# hmmscan :: search sequence(s) against a profile database
# HMMER 3.2.1 (June 2018); http://hmmer.org/
# Copyright (C) 2018 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query sequence file:             /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Thermoplasmatales_archaeon_BRNA1_uid195930/NC_020892.faa
# target HMM database:             /oak/stanford/groups/akundaje/marinovg/genomes/PFam/PFam32.0/Pfam-A.hmm
# output directed to file:         /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Thermoplasmatales_archaeon_BRNA1_uid195930/NC_020892.PFam32-A
# per-seq hits tabular output:     /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Thermoplasmatales_archaeon_BRNA1_uid195930/NC_020892.PFam32-A.tblout
# number of worker threads:        20
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       gi|474933594|ref|YP_007687176.1|  [L=411]
Description: orc1/cdc6 family replication initiation protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-17   63.9   0.1    2.2e-17   62.8   0.1    1.5  1  Cdc6_C           CDC6, C terminal winged helix domain
    1.6e-10   41.4   0.0    3.8e-10   40.2   0.0    1.6  1  AAA_22           AAA domain
    7.1e-10   39.4   0.0    1.8e-09   38.1   0.0    1.7  1  AAA              ATPase family associated with various cellul
    1.1e-09   38.8   0.0    1.7e-08   35.1   0.0    2.4  1  AAA_16           AAA ATPase domain
    3.5e-07   29.8   0.0    8.8e-07   28.5   0.0    1.6  1  TniB             Bacterial TniB protein
    0.00031   21.0   0.1    0.00092   19.5   0.1    1.8  1  AAA_assoc_2      AAA C-terminal domain
    0.00034   20.4   0.0    0.00088   19.0   0.0    1.7  1  Sigma54_activat  Sigma-54 interaction domain
     0.0004   19.6   0.1     0.0013   17.9   0.0    1.8  2  DUF815           Protein of unknown function (DUF815)
    0.00045   20.2   0.0    0.00073   19.5   0.0    1.3  1  NACHT            NACHT domain
     0.0061   16.1   0.0      0.013   15.1   0.0    1.5  1  AAA_7            P-loop containing dynein motor region
     0.0066   16.2   0.1      0.019   14.7   0.1    1.8  1  AAA_24           AAA domain
     0.0078   16.2   0.1      0.054   13.5   0.0    2.2  2  ResIII           Type III restriction enzyme, res subunit
      0.008   15.6   0.0      0.073   12.4   0.0    2.1  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
      0.009   14.8   0.5       0.24   10.1   0.0    2.2  2  AAA_32           AAA domain
  ------ inclusion threshold ------
      0.015   15.1   0.0      0.042   13.6   0.0    1.8  1  PduV-EutP        Ethanolamine utilisation - propanediol utili
      0.015   15.3   0.0      0.055   13.5   0.0    2.1  1  AAA_5            AAA domain (dynein-related subfamily)
      0.016   15.7   0.0      0.078   13.5   0.0    2.3  2  AAA_18           AAA domain
      0.019   15.0   0.2       0.06   13.4   0.2    1.9  1  AAA_14           AAA domain
      0.028   13.6   0.0      0.052   12.7   0.0    1.3  1  PIF1             PIF1-like helicase
      0.029   14.1   0.1      0.057   13.2   0.1    1.5  1  AAA_lid_4        RuvB AAA lid domain
      0.038   13.7   0.1       0.38   10.5   0.0    2.2  2  IstB_IS21        IstB-like ATP binding protein
      0.042   13.6   0.1        5.8    6.6   0.0    2.4  2  DEAD             DEAD/DEAH box helicase
      0.043   13.9   1.6        0.2   11.7   0.0    2.5  2  DUF87            Helicase HerA, central domain
      0.059   12.6   0.7        4.7    6.3   0.0    2.2  2  KAP_NTPase       KAP family P-loop domain
      0.077   12.9   4.5      0.033   14.1   1.1    2.1  1  ATPase_2         ATPase domain predominantly from Archaea
      0.077   12.3   0.0       0.16   11.2   0.0    1.4  1  Zeta_toxin       Zeta toxin
      0.077   13.4   0.2       0.25   11.8   0.1    2.0  1  RNA_helicase     RNA helicase
      0.089   13.1   0.0       0.25   11.7   0.0    1.7  1  AAA_19           AAA domain
      0.099   13.2   0.0       0.48   10.9   0.0    2.0  2  ABC_tran         ABC transporter
       0.11   11.4   0.0       0.55    9.1   0.0    1.9  2  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
       0.13   12.2   0.3       0.58   10.2   0.1    2.1  2  CTK3             CTD kinase subunit gamma CTK3
       0.13   12.1   1.7        3.4    7.6   0.1    2.7  2  NTPase_1         NTPase


Domain annotation for each model (and alignments):
>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.8   0.1     4e-20   2.2e-17      11      79 ..     318     385 ..     309     388 .. 0.90

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 4e-20
                                       CSSS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSSCH CS
                            Cdc6_C  11 sgkeevttgevyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtrkisLnvdpd 79 
                                       +++  +ttg+vy vYk+++ ++g++ ltqr+v dl+seL+mlgi++++ +s Gr +grt+ i+Ln++++
  gi|474933594|ref|YP_007687176.1| 318 NDEGKITTGDVYFVYKEIATELGYNLLTQRRVGDLISELDMLGIINARIKSLGR-KGRTKIIELNISKE 385
                                       678899***********************************************9.5*********9986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.0   6.7e-13   3.8e-10       5     126 ..      56     184 ..      52     196 .. 0.86

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 6.7e-13
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka....erlssee 77 
                                        + ++++G +GtGKT +++ + e+l + a+++  + +++++++    ++ ++l ++ + + ++ ++     + s+e+
  gi|474933594|ref|YP_007687176.1|  56 PSNIMIIGKTGTGKTAVVKYIGEEL-RKADPDGSKCSYIYINCETVDTPYSILYNISNHVISDPNKripfTGWSLER 131
                                       6789********************9.4556666******************************************** PP

                            AAA_22  78 llealeqalraravielliiDEaqh.lr..seealeeLrsllnl.srkgvqli 126
                                       +++ l ++++++++i ++++DE++   r   ++++ +L ++ +  s++ v++i
  gi|474933594|ref|YP_007687176.1| 132 MFNVLIKYIDEADKIFIIVLDEIDQsYRknGDDIFYFLTTINEMlSQSRVSII 184
                                       **************99********96656437777777666665668888877 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.0   3.2e-12   1.8e-09       1     126 [.      59     206 ..      59     212 .. 0.76

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 3.2e-12
                                       EEEESSTTSSHHHHHHHHHHHH........THEEEEEETTTCSSS....................STTHHHHHHHHH CS
                               AAA   1 vllyGppGtGKTllakavakel........gvefleisgsellsk....................yvgesekkirel 49 
                                       ++++G  GtGKT+++k + +el        + +++ i++ ++                       + g s +++ ++
  gi|474933594|ref|YP_007687176.1|  59 IMIIGKTGTGKTAVVKYIGEELrkadpdgsKCSYIYINCETVDTPysilynisnhvisdpnkripFTGWSLERMFNV 135
                                       5789*****************866555554577999999988855899999999999999*****666665555554 PP

                                       HHH.HHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS...GGGSTHHHHST CS
                               AAA  50 fke.akekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnr...pdkldpallrg 122
                                       + + + e  k  i+++DEid+  +++       ++++   L t  + +++  s+v +ig+tn+    + l+p+++ +
  gi|474933594|ref|YP_007687176.1| 136 LIKyIDEADKIFIIVLDEIDQSYRKN-------GDDIFYFLTTINEMLSQ--SRVSIIGITNNskfNEILSPKIR-S 202
                                       444155555679***********999.......66666655555555555..68*********995566666676.8 PP

                                       TSSE CS
                               AAA 123 Rfdr 126
                                       R+ +
  gi|474933594|ref|YP_007687176.1| 203 RLGE 206
                                       8865 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.0     3e-11   1.7e-08       1     147 [.      32     157 ..      32     184 .. 0.75

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 3e-11
                            AAA_16   1 rlvGReeeleqLlsale.rvrsgrpelvllsGesGvGKsslvrellralekd.....ggiflrgkcdqlesaipysa 71 
                                       +l+ R+++++++ +++  ++ ++ p++++++G  G+GK+++v+ + ++l+k+     ++ +++ +c+    ++pys+
  gi|474933594|ref|YP_007687176.1|  32 QLIHRDDQIREIVDIVApSLQKDKPSNIMIIGKTGTGKTAVVKYIGEELRKAdpdgsKCSYIYINCETV--DTPYSI 106
                                       6899*************55555556*********************999999999766777******99..99**99 PP

                            AAA_16  72 laqalareellrqlldeaesaeleawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlqwa 147
                                       l ++  + +++ + + +     +  w+                  +r++++l + ++ + +    +++vlD++++ 
  gi|474933594|ref|YP_007687176.1| 107 LYNIS-N-HVISDPNKR---IPFTGWSL-----------------ERMFNVLIKYIDEADK---IFIIVLDEIDQS 157
                                       88888.5.776655555...45566666.................6777887777755544...588888887754 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   1.6e-09   8.8e-07      29     170 ..      50     196 ..      31     210 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.6e-09
                              TniB  29 ypkrkrmpnlllvGdsnnGKtmivekFarlhppekdedaekvpvlvvqappkpdekrlyaaiLealgaplkara... 102
                                         ++++++n++++G++ +GKt++v+ +  ++ ++ d+d +k+  +++++ +  +   +  +i +++  + ++r    
  gi|474933594|ref|YP_007687176.1|  50 SLQKDKPSNIMIIGKTGTGKTAVVK-YIGEELRKADPDGSKCSYIYINCETVDTPYSILYNISNHVISDPNKRIpft 125
                                       5679999**************9995.7888899999************99988877766666666655444443222 PP

                              TniB 103 ..rvskleqqvlrllrel.kvrvLiiDEihnllagsarkqreflnalksLgnelkipivlvGteealralr 170
                                         +++++ +  +++++e  k+ ++++DEi++  + + ++   fl ++  +  + +++i+++  ++ ++ + 
  gi|474933594|ref|YP_007687176.1| 126 gwSLERMFNVLIKYIDEAdKIFIIVLDEIDQSYRKNGDDIFYFLTTINEMLSQSRVSIIGITNNSKFNEIL 196
                                       2378888888888887763678999***********************************98888777664 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   1.6e-06   0.00092      19      57 ..     251     288 ..     235     296 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.6e-06
                                       XXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXX CS
                       AAA_assoc_2  19 adGDaRkaLnlLElaaeaaeakegkieitledleealqr 57 
                                        +GDaRkaL lL + a+aae+ +g+ +it+++++ a+q+
  gi|474933594|ref|YP_007687176.1| 251 DSGDARKALDLLRISADAAER-NGDPRITEAHVKYAIQK 288
                                       37****************987.9*************997 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.6e-06   0.00088       2      61 ..      34     100 ..      33     109 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.6e-06
                                       ---SHHHHHHHHHHHHHCTSS..S-EEEECSTTSSHHHHHHHHHHHSTT.....TTS-EEEEETTTS CS
                   Sigma54_activat   2 igesealkelleqikkvaktd..lsvlitGesGtGKellaraiheaskr.....kekpfvavncaai 61 
                                       i ++++++e+++ ++   ++d  ++++i G++GtGK+ + + i e+ ++     ++ +++ +nc  +
  gi|474933594|ref|YP_007687176.1|  34 IHRDDQIREIVDIVAPSLQKDkpSNIMIIGKTGTGKTAVVKYIGEELRKadpdgSKCSYIYINCETV 100
                                       566777888888877777665569*******************885554111124558999999755 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   2.3e-06    0.0013      28      79 ..      31      82 ..       9     117 .. 0.87
   2 ?   -1.6   0.2       2.2   1.2e+03      95     116 ..     133     154 ..     128     174 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.3e-06
                            DUF815 28 ddLvgidkqkealventeqfleglpannvLLwGarGtGKSslvkallneyae 79
                                      ++L+  d+q +++v+ ++  l++ + +n++++G+ GtGK ++vk + +e+++
  gi|474933594|ref|YP_007687176.1| 31 AQLIHRDDQIREIVDIVAPSLQKDKPSNIMIIGKTGTGKTAVVKYIGEELRK 82
                                      57888999************************************99988876 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.2
                            DUF815  95 lpklvellrerperfilfvDDL 116
                                       ++ l++ + e+++ fi+++D +
  gi|474933594|ref|YP_007687176.1| 133 FNVLIKYIDEADKIFIIVLDEI 154
                                       5678899999*********965 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.3e-06   0.00073       3      99 ..      59     163 ..      57     206 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.3e-06
                                       EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-...-HCHHHCCCC.TS--SSS-C....... CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgnarsladllfsql.pepaapvse....... 71 
                                       +++ G+ G GKT+ ++ + +++++ ++++ + +  +++++ ++ ++    s+ + +  +   +p+++++        
  gi|474933594|ref|YP_007687176.1|  59 IMIIGKTGTGKTAVVKYIGEELRKADPDGSK-CSYIYINCETVDTPY---SILYNISNHViSDPNKRIPFtgwsler 131
                                       789**************************97.9999*******9985...555555554413444444334444555 PP

                                       ...CHHHHCCSCCCEE............EEEE-STT-SS-TCH CS
                             NACHT  72 ...vwavllelperlL............lilDglDelvtdlgq 99 
                                          v           L            ++lD +D+  +++g 
  gi|474933594|ref|YP_007687176.1| 132 mfnV-----------LikyideadkifiIVLDEIDQSYRKNGD 163
                                       4442...........2233333333334778888887777666 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.3e-05     0.013      34      60 ..      57      83 ..      45     114 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.3e-05
                             AAA_7 34 kpvllvGptGtGKtviikdllkkldke 60
                                       +++++G+tGtGKt+++k + ++l k 
  gi|474933594|ref|YP_007687176.1| 57 SNIMIIGKTGTGKTAVVKYIGEELRKA 83
                                      689**************9887776643 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   3.3e-05     0.019       3      80 ..      57     160 ..      55     166 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.3e-05
                            AAA_24   3 lkiliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie..........................swedfl 53 
                                        +i+i+G+ g+GKT ++k +g++    d +++  s   ++ +++                           s+e + 
  gi|474933594|ref|YP_007687176.1|  57 SNIMIIGKTGTGKTAVVKYIGEELRKADPDGSKCSYIYINCETVDtpysilynisnhvisdpnkripftgwSLERMF 133
                                       589*****************666666666665555555555555555566666667777788899999988888888 PP

                            AAA_24  54 devvelaaeladyktlviDtideleel 80 
                                       + + +  +e +++ ++v+D id+ ++ 
  gi|474933594|ref|YP_007687176.1| 134 NVLIKYIDEADKIFIIVLDEIDQSYRK 160
                                       888888999999*********998875 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   9.6e-05     0.054       6      50 ..      37      82 ..      32      89 .. 0.74
   2 ?   -0.7   0.0       2.2   1.2e+03      45      71 ..     154     180 ..     129     211 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.6e-05
                                      HHHHHHH.HHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S CS
                            ResIII  6 eyQeeai.enlleklkskrdkrglikmaTGtGKTlvaaklierllk 50
                                      + Q++ i + ++ +l++++  +++i   TGtGKT v   + e+l+k
  gi|474933594|ref|YP_007687176.1| 37 DDQIREIvDIVAPSLQKDKPSNIMIIGKTGTGKTAVVKYIGEELRK 82
                                      555544404445788888999**************98777777666 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.2
                                       HHHH-S.....-EEEEESSHHHHHHHH CS
                            ResIII  45 ierllkkgkeekflflvprkslleqtl 71 
                                       i++ ++k++ + f fl   +++l+q +
  gi|474933594|ref|YP_007687176.1| 154 IDQSYRKNGDDIFYFLTTINEMLSQSR 180
                                       333333333344444444444444444 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00013     0.073      26      57 ..      43      74 ..      24      76 .. 0.81
   2 ?    0.7   0.0      0.48   2.7e+02     139     170 ..     137     176 ..     128     206 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                                      TTS-EEEEEGGGS-.SEEEE--TTSSHHHHHH CS
                      FtsK_SpoIIIE 26 isgnplvldlkkmashllvaGatgsGKStaln 57
                                      i++++  + +k  +s+++++G tg+GK+ +++
  gi|474933594|ref|YP_007687176.1| 43 IVDIVAPSLQKDKPSNIMIIGKTGTGKTAVVK 74
                                      55555556677788**************9875 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.48
                                       HHHHHTT---B-TT-......................... CS
                      FtsK_SpoIIIE 139 aedpldifgdvflvlDnyddlaaene........ritsLs 170
                                        +++++++++  +vlD+ d+ + +n          i+++ 
  gi|474933594|ref|YP_007687176.1| 137 IKYIDEADKIFIIVLDEIDQSYRKNGddifyfltTINEML 176
                                       5678999999************999877776655444444 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00043      0.24      31      77 ..      57     104 ..      51     108 .. 0.85
   2 ?    2.5   0.2     0.091        51     477     510 ..     255     288 ..     245     290 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00043
                            AAA_32  31 YNifvlGesgtGrttlvkrlleeiakkeptpdDwcYvn.nfdnpeePk 77 
                                        Ni ++G++gtG+t +vk + ee  k  p  + + Y++ n ++ ++P 
  gi|474933594|ref|YP_007687176.1|  57 SNIMIIGKTGTGKTAVVKYIGEELRKADPDGSKCSYIYiNCETVDTPY 104
                                       59**************************99998888875777777776 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.091
                            AAA_32 477 fseiadllrEAdywakkegaevveaehVekAlee 510
                                        ++  dllr ++  a+++g+  ++++hV+ A+++
  gi|474933594|ref|YP_007687176.1| 255 ARKALDLLRISADAAERNGDPRITEAHVKYAIQK 288
                                       567899*************************986 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   7.5e-05     0.042       3      44 ..      58     103 ..      56     114 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.5e-05
                         PduV-EutP   3 killiGkvgsGKttLtqalkg....eelkYkktqaiefsdeviDtP 44 
                                       +i++iGk+g+GKt++ + + +     +   +k  +i ++ e++DtP
  gi|474933594|ref|YP_007687176.1|  58 NIMIIGKTGTGKTAVVKYIGEelrkADPDGSKCSYIYINCETVDTP 103
                                       79************99977552211455567999999999999999 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   9.8e-05     0.055       1      76 [.      58     156 ..      58     204 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.8e-05
                                       EEEEE--SSSSHHHHHHHGGGGB........S--EEEEE--TT--HHHHH--B--..............-------- CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaal........nreveyvqltrdtteedlkgrreik.....ngttslvdsplvraar 64 
                                       +++++G++GtgK+ +++++ + l        ++++ y+++    t+  +++ ++       n++  ++  +l r ++
  gi|474933594|ref|YP_007687176.1|  58 NIMIIGKTGTGKTAVVKYIGEELrkadpdgsKCSYIYINCETVDTPYSILYNISNHvisdpNKRIPFTGWSLERMFN 134
                                       589*****************999999999999999999998877777788777755677877777777777777777 PP

                                       ..........G-SEEEEESGGG CS
                             AAA_5  65 ..........egeilvlDEver 76 
                                                 +  i+vlDE+++
  gi|474933594|ref|YP_007687176.1| 135 vlikyideadKIFIIVLDEIDQ 156
                                       7777777777777777777775 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   0.00014     0.078       1      25 [.      59      91 ..      59     182 .. 0.76
   2 ?   -1.5   0.0         6   3.4e+03      50      87 ..     275     317 ..     217     329 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00014
                            AAA_18  1 IlltGtpGvGKttlakeLskrl.gf.......g 25
                                      I++ G+ G+GKt + k++ ++l +        +
  gi|474933594|ref|YP_007687176.1| 59 IMIIGKTGTGKTAVVKYIGEELrKAdpdgskcS 91
                                      99****************999744455544440 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 6
                            AAA_18  50 krldedkldklldaleenss.....aleegknlvidghlaele 87 
                                        r+ e  ++++++++e  +s     +l++++ lv+ +++ ++ 
  gi|474933594|ref|YP_007687176.1| 275 PRITEAHVKYAIQKIEIDASaeivkSLTDQSKLVLMSIIKNPG 317
                                       3444444444444444444455555556666666666665555 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   0.00011      0.06       5      77 ..      59     163 ..      55     218 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00011
                            AAA_14   5 lvitGaRrvGKTtllkqlikell.....vkkesilyinldderd...............kkladpe........... 50 
                                       ++i G   +GKT ++k + +el       +k s++yin+++ ++                     +           
  gi|474933594|ref|YP_007687176.1|  59 IMIIGKTGTGKTAVVKYIGEELRkadpdGSKCSYIYINCETVDTpysilynisnhvisdP-----Nkripftgwsle 130
                                       7899999********99998888*99998899*********9998888877766554440.....233444455333 PP

                            AAA_14  51 kllelileklke.ekktylflDEiqev.....p 77 
                                       ++ +++ + + e +k  +++lDEi ++     +
  gi|474933594|ref|YP_007687176.1| 131 RMFNVLIKYIDEaDKIFIIVLDEIDQSyrkngD 163
                                       333333333322356677999999876555553 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   9.3e-05     0.052       5      48 ..      39      82 ..      36      88 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.3e-05
                                      HHHHHHHHH......HCTS-EEEEESTTSSCHHHHHHHHHHCHC CS
                              PIF1  5 eQkkvfdaiieavlnekgklfFvtGsgGtgKtflwkallkklrs 48
                                      + ++++d +  +++++k+ ++ + G  GtgKt + k + + lr+
  gi|474933594|ref|YP_007687176.1| 39 QIREIVDIVAPSLQKDKPSNIMIIGKTGTGKTAVVKYIGEELRK 82
                                      44889999999**************************9999987 PP

>> AAA_lid_4  RuvB AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1    0.0001     0.057       1      74 []     214     292 ..     214     292 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.0001
                         AAA_lid_4   1 YeeeeLeeivk.rsakilgveieeega....aeiarRsRGTPRianrLLrRvrDfaqvkgdgkitkevakkaLelle 72 
                                       Y+++eL +i+k r+a+ +  ++ +eg     a ++    G  R a  LLr   D a+ +gd +it++ +k a++++e
  gi|474933594|ref|YP_007687176.1| 214 YSPKELVDILKdRAAEAFYSDVMDEGVlpyvAAVSAQDSGDARKALDLLRISADAAERNGDPRITEAHVKYAIQKIE 290
                                       9999*****9669************97222246777778************************************** PP

                         AAA_lid_4  73 vd 74 
                                       +d
  gi|474933594|ref|YP_007687176.1| 291 ID 292
                                       98 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00067      0.38      45      73 ..      54      82 ..      32      96 .. 0.77
   2 ?    0.4   0.1      0.86   4.8e+02      99     157 ..     136     195 ..     128     201 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00067
                         IstB_IS21 45 ekkenivllGpsGvGKshlaialgveavr 73
                                      +k  ni+++G +G+GK+ +   +g e  +
  gi|474933594|ref|YP_007687176.1| 54 DKPSNIMIIGKTGTGKTAVVKYIGEELRK 82
                                      5668*************999999887554 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.86
                         IstB_IS21  99 laralkrllkvdllilDdlgll.pldqaeaellfeviekryerrsiiitsnlpfaewdev 157
                                       l + +++  k+ +++lD++      + ++  +++  i++   ++ + i    + ++++e+
  gi|474933594|ref|YP_007687176.1| 136 LIKYIDEADKIFIIVLDEIDQSyRKNGDDIFYFLTTINEMLSQSRVSIIGITNNSKFNEI 195
                                       5667888899999****9976425677788888888888877665555555555555555 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0      0.01       5.8      15      31 ..      57      73 ..      38      89 .. 0.82
   2 ?    4.5   0.0     0.049        27     120     156 ..     144     179 ..     119     190 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.01
                                      CEEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxxx RF
                              DEAD 15 gdvlvaaeTGsGKTlaf 31
                                       ++++ ++TG+GKT++ 
  gi|474933594|ref|YP_007687176.1| 57 SNIMIIGKTGTGKTAVV 73
                                      6999**********985 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.049
                                       TTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 120 sqvrflVlDEadrlldqgfsdfinrilnqlpqitcdg 156
                                       +++ ++VlDE+d+   +  +d+i   l++++++ ++ 
  gi|474933594|ref|YP_007687176.1| 144 DKIFIIVLDEIDQSYRK-NGDDIFYFLTTINEMLSQS 179
                                       566789*******9998.8888888888886665554 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00036       0.2      28      49 ..      61      82 ..      56      89 .. 0.86
   2 ?    0.9   0.4      0.73   4.1e+02     170     215 ..     354     387 ..     133     399 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00036
                             DUF87 28 ilgsTGsGKSntvavLleelle 49
                                      i+g+TG+GK+  v+++ eel +
  gi|474933594|ref|YP_007687176.1| 61 IIGKTGTGKTAVVKYIGEELRK 82
                                      9****************99975 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.73
                             DUF87 170 dkledllrkggsfsnsstdliallleklekegkitiidlsgvdela 215
                                       + l+ l   ++              + l+++g+  ii+l+  +e +
  gi|474933594|ref|YP_007687176.1| 354 SELDMLGIINAR------------IKSLGRKGRTKIIELNISKEIQ 387
                                       222222222222............2334566666666666544444 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0084       4.7       7      47 ..      42      83 ..      36     116 .. 0.83
   2 ?    4.0   0.6     0.044        25     158     222 ..     130     197 ..     125     210 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0084
                        KAP_NTPase  7 aladilseptl..atpivvgLygkWGsGKssllnkledelkef 47
                                       ++di+  p+l   +p+ +++ gk G+GK+++++ + +el++ 
  gi|474933594|ref|YP_007687176.1| 42 EIVDIVA-PSLqkDKPSNIMIIGKTGTGKTAVVKYIGEELRKA 83
                                      5555555.6665578999*******************999987 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.044
                        KAP_NTPase 158 eelladmektLdalqkrlVvviDdLDrceteevlql...leavkllfslkpvvfilavDphviakaie 222
                                       e +++ ++k++d+++k  ++v+D++D    ++   +   l +++ ++s ++v+ i +++ ++  +++ 
  gi|474933594|ref|YP_007687176.1| 130 ERMFNVLIKYIDEADKIFIIVLDEIDQSYRKNGDDIfyfLTTINEMLSQSRVSIIGITNNSKFNEILS 197
                                       55777889999***************765555554400055555555558888887777776666665 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   1.1   5.9e-05     0.033       4     131 ..      36     158 ..      33     203 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.9e-05
                          ATPase_2   4 Rekelkeleei....lerepneiyfiYGpegsGKtaLlkeiienledkdk...yviy.yialreesiskldefieee 72 
                                       R+  ++e+  i    l++++ + ++i G  g GKta++k i e+l++ d    +  y yi+ +++++ +   +    
  gi|474933594|ref|YP_007687176.1|  36 RDDQIREIVDIvapsLQKDKPSNIMIIGKTGTGKTAVVKYIGEELRKADPdgsKCSYiYINCETVDTPYSILY---- 108
                                       555556555552222577788889999******************8877656644442678888888888877.... PP

                          ATPase_2  73 eekkklekalgiavpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqkli 131
                                          +  + +++++ ++  +      +   +++ ++ l++ i +  k  ii++De+ +  
  gi|474933594|ref|YP_007687176.1| 109 ---NISNHVISDPNKRIPF------TGWSLERMFNVLIKYIDEADKIFIIVLDEIDQSY 158
                                       ...2223334444444444......4567788899999999999888999999998876 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00029      0.16      10      42 ..      50      82 ..      41      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00029
                        Zeta_toxin 10 ypsqerPklillgGqpGAGKselaellkdeler 42
                                      + ++++P  i++ G +G GK+++ +++ +el++
  gi|474933594|ref|YP_007687176.1| 50 SLQKDKPSNIMIIGKTGTGKTAVVKYIGEELRK 82
                                      45779**********************999964 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00044      0.25       1      39 [.      59      97 ..      59     138 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00044
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnp 39
                                      i++ G++g+GK+ ++k++ ++l k+  + +k s+++ n+
  gi|474933594|ref|YP_007687176.1| 59 IMIIGKTGTGKTAVVKYIGEELRKADPDGSKCSYIYINC 97
                                      7899******************98876666555555444 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00045      0.25      10      38 ..      56      84 ..      49      99 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00045
                            AAA_19 10 ekvllvtaGpGtGKTrvlkhivallvelg 38
                                       +++++++  GtGKT v+k i ++l ++ 
  gi|474933594|ref|YP_007687176.1| 56 PSNIMIIGKTGTGKTAVVKYIGEELRKAD 84
                                      57899***************999988765 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00085      0.48      11      36 ..      56      81 ..      48     103 .. 0.85
   2 ?   -1.0   0.0       4.2   2.3e+03      79     102 ..     316     366 ..     261     396 .. 0.50

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00085
                                      TSEEEEEESTTSSHHHHHHHHTTSS- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 11 gekvaivGenGaGKStLlkllagllk 36
                                       + + i+G++G+GK+ ++k + ++l+
  gi|474933594|ref|YP_007687176.1| 56 PSNIMIIGKTGTGKTAVVKYIGEELR 81
                                      56799**************9987765 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 4.2
                                       H...........................HHHTCHHHHHHHSTTGGTTCBGE CS
                                       x...........................xxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n...........................esdeeiekalsklglkelkdtvv 102
                                                                     ++++ +++s+l++ ++ + ++
  gi|474933594|ref|YP_007687176.1| 316 PgndegkittgdvyfvykeiatelgynlLTQRRVGDLISELDMLGIINARI 366
                                       143444444444444444444444444444444555555555555444444 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00098      0.55      12      41 ..      53      82 ..      43      87 .. 0.80
   2 ?   -0.7   0.0      0.89     5e+02     335     364 ..     368     397 ..     363     404 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00098
                     TrwB_AAD_bind 12 eretqhilivGttGsGKtqalekllraira 41
                                      ++  + i+i+G tG+GKt +++ + +++r+
  gi|474933594|ref|YP_007687176.1| 53 KDKPSNIMIIGKTGTGKTAVVKYIGEELRK 82
                                      556688*************99887666665 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.89
                     TrwB_AAD_bind 335 sygannsrdgvslgrqrevrpvVlaselqn 364
                                       s g++   +++ l+  +e++++V+++e+ +
  gi|474933594|ref|YP_007687176.1| 368 SLGRKGRTKIIELNISKEIQKLVISDEIFQ 397
                                       6788888889999**************965 PP

>> CTK3  CTD kinase subunit gamma CTK3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       4.6   2.6e+03      89     106 ..      39      59 ..      20      67 .. 0.72
   2 ?   10.2   0.1     0.001      0.58      25      73 ..     130     178 ..     125     200 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 4.6
                                       THHHHHHHHS-...HHHHHHH CS
                              CTK3  89 dilklvdsvvP...gsgaaNl 106
                                       +i ++vd v+P   ++++ N+
  gi|474933594|ref|YP_007687176.1|  39 QIREIVDIVAPslqKDKPSNI 59 
                                       589999999996655555555 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.001
                                       HHHHHHHHHTGGGHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHH CS
                              CTK3  25 qkaaqfAlknkdkeedlfscileqlesadlNtranilyfidllleeslk 73 
                                       ++  +  +k+ d+++ +f  +l++++++   +   i+yf+ ++ e+  +
  gi|474933594|ref|YP_007687176.1| 130 ERMFNVLIKYIDEADKIFIIVLDEIDQSYRKNGDDIFYFLTTINEMLSQ 178
                                       55666679********************999999******999998665 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1     0.006       3.4       1      26 [.      58      83 ..      58      93 .. 0.89
   2 ?    2.9   0.3      0.16        91      86     147 ..     133     203 ..     120     210 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.006
                                      EEEEE--TTSSHHHHHHHHHHHH... CS
                          NTPase_1  1 kvfiTGppGvGKtTlvkkvlellkss 26
                                      +++i G+ G+GKt +vk + e+l++ 
  gi|474933594|ref|YP_007687176.1| 58 NIMIIGKTGTGKTAVVKYIGEELRKA 83
                                      58999*****************9875 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.16
                                       HHHHHHHHHHH-...EEEE---STTGGG....-HHHHHHHHHHHT.TTSEEEEE--SS-.-SHHHHHHHT- CS
                          NTPase_1  86 lealrkalsead...viviDEiGkmElk....skkfkeaveevLk.sekpvlavihrrk.dlalveeirer 147
                                        ++l k + ead   +iv+DEi +   k    +  f ++++e+L+ s + ++++  ++k ++ l  +ir+r
  gi|474933594|ref|YP_007687176.1| 133 FNVLIKYIDEADkifIIVLDEIDQSYRKngddIFYFLTTINEMLSqSRVSIIGITNNSKfNEILSPKIRSR 203
                                       44555555666667799999998765551111345888888888866666666666665555555666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                        32  (0.00178482); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              32  [number of targets reported over threshold]
# CPU time: 0.69u 0.31s 00:00:01.00 Elapsed: 00:00:00.52
# Mc/sec: 2370.01
//
Query:       gi|474933595|ref|YP_007687177.1|  [L=269]
Description: Signal peptidase I [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1572.33
//
Query:       gi|474933596|ref|YP_007687178.1|  [L=151]
Description: Deoxycytidylate deaminase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-27   93.8   0.5    6.4e-27   93.4   0.5    1.2  1  dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-
    2.7e-19   69.3   0.0    3.2e-19   69.1   0.0    1.1  1  MafB19-deam      MafB19-like deaminase
     0.0051   16.9   0.0      0.007   16.5   0.0    1.2  1  APOBEC3          APOBEC3
  ------ inclusion threshold ------
      0.048   13.5   2.1        1.3    8.9   2.0    2.7  1  Inv-AAD          Invertebrate-AID/APOBEC-deaminase


Domain annotation for each model (and alignments):
>> dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.4   0.5   1.4e-30   6.4e-27       8      99 ..       1     113 [.       1     115 [. 0.98

  Alignments for each domain:
  == domain 1  score: 93.4 bits;  conditional E-value: 1.4e-30
                                       HHHHHHHHHHHHTTTSCSEEEEEEETTEEEEEEESBHHCCTG.......................TTB-HHHHHHHH CS
                   dCMP_cyt_deam_1   8 lelalkaakeaqkcsnfkVGavivkngeiistgyngepaggs.......................ktiHAEvnAilk 61 
                                       +++a+++a+++ +c + +VGaviv+++++istgyng p+g +                       + +HAE+nAi++
  gi|474933596|ref|YP_007687178.1|   1 MDMAQLVATRS-TCLRRHVGAVIVRDKHVISTGYNGAPRGIThceekgclretlnvpsgtrhelcRGVHAEQNAITQ 76 
                                       89*********.***************************************************************** PP

                                       HHHHTSSCETTEEEEEEE--BHHHHHHHHHHT-SEEEE CS
                   dCMP_cyt_deam_1  62 aaknggsklegatlyvtlePCsmCakaiiqsgikkvvv 99 
                                       aa+  g++++gat+y+t++PCs Cak++i++gi+++v+
  gi|474933596|ref|YP_007687178.1|  77 AASF-GISVDGATIYTTTFPCSLCAKILINAGIREIVY 113
                                       **99.999****************************98 PP

>> MafB19-deam  MafB19-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.1   0.0   7.1e-23   3.2e-19      10     109 ..       3     123 ..       1     147 [. 0.90

  Alignments for each domain:
  == domain 1  score: 69.1 bits;  conditional E-value: 7.1e-23
                       MafB19-deam  10 alaevekatkikedkigavivkdkkviargsn.......................ekelnakataHaEiaalqqAak 63 
                                        +++v  ++ +  + +gaviv dk vi +g+n                        +  +   + HaE +a+ qAa 
  gi|474933596|ref|YP_007687178.1|   3 MAQLVATRSTCLRRHVGAVIVRDKHVISTGYNgaprgithceekgclretlnvpsGTRHELCRGVHAEQNAITQAAS 79 
                                       5678899999******************************************9994444577899************ PP

                       MafB19-deam  64 klkskrlddatlyvtlepCdmCagaivqaglkklvygagnpkslnk 109
                                       +++s   d+at+y+t  pC+ Ca+++++ag++++vy  g+ + l k
  gi|474933596|ref|YP_007687178.1|  80 FGISV--DGATIYTTTFPCSLCAKILINAGIREIVYDDGYMDDLAK 123
                                       *9999..*****************************9999887654 PP

>> APOBEC3  APOBEC3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.6e-06     0.007      31      72 ..      67     105 ..      44     110 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.6e-06
                           APOBEC3  31 kHAEerfidkirslnldslkqykitcylswsPcpkCaeelve 72 
                                        HAE+ +i + +s  ++ +     t+y +  Pc+ Ca+ l++
  gi|474933596|ref|YP_007687178.1|  67 VHAEQNAITQAASFGISVDG---ATIYTTTFPCSLCAKILIN 105
                                       6***************9999...8**************9997 PP

>> Inv-AAD  Invertebrate-AID/APOBEC-deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   2.0   0.00028       1.3       2      35 ..      20      52 ..      19     102 .. 0.57

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00028
                           Inv-AAD  2 avlvdadkneilatGytleleGnthae.qcclikl 35
                                      av+v   ++++++tGy     G th e + cl   
  gi|474933596|ref|YP_007687178.1| 20 AVIVR--DKHVISTGYNGAPRGITHCEeKGCLRET 52
                                      66664..568***************9725787643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1095.55
//
Query:       gi|474933597|ref|YP_007687179.1|  [L=116]
Description: ATP synthase H subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.031   14.8  19.1      0.075   13.6  19.1    1.6  1  V-ATPase_G     Vacuolar (H+)-ATPase G subunit
       0.11   13.0  21.9       0.15   12.4  21.9    1.3  1  V-ATPase_G_2   Vacuolar (H+)-ATPase G subunit
       0.35   10.2   6.8       0.42    9.9   6.8    1.0  1  Aminopep       Putative aminopeptidase
       0.84   10.0   7.0        1.5    9.1   7.0    1.5  1  Muted          Organelle biogenesis, Muted-like protein
          2    9.1  16.3        1.8    9.2  10.9    2.0  2  DUF883         Bacterial protein of unknown function (DUF883)
        2.1    7.4   5.9        2.4    7.2   5.9    1.0  1  Pannexin_like  Pannexin-like TM region of LRRC8


Domain annotation for each model (and alignments):
>> V-ATPase_G  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6  19.1   2.5e-05     0.075      10      97 ..      17     104 ..       8     114 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.5e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHSSHHHHHHHHHH CS
                        V-ATPase_G  10 LqAEkeAaeivkeArkrkakrlkqAkeeAekEieeyrakkekefkekeaeklgseeelekkieketeekikelkesv 86 
                                        +AE +A++ v++A  +k++ + qA+ +  k i+  ra + + +++  a++ ++ ++ ++++ ++ ee+ + ++ ++
  gi|474933597|ref|YP_007687179.1|  17 KEAESRADQTVAQAEADKKAAVAQARRDSVKRIQDERAAMSAAYESAVAAEQAALDKEKAEVLAKGEEEAAAIDAAA 93 
                                       58999******************************999999999999999999988888888888888888888877 PP

                                       HHHHHHHHHHH CS
                        V-ATPase_G  87 kknkeavvkel 97 
                                       + + ++v + l
  gi|474933597|ref|YP_007687179.1|  94 QDKIKEVNDFL 104
                                       77777776555 PP

>> V-ATPase_G_2  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4  21.9   5.2e-05      0.15       5      93 ..      11      99 ..       8     110 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.2e-05
                                      HHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHH CS
                      V-ATPase_G_2  5 rllkeLaerEaeLdqrlEaArkeaereveaAeaeAarilreAeakakalqaeyeqelaeeva...rireeararaeaea 80
                                       +l+e++e E+  dq + +A  + +++v++A+ +     +  +++  a+ a+ye ++a+e a   ++++e+ a++e+ea
  gi|474933597|ref|YP_007687179.1| 11 DILSEIKEAESRADQTVAQAEADKKAAVAQARRDSV---KRIQDERAAMSAAYESAVAAEQAaldKEKAEVLAKGEEEA 86
                                      689999999999999999999999999999888863...3335566789999999888776611156778899****** PP

                                      HHHHHHHHCSHHH CS
                      V-ATPase_G_2 81 qavrkraearlqq 93
                                       a+ ++a++++++
  gi|474933597|ref|YP_007687179.1| 87 AAIDAAAQDKIKE 99
                                      ***********98 PP

>> Aminopep  Putative aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   6.8   0.00014      0.42     192     271 ..      28     108 ..      13     112 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00014
                          Aminopep 192 gsaaareeaaaekarreqfralvkatrerLealYas..dlsaeekraakaeileelraeyaelkaeelkglagydew 266
                                       ++a+ +++ aa ++ r++ ++ +++ r++++a Y+s  ++++++  ++kae+l++  +e a++ a+   + ++ + +
  gi|474933597|ref|YP_007687179.1|  28 AQAE-ADKKAAVAQARRDSVKRIQDERAAMSAAYESavAAEQAALDKEKAEVLAKGEEEAAAIDAAAQDKIKEVNDF 103
                                       2333.44444556666677788999***********66677778899999*****9999999999988888888888 PP

                          Aminopep 267 vakpl 271
                                       + k++
  gi|474933597|ref|YP_007687179.1| 104 LTKEF 108
                                       88766 PP

>> Muted  Organelle biogenesis, Muted-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   7.0   0.00051       1.5      70     137 ..      35     102 ..       5     110 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00051
                             Muted  70 lnkkleaalekverllqkeleeekrkseqlqekeeerkaeweeflkelqekkeevDeefeekveelke 137
                                         +  +a +++v+r++++ +      ++ + +++ ++ +e++e+l + +e+ + +D   ++k++e+++
  gi|474933597|ref|YP_007687179.1|  35 KAAVAQARRDSVKRIQDERAAMSAAYESAVAAEQAALDKEKAEVLAKGEEEAAAIDAAAQDKIKEVND 102
                                       222234567899********9999****************************************9987 PP

>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2  10.9   0.00059       1.8       2      64 ..      11      73 ..      10      78 .. 0.92
   2 ?    4.2   0.8     0.022        65       3      43 ..      71     111 ..      69     116 .] 0.78

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00059
                            DUF883  2 eleaeleslladleellkeaadeageeaeelRerleerlerarerlrdaeeavaerakeaaea 64
                                      ++ +e++++ + +++ + +a+++ +  ++++R+   +r+++ r+++++a+e++++  ++a ++
  gi|474933597|ref|YP_007687179.1| 11 DILSEIKEAESRADQTVAQAEADKKAAVAQARRDSVKRIQDERAAMSAAYESAVAAEQAALDK 73
                                      5789************************************************99988888765 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.022
                            DUF883   3 leaeleslladleellkeaadeageeaeelRerleerlera 43 
                                       l +e +++la+ ee + +  + a+++++e+ + l++++era
  gi|474933597|ref|YP_007687179.1|  71 LDKEKAEVLAKGEEEAAAIDAAAQDKIKEVNDFLTKEFERA 111
                                       56677788888888888888889999998888888888877 PP

>> Pannexin_like  Pannexin-like TM region of LRRC8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   5.9    0.0008       2.4     173     250 ..      11      87 ..       4     103 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0008
                     Pannexin_like 173 kalsetakedseekkqeaeekksaskslssesssseesseeesallkkkssvkskaekkvvekkssvsvLdkkegeq 249
                                         lse  + +s+ +++ a++++ +++++++++++s ++ ++e+a ++ + ++ ++ae+++++ k++++vL k e e 
  gi|474933597|ref|YP_007687179.1|  11 DILSEIKEAESRADQTVAQAEADKKAAVAQARRDSVKRIQDERAAMSAAYESAVAAEQAALD-KEKAEVLAKGEEEA 86 
                                       56899999888888887777777777888888888888999999999999999999999999.6779****999887 PP

                     Pannexin_like 250 A 250
                                       A
  gi|474933597|ref|YP_007687179.1|  87 A 87 
                                       6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2023  (0.112834); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 797.72
//
Query:       gi|474933598|ref|YP_007687180.1|  [L=711]
Description: Archaeal/vacuolar-type H+-ATPase subunit I [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.2e-19   67.2  21.5    9.6e-12   43.7   2.4    3.6  3  V_ATPase_I      V-type ATPase 116kDa subunit family
  ------ inclusion threshold ------
        6.9    6.8   5.7        1.1    9.3   1.1    2.0  2  Cauli_DNA-bind  Caulimovirus DNA-binding protein


Domain annotation for each model (and alignments):
>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   1.7     0.092   8.3e+02      37     101 ..      49     113 ..      41     121 .. 0.69
   2 !   43.7   2.4   1.1e-15   9.6e-12     302     538 ..     259     504 ..     193     536 .. 0.67
   3 !   33.9   2.6   9.5e-13   8.5e-09     716     811 ..     580     692 ..     571     693 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.092
                        V_ATPase_I  37 rklrfleeeieklekavikeeeaeesleapeekeldeleeelekleeelkelnenleklkkelne 101
                                        k+r +e+e+  ++ka++ +   e+ +++ e+ e++++e+e+ k+ +  ++l+++ ++l++++++
  gi|474933598|ref|YP_007687180.1|  49 LKVRAMEKELGIKKKAKTANIAVEDVQARIEAGEIESVEDEVLKTVDARNDLTQKITELNAKKKT 113
                                       56778888877767777777776777777777778888777777777777777777777666554 PP

  == domain 2  score: 43.7 bits;  conditional E-value: 1.1e-15
                        V_ATPase_I 302 ldvtkkvliaegWvpkeeleeiqkalkeateess..ssvpsilneietk..etp.....PTyfrtnkfteafQeivd 369
                                       + v+k  ++ ++Wvp+++++ei+  l+++  +    + v++  +++  +   +p     PT     k+ + f     
  gi|474933598|ref|YP_007687180.1| 259 IAVSKYAYVMDAWVPTKKVDEIKAHLEQKLGDDVyvEFVETRSRKMADSeaAEPrfqpvPTKQSNGKIASEFEYATS 335
                                       5677888999******************8865546633333333343321233345557****************** PP

                        V_ATPase_I 370 aYGiarYrEvNpalftiitFPFlFavMFGDiGHGlllllfalllvlkekklkkkkkdeilemlfsgRYiillmGlfs 446
                                         +i++Y+E+ p+++ ++  P  F+ M GD+G ++  ++++++ + k    ++k+   i+ ++f g    +l G+f 
  gi|474933598|ref|YP_007687180.1| 336 LVAIPKYQEIDPTILIMVFLPLFFGFMVGDAGYAIPFIILGIYGLRKT---HHKDWRAIALVFFFGGLWAFLFGFF- 408
                                       ****************************************99866544...4444557888888777777788887. PP

                        V_ATPase_I 447 iYtGliYNdifskslnlfgSswevkeka.....veeeelk........kekkeekvYpfGlDpaWklaenellflnS 510
                                        + G +    f    +  g  we+++++     +   +++          +  +++ +   D +  ++ ++++f   
  gi|474933598|ref|YP_007687180.1| 409 -FYGEMLGMHFVGG-EEIGGVWEWEHNSvavggT---AVTwdwllgehFPEWFSSMMAQVDDGVGIGKLEDVTF--- 477
                                       .4444444444333.3456778886555443320...2223333222211111111111112222333344444... PP

                        V_ATPase_I 511 lKmKlsvilGviqMlfgvllslvNalyf 538
                                         +Kls+ +G++++ +g++  l+N + +
  gi|474933598|ref|YP_007687180.1| 478 -LLKLSIYIGIVHLGIGYVCGLYNRTIQ 504
                                       .478888888888888888888877655 PP

  == domain 3  score: 33.9 bits;  conditional E-value: 9.5e-13
                        V_ATPase_I 716 ciSnTASYLRLWALSLAHaqLs....eVlwemvlkkal.............lksksvlgvillvilfavfavltvav 775
                                       +i n  SY RL A+ ++ a ++     ++++m+++++              +   +  g+i+l+il ++ + +   v
  gi|474933598|ref|YP_007687180.1| 580 VIGNVLSYARLGAIAMSKAGMAlafnYIVFSMIMHTTEtgavqivdgvahnIVAFNPSGAIVLCILGLLLFGFLHLV 656
                                       6888999***9988777776652133477999998855778887777666544455666688887777777777788 PP

                        V_ATPase_I 776 LllmeglsafLHaLRLhWVEfqsKFykgdGykFepf 811
                                       + ++  lsa LHaLRL+ VE + KFy g   +F+p+
  gi|474933598|ref|YP_007687180.1| 657 VWTLAILSAGLHALRLQFVELMMKFYDGGTLQFAPL 692
                                       8999******************************97 PP

>> Cauli_DNA-bind  Caulimovirus DNA-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   1.1   0.00012       1.1      11      72 ..      60     122 ..      51     128 .. 0.76
   2 ?   -1.9   0.2      0.36   3.2e+03       4      31 ..     210     237 ..     207     314 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00012
                                       HHHHHHHHHHHHHHHHHHHHTS--HHHHHHHHHHHHH...HHHHHHHHT-TTHHHHHHHHTXXXX CS
                    Cauli_DNA-bind  11 vlsdqkkieaeikaileklgstkpekesleevaakii...kdltkkidececnkeiveildkkqd 72 
                                       ++++ k+ +  ++ + +++ +++   es+e+   k +   +dlt+ki e + +k+  e+l+k qd
  gi|474933598|ref|YP_007687180.1|  60 IKKKAKTANIAVEDVQARIEAGEI--ESVEDEVLKTVdarNDLTQKITELNAKKKTFELLGKLQD 122
                                       566677777788888888888876..555555555553338********************9886 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.36
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                    Cauli_DNA-bind   4 iaseieevlsdqkkieaeikaileklgs 31 
                                       + sei e  ++   ++  i+a+ ek  s
  gi|474933598|ref|YP_007687180.1| 210 VDSEIAEAQAKIDATAFTIEALKEKYQS 237
                                       5667777777777777777777666544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (711 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       952  (0.0530983); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.80u 0.36s 00:00:01.16 Elapsed: 00:00:00.59
# Mc/sec: 3644.36
//
Query:       gi|474933599|ref|YP_007687181.1|  [L=80]
Description: ATP synthase subunit C [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    9.1e-18   64.4   9.3    1.1e-17   64.0   9.3    1.1  1  ATP-synt_C  ATP synthase subunit C


Domain annotation for each model (and alignments):
>> ATP-synt_C  ATP synthase subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.0   9.3   6.4e-22   1.1e-17       1      59 [.      17      75 ..      17      76 .. 0.98

  Alignments for each domain:
  == domain 1  score: 64.0 bits;  conditional E-value: 6.4e-22
                                      HHHHHHH.GGGHHHHHHHHHHHHHHHHHHHHSGHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        ATP-synt_C  1 lgaglavGlsalgsGigiGkagsagiravarnpklftksliilafaeaialygLivali 59
                                      +gaglavGl++lgsG+g   +g+a+++a+ ++p+lf++++i+ +++e++ ++gL++a++
  gi|474933599|ref|YP_007687181.1| 17 IGAGLAVGLAGLGSGLGEKDIGAAAVGAITEDPSLFGRAMIFTVLPETVVIFGLVIAIM 75
                                      7********************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.36s 00:00:00.88 Elapsed: 00:00:00.55
# Mc/sec: 438.90
//
Query:       gi|474933600|ref|YP_007687182.1|  [L=185]
Description: Archaeal/vacuolar-type H+-ATPase subunit E [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      5e-07   29.3  23.3    6.1e-05   22.5  21.7    2.1  2  vATP-synt_E    ATP synthase (E/31 kDa) subunit
     0.0074   16.3   4.2     0.0082   16.2   4.2    1.2  1  Sds3           Sds3-like
  ------ inclusion threshold ------
      0.013   15.3   0.9       0.02   14.7   0.4    1.5  2  Peptidase_C93  Bacterial transglutaminase-like cysteine prote
       0.04   12.9   5.4      0.052   12.5   5.4    1.1  1  DUF2362        Uncharacterized conserved protein (DUF2362)
       0.36    8.7   5.2       0.37    8.7   5.2    1.0  1  V_ATPase_I     V-type ATPase 116kDa subunit family
        4.8    6.3   5.7        5.8    6.1   5.7    1.2  1  TMPIT          TMPIT-like protein


Domain annotation for each model (and alignments):
>> vATP-synt_E  ATP synthase (E/31 kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5  21.7   2.1e-08   6.1e-05       5     116 ..       9     122 ..       5     128 .. 0.79
   2 !    7.1   0.0    0.0011       3.2     158     199 .]     143     184 ..     112     184 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 2.1e-08
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       vATP-synt_E   5 eAeekAeeIkakaeeefeiekaklveeeeekieeayekkeKqaelqk....kiaiSnalnkarlkvLkareevleev 77 
                                       e e+ A++  ak  ee + e + + e++  +i+e +ek+eK+++ +k    +++ S+a +++++ vL  ++e+l+++
  gi|474933600|ref|YP_007687182.1|   9 EIEASAQASVAKLREEQAAEIKAINEQADAEIAEMKEKQEKRISETKdmlaRQERSSADLESKKIVLAKKKEILNRA 85 
                                       55666666667777888889999999****************97666344389************************ PP

                                       HHHHHHHHHHHTTSHHCCCCHHHHHHCCCCCCC-SSCEE CS
                       vATP-synt_E  78 feeaekkLaeveedkdeYkellkkLivqalvkleepevi 116
                                       fe a  +L++++  k   k   k ++++a   + ep+++
  gi|474933600|ref|YP_007687182.1|  86 FESALVELENMPASK--KKAYYKAMVKAAKKIIPEPKAL 122
                                       ***********9988..4555555555555555566665 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0011
                                       TTSSSEEEECCSSSCEEECCCHHHCHHHHHHHHHHCCCCCHC CS
                       vATP-synt_E 158 edvlGGvvleaadgkikvnnTlearLelvleqllpeirkaLF 199
                                        ++  G +l++adg  +v+     +L+ +++++l++ +  LF
  gi|474933600|ref|YP_007687182.1| 143 SKIRSGLILQSADGSLEVDMQYSVLLQNIWDSNLKQLSDILF 184
                                       46778*********************************9998 PP

>> Sds3  Sds3-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   4.2   2.7e-06    0.0082      46     142 ..       7     133 ..       2     185 .] 0.66

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.7e-06
                              Sds3  46 lrdleeerDaeLkrlrlreeyqlkriekefkadiekakqeheklvkllkekly......eelekkikrLkeeklllD 116
                                       ++++e + +a+ ++lr  +  ++k i+++ +a+i  +k++ ek + ++k+ l       ++le+k+  L + k+ l+
  gi|474933600|ref|YP_007687182.1|   7 TKEIEASAQASVAKLREEQAAEIKAINEQADAEIAEMKEKQEKRISETKDMLArqerssADLESKKIVLAKKKEILN 83 
                                       578999****************************************9997664222222789999999999999999 PP

                              Sds3 117 lanansl.........kktrshta...g............lanesatste 142
                                        a +++l         kk++  +a   +            ++n s+t ++
  gi|474933600|ref|YP_007687182.1|  84 RAFESALvelenmpasKKKAYYKAmvkAakkiipepkalmSENDSFTASD 133
                                       99998887776655442222222233302333334444444444444443 PP

>> Peptidase_C93  Bacterial transglutaminase-like cysteine proteinase BTLCP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.4   6.6e-06      0.02      26      97 ..      13      89 ..       4     112 .. 0.76
   2 ?   -2.3   0.0       1.1   3.3e+03      93     127 ..     128     161 ..     120     169 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.6e-06
                     Peptidase_C93 26 kkekaevklteerlkeleevnasvNeeikpvtdkely...gveerWeypkdgaGdCe..dyallKrkeLieaGlpas 97
                                      +++++ +kl+ee+++e++++n++  +ei+++++k+     +++++ +  +++ +d e   ++l K+ke++++ + ++
  gi|474933600|ref|YP_007687182.1| 13 SAQASVAKLREEQAAEIKAINEQADAEIAEMKEKQEKrisETKDMLARQERSSADLEskKIVLAKKKEILNRAFESA 89
                                      34555689********************99988765511155666777777888876336999*****999988765 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.1
                     Peptidase_C93  93 GlpasallltvvrdekgegHavLtvrtdrGdlvLD 127
                                        + as+l +t v++   +  + L+++  +G l +D
  gi|474933600|ref|YP_007687182.1| 128 SFTASDLGVTAVEKD-SKIRSGLILQSADGSLEVD 161
                                       577888889988764.4555566667777766555 PP

>> DUF2362  Uncharacterized conserved protein (DUF2362)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   5.4   1.7e-05     0.052      89     201 ..       6     124 ..       3     149 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.7e-05
                           DUF2362  89 yhklvhspaletllqlehtyakavedlveernkelekleekqteemekaiqel.dksltdedvnelaakhfeeqqll 164
                                       ++k ++ +a  ++ +l ++ a++++ ++e+ + e+ +++ekq++ ++++ + l  ++++++d  + +    +++++l
  gi|474933600|ref|YP_007687182.1|   6 VTKEIEASAQASVAKLREEQAAEIKAINEQADAEIAEMKEKQEKRISETKDMLaRQERSSADLESKKIVLAKKKEIL 82 
                                       56778889999999999999********************9999997777766545556666666655566666667 PP

                           DUF2362 165 kkklns...eleelketQkkeYrewvmklveelk.sptns.s 201
                                       +  ++s   ele++  + kk Y+++++k ++++  +p+   s
  gi|474933600|ref|YP_007687182.1|  83 NRAFESalvELENMPASKKKAYYKAMVKAAKKIIpEPKALmS 124
                                       777776222667777899*********999999843333322 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   5.2   0.00012      0.37      44     134 ..       8     101 ..       2     183 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00012
                        V_ATPase_I  44 eeieklekavikeeea..eesleapeekeldeleeelekleeelkelnenleklkkelnelvelkavlekakeflee 118
                                       +eie  ++a + + ++  +++ +a +e+   e+ e  ek e++++e+++ l + +++  +l+ +k vl k ke+l++
  gi|474933600|ref|YP_007687182.1|   8 KEIEASAQASVAKLREeqAAEIKAINEQADAEIAEMKEKQEKRISETKDMLARQERSSADLESKKIVLAKKKEILNR 84 
                                       45554444444333332233444444444455566667777777777777777777777888888888888877776 PP

                        V_ATPase_I 119 e.eeeeeeeeseeeeee 134
                                       + e+   e e++ ++++
  gi|474933600|ref|YP_007687182.1|  85 AfESALVELENMPASKK 101
                                       64333333222222222 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   5.7    0.0019       5.8      10      96 ..      17     104 ..       5     140 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0019
                             TMPIT  10 efkeleetakeykqkleelsklqs.kcskeikkqkkrlkelksslkklkksvk.eeeeeeveelkeelker..kkvl 82 
                                       ++ +l+e++    ++++ ++++ + ++++  +kq+kr++e k++l + ++s+   e++++v   k+e+ +r  ++ l
  gi|474933600|ref|YP_007687182.1|  17 SVAKLREEQ---AAEIKAINEQADaEIAEMKEKQEKRISETKDMLARQERSSAdLESKKIVLAKKKEILNRafESAL 90 
                                       333333333...33444444433314555566788888888888888777744244444444445555444113344 PP

                             TMPIT  83 kevesllpkkngly 96 
                                        e+e++  +k+  y
  gi|474933600|ref|YP_007687182.1|  91 VELENMPASKKKAY 104
                                       46666655553333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2447  (0.136483); expected 358.6 (0.02)
Passed bias filter:                      750  (0.0418317); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1130.61
//
Query:       gi|474933601|ref|YP_007687183.1|  [L=350]
Description: ATP synthase A1, C subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.4e-60  203.7   5.6      6e-60  203.5   5.6    1.0  1  vATP-synt_AC39  ATP synthase (C/AC39) subunit


Domain annotation for each model (and alignments):
>> vATP-synt_AC39  ATP synthase (C/AC39) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.5   5.6   3.3e-64     6e-60       3     334 ..      15     345 ..      13     347 .. 0.94

  Alignments for each domain:
  == domain 1  score: 203.5 bits;  conditional E-value: 3.3e-64
                                       HHHHHHGGGS--HHHHHHHTTS.-HHHHHHHHHTSGGGGG--.....SSSHHHHHHHHHHHHHHHTTTGGGGS-H.H CS
                    vATP-synt_AC39   3 ArvramrsglLteedyenLlqcesledvkryLketdYgnfladelseplsrsdiekalreklarefnklreqapgps 79 
                                       Arv+ ++++l+++edy++Ll  +s++++  y++e +Y++++ d ++++++ s +e+a   ++a+ f+++++ ++g++
  gi|474933601|ref|YP_007687183.1|  15 ARVKSKKAKLMKAEDYNKLL-VMSVPEISHYISEAGYAKEMTDLATRYSGLSLLEYATYTNMAKAFRSILTSSKGEL 90 
                                       9******************5.55**********************99*****************************5 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHH.T--GGGS-..--.SSSS-HHHHHHHHHSSSHHHHHHHHHT-HHHHHHHHHH CS
                    vATP-synt_AC39  80 refldyllyrydidNvklllrgklsgdldleeleeklhplgelsaldldklieaksveelyeallgtpyakyleeal 156
                                        ++++++l ++di N ++++r+k   +++ e  +e+l+p+g+l ++dldkl++  +v++ ++a       k+ ee++
  gi|474933601|ref|YP_007687183.1|  91 ANMVQAYLTKWDIYNAMIIMRAKKF-GVSMESAREDLVPAGKLNMDDLDKLLAYPTVDDTLAAYCTMVHIKVPEEYM 166
                                       5************************.6888***********************************8888899999** PP

                                       CC...--SHHHHHHHHHHHHHHHHHHHHHTSS-HH...HHHHHHHHHHHHHHHHHHHTTTSS......T...--SS- CS
                    vATP-synt_AC39 157 deleetgdleiienaLdkayledllkfckklggetaeilreilgfeiDlrniniilrskkygelskedrkkllipgg 233
                                       + +++ + l+++e   ++ y+++llk ++  +++t +i+ +++++ iD +n+ ++l++k+  + s+e + +++ipgg
  gi|474933601|ref|YP_007687183.1| 167 QMYRDRNILAPVEDFFYRDYYKNLLKNIDAHDRPT-NIFLSYIKHVIDHKNLETALKLKN-DKISPEIIMAFFIPGG 241
                                       *****9999********************999888.9***********************.669************* PP

                                       .S--HHHHHHHHTT-G.....GG..GGSSTSSTTGGGTT-.-S.HHHHHHHHHHHHHHHHHT.TTSSSTSTHHHHHH CS
                    vATP-synt_AC39 234 .slypeglealaeaedveellaal.kyteygelleealee.agslksledaldealvkllkk.afrqqfsvgvfyaY 306
                                        +++++ ++a+a+a+dv  +l+   +   y +l +++++e ++s  ++  al e    ++ k +++++ s+ +++ Y
  gi|474933601|ref|YP_007687183.1| 242 aEIDEKVMTAMANADDVAGVLSEAsQLKLYVDL-KDIISEeTDSVLKISAALSELGAVMANKvSHMYPPSIIPVMDY 317
                                       ************************555666665.5555554788********************************* PP

                                       HHHHHHHHHHHHHHHHHHHHT--SHHHH CS
                    vATP-synt_AC39 307 lklkeqEirnlrwIaegiaqglpkekIr 334
                                       +++ke+E+rn+r+Ia g+  gl+ e ++
  gi|474933601|ref|YP_007687183.1| 318 MIHKENEVRNIRMIAHGVDSGLDVEIMK 345
                                       **********************997554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 2057.13
//
Query:       gi|474933602|ref|YP_007687184.1|  [L=101]
Description: Archaeal/vacuolar-type H+-ATPase subunit F [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.9e-15   55.1   0.1    8.2e-15   54.9   0.1    1.1  1  ATP-synt_F  ATP synthase (F/14-kDa) subunit


Domain annotation for each model (and alignments):
>> ATP-synt_F  ATP synthase (F/14-kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   0.1   4.5e-19   8.2e-15       1      84 [.       3      87 ..       3      92 .. 0.89

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 4.5e-19
                                      EEEEESHHHHHHHHHTTCEEEECSSHHHHHHHHHHHHHHTTEEEEEEEHHHHCCCHHHHHHCTCS.SSSEEEEESCSCC CS
                        ATP-synt_F  1 iavIGdedtvtgfrlaGvgevevtdeeeieealkelleredigiilitekiaeeirelideykee.alPaileIPskeg 78
                                      i+vIG+ ++++gfrlaGv++v v+d+e+ +++++e++++ digi+++  + +++++++ ++  +e   P+++++ + ++
  gi|474933602|ref|YP_007687184.1|  3 IGVIGSDEFTLGFRLAGVRKVFVADAENYQAKMQEAMADADIGILAVMSDDLQNLPTNYKNKIMEsIQPVVVPVGGDSN 81
                                      89******************************************************7777666665********88888 PP

                                      GGSHHC CS
                        ATP-synt_F 79 pydeek 84
                                      + +e+ 
  gi|474933602|ref|YP_007687184.1| 82 DLREKV 87
                                      776664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 621.52
//
Query:       gi|474933603|ref|YP_007687185.1|  [L=553]
Description: Archaeal/vacuolar-type H+-ATPase subunit A [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-91  306.2   0.0    1.8e-91  305.6   0.0    1.3  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
      3e-38  130.4   0.0    6.7e-38  129.3   0.0    1.6  1  ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extens
    3.5e-08   33.8   1.3    6.8e-08   32.9   0.2    2.1  2  ATP-synt_ab_N    ATP synthase alpha/beta family, beta-barrel 
  ------ inclusion threshold ------
      0.062   13.5   0.6        1.3    9.3   0.0    2.5  2  Peptidase_M23    Peptidase family M23


Domain annotation for each model (and alignments):
>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  305.6   0.0   3.9e-95   1.8e-91       1     212 [.     184     404 ..     184     405 .. 0.97

  Alignments for each domain:
  == domain 1  score: 305.6 bits;  conditional E-value: 3.9e-95
                                       SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEEESEEHHHHHHHHHHCHH.......SSGGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxx RF
                       ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsddaiiyvgiGergnevaevleefpe.......gtimk 70 
                                       G+rvlD++fp+++G+  +ipgafg+Gktv +qsl+k+s+++ +++y+g+Gergne++evl+efp        +++mk
  gi|474933603|ref|YP_007687185.1| 184 GLRVLDTMFPLAKGGAAAIPGAFGTGKTVTQQSLAKYSDAQ-IVVYIGCGERGNEMTEVLTEFPAlkdpttgESLMK 259
                                       89***********************************9877.***********************999877445*** PP

                                       GEEEEEEETTS-HHHHHHHHHHHHHHHHHHHHTTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  71 rtvlvantsnepvaareasiytgitlAEyfrdqgknvlliadslsrwaeAlreislrlgempadqgypaylgaklas 147
                                       rt+l+antsn+pvaareas+ytg+t+AEyfrd+g+nv l+ads+srwaeA+reis rl+emp+++gypayl  +l++
  gi|474933603|ref|YP_007687185.1| 260 RTILIANTSNMPVAAREASVYTGMTIAEYFRDMGYNVALMADSTSRWAEAMREISSRLEEMPGEEGYPAYLSGRLSE 336
                                       ***************************************************************************** PP

                                       HHTTSEEE...TSSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEE CS
                                       xxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab 148 lyERagka...pdrtGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSv 212
                                       +yERa++      + Gs++++ avsp+ggD+s+pvt++tl+i+ +f+ Ld+kl +r+hfP in+l+S+
  gi|474933603|ref|YP_007687185.1| 337 FYERACRGktlCGEDGSISVIGAVSPPGGDLSEPVTQNTLRIVRVFWALDTKLRERRHFPTINWLTSY 404
                                       *****9996665669****************************************************9 PP

>> ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.3   0.0   1.5e-41   6.7e-38       1     120 [.      61     174 ..      61     175 .. 0.95

  Alignments for each domain:
  == domain 1  score: 129.3 bits;  conditional E-value: 1.5e-41
                                       EETTS-BHHHHHHHHTSBE-TT----SS-SSS-EEEEESS-TT-EEETT-EEEEEECTTCEEEEEE--TT-.EEEEE CS
                   ATP-synt_ab_Xtn   1 yDGiqrpLekiaeksgsfierGvkvpaldrekkwefkpkvkvgdkvsggdilGtvqeteliehkimvppkv.egkvk 76 
                                       yDGiqrpL  +++k+g+fi rG+++p l+re kw+f+p+v+vgd+v++g+++Gtvqe  +  h+im+pp++  gkv+
  gi|474933603|ref|YP_007687185.1|  61 YDGIQRPLPVLRDKMGDFIYRGATAPGLNREAKWDFVPAVSVGDEVKAGTVIGTVQEGPI-VHRIMLPPNAkGGKVE 136
                                       9*********************************************************99.6*******983567** PP

                                       EE--EEEE-TTSECEEECETT.ECEEEESSEEEETTS---ESEE CS
                   ATP-synt_ab_Xtn  77 eiaeegeytvedtiaeveteegkekeltllqkwPvrkprpvkek 120
                                       +i+ +g++tve+ +++v+      +e+ ++qkwPvr prpv ek
  gi|474933603|ref|YP_007687185.1| 137 KIE-AGSFTVEESVITVDG-----AEYPMMQKWPVRAPRPVIEK 174
                                       *98.*************93.....579**************998 PP

>> ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.2   1.5e-11   6.8e-08      21      69 .]       1      45 [.       1      45 [. 0.97
   2 ?   -2.7   0.1         2   8.8e+03      35      46 ..     439     450 ..     431     463 .. 0.56

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 1.5e-11
                                      TTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBTTSEEEEES CS
                     ATP-synt_ab_N 21 iynalevelvefgtlllgvalnlgedkVrvivmgstdGlsrGteVkrTG 69
                                      +y++++v+  +  ++l+g+++ + +dk +++v+++t+G+++G++V +TG
  gi|474933603|ref|YP_007687185.1|  1 MYDVVHVG--N--EQLMGEVIKIVGDKSIIQVYEDTTGIKPGEPVSNTG 45
                                      79999***..8..9**********************************8 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2
                                       EEEEEEEEEETT CS
                     ATP-synt_ab_N  35 lllgvalnlged 46 
                                        l++v++ +g d
  gi|474933603|ref|YP_007687185.1| 439 ELQEVVQMVGSD 450
                                       455555555544 PP

>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1     0.071   3.2e+02      24      63 ..       4      41 ..       3      45 .. 0.83
   2 ?    9.3   0.0   0.00029       1.3      56      73 ..      99     116 ..      92     123 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.071
                                      EEEEEEETTTEEEEEEEECTCEEEEEEEESEESS-TTEEE CS
                     Peptidase_M23 24 VvfagkkegyGnvviidhgdgystlyahlskisvkegqkV 63
                                      Vv++g+++ +G+v+ i  ++ ++++y       +k+g+ V
  gi|474933603|ref|YP_007687185.1|  4 VVHVGNEQLMGEVIKIVGDKSIIQVYEDTTG--IKPGEPV 41
                                      8999998788***************988766..6777666 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00029
                                       SS-TTEEE-TTCEEEEEB CS
                     Peptidase_M23  56 svkegqkVkaGqvIGtvg 73 
                                       +v++g++VkaG+vIGtv 
  gi|474933603|ref|YP_007687185.1|  99 AVSVGDEVKAGTVIGTVQ 116
                                       499*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (553 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.73u 0.34s 00:00:01.07 Elapsed: 00:00:00.58
# Mc/sec: 2882.47
//
Query:       gi|474933604|ref|YP_007687186.1|  [L=460]
Description: Archaeal/vacuolar-type H+-ATPase subunit B [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.3e-67  225.6   0.0    9.2e-67  224.8   0.0    1.4  1  ATP-synt_ab    ATP synthase alpha/beta family, nucleotide-bin
    9.6e-13   48.5   0.2      2e-12   47.4   0.2    1.6  1  ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel do
  ------ inclusion threshold ------
       0.01   15.9   0.2      0.032   14.4   0.1    1.9  2  HAS-barrel     HAS barrel domain


Domain annotation for each model (and alignments):
>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  224.8   0.0   1.5e-70   9.2e-67       1     213 []     134     352 ..     134     352 .. 0.98

  Alignments for each domain:
  == domain 1  score: 224.8 bits;  conditional E-value: 1.5e-70
                                       SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTS....S.EEEEEEESEEHHHHHHHHHHCHHSSGGGGE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsd....d.aiiyvgiGergnevaevleefpegtimkrt 72 
                                       Gi+++D + ++v+Gq++ i++a+g++++ i+ ++++q++ +    + a+++++ G  ++e +++++ef++++++k+ 
  gi|474933604|ref|YP_007687186.1| 134 GISTIDGMNTLVRGQKLPIFSASGLPHNDIALQIARQAKVRgeneEfAVVFIALGITNEEKQKFMNEFERTGALKNA 210
                                       899**********************************9888999768****************************** PP

                                       EEEEEETTS-HHHHHHHHHHHHHHHHHHHH.TTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  73 vlvantsnepvaareasiytgitlAEyfrd.qgknvlliadslsrwaeAlreislrlgempadqgypaylgaklasl 148
                                       v+++n +++p+++r+ ++++g+t+AEy++   g++vl+i++++++++eAlr+i+++ +e+p+++gyp+y++++la+l
  gi|474933604|ref|YP_007687186.1| 211 VVFLNLADDPAVERISTPRLGLTTAEYMAFdLGMQVLVIMTDITNYCEALRQIGAARDEVPGRRGYPGYMYTDLAQL 287
                                       ****************************9779********************************************* PP

                                       HTTSEEETSSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab 149 yERagkapdrtGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                       yERag+++ ++Gs+t++++++++g+D+++p+++   +it+g+ivL+++l++++++P++nv+ S+S
  gi|474933604|ref|YP_007687186.1| 288 YERAGRIKGKNGSITQIPILTMPGDDITHPIPDLSGYITEGQIVLSRELHRNGIYPPVNVSSSLS 352
                                       ***************************************************************98 PP

>> ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.4   0.2   3.3e-16     2e-12       3      69 .]      14      77 ..      12      77 .. 0.96

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 3.3e-16
                                      EEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBTTSEEEEES CS
                     ATP-synt_ab_N  3 qviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsrGteVkrTG 69
                                       + Gp+v v++ +    g+ ++++v+l + g+  +g++l  ++d+V ++++++t+G++r + V+++G
  gi|474933604|ref|YP_007687186.1| 14 NIAGPLVFVKNTEP--VGYQEMVSVRLSD-GSIKRGQVLDTSDDMVCIQIFEGTTGIDRAAAVRFLG 77
                                      799***********..9*********999.***********************************98 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   5.4e-06     0.032       4      48 ..       8      53 ..       5      92 .. 0.81
   2 ?   -3.0   0.0       1.4   8.4e+03       4      21 ..     132     149 ..     131     154 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.4e-06
                        HAS-barrel  4 vigests.sslifrvegskdvkvGeyVeielpdgeivlGmvtdirr 48
                                      ++ +  +  +++++v+++++v++ e+V+++l dg+i  G+v+d + 
  gi|474933604|ref|YP_007687186.1|  8 EYKTIENiAGPLVFVKNTEPVGYQEMVSVRLSDGSIKRGQVLDTSD 53
                                      555555558999******************************9876 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.4
                        HAS-barrel   4 vigestssslifrvegsk 21 
                                       ++g st+++  + v+g+k
  gi|474933604|ref|YP_007687186.1| 132 ETGISTIDGMNTLVRGQK 149
                                       789999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 2687.29
//
Query:       gi|474933605|ref|YP_007687187.1|  [L=212]
Description: H(+)-transporting ATP synthase, vacuolar type, subunit D [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.4e-52  177.6   6.7    2.7e-52  177.5   6.7    1.0  1  ATP-synt_D  ATP synthase subunit D
  ------ inclusion threshold ------
      0.026   15.2   0.1      0.047   14.3   0.1    1.4  1  Ead_Ea22    Ead/Ea22-like protein
      0.034   14.4   1.6       0.21   11.9   0.1    2.2  2  DUF1811     Protein of unknown function (DUF1811)
      0.054   13.3   0.1       0.13   12.1   0.1    1.6  1  CCDC92      Coiled-coil domain of unknown function
       0.11   12.0   0.0       0.13   11.8   0.0    1.1  1  SMRP1       Spermatid-specific manchette-related protein 1


Domain annotation for each model (and alignments):
>> ATP-synt_D  ATP synthase subunit D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.5   6.7   7.6e-56   2.7e-52       2     195 ..      16     207 ..      15     208 .. 0.95

  Alignments for each domain:
  == domain 1  score: 177.5 bits;  conditional E-value: 7.6e-56
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTSTTSTSHHHHHHHSSS.SS-.. CS
                        ATP-synt_D   2 LirlkkrlklaqrghslLkkKrdaLilefreilkelkelreeleeelkeayfslaeafaaggeediesavlesvkla 78 
                                       L+ lk+r+kl q gh++Lk+Krd Li+ef+e+l++++++r  +++ ++ a   ++ a+a++ge +++sa+ + ++  
  gi|474933605|ref|YP_007687187.1|  16 LLDLKRRIKLSQSGHKILKMKRDGLIIEFFEVLEKARQMRAGVATDFEVAMRNITIARAVDGEIAVKSAAYALKS-- 90 
                                       789********************************************************************6655.. PP

                                       TSS-SEEEEEEBTTSEEEEEEE-.......S.SSTSSSSSSSSTCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHH CS
                        ATP-synt_D  79 kvvkvelktenvaGVkvpvfeleee.....ksdstelygllrtgaqldeavealrellellvelasletslelLdee 150
                                        + +v+l++++++G  vp++e e+      ++     yg+l+t+a+++ a++++++lle+l+++a++et++++L +e
  gi|474933605|ref|YP_007687187.1|  91 -HPTVKLTSHSIMGMMVPKVEAEKIhtdiiGR----GYGILNTSAYVAAAADSFEKLLETLIRAAEVETTMKKLLDE 162
                                       .699****************987667555544....5**************************************** PP

                                       HHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        ATP-synt_D 151 ikktnrRvNaLekvvIPrleetikyIkseLdEqereeffrlkkvk 195
                                       i+kt+rRvNaLe +vIP l+e  ++++s+L+E+ere++++lk +k
  gi|474933605|ref|YP_007687187.1| 163 IEKTKRRVNALEFKVIPDLQESQRFVRSRLEEMERETTTSLKHLK 207
                                       ******************************************998 PP

>> Ead_Ea22  Ead/Ea22-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   1.3e-05     0.047      24     111 ..     105     197 ..      95     211 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.3e-05
                          Ead_Ea22  24 iipgisssrityectgegnddefklgrtvakeh......daefiaaan.patvlaLLDelekkqqrikeleeeaene 93 
                                       ++p+  + +i++ + g+g++  +  + +va+ +       ++ i aa+   t+  LLDe+ek ++r+ +le      
  gi|474933605|ref|YP_007687187.1| 105 MVPKVEAEKIHTDIIGRGYGILN-TSAYVAAAAdsfeklLETLIRAAEvETTMKKLLDEIEKTKRRVNALEFK-VIP 179
                                       56777778888888888887774.3333333335788999999999864788999**************9933.456 PP

                          Ead_Ea22  94 dialtvgklrveleaaek 111
                                       d+++  +  r+ le++e+
  gi|474933605|ref|YP_007687187.1| 180 DLQESQRFVRSRLEEMER 197
                                       666666666667777776 PP

>> DUF1811  Protein of unknown function (DUF1811)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   5.7e-05      0.21       6      79 ..      35     105 ..      30     112 .. 0.82
   2 ?    1.4   0.1       0.1   3.8e+02       8      37 ..     149     178 ..     146     186 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.7e-05
                                       --HHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHS-GGGS-TT-EEEET.TSS-EEEEEEEETTE CS
                           DUF1811   6 mseeeLkqeiaklkekarkaeqlgivnelavlerkialAksYlldpsdfkpgelYeieedeeelfkvdylnGvf 79 
                                       m +  L  e  ++ ekar+ +  g   +++v +r i++A++  +d +   +   Y +++ +  +++ + + G++
  gi|474933605|ref|YP_007687187.1|  35 MKRDGLIIEFFEVLEKARQMR-AGVATDFEVAMRNITIARA--VDGEIAVKSAAYALKSHPTVKLTSHSIMGMM 105
                                       555566666667778888876.8*****************8..8888888889999999999888888888887 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.1
                                       HHHHHHHHHHHHHHHHHHHHTT-HHHHHHH CS
                           DUF1811   8 eeeLkqeiaklkekarkaeqlgivnelavl 37 
                                        +e+++ ++kl ++ +k++++ +  e++v+
  gi|474933605|ref|YP_007687187.1| 149 AAEVETTMKKLLDEIEKTKRRVNALEFKVI 178
                                       57999999***9999999999999999886 PP

>> CCDC92  Coiled-coil domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   3.6e-05      0.13      19      44 ..     153     178 ..     150     187 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.6e-05
                            CCDC92  19 aatLkgLHkEIekLqkenkdLtfkli 44 
                                       ++t k+L +EIek ++++  L+fk+i
  gi|474933605|ref|YP_007687187.1| 153 ETTMKKLLDEIEKTKRRVNALEFKVI 178
                                       6799********************97 PP

>> SMRP1  Spermatid-specific manchette-related protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.6e-05      0.13      88     168 ..     105     184 ..      55     208 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.6e-05
                             SMRP1  88 wlseeeaekcspaylssdryatwrtapynssywnkyttclprlpkeagmetvvrgmpleyppkperlnayerevvvn 164
                                        + + eaek+    + +  y+   t+ y ++  + +   l  l + a +et ++ +  e+     r+na e +v+ +
  gi|474933605|ref|YP_007687187.1| 105 MVPKVEAEKIHTDII-GRGYGILNTSAYVAAAADSFEKLLETLIRAAEVETTMKKLLDEIEKTKRRVNALEFKVIPD 180
                                       566788898887766.568*************************************999999999********9988 PP

                             SMRP1 165 mlns 168
                                       + +s
  gi|474933605|ref|YP_007687187.1| 181 LQES 184
                                       7766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1375  (0.0766914); expected 358.6 (0.02)
Passed bias filter:                      736  (0.0410508); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1264.26
//
Query:       gi|474933606|ref|YP_007687188.1|  [L=49]
Description: hypothetical protein TALC_00013 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      0.005   16.6   0.1     0.0063   16.3   0.1    1.1  1  Asp4      Accessory secretory protein Sec Asp4
  ------ inclusion threshold ------
      0.043   13.5   0.3      0.045   13.5   0.3    1.1  1  TMEM252   Transmembrane protein 252 family


Domain annotation for each model (and alignments):
>> Asp4  Accessory secretory protein Sec Asp4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1     7e-07    0.0063       7      50 ..       2      45 ..       1      47 [. 0.89

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7e-07
                              Asp4  7 keveGrmeslkrrPaekekttrsekinvtfnviiGlvillGvif 50
                                      k +e r+e +   Pa k k  +   i     +++G+vi+l v+f
  gi|474933606|ref|YP_007687188.1|  2 KSLEERLEEFAEDPAKKAKLFKWTIIIAYSMLMLGIVIILAVLF 45
                                      7899****************99987777777889*********9 PP

>> TMEM252  Transmembrane protein 252 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.3     5e-06     0.045       9      31 ..      23      45 ..      15      49 .] 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5e-06
                           TMEM252  9 rknlilaylllPlGfvillsGif 31
                                      ++ +i+ay +l lG vi+l+ +f
  gi|474933606|ref|YP_007687188.1| 23 KWTIIIAYSMLMLGIVIILAVLF 45
                                      6789***************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1238  (0.0690501); expected 358.6 (0.02)
Passed bias filter:                      708  (0.0394891); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 359.46
//
Query:       gi|474933607|ref|YP_007687189.1|  [L=480]
Description: Archaeal DNA polymerase II, small subunit/DNA polymerase delta, subunit B [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-14   54.3   0.2    4.4e-14   53.5   0.2    1.4  1  Metallophos    Calcineurin-like phosphoesterase
    4.6e-13   49.0   0.0    6.9e-13   48.4   0.0    1.2  1  DNA_pol_E_B    DNA polymerase alpha/epsilon subunit B
    3.2e-05   24.2   0.0      6e-05   23.3   0.0    1.4  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   0.2   7.4e-18   4.4e-14       2     202 ..     226     425 ..     225     427 .. 0.78

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 7.4e-18
                                       EEEEEESBTB...TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS................HHHHHHHHHHHH CS
                       Metallophos   2 rilvigDlHl...algggqlddllkllddllreekpdlvllaGDlvdrg................dlekellellaa 59 
                                       ++++++D+H+   +   g++++ +++l+   +++++++++++GD+vd+                 d        + a
  gi|474933607|ref|YP_007687189.1| 226 SVAFLSDIHIgskEFLRGSWEKMIAFLKAHSDDQQINYIIMPGDVVDGIgaypgqeadleiddiyDQ-------YHA 295
                                       699**********8888*******************************8899999998755443333.......444 PP

                                       HHHH......TSEEEEEC-TTS..CHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEET CS
                       Metallophos  60 lvky......pipvylllGNHe..gfeeellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGgspell 128
                                       l +y      +i+++l +GNH+        +++ + ++i+ + + s+   + + p++  ++g  ++++ ++g     
  gi|474933607|ref|YP_007687189.1| 296 LSEYikeipdDIRLVLHPGNHDacR---LAEPQPALNEIYTKSFDSN-VAMVGNPINMKIEG--RIVTSYHG----- 361
                                       44445556668999********331...3344444444556666665.44456677777999..9******9..... PP

                                       HHHHHHHHHHHSCHHHHCC..HHHHHHHHHHTTCSEEEEEESSESSCSSSCSCCHHHHHHHHHHTTESEEEEESSS CS
                       Metallophos 129 vsldklgslnleleapepg..dewlkdlekrekadwvivlgHsplyrgsgylfgdealedllkkygvdlvisGHtH 202
                                       +s+d++ s ++el+++ p    + +++             +  p+y g  +  ++e  + l  ++ +d+ +sGH+H
  gi|474933607|ref|YP_007687189.1| 362 KSIDDWISGVRELTYENPLlvMKYMAE-----------RRHLAPMY-GQRNALAPEKKDYLVMDNVPDIFVSGHVH 425
                                       899999999999999888666666666...........56688999.99999999999999*************** PP

>> DNA_pol_E_B  DNA polymerase alpha/epsilon subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.4   0.0   1.1e-16   6.9e-13       1     203 [.     227     422 ..     227     426 .. 0.90

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 1.1e-16
                                       EEEEES--S-TT---...-HHHHHHHHHHH.HTT--SEEEEES-SSBTTSHHHHHT---S--SSHHHHHHHHTHHHH CS
                       DNA_pol_E_B   1 vvivsglnldndnrs...leaLrkiLqgyapeesppdvlilaGnfvdaahkaiasskvstdekkenfdalalllsil 74 
                                       v+++s++++ ++++     e++  +L+ +  +++++  +i+ G  vd   +  +++ + + e ++  d   +l++ +
  gi|474933607|ref|YP_007687189.1| 227 VAFLSDIHIGSKEFLrgsWEKMIAFLKAHS-DDQQINYIIMPGDVVDGIGAYPGQE-A-DLEIDDIYDQYHALSEYI 300
                                       678999999977777777888888888888.****************555555444.4.4799999999999999** PP

                                       TTS-TTSEEEEE--TTBTT-S-SBSB----TTTTT--TTT...EEE--BSEEEEETTEEEEE--S-HHHH---EEES CS
                       DNA_pol_E_B  75 esllekttvvlvPgpnDpanstvlPqqPlprlllsrikrvfkelklvtNPsrielnsvevvltsddivkdlkreslk 151
                                       +++   +++vl Pg  D++   + Pq++l++++++  +++   + +v NP  +++++  v  + +  ++d    + +
  gi|474933607|ref|YP_007687189.1| 301 KEIPDDIRLVLHPGNHDACRL-AEPQPALNEIYTKSFDSN---VAMVGNPINMKIEGRIVTSYHGKSIDDWISGVRE 373
                                       *********************.*****************8...99*************************9998888 PP

                                       HHHHHS-HHHHHHHHHHHHTBS---SS--B-GGGGGGGB-GGG---SEEE-- CS
                       DNA_pol_E_B 152 esntdverlrklvktildqrhlaPlaptlrpvswdkddalvleplPdvlvlp 203
                                        +    e+ + ++k++ + rhlaP++ +  +   +k+d lv++ +Pd++v +
  gi|474933607|ref|YP_007687189.1| 374 LTY---ENPLLVMKYMAERRHLAPMYGQRNALAPEKKDYLVMDNVPDIFVSG 422
                                       888...799****************************************987 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0     1e-08     6e-05       3     147 ..     227     444 ..     226     454 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1e-08
                     Metallophos_2   3 laiiSDlH.........snldaleavlealkevgvdaiihaGD.......leeeep...............evleel 48 
                                       +a++SD+H         s+ + ++ + ++ +++++++ii+ GD       +    p               ++l e 
  gi|474933607|ref|YP_007687189.1| 227 VAFLSDIHigskeflrgSWEKMIAFLKAHSDDQQINYIIMPGDvvdgigaY----PgqeadleiddiydqyHALSEY 299
                                       789*******9999995444444444455556889********55555541....2444555665555333344444 PP

                     Metallophos_2  49 lela....pvlaVrGNnD.......eev.veedvlreaaelgtdlpeeaelelagekvlliHgdpl........... 102
                                       ++      +++  +GN+D       +   + e   +++      + +  +++++g+ v  +Hg+             
  gi|474933607|ref|YP_007687189.1| 300 IKEIpddiRLVLHPGNHDacrlaepQ-PaLNEIYTKSFDSNVAMVGNPINMKIEGRIVTSYHGKSIddwisgvrelt 375
                                       44447844555558****88887632.34667777777777777799999999**99******977*********** PP

                     Metallophos_2 103 .....................gvkdalaellke...aeegsdvvvcGHtHvpevekeggvlvvnPGsvg 147
                                                            g ++ala+  k+   ++++ d++v+GH H ++  + +gv+++n+   +
  gi|474933607|ref|YP_007687189.1| 376 yenpllvmkymaerrhlapmyGQRNALAPEKKDylvMDNVPDIFVSGHVHGAGTMEYHGVRMINASTWQ 444
                                       ***********9999999999666666666666554557778**********************86655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (480 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.49
# Mc/sec: 2949.66
//
Query:       gi|474933608|ref|YP_007687190.1|  [L=175]
Description: Carbonic anhydrase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-28   99.3   2.8    8.1e-28   97.7   2.8    1.7  1  Pro_CA    Carbonic anhydrase


Domain annotation for each model (and alignments):
>> Pro_CA  Carbonic anhydrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.7   2.8   4.5e-32   8.1e-28       2     113 ..      44     148 ..      43     172 .. 0.80

  Alignments for each domain:
  == domain 1  score: 97.7 bits;  conditional E-value: 4.5e-32
                                       EEEEETTTTS-HHHHTTS-TTSEEEEEETTG---TT-HHHHHHHHHHHHTS--SEEEEEEETT-HHHHHHHSHHCCS CS
                            Pro_CA   2 lvigCsDSRvppelitdagpGdlFvvrnvgnlvppadssvlaaleyAvevlkvkhivVlGHskCGavkaalkaekse 78 
                                       ++++CsDSRv+pe+++++g+G+lFv+r++gn++    ++ l++++yAv++l+   +vV+ H++CGav+aal+     
  gi|474933608|ref|YP_007687190.1|  44 AIVTCSDSRVVPEIVFNTGIGELFVIRTAGNTI---FDGELGSIDYAVSHLGCGIVVVMAHTHCGAVHAALNG---- 113
                                       79*******************************...9*******************************99974.... PP

                                       TTSSHHHHHHHHHHHHHHHCHHHHHTTSSHHHHHH CS
                            Pro_CA  79 eeagaidkwlekirealekveeelesekekearer 113
                                       +++g++++++++i e++   e+ +e + ++++ ++
  gi|474933608|ref|YP_007687190.1| 114 HNHGHVGAIVDRISESIGDEEDPTEVSVQNARNSA 148
                                       33689999999999988876654444332222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1243.34
//
Query:       gi|474933609|ref|YP_007687191.1|  [L=130]
Description: archaeal conserved hypothetical protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-12   47.7   0.0    7.7e-11   42.3   0.0    2.1  1  RNA_binding  RNA binding
  ------ inclusion threshold ------
       0.26   11.1   0.4       0.54   10.0   0.4    1.5  1  Zn_Tnp_IS1   InsA N-terminal domain


Domain annotation for each model (and alignments):
>> RNA_binding  RNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.0   8.6e-15   7.7e-11       2     115 ..       4     104 ..       3     107 .. 0.76

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 8.6e-15
                                       EEEEEEE-TTC-HHHHHHHHHTTSTTSE---EEEEEE-CCC-EEEEEEEEESSHHHHHHHHHHHHHHCCCCH..... CS
                       RNA_binding   2 ievrafvhaTEdeekVlealsnllpeeeveieeeeaeGhygnpitileaelekkkakkvlkkllellreeei..... 73 
                                       ++v++ v+++Ed ekV++al +++p+ +                ++  +++++    + l+++ +l+r+++i     
  gi|474933609|ref|YP_007687191.1|   4 VTVSCPVYPSEDPEKVKKALLSIFPTGD---------------FQLEDGTMSG---TADLDNFSNLIRKQRIldttr 62 
                                       899**********************554...............4466666667...444455555555555555577 PP

                                       HHHHHCCHCCB-TTSEEEEEEEHHHHHTT---BESSSS...EEEE CS
                       RNA_binding  74 keLlkeleervdekgklylrldKQaaylgklslvegdd...vIkv 115
                                       +++lk++ +    + k+ + l+KQ a +gk+s+ve       I+v
  gi|474933609|ref|YP_007687191.1|  63 SQMLKGMGR---STRKTRFNLNKQVATVGKVSFVEYRIalgTIEV 104
                                       999999999...689******************997655555555 PP

>> Zn_Tnp_IS1  InsA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.4   6.1e-05      0.54       1      10 [.       1      10 [.       1      16 [. 0.84

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 6.1e-05
                        Zn_Tnp_IS1  1 MAsVsihCPr 10
                                      MA+V+++CP 
  gi|474933609|ref|YP_007687191.1|  1 MAAVTVSCPV 10
                                      9********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.35s 00:00:00.89 Elapsed: 00:00:00.66
# Mc/sec: 590.97
//
Query:       gi|474933610|ref|YP_007687192.1|  [L=254]
Description: Sugar phosphate isomerase/epimerase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.2e-25   88.1   0.2    6.5e-25   87.8   0.2    1.1  1  AP_endonuc_2   Xylose isomerase-like TIM barrel
  ------ inclusion threshold ------
      0.042   12.6   0.1      0.048   12.4   0.1    1.1  1  ThiC_Rad_SAM   Radical SAM ThiC family
      0.062   13.6   0.0         17    5.8   0.0    2.6  3  Ta0938         Ta0938
      0.083   13.0   1.2       0.28   11.3   0.5    2.1  2  Lipase_GDSL_3  GDSL-like Lipase/Acylhydrolase family


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.8   0.2   1.4e-28   6.5e-25      51     210 .]      62     216 ..      33     216 .. 0.90

  Alignments for each domain:
  == domain 1  score: 87.8 bits;  conditional E-value: 1.4e-28
                                       CCHSTCTHCHTTCS.HHHHHHHHHHHHHHHHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSE CS
                      AP_endonuc_2  51 trfgypdederear.reesvdalkraielaaaLGapllvlhpGtagagpkgseeeawerlaeslneladyaekegvk 126
                                       t+ + ++    ++r re+sv ++ +++e+a ++G+++l++hpG+ +   +g+++  ++ + +s + + + a ++g +
  gi|474933610|ref|YP_007687192.1|  62 TDISCVNIAAVNERmREASVMEIVSEMEAAVEMGIDTLTVHPGIINLAVSGTRDRSVRSAKNSARFISRAANEYGLR 138
                                       3333333334555689999*************************9999***************************** PP

                                       EEEE--TTTTSSSTC..HHHHHHHHHHTTTTEEEEEEHHHHHHHTTTHHHHHHHHHGGEEEEEE.EESSTTTTSSTT CS
                      AP_endonuc_2 127 lalEtlagsgvelgd..eelarlldavdspnvgvclDtgHlliaeedvddalraladrikhvHikDakgdlgagrdr 201
                                       +++E++++ ++  g   eel++++d +d   +gv++D+gH++   + +d+++++++dri+ vHi+D+ g    +rd+
  gi|474933610|ref|YP_007687192.1| 139 VCMENMPNVPMLIGTsvEELQEIVDGTD---LGVTFDIGHANTL-GMIDSMIDTFGDRIGNVHIHDNLG----KRDD 207
                                       ***********99889999999999999...***********99.99**********************....**** PP

                                       EESTTSSSS CS
                      AP_endonuc_2 202 hvpigeGei 210
                                       h+ +geG+i
  gi|474933610|ref|YP_007687192.1| 208 HLTLGEGNI 216
                                       *******87 PP

>> ThiC_Rad_SAM  Radical SAM ThiC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   1.1e-05     0.048     126     172 ..      70     116 ..      34     197 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.1e-05
                      ThiC_Rad_SAM 126 eekekkveelteeellevieeqaedGvdfltiHagvtlellellkke 172
                                       + +++++ e ++ e+++ +e  +e G+d lt+H g+ + +++ ++++
  gi|474933610|ref|YP_007687192.1|  70 AAVNERMREASVMEIVSEMEAAVEMGIDTLTVHPGIINLAVSGTRDR 116
                                       33678899999999*********************998888766532 PP

>> Ta0938  Ta0938
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0    0.0037        17      39      61 ..       8      30 ..       5      56 .. 0.85
   2 ?   -2.3   0.0       1.2   5.5e+03      57      57 ..      91      91 ..      47     137 .. 0.61
   3 ?    5.1   0.0    0.0059        27      19      74 ..     150     204 ..     146     234 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0037
                                      S--SSSS-TTS-THHHHHHHHHH CS
                            Ta0938 39 ccdicakefvnllnevkkrtgls 61
                                      c d c+++f ++l+ + k +++ 
  gi|474933610|ref|YP_007687192.1|  8 CPDFCTTDFYEMLESISKDFSHW 30
                                      99**************9988654 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.2
                                      H CS
                            Ta0938 57 r 57
                                       
  gi|474933610|ref|YP_007687192.1| 91 A 91
                                      1 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.0059
                                       S---S---SS-B-TT--BSSS--SSSS-TTS-THHHHHHHHHHHS---EE---TTT CS
                            Ta0938  19 lcgatwgdyyeevdgeklffccdicakefvnllnevkkrtglskideleingnyyk 74 
                                       l g++  +  e vdg +l    di  ++ + +++ +   +g ++i +++i+ n  k
  gi|474933610|ref|YP_007687192.1| 150 LIGTSVEELQEIVDGTDLGVTFDIGHANTLGMIDSMIDTFG-DRIGNVHIHDNLGK 204
                                       678888899999***********************998876.89999999988754 PP

>> Lipase_GDSL_3  GDSL-like Lipase/Acylhydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.5   6.3e-05      0.28      13      67 ..      44      98 ..      42     164 .. 0.82
   2 ?    0.1   0.1      0.18   7.9e+02     150     167 ..     165     182 ..     111     186 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.3e-05
                     Lipase_GDSL_3 13 qGasasRpglaytailsrklgrevvnLgfsGnalleaeladvlaevdasvfv.ldl 67
                                      +G+ a+R+ + y + +s +++  +vn++   + + ea ++++++e++a+v + +d+
  gi|474933610|ref|YP_007687192.1| 44 SGGFADRAEM-YKMTFSIHTDISCVNIAAVNERMREASVMEIVSEMEAAVEMgIDT 98
                                      799999*988.9******************99999*************88543665 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.18
                     Lipase_GDSL_3 150 kdeeatvdgiHpsdlGll 167
                                       +d   t d+ H++ lG++
  gi|474933610|ref|YP_007687192.1| 165 TDLGVTFDIGHANTLGMI 182
                                       334457788888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 1429.94
//
Query:       gi|474933611|ref|YP_007687193.1|  [L=366]
Description: CAAX amino terminal protease family [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.1e-10   39.3   8.3    6.1e-10   39.3   8.3    2.9  2  CPBP            CPBP intramembrane metalloprotease
      1e-08   35.1  21.5    4.4e-08   33.0   8.8    2.4  3  DZR             Double zinc ribbon
    4.3e-05   22.8   8.5      0.017   14.5   1.0    2.5  2  zf-ribbon_3     zinc-ribbon domain
  ------ inclusion threshold ------
       0.17   11.9  10.7       0.98    9.4  10.3    2.2  2  zinc-ribbons_6  zinc-ribbons
       0.52    9.0   5.2       0.16   10.7   1.9    1.6  2  tRNA-synt_1g    tRNA synthetases class I (M)
       0.66   10.8  11.1        1.5    9.7   1.5    2.5  2  zinc_ribbon_15  zinc-ribbon family
        1.3    6.8   6.4        1.6    6.5   6.4    1.1  1  PolC_DP2        DNA polymerase II large subunit DP2
        2.1    8.5  13.4       0.37   10.9   1.7    3.0  3  UPF0547         Uncharacterised protein family UPF0547
        4.5    7.1  19.9        2.6    7.9   2.9    3.7  4  zinc_ribbon_2   zinc-ribbon domain


Domain annotation for each model (and alignments):
>> CPBP  CPBP intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -6.3   8.6         9   1.8e+04      38      56 ..      95     117 ..      73     181 .. 0.49
   2 !   39.3   8.3   3.1e-13   6.1e-10       8      91 ..     196     302 ..     164     303 .. 0.83

  Alignments for each domain:
  == domain 1  score: -6.3 bits;  conditional E-value: 9
                                       HHHHHHHHHHHHHCSGGG....H CS
                              CPBP  38 tlailissilFglaHlpn....g 56 
                                       ++ai++  i+Fg + ++     +
  gi|474933611|ref|YP_007687193.1|  95 IVAIAYGFIFFGDLMAVAspvgK 117
                                       33333334444433333333331 PP

  == domain 2  score: 39.3 bits;  conditional E-value: 3.1e-13
                                       HHHHHHHHHHHHHHHHTTCHHHH........................HHHH.S-HHHHHHHHHHHHHCSGGG.HHH. CS
                              CPBP   8 fllalllapllEEllfRglllql........................lqergsstlailissilFglaHlpn.gps. 58 
                                       + ++ll a+  EE++fR+l +                          ++  ++ ++ ++is+++Fg aHl   g++ 
  gi|474933611|ref|YP_007687193.1| 196 LAYLLLTAGPEEEFIFRVLPIGIpmvivalcygrgrssfryllggfgMS--RWAWIFLAISAVIFGYAHLGGwGWTk 270
                                       45588999999*******9977677777777777777777775554333..3556****************999999 PP

                                       HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              CPBP  59 vllaalaGlvlgylylktgsllaaillHallnl 91 
                                       ++ aa+ G+++g++y + g l a+il+H+++++
  gi|474933611|ref|YP_007687193.1| 271 IIDAAMGGVIFGFIYCEFG-LYACILAHTVNDT 302
                                       *******************.**********997 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   8.8   2.2e-11   4.4e-08       1      49 []       5      50 ..       5      50 .. 0.98
   2 !   15.6   4.8     6e-06     0.012       1      32 [.      32      63 ..      32      64 .. 0.96
   3 ?   -1.0   0.2      0.94   1.9e+03      28      35 ..     153     160 ..     140     165 .. 0.73

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 2.2e-11
                               DZR  1 CpqCgeelppdarfCseCgtklkavaaedrCpsCgekvdpearfCpeCG 49
                                      Cp+C+e    +arfC +Cg++l +   +++Cp+C+   + +a++C +CG
  gi|474933611|ref|YP_007687193.1|  5 CPECEEWRARGARFCRNCGKALAE---SEVCPECDVWRQRGANYCRNCG 50
                                      **********************85...9********************9 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 6e-06
                               DZR  1 CpqCgeelppdarfCseCgtklkavaaedrCp 32
                                      Cp+C    + +a++C +Cg kl +++++  Cp
  gi|474933611|ref|YP_007687193.1| 32 CPECDVWRQRGANYCRNCGRKLGNAPEPLPCP 63
                                      **********************9999999997 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.94
                               DZR  28 edrCpsCg 35 
                                       +  C++C+
  gi|474933611|ref|YP_007687193.1| 153 SGLCMACT 160
                                       67899997 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   1.0   8.8e-06     0.017       5      24 ..       5      24 ..       3      26 .. 0.92
   2 !   12.0   1.2   5.3e-05      0.11       5      26 .]      32      53 ..      29      53 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 8.8e-06
                       zf-ribbon_3  5 CPnCGa.plssddnvCpyCGt 24
                                      CP+C +   + ++++C +CG+
  gi|474933611|ref|YP_007687193.1|  5 CPECEEwR-ARGARFCRNCGK 24
                                      ******88.***********7 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 5.3e-05
                       zf-ribbon_3  5 CPnCGa.plssddnvCpyCGtkl 26
                                      CP+C+    + ++n C +CG kl
  gi|474933611|ref|YP_007687193.1| 32 CPECDVwR-QRGANYCRNCGRKL 53
                                      ******88.***********876 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4  10.3   0.00049      0.98       2      37 ..       4      37 ..       3      52 .. 0.70
   2 ?    0.6   0.2      0.28   5.5e+02       2      19 ..      45      62 ..      44      73 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00049
                                      --SSS-S--EE-SSEEE-TTT--EEEEEEE-SSS-S CS
                    zinc-ribbons_6  2 kCpeCqqelekrgeqyhCeaCqedlkkealCpeCeq 37
                                       CpeC++  + rg   +C++C + l +  +CpeC+ 
  gi|474933611|ref|YP_007687193.1|  4 DCPECEEW-RARG-ARFCRNCGKALAESEVCPECDV 37
                                      59***864.4444.689*****************63 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.28
                                      --SSS-S--EE-SSEEE- CS
                    zinc-ribbons_6  2 kCpeCqqelekrgeqyhC 19
                                      +C++C ++l +  e + C
  gi|474933611|ref|YP_007687193.1| 45 YCRNCGRKLGNAPEPLPC 62
                                      688887777766655555 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.3    0.0028       5.6     138     162 ..       4      29 ..       1      31 [. 0.84
   2 ?   10.7   1.9   8.1e-05      0.16     121     160 ..      17      54 ..      11      84 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0028
                                       ........-TTS-E.E-TTSSB-E.. CS
                      tRNA-synt_1g 138 tCPkckseeargdq.ceecgkklept 162
                                        CP+c++ +arg + c +cgk l  +
  gi|474933611|ref|YP_007687193.1|   4 DCPECEEWRARGARfCRNCGKALAES 29 
                                       7***********9846*****99855 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 8.1e-05
                                       EEETTTTEEE-GGG-EE........-TTS-EE.-TTSSB-E CS
                      tRNA-synt_1g 121 lycpkderflpdryvegtCPkckseeargdqc.eecgkkle 160
                                        +c ++++ l++++v   CP+c   ++rg ++  +cg+kl 
  gi|474933611|ref|YP_007687193.1|  17 RFCRNCGKALAESEV---CPECDVWRQRGANYcRNCGRKLG 54 
                                       59************8...***********9866*****995 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   2.5     0.013        27      67      86 .]       4      23 ..       2      23 .. 0.94
   2 ?    9.7   1.5   0.00074       1.5      64      86 .]      28      50 ..      24      50 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.013
                    zinc_ribbon_15 67 eCknCgkeveeefkyCpkCg 86
                                       C++C++      ++C +Cg
  gi|474933611|ref|YP_007687193.1|  4 DCPECEEWRARGARFCRNCG 23
                                      7******************9 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00074
                    zinc_ribbon_15 64 ekkeCknCgkeveeefkyCpkCg 86
                                      e+++C++C+   +   +yC +Cg
  gi|474933611|ref|YP_007687193.1| 28 ESEVCPECDVWRQRGANYCRNCG 50
                                      5789******************9 PP

>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   6.4   0.00083       1.6     619     665 ..       3      53 ..       1      58 [. 0.78

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.00083
                          PolC_DP2 619 rkCkkCgketl..earCeeCgekteeklvCkkcee.eve.eekcekcekea 665
                                         C++C++      + C++Cg+   e+ vC++c+  +++ ++ c +c+++ 
  gi|474933611|ref|YP_007687193.1|   3 DDCPECEEWRArgARFCRNCGKALAESEVCPECDVwRQRgANYCRNCGRKL 53 
                                       579***9876512578******************953334677****9875 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.7   0.00019      0.37       3      21 ..       5      23 ..       4      23 .. 0.97
   2 ?    5.0   0.5     0.013        27       2       7 ..      31      36 ..      30      40 .. 0.90
   3 ?   -1.7   0.2       1.6   3.2e+03      16      21 ..      45      50 ..      41      50 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00019
                           UPF0547  3 CPeCeakvPvaaqfCphCG 21
                                      CPeCe+  +  a+fC+ CG
  gi|474933611|ref|YP_007687193.1|  5 CPECEEWRARGARFCRNCG 23
                                      ******************9 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.013
                           UPF0547  2 vCPeCe 7 
                                      vCPeC+
  gi|474933611|ref|YP_007687193.1| 31 VCPECD 36
                                      7****8 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.6
                           UPF0547 16 fCphCG 21
                                       C+ CG
  gi|474933611|ref|YP_007687193.1| 45 YCRNCG 50
                                      6999*9 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   2.9    0.0013       2.6      11      22 ..      14      25 ..       5      26 .. 0.71
   2 ?    2.3   6.8     0.074   1.5e+02       1      13 [.      18      30 ..      18      35 .. 0.70
   3 ?    5.7   5.5    0.0063        13       2      23 .]      32      53 ..      31      53 .. 0.74
   4 ?   -3.9   0.1       6.6   1.3e+04      16      19 ..     156     159 ..     148     160 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0013
                     zinc_ribbon_2 11 dnakFCpyCGtp 22
                                       +a+FC +CG  
  gi|474933611|ref|YP_007687193.1| 14 RGARFCRNCGKA 25
                                      5899*****976 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.074
                     zinc_ribbon_2  1 fCpnCGaelqdna 13
                                      fC nCG+ l + +
  gi|474933611|ref|YP_007687193.1| 18 FCRNCGKALAESE 30
                                      8999999876554 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.0063
                     zinc_ribbon_2  2 CpnCGaelqdnakFCpyCGtpl 23
                                      Cp+C    q +a++C +CG +l
  gi|474933611|ref|YP_007687193.1| 32 CPECDVWRQRGANYCRNCGRKL 53
                                      6666666667999999999886 PP

  == domain 4  score: -3.9 bits;  conditional E-value: 6.6
                     zinc_ribbon_2  16 CpyC 19 
                                       C  C
  gi|474933611|ref|YP_007687193.1| 156 CMAC 159
                                       8888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1064  (0.0593452); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.51
# Mc/sec: 2140.20
//
Query:       gi|474933612|ref|YP_007687194.1|  [L=196]
Description: hypothetical protein TALC_00019 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1401.80
//
Query:       gi|474933613|ref|YP_007687195.1|  [L=319]
Description: putative transcriptional regulator [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-07   31.2   0.2    4.5e-07   29.8   0.1    1.8  2  HTH_3     Helix-turn-helix
    5.4e-06   26.3   0.1    1.2e-05   25.2   0.1    1.6  1  HTH_19    Helix-turn-helix domain
    0.00072   19.8   0.1     0.0015   18.8   0.1    1.5  1  HTH_31    Helix-turn-helix domain
  ------ inclusion threshold ------
      0.019   14.9   0.0      0.059   13.3   0.0    1.9  1  HTH_11    HTH domain
      0.026   14.4   0.2       0.05   13.5   0.2    1.5  1  HTH_25    Helix-turn-helix domain
       0.14   11.9   0.0        0.3   10.9   0.0    1.5  1  MerR      MerR family regulatory protein


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       3.2   9.6e+03      38      51 ..      59      72 ..      56      74 .. 0.78
   2 !   29.8   0.1   1.5e-10   4.5e-07       1      50 [.     132     180 ..     132     183 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.2
                                      HHHHHHHHHHHTSE CS
                             HTH_3 38 letlkklakaLgvs 51
                                       + +k +a+aL+ s
  gi|474933613|ref|YP_007687195.1| 59 ADEMKIMADALQAS 72
                                      67899999999855 PP

  == domain 2  score: 29.8 bits;  conditional E-value: 1.5e-10
                                       HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTS CS
                             HTH_3   1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgv 50 
                                       l+ +R+ +g+s+  LAe +Gvsr+ti+ +E+G     ++ +++l+++L+ 
  gi|474933613|ref|YP_007687195.1| 132 LRDIREMRGISLGTLAETAGVSRRTIQLYESGMG-AMIDAALRLEEYLDA 180
                                       799*****************************66.99*******999985 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.1   4.1e-09   1.2e-05       3      41 ..     131     169 ..     130     180 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 4.1e-09
                            HTH_19   3 rLkeaReelgltqeelaerlgisrskisaiEng.kkdvps 41 
                                        L+ +Re++g+++  lae++g+sr+ i  +E+g    +++
  gi|474933613|ref|YP_007687195.1| 131 ALRDIREMRGISLGTLAETAGVSRRTIQLYESGmG-AMID 169
                                       69*****************************9933.3555 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   5.1e-07    0.0015       4      39 ..     130     165 ..     129     182 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 5.1e-07
                            HTH_31   4 alLralReraGLsqeevAerlgvsestlsrlEqGrr 39 
                                       + Lr+ Re +G+s+  +Ae +gvs+ t+  +E+G  
  gi|474933613|ref|YP_007687195.1| 130 DALRDIREMRGISLGTLAETAGVSRRTIQLYESGMG 165
                                       579******************************965 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     2e-05     0.059      13      33 ..     139     158 ..     130     160 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2e-05
                            HTH_11  13 rgpisgeeLAeeLnvSrrtvr 33 
                                       rg is  +LAe  +vSrrt++
  gi|474933613|ref|YP_007687195.1| 139 RG-ISLGTLAETAGVSRRTIQ 158
                                       44.9***************96 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   1.7e-05      0.05       2      41 ..     132     171 ..     131     180 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.7e-05
                                       HHHHHHTTT--HHHHHHHSS--HHHHHHHHCT--TTSS-H CS
                            HTH_25   2 LraaRearglsleevaketkIrkdylealEeddfdalpep 41 
                                       Lr  Re rg+sl  +a+   ++ ++++  E+++ + + ++
  gi|474933613|ref|YP_007687195.1| 132 LRDIREMRGISLGTLAETAGVSRRTIQLYESGMGAMIDAA 171
                                       9**************************9999986666655 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0    0.0001       0.3       3      21 ..     144     162 ..     142     168 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0001
                                       HHHHHHHTTTHHHHHHHHH CS
                              MerR   3 gevAeltGvsprtLRyYEr 21 
                                       g +Ae +Gvs rt+  YE+
  gi|474933613|ref|YP_007687195.1| 144 GTLAETAGVSRRTIQLYES 162
                                       89***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2300.18
//
Query:       gi|474933614|ref|YP_007687196.1|  [L=165]
Description: Molecular chaperone (small heat shock protein) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.5e-10   40.4   0.1    5.8e-09   36.0   0.1    2.1  1  HSP20       Hsp20/alpha crystallin family
    2.4e-07   30.2   0.0    3.5e-07   29.7   0.0    1.3  1  ArsA_HSP20  HSP20-like domain found in ArsA
     0.0051   17.8   0.0     0.0086   17.1   0.0    1.3  1  CS          CS domain


Domain annotation for each model (and alignments):
>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.1   9.7e-13   5.8e-09      11     101 ..      90     164 ..      80     165 .] 0.75

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 9.7e-13
                                       EEEE-TT--CCCEEEEEETTEEEEEEE--..---TT----SS---EEEEEE--STTB-TTT-EEEEETTEEEEEEEB CS
                             HSP20  11 vkldvpglkkeelkvkvednrvlvkgeheeeeedekglikerssrkFsrkftLPenvdadkvkaslkdGvLtvtvpk 87 
                                        ++++pg++ke+++++ +  +++v+   e              +rkFs++++LP +vd d+ +a++++G+L+vt++ 
  gi|474933614|ref|YP_007687196.1|  90 ATFEIPGVAKEDVNLEGTPSSLTVTVDTE--------------KRKFSKTVALPCDVDMDSAEATCNNGILEVTLKT 152
                                       55666666666666666666666665555..............599******************************* PP

                                       SS--..-------- CS
                             HSP20  88 kepekkkkerkiqi 101
                                        +p++   ++ki+i
  gi|474933614|ref|YP_007687196.1| 153 VKPAET--KKKISI 164
                                       ***955..666666 PP

>> ArsA_HSP20  HSP20-like domain found in ArsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   5.9e-11   3.5e-07       7      63 .]      91     150 ..      84     150 .. 0.88

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 5.9e-11
                        ArsA_HSP20   7 kldLPfvdkeeidlsrsgdeLtIkig....nfrRqitLPsvlarkevtsAkfedgvLeIrF 63 
                                       + ++P+v ke+++l+ + + Lt++++    +f+++++LP  ++ + +  A+ ++g Le+++
  gi|474933614|ref|YP_007687196.1|  91 TFEIPGVAKEDVNLEGTPSSLTVTVDtekrKFSKTVALPCDVDMDSA-EATCNNGILEVTL 150
                                       5689**********************666666666********9977.***********96 PP

>> CS  CS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.4e-06    0.0086       6      75 ..      82     151 ..      78     151 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.4e-06
                                       EEETTEEEEEEE-TTCTTTTTCEEEEEETTEEEEEE.TS.CEEEEECEBSS-BETTTEEEEEETTEEEEEEE CS
                                CS   6 yQtldeVvvtiyvkkvnikkkdvkvefkerslkvki.gk.eklliegeLfgpIdpeesswtieskkveitLk 75 
                                       +Q+ + V  t+++++v   k+dv++e +++sl+v +  + +k+ +   L   +d +++  t  +  +e+tLk
  gi|474933614|ref|YP_007687196.1|  82 QQDGEVVRATFEIPGV--AKEDVNLEGTPSSLTVTVdTEkRKFSKTVALPCDVDMDSAEATCNNGILEVTLK 151
                                       688999*********9..******************955588887777*************99999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1204.36
//
Query:       gi|474933615|ref|YP_007687197.1|  [L=713]
Description: AAA family ATPase, CDC48 subfamily [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-99  328.8   0.0    7.4e-49  165.6   0.0    2.6  2  AAA              ATPase family associated with various cellul
    1.6e-33  114.3   4.0    1.1e-16   60.3   0.4    3.0  2  AAA_lid_3        AAA+ lid domain
    1.2e-23   83.0   0.6    6.5e-23   80.7   1.0    2.1  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    3.5e-16   59.3   0.0      1e-07   31.8   0.0    3.2  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    9.7e-15   55.1   0.0    5.3e-06   26.7   0.0    2.6  2  AAA_2            AAA domain (Cdc48 subfamily)
    1.2e-13   51.8   0.1      4e-05   24.0   0.0    3.7  3  AAA_16           AAA ATPase domain
    4.6e-12   45.5   0.0    1.6e-11   43.8   0.0    2.0  1  CDC48_2          Cell division protein 48 (CDC48), domain 2
    1.7e-10   41.3   1.4     0.0036   17.6   0.0    3.9  4  AAA_22           AAA domain
    2.8e-10   40.3   8.6     0.0002   21.3   0.1    5.1  2  AAA_5            AAA domain (dynein-related subfamily)
      5e-10   39.7   0.0    0.00069   19.8   0.0    2.7  2  AAA_33           AAA domain
      1e-09   38.1   0.6    0.00086   18.6   0.0    2.8  3  TIP49            TIP49 P-loop domain
    3.4e-09   36.8   0.0     0.0011   19.0   0.0    2.4  2  AAA_14           AAA domain
    1.6e-08   34.2   0.4     0.0037   16.7   0.0    2.5  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    7.6e-08   32.3   0.0      0.014   15.1   0.0    2.4  2  IstB_IS21        IstB-like ATP binding protein
    2.8e-07   31.1   0.0      0.034   14.7   0.0    2.6  2  AAA_18           AAA domain
    4.6e-07   29.6   1.9       0.35   10.4   0.1    3.5  3  AAA_25           AAA domain
    5.3e-07   29.7   0.0      0.022   14.6   0.0    3.0  2  Bac_DnaA         Bacterial dnaA  protein
    5.7e-07   29.0   0.1      0.036   13.4   0.0    2.4  2  Zeta_toxin       Zeta toxin
      6e-07   29.3   0.1       0.06   13.0   0.0    3.4  2  Sigma54_activat  Sigma-54 interaction domain
      6e-07   29.5   0.2      0.012   15.6   0.1    2.7  3  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    6.4e-07   29.4   0.3       0.14   12.1   0.1    3.4  3  NACHT            NACHT domain
    7.7e-07   29.5   0.0      0.023   15.1   0.0    2.8  2  RNA_helicase     RNA helicase
    7.9e-07   29.5   0.0       0.03   14.6   0.0    2.5  2  AAA_28           AAA domain
    1.5e-06   27.9   0.1      0.063   12.8   0.0    2.8  2  AAA_7            P-loop containing dynein motor region
    1.9e-06   27.7   0.1      0.025   14.3   0.0    2.8  2  AAA_24           AAA domain
    1.6e-05   24.2   0.0       0.03   13.5   0.0    2.6  2  DUF815           Protein of unknown function (DUF815)
    1.7e-05   25.3   0.0       0.14   12.7   0.0    2.5  2  ABC_tran         ABC transporter
    1.8e-05   24.2   0.2        1.7    8.0   0.0    3.5  3  ATPase           KaiC
    3.2e-05   23.0   0.0       0.15   10.9   0.0    2.4  2  AFG1_ATPase      AFG1-like ATPase
    5.8e-05   23.0   0.0       0.25   11.1   0.0    2.4  2  AAA_11           AAA domain
    9.3e-05   22.3   0.0       0.58   10.0   0.0    2.7  2  AAA_3            ATPase family associated with various cellul
    0.00011   21.7   0.5       0.55    9.6   0.0    2.8  2  PhoH             PhoH-like protein
    0.00013   21.8   0.5       0.55    9.9   0.0    2.6  2  AAA_30           AAA domain
    0.00018   21.0   0.1          1    8.8   0.0    3.3  3  TniB             Bacterial TniB protein
     0.0002   20.5   0.1       0.16   11.0   0.0    2.2  2  Parvo_NS1        Parvovirus non-structural protein NS1
    0.00024   20.4   0.0       0.49    9.6   0.0    2.3  2  DUF2075          Uncharacterized conserved protein (DUF2075)
    0.00052   19.3   0.0          1    8.5   0.0    2.3  2  NB-ARC           NB-ARC domain
     0.0015   18.9   0.0          2    8.8   0.0    2.7  2  AAA_17           AAA domain
     0.0017   18.7   2.0        1.4    9.3   0.0    3.0  2  AAA_19           AAA domain
     0.0018   18.2   3.9        2.1    8.2   0.1    4.2  4  NTPase_1         NTPase
     0.0018   18.2   0.1       0.42   10.5   0.0    3.0  2  ATPase_2         ATPase domain predominantly from Archaea
     0.0031   17.5   0.1        4.5    7.3   0.0    2.7  2  ResIII           Type III restriction enzyme, res subunit
     0.0095   15.6   0.2        9.6    5.8   0.0    3.5  3  Guanylate_kin    Guanylate kinase
  ------ inclusion threshold ------
       0.01   15.6   0.5        5.6    6.6   0.0    2.7  2  Cytidylate_kin   Cytidylate kinase
      0.011   15.6   0.0        4.8    7.0   0.0    2.5  2  CPT              Chloramphenicol phosphotransferase-like prot
      0.011   15.2   0.0      0.018   14.5   0.0    1.4  1  UFD1             Ubiquitin fusion degradation protein UFD1
      0.014   14.5   0.0        4.2    6.3   0.0    2.6  2  T2SSE            Type II/IV secretion system protein
      0.017   14.3   0.0        2.1    7.4   0.0    2.3  2  DAP3             Mitochondrial ribosomal death-associated pro
      0.021   14.9   0.0         10    6.3   0.0    2.6  2  Sigma54_activ_2  Sigma-54 interaction domain
      0.027   14.6   0.0         11    6.2   0.0    2.9  2  Torsin           Torsin
       0.04   13.9   0.2         10    6.2   0.0    3.3  2  Vps4_C           Vps4 C terminal oligomerisation domain
      0.045   13.5   0.0         11    5.9   0.0    2.5  2  AAA_29           P-loop containing region of AAA domain
      0.071   12.5   0.6        9.8    5.5   0.0    2.4  2  IPT              Isopentenyl transferase
      0.084   12.6   0.0         19    5.0   0.0    2.5  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
      0.087   12.0   0.3         21    4.2   0.0    3.2  4  KAP_NTPase       KAP family P-loop domain
        0.1   12.3   0.0          8    6.1   0.0    2.3  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.13   11.7   0.0         16    4.8   0.0    2.4  2  SRPRB            Signal recognition particle receptor beta su
       0.13   11.8   0.3         15    5.1   0.0    2.7  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
       0.14   11.3   0.0        3.9    6.5   0.0    2.4  2  PIF1             PIF1-like helicase
       0.76   10.0   2.9         31    4.8   0.1    2.8  2  Hydin_ADK        Hydin Adenylate kinase-like domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.6   0.0   2.5e-51   7.4e-49       1     131 [.     207     336 ..     207     337 .. 0.98
   2 !  160.7   0.0   7.8e-50   2.3e-47       1     130 [.     480     609 ..     480     611 .. 0.97

  Alignments for each domain:
  == domain 1  score: 165.6 bits;  conditional E-value: 2.5e-51
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgs 77 
                                       vll+GppGtGKT+lakava e++++f++i g+e++sk+ gese k+re+fk+a+e+a psi+fiDEid++a++r+++
  gi|474933615|ref|YP_007687197.1| 207 VLLHGPPGTGKTMLAKAVAGETSSNFISIGGPEIVSKFYGESEGKLREIFKDAEENA-PSIIFIDEIDSIAPKREET 282
                                       79******************************************************9.******************* PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       + eee+r+v+qLl+ +dg++++ ++v+vigatnrp+++d+al+r gRfdr+iei+
  gi|474933615|ref|YP_007687197.1| 283 QGEEERRIVAQLLSLMDGLNSR-GRVVVIGATNRPNSIDEALRRpGRFDREIEIG 336
                                       *********************6.77***************************996 PP

  == domain 2  score: 160.7 bits;  conditional E-value: 7.8e-50
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.TT CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.sg 76 
                                       +llyGppGtGKT+lakava+e++++f++++g+e+l+kyvgesek +re+f++a++ + p+++f+DEid++a+ r  g
  gi|474933615|ref|YP_007687197.1| 480 ILLYGPPGTGKTMLAKAVATESEANFISVKGPEFLNKYVGESEKAVRETFRKARQAS-PCVVFMDEIDSIAPVRgIG 555
                                       69******************************************************9.****************989 PP

                                       CCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEET CS
                               AAA  77 seseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkiei 130
                                       +++ ++e+vv+q+lteldg++   ++v+vi+atnrpd++dpallr gRfd+ i +
  gi|474933615|ref|YP_007687197.1| 556 DDTHVTENVVSQMLTELDGLEPM-NNVVVIAATNRPDRIDPALLRpGRFDKSILV 609
                                       99********************6.66*************************9987 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   0.4   3.8e-19   1.1e-16       1      42 [.     359     400 ..     359     420 .. 0.84
   2 !   54.1   0.3   3.2e-17   9.6e-15       1      43 [.     633     688 ..     633     690 .. 0.85

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 3.8e-19
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitmed 42 
                                       dvdl  +A +T+Gy+GADlaalcreAa++Alrr+++ +++ed
  gi|474933615|ref|YP_007687197.1| 359 DVDLGVIADKTHGYVGADLAALCREAAMAALRRVLPDVNTED 400
                                       9********************************877666655 PP

  == domain 2  score: 54.1 bits;  conditional E-value: 3.2e-17
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrr...........gik..eitmedf 43 
                                       +vdl+++AerTeG++GAD+ a+++eA++ A+rr            i+  ++tm+d+
  gi|474933615|ref|YP_007687197.1| 633 NVDLDDIAERTEGCTGADIGAIVNEAVMTAVRRlvasgsvpsqeEIDacKVTMDDL 688
                                       7********************************77777777665566555999987 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.7   1.0   2.2e-25   6.5e-23       8      85 .]       4      81 ..       1      81 [. 0.95

  Alignments for each domain:
  == domain 1  score: 80.7 bits;  conditional E-value: 2.2e-25
                                      SS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEEEEEE-- CS
                           CDC48_N  8 pqedvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVtVrkaev 85
                                      +  ++g+g++r+dp+ m+ l+++ gd+  ++g++kT++++++++pede+ g+Ir+dg tR+nagvsiGd+V V+kaev
  gi|474933615|ref|YP_007687197.1|  4 KAGEAGKGVARLDPALMDILKIKVGDIAIVTGNKKTAVKILRGAPEDENLGVIRIDGSTRRNAGVSIGDRVDVKKAEV 81
                                      55678**********************************************************************985 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.0   3.5e-10     1e-07      31     103 ..     202     282 ..     180     330 .. 0.86
   2 !   23.9   0.0   9.6e-08   2.9e-05      26      69 ..     470     513 ..     449     552 .. 0.73

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 3.5e-10
                            RuvB_N  31 ealdhvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsra 99 
                                       ea   vll+GpPG Gkt lak +a e  +++ +  gP +      e +g l  ++++ ee+   ++fidei  ++++
  gi|474933615|ref|YP_007687197.1| 202 EAPKGVLLHGPPGTGKTMLAKAVAGETSSNFISIGGPEIvskfygESEGKLREIFKDAEENapSIIFIDEIDSIAPK 278
                                       566789*******************************985555555679999999999876447**********999 PP

                            RuvB_N 100 veev 103
                                        ee 
  gi|474933615|ref|YP_007687197.1| 279 REET 282
                                       9986 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 9.6e-08
                            RuvB_N  26 akkreealdhvllyGpPGlGkttlakiiakelgvklkitsgPvl 69 
                                       a++  ++   +llyGpPG Gkt lak +a+e ++++ +  gP  
  gi|474933615|ref|YP_007687197.1| 470 AHMNAKPPKGILLYGPPGTGKTMLAKAVATESEANFISVKGPEF 513
                                       55566777889***************************999964 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   1.8e-08   5.3e-06       6     105 ..     207     300 ..     204     307 .. 0.92
   2 !   25.6   0.0   3.8e-08   1.1e-05       6     104 ..     480     573 ..     475     576 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 1.8e-08
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       +ll gp g+Gkt+laka+a   +    +++i +   e+      + + +++   ++  + aee+   i+++DEid i
  gi|474933615|ref|YP_007687197.1| 207 VLLHGPPGTGKTMLAKAVAGETS----SNFISIGGPEIVS----KFYGESEGKLREIFKDAEENApsIIFIDEIDSI 275
                                       5789***************9998....5************....888888888899999999999************ PP

                                       ------------HHHHHHHHHHHH- CS
                             AAA_2  81 hpkessgadvSregVqrdLLqileg 105
                                       +pk+++++   +  ++  LL +++g
  gi|474933615|ref|YP_007687197.1| 276 APKREETQGEEERRIVAQLLSLMDG 300
                                       ***999999999999999****998 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 3.8e-08
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       ill gp g+Gkt+laka+a   ++    ++i +   e+l     + + ++++  ++   +a +    +v++DEid i
  gi|474933615|ref|YP_007687197.1| 480 ILLYGPPGTGKTMLAKAVATESEA----NFISVKGPEFLN----KYVGESEKAVRETFRKARQASpcVVFMDEIDSI 548
                                       8999***************99985....************....55555555566666666666689********** PP

                                       ----------.--HHHHHHHHHHHH CS
                             AAA_2  81 hpkessgadv.SregVqrdLLqile 104
                                       +p + +g d    e+V+  +L  l+
  gi|474933615|ref|YP_007687197.1| 549 APVRGIGDDThVTENVVSQMLTELD 573
                                       **98888776246778777776665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   1.4e-07     4e-05      17     139 ..     197     309 ..     193     311 .. 0.72
   2 !   20.4   0.0   1.8e-06   0.00053      22      63 ..     475     513 ..     466     521 .. 0.80
   3 ?    2.4   0.0       0.6   1.8e+02     123     148 ..     525     549 ..     519     584 .. 0.69

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.4e-07
                            AAA_16  17 ervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesae 93 
                                       +r+    p  vll+G++G+GK+ l+++++ + + +   f++    +       s +    +  +l +  +d++e+a 
  gi|474933615|ref|YP_007687197.1| 197 KRLGVEAPKGVLLHGPPGTGKTMLAKAVAGETSSN---FISIGGPEI-----VSKFYGESEG-KLREIFKDAEENAP 264
                                       5555567899*******************877777...766666666.....2234444423.55555555555567 PP

                            AAA_16  94 leawrekleealaavpelagaeasrllellkrllallsrderplvl 139
                                          + +++++ +    e  g+e++r+ ++l +l++ l +++r +v+
  gi|474933615|ref|YP_007687197.1| 265 SIIFIDEIDSIAPKREETQGEEERRIVAQLLSLMDGLNSRGR-VVV 309
                                       77777777777778888889999***********77777687.555 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 1.8e-06
                            AAA_16  22 grpelvllsGesGvGKsslvrellralekdggiflrgkcdql 63 
                                         p  +ll+G++G+GK+ l+++++++ e++   f++ k  ++
  gi|474933615|ref|YP_007687197.1| 475 KPPKGILLYGPPGTGKTMLAKAVATESEAN---FISVKGPEF 513
                                       44689*******************988877...776666555 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.6
                            AAA_16 123 lkrllallsrderplvlvlDdlqwad 148
                                       +++ ++++++ ++p v+++D+++ + 
  gi|474933615|ref|YP_007687197.1| 525 VRETFRKARQ-ASPCVVFMDEIDSIA 549
                                       6677889999.999********9554 PP

>> CDC48_2  Cell division protein 48 (CDC48), domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.0   5.3e-14   1.6e-11       1      63 [.      96     158 ..      96     159 .. 0.96

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 5.3e-14
                                       ..SCCCCHHHHCCCTTEEE-TTEEEEECCTCCCEEEEEEEECCCC.SCEEECTSCCEEESTTCC CS
                           CDC48_2   1 ridgdemaylkrqFlgrpvtkGdlvvfefkgqeiklvVvstePkg.pvgitetTeielgtkpve 63 
                                       r++g+ ++yl ++++gr+++kGd++  + +g+ ++lvV+s +P+  +v+i  +T++++  kpv+
  gi|474933615|ref|YP_007687197.1|  96 RLQGG-EEYLAQALEGRAFAKGDILSLNIMGNKMDLVVTSFTPAAeAVIIGAETKVKINAKPVS 158
                                       57888.89***********************************999****************96 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.6e-05    0.0047       8      60 ..     207     259 ..     202     264 .. 0.74
   2 ?    3.4   0.0       0.3        89      84     128 ..     258     310 ..     240     317 .. 0.63
   3 !   17.6   0.0   1.2e-05    0.0036       8      40 ..     480     503 ..     473     534 .. 0.75
   4 ?   -0.3   0.0         4   1.2e+03      78     104 ..     525     549 ..     514     584 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.6e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsstsskdllrel 60 
                                       ++++G++GtGKT+l++ ++ +     ++   +pe+v +++  s++++++++++ 
  gi|474933615|ref|YP_007687197.1| 207 VLLHGPPGTGKTMLAKAVAGETSSN-FISIGGPEIVsKFYGESEGKLREIFKDA 259
                                       689***************9997543.3333466655678888888888877765 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.3
                            AAA_22  84 qalraravielliiDEaqhlr...s.......eealeeLrsllnlsrkgvqliLv 128
                                       +a +++  ++++ iDE++ +    +        +++ +L sl++   +  +++++
  gi|474933615|ref|YP_007687197.1| 258 DAEENA--PSIIFIDEIDSIApkrEetqgeeeRRIVAQLLSLMDGLNSRGRVVVI 310
                                       333333..469*********88651445566677777777777754444455555 PP

  == domain 3  score: 17.6 bits;  conditional E-value: 1.2e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerp 40 
                                       ++++G++GtGKT+l++ ++ + +         +
  gi|474933615|ref|YP_007687197.1| 480 ILLYGPPGTGKTMLAKAVATESE---------A 503
                                       89****************99973.........2 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 4
                            AAA_22  78 llealeqalrarav..ielliiDEaqhlr 104
                                       ++e++++a        + ++  DE++ + 
  gi|474933615|ref|YP_007687197.1| 525 VRETFRKAR----QasPCVVFMDEIDSIA 549
                                       334444443....34456********986 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.8   1.3e-05    0.0038       1     135 [.     206     324 ..     206     327 .. 0.67
   2 !   21.3   0.1   6.8e-07    0.0002       2     136 ..     480     599 ..     479     600 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.3e-05
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------.....G-SEEEEE CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar.....egeilvlD 72 
                                       +vlL GppGtgK++la+ +a  + +++  + +++    +++ g+ e          ++l + ++      ++i+++D
  gi|474933615|ref|YP_007687197.1| 206 GVLLHGPPGTGKTMLAKAVAGETSSNFISIGGPEI--VSKFYGESE----------GKLREIFKdaeenAPSIIFID 270
                                       59******************999999888888873..445666666..........333333333335577888888 PP

                                       SGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHH CS
                             AAA_5  73 EveraesevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalr 135
                                       E++ + ++  ++     ee+r+ ++++  l++  n     r+ vi+++n+++    ++++alr
  gi|474933615|ref|YP_007687197.1| 271 EIDSIAPKREETQ---GEEERRIVAQLLSLMDGLNS--RGRVVVIGATNRPN----SIDEALR 324
                                       8887776665555...55666666677777766663..33477777777777....6666666 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 6.8e-07
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEver 76 
                                       +lL GppGtgK++la+ +a   ++++  v +++++++   +g+ e      + v     r+ar  +++++++DE++ 
  gi|474933615|ref|YP_007687197.1| 480 ILLYGPPGTGKTMLAKAVATESEANFISVKGPEFLNKY--VGESE------KAVRE-TFRKARqaSPCVVFMDEIDS 547
                                       89******************************988764..34433......33444.4445555899*********7 PP

                                       --..HHHHHHHHHHHHSSEE.E..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHT CS
                             AAA_5  77 ae..sevlnsLlslleerrl.lleeggelvkaknddllerfrviatanpldrslnelspalrs 136
                                       +   + + +    + e+    +l e+++l+  +n      + via++n++d    +++pal++
  gi|474933615|ref|YP_007687197.1| 548 IApvRGIGDDT-HVTENVVSqMLTELDGLEPMNN------VVVIAATNRPD----RIDPALLR 599
                                       76422233333.3333333303334444444444......99999999999....88888865 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   2.3e-06   0.00069       2      81 ..     207     316 ..     207     340 .. 0.71
   2 !   17.0   0.0   1.7e-05    0.0052       2      47 ..     480     556 ..     480     596 .. 0.65

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2.3e-06
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt............................dy 48 
                                       vll+G+pG+GK+ la+ ++ ++   ++ +  +++ ++ +g+ + +++                             +
  gi|474933615|ref|YP_007687197.1| 207 VLLHGPPGTGKTMLAKAVAGETSsnFISIGGPEIVSKFYGESEGKLReifkdaeenapsiifideidsiapkreeTQ 283
                                       799****************9999999999999977777774443333445555555556666666666666654444 PP

                            AAA_33  49 trvldrlyqilnelarkalsagrnvildatnls 81 
                                        + + r+ ++l  l +   s+gr v++ atn+ 
  gi|474933615|ref|YP_007687197.1| 284 GEEERRIVAQLLSLMDGLNSRGRVVVIGATNRP 316
                                       445556777777888888888888888888875 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 1.7e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt.............................d 47 
                                       +ll G+pG+GK+ la+ ++ +    ++ +  ++++++++g+ ++  +                             d
  gi|474933615|ref|YP_007687197.1| 480 ILLYGPPGTGKTMLAKAVATESEanFISVKGPEFLNKYVGESEKAVRetfrkarqaspcvvfmdeidsiapvrgigD 556
                                       6789***************9999788888889988888885444333224444444455555555555555555555 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1         5   1.5e+03     136     228 ..      78     171 ..      68     181 .. 0.77
   2 !   16.5   0.0   1.2e-05    0.0037      50      92 ..     204     244 ..     195     261 .. 0.84
   3 !   18.6   0.0   2.9e-06   0.00086      51     106 ..     478     532 ..     469     536 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 5
                                       ..TTS--EEEEEE-SS-EEEEEE-HHHHHHHHHHT--TT-EEEEETTT--EEE-SSS-SS------.S--------S CS
                             TIP49 136 kekkikevkitlktakeekklklgskiaeellkekvkegDviviekesGkvkklGrsearakefDi.ekdefvelPk 211
                                       k++ ++++kit+  ++e +    ++ +a++l+ +   +gD++ ++    k+  + +s++ a e  i  +++ v++  
  gi|474933615|ref|YP_007687197.1|  78 KAEVKEATKITFSPTEELRLQGGEEYLAQALEGRAFAKGDILSLNIMGNKMDLVVTSFTPAAEAVIiGAETKVKINA 154
                                       55667778888888888877777888999999999999999999999999998888888776655548888888888 PP

                                       ---S----XXXXXXXXX CS
                             TIP49 212 GevekkkevvqevtLhd 228
                                         v+k+   v +v+  d
  gi|474933615|ref|YP_007687197.1| 155 KPVSKEGMDVPKVSYDD 171
                                       88888877777777665 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.2e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  50 GravLlaGpsgtGktalaiaiskelgedvpfvalsgsevysle 92 
                                        ++vLl Gp+gtGkt la a++ e +    f+++ g e+ s  
  gi|474933615|ref|YP_007687197.1| 204 PKGVLLHGPPGTGKTMLAKAVAGETS--SNFISIGGPEIVSKF 244
                                       699********************987..679999999998865 PP

  == domain 3  score: 18.6 bits;  conditional E-value: 2.9e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte.vltqalrks 106
                                       +++Ll Gp+gtGkt la a++ e  ++  f++++g e+    v  +e ++ +++rk+
  gi|474933615|ref|YP_007687197.1| 478 KGILLYGPPGTGKTMLAKAVATE--SEANFISVKGPEFLNKYVGESEkAVRETFRKA 532
                                       89*******************98..5689*********9999998884688999997 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   3.7e-06    0.0011       4     104 ..     206     316 ..     203     335 .. 0.78
   2 !   15.4   0.0   4.6e-05     0.014       5      77 ..     480     549 ..     477     573 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 3.7e-06
                            AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe.kllelileklkeekktylflDEiqev... 76 
                                        +++ G+  +GKT+l+k ++ e     ++++ i   +   k + ++e kl e++++  +e+  +++f+DEi  +   
  gi|474933615|ref|YP_007687197.1| 206 GVLLHGPPGTGKTMLAKAVAGETS---SNFISIGGPEIVSKFYGESEgKLREIFKDA-EENAPSIIFIDEIDSIapk 278
                                       5899****************9988...999999988877766666664666666665.55699***********999 PP

                            AAA_14  77 .........pewekalkslvd..egknldvivtGSnskl 104
                                                +++   l sl+d  + ++++v+v G  +  
  gi|474933615|ref|YP_007687197.1| 279 reetqgeeeRRIVAQLLSLMDglN-SRGRVVVIGATNRP 316
                                       999999888888888888888533.57899999877655 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 4.6e-05
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevp 77 
                                       +++ G+  +GKT+l+k ++ e+     +++ ++  +  +k   ++ek  ++ ++k+++    ++f+DEi  + 
  gi|474933615|ref|YP_007687197.1| 480 ILLYGPPGTGKTMLAKAVATESE---ANFISVKGPEFLNKYVGESEKAVRETFRKARQASPCVVFMDEIDSIA 549
                                       7899**************98877...6666666666555555555544444444444458899******9875 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   4.1e-05     0.012      25      43 ..     207     225 ..     200     229 .. 0.90
   2 !   16.7   0.0   1.2e-05    0.0037      24      43 ..     479     498 ..     466     536 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.1e-05
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll GppG+GKtmlak+++
  gi|474933615|ref|YP_007687197.1| 207 VLLHGPPGTGKTMLAKAVA 225
                                       89*************9875 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 1.2e-05
                      Mg_chelatase  24 nlllvGppGsGKtmlakrlp 43 
                                        +ll+GppG+GKtmlak+++
  gi|474933615|ref|YP_007687197.1| 479 GILLYGPPGTGKTMLAKAVA 498
                                       589*************9975 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   6.8e-05      0.02      44      71 ..     201     228 ..     189     272 .. 0.90
   2 !   15.1   0.0   4.8e-05     0.014      48      73 ..     478     503 ..     466     515 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.8e-05
                         IstB_IS21  44 iekkenivllGpsGvGKshlaialgvea 71 
                                       +e+ ++++l Gp+G+GK+ la a++ e+
  gi|474933615|ref|YP_007687197.1| 201 VEAPKGVLLHGPPGTGKTMLAKAVAGET 228
                                       5677899****************98765 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 4.8e-05
                         IstB_IS21  48 enivllGpsGvGKshlaialgveavr 73 
                                       ++i+l Gp+G+GK+ la a+++e  +
  gi|474933615|ref|YP_007687197.1| 478 KGILLYGPPGTGKTMLAKAVATESEA 503
                                       5799****************998755 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   0.00022     0.066       1      56 [.     207     268 ..     207     315 .. 0.65
   2 !   14.7   0.0   0.00011     0.034       1      22 [.     480     501 ..     480     551 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00022
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.......gvnlrdvakenglllevdpealdeskrldedk 56 
                                       +ll G+pG+GKt lak+++ ++  +        ++++++   +g l e +++   e++   + +
  gi|474933615|ref|YP_007687197.1| 207 VLLHGPPGTGKTMLAKAVAGETsSNfisiggpEIVSKFYGESEGKLREIFKD--AEENAPSIIF 268
                                       7899**************8887433588888755555555555555555555..4444444444 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 0.00011
                            AAA_18   1 IlltGtpGvGKttlakeLskrl 22 
                                       Ill G+pG+GKt lak+++ + 
  gi|474933615|ref|YP_007687197.1| 480 ILLYGPPGTGKTMLAKAVATES 501
                                       99****************6654 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.1    0.0026      0.78      36      54 ..     207     225 ..     198     232 .. 0.86
   2 ?    7.1   0.0     0.012       3.7     129     177 ..     251     299 ..     243     312 .. 0.82
   3 !   10.4   0.1    0.0012      0.35      36      54 ..     480     498 ..     477     501 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0026
                            AAA_25  36 allaGapgtGKttlaldla 54 
                                       +ll G+pgtGKt+la  +a
  gi|474933615|ref|YP_007687197.1| 207 VLLHGPPGTGKTMLAKAVA 225
                                       69************97776 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.012
                            AAA_25 129 dvdaleaaieevegvrlvviDplsralgg.densnsdvgalvealeriar 177
                                       +++++ +++ee + +  + iD ++++ +  +e+  ++++++v++l ++ +
  gi|474933615|ref|YP_007687197.1| 251 KLREIFKDAEE-NAPSIIFIDEIDSIAPKrEETQGEEERRIVAQLLSLMD 299
                                       67889999999.77***************555555556******988865 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.0012
                            AAA_25  36 allaGapgtGKttlaldla 54 
                                       +ll+G+pgtGKt+la  +a
  gi|474933615|ref|YP_007687197.1| 480 ILLYGPPGTGKTMLAKAVA 498
                                       69************97666 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00058      0.17      37     184 ..     207     354 ..     201     393 .. 0.74
   2 !   14.6   0.0   7.5e-05     0.022      36     179 ..     479     625 ..     463     668 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00058
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHTT-.SEEEEE-GGGGTT- CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklrkv.DvLliDDiqflagk 112
                                       ++++g+ G Gkt L ka++ e+ +n+       + + e ++++    + k  e fk+   ++  ++ iD+i  +a k
  gi|474933615|ref|YP_007687197.1| 207 VLLHGPPGTGKTMLAKAVAGETSSNFI-----SIGGPEIVSKFYGESEGKLREIFKDAEENApSIIFIDEIDSIAPK 278
                                       79*****************99988875.....57899999999999999999999998775527899*******977 PP

                                       .HHHHHH........HHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHHHHHH CS
                          Bac_DnaA 113 .ektqee........lfhtfnalleegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailkkkie 180
                                        e+tq e        l+ +++ l   g+ vv+ +   P++++e   r   rf++   ++i  pd++ r +il+   +
  gi|474933615|ref|YP_007687197.1| 279 rEETQGEeerrivaqLLSLMDGLNSRGRVVVIGATNRPNSIDEALRR-PGRFDRE--IEIGVPDRNGRNEILQI--H 350
                                       3456633233433337777788888999999*******988765433.5677775..66677999999999964..3 PP

                                       HTT- CS
                          Bac_DnaA 181 aekl 184
                                       + ++
  gi|474933615|ref|YP_007687197.1| 351 TRGM 354
                                       4444 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 7.5e-05
                                       -EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHT.T-SEEEEE-GGGGT. CS
                          Bac_DnaA  36 PlfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklr.kvDvLliDDiqfla. 110
                                        +++yg+ G Gkt L ka++ e ++n+     + +++ eFln+ v   ++   e+f++  + +  v+ +D+i  +a 
  gi|474933615|ref|YP_007687197.1| 479 GILLYGPPGTGKTMLAKAVATESEANF-----ISVKGPEFLNKYVGESEKAVRETFRKARQaSPCVVFMDEIDSIAp 550
                                       589***************998776665.....557899*******99999999999987663456778898888762 PP

                                       .....T....-HHHHHHHHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHHHH CS
                          Bac_DnaA 111 .....g....kektqeelfhtfnalleegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailkkk 178
                                            +     e++  ++++ ++ l   ++ vv+++   P +++    r   rf+  +   + ppd+e r +i + +
  gi|474933615|ref|YP_007687197.1| 551 vrgigDdthvTENVVSQMLTELDGLEPMNNVVVIAATNRPDRIDPALLR-PGRFDKSIL--VGPPDKESRKSIFEIH 624
                                       2222121001122222334444445556777888888888877654333.356766544..5677777777777665 PP

                                       H CS
                          Bac_DnaA 179 i 179
                                       +
  gi|474933615|ref|YP_007687197.1| 625 V 625
                                       5 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   0.00012     0.036      14      50 ..     202     236 ..     193     244 .. 0.87
   2 !   13.1   0.0   0.00014     0.043      13      51 ..     474     510 ..     465     529 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00012
                        Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrld 50 
                                       e Pk +ll G pG GK+ la++++ e+   +n++ + 
  gi|474933615|ref|YP_007687197.1| 202 EAPKGVLLHGPPGTGKTMLAKAVAGET--SSNFISIG 236
                                       89************************8..89998875 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00014
                        Zeta_toxin  13 qerPklillgGqpGAGKselaellkdelerqgnvvrldp 51 
                                        + Pk ill G pG GK+ la+++++e   + n++ +++
  gi|474933615|ref|YP_007687197.1| 474 AKPPKGILLYGPPGTGKTMLAKAVATES--EANFISVKG 510
                                       4789***********************8..888888876 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.1   0.00052      0.16      21      77 ..     203     251 ..     192     283 .. 0.65
   2 !   13.0   0.0    0.0002      0.06      18      57 ..     473     509 ..     458     591 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00052
                                       SSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSS CS
                   Sigma54_activat  21 tdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGa 77 
                                        +  vl++G  GtGK++la+a+  +++   ++f+++   +i      s+++G ++G 
  gi|474933615|ref|YP_007687197.1| 203 APKGVLLHGPPGTGKTMLAKAVAGETS---SNFISIGGPEI-----VSKFYGESEGK 251
                                       56789***************9975543...56666654443.....34555555554 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.0002
                                       HCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEE CS
                   Sigma54_activat  18 vaktdlsvlitGesGtGKellaraiheaskrkekpfvavn 57 
                                        ak +  +l+ G  GtGK++la+a+ ++s+   ++f++v 
  gi|474933615|ref|YP_007687197.1| 473 NAKPPKGILLYGPPGTGKTMLAKAVATESE---ANFISVK 509
                                       45556889****************998876...5666665 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0    0.0012      0.36      11      43 ..     196     228 ..     182     245 .. 0.80
   2 ?   -0.7   0.0       4.6   1.4e+03      79     107 ..     441     469 ..     437     478 .. 0.75
   3 !   15.6   0.1   4.1e-05     0.012      21      53 ..     472     513 ..     447     526 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0012
                                       HHHHHHCHTEEEEEEESTTSSHHHHHHHHHHHT CS
                              TsaE  11 gkklakalgdvilLeGdLGaGKTtlvrglakal 43 
                                        k+l+ ++ + +lL+G+ G+GKT+l++++a + 
  gi|474933615|ref|YP_007687197.1| 196 FKRLGVEAPKGVLLHGPPGTGKTMLAKAVAGET 228
                                       45555544567*****************99766 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 4.6
                                       HHHHCTTCCCCSTSCEEEEETGGGGCCCS CS
                              TsaE  79 eleelgleeyleeeavvlvEWpekleell 107
                                       ++e++g  e  +++   +vEWp k+++++
  gi|474933615|ref|YP_007687197.1| 441 KWEDIGALEDAKQQLKEAVEWPLKYSKVF 469
                                       578888888877667889****9976654 PP

  == domain 3  score: 15.6 bits;  conditional E-value: 4.1e-05
                                       E.......EEEEESTTSSHHHHHHHHHHHTT--..----TTT CS
                              TsaE  21 v.......ilLeGdLGaGKTtlvrglakalgve..evkSPTF 53 
                                       +       ilL+G+ G+GKT+l++++a + + +  +vk P F
  gi|474933615|ref|YP_007687197.1| 472 MnakppkgILLYGPPGTGKTMLAKAVATESEANfiSVKGPEF 513
                                       13334444**********************999999999988 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.1   0.00046      0.14       3      22 ..     207     226 ..     205     232 .. 0.88
   2 ?    1.4   0.0      0.91   2.7e+02      63     142 ..     246     326 ..     238     348 .. 0.70
   3 !   11.7   0.0   0.00061      0.18       3      23 ..     480     500 ..     478     505 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00046
                                       EEEEC-TTTCHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklal 22 
                                       v+l+G++G GKT+L++ +a 
  gi|474933615|ref|YP_007687197.1| 207 VLLHGPPGTGKTMLAKAVAG 226
                                       79**************9985 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.91
                                       TS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH............HHHHHCTTTTT--EEEEEEECCCHHHHC CS
                             NACHT  63 pepaapvsevwavllelperlLlilDglDelvtdlgq...kekqpvrtlLselirkkllpeasllltvrpralrdle 136
                                        e++++ +e+++   e++ ++ + +D +D ++ + ++   +e++++   L +l+ + l ++ +++++  +++ + + 
  gi|474933615|ref|YP_007687197.1| 246 GESEGKLREIFKDAEENAPSIIF-IDEIDSIAPKREEtqgEEERRIVAQLLSLMDG-LNSRGRVVVIGATNRPNSID 320
                                       56667777777777777777776.59999999988888896666666666688888.77777777776666666677 PP

                                       TTSSCE CS
                             NACHT 137 eqleea 142
                                       e l+++
  gi|474933615|ref|YP_007687197.1| 321 EALRRP 326
                                       777666 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00061
                                       EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                       ++l G++G GKT+L++ +a++
  gi|474933615|ref|YP_007687197.1| 480 ILLYGPPGTGKTMLAKAVATE 500
                                       7899************99986 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0    0.0011      0.33       1      26 [.     207     232 ..     207     288 .. 0.77
   2 !   15.1   0.0   7.5e-05     0.023       1      56 [.     480     526 ..     480     552 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0011
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                       ++l+Gp+g+GK++lak +a + ++++
  gi|474933615|ref|YP_007687197.1| 207 VLLHGPPGTGKTMLAKAVAGETSSNF 232
                                       689**************887777655 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 7.5e-05
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvid 56 
                                       i+lyGp+g+GK++lak +a++ +         +++   +  +f+++Y g+    + 
  gi|474933615|ref|YP_007687197.1| 480 ILLYGPPGTGKTMLAKAVATESE--------ANFI-SVKGPEFLNKYVGESEKAVR 526
                                       789**************555444........3333.35566666666655544444 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   0.00044      0.13       2      48 ..     207     258 ..     206     300 .. 0.63
   2 !   14.6   0.0   9.9e-05      0.03       2      39 ..     480     522 ..     479     542 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00044
                            AAA_28   2 ivitGgestGKTtlleaLa.ar..gypvv..pEaareileeklakgedalpw 48 
                                       + + G+++tGKT l++a a ++  ++  +  pE++ +++ e   k +++ ++
  gi|474933615|ref|YP_007687197.1| 207 VLLHGPPGTGKTMLAKAVAgETssNFISIggPEIVSKFYGESEGKLREIFKD 258
                                       6799***************633554444457777777776666555544444 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 9.9e-05
                            AAA_28   2 ivitGgestGKTtlleaLaar...gypvv..pEaareileekl 39 
                                       i + G+++tGKT l++a a +   ++  v  pE+  +++ e  
  gi|474933615|ref|YP_007687197.1| 480 ILLYGPPGTGKTMLAKAVATEseaNFISVkgPEFLNKYVGESE 522
                                       7899***************554454444449999988886655 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0    0.0004      0.12      30      58 ..     201     229 ..     193     237 .. 0.80
   2 !   12.8   0.0   0.00021     0.063      25      61 ..     469     504 ..     464     549 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0004
                             AAA_7  30 lknkkpvllvGptGtGKtviikdllkkld 58 
                                       +++ k vll Gp GtGKt+++k +  + +
  gi|474933615|ref|YP_007687197.1| 201 VEAPKGVLLHGPPGTGKTMLAKAVAGETS 229
                                       778899***************99877766 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00021
                             AAA_7  25 llelllknkkpvllvGptGtGKtviikdllkkldkek 61 
                                       + ++  k  k +ll+Gp GtGKt+++k + ++ +  +
  gi|474933615|ref|YP_007687197.1| 469 FAHMNAKPPKGILLYGPPGTGKTMLAKAVATESE-AN 504
                                       55666677789****************9887777.33 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0    0.0013       0.4       4      22 ..     206     224 ..     203     283 .. 0.80
   2 !   14.3   0.0   8.3e-05     0.025       5      23 ..     480     500 ..     477     549 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0013
                            AAA_24   4 kiliyGpsgiGKTtlakel 22 
                                        +l+ Gp+g+GKT+lak  
  gi|474933615|ref|YP_007687197.1| 206 GVLLHGPPGTGKTMLAKAV 224
                                       5899************987 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 8.3e-05
                            AAA_24   5 iliyGpsgiGKTtlakel..g 23 
                                       il+yGp+g+GKT+lak    +
  gi|474933615|ref|YP_007687197.1| 480 ILLYGPPGTGKTMLAKAVatE 500
                                       89*************987553 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0048       1.4      54      84 ..     205     235 ..     196     331 .. 0.69
   2 !   13.5   0.0    0.0001      0.03      24      81 ..     439     505 ..     420     546 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0048
                            DUF815  54 nnvLLwGarGtGKSslvkallneyaeegLrl 84 
                                       + vLL G  GtGK  l ka+  e++++ + +
  gi|474933615|ref|YP_007687197.1| 205 KGVLLHGPPGTGKTMLAKAVAGETSSNFISI 235
                                       579******************9999987654 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.0001
                            DUF815  24 evklddLvgidkqkealvente.........qfleglpannvLLwGarGtGKSslvkallneyaeeg 81 
                                       +vk++d+  +++ k++l+e +e         ++++ +p + +LL+G  GtGK  l ka+ +e +++ 
  gi|474933615|ref|YP_007687197.1| 439 NVKWEDIGALEDAKQQLKEAVEwplkyskvfAHMNAKPPKGILLYGPPGTGKTMLAKAVATESEANF 505
                                       5666666666666666666543222222222678889999*******************99987765 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   0.00047      0.14       7      51 ..     200     242 ..     197     320 .. 0.73
   2 !   10.1   0.0    0.0029      0.87       9      51 ..     475     515 ..     470     582 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00047
                                       EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke 51 
                                        +++ + v + G+ G+GK+ L+k++ag+++  +  i + g ++ +
  gi|474933615|ref|YP_007687197.1| 200 GVEAPKGVLLHGPPGTGKTMLAKAVAGETS--SNFISIGGPEIVS 242
                                       667778899******************987..4555555555555 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0029
                                       ETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   9 kegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke 51 
                                       k+ + + + G+ G+GK+ L+k++a +++     i ++g ++ +
  gi|474933615|ref|YP_007687197.1| 475 KPPKGILLYGPPGTGKTMLAKAVATESEA--NFISVKGPEFLN 515
                                       555668899***************99864..555555555554 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0068         2      15      37 ..     200     222 ..     193     235 .. 0.83
   2 ?    4.3   0.0     0.074        22     121     155 ..     265     302 ..     241     313 .. 0.70
   3 !    8.0   0.0    0.0056       1.7      22      42 ..     480     500 ..     476     530 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0068
                            ATPase  15 GipegrvvlitGepGtGKtifal 37 
                                       G+   + vl+ G pGtGKt++a+
  gi|474933615|ref|YP_007687197.1| 200 GVEAPKGVLLHGPPGTGKTMLAK 222
                                       55566779*************97 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.074
                            ATPase 121 krvviDsitgl...ayeekeavaReilrqlvrvlkklg 155
                                       + + iD i+++    +e++ ++ R+i+ ql++ + +l+
  gi|474933615|ref|YP_007687197.1| 265 SIIFIDEIDSIapkREETQGEEERRIVAQLLSLMDGLN 302
                                       55566666655431566667789*********998775 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0056
                            ATPase  22 vlitGepGtGKtifalqFlik 42 
                                       +l++G pGtGKt++a+  + +
  gi|474933615|ref|YP_007687197.1| 480 ILLYGPPGTGKTMLAKAVATE 500
                                       89************9876655 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0    0.0014      0.41      55      79 ..     197     221 ..     180     225 .. 0.86
   2 !   10.9   0.0    0.0005      0.15      46      79 ..     463     494 ..     427     504 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0014
                       AFG1_ATPase  55 krksvepvrglYlwGgvGrGKtylm 79 
                                       kr  ve+++g+ l+G+ G GKt+l 
  gi|474933615|ref|YP_007687197.1| 197 KRLGVEAPKGVLLHGPPGTGKTMLA 221
                                       345789*****************95 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0005
                       AFG1_ATPase  46 salgklfgrkrksvepvrglYlwGgvGrGKtylm 79 
                                        ++ k+f++   + +p++g+ l+G+ G GKt+l 
  gi|474933615|ref|YP_007687197.1| 463 LKYSKVFAHM--NAKPPKGILLYGPPGTGKTMLA 494
                                       3567788854..689*****************96 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00085      0.25      16      35 ..     203     222 ..     187     263 .. 0.83
   2 !    9.5   0.0    0.0026      0.79      20      41 ..     480     501 ..     457     570 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00085
                            AAA_11  16 eseitliqGPPGtgKTktiv 35 
                                        ++ +l++GPPGtgKT    
  gi|474933615|ref|YP_007687197.1| 203 APKGVLLHGPPGTGKTMLAK 222
                                       555689**********6544 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0026
                            AAA_11  20 tliqGPPGtgKTktivellsql 41 
                                        l+ GPPGtgKT    ++  + 
  gi|474933615|ref|YP_007687197.1| 480 ILLYGPPGTGKTMLAKAVATES 501
                                       6899********8777777666 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0    0.0029      0.87       2      28 ..     207     233 ..     206     242 .. 0.89
   2 !   10.0   0.0    0.0019      0.58       2      30 ..     480     508 ..     479     590 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0029
                             AAA_3   2 vllegvPGlaktllvkalakaldlefk 28 
                                       vll+g PG++kt+l+ka+a   + +f 
  gi|474933615|ref|YP_007687197.1| 207 VLLHGPPGTGKTMLAKAVAGETSSNFI 233
                                       89*****************99888875 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0019
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                       +ll g PG++kt+l+ka+a+  +++f  +
  gi|474933615|ref|YP_007687197.1| 480 ILLYGPPGTGKTMLAKAVATESEANFISV 508
                                       7999****************999999766 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.1    0.0027       0.8      22      41 ..     207     226 ..     197     233 .. 0.85
   2 !    9.6   0.0    0.0018      0.55      23      42 ..     481     500 ..     466     507 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0027
                                       EEEE--TTSSTTHHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavalav 41 
                                       v   Gp GtGKt+la a+a 
  gi|474933615|ref|YP_007687197.1| 207 VLLHGPPGTGKTMLAKAVAG 226
                                       6789***********99985 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0018
                                       EEE--TTSSTTHHHHHHHHH CS
                              PhoH  23 faiGpaGtGKtylavalave 42 
                                          Gp GtGKt+la a+a e
  gi|474933615|ref|YP_007687197.1| 481 LLYGPPGTGKTMLAKAVATE 500
                                       678************99976 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.1    0.0027      0.81      21      39 ..     207     225 ..     195     232 .. 0.86
   2 !    9.9   0.0    0.0018      0.55      16      44 ..     475     503 ..     466     511 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0027
                            AAA_30  21 avltGpAGtGKttalkalr 39 
                                       ++l+Gp+GtGKt++ ka++
  gi|474933615|ref|YP_007687197.1| 207 VLLHGPPGTGKTMLAKAVA 225
                                       689**********999986 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0018
                            AAA_30  16 sgdrvavltGpAGtGKttalkalreawea 44 
                                       ++ +  +l Gp+GtGKt++ ka++   ea
  gi|474933615|ref|YP_007687197.1| 475 KPPKGILLYGPPGTGKTMLAKAVATESEA 503
                                       555567899************99876665 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0096       2.9      25      55 ..     194     224 ..     182     232 .. 0.84
   2 ?   -0.1   0.0       1.7   5.1e+02     119     154 ..     263     302 ..     247     332 .. 0.66
   3 !    8.8   0.0    0.0034         1      25      59 ..     467     501 ..     452     511 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0096
                              TniB  25 eLleypkrkrmpnlllvGdsnnGKtmivekF 55 
                                       eL+++   + ++ +ll+G++ +GKtm+++  
  gi|474933615|ref|YP_007687197.1| 194 ELFKRLGVEAPKGVLLHGPPGTGKTMLAKAV 224
                                       5777777788899**************9865 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.7
                              TniB 119 kvrvLiiDEihnll....agsarkqreflnalksLgnelk 154
                                        + ++ iDEi+++     + + ++ r+++++l sL++ l+
  gi|474933615|ref|YP_007687197.1| 263 APSIIFIDEIDSIApkreETQGEEERRIVAQLLSLMDGLN 302
                                       567899*****99722224455556777777777777664 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0034
                              TniB  25 eLleypkrkrmpnlllvGdsnnGKtmivekFarlh 59 
                                       +++++ ++k ++ +ll+G++ +GKtm+++  a + 
  gi|474933615|ref|YP_007687197.1| 467 KVFAHMNAKPPKGILLYGPPGTGKTMLAKAVATES 501
                                       5667777888899**************99877665 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0083       2.5     117     135 ..     207     225 ..     204     232 .. 0.90
   2 !   11.0   0.0   0.00054      0.16     117     136 ..     480     499 ..     463     504 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0083
                         Parvo_NS1 117 vwfyGpantGktnlaeaIa 135
                                       v+++Gp+ tGkt+la+a a
  gi|474933615|ref|YP_007687197.1| 207 VLLHGPPGTGKTMLAKAVA 225
                                       7899************987 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00054
                         Parvo_NS1 117 vwfyGpantGktnlaeaIak 136
                                       +++yGp+ tGkt+la+a a+
  gi|474933615|ref|YP_007687197.1| 480 ILLYGPPGTGKTMLAKAVAT 499
                                       89***************997 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0    0.0016      0.49       4      75 ..     207     273 ..     204     294 .. 0.63
   2 !    8.8   0.0    0.0029      0.86       4      48 ..     480     517 ..     477     565 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0016
                           DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavyls.vNhplvlvlrealakkeekkkkkeafek.ls.sfinnls 75 
                                       vl +G +GtGKt+++ +++ e        +++++s +  + v + + + ++k  ++ +k+a e+ +s  fi +++
  gi|474933615|ref|YP_007687197.1| 207 VLLHGPPGTGKTMLAKAVAGET-------SSNFISiGGPEIVSKFYGESEGKL-REIFKDAEENaPSiIFIDEID 273
                                       6889*************99998.......455554144455678888888888.444444333303313555555 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0029
                           DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlr 48 
                                       +l  G +GtGKt+++ ++++e        +a+++sv +p+ l  +
  gi|474933615|ref|YP_007687197.1| 480 ILLYGPPGTGKTMLAKAVATES-------EANFISVKGPEFLNKY 517
                                       6789************999998.......6666666666654433 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0034         1      22      43 ..     206     227 ..     193     235 .. 0.80
   2 !    8.2   0.0    0.0041       1.2      23      44 ..     480     501 ..     465     508 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0034
                                       EEEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC  22 vvalvGmgGvGKttlakqilnk 43 
                                        v l+G +G GKt lak +  +
  gi|474933615|ref|YP_007687197.1| 206 GVLLHGPPGTGKTMLAKAVAGE 227
                                       4889*************99766 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0041
                                       EEEEESTTSSHHHHHHHHCCSH CS
                            NB-ARC  23 valvGmgGvGKttlakqilnks 44 
                                       + l+G +G GKt lak +  +s
  gi|474933615|ref|YP_007687197.1| 480 ILLYGPPGTGKTMLAKAVATES 501
                                       789*************999874 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0     0.019       5.5       2      27 ..     211     236 ..     210     282 .. 0.89
   2 !    8.8   0.0    0.0068         2       1      31 [.     483     514 ..     483     585 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.019
                                       E-TTSSHHHHHHHHHHHHTEEEEEHH CS
                            AAA_17   2 GgPGsGKgtqceklvekygfthlsaG 27 
                                       G+PG GK+ +++ ++ +    ++s G
  gi|474933615|ref|YP_007687197.1| 211 GPPGTGKTMLAKAVAGETSSNFISIG 236
                                       9**************99999999987 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0068
                                       EE-TTSSHHHHHHHHHHHHTEEEEEH.HHHHH CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsa.Gdllr 31 
                                       +G+PG GK+ +++ ++ + +  ++s  G  + 
  gi|474933615|ref|YP_007687197.1| 483 YGPPGTGKTMLAKAVATESEANFISVkGPEFL 514
                                       7***********99998876666654344444 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.2     0.015       4.6      11      30 ..     205     224 ..     200     234 .. 0.82
   2 !    9.3   0.0    0.0045       1.4       9      32 ..     476     499 ..     470     545 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.015
                            AAA_19  11 kvllvtaGpGtGKTrvlkhi 30 
                                       k +l+ ++pGtGKT + k++
  gi|474933615|ref|YP_007687197.1| 205 KGVLLHGPPGTGKTMLAKAV 224
                                       55899*********987765 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0045
                            AAA_19   9 kekvllvtaGpGtGKTrvlkhiva 32 
                                       + k +l+ ++pGtGKT + k++ +
  gi|474933615|ref|YP_007687197.1| 476 PPKGILLYGPPGTGKTMLAKAVAT 499
                                       567799**********98776654 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.1     0.007       2.1       2      32 ..     207     237 ..     206     257 .. 0.89
   2 ?   -1.4   0.0       6.3   1.9e+03      87     104 ..     254     272 ..     241     296 .. 0.74
   3 ?    0.1   0.0       2.2   6.4e+02     103     125 ..     444     466 ..     411     472 .. 0.79
   4 ?    7.4   0.0     0.013       3.8       2      32 ..     480     510 ..     479     530 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.007
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                       v++ GppG+GKt l k v+ + +s+ +++gG
  gi|474933615|ref|YP_007687197.1| 207 VLLHGPPGTGKTMLAKAVAGETSSNFISIGG 237
                                       6789***************999888888887 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 6.3
                                       HHHHHHH.HHH-EEEE--- CS
                          NTPase_1  87 ealrkal.seadviviDEi 104
                                       e+++ a  + + +i iDEi
  gi|474933615|ref|YP_007687197.1| 254 EIFKDAEeNAPSIIFIDEI 272
                                       445555535566******9 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 2.2
                                       --STTGGG-HHHHHHHHHHHTTT CS
                          NTPase_1 103 EiGkmElkskkfkeaveevLkse 125
                                        iG +E   +++keave  Lk +
  gi|474933615|ref|YP_007687197.1| 444 DIGALEDAKQQLKEAVEWPLKYS 466
                                       6***************9888744 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.013
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                       +++ GppG+GKt l k v+ + + + ++v+G
  gi|474933615|ref|YP_007687197.1| 480 ILLYGPPGTGKTMLAKAVATESEANFISVKG 510
                                       6788**************9999888888887 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0      0.14        41      23      48 ..     207     231 ..     194     312 .. 0.54
   2 !   10.5   0.0    0.0014      0.42      17      46 ..     474     503 ..     466     569 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.14
                          ATPase_2  23 yfiYGpegsGKtaLlkeiienledkd 48 
                                       +++ Gp g GKt L k ++ + ++ +
  gi|474933615|ref|YP_007687197.1| 207 VLLHGPPGTGKTMLAKAVAGETSS-N 231
                                       678999999999999998877643.3 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0014
                          ATPase_2  17 repneiyfiYGpegsGKtaLlkeiienled 46 
                                        +p + +++YGp g GKt L k +++++e 
  gi|474933615|ref|YP_007687197.1| 474 AKPPKGILLYGPPGTGKTMLAKAVATESEA 503
                                       56667789***************9999854 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0     0.015       4.6      14      46 ..     181     226 ..     176     235 .. 0.70
   2 ?    7.3   0.0     0.015       4.5      14      46 ..     450     499 ..     440     514 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.015
                                       HHT...................TTSEEEEEESTTSTHHHHHHHHHH CS
                            ResIII  14 nlleklks.............krdkrglikmaTGtGKTlvaaklie 46 
                                       +++e ++              +  k +l++ + GtGKT++a +++ 
  gi|474933615|ref|YP_007687197.1| 181 QVREMIELplkhpelfkrlgvEAPKGVLLHGPPGTGKTMLAKAVAG 226
                                       5554444455555566666668889999***********9976665 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.015
                                       HHT.......................TTSEEEEEESTTSTHHHHHHHHHH CS
                            ResIII  14 nlleklks.................krdkrglikmaTGtGKTlvaaklie 46 
                                       + +++lk+                 k  k +l+  + GtGKT++a +++ 
  gi|474933615|ref|YP_007687197.1| 450 DAKQQLKEavewplkyskvfahmnaKPPKGILLYGPPGTGKTMLAKAVAT 499
                                       55555555555566666667776668888999***********9965554 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.044        13       3      31 ..     205     233 ..     203     251 .. 0.87
   2 ?    5.8   0.0     0.032       9.6       3      30 ..     478     505 ..     476     512 .. 0.87
   3 ?   -0.9   0.0       3.9   1.2e+03      74      96 ..     513     538 ..     509     553 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.044
                                       SEEEEESTTTSSHHHHHHHHHHHSTTTEE CS
                     Guanylate_kin   3 rpvvlvgpsgaGksslkkaLlselpekfg 31 
                                       + v l gp g+Gk +l ka+  e +++f 
  gi|474933615|ref|YP_007687197.1| 205 KGVLLHGPPGTGKTMLAKAVAGETSSNFI 233
                                       56899***************999999884 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.032
                                       SEEEEESTTTSSHHHHHHHHHHHSTTTE CS
                     Guanylate_kin   3 rpvvlvgpsgaGksslkkaLlselpekf 30 
                                       + + l gp g+Gk +l ka+ +e + +f
  gi|474933615|ref|YP_007687197.1| 478 KGILLYGPPGTGKTMLAKAVATESEANF 505
                                       56899***************99988887 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 3.9
                                       ETTEEEEEEHHHHHHHHHTTSE...E CS
                     Guanylate_kin  74 fsgnlygtsveaieevlekgki...v 96 
                                       f +++ g+s +a++e + k+++   +
  gi|474933615|ref|YP_007687197.1| 513 FLNKYVGESEKAVRETFRKARQaspC 538
                                       5678999*********9999986663 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1     0.023       6.9       3      30 ..     209     236 ..     207     237 .. 0.89
   2 ?    6.6   0.0     0.019       5.6       3      28 ..     482     507 ..     480     509 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.023
                                       EE-STTSSHHHHHHHHHHHHT-EEEEHH CS
                    Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyldtg 30 
                                       + GP g+GK  +a+a+a + + ++++ g
  gi|474933615|ref|YP_007687197.1| 209 LHGPPGTGKTMLAKAVAGETSSNFISIG 236
                                       68*****************999998765 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.019
                                       EE-STTSSHHHHHHHHHHHHT-EEEE CS
                    Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyld 28 
                                       + GP g+GK  +a+a+a++ ++++++
  gi|474933615|ref|YP_007687197.1| 482 LYGPPGTGKTMLAKAVATESEANFIS 507
                                       67*****************9999986 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.035        11       4      33 ..     207     236 ..     205     286 .. 0.89
   2 ?    7.0   0.0     0.016       4.8       4      40 ..     480     516 ..     478     544 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.035
                                       EEEEE-TTSSHHHHHHHHHHHSSS-EEEEE CS
                               CPT   4 ilLnGgsssGKsslaralqevldepwlhlg 33 
                                       +lL+G + +GK+ la+a+   +   ++ +g
  gi|474933615|ref|YP_007687197.1| 207 VLLHGPPGTGKTMLAKAVAGETSSNFISIG 236
                                       89****************999999998887 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.016
                                       EEEEE-TTSSHHHHHHHHHHHSSS-EEEEEHHHHHHH CS
                               CPT   4 ilLnGgsssGKsslaralqevldepwlhlgvDafvea 40 
                                       ilL G + +GK+ la+a+ + +++ ++ ++  +f+++
  gi|474933615|ref|YP_007687197.1| 480 ILLYGPPGTGKTMLAKAVATESEANFISVKGPEFLNK 516
                                       89************************99988888776 PP

>> UFD1  Ubiquitin fusion degradation protein UFD1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   6.1e-05     0.018      79     170 ..      64     152 ..      17     156 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.1e-05
                              UFD1  79 enlgleegdlveiesvslpkgkfvklqpqsedfldisdpkavLekaLrnfatLtkgdvieikyndkvyelkvlevkp 155
                                       +n g++ gd v+++++++++++ +++ p +e  l+++   + L +aL    + +kgd+++++   ++++l v+  +p
  gi|474933615|ref|YP_007687197.1|  64 RNAGVSIGDRVDVKKAEVKEATKITFSPTEE--LRLQGGEEYLAQALEG-RAFAKGDILSLNIMGNKMDLVVTSFTP 137
                                       6788999*********************955..899999********86.6789*********************** PP

                              UFD1 156 esavsiietdlevdf 170
                                       +    ii ++ +v +
  gi|474933615|ref|YP_007687197.1| 138 AAEAVIIGAETKVKI 152
                                       995556655555554 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.026       7.7     125     153 ..     200     228 ..      80     236 .. 0.82
   2 ?    6.3   0.0     0.014       4.2     129     153 ..     477     501 ..     372     511 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.026
                             T2SSE 125 avrerglilvsGgTgsGKttllyallkei 153
                                        v++ + +l+ G+ g+GKt l+ a+  e 
  gi|474933615|ref|YP_007687197.1| 200 GVEAPKGVLLHGPPGTGKTMLAKAVAGET 228
                                       46667889*************99987765 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.014
                             T2SSE 129 rglilvsGgTgsGKttllyallkei 153
                                        + il+ G+ g+GKt l+ a+ +e 
  gi|474933615|ref|YP_007687197.1| 477 PKGILLYGPPGTGKTMLAKAVATES 501
                                       5679*************99987764 PP

>> DAP3  Mitochondrial ribosomal death-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.056        17      24      53 ..     205     233 ..     194     240 .. 0.77
   2 ?    7.4   0.0    0.0072       2.1      17      53 ..     471     506 ..     456     527 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.056
                                       -EEEEE-SSSSSTTTTHHHHHHHGGGS--E CS
                              DAP3  24 krlvltGekgsGKSvlLlqalayAlekgwv 53 
                                       k ++l+G +g+GK++ L++a+a  ++++++
  gi|474933615|ref|YP_007687197.1| 205 KGVLLHGPPGTGKTM-LAKAVAGETSSNFI 233
                                       5579*********97.67777766666655 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0072
                                       S-SSS---EEEEE-SSSSSTTTTHHHHHHHGGGS--E CS
                              DAP3  17 adkkkkvkrlvltGekgsGKSvlLlqalayAlekgwv 53 
                                         ++k+ k ++l+G +g+GK++ L++a+a   e++++
  gi|474933615|ref|YP_007687197.1| 471 HMNAKPPKGILLYGPPGTGKTM-LAKAVATESEANFI 506
                                       4678899999**********97.56666655555554 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.034        10      22      45 ..     205     228 ..     194     281 .. 0.81
   2 ?    5.8   0.0     0.047        14      24      47 ..     480     503 ..     471     549 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.034
                                       S-EEEEEETT--HHHHHHCC--TT CS
                   Sigma54_activ_2  22 lpvfltGekGsgkelvArlLhkns 45 
                                         v+l G++G+gk++ A++ + + 
  gi|474933615|ref|YP_007687197.1| 205 KGVLLHGPPGTGKTMLAKAVAGET 228
                                       569***************987554 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.047
                                       EEEEEETT--HHHHHHCC--TTS- CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgp 47 
                                       ++l G++G+gk++ A++ + +s+ 
  gi|474933615|ref|YP_007687197.1| 480 ILLYGPPGTGKTMLAKAVATESEA 503
                                       89***************9988775 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.036        11      56      76 ..     207     227 ..     197     240 .. 0.86
   2 ?    4.8   0.0     0.097        29      45      76 ..     472     500 ..     459     530 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.036
                                       EEEEE-TTSSHHHHHHHHHHH CS
                            Torsin  56 lsfhGwtGtGknfvaeiiaen 76 
                                       + +hG +GtGk  +a+ +a +
  gi|474933615|ref|YP_007687197.1| 207 VLLHGPPGTGKTMLAKAVAGE 227
                                       569*************99866 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.097
                                       HT-SS-SS-EEEEEEE-TTSSHHHHHHHHHHH CS
                            Torsin  45 lenekpkkpLvlsfhGwtGtGknfvaeiiaen 76 
                                       ++   +k p  + ++G +GtGk  +a+ +a +
  gi|474933615|ref|YP_007687197.1| 472 MN---AKPPKGILLYGPPGTGKTMLAKAVATE 500
                                       33...3334456689************99864 PP

>> Vps4_C  Vps4 C terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.034        10      19      44 ..     403     428 ..     381     436 .. 0.81
   2 ?    3.6   0.0      0.23        68      21      41 ..     675     695 ..     667     701 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.034
                            Vps4_C  19 ipsdkllePpvtlkDflkalkkarpt 44 
                                       ip++ l   +vt++Df  a++   p+
  gi|474933615|ref|YP_007687197.1| 403 IPTEVLNSINVTMEDFRHAMNGLTPS 428
                                       677777777**********9988777 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.23
                            Vps4_C  21 sdkllePpvtlkDflkalkka 41 
                                       ++++ + +vt++D+lka+ k 
  gi|474933615|ref|YP_007687197.1| 675 QEEIDACKVTMDDLLKAVDKF 695
                                       6788888**********9875 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.079        24      21      39 ..     204     221 ..     195     225 .. 0.81
   2 ?    5.9   0.0     0.037        11      21      42 ..     477     497 ..     463     499 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.079
                            AAA_29  21 lkgatlltGpsGsGKSTll 39 
                                       +kg +ll Gp G+GK+ l 
  gi|474933615|ref|YP_007687197.1| 204 PKG-VLLHGPPGTGKTMLA 221
                                       467.9**********9875 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.037
                            AAA_29  21 lkgatlltGpsGsGKSTllDAi 42 
                                       +kg +ll Gp G+GK+ l  A+
  gi|474933615|ref|YP_007687197.1| 477 PKG-ILLYGPPGTGKTMLAKAV 497
                                       466.9**********9887666 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.057        17       5      31 ..     208     234 ..     205     237 .. 0.91
   2 ?    5.5   0.0     0.033       9.8       5      31 ..     481     507 ..     478     511 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.057
                               IPT   5 lifGatttGKtaeaiklaketgapviv 31 
                                       l++G+ +tGKt  a ++a et+   i+
  gi|474933615|ref|YP_007687197.1| 208 LLHGPPGTGKTMLAKAVAGETSSNFIS 234
                                       899******************998887 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.033
                               IPT   5 lifGatttGKtaeaiklaketgapviv 31 
                                       l++G+ +tGKt  a ++a e  a  i+
  gi|474933615|ref|YP_007687197.1| 481 LLYGPPGTGKTMLAKAVATESEANFIS 507
                                       89****************999888776 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.065        19       2      24 ..     205     227 ..     204     231 .. 0.90
   2 ?    4.9   0.0     0.066        20       2      24 ..     478     500 ..     477     509 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.065
                         PduV-EutP   2 kkilliGkvgsGKttLtqalkge 24 
                                       k +ll G+ g+GKt L++a+ ge
  gi|474933615|ref|YP_007687197.1| 205 KGVLLHGPPGTGKTMLAKAVAGE 227
                                       5699***************9987 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.066
                         PduV-EutP   2 kkilliGkvgsGKttLtqalkge 24 
                                       k ill G+ g+GKt L++a+  e
  gi|474933615|ref|YP_007687197.1| 478 KGILLYGPPGTGKTMLAKAVATE 500
                                       6699**************99765 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0         9   2.7e+03      23      43 ..     207     227 ..     194     233 .. 0.82
   2 ?    2.7   0.0      0.21        61     167     189 ..     258     279 ..     241     313 .. 0.86
   3 ?    4.2   0.0     0.069        21       9      43 ..     466     500 ..     463     509 .. 0.83
   4 ?    0.0   0.0       1.3   3.9e+02     167     187 ..     528     550 ..     511     556 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 9
                        KAP_NTPase  23 vgLygkWGsGKssllnklede 43 
                                       v L g+ G+GK+ l + +  e
  gi|474933615|ref|YP_007687197.1| 207 VLLHGPPGTGKTMLAKAVAGE 227
                                       7899999*****998877665 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.21
                        KAP_NTPase 167 tLdalqkrlVvviDdLDrcetee 189
                                         + ++ + +++iD++D++ +++
  gi|474933615|ref|YP_007687197.1| 258 DAE-ENAPSIIFIDEIDSIAPKR 279
                                       333.58899*********99876 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.069
                        KAP_NTPase   9 adilseptlatpivvgLygkWGsGKssllnklede 43 
                                        ++  ++++++p  + Lyg+ G+GK+ l + +  e
  gi|474933615|ref|YP_007687197.1| 466 SKVFAHMNAKPPKGILLYGPPGTGKTMLAKAVATE 500
                                       567778889999**************999887665 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 1.3
                        KAP_NTPase 167 tLda..lqkrlVvviDdLDrcet 187
                                       t+++  + ++ Vv+ D++D++ +
  gi|474933615|ref|YP_007687197.1| 528 TFRKarQASPCVVFMDEIDSIAP 550
                                       4444568899*********9866 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0      0.13        38       2      70 ..     208     271 ..     207     276 .. 0.60
   2 ?    6.1   0.0     0.027         8       4      71 ..     483     545 ..     480     550 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.13
                   Viral_helicase1   2 vvhGvpGcGKStlirkllrts..liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDE 70 
                                       + hG pG GK+ l + ++ +     ++++ p  e++++   +++ +  + ++++++++       i+++DE
  gi|474933615|ref|YP_007687197.1| 208 LLHGPPGTGKTMLAKAVAGETssNFISIGGP--EIVSKFYGESEGKLREIFKDAEENAP-----SIIFIDE 271
                                       68***********999998866433333333..44444333444444455555555543.....2566665 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.027
                   Viral_helicase1   4 hGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                        G pG GK+ l + ++ +s  ++ +++   e l++ + ++++   +t++++ +a  +     ++++DE+
  gi|474933615|ref|YP_007687197.1| 483 YGPPGTGKTMLAKAVATESeANFISVKG-PEFLNKYVGESEKAVRETFRKARQASPC-----VVFMDEI 545
                                       588*************999966666666.7999999988888888888888887764.....7999997 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.072        22       5      46 ..     206     247 ..     202     258 .. 0.77
   2 ?    4.8   0.0     0.055        16       5      46 ..     479     520 ..     475     528 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.072
                                       EEEEE-STTSSHHHHHHHHHHSS---B---S.S-EEETTG... CS
                             SRPRB   5 avllvGlsdsGKTslftrLttdsvkktvtSq.essaalkvkse 46 
                                        vll G+  +GKT+l +    +++ +  +S+  ++++ k+ +e
  gi|474933615|ref|YP_007687197.1| 206 GVLLHGPPGTGKTMLAK-AVAGETSSNFISIgGPEIVSKFYGE 247
                                       699**********8865.5667788888999888888887444 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.055
                                       EEEEE-STTSSHHHHHHHHHHSS---B---S.S-EEETTG... CS
                             SRPRB   5 avllvGlsdsGKTslftrLttdsvkktvtSq.essaalkvkse 46 
                                        +ll G+  +GKT+l + + t+s  +   S+  +++ +k+ +e
  gi|474933615|ref|YP_007687197.1| 479 GILLYGPPGTGKTMLAKAVATESEANFI-SVkGPEFLNKYVGE 520
                                       589************9999998766544.44477777777444 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1      0.14        40       4      21 ..     208     225 ..     206     235 .. 0.81
   2 ?    5.1   0.0     0.051        15       4      28 ..     481     505 ..     479     532 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.14
                                       EEEESTTCCHHHHHHHHH CS
                              cobW   4 vltGflGsGKTtLlnhll 21 
                                       +l G++G+GKT+L +++ 
  gi|474933615|ref|YP_007687197.1| 208 LLHGPPGTGKTMLAKAVA 225
                                       689*********988776 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.051
                                       EEEESTTCCHHHHHHHHHCT--SS- CS
                              cobW   4 vltGflGsGKTtLlnhllenraglk 28 
                                       +l G++G+GKT+L +++ ++++ + 
  gi|474933615|ref|YP_007687197.1| 481 LLYGPPGTGKTMLAKAVATESEANF 505
                                       689**********999987766655 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.33        97      20      44 ..     202     226 ..     194     233 .. 0.81
   2 ?    6.5   0.0     0.013       3.9      11      44 ..     466     499 ..     463     508 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.33
                                       HCTS-EEEEESTTSSCHHHHHHHHH CS
                              PIF1  20 ekgklfFvtGsgGtgKtflwkallk 44 
                                       e +k + ++G  GtgKt+l ka+  
  gi|474933615|ref|YP_007687197.1| 202 EAPKGVLLHGPPGTGKTMLAKAVAG 226
                                       567778899**********999865 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.013
                                       HHH......HCTS-EEEEESTTSSCHHHHHHHHH CS
                              PIF1  11 daiieavlnekgklfFvtGsgGtgKtflwkallk 44 
                                        ++ + ++++ +k + ++G  GtgKt+l ka+ +
  gi|474933615|ref|YP_007687197.1| 466 SKVFAHMNAKPPKGILLYGPPGTGKTMLAKAVAT 499
                                       567777888999****************999876 PP

>> Hydin_ADK  Hydin Adenylate kinase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1       0.1        31       2      28 ..     207     233 ..     206     241 .. 0.81
   2 ?    4.8   0.1       0.1        31       2      30 ..     480     508 ..     479     510 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.1
                         Hydin_ADK   2 iivhGaPlsGKtatavtLakkYeaAll 28 
                                       +++hG+P +GKt  a ++a +    ++
  gi|474933615|ref|YP_007687197.1| 207 VLLHGPPGTGKTMLAKAVAGETSSNFI 233
                                       689**********99999876655555 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.1
                         Hydin_ADK   2 iivhGaPlsGKtatavtLakkYeaAllti 30 
                                       i++ G+P +GKt  a ++a + ea ++++
  gi|474933615|ref|YP_007687197.1| 480 ILLYGPPGTGKTMLAKAVATESEANFISV 508
                                       7889*****************99999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (713 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                        60  (0.00334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              60  [number of targets reported over threshold]
# CPU time: 0.88u 0.35s 00:00:01.23 Elapsed: 00:00:00.56
# Mc/sec: 3850.98
//
Query:       gi|474933616|ref|YP_007687198.1|  [L=211]
Description: putative transcriptional regulator [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-10   40.4   0.0    7.1e-10   38.8   0.0    1.8  2  HTH_20          Helix-turn-helix domain
      6e-10   38.8   0.0    1.4e-07   31.3   0.0    2.3  2  HTH_5           Bacterial regulatory protein, arsR family
    8.3e-08   32.0   0.0    0.00029   20.7   0.0    2.3  2  MarR_2          MarR family
    7.5e-07   28.6   0.0    0.00019   20.9   0.1    2.8  2  HTH_24          Winged helix-turn-helix DNA-binding
    1.1e-06   28.5   0.0      0.042   13.8   0.0    2.4  2  MarR            MarR family
    8.3e-06   25.7   0.0      0.034   14.1   0.0    2.4  2  HTH_11          HTH domain
    0.00013   21.7   0.1       0.49   10.3   0.1    2.3  2  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00092   19.5   0.1     0.0013   19.0   0.1    1.2  1  TerB_C          TerB-C domain
     0.0019   17.9   0.0       0.31   10.9   0.0    2.8  3  HTH_23          Homeodomain-like domain
     0.0037   17.2   0.0        0.4   10.7   0.0    2.5  2  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0038   17.4   0.0       0.88    9.8   0.1    2.3  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
  ------ inclusion threshold ------
      0.014   15.4   0.0      0.081   13.0   0.0    2.2  2  HTH_29          Winged helix-turn helix
      0.016   15.7   0.1        2.9    8.5   0.0    2.7  2  HTH_27          Winged helix DNA-binding domain
      0.019   14.6   0.0       0.48   10.0   0.0    2.1  2  ArsR            ArsR transcriptional regulator
      0.022   14.7   0.0      0.075   13.0   0.0    1.9  1  PadR            Transcriptional regulator PadR-like family
       0.03   14.7   0.0          2    8.8   0.0    2.3  2  Rrf2            Transcriptional regulator
      0.056   13.3   0.3         11    5.9   0.0    2.9  3  TFIIE_alpha     TFIIE alpha subunit
      0.075   13.1   0.0       0.19   11.9   0.0    1.7  1  DUF2250         Uncharacterized protein conserved in archaea 
       0.08   12.5   0.3        8.8    5.9   0.0    2.9  3  Sigma70_r4      Sigma-70, region 4
       0.18   11.9   0.0         12    6.0   0.0    2.4  2  FeoC            FeoC like transcriptional regulator


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.0   7.9e-13   7.1e-10       1      60 [.       5      63 ..       5      64 .. 0.96
   2 ?   -1.8   0.0       3.9   3.5e+03      17      42 ..     173     197 ..     171     205 .. 0.67

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 7.9e-13
                                      HHHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20  1 dqiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                      d i++++ +P+Rr+il+a   +e++ + +l ++l++s++ + ++L+ +e+ g+v + re+
  gi|474933616|ref|YP_007687198.1|  5 DSILSIVENPTRRKILQAV-VREPHYPLQLSKELGISQQAVVKNLNLMEKEGIVVSYRES 63
                                      579999*************.**********************************999986 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.9
                                       HHHSTCTTB-HHHHHHHHTS-HHHHH CS
                            HTH_20  17 raLaraegltaselaerldlskntls 42 
                                       ++L  +   +a+++ + l+   + +s
  gi|474933616|ref|YP_007687198.1| 173 DML-NRPNWSAEDISRNLGFNESMVS 197
                                       666.6667789999998876555555 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.0   1.5e-10   1.4e-07       1      45 [.      13      57 ..      13      59 .. 0.98
   2 ?    5.4   0.0     0.018        16      11      34 ..     174     198 ..     167     205 .. 0.75

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 1.5e-10
                                      SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  1 dptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLV 45
                                      +ptR+kIL+++ +++++  +l++elg+sq +v   L+ ++++G+V
  gi|474933616|ref|YP_007687198.1| 13 NPTRRKILQAVVREPHYPLQLSKELGISQQAVVKNLNLMEKEGIV 57
                                      69******************************************9 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.018
                                       HTTSS.EEHHHHHHHHTS-HHHHHH CS
                             HTH_5  11 Laege.lcvcelaeelglsqstvSh 34 
                                       + +++  ++ ++++ lg ++s vS+
  gi|474933616|ref|YP_007687198.1| 174 MLNRPnWSAEDISRNLGFNESMVSR 198
                                       4454447889**************8 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   3.3e-07   0.00029       5      53 ..      14      59 ..      11      70 .. 0.86
   2 !    9.1   0.0    0.0013       1.2       6      45 ..     166     203 ..     162     205 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 3.3e-07
                                      HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2  5 paqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                      p+ + +L a+ r+p     + +l ++lg+s++av + l+ +++ G v+ 
  gi|474933616|ref|YP_007687198.1| 14 PTRRKILQAVVREPH---YPLQLSKELGISQQAVVKNLNLMEKEGIVVS 59
                                      889999999999995...999*************************954 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0013
                                       HHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHH CS
                            MarR_2   6 aqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrL 45 
                                        ++ +L+   +rp    ++ ++ r lg   s vsr++++L
  gi|474933616|ref|YP_007687198.1| 166 EHRELLYDMLNRPN--WSAEDISRNLGFNESMVSRMIDDL 203
                                       57889999999998..7********************998 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.1   2.1e-07   0.00019       2      47 ..      13      57 ..      12      58 .. 0.94
   2 ?    4.7   0.0     0.024        22      20      42 ..     182     204 ..     169     206 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.1e-07
                            HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      + t+rkIL+++ ++p+ +  +L+++lg+S+++v + l+ +e+eG++
  gi|474933616|ref|YP_007687198.1| 13 NPTRRKILQAVVREPHYP-LQLSKELGISQQAVVKNLNLMEKEGIV 57
                                      789*************98.58************************9 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.024
                            HTH_24  20 qreLAerlglSpstvnrrlkrLe 42 
                                         ++++ lg   s v+r ++ L 
  gi|474933616|ref|YP_007687198.1| 182 AEDISRNLGFNESMVSRMIDDLL 204
                                       579****************9996 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   4.7e-05     0.042      16      56 ..      26      66 ..      22      66 .. 0.93
   2 !   12.0   0.0   0.00016      0.15       8      42 ..     170     204 ..     164     205 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.7e-05
                                      TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTST CS
                              MarR 16 gplsvseLakklgvskstvtrvldrLekkGlieRskspeDr 56
                                      +p++  +L k lg+s+ +v + l  +ek+G + +++  ++r
  gi|474933616|ref|YP_007687198.1| 26 EPHYPLQLSKELGISQQAVVKNLNLMEKEGIVVSYRESSNR 66
                                      7888889****************************998887 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00016
                                       HHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHH CS
                              MarR   8 iLrilyeqgplsvseLakklgvskstvtrvldrLe 42 
                                       +L+   ++++ s  ++ + lg + s+v+r++d L 
  gi|474933616|ref|YP_007687198.1| 170 LLYDMLNRPNWSAEDISRNLGFNESMVSRMIDDLL 204
                                       677778999***********************996 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   3.8e-05     0.034      20      46 ..      32      58 ..      15      65 .. 0.85
   2 !    9.3   0.0    0.0012       1.1       8      39 ..     174     203 ..     167     208 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.8e-05
                            HTH_11 20 eLAeeLnvSrrtvrrdIkaLeelgvpI 46
                                      +L++eL++S ++v++ +  +e+ g+ +
  gi|474933616|ref|YP_007687198.1| 32 QLSKELGISQQAVVKNLNLMEKEGIVV 58
                                      79*********************9654 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0012
                            HTH_11   8 lLleargpisgeeLAeeLnvSrrtvrrdIkaL 39 
                                       +L  +r+++s+e++++ L+  ++ v r I++L
  gi|474933616|ref|YP_007687198.1| 174 ML--NRPNWSAEDISRNLGFNESMVSRMIDDL 203
                                       55..8999**********************99 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.1   0.00054      0.49      20      64 ..      25      75 ..      18      77 .. 0.79
   2 !    9.2   0.0    0.0013       1.1      15      48 ..     172     205 ..     161     206 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00054
                                      HCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST......TTEEEE CS
                              TrmB 20 lgpatadeiaeelgvprskvYevLrsLedkGlVerekgr......pklYra 64
                                      ++p    ++++elg++++ v + L+ +e+ G+V   +++      + +Y++
  gi|474933616|ref|YP_007687198.1| 25 REPHYPLQLSKELGISQQAVVKNLNLMEKEGIVVSYRESsnrgpdRIFYKP 75
                                      566666789************************877766667766556665 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0013
                                       HHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHH CS
                              TrmB  15 laLlklgpatadeiaeelgvprskvYevLrsLed 48 
                                         +l++ + +a++i+++lg  +s v +++  L+d
  gi|474933616|ref|YP_007687198.1| 172 YDMLNRPNWSAEDISRNLGFNESMVSRMIDDLLD 205
                                       56899999*********************99986 PP

>> TerB_C  TerB-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   1.5e-06    0.0013      45     121 ..     115     203 ..      92     207 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.5e-06
                            TerB_C  45 eer.eeeeepakpevteepeaeeaetaladkvaes...........egLdeaeaalLraLlareswpreeveslare 109
                                       eer  ee++  + +++++ ++ ++  a+++++ +s            +Ld ++++lL ++l r++w++e++ + +  
  gi|474933616|ref|YP_007687198.1| 115 EERrLEEVRGRISSIDRQIAEFDKRRAEMVRERNSlingflastdlGNLDYEHRELLYDMLNRPNWSAEDISRNLGF 191
                                       33334555556666666666666666666665555888888889********************************* PP

                            TerB_C 110 kglmpdvliesI 121
                                       ++ m + +i+++
  gi|474933616|ref|YP_007687198.1| 192 NESMVSRMIDDL 203
                                       *********975 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.064        57      22      45 ..      32      55 ..      28      57 .. 0.79
   2 ?   -2.5   0.1       5.7   5.1e+03       4      12 ..     137     145 ..     134     148 .. 0.79
   3 !   10.9   0.0   0.00034      0.31      16      38 ..     177     200 ..     165     204 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.064
                            HTH_23 22 eIAreLgvsrrTvyrwlkryreeG 45
                                      + ++eLg+s++ v + l+  ++eG
  gi|474933616|ref|YP_007687198.1| 32 QLSKELGISQQAVVKNLNLMEKEG 55
                                      56899****999988877765566 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.7
                            HTH_23   4 ereRlrill 12 
                                        ++R+++++
  gi|474933616|ref|YP_007687198.1| 137 DKRRAEMVR 145
                                       589999997 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00034
                            HTH_23  16 e.GlsvreIAreLgvsrrTvyrwl 38 
                                       +  +s ++I+r Lg +++ v+r +
  gi|474933616|ref|YP_007687198.1| 177 RpNWSAEDISRNLGFNESMVSRMI 200
                                       378******************987 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00045       0.4      26      53 ..      32      60 ..      18      70 .. 0.89
   2 ?    4.0   0.0     0.054        49      21      45 ..     179     203 ..     159     205 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00045
                                      HHHHHTTSSHHHHHHHHHHHHHTTSEE.E CS
                         HTH_Crp_2 26 elAsmlGltretvsrilseLkreglis.r 53
                                      +l+  lG++++ v + l+ +++eg++   
  gi|474933616|ref|YP_007687198.1| 32 QLSKELGISQQAVVKNLNLMEKEGIVVsY 60
                                      78999********************9842 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.054
                                       EHHHHHHHHHTTSSHHHHHHHHHHH CS
                         HTH_Crp_2  21 pltqeelAsmlGltretvsrilseL 45 
                                       + + e++++ lG + + vsr++ +L
  gi|474933616|ref|YP_007687198.1| 179 NWSAEDISRNLGFNESMVSRMIDDL 203
                                       56889****************9887 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.1   0.00098      0.88      27      53 ..      32      58 ..      22      63 .. 0.91
   2 ?    5.2   0.0     0.028        25      24      46 ..     181     203 ..     169     205 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00098
                                      HHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                    Fe_dep_repress 27 dlaerLnvspssVsemlkkLekdGyve 53
                                      +l+++L++s   V + l+ +ek+G v+
  gi|474933616|ref|YP_007687198.1| 32 QLSKELGISQQAVVKNLNLMEKEGIVV 58
                                      8***********************986 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.028
                                       -HHHHHHHHTS-HHHHHHHHHHH CS
                    Fe_dep_repress  24 ktkdlaerLnvspssVsemlkkL 46 
                                       +  d+++ L+   s Vs m+  L
  gi|474933616|ref|YP_007687198.1| 181 SAEDISRNLGFNESMVSRMIDDL 203
                                       6689***************9765 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     9e-05     0.081      17      51 ..      32      67 ..      16      72 .. 0.80
   2 ?   -0.7   0.0       1.7   1.5e+03      13      34 ..     181     201 ..     174     203 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9e-05
                            HTH_29 17 qiAkllglsrrtvyrwlkrfeegGlaalld.rrrsg 51
                                      q+ k lg+s + v + l+++e++G+    + + ++g
  gi|474933616|ref|YP_007687198.1| 32 QLSKELGISQQAVVKNLNLMEKEGIVVSYReSSNRG 67
                                      899*********************977666444444 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.7
                            HTH_29  13 stvsqiAkllglsrrtvyrwlk 34 
                                       s   +i ++lg  ++ v r ++
  gi|474933616|ref|YP_007687198.1| 181 S-AEDISRNLGFNESMVSRMID 201
                                       4.78999****99999999876 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0032       2.9      23      59 ..      32      68 ..       7      74 .. 0.88
   2 ?    4.6   0.0     0.053        48      12      43 ..     174     204 ..     163     206 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0032
                            HTH_27 23 dlcgrlnvedshisyslkkLtekGLvertgdeadrre 59
                                      +l++ l +++++++++l+ +++ G v++ +   +r++
  gi|474933616|ref|YP_007687198.1| 32 QLSKELGISQQAVVKNLNLMEKEGIVVSYRESSNRGP 68
                                      79999*********************88888788876 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.053
                            HTH_27  12 irhrrrrkkl.adlcgrlnvedshisyslkkLt 43 
                                       +   +r++   +d+++ l ++ s +s +++ L 
  gi|474933616|ref|YP_007687198.1| 174 ML--NRPNWSaEDISRNLGFNESMVSRMIDDLL 204
                                       44..4444444******************9996 PP

>> ArsR  ArsR transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00054      0.48       6      84 ..       3      82 ..       1     140 [. 0.77
   2 ?    2.7   0.0     0.098        88     111     139 ..     169     197 ..     155     202 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00054
                              ArsR  6 eLvpllqvfdsetkkkvyeelskeWlteeeleeklgee...veealklLkkikliEsqWrmpepgekpekeYhtsYskv 81
                                      ++ ++l +++++t +k+++++ +e     +l+++lg +   v + l+l++k +++ s  ++++   +p++ +    s++
  gi|474933616|ref|YP_007687198.1|  3 DMDSILSIVENPTRRKILQAVVREPHYPLQLSKELGISqqaVVKNLNLMEKEGIVVSYRESSN--RGPDRIFYKPSSEF 79
                                      6779*****************************9986545689999*******9977655555..67777666555555 PP

                              ArsR 82 qan 84
                                      ++ 
  gi|474933616|ref|YP_007687198.1| 80 SIT 82
                                      544 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.098
                              ArsR 111 ekiekeveegntsisdlsrklglsplfir 139
                                       e + +++++ n s +d+sr+lg ++ ++ 
  gi|474933616|ref|YP_007687198.1| 169 ELLYDMLNRPNWSAEDISRNLGFNESMVS 197
                                       5678999999************9988875 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   8.4e-05     0.075       6      63 ..      24      73 ..      19      75 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.4e-05
                                      CCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEE CS
                              PadR  6 eeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyY 63
                                       ++p y +++ kel         +s+  + ++L+ +ekeg+v+s++e s++gp r +Y
  gi|474933616|ref|YP_007687198.1| 24 VREPHYPLQLSKELG--------ISQQAVVKNLNLMEKEGIVVSYRESSNRGPDRIFY 73
                                      555555555555553........344456689***********************999 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0023         2      30      59 ..      32      61 ..      24      64 .. 0.94
   2 ?    3.5   0.0       0.1        90      26      49 ..     180     203 ..     163     205 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0023
                                      HHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                              Rrf2 30 eiaerqnispsylekilakLrkaglvksvr 59
                                      +++++ +is++ + k l+ ++k+g+v s r
  gi|474933616|ref|YP_007687198.1| 32 QLSKELGISQQAVVKNLNLMEKEGIVVSYR 61
                                      6899**********************9986 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.1
                                       B-HHHHHHHHTS-HHHHHHHHHHH CS
                              Rrf2  26 vsseeiaerqnispsylekilakL 49 
                                        s+e+i+++ + ++s++++++  L
  gi|474933616|ref|YP_007687198.1| 180 WSAEDISRNLGFNESMVSRMIDDL 203
                                       699****************99887 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.076        68      32      63 ..      32      64 ..      17      83 .. 0.80
   2 ?    0.2   0.0      0.75   6.8e+02      49      69 ..      87     107 ..      76     139 .. 0.67
   3 ?    5.9   0.0     0.012        11      14      53 ..     166     205 ..     160     206 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.076
                                      HHHHHHTS-HHHHHHHHHHHHHCTS.EEEEEEE CS
                       TFIIE_alpha 32 dlakelkidlnelrklLnrLyearl.vkykrrr 63
                                      +l+kel+i ++ + k Ln + ++++ v+y+ + 
  gi|474933616|ref|YP_007687198.1| 32 QLSKELGISQQAVVKNLNLMEKEGIvVSYRESS 64
                                      79***************9998877515776654 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.75
                                       HHHHHCTSEEEEEEEETTTEE CS
                       TFIIE_alpha  49 nrLyearlvkykrrrdeeksw 69 
                                       n+++e rlv + +++++  + 
  gi|474933616|ref|YP_007687198.1|  87 NNMFEMRLVPIAQAKEQVPKE 107
                                       788999999999999854333 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.012
                                       HHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHH CS
                       TFIIE_alpha  14 eavlvldvLlekgevteedlakelkidlnelrklLnrLye 53 
                                       e+ + l  +l + + + ed++++l+++   + +++ +L +
  gi|474933616|ref|YP_007687198.1| 166 EHRELLYDMLNRPNWSAEDISRNLGFNESMVSRMIDDLLD 205
                                       56666666777888999******************99976 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00021      0.19      12      58 ..      18      63 ..       9      78 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00021
                           DUF2250 12 kvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlervegk 58
                                      k+l+ +   ++ Y+++++kel i+++ v + l+ +e+ G++  + ++
  gi|474933616|ref|YP_007687198.1| 18 KILQAV-VREPHYPLQLSKELGISQQAVVKNLNLMEKEGIVVSYRES 63
                                      555544.45899***************************99887765 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.069        62       7      37 ..      14      44 ..      13      45 .. 0.75
   2 ?   -1.6   0.4       2.2   1.9e+03      34      43 ..     123     132 ..     117     134 .. 0.80
   3 ?    5.9   0.0    0.0098       8.8       3      41 ..     161     200 ..     160     205 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.069
                                      HHHHHHHHHHHTTT--HHHHHHHHTS-HHHH CS
                        Sigma70_r4  7 ererevlelrfgeglTleEIgerlgiSrerV 37
                                      +  r++l+ +  e++   +++++lgiS+ +V
  gi|474933616|ref|YP_007687198.1| 14 PTRRKILQAVVREPHYPLQLSKELGISQQAV 44
                                      556777777775555556899******9987 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.2
                                       HHHHHHHHHH CS
                        Sigma70_r4  34 rerVrqiekr 43 
                                       r+r+++i ++
  gi|474933616|ref|YP_007687198.1| 123 RGRISSIDRQ 132
                                       8999999775 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.0098
                                       HHS-HHHHHHHHHHH.TTT--HHHHHHHHTS-HHHHHHHH CS
                        Sigma70_r4   3 asLpererevlelrf.geglTleEIgerlgiSrerVrqie 41 
                                         L+ ++re l+      +++ e+I++ lg  ++ V++ +
  gi|474933616|ref|YP_007687198.1| 161 GNLDYEHRELLYDMLnRPNWSAEDISRNLGFNESMVSRMI 200
                                       5688889999999998889*****************9976 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.093        83      19      49 ..      32      62 ..      30      68 .. 0.87
   2 ?    6.0   0.0     0.014        12      13      37 ..     178     202 ..     171     205 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.093
                              FeoC 19 eLsrhfkaspealeamLeqwvrkGrvekvaa 49
                                      +Ls+++ +s++a+ + L+++++ G v    +
  gi|474933616|ref|YP_007687198.1| 32 QLSKELGISQQAVVKNLNLMEKEGIVVSYRE 62
                                      69*********************99876655 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.014
                              FeoC  13 grvslkeLsrhfkaspealeamLeq 37 
                                          s +++sr +  +++++  m++ 
  gi|474933616|ref|YP_007687198.1| 178 PNWSAEDISRNLGFNESMVSRMIDD 202
                                       56799*****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       962  (0.0536561); expected 358.6 (0.02)
Passed bias filter:                      776  (0.0432818); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 1670.05
//
Query:       gi|474933617|ref|YP_007687199.1|  [L=319]
Description: ABC-type multidrug transport system, ATPase component [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-26   93.3   0.0    4.2e-26   92.1   0.0    1.6  2  ABC_tran  ABC transporter
    3.3e-13   50.1   0.8    8.7e-08   32.3   0.0    2.3  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    0.00042   20.6   0.0     0.0011   19.3   0.0    1.7  2  AAA_22    AAA domain
    0.00057   20.3   0.5     0.0069   16.8   0.5    2.2  1  AAA       ATPase family associated with various cellular acti
      0.001   18.7   0.1     0.0024   17.5   0.1    1.6  2  AAA_27    AAA domain
     0.0012   18.7   0.0      0.018   14.8   0.0    2.1  2  AAA_15    AAA ATPase domain
     0.0015   18.2   0.4     0.0032   17.2   0.4    1.5  1  AAA_29    P-loop containing region of AAA domain
     0.0017   17.8   0.1        0.4   10.1   0.1    2.2  2  SMC_N     RecF/RecN/SMC N terminal domain
     0.0029   18.1   0.1     0.0043   17.6   0.1    1.4  1  AAA_23    AAA domain
     0.0041   16.9   0.0       0.01   15.6   0.0    1.6  1  AAA_30    AAA domain
     0.0065   16.5   0.4        0.4   10.7   0.0    2.4  2  MutS_V    MutS domain V
  ------ inclusion threshold ------
      0.018   15.0   0.0      0.029   14.3   0.0    1.4  1  Rad17     Rad17 P-loop domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.1   0.0   2.8e-29   4.2e-26       2     137 .]      28     171 ..      27     171 .. 0.96
   2 ?   -2.2   0.0       3.5   5.3e+03      80     122 ..     202     244 ..     180     246 .. 0.59

  Alignments for each domain:
  == domain 1  score: 92.1 bits;  conditional E-value: 2.8e-29
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       ++++l++k+++ ++++G+nGaGKSt lk+l++l + t+G+  ++g d+ + + + + + +g++ ++p++   lt re
  gi|474933617|ref|YP_007687199.1|  28 DDLNLEIKKNSFTGLLGPNGAGKSTSLKILTNLITATSGHAFINGYDVAK-DPKNALQGVGTVVETPEFYLYLTPRE 103
                                       899***********************************************.778888899******99999999999 PP

                                       H.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       x.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       +               ++e +++l+k++++e++d+++     ++S+G++qr+ l  +ll++p++++lDEpt+
  gi|474933617|ref|YP_007687199.1| 104 TfryvgeifgmsreSISAETDTILAKVKMSEWEDKRL----GTFSKGMRQRITLGLSLLNDPSVIILDEPTS 171
                                       99999****9999888999******************....*****************************96 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.5
                                       HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalara 122
                                       ++  e++++ +++ l++  +  ++++ ss+ +G  +r  ++r+
  gi|474933617|ref|YP_007687199.1| 202 HMMHEVTDLCDRIALINHGQLLMHDDISSFIEGSDVRTLIVRT 244
                                       5666666777777777755555555557777777777777665 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.9   7.8e-06     0.012       1      25 [.      39      63 ..      39     136 .. 0.79
   2 !   32.3   0.0   5.8e-11   8.7e-08     236     297 ..     142     202 ..     136     206 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.8e-06
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarl 25
                                      +++l GpNg+GKS+ L++l  l  +
  gi|474933617|ref|YP_007687199.1| 39 FTGLLGPNGAGKSTSLKILTNLITA 63
                                      79*****************888554 PP

  == domain 2  score: 32.3 bits;  conditional E-value: 5.8e-11
                            AAA_21 236 elSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr..ngaQviltTH 297
                                        +S G+++ + l ++ll ++   s++++DEp +gL+P+ +++  e+lk+ ++  n+  v++++H
  gi|474933617|ref|YP_007687199.1| 142 TFSKGMRQRITLGLSLLNDP---SVIILDEPTSGLDPRGMAEMREILKNIRNdnNNLTVLMSSH 202
                                       68****************99...*****************999999999988999********* PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   7.3e-07    0.0011       4     118 ..      36     191 ..      32     208 .. 0.75
   2 ?    4.6   0.0     0.024        36      38      91 ..     159     216 ..     128     261 .. 0.63

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 7.3e-07
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee...........erpevv......fvtlpsst...sskdllrel 60 
                                       + +++ + G+ G+GK+t+l+ l++  ++ + ++            +    +       v+ p+     ++++ +r +
  gi|474933617|ref|YP_007687199.1|  36 KNSFTGLLGPNGAGKSTSLKILTNLITATSGHAFingydvakdpkN----AlqgvgtVVETPEFYlylTPRETFRYV 108
                                       56778899*****************998888888*99***965541....335556555555555788999999999 PP

                            AAA_22  61 lralglelka.....................erlsseellealeqalraravielliiDEaqh.lr.s..eealeeL 112
                                        +++g ++++                      +  s+ ++++++  l+   +++++i+DE    l+ +  +e+ e L
  gi|474933617|ref|YP_007687199.1| 109 GEIFGMSRESisaetdtilakvkmsewedkrLGTFSKGMRQRITLGLSLLNDPSVIILDEPTSgLDpRgmAEMREIL 185
                                       99999988889999999*****999997764444455555677666666666**********999873566666666 PP

                            AAA_22 113 rsllnl 118
                                       +++ n+
  gi|474933617|ref|YP_007687199.1| 186 KNIRND 191
                                       888774 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.024
                            AAA_22  38 erpevvfvtlpsst.sskdl..lrellralglelka.erlsseellealeqalrarav 91 
                                       ++p+v+  + p s+ +++ +  +re+l+++ +++++   l s+++++ +++ +++ a 
  gi|474933617|ref|YP_007687199.1| 159 NDPSVIILDEPTSGlDPRGMaeMREILKNIRNDNNNlTVLMSSHMMHEVTDLCDRIAL 216
                                       5666666666666666666655566666666666654445555555555555555555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.5   4.6e-06    0.0069       3     117 ..      42     209 ..      40     218 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.6e-06
                                       EESSTTSSHHHHHHHHHHHHTHE...................................................... CS
                               AAA   3 lyGppGtGKTllakavakelgve...................................................... 25 
                                       l Gp G GK++  k + + + ++                                                      
  gi|474933617|ref|YP_007687199.1|  42 LLGPNGAGKSTSLKILTNLITATsghafingydvakdpknalqgvgtvvetpefylyltpretfryvgeifgmsres 118
                                       78999999999999999997655555566667777777888888888888888888888888888888888888888 PP

                                       ........EEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHH CS
                               AAA  26 ........fleisgsellskyvgesekkirelfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLltel 93 
                                               + ++++se  +k +g  +k +r+ ++   +   +ps++++DE  +    r           ++++ + l
  gi|474933617|ref|YP_007687199.1| 119 isaetdtiLAKVKMSEWEDKRLGTFSKGMRQRITLGLSLLnDPSVIILDEPTSGLDPR----------GMAEMREIL 185
                                       88888888899999999999*************9966555799*******99999888..........799****** PP

                                       HHTTTSSSTEEEEEEESSGGGSTH CS
                               AAA  94 dgvkkkeskvivigatnrpdkldp 117
                                       ++ ++++++++v++ ++ ++++++
  gi|474933617|ref|YP_007687199.1| 186 KNIRNDNNNLTVLMSSHMMHEVTD 209
                                       ******99*******999988765 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   1.6e-06    0.0024      10      50 ..      20      61 ..      12      73 .. 0.84
   2 ?   -3.9   0.0       5.7   8.5e+03     121     139 ..     110     128 ..      99     129 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.6e-06
                            AAA_27 10 ryGkftd.rsldfsaeeadlhliyGpNEAGKstalrAisdll 50
                                       yG+f     l+++ ++++++ ++GpN AGKst+l+ +++l+
  gi|474933617|ref|YP_007687199.1| 20 VYGSFVAvDDLNLEIKKNSFTGLLGPNGAGKSTSLKILTNLI 61
                                      5898865247888888*******************9999885 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 5.7
                            AAA_27 121 alFgLdherLreGGealle 139
                                       ++Fg++ e++ +  +++l+
  gi|474933617|ref|YP_007687199.1| 110 EIFGMSRESISAETDTILA 128
                                       5799999999888888775 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.2e-05     0.018      15      50 ..      28      64 ..      21     138 .. 0.84
   2 ?    1.8   0.0       0.1   1.5e+02     322     364 ..     159     202 ..     143     205 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.2e-05
                            AAA_15 15 kdveidlsee.ltvliGkNnsGKSsilealdlFlnnk 50
                                      +d  ++++++ +t l G+N++GKS+ l++l  +++ +
  gi|474933617|ref|YP_007687199.1| 28 DDLNLEIKKNsFTGLLGPNGAGKSTSLKILTNLITAT 64
                                      56778888888*******************9888765 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.1
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnkt.QviitTH 364
                                       +++ +++++EP   L p    ++ + lk++ ndn++  v++++H
  gi|474933617|ref|YP_007687199.1| 159 NDPSVIILDEPTSGLDPRGMAEMREILKNIRNDNNNlTVLMSSH 202
                                       578899*****************************999999999 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.4   2.2e-06    0.0032      14      53 ..      29      68 ..      22      72 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.2e-06
                            AAA_29 14 ghtieidlkgatlltGpsGsGKSTllDAiqalLvpakkvr 53
                                      +  +ei+ +++t l Gp+G+GKST l  ++ l+++++ ++
  gi|474933617|ref|YP_007687199.1| 29 DLNLEIKKNSFTGLLGPNGAGKSTSLKILTNLITATSGHA 68
                                      456788877799*************999999999988443 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.1   0.00027       0.4      23      41 ..      36      54 ..      23      69 .. 0.82
   2 !    5.6   0.0    0.0063       9.4     158     208 ..     160     210 ..     143     221 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00027
                                      TSSEEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxxxxx RF
                             SMC_N 23 sksftaivGpNGSGKsnll 41
                                      ++sft ++GpNG+GKs  l
  gi|474933617|ref|YP_007687199.1| 36 KNSFTGLLGPNGAGKSTSL 54
                                      468*************755 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0063
                                       --SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 158 paplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadkl 208
                                         ++ +lDe  + LD + ++++ e+lk+ +++   + + ++++m++++  l
  gi|474933617|ref|YP_007687199.1| 160 DPSVIILDEPTSGLDPRGMAEMREILKNIRNDNNNLTVLMSSHMMHEVTDL 210
                                       556789*********************999999999999999999887544 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   2.9e-06    0.0043       8      43 ..      22      61 ..      12     150 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.9e-06
                            AAA_23  8 rsf...rdqeidF.skgltlItGpNGaGKTTildAiklaL 43
                                      +sf   +d +++  ++ +t + GpNGaGK+T l  ++   
  gi|474933617|ref|YP_007687199.1| 22 GSFvavDDLNLEIkKNSFTGLLGPNGAGKSTSLKILTNLI 61
                                      566777888888866689*************988877555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   6.8e-06      0.01      18      96 ..      37     168 ..      31     200 .. 0.55

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 6.8e-06
                            AAA_30  18 drvavltGpAGtGKttalkalreaweaa.ggrvi.glAptgkaAkvLa............................. 63 
                                       + ++ l Gp G+GK+t+lk l+++++a  g+  i g+   +   ++L+                             
  gi|474933617|ref|YP_007687199.1|  37 NSFTGLLGPNGAGKSTSLKILTNLITATsGHAFInGYDVAKDPKNALQgvgtvvetpefylyltpretfryvgeifg 113
                                       5678899*******************997865553332222222233322244444444444444444444444444 PP

                            AAA_30  64 ...eelgieastiakllkrlk...................grarlepgtllivDE 96 
                                          e++ +e++ti   +k  +                   g   l++ +++i DE
  gi|474933617|ref|YP_007687199.1| 114 msrESISAETDTILAKVKMSEwedkrlgtfskgmrqritlGLSLLNDPSVIILDE 168
                                       4433444444444444433335566666666666666666434445556666666 PP

>> MutS_V  MutS domain V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.038        57       4      18 ..      43      57 ..      40      72 .. 0.79
   2 !   10.7   0.0   0.00027       0.4      40     141 ..     122     225 ..     105     262 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.038
                                      E-STTSSHHHHHHHH CS
                            MutS_V  4 tGpnmaGkstylrqv 18
                                       Gpn aGkst l+  
  gi|474933617|ref|YP_007687199.1| 43 LGPNGAGKSTSLKIL 57
                                      59********99865 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00027
                                       --SEEEEEE--------SS-HHHHHHHH.HHHHHTT--TTSEEEEESTS-SS-HHHHHHHHHHHHHHHHHT.T--EE CS
                            MutS_V  40 ivdkiftRvgasDdlakgkstFmvEmlE.tasilknatekslvilDElGRGtstydGlaialavaeyllek.ikakt 114
                                        +d+i+++v  s+   k   tF   m   ++  l+  ++ s++ilDE   G     G+a    +++ + +  ++ ++
  gi|474933617|ref|YP_007687199.1| 122 ETDTILAKVKMSEWEDKRLGTFSKGMRQrITLGLSLLNDPSVIILDEPTSGLDP-RGMAEMREILKNIRNDnNNLTV 197
                                       4799999999999999999*******8725566999***********7666543.4777778999999865155677 PP

                                       EEEES-.GGGGGHHHHSTTEEEEEEEEE CS
                            MutS_V 115 lfatHy.heltklaekleevknlhlavk 141
                                       l++ H  he+t+l ++++ +++ +l ++
  gi|474933617|ref|YP_007687199.1| 198 LMSSHMmHEVTDLCDRIALINHGQLLMH 225
                                       899995489***9999988887776655 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.9e-05     0.029      39      92 ..      31      86 ..      15     134 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.9e-05
                             Rad17 39 vLesrkkriLLisGPsGCgkstvvkvLskel.giklrewlnpvsl.kepdnqksdf 92
                                       Le +k+    + GP G gkst +k+L+    +++ + ++n+  + k+p+n  + +
  gi|474933617|ref|YP_007687199.1| 31 NLEIKKNSFTGLLGPNGAGKSTSLKILTNLItATSGHAFINGYDVaKDPKNALQGV 86
                                      5777777788899**************98651567788999987535666654444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2209.64
//
Query:       gi|474933618|ref|YP_007687200.1|  [L=262]
Description: ABC-2 type transporter [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.6e-19   68.3  27.1    1.9e-18   66.8  19.0    2.2  2  ABC2_membrane_2  ABC-2 family transporter protein
    1.2e-11   44.5  17.7    1.7e-11   44.0  17.7    1.2  1  ABC2_membrane    ABC-2 type transporter
    6.4e-09   36.0  19.1    9.5e-09   35.5  17.4    1.9  2  ABC2_membrane_4  ABC-2 family transporter protein
    1.2e-08   34.5  21.9    1.2e-08   34.5  21.9    1.9  2  ABC2_membrane_3  ABC-2 family transporter protein
  ------ inclusion threshold ------
      0.049   13.4   8.2       0.13   12.0   8.2    1.6  1  Per1             Per1-like family
       0.47   10.1   3.0       0.17   11.5   0.2    1.7  2  Orbi_NS3         Orbivirus NS3
       0.66    9.5  26.7       0.48   10.0  24.0    2.1  1  ABC2_membrane_5  ABC-2 family transporter protein
        1.8    8.8  12.3        3.7    7.8   1.4    3.6  4  Holin_SPP1       SPP1 phage holin
        1.9    7.7  12.0      0.073   12.4   1.1    2.4  2  SLATT_5          SMODS and SLOG-associating 2TM effector doma


Domain annotation for each model (and alignments):
>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   1.0    0.0018       3.7       3      31 ..      16      44 ..      14      59 .. 0.77
   2 !   66.8  19.0   9.5e-22   1.9e-18      77     287 ..      64     261 ..      50     262 .] 0.81

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0018
                   ABC2_membrane_2  3 iakkEfrdlvrsrrfllltvllplidval 31
                                      ++++E+ +++r r+++l+t+l++ + + l
  gi|474933618|ref|YP_007687200.1| 16 VMRNEITKFLRGRKIILFTLLIVSVLALL 44
                                      789*****************999882333 PP

  == domain 2  score: 66.8 bits;  conditional E-value: 9.5e-22
                   ABC2_membrane_2  77 vstimavlipvia.alfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilal 152
                                       v++++a li+++a +lf++++ia E e++T  +l++kP+ +++i++gKf ++++i       l+a + ++++++la 
  gi|474933618|ref|YP_007687200.1|  64 VYASFASLIVLVAvTLFSSTSIASEFEERTALILFTKPIRKWSIYFGKFMASILI---ETAYLVAFYAITIGVSLAK 137
                                       67788889999972589**************************************...77777777788******** PP

                   ABC2_membrane_2 153 givlaledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqei 229
                                         ++++++ + lv+a+  +l    +++++ll+Ssv+++s+++  + ++ +++l+ +v+++l ++a+   +  + q  
  gi|474933618|ref|YP_007687200.1| 138 TGEFPGAMGTSLVLAFCYMLG---ATGIALLISSVMKKSSTSSIMTFVTLLLLLSVVSMSL-TIADYDPYWMFDQAA 210
                                       *******99999999995555...69***********999999999999999999999999.556555555553444 PP

                   ABC2_membrane_2 230 ndflsllsptsayntllneilagsdlnalgstatnllilllllavllvlgyvlFkrkD 287
                                       n +   ++   +  t ++ i+       ++  a  + +++++ ++ l+ g++lF+++D
  gi|474933618|ref|YP_007687200.1| 211 NSITYCITGLGVDITTYERIP-------YTHEARDASVMIIWGVAALIAGFFLFRKRD 261
                                       443334444444444455555.......555899**********************99 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0  17.7   8.4e-15   1.7e-11       2     205 ..      12     220 ..      11     222 .. 0.86

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 8.4e-15
                     ABC2_membrane   2 qikallkreflqrwrdpslgllwrliqplllalvfgtvfgnlg....nsedglnrpgllffsvlflafsaltsvapv 74 
                                       q +++++ e+ +++r + ++ l+ l+   +lal+  ++f   g    + +d+ +    ++ +++ +a+++++s+++ 
  gi|474933618|ref|YP_007687200.1|  12 QAFVVMRNEITKFLRGRKII-LFTLLIVSVLALLTAVLFIF-GdddmTGKDVCEVYASFASLIVLVAVTLFSSTSIA 86 
                                       8899*************999.66777777777777766663.22444455555556666666677777999999999 PP

                     ABC2_membrane  75 ferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldls.rf....flflllllltalaass 146
                                       +e e+++   +++ p+ + ++++++k+++++++ ++  ++f +i++ + +l  +  f    +  l+l+++++l a++
  gi|474933618|ref|YP_007687200.1|  87 SEFEERTALILFTKPI-RKWSIYFGKFMASILIETAYLVAFYAITIGV-SLAKTgEFpgamGTSLVLAFCYMLGATG 161
                                       9***************.******************************8.888888445567**************** PP

                     ABC2_membrane 147 lgllisalapsfedasqlaslvllpllllsGffipidsm.pkwlqwiaylnPltyaveal 205
                                       ++llis+++++  + s+++++ ll+ll +  +  +i +  p ++ + + +n +ty + +l
  gi|474933618|ref|YP_007687200.1| 162 IALLISSVMKKSSTSSIMTFVTLLLLLSVVSMSLTIADYdP-YWMFDQAANSITYCITGL 220
                                       ********************999999999999999999988.999999999999999876 PP

>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5  17.4   4.8e-12   9.5e-09       3     175 ..      18     183 ..      16     192 .. 0.70
   2 ?    2.0   1.2     0.089   1.8e+02      10      56 ..     171     215 ..     165     222 .. 0.54

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 4.8e-12
                   ABC2_membrane_4   3 ktEflK.lkrskivwllvlaallvpllallyfnllgktgldpaefyslsvfgftlllllplilgiiasylifrEeqn 78 
                                       ++E++K l+ +ki+++++l++ +++ll+ ++f  +g++++  + +      +f  l++l+++ ++++s++i  E+++
  gi|474933618|ref|YP_007687200.1|  18 RNEITKfLRGRKIILFTLLIVSVLALLTAVLFI-FGDDDMTGKDVCEV-YASFASLIVLVAV-TLFSSTSIASEFEE 91 
                                       689999456699999999999999888777764.56666654444443.3344455555555.589*********** PP

                   ABC2_membrane_4  79 dtlknLltiPvsrtklllaKlivllllsvllmlvtflitvlfallsgfvgfsvklvlellkkclelgllvffavlpi 155
                                        t   L+t P+ + +++++K+++ +l+  ++++++++it+ ++l  ++  f +++ ++     l+l+ + ++  + i
  gi|474933618|ref|YP_007687200.1|  92 RTALILFTKPIRKWSIYFGKFMASILIETAYLVAFYAITIGVSLAKTGE-FPGAMGTS-----LVLAFCYMLGATGI 162
                                       *******************************999999888887766654.44333333.....32222222222333 PP

                   ABC2_membrane_4 156 .ialvllkksyvlpliltlvy 175
                                        ++++++ k++ ++ i+t+v 
  gi|474933618|ref|YP_007687200.1| 163 aLLISSVMKKSSTSSIMTFVT 183
                                       145667777777777777765 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.089
                   ABC2_membrane_4  10 krskivwllvlaallvpllallyfnllgktgldpaefyslsvfgftl 56 
                                       k+s+   ++ +++ll+  l ++ +  l+  + dp ++++++++++t+
  gi|474933618|ref|YP_007687200.1| 171 KKSSTSSIMTFVTLLLL-LSVVSMS-LTIADYDPYWMFDQAANSITY 215
                                       44444444455555442.2333332.333455777888877777665 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   2.5      0.56   1.1e+03     242     264 ..      30      52 ..      13      59 .. 0.64
   2 !   34.5  21.9     6e-12   1.2e-08     162     343 ..      64     253 ..      55     257 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.56
                   ABC2_membrane_3 242 lllfllfglayialgyllsslfk 264
                                       ++lf l + +++al +++ ++f 
  gi|474933618|ref|YP_007687200.1|  30 IILFTLLIVSVLALLTAVLFIFG 52 
                                       45555555555555555555554 PP

  == domain 2  score: 34.5 bits;  conditional E-value: 6e-12
                   ABC2_membrane_3 162 flvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilllafgl.....gi 233
                                        +++++ +i++  + +f ++si++E e r+  ++++ ++++++++++k+ ++ l+    l+ + ++ +g+     g 
  gi|474933618|ref|YP_007687200.1|  64 VYASFASLIVLVAVTLFSSTSIASEFEERTALILFTKPIRKWSIYFGKFMASILIETAYLVAFYAITIGVslaktGE 140
                                       56665555555555666889***********************************9999988888877764444433 PP

                   ABC2_membrane_3 234 pfgnlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfp..ledlpsalkwifsiiPffa 308
                                       + g +g  l+l ++++l ++ +++l+ss++k+s+t +i++f+++lll+ ++ ++ +    d+  ++ +++  i  + 
  gi|474933618|ref|YP_007687200.1| 141 FPGAMGTSLVLAFCYMLGATGIALLISSVMKKSSTSSIMTFVTLLLLLSVVSMSLTiaDYDPYWMFDQAANSITYCI 217
                                       334778899************************99888666666644443333333122335577777777776666 PP

                   ABC2_membrane_3 309 pglgllrlitgd..plweillsliilalfavvyllla 343
                                        glg  ++ t++  p+   +++  ++++ +v+ l+++
  gi|474933618|ref|YP_007687200.1| 218 TGLGV-DITTYEriPYTHEARDASVMIIWGVAALIAG 253
                                       66666.5554442444445566666666666665554 PP

>> Per1  Per1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   8.2   6.5e-05      0.13      70     240 ..      15     218 ..       9     228 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.5e-05
                              Per1  70 kklrkeipkssplkkvylvy.alvslnawvwSaiFHtrDveltEk..lDYfsAgavvlsglylavvrlfr....... 136
                                         +r+ei+k  + +k++l +  +vs++a +  ++F + D ++t k        +a+ +s ++l++v lf+       
  gi|474933618|ref|YP_007687200.1|  15 VVMRNEITKFLRGRKIILFTlLIVSVLALLTAVLFIFGDDDMTGKdvC---EVYASFASLIVLVAVTLFSstsiase 88 
                                       556666666666665544444899999999999999999999977442...33333333333333333332222222 PP

                              Per1 137 ....larekkrvk......................llltalllalyllHvlyLllv.......rfdYtYnmaanvvv 180
                                           +       +                      l+ ta l+a+y++ +  ++l         +  +  +a++ ++
  gi|474933618|ref|YP_007687200.1|  89 feerT-------AlilftkpirkwsiyfgkfmasiLIETAYLVAFYAITI-GVSLAktgefpgAMGTSLVLAFCYML 157
                                       22330.......13456666666677777766664333333333333332.22222112111223344455566666 PP

                              Per1 181 gllqnllwlllslktlakklvslklillvlllllamllEllDFppllrl.lDAhalwhlaT 240
                                       g + ++l++  ++k+ +++++++ ++ll+ll +++m+l + D+ p++ +   A ++  ++T
  gi|474933618|ref|YP_007687200.1| 158 GATGIALLISSVMKKSSTSSIMTFVTLLLLLSVVSMSLTIADYDPYWMFdQAANSITYCIT 218
                                       66666666665556556677888999999999*************9765344666666655 PP

>> Orbi_NS3  Orbivirus NS3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   8.8e-05      0.17      71     132 ..      16      74 ..       7      89 .. 0.74
   2 ?   -2.7   0.2         2     4e+03      96     110 ..     162     177 ..     151     194 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.8e-05
                          Orbi_NS3  71 klksdlselkkkraiihttllvaavvalltsvctlssdmsvafkingtktevpswfkslnpm 132
                                        ++ +++++ + r ii  tll+ +v+allt+v  +  d  ++ k      ev + f sl  +
  gi|474933618|ref|YP_007687200.1|  16 VMRNEITKFLRGRKIILFTLLIVSVLALLTAVLFIFGDDDMTGK---DVCEVYASFASLIVL 74 
                                       567788888999********************998877665544...234566666665555 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2
                          Orbi_NS3  96 vallt.svctlssdms 110
                                       +all  sv   ss  s
  gi|474933618|ref|YP_007687200.1| 162 IALLIsSVMKKSSTSS 177
                                       4443303333333333 PP

>> ABC2_membrane_5  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0  24.0   0.00024      0.48      23     167 ..      43     194 ..      24     227 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00024
                   ABC2_membrane_5  23 llaiiilifl.........ndsvllifsilslvisiililttlsyDekskwnkylltLPvtrkeiVksKYlfvlili 90 
                                       ll  +++if+          + ++ + s+++lv + +   t+++ +  +++  +l+t P++++ i   K++ ++++ 
  gi|474933618|ref|YP_007687200.1|  43 LLTAVLFIFGdddmtgkdvCEVYASFASLIVLVAVTLFSSTSIASEFEERTALILFTKPIRKWSIYFGKFMASILIE 119
                                       334444455523333211111122444555555555556799999******************************** PP

                   ABC2_membrane_5  91 liailitlllliiavlikgnvtisevllsiliglvialiflaivlPlyfkfgvekgrivliiiifgiifllvaifsl 167
                                       +++++ +++++i ++l k   +   + +s++++++++l ++ i l +    +  k+ + +i+ ++ +  ll+ ++++
  gi|474933618|ref|YP_007687200.1| 120 TAYLVAFYAITIGVSLAKTGEFPGAMGTSLVLAFCYMLGATGIALLISSVMK--KSSTSSIMTFVTLLLLLSVVSMS 194
                                       9999999999876666555554456777777777777777777777777776..55554555554444444433333 PP

>> Holin_SPP1  SPP1 phage holin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   1.4    0.0019       3.7      10      52 ..      36      80 ..      32      82 .. 0.86
   2 ?   -1.1   0.1       1.1   2.2e+03      24      52 ..     108     136 ..      94     137 .. 0.78
   3 ?   -1.5   0.0       1.5     3e+03      15      31 ..     147     163 ..     144     184 .. 0.61
   4 ?    6.8   0.2    0.0038       7.6      10      50 ..     183     222 ..     175     255 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0019
                        Holin_SPP1 10 tillllallnqlltilGknplpidee..alytaitlvftvataiv 52
                                       i+ +lall ++l i+G   ++ ++      ++ +l+++va+++ 
  gi|474933618|ref|YP_007687200.1| 36 LIVSVLALLTAVLFIFGDDDMTGKDVceVYASFASLIVLVAVTLF 80
                                      699****************99999976466789999999999986 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.1
                        Holin_SPP1  24 ilGknplpideealytaitlvftvataiv 52 
                                        +Gk    i  e+ y +  +++t++++++
  gi|474933618|ref|YP_007687200.1| 108 YFGKFMASILIETAYLVAFYAITIGVSLA 136
                                       67888888888888888888999888775 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.5
                        Holin_SPP1  15 lallnqlltilGknplp 31 
                                        +l+ +++ +lG + ++
  gi|474933618|ref|YP_007687200.1| 147 TSLVLAFCYMLGATGIA 163
                                       67777777777776554 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.0038
                        Holin_SPP1  10 tillllallnqlltilGknplpideealytaitlvftvata 50 
                                       t+llll+ +++ lti    p ++ ++a +++ t+ +t++ +
  gi|474933618|ref|YP_007687200.1| 183 TLLLLLSVVSMSLTIADYDPYWMFDQAANSI-TYCITGLGV 222
                                       899*******************999876665.555554444 PP

>> SLATT_5  SMODS and SLOG-associating 2TM effector domain family 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.1   3.7e-05     0.073      25      84 ..      23      82 ..      19      92 .. 0.91
   2 ?   -0.2   3.8      0.26   5.1e+02      33      79 ..     150     196 ..     147     220 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.7e-05
                           SLATT_5 25 RlrrknklstfslsllSvylivlsllsnkssestinenlldflsiilSilvlvislless 84
                                      +++r  k+++f+l ++Sv +++ ++l  + + +   +++ ++++ ++S +vlv+ +l ss
  gi|474933618|ref|YP_007687200.1| 23 KFLRGRKIILFTLLIVSVLALLTAVLFIFGDDDMTGKDVCEVYASFASLIVLVAVTLFSS 82
                                      5788899********************999***********************9887665 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.26
                           SLATT_5  33 stfslsllSvylivlsllsnkssestinenlldflsiilSilvlvis 79 
                                       ++ ++ +l++ +i+l + s+  + st++   +  l ++lS++ + ++
  gi|474933618|ref|YP_007687200.1| 150 VLAFCYMLGATGIALLISSVMKKSSTSSIMTFVTLLLLLSVVSMSLT 196
                                       56677788888888888886666666666666666667777766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1358  (0.0757432); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 1632.98
//
Query:       gi|474933619|ref|YP_007687201.1|  [L=442]
Description: pyridoxal-phosphate dependent TrpB-like enzyme [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-42  144.0   0.0    9.2e-42  143.4   0.0    1.2  1  PALP      Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.4   0.0   5.1e-46   9.2e-42       5     294 .]      80     418 ..      77     418 .. 0.85

  Alignments for each domain:
  == domain 1  score: 143.4 bits;  conditional E-value: 5.1e-46
                                       SSS--EEEECCTCCCCCCE..EEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBS.SHHHHHHHHHHHHHT CS
                              PALP   5 igpTPlvrlprlskelgvp..lflKlEslnptgSfKdRgaeyllarlkegtgaktvveass.GNhgralAaaaallG 78 
                                        +p+Pl r+ rl+k l++p  +++K+E+l p+gS+K ++a    ++ +++ g  t+++ ++ G++g alA++++l+ 
  gi|474933619|ref|YP_007687201.1|  80 NRPSPLQRAFRLEKYLKTPakIYFKREDLSPLGSHKGNTALAQAYYNANA-GIHTLTTETGaGQWGTALAMVSNLFD 155
                                       589**************************************999997777.56666555555*************** PP

                                       -EEEEEEETTS-...HHHHHHHHHTT-EEEEE..................CCHHHHHHHHHHHHHHHSTTCEE--TT CS
                              PALP  79 lkvtivvpadas...pekvallrllGaevvev..................ggdydeavaaaaelaaegegaylvsqf 134
                                       +k t+++ +++    p ++  +  +Ga+v  +                   g+   a + a e+aa++e+  ++  +
  gi|474933619|ref|YP_007687201.1| 156 IKTTVFMVKGSFmakPLRKTIINTYGATVYASpseyteygrkvlkehpetSGSLGIAISEACEMAAKDEHTCYALGS 232
                                       **********998889****************666666666666665555555777777777777776666666666 PP

                                       TSHHHHHHHHTHHHHHHHHTT...TTEEEEEEE-SSSHHHHHHHHHHHH..HSTT...-EEEEEEECTTCGGTTCC. CS
                              PALP 135 dnptviegygtiglEileqlg...gkpdavvvpvGgGgliaGiaaglke..rrpd...vrvigvepegsdalarsl. 202
                                          +v++ ++ ig E l q+     +pd+++++vGgG+++aG+ +++     +++    ++i+vep+ +++l+++  
  gi|474933619|ref|YP_007687201.1| 233 VMNHVMLHQTVIGEEALLQFRkaeIEPDYMIACVGGGSNFAGFTFPFIReqMNGKykgAEIIAVEPKAAPSLTKGKf 309
                                       67899999*********666666699**********************97733336679*****************6 PP

                                       ..S..S.SS..B..............SSS.CCSTCSCGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B- CS
                              PALP 203 ..ragrrvtvpvs.............dtiadglavgspselafelldrlvdeivtvsdeealeamrllarregivve 264
                                         + g+   +++              +  a gl+ +  s+l+ +++d++  ++ + ++ ++++a  l+ar+egi++ 
  gi|474933619|ref|YP_007687201.1| 310 dyDYGDTAGMTPLmmmyslgsqyippSIHAGGLRYHGMSPLVSAAFDQHKITATSYDQPDTFQAGLLFARTEGIIPA 386
                                       6666666666666********777777777777777***************************************** PP

                                       HHHHHHHHHH..HHHHHHCCTTCEEEEEEE-B CS
                              PALP 265 pssaaalaal..klreagelkegdrvvviltg 294
                                       p s +al  +  k++e++e +e++++v+ l+g
  gi|474933619|ref|YP_007687201.1| 387 PESCHALKCAidKALECKEKGEEKTIVFNLSG 418
                                       *8888888887999999999999*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2896.55
//
Query:       gi|474933620|ref|YP_007687202.1|  [L=1104]
Description: hypothetical protein TALC_00027 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        4.1    7.4  10.0         30    4.6   0.1    5.9  7  CE2_N     Carbohydrate esterase 2 N-terminal


Domain annotation for each model (and alignments):
>> CE2_N  Carbohydrate esterase 2 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0      0.66   1.2e+04      79     106 ..      98     125 ..      95     126 .. 0.84
   2 ?   -2.4   0.0      0.26   4.7e+03      38      56 ..     234     252 ..     214     289 .. 0.53
   3 ?    1.5   0.2     0.016   2.9e+02      31      71 ..     292     337 ..     263     344 .. 0.82
   4 ?    1.1   0.1     0.021   3.8e+02      23      70 ..     345     390 ..     340     403 .. 0.76
   5 ?   -1.3   0.0      0.12   2.1e+03       1      27 [.     459     485 ..     459     491 .. 0.85
   6 ?   -0.9   0.0      0.09   1.6e+03      58     101 ..     553     595 ..     548     601 .. 0.83
   7 ?    4.6   0.1    0.0017        30      37      72 ..     850     890 ..     782     892 .. 0.70

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 0.66
                                       EEEEEE-S-GGG--EEEEEEEEE.EEEE CS
                             CE2_N  79 tvrlvkrtEaeagkteflgfvldeggkl 106
                                       t+ +v  ++ ++++t ++ f +++g+++
  gi|474933620|ref|YP_007687202.1|  98 TLLIVVGQDFKMKATDLASFQFNDGSRI 125
                                       6788888999999999999999999876 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.26
                                       ..SSS-EEEEEEETTS--E CS
                             CE2_N  38 kedkgknrlaviiDgkrvk 56 
                                        + kg+ ++++ +Dg   +
  gi|474933620|ref|YP_007687202.1| 234 IKFKGDGSYDIKVDGPSSA 252
                                       3444556666666664422 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.016
                                       EEEEEEE........SSS-EEEEEEETTS--EEEEE-SS-EEEEEEE CS
                             CE2_N  31 lsvrlkd......kedkgknrlaviiDgkrvkdlkldgeektytlae 71 
                                       l+v+++d       ++++++++++++Dg+   d+++d+ +k y++ +
  gi|474933620|ref|YP_007687202.1| 292 LDVKVTDyrnsftADTEDDKQMKLYVDGDFGLDISVDDIKK-YEIRD 337
                                       55666666666766778999**********99999999888.87755 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.021
                                       EEEEEEEEEEEEEEE..SSS-EEEEEEETTS--EEEEE-SS-EEEEEE CS
                             CE2_N  23 efrftGtslsvrlkdkedkgknrlaviiDgkrvkdlkldgeektytla 70 
                                        f+ tG ++s+ ++   +k+ + ++v++D  +  + + +g+e+t  ++
  gi|474933620|ref|YP_007687202.1| 345 IFTLTGAKASLDIDI--SKNVADVGVSVDLGKYEVTEYEGAESTTATY 390
                                       588899999999988..99**********8776666666666655444 PP

  == domain 5  score: -1.3 bits;  conditional E-value: 0.12
                                       EES--EE-TTS-EEE-STT-EEEEEEE CS
                             CE2_N   1 yiGRvdfsdpgaprfawpGtsvefrft 27 
                                       ++G +d + ++ + f+ +Gts++++f+
  gi|474933620|ref|YP_007687202.1| 459 FMGKIDGTVNDVLPFDVTGTSAKAKFS 485
                                       688888888889999999999999985 PP

  == domain 6  score: -0.9 bits;  conditional E-value: 0.09
                                       EEE-SS-EEEEEEEEEEEEEEEEEEEE-S-GGG--EEEEEEEEE CS
                             CE2_N  58 lkldgeektytlaeglepgehtvrlvkrtEaeagkteflgfvld 101
                                       ++l+ge ++y++ +g   g++ v+ +k   + a++++f g+++ 
  gi|474933620|ref|YP_007687202.1| 553 FNLTGEMRIYSI-DGRMVGNVYVKNFKVKATLAKEFTFTGLTVG 595
                                       667888886666.9999999999999999999999999999876 PP

  == domain 7  score: 4.6 bits;  conditional E-value: 0.0017
                                       E.......SSS-EEEEEEETTS--EEEEE-SS-EEEEEEEE CS
                             CE2_N  37 d.....kedkgknrlaviiDgkrvkdlkldgeektytlaeg 72 
                                       d     +++     + v+iDgk+v+d   +g+  + t+a+g
  gi|474933620|ref|YP_007687202.1| 850 DlgataSYTASAVPFSVYIDGKKVTDEARNGTAIQATVASG 890
                                       2555555566777899********99999999888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.75u 0.29s 00:00:01.04 Elapsed: 00:00:00.44
# Mc/sec: 7587.86
//
Query:       gi|474933621|ref|YP_007687203.1|  [L=149]
Description: hypothetical protein TALC_00028 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1133.72
//
Query:       gi|474933622|ref|YP_007687204.1|  [L=351]
Description: tRNA intron endonuclease [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-40  135.5   0.2    3.3e-24   84.8   0.1    2.3  2  tRNA_int_endo    tRNA intron endonuclease, catalytic C-termin
    3.6e-34  116.2   0.9    1.8e-17   62.7   0.0    2.6  2  tRNA_int_endo_N  tRNA intron endonuclease, N-terminal domain
  ------ inclusion threshold ------
       0.15   12.3   0.1       0.51   10.6   0.0    1.9  2  YorP             YorP protein


Domain annotation for each model (and alignments):
>> tRNA_int_endo  tRNA intron endonuclease, catalytic C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   0.0     1e-16   6.1e-13       1      85 []      77     162 ..      77     162 .. 0.98
   2 !   84.8   0.1   5.5e-28   3.3e-24       1      85 []     259     343 ..     259     343 .. 0.98

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 1e-16
                                       HHHHHHHHHHHHHTT-EEEECGGGTSSEEEE..TSCTTTSSCSEEEEEEETTSEEEHHHHHHHHHHHHHTTSEEEEE CS
                     tRNA_int_endo   1 falkyavyrdLrekGyvvrsGlkFGadFrvY..qrrpslehseylVvvvsedeeldwpdlsaavrlahsvkKklila 75 
                                       f++ky+v++dLre+G++v++ +    d+rvY  ++ ps++   ylV  vse+++  ++ +s++v  ++ + K+l++ 
  gi|474933622|ref|YP_007687204.1|  77 FDIKYRVFKDLRERGFIVKPESG-SFDLRVYprGKLPSEVPPVYLVCAVSERSATNLSVFSRDVSESEDMGKRLLYG 152
                                       899******************99.9******99999***************************************** PP

                                       EETTTSCEEE CS
                     tRNA_int_endo  76 ivdaegdvty 85 
                                       + d+egd+ty
  gi|474933622|ref|YP_007687204.1| 153 VADEEGDITY 162
                                       *********9 PP

  == domain 2  score: 84.8 bits;  conditional E-value: 5.5e-28
                                       HHHHHHHHHHHHHTT-EEEECGGGTSSEEEETSCTTTSSCSEEEEEEETTSEEEHHHHHHHHHHHHHTTSEEEEEEE CS
                     tRNA_int_endo   1 falkyavyrdLrekGyvvrsGlkFGadFrvYqrrpslehseylVvvvsedeeldwpdlsaavrlahsvkKklilaiv 77 
                                       f+l++++y dLr +G+vv++G+k+G++FrvY+++p++ h++ylV+ v  ++   wp++s++vrl+ +v+K+ +++ +
  gi|474933622|ref|YP_007687204.1| 259 FDLRLKAYYDLRARGLVVKTGFKYGTHFRVYEGSPDECHARYLVHAVTASKIAMWPEISRTVRLSGGVRKEILFCRI 335
                                       899************************************************************************** PP

                                       TTTSCEEE CS
                     tRNA_int_endo  78 daegdvty 85 
                                        + ++++y
  gi|474933622|ref|YP_007687204.1| 336 GDGEKIDY 343
                                       99988987 PP

>> tRNA_int_endo_N  tRNA intron endonuclease, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.7   0.0   3.1e-21   1.8e-17       1      66 [.       1      66 [.       1      67 [. 0.97
   2 !   51.8   0.2     8e-18   4.8e-14       3      66 ..     185     248 ..     183     249 .. 0.95

  Alignments for each domain:
  == domain 1  score: 62.7 bits;  conditional E-value: 3.1e-21
                                      EEEEEETTEEEESSHHHHHHHHHTTT-SEECCTSSEEEEHHHHHHHHHTTSEEEETTSEEE-HHHH CS
                   tRNA_int_endo_N  1 vegeLsgdrvlvedeeaakrlyekgfYGkplidepLqLslvEAlYLlekGklevvkggeplsfeel 66
                                      + geL+g +v ++d  +a++ y+kg++G p+ +  L+L+lvEA++Ll+ ++lev+kg+++++f  l
  gi|474933622|ref|YP_007687204.1|  1 MPGELEGQSVFIRDVREASQTYSKGCFGYPMSGGFLELDLVEAAFLLSLNRLEVRKGKKKMDFPSL 66
                                      78************************************************************9887 PP

  == domain 2  score: 51.8 bits;  conditional E-value: 8e-18
                                       EEEETTEEEESSHHHHHHHHHTTT-SEECCTSSEEEEHHHHHHHHHTTSEEEE.TTSEEE-HHHH CS
                   tRNA_int_endo_N   3 geLsgdrvlvedeeaakrlyekgfYGkplidepLqLslvEAlYLlekGklevv.kggeplsfeel 66 
                                       g+L+gd + v+de++ k+lye+ f+Gk   +  LqLsl+E++YL+ +G l+v  ++g +++   l
  gi|474933622|ref|YP_007687204.1| 185 GKLVGDIIFVFDESEGKSLYEEAFFGK-QSGGILQLSLIEGCYLIHTGELRVFdRKGNEMDEAAL 248
                                       89*************************.*************************999999998776 PP

>> YorP  YorP protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       2.2   1.3e+04      40      55 ..      65      81 ..      55      86 .. 0.59
   2 ?   10.6   0.0   8.5e-05      0.51      44      58 ..     151     165 ..     146     172 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.2
                                      SS-SEEEEE.TTS-EEE CS
                              YorP 40 atydyavsd.etgdity 55
                                      + +dya    e  di y
  gi|474933622|ref|YP_007687204.1| 65 SLFDYASGRvEGFDIKY 81
                                      45788876414447766 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 8.5e-05
                                       EEEEETTS-EEEE-G CS
                              YorP  44 yavsdetgdityfke 58 
                                       y v+de gdity+k 
  gi|474933622|ref|YP_007687204.1| 151 YGVADEEGDITYYKM 165
                                       99***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       223  (0.0124379); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.21s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2720.13
//
Query:       gi|474933623|ref|YP_007687205.1|  [L=182]
Description: HpaII restriction endonuclease [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-13   50.5   0.0    3.7e-13   49.6   0.0    1.3  1  RE_HpaII  HpaII restriction endonuclease


Domain annotation for each model (and alignments):
>> RE_HpaII  HpaII restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.0   2.1e-17   3.7e-13     152     277 ..       6     144 ..       2     148 .. 0.85

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 2.1e-17
                          RE_HpaII 152 LLnagkttnfkfevtgv..vpeenkineink...........ietkskvkdRiekieelggklkyakvedkvfrsNL 215
                                       +L +++ t f+++++g    ++ ++++++++           ++ + ++ +R++++++ +  l++ +ve+k + s L
  gi|474933623|ref|YP_007687205.1|   6 ILPGSERTSFVYRIEGGmdDRDRDEMEAMDSgyvmgenwpaiVSDSVDIGHRMRYMRKRNLGLRFLRVESKDYLSEL 82 
                                       6889999999999999878667777777764333222222223455679999************************* PP

                          RE_HpaII 216 llidsslprilAemlrlfylegiskvselvekikeenplkiklinkhafyeyklkqFLlala 277
                                       + +d +lp il++m+ + yl g+ +++++++++++ npl +        y+ k+ +FL ++ 
  gi|474933623|ref|YP_007687205.1|  83 SALDPDLPAILGWMVSEAYLGGTPRIDDIIDNLESVNPLRYPRPAVSGIYREKVGRFLESVG 144
                                       **********************************************************8775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       183  (0.0102069); expected 358.6 (0.02)
Passed bias filter:                      176  (0.0098165); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1271.04
//
Query:       gi|474933624|ref|YP_007687206.1|  [L=311]
Description: Transcription initiation factor IIB (TFIIB) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.5e-43  144.9   2.5    7.1e-22   77.2   0.2    2.2  2  TFIIB            Transcription factor TFIIB repeat
    4.9e-21   74.0   3.6    6.6e-21   73.6   1.3    2.1  2  TF_Zn_Ribbon     TFIIB zinc-binding
    0.00012   22.3   0.3     0.0073   16.7   0.2    2.6  2  Lar_restr_allev  Restriction alleviation protein Lar
    0.00071   19.0   0.4     0.0094   15.4   0.1    2.7  3  Sigma70_r4       Sigma-70, region 4
     0.0092   15.8   0.1      0.022   14.6   0.1    1.6  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
     0.0096   15.8   2.2      0.014   15.3   0.3    2.2  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
  ------ inclusion threshold ------
       0.01   16.1   0.1       0.18   12.1   0.1    2.4  2  UPF0253          Uncharacterised protein family (UPF0253)
      0.011   15.7   1.4       0.14   12.2   0.1    2.5  2  DZR              Double zinc ribbon
      0.011   15.6   2.2      0.018   15.0   0.4    2.2  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.012   16.2   0.0       0.57   10.8   0.0    2.5  2  RPA_interact_C   Replication protein A interacting C-terminal
      0.027   14.6   5.0        0.2   11.8   0.3    3.2  3  Zn-ribbon_8      Zinc ribbon domain
      0.039   13.7   4.1       0.16   11.7   2.2    2.7  2  A2L_zn_ribbon    A2L zinc ribbon domain
       0.12   12.4   0.0       0.75    9.8   0.0    2.0  2  RB_B             Retinoblastoma-associated protein B domain
       0.19   11.9   3.6        2.6    8.3   1.5    2.5  2  Auto_anti-p27    Sjogren's syndrome/scleroderma autoantigen 1
        0.2   11.3   2.1        1.5    8.5   0.4    2.9  2  GATA             GATA zinc finger
       0.28   10.7   5.3       0.43   10.0   1.6    2.8  2  zf-ribbon_3      zinc-ribbon domain
       0.34   10.3   3.0        2.4    7.6   0.0    3.0  3  Vps36-NZF-N      Vacuolar protein sorting 36 NZF-N zinc-finge
       0.39   11.1   4.4         10    6.5   0.0    3.9  4  HTH_31           Helix-turn-helix domain
       0.52   10.5   2.2         33    4.7   1.0    2.8  2  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
        0.6   10.8   4.1        3.7    8.3   0.3    2.8  2  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
       0.75   10.1   3.4        1.1    9.6   0.7    2.4  2  Prim_Zn_Ribbon   Zinc-binding domain of primase-helicase
        5.7    6.9   7.0       0.84    9.5   0.1    2.9  3  HTH_23           Homeodomain-like domain
        6.3    6.9   5.4    1.1e+02    2.9   1.5    4.1  5  zinc_ribbon_6    Zinc-ribbon


Domain annotation for each model (and alignments):
>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.9   0.2   7.5e-22   5.9e-19       2      71 .]     131     200 ..     130     200 .. 0.98
   2 !   77.2   0.2   9.2e-25   7.1e-22       1      71 []     224     294 ..     224     294 .. 0.99

  Alignments for each domain:
  == domain 1  score: 67.9 bits;  conditional E-value: 7.5e-22
                                       HHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   2 krfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                        r+a+a++Lp  V++ A  ++++a++++++ Grs +g++AA+ly Acr+++v rt+ e+++ ++V  k+i
  gi|474933624|ref|YP_007687206.1| 131 DRMASAMGLPRNVRETAAMIYRKAVNKNLIRGRSIEGVVAASLYAACRQCGVPRTLDEVANSSRVGRKEI 200
                                       69****************************************************************9997 PP

  == domain 2  score: 77.2 bits;  conditional E-value: 9.2e-25
                                       HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                       ++rf+++l+L+ +V+ +A e++k a+++++++Gr p+g+aAA++yi + +++++rtq+e+++v+ V+e+ti
  gi|474933624|ref|YP_007687206.1| 224 VQRFCSELKLSGEVQTKAAEILKDASDKELTSGRGPTGVAAAAIYISSILCNERRTQREVADVAGVTEVTI 294
                                       79*******************************************************************98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.6   1.3   8.4e-24   6.6e-21       2      43 .]      14      55 ..      14      55 .. 0.99
   2 ?   -0.4   0.0         1   8.1e+02       3      11 ..     177     185 ..     175     194 .. 0.70

  Alignments for each domain:
  == domain 1  score: 73.6 bits;  conditional E-value: 8.4e-24
                                      EETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCHHHHH CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlVlednsidegpewref 43
                                      +CP+Cgs++lv+D+ergelvC+dCGlVl+dn id gpewr+f
  gi|474933624|ref|YP_007687206.1| 14 VCPECGSRHLVRDYERGELVCEDCGLVLDDNFIDQGPEWRAF 55
                                      7***************************************98 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1
                                       ETTTTCEEC CS
                      TF_Zn_Ribbon   3 CPnCgstnl 11 
                                       C  Cg +++
  gi|474933624|ref|YP_007687206.1| 177 CRQCGVPRT 185
                                       888988763 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2   9.4e-06    0.0073       1      37 [.      10      41 ..      10      66 .. 0.77
   2 ?    2.9   0.0      0.18   1.4e+02      27      36 ..     167     182 ..     138     200 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 9.4e-06
                   Lar_restr_allev  1 eeLkpCPfCggravlersqrvvaeigqcvyCadCga.s 37
                                      ee+k CP Cg+r  +   +r+         C+dCg   
  gi|474933624|ref|YP_007687206.1| 10 EEIKVCPECGSRHLVRDYERGE------LVCEDCGLvL 41
                                      689**********999998885......8******952 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.18
                   Lar_restr_allev  27 q......cvyCadCga 36 
                                              + +C +Cg+
  gi|474933624|ref|YP_007687206.1| 167 GvvaaslYAACRQCGV 182
                                       1445555999*****9 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       4.5   3.5e+03      34      47 ..     144     157 ..     134     157 .. 0.76
   2 ?    0.1   0.0      0.76   5.9e+02      18      30 ..     181     193 ..     174     204 .. 0.77
   3 !   15.4   0.1   1.2e-05    0.0094      19      48 ..     276     305 ..     267     306 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4.5
                                       HHHHHHHHHHHHHH CS
                        Sigma70_r4  34 rerVrqiekrAlrk 47 
                                       re++ +i ++A++k
  gi|474933624|ref|YP_007687206.1| 144 RETAAMIYRKAVNK 157
                                       67888888888876 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.76
                                       TTT--HHHHHHHH CS
                        Sigma70_r4  18 geglTleEIgerl 30 
                                       g ++Tl E+++  
  gi|474933624|ref|YP_007687206.1| 181 GVPRTLDEVANSS 193
                                       6689****99865 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 1.2e-05
                                       TT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4  19 eglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                       e +T+ E++++ g+++ ++r + k+  +kL
  gi|474933624|ref|YP_007687206.1| 276 ERRTQREVADVAGVTEVTIRNRYKELTEKL 305
                                       789*********************998887 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   2.8e-05     0.022      15      41 ..     275     301 ..     273     302 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.8e-05
                     HTH_AsnC-type  15 daRisyaeLAervGlSestvlrRvrrL 41 
                                       + R++ +e+A+  G++e t+++R++ L
  gi|474933624|ref|YP_007687206.1| 275 NERRTQREVADVAGVTEVTIRNRYKEL 301
                                       569*********************998 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.3   1.8e-05     0.014      29      57 ..      13      42 ..      12      45 .. 0.91
   2 ?   -2.3   0.0       5.5   4.3e+03      49      54 ..     177     182 ..     168     194 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.8e-05
                    OrfB_Zn_ribbon 29 ktCseCgsknke.alsgrtfkCpnCgfead 57
                                      k C+eCgs++   + ++ +++C++Cg+++d
  gi|474933624|ref|YP_007687206.1| 13 KVCPECGSRHLVrDYERGELVCEDCGLVLD 42
                                      68*******988799***********9987 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.5
                    OrfB_Zn_ribbon  49 CpnCgf 54 
                                       C++Cg+
  gi|474933624|ref|YP_007687206.1| 177 CRQCGV 182
                                       555554 PP

>> UPF0253  Uncharacterised protein family (UPF0253)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00023      0.18      27      52 ..     123     148 ..     117     155 .. 0.91
   2 ?    0.9   0.0      0.75   5.8e+02      32      44 ..     184     196 ..     176     200 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00023
                           UPF0253  27 iscalktLdevaanealpeevrekAA 52 
                                       ++ al  Ld++a+   lp++vre AA
  gi|474933624|ref|YP_007687206.1| 123 LAFALSELDRMASAMGLPRNVRETAA 148
                                       677999*******************9 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.75
                           UPF0253  32 ktLdevaanealp 44 
                                       +tLdeva+ +++ 
  gi|474933624|ref|YP_007687206.1| 184 RTLDEVANSSRVG 196
                                       89******99875 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00018      0.14       9      40 ..       9      43 ..       5      46 .. 0.79
   2 ?    1.9   0.0      0.31   2.4e+02      15      20 ..     177     182 ..     162     198 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00018
                               DZR  9 ppdarfCseCgtk..lkavaa.edrCpsCgekvdp 40
                                      +++ ++C+eCg++  ++ +++ e +C  Cg  +d 
  gi|474933624|ref|YP_007687206.1|  9 TEEIKVCPECGSRhlVRDYERgELVCEDCGLVLDD 43
                                      667799******987776666999*****987765 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.31
                               DZR  15 CseCgt 20 
                                       C +Cg 
  gi|474933624|ref|YP_007687206.1| 177 CRQCGV 182
                                       444443 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.4   2.3e-05     0.018      20      44 ..      14      38 ..       7      39 .. 0.88
   2 ?   -1.4   0.1       3.1   2.4e+03      20      26 ..     176     182 ..     174     190 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.3e-05
                     Zn_Tnp_IS1595 20 vCPhCgsrkayriktrglfqCkeCr 44
                                      vCP Cgsr++ r   rg + C++C+
  gi|474933624|ref|YP_007687206.1| 14 VCPECGSRHLVRDYERGELVCEDCG 38
                                      8*******88887778********7 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.1
                     Zn_Tnp_IS1595  20 vCPhCgs 26 
                                        C  Cg+
  gi|474933624|ref|YP_007687206.1| 176 ACRQCGV 182
                                       4888886 PP

>> RPA_interact_C  Replication protein A interacting C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00073      0.57       1      27 [.      14      43 ..      14      95 .. 0.83
   2 ?    3.0   0.0      0.19   1.5e+02      66      78 ..     170     182 ..     127     185 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00073
                    RPA_interact_C  1 lCPvCkkrklkets..evifCe.Cglrlet 27
                                      +CP C +r+l ++     ++Ce Cgl l+ 
  gi|474933624|ref|YP_007687206.1| 14 VCPECGSRHLVRDYerGELVCEdCGLVLDD 43
                                      6********998553478********9987 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.19
                    RPA_interact_C  66 veaLlaeCeeCdf 78 
                                        ++L+a C++C++
  gi|474933624|ref|YP_007687206.1| 170 AASLYAACRQCGV 182
                                       578********86 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.3   0.00026       0.2      23      38 ..       8      25 ..       3      27 .. 0.78
   2 ?    2.3   0.1      0.25   1.9e+02       5      13 ..      31      39 ..      26      51 .. 0.75
   3 ?    0.7   0.0      0.74   5.8e+02      28      33 ..     175     181 ..     162     186 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00026
                       Zn-ribbon_8 23 daplta.CPeCgs.evrr 38
                                      + ++++ CPeCgs ++ r
  gi|474933624|ref|YP_007687206.1|  8 ETEEIKvCPECGSrHLVR 25
                                      5567777******99988 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.25
                       Zn-ribbon_8  5 eYrCeeCgh 13
                                      e  Ce+Cg 
  gi|474933624|ref|YP_007687206.1| 31 ELVCEDCGL 39
                                      445888885 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.74
                       Zn-ribbon_8  28 a.CPeCg 33 
                                       a C +Cg
  gi|474933624|ref|YP_007687206.1| 175 AaCRQCG 181
                                       4477776 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   2.2   0.00021      0.16       3      30 ..      12      40 ..      10      41 .. 0.91
   2 ?   -2.0   0.0       4.1   3.2e+03      18      28 ..     171     181 ..     166     182 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00021
                     A2L_zn_ribbon  3 lkvCsvCggngiln.seqgylvCieCgas 30
                                      +kvC  Cg+  ++   e+g+lvC +Cg++
  gi|474933624|ref|YP_007687206.1| 12 IKVCPECGSRHLVRdYERGELVCEDCGLV 40
                                      699**********8889**********86 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.1
                     A2L_zn_ribbon  18 eqgylvCieCg 28 
                                       ++ y  C  Cg
  gi|474933624|ref|YP_007687206.1| 171 ASLYAACRQCG 181
                                       55566788898 PP

>> RB_B  Retinoblastoma-associated protein B domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00096      0.75      10      94 ..     123     205 ..     115     219 .. 0.82
   2 ?   -0.0   0.0       1.1   8.4e+02      17      40 ..     224     247 ..     214     286 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00096
                              RB_B  10 yklaavrlrdLcerLklsselrekiwtlfehvlveetellkdRhlDqillcavYvvakvtkeelsFkeiikaYrkqp 86 
                                       +  a + l ++ + + l +++re +  + +++++  ++l++ R ++ ++ +++Y+ ++ +   +++ e+ ++ r   
  gi|474933624|ref|YP_007687206.1| 123 LAFALSELDRMASAMGLPRNVRETAAMIYRKAVN--KNLIRGRSIEGVVAASLYAACRQCGVPRTLDEVANSSRVGR 197
                                       5667788888899999999999988888777775..68**********************99999999998887766 PP

                              RB_B  87 qasskvyr 94 
                                       ++  ++yr
  gi|474933624|ref|YP_007687206.1| 198 KEIGRTYR 205
                                       66666665 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.1
                              RB_B  17 lrdLcerLklsselrekiwtlfeh 40 
                                       +++ c++Lkls e+++k+ ++++ 
  gi|474933624|ref|YP_007687206.1| 224 VQRFCSELKLSGEVQTKAAEILKD 247
                                       678999999999999988776665 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   1.5    0.0034       2.6      16      40 .]      13      38 ..      12      38 .. 0.85
   2 ?    2.9   0.0      0.16   1.2e+02      16      25 ..     175     184 ..     172     193 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0034
                     Auto_anti-p27 16 etCpvC.gvPLmrdrkggkvyCvaCd 40
                                      ++Cp+C +  L+rd ++g+++C  C+
  gi|474933624|ref|YP_007687206.1| 13 KVCPECgSRHLVRDYERGELVCEDCG 38
                                      58****66678999899*****9996 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.16
                     Auto_anti-p27  16 etCpvCgvPL 25 
                                       + C +CgvP 
  gi|474933624|ref|YP_007687206.1| 175 AACRQCGVPR 184
                                       56*******6 PP

>> GATA  GATA zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.4    0.0019       1.5       1      28 [.      15      39 ..      15      41 .. 0.93
   2 ?    0.6   0.1      0.56   4.3e+02       1       9 [.     177     185 ..     177     187 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0019
                              GATA  1 CsnCgttkTplWRrgpdgnksLCnaCGl 28
                                      C  Cg++   l R  ++g+  +C++CGl
  gi|474933624|ref|YP_007687206.1| 15 CPECGSRH--LVRDYERGEL-VCEDCGL 39
                                      88999999..99999*****.******9 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.56
                              GATA   1 CsnCgttkT 9  
                                       C++Cg+  T
  gi|474933624|ref|YP_007687206.1| 177 CRQCGVPRT 185
                                       999998665 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.6   0.00056      0.43       4      26 .]      14      41 ..      11      41 .. 0.80
   2 ?   -0.1   0.1      0.88   6.8e+02      18      24 ..     176     182 ..     173     184 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00056
                       zf-ribbon_3  4 rCPnCGa.pl....ssddnvCpyCGtkl 26
                                       CP+CG+ +l    + +  vC  CG +l
  gi|474933624|ref|YP_007687206.1| 14 VCPECGSrHLvrdyERGELVCEDCGLVL 41
                                      7*******95455556999999999986 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.88
                       zf-ribbon_3  18 vCpyCGt 24 
                                       +C  CG 
  gi|474933624|ref|YP_007687206.1| 176 ACRQCGV 182
                                       5888885 PP

>> Vps36-NZF-N  Vacuolar protein sorting 36 NZF-N zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.2      0.86   6.7e+02      28      40 ..       7      19 ..       2      26 .. 0.83
   2 ?   -0.9   2.2       1.4   1.1e+03      34      46 ..      32      44 ..      14      51 .. 0.77
   3 ?    7.6   0.0    0.0031       2.4      35      54 ..     176     195 ..     169     203 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.86
                       Vps36-NZF-N 28 nastplPpClaCG 40
                                      ++++++ +C  CG
  gi|474933624|ref|YP_007687206.1|  7 EETEEIKVCPECG 19
                                      5788899999999 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.4
                       Vps36-NZF-N 34 PpClaCGvkpdle 46
                                       +C+ CG   d +
  gi|474933624|ref|YP_007687206.1| 32 LVCEDCGLVLDDN 44
                                      58****9887765 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0031
                       Vps36-NZF-N  35 pClaCGvkpdlelikksika 54 
                                        C +CGv+ +l+ + +s  +
  gi|474933624|ref|YP_007687206.1| 176 ACRQCGVPRTLDEVANSSRV 195
                                       6***********99998765 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0         7   5.4e+03      27      39 ..      20      32 ..      20      35 .. 0.80
   2 ?    2.9   0.1      0.19   1.4e+02      44      62 ..     127     145 ..     101     147 .. 0.83
   3 ?   -0.0   0.1       1.5   1.2e+03      16      33 ..     185     202 ..     169     205 .. 0.72
   4 ?    6.5   0.0     0.013        10      14      32 ..     277     295 ..     262     296 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 7
                            HTH_31 27 sestlsrlEqGrr 39
                                      s+  ++++E+G+ 
  gi|474933624|ref|YP_007687206.1| 20 SRHLVRDYERGEL 32
                                      6778999***986 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.19
                            HTH_31  44 pavlealaralgldpaera 62 
                                       ++ l+++a a gl+++ r+
  gi|474933624|ref|YP_007687206.1| 127 LSELDRMASAMGLPRNVRE 145
                                       5789**********99887 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 1.5
                            HTH_31  16 sqeevAerlgvsestlsr 33 
                                       +++evA  ++v +  ++r
  gi|474933624|ref|YP_007687206.1| 185 TLDEVANSSRVGRKEIGR 202
                                       778888888888887776 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.013
                            HTH_31  14 GLsqeevAerlgvsestls 32 
                                       + +q+evA+ +gv+e t++
  gi|474933624|ref|YP_007687206.1| 277 RRTQREVADVAGVTEVTIR 295
                                       569***********99986 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   1.0     0.042        33       2      25 ..      15      40 ..       4      42 .. 0.85
   2 ?    3.6   0.0     0.089        69      17      28 ..     175     186 ..     163     192 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.042
                          zf-Mss51  2 CPvpkhkqt..apkhvdfeCpdCGip 25
                                      CP + +++   + ++ ++ C dCG++
  gi|474933624|ref|YP_007687206.1| 15 CPECGSRHLvrDYERGELVCEDCGLV 40
                                      8888888877778888999****985 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.089
                          zf-Mss51  17 feCpdCGiptyc 28 
                                         C +CG+p   
  gi|474933624|ref|YP_007687206.1| 175 AACRQCGVPRTL 186
                                       57*******765 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.3    0.0047       3.7       4      15 ..      14      25 ..      12      33 .. 0.81
   2 ?    3.2   0.0      0.18   1.4e+02       4      13 ..     176     185 ..     174     215 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0047
                           zf-ISL3  4 rCPnCgsktvvk 15
                                      +CP+Cgs+++v+
  gi|474933624|ref|YP_007687206.1| 14 VCPECGSRHLVR 25
                                      6*******8754 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.18
                           zf-ISL3   4 rCPnCgsktv 13 
                                       +C++Cg +  
  gi|474933624|ref|YP_007687206.1| 176 ACRQCGVPRT 185
                                       8*****9844 PP

>> Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.7    0.0014       1.1       6      33 ..      15      38 ..      13      45 .. 0.88
   2 ?   -0.4   0.1       1.8   1.4e+03      28      33 ..     177     181 ..     175     187 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0014
                                      -TTTT-TTTEE.ETT....S-EEETTTTB CS
                    Prim_Zn_Ribbon  6 CPvCGGrDrFr.fddkdgrGtwfCrqCgg 33
                                      CP CG+r   r +++    G  +C  C g
  gi|474933624|ref|YP_007687206.1| 15 CPECGSRHLVRdYER----GELVCEDC-G 38
                                      *********999999....********.5 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.8
                                       ETTTTB CS
                    Prim_Zn_Ribbon  28 CrqCgg 33 
                                       CrqC g
  gi|474933624|ref|YP_007687206.1| 177 CRQC-G 181
                                       ****.4 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   1.5       6.2   4.9e+03      30      40 ..      99     109 ..      98     116 .. 0.76
   2 ?   -0.7   0.0       1.8   1.4e+03      20      31 ..     173     184 ..     170     185 .. 0.82
   3 ?    9.5   0.1    0.0011      0.84      14      41 ..     274     301 ..     271     308 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 6.2
                            HTH_23  30 srrTvyrwlkr 40 
                                       +r ++yr +k+
  gi|474933624|ref|YP_007687206.1|  99 NRAQLYRLRKW 109
                                       67888888887 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.8
                            HTH_23  20 vreIAreLgvsr 31 
                                         +++r++gv+r
  gi|474933624|ref|YP_007687206.1| 173 LYAACRQCGVPR 184
                                       5689******98 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0011
                            HTH_23  14 laeGlsvreIAreLgvsrrTvyrwlkry 41 
                                       + e+ ++re+A+  gv++ T+++  k  
  gi|474933624|ref|YP_007687206.1| 274 CNERRTQREVADVAGVTEVTIRNRYKEL 301
                                       55689*****************665554 PP

>> zinc_ribbon_6  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   1.5      0.14   1.1e+02      19      54 ..       2      38 ..       1      39 [. 0.76
   2 ?   -2.9   0.0       9.2   7.1e+03       8      30 ..     128     150 ..     124     151 .. 0.80
   3 ?   -0.4   0.1       1.5   1.2e+03      45      54 ..     172     181 ..     166     182 .. 0.84
   4 ?    1.2   0.0      0.48   3.7e+02       5      29 ..     202     226 ..     199     239 .. 0.84
   5 ?   -1.8   0.0       4.2   3.3e+03      26      34 ..     268     276 ..     249     284 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.14
                     zinc_ribbon_6 19 mpeeyknkkvkilCnDCekkse.vkfhvlglkCkeCg 54
                                      mp++ +++    +C  C+++    ++    l C+ Cg
  gi|474933624|ref|YP_007687206.1|  2 MPKQREETEEIKVCPECGSRHLvRDYERGELVCEDCG 38
                                      8888888877778999999888456777778888885 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 9.2
                     zinc_ribbon_6   8 raldaeiaeqpmpeeyknkkvki 30 
                                       ++ld+  ++  +p +++++ + i
  gi|474933624|ref|YP_007687206.1| 128 SELDRMASAMGLPRNVRETAAMI 150
                                       57888888899999999888777 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.5
                     zinc_ribbon_6  45 vlglkCkeCg 54 
                                        l+ +C++Cg
  gi|474933624|ref|YP_007687206.1| 172 SLYAACRQCG 181
                                       58999****6 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.48
                     zinc_ribbon_6   5 ayfraldaeiaeqpmpeeyknkkvk 29 
                                       +++r + +e++ + mp++ ++++++
  gi|474933624|ref|YP_007687206.1| 202 RTYRFMTRELKLKLMPTKPQDYVQR 226
                                       6799999**********99987654 PP

  == domain 5  score: -1.8 bits;  conditional E-value: 4.2
                     zinc_ribbon_6  26 kkvkilCnD 34 
                                       ++ +ilCn 
  gi|474933624|ref|YP_007687206.1| 268 YISSILCNE 276
                                       457899985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       771  (0.043003); expected 358.6 (0.02)
Passed bias filter:                      655  (0.036533); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 1948.46
//
Query:       gi|474933625|ref|YP_007687207.1|  [L=96]
Description: hypothetical protein TALC_00032 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
        4.1    7.3  11.2       0.92    9.4   3.6    2.1  2  DUF3611    Protein of unknown function (DUF3611)


Domain annotation for each model (and alignments):
>> DUF3611  Protein of unknown function (DUF3611)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   3.6   5.1e-05      0.92      33      71 ..      11      51 ..       1      55 [. 0.63
   2 ?    3.0   0.9    0.0047        85     103     126 ..      71      94 ..      62      96 .] 0.69

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 5.1e-05
                           DUF3611 33 llfallgrslae..etnaglgfglflavlglvvllfsifwa 71
                                       ++ +++  +++   + ++ gfgl++a++gl+vl+f ++++
  gi|474933625|ref|YP_007687207.1| 11 GITMIAAGAFSAyfGKGKSKGFGLLVAAIGLIVLIFWLYLT 51
                                      22222222222245667888****************99975 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.0047
                           DUF3611 103 livnlvGmllallgaeatvgvLla 126
                                        i+nl+G+l+  l+a  +  v ++
  gi|474933625|ref|YP_007687207.1|  71 AIINLIGILIGALIAVGIFLVTVI 94 
                                       589999999877776555544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1111  (0.0619666); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.51
# Mc/sec: 571.43
//
Query:       gi|474933626|ref|YP_007687208.1|  [L=161]
Description: 5-(carboxyamino)imidazole ribonucleotide mutase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-51  174.0   0.5    1.6e-51  173.7   0.5    1.1  1  AIRC      AIR carboxylase


Domain annotation for each model (and alignments):
>> AIRC  AIR carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.7   0.5   9.1e-56   1.6e-51       3     147 ..       5     144 ..       3     145 .. 0.95

  Alignments for each domain:
  == domain 1  score: 173.7 bits;  conditional E-value: 9.1e-56
                                       EEEESSGGGHHHHHHHHHHHHHTT-EEEEEE--TTTSHHHHHHHHHHCHTTTEEEEEEEEESS--HHHHHHHHSSS- CS
                              AIRC   3 giimGSdsDlevmkkaaeilkelgveyevrvvSahrtpeelleyaeeaeerglkviIagAGgaahLpgvvaslttlP 79 
                                        iimGS+sD+ev++ka+++lk++gv++++ v Sahrtpe++++++++ +    +v+Ia+AG +a+Lpgv+as tt P
  gi|474933626|ref|YP_007687208.1|   5 FIIMGSKSDFEVASKAIKVLKKFGVDFDIAVSSAHRTPERTQTLVTNSD---ADVFIAIAGLSAALPGVIASFTTKP 78 
                                       69******************************************99765...68*********************** PP

                                       EEEEEE--STTCCHHHHHHHHT--TTS--EE-SSTHHHHHHHHHHHHHTTT-HHHHHHHHHHHHHHHH CS
                              AIRC  80 VigvPvkskalkgldsllSivqmPsgvpvatvaigkaknAallAaqilalkdeelaekleeyreelke 147
                                       VigvPvk       d+llSivqmP+g+pva+v++g+a+nAa lAa+i+alkd++l +kl+e r +++e
  gi|474933626|ref|YP_007687208.1|  79 VIGVPVKG--DLNYDALLSIVQMPPGIPVACVGLGRADNAATLAAEIMALKDPALGKKLQEDRLAQAE 144
                                       *******9..4579**********************************************99987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1064.51
//
Query:       gi|474933627|ref|YP_007687209.1|  [L=320]
Description: GMP synthase (glutamine-hydrolyzing) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.1e-36  122.9   0.1    7.8e-36  122.0   0.1    1.5  1  GMP_synt_C     GMP synthase C terminal domain
    1.6e-09   37.2   0.0    8.1e-07   28.4   0.0    2.2  2  NAD_synthase   NAD synthase
      4e-09   36.3   0.0    9.6e-07   28.5   0.0    2.1  1  QueC           Queuosine biosynthesis protein QueC
    1.2e-05   25.2   0.0    1.9e-05   24.5   0.0    1.3  1  ATP_bind_3     PP-loop family
    0.00019   20.4   0.2      0.032   13.0   0.1    2.3  2  tRNA_Me_trans  tRNA methyl transferase
     0.0002   21.4   0.0    0.00031   20.8   0.0    1.3  1  PAPS_reduct    Phosphoadenosine phosphosulfate reductase fami
     0.0034   17.0   0.1      0.018   14.6   0.1    2.0  1  ThiI           Thiamine biosynthesis protein (ThiI)
  ------ inclusion threshold ------
      0.051   13.7   0.1        1.3    9.2   0.0    2.8  2  TmoB           Toluene-4-monooxygenase system protein B (TmoB


Domain annotation for each model (and alignments):
>> GMP_synt_C  GMP synthase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.0   0.1   3.5e-39   7.8e-36      10      92 .]     236     319 ..     224     319 .. 0.92

  Alignments for each domain:
  == domain 1  score: 122.0 bits;  conditional E-value: 3.5e-39
                                       GGSSEEEEEEEEEEE----------EEEEEEEEE---------B----HHHHHHHHHHHHHHST.T---EEEE---T CS
                        GMP_synt_C  10 kkiwQafavllpvksvGvmgdkRtyeyvvalRaveseDamtadvaelpyevLekissrivnevk.gvnrvvyditsk 85 
                                        + wQ+favllp+k+vGv+gd+R+y+y++a+Rav+s D+mta++++lp evL++is ri++ +k +vnrvvyditsk
  gi|474933627|ref|YP_007687209.1| 236 VRPWQYFAVLLPTKTVGVQGDRRAYGYTIAVRAVDSVDGMTATFSRLPLEVLNRISVRITDTMKsQVNRVVYDITSK 312
                                       456**********************************************************99747*********** PP

                                       TTS-S-- CS
                        GMP_synt_C  86 PpatiEw 92 
                                       Ppat+Ew
  gi|474933627|ref|YP_007687209.1| 313 PPATVEW 319
                                       ******* PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   3.6e-10   8.1e-07      19      90 ..      26      97 ..      10     120 .. 0.82
   2 !    6.6   0.0    0.0017       3.8     148     168 ..     166     186 ..     159     195 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 3.6e-10
                                      SEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE---HHHH.HHHHH CS
                      NAD_synthase 19 kgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidikpiv.rafeq 90
                                       ++++  SGGvDS ++a++a ka+  ++ la+++ s    + ++e+  a+++++gi++ +  +++ + +a++ 
  gi|474933627|ref|YP_007687209.1| 26 AKAIIACSGGVDSMVAATIASKAI-GDRLLAIYVDSGLMRKGETEEVEAMMKHMGINYRVARVADEYfEALKG 97
                                      5789999*****************.689*******************************99998754145444 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0017
                                       BETTTTS-HHHHHHHHHHTT- CS
                      NAD_synthase 148 lapiaellKtevkeLakelnv 168
                                       ++p+ +l+K ev++ a++l+v
  gi|474933627|ref|YP_007687209.1| 166 VEPLRDLYKDEVRQVARKLGV 186
                                       68*****************98 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   4.3e-10   9.6e-07       1     177 [.      27     188 ..      27     192 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 4.3e-10
                                       EEEEE--SSHHHHHHHHHHHHH.-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-GGGGGGSCGGG---- CS
                              QueC   1 kavvllSGGlDSttvlalakke.gkevealtfdYgqrhkkeleaakkiakelgveehkildldllkelggsaLtdee 76 
                                       ka++  SGG+DS +++++a+k+ g+++ a+ +d g  +k e+e +++++k++g+ + ++  +    +   +aL    
  gi|474933627|ref|YP_007687209.1|  27 KAIIACSGGVDSMVAATIASKAiGDRLLAIYVDSGLMRKGETEEVEAMMKHMGI-NYRVARVA---DEYFEALK--- 96 
                                       799*************999887269*****************************.66665555...22222332... PP

                                       -------...--------TTHHHHHHHHHHHHHHHHT-SEEEE---S-STT--GGGSHHHHHHHHHHHHHHHTS--E CS
                              QueC  77 ievpkeeleeeelpntfVpaRNliflslaasyaealgaeaiiiGvneedfsgYPDcrdefvkalnkalnlgedkkie 153
                                         v++ e +++ + +         f+ +   ya++ ga+ ++ G  + d     D  ++++k+ +++  l +d  ++
  gi|474933627|ref|YP_007687209.1|  97 -GVTDPEEKRKIIGEK--------FIRVFERYAKEFGATYLFQGTIAPDWIESGDGVRDTIKSHHNVGGLPKDLGMT 164
                                       .234423333444444........6778899********************************************** PP

                                       EE-TTTT--HHHHHHHHHHTTHHH CS
                              QueC 154 ieaPlidlsKaeivklgkelgvpl 177
                                       ++ Pl dl K e+ +++ +lgv+ 
  gi|474933627|ref|YP_007687209.1| 165 LVEPLRDLYKDEVRQVARKLGVEA 188
                                       *********************976 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   8.5e-09   1.9e-05       2     161 ..      28     186 ..      27     190 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 8.5e-09
                                       EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H...HHCTTST CS
                        ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvdv...akkkgkn 75 
                                       +++A SgG+DSm+   ++ k     g +l ai+vd gl  +   e+e v+++ k+++i++++++v     ++ kg +
  gi|474933627|ref|YP_007687209.1|  28 AIIACSGGVDSMVAATIASKA---IGDRLLAIYVDSGLMRK--GETEEVEAMMKHMGINYRVARVADeyfEALKGVT 99 
                                       79**********998888877...4559*********9865..56677*****************988884444555 PP

                                       CCCHHHHH....HHHHHHHCHHCCT.CEEE---BHHHHHHHHHHHHCCT--CCHHH-S-SEEEETTCCEE-CCCT-- CS
                        ATP_bind_3  76 leeaARel....RYevlkealkkegievlllAhhadDqaEtfllrlargsglaglagikeaseiasirlvRPlLkvs 148
                                         e+ R++      +v+++++k+ g+++l  +  a D +E         ++ +++ g+++     +++lv Pl +++
  gi|474933627|ref|YP_007687209.1| 100 DPEEKRKIigekFIRVFERYAKEFGATYLFQGTIAPDWIESGDGVRDTIKSHHNVGGLPKDL---GMTLVEPLRDLY 173
                                       5555565422215689999*******************999877777777777888888866...899999999999 PP

                                       HHHHHHHHHHTT- CS
                        ATP_bind_3 149 keeleeylkekki 161
                                       k+e+++++++ ++
  gi|474933627|ref|YP_007687209.1| 174 KDEVRQVARKLGV 186
                                       9999999988665 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.1   1.4e-05     0.032       2      76 ..      27      93 ..      26      99 .. 0.76
   2 !    5.0   0.0    0.0039       8.7     164     190 ..     165     191 ..     157     194 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.4e-05
                     tRNA_Me_trans  2 kvvvalSgGVDSsvaaallkeq.gyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfekeyke 76
                                      k ++a SgGVDS vaa++  ++ g  + ++++               + +++++e++ +++gi+++v  +++ey e
  gi|474933627|ref|YP_007687209.1| 27 KAIIACSGGVDSMVAATIASKAiGDRLLAIYVDSG---------LMRKGETEEVEAMMKHMGINYRVARVADEYFE 93
                                      56899***********9988762455556655433.........34466788999999999999999999999976 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0039
                     tRNA_Me_trans 164 llfPlgeltKeevrkiAkeaglavaek 190
                                       l+ Pl +l K+evr++A++ g++  e+
  gi|474933627|ref|YP_007687209.1| 165 LVEPLRDLYKDEVRQVARKLGVEASER 191
                                       566*****************9998776 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   1.4e-07   0.00031       2      77 ..      28     104 ..      27     132 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.4e-07
                                       EEEE--SSCTCHHHHHHHHHHCTTH.EEEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-TH CS
                       PAPS_reduct   2 lvvsvsgGkdslVllhLalkafkpv.pvvfvdtghefpetiefvdeleeryglrlkvyepeeevaekinaekhgssl 77 
                                        ++++sgG ds+V   +a+ka  ++   ++vd g   +  +e v+++ +++g++  v++  +e  e+++  + ++++
  gi|474933627|ref|YP_007687209.1|  28 AIIACSGGVDSMVAATIASKAIGDRlLAIYVDSGLMRKGETEEVEAMMKHMGINYRVARVADEYFEALKGVTDPEEK 104
                                       5799********************746***************************99999999988888877777665 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1     8e-06     0.018       5     161 ..      27     186 ..      24     217 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8e-06
                              ThiI   5 kvlaLlSgGiDSpVaaylllkR.Gcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlkeil 80 
                                       k++   SgG+DS Vaa ++ k  G r  ++++++ ++ + e++e+  ++ ++  +y     v  v+ ++ e lk ++
  gi|474933627|ref|YP_007687209.1|  27 KAIIACSGGVDSMVAATIASKAiGDRLLAIYVDSGLMRKGETEEVEAMMKHMGINYR----VARVADEYFEALKGVT 99 
                                       677889**********9998855*********9888888777766555555544554....4444555555555544 PP

                              ThiI  81 ekvkekltivllkrkmlriAekvaeeegakalvtGe......sLgqVaSqtle...NlrvisavvnllilrPLigld 148
                                       +  +e+ +  ++  k++r+ e++a+e+ga+ l +G         g     t++   N+  + +   +++++PL  l 
  gi|474933627|ref|YP_007687209.1| 100 D--PEEKRK-IIGEKFIRVFERYAKEFGATYLFQGTiapdwiESGDGVRDTIKshhNVGGLPKDLGMTLVEPLRDLY 173
                                       3..344444.5567899***********9999998621111112333334553222455555555666666666666 PP

                              ThiI 149 KeeiiklAkeigt 161
                                       K+e+ ++A+++g 
  gi|474933627|ref|YP_007687209.1| 174 KDEVRQVARKLGV 186
                                       6666666666665 PP

>> TmoB  Toluene-4-monooxygenase system protein B (TmoB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.18   4.1e+02      27      43 ..      39      55 ..      36      87 .. 0.79
   2 ?    9.2   0.0   0.00057       1.3      22      64 ..     174     214 ..     155     224 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.18
                              TmoB 27 qVaekvahhavGrrvrp 43
                                       Va+ +a+ a+G r+ +
  gi|474933627|ref|YP_007687209.1| 39 MVAATIASKAIGDRLLA 55
                                      5999********99865 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00057
                              TmoB  22 edtmdqVaekvahhavGrrvrpkpgaplrVrrqGevlprsmtv 64 
                                       +d ++qVa k+ + a  r+  p p   l Vr+ Gev p+++ v
  gi|474933627|ref|YP_007687209.1| 174 KDEVRQVARKLGVEASERQPFPGP--ALAVRCLGEVTPEKIEV 214
                                       6899***********999977777..9************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 1858.27
//
Query:       gi|474933628|ref|YP_007687210.1|  [L=131]
Description: transcriptional regulator, MarR family [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-16   58.7   0.0    5.9e-16   58.1   0.0    1.3  1  MarR             MarR family
    5.1e-10   39.1   0.0      8e-10   38.5   0.0    1.3  1  MarR_2           MarR family
    2.1e-09   37.7   0.0    3.3e-09   37.1   0.0    1.4  1  HTH_27           Winged helix DNA-binding domain
    9.2e-06   25.7   0.0    1.3e-05   25.3   0.0    1.3  1  HTH_34           Winged helix DNA-binding domain
    8.7e-05   22.3   0.0    0.00016   21.5   0.0    1.4  1  TrmB             Sugar-specific transcriptional regulator Trm
    0.00013   21.4   0.0    0.00023   20.7   0.0    1.4  1  HTH_24           Winged helix-turn-helix DNA-binding
    0.00027   21.0   0.0    0.00056   19.9   0.0    1.5  1  HTH_20           Helix-turn-helix domain
    0.00047   19.9   0.0    0.00063   19.5   0.0    1.3  1  HxlR             HxlR-like helix-turn-helix
     0.0005   20.0   0.2    0.00095   19.1   0.0    1.5  2  PadR             Transcriptional regulator PadR-like family
    0.00082   19.3   0.0     0.0014   18.5   0.0    1.4  1  HTH_45           Winged helix-turn-helix
     0.0012   17.8   0.1     0.0014   17.5   0.1    1.1  1  HTH_micro        HTH-like
  ------ inclusion threshold ------
      0.013   15.6   0.0      0.023   14.7   0.0    1.4  1  FeoC             FeoC like transcriptional regulator
      0.017   15.0   0.1      0.045   13.6   0.0    1.6  2  TFIIE_alpha      TFIIE alpha subunit
       0.02   14.8   0.0      0.033   14.1   0.0    1.4  1  HTH_5            Bacterial regulatory protein, arsR family
      0.023   14.6   0.1      0.075   13.0   0.1    1.9  1  HTH_12           Ribonuclease R winged-helix domain
      0.053   13.9   0.0      0.077   13.4   0.0    1.5  1  Penicillinase_R  Penicillinase repressor
      0.069   13.0   0.0       0.13   12.1   0.0    1.4  1  HTH_IclR         IclR helix-turn-helix domain


Domain annotation for each model (and alignments):
>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.1   0.0   5.6e-19   5.9e-16       1      58 [.      25      82 ..      25      83 .. 0.98

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 5.6e-19
                                      --HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTTS CS
                              MarR  1 ltltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRskspeDrRe 58
                                      +t+tq+ + + l+e+++ls+ e+ ++l+++++t+t +l+++e +G+i+R++s++D R+
  gi|474933628|ref|YP_007687210.1| 25 ITYTQYIVFMVLWERDDLSIGEICERLNLDNGTLTPLLKKMESNGFINRTRSKSDERV 82
                                      79*******************************************************7 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.0   7.6e-13     8e-10       1      61 [.      23      81 ..      23      82 .. 0.97

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 7.6e-13
                                      TT--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                            MarR_2  1 lgltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkR 61
                                      lg+t +q+ v ++L  r++  l++ge+++rl+l+ ++++ +lk++++ G++ r+++  D R
  gi|474933628|ref|YP_007687210.1| 23 LGITYTQYIVFMVLWERDD--LSIGEICERLNLDNGTLTPLLKKMESNGFINRTRSKSDER 81
                                      699***************9..*********************************9999998 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.0   3.2e-12   3.3e-09      15      68 .]      38      91 ..      25      91 .. 0.89

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 3.2e-12
                            HTH_27 15 rrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      +r+  ++ ++c+rln++  +    lkk++ +G++ rt+++ d r  rv+lTdkG
  gi|474933628|ref|YP_007687210.1| 38 ERDDLSIGEICERLNLDNGTLTPLLKKMESNGFINRTRSKSDERVIRVTLTDKG 91
                                      7889999**********************************************9 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   1.3e-08   1.3e-05       5      72 ..      32      98 ..      29     109 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.3e-08
                            HTH_34  5 vlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkky 72
                                      v+ +L + d  +  e+ e l++ +g L   lkk+e++g+i+++ ++++  + + +++T++G+e  +k 
  gi|474933628|ref|YP_007687210.1| 32 VFMVLWERDDLSIGEICERLNLDNGTLTPLLKKMESNGFINRTRSKSDE-RVIRVTLTDKGKELREKA 98
                                      78899999*************************************9998.9***********987765 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   1.5e-07   0.00016       1      58 [.      20      77 ..      20      91 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.5e-07
                                      HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                      L+ lG++ +   v+ +L +++ +++ ei e+l+++  +    L+++e+ G+++r +++
  gi|474933628|ref|YP_007687210.1| 20 LKPLGITYTQYIVFMVLWERDDLSIGEICERLNLDNGTLTPLLKKMESNGFINRTRSK 77
                                      6779**************************************************9987 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   2.2e-07   0.00023      12      47 ..      36      71 ..      35      72 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.2e-07
                            HTH_24 12 LqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      L +  ++s+ e++erl+l  +t++  lk++e++G+I
  gi|474933628|ref|YP_007687210.1| 36 LWERDDLSIGEICERLNLDNGTLTPLLKKMESNGFI 71
                                      6677889***************************99 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   5.3e-07   0.00056      16      59 ..      33      76 ..      26      78 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 5.3e-07
                                      HHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                            HTH_20 16 lraLaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                                      +  L++++ l+ +e++erl l+  tl   L+++e+ g++ ++r+
  gi|474933628|ref|YP_007687210.1| 33 FMVLWERDDLSIGEICERLNLDNGTLTPLLKKMESNGFINRTRS 76
                                      5568**************************************97 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0     6e-07   0.00063      19      75 ..      42      97 ..      27     112 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 6e-07
                                      EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHH CS
                              HxlR 19 kRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepv 75
                                         +e+ ++l ++ + +L+  L+++e++g+i+r+  ++    +  +lt+kG++l++ 
  gi|474933628|ref|YP_007687210.1| 42 LSIGEICERL-NLDNGTLTPLLKKMESNGFINRTRSKSDERVIRVTLTDKGKELREK 97
                                      5567777777.888999**********************9999***********975 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0     9e-07   0.00095      27      73 ..      51      95 ..      43      97 .. 0.80
   2 ?   -2.8   0.0       5.9   6.2e+03      27      27 ..     117     117 ..     104     129 .. 0.48

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 9e-07
                                      CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHH CS
                              PadR 27 lelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrel 73
                                      l+l +G+l p+Lk++e +g++++++++s+e+  r   +lTd+G++  
  gi|474933628|ref|YP_007687210.1| 51 LNLDNGTLTPLLKKMESNGFINRTRSKSDERVIRV--TLTDKGKELR 95
                                      56789*********************985444444..8*****9865 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5.9
                                       C CS
                              PadR  27 l 27 
                                       +
  gi|474933628|ref|YP_007687210.1| 117 I 117
                                       2 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.4e-06    0.0014      19      69 ..      41      98 ..      28     103 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.4e-06
                            HTH_45 19 eakkTkimykanLsykllnkYLdmLvekgli.......kkskekYvlTekGlellekl 69
                                      + +  +i  + nL+  +l   L+++ ++g+i       +++    +lT+kG+el ek 
  gi|474933628|ref|YP_007687210.1| 41 DLSIGEICERLNLDNGTLTPLLKKMESNGFInrtrsksDERVIRVTLTDKGKELREKA 98
                                      5667789999*********************9988643334456789*******9986 PP

>> HTH_micro  HTH-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   1.3e-06    0.0014      95     166 ..      30     101 ..      25     127 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.3e-06
                         HTH_micro  95 kivdflvkakdyvkaaelraklnidpKklfYvikkLakkglieqktkeeakivikinkDesgsvvkkldkek 166
                                       +iv +++  +d  +  e+ ++ln+d  +l  ++kk++++g+i+  +++  + vi++    +g++ ++ +++ 
  gi|474933628|ref|YP_007687210.1|  30 YIVFMVLWERDDLSIGEICERLNLDNGTLTPLLKKMESNGFINRTRSKSDERVIRVTLTDKGKELREKAVSV 101
                                       567788888999999*****************************************9978888888777765 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   2.2e-05     0.023      10      50 ..      37      77 ..      32      82 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.2e-05
                              FeoC 10 eergrvslkeLsrhfkaspealeamLeqwvrkGrvekvaat 50
                                       er   s++e++ +++ +  +l ++L  ++  G ++++  +
  gi|474933628|ref|YP_007687210.1| 37 WERDDLSIGEICERLNLDNGTLTPLLKKMESNGFINRTRSK 77
                                      578899***************************99887665 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   4.3e-05     0.045      17      67 ..      31      81 ..      24      88 .. 0.91
   2 ?   -1.7   0.0       2.5   2.7e+03      28      35 ..     112     119 ..      98     128 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.3e-05
                                      HHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTT CS
                       TFIIE_alpha 17 lvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeek 67
                                       v +vL e+  ++  ++ + l++d   l +lL ++ + ++++  r++ +e 
  gi|474933628|ref|YP_007687210.1| 31 IVFMVLWERDDLSIGEICERLNLDNGTLTPLLKKMESNGFINRTRSKSDER 81
                                      58899999999999*********************************9886 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.5
                                       EBHHHHHH CS
                       TFIIE_alpha  28 vteedlak 35 
                                       +t+e++++
  gi|474933628|ref|YP_007687210.1| 112 LTDEEIKQ 119
                                       45555554 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.1e-05     0.033      14      46 ..      40      72 ..      30      73 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.1e-05
                                      SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5 14 gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                        l+++e++e l+l  +t+   Lkk++  G+++
  gi|474933628|ref|YP_007687210.1| 40 DDLSIGEICERLNLDNGTLTPLLKKMESNGFIN 72
                                      679****************************97 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   7.2e-05     0.075       8      64 ..      37      93 ..      30      95 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.2e-05
                            HTH_12  8 aesdkpigakeiaeeLkkrgydigeravRyrLrkleergltrrvgya......greltEkGle 64
                                       e+d+ ++ +ei e L++ +  +        L+k+e +g+++r +          +lt+kG e
  gi|474933628|ref|YP_007687210.1| 37 WERDD-LSIGEICERLNLDNGTL-----TPLLKKMESNGFINRTRSKsderviRVTLTDKGKE 93
                                      55555.66666666666553333.....4569***********99887888877889999976 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   7.3e-05     0.077       5      57 ..      29      77 ..      25     125 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.3e-05
                                      -SHHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEET CS
                   Penicillinase_R  5 EaevmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsrekeg 57
                                      +  v  +lwe+++++++e+ e+l+ +    + T + ll++++  g+++r +++
  gi|474933628|ref|YP_007687210.1| 29 QYIVFMVLWERDDLSIGEICERLNLD----NGTLTPLLKKMESNGFINRTRSK 77
                                      567899*****************988....99***************998864 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00012      0.13      16      50 ..      39      73 ..      37      75 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00012
                                      BSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 16 pqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      + +l++ e+++r+ l   t   lL+ ++  G++ +
  gi|474933628|ref|YP_007687210.1| 39 RDDLSIGEICERLNLDNGTLTPLLKKMESNGFINR 73
                                      5679***************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      628  (0.0350271); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 851.43
//
Query:       gi|474933629|ref|YP_007687211.1|  [L=191]
Description: GMP synthase (glutamine-hydrolyzing), N-terminal domain or A subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.8e-35  121.1   0.0    5.3e-35  120.9   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
    1.5e-13   51.0   0.3    5.6e-11   42.6   0.0    2.7  2  Peptidase_C26  Peptidase C26
      5e-05   23.0   0.0    7.6e-05   22.4   0.0    1.3  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    0.00012   22.0   0.0     0.0035   17.2   0.0    2.1  2  SNO            SNO glutamine amidotransferase family


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.9   0.0   1.2e-38   5.3e-35       2     187 ..       5     183 ..       4     186 .. 0.93

  Alignments for each domain:
  == domain 1  score: 120.9 bits;  conditional E-value: 1.2e-38
                                       EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT..TTTHHHHHHHHCTSTS-EEE CS
                            GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg..vegkieaikearenkiPiLG 76 
                                       ++Dn+ + t+   + l  l+v+++++p+++++eei    ++ dg+++sgG  +++   + + ++++++  +  P++G
  gi|474933629|ref|YP_007687211.1|   5 VVDNGGQWTHREWRVLKYLKVETKIIPNTTPFEEI----SDLDGLILSGGAPNVAcdGDRMGNNAEYIDRATFPVFG 77 
                                       79*********************************....69**************7777788899999999****** PP

                                       ETHHHHHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEE CS
                            GATase  77 ICLGmQllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddee 153
                                       IC GmQ +++ fg ++ ++   e    + ++ d +++l+++ ++e++++ +H++ev++   +p g++ ta s  +++
  gi|474933629|ref|YP_007687211.1|  78 ICAGMQYMCQHFGSQLGPADMPEFGEVKLKVSD-HSDLFKNVPDEFTVWGSHNDEVKQ---VPPGFRLTASS-PSCR 149
                                       ********************7777777778777.77**********************...***********.5579 PP

                                       EEEEEEETTTEEEESSBTTSTTSTTHHHHHHHHH CS
                            GATase 154 lmeiiekknpfvgvQFHPEststpegpellfnfl 187
                                       ++++   ++p++gvQFHPE+  t++g+e+++nfl
  gi|474933629|ref|YP_007687211.1| 150 VEGVACIDRPLFGVQFHPEVENTEHGAEIFQNFL 183
                                       *******************************996 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.2   0.0    0.0035        16      56      71 ..      39      55 ..      29      67 .. 0.84
   2 !   42.6   0.0   1.3e-14   5.6e-11     104     216 .]      71     168 ..      63     168 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0035
                     Peptidase_C26 56 ldkldgllltGgq.dve 71
                                      ++ ldgl+l+Gg+ +v+
  gi|474933629|ref|YP_007687211.1| 39 ISDLDGLILSGGApNVA 55
                                      6789********99996 PP

  == domain 2  score: 42.6 bits;  conditional E-value: 1.3e-14
                     Peptidase_C26 104 rgvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllaellgseeievnslHhqaike 180
                                       + +P++giC G+q +   +G +l  +        d+     ++ + ++kv   s l + +  +e+ v   H+  +k+
  gi|474933629|ref|YP_007687211.1|  71 ATFPVFGICAGMQYMCQHFGSQLGPA--------DM----PEFGEVKLKVSDHSDLFKNVP-DEFTVWGSHNDEVKQ 134
                                       679************66666666543........22....245677899999998888888.8************** PP

                     Peptidase_C26 181 laeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                       + +++r +A ++   +E +  +++  +++gvQ+HPE
  gi|474933629|ref|YP_007687211.1| 135 VPPGFRLTASSPSCRVEGVACIDR--PLFGVQFHPE 168
                                       ***********************4..6********9 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   1.7e-08   7.6e-05      17      96 ..      18      93 ..       3     108 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.7e-08
                          GATase_3 17 dpLeaepevrvrfvplkdeslg..edadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGeeie 93
                                      ++L++ + v+ +++p +++ ++  +d+d +il Gg + ++        ++ ++ +   +a  pv+giC+G+q++++++ 
  gi|474933629|ref|YP_007687211.1| 18 RVLKYLK-VETKIIP-NTTPFEeiSDLDGLILSGGAPNVACDG----DRMGNNAEYIDRATFPVFGICAGMQYMCQHFG 90
                                      5666644.5555665.5554445578*********99886543....344444444445679**************986 PP

                          GATase_3 94 dpe 96
                                       + 
  gi|474933629|ref|YP_007687211.1| 91 SQL 93
                                      655 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   7.8e-07    0.0035      28      88 ..      36      92 ..      13     112 .. 0.76
   2 ?    2.7   0.0     0.021        96     159     184 ..     157     184 ..     142     188 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 7.8e-07
                                      GGGGCC-SEEEE-SS-HHHHHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCEETTB CS
                               SNO 28 kedlaevdaliiPGGestamskliertglyedllefvknsekvvlGtCaGlillskelene 88
                                       e++ ++d+li+ GG    ++   +r+g   +  e++ ++  +v+G CaG+ +++++ +++
  gi|474933629|ref|YP_007687211.1| 36 FEEISDLDGLILSGGAPN-VACDGDRMG---NNAEYIDRATFPVFGICAGMQYMCQHFGSQ 92
                                      4789999*******9754.444456666...889********************9988776 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.021
                                       ETTEEEESS-GGG..STTHCHHHHHHHH CS
                               SNO 159 qkkilatsfhPel..aeddirvhdyfve 184
                                        + ++++ fhPe+  +e++  + + f+e
  gi|474933629|ref|YP_007687211.1| 157 DRPLFGVQFHPEVenTEHGAEIFQNFLE 184
                                       45678999***98335666778888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1224.65
//
Query:       gi|474933630|ref|YP_007687212.1|  [L=85]
Description: archaeal conserved hypothetical protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-31  106.1   0.3    7.6e-31  106.0   0.3    1.0  1  UPF0147   Uncharacterised protein family (UPF0147)
    0.00037   20.7   0.6       0.08   13.2   0.1    2.1  2  UPF0253   Uncharacterised protein family (UPF0253)
  ------ inclusion threshold ------
      0.059   12.8   0.1      0.066   12.6   0.1    1.2  1  Med14     Mediator complex subunit MED14


Domain annotation for each model (and alignments):
>> UPF0147  Uncharacterised protein family (UPF0147)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.0   0.3   1.3e-34   7.6e-31       3      80 ..       3      80 ..       1      81 [. 0.97

  Alignments for each domain:
  == domain 1  score: 106.0 bits;  conditional E-value: 1.3e-34
                                      HHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHHH CS
                           UPF0147  3 ekikevielLeeiiedtsvPrniRraakeakekLkdekeslavraataisiLdeisnDpnmPlhaRtliwevvskLEt 80
                                      +k+k+v++ ++ +++d+svPrniR+ a++ak++L d++++l+vr+a a++iLd+++nDpn+P+haR liw+++s+LE 
  gi|474933630|ref|YP_007687212.1|  3 DKVKQVTDAMDMLADDNSVPRNIRKGATDAKARLLDTSDALDVRCAGAMNILDDLANDPNIPMHARSLIWQILSQLEM 80
                                      789**************************************************************************7 PP

>> UPF0253  Uncharacterised protein family (UPF0253)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.1   1.3e-05      0.08      26      59 ..       4      37 ..       1      44 [. 0.86
   2 !    6.5   0.0    0.0017        10      29      48 ..      49      68 ..      40      70 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.3e-05
                           UPF0253 26 AiscalktLdevaanealpeevrekAAyAAANLl 59
                                       ++ +  ++d +a+++++p+++r  A  A A Ll
  gi|474933630|ref|YP_007687212.1|  4 KVKQVTDAMDMLADDNSVPRNIRKGATDAKARLL 37
                                      5778889*********************999987 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0017
                           UPF0253 29 calktLdevaanealpeevr 48
                                       a++ Ld++a++ ++p + r
  gi|474933630|ref|YP_007687212.1| 49 GAMNILDDLANDPNIPMHAR 68
                                      489************98876 PP

>> Med14  Mediator complex subunit MED14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   1.1e-05     0.066      91     148 ..      23      79 ..       1      83 [. 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.1e-05
                                       CCHHHHHHCCHHHHHHHHCHHCHCTTCHCHCCCCCCSCSH--S--.-SHHHHHHHHHHH CS
                             Med14  91 kelkeslanaklpnpdlktAleVLstGrysrlpslikeeyppkpl.takeilktlkdln 148
                                       +++++  + ak++  d + Al+V + G ++ l +l ++  p+ p+ +++ i + l++l+
  gi|474933630|ref|YP_007687212.1|  23 RNIRKGATDAKARLLDTSDALDVRCAGAMNILDDLAND--PNIPMhARSLIWQILSQLE 79 
                                       578888999********************999999933..6666634455556666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 594.94
//
Query:       gi|474933631|ref|YP_007687213.1|  [L=54]
Description: hypothetical protein TALC_00038 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 379.18
//
Query:       gi|474933632|ref|YP_007687214.1|  [L=77]
Description: protein translocase SEC61 complex gamma subunit, archaeal and eukaryotic [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-06   26.9   0.1    4.2e-06   26.6   0.1    1.1  1  SecE      SecE/Sec61-gamma subunits of protein translocation 


Domain annotation for each model (and alignments):
>> SecE  SecE/Sec61-gamma subunits of protein translocation complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.1   2.4e-10   4.2e-06      15      50 ..      38      73 ..      32      77 .] 0.91

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 2.4e-10
                                      CCCHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SecE 15 tWPtrkEllkttvvVlvfvvimglflflvDlvfskl 50
                                      + P+++E++kt+++ +++++++g+++f++ +++++l
  gi|474933632|ref|YP_007687214.1| 38 HTPDKEEFIKTSKISAIGIIVLGALGFFIMWLMTYL 73
                                      67*****************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 494.84
//
Query:       gi|474933633|ref|YP_007687215.1|  [L=274]
Description: ribosomal protein L24p/L26e, archaeal [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-15   54.7   0.3    1.2e-14   54.0   0.3    1.4  1  Spt5-NGN  Early transcription elongation factor of RNA pol II
    4.1e-07   29.7   1.5    1.2e-06   28.3   0.2    2.5  3  KOW       KOW motif
  ------ inclusion threshold ------
      0.013   15.9   0.4       0.75   10.3   0.0    2.3  2  MG1       Macroglobulin domain MG1


Domain annotation for each model (and alignments):
>> Spt5-NGN  Early transcription elongation factor of RNA pol II, NGN section
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   0.3     2e-18   1.2e-14       1      84 []     129     208 ..     129     208 .. 0.94

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 2e-18
                          Spt5-NGN   1 siwavkctagqErevalslmkkilelakkenleIkSvfapdelkGyiyvEAdrkaaveralegipnvrgvvqglvpi 77 
                                       si ++k+++ qE+ v+ sl +k    a + + +I++v+ p ++ Gy++vE ++++++ +  ++i+++r++  g+v+i
  gi|474933633|ref|YP_007687215.1| 129 SIVILKTQMDQEKVVVQSLIAK----ADQGEKDIYAVLSPAGMRGYVFVEGMNTDRMHEKTRDIKKARAFIDGEVSI 201
                                       57889**************999....555567********************************************* PP

                          Spt5-NGN  78 kEvedll 84 
                                       +E++++l
  gi|474933633|ref|YP_007687215.1| 202 EEISNYL 208
                                       ***9987 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       1.7     1e+04      23      32 .]     187     196 ..     186     196 .. 0.82
   2 !   28.3   0.2   1.9e-10   1.2e-06       1      32 []     219     250 ..     219     250 .. 0.95
   3 ?   -2.0   0.0      0.68   4.1e+03       1       8 [.     263     270 ..     263     271 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.7
                                       ETTTTEEEEE CS
                               KOW  23 dqhkvrVfvd 32 
                                       d +k+r+f+d
  gi|474933633|ref|YP_007687215.1| 187 DIKKARAFID 196
                                       6689999998 PP

  == domain 2  score: 28.3 bits;  conditional E-value: 1.9e-10
                                       TTSEEEESSSTTTTCEEEEEEEETTTTEEEEE CS
                               KOW   1 pGdhVkVvsGphkGktGkVvkvdqhkvrVfvd 32 
                                       +Gd+V+ v Gp+kG++++V+k+d+ k+ ++v+
  gi|474933633|ref|YP_007687215.1| 219 EGDIVELVNGPFKGEKARVTKIDETKEEITVE 250
                                       59************************999997 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.68
                                       TTSEEEES CS
                               KOW   1 pGdhVkVv 8  
                                       +Gd V+ +
  gi|474933633|ref|YP_007687215.1| 263 KGDSVRLI 270
                                       7****976 PP

>> MG1  Macroglobulin domain MG1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00012      0.75      39      93 ..      80     141 ..      72     148 .. 0.84
   2 ?    3.4   0.1     0.017     1e+02      15      36 ..     242     263 ..     239     271 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00012
                                       ETTTTTSEEEEEEEEESTTTTTEEEEEEEB-SG.......CSSSSSSTT-EEEEEEEESS-E CS
                               MG1  39 dfpqkkkelasesvtLnsdnnfqalvkikippk.......dlkkdrkekqyvylqakskeet 93 
                                       dfp k+ +l++ +v   ++ ++ ++v+i+i++k       +++     +++v+l++++++e+
  gi|474933633|ref|YP_007687215.1|  80 DFPGKSGKLLTLEVICPKGARYDESVNIEITAKsdageasQHFGAAARQSIVILKTQMDQEK 141
                                       9******************************9977776666888888999999999996554 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.017
                                       TSEEEEEEEEES-SS-EEEEEE CS
                               MG1  15 gseetivveahgltkeveVtit 36 
                                       +++e+i+ve+ ++  +++Vt+ 
  gi|474933633|ref|YP_007687215.1| 242 ETKEEITVELVDAMVPIPVTVK 263
                                       799**********999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1761.23
//
Query:       gi|474933634|ref|YP_007687216.1|  [L=150]
Description: LSU ribosomal protein L11P [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-20   72.7   1.7    3.5e-20   71.6   1.7    1.6  1  Ribosomal_L11_N  Ribosomal protein L11, N-terminal domain
    1.7e-18   66.9   0.4    3.1e-18   66.0   0.4    1.4  1  Ribosomal_L11    Ribosomal protein L11, RNA binding domain


Domain annotation for each model (and alignments):
>> Ribosomal_L11_N  Ribosomal protein L11, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.6   1.7   3.9e-24   3.5e-20      14      65 .]       3      54 ..       1      54 [. 0.98

  Alignments for each domain:
  == domain 1  score: 71.6 bits;  conditional E-value: 3.9e-24
                   Ribosomal_L11_N 14 aGkAtpaPplGpaLGplGlnikkfckefnkaTkdkkglripVkitvyqdrsf 65
                                      +GkAt++PplGpaLGp+G+ni +++ ++n++Tk ++g+++pVki +++d++f
  gi|474933634|ref|YP_007687216.1|  3 GGKATAGPPLGPALGPKGVNIGQIIAKINEKTKAFEGMKVPVKILINPDKTF 54
                                      9*************************************************98 PP

>> Ribosomal_L11  Ribosomal protein L11, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.0   0.4   3.4e-22   3.1e-18       2      70 .]      60     127 ..      59     127 .. 0.95

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 3.4e-22
                                       --SHHHHHHHHHTXSSXXSSTTTSXXEEEEHHHHHHHHHHHGGGHTXS.SHHHHHHHHHHHHCTTTEEE CS
                     Ribosomal_L11   2 tPptsylLkkaagiekgsgkpgketvGtvslkqvyeIAkiKksdlnaalsleaavksilgtArsmGikV 70 
                                       tPp+s+l+k+++gi+k sg+p++e+vG++s++q+++IA +K+++l  + + +a v +++g + s+G++V
  gi|474933634|ref|YP_007687216.1|  60 TPPVSALIKNELGISKESGNPKTEIVGNLSVDQIKKIAAQKQDSLL-GATEKARVLEVAGNCVSCGVTV 127
                                       9*****************************************6555.559*****************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1020.20
//
Query:       gi|474933635|ref|YP_007687217.1|  [L=185]
Description: LSU ribosomal protein L1P [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-38  133.1   0.1    1.2e-38  132.9   0.1    1.0  1  Ribosomal_L1  Ribosomal protein L1p/L10e family


Domain annotation for each model (and alignments):
>> Ribosomal_L1  Ribosomal protein L1p/L10e family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.9   0.1   6.7e-43   1.2e-38      16     204 .]       2     180 ..       1     180 [. 0.97

  Alignments for each domain:
  == domain 1  score: 132.9 bits;  conditional E-value: 6.7e-43
                                       EEEESSS-TTSGGG--EEEEE-STSTSSCS-EEEEE-HHHHH...HHHHTT..-SEEETCHHHHHHT-HHHHHHTCC CS
                      Ribosomal_L1  16 alnlttkkpkkadqrkpgkipLphplgkevkiclitkdpqaeyakeakeagriakviglkklkkkyksfeakrkllk 92 
                                       a+nl++++   +++r+++ i+Lp++ gk vk+ +i  ++ a    +ak+    + vig +++ +   ++++ +k+++
  gi|474933635|ref|YP_007687217.1|   2 AVNLRDIDLTLPKNRIQEDIVLPKGRGKAVKVTVIGGGELAL---KAKDVA--DLVIGPDEIGALADNKKQAKKVAN 73 
                                       78999**********************************999...888888..9*********************** PP

                                       H-SEEEEEGGGHHHHHHHCHHHHGGGT-S-ECC..CT.BTS-HHHHHHHHCTTEEEEE-TTTSEEEEEEEETTSSHH CS
                      Ribosomal_L1  93 efdlfladdrimpllpklLGkvfgkrkkmPipvltkgtvkedvkkevekalkstvvvrldkgtclsvkvGklsftae 169
                                       + ++f+a+  +m +++k LG v+g+r+kmP p+ +     +d ++ ++++ k +v vr++++++++v+vG+++++ae
  gi|474933635|ref|YP_007687217.1|  74 DTEFFIAEAPLMAQVGKRLGTVLGPRGKMPKPI-AP---GADPSAMIDNLRK-SVTVRTKDHKTFHVPVGTVEMSAE 145
                                       *********************************.43...579**********.99********************** PP

                                       HHHHHHHHHHHHHHHTSTTTSGSEEEEEEEETTS- CS
                      Ribosomal_L1 170 elaeNieavvkalvekvpkkwkniksiylkttmsp 204
                                       ++aeNi+ v++ ++ +++k++ ni s+y+kt+m+p
  gi|474933635|ref|YP_007687217.1| 146 DIAENIDVVMSRVIGHLEKGKHNIDSVYIKTSMGP 180
                                       **********************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1328.45
//
Query:       gi|474933636|ref|YP_007687218.1|  [L=334]
Description: Ribosomal protein L10 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-23   81.9   0.2    4.1e-23   81.1   0.2    1.4  1  RL10P_insert   Insertion domain in 60S ribosomal protein L10P
      3e-21   75.4   0.3    8.4e-21   74.0   0.3    1.8  1  Ribosomal_L10  Ribosomal protein L10
    2.5e-09   37.6  11.1    2.5e-09   37.6  11.1    2.7  2  Ribosomal_60s  60s Acidic ribosomal protein
  ------ inclusion threshold ------
       0.15   12.6   0.0       0.26   11.8   0.0    1.3  1  MPP6           M-phase phosphoprotein 6


Domain annotation for each model (and alignments):
>> RL10P_insert  Insertion domain in 60S ribosomal protein L10P
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.1   0.2   9.2e-27   4.1e-23       1      71 []     109     179 ..     109     179 .. 0.99

  Alignments for each domain:
  == domain 1  score: 81.1 bits;  conditional E-value: 9.2e-27
                      RL10P_insert   1 AraGtiAtedviipagplelaPgsiepeLrklglptklkkGkivleedylvckkGetltseqaqlLklLgi 71 
                                       AraGt A+ed+++p+gp+   Pg+i+ eL+klglp+++  Gkiv+++d++v+kkGe++++e a++L +L+i
  gi|474933636|ref|YP_007687218.1| 109 ARAGTAAPEDIVVPEGPTPFGPGPIIGELQKLGLPAQIMAGKIVIKKDTTVVKKGEEISAELAAMLPKLEI 179
                                       9********************************************************************98 PP

>> Ribosomal_L10  Ribosomal protein L10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.0   0.3   1.9e-24   8.4e-21       4      98 ..       6     103 ..       3     105 .. 0.94

  Alignments for each domain:
  == domain 1  score: 74.0 bits;  conditional E-value: 1.9e-24
                                       CCHCCCCCCCCCCCTTSSEEEEEE-TTS-HHHHHHCCCHHHHHGCEEEEESCCCCCCCCHCCTSS.S....SCGCCS CS
                     Ribosomal_L10   4 ekKeelvkelkellkkyksvvvvdyegltvaqlqelRkklrengaelkvvKntlmrrAleetgeeek....lkellk 76 
                                        +K+++v+e+   +k+y +++vv++eg++++q+q +R+ lr++ a++k++Kn+l+ +Al+e+++e+     l + + 
  gi|474933636|ref|YP_007687218.1|   6 SWKKDVVEEIVADIKQYPTIAVVNVEGIGATQFQSMRAGLRGH-AKIKMAKNKLLALALQEAAAEKAgvdqLVDAID 81 
                                       79*****************************************.********************853789999**** PP

                                       SSEEEEEESS-TCHHHHCCCCC CS
                     Ribosomal_L10  77 gpvalvftnedpvalakvleef 98 
                                       g++a+v t+ +p++l  +l+++
  gi|474933636|ref|YP_007687218.1|  82 GQCAIVATDLNPFKLFNKLKAT 103
                                       **************99988865 PP

>> Ribosomal_60s  60s Acidic ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   1.5      0.22   9.8e+02      25      62 ..      63     115 ..      49     120 .. 0.63
   2 !   37.6  11.1   5.5e-13   2.5e-09       2      88 .]     231     333 ..     230     333 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.22
                                       XXXXXXXXXXXXXXXXXXXXXXX...............XXXXXXXXXXXXXXX CS
                     Ribosomal_60s  25 llvkalegkdieellangaakla...............aaaaaaaaaaaaaaa 62 
                                       l  +a e+  ++ l+ ++  + a                a+  +a+a a  aa
  gi|474933636|ref|YP_007687218.1|  63 LQEAAAEKAGVDQLVDAIDGQCAivatdlnpfklfnklKATQTPAPARAGTAA 115
                                       55566667777777777777766777777778888776444444444444443 PP

  == domain 2  score: 37.6 bits;  conditional E-value: 5.5e-13
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..................XXXXXXXXXXXXX CS
                     Ribosomal_60s   2 ptaenikkvlkaagveveaarvkllvkalegkdieellangaakla..................aaaaaaaaaaaaa 60 
                                       p +e+i  ++++a+   + ++++l+++  ++++i  l a++ ++++                  aaaaa+ aaa++a
  gi|474933636|ref|YP_007687218.1| 231 PAKETIVPLVQKAYR--QTYALSLEAAIPTKETIGALFAKADSQMLalasasgftnddiagrlsAAAAAPVAAAEPA 305
                                       8899***********..99**************************9*****************999999******** PP

                                       XXXXXXXXXXXXXXX.XX--SS--.STTT CS
                     Ribosomal_60s  61 aaaaaaeekkkeeeeeEeedddmG.fgLF 88 
                                       +a+++aee  +eee   ee+ ++G  +LF
  gi|474933636|ref|YP_007687218.1| 306 NAEQKAEENTEEEEV-SEEEAAAGlSALF 333
                                       ***********9999.58999***99999 PP

>> MPP6  M-phase phosphoprotein 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.7e-05      0.26      57     109 ..     276     326 ..     245     331 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.7e-05
                              MPP6  57 evsnvgfedlessvifGRrsFggfnkeve.ekkeeeeeeeekekeedvsdeela 109
                                         s  gf++    +i+GR+s  +  +    e +++e+++ee+ +ee+vs+ee a
  gi|474933636|ref|YP_007687218.1| 276 LASASGFTND---DIAGRLSAAAAAPVAAaEPANAEQKAEENTEEEEVSEEEAA 326
                                       6678888888...9********99996665599999999999999999999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       911  (0.0508115); expected 358.6 (0.02)
Passed bias filter:                      590  (0.0329076); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2161.72
//
Query:       gi|474933637|ref|YP_007687219.1|  [L=108]
Description: LSU ribosomal protein L12AE [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.7e-19   69.1  26.8    4.3e-19   68.9  26.8    1.1  1  Ribosomal_60s  60s Acidic ribosomal protein
  ------ inclusion threshold ------
      0.029   13.9   1.9      0.031   13.8   1.9    1.1  1  CAP_N          Adenylate cyclase associated (CAP) N terminal
        1.3    8.6   6.4        1.8    8.2   6.4    1.1  1  TraT           Enterobacterial TraT complement resistance pro


Domain annotation for each model (and alignments):
>> Ribosomal_60s  60s Acidic ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.9  26.8   7.2e-23   4.3e-19       1      88 []      21     107 ..      21     107 .. 0.81

  Alignments for each domain:
  == domain 1  score: 68.9 bits;  conditional E-value: 7.2e-23
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.. CS
                     Ribosomal_60s   1 eptaenikkvlkaagveveaarvkllvkalegkdieellangaaklaaaaaaaaaaaaaaaaaaaaeekkkeeeee. 76 
                                       e+t++ i ++l aag+ev+aa+vk+lv++leg+di+e++an+a +   a+aaaaa aaaaaaa+aaeekk+eeee+ 
  gi|474933637|ref|YP_007687219.1|  21 EITEDAISAILTAAGAEVDAAKVKALVASLEGVDIKEAIANAAVA---APAAAAAPAAAAAAAPAAEEKKEEEEEAv 94 
                                       79****************************************854...55555555555556666666666666658 PP

                                       XX--SS--.STTT CS
                     Ribosomal_60s  77 EeedddmG.fgLF 88 
                                        ee+ ++G  +LF
  gi|474933637|ref|YP_007687219.1|  95 SEEEAAAGlSALF 107
                                       89999***99999 PP

>> CAP_N  Adenylate cyclase associated (CAP) N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.9   5.2e-06     0.031     222     280 ..      49     107 ..      26     108 .] 0.68

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.2e-06
                                       -TTSBE.......SSC--XXXXXXX....XXXXXXXX.....XXXXXXXXXXXXXXXXX CS
                             CAP_N 222 nkkGkdaeealkaaaaaasaaaaggpppPpPpPppasvfeeesaaasasaaaggmsavF 280
                                       + +G+d++ea+++aa aa+aaaa+ +++++  P+  + +eee++a s+++aa+g+sa+F
  gi|474933637|ref|YP_007687219.1|  49 SLEGVDIKEAIANAAVAAPAAAAAPAAAAAAAPAAEEKKEEEEEAVSEEEAAAGLSALF 107
                                       557999999998555544444433333334444444455777778999999*******9 PP

>> TraT  Enterobacterial TraT complement resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   6.4    0.0003       1.8      60     130 ..       5      75 ..       2      83 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0003
                              TraT  60 eAayiLqanvly.vdkktdkaaaegalkaGfggalagaaagaaigaanggsagaalggglvGglvgaiagal 130
                                       e +yi +a vly ++k+ ++ a++++l+a+ g+ + +a + a ++ ++g + ++a++ ++v++ ++a+a+a+
  gi|474933637|ref|YP_007687219.1|   5 EMQYIYSAMVLYsAGKEITEDAISAILTAA-GAEVDAAKVKALVASLEGVDIKEAIANAAVAAPAAAAAPAA 75 
                                       669********9568988888888888888.788**************************999999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1197  (0.0667633); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 711.75
//
Query:       gi|474933638|ref|YP_007687220.1|  [L=96]
Description: hypothetical protein TALC_00045 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.019   15.0   0.0      0.022   14.8   0.0    1.1  1  Neugrin   Neugrin
       0.37   10.8   4.1       0.35   10.9   0.5    2.5  2  RHH_1     Ribbon-helix-helix protein, copG family


Domain annotation for each model (and alignments):
>> Neugrin  Neugrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   2.4e-06     0.022      37      72 ..      27      65 ..      20      94 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.4e-06
                           Neugrin 37 eGFdvstDvirRv....lkskfvPtlerklkqDakvlkkl 72
                                       GFd ++Dv+rRv    l  +f+P ++ k+  Da   +++
  gi|474933638|ref|YP_007687220.1| 27 QGFDSASDVVRRVvedyLSERFTPEERAKALEDAER-RRA 65
                                      6************33334579*********999987.443 PP

>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.5   3.9e-05      0.35       1      37 [.       6      44 ..       6      46 .. 0.87
   2 ?   -2.0   0.2      0.45     4e+03      16      16 ..      61      61 ..      51      70 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.9e-05
                                      EEEEEEEHHHHHHH.HHHHHHHT.SSHHHHHHHHHHHHH CS
                             RHH_1  1 rvsirldeellerL.delarrrg.rSrSelIReAlreyl 37
                                      rv++rl++e++++L     r++g  S S+++R+ +++yl
  gi|474933638|ref|YP_007687220.1|  6 RVTVRLSREDVDLLlFVASREQGfDSASDVVRRVVEDYL 44
                                      89*****9999986257778888*************998 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.45
                                      H CS
                             RHH_1 16 e 16
                                      e
  gi|474933638|ref|YP_007687220.1| 61 E 61
                                      3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.32s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 600.67
//
Query:       gi|474933639|ref|YP_007687221.1|  [L=278]
Description: Cell division GTPase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-10   39.8   0.2    3.6e-08   33.9   0.0    2.2  2  Tubulin   Tubulin/FtsZ family, GTPase domain
  ------ inclusion threshold ------
        0.1   12.3   0.0        1.9    8.1   0.0    2.2  2  MtrA      Tetrahydromethanopterin S-methyltransferase, subuni


Domain annotation for each model (and alignments):
>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.1   0.2    0.0053        47       2      20 ..       4      22 ..       3      37 .. 0.88
   2 !   33.9   0.0     4e-12   3.6e-08      84     194 ..      46     149 ..      29     152 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0053
                                      EEEEEEHHHHHHHHHHHHH CS
                           Tubulin  2 iivigvGqcGnqignelwe 20
                                       ivig+G+ G++i++++ +
  gi|474933639|ref|YP_007687221.1|  4 AIVIGCGGPGCNIVSRVRD 22
                                      59************99866 PP

  == domain 2  score: 33.9 bits;  conditional E-value: 4e-12
                                       TTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE.SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEEEEE--GG CS
                           Tubulin  84 gnngaggypevgkeaaeeileeirkevekcdslqgffitaslgGGTGSGlgpvilevlkeeypkalvvtvvvlPsef 160
                                       ++n ++g+ e+++++ e+ ++ei  ++++      +++++ lgGG GS++  +i + ++    +  +++ +v+P++f
  gi|474933639|ref|YP_007687221.1|  46 AENEVHGNAELAAKCLEAKRNEILLNIDGYSE---IILVTALGGGLGSAAVEFISKCARLA--DSKLIAAIVIPFKF 117
                                       5666899*************************...************************99..88999999****99 PP

                                       .G-HHHHHHHHHHHHHHHHT-SEEEEEEHHHHHC CS
                           Tubulin 161 sevvvepynailalkelieesdavividNdaLlk 194
                                         +  +   ++     + e +d ++++dN+++++
  gi|474933639|ref|YP_007687221.1| 118 --EDERRAHTLRDAFGMEELADRILLMDNQRFIE 149
                                       ..4457778888888899999*********9876 PP

>> MtrA  Tetrahydromethanopterin S-methyltransferase, subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.022     2e+02      53     116 ..     129     189 ..     121     198 .. 0.70
   2 ?    8.1   0.0   0.00021       1.9      46      82 ..     228     264 ..     199     270 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.022
                                       THHHHHHHHHHHT-TT--EEEEEE---TTT-HHHHHHHHHHH-B-TTSBBTT--SSS-B-SSS- CS
                              MtrA  53 nlGiekvvanvisnpnirflivtGaevkGhitGqalkalhenGvdkekkivgakGaiPfienlt 116
                                        +G+e +  +++   n rf+ + G+e     +  a++ + ++ v +  ++++   ++Pf   lt
  gi|474933639|ref|YP_007687221.1| 129 AFGMEELADRILLMDNQRFIETGGTEYVANDALGAVEDMLKDAVVELARLLD---TVPFFSTLT 189
                                       6799999999999999***999999966555555555555555544444443...456655555 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00021
                                       EE----TTHHHHHHHHHHHT-TT--EEEEEE---TTT CS
                              MtrA  46 aGplktenlGiekvvanvisnpnirflivtGaevkGh 82 
                                       +      ++  e+v +nv   + ir  i++G+e kGh
  gi|474933639|ref|YP_007687221.1| 228 CCDAAISDIEAERVCSNVTDHTGIRPEIISGTEPKGH 264
                                       55556677889************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1892.80
//
Query:       gi|474933640|ref|YP_007687222.1|  [L=238]
Description: RNA methyltransferase, TrmH family, group 1 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-31  108.0   0.0    5.4e-31  107.7   0.0    1.2  1  SpoU_methylase   SpoU rRNA Methylase family
     0.0022   17.9   0.0       0.15   11.9   0.0    2.2  1  Methyltrn_RNA_4  SAM-dependent RNA methyltransferase


Domain annotation for each model (and alignments):
>> SpoU_methylase  SpoU rRNA Methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.7   0.0     6e-35   5.4e-31       2     142 .]       4     154 ..       3     154 .. 0.88

  Alignments for each domain:
  == domain 1  score: 107.7 bits;  conditional E-value: 6e-35
                                       EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHH.EEEESSHHHHHHHHCCCTEE CS
                    SpoU_methylase   2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevle.lkvvdsleealkelkeegfa 77 
                                       ++vv+v+++ +gN+GaiaR++++fg++el+lv+p++     ++a++ + +   +l+ +++ +++eea+k++  + + 
  gi|474933640|ref|YP_007687222.1|   4 IRVVVVGPKFEGNVGAIARCCANFGVTELYLVNPCEI---GETAMNRSKHGDYILQnAVICTTFEEAVKDCFLV-VG 76 
                                       79*******************************8886...77777777788888877****************9.66 PP

                                       EEEEST.T-SEGCCSHHH............TTEEEEEEBTTTBS-HHHHCTSSEEEE----TTSSS--HHHHHHHHH CS
                    SpoU_methylase  78 lvatsl.kgkslseidlk............ekvalvfGnEdkGlsnelleladrlvkIpmsgeveSLNvavAvaill 141
                                       + +t + ++k++++i ++            ek+alvfG+Ed Gl + +l+++d lv+Ip + +++ +N++++v+++l
  gi|474933640|ref|YP_007687222.1|  77 TSGTVTkGDKNYTRIPVPirefaegcrgysEKIALVFGREDIGLFQTELNRCDVLVTIPAHDDYPVMNLSHSVGVVL 153
                                       666655577788877544555557777777**********************************************9 PP

                                       H CS
                    SpoU_methylase 142 y 142
                                       y
  gi|474933640|ref|YP_007687222.1| 154 Y 154
                                       9 PP

>> Methyltrn_RNA_4  SAM-dependent RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   1.6e-05      0.15      30     164 ..      19     140 ..      14     158 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.6e-05
                                       HHHHHHHHTT-SEEEEE---HHHHHHHHHHHHHHHTSGGGGT-SSSHHHHTTEEEESSHHHHHHHHHHHHSS--EEE CS
                   Methyltrn_RNA_4  30 DiaRsartygvkkyyvvtpleaqrelverilehWtegagaeynpdRkealslvkvvesleealeeiekeegkkplvv 106
                                        iaR++  +gv+++y+v+p+e  ++ ++r  +h     g          l++  +++++eea+++     g++ +v 
  gi|474933640|ref|YP_007687222.1|  19 AIARCCANFGVTELYLVNPCEIGETAMNRS-KH-----G-------DYILQNAVICTTFEEAVKDCFLVVGTSGTVT 82 
                                       69*****************98766555442.22.....2.......2346666666667777777766667666666 PP

                                       E--SS--SS-B-HHHHHHHHHH--S-EEEEE--.TT---HHHHTT-SEEB--TTTTSS- CS
                   Methyltrn_RNA_4 107 atsArkkentvsyeelrelleeeekpvlllfGt.gwGlaeevlekadyiLepirgasey 164
                                         + + ++  v ++e+ e ++  ++++ l+fG    Gl +  l+++d+ L  i ++++y
  gi|474933640|ref|YP_007687222.1|  83 KGDKNYTRIPVPIREFAEGCRGYSEKIALVFGReDIGLFQTELNRCDV-LVTIPAHDDY 140
                                       666666666666777777777777777777775246777777777764.4456666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1615.96
//
Query:       gi|474933641|ref|YP_007687223.1|  [L=107]
Description: hypothetical protein TALC_00048 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       208  (0.0116013); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 703.77
//
Query:       gi|474933642|ref|YP_007687224.1|  [L=302]
Description: Sugar kinase, ribokinase family [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-39  134.1   0.0    6.8e-39  134.0   0.0    1.0  1  PfkB      pfkB family carbohydrate kinase


Domain annotation for each model (and alignments):
>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.0   0.0   3.8e-43   6.8e-39       3     301 ..       4     289 ..       2     290 .. 0.92

  Alignments for each domain:
  == domain 1  score: 134.0 bits;  conditional E-value: 3.8e-43
                                       EEEEEEEEEEEEEEECSSH..TTSEEEESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTTE CS
                              PfkB   3 kvvviGealidliavsekl..egelvevktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkegv 77 
                                        + v+G++ id i    k+   +e+v v t + + GG g N+A+++a+lg+ +++ ++vG D+  +++++ l+ +g+
  gi|474933642|ref|YP_007687224.1|   4 FLTVYGHVTIDQIVSIGKFpgINETVDVLTKKTTLGGTGSNIAMVAAKLGVPTSLSSFVGPDF-PDRFRRDLEGSGL 79 
                                       5789******9999999999999999*************************************.************* PP

                                       EETTEEEESSSEEEEEEEEETTTSEEEEEEEEGGGGGHHHHHHHHHHHHHGCTSEEEEESEECTTSHHHHHHHHHHH CS
                              PfkB  78 dtdyvkidedtrtglalivvdedgertivfnrgaaadltkeeleededlleeadllyisgllsselpeavleelaea 154
                                         d  + ++d +t+ a+++++ + ++  +f++g+   +tk    + +++ + ++ +++++    + p+ +l++++e+
  gi|474933642|ref|YP_007687224.1|  80 IMDEFVTVDDYETSQATVINTPELQQKCIFYQGPLGFATKIGK-DLLNNASRSERVHFCT----GEPDYYLHLMEEL 151
                                       ***********************99***************753.6666667777777777....9************ PP

                                       HHHTTEEEEEECESSSHH....HHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEE CS
                              PfkB 155 aknggtfdpnlldplgaq....fkeallellaladllkpneeElealtgekledieealaalhklkakgaktvvvtl 227
                                       + + +      ldp+ +      ke+l++ l+la++l++ne+E++ + ++   + +++l+           +vv t 
  gi|474933642|ref|YP_007687224.1| 152 RGKTDV----ALDPSQETyrlwPKERLEKGLPLASALFCNEYEAKVIEERL--NLKSVLDIDL-------PLVVRTD 215
                                       **9995....5555555555557**********************999999..8888888854.......6****** PP

                                       GGGEEEEEETTEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHTSSSSSTCSCC CS
                              PfkB 228 GkeGalvvekdgelkvpavpkvkvvDttGAGDsfvggflaallegksleealrfanavAalvvqkkgaiaslpt 301
                                       G++G++++ +++   +p v++ +vvD+tG GDs+ +gf ++l +g s++++l +a+ ++++v++k+ga +++pt
  gi|474933642|ref|YP_007687224.1| 216 GERGSQAKIGGKIESIPCVKADNVVDPTGCGDSYRAGFYSGLFHGYSVKDSLILASSTSSFVIEKTGALTNIPT 289
                                       ********************************************************************999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1939.20
//
Query:       gi|474933643|ref|YP_007687225.1|  [L=177]
Description: putative nucleotide kinase (CMP and AMP kinases -like protein) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-24   85.0   0.2    8.1e-24   84.6   0.2    1.1  1  AAA_18    AAA domain
    2.5e-08   34.3   0.0    3.4e-08   33.9   0.0    1.3  1  AAA_28    AAA domain
    5.1e-06   26.7   0.6      0.037   14.2   0.1    2.4  2  AAA_33    AAA domain
    4.4e-05   23.2   0.0     0.0019   17.9   0.0    2.1  2  CoaE      Dephospho-CoA kinase
    0.00052   19.5   0.0    0.00066   19.2   0.0    1.2  1  KTI12     Chromatin associated protein KTI12
    0.00055   20.0   0.1       0.39   10.9   0.0    2.3  2  UPF0180   Uncharacterised protein family (UPF0180)
     0.0026   18.2   0.2      0.023   15.1   0.2    2.0  1  AAA_17    AAA domain
  ------ inclusion threshold ------
      0.028   14.7   0.1      0.036   14.3   0.1    1.5  1  AAA_22    AAA domain
      0.037   13.9   0.1        5.6    6.8   0.0    2.1  2  dNK       Deoxynucleoside kinase
      0.055   12.8   0.1       0.15   11.4   0.1    1.6  1  ATPase    KaiC
      0.085   13.2   0.2        0.1   13.0   0.2    1.4  1  AAA_16    AAA ATPase domain
       0.97    9.3   2.5        5.1    7.0   1.3    2.2  2  NTPase_1  NTPase


Domain annotation for each model (and alignments):
>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.6   0.2   5.4e-27   8.1e-24       1     130 []       4     121 ..       4     121 .. 0.92

  Alignments for each domain:
  == domain 1  score: 84.6 bits;  conditional E-value: 5.4e-27
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegkn 76 
                                       I++tGtpG+GKt+++ eL++r g+ +v  ++ ++++gll e d++  +++  +d++  ++ l++ ++      + + 
  gi|474933643|ref|YP_007687225.1|   4 IAITGTPGTGKTSVSGELRDR-GYeVVDANEHLRKHGLLGEKDEA--RDTYNVDMEAFNSSLEEYRR------KDGL 71 
                                       89******************9.799********************..99999999995555555555......5689 PP

                            AAA_18  77 lvidghlaeleseaakdikkvvLtaspeelleRlekRgyeeakikeneeaeild 130
                                       + id+hla+ ++ +++    +vL+++p+el+ Rl+kRgy+eak +en +ae ld
  gi|474933643|ref|YP_007687225.1|  72 VFIDSHLAHQCDCSRI----IVLRCEPHELAGRLRKRGYSEAKVRENVQAEVLD 121
                                       9**************9....*******************************985 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0   2.3e-11   3.4e-08       2      89 ..       4      85 ..       3     121 .. 0.76

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 2.3e-11
                            AAA_28  2 ivitGgestGKTtlleaLaargypvv..pEaareileeklakgedalpwvedllafaervleeqleeeaaaaankvlfc 78
                                      i+itG+++tGKT+++ +L +rgy+vv   E  r+    + +++ ++   v d+ af++ ++e ++       +++++f+
  gi|474933643|ref|YP_007687225.1|  4 IAITGTPGTGKTSVSGELRDRGYEVVdaNEHLRKHGLLGEKDEARDTYNV-DMEAFNSSLEEYRR-------KDGLVFI 74
                                      99************************999999987666655555555555.9****999887765.......4677777 PP

                            AAA_28 79 DrglldtlaYa 89
                                      D  l   +  +
  gi|474933643|ref|YP_007687225.1| 75 DSHLAHQCDCS 85
                                      77776665555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.1   2.4e-05     0.037       1      39 [.       3      40 ..       3      75 .. 0.69
   2 !   10.6   0.1   0.00032      0.48      91     134 ..      78     121 ..      76     125 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.4e-05
                            AAA_33  1 lvllvGlpGsGKstlaerllkklgavllssdtlrrrlfg 39
                                      l+ + G pG+GK+ ++ +l + +g+++++ ++ +r++  
  gi|474933643|ref|YP_007687225.1|  3 LIAITGTPGTGKTSVSGEL-RDRGYEVVDANEHLRKHGL 40
                                      67789************96.599*******996665543 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00032
                            AAA_33  91 larrlgvpvrivvvetdeetlkeRlakRaang.ddrsevpeeald 134
                                       la+++++  ri+v+++ + +l+ Rl+kR  ++ ++r +v  e+ld
  gi|474933643|ref|YP_007687225.1|  78 LAHQCDCS-RIIVLRCEPHELAGRLRKRGYSEaKVRENVQAEVLD 121
                                       78888866.9********************987789999999988 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.3e-06    0.0019       2      33 ..       3      34 ..       2      49 .. 0.90
   2 ?    3.5   0.0     0.032        48     121     157 ..      83     118 ..      55     123 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.3e-06
                                      EEEEEESTTSSHHHHHHHHHHTT-EEEEHHHH CS
                              CoaE  2 ivgltGgiasGKstvanlfadlgvpivDaDlv 33
                                      ++++tG  ++GK+ v+  ++d g+++vDa   
  gi|474933643|ref|YP_007687225.1|  3 LIAITGTPGTGKTSVSGELRDRGYEVVDANEH 34
                                      699**************************875 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.032
                                       GSSEEEEEE--HHHHHHHHHHCCTSTHHHHHHHHHHS CS
                              CoaE 121 liervlvvdvelelqveRlvardgvseeevkaiiaaQ 157
                                        ++r++v+ +e+++   Rl +++g se++v++ ++a 
  gi|474933643|ref|YP_007687225.1|  83 DCSRIIVLRCEPHELAGRL-RKRGYSEAKVRENVQAE 118
                                       4689*******98877775.66799999999988876 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   4.4e-07   0.00066       1      41 [.       1      59 [.       1      81 [. 0.69

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4.4e-07
                                      E.EEEEE--TTSSHHHHHHHHHHHHHH..................TT--EEEE-THHHH CS
                             KTI12  1 MpLvvltGlPssGKstrakeLakalee..................ekrsvvviddeslg 41
                                      MpL+ +tG P +GK++++ eL++   e                  e r+ + +d e+++
  gi|474933643|ref|YP_007687225.1|  1 MPLIAITGTPGTGKTSVSGELRDRGYEvvdanehlrkhgllgekdEARDTYNVDMEAFN 59
                                      *********************98776655555555555555555444555555555555 PP

>> UPF0180  Uncharacterised protein family (UPF0180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00026      0.39      11      28 ..      16      33 ..      13      55 .. 0.84
   2 !    6.9   0.0    0.0047       7.1      13      49 ..      98     134 ..      95     149 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00026
                           UPF0180 11 nvkeaLrekGYeVvdlet 28
                                       v+ +Lr++GYeVvd ++
  gi|474933643|ref|YP_007687225.1| 16 SVSGELRDRGYEVVDANE 33
                                      68899**********997 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0047
                           UPF0180  13 keaLrekGYeVvdleteedaqsvdaiVvtGqdtnvmg 49 
                                       +  Lr++GY+  +++++ +a+  d+i ++ +dt++  
  gi|474933643|ref|YP_007687225.1|  98 AGRLRKRGYSEAKVRENVQAEVLDVILCEAMDTDIPV 134
                                       6679***********9999*********999999843 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.2   1.5e-05     0.023       1     122 [.       7     104 ..       7     121 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.5e-05
                                       EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEE CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrklpleekkelqkeaaekiaeeakkkgvlvd 77 
                                       +G PG GK+ ++ +l ++ g++++ a + lr+     gl  ++de r+ ++++ +++   ++e  ++   ++ v +d
  gi|474933643|ref|YP_007687225.1|   7 TGTPGTGKTSVSGEL-RDRGYEVVDANEHLRKH----GLLGEKDEARDTYNVDMEAFNSSLEEYRRK---DGLVFID 75 
                                       69**********888.677*******9999976....887889999999999999888888764444...5678999 PP

                                       E-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHH CS
                            AAA_17  78 ghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkd 122
                                        h                  ++ + + ii+l ++p e+  r+ k+
  gi|474933643|ref|YP_007687225.1|  76 SHLA----------------HQCDCSRIIVLRCEPHELAGRLRKR 104
                                       9984................4566688888888888888888877 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   2.4e-05     0.036       7      51 ..       3      59 ..       2     156 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.4e-05
                            AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeakaee............erpevvfvtlpsst 51
                                      ++++tG +GtGKT +  +l+++  e+ +a+e            e ++++ v++ + +
  gi|474933643|ref|YP_007687225.1|  3 LIAITGTPGTGKTSVSGELRDRGYEVVDANEhlrkhgllgekdEARDTYNVDMEAFN 59
                                      689*************99999987777777777777777766655555666655555 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0037       5.6       1      68 [.       4      65 ..       4      79 .. 0.73
   2 ?    5.2   0.0     0.011        16     123     149 ..      84     110 ..      73     124 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0037
                                      EEEEESTTSSHHHHHHHHHCCSTCEEEE-HHHHCCSSSS.HHHHHHHHSHHHHHHHHHHHHHHHHHHHH CS
                               dNK  1 ivveGnIgaGKstlvklLskklgvkvfeEpvdkwtnvqk.nlLekfYkdpsrwsfalqtyvllsrlkqq 68
                                      i++ G+ g GK+++   L+++      +E+vd ++  +k  lL    kd +r ++++++++++s l+++
  gi|474933643|ref|YP_007687225.1|  4 IAITGTPGTGKTSVSGELRDRG-----YEVVDANEHLRKhGLLG--EKDEARDTYNVDMEAFNSSLEEY 65
                                      899****************998.....77888885555433333..36777777777777777777666 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.011
                                       -SEEEEEE--HHHHHHHHHHCTTCCCT CS
                               dNK 123 pdlliYLkasletclerikkRgreeek 149
                                        + +i L++++ ++  r++kRg +e k
  gi|474933643|ref|YP_007687225.1|  84 CSRIIVLRCEPHELAGRLRKRGYSEAK 110
                                       67899*****************98866 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   9.7e-05      0.15      22      93 ..       4      81 ..       2     111 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.7e-05
                            ATPase 22 vlitGepGtGKtifalqFlikgaekyg......epgvfvtveepaedlrenakslGwdlekleeegklaiidasesae 93
                                      + itG+pGtGKt ++ +   +g e ++      + g++   +e       +++++   le++++++ l++id     +
  gi|474933643|ref|YP_007687225.1|  4 IAITGTPGTGKTSVSGELRDRGYEVVDanehlrKHGLLGEKDEARDTYNVDMEAFNSSLEEYRRKDGLVFIDSHLAHQ 81
                                      78**********999876555544433111111568888888888888889999999999999998888888765554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   6.8e-05       0.1      26      46 ..       3      23 ..       1     122 [. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.8e-05
                            AAA_16 26 lvllsGesGvGKsslvrellr 46
                                      l+ ++G +G+GK+s+  el++
  gi|474933643|ref|YP_007687225.1|  3 LIAITGTPGTGKTSVSGELRD 23
                                      789************999996 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   1.3    0.0034       5.1       2      16 ..       4      18 ..       3      31 .. 0.79
   2 ?    1.7   0.0      0.14   2.2e+02      45     102 ..      24      75 ..      17      76 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0034
                                      EEEE--TTSSHHHHH CS
                          NTPase_1  2 vfiTGppGvGKtTlv 16
                                      ++iTG pG+GKt + 
  gi|474933643|ref|YP_007687225.1|  4 IAITGTPGTGKTSVS 18
                                      78**********754 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.14
                                       -EEEEEET.T--EEEEEETT..---SSEETTEEE-HHHHHHHHHHHHHHHHHHH-EEEE- CS
                          NTPase_1  45 igFkivdlasgeegiLarve..akreprvgkyvvdvesfeelalealrkalseadviviD 102
                                        g+++vd     ++ L + +  +++    + y vd+e+f++     l++  ++ +++ iD
  gi|474933643|ref|YP_007687225.1|  24 RGYEVVDA----NEHLRKHGllGEKDEARDTYNVDMEAFNSS----LEEYRRKDGLVFID 75 
                                       57888888....344444444455667889999999998875....44444566777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1153.27
//
Query:       gi|474933644|ref|YP_007687226.1|  [L=221]
Description: Phosphatidylglycerophosphate synthase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-11   45.3   5.4    2.6e-11   44.1   0.6    2.7  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
  ------ inclusion threshold ------
        0.2   12.1  10.9        2.7    8.5   0.9    2.4  2  MerC             MerC mercury resistance protein
       0.71   10.4   3.1       0.76   10.3   0.2    2.3  2  DUF4231          Protein of unknown function (DUF4231)


Domain annotation for each model (and alignments):
>> CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.6   4.3e-15   2.6e-11       3      66 .]      26      93 ..      24      93 .. 0.89
   2 ?    2.8   0.4     0.033     2e+02      10      40 ..     115     164 ..      98     196 .. 0.70

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 4.3e-15
                                      HHHHHHHHHHHHHHHHHGGGS-H.......HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
                   CDP-OH_P_transf  3 PnaiTllrlllsvlailllltyyp.....lvlailllliasltDalDGklARrlnqvstlGkllDslaD 66
                                      Pn+i++l+l+ ++l+ + l +++      l+la  l+++++ +DalDGk+A+  n+ s  G++lD++ D
  gi|474933644|ref|YP_007687226.1| 26 PNVISWLGLIVAFLSGVAL-YFSFdhhwmLILASGLVILSGYFDALDGKIAKLANKCSVKGDFLDHVFD 93
                                      ***********99999755.33336799999999999*******************999*******998 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.033
                                       HHHHHHHHHHGGGS-H.......................HHHHHHHHHHHHH CS
                   CDP-OH_P_transf  10 rlllsvlailllltyyp.....................lvlailllliaslt 40 
                                       ++++ ++ + ll +y++                     +vl++l+ li+ l+
  gi|474933644|ref|YP_007687226.1| 115 GIFA-IIGV-LLTSYMGtqaqaigakrlydgllgradrVVLCFLFPLIQYLA 164
                                       4443.2233.333444477888888888888888888877777777654433 PP

>> MerC  MerC mercury resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   3.3   0.00064       3.8      25      79 ..      15      74 ..      12     128 .. 0.57
   2 ?    8.5   0.9   0.00045       2.7      12      60 ..     151     200 ..     150     208 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00064
                              MerC 25 lpllglsflasellhqvllilvvaigllalvvgyrrhrktsvlvlgalGllill......v 79
                                      +p+   ++  ++ +  +l ++v+ ++++al++++  h+ +++l+ g++ l  ++      +
  gi|474933644|ref|YP_007687226.1| 15 APVARRLINVNPNVISWLGLIVAFLSGVALYFSFD-HHWMLILASGLVILSGYFdaldgkI 74
                                      55555554448889999999999999999999976.5556666666555555554444442 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00045
                              MerC  12 vvhClllPvllallpllglsfla.sellhqvllilvvaigllalvvgyrr 60 
                                       vv C+l+P++  l+  l  ++++ + l   +l+++++ +++++++ + +r
  gi|474933644|ref|YP_007687226.1| 151 VVLCFLFPLIQYLACYLDYGWIDpDNLAISWLAVMMIWFAVVGNLTAIQR 200
                                       688******************77699999999999999999888877665 PP

>> DUF4231  Protein of unknown function (DUF4231)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.2   0.00013      0.76      43      74 ..      22      53 ..      12      55 .. 0.89
   2 ?   -0.0   0.2       0.2   1.2e+03      25      54 ..     151     190 ..     113     211 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00013
                           DUF4231 43 vsvlkiltallsalvailaaleeffrykerWr 74
                                       +v + ++++l+++va+l+++   f +  +W+
  gi|474933644|ref|YP_007687226.1| 22 INVNPNVISWLGLIVAFLSGVALYFSFDHHWM 53
                                      6788999************************7 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.2
                           DUF4231  25 ivlgallpilvs..........sklgagvsvlkiltalls 54 
                                       +vl++l+p+++           + ++   s+l+++  + +
  gi|474933644|ref|YP_007687226.1| 151 VVLCFLFPLIQYlacyldygwiDPDNLAISWLAVMMIWFA 190
                                       4566666666656666665544333444444444433333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1385.37
//
Query:       gi|474933645|ref|YP_007687227.1|  [L=83]
Description: Eukaryotic-type DNA primase, large subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-09   37.3   1.5    1.8e-08   34.1   1.5    1.8  1  DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large s


Domain annotation for each model (and alignments):
>> DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   1.5   9.9e-13   1.8e-08     142     260 ..       1      63 [.       1      69 [. 0.82

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 9.9e-13
                                       --CHHHHCCCHCHST..HHHHHH.HTHCHCHHHCC-STT--------HHHHHHS....TT---S.-HHHH.HHHHHH CS
                   DNA_primase_lrg 142 lsldeilelwkeaftrteekFdk.eyrynirhnyGkegkrtnyspysCekiltkpppgkgdahg.Cpfrhdpdklkt 216
                                       ++ ++i++++ ++     ++Fd+   +y+i+h+ G+  +   y+p++C ++         +++g C+   +pd+l +
  gi|474933645|ref|YP_007687227.1|   1 MTYEQIVAVFAQS-----PDFDEsVSEYQIKHITGELNGTEGYTPPECGTM---------KTNGiCF---NPDSLCE 60 
                                       78899******98.....*****7777********6666667*********.........99999*4...8999943 PP

                                       HHHHTT..HHHHHHHHHHHHTT.HHHHHHHHHHHHHS-TTT-SS CS
                   DNA_primase_lrg 217 lLqeyglseediedilesvkegeyqvaCtkvFelthkcerdeik 260
                                                                                 ik
  gi|474933645|ref|YP_007687227.1|  61 H-----------------------------------------IK 63 
                                       3.........................................33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.33s 00:00:00.83 Elapsed: 00:00:00.53
# Mc/sec: 475.24
//
Query:       gi|474933647|ref|YP_007687229.1|  [L=244]
Description: Eukaryotic-type DNA primase, large subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-06   26.6   0.0    5.1e-06   26.1   0.0    1.2  1  DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large s
  ------ inclusion threshold ------
       0.11   11.4   0.0       0.18   10.7   0.0    1.3  1  DUF3480          Domain of unknown function (DUF3480)


Domain annotation for each model (and alignments):
>> DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   5.6e-10   5.1e-06       9     117 ..     139     239 ..     132     244 .] 0.80

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 5.6e-10
                                       HHHHHTT.-G.......GS-EETTEEEE-HHHHHHHHHHHHHHHHHH..........HHGGGSSS---HHHHHHHCT CS
                   DNA_primase_lrg   9 dvldlvk.rr.......rvllkkGyaylpkeeleslllekfrkrlekalestkeslpeleeeikederekleellea 77 
                                       d+l++    r       ++ l++Gy+ l+ke++ +ll +++r+r+e +l     + p+  ++i +++ +k++ +l++
  gi|474933647|ref|YP_007687229.1| 139 DFLRFSYvMRavewkliNMDLRDGYVRLEKEKFTRLLQNAYRSRIEAELPL---NVPDSFRKIVSQDVSKVQLALNE 212
                                       55544443333455578******************************9999...55555566789999999999999 PP

                                       --.............TTSSTTGGSHHHHTT--HHHHCCHH CS
                   DNA_primase_lrg  78 lsesyvaedvqeeedskisaknidklakesfPpCmrelle 117
                                       ++             +++s+   + ++ e +PpC++++++
  gi|474933647|ref|YP_007687229.1| 213 MK-------------NRLSPTGGEGVKDEYLPPCIKAIIS 239
                                       99.............7888888889999*********987 PP

>> DUF3480  Domain of unknown function (DUF3480)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0     2e-05      0.18      58     105 ..     132     179 ..     102     185 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 2e-05
                           DUF3480  58 tilnlLvDfrnyqYtlpkikglvihleekkttikipknrydevlkvln 105
                                       t+   ++Df  ++Y ++ ++  +i+++ +  ++++ k+++  +l+   
  gi|474933647|ref|YP_007687229.1| 132 TVNMHFADFLRFSYVMRAVEWKLINMDLRDGYVRLEKEKFTRLLQNAY 179
                                       666679**********************************99887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1742.84
//
Query:       gi|474933648|ref|YP_007687230.1|  [L=38]
Description: hypothetical protein TALC_00055 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       184  (0.0102627); expected 358.6 (0.02)
Passed bias filter:                      173  (0.00964917); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.42
# Mc/sec: 269.53
//
Query:       gi|474933649|ref|YP_007687231.1|  [L=539]
Description: putative Fe-S oxidoreductase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.2e-18   66.3   0.0    1.2e-17   64.7   0.0    1.8  2  Radical_SAM  Radical SAM superfamily
    0.00071   19.8   0.0     0.0016   18.7   0.0    1.5  1  HHH_3        Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.057   13.3   0.0       0.16   11.9   0.0    1.8  1  HHH          Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.83     5e+03      25      72 ..      77     122 ..      58     159 .. 0.72
   2 !   64.7   0.0   2.1e-21   1.2e-17       3     166 ..     174     367 ..     172     368 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.83
                                       HHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  25 rgrslsveeileevkelkaekgvkevilgggepllypdfvellerlak 72 
                                         + +s+ +  +e++el + +  ++  ++gg   + pd + + +r ++
  gi|474933649|ref|YP_007687231.1|  77 GKYLRSMPMSGRELREL-VPR-LEGWKMVGGSAAFSPDSEGFDFRVKR 122
                                       55667777777788888.666.88888888877777776655555554 PP

  == domain 2  score: 64.7 bits;  conditional E-value: 2.1e-21
                                       EESEESS-....-TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS..............T CS
                                       xxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..............x RF
                       Radical_SAM   3 vtrgCnlr....CsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly..............p 61 
                                        +rgC++     CsfC+ p+     g++ ++s+e+il+e+++l +e gv++v +gg++ ++               p
  gi|474933649|ref|YP_007687231.1| 174 SYRGCHRWksggCSFCIEPS----KGKVLMRSPEDILAEARRL-KELGVRNVRIGGQTCIVSygatdlesgcprpnP 245
                                       667777655555*******5....8******************.7**********7777776555555555555557 PP

                                       THHHHHHHHHHTC......CCTEEEEEEECSSCHGHHHHHHHHHTT..-SEEEEEEBSSSHHHHHHHHTCTSHHHHH CS
                                       xxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  62 dfvellerlakla......vpgiritvetngtlpdeeklerllelg..vdrvslgleaaddekvlklmnrghtfeev 130
                                         ve+l++  k+       v++ + +v++ ++  + +++e+l++     +++++gle+ad+  v+k +n + + e+v
  gi|474933649|ref|YP_007687231.1| 246 GAVEELFEGLKELgfdnlcVDNANPSVIAAYPEESSRIIETLARCCssGNVLAMGLESADPA-VQKANNLNSSAEQV 321
                                       7777777777777899999999999999999998899999999988999*************.******99****** PP

                                       HHHHHHHHHTTSET..........EEEEEEEBTTTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 131 lealeklreagikr..........vvdrivglpGendeeleellel 166
                                       lea+++ ++ g++r            ++i gl Ge+ ++++  l+l
  gi|474933649|ref|YP_007687231.1| 322 LEAVRLVNRIGGERgetglprilpGLNIICGLDGETAATYDMDLDL 367
                                       ***********8888888888999************9998888776 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   2.7e-07    0.0016       4      47 ..     482     521 ..     480     523 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.7e-07
                             HHH_3   4 vgvdiNtAsaeeLqklpGlgpklAknIvayReknGpfksreeLl 47 
                                       +++diNt   + L+ lpG+g k A  +   R    pf++ ++L 
  gi|474933649|ref|YP_007687231.1| 482 HPFDINTMPMSALSALPGIGRKRAATLAVKR----PFRDYDDLS 521
                                       689****************************....*******96 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.7e-05      0.16      13      26 ..     494     507 ..     491     509 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.7e-05
                                       HHTSTT-SHHHHHH CS
                               HHH  13 LlalPGVGpktAea 26 
                                       L alPG+G+k+A  
  gi|474933649|ref|YP_007687231.1| 494 LSALPGIGRKRAAT 507
                                       89**********75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (539 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.47
# Mc/sec: 3416.14
//
Query:       gi|474933650|ref|YP_007687232.1|  [L=480]
Description: Malic enzyme [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-30  105.7   0.0      4e-28   98.4   0.0    2.5  1  malic          Malic enzyme, N-terminal domain
    2.6e-21   76.1   0.7      7e-20   71.4   0.7    2.2  1  Malic_M        Malic enzyme, NAD binding domain
  ------ inclusion threshold ------
      0.079   13.2   0.1       0.23   11.7   0.1    1.8  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain


Domain annotation for each model (and alignments):
>> malic  Malic enzyme, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.4   0.0   6.8e-32     4e-28       2     182 .]      60     192 ..      59     192 .. 0.96

  Alignments for each domain:
  == domain 1  score: 98.4 bits;  conditional E-value: 6.8e-32
                                       TTECCCCCCHHCCCHHHHHHHHSTTCHHHHHHHHHHHGGCHHSCCCEGGGETCHHHHHTTSS.SS..EEEEE-SSSB CS
                             malic   2 eknetlfykllkekleellpivYtPtvgeacqeyseeyrkarglylsikdkekikeilknlpeedvkvivvtdgeri 78 
                                       +k+et++++ +++   ++++i+Y+P+v+++c++++ +++ ++ +++ + ++                v+vv+dg+r+
  gi|474933650|ref|YP_007687232.1|  60 GKIETVPKACIRNF--DDFSIWYSPGVAAPCKDIAANPDMVY-EHTWKWNT----------------VAVVSDGTRV 117
                                       58899999999999..9*************************.99999999................9********* PP

                                       TTTBS-G.HHHHHHHHHHHHHHHHHHS-EGGGEEEEEECS-BS.HHHHC.TT..S.SSB...SHHHHHHHHHHHHHH CS
                             malic  79 LGlGdlG.vagvgimvGKlaLytalagidPekvlpvvldvgtnneelledplYlGlrkkRvkgeeydefvdefveav 154
                                       LGlGd+G  a++++m+GK +L++ l+g+d   ++p++ld++                           + d+++e+v
  gi|474933650|ref|YP_007687232.1| 118 LGLGDIGpEAAMPVMEGKSMLFKYLGGVD---CVPICLDTK---------------------------DPDKIIETV 164
                                       *****************************...*********...........................99******* PP

                                       HHHHGCTSEEEE-S--CCHHHHHHHHHC CS
                             malic 155 kelfppkaliqfEDfkaknafeileryr 182
                                       + ++p++++i++ED++++++f+il+ +r
  gi|474933650|ref|YP_007687232.1| 165 RLIAPSFGGINLEDISNPKCFDILDELR 192
                                       ************************9886 PP

>> Malic_M  Malic enzyme, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.4   0.7   1.2e-23     7e-20       2     245 ..     205     422 ..     204     437 .. 0.86

  Alignments for each domain:
  == domain 1  score: 71.4 bits;  conditional E-value: 1.2e-23
                                       HHHHHHHHHHHHHHHHHH-S-GGG--EEEEC-SHHHHHHHHHHHHHHHTTTS-HHHHHTTEEEEETTEE-BTT-S-- CS
                           Malic_M   2 qgTaavalagllaalkitgkklseqkivvlGaGsagiGiaeqivealvkeGlseeeakkkiylvDrkGLltedrekl 78 
                                       qgTa+v +ag ++a+k  gk++ + ++ ++GaG+a++ ia +++++    G +     +++ + D+kG+l  +r++l
  gi|474933650|ref|YP_007687232.1| 205 QGTATVEVAGAMNAMKFVGKRFDDANVTIVGAGAASLAIARLLLST----GFKP----DHLCMCDSKGILNGERDDL 273
                                       9**************************************9988765....5544....5899*************** PP

                                       -TTTGGGSBS--SS--S....SHHHHHHHH--SEEEE-SS.SSS-S-HHHHHHHHHHSSS-EEEE--SSGGGSSS-H CS
                           Malic_M  79 eeekkpfakkkeelkeakdkltLeevvkkvkptvliGlsg.vagafteeivremaksterPiilplSNPtskaEata 154
                                       ++ ++   + +++++ a +k  ++e++k   ++ li +s   +g++  e +  ma+     ++++  NP    E  +
  gi|474933650|ref|YP_007687232.1| 274 DDSHRLKREIAQKTNGAGKKGGMKEAIKG--ADLLIAASKpGPGTIPGEYLDGMADD---AVVFATANPVP--EIWP 343
                                       999887777778888888999******97..68999999725799******999875...69*******97..6778 PP

                                       HHHHHHTTT-SEEEESS----EEETSEEE--EE--GGGTHHHHHHHHHHTT-SS--HHHHHHHHHHHHTT--HHHHH CS
                           Malic_M 155 edvlkwtdgkalvasGsPfkpvelngktyeigQaNNayifPglglgvivarakritdemllaaaealaelvseeelk 231
                                        ++ +  +g  ++a+G          +   ++Q NN+  fP++  gv+ +rak+itdem  aaa++la++++e+ ++
  gi|474933650|ref|YP_007687232.1| 344 WEAKE--HGVKIFATG----------RSDFPNQVNNSMGFPAIFRGVLDVRAKTITDEMCIAAATELARYAEEKGIT 408
                                       77765..6899***98..........456799********************************************* PP

                                       TT-SS--GGGHHHH CS
                           Malic_M 232 egsllPelseirev 245
                                       e+ + P++se   +
  gi|474933650|ref|YP_007687232.1| 409 EDYIIPNMSEEDVF 422
                                       *******9974333 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   3.9e-05      0.23       1      21 [.     233     253 ..     233     259 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.9e-05
                                       EE--SHHHHHHHHHHHCCTEE CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfd 21 
                                       IvGaG+++l++A+lL   gf+
  gi|474933650|ref|YP_007687232.1| 233 IVGAGAASLAIARLLLSTGFK 253
                                       9*************9888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (480 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.26s 00:00:00.90 Elapsed: 00:00:00.45
# Mc/sec: 3204.49
//
Query:       gi|474933651|ref|YP_007687233.1|  [L=89]
Description: Translation elongation factor EF-1beta [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.7e-07   29.2   0.0    9.7e-07   28.9   0.0    1.1  1  EF1_GNE   EF-1 guanine nucleotide exchange domain


Domain annotation for each model (and alignments):
>> EF1_GNE  EF-1 guanine nucleotide exchange domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   5.4e-11   9.7e-07       5      87 ..       9      86 ..       6      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 5.4e-11
                                      EEEESSS---HHHHHHHHHH.HS-TSEE--.--EEE-SSS-EEEEEEEEESSS-G.GGGHHHHHHTTS-S.....SEEE CS
                           EF1_GNE  5 evkPeddetdleelekkvksikleglvwgeasklepiafGlkkLqiscvieddkv.stdeleekieeiegeledlVqsv 82
                                      +  Pe++e dl+ + +++  +  eg+++ e  k+ p+afGl k++  + i++       +le ++ +i g     +++v
  gi|474933651|ref|YP_007687233.1|  9 DLLPESTEIDLNTVIAAIPGVLPEGVKLLE-TKILPLAFGLMKVNAGFLIDEVSDhIGSDLEAALVSIAG-----IENV 81
                                      678*****************99999****6.*******************86544144688999888988.....7777 PP

                                      EEEEE CS
                           EF1_GNE 83 eivsf 87
                                      e vs 
  gi|474933651|ref|YP_007687233.1| 82 ECVST 86
                                      77765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       198  (0.0110436); expected 358.6 (0.02)
Passed bias filter:                      172  (0.0095934); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 584.13
//
Query:       gi|474933652|ref|YP_007687234.1|  [L=45]
Description: protein of unknown function (DUF1610) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.6e-05   22.8   8.4      0.064   13.2   0.3    2.4  2  DUF1610         Domain of unknown function (DUF1610)
  ------ inclusion threshold ------
      0.034   14.2  11.1      0.066   13.3   0.3    3.1  3  zf-ACC          Acetyl-coA carboxylase zinc finger domain
      0.047   13.4   8.8       0.83    9.4   0.1    2.5  2  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
      0.055   13.6   8.5        2.3    8.4   0.1    2.2  2  zf-Mss51        Zinc-finger of mitochondrial splicing suppres
      0.082   13.4   0.5      0.082   13.4   0.5    2.8  3  zf-H2C2_2       Zinc-finger double domain
      0.083   12.9   5.4        2.9    7.9   0.1    2.9  3  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
      0.099   12.5  10.1       0.28   11.1   0.1    2.9  3  TFIIS_C         Transcription factor S-II (TFIIS)
       0.16   12.4   7.1       0.43   11.1   7.1    1.6  1  zf-CHY          CHY zinc finger
       0.18   10.7   0.3       0.17   10.8   0.3    1.0  1  tRNA-synt_1f    tRNA synthetases class I (K)
       0.18   11.8  11.7       0.32   11.1  11.7    1.5  1  DZR             Double zinc ribbon
        0.2   11.6   8.1       0.75    9.7   0.3    2.6  3  HalOD2          Halobacterial output domain 2
        0.2   11.0  12.9        1.6    8.1   0.2    3.1  3  zf-TFIIB        Transcription factor zinc-finger
       0.24   10.9   0.8       0.24   10.9   0.8    3.1  3  zf-ribbon_3     zinc-ribbon domain
       0.26   11.2  13.7        4.1    7.4   0.1    3.0  2  zf-HIT          HIT zinc finger
       0.27   10.8   0.9       0.27   10.8   0.9    2.6  3  zf_C2H2_10      C2H2 type zinc-finger
       0.63   10.0   8.6       0.32   10.9   0.5    2.3  2  DUF3797         Domain of unknown function (DUF3797)
       0.79    9.7   8.2        1.6    8.7   8.2    1.6  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.97    9.4  11.9        1.9    8.5   0.1    3.1  3  zinc_ribbon_4   zinc-ribbon domain
       0.99    9.6   9.5         11    6.2   0.0    3.0  2  zf-RING_7       C4-type zinc ribbon domain
        1.1    8.9  10.1        1.6    8.4   0.3    2.7  3  Sgf11           Sgf11 (transcriptional regulation protein)
        1.1    9.6  11.4         51    4.3  11.4    2.1  1  C1_2            C1 domain
        1.4    9.1   9.4        8.9    6.6   0.1    2.1  2  Ribosomal_L37e  Ribosomal protein L37e
        1.5    8.5  15.6       0.19   11.4   2.9    2.2  2  zf-tcix         Putative treble-clef, zinc-finger, Zn-binding
        2.1    8.2  17.7        0.3   10.9   0.9    3.1  2  zinc_ribbon_2   zinc-ribbon domain
        2.1    6.1   5.5        2.1    6.1   5.5    1.0  1  PolC_DP2        DNA polymerase II large subunit DP2
        2.5    8.3  14.8        4.1    7.6   1.1    2.8  3  zf-AN1          AN1-like Zinc finger
        2.8    7.9   7.5       0.31   11.0   0.8    2.3  2  VP_N-CPKC       Virion protein N terminal domain
          3    8.0   7.0        7.2    6.8   0.2    2.1  2  DUF2752         Protein of unknown function (DUF2752)
        3.4    6.3   7.0        3.6    6.3   7.0    1.1  1  Dynactin_p62    Dynactin p62 family
        3.8    7.1  16.2       0.36   10.4   0.7    2.7  3  TF_Zn_Ribbon    TFIIB zinc-binding
        6.1    7.0  13.9         12    6.1   2.6    2.5  2  Zn-ribbon_8     Zinc ribbon domain
        7.8    6.3  17.7         10    5.9   0.9    3.2  3  Rubredoxin_2    Rubredoxin metal binding domain
        8.5    6.4   9.8    1.1e+02    2.9   9.8    2.0  1  HypA            Hydrogenase/urease nickel incorporation, meta


Domain annotation for each model (and alignments):
>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   2.5   0.00015     0.084      15      24 .]      10      19 ..       7      19 .. 0.89
   2 !   13.2   0.3   0.00012     0.064      13      23 ..      31      41 ..      29      41 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00015
                           DUF1610 15 vvFpCPNCGE 24
                                      + F CP+CGE
  gi|474933652|ref|YP_007687234.1| 10 TFFKCPKCGE 19
                                      679******9 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00012
                           DUF1610 13 ravvFpCPNCG 23
                                       +v + CPNCG
  gi|474933652|ref|YP_007687234.1| 31 QSVPYKCPNCG 41
                                      578899****9 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   0.00012     0.066       1      10 [.      11      20 ..      11      20 .. 0.90
   2 ?    1.8   0.2      0.48   2.6e+02       3       8 ..      24      29 ..      24      31 .. 0.80
   3 ?    5.4   1.0     0.035        19       3       8 ..      36      41 ..      35      41 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00012
                            zf-ACC  1 WtKCpsCgem 10
                                      ++KCp+Cge+
  gi|474933652|ref|YP_007687234.1| 11 FFKCPKCGEV 20
                                      79******96 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.48
                            zf-ACC  3 KCpsCg 8 
                                      +C++C 
  gi|474933652|ref|YP_007687234.1| 24 RCDRCR 29
                                      6****6 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.035
                            zf-ACC  3 KCpsCg 8 
                                      KCp Cg
  gi|474933652|ref|YP_007687234.1| 36 KCPNCG 41
                                      899998 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.1    0.0015      0.83      38      53 ..       5      20 ..       1      21 [. 0.78
   2 ?    5.2   5.2     0.031        17      41      52 ..      31      42 ..      25      43 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0015
                    zinc_ribbon_10 38 eeleevkyrCpkCgal 53
                                      e+  ++ ++CpkCg++
  gi|474933652|ref|YP_007687234.1|  5 EKHGNTFFKCPKCGEV 20
                                      5666788******985 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.031
                    zinc_ribbon_10 41 eevkyrCpkCga 52
                                      + v y+Cp+Cg+
  gi|474933652|ref|YP_007687234.1| 31 QSVPYKCPNCGF 42
                                      5789******96 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1    0.0043       2.3      12      23 ..       7      18 ..       2      22 .. 0.81
   2 ?    7.3   4.8     0.009       4.9      12      24 ..      30      42 ..      24      44 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0043
                          zf-Mss51 12 pkhvdfeCpdCG 23
                                      + +  f+Cp+CG
  gi|474933652|ref|YP_007687234.1|  7 HGNTFFKCPKCG 18
                                      56778******9 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.009
                          zf-Mss51 12 pkhvdfeCpdCGi 24
                                       ++v ++Cp+CG+
  gi|474933652|ref|YP_007687234.1| 30 DQSVPYKCPNCGF 42
                                      6789********7 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.5   0.00015     0.082       9      21 ..       6      18 ..       2      20 .. 0.85
   2 ?   -0.3   0.1       3.3   1.8e+03      17      22 ..      25      30 ..      24      33 .. 0.77
   3 ?    8.2   2.3    0.0063       3.4      14      21 ..      34      41 ..      29      44 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00015
                         zf-H2C2_2  9 HtgekpyeCplCd 21
                                       +g ++++Cp+C+
  gi|474933652|ref|YP_007687234.1|  6 KHGNTFFKCPKCG 18
                                      58999*******8 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 3.3
                         zf-H2C2_2 17 CplCdk 22
                                      C+ C++
  gi|474933652|ref|YP_007687234.1| 25 CDRCRD 30
                                      999987 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0063
                         zf-H2C2_2 14 pyeCplCd 21
                                      py+Cp C+
  gi|474933652|ref|YP_007687234.1| 34 PYKCPNCG 41
                                      8******8 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1    0.0054       2.9      15      26 ..       7      18 ..       3      19 .. 0.71
   2 ?    0.6   0.1         1   5.5e+02      22      26 ..      25      29 ..      21      31 .. 0.72
   3 ?    5.8   0.4     0.024        13       4       9 ..      36      41 ..      32      41 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0054
                    PhnA_Zn_Ribbon 15 edgallvCpeCa 26
                                      ++++ + Cp+C+
  gi|474933652|ref|YP_007687234.1|  7 HGNTFFKCPKCG 18
                                      566677777776 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1
                    PhnA_Zn_Ribbon 22 CpeCa 26
                                      C+ C 
  gi|474933652|ref|YP_007687234.1| 25 CDRCR 29
                                      77776 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.024
                    PhnA_Zn_Ribbon  4 kCplCa 9 
                                      kCp+C+
  gi|474933652|ref|YP_007687234.1| 36 KCPNCG 41
                                      888885 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00051      0.28      27      36 ..      10      19 ..       2      22 .. 0.81
   2 ?    1.3   0.3      0.58   3.1e+02       3       8 ..      25      30 ..      23      35 .. 0.68
   3 ?    6.8   0.7     0.011       6.2      27      35 ..      33      41 ..      30      43 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00051
                           TFIIS_C 27 vfykCtkCgh 36
                                      +f+kC kCg+
  gi|474933652|ref|YP_007687234.1| 10 TFFKCPKCGE 19
                                      6888888876 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.58
                           TFIIS_C  3 CpkCgs 8 
                                      C +C+ 
  gi|474933652|ref|YP_007687234.1| 25 CDRCRD 30
                                      777765 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.011
                           TFIIS_C 27 vfykCtkCg 35
                                      v ykC +Cg
  gi|474933652|ref|YP_007687234.1| 33 VPYKCPNCG 41
                                      668888887 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   7.1   0.00079      0.43      38      73 ..       8      41 ..       2      43 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00079
                            zf-CHY 38 evkevlcllCeteqekavlCkkCkkefaeyfCpiCk 73
                                        + ++c +C ++  +   C +C+ +   y+Cp+C 
  gi|474933652|ref|YP_007687234.1|  8 GNTFFKCPKCGEV--EIGRCDRCRDQSVPYKCPNCG 41
                                      4555778899886..6778****************7 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.3   0.00031      0.17     176     208 ..      13      43 ..       2      45 .] 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00031
                      tRNA-synt_1f 176 vcekcgrvdttevvevdaeeeeieYkceecGee 208
                                        c+kcg+v+  +   +   ++++ Ykc +cG+ 
  gi|474933652|ref|YP_007687234.1|  13 KCPKCGEVEIGRCDRCR--DQSVPYKCPNCGFC 43 
                                       6******9999999998..99**********86 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1  11.7   0.00058      0.32      13      49 .]      12      44 ..       4      44 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00058
                               DZR 13 rfCseCgtklkavaaedrCpsCgek.vdpearfCpeCG 49
                                        C++Cg+         rC++C  + v+ ++  C+ CG
  gi|474933652|ref|YP_007687234.1| 12 FKCPKCGEVEI-----GRCDRCRDQsVPYKCPNCGFCG 44
                                      56*****9987.....9*****9999999999999998 PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.3    0.0014      0.75      26      42 ..       6      22 ..       4      25 .. 0.84
   2 ?   -0.4   0.2       2.1   1.1e+03      33      37 ..      24      28 ..      21      32 .. 0.67
   3 ?    6.0   0.8      0.02        11       2      10 ..      34      42 ..      33      44 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0014
                            HalOD2 26 qLGayvWkCtrCGevqa 42
                                      + G   +kC +CGev  
  gi|474933652|ref|YP_007687234.1|  6 KHGNTFFKCPKCGEVEI 22
                                      6688899*******976 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2.1
                            HalOD2 33 kCtrC 37
                                      +C rC
  gi|474933652|ref|YP_007687234.1| 24 RCDRC 28
                                      56666 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.02
                            HalOD2  2 PekCseCsl 10
                                      P kC++C++
  gi|474933652|ref|YP_007687234.1| 34 PYKCPNCGF 42
                                      889999987 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.2    0.0029       1.6      12      26 ..       4      18 ..       1      18 [. 0.70
   2 ?    7.7   0.7    0.0041       2.2      15      26 ..      18      29 ..      18      29 .. 0.92
   3 ?    3.9   1.1     0.064        35       1       6 [.      36      41 ..      35      41 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0029
                          zf-TFIIB 12 serggveidyCpqCr 26
                                      se++g ++++Cp+C+
  gi|474933652|ref|YP_007687234.1|  4 SEKHGNTFFKCPKCG 18
                                      667777788888886 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0041
                          zf-TFIIB 15 ggveidyCpqCr 26
                                      g+vei +C++Cr
  gi|474933652|ref|YP_007687234.1| 18 GEVEIGRCDRCR 29
                                      689********8 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.064
                          zf-TFIIB  1 kCPkCq 6 
                                      kCP+C+
  gi|474933652|ref|YP_007687234.1| 36 KCPNCG 41
                                      577774 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.8   0.00043      0.24       4      11 ..      13      20 ..      11      24 .. 0.76
   2 ?   -0.4   0.3       1.6   8.6e+02       4       8 ..      24      28 ..      21      28 .. 0.87
   3 ?    7.6   2.5    0.0046       2.5       4       9 ..      36      41 ..      35      42 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00043
                       zf-ribbon_3  4 rCPnCGap 11
                                      +CP+CG++
  gi|474933652|ref|YP_007687234.1| 13 KCPKCGEV 20
                                      79999886 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.6
                       zf-ribbon_3  4 rCPnC 8 
                                      rC +C
  gi|474933652|ref|YP_007687234.1| 24 RCDRC 28
                                      79998 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0046
                       zf-ribbon_3  4 rCPnCG 9 
                                      +CPnCG
  gi|474933652|ref|YP_007687234.1| 36 KCPNCG 41
                                      566666 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1    0.0075       4.1      15      21 ..      13      19 ..      11      20 .. 0.87
   2 ?    3.7  10.1      0.11        57       4      20 ..      24      41 ..      23      44 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0075
                                      E-TTT-- CS
                            zf-HIT 15 kCpkCnt 21
                                      kCpkC++
  gi|474933652|ref|YP_007687234.1| 13 KCPKCGE 19
                                      9****96 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.11
                                      B-TTT-S.B-SEE-TTT- CS
                            zf-HIT  4 lCgvCgf.pakYkCpkCn 20
                                       C  C      YkCp+C+
  gi|474933652|ref|YP_007687234.1| 24 RCDRCRDqSVPYKCPNCG 41
                                      58888888889******8 PP

>> zf_C2H2_10  C2H2 type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.9    0.0005      0.27       3      11 ..      12      20 ..      11      21 .. 0.88
   2 ?   -1.8   0.1       4.3   2.3e+03       5      10 ..      25      30 ..      24      32 .. 0.73
   3 ?   -0.1   4.8       1.3   6.9e+02       3      11 ..      35      43 ..      34      45 .] 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0005
                        zf_C2H2_10  3 fsCPKCqek 11
                                      f CPKC+e+
  gi|474933652|ref|YP_007687234.1| 12 FKCPKCGEV 20
                                      78*****96 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.3
                        zf_C2H2_10  5 CPKCqe 10
                                      C +C  
  gi|474933652|ref|YP_007687234.1| 25 CDRCRD 30
                                      778876 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 1.3
                        zf_C2H2_10  3 fsCPKCqek 11
                                      + CP C+  
  gi|474933652|ref|YP_007687234.1| 35 YKCPNCGFC 43
                                      56****875 PP

>> DUF3797  Domain of unknown function (DUF3797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.5    0.0006      0.32       8      25 ..       2      23 ..       1      28 [. 0.83
   2 ?    0.8   4.9      0.83   4.5e+02      15      20 ..      36      41 ..      23      43 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0006
                           DUF3797  8 kLdek....YvqCPeCgNnkvl 25
                                      +L+ek    + +CP+Cg   ++
  gi|474933652|ref|YP_007687234.1|  2 RLSEKhgntFFKCPKCGEVEIG 23
                                      57888888899******98886 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.83
                           DUF3797 15 qCPeCg 20
                                      +CP+Cg
  gi|474933652|ref|YP_007687234.1| 36 KCPNCG 41
                                      7****8 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   8.2    0.0029       1.6      30      54 ..      13      42 ..       5      44 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0029
                    OrfB_Zn_ribbon 30 tCseCgsknke.....alsgrtfkCpnCgf 54
                                      +C++Cg++        ++++  +kCpnCgf
  gi|474933652|ref|YP_007687234.1| 13 KCPKCGEVEIGrcdrcRDQSVPYKCPNCGF 42
                                      8******998889999999999*******8 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1    0.0035       1.9      26      34 ..      12      20 ..       3      20 .. 0.83
   2 ?    2.8   1.0      0.21   1.1e+02      27      32 ..      24      29 ..      23      32 .. 0.76
   3 ?    5.1   1.2     0.039        21      27      32 ..      36      41 ..      29      43 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0035
                     zinc_ribbon_4 26 vrCskCghv 34
                                       +C+kCg+v
  gi|474933652|ref|YP_007687234.1| 12 FKCPKCGEV 20
                                      589999976 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.21
                     zinc_ribbon_4 27 rCskCg 32
                                      rC +C+
  gi|474933652|ref|YP_007687234.1| 24 RCDRCR 29
                                      788887 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.039
                     zinc_ribbon_4 27 rCskCg 32
                                      +C++Cg
  gi|474933652|ref|YP_007687234.1| 36 KCPNCG 41
                                      666665 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.021        11      19      30 ..       7      18 ..       1      18 [. 0.75
   2 ?    2.6   6.6       0.3   1.6e+02      23      30 ..      34      41 ..      20      41 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.021
                                      CSTB-EE-TTT- CS
                         zf-RING_7 19 agdevvtCpeCG 30
                                       g+  ++Cp CG
  gi|474933652|ref|YP_007687234.1|  7 HGNTFFKCPKCG 18
                                      346789*****9 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.3
                                      -EE-TTT- CS
                         zf-RING_7 23 vvtCpeCG 30
                                        +Cp+CG
  gi|474933652|ref|YP_007687234.1| 34 PYKCPNCG 41
                                      589****9 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.3    0.0029       1.6       2      11 ..       9      18 ..       8      24 .. 0.89
   2 ?   -1.1   0.2       2.6   1.4e+03       6      10 ..      24      28 ..      19      29 .. 0.71
   3 ?    7.3   0.4    0.0065       3.5       4      11 ..      34      41 ..      31      41 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0029
                                      C-EEE-TTTS CS
                             Sgf11  2 seyvtCpnCg 11
                                      +++++Cp Cg
  gi|474933652|ref|YP_007687234.1|  9 NTFFKCPKCG 18
                                      789******8 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.6
                                      E-TTT CS
                             Sgf11  6 tCpnC 10
                                      +C+ C
  gi|474933652|ref|YP_007687234.1| 24 RCDRC 28
                                      46666 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0065
                                      EEE-TTTS CS
                             Sgf11  4 yvtCpnCg 11
                                       ++CpnCg
  gi|474933652|ref|YP_007687234.1| 34 PYKCPNCG 41
                                      589****7 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3  11.4     0.094        51      17      40 ..      21      42 ..       2      43 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.094
                              C1_2 17 esfnCsaCgrkidgffYsCseCdf 40
                                      e ++C+ C+ ++    Y+C+ C f
  gi|474933652|ref|YP_007687234.1| 21 EIGRCDRCRDQS--VPYKCPNCGF 42
                                      457899998885..55******99 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1     0.016       8.9      11      24 ..       6      19 ..       4      22 .. 0.85
   2 ?    5.5   4.6     0.035        19      18      38 ..      24      44 ..      21      44 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.016
                    Ribosomal_L37e 11 qkkktHilCrrCgk 24
                                      ++ +t+ +C +Cg+
  gi|474933652|ref|YP_007687234.1|  6 KHGNTFFKCPKCGE 19
                                      47789********7 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.035
                    Ribosomal_L37e 18 lCrrCgkrsyhvqkktCascG 38
                                      +C rC  +s  ++  +C+ cG
  gi|474933652|ref|YP_007687234.1| 24 RCDRCRDQSVPYKCPNCGFCG 44
                                      8*********99999999998 PP

>> zf-tcix  Putative treble-clef, zinc-finger, Zn-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   2.9   0.00035      0.19      12      30 ..      13      31 ..      12      35 .. 0.89
   2 ?    3.4   4.8      0.11        60      12      18 ..      36      42 ..      35      45 .] 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00035
                           zf-tcix 12 kCpkCGtyNGtRglsCkNk 30
                                      kCpkCG     R+ +C+ +
  gi|474933652|ref|YP_007687234.1| 13 KCPKCGEVEIGRCDRCRDQ 31
                                      9*******999*****976 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.11
                           zf-tcix 12 kCpkCGt 18
                                      kCp+CG 
  gi|474933652|ref|YP_007687234.1| 36 KCPNCGF 42
                                      9*****5 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.9   0.00055       0.3      15      21 ..      11      19 ..       6      20 .. 0.62
   2 ?    7.8   2.3    0.0052       2.8       1       6 [.      36      41 ..      36      42 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00055
                     zinc_ribbon_2 15 F..CpyCGt 21
                                      F  Cp+CG+
  gi|474933652|ref|YP_007687234.1| 11 FfkCPKCGE 19
                                      555666664 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0052
                     zinc_ribbon_2  1 fCpnCG 6 
                                      +CpnCG
  gi|474933652|ref|YP_007687234.1| 36 KCPNCG 41
                                      688888 PP

>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   5.5    0.0039       2.1     620     650 ..      13      41 ..       4      44 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0039
                          PolC_DP2 620 kCkkCgketlearCeeCgekteeklvCkkce 650
                                       kC+kCg+  +  rC++C  +  + ++C++c+
  gi|474933652|ref|YP_007687234.1|  13 KCPKCGEVEI-GRCDRCRDQSVP-YKCPNCG 41 
                                       5666665554.356666666655.6666664 PP

>> zf-AN1  AN1-like Zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   1.1    0.0076       4.1      11      21 ..       9      19 ..       3      21 .. 0.77
   2 ?    4.4   3.9     0.077        42       1      21 [.      14      30 ..      14      32 .. 0.85
   3 ?    5.0   6.6     0.051        28       1      20 [.      25      41 ..      21      44 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0076
                            zf-AN1 11 flpfkCryCgk 21
                                      ++ fkC++Cg+
  gi|474933652|ref|YP_007687234.1|  9 NTFFKCPKCGE 19
                                      466******97 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.077
                            zf-AN1  1 CsfksCkkkdflpfkCryCgk 21
                                      C   +C++ +   ++C++C+ 
  gi|474933652|ref|YP_007687234.1| 14 CP--KCGEVEI--GRCDRCRD 30
                                      54..8****99..******86 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.051
                            zf-AN1  1 CsfksCkkkdflpfkCryCg 20
                                      C+  +C+ +   p+kC++Cg
  gi|474933652|ref|YP_007687234.1| 25 CD--RCRDQSV-PYKCPNCG 41
                                      54..6888876.*******8 PP

>> VP_N-CPKC  Virion protein N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.8   0.00057      0.31      12      23 ..       7      18 ..       5      25 .. 0.89
   2 ?    0.7   1.0      0.96   5.2e+02      18      22 ..      36      40 ..      26      42 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00057
                         VP_N-CPKC 12 HsLtFEECPKCs 23
                                      H  tF  CPKC 
  gi|474933652|ref|YP_007687234.1|  7 HGNTFFKCPKCG 18
                                      888********6 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.96
                         VP_N-CPKC 18 ECPKC 22
                                       CP C
  gi|474933652|ref|YP_007687234.1| 36 KCPNC 40
                                      59*99 PP

>> DUF2752  Protein of unknown function (DUF2752)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.2     0.013       7.2       6      15 ..       9      18 ..       7      20 .. 0.88
   2 ?    4.1   2.1     0.087        47       9      16 ..      35      42 ..      32      43 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.013
                           DUF2752  6 ltGipCPGCG 15
                                       t ++CP CG
  gi|474933652|ref|YP_007687234.1|  9 NTFFKCPKCG 18
                                      589******9 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.087
                           DUF2752  9 ipCPGCGl 16
                                      ++CP CG 
  gi|474933652|ref|YP_007687234.1| 35 YKCPNCGF 42
                                      78*****5 PP

>> Dynactin_p62  Dynactin p62 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   7.0    0.0066       3.6       8      35 ..      14      43 ..       9      45 .] 0.76

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0066
                      Dynactin_p62  8 CedChqi...rCpRCvteeivtyyCPnCLFe 35
                                      C +C ++   rC RC  +  v y CPnC F 
  gi|474933652|ref|YP_007687234.1| 14 CPKCGEVeigRCDRC-RDQSVPYKCPNCGFC 43
                                      677766544589999.7899********985 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.7   0.00067      0.36      19      28 ..      11      20 ..       3      23 .. 0.66
   2 ?    5.5   4.4     0.021        12       1      10 [.      12      21 ..      12      28 .. 0.78
   3 ?    6.0   3.8     0.016       8.7       1       7 [.      35      41 ..      35      44 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00067
                                      CEEESSSSBE CS
                      TF_Zn_Ribbon 19 elvCtdCGlV 28
                                       + C++CG+V
  gi|474933652|ref|YP_007687234.1| 11 FFKCPKCGEV 20
                                      5566666666 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.021
                                      EEETTTTCEE CS
                      TF_Zn_Ribbon  1 ykCPnCgstn 10
                                      +kCP+Cg  +
  gi|474933652|ref|YP_007687234.1| 12 FKCPKCGEVE 21
                                      6888888754 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.016
                                      EEETTTT CS
                      TF_Zn_Ribbon  1 ykCPnCg 7 
                                      ykCPnCg
  gi|474933652|ref|YP_007687234.1| 35 YKCPNCG 41
                                      89****8 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   2.6     0.022        12       7      35 ..      13      21 ..       6      25 .. 0.68
   2 ?    5.4  13.0     0.036        20       6      33 ..      12      41 ..      11      42 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.022
                       Zn-ribbon_8  7 rCeeCghefevlqsisdapltaCPeCgs.e 35
                                      +                     CP+Cg+ e
  gi|474933652|ref|YP_007687234.1| 13 K---------------------CPKCGEvE 21
                                      4.....................66666544 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.036
                       Zn-ribbon_8  6 YrCeeCghefe..vlqsisdaplta.CPeCg 33
                                      ++C +Cg e e  +  +  d + +  CP+Cg
  gi|474933652|ref|YP_007687234.1| 12 FKCPKCG-EVEigRCDRCRDQSVPYkCPNCG 41
                                      89*****.999886666678888999****9 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.9     0.019        10      16      22 ..      13      19 ..       6      21 .. 0.82
   2 ?    2.5   6.9      0.23   1.2e+02       1      21 [.      12      29 ..      12      30 .. 0.74
   3 ?    5.3   2.9     0.029        16       1       8 [.      35      42 ..      35      45 .] 0.75

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.019
                      Rubredoxin_2 16 rCpsCgs 22
                                      +Cp Cg+
  gi|474933652|ref|YP_007687234.1| 13 KCPKCGE 19
                                      7999986 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.23
                      Rubredoxin_2  1 YvCsqCGfesakwfGrCpsCg 21
                                      + C +CG +     GrC  C+
  gi|474933652|ref|YP_007687234.1| 12 FKCPKCGEVE---IGRCDRCR 29
                                      6788888877...48888887 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.029
                      Rubredoxin_2  1 YvCsqCGf 8 
                                      Y C +CGf
  gi|474933652|ref|YP_007687234.1| 35 YKCPNCGF 42
                                      77888877 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   9.8       0.2   1.1e+02      69      93 ..      10      41 ..       1      44 [. 0.58

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.2
                                      -EEEETTTS-EEECHH.HHH.......S-TTTS CS
                              HypA 69 vkvrCreCgkefelee.kal.......rCpkCg 93
                                        ++C +Cg e+e+ + ++        +Cp+Cg
  gi|474933652|ref|YP_007687234.1| 10 TFFKCPKCG-EVEIGRcDRCrdqsvpyKCPNCG 41
                                      567888888.66655321112334455777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                        43  (0.00239835); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              33  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.51
# Mc/sec: 267.58
//
Query:       gi|474933653|ref|YP_007687235.1|  [L=278]
Description: hypothetical protein TALC_00060 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.8e-44  150.1   0.0    9.2e-44  149.8   0.0    1.0  1  DUF89     Protein of unknown function DUF89


Domain annotation for each model (and alignments):
>> DUF89  Protein of unknown function DUF89
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.8   0.0   5.1e-48   9.2e-44      69     350 ..      41     270 ..      23     273 .. 0.92

  Alignments for each domain:
  == domain 1  score: 149.8 bits;  conditional E-value: 5.1e-48
                                       HHHHHHHHHHHHTHSGGGTTS-TTHHHHHHHHHHHHHHHHHHHHHHHHCCSHHHHHHHHHHHHHHHCG--CCCHTSH CS
                             DUF89  69 ecylyrrllelfglskelknyDpFkeqKeesnksalkaveelakrleeledekelfkellkislwGNaiDlsllate 145
                                       ++ ++ + +e +g       +Dp++++K ++ + a+++v+e ++ ++++ d    f ++++++++GN++D+++ + +
  gi|474933653|ref|YP_007687235.1|  41 ATAVHGKAYESMG------CDDPYRQMKIDADEVAQQYVPEAQSFIDSSDDR---FAAAVRACIVGNIMDFGSGI-A 107
                                       5667777777778......99****************************999...*****************999.9 PP

                                       HCHHHHHHHHHHHHHHCTESEE-HHHHHHHHCTCHTSEEEEE--BTTHHHHHHHHHHHHHHHCTTTSEEEEEEBSS- CS
                             DUF89 146 ediqkdqeeearkaleknilvddleklweklkkkkakrvdivlDNaGfElvfDlllaeeLlesglatkVvlhvkaiP 222
                                        d++++ +  +r+ le+ i  d++e+l + +  +++ +v++ +DN+G E vfD l+++e+++  ++++Vv +v+++P
  gi|474933653|ref|YP_007687235.1| 108 IDSPSEFGRVFRSLLEQGIGLDQTEELRRLV--ESSDTVLYAFDNCG-EDVFDKLFIREIKS--MGKRVVAVVRGKP 179
                                       9******************************..**************.**************..************* PP

                                       -TTTB-BHHHHHHHHHHHH-TTTSHHHHCHTTHHHHHHTSEEEEESSCGGSSS--CCGSSSHHHHHHHHHC-SEEEE CS
                             DUF89 223 wfvsDvtpeDfewlleqladsksfelsalgagldellkegklvlrgssfwttglsysempeapelyeelekadLvif 299
                                        +++Dvt+eD+                  + g+d+  +++++v++g     +g+   +++++p + eel ka + i+
  gi|474933653|ref|YP_007687235.1| 180 -ILNDVTMEDAL-----------------RVGMDR--EVDRIVSTGEF--AVGF--PRVNRDPGFNEELPKAGVMIV 232
                                       .***********.................******..9*******988..5555..55555**************** PP

                                       EHHHHHHHHTTSCTTTTTSEHHHHTGTSS--EEEEEE--SHHHHHHH.STTT CS
                             DUF89 300 KGdlNyrkLtgdrkwppttpfttalgfspvpvlaLrtvKadvvagll.egeg 350
                                       KG++Ny++L+ d +              ++pv++L+++K+ +va+ + ++ g
  gi|474933653|ref|YP_007687235.1| 233 KGMANYEALS-DFDY-------------GIPVAFLLRAKCIPVARSIgVEPG 270
                                       *********5.4343.............477*************99876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1800.02
//
Query:       gi|474933654|ref|YP_007687236.1|  [L=343]
Description: Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis/translation initiation factor 2B, gamma/epsilon subunits (eIF-2Bgamma/eIF-2Bepsilon) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-43  148.3   0.0    3.3e-43  148.0   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase
    6.4e-08   33.1   0.0    7.7e-08   32.9   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
     0.0095   15.6   4.5      0.025   14.3   1.4    3.1  3  Hexapep          Bacterial transferase hexapeptide (six repea
  ------ inclusion threshold ------
      0.031   14.0   2.6        0.3   10.9   0.9    2.9  2  Hexapep_2        Hexapeptide repeat of succinyl-transferase
      0.032   12.4   1.6      0.059   11.5   1.7    1.4  1  DUF4954          Domain of unknown function (DUF4954)
      0.062   12.2   0.5       0.11   11.4   0.5    1.4  1  Fucokinase       L-fucokinase


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.0   0.0   1.1e-46   3.3e-43       2     246 ..       8     237 ..       7     239 .. 0.96

  Alignments for each domain:
  == domain 1  score: 148.0 bits;  conditional E-value: 1.1e-46
                                       EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEE CS
                   NTP_transferase   2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlia 78 
                                       avI++GG GtRL PLt t++k+++pvl+  + +++ +  +a++giee+i+ +  ++s ++++++++gs++gv++l++
  gi|474933654|ref|YP_007687236.1|   8 AVIMVGGLGTRLLPLTETRPKPAMPVLDR-PFLKYLIDSIARAGIEEVILACG-YKSDILAKEIGDGSDMGVRILYS 82 
                                       8****************************.*****************777777.8999******************* PP

                                       EESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECT CS
                   NTP_transferase  79 lepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieade 155
                                        e+ + gt +A++  ++ l+d +     +  +gD l++ ++ + ++++ +++a  +vt+ +++ve++++ Gv+ +d+
  gi|474933654|ref|YP_007687236.1|  83 DEDTPLGTGGAIKSLEDRLDDVF-----VAANGDTLTSVDVGAQIEEHFSSGA--MVTVSLSEVEDPSSSGVAVIDS 152
                                       *************9999998655.....899**********************..********************** PP

                                       TSBEEEEECS-SSHSH.CSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEE CS
                   NTP_transferase 156 egrverfvEKPkeaka.selassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsD 231
                                       egr++ f+EKPk+++a s+l++sG+Yv ++ vl ++     + k+  d+ ++++p +le+g++ + +++++   W D
  gi|474933654|ref|YP_007687236.1| 153 EGRITAFQEKPKREEAlSHLVNSGLYVVDKRVLRYI-----PEKSFYDFSKELFPLLLEKGERMQGHMARG--IWID 222
                                       **************999*******************.....889***************************..7*** PP

                                       XSSHHHHHHHHHHHH CS
                   NTP_transferase 232 vGtldslleanekla 246
                                       +G++ +l+++n  +a
  gi|474933654|ref|YP_007687236.1| 223 IGKPLDLIRMNLTMA 237
                                       ********9998765 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0   2.6e-11   7.7e-08       1     107 [.       8     122 ..       8     213 .. 0.79

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 2.6e-11
                                       EEEEEESS-TTT.....TTTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSHC.HHHH....HHTTCTS-EEE-TT CS
                      NTP_transf_3   1 aviLAGGrSsRm.....ggdKallplggkpllervldalraagvdevvvvggde.evla....alarlgvrvveded 67 
                                       avi+ GG ++R+      ++K+ +p+ ++p+l++++d++++ag++ev++++g++ ++la    +  + gvr+++ ++
  gi|474933654|ref|YP_007687236.1|   8 AVIMVGGLGTRLlplteTRPKPAMPVLDRPFLKYLIDSIARAGIEEVILACGYKsDILAkeigDGSDMGVRILYSDE 84 
                                       79**********7776446**********************************5334433333457779**987765 PP

                                       S.S-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHH CS
                      NTP_transf_3  68 p.gkgplaslaaalraaadadavlvlacDmPlltpelverl 107
                                           g+++++++  +++  +d ++ + +D+   + ++ +++
  gi|474933654|ref|YP_007687236.1|  85 DtPLGTGGAIKSLEDRL--DDVFVAANGDTL-TSVDVGAQI 122
                                       5269********99998..577777778873.344444444 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.56   1.7e+03      25      34 ..     274     283 ..     273     285 .. 0.56
   2 !   11.3   2.0   7.2e-05      0.21       3      35 ..     292     322 ..     289     323 .. 0.68
   3 !   14.3   1.4   8.4e-06     0.025       2      33 ..     307     337 ..     306     340 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.56
                                       TEEEETTEEE CS
                           Hexapep  25 nvkIgagvvi 34 
                                       ++++ +g++i
  gi|474933654|ref|YP_007687236.1| 274 DSVVSEGCTI 283
                                       5556666665 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 7.2e-05
                                       EEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   3 vIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                       +I +++ I  +a++    ++G++++I +g+v++
  gi|474933654|ref|YP_007687236.1| 292 FIMKGSCIE-GATVVR-SIVGEGCIIKNGSVVT 322
                                       455555555.444444.45************97 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 8.4e-06
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvv 33 
                                       +++G++++I +++v+  + ++ d+++++ag+v
  gi|474933654|ref|YP_007687236.1| 307 SIVGEGCIIKNGSVV-TDSVLRDGTVLEAGSV 337
                                       579999999999999.7777999999999998 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.9   9.9e-05       0.3      19      33 ..     308     322 ..     297     323 .. 0.94
   2 ?    1.1   0.0      0.11   3.3e+02      20      31 ..     326     337 ..     325     337 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 9.9e-05
                                       EE-TT-EE-TT-EE- CS
                         Hexapep_2  19 slGdncvvgaGvvit 33 
                                       ++G++c++ +G+v+t
  gi|474933654|ref|YP_007687236.1| 308 IVGEGCIIKNGSVVT 322
                                       69************9 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.11
                                       E-TT-EE-TT-E CS
                         Hexapep_2  20 lGdncvvgaGvv 31 
                                       l+d+ v++aG+v
  gi|474933654|ref|YP_007687236.1| 326 LRDGTVLEAGSV 337
                                       789*******97 PP

>> DUF4954  Domain of unknown function (DUF4954)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.7     2e-05     0.059     227     274 ..     289     335 ..     250     339 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2e-05
                           DUF4954 227 edfiissGskikdgavisrcfvGqavklkkqfsaedsllfaNcqgeng 274
                                       + + i++Gs i+ ga+++r++vG+++ +k++  ++ds+l + + +e g
  gi|474933654|ref|YP_007687236.1| 289 SGSFIMKGSCIE-GATVVRSIVGEGCIIKNGSVVTDSVLRDGTVLEAG 335
                                       345678899985.88899*********************988877776 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.5   3.6e-05      0.11     232     311 ..     260     339 ..     255     342 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.6e-05
                        Fucokinase 232 HlgttaeylehltkdaslkeelsltstafsaiknkkekkkesavvinSvlessvsvgegsviehsslkgnvsigsns 308
                                       ++g+ +e+ +  ++d+   e   ++++  s     k +  e+a+v+ S++ +++ +++gsv+ +s l++++  +++s
  gi|474933654|ref|YP_007687236.1| 260 YIGEGSEFSHSASSDSVVSEGCTIKESKLSGSFIMKGSCIEGATVVRSIVGEGCIIKNGSVVTDSVLRDGTVLEAGS 336
                                       677777777777777777777777777777666566566899**************************998888888 PP

                        Fucokinase 309 ivs 311
                                       + +
  gi|474933654|ref|YP_007687236.1| 337 VTV 339
                                       765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2384.50
//
Query:       gi|474933655|ref|YP_007687237.1|  [L=342]
Description: putative kinase (galactokinase and mevalonate kinase -like protein) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.1e-17   61.4   0.2    2.2e-16   59.8   0.2    1.9  1  GHMP_kinases_N  GHMP kinases N terminal domain
      3e-13   50.0   0.0      3e-13   50.0   0.0    1.7  2  GHMP_kinases_C  GHMP kinases C terminal


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.8   0.2   2.4e-20   2.2e-16       1      66 []     101     169 ..     101     169 .. 0.93

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 2.4e-20
                                       EEEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHH...HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                    GHMP_kinases_N   1 divikseiPvgaGLGSSAAlavalvaAllallglslee...aklaleaerlaqggngsggDvaasvyGg 66 
                                       d++i+s++P g+GLG+S++++v+++ Al+++l++++++   a+la+  er++ g +g+++D++a+v+Gg
  gi|474933655|ref|YP_007687237.1| 101 DLSIRSDVPAGSGLGGSSTMIVSMIEALANWLDVDMSKvemAQLAYHLEREVIGLKGGMQDQYAAVFGG 169
                                       689*****************************999744455************9**************8 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.9         2   1.8e+04      55      63 ..     111     119 ..     110     123 .. 0.75
   2 !   50.0   0.0   3.3e-17     3e-13       2      78 ..     241     319 ..     240     324 .. 0.87

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 2
                    GHMP_kinases_C  55 GaGgGptvf 63 
                                       G+G+G++  
  gi|474933655|ref|YP_007687237.1| 111 GSGLGGSST 119
                                       999999855 PP

  == domain 2  score: 50.0 bits;  conditional E-value: 3.3e-17
                    GHMP_kinases_C   2 lealergdlellgellnlsqrselkavvgilppeleellealselGalgaklsGaGgGptvfalf..kdkdeaeqva 76 
                                       ++ l++gd++  g+ll +s++ +++   +i++pe+++l +a+ ++Ga+g+k+sGaGgG++ + ++  ++k+++ +++
  gi|474933655|ref|YP_007687237.1| 241 RSSLRHGDIDDCGRLLGESWEYKKRFSNKISNPEIDDLYNAAVKAGAIGGKVSGAGGGGFMYFICgyDKKPAVTKAL 317
                                       567999****************9999***************************************666666655444 PP

                    GHMP_kinases_C  77 ra 78 
                                        a
  gi|474933655|ref|YP_007687237.1| 318 AA 319
                                       43 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2264.98
//
Query:       gi|474933656|ref|YP_007687238.1|  [L=163]
Description: histidinol-phosphate phosphatase family domain/HAD-superfamily hydrolase, subfamily IIIA [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-12   47.2   0.0    3.4e-12   46.2   0.0    1.5  1  Hydrolase_like  HAD-hyrolase-like
    1.5e-06   28.4   0.0    1.1e-05   25.6   0.0    1.9  2  HAD_2           Haloacid dehalogenase-like hydrolase
    9.7e-06   25.4   0.0    1.1e-05   25.2   0.0    1.1  1  PNK3P           Polynucleotide kinase 3 phosphatase
     0.0014   19.0   0.0     0.0072   16.6   0.0    2.1  2  Hydrolase       haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.062   13.4   0.0      0.086   13.0   0.0    1.3  1  Hydrolase_6     Haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.0   9.5e-16   3.4e-12       2      58 ..     102     157 ..     101     161 .. 0.94

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 9.5e-16
                                       .STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTTH CS
                    Hydrolase_like   2 lgKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrpedl 58 
                                       ++KPe +m ++al + g dp+ ++m+GD+ + Di+++++ G++++ V +G t ++++
  gi|474933656|ref|YP_007687238.1| 102 CRKPETGMGEQALSKWGFDPSVSFMVGDS-DKDIEFGRRLGLRTIKVSSGHTFADAV 157
                                       89***************************.********************9877665 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.16   5.6e+02      76     105 ..      27      56 ..      14      59 .. 0.84
   2 !   25.6   0.0     3e-09   1.1e-05     134     178 .]     103     147 ..      94     147 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.16
                             HAD_2  76 kevkpydgvkelLeeLkeagyklgivTsks 105
                                        ++++++ v  +++ L++ag+ + +vT++s
  gi|474933656|ref|YP_007687238.1|  27 AKMHVFPFVPAAVKRLNDAGFLVIVVTNQS 56 
                                       567888999999***************986 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 3e-09
                             HAD_2 134 kKPdpeviekaleklklkkeeviyvGDsptDieaakkagikviav 178
                                       +KP++ + e+al k +++++  ++vGDs +Die ++++g+++i v
  gi|474933656|ref|YP_007687238.1| 103 RKPETGMGEQALSKWGFDPSVSFMVGDSDKDIEFGRRLGLRTIKV 147
                                       7*****************************************976 PP

>> PNK3P  Polynucleotide kinase 3 phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   3.1e-09   1.1e-05      32     127 ..      33     130 ..      10     156 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 3.1e-09
                             PNK3P  32 esvlekLkklkeegykivifsNqggvvekktkkslekfkekieallkel.....dvpllvyaatkkd...kyRKPet 100
                                       + v++ +k+l++ g+ +++++Nq+g+ +  +  s+e++     ++ +++     +++ ++++  + d     RKPet
  gi|474933656|ref|YP_007687238.1|  33 PFVPAAVKRLNDAGFLVIVVTNQSGIGR--GLYSVEDMEATNAEMESQIsreggHIDDVFFCPHRPDegcSCRKPET 107
                                       4589999*********************..777777777777777777744444444566666666656789***** PP

                             PNK3P 101 GmweelkkdleekleidkeksfyvGDa 127
                                       Gm e+  ++       d + sf vGD 
  gi|474933656|ref|YP_007687238.1| 108 GMGEQALSKWGF----DPSVSFMVGDS 130
                                       **9988776654....88888889986 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.013        47     119     143 ..      31      55 ..       6      85 .. 0.81
   2 !   16.6   0.0     2e-06    0.0072     119     210 .]      31     141 ..      26     141 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.013
                                       BHTTHHHHHHHHHHTTEEEEEEESS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 119 vkpeaaeavasLkaagievvlltgd 143
                                       v+p +  av++L++ag+ v+++t++
  gi|474933656|ref|YP_007687238.1|  31 VFPFVPAAVKRLNDAGFLVIVVTNQ 55 
                                       6777788888888888877777775 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 2e-06
                                       BHTTHHHHHHHHHHTTEEEEEEESSEH................HHHHHHHHHTT..GGGESEEEEHHCES....STT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx................xxxxxxxxxxx..xxxxxxxxxxxxxx....xxx RF
                         Hydrolase 119 vkpeaaeavasLkaagievvlltgdnp................etaeraanqlG..ddyfdaviasdiet....vak 173
                                       v+p +  av++L++ag+ v+++t+++                 e+   + ++ G  dd f +   +        + k
  gi|474933656|ref|YP_007687238.1|  31 VFPFVPAAVKRLNDAGFLVIVVTNQSGigrglysvedmeatnaEMESQISREGGhiDDVF-FCPHRP--DegcsCRK 104
                                       788889999******997788887776888888886665544222223333333532222.222233..245889** PP

                                       TSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 174 pspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                       p+  + ++a+ + + +p+   mVGD+  D++++++ g
  gi|474933656|ref|YP_007687238.1| 105 PETGMGEQALSKWGFDPSVSFMVGDSDKDIEFGRRLG 141
                                       *******************************998765 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.4e-05     0.086      11      44 ..      27      60 ..       8      79 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.4e-05
                                      ETTEE-TTHHHHHHHHHHTT-EEEEEE---SS-H CS
                       Hydrolase_6 11 rgdkaipgaaealnalraagkpvvllTNnsskse 44
                                       +++++p ++ a+++l++ag  v+++TN+s+  +
  gi|474933656|ref|YP_007687238.1| 27 AKMHVFPFVPAAVKRLNDAGFLVIVVTNQSGIGR 60
                                      578899***********************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1166.39
//
Query:       gi|474933657|ref|YP_007687239.1|  [L=222]
Description: Phosphoheptose isomerase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-16   60.0   0.0    4.9e-08   33.1   0.1    2.2  2  SIS_2     SIS domain
      1e-09   38.3   0.0    1.6e-09   37.7   0.0    1.4  1  SIS       SIS domain


Domain annotation for each model (and alignments):
>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   1.9e-09   1.7e-05      19      67 ..      29      77 ..      22      83 .. 0.91
   2 !   33.1   0.1   5.5e-12   4.9e-08      98     138 .]     134     174 ..     109     174 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.9e-09
                                      HHHHHHHHHHHHHHHTT--EEEEESGGGHHHHHHTSSSTT-BTTEEEE- CS
                             SIS_2 19 eaiekaaeliadslenggkvlvfGsGhSaalaeelaaragglaeferia 67
                                      ++ ++a  +i d+ +++gk+++ G+G+Saa++ ++  ++ + ++f r +
  gi|474933657|ref|YP_007687239.1| 29 KEFDEAYSVILDCYRKDGKLMLAGNGGSAADSDHFTGEMTKSFKFSRRL 77
                                      56788999************************************99866 PP

  == domain 2  score: 33.1 bits;  conditional E-value: 5.5e-12
                                       HTT--TT-EEEEE-SS--SHHHHHHHHHHHHHT-EEEEEE- CS
                             SIS_2  98 lvrlkpgDvLlviSnsGnnavvveaaeaakergmkviAlts 138
                                       ++ ++++Dv++ iS+sGn+ +++ a++aak+rg++++ lt+
  gi|474933657|ref|YP_007687239.1| 134 QTFGRENDVFIGISTSGNSRNIILALMAAKARGVRTVCLTG 174
                                       3457***********************************97 PP

>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.0   1.7e-13   1.6e-09      41     110 ..     127     196 ..     103     215 .. 0.86

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 1.7e-13
                                       HHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTTSEEEEEESSTTSHHHHHSSEEEEEEEECHC CS
                               SIS  41 selkhgvlalideddlvilisfsgetkdlvaaaelakergakiiaITdskgsplareadlalyinaepet 110
                                       +++ + v    +e+d++i is+sg++++ ++a+  ak+rg++++++T+ +g    ++ad++++ ++ + +
  gi|474933657|ref|YP_007687239.1| 127 AAFAQLVQTFGRENDVFIGISTSGNSRNIILALMAAKARGVRTVCLTGATGGKCREFADVCICAPETETF 196
                                       5556666666689***************************************************999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1413.38
//
Query:       gi|474933658|ref|YP_007687240.1|  [L=120]
Description: Acetolactate synthase, small (regulatory) subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-06   27.2   0.0      4e-06   26.6   0.0    1.3  1  ACT_5     ACT domain
    9.5e-05   22.1   0.0     0.0002   21.1   0.0    1.6  1  ACT       ACT domain
    0.00033   21.2   0.0    0.00059   20.4   0.0    1.4  2  ACT_4     ACT domain
  ------ inclusion threshold ------
       0.11   12.4   0.0       0.13   12.1   0.0    1.2  1  L1R_F9L   Lipid membrane protein of large eukaryotic DNA viru


Domain annotation for each model (and alignments):
>> ACT_5  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0     9e-10     4e-06       4      61 ..      13      70 ..      10      71 .. 0.96

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 9e-10
                             ACT_5  4 gvLeRvlrvvrrrgFevkslnmsttedggtvrieltVesersvelLsnQleKLidVlk 61
                                      gv +Rv++ ++r + +v+++++ ++e+ g++r+ l+V +  +  l++ +l+KL dV  
  gi|474933658|ref|YP_007687240.1| 13 GVMQRVMGEFTRNKINVETIVVGKCEKPGKSRMVLSVIDGGEAKLVMGRLQKLQDVYD 70
                                      899****************************************************976 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   4.4e-08    0.0002       2      65 ..       3      65 ..       2      67 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 4.4e-08
                                      EEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTT CS
                               ACT  2 vlrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkl 65
                                      v+++ v+++ G++ rv g ++++ iN++ i ++  e   ++  +v  v+d  +++ v+ +l+kl
  gi|474933658|ref|YP_007687240.1|  3 VISLIVKNEFGVMQRVMGEFTRNKINVETIVVGKCEKP-GKSRMVLSVIDGGEAKLVMGRLQKL 65
                                      7999****************************998887.9999999999999999999999998 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   1.3e-07   0.00059       9      78 ..       4      71 ..       1      72 [. 0.94
   2 ?   -3.3   0.0       3.3   1.5e+04      59      68 ..      98     107 ..      95     115 .. 0.66

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.3e-07
                             ACT_4  9 leveaedrkglLaditqviseekanivsvnaktrkkdglaeikitveVkdvehLsrviakLraipgVisV 78
                                      ++++++++ g++++++  ++ +k+n++ + + +   ++  + ++ ++V d  + + v+ +L+++++V++ 
  gi|474933658|ref|YP_007687240.1|  4 ISLIVKNEFGVMQRVMGEFTRNKINVETIVVGKC--EKPGKSRMVLSVIDGGEAKLVMGRLQKLQDVYDC 71
                                      8999*****************************6..679999**************************96 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.3
                             ACT_4  59 vehLsrviak 68 
                                       +++++++ia+
  gi|474933658|ref|YP_007687240.1|  98 SDQVEEIIAR 107
                                       6777777776 PP

>> L1R_F9L  Lipid membrane protein of large eukaryotic DNA viruses
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     3e-05      0.13     122     151 ..      24      56 ..      16      81 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3e-05
                           L1R_F9L 122 nnsidvqnieigeCvape...tslqfintgtaa 151
                                       +n+i+v++i +g+C +p    + l +i+ g a+
  gi|474933658|ref|YP_007687240.1|  24 RNKINVETIVVGKCEKPGksrMVLSVIDGGEAK 56 
                                       79**************9889999****998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 787.35
//
Query:       gi|474933659|ref|YP_007687241.1|  [L=308]
Description: branched-chain amino acid aminotransferase, group I [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.8e-42  143.3   0.0    1.2e-41  143.1   0.0    1.1  1  Aminotran_4  Amino-transferase class IV
  ------ inclusion threshold ------
       0.25   11.3   0.0       0.53   10.3   0.0    1.5  1  BORCS8       BLOC-1-related complex sub-unit 8


Domain annotation for each model (and alignments):
>> Aminotran_4  Amino-transferase class IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.1   0.0   1.3e-45   1.2e-41       1     221 [.      33     266 ..      33     268 .. 0.94

  Alignments for each domain:
  == domain 1  score: 143.1 bits;  conditional E-value: 1.3e-45
                       Aminotran_4   1 glfEtmrvy....ngeiffldeHleRLrksaellgl.....elpfdeeelrkileelleannsengrlrllvsrggg 68 
                                       g+fE++rvy       if+l++H+ RL  +++llg      +  +d + + ++++e+++an++   ++++ ++  g+
  gi|474933659|ref|YP_007687241.1|  33 GVFEGIRVYqtpkGPAIFRLKDHVRRLVDGCKLLGFdmkfgGKQYDFDSICEAIKEAVRANDKVD-YVKPCIFLSGE 108
                                       89*******99988899*****************88667776678999***************99.9*********9 PP

                       Aminotran_4  69 glg..aatsepsvavyvsalppgpeseke..lplvtssdvrrdapsplpgaKtln.yldnvlarreakergadevll 140
                                       + g  + ++  s+a++ + +   +   ++  ++lvt+s++r d  +  +gaK    y  + la+rea ++ga e+l+
  gi|474933659|ref|YP_007687241.1| 109 EVGlnPVGVPESFAITCIYMGSYLGKGAAsgTKLVTASWQRPDYLCGPAGAKVNGsYVASCLAKREAIRQGAGEALM 185
                                       999999999999999888888877777778999*******************8766********************* PP

                       Aminotran_4 141 vdedgnvtEgstsNvfivkggelitPplssgiLpGitrrallelakalgleveereitlkdleeadeafltntlrgv 217
                                       ++++g+  E+s  N+fi k g+++tP +s+giL+G+tr +++  a++lg ev e++it  +l  ade+++t+t++++
  gi|474933659|ref|YP_007687241.1| 186 LNKEGRPAECSGENIFIYKFGKIYTPAVSEGILQGVTRGSIITVARDLGYEVVEAPITRFQLTSADEIWMTGTAAEI 262
                                       ***************************************************************************** PP

                       Aminotran_4 218 lpvr 221
                                        pv+
  gi|474933659|ref|YP_007687241.1| 263 APVT 266
                                       ***8 PP

>> BORCS8  BLOC-1-related complex sub-unit 8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   5.9e-05      0.53      29      85 ..      48      99 ..      36     106 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 5.9e-05
                            BORCS8 29 alYrlQeHvrkalPelvekkkevkeleeelqgacydveyaisavksikesessfeni 85
                                      a++rl +Hvr+ +        ++   + +  g++yd +  ++a+k+   ++++++ +
  gi|474933659|ref|YP_007687241.1| 48 AIFRLKDHVRRLVDGC-----KLLGFDMKFGGKQYDFDSICEAIKEAVRANDKVDYV 99
                                      89*********99875.....677888889999999999999999998888777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1969.82
//
Query:       gi|474933660|ref|YP_007687242.1|  [L=187]
Description: Glycosyl transferase family 2 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.8e-08   32.3   0.0    1.1e-07   31.8   0.0    1.3  1  Glycos_transf_2  Glycosyl transferase family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.0   6.4e-12   1.1e-07      68     167 ..       2      98 ..       1     101 [. 0.93

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 6.4e-12
                                       HHHHHHHHHH--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCH CS
                   Glycos_transf_2  68 agalnaglraatgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerk 144
                                       a+++++g+  +++dy + +D D +++   + +l+++++k gadv +g r  + ++ +++   +     e++++   +
  gi|474933660|ref|YP_007687242.1|   2 AASIMEGFYLSDTDYTMSMDCDFQHPVSAIGDLIAEMDK-GADVCVGVRNSRMSMGRKRALGSS--AVENFNKLFFR 75 
                                       7899***********************************.*******99999999999999987..89999999999 PP

                                       CCCCCCSTTCSTCCCEEEEHHHH CS
                   Glycos_transf_2 145 rslkgnlsfeigsaallrreale 167
                                          k+++ ++ ++ ++lr e+++
  gi|474933660|ref|YP_007687242.1|  76 LHGKQTTKDFMSGLFALRCEVFR 98 
                                       99999999999999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1139.55
//
Query:       gi|474933661|ref|YP_007687243.1|  [L=59]
Description: Glycosyltransferases involved in cell wall biogenesis [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.5e-11   41.9   0.0    8.5e-11   41.9   0.0    1.0  1  Glycos_transf_2  Glycosyl transferase family 2
    7.1e-05   22.8   0.0    7.5e-05   22.7   0.0    1.0  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
     0.0063   16.0   0.0     0.0063   16.0   0.0    1.0  1  Glyco_tranf_2_2  Glycosyltransferase like family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.0   1.4e-14   8.5e-11       1      50 [.       2      49 ..       2      59 .] 0.86

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 1.4e-14
                                      EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGC CS
                   Glycos_transf_2  1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileela 50
                                      +vviptyNe+ ++  + + +++q  ypd++i+++DDgStD+t +++++l 
  gi|474933661|ref|YP_007687243.1|  2 TVVIPTYNEAGNVIPMAK-AIRQ-SYPDVKILFMDDGSTDGTIDLVRNLG 49
                                      69*************999.6666.6********************99984 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   1.3e-08   7.5e-05       5      56 ..       2      52 ..       1      58 [. 0.86

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.3e-08
                   Glyco_tranf_2_3  5 avlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaal 56
                                      +v++pt+ne+  +  +  ++ +q+yp+v++ +++d+s+++t++ ++ l ++l
  gi|474933661|ref|YP_007687243.1|  2 TVVIPTYNEAGNVIPMAKAI-RQSYPDVKILFMDDGSTDGTIDLVRNLGDPL 52
                                      79**********99997766.667*******************999877665 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.1e-06    0.0063       1      52 [.       2      50 ..       2      59 .] 0.80

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.1e-06
                   Glyco_tranf_2_2  1 svviplraseerhyieervlqkakyydeeielivvddgSsekfleevssiid 52
                                      +vvip +++ ++  +    + +++ y ++++++++ddgS++ +++ v+++ d
  gi|474933661|ref|YP_007687243.1|  2 TVVIPTYNEAGN--VIPMAKAIRQSY-PDVKILFMDDGSTDGTIDLVRNLGD 50
                                      79**********..555555555443.899***************9999866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 393.27
//
Query:       gi|474933662|ref|YP_007687244.1|  [L=295]
Description: Glycosyltransferase, probably involved in cell wall biogenesis [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.3e-23   81.7   0.0    1.4e-22   80.3   0.0    1.7  2  Glycos_transf_2  Glycosyl transferase family 2
    1.8e-12   47.7   0.0    2.8e-11   43.8   0.0    2.5  2  Glyco_tranf_2_3  Glycosyltransferase like family 2
    0.00019   21.9   0.0    0.00048   20.6   0.0    1.7  1  Glyco_tranf_2_4  Glycosyl transferase family 2
     0.0089   16.0   0.0      0.014   15.4   0.0    1.5  1  Glyco_trans_2_3  Glycosyl transferase family group 2
  ------ inclusion threshold ------
      0.013   15.8   0.0      0.034   14.5   0.0    1.6  2  NTP_transf_3     MobA-like NTP transferase domain


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.3   0.0     4e-26   1.4e-22       2     128 ..       8     137 ..       7     164 .. 0.92
   2 ?   -1.8   0.0      0.64   2.3e+03       4      23 ..     232     251 ..     232     285 .. 0.69

  Alignments for each domain:
  == domain 1  score: 80.3 bits;  conditional E-value: 4e-26
                                       EEEEESS-TTTHHHHHHHHHHH..GGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHH CS
                   Glycos_transf_2   2 vviptyNeektlletlesllaq..dpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglr 76 
                                       v i++yNee+ ++++++s+ +q       +e++vv  gStD+t +i+++l++e+p+++++r+e+++Gk +a+n+ l+
  gi|474933662|ref|YP_007687244.1|   8 VGICAYNEEQIIERSIRSVYSQklSGVTVKEVLVVSSGSTDRTDDIVRRLSNEFPNLKLFRQEKREGKNSAINCYLD 84 
                                       679*******************999999************************************************* PP

                                       H--SSEEEEEESSEEE-TT.HHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCH CS
                   Glycos_transf_2  77 aatgdyilflDaDdepdpd.wleklvealekdgadvvlgqrprifgetdeier 128
                                       + t d+++ l+aD ++  +  l+klve+l ++ +++  g+++ ++++t++i  
  gi|474933662|ref|YP_007687244.1|  85 NKTCDIVVMLNADNAFGTEdSLQKLVEPLFDGHVGITGGHPVPTNDKTTKIGF 137
                                       ****************8877***********9999999999999998887765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.64
                                       EEESS-TTTHHHHHHHHHHH CS
                   Glycos_transf_2   4 iptyNeektlletlesllaq 23 
                                       ipt N + + +++l+s+++ 
  gi|474933662|ref|YP_007687244.1| 232 IPTWNKKYLAKAMLASVREL 251
                                       78889888888888888887 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.0   7.7e-15   2.8e-11       4     227 ..       6     217 ..       3     220 .. 0.81
   2 ?   -1.1   0.0      0.41   1.5e+03       8      39 ..     232     263 ..     231     285 .. 0.73

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 7.7e-15
                   Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqey.pr..vevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksr 77 
                                       +av ++++nee+ +++ ++s+ +q+  +    ev vv  +s++ t + ++ l  ++p+  +++ +++++    gk  
  gi|474933662|ref|YP_007687244.1|   6 IAVGICAYNEEQIIERSIRSVYSQKLsGVtvKEVLVVSSGSTDRTDDIVRRLSNEFPN--LKLFRQEKR---EGKNS 77 
                                       89**********************9643353566666699******************..577777775...46777 PP

                   Glyco_tranf_2_3  78 alnealravksdlvllvDdDtvv.ePdtlkrllqffltpkvgavgtpvfllnrstlvsalgalefaerhlrflaarr 153
                                       a+n  l++ ++d+v+++++D+     d+l++l+  +++  vg+ g++    n++t+     ++ fa + + ++ +++
  gi|474933662|ref|YP_007687244.1|  78 AINCYLDNKTCDIVVMLNADNAFgTEDSLQKLVEPLFDGHVGITGGHPVPTNDKTT-----KIGFAVNLMWCMHHQL 149
                                       788********************9999********977788888888777777764.....4678888999999999 PP

                   Glyco_tranf_2_3 154 algvltlnGsgslirrevlkelegldp.lflltdDyelglrlrragfrtayvpgaavrevfpsslkayikqrnRw 227
                                       al  +   G++ ++r ++ ++l    p      +D ++ +r+  ag+  +yvp+ +v    p++ +++ikqr R 
  gi|474933662|ref|YP_007687244.1| 150 ALQHPK-IGELIAFR-DIGTRL----PtDMQSDED-IIRMRIEDAGMICVYVPDCIVVNRGPETEEDFIKQRVRV 217
                                       998875.89999996.445555....412233444.577888889999999999999999999999999999885 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.41
                   Glyco_tranf_2_3   8 Vptfneedvlgevlesllaqeyprvevvvvvd 39 
                                       +pt+n      ++l+s+     ++++  + + 
  gi|474933662|ref|YP_007687244.1| 232 IPTWNKKYLAKAMLASVRELGFHPFKMLYTAK 263
                                       89999988888899999888888888766654 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.3e-07   0.00048       1      94 [.      13     108 ..      13     111 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.3e-07
                   Glyco_tranf_2_4   1 rneadiLpeflahhlalg.....fdrilvydndstDgtrailkel....pevkllhvdksyederrqvellkallar 68 
                                       +ne++i+++ ++  ++       ++++lv++ +stD+t++i+++l    p++kl++ +k     + ++++++  l++
  gi|474933662|ref|YP_007687244.1|  13 YNEEQIIERSIRSVYSQKlsgvtVKEVLVVSSGSTDRTDDIVRRLsnefPNLKLFRQEKR----EGKNSAINCYLDN 85 
                                       69**********7665554466689*****************997211244555544443....3346677766644 PP

                   Glyco_tranf_2_4  69 yaeadwvlvvDaDEflvvpdsrslra 94 
                                        +  d v+++ aD+ + ++d  sl++
  gi|474933662|ref|YP_007687244.1|  86 -KTCDIVVMLNADNAFGTED--SLQK 108
                                       .7899********9999998..5555 PP

>> Glyco_trans_2_3  Glycosyl transferase family group 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   3.8e-06     0.014     103     165 ..     180     242 ..      90     264 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.8e-06
                   Glyco_trans_2_3 103 mglrlqrkGyrvrfvpeslvkekspltlraalrQrkRwayGc...el..eklillvrllgylgsllws 165
                                       + +r+  +G+++++vp+ +v   +p t  ++++Qr R   G    +   ++ i       +  ++l++
  gi|474933662|ref|YP_007687244.1| 180 IRMRIEDAGMICVYVPDCIVVNRGPETEEDFIKQRVRVNVGEctmKKkyGYEI-P----TWNKKYLAK 242
                                       56999*************99*****************9999333211222222.2....222333333 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   9.4e-06     0.034      23     110 ..      15     112 ..      10     150 .. 0.77
   2 ?   -2.0   0.0       1.1     4e+03      59      59 ..     231     231 ..     192     270 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 9.4e-06
                                       CCCHHHHHHHHH.....CTT.-CEEEEECSH..CHHHHHHTTC.....TS-EEE-TTSS-SHHHHHHHHHHHH.SSS CS
                      NTP_transf_3  23 gkpllervldal.....raagvdevvvvggd..eevlaalarl.....gvrvvededpgkgplaslaaalraaadad 87 
                                       ++ ++er+++++     + ++v+ev+vv     +   + ++rl     +++++++e + +g  +++ + l++    d
  gi|474933662|ref|YP_007687244.1|  15 EEQIIERSIRSVysqklSGVTVKEVLVVSSGstDRTDDIVRRLsnefpNLKLFRQE-KREGKNSAINCYLDNK-TCD 89 
                                       56666666666622222666778999996443445555555554444468888887.689***********97.8** PP

                                       CEEEEETT-TT--HHHHHHHHHC CS
                      NTP_transf_3  88 avlvlacDmPlltpelverllaa 110
                                        v++l +D ++ t++ +++l++ 
  gi|474933662|ref|YP_007687244.1|  90 IVVMLNADNAFGTEDSLQKLVEP 112
                                       ********************985 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.1
                                       T CS
                      NTP_transf_3  59 g 59 
                                       +
  gi|474933662|ref|YP_007687244.1| 231 E 231
                                       2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2167.23
//
Query:       gi|474933663|ref|YP_007687245.1|  [L=251]
Description: hypothetical protein TALC_00070 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-06   28.6   3.5    6.6e-06   26.8   0.4    2.6  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase


Domain annotation for each model (and alignments):
>> CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.4   3.7e-10   6.6e-06       1      62 [.      43     106 ..      43     109 .. 0.71
   2 ?    2.2   0.2     0.017   3.1e+02      26      44 ..     163     221 ..     117     224 .. 0.62

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 3.7e-10
                                       S-HHHHHHHHHHHHHHHHHGGGS-H.....HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHH CS
                   CDP-OH_P_transf   1 nlPnaiTllrlllsvlailllltyyp...lvlailllliasltDalDGklARrlnqvstlGkllD 62 
                                       ++Pn+iT++  +l+++  + +l+ ++   ++++i ++++++l D+ DG lAR ++ +s  G++ D
  gi|474933663|ref|YP_007687245.1|  43 VTPNQITYFWGALMLVCSIGFLFNDYllnILCGIGWVVAYAL-DCADGPLARYTGIKSARGDYQD 106
                                       58******8666655544455555555655555555556666.***********99888999988 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.017
                                       ...........................................HHHHHHHHHHHHHTTHH CS
                   CDP-OH_P_transf  26 p.........................................lvlailllliasltDalD 44 
                                                                                 + +++l+ ++a++ D+lD
  gi|474933663|ref|YP_007687245.1| 163 VhdrvnpiegftanggslgiegekmknrsllkaammlnplafTNMMVLIPVFAAI-DCLD 221
                                       2666666666666666666666666666654444444444423333333356666.8888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1858.77
//
Query:       gi|474933664|ref|YP_007687246.1|  [L=311]
Description: Nucleoside-diphosphate-sugar epimerase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.5e-29  100.5   0.0    1.1e-28  100.3   0.0    1.1  1  Epimerase      NAD dependent epimerase/dehydratase family
    7.5e-15   55.1   0.0    1.3e-14   54.4   0.0    1.4  1  GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
     0.0083   15.3   0.0      0.019   14.1   0.0    1.6  2  NAD_binding_4  Male sterility protein
  ------ inclusion threshold ------
      0.037   13.0   0.0      0.064   12.3   0.0    1.4  1  3Beta_HSD      3-beta hydroxysteroid dehydrogenase/isomerase 


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.3   0.0   2.5e-32   1.1e-28      47     240 ..      43     235 ..       1     236 [. 0.81

  Alignments for each domain:
  == domain 1  score: 100.3 bits;  conditional E-value: 2.5e-32
                                       E--TT-HHHHHHHHHHHT-SEEEE--S---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCS CS
                         Epimerase  47 eldltdrsalerlfkeeqpdavihlAavggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkda 123
                                       + ++ +++    + ++  +d ++ +A   ++++++ dp  ++++n+ g  n l++ +  +  r++f sS+e+YG++ 
  gi|474933664|ref|YP_007687246.1|  43 YFEIIEQDVNMPFADRGVFDSIFECASNTCPEQYAGDPIGTVMTNISGLKNSLDVFSGEKGGRFVFTSSVEIYGQNR 119
                                       444444444444455558899************************************99888************999 PP

                                       S.SS..BSTCSTTS--.--SSHHHHHHHHHHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTT CS
                         Epimerase 124 e.qp..keettltgpl.kpnspYaaaKlageklveayaaqyglnaiilrlfnlyGprngegevsrvipalirkileg 196
                                         +    e+++ +  +   +  Y  +K+age+l++ay a  ++++ii r++  yGp    +++++ ++++ir++ +g
  gi|474933664|ref|YP_007687246.1| 120 GdVGkfSEDYCGYIDCnTVRAGYNESKRAGESLCQAYGAVKDIDFIIPRISRSYGPT-LRDSDNKALSQFIRNAVSG 195
                                       9522469*********888999**********************************9.7778*************** PP

                                       SSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-STTEEEEE CS
                         Epimerase 197 kqevtllgdgtalRdflyveDvaeaillvlehvdagdkgeiyni 240
                                       + +++l + gt+l+ ++y+ D+++ail++  +   g  ge+yn+
  gi|474933664|ref|YP_007687246.1| 196 E-DIVLKSAGTQLYSYVYSADAVDAILFLFFN---GIRGEAYNV 235
                                       *.*****************************9...888999998 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.4   0.0   2.9e-18   1.3e-14      70     331 ..      55     302 ..       2     303 .. 0.70

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 2.9e-18
                                       HHHHHT-SEEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-S..SSSB-TT CS
                     GDP_Man_Dehyd  70 llaevqpdevynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvq..evpqtEt 144
                                         ++  +d ++  A   + ++   +P  t+ +n+ G  + L++      ek  rf+++S+ E+YG+ +    +++E+
  gi|474933664|ref|YP_007687246.1|  55 FADRGVFDSIFECASNTCPEQYAGDPIGTVMTNISGLKNSLDVFSG---EKGGRFVFTSSVEIYGQNRgdVGKFSED 128
                                       444556788999999999999999*******************965...5789**************75234599*9 PP

                                       .....S-----SHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTT CS
                     GDP_Man_Dehyd 145 .....tpfyPrsPYaaaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGn 216
                                               + r  Y  +K + + ++++y    ++  ++ +++  ++p   ++   + +++++ ++  g+  vl    
  gi|474933664|ref|YP_007687246.1| 129 ycgyiDCNTVRAGYNESKRAGESLCQAYGAVKDIDFIIPRISRSYGPTL-RDSDNKALSQFIRNAVSGEDIVL-KSA 203
                                       55554455579*************************************7.55699************996665.588 PP

                                       TT-EEEEEEHHHHHHHHHHHHHCSS---EEE-TT-E..EECHHCHHCCHHCCCHHHHHH............TTGGCC CS
                     GDP_Man_Dehyd 217 ldakRdwghvkDyveamwlmlqqdkpedyviatget..hsvrefvelaflelgktiewegkgeeevgrakesgkvvv 291
                                       + +  ++ +  D v+a+  ++ ++   + +  +g++   +++e++e+ +  +g ++                     
  gi|474933664|ref|YP_007687246.1| 204 GTQLYSYVYSADAVDAILFLFFNGIRGEAYNVSGREpnLTLKEIAEALADIAGTQLR------------------FE 262
                                       899*************99888777543333333332002333333333333333333..................33 PP

                                       CEECGG--S.S--SB--B-THHHHHHH----SS-HHHHHHH CS
                     GDP_Man_Dehyd 292 evdpkyfrp.gevdlllgdaskakeeLgWkpkvsfeelvre 331
                                       +v+++ +r  + +++ + d+sk+k +LgW+p++++ee++r+
  gi|474933664|ref|YP_007687246.1| 263 QVSEEENRGySKATTAVLDISKIK-KLGWEPRFGMEEGLRR 302
                                       444445554234456799*****9.9************986 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.48   2.2e+03       9      51 ..       3      44 ..       1      52 [. 0.68
   2 !   14.1   0.0   4.3e-06     0.019      90     208 ..      63     174 ..      58     213 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.48
                                      HHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHHHHHT-SS-HH CS
                     NAD_binding_4  9 GkvLlekLLrttpevkiyllvRaksgesaeeRleeelekkelf 51
                                      G+ L   LL + +e+  ++ + ++ g+++eeR+ + +  k+ f
  gi|474933664|ref|YP_007687246.1|  3 GSLLADVLLGKAEEYGFTVAALSRHGKAIEERF-SDFVGKGYF 44
                                      777778888888888455555555557899999.666666655 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 4.3e-06
                                       EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H......HHH- CS
                     NAD_binding_4  90 viihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegekeeklde 163
                                        i+ +a ++  ++   +    + +N+ G ++ l+  ++ k    +++ S+  ++g+++g v +           +d 
  gi|474933664|ref|YP_007687246.1|  63 SIFECASNTCPEQYAGDpigTVMTNISGLKNSLDVFSGEKGG-RFVFTSSVEIYGQNRGDVGK---------FSEDY 129
                                       556666555544444333336789***********9999998.9******7777888878722.........22455 PP

                                       -EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE- CS
                     NAD_binding_4 164 deraklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg 208
                                           + + +  +Y+ sK ++E l+++++  +++ ++i R+s  +g
  gi|474933664|ref|YP_007687246.1| 130 CGYIDCNTVRAGYNESKRAGESLCQAYGAVKDIDFIIPRISRSYG 174
                                       55667788899****************************997665 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.4e-05     0.064      91     225 ..      86     220 ..      61     261 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.4e-05
                         3Beta_HSD  91 vnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyesl.hqdaypesKalaEklvlkaNgrtlk 166
                                        n+ G +n l+        ++v+tSs+e+ g+n         d   +++ +   + y+esK+  E l  +a g  +k
  gi|474933664|ref|YP_007687246.1|  86 TNISGLKNSLDVFSGEKGGRFVFTSSVEIYGQNRGDVGKFSEDYCGYIDCNtVRAGYNESKRAGESLC-QAYG-AVK 160
                                       5999*******99999999*************765443332333333433348889******999986.6777.788 PP

                         3Beta_HSD 167 nggrlyTcaLRpagiyGeg.....dkllvpllkqlaklglalfkigdeevlsdrvYvgNvawah 225
                                       ++  ++    R +  yG+      +k l++++++++  + +++k++  + l ++vY+   ++a+
  gi|474933664|ref|YP_007687246.1| 161 DIDFII---PRISRSYGPTlrdsdNKALSQFIRNAVSGEDIVLKSAGTQ-LYSYVYSADAVDAI 220
                                       884333...4556667774332225677778888877776666666554.58888888777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 1836.89
//
Query:       gi|474933665|ref|YP_007687247.1|  [L=240]
Description: 4-diphosphocytidyl-2-methyl-D-erithritol synthase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-35  123.0   0.0    1.8e-35  122.7   0.0    1.0  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
    1.6e-09   38.3   0.0    1.9e-09   38.1   0.0    1.1  1  NTP_transf_3     MobA-like NTP transferase domain
     0.0035   17.0   0.0     0.0046   16.6   0.0    1.3  1  NTP_transferase  Nucleotidyl transferase
  ------ inclusion threshold ------
      0.023   14.6   0.0      0.028   14.3   0.0    1.1  1  CTP_transf_3     Cytidylyltransferase
      0.066   13.3   0.1       0.13   12.3   0.1    1.5  1  B1               Protein L b1 domain


Domain annotation for each model (and alignments):
>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.7   0.0   4.9e-39   1.8e-35       1     216 [.       2     224 ..       2     228 .. 0.88

  Alignments for each domain:
  == domain 1  score: 122.7 bits;  conditional E-value: 4.9e-39
                                       EEEEEECTTSSCTT-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGG....CCEEEEE- CS
                              IspD   1 vvvvipAAGsGkRmkaglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllld....ksiqlvaG 73 
                                       +++++ A G GkR++  +pKqfle+kg+++++ ++d +++++ vd+i vv  +   e+ +++  +    k  +++ G
  gi|474933665|ref|YP_007687247.1|   2 ITAILLAGGIGKRVGDPTPKQFLEIKGKPIIAYALDYFQNNQYVDRIAVVCLHTWEERLSEIKEKynytKLTHVIPG 78 
                                       5799*******************************************999988888999999998888777899*** PP

                                       -SSHHHHHHHHHHTTSS...TTSEEEE--TT-TT--HHHHHHHHHHHHTTCSEEEEEEE-SSEEEEEETTT.BEEEE CS
                              IspD  74 GdeRaesVlnglkaleg...eakfVLvHDaARpllkaadiaellaaaeqstqgailalpvkDtikrveadg.lvaet 146
                                       G++  es +ngl+ +++   e+++V++HDa Rpl++++ +++ + + ++ +  a   +++++ti r++ dg      
  gi|474933665|ref|YP_007687247.1|  79 GKNGMESTYNGLRGIADvmhEDDMVIIHDAVRPLISEDIVDDCIYICKK-HGNACSSVAMQETIVRTN-DGiSGNVN 153
                                       ***********99877522267*************************98.7888999***********.66144456 PP

                                       ETGTTEEEEEEEEEEEHHHHHHHHHHHHHCT---SSHH.HHHHHTT--EEEEE--TTG----SHHHHHHHH CS
                              IspD 147 edRegLwaaqtPqgFrvdlllaahakgeqegaeitDda.slvekiGlsvkvVeGeednlKittpeDlalAe 216
                                       +dR+++ ++qtPq++r   +l+ ++++ ++g++ +  a  l  ++G+++    G+  nlK+t  eDl    
  gi|474933665|ref|YP_007687247.1| 154 IDRSDVMRVQTPQAYRYGDILSKYEQAYKQGITDSVYAnTLYMEMGGRIFFSRGSVYNLKVTMLEDLDYIR 224
                                       8**************************999654444442456789*********************97655 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.0   5.3e-13   1.9e-09       1     117 [.       4     131 ..       4     169 .. 0.83

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 5.3e-13
                                       EEEEEESS-TTTTT..THHHHCCCCCCHHHHHHHHHCTT..-CEEEEECSH..CHHHHHH.TTCTS-EEE-TTS.S- CS
                      NTP_transf_3   1 aviLAGGrSsRmgg..dKallplggkpllervldalraag.vdevvvvggd..eevlaal.arlgvrvvededp.gk 70 
                                       a++LAGG ++R g   +K++l+++gkp+++++ld ++  + vd++ vv+ +  ee l+++ ++++++ ++   p gk
  gi|474933665|ref|YP_007687247.1|   4 AILLAGGIGKRVGDptPKQFLEIKGKPIIAYALDYFQNNQyVDRIAVVCLHtwEERLSEIkEKYNYTKLTHVIPgGK 80 
                                       799**********777********************999769******98866554444415667777777666369 PP

                                       SHHHHHHHHHHHH.....SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSS CS
                      NTP_transf_3  71 gplaslaaalraaa....dadavlvlacDmPlltpelverllaaaaasgad 117
                                       + ++s + +lr +a    ++d v++  +  Pl+++++v+  +  ++++g++
  gi|474933665|ref|YP_007687247.1|  81 NGMESTYNGLRGIAdvmhEDDMVIIHDAVRPLISEDIVDDCIYICKKHGNA 131
                                       999999999998665776888888888989999999999888877777755 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.3e-06    0.0046       2      84 ..       4      80 ..       3     142 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.3e-06
                                      EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHH.TT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEE CS
                   NTP_transferase  2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlan.sgieeiivvltqehsflveeqlkegskfgvevlial 79
                                      a++LaGG G+R+ + t    +k+++  +++++i + l    n + +++i vv+ +  ++++ e +ke+++++   l  +
  gi|474933665|ref|YP_007687247.1|  4 AILLAGGIGKRVGDPT----PKQFLEIKGKPIIAYALDYFQNnQYVDRIAVVCLHTWEERLSE-IKEKYNYT--KLTHV 75
                                      89*********97644....5555555555**********99566788888888777766665.44455444..33333 PP

                                      ESS-- CS
                   NTP_transferase 80 epegk 84
                                       p gk
  gi|474933665|ref|YP_007687247.1| 76 IPGGK 80
                                      33333 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   7.8e-06     0.028      16     129 ..      21     147 ..      13     230 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.8e-06
                                       GGGSEETTEEHHHHHHHHHHHTTTTSE...EEEEES-HHHHHHHHHTT.SEEEE--TTCSSHHHHHHHHHHHHTTT. CS
                      CTP_transf_3  16 Knlldlggkpliayvleaalkskafek...vivaTDseeiknvakefg.asvlvtrsslesdterflevvkaflms. 87 
                                       K  l++ gkp+iay l+   + + +++   v++ T +e+  ++ +++   +     +  ++++e++++ ++ ++   
  gi|474933665|ref|YP_007687247.1|  21 KQFLEIKGKPIIAYALDYFQNNQYVDRiavVCLHTWEERLSEIKEKYNyTKLTHVIPGGKNGMESTYNGLRGIADVm 97 
                                       77899**********************999999***************988888888999********998776440 PP

                                       .TTSEEEEE-TT-TT--HHHHHHHHHHHHHSTTS........SEEEEEEE CS
                      CTP_transf_3  88 eneeiivnlqGdnPllqeevikkaietlkenqed........ylstlvkk 129
                                       +++++++   +  Pl++e  ++  i   k+ ++          ++ +++ 
  gi|474933665|ref|YP_007687247.1|  98 HEDDMVIIHDAVRPLISEDIVDDCIYICKKHGNAcssvamqeTIVRTNDG 147
                                       445588888889***********999999999987766554433333333 PP

>> B1  Protein L b1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   3.6e-05      0.13      34      60 ..     164     190 ..     145     201 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.6e-05
                                B1  34 taeayryadllkkenGeytadledgGy 60 
                                       t +ayry d+l+k +  y   + d  y
  gi|474933665|ref|YP_007687247.1| 164 TPQAYRYGDILSKYEQAYKQGITDSVY 190
                                       779****************99999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1673.76
//
Query:       gi|474933666|ref|YP_007687248.1|  [L=521]
Description: hypothetical protein TALC_00073 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.4e-10   39.7  14.8    4.4e-10   39.7  14.8    3.3  3  GT87           Glycosyltransferase family 87
    1.6e-05   24.2   5.9    1.6e-05   24.2   5.9    2.8  3  PIG-U          GPI transamidase subunit PIG-U
  ------ inclusion threshold ------
       0.03   13.9   1.0       0.03   13.9   1.0    3.1  4  AcrZ           Multidrug efflux pump-associated protein AcrZ
      0.078   13.1   0.0       0.18   12.0   0.0    1.6  1  Acyl-CoA_dh_C  Acetyl-CoA dehydrogenase C-terminal like


Domain annotation for each model (and alignments):
>> GT87  Glycosyltransferase family 87
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7  14.8   9.7e-14   4.4e-10      18     232 ..     119     323 ..     103     332 .. 0.72
   2 ?   -3.5   9.6       1.5   6.8e+03     128     211 ..     322     404 ..     316     446 .. 0.52
   3 ?    2.7   0.6     0.019        86      11      45 ..     429     463 ..     428     498 .. 0.86

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 9.7e-14
                              GT87  18 pyglalalwallnlaalllalrlllrrlgral.asavalalllaalalepv.lstlgfGqinllllllvlldllllr 92 
                                        + +++  ++++  ++ ++++r+++  l+ ++ +  va+al   +++++ +  +   +G +++   ll+l ++    
  gi|474933666|ref|YP_007687248.1| 119 GFLASFKFMMVVGDVLCAFLVRWMVAKLTDDQsKGDVAFAL---IFLSPIIlVESSIHGMFDIYCGLLALISVYFAA 192
                                       45556655666665555555555555555555599999997...555555579999********************* PP

                              GT87  93 rrrpllaGlliGlaaaiKltPalfllylll......rrrwralaaaaatalvltalpllllppssleyfle.tlfdt 162
                                       r++ +laGl +G+a+++K++P+ +  +ll+      r++ ra++ +++ a++ ++ ++ ll    + + l+ t+ dt
  gi|474933666|ref|YP_007687248.1| 193 REKYYLAGLSLGIATLMKIFPVYLFPILLAfllkqnRGDSRAIVNGVFMAVLGVLSAFFLLY---YPQLLDgTFSDT 266
                                       *********************9777766666779**********************999999...888888888888 PP

                              GT87 163 seriaedvgnqsllslagllaralalglsavtllwlvlvllvvalaavaawrlrrrerllalaaallval 232
                                       +  +  + +  s  +++g +a   +++          l++ +++l+a++++++rr+   +++ ++++ a+
  gi|474933666|ref|YP_007687248.1| 267 WAFL--FGRVDSAGGIVGKFAG--HIPE---------LAVGAIVLVAIIIYIYRRGVGKVEIHLSSMQAI 323
                                       8844..4444455599999999..7777.........455556666666666665544444443333333 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.5
                              GT87 128 alaaaaatalvltalpllllppssleyfletlfdtseriaedvgnqsllslagllaralalgl..s.avtllwlvlv 201
                                       a+a++a+ +l+++a  + + +   +e+ ++ lf ts  i    g q l  +++ ++ ++ ++   + +++l+++v  
  gi|474933666|ref|YP_007687248.1| 322 AIAVMALMVLAVFAGLVFVNG--GVENMFSDLFHTSY-I-VGIGMQGLALIVSFYLAHKLYYSelEdQTKLVMMVGT 394
                                       666666666666665444444..68888888888844.4.5556666666666665556566534244555555553 PP

                              GT87 202 llvvalaava 211
                                       l+v++  +++
  gi|474933666|ref|YP_007687248.1| 395 LAVATGFLWV 404
                                       3333333333 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.019
                              GT87  11 faplallpyglalalwallnlaalllalrlllrrl 45 
                                       ++p+ l+++g+a++++++   aal+++++  + ++
  gi|474933666|ref|YP_007687248.1| 429 LTPFLLISFGAAFFIIMVEGPAALFVSVAQYTDLI 463
                                       689***********************998777665 PP

>> PIG-U  GPI transamidase subunit PIG-U
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   5.9   3.5e-09   1.6e-05      82     234 ..     124     258 ..     101     274 .. 0.73
   2 ?    0.1   2.2     0.073   3.3e+02     183     245 ..     296     351 ..     288     403 .. 0.60
   3 ?   -1.6   0.5      0.23     1e+03     154     195 ..     368     422 ..     357     469 .. 0.54

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 3.5e-09
                             PIG-U  82 asllflliDllialllykiknkslaksekkreksktkkslsplliaavYlfNPltilsc.vslStsvlsnlllllsl 157
                                       +++++++ D+l+a+l++ +     ak         t+++++ ++++a+ ++ P++++ + + + +++   ll l+s+
  gi|474933666|ref|YP_007687248.1| 124 FKFMMVVGDVLCAFLVRWM-V---AKL--------TDDQSKGDVAFALIFLSPIILVESsIHGMFDIYCGLLALISV 188
                                       5667778888888888888.2...222........2334678999999999**999865156678999999999*** PP

                             PIG-U 158 ylalkgkallsalslalatylslypllllapllllllkllkaskskkpsksnklskllrllllfllyllvLllaSfl 234
                                       y+a ++k  l+ lsl++at +++ p++l+++ll++llk       +++ +s+ + + +++++l +l+ + Ll+   l
  gi|474933666|ref|YP_007687248.1| 189 YFAAREKYYLAGLSLGIATLMKIFPVYLFPILLAFLLK-------QNRGDSRAIVNGVFMAVLGVLSAFFLLYYPQL 258
                                       *********************************99999.......45555566666666555555555555554444 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.073
                             PIG-U 183 llllapllllllkllkaskskkpsksnklskllrllllfllyllvLll.aSfllggswsflrat 245
                                       ++l+a++++++ +           k++++ + ++ +++++l++l+++  + f++gg +++++  
  gi|474933666|ref|YP_007687248.1| 296 IVLVAIIIYIYRR--------GVGKVEIHLSSMQAIAVMALMVLAVFAgLVFVNGGVENMFSDL 351
                                       5566666644444........3333444444444333333333333332444455555544433 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.23
                             PIG-U 154 llslylalk.........gk....allsalslalatylslypllllapllllllk 195
                                       ++s+yla k         +k    + + a++ +++    + +l+ll+pl+ +++ 
  gi|474933666|ref|YP_007687248.1| 368 IVSFYLAHKlyyseledqTKlvmmVGTLAVATGFLWVPMPEYLILLLPLICVYAM 422
                                       4444444443333333322233223333444444444445555666666533333 PP

>> AcrZ  Multidrug efflux pump-associated protein AcrZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.4       1.7   7.5e+03      16      26 ..      24      34 ..      23      37 .. 0.83
   2 ?   -2.9   0.2       1.2   5.4e+03      10      23 ..     212     225 ..     203     226 .. 0.78
   3 ?   -4.7   1.2         4   1.8e+04      12      22 ..     296     302 ..     293     306 .. 0.50
   4 ?   13.9   1.0   6.7e-06      0.03       5      41 ..     317     353 ..     314     356 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.7
                              AcrZ 16 PvvmAiiLglI 26
                                      Pv+  +i+gl+
  gi|474933666|ref|YP_007687248.1| 24 PVLTVLIIGLV 34
                                      88999999997 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.2
                              AcrZ  10 vaviMvPvvmAiiL 23 
                                       + v + P+++A +L
  gi|474933666|ref|YP_007687248.1| 212 FPVYLFPILLAFLL 225
                                       55777899999877 PP

  == domain 3  score: -4.7 bits;  conditional E-value: 4
                              AcrZ  12 viMvPvvmAii 22 
                                       +++v    Aii
  gi|474933666|ref|YP_007687248.1| 296 IVLV----AII 302
                                       4444....444 PP

  == domain 4  score: 13.9 bits;  conditional E-value: 6.7e-06
                              AcrZ   5 LksLvvaviMvPvvmAiiLglIygLGEvfNviSkiGh 41 
                                       L s+   ++M+ +v+A+  gl++  G v N++S + h
  gi|474933666|ref|YP_007687248.1| 317 LSSMQAIAVMALMVLAVFAGLVFVNGGVENMFSDLFH 353
                                       789999***************************8765 PP

>> Acyl-CoA_dh_C  Acetyl-CoA dehydrogenase C-terminal like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     4e-05      0.18      48      86 ..     120     156 ..     112     190 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4e-05
                     Acyl-CoA_dh_C  48 laaavpyLelfGdvvigwlllrqalaAqaklaagekdaa 86 
                                       ++a+  +++++Gdv++++l  ++++   +++++  +d a
  gi|474933666|ref|YP_007687248.1| 120 FLASFKFMMVVGDVLCAFLVRWMVAKLTDDQSK--GDVA 156
                                       68999******************9887666554..4555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (521 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       995  (0.0554967); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.71u 0.32s 00:00:01.03 Elapsed: 00:00:00.48
# Mc/sec: 3244.72
//
Query:       gi|474933667|ref|YP_007687249.1|  [L=328]
Description: hypothetical protein TALC_00074 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2323.39
//
Query:       gi|474933668|ref|YP_007687250.1|  [L=380]
Description: Glycosyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-30  105.9   0.0    3.4e-30  104.8   0.0    1.6  1  Glycos_transf_1  Glycosyl transferases group 1
    5.9e-24   85.0   0.1    2.2e-23   83.2   0.0    2.0  2  Glyco_trans_1_4  Glycosyl transferases group 1
    6.7e-22   78.3   0.0      1e-21   77.7   0.0    1.3  1  Glyco_transf_4   Glycosyltransferase Family 4
    1.7e-08   35.1   0.0    3.3e-08   34.1   0.0    1.5  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    4.9e-05   23.4   0.1     0.0001   22.4   0.1    1.6  1  Glyco_trans_4_2  Glycosyl transferase 4-like
    0.00012   22.5   0.0    0.00024   21.4   0.0    1.6  1  Glyco_trans_1_2  Glycosyl transferases group 1
     0.0042   16.1   0.1     0.0065   15.4   0.1    1.3  1  Glyco_hydro_130  beta-1,4-mannooligosaccharide phosphorylase


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.8   0.0   1.3e-33   3.4e-30      13     163 ..     200     342 ..     191     375 .. 0.94

  Alignments for each domain:
  == domain 1  score: 104.8 bits;  conditional E-value: 1.3e-33
                                       TT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHH CS
                   Glycos_transf_1  13 ekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleel 89 
                                       ++k++++ vgr++ eK ++++++ +++l    +++++l+++G+g+  + lk++a+el+++d+v f g+v++e+l e+
  gi|474933668|ref|YP_007687250.1| 200 QGKRVMVHVGRVSFEKEINRIVEIMPRL----DEDIVLLVVGKGPAMEPLKQQAKELGVEDRVVFAGFVPDEELTEY 272
                                       689***********************99....899****************************************** PP

                                       HHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHH CS
                   Glycos_transf_1  90 lknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelre 163
                                       + + di ++ s++E  ++++l A+a+glpv +s+a  ++++ +dg +G+l+    +++++ea++k   ++    
  gi|474933668|ref|YP_007687250.1| 273 YGAGDICIMASRWETECLTVLHALACGLPVACSDARALRDYMTDGYNGFLFGDS-PDDIVEAVNKCFASG---T 342
                                       ***************************************************999.**********99888...3 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0         1   2.7e+03      87     100 ..     100     113 ..       5     122 .. 0.68
   2 !   83.2   0.0   8.7e-27   2.2e-23       2     132 ..     203     338 ..     202     340 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1
                                       HHHHHHTT-EEEE- CS
                   Glyco_trans_1_4  87 llEamaaglpvVat 100
                                       ++ a  +g+pv++t
  gi|474933668|ref|YP_007687250.1| 100 VIAAHRLGIPVICT 113
                                       34455566666666 PP

  == domain 2  score: 83.2 bits;  conditional E-value: 8.7e-27
                                       EEEEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---...HHHHHHHT..T-T.TEEEE---..THHHHHHHH- CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkkdvrlvivGdgp.rpeeleelaa..gleerveftGfv..edlaellaaa 73 
                                       +v+++vGr++ + k +  ++e +p+l  +d+ l++vG+gp + e l+++a+  g+e+rv+f+Gfv  e+l e++ a 
  gi|474933668|ref|YP_007687250.1| 203 RVMVHVGRVSFE-KEINRIVEIMPRLD-EDIVLLVVGKGPaM-EPLKQQAKelGVEDRVVFAGFVpdEELTEYYGAG 276
                                       6899*****556.**************.66*********976.4899999779************8667******** PP

                                       SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-.HHHHHHHHHHHH CS
                   Glyco_trans_1_4  74 dvfvaPs..egfglkllEamaaglpvVatdvggiaevv..gengllvppgd.pealaeailrLl 132
                                       d++++ s  e+  l++l a+a+glpv ++d+ ++++++  g ng+l+   d p++++ea+ +++
  gi|474933668|ref|YP_007687250.1| 277 DICIMASrwETECLTVLHALACGLPVACSDARALRDYMtdGYNGFLFG--DsPDDIVEAVNKCF 338
                                       *******99899*******************9****999********7..55*******99875 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.7   0.0     4e-25     1e-21       9     170 .]      21     184 ..      16     184 .. 0.91

  Alignments for each domain:
  == domain 1  score: 77.7 bits;  conditional E-value: 4e-25
                    Glyco_transf_4   9 leLaraLarrG.heVtvvtpgddgpleeevelvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHahspaal 84 
                                       +++ ++L  +G +  ++v+p+++ +++ + ++v+  +++ l + +  ++ + f+++ +r+lk+ + Dv Ha+++  +
  gi|474933668|ref|YP_007687250.1|  21 VDIMEELLNDGeYSAEIVAPDSGNAADHR-PNVHYCKSIKL-STYEGYFVPIFPSHTKRILKNMGADVMHAQGYTLM 95 
                                       56677777777688899********9999.99999999985.5556679999************************* PP

                    Glyco_transf_4  85 gaallalrrrlgiplVltvHglye.....krllkarlkplsrllralerrllrradrviavSeatadelrerygvpp 156
                                        + ++ +++rlgip+++t+H+l       +++ k  ++++ +l + + r+l ++ d ++++S+ ta+elr+  g+  
  gi|474933668|ref|YP_007687250.1|  96 TLKGVIAAHRLGIPVICTFHTLGGdalqyYSPIKIPKNLGVKLSWIYFRQLSKWIDIIVTPSKDTAEELRA-NGIT- 170
                                       9999999999*****************99999999************************************.****. PP

                    Glyco_transf_4 157 ekitVipnGvDler 170
                                       + i+ ip++vD++r
  gi|474933668|ref|YP_007687250.1| 171 KEIRAIPTPVDTNR 184
                                       8***********87 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0   1.3e-11   3.3e-08      56     159 ..      68     178 ..      17     179 .. 0.68

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 1.3e-11
                   Glyco_trans_4_4  56 dlaalralrrllrqrrerpdvvhahspt.aglaarlarrrrgiplvvtlh...glllrrg........sgavrrlyr 120
                                        + ++   +r+l  +  + dv+ha+++t   l +++a+ r gip+++t+h   g++l+++         g +  l  
  gi|474933668|ref|YP_007687250.1|  68 VPIFPSHTKRIL--KNMGADVMHAQGYTlMTLKGVIAAHRLGIPVICTFHtlgGDALQYYspikipknLGVK--L-S 139
                                       445555567788..8899********875788899999788*********4432444444344443222222..2.3 PP

                   Glyco_trans_4_4 121 al.errllrradavlvvseaeaeelralgvpadrvvvvpn 159
                                       ++  r l +  d ++++s + aeelra+g+    ++ +p 
  gi|474933668|ref|YP_007687250.1| 140 WIyFRQLSKWIDIIVTPSKDTAEELRANGIT-KEIRAIPT 178
                                       33379*************************9.57888885 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.1   3.9e-08    0.0001       1     110 [.       2     118 ..       2     156 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 3.9e-08
                   Glyco_trans_4_2   1 killlanlssvh......tlrlake.LakrgyeVhvitpkkgakdeleaegihvhrlkvdrkgpleylkaf..klkk 68 
                                       ki+++++   +h      ++ +++e L +  y  +++ p+ g   + + +  +++++k  + +   ++ +f  + k+
  gi|474933668|ref|YP_007687250.1|   2 KIAIVTDSYHPHmdgviaCVDIMEElLNDGEYSAEIVAPDSGNAADHRPNVHYCKSIK-LSTYEGYFVPIFpsHTKR 77 
                                       7899999888884442222444666566668********9997666666655677777.3444544455766588** PP

                   Glyco_trans_4_2  69 likkikPDvvhahyakpygllgslaarlsgvipvvlsvwGld 110
                                       ++k  + Dv+ha+  + + l g +aa ++g ipv+ +++ l+
  gi|474933668|ref|YP_007687250.1|  78 ILKNMGADVMHAQGYTLMTLKGVIAAHRLG-IPVICTFHTLG 118
                                       ******************************.*****999776 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   9.5e-08   0.00024      14      61 ..     291     339 ..     270     365 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 9.5e-08
                   Glyco_trans_1_2  14 rlfEaaacGafaltddaegleelftpgkevilfe.dleelaekirylla 61 
                                        ++ a+acG ++ ++da +l+++ t+g  ++lf  ++++++e+++++ a
  gi|474933668|ref|YP_007687250.1| 291 TVLHALACGLPVACSDARALRDYMTDGYNGFLFGdSPDDIVEAVNKCFA 339
                                       67889****************************************9876 PP

>> Glyco_hydro_130  beta-1,4-mannooligosaccharide phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   2.5e-06    0.0065     252     317 ..     227     290 ..     199     295 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.5e-06
                                       E-SS-SEEEEBSS-SB-S.-SHHHHSSSSSSBEEEEEEEE-TTEEEEEEEETTTEEEEEEEEHHHHH CS
                   Glyco_hydro_130 252 ldlegkvlartkeyileP.eeeyEeyGdrpnvvFpcgalveeekvlvyyGaaDtaiglaeisveeil 317
                                       ld +  +l + k + +eP +++  e G   +vvF  g + +ee +  yyGa D +i    ++  e l
  gi|474933668|ref|YP_007687250.1| 227 LDEDIVLLVVGKGPAMEPlKQQAKELGVEDRVVF-AGFVPDEE-LTEYYGAGDICIMASRWE-TECL 290
                                       56555789999*******6667899*********.66666666.************988888.5544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2447.02
//
Query:       gi|474933669|ref|YP_007687251.1|  [L=412]
Description: adenosylhomocysteinase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-54  184.9   0.0    2.7e-26   92.4   0.0    2.0  2  AdoHcyase      S-adenosyl-L-homocysteine hydrolase
    6.4e-53  179.1   0.8      1e-52  178.4   0.8    1.3  1  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi
    1.1e-07   31.4   0.0    2.2e-07   30.4   0.0    1.5  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    5.6e-07   29.3   0.1    1.3e-06   28.1   0.1    1.6  1  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
  ------ inclusion threshold ------
      0.047   13.0   1.4       0.13   11.6   1.4    1.7  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain


Domain annotation for each model (and alignments):
>> AdoHcyase  S-adenosyl-L-homocysteine hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.7   0.0   1.3e-29   4.6e-26      12     140 ..       7     131 ..       3     137 .. 0.93
   2 !   92.4   0.0   7.6e-30   2.7e-26     175     291 ..     133     411 ..     127     412 .] 0.98

  Alignments for each domain:
  == domain 1  score: 91.7 bits;  conditional E-value: 1.3e-29
                                       HHHHHHHHHHCC-HHHHHHHHHCTTT-TTTT-EEEEES--SHHHHHHHHHHHHTT-EEEEE-SSTTT--HHHHHHHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase  12 fGrkeielaekempglmalreeyaeekplkgariaGslhmtiqtavLietLvalGaevrWasCnifstqdeaaaaia 88 
                                        G  +++ a + mp + ++ +++++e+pl+g +i  +lh  ++t +L  tL + Gae+r asCn  st+d +aaa+ 
  gi|474933669|ref|YP_007687251.1|   7 KGSLRLHWAYEHMPVIQEIDKKFRKEQPLAGLKIGMALHTEAKTGMLAVTLANAGAEIRLASCNPLSTDDSVAAALR 83 
                                       6777888999******************************************************************* PP

                                       CT.TEEEE--TT--HHHHHHHHHHCHS-SSTS-S-SEEEESSSHHHHHHHHHH CS
                                       xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase  89 ea.gvpvfawkgetleeywwcieqalkwaedekepnlilDdGGDltllvhkgv 140
                                       e+ g++v+a k e+ eey   ++++l++     +p++++DdG Dl ++ h+  
  gi|474933669|ref|YP_007687251.1|  84 EEfGLKVYAKKFESDEEYYANLNSVLDM-----KPDFVIDDGADLITMAHTSR 131
                                       999***********************66.....7***********99999854 PP

  == domain 2  score: 92.4 bits;  conditional E-value: 7.6e-30
                                       CCHCC--EEEE-SHHHHHHHHHHHHTT---SEEEESTTSHHHCTTH............................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................... RF
                         AdoHcyase 175 ellkkikGvseetttGvhrLyelakkgkLlvpainvndsvtkskfD............................... 220
                                       ++l++ikG  eetttG+ rL+ +a+++kL++p ++vnds  k  fD                               
  gi|474933669|ref|YP_007687251.1| 133 DALSNIKGGNEETTTGIVRLKAMAADKKLEFPVMDVNDSKMKYLFDnrygtgqsvfdgwmnatnlivagknvvvagy 209
                                       56899************************************************************************ PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                         AdoHcyase 221 ............................................................................. 220
                                                                                                                    
  gi|474933669|ref|YP_007687251.1| 210 gwcgkgvamrskglgalvtvtevdpvkaiearmdgfevkpmreavrnadivltvtgckdivtkedflnmkdgcvmgn 286
                                       ***************************************************************************** PP

                                       ......................................................S-HHHHHHHHHHHHHHHHHHHHT CS
                                       ......................................................xxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase 221 ......................................................hpsfvmsasftnqvlaqielfkk 243
                                                                                             hp+ +m++sf++q++a + + ++
  gi|474933669|ref|YP_007687251.1| 287 aghfdneiskkdlneisvskepvrdfidcytlkdgrklyligegrlmnlaagqgHPAEIMDTSFSTQAMAIVYMVEN 363
                                       ***************************************************************************** PP

                                       TSSS-SSEEE--CHHHHHHHHHCCCCCT-------HHHHHCCTSXTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase 244 ekkyekkvyvlpkklDekvarlhleklgaklteltkeqaeyigveveG 291
                                       ++k +++v  +p ++D+++ar++l++lg++++++t+eq +yi+  +eG
  gi|474933669|ref|YP_007687251.1| 364 HDKLSNQVIPVPDEIDNELARIKLRTLGIEIDSFTEEQYNYIHSWQEG 411
                                       ******************************************977776 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.4   0.8   2.9e-56     1e-52       1     161 [.     179     339 ..     179     340 .. 0.99

  Alignments for each domain:
  == domain 1  score: 178.4 bits;  conditional E-value: 2.9e-56
                                       HHHHHCCCCCHHHHHHH-S--TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTT CS
                     AdoHcyase_NAD   1 nlygcreslvdgikratdvllaGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvk 77 
                                       n yg+ +s+ dg + at++++aGk++vvaGyG  GkG a   kglGa v+vtevdP+ a+ a m+Gfev+ + e+v+
  gi|474933669|ref|YP_007687251.1| 179 NRYGTGQSVFDGWMNATNLIVAGKNVVVAGYGWCGKGVAMRSKGLGALVTVTEVDPVKAIEARMDGFEVKPMREAVR 255
                                       78*************************************************************************** PP

                                       T-SEEEE-SSSSSSB-HHHHCCS-TTEEEEE-SSTTTTBTHHHHHTTT-EEEEEETTEEEEE-TTS-EEEEEGGGSB CS
                     AdoHcyase_NAD  78 kadivvtttGnkdiitlehlkkmkddaivcniGhfdseidvaaleanalkkeevkpqvdrvtlkdgkkiillaeGrl 154
                                       +adiv+t+tG+kdi+t+e++ +mkd ++++n Ghfd+ei  + l++ +++ke v+  +d +tlkdg+k+ l+ eGrl
  gi|474933669|ref|YP_007687251.1| 256 NADIVLTVTGCKDIVTKEDFLNMKDGCVMGNAGHFDNEISKKDLNEISVSKEPVRDFIDCYTLKDGRKLYLIGEGRL 332
                                       ***************************************************************************** PP

                                       CHHHTS- CS
                     AdoHcyase_NAD 155 lnlgcat 161
                                       +nl++ +
  gi|474933669|ref|YP_007687251.1| 333 MNLAAGQ 339
                                       ***9865 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   6.3e-11   2.2e-07      33     127 ..     198     288 ..     178     316 .. 0.88

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 6.3e-11
                                       -GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S--STTTTTSB CS
                      2-Hacid_dh_C  33 elsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDivslhlpltpetrhli 109
                                        ++gk v + G+G  G+ va r k++g+ v+++++ + k  e++  g+e+  + e+++++Div  ++      ++++
  gi|474933669|ref|YP_007687251.1| 198 IVAGKNVVVAGYGWCGKGVAMRSKGLGALVTVTEVDPVKAIEARMDGFEVKPMREAVRNADIVLTVTG----CKDIV 270
                                       479*************************999999999988899999****************988776....678** PP

                                       SHHHHHCSTTTEEEEESS CS
                      2-Hacid_dh_C 110 naeelakmkkgailiNta 127
                                       ++e +  mk+g ++ N++
  gi|474933669|ref|YP_007687251.1| 271 TKEDFLNMKDGCVMGNAG 288
                                       ***********9998887 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.1   3.5e-10   1.3e-06       2      68 ..     199     264 ..     198     296 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 3.5e-10
                                       HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-H.HHHHHHHTT-EEEEHHHHHHT-SEEEE-S CS
                              IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsk.svkkAkeegfevltvaeavkkadvvmili 68 
                                       + gk+++v GyG  G+  a  +r  gl   v++ e +  ++ +A+ +gfev+ ++eav++ad+v++++
  gi|474933669|ref|YP_007687251.1| 199 VAGKNVVVAGYGWCGKGVA--MRSKGLGALVTVTEVDPvKAIEARMDGFEVKPMREAVRNADIVLTVT 264
                                       679************9877..6666666666666555437889*********************9875 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.4   3.5e-05      0.13      27     123 ..     200     283 ..     179     284 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.5e-05
                                       ---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHHHHH-SEEEE---BTT CS
                       AlaDh_PNT_C  27 epakvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeellaeavkeadvvigtvlipG 103
                                       +  +v+v G G  G   +  +kglga Vtv++v+p ++ + +  g         + + ++eav++ad+v +   ++G
  gi|474933669|ref|YP_007687251.1| 200 AGKNVVVAGYGWCGKGVAMRSKGLGALVTVTEVDPVKAIEARMDGF--------EVKPMREAVRNADIVLT---VTG 265
                                       55689****************************9976655544333........34567788888888876...455 PP

                                       SS---SC-HHHHHTS-TTEE CS
                       AlaDh_PNT_C 104 kkaPkLvteemvksMkpgsV 123
                                        k   +vt+e   +Mk+g V
  gi|474933669|ref|YP_007687251.1| 266 CK--DIVTKEDFLNMKDGCV 283
                                       54..5777777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 2730.00
//
Query:       gi|474933670|ref|YP_007687252.1|  [L=249]
Description: archaeal conserved hypothetical protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-67  225.8   0.5    3.2e-67  225.5   0.5    1.1  1  PPS_PS    Phosphopantothenate/pantothenate synthetase
  ------ inclusion threshold ------
       0.16   11.9   0.1       0.32   10.9   0.0    1.5  2  Sec34     Sec34-like family


Domain annotation for each model (and alignments):
>> PPS_PS  Phosphopantothenate/pantothenate synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.5   0.5   3.5e-71   3.2e-67       1     176 []      65     239 ..      65     239 .. 0.98

  Alignments for each domain:
  == domain 1  score: 225.5 bits;  conditional E-value: 3.5e-71
                            PPS_PS   1 lllakkpvisvNGNtaaLvaeeiveLaealgaklevNlfyrteeRvekiaellkeagaeevlgleedaripeleseR 77 
                                       ll+akkp+++vNGN++aL +  +++La+++ ak+evN+f+rteeR+e++ e+++++ga+ +lg++ darip+l+s+R
  gi|474933670|ref|YP_007687252.1|  65 LLKAKKPIVCVNGNSIALEPGGLIALAQSVPAKMEVNIFHRTEERMEQLIEYMESQGAKGILGRNPDARIPNLTSDR 141
                                       799************************************************************************** PP

                            PPS_PS  78 akvskeGiysaDvvlvplEDGDRaeaLvkmgKkviaiDLNPlsRtartatitivdnvvRalpnlteavkelkkkske 154
                                       a ++keGi+++Dv++vp+EDGDRaeaL +mgK+vi+iDLNPlsRt+r+a+++i d++ Ra++n+ ++v+el+  +++
  gi|474933670|ref|YP_007687252.1| 142 ALCTKEGIFDSDVIVVPIEDGDRAEALIAMGKTVISIDLNPLSRTSRVASVPISDEISRAVENIRKFVEELRG-KDD 217
                                       ***********************************************************************65.778 PP

                            PPS_PS 155 eleeivkefdnkkvlkealkei 176
                                       e+++i+k+f++ ++ ++++++i
  gi|474933670|ref|YP_007687252.1| 218 EIDAIIKQFSSVRTRRDTIDHI 239
                                       9**********99999998876 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0      0.65   5.8e+03      97     109 ..     106     118 ..      90     120 .. 0.61
   2 ?   10.9   0.0   3.6e-05      0.32       3      53 ..     196     246 ..     194     249 .] 0.94

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.65
                             Sec34  97 mLkklDeclefle 109
                                       + +++++ +e++e
  gi|474933670|ref|YP_007687252.1| 106 TEERMEQLIEYME 118
                                       3345555566665 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 3.6e-05
                             Sec34   3 dqLeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqllee 53 
                                       d++++  e++++++e+++   ++++ + ++f+sv ++  ++++ c++l++e
  gi|474933670|ref|YP_007687252.1| 196 DEISRAVENIRKFVEELRGKDDEIDAIIKQFSSVRTRRDTIDHICKSLMSE 246
                                       67889999****************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       822  (0.0458475); expected 358.6 (0.02)
Passed bias filter:                      769  (0.0428914); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1619.43
//
Query:       gi|474933671|ref|YP_007687253.1|  [L=222]
Description: hypothetical protein TALC_00078 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
        1.8    8.1   6.6       0.43   10.1   0.5    2.2  2  E1-E2_ATPase    E1-E2 ATPase
        2.5    7.6   4.8       0.72    9.4   0.4    2.1  2  DUF5527         Family of unknown function (DUF5527)
        5.7    5.4   8.0        8.5    4.9   8.0    1.2  1  Chitin_synth_2  Chitin synthase


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.5   7.2e-05      0.43     110     160 ..       5      58 ..       2      60 .. 0.87
   2 ?    0.9   0.9     0.048   2.9e+02     116     138 ..      99     121 ..      65     146 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 7.2e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTT...HHHHHHHHHHHHHS- CS
                      E1-E2_ATPase 110 plqkkldklgkvlvpvvlliallvflialllgksla...eallralallvaaiP 160
                                       ++++k+d    +l+p++lli+++++ + + +g+       a   ++a+lva+iP
  gi|474933671|ref|YP_007687253.1|   5 EFERKIDLACIFLFPAGLLIFFVLARLGYATGEYGDtyiAATHIVIAMLVAIIP 58 
                                       799*************************99888887775666669********9 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.048
                                       HHHHHHHHHHHHHHHHHHHHS-S CS
                      E1-E2_ATPase 116 dklgkvlvpvvlliallvflial 138
                                       d+++ +++++ + ++++v+l ++
  gi|474933671|ref|YP_007687253.1|  99 DEFAHWMSTLFVSMVVFVALCLI 121
                                       45555655555555555544444 PP

>> DUF5527  Family of unknown function (DUF5527)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.4   0.00012      0.72      45      65 ..      10      30 ..       6      33 .. 0.91
   2 ?   -1.5   0.4      0.28   1.7e+03      53      64 ..     108     119 ..     105     128 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00012
                           DUF5527 45 ialvCiflllatflifvtlCk 65
                                      i l+Cifl+ a +lif++l +
  gi|474933671|ref|YP_007687253.1| 10 IDLACIFLFPAGLLIFFVLAR 30
                                      679**************9976 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.28
                           DUF5527  53 llatflifvtlC 64 
                                       l+ ++++fv+lC
  gi|474933671|ref|YP_007687253.1| 108 LFVSMVVFVALC 119
                                       567889999999 PP

>> Chitin_synth_2  Chitin synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   8.0    0.0014       8.5     401     492 ..      10     107 ..       3     112 .. 0.61

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0014
                    Chitin_synth_2 401 ieligtvvlPvaiaftlylivasilksklv.pviplvllaivlGlpailivlt.arkleyvawllvyllalPifnfv 475
                                       i+l    + P+ ++  + l      + ++   +i+     ++  l ai+  ++ +rkl++  w+++ +++l i+++ 
  gi|474933671|ref|YP_007687253.1|  10 IDLACIFLFPAGLLIFFVLARLGYATGEYGdTYIAAT-HIVIAMLVAIIPAIRyTRKLVFPYWFVI-IITLNIYAYG 84 
                                       5666666666655444444333333333330333333.3345557777776654799999999877.789******* PP

                    Chitin_synth_2 476 lPly.....afwhlddfs.wGet 492
                                       +Pl+      fw  d+f+ w  t
  gi|474933671|ref|YP_007687253.1|  85 IPLFlgfydNFWWWDEFAhWMST 107
                                       99874444569999999646665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1495.96
//
Query:       gi|474933672|ref|YP_007687254.1|  [L=188]
Description: hypothetical protein TALC_00079 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.91    8.9  13.9        1.3    8.4  13.9    1.2  1  TssN       Type VI secretion system, TssN
        1.7    8.3  12.3       0.15   11.7   5.6    2.0  2  CPP1-like  Protein CHAPERONE-LIKE PROTEIN OF POR1-like
        2.3    7.9  14.6      0.037   13.7   3.5    2.7  2  MlaE       Permease MlaE


Domain annotation for each model (and alignments):
>> TssN  Type VI secretion system, TssN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4  13.9   0.00021       1.3      18     147 ..      36     171 ..      24     178 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00021
                              TssN  18 lsliakknkllkkkkliiyiLlaglvlalpgllgf.lknefvpygyillqilylllGilhlylllkkffkelkekk. 92 
                                       +s++   +++l +   i++ +l ++ la+   l++ +++e    g+ l++i y +lG++ ++ l+  f+ ++  +  
  gi|474933672|ref|YP_007687254.1|  36 ISVLYIVEAFLGRNIRIVFPILHIIALAVSLALAYgIDTECY-PGFRLCVIPYPVLGFCAVISLIAFFNLKFYRELi 111
                                       333333345666666788888999999999999996666666.69*****************999999999998887 PP

                              TssN  93 ilfeilltlivillglvlfvlvfn.....llselqygvwaatsllvfiipllflktykal 147
                                        +f +l+ l +  +  v+ +++++      +++   +   a+++++ i+  + +++y+++
  gi|474933672|ref|YP_007687254.1| 112 ATFIFLFGLAISSFTGVVIYMLYHsefdiTVNNALNTQEFAAAFVWCIVFAVAFMVYEKM 171
                                       777777777665555555555544111122333334445566667777777777777766 PP

>> CPP1-like  Protein CHAPERONE-LIKE PROTEIN OF POR1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   1.7     0.072   4.3e+02     102     152 ..       6      57 ..       1      85 [. 0.62
   2 ?   11.7   5.6   2.6e-05      0.15     122     194 ..      90     164 ..      52     167 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.072
                         CPP1-like 102 vflvlavltlvapaes.vpalllalglgasiyflnrKekklgravlltlvgL 152
                                       v ++++v++l+a+ +  +p+l+ a ++ + i +l+  e  lgr + + +  L
  gi|474933672|ref|YP_007687254.1|   6 VTVLFSVISLAAGISLeSPPLVSASAVSVFISVLYIVEAFLGRNIRIVFPIL 57 
                                       4444555555555544677777777777777777777777777766666555 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 2.6e-05
                         CPP1-like 122 llalglgasiyflnrKekklgravlltlvgLvvGlllGsllasllqvd..valsglsseellvslvtlvllwlvs 194
                                       l  +++++ i f n K  + + a  + l gL+++ + G ++  l +++  ++++++ + + ++++++ ++ ++v+
  gi|474933672|ref|YP_007687254.1|  90 LGFCAVISLIAFFNLKFYRELIATFIFLFGLAISSFTGVVIYMLYHSEfdITVNNALNTQEFAAAFVWCIVFAVA 164
                                       55689999************************************99999999999999999*********99997 PP

>> MlaE  Permease MlaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.4     0.031   1.9e+02     110     130 ..      52      72 ..      48      79 .. 0.87
   2 ?   13.7   3.5   6.1e-06     0.037     115     178 ..     111     174 ..      90     184 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.031
                              MlaE 110 ialplLtviadlvgilggylv 130
                                       i++p+L +ia++v+++ +y +
  gi|474933672|ref|YP_007687254.1|  52 IVFPILHIIALAVSLALAYGI 72 
                                       899***********9999865 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 6.1e-06
                              MlaE 115 LtviadlvgilggylvavlllgispgaylqsvqealslkdllvgllKalvfGliialiacyqGl 178
                                       ++ +++l+g++++ +++v+++ +  +++  +v +al+++++  +++ ++vf+++ ++   ++Gl
  gi|474933672|ref|YP_007687254.1| 111 IATFIFLFGLAISSFTGVVIYMLYHSEFDITVNNALNTQEFAAAFVWCIVFAVAFMVYEKMKGL 174
                                       56788999************************************************99999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       990  (0.0552178); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1327.65
//
Query:       gi|474933673|ref|YP_007687255.1|  [L=249]
Description: LPS biosynthesis protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-27   96.5   0.2      2e-18   67.4   0.5    2.1  2  LicD          LicD family
  ------ inclusion threshold ------
      0.012   15.2   0.0      0.018   14.7   0.0    1.3  1  NTP_transf_5  Uncharacterised nucleotidyltransferase
        0.1   12.7   0.1       0.37   10.9   0.0    1.9  2  Polbeta       Polymerase beta, Nucleotidyltransferase


Domain annotation for each model (and alignments):
>> LicD  LicD family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.4   0.5   3.3e-22     2e-18       2     109 ..      20     119 ..      19     152 .. 0.74
   2 !   27.0   0.0   7.2e-10   4.3e-06     188     227 .]     176     217 ..     154     217 .. 0.85

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 3.3e-22
                              LicD   2 kkngleywLsgGTllGavRhggfIPWDDDiDlqmprkdyerLaevfnqlilk..kedlreaekdknylenfaklldk 76 
                                       +++g++++L++G++lGavRh gfIPWDDDiDl    kd+ r  +++ q  l+  k++            + a+   +
  gi|474933673|ref|YP_007687255.1|  20 ESHGIPFYLCYGSALGAVRHDGFIPWDDDIDLAVWEKDLPRIDDAMTQ-DLDsnKYYWHF---------PSADTHPH 86 
                                       58******************************************9999.44322444433.........22333333 PP

                              LicD  77 ntsiterkngngkndsglyiDIfpldyvpkskl 109
                                           te  +++ kn+   +iD f l+  p +k 
  gi|474933673|ref|YP_007687255.1|  87 VILKTEDFEDDLKNKRAPFIDLFVLSDSPSTKV 119
                                       333333333333345567999999988887664 PP

  == domain 2  score: 27.0 bits;  conditional E-value: 7.2e-10
                              LicD 188 l..rnkeilpleelsplkkvkFegvevpipnnydkyLtelYg 227
                                       +  r++ ++p+e++ +++++ Fe++ vp p++yd++Lt+lYg
  gi|474933673|ref|YP_007687255.1| 176 CaiRQNDVFPKEWWGEPIMHRFEDTDVPLPKEYDAVLTQLYG 217
                                       144799***********************************8 PP

>> NTP_transf_5  Uncharacterised nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0     3e-06     0.018      54     115 ..       6      67 ..       2     151 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3e-06
                      NTP_transf_5  54 llllaeleellalleeegipvllLKGpalaqlYpdpalRemgDiDllvkredldraeelLee 115
                                       ++l+   + + + le +gip+ l  G+al ++  d +  +  DiDl v ++dl+r+++ +++
  gi|474933673|ref|YP_007687255.1|   6 ARLISMYKDVSEVLESHGIPFYLCYGSALGAVRHDGFIPWDDDIDLAVWEKDLPRIDDAMTQ 67 
                                       66777889999************************************************953 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   6.2e-05      0.37       2      48 ..      14      64 ..      13      77 .. 0.81
   2 ?   -1.4   0.0      0.42   2.5e+03      33      45 ..     106     118 ..      88     141 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6.2e-05
                                      STTTTHHHHHHHHSTTEEEEEE-S---.....---EEEEEEEESS---HHHH CS
                           Polbeta  2 kikeilekekeielaylFGSrakgkar.....eeSDiDlavllkekldleee 48
                                       ++e+le++ +i + + +GS +    +      + DiDlav  k+  ++++ 
  gi|474933673|ref|YP_007687255.1| 14 DVSEVLESH-GIPFYLCYGSALGAVRHdgfipWDDDIDLAVWEKDLPRIDDA 64
                                      67899****.**********99666666667669*******99988666654 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.42
                                       EEEEEEESS---H CS
                           Polbeta  33 iDlavllkekldl 45 
                                       iDl+vl ++  ++
  gi|474933673|ref|YP_007687255.1| 106 IDLFVLSDSPSTK 118
                                       5666666655443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1732.31
//
Query:       gi|474933674|ref|YP_007687256.1|  [L=609]
Description: 2-aminoethylphosphonate aminotransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.2e-29  100.9   0.0    1.1e-28  100.3   0.0    1.2  1  Aminotran_5      Aminotransferase class-V
      4e-09   37.0   0.0    6.6e-09   36.3   0.0    1.4  1  NTP_transf_3     MobA-like NTP transferase domain
    5.9e-06   26.1   0.0      1e-05   25.2   0.0    1.4  1  NTP_transferase  Nucleotidyl transferase
     0.0031   16.1   0.0     0.0073   14.9   0.0    1.6  2  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
  ------ inclusion threshold ------
      0.012   15.4   0.0      0.021   14.5   0.0    1.4  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
      0.083   12.6   0.0       0.16   11.7   0.0    1.4  1  Ad_Cy_reg        Adenylate cyclase regulatory domain


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.3   0.0   3.7e-32   1.1e-28      27     327 ..     267     560 ..     262     590 .. 0.84

  Alignments for each domain:
  == domain 1  score: 100.3 bits;  conditional E-value: 3.7e-32
                                       CCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHH.HHHHHHHHCCCC-TTTSEEEEETTSHGGGT CS
                       Aminotran_5  27 nanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtte.ainlvalslarslkpgdeivvteaehhanl 102
                                       +a+v+  +  +++e+ + ve + +++a + + + + e++   G+++ + ++++ s    + +  + ++++++  +++
  gi|474933674|ref|YP_007687256.1| 267 YAQVQADICPRENEFGDVVEWVADELALMAGKPGRVETVLFGGSGTaGDEAMISSC---VPDSGKLLIVDNGAYGKR 340
                                       6777778888999999999999999**99999998887776666664888888888...99**************** PP

                                       HHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH-.-TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TT CS
                       Aminotran_5 103 vpwqelakrtgakvkvipldeegeldldelekll.nektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaq 178
                                         ++++a+  g++ +v+  d   +ld+ ++ek l + k    a+  ++++tG+++pv+++++ ++ kg++++vDa++
  gi|474933674|ref|YP_007687256.1| 341 --MAKMAEIYGLDFEVYHSDGVNRLDIPDIEKRLvDGKFTHFAVIYHETTTGILNPVPQLCRFCHSKGIVTIVDAVS 415
                                       ..7788889*****************999988874799*************************************** PP

                                       TTTTS---HHHHTESEEEEETTT.TTSSTT-EEEEEEHHHHHTS..SS.STTSEEEEETTEEEEHCTTGGGS.SS-- CS
                       Aminotran_5 179 avghipidvkklgvDflafsghK.llgPtGiGvlyvrkellekleplllggemveevsleettfaeapskfeaGTpn 254
                                       a+   pid+++  +Df+a+++ K + g +Gi ++++rk++le+++   +  ++++ ++ + + +++  ++f   Tp+
  gi|474933674|ref|YP_007687256.1| 416 AFAAVPIDMDEDCIDFMASTSNKnIQGMAGIAFVFCRKDALEAIKDYPMRNYYLNIYDQNAYFQKTHQMRF---TPP 489
                                       ***********************999*******************99999999999999888888888888...6** PP

                                       HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEETTCSHHHHHHH CS
                       Aminotran_5 255 vagiiglgaaleyleeigleaiekhekelaeyllerlkslpgvrlygpdkaerrasivsfnfkgvhaedvatl 327
                                       v  +++l++a+   +   +e   ++ +e  + l++++k+l+   +   +++e+++ i+s+  ++ +  d+ tl
  gi|474933674|ref|YP_007687256.1| 490 VQTFYALRQAIIETKLETIEGRYARYTECWHILMDAVKKLGLRSI--VSEEEQSHLIISIENPSSEKYDFNTL 560
                                       **********97665555555555555666666666666666666..36789999999*99999999888776 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.0   2.2e-12   6.6e-09       1      95 [.       5     106 ..       5     189 .. 0.86

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 2.2e-12
                                       EEEEEESS-TTTTT.....THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH.CHHHHHH.TTCT.S-EEE-TTSS CS
                      NTP_transf_3   1 aviLAGGrSsRmgg.....dKallplggkpllervldalraagvdevvvvggd.eevlaal.arlg.vrvvededpg 69 
                                       avi+AGG +sR++      +K +l+++g  ++e ++++l  agv+e+++ +g+ +e ++ l +++  +++++++d+ 
  gi|474933674|ref|YP_007687256.1|   5 AVIMAGGLGSRLKDrtatmPKGFLEIDGMAIVESSVRKLIWAGVEEIIIGTGHcSEYYEKLaEKYScITLAHNPDYA 81 
                                       79**********8335668**********************************755555550555568889999995 PP

                                       .-SHHHHHHHHHHHH.SSSCEEEEETT CS
                      NTP_transf_3  70 .kgplaslaaalraaadadavlvlacD 95 
                                        +g +++la+ ++++     +l+l  D
  gi|474933674|ref|YP_007687256.1|  82 nTGSMGTLACCAEKV--YGEFLLLESD 106
                                       499999999999876..4555555555 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   3.5e-09     1e-05       2     116 ..       5     110 ..       4     122 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 3.5e-09
                                       EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEE CS
                   NTP_transferase   2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlia 78 
                                       avI+aGG G+RL + t t++k  + + g   +++  + +l+ +g+ee i++ t + s+ +e+ +++ s+    ++ a
  gi|474933674|ref|YP_007687256.1|   5 AVIMAGGLGSRLKDRTATMPKGFLEIDGM-AIVESSVRKLIWAGVEE-IIIGTGHCSEYYEKLAEKYSC----ITLA 75 
                                       8*****************99999988888.*****************.889888888888888777775....4455 PP

                                       EESS--..BGGHHHHHTHHHHTTSSE..EEEEETTEEEES CS
                   NTP_transferase  79 lepegk..gtAdAvalaaelledeksdelvlvLggDhlik 116
                                       + p     g+ + +a  ae +  e     +l L +D +++
  gi|474933674|ref|YP_007687256.1|  76 HNPDYAntGSMGTLACCAEKVYGE-----FLLLESDLVYD 110
                                       555555114444444444444433.....57888888876 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.4e-06    0.0073      68     202 ..     303     442 ..     289     532 .. 0.82
   2 ?   -2.3   0.0       0.4   1.2e+03     131     169 ..     532     570 ..     510     572 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.4e-06
                                       SEEEEESSHHHHHHHHHHTTS-T.TEEEEEESTSSHHHHHHHHHTHHH.TTC.EEEEESTTSHHHHHHHCCT....T CS
                   Cys_Met_Meta_PP  68 eaalavssGmaAiaaailallka.GdeivvsddlYggtqrllkkvlkk.lgi.evkfvdtsdleelekaike....n 137
                                       e +l   sG+a  +a+i + +   G+ ++v++ +Yg+  + + +++   +++ +++ v+  d+ ++ek + +    +
  gi|474933674|ref|YP_007687256.1| 303 ETVLFGGSGTAGDEAMISSCVPDsGKLLIVDNGAYGKRMAKMAEIYGLdFEVyHSDGVNRLDIPDIEKRLVDgkftH 379
                                       5556668************99766999**********998888876543555256789999999**99998876556 PP

                                       EEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTHTTTS-GGGGT...-SEEEEETTTTTTC CS
                   Cys_Met_Meta_PP 138 tklvylEtptnpllkvvDiekiaklakkagvlvvvDntfaspllqrplklg...aDivvhSaTKylgG 202
                                         ++y Et t +l  v   ++++++++++g++++vD++  s +   p++++   +D       K ++G
  gi|474933674|ref|YP_007687256.1| 380 FAVIYHETTTGILNPV---PQLCRFCHSKGIVTIVDAV--SAFAAVPIDMDedcIDFMASTSNKNIQG 442
                                       789********99876...57899************86..6666777777744555566666676666 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.4
                                       HHHCCTTEEEEEEESS-TTTT----HHHHHHHHHHTT-E CS
                   Cys_Met_Meta_PP 131 ekaikentklvylEtptnpllkvvDiekiaklakkagvl 169
                                       ++ ++e+ +  ++ ++ np  +  D++++ +la+++g +
  gi|474933674|ref|YP_007687256.1| 532 RSIVSEEEQSHLIISIENPSSEKYDFNTLHDLARSRGFT 570
                                       55566666666777999*************999998855 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   7.2e-06     0.021       3      51 ..       5      55 ..       3      76 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.2e-06
                                      EEEECTTSSCTT-...SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE CS
                              IspD  3 vvipAAGsGkRmk...aglpKqflelkgqtllehtvdallaskavdkivvvv 51
                                      +vi A G G+R+k   a +pK fle++g +++e +v+ l     v++i++  
  gi|474933674|ref|YP_007687256.1|  5 AVIMAGGLGSRLKdrtATMPKGFLEIDGMAIVESSVRKLIW-AGVEEIIIGT 55
                                      89**********8333578******************9987.6788888754 PP

>> Ad_Cy_reg  Adenylate cyclase regulatory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   5.4e-05      0.16      94     149 ..     140     192 ..     127     210 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.4e-05
                         Ad_Cy_reg  94 vllraDaeaaarakrfldlGldedqivavarvLaegLsraaevlReaalkallepg 149
                                       + ++aD ++ +++k+  ++G  + ++v ++++  + Lsr +e +     ++ ++p 
  gi|474933674|ref|YP_007687256.1| 140 LETDADGNLLRHSKKREEIGTVAGELVGITKLSKDTLSRMVEYMN---AEKAVQPK 192
                                       34689999***********************************93...34455554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (609 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.49
# Mc/sec: 3711.70
//
Query:       gi|474933675|ref|YP_007687257.1|  [L=372]
Description: phosphonopyruvate decarboxylase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-18   66.1   1.1    2.4e-17   63.1   0.5    2.4  2  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    6.7e-14   51.9   0.0    1.9e-13   50.4   0.0    1.7  2  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
  ------ inclusion threshold ------
      0.016   14.6   0.0       0.13   11.7   0.0    2.0  2  PALP          Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0     0.068     4e+02      30      78 ..      47      97 ..      29     161 .. 0.80
   2 !   63.1   0.5   4.1e-21   2.4e-17      24     153 .]     226     342 ..     203     342 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.068
                                      TTTHHHHHHHHHHHSTTSEEE..EEEEHHHHHHTGGGHHHHHHTT-SEEEE CS
                      TPP_enzyme_C 30 mGyglpaAiGaklakpdrevv..aivGDGgflmilqelatavrrnlpitvv 78
                                       G++++ A G  la  + +vv    +G G ++  l  l+    + +p +++
  gi|474933675|ref|YP_007687257.1| 47 EGNSVGLAAGYHLATGKVPVVylQNSGEGNIINPLASLISEEVYAIPCIFI 97
                                      589999999999987777887334467777766666666655555555555 PP

  == domain 2  score: 63.1 bits;  conditional E-value: 4.1e-21
                                       ETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-.SEEEEEEE-SBCCCHHHHHHHHTCCT CS
                      TPP_enzyme_C  24 sgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnl.pitvvvlnNegygmtggqqepfggkr 99 
                                         + g+mG + ++A+G+++ kp+ ++++i GDG+ lm++  +at+   +  +++++++nN +   +gg ++ +    
  gi|474933675|ref|YP_007687257.1| 226 FLTVGSMGHSSSIALGIAINKPKTRIWCIDGDGSALMHMGSMATVGAVKPvNLIHIIINNFAHESVGGMPTVA---- 298
                                       3379**********************************9999999888888**************99977655.... PP

                                       TTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                      TPP_enzyme_C 100 ksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpaliev 153
                                                ++vdf+ +a+a+G   +++v+++  e+l+ ++    + +gp++ie+
  gi|474933675|ref|YP_007687257.1| 299 ---------NSVDFVSVAKACGYAyAVKVDTY--EDLKWKFTVVKSIEGPCFIEI 342
                                       .........469************67799999..*******************97 PP

>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   0.0   3.1e-17   1.9e-13      14     114 ..      10     118 ..       5     142 .. 0.87
   2 ?   -2.1   0.0      0.44   2.6e+03      88     123 ..     273     309 ..     237     326 .. 0.56

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 3.1e-17
                                       CT--EEEE---CCCHHHHCCHHCT....TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-C.HH.HHHHCHHHHHH CS
                      TPP_enzyme_N  14 lgvehvfgvpGsrilplldalseeq...girvvlarhEqgaafaAdgyaratgkpgvvlvts.gp.Gatnaltalae 85 
                                       lg++ + gvp+s++ +l+d+l +       +++ a +E++ ++ A gy+ atgk+ vv++++ g  +++n l +l++
  gi|474933675|ref|YP_007687257.1|  10 LGADFFTGVPDSQLRQLCDYLMDTYgidPKHHLIAANEGNSVGLAAGYHLATGKVPVVYLQNsGEgNIINPLASLIS 86 
                                       79999******************99775667999**************************99887689********* PP

                                       HHHHT--EEEEEEE--CCCHH...S..TC--T CS
                      TPP_enzyme_N  86 AkvdriPllvlsgdrptslrg...qgvlqqel 114
                                         v  iP++++ g+r++  ++   q+ +q+ +
  gi|474933675|ref|YP_007687257.1|  87 EEVYAIPCIFIIGWRGEPGVHdepQHIQQGKV 118
                                       *****************999955444444333 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.44
                                       HHT--EEEEEEE--CCCHHS..TC--T...-CCHHHCCC CS
                      TPP_enzyme_N  88 vdriPllvlsgdrptslrgqgvlqqel...dqlalfrpv 123
                                       v  + l+++  ++++++   g++  +    d +++++  
  gi|474933675|ref|YP_007687257.1| 273 VKPVNLIHIIINNFAHESVGGMPT-VAnsvDFVSVAK-A 309
                                       555555555555555555522222.221113333322.2 PP

>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.05     3e+02     155     194 ..      35      73 ..      23      90 .. 0.77
   2 ?   11.7   0.0   2.1e-05      0.13     136     202 ..     197     266 ..     167     324 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.05
                                       TTTEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECT CS
                              PALP 155 ggkpdavvvpvGgGgliaGiaaglkerrpdvrvigvepeg 194
                                       g +p++ + ++  G +  G+aag++ + ++v v+  +++g
  gi|474933675|ref|YP_007687257.1|  35 GIDPKHHLIAANEG-NSVGLAAGYHLATGKVPVVYLQNSG 73 
                                       55566555555555.899*************999998876 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 2.1e-05
                                       SHHHHHHHHTHHHHHH...HHTTTTEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCC CS
                              PALP 136 nptviegygtiglEil...eqlggkpdavvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarsl 202
                                       +  ++   g +  E+    e lg+  +  +++vG+ g  + ia g++ ++p++r+  ++ +gs+ ++ + 
  gi|474933675|ref|YP_007687257.1| 197 DDPIVSTTGKTSRELFevrESLGQGHNNDFLTVGSMGHSSSIALGIAINKPKTRIWCIDGDGSALMHMGS 266
                                       444555566666777655699996666669********************************99998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2729.89
//
Query:       gi|474933676|ref|YP_007687258.1|  [L=431]
Description: phosphoenolpyruvate phosphomutase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-66  224.7   0.1    2.3e-66  223.7   0.1    1.5  2  PEP_mutase       Phosphoenolpyruvate phosphomutase
    6.1e-13   49.2   0.0    5.9e-12   46.0   0.0    2.2  2  CTP_transf_like  Cytidylyltransferase-like


Domain annotation for each model (and alignments):
>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.42   3.7e+03     215     237 ..      85     107 ..      49     108 .. 0.60
   2 !  223.7   0.1   2.5e-70   2.3e-66       9     239 .]     156     406 ..     148     406 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.42
                        PEP_mutase 215 arislgnhllraalaalreaaee 237
                                         i++g +    a++a+r+ ae+
  gi|474933676|ref|YP_007687258.1|  85 DYIIHGDNWKTGAMKAIRDNAEK 107
                                       55777777777777777777765 PP

  == domain 2  score: 223.7 bits;  conditional E-value: 2.5e-70
                        PEP_mutase   9 eplvlpnawDalsakiveeag.........fkalatsSlavaaslGvpDgeelpleellaavraiaevvslPlivDl 76 
                                        ++ +++++++l+  ive++          f+a+++sSl+ ++++G+pD+e ++++++++++ +++ev++ P+i+D 
  gi|474933676|ref|YP_007687258.1| 156 PIVKAMEVHSGLTGLIVEKTCvehngeidqFDAMWLSSLCDSTAKGKPDIEVVDMTSRFRTIDDVMEVTTKPIIFDG 232
                                       57789***************5556667777*********************************************** PP

                        PEP_mutase  77 edGygespeevaetvrrliaaGvvgvniEDk...kkn..d..aerqll.dieefaekiaaaraaaeeagfvinARtd 145
                                       ++G g  pe++ + vr+l+++Gv++v+iEDk   kkn  +  + +q++ +ie+f+eki+a+++ + +++f+i+AR++
  gi|474933676|ref|YP_007687258.1| 233 DTG-GL-PEHFVYIVRSLERMGVSAVIIEDKtglKKNslFgtEVKQTQdSIENFCEKIKAGKRVQLTDDFMIIARIE 307
                                       ***.99.**************************9666673569999999**************************** PP

                        PEP_mutase 146 alllsagagleeaieRaraYaeAGAdgvfvpglqkdae.iaelvaavd.....vplnvvp.lkgtlsvaelaelGva 215
                                       +l+   ++g+++a++RaraY++AGAdg++++++++d++ i e+++ ++     +p++vvp + ++++ +elae+Gv+
  gi|474933676|ref|YP_007687258.1| 308 SLI--LEQGMDDALARARAYVAAGADGIMIHSRKNDPAeILEFCDLFRkenkdTPIVVVPtSFNSITESELAEHGVN 382
                                       ***..89**************************999888********559**********44778************ PP

                        PEP_mutase 216 rislgnhllraalaalreaaeeil 239
                                       +++++n+l r+a+ a++++a++il
  gi|474933676|ref|YP_007687258.1| 383 IVIYANQLTRSAFPAMEQTAKDIL 406
                                       *********************996 PP

>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.0   0.0   6.6e-16   5.9e-12       7      97 ..      11      97 ..       5     144 .. 0.87
   2 ?    0.6   0.0     0.065   5.9e+02      55     118 ..     291     357 ..     270     393 .. 0.67

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 6.6e-16
                                      TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST.-SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHHHHHTTTTE CS
                   CTP_transf_like  7 DpiHlGHlrlleqakklleedlivgvpsdeppkkk.kkplasaeeRlemlelakevdevisvdpweltrevlkklkpdk 84
                                      D++H GHl+++++a k+++  ++vgv sd+ + ++ k p +s e+R +m+e++  v +v++ d+   +  ++k+++pd 
  gi|474933676|ref|YP_007687258.1| 11 DIVHEGHLNIIKNAQKYGD--VYVGVLSDKATIRYnKFPTVSFEDRFKMIEAIPGVTRVLVQDDVMYDG-IVKQIRPD- 85
                                      9******************..7************956*********************88888888886.********. PP

                                      EEEEEEHHHHHHH CS
                   CTP_transf_like 85 lylvigadvledf 97
                                       y+++g+   + +
  gi|474933676|ref|YP_007687258.1| 86 -YIIHGDNWKTGA 97
                                      .*****9876665 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.065
                                       HHHHTTCTTEEEEEEESEHHHHHHHTTTT......EEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEE CS
                   CTP_transf_like  55 lelakevdevisvdpweltrevlkklkpd......klylvigadvledfsewkeleeilgnvklvvvsrp 118
                                        ++ + +d+++ ++ +e+    + +++ d        y+++gad ++  s+ ++  eil+ + l  ++ +
  gi|474933676|ref|YP_007687258.1| 291 GKRVQLTDDFMIIARIESL---ILEQGMDdalaraRAYVAAGADGIMIHSRKNDPAEILEFCDLFRKENK 357
                                       4444445555555555444...444455445666677999999999988889999999999888777555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.24s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 2977.04
//
Query:       gi|474933677|ref|YP_007687259.1|  [L=253]
Description: hypothetical protein TALC_00084 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.8e-13   49.7   1.6    3.8e-13   49.7   1.6    1.7  2  GT87           Glycosyltransferase family 87
  ------ inclusion threshold ------
      0.048   13.4   0.9      0.048   13.4   0.9    2.6  2  Cation_efflux  Cation efflux family
       0.16   12.0   7.8       0.22   11.5   1.5    2.4  2  AmiS_UreI      AmiS/UreI family transporter


Domain annotation for each model (and alignments):
>> GT87  Glycosyltransferase family 87
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   1.6   6.4e-17   3.8e-13      81     231 ..      14     162 ..       2     172 .. 0.78
   2 ?   -1.3   0.2      0.24   1.4e+03       7      26 ..     201     220 ..     175     233 .. 0.64

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 6.4e-17
                              GT87  81 lllvlldllllrrrrpl...laGlliGlaaaiKltPalfllylllrrrwralaaaaatalvltalpllllppssley 154
                                       ++ +ll+ l++r+++++   ++ +++++a++iKl+Pal++++ l  r  + ++  ++ +++++++++l+  ++++  
  gi|474933677|ref|YP_007687259.1|  14 IVFMLLFILGYRSEKKWiryASYVCLAIATGIKLYPALLAILILREREIKEFLICVGLVAGVFLVSFLFTDGDPI-S 89 
                                       445555666666666676669**************************************************7775.6 PP

                              GT87 155 fletlfdtseriaedvgnqsllslagllaralalglsavtllwlvlvllvvalaavaawrlr.rrerllalaaallv 230
                                       fl+ lf+ s+  ++d+ + s  +++  +a    + +   +l ++ l + ++ la+ ++++++ r+ +l+    +ll+
  gi|474933677|ref|YP_007687259.1|  90 FLDNLFSFSS--PHDT-SRSRIGIREWFAAFGLYFF-DDNLNYIGLPVTLFFLAGSLLLIVFdREMPLWQAI-TLLG 161
                                       8888999989..8995.555599*******554444.68999999999998888888887773555555444.4444 PP

                              GT87 231 a 231
                                       +
  gi|474933677|ref|YP_007687259.1| 162 C 162
                                       3 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.24
                              GT87   7 aallfaplallpyglalalw 26 
                                       ++l+ +++al+p  + +  +
  gi|474933677|ref|YP_007687259.1| 201 TVLFALIFALVPSVPMIKSF 220
                                       34444555555544444444 PP

>> Cation_efflux  Cation efflux family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   2.3      0.26   1.5e+03     155     169 ..     114     128 ..       9     149 .. 0.56
   2 ?   13.4   0.9     8e-06     0.048     151     194 ..     200     240 ..     197     242 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.26
                     Cation_efflux 155 vsalvillfnlksgp 169
                                       ++a++ ++f+++ ++
  gi|474933677|ref|YP_007687259.1| 114 FAAFGLYFFDDNLNY 128
                                       455555555555554 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 8e-06
                     Cation_efflux 151 lgvlvsalvillfnlksgplaDpvaslligliilysalkllkes 194
                                       + vl++++++l+   +s p++ +++++ i+liilys+ k lkes
  gi|474933677|ref|YP_007687259.1| 200 ITVLFALIFALV---PSVPMIKSFCTFGIMLIILYSSIKHLKES 240
                                       456666666666...34489**********************98 PP

>> AmiS_UreI  AmiS/UreI family transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.6    0.0072        43     119     162 ..      10      53 ..       6      82 .. 0.64
   2 ?   11.5   1.5   3.7e-05      0.22     118     164 ..     171     218 ..     126     220 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0072
                         AmiS_UreI 119 laWavLwllfflllalkkkkleklvgwlaivegilTawiPalll 162
                                       +++a+ ++l f+l   ++kk+ ++  ++ ++ +    + Pall 
  gi|474933677|ref|YP_007687259.1|  10 IFYAIVFMLLFILGYRSEKKWIRYASYVCLAIATGIKLYPALLA 53 
                                       45666667777666666666666666665555554455555554 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 3.7e-05
                         AmiS_UreI 118 WlaWavLwll.fflllalkkkkleklvgwlaivegilTawiPallllt 164
                                        +++++L+ll  f++ +++ +++++ +++++++ +++ a++P++ +++
  gi|474933677|ref|YP_007687259.1| 171 STTYGFLYLLpGFIFFITQYERWDRPTQIITVLFALIFALVPSVPMIK 218
                                       4589****9868*******************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       828  (0.0461822); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1623.67
//
Query:       gi|474933678|ref|YP_007687260.1|  [L=364]
Description: Nucleoside-diphosphate-sugar epimerase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-40  138.7   0.0    2.6e-40  138.4   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    1.5e-35  123.2   0.0    1.8e-35  123.0   0.0    1.0  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    4.9e-11   42.1   0.0    6.9e-11   41.7   0.0    1.2  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    0.00054   19.2   0.0     0.0054   15.9   0.0    2.1  2  NAD_binding_4    Male sterility protein
    0.00091   18.4   0.0     0.0022   17.2   0.0    1.6  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
  ------ inclusion threshold ------
      0.023   14.6   0.0        1.4    8.8   0.0    2.2  2  KR               KR domain


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.4   0.0   8.6e-44   2.6e-40       1     241 []      30     277 ..      30     277 .. 0.88

  Alignments for each domain:
  == domain 1  score: 138.4 bits;  conditional E-value: 8.6e-44
                                       EEEETTTSHHHHHHHHHHHHCT.....SEEEEEES-STTTTCHHCHHC......EEEE--TT-HHHHHHHHHHHT-S CS
                         Epimerase   1 ilVtGatGfiGsalvkallekg.....yevigldrlssasntarledl......elveldltdrsalerlfkeeqpd 66 
                                       +l+tG +Gf+G ++++ + e g      +vi+ld+   + + +++e         + + d+ + +++e + + ++++
  gi|474933678|ref|YP_007687260.1|  30 VLITGCAGFLGFYFMHFFREFGdklavKKVIALDNFMLGTPDWLKE-FekdnrfIIRKFDIIK-DRIESIEEAKDAN 104
                                       79******************999999555******95555544444.3589955555666653.3455555555*** PP

                                       EEEE--S---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSS..SS.BSTCSTTS--.--S CS
                         Epimerase  67 avihlAavggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdae..qp.keettltgpl.kpn 139
                                       ++ih+A ++++  + ++p +++++n+ g +nl+++  +++v+ +lf+sSse+YG++ +  +p  e++  + ++  p+
  gi|474933678|ref|YP_007687260.1| 105 YIIHMASIASPTFYRQYPIETLDANIWGLRNLFDYYVDKKVDGFLFFSSSEIYGDPVPeaVPtSEDYFGNVSCtGPR 181
                                       ******************************************************9988655888888888888**** PP

                                       SHHHHHHHHHHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHH CS
                         Epimerase 140 spYaaaKlageklveayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyve 216
                                       s Y  +K+ ge ++  +a++yg+++ ++r+fn+yGp+     ++rv + +++++ egk ++++l++g++ R f+yv 
  gi|474933678|ref|YP_007687260.1| 182 SCYDESKRFGETMCMLFAQKYGMPIAVVRPFNNYGPG-MRLGDKRVPADFLKNVIEGK-DIVILSNGSPTRTFCYVA 256
                                       *************************************.7777****************.****************** PP

                                       HHHHHHHHHHHHHTT-STTEEEEES CS
                         Epimerase 217 DvaeaillvlehvdagdkgeiyniG 241
                                       D + ++l  l h     + + +niG
  gi|474933678|ref|YP_007687260.1| 257 DSVAGYLKSLLH----GEYDYFNIG 277
                                       ************....567899998 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.0   0.0   5.9e-39   1.8e-35       1     331 [.      31     349 ..      31     350 .. 0.83

  Alignments for each domain:
  == domain 1  score: 123.0 bits;  conditional E-value: 5.9e-39
                                       EEETTTSHHHHHHHHHHHHCT-CCEE..EEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhg..ivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevq 75 
                                       LiTG aGf G y+++++ e g +  +  ++   ++f +g+ + l++   +e+++++ + k D+   +++e++ +  +
  gi|474933678|ref|YP_007687260.1|  31 LITGCAGFLGFYFMHFFREFGDKLAVkkVIA-LDNFMLGTPDWLKE---FEKDNRFIIRKFDIIK-DRIESIEEAKD 102
                                       9*****************9988754410444.46788999999986...56689********997.679******** PP

                                       -SEEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-..SSSSB-TT.....S CS
                     GDP_Man_Dehyd  76 pdevynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkv..qevpqtEt.....t 145
                                        + ++++A         + P +t+++n+ G  +L++   + +++    f++ S+sE+YG++  ++vp +E+      
  gi|474933678|ref|YP_007687260.1| 103 ANYIIHMASIASPTFYRQYPIETLDANIWGLRNLFDYYVDKKVD---GFLFFSSSEIYGDPvpEAVPTSEDyfgnvS 176
                                       *************************************9887665...7999*********95558999998777767 PP

                                       -----SHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEE CS
                     GDP_Man_Dehyd 146 pfyPrsPYaaaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRd 222
                                        + Prs+Y  +K + +++++ + ++yg+++ + + fn+++p +     +r   +++ ++ +gk ++++l n++++R 
  gi|474933678|ref|YP_007687260.1| 177 CTGPRSCYDESKRFGETMCMLFAQKYGMPIAVVRPFNNYGPGMRL-GDKRVPADFLKNVIEGK-DIVILSNGSPTRT 251
                                       889***************************************844.46677778888888887.8899********* PP

                                       EEEHHHHHHHHHHHHHCSS---EEE-TT-.EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG- CS
                     GDP_Man_Dehyd 223 wghvkDyveamwlmlqqdkpedyviatge.thsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyf 298
                                       + +v D v ++ + l +++ + ++i+    + s+ +++e+  +e+gk+i   +    ev       k   + d++y 
  gi|474933678|ref|YP_007687260.1| 252 FCYVADSVAGYLKSLLHGEYDYFNIGVESpEISMTQLAEI-YKEAGKEIFDYN---GEV-------KYATSEDRQYL 317
                                       *******************999988765415566666664.466677765432...222.......33334444554 PP

                                       -SS--SB--B-THHHHHHH----SS-HHHHHHH CS
                     GDP_Man_Dehyd 299 rpgevdlllgdaskakeeLgWkpkvsfeelvre 331
                                          + ++++ ++ska++ L+++p+++++e+vr+
  gi|474933678|ref|YP_007687260.1| 318 -TNNPQRRCPNISKARKILDYNPTIKVDEGVRR 349
                                       .4567899***********************97 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   0.0   2.3e-14   6.9e-11       1     188 [.      31     221 ..      31     260 .. 0.79

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 2.3e-14
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrlee...lkevrvlD..lrespelleelskvnvkkviegDvtdk..dkleealegvdvv 70 
                                       ++tG aGFlG + ++ + ++++   +k+v +lD  +   p +l+e++k n+  + + D+ +   +++eea ++++ +
  gi|474933678|ref|YP_007687260.1|  31 LITGCAGFLGFYFMHFFREFGDklaVKKVIALDnfMLGTPDWLKEFEKDNRFIIRKFDIIKDriESIEEA-KDANYI 106
                                       69**********99999998885446777788877667888999999999998999**986522455555.78999* PP

                         3Beta_HSD  71 ihlaslvd.vagkltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyesl..hqd 144
                                       ih+as+    + +++  e  ++n+ G rn+ +  v++ v  +++ Ss e+ g+    e++  +++     s+  + +
  gi|474933678|ref|YP_007687260.1| 107 IHMASIASpTFYRQYPIETLDANIWGLRNLFDYYVDKKVDGFLFFSSSEIYGD-PVPEAVPTSEDYFGNVSCtgPRS 182
                                       *****8751566899999**********************************9.777888866666655555789** PP

                         3Beta_HSD 145 aypesKalaEklvlkaNgrtlknggrlyTcaLRpagiyGegdkl 188
                                       +y esK+  E + +   +   k g  +    +Rp   yG+g +l
  gi|474933678|ref|YP_007687260.1| 183 CYDESKRFGETMCMLFAQ---KYG--MPIAVVRPFNNYGPGMRL 221
                                       ************999888...667..888999********9765 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.4       0.1   3.1e+02       1      13 [.      32      44 ..      32      47 .. 0.88
   2 !   15.9   0.0   1.8e-06    0.0054      84     203 ..      97     211 ..      83     244 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.1
                                      EE-TTSHHHHHHH CS
                     NAD_binding_4  1 lTGaTGFLGkvLl 13
                                      +TG  GFLG +++
  gi|474933678|ref|YP_007687260.1| 32 ITGCAGFLGFYFM 44
                                      8********8876 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.8e-06
                                       H..HHH--EEEE--..SS-S.STTSSE.EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TT.T--SSS-H. CS
                     NAD_binding_4  84 l..aeevdviihsa..Atvnfdepyke.llrvNveGtrevlelakklkklkvllhvSTayvngereg.eveekvyee 154
                                       +  a+  + iih+a  A+ +f ++y+   l++N+ G r++++     k    +l++S++ ++g+    +v   +   
  gi|474933678|ref|YP_007687260.1|  97 IeeAKDANYIIHMAsiASPTFYRQYPIeTLDANIWGLRNLFDYYVDKKVD-GFLFFSSSEIYGDPVPeAV---P--- 166
                                       433788999***99667889*****9669*************99966666.8999999555555543033...2... PP

                                       .....HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE CS
                     NAD_binding_4 155 gekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRp 203
                                             +d     + +g    Y  sK  +E ++   +++ g+p+++vRp
  gi|474933678|ref|YP_007687260.1| 167 ----TSEDYFGNVSCTGPRSCYDESKRFGETMCMLFAQKYGMPIAVVRP 211
                                       ....3466677778889999****************************9 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   7.5e-07    0.0022       1     128 [.      30     153 ..      30     157 .. 0.79
   2 ?   -2.3   0.0      0.61   1.8e+03     137     167 ..     183     210 ..     178     290 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 7.5e-07
                                       EEEETTTSHHHHHHHHHHHHH....B-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHT CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkk....kpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekal 73 
                                       vl+tG +G +G  +++ + ++     +kk+i l++  l   +  ke+e   k++++ ++ +    d+  k+r+e++ 
  gi|474933678|ref|YP_007687260.1|  30 VLITGCAGFLGFYFMHFFREFgdklAVKKVIALDNFMLGTPDWLKEFE---KDNRFIIRKF----DII-KDRIESIE 98 
                                       899999999998887766665444678888888888888888777774...3333323322....332.45788888 PP

                                       T..T-SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEE CS
                   Polysacc_synt_2  74 eelkvdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliSt 128
                                       e+ + ++++h A +       ++p+e+++ N+ g +n+ +  ++++v+ +++ S+
  gi|474933678|ref|YP_007687260.1|  99 EAKDANYIIHMASIASPTFYRQYPIETLDANIWGLRNLFDYYVDKKVDGFLFFSS 153
                                       8889************999*******************************99986 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.61
                                       HHHHHHHHHHHHHHHGGG--SSS--EEEEEE CS
                   Polysacc_synt_2 137 vmGatKrlaekllqalakeseekktkfvvvR 167
                                        +  +Kr+ e +++ +a++     + ++vvR
  gi|474933678|ref|YP_007687260.1| 183 CYDESKRFGETMCMLFAQKY---GMPIAVVR 210
                                       55566666666666666555...34444444 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.018        54       2      24 ..      29      51 ..      28      62 .. 0.86
   2 ?    8.8   0.0   0.00048       1.4      80     137 ..     101     154 ..      78     161 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.018
                                      EEEEETTTSHHHHHHHHHHHHHH CS
                                KR  2 tylitGGlGgLGlelarwlaekg 24
                                      t+litG++G LG  ++++  e g
  gi|474933678|ref|YP_007687260.1| 29 TVLITGCAGFLGFYFMHFFREFG 51
                                      78***********9998877665 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00048
                                       S---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEH CS
                                KR  80 ppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelledesldffvlfSSi 137
                                       +  + +ih+A ++  +   +   e+    l + + G++nL  +  d+++d f++fSS 
  gi|474933678|ref|YP_007687260.1| 101 KDANYIIHMASIASPTFYRQYPIET----LDANIWGLRNLFDYYVDKKVDGFLFFSSS 154
                                       4566788888888887777776665....567899*********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2494.96
//
Query:       gi|474933679|ref|YP_007687261.1|  [L=81]
Description: putative UDP-glucose 6-dehydrogenase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-14   54.3   0.0    1.3e-14   54.2   0.0    1.0  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
  ------ inclusion threshold ------
      0.014   16.0   0.2      0.019   15.5   0.2    1.4  1  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
      0.028   13.8   0.1       0.05   13.0   0.1    1.6  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
      0.034   13.4   0.0      0.034   13.4   0.0    1.1  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
       0.07   13.0   0.0      0.093   12.6   0.0    1.4  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
       0.16   11.1   0.0       0.17   11.1   0.0    1.0  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.2   0.0   4.4e-18   1.3e-14       2      80 ..       3      80 ..       2      81 .] 0.97

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 4.4e-18
                                      EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTHHHHHHHHCHTTTEEEES-HHHHHHC-SEE CS
                    UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepgLeelvkkavesgrlsfttdvekaveeadvi 80
                                      +++v+GlG+vGl+ta+ +++ig +v g+ +de++ d l+sgk+p+ ep +e++++k++  +++    dv++av+++d i
  gi|474933679|ref|YP_007687261.1|  3 TVTVFGLGFVGLTTALGFSHIGCKVYGIEVDERRKDILRSGKLPFSEPYMEDVLNKHL-GKQFIVCDDVKEAVRSSDYI 80
                                      699*******************************************************.899999***********976 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.2   6.3e-06     0.019       2      32 ..       4      34 ..       3      78 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.3e-06
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversd 32
                                      v+v G G++gl  A  ++++g+kV+ +e  +
  gi|474933679|ref|YP_007687261.1|  4 VTVFGLGFVGLTTALGFSHIGCKVYGIEVDE 34
                                      7899********************8776433 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   1.7e-05      0.05      38      73 ..       3      38 ..       2      81 .] 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.7e-05
                                      EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydrskkkee 73
                                      tv ++GlG +G ++a  ++ +g+kv+++++ +++++
  gi|474933679|ref|YP_007687261.1|  3 TVTVFGLGFVGLTTALGFSHIGCKVYGIEVDERRKD 38
                                      899*************************99988776 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.1e-05     0.034      30      71 ..       3      44 ..       1      78 [. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.1e-05
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTT CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslg 71
                                      +v+v+G G +Gl  +   + +g kV+ ++v+++r+  l+s +
  gi|474933679|ref|YP_007687261.1|  3 TVTVFGLGFVGLTTALGFSHIGCKVYGIEVDERRKDILRSGK 44
                                      69********************************99888744 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.1e-05     0.093       1      34 [.       3      36 ..       3      77 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.1e-05
                                      EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHH CS
                           3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdiseea 34
                                      +v+v G G +G   a  f + g++V  ++++e++
  gi|474933679|ref|YP_007687261.1|  3 TVTVFGLGFVGLTTALGFSHIGCKVYGIEVDERR 36
                                      69*************************9997654 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   5.7e-05      0.17     145     210 ..       4      74 ..       1      80 [. 0.71

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.7e-05
                                       EEEES-SHHHHHHHHHHHHHT-EEE...EEESSSSSSTTS-.HHHHHHHHHHHHHT.TEEEEESCEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxx.xxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                       Pyr_redox_2 145 ivvvGgGyiGvElAaalaklgkevt...lveardrllrald.kelsaaleealeke.Gvevklgtsvkeid 210
                                       ++v G G++G+ +A  ++ +g++v+   + e+r+ +lr+ + +  + ++e++l+k+ G ++ +   vke+ 
  gi|474933679|ref|YP_007687261.1|   4 VTVFGLGFVGLTTALGFSHIGCKVYgieVDERRKDILRSGKlPFSEPYMEDVLNKHlGKQFIVCDDVKEAV 74 
                                       789999****************9983334456777775555144455677778887777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 571.34
//
Query:       gi|474933680|ref|YP_007687262.1|  [L=518]
Description: Transposase DDE domain protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.2e-12   45.9   0.0    9.2e-12   45.0   0.0    1.3  1  DDE_Tnp_1  Transposase DDE domain
  ------ inclusion threshold ------
      0.038   14.0   0.1      0.065   13.2   0.1    1.4  1  DUF5028    Domain of unknown function (DUF5028)


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.0     1e-15   9.2e-12      29     189 ..     203     392 ..     178     401 .. 0.78

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 1e-15
                         DDE_Tnp_1  29 ggkykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrprkgklvlaDaGYasaelldtle.ekgvdyii 104
                                       + k+++ + ++ a+d++ + i+  +++pgn+ d  ++ +++   +  ++ ++++D+G+   ++ ++l+   ++++i 
  gi|474933680|ref|YP_007687262.1| 203 RVKGIRNISVIFAYDLEKKEIVCSEVFPGNEIDAAAYSAFICDNDV-RSGILVTDKGFPPSKISKELDeRPNLHFIT 278
                                       5568889999*****************************8877666.*********************999****** PP

                         DDE_Tnp_1 105 rlkkntklyrk........gaeskrrgrlrkhdrnkiltksqkrrnk.............................s 144
                                       +lk n +  ++                 l + d +  ++k++ + ++                             +
  gi|474933680|ref|YP_007687262.1| 279 PLKRNDTRIKTnkmmeftgL--------LPGYDSGILFKKTRLKGGRflysfrdpekaaieeaaylrrlngefdndK 347
                                       **555433333244444441........4444444444444444444555555556666777777777777777777 PP

                         DDE_Tnp_1 145 kkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfg 189
                                        +ek+   ++t++++e+l++e+  ++y+ Rw iE vF++ k++  
  gi|474933680|ref|YP_007687262.1| 348 FSEKEQFGTITFLSDEDLKPEDAYAIYSERWLIEMVFRFYKNDID 392
                                       7777777777*******************************9755 PP

>> DUF5028  Domain of unknown function (DUF5028)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   7.3e-06     0.065      55     111 ..     367     422 ..     343     436 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.3e-06
                           DUF5028  55 adeagntvkrteyvydlkvkivnkdneeGtldmldrlllnGdelmllvdeylfdemy 111
                                        ++a  +++   +++++  +++ +d +  t d+ d +++ G+e++ l+   + + m 
  gi|474933680|ref|YP_007687262.1| 367 PEDA-YAIYSERWLIEMVFRFYKNDIDLATTDVQDDYTVIGEEFVNLIATTITCRML 422
                                       4445.89********************************************999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (518 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 3448.89
//
Query:       gi|474933681|ref|YP_007687263.1|  [L=41]
Description: hypothetical protein TALC_00088 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      184  (0.0102627); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 306.67
//
Query:       gi|474933682|ref|YP_007687264.1|  [L=369]
Description: Transposase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.5e-10   39.5   0.1    0.00099   18.8   0.0    2.3  2  DDE_Tnp_1  Transposase DDE domain


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   5.5e-08   0.00099      46     115 ..      44     115 ..       7     144 .. 0.87
   2 !   18.7   0.0   6.1e-08    0.0011     158     210 ..     231     283 ..     170     284 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 5.5e-08
                         DDE_Tnp_1  46 sglilsvvitpgnvhdskglkqlldelrpr..kgklvlaDaGYasaelldtleekgvdyiirlkkntklyrk 115
                                       s+++  ++   gn++d +++++ l  +  +  +g+++++D G as ++ld + ++g +y+ r+k n+   ++
  gi|474933682|ref|YP_007687264.1|  44 SRIPFFMRAYKGNTSDPEQYRDALPDIFSMirEGSWIIVDNGGASGDILDSIVKSGHKYLTRVKMNASDDKR 115
                                       56677778889***********9999998899*******************************999976655 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 6.1e-08
                         DDE_Tnp_1 158 nsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllll 210
                                       +se+l++ e  + yr R ++E+ +++lkr+ gl  lr+ +   ++  ++l ll
  gi|474933682|ref|YP_007687264.1| 231 SSEQLTPLEALDKYRARVTVEHLIHSLKRVTGLKPLRVWSESSIRGSMMLALL 283
                                       56788999999**************************9999999998888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2618.00
//
Query:       gi|474933683|ref|YP_007687265.1|  [L=129]
Description: hypothetical protein TALC_00090 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00047   20.5   0.0    0.00062   20.1   0.0    1.2  1  DUF4277          Domain of unknown function (DUF4277)
  ------ inclusion threshold ------
       0.12   12.1   0.0       0.15   11.8   0.0    1.1  1  Ad_Cy_reg        Adenylate cyclase regulatory domain
       0.15   12.1   0.0       0.22   11.5   0.0    1.3  1  DDE_Tnp_1_assoc  DDE_Tnp_1-associated


Domain annotation for each model (and alignments):
>> DUF4277  Domain of unknown function (DUF4277)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0     1e-07   0.00062       9      85 ..      23      99 ..      17     112 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1e-07
                           DUF4277  9 lglvaglidelglaelidelipkksqekvsagevvkalilngLgfvsrpLylfpeffedkplerLlg..egveaehlnd 85
                                       glv+ + + lg   ++d ++ + +++ v ++ +++a++ ++L + s+++ ++++++++ ++ + lg  +g++++ +n+
  gi|474933683|ref|YP_007687265.1| 23 TGLVKTIEHYLGATGVLD-FVDTFKHRGVPMSRILTAMCTHIL-MGSNSMSRCSDWLKNRDVRKELGldSGLSQRTINR 99
                                      588999999999887776.6899999*****************.9****************987666447777777776 PP

>> Ad_Cy_reg  Adenylate cyclase regulatory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.5e-05      0.15      24      92 ..      42     110 ..      37     122 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.5e-05
                         Ad_Cy_reg  24 iewLlerGvsieeiraaaepmLLaaervlgddgtyvsareisektGidlellqr.lqrAvGLprvddpDa 92 
                                       +++  +rGv++ +i +a+   +L     ++    +   r++ ++ G+d  l qr ++rA+ L   d  D+
  gi|474933683|ref|YP_007687265.1|  42 VDTFKHRGVPMSRILTAMCTHILMGSNSMSRCSDWLKNRDVRKELGLDSGLSQRtINRAISLIG-DHSDE 110
                                       677789***********8888888888888888899*****************94589*99865.55554 PP

>> DDE_Tnp_1_assoc  DDE_Tnp_1-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.8e-05      0.22      19      77 ..      51     106 ..      45     116 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.8e-05
                   DDE_Tnp_1_assoc  19 pladiLlialcaviagadsweeieefakekeewlreflelengiPshdtirrvlsridp 77 
                                       p++ iL+ +   ++ g +s++  +++ k+  + +r+ l l+ g  s++ti+r +s i  
  gi|474933683|ref|YP_007687265.1|  51 PMSRILTAMCTHILMGSNSMSRCSDWLKN--RDVRKELGLDSG-LSQRTINRAISLIGD 106
                                       67899*********************765..678999999886.5999*****999965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 921.84
//
Query:       gi|474933684|ref|YP_007687266.1|  [L=127]
Description: Sel1 repeat protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-18   67.1   7.1    5.5e-06   26.9   0.2    3.4  4  Sel1      Sel1 repeat
  ------ inclusion threshold ------
      0.088   13.0   5.3         37    4.8   0.0    4.3  4  TPR_2     Tetratricopeptide repeat
       0.12   12.0   0.0       0.14   11.8   0.0    1.1  1  NAPRTase  Nicotinate phosphoribosyltransferase (NAPRTase) fam


Domain annotation for each model (and alignments):
>> Sel1  Sel1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   5.8e-07    0.0035      12      37 ..       1      26 [.       1      27 [. 0.95
   2 !   26.9   0.2   9.3e-10   5.5e-06       2      38 .]      29      63 ..      28      63 .. 0.93
   3 !   25.2   0.1   3.1e-09   1.8e-05       1      38 []      64      99 ..      64      99 .. 0.95
   4 ?   -2.4   0.0       1.5   8.9e+03       2      14 ..     101     111 ..     100     114 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 5.8e-07
                              Sel1 12 lylnGlgvpkDpekAiewyekAAeqG 37
                                      +yl+G g ++  +kA++w  +AAeq+
  gi|474933684|ref|YP_007687266.1|  1 MYLDGEGGEQSDKKAFKWVSLAAEQN 26
                                      67**********************97 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 9.3e-10
                              Sel1  2 eAmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38
                                      +A+  LG  y+y++G+g+++  ekA+ ++ ++Ae G+
  gi|474933684|ref|YP_007687266.1| 29 YALDYLG--YMYYEGKGTEQSFEKALDCFTRSAEEGN 63
                                      67778**..999**********************997 PP

  == domain 3  score: 25.2 bits;  conditional E-value: 3.1e-09
                              Sel1  1 aeAmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38
                                      +e +++ +   ++l G g++kD  kA+e++  AA+ Gd
  gi|474933684|ref|YP_007687266.1| 64 PEGAFNAA--SMHLQGEGTEKDLAKAEEYFLVAADSGD 99
                                      68899***..999**********************997 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 1.5
                              Sel1   2 eAmyrLGmfylyl 14 
                                        A+  L+   +y+
  gi|474933684|ref|YP_007687266.1| 101 MALIELA--KIYM 111
                                       5788898..4443 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.3     0.031   1.8e+02       1      13 [.      28      40 ..      28      42 .. 0.87
   2 ?    4.8   0.0    0.0062        37      17      29 ..      48      60 ..      45      63 .. 0.85
   3 ?    2.7   0.2     0.029   1.7e+02      15      27 ..      82      94 ..      80      96 .. 0.83
   4 ?    2.1   0.0     0.046   2.7e+02       3      14 ..     102     113 ..     100     115 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.031
                             TPR_2  1 aealynlGlayyk 13
                                      ++al +lG+ yy+
  gi|474933684|ref|YP_007687266.1| 28 PYALDYLGYMYYE 40
                                      57999******96 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0062
                             TPR_2 17 yeeAleafekAle 29
                                      +e+Al++f ++ e
  gi|474933684|ref|YP_007687266.1| 48 FEKALDCFTRSAE 60
                                      89******99876 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.029
                             TPR_2 15 gdyeeAleafekA 27
                                      +d+++A+e+f  A
  gi|474933684|ref|YP_007687266.1| 82 KDLAKAEEYFLVA 94
                                      799******9755 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.046
                             TPR_2   3 alynlGlayykl 14 
                                       al +l+++y+k 
  gi|474933684|ref|YP_007687266.1| 102 ALIELAKIYMKT 113
                                       899*******97 PP

>> NAPRTase  Nicotinate phosphoribosyltransferase (NAPRTase) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.3e-05      0.14     103     140 ..      81     115 ..      37     120 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.3e-05
                                       HCCS-CC.HHHSEEEEE-SS-HHHHHHHHHHHHHCTCTT CS
                          NAPRTase 103 lkdfrle.akaylgvRpDSGdpvevieklaahygstlns 140
                                        kd  l  a+ y  v  DSGdp+++ie la++y +t ns
  gi|474933684|ref|YP_007687266.1|  81 EKD--LAkAEEYFLVAADSGDPMALIE-LAKIYMKT-NS 115
                                       333..334999**************98.67889888.65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 895.58
//
Query:       gi|474933685|ref|YP_007687267.1|  [L=79]
Description: hypothetical protein TALC_00092 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 605.94
//
Query:       gi|474933686|ref|YP_007687268.1|  [L=617]
Description: hypothetical protein TALC_00093 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-07   32.0  20.7    1.3e-07   32.0  20.7    3.9  5  PMT_2      Dolichyl-phosphate-mannose-protein mannosyltransfe
  ------ inclusion threshold ------
       0.19   10.3   0.0       0.28    9.7   0.0    1.1  1  Adaptin_N  Adaptin N terminal region


Domain annotation for each model (and alignments):
>> PMT_2  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.2       1.8   1.6e+04      26      31 ..      26      31 ..      19      47 .. 0.47
   2 !   32.0  20.7   1.4e-11   1.3e-07       4     152 ..      70     227 ..      67     235 .. 0.79
   3 ?   -2.1   2.0      0.45   4.1e+03      82     152 ..     261     287 ..     222     295 .. 0.53
   4 ?   -1.9   3.1      0.39   3.5e+03      70      94 ..     336     360 ..     304     391 .. 0.63
   5 ?   -1.5   2.9      0.29   2.6e+03      51      91 ..     373     417 ..     333     448 .. 0.46

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 1.8
                             PMT_2 26 lvsala 31
                                      l++a++
  gi|474933686|ref|YP_007687268.1| 26 LFTAVW 31
                                      112222 PP

  == domain 2  score: 32.0 bits;  conditional E-value: 1.4e-11
                             PMT_2   4 Pliawllalftklfgfselairlvsalagvltilllyllarrlfgkraallaalllavvplfvalsa.lftpdaplv 79 
                                       Pl+ +++a + ++fg++  + r++  ++ vlt +l ++l+r +f +++all++l+  + +lf+   +  +    ++ 
  gi|474933686|ref|YP_007687268.1|  70 PLYTYFTAGVNAVFGDHLIVWRIIGSILFVLTGVLAFKLFRLFFPTETALLSTLISVM-ILFAEGIFiSYDYVYFFN 145
                                       9****************************************************98655.557777775666677888 PP

                             PMT_2  80 llwalalylllrale.......knklkywllagvlfGlgflsKytaallliaall.yllisarrilke.kkpyl.al 146
                                       +++ l+ ylll++l         ++  ++ll+g+l+Gl+f  +   +l+li +ll +ll+   +  k+ ++ y+  l
  gi|474933686|ref|YP_007687268.1| 146 FVVFLLSYLLLKVLGqqeevsmARQNLDLLLIGILAGLSFWLRQSTGLILIVYLLiFLLVV-AKFQKQyRVNYVnLL 221
                                       99999999999998755666665555699******************99998777688887.443333355555333 PP

                             PMT_2 147 llalll 152
                                       ++ + +
  gi|474933686|ref|YP_007687268.1| 222 AFLAGV 227
                                       222223 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.45
                             PMT_2  82 walalylllraleknklkywllagvlfGlgflsKytaallliaallyllisarrilkekkpylalllalll 152
                                       +++++ +l+r +e++                                            +++l + ++++l
  gi|474933686|ref|YP_007687268.1| 261 VVMLTGFLVRIVEER--------------------------------------------WIFLLIGIGFAL 287
                                       333333444444443............................................333333333333 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 0.39
                             PMT_2  70 alftpdaplvllwalalylllrale 94 
                                       +l+ +d   +++  +++y+l+ +++
  gi|474933686|ref|YP_007687268.1| 336 VLGPMDLCAIVFSFICTYFLVVLVK 360
                                       3455666666666666666665554 PP

  == domain 5  score: -1.5 bits;  conditional E-value: 0.29
                             PMT_2  51 aallaalllavvplfvalsa....lftpdaplvllwalalylllr 91 
                                        + +++l+ a +++++a +      +t    ++++ +l+  l+l+
  gi|474933686|ref|YP_007687268.1| 373 PGRMSILFFAGILFVIAFGGgtsaDVTFRHCFMCFGLLTGMLILK 417
                                       234444444444433333331111444444444444554444444 PP

>> Adaptin_N  Adaptin N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   3.1e-05      0.28     139     179 ..     479     518 ..     476     528 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 3.1e-05
                                       HHCCCCCHHCCCCCHHHHHHHCTT-SSHHHHHHHHHHHHHH CS
                         Adaptin_N 139 lklykkdpdllrkqlveeikellsdkdpgvvlaAvalleei 179
                                       +kl + ++  ++++ v+ ++  lsd+dp+ v+aA+ +++ +
  gi|474933686|ref|YP_007687268.1| 479 IKLTDTEKYVYEDF-VSICQTELSDSDPMYVYAATPVFYTL 518
                                       78889999999996.************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (617 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1153  (0.0643092); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.78u 0.34s 00:00:01.12 Elapsed: 00:00:00.50
# Mc/sec: 3726.69
//
Query:       gi|474933687|ref|YP_007687269.1|  [L=321]
Description: Nucleoside-diphosphate-sugar epimerase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-37  129.6   0.0    1.6e-37  129.3   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    2.3e-30  106.1   0.0    2.9e-30  105.8   0.0    1.0  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    2.3e-08   33.4   0.0      3e-08   33.0   0.0    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
     0.0017   17.6   0.0     0.0025   17.0   0.0    1.3  1  NAD_binding_4    Male sterility protein
     0.0017   17.5   0.0     0.0036   16.5   0.0    1.4  1  Polysacc_synt_2  Polysaccharide biosynthesis protein


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.3   0.0   4.5e-41   1.6e-37      47     241 .]      43     234 ..      13     234 .. 0.93

  Alignments for each domain:
  == domain 1  score: 129.3 bits;  conditional E-value: 4.5e-41
                                       E--TT-HHHHHHHHHHHT-SEEEE--S---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCS CS
                         Epimerase  47 eldltdrsalerlfkeeqpdavihlAavggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkda 123
                                       + d+  ++++e +++ ++++++ih+A ++++  + ++p +++++n+ g +nl+++  +++v+ +lf+sSse+YG+++
  gi|474933687|ref|YP_007687269.1|  43 KFDII-KDRIESILEAKDANYIIHMASIASPTFYRQYPIETLDANIWGLRNLFDYYVEKKVDGFLFFSSSEIYGDPT 118
                                       55555.57799999999************************************************************ PP

                                       S..SS.BSTCSTTS--.--SSHHHHHHHHHHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTT CS
                         Epimerase 124 e..qp.keettltgpl.kpnspYaaaKlageklveayaaqyglnaiilrlfnlyGprngegevsrvipalirkileg 196
                                       +  +p +e++    ++  p+  Y  +K+ ge ++  + ++yg+++ ++r+fn+yGp+     ++rv + +++++ e 
  gi|474933687|ref|YP_007687269.1| 119 PdaIPtQEDYRGFVSCtGPRACYDESKRFGETMCMLFSQKYGMPIAVVRPFNNYGPG-MRLGDKRVPADFLKNVVEH 194
                                       *877989999999999*****************************************.7777*************** PP

                                       SSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-STTEEEEES CS
                         Epimerase 197 kqevtllgdgtalRdflyveDvaeaillvlehvdagdkgeiyniG 241
                                       k ++++l++g++ R f+yv D + ++l +l h     + + +niG
  gi|474933687|ref|YP_007687269.1| 195 K-DIVILSNGSPTRTFCYVADSVAGYLKALLH----GTYDYFNIG 234
                                       *.******************************....789999998 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.8   0.0     8e-34   2.9e-30      40     331 ..      28     306 ..      10     307 .. 0.82

  Alignments for each domain:
  == domain 1  score: 105.8 bits;  conditional E-value: 8e-34
                                       HHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHC CS
                     GDP_Man_Dehyd  40 ehlakdpkeeleenlklhkgDltDssslerllaevqpdevynLAAqshVdvsfekPeytaevnvlGtlrLLeairal 116
                                       + l++   ++ ++++ + k D+   +++e++l+  + + ++++A         + P +t+++n+ G  +L++   + 
  gi|474933687|ref|YP_007687269.1|  28 DWLED---FKEDKRFIIRKFDIIK-DRIESILEAKDANYIIHMASIASPTFYRQYPIETLDANIWGLRNLFDYYVEK 100
                                       44543...3457899999***986.68**********************************************9886 PP

                                       T..TTSEEEEEEEGGGG-S-S..SSSB-TT.....S-----SHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEEST CS
                     GDP_Man_Dehyd 117 glekkvrfyqaStsEvYGkvq..evpqtEt.....tpfyPrsPYaaaKlyadwivvnyreayglfavngilfnhesp 186
                                       +++    f++ S+sE+YG+++  ++p +E+       + Pr +Y  +K + +++++ + ++yg+++ + + fn+++p
  gi|474933687|ref|YP_007687269.1| 101 KVD---GFLFFSSSEIYGDPTpdAIPTQEDyrgfvSCTGPRACYDESKRFGETMCMLFSQKYGMPIAVVRPFNNYGP 174
                                       665...7999*********96548899998666667789************************************** PP

                                       TS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHCSS---EEE-TT-.EEECHHCHHCC CS
                     GDP_Man_Dehyd 187 rrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyveamwlmlqqdkpedyviatge.thsvrefvela 262
                                        +  +   + ++    +  ++++++++l n++++R + +v D v ++ ++l +++ + ++i+  + + ++ +++e+ 
  gi|474933687|ref|YP_007687269.1| 175 GM--RLGDKRVPADFLKNVVEHKDIVILSNGSPTRTFCYVADSVAGYLKALLHGTYDYFNIGVETpEITMAQLAEI- 248
                                       98..66678888777777777889*******************************988888765413455555554. PP

                                       HHCCCHHHHHH............TTGGCCCEECGG--SS--SB--B-THHHHHHH----SS-HHHHHHH CS
                     GDP_Man_Dehyd 263 flelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlllgdaskakeeLgWkpkvsfeelvre 331
                                        +++gk+i      e ev+ a        + d++y    + ++++ +++ka++ L++ p++++ee+vr+
  gi|474933687|ref|YP_007687269.1| 249 YKQAGKEIFGY---EGEVKYA-------QSEDKQYL-TNNPQRRCPNIEKARKVLDYDPTIRVEEGVRR 306
                                       45666666554...2233332.......23344444.45677899**********************97 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.0   8.3e-12     3e-08      26     218 ..      16     212 ..       4     222 .. 0.75

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 8.3e-12
                         3Beta_HSD  26 vrvlD..lrespelleelskvnvkkviegDvtdkdkleeale..gvdvvihlaslvd.vagkltedeimkvnvkGTr 97 
                                       v +lD  +   p +le++++ ++  + + D+ + d++e  le  +++ +ih+as+    + +++  e  ++n+ G r
  gi|474933687|ref|YP_007687269.1|  16 VIALDnfMLGTPDWLEDFKEDKRFIIRKFDIIK-DRIESILEakDANYIIHMASIASpTFYRQYPIETLDANIWGLR 91 
                                       555554444567788888888887788899985.677877753378899*****8751566899999********** PP

                         3Beta_HSD  98 nvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyesl...hqdaypesKalaEklvlkaNgrtlknggrl 171
                                       n+ +  v++ v  +++ Ss e+ g+  + ++i   +E+ + + +   + ++y esK+  E + +   +   k g  +
  gi|474933687|ref|YP_007687269.1|  92 NLFDYYVEKKVDGFLFFSSSEIYGD-PTPDAIP-TQEDYRGFVSctgPRACYDESKRFGETMCMLFSQ---KYG--M 161
                                       ************************9.6666666.677766655447899**************99888...677..8 PP

                         3Beta_HSD 172 yTcaLRpagiyGegdkll.....vpllkqlaklglalfkigdeevlsdrvYv 218
                                           +Rp   yG+g +l        +lk+++ ++  ++ + + + +  + Yv
  gi|474933687|ref|YP_007687269.1| 162 PIAVVRPFNNYGPGMRLGdkrvpADFLKNVVEHK-DIVILSNGSPTRTFCYV 212
                                       89999********976431111145667777666.55555555555666665 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0     7e-07    0.0025      82     203 ..      52     168 ..      40     205 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 7e-07
                                       HHH..HHH--EEEE--..SS-S.STTSSE.EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-T.TT--SSS- CS
                     NAD_binding_4  82 qel..aeevdviihsa..Atvnfdepyke.llrvNveGtrevlelakklkklkvllhvSTayvngere.geveekvy 152
                                       + +  a+  + iih+a  A+ +f ++y+   l++N+ G r++++   + k    +l++S++ ++g+ + +++     
  gi|474933687|ref|YP_007687269.1|  52 ESIleAKDANYIIHMAsiASPTFYRQYPIeTLDANIWGLRNLFDYYVEKKVD-GFLFFSSSEIYGDPTpDAI----- 122
                                       55545788999***99667889*****9669**************9977666.8999999655555550344..... PP

                                       H......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE CS
                     NAD_binding_4 153 eegekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRp 203
                                            + ++d     + +g    Y  sK  +E ++   +++ g+p+++vRp
  gi|474933687|ref|YP_007687269.1| 123 -----PTQEDYRGFVSCTGPRACYDESKRFGETMCMLFSQKYGMPIAVVRP 168
                                       .....23477777888999999****************************9 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0     1e-06    0.0036      66     128 ..      48     110 ..      33     114 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1e-06
                                       HHHHHHHTT..T-SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEE CS
                   Polysacc_synt_2  66 kerlekaleelkvdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliSt 128
                                       k+r+e++le+ + ++++h A +       ++p+e+++ N+ g +n+ +  +e++v+ +++ S+
  gi|474933687|ref|YP_007687269.1|  48 KDRIESILEAKDANYIIHMASIASPTFYRQYPIETLDANIWGLRNLFDYYVEKKVDGFLFFSS 110
                                       6799********************999*******************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 1891.56
//
Query:       gi|474933688|ref|YP_007687270.1|  [L=422]
Description: nucleotide sugar dehydrogenase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      9e-43  146.0   0.0    1.4e-42  145.4   0.0    1.3  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
    1.1e-27   96.0   0.0    2.6e-27   94.8   0.0    1.6  1  UDPG_MGDP_dh    UDP-glucose/GDP-mannose dehydrogenase family,
    8.8e-21   74.3   0.0    1.4e-18   67.3   0.0    3.3  4  UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family,
     0.0045   16.8   0.0     0.0085   15.9   0.0    1.4  1  HGD-D           2-hydroxyglutaryl-CoA dehydratase, D-componen
  ------ inclusion threshold ------
      0.069   12.4   0.0       0.13   11.5   0.0    1.4  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
      0.085   12.2   0.0         12    5.2   0.0    2.3  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase


Domain annotation for each model (and alignments):
>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.4   0.0   4.8e-46   1.4e-42       3     185 ..       4     192 ..       2     194 .. 0.94

  Alignments for each domain:
  == domain 1  score: 145.4 bits;  conditional E-value: 4.8e-46
                                       EEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTHHHHHHHHCHTTTEEEES-HHHHHHC-SE CS
                    UDPG_MGDP_dh_N   3 isviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepgLeelvkkavesgrlsfttdvekaveeadv 79 
                                       ++v+GlG+vGl+ta+ ++++g +v g+ +de++ + l+sg++p++ep ++e++k+++  + ++   dv++av+++d 
  gi|474933688|ref|YP_007687270.1|   4 VTVFGLGFVGLTTALGFSHLGYTVYGIEVDERRKEILRSGQLPFVEPYMDEVLKEHL-GKDFFVCDDVKRAVQKSDY 79 
                                       89*******************************************************.8999999************ PP

                                       EEE-----B-TTTTCB-THHHHHHHHHHHHHHHC.........EEEEEE-S---TTHHHHCHHHHHHHHCSS-TTCE CS
                    UDPG_MGDP_dh_N  80 ifiaVgTPskkkgkaaDlkyvesaarsiaealkk.........gkvvvvkSTvpvgtaeelvkkileeaskkkgvdf 147
                                       i+ +VgTP  k + aaDl+y+ sa+++  eal +          + +v+kST+p+ t+ + + + ++++ k  + ++
  gi|474933688|ref|YP_007687270.1|  80 IYYCVGTPYGK-DGAADLTYLFSAIDTTIEALTDangnpiddkFRCLVTKSTIPPSTTSDKIVPYVQSKGKI-ADNL 154
                                       ***********.8888**********99999987777788777789****************9*99988875.59** PP

                                       EEEE------TTSHHHHHHS-S-EEEEESSCHHHHHHH CS
                    UDPG_MGDP_dh_N 148 dvvsnPEflregsavkdllnpdrvviGveekkaeaale 185
                                       ++  nPEflreg+  +d++n dr+viGv+++k+++++ 
  gi|474933688|ref|YP_007687270.1| 155 GICNNPEFLREGKCWEDFINSDRIVIGVDKEKSKELMG 192
                                       ********************************998775 PP

>> UDPG_MGDP_dh  UDP-glucose/GDP-mannose dehydrogenase family, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.8   0.0   8.8e-31   2.6e-27       2      93 ..     209     305 ..     208     306 .. 0.95

  Alignments for each domain:
  == domain 1  score: 94.8 bits;  conditional E-value: 8.8e-31
                      UDPG_MGDP_dh   2 tAEliKlaaNaflatkIsfiNelanlceal.gidveeVieavgldprigp....kflkpglGvGGsclpkDvkaLva 73 
                                       t E+iK+++N++lat Is++Ne+a++++++ gidv++ ++++++d+r++     ++++pg+G+GG+clpkD+ aL++
  gi|474933688|ref|YP_007687270.1| 209 TGEFIKYLSNTLLATLISYSNEMAHVADTIgGIDVASAFKILHMDKRWNGcnmtSYVYPGCGYGGYCLPKDTCALLS 285
                                       68****************************88***************7557888*********************** PP

                      UDPG_MGDP_dh  74 laeelgleaelleavrevNe 93 
                                       ++e +g+e+ +l++v+++N+
  gi|474933688|ref|YP_007687270.1| 286 QSEVKGYEPAILREVINTNA 305
                                       *******************7 PP

>> UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.16   4.7e+02      35      74 ..      47      84 ..      37      90 .. 0.82
   2 ?    0.8   0.0      0.22   6.6e+02      61      96 ..     169     203 ..     142     207 .. 0.83
   3 ?   -2.2   0.0       1.8   5.5e+03      30      49 ..     286     305 ..     279     321 .. 0.71
   4 !   67.3   0.0   4.6e-22   1.4e-18       2     101 ..     327     420 ..     326     422 .] 0.92

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.16
                                      EE-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S CS
                    UDPG_MGDP_dh_C 35 iyDPkvkeeaveaeleekgvevvdsleealkgadaivilt 74
                                       ++P+++e  +e+ +  k+  v+d++++a++++d i  ++
  gi|474933688|ref|YP_007687270.1| 47 FVEPYMDEVLKEHLG--KDFFVCDDVKRAVQKSDYIYYCV 84
                                      567888888887766..6999*************987665 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.22
                                       HHHHTT-SEEEE-S--GGGGGS-HHHHHHCCSS-EE CS
                    UDPG_MGDP_dh_C  61 eealkgadaiviltehdefkeldlaklkelmkpavv 96 
                                        e + ++d ivi ++ ++ kel + kl+e m ++++
  gi|474933688|ref|YP_007687270.1| 169 WEDFINSDRIVIGVDKEKSKEL-MGKLYEPMGRPIF 203
                                       6788999************997.7888888855554 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.8
                                       TSEEEEE-SSTHHCCCCHHG CS
                    UDPG_MGDP_dh_C  30 gaevkiyDPkvkeeaveael 49 
                                       + evk y+P + +e ++ ++
  gi|474933688|ref|YP_007687270.1| 286 QSEVKGYEPAILREVINTNA 305
                                       45899999999988877655 PP

  == domain 4  score: 67.3 bits;  conditional E-value: 4.6e-22
                                       EE-SSSSTT-S--TT-HHHHHHHHHHHCTSE.EEEE-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S--G CS
                    UDPG_MGDP_dh_C   2 ilGlafKkdtdDlReSpaldiieeLleegae.vkiyDPkvkeeaveaeleekgvevvdsleealkgadaiviltehd 77 
                                       ilGl+fK+++dD+R++pa +ii+eL ++g+  +++yDP +++e + + ++  +++++ds+ +  ++ad+i i+t+++
  gi|474933688|ref|YP_007687270.1| 327 ILGLSFKPESDDVRDTPASKIIKELMAMGYSnIVAYDPIANKEFAFRFPD-IKITLLDSARDVYQKADVIAITTAWK 402
                                       9****************************966***************996.79************************ PP

                                       GGGGS-HHHHHHCCSS-EEEESSS CS
                    UDPG_MGDP_dh_C  78 efkeldlaklkelmkpavvfDgrn 101
                                       efke+       +  ++ +fD+r 
  gi|474933688|ref|YP_007687270.1| 403 EFKEV------PKFGDKKIFDCRY 420
                                       ****5......5567778888886 PP

>> HGD-D  2-hydroxyglutaryl-CoA dehydratase, D-component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.8e-06    0.0085      64     115 ..      67     121 ..      40     123 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.8e-06
                                       SHHHHHHHHHHTTTS-EEEE---.....HHHHHHHHHHHHHHHHHHHHHHT----HH CS
                             HGD-D  64 CdqvkkilenlakiipytvldiP.....eeavkyledelenliaaleeitgkridee 115
                                       Cd vk++ + ++ i  y+++ +P      +++ yl + ++  i+al+++ g++id++
  gi|474933688|ref|YP_007687270.1|  67 CDDVKRAVQKSDYI--YYCVGTPygkdgAADLTYLFSAIDTTIEALTDANGNPIDDK 121
                                       **************..**************************************975 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   4.3e-05      0.13      31      79 ..       4      52 ..       2      81 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.3e-05
                                      EEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHC CS
                       AlaDh_PNT_C 31 vlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlk 79
                                      v+v+G G +Gl  +   + lg +V+ ++v+++r+e l+s +  fve ++
  gi|474933688|ref|YP_007687270.1|  4 VTVFGLGFVGLTTALGFSHLGYTVYGIEVDERRKEILRSGQLPFVEPYM 52
                                      99***********************************998888887644 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0    0.0056        17      39      77 ..       4      42 ..       2      80 .. 0.81
   2 ?    5.2   0.0    0.0041        12      49     100 ..     345     400 ..     344     406 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0056
                                      EEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHH CS
                      2-Hacid_dh_C 39 vGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeee 77
                                      v ++GlG +G ++a  ++ +g  v+++++ ++++e  ++
  gi|474933688|ref|YP_007687270.1|  4 VTVFGLGFVGLTTALGFSHLGYTVYGIEVDERRKEILRS 42
                                      789************************999988774443 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0041
                                       HHHHHHHHHTT-.EEEEESSSHHHHH..CHHHHTC.EECSHHHHHHH-SEEEE-S- CS
                      2-Hacid_dh_C  49 qavakrlkafgm.kviaydrskkkee..eeeelgv.elvsleellaesDivslhlp 100
                                       ++++k l a+g  +++ayd+  +ke   ++ + ++  l+s  ++++++D++ +++ 
  gi|474933688|ref|YP_007687270.1| 345 SKIIKELMAMGYsNIVAYDPIANKEFafRFPDIKItLLDSARDVYQKADVIAITTA 400
                                       57888999999989*******9998855455555523459999********99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.63u 0.25s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 2704.44
//
Query:       gi|474933689|ref|YP_007687271.1|  [L=437]
Description: putative pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-89  301.0   0.0    1.8e-89  300.6   0.0    1.1  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    1.6e-05   23.6   0.0    2.7e-05   22.9   0.0    1.3  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    2.4e-05   23.7   0.0    3.9e-05   23.0   0.0    1.2  1  Aminotran_1_2    Aminotransferase class I and II
      3e-05   23.1   0.0     0.0015   17.5   0.0    2.1  2  Aminotran_5      Aminotransferase class-V
    0.00076   18.9   0.0     0.0028   17.0   0.0    1.8  2  Beta_elim_lyase  Beta-eliminating lyase


Domain annotation for each model (and alignments):
>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  300.6   0.0     5e-93   1.8e-89       4     360 ..      39     430 ..      36     431 .. 0.88

  Alignments for each domain:
  == domain 1  score: 300.6 bits;  conditional E-value: 5e-93
                                       HHHHHHHHHHHTSS-SSSSHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHH........TTTTTT-EEEEESSS CS
                   DegT_DnrJ_EryC1   4 eeeleaveevlksgwltsgpeveeFEkafaaylgvkhaiavssGtaAlhlaLra........lgvgpgdeVIvpslt 72 
                                       ee+ + v  +l+  wlt g++v++FEk++a+ylgv+++ +v+sG++A+++a +a         ++ +gdeVI +++ 
  gi|474933689|ref|YP_007687271.1|  39 EEIVNIVDSALDF-WLTAGKYVDQFEKNLAEYLGVQFVSTVNSGSSANLIAFMAltspllgdRQIRRGDEVICVAAA 114
                                       4555556666665.9999************************************877765555567*********** PP

                                       -THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-T CS
                   DegT_DnrJ_EryC1  73 FvatanavlelgakpvfvDvdpdtynidpaaieaaitertkaIlpVhlyGqvadmdalkaiaakhglkvieDaAhAl 149
                                       F ++++++l+ ga+pvfvDv+p t+ id++++eaa+  +tk ++++h++G+++d++++k+ ++kh+l++ieD ++Al
  gi|474933689|ref|YP_007687271.1| 115 FPTSVAPILQYGAVPVFVDVEPRTCDIDVSKMEAALSDKTKLVFMAHTLGNPFDLAKVKEFCDKHNLWLIEDNCDAL 191
                                       ***************************************************************************** PP

                                       T-EETT....EECCCSSSEEEEE-BTTSSS-SSS-EEEEESTHHHHHHHHHHHBTTCEC........CTCSSCECCS CS
                   DegT_DnrJ_EryC1 150 Gatykg....kkvGalgdaavfSFyptKnlttGeGGavvtndeelaekarvlrnhGlkr........kaekryvgev 214
                                       G +y       k+G++gd+++ SFyp++++t+GeGGav t+++ l++ +r +r  G++         +  +      
  gi|474933689|ref|YP_007687271.1| 192 GGEYTLngktYKTGTIGDIGTSSFYPAHQMTMGEGGAVYTDNPLLHKLIRSFRDWGRECvctggqdnSCGQ-----R 263
                                       *877533355699*************************************777777665443211113344.....1 PP

                                       ...................S---B-B-BHHHHHHHHHHHCTHHHHHHHHHHHHHHHHHHHHTCCCCEESCGGTTSSS CS
                   DegT_DnrJ_EryC1 215 ...................elGynyrlteiqAAiglaqLerldelvarRreiaelykeeLaelegtaelttpketkk 272
                                                          +lGyn+++te+qAA+g+aqL++l ++va+Rre++++++ +L  l+ +++l++++ +++
  gi|474933689|ref|YP_007687271.1| 264 fmgqfgklpfgydhkyvysHLGYNLKITEMQAAVGVAQLKKLPDFVAKRREHWDYLRANLDCLKDVLTLPEKQANAN 340
                                       45555999********************************************************9988888877777 PP

                                       EEESCEEEEEHCCHHHCHHHHHHHHHHCCEE-B-SGSCHGGGSCCHHHHH....HCCCHC-HHHHHHHHHEEEEEGG CS
                   DegT_DnrJ_EryC1 273 hawhlyavlveeeaevkrdelvealkeegigtrvhypnplhrqpvyaerk....eeasgdlpnaerlaervlsLply 345
                                         w+ ++++ +++   +++++   l++++i+tr ++   + ++p +++ +    ++  gdl+++++l++++++  +y
  gi|474933689|ref|YP_007687271.1| 341 PCWFGFLMIAKSN--KDCNRITSYLESHNIQTRKLFAGNIILHPCFTNLVegkdYRVVGDLTVTNTLMNNAFWVGVY 415
                                       99***99999976..3699*****************888999999776651111566799***************** PP

                                       TTGSHHHHHHHHHHH CS
                   DegT_DnrJ_EryC1 346 pelteedvdrVveal 360
                                       p++t+  +d++++++
  gi|474933689|ref|YP_007687271.1| 416 PGMTQPMMDEIIACI 430
                                       ***********9987 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   7.4e-09   2.7e-05      54     175 ..      59     188 ..      46     198 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 7.4e-09
                                       HHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHTTS-T..TEE.......EEEESTSSHHHHH.HHHHTHHHTTCEEE CS
                   Cys_Met_Meta_PP  54 rsvleeriaaLeggeaalavssGmaAiaaailallka..Gde.......ivvsddlYggtqr.llkkvlkklgievk 120
                                       ++ +e+++a+  g++ +  v+sG +A   a++al +   Gd+       +++   ++  + + +l++ +        
  gi|474933689|ref|YP_007687271.1|  59 VDQFEKNLAEYLGVQFVSTVNSGSSANLIAFMALTSPllGDRqirrgdeVICVAAAFPTSVApILQYGAVP-----V 130
                                       5789***********************99999997644455522222226666666665544133333333.....3 PP

                                       EEST......TSHHHHHHHCCTTEEEEEE.ESS-TTTT----HHHHHHHHHHTT-EEEEEGT CS
                   Cys_Met_Meta_PP 121 fvdt......sdleelekaikentklvyl.EtptnpllkvvDiekiaklakkagvlvvvDnt 175
                                       fvd+       d++++e+a++++tklv++  t++np+    D++k+ +++ k+++ ++ Dn+
  gi|474933689|ref|YP_007687271.1| 131 FVDVeprtcdIDVSKMEAALSDKTKLVFMaHTLGNPF----DLAKVKEFCDKHNLWLIEDNC 188
                                       44433333334899**************846999995....*******************97 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   1.1e-08   3.9e-05      47     187 ..      60     186 ..      54     188 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.1e-08
                                       HHHHHHHHHHHCTCTTCHTTGGEGE.EEESHHHHHHHHHHHHHH.......HTTT-EEEEEESS-THHHHHHHHTTS CS
                     Aminotran_1_2  47 peleealakflgrseklklkreaav.vvgsGagaliealifllk.......lnpgdeilvpdptyasyknilrlsgg 115
                                       +++e++la++lg         +  v +v sG++a++ a+++l++       + +gde++  +  ++     +  +g+
  gi|474933689|ref|YP_007687271.1|  60 DQFEKNLAEYLG--------VQ-FVsTVNSGSSANLIAFMALTSpllgdrqIRRGDEVICVAAAFPTSVAPILQYGA 127
                                       78**********........66.441578899999999999998*********************977777777788 PP

                                       EEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEE CS
                     Aminotran_1_2 116 evvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvD 187
                                         v + ++ + ++ +d+ ++e+al++      ktk+++ +   +  G  ++l+++++    ++k+nl+l+ D
  gi|474933689|ref|YP_007687271.1| 128 VPVFVDVE-PRTCDIDVSKMEAALSD------KTKLVFMA---HTLGNPFDLAKVKEF---CDKHNLWLIED 186
                                       88888855.99***************......9*****87...778999999999999...********987 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   4.2e-07    0.0015      35     181 ..      49     192 ..      31     196 .. 0.79
   2 !    3.4   0.0    0.0082        29     262     349 ..     294     387 ..     288     406 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.2e-07
                                       SHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC.......-TTTSEEEEETTSHGGGTHH CS
                       Aminotran_5  35 hhlgkeatkaveearekvaelinaeseeeiiftsGtteainlvalslars.......lkpgdeivvteaehhanlvp 104
                                        ++   a k v++ ++++ae ++++     + t +++++ nl+a  ++ s       +++gde++ ++a     + p
  gi|474933689|ref|YP_007687271.1|  49 LDFWLTAGKYVDQFEKNLAEYLGVQF----VSTVNSGSSANLIAFMALTSpllgdrqIRRGDEVICVAAAFPTSVAP 121
                                       55566788899999***********8....777777777777776665544545567999*********99999977 PP

                                       HHHHHHHHTEEEEEEEBE.TTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTT CS
                       Aminotran_5 105 wqelakrtgakvkvipld.eegeldldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqav 180
                                       + +   +  + v ++ ++ ++  +d++++e++l++ktklv+++h+   +G+ ++++++++ + k++ +++ D + a+
  gi|474933689|ref|YP_007687271.1| 122 ILQYG-A--VPV-FVDVEpRTCDIDVSKMEAALSDKTKLVFMAHT---LGNPFDLAKVKEFCDKHNLWLIEDNCDAL 191
                                       77765.3..333.44444146789*******************95...9********************99988777 PP

                                       T CS
                       Aminotran_5 181 g 181
                                       g
  gi|474933689|ref|YP_007687271.1| 192 G 192
                                       6 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.0082
                                       HHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEE...TTCSHHHHHHHHHHTTEEE CS
                       Aminotran_5 262 gaaleyleeigleaiekhekelaeyllerlkslpgvrlygpdkaerrasivsfnf...kgvhaedvatlLdeegIav 335
                                       +aa+   +  +l    ++ +e  +yl++ l+ l++v ++  ++a++++  + f +    + +++ + ++L++++I  
  gi|474933689|ref|YP_007687271.1| 294 QAAVGVAQLKKLPDFVAKRREHWDYLRANLDCLKDVLTLPEKQANANPCWFGFLMiakSNKDCNRITSYLESHNIQT 370
                                       556666666666667788899999**************888788888877666554336777899***********9 PP

                                       EE...E-TTTHHHHHHT CS
                       Aminotran_5 336 rs...Ghhcaqplmkrl 349
                                       r    G+  ++p ++ l
  gi|474933689|ref|YP_007687271.1| 371 RKlfaGNIILHPCFTNL 387
                                       98888999888887766 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   7.9e-07    0.0028      34     168 ..      59     187 ..      54     191 .. 0.75
   2 ?   -1.3   0.0      0.29     1e+03      18      44 ..     220     267 ..     209     319 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 7.9e-07
                                       HHHHHHHHHHHTT-SEEEEES-HHHHHHHHH.........HHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE CS
                   Beta_elim_lyase  34 vnrLedavaelfgkeaalfvpqGtaAnsill.........killqrgeevivtepahihfdetgaiaelagvklrdl 101
                                       v ++e+++ae++g + +  v +G  An i++            ++rg+evi+       f +  a+    g+ ++ +
  gi|474933689|ref|YP_007687271.1|  59 VDQFEKNLAEYLGVQFVSTVNSGSSANLIAFmaltspllgDRQIRRGDEVICVA---AAFPTSVAPILQYGAVPVFV 132
                                       6789999************************33333333333344555555554...45778877777777778888 PP

                                       -EBTT.TBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEE CS
                   Beta_elim_lyase 102 knkea.GkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDg 168
                                       + +    ++d+ k+eaa+ +      k+kl+ ++ T       +     l++v+++++k+++ l+ D 
  gi|474933689|ref|YP_007687271.1| 133 DVEPRtCDIDVSKMEAALSD------KTKLVFMAHTLGN----P---FDLAKVKEFCDKHNLWLIEDN 187
                                       76655599**********99......6899999999864....5...456778899999999888775 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.29
                                       HHCS----CCCT--HHHHHHHHHHHH.....................H CS
                   Beta_elim_lyase  18 qaaamlGdesYgedktvnrLedavae.....................l 44 
                                       q+++  G ++Y +++  ++L   +++                      
  gi|474933689|ref|YP_007687271.1| 220 QMTMGEGGAVYTDNPLLHKLIRSFRDwgrecvctggqdnscgqrfmgQ 267
                                       477777888999999999998888885555555555555555554440 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.52
# Mc/sec: 2509.39
//
Query:       gi|474933690|ref|YP_007687272.1|  [L=599]
Description: thiamine pyrophosphate-requiring protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.8e-46  156.5   0.0      7e-46  156.0   0.0    1.2  1  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
    4.4e-31  107.7   0.0    1.6e-30  105.9   0.0    1.9  2  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
      2e-29  102.0   0.0    3.5e-29  101.3   0.0    1.4  1  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain


Domain annotation for each model (and alignments):
>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.0   0.0   1.2e-49     7e-46       2     169 ..       4     178 ..       3     181 .. 0.97

  Alignments for each domain:
  == domain 1  score: 156.0 bits;  conditional E-value: 1.2e-49
                                       EHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHH CS
                      TPP_enzyme_N   2 tvaealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatn 78 
                                       +v+++++++L ++g++ +f+++G++ ++l d++ +++g++++  +hEq++a+aA++yar+t++++ v+vt+gpG tn
  gi|474933690|ref|YP_007687272.1|   4 KVSDYIAQYLVDYGITDAFTIVGGGAMHLNDSFGKQKGLKCYYNHHEQACAIAAEAYARVTNRLALVCVTTGPGGTN 80 
                                       799************************************************************************** PP

                                       CHHHHHHHHHHT--EEEEEEE--CCCHH.......S..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHH CS
                      TPP_enzyme_N  79 altalaeAkvdriPllvlsgdrptslrg.......qgvlqqeldqlalfrpvtkyaervtspeelpealrrAirtal 148
                                       a+t++++ ++d+iP+l++sg++ ++ +        + +  qe+d+   ++++tky+e v +p++++  l++A+++a+
  gi|474933690|ref|YP_007687272.1|  81 AITGVVGGWLDSIPMLIISGQVRYDTTArstglplRAMGDQEFDICTSVASMTKYCEMVIDPNRIRYCLHKALTIAT 157
                                       ************************999999****988888899********************************** PP

                                       SSS--EEEEEEEHHHCC-EEE CS
                      TPP_enzyme_N 149 sgrpgPvylelpkdvlleevd 169
                                       +grpgPv+l++p++v+ + ++
  gi|474933690|ref|YP_007687272.1| 158 NGRPGPVWLDIPLNVQGAFIE 178
                                       ****************88666 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.25   1.5e+03      82     150 ..      80     165 ..      78     168 .. 0.63
   2 !  105.9   0.0   2.7e-34   1.6e-30       2     145 ..     408     544 ..     401     552 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.25
                                       -SBCCCHHHH......HHHHTCCTTTTSBB.........BS----HHHHHHHTTSEEE.EESSH.HHHHHHHHHHHH CS
                      TPP_enzyme_C  82 Negygmtggq......qepfggkrksgpagk........dlkpvdfaklaealGakga.rvekadveeleealkeal 143
                                       N+++g +gg+          g+ r+ ++a++        +++++d++  ++++  k +  v ++  + ++  l +al
  gi|474933690|ref|YP_007687272.1|  80 NAITGVVGGWldsipmLIISGQVRYDTTARStglplramGDQEFDICTSVASM-TKYCeMVIDP--NRIRYCLHKAL 153
                                       77778888887777653445555555555556667778778889999999999.4433343344..78887787777 PP

                                       .....CSSSEEE CS
                      TPP_enzyme_C 144 .....ekkgpal 150
                                             + gp+ 
  gi|474933690|ref|YP_007687272.1| 154 tiatnGRPGPVW 165
                                       666555556655 PP

  == domain 2  score: 105.9 bits;  conditional E-value: 2.7e-34
                                       SSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEEE CS
                      TPP_enzyme_C   2 iGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnlpitvv 78 
                                       +G      ++ + +k+ ++y+t++  ++mGy lpaAiG+++a++ r vv+++GDG+++m+lqel t++ +nlpi+++
  gi|474933690|ref|YP_007687272.1| 408 VG------SHSYVIKKSQRYITNSAIASMGYDLPAAIGVCVANKCRSVVCLAGDGSIMMNLQELQTVITNNLPIKIF 478
                                       33......334578999*************************9999******************************* PP

                                       EEE-SBCCCHHHHHHHHTCCTTTTSBB...BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHHCS CS
                      TPP_enzyme_C  79 vlnNegygmtggqqepfggkrksgpagk..dlkpvdfaklaealGakgarvekadveeleealkealek 145
                                       ++nN+gy+ ++  q+  ++k+++g  ++  dl  +d++kla a+G + +r+ ++  +e+e+ l++ l++
  gi|474933690|ref|YP_007687272.1| 479 IINNSGYQSIRLTQTNIFDKHFVGIGKDsgDLSFPDYEKLATAFGYPYYRICSN--AEMEK-LDQILNE 544
                                       ************************88779878999************8865555..44433.3444444 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.3   0.0   5.8e-33   3.5e-29       4     136 ..     206     339 ..     203     340 .. 0.95

  Alignments for each domain:
  == domain 1  score: 101.3 bits;  conditional E-value: 5.8e-33
                                       HHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEEESGGGSCHHHHHHHHH-SE CS
                      TPP_enzyme_M   4 aaellkaakrpvilvGggvarsgaseelrelaeklgiPvvttlmgkgvipedhplylgmlglhgskaanealeeaDl 80 
                                       +++ +k+a+rpv+++G+g++ sga + + +++ekl+iPvvt +   +++p+dh+ly+g+ g +g++ +n a++++Dl
  gi|474933690|ref|YP_007687272.1| 206 ILDKVKNAERPVFYAGNGIRLSGAYDTFLQVIEKLNIPVVTNWDSVDMLPDDHHLYAGRGGSLGTRGGNFAVQNSDL 282
                                       67899************************************************************************ PP

                                       EEEES-SSSTCCCTT.TTTTTTTT-EEEEEESSCCCCTTCC.--SEEEECTHHHHHHH CS
                      TPP_enzyme_M  81 vlalGarfddirttg.sepefapeakiihididpaeigkny.qvdlaivgdvketlea 136
                                       v+ +G+r++  r+t+ +++++a++a +i  did+ae++k   +vd+++  d+k  lea
  gi|474933690|ref|YP_007687272.1| 283 VISIGSRLSL-RQTSfNWKRWASHAYVIMEDIDEAELKKPIlHVDMPLHVDAKVLLEA 339
                                       ********99.77777***********************88679*********99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (599 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.37s 00:00:01.03 Elapsed: 00:00:00.53
# Mc/sec: 3377.27
//
Query:       gi|474933691|ref|YP_007687273.1|  [L=301]
Description: Nucleoside-diphosphate-sugar epimerase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-33  116.6   0.0    1.4e-33  116.3   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    2.2e-17   63.5   0.0      5e-17   62.3   0.0    1.5  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    3.6e-08   33.3   0.1    4.7e-08   32.9   0.1    1.2  1  NmrA             NmrA-like family
    1.2e-07   31.8   0.0    1.6e-07   31.4   0.0    1.2  1  NAD_binding_10   NAD(P)H-binding
    0.00013   21.1   0.0     0.0008   18.5   0.0    1.9  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    0.00014   21.1   0.0    0.00043   19.5   0.0    1.8  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    0.00064   18.9   0.0     0.0016   17.6   0.0    1.7  1  RmlD_sub_bind    RmlD substrate binding domain
     0.0017   18.9   1.0      0.004   17.7   0.3    1.9  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
       0.01   15.3   0.6      0.016   14.7   0.2    1.5  2  adh_short        short chain dehydrogenase
      0.042   14.0   0.1      0.067   13.3   0.1    1.3  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
      0.054   12.6   0.0        0.9    8.7   0.0    2.2  2  NAD_binding_4    Male sterility protein


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.3   0.0   8.7e-37   1.4e-33       1     241 []       3     229 ..       3     229 .. 0.91

  Alignments for each domain:
  == domain 1  score: 116.3 bits;  conditional E-value: 8.7e-37
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC..EEEE--TT-HHHHHHHHHHHT-SEEEE--S-- CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl..elveldltdrsalerlfkeeqpdavihlAavg 75 
                                       i +tG tG iG+al+k+  ++g+evi++ r  s++ ++   ++  e++e+d+ d ++l+    + q+da +hlA  +
  gi|474933691|ref|YP_007687273.1|   3 IAITGPTGAIGTALIKEAISAGHEVIAIVRPGSSRMSNVAVTKgvEIIECDISDYASLHG---KRQCDAFFHLAWMK 76 
                                       689***************************988877776666688**********99998...459*******9999 PP

                                       -HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHH CS
                         Epimerase  76 gvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlagekl 152
                                       + +a  +d  +   +n++++ln ++ a   g+k ++ ++S + YG ++ +  + ++   p+ p+s Y++aK+ + kl
  gi|474933691|ref|YP_007687273.1|  77 TFGAARDD-VYSQVDNIRYALNAVDLAESWGAKAFVGAGSQAEYGHSEVS-LNGSV---PVDPTSGYGIAKYSAGKL 148
                                       99885555.677778******************************87774.66666...88**************** PP

                                       HHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHH CS
                         Epimerase 153 veayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehv 229
                                       ++ + +q gl++   r+ ++yG++   + ++ +i +li  +leg   v  l + ++ +d++y++D+a a+l++ e+ 
  gi|474933691|ref|YP_007687273.1| 149 CRLFCQQKGLRFNWARILSVYGEN---DADHTLIMYLIHTLLEGG--VPELTKCEQMWDYIYSKDAAYALLCIGEK- 219
                                       ************************...7799************98..9999999**********************. PP

                                       TT-STTEEEEES CS
                         Epimerase 230 dagdkgeiyniG 241
                                         g +g++y iG
  gi|474933691|ref|YP_007687273.1| 220 --GVDGKVYCIG 229
                                       ..8999999998 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.3   0.0   3.1e-20     5e-17       2     331 ..       5     293 ..       4     294 .. 0.85

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 3.1e-20
                                       EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SE CS
                     GDP_Man_Dehyd   2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpde 78 
                                       iTG +G iG  l++  ++ g+ev+ ivr  ss    r++++a       ++ ++++++D++D +sl     + q+d+
  gi|474933691|ref|YP_007687273.1|   5 ITGPTGAIGTALIKEAISAGHEVIAIVRPGSS----RMSNVAV------TKGVEIIECDISDYASL---HGKRQCDA 68 
                                       9**************************99988....6667653......34689********8865...5799**** PP

                                       EEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHHH CS
                     GDP_Man_Dehyd  79 vynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYaa 155
                                        ++LA ++  +   ++  y    n+  +l+ ++++ + g    + f+ a++   YG+  ev  + + p++P+s Y++
  gi|474933691|ref|YP_007687273.1|  69 FFHLAWMKTFGAARDDV-YSQVDNIRYALNAVDLAESWGA---KAFVGAGSQAEYGHS-EVSLNGSVPVDPTSGYGI 140
                                       ************99984.4444468888999999988875...58***********98.6999************** PP

                                       HHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHH CS
                     GDP_Man_Dehyd 156 aKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyvea 232
                                       aK +a  +++ + ++ gl    +++   ++          +i+  ++  ++g   v++l + ++  d+ + kD + a
  gi|474933691|ref|YP_007687273.1| 141 AKYSAGKLCRLFCQQKGLRFNWARILSVYGEND---ADHTLIMYLIHTLLEGG--VPELTKCEQMWDYIYSKDAAYA 212
                                       ******************************995...66799******999998..77789***************** PP

                                       HHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB--B- CS
                     GDP_Man_Dehyd 233 mwlmlqqdkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlllgd 309
                                       +  + +++        +g+++ +++   + +++ ++++         v   +   +++v++  k++ p ++  l++d
  gi|474933691|ref|YP_007687273.1| 213 LLCIGEKGV-------DGKVYCIGSGECRPLKAYVEDLRDA------V---DP--SKEVRFGVKPYYPHQAMYLCAD 271
                                       *99999886.......5666666555555555555544332......1...22..3457777888889999****** PP

                                       THHHHHHH----SS-HHHHHHH CS
                     GDP_Man_Dehyd 310 askakeeLgWkpkvsfeelvre 331
                                       +s +  + g++p+++f+++++e
  gi|474933691|ref|YP_007687273.1| 272 ISELTADTGFRPRYGFKKGISE 293
                                       *******************987 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.1   2.9e-11   4.7e-08       1      60 [.       3      62 ..       3     122 .. 0.83

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 2.9e-11
                                      EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHH CS
                              NmrA  1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslve 60
                                      I+++G+TG++G ++++ +++agh+v a+vR  +s  ++   ++Gve+++ d+ d++sl+ 
  gi|474933691|ref|YP_007687273.1|  3 IAITGPTGAIGTALIKEAISAGHEVIAIVRPGSSRMSNVAVTKGVEIIECDISDYASLHG 62
                                      89*******************************************************974 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.0     1e-10   1.6e-07       1      98 [.       7     115 ..       7     160 .. 0.77

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 1e-10
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETT.HHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES-......-- CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRn.peklaeleaeeglevvegdvtdvedlaealkgadaVvsal......gg 70 
                                       G tG +G +l+ke++++ ghev a+vR  ++++++++ ++g+e++e d++d ++l    +++da +  +      ++
  gi|474933691|ref|YP_007687273.1|   7 GPTGAIGTALIKEAISA-GHEVIAIVRPgSSRMSNVAVTKGVEIIECDISDYASLHGK-RQCDAFFHLAwmktfgAA 81 
                                       669**************.5********978999***999***************9876.789988777778776433 PP

                                       TCC...HHHH.....HHHHHHHHHHCT--EEEEEEE CS
                    NAD_binding_10  71 ggk...deeg.....aknivdaakeagvkRfvlvsa 98 
                                       +++   +  +     a n+vd a+  g k fv  ++
  gi|474933691|ref|YP_007687273.1|  82 RDDvysQ--VdniryALNAVDLAESWGAKAFVGAGS 115
                                       3334330..255567888899999999888887665 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   4.9e-07    0.0008       1     121 [.       4     120 ..       4     224 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 4.9e-07
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslv 77 
                                       ++tG +G +G al+ke +++++  ev ++ +r +++  +++  ++  ++ie+D+ d ++l+   ++ d+ +hl + +
  gi|474933691|ref|YP_007687273.1|   4 AITGPTGAIGTALIKEAISAGH--EVIAI-VRPGSSRMSNVAVTKGVEIIECDISDYASLHG-KRQCDAFFHL-AWM 75 
                                       59*******************5..77666.455554445555444445************86.6889******.788 PP

                         3Beta_HSD  78 dvagkltedeimkv.nvkGTrnvleacvkagvrvlvYtSsaevvg 121
                                       + +g  ++d + +v n++   n ++ + + g +++v   s    g
  gi|474933691|ref|YP_007687273.1|  76 KTFGAARDDVYSQVdNIRYALNAVDLAESWGAKAFVGAGSQAEYG 120
                                       89999****999998899999999999999999998766655444 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   2.7e-07   0.00043       1     125 [.       3     112 ..       3     254 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.7e-07
                                       EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelk 77 
                                       + +tG +G+iG +l+++ ++   + i ++     ++ +++ ++       ++      + +d+ d ++l+   +   
  gi|474933691|ref|YP_007687273.1|   3 IAITGPTGAIGTALIKEAISAGHEVIAIVRPGSSRMSNVAVTK-----GVEI------IECDISDYASLHGKRQ--- 65 
                                       679***************************9999999988765.....2223......3499****99987655... PP

                                       -SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEE CS
                   Polysacc_synt_2  78 vdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvl 125
                                       +d+ fh A +K   ++   +++ ++ N+  + n ++ a + g k++v 
  gi|474933691|ref|YP_007687273.1|  66 CDAFFHLAWMKTFGAARDDVYSQVD-NIRYALNAVDLAESWGAKAFVG 112
                                       ********************99996.8*****************9995 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   9.7e-07    0.0016       1      44 [.       1      61 [.       1     184 [. 0.76

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 9.7e-07
                                      EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT.................T--TTSHHHHH CS
                     RmlD_sub_bind  1 mkilvtGanGqlGseLakqlaeeglevlaltre.................eldltdaeava 44
                                      m+i +tG +G++G++L+k++ ++g+ev+a+ r+                 e+d++d ++++
  gi|474933691|ref|YP_007687273.1|  1 MRIAITGPTGAIGTALIKEAISAGHEVIAIVRPgssrmsnvavtkgveiiECDISDYASLH 61
                                      89****************************9997888887777777777777777776665 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.3   2.5e-06     0.004       1      58 [.       2      57 ..       2      62 .. 0.88
   2 ?   -1.8   0.0         3   4.9e+03       3      12 ..     109     118 ..     109     129 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.5e-06
                                      EEEEET.TSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHH CS
                     F420_oxidored  1 kigiiG.aGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneea 58
                                      +i+i G +G +g al++ +++ag   he++ + ++  +++   a + gv++++ d ++ 
  gi|474933691|ref|YP_007687273.1|  2 RIAITGpTGAIGTALIKEAISAG---HEVIAIVRPGSSRMSNVAVTKGVEIIECDISDY 57
                                      57788549***************...****999***************99999777665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3
                                       EEETTSHHHH CS
                     F420_oxidored   3 giiGaGnmge 12 
                                       +++GaG+++e
  gi|474933691|ref|YP_007687273.1| 109 AFVGAGSQAE 118
                                       799****997 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.2   9.7e-06     0.016       3      64 ..       3      60 ..       1      63 [. 0.81
   2 ?   -3.4   0.0       3.4   5.5e+03     136     157 ..     125     146 ..     124     153 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 9.7e-06
                                      EEEESTTSHHHHHHHHHHHHTT-EEEE.EESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHH CS
                         adh_short  3 vlvtGassGIGraiakelakeGakvvv.vdrseekleevakelkeegakalaiqvDvtdreev 64
                                      + +tG ++ IG a+ ke +++G +v++ v   ++++ +va   k     + +i++D++d++++
  gi|474933691|ref|YP_007687273.1|  3 IAITGPTGAIGTALIKEAISAGHEVIAiVRPGSSRMSNVAVT-KG----VEIIECDISDYASL 60
                                      78*************************555566666555444.43....89*******99875 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.4
                                       EGGGTSB-TTBHHHHHHHHHHH CS
                         adh_short 136 SvagkvpvagvaaYsAsKaava 157
                                       S +g vpv  ++ Y+ +K    
  gi|474933691|ref|YP_007687273.1| 125 SLNGSVPVDPTSGYGIAKYSAG 146
                                       6677777777777777775544 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   4.1e-05     0.067       1      52 [.       1      51 [.       1      66 [. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.1e-05
                                      EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS- CS
                            DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgk 52
                                      +++a++G +G +G++++k + + +++e+ a v   +s++++  + + +++ +
  gi|474933691|ref|YP_007687273.1|  1 MRIAITGPTGAIGTALIKEAIS-AGHEVIAIVRPGSSRMSNVAVTKGVEIIE 51
                                      89******************99.999*9999999888777776665555544 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00055       0.9       1      37 [.       5      39 ..       5      65 .. 0.87
   2 ?    1.9   0.0     0.065   1.1e+02     169     212 ..     131     174 ..      61     200 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00055
                                      EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHH CS
                     NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksgesa 37
                                      +TG TG +G+ L+++ ++     ++++ vR+ s++  
  gi|474933691|ref|YP_007687273.1|  5 ITGPTGAIGTALIKEAISAGH--EVIAIVRPGSSRMS 39
                                      8****************9998..8******9987654 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.065
                                       TTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE--SSS CS
                     NAD_binding_4 169 lkglpntYeqsKalaEklvrearrrsglpvvivRpsiitgeskt 212
                                         + + +Y   K+ a kl+r   +++gl+++  R+  ++ge   
  gi|474933691|ref|YP_007687273.1| 131 PVDPTSGYGIAKYSAGKLCRLFCQQKGLRFNWARILSVYGENDA 174
                                       5567789****************999*99999998888876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.56u 0.35s 00:00:00.91 Elapsed: 00:00:00.48
# Mc/sec: 1868.11
//
Query:       gi|474933692|ref|YP_007687274.1|  [L=215]
Description: putative phosphatase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-34  120.2   0.0    1.2e-34  120.0   0.0    1.0  1  HAD_2           Haloacid dehalogenase-like hydrolase
    1.6e-12   48.2   0.0    1.3e-07   32.2   0.0    2.1  2  Hydrolase       haloacid dehalogenase-like hydrolase
    4.6e-07   30.4   0.0    3.3e-06   27.6   0.0    1.9  1  HAD             haloacid dehalogenase-like hydrolase
    2.3e-06   27.6   0.0    3.8e-06   26.9   0.0    1.3  1  Hydrolase_like  HAD-hyrolase-like
     0.0034   17.2   1.1       0.48   10.1   0.2    2.8  3  Hydrolase_3     haloacid dehalogenase-like hydrolase
     0.0035   17.1   0.0       0.03   14.1   0.0    2.0  1  NIF             NLI interacting factor-like phosphatase


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.0   0.0     4e-38   1.2e-34       1     178 []       7     183 ..       7     183 .. 0.92

  Alignments for each domain:
  == domain 1  score: 120.0 bits;  conditional E-value: 4e-38
                             HAD_2   1 iiFDlDgTlldteeliiqafnelleeyglselseeelrkliglslrellr.klgeseeeee.kieellrkyneekkk 75 
                                       +iFDlDgTl+d++e i++++ e+++ +gl++ls+e ++++ig++  +++  k+g see+    ++ ++ +y++++  
  gi|474933692|ref|YP_007687274.1|   7 VIFDLDGTLIDSSEGIVNSVVETIDIMGLETLSREFIESCIGPPIGDSIGsKMGYSEETIRrFYDVFRPIYKDKHLM 83 
                                       7*******************************************988776155555443336778888888888888 PP

                             HAD_2  76 kevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekaleklklkk 152
                                        e++++dg+  +LeeL + +++lgi+T+k+ + +   l++lg+++yF  i+++++ ++ K +p+++++++++l++++
  gi|474933692|ref|YP_007687274.1|  84 -ECEVFDGIPAMLEEL-QGRFRLGIATNKRIDYTLTLLDNLGLKQYFGSICGGDQYNRLK-KPDILNNCMKELGVDP 157
                                       .***************.99***************************************99.9*************** PP

                             HAD_2 153 eeviyvGDsptDieaakkagikviav 178
                                       + +++vGD+++D+ aa +  +++i+v
  gi|474933692|ref|YP_007687274.1| 158 SGTVMVGDTSSDLNAAVQCDTDFIGV 183
                                       ***********************987 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   1.1e-05     0.034       3      26 ..       6      29 ..       4      72 .. 0.78
   2 !   32.2   0.0   4.2e-11   1.3e-07     117     210 .]      85     177 ..      74     177 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.1e-05
                                      EEEEESBTTTBCHHHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  3 tvvfDkdGTLttgepsvedvivsa 26
                                      +v+fD+dGTL++++  ++  +v+ 
  gi|474933692|ref|YP_007687274.1|  6 AVIFDLDGTLIDSSEGIVNSVVET 29
                                      89*********9995555555554 PP

  == domain 2  score: 32.2 bits;  conditional E-value: 4.2e-11
                                       HHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT.GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 117 lkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG.ddyfdaviasdietvakpspegkvaaireLqgkpee 192
                                       ++v++++  ++++L+ + ++++++t+        ++++lG ++yf  + ++d     k +p++++  ++eL+++p+ 
  gi|474933692|ref|YP_007687274.1|  85 CEVFDGIPAMLEELQGR-FRLGIATNKRIDYTLTLLDNLGlKQYFGSICGGDQYNRLK-KPDILNNCMKELGVDPSG 159
                                       5799***********54.59*********9999************7777777777443.57**************** PP

                                       EEEEESSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxx RF
                         Hydrolase 193 vamVGDgvnDaaalaaAg 210
                                       ++mVGD+  D+ a+ + +
  gi|474933692|ref|YP_007687274.1| 160 TVMVGDTSSDLNAAVQCD 177
                                       *************98765 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   1.1e-09   3.3e-06       1     187 [.       7     173 ..       7     173 .. 0.69

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 1.1e-09
                               HAD   1 alfDfDgTLldgdslelllrfllrrgaprlwralreklllal.....frellrldraglaelleallaglseelaae 72 
                                       ++fD+DgTL+d++ ++  +  ++++ +   +++l +++ ++           +               g+see +++
  gi|474933692|ref|YP_007687274.1|   7 VIFDLDGTLIDSSEGI--VNSVVETIDIMGLETLSREFIESCigppiG----D---------SIGSKMGYSEETIRR 68 
                                       79**********7665..455666666666777777777777322221....1.........233456677777777 PP

                               HAD  73 lerfvaevirpk......lldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelg 143
                                       + + ++ +++ k      ++  g+ ++l+  ++  +r+ + ++    ++  ll++lg ++  ++       + g   
  gi|474933692|ref|YP_007687274.1|  69 FYDVFRPIYKDKhlmeceVF-DGIPAMLE-ELQGRFRLGIATNKRIDYTLTLLDNLGLKQYFGS------ICGG--- 134
                                       77777666666653333334.36666666.335669*********************5555555......4444... PP

                               HAD 144 legkpvrgegkvaalrewlaaegegidleevvayGDspsDlpll 187
                                        ++ +  +  k++ l+    +++ g d++ +v +GD+ sDl ++
  gi|474933692|ref|YP_007687274.1| 135 -DQYNRLK--KPDILNN--CMKELGVDPSGTVMVGDTSSDLNAA 173
                                       .4444444..6699999..99999999999***********886 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   1.3e-09   3.8e-06       7      73 ..     143     209 ..     140     211 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 1.3e-09
                                       SHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSS..S-TTTHHHHHHHHT---SEEE CS
                    Hydrolase_like   7 pemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGv..trpedleepehkptyvaddla 73 
                                       p ++   +++lg+dp+ ++m+GD+  +D+ +A +   +++ V  G    rp+d + ++++ ++ +ddl+
  gi|474933692|ref|YP_007687274.1| 143 PDILNNCMKELGVDPSGTVMVGDT-SSDLNAAVQCDTDFIGVGFGFgfRRPSDIP-EKYHFAATVDDLR 209
                                       457888999***************.*****************9976558889988.5577777888876 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.2   0.00016      0.48       1      24 [.       7      30 ..       7      33 .. 0.89
   2 ?   -0.3   0.0      0.25   7.5e+02      32      60 ..     102     130 ..      91     141 .. 0.82
   3 !    4.3   0.0    0.0097        29     188     216 ..     142     170 ..     136     173 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00016
                                      EEEEIIIIIS-TTS---HHHHHHH CS
                       Hydrolase_3  1 ialDlDGTLlnsdkkisektkeai 24
                                      +++DlDGTL++s + i ++ +e+i
  gi|474933692|ref|YP_007687274.1|  7 VIFDLDGTLIDSSEGIVNSVVETI 30
                                      69***********99999988887 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.25
                                       SEEEEE-SS-HHHHHHHHHHCCCCSEEEE CS
                       Hydrolase_3  32 ikvviATGRslravlpvleelgldlpvia 60 
                                       + + iAT   +  +l +l++lgl++++ +
  gi|474933692|ref|YP_007687274.1| 102 FRLGIATNKRIDYTLTLLDNLGLKQYFGS 130
                                       56789******************988755 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.0097
                                       HHHHHHHHHHHCT--GGGEEEEESSGGGH CS
                       Hydrolase_3 188 KgtalkklakelnisleeviafGDgeNDi 216
                                       K   l++ +kel+++++ ++ +GD   D+
  gi|474933692|ref|YP_007687274.1| 142 KPDILNNCMKELGVDPSGTVMVGDTSSDL 170
                                       66778999*****************9997 PP

>> NIF  NLI interacting factor-like phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0     1e-05      0.03       3     115 ..       7     168 ..       5     177 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1e-05
                               NIF   3 LVLDLDetLvhskleksk...............................................kl.kvegekvev 31 
                                       +++DLD+tL+ s++   +                                                + ++++ k+ +
  gi|474933692|ref|YP_007687274.1|   7 VIFDLDGTLIDSSEGIVNsvvetidimgletlsrefiescigppigdsigskmgyseetirrfydVFrPIYKDKHLM 83 
                                       899*******9996222135557778888888888888888898888888877776666555444222344666778 PP

                               NIF  32 svlkRpgldefLkelsklyevvifTasseeyaeavidildpekkllshrlyrescvkkkg.....eyvKdLsllgrd 103
                                          +  g   +L+el   + ++i T++  +y    +d l  ++ +++     ++  + k+     +++K+L +   d
  gi|474933692|ref|YP_007687274.1|  84 ECEVFDGIPAMLEELQGRFRLGIATNKRIDYTLTLLDNLGLKQ-YFGSICGGDQYNRLKKpdilnNCMKELGV---D 156
                                       8888899********************************9997.79988777777422333455588888888...* PP

                               NIF 104 lsrvvivDdspd 115
                                        s +v+v d++ 
  gi|474933692|ref|YP_007687274.1| 157 PSGTVMVGDTSS 168
                                       ******998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1340.23
//
Query:       gi|474933693|ref|YP_007687275.1|  [L=533]
Description: Isopropylmalate/homocitrate/citramalate synthase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.8e-24   86.1   0.0    1.6e-23   83.7   0.0    2.1  2  HMGL-like  HMGL-like
  ------ inclusion threshold ------
      0.029   14.2   0.0      0.056   13.3   0.0    1.4  1  PDZ_3      PDZ domain


Domain annotation for each model (and alignments):
>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.7   0.0   1.7e-27   1.6e-23       2     258 ..       8     262 ..       7     268 .. 0.83
   2 ?   -2.1   0.0      0.25   2.2e+03      57     103 ..     310     356 ..     303     363 .. 0.71

  Alignments for each domain:
  == domain 1  score: 83.7 bits;  conditional E-value: 1.7e-27
                                       -EEEE-TTTHHHHTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHH CS
                         HMGL-like   2 vkivdttLRDGeqalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkarilalvrarekdi 78 
                                       ++++d tLRDG       +  +    i++ L+ea vd iE+gf     ++ +  r i+ +   ++i      ++k  
  gi|474933693|ref|YP_007687275.1|   8 IRLLDCTLRDGGYVNDWNFGNSTITGIFDRLNEAHVDIIEIGFLDDR-NPEDINRSIQPNT--QAIAKTFSNTIKPT 81 
                                       789**************************************997655.4444445554443..33555555555555 PP

                                       HHHHH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--HHHHHHHHHHH CS
                         HMGL-like  79 kaavealkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkdvelsledasrtdleflaevveaa 155
                                        + v+ +   g   ++ + ++ +  l     + ++e + ka++  k   +lg +v l l + ++ + +++ + +e +
  gi|474933693|ref|YP_007687275.1|  82 SMVVA-MIDYGTCDIKNVQPCKDTILDGIRVIFKKENMYKAADFGKQLMDLGYKVFLQLVSITDYEEQDIRDFCEYV 157
                                       55544.444666677777777776666666666667799999999******************************** PP

                                       HHHT-SEEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--E...EEEBTTS--S CS
                         HMGL-like 156 eeaGatriniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadr...vdgtvnGlGe 229
                                        ++G+  i+i Dt G++   +a + +  l + +++ +++  H Hn++ lA  nt++ +  G+dr   +dg++ G+G 
  gi|474933693|ref|YP_007687275.1| 158 NKIGPHAISIVDTYGLMHKPQATNYFILLNKYLNKDIAIGYHSHNNFQLAYTNTVEILDLGIDRdivLDGSLYGMGK 234
                                       ***************************************************************77769********* PP

                                       SBBB-BHHHHHHHHHHTT-B----HHHHH CS
                         HMGL-like 230 raGnaaleelvaalealgvdtgldlqklr 258
                                        aGna+le ++++l+++   +++d+ ++ 
  gi|474933693|ref|YP_007687275.1| 235 SAGNAPLELIAMNLNQR-FGKKYDIDQIL 262
                                       *************9865.55566666665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.25
                                       HS---TT-B..--EE-SSHHHHHHHHH....TT-SEEEEEEES-HHH CS
                         HMGL-like  57 aiakavkkarilalvrarekdikaavealkgagakrvhvfiatselh 103
                                        +   ++k ++   +r++e+ i+  +e+   +g + v+ + a s+  
  gi|474933693|ref|YP_007687275.1| 310 DVNTILQKIELERKLRYKEEYIESLYERYILNGINDVEYVEALSQTL 356
                                       44444444456677889999999999999999999999998888744 PP

>> PDZ_3  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   6.2e-06     0.056      41      93 ..     165     217 ..     144     226 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.2e-06
                             PDZ_3  41 irlldralygileeedqevvlLsqvLaselntGyenianlqlkkvNgtkvknL 93 
                                       i+++d++   ++ ++++ ++lL++ L++++ +Gy+++ n ql   N  ++++L
  gi|474933693|ref|YP_007687275.1| 165 ISIVDTYGLMHKPQATNYFILLNKYLNKDIAIGYHSHNNFQLAYTNTVEILDL 217
                                       5666666666666778889***************************9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (533 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.47
# Mc/sec: 3420.02
//
Query:       gi|474933694|ref|YP_007687276.1|  [L=312]
Description: Glycosyltransferases involved in cell wall biogenesis [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-25   89.2   0.0    3.8e-25   88.6   0.0    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    6.9e-07   29.4   0.0    8.7e-07   29.1   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    0.00082   18.9   0.0     0.0012   18.4   0.0    1.3  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
  ------ inclusion threshold ------
       0.54    9.9   2.5       0.77    9.4   2.5    1.2  1  Tetraspanin      Tetraspanin family


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.6   0.0   8.6e-29   3.8e-25       1     145 [.       5     150 ..       5     168 .. 0.92

  Alignments for each domain:
  == domain 1  score: 88.6 bits;  conditional E-value: 8.6e-29
                                       EEEEEESS-TTTHHHHHHHHHHH...GGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaq...dpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnag 74 
                                       sv +ptyNee++++   +++++q    p +d+e++++D++S+D+t+ei+++l++e+p+++ i + +n G+ ++   g
  gi|474933694|ref|YP_007687276.1|   5 SVMVPTYNEEENVEPISKAIIEQleqFPQYDYELLFIDNCSKDSTREIIRRLCAENPKIKAIFNAKNYGQFSSPYYG 81 
                                       89*************************************************************************** PP

                                       HHH--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHC CS
                   Glycos_transf_2  75 lraatgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkr 145
                                       + ++tgd+ + + aD + +p+ ++k ++a+e+ g+++v+gq   ++ +   ++ +++ ++n++ ++    +
  gi|474933694|ref|YP_007687276.1|  82 ILQTTGDCTISMCADFQDPPEMIPKYIAAWEE-GYKLVMGQKTSSKESFLVYRARSF-YYNYMKKHSNIGF 150
                                       ********************************.9*9*****9999999999998876.5666666665544 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   1.9e-10   8.7e-07       4     134 ..       4     132 ..       2     210 .. 0.85

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 1.9e-10
                   Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaq.ey.pr..vevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgks 76 
                                       ++v+Vpt+nee+ ++ +  +++ q e  p   +e+ ++++ s+++t+e ++ l a+ p++  + ++na+n g  +  
  gi|474933694|ref|YP_007687276.1|   4 ISVMVPTYNEEENVEPISKAIIEQlEQfPQydYELLFIDNCSKDSTREIIRRLCAENPKI--KAIFNAKNYGQFSS- 77 
                                       89**************9999997745347777***********************99996..89*****9885333. PP

                   Glyco_tranf_2_3  77 ralnealravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrstlvs 134
                                          + ++ ++++d ++ + +D    P+ ++++ ++   ++++ v +++ +  +s lv 
  gi|474933694|ref|YP_007687276.1|  78 --PYYGILQTTGDCTISMCADFQDPPEMIPKYIAAW-EEGYKLVMGQKTSSKESFLVY 132
                                       ..46999999*************************9.*********999988774433 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   2.7e-07    0.0012       1      87 [.       5      92 ..       5     110 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.7e-07
                   Glyco_tranf_2_2  1 svviplraseer.hyieervlqkakyy.deeielivvddgSsekfleevssiidlnllv.ylkdeddkayslaaarNrG 76
                                      sv++p +++ee+ + i   + ++  ++   + el+++d+ S + + e ++ +++ n ++  + +   k y++  +   G
  gi|474933694|ref|YP_007687276.1|  5 SVMVPTYNEEENvEPISKAIIEQLEQFpQYDYELLFIDNCSKDSTREIIRRLCAENPKIkAIFN--AKNYGQFSSPYYG 81
                                      7999***999983468899999999998889***************************954444..4899998888888 PP

                   Glyco_tranf_2_2 77 askaesdlvlF 87
                                      + ++ +d  + 
  gi|474933694|ref|YP_007687276.1| 82 ILQTTGDCTIS 92
                                      88887776554 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   2.5   0.00017      0.77      48     103 ..     230     285 ..     209     298 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00017
                                       .....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Tetraspanin  48 ilaillivvGvllfllgflGcigalkenkcllltfsllllvlfllelaagilgfvf 103
                                       +++++li++ + +f +  +G++  l+ n++ l+ + l ll++f++ l + +lgf+ 
  gi|474933694|ref|YP_007687276.1| 230 TISTGLILTFASIFTIVGFGIYKLLNWNTFSLMPYGLDLLIFFAVSLNIFFLGFIG 285
                                       5667888888888888889******************************9999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2101.84
//
Query:       gi|474933695|ref|YP_007687277.1|  [L=413]
Description: hypothetical protein TALC_00102 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-06   26.6  10.6    5.1e-06   26.6  10.6    4.4  5  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
  ------ inclusion threshold ------
        3.3    7.9   9.4        1.9    8.7   3.2    3.7  3  SpoIIIAC         Stage III sporulation protein AC/AD protein 
        3.8    7.4   9.1        4.1    7.3   0.2    4.1  4  DUF2976          Protein of unknown function (DUF2976)


Domain annotation for each model (and alignments):
>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.4      0.27   1.6e+03      12      51 ..      21      60 ..      14      65 .. 0.69
   2 ?   -1.2  20.6      0.32   1.9e+03      38     138 ..      78     180 ..      41     183 .. 0.72
   3 ?   -0.9   0.1      0.26   1.6e+03      81     119 ..     200     236 ..     193     257 .. 0.67
   4 !    6.7   0.7    0.0012       7.1      65     114 ..     258     305 ..     250     317 .. 0.73
   5 !   26.6  10.6   8.5e-10   5.1e-06       2      77 ..     324     399 ..     323     403 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.27
                   Polysacc_synt_C 12 lslstvlssiLqglgrqkialkalvigalvklilnlllip 51
                                      + l+++   iL+   ++  +++a+ ++ +++ i  + l+p
  gi|474933695|ref|YP_007687277.1| 21 QWLIIMIIPILTDFSEAGVFAVAVSVSSILNQIALFSLTP 60
                                      5566677777777777777777777777777777777766 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.32
                   Polysacc_synt_C  38 galvklilnllli.plfgivGaaiatvlallvvavlnlyalrrllgikl.ellrrl...lkpllaalvmgivvylll 109
                                       + ++ ++l++ li p  gi G  +  +l  ++++++   + + +l+++  +++++l    k +++  +++  v+ + 
  gi|474933695|ref|YP_007687277.1|  78 TRFITIVLSFALIlPISGIFGYGLNQILIIVAYTIYRNLINYAYLHLSSlQIINHLdyaGKCMILEGMVSFTVF-VG 153
                                       55789********9999******************999999999999999766666221343333333333344.44 PP

                   Polysacc_synt_C 110 llllgllllaalalllavlvgalvYllll 138
                                       +++l+ +ll  l++ll +lvg+ ++l+l+
  gi|474933695|ref|YP_007687277.1| 154 CYVLTYNLL--LSTLLMALVGGGIFLYLM 180
                                       444444443..37777777*****99987 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.26
                   Polysacc_synt_C  81 lgiklellrrllkpllaalvmgivvylllllllglllla 119
                                        +++   l  +  pll++ ++ iv+++l +l+l+  ++ 
  gi|474933695|ref|YP_007687277.1| 200 GNVRA--LLLVGTPLLLSTLCPIVITALPKLILENMWNT 236
                                       55555..44555788888888888787888888777766 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.0012
                   Polysacc_synt_C  65 allvvavlnlyalrrllgiklellrrllkpllaalvmgivvylllllllg 114
                                       a +v + + + +l r+ +++l l r+  k lla++  ++v+y ++++l+ 
  gi|474933695|ref|YP_007687277.1| 258 AVFVPFTVYFARLCRENNFSL-LKRQYGKFLLAMASGAVVCY-FVSVLFA 305
                                       6688899999***********.78888776666666666655.5554443 PP

  == domain 5  score: 26.6 bits;  conditional E-value: 8.5e-10
                   Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyal 77 
                                       + il+++i+f+sl + + ++L++  + ++a +++++++++ +++ ++lip+ gi Ga ++  la+ +  +l+  ++
  gi|474933695|ref|YP_007687277.1| 324 FNILIVGIFFYSLGICGITVLIAKEQGRAAGYSAIVSLIASIAIFFMLIPEHGIDGATWGLFLAYGLFGILITACI 399
                                       679**************************************************************99988886665 PP

>> SpoIIIAC  Stage III sporulation protein AC/AD protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.19   1.1e+03      23      48 ..       9      33 ..       3      36 .. 0.69
   2 ?   -3.2   0.1       1.7     1e+04      28      41 ..     286     299 ..     276     304 .. 0.64
   3 ?    8.7   3.2   0.00032       1.9      11      44 ..     339     373 ..     326     374 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.19
                          SpoIIIAC 23 eeeiAslielagkiiilllalpllsa 48
                                      ++ +++  +l+g  +i ++++p+l++
  gi|474933695|ref|YP_007687277.1|  9 YNTLGNVASLFGQWLI-IMIIPILTD 33
                                      6677777777777766.577788765 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.7
                          SpoIIIAC  28 slielagkiiilll 41 
                                       +l+ +a ++++ ++
  gi|474933695|ref|YP_007687277.1| 286 FLLAMASGAVVCYF 299
                                       56666666666555 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.00032
                          SpoIIIAC  11 aalladilkdag.eeeiAslielagkiiilllalp 44 
                                       + +  +i k++g    ++  ++l++ i+i+++++p
  gi|474933695|ref|YP_007687277.1| 339 CGITVLIAKEQGrAAGYSAIVSLIASIAIFFMLIP 373
                                       445556667777434699****************9 PP

>> DUF2976  Protein of unknown function (DUF2976)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.2      0.13   7.8e+02      34      70 ..      49      85 ..      24      96 .. 0.56
   2 ?   -2.9   0.0         1   6.1e+03      23      40 ..     195     212 ..     191     215 .. 0.75
   3 ?    7.3   0.2   0.00069       4.1      15      84 ..     237     306 ..     231     310 .. 0.86
   4 ?    2.8   0.2     0.017     1e+02      57      82 ..     378     402 ..     352     407 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.13
                           DUF2976 34 vlaavaflaVa.kaalkkfneisegkaewgkfgltlvv 70
                                      +l  +a++    ++++ +++  s+++   + f++++  
  gi|474933695|ref|YP_007687277.1| 49 ILNQIALFSLTpYQVVDQYKRFSKNDYAVTRFITIV-L 85
                                      334455555432667777777777777777776543.3 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1
                           DUF2976  23 ylkdgvillgLvlaavaf 40 
                                       ylkd   + +L+l+++ +
  gi|474933695|ref|YP_007687277.1| 195 YLKDRGNVRALLLVGTPL 212
                                       888888888888877655 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.00069
                           DUF2976  15 dllelikgylkdgvillgLvlaavaflaVakaalkkfneisegkaewgkfgltlvvGvvllvvviwLltk 84 
                                       +++++++  +   +i+  Lv a++  ++V  a l + n+ s  k ++gkf l+++ G+v+  +v+ L ++
  gi|474933695|ref|YP_007687277.1| 237 EIVGIFNTLTSPTIIIPTLVQAVFVPFTVYFARLCRENNFSLLKRQYGKFLLAMASGAVVCYFVSVLFAE 306
                                       56667777777788899999999999999999999999999***********************999765 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.017
                           DUF2976  57 gkaewgkfgltlvvGvvllvvviwLl 82 
                                       + a+wg f +  + G+ l+ ++i+L+
  gi|474933695|ref|YP_007687277.1| 378 DGATWGLFLAYGLFGI-LITACIYLI 402
                                       5689999999999995.899****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       886  (0.0494171); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2861.34
//
Query:       gi|474933696|ref|YP_007687278.1|  [L=301]
Description: Nucleoside-diphosphate-sugar epimerase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-29  102.4   0.1    3.2e-29  102.1   0.1    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    1.3e-15   57.7   0.0    1.7e-14   54.0   0.0    2.4  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    8.6e-07   28.2   0.9    5.7e-06   25.5   0.9    1.9  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    1.2e-05   25.3   0.0    1.8e-05   24.7   0.0    1.2  1  NAD_binding_10   NAD(P)H-binding
    2.7e-05   23.7   0.0    0.00071   19.1   0.0    2.2  2  adh_short        short chain dehydrogenase
    0.00014   21.5   0.1    0.00025   20.7   0.1    1.3  1  NmrA             NmrA-like family
  ------ inclusion threshold ------
      0.011   15.0   0.0       0.74    8.9   0.0    2.3  2  NAD_binding_4    Male sterility protein
      0.011   14.8   0.0      0.015   14.4   0.0    1.3  1  RmlD_sub_bind    RmlD substrate binding domain
      0.013   15.4   0.0      0.022   14.7   0.0    1.3  1  KR               KR domain
      0.023   14.8   0.0      0.041   14.0   0.0    1.4  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
      0.029   13.5   0.1       0.15   11.1   0.0    2.1  3  Polysacc_synt_2  Polysaccharide biosynthesis protein


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.1   0.1     2e-32   3.2e-29       2     234 ..       5     220 ..       4     227 .. 0.82

  Alignments for each domain:
  == domain 1  score: 102.1 bits;  conditional E-value: 2e-32
                                       EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HH CS
                         Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggva 78 
                                       +VtGa+GfiGs++++ l+e g++v +l ++ +++n    +++ +++ +  + ++l   ++e ++d+ +h+A +g  +
  gi|474933696|ref|YP_007687278.1|   5 VVTGANGFIGSNVCNTLAESGVKVFALVNE-RSDNLRDSDNIVIIKTNSVHVEELSVRIHE-DIDCFFHFAWEGAFN 79 
                                       8****************************9.555555555556666666666666666664.9*******7766554 PP

                                       HHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHH CS
                         Epimerase  79 assedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklvea 155
                                          +dp+    kn+  t  ++++a++ +++r++f +++  Y  ++ +  ++++   +   ++ Y aaK+a+  +++ 
  gi|474933696|ref|YP_007687278.1|  80 S--SDPTI-QAKNISFTCSMVKVAKELNADRFVFSGTVMEYSFGKVV-CSDDS---QPGLRNLYYAAKQASNLMART 149
                                       4..44443.348*****************************988885.33444...6699***************** PP

                                       HHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT- CS
                         Epimerase 156 yaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvdag 232
                                       +    g++++   + n yGp+   +++++++  +++k+l+++ +++l  +g + +df+y+ D+a+ai+l+ e+   g
  gi|474933696|ref|YP_007687278.1| 150 LCYNLGIKYVEAAIMNGYGPG---SNRNSFMNSVLTKMLANE-PIKLT-KGLQDYDFIYITDLANAIILLGEK---G 218
                                       *********************...667777777777777788.88886.6*******************9999...4 PP

                                       ST CS
                         Epimerase 233 dk 234
                                       ++
  gi|474933696|ref|YP_007687278.1| 219 KA 220
                                       44 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   0.0     1e-17   1.7e-14       2     331 ..       6     291 ..       5     292 .. 0.80

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 1e-17
                                       EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SE CS
                     GDP_Man_Dehyd   2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpde 78 
                                       +TG +GfiGs++++ L e g +v+ +v+  s        +l++      ++n+ ++k +    ++l   ++e ++d 
  gi|474933696|ref|YP_007687278.1|   6 VTGANGFIGSNVCNTLAESGVKVFALVNERSD-------NLRD------SDNIVIIKTNSVHVEELSVRIHE-DIDC 68 
                                       9************************9986654.......5543......34667778777777777766766.59** PP

                                       EEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHHH CS
                     GDP_Man_Dehyd  79 vynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYaa 155
                                        +++A + + + s  +P   a+ n+  t  +++++++l+ +   rf++++t   Y +  +v ++++ +   r+ Y a
  gi|474933696|ref|YP_007687278.1|  69 FFHFAWEGAFNSS--DPTIQAK-NISFTCSMVKVAKELNAD---RFVFSGTVMEY-SFGKVVCSDDSQPGLRNLYYA 138
                                       *****99876664..5555554.47779*********9865...9******9988.6677889999999******** PP

                                       HHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TT.SCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHH CS
                     GDP_Man_Dehyd 156 aKlyadwivvnyreayglfavngilfnhesprrget.fvtrkitravarialgkqevlylGnldakRdwghvkDyve 231
                                       aK +++ +++    + g+  v + + n ++p  +++ f+   +t+++a+      e ++l ++ +  d+ ++ D ++
  gi|474933696|ref|YP_007687278.1| 139 AKQASNLMARTLCYNLGIKYVEAAIMNGYGPGSNRNsFMNSVLTKMLAN------EPIKLTKGLQDYDFIYITDLAN 209
                                       *******************************987653777777766665......56778889999*********** PP

                                       HHHHHHHCSS---.EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB-- CS
                     GDP_Man_Dehyd 232 amwlmlqqdkped.yviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlll 307
                                       a+ l+ +++k++  y++++ +  ++r+ ve     +g +                    +  +    + p   d + 
  gi|474933696|ref|YP_007687278.1| 210 AIILLGEKGKANCcYYVGSDTPRRIRDYVESMKSIVGSS-------------------SELLFGAIEDSPVGLDVTQ 267
                                       ********9976437778888888888888544444432...................2233444456778888889 PP

                                       B-THHHHHHH----SS-HHHHHHH CS
                     GDP_Man_Dehyd 308 gdaskakeeLgWkpkvsfeelvre 331
                                        d+ ++ +eLg++++v++ e+v++
  gi|474933696|ref|YP_007687278.1| 268 FDIGRIYSELGFRQTVDLAEGVAR 291
                                       999999999999999999999986 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.9   3.5e-09   5.7e-06       1     227 [.       5     213 ..       5     248 .. 0.63

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 3.5e-09
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegD.vtdkdkleealegvdvvihlasl 76 
                                       vvtG+ GF+G++++++L + +    v+v+ l+++ +  ++l+ ++++ +i++  v  ++   +  e++d+ +h a  
  gi|474933696|ref|YP_007687278.1|   5 VVTGANGFIGSNVCNTLAESG----VKVFALVNERS--DNLRDSDNIVIIKTNsVHVEELSVRIHEDIDCFFHFAWE 75 
                                       8****************9988....89998765443..3555555555555541444444468999********666 PP

                         3Beta_HSD  77 vdvagkltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKala 153
                                           +  ++ +i+  n+  T+++++ +++ +  ++v+  ++    + s g+ +  +d++++      + y   K+ +
  gi|474933696|ref|YP_007687278.1|  76 GAFNS--SDPTIQAKNISFTCSMVKVAKELNADRFVFSGTV---MEYSFGKVVC-SDDSQP---GLRNLYYAAKQAS 143
                                       65555..67789*************************9774...3334456666.333332...3334444444433 PP

                         3Beta_HSD 154 EklvlkaNgrtlkngg.rlyTcaLRpagiyGegdkllvpllkqlakl.glalfkigdeevlsdrvYvgNvawahil 227
                                         +          n g + +  a+  +  yG+g+++ + +   l+k+  ++ +k+ +  +  d++Y   +a a+il
  gi|474933696|ref|YP_007687278.1| 144 NLMA---RT-LCYNLGiKYVEAAI--MNGYGPGSNRNSFMNSVLTKMlANEPIKLTKGLQDYDFIYITDLANAIIL 213
                                       3221...11.12233335555555..44566666554444444444312334445555555577777777777766 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   1.1e-08   1.8e-05       1     128 [.       8     143 ..       8     158 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.1e-08
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHH.TT-SEEEES-...--TCC CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaeal.kgadaVvsal...ggggk 73 
                                       GA+G +G+ +++ l+++ g++v alv + +  ++l++++++ +++ +   ve+l   + +++d  +  +   +  ++
  gi|474933696|ref|YP_007687278.1|   8 GANGFIGSNVCNTLAES-GVKVFALVNERS--DNLRDSDNIVIIKTNSVHVEELSVRIhEDIDCFFHFAwegA-FNS 80 
                                       9****************.599999996544..467899*************9998877357776555556642.222 PP

                                       .HHHH.......HHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHHHCCHHHHHHHHHHH CS
                    NAD_binding_10  74 .deeg.......aknivdaakeagvkRfvlvsaigvgdevpgefgewnkellkaylaakraae 128
                                        d ++       + ++v++ake +  Rfv+ +++  +   +   ++  +  l++ + a ++a 
  gi|474933696|ref|YP_007687278.1|  81 sDPTIqaknisfTCSMVKVAKELNADRFVFSGTVMEYSFGKVVCSDDSQPGLRNLYYAAKQAS 143
                                       3444465666889999**************998776643333344444455655555555544 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   4.4e-07   0.00071       1      37 [.       2      39 ..       2      75 .. 0.82
   2 ?    2.5   0.0     0.052        84     147     175 ..     134     162 ..     122     180 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 4.4e-07
                                      SEEEEESTTSHHHHHHHHHHHHTT-EEEE.EESCHHHH CS
                         adh_short  1 kvvlvtGassGIGraiakelakeGakvvv.vdrseekl 37
                                      k+++vtGa + IG +++++la++G+kv++ v++++++l
  gi|474933696|ref|YP_007687278.1|  2 KTAVVTGANGFIGSNVCNTLAESGVKVFAlVNERSDNL 39
                                      79**************************9777766665 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.052
                                       HHHHHHHHHHHHHHHHHHHHHGGGTEEEE CS
                         adh_short 147 aaYsAsKaavagltrslakelaptgirvn 175
                                         Y A+K a + ++r+l   l  + ++  
  gi|474933696|ref|YP_007687278.1| 134 NLYYAAKQASNLMARTLCYNLGIKYVEAA 162
                                       679**************999988877655 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.1   1.5e-07   0.00025       2     103 ..       5     114 ..       4     123 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.5e-07
                                       EESSTTSHHHHHHHHHHHHHT-EEEEEES-S.....-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-.SEEEE-- CS
                              NmrA   2 lviGaTGrqGksvvrallkaghkvralvRdt.....kselakslkeaGvelvkgdlddkeslvealkgv.dvvfsvt 72 
                                       +v+Ga G +G+ v + l+++g kv+alv +      +s+++  +k++ v + + ++  +e ++  ++ + +++f + 
  gi|474933696|ref|YP_007687278.1|   5 VVTGANGFIGSNVCNTLAESGVKVFALVNERsdnlrDSDNIVIIKTNSVHVEELSVRIHEDIDCFFHFAwEGAFNSS 81 
                                       69**************************9887777777777777777777777777777777777765534555544 PP

                                       -GG..S-HHHHHHHHHHHHHHHS-SEEEEEE-- CS
                              NmrA  73 gfy..skeiedgkklvdAakeaGvkhfiySslg 103
                                         +   k+i     +v++ake    +f++S+ +
  gi|474933696|ref|YP_007687278.1|  82 DPTiqAKNISFTCSMVKVAKELNADRFVFSGTV 114
                                       43367999**********************876 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00045      0.74       1      34 [.       6      37 ..       6      46 .. 0.88
   2 ?    4.0   0.0     0.014        23      83     137 ..      61     116 ..      54     186 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00045
                                      EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSH CS
                     NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksg 34
                                      +TGa GF+G+ + + L ++   vk+++lv ++s+
  gi|474933696|ref|YP_007687278.1|  6 VTGANGFIGSNVCNTLAESG--VKVFALVNERSD 37
                                      7***************9997..59****987765 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.014
                                       HHHHH--EEEE--SS-S.STTSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEE..G CS
                     NAD_binding_4  83 elaeevdviihsaAtvnfdepykellrvNveGtrevlelakklkklkvllhvST..a 137
                                       ++ e +d+ +h a    f+++ +++ + N+  t  +++ ak+l++   +++  T   
  gi|474933696|ref|YP_007687278.1|  61 RIHEDIDCFFHFAWEGAFNSSDPTIQAKNISFTCSMVKVAKELNAD-RFVFSGTvmE 116
                                       67899************************************99988.8888777543 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   9.3e-06     0.015       3      42 ..       4      44 ..       1     106 [. 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 9.3e-06
                                      EEEESTTSHHHHHHHHHCTTTSEEEEEE.-TTT--TTSHHH CS
                     RmlD_sub_bind  3 ilvtGanGqlGseLakqlaeeglevlal.treeldltdaea 42
                                       +vtGanG +Gs++ + lae+g++v al ++++ +l+d+++
  gi|474933696|ref|YP_007687278.1|  4 AVVTGANGFIGSNVCNTLAESGVKVFALvNERSDNLRDSDN 44
                                      689*************************4444455555554 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.4e-05     0.022       3      62 ..       4      62 ..       2      68 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.4e-05
                                      EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----T CS
                                KR  3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDv 62
                                       ++tG+ G +G  ++++lae+g +  +l+  ++  + +++++i  ++ + ++ve +++ +
  gi|474933696|ref|YP_007687278.1|  4 AVVTGANGFIGSNVCNTLAESGVKVFALVNERSD-NLRDSDNIVIIKTNSVHVEELSVRI 62
                                      68***************************99954.4455558888888888888776655 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.5e-05     0.041       4      68 ..       5      66 ..       2      99 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.5e-05
                                      EEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH- CS
                            DapB_N  4 avvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavtddleevleka 68
                                      +v+Ga+G +G++v++++ e +++++ a v++++ +l+++d   ++++  ++v v++   ++ e+ 
  gi|474933696|ref|YP_007687278.1|  5 VVTGANGFIGSNVCNTLAE-SGVKVFALVNERSDNLRDSDNIVIIKT--NSVHVEELSVRIHEDI 66
                                      79***************99.9**********9998988887644444..4444444444444444 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   9.3e-05      0.15       2      41 ..       5      44 ..       4      71 .. 0.79
   2 ?   -3.0   0.0       1.9   3.2e+03     103     125 ..      88     110 ..      83     113 .. 0.83
   3 ?   -0.6   0.0      0.34   5.6e+02     189     250 ..     187     248 ..     132     263 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.3e-05
                                      EEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHH CS
                   Polysacc_synt_2  2 lvtGagGsiGselvrqilkkkpkkiillerdElklyeiek 41
                                      +vtGa G iGs+++++++++ +k   l+++   +l + ++
  gi|474933696|ref|YP_007687278.1|  5 VVTGANGFIGSNVCNTLAESGVKVFALVNERSDNLRDSDN 44
                                      69*********************99999887777766554 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHHHHHHTT-SEEEE CS
                   Polysacc_synt_2 103 tNvlgtenvieaaieagvkkvvl 125
                                        N+  t +++++a+e + +++v+
  gi|474933696|ref|YP_007687278.1|  88 KNISFTCSMVKVAKELNADRFVF 110
                                       68999999999999999999997 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.34
                                       TSSEEES-TT-EEEEE-HHHHHHHHHHHHHH--SS-EEEE--.-EEEHHHHHHHH....... CS
                   Polysacc_synt_2 189 ggpvtvTdpemtRyfmtieeavqLvlqalalakggeifvldmGepvkivdlakalielsgle 250
                                       ++p+ +T       f+ i++ ++ ++  ++++k +  + +    p +i+d ++++ +++g +
  gi|474933696|ref|YP_007687278.1| 187 NEPIKLTKGLQDYDFIYITDLANAIILLGEKGKANCCYYVGSDTPRRIRDYVESMKSIVGSS 248
                                       55666665544444777888888888888888888877777778888888888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.54u 0.41s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 1745.79
//
Query:       gi|474933697|ref|YP_007687279.1|  [L=388]
Description: UDP-galactopyranose mutase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-64  216.8   4.8    2.4e-64  216.8   4.8    1.5  2  GLF              UDP-galactopyranose mutase
    2.9e-13   49.8   0.0    8.8e-13   48.3   0.0    1.8  2  NAD_binding_8    NAD(P)-binding Rossmann-like domain
    8.7e-05   22.6   0.0    0.00015   21.8   0.0    1.4  1  NAD_binding_9    FAD-NAD(P)-binding
    0.00021   21.0   0.0    0.00027   20.6   0.0    1.5  1  DAO              FAD dependent oxidoreductase
     0.0016   17.9   0.0     0.0025   17.3   0.0    1.3  1  GMC_oxred_N      GMC oxidoreductase
     0.0042   16.4   0.0      0.011   15.0   0.0    1.6  2  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
  ------ inclusion threshold ------
       0.01   15.1   0.0      0.028   13.6   0.0    1.6  2  Thi4             Thi4 family
      0.014   15.6   0.0      0.024   14.9   0.0    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.021   14.5   0.0      0.034   13.8   0.0    1.3  1  ApbA             Ketopantoate reductase PanE/ApbA
      0.046   13.8   0.0      0.086   12.9   0.0    1.3  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
      0.051   13.8   0.0        0.1   12.9   0.0    1.5  1  TrkA_N           TrkA-N domain
       0.15   12.7   0.0       0.76   10.4   0.0    2.2  2  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
       0.17   10.9   0.0       0.26   10.3   0.0    1.2  1  Lycopene_cycl    Lycopene cyclase protein
       0.18   11.1   0.0        7.9    5.7   0.0    2.2  2  FAD_oxidored     FAD dependent oxidoreductase


Domain annotation for each model (and alignments):
>> GLF  UDP-galactopyranose mutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       3.1   3.9e+03     119     119 ..      97      97 ..      57     125 .. 0.52
   2 !  216.8   4.8   1.9e-67   2.4e-64       3     204 .]     157     368 ..     155     368 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.1
                                       S CS
                               GLF 119 f 119
                                       +
  gi|474933697|ref|YP_007687279.1|  97 Y 97 
                                       1 PP

  == domain 2  score: 216.8 bits;  conditional E-value: 1.9e-67
                                       THHHHHHHHTSSGGGSBGGGGCGS-B-SSS--BS--SSEEEEBTTHHHHHHHHHTTSTTEEEESS--HHHHHH.... CS
                               GLF   3 fkgYtkKqWglkpeeldasvlkrvpvrlsyddrYfndkyqglPkeGYtklfekmldhenievrlntdffdvke.... 75 
                                       +k Yt KqWg+kpee+++s+l+rv+v lsyddrYf++kyq  P++G+t++f++ml+h+nie+rl+tdf+d+ +    
  gi|474933697|ref|YP_007687279.1| 157 YKPYTCKQWGRKPEEIEPSILSRVKVALSYDDRYFTNKYQFTPRDGFTEMFKRMLNHPNIELRLETDFKDMISfdgd 233
                                       689**********************************************************************99*9 PP

                                       ...HHHHTTEEEEEE-S-HHHHTTTTTS---EEEEEEEEEEESSS-SSSSSEEEESSTTSSSSEEEEGGGGCTCS.S CS
                               GLF  76 ...aeekeeakkvvytgpideyFdyklgeLeYrsldfeketldeekfqenavvnYpdeevpytrivEykhltkqk.s 148
                                          ++  + ++k+vytg++d++Fdy++g+L+Yr++ fe+ t + + + ++  v Yp +  ++tr++E+k +t+qk +
  gi|474933697|ref|YP_007687279.1| 234 rvvVDGVNPDAKIVYTGALDDLFDYQYGQLPYRTIGFEFFTEHVDYYLNAPFVAYPMHP-TMTRMTEFKSITGQKkA 309
                                       99977888889***********************************************9.**************758 PP

                                       SSEEEEEEEEEE....STTS.--EE--SHHHHHHHHHHHHHHHHCTTEEE-HHHHTTS- CS
                               GLF 149 kktvivreypkea...eegdepyYpinteenrelyekYkelakkeekvlfvGRLaeYkY 204
                                        +tv+ +e+p e+    +++ep+Ypi +e+n+++yekYk+l  k+++++++GRLa+YkY
  gi|474933697|ref|YP_007687279.1| 310 GTTVVLKEFPGEYdhtVKDSEPFYPILSEANQQIYEKYKQLSGKYSNLTICGRLADYKY 368
                                       8999*******9944434559*************************************9 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.0   6.9e-16   8.8e-13       1      67 [.      11      78 ..      11      79 .. 0.89
   2 ?   -2.1   0.0       3.6   4.6e+03      24      47 ..     343     366 ..     340     385 .. 0.66

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 6.9e-16
                                      EE--SHHHHHHHHHHHCC.TEEEEEE-SSSSSSGGG-EECE.TTCEEC.TS---EEETTHHHHCHHHHCC CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLaka.gfdvlllekrdrlGGraasyev.pgvrvd.ygahifhgsgyypnvrrllre 67
                                      +vG G+ G+v+A++La++  ++vl+l++r+++ G+++++ + +g+ v+ yg+h+fh+  + +n++++l +
  gi|474933697|ref|YP_007687279.1| 11 VVGCGFCGSVIARRLAEEqSAKVLILDRRNHIAGNMYDEYDsDGILVQkYGVHVFHT--DKDNIFEYLSR 78
                                      8***************98688****************986658955555********..689***99987 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.6
                                       EE-SSSSSSGGG-EECETTCEECT CS
                     NAD_binding_8  24 llekrdrlGGraasyevpgvrvdy 47 
                                       ++ek  +l+G+ +  ++ g+ +dy
  gi|474933697|ref|YP_007687279.1| 343 IYEKYKQLSGKYSNLTICGRLADY 366
                                       778888888887777776666665 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   1.2e-07   0.00015       1      77 [.      10      80 ..      10     100 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.2e-07
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsepgagrvwrtdqseelllNvpasemslftddpptfaeWlrerg 77
                                      ++vG+G+ G  +++rL+++    ++ ++ + d++++ ag ++++ +s+  l  v+   +++f+ d+++  e+l++  
  gi|474933697|ref|YP_007687279.1| 10 VVVGCGFCGSVIARRLAEE----QSAKVLILDRRNHIAGNMYDEYDSDGIL--VQKYGVHVFHTDKDNIFEYLSRFT 80
                                      69****************9....59********99989*******999966..678889999999977777766544 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   2.1e-07   0.00027       1      36 [.       8      45 ..       8     352 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.1e-07
                                      EEEEECTSHHHHHHHHHHHHTT...EEEEESSSSTTSSG CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg...Vtllekgdiagsga 36
                                      d v++G G  G+ +A+ La++    V++l++++ ++ g 
  gi|474933697|ref|YP_007687279.1|  8 DYVVVGCGFCGSVIARRLAEEQsakVLILDRRNHIA-GN 45
                                      89****************9775589*******8888.54 PP

>> GMC_oxred_N  GMC oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.9e-06    0.0025       1      31 [.       7      37 ..       7      58 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.9e-06
                       GMC_oxred_N  1 vdelveggGsagsvvAaRLsedpstsvlvle 31
                                      vd++v+g G +gsv+A RL+e++s++vl+l+
  gi|474933697|ref|YP_007687279.1|  7 VDYVVVGCGFCGSVIARRLAEEQSAKVLILD 37
                                      69**************************996 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   8.2e-06     0.011       2      36 ..       8      43 ..       7      55 .. 0.81
   2 ?   -2.9   0.0       2.5   3.2e+03     185     213 ..     203     231 ..     199     247 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.2e-06
                                      SEEEE--SHHHHHHHHHHHH.HTS-EEEEETTHCHH CS
                                      xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaq.agakvtlvelegtcl 36
                                      d+vv+G G+ G   a++la+ ++akv+++++++++ 
  gi|474933697|ref|YP_007687279.1|  8 DYVVVGCGFCGSVIARRLAEeQSAKVLILDRRNHIA 43
                                      789999999999999999997799999995554443 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.5
                                       HHHHHHHHHHHTTEEEEESCEEEEEEETT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 185 lsaaleealekeGvevklgtsvkeidgng 213
                                       ++++ ++ l++ ++e++l+t +k++++ +
  gi|474933697|ref|YP_007687279.1| 203 FTEMFKRMLNHPNIELRLETDFKDMISFD 231
                                       56666777777788888888888766544 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.2e-05     0.028      18      57 ..       7      46 ..       2      59 .. 0.90
   2 ?   -2.3   0.0       1.6     2e+03     102     135 ..     205     240 ..     175     248 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.2e-05
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTT CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersvspGGGa 57
                                       D v+vG G +G   a+ la++   kv+il+r+  + G +
  gi|474933697|ref|YP_007687279.1|  7 VDYVVVGCGFCGSVIARRLAEEQSAKVLILDRRNHIAGNM 46
                                      688*****************************98888765 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.6
                                       HHHHHHHTSTTEEEEESEEEEEEEEETB..TEEEEE CS
                              Thi4 102 tllskvlqlanvkllnavaveDlivreg..egvaGv 135
                                       ++  ++l+ +n+ l   +   D+i  +g  + v Gv
  gi|474933697|ref|YP_007687279.1| 205 EMFKRMLNHPNIELRLETDFKDMISFDGdrVVVDGV 240
                                       566778888888888888888888877623334454 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.9e-05     0.024       2      47 ..      10      60 ..       9      81 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.9e-05
                                      EEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH.......TTT CS
                   Sacchrp_dh_NADP  2 liiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka.......lgv 47
                                      +++G+G+ G+++a+ la++++   ++ + dr ++ + ++ ++        ++ 
  gi|474933697|ref|YP_007687279.1| 10 VVVGCGFCGSVIARRLAEEQSA--KVLILDRRNHIAGNMYDEYdsdgilvQKY 60
                                      79******************99..9******9998777776665555555555 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.7e-05     0.034       2      34 ..      10      43 ..       9      72 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.7e-05
                                      EEES-SHHHHHHHHHHHH.HTHCEEEE-SCHHHH CS
                              ApbA  2 ailGaGaiGsllaakLak.agadvtlilrsrrle 34
                                      +++G+G  Gs++a +La+ + a+v +++r+++++
  gi|474933697|ref|YP_007687279.1| 10 VVVGCGFCGSVIARRLAEeQSAKVLILDRRNHIA 43
                                      79****************99999******99875 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.7e-05     0.086      14      59 ..       8      53 ..       2      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.7e-05
                                      EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.E CS
                      Shikimate_DH 14 kvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkge 59
                                        +++G G  ++ +a+ L++++  kv+++ R  + a ++ +e++++
  gi|474933697|ref|YP_007687279.1|  8 DYVVVGCGFCGSVIARRLAEEQSAKVLILDRRNHIAGNMYDEYDSD 53
                                      568****************************999999998888665 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.9e-05       0.1       1      33 [.       9      42 ..       9      59 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.9e-05
                                      EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHH CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeer 33
                                      ++++G+G  G+ +a++L e ++ +v++ d++   
  gi|474933697|ref|YP_007687279.1|  9 YVVVGCGFCGSVIARRLAEeQSAKVLILDRRNHI 42
                                      79*****************555779999987655 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00059      0.76       3      40 ..      10      49 ..       8      58 .. 0.90
   2 ?   -1.8   0.0       3.6   4.7e+03      44      64 ..     205     225 ..     199     237 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00059
                                      EEECSSHHHHHHHHHHHHTT.SEEEEEESSSSSS.TTSSH CS
                         Pyr_redox  3 vvvGgGyiglElAgalaelg.kkVtvversdkll.rllDe 40
                                      vvvG G+ g   A  lae + +kV +++r++++  +++De
  gi|474933697|ref|YP_007687279.1| 10 VVVGCGFCGSVIARRLAEEQsAKVLILDRRNHIAgNMYDE 49
                                      9***************997647************999997 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.6
                                       HHHHHHHHHTTEEEECSEEEE CS
                         Pyr_redox  44 kilqeklekngievllntkve 64 
                                       +++++ l + +ie++l+t  +
  gi|474933697|ref|YP_007687279.1| 205 EMFKRMLNHPNIELRLETDFK 225
                                       455556666699999998765 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0    0.0002      0.26       1      36 [.       8      42 ..       8      55 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0002
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsl 36
                                      D vv+G+G  g  +A rl ++++  kv++++  +++
  gi|474933697|ref|YP_007687279.1|  8 DYVVVGCGFCGSVIARRL-AEEQSAKVLILDRRNHI 42
                                      789***************.77888999999876665 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0    0.0061       7.9       1      38 [.       8      46 ..       8      85 .. 0.90
   2 ?    3.3   0.0     0.034        44      83     120 ..     197     237 ..     159     250 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0061
                      FAD_oxidored  1 DvvVvGGgpaG.vaAAiaAaraGakvlLveergvlGGll 38
                                      D vVvG g  G v+A   A ++ akvl++++r+++ G++
  gi|474933697|ref|YP_007687279.1|  8 DYVVVGCGFCGsVIARRLAEEQSAKVLILDRRNHIAGNM 46
                                      669***9988735666779999*************9998 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.034
                      FAD_oxidored  83 tfepevakavleemlaeagvtvllntrlvevek.egkr..i 120
                                       +   + ++++++ ml+ +++++ l+t++++++  +g+r  +
  gi|474933697|ref|YP_007687279.1| 197 FTPRDGFTEMFKRMLNHPNIELRLETDFKDMISfDGDRvvV 237
                                       344457999*******************9998855656444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.64u 0.38s 00:00:01.02 Elapsed: 00:00:00.54
# Mc/sec: 2175.04
//
Query:       gi|474933698|ref|YP_007687280.1|  [L=338]
Description: Glycosyltransferases involved in cell wall biogenesis [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.2e-31  107.1   0.0    1.8e-30  106.0   0.0    1.5  1  Glycos_transf_2  Glycosyl transferase family 2
    2.3e-11   43.7   0.1      6e-11   42.3   0.0    1.7  2  Glyco_tranf_2_2  Glycosyltransferase like family 2
    3.8e-11   43.3   0.0    5.7e-11   42.8   0.0    1.3  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    2.6e-05   24.6   0.1    0.00014   22.3   0.1    2.1  2  Glyco_tranf_2_4  Glycosyl transferase family 2
  ------ inclusion threshold ------
      0.051   13.1   0.0      0.082   12.4   0.0    1.3  1  Glyco_transf_21  Glycosyl transferase family 21
      0.053   14.1   1.3       0.11   13.0   0.0    2.2  3  Chitin_bind_4    Insect cuticle protein


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.0   0.0   5.9e-34   1.8e-30       1     145 [.       5     150 ..       5     164 .. 0.90

  Alignments for each domain:
  == domain 1  score: 106.0 bits;  conditional E-value: 5.9e-34
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCH..C-TTEEEEEESSS-HHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelak..edprvrvirreenvGkagalnagl 75 
                                       svv ++yN +++l+++l s+++q +  d+e+i+v++gStD+t+e+ ++++k   +  ++++  e n+G+a++ n+g+
  gi|474933698|ref|YP_007687280.1|   5 SVVLICYNYAHLLPRVLGSIAEQ-TFTDYELILVNNGSTDNTAEVFDQFVKdhPEISCKIVYIEVNKGPANGDNEGA 80 
                                       8**********************.***************************888888899999************** PP

                                       HH--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHC CS
                   Glycos_transf_2  76 raatgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkr 145
                                       ++atg+y++f+DaDd++dp++le l  ++++++ad v+g+ ++ +++  +i+ +   ge  + +f++ ++
  gi|474933698|ref|YP_007687280.1|  81 SKATGEYLMFVDADDWMDPNCLECLTSKAKETDADRVIGSYRYVNQNGETIKTMAMEGEGLNKWFYTMQQ 150
                                       *************************************************999876555555555555544 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.0     2e-14     6e-11       3     105 ..       8     108 ..       5     138 .. 0.79
   2 ?   -1.6   0.0      0.48   1.4e+03     232     258 ..     180     206 ..     155     228 .. 0.82

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 2e-14
                   Glyco_tranf_2_2   3 viplraseerhyieervlqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddk.ayslaaarNrGas 78 
                                       +i+ +  +  + +   + ++++    + eli+v++gS+++++e+  ++++ + +++ k    +   ++a   N Gas
  gi|474933698|ref|YP_007687280.1|   8 LICYNYAHLLPRVLGSIAEQTFT---DYELILVNNGSTDNTAEVFDQFVKDHPEISCKIVYIEvNKGPANGDNEGAS 81 
                                       45665555666666677777777...89*********************99999987776555588*********** PP

                   Glyco_tranf_2_2  79 kaesdlvlFlDaDcfissDkfekilkl 105
                                       ka +++++F+DaD+++ ++ +e + + 
  gi|474933698|ref|YP_007687280.1|  82 KATGEYLMFVDADDWMDPNCLECLTSK 108
                                       *******************99988772 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.48
                   Glyco_tranf_2_2 232 lealakeaaalglvvfhlYheepksed 258
                                       ++ ++k   ++  v +  Y +e+ s++
  gi|474933698|ref|YP_007687280.1| 180 FSVVSKSTVFVPTVCYNYYVHESTSNN 206
                                       678888888888888888888777764 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.8   0.0   1.9e-14   5.7e-11       4     131 ..       4     130 ..       3     200 .. 0.83

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 1.9e-14
                   Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksraln 80 
                                       ++v+  ++n +  l +vl s++ q+  ++e+++v ++s++ t+ev++++++++p +  ++v  + n g+   +++ n
  gi|474933698|ref|YP_007687280.1|   4 VSVVLICYNYAHLLPRVLGSIAEQTFTDYELILVNNGSTDNTAEVFDQFVKDHPEISCKIVYIEVNKGP---ANGDN 77 
                                       689999************************************************887777655655576...5666* PP

                   Glyco_tranf_2_3  81 ealravksdlvllvDdDtvvePdtlkrllqff.ltpkvgavgtpvfll.nrst 131
                                       e+ + ++++++ +vD+D+  +P+ l+ l+  + +t+  +++g  ++++ n++t
  gi|474933698|ref|YP_007687280.1|  78 EGASKATGEYLMFVDADDWMDPNCLECLTSKAkETDADRVIGSYRYVNqNGET 130
                                       ***************************99999766666666666666624544 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.1   4.7e-08   0.00014       1      83 [.      11      96 ..      11     101 .. 0.71
   2 ?   -3.1   0.0       3.9   1.2e+04      57      79 ..     205     227 ..     183     228 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 4.7e-08
                   Glyco_tranf_2_4  1 rneadiLpeflahhlalgfdr..ilvydndstDgtrailke....lpe..vkllhvdksyederrqvellkallaryae 71
                                      +n a++Lp++l+ + +  f++  +++++n+stD+t+++ ++    +pe  +k+++++   ++ +   +   a   + a 
  gi|474933698|ref|YP_007687280.1| 11 YNYAHLLPRVLGSIAEQTFTDyeLILVNNGSTDNTAEVFDQfvkdHPEisCKIVYIEV--NKGPANGDNEGA---SKAT 84
                                      5889********99888886335************99997754446663344555554..333444444443...4467 PP

                   Glyco_tranf_2_4 72 adwvlvvDaDEf 83
                                      ++++++vDaD  
  gi|474933698|ref|YP_007687280.1| 85 GEYLMFVDADDW 96
                                      89*******975 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.9
                   Glyco_tranf_2_4  57 rqvellkallaryaeadwvlvvD 79 
                                         +++ ++++++ ++ ++  ++D
  gi|474933698|ref|YP_007687280.1| 205 NNNKMVHNVIEDTGRFTYTGFID 227
                                       34567888888888888888888 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.7e-05     0.082      25      78 ..      79     132 ..      69     158 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.7e-05
                   Glyco_transf_21  25 aleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdakglaaa 78 
                                       + ++a  ++l++ D+d  ++p+ Le l  + +++++  V + +++++++g + +
  gi|474933698|ref|YP_007687280.1|  79 GASKATGEYLMFVDADDWMDPNCLECLTSKAKETDADRVIGSYRYVNQNGETIK 132
                                       5567999*************************************9999873333 PP

>> Chitin_bind_4  Insect cuticle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       5.1   1.5e+04      20      32 ..      75      87 ..      68      95 .. 0.67
   2 ?   13.0   0.0   3.8e-05      0.11      20      43 ..     109     132 ..      99     134 .. 0.89
   3 ?   -2.2   0.5       2.1   6.4e+03       3      35 ..     195     223 ..     195     224 .. 0.61

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 5.1
                     Chitin_bind_4 20 gtedeglvvqGsY 32
                                      g+++++ +++G+Y
  gi|474933698|ref|YP_007687280.1| 75 GDNEGASKATGEY 87
                                      4555666777888 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 3.8e-05
                     Chitin_bind_4  20 gtedeglvvqGsYsyvdpdGktrt 43 
                                        +e+++++v GsY+yv+ +G+t++
  gi|474933698|ref|YP_007687280.1| 109 AKETDADRVIGSYRYVNQNGETIK 132
                                       57899***************9986 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2.1
                     Chitin_bind_4   3 fsYetsdgikreeegrtgtedeglvvqGsYsyv 35 
                                       ++Y ++ +++ + + +    +  ++ +G ++y+
  gi|474933698|ref|YP_007687280.1| 195 YNYYVHESTSNNNKMV----HNVIEDTGRFTYT 223
                                       6666666655555555....5666667888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 2003.20
//
Query:       gi|474933699|ref|YP_007687281.1|  [L=479]
Description: Dolichyl-phosphate-mannose-protein mannosyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.1e-16   58.6  10.8    8.1e-16   58.6  10.8    3.2  3  PMT_2     Dolichyl-phosphate-mannose-protein mannosyltransfer
     0.0002   21.0   1.0     0.0002   21.0   1.0    3.5  3  PMT       Dolichyl-phosphate-mannose-protein mannosyltransfer
    0.00056   19.9   1.7    0.00056   19.9   1.7    3.3  3  DUF2723   Protein of unknown function (DUF2723)
  ------ inclusion threshold ------
       0.37   10.9   1.0        9.3    6.4   0.1    2.7  2  Tom5      Mitochondrial import receptor subunit or translocas


Domain annotation for each model (and alignments):
>> PMT_2  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.3      0.82   3.7e+03      51      62 ..      23      34 ..       7      43 .. 0.52
   2 !   58.6  10.8   1.8e-19   8.1e-16       6     158 ..      70     230 ..      65     231 .. 0.91
   3 ?   -5.5  16.0         4   1.8e+04      24      92 ..     215     280 ..     212     361 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.82
                             PMT_2 51 aallaalllavv 62
                                      + l+a+llla++
  gi|474933699|ref|YP_007687281.1| 23 VLLVASLLLAFF 34
                                      223333333333 PP

  == domain 2  score: 58.6 bits;  conditional E-value: 1.8e-19
                             PMT_2   6 iawllalftklfgfselairlvsalagvltilllyllarrlfg.kraallaalllavvplfvalsalftpdaplvll 81 
                                       ++ +   ++k fg sel +r++sa+   l++ ++yll  +l++ ++ a l+al+l v+p+++++++ ++p+++ +ll
  gi|474933699|ref|YP_007687281.1|  70 YFLVEGSILKTFGISELTVRILSAISFGLSVPMIYLLTLKLTDsEHMAGLTALMLLVSPFVLFYAQDGRPYSIDLLL 146
                                       44455557899********************************99******************************** PP

                             PMT_2  82 walalylllraleknklkywllagvlfGlgflsKytaallliaallyllis.arr.ilke....kkpyl.alllall 151
                                       ++  lyl l+ + +n  k+w+   ++ +l +++ y a+l ++ +++ylli   r  ++k+      ++l  ++++ +
  gi|474933699|ref|YP_007687281.1| 147 TLVELYLCLEIIRNNDRKDWYKYCLVSALTIYFNYLAILPIVCFFVYLLIAeYREnRFKNllrcLLHWLlFIAIICV 223
                                       ******************************************9999****995545888877667788889999999 PP

                             PMT_2 152 lfspvli 158
                                       l+sp+l+
  gi|474933699|ref|YP_007687281.1| 224 LCSPILY 230
                                       9999998 PP

  == domain 3  score: -5.5 bits;  conditional E-value: 4
                             PMT_2  24 irlvsalagvltilllyllarrlfgkraallaalllavvplfvalsalftpdaplvllwalalylllra 92 
                                       + ++++++++++ +l+ +++  ++ ++ +++a+ l+a++ +f    a f +d ++v ++a+a+   +++
  gi|474933699|ref|YP_007687281.1| 215 LLFIAIICVLCSPILYHAIFAVRTVTNMGVWASGLAALMDIFE---AFFLTDYLMVIALAAAVVGAIKL 280
                                       578999**************99999************988544...44557888888888877665554 PP

>> PMT  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   1.0   4.5e-08    0.0002      57     127 ..      60     130 ..      50     135 .. 0.88
   2 ?    1.2   1.2     0.051   2.3e+02     187     234 ..     144     191 ..     140     198 .. 0.83
   3 ?   -8.1  13.6         4   1.8e+04      87     169 ..     216     298 ..     212     365 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 4.5e-08
                               PMT  57 gyLagkdgnftfesigaeyypenvpyvslRlfsallgslivplvyltllelgfskltallaallvllensl 127
                                       ++ +++ +  +f ++g+  ++++ +++++R++sa+   l+vp+ yl++l+l+ s  +a l+al++l+++ +
  gi|474933699|ref|YP_007687281.1|  60 WASNDFTPIGYFLVEGSILKTFGISELTVRILSAISFGLSVPMIYLLTLKLTDSEHMAGLTALMLLVSPFV 130
                                       55677888889999999999999*****************************************9998755 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.051
                               PMT 187 ftvllvgllliwelwqllgdkslllksivkhllaralaliviPvtlyl 234
                                       ++++lv l+l+ e+ + + +k + ++  v  l++++++l ++P++ ++
  gi|474933699|ref|YP_007687281.1| 144 LLLTLVELYLCLEIIRNNDRKDWYKYCLVSALTIYFNYLAILPIVCFF 191
                                       56778999**********988888887899999999999999998775 PP

  == domain 3  score: -8.1 bits;  conditional E-value: 4
                               PMT  87 lfsallgslivplvyltllelgfskltallaallvllenslitlsryilldspLlfftllsmyclvkfe...rkapf 160
                                       lf a+  +l++p++y   +      +++++a+ l +l  ++     + l+d  +++ ++++++  +k +   ++++f
  gi|474933699|ref|YP_007687281.1| 216 LFIAIICVLCSPILYHAIFAVRTVTNMGVWASGLAALMDIFE---AFFLTDYLMVIALAAAVVGAIKLFcmlKQKEF 289
                                       678899999999999999999999999999999999999885...58999999999999999999999988777778 PP

                               PMT 161 srswwlwll 169
                                       ++  + +l 
  gi|474933699|ref|YP_007687281.1| 290 RCILFVQLS 298
                                       775555444 PP

>> DUF2723  Protein of unknown function (DUF2723)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.043   1.9e+02      72     107 ..      17      56 ..       2      59 .. 0.79
   2 !   19.9   1.7   1.3e-07   0.00056      36     166 ..      81     200 ..      68     204 .. 0.84
   3 ?   -1.0   1.6      0.34   1.5e+03      30      84 ..     256     278 ..     206     312 .. 0.60

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.043
                           DUF2723  72 kiailgaglvgalafaf....sdtfWfsaveaeVYalssl 107
                                         ++l+  lv++l++af     +++W+   ++  Y++ sl
  gi|474933699|ref|YP_007687281.1|  17 RRTALIVLLVASLLLAFfrltYQSIWCDEGSTIHYSMMSL 56 
                                       4567788899999999977778899999999999999876 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 1.3e-07
                           DUF2723  36 aekvalrvnllsalssaltilflfltitlllrskakkiailgaglvgalafafsdtfWfsaveaeVYalsslftalv 112
                                       ++   l v +lsa+s +l++ +++l++ +l++s       ++ag + al++ +s  + f a  +  Y++  l+t + 
  gi|474933699|ref|YP_007687281.1|  81 FGISELTVRILSAISFGLSVPMIYLLTLKLTDS------EHMAG-LTALMLLVSPFVLFYAQDGRPYSIDLLLTLVE 150
                                       455667889999999999999999999999983......44555.468999************************** PP

                           DUF2723 113 lwlilkweeeadekrsdrwlvliayligLslgvhllnllllpaiallyyfkkyk 166
                                       l+l l++ +++d+    + ++  +++ +L +    l++l ++ +++ +++ +y+
  gi|474933699|ref|YP_007687281.1| 151 LYLCLEIIRNNDR----KDWYKYCLVSALTIYFNYLAILPIVCFFVYLLIAEYR 200
                                       ***********98....9999999999999999999999888877777776665 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.34
                           DUF2723  30 fslladaekvalrvnllsalssaltilflfltitlllrskakkiailgaglvgal 84 
                                       f+ ++  ++                                 ++++l+a++vga+
  gi|474933699|ref|YP_007687281.1| 256 FEAFF-LTD-------------------------------YLMVIALAAAVVGAI 278
                                       11111.222...............................223333444444443 PP

>> Tom5  Mitochondrial import receptor subunit or translocase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1    0.0021       9.3      27      46 ..     116     135 ..     115     136 .. 0.89
   2 ?    2.1   0.1     0.044     2e+02      26      44 ..     344     362 ..     337     364 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0021
                              Tom5  27 nfaaaaalLylsPfvidfvk 46 
                                       +++++a++L +sPfv+ +++
  gi|474933699|ref|YP_007687281.1| 116 MAGLTALMLLVSPFVLFYAQ 135
                                       7999***********98875 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.044
                              Tom5  26 knfaaaaalLylsPfvidf 44 
                                          +a a++L  +Pfv ++
  gi|474933699|ref|YP_007687281.1| 344 SLITACAIVLVSAPFVYNY 362
                                       56678899********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1025  (0.0571699); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.71u 0.35s 00:00:01.06 Elapsed: 00:00:00.52
# Mc/sec: 2778.82
//
Query:       gi|474933700|ref|YP_007687282.1|  [L=257]
Description: glucose-1-phosphate cytidylyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-15   58.0   0.0    2.2e-15   56.9   0.0    1.5  1  NTP_transferase  Nucleotidyl transferase
    2.2e-09   37.9   0.0    2.4e-09   37.7   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
  ------ inclusion threshold ------
      0.033   13.9   0.0       0.05   13.3   0.0    1.3  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.9   0.0   3.7e-19   2.2e-15       1     193 [.       2     203 ..       2     247 .. 0.80

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 3.7e-19
                                       EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGT..... CS
                   NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfg..... 72 
                                       k+vILaGG GtR+   +  ++k+++ ++g  +++ + ++   ++g++e  +++  +++++++e++++    +     
  gi|474933700|ref|YP_007687282.1|   2 KTVILAGGLGTRISEESYLRPKPMIEIGGY-PILWHIMKIFYSQGVDE-FIICAGYKQHMIKEYFADYFLHRsditf 76 
                                       68**************************99.*****************.*****************98644477778 PP

                                       ...............SEEEEEEESS--............BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHH CS
                   NTP_transferase  73 ...............vevlialepegk............gtAdAvalaaelledeksdelvlvLggDhlikdayeea 122
                                                                 k             t + ++ +a++l++e     +l   gD + + +++++
  gi|474933700|ref|YP_007687282.1|  77 dftdeyhmtvhanssE----------KwkvtvvdtglntLTGGRIKRVAKYLGNEP----FLLTYGDGVSDVDIKKL 139
                                       8887755333333331..........255667766663345666888888888777....8**************** PP

                                       HHHHHTHSSTTSEEEEEEESS-CTTSEEEEECTTSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHC CS
                   NTP_transferase 123 vkkaiekaakgtvtfgivpveeateyGvieadeegrverfvEKPkeakaselassGiYvfnsevllflakd 193
                                       +k+++++++    +  ++ v++  ++Gv   ++ +++++f EK + ++  ++++ G  v +++v++ +  d
  gi|474933700|ref|YP_007687282.1| 140 IKFHKSHGK----LATLTAVHPVGRFGVLDLSG-DQITSFGEKTESQT--DWINGGFMVLDPKVIDLIDGD 203
                                       *********....55567899********9987.69*******99999..9**************999332 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.0     4e-13   2.4e-09       2     116 ..       4     148 ..       3     245 .. 0.72

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 4e-13
                                       EEEEESS-TTTTT.....THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHHTTC............. CS
                      NTP_transf_3   2 viLAGGrSsRmgg.....dKallplggkpllervldalraagvdevvvvggd..eevlaalarl............. 58 
                                       viLAGG ++R  +     +K+++++gg p+l+++++ + ++gvde ++++g+  + +++++a++             
  gi|474933700|ref|YP_007687282.1|   4 VILAGGLGTRISEesylrPKPMIEIGGYPILWHIMKIFYSQGVDEFIICAGYkqHMIKEYFADYflhrsditfdftd 80 
                                       9**********8545666********************************995556777554443333333333333 PP

                                       ..TS-EEE-TTSS-SHHHHHHHHH............HHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTS CS
                      NTP_transf_3  59 ..gvrvvededpgkgplaslaaal............raaadadavlvlacDmPlltpelverllaaaaasga 116
                                          ++v +++ ++k+ +  + ++l            + + +++++l++ +D   ++   +++l++ ++++g+
  gi|474933700|ref|YP_007687282.1|  81 eyHMTVHANS-SEKWKVTVVDTGLntltggrikrvaKYL-GNEPFLLTYGDG--VSDVDIKKLIKFHKSHGK 148
                                       2134444443.4566666666666555555554331223.777777777776..455666666666655554 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   8.4e-06      0.05       2      55 ..       2      58 ..       1      76 [. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.4e-06
                                      EEEEECTTSSCTT-SS...S-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGG CS
                              IspD  2 vvvipAAGsGkRmkag...lpKqflelkgqtllehtvdallaskavdkivvvvsedd 55
                                        vi A G G+R+ ++   +pK  +e+ g ++l h ++ + ++++ + i+ +  +++
  gi|474933700|ref|YP_007687282.1|  2 KTVILAGGLGTRISEEsylRPKPMIEIGGYPILWHIMKIFYSQGVDEFIICAGYKQH 58
                                      579***********995556*********************9766666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1628.05
//
Query:       gi|474933701|ref|YP_007687283.1|  [L=210]
Description: hypothetical protein TALC_00108 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00071   19.4   0.2      0.018   14.8   0.0    2.2  2  Collectrin      Renal amino acid transporter
     0.0028   17.9   4.4     0.0028   17.9   4.4    2.0  2  PMT_2           Dolichyl-phosphate-mannose-protein mannosyltr
  ------ inclusion threshold ------
       0.18   10.6   0.0       0.27   10.1   0.0    1.3  1  DUF5565         Family of unknown function (DUF5565)
        2.5    7.7   6.5        3.7    7.2   1.1    2.8  3  DUF4131         Domain of unknown function (DUF4131)
        2.7    7.6   8.0       0.37   10.4   3.2    1.8  2  Peptidase_M50B  Peptidase M50B-like
        7.6    7.0  10.7        5.4    7.5   0.1    3.1  4  HRG             Haem-transporter, endosomal/lysosomal, haem-r


Domain annotation for each model (and alignments):
>> Collectrin  Renal amino acid transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1     0.039   1.2e+02     122     149 ..      13      39 ..       4      44 .. 0.72
   2 !   14.8   0.0   6.1e-06     0.018     117     153 ..     107     143 ..      97     144 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.039
                        Collectrin 122 pvtiWlivfgvvmgvvvvgivlLivsgi 149
                                         ++W i ++ v+ ++ +  vlLi+ ++
  gi|474933701|ref|YP_007687283.1|  13 CSETWYIYYPAVVLIISLS-VLLITLAV 39 
                                       5689******999887765.55666665 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 6.1e-06
                        Collectrin 117 ppveppvtiWlivfgvvmgvvvvgivlLivsgirerk 153
                                       +p +p+++ +l  fg++mg+ +v ++l+++  ++er+
  gi|474933701|ref|YP_007687283.1| 107 TPSDPNIPYFLAEFGIMMGLCIVVTILILYKEVKERR 143
                                       6899***************************999998 PP

>> PMT_2  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.2       0.3   8.9e+02     117     130 ..      22      35 ..      14      53 .. 0.46
   2 !   17.9   4.4   9.3e-07    0.0028      76     153 ..     122     203 ..     104     208 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.3
                             PMT_2 117 taallliaallyll 130
                                        a++l+i++ + l+
  gi|474933701|ref|YP_007687283.1|  22 PAVVLIISLSVLLI 35 
                                       44444443222111 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 9.3e-07
                             PMT_2  76 aplvllwalalylllraleknklkywllagvlfG...lgflsKytaallliaallyllis.arr.ilkekkpylall 147
                                       +++ l+++ ++++l++ ++++++   l++ +l+G   + +  + ++++l++++lly++++  +   +k+k +    l
  gi|474933701|ref|YP_007687283.1| 122 IMMGLCIVVTILILYKEVKERRILSILILLLLLGtpmIWMIERGNIIFLGFTFLLYFYFNyDSDtEWKKKTAV-FCL 197
                                       78999*****************99999999999955556778******************7444233333333.344 PP

                             PMT_2 148 lalllf 153
                                       ++++ +
  gi|474933701|ref|YP_007687283.1| 198 IMACSI 203
                                       444444 PP

>> DUF5565  Family of unknown function (DUF5565)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   8.9e-05      0.27     187     220 ..      55      88 ..      15     103 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 8.9e-05
                           DUF5565 187 eelleqtleliGtnvnanPyglGskkkPvhllvp 220
                                       + l     e++    n+nPy++Gs   P+ +l+ 
  gi|474933701|ref|YP_007687283.1|  55 DSLIPDFTEVVWKAYNGNPYDMGSTYLPITFLIF 88 
                                       55677778999999***************99985 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.22   6.5e+02       5      25 ..      21      41 ..      18      59 .. 0.71
   2 ?    7.2   1.1    0.0012       3.7      10      46 ..     122     158 ..     114     166 .. 0.65
   3 ?    1.8   0.0     0.055   1.6e+02      12      40 ..     169     200 ..     164     208 .. 0.51

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.22
                           DUF4131  5 lalvllalllllllllllllr 25
                                      +++v+l++ l +ll+ l++++
  gi|474933701|ref|YP_007687283.1| 21 YPAVVLIISLSVLLITLAVNN 41
                                      566777777777777777654 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0012
                           DUF4131  10 lalllllllllllllrrrprrrvllllllllllallg 46 
                                       ++++l++ +++l+l+++ + rr+l +l+lllll++ +
  gi|474933701|ref|YP_007687283.1| 122 IMMGLCIVVTILILYKEVKERRILSILILLLLLGTPM 158
                                       4555555555555556577888888888877777644 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.055
                           DUF4131  12 lllllllllllllrr....rprrrvllllllll 40 
                                       +l++ ++ll+++++      +++++++++l+ +
  gi|474933701|ref|YP_007687283.1| 169 FLGF-TFLLYFYFNYdsdtEWKKKTAVFCLIMA 200
                                       3344.4444444433489844444444444333 PP

>> Peptidase_M50B  Peptidase M50B-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.2       0.4   1.2e+03     117     133 ..      24      40 ..      12      52 .. 0.53
   2 ?   10.4   3.2   0.00012      0.37      76     152 ..     125     202 ..     111     207 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.4
                    Peptidase_M50B 117 lvlllllgallllvlll 133
                                       +vl++ l++ll+ +++ 
  gi|474933701|ref|YP_007687283.1|  24 VVLIISLSVLLITLAVN 40 
                                       23333333333333333 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00012
                    Peptidase_M50B  76 gpallGlllillsasgkarlllv.llvllllvllllvrnlfglvlllllgallllvlllaedelleflllflgvfll 151
                                       g +++  +lil+   +  r+l + +l+lll + ++++ +  ++++l ++++l + + +   +e+++  ++f  ++++
  gi|474933701|ref|YP_007687283.1| 125 GLCIVVTILILYKEVKERRILSIlILLLLLGTPMIWMIERGNIIFLGFTFLLYFYFNYDSDTEWKKKTAVFCLIMAC 201
                                       446666677777766777776663666667777999999999****************9999999999999999887 PP

                    Peptidase_M50B 152 l 152
                                        
  gi|474933701|ref|YP_007687283.1| 202 S 202
                                       5 PP

>> HRG  Haem-transporter, endosomal/lysosomal, haem-responsive gene
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1    0.0018       5.4       5      34 ..      19      46 ..      17      70 .. 0.87
   2 ?    6.2   0.2    0.0047        14       9      29 ..     119     137 ..     113     157 .. 0.86
   3 ?   -3.6   0.1       5.3   1.6e+04      13      21 ..     169     177 ..     166     184 .. 0.54
   4 ?   -1.6   0.1       1.2   3.6e+03      42      50 ..     192     200 ..     191     208 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0018
                               HRG  5 iaygifgsilglsaflvylvlaivnkqgvs 34
                                      i y ++++i++ls+ l+ l++   n q+v+
  gi|474933701|ref|YP_007687283.1| 19 IYYPAVVLIISLSVLLITLAV--NNAQTVL 46
                                      78999**********999999..9999998 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0047
                               HRG   9 ifgsilglsaflvylvlaivn 29 
                                        fg+++gl++ ++ l+l  ++
  gi|474933701|ref|YP_007687283.1| 119 EFGIMMGLCIVVTILIL--YK 137
                                       59**************9..54 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 5.3
                               HRG  13 ilglsaflv 21 
                                       +lg+   l+
  gi|474933701|ref|YP_007687283.1| 169 FLGFTFLLY 177
                                       444444444 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 1.2
                               HRG  42 savWslltl 50 
                                       +av++l+++
  gi|474933701|ref|YP_007687283.1| 192 TAVFCLIMA 200
                                       688888764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1071  (0.0597356); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.32s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1376.60
//
Query:       gi|474933702|ref|YP_007687284.1|  [L=202]
Description: hypothetical protein TALC_00109 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1003  (0.0559429); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1257.31
//
Query:       gi|474933703|ref|YP_007687285.1|  [L=459]
Description: hypothetical protein TALC_00110 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-21   78.1   5.2    1.3e-20   74.5   5.2    2.4  1  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    2.2e-14   54.0   0.1    3.2e-13   50.1   0.1    2.2  1  AAA_15    AAA ATPase domain
    7.8e-08   32.0   0.0    7.4e-06   25.6   0.0    2.2  2  SMC_N     RecF/RecN/SMC N terminal domain
    1.8e-06   28.6   0.3    6.1e-06   26.9   0.2    2.1  1  AAA_23    AAA domain
    0.00036   19.3   0.4      0.037   12.7   0.0    2.4  3  AAA_13    AAA domain
    0.00099   19.5   0.0     0.0064   16.9   0.0    2.0  2  AAA_16    AAA ATPase domain
  ------ inclusion threshold ------
       0.03   14.2   0.3       0.17   11.8   0.0    2.4  4  ATPase_2  ATPase domain predominantly from Archaea
      0.034   14.4   0.1        1.6    9.0   0.0    2.4  2  AAA_22    AAA domain
      0.069   12.9   0.0       0.22   11.3   0.0    1.8  2  AAA_29    P-loop containing region of AAA domain
      0.078   13.5   0.0       0.22   12.1   0.0    1.8  1  ABC_tran  ABC transporter
        0.1   12.9   0.0       0.18   12.2   0.0    1.4  1  DUF4378   Domain of unknown function (DUF4378)
       0.13   11.8   0.0       0.26   10.8   0.0    1.5  1  AAA_27    AAA domain
       0.16   11.9   0.0       0.53   10.2   0.0    1.8  1  NACHT     NACHT domain


Domain annotation for each model (and alignments):
>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.5   5.2   9.2e-24   1.3e-20       3     302 ..      33     388 ..      31     389 .. 0.90

  Alignments for each domain:
  == domain 1  score: 74.5 bits;  conditional E-value: 9.2e-24
                            AAA_21   3 vliGpNgsGKSnLLdaldllarl.................................drdvegltdelsggggirkip 46 
                                       +++G NgsGK+nLL+++++l++                                  + ++ ++  +    ++i+  +
  gi|474933703|ref|YP_007687285.1|  33 FVYGENGSGKTNLLETISYLKDSvltlsrgnevvdrgreyveafgtligsmghdfdREEFGQSFMDILLPKDITHLA 109
                                       79*******************************************99999999998777777777777788888888 PP

                            AAA_21  47 slldlydpeipfefeieeflsqgvryryglrlersqv..eeklssvetllesgllldkrsleeedvfnpeargirgg 121
                                       s+ + +   +++++ i  f+++g + +y++ ++ ++   +e+l++v + + s+l++         ++ + a  +  +
  gi|474933703|ref|YP_007687285.1| 110 SRHRMIGSAEDMRICIV-FDIDGRDATYEMVFNGDNNlvSESLKCVANERTSTLYQLTA------DSGAIAAKFSRT 179
                                       88899999999999999.99999999999999999999999999999999999999766......566677777889 PP

                            AAA_21 122 vsvfslkelsvsepndlqfgkaltditsrawsllllldglrke.......rigllnifadyfgfakekrllqrlvrs 191
                                        +v s +e++v e ++++ gk+  +++  +++ + +++++ k         ++ l++ + + g+++e  +++r vr 
  gi|474933703|ref|YP_007687285.1| 180 FFVSSTYEKTVRELISKHWGKHSFLSIMNYETVRNNSEFMEKSvsgsffrFMAALEDIKVENGPYSEMIFRERSVRY 256
                                       9**************************************99999999999999999999999999999999999999 PP

                            AAA_21 192 lklveielsdlgegeeliasvderlrer........................gvvflengdgqelparelSdGtkrl 244
                                         + +i     +   + ++s+ +    r                         +v + +g+++e++a  +S+Gt +l
  gi|474933703|ref|YP_007687285.1| 257 NPESGIIEKSRMGELKRYESALNKAFTRiysdvrrvyfelsdrgedrveyslIFVRHIHGQDREISAEFESSGTEKL 333
                                       9999988877777777777777776666999********************************************** PP

                            AAA_21 245 lalltallralkkgsllliDEpEngLHPkllrrll.ellkelsrngaQviltTHSplll 302
                                       l +l+ ll+ +   + +liDE+++g+H kl+  l+ e+l e +   +Q+i+tTH+++ll
  gi|474933703|ref|YP_007687285.1| 334 LEILPFLLDCANG-KAVLIDEMDSGIHDKLVFDLIrEVLGEIK---GQLIVTTHNTSLL 388
                                       ***********99.*****************999956665554...6*********998 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   0.1   2.3e-16   3.2e-13       3     367 ..       4     386 ..       3     388 .. 0.62

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 2.3e-16
                            AAA_15   3 IkkikikNFRslkdveidlsee.....ltvliGkNnsGKSsilealdlFlnnkekkn.................... 54 
                                       I++i++ N++s+ +v+ dl +      + ++ G+N+sGK+++le + ++++     +                    
  gi|474933703|ref|YP_007687285.1|   4 IRRITLDNYKSFGHVDFDLTDGkdplpYAFVYGENGSGKTNLLETISYLKDSVLTLSrgnevvdrgreyveafgtli 80 
                                       899****************9999***999**********************775555888999******99997777 PP

                            AAA_15  55 ......................kkvikiekedleifeniseskdikIdvefaekekakeyektlkskekkkadlllk 109
                                                             k    +  +  +  + i    d++I + f        +++  + + ++  +++ +
  gi|474933703|ref|YP_007687285.1|  81 gsmghdfdreefgqsfmdillpK----DITHLASRHRMIGSAEDMRICIVF--------DIDGRDATYEMVFNGDNN 145
                                       77666666666665554422221....333444445555556666666666........222222223333333334 PP

                            AAA_15 110 kkesdlkktikdkklklkknelsdekisvekkkskkelpkekeeklekekeelkidkedlkklikkleeslkkeeel 186
                                         +++lk   ++++  l++   ++  i     k ++ ++++++++++ ++   k+  +  +  i  +e+  + +e +
  gi|474933703|ref|YP_007687285.1| 146 LVSESLKCVANERTSTLYQLTADSGAI---AAKFSRTFFVSSTYEKTVRELISKHWGKHSFLSIMNYETVRNNSEFM 219
                                       444444444444444444222222111...12222233333333333333333333333333333344443333322 PP

                            AAA_15 187 knvlksaiiklllisakRnvsdedsekkssllgklkekileealqekl................eeelteklkeiqe 247
                                       +++ +     +++  a  +++ e+   ++                  +                e++   +lk+ ++
  gi|474933703|ref|YP_007687285.1| 220 EKSVSG--SFFRFMAALEDIKVENGPYSE------------------MifrersvrynpesgiiEKSRMGELKRYES 276
                                       222211..124444444444444333333..................244544444444444557788888888888 PP

                            AAA_15 248 klkeidkklaeelkkilkkkidkikkfnykgkkneeieik.........ddeelplnknGsGvqrllllillileae 315
                                       +l+++   + ++  +++++  d        +  +e+   +          d e++++  +sG+  ll ++ ++l++ 
  gi|474933703|ref|YP_007687285.1| 277 ALNKAFTRIYSDVRRVYFELSDRG------EDRVEY---SlifvrhihgQDREISAEFESSGTEKLLEILPFLLDCA 344
                                       888888888777777777777763......122222...233466778***************************** PP

                            AAA_15 316 kkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSph 367
                                       ++       + +li+E +  +H +    +++l++e++ + k+Q+i+tTH+  
  gi|474933703|ref|YP_007687285.1| 345 NG-------KAVLIDEMDSGIHDK---LVFDLIREVLGEIKGQLIVTTHNTS 386
                                       **.......*************75...6899999***************975 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   5.4e-09   7.4e-06       2      47 ..       4      52 ..       3      68 .. 0.81
   2 ?    4.6   0.0     0.013        19     138     203 ..     328     389 ..     103     400 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 5.4e-09
                                      EEEEEEESETTEECEEEEEETTSS.....EEEEEESTTSSHHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  2 lkrleienFksyagktvilpfsks.....ftaivGpNGSGKsnlldAilFv 47
                                      ++r++++n+ks+   +v+ +++++       +++G+NGSGK+nll+ i+++
  gi|474933703|ref|YP_007687285.1|  4 IRRITLDNYKSFG--HVDFDLTDGkdplpYAFVYGENGSGKTNLLETISYL 52
                                      89**********6..5555555542233378*****************985 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.013
                                       -HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHH.HHHHHHHHHHCTTSEEEEE-SSHHHCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 138 SgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknv.kkvaellkeksknaQfivislreemle 203
                                       Sg ek L  l +l+   + k    +l+De+d+ + +k v   + e+l e +   Q+iv+++++ +l+
  gi|474933703|ref|YP_007687285.1| 328 SGTEKLLEILPFLLDCANGK---AVLIDEMDSGIHDKLVfDLIREVLGEIK--GQLIVTTHNTSLLR 389
                                       66666666666665444443...4689****99866655145556666666..9*******998876 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.2   4.4e-09   6.1e-06       1      42 [.       6      52 ..       6     287 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 4.4e-09
                            AAA_23  1 kLkienfrsfrdqeidF....sk.gltlItGpNGaGKTTildAikla 42
                                      ++++ n++sf+++++d+    ++ +   ++G+NG+GKT +l+ i + 
  gi|474933703|ref|YP_007687285.1|  6 RITLDNYKSFGHVDFDLtdgkDPlPYAFVYGENGSGKTNLLETISYL 52
                                      79***************8775446799*****************985 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   2.7e-05     0.037       2      39 ..      15      52 ..      14      67 .. 0.84
   2 ?   -4.0   0.0       3.1   4.2e+03     603     627 ..     262     287 ..     226     291 .. 0.65
   3 !    4.5   0.0     0.008        11     546     578 ..     362     392 ..     354     427 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.7e-05
                            AAA_13  2 vrifdfrgaeledfkriNliYGwNGaGKTtLSrllrsl 39
                                      ++++df  ++ +d   + ++YG NG+GKT L + ++ l
  gi|474933703|ref|YP_007687285.1| 15 FGHVDFDLTDGKDPLPYAFVYGENGSGKTNLLETISYL 52
                                      677777888888888899************99988877 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 3.1
                            AAA_13 603 ki..kelkrllneieseYellfkevkr 627
                                       +i  +++ + l+ +es+ + +f ++++
  gi|474933703|ref|YP_007687285.1| 262 IIekSRMGE-LKRYESALNKAFTRIYS 287
                                       232245555.88899999999988875 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.008
                            AAA_13 546 ivfsliksrllkkkkak.QlfiLTHnleffkevk 578
                                       +vf li+++l    ++k Ql++ THn+++++ ++
  gi|474933703|ref|YP_007687285.1| 362 LVFDLIREVL---GEIKgQLIVTTHNTSLLRILD 392
                                       5899999999...55544***********99765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   4.7e-06    0.0064      23      81 ..      27      79 ..      20     128 .. 0.78
   2 ?   -0.1   0.0      0.77   1.1e+03     106     145 ..     290     355 ..     245     380 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.7e-06
                            AAA_16 23 rp.elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareel 81
                                      +p ++ +++Ge G+GK+ l++++  +l+++ +++l+  ++  +++++y+   +a+   +l
  gi|474933703|ref|YP_007687285.1| 27 DPlPYAFVYGENGSGKTNLLETIS-YLKDS-VLTLSRGNEVVDRGREYV---EAF-G-TL 79
                                      456899*****************9.88888.888777776667887774...444.2.33 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.77
                            AAA_16 106 a..........................avpelagaeasrllellkrll.allsrderplvlvlDdlq 145
                                       +                          + +e++++ +s+  e+l ++l  ll + +    +++D+++
  gi|474933703|ref|YP_007687285.1| 290 RrvyfelsdrgedrveyslifvrhihgQDREISAEFESSGTEKLLEILpFLLDC-ANGKAVLIDEMD 355
                                       344444444444444455555555444555555555577777777777666666.555677777776 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00012      0.17      21      40 ..      30      49 ..      25      72 .. 0.85
   2 ?   -2.2   0.0       2.3   3.2e+03     125     151 ..     130     156 ..     111     166 .. 0.74
   3 ?   -3.1   0.0       4.4   6.1e+03      50     112 ..     307     373 ..     299     377 .. 0.49
   4 ?   -4.0   0.1       8.1   1.1e+04       5      20 ..     406     421 ..     404     422 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                          ATPase_2 21 eiyfiYGpegsGKtaLlkei 40
                                      +  f+YG  gsGKt Ll  i
  gi|474933703|ref|YP_007687285.1| 30 PYAFVYGENGSGKTNLLETI 49
                                      567*************9876 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.3
                          ATPase_2 125 DelqklidlglngaellvkeLlnlies 151
                                       D      ++ +ng+++lv+e l+++ +
  gi|474933703|ref|YP_007687285.1| 130 DGRDATYEMVFNGDNNLVSESLKCVAN 156
                                       444455678999999999999988876 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 4.4
                          ATPase_2  50 yviyyialreesiskldefieeeeekkklekal........giavpkaeleeilk.eksklvfkaielllek 112
                                         i++  +++++ +   ef  e++  +kl + l        g+av  +e+    +  + klvf  i ++l +
  gi|474933703|ref|YP_007687285.1| 307 SLIFVRHIHGQDREISAEF--ESSGTEKLLEILpflldcanGKAVLIDEM---DSgIHDKLVFDLIREVLGE 373
                                       5566666666666666666..55555555555544443222222222222...2234555555555555555 PP

  == domain 4  score: -4.0 bits;  conditional E-value: 8.1
                          ATPase_2   5 ekelkeleeilerepn 20 
                                       e+e++ +++il++++n
  gi|474933703|ref|YP_007687285.1| 406 EREIRCVKKILRTQKN 421
                                       89********999877 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0    0.0012       1.6       9      32 ..      33      56 ..      30      97 .. 0.82
   2 ?    3.0   0.1      0.08   1.1e+02      86     128 ..     340     381 ..     271     391 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0012
                            AAA_22  9 vvtGesGtGKTtllrrlleqldee 32
                                      +v+Ge G+GKT ll+++ + +d +
  gi|474933703|ref|YP_007687285.1| 33 FVYGENGSGKTNLLETISYLKDSV 56
                                      79*************999887765 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.08
                            AAA_22  86 lraravielliiDEaqh.lrseealeeL.rsllnlsrkgvqliLv 128
                                       l ++a  ++++iDE++  + +++++ +L r+ l   + + qli+ 
  gi|474933703|ref|YP_007687285.1| 340 LLDCANGKAVLIDEMDSgI-HDKLVFDLiREVLG--EIKGQLIVT 381
                                       3344444899*******88.75555555355555..666666655 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00016      0.22       2      45 ..       5      52 ..       4      54 .. 0.79
   2 ?   -3.0   0.0       4.7   6.5e+03      33      40 ..     345     352 ..     343     355 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00016
                            AAA_29  2 krlqlvNWgtfdghtieidlkg....atlltGpsGsGKSTllDAiqal 45
                                      +r+ l N  +f + +++++         ++ G++GsGK+ ll  i++l
  gi|474933703|ref|YP_007687285.1|  5 RRITLDNYKSFGHVDFDLTDGKdplpYAFVYGENGSGKTNLLETISYL 52
                                      577778888888888888744467767899************988876 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.7
                            AAA_29  33 sGKSTllD 40 
                                       +GK  l+D
  gi|474933703|ref|YP_007687285.1| 345 NGKAVLID 352
                                       69*****9 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00016      0.22      15      36 ..      33      54 ..      17      91 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00016
                                      EEEESTTSSHHHHHHHHTTSS- CS
                                      xxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 15 aivGenGaGKStLlkllagllk 36
                                       + GenG+GK+ Ll++++ l +
  gi|474933703|ref|YP_007687285.1| 33 FVYGENGSGKTNLLETISYLKD 54
                                      578**************97765 PP

>> DUF4378  Domain of unknown function (DUF4378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00013      0.18      55      80 ..     355     383 ..     318     456 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                           DUF4378  55 eerserklLFDlvneiLaeilalel....k 80 
                                       ++ ++ kl+FDl+ e+L ei   +l    +
  gi|474933703|ref|YP_007687285.1| 355 DSGIHDKLVFDLIREVLGEIKG-QLivttH 383
                                       67789***************32.2245431 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00019      0.26       3      49 ..       4      52 ..       2      75 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00019
                            AAA_27  3 lerLdLeryGkftdrsldfsaeeadl..hliyGpNEAGKstalrAisdl 49
                                      ++r++L+ y +f    +d+  +++ l   ++yG N +GK+ +l+ is l
  gi|474933703|ref|YP_007687285.1|  4 IRRITLDNYKSFGHVDFDLTDGKDPLpyAFVYGENGSGKTNLLETISYL 52
                                      8999*********99999998766653389**************99876 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00039      0.53       4      21 ..      33      50 ..      31      55 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00039
                                      EEEC-TTTCHHHHHHHHH CS
                             NACHT  4 ilqGeaGsGKTtLlqkla 21
                                      ++ Ge+GsGKT Ll+ + 
  gi|474933703|ref|YP_007687285.1| 33 FVYGENGSGKTNLLETIS 50
                                      799***********9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 2829.51
//
Query:       gi|474933704|ref|YP_007687286.1|  [L=196]
Description: hypothetical protein TALC_00111 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.038   13.6   0.0        0.1   12.2   0.0    1.7  2  PRY       SPRY-associated domain


Domain annotation for each model (and alignments):
>> PRY  SPRY-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.23   4.2e+03       9      29 ..      57      77 ..      57      81 .. 0.77
   2 ?   12.2   0.0   5.7e-06       0.1       3      23 ..     150     170 ..     149     179 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.23
                               PRY  9 hpkLvlSedlksVrysedrqs 29
                                      h +L+l +  ++ +ys++ ++
  gi|474933704|ref|YP_007687286.1| 57 HDDLSLHKMFDGLQYSPKGRP 77
                                      678888888889999998876 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 5.7e-06
                               PRY   3 LDpnTAhpkLvlSedlksVry 23 
                                       +D  TA  +L+lSe lk+V  
  gi|474933704|ref|YP_007687286.1| 150 FDSMTAEGYLQLSEQLKTVPE 170
                                       9*****************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1264.68
//
Query:       gi|474933705|ref|YP_007687287.1|  [L=121]
Description: LSU ribosomal protein L7AE [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.2e-29   99.0   0.1    1.1e-28   98.8   0.1    1.1  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil
      0.005   16.7   0.0     0.0069   16.3   0.0    1.3  1  PELOTA_1        PELOTA RNA binding domain
  ------ inclusion threshold ------
      0.018   15.1   0.0      0.018   15.1   0.0    1.1  1  RNase_P_pop3    RNase P subunit Pop3


Domain annotation for each model (and alignments):
>> Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.8   0.1   1.8e-32   1.1e-28       2      91 ..      16     105 ..      15     109 .. 0.95

  Alignments for each domain:
  == domain 1  score: 98.8 bits;  conditional E-value: 1.8e-32
                                       HHHHHHHHHHHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHHHTTEEEEEESCHHHHHHHTTSSS CS
                    Ribosomal_L7Ae   2 aieevlkkakkagklvlGlkevtkalergeaklvilAedvepeekkkllealckekevpyvkvkskkeLGelvgkkr 78 
                                       +++ v + a+++gkl++G++evtk +ergea +vi+A+dvep+e+ ++++alc e++vpy +v+sk+eLG+++g+++
  gi|474933705|ref|YP_007687287.1|  16 KAYAVAEIARDSGKLKKGTNEVTKVVERGEAVFVIMAADVEPPEILAHMPALCDERNVPYAYVPSKEELGKAIGLEK 92 
                                       67888999********************************************************************* PP

                                       ECSEEEEEESTTT CS
                    Ribosomal_L7Ae  79 pvsalaikdegds 91 
                                       p++++ai+d+g+ 
  gi|474933705|ref|YP_007687287.1|  93 PTASVAIVDAGNG 105
                                       *********9975 PP

>> PELOTA_1  PELOTA RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.2e-06    0.0069      17      71 ..      25      81 ..      11      93 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.2e-06
                          PELOTA_1 17 edinliKPgigEaTRvlLRRvPekvlvrdeee..pdlahlllLakekgvpveevpdl 71
                                      +d    K g  E T+v+ R     v+++++ e  + lah+ +L++e++vp+  vp++
  gi|474933705|ref|YP_007687287.1| 25 RDSGKLKKGTNEVTKVVERGEAVFVIMAADVEppEILAHMPALCDERNVPYAYVPSK 81
                                      56678999**************999999977765679**************999876 PP

>> RNase_P_pop3  RNase P subunit Pop3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   3.1e-06     0.018      55     107 ..      29      79 ..      13     118 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.1e-06
                      RNase_P_pop3  55 eltvglneivelLecsesddvvllvcnkD.tPsvLlsqlpllvavanltvklvq 107
                                       +l  g ne+ ++ e    +++v++++  D +P  +l ++p l+   n+  + v+
  gi|474933705|ref|YP_007687287.1|  29 KLKKGTNEVTKVVE---RGEAVFVIMAADvEPPEILAHMPALCDERNVPYAYVP 79 
                                       788999*****999...8889999999997799999********9996555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 861.32
//
Query:       gi|474933706|ref|YP_007687288.1|  [L=71]
Description: SSU ribosomal protein S28E [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.7e-31  106.1   2.1    7.2e-31  106.0   2.1    1.0  1  Ribosomal_S28e  Ribosomal protein S28e


Domain annotation for each model (and alignments):
>> Ribosomal_S28e  Ribosomal protein S28e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.0   2.1     4e-35   7.2e-31       4      64 .]       7      67 ..       4      67 .. 0.97

  Alignments for each domain:
  == domain 1  score: 106.0 bits;  conditional E-value: 4e-35
                                      EEEEEEEEEE---SSSSEEEEEEEE-S-SS-S-EEEEEEES---TT-EEEES--S--TT-- CS
                    Ribosomal_S28e  4 klAeVikvlgrtGsrGevtqVrvellegkdkgriiiRnVkGPvreGDiLtLlEterEArrL 64
                                       + eV++++grtG++Ge+tqV+v++l+g+dkgrii+Rn++GPvr+GDiL+L+Et rEAr+L
  gi|474933706|ref|YP_007687288.1|  7 IPSEVVEIIGRTGMTGEATQVKVRVLDGRDKGRIITRNIMGPVRMGDILMLRETSREARKL 67
                                      5789********************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       221  (0.0123264); expected 358.6 (0.02)
Passed bias filter:                      183  (0.0102069); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 484.86
//
Query:       gi|474933707|ref|YP_007687289.1|  [L=79]
Description: LSU ribosomal protein L24E [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-21   76.8   0.6    1.4e-21   76.5   0.6    1.1  1  Ribosomal_L24e  Ribosomal protein L24e
  ------ inclusion threshold ------
      0.032   14.2   0.1      0.064   13.2   0.1    1.5  1  zf-FCS          MYM-type Zinc finger with FCS sequence motif
       0.06   13.8   0.0      0.069   13.6   0.0    1.2  1  DUF1140         Protein of unknown function (DUF1140)
      0.074   13.0   0.0      0.096   12.7   0.0    1.2  1  Exc             Excisionase-like protein
        0.1   12.7   1.0          7    6.8   0.0    2.1  2  Acyltransf_C    Acyltransferase C-terminus


Domain annotation for each model (and alignments):
>> Ribosomal_L24e  Ribosomal protein L24e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.5   0.6   3.8e-25   1.4e-21       2      65 ..       3      67 ..       2      68 .. 0.95

  Alignments for each domain:
  == domain 1  score: 76.5 bits;  conditional E-value: 3.8e-25
                                      XX-B-TTT-SB--SS--EEEE-TTS-EEEESSHHH.HHHHHTT--GGGSTTSTTT-XXXXXXXX. CS
                    Ribosomal_L24e  2 ktekCsFsgykiyPGhGkrfvrnDgkvfrFlssKc.eklfkqkrnPrklkWTkayRrahkkelte 65
                                      +++kCsF+g+ i PG+Gk+fv++Dg+v+ F  ++c +++++ kr Pr ++WT++++ ++  +l++
  gi|474933707|ref|YP_007687289.1|  3 EIRKCSFCGQDIPPGTGKMFVKKDGTVLYFDANRCyKNMIQLKRVPRTTRWTQKAHDEKDARLKN 67
                                      689********************************99*******************999988776 PP

>> zf-FCS  MYM-type Zinc finger with FCS sequence motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   1.8e-05     0.064       4      18 ..       5      19 ..       4      32 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.8e-05
                            zf-FCS  4 krCwfCkkyikgkpe 18
                                      ++C+fC+++i+ +++
  gi|474933707|ref|YP_007687289.1|  5 RKCSFCGQDIPPGTG 19
                                      58********88774 PP

>> DUF1140  Protein of unknown function (DUF1140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.9e-05     0.069      55      85 ..      31      61 ..      17      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.9e-05
                           DUF1140 55 efyikeiskkldqllelDrsfrWsekLhqdr 85
                                       f  +  +k++ ql+++ r++rW++k h ++
  gi|474933707|ref|YP_007687289.1| 31 YFDANRCYKNMIQLKRVPRTTRWTQKAHDEK 61
                                      566788999*******************987 PP

>> Exc  Excisionase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.7e-05     0.096      37      71 ..      25      59 ..      17      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.7e-05
                                      EETTEEEEETT-EE--SSX....XXXXXXXXXXXX CS
                               Exc 37 kdGreylveedavkvelerlprvPvtsgllkrias 71
                                      kdG   +++++ +++++ +l rvP t+   ++  +
  gi|474933707|ref|YP_007687289.1| 25 KDGTVLYFDANRCYKNMIQLKRVPRTTRWTQKAHD 59
                                      89**********************99877666655 PP

>> Acyltransf_C  Acyltransferase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0019         7      35      62 ..      20      45 ..      18      51 .. 0.77
   2 ?    6.1   0.1    0.0034        12      20      45 ..      45      66 ..      40      67 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0019
                      Acyltransf_C 35 elfeeKDklleeFyktgtFepgkevkip 62
                                      ++f++KD ++ +F ++ +++  ++ +++
  gi|474933707|ref|YP_007687289.1| 20 KMFVKKDGTVLYFDANRCYK--NMIQLK 45
                                      79****************93..444444 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0034
                      Acyltransf_C 20 eevPedeeelaeWlhelfeeKDklle 45
                                      + vP +    ++W ++   eKD++l+
  gi|474933707|ref|YP_007687289.1| 45 KRVPRT----TRWTQKAHDEKDARLK 66
                                      555555....49***********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1186  (0.0661498); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 517.58
//
Query:       gi|474933708|ref|YP_007687290.1|  [L=153]
Description: nucleoside diphosphate kinase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-57  193.6   0.0    1.5e-57  193.4   0.0    1.0  1  NDK       Nucleoside diphosphate kinase


Domain annotation for each model (and alignments):
>> NDK  Nucleoside diphosphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.4   0.0   8.2e-62   1.5e-57       1     132 [.       7     138 ..       7     141 .. 0.99

  Alignments for each domain:
  == domain 1  score: 193.4 bits;  conditional E-value: 8.2e-62
                                       EEEEEEE-HHHHHTT-HHHHHHHHHHHT-EEEEEEEECE-HHHHHHHTGGGTTSTTHHHHHHHHTSSEEEEEEEEST CS
                               NDK   1 ertlvliKPdavkrgligeiisrleekglkivalkmlrlteeqaeehYaehkgkpffeelvefmtsgpvvalvlege 77 
                                       ert++++KPd+v+rgl+gei+sr+e+kglk+va+k++ + +e+ae+hYaehk+k+ff++l++++tsgpv+a+v+ege
  gi|474933708|ref|YP_007687290.1|   7 ERTYLMVKPDGVQRGLVGEILSRFEKKGLKLVAAKLMVIPKETAEKHYAEHKDKKFFPSLISYITSGPVFAMVWEGE 83 
                                       89*************************************************************************** PP

                                       THHHHHHHHH--SSTTTSSTTSHHHHH-SSSTT-SEEE-SSHHHHHHHHHHHSTG CS
                               NDK  78 daiekvreliGatnpaeaapgtiRadfgvslgeNlvHgSdseesaereiklfFke 132
                                       +a++++r+l+G+tnp+e+apgtiR+d+++ +g N++HgSds+esa+rei++fF+e
  gi|474933708|ref|YP_007687290.1|  84 NAVQVCRNLMGKTNPQESAPGTIRGDYCMVTGVNIIHGSDSPESAAREIGIFFPE 138
                                       *****************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 929.91
//
Query:       gi|474933709|ref|YP_007687291.1|  [L=582]
Description: translation initiation factor aIF-2/yIF-2 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-32  112.7   0.2    2.1e-31  109.0   0.0    2.6  2  GTP_EFTU     Elongation factor Tu GTP binding domain
    7.1e-24   83.5   3.9      9e-24   83.2   1.6    2.4  3  GTP_EFTU_D4  Elongation factor Tu domain 4
    7.9e-18   64.5   2.3      6e-17   61.7   0.3    2.5  2  IF-2         Translation-initiation factor 2
    5.6e-13   49.1   5.6    2.3e-10   40.7   0.1    2.8  2  GTP_EFTU_D2  Elongation factor Tu domain 2
    1.8e-06   28.0   0.0    3.8e-06   27.0   0.0    1.6  1  MMR_HSR1     50S ribosome-binding GTPase
      0.005   16.6   0.0      0.011   15.6   0.0    1.5  1  ATP_bind_1   Conserved hypothetical ATP binding protein


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.0   0.0     7e-35   2.1e-31       6     192 ..       8     214 ..       4     216 .. 0.80
   2 ?   -0.8   0.0       0.3   9.1e+02      43      61 ..     339     357 ..     323     365 .. 0.75

  Alignments for each domain:
  == domain 1  score: 109.0 bits;  conditional E-value: 7e-35
                                       EEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESSSGG CS
                          GTP_EFTU   6 igiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisleketkkylinliDtPGHvd 82 
                                       ++++ghvDhGKt L+dr+  ++   +++g+ ++    +  ++    r   +  + i  + + +   + +iDtPGH+ 
  gi|474933709|ref|YP_007687291.1|   8 VSVLGHVDHGKTKLLDRIRGTAVGAREAGAITQ---HIGATEVPIDRIYEMCGSIIGQK-KFTVPGLLFIDTPGHQA 80 
                                       89*****************87777777565554...45666666666665555555555.667889*********** PP

                                       GHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGST...............HHHHHHHHH CS
                          GTP_EFTU  83 FskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrl...............kaelkeive 144
                                       F++   rg + +D+avlv+d++eG +pqt e +++++++++p+++++NK+D +               k++++++ +
  gi|474933709|ref|YP_007687291.1|  81 FTSLRARGGSLADLAVLVIDIREGLMPQTIESIHILRQYKTPFVIALNKVDTVdgwiaepdrpfilaeKQQMDHTRQ 157
                                       ********************************************************999988886665555555555 PP

                                       HHHHHHHHHHHHHHHH.HHTTT............TTEEEEEEBTTTTBTHHHHHHHHHHHS CS
                          GTP_EFTU 145 evkqklsrkeekleky.gekge............kevpvvfgSalkgegvktllealvell 192
                                       + ++++    +++ ++  e+g             k v ++++Sa++gegv +l+ +l+ l+
  gi|474933709|ref|YP_007687291.1| 158 MFETHM----YNIISQlSENGVfadrydriedftKAVALIPMSAKTGEGVPDLMLMLIGLA 214
                                       555555....33333313333366678888999899*******************998765 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.3
                                       HCHSHHHHHHTSCSSCEEE CS
                          GTP_EFTU  43 lDtlkeErergiTiksaai 61 
                                       +    e +e+giTik+ ai
  gi|474933709|ref|YP_007687291.1| 339 TSIKIETEEKGITIKADAI 357
                                       5555567899*****9886 PP

>> GTP_EFTU_D4  Elongation factor Tu domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0         2   5.9e+03      60      70 ..     255     265 ..     242     274 .. 0.75
   2 ?   -2.1   0.0       1.2   3.7e+03      46      71 ..     285     310 ..     279     322 .. 0.63
   3 !   83.2   1.6     3e-27     9e-24       2      86 .]     457     542 ..     456     542 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2
                                       EETT-EEEEEE CS
                       GTP_EFTU_D4  60 akaGqevaisi 70 
                                       +k+G+ vai  
  gi|474933709|ref|YP_007687291.1| 255 IKTGDTVAIGT 265
                                       56788888765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.2
                                       EEEEEEETTEEESEEETT-EEEEEEE CS
                       GTP_EFTU_D4  46 eilqiqdkgkkleeakaGqevaisie 71 
                                       ei++ qd+ ++++e++a + v i+ +
  gi|474933709|ref|YP_007687291.1| 285 EIRDPQDTFERVKEVHAAAGVKIACK 310
                                       56677777888888766555555443 PP

  == domain 3  score: 83.2 bits;  conditional E-value: 3e-27
                                       -CEEEEEEEEEEETCCCEEEEEEEEEEEEETT-EEEETTE.EEEEEEEEEET.TEEESEEETT-EEEEEEESS-TTT CS
                       GTP_EFTU_D4   2 PgkikilpgvvfrrsdpaivGvevlgGvikpgvklikedGrevGeilqiqdk.gkkleeakaGqevaisiegkivGr 77 
                                       P+k++ilp+ +fr  +pa+vGv+vl+G+i++g++li+++G++ G i++++   g  l e  +G+ev+++i+g +vGr
  gi|474933709|ref|YP_007687291.1| 457 PAKFTILPDHIFRVNKPAVVGVRVLAGRIRVGMPLINKEGKDCGIIKSVRADdGTVLAEGVQGDEVSVAIDGVTVGR 533
                                       9************************************************9651577899****************** PP

                                       S--TT-EEE CS
                       GTP_EFTU_D4  78 qikegdily 86 
                                       qi+e+di+y
  gi|474933709|ref|YP_007687291.1| 534 QINENDIIY 542
                                       *******98 PP

>> IF-2  Translation-initiation factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   0.3     2e-20     6e-17       6     104 ..     339     435 ..     333     436 .. 0.91
   2 ?    1.9   0.1     0.081   2.4e+02      38      63 ..     518     544 ..     511     554 .. 0.81

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 2e-20
                                       HCCCSCSSCCEEEEEESSHHHHHHHHHHHHCTT.SSTEEEECEEEESSB-HHHHHHHHHST...EEEEEESSSCTHH CS
                              IF-2   6 eeikeegkelnviikaDvqGsleAlkeaLekleseevkvkvihsgvGaitesDvelasasn...aiiigFnvkvskk 79 
                                       ++ik e++e ++ ikaD  GsleAl+   +        +++ + g+G+it++D+   s  n    +++gFnv+++k+
  gi|474933709|ref|YP_007687291.1| 339 TSIKIETEEKGITIKADAIGSLEALAFEAKAA-----GIPIRKYGIGDITRRDILESSYGNdtyHVLLGFNVTLTKD 410
                                       5677778999***************9888776.....6*******************9966677************* PP

                                       HHHCCCCCTSEEEEESSHHHHHHHH CS
                              IF-2  80 akklaekegvkirlynvIYkliddv 104
                                       a+++ e++  k++++n++Y lidd+
  gi|474933709|ref|YP_007687291.1| 411 AEAALESQPLKVFTNNIVYALIDDY 435
                                       ***********************97 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.081
                                       T.SSTEEEECEEEESS.B-HHHHHHHH CS
                              IF-2  38 eseevkvkvihsgvGa.itesDvelas 63 
                                       + +ev+v +  + vG  i+e+D+ + +
  gi|474933709|ref|YP_007687291.1| 518 QGDEVSVAIDGVTVGRqINENDIIYTD 544
                                       3499***********65******8765 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.1   7.6e-14   2.3e-10       1      73 [.     243     321 ..     243     322 .. 0.91
   2 !    9.0   2.0   0.00061       1.8       3      60 ..     475     528 ..     474     541 .. 0.70

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 7.6e-14
                                       EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEE...........ETTSEEEEEEEESSCCSG CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededea...........vaganaGvivaikgleda 66 
                                       G+++++++ysGt+k+Gd+v i+ n+    + vtr+++++++++ +de            ++ a+aGv++a k+ +  
  gi|474933709|ref|YP_007687291.1| 243 GQTIDMILYSGTIKTGDTVAIGTNS---APLVTRVKAILKPRP-LDEIrdpqdtfervkEVHAAAGVKIACKESDG- 314
                                       889******************3354...49***********55.888889**************************. PP

                                       SSTTCEE CS
                       GTP_EFTU_D2  67 iivGdtl 73 
                                       ii+G+++
  gi|474933709|ref|YP_007687291.1| 315 IIAGAPI 321
                                       ****987 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00061
                                       EEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETE.EESEEETTSEEEEEEEE CS
                       GTP_EFTU_D2   3 valgrvysGtlkkGdevrilgndtskkeivtrissletfhe.dedeavaganaGvivai 60 
                                       v+++rv  G +++G+ + +  ++ +k+   + i+s+ +  +  + e v g+ + v + +
  gi|474933709|ref|YP_007687291.1| 475 VVGVRVLAGRIRVGMPLIN--KE-GKD--CGIIKSVRADDGtVLAEGVQGDEVSVAIDG 528
                                       99****************9..75.444..466677666666333444666665555554 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   1.3e-09   3.8e-06       2     114 .]       8     129 ..       7     129 .. 0.69

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 1.3e-09
                                       EEEEESTTSSHHHHHHHHHT......STEEESSSTTSSSSEEEEEEE.....ETTEE........EEEEECGGCSSH CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltg......ekaivsdkpgtTrdinegrvk.....lkgke........ielvDtpGlieg 59 
                                       v ++G+   GK+ L+ ++ g      e+  ++++ g+T  ++ + ++     +            + ++DtpG  + 
  gi|474933709|ref|YP_007687291.1|   8 VSVLGHVDHGKTKLLDRIRGtavgarEAGAITQHIGATEVPIDRIYEmcgsiI---GqkkftvpgLLFIDTPG-HQ- 79 
                                       789***************98333321233556666666666666665444441...0444555559*******.33. PP

                                       HHHHHHHHHHHHHHHC.TSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                          MMR_HSR1  60 aseekglgkaflalee.adlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                             ++   ++  + adl++lv+d++ e+l p+  e   +l++ k p++++lnk
  gi|474933709|ref|YP_007687291.1|  80 ---A--FTSLRARGGSlADLAVLVIDIR-EGLMPQTIESIHILRQYKTPFVIALNK 129
                                       ...2..222222222348********99.7799999999999999*********98 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   3.6e-06     0.011      93     232 ..      70     207 ..      38     215 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.6e-06
                        ATP_bind_1  93 yllfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltdptkfisgllsalsamlrlelPhvvvlnkfDll 169
                                       +l +DtPG + +  +++ +         + a  +v ++D +       ++ +++ ++ ++ ++++P+v++lnk+D +
  gi|474933709|ref|YP_007687291.1|  70 LLFIDTPGHQAFTSLRARGG--------SLADLAVLVIDIREG-----LMPQTIESIHILRQYKTPFVIALNKVDTV 133
                                       67788888888888888888........666688888887754.....45555556799*****************9 PP

                        ATP_bind_1 170 kek.....lekeleffedvealslllekee......ekykklaeaiaelleefalvlrflplssekeesiedll 232
                                       +       + + l   +++++ +++ e+++         +  +++  + +e+f+    ++p+s++++e++ dl+
  gi|474933709|ref|YP_007687291.1| 134 DGWiaepdRPFILAEKQQMDHTRQMFETHMyniisqLSENGVFADRYDRIEDFTKAVALIPMSAKTGEGVPDLM 207
                                       94453333444444444444444444444465554322233444555667777777777777777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (582 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.49
# Mc/sec: 3593.72
//
Query:       gi|474933710|ref|YP_007687292.1|  [L=401]
Description: hypothetical protein TALC_00117 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-19   70.7   0.0    4.3e-19   69.2   0.0    1.8  2  Fic       Fic/DOC family
    0.00076   19.2   0.0      0.002   17.9   0.0    1.7  1  HTH_DeoR  DeoR-like helix-turn-helix domain
     0.0079   16.1   0.1      0.024   14.6   0.1    1.8  1  HTH_11    HTH domain
  ------ inclusion threshold ------
       0.07   13.2   0.1       0.15   12.2   0.1    1.5  1  Fic_N     Fic/DOC family N-terminal
       0.11   12.8   1.1       0.42   10.9   1.1    2.0  1  GFD1      GFD1 mRNA transport factor
       0.13   12.0   0.0        0.4   10.4   0.0    1.9  1  GntR      Bacterial regulatory proteins, gntR family


Domain annotation for each model (and alignments):
>> Fic  Fic/DOC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.2   0.0   1.4e-22   4.3e-19       1      96 [.     150     255 ..     150     256 .. 0.94
   2 ?   -3.1   0.0       5.3   1.6e+04      33      58 ..     293     319 ..     270     331 .. 0.61

  Alignments for each domain:
  == domain 1  score: 69.2 bits;  conditional E-value: 1.4e-22
                                       --SHHHHHHHHCHS-S----...--TS--SS-S......T..EEEE---SCCCHHHHHHHHHHHHC.HHT-S-HHHH CS
                               Fic   1 pltledllelhrlllqdige...eagefrdeev......segklesalappeevpaeleelleyln.elekeeplek 67 
                                       pl+le ++++hr +++ + +   + gefr+++       +e+ +++++ ++ e+ + + +l++y+n + e ++pl+k
  gi|474933710|ref|YP_007687292.1| 150 PLSLELIKDVHRVITESLMDdpqTSGEFRTDDSiavrdvYEDVTYHVPVSHTEIGKMIVDLCDYVNeDAEFIHPLIK 226
                                       699***********98888877777***9988899999999*************************999999***** PP

                                       HHHHHHHHHHH--SSS-HHHHHHHHHHHH CS
                               Fic  68 aaalhyefekiHPFaDGNgRtarlllnll 96 
                                         ++h+ +++iHPF DGNgR++r+l+ ++
  gi|474933710|ref|YP_007687292.1| 227 GIMIHFILAYIHPFLDGNGRVSRALFYWY 255
                                       **************************998 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.3
                                       .EEEE---SCCCHHHHHHHHHHHHC.H CS
                               Fic  33 gklesalappeevpaeleelleyln.e 58 
                                       + +++a  + ++v+++++ ++ yl+ +
  gi|474933710|ref|YP_007687292.1| 293 DATYFARYNLKMVSEAIDVFDTYLKrK 319
                                       444555555567777777777777742 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   6.6e-07     0.002       1      44 [.     338     382 ..     338     384 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 6.6e-07
                          HTH_DeoR   1 Rieqile.llkqqgklsveelvellgvSeaTiRRDLneLeeqgll 44 
                                       R+ qil+ ++++   +s  el+  ++++  TiRRDL  L e+g +
  gi|474933710|ref|YP_007687292.1| 338 RQSQILKdMVRSGEPVSQYELSVKYQTTVPTIRRDLIALLESGYI 382
                                       888888548888889************************999976 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   7.9e-06     0.024       1      44 [.     338     381 ..     338     399 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 7.9e-06
                            HTH_11   1 RllqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44 
                                       R++qil+   ++ +p+s  eL+ +   +  t+rrd+ aL e+g+
  gi|474933710|ref|YP_007687292.1| 338 RQSQILKDMVRSGEPVSQYELSVKYQTTVPTIRRDLIALLESGY 381
                                       899****999*****************************99994 PP

>> Fic_N  Fic/DOC family N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   4.9e-05      0.15      27      78 ..      90     141 ..      82     142 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.9e-05
                             Fic_N  27 LirplvrkEAvlSSeIEgtqttld...dlleaeadeeeekskdvkEVlnYvkAle 78 
                                       L  + +++E+ +SS++Eg+ tt +   +ll+++ ++++    + + +ln  +A++
  gi|474933710|ref|YP_007687292.1|  90 LSVSSMMEESIASSQLEGASTTTKlakKLLRSNLEPKDR---SQRMILNNYHAMQ 141
                                       55567889***********99975222666666666665...5578888877775 PP

>> GFD1  GFD1 mRNA transport factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.1   0.00014      0.42       5      17 ..     316     328 ..     315     330 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00014
                              GFD1   5 LKKKIEEQrkIle 17 
                                       LK+K +EQ+k+ e
  gi|474933710|ref|YP_007687292.1| 316 LKRKMDEQKKLIE 328
                                       9*********976 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00013       0.4      12      61 ..     341     389 ..     339     391 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00013
                                       HHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTCE CS
                              GntR  12 dIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglverrqgrG 61 
                                       +Il+  +r G++  s+ eL+ ++ ++ +t+R+ L+ L + g++    + G
  gi|474933710|ref|YP_007687292.1| 341 QILKDMVRSGEPV-SQYELSVKYQTTVPTIRRDLIALLESGYISLAGKDG 389
                                       688888999****.***********************9999998777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       794  (0.0442858); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2618.27
//
Query:       gi|474933711|ref|YP_007687293.1|  [L=133]
Description: SSU ribosomal protein S6E [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-36  124.5   0.5    2.7e-36  124.3   0.5    1.0  1  Ribosomal_S6e  Ribosomal protein S6e


Domain annotation for each model (and alignments):
>> Ribosomal_S6e  Ribosomal protein S6e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.3   0.5   1.5e-40   2.7e-36       2     122 ..       5     122 ..       4     125 .. 0.98

  Alignments for each domain:
  == domain 1  score: 124.3 bits;  conditional E-value: 1.5e-40
                                       EEEEEETTTTEEEEEE-CHHHCTTCTT-BSSEEEECCTTTSSSTS-EEEEEEEEETTC-BB-TTS-SSSEEEEEEET CS
                     Ribosomal_S6e   2 klnisdpatgkqklievdekklrtligkrigeevdgdalGeelkgyvlkitggsdkqGfpmkqgvltpgrvrlLlsk 78 
                                       k++i d +tgk++++ v+++ +++l gk+ige vdg ++G  l+gy+l+itggsd +G+pm++++++++rv+lLls+
  gi|474933711|ref|YP_007687293.1|   5 KVVINDVKTGKSYNVTVSGNYANSLDGKNIGEIVDGIFVG--LPGYKLQITGGSDSTGTPMRKDLPGKKRVKLLLSD 79 
                                       99**************************************..*********************************** PP

                                       TSSSS-SSSSS-EEEEEEE-SB--SSEEEEEEEEEE--SS--TT CS
                     Ribosomal_S6e  79 ggvgyrprrkGerkrksvrGcivsadisqlnlvivkkgekdieg 122
                                        g+g+++  +Ger+++  rG+ +s++i+q+n++++++g k+ie+
  gi|474933711|ref|YP_007687293.1|  80 -GQGFHEIYQGERRKVAQRGSAISSEIVQINMKVTEYGGKSIEE 122
                                       .*****************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 800.71
//
Query:       gi|474933712|ref|YP_007687294.1|  [L=412]
Description: translation initiation factor 2 subunit gamma (aeIF-2g) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-29  102.5   0.1    2.5e-29  101.3   0.1    1.7  1  eIF2_C           Initiation factor eIF2 gamma, C terminal
    2.9e-29  102.0   0.4      2e-28   99.3   0.4    2.0  1  GTP_EFTU         Elongation factor Tu GTP binding domain
    1.5e-07   31.7   1.7    5.3e-07   29.9   1.7    2.0  1  GTP_EFTU_D2      Elongation factor Tu domain 2
    2.7e-05   24.1   0.5    0.00067   19.6   0.1    2.3  2  RsgA_GTPase      RsgA GTPase
    0.00039   20.2   0.3       0.16   11.7   0.0    2.4  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
     0.0019   18.3   0.0     0.0046   17.0   0.0    1.8  1  MMR_HSR1         50S ribosome-binding GTPase
     0.0045   16.3   0.3       0.25   10.7   0.1    2.5  2  zf-TFIIB         Transcription factor zinc-finger
     0.0068   16.4   0.2      0.016   15.2   0.2    1.6  1  MMR_HSR1_Xtn     C-terminal region of MMR_HSR1 domain
  ------ inclusion threshold ------
      0.034   14.5   0.2      0.069   13.5   0.2    1.4  1  DnaJ_CXXCXGXG    DnaJ central domain
      0.041   13.9   1.2        1.3    9.1   0.1    2.6  2  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
      0.078   12.4   0.2         13    5.3   0.0    2.4  2  zf_Rg            Reverse gyrase zinc finger
       0.22   11.1   0.8         15    5.2   0.0    2.4  2  TF_Zn_Ribbon     TFIIB zinc-binding
       0.38   11.1   2.1          1    9.7   0.1    2.2  2  Prim_Zn_Ribbon   Zinc-binding domain of primase-helicase
       0.67   10.4   3.3       0.93    9.9   0.2    2.2  2  Lar_restr_allev  Restriction alleviation protein Lar
       0.76    9.6   3.2        4.3    7.2   3.8    1.9  2  PADR1            PADR1 (NUC008) domain


Domain annotation for each model (and alignments):
>> eIF2_C  Initiation factor eIF2 gamma, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.3   0.1   2.1e-32   2.5e-29       2      86 .]     326     410 ..     325     410 .. 0.98

  Alignments for each domain:
  == domain 1  score: 101.3 bits;  conditional E-value: 2.1e-32
                                       EEEEEEEE-SBESSSSSCCC-----TTEEEEEEETTEEEEEEEEEEESSEEEEEEEEEEE-STTEEEEEEEEETTSE CS
                            eIF2_C   2 eleieyellerlvgvkeekkveklkkkEvLmlniGsastggvvtsvkkdeakvkLkkPvcaekgekialsRrvekrW 78 
                                       ++++++ ll+r+vg+ +e +v+++k++E+Lml++G+a+t+gvv+s++k +a+v+Lk Pvc+  g+++a+sRr++++W
  gi|474933712|ref|YP_007687294.1| 326 TFKMKTVLLDRVVGSASELDVDEIKSNEPLMLSVGTATTVGVVKSAHKGNADVALKLPVCILPGQRVAISRRISNKW 402
                                       5799************************************************************************* PP

                                       EEEEEEEE CS
                            eIF2_C  79 rLiGwGei 86 
                                       rLiG+G++
  gi|474933712|ref|YP_007687294.1| 403 RLIGYGIV 410
                                       ******86 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.3   0.4   1.7e-31     2e-28       4     191 ..       9     198 ..       6     201 .. 0.89

  Alignments for each domain:
  == domain 1  score: 99.3 bits;  conditional E-value: 1.7e-31
                                       EEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE................ CS
                          GTP_EFTU   4 rnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle................ 64 
                                       +nig+ighvDhGKtTLt +L    g            + +D+++eE +rgi+i    + +                 
  gi|474933712|ref|YP_007687294.1|   9 INIGMIGHVDHGKTTLTKALS---G------------EWTDRHSEEVKRGISIRLGYADVAfyrcpncegvaaygta 70 
                                       8******************98...1............2589999***********99999999************** PP

                                       ........TTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTB.STHHHHHHHHHHHHTTTE.EEEEEES CS
                          GTP_EFTU  65 ........ketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveG.vepqteevlrlalkegvp.iivfiNK 131
                                               + +  + ++++D+PGH+  + ++  g++ +Dga+l+v+a+e  ++pqt+e+l  ++  g+  i+++ NK
  gi|474933712|ref|YP_007687294.1|  71 kkcpvcggEAEFLRAVSFVDAPGHETLMATMLSGAALMDGALLLVAANERcPQPQTKEHLMALSIIGIDkIVIVQNK 147
                                       ****99877888999*********************************9879****************9899999** PP

                                       CGST.HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHH CS
                          GTP_EFTU 132 mDrl.kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvel 191
                                       +D + +++  +  +e+k ++      ++  +++   + p++++Sa +g +++ l++a+ ++
  gi|474933712|ref|YP_007687294.1| 148 IDLVtREQALQNYREIK-EF------VKGTVAE---NAPIIPVSAQSGVNIDMLIKAIEDN 198
                                       ****7566666667777.66......4444444...57*****************999876 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   1.7   4.4e-10   5.3e-07       1      62 [.     233     301 ..     233     310 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 4.4e-10
                                       EEEEEEEEEESEEETTEEEEEEC.TCTTSEE.........EEEEEEEEEEETEEESEEETTSEEEEEEEESS CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskke.........ivtrissletfhededeavaganaGvivaikg 62 
                                       G+v++g++++G+lk+Gde++i++  ++   e         i+ ++ sle+ +  ++e+ +g+ + +++ +++
  gi|474933712|ref|YP_007687294.1| 233 GGVIGGSLIQGKLKVGDEIEIVPgRKV---EvagkttyepITAKVVSLEAGERSVKEVLPGGLIAIGTQLDP 301
                                       89*******************997666...3566****************************9999988765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.12   1.4e+02     104     137 ..      13      43 ..       7      45 .. 0.77
   2 !   19.6   0.1   5.6e-07   0.00067      13     102 ..     105     200 ..      84     203 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.12
                                       EECSTTSSHHHHHHHHCTT-----S--------- CS
                       RsgA_GTPase 104 lvGqSGvGKStLinallpelelktgevseklgrG 137
                                       ++G+   GK+tL +al +e    t   se+ +rG
  gi|474933712|ref|YP_007687294.1|  13 MIGHVDHGKTTLTKALSGE---WTDRHSEEVKRG 43 
                                       6888899**********98...555555555555 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 5.6e-07
                                       EES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-.EEEEEEE-GGG--HHH......HHHHHHHHHHHTTSEEEE- CS
                       RsgA_GTPase  13 vaNvdqllivvslkepelslnlldrfLvlaeekgi.epvivlnKiDlleeee......eleelkeelealgyevllv 82 
                                       +a +d +l++v+++ +++ + + +  L+++   gi ++viv nKiDl+++e+      e++e+ + + a + +++ v
  gi|474933712|ref|YP_007687294.1| 105 AALMDGALLLVAAN-ERCPQPQTKEHLMALSIIGIdKIVIVQNKIDLVTREQalqnyrEIKEFVKGTVAENAPIIPV 180
                                       7889999******9.5566666677788888888878999************9998888888888888999****** PP

                                       -TTTHTTHHHHHHHCTTSEE CS
                       RsgA_GTPase  83 saktkegleelkellkdkts 102
                                       sa+++ +++ l ++++d+++
  gi|474933712|ref|YP_007687294.1| 181 SAQSGVNIDMLIKAIEDNIV 200
                                       *************9999876 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00013      0.16       4      24 ..      11      31 ..       9      38 .. 0.89
   2 !    6.1   0.1    0.0075       8.9      55     142 ..      99     196 ..      83     197 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                         PduV-EutP  4 illiGkvgsGKttLtqalkge 24
                                      i +iG+v+ GKttLt+al+ge
  gi|474933712|ref|YP_007687294.1| 11 IGMIGHVDHGKTTLTKALSGE 31
                                      568***************997 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0075
                         PduV-EutP  55 salivtsaeadvialvqdateeesvfppgfasvfnkeviGi....i..tkidlaedeenieavee...lLks..aGa 120
                                        ++ + +a  d  al++ a +e++  p++  ++++  +iGi    i   kidl++ e+++++ +e   ++k   a  
  gi|474933712|ref|YP_007687294.1|  99 ATMLSGAALMDG-ALLLVAANERCPQPQTKEHLMALSIIGIdkivIvqNKIDLVTREQALQNYREikeFVKGtvAEN 174
                                       444444444454.4455566677888899999999999996443322369999999888887655111454411344 PP

                         PduV-EutP 121 ekifevsavekegieellkyle 142
                                       + i+ vsa + ++i+ l+k +e
  gi|474933712|ref|YP_007687294.1| 175 APIIPVSAQSGVNIDMLIKAIE 196
                                       5589999999999999999886 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   3.8e-06    0.0046       1     100 [.      10     132 ..      10     180 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.8e-06
                                       EEEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEE...ETTEE.......................... CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvk...lkgke.......................... 47 
                                       +++ +G+   GK+tL +al+ge + + s++    + i+ g  +   +   +                          
  gi|474933712|ref|YP_007687294.1|  10 NIGMIGHVDHGKTTLTKALSGEwTDRHSEEVKRGISIRLGYADvafY---Rcpncegvaaygtakkcpvcggeaefl 83 
                                       5899*****************98666666666666666555442231...122355555666666777777777777 PP

                                       ..EEEEECGGCSSHHHHHHHHHHHHHHHHC.TSEEEEEEETTTTCSHHHHHHHHHH CS
                          MMR_HSR1  48 ..ielvDtpGliegaseekglgkaflalee.adlillvvdaseeklkpldeeleel 100
                                         + +vD pG  e       l  ++l+    +d +ll+v a+e+  +p+ +e    
  gi|474933712|ref|YP_007687294.1|  84 raVSFVDAPG-HE------TLMATMLSGAAlMDGALLLVAANERCPQPQTKEHLMA 132
                                       77********.44......6778888766657999999987744444444443333 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.1   0.00021      0.25      15      28 ..      51      64 ..      38      64 .. 0.85
   2 ?    3.0   0.0     0.055        66       1       9 [.      72      80 ..      72      88 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00021
                          zf-TFIIB 15 ggveidyCpqCrGv 28
                                       +v +++Cp+C+Gv
  gi|474933712|ref|YP_007687294.1| 51 ADVAFYRCPNCEGV 64
                                      799**********8 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.055
                          zf-TFIIB  1 kCPkCqdel 9 
                                      kCP+C+ e 
  gi|474933712|ref|YP_007687294.1| 72 KCPVCGGEA 80
                                      799999876 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.2   1.4e-05     0.016      58     100 ..     141     195 ..     138     200 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.4e-05
                      MMR_HSR1_Xtn  58 clyvlNKiDlisleeldelare............pnsvviSaekelnldeLkeki 100
                                        ++v NKiDl++ e+  + +re              ++++Sa++++n+d L ++i
  gi|474933712|ref|YP_007687294.1| 141 IVIVQNKIDLVTREQALQNYREikefvkgtvaenAPIIPVSAQSGVNIDMLIKAI 195
                                       68999*****98887766666556788889987668999************9988 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   5.8e-05     0.069       1      24 [.      58      80 ..      56     103 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.8e-05
                     DnaJ_CXXCXGXG  1 CkkCkGsgakkgkkktCktCkGsG 24
                                      C++C+G  a  g++k+C+ C+G+ 
  gi|474933712|ref|YP_007687294.1| 58 CPNCEGVAA-YGTAKKCPVCGGEA 80
                                      999999986.57788899999987 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1     0.089   1.1e+02      16      22 ..      53      60 ..      37      63 .. 0.80
   2 ?    9.1   0.1    0.0011       1.3       1      10 [.      72      81 ..      72      85 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.089
                    DNA_ligase_ZBD 16 ai.yRCtn 22
                                      ++ yRC+n
  gi|474933712|ref|YP_007687294.1| 53 VAfYRCPN 60
                                      55599999 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0011
                    DNA_ligase_ZBD  1 hCPvCGsavv 10
                                      +CPvCG +++
  gi|474933712|ref|YP_007687294.1| 72 KCPVCGGEAE 81
                                      6*****9987 PP

>> zf_Rg  Reverse gyrase zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.011        13       9      15 ..      57      63 ..      52      67 .. 0.86
   2 ?    4.7   0.0     0.017        20       8      18 ..      71      81 ..      69      86 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.011
                             zf_Rg  9 lCPNCgG 15
                                       CPNC+G
  gi|474933712|ref|YP_007687294.1| 57 RCPNCEG 63
                                      5*****9 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.017
                             zf_Rg  8 klCPNCgGdis 18
                                      k CP CgG+ +
  gi|474933712|ref|YP_007687294.1| 71 KKCPVCGGEAE 81
                                      78******976 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.2     0.033        39       1       8 [.      56      63 ..      55      66 .. 0.79
   2 ?    5.2   0.0     0.012        15       2      10 ..      72      80 ..      71      91 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.033
                                      EEETTTTC CS
                      TF_Zn_Ribbon  1 ykCPnCgs 8 
                                      y+CPnC +
  gi|474933712|ref|YP_007687294.1| 56 YRCPNCEG 63
                                      68999975 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.012
                                      EETTTTCEE CS
                      TF_Zn_Ribbon  2 kCPnCgstn 10
                                      kCP+Cg++ 
  gi|474933712|ref|YP_007687294.1| 72 KCPVCGGEA 80
                                      8*****964 PP

>> Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.2      0.61   7.3e+02       6      11 ..      58      63 ..      56      67 .. 0.85
   2 ?    9.7   0.1   0.00086         1       5      15 ..      72      82 ..      68      94 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.61
                                      -TTTT- CS
                    Prim_Zn_Ribbon  6 CPvCGG 11
                                      CP+C G
  gi|474933712|ref|YP_007687294.1| 58 CPNCEG 63
                                      ****77 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00086
                                      --TTTT-TTTE CS
                    Prim_Zn_Ribbon  5 pCPvCGGrDrF 15
                                       CPvCGG+  F
  gi|474933712|ref|YP_007687294.1| 72 KCPVCGGEAEF 82
                                      6******9766 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.3      0.33     4e+02       4      17 ..      56      69 ..      53      72 .. 0.79
   2 ?    9.9   0.2   0.00078      0.93       3      18 ..      70      85 ..      68     101 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.33
                   Lar_restr_allev  4 kpCPfCggravler 17
                                      + CP C g a +++
  gi|474933712|ref|YP_007687294.1| 56 YRCPNCEGVAAYGT 69
                                      78****99988776 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00078
                   Lar_restr_allev  3 LkpCPfCggravlers 18
                                       k CP Cgg+a+  r+
  gi|474933712|ref|YP_007687294.1| 70 AKKCPVCGGEAEFLRA 85
                                      699********98765 PP

>> PADR1  PADR1 (NUC008) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.2      0.35   4.2e+02      14      22 ..      56      63 ..      54      67 .. 0.74
   2 ?    7.2   3.8    0.0036       4.3       4      26 ..      61      82 ..      58      89 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.35
                             PADR1 14 ekCpeCkeg 22
                                       +Cp+C+ g
  gi|474933712|ref|YP_007687294.1| 56 YRCPNCE-G 63
                                      68****9.4 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0036
                             PADR1  4 vaDgmlfGalekCpeCkegqlvf 26
                                      +  + ++G  +kCp C+ g+ +f
  gi|474933712|ref|YP_007687294.1| 61 CEGVAAYGTAKKCPVCG-GEAEF 82
                                      777899***********.87776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      594  (0.0331307); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.70u 0.31s 00:00:01.01 Elapsed: 00:00:00.55
# Mc/sec: 2263.59
//
Query:       gi|474933713|ref|YP_007687295.1|  [L=104]
Description: putative PilT protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-16   60.4   0.0    2.2e-16   60.2   0.0    1.0  1  PIN_9          PIN like domain
    0.00024   21.4   0.0    0.00036   20.9   0.0    1.3  1  Fcf1           Fcf1
  ------ inclusion threshold ------
      0.081   13.0   0.1      0.099   12.7   0.1    1.2  1  Mut7-C         Mut7-C RNAse domain
      0.088   12.6   0.0        0.1   12.4   0.0    1.2  1  RNase_Zc3h12a  Zc3h12a-like Ribonuclease NYN domain
       0.13   12.2   0.0       0.16   11.9   0.0    1.0  1  Med19          Mediator of RNA pol II transcription subunit 1


Domain annotation for each model (and alignments):
>> PIN_9  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.2   0.0     6e-20   2.2e-16      16     115 ..       3      95 ..       1      96 [. 0.91

  Alignments for each domain:
  == domain 1  score: 60.2 bits;  conditional E-value: 6e-20
                             PIN_9  16 vdifeelerllgsvelvvpkavleELerlakagkgkertaakvalsLaerceiveaeeekaDdailelakeldaavl 92 
                                       +++ ++++ +lg+v++vvp + + EL++l      ++++ ak al+La+  eiv+ + + +Dda++e+a++ +  ++
  gi|474933713|ref|YP_007687295.1|   3 INLDAQVRNVLGDVRFVVPGPLIGELKHL-----TETNRHAKPALALARTKEIVQCD-SFGDDAVIEVAEREH-GYI 72 
                                       666678899********************.....5666789****************.************987.566 PP

                             PIN_9  93 vTnDreLkkrllekgipvilLRq 115
                                        TnD+eL++r++++ ip ++LR 
  gi|474933713|ref|YP_007687295.1|  73 LTNDKELRRRARKQLIPLLFLRS 95 
                                       6*********************6 PP

>> Fcf1  Fcf1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0     1e-07   0.00036      16      94 ..      28      97 ..      11     102 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1e-07
                                      HHHHHHCT..-HHHHHHHTTSEEE----SS---HHHHHHHHH-BTB-TT-EEEE-S-HHHHHHHHTSTT--EEEEE--E CS
                              Fcf1 16 iaeleklgkklkealkiaktferlkCnhkkptsaddClvsvvkkkknkkryivAtqDkdlrrrlrkipgvPilyikrsv 94
                                      +++l +++++ k al++a+t e ++C+       dd + +v + +  ++ y + t+Dk+lrrr+rk   +P+l++++++
  gi|474933713|ref|YP_007687295.1| 28 LKHLTETNRHAKPALALARTKEIVQCDS----FGDDAVIEVAE-R--EHGY-ILTNDKELRRRARKQ-LIPLLFLRSNT 97
                                      34555555778999*****99*****99....67888999888.3..4555.569**********95.69999987664 PP

>> Mut7-C  Mut7-C RNAse domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   2.8e-05     0.099      28      61 ..      55      88 ..      31     102 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.8e-05
                            Mut7-C 28 dvedeellalaakekrillTrdreLlkraklkkg 61
                                      ++ d+++++ a++e+  +lT d+eL +ra+++  
  gi|474933713|ref|YP_007687295.1| 55 SFGDDAVIEVAEREHGYILTNDKELRRRARKQLI 88
                                      357999**********************998754 PP

>> RNase_Zc3h12a  Zc3h12a-like Ribonuclease NYN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.8e-05       0.1      87     111 ..      53      77 ..      28      87 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.8e-05
                     RNase_Zc3h12a  87 svsyddrlilelAeekdGvivsndn 111
                                         s+ d  ++e+Ae++ G i++nd+
  gi|474933713|ref|YP_007687295.1|  53 CDSFGDDAVIEVAEREHGYILTNDK 77 
                                       56788999****************7 PP

>> Med19  Mediator of RNA pol II transcription subunit 19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   4.4e-05      0.16      93     160 ..      20      85 ..      10      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.4e-05
                             Med19  93 haGPlpeqyrllkkqePkkknkekhkkskvkdakseetlsdseteegfekkhkkkkkedDkerkkkkk 160
                                        +GPl  + ++l+++  +++ k  +   ++k+ ++ +++ d++  e  e+ h     +d + r++ +k
  gi|474933713|ref|YP_007687295.1|  20 VPGPLIGELKHLTET--NRHAKPALALARTKEIVQCDSFGDDAVIEVAEREHGYILTNDKELRRRARK 85 
                                       59**********999..8888999****************************9988555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 617.15
//
Query:       gi|474933714|ref|YP_007687296.1|  [L=276]
Description: putative methanogenesis marker protein 8 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.7e-92  307.3   1.0    7.5e-92  307.1   1.0    1.0  1  DUF2099      Uncharacterized protein conserved in archaea (DU
  ------ inclusion threshold ------
      0.083   13.1   0.0       0.21   11.8   0.0    1.6  1  FrhB_FdhB_N  Coenzyme F420 hydrogenase/dehydrogenase, beta su


Domain annotation for each model (and alignments):
>> DUF2099  Uncharacterized protein conserved in archaea (DUF2099)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  307.1   1.0   8.4e-96   7.5e-92       1     256 [.       5     255 ..       5     256 .. 0.98

  Alignments for each domain:
  == domain 1  score: 307.1 bits;  conditional E-value: 8.4e-96
                           DUF2099   1 HiiealgkarvvvkdgkvvevgepkikyCPlfkklrgikeitkeaikkniefrikefGlftkkRkleskedfvsfGa 77 
                                       H++e+lg+a vvv+dgk+ve+  p ++yCP+f+k+r+i++i+++a+++niefri++fGlft++R++++  d+v+fG+
  gi|474933714|ref|YP_007687296.1|   5 HVMEVLGMATVVVSDGKIVEMRPPVLRYCPMFNKMRNIETIDEDAVRQNIEFRIRDFGLFTEDRVVRAP-DIVTFGV 80 
                                       9********************************************************************.******* PP

                           DUF2099  78 sEilstalkeglidaavivcdgaGtvivtnpelvqglggrisGlveTePieevierieeeggivldketaeidqveG 154
                                       sEil +a+++g idaaviv+dg+G+ +vt+pe++qgl+grisG++eT+P++ v++ +++++  v+d++t+ idq++G
  gi|474933714|ref|YP_007687296.1|  81 SEILNKAIRDGKIDAAVIVADGCGSAVVTDPEVLQGLCGRISGIIETSPLNVVLDAVGRDN--VVDPRTTPIDQAAG 155
                                       *************************************************************..************** PP

                           DUF2099 155 vkkAiekgykkiavtvaeaedakklrelekeegvkilifavhttgiskeeaeelveaaDlvtacAskeireivkkk. 230
                                       ++ A++kg++k+avtv+++ da ++r+   + g +++i++vht+++++++ae+l++++D++tacAs  irei+ ++ 
  gi|474933714|ref|YP_007687296.1| 156 AALAFSKGFRKFAVTVSRPLDALAIRK---AFGDSAVIVGVHTSTLNRKQAEMLFDNCDFTTACASGPIREIMMSRk 229
                                       ***************************...6789*************************************987653 PP

                           DUF2099 231 allqvgksvpvfaltekGkelilerl 256
                                       ++l +g++v++ a+t+ Gk+l+ ++l
  gi|474933714|ref|YP_007687296.1| 230 DVLIAGNKVQIVAITDFGKDLVGSKL 255
                                       8999******************9887 PP

>> FrhB_FdhB_N  Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.3e-05      0.21      21      64 ..      80     118 ..      79     128 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.3e-05
                       FrhB_FdhB_N  21 vtallkylLeegiidgvivvapskdpwrpkpviattkeellaaa 64 
                                       v+++l ++ + g+id+++ va +        +++t++e l   +
  gi|474933714|ref|YP_007687296.1|  80 VSEILNKAIRDGKIDAAVIVADG-----CGSAVVTDPEVLQGLC 118
                                       899******************88.....5678888888776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1682.06
//
Query:       gi|474933715|ref|YP_007687297.1|  [L=159]
Description: Peptidyl-prolyl cis-trans isomerase (rotamase) - cyclophilin family [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-45  155.4   0.0    1.6e-45  155.2   0.0    1.0  1  Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans iso
  ------ inclusion threshold ------
      0.015   15.5   0.0      0.021   15.0   0.0    1.2  1  Tau95_N        Tau95 Triple barrel domain


Domain annotation for each model (and alignments):
>> Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.2   0.0   1.8e-49   1.6e-45       2     158 .]       4     157 ..       3     157 .. 0.93

  Alignments for each domain:
  == domain 1  score: 155.2 bits;  conditional E-value: 1.8e-49
                     Pro_isomerase   2 vdietsskGrivieLfadkaPktvenFlklvkegfYdgttFhRvikgfmvqgGdptgktsageqekkggesiraipd 78 
                                       v ++t+ +G+i++++++d  P+tv+nF+kl+k+gfYdgt+FhRvi+gfm+qgGdp+g++        gg   ++i+d
  gi|474933715|ref|YP_007687297.1|   4 VILHTN-MGDIALRMYDDM-PITVGNFVKLAKSGFYDGTIFHRVIDGFMIQGGDPEGTGC-------GG-PGYTIDD 70 
                                       668997.*********998.**********************************999855.......33.2469*** PP

                     Pro_isomerase  79 EitsklkhkrGalamartgkepnsagsqFfItlkeaphldg.......kytvFGkVveGmdvvekiekvetde.erp 147
                                       E  +  ++++G++ama+tg  p+s+gsqFfI+++++ +ld         + vFG+V++G+++v ki++v++++ +rp
  gi|474933715|ref|YP_007687297.1|  71 EKVKGHSNQPGTIAMANTG-RPHSGGSQFFINVADNGYLDWdnpstpyAHPVFGEVTQGYELVVKISEVPRSRnDRP 146
                                       ***9999***********8.6****************99999999999***************************** PP

                     Pro_isomerase 148 kknvkivsaev 158
                                        k+v+i++aev
  gi|474933715|ref|YP_007687297.1| 147 LKDVVIERAEV 157
                                       *******9975 PP

>> Tau95_N  Tau95 Triple barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   2.3e-06     0.021      43      73 ..     112     142 ..      95     156 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.3e-06
                                       -TT-TT---EE-EEE----EEEEE....... CS
                           Tau95_N  43 rpedpfshpilgeraptnnlllkvtvpkrtg 73 
                                       +p+ p++hp++ge+++ ++l++k++   r +
  gi|474933715|ref|YP_007687297.1| 112 NPSTPYAHPVFGEVTQGYELVVKISEVPRSR 142
                                       4889********************7543332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 965.38
//
Query:       gi|474933716|ref|YP_007687298.1|  [L=37]
Description: hypothetical protein TALC_00123 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.45   10.5   3.8       0.57   10.2   3.8    1.2  1  Fer4_5    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4_5  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   3.8   3.2e-05      0.57       2      21 ..      15      34 ..      14      35 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 3.2e-05
                            Fer4_5  2 allllilflaivlvtllfGR 21
                                      a ++++ ++a+++v++++G 
  gi|474933716|ref|YP_007687298.1| 15 AAVMIVAVVAVLVVSFVWGP 34
                                      678999999**********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1374  (0.0766356); expected 358.6 (0.02)
Passed bias filter:                      698  (0.0389313); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 266.78
//
Query:       gi|474933717|ref|YP_007687299.1|  [L=209]
Description: putative cobalamin binding protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00047   20.2   0.2     0.0011   19.0   0.2    1.6  1  B12-binding   B12 binding domain
  ------ inclusion threshold ------
      0.043   13.2   0.1      0.079   12.4   0.1    1.5  1  Aldolase      KDPG and KHG aldolase
      0.093   12.7   0.1       0.16   11.9   0.1    1.4  1  Fimbrial_K88  Fimbrial, major and minor subunit


Domain annotation for each model (and alignments):
>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.2   1.8e-07    0.0011       8     110 ..      87     186 ..      82     196 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.8e-07
                       B12-binding   8 vggdlhplGlavlaaalrdagfeVqllganvenedivaairae..kpdv.vgl.Salltsqleavkelvel..lkri 78 
                                        + d h+ G a+ a  l+ agf+V     +v+++ +++ ir++  +pdv v+  S+ + ++  + ke+ +    ++i
  gi|474933717|ref|YP_007687299.1|  87 CTVDNHTNGRALMALLLQVAGFDV----NEVSKDYVMDDIRRLcmDPDVhVCTaSSAFATTEVKLKEINQCliDAGI 159
                                       56799*******************....5677777888777776667775443344488888888888888****** PP

                       B12-binding  79 rprvkvvvGGahpsldpeetleaklgiddvvv 110
                                       r+r+   vGG ++s  ++e   +  g +dv  
  gi|474933717|ref|YP_007687299.1| 160 RDRIVFNVGGSPVSGFAAE---K-VG-ADVYA 186
                                       ***************9999...7.88.44333 PP

>> Aldolase  KDPG and KHG aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   1.3e-05     0.079       8      45 ..       4      41 ..       1      72 [. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.3e-05
                                      HSEEEEE--SSGGGHHHHHHHHHHTT--EEEEETTSTT CS
                          Aldolase  8 akvvpvivikdkedalplaeaLvagGlrvlevtlrtea 45
                                       +vv+ i   d e a+  a+ Lva G+ + +vt+rt  
  gi|474933717|ref|YP_007687299.1|  4 EEVVAFIENCDSESAVSAAKELVASGMDAQDVTVRTAE 41
                                      579999*****************************843 PP

>> Fimbrial_K88  Fimbrial, major and minor subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   2.7e-05      0.16      64     129 ..      47     111 ..      14     120 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.7e-05
                      Fimbrial_K88  64 iesaasqggvglspvvtittstgevevigpnmpqggitdvvldvtegtggdqvaslqmqisgvtag 129
                                       ie   + g vgl+p++ +  ++ +v      +p+ g   vv  v + t g  + +l +q++g    
  gi|474933717|ref|YP_007687299.1|  47 IEKKFTLGAVGLAPMMKVVKAANDVREALGTVPDFGK-AVVCTVDNHTNGRALMALLLQVAGFDVN 111
                                       7888899*****************9877778999996.69999******************98665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1311.28
//
Query:       gi|474933718|ref|YP_007687300.1|  [L=365]
Description: Prephenate dehydrogenase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      7e-60  202.2   0.0    9.2e-60  201.8   0.0    1.1  1  PDH             Prephenate dehydrogenase
    6.8e-07   29.6   0.0    2.3e-06   27.9   0.0    1.9  2  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    4.6e-06   27.1   0.0    0.00071   20.1   0.0    2.8  3  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
    0.00014   22.4   0.4     0.0005   20.6   0.4    1.9  1  ACT_4           ACT domain
    0.00094   19.6   0.0     0.0028   18.1   0.0    1.8  1  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai
     0.0038   16.6   0.0     0.0073   15.7   0.0    1.5  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
  ------ inclusion threshold ------
       0.12   12.2   0.2        2.5    8.0   0.1    2.5  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 


Domain annotation for each model (and alignments):
>> PDH  Prephenate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.8   0.0   3.6e-63   9.2e-60       1     256 [.      17     273 ..      17     275 .. 0.96

  Alignments for each domain:
  == domain 1  score: 201.8 bits;  conditional E-value: 3.6e-63
                                       HHHHHHHT.T--SEEEEE-SSHHHHHHHHHTTSSSEEES-.GGGGCCGSEEEE-S-GGGHHHHHHHHHHHS-TT-EE CS
                               PDH   1 laralrrk.gfkvtvigydideekaeaalelglvdeatdd.ieavkeadivvlavPvevilevlkelaphlkedali 75 
                                       +ara +++   +v++   d d ++   a e g+ d    d     +++d v+l+ P++  +e ++ l p lk +a++
  gi|474933718|ref|YP_007687300.1|  17 IARAFKANpEADVKIKAFDSDRKAVTLAFEEGVTDVMVSDiGPDFSDCDYVFLCAPIDFNIENAERLRPYLKDGAVL 93 
                                       57777766245899**************************5579********************************* PP

                                       EE--S--CHHHHHHHHHCC..GCEEEEEES---S-SSGGG--TTTTTT-EEEEEE-TTS-HHHHHHHHHHHHHCT-E CS
                               PDH  76 tDvgsvKekvvreleellkegksfvgghPmaGteksGvdaareelfenavviLtPtektdkealekvkelleevgar 152
                                       tDvgs+K  ++  +++l     +f+gghPmaG+e  G ++++++l+ena +i+t t +t    +e    l++ +ga 
  gi|474933718|ref|YP_007687300.1|  94 TDVGSIKGPMHARIHALGL-DGRFIGGHPMAGSERTGFANSKAKLLENAYYIITRTPETTDAMVERYEGLVRMMGAI 169
                                       *****************99.789***********************************999**************** PP

                                       EEE--HHHHHHHHHHHTHHHHHHHHHHHHHHHCHHCCCCHHHHCGTCCHHHHHCGGGS-HHHHHHHHHHTHHHHHHH CS
                               PDH 153 vilmspeeHDrvvavvshlphvvaialaatlkekkndekeirklasggfrdvtRiaksnPelwadilleNkeavlea 229
                                         +m+peeHD+++a vsh+phv++++l++ +  + n e e+r  a+ggf+d+tRi++s+P++w++i l N e++ + 
  gi|474933718|ref|YP_007687300.1| 170 PLVMTPEEHDYITAAVSHVPHVISASLVNLVRDSDNPEGEMRMIAAGGFKDITRISSSSPAMWQQICLGNSENITKL 246
                                       *****************************999999****************************************** PP

                                       HHHHHHHHHHHHHHHHTT-HHHHHHHH CS
                               PDH 230 ldkfikelkklkelienedaeeLvell 256
                                       l ++i+ l++++  i ++d ++L++ +
  gi|474933718|ref|YP_007687300.1| 247 LGDYIARLTEIRDGIVSGDSDSLLRFF 273
                                       ***********************9987 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   8.9e-10   2.3e-06       1     101 [.       4     108 ..       4     128 .. 0.88
   2 ?   -2.5   0.0         2   5.2e+03      26      43 ..     143     163 ..     133     196 .. 0.60

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 8.9e-10
                                       EEEEE--SHHHHHHHHHH...HHTT-EEEEE-SSHHHHHHHHHTT..EEE-SSHHHHHHHCSEEEE-SSSHHHHHHH CS
                     NAD_binding_2   1 kigfiGlGvMGsnmalnl...lkagykvavynrtkekveelvaeg..akaaesieelvasldvvitmvkagkavdev 72 
                                       +igfiGlG +G ++a+ +    +a+ k+ +++ ++++v+ + +eg   +++++i   ++++d v+++ + + ++++ 
  gi|474933718|ref|YP_007687300.1|   4 TIGFIGLGLIGGSIARAFkanPEADVKIKAFDSDRKAVTLAFEEGvtDVMVSDIGPDFSDCDYVFLCAPIDFNIEN- 79 
                                       69****************54448999******************96556889999999***********9999876. PP

                                       HHSHCCC--TT-EEEE-S---HHHHHHHH CS
                     NAD_binding_2  73 iegllealkkgdilidgstsspedtrela 101
                                        e+l ++lk g++l d+++++     +++
  gi|474933718|ref|YP_007687300.1|  80 AERLRPYLKDGAVLTDVGSIKGPMHARIH 108
                                       688*****************988777776 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2
                                       EEE-SSHHHHHHHHHTT...E CS
                     NAD_binding_2  26 avynrtkekveelvaeg...a 43 
                                       +++ rt+e ++++v++    +
  gi|474933718|ref|YP_007687300.1| 143 YIITRTPETTDAMVERYeglV 163
                                       556677777777776643442 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   2.8e-07   0.00071       1      93 [.       4      95 ..       4      98 .. 0.81
   2 ?    3.9   0.0     0.032        81       4      48 ..     116     163 ..     115     202 .. 0.75
   3 ?   -1.7   0.0       1.8   4.7e+03      18      64 ..     315     362 ..     309     364 .. 0.56

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.8e-07
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHH CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevls 79
                                      +ig+iG G +g ++a+ + a+ +++ +i  a +++ + ++ + ee   +v+ +d     +++d v+l+ +     e ++
  gi|474933718|ref|YP_007687300.1|  4 TIGFIGLGLIGGSIARAFKANPEADVKIK-AFDSDRKAVTLAFEEGVTDVMVSDIGPDFSDCDYVFLCAPIDFNIENAE 81
                                      69**************9999976666777.656666666666677778999999999999************9999999 PP

                                      HCGHHHHTTSEEEE CS
                     F420_oxidored 80 elakdalkgklvis 93
                                       l++ ++ g ++ +
  gi|474933718|ref|YP_007687300.1| 82 RLRPYLKDGAVLTD 95
                                      99777777777665 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.032
                                       EETTSHHHHHHHHHHHHTTS.-GGCEEEEEESSCCCHHHHHHHHC..- CS
                     F420_oxidored   4 iiGaGnmgealasgllaaga.qpheivvansrnpekaeelaeelg..v 48 
                                       +iG+  m+ +   g++++ a   ++ + + +r+pe+ +++ e+++  v
  gi|474933718|ref|YP_007687300.1| 116 FIGGHPMAGSERTGFANSKAkLLENAYYIITRTPETTDAMVERYEglV 163
                                       7888889999999999999995555555669************99552 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.8
                                       HHHTTS-GGCEEEEEESSCCCHHHHHHHHC..-EEECECHHHHHHH-SE CS
                     F420_oxidored  18 llaagaqpheivvansrnpekaeelaeelg..vkvtavdneeaaeeadv 64 
                                       ++++g + +++ ++ +r+ e+  +l+ el    +v++v+   aa+  dv
  gi|474933718|ref|YP_007687300.1| 315 IASRGIDVKNVGIIHNREVETG-SLRIELHdeKDVKTVHDMLAAKGYDV 362
                                       5566777788888877776653.22222222245555556666666665 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.4     2e-07    0.0005       9      69 ..     297     355 ..     294     358 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2e-07
                             ACT_4   9 leveaedrkglLaditqviseekanivsvnaktrkkdglaeikitveVkdvehLsrviakL 69 
                                       ++ve  d++g+La +++ i++ ++++++v + +++  ++ ++++++e++d +++++v + L
  gi|474933718|ref|YP_007687300.1| 297 VHVEIPDEPGALAIVVTMIASRGIDVKNVGIIHNR--EVETGSLRIELHDEKDVKTVHDML 355
                                       68999****************************64..699*************99998766 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.1e-06    0.0028       2      95 ..       5      95 ..       4      99 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.1e-06
                                      EEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SCHHHHH CS
                    Semialdhyde_dh  2 vaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeelkevdivflalpagvsk 80
                                      ++++G  G +G  ++r  + +pe+++   +  s  +  +la+     e+++d+ v+d    +++++d+vfl++p +   
  gi|474933718|ref|YP_007687300.1|  5 IGFIG-LGLIGGSIARAFKANPEADVKIKAFDSDRKAVTLAFE----EGVTDVMVSD-IGPDFSDCDYVFLCAPIDFNI 77
                                      78999.9****************99987666666578888888....569*******.778999************999 PP

                                      HHHHHH...HHTTSEEEE CS
                    Semialdhyde_dh 81 elapkl...aeagvkviD 95
                                      e a++l   ++ g+++ D
  gi|474933718|ref|YP_007687300.1| 78 ENAERLrpyLKDGAVLTD 95
                                      999998555666666555 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.9e-06    0.0073      37     102 ..       3      74 ..       1      98 [. 0.76

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.9e-06
                                       SEEEEES-SHHHHHHHHHHH...HTT-EEEEESSSHHHHH...CHHHHTCEECSHHHHHHH-SEEEE-S--S CS
                      2-Hacid_dh_C  37 ktvGiiGlGrIGqavakrlk...afgmkviaydrskkkee...eeeelgvelvsleellaesDivslhlplt 102
                                        t+G iGlG IG ++a+ +k   + ++k+ a+d  +k+ +   ee  + v + ++   ++++D+v+l++p+ 
  gi|474933718|ref|YP_007687300.1|   3 VTIGFIGLGLIGGSIARAFKanpEADVKIKAFDSDRKAVTlafEEGVTDVMVSDIGPDFSDCDYVFLCAPID 74 
                                       599****************95555899********998886444444444455777779*********9975 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1   0.00097       2.5       1      36 [.       4      42 ..       4      55 .. 0.72
   2 ?    1.3   0.0      0.11   2.7e+02     149     177 ..     145     173 ..     133     176 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00097
                                      EEEEE--SCCHHHHHHHHHHT...T-EEEEE-S-HHHHH CS
                           3HCDH_N  1 kvaviGaGtmGagiaavfasa...gleVvlvdiseeale 36
                                      +++ iG G++G +ia +f ++   +++++ +d +++a++
  gi|474933718|ref|YP_007687300.1|  4 TIGFIGLGLIGGSIARAFKANpeaDVKIKAFDSDRKAVT 42
                                      5899************99765422455555566666555 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.11
                                       EEE-TT--HHHHHHHHHHHHHTT-EEEEE CS
                           3HCDH_N 149 vvrgekTseetvatvvelakkigktpvvv 177
                                       + r+++T +++v++   l++ +g  p v+
  gi|474933718|ref|YP_007687300.1| 145 ITRTPETTDAMVERYEGLVRMMGAIPLVM 173
                                       56899******************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.58
# Mc/sec: 1893.40
//
Query:       gi|474933719|ref|YP_007687301.1|  [L=205]
Description: hypothetical protein TALC_00126 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0011   18.6   3.1     0.0011   18.6   3.1    2.9  2  L6_membrane      L6 membrane protein
  ------ inclusion threshold ------
      0.018   15.4   0.6      0.018   15.4   0.6    3.3  3  DUF308           Short repeat of unknown function (DUF308)
      0.049   13.1  20.3      0.081   12.4   6.4    2.8  3  DUF1129          Protein of unknown function (DUF1129)
      0.055   13.7   0.6      0.055   13.7   0.6    4.5  5  Chordopox_A13L   Chordopoxvirus A13L protein
       0.38   10.4  11.8      0.038   13.6   2.1    2.7  2  DUF5336          Family of unknown function (DUF5336)
        1.7    8.4  30.9         33    4.2  30.9    2.2  1  Yip1             Yip1 domain
        8.4    4.7   6.3       0.75    8.1   1.6    1.6  2  DUF515           Protein of unknown function (DUF515)


Domain annotation for each model (and alignments):
>> L6_membrane  L6 membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   3.1   4.4e-07    0.0011       7     102 ..       7     101 ..       1     112 [. 0.80
   2 ?   -2.9   7.4       1.7   4.2e+03       4      32 ..     136     164 ..     133     193 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 4.4e-07
                       L6_membrane   7 akclGlsLlplallsivaNilllfpngkteylkeekiskevwlfgGilGgGllvllpaivilllgkkracscgnrck 83 
                                       +k  Gl+L++ a+lsi+  ill++  + ++++ke++i   +  +g ++ g +++ +  ++ +  + +++ +  +r+ 
  gi|474933719|ref|YP_007687301.1|   7 TKNAGLALYIAAILSIIGAILLIVCAFVDDDMKEDDIGWAIQGVGDLICGFIMLGFGKMIKSG-ELSDKFDIVTRFV 82 
                                       6778**********************************9988888888766666654444333.3333356888999 PP

                       L6_membrane  84 mllsillavlgvlGalycl 102
                                       m++++++ + g++ a+ c+
  gi|474933719|ref|YP_007687301.1|  83 MVVAMVTIIGGIFTAISCI 101
                                       9998888888888888886 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.7
                       L6_membrane   4 ekcakclGlsLlplallsivaNilllfpn 32 
                                       +++ +++ ++Ll++ ++ i++N l lf  
  gi|474933719|ref|YP_007687301.1| 136 GTFDRIMWIILLVIFVIMIILNFLALFGA 164
                                       67778888999999999999999988865 PP

>> DUF308  Short repeat of unknown function (DUF308)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.6   6.9e-06     0.018      25      72 ..      14      60 ..       4      61 .. 0.78
   2 ?   10.2   8.4   0.00028      0.71      24      73 .]      81     125 ..      75     125 .. 0.82
   3 ?   -2.8  12.8       3.3   8.4e+03      30      71 ..     148     186 ..     137     189 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.9e-06
                            DUF308 25 vllfGilllvsGivqiiaafaarkknrggrwlglllGilyliaGllll 72
                                       ++ +il ++++i+ i+ af   +  +   + + + G+  li+G+++l
  gi|474933719|ref|YP_007687301.1| 14 LYIAAILSIIGAILLIVCAFVDDD-MKEDDIGWAIQGVGDLICGFIML 60
                                      578888889999999998885555.5555555566***********98 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00028
                            DUF308  24 lvllfGilllvsGivqiiaafaarkknrggrwlglllGilyliaGllllf 73 
                                       +v++++++ +++Gi+  i+ + + +   +g +    +Gi+++i+Gl++ f
  gi|474933719|ref|YP_007687301.1|  81 FVMVVAMVTIIGGIFTAISCIGFDD---KGAV--AGSGIVSIIIGLIIYF 125
                                       799***************9995555...4433..459**********976 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 3.3
                            DUF308  30 illlvsGivqiiaafaarkknrggrwlglllGilyliaGlll 71 
                                       +++++  i++++a f a ++    + l +++++++ i+G+++
  gi|474933719|ref|YP_007687301.1| 148 VIFVIMIILNFLALFGAFGYD---GALAIVVALISAICGIII 186
                                       334444444444444333444...45788***********98 PP

>> DUF1129  Protein of unknown function (DUF1129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   6.4   3.2e-05     0.081      83     194 ..      15     127 ..       5     130 .. 0.83
   2 ?    5.6   9.5    0.0037       9.5     118     169 ..     114     165 ..     103     190 .. 0.57
   3 ?    2.1   7.5     0.046   1.2e+02      86     142 ..     149     201 ..     141     205 .] 0.59

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.2e-05
                           DUF1129  83 DnsLlllalfallfgilalfskkkqtasiGlitlllvalvgGlamvlvyrlltrekkkkkrpplwkrllilllllvv 159
                                       + + +l ++ a+l  + a+++++ ++ +iG     +  l+ G++m+ + ++++   + +++  ++ r++++++++ +
  gi|474933719|ref|YP_007687301.1|  15 YIAAILSIIGAILLIVCAFVDDDMKEDDIGWAIQGVGDLICGFIMLGFGKMIKS-GELSDKFDIVTRFVMVVAMVTI 90 
                                       4444444555555555566666666666************************97.********************** PP

                           DUF1129 160 wlvlftlval..lpaviNpvLpplvliiigviafvvr 194
                                       +  +ft+++   +  +  +  + +v+iiig i+++++
  gi|474933719|ref|YP_007687301.1|  91 IGGIFTAISCigFDDKGAVAGSGIVSIIIGLIIYFIY 127
                                       ******9999677899999999**********99886 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0037
                           DUF1129 118 lvalvgGlamvlvyrlltre.kkkkkrpplwkrllilllllvvwlvlftlval 169
                                       +v+++ Gl+++++y+ +t++   + +r+ +w +ll+++++++++ +l ++ a+
  gi|474933719|ref|YP_007687301.1| 114 IVSIIIGLIIYFIYTKITNDsVGTFDRI-MWIILLVIFVIMIILNFLALFGAF 165
                                       6899**************9643444444.444444444444444443333333 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.046
                           DUF1129  86 LlllalfallfgilalfskkkqtasiGlitlllvalvgGlamvlvyrlltrekkkkk 142
                                        ++++++  + +++++f+      +   i+++l++++ G+++++++++++ + + k 
  gi|474933719|ref|YP_007687301.1| 149 IFVIMIILNFLALFGAFGY---DGAL-AIVVALISAICGIIIYIFMTIFMLDGDVKA 201
                                       2333333344455555554...3322.256778999999999999999987655554 PP

>> Chordopox_A13L  Chordopoxvirus A13L protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   1.0       0.5   1.3e+03       5      14 ..      25      34 ..      21      35 .. 0.79
   2 ?   -2.1   2.0       1.8   4.7e+03       2      19 ..      78      95 ..      77      99 .. 0.70
   3 ?   13.7   0.6   2.2e-05     0.055      10      30 ..     114     134 ..     112     137 .. 0.87
   4 ?   -3.6   3.9       5.3   1.4e+04       5      17 ..     144     156 ..     140     162 .. 0.70
   5 ?   -4.5   5.3         7   1.8e+04       8      20 ..     175     187 ..     170     192 .. 0.58

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.5
                    Chordopox_A13L  5 lllliiCvai 14
                                      ++lli+C+ +
  gi|474933719|ref|YP_007687301.1| 25 AILLIVCAFV 34
                                      7999***865 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.8
                    Chordopox_A13L  2 iadlllliiCvaivgliv 19
                                      ++ +++++  v i+g i 
  gi|474933719|ref|YP_007687301.1| 78 VTRFVMVVAMVTIIGGIF 95
                                      567888888888888765 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 2.2e-05
                    Chordopox_A13L  10 iCvaivglivYgiYnrkketq 30 
                                       i  +i+gli+Y iY+++++ +
  gi|474933719|ref|YP_007687301.1| 114 IVSIIIGLIIYFIYTKITNDS 134
                                       6679*************9875 PP

  == domain 4  score: -3.6 bits;  conditional E-value: 5.3
                    Chordopox_A13L   5 lllliiCvaivgl 17 
                                       ++ll+i v+++ l
  gi|474933719|ref|YP_007687301.1| 144 IILLVIFVIMIIL 156
                                       6777777777655 PP

  == domain 5  score: -4.5 bits;  conditional E-value: 7
                    Chordopox_A13L   8 liiCvaivglivY 20 
                                       +++  ai g+i+Y
  gi|474933719|ref|YP_007687301.1| 175 VALISAICGIIIY 187
                                       4444455566665 PP

>> DUF5336  Family of unknown function (DUF5336)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.3     0.024        61     105     126 ..      16      37 ..       9      58 .. 0.77
   2 ?   13.6   2.1   1.5e-05     0.038      51     147 ..      59     155 ..      46     166 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.024
                           DUF5336 105 vaAvlsvlgfLlvlaevinape 126
                                       +aA+ls++g++l++   +  ++
  gi|474933719|ref|YP_007687301.1|  16 IAAILSIIGAILLIVCAFVDDD 37 
                                       79********999988876653 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 1.5e-05
                           DUF5336  51 llgFgplltvsassadleeasatsgglglavvllLlagLlAgvslLPkqks.ktavaAvlsvlgfL..lvlaevina 124
                                       +lgFg++++  + s    ++++++  +++  ++++++g++ ++s +   ++  +a   ++s++  L   ++++ i+ 
  gi|474933719|ref|YP_007687301.1|  59 MLGFGKMIKSGELS---DKFDIVTRFVMVVAMVTIIGGIFTAISCIGFDDKgAVAGSGIVSIIIGLiiYFIYTKITN 132
                                       68999999888877...67777777777778899************9776213334457787644412578899999 PP

                           DUF5336 125 pegvsiawglwvvlvlallqaaa 147
                                       ++  + + ++w++l ++++ +++
  gi|474933719|ref|YP_007687301.1| 133 DSVGTFDRIMWIILLVIFVIMII 155
                                       999999********999998876 PP

>> Yip1  Yip1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2  30.9     0.013        33      13     153 ..       8     195 ..       1     201 [. 0.56

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.013
                              Yip1  13 kkeppilrapdlallllalltlllgllas...........lnlgqtlasg........................... 51 
                                       k ++        al ++a+l+++ ++l+              +g+ +++                            
  gi|474933719|ref|YP_007687301.1|   8 KNAGL-------ALYIAAILSIIGAILLIvcafvdddmkeDDIGWAIQGVgdlicgfimlgfgkmiksgelsdkfdi 77 
                                       44444.......44444444444444444444677777773333333333455555555555555555566665544 PP

                              Yip1  52 ..eevqgltlssllgaiiggylgl................llgllllalllhl.iakllg.gkgsfkqtlsvvgya. 107
                                         ++v++ + ++++g+    +++                 +   ++++l++++   k+   + g+f +++ ++ +  
  gi|474933719|ref|YP_007687301.1|  78 vtRFVMVVAMVTIIGG----IFTAiscigfddkgavagsgI-VSIIIGLIIYFiYTKITNdSVGTFDRIMWIILLVi 149
                                       4422222222222222....222233334455555555532.2222222222212233335**************99 PP

                              Yip1 108 llPlilgaliaillllllgtllllvgllaliWslvllylglkaahn 153
                                       ++++i++ ++a++ ++ ++++l++v++l+++ + +++y+++ +++ 
  gi|474933719|ref|YP_007687301.1| 150 FVIMIILNFLALFGAFGYDGALAIVVALISAICGIIIYIFMTIFML 195
                                       9999999999999888888899999999999999999999988775 PP

>> DUF515  Protein of unknown function (DUF515)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   1.6   0.00029      0.75      33      59 ..     109     135 ..     104     140 .. 0.89
   2 ?   -2.9   0.2      0.67   1.7e+03      33      46 ..     144     157 ..     134     163 .. 0.52

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00029
                            DUF515  33 iiGasvlvvivillvfaiYsyienkel 59 
                                       + G+ ++++i++l+ + iY++i n  +
  gi|474933719|ref|YP_007687301.1| 109 VAGSGIVSIIIGLIIYFIYTKITNDSV 135
                                       67999******************9876 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.67
                            DUF515  33 iiGasvlvvivill 46 
                                       ii  ++ v+++il 
  gi|474933719|ref|YP_007687301.1| 144 IILLVIFVIMIILN 157
                                       44234444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1571  (0.0876234); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                       115  (0.00641419); expected 17.9 (0.001)
Passed Fwd filter:                        50  (0.00278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.90u 0.36s 00:00:01.26 Elapsed: 00:00:00.57
# Mc/sec: 1087.22
//
Query:       gi|474933720|ref|YP_007687302.1|  [L=277]
Description: Indolepyruvate ferredoxin oxidoreductase, alpha and beta subunits [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-14   51.0  10.3    5.3e-07   29.2   2.0    2.8  2  Fer4      4Fe-4S binding domain
    1.7e-07   31.7  11.0    1.7e-07   31.7  11.0    2.4  1  Fer4_7    4Fe-4S dicluster domain
    4.6e-07   29.9  22.2      9e-06   25.8  11.5    2.6  3  Fer4_9    4Fe-4S dicluster domain
    2.9e-06   27.3   8.3    2.9e-06   27.3   8.3    2.6  2  Fer4_21   4Fe-4S dicluster domain
    2.1e-05   24.4  10.8     0.0016   18.5   1.8    3.1  2  Fer4_6    4Fe-4S binding domain
    7.9e-05   22.7   0.3    7.9e-05   22.7   0.3    3.2  3  Fer4_10   4Fe-4S dicluster domain
    0.00073   20.4   6.5     0.0027   18.6   0.9    3.4  3  Fer4_16   4Fe-4S double cluster binding domain
     0.0015   18.5  12.3       0.01   15.9   1.9    3.3  2  Fer4_2    4Fe-4S binding domain
     0.0039   17.4   4.0     0.0039   17.4   4.0    1.8  1  Fer4_18   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.014   16.2   1.6      0.014   16.2   1.6    3.3  2  Fer4_22   4Fe-4S dicluster domain
        7.3    7.4  20.2         12    6.7  11.6    3.4  4  Fer4_15   4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   2.0   3.2e-10   5.3e-07       2      24 .]     205     227 ..     204     227 .. 0.93
   2 !   25.8   1.4   3.8e-09   6.1e-06       3      24 .]     235     256 ..     233     256 .. 0.90

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 3.2e-10
                                       EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                        +d+ kC+gCG Cve C v AI+
  gi|474933720|ref|YP_007687302.1| 205 SVDPGKCTGCGFCVELCFVRAIS 227
                                       69*******************95 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 3.8e-09
                                       EETTTSSS-THHHHHSTTTEEE CS
                              Fer4   3 ideekCigCGaCvevCPvgAIt 24 
                                        +  kC gCG+C e CP +AI+
  gi|474933720|ref|YP_007687302.1| 235 LNDAKCRGCGRCSEQCPSEAIS 256
                                       5788****************96 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7  11.0     1e-10   1.7e-07       1      52 []     210     254 ..     210     254 .. 0.94

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 1e-10
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       +C+gCg+Cv+ C v+ai++++        k+e++  kC gCg+C + CP++a
  gi|474933720|ref|YP_007687302.1| 210 KCTGCGFCVELCFVRAISVRDG-------KAELNDAKCRGCGRCSEQCPSEA 254
                                       7******************774.......789*****************986 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3  13.5     0.058        95       5      50 ..     173     225 ..     171     226 .. 0.69
   2 !   25.8  11.5   5.5e-09     9e-06       1      51 []     210     255 ..     210     255 .. 0.93
   3 !   17.2   2.8   2.7e-06    0.0043       1      26 [.     239     264 ..     239     270 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.058
                            Fer4_9   5 CgaCveaCpagvvvedaaerkarlraase........eaCigCgaCveaCpkga 50 
                                       C+ C + C  + + +d  +++  + ++ +         +C+gCg Cve C   a
  gi|474933720|ref|YP_007687302.1| 173 CN-CCPCCCLWNIARDIDPGISDVYRRLDgvtvsvdpGKCTGCGFCVELCFVRA 225
                                       66.666666666655555555555554446899999999***********7665 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 5.5e-09
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       kCtgCg Cve C   +++ ++++ + +       +C gCg+C e Cp++ai
  gi|474933720|ref|YP_007687302.1| 210 KCTGCGFCVELCFVRAISVRDGKAELNDA-----KCRGCGRCSEQCPSEAI 255
                                       7****************999999998874.....6*************987 PP

  == domain 3  score: 17.2 bits;  conditional E-value: 2.7e-06
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerka 26 
                                       kC gCg+C e+Cp+++++ +  +  +
  gi|474933720|ref|YP_007687302.1| 239 KCRGCGRCSEQCPSEAISISYDTSVI 264
                                       7**************99988877665 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3  17.0      0.75   1.2e+03      11      57 ..     173     226 ..     167     228 .. 0.63
   2 !   27.3   8.3   1.8e-09   2.9e-06       3      58 ..     206     256 ..     204     257 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.75
                           Fer4_21  11 CgkCliaCedtshqai.........eidaktvlkvvedeCvGCnlCssvCPvedci 57 
                                       C+ C   C  +    i         ++d+  ++ v   +C+GC  C++ C v  +i
  gi|474933720|ref|YP_007687302.1| 173 CNCCPCCCLWNIARDIdpgisdvyrRLDG-VTVSVDPGKCTGCGFCVELCFV-RAI 226
                                       66666666666666564443332212222.23366788************98.565 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 1.8e-09
                           Fer4_21   3 idedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58 
                                       +d+ kC gCg C+  C    + ai++  + ++++ + +C GC  Cs+ CP +++i+
  gi|474933720|ref|YP_007687302.1| 206 VDPGKCTGCGFCVELCF---VRAISVR-DGKAELNDAKCRGCGRCSEQCP-SEAIS 256
                                       8999*************...89**997.555699****************.58886 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   1.8   9.5e-07    0.0016       2      22 ..     204     224 ..     203     226 .. 0.85
   2 !   18.2   2.0   1.1e-06    0.0018       5      24 .]     236     255 ..     232     255 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 9.5e-07
                            Fer4_6   2 veidpdkCigCgdCvrvCPeg 22 
                                       v +dp kC+gCg Cv  C   
  gi|474933720|ref|YP_007687302.1| 204 VSVDPGKCTGCGFCVELCFVR 224
                                       88*************999655 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 1.1e-06
                            Fer4_6   5 dpdkCigCgdCvrvCPegai 24 
                                       ++ kC gCg+C   CP  ai
  gi|474933720|ref|YP_007687302.1| 236 NDAKCRGCGRCSEQCPSEAI 255
                                       789*************9998 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   2.3       4.6   7.5e+03      29      51 ..     120     142 ..      92     144 .. 0.50
   2 ?    3.6  12.4     0.044        72      15      55 ..     176     221 ..     171     222 .. 0.67
   3 !   22.7   0.3   4.8e-08   7.9e-05       2      24 ..     233     257 ..     232     275 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.6
                           Fer4_10  29 kgeaseeeavrkkvekCtgcgaC 51 
                                       + + s+ ++  ++ e+C+++ +C
  gi|474933720|ref|YP_007687302.1| 120 QSIPSKYGHFADAEEACDFIDEC 142
                                       33333334444445677777777 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.044
                           Fer4_10  15 CvkaCPadl.......tsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                       C   C   +        + +  + + ++ +v+++++kCtgcg Cve C
  gi|474933720|ref|YP_007687302.1| 176 CPCCCL--WniardidPGISDVYRRLDGVTVSVDPGKCTGCGFCVELC 221
                                       444442..1456666545555566777778888999999999999999 PP

  == domain 3  score: 22.7 bits;  conditional E-value: 4.8e-08
                           Fer4_10   2 vvidddtCirCgkCvkaCPadl..t 24 
                                       ++++d +C +Cg+C + CP+ +   
  gi|474933720|ref|YP_007687302.1| 233 AELNDAKCRGCGRCSEQCPSEAisI 257
                                       67899***************66442 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   3.9       3.3   5.4e+03      52      67 .]     167     183 ..     126     183 .. 0.76
   2 !   12.2   0.5   0.00016      0.27       1      20 [.     210     229 ..     210     238 .. 0.82
   3 !   18.6   0.9   1.6e-06    0.0027       1      20 [.     239     258 ..     239     273 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 3.3
                           Fer4_16  52 eai.tgCdiCqdvCPan 67 
                                       +++ t C+ C  +C +n
  gi|474933720|ref|YP_007687302.1| 167 KDLlTICNCCPCCCLWN 183
                                       333499****9999998 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00016
                           Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                       +C++Cg C+e C ++ai+ +
  gi|474933720|ref|YP_007687302.1| 210 KCTGCGFCVELCFVRAISVR 229
                                       5****************977 PP

  == domain 3  score: 18.6 bits;  conditional E-value: 1.6e-06
                           Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                       +C +Cg+C e CP++ai+  
  gi|474933720|ref|YP_007687302.1| 239 KCRGCGRCSEQCPSEAISIS 258
                                       5****************966 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   3.0   9.6e-06     0.016       4      20 ..     205     221 ..     202     221 .. 0.91
   2 !   15.9   1.9   6.4e-06      0.01       3      21 ..     233     251 ..     231     252 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 9.6e-06
                            Fer4_2   4 vvdtdrCigCgaCvsaC 20 
                                        vd+ +C+gCg Cv  C
  gi|474933720|ref|YP_007687302.1| 205 SVDPGKCTGCGFCVELC 221
                                       589***********999 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 6.4e-06
                            Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                       ++ + ++C gCg C   CP
  gi|474933720|ref|YP_007687302.1| 233 AELNDAKCRGCGRCSEQCP 251
                                       567889********999** PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   4.0   2.4e-06    0.0039      57     110 ..     207     265 ..     194     269 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.4e-06
                           Fer4_18  57 gagdcidcescvkvcPt.gidirkGl....qleciscllcidacdkvmeklgkpkglir 110
                                       + g+c+ c++cv++c +  i +r+G       +c  c++c + c +   ++++++++i+
  gi|474933720|ref|YP_007687302.1| 207 DPGKCTGCGFCVELCFVrAISVRDGKaelnDAKCRGCGRCSEQCPSEAISISYDTSVIH 265
                                       5689***********87369*****63333579***********998888888888775 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.8     0.001       1.6      67      94 ..     196     223 ..     192     225 .. 0.81
   2 ?   16.2   1.6   8.6e-06     0.014      74      95 ..     232     253 ..     226     254 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.001
                           Fer4_22  67 lhklsefkekfgesgCvGCgRCieacpv 94 
                                       +++l  ++ +++  +C+GCg C+e c v
  gi|474933720|ref|YP_007687302.1| 196 YRRLDGVTVSVDPGKCTGCGFCVELCFV 223
                                       566677777888899***********86 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 8.6e-06
                           Fer4_22  74 kekfgesgCvGCgRCieacpvk 95 
                                       k++ +  +C GCgRC+e+cp++
  gi|474933720|ref|YP_007687302.1| 232 KAELNDAKCRGCGRCSEQCPSE 253
                                       56678999***********975 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       8.2   1.3e+04      44      57 ..      41      54 ..      35      55 .. 0.75
   2 ?   -3.2   0.2       9.1   1.5e+04       6      14 ..     134     142 ..     131     145 .. 0.75
   3 ?    6.7  11.6    0.0075        12       1      66 []     204     257 ..     204     257 .. 0.71
   4 ?    5.3   2.9      0.02        32       5      20 ..     237     252 ..     234     270 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 8.2
                           Fer4_15 44 vpddeeeaaqeAar 57
                                      ++dd++  + +Aa+
  gi|474933720|ref|YP_007687302.1| 41 FEDDDMVVVPKAAS 54
                                      67888888888886 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 9.1
                           Fer4_15   6 daCigcglC 14 
                                       +aC+ +  C
  gi|474933720|ref|YP_007687302.1| 134 EACDFIDEC 142
                                       688888888 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0075
                           Fer4_15   1 VvvDrdaCigcglCvaeapevfeldedglasvllddgeiaegevpddeeeaaqeAaraCPvdAIrv 66 
                                       V vD  +C+gcg Cv+++  +     dg+            +e++d +     +  ++CP +AI++
  gi|474933720|ref|YP_007687302.1| 204 VSVDPGKCTGCGFCVELCFVRAISVRDGK------------AELNDAKCRGCGRCSEQCPSEAISI 257
                                       789**************953333333444............5777777777777777777777765 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.02
                           Fer4_15   5 rdaCigcglCvaeape 20 
                                         +C gcg+C + +p 
  gi|474933720|ref|YP_007687302.1| 237 DAKCRGCGRCSEQCPS 252
                                       678*********9974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1764.41
//
Query:       gi|474933721|ref|YP_007687303.1|  [L=433]
Description: Arabinose efflux permease [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.8e-62  211.3  62.4    2.2e-53  181.5  34.4    2.0  2  MFS_1       Major Facilitator Superfamily
    2.1e-57  195.0  16.6    2.7e-57  194.7  16.6    1.0  1  Sugar_tr    Sugar (and other) transporter
    3.1e-05   23.0  21.6    8.4e-05   21.6   7.0    2.9  3  MFS_1_like  MFS_1 like family
    6.7e-05   21.6   6.6    6.7e-05   21.6   6.6    3.3  3  MFS_2       MFS/sugar transport protein
    0.00086   18.7   7.5    0.00086   18.7   7.5    2.4  2  MFS_4       Uncharacterised MFS-type transporter YbfB
  ------ inclusion threshold ------
        5.6    5.1   9.2      0.055   11.8   0.6    1.9  3  OATP        Organic Anion Transporter Polypeptide (OATP) fami


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.5  34.4   7.3e-57   2.2e-53       2     353 .]      13     382 ..      12     382 .. 0.89
   2 !   43.7  20.0   5.4e-15   1.6e-11      40     172 ..     284     420 ..     281     433 .] 0.86

  Alignments for each domain:
  == domain 1  score: 181.5 bits;  conditional E-value: 7.3e-57
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglll 78 
                                        +++++ a++ ++++ ++  a+++d  +s+ e+g+l+++  +g++v++ + G l dr+Grr v+l++ll++++g++l
  gi|474933721|ref|YP_007687303.1|  13 GIGLMFDAMDQGMVSGVIA-AIGDDWDLSKYELGWLTSAGVIGMIVGAAISGELCDRMGRRTVILCTLLIYSAGSFL 88 
                                       68999**************.******************************************************666 PP

                             MFS_1  79 llfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfy 155
                                       + +a+ +w+l+v+r+l+G+g g+ +pa+++l+++++p + rgr + l+ ++++ G + + l++ ll+ s gWr++f+
  gi|474933721|ref|YP_007687303.1|  89 CGIATEYWMLMVFRFLTGFGLGGELPAAITLASEISPLRSRGRNVVLVESFWAWGWLAASLVAFLLIPSHGWRVAFF 165
                                       665799*********************************************************************** PP

                             MFS_1 156 ilaivsllafvlfllllpeepperkrkspkeee.......................kgtgpaplvpawkallkdpvl 209
                                       + a+ +l+a++l   + + e p+    ++++ee                       ++ +++p+   +k l+ +  +
  gi|474933721|ref|YP_007687303.1| 166 AGAVPALFAAIL--RFKVPESPRYLELNGRREEaerivgvferaagvepvaddtpaEKAEKRPWYVEFKGLWGRENI 240
                                       *********995..44444444444444444447****************999998888888888899999999999 PP

                             MFS_1 210 w...illialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllalll 283
                                           +l+++++++ fg++g++ ++p+ l  ++g++    + ++  +++l+ +++ + a++l+ r+gr+++l++++l+
  gi|474933721|ref|YP_007687303.1| 241 RstaVLWVIWFGINFGYYGFVLWTPT-LLIDRGFD-ITKSFGYTVIMCLAQLPGYFSAAYLIERMGRKPTLIMFFLG 315
                                       556789999999999***********.5*******.788888899999999999*************8888888877 PP

                             MFS_1 284 lllaalglallavtssavllllvlvliGfglgfvfpsllalasdlappeeagtasglfntagslggalgp 353
                                       +++aa ++  +     +++l++++vl+ f+lg +++s+ +++ +++p++ +g+ sg+++ +g +g++++p
  gi|474933721|ref|YP_007687303.1| 316 TAAAAWFFGHADSD--TSILAAGCVLYFFALG-AWGSIYSYTPEVYPTDVRGSGSGWASAFGRVGAFIAP 382
                                       77777777777777..6666667777778888.599********************************98 PP

  == domain 2  score: 43.7 bits;  conditional E-value: 5.4e-15
                             MFS_1  40 lyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslwlllvlrvlqGlgagalfpagaaliadwfpk 116
                                       +  l+++ + + +++l++r+Gr+++l++ +l++a++++++  a s + +l++ ++  ++a +++ ++++++ +++p 
  gi|474933721|ref|YP_007687303.1| 284 IMCLAQLPGYFSAAYLIERMGRKPTLIMFFLGTAAAAWFFGHADSDTSILAAGCVLYFFALGAWGSIYSYTPEVYPT 360
                                       567899999999************************7777733666679999999999999**************** PP

                             MFS_1 117 eergraigllsagfslGailgpllggllasslg....Wravfyilaivsllafvlfllll 172
                                       + rg++ g++sa+  +Ga ++p + ++l+ ++g    + +vf +la+++++++++++++ 
  gi|474933721|ref|YP_007687303.1| 361 DVRGSGSGWASAFGRVGAFIAPFVVPVLYNAYGteqgFALVFSVLAAAFAVVAIVIAVFG 420
                                       *****************************9999888888888888888888888655554 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  194.7  16.6   8.9e-61   2.7e-57      44     446 ..      40     429 ..      15     432 .. 0.86

  Alignments for each domain:
  == domain 1  score: 194.7 bits;  conditional E-value: 8.9e-61
                                       ...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHH CS
                          Sugar_tr  44 ssvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlas 120
                                       s+  +g+++s+ ++G i+G+ ++g l dr+GR+ ++l++ +++++g++l+++a+   ++++l+v R+l+G+g+G++ 
  gi|474933721|ref|YP_007687303.1|  40 SKYELGWLTSAGVIGMIVGAAISGELCDRMGRRTVILCTLLIYSAGSFLCGIAT---EYWMLMVFRFLTGFGLGGEL 113
                                       56679*************************************************...9******************* PP

                                       HHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS---HHH CS
                          Sugar_tr 121 vlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllflPESPry 197
                                         + +++sEi+p + Rg+ v+l ++++++G l a+ + + l  +++   wr+ ++  +vpal+ +il++ +PESPry
  gi|474933721|ref|YP_007687303.1| 114 PAAITLASEISPLRSRGRNVVLVESFWAWGWLAASLVAFLLIPSHG---WRVAFFAGAVPALFAAILRFKVPESPRY 187
                                       *****************************************99999...**************************** PP

                                       HHHTT-HHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH.....HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHH CS
                          Sugar_tr 198 lvekgkeeeakevlaklrgeedadrelaeekdsleaeqeeekaswkellssktvrqrlligvvlqifqqltGinaim 274
                                       l  +g++eea++++   +  +++++ +++  ++  +++    +  k l+++ +  + + +  v++++ ++ +   + 
  gi|474933721|ref|YP_007687303.1| 188 LELNGRREEAERIVGVFERAAGVEPVADDTPAEKAEKRPW-YVEFKGLWGREN-IRSTAVLWVIWFGINFGY-YGFV 261
                                       ************9988777766666666666655555332.578999**9977.566666666777777755.5555 PP

                                       HHTTTHHHHSS-THH..HHHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...C CS
                          Sugar_tr 275 yysptifenlglsks..llvtiivgvvnfvatfvaiflvdrfGRRtllllGaagmaicfvilgivalllvakskaas 349
                                          pt++ + g++ +  +  t+i+   +    f a++l++r+GR+++l++ ++g a++++++g   ++ +++     
  gi|474933721|ref|YP_007687303.1| 262 LWTPTLLIDRGFDITksFGYTVIMCLAQLPGYFSAAYLIERMGRKPTLIMFFLGTAAAAWFFG---HADSDT----- 330
                                       6666666666655444499*******************************************9...333333..... PP

                                       HHHHHHHHHHHHHHHTTTTHHHHHHHHHHSHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHH....T-HHHHHH CS
                          Sugar_tr 350 ivaivfialfialfalgwgpvpwvlvsElfpqsvRskalaiavavnwlanflisllfpiiteaig....ggyvflvf 422
                                        ++ ++++l+  +falg  + ++ + +E++p++vR++++  a a   +  f+  ++ p++ +a+g     + vf v 
  gi|474933721|ref|YP_007687303.1| 331 SILAAGCVLY--FFALGAWGSIYSYTPEVYPTDVRGSGSGWASAFGRVGAFIAPFVVPVLYNAYGteqgFALVFSVL 405
                                       4666777777..55555545556999***************************************987667778888 PP

                                       HHHHHHHHHHHHHHS--STT--CC CS
                          Sugar_tr 423 aglavlfiifvfffvpetkgrtle 446
                                       a+  ++++i++ +f  et g++l 
  gi|474933721|ref|YP_007687303.1| 406 AAAFAVVAIVIAVFGKETMGSSLR 429
                                       888888888999999999999985 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   7.0   2.8e-08   8.4e-05     254     370 ..      36     151 ..      11     166 .. 0.86
   2 !    9.7   2.1   0.00011      0.33     266     377 ..     282     392 ..     276     400 .. 0.76
   3 ?    1.6   0.9     0.032        97     152     206 ..     372     425 ..     368     431 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.8e-08
                        MFS_1_like 254 elgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgll 330
                                       + + s++ lG l+  gv++ i+   ++ +l +++G +++++ +ll+y +  +l +i ++ w+++++ +L g+ +g  
  gi|474933721|ref|YP_007687303.1|  36 DWDLSKYELGWLTSAGVIGMIVGAAISGELCDRMGRRTVILCTLLIYSAGSFLCGIATEYWMLMVFRFLTGFGLGGE 112
                                       567899*********************************************************************** PP

                        MFS_1_like 331 waaaveyvskiapksleatgqgllsglyfglGralGsliG 370
                                         aa++ +s+i p + +++   l++++ +  G    sl++
  gi|474933721|ref|YP_007687303.1| 113 LPAAITLASEISPLRSRGRNVVLVESF-WAWGWLAASLVA 151
                                       ****************99999888877.666665555555 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00011
                        MFS_1_like 266 valgvvaeiplfffaeklleklGhvklliiallayilrfllyaii.enawlvlpievLhgisfgllwaaaveyvski 341
                                       +++ ++a++p +f a +l+e++G    li+ +l +++  +  +   ++++++    vL+ +++g  w+++ +y  ++
  gi|474933721|ref|YP_007687303.1| 282 TVIMCLAQLPGYFSAAYLIERMGRKPTLIMFFLGTAAAAWFFGHAdSDTSILAAGCVLYFFALG-AWGSIYSYTPEV 357
                                       456799*****************99776666666555555555553888888888899999998.59********** PP

                        MFS_1_like 342 apksleatgqgllsglyfglGralGsliGGllwdlk 377
                                        p  +++ g g  s++   +G ++  ++  +l++ +
  gi|474933721|ref|YP_007687303.1| 358 YPTDVRGSGSGWASAF-GRVGAFIAPFVVPVLYNAY 392
                                       *******999988776.3456666666655555555 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.032
                        MFS_1_like 152 lfGsvGyaifafitGilidhysvnllpysallyvlaallvisllvvlilneteke 206
                                        fG vG  i+ f++ +l + y +++ ++  ++ vlaa + ++ +v++++ + + +
  gi|474933721|ref|YP_007687303.1| 372 AFGRVGAFIAPFVVPVLYNAYGTEQ-GFALVFSVLAAAFAVVAIVIAVFGKETMG 425
                                       5899999999999999999999976.54556666666666666666666665555 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   6.6   2.2e-08   6.7e-05     257     363 ..      40     141 ..       8     179 .. 0.84
   2 ?    2.5   4.3     0.015        43     265     334 ..     282     349 ..     218     362 .. 0.71
   3 !    6.9   1.6   0.00067         2     130     194 ..     361     421 ..     349     431 .. 0.57

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.2e-08
                             MFS_2 257 ngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlllqpsnlllflvllviagfgvgvaal 333
                                       ++ +  +++ + +i++++g+++   l+ r+g+++++l+ +l++ ++++l+ ++  + +++++v+ +++gfg+g+   
  gi|474933721|ref|YP_007687303.1|  40 SKYELGWLTSAGVIGMIVGAAISGELCDRMGRRTVILCTLLIYSAGSFLCGIA--TEYWMLMVFRFLTGFGLGGE-- 112
                                       556778999999*****************************************..99**************6543.. PP

                             MFS_2 334 lpwsmladvvDygelktGkrregvffavls 363
                                        +++ ++ + + + l++  r+  ++ ++++
  gi|474933721|ref|YP_007687303.1| 113 -LPAAITLASEISPLRSRGRNVVLVESFWA 141
                                       .33334445566677777777777777766 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.015
                             MFS_2 265 llvvtisallgiplwqplakrlgkkntyllgalltivllvlvlllqpsnlllflvllviagfgvgvaall 334
                                       ++++ +++l g + +++l  r+g+k t ++++l t++   ++  +  s++ ++ + +v+++f++g+ +  
  gi|474933721|ref|YP_007687303.1| 282 TVIMCLAQLPGYFSAAYLIERMGRKPTLIMFFLGTAAAAWFFGHA-DSDTSILAAGCVLYFFALGA-WGS 349
                                       222345555788899**********88888777777776666666.68888888888888777655.434 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.00067
                             MFS_2 130 deRtsltsvrsflsvlggvlaailafllvlilgglkserkgylifaliialLmllgviivvlgtk 194
                                       d R s +++ s +  +g ++a +++++l  ++g+    ++g+ ++ ++ a+ +++++i+++ + k
  gi|474933721|ref|YP_007687303.1| 361 DVRGSGSGWASAFGRVGAFIAPFVVPVLYNAYGT----EQGFALVFSVLAAAFAVVAIVIAVFGK 421
                                       5555555555555555555555555555555554....666666666666655555555555555 PP

>> MFS_4  Uncharacterised MFS-type transporter YbfB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   7.5   2.9e-07   0.00086      22      97 ..      36     111 ..      28     186 .. 0.78
   2 ?    3.0  10.2     0.017        50     200     362 ..     250     417 ..     235     418 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.9e-07
                             MFS_4  22 egqlslsqagllaaaNylGYLvGallaafalsagaeRlrllagllatvllllamaltesfaaflliRflaGvasAv 97 
                                       +  ls  ++g+l +a  +G +vGa +      +   R+++l+ ll   +  + ++++++ +++++ Rfl+G + + 
  gi|474933721|ref|YP_007687303.1|  36 DWDLSKYELGWLTSAGVIGMIVGAAISGELCDRMGRRTVILCTLLIYSAGSFLCGIATEYWMLMVFRFLTGFGLGG 111
                                       55688889****************999888888888999*******************************987554 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.017
                             MFS_4 200 YglaGfGYiitatFlvaiardgaggalleallWllvGlaaivgvlvwlrvakrsglrralaaallieavgvllslls 276
                                       ++ + fGY     + + +  d++      + + +++ la ++g +    + +r g ++ l + +l  a+++      
  gi|474933721|ref|YP_007687303.1| 250 WFGINFGYYGFVLWTPTLLIDRGFDITKSFGYTVIMCLAQLPGYFSAAYLIERMGRKPTLIMFFLGTAAAAWFFGHA 326
                                       5555566666666666666665555566666778999**********************999988888777777777 PP

                             MFS_4 277 psplglivssvllGltflaitalvlqlarelappatrrllglmTasfg.igQilGpllasllaeatgsla...lall 349
                                       +s ++++ ++ +l  + l+   +   ++ e++p  +r   +    +fg +g  ++p ++ +l++a g+ +   l+  
  gi|474933721|ref|YP_007687303.1| 327 DSDTSILAAGCVLYFFALGAWGSIYSYTPEVYPTDVRGSGSGWASAFGrVGAFIAPFVVPVLYNAYGTEQgfaLVFS 403
                                       777776666667778889999999*************9999999999989**************9997542114433 PP

                             MFS_4 350 .vaaaalvlaaliv 362
                                        +aaa +v+a++i+
  gi|474933721|ref|YP_007687303.1| 404 vLAAAFAVVAIVIA 417
                                       4999******9996 PP

>> OATP  Organic Anion Transporter Polypeptide (OATP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.6   1.8e-05     0.055       3      84 ..       9      90 ..       6      95 .. 0.92
   2 ?   -3.5   0.4      0.77   2.3e+03     312     368 ..     259     313 ..     250     325 .. 0.61
   3 ?   -2.9   0.1      0.49   1.5e+03     219     243 ..     402     426 ..     400     432 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.8e-05
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP  3 lvllsllglvqamvsgyfkstittiEkrFklpsstsgliassneignillilfvsYfggrghrPrwigigallmalgsl 81
                                      l+l+++  ++ am  g+++ +i  i   ++l++++ g+++s+  ig i+ +++ + + +r+ r  +i + +l+ + gs+
  gi|474933721|ref|YP_007687303.1|  9 LLLIGIGLMFDAMDQGMVSGVIAAIGDDWDLSKYELGWLTSAGVIGMIVGAAISGELCDRMGRRTVILCTLLIYSAGSF 87
                                      56677777777******************************************************************** PP

                                      xxx RF
                              OATP 82 lla 84
                                      l+ 
  gi|474933721|ref|YP_007687303.1| 88 LCG 90
                                      985 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 0.77
                                       xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 312 GfitFlpky.lEtqFslsaseAnlltGvvvipgaalGillgGllvkklklsakklakl 368
                                       Gf+ ++p   + + F +++s   ++   ++ ++   G + + +l++++  ++  ++++
  gi|474933721|ref|YP_007687303.1| 259 GFVLWTPTLlIDRGFDITKSFGYTV---IMCLAQLPGYFSAAYLIERMGRKPTLIMFF 313
                                       5555555531455666666655444...455556667777777777776666655555 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 0.49
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 219 flilgvllllaaiplffFPkelpkk 243
                                       f +l+++ +++ai++++F ke  ++
  gi|474933721|ref|YP_007687303.1| 402 FSVLAAAFAVVAIVIAVFGKETMGS 426
                                       7788999999999999999986655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 3146.82
//
Query:       gi|474933722|ref|YP_007687304.1|  [L=329]
Description: protein of unknown function (DUF1814) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-45  156.5   0.0    1.4e-45  156.1   0.0    1.1  1  AbiEii    Nucleotidyl transferase AbiEii toxin, Type IV TA sy


Domain annotation for each model (and alignments):
>> AbiEii  Nucleotidyl transferase AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.1   0.0   7.9e-50   1.4e-45       3     238 ..      46     313 ..      42     314 .. 0.88

  Alignments for each domain:
  == domain 1  score: 156.1 bits;  conditional E-value: 7.9e-50
                            AbiEii   3 LfalslsaladklvFkGGTaLslayglipRfSeDIDlsllr................gdrkellealkealeeiaaa 63 
                                       L++  +s+++++l FkGGT+Ls++yg i RfSeDIDl+l++                +++++++++l +  e +  +
  gi|474933722|ref|YP_007687304.1|  46 LYS--DSPWKHRLLFKGGTSLSKCYGAIRRFSEDIDLLLDWrelgypeegpkeektrKKQEQSNDQLMAKTEMFLLE 120
                                       444..9***************************************************66666666666666666666 PP

                            AbiEii  64 laeeglkvklaasigege....dyeglrlrypaef.ggyarqkikieigfreavppaerreippyleel....ggpa 131
                                        +++  k +l++ ++++     d++ + +ryp++f    ++ +i +eig r+ +  ++ r+i++y++e      g++
  gi|474933722|ref|YP_007687304.1| 121 HMRPRMKSDLDKILKKEFeietDGPNIIFRYPCAFdTSTIKNEILMEIGPRGLWGSPVSRSIQSYVAERlpklCGEQ 197
                                       6665555555555555556667******************************************************* PP

                            AbiEii 132 fevpvysleellaeKllall..drgrdrsr..aRDlyDlalLle.aeldaealaeallaylasrgr........pge 195
                                       ++v+++sle++++eKl++l+   ++ + ++  +R++yD+ ++ + ++l+++   +++++  +++ r        ++ 
  gi|474933722|ref|YP_007687304.1| 198 ISVRTLSLERTFCEKLVILHtvACREKVPErySRHYYDVSCIHRyDKLSPNP--DLIKEIAEFKSRffpgtsygYDL 272
                                       ********************984444444467********************..********************888 PP

                            AbiEii 196 lrlaplellreaeadealradwkaflamllggepdpafdaale 238
                                         +  l+l +   ++ alr+d+ ++++m++g++p+  fd++l+
  gi|474933722|ref|YP_007687304.1| 273 ACEGILKLVPPDSVRSALRKDYGSMADMIFGNPPN--FDDVLK 313
                                       8888888888************************9..**9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2159.57
//
Query:       gi|474933723|ref|YP_007687305.1|  [L=200]
Description: hypothetical protein TALC_00130 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0028   17.7   0.0     0.0064   16.5   0.0    1.6  2  AbiEi_3_N      Transcriptional regulator, AbiEi antitoxin N-t
  ------ inclusion threshold ------
      0.076   13.4   0.0       0.14   12.5   0.0    1.4  1  ECSIT_C        C-terminal domain of the ECSIT protein
       0.13   12.4   0.1       0.38   10.9   0.0    1.8  2  AbiEi_4        Transcriptional regulator, AbiEi antitoxin
        0.5   10.5   1.8       0.64   10.2   0.6    1.7  2  Fibrillin_U_N  Fibrillin 1 unique N-terminal domain


Domain annotation for each model (and alignments):
>> AbiEi_3_N  Transcriptional regulator, AbiEi antitoxin N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.4e-06    0.0064      35      90 ..      39     102 ..       8     105 .. 0.89
   2 ?   -2.4   0.0       1.1     5e+03      20      44 ..     165     189 ..     155     192 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.4e-06
                         AbiEi_3_N  35 kyvksgwLerlatGvyarpgde........lswegvvasLqrqlklpvhvGglsALelqGlshy 90 
                                        + k g++ r+++G+y++p+ +         + ++v +++ r ++  ++ Gg s L+l Gls  
  gi|474933723|ref|YP_007687305.1|  39 VACKRGRIVRIMRGIYYKPKYNkllgimipYNPDDVAYAIARNNGWHIIPGGNSCLNLTGLSTQ 102
                                       567999*************999999*99999999**************************9965 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.1
                         AbiEi_3_N  20 aswLaeqGisadlakkyvksgwLer 44 
                                       ++  +++Gi  d a+  +   w++r
  gi|474933723|ref|YP_007687305.1| 165 SEYVRSHGIAMDSAEYSRTAPWIKR 189
                                       5566778888888877777777765 PP

>> ECSIT_C  C-terminal domain of the ECSIT protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.1e-05      0.14      81     108 ..       5      33 ..       1      39 [. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.1e-05
                           ECSIT_C  81 vvkksvheqedGtvlAmc.atgtsskdsl 108
                                       +v+k v+ ++dGtv+A+c +  +ss ds+
  gi|474933723|ref|YP_007687305.1|   5 AVAKYVDSIDDGTVFAICdILNDSSSDSI 33 
                                       57889*************44556666665 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   8.5e-05      0.38      28      46 ..      36      54 ..      27      55 .. 0.87
   2 ?   -3.9   0.0       3.6   1.6e+04      27      35 ..     162     170 ..     160     172 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8.5e-05
                           AbiEi_4 28 alrrLvrkGwLvrlrrGvY 46
                                      +l+ ++++G++vr+ rG+Y
  gi|474933723|ref|YP_007687305.1| 36 QLSVACKRGRIVRIMRGIY 54
                                      467789************* PP

  == domain 2  score: -3.9 bits;  conditional E-value: 3.6
                           AbiEi_4  27 salrrLvrk 35 
                                       ++l+++vr+
  gi|474933723|ref|YP_007687305.1| 162 RTLSEYVRS 170
                                       568888886 PP

>> Fibrillin_U_N  Fibrillin 1 unique N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.6   0.00014      0.64      25      36 ..      83      94 ..      81      95 .. 0.92
   2 ?   -3.0   0.0       1.9   8.4e+03      16      28 ..     105     117 ..     104     123 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00014
                     Fibrillin_U_N 25 GWktLPGGnqCi 36
                                      GW  +PGGn C+
  gi|474933723|ref|YP_007687305.1| 83 GWHIIPGGNSCL 94
                                      9**********6 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.9
                     Fibrillin_U_N  16 sRfhsYCCPGWkt 28 
                                       sRf  Y    +kt
  gi|474933723|ref|YP_007687305.1| 105 SRFIYYSDGPYKT 117
                                       8998887766777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1606.33
//
Query:       gi|474933724|ref|YP_007687306.1|  [L=367]
Description: hypothetical protein TALC_00131 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
        0.1   12.7   0.1       0.22   11.7   0.1    1.5  1  Bac_small_YrzI  Probable sporulation protein (Bac_small_yrzI)


Domain annotation for each model (and alignments):
>> Bac_small_YrzI  Probable sporulation protein (Bac_small_yrzI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   1.2e-05      0.22       4      22 ..     118     136 ..     116     141 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.2e-05
                    Bac_small_YrzI   4 nlFFLTITIqKRkyseeEi 22 
                                       +++F+T+T + ++ys+eE+
  gi|474933724|ref|YP_007687306.1| 118 KVLFFTLTFSHKRYSQEEA 136
                                       69***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2496.02
//
Query:       gi|474933725|ref|YP_007687307.1|  [L=321]
Description: CfrBI restriction endonuclease [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.9e-83  277.7   6.9    1.1e-82  277.2   6.9    1.2  1  RE_CfrBI  CfrBI restriction endonuclease
  ------ inclusion threshold ------
      0.052   13.1   0.3       0.66    9.5   0.1    2.3  2  DUF3400   Domain of unknown function (DUF3400)


Domain annotation for each model (and alignments):
>> RE_CfrBI  CfrBI restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  277.2   6.9   1.3e-86   1.1e-82       2     245 ..      25     234 ..      24     238 .. 0.97

  Alignments for each domain:
  == domain 1  score: 277.2 bits;  conditional E-value: 1.3e-86
                          RE_CfrBI   2 evidklvkklltGedYReevlesinkvfldltdlllseivevkrk......keeileelldktykkkskeekfkslw 72 
                                       ++++kl+k+ll+G++YR+ ++e+++k++++ltdl+ls++vev+rk      ke++l++lldk  kkk++eek++++w
  gi|474933725|ref|YP_007687307.1|  25 DSLKKLTKHLLCGGNYRA-ITEFNTKCKIALTDLWLSDVVEVARKeyglawKEKMLAALLDK--KKKTTEEKYLQYW 98 
                                       89****************.*******************************************..************* PP

                          RE_CfrBI  73 laGlnkktvknidGsaakdvvldlakknikeLssLleelkedatDelqisiklekedvkveldllesllimnilaak 149
                                       l+Gl++kt++nidG             n+keL+sLl+el+e++tD+l +sik+eke        l++++im++++++
  gi|474933725|ref|YP_007687307.1|  99 LLGLTQKTFNNIDG-------------NTKELPSLLSELEEQLTDTL-TSIKREKE--------LDNVWIMMMCGSA 153
                                       **************.............********************.********........9************ PP

                          RE_CfrBI 150 kltirGgawsevGkkvekvLlkkllkllgvpeeknilsdlkrdkelvkeRevDakvletkreairvelkLlgsGnpe 226
                                       +ltirG+++s++Gk+ve+vLlk++l+llg++e+kn+++dl+rd+e+  eRe+Da+v etkr++ir+el+L++sGn+e
  gi|474933725|ref|YP_007687307.1| 154 ALTIRGSDKSKNGKWVERVLLKSMLTLLGFTENKNFWVDLQRDNEV--ERETDAEV-ETKRGRIRIELGLIASGNQE 227
                                       **********************************************..********.******************** PP

                          RE_CfrBI 227 vadviyardvklfieDkls 245
                                       v            ieDk++
  gi|474933725|ref|YP_007687307.1| 228 V------------IEDKIN 234
                                       9............444444 PP

>> DUF3400  Domain of unknown function (DUF3400)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1   7.4e-05      0.66      15      33 ..      62      80 ..      61      84 .. 0.90
   2 ?    1.1   0.0     0.033   2.9e+02      39      45 .]     168     174 ..     161     174 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 7.4e-05
                           DUF3400 15 VvElArhllGedWmqdfve 33
                                      VvE+Ar+ +G  W+++ ++
  gi|474933725|ref|YP_007687307.1| 62 VVEVARKEYGLAWKEKMLA 80
                                      9*************99876 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.033
                           DUF3400  39 GIErVLl 45 
                                       ++ErVLl
  gi|474933725|ref|YP_007687307.1| 168 WVERVLL 174
                                       9*****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       932  (0.0519828); expected 358.6 (0.02)
Passed bias filter:                      621  (0.0346366); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2158.64
//
Query:       gi|474933726|ref|YP_007687308.1|  [L=379]
Description: DNA modification methylase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-42  146.3   0.4    1.1e-42  146.3   0.4    1.5  2  N6_N4_Mtase      DNA methylase
  ------ inclusion threshold ------
      0.011   15.5   0.2        5.3    6.6   0.1    2.4  2  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran
        0.1   12.3   0.0       0.31   10.7   0.0    1.8  2  UPF0020          Putative RNA methylase family UPF0020


Domain annotation for each model (and alignments):
>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1      0.42   2.5e+03      77     104 ..      44      75 ..      12     110 .. 0.53
   2 !  146.3   0.4   1.9e-46   1.1e-42       1     230 [.     126     357 ..     126     358 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.42
                                       EEEEEEEEEESSSTTTSTCC....S-B--EEE CS
                       N6_N4_Mtase  77 fllnvivwkkpnsmpesnkd....rltsthEy 104
                                       +  + ++++++++++e + d    ++++t+E+
  gi|474933726|ref|YP_007687308.1|  44 WHVSIMIKNNSENIGEIRIDsgltKVVETTEL 75 
                                       33333344333333333333323333333333 PP

  == domain 2  score: 146.3 bits;  conditional E-value: 1.9e-46
                                       EEEEEE--SSSSSCS.....GCCGCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEEE-CCCHHT.............. CS
                       N6_N4_Mtase   1 vdlivtdpPYntgkdyendeqyeeedsyeeyleflekvlkevrrvLkddgsifiniddseikk.............. 63 
                                       v+l++t+pPY + k      +y e  +y+eyl+ l+kv+  +r++L+++ +++ini+   ik+              
  gi|474933726|ref|YP_007687308.1| 126 VQLVFTSPPYYNAKP-----EYSEYVDYQEYLDALRKVIVRCRDILSEGRFFIINISPVLIKRtsrntsskripipf 197
                                       79*************.....9******************************************************97 PP

                                       HHHHHHHHHTT-EEEEEEEEEEESSSTTTSTCC.............S-B--EEEEEEEESSTT-..---GGGSSBSS CS
                       N6_N4_Mtase  64 elkaladeifggffllnvivwkkpnsmpesnkd.............rltsthEyilvfsknkkyllkfnldaikvpy 127
                                       ++  ++ ++ g f ++++i+w+kp++ + ++++             + ++ +Ey+lv++k+ ++   + +  i+++y
  gi|474933726|ref|YP_007687308.1| 198 DINTIMVNN-G-FEFIDDIIWEKPEGAGWNVGRgrrfkadrnplqyKPVPVTEYVLVYRKSTDK---LIDWNIRNHY 269
                                       777777766.7.************8777777777788999999999******************...99999***** PP

                                       -HHHHHHHHHHCHHHCC-B--BSEEE-SCCCTTSTTS-CHH----SS---HHHHHHHHHHHS-TT-EEEETT-TTTH CS
                       N6_N4_Mtase 128 eekdklekrgaytskkkgkkiediWdlseiqsnekkskgdtkkkHpaqkPvallerlIklstkkgdivlDpFaGSGt 204
                                       ++++ ++++        + ++++iW   +i+++++k       +Hpa++P++l +r+I+ ++  gd+vlDpFaG+Gt
  gi|474933726|ref|YP_007687308.1| 270 DQQAVKDSKI-----LGEYDVTNIW---KIKPSNNK-------LHPATFPEELCRRVIRYYSFIGDMVLDPFAGTGT 331
                                       ********99.....88999*****...66666665.......6********************************* PP

                                       HHHHHHHTT-EEEEEESSHHHHHHHH CS
                       N6_N4_Mtase 205 TavaakelgrkfiGieieeeyvelae 230
                                        a++a+e+gr+f  i++e++y++  +
  gi|474933726|ref|YP_007687308.1| 332 VAKVAHEMGRRFMVIDKERSYYDYMK 357
                                       *********************99765 PP

>> MethyltransfD12  D12 class N6 adenine-specific DNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1   0.00089       5.3     121     203 ..      64     149 ..      11     177 .. 0.79
   2 ?    6.6   0.0   0.00093       5.5      23      61 ..     321     359 ..     313     376 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.00089
                                       GG---B-TTS-B---B-S-SS-....HHHHHHHHHHHHH....CCEEEC-CHHHHTT-.-TTE.EEEE--S-T.S.. CS
                   MethyltransfD12 121 sglervnkkgnfnvpygaykkpkkvaekelklrseklkn....akiecgdfdavllka.kieddivYlDPPYnprqy 192
                                       sgl+ v ++ + +    + +k+k  a k+ ++++e +k     +ki  gd  +vl+++  ++ ++v+  PPY     
  gi|474933726|ref|YP_007687308.1|  64 SGLTKVVETTELTLIKERIAKNKDAAPKKRSSKKEIFKPvpmgNKIILGDSCKVLEDYpPNSVQLVFTSPPYYN--A 138
                                       78888888889999999999997777777777777666689999999999999999998999*********975..5 PP

                                       .TS--GGGG.C CS
                   MethyltransfD12 193 tanytlyetla 203
                                       +  y  y + +
  gi|474933726|ref|YP_007687308.1| 139 KPEYSEYVDYQ 149
                                       55555554444 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.00093
                                       EEEETT-TTSCCHHCS...SSCEEEEES-HHHHHHHHHH CS
                   MethyltransfD12  23 tfvepFaGggaVffeakkqgkkvlinDinedlinlykal 61 
                                        + +pFaG+g V+  a + g + ++ D +   +  +k++
  gi|474933726|ref|YP_007687308.1| 321 MVLDPFAGTGTVAKVAHEMGRRFMVIDKERSYYDYMKDT 359
                                       578**********76666777777777776666666655 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       0.4   2.4e+03     120     133 ..     124     137 ..     113     165 .. 0.74
   2 ?   10.7   0.0   5.3e-05      0.31      29      65 ..     319     356 ..     296     377 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.4
                                       S---EEEE------ CS
                           UPF0020 120 gevdvivtnpPYGe 133
                                       ++v ++ t pPY +
  gi|474933726|ref|YP_007687308.1| 124 NSVQLVFTSPPYYN 137
                                       5899999****965 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 5.3e-05
                                       TS-EEETT-TTSHHHHHHHHHHTT--TTTT----SS.H CS
                           UPF0020  29 gepllDPmCGsGtilIEaallganiapgllrefvle.l 65 
                                       g++ lDP+ G+Gt++  a  +g++ + +   +  +  +
  gi|474933726|ref|YP_007687308.1| 319 GDMVLDPFAGTGTVAKVAHEMGRRFMVIDKERSYYDyM 356
                                       7999**********988888888877544444444353 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2308.41
//
Query:       gi|474933727|ref|YP_007687309.1|  [L=114]
Description: hypothetical protein TALC_00134 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.063   13.2   0.0        0.1   12.5   0.0    1.3  1  DUF2507   Protein of unknown function (DUF2507)


Domain annotation for each model (and alignments):
>> DUF2507  Protein of unknown function (DUF2507)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.7e-06       0.1      29      83 ..      22      74 ..      20      81 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.7e-06
                           DUF2507 29 kelArkfplesledlieffekagwGtLellkekkkelefeLsgeiveerlkekee 83
                                      +e+A  ++le+ ed ++ff +   G+L ++k++kk  +f  +g+ +++rl+  ee
  gi|474933727|ref|YP_007687309.1| 22 REIAELMNLEKGEDYVSFFLHE--GRLIVKKDTKKYGTFDFEGDEIADRLRDYEE 74
                                      6799999************765..9************************987554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       679  (0.0378716); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 748.90
//
Query:       gi|474933728|ref|YP_007687310.1|  [L=70]
Description: hypothetical protein TALC_00135 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 519.18
//
Query:       gi|474933729|ref|YP_007687311.1|  [L=323]
Description: Site-specific recombinase XerD [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-10   40.4   0.0    3.4e-10   40.0   0.0    1.2  1  Phage_integrase  Phage integrase family
  ------ inclusion threshold ------
       0.15   12.4   0.0       0.47   10.8   0.0    1.9  1  Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.0   3.7e-14   3.4e-10       3     170 ..     120     301 ..     118     303 .. 0.83

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 3.7e-14
                                       HHHHHHHHHHHCCGC.....HHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSE....EEE CS
                   Phage_integrase   3 ltedeverllaalee.....slkirdklllellyetGlRisEllsLrvkdldlengvilvheregKgske....rav 70 
                                       ++ed v+r+++ +e+       k++ + ++ ++  tGlR  El+ L++ +++  +  + + +++ Kg+      r v
  gi|474933729|ref|YP_007687311.1| 120 MEEDTVQRIIEKAEKlniadWPKMEAYGVVVIAICTGLRPQELRMLSIRNVHETDTSVEIYAEHVKGEGTygseRLV 196
                                       7899***********99988789999999**********************99999999997777777666666999 PP

                                       ECTHHHHHHHHHHHHHH....CHCCTTTSBSSBETTSSB--HHHHHHHHHHHHHHCT-SSC--TTHHHHHHHHHHHH CS
                   Phage_integrase  71 plseealellkellska....leeaeksellfaskrgkplsrqtvrkafkraveeagiekpltpHtlRhsfataLle 143
                                        +    ++ +k+ l+ +     ++ + ++ lf+  ++k  + +  r ++ +++ e++++  +   + R++f+ + + 
  gi|474933729|ref|YP_007687311.1| 197 VVHPDGVPFVKKFLAARrlrlEKAGKFEDSLFPPLKNKGGYLSYNRIRMLKTKVEQDLDITFELRKCRRTFGQRAID 273
                                       99999999999999999888655666788999888555544444444455555555666669999************ PP

                                       HCTSHHHHHHHHT-SSCCHH.HHHHCCC CS
                   Phage_integrase 144 agvdlrvvqkllGHssistt.qiYthva 170
                                       +g dl+ v  ++GH+ ++tt + Y +++
  gi|474933729|ref|YP_007687311.1| 274 EGQDLHNVSLVMGHTTLNTTqKDYCDKD 301
                                       ********************88887765 PP

>> Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   5.2e-05      0.47      14      79 ..      21      92 ..      11      96 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.2e-05
                                      S-HHHHHHHHHHHHHHHHHHHH.......TS--TTT--HHHHHHHHHS----------HHHHHHHHHHHHHH CS
                   Phage_int_SAM_1 14 lspnTlraYrrdLrrflkflae......rgkesleqlttedvraflaeleeeglsatslarrlsalrsFfqf 79
                                      +++ T+ +  r+Lr +   +++          + +++t++dv  f+  ++++g + t+l++ l  l +F+++
  gi|474933729|ref|YP_007687311.1| 21 IAKSTMGTTSRRLRQIGSIFHYlrgeglVSTDNPREITPKDVDVFVGFRRKNGIKNTTLHKDLGLLSKFLAY 92
                                      5666777777777766666665322222223456789********************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2107.47
//
Query:       gi|474933730|ref|YP_007687312.1|  [L=152]
Description: putative transcriptional regulator, contains C-terminal CBS domains [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.5e-23   83.0   4.0    6.7e-12   45.7   0.4    2.2  2  CBS         CBS domain
  ------ inclusion threshold ------
      0.052   12.1   0.2       0.06   11.9   0.2    1.1  1  ADP_PFK_GK  ADP-specific Phosphofructokinase/Glucokinase cons


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   0.4   7.5e-16   6.7e-12       5      56 ..       1      52 [.       1      53 [. 0.93
   2 !   38.8   0.2   1.1e-13   9.7e-10       1      55 [.      94     147 ..      94     149 .. 0.93

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 7.5e-16
                                      SBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS  5 mtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56
                                      mt++v+tv+p++t++ a+ +m+  +vs+ PVVd+ ++++Gi+++ D+l+++l
  gi|474933730|ref|YP_007687312.1|  1 MTTQVITVKPTDTVRHAVIRMAIDNVSGAPVVDNRNHVLGILSQNDILKLIL 52
                                      9********************7445*******99999************997 PP

  == domain 2  score: 38.8 bits;  conditional E-value: 1.1e-13
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       V+d+m r  ++ +pd+ + eal+ m + +v+rlPV+ e+g lvG v+++D++ ++
  gi|474933730|ref|YP_007687312.1|  94 VEDLMVRSTLCTTPDAEIMEALKAMMKMDVGRLPVL-EQGVLVGTVSRSDIIFYI 147
                                       89**********************75666*******.9**************998 PP

>> ADP_PFK_GK  ADP-specific Phosphofructokinase/Glucokinase conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   6.7e-06      0.06     192     245 ..      61     115 ..      31     123 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.7e-06
                                       EE--GGG--TB-TTSTCHHHHHHHHHHHHHHHCC.T-EEEEE----S-HHHHHHH CS
                        ADP_PFK_GK 192 vlsGlqmleeqykegkereerlekvkeqlkslkn.kikiHlElAsfqdeellkei 245
                                         sGl++l++   + ++  + +ek+k++++++k  ++ +   l ++ d+e+++++
  gi|474933730|ref|YP_007687312.1|  61 GTSGLHLLDNPLDSANTEADIIEKAKQEISDMKVeDLMVRSTLCTTPDAEIMEAL 115
                                       56*********9999******************5599999999999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 994.85
//
Query:       gi|474933731|ref|YP_007687313.1|  [L=254]
Description: Metal-dependent hydrolases of the beta-lactamase superfamily I [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.8e-16   57.9   0.0    1.3e-15   57.5   0.0    1.2  1  Lactamase_B_2  Beta-lactamase superfamily domain
    5.2e-13   49.5   0.0    7.8e-13   48.9   0.0    1.5  1  Lactamase_B    Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
      0.032   14.1   0.0      0.058   13.3   0.0    1.4  1  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.5   0.0   2.2e-19   1.3e-15       3     192 ..      25     201 ..      23     213 .. 0.83

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 2.2e-19
                                       EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHC CS
                     Lactamase_B_2   3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylal 79 
                                       ++iDag++  +  ++++  ve +de   i+a l+th+H DH+ g+  +++    ++p+y+++ + +   ++      
  gi|474933731|ref|YP_007687313.1|  25 VVIDAGLSYKKL-HSLM-SVEGVDE-GCIKAMLITHEHNDHILGAGAMARKL--DIPMYCNLPTFDAFGHG------ 90 
                                       789999996555.4444.4453444.59*********************943..49**********99999...... PP

                                       HTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HHHHHHHCT CS
                     Lactamase_B_2  80 eeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipeeigerlgg 156
                                            v+ +++ +  +f+l   g++it+ p +h++++          ++++e ++++v+ ++Dtg+++e  ++ l+ 
  gi|474933731|ref|YP_007687313.1|  91 ----SVSYRQIFTSRPFDLC--GMRITPLPTSHDAAE--------PNAFVFEAEDRNVLLATDTGRLTEPCQAALQR 153
                                       ....578889999******6..799************........9******************************* PP

                                       -SEEEEE-S-SSTTHHHH.............HHT---STSHHHHCTTSS CS
                     Lactamase_B_2 157 adllllditayeddemir.............hmgHltpeeaveaaadlg 192
                                       adl++++ + y+ ++ ++             + gH+  + +  +++ + 
  gi|474933731|ref|YP_007687313.1| 154 ADLAIIESN-YDLRMLKEgpypyplkqriasDSGHMCNDATGNWIRTTA 201
                                       *******88.666555558999999999999999998877777777665 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.0   1.3e-16   7.8e-13       5     153 ..      12     142 ..       8     212 .. 0.87

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 1.3e-16
                                       SSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHC CS
                       Lactamase_B   5 pvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapa 81 
                                        +n+++i+ d+++++iD+G+s  +   +  +  +g++   ++a ++TH H DHi g+g  +++ d+p +++  +  a
  gi|474933731|ref|YP_007687313.1|  12 DGNCTVIQLDDEAVVIDAGLSYKKLHSL--MSVEGVDEGCIKAMLITHEHNDHILGAGAMARKLDIPMYCNLPTFDA 86 
                                       68**********************9998..7*********************************************9 PP

                                       CHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTS CS
                       Lactamase_B  82 lfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDall 153
                                       + +  +                   ++++    +  g+r +  +t + +  +  +v+e+++++vl++ D++ 
  gi|474933731|ref|YP_007687313.1|  87 FGHGSVSY----------------RQIFTSRPFDLCGMRITPLPTSHDAAEPNAFVFEAEDRNVLLATDTGR 142
                                       99999943................457788888888888888889999999999999999999999999986 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   9.8e-06     0.058       6     134 ..      12     159 ..      11     161 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.8e-06
                     Lactamase_B_3   6 ghnsflletagarilvDPfkanlgyeppa.......eeaDlvlisqaledHahletlkql................. 58 
                                       + n+ +++ ++  +++D +  ++++             + + li+++++dH   +   +                  
  gi|474933731|ref|YP_007687313.1|  12 DGNCTVIQLDDEAVVIDAGLSYKKLHSLMsvegvdeGCIKAMLITHEHNDHILGAGAMARkldipmycnlptfdafg 88 
                                       679**************986522222222455665577889999999999986655444345777766666666665 PP

                     Lactamase_B_3  59 ..aenvkvleegeslevggleiravatshdavggsergenngflleqdgltiyhlGhlahelsseelkelgrvDvvl 133
                                            ++ + +   +++ g++i+  +tshda       e n+f++e ++ +++   +++  l+++ +++l+r+D+ +
  gi|474933731|ref|YP_007687313.1|  89 hgSVSYRQIFTSRPFDLCGMRITPLPTSHDAA------EPNAFVFEAEDRNVLLATDTGR-LTEPCQAALQRADLAI 158
                                       55555555555677888888888888888765......4578999999999999999997.9999999999999877 PP

                     Lactamase_B_3 134 t 134
                                       +
  gi|474933731|ref|YP_007687313.1| 159 I 159
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1649.12
//
Query:       gi|474933732|ref|YP_007687314.1|  [L=293]
Description: hypothetical protein TALC_00140 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1818.55
//
Query:       gi|474933733|ref|YP_007687315.1|  [L=98]
Description: conserved hypothetical protein TIGR00251 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-18   64.9   0.2      7e-18   64.5   0.2    1.2  1  DUF167    Uncharacterised ACR, YggU family COG1872
  ------ inclusion threshold ------
      0.051   13.4   0.0      0.071   12.9   0.0    1.3  1  KH_1      KH domain


Domain annotation for each model (and alignments):
>> DUF167  Uncharacterised ACR, YggU family COG1872
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.5   0.2   7.8e-22     7e-18       2      76 ..      14      83 ..      13      84 .. 0.95

  Alignments for each domain:
  == domain 1  score: 64.5 bits;  conditional E-value: 7.8e-22
                                      EEEEEES---SSS----...--TTTT-------TTIIIIIHHHHHHHHHHHHHS...SEEEE-S-GGGSEEEEEE CS
                            DUF167  2 vilavrvkPgakkdaigleedaegrealkvrvaappvdGkANkalikfLakalgvpksdveivsGeksreKvvri 76
                                      v ++v v+P+a+++ ig  + +e+r++l v+v+appv+GkANk++  +++++ g    +  ++sG +s++K+v i
  gi|474933733|ref|YP_007687315.1| 14 VEVDVLVSPKASRSGIG--GIDEWRKRLIVKVRAPPVEGKANKEVADVFSEVTG---CRAAVTSGMTSHQKTVTI 83
                                      6799*************..9899*******************************...56789***********98 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.9e-06     0.071      22      58 ..      56      91 ..      37      96 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.9e-06
                                      HHHHHHH.HT-EEEEESSTT...T.-EEEEEESHHHHH CS
                              KH_1 22 IkeIree.tgakIkvpksedegsderevtisGspeave 58
                                      + +  +e tg++  v  s +  s++++vti+G+p+++ 
  gi|474933733|ref|YP_007687315.1| 56 VADVFSEvTGCRAAVT-SGMT-SHQKTVTITGDPDDIC 91
                                      555554428***9999.7777.89********999775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 613.91
//
Query:       gi|474933734|ref|YP_007687316.1|  [L=131]
Description: hypothetical protein TALC_00142 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.08   13.4   0.0       0.11   12.9   0.0    1.2  1  Toprim_2  Toprim-like


Domain annotation for each model (and alignments):
>> Toprim_2  Toprim-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.2e-06      0.11       2      74 ..      27      98 ..      26     116 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.2e-06
                          Toprim_2  2 vfEgaiDalSlaqlgikektnvvalgGtalteaalkllerypekkvvlalDnDkaGrkaakrlaellreag..vr 74
                                      + Ega D  +la++gi+ ++  + +gG   + +a++++e++   k v+ +D D+ G   +++l+++l  ++  ++
  gi|474933734|ref|YP_007687316.1| 27 LIEGAKDREALAHVGIDGDMFQIQSGGG--PIKAAEYVESH-GGKAVILTDWDRRGGSLCRQLRDILGRDNpdID 98
                                      78999999999*****866666666666..88999999999.6569999****************9976554544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 867.86
//
Query:       gi|474933735|ref|YP_007687317.1|  [L=198]
Description: thymidylate kinase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-44  150.8   0.0    3.9e-44  150.6   0.0    1.0  1  Thymidylate_kin  Thymidylate kinase
    3.2e-14   53.5   0.0    3.9e-14   53.2   0.0    1.1  1  AAA_28           AAA domain
    2.7e-06   27.4   0.0      0.027   14.3   0.0    2.1  2  dNK              Deoxynucleoside kinase
    2.8e-06   27.9   0.0    6.8e-05   23.4   0.0    2.3  1  AAA_18           AAA domain
    1.1e-05   25.6   0.0    3.1e-05   24.1   0.0    1.8  1  AAA_33           AAA domain
     0.0001   22.7   0.0       0.52   10.7   0.0    2.3  2  AAA_17           AAA domain
     0.0016   18.6   0.2       0.92    9.6   0.0    2.1  2  SKI              Shikimate kinase
     0.0048   17.3   0.0     0.0055   17.1   0.0    1.2  1  AAA_16           AAA ATPase domain
     0.0056   16.6   0.0      0.009   15.9   0.0    1.3  1  NACHT            NACHT domain
     0.0061   16.8   0.0      0.013   15.8   0.0    1.6  2  AAA_22           AAA domain
  ------ inclusion threshold ------
      0.024   14.5   0.0      0.065   13.1   0.0    1.8  1  CPT              Chloramphenicol phosphotransferase-like prot
      0.048   13.1   0.0      0.076   12.5   0.0    1.3  1  Arf              ADP-ribosylation factor family
      0.055   13.0   0.0        3.2    7.2   0.0    2.1  2  Ploopntkinase1   P-loop Nucleotide Kinase1
      0.062   13.7   0.0       0.13   12.7   0.0    1.5  1  AAA              ATPase family associated with various cellul
       0.12   11.7   0.1        1.1    8.5   0.0    2.3  2  Zeta_toxin       Zeta toxin
       0.13   11.9   0.1        0.3   10.7   0.0    1.6  2  SRP54            SRP54-type protein, GTPase domain
       0.14   11.7   0.2       0.35   10.4   0.1    1.7  2  AAA_25           AAA domain
       0.16   12.0   0.0       0.37   10.8   0.0    1.6  2  AAA_14           AAA domain
       0.16   12.0   0.0       0.25   11.3   0.0    1.3  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro


Domain annotation for each model (and alignments):
>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.6   0.0   4.1e-47   3.9e-44       1     183 [.       8     183 ..       8     185 .. 0.94

  Alignments for each domain:
  == domain 1  score: 150.6 bits;  conditional E-value: 4.1e-47
                                       EEESTTSSHHHHHHHHHHHHHHTTE.EEEESSSTTSHHHHHHHHHHHTCS---HHHHHHHHHHHHHHTTHHHHHHHH CS
                   Thymidylate_kin   1 iEGlDGaGKttqaellkerlkeegikvvltrepggteiGekirelllkeeeleeqteallfaadriehleekikpal 77 
                                       +EG+DG+GKtt a+ l++   +++    +t+ep++++iG+ +r+      ++ + +eallfaadr+ h++ +i +al
  gi|474933735|ref|YP_007687317.1|   8 LEGIDGSGKTTLAKRLAADAGDAW----VTFEPTDGKIGSALRSGEY--GDIPPAAEALLFAADRSIHTA-EIAKAL 77 
                                       6***************99999888....6****************66..9***************99999.89999* PP

                                       HTT-EEEEES-HHHHHHHHHT..TTTTTCHHHHHHGGGTTSE-SEEEEEESSHHHHHTSCCTTSSTTTSHHHHHHHH CS
                   Thymidylate_kin  78 kqgktvivdRylfSslaYqga..kegvdldlvlslnedvllkPdltflldvdpevalkRlakrdeldeeeeeqldfl 152
                                       + g++vi+dRy+ S++aYq+a  + + d+d++ s+++d++ +Pd+++lld+dpev++ R++ r+e +   +e+l+f+
  gi|474933735|ref|YP_007687317.1|  78 DGGRWVICDRYMGSTVAYQSAsmGDSADWDWLVSMQKDAVIQPDAVILLDMDPEVSMSRVGNRGE-ELSRFEKLEFQ 153
                                       ********************9666789************99************************.9********** PP

                                       HHHHHHHHHHHHTTSTEEEEETTS-HHHHHH CS
                   Thymidylate_kin 153 rkvrerylelakederiliidasksieevhe 183
                                       r+vr  yl+la +   +++idask  + v e
  gi|474933735|ref|YP_007687317.1| 154 RRVRDAYLRLA-QMFGYIVIDASKDADSVYE 183
                                       ***********.5999*******99887765 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.2   0.0   4.1e-17   3.9e-14       2     148 ..       6     163 ..       5     179 .. 0.77

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 4.1e-17
                            AAA_28   2 ivitGgestGKTtlleaLaar.gypvv.pEaareileeklakge.dalpwvedllafaervleeqleeeaaaaankv 75 
                                       iv+ G  ++GKTtl+++Laa+ g  +v  E+    + + l++ge +++p ++++l fa+ +  + +e ++a +++++
  gi|474933735|ref|YP_007687317.1|   6 IVLEGIDGSGKTTLAKRLAADaGDAWVtFEPTDGKIGSALRSGEyGDIPPAAEALLFAADRSIHTAEIAKALDGGRW 82 
                                       899****************9888888887877777777765544455555579*****99999999999999***** PP

                            AAA_28  76 lfcDrglldtlaYarayggeaeaelea...aar..ekrydlvfllppapei..dddgeRre..dleereaiderlre 143
                                       ++cDr +  t+aY  a++g+ +a+++      +    + d+v+ll+ +pe+  ++ g+R e  +  e  ++++r+r+
  gi|474933735|ref|YP_007687317.1|  83 VICDRYMGSTVAYQSASMGD-SADWDWlvsMQKdaVIQPDAVILLDMDPEVsmSRVGNRGEelSRFEKLEFQRRVRD 158
                                       ********************.66654422233311333599******998888999***762455578899****** PP

                            AAA_28 144 alrel 148
                                       a+ +l
  gi|474933735|ref|YP_007687317.1| 159 AYLRL 163
                                       99884 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   2.8e-05     0.027       1      29 [.       6      35 ..       6      44 .. 0.83
   2 !   11.3   0.0   0.00024      0.23      88     182 ..      87     176 ..      63     190 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.8e-05
                                      EEEEESTTSSHHHHHHHHHCCST..CEEEE- CS
                               dNK  1 ivveGnIgaGKstlvklLskklg..vkvfeE 29
                                      iv+eG  g+GK+tl+k+L+  +g  +++f E
  gi|474933735|ref|YP_007687317.1|  6 IVLEGIDGSGKTTLAKRLAADAGdaWVTF-E 35
                                      89*****************9998755444.4 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00024
                                       HHTHHHHHHHTTSS-H.HHHHHHHHHHHHHHHHCCH-SEEEEEE--HHHHHHHHHHCTTCCCTTS-HHHHHHHHHHH CS
                               dNK  88 ryiFakalaekgtlse.eelkiykelldnlleelakpdlliYLkasletclerikkRgreeekkieldYlekLheky 163
                                       ry+   +++++ ++ +  +++ + ++ + ++  ++ pd +i L++++e+ + r+ +Rg+e     +l++ +++   y
  gi|474933735|ref|YP_007687317.1|  87 RYMGSTVAYQSASMGDsADWDWLVSMQKDAV--IQ-PDAVILLDMDPEVSMSRVGNRGEELSRFEKLEFQRRVRDAY 160
                                       5555555566666654145666666666665..55.***********************998888888888888777 PP

                                       HHHHTSGGCS-EEEEETSS CS
                               dNK 164 eewlkklnevpvlvidvee 182
                                           +    +  +vid+++
  gi|474933735|ref|YP_007687317.1| 161 LRLAQM---FGYIVIDASK 176
                                       654443...5556666665 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   7.2e-08   6.8e-05       1     119 [.       6     146 ..       6     156 .. 0.57

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 7.2e-08
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.......gvnlrdvakenglllevdpealdeskrldedkldklldaleenss 69 
                                       I+l G+ G+GKttlak+L+               ++++ ++         ++   +   + e  l ++ + ++ +  
  gi|474933735|ref|YP_007687317.1|   6 IVLEGIDGSGKTTLAKRLAADAgDAwvtfeptDGKIGSALRS-------GEY--GDIPPAAEALLFAADRSIHTAEI 73 
                                       89****************888633355554442222222222.......222..22222222222222222222211 PP

                            AAA_18  70 .......aleegknl...vidghlaeleseaakdikk.............vvLtaspeelleRlekRgyeeak 119
                                              ++  ++ +    +  + a + + a++d+               + L+ +pe+ + R+ +Rg+e  +
  gi|474933735|ref|YP_007687317.1|  74 akaldggRWVICDRYmgsTVAYQSASMGDSADWDWLVsmqkdaviqpdavILLDMDPEVSMSRVGNRGEELSR 146
                                       22122342333333333345555555665555555559999999999999*****************987655 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   3.3e-08   3.1e-05       2     127 ..       6     148 ..       5     165 .. 0.64

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 3.3e-08
                            AAA_33   2 vllvGlpGsGKstlaerllkklg.avllssdt.......lrrrlfgtdqqsktdytrvldrlyqilnelarkalsag 70 
                                       ++l G  GsGK+tla+rl++  g a +  ++t       lr+  +g+ ++  + +  ++dr + ++ + ++kal  g
  gi|474933735|ref|YP_007687317.1|   6 IVLEGIDGSGKTTLAKRLAADAGdAWVTFEPTdgkigsaLRSGEYGDIPPAAEALLFAADRSI-HT-AEIAKALDGG 80 
                                       6899*****************997444445556787764444444444444444333444444.33.3455899999 PP

                            AAA_33  71 rnvildat...........nlsrrerarflklarrlgv.pvrivvvetdeetlkeRlakRaangddrse 127
                                       r vi d             + + +++++++++ +++   p++++ ++ d+e+  +R+  R ++  +r+e
  gi|474933735|ref|YP_007687317.1|  81 RWVICDRYmgstvayqsasMGDSADWDWLVSMQKDAVIqPDAVILLDMDPEVSMSRVGNRGEE-LSRFE 148
                                       99999654333343333334445666555555554332269999****************996.44433 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00095      0.89       2      20 ..      10      28 ..       9      35 .. 0.88
   2 !   10.7   0.0   0.00055      0.52      98     123 ..     116     142 ..      71     151 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00095
                                      E-TTSSHHHHHHHHHHHHT CS
                            AAA_17  2 GgPGsGKgtqceklvekyg 20
                                      G+ GsGK+t++++l+ + g
  gi|474933735|ref|YP_007687317.1| 10 GIDGSGKTTLAKRLAADAG 28
                                      899***********99876 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00055
                                       HHH..SEEEEEE--HHHHHHHHHHH.T CS
                            AAA_17  98 eelkpdaiilleadpeeilerrlkd.r 123
                                       + ++pda+ill+ dpe+ ++r+ ++ +
  gi|474933735|ref|YP_007687317.1| 116 AVIQPDAVILLDMDPEVSMSRVGNRgE 142
                                       4579***************99987643 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0056       5.3       2      17 ..      13      28 ..      12      35 .. 0.85
   2 !    9.6   0.0   0.00098      0.92      86     157 ..     121     189 ..     109     190 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0056
                                      TSSHHHHHHHHHHHHT CS
                               SKI  2 GaGKstvGkllAkklg 17
                                      G+GK+t++k+lA   g
  gi|474933735|ref|YP_007687317.1| 13 GSGKTTLAKRLAADAG 28
                                      9***********8765 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00098
                                       SEEEEEE--HHHHHHHHHHTTSSGGGCSCHHHHHHHHHHH.HHHHHHCCSSCEEEECTSSHHHHHHHHHHHHH CS
                               SKI  86 giviyLdvsleellerlkadkeRPllqekskeeelleela.ereplyeeaadvvvdeseeskeevaeeileal 157
                                         vi+Ld+++e+ ++r+ ++ e   l+  +k  e ++  + +  +l + +  +v+d+s+ + + v ee ++al
  gi|474933735|ref|YP_007687317.1| 121 DAVILLDMDPEVSMSRVGNRGE--ELSRFEK-LEFQRRVRdAYLRLAQMFGYIVIDASKDA-DSVYEEAVSAL 189
                                       579***************9999..5666666.33344444356667777788899988888.89998888876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   5.8e-06    0.0055      25     107 ..       4     121 ..       1     193 [. 0.63

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.8e-06
                            AAA_16  25 elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekl 101
                                       + ++l G  G+GK++l+++l+  + ++  +++ + +d          + +al r++ + ++  +ae+ +++a+r   
  gi|474933735|ref|YP_007687317.1|   4 RFIVLEGIDGSGKTTLAKRLAADAGDA--WVTFEPTDGK--------IGSAL-RSGEYGDIPPAAEALLFAADRSIH 69 
                                       67999****************877766..5555555555........77777.778888888888887777777777 PP

                            AAA_16 102 eeala..............................................a 107
                                       ++++a                                              +
  gi|474933735|ref|YP_007687317.1|  70 TAEIAkaldggrwvicdrymgstvayqsasmgdsadwdwlvsmqkdaviqpD 121
                                       7666655555555555555566666655555555555555555555555550 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   9.6e-06     0.009       1      24 [.       4      27 ..       4      32 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9.6e-06
                                      SCEEEEC-TTTCHHHHHHHHHHHH CS
                             NACHT  1 rlvilqGeaGsGKTtLlqklalaw 24
                                      r ++l+G  GsGKTtL+++la ++
  gi|474933735|ref|YP_007687317.1|  4 RFIVLEGIDGSGKTTLAKRLAADA 27
                                      5799****************9876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.4e-05     0.013       5      29 ..       3      27 ..       1      46 [. 0.86
   2 ?   -3.0   0.0       8.8   8.3e+03      93      98 ..     168     173 ..     141     192 .. 0.53

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.4e-05
                            AAA_22  5 agilvvtGesGtGKTtllrrlleql 29
                                       +++v+ G  G+GKTtl++rl+  +
  gi|474933735|ref|YP_007687317.1|  3 GRFIVLEGIDGSGKTTLAKRLAADA 27
                                      689******************9765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 8.8
                            AAA_22  93 elliiD 98 
                                       + ++iD
  gi|474933735|ref|YP_007687317.1| 168 GYIVID 173
                                       333333 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   6.9e-05     0.065       1      33 [.       3      35 ..       3     100 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.9e-05
                                      --EEEEEE-TTSSHHHHHHHHHHHSSS-EEEEE CS
                               CPT  1 ariilLnGgsssGKsslaralqevldepwlhlg 33
                                      +r i+L+G   sGK++la+ l + + ++w+ ++
  gi|474933735|ref|YP_007687317.1|  3 GRFIVLEGIDGSGKTTLAKRLAADAGDAWVTFE 35
                                      689**************************9885 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     8e-05     0.076      17      47 ..       6      39 ..       1      50 [. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8e-05
                                      EEEEESTTSSHHHHHHHHHHSS...CEECSSSSS CS
                               Arf 17 illlGLDnaGKtTilkklklee...lvttvPTig 47
                                      i+l G+D++GKtT+ k+l  +     vt  PT g
  gi|474933735|ref|YP_007687317.1|  6 IVLEGIDGSGKTTLAKRLAADAgdaWVTFEPTDG 39
                                      6677**************9764111566778766 PP

>> Ploopntkinase1  P-loop Nucleotide Kinase1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.035        33      17      48 ..       3      34 ..       1      44 [. 0.83
   2 ?    7.2   0.0    0.0034       3.2     129     188 ..     122     179 ..     105     187 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.035
                    Ploopntkinase1 17 gelyyvkgsngsgkstvpsylaekdpeayvvt 48
                                      g +  + g +gsgk+t+   la    +a+v  
  gi|474933735|ref|YP_007687317.1|  3 GRFIVLEGIDGSGKTTLAKRLAADAGDAWVTF 34
                                      666677899**************999999975 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0034
                    Ploopntkinase1 129 vvlfldtpletclsrvdsrnggedfnedlvvekfkrveshkerhkelfptvpagmikseg 188
                                        v++ld + e+ +srv  r  ge+  +   +e  +rv++   r  ++f  +     k   
  gi|474933735|ref|YP_007687317.1| 122 AVILLDMDPEVSMSRVGNR--GEELSRFEKLEFQRRVRDAYLRLAQMFGYIVIDASKDAD 179
                                       6899************865..9999999999999*****999999999887666655555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00013      0.13       2      25 ..       7      30 ..       6      50 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00013
                                      EEESSTTSSHHHHHHHHHHHHTHE CS
                               AAA  2 llyGppGtGKTllakavakelgve 25
                                      +l G  G GKT+lak +a ++g  
  gi|474933735|ref|YP_007687317.1|  7 VLEGIDGSGKTTLAKRLAADAGDA 30
                                      7899**************999744 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0012       1.1      19      53 ..       6      38 ..       2      93 .. 0.87
   2 ?    1.0   0.0      0.23   2.2e+02     126     161 ..     123     155 ..     121     184 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0012
                        Zeta_toxin 19 illgGqpGAGKselaellkdelerqgnvvrldpDd 53
                                      i+l G  G+GK++la+ l+++   ++  v+++p+d
  gi|474933735|ref|YP_007687317.1|  6 IVLEGIDGSGKTTLAKRLAADA--GDAWVTFEPTD 38
                                      788999***********99997..78888887766 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.23
                        Zeta_toxin 126 vvvvavkkelSrlgvldRyeeevaegRlvpkeehde 161
                                       v+++  ++e+S ++v +R ee     R+ + e++ +
  gi|474933735|ref|YP_007687317.1| 123 VILLDMDPEVSMSRVGNRGEEL---SRFEKLEFQRR 155
                                       6778899***********9999...66666665554 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00031       0.3       3      23 ..       5      25 ..       3      30 .. 0.89
   2 ?   -3.5   0.0       7.3   6.8e+03     171     193 ..     133     155 ..     127     156 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00031
                                      EEEEEESTTSSHHHHHHHHHH CS
                             SRP54  3 villvGlqGaGKTttlaKLaa 23
                                       i+l G+ G+GKTt + +Laa
  gi|474933735|ref|YP_007687317.1|  5 FIVLEGIDGSGKTTLAKRLAA 25
                                      58999**************97 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 7.3
                                       EEEE-SSSTTGEEE--HHHHHHH CS
                             SRP54 171 kfigvGekiedleefdperlvsr 193
                                       ++  vG++ e+l++f++ ++ +r
  gi|474933735|ref|YP_007687317.1| 133 SMSRVGNRGEELSRFEKLEFQRR 155
                                       56668888899999988887665 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00037      0.35      32      57 ..       2      27 ..       1      44 [. 0.81
   2 ?   -2.3   0.0       2.9   2.7e+03     143     158 ..     167     182 ..     145     192 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00037
                            AAA_25 32 agelallaGapgtGKttlaldlalav 57
                                      +g +++l G  g+GKttla  la++ 
  gi|474933735|ref|YP_007687317.1|  2 KGRFIVLEGIDGSGKTTLAKRLAADA 27
                                      6899******************9985 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.9
                            AAA_25 143 vrlvviDplsralggd 158
                                        + +viD  + a +  
  gi|474933735|ref|YP_007687317.1| 167 FGYIVIDASKDADSVY 182
                                       4566666666665554 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00039      0.37       2      26 ..       3      27 ..       2      39 .. 0.86
   2 ?   -2.3   0.0       4.6   4.3e+03      52      71 ..     156     173 ..     115     191 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00039
                            AAA_14  2 rkilvitGaRrvGKTtllkqlikel 26
                                      ++ +v++G+  +GKTtl+k+l+ + 
  gi|474933735|ref|YP_007687317.1|  3 GRFIVLEGIDGSGKTTLAKRLAADA 27
                                      5789****************99765 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.6
                            AAA_14  52 llelileklkeekktylflD 71 
                                       + +++l+++ +    y+++D
  gi|474933735|ref|YP_007687317.1| 156 VRDAYLRLA-Q-MFGYIVID 173
                                       333333331.1.23455555 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00027      0.25      20      44 ..       4      28 ..       1      37 [. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00027
                                      EEEEEEESTTSSHHHHHHHHHHHTT CS
                              TsaE 20 dvilLeGdLGaGKTtlvrglakalg 44
                                      ++i+LeG  G+GKTtl++ la+  g
  gi|474933735|ref|YP_007687317.1|  4 RFIVLEGIDGSGKTTLAKRLAADAG 28
                                      6799****************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1217.69
//
Query:       gi|474933736|ref|YP_007687318.1|  [L=396]
Description: phosphopantothenoylcysteine decarboxylase/phosphopantothenate--cysteine ligase, prokaryotic [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-36  125.0   1.0    4.1e-36  124.1   1.0    1.5  1  Flavoprotein  Flavoprotein
    3.7e-35  121.4   0.0    1.8e-34  119.2   0.0    1.9  2  DFP           DNA / pantothenate metabolism flavoprotein
  ------ inclusion threshold ------
      0.096   12.8   0.0       0.22   11.6   0.0    1.6  1  PglZ          PglZ domain


Domain annotation for each model (and alignments):
>> Flavoprotein  Flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.1   1.0   6.9e-40   4.1e-36       1     156 [.      18     185 ..      18     187 .. 0.94

  Alignments for each domain:
  == domain 1  score: 124.1 bits;  conditional E-value: 6.9e-40
                                       EEEEEEE-SSCGGGCHHHHHHHHHHTTEEEEEEESCHHHHCCHHGGS...........TCSSHHHHHH...CTTESE CS
                      Flavoprotein   1 kkillgiTGsvaaikalellekLkkegievqvvltkaAkkfiskeklklaa.......redpilhiel...rrwadl 67 
                                       k i++giTGs+aa+   +l+++L k+g++v  v+t+aA+++  ++ +++a+       ++++ +hi++      adl
  gi|474933736|ref|YP_007687318.1|  18 KTIVVGITGSIAAVDSFHLIRELVKNGAKVVPVMTQAATRLSAPDAIEFASgmkpiteITGQCEHIKYlgsPSDADL 94 
                                       679******************************************9999999999999999999999877666**** PP

                                       EEEEEEEHHHHHHHHTT--SSHHHHHHHT..HCCTTEEEEE.--HHCCTCSTCHHHHHHH.HT.............. CS
                      Flavoprotein  68 lviaPasantlakianGiadnlltlilra..takkpiliaPamnpamyenpqtlknlekl.eegvtvikPsegdigk 141
                                       ++i+P++ant++k+anGi d+++t+++ +  ++++p+ iaPam+  m+enp++ knle+l e gv +i+P   d + 
  gi|474933736|ref|YP_007687318.1|  95 FLIYPCTANTISKMANGIDDSPVTTMATValGSRTPVAIAPAMHGYMMENPAVEKNLETLaEWGVNIIGPH-IDRER 170
                                       ***********************999955589****************************88*********.99999 PP

                                       ..GHHHHHHHHHHCH CS
                      Flavoprotein 142 gkmaeieeivgkild 156
                                       +k+a+++e+v + ++
  gi|474933736|ref|YP_007687318.1| 171 AKVASVNEVVAWAIR 185
                                       9*********98775 PP

>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.18   1.1e+03      34      62 ..      35      65 ..      32      82 .. 0.74
   2 !  119.2   0.0     3e-38   1.8e-34       3     175 ..     194     362 ..     192     371 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.18
                                      HHHHHHHHTT-EEEEEE-S..-SS---TT-E CS
                               DFP 34 alAeaaaarGaeVtlvsgp..vsletpegve 62
                                       l +++++ Ga+V  v  +  ++l++p+++e
  gi|474933736|ref|YP_007687318.1| 35 HLIRELVKNGAKVVPVMTQaaTRLSAPDAIE 65
                                      67789999*****999888323566665555 PP

  == domain 2  score: 119.2 bits;  conditional E-value: 3e-38
                                       T-EEEEEES-EEEECCTTEEEEE----HHHHHHHHHHHHTT-EEEEEE-S-SS---TT-EEEE--SHHHHHHHHHHH CS
                               DFP   3 gkkvlvtaGpTrEaiDpVRfisNrSSGkmGyalAeaaaarGaeVtlvsgpvsletpegvevvkvesaeemleaveea 79 
                                       gkk+l+ +G + E++D++R+i+NrS+G m+++lA+ a +rGaeV+l  g +s++ p+ + v ++ +++++   +++ 
  gi|474933736|ref|YP_007687318.1| 194 GKKILIIGGRSEEPMDSMRLITNRSTGLMAVSLAQSAFERGAEVELWMGASSVPMPDYIPVRRYGTVDDLIGLLKDI 270
                                       89**********************************************************************99987 PP

                                       HTT-SEEEE---S--EEES-------------..----EEE---HHHHHHHC-S.S-EEEEEEE-SS....-HHHHH CS
                               DFP  80 lkeadivimaAAvaDyrpkeaaeeKikkeeeeeeltleleknpdilaelaekkkkkqllvGFaaete....ellena 152
                                         ++d+vi+ AA aD+ p+++ ++Ki     e+ ++++l++ p++l  ++   +k ++++G++ae+     +l+++a
  gi|474933736|ref|YP_007687318.1| 271 --DHDVVIVPAALADFAPESVFDGKIPS---EKGFSMKLRSVPKVLPLIR---EKCSYVIGYKAESGlsgdRLIARA 339
                                       ..79**********************96...34599*************3...44569*******755677****** PP

                                       HHHHHHTT-SEEEEEEGGGTTGG CS
                               DFP 153 reklerkgldlivaNdvskeeag 175
                                       re+le+ +l ++vaNdv+ ++++
  gi|474933736|ref|YP_007687318.1| 340 RERLEQYDLVAVVANDVDAAGKT 362
                                       *****************987544 PP

>> PglZ  PglZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   3.7e-05      0.22     104     147 ..     338     381 ..     314     391 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.7e-05
                              PglZ 104 errellkdkevvyivhnkvDalgdkasteqksfeaveeslkelk 147
                                        +re l+++++v++v n vDa g  +++++ + +   + ++ +k
  gi|474933736|ref|YP_007687318.1| 338 RARERLEQYDLVAVVANDVDAAGKTSASMHLVTKNDVRNITGTK 381
                                       5788999*****************99999988777666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2493.76
//
Query:       gi|474933737|ref|YP_007687319.1|  [L=288]
Description: putative archaeal kinase (sugar kinase superfamily) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-07   31.6   2.4    1.4e-07   31.6   2.4    2.1  2  GHMP_kinases_N  GHMP kinases N terminal domain


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   2.4   7.8e-12   1.4e-07       2      63 ..      81     140 ..      80     142 .. 0.86
   2 ?   -2.1   0.0      0.26   4.7e+03      20      51 ..     193     216 ..     191     221 .. 0.71

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 7.8e-12
                                       EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHH.HHHHHHHHHHHHHHHHHSHHHHHHH CS
                    GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglslee.aklaleaerlaqggngsggDvaasv 63 
                                       +++++++P+g G+G SAA a a++++ ++  g++ +  ++ a +ae     g g+ gDv+a++
  gi|474933737|ref|YP_007687319.1|  81 VRVENDVPMGEGFGMSAAGAIAVALCCAEIAGVDDSVaYQVAHRAE---IAGGGGLGDVSAIM 140
                                       789*****************************99755576677666...34899*****9986 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.26
                                       HHHHHHHHHHHHTTEHHHHHHHHHHHHHHHHH CS
                    GHMP_kinases_N  20 lavalvaAllallglsleeaklaleaerlaqg 51 
                                       +++a+  A+ ++ +        +++ e+l+ +
  gi|474933737|ref|YP_007687319.1| 193 IVAAGSEAMKEFGQ--------CQTKEKLFEV 216
                                       57788888888775........7777777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1912.16
//
Query:       gi|474933738|ref|YP_007687320.1|  [L=100]
Description: archaeal conserved hypothetical protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-26   92.5   0.0    1.5e-26   92.2   0.0    1.1  1  DUF357    Protein of unknown function (DUF357)


Domain annotation for each model (and alignments):
>> DUF357  Protein of unknown function (DUF357)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.2   0.0   8.4e-31   1.5e-26       1      72 [.      16      87 ..      16      88 .. 0.99

  Alignments for each domain:
  == domain 1  score: 92.2 bits;  conditional E-value: 8.4e-31
                                      HHHHHHHHHHHHHH.....TS---HHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTST CS
                            DUF357  1 rYirlleealekvkiapdeesplgeaaeevlemaesYleDakyflekgdlvnAlasfsYaeGwLDagarlgl 72
                                      rY++++++al+k+k+ ++e++  +  a+++l+ma++Y++Dak+f+e+gdlv+A+a+++Y++Gw+D+garlgl
  gi|474933738|ref|YP_007687320.1| 16 RYLSITRKALDKLKVVTPERTIGKSIADNFLQMANAYYNDAKHFRETGDLVTAFAAVNYSHGWIDCGARLGL 87
                                      8**********************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 685.99
//
Query:       gi|474933739|ref|YP_007687321.1|  [L=281]
Description: ribose-phosphate pyrophosphokinase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.5e-27   93.8   0.0    5.3e-24   84.4   0.0    2.4  2  Pribosyltran_N  N-terminal domain of ribose phosphate pyropho
      7e-20   71.1   0.8    1.8e-19   69.8   0.4    1.9  3  Pribosyltran    Phosphoribosyl transferase domain
    1.5e-10   41.4   0.7    1.5e-10   41.4   0.7    2.1  2  Pribosyl_synth  Phosphoribosyl synthetase-associated domain
    1.8e-05   24.3   0.1    3.5e-05   23.3   0.0    1.5  2  UPRTase         Uracil phosphoribosyltransferase
  ------ inclusion threshold ------
      0.012   15.1   0.0      0.021   14.4   0.0    1.4  1  PRTase_2        Phosphoribosyl transferase
      0.051   13.3   0.1          1    9.0   0.1    2.2  2  His_Phos_1      Histidine phosphatase superfamily (branch 1)
      0.098   12.3   0.1        2.1    7.9   0.0    2.2  2  Amdase          Arylmalonate decarboxylase
       0.13   12.6   0.2       0.56   10.6   0.0    2.1  2  Nitro_FeMo-Co   Dinitrogenase iron-molybdenum cofactor


Domain annotation for each model (and alignments):
>> Pribosyltran_N  N-terminal domain of ribose phosphate pyrophosphokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.4   0.0   2.4e-27   5.3e-24      11     112 ..       2     102 ..       1     104 [. 0.97
   2 !    6.9   0.0    0.0025       5.6      13      58 ..     159     205 ..     155     239 .. 0.85

  Alignments for each domain:
  == domain 1  score: 84.4 bits;  conditional E-value: 2.4e-27
                    Pribosyltran_N  11 eLaekiakrlgvelgkakvsrfadgEikveieesvrgkdvfiiqslskpvndnlmelllmidalrrasakritaViP 87 
                                       +La+++a  l+++ ++a  +rf+dgE++++i+e+  ++dv+i+q++ ++   nl+e++l+ da+rr  akri +ViP
  gi|474933739|ref|YP_007687321.1|   2 DLAKELAGALDCKYIQAASNRFPDGECYIRIDEEKLDDDVIIVQNTYPD--GNLVEMFLLQDAVRRLGAKRIALVIP 76 
                                       79*******************************************9977..9************************* PP

                    Pribosyltran_N  88 ylgysrqdrk.ksrepisaklvaklL 112
                                       y+gy+rqd+  k  ep sak++ klL
  gi|474933739|ref|YP_007687321.1|  77 YFGYARQDKVfKLGEPESAKVMCKLL 102
                                       **********888**********998 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0025
                    Pribosyltran_N  13 aekiakrlgvelgkakvsrfadgEikveiee.svrgkdvfiiqslsk 58 
                                       a+++a+++g++  + + +r +  E+++e  + +v++k+v i+ ++ +
  gi|474933739|ref|YP_007687321.1| 159 AKAVADYMGLPYDHLNKTRLSGTEVRIEPATaDVKDKKVLIVDDMIS 205
                                       799*************************98879*********99874 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.8     4e+03      44      56 ..       4      16 ..       3      45 .. 0.71
   2 ?   -2.9   0.0       1.9   4.2e+03     109     125 ..      62      81 ..      58      90 .. 0.66
   3 !   69.8   0.4   8.2e-23   1.8e-19      14     147 ..     131     258 ..     126     268 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.8
                                      HHHHHHHSTT-EE CS
                      Pribosyltran 44 akiladeLevpla 56
                                      ak+la +L++++ 
  gi|474933739|ref|YP_007687321.1|  4 AKELAGALDCKYI 16
                                      7788888887654 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.9
                                       HHHCC-BSEEEEEEEE...E CS
                      Pribosyltran 109 lLkekgpeevriavlv...d 125
                                       ++++ g++++ ++ ++   +
  gi|474933739|ref|YP_007687321.1|  62 AVRRLGAKRIALVIPYfgyA 81 
                                       77888888888888874433 PP

  == domain 3  score: 69.8 bits;  conditional E-value: 8.2e-23
                                       EEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----TTSEE CS
                      Pribosyltran  14 avarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpagkkV 90 
                                       ++a+++a++++e    +d+v+ ++ g+  +ak++ad++++p++ ++k++ ++      +        +++d+++kkV
  gi|474933739|ref|YP_007687321.1| 131 KAAKAIADYFSE--KGIDIVISPDIGAAGRAKAVADYMGLPYDHLNKTRLSGTEVRIEP--------ATADVKDKKV 197
                                       578889999999..99*****************************99999888888777........99******** PP

                                       EEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEE...E-HHHHHHHHHH-TTS......EE CS
                      Pribosyltran  91 liVDDildtGgTllaalelLkekgpeevriavlv...dkpateeevdknakrvfsls.pdn 147
                                       liVDD+++tGgT++aa ++Lke+g++ v +a+ +    ++a e+    + ++++s++    
  gi|474933739|ref|YP_007687321.1| 198 LIVDDMISTGGTIIAASNALKEAGAKGVSVACTHgmfVNNALERFAGSSLDNILSCNtLNS 258
                                       **************************99999998777777776666666666666664444 PP

>> Pribosyl_synth  Phosphoribosyl synthetase-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       0.7   1.6e+03     149     163 ..     101     115 ..      94     119 .. 0.82
   2 !   41.4   0.7   6.8e-14   1.5e-10      79     152 ..     190     263 ..     174     278 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.7
                                       HHHHT-TTEEEE--H CS
                    Pribosyl_synth 149 iqklrcskiktvdis 163
                                       +  l+c++i t+di 
  gi|474933739|ref|YP_007687321.1| 101 LLDLNCDRIITIDIH 115
                                       55789********95 PP

  == domain 2  score: 41.4 bits;  conditional E-value: 6.8e-14
                                       S--TTSEEEEEEEEE-S-HHHHHHHHHHHHTT--EEEEEEEEE---TTHHHHHHHSS--EEEEESSS--HHHHH CS
                    Pribosyl_synth  79 GdvgGriaiivddliddvesfvaaaevlkerGaykiyvlathGllssdaprlleesaidevvvtntipheiqkl 152
                                        dv+ +  +ivdd+i    +++aa++ lke Ga  + v +thG++ ++a +++  s++d+++  nt+   + ++
  gi|474933739|ref|YP_007687321.1| 190 ADVKDKKVLIVDDMISTGGTIIAASNALKEAGAKGVSVACTHGMFVNNALERFAGSSLDNILSCNTLNSAVSHI 263
                                       699***************************************************************98877554 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0         3   6.7e+03     167     194 ..      17      44 ..      15      47 .. 0.66
   2 !   23.3   0.0   1.6e-08   3.5e-05     118     170 ..     191     243 ..     169     261 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3
                           UPRTase 167 krlaeefpkvkvvtaavDeeldekgyiv 194
                                       ++++++fp+ + ++   +e+ld++ +iv
  gi|474933739|ref|YP_007687321.1|  17 QAASNRFPDGECYIRIDEEKLDDDVIIV 44 
                                       6677777777777775556677776665 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 1.6e-08
                           UPRTase 118 kiaertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkrla 170
                                       ++++++vl++D +i+TGg+++aa + Lke+g++  ++ +   +  +++++r+a
  gi|474933739|ref|YP_007687321.1| 191 DVKDKKVLIVDDMISTGGTIIAASNALKEAGAKGVSVACTHGMFVNNALERFA 243
                                       568999***********************999988888888888888887776 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   9.2e-06     0.021     120     150 ..     193     223 ..     172     246 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 9.2e-06
                          PRTase_2 120 aakelvLvDDEistGktalnliralqeklpr 150
                                       ++k++++vDD istG t+++  +al+e+  +
  gi|474933739|ref|YP_007687321.1| 193 KDKKVLIVDDMISTGGTIIAASNALKEAGAK 223
                                       67899*******************9987655 PP

>> His_Phos_1  Histidine phosphatase superfamily (branch 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.078   1.7e+02      31      73 ..     131     172 ..     127     177 .. 0.78
   2 ?    9.0   0.1   0.00045         1     131     182 ..     215     266 ..     209     271 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.078
                                       HHHHHHHHHHTTS---EEEE-SSHHHHHHHHHHHHCTT--EEE CS
                        His_Phos_1  31 eqAealaerlagepidaiysSplkRarqTaeliaealglpvel 73 
                                       + A+a+a+++++ +id +  Sp   a   a+++a+ +glp+ +
  gi|474933739|ref|YP_007687321.1| 131 KAAKAIADYFSEKGIDIV-ISPDIGAAGRAKAVADYMGLPYDH 172
                                       6799********999965.566666777788888888888765 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00045
                                       HHHHHHTTTSEEEEEE-HHHHHHHHHHHHT--GGGGGGB---TT-EEEEEE- CS
                        His_Phos_1 131 eelaarhegetvlvVsHggvirallarllglpleelrrleldnaslsvlefd 182
                                       ++l+++ +++  + ++Hg++++ +l r+ g +l+++   +  n ++s++++ 
  gi|474933739|ref|YP_007687321.1| 215 NALKEAGAKGVSVACTHGMFVNNALERFAGSSLDNILSCNTLNSAVSHISVA 266
                                       5566666666699****************************99999999875 PP

>> Amdase  Arylmalonate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.053   1.2e+02      91     111 ..      61      81 ..      57     150 .. 0.79
   2 ?    7.9   0.0   0.00093       2.1      90     133 ..     214     257 ..     202     279 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.053
                            Amdase  91 ealralgarRvAvataYidev 111
                                       +a+r+lga+R+A++  Y    
  gi|474933739|ref|YP_007687321.1|  61 DAVRRLGAKRIALVIPYFGYA 81 
                                       789*********999987655 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00093
                            Amdase  90 vealralgarRvAvataYidevnerLvayLeesglevaalesLd 133
                                        +al++ ga+ v va +    vn++L ++  +s  ++ + ++L+
  gi|474933739|ref|YP_007687321.1| 214 SNALKEAGAKGVSVACTHGMFVNNALERFAGSSLDNILSCNTLN 257
                                       5799*************************999888888888776 PP

>> Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00025      0.56      17      70 ..     109     160 ..     105     165 .. 0.83
   2 ?   -1.2   0.0       1.2   2.6e+03      66      91 ..     215     240 ..     180     243 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00025
                                       EEEESSSCEEEEEEEE.GCCCTSS.CSSTHHHHHHHHTT-SEEEESSSCHHHHHH CS
                     Nitro_FeMo-Co  17 iyeveegevkivenrveeaadaeg.ggggklaqllaeegvdvvivgkiGpralak 70 
                                       i+ ++ +++++++n    +++++  ++ +++a+  +e+g+d+vi   iG   +ak
  gi|474933739|ref|YP_007687321.1| 109 IITIDIHKESVLDNF---SCPHKDlKAAKAIADYFSEKGIDIVISPDIGAAGRAK 160
                                       455555588899999...88888889999********************987776 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.2
                                       HHHHHHCTTTSEEEES-SSBHHHHHH CS
                     Nitro_FeMo-Co  66 ralakleaagievykgaggtveealk 91 
                                       +al++  a+g+ v  + g  v +al+
  gi|474933739|ref|YP_007687321.1| 215 NALKEAGAKGVSVACTHGMFVNNALE 240
                                       23333333444444445555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1754.95
//
Query:       gi|474933740|ref|YP_007687322.1|  [L=469]
Description: prolyl-tRNA synthetase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-23   84.2   0.0    1.8e-23   83.4   0.0    1.4  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
    1.9e-19   69.6   0.0      5e-19   68.2   0.0    1.7  1  HGTP_anticodon  Anticodon binding domain
    7.2e-09   35.7   1.3    1.3e-08   34.9   0.3    1.9  2  ProRS-C_1       Prolyl-tRNA synthetase, C-terminal


Domain annotation for each model (and alignments):
>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.4   0.0     3e-27   1.8e-23       8     177 ..      98     266 ..      87     268 .. 0.88

  Alignments for each domain:
  == domain 1  score: 83.4 bits;  conditional E-value: 3e-27
                                       SEEEEE-SSSHHHHHHHHHHHEEEB.GGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEES.GGGHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                      tRNA-synt_2b   8 dreyiLkPtneetfvelirdevlrs.krLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfha.easlddslrd 82 
                                       d +++++Pt+e++++ +++ + +rs ++LPlk+yqi   +R+E++++r  +Rvre+h  + + +ha  ++++ ++++
  gi|474933740|ref|YP_007687322.1|  98 DVRLVVRPTSETAMYPMFSLW-VRShQDLPLKVYQIVNTFRYETKQTRAFMRVREIHFFESHTCHAdREDAERQVAQ 173
                                       66899**************88.9**788*****************9********************88999999999 PP

                                       HHHHHHHHHHHTT.SCEEEEEE.GTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTSSEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  83 likaisriferlglefraiiel.msaksadykdkkefeavsesltkgieigtiqklgtrlserlgatvldennreks 158
                                        ++ ++r+ +++ +++  +i+  ++++ + ++++  ++ v++  +++++ig+++   t++s+  ++t+ d n++++ 
  gi|474933740|ref|YP_007687322.1| 174 DVEIVDRLCRSICIPYSLLIRTdWDKF-PGANYTVGIDTVMP-NGRTLQIGSAHYYATNFSKPYEITYEDDNGEHQY 248
                                       9*************9976666548854.89999999******.9************************888888777 PP

                                       EEEEEEEEE.HHHHHHHHHH CS
                                       xxxxxxxxx.xxxxxxxxxx RF
                      tRNA-synt_2b 159 vimicaaig.veRllsaile 177
                                        + +   +g +eRll+a++ 
  gi|474933740|ref|YP_007687322.1| 249 AHQTT--LGmTERLLGAVVG 266
                                       75555..5555******985 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.2   0.0   8.4e-23     5e-19       1      89 [.     284     374 ..     284     376 .. 0.98

  Alignments for each domain:
  == domain 1  score: 68.2 bits;  conditional E-value: 8.4e-23
                                       SEEEEESSSS..HHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETT CS
                    HGTP_anticodon   1 qvvviplnek..aeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrd 75 
                                       q+v++p+ +k  a+e+++ ++ + e Lr+agirv+ldd ++++g k+  ++ +g+p++++vG ++le+++v+  +rd
  gi|474933740|ref|YP_007687322.1| 284 QIVIVPIFKKdnADEVLKACRGIEEVLRKAGIRVKLDDGDDRPGAKFFAWEVKGVPLRFEVGGRDLENNVVSWARRD 360
                                       89******9999999************************************************************** PP

                                       TCEEEEEETTHHHH CS
                    HGTP_anticodon  76 treqervsldelve 89 
                                       ++e+ ++sld+lv+
  gi|474933740|ref|YP_007687322.1| 361 NGEKGTMSLDSLVD 374
                                       ***********986 PP

>> ProRS-C_1  Prolyl-tRNA synthetase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.3   7.7e+03      20      41 ..     163     189 ..     156     194 .. 0.72
   2 !   34.9   0.3   2.2e-12   1.3e-08       6      67 ..     408     467 ..     406     468 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.3
                                       SGHHHHHHHHHHH.....S-EEEEEES CS
                         ProRS-C_1  20 geeecEekIkeet.....gakslcipf 41 
                                       ++e++E+++ +++        s cip 
  gi|474933740|ref|YP_007687322.1| 163 DREDAERQVAQDVeivdrLCRSICIPY 189
                                       567777777777766666677888885 PP

  == domain 2  score: 34.9 bits;  conditional E-value: 2.2e-12
                                       HHHHTT-EEEEEESSGHHHHHHHHHHHS-EEEEEESSB-SSCCCSB-TTT-SB-SEEEEEE- CS
                         ProRS-C_1   6 ealekkgfvlapWcgeeecEekIkeetgakslcipfdqepseegtkCivcgkpakkwvlfgr 67 
                                       + + ++++v++ Wcg +ec  k +++   k+l+ p    p+e + kCivcgk+  k ++ +r
  gi|474933740|ref|YP_007687322.1| 408 DSIPEGRIVRFGWCGCAECGHKFEDKYDIKILGTPYR--PEEFTGKCIVCGKEGAKPAYAAR 467
                                       5677889*****************************6..688999**************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 3064.72
//
Query:       gi|474933741|ref|YP_007687323.1|  [L=255]
Description: tRNA(1-methyladenosine) methyltransferase-related methyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-33  116.7   0.0      5e-30  105.0   0.0    2.0  2  GCD14            tRNA methyltransferase complex GCD14 subunit
    2.2e-10   40.6   0.0    2.8e-10   40.2   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    8.3e-09   36.1   0.0    1.5e-08   35.2   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    1.6e-07   31.3   0.0    2.4e-07   30.7   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      4e-07   29.6   0.0    5.9e-07   29.1   0.0    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      1e-05   26.2   0.0      2e-05   25.3   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
    1.8e-05   24.5   0.0    2.1e-05   24.2   0.0    1.2  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    2.3e-05   25.0   0.0    4.4e-05   24.0   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
     0.0018   17.4   0.0     0.0021   17.2   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
     0.0021   17.9   0.0      0.004   17.0   0.0    1.4  1  Methyltransf_23  Methyltransferase domain
      0.003   17.6   0.0     0.0041   17.1   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
     0.0033   16.6   0.0     0.0061   15.7   0.0    1.4  1  Fibrillarin      Fibrillarin
      0.007   15.6   0.1      0.098   11.8   0.0    2.0  2  Methyltransf_3   O-methyltransferase
  ------ inclusion threshold ------
      0.011   16.8   0.0      0.021   15.8   0.0    1.5  1  Methyltransf_24  Methyltransferase domain
      0.019   14.6   0.0      0.026   14.2   0.0    1.3  1  Methyltransf_28  Putative S-adenosyl-L-methionine-dependent m
      0.019   14.5   0.1      0.033   13.7   0.1    1.4  2  MTS              Methyltransferase small domain
       0.05   13.5   0.1      0.079   12.9   0.1    1.2  1  Methyltransf_18  Methyltransferase domain
       0.11   12.2   0.0       0.73    9.5   0.0    2.1  2  UPF0020          Putative RNA methylase family UPF0020
       0.13   12.5   1.3        4.7    7.5   1.1    3.0  3  NAD_binding_8    NAD(P)-binding Rossmann-like domain
       0.17   11.5   0.0       0.24   11.0   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95
       0.22   10.8   0.1        0.3   10.3   0.1    1.3  1  CMAS             Mycolic acid cyclopropane synthetase


Domain annotation for each model (and alignments):
>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.0   0.0   5.8e-33     5e-30      15     179 ..      69     229 ..      57     233 .. 0.94
   2 !    9.9   0.0   0.00061      0.52     229     247 .]     234     252 ..     230     252 .. 0.90

  Alignments for each domain:
  == domain 1  score: 105.0 bits;  conditional E-value: 5.8e-33
                             GCD14  15 laLphrtqilytaDisliimkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehels 91 
                                        +L+  +qi+  +D s ii + ++++G++v+e G+Gsg l++a++ +v+ tGh++t+e  eq ae+ ++++++++l+
  gi|474933741|ref|YP_007687323.1|  69 ESLDRGAQIITPKDASAIILECDIHEGTKVIEVGAGSGGLTTALLAAVGKTGHVHTLEIKEQNAERVLKNLKRTGLD 145
                                       5788999********************************************************************** PP

                             GCD14  92 qlvtvthrDvckeGfdeevsgkvDavfLDlPaPweaiphaakalkkeggrlCsfsPCieqvqrtceaLrelgfteie 168
                                            +  D+ +   d ++   +D v  D+P P +ai++++k+l ++ggr+C++ P  +q+  +++aLr+ gf++++
  gi|474933741|ref|YP_007687323.1| 146 ASWSYQIGDAREMEIDYGM---ADVVTTDMPDPENAIDNLSKHL-RNGGRICTYVPNANQLDLAVRALRDRGFVDVR 218
                                       *999*****9998886655...**********************.99****************************** PP

                             GCD14 169 tlevllrtyev 179
                                       ++e++ r  ev
  gi|474933741|ref|YP_007687323.1| 219 SFEIMRRGMEV 229
                                       *****998877 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00061
                             GCD14 229 lkPvselkghtgyLtfatk 247
                                       ++P  e+ ghtgyLtfa+k
  gi|474933741|ref|YP_007687323.1| 234 VRPSFEMLGHTGYLTFARK 252
                                       589999***********85 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.0   3.3e-13   2.8e-10       2     119 ..      93     203 ..      92     229 .. 0.87

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 3.3e-13
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDl 77 
                                       ++g++v+++G+G+G lt +l   +g+ ++v+ ++i+e+  e+  +n+++ gld   + ++gd+ e+e       +D+
  gi|474933741|ref|YP_007687323.1|  93 HEGTKVIEVGAGSGGLTTALLAAVGKTGHVHTLEIKEQNAERVLKNLKRTGLDaSWSYQIGDAREME-------IDY 162
                                       7899*************************************************99************.......455 PP

                   Methyltransf_31  78 ilsnevlnaladpdkileeiervlkpggilliedprllaelp 119
                                        +++ v  +++dp++++ ++++ l++gg++++  p+ + +l+
  gi|474933741|ref|YP_007687323.1| 163 GMADVVTTDMPDPENAIDNLSKHLRNGGRICTYVPN-ANQLD 203
                                       445444457*********************987777.55544 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.0   1.8e-11   1.5e-08       1      97 []      98     190 ..      98     190 .. 0.93

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 1.8e-11
                                       EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEESTG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssgal 74 
                                       v+++G+G+G lt al++++g  ++v+ ++i e+  e++ +++++ gl  +++++ gda++++ + g  D+v+     
  gi|474933741|ref|YP_007687323.1|  98 VIEVGAGSGGLTTALLAAVGkTGHVHTLEIKEQNAERVLKNLKRTGLdaSWSYQIGDAREMEIDYGMADVVTTD--- 171
                                       89****************9669**********************999889999********************3... PP

                                       GGSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  75 hhlsdedlekalkeiarvLkpgG 97 
                                            +d e+a+++++++L++gG
  gi|474933741|ref|YP_007687323.1| 172 ----MPDPENAIDNLSKHLRNGG 190
                                       ....357789************9 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0   2.8e-10   2.4e-07      52     179 ..      73     201 ..      52     221 .. 0.80

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 2.8e-10
                                       TTEEE--HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC.SEE CS
                              PCMT  52 ynatiSaphmvalalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle.nvi 127
                                        +a i  p+  ++++   ++++g++v+evG+GsG lt  l   vg++g+v ++e  ++ +e+  +nlk+ +l+ + +
  gi|474933741|ref|YP_007687323.1|  73 RGAQIITPKDASAIILECDIHEGTKVIEVGAGSGGLTTALLAAVGKTGHVHTLEIKEQNAERVLKNLKRTGLDaSWS 149
                                       55555555554444444679****************************************************98999 PP

                                       EEES-GGGTTGGG-SEEEEEESSBBSS.--HHHHHTEEEEEEEEEEESBSSSE CS
                              PCMT 128 vvvgDGrkGyeekaPYdaihvgaaape.iPealidQLkeGGrlvvPvgeeeeQ 179
                                        ++gD r+   ++   d++ +    pe   ++l + L +GGr+   v  + +Q
  gi|474933741|ref|YP_007687323.1| 150 YQIGDAREMEIDYGMADVVTTDMPDPEnAIDNLSKHLRNGGRICTYVP-NANQ 201
                                       9*****998888888888888877655155788889999999988887.3333 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   6.9e-10   5.9e-07      46     150 ..      93     193 ..      80     218 .. 0.92

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 6.9e-10
                                       --TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE--TTT-TTS-T-EEEEE CS
                   Ubie_methyltran  46 krgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.nieflqanaeeLpfeddsfDvvt 121
                                       ++g+kv++v +G+g l+ +l+ +vg++g+v+ l+i+e+  +   k lk++g   +  +  ++a e++ + +  Dvvt
  gi|474933741|ref|YP_007687323.1|  93 HEGTKVIEVGAGSGGLTTALLAAVGKTGHVHTLEIKEQNAERVLKNLKRTGLDaSWSYQIGDAREMEIDYGMADVVT 169
                                       689************************************************98799********************* PP

                                       EES-GGG-S-HHHHHHHHHHHEEEEEEEE CS
                   Ubie_methyltran 122 vsfGlrnvtDklkaLkeayrvlkpGGrlv 150
                                             +++D ++a+ ++ + l+ GGr+ 
  gi|474933741|ref|YP_007687323.1| 170 T-----DMPDPENAIDNLSKHLRNGGRIC 193
                                       6.....68999999999999999999975 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   2.3e-08     2e-05       2      99 .]     100     192 ..      99     192 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 2.3e-08
                   Methyltransf_12   2 eiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       e+G+G+G l+ all++  ++ +++ ++i ++  e+  + l++ + +    +++ +            D+  a  v  
  gi|474933741|ref|YP_007687323.1| 100 EVGAGSGGLTTALLAAVgKTGHVHTLEIKEQNAERVLKNLKRTGLDASWSYQIGDAREM------EIDYGMADVVTT 170
                                       9****************9***************99999999999988888888877766......899999999999 PP

                   Methyltransf_12  78 hlkdirevldnirklLkpgGrl 99 
                                        ++d++ ++dn+ k+L++gGr+
  gi|474933741|ref|YP_007687323.1| 171 DMPDPENAIDNLSKHLRNGGRI 192
                                       ********************86 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   2.5e-08   2.1e-05       6      88 ..      92     173 ..      85     215 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 2.5e-08
                                       --TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--.SEEEEES-CTCCHHHHCC..EE CS
                   Methyltr_RsmB-F   6 pqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvt.ntivleaDarkidkvlggelfD 81 
                                        +e+ +++++ a+ Gg Tt +++ + ++g+v  ++++++ ++rv +nlkr g+  +     +Dar+++ + g    D
  gi|474933741|ref|YP_007687323.1|  92 IHEGTKVIEVGAGSGGLTTALLAAVGKTGHVHTLEIKEQNAERVLKNLKRTGLDaSWSYQIGDAREMEIDYGM--AD 166
                                       578888***************9999****************************94556667899999888774..77 PP

                                       EEEEEE- CS
                   Methyltr_RsmB-F  82 riLlDaP 88 
                                        +  D P
  gi|474933741|ref|YP_007687323.1| 167 VVTTDMP 173
                                       7777777 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   5.2e-08   4.4e-05       2      95 ..     100     193 ..      99     194 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 5.2e-08
                                       EET-TTSHHHHHHH.HTT..SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES-CCC CS
                   Methyltransf_11   2 dvGcGtGrlaeala.krg..arvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvssevlhh 73 
                                       +vG+G+G l+ al    g  ++v ++++ ++  +++ ++ ++ gl  + +++ +da+++ +  +  D+v+     + 
  gi|474933741|ref|YP_007687323.1| 100 EVGAGSGGLTTALLaAVGktGHVHTLEIKEQNAERVLKNLKRTGLdaSWSYQIGDAREMEIDYGMADVVT-----TD 171
                                       89***8888877773444889*********************9999977899999999876666666665.....56 PP

                                       -CCHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  74 vedpekalkeiaRvLkpgGllv 95 
                                       ++dpe a++++ + L++gG+++
  gi|474933741|ref|YP_007687323.1| 172 MPDPENAIDNLSKHLRNGGRIC 193
                                       7******************985 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.4e-06    0.0021      19      72 ..      83     139 ..      76     210 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.4e-06
                                       HHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-...SEEEEE-S-HHHHHHHHCHT CS
                            RrnaAD  19 ineIldklnleekltvleigpGkGilTeeLakra...kqvvvlElderLakllqkkl 72 
                                       +  I+ + ++ e ++v+e+g+G G lT+ L+  +    +v  lE+ e+ a+++ k+l
  gi|474933741|ref|YP_007687323.1|  83 ASAIILECDIHEGTKVIEVGAGSGGLTTALLAAVgktGHVHTLEIKEQNAERVLKNL 139
                                       56799999**********************988886567778898887777666655 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   4.7e-06     0.004      23     125 ..      95     207 ..      63     238 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.7e-06
                   Methyltransf_23  23 ggrvLdiGcGtG.illevlrengf..svtgvDlspeaveiaekakkaqkdqfdeqeaaepqg.....kfdlIvlrev 91 
                                       g +v+++G+G+G  ++ +l++ g+  +v   ++ +++ e++   k+ + +     +++++ g      +d+  +  v
  gi|474933741|ref|YP_007687323.1|  95 GTKVIEVGAGSGgLTTALLAAVGKtgHVHTLEIKEQNAERV--LKNLKRTGL-DASWSYQIGdaremEIDYGMADVV 168
                                       458*********66777779999989999999999988886..444444444.33444433355667999999999* PP

                   Methyltransf_23  92 lehvpdppellrqiatllkpgGylllseplasl.....k 125
                                       +  +pdp+ +++++ ++l+ gG++   +p+a++      
  gi|474933741|ref|YP_007687323.1| 169 TTDMPDPENAIDNLSKHLRNGGRICTYVPNANQldlavR 207
                                       ************************999999987443330 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   4.8e-06    0.0041      22      81 ..      91     147 ..      70     178 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.8e-06
                   Methyltransf_32  22 kesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkr 81 
                                       + ++ ++v++vGaG g L+ +l   ++ +  +v+ +++ke+++e+  k  ++ g  ++++
  gi|474933741|ref|YP_007687323.1|  91 DIHEGTKVIEVGAGSGGLTTALLA-AVGKTGHVHTLEIKEQNAERVLKNLKRTG--LDAS 147
                                       5567789***************99.77899**************9999888887..5554 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   7.2e-06    0.0061      65     175 ..      89     196 ..      79     210 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 7.2e-06
                                       --S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHHHHHH.HHHTTS..TTEEEEES-TTSGGGGTTTS CS
                       Fibrillarin  65 elpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvlreli.evakkR..knivPileDArkPekYralv 138
                                       e+ i++g+kv+ +Ga+sG     +   vg++g v+++e  ++    ++ ++ ++         ++DAr+ e      
  gi|474933741|ref|YP_007687323.1|  89 ECDIHEGTKVIEVGAGSGGLTTALLAAVGKTGHVHTLEIKEQNAERVLkNLKRTGldASWSYQIGDAREME---IDY 162
                                       5779*************9999999999***********977655444314433321123455689998643...444 PP

                                       --EEEEEEESSSTTHHHHHHHHHHHHEEEEEEEEEEE CS
                       Fibrillarin 139 ekvDvifaDvaqpdqarilaknaklflkeggyllisi 175
                                        + Dv+ +D+ +p++a   ++n + +l++gg +  ++
  gi|474933741|ref|YP_007687323.1| 163 GMADVVTTDMPDPENA---IDNLSKHLRNGGRICTYV 196
                                       689**********986...89**********998777 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.13   1.1e+02     134     189 ..      15      71 ..       4      80 .. 0.74
   2 !   11.8   0.0   0.00011     0.098      38     110 ..      85     157 ..      72     166 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.13
                                       GGHHHHHHHHHHTEEEEEEEEEE-TTGGGGGG-S.S--SHHHHH.....HHHHHHHH CS
                    Methyltransf_3 134 ssyvnyyeklleLvkvGgliaiDntLWeGkvvee.ddeeakalreyravllelnkkl 189
                                       s  + +++  + +vk+Ggl +iD   ++G    +  d + k+ +++r  + +l ++l
  gi|474933741|ref|YP_007687323.1|  15 SGKKFWFRLEFGMVKMGGLGVIDGKKFQGLDDGDtVDIVGKQFAVFRPTVTDLMESL 71 
                                       5555566777899***********999998766545666777777777777776666 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHT--EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES-HHH CS
                    Methyltransf_3  38 fLslLvklvnakrvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvaekieliegdalk 110
                                        + l  ++ +  +v+e+G   G    a+  a+ + G++ +++i ++++e  lk +++ g++   +++ gda++
  gi|474933741|ref|YP_007687323.1|  85 AIILECDIHEGTKVIEVGAGSGGLTTALLAAVGKTGHVHTLEIKEQNAERVLKNLKRTGLDASWSYQIGDARE 157
                                       4556677889999*****877755555555999************************************9986 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   0.0   2.5e-05     0.021       1     100 [.      99     191 ..      99     194 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.5e-05
                   Methyltransf_24   1 vEiGvysGvstlwllralrrngagrlvavdhdpg.aeeaaalareaglddrvrlikadseealaslaagsiDllfiD 76 
                                       +E+G+ sG  t +ll+a+ ++g  ++++++ +++ ae++ ++++++gld+ +    +d++e   + + g  D++  D
  gi|474933741|ref|YP_007687323.1|  99 IEVGAGSGGLTTALLAAVGKTG--HVHTLEIKEQnAERVLKNLKRTGLDASWSYQIGDAREM--EIDYGMADVVTTD 171
                                       699****************999..589999888657778888888*************9999..6666788999999 PP

                   Methyltransf_24  77 gghaaeavledleallprlapggv 100
                                       ++    +  +++++l ++l++gg 
  gi|474933741|ref|YP_007687323.1| 172 MP----DPENAIDNLSKHLRNGGR 191
                                       88....666667788888888885 PP

>> Methyltransf_28  Putative S-adenosyl-L-methionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0     3e-05     0.026      18      73 ..      94     142 ..      85     181 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3e-05
                   Methyltransf_28  18 kklrliElGpGkGtLmadvLrtlrkflpefyealeyhlvEaSpqlrerQknrLkek 73 
                                       +++++iE+G+G+G L   +L ++ k+        ++h +E+ +q +er  ++Lk++
  gi|474933741|ref|YP_007687323.1|  94 EGTKVIEVGAGSGGLTTALLAAVGKT-------GHVHTLEIKEQNAERVLKNLKRT 142
                                       4689********************99.......47999999999999999999986 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   3.8e-05     0.033      23      84 ..      87     148 ..      68     173 .. 0.75
   2 ?   -3.7   0.0         9   7.7e+03     126     136 ..     183     193 ..     176     201 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.8e-05
                                       HHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.E.EEEEESBHHHHHHHHHHHHHTTGCEEE CS
                               MTS  23 LletlpkelsgkvlDlGcGaGvlgaalakespeae.vtlvdvdarAlesakenleanklevev 84 
                                       +le+   ++  kv+ +G+G G l++al+++  ++  v+ ++++ +  e   +nl++++l+++ 
  gi|474933741|ref|YP_007687323.1|  87 ILECDI-HEGTKVIEVGAGSGGLTTALLAAVGKTGhVHTLEIKEQNAERVLKNLKRTGLDASW 148
                                       333322.26778***********9988777766655********************9998543 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 9
                                       HHHEEEEEEEE CS
                               MTS 126 keaLkegGeLl 136
                                        ++L++gG++ 
  gi|474933741|ref|YP_007687323.1| 183 SKHLRNGGRIC 193
                                       68999999875 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   9.2e-05     0.079      12      75 ..      92     156 ..      87     171 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.2e-05
                   Methyltransf_18  12 vekgsrvaDiGtDHgylpiylv.kegkakkviasDinegplekakeniekagledkievrlsdGl 75 
                                       +++g++v+ +G+  g l+ +l+   gk+ +v+  +i+e+  e+  +n++++gl+ +++  ++d  
  gi|474933741|ref|YP_007687323.1|  92 IHEGTKVIEVGAGSGGLTTALLaAVGKTGHVHTLEIKEQNAERVLKNLKRTGLDASWSYQIGDAR 156
                                       678999*******9999988762679*******************************99999865 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00086      0.73      82     130 ..     125     173 ..     109     174 .. 0.88
   2 ?   -0.5   0.0      0.98   8.3e+02     150     177 ..     180     207 ..     176     227 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00086
                                       EES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE--- CS
                           UPF0020  82 sDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpP 130
                                       ++++++  ++  +N++++g++ +++++  da++++ + g  dv+ t++P
  gi|474933741|ref|YP_007687323.1| 125 LEIKEQNAERVLKNLKRTGLDASWSYQIGDAREMEIDYGMADVVTTDMP 173
                                       5666666777789**********************9999*********9 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.98
                                       HHHHHH-TT..-EEEEEESSHHHHHCC- CS
                           UPF0020 150 relkrvlrgggrlvlltsenkalekale 177
                                       + l+++lr+ggr++  +++ ++l  a++
  gi|474933741|ref|YP_007687323.1| 180 DNLSKHLRNGGRICTYVPNANQLDLAVR 207
                                       678999********99998888765554 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0         5   4.3e+03      43      54 ..      69      80 ..      46      85 .. 0.72
   2 ?    7.5   1.1    0.0055       4.7       2      49 ..     101     164 ..     101     186 .. 0.71
   3 ?    1.5   0.0      0.42   3.6e+02      26      54 ..     183     211 ..     176     220 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 5
                                      CEECTS---EEE CS
                     NAD_binding_8 43 vrvdygahifhg 54
                                        +d ga+i+++
  gi|474933741|ref|YP_007687323.1| 69 ESLDRGAQIITP 80
                                      457888888776 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0055
                                       E--SHHHHHHHHHHH............CCTEEEEEE-SSSSSSGGG-.EECETT...CEECTS- CS
                     NAD_binding_8   2 vGaGlsGlvaAylLa............kagfdvlllekrdrlGGraa.syevpg...vrvdyga 49 
                                       vGaG +Gl++A l+a            k++    +l +  r+G +a+ sy++++   + +dyg+
  gi|474933741|ref|YP_007687323.1| 101 VGAGSGGLTTALLAAvgktghvhtleiKEQNAERVLKNLKRTGLDASwSYQIGDareMEIDYGM 164
                                       9**********99986665555555554555666677777777776666666444446777766 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.42
                                       -SSSSSSGGG-EECETTCEECTS---EEE CS
                     NAD_binding_8  26 ekrdrlGGraasyevpgvrvdygahifhg 54 
                                        k+ r GGr+ +y  + + +d+ ++++++
  gi|474933741|ref|YP_007687323.1| 183 SKHLRNGGRICTYVPNANQLDLAVRALRD 211
                                       578899*******9999999999999876 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00028      0.24      41     103 ..      94     158 ..      61     195 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00028
                                       CC-EEEETT-TTSHHH..HHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHH CS
                     Cons_hypoth95  41 egarvLDlfaGsGalg..lEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedalea 103
                                       eg +v+++ aGsG+l   l A+  +  +++ +e +++ ++ + +nl++++l+++++  + da e 
  gi|474933741|ref|YP_007687323.1|  94 EGTKVIEVGAGSGGLTtaLLAAVGKTGHVHTLEIKEQNAERVLKNLKRTGLDASWSYQIGDAREM 158
                                       67899********99633567777889************************99888777777654 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00035       0.3      57     136 ..      89     172 ..      74     246 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00035
                                       TTT--TT-EEEEES-TTSHHHHH...HHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---..-- CS
                              CMAS  57 klelkpGmtlLdiGcGWGslvrr...averydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedlde..kv 128
                                         ++++G +++++G+G G+l++    av +   +v  l + +++a+++ k++++++l+ + + ++ d ++++    +
  gi|474933741|ref|YP_007687323.1|  89 ECDIHEGTKVIEVGAGSGGLTTAllaAVGK-TGHVHTLEIKEQNAERVLKNLKRTGLDASWSYQIGDAREMEIdyGM 164
                                       56789*************987651114444.679999999999999***********99999999999888762344 PP

                                       SEEEEES- CS
                              CMAS 129 drvvsvga 136
                                         vv+ ++
  gi|474933741|ref|YP_007687323.1| 165 ADVVTTDM 172
                                       45665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 1551.66
//
Query:       gi|474933742|ref|YP_007687324.1|  [L=80]
Description: phosphoribosylformylglycinamidine synthase, purS protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-22   79.6   0.2    1.6e-22   79.4   0.2    1.0  1  PurS      Phosphoribosylformylglycinamidine (FGAM) synthase
  ------ inclusion threshold ------
        0.1   12.6   0.0       0.11   12.4   0.0    1.1  1  PGDH_C    Phosphogluconate dehydrogenase (decarboxylating) C-


Domain annotation for each model (and alignments):
>> PurS  Phosphoribosylformylglycinamidine (FGAM) synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.4   0.2   1.8e-26   1.6e-22       3      76 ..       5      77 ..       3      78 .. 0.95

  Alignments for each domain:
  == domain 1  score: 79.4 bits;  conditional E-value: 1.8e-26
                                      EEEEEE-TTS--HHHHHHHHHHHHTTHTTEEEEEEEEEEEEEEE-SSHHHHHHHHHHHHHHTTS-TTTEEEEEE CS
                              PurS  3 kveVtlKkgvlDpqGkavkkalkslgyeevedvrvgkyieleleaedeeeaeeeveemceklLaNpviedyeie 76
                                       + ++lKkgv Dp+G+  kk+l+slg+++++ v+  k++e+el+  + eea +  ee c+klLaNpv+++y+++
  gi|474933742|ref|YP_007687324.1|  5 DIRIELKKGVADPEGSNTKKTLESLGFKGIKAVKSVKCFEVELDM-SGEEAVKAGEEYCKKLLANPVVQSYKVT 77
                                      799*****************************************6.667899*******************997 PP

>> PGDH_C  Phosphogluconate dehydrogenase (decarboxylating) C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.3e-05      0.11      13      57 ..      31      79 ..      20      80 .] 0.68

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.3e-05
                                      SSSS.S-EEEEEEE....EES-TTHHHHHHHHHHHHT.-SEEEEEE--HH CS
                            PGDH_C 13 fGGiaakqsivaal....lqgpeekyalgeevaktiy.aPverayrvtve 57
                                      f Gi+a +s+ +      ++g ee++++gee +k++  +Pv+++y+vt++
  gi|474933742|ref|YP_007687324.1| 31 FKGIKAVKSVKCFEveldMSG-EEAVKAGEEYCKKLLaNPVVQSYKVTLR 79
                                      789999999877531111445.66677777777766516********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 519.24
//
Query:       gi|474933743|ref|YP_007687325.1|  [L=778]
Description: phosphoribosylformylglycinamidine synthase II [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.7e-46  156.1   2.9    1.4e-32  113.0   0.1    2.2  2  AIRS_C          AIR synthase related protein, C-terminal doma
      3e-39  133.6   0.4    4.1e-19   69.0   0.1    2.5  2  AIRS            AIR synthase related protein, N-terminal doma
    6.9e-16   58.5   0.2    1.2e-15   57.7   0.2    1.4  1  FGAR-AT_linker  Formylglycinamide ribonucleotide amidotransfe


Domain annotation for each model (and alignments):
>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.0   0.1   2.4e-36   1.4e-32       2     154 ..     235     389 ..     234     391 .. 0.92
   2 !   43.3   0.5   6.4e-15   3.8e-11       2     148 ..     612     745 ..     611     750 .. 0.76

  Alignments for each domain:
  == domain 1  score: 113.0 bits;  conditional E-value: 2.4e-36
                                       TTEEEEEEET....SSCTCCHHHHHHHCHHHCTSHTT.TSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHH CS
                            AIRS_C   2 pGdvliltgs....lGlggagtslkrkileeegldds.avqlgdvlleptliyvkralaalkglvkaahDvTgGGLl 73 
                                       pG   il g+    +G++g+++++ + i ++++ d + avqlgd++ ++ +i ++++la++ +lv++++D++gGGL+
  gi|474933743|ref|YP_007687325.1| 235 PGEIMILFGGrtgrDGIHGVNFAS-KDITATSEDDSRgAVQLGDPITKEPVIHACLELAQK-HLVTGMKDLGGGGLS 309
                                       78888999999999*******555.5577777666568**********************7.*************** PP

                                       HHHHHHHHTTTEEEEEECGTHHHHHHHHHHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEESSS CS
                            AIRS_C  74 galaemapasgvgaeidldkvpifdelesplemllsensGrllvavppeeadavlaileeeglpeaavIGevtakee 150
                                       + + ema + g+ga +dldkvp+ +    p+e+++se+++r++++v+pe+ d+v+ai++ +++  a+ + ++t+ ++
  gi|474933743|ref|YP_007687325.1| 310 CVVGEMAIELGCGADVDLDKVPLKETGLAPWEIWVSESQERMMCTVKPENVDKVMAIFDLWDII-ATPVAKTTDTGR 385
                                       **************************99***********************************5.**********99 PP

                                       EEEE CS
                            AIRS_C 151 lsvi 154
                                       +++ 
  gi|474933743|ref|YP_007687325.1| 386 TRLF 389
                                       9876 PP

  == domain 2  score: 43.3 bits;  conditional E-value: 6.4e-15
                                       TTEEEEEEET..SSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHH..HTTECEEEE--TTHHHH CS
                            AIRS_C   2 pGdvliltgs..lGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaal..kglvkaahDvTgGGLlg 74 
                                        G +++++g   + +g++  + ++ +++  +++     ++ ++l+  +    ++   +  +glv ++hD+++GGL  
  gi|474933743|ref|YP_007687325.1| 612 SGSCIFVVGDtkDEMGASL-LFRKYGGKGGDVP----DVVIPRLK-EVSGRLLE---AmgEGLVLGCHDCSDGGLGI 679
                                       6889999999644444444.5555555555555....23333333.33333333...2246**************** PP

                                       HHHHHHHTTTEEEEEECGTHHHHHHHHHHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEES CS
                            AIRS_C  75 alaemapasgvgaeidldkvpifdelesplemllsensGrllvavppeeadavlaileeeglpeaavIGevtak 148
                                       a++em+  ++vga+++l+++p  d     +  l+se+  r +  v+ ++ d++++i++++    a+ IG + ++
  gi|474933743|ref|YP_007687325.1| 680 AVSEMCISGQVGAQLNLSQMPGDDI----MVKLFSESASRWIAEVDGADVDRFTQIMGDA----ATLIGITKGD 745
                                       ***********************94....799**************************84....8888877655 PP

>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.0   0.1   6.9e-23   4.1e-19       1      94 []     109     222 ..     100     222 .. 0.93
   2 !   62.3   0.0   8.9e-21   5.3e-17       5      94 .]     493     598 ..     478     598 .. 0.91

  Alignments for each domain:
  == domain 1  score: 69.0 bits;  conditional E-value: 6.9e-23
                                       SSSEEEEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.................HHHHHHH CS
                              AIRS   1 dDaavvvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp.................wleevvr 60 
                                       dD + ++ ++shn+p+++ep+ + +a++++++++D+++mGA+P++l + l+++                  +++vv+
  gi|474933743|ref|YP_007687325.1| 109 DDYGYALRVESHNHPSAIEPYGG-AATGIGGIVRDVICMGAQPIGLADPLCFGpidtkkeipagikhpryLINGVVS 184
                                       3444599****************.***************************************************** PP

                                       HHHHHHHHTT-EEEEEEEEEESS....EEEEEEEEEEE CS
                              AIRS  61 glaeaaeelgvplvgGdtsfsne....ptisvtavGlv 94 
                                       g++++++++g+p+++G   f+++    ++++v+++G+v
  gi|474933743|ref|YP_007687325.1| 185 GIRDYGNRIGIPTITGGFFFDDSytgnCLVNVCCFGIV 222
                                       ********************9989999*********97 PP

  == domain 2  score: 62.3 bits;  conditional E-value: 8.9e-21
                                       EEEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.........HHHHHHHHHHHHHHHTT-E CS
                              AIRS   5 vvvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp.........wleevvrglaeaaeelgvp 72 
                                       +++++ +++  +  +p+++ G+ ++ ++ ++++a+GArP a++++l+++         +++e+vrg++e a+el++p
  gi|474933743|ref|YP_007687325.1| 493 LAAAVGCNPWFTGADPYRG-GKVCIDEAFRNVVAVGARPNAFTDCLNFGnpekperlgEFREAVRGIGEIAKELNIP 568
                                       4778889999999******.********************************************************* PP

                                       EEEEEEEEESS........EEEEEEEEEEE CS
                              AIRS  73 lvgGdtsfsne........ptisvtavGlv 94 
                                       + +G++s +ne        pt+++++ Gl+
  gi|474933743|ref|YP_007687325.1| 569 IPSGNVSMYNEapggehilPTPMIVCCGLI 598
                                       *********999*************99985 PP

>> FGAR-AT_linker  Formylglycinamide ribonucleotide amidotransferase linker domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.7   0.2   2.1e-19   1.2e-15       1      50 []      29      78 ..      29      78 .. 0.98

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 2.1e-19
                    FGAR-AT_linker  1 LeeankelglaLsdeEidylqeafeklgrnPtdvElemfaqvwSEHCrHK 50
                                      L+++++ l l+Lsd+E+  +q+ + + +r+ tdvEl+ ++q+wSEHC++K
  gi|474933743|ref|YP_007687325.1| 29 LSQISEALSLGLSDDEMLEIQKFYVRENREATDVELQSLGQAWSEHCCYK 78
                                      7899********************99***********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (778 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.49
# Mc/sec: 4795.30
//
Query:       gi|474933744|ref|YP_007687326.1|  [L=272]
Description: phosphoribosylformylglycinamidine synthase I [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-71  240.6   0.0    1.7e-71  240.4   0.0    1.0  1  GATase_5       CobB/CobQ-like glutamine amidotransferase doma
    7.1e-07   29.2   0.0    1.1e-06   28.5   0.0    1.5  1  DJ-1_PfpI      DJ-1/PfpI family
    5.1e-06   26.2   0.0    9.1e-06   25.4   0.0    1.3  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    0.00073   19.4   0.0     0.0017   18.2   0.0    1.5  1  GATase         Glutamine amidotransferase class-I
  ------ inclusion threshold ------
      0.013   15.4   0.0      0.029   14.2   0.0    1.6  2  SNO            SNO glutamine amidotransferase family
      0.014   15.1   0.0      0.021   14.6   0.0    1.3  1  Peptidase_C26  Peptidase C26


Domain annotation for each model (and alignments):
>> GATase_5  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  240.4   0.0   5.6e-75   1.7e-71       2     259 ..       6     268 ..       5     269 .. 0.94

  Alignments for each domain:
  == domain 1  score: 240.4 bits;  conditional E-value: 5.6e-75
                          GATase_5   2 pkvailreeGvngeyemaaafekaGfeavdvhmsdlleg.....rvslddfqilalpGGfsygDelgsgkgwaksll 73 
                                       +kv+++r eG+n+e ema+afe+ G++a++vh+++ll +     + +l+++  la+pGGfs+gD   +g+++a++++
  gi|474933744|ref|YP_007687326.1|   6 VKVCVIRIEGTNCEDEMANAFEMVGAKAEKVHLKQLLGQcapelKRNLEEYDALAFPGGFSAGDYVRAGAIFAARIK 82 
                                       69**********************************9663333366******************************9 PP

                          GATase_5  74 lneklrealekflnredtlaLGiCnGfqlLvklglvpggeiee.aeksptltrNksgrfesrlvsvvvsekspsvfl 149
                                         + + +++++f++  ++ +LG+CnGfq+Lv+lgl+p+ + +  ++ +++l  N+sgrfe+r + ++ ++  ++vf+
  gi|474933744|ref|YP_007687326.1|  83 --AGIGKDVRDFVEA-GKPVLGVCNGFQILVELGLLPALDGTMsDRPTAALYTNDSGRFECRPSVLRNDNRGKCVFT 156
                                       ..8************.**********************9998878999***************999*9********* PP

                          GATase_5 150 kgme...glslpvahGeGrfvfkseevlkeleangqvalrYvdeegkpteeyplNPNgSpegiagitspdGRvlalm 223
                                       +++     + +p ah+eG++  + +  +++le+n qv++rYv ++g    +yp+NPNgSp++iagi++p G vl++m
  gi|474933744|ref|YP_007687326.1| 157 SDIPkgsLMVCPSAHAEGKLLSEIPGFVQKLEENDQVVFRYVTPDGGR-ASYPWNPNGSPSDIAGICNPAGNVLGMM 232
                                       999434477888********************************8876.68************************** PP

                          GATase_5 224 pHpervveavqksiipeeeeeevspwlrlFenavky 259
                                       pHperv++ +  + +++++  e +p+  +F + +ky
  gi|474933744|ref|YP_007687326.1| 233 PHPERVMTGYTVPDWTRSKAGEDGPGKAIFTSVMKY 268
                                       ****************9988767**********999 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   3.8e-10   1.1e-06      46     126 ..      34     128 ..       1     164 [. 0.72

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 3.8e-10
                                       EEEE-SEEGG......GCTCCG-SEEEE--BHHHHHHHHTSH........HHHHHHHHHHHTT-EEEEETTTHHHHH CS
                         DJ-1_PfpI  46 lkvtvdasld......dvkaaeyDalvlpGGragperlrene........kvvelvkefaekgklvaaICagpqlLa 108
                                       +kv + + l+      + + +eyDal  pGG +  +++r+ +         +++ v++f+e+gk+v  +C g q+L+
  gi|474933744|ref|YP_007687326.1|  34 EKVHLKQLLGqcapelKRNLEEYDALAFPGGFSAGDYVRAGAifaarikaGIGKDVRDFVEAGKPVLGVCNGFQILV 110
                                       5555555555333333335679***************998664433333367888********************** PP

                                       HTTTTTTSEE--SGGGHH CS
                         DJ-1_PfpI 109 aagvlkgrrvTsypavkd 126
                                       + g+l+    T     + 
  gi|474933744|ref|YP_007687326.1| 111 ELGLLPALDGTMSDRPTA 128
                                       *****9887776655555 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   3.1e-09   9.1e-06      28      89 ..      44     110 ..      33     114 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 3.1e-09
                          GATase_3  28 rfvplkdeslgedadlvilpGgkdtiq...d...lallresgldeaikeaaeaggpvlgiCGGlqmLG 89 
                                       + +p  +++l+ ++d++ +pGg++  +   +    a+  + g+ +++++++eag+pvlg+C G+q+L 
  gi|474933744|ref|YP_007687326.1|  44 QCAPELKRNLE-EYDALAFPGGFSAGDyvrAgaiFAARIKAGIGKDVRDFVEAGKPVLGVCNGFQILV 110
                                       55666778895.5*********97543111211133444699************************96 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   5.7e-07    0.0017      36      86 ..      49     111 ..      17     114 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 5.7e-07
                                       HHH.THHSTSEEEEEEESSCTT.........TTTHHHHHHHHCT...STS-EEEETHHHHHHHH CS
                            GATase  36 ile.llknpdgilvsgGpgspg.........vegkieaikeare...nkiPiLGICLGmQllai 86 
                                         + +l+++d++ ++gG+ +           +  k  + k +r+   +++P+LG+C G+Q+l++
  gi|474933744|ref|YP_007687326.1|  49 L-KrNLEEYDALAFPGGFSAGDyvragaifaARIKAGIGKDVRDfveAGKPVLGVCNGFQILVE 111
                                       3.335899999999***9988888777776644444444444434449*************986 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   9.8e-06     0.029      28      81 ..      50     109 ..      20     114 .. 0.76
   2 ?   -3.5   0.0       2.7     8e+03     160     181 ..     226     247 ..     217     248 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.8e-06
                                       GGGGCC-SEEEE-SS-HH.......HHHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHH CS
                               SNO  28 kedlaevdaliiPGGest.......amskliertglyedllefvknsekvvlGtCaGlill 81 
                                       k +l+e dal  PGG s+       a+     + g+ +d+++fv+ + k+vlG C G+ +l
  gi|474933744|ref|YP_007687326.1|  50 KRNLEEYDALAFPGGFSAgdyvragAIFAARIKAGIGKDVRDFVEAG-KPVLGVCNGFQIL 109
                                       568************9863333222344444578999********99.*********9776 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.7
                                       TTEEEESS-GGGSTTHCHHHHH CS
                               SNO 160 kkilatsfhPelaeddirvhdy 181
                                       +++l++  hPe    ++ v d+
  gi|474933744|ref|YP_007687326.1| 226 GNVLGMMPHPERVMTGYTVPDW 247
                                       6889999999988888887777 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0     7e-06     0.021      99     123 ..      90     113 ..      46     126 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 7e-06
                     Peptidase_C26  99 raalergvPilgiCrGlqllnvalG 123
                                       r  +e+g+P+lg+C G+q+l v lG
  gi|474933744|ref|YP_007687326.1|  90 RDFVEAGKPVLGVCNGFQIL-VELG 113
                                       677899*************9.7666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1639.91
//
Query:       gi|474933745|ref|YP_007687327.1|  [L=229]
Description: Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-40  137.1   0.0    4.9e-40  136.4   0.0    1.3  1  CTP-dep_RFKase  Domain of unknown function DUF120
     0.0098   15.8   0.2      0.016   15.1   0.2    1.3  1  MarR_2          MarR family
  ------ inclusion threshold ------
      0.031   13.8   0.1      0.057   13.0   0.1    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
      0.043   12.2   0.0      0.053   11.9   0.0    1.1  1  Glyco_hydro_1   Glycosyl hydrolase family 1
      0.047   13.9   0.0       0.13   12.5   0.0    1.7  1  ROF             Modulator of Rho-dependent transcription term
      0.047   14.2   0.1      0.086   13.3   0.1    1.4  1  HTH_27          Winged helix DNA-binding domain
      0.054   13.4   0.0        0.1   12.6   0.0    1.3  1  MarR            MarR family
      0.086   12.8   0.2       0.15   12.0   0.2    1.4  1  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.091   12.8   0.0       0.44   10.7   0.1    1.9  2  HTH_20          Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> CTP-dep_RFKase  Domain of unknown function DUF120
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.4   0.0   2.4e-43   4.9e-40       1     121 []     108     227 ..     108     227 .. 0.99

  Alignments for each domain:
  == domain 1  score: 136.4 bits;  conditional E-value: 2.4e-43
                                       EE--SSHHHHHHCSHHHHHHHHHHHSS---SS-EEEEESCCGHHHHCHHHHS--EEE--EEETTEEE--EEEEEEEE CS
                    CTP-dep_RFKase   1 VvsGlgeGkyyvslegykeqfeeklgfepypGTLNvkldeeslelrkaleklkgieiegfedeertfgavkvypaki 77 
                                       V++G+geG yy+ ++gy++qfe+klgf+p+ GTLNv +d+e++ + + ++++ gi i gf+de+r+fg+v +y+aki
  gi|474933745|ref|YP_007687327.1| 108 VMDGMGEGGYYICQKGYMDQFESKLGFKPFFGTLNVGVDKEDIGKLDVVKSTAGILIAGFTDEGRSFGDVIAYKAKI 184
                                       899************************************************************************** PP

                                       CCEEEEEEEESS-SS.TTEEEEE-SS-HHHHTT--TT-EEEEEE CS
                    CTP-dep_RFKase  78 ekikaavvvperthyeedvlEiiapekLReklelkdgdevevev 121
                                       +++++avvvp r+hy  dv+Eii+p++LR++l+l+ gd+v+v++
  gi|474933745|ref|YP_007687327.1| 185 RNVECAVVVPARSHY-MDVIEIICPYHLRRTLSLNTGDRVDVRI 227
                                       ***************.9************************987 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.2   8.1e-06     0.016      19      56 ..      34      69 ..      18      75 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8.1e-06
                                      TSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2 19 grdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                         ++ +el ++l +s++++s+++ +L + GL++r  g
  gi|474933745|ref|YP_007687327.1| 34 A--VSSRELGDALEMSQQSASKRILELLDLGLIVRDLG 69
                                      3..7899**************************98644 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   2.9e-05     0.057      19      47 ..      36      64 ..      35      65 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.9e-05
                            HTH_24 19 sqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      s reL ++l +S++  ++r+ +L + GlI
  gi|474933745|ref|YP_007687327.1| 36 SSRELGDALEMSQQSASKRILELLDLGLI 64
                                      789*************************9 PP

>> Glyco_hydro_1  Glycosyl hydrolase family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.7e-05     0.053     363     429 ..      82     145 ..      46     153 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.7e-05
                                       --EE-BSSSHHH--HHHHHHHHHHHHHHHHHHHTT--EEEEEE..E-SB----GGGTTSEE--SEEEET CS
                     Glyco_hydro_1 363 lgakdeieegkveDdkRidYlkehlnevkkaiedgvdlkgYva..wsllDnfewaegyskrfGlvyvdr 429
                                       + +     + + ++++Ri  l +h+ +v+ a+ dg+   gY++   + +D+fe   g++  fG + v  
  gi|474933745|ref|YP_007687327.1|  82 VDEL----KREYNEYRRIFELTDHM-TVRGAVMDGMGEGGYYIcqKGYMDQFESKLGFKPFFGTLNVGV 145
                                       4333....367899**********8.5899***********763368****************988764 PP

>> ROF  Modulator of Rho-dependent transcription termination (ROF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.4e-05      0.13       7      31 ..     200     224 ..     196     228 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.4e-05
                                       HHHHHHHHTTTT-EEEE-TTT--EE CS
                               ROF   7 yDylEiaClyryrlkleLkdgetie 31 
                                        D++Ei+C y++r +l L+ g++++
  gi|474933745|ref|YP_007687327.1| 200 MDVIEIICPYHLRRTLSLNTGDRVD 224
                                       49******************99875 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   4.3e-05     0.086      19      65 ..      35      78 ..      20      81 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.3e-05
                            HTH_27 19 kkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlT 65
                                      ++ ++l ++l ++++++s+ + +L   GL++r   +   r  r++ T
  gi|474933745|ref|YP_007687327.1| 35 VSSRELGDALEMSQQSASKRILELLDLGLIVRDLGA---RKQRIKMT 78
                                      5779**************************999888...55555555 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0     5e-05       0.1       8      49 ..      25      66 ..      20      71 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5e-05
                                      HHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR  8 iLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieR 49
                                      +L  +++  + s  eL+++l++s+ ++++ + +L + Gli R
  gi|474933745|ref|YP_007687327.1| 25 LLGGIDDYIAVSSRELGDALEMSQQSASKRILELLDLGLIVR 66
                                      55567888899999**************************88 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   7.7e-05      0.15      20      54 ..      33      69 ..      19      80 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.7e-05
                                      EEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEE..T CS
                         HTH_Crp_2 20 lpltqeelAsmlGltretvsrilseLkreglisr..g 54
                                      + ++ +el++ l +++++ s+ + eL + gli r  g
  gi|474933745|ref|YP_007687327.1| 33 IAVSSRELGDALEMSQQSASKRILELLDLGLIVRdlG 69
                                      67999***************************94234 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00022      0.44      24      55 ..      34      65 ..      31      68 .. 0.92
   2 ?   -1.2   0.0       1.1   2.2e+03       2      14 ..      94     107 ..      93     115 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00022
                                      TB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20 24 gltaselaerldlskntlsyHLrvLeeagLve 55
                                      +++  el ++l++s++++s+++ +L + gL+ 
  gi|474933745|ref|YP_007687327.1| 34 AVSSRELGDALEMSQQSASKRILELLDLGLIV 65
                                      57889*************************86 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.1
                                       HHHHHHS-.HHHHH CS
                            HTH_20   2 qiaeALah.PvRrr 14 
                                       +i+e+++h  vR +
  gi|474933745|ref|YP_007687327.1|  94 RIFELTDHmTVRGA 107
                                       68999999666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1339.54
//
Query:       gi|474933746|ref|YP_007687328.1|  [L=98]
Description: hypothetical protein TALC_00154 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 693.50
//
Query:       gi|474933747|ref|YP_007687329.1|  [L=157]
Description: hypothetical protein TALC_00155 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       185  (0.0103185); expected 358.6 (0.02)
Passed bias filter:                      175  (0.00976072); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 1148.78
//
Query:       gi|474933748|ref|YP_007687330.1|  [L=128]
Description: hypothetical protein TALC_00156 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
        6.3    6.7  18.4        4.2    7.2   4.4    2.9  2  DUF4118          Domain of unknown function (DUF4118)
        6.4    6.5  17.4       0.49   10.1   9.6    2.0  2  DUF1282          Protein of unknown function (DUF1282)


Domain annotation for each model (and alignments):
>> DUF4118  Domain of unknown function (DUF4118)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   4.4   0.00047       4.2       4      44 ..      21      63 ..      17      68 .. 0.84
   2 ?    3.2   6.3    0.0083        75      37      64 ..      89     116 ..      63     126 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00047
                           DUF4118  4 avlllalatllallldkl.lsl.anivllfllavllvallggl 44
                                       v+++a+a++la+++d   +++ a + l +l+avl+ al gg+
  gi|474933748|ref|YP_007687330.1| 21 IVAFFAMAFALAYAVDGSgMDTvADAGLYLLMAVLFFALAGGF 63
                                      467899999999999777655559*****************98 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.0083
                           DUF4118  37 lvallgglgpgllaallsvllfnyfftp 64 
                                       ++a ++ l+ g++ a+l++l++   f+ 
  gi|474933748|ref|YP_007687330.1|  89 FAAGYFELWFGIIEAVLGALCVAAAFMN 116
                                       3455667899999999999999999976 PP

>> DUF1282  Protein of unknown function (DUF1282)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   1.3     0.031   2.8e+02      62      82 ..      16      35 ..       3      46 .. 0.56
   2 ?   10.1   9.6   5.5e-05      0.49      72     137 ..      46     112 ..      40     126 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.031
                           DUF1282 62 sliisvvfylalgvlvlayli 82
                                      +li ++v+ +a+  ++lay++
  gi|474933748|ref|YP_007687330.1| 16 ALIGGIVAFFAM-AFALAYAV 35
                                      333333333333.55555554 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 5.5e-05
                           DUF1282  72 algvlvlayl.iklmgrtyd.sqhsyskifafaayalvplflgglalglsllllvalvslllllyvvv 137
                                       a+++l++a l + l+g +   +q + +++++f+a+ +  + +gg+a+g+  l+++++ ++l +l+v++
  gi|474933748|ref|YP_007687330.1|  46 AGLYLLMAVLfFALAGGFTRyAQWT-QNVLIFMAFLTLGAAIGGFAAGYFELWFGIIEAVLGALCVAA 112
                                       5567777777455555554435555.6899**************************888877776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       941  (0.0524848); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 821.35
//
Query:       gi|474933749|ref|YP_007687331.1|  [L=207]
Description: hypothetical protein TALC_00157 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      7e-09   35.5  20.4    1.1e-08   34.9  20.4    1.4  1  DUF998         Protein of unknown function (DUF998)
  ------ inclusion threshold ------
      0.095   12.6   0.5       0.18   11.6   0.5    1.6  1  Rossmann-like  Rossmann-like domain
       0.13   11.9   0.1       0.19   11.4   0.1    1.2  1  CBM9_2         Carbohydrate-binding family 9


Domain annotation for each model (and alignments):
>> DUF998  Protein of unknown function (DUF998)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9  20.4   1.9e-12   1.1e-08       1     182 [.      17     192 ..      17     195 .. 0.75

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 1.9e-12
                            DUF998   1 vaaallalavilaaallrpgydplrhaiSeLgaeg.gpggwlfnaglvllgllvlalavgllraargragragrlll 76 
                                       ++a+++++ +++aa  +++ ++++++ + + g  +  +   +fn+g++l+g+l++a+++g ++   + + ++++ll 
  gi|474933749|ref|YP_007687331.1|  17 ILAIAVFICAWIAAYSADSSWSWTESCLGDFGISDnEDAVHYFNYGCLLSGILLAAYGAGKASYEAKIGYKISGLLT 93 
                                       689999***************************9999999999*****************99977777888888888 PP

                            DUF998  77 avaglglvlagvfptdpgggspslsglvHglasavaflalavavl..llasaarrrawallrlvggvallllvaalv 151
                                       a  g+++++ gvf +d +gg +       ++++++a +++a++++  +++  +  ++ +++ + +g+++++ v   +
  gi|474933749|ref|YP_007687331.1|  94 AFVGISVLFLGVFTLDYAGG-D-----YFRFFGMLAAILVACSLIaeCAG-LWIDGGSKRAIAGIGIVFAIVVGTCA 163
                                       899*************9974.4.....88888888888888888755333.33344444443333333333333333 PP

                            DUF998 152 wllaaaldgslllGlaerllvlaitawllal 182
                                       ++la  l++   +G+a  l+ ++i  +++++
  gi|474933749|ref|YP_007687331.1| 164 LGLA--LEEAEHVGVALALAWFVIDGVVFLA 192
                                       3333..3667777777777777777776665 PP

>> Rossmann-like  Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.5   3.1e-05      0.18       8      39 ..     146     178 ..     140     202 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.1e-05
                     Rossmann-like   8 sarlsvGiisaGrvGt.algaaleraghvvvgi 39 
                                       +a  ++Gi+ a  vGt alg ale a+hv v++
  gi|474933749|ref|YP_007687331.1| 146 RAIAGIGIVFAIVVGTcALGLALEEAEHVGVAL 178
                                       556689*********868**********97775 PP

>> CBM9_2  Carbohydrate-binding family 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   3.2e-05      0.19      53     102 ..      27      78 ..      12      89 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.2e-05
                            CBM9_2  53 vravatedngrvweDsCveff.ispeedg.iyynlevnCigtlligagaere 102
                                         a+++ d    w++sC   f is++ed   y+n  +   g ll+++ga + 
  gi|474933749|ref|YP_007687331.1|  27 WIAAYSADSSWSWTESCLGDFgISDNEDAvHYFNYGCLLSGILLAAYGAGKA 78 
                                       56889999999******96661555555436889999999999999887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       917  (0.0511462); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1330.67
//
Query:       gi|474933750|ref|YP_007687332.1|  [L=255]
Description: Conserved hypothetical ATP binding protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.5e-60  202.7   0.0    8.9e-60  202.5   0.0    1.0  1  ATP_bind_1      Conserved hypothetical ATP binding protein
     0.0025   17.5   0.0       0.57    9.8   0.0    2.2  2  SRP54           SRP54-type protein, GTPase domain
     0.0088   15.0   0.0        0.1   11.6   0.0    2.1  2  MeaB            Methylmalonyl Co-A mutase-associated GTPase M
  ------ inclusion threshold ------
      0.012   15.3   0.0      0.024   14.4   0.0    1.5  1  AAA_29          P-loop containing region of AAA domain
      0.015   14.8   0.0      0.025   14.1   0.0    1.3  1  AAA_7           P-loop containing dynein motor region
      0.027   14.2   0.0       0.04   13.6   0.0    1.2  1  AAA_24          AAA domain
      0.041   13.1   0.0       0.23   10.6   0.0    1.9  2  ArsA_ATPase     Anion-transporting ATPase
      0.042   14.2   0.0      0.083   13.3   0.0    1.5  1  AAA_16          AAA ATPase domain
      0.047   13.9   0.0       0.17   12.2   0.0    1.8  2  AAA_22          AAA domain
      0.068   12.5   0.0       0.86    8.9   0.0    1.9  2  Gtr1_RagA       Gtr1/RagA G protein conserved region
      0.068   13.1   0.0        2.9    7.8   0.0    2.8  3  RsgA_GTPase     RsgA GTPase
      0.074   12.8   0.0       0.13   11.9   0.0    1.4  1  AAA_30          AAA domain
        0.1   12.1   0.0         32    4.0   0.0    2.9  3  GTP_EFTU        Elongation factor Tu GTP binding domain
        0.1   12.7   0.2        3.2    7.9   0.2    2.3  1  MMR_HSR1        50S ribosome-binding GTPase
       0.18   11.7   0.0       0.35   10.8   0.0    1.4  1  Ploopntkinase3  P-loop Nucleotide Kinase3


Domain annotation for each model (and alignments):
>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.5   0.0   7.4e-63   8.9e-60       1     236 [.       6     242 ..       6     246 .. 0.95

  Alignments for each domain:
  == domain 1  score: 202.5 bits;  conditional E-value: 7.4e-63
                        ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPAaeelpYeaavdirelitledvmedlglgpngalvvaleflre 77 
                                       +vG+aGsGK+t+vga+ e+l++++ ++ v+NLDP+ae+lpY +++dire+i l++vm ++glgpnga +va+++++ 
  gi|474933750|ref|YP_007687332.1|   6 FVGTAGSGKSTMVGAFKEWLDDNEIDSVVINLDPGAEKLPYVPDIDIREWIGLDEVMSEYGLGPNGAQIVAADLMAV 82 
                                       58*************************************************************************** PP

                        ATP_bind_1  78 sldwldeelekeeddyllfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltdptkfisgllsalsamlr 154
                                       ++d ++++l+ ++ dy+l+DtPGQ+elf ++es + +v++L  + + +  yL D++  +++  f+s++ +++ + +r
  gi|474933750|ref|YP_007687332.1|  83 NIDRVKDALGSYNVDYVLIDTPGQLELFAFRESSSVVVDALG-KSRSMLCYLSDPTLYKSANGFVSAMTLSSLVQFR 158
                                       ******************************************.5999999*************************** PP

                        ATP_bind_1 155 lelPhvvvlnkfDllkek.lekeleffedvealslllekee.ekykklaeaiaelleefalvlrflplssekeesie 229
                                       ++lP+++ l+k+D+l+e+ +++ +++++++++l   l +e+ + ++ +  ++ +++e+++   ++ ++s++k+ ++ 
  gi|474933750|ref|YP_007687332.1| 159 MDLPMINLLSKCDVLQESeADRIVDWYNNPDTLYGSLLDEDrDPQSVMGMELFRAMEDTGVFGEMRQVSASKGVGLP 235
                                       ****************99999***********997655554378888999***********************9999 PP

                        ATP_bind_1 230 dllslid 236
                                       +++++++
  gi|474933750|ref|YP_007687332.1| 236 EIYAAVQ 242
                                       9998886 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0   0.00048      0.57       3      38 ..       3      38 ..       1      39 [. 0.88
   2 !    5.5   0.0    0.0098        12      69      96 ..      80     108 ..      69     127 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00048
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                       + +vG+ G+GK t ++   ++l +++ + +++ +D
  gi|474933750|ref|YP_007687332.1|  3 NVYFVGTAGSGKSTMVGAFKEWLDDNEIDSVVINLD 38
                                      5789*******************9998888887776 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0098
                                       HHHHHHHHHHH.HHTTSSEEEEEE--SST CS
                             SRP54  69 aavakeaveka.keekidvvlvDTaGrlq 96 
                                       +av  + v+ a  + ++d+vl+DT G+l+
  gi|474933750|ref|YP_007687332.1|  80 MAVNIDRVKDAlGSYNVDYVLIDTPGQLE 108
                                       55666666555145689*********986 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   8.4e-05       0.1      33      69 ..       5      41 ..       2      44 .. 0.91
   2 ?    1.1   0.0      0.13   1.5e+02     200     226 ..     216     242 ..     159     251 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.4e-05
                                      EEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE---- CS
                              MeaB 33 GltGvPGaGkstlvealglelrrrGkrvavlavDPss 69
                                       + G+ G+Gkst+v a+ + l ++     v+ +DP++
  gi|474933750|ref|YP_007687332.1|  5 YFVGTAGSGKSTMVGAFKEWLDDNEIDSVVINLDPGA 41
                                      5789*******************************97 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.13
                                       BTTB--EEEEEBCCCTBSHHHHHHHHH CS
                              MeaB 200 ekeWrpkvlktsavegeGidelvdaie 226
                                       +++   ++ ++sa++g G+ e+ +a++
  gi|474933750|ref|YP_007687332.1| 216 DTGVFGEMRQVSASKGVGLPEIYAAVQ 242
                                       55566788999***********99997 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0     2e-05     0.024      24      43 ..       3      22 ..       1      31 [. 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2e-05
                            AAA_29 24 atlltGpsGsGKSTllDAiq 43
                                      ++ ++G+ GsGKST++ A++
  gi|474933750|ref|YP_007687332.1|  3 NVYFVGTAGSGKSTMVGAFK 22
                                      47899***********9976 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.1e-05     0.025      34      69 ..       2      37 ..       1      42 [. 0.93

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.1e-05
                             AAA_7 34 kpvllvGptGtGKtviikdllkkldkekylsltinf 69
                                      ++v +vG++G+GK++++  + + ld++++ s++in+
  gi|474933750|ref|YP_007687332.1|  2 NNVYFVGTAGSGKSTMVGAFKEWLDDNEIDSVVINL 37
                                      5899****************************9997 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.4e-05      0.04       5      79 ..       4     109 ..       2     127 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.4e-05
                            AAA_24   5 iliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdieswedfldevvel............... 59 
                                       +  +G +g+GK+t++  +       + + ++i+++ G+ +l      di+ w+ + + + e                
  gi|474933750|ref|YP_007687332.1|   4 VYFVGTAGSGKSTMVGAFkewlddnEIDSVVINLDPGAEKLPYVPDIDIREWIGLDEVMSEYglgpngaqivaadlm 80 
                                       5678******************999999*************************999999999888888888888888 PP

                            AAA_24  60 .........aaeladyktlviDtidelee 79 
                                                a    + + + iDt ++le 
  gi|474933750|ref|YP_007687332.1|  81 avnidrvkdALGSYNVDYVLIDTPGQLEL 109
                                       88887775544444456677777777665 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00019      0.23       3      40 ..       3      40 ..       1      50 [. 0.92
   2 ?   -0.0   0.0      0.33     4e+02     112     169 ..      83     137 ..      76     167 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00019
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STT CS
                       ArsA_ATPase  3 vilvgGKGGVGKttvsaatavklsekgkkvllistDPA 40
                                       + + G  G GK+t+  a+  +l +++ + ++i +DP 
  gi|474933750|ref|YP_007687332.1|  3 NVYFVGTAGSGKSTMVGAFKEWLDDNEIDSVVINLDPG 40
                                      68899********************************5 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.33
                                       HHHHHHHHHHCSSSSEEEEESBSCCHTCGGGGHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       ArsA_ATPase 112 sfeellkyvkeeeydvvvlDtaPTGhtlrllslpevleklleklvklkeklsplakql 169
                                         +++++ + + + d+v++Dt+     l l+ + e  + +++ l k + +l  l+ ++
  gi|474933750|ref|YP_007687332.1|  83 NIDRVKDALGSYNVDYVLIDTP---GQLELFAFRESSSVVVDALGKSRSMLCYLSDPT 137
                                       5678888888999999***997...358888888888888888888888877777766 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   6.9e-05     0.083      25      51 ..       2      28 ..       1      66 [. 0.73

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.9e-05
                            AAA_16 25 elvllsGesGvGKsslvrellralekd 51
                                      ++v+++G +G+GKs++v ++++ l ++
  gi|474933750|ref|YP_007687332.1|  2 NNVYFVGTAGSGKSTMVGAFKEWLDDN 28
                                      5899****************9755555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00014      0.17       8      32 ..       4      28 ..       2      50 .. 0.82
   2 ?   -1.9   0.0       3.2   3.8e+03      17      35 ..     124     142 ..     122     175 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                            AAA_22  8 lvvtGesGtGKTtllrrlleqldee 32
                                      ++ +G +G+GK+t +  ++e+ld  
  gi|474933750|ref|YP_007687332.1|  4 VYFVGTAGSGKSTMVGAFKEWLDDN 28
                                      5789******************743 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.2
                            AAA_22  17 GKTtllrrlleqldeeaka 35 
                                       GK++++  +l+  + +++a
  gi|474933750|ref|YP_007687332.1| 124 GKSRSMLCYLSDPTLYKSA 142
                                       8999998888876655554 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.11   1.3e+02       2      16 ..       4      18 ..       3      65 .. 0.90
   2 ?    8.9   0.0   0.00072      0.86      45     133 ..      93     182 ..      71     188 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.11
                         Gtr1_RagA  2 vLLmGksgsGKtsmr 16
                                      v ++G  gsGK++m 
  gi|474933750|ref|YP_007687332.1|  4 VYFVGTAGSGKSTMV 18
                                      6689*********95 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00072
                         Gtr1_RagA  45 lgnltlnlwDcgGqeafvee..ylssqkeeifrnvgvliyVfDvesreleedletlke..ilealrqyspeakvfvl 117
                                       + n++  l+D +Gq ++++   + s   + + ++ + l y+ D +   l ++ + +++  +l+ l+q+  ++ +  l
  gi|474933750|ref|YP_007687332.1|  93 SYNVDYVLIDTPGQLELFAFreSSSVVVDALGKSRSMLCYLSDPT---LYKSANGFVSamTLSSLVQFRMDLPMINL 166
                                       45788889******9987642277788899999999*******99...6666666665115689************* PP

                         Gtr1_RagA 118 ihKmDliqedereeif 133
                                       + K+D +qe+e ++i+
  gi|474933750|ref|YP_007687332.1| 167 LSKCDVLQESEADRIV 182
                                       ********99988876 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0024       2.9     102     121 ..       4      23 ..       2      42 .. 0.76
   2 ?    0.1   0.0      0.56   6.7e+02     152     161 ..      97     106 ..      88     111 .. 0.77
   3 ?    0.8   0.0      0.34   4.1e+02      47      73 ..     161     186 ..     150     204 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0024
                                       EEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase 102 svlvGqSGvGKStLinallp 121
                                       + +vG  G GKSt++ a+++
  gi|474933750|ref|YP_007687332.1|   4 VYFVGTAGSGKSTMVGAFKE 23 
                                       579***********998876 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.56
                                       TEEEESS-SS CS
                       RsgA_GTPase 152 gglliDtPGf 161
                                       + +liDtPG 
  gi|474933750|ref|YP_007687332.1|  97 DYVLIDTPGQ 106
                                       6789*****5 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.34
                                       -EEEEEEE-GGG--HHHHHHHHHHHHH CS
                       RsgA_GTPase  47 iepvivlnKiDlleeeeeleelkeele 73 
                                       ++++ +l+K+D+l+e+e ++++ + ++
  gi|474933750|ref|YP_007687332.1| 161 LPMINLLSKCDVLQESE-ADRIVDWYN 186
                                       5566689********99.777666665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00011      0.13      23      46 ..       6      29 ..       2      42 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                            AAA_30 23 ltGpAGtGKttalkalreaweaag 46
                                       +G AG+GK+t+++a +e +++++
  gi|474933750|ref|YP_007687332.1|  6 FVGTAGSGKSTMVGAFKEWLDDNE 29
                                      68**************99988764 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.072        86       5      22 ..       3      20 ..       1      32 [. 0.89
   2 ?    2.0   0.0      0.11   1.3e+02      69      82 ..      95     108 ..      75     123 .. 0.76
   3 ?    4.0   0.0     0.027        32     118     183 ..     156     236 ..     137     245 .. 0.57

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.072
                                      EEEEEESTTSSHHHHHHH CS
                          GTP_EFTU  5 nigiighvDhGKtTLtdr 22
                                      n+ ++g   +GK+T++++
  gi|474933750|ref|YP_007687332.1|  3 NVYFVGTAGSGKSTMVGA 20
                                      9999***********986 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.11
                                       SEEEEEEEESSSGG CS
                          GTP_EFTU  69 kylinliDtPGHvd 82 
                                       +  + liDtPG  +
  gi|474933750|ref|YP_007687332.1|  95 NVDYVLIDTPGQLE 108
                                       56789******876 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.027
                                       HHHTTTEEEEEEESCGST.HHHHHHHHHHHHHHHHHH................HHHHHHHHHTTTTTEEEEEEBTTT CS
                          GTP_EFTU 118 alkegvpiivfiNKmDrl.kaelkeiveevkqklsrk................eeklekygekgekevpvvfgSalk 177
                                         ++++p+i ++ K+D l ++e ++iv+ +++   +                 +e  ++++  g  + ++  +Sa k
  gi|474933750|ref|YP_007687332.1| 156 QFRMDLPMINLLSKCDVLqESEADRIVDWYNNPD-TLygslldedrdpqsvmgMELFRAMEDTG-VFGEMRQVSASK 230
                                       4568999***********7666666666555322.22344444455555554433332222222.355555666666 PP

                                       TBTHHH CS
                          GTP_EFTU 178 gegvkt 183
                                       g g+ +
  gi|474933750|ref|YP_007687332.1| 231 GVGLPE 236
                                       666555 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.2    0.0027       3.2       2      56 ..       4     106 ..       3     150 .. 0.52

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0027
                                       EEEEESTTSSHHHHHHHHHT.....S..TEEESSSTTSSSSEEEEEEEETTEE........................ CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltg.....e..kaivsdkpgtTrdinegrvklkgke........................ 47 
                                       v +vG   +GKSt++ a  +     e   + ++  pg+ + +    ++++  e                        
  gi|474933750|ref|YP_007687332.1|   4 VYFVGTAGSGKSTMVGAFKEwlddnEidSVVINLDPGAEKLPYVPDIDIR--Ewigldevmseyglgpngaqivaad 78 
                                       77888888888888777654333321212233334444444444434322..1112222333333333333344444 PP

                                       ...................EEEEECGGC CS
                          MMR_HSR1  48 ...................ielvDtpGl 56 
                                                          ++l+DtpG 
  gi|474933750|ref|YP_007687332.1|  79 lmavnidrvkdalgsynvdYVLIDTPGQ 106
                                       4444444444444444444777777774 PP

>> Ploopntkinase3  P-loop Nucleotide Kinase3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00029      0.35       6      33 ..       4      31 ..       1      39 [. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00029
                    Ploopntkinase3  6 iylvGqPGaGkstlmaeltkgfdrskve 33
                                      +y+vG+ G+Gkst++ ++ + +d ++++
  gi|474933750|ref|YP_007687332.1|  4 VYFVGTAGSGKSTMVGAFKEWLDDNEID 31
                                      8**************9999988887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1561.44
//
Query:       gi|474933751|ref|YP_007687333.1|  [L=342]
Description: hypothetical protein TALC_00159 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.016   15.6   0.2      0.043   14.2   0.2    1.8  1  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2   2.4e-06     0.043       7     144 ..      76     204 ..      71     228 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.4e-06
                                       ESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC...CCTEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxx RF
                       Radical_SAM   7 CnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla...vpgiri 80 
                                       C+l+C fC + e+  +  +  +   +++l+++       g   v +   e + ++d+ +l+++    +   ++g ri
  gi|474933751|ref|YP_007687333.1|  76 CPLNCGFCRFAES--TSSCRFFDIDDSVLAKFANE--ITGFSDVRSIRLETTGDADIGDLARQVGIVRdnsKRGTRI 148
                                       ************7..88888888888999888554..4568888888889999999999999988888888999999 PP

                                       EEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  81 tvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikr 144
                                        v t  +   e+  + l+++g    +++  ++  +     +    ++e++l ++++l +ag+ +
  gi|474933751|ref|YP_007687333.1| 149 IVDTKDLD--EDGCRMLKDAGAFGAYHSCRIGEGK----DT--SISPERRLSTIRNLVDAGFWV 204
                                       99999999..999********99999999999888....33..478999999999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2101.83
//
Query:       gi|474933752|ref|YP_007687334.1|  [L=400]
Description: Proteasome-activating nucleotidase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-42  144.9   0.1    4.5e-42  143.6   0.0    1.8  1  AAA              ATPase family associated with various cellul
    8.1e-15   54.4   0.5    2.2e-14   53.0   0.5    1.8  1  AAA_lid_3        AAA+ lid domain
    4.3e-12   45.8   1.2    1.1e-11   44.5   0.6    2.0  2  Prot_ATP_ID_OB   Proteasomal ATPase OB C-terminal domain
    2.6e-07   30.9   0.0      5e-07   30.0   0.0    1.4  1  AAA_2            AAA domain (Cdc48 subfamily)
    7.2e-06   26.0   0.3    4.8e-05   23.4   0.1    2.5  1  AAA_5            AAA domain (dynein-related subfamily)
    1.9e-05   25.1   0.3     0.0083   16.5   0.1    2.6  2  AAA_16           AAA ATPase domain
    0.00018   21.3   0.0    0.00047   19.9   0.0    1.7  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00051   20.3   0.2      0.012   15.8   0.2    2.5  1  AAA_22           AAA domain
    0.00063   19.0   0.1     0.0015   17.8   0.0    1.6  2  DUF815           Protein of unknown function (DUF815)
    0.00078   19.0   0.9     0.0033   17.0   0.2    2.4  2  Prot_ATP_OB_N    Proteasomal ATPase OB N-terminal domain
    0.00095   18.5   0.0     0.0016   17.7   0.0    1.3  1  TIP49            TIP49 P-loop domain
      0.001   19.2   0.0     0.0023   18.1   0.0    1.7  1  AAA_33           AAA domain
     0.0029   18.2   0.0      0.018   15.6   0.0    2.2  2  AAA_18           AAA domain
      0.005   16.2   0.2      0.098   12.0   0.0    2.7  3  ATPase           KaiC
     0.0085   15.8   0.3      0.023   14.4   0.3    1.8  1  AAA_30           AAA domain
     0.0085   15.5   0.1      0.017   14.5   0.1    1.4  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0092   15.5   0.0      0.019   14.5   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
  ------ inclusion threshold ------
       0.01   15.6   0.3      0.025   14.3   0.0    1.8  2  IstB_IS21        IstB-like ATP binding protein
      0.012   15.5   0.0      0.026   14.4   0.0    1.7  1  AAA_3            ATPase family associated with various cellul
      0.018   15.3   0.1      0.047   13.9   0.0    1.8  1  AAA_28           AAA domain
      0.023   14.5   0.0        6.6    6.4   0.0    2.3  2  DUF1845          Domain of unknown function (DUF1845)
      0.046   14.1   0.0       0.13   12.6   0.0    1.8  1  RNA_helicase     RNA helicase
      0.052   13.2   0.0        0.2   11.3   0.0    2.0  2  Sigma54_activat  Sigma-54 interaction domain
      0.055   13.0   1.6       0.31   10.6   0.1    2.5  2  AAA_25           AAA domain
      0.079   12.2   0.0       0.14   11.4   0.0    1.4  1  Zeta_toxin       Zeta toxin
       0.09   12.6   1.4       0.21   11.4   1.4    1.6  1  KASH_CCD         Coiled-coil region of CCDC155 or KASH
        0.1   11.7   0.1        0.2   10.7   0.1    1.4  1  Parvo_NS1        Parvovirus non-structural protein NS1
        0.1   12.5   0.1          1    9.2   0.0    2.4  2  NTPase_1         NTPase
       0.11   12.6   0.0       0.24   11.4   0.0    1.6  1  AAA_14           AAA domain
       0.13   11.1   0.6       0.21   10.4   0.6    1.2  1  CALCOCO1         Calcium binding and coiled-coil domain (CALC
       0.18   11.8   0.0       0.35   10.9   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.19   12.1   1.3       0.48   10.9   0.7    2.0  1  CENP-H           Centromere protein H (CENP-H)
       0.44   10.4   1.7       0.54   10.1   0.2    1.9  1  DUF2642          Protein of unknown function (DUF2642)
       0.46   10.8   6.3       0.66   10.3   4.3    2.1  2  ABC_tran_CTD     ABC transporter C-terminal domain
       0.48   10.4   3.6       0.88    9.5   2.2    2.0  2  YscO             Type III secretion protein YscO
        2.1    8.2   5.4        2.9    7.7   2.5    2.5  2  DivIC            Septum formation initiator


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.6   0.0   9.1e-45   4.5e-42       1     131 [.     179     311 ..     179     312 .. 0.97

  Alignments for each domain:
  == domain 1  score: 143.6 bits;  conditional E-value: 9.1e-45
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH... CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr... 74 
                                       vll+GppGtGKTl+akava+ ++++f+++ gsel++ky+ge+++ +relf+ ake a psi+fiDE+d+++ +r   
  gi|474933752|ref|YP_007687334.1| 179 VLLVGPPGTGKTLMAKAVANATDATFIRLVGSELVQKYIGEGARLVRELFELAKERA-PSIVFIDELDSVGAKRadv 254
                                       79******************************************************9.****************998 PP

                                       TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  75 sgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                        +s ++e +r++ qLl+eldg++   +++ +igatnrpd ld+allr gRfdr+iei+
  gi|474933752|ref|YP_007687334.1| 255 ATSGDREVQRTLMQLLSELDGFTPT-ADIKIIGATNRPDILDDALLRpGRFDRIIEIG 311
                                       888999999***************6.77***************************997 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.5   4.3e-17   2.2e-14       2      44 ..     335     377 ..     334     378 .. 0.96

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 4.3e-17
                         AAA_lid_3   2 vdlkeLAerTeGySGADlaalcreAallAlrrgikeitmedfe 44 
                                       +d+ +LAe+TeG SGA+++a+c eA++lA+r++++++  edf+
  gi|474933752|ref|YP_007687334.1| 335 IDIRKLAEETEGASGAEIKAICTEAGMLAIRDNRDTVAPEDFQ 377
                                       89************************************99997 PP

>> Prot_ATP_ID_OB  Proteasomal ATPase OB C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   0.6   2.2e-14   1.1e-11       1      57 []      66     121 ..      66     121 .. 0.99
   2 ?   -1.4   0.0       4.9   2.4e+03      10      22 ..     215     260 ..     151     263 .. 0.47

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 2.2e-14
                                       EEEEEEE-TTSSEEEEE-TTS-EEEEEE-GGGSSST--TTEEEEEETTTTEEEEEE- CS
                    Prot_ATP_ID_OB   1 VatVsEvlddteraiVktssdeevvvslagavpremLrpgDlVavdkdtgfifEkLP 57 
                                       ++++++vl+d ++++V +s++  ++vs++  v++++L +g +V+++k+t +++E+LP
  gi|474933752|ref|YP_007687334.1|  66 IGSLRDVLPD-HKVVVHSSTGPDFIVSVSQYVDEKDLVAGSRVSLNKQTLAVMEVLP 121
                                       799*******.*********************************************9 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.9
                                       T.................................SSEEEEE-TTS- CS
                    Prot_ATP_ID_OB  10 d.................................teraiVktssde 22 
                                       +                                  +ra V ts+d 
  gi|474933752|ref|YP_007687334.1| 215 KyigegarlvrelfelakerapsivfideldsvgAKRADVATSGDR 260
                                       0444444444444444444444444444444444566666676665 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0     1e-09     5e-07       6     103 ..     179     270 ..     175     274 .. 0.87

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 1e-09
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       +ll+gp g+Gkt++aka+a+  ++    ++ir+  sel +    + + +     ++    a+e+   iv++DE+d +
  gi|474933752|ref|YP_007687334.1| 179 VLLVGPPGTGKTLMAKAVANATDA----TFIRLVGSELVQ----KYIGEGARLVRELFELAKERApsIVFIDELDSV 247
                                       6899******************96....************....77778888888888888888889********** PP

                                       ------------HHHHHHHHHHH CS
                             AAA_2  81 hpkessgadvSregVqrdLLqil 103
                                        +k+   a     +Vqr L+q+l
  gi|474933752|ref|YP_007687334.1| 248 GAKRADVATSGDREVQRTLMQLL 270
                                       **655555556789*******98 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.1   9.6e-08   4.8e-05       1     124 [.     178     292 ..     178     301 .. 0.65

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 9.6e-08
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG- CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEvera 77 
                                       +vlLvGppGtgK+ +a+ +a a+ +++    +++      l++++  ++ + +++  +l  + r ++i+++DE++ +
  gi|474933752|ref|YP_007687334.1| 178 GVLLVGPPGTGKTLMAKAVANATDATFIRLVGSE------LVQKYIGEGARLVRELFELA-KERAPSIVFIDELDSV 247
                                       59*********************99888777765......88888754555555555555.5568999999999988 PP

                                       -HHHHHHHHHHHHSSEEE..-SSSEEE.---......-EEEEEESS-- CS
                             AAA_5  78 esevlnsLlslleerrllleeggelvk.aknddllerfrviatanpld 124
                                         + +++  s   e ++ l+++  + + + +   + ++ +i+++n++d
  gi|474933752|ref|YP_007687334.1| 248 GAKRADVATSGDREVQRTLMQLLSELDgFTP---TADIKIIGATNRPD 292
                                       7666665555444444444443333320222...23377777777766 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   1.7e-05    0.0083      24      49 ..     176     201 ..     153     215 .. 0.81
   2 ?    5.8   0.0     0.032        16     121     161 ..     222     269 ..     211     277 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.7e-05
                            AAA_16  24 pelvllsGesGvGKsslvrellrale 49 
                                       p  vll+G++G+GK+ +++++++a  
  gi|474933752|ref|YP_007687334.1| 176 PKGVLLVGPPGTGKTLMAKAVANATD 201
                                       589******************96433 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.032
                            AAA_16 121 ellkrllallsrderplvlvlDdlq........wadeaslqllaaLlrl 161
                                       +l+++l++l+++ + p ++++D+l+         a ++++++ ++L++l
  gi|474933752|ref|YP_007687334.1| 222 RLVRELFELAKE-RAPSIVFIDELDsvgakradVATSGDREVQRTLMQL 269
                                       567788899999.777*********777775554444555555455444 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   9.4e-07   0.00047      36      97 ..     179     248 ..     175     307 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 9.4e-07
                            RuvB_N  36 vllyGpPGlGkttlakiiakelgvk.lkitsgPvleka.gd...laalltnleek...dvlfideihrls 97 
                                       vll+GpPG Gkt +ak +a+  +++ ++   +  ++k  g+   l+  l +l ++    ++fide+  + 
  gi|474933752|ref|YP_007687334.1| 179 VLLVGPPGTGKTLMAKAVANATDATfIRLVGSELVQKYiGEgarLVRELFELAKErapSIVFIDELDSVG 248
                                       9*********************988246666666666334411155555555543233799999987665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.2   2.5e-05     0.012       8      31 ..     179     202 ..     176     293 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.5e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqlde 31 
                                       ++++G++GtGKT+ ++ +++  d+
  gi|474933752|ref|YP_007687334.1| 179 VLLVGPPGTGKTLMAKAVANATDA 202
                                       589****************99853 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1         9   4.5e+03      96     125 ..       8      37 ..       6      39 .. 0.74
   2 !   17.8   0.0   2.9e-06    0.0015      52     116 ..     175     244 ..     132     253 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 9
                            DUF815  96 pklvellrerperfilfvDDLsFeeeeeey 125
                                       ++l +++ + +er + ++ DL   e++++y
  gi|474933752|ref|YP_007687334.1|   8 EELKAKIITLEERNVRLMEDLQNAENDKRY 37 
                                       566677778888888888888888888877 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 2.9e-06
                            DUF815  52 pannvLLwGarGtGKSslvkallneyaeegLrli..evekedlkelpklvellr...erperfilfvDDL 116
                                       p + vLL+G  GtGK  + ka+ n++ ++ +rl+  e+ ++ + e  +lv++l    +++   i+f+D L
  gi|474933752|ref|YP_007687334.1| 175 PPKGVLLVGPPGTGKTLMAKAVANATDATFIRLVgsELVQKYIGEGARLVRELFelaKERAPSIVFIDEL 244
                                       56789****************************988899999999999998765221556678*****98 PP

>> Prot_ATP_OB_N  Proteasomal ATPase OB N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.2   6.6e-06    0.0033      14      52 ..      78     116 ..      65     124 .. 0.77
   2 ?   -1.7   0.0       4.8   2.4e+03      12      23 ..     249     260 ..     239     262 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.6e-06
                     Prot_ATP_OB_N  14 tadVlvggrrmrVavsPlvdaeeLrpGqeVlLnEalvvV 52 
                                        +  ++ g ++ V+vs  vd+++L +G +V Ln +  +V
  gi|474933752|ref|YP_007687334.1|  78 VVVHSSTGPDFIVSVSQYVDEKDLVAGSRVSLNKQTLAV 116
                                       344456799************************876666 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4.8
                     Prot_ATP_OB_N  12 dgtadVlvggrr 23 
                                       +++adV ++g r
  gi|474933752|ref|YP_007687334.1| 249 AKRADVATSGDR 260
                                       6789****9976 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   3.2e-06    0.0016      48      91 ..     174     215 ..     164     229 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.2e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  48 laGravLlaGpsgtGktalaiaiskelgedvpfvalsgsevysl 91 
                                       +  ++vLl+Gp+gtGkt +a a++++  +d  f+ l+gse+ + 
  gi|474933752|ref|YP_007687334.1| 174 IPPKGVLLVGPPGTGKTLMAKAVANA--TDATFIRLVGSELVQK 215
                                       56799******************997..5689********9765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   4.6e-06    0.0023       2      39 ..     179     218 ..     179     352 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 4.6e-06
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfg 39 
                                       vllvG+pG+GK+  a+ ++++++  +++l   +l +++ g
  gi|474933752|ref|YP_007687334.1| 179 VLLVGPPGTGKTLMAKAVANATDatFIRLVGSELVQKYIG 218
                                       799****************999977666666664444333 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   3.5e-05     0.018       1      60 [.     179     269 ..     179     308 .. 0.74
   2 ?   -0.6   0.0       3.6   1.8e+03      16      62 ..     338     382 ..     330     396 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.5e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf....................gvnlrdvakenglllevdpe..........al 46 
                                       +ll G+pG+GKt +ak++++ + +                     +++l ++ake+ +++ + +e            
  gi|474933752|ref|YP_007687334.1| 179 VLLVGPPGTGKTLMAKAVANATdATfirlvgselvqkyigegarlVRELFELAKERAPSIVFIDEldsvgakradVA 255
                                       799***************99874337777877888888888888888888888888888888888777655544433 PP

                            AAA_18  47 deskrldedkldkl 60 
                                        + +r+++  l++l
  gi|474933752|ref|YP_007687334.1| 256 TSGDREVQRTLMQL 269
                                       33344444444444 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 3.6
                            AAA_18  16 keLskrl.gf.gvnlrdvakenglllevdpealdeskrldedkldklld 62 
                                       + L++++ g  g +++ +++e g+l  +d+       ++ ed++++ ++
  gi|474933752|ref|YP_007687334.1| 338 RKLAEETeGAsGAEIKAICTEAGMLAIRDNR----DTVAPEDFQAAKVK 382
                                       5566766555799999999999999999999....45555555444444 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.1   5.4e+02      53      85 ..      14      45 ..       7      83 .. 0.68
   2 !   12.0   0.0    0.0002     0.098      14      37 ..     171     194 ..     163     200 .. 0.86
   3 ?   -0.4   0.0       1.2   6.1e+02     106     152 ..     222     271 ..     209     280 .. 0.65

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.1
                            ATPase 53 fvtveepaedlrenakslGwdlekleeegklai 85
                                      ++t+ee+++ l e+ ++   d +  e+e ++ +
  gi|474933752|ref|YP_007687334.1| 14 IITLEERNVRLMEDLQNAENDKRYSESE-LFRL 45
                                      6999999999999999888886555554.4443 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.0002
                            ATPase  14 gGipegrvvlitGepGtGKtifal 37 
                                        Gi   + vl++G pGtGKt++a+
  gi|474933752|ref|YP_007687334.1| 171 VGIIPPKGVLLVGPPGTGKTLMAK 194
                                       588888899*************97 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.2
                            ATPase 106 elieelaeaikeikakrvviDsitgl.ayeekeav..aReilrqlvrvlk 152
                                        l++el e  ke   + v iD ++++ a++++ a+   Re  r+l++ l+
  gi|474933752|ref|YP_007687334.1| 222 RLVRELFELAKERAPSIVFIDELDSVgAKRADVATsgDREVQRTLMQLLS 271
                                       57788888888888899999998888544444333223444444444444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.3   4.7e-05     0.023      21      48 ..     179     206 ..     175     257 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.7e-05
                            AAA_30  21 avltGpAGtGKttalkalreaweaaggr 48 
                                       ++l+Gp+GtGKt + ka+++a +a   r
  gi|474933752|ref|YP_007687334.1| 179 VLLVGPPGTGKTLMAKAVANATDATFIR 206
                                       579****************999876544 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   3.4e-05     0.017      24      43 ..     178     197 ..     169     203 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.4e-05
                      Mg_chelatase  24 nlllvGppGsGKtmlakrlp 43 
                                        +llvGppG+GKt++ak+++
  gi|474933752|ref|YP_007687334.1| 178 GVLLVGPPGTGKTLMAKAVA 197
                                       589*************9875 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   3.8e-05     0.019      34      60 ..     177     202 ..     172     216 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.8e-05
                             AAA_7  34 kpvllvGptGtGKtviikdllkkldke 60 
                                       k vllvGp GtGKt+++k + ++ d  
  gi|474933752|ref|YP_007687334.1| 177 KGVLLVGPPGTGKTLMAKAVANATD-A 202
                                       679***************9999887.3 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       9.7   4.8e+03      84     101 ..      22      39 ..      19      47 .. 0.80
   2 ?   14.3   0.0     5e-05     0.025      48      70 ..     177     199 ..     166     215 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 9.7
                         IstB_IS21  84 edLveelkrarrdgklar 101
                                        +L+e l+ a++d ++++
  gi|474933752|ref|YP_007687334.1|  22 VRLMEDLQNAENDKRYSE 39 
                                       689999999999999864 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 5e-05
                         IstB_IS21  48 enivllGpsGvGKshlaialgve 70 
                                       ++++l+Gp+G+GK+ +a a++ +
  gi|474933752|ref|YP_007687334.1| 177 KGVLLVGPPGTGKTLMAKAVANA 199
                                       5799***************9876 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   5.3e-05     0.026       2      30 ..     179     207 ..     178     248 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.3e-05
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                       vll g PG++ktl++ka+a+a d++f r+
  gi|474933752|ref|YP_007687334.1| 179 VLLVGPPGTGKTLMAKAVANATDATFIRL 207
                                       7999**********************996 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   9.5e-05     0.047       2      39 ..     179     221 ..     178     245 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.5e-05
                            AAA_28   2 ivitGgestGKTtlleaLaar....gypvv.pEaareileekl 39 
                                       + ++G+++tGKT +++a a+      ++ v  E + +++ e++
  gi|474933752|ref|YP_007687334.1| 179 VLLVGPPGTGKTLMAKAVANAtdatFIRLVgSELVQKYIGEGA 221
                                       689****************554555777777888888876665 PP

>> DUF1845  Domain of unknown function (DUF1845)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.013       6.6      33      81 ..      11      59 ..       3      75 .. 0.87
   2 ?    5.7   0.0     0.022        11     136     187 ..     200     261 ..     194     291 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.013
                           DUF1845 33 kpaIiglprfasrlrqiwrdasaddPYAdaaLlkleekleeareelqkl 81
                                      k +Ii l++   rl +  ++a++d  Y++  L++l++ ++ +r el+ l
  gi|474933752|ref|YP_007687334.1| 11 KAKIITLEERNVRLMEDLQNAENDKRYSESELFRLQKDIARIRGELERL 59
                                      67888888887777777889***********************999865 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.022
                           DUF1845 136 ltarhiglisrkevedllkkgaravRkvfglvqrYrasg............vtraDiaaktara 187
                                         a  i l+ ++ v++++ +gar+vR++f+l+++   +             ++raD+a + +r 
  gi|474933752|ref|YP_007687334.1| 200 TDATFIRLVGSELVQKYIGEGARLVRELFELAKE--RAPsivfideldsvgAKRADVATSGDRE 261
                                       55677788899999******************93..3334566667777777777777766665 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00027      0.13       1      58 [.     179     227 ..     179     247 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00027
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDf 58 
                                       ++l+Gp+g+GK+++ak +a+          +d +++r + ++ +++Y g+ + ++ ++
  gi|474933752|ref|YP_007687334.1| 179 VLLVGPPGTGKTLMAKAVAN---------ATDATFIRLVGSELVQKYIGEGARLVREL 227
                                       6799*************444.........44555666666666666666666555555 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0004       0.2      23      47 ..     177     201 ..     152     217 .. 0.84
   2 ?   -2.2   0.0       5.7   2.9e+03     132     143 ..     279     290 ..     261     308 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0004
                                       S-EEEECSTTSSHHHHHHHHHHHST CS
                   Sigma54_activat  23 lsvlitGesGtGKellaraiheask 47 
                                         vl++G  GtGK+l+a+a+ +a++
  gi|474933752|ref|YP_007687334.1| 177 KGVLLVGPPGTGKTLMAKAVANATD 201
                                       569****************987665 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.7
                                       E--EEEEEEESS CS
                   Sigma54_activat 132 kvdvriiaatne 143
                                       ++d++ii atn+
  gi|474933752|ref|YP_007687334.1| 279 TADIKIIGATNR 290
                                       579999999997 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00062      0.31      20      54 ..     163     197 ..     147     204 .. 0.72
   2 ?    0.4   0.0      0.83   4.1e+02     129     157 ..     223     250 ..     206     273 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00062
                            AAA_25  20 pprrwlvk.gllpagelallaGapgtGKttlaldla 54 
                                       ++++ + k g++p ++ +ll+G+pgtGKt +a  +a
  gi|474933752|ref|YP_007687334.1| 163 KRPELYKKvGIIPPKG-VLLVGPPGTGKTLMAKAVA 197
                                       4555444467777655.5899*********996655 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.83
                            AAA_25 129 dvdaleaaieevegvrlvviDplsralgg 157
                                        v++l + ++e+  +  v iD l+++ + 
  gi|474933752|ref|YP_007687334.1| 223 LVRELFELAKER-APSIVFIDELDSVGAK 250
                                       578899999995.5*********996554 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00029      0.14      16      51 ..     176     209 ..     166     228 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00029
                        Zeta_toxin  16 PklillgGqpGAGKselaellkdelerqgnvvrldp 51 
                                       Pk +ll+G pG GK+ +a+++++++  +  ++rl +
  gi|474933752|ref|YP_007687334.1| 176 PKGVLLVGPPGTGKTLMAKAVANAT--DATFIRLVG 209
                                       999*******************998..677777765 PP

>> KASH_CCD  Coiled-coil region of CCDC155 or KASH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.4   0.00043      0.21      68     123 ..       6      61 ..       2      64 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00043
                          KASH_CCD  68 EleelkalvkeleEkrarlkaqnkqlekenqsLiakiesLqeenikllaekdelkk 123
                                       ++eelka + +leE++ rl    +++e ++   ++++  Lq ++ +++ e + lk+
  gi|474933752|ref|YP_007687334.1|   6 DIEELKAKIITLEERNVRLMEDLQNAENDKRYSESELFRLQKDIARIRGELERLKS 61 
                                       689*********************************************99999885 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1    0.0004       0.2     117     139 ..     179     201 ..     173     205 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0004
                         Parvo_NS1 117 vwfyGpantGktnlaeaIakavp 139
                                       v+++Gp+ tGkt +a+a a+a++
  gi|474933752|ref|YP_007687334.1| 179 VLLVGPPGTGKTLMAKAVANATD 201
                                       7899****************986 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0       1.1   5.5e+02      95     124 ..     136     164 ..     112     176 .. 0.83
   2 ?    9.2   0.0    0.0021         1       2      57 ..     179     235 ..     178     285 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.1
                                       HH-EEEE---STTGGG-HHHHHHHHHHHTT CS
                          NTPase_1  95 eadviviDEiGkmElkskkfkeaveevLks 124
                                       ++d+   D iG +  ++ +++eave+ Lk+
  gi|474933752|ref|YP_007687334.1| 136 KPDI-TYDDIGGLKQQMVELREAVEDPLKR 164
                                       5554.4699****************99884 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0021
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEEE.EEEEE-------EEEEEET.T--E CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgGf.yteevreggrrigFkivdlasgee 57 
                                       v++ GppG+GKt + k v+++ +   +++ G  +++++  +g r   ++ +la+++ 
  gi|474933752|ref|YP_007687334.1| 179 VLLVGPPGTGKTLMAKAVANATDATFIRLVGSeLVQKYIGEGARLVRELFELAKERA 235
                                       6899****************9998888887763567777888888888888866654 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00049      0.24       5      76 ..     179     247 ..     176     284 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00049
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                                       ++++G+  +GKT ++k +++        ++ +   +  +k + + ++l ++++e++ke+  +++f+DE   v
  gi|474933752|ref|YP_007687334.1| 179 VLLVGPPGTGKTLMAKAVANATD---ATFIRLVGSELVQKYIGEGARLVRELFELAKERAPSIVFIDELDSV 247
                                       789************99996655...556665555555555555557889999987777899******9877 PP

>> CALCOCO1  Calcium binding and coiled-coil domain (CALCOCO1) like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.6   0.00042      0.21     170     223 ..       4      57 ..       2      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00042
                          CALCOCO1 170 eaerkqlqakleqseeelrslskelqelrnslaerdtqvlqLqdtittltqkLt 223
                                       e + ++l+ak+ + ee + +l ++lq++ n +   ++++ +Lq++i++++ +L+
  gi|474933752|ref|YP_007687334.1|   4 EPDIEELKAKIITLEERNVRLMEDLQNAENDKRYSESELFRLQKDIARIRGELE 57 
                                       56778999****************************************998886 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00069      0.35      21      46 ..     174     203 ..     148     233 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00069
                                       E....EEEEESTTSSHHHHHHHHHHHTT-- CS
                              TsaE  21 v....ilLeGdLGaGKTtlvrglakalgve 46 
                                       +    +lL G+ G+GKT +++++a+a + +
  gi|474933752|ref|YP_007687334.1| 174 IppkgVLLVGPPGTGKTLMAKAVANATDAT 203
                                       144449******************998876 PP

>> CENP-H  Centromere protein H (CENP-H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.7   0.00096      0.48      28      77 ..       6      58 ..       2      63 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00096
                            CENP-H 28 eltevekenlrlkrknrelaaellelakekesek...eklkeelekleaelkk 77
                                      +++e++++++ l+++n+ l+++l+  +++k++ +    +l++ +++++ el++
  gi|474933752|ref|YP_007687334.1|  6 DIEELKAKIITLEERNVRLMEDLQNAENDKRYSEselFRLQKDIARIRGELER 58
                                      6889*******************877777777775665588888888888765 PP

>> DUF2642  Protein of unknown function (DUF2642)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2    0.0011      0.54      31      53 ..      65      88 ..      63      96 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0011
                           DUF2642 31 vrGiLkdvkPDH.ivveigntvfy 53
                                      v G L+dv+PDH +vv+++  + +
  gi|474933752|ref|YP_007687334.1| 65 VIGSLRDVLPDHkVVVHSSTGPDF 88
                                      669*********777777744433 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   4.3    0.0013      0.66       9      60 ..       6      59 ..       2      61 .. 0.92
   2 ?   -0.8   0.0       3.9   1.9e+03      16      35 ..     143     162 ..     134     171 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0013
                      ABC_tran_CTD  9 eleeleaeIeaLEeeiaeleaeladpelysdp..eklaelsaeleeleaeLeel 60
                                       +eel a+I  LEe+   l + l+++e  +++   +l +l++ +++++ eLe+l
  gi|474933752|ref|YP_007687334.1|  6 DIEELKAKIITLEERNVRLMEDLQNAENDKRYseSELFRLQKDIARIRGELERL 59
                                      589************************999998778****************87 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 3.9
                      ABC_tran_CTD  16 eIeaLEeeiaeleaeladpe 35 
                                       +I  L +++ el ++++dp 
  gi|474933752|ref|YP_007687334.1| 143 DIGGLKQQMVELREAVEDPL 162
                                       56667777777777777774 PP

>> YscO  Type III secretion protein YscO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   2.2    0.0018      0.88      67     120 ..       6      59 ..       1      61 [. 0.91
   2 ?   -1.2   0.0       3.6   1.8e+03      66      83 ..     142     159 ..     135     164 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0018
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YscO  67 elekvkqqvalLrekeaelekqveeakqqleaerealrqarkelqearraveKf 120
                                       ++e++k+++  L+e+  +l ++++ a++  +  + +l +++k ++  r ++e++
  gi|474933752|ref|YP_007687334.1|   6 DIEELKAKIITLEERNVRLMEDLQNAENDKRYSESELFRLQKDIARIRGELERL 59 
                                       8*********************************99999999999998888875 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.6
                                       HHHHHHHHHHHHHHHHHH CS
                              YscO  66 kelekvkqqvalLrekea 83 
                                       +++  +kqq   Lre+++
  gi|474933752|ref|YP_007687334.1| 142 DDIGGLKQQMVELREAVE 159
                                       677777888888888776 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   2.5    0.0058       2.9      22      56 ..       3      37 ..       1      41 [. 0.90
   2 ?    0.0   0.0       1.5   7.4e+02      20      51 ..      43      60 ..      38      63 .. 0.47

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0058
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXX CS
                             DivIC 22 lkqeiaalqaelaklkaeneeLeaevkdLksdedy 56
                                      ++ +i++l+a++ +l ++n +L + +++ ++d+ y
  gi|474933752|ref|YP_007687334.1|  3 QEPDIEELKAKIITLEERNVRLMEDLQNAENDKRY 37
                                      6779*************************999998 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.5
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-X CS
                             DivIC 20 kqlkqeiaalqaelaklkaeneeLeaevkdLk 51
                                      +              +l++++++   e+++Lk
  gi|474933752|ref|YP_007687334.1| 43 F--------------RLQKDIARIRGELERLK 60
                                      3..............44444444444444442 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       822  (0.0458475); expected 358.6 (0.02)
Passed bias filter:                      727  (0.0405488); expected 358.6 (0.02)
Passed Vit filter:                       167  (0.00931452); expected 17.9 (0.001)
Passed Fwd filter:                        36  (0.00200792); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              36  [number of targets reported over threshold]
# CPU time: 0.72u 0.35s 00:00:01.06 Elapsed: 00:00:00.50
# Mc/sec: 2418.62
//
Query:       gi|474933753|ref|YP_007687335.1|  [L=176]
Description: putative transcription factor, eukaryotic MBF1 -like protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-11   44.0   0.3    2.5e-11   43.4   0.3    1.3  1  HTH_3           Helix-turn-helix
    2.4e-08   33.8   0.1    3.7e-08   33.3   0.1    1.3  1  HTH_19          Helix-turn-helix domain
    5.3e-07   29.9   0.0    7.7e-07   29.4   0.0    1.2  1  HTH_31          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.021   14.2   0.6        1.7    8.1   0.1    2.6  2  zf_Rg           Reverse gyrase zinc finger
      0.088   13.3   0.2       0.19   12.2   0.2    1.5  1  HTH_26          Cro/C1-type HTH DNA-binding domain
       0.15   12.2   2.4        0.2   11.7   0.1    2.2  2  MqsA_antitoxin  Antitoxin component of bacterial toxin-antito
       0.15   12.0   4.6       0.25   11.3   2.5    2.2  2  zf-FCS          MYM-type Zinc finger with FCS sequence motif
       0.16   11.7   0.1       0.27   11.0   0.1    1.4  1  SUKH_5          SMI1-KNR4 cell-wall
        5.1    7.2   8.1       0.58   10.2   1.9    2.3  2  Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   0.3   1.3e-14   2.5e-11       1      55 []      93     147 ..      93     147 .. 0.98

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 1.3e-14
                                       HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHHHH CS
                             HTH_3   1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvsldel 55 
                                       ++++R+++gls +++A+ +G +  tis++E+ +  P+ +++ kl+kaL+++l+el
  gi|474933753|ref|YP_007687335.1|  93 IRQAREKKGLSCKDFAASIGEKEMTISKYESQRLTPDDKMIAKLEKALNIKLTEL 147
                                       8*******************************999*****************997 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.1   1.8e-11   3.7e-08       1      62 [.      90     150 ..      90     153 .. 0.95

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 1.8e-11
                            HTH_19   1 GerLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgidleyllqg 62 
                                       G r+++aRe++gl+ ++ a  +g     is++E+ +  +p+ +++ k+ +al+i l++l q 
  gi|474933753|ref|YP_007687335.1|  90 GTRIRQAREKKGLSCKDFAASIGEKEMTISKYESQRL-TPDDKMIAKLEKALNIKLTELVQD 150
                                       77*******************************9998.********************9885 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   3.9e-10   7.7e-07       3      60 ..      90     146 ..      88     149 .. 0.92

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 3.9e-10
                            HTH_31   3 GalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgldpae 60 
                                       G + r++Re+ GLs ++ A+ +g  e t+s++E+ r + p    +++l  al+    e
  gi|474933753|ref|YP_007687335.1|  90 GTRIRQAREKKGLSCKDFAASIGEKEMTISKYESQRLT-PDDKMIAKLEKALNIKLTE 146
                                       899**********************************6.*************986555 PP

>> zf_Rg  Reverse gyrase zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1   0.00086       1.7       4      14 ..      25      35 ..      22      47 .. 0.70
   2 ?    3.9   0.0     0.018        36      16      29 ..      92     105 ..      89     107 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00086
                             zf_Rg  4 avfeklCPNCg 14
                                       v  +lCPNC 
  gi|474933753|ref|YP_007687335.1| 25 GVRMNLCPNCA 35
                                      56779*****7 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.018
                             zf_Rg  16 disdeRlekGLpCk 29 
                                        i + R +kGL Ck
  gi|474933753|ref|YP_007687335.1|  92 RIRQAREKKGLSCK 105
                                       58899********8 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   9.4e-05      0.19       1      58 [.      92     148 ..      92     150 .. 0.96

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.4e-05
                            HTH_26   1 kLrelmadrgitkseLargtgisaatlsrlvkgkpervsldtLdkiCdaLgctpgDLl 58 
                                       ++r++  ++g++ +++a  +g  + t+s++ +++  +++ + ++k+ +aL++++ +L+
  gi|474933753|ref|YP_007687335.1|  92 RIRQAREKKGLSCKDFAASIGEKEMTISKYESQRL-TPDDKMIAKLEKALNIKLTELV 148
                                       789999****************************8.******************9997 PP

>> MqsA_antitoxin  Antitoxin component of bacterial toxin-antitoxin system, MqsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.51     1e+03      26      42 ..      20      36 ..      14      41 .. 0.84
   2 ?   11.7   0.1    0.0001       0.2      54     116 ..      71     135 ..      47     150 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.51
                    MqsA_antitoxin 26 ktvikavtgdfCarCGe 42
                                       +v++ v+ + C++C +
  gi|474933753|ref|YP_007687335.1| 20 PFVVQGVRMNLCPNCAK 36
                                      5789999********75 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.0001
                    MqsA_antitoxin  54 seellefrkkvnaelv..dpafiarvrkkleldqreaaeifGgGvnafsryekGkvrpplalvkl 116
                                       +++   +  + n +lv   ++ i++ r+k +l+ ++ a+  G   ++ s+ye+ +  p+  ++  
  gi|474933753|ref|YP_007687335.1|  71 MQTKDIYAGTANIALVddYGTRIRQAREKKGLSCKDFAASIGEKEMTISKYESQRLTPDDKMIAK 135
                                       3333444444455555225899*********************************9998776643 PP

>> zf-FCS  MYM-type Zinc finger with FCS sequence motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   2.5   0.00012      0.25       3      20 ..       6      22 ..       5      31 .. 0.82
   2 ?    0.2   0.2      0.38   7.5e+02       3      12 ..      28      37 ..      26      40 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                            zf-FCS  3 kkrCwfCkkyikgkpeft 20
                                      k++C++C+k +++ p f+
  gi|474933753|ref|YP_007687335.1|  6 KSTCEMCGKACPTRP-FV 22
                                      78*************.73 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.38
                            zf-FCS  3 kkrCwfCkky 12
                                      ++ C +C k+
  gi|474933753|ref|YP_007687335.1| 28 MNLCPNCAKF 37
                                      899****986 PP

>> SUKH_5  SMI1-KNR4 cell-wall
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00014      0.27       7      37 ..     120     146 ..     104     150 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00014
                                       HCGGG......---HHHHHHHHHHHTS---H CS
                            SUKH_5   7 elkeaeeevlvlpddeeikeaEekLgikfpn 37 
                                       +++     +  +pdd+ i ++E++L+ik+++
  gi|474933753|ref|YP_007687335.1| 120 KYES----QRLTPDDKMIAKLEKALNIKLTE 146
                                       2222....2349****************986 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.9   0.00029      0.58       3      18 ..       4      19 ..       2      29 .. 0.83
   2 ?    0.1   0.4      0.42   8.3e+02       6      12 ..      29      35 ..      24      36 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00029
                                      EEEEE-SSBTT--EEE CS
                    Molybdop_Fe4S4  3 vvktaCpyCgvgCgle 18
                                       +k++C++Cg  C+ +
  gi|474933753|ref|YP_007687335.1|  4 RTKSTCEMCGKACPTR 19
                                      79***********865 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.42
                                      EE-SSBT CS
                    Molybdop_Fe4S4  6 taCpyCg 12
                                      ++Cp+C 
  gi|474933753|ref|YP_007687335.1| 29 NLCPNCA 35
                                      68****5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1207.68
//
Query:       gi|474933754|ref|YP_007687336.1|  [L=244]
Description: ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase component [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-18   67.4   0.0    2.5e-18   66.9   0.0    1.2  1  ABC_tran  ABC transporter
     0.0028   17.5   0.0     0.0035   17.2   0.0    1.2  1  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.9   0.0   2.8e-22   2.5e-18      28     137 .]       2     121 ..       1     121 [. 0.92

  Alignments for each domain:
  == domain 1  score: 66.9 bits;  conditional E-value: 2.8e-22
                                       HHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH...............HHHTCHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...............xxxxxxxxxx RF
                          ABC_tran  28 lkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren...............esdeeiekal 89 
                                       lk+l+g++kp++G+++++gk +++ + ++l kei+++pq  +   ++tv ++               e+ e++e +l
  gi|474933754|ref|YP_007687336.1|   2 LKCLCGMYKPASGSVEVNGKAVSTLRGKELAKEIAFVPQS-TPATRTTVFDTvllgrkpyidwyaskEDYEKVESVL 77 
                                       89**************************************.666667799999**********98877777799999 PP

                                       HHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  90 sklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       + l++++l+ + +     ++SgG+ q+ ++ara++++p++l+lDEp++
  gi|474933754|ref|YP_007687336.1|  78 TALKMEDLALKYA----DQISGGELQKAQIARAIVQEPSVLILDEPSN 121
                                       9999999888888....*****************************86 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   3.9e-07    0.0035     220     294 ..      76     148 ..      20     156 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.9e-07
                            AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQvil 294
                                        ++ l+++d     a+++S G ++ + ++ a+ + +   s+l++DEp n+L+ + ++r + ++ +l r +g   i+
  gi|474933754|ref|YP_007687336.1|  76 VLTALKMEDLALKYADQISGGELQKAQIARAIVQEP---SVLILDEPSNNLDIANQHRTMHMIMDLVRsRGMSTIM 148
                                       667788888888899999*******77777777777...*****************99998885444435555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 1432.89
//
Query:       gi|474933755|ref|YP_007687337.1|  [L=34]
Description: hypothetical protein TALC_00163 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (34 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                        86  (0.0047967); expected 358.6 (0.02)
Passed bias filter:                       74  (0.00412739); expected 358.6 (0.02)
Passed Vit filter:                         2  (0.000111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 203.11
//
Query:       gi|474933756|ref|YP_007687338.1|  [L=327]
Description: ABC-type Fe3+-siderophore transport system, permease component [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-86  290.2  37.6    1.7e-86  290.1  37.6    1.0  1  FecCD     FecCD transport family
    1.9e-09   37.4  30.3    3.9e-09   36.4  30.3    1.5  1  ABC-3     ABC 3 transport family


Domain annotation for each model (and alignments):
>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  290.1  37.6   1.9e-90   1.7e-86       2     312 .]       2     322 ..       1     322 [. 0.99

  Alignments for each domain:
  == domain 1  score: 290.1 bits;  conditional E-value: 1.9e-90
                             FecCD   2 lllllllslllgavkispsevfeallgkadsleaeivlelrlprvlaallvGaaLavaGallQtvtrNpLadPsilG 78 
                                       l++l ++++ lga+++s+ +++++l++ +ds+++++v++lr+  ++aa+++GaaL++aGa++Q+++rNp+a+P +lG
  gi|474933756|ref|YP_007687338.1|   2 LAVLSVFTIHLGATDLSYFDIIRYLFHPDDSWNSTVVWDLRFRMIVAAIVAGAALGCAGAVMQSILRNPMASPFTLG 78 
                                       789999*********************************************************************** PP

                             FecCD  79 issgaalgavlallll............lgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsal 143
                                       is+++a+ga+la+++l            +  ++ f ++++af++a++a++++lll+ k ++ +p++++LaG+a+s++
  gi|474933756|ref|YP_007687338.1|  79 ISNASAFGAALAIMFLdggiivgqtaayTNVTNPFLVTALAFVFAMVATGIMLLLV-KLTECTPETIVLAGLAISSI 154
                                       ***************************99999************************.******************** PP

                             FecCD 144 lsaltsllllllneealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnverv 220
                                       +sa  ++l++++++ al++i++w +Gsls++sw+++++l+ +l+l+++++++++ ++++++ g+++A+slG nv+ +
  gi|474933756|ref|YP_007687338.1| 155 FSAGLAFLQYMASDVALSAIVYWQFGSLSKVSWDQLYMLMGVLVLVFVFFFWNRWNYNAMESGEDVARSLGTNVNLT 231
                                       ***************************************************************************** PP

                             FecCD 221 rllllllvalltavavalvGpigFvGLivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgiv 297
                                       rll l+++a+ltav+v+++G+igF+GLi Phi+++l+g+d+r++lp ++l+Ga++lll+ +++ +++ +t lpvgi+
  gi|474933756|ref|YP_007687338.1| 232 RLLGLIMSAILTAVVVSFMGIIGFIGLIGPHIVKRLIGNDTRYVLPGAMLVGAVVLLLSYIVGSYAF-ETVLPVGII 307
                                       *****************************************************************98.6999***** PP

                             FecCD 298 taliGapffiylllr 312
                                       t++iG+p+fi++l+r
  gi|474933756|ref|YP_007687338.1| 308 TSAIGGPIFIAILVR 322
                                       ************997 PP

>> ABC-3  ABC 3 transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4  30.3   4.3e-13   3.9e-09       3     238 ..      44     301 ..      42     322 .. 0.86

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 4.3e-13
                             ABC-3   3 eflqrallasilvslacallgsfvvlrrqsllgdalsHaalpGvalayllgvn..................lllgai 61 
                                        +++ a++a++++++a a++ s +    +s +  ++s a+  G ala+++                     +++ a+
  gi|474933756|ref|YP_007687338.1|  44 RMIVAAIVAGAALGCAGAVMQSILRNPMASPFTLGISNASAFGAALAIMFLDGgiivgqtaaytnvtnpflVTALAF 120
                                       67899*****************99999999****************987643336788999999****98778889* PP

                             ABC-3  62 lvgliaavalellkrktklkedtai..givlsvflalglvlvslikk..skvdldsyLfGniltisqedliliaiie 134
                                       +++++a+ ++ ll + t    +t++  g+ +s++++ gl++++++ +  + + +  + fG++  +s ++l++++ + 
  gi|474933756|ref|YP_007687338.1| 121 VFAMVATGIMLLLVKLTECTPETIVlaGLAISSIFSAGLAFLQYMASdvALSAIVYWQFGSLSKVSWDQLYMLMGVL 197
                                       ******************999986444******************95543444445569*****************9 PP

                             ABC-3 135 avvllllllfwkelllitfdeelAkveglsvkllkllllalialavvvalqavGviLvialliiPaatArrltrsle 211
                                       ++v++ +++ + +  ++   e++A++ g +v+l +ll l++ a+  +v++ ++G+i  i  li P ++ r+++++ +
  gi|474933756|ref|YP_007687338.1| 198 VLVFVFFFWNRWNYNAMESGEDVARSLGTNVNLTRLLGLIMSAILTAVVVSFMGIIGFIG-LIGPHIVKRLIGNDTR 273
                                       999999999999*************************999999999********999998.589************* PP

                             ABC-3 212 sllivAillglvsvvaGlll.Syyldla 238
                                        +l  A+l+g+v +++  ++ Sy +++ 
  gi|474933756|ref|YP_007687338.1| 274 YVLPGAMLVGAVVLLLSYIVgSYAFETV 301
                                       **********999887765548888743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1177  (0.0656478); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 1985.16
//
Query:       gi|474933757|ref|YP_007687339.1|  [L=405]
Description: hypothetical protein TALC_00165 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-12   47.0   0.1    3.4e-12   46.4   0.1    1.3  1  Peripla_BP_2  Periplasmic binding protein
     0.0077   16.3   0.1      0.015   15.4   0.1    1.4  1  DUF2532       Protein of unknown function (DUF2532)


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.1   3.8e-16   3.4e-12      47     208 ..     114     288 ..      59     302 .. 0.77

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 3.8e-16
                                       SSSB-HHHHHHH--SEEEE-GGG...GGGHHHHHHHS-EEE----TTS...........HHHHHHHHHHHHHTT-HH CS
                      Peripla_BP_2  47 dgeidvEklaalkPDlvilskglgltdedeellksgiptvivessntg...........eslkeqiralgellgled 112
                                         +++vEk+a+ +P lvi+ +++ ++ ++  +l +++ tviv +++t            + l ++i+ +g ++++ +
  gi|474933757|ref|YP_007687339.1| 114 LESATVEKIAEKHPSLVIVGNNIWTNYQTNVELLAKACTVIVLYNQTMatmwddnnkleATLRDNIKLVGNMVNESS 190
                                       345667****************978888888888888899999999999**************************** PP

                                       HHHHHHHHHHHHHHHHHHTS-TT.-EEEEEEEETTE..EEEE-TTSTTTHH.HHTS--EESTTT--STT-EEE-HHH CS
                      Peripla_BP_2 113 eaeklvaeidsklaaaksaidsekpkpvlvfggadeggyvvagsnsyigdl.ldalgieniaaeskkseyeeisaEq 188
                                       +a+k+++ i++ ++++++ + +  +k v v g   +   + + + ++ ++l +  +g++n++  + +s+  +i+ E 
  gi|474933757|ref|YP_007687339.1| 191 RADKVIKGIEDIMDDIRAHTGTS-DKYVYVAGVTIS--GSNTFNTTFPTYLpFKLIGAKNAYVGGSTSSKVTIPVES 264
                                       ***********************.777777776666..4444445555555455599999966666*********** PP

                                       HHH....H--SEEEEEEHHHHT-S CS
                      Peripla_BP_2 189 ila....sdpdvifvsgraeadnk 208
                                       ++      +pd+i+++++ +++ k
  gi|474933757|ref|YP_007687339.1| 265 FSDasviHSPDLIVIDPSSSDKIK 288
                                       *99989999*****9999333333 PP

>> DUF2532  Protein of unknown function (DUF2532)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   1.7e-06     0.015      41     108 ..     321     391 ..     283     404 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.7e-06
                           DUF2532  41 ndctaihkfleeklffseqqikk.enkihekykqfyl.qhnnklsdfsmqflekkseinsvet.lisgflk 108
                                        dc+    +  e l++    + + ++ki + +k fy  +h +k+ d  + f+e ks  n ve  l+s +  
  gi|474933757|ref|YP_007687339.1| 321 YDCALASAYYIEALLYGTLSVDEvKEKINNIFKVFYGkEHGKKVYDSMVTFFEGKSSTNGVEFpLLSQVHI 391
                                       389888888888888888777542689*********6269999****9*************9625555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       940  (0.052429); expected 358.6 (0.02)
Passed bias filter:                      639  (0.0356406); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 2339.55
//
Query:       gi|474933758|ref|YP_007687340.1|  [L=175]
Description: formylmethanofuran dehydrogenase, subunit E [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-27   94.7   0.0    6.3e-27   94.2   0.0    1.2  1  FmdE          FmdE, Molybdenum formylmethanofuran dehydrogena
  ------ inclusion threshold ------
       0.01   15.8   2.8       0.01   15.8   2.8    2.1  2  zf-dskA_traR  Prokaryotic dksA/traR C4-type zinc finger


Domain annotation for each model (and alignments):
>> FmdE  FmdE, Molybdenum formylmethanofuran dehydrogenase operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.2   0.0     7e-31   6.3e-27       1      88 [.      12     102 ..      12     123 .. 0.87

  Alignments for each domain:
  == domain 1  score: 94.2 bits;  conditional E-value: 7e-31
                                       HHSS--CHHHHHHHHHHHHHHCC....-TT.SSSEEEEES-STCHHHHHHHHCS--TTTTSEEE--SS-SEEEEEET CS
                              FmdE   1 fHGHlCpglvlGyrmakaalkelgpkeeeg.deelvaivetdsCldDAiqvltgctlGkgnlivmdygkkaltfkkr 76 
                                       fHGH Cpgl+ G r+a  a + lg+  e+  dee+v+++e+d+C  DAiq l+gctlGkg++i++  gk a++f +r
  gi|474933758|ref|YP_007687340.1|  12 FHGHGCPGLATGCRAAYEAARILGIPLETArDEEIVCVTENDACGIDAIQRLLGCTLGKGSMIMRMRGKAAYSFFDR 88 
                                       9************************98888*********************************************** PP

                                       TT-EEEEEEE-..C CS
                              FmdE  77 ktgkavrlklk..e 88 
                                       ++gk+vrl++k  +
  gi|474933758|ref|YP_007687340.1|  89 RSGKKVRLVAKfdR 102
                                       *********99331 PP

>> zf-dskA_traR  Prokaryotic dksA/traR C4-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0      0.87   7.8e+03      20      28 ..      41      49 ..      41      50 .. 0.75
   2 ?   15.8   2.8   1.1e-06      0.01       5      34 ..     142     171 ..     137     172 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.87
                      zf-dskA_traR 20 alPgarlCv 28
                                      a++  ++Cv
  gi|474933758|ref|YP_007687340.1| 41 ARDEEIVCV 49
                                      677788997 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.1e-06
                      zf-dskA_traR   5 sCeeCGEpIpeaRlralPgarlCveCqeka 34 
                                       +C++CGE   e  +r ++g+++C++C++++
  gi|474933758|ref|YP_007687340.1| 142 KCDCCGEWCREDLVRFQDGKIVCLDCFRDY 171
                                       3**************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1222.49
//
Query:       gi|474933759|ref|YP_007687341.1|  [L=176]
Description: archaeal conserved hypothetical protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      5e-25   87.8   0.0    5.9e-25   87.6   0.0    1.1  1  DUF2240   Uncharacterized protein conserved in archaea (DUF22


Domain annotation for each model (and alignments):
>> DUF2240  Uncharacterized protein conserved in archaea (DUF2240)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.6   0.0   3.3e-29   5.9e-25       4     144 .]      11     169 ..       8     169 .. 0.96

  Alignments for each domain:
  == domain 1  score: 87.6 bits;  conditional E-value: 3.3e-29
                           DUF2240   4 iavaapfkkkrkdklsesdfvfalsldrkwlspdqakklldraeeegLlekkdgdlvpnfdvaeveiPlgFkpdeel 80 
                                       i  aa f++k+kd ++e++f + + ld++w+s ++a  ll++  +eg ++ +dg++ p+ d ++v++P ++kp+e+l
  gi|474933759|ref|YP_007687341.1|  11 ICTAAFFRAKGKDVVTEKEFTMGIGLDLRWMSVKEAAVLLKMLVSEGCVSLNDGYVRPAKDFSDVQVPIAYKPSEDL 87 
                                       6789************************************************************************9 PP

                           DUF2240  81 l.....................kekstferildaiaastgiekkevvaeinelqeelkglvdveaaalvvakkegvd 136
                                                             +++++f  ++d+++    i+k + v+e n+++++l+  +d+  aal+v+++ g d
  gi|474933759|ref|YP_007687341.1|  88 RrkvnghlsgpalsappkpkadDSEDMFPVMVDIATD-NDIPKGKFVGECNRVRQNLG--IDMISAALIVLRDSGAD 161
                                       9******************998888899988987777.9*******************..***************** PP

                           DUF2240 137 vddlieev 144
                                       v+dl e+v
  gi|474933759|ref|YP_007687341.1| 162 VSDLYEKV 169
                                       ****9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       248  (0.0138323); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1153.60
//
Query:       gi|474933760|ref|YP_007687342.1|  [L=61]
Description: DNA-directed RNA polymerase, subunit K [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.5e-13   48.4   0.1    7.9e-13   48.1   0.1    1.1  1  RNA_pol_Rpb6  RNA polymerase Rpb6


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb6  RNA polymerase Rpb6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   0.1   4.4e-17   7.9e-13       8      49 .]       9      56 ..       6      56 .. 0.82

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 4.4e-17
                                      -HHHHHHHHHHHHHHH....HT.........SS-..SSSSTTCHHHHTT-S-- CS
                      RNA_pol_Rpb6  8 trYelvriaakRArQieegesl.........etq..kpvviAlrEiaegkipi 49
                                      tr+e++ri+++RA+Qi    s          e +  +p++iAl E +++ ipi
  gi|474933760|ref|YP_007687342.1|  9 TRFEKARIIGARALQI----SYgapvlvdypE-TmiDPIDIALTEFEKDVIPI 56
                                      9***************....655555566554.247***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       205  (0.011434); expected 358.6 (0.02)
Passed bias filter:                      189  (0.0105416); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 401.84
//
Query:       gi|474933761|ref|YP_007687343.1|  [L=208]
Description: SSU ribosomal protein S2P [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-27   95.3   0.0    7.4e-15   54.8   0.1    2.0  2  Ribosomal_S2  Ribosomal protein S2


Domain annotation for each model (and alignments):
>> Ribosomal_S2  Ribosomal protein S2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.0   2.8e-14   5.1e-10       2      95 ..      22     112 ..      21     118 .. 0.92
   2 !   54.8   0.1   4.1e-19   7.4e-15     148     212 ..     120     184 ..     113     187 .. 0.95

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 2.8e-14
                      Ribosomal_S2   2 LeagvhfGhqtrrwnpkmkpyIygern.gihiidlektlaalrraykvvkevaakggkilfvgtkkqakeavkeaak 77 
                                       L +gvh+G q +    +mk +Iy++r+ g +++d++kt + +r a++++ ++  + +++l  + ++  ++  +e +k
  gi|474933761|ref|YP_007687343.1|  22 LTSGVHIGTQFK--SSDMKDFIYKVRQdGLYVLDIKKTDERIRAAANFLAKF--DPQRVLVASMRQYGQRPAREFSK 94 
                                       789*****7766..899*******99659********************987..5678999999************* PP

                      Ribosomal_S2  78 rangyyvnerWlgGtLTN 95 
                                         +++    r+++GtLTN
  gi|474933761|ref|YP_007687343.1|  95 AIGAPAFAGRFVPGTLTN 112
                                       ****************** PP

  == domain 2  score: 54.8 bits;  conditional E-value: 4.1e-19
                      Ribosomal_S2 148 lPdlvvvldpkkekiavkEakklgipviaivDtnvdpdlvdypIpaNddsirsiklilgvladai 212
                                        Pd++vv+dp  +k  ++Ea +lgip++a++D n ++++vd +Ip N++  rs+  i+ +l++ +
  gi|474933761|ref|YP_007687343.1| 120 EPDVLVVTDPAADKQSLSEALNLGIPIVALCDANNETRNVDLVIPTNNKGRRSLACIYWLLTREV 184
                                       69*********************************************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1279.75
//
Query:       gi|474933762|ref|YP_007687344.1|  [L=267]
Description: putative dioxygenase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-50  172.2   0.0    1.3e-50  172.0   0.0    1.0  1  Memo      Memo-like protein
  ------ inclusion threshold ------
      0.088   11.9   0.0        2.5    7.1   0.0    2.1  2  LigB      Catalytic LigB subunit of aromatic ring-opening dio


Domain annotation for each model (and alignments):
>> Memo  Memo-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.0   0.0   1.5e-54   1.3e-50       5     271 .]       2     261 ..       1     261 [. 0.91

  Alignments for each domain:
  == domain 1  score: 172.0 bits;  conditional E-value: 1.5e-54
                              Memo   5 AGsfYpedeeelkkqleeflekntgkkei...arviis...PHagyvysgevaakayaeles.skvervvilGpsHt 74 
                                       A  fYp++e  l++q+ ++++   g+ ++   +r i     PHagy  sg  aa+a++e+++   ++  v++Gp H+
  gi|474933762|ref|YP_007687344.1|   2 ADRFYPSQEGVLRNQIIQCFRMGPGEPKEcsnKRSISAvvvPHAGYQCSGSCAAYAFKEIAEdGLPDAYVVIGPDHY 78 
                                       668******************99998877888444433556*********************999************ PP

                              Memo  75 ilgskvsvlaaseleTPlGdlkvDeelveeLvkkeeiadldetaalaEHSlEvqlpfLkellkekkfkivPilvsaq 151
                                       ++  ++ +++ +++ TP+G   vD+ ++ +L++   ++  d +a+  EHS+Ev+lpfLk++ ++   kivPi++++q
  gi|474933762|ref|YP_007687344.1|  79 GVPYEFVMSS-EDYWTPFGPCMVDQGIASKLRE---YIPDDPRAHTREHSIEVELPFLKYIDPK--AKIVPIIMGRQ 149
                                       ***9998888.9999****************98...466677888******************9..5********** PP

                              Memo 152 seetakevgealakvikdesnlviiSsDlsHygrrFgspqeiaesieDrevikaleelneeelkeylektnnticGe 228
                                       s ++a+ +++a++ +   +++++i+SsDl+Hy      p+++a  + D+ ++  + + + ++++  + ++n ++cG+
  gi|474933762|ref|YP_007687344.1| 150 SRSSAERLAQAIKMATIGKDVIIIASSDLCHYV-----PKSYADTA-DAGFLGFVRNGDVDGMYRDVMSNNLSVCGY 220
                                       *********************************.....99999999.****************************** PP

                              Memo 229 kpiavilkalkklgakkakllkYaqssdv.tsdtdsvVsyaslv 271
                                       +pia ++ a       + ++lk + s ++ +  +dsvV+y+s+v
  gi|474933762|ref|YP_007687344.1| 221 GPIATAMLATGMG---RTEILKQTDSFEAlNFGRDSVVGYGSAV 261
                                       ****999776544...699999999988725579******9985 PP

>> LigB  Catalytic LigB subunit of aromatic ring-opening dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.005        45      36      67 ..      59      90 ..      38     114 .. 0.80
   2 ?    7.1   0.0   0.00028       2.5     136     194 ..     141     192 ..     122     229 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.005
                              LigB 36 eriaek.sPdtiivvsphhltdvnpvfvlgvae 67
                                      ++iae+  Pd+ +v+ p+h+  v++ fv++ ++
  gi|474933762|ref|YP_007687344.1| 59 KEIAEDgLPDAYVVIGPDHYG-VPYEFVMSSED 90
                                      66777779************8.66666666554 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.00028
                              LigB 136 vikvslntvaypllsferlykLGeAlrkaveeldknvlilgsGglsHqlegdeaakada 194
                                        +++++        s     +L +A++ a+    k v i++s +l H+ ++  a  ada
  gi|474933762|ref|YP_007687344.1| 141 IVPIIMG-----RQSRSSAERLAQAIKMAT--IGKDVIIIASSDLCHYVPKSYADTADA 192
                                       4444443.....367777789999***999..9***************99988776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1919.09
//
Query:       gi|474933763|ref|YP_007687345.1|  [L=307]
Description: archaeal conserved hypothetical protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.026   14.8   0.1       0.31   11.3   0.0    2.4  2  Mnd1      Mnd1 HTH domain
      0.074   13.6   0.2       0.28   11.8   0.0    2.0  2  DUF4473   Domain of unknown function (DUF4473)


Domain annotation for each model (and alignments):
>> Mnd1  Mnd1 HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0     0.088   7.9e+02      38      52 ..      47      61 ..      20      63 .. 0.84
   2 ?   11.3   0.0   3.5e-05      0.31      16      45 ..     268     296 ..     266     299 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.088
                              Mnd1 38 sLvdDglveveKiGs 52
                                       Lv+  lve+e +G+
  gi|474933763|ref|YP_007687345.1| 47 VLVAGVLVEKENVGT 61
                                      688888999999998 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 3.5e-05
                              Mnd1  16 eleklapkekgivsqsVkdvlqsLvdDglv 45 
                                       ele +a    gi+s++ +++ +sL+d glv
  gi|474933763|ref|YP_007687345.1| 268 ELETRAMQ-EGISSMELEELTNSLMDKGLV 296
                                       89999999.9******************99 PP

>> DUF4473  Domain of unknown function (DUF4473)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.76   6.8e+03      62      71 ..     111     120 ..     109     123 .. 0.78
   2 ?   11.8   0.0   3.1e-05      0.28       4      25 ..     161     182 ..     159     194 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.76
                           DUF4473  62 tqseeDqaay 71 
                                       + + eDq+ y
  gi|474933763|ref|YP_007687345.1| 111 SYTTEDQKTY 120
                                       66789**999 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 3.1e-05
                           DUF4473   4 aeeakaeLvaaGlsekaadglv 25 
                                       ++ + ++L  aG+se+aa g+ 
  gi|474933763|ref|YP_007687345.1| 161 GDATYEDLKNAGMSEQAASGIS 182
                                       5666789*************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 1948.40
//
Query:       gi|474933764|ref|YP_007687346.1|  [L=453]
Description: Single-stranded DNA-binding replication protein A (RPA), large (70 kD) subunit-related ssDNA-binding protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-05   24.9   6.3      0.017   15.1   0.1    4.1  4  tRNA_anti-codon  OB-fold nucleic acid binding domain
     0.0022   17.7   0.9       0.99    9.1   0.0    3.2  3  CDC24_OB3        Cell division control protein 24, OB domain 
     0.0053   16.5   0.1      0.054   13.2   0.0    2.4  3  Rep_fac-A_C      Replication factor-A C terminal domain


Domain annotation for each model (and alignments):
>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   0.1    0.0024        14       8      51 ..      96     132 ..      81     162 .. 0.71
   2 !   15.1   0.1   2.8e-06     0.017       2      69 ..     201     268 ..     200     273 .. 0.86
   3 ?   -3.3   0.1       1.6   9.6e+03       2      16 ..     308     320 ..     307     323 .. 0.62
   4 !    5.0   0.0    0.0039        23      22      37 ..     356     374 ..     352     397 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0024
                                       EEEEEEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSE CS
                   tRNA_anti-codon   8 tsisdrsggkvifidlrDgtgriqvvlfreeatklaenlkeGdv 51 
                                        ++  + ++ +i+ +  D+tg+ + ++++      a +++ G+v
  gi|474933764|ref|YP_007687346.1|  96 NAK--GVSKTIISGIAGDETGSTNFTIWS-----DAGEFQAGQV 132
                                       344..89999999999*************.....3333333443 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 2.8e-06
                                       EEEEEEEEEE......EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEECTTSSEEEE CS
                   tRNA_anti-codon   2 tvaGrvtsis......drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvt.Grvkrrpggelelk 69 
                                       tv+G++ s++      +++ + v    + D +g+iq ++++        nl eG+ vr++  ++++++g  ++l+
  gi|474933764|ref|YP_007687346.1| 201 TVVGKILSVEtrnitvKGEARTVWGGLIADSSGKIQFTAWD------DHNLSEGQTVRIEnAYIRSWKGI-PQLN 268
                                       799999999988877777777777777**************......******************99987.6665 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 1.6
                                       EEEEEEEEEEEEEET CS
                   tRNA_anti-codon   2 tvaGrvtsisdrsgg 16 
                                       ++ G ++++  + g+
  gi|474933764|ref|YP_007687346.1| 308 SITGTIVDV--KTGS 320
                                       677888877..4444 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.0039
                                       EEEETTEEEEEEEET...H CS
                   tRNA_anti-codon  22 dlrDgtgriqvvlfr...e 37 
                                       +++Dgtg i v+++r   e
  gi|474933764|ref|YP_007687346.1| 356 TIDDGTGAISVIINRrdtE 374
                                       89************95441 PP

>> CDC24_OB3  Cell division control protein 24, OB domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.1   0.0    0.0055        33       7      57 ..      79     130 ..      73     151 .. 0.71
   2 !    9.1   0.0   0.00017      0.99       3      69 ..     194     255 ..     192     271 .. 0.78
   3 ?    1.5   0.0     0.035   2.1e+02     160     192 ..     325     368 ..     305     390 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0055
                         CDC24_OB3   7 lnvtLlGrvvaifr.eknsek.kkmdryslrieDttGaidatlweeagklhfk 57 
                                       + v + +++  + + e+n +   k ++ s    D+tG+++ t+w+ ag+ +  
  gi|474933764|ref|YP_007687346.1|  79 VAVNVTAKILFVAKkEINAKGvSK-TIISGIAGDETGSTNFTIWSDAGEFQAG 130
                                       567777889999775666655333.33345568*************9876654 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00017
                         CDC24_OB3   3 rekmlnvtLlGrvvaifreknsek.kkmdryslrieDttGaidatlweeagklhfkrlrvGhlvllsg 69 
                                        e+++  t++G++  +   + ++k ++ ++    i+D++G+i+ t w+       + l+ G++v +++
  gi|474933764|ref|YP_007687346.1| 194 TENTSSATVVGKILSVETRNITVKgEARTVWGGLIADSSGKIQFTAWDD-----HN-LSEGQTVRIEN 255
                                       6788899*********443334444666667999**********99998.....44.67799998887 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.035
                         CDC24_OB3 160 eCefCqcsv...........aevvrefeleitLdddtssaklfa 192
                                        C  C++s+             +v    l+ t+dd+t+ ++++ 
  gi|474933764|ref|YP_007687346.1| 325 RCPECNRSIlnedcaihghvDSPVIDLRLKTTIDDGTGAISVII 368
                                       68888888888888888887667788999999999988866544 PP

>> Rep_fac-A_C  Replication factor-A C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.13   7.5e+02      54      77 ..     103     126 ..      93     149 .. 0.83
   2 ?   -3.7   0.0       1.5   8.7e+03      60      74 ..     228     242 ..     227     244 .. 0.88
   3 !   13.2   0.0   9.1e-06     0.054       3     143 ..     308     442 ..     307     445 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.13
                                       EEEEEEEE-SS-EEEEEEEHHHHH CS
                       Rep_fac-A_C  54 yilsikvsDstgqlwvtlFneaae 77 
                                        i+s    D+tg++  t++++a+e
  gi|474933764|ref|YP_007687346.1| 103 TIISGIAGDETGSTNFTIWSDAGE 126
                                       57777789************9997 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.5
                                       EE-SS-EEEEEEEHH CS
                       Rep_fac-A_C  60 vsDstgqlwvtlFne 74 
                                       ++Ds+g++  t++++
  gi|474933764|ref|YP_007687346.1| 228 IADSSGKIQFTAWDD 242
                                       78*********9998 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 9.1e-06
                                       EEEEEEEEEETTTTEEEB--STT---B-EEETTTEEEETTTTEEESS--EEEEEEEEEE-SS-EEEEEEEHHHHHHH CS
                       Rep_fac-A_C   3 svkatvsfikkdnlvYkACpsedCnkKvveeedgewrCekCdkeveepkyryilsikvsDstgqlwvtlFneaaekl 79 
                                       s+ +t++ +k+ + + k Cp  +Cn+ +++e+     C+    +v++p   + l++ + D tg + v +     e +
  gi|474933764|ref|YP_007687346.1| 308 SITGTIVDVKTGSGLIKRCP--ECNRSILNED-----CAI-HGHVDSPVIDLRLKTTIDDGTGAISVIINRRDTEAI 376
                                       78999***************..*****99985.....553.567899****************************** PP

                                       HSS-HHHHHHHCC...C-HHHHHHHHHHTTT-EEEEEEE.EE----------EEEEEEEEE--HHHHH CS
                       Rep_fac-A_C  80 lglsaeelkklke...edeeefekiiekvklkeflfrlr.vkeesyndesrvrytvvkvepvdykkes 143
                                        g++ ee ++l          ++k++  v lk+++     ++ e+++ ++  r tv++  +v  +  +
  gi|474933764|ref|YP_007687346.1| 377 TGMTLEEAQDLARekgDMGVVANKMAAAVLLKKVTVTGNiMTDEKFGPQMSARSTVLTNTDVKAE--A 442
                                       ***99999888764432233445555556666665554414677899999999999887777444..4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 3093.63
//
Query:       gi|474933765|ref|YP_007687347.1|  [L=68]
Description: hypothetical protein TALC_00173 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 446.02
//
Query:       gi|474933766|ref|YP_007687348.1|  [L=357]
Description: ATP-utilizing enzymes of ATP-grasp superfamily (probably carboligases) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      8e-53  178.8   0.0    1.1e-52  178.3   0.0    1.1  1  DUF1297      Domain of unknown function (DUF1297)
    3.1e-42  143.4   0.0    5.8e-42  142.5   0.0    1.5  1  DUF1246      Protein of unknown function (DUF1246)
  ------ inclusion threshold ------
      0.069   12.6   0.0        0.2   11.1   0.0    1.7  2  CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP bindin


Domain annotation for each model (and alignments):
>> DUF1297  Domain of unknown function (DUF1297)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.3   0.0   1.8e-56   1.1e-52      22     187 ..     183     356 ..     176     357 .] 0.94

  Alignments for each domain:
  == domain 1  score: 178.3 bits;  conditional E-value: 1.8e-56
                                       CEEEEE---SEEEEEEEEEETTT.........TEEEEEEEEEEEEEECCCHCCS-HHHH.HCCT----EEEEEEEEE CS
                           DUF1297  22 kasieeyvvGanfnlnyfysplk.........eevellgidrRyesnldglvrlpakeq.lelevepeyvvvGnipv 88 
                                         +i+ey +G++++l++fy plk         + +ell+idrR esn+d++++l + e   +    p++vv+Gn+pv
  gi|474933766|ref|YP_007687348.1| 183 PYTIQEYCLGTRYYLHFFYDPLKtdgyrikqgGSLELLSIDRRDESNIDEMYKLGSIEDaKRHGLYPSFVVTGNTPV 259
                                       568****************************99*********************87655055666************ PP

                                       EE-GGGHHHHHHHHHHHHHHHHHHSTT---EEEEEEEEE-TTS-EEEEEEESSB-GGGGGGTT--CCHHHTTSS--- CS
                           DUF1297  89 vlREsllekvfelgekfveaakklvppGiiGpFcLqsvvtkdlelvvfdvsaRivggtnvymegspyskllfgepls 165
                                       v+REsll+k+fe++e++v+ + +l+  G++GpFcL++vv+++le+ vf++s+Riv+gtn +++gspy+++++   ls
  gi|474933766|ref|YP_007687348.1| 260 VIRESLLPKAFEMAENIVNRSYELFG-GMWGPFCLETVVNDKLEFRVFEISTRIVAGTNPFINGSPYAEMIYP-GLS 334
                                       **********************9997.*****************************************99995.79* PP

                                       HHHHHHHHHHHHHHCT-GGGCE CS
                           DUF1297 166 mGrrialEikeaiekdrleeiv 187
                                       +G r+a+Ei++ai++++l+ ++
  gi|474933766|ref|YP_007687348.1| 335 TGGRMAMEIRDAIASKELKTLI 356
                                       ******************9987 PP

>> DUF1246  Protein of unknown function (DUF1246)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.5   0.0   9.7e-46   5.8e-42       1     121 [.      21     141 ..      21     142 .. 0.98

  Alignments for each domain:
  == domain 1  score: 142.5 bits;  conditional E-value: 9.7e-46
                                       EEEESSTTHHHHHHHHHHTT--EEEEC-CCCHHHHHTTTT-..SEEEE.S.S..TTSS--HHHHHHTTCEE--BTTH CS
                           DUF1246   1 iatlaSHsalqilkgAkkegfrtlavcekgreklYekfkvi..devivldkfkdilkeevqeklreenailvPhgsf 75 
                                       iatl+SHs+lqi++gA+k gfrt+ +++k++ek+Y++f+++  de+i++ +f+d+ +++   +l ++nail+Phgsf
  gi|474933766|ref|YP_007687348.1|  21 IATLCSHSSLQIFHGARKMGFRTIGLVTKKNEKIYDAFPLAkpDEFIEYADFDDMNERT--GELLDKNAILIPHGSF 95 
                                       89************************************99999************9887..9*************** PP

                                       HHHC-HHHHHC-SS-EES-TTHHHHHCSHHHHHHHHHHTT-BB--B CS
                           DUF1246  76 veYvgiekieelkvpifGnrkllrwEerrekkrkyLekAgiriPkk 121
                                       veY+g++k+e+++vp +Gnr +l+wE++r  +r+++++Ag ++P+ 
  gi|474933766|ref|YP_007687348.1|  96 VEYMGAKKFEDFEVPSYGNRGVLQWESDRALQRQWITSAGAPMPRL 141
                                       ********************************************96 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   3.4e-05       0.2      31      70 ..     142     181 ..     129     196 .. 0.85
   2 ?   -2.4   0.0      0.45   2.7e+03     163     180 ..     296     312 ..     287     315 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.4e-05
                                       HHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHH CS
                       CPSase_L_D2  31 laiakeigyPviikaafglGGkGmrvarneeelaelvkka 70 
                                       ++ a+ei+ Pv++k   + GG+G  +a++  +++  + ++
  gi|474933766|ref|YP_007687348.1| 142 ITDAREIKEPVMVKYHGAKGGRGFFIAKDYPDFKMGIDNS 181
                                       56799***********************998888776665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.45
                                       EEETTTTEEEEEEEESS- CS
                       CPSase_L_D2 163 lldpkskeyyviEvNtRl 180
                                       +++ ++ e+ v E+ tR+
  gi|474933766|ref|YP_007687348.1| 296 VVN-DKLEFRVFEISTRI 312
                                       455.4899*********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       226  (0.0126053); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2500.01
//
Query:       gi|474933767|ref|YP_007687349.1|  [L=386]
Description: Aspartate/tyrosine/aromatic aminotransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.2e-66  223.0   0.0      7e-66  222.9   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    2.4e-13   50.1   0.0    3.5e-13   49.6   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    2.9e-06   26.1   0.1    5.7e-06   25.1   0.0    1.5  2  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    2.1e-05   23.7   0.0    0.00019   20.5   0.0    2.1  2  Aminotran_5      Aminotransferase class-V
    0.00015   21.2   0.0    0.00027   20.3   0.0    1.4  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.096   11.5   0.0        0.6    8.9   0.0    1.9  2  Alliinase_C      Allinase


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  222.9   0.0   2.3e-69     7e-66       2     363 .]      32     379 ..      31     379 .. 0.94

  Alignments for each domain:
  == domain 1  score: 222.9 bits;  conditional E-value: 2.3e-69
                                       EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHH CS
                     Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGag 78 
                                       d++ ++ +e+++     t+++++ a+k+  +  ++++ y+p+ g p+l+ea+a  ++++++++     +v+v++  +
  gi|474933767|ref|YP_007687349.1|  32 DIVSFSMGEPDFV----TPENIIGAAKK--SLDEGFTHYTPSMGVPDLREAIANAVRKDNGINASSY-NVLVTPTKQ 101
                                       68899*******9....**********9..9999*********************************.**9999666 PP

                                       HHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEE CS
                     Aminotran_1_2  79 aliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilve 155
                                       a+  ++ + l  +pgde+++pdp + sy+ +++l+g++ v++pl   edf l  e +e+a++       kt++i+++
  gi|474933767|ref|YP_007687349.1| 102 AIFLTALAYL--DPGDEVILPDPGWVSYEADIKLCGAKPVYVPLFYDEDFILSPERVEAAITP------KTRMIVLN 170
                                       6666666555..6**************************************************......******** PP

                                       SS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHH..HGGSTTSTTEEEEEESSSTTSSGGG-E CS
                     Aminotran_1_2 156 sphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavat..ranveeepnllivgslsKafGlaGeRv 230
                                       +p NPtG v++++++++++++a+k+ l+++ De+Y++  +    + ++  +++++++  +++v++lsK ++++G+Rv
  gi|474933767|ref|YP_007687349.1| 171 TPANPTGCVLPEATIRAIAEIAEKHDLMVLADEIYEKVIYSGRHF-SIasIPGMMDR--TITVSGLSKTYAMTGWRV 244
                                       **************************************9996643.43458888886..89**************** PP

                                       EEEEEEHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS.TEEEECCSC CS
                     Aminotran_1_2 231 Gyilgnaavvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael.glkvlasqs 304
                                       G+++++ + ++ ++kl+++ +s  +s +q  +++al+ + +   + + m+++++krr+   d Lae  g+++ ++++
  gi|474933767|ref|YP_007687349.1| 245 GWAVSSVENIKSINKLQTHSISccTSFAQMGAVEALNGPTD---SRDRMVAEFKKRRDLALDLLAEVkGIECKKPEG 318
                                       ***********************9999*************7...89******************999********** PP

                                       SSEEEEEETHH.CHHHHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHHH CS
                     Aminotran_1_2 305 gmflltdlsae.takelskkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelveal 363
                                       +++l+  ++a     +l+ kLl+e +v+vtpg  f+   +g++Ri++ ++++++++e ++++
  gi|474933767|ref|YP_007687349.1| 319 AFYLFPKYDADiHSADLATKLLKEAHVAVTPGAAFGPhgEGFFRISY-ATSDDQIREGISRI 379
                                       ***********9999********************************.99999999999887 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.0   1.2e-16   3.5e-13      52     144 ..     102     202 ..      47     203 .. 0.84

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 1.2e-16
                                       HHHHHH.TTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B.-TTTSSB-GGGCGGG--TTEEEEE...EB-GGGB CS
                   DegT_DnrJ_EryC1  52 hlaLra.lgvgpgdeVIvpsltFvatanavlelgakpvfvDv.dpdtynidpaaieaaitertkaIl...pVhlyGq 123
                                       ++ L+a   ++pgdeVI p  ++v+  + +  +gakpv+v     +++ ++p+++eaait++t+ I+   p++  G 
  gi|474933767|ref|YP_007687349.1| 102 AIFLTAlAYLDPGDEVILPDPGWVSYEADIKLCGAKPVYVPLfYDEDFILSPERVEAAITPKTRMIVlntPANPTGC 178
                                       46677745578*****************************9735689*******************75557899998 PP

                                       --...-HHHHHHHHHHCT-EEEEE CS
                   DegT_DnrJ_EryC1 124 va...dmdalkaiaakhglkvieD 144
                                       v     + a+ +ia+kh+l+v+ D
  gi|474933767|ref|YP_007687349.1| 179 VLpeaTIRAIAEIAEKHDLMVLAD 202
                                       7443489**************998 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.1         1   3.1e+03      74      96 ..      13      35 ..      11      37 .. 0.78
   2 !   25.1   0.0   1.9e-09   5.7e-06      72     175 ..      95     204 ..      73     211 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1
                                      SSHHHHHHHHHHTTS-TTEEEEE CS
                   Cys_Met_Meta_PP 74 ssGmaAiaaailallkaGdeivv 96
                                      +sG+ Ai++ + ++  +G +iv+
  gi|474933767|ref|YP_007687349.1| 13 ASGTIAISNLVSEMKAHGVDIVS 35
                                      68888888888888888888876 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 1.9e-09
                                       EESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEEST...TSHHHHHHHCCTTEEEEEEES CS
                   Cys_Met_Meta_PP  72 avssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdt...sdleelekaikentklvylEt 145
                                       +v+    Ai+++ la l  Gde+++ d  + + ++ +k +  k      f+d     ++e++e+ai+++t+++ l t
  gi|474933767|ref|YP_007687349.1|  95 LVTPTKQAIFLTALAYLDPGDEVILPDPGWVSYEADIKLCGAKPVYVPLFYDEdfiLSPERVEAAITPKTRMIVLNT 171
                                       45555678889999999**********99999999999988888888888888344579****************** PP

                                       S-TTTT--...--HHHHHHHHHHTT-EEEEEGT CS
                   Cys_Met_Meta_PP 146 ptnpllkv...vDiekiaklakkagvlvvvDnt 175
                                       p+np+  v   + i++ia++a k++++v+ D  
  gi|474933767|ref|YP_007687349.1| 172 PANPTGCVlpeATIRAIAEIAEKHDLMVLADEI 204
                                       ****966622268***************99975 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   6.5e-08   0.00019      56     175 ..      87     202 ..      65     205 .. 0.83
   2 ?    0.4   0.0     0.084   2.5e+02     282     342 ..     296     354 ..     286     371 .. 0.63

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 6.5e-08
                                       HT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEB..ETTSCBEGG CS
                       Aminotran_5  56 inaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipl..deegeldld 130
                                       ina+s +++++t  t +ai l al++   l+pgde+++ + +  +     ++++  +gak +++pl  de+  l ++
  gi|474933767|ref|YP_007687349.1|  87 INASS-YNVLVTP-TKQAIFLTALAY---LDPGDEVILPDPGWVSYE---ADIK-LCGAKPVYVPLfyDEDFILSPE 154
                                       88887.9988885.666*********...*************99999...6665.66777777765448999999** PP

                                       GHHHH--TTEEEEEEESBETTTTEB--...HHHHHHHHHHTT-EEEEE CS
                       Aminotran_5 131 elekllnektklvaithvsnvtGtiqp...veeigklakkkgalvlvD 175
                                       ++e+++++kt+++ ++   n tG + p   + +i+++a k++ +vl+D
  gi|474933767|ref|YP_007687349.1| 155 RVEAAITPKTRMIVLNTPANPTGCVLPeatIRAIAEIAEKHDLMVLAD 202
                                       ************************988333566778888999999998 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.084
                                       HHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEE..TTCSHHHHHHHHHHT.TEEEEEE-TTT CS
                       Aminotran_5 282 elaeyllerlkslpgvrlygpdkaerrasivsfnf..kgvhaedvatlLdee.gIavrsGhhca 342
                                       + ++ +l+ l++++g+++  +   + + +   f+   +++h++d+at L +e  +av+ G +  
  gi|474933767|ref|YP_007687349.1| 296 KRRDLALDLLAEVKGIEC--K---KPEGAFYLFPKydADIHSADLATKLLKEaHVAVTPGAAFG 354
                                       556666777777777777..2...23333333333346788888887666666****9998765 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   9.1e-08   0.00027     108     167 ..     150     202 ..     101     203 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 9.1e-08
                                       BE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEE CS
                   Beta_elim_lyase 108 kmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlD 167
                                        +++e++eaai++      k+++i+l +  n   G v++ + +r++a+ia+k+++ ++ D
  gi|474933767|ref|YP_007687349.1| 150 ILSPERVEAAITP------KTRMIVLNTPANP-TGCVLPEATIRAIAEIAEKHDLMVLAD 202
                                       5788899999988......6899999887774.8**********************9988 PP

>> Alliinase_C  Allinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0002       0.6     164     213 ..     202     254 ..     161     279 .. 0.71
   2 ?    0.2   0.0     0.093   2.8e+02     318     362 ..     337     382 ..     321     383 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0002
                                       EEEEE-TT-ST.TT..S---S-B--SEEEEEHHHHHS-GGG-EEEEEES-HHH CS
                       Alliinase_C 164 kviyDlayYWP.hy..tpitskadedimLftlskltGhaGsrlGWalvkdkev 213
                                         iy+ + Y   h+  + i    d  i +  lsk+   +G r+GWa+   +++
  gi|474933767|ref|YP_007687349.1| 202 DEIYEKVIYSGrHFsiASIPGMMDRTITVSGLSKTYAMTGWRVGWAVSSVENI 254
                                       44677776764144224677889***********************8544443 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.093
                                       HHHHHTTTEEEEEGGGGT.S-TTEEEEESSS-HHHHHHHHHHHHTS CS
                       Alliinase_C 318 aevlrekkiltrsGevfe.aesryvrlsllkrdddfdvllerlkkl 362
                                       +++l+e+++    G  f+  ++ + r+s   +dd+    ++r+kk+
  gi|474933767|ref|YP_007687349.1| 337 TKLLKEAHVAVTPGAAFGpHGEGFFRISYATSDDQIREGISRIKKF 382
                                       57899************9446889***********99999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2642.22
//
Query:       gi|474933768|ref|YP_007687350.1|  [L=357]
Description: Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-25   89.4   0.0    2.9e-25   89.0   0.0    1.2  1  Aminotran_5  Aminotransferase class-V
  ------ inclusion threshold ------
      0.064   13.8   0.1       0.15   12.6   0.1    1.6  1  SF3b1        Splicing factor 3B subunit 1


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.0   0.0   3.2e-29   2.9e-25     107     371 .]      91     344 ..      16     344 .. 0.87

  Alignments for each domain:
  == domain 1  score: 89.0 bits;  conditional E-value: 3.2e-29
                                       HHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHH.T.T-EEEEE-TTTTT CS
                       Aminotran_5 107 elakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGtiqpveeigklakk.k.galvlvDaaqavg 181
                                       e+ak  g +v+v+++  +   ++ +le +++ ++++v+   +++++G+  +  +++k +++ + +a+v++Da++++ 
  gi|474933768|ref|YP_007687350.1|  91 EVAKLNGRQVDVLKKPMGIGFTPADLEGKVTSDIDAVHWVSNESSSGVQLDNVALAKEVRDqNpDAIVMIDAVTSMF 167
                                       789999*********99999****************************999999*****99548************* PP

                                       TS---HHHHTESEEEEETTT.TTSSTT-EEEEEEHHHHHTS..SS.STTSEEEEETTEEEEHCTTGGGS.SS--HHH CS
                       Aminotran_5 182 hipidvkklgvDflafsghK.llgPtGiGvlyvrkellekleplllggemveevsleettfaeapskfeaGTpnvag 257
                                            +k+l++D ++f+++K l  P+Gi +++v+ke+ ++ e+++  g + + v+l+e+   + ++ +   Tp+v  
  gi|474933768|ref|YP_007687350.1| 168 ALDHRMKELQADSVVFGSQKdLALPPGIAFVVVSKEMMKRSEKMENKGFYADFVKLKEKN--DEDYALT--TPPVSL 240
                                       ********************9999********************************9988..7888888..****** PP

                                       HHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEETTCSHHHHHHHHHHTTEE CS
                       Aminotran_5 258 iiglgaaleyleeigleaiekhekelaeyllerlkslpgvrlygpdkaerrasivsfnfkgvhaedvatlLdeegIa 334
                                       ++gl   l+ + + g+++  ++++e+ae++++  ++  +  +  p+k  ++++i  ++  +++ + + ++++++g +
  gi|474933768|ref|YP_007687350.1| 241 MYGLDYQLDKMLKEGMATRYRRHEEMAEMVRKWADEKMEGIF--PEKGFESKTIGVVKRGDLDFDRFHSIIKSKGME 315
                                       ******************************999887555556..677888888888888999999999999999999 PP

                                       EEEE-TTTHHHHHHTT.S-EEEEE--TTS-HHHHHHH CS
                       Aminotran_5 335 vrsGhhcaqplmkrlalegtvRaSlyiynteeevdrl 371
                                       ++ G   a         ++t+R++ +   t++++++l
  gi|474933768|ref|YP_007687350.1| 316 ISNGYGDA--------KKSTFRIGTMGDLTKDDIKQL 344
                                       99988888........778888888888888888876 PP

>> SF3b1  Splicing factor 3B subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   1.7e-05      0.15      30      78 ..     231     288 ..     202     290 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.7e-05
                             SF3b1  30 mgmatPpgala........amtP.eqlqalrlekeidernrpltDeeLdallPkeGYk 78 
                                        +++tPp +l+        +m     ++++r ++e+ e  r  +De ++ ++P++G++
  gi|474933768|ref|YP_007687350.1| 231 YALTTPPVSLMygldyqldKMLKeGMATRYRRHEEMAEMVRKWADEKMEGIFPEKGFE 288
                                       56778877766778777774444145678999************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2280.64
//
Query:       gi|474933769|ref|YP_007687351.1|  [L=531]
Description: D-3-phosphoglycerate dehydrogenase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.8e-57  191.7   0.0    1.3e-56  190.8   0.0    1.5  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    2.8e-38  130.6   0.3    6.1e-38  129.5   0.0    1.6  2  2-Hacid_dh      D-isomer specific 2-hydroxyacid dehydrogenase
    1.1e-08   34.6   0.2    2.9e-08   33.3   0.2    1.7  1  ACT             ACT domain
  ------ inclusion threshold ------
       0.11   12.3   0.1       0.32   10.8   0.1    1.8  1  ACT_7           ACT domain
       0.11   12.6   2.2       0.38   10.9   0.0    2.6  4  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
       0.12   12.8   0.0       0.59   10.6   0.0    2.1  2  UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family,


Domain annotation for each model (and alignments):
>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.8   0.0   4.3e-60   1.3e-56       2     178 .]     108     284 ..     107     284 .. 0.96

  Alignments for each domain:
  == domain 1  score: 190.8 bits;  conditional E-value: 4.3e-60
                                       HHHHHHHTTHHHHHHHHHTTCCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHH CS
                      2-Hacid_dh_C   2 alllallrrlaeadeevregewksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeel 78 
                                       a++++l+r+++ a+++++eg+w ++++++g el+gk +GiiG+Gr+G +vakrlk+f+m +i+yd++  +e  +++l
  gi|474933769|ref|YP_007687351.1| 108 AMIMSLARNIPFAHKSMHEGKW-DRSKFTGVELNGKVLGIIGVGRVGGEVAKRLKPFNMTMIGYDPFLPREV-ADSL 182
                                       79********************.9*******************************************99887.9999 PP

                                       TC.EECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEES-- CS
                      2-Hacid_dh_C  79 gv.elvsleellaesDivslhlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiagaalDvf 154
                                       gv  +++ ee+++++D+ ++h+pl p+t+++i+  ++++mk++a l N+aRGg+v+e++L++aLk++ iagaa+Dv+
  gi|474933769|ref|YP_007687351.1| 183 GVkLYDNPEEIYKQADFMTIHTPLLPSTKNMISMPQFKMMKPSARLANVARGGIVNEDDLYTALKEKIIAGAAFDVW 259
                                       995567*********************************************************************** PP

                                       SSSSSGTC.HHHHHSTTEEE-SS-T CS
                      2-Hacid_dh_C 155 eeeplped.spllelpnviltPHia 178
                                        +epl+e+ ++llel+n++ tPH++
  gi|474933769|ref|YP_007687351.1| 260 CNEPLDESeQKLLELDNLVTTPHLG 284
                                       *****965269************97 PP

>> 2-Hacid_dh  D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.5   0.0     2e-41   6.1e-38       1     134 []       5     316 ..       5     316 .. 0.99
   2 ?   -2.3   0.0       1.1   3.3e+03      77      90 ..     392     405 ..     370     411 .. 0.83

  Alignments for each domain:
  == domain 1  score: 129.5 bits;  conditional E-value: 2e-41
                                       EEEEST.CHHHHHHHHHTTEEEEEESCSSHHHCHHHHTTESEEEE-TTS-BSHHHHHHHTT--EEEESSSSCTTB-H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh   1 vlileplreeelellkeegvevevkdellteellekakdadalivrsntkvtaevlealpkLkviaragvGvDnvDl 77 
                                       +l++++l++++l++lk+ g+ v++k  ++++el++++ d+dali+rs tkvt++v++a++kL++i+ragvGvDnvD+
  gi|474933769|ref|YP_007687351.1|   5 ILVSDKLSNDGLDILKASGFPVVMKPGMTEDELCKEIVDYDALIIRSGTKVTRKVIDAAKKLRLIGRAGVGVDNVDI 81 
                                       7999*************888********************************************************* PP

                                       HHHHHTT-EEEE-TTTTHHHHHHHH.................................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.................................................... RF
                        2-Hacid_dh  78 daakerGilVtnvpgystesvAElt.................................................... 102
                                       ++a+e+Gil++n+p+++  s+AE+t                                                    
  gi|474933769|ref|YP_007687351.1|  82 PYATEKGILIMNTPTANILSAAEHTcamimslarnipfahksmhegkwdrskftgvelngkvlgiigvgrvggevak 158
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                        2-Hacid_dh 103 ............................................................................. 102
                                                                                                                    
  gi|474933769|ref|YP_007687351.1| 159 rlkpfnmtmigydpflprevadslgvklydnpeeiykqadfmtihtpllpstknmismpqfkmmkpsarlanvargg 235
                                       ***************************************************************************** PP

                                       .................................................T-BHHHHHHHHHHHHHHHHHHHTTCCGT CS
                                       .................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh 103 .................................................aaTeeaqeniaeeaaenlvaflkgespa 130
                                                                                        a+Teeaq ++a  +ae+ v++lk++  +
  gi|474933769|ref|YP_007687351.1| 236 ivneddlytalkekiiagaafdvwcnepldeseqklleldnlvttphlgASTEEAQVRVAVDVAEAAVKYLKEGIIT 312
                                       ***************************************************************************** PP

                                       TBCS CS
                                       xxxx RF
                        2-Hacid_dh 131 navn 134
                                       na+n
  gi|474933769|ref|YP_007687351.1| 313 NAIN 316
                                       *997 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.1
                                       HHHHHHTT-EEEE- CS
                                       xxxxxxxxxxxxxx RF
                        2-Hacid_dh  77 ldaakerGilVtnv 90 
                                       l+ ak++Gi V++ 
  gi|474933769|ref|YP_007687351.1| 392 LPVAKAKGIEVSES 405
                                       56799999999875 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.2   9.6e-12   2.9e-08       3      65 ..     458     518 ..     457     520 .. 0.95

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 9.6e-12
                                       EEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTT CS
                               ACT   3 lrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkl 65 
                                       ++v  +D+ G+ ++v+++l++ +iNi  + ++  e    +i+ +vi vd+ ++++v +++ k 
  gi|474933769|ref|YP_007687351.1| 458 VFVTYKDVTGVVGKVGSILGEENINIQQMAVSMKEG--SDIALMVIAVDQPVADAVTDKIAKA 518
                                       678999******************************..8*********************986 PP

>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00011      0.32      19      43 ..     464     489 ..     457     498 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00011
                                       SS--HHHHHHHHHHTTT---EEEE.- CS
                             ACT_7  19 dvtGivaklaspLaeagIsifqiS.t 43 
                                       dvtG+v k+ s L e++I+i q++ +
  gi|474933769|ref|YP_007687351.1| 464 DVTGVVGKVGSILGEENINIQQMAvS 489
                                       79******************999854 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       3.6   1.1e+04      81     105 ..      43      67 ..      34      76 .. 0.67
   2 ?   10.9   0.0   0.00013      0.38       2     106 ..     144     248 ..     143     254 .. 0.76
   3 ?   -3.4   0.0       3.3   9.9e+03      94     128 ..     288     322 ..     283     323 .. 0.65
   4 ?    0.0   0.2      0.28   8.4e+02      49      89 ..     487     528 ..     462     530 .. 0.69

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 3.6
                                       -TT-EEEE-S---HHHHHHHHHHHH CS
                     NAD_binding_2  81 kkgdilidgstsspedtrelakelk 105
                                       + ++++i ++t   ++ ++ ak+l+
  gi|474933769|ref|YP_007687351.1|  43 DYDALIIRSGTKVTRKVIDAAKKLR 67 
                                       4567777777777777777776665 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00013
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-.SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS.H CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavyn.rtkekveelvaegakaaesieelvasldvvitmvkagkavdevieg.l 76 
                                       +g+iG+G  G + a++l+  ++++++y+   + +v + +  g+k+++++ee+ +++d++ +  +  + ++++i+   
  gi|474933769|ref|YP_007687351.1| 144 LGIIGVGRVGGEVAKRLKPFNMTMIGYDpFLPREVADSL--GVKLYDNPEEIYKQADFMTIHTPLLPSTKNMISMpQ 218
                                       69**************************43333333333..8***************99999988888888888776 PP

                                       CCC--TT-EEEE-S---HHHHHHHHHHHHH CS
                     NAD_binding_2  77 lealkkgdilidgstsspedtrelakelke 106
                                       ++ +k+++ l +++   + +  +l+++lke
  gi|474933769|ref|YP_007687351.1| 219 FKMMKPSARLANVARGGIVNEDDLYTALKE 248
                                       777777766666655555555555555555 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 3.3
                                       HHHHHHHHHHHHHTT-EEEEEEEESHHHHHHHT-E CS
                     NAD_binding_2  94 pedtrelakelkekglkfldaPVSGGeegAekGtL 128
                                        e++ ++a +++e+ +k+l  ++   + +A +G+L
  gi|474933769|ref|YP_007687351.1| 288 EEAQVRVAVDVAEAAVKYLKEGIITNAINAPRGKL 322
                                       45566777777777777777777766666666665 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 0.28
                                       HHHHHHHCSEEEE-SSSHHHHHHHHHS.HCCC--TT-EEEE- CS
                     NAD_binding_2  49 ieelvasldvvitmvkagkavdevieg.llealkkgdilidg 89 
                                       + ++ ++ d+ ++++  +++v + +++ +++al   + ++d 
  gi|474933769|ref|YP_007687351.1| 487 AVSMKEGSDIALMVIAVDQPVADAVTDkIAKALGGTAKFVDL 528
                                       333444558888888888887665555599999888888876 PP

>> UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0    0.0002      0.59      22      75 ..     156     205 ..     154     226 .. 0.89
   2 ?   -2.6   0.0       2.6   7.6e+03      34      71 ..     254     294 ..     241     305 .. 0.46

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0002
                                       HHHHHHHCTSEEEEE-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S- CS
                    UDPG_MGDP_dh_C  22 iieeLleegaevkiyDPkvkeeaveaeleekgvevvdsleealkgadaivilte 75 
                                       ++++L+  ++ +  yDP  ++e +       gv+++d++ee  k+ad + i+t+
  gi|474933769|ref|YP_007687351.1| 156 VAKRLKPFNMTMIGYDPFLPREVADS----LGVKLYDNPEEIYKQADFMTIHTP 205
                                       7899999**************99987....59*****************99996 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.6
                                       EEE-SSTHHCCCCHHGG...BTCCEEES-CHHHHTT-SEEE CS
                    UDPG_MGDP_dh_C  34 kiyDPkvkeeaveaele...ekgvevvdsleealkgadaiv 71 
                                        ++D +++e   e e++   +++++++ +l    ++a++ v
  gi|474933769|ref|YP_007687351.1| 254 AAFDVWCNEPLDESEQKlleLDNLVTTPHLGASTEEAQVRV 294
                                       55555555544444443444334444434444444443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (531 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 3230.12
//
Query:       gi|474933770|ref|YP_007687352.1|  [L=129]
Description: hypothetical protein TALC_00178 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.077   11.7   0.1      0.078   11.6   0.1    1.1  1  EVC2_like    Ellis van Creveld protein 2 like protein
       0.11   12.3   0.8       0.19   11.6   0.4    1.5  1  TFIIE_alpha  TFIIE alpha subunit


Domain annotation for each model (and alignments):
>> EVC2_like  Ellis van Creveld protein 2 like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   8.7e-06     0.078     105     168 ..      14      78 ..       2     128 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.7e-06
                         EVC2_like 105 knreeskleksq.fnsaegvkeelaledkivdiLvledpqnmlqaLenleiasllradadLeacR 168
                                       + ++e++le+++ fn+a+ v + +  +d+i+d     + +  +  Le+  i ++ r ++ L   R
  gi|474933770|ref|YP_007687352.1|  14 SIDHEQDLEYEDaFNLAQHVLNFFGYSDRIIDNVLEPEDRDAFYMLEDSGILTTEREEITLYDGR 78 
                                       35899999987549******************8888888889999**************996544 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.4   2.2e-05      0.19      45      90 ..      53     101 ..      46     106 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.2e-05
                                       HHHHHHHHHCTSEEEEEEEE...TTTEEEEEEEEEECCCHCCCHHHHHH CS
                       TFIIE_alpha  45 rklLnrLyearlvkykrrrd...eekswykyywrinyeklvdvvkrkle 90 
                                       r + + L + ++    r+     ++ +w+  yw++ ++k+   + +k++
  gi|474933770|ref|YP_007687352.1|  53 RDAFYMLEDSGILTTEREEItlyDGREWRIHYWLFRKDKIASLMEKKHS 101
                                       77889999999998888766899********************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 950.26
//
Query:       gi|474933771|ref|YP_007687353.1|  [L=625]
Description: Rad3-related DNA helicase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-57  193.9   0.0      9e-56  188.6   0.0    2.1  2  HBB           Helical and beta-bridge domain
    1.9e-32  112.8   0.0    3.2e-32  112.0   0.0    1.3  1  Helicase_C_2  Helicase C-terminal domain
    6.5e-22   78.0   0.0    9.2e-22   77.5   0.0    1.2  1  DEAD_2        DEAD_2
     0.0016   18.3   0.0     0.0085   15.9   0.0    2.0  2  DEAD          DEAD/DEAH box helicase
     0.0024   17.9   0.0       0.51   10.3   0.0    2.2  2  ResIII        Type III restriction enzyme, res subunit


Domain annotation for each model (and alignments):
>> HBB  Helical and beta-bridge domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.018        66      86     121 ..     190     227 ..     173     236 .. 0.82
   2 !  188.6   0.0   2.5e-59     9e-56       2     190 .]     244     436 ..     243     436 .. 0.99

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.018
                                       -SHHHHHHHHHHHHHHHTS.TTTEEEEEE.STT...EE CS
                               HBB  86 sPrsflsrlaefllawlssdeedYvrlvskeeg..esL 121
                                        P  f+  ++++l+ w+ + e+d v+++ + ++  e+L
  gi|474933771|ref|YP_007687353.1| 190 YPFFFIPAVRSRLMDWMGTAEKDVVAIIDEAHNlpEYL 227
                                       5999************************9988755555 PP

  == domain 2  score: 188.6 bits;  conditional E-value: 2.5e-59
                                       CHCHCCCCHHCCCCCCCH..HHHHHHHHCCCCHHHHSTTTE.CCHCHHHHHCHCHHHCHHHHHHHHHHHHHHHHHHH CS
                               HBB   2 ikeaketdepklqdeysr..LvegLreaeeereeeyvleee.pilpdeileeavpglirsaehflsllkrlveygka 75 
                                        +ea+++++p l +++++  Lv+++r++++++++e++++e+ pi+pd++ +++++++ rs+ ++++l+  l+e+g+a
  gi|474933771|ref|YP_007687353.1| 244 RSEAEANGNPLLGSDVRAtdLVDAVRDVMDDATDEFLTRENdPIPPDYLSTKLMSRFSRSTVGIKNLFVLLHEAGMA 320
                                       589***********************************9999*********************************** PP

                                       CCHHCCCTCC-SHHHHHHHHHHHHHHHTS.TTTEEEEEE.STT.EECCCCS-TCCHHHHHHHCHCCCCCCTS-SSHH CS
                               HBB  76 rreekieksesPrsflsrlaefllawlssdeedYvrlvskeegesLeavcldPskalrflkerlssllmsgtltple 152
                                       ++e+k++k+++Prs+l +la f+l wl++d+e++v+l++ ++++sLea+cldP++a+++l+ ++ss++msgtl+pl+
  gi|474933771|ref|YP_007687353.1| 321 IAEKKKAKRKLPRSHLATLALFILGWLECDDESHVFLIAGGDNPSLEAYCLDPADAAEPLRLCRSSVSMSGTLEPLR 397
                                       ***************************************************************************** PP

                                       HHHHHHT.....EEE.S..S.GGHCCCCCCCCCSHTCCC CS
                               HBB 153 eysdiiGle.aklkkfpspfpkEnlivlfatdVsTkyke 190
                                       +y++ +Gl+ +++++fpspfp+En+ ++f++d+sT+y +
  gi|474933771|ref|YP_007687353.1| 398 NYAWELGLRePETETFPSPFPPENRRTVFVRDISTRYAD 436
                                       ************************************975 PP

>> Helicase_C_2  Helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.0   0.0     9e-36   3.2e-32       4     155 ..     454     602 ..     451     606 .. 0.88

  Alignments for each domain:
  == domain 1  score: 112.0 bits;  conditional E-value: 9e-36
                      Helicase_C_2   4 llevvpggvlvffpSyklleevverlkeeleskkieifvee...keesrekvleeykekkkkgaillavcrGklsEG 77 
                                       ++++ + ++ vffpSy+l+e++++   +     + ++f e+   ++++  + +  +++    g++l+av +G++sEG
  gi|474933771|ref|YP_007687353.1| 454 IVDAAKVNTAVFFPSYSLMERFIDDGVDFAL--RRDVFYERagsTQAELMDQVMGFRT--TPGSVLFAVTGGRISEG 526
                                       566778899***************8888665..7789999844444444445555666..***************** PP

                      Helicase_C_2  78 idfsddllraviivglPfpnpkdpeveakreyldekgkknsgkewylpealravnQaiGRliRhkdDygaivllDeR 154
                                       +df+++++++ +ivg+P+  p + +++a  +y++ +++ +++  +++ +a+r+++QaiGRliR+++D+g+ v+lD+R
  gi|474933771|ref|YP_007687353.1| 527 LDFPGREMELAVIVGIPYGRP-SAKTDALIRYCQGRFG-DGFGMAMKVPAVRKMRQAIGRLIRSENDRGIAVILDNR 601
                                       *********************.6888************.************************************** PP

                      Helicase_C_2 155 f 155
                                       +
  gi|474933771|ref|YP_007687353.1| 602 V 602
                                       7 PP

>> DEAD_2  DEAD_2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.5   0.0   2.6e-25   9.2e-22       1     176 []      62     240 ..      62     240 .. 0.87

  Alignments for each domain:
  == domain 1  score: 77.5 bits;  conditional E-value: 2.6e-25
                                       EEESSHHHHHHHHHHHHHHHHHCHHHS---EEEE--CC.CC-...SCHHCCCHHCCCCHHHHHHHHHCCHHCCHTTT CS
                            DEAD_2   1 ycsRThsqleqvvkelkklesykkkkekvkvviLgSRk.nlC...ineevkkekkekavneaCkelkkkkaeekeek 73 
                                       y +RT+sq +qv  e + +++       +  v +++R+  +C    +++ +++ + ++++++C++lkk        k
  gi|474933771|ref|YP_007687353.1|  62 YLTRTKSQQRQVALECRAISDNI----PLISVAVQGRSaSTCpmmAHDRDLSDGTPEELSRLCSDLKKGDGP--AGK 132
                                       89*****************7544....588888888872467322344444455688999*******99964..599 PP

                                       TTT-SCC..CCHHHHHHHHHHC---CHHHHHHHHHCT--HHHHHHHHHCCTSEEEEEHHHHTSCCCHHHHH...T.. CS
                            DEAD_2  74 Csffenl..eelkklkkllleevvdiedlvelgeklklCPYylsrelledadiiilpYqyLldekireslk...gis 145
                                       C++fe++  +++++  + + +   d e++ e++  +++CPY +++++l+ ad++ +pY +++ + +r++l    g  
  gi|474933771|ref|YP_007687353.1| 133 CEYFEAMgsTQVEACISYIRTAHPDPEEFAEFCGAMGVCPYEMAKKVLPYADVVSAPYPFFFIPAVRSRLMdwmGTA 209
                                       ******98777777799****************************************************99898889 PP

                                       GCGCEEEECTCCCHHHHHHHCC-EEEECHHH CS
                            DEAD_2 146 lknsivilDEAhNiedvceeaasveiseesl 176
                                        k+ + i+DEAhN+ + ++e++ + ++ +sl
  gi|474933771|ref|YP_007687353.1| 210 EKDVVAIIDEAHNLPEYLREIQTYTVTARSL 240
                                       9**********************99998776 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.4e-06    0.0085       3     112 ..      14     120 ..      12     133 .. 0.74
   2 ?   -0.6   0.0      0.27   9.6e+02     124     135 ..     214     225 ..     197     241 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.4e-06
                                       HHHHHHHHHH....TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST CS
                                       xxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   3 iQaeaiplil....gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyid 75 
                                        Q+++++ +     g+g v+++  TG+GKT++ l  +++      + +  ++++++ t++  +q++ +++ + ++i 
  gi|474933771|ref|YP_007687353.1|  14 CQKAMVEFVRsgvaGDGTVVMESGTGTGKTAVSLSGAIEG-----RGRSARIVYLTRTKSQQRQVALECRAISDNIP 85 
                                       566666666633335599***************9999944.....456679*********************99988 PP

                                       SEEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  76 lrvlliiggvaardqlskldngvdivvgtpgrlddll 112
                                       l  ++ ++g +a+       ++ d+  gtp+ l +l+
  gi|474933771|ref|YP_007687353.1|  86 LISVA-VQGRSASTCPMMA-HDRDLSDGTPEELSRLC 120
                                       55554.4555554444333.66777778887777776 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.27
                                       EEEEETHHHHHH CS
                                       xxxxxxxxxxxx RF
                              DEAD 124 flVlDEadrlld 135
                                       + ++DEa++l +
  gi|474933771|ref|YP_007687353.1| 214 VAIIDEAHNLPE 225
                                       579*****9865 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00014      0.51       3      47 ..      10      52 ..       8     108 .. 0.79
   2 !    5.3   0.0    0.0048        17     131     164 ..     210     241 ..     192     243 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00014
                                      EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHH CS
                            ResIII  3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklier 47
                                      + r++Q+ ++e +++ +   +d  ++++  TGtGKT v+++ + +
  gi|474933771|ref|YP_007687353.1| 10 SYRPCQKAMVEFVRSGV--AGDGTVVMESGTGTGKTAVSLSGAIE 52
                                      57999999999999998..6999***************9765544 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0048
                                       TT-SEEEEETGGGTTS.TTTHHHHHT---SEEEE CS
                            ResIII 131 drfdviiiDEaHrlgakkswreilekfkeavllg 164
                                       ++  v iiDEaH+l +    rei  +   a  l+
  gi|474933771|ref|YP_007687353.1| 210 EKDVVAIIDEAHNLPE--YLREIQTYTVTARSLE 241
                                       344589********99..6666766665555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (625 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.69u 0.29s 00:00:00.98 Elapsed: 00:00:00.52
# Mc/sec: 3621.19
//
Query:       gi|474933772|ref|YP_007687354.1|  [L=95]
Description: hypothetical protein TALC_00180 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.035   14.3   0.1      0.043   14.0   0.1    1.1  1  Fe-S_biosyn  Iron-sulphur cluster biosynthesis


Domain annotation for each model (and alignments):
>> Fe-S_biosyn  Iron-sulphur cluster biosynthesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   2.4e-06     0.043      19      88 ..       7      71 ..       2      78 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.4e-06
                                      CTTECEEEEEECCTSCCGGS.TT.EEEEEEEEESSTS.TTTEEEEEETTEEEEEEGGGHHHS.TTEEEEEE CS
                       Fe-S_biosyn 19 edkkelrLdvddgggpyskggCsiggkyslvlvdeed.eeydevlesnggkvyvksyslvfldeglvldfv 88
                                      ed k+l++d +++       +C+      lv ++ +  ++ d+++  ++  +yv++ ++++l e++++d+ 
  gi|474933772|ref|YP_007687354.1|  7 EDVKKLIMDAKHDY-----RVCTACLGPALVSTEVKPpKDSDTKIPVGDYILYVSKVQAPYL-ERVTMDML 71
                                      45555888888886.....5588888889998885555************************.99999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 661.12
//
Query:       gi|474933773|ref|YP_007687355.1|  [L=208]
Description: Thiamine biosynthesis ATP pyrophosphatase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.6e-58  196.1   0.1    5.2e-58  195.9   0.1    1.0  1  ThiI           Thiamine biosynthesis protein (ThiI)
    1.5e-06   27.8   0.1    0.00039   20.0   0.0    3.0  2  QueC           Queuosine biosynthesis protein QueC
    2.8e-05   23.1   0.0    5.1e-05   22.2   0.0    1.4  1  tRNA_Me_trans  tRNA methyl transferase
    0.00081   19.8   0.1     0.0014   19.0   0.1    1.5  1  DUF3280        Protein of unknown function (DUF2380)
     0.0033   17.2   0.0      0.015   15.1   0.0    1.9  1  ATP_bind_3     PP-loop family
     0.0039   16.3   0.0     0.0094   15.1   0.0    1.7  2  NAD_synthase   NAD synthase
  ------ inclusion threshold ------
      0.032   14.3   0.0      0.043   13.9   0.0    1.2  1  PAPS_reduct    Phosphoadenosine phosphosulfate reductase fami
       0.16   12.1   0.0       0.22   11.7   0.0    1.2  1  PDDEXK_4       PD-(D/E)XK nuclease superfamily


Domain annotation for each model (and alignments):
>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.9   0.1   2.3e-61   5.2e-58       5     195 ..       2     191 ..       1     193 [. 0.98

  Alignments for each domain:
  == domain 1  score: 195.9 bits;  conditional E-value: 2.3e-61
                              ThiI   5 kvlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlkeile 81 
                                       k+++L+SgGiDSpVaay++ k G  vvl+h++n+p+  ++  e+v++lae l +  +  e+ l+  ++ + +++i +
  gi|474933773|ref|YP_007687355.1|   2 KAVCLISGGIDSPVAAYVMSKVGADVVLLHMDNRPFADDRSLERVKMLAEQLRKVTG-KELPLYSAPHGPSQDKIAK 77 
                                       79***************************************************9986.9****************** PP

                              ThiI  82 kvkekltivllkrkmlriAekvaeeegakalvtGesLgqVaSqtleNlrvisavvnllilrPLigldKeeiiklAke 158
                                        v+  +++vl+k +m   A+k+a++ ga+a++ G+sLgqVaSqtl N+r  ++ v+ +ilrPLig+dK ei ++A++
  gi|474933773|ref|YP_007687355.1|  78 TVDRMYQCVLCKHCMQLTAKKLAKKLGADAIIMGDSLGQVASQTLLNIRSETMFVDFPILRPLIGYDKLEIERIAQD 154
                                       ***************************************************************************** PP

                              ThiI 159 igtyeisiekedkCsvlakhPttkakleevekaeekl 195
                                       igt++isi +   C++l+++  t+ak+e+ +k ++ +
  gi|474933773|ref|YP_007687355.1| 155 IGTFDISIMEVSGCTILPNKVITEAKPEKAQKFYDDV 191
                                       *******************************998876 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.8e-07   0.00039       1      52 [.       2      54 ..       2      68 .. 0.85
   2 ?    3.9   0.0     0.014        32     148     174 ..     130     156 ..      89     169 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.8e-07
                                      EEEEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-T.TSHHHHHHHHHHHHT- CS
                              QueC  1 kavvllSGGlDSttvlalakkegkevealtfdYgqr.hkkeleaakkiakelg 52
                                      kav+l+SGG+DS +++++++k g+ v +l++d      ++ le +k +a++l 
  gi|474933773|ref|YP_007687355.1|  2 KAVCLISGGIDSPVAAYVMSKVGADVVLLHMDNRPFaDDRSLERVKMLAEQLR 54
                                      79*****************************9876667788888888887765 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.014
                                       HTS--EEE-TTTT--HHHHHHHHHHTT CS
                              QueC 148 edkkieieaPlidlsKaeivklgkelg 174
                                       +  ++ i  Pli  +K ei ++++++g
  gi|474933773|ref|YP_007687355.1| 130 MFVDFPILRPLIGYDKLEIERIAQDIG 156
                                       556778888999999999999888888 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   2.3e-08   5.1e-05       1      42 [.       1      42 [.       1      58 [. 0.80

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 2.3e-08
                     tRNA_Me_trans  1 kkvvvalSgGVDSsvaaallkeqgyevigvflklweeedeeg 42
                                      +k v+++SgG+DS vaa+++ + g +v+ +++ +   +d+ +
  gi|474933773|ref|YP_007687355.1|  1 MKAVCLISGGIDSPVAAYVMSKVGADVVLLHMDNRPFADDRS 42
                                      5789*****************************987766655 PP

>> DUF3280  Protein of unknown function (DUF2380)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   6.4e-07    0.0014      21      86 ..      39     112 ..      20     129 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 6.4e-07
                           DUF3280  21 taeearRlaavteqlreaLaesgryevvdlapaaaeiekesn.lrkCngceadi.......ArklgAdlvlvge 86 
                                       ++   +R+++++eqlr+   ++  +      p++++i+k+ + +++C  c+  +       A+klgAd +++g 
  gi|474933773|ref|YP_007687355.1|  39 DDRSLERVKMLAEQLRKVTGKELPLYSAPHGPSQDKIAKTVDrMYQCVLCKHCMqltakklAKKLGADAIIMGD 112
                                       667789********************************77777*******98888888888*********9984 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   6.7e-06     0.015       6     158 ..       7     154 ..       2     158 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.7e-06
                                       --SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSST.CHHHHHHHHHHHHHHTT-EEEEEE--H.HHCTTSTCCCHH CS
                        ATP_bind_3   6 vSgGlDSmaLllllaklkkklgiklvaihvdhglre.eskeeaelvkelckklnikleiekvdv.akkkgknleeaA 80 
                                       +SgG+DS +  +++ k       ++v++h+d   r+   ++  e vk l+++l  k++ +++++ ++ +g + ++ A
  gi|474933773|ref|YP_007687355.1|   7 ISGGIDSPVAAYVMSKVGA----DVVLLHMD--NRPfADDRSLERVKMLAEQL-RKVTGKELPLySAPHGPSQDKIA 76 
                                       7999999999999999844....45555555..56425567778888888888.67777777775444455555555 PP

                                       HHHH..HH.HHHHCHHCCT.CEEE---BHHHHHHHHHHHHCCT--C.CHHH-S-SEEEETTCCEE-CCCT--HHHHH CS
                        ATP_bind_3  81 RelR..Ye.vlkealkkegievlllAhhadDqaEtfllrlargsgl.aglagikeaseiasirlvRPlLkvskeele 153
                                        ++   Y+ vl +++ +  ++ l+  ++    a  +++  + g+   ++l+ i++++ + +  ++RPl+ + k e+e
  gi|474933773|ref|YP_007687355.1|  77 KTVDrmYQcVLCKHCMQLTAKKLA--KK--LGADAIIMGDSLGQVAsQTLLNIRSETMFVDFPILRPLIGYDKLEIE 149
                                       554311331445555555444443..22..2356788887777766488999************************* PP

                                       HHHHH CS
                        ATP_bind_3 154 eylke 158
                                       +++++
  gi|474933773|ref|YP_007687355.1| 150 RIAQD 154
                                       *9986 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   4.2e-06    0.0094      20      73 ..       2      54 ..       1      84 [. 0.87
   2 ?   -2.7   0.0       1.2   2.6e+03      51      76 ..     170     195 ..     165     199 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.2e-06
                                      EEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--.SSSTTHHHHHHHHHHHHHHT CS
                      NAD_synthase 20 gvvlGlSGGvDSslvaalavkalgkenvlalllP.ssvsseedvedalalaenlg 73
                                      ++v  +SGG+DS ++a++  k+   + v+ l +    +++++++e  ++lae+l 
  gi|474933773|ref|YP_007687355.1|  2 KAVCLISGGIDSPVAAYVMSKVG--ADVVLLHMDnRPFADDRSLERVKMLAEQLR 54
                                      567779************99986..778889999899***************985 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.2
                                       E--SSSTTHHHHHHHHHHHHHHTSEE CS
                      NAD_synthase  51 llPssvsseedvedalalaenlgiev 76 
                                       +lP++v +e   e+a+++ ++++ie 
  gi|474933773|ref|YP_007687355.1| 170 ILPNKVITEAKPEKAQKFYDDVSIEE 195
                                       78999999999999999999888875 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.9e-05     0.043       2     119 ..       3     124 ..       2     156 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.9e-05
                                       EEEE--SSCTCHHHHHHHHHHCTTHEEEEEE-S.....TB-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH- CS
                       PAPS_reduct   2 lvvsvsgGkdslVllhLalkafkpvpvvfvdtg.....hefpetiefvdeleeryglrlkvyepeeevaekinaekh 73 
                                        v ++sgG+ds V    ++k+  +v ++++d +     +  + +  + ++l++  g +l +y+ +++ ++  +a++ 
  gi|474933773|ref|YP_007687355.1|   3 AVCLISGGIDSPVAAYVMSKVGADVVLLHMDNRpfaddRSLERVKMLAEQLRKVTGKELPLYSAPHGPSQDKIAKT- 78 
                                       5889***************************873222123333444445555555777999**9999888888877. PP

                                       S-THHHCHHHHHHTHHHHHHHHHCTTECEEE----CCCTTTTTTSS CS
                       PAPS_reduct  74 gsslyeeaaeriaKveplkkaLekldedalltGaRrdesksraklp 119
                                         + y+  +++ +   ++kk  +kl++da+++G    + +s+  l+
  gi|474933773|ref|YP_007687355.1|  79 VDRMYQCVLCKHCMQLTAKKLAKKLGADAIIMGDSLGQVASQTLLN 124
                                       68888886666666677778799*********97655555555555 PP

>> PDDEXK_4  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   9.8e-05      0.22      38     114 ..     120     194 ..      97     207 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.8e-05
                          PDDEXK_4  38 kafldllrerlfssdeisasvadlesaeverenasekngriDlllqenkivvlIEnKvaAkdqkeQlarYeefakkk 114
                                       +++l+++ e +f + +i +++  +++ e+er    ++ g++D+++ e +++ ++ nKv + +++e  ++ +++++ +
  gi|474933773|ref|YP_007687355.1| 120 QTLLNIRSETMFVDFPILRPLIGYDKLEIERI--AQDIGTFDISIMEVSGCTILPNKVITEAKPEKAQKFYDDVSIE 194
                                       45558888888988888888556666666665..9999**************************9999999988755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       806  (0.0449551); expected 358.6 (0.02)
Passed bias filter:                      647  (0.0360868); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1314.45
//
Query:       gi|474933774|ref|YP_007687356.1|  [L=60]
Description: hypothetical protein TALC_00182 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.08   12.8   0.4       0.13   12.1   0.3    1.4  1  WD40_alt  Alternative WD40 repeat motif


Domain annotation for each model (and alignments):
>> WD40_alt  Alternative WD40 repeat motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.3   7.4e-06      0.13      15      38 ..      11      34 ..       6      36 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.4e-06
                          WD40_alt 15 qlkvrvseLeeEVrtLrKInkdLf 38
                                       l++ v  L +EV+tLr   + L+
  gi|474933774|ref|YP_007687356.1| 11 DLRMEVISLRNEVKTLRDFVRGLY 34
                                      699**************9999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.37
# Mc/sec: 485.52
//
Query:       gi|474933775|ref|YP_007687357.1|  [L=181]
Description: putative RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-09   37.5   0.0    4.2e-09   36.0   0.0    1.8  1  ECR1_N          Exosome complex exonuclease RRP4 N-terminal r
     0.0003   21.1   0.0       0.58   10.5   0.0    2.5  2  S1              S1 RNA binding domain
     0.0029   17.6   0.1     0.0048   16.9   0.1    1.4  1  Zn_Tnp_IS91     Transposase zinc-binding domain
     0.0033   18.0   0.3          2    9.0   0.0    2.6  3  EXOSC1          Exosome component EXOSC1/CSL4
     0.0061   16.5   1.6      0.015   15.3   1.6    1.6  1  DZR             Double zinc ribbon
     0.0076   16.2   0.8      0.018   14.9   0.8    1.6  1  Prok-RING_1     Prokaryotic RING finger family 1
     0.0083   16.1   1.5      0.018   15.0   1.5    1.5  1  zinc-ribbons_6  zinc-ribbons
  ------ inclusion threshold ------
      0.022   14.8   1.5      0.043   13.9   1.5    1.6  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.031   14.4   1.7      0.057   13.6   1.7    1.4  1  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
      0.039   13.5   0.1      0.086   12.4   0.1    1.5  1  DUF5029         Domain of unknown function (DUF5029)
       0.15   12.0   2.6       0.33   10.9   2.6    1.5  1  zf-C3HC4        Zinc finger, C3HC4 type (RING finger)
          1    9.2   3.6       0.55   10.0   1.0    1.8  2  DUF3039         Protein of unknown function (DUF3039)


Domain annotation for each model (and alignments):
>> ECR1_N  Exosome complex exonuclease RRP4 N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.0   2.8e-12   4.2e-09       1      36 [.       1      36 [.       1      38 [. 0.95

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 2.8e-12
                                      EE-TT-EEEETTTSEE-TTEEEETTEEEESSSEEEE CS
                            ECR1_N  1 iVtPGevlttdeefmrGhGTYvrggtiyAsvaGtve 36
                                      +V+PG+ ++ +ee++++ GT+v++g+iyAs  G ++
  gi|474933775|ref|YP_007687357.1|  1 MVLPGDEVAVEEEYVASDGTFVKDGKIYASQFGRLI 36
                                      7*****************************999875 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0024       3.5      45      66 ..      50      71 ..      25      75 .. 0.88
   2 !   10.5   0.0   0.00039      0.58      30      63 ..      93     125 ..      89     130 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0024
                                      CHHHCEETTEEEEEEEEEEETT CS
                                S1 45 dpdevlkvGdevkvkvlkvdkd 66
                                      +   vlk+Gd v++ +++v+k+
  gi|474933775|ref|YP_007687357.1| 50 NAPNVLKIGDIVYASIDDVRKT 71
                                      66789**************997 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00039
                                       EEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEE CS
                                S1  30 gfvpaselsrdarvedpdevlkvGdevkvkvlkv 63 
                                       + +++s +s d  + d   ++++Gd ++++v++v
  gi|474933775|ref|YP_007687357.1|  93 ATIHVSKISPD-YTNDVANEFRKGDLIRARVIGV 125
                                       569********.9*******************98 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   3.2e-06    0.0048      30      72 ..     133     173 ..     105     178 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.2e-06
                       Zn_Tnp_IS91  30 CrtaalGfaryeCeeCghekivyfsCksrhCpsCqkkateewl 72 
                                        ++++lG+ r  C +C+    +  + k+ +Cp+C+k + ++ +
  gi|474933775|ref|YP_007687357.1| 133 TKDEHLGVIRALCGTCKT--EMTKRGKNVFCPKCKKSQPRKLA 173
                                       57899***********85..68899***********9988776 PP

>> EXOSC1  Exosome component EXOSC1/CSL4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0014         2       3      41 ..      56      94 ..      52     108 .. 0.86
   2 !    6.4   0.1    0.0092        14      92     107 ..     108     123 ..     105     125 .. 0.86
   3 ?   -2.6   0.0       5.5   8.2e+03      83      99 ..     130     156 ..     127     159 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0014
                                      -TT-EEEEEEEEEESSEEEEEEEEECTBSBCCCEEECCC CS
                            EXOSC1  3 kegdvVLarvtrlrkkqalveilsvegennvlsdsgvga 41
                                      k+gd+V a + ++rk  a    l +eg+++ +s s v  
  gi|474933775|ref|YP_007687357.1| 56 KIGDIVYASIDDVRKTMAPATALCKEGSGRNISSSTVAT 94
                                      68**************************99988887765 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0092
                                       GGCTEECTTEEEEEEE CS
                            EXOSC1  92 viemfrpGDIvraqvi 107
                                       v + fr+GD++ra+vi
  gi|474933775|ref|YP_007687357.1| 108 VANEFRKGDLIRARVI 123
                                       5678***********9 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 5.5
                                       ECCSSSTT-..........GGCTEECT CS
                            EXOSC1  83 Ratekdrvk..........viemfrpG 99 
                                        +t+kd+            ++em + G
  gi|474933775|ref|YP_007687357.1| 130 QLTTKDEHLgviralcgtcKTEMTKRG 156
                                       577788776667777777778888777 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   1.6     1e-05     0.015      14      39 ..     144     169 ..     140     173 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1e-05
                               DZR  14 fCseCgtklkavaaedrCpsCgekvd 39 
                                        C++C+t++ +  ++ +Cp+C+++ +
  gi|474933775|ref|YP_007687357.1| 144 LCGTCKTEMTKRGKNVFCPKCKKSQP 169
                                       7*********9999*******99866 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.8   1.2e-05     0.018       6      33 ..     144     171 ..     140     178 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.2e-05
                       Prok-RING_1   6 kCpvCgkelkeedDiVvCpeCgtpyHra 33 
                                        C  C+ e+++    V Cp+C+ ++ r+
  gi|474933775|ref|YP_007687357.1| 144 LCGTCKTEMTKRGKNVFCPKCKKSQPRK 171
                                       7*********************998776 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   1.5   1.2e-05     0.018       2      25 ..     144     167 ..     143     175 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.2e-05
                                       --SSS-S--EE-SSEEE-TTT--E CS
                    zinc-ribbons_6   2 kCpeCqqelekrgeqyhCeaCqed 25 
                                        C +C++e++krg++++C +C+++
  gi|474933775|ref|YP_007687357.1| 144 LCGTCKTEMTKRGKNVFCPKCKKS 167
                                       6********************985 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   1.5   2.8e-05     0.043      68      96 ..     140     168 ..      65     175 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.8e-05
                                       --EEEETTTS-EEECHHHHHS-TTTSSS- CS
                              HypA  68 pvkvrCreCgkefeleekalrCpkCgsad 96 
                                        +++ C +C++e++++ k++ CpkC++++
  gi|474933775|ref|YP_007687357.1| 140 VIRALCGTCKTEMTKRGKNVFCPKCKKSQ 168
                                       36789*********8877788****9976 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.7   3.8e-05     0.057      10      33 ..     144     168 ..     140     176 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.8e-05
                      NOB1_Zn_bind  10 rChaCfk.vtkdmtkkFCpkCGnkt 33 
                                        C +C + +tk+ + +FCpkC +++
  gi|474933775|ref|YP_007687357.1| 144 LCGTCKTeMTKRGKNVFCPKCKKSQ 168
                                       599**8736677999******9876 PP

>> DUF5029  Domain of unknown function (DUF5029)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   5.8e-05     0.086     112     164 ..      53     109 ..      47     126 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.8e-05
                           DUF5029 112 ngvrqgdsvyvvvndpqmtlataqtlahqgd....kseaairayisnlsksylndlt 164
                                       n ++ gd vy  ++d + t+a a +l+++g      s +    ++s++s  y nd++
  gi|474933775|ref|YP_007687357.1|  53 NVLKIGDIVYASIDDVRKTMAPATALCKEGSgrniSSSTVATIHVSKISPDYTNDVA 109
                                       66789**********************999622222444556789*********986 PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   2.6   0.00022      0.33      21      41 .]     144     164 ..     143     164 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00022
                                       B-CHHHHHHHHCTSSB--TTT CS
                          zf-C3HC4  21 fCskCirkilksrkkvkCPlC 41 
                                       +C +C ++++k  k+v CP+C
  gi|474933775|ref|YP_007687357.1| 144 LCGTCKTEMTKRGKNVFCPKC 164
                                       8**********999999**** PP

>> DUF3039  Protein of unknown function (DUF3039)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.1       7.9   1.2e+04      26      30 ..      75      79 ..      73      81 .. 0.70
   2 ?   10.0   1.0   0.00037      0.55      26      51 ..     141     166 ..     137     168 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 7.9
                           DUF3039 26 VvALC 30
                                       +ALC
  gi|474933775|ref|YP_007687357.1| 75 ATALC 79
                                      57888 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00037
                           DUF3039  26 VvALCGkvwvptrdpkkfPvCpeCke 51 
                                       ++ALCG + + + +  k   Cp+Ck+
  gi|474933775|ref|YP_007687357.1| 141 IRALCGTCKTEMTKRGKNVFCPKCKK 166
                                       89******999999999999****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1310.99
//
Query:       gi|474933776|ref|YP_007687358.1|  [L=197]
Description: putative RNA methylase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-13   51.0   0.0    1.7e-13   50.5   0.0    1.2  1  MTS              Methyltransferase small domain
    1.6e-13   50.7   0.0    1.8e-13   50.5   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    4.5e-11   43.3   0.0    7.1e-11   42.7   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    1.4e-10   41.0   0.4      2e-10   40.5   0.4    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    8.3e-07   29.6   0.0    1.3e-06   29.0   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    6.7e-05   22.8   0.0    8.2e-05   22.5   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    0.00017   21.0   0.0    0.00021   20.7   0.0    1.3  1  CMAS             Mycolic acid cyclopropane synthetase
    0.00017   21.7   0.0    0.00021   21.4   0.0    1.2  1  FtsJ             FtsJ-like methyltransferase
    0.00023   20.9   1.0     0.0021   17.8   1.0    2.0  1  UPF0020          Putative RNA methylase family UPF0020
    0.00043   21.0   0.1    0.00066   20.4   0.1    1.5  1  Methyltransf_12  Methyltransferase domain
    0.00076   19.2   0.0      0.001   18.8   0.0    1.2  1  Cons_hypoth95    Conserved hypothetical protein 95
     0.0021   17.5   0.0     0.0039   16.6   0.0    1.4  1  TehB             Tellurite resistance protein TehB
     0.0025   17.2   0.3     0.0036   16.7   0.2    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
     0.0042   17.0   0.0     0.0067   16.4   0.0    1.3  1  Methyltransf_18  Methyltransferase domain
     0.0044   17.0   0.0     0.0052   16.8   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
  ------ inclusion threshold ------
      0.016   14.9   0.1      0.023   14.4   0.1    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.019   13.9   0.1      0.028   13.4   0.1    1.2  1  Methyltransf_9   Protein of unknown function (DUF1698)
      0.031   13.4   0.1      0.044   12.9   0.1    1.2  1  Methyltrans_SAM  S-adenosylmethionine-dependent methyltransfe
      0.059   13.1   0.0      0.086   12.6   0.0    1.2  1  Met_10           Met-10+ like-protein
      0.067   12.2   0.0      0.094   11.7   0.0    1.2  1  DUF4655          Domain of unknown function (DUF4655)
       0.15   11.8   0.1       0.21   11.3   0.1    1.2  1  Methyltransf_16  Lysine methyltransferase


Domain annotation for each model (and alignments):
>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5   0.0     2e-16   1.7e-13      32     116 ..      48     129 ..      34     145 .. 0.84

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 2e-16
                                       CSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE---ST CS
                               MTS  32 sgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdlivsNPPfh 108
                                         kv+DlGcG+G+ ++a+a +     v+ +dv+  Ale ake +++ +l+v++  sd+ +    +  d++++NPPf 
  gi|474933776|ref|YP_007687358.1|  48 GMKVMDLGCGTGMFSVAAALMGAG-MVVGYDVSEGALEQAKECARSMNLDVSFKLSDIRDVN--EGADTVLMNPPFG 121
                                       468*************99998887.69******************************98755..59**********9 PP

                                       TTCHCHHH CS
                               MTS 109 agkatela 116
                                       ++++  ++
  gi|474933776|ref|YP_007687358.1| 122 SQNKHADR 129
                                       98864332 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5   0.0   2.1e-16   1.8e-13       4     103 ..      48     145 ..      45     190 .. 0.86

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 2.1e-16
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlils 80 
                                       g++v+DlGCGtG ++ ++a ++g  + vvG D se a+e+A+e a++ +ld v+F+ +di + +     e  D +l 
  gi|474933776|ref|YP_007687358.1|  48 GMKVMDLGCGTGMFSVAAA-LMG-AGMVVGYDVSEGALEQAKECARSMNLD-VSFKLSDIRDVN-----EGADTVLM 116
                                       89*****************.665.699***********************8.**********88.....679***** PP

                   Methyltransf_31  81 nevl......naladpdkileeiervlkp 103
                                       n ++      ++ ++++k+l ++e+v + 
  gi|474933776|ref|YP_007687358.1| 117 NPPFgsqnkhADRPFLEKALDSAEKVYSI 145
                                       *8888888778889999999988888664 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   0.0   8.4e-14   7.1e-11       1      75 [.      51     121 ..      51     144 .. 0.79

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 8.4e-14
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEEST.GG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssga.lh 75 
                                       v+dlGcGtG ++ a+a   g++ v+g D+se++le+a+e a++ +l+v+f   d++d+++     D v+++   + 
  gi|474933776|ref|YP_007687358.1|  51 VMDLGCGTGMFSVAAALM-GAGMVVGYDVSEGALEQAKECARSMNLDVSFKLSDIRDVNEG---ADTVLMN-PpFG 121
                                       89************9977.79************************************9854...5777773.3244 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   0.4   2.4e-13     2e-10     161     233 ..      47     117 ..      34     117 .. 0.85

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 2.4e-13
                              PrmA 161 egeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellkeekadvivaN 233
                                       eg +v+D+G+G+G+ ++aaa++ga  vv++D+ e A++ ake a+  +++ ++++   +++   e ad ++ N
  gi|474933776|ref|YP_007687358.1|  47 EGMKVMDLGCGTGMFSVAAALMGAGMVVGYDVSEGALEQAKECARSMNLDVSFKLSDIRDVN--EGADTVLMN 117
                                       5679****************************************999999888775555554..467777765 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   1.5e-09   1.3e-06       2      56 ..      53     108 ..      52     143 .. 0.90

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 1.5e-09
                                       EET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTS CS
                   Methyltransf_11   2 dvGcGtGrlaealakrg.arvvgvDlskemlklakekaseeglkvefvvadaeklp 56 
                                       d+GcGtG ++ a a  g + vvg D+s+ +l++ake+a+  +l v+f  +d+++++
  gi|474933776|ref|YP_007687358.1|  53 DLGCGTGMFSVAAALMGaGMVVGYDVSEGALEQAKECARSMNLDVSFKLSDIRDVN 108
                                       9*************9999***********************999999999999863 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   9.6e-08   8.2e-05      21      89 ..      46     117 ..      24     160 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 9.6e-08
                   Methyltransf_23  21 raggrvLdiGcGtGillevlrengf.svtgvDlspeaveiae......kakkaqkdqfdeqeaaepqgkfdlIvlr 89 
                                        +g++v+d+GcGtG ++  ++  g+  v+g+D s+ a e a+      +     +++f  +++++ ++  d++ ++
  gi|474933776|ref|YP_007687358.1|  46 IEGMKVMDLGCGTGMFSVAAALMGAgMVVGYDVSEGALEQAKecarsmN----LDVSFKLSDIRDVNEGADTVLMN 117
                                       57889********************8899******99999878744441....34444444455555555555444 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   2.4e-07   0.00021      62     131 ..      47     114 ..      16     155 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.4e-07
                                       TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-----SEE CS
                              CMAS  62 pGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedldekvdrv 131
                                       +Gm+++d+GcG G   + a+      vvg  +S+   ++ak+   +++   +v+ kl+d +d++e  d v
  gi|474933776|ref|YP_007687358.1|  47 EGMKVMDLGCGTGMFSVAAALMGAGMVVGYDVSEGALEQAKECARSMN--LDVSFKLSDIRDVNEGADTV 114
                                       7*************999999997779***************9988887..568899*********99987 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   2.5e-07   0.00021      21      92 ..      47     115 ..      29     153 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.5e-07
                                       TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSSHHH...TTEEEECS-C.CCSSHHHHHCHCHHHSSEEEEE CS
                              FtsJ  21 pgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpmapl...pgvttiqgdi.tdpetiekikealserkvdlvv 92 
                                       +g++v+Dlg+++G +s  +   +ga g+vv++D+ ++a+    +  ++++ d+ ++ + i+ ++e     ++d v+
  gi|474933776|ref|YP_007687358.1|  47 EGMKVMDLGCGTGMFSVAA-ALMGA-GMVVGYDVSEGALEqakECARSMNLDVsFKLSDIRDVNE-----GADTVL 115
                                       6899***********9666.55598.**********95443236666667777666677766664.....455555 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   1.0   2.4e-06    0.0021      28     154 ..      47     141 ..      27     152 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.4e-06
                                       TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHHHHHHHHHHTT-GGG CS
                           UPF0020  28 pgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDldrrvvqgareNaekagvgdl 104
                                       +g + +D  CG+G + + aal+ga ++                         +g D  + ++++a+e a++++++ +
  gi|474933776|ref|YP_007687358.1|  47 EGMKVMDLGCGTGMFSVAAALMGAGMV-------------------------VGYDVSEGALEQAKECARSMNLDVS 98 
                                       5666677779************99999.........................8*****************9998765 PP

                                       EEEEE--GGG--STTS---EEEE----------HHHHHHHHHHHHHHHHH CS
                           UPF0020 105 iefsqadaakLrlkegevdvivtnpPYGerlgskkalekLYseflrelkr 154
                                         f+  d+++++  e   d+++ npP+G     k+a + + ++ l+++++
  gi|474933776|ref|YP_007687358.1|  99 --FKLSDIRDVN--E-GADTVLMNPPFGSQN--KHADRPFLEKALDSAEK 141
                                       ..5556699998..3.48**********864..44445555555555555 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1   7.8e-07   0.00066       1      73 [.      52     117 ..      52     156 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 7.8e-07
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvas 73 
                                       +++GcGtG ++ a +       ++g+D+s+ a+e+ake  ++ +      v ++  d+ d  +    D+v+++
  gi|474933776|ref|YP_007687358.1|  52 MDLGCGTGMFSVAAALM-GAGMVVGYDVSEGALEQAKECARSMNL----DVSFKLSDIRDVNE--GADTVLMN 117
                                       69******887777666.667777*********665554444433....44444444433333..67777775 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.2e-06     0.001      30     128 ..      35     125 ..      23     169 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.2e-06
                                       HHHHHH.HCCCHCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHC CS
                     Cons_hypoth95  30 ealFni.laaeiegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleall 105
                                       e +F+  +a +ieg +v+Dl +G+G  ++ A+  ga  +v  + ++ a+++ ke  ++++l+     +k ++ ++++
  gi|474933776|ref|YP_007687358.1|  35 EIVFDAyCAGDIEGMKVMDLGCGTGMFSVAAALMGAGMVVGYDVSEGALEQAKECARSMNLD---VSFKLSDIRDVN 108
                                       56777515566*************************************************88...577777777775 PP

                                       TS--SS-EEEEEEE--SSSTTCH CS
                     Cons_hypoth95 106 klakkkeefdivflDPPyakell 128
                                       +        d v ++PP+ +++ 
  gi|474933776|ref|YP_007687358.1| 109 EG------ADTVLMNPPFGSQNK 125
                                       55......699*******99875 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   4.6e-06    0.0039      29      90 ..      46     107 ..      28     116 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.6e-06
                                       S-S-EEEEES-TTSHHHHHHHHTT-E.EEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG- CS
                              TehB  29 vkpgkvldlgcgqgrnslylsllgyd.vtawdknensiafleeikekenlknistalydinea 90 
                                       ++  kv+dlgcg g  s+  +l+g   v  +d  e +++  +e +   nl+ +s +l di ++
  gi|474933776|ref|YP_007687358.1|  46 IEGMKVMDLGCGTGMFSVAAALMGAGmVVGYDVSEGALEQAKECARSMNLD-VSFKLSDIRDV 107
                                       6778*******************9863789********************9.99999988765 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2   4.3e-06    0.0036      41     106 ..      41     103 ..      35     143 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.3e-06
                                       HH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE-- CS
                   Ubie_methyltran  41 klvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqan 106
                                        + ++ +g kv+D+ +Gtg   f+++ ++   g vv+ D++e  L+++++ ++     ++ f  ++
  gi|474933776|ref|YP_007687358.1|  41 YCAGDIEGMKVMDLGCGTGM--FSVAAALMGAGMVVGYDVSEGALEQAKECARSM-NLDVSFKLSD 103
                                       578999*************6..6678889999***************99977654.3466665555 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   7.9e-06    0.0067      15      73 ..      48     103 ..      41     117 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.9e-06
                   Methyltransf_18  15 gsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsd 73 
                                       g +v+D G+  g+ +++++  g a  v+  D++eg+le+ake +++ +l  ++++ lsd
  gi|474933776|ref|YP_007687358.1|  48 GMKVMDLGCGTGMFSVAAALMG-AGMVVGYDVSEGALEQAKECARSMNL--DVSFKLSD 103
                                       779*************999766.669*******************9999..46666666 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   6.1e-06    0.0052      26      86 ..      48     105 ..      30     163 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6.1e-06
                   Methyltransf_32  26 altvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfae 86 
                                        ++v+D+G+G g  s + al        vvg d++e   e+a++ a+ ++ +++ +ls + 
  gi|474933776|ref|YP_007687358.1|  48 GMKVMDLGCGTGMFSVAAAL---MGAGMVVGYDVSEGALEQAKECARSMNLDVSFKLSDIR 105
                                       5789***************9...6699********************99955544444443 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   2.7e-05     0.023      73     132 ..      47     103 ..      31     112 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.7e-05
                                       TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES- CS
                              PCMT  73 kgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgD 132
                                       +g++v+++G+G+G  ++  a l+g+ g vv+ + ++   e+ak+  +  +l+ v+++ +D
  gi|474933776|ref|YP_007687358.1|  47 EGMKVMDLGCGTGMFSV-AAALMGA-GMVVGYDVSEGALEQAKECARSMNLD-VSFKLSD 103
                                       69***********9865.5556665.66*************99887766654.6666555 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   3.2e-05     0.028     113     164 ..      45      96 ..      41     115 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.2e-05
                                       --TT-EEEEET-TTSHHHHHHHHCT-SEEEEE---HHHHHHHHHHHCCTTTT CS
                    Methyltransf_9 113 dlkgrtildvGcgnGyhlwrmvgegaklvvGidPselfliqfeavrkllged 164
                                       d++g +++d+Gcg+G +    +  ga +vvG d se  l q +   + ++ d
  gi|474933776|ref|YP_007687358.1|  45 DIEGMKVMDLGCGTGMFSVAAALMGAGMVVGYDVSEGALEQAKECARSMNLD 96 
                                       788999**************99************999998888777766555 PP

>> Methyltrans_SAM  S-adenosylmethionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   5.2e-05     0.044     123     170 ..      47      94 ..      39     105 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.2e-05
                   Methyltrans_SAM 123 kdknvlnlfaytcgfsvaaiaggaskvvnvdmargslnkgrdnhrlng 170
                                       ++ +v++l + t  fsvaa   ga  vv  d++ g+l++ ++  r  +
  gi|474933776|ref|YP_007687358.1|  47 EGMKVMDLGCGTGMFSVAAALMGAGMVVGYDVSEGALEQAKECARSMN 94 
                                       56789999999999**************************99887555 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0    0.0001     0.086     100     178 ..      47     120 ..      44     147 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0001
                                       TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---TT-EEEEEE-- CS
                            Met_10 100 egevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevireqladrvvmnl 176
                                       eg  V+d+  G G f++++a +  a +v++ d+   + +  ke  +  +++  v+  l+D r+v  ++ ad v+mn 
  gi|474933776|ref|YP_007687358.1|  47 EGMKVMDLGCGTGMFSVAAALM-GAGMVVGYDVSEGALEQAKECARSMNLD--VSFKLSDIRDV--NEGADTVLMNP 118
                                       57789***************85.5667*************99999876665..656799*****..5999*****98 PP

                                       TT CS
                            Met_10 177 pk 178
                                       p 
  gi|474933776|ref|YP_007687358.1| 119 PF 120
                                       74 PP

>> DUF4655  Domain of unknown function (DUF4655)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00011     0.094     256     299 ..      82     126 ..      75     135 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                           DUF4655 256 illepkalkrnlnlesslklsvlkdldsgh.rvsarpdpeslhkk 299
                                       +l ++k   r++nl+ s+kls ++d+++g   v++ p   s +k+
  gi|474933776|ref|YP_007687358.1|  82 ALEQAKECARSMNLDVSFKLSDIRDVNEGAdTVLMNPPFGSQNKH 126
                                       67789999*****************98765155777777777776 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00025      0.21      44      82 ..      45      87 ..      30     106 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00025
                   Methyltransf_16 44 elsklsvlELGsGtGlvGlavael....lpeakviltDleell 82
                                      + ++++v++LG GtG++ +a+a++    + + +v    le++ 
  gi|474933776|ref|YP_007687358.1| 45 DIEGMKVMDLGCGTGMFSVAAALMgagmVVGYDVSEGALEQAK 87
                                      67899*****************994442244444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1302.37
//
Query:       gi|474933777|ref|YP_007687359.1|  [L=542]
Description: IMP cyclohydrolase /phosphoribosylaminoimidazolecarboxamide formyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   5.5e-105  351.0   0.0   7.4e-105  350.6   0.0    1.2  1  AICARFT_IMPCHas  AICARFT/IMPCHase bienzyme
    6.2e-30  103.3   0.1    2.1e-29  101.6   0.1    2.0  1  MGS              MGS-like domain
     0.0074   15.6   0.0      0.014   14.7   0.0    1.3  1  tRNA-synt_2e     Glycyl-tRNA synthetase alpha subunit
      0.008   16.7   0.1      0.095   13.2   0.0    2.8  4  CoA_binding_2    CoA binding domain
  ------ inclusion threshold ------
      0.064   13.3   0.0       0.16   12.0   0.0    1.7  1  DUF4943          Domain of unknown function (DUF4943)
       0.15   11.9   0.0       0.39   10.5   0.0    1.7  1  BING4CT          BING4CT (NUC141) domain


Domain annotation for each model (and alignments):
>> AICARFT_IMPCHas  AICARFT/IMPCHase bienzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  350.6   0.0  2.5e-108  7.4e-105       1     294 [.     160     473 ..     160     475 .. 0.94

  Alignments for each domain:
  == domain 1  score: 350.6 bits;  conditional E-value: 2.5e-108
                                       HHHTTTT-EEE-SGGGHHHHHHHHHC.T.B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.....CSE...EEEEEE CS
                   AICARFT_IMPCHas   1 AAKNhksVtvvvdpadYeevleelkk.gevsletrkklaakaFahtaaYDaaiaeylskq.....lpetlklslekk 71 
                                       AAKN++sV+vv+dp++Y +v+ +l + ge+ +   k+++a+aF+ ta+YDa+++++++k+     +p+ +   +ek+
  gi|474933777|ref|YP_007687359.1| 160 AAKNWQSVAVVTDPKQYGTVTGHLIAdGEIPEFILKRFMAQAFTVTAQYDAMVSQVMQKSfgnemFPSFFPQPCEKV 236
                                       9**********************99989*****************************98888777778888899*** PP

                                       EEESSSSSTTS-EEEEE-TT..STTHHH-EEEESS---HHHHHHHHHHHHHHCTS...EEEEEEETTEEEEEEEESS CS
                   AICARFT_IMPCHas  72 qkLrYGeNphQkaalyeeee..eeglakaeqlqGkelsynNllDadaalelvkef...aavaivKHanpcGvAvget 143
                                       ++LrYGeNp+Qkaa+y++      ++a+a+ql Gk+lsynN++D+d+al++v +f   + ++++KH+npcG+A++et
  gi|474933777|ref|YP_007687359.1| 237 ADLRYGENPNQKAAFYKDPFtkGCTVANAQQLGGKQLSYNNIIDLDKALDIVLDFerpT-AVVMKHTNPCGLASDET 312
                                       ****************977666667899***************************7643.55*************** PP

                                       HHHHHHHHHCCSHHHHTTEEEEECCEE-HHHHHHHTTS-ECEEEECEE-CCHHHCCTTSSS-EEEE-SS....-... CS
                   AICARFT_IMPCHas 144 laeAyekAlaaDpvSaFGgiialnrevdaetaeeikkefleviiApsfeeealeilkkkknlrvlelke....e... 213
                                       +++A+++A++ Dp+SaFG +ialnre+daeta+ i++ f+e +iApsf+++al++l+ kk +r+l ++     +   
  gi|474933777|ref|YP_007687359.1| 313 ISKAFRTAYDVDPISAFGCVIALNRECDAETATMIHEYFVEAVIAPSFTQDALDVLRLKKGVRILATNMpigpDtri 389
                                       ******************************************************************98866551567 PP

                                       ...EEEEETTEEEEEE--G..TTCCCSEEECSC---HHHHHHHHHHHHHCCCS-SS-EEEEETTEEEEEE-SSSSHH CS
                   AICARFT_IMPCHas 214 ...elrsvsgglLvqerdeakieeeelkvvtkkkpteeeledllfawkvvkhvkSNaivlakdgqtvgiGaGqmsRv 287
                                          ++r+v+gg+Lvq+ ++  ++e++lkvvtk++pt+ee++ llfawk +khv SNa+v+++ +++vgiGaGqmsRv
  gi|474933777|ref|YP_007687359.1| 390 remKVRRVQGGVLVQTDEDIGLNESNLKVVTKRAPTKEEVHSLLFAWKLAKHVMSNAVVYVRGEHAVGIGAGQMSRV 466
                                       7779************************************************************************* PP

                                       HHHHHHH CS
                   AICARFT_IMPCHas 288 dsarlAv 294
                                       dsa++A+
  gi|474933777|ref|YP_007687359.1| 467 DSAKIAG 473
                                       *****97 PP

>> MGS  MGS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.6   0.1   6.9e-33   2.1e-29       1      94 [.      40     154 ..      40     155 .. 0.98

  Alignments for each domain:
  == domain 1  score: 101.6 bits;  conditional E-value: 6.9e-33
                                       THHHHHHHHHHTTCEEEEEHHHHHHHHHTT--EEECCCCHSTGSGGTHCH..................HHHHHHHTT CS
                               MGS   1 glvelakklkelgfellATgGTakllkeagipvtevvektgegerlggrv..................eildaikng 59 
                                       g+ve+akkl+e ++e+++TgGT+kllk++g++v+ev+e+tg++e+l+grv                  e+++aik+ 
  gi|474933777|ref|YP_007687359.1|  40 GIVEFAKKLEEYKVEIISTGGTYKLLKDNGVKVKEVSEVTGFPEMLDGRVktlhpfihagilarrdvpEHMKAIKDM 116
                                       69*************************************************************************** PP

                                       SCC...EEEEE--THHHHHHCHHHHHHHHHHHTTSHEE CS
                               MGS  60 eid...lvintlypfkatvakdgykirraaenidIplp 94 
                                       +i+   +++++lypf+ tv k+g+++++++enidI++p
  gi|474933777|ref|YP_007687359.1| 117 KIQpvdMIVVNLYPFRNTVLKEGVSMEEIIENIDIGGP 154
                                       **9999******************************98 PP

>> tRNA-synt_2e  Glycyl-tRNA synthetase alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   4.6e-06     0.014      22      74 ..     201     253 ..     195     268 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.6e-06
                                       --SS--SSGGGSHHHHTCCCSSS-EEEEEEEEEE-GGG--TT-STT--SEEEE CS
                      tRNA-synt_2e  22 pydlevGagtlhpatflralgpepwkvayvepsrRptDgrygenpnrlqkyyq 74 
                                       ++ +      +  + + ++ g+e +   + +p+ + +D rygenpn+   +y+
  gi|474933777|ref|YP_007687359.1| 201 AFTVTAQYDAMVSQVMQKSFGNEMFPSFFPQPCEKVADLRYGENPNQKAAFYK 253
                                       5555555566778888999***************************9998885 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.8   5.4e+03      66      81 ..     104     119 ..      97     154 .. 0.72
   2 ?   -1.2   0.0      0.94   2.8e+03      57      79 ..     156     187 ..     110     208 .. 0.66
   3 ?   -3.7   0.0       5.7   1.7e+04      41      68 ..     269     297 ..     264     301 .. 0.64
   4 !   13.2   0.0   3.2e-05     0.095      70     115 ..     495     541 ..     492     542 .] 0.85

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.8
                                       HHHGGGHHHHHHH--S CS
                     CoA_binding_2  66 eatpeivkealalgak 81 
                                        ++pe++k++++++++
  gi|474933777|ref|YP_007687359.1| 104 RDVPEHMKAIKDMKIQ 119
                                       5666777777666643 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.94
                                       -.........EEEE-S-HHHHGGGHHHHHHH- CS
                     CoA_binding_2  57 d.........lvdvftppeatpeivkealalg 79 
                                                 +v v+t p+   ++   ++a g
  gi|474933777|ref|YP_007687359.1| 156 MiraaaknwqSVAVVTDPKQYGTVTGHLIADG 187
                                       03333333448888888888777777776665 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 5.7
                                       TTEE.S----T.....T--EEEE-S-HHHH CS
                     CoA_binding_2  41 lgek.vyaslae.dpepvdlvdvftppeat 68 
                                        g++ +y ++ + d +++d+v  f +p+a+
  gi|474933777|ref|YP_007687359.1| 269 GGKQlSYNNIIDlD-KALDIVLDFERPTAV 297
                                       55334788888755.889988766666554 PP

  == domain 4  score: 13.2 bits;  conditional E-value: 3.2e-05
                                       GGHHHHHHH--SEEEE-TT..---HHHHHHHHHTT-EEE.ES-HHHHH CS
                     CoA_binding_2  70 eivkealalgakavwlqpg..sedeeaaelaeeagirvvgdrCilveg 115
                                       + v++a+++g+ a+ +qpg  ++d+e +++a+e+gi +v  +C  +++
  gi|474933777|ref|YP_007687359.1| 495 DAVDAAAEAGITAI-IQPGgsIRDQESIDAANEHGIAMVYTGCRVFRH 541
                                       57888999998765.678879**********************77765 PP

>> DUF4943  Domain of unknown function (DUF4943)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   5.5e-05      0.16      26     109 ..      94     173 ..      82     180 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.5e-05
                           DUF4943  26 gvvevpkfteedipkllkyaedltlits.fplpsvsayvsgkirlgecmlwivesirlgdyaslgcklvranaenye 101
                                        ++    +  +d+p+ +k  +d+ + +  + + +++++ +  ++ g  m  i+e+i +g     g  ++ra a+n++
  gi|474933777|ref|YP_007687359.1|  94 PFIHAGILARRDVPEHMKAIKDMKIQPVdMIVVNLYPFRNTVLKEGVSMEEIIENIDIG-----GPSMIRAAAKNWQ 165
                                       56677778899************997642667899************************.....5579********* PP

                           DUF4943 102 aiyfltde 109
                                       ++  +td 
  gi|474933777|ref|YP_007687359.1| 166 SVAVVTDP 173
                                       **999995 PP

>> BING4CT  BING4CT (NUC141) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00013      0.39       9      41 ..     482     514 ..     476     527 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00013
                           BING4CT   9 gskieslrFvpfeDvlgvghskgissiivPGsG 41 
                                       g  ++s +F pf+D +  + + gi+ ii PG  
  gi|474933777|ref|YP_007687359.1| 482 GCVMASDAFFPFRDAVDAAAEAGITAIIQPGGS 514
                                       55667789**********************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (542 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 3241.56
//
Query:       gi|474933778|ref|YP_007687360.1|  [L=128]
Description: hypothetical protein TALC_00186 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.6e-05   23.1   0.0    9.3e-05   22.6   0.0    1.2  1  PAS_9     PAS domain
     0.0099   16.1   0.0      0.034   14.4   0.0    1.8  1  PAS_4     PAS fold
  ------ inclusion threshold ------
      0.082   13.0   0.0       0.12   12.5   0.0    1.3  1  PAS_8     PAS domain
       0.14   12.1   0.0        0.2   11.7   0.0    1.4  1  PAS       PAS fold


Domain annotation for each model (and alignments):
>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   2.1e-08   9.3e-05       2      94 ..      20     109 ..      19     112 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 2.1e-08
                             PAS_9   2 dgilidnpdgrilyaNeaalrllG.yspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfw 77 
                                       ++++++n+ ++i+y+N+aa + +   + e ++g +i d+    +e++  +++++   + k re ++v++  +++   
  gi|474933778|ref|YP_007687360.1|  20 MPVVVCNTLHEIIYMNPAAVEAYAhRGGEKLIGLNIMDCH--GKESRVMIDRVFSWFQ-KSRENNIVHTFYKESSNE 93 
                                       578999****************98777999**********..**************99.666666666666555554 PP

                             PAS_9  78 vlltaspvkdddgelvg 94 
                                        ++ +++++d++g+l+g
  gi|474933778|ref|YP_007687360.1|  94 -DVYMVALRDGEGNLIG 109
                                       .6999999999999987 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   7.5e-06     0.034       2      49 ..      16      64 ..      15     115 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.5e-06
                             PAS_4  2 dslpdalavldpdgrvlyaNaaaae.lfgappeellGktlaellpeeda 49
                                      d+   +++v+++   ++y+N+aa e ++++ +e l+G    + + +e++
  gi|474933778|ref|YP_007687360.1| 16 DQDGMPVVVCNTLHEIIYMNPAAVEaYAHRGGEKLIGLNIMDCHGKESR 64
                                      678899****************999899999*****9888776555444 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.6e-05      0.12       2      51 ..      10      58 ..      10      77 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.6e-05
                             PAS_8  2 rlralfesspdgiavvd.lgdrivdvNqaalellGysadlkgellg.qllpv 51
                                      ++++++++   +++v++ l + i+++N+aa e +  +    ++l+g ++++ 
  gi|474933778|ref|YP_007687360.1| 10 FFKSIIDQDGMPVVVCNtLHE-IIYMNPAAVEAYAHR--GGEKLIGlNIMDC 58
                                      58999999999***9995545.********9988655..5555555555555 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   4.4e-05       0.2       3      48 ..      11      57 ..      10     110 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.4e-05
                                      HHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTH.HHCTTSBGGG CS
                               PAS  3 lraileslpdpifvvDedgrilyvNaaaeellGlsr.eevlgkslld 48
                                      +++i+++   p++v +  ++i+y+N+aa e    +  e ++g +++d
  gi|474933778|ref|YP_007687360.1| 11 FKSIIDQDGMPVVVCNTLHEIIYMNPAAVEAYAHRGgEKLIGLNIMD 57
                                      67888888899*****************99988888899***99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 829.93
//
Query:       gi|474933779|ref|YP_007687361.1|  [L=77]
Description: hypothetical protein TALC_00187 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 502.52
//
Query:       gi|474933780|ref|YP_007687362.1|  [L=272]
Description: nicotinate-nucleotide pyrophosphorylase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.5e-44  150.2   0.0    6.8e-44  149.6   0.0    1.3  1  QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal
    3.3e-28   97.6   0.5      1e-27   96.0   0.1    1.9  2  QRPTase_N  Quinolinate phosphoribosyl transferase, N-terminal
  ------ inclusion threshold ------
       0.12   12.4   0.0       0.29   11.1   0.0    1.6  1  RnfC_N     RnfC Barrel sandwich hybrid domain


Domain annotation for each model (and alignments):
>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.6   0.0   1.1e-47   6.8e-44       1     169 []     102     270 ..     102     270 .. 0.96

  Alignments for each domain:
  == domain 1  score: 149.6 bits;  conditional E-value: 1.1e-47
                                       HHHHHHHHHHHHHCT..SSEEEE-S---TTTHHHHHHHHHHTTSB--TSSTTTSEEE-HHHHHHHSSHHHHHHHHHH CS
                         QRPTase_C   1 iAtltarmveaaksa..kvrildTRkttPglrllekyAvliGGgdnhrlgLsdmvlikdnhiaaagsiveavksvre 75 
                                       iA +t ++ ++++++    ri++ RkttPg+r++ek+A+ +GGg  hr+gL+dm+++kdnhiaaag+i  + +++++
  gi|474933780|ref|YP_007687362.1| 102 IAEATWSISKRVHEKdpDLRIAGSRKTTPGFRYFEKKAIALGGGWPHRMGLYDMAMVKDNHIAAAGGIDAIAEKMKD 178
                                       899999999999999999**************************************************988888876 PP

                                       HHTTTSEEEEEESSHHHHHHHHHHT-SEEEEES--HHHHHHHHHHHHHHSTTSEEEEESS--TTTHHHHHCTT-SEE CS
                         QRPTase_C  76 avdkevkievevesleeleevleaeadiimLDnfsveelkkaveelkeknkrvlievSGgvtlenveeyaksgvdvi 152
                                        v+k +++e+ev   ee  ++++a+a+i+m D +s+ +++++ e+l+e+n+r+ +e+SG++t e+ +++a    d++
  gi|474933780|ref|YP_007687362.1| 179 -VPKGIPVEIEVLDIEEGIKAAKAGASIVMGDHMSPADVRTMREKLREINPRIFVEASGNITAETAADFAGCA-DIV 253
                                       .667778******************************************************************.*** PP

                                       EECHHCHTB----EEEE CS
                         QRPTase_C 153 svgalthsvkalDislk 169
                                       s+galths+++  +s++
  gi|474933780|ref|YP_007687362.1| 254 SLGALTHSARSTHFSMD 270
                                       ************99996 PP

>> QRPTase_N  Quinolinate phosphoribosyl transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.0   0.1   1.7e-31     1e-27       1      89 []      14     100 ..      14     100 .. 0.99
   2 ?   -1.2   0.0      0.36   2.1e+03      31      54 ..     167     191 ..     156     206 .. 0.71

  Alignments for each domain:
  == domain 1  score: 96.0 bits;  conditional E-value: 1.7e-31
                                       CTT--HHHHHHGCTTSEEEEEEEESSSEEE-SHHHHHHHHHHHTTTEEEESS-TT-EEETTEEEEEEEEEHHHHHHH CS
                         QRPTase_N   1 igrgDlttealipeekkakaeiiakeegvvaGlevaeevfellpglevellvkDGervekgdvlleieGnarallsa 77 
                                       +g+gD+t+ +++++++ +ka+i + e+ vvaGl++a  +f+++ g+++e++vkDG+rv++g+++le++G++r+l+++
  gi|474933780|ref|YP_007687362.1|  14 VGTGDVTS-ETFLPDRDGKAVITCEEDSVVAGLDEAVTIFSIM-GVSCETFVKDGDRVAAGTKVLEASGPLRSLMTC 88 
                                       689*****.9*********************************.********************************* PP

                                       HHHHHHHHHHHH CS
                         QRPTase_N  78 ERvaLnllqrlS 89 
                                       ER+aLn+l+r+S
  gi|474933780|ref|YP_007687362.1|  89 ERTALNFLMRMS 100
                                       ***********9 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.36
                                       -SHHHHHHHHHHH.TTTEEEESS-T CS
                         QRPTase_N  31 aGlevaeevfell.pglevellvkD 54 
                                        G+++++e ++ + +g+ ve++v D
  gi|474933780|ref|YP_007687362.1| 167 GGIDAIAEKMKDVpKGIPVEIEVLD 191
                                       3888888888888888888866544 PP

>> RnfC_N  RnfC Barrel sandwich hybrid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   4.9e-05      0.29      37      63 ..      54      80 ..      37      87 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.9e-05
                            RnfC_N 37 hiGapakplvkvgdkVlkGqkiaeaeg 63
                                       +G +++  vk gd+V  G k+ ea+g
  gi|474933780|ref|YP_007687362.1| 54 IMGVSCETFVKDGDRVAAGTKVLEASG 80
                                      4799******************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1641.32
//
Query:       gi|474933781|ref|YP_007687363.1|  [L=410]
Description: putative exonuclease of the beta-lactamase fold involved in RNA processing [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.8e-16   59.4   0.0      7e-16   58.5   0.0    1.4  1  Beta-Casp      Beta-Casp domain
    4.1e-11   42.7   0.1    9.8e-11   41.4   0.1    1.6  1  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    1.7e-09   38.0   0.2    3.1e-09   37.1   0.2    1.4  1  Lactamase_B    Metallo-beta-lactamase superfamily
    3.3e-08   33.2   0.0    5.2e-08   32.6   0.0    1.3  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
    3.1e-07   30.1   0.1    2.7e-06   27.0   0.0    2.1  2  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.018   14.9   0.0      0.045   13.7   0.0    1.8  1  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Beta-Casp  Beta-Casp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.5   0.0   2.3e-19     7e-16       1     110 []     225     332 ..     225     332 .. 0.78

  Alignments for each domain:
  == domain 1  score: 58.5 bits;  conditional E-value: 2.3e-19
                                       HHHHHHHH..HCTT..TTS-S-EEEEE-HHHHHHHHHGGGGGG........E-SHH....HHH.H...HH....HS- CS
                         Beta-Casp   1 aqellylLeelwkekkledlklpiyldsplaskatevYkeyae........veakslewmesk.ke.eln....ssk 63 
                                       +qe+++lL++l             y+d+ +++++t+++ +y+e        +      + ++  +e + n    +  
  gi|474933781|ref|YP_007687363.1| 225 TQEIMLLLKNLGY---------DMYVDG-MGRSVTNLFLDYPEyirnakslK------AAKRTfNEiKNNsmrkKAL 285
                                       6888888888773.........57****.***************75555542......4444432222222222344 PP

                                       SSEEEEES-TTSSSSHHHHHHHHHTTSTTSEEEESS---TTSHHHHH CS
                         Beta-Casp  64 gpkvilassgmlegGrsrellkklledprntvilvgyqaegTlgrkl 110
                                       g ++i+++ gml+gG++  +l+ l edp+n+++lvgyqae+T gr l
  gi|474933781|ref|YP_007687363.1| 286 GAQIIVTTGGMLDGGPVLSYLRYLREDPKNAILLVGYQAEDTNGRML 332
                                       779*****************************************975 PP

>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.1   3.3e-14   9.8e-11       2      44 ..     345     387 ..     344     389 .. 0.95

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 3.3e-14
                             RMMBL   2 ipvkarieeidfSgHadknellelirklkprnvilvHGeeeat 44 
                                       ++v +++e++dfS+Ha++++l +++r   p+nvi+ H e +++
  gi|474933781|ref|YP_007687363.1| 345 VKVECEVEKFDFSAHAGHDQLVQFVRDCDPENVIIMHSESREL 387
                                       79*************************************9886 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.2     1e-12   3.1e-09      11     162 ..      19     172 ..      17     209 .. 0.77

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 1e-12
                                       EEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHH CS
                       Lactamase_B  11 iegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeea 87 
                                       iegd++ +L+  G+s+ ++ +         +  ++d+v+lTH+HlDH+G  + ++ + d+  +  +++a+  +  + 
  gi|474933781|ref|YP_007687363.1|  19 IEGDNKRMLVEYGISPTKPPQY-----PLAPEGKIDHVFLTHSHLDHCGMIPAVCGKNDCELFTTPLTAEIAELMMY 90 
                                       7999999999999999999997.....6999*********************************9998887776666 PP

                                       HHHHHHCCHH........TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHH CS
                       Lactamase_B  88 ddaasrkgll........lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallage 156
                                       d    +k           + + + +++++ + ++++++g +  + +  g+++g+  +  ++g+g+++++GD   +  
  gi|474933781|ref|YP_007687363.1|  91 DSLKIAKAEGypqpytakDVETTMKHVVPLTFGDTIELGKIDVTLHSAGHVPGAAMF-EFIGDGSTIYSGDIHTEDQ 166
                                       6655555555779****6666666666666666666666666666666666666555.678**********987666 PP

                                       CCCCCC CS
                       Lactamase_B 157 tgridl 162
                                        + ++ 
  gi|474933781|ref|YP_007687363.1| 167 KLVLGA 172
                                       665555 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.0   1.7e-11   5.2e-08       5     167 ..      22     166 ..      18     180 .. 0.79

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 1.7e-11
                     Lactamase_B_6   5 dnvkiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallyakfksklllnipvyatlpvvkLGrv 81 
                                       dn ++L++ G + +k        +      ++d++ L+h+ l+h G  + ++ k       +++ ++t  +++++++
  gi|474933781|ref|YP_007687363.1|  22 DNKRMLVEYGISPTKPPQ-----YPLAPEGKIDHVFLTHSHLDHCGMIPAVCGK------NDCELFTTPLTAEIAEL 87 
                                       666666666666664432.....222223489**************87777754......589************** PP

                     Lactamase_B_6  82 slldlyaskgllgpedseeleledideafdkiktlkYsQklelkskldgltitaynaGhtlGGtiWkiskesekivY 158
                                       +++d+ + ++++g  +    + +d+++ ++++ +l +  ++el     ++ +t ++aGh++G+++++      + +Y
  gi|474933781|ref|YP_007687363.1|  88 MMYDSLKIAKAEGYPQ--PYTAKDVETTMKHVVPLTFGDTIELG----KIDVTLHSAGHVPGAAMFEFIGD-GSTIY 157
                                       ******9999988665..5688******************9998....599999************98654.34567 PP

                     Lactamase_B_6 159 avdwnhake 167
                                         d++ +  
  gi|474933781|ref|YP_007687363.1| 158 SGDIHTEDQ 166
                                       777755554 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   9.2e-10   2.7e-06      24     172 ..      41     192 ..      27     208 .. 0.69
   2 ?    0.3   0.0      0.14   4.1e+02     177     200 ..     358     381 ..     336     382 .. 0.89

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 9.2e-10
                                       SS--..SEEEEE-SS--HHHHGGGGCCCCC--EE.EEEEEEHHHHHHCCTTCGHHHCHTT................T CS
                     Lactamase_B_2  24 lrdelppidaVllthaHyDHlaglltlrelrpkk.lplyapkgvlavleanfvylaleee................p 83 
                                       +++   +id V+lth+H DH+  ++ +     k+  +l+ ++ +++ +++ + y+ l+ +                 
  gi|474933781|ref|YP_007687363.1|  41 PLAPEGKIDHVFLTHSHLDHCGMIPAVCG---KNdCELFTTPLTAE-IAELMMYDSLKIAkaegypqpytakdvetT 113
                                       3333359**************65555555...33388886655554.444555555555556666666666666677 PP

                                       TEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HH..HHHHHCT-S CS
                     Lactamase_B_2  84 avnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipee..igerlggad 158
                                         +v++l+ g+++elg  ++++t++ a h  g         ++   i  g+ +  y+gD  + +++  +g+r ++++
  gi|474933781|ref|YP_007687363.1| 114 MKHVVPLTFGDTIELG--KIDVTLHSAGHVPGA--------AMFEFI--GDGSTIYSGDIHTEDQKlvLGARPRDCK 178
                                       7788888899999998..566888887777776........333333..4788899***997775555789999999 PP

                                       EEEEE-S-SSTTHH CS
                     Lactamase_B_2 159 llllditayeddem 172
                                        l++++t+   + +
  gi|474933781|ref|YP_007687363.1| 179 NLFIEGTYAGRNHP 192
                                       99999998776655 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.14
                                       T---STSHHHHCTTSSSSEEEEES CS
                     Lactamase_B_2 177 gHltpeeaveaaadlgakrlvliH 200
                                        H+  ++ v++++d++++ ++ +H
  gi|474933781|ref|YP_007687363.1| 358 AHAGHDQLVQFVRDCDPENVIIMH 381
                                       588899*****************9 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.5e-05     0.045      10      52 ..      17      63 ..      11     172 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.5e-05
                     Lactamase_B_3 10 flletagarilvDPf....kanlgyeppaeeaDlvlisqaledHahl 52
                                      + +e++++r+lv ++    k+ +   +p+ ++D v +++++ dH+ +
  gi|474933781|ref|YP_007687363.1| 17 MTIEGDNKRMLVEYGisptKPPQYPLAPEGKIDHVFLTHSHLDHCGM 63
                                      579999********9544322122223459**************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 2954.76
//
Query:       gi|474933782|ref|YP_007687364.1|  [L=442]
Description: hypothetical protein TALC_00190 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00062   19.4   1.4     0.0014   18.3   1.4    1.6  1  FAM176          FAM176 family
  ------ inclusion threshold ------
      0.071   13.3   0.6       0.24   11.6   0.1    2.1  2  Shisa           Wnt and FGF inhibitory regulator
      0.079   11.4   6.3       0.11   10.9   6.3    1.1  1  MCM_bind        Mini-chromosome maintenance replisome factor
        0.1   13.6   2.3       0.19   12.7   1.8    1.7  1  DUF2547         Protein of unknown function (DUF2547)
       0.13   10.6   1.3       0.23    9.8   1.3    1.5  1  CBP_BcsG        Cellulose biosynthesis protein BcsG
       0.15   11.9   0.0        0.3   10.9   0.0    1.5  1  DUF559          Protein of unknown function (DUF559)
       0.36    8.7   1.2       0.54    8.1   1.2    1.2  1  V_ATPase_I      V-type ATPase 116kDa subunit family
       0.45   10.2   2.2       0.73    9.5   2.2    1.3  1  DUF4569         Domain of unknown function (DUF4569)
        5.3    5.7   8.2        7.3    5.3   7.9    1.3  1  NPR3            Nitrogen Permease regulator of amino acid tra
        5.5    5.6   6.1        8.1    5.1   6.1    1.2  1  SAPS            SIT4 phosphatase-associated protein
        5.8    6.5  10.3        4.8    6.8   5.4    2.3  2  Tetraspanin     Tetraspanin family
        8.8    5.2   6.1         14    4.6   6.1    1.2  1  SLC12           Solute carrier family 12
        9.8    6.2   8.3       0.38   10.7   0.8    2.4  3  RelB            RelB antitoxin


Domain annotation for each model (and alignments):
>> FAM176  FAM176 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   1.4   9.8e-07    0.0014       5      96 ..     141     233 ..     137     270 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 9.8e-07
                            FAM176   5 lSnslaayayikenpEraaLlFvlgvcvGLlltLcllviriscrkdlerlkkkkkklkeesekasededeeeeeeee 81 
                                       +  ++ a ayi ++    ++l  ++++v Ll+  +l +++i c+++l +++kk  +++  ++ a++ e + +  e++
  gi|474933782|ref|YP_007687364.1| 141 IMAAFVALAYILKDEVIEGMLLPIAIAVSLLVINILAIVAIPCKAKLAEEEKKAAEEAAAKAAAEKAEADKKAAERQ 217
                                       55667889***9999999****************************9977666666555544333333233333333 PP

                            FAM176  82 dssesea.eeelsefe 96 
                                        + e+e  e+++ + +
  gi|474933782|ref|YP_007687364.1| 218 AQIEKEYaEKKAAKAQ 233
                                       3333332022222222 PP

>> Shisa  Wnt and FGF inhibitory regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00018      0.24      80     173 ..     158     244 ..     142     274 .. 0.47
   2 ?   -1.4   0.1       1.7   2.4e+03     136     160 ..     281     305 ..     250     314 .. 0.43

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00018
                             Shisa  80 kdiyvpvlivktifivfvivgvvvivcccgclkkkqrekrpgrenlssalaev.gpivtettsattvvhsrysepqq 155
                                       +++ +p++i ++++++ ++  +v+i c  +       ek++ +e++ +a ae  ++  ++ ++ ++ ++ +y   ++
  gi|474933782|ref|YP_007687364.1| 158 EGMLLPIAIAVSLLVINILA-IVAIPCKAKLAEE---EKKAAEEAAAKAAAEKaEA-DKKAAERQAQIEKEY---AE 226
                                       34889************777.4555555444222...2223344444444444221.111222222222233...22 PP

                             Shisa 156 ssssssypgatnqgyqpv 173
                                       +++++++++a +q  +  
  gi|474933782|ref|YP_007687364.1| 227 KKAAKAQAKADEQAKKDA 244
                                       222222222222222222 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.7
                             Shisa 136 vtettsattvvhsrysepqqsssss 160
                                       +t++t+   ++++++ ep+++++++
  gi|474933782|ref|YP_007687364.1| 281 KTAETKPVEAAPAKKEEPAPAAVAA 305
                                       1113333444444444444444444 PP

>> MCM_bind  Mini-chromosome maintenance replisome factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   6.3   8.2e-05      0.11      93     177 ..     175     258 ..     169     287 .. 0.45

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8.2e-05
                          MCM_bind  93 tlycvpiPgeneWvkesee..keksqekvesststlssrkKRsleeeeedeemdvsksekkeeissestkekeeesk 167
                                       +l +v+iP++++ ++e+++  +e+  +  ++++++ +++++R+++ e+e  e+++ k+++k +++ ++    ++ + 
  gi|474933782|ref|YP_007687364.1| 175 ILAIVAIPCKAKLAEEEKKaaEEAAAKAAAEKAEADKKAAERQAQIEKEYAEKKAAKAQAKADEQAKK---DAAAKA 248
                                       6889**********999983222222223333333344444444422222222222222222222111...111111 PP

                          MCM_bind 168 ssetekkskk 177
                                       ++e++++ ++
  gi|474933782|ref|YP_007687364.1| 249 AAEKKAAPAA 258
                                       1111111111 PP

>> DUF2547  Protein of unknown function (DUF2547)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.8   0.00014      0.19       6      73 ..     169     233 ..     167     256 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00014
                           DUF2547   6 sqLllgivAifaLPeaqelaneeavenyqntqsvqqqvletaallqqveqqqlfiaeaklvvveskkq 73 
                                       s L++ i+Ai a+P+  +la+ee+     +++ ++++++e a+  +++++ q  i++    ++ +k q
  gi|474933782|ref|YP_007687364.1| 169 SLLVINILAIVAIPCKAKLAEEEKK---AAEEAAAKAAAEKAEADKKAAERQAQIEKEYAEKKAAKAQ 233
                                       7799***************998644...3344445555555555554444443442222222222223 PP

>> CBP_BcsG  Cellulose biosynthesis protein BcsG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   1.3   0.00017      0.23     101     179 ..     145     239 ..     123     286 .. 0.46

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00017
                          CBP_BcsG 101 vllivylllsqwirvttlvllalialsvle.................ksaksaaaaaaakaaeaeaakaaaaaaqaa 160
                                        ++++y+l  ++i    l +++ + l v++                 k   +aa++aaakaa+++a+  ++aa+++a
  gi|474933782|ref|YP_007687364.1| 145 FVALAYILKDEVIEGMLLPIAIAVSLLVINilaivaipckaklaeeeK---KAAEEAAAKAAAEKAEADKKAAERQA 218
                                       334444444444443333222222222222222333323334443221...11111111111111111111111111 PP

                          CBP_BcsG 161 eansa..nldealeaFyekek 179
                                       +++++  + ++a+++  ++e+
  gi|474933782|ref|YP_007687364.1| 219 QIEKEyaEKKAAKAQAKADEQ 239
                                       111111122222222222222 PP

>> DUF559  Protein of unknown function (DUF559)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00022       0.3      53      99 ..     368     408 ..     328     417 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00022
                                       TTEEEEEE-----------HHHHHHHHHTT-EEEEEEHHHHHH-HHH CS
                            DUF559  53 aklivelDGaqhdeeeeyDaeRtelLeslGftvlRfkndevlkniee 99 
                                        ++ v +DGa        D++ +++L+  G+tvl fk  +v+  + e
  gi|474933782|ref|YP_007687364.1| 368 GRVAVYVDGA------VPDHSNDAALADEGWTVLHFKEADVTDGEAE 408
                                       5555555555......45788999***************99654333 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   1.2   0.00039      0.54     617     690 ..     168     241 ..     144     258 .. 0.34

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00039
                        V_ATPase_I 617 lalvcvpvlll.vkPlilklkhkkkkkkkekkkeeeeeeeeeeeeeeeeeeeeaeeeeeeeeeeeeeeeeeeeee 690
                                       ++l+ + +l + + P+  kl +++kk+++e+ +++++e++e+++ +++e++ + e+e  e+++++++++++e+++
  gi|474933782|ref|YP_007687364.1| 168 VSLLVINILAIvAIPCKAKLAEEEKKAAEEAAAKAAAEKAEADK-KAAERQAQIEKEYAEKKAAKAQAKADEQAK 241
                                       22222222222022333333222222222222222221111111.111111111111111111111111111111 PP

>> DUF4569  Domain of unknown function (DUF4569)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   2.2   0.00053      0.73      22      98 ..     183     261 ..     146     282 .. 0.52

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00053
                           DUF4569  22 kkeekeeekeklldseeakslsseaeaqskslskl..sgklissvksseeenskkqqqeleeekkvaksqslllerq 96 
                                       +k + +ee++k ++++ ak+++++aea +k++++    +k  +++k  + + ++++q ++ +++k a +++ +   +
  gi|474933782|ref|YP_007687364.1| 183 CKAKLAEEEKKAAEEAAAKAAAEKAEADKKAAERQaqIEKEYAEKKAAKAQAKADEQAKKDAAAKAAAEKKAAPAAE 259
                                       34445555555555555555555555555551111123333333333333333333333333333333333333333 PP

                           DUF4569  97 vs 98 
                                       + 
  gi|474933782|ref|YP_007687364.1| 260 AK 261
                                       33 PP

>> NPR3  Nitrogen Permease regulator of amino acid transport activity 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   7.9    0.0053       7.3      24     111 ..     171     259 ..     152     297 .. 0.53

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0053
                              NPR3  24 ltvDdlaFlGlPvhvdedgkwrkskkkk.........kkskrkrssrskekkskesskksesssksesseekksske 91 
                                       l+++ la + +P+ ++  ++ +k  ++          +         +k++ +++ + ++e  +k+ ++++ k++++
  gi|474933782|ref|YP_007687364.1| 171 LVINILAIVAIPCKAKLAEEEKKAAEEAaakaaaekaE--------ADKKAAERQAQIEKEYAEKKAAKAQAKADEQ 239
                                       78999999999999999998888866665443222211........1222222222222222222222222222222 PP

                              NPR3  92 seeseekesneeeeeeeded 111
                                       ++++++++  +e++ +  ++
  gi|474933782|ref|YP_007687364.1| 240 AKKDAAAKAAAEKKAAPAAE 259
                                       22222222222222222222 PP

>> SAPS  SIT4 phosphatase-associated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   6.1    0.0059       8.1     265     344 ..     192     260 ..     152     298 .. 0.46

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0059
                              SAPS 265 eealedvsdeaskeesaesedltdkdedvsleesksakdenkesdesesdtaeesseededdasseesalaeeteek 341
                                       ++       +a++  ++++++++++d++ ++++ + +k+    ++e+++ +a+ + +e+++++++ ++a +++ +++
  gi|474933782|ref|YP_007687364.1| 192 KK-------AAEEAAAKAAAEKAEADKKAAERQAQIEKE----YAEKKAAKAQAKADEQAKKDAAAKAAAEKKAAPA 257
                                       12.......222222222222222222222222222222....1111111111111111111222222222222221 PP

                              SAPS 342 lrk 344
                                        + 
  gi|474933782|ref|YP_007687364.1| 258 AEA 260
                                       111 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   5.4    0.0035       4.8      15      96 ..      14      95 ..       2      99 .. 0.70
   2 ?    2.1   0.2       0.1   1.4e+02      11      70 ..     115     180 ..     107     233 .. 0.49

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0035
                                      XXXXXXXXXXXXXX...XXX.....................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                      xxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Tetraspanin 15 igivllavGvwlrl...khaeaalacllsesaedpailaillivvGvllfllgflGcigalkenkcllltfsllllvlf 90
                                      +++v++++++   +    ++  +  +++ e   +++ +a ++ ++G+l++++g + +    + ++    ++ +ll+   
  gi|474933782|ref|YP_007687364.1| 14 AAAVVVFMAI---VigiVNEDLSVGTDSFEAFAANSNVAQIFAIAGALMIVTGAFAFADGARTRRSWASVYGFLLIAGG 89
                                      2333333332...13443444555566666677777777889999**************99999999999999999887 PP

                                      XXXXXX CS
                                      xxxxxx RF
                       Tetraspanin 91 llelaa 96
                                      ll+ +a
  gi|474933782|ref|YP_007687364.1| 90 LLFAIA 95
                                      777665 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.1
                                       XXXXXXXXXXXXXXXXXX.........XXX.....................XXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Tetraspanin  11 lfwligivllavGvwlrl.........khaeaalacllsesaedpailaillivvGvllfllgflGcig 70 
                                       +f  ++i+++av +  r+          +a+ ala  l+++  +   l    i++ v l+++ +l +++
  gi|474933782|ref|YP_007687364.1| 115 VFAAVAIAAVAVQIADRCyilasvdiiMAAFVALAYILKDEVIEGMLL---PIAIAVSLLVINILAIVA 180
                                       444444444444211111222233333233333333322222222222...333333333333333333 PP

>> SLC12  Solute carrier family 12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   6.1      0.01        14     133     210 ..     190     266 ..     164     299 .. 0.41

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.01
                             SLC12 133 eeeeeeekekkeaeesekeeeekkkakkkklleekskekeekekleekdsnlslseekkeeekekkkekkkkkekke 209
                                       ee++++ +e++ ++++ek+e++kk+a+++ ++e++  ek+ +++  ++d++++ +  +k  +++k+ ++ + k + e
  gi|474933782|ref|YP_007687364.1| 190 EEKKAA-EEAAAKAAAEKAEADKKAAERQAQIEKEYAEKKAAKAQAKADEQAKKDAAAKAAAEKKAAPAAEAKPAAE 265
                                       211111.1111111122222233333333333333333333333333333333333333222222222222222222 PP

                             SLC12 210 k 210
                                       k
  gi|474933782|ref|YP_007687364.1| 266 K 266
                                       2 PP

>> RelB  RelB antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.8   0.00028      0.38      17      80 ..     154     214 ..     151     222 .. 0.73
   2 ?   -1.9   0.1       2.5   3.4e+03      61      75 ..     224     238 ..     212     255 .. 0.52
   3 ?   -1.6   0.3         2   2.8e+03      55      75 ..     409     430 ..     401     438 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00028
                                       HHHHHCCT--HHHHHHHHHHHHHHHTS-STT-CHHHHHHHHHHHHHHHHCCTTEEEESCCCCHC CS
                              RelB  17 tdvlekmGltiSqairlfLekiaktkalPfdlrlpepnqetlvaikeleagkdeskaksaeetl 80 
                                       ++v+e m l+i  a+ l++ +i    a+P + +l e++++ +++     a  +  ka+ ++++ 
  gi|474933782|ref|YP_007687364.1| 154 DEVIEGMLLPIAIAVSLLVINILAIVAIPCKAKLAEEEKKAAEEA---AAKAAAEKAEADKKAA 214
                                       68*********************************6666555443...3333333344444433 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.5
                                       HHHHHCCTTEEEESC CS
                              RelB  61 ikeleagkdeskaks 75 
                                       + e++a k++ ka +
  gi|474933782|ref|YP_007687364.1| 224 YAEKKAAKAQAKADE 238
                                       333333333322222 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2
                                       HHHHHHHHHHHCCTTE.EEESC CS
                              RelB  55 qetlvaikeleagkde.skaks 75 
                                       ++ ++a ++++ + d+  kak 
  gi|474933782|ref|YP_007687364.1| 409 AVQIAAAVKENLRADKaAKAKA 430
                                       5555555555555554322222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2992  (0.16688); expected 358.6 (0.02)
Passed bias filter:                      938  (0.0523175); expected 358.6 (0.02)
Passed Vit filter:                       263  (0.014669); expected 17.9 (0.001)
Passed Fwd filter:                        76  (0.00423894); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 1.13u 0.35s 00:00:01.48 Elapsed: 00:00:00.48
# Mc/sec: 2759.48
//
Query:       gi|474933783|ref|YP_007687365.1|  [L=92]
Description: DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.2e-17   61.7   6.0    4.2e-17   61.7   6.0    2.0  2  TFIIS_C         Transcription factor S-II (TFIIS)
     0.0054   16.6   8.0      0.038   13.8   0.1    3.2  3  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
     0.0079   16.1   5.5      0.046   13.6   5.4    2.1  1  zinc_ribbon_4   zinc-ribbon domain
  ------ inclusion threshold ------
       0.01   15.5   0.9       0.01   15.5   0.9    1.5  2  Baculo_LEF5_C   Baculoviridae late expression factor 5 C-term
      0.029   14.5   4.0       0.55   10.4   0.2    2.5  2  UPF0547         Uncharacterised protein family UPF0547
      0.045   13.7  10.3      0.051   13.5   6.3    2.3  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
       0.05   13.8   0.1       0.05   13.8   0.1    2.8  3  zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ri
       0.13   12.0   8.8        3.4    7.5   0.1    3.3  3  A2L_zn_ribbon   A2L zinc ribbon domain
       0.28   11.2   5.2         25    4.9   0.0    2.5  2  zf-DNL          DNL zinc finger
        1.1    9.2   0.0        1.1    9.2   0.0    2.6  2  Ogr_Delta       Ogr/Delta-like zinc finger
        1.2    9.1  12.2       0.27   11.2   1.2    3.1  3  DUF1936         Domain of unknown function (DUF1936)
        2.3    8.0   9.4       0.76    9.5   5.0    2.3  2  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal


Domain annotation for each model (and alignments):
>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.39   5.8e+02      29      36 ..       8      17 ..       7      27 .. 0.62
   2 !   61.7   6.0   2.8e-20   4.2e-17       2      38 ..      53      89 ..      52      90 .. 0.97

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.39
                           TFIIS_C 29 ykCt..kCgh 36
                                      y+C   +Cg+
  gi|474933783|ref|YP_007687365.1|  8 YVCRnpDCGY 17
                                      5555445554 PP

  == domain 2  score: 61.7 bits;  conditional E-value: 2.8e-20
                           TFIIS_C  2 kCpkCgsreayffqlQtRsaDEpmtvfykCtkCghrW 38
                                      +Cp Cg +eay+  +QtR+aDEp+t++y+C+kC++rW
  gi|474933783|ref|YP_007687365.1| 53 TCPACGYTEAYYNVRQTRAADEPETIMYRCCKCNNRW 89
                                      8************************************ PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   2.6e-05     0.038      11      35 ..       1      23 [.       1      24 [. 0.87
   2 ?    4.0   0.0     0.032        47      22      31 ..      52      61 ..      40      62 .. 0.75
   3 ?    1.8   1.4      0.15   2.3e+02       4       9 ..      82      87 ..      73      88 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.6e-05
                                      EEEEECSCCCEEEESS..SS-EEESSC CS
                    RNA_POL_M_15KD 11 LlpkedkegknfeCrq..CgYeepadq 35
                                      + pk++k +    Cr+  CgYeep+++
  gi|474933783|ref|YP_007687365.1|  1 MFPKDGKYV----CRNpdCGYEEPISG 23
                                      789999999....**777*******97 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.032
                                      EEESSSS-EE CS
                    RNA_POL_M_15KD 22 feCrqCgYee 31
                                      + C  CgY e
  gi|474933783|ref|YP_007687365.1| 52 VTCPACGYTE 61
                                      6799999975 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.15
                                      ESTTTS CS
                    RNA_POL_M_15KD  4 CpkCgN 9 
                                      C kC+N
  gi|474933783|ref|YP_007687365.1| 82 CCKCNN 87
                                      889998 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   5.4   3.1e-05     0.046       2      36 .]      51      90 ..      50      90 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.1e-05
                     zinc_ribbon_4  2 kitCpsCk...akyeiddeklp..akgvkvrCskCghvFr 36
                                      ++tCp+C+   a y+++  + +  +++ + rC kC++ ++
  gi|474933783|ref|YP_007687365.1| 51 RVTCPACGyteAYYNVRQTRAAdePETIMYRCCKCNNRWN 90
                                      69*****744478*******88678899**********96 PP

>> Baculo_LEF5_C  Baculoviridae late expression factor 5 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.2       6.8     1e+04      37      41 ..      54      58 ..      53      59 .. 0.77
   2 ?   15.5   0.9   6.8e-06      0.01      22      41 ..      67      86 ..      64      87 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 6.8
                     Baculo_LEF5_C 37 CskCg 41
                                      C  Cg
  gi|474933783|ref|YP_007687365.1| 54 CPACG 58
                                      88898 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 6.8e-06
                     Baculo_LEF5_C 22 iQnRagDEivsfvryCskCg 41
                                      +Q+Ra DE   ++  C kC+
  gi|474933783|ref|YP_007687365.1| 67 RQTRAADEPETIMYRCCKCN 86
                                      7******************9 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.4     0.019        28      17      23 ..      10      18 ..       8      18 .. 0.86
   2 ?   10.4   0.2   0.00037      0.55       8      22 ..      45      59 ..      44      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.019
                           UPF0547 17 C..phCGyv 23
                                      C  p+CGy+
  gi|474933783|ref|YP_007687365.1| 10 CrnPDCGYE 18
                                      888*****7 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00037
                           UPF0547  8 akvPvaaqfCphCGy 22
                                      a++P a + Cp CGy
  gi|474933783|ref|YP_007687365.1| 45 ATLPKARVTCPACGY 59
                                      68999999******9 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.18   2.7e+02      22      30 ..      13      21 ..       4      29 .. 0.67
   2 ?   13.5   6.3   3.4e-05     0.051      17      44 ..      50      86 ..      45      88 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.18
                     Zn_Tnp_IS1595 22 PhCgsrkay 30
                                      P Cg+++++
  gi|474933783|ref|YP_007687365.1| 13 PDCGYEEPI 21
                                      778887766 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 3.4e-05
                     Zn_Tnp_IS1595 17 ngfvCPhCgsr.kayrikt........rglfqCkeCr 44
                                      ++++CP+Cg++  +y +++           ++C +C+
  gi|474933783|ref|YP_007687365.1| 50 ARVTCPACGYTeAYYNVRQtraadepeTIMYRCCKCN 86
                                      5678*******99999999999***99999***9997 PP

>> zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.57   8.5e+02      40      45 ..      14      19 ..       8      38 .. 0.74
   2 ?   13.8   0.1   3.3e-05      0.05      36      50 ..      52      66 ..      50      77 .. 0.82
   3 ?   -1.5   2.3         2   2.9e+03       1       8 [.      81      88 ..      81      91 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.57
                    zinc_ribbon_13 40 nCgYte 45
                                      +CgY e
  gi|474933783|ref|YP_007687365.1| 14 DCGYEE 19
                                      499987 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 3.3e-05
                    zinc_ribbon_13 36 vsCknCgYtelYkae 50
                                      v+C  CgYte Y + 
  gi|474933783|ref|YP_007687365.1| 52 VTCPACGYTEAYYNV 66
                                      9*********99654 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2
                    zinc_ribbon_13  1 kCpKCgnt 8 
                                      +C KC+n+
  gi|474933783|ref|YP_007687365.1| 81 RCCKCNNR 88
                                      599**986 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1    0.0023       3.4      18      33 .]       4      21 ..       1      21 [. 0.86
   2 ?    6.0   0.1    0.0069        10      24      33 .]      54      63 ..      50      63 .. 0.90
   3 ?    1.6   2.0      0.16   2.4e+02      23      29 ..      81      87 ..      79      88 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0023
                     A2L_zn_ribbon 18 eqgylvC..ieCgasfpy 33
                                      ++g +vC  ++Cg+++p+
  gi|474933783|ref|YP_007687365.1|  4 KDGKYVCrnPDCGYEEPI 21
                                      68999998889****996 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0069
                     A2L_zn_ribbon 24 CieCgasfpy 33
                                      C+ Cg++++y
  gi|474933783|ref|YP_007687365.1| 54 CPACGYTEAY 63
                                      *******987 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.16
                     A2L_zn_ribbon 23 vCieCga 29
                                       C++C++
  gi|474933783|ref|YP_007687365.1| 81 RCCKCNN 87
                                      5888875 PP

>> zf-DNL  DNL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.016        25      28      62 ..       9      43 ..       4      45 .. 0.85
   2 ?    3.8   5.3     0.037        55       5      37 ..      53      88 ..      49      90 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.016
                            zf-DNL 28 ivqCpgCknrHliaDnLgwfedkkktiedilkekg 62
                                      +++ p+C  +  i+ n + f++k+k+ e i+ e+g
  gi|474933783|ref|YP_007687365.1|  9 VCRNPDCGYEEPISGNAQTFTTKAKNTETIVMEEG 43
                                      566689999999****************9998876 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.037
                            zf-DNL  5 tCkaCetrss...keiskkaYekGvVivqCpgCknr 37
                                      tC aC+  ++    + ++ a e  +++ +C +C+nr
  gi|474933783|ref|YP_007687365.1| 53 TCPACGYTEAyynVRQTRAADEPETIMYRCCKCNNR 88
                                      888998776521145677888899999999999997 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00076       1.1      26      36 ..       8      18 ..       4      35 .. 0.89
   2 ?   -0.7   8.2      0.96   1.4e+03       1      30 [.      53      87 ..      53      90 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00076
                         Ogr_Delta 26 yqCsnfeCgat 36
                                      y+C+n++Cg+ 
  gi|474933783|ref|YP_007687365.1|  8 YVCRNPDCGYE 18
                                      9********95 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.96
                         Ogr_Delta  1 rCPhCgapaaartsrnlskdvre......ryyqCsn 30
                                      +CP Cg   a  ++r++ +   e      r + C+n
  gi|474933783|ref|YP_007687365.1| 53 TCPACGYTEAYYNVRQTRA-ADEpetimyRCCKCNN 87
                                      6*****9988888888876.3334565556666665 PP

>> DUF1936  Domain of unknown function (DUF1936)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.2   0.00018      0.27      25      34 .]      10      19 ..       7      19 .. 0.91
   2 ?    4.0   0.1     0.032        47      27      34 .]      54      61 ..      50      61 .. 0.75
   3 ?    0.2   0.7       0.5   7.4e+02       2       6 ..      82      86 ..      74      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00018
                                      ES-TT---EE CS
                           DUF1936 25 CdredCdYiE 34
                                      C ++dC+Y+E
  gi|474933783|ref|YP_007687365.1| 10 CRNPDCGYEE 19
                                      *********9 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.032
                                      -TT---EE CS
                           DUF1936 27 redCdYiE 34
                                       ++C+Y E
  gi|474933783|ref|YP_007687365.1| 54 CPACGYTE 61
                                      68999987 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.5
                                      -TTTS CS
                           DUF1936  2 CPKCn 6 
                                      C KCn
  gi|474933783|ref|YP_007687365.1| 82 CCKCN 86
                                      88887 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.95   1.4e+03      43      49 ..       6      12 ..       3      17 .. 0.64
   2 ?    9.5   5.0   0.00051      0.76      23      52 ..      52      87 ..      38      89 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.95
                    zinc_ribbon_10 43 vkyrCpk 49
                                       ky+C +
  gi|474933783|ref|YP_007687365.1|  6 GKYVCRN 12
                                      5899964 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00051
                    zinc_ribbon_10 23 lICskChshnGlap......keeleevkyrCpkCga 52
                                      + C+ C  +  ++        +e+e++ yrC kC+ 
  gi|474933783|ref|YP_007687365.1| 52 VTCPACGYTEAYYNvrqtraADEPETIMYRCCKCNN 87
                                      679999998888887777777899**********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 545.48
//
Query:       gi|474933784|ref|YP_007687366.1|  [L=245]
Description: DNA polymerase sliding clamp subunit (PCNA-like protein) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-12   47.0   2.6    1.4e-11   44.2   1.0    2.1  2  PCNA_N    Proliferating cell nuclear antigen, N-terminal doma
    1.3e-05   25.3   1.4    0.00016   21.8   0.1    2.6  2  PCNA_C    Proliferating cell nuclear antigen, C-terminal doma
  ------ inclusion threshold ------
       0.14   11.6   0.0       0.21   11.0   0.0    1.3  1  Rad9      Rad9


Domain annotation for each model (and alignments):
>> PCNA_N  Proliferating cell nuclear antigen, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   1.0   2.4e-15   1.4e-11       1     105 [.       1     103 [.       1     129 [. 0.89
   2 ?    2.6   0.0     0.017     1e+02      12     102 ..     137     224 ..     132     239 .. 0.75

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 2.4e-15
                                       CEEEEESSHHHHHHHHHHHTTTCSEEEEEEETTEEEEEEE-TTSSEEEEEEEEGGGSSEEEESS-EEEEEEHHHHHH CS
                            PCNA_N   1 mlearleqasllkklleaikdlvneanfdcddsGislqalDsshvaLvslelrsegfekyrCDrnlalgvnlnslsk 77 
                                       m+ a+++ a  lk l+  +  lv+e+ + + ++ + ++a+D +hva+  +++ s++f ++  D    +g++l  +  
  gi|474933784|ref|YP_007687366.1|   1 MFKAEIK-ADTLKSLVYIVSTLVDEVKMSIRSDSVVMKAIDPAHVAMLDIKVSSDAFISFSADE-ADIGLDLDKVKS 75 
                                       7777775.6679**************************************************95.689********* PP

                                       HHTTSTTTSEEEEEEETTSSEEEEEEEE CS
                            PCNA_N  78 ilkcannedsvtlkaedeadtlalvfes 105
                                       +lk+a+ +d+++++ + ++  l+l + +
  gi|474933784|ref|YP_007687366.1|  76 VLKLADGDDTIIMEHDPDQGRLTLRIGN 103
                                       **************99999999887655 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.017
                                       HHHHHHHHTTTCSEEEEEEETTEEEEEEE-TTSSEEEEEEEEGGGSSEEEESS-EEEEEEHHHHHHHHTTSTTTSEE CS
                            PCNA_N  12 lkklleaikdlvneanfdcddsGislqalDsshvaLvslelrsegfekyrCDrnlalgvnlnslskilkcannedsv 88 
                                       lkk + a   + +++++++d+ G++l +  ++   + sl++ +      + D ++     l  +s i+k+  ++ +v
  gi|474933784|ref|YP_007687366.1| 137 LKKGIKASESISDHISLEADQYGFELACEGDT--DMASLRIPVADLAGLKADSKVRSLYPLDYFSNIVKVIPDKTVV 211
                                       67777777778888888889999988775554..46688999999999999999999999999999***99999999 PP

                                       EEEEETTSSEEEEE CS
                            PCNA_N  89 tlkaedeadtlalv 102
                                        ++ +++  + + +
  gi|474933784|ref|YP_007687366.1| 212 DIQLDNDYPVKI-L 224
                                       999887654432.2 PP

>> PCNA_C  Proliferating cell nuclear antigen, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1     0.046   2.8e+02      39      74 ..      55      91 ..      23     119 .. 0.81
   2 !   21.8   0.1   2.7e-08   0.00016       2     127 ..     121     240 ..     120     241 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.046
                                      TEEEEEEE.ETTEEEEEEE--BEESSSGGGCBEEEES CS
                            PCNA_C 39 egvkfsas.GdiGsasivlkqvkdvdkeeeavklelk 74
                                        + fsa+  diG    ++k v ++++ ++++++e +
  gi|474933784|ref|YP_007687366.1| 55 AFISFSADeADIGLDLDKVKSVLKLADGDDTIIMEHD 91
                                      3478999637999999999999999999999999865 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 2.7e-08
                                       ---SS-SEEEEEEHHHHHHHHHHHTTT-SEEEEEEETTEEEEEEEETTEEEEEEE--BEESSSGGGCBEEEESS-EE CS
                            PCNA_C   2 ipdseydavvklpssefaricrdlsqlsdsvvisvtkegvkfsasGdiGsasivlkqvkdvdkeeeavklelkepvt 78 
                                       +p+++ ++ + +   + ++ ++   ++sd + + + + g    ++Gd   as+ +          +   l+++  v 
  gi|474933784|ref|YP_007687366.1| 121 VPQIDLSTDIMVGIEQLKKGIKASESISDHISLEADQYGFELACEGDTDMASLRIPV-------ADLAGLKADSKVR 190
                                       67777777777788888888999999**********************999887743.......2456799****** PP

                                       EEEEHHHHHHHGGGGGC-SEEEEEEETTSEEEEEEEETT.CEEEEEEE-B CS
                            PCNA_C  79 ltfalkYlaeftkatsLservtlslssevPlvveykikd.vgllayllak 127
                                         + l+Y+ +++k  +  + v ++l ++ P+++ +++++    + y+la+
  gi|474933784|ref|YP_007687366.1| 191 SLYPLDYFSNIVKVIPDKTVVDIQLDNDYPVKILFSLAEdKINVIYFLAP 240
                                       ************************************97515566788887 PP

>> Rad9  Rad9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   3.4e-05      0.21       5      68 ..      15      78 ..      11     132 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.4e-05
                              Rad9  5 lqclsrigdelyleisedglelrtvnssrSayalvtlkksfFdkyekevseqircki.lvKsvls 68
                                      +  +s + de+ + i+ d + +++++ ++ a   ++ +++ F +++ + + +i + + +vKsvl+
  gi|474933784|ref|YP_007687366.1| 15 VYIVSTLVDEVKMSIRSDSVVMKAIDPAHVAMLDIKVSSDAFISFSAD-EADIGLDLdKVKSVLK 78
                                      66789999*************************************443.3333333325666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1448.27
//
Query:       gi|474933785|ref|YP_007687367.1|  [L=272]
Description: Transketolase, N-terminal subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-61  206.2   0.0    9.2e-61  205.6   0.0    1.2  1  Transketolase_N  Transketolase, thiamine diphosphate binding 
    1.6e-12   47.2   0.0    1.9e-10   40.4   0.0    2.1  2  DXP_synthase_N   1-deoxy-D-xylulose-5-phosphate synthase
    1.7e-10   40.3   0.0    2.5e-10   39.8   0.0    1.3  1  E1_dh            Dehydrogenase E1 component
      8e-07   29.0   0.1    7.6e-06   25.8   0.1    2.1  1  TPP_enzyme_C     Thiamine pyrophosphate enzyme, C-terminal TP
    0.00076   18.4   0.0     0.0019   17.1   0.1    1.6  1  XFP_N            XFP N-terminal domain


Domain annotation for each model (and alignments):
>> Transketolase_N  Transketolase, thiamine diphosphate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.6   0.0   2.6e-64   9.2e-61       3     267 ..       7     260 ..       5     269 .. 0.94

  Alignments for each domain:
  == domain 1  score: 205.6 bits;  conditional E-value: 2.6e-64
                                       HHHHHHHHHHHHHHHHHHT-S--HHHHHHHHHHHHHHHHT--B-TTBTT-TTS-EEEESSGGGHHHHHHHHHHTTSS CS
                   Transketolase_N   3 kkavnaiRvLavDavekaksGhPGaplgladiaevlfkkllkhnPndpkwidRDRfvLsnGhaslllYsllhLtGyd 79 
                                       +k++n +R+ +v++  +a+sGhPG +l+ ad+  +l+ ++++++P+dp   dRDRf+Ls Gha+ +lY+ l   Gy 
  gi|474933785|ref|YP_007687367.1|   7 QKMANKLRLDVVEMTTEAGSGHPGGSLSSADLLAALYFRIMNVDPADPYKEDRDRFILSKGHAAPILYAALAERGY- 82 
                                       6899************************************************************************. PP

                                       --HHHHTTTTSTT-SS-SS--TTTSTT--S---STTHHHHHHHHHHHHHHHHHHHH-BTTB-S----EEEEEEHHHH CS
                   Transketolase_N  80 lsledlksfrqlgsktpGhPelghtagvevttGPLGqGianavglalaektlaatynkpgfdivdhytyvilgDgcl 156
                                       +++e+lk +r++gs+  GhP +++ +gvevttG LGqG++ a g+a+a ++    y           +y++lgDg l
  gi|474933785|ref|YP_007687367.1|  83 FPVEELKTLRKIGSRLQGHPAYRDVPGVEVTTGSLGQGLSMACGIAMAGRMDGKDY----------RVYCLLGDGEL 149
                                       89**********************************************99865555..........59********* PP

                                       HSHHHHHHHHHHHHTT-TTEEEEEEESSEETTEEGGGT--.S-HHHHHHHTT-EEEEETTTT-HHHHHHHHHHHHH- CS
                   Transketolase_N 157 meGvsseasslagtlkLgkLivlyDdnkisidGeteisft.edvakrfeaygWhvievedgedveaikaaieeakae 232
                                       +eG   ea+ +a + +L ++ ++ D nk+ i G+te  ++ +  +++++ +gW+vi   dg+++++i +a ++a ++
  gi|474933785|ref|YP_007687367.1| 150 QEGQNWEAAMFAHQYNLSNITAFVDRNKLQICGNTEEVMAlDPLMEKWRYFGWNVIV-IDGHNIRQIIDACDKAARS 225
                                       ***********************************98876255899*********97.9****************** PP

                                       TTS-EEEEEE--TTTTSTTTTTSGGGTSS---HHH CS
                   Transketolase_N 233 kdkPsliklrtviGygspakagtedvhGapLgede 267
                                       k+ Ps+i l+tv G g    ++++  hG +   +e
  gi|474933785|ref|YP_007687367.1| 226 KKNPSMIILNTVKGKGVSFMENNAGFHGKSCSPEE 260
                                       ****************************8877666 PP

>> DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.0   5.4e-14   1.9e-10      15     176 ..       3     181 ..       1     198 [. 0.82
   2 !    5.1   0.0    0.0032        12     244     269 ..     206     232 ..     186     236 .. 0.74

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 5.4e-14
                    DXP_synthase_N  15 keeleelaeelrefliesvsktg.gHlasnLgvveLtlalh.yv........fdtpkDklvwDvgHqa.YvhKiltg 80 
                                        eel+++a++lr  ++e+ ++ g gH + +L+  +L  al+ ++        ++ ++D+++   gH a   +  l++
  gi|474933785|ref|YP_007687367.1|   3 MEELQKMANKLRLDVVEMTTEAGsGHPGGSLSSADLLAALYfRImnvdpadpYKEDRDRFILSKGHAApILYAALAE 79 
                                       589**************98776549**************974342234444477889*********99345899*** PP

                    DXP_synthase_N  81 Rk....dkfktlrqkgG.lsgfpkrsEseyDafeagHsstsisaalGlavardlkgekkkvvaviGDgaltgGmafe 152
                                       R     +++ktlr+ g  l+g+p  ++ +   +++g  +  +s+a G+a+a +++g++++v +++GDg l  G  +e
  gi|474933785|ref|YP_007687367.1|  80 RGyfpvEELKTLRKIGSrLQGHPAYRDVPGVEVTTGSLGQGLSMACGIAMAGRMDGKDYRVYCLLGDGELQEGQNWE 156
                                       *6555589******87559********************************************************** PP

                    DXP_synthase_N 153 alnnigelk.kkllvilNdNemsis 176
                                       a   + + + +++   +  N+  i 
  gi|474933785|ref|YP_007687367.1| 157 AAMFAHQYNlSNITAFVDRNKLQIC 181
                                       9777655542566666666776665 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0032
                    DXP_synthase_N 244 pidGhdleelikvleevkkl.kgpvll 269
                                        idGh+++++i++ +++ +  k+p ++
  gi|474933785|ref|YP_007687367.1| 206 VIDGHNIRQIIDACDKAARSkKNPSMI 232
                                       69**********998876542678776 PP

>> E1_dh  Dehydrogenase E1 component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   0.0   6.9e-14   2.5e-10      95     224 ..     111     236 ..      74     255 .. 0.85

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 6.9e-14
                                       .BEEE-SSTTTHHHHHHHHHHHHHHHTS---EEEEEEGGGTT-HHHHHHHHHHHHTT--EE.EEEEEESEETTEEHH CS
                             E1_dh  95 rilggngivgaqvplvaGialaakiegkkevailliGDgAanqGdvyealnlaalwklpvi.fvveNNkygisTeae 170
                                       ++  + g +g   ++++Gia+a++++gk+  + +l GDg   +G+ +ea+ +a+ ++l  i  +v  Nk  i  ++e
  gi|474933785|ref|YP_007687367.1| 111 EV--TTGSLGQGLSMACGIAMAGRMDGKDYRVYCLLGDGELQEGQNWEAAMFAHQYNLSNItAFVDRNKLQICGNTE 185
                                       34..4455666677********************************************98626899*********** PP

                                       HH-S---GGG..TTTTS-EEEEETTSHHHHHHHHHHHHHHHHTTT--EEEEEEE CS
                             E1_dh 171 kasaskeladrargvgipglrVdgnDplavyeAvkfAaeraregkgpllielvt 224
                                       +  a + l+++ r +g   + +dg  +  +  A+  Aa+   + k p++i l t
  gi|474933785|ref|YP_007687367.1| 186 EVMALDPLMEKWRYFGWNVIVIDGHNIRQIIDACDKAAR---SKKNPSMIILNT 236
                                       **********************************99965...455577776665 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.1   2.1e-09   7.6e-06      26     142 ..     113     222 ..      96     234 .. 0.66

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 2.1e-09
                                       TTS-TTTHHHHHHHHHHH....STTSEEEEEEEHHHHHHT..GGGHHHHHHTT-.SEEEEEEE-SBCCCHHHHHHHH CS
                      TPP_enzyme_C  26 glgtmGyglpaAiGakla....kpdrevvaivGDGgflmi..lqelatavrrnl.pitvvvlnNegygmtggqqepf 95 
                                       ++g++G gl++A+G+++a     +d +v+++ GDG ++     ++ + a+++nl +it +v  N+    +g+ +e +
  gi|474933785|ref|YP_007687367.1| 113 TTGSLGQGLSMACGIAMAgrmdGKDYRVYCLLGDGELQEGqnWEAAMFAHQYNLsNITAFVDRNKLQ-ICGNTEEVM 188
                                       789**************755533478**********99755378888999****7777777777544.444444433 PP

                                       TCCTTTTSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHH CS
                      TPP_enzyme_C  96 ggkrksgpagkdlkpvdfaklaealGakgarvekadveeleealkea 142
                                                    +p  + +  + +G ++++++ +++ ++ +a ++a
  gi|474933785|ref|YP_007687367.1| 189 AL-----------DP--LMEKWRYFGWNVIVIDGHNIRQIIDACDKA 222
                                       32...........22..334445555555555555555555555555 PP

>> XFP_N  XFP N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   5.3e-07    0.0019     130     239 ..     105     214 ..      94     246 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.3e-07
                             XFP_N 130 aetPGsiheGGelGyalshayGav....ldnPdlivacvvGdGeaetGPlatswhsnkflnPaedGavlPilelnGy 202
                                        ++PG     G lG  ls a G +    +d  d  v c++GdGe + G     w++  f    +   +   ++ n  
  gi|474933785|ref|YP_007687367.1| 105 RDVPGVEVTTGSLGQGLSMACGIAmagrMDGKDYRVYCLLGDGELQEGQ---NWEAAMFAHQYNLSNITAFVDRNKL 178
                                       589**9999***********997633446999**************995...8************************ PP

                             XFP_N 203 kisnptilarisdeelkklfeGlGyepafvededtes 239
                                       +i   t    +  + l + ++ +G+++ ++++++  +
  gi|474933785|ref|YP_007687367.1| 179 QICGNTE-EVMALDPLMEKWRYFGWNVIVIDGHNIRQ 214
                                       *998885.55667788888999999999999987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1729.28
//
Query:       gi|474933786|ref|YP_007687368.1|  [L=316]
Description: Transketolase, C-terminal subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.5e-41  140.0   0.0      1e-40  139.3   0.0    1.3  1  Transket_pyr     Transketolase, pyrimidine binding domain
    1.8e-38  131.2   1.5    2.9e-38  130.6   0.5    1.8  2  Transketolase_C  Transketolase, C-terminal domain
    0.00037   20.7   0.2      0.002   18.4   0.1    2.2  3  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma


Domain annotation for each model (and alignments):
>> Transket_pyr  Transketolase, pyrimidine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.3   0.0   1.7e-44     1e-40       2     175 ..       5     169 ..       4     171 .. 0.97

  Alignments for each domain:
  == domain 1  score: 139.3 bits;  conditional E-value: 1.7e-44
                                       EEEHHHHHHHHHHHHHCTTTTEEEEESSTHHHHTTCHCCHHEGGTTEGEEE--S-HHHHHHHHHHHHHHCTTEEEEE CS
                      Transket_pyr   2 kiawrkaeaealaellkedpevvligaDvaggtfsvrkgllhdqgegrvidsgisEqavlgfavGaalagpllvive 78 
                                       k+a r  +++ala+l++++p+vv+++aD+ag+t +  ++++ ++   r+i++gi+E++++g+a+G+a++g  ++++ 
  gi|474933786|ref|YP_007687368.1|   5 KLAQRSYYGKALAKLAETNPDVVVLDADLAGSTKTGDFQKVCPE---RFIECGIAEANMVGVAAGLATSG--KIPFA 76 
                                       6778999*************************************...***********************..9**** PP

                                       EEEHHHHGGGHHGGHHHHHCHHHHHT--EE.EEESBSGGGSTTGTTTSBSSHHHHHHTSTTEEEE--SSHHHHHHHH CS
                      Transket_pyr  79 aqFgdFangAqiyadqairsgeakgklkvg.vvtrlpigvgedGpehqsaeleaflrlipglkvvrPsdpaetkhll 154
                                        +Fg+Fa+    +++++ir+ +a  +l+v+ v t+++++vg dG++hq++e++a+ r++p+++v++P+d+ e++++ 
  gi|474933786|ref|YP_007687368.1|  77 STFGVFAS---GRCWEQIRMAVAYPRLNVKiVATHCGLSVGPDGATHQALEDIAITRALPNMTVIVPCDAHEAYAAT 150
                                       ********...9***************************************************************** PP

                                       HHHHHSSS.SEEEEEE-SSEE CS
                      Transket_pyr 155 rrairredrkPvvlrlpksll 175
                                        + +   +++Pv++r+ +s+ 
  gi|474933786|ref|YP_007687368.1| 151 LAIAD--YDGPVYMRMGRSSF 169
                                       99999..789******99976 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.53   3.2e+03      27      43 ..      15      31 ..      13      65 .. 0.74
   2 !  130.6   0.5   4.8e-42   2.9e-38       1     124 []     182     302 ..     182     302 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.53
                                      HHHHHHTTTTCEEEEE- CS
                   Transketolase_C 27 AaeeLekegisaeVvdl 43
                                      A ++L++ + ++ V+d+
  gi|474933786|ref|YP_007687368.1| 15 ALAKLAETNPDVVVLDA 31
                                      66677777777777775 PP

  == domain 2  score: 130.6 bits;  conditional E-value: 4.8e-42
                                       TEEEEEETTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHH CS
                   Transketolase_C   1 gkaeilregkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGig 77 
                                       gka++lreg+d+ ++a G mv+ ++ Aae+L++egisaeVv++ tvkplD++ +l+ +kktg +v+vee++++gG+g
  gi|474933786|ref|YP_007687368.1| 182 GKADVLREGSDISIIACGQMVQSCMVAAEQLASEGISAEVVNMATVKPLDRDAVLATAKKTGAVVTVEEHSIIGGLG 258
                                       89*************************************************************************** PP

                                       HHHHHHHHHCCCTTCSSEEEEEEE-SS.SSSSGHHHHHHHTT-SHHHH CS
                   Transketolase_C  78 sevaaalaeeafdgldapvkrvggpdv.iepgsaeelekafgldaeki 124
                                       s v+++l+e    + ++pv+rvg +d+ +e+g aeel++ +gl +++i
  gi|474933786|ref|YP_007687368.1| 259 SVVCECLSE----EYPVPVLRVGTKDTfGESGEAEELLEKYGLGVKDI 302
                                       *********....99****************************99887 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.1   6.7e+03      44      63 ..      15      34 ..      13      42 .. 0.75
   2 ?   -1.7   0.0      0.59   3.5e+03      64      94 ..      79     110 ..      59     116 .. 0.68
   3 !   18.4   0.1   3.4e-07     0.002       2      74 ..     192     264 ..     191     279 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.1
                                      HHHHHSTT-SEEEEEE-S-- CS
                           PFOR_II 44 elkellkkvkkvvvldrnis 63
                                      +l++l++    vvvld + +
  gi|474933786|ref|YP_007687368.1| 15 ALAKLAETNPDVVVLDADLA 34
                                      67788888889999998873 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.59
                                       TT-G..-HHHHHHHHHTGGGTSEEEEEE--GGG CS
                           PFOR_II  64 fgse..GqlveevkaalkkskvkvvnfvaglgG 94 
                                       fg+   G  +e +++a+      +v++va ++G
  gi|474933786|ref|YP_007687368.1|  79 FGVFasGRCWEQIRMAVAYP-RLNVKIVATHCG 110
                                       55444588888888887655.455666666665 PP

  == domain 3  score: 18.4 bits;  conditional E-value: 3.4e-07
                                       SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHH CS
                           PFOR_II   2 evvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveev 74 
                                       ++ i+a G +++++  a+++l  egi++ ++ + t+ P  ++++   +kk+ +vv+++    +g  G +v e 
  gi|474933786|ref|YP_007687368.1| 192 DISIIACGQMVQSCMVAAEQLASEGISAEVVNMATVKPLDRDAVLATAKKTGAVVTVEEHSIIGGLGSVVCEC 264
                                       789*******************************************************999999888877664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 1794.38
//
Query:       gi|474933787|ref|YP_007687369.1|  [L=219]
Description: transaldolase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-55  188.7   1.2    3.7e-54  184.0   1.2    2.1  1  TAL_FSA   Transaldolase/Fructose-6-phosphate aldolase


Domain annotation for each model (and alignments):
>> TAL_FSA  Transaldolase/Fructose-6-phosphate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.0   1.2     2e-58   3.7e-54       1     281 [.       5     213 ..       5     219 .] 0.91

  Alignments for each domain:
  == domain 1  score: 184.0 bits;  conditional E-value: 2e-58
                                       EEEE---HHHHHHHHHTT---EEE--HHHHHH..TTS.-HHHHHHHHHHH........................H-S CS
                           TAL_FSA   1 lvlDtadrelikklleekgiqgvTtNPsliekaikykalydeaieeikkegkkvkeaydkLavedilealdllgadg 77 
                                       +++Dta++++ik++  +++++gvTtNPsl++k  +++ +  + ++ei+k+                      l  d 
  gi|474933787|ref|YP_007687369.1|   5 FFIDTANLDMIKEINSWGILDGVTTNPSLVAK--EGT-DTPTRVAEIAKI----------------------L-GDR 55 
                                       69******************************..544.667777777766......................6.89* PP

                                       -EEEE-S-...-SHHHHHHHHHHHHTT-T..TEEEEEESSHHHHHHHHHHHHTT--EEEEEE-SHHHHHHHHHHT-S CS
                           TAL_FSA  78 rvslEVdarlsddteatieeArrlialyerenvlIKiPateeGikAikeLkkeGinvnvTliFsleqalaaaeagas 154
                                       +vs+E +a    d+e++i+e+++l+a++   nv +K+P++ e++kA k+L++ Gi vn+TliFs+ qal+aa+aga+
  gi|474933787|ref|YP_007687369.1|  56 PVSAEAMA---VDAEGMIAEGKKLAAIAP--NVNVKLPMCIESLKATKALSEIGIDVNMTLIFSPLQALMAAKAGAR 127
                                       ********...**************9998..********************************************** PP

                                       EEEEBHHHHHTTT............S-HHHHHHHHHHHHHHHT-S-EEEEBS--SHHHHH..HHHT-SEEEE-HHHH CS
                           TAL_FSA 155 viSpFvgRiddllkkleekdklkgkddgvalvkeiynyykklgysTkvmaasfrnveeve..elagcdtvTippkll 229
                                       ++SpFvgR+dd++            + g  + +e + +++++g++T+v+aas+r++ +v+  + +gcd+ Tip ++l
  gi|474933787|ref|YP_007687369.1| 128 YVSPFVGRLDDIG------------THGNDMLTETVGILRTYGFETEVIAASIRHPVHVLdaAEMGCDIATIPYDIL 192
                                       *************............7999********************************9*************** PP

                                       HHHT--HHH...............................HHHHHHHHHHHH CS
                           TAL_FSA 230 ealakhgktsekleeeeieklleklfrlginedavaeelldegikkFakdle 281
                                       +++  h+kt+e +++                               F++d+e
  gi|474933787|ref|YP_007687369.1| 193 KKMVSHPKTDEGIAK-------------------------------FKADYE 213
                                       *********444444...............................333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1483.09
//
Query:       gi|474933788|ref|YP_007687370.1|  [L=387]
Description: geranylgeranyl reductase family [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.6e-18   64.5   2.1    2.7e-16   59.8   2.1    2.6  1  FAD_binding_3   FAD binding domain
    2.3e-13   49.8   0.4    8.3e-09   34.8   0.0    2.2  2  Trp_halogenase  Tryptophan halogenase
    8.7e-11   41.5   0.1    1.2e-10   41.1   0.1    1.2  1  Lycopene_cycl   Lycopene cyclase protein
    1.1e-08   34.7   3.7    0.00071   18.9   0.1    2.5  3  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    4.4e-08   33.1   1.0    2.4e-05   24.1   0.3    2.2  2  DAO             FAD dependent oxidoreductase
    3.7e-07   30.3   0.1    9.6e-07   28.9   0.1    1.7  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    5.2e-06   25.4   0.2    0.00026   19.8   0.0    2.1  2  HI0933_like     HI0933-like protein
    4.1e-05   23.1   0.4      6e-05   22.6   0.4    1.3  1  FAD_oxidored    FAD dependent oxidoreductase
    0.00099   19.6   0.1        1.1    9.9   0.1    2.4  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
     0.0026   16.9   0.3     0.0045   16.1   0.3    1.3  1  FAD_binding_2   FAD binding domain
     0.0046   16.1   0.1     0.0058   15.8   0.1    1.2  1  GIDA            Glucose inhibited division protein A
  ------ inclusion threshold ------
       0.01   15.1   0.2      0.034   13.4   0.0    1.9  3  Thi4            Thi4 family
      0.015   14.6   0.2        2.2    7.5   0.1    2.1  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
      0.067   13.1   0.3        0.2   11.5   0.1    1.8  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 


Domain annotation for each model (and alignments):
>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.8   2.1   2.1e-19   2.7e-16       3     304 ..       7     276 ..       6     277 .. 0.78

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 2.1e-19
                                       EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEEEE CS
                     FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrtmellrqlGledrilaegapnelmgealyne 79 
                                       dV +VG+GpaG ++a+lL+  G +vvl+e ++++ v +   g+ +   ++++++G+  +i+++  + +     ++ +
  gi|474933788|ref|YP_007687370.1|   7 DVTVVGGGPAGSLTARLLAASGRDVVLLEEHNEAGVPTHCAGFVSD--DVIQKMGVRPNIYSTICRAD-----VKLP 76 
                                       79******************************99888866666544..89***********9995555.....4555 PP

                                       CCCCCEEEEEHHCHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEE CS
                     FAD_binding_3  80 lsdtpkaradlelesspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrak 156
                                                 le+  + +   ++   +l+  +v+ a+++g++v+++++ + +++++  vta+  d       +++++
  gi|474933788|ref|YP_007687370.1|  77 ------DGRVLEIGRKSPIGFIVDRADLDAKMVDLAAKHGVDVHMGERCTEVTATDAYVTAKTNDG------EIKSD 141
                                       ......2335665677777778888999**********************9999999999998888......49*** PP

                                       EEEE--GTT-HHHHHHTGGEEEEEEEEEEEEEEEEEEC-SCCCTTCCEEEEECCTTEEEEEECCETEEEEEEEEECC CS
                     FAD_binding_3 157 YlvGaDGgrStvrktlgiefegeetvyeagvldvlfdadlsdiveplvlilsaesrgvmviPlentlerfyvqvear 233
                                        lvGaDG +St++++ g ++  e    +   +dv  + d +       +il+  +++        +   f +q++++
  gi|474933788|ref|YP_007687370.1| 142 LLVGADGQNSTIAASWGNNMAREY--LRGFQMDVRHTMDEQ-----DRMILRVGNDI--------APGLFAWQLPMG 203
                                       *****************8877666..234445555444444.....23333333333........222234444444 PP

                                       E-GGGS....CCCHHHHHHHHHHHHHHTTSSCEEEEEEEEEEEEEEEEESSSEETTEEE-GGGTEEE-STTSHHH CS
                     FAD_binding_3 234 aekeer....sekfteeevkarlreivgektldveieevsawtvaqrvaekyrkgrvflaGDAaHihpPtgGqGl 304
                                       +  +      +++ t++e+++rl + +g ++ +ve +   +++++ r ++   ++rv+l+GDAa  + P+ + Gl
  gi|474933788|ref|YP_007687370.1| 204 DLTRVGvcvsPNAGTPAEYVKRLLKNIGLADCKVEQSFGGKVPIGGRRTSV--NNRVMLIGDAAGQVKPVSAGGL 276
                                       43333333448899********************9999999****998874..68**************999886 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.2   1.9e-05     0.024       1      34 [.       7      37 ..       7      76 .. 0.82
   2 !   34.8   0.0   6.5e-12   8.3e-09     147     372 ..      89     316 ..      56     321 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.9e-05
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-S CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlvese 34
                                      ++++vGGG+aG+l+A +la  +    +v l+e  
  gi|474933788|ref|YP_007687370.1|  7 DVTVVGGGPAGSLTARLLAASG---RDVVLLEEH 37
                                      589****************999...568888754 PP

  == domain 2  score: 34.8 bits;  conditional E-value: 6.5e-12
                                       -EEEE-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGGG-IIIIIIT---EE CS
                    Trp_halogenase 147 yAyhldaalyakfLrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsGfrgllieqaLktgfe 223
                                        ++ +d+a ++  + + a ++Gv++  g+  + ++  d +v++ +++dg+ ++ dl + + G ++ + ++  ++  +
  gi|474933788|ref|YP_007687370.1|  89 IGFIVDRADLDAKMVDLAAKHGVDVHMGERCTEVTATDAYVTA-KTNDGE-IKSDLLVGADGQNSTIAASWGNNMAR 163
                                       67899************************99999999999998.555777.*******************9888888 PP

                                       E-TTT----EEEEEEEE--H.---SSEEEEE-SSEEEEEEEETTEEEEEEEE-TTTS-HHHHHHHHHHHCT--TTTS CS
                    Trp_halogenase 224 dwsdvLltdrAlavqvesee.lvepytrataekaGWtWkiPLqhrlgnGyvyssahadddeAlaellaeldgkleae 299
                                       ++ + + +d   +  +++++  +  + + +a      W+ P+ + +  G+ +s +  + +e +++ll++++++  + 
  gi|474933788|ref|YP_007687370.1| 164 EYLRGFQMDVRHT--MDEQDrMILRVGNDIA-PGLFAWQLPMGDLTRVGVCVSPNAGTPAEYVKRLLKNIGLADCKV 237
                                       8888887776655..4455524444555555.45589*********************************9875544 PP

                                       -..EEEE---EEES-SEETTEEE-CCCTEE--CCCS-HHHHHHHHHHHHHHT--B....TT--HHHHHHHHHHHHHH CS
                    Trp_halogenase 300 p..rkirfttGrrkqawvknvvalGlasgfvePlestsihliqaalrrLlallpd....ksdepaaiaefnrevare 370
                                       +     ++  G r+++ ++ v+++G+a+g v P+ + +++ i +a+  L+ +  +    ++++ a +a ++r  +re
  gi|474933788|ref|YP_007687370.1| 238 EqsFGGKVPIGGRRTSVNNRVMLIGDAAGQVKPVSAGGLYPIAVAAPILADTVSKayemNVFSTAVLALYERGWKRE 314
                                       413556899999********************************998887776651111455666667777766666 PP

                                       HH CS
                    Trp_halogenase 371 le 372
                                       l+
  gi|474933788|ref|YP_007687370.1| 315 LG 316
                                       65 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.1   9.2e-14   1.2e-10       1     297 [.       7     297 ..       7     344 .. 0.79

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 9.2e-14
                     Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnny...vWsdefedlgaleecvehsWsgtivylddgkk 74 
                                       Dv v+G+GpAg + A  l  a+ g  vvl+e  ++   p      v  d  + +g     +  +  ++ v+l+dg+ 
  gi|474933788|ref|YP_007687370.1|   7 DVTVVGGGPAGSLTARLL--AASGRDVVLLEEHNEAGVPTHCagfVSDDVIQKMG-VRPNIYSTICRADVKLPDGRV 80 
                                       9**********9999888..9999******9988876665543225566667777.9999999************** PP

                     Lycopene_cycl  75 illgraY...grvsskrlkeellerlvengvkllea.kvesveeeeageslvvleggr.kirarlvvdarglaslk. 145
                                        ++gr+      v +++l +++    +++gv  + + + ++v++ +a   +v+ + +  +i++ l v a g  s   
  gi|474933788|ref|YP_007687370.1|  81 LEIGRKSpigFIVDRADLDAKMVDLAAKHGVDVHMGeRCTEVTATDA---YVTAKTNDgEIKSDLLVGADGQNSTIa 154
                                       ****654111469***********999****9998724566666555...6655555558***********555446 PP

                     Lycopene_cycl 146 ..karrlglQtfyGvevevdnppfdldkmvlMDfrveqklkgltFlYalPlds.drllvEeTelaskpeLpadalkk 219
                                          + ++     +G  + v++    +d+ + M  rv +++    F + lP+++ +r+     + +++   pa+ +k+
  gi|474933788|ref|YP_007687370.1| 155 asWGNNMAREYLRGFQMDVRHT---MDEQDRMILRVGNDIAPGLFAWQLPMGDlTRV---GVCVSPNAGTPAEYVKR 225
                                       6677888888899998888766...777777778*****99999*******873555...45889988888887765 PP

                     Lycopene_cycl 220 rlaaylralglkvkevveeEqgviPvtlggslprleqkvlaiGaaaglvhPaTGYsvarslaeapllasaiaaalre 296
                                            l++ gl+  +v++   g +P+  gg    ++++v+ iG aag v+P     +     +ap+la+ +++a + 
  gi|474933788|ref|YP_007687370.1| 226 L----LKNIGLADCKVEQSFGGKVPI--GGRRTSVNNRVMLIGDAAGQVKPVSAGGLYPIAVAAPILADTVSKAYEM 296
                                       4....5789*****************..***********************665555556667999******99886 PP

                     Lycopene_cycl 297 s 297
                                       +
  gi|474933788|ref|YP_007687370.1| 297 N 297
                                       5 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   5.5e-07   0.00071       2      34 ..       7      43 ..       6      89 .. 0.75
   2 !   16.6   0.2   2.7e-06    0.0035     186     243 ..      99     155 ..      92     192 .. 0.76
   3 ?   -3.7   0.0       4.3   5.4e+03     265     283 ..     251     269 ..     248     273 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 5.5e-07
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEE....TTHC CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlve....legt 34
                                      dv v+GgGpAG  +a+ la++g +v+l+e    ++  
  gi|474933788|ref|YP_007687370.1|  7 DVTVVGGGPAGSLTARLLAASGRDVVLLEehneAGVP 43
                                      89**************************755443333 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 2.7e-06
                                       HHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 186 saaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrpstel 243
                                        a + +   k+Gv+v++g++ +e+++ +  ++ +++dge i+ dl+v a G     + 
  gi|474933788|ref|YP_007687370.1|  99 DAKMVDLAAKHGVDVHMGERCTEVTATDAYVTAKTNDGE-IKSDLLVGADGQNSTIAA 155
                                       566677889****************99985556666665.9********999877655 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 4.3
                                       BES.STTEEE-GGGCTECCS CS
                                       xxx.xxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 265 rtn.vpgiyaiGDvaggkgg 283
                                       rt+    + +iGD a g+ +
  gi|474933788|ref|YP_007687370.1| 251 RTSvNNRVMLIGDAA-GQVK 269
                                       566566799999999.4444 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.3   1.9e-08   2.4e-05       1      33 [.       7      41 ..       7      54 .. 0.90
   2 !    7.7   0.0    0.0018       2.3     140     205 ..      90     152 ..      70     229 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.9e-08
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                      dv ++GGG +G+ tA+ La+ g  V+lle +++ag
  gi|474933788|ref|YP_007687370.1|  7 DVTVVGGGPAGSLTARLLAASGrdVVLLEEHNEAG 41
                                      89******************999********9887 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0018
                                       EEEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHH CS
                               DAO 140 tgqvdpakltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsd 205
                                       + +vd a l a + + a+++Gv+++ g++ t++ ++d   + v  +t+ ge+++ d +V a G  s+
  gi|474933788|ref|YP_007687370.1|  90 GFIVDRADLDAKMVDLAAKHGVDVHMGERCTEVTATD---AYVTAKTNdGEIKS-DLLVGADGQNST 152
                                       56789999999****************9999996664...33333555587655.788888887776 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.1   7.5e-10   9.6e-07       1      36 [.      10      47 ..      10      67 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 7.5e-10
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSS..GGG- CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlG..Graa 36
                                      +vG+G +G+++A+lLa  g+dv+lle ++  G   ++a
  gi|474933788|ref|YP_007687370.1| 10 VVGGGPAGSLTARLLAASGRDVVLLEEHNEAGvpTHCA 47
                                      8*****************************99444554 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   2.1e-07   0.00026       2      36 ..       7      41 ..       6      49 .. 0.91
   2 ?    3.7   0.0     0.016        21     119     167 ..     106     152 ..      97     175 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2.1e-07
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                      dv v+GgG+AG ++A  +a+ g++V+lle+ +++g
  gi|474933788|ref|YP_007687370.1|  7 DVTVVGGGPAGSLTARLLAASGRDVVLLEEHNEAG 41
                                      89*****************************9988 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.016
                                       HHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS- CS
                       HI0933_like 119 lkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGlSi 167
                                       + + gv++++ ++ ++v+++ d  ++ kt +++e+++d lv A G +S 
  gi|474933788|ref|YP_007687370.1| 106 AAKHGVDVHMGERCTEVTAT-DAYVTAKT-NDGEIKSDLLVGADGQNST 152
                                       6789*************775.55488888.9**********99998874 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.4   4.7e-08     6e-05       1     117 [.       7     126 ..       7     156 .. 0.67

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 4.7e-08
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaeeqvvtgiareflerlrq.rgga..r 74 
                                       Dv VvGGgpaG   A   a +G+ v+L+ee++  G  +  ++  +d+  ++ + v   i+  ++++  +  +g   +
  gi|474933788|ref|YP_007687370.1|   7 DVTVVGGGPAGSLTARLLAASGRDVVLLEEHNEAGVPTHCAGFVSDDVIQKMG-VRPNIYSTICRADVKlPDGRvlE 82 
                                       9*******************************997444444444444444333.66666666666655543333232 PP

                      FAD_oxidored  75 lkkrskw..ntfepevakavleemlaeagvtvllntrlvevekeg 117
                                       ++ r+++   +++   + a + ++ a++gv+v +++r +ev+ ++
  gi|474933788|ref|YP_007687370.1|  83 IG-RKSPigFIVDRADLDAKMVDLAAKHGVDVHMGERCTEVTATD 126
                                       22.222223377777777777777788888888888887777766 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.1   0.00082       1.1       2      40 ..       8      44 ..       7      62 .. 0.80
   2 !    7.2   0.0    0.0058       7.4      41      72 ..      97     128 ..      90     136 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00082
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSH CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDe 40
                                      v+vvGgG  g   A  la+ g +V ++e +++     + 
  gi|474933788|ref|YP_007687370.1|  8 VTVVGGGPAGSLTARLLAASGRDVVLLEEHNEAG--VPT 44
                                      89**************************999877..444 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0058
                                       HHHHHHHHHHHHTTEEEECSEEEEEEEEETTS CS
                         Pyr_redox  41 easkilqeklekngievllntkveeiegsedg 72 
                                       ++ + + +   k+g++v+++++ +e++ ++  
  gi|474933788|ref|YP_007687370.1|  97 DLDAKMVDLAAKHGVDVHMGERCTEVTATDAY 128
                                       5667889999*****************88864 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.3   3.5e-06    0.0045       1      42 [.       7      48 ..       7      56 .. 0.96

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.5e-06
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG-- CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsq 42
                                      Dv V+G+G AG   A  +a  G++v+++e  +e g  t++++
  gi|474933788|ref|YP_007687370.1|  7 DVTVVGGGPAGSLTARLLAASGRDVVLLEEHNEAGVPTHCAG 48
                                      999********************************9999985 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   4.5e-06    0.0058       1      34 [.       7      40 ..       7     134 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.5e-06
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGG CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkldt 34
                                      dv+V+GgG AG+  A  +a +G +v+L+ ++ + 
  gi|474933788|ref|YP_007687370.1|  7 DVTVVGGGPAGSLTARLLAASGRDVVLLEEHNEA 40
                                      79**************************555443 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.6e-05     0.034      18      63 ..       6      50 ..       1      62 [. 0.83
   2 ?   -2.5   0.0         2   2.5e+03     162     193 ..      92     123 ..      85     151 .. 0.69
   3 ?   -2.4   0.1       1.8   2.3e+03     157     216 ..     138     196 ..     100     200 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.6e-05
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTT CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGql 63
                                       Dv +vG+G++G  +a+ la + +  v++le++   G  +   G +
  gi|474933788|ref|YP_007687370.1|  6 PDVTVVGGGPAGSLTARLLAAS-GRDVVLLEEHNEAGVPTHCAGFV 50
                                      59*******************9.99******998888776666655 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2
                                       EEE--GSSSTTTTHHHHHHHHCTTTS-----E CS
                              Thi4 162 vvdatGhdgeivavvvkkikleakiekvkgek 193
                                       +vd +  d+++v++++k+ ++ ++ e+ ++  
  gi|474933788|ref|YP_007687370.1|  92 IVDRADLDAKMVDLAAKHGVDVHMGERCTEVT 123
                                       67777778888888887777766554444443 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.8
                                       EEEEEEEE--GSSSTTTTHHHHHHHHCTTTS-----ECB-HHHHHHHHHHHECEEETTEE CS
                              Thi4 157 irakvvvdatGhdgeivavvvkkikleakiekvkgeksldaekaedaivkktrevvpnly 216
                                       i++ ++v a G ++ i a     ++ e       + +   +++ ++ i++  +++ p+l+
  gi|474933788|ref|YP_007687370.1| 138 IKSDLLVGADGQNSTIAASWGNNMAREYLRGFQMDVR-HTMDEQDRMILRVGNDIAPGLF 196
                                       5556666666666666666555555555333333333.3566667777777777777776 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1    0.0017       2.2       2      31 ..      10      38 ..       9      43 .. 0.91
   2 ?    5.0   0.0    0.0094        12      90     134 ..     105     149 ..      92     162 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0017
                       Pyr_redox_3  2 IiGaGPaGlaaaielkkagledylilEkgn 31
                                      ++G+GPaG  +a  l  +g  d++ lE +n
  gi|474933788|ref|YP_007687370.1| 10 VVGGGPAGSLTARLLAASGR-DVVLLEEHN 38
                                      8******************9.899**9985 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0094
                       Pyr_redox_3  90 vaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGe 134
                                       +a+++ +++++ e+ ++v+ +d   + +t+ ++++++ ++ A G+
  gi|474933788|ref|YP_007687370.1| 105 LAAKHGVDVHMGERCTEVTATDAYVTAKTNDGEIKSDLLVGADGQ 149
                                       678899999999999999999999999999999999999999886 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00015       0.2       2      34 ..       8      40 ..       7      45 .. 0.93
   2 ?   -1.5   0.0       1.5     2e+03      15      35 ..     103     123 ..      99     153 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00015
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseea 34
                                      v+v+G G  G+  a ++a++g +Vvl++ ++ea
  gi|474933788|ref|YP_007687370.1|  8 VTVVGGGPAGSLTARLLAASGRDVVLLEEHNEA 40
                                      9**************************998875 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.5
                                       HHHHHHTT-EEEEE-S-HHHH CS
                           3HCDH_N  15 aavfasagleVvlvdiseeal 35 
                                         ++a++g++V++ ++ +e  
  gi|474933788|ref|YP_007687370.1| 103 VDLAAKHGVDVHMGERCTEVT 123
                                       567888888888887754443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2588.84
//
Query:       gi|474933789|ref|YP_007687371.1|  [L=336]
Description: putative methyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.2e-57  192.4   0.0    8.9e-57  192.0   0.0    1.1  1  Met_10           Met-10+ like-protein
     0.0049   16.7   0.3      0.011   15.6   0.0    1.7  2  Trm5_N           tRNA methyltransferase 5 N-terminal domain
     0.0073   15.9   0.0      0.011   15.3   0.0    1.2  1  MTS              Methyltransferase small domain
  ------ inclusion threshold ------
      0.027   13.5   0.0      0.038   13.0   0.0    1.1  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
      0.028   14.0   0.0      0.051   13.2   0.0    1.4  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
      0.049   13.2   0.0      0.077   12.6   0.0    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
       0.18   11.4   0.0       0.41   10.3   0.0    1.5  2  Cons_hypoth95    Conserved hypothetical protein 95


Domain annotation for each model (and alignments):
>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.0   0.0   3.5e-60   8.9e-57       2     199 .]      89     285 ..      88     285 .. 0.99

  Alignments for each domain:
  == domain 1  score: 192.0 bits;  conditional E-value: 3.5e-60
                                       EEEEETTEEEEEB-TTSSHHHHHHHHHHHHHSS-SCEEEE-S-SBTTTTB--EEEEEES-.SEEEEEETTEEEEEET CS
                            Met_10   2 kfeiiGdvvilnlreelkeykkvigevildktkvktvlrkvsevegefRtfelevlaGsdstetihkEngcrfklDv 78 
                                       k+ei+Gdvv l+++  l +  ++ig+++++  +v tv+ + s v+gefR +++++l G+     +++Eng+ ++ Dv
  gi|474933789|ref|YP_007687371.1|  89 KWEIAGDVVTLKMDPVLYPEGREIGKAYAEALEVSTVYADISGVAGEFRLPDMKLLFGEP-RLSVKTENGIVYEYDV 164
                                       79*********************************************************9.677899********** PP

                                       TTS---GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEE CS
                            Met_10  79 skvyfsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkp 155
                                       +kv+f s++ aEr+r+ +l   ge+Vvd+fAGiG+f++p+ak+s a+rv+a ++nP+s+ +l +n+++N ve+vv p
  gi|474933789|ref|YP_007687371.1| 165 TKVMFASGNLAERKRMEALDCRGETVVDMFAGIGYFTLPLAKFSGARRVFACEKNPDSYGFLVNNVRRNGVEDVVIP 241
                                       ***************************************************************************** PP

                                       EES-GGG---TT-EEEEEE--TTTGGGGHHHHHHHEEEEEEEEE CS
                            Met_10 156 ileDgrevireqladrvvmnlpksaieFldkvlaalkdggvihy 199
                                       il+D+r +  + +adr++m++++++ eF+  +l+++k g +ihy
  gi|474933789|ref|YP_007687371.1| 242 ILADNRSLCGTAFADRILMGYVQTTSEFVPYALRMAKPGCIIHY 285
                                       *******************************************9 PP

>> Trm5_N  tRNA methyltransferase 5 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   4.2e-06     0.011       3      42 ..       3      42 ..       3      47 .. 0.91
   2 ?   -3.5   0.0         4     1e+04      34      42 ..     237     245 ..     236     246 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.2e-06
                                      EEEGGGHHHHHHHHHHTT-B-TTS--EEETTEEEEEB-S- CS
                            Trm5_N  3 kVpkkegEkvRkkLlekglLdrnyKIksdddylyIPvkee 42
                                      +Vp  ++ +++ +L+ekg+Ld++ +I+  d++ ++P++  
  gi|474933789|ref|YP_007687371.1|  3 RVPSDKASEIIPVLREKGILDPSARISGGDGFRLVPIVPG 42
                                      79999999************************99999876 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4
                                       EEEEEB-S- CS
                            Trm5_N  34 ylyIPvkee 42 
                                        + IP+  +
  gi|474933789|ref|YP_007687371.1| 237 DVVIPILAD 245
                                       6889*9875 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   4.2e-06     0.011      26      82 ..     182     238 ..     156     259 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.2e-06
                                       HCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.E CS
                               MTS  26 tlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.v 82 
                                       +l+  + ++v+D+ +G+G+ ++ lak+s   +v +++++  +  +  +n+++n++e v
  gi|474933789|ref|YP_007687371.1| 182 ALDC-RGETVVDMFAGIGYFTLPLAKFSGARRVFACEKNPDSYGFLVNNVRRNGVEdV 238
                                       4444.6778********************************************99852 PP

>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.5e-05     0.038     196     254 ..     181     241 ..     146     249 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.5e-05
                   tRNA_U5-meth_tr 196 evtqeskgdllelycGnGnfslalarn..fekvlateiakssveaaqyniaankidnvqii 254
                                       e+++ + + +++++ G G f+l+la++   ++v+a e    s  +   n+  n +++v i 
  gi|474933789|ref|YP_007687371.1| 181 EALDCRGETVVDMFAGIGYFTLPLAKFsgARRVFACEKNPDSYGFLVNNVRRNGVEDVVIP 241
                                       5555666778999************984469*************************99875 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0     2e-05     0.051       9      85 ..     187     260 ..     180     262 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2e-05
                                       T-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEE.EES-CTCCHHHHCC..EEEEE CS
                   Methyltr_RsmB-F   9 eetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntiv.leaDarkidkvlggelfDriL 84 
                                       +et++D+ a+ G  T  +a++ + + +v+A ++n      +++n++r gv+++ + + aD r     +g ++ DriL
  gi|474933789|ref|YP_007687371.1| 187 GETVVDMFAGIGYFTLPLAKF-SGARRVFACEKNPDSYGFLVNNVRRNGVEDVVIpILADNRSL---CGTAFADRIL 259
                                       799*****************9.8899*************************8766478898887...888999***9 PP

                                       E CS
                   Methyltr_RsmB-F  85 l 85 
                                       +
  gi|474933789|ref|YP_007687371.1| 260 M 260
                                       7 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0     3e-05     0.077       2      61 ..     188     249 ..     187     284 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3e-05
                   Methyltransf_15   2 rvilDlfsGaGGnviqfalv..fekviaieinleklacaqhNaevYgvsdkitlvlgdvfel 61 
                                       ++++D+f+G G  +  +a+    ++v+a e+n++      +N +  gv+d + ++l+d  +l
  gi|474933789|ref|YP_007687371.1| 188 ETVVDMFAGIGYFTLPLAKFsgARRVFACEKNPDSYGFLVNNVRRNGVEDVVIPILADNRSL 249
                                       579***************9877789*******************************998774 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       2.9   7.4e+03      19      32 ..      62      75 ..      60      80 .. 0.82
   2 ?   10.3   0.0   0.00016      0.41      40      97 ..     185     243 ..     171     259 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.9
                                      XXXXSSSHHHHHHH CS
                     Cons_hypoth95 19 kstRPttdrvreal 32
                                      +s RP ++ +re l
  gi|474933789|ref|YP_007687371.1| 62 ESSRPPMEHIRECL 75
                                      67899999999976 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00016
                                       HCC-EEEETT-TTSHHHHH.HHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEE CS
                     Cons_hypoth95  40 iegarvLDlfaGsGalglE.AlSRgakkavlvekdkeavkilkenleelkleeetaelk 97 
                                        +g++v+D+faG G   l  A   ga+++ + ek++  +  l +n+++ ++e+ +  + 
  gi|474933789|ref|YP_007687371.1| 185 CRGETVVDMFAGIGYFTLPlAKFSGARRVFACEKNPDSYGFLVNNVRRNGVEDVVIPIL 243
                                       67899*********8877535567***********************999887554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2217.53
//
Query:       gi|474933790|ref|YP_007687372.1|  [L=502]
Description: hypothetical protein TALC_00198 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (502 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 3240.06
//
Query:       gi|474933791|ref|YP_007687373.1|  [L=311]
Description: ribose 1,5-bisphosphate isomerase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-83  278.6   0.5    5.6e-83  278.4   0.5    1.0  1  IF-2B     Initiation factor 2 subunit family
  ------ inclusion threshold ------
      0.042   12.2   0.1      0.046   12.1   0.1    1.1  1  ACD       Actin cross-linking domain


Domain annotation for each model (and alignments):
>> IF-2B  Initiation factor 2 subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  278.4   0.5   6.2e-87   5.6e-83       1     282 []      18     292 ..      18     292 .. 0.98

  Alignments for each domain:
  == domain 1  score: 278.4 bits;  conditional E-value: 6.2e-87
                                       SS-SHHHHHHHHHHHHHHHHHHCCCSTHHHHHHHHHHHHHHHHTSSTS-HHHHHHHHHHHHHHHCCTTTSSHHHHHH CS
                             IF-2B   1 kvrGspaiaiaalevllevikdaktskvaeLkeelrkaidlLkkarPtavslgnairrllkeiselksssdvkeakk 77 
                                       kvrG+ +ia+a++ +l+++++ ++ s+ + ++ ++ ka +++  +rPtavsl n ++   k    ++  +d ++a++
  gi|474933791|ref|YP_007687373.1|  18 KVRGAGRIARAGASALAQFAESYQGSDLERFRADIGKAERTILDSRPTAVSLWNGVNATVK---GVDRATDFESARQ 91 
                                       69********************************************************999...799********** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHTTC-TTEEEEEES--SHHHHHHHHHHHTTEEEEEEEEEXTTTTHHHTHHHHH CS
                             IF-2B  78 sliekikelikeieeadekigdiaaelikdgdtilTicnsktvlevlraaakekkkfkVivvEsrPrlqGrltakeL 154
                                       s+i++ + ++++ e+a  +i++i+a++ikdgd+i+T+cns+++++v+ +a++++k++kV+++EsrP  qG lt+  L
  gi|474933791|ref|YP_007687373.1|  92 SVIDNGRLFVEKSEKAVGVIAKIGAKRIKDGDVIMTHCNSSAAIGVIAEAVRQGKDIKVYATESRPWRQGILTVNDL 168
                                       ***************************************************************************** PP

                                       HHTTXEEEEEEGGGHHHHHHCTESEEEEEXSEEETTSEEEEETTHHHHHHHHHHTTXEEEEEXXGGGBESTSSSGGG CS
                             IF-2B 155 vqagipvtlitdsavayvmseevdkvivGAdrilenGaiankiGTsslAvlAkefnipvlvvaeslkfservqlded 231
                                       ++ag+++t+i+dsav++vm++ vd v+vGAd+i++ G+++nkiGTs++A++A+e+  ++ v+ e++kfs+++ +++ 
  gi|474933791|ref|YP_007687373.1| 169 AKAGVDTTMIIDSAVRTVMKR-VDRVFVGADTITSSGSLINKIGTSQVALCANEAGAEFNVCSETYKFSPKTLFGDS 244
                                       *********************.******************************************************* PP

                                       SSXXBEXTHHHHEETTEESSTTTEEEEEBSEEEEEGGGXSEEEETTEEEXC CS
                             IF-2B 232 ifieerdpeellnitgeriaeeelkvvnpafDvtPpelItliITevGvlpp 282
                                       + ieer+  e++   +  i +e++kv+np+fD tP+++I+ iITe+G++ p
  gi|474933791|ref|YP_007687373.1| 245 VTIEERNVSEVVKPGE--I-PESVKVFNPVFDRTPAKYIDNIITEIGIMSP 292
                                       ***********99988..4.67**************************987 PP

>> ACD  Actin cross-linking domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   5.1e-06     0.046     112     203 ..      80     171 ..      37     256 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.1e-06
                                       HHH.STTB-----B-TTSSEEEEES--S-EEEETTS-SSS------EEEEEEEEEEEEEEGGGTTT--SHHHHHHHT CS
                               ACD 112 idq.snhqsladlvsedgrftlvisnakhviaagngisadaqgktigmtpsgqqatvavsakefgtssspevrlles 187
                                       +d+ ++ +s  + v ++gr+ ++ s+    + a  g+ +  +g+ i mt     a+++v a +   +   +v   es
  gi|474933791|ref|YP_007687373.1|  80 VDRaTDFESARQSVIDNGRLFVEKSEKAVGVIAKIGAKRIKDGDVI-MTHCNSSAAIGVIAEAVRQGKDIKVYATES 155
                                       5541456677778899***999999888778888999999999877.9***************************** PP

                                       -TT--TTHHHHHHHHT CS
                               ACD 188 apwyqkelkdellsna 203
                                        pw q  l  + l++a
  gi|474933791|ref|YP_007687373.1| 156 RPWRQGILTVNDLAKA 171
                                       ****998865544443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1987.59
//
Query:       gi|474933792|ref|YP_007687374.1|  [L=412]
Description: Ribulose 1,5-bisphosphate carboxylase, large subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-72  244.4   2.3      5e-72  242.6   2.3    1.8  1  RuBisCO_large    Ribulose bisphosphate carboxylase large chai
    2.1e-23   82.7   0.1    1.2e-22   80.3   0.0    2.1  3  RuBisCO_large_N  Ribulose bisphosphate carboxylase large chai
  ------ inclusion threshold ------
       0.01   15.9   0.0      0.021   14.9   0.0    1.5  1  Glyco_transf_28  Glycosyltransferase family 28 N-terminal dom
       0.26   11.1   0.7        2.3    8.0   0.0    2.6  3  Nsp1_C           Nsp1-like C-terminal region


Domain annotation for each model (and alignments):
>> RuBisCO_large  Ribulose bisphosphate carboxylase large chain, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  242.6   2.3   1.1e-75     5e-72       5     299 .]     134     409 ..     132     409 .. 0.96

  Alignments for each domain:
  == domain 1  score: 242.6 bits;  conditional E-value: 1.1e-75
                                       HHHHH...T--EEEEE-SSSS---HHHHHHHHHHHHTT-.SEEE--TT-SSBTTB-HHHHHHHHHHHHHHHHHHHSS CS
                     RuBisCO_large   5 erevlnkegrpilGtiiKPklGLspknyarvvyelllgglDfiKdDEnlnsqpfarlkdrieavaeaikraqdetGe 81 
                                        re+l+  ++p++Gti+KPk+GLsp+++a+ +ye+ +ggl   KdDE l +q f++++ r +avae+++r ++  G+
  gi|474933792|ref|YP_007687374.1| 134 LREILGRPEKPLVGTIVKPKIGLSPEDTAKYIYEAGSGGLTNSKDDETLVDQKFCPIEARTKAVAEVLDRLEE-EGH 209
                                       6999*****************************************************************9876.5** PP

                                       --EEEEE---SSHHHHHHHHHHHHHHHGGEEEEEHHHH-HHHHHHHHHHSTTS..EEEEE-TTTHHHHST--SEE-H CS
                     RuBisCO_large  82 kklyalnitaddleemlrraefvketggeivlvdvlviGfaaitslrkafrknelllHlHraghgaltrqskhGisf 158
                                       k l+a+ni+ +  +++l+ ae v++ g++ +++dvl++G++ai+ +++  +k ++ +H+Hr +hga+t+++  Gis+
  gi|474933792|ref|YP_007687374.1| 210 KMLHAVNISTN-GQDILQLAEDVQSWGAKQIMIDVLTCGYGAIQAVAED-PKIKVPIHVHRTMHGAMTKDPFNGISM 284
                                       *********55.59***********************************.8889*********************** PP

                                       HHHHHHHHHHT-SEEE---TTSSSBS--GG......GHHHHHHHHSSEEE-SS-EEE-TT----EEEEESS--TTTH CS
                     RuBisCO_large 159 rvlakllRLlGvdhlhtgtvgvgklegdesvvkgfkdtlrekmleedeaegiffeqdlaslkavlpvasgGihagql 235
                                       rv++kl+R++G d lh+gt+gvgk+ g                  e +a+ +++++  +  k+v+pv sgG++ g +
  gi|474933792|ref|YP_007687374.1| 285 RVISKLVRMCGGDALHIGTLGVGKMAGGIG---------------EGRANQEACQSGDVPFKTVMPVCSGGMYPGIV 346
                                       **************************9887...............455677889999999***************** PP

                                       HHHHHHHS---SEEE-HHHHHTSTT-HHHHHHHHHHHHHHHHHT--HHHHHTT-HHHHHHHHHX CS
                     RuBisCO_large 236 pellenlgesdvilqaGGGilgHpdgaaaGakalrqaleaaveGadleeyAkehkeLarAlesw 299
                                       p+++++ g+ ++ +qaGGG+ gHp+g  +Ga a+ qa++a   G++l eyAk+hkeL++Ale w
  gi|474933792|ref|YP_007687374.1| 347 PAVMKAAGN-NIQIQAGGGVAGHPEGVRGGALAMCQAVDAGFLGVSLDEYAKDHKELREALERW 409
                                       *********.****************************************************99 PP

>> RuBisCO_large_N  Ribulose bisphosphate carboxylase large chain, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.3   0.0   2.7e-26   1.2e-22      12     119 ..      17     119 ..      11     120 .. 0.90
   2 ?   -2.1   0.0      0.95   4.3e+03      19      40 ..     149     170 ..     145     187 .. 0.80
   3 ?   -1.6   0.0      0.67     3e+03      66     103 ..     216     254 ..     190     262 .. 0.70

  Alignments for each domain:
  == domain 1  score: 80.3 bits;  conditional E-value: 2.7e-26
                   RuBisCO_large_N  12 tdllaafrvePaegvsveeaaaavAaeSStgtwtevsttkdellkklkakvyeieeveeekelvkiAYplelF..ee 86 
                                         ++  +rv+  +++ +e+aa+ +Aae Stgtwt +st +d++++k+ akv ei+       +v+iAYp e F  e 
  gi|474933792|ref|YP_007687374.1|  17 AYVVTKYRVS--TDLPMEKAAESIAAEQSTGTWTGISTLNDDVFTKYAAKVTEIDG-----DMVTIAYPEEDFsvEV 86 
                                       4567777776..799***************************************55.....79**********5556 PP

                   RuBisCO_large_N  87 gsipqllssiaGnifgmkavkalrleDirlPka 119
                                       g ipq+ls i Gn  g++++k +rleD+++P++
  gi|474933792|ref|YP_007687374.1|  87 GAIPQILSVISGNLYGLETLKGVRLEDVEFPSS 119
                                       6******************************85 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.95
                   RuBisCO_large_N  19 rvePaegvsveeaaaavAaeSS 40 
                                        v+P+ g+s+e++a+ +    S
  gi|474933792|ref|YP_007687374.1| 149 IVKPKIGLSPEDTAKYIYEAGS 170
                                       589999*****99998866555 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.67
                   RuBisCO_large_N  66 eeveeekelvkiAYplelFeeg.sipqllssiaGnifgm 103
                                       + +++++ +++ A +++ +  +  +  +l++  G i+ +
  gi|474933792|ref|YP_007687374.1| 216 NISTNGQDILQLAEDVQSWGAKqIMIDVLTCGYGAIQAV 254
                                       334458888888888888887635678888888888876 PP

>> Glyco_transf_28  Glycosyltransferase family 28 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   4.6e-06     0.021      54     117 ..     205     267 ..     180     270 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.6e-06
                                       --GHCTT..CHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHCCCCCHCCCTTHCCCC CS
                   Glyco_transf_28  54 ageklrrklspknlkeilkvlkavvkakkilkeakpdavvgtggyvslpaviaaplaripviih 117
                                       + e++++ l+  n+++  + + ++ +  +++  +++ ++v t+gy +++av + p+ ++p+++h
  gi|474933792|ref|YP_007687374.1| 205 EEEGHKM-LHAVNISTNGQDILQLAEDVQSWGAKQIMIDVLTCGYGAIQAVAEDPKIKVPIHVH 267
                                       3347777.78888888888888999999***********************************9 PP

>> Nsp1_C  Nsp1-like C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.24   1.1e+03      35      50 ..      55      70 ..      45      75 .. 0.78
   2 ?    8.0   0.0   0.00052       2.3      68     113 ..     175     220 ..     170     223 .. 0.87
   3 ?   -2.8   0.0       1.2   5.5e+03      84      96 ..     396     408 ..     390     411 .. 0.51

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.24
                            Nsp1_C 35 ekeFeeqakkvneWDr 50
                                       + F+++a+kv+e D 
  gi|474933792|ref|YP_007687374.1| 55 DDVFTKYAAKVTEIDG 70
                                      57899*****998775 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00052
                            Nsp1_C  68 eaeqeqnkidqeLeyiesqqdeLeslLdnyEkeleellsklesqks 113
                                       + + +++ +dq+   ie+  +   ++Ld++E+e +++l+ ++ + +
  gi|474933792|ref|YP_007687374.1| 175 NSKDDETLVDQKFCPIEARTKAVAEVLDRLEEEGHKMLHAVNISTN 220
                                       56889999****************************9988777665 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.2
                            Nsp1_C  84 esqqdeLeslLdn 96 
                                       +++++eL + L++
  gi|474933792|ref|YP_007687374.1| 396 AKDHKELREALER 408
                                       4455555555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 2949.20
//
Query:       gi|474933793|ref|YP_007687375.1|  [L=504]
Description: putative thymidine phosphorylase/AMP phosphorylase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.3e-15   54.2   0.0    2.2e-14   53.0   0.0    1.7  1  Glycos_trans_3N  Glycosyl transferase family, helical bundle 
    5.8e-14   52.3   0.1    2.9e-13   50.0   0.1    2.0  1  Glycos_transf_3  Glycosyl transferase family, a/b domain
    1.2e-11   44.1   0.1    3.7e-11   42.5   0.1    1.8  1  PYNP_C           Pyrimidine nucleoside phosphorylase C-termin
    1.7e-05   24.8   0.0      3e-05   24.0   0.0    1.3  1  Molydop_binding  Molydopterin dinucleotide binding domain
      0.001   18.8   0.2       0.02   14.7   0.1    2.6  2  Biotin_lipoyl_2  Biotin-lipoyl like
     0.0013   18.9   0.0     0.0038   17.4   0.0    1.8  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
  ------ inclusion threshold ------
      0.015   14.1   0.0      0.023   13.5   0.0    1.2  1  DUF2254          Predicted membrane protein (DUF2254)


Domain annotation for each model (and alignments):
>> Glycos_trans_3N  Glycosyl transferase family, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.0   8.6e-18   2.2e-14       4      63 .]      92     151 ..      89     151 .. 0.97

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 8.6e-18
                                       HHHHHTT.---HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH---HHHHHHHHHHHHHHS CS
                   Glycos_trans_3N   4 ikklrdgeeLtaeeirfaihgilkgevtdaqiaAfLmAlrlkGetaeEiaalaeAmresg 63 
                                       i++++dg  L+++ei +++++i  g+++ ++++A+L+Al+++G++ +Eiaa+a Am++ g
  gi|474933793|ref|YP_007687375.1|  92 IRRKMDGLVLDPAEISAVVKDIYGGNLSGIEVSAWLTALYINGMNIDEIAAFAVAMVDTG 151
                                       89*******************************************************976 PP

>> Glycos_transf_3  Glycosyl transferase family, a/b domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   0.1   1.1e-16   2.9e-13       3     253 .]     160     385 ..     158     385 .. 0.83

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 1.1e-16
                                       TBEEEEESS-SSSTHHHHHHHHHHHHHHTT-BEEEEE-STCTTCS-HHHHHCTST--ST--HHHHHHHHHHHSEEEE CS
                   Glycos_transf_3   3 dlvDivgTGGdgantfNiStaaaivvAaaGvkvakhgnrsvssksGsaDvLealgvnleltpeeveklleevgvgfl 79 
                                       ++ D ++ GG+  n   i+     +vAaaG+ ++k + r++ss +G++D +e + + +e++++++ ++ e+vg +f+
  gi|474933793|ref|YP_007687375.1| 160 PVFDFHSMGGVPGNK--ITPIVVSIVAAAGLMIPKTSSRAISSACGTSDFVELF-CPVEVDAQQLSEIGENVGGAFV 233
                                       67899******9999..99999999**************************966.99*******************9 PP

                                       EHHSS.SSHHHH.HHHHHHHHTT.-SSHHHCHHHHHT..SEEEEHHHHHHHHTCHSEEEEEEEESTTSSCCSTSHHH CS
                   Glycos_transf_3  80 fapey.hkamkh.vapvrrelgirTvfnlLGPLinparvkkqllgvyskelaeklaevlkelgveralvvhgdGlde 154
                                          ++  ++++  v+++   lg           inp    + l +++sk+la ++  +l +++++++  v++  lde
  gi|474933793|ref|YP_007687375.1| 234 WGGSMnIAPVDDiVIKIEHPLG-----------INP--RAQMLASIISKKLAIGAQYLLVDIPTGSGTKVKT--LDE 295
                                       7654403444331444444444...........588..5566789***************************..*** PP

                                       HHHHHHHHHHHHH.TTEEEEEEEEEGSSTSSSEEESHHHHSSHHHHHHHHTTHHTSCHHHHHHHHHHHHHHHHHHHT CS
                   Glycos_transf_3 155 vsllakttvaelk.dgeiteytlepedfglkraelealeggepkenaeilkavlegkksaakrdlvllnagaalvla 230
                                       +++ a   +   +  g   e +++ +d+++++a + ale    +e ++il++  e++ s      v+  a +   + 
  gi|474933793|ref|YP_007687375.1| 296 ARAYARDFMDLGDkLGIHIECAITYADQPIGSAVGPALEA---RECLRILEGY-EHPAS------VIEKACECAGIV 362
                                       **********999899999*******************99...8888888776.33333......444444444444 PP

                                       TSSSSHHHHHHHHHHHHHTSHHH CS
                   Glycos_transf_3 231 gkadslkegvakaeevidsGkAl 253
                                        ++    +gvaka+e+++sG+Al
  gi|474933793|ref|YP_007687375.1| 363 LEMGGFSNGVAKAHEILSSGAAL 385
                                       4456699**************95 PP

>> PYNP_C  Pyrimidine nucleoside phosphorylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   0.1   1.4e-14   3.7e-11       1      69 [.     422     483 ..     422     488 .. 0.95

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 1.4e-14
                                       EEEEE-HHHHHHHHHHTTTSBSSTTS---TT-EEEES--TT-EEBTTSEEEEEEESSSCHHHHHHHHHH CS
                            PYNP_C   1 yvseidareiGlaaveLGAGRakkeDpidlavGielhkklGdkVkkGeplatiYankeekleeavkklk 69 
                                       yv++id++e+  +a +LGA       p d+++G  l kk G++V++G++l+ ++a+++ kl++a + ++
  gi|474933793|ref|YP_007687375.1| 422 YVHSIDNKEVVAIAKALGA-------PTDKGAGMLLLKKKGQRVEQGDVLFQLFADNKTKLDRAKDLAE 483
                                       89*****************.......************************************9988775 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   1.2e-08     3e-05      29      82 ..      13      68 ..       2      89 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.2e-08
                                      S.-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESS.B-TTEEEEESSHCC CS
                   Molydop_binding 29 p.evveinpedAaalGikdGdlVevesrrGsvevrakvter.vrpGvvfmpfgwwe 82
                                      + +v+++ p dA + G+k++++ ++  ++ +v+v   ++e  + pG+v++p+g  +
  gi|474933793|ref|YP_007687375.1| 13 GaAVACLDPSDAMEIGVKENERMHIVGPKSEVTVFTILSEKlIEPGTVAVPSGIMK 68
                                      346999***********************************9**********9887 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.18   4.7e+02       4      16 ..     414     426 ..     412     430 .. 0.83
   2 !   14.7   0.1   7.8e-06      0.02      19      33 ..     453     467 ..     450     482 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.18
                   Biotin_lipoyl_2   4 sIaapvsGrVaql 16 
                                        Iaa++sG V+++
  gi|474933793|ref|YP_007687375.1| 414 DIAARQSGYVHSI 426
                                       79********988 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 7.8e-06
                   Biotin_lipoyl_2  19 kdGqrVkaGdvLael 33 
                                       k GqrV++GdvL++l
  gi|474933793|ref|YP_007687375.1| 453 KKGQRVEQGDVLFQL 467
                                       89************8 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.5e-06    0.0038       9      80 ..       9      80 ..       2      82 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.5e-06
                                      S-CSSTTEEEE-HHHHHHHTS-TTSEEEEEC.CCC.EEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEEE CS
                           CDC48_N  9 qedvgrgivridpedmeelglepgdvveieg.krk.TvaivwpaepedegkgiIrmdgvtRknagvsiGdkVtV 80
                                      + ++g  ++ +dp+d  e+g+++ + + i+g k + Tv  +++ +    ++g++++ + + k +g+s Gd  +V
  gi|474933793|ref|YP_007687375.1|  9 DALSGAAVACLDPSDAMEIGVKENERMHIVGpKSEvTVFTILSEKLI--EPGTVAVPSGIMKRIGASEGDILSV 80
                                      668999*************************9998888888888766..48*******************9888 PP

>> DUF2254  Predicted membrane protein (DUF2254)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   9.1e-06     0.023     187     246 ..     407     477 ..     374     489 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.1e-06
                           DUF2254 187 seeeeatpiraersGylqaidveaLvklae......ehdlvielevrpGdfvvkgeplakvwgee.....d 246
                                       +  + +  i a++sGy+ +id +++v++a+      ++++ + l ++ G+ v +g++l++++ ++     +
  gi|474933793|ref|YP_007687375.1| 407 PLGQFTADIAARQSGYVHSIDNKEVVAIAKalgaptDKGAGMLLLKKKGQRVEQGDVLFQLFADNktkldR 477
                                       4456678899*******************822222246778999***************999888544432 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (504 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 3193.38
//
Query:       gi|474933794|ref|YP_007687376.1|  [L=260]
Description: putative xylanase/chitin deacetylase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-16   60.3   0.0    8.6e-15   54.7   0.0    2.1  2  Polysacc_deac_1  Polysaccharide deacetylase
  ------ inclusion threshold ------
        0.2   10.8   0.0       0.26   10.4   0.0    1.1  1  Glyco_hydro_57   Glycosyl hydrolase family 57


Domain annotation for each model (and alignments):
>> Polysacc_deac_1  Polysaccharide deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.7   0.0   9.6e-19   8.6e-15      25     123 ..      41     137 ..      38     138 .. 0.94
   2 !    3.6   0.0    0.0066        59      46      94 ..     189     241 ..     168     250 .. 0.84

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 9.6e-19
                                       HHHHHHCT--EEEEE-HHHHCH-HHHHHHHHHTTEEEEE--SS--EGGGSHHHHHHHHHHHHHHHHHHHHS----EE CS
                   Polysacc_deac_1  25 lpvLkkykvkatffvigglvedypdevremaasGveignHtinhsnlkrlseeevrreierakdalrkalgreprlf 101
                                        ++L++ +++atff  g++ e+  d +     +G+eig H+++h+ l  + ++++   +e   +a+r+++gr+p+ f
  gi|474933794|ref|YP_007687376.1|  41 ADLLDEMGIPATFFCEGRTLEEMRDSAG--ILDGFEIGVHGYDHEFLPGMIRPDAISAVEHGCQAIRDVTGRNPTCF 115
                                       589*****************99977665..457******************************************** PP

                                       E-GGGEE-HHHHHHHHHTT.EE CS
                   Polysacc_deac_1 102 ryPygsasatvlevarelgfay 123
                                       r+Py ++ +++ + ++++g+++
  gi|474933794|ref|YP_007687376.1| 116 RAPYMKQPRDIADFLKNTGIRV 137
                                       ******************9986 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.0066
                                       H-HHHHHHHHHTT.EEEEE--SS--EG...GGSHHHHHHHHHHHHHHHHHHHH CS
                   Polysacc_deac_1  46 dypdevremaasG.veignHtinhsnl...krlseeevrreierakdalrkal 94 
                                       dy d++  + ++G + ++ H+++   l     lsee+v++ +e  ++al+ +l
  gi|474933794|ref|YP_007687376.1| 189 DYSDLAGCVPEEGcFVLADHSWHICELrerGVLSEEDVKENLELERRALQGIL 241
                                       5577777888999999******999887778899********99999999876 PP

>> Glyco_hydro_57  Glycosyl hydrolase family 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   2.9e-05      0.26     129     197 ..      70     137 ..      47     162 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 2.9e-05
                                       CTSEEEEEE-TT-B-GGG-S-HHHHHHHHHHHHHHHHHHHSS--SBEE-GGG-B--SHHHHHHHTT--E CS
                    Glyco_hydro_57 129 sgqvElltspyyHpllpllpdsedieaqvkkarelyeeyfgqePrgfwlpElavspeileilaelGfey 197
                                        +  E+ + +y H +lp + +  d ++ v+++ + +++  g++P+ f++p +    +i+ +l++ G+++
  gi|474933794|ref|YP_007687376.1|  70 LDGFEIGVHGYDHEFLPGMIR-PDAISAVEHGCQAIRDVTGRNPTCFRAPYMKQPRDIADFLKNTGIRV 137
                                       46679999***********99.99******************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1606.01
//
Query:       gi|474933795|ref|YP_007687377.1|  [L=294]
Description: methenyltetrahydrofolate cyclohydrolase/5,10-methylenetetrahydrofolate dehydrogenase (NADP+) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-67  226.4   4.8    1.7e-67  225.7   4.8    1.3  1  THF_DHG_CYH_C    Tetrahydrofolate dehydrogenase/cyclohydrolas
      3e-42  143.6   0.1      5e-42  142.9   0.1    1.4  1  THF_DHG_CYH      Tetrahydrofolate dehydrogenase/cyclohydrolas
  ------ inclusion threshold ------
       0.11   12.7   0.5        0.5   10.6   0.5    2.1  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma


Domain annotation for each model (and alignments):
>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.7   4.8   2.9e-71   1.7e-67       1     158 [.     123     290 ..     123     292 .. 0.98

  Alignments for each domain:
  == domain 1  score: 225.7 bits;  conditional E-value: 2.9e-71
                                       SHHHHHHHHTT--SS--HHHHHHHHHHHHCT---TT-EEEEE---TTTHHHHHHHHHCT....T-EEEEE-TTSCCH CS
                     THF_DHG_CYH_C   1 hplnlgrlvkgeeallpctpkgvvellketgielegkkvvvvGrsnivgkplallLlek....natVtvchsktkdl 73 
                                       hp+n+g+++ ge+ ++p+tp+gv ++l + +ie++gk+vvvvGrsnivgkp+a+++++k    ++tVtv++s+t++l
  gi|474933795|ref|YP_007687377.1| 123 HPFNVGKMLIGEPDFMPATPAGVQQMLIRRNIETKGKHVVVVGRSNIVGKPMAAIMMQKgkgaDSTVTVTNSRTENL 199
                                       899*****************************************************9977888************** PP

                                       HHHHCCSSEEEE-SS-TT-B-GGGS-TT-EEEE---EEC......-TTEEE-SB-HHHHCTTSSEE--TTTSCHHHH CS
                     THF_DHG_CYH_C  74 aeitreadivvvavGkpelikaemvkegavviDvGinrv......ekgklvGDvdfeevkevasaitPvpgGVGpmT 144
                                       aeitr+adi++va+Gkp++++a+mvkegavviDvG+nrv      ++++lvGDvdf++v+++as+itPvpgGVGpmT
  gi|474933795|ref|YP_007687377.1| 200 AEITRTADILIVAIGKPKFVTADMVKEGAVVIDVGTNRVddpaakNGSRLVGDVDFDAVEKKASYITPVPGGVGPMT 276
                                       *******************************************988999**************************** PP

                                       HHHHHHHHHHHHHC CS
                     THF_DHG_CYH_C 145 vamllkntleaakr 158
                                       + ml++n ++aa+r
  gi|474933795|ref|YP_007687377.1| 277 ICMLMANAVHAAER 290
                                       ***********997 PP

>> THF_DHG_CYH  Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.9   0.1   8.3e-46     5e-42       1     116 []       5     120 ..       5     120 .. 0.99

  Alignments for each domain:
  == domain 1  score: 142.9 bits;  conditional E-value: 8.3e-46
                                       E--HHHHHHHHHHHHHHHHHHHHHHT---EEEEEEES--HHHHHHHHHHHHHHHHTT-EEEEEEE-TT--HHHHHHH CS
                       THF_DHG_CYH   1 lldGkalakeireelkeeveklkekgvkpkLavilvgddpasevYvrnkkkaceevGieseliklpedvseeellkl 77 
                                       l+ Gk++++ei +el++++e+lk+kg+ p+Lav+lvg+dpas+vYvr+k k+cee+G++s +i +pe++++e ll++
  gi|474933795|ref|YP_007687377.1|   5 LILGKEVSEEIYAELRQRIEALKSKGIMPGLAVVLVGEDPASQVYVRMKGKKCEELGMHSVTIVMPESTTQEGLLAK 81 
                                       588************************************************************************** PP

                                       HHHHHH-TT--EEEE-SS-STTS-HHHHHCCS-GGGBTT CS
                       THF_DHG_CYH  78 ieelneddsvdGilvqlPlpkhidekaileaispeKDVD 116
                                       + eln+d+s+dG lvqlPlpkhide+ai++ai+p+KDVD
  gi|474933795|ref|YP_007687377.1|  82 VAELNADKSIDGFLVQLPLPKHIDENAIINAIDPAKDVD 120
                                       **************************************9 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.51     3e+03      88     119 ..      56      86 ..      54      93 .. 0.68
   2 ?   10.6   0.5   8.4e-05       0.5       1      83 [.     161     240 ..     150     245 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.51
                                       HHHHHT-EEEESS-BCGCCSCHCCSHHHHHTH CS
                   Sacchrp_dh_NADP  88 aCietgvhyvdtsiskeertnyalreavlklk 119
                                        C e g+h v++++ +e+ t   l  +v +l+
  gi|474933795|ref|YP_007687377.1|  56 KCEELGMHSVTIVM-PESTTQEGLLAKVAELN 86 
                                       58899999999888.66555555555555554 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 8.4e-05
                                       EEEE--.SHHHHHHHHHHHCTCCT-G.EEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE CS
                   Sacchrp_dh_NADP   1 vliiGa.GsvGqavaellarhfdvda.eitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvn 75 
                                       v+++G    vG+++a  + ++++  + ++tv     e+l+++       ++++  + + +++ v+a ++keg +v++
  gi|474933795|ref|YP_007687377.1| 161 VVVVGRsNIVGKPMAAIMMQKGKGADsTVTVTNSRTENLAEITR-----TADILIVAIGKPKFVTADMVKEGAVVID 232
                                       5677776679******9999998766899999999999888874.....5788899999999999************ PP

                                       -SSGGGHH CS
                   Sacchrp_dh_NADP  76 lsppissl 83 
                                       + ++  + 
  gi|474933795|ref|YP_007687377.1| 233 VGTNRVDD 240
                                       *9987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1829.55
//
Query:       gi|474933796|ref|YP_007687378.1|  [L=216]
Description: RNA:NAD 2'-phosphotransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.9e-19   69.1   0.0    6.5e-19   68.7   0.0    1.0  1  PTS_2-RNA    RNA 2'-phosphotransferase, Tpt1 / KptA family
     0.0052   17.4   0.1      0.009   16.7   0.1    1.4  1  Zn_ribbon_2  Putative zinc ribbon domain


Domain annotation for each model (and alignments):
>> PTS_2-RNA  RNA 2'-phosphotransferase, Tpt1 / KptA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.7   0.0   7.2e-23   6.5e-19       4     179 ..      33     196 ..      31     197 .. 0.85

  Alignments for each domain:
  == domain 1  score: 68.7 bits;  conditional E-value: 7.2e-23
                         PTS_2-RNA   4 vqlskaLsyiLRhgaekegLkiredGyvkvedlLelpklkslk...vtleeikevVesndKqRFelveleelliran 77 
                                       ++l+++L+ +LRhg+    L+++++G+v+++d+++  k ++ +   +  ++i+++  +++K R++   +++  ira+
  gi|474933796|ref|YP_007687378.1|  33 EKLGRTLAAVLRHGK--YDLEMDPQGFVDMRDIISIVKENNPRmkwLRSRHIEALALTDPKGRYQ---IRGHNIRAT 104
                                       5799*********95..789*************99543333223348899***************...55567**** PP

                         PTS_2-RNA  78 qghsikkvesselllepiesaeelpevvvHgTylkawesilasggLkrmsrnhihlatglpgekevisgmrk.saev 153
                                        gh+ik        l+    ++ +p+ +++  + ++ + i+ ++g+++  r  +hl+++    ++v  g  + +  +
  gi|474933796|ref|YP_007687378.1| 105 YGHTIKL------DLQL--PTDRVPAYLYYPVSEEEGDIIM-ETGIRPTDRAMVHLSATYR--DAVNAGRAHlDDPL 170
                                       ****742......2444..33568*****************.99**************876..5799998887888* PP

                         PTS_2-RNA 154 liyidvekaladgikfyvsengviLt 179
                                       ++ +d+e+++++g ++ +++  v+L+
  gi|474933796|ref|YP_007687378.1| 171 ILEVDTEACAEAGHPIGRAAKTVYLC 196
                                       ***********************998 PP

>> Zn_ribbon_2  Putative zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1     1e-06     0.009      18      57 ..       6      45 ..       3      75 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1e-06
                       Zn_ribbon_2 18 eadgsksedYCkyCykdGeftepdltmeemiekcvkklae 57
                                      e++g   +dYC  C ++G+f+  d+++e++ + ++  l++
  gi|474933796|ref|YP_007687378.1|  6 EQHGYYRDDYCPVCGEKGKFVMSDFEVEKLGRTLAAVLRH 45
                                      67888999********************998888776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1432.12
//
Query:       gi|474933797|ref|YP_007687379.1|  [L=316]
Description: protein of unknown function (DUF1743) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-09   35.8   3.3    1.9e-06   27.9   0.3    3.4  2  DUF1743   Domain of unknown function (DUF1743)


Domain annotation for each model (and alignments):
>> DUF1743  Domain of unknown function (DUF1743)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.3   1.1e-10   1.9e-06       1     114 [.     165     253 ..     165     255 .. 0.87
   2 ?    1.4   0.2     0.018   3.3e+02       3      13 ..     291     301 ..     290     307 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.1e-10
                                       TTHHHHHHHHHH-..-TT..S-EEEEEEEE-GGGTT---EEHHHHHHHHHHHTTCECTSEBTTTTCECCS-STTSS. CS
                           DUF1743   1 grgiiGAtaalganiale..dstyEllaYreperwgerevdeesvieadektypetfdnvDlshklvvlvPhtpdp. 74 
                                       +++++GAt+a ++ +a++    ++                                     ++hkl++l+P++p++ 
  gi|474933797|ref|YP_007687379.1| 165 DTKEKGATWATALAMARDcpIGKF-------------------------------------MEHKLIQLNPKAPNKt 204
                                       567777777777777776544555.....................................89************** PP

                                       .......EEEEEEES-HHHHHHHHHCSEE..S-EEC..EEEEEESTTS- CS
                           DUF1743  75 .......vlfGirgedpeallkaakeilskeeesee..mavfrtnqgtd 114
                                              v f+++++d  al+++++ + ++++ se+  m+vf++++ ++
  gi|474933797|ref|YP_007687379.1| 205 tncvasaVSFAVKEKDIPALIEFCHGYIKEHSYSEDavMTVFQGLEIPK 253
                                       *******************************************998876 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.018
                                       HHHHHHHHHH- CS
                           DUF1743   3 giiGAtaalga 13 
                                       giiGA+aa+g+
  gi|474933797|ref|YP_007687379.1| 291 GIIGAVAAIGC 301
                                       89*******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2416.18
//
Query:       gi|474933798|ref|YP_007687380.1|  [L=260]
Description: Undecaprenyl pyrophosphate synthetase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-80  269.2   0.0    2.9e-80  269.0   0.0    1.0  1  Prenyltransf  Putative undecaprenyl diphosphate synthase


Domain annotation for each model (and alignments):
>> Prenyltransf  Putative undecaprenyl diphosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  269.0   0.0   1.6e-84   2.9e-80       1     224 []      36     259 ..      36     259 .. 0.94

  Alignments for each domain:
  == domain 1  score: 269.0 bits;  conditional E-value: 1.6e-84
                                       EE--HHHHHHHTT.S-HHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEEGGGGGS-HHHHHHHHHHHHHHHHHHH.H CS
                      Prenyltransf   1 imDGNrRwAkkrgleereeGhkaGaealkeilelclelgvkvvtvYafSteNfkRskeevdalmellkeellkee.l 76 
                                       imDGNrR+Ak+    +  eGh+ G +++++++++c +lg+++vtv+afS+eNfkR++eevd+lm+l+++++l     
  gi|474933798|ref|YP_007687380.1|  36 IMDGNRRYAKEFLGDNIDEGHELGEKKIEDVIDWCFDLGIRYVTVFAFSSENFKRDAEEVDFLMDLAENSFLMMAdN 112
                                       9**********9999****************************************************9665544326 PP

                                       HHHHHTTEEEEEESSGGGS-HHHHHHHHHHHHHHT.TTTSEEEEEEEEE-HHHHHHHHHHHHHHTT..SSSG.GGHS CS
                      Prenyltransf  77 kellkegvrvrviGdlellpedvlealekaeeatkknnkklvlniavnYgsrdeiveavrelvkekseekkk.eeid 152
                                        +++ ++vr+r+iG++++lpe+v++a++ a e+t++ ++ +v+ ++++Yg+r+eiv+avre++k+ ++ + + ++id
  gi|474933798|ref|YP_007687380.1| 113 PKIHANKVRIRAIGQIDKLPENVRKAIAYADERTSSYSD-FVVSVCIAYGGRQEIVAAVREIAKKIQNGEIQpDDID 188
                                       7999*******************************6666.**********************999987776657889 PP

                                       HHHHHCTSTT..TSSS-SEEEEESS--S-TTSSTTTTTT-EEEEESSSGGG--HHHHHHHHHHHHHCHHHTT CS
                      Prenyltransf 153 eetlekhlytakalpdpDlliRtsGeeRlSnFllwqlayselyfldvlWPdfskedllealleyqkrerrfg 224
                                       ee+l+ h+yt+ ++pdpDl++RtsGe R+SnFllwqlayselyf+dv+WP f++ dll+a+++yq+r rr+g
  gi|474933798|ref|YP_007687380.1| 189 EEMLSLHMYTS-DIPDPDLILRTSGEVRVSNFLLWQLAYSELYFTDVYWPGFRRIDLLRAIRTYQQRVRRYG 259
                                       *********94.46********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1620.83
//
Query:       gi|474933799|ref|YP_007687381.1|  [L=577]
Description: Fe-S oxidoreductase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.5e-10   40.0   0.0    6.7e-10   39.1   0.0    1.4  1  B12-binding  B12 binding domain
    8.4e-09   36.0   0.0    3.3e-08   34.1   0.0    1.9  2  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.0   7.5e-14   6.7e-10       9     115 ..      36     146 ..      29     150 .. 0.87

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 7.5e-14
                       B12-binding   9 ggdlhplGlavlaaalrdagfeVqllganven.....edivaairaekpdvvglSalltsqleavkelvellkrirp 80 
                                        ++++p+G++ + a+l +agf+ +++++   +      d +++ir +++ v ++ +++  +  ++ el++ +k+++p
  gi|474933799|ref|YP_007687381.1|  36 VFEMYPIGFMTISAHLMAAGFRARIVNIANLMlssekFDAEKKIRGLDATVFAIDLHWMPHAHGAIELAKIVKKYHP 112
                                       5789*****************666654444444444488899*********************************** PP

                       B12-binding  81 rvkvvvGGahpsldpeetleaklgiddvvvgeged 115
                                       ++kv +GG   s+ ++e+++  ++id v++g+ ++
  gi|474933799|ref|YP_007687381.1| 113 DAKVEFGGFTSSYFYDELIRR-PEIDLVMRGDTTE 146
                                       *****************9998.*****99998765 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.31   2.8e+03      91     131 ..     101     140 ..      70     142 .. 0.71
   2 !   34.1   0.0   3.7e-12   3.3e-08       3     164 ..     228     393 ..     226     394 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.31
                                       HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHHHHHH CS
                                       xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  91 eeklerllelg.vdrvslgleaaddekvlklmnrghtfeevl 131
                                        e ++  ++++    v++g  + +++ + +l+ r+++++ v+
  gi|474933799|ref|YP_007687381.1| 101 IELAKIVKKYHpDAKVEFGGFTSSYF-YDELI-RRPEIDLVM 140
                                       67777788888777788888888888.88888.667777666 PP

  == domain 2  score: 34.1 bits;  conditional E-value: 3.7e-12
                                       EESEESS--TTTSCCTT....HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCC CS
                                       xxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpet....vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklav 75 
                                       ++rgC+ +C  C  ++     v  + r++++s+e+++e ++ + ++  +  ++++g+   +  d+ + l+++a++  
  gi|474933799|ref|YP_007687381.1| 228 TVRGCSVNCAECGGSHYanrkVVCRSRPAFRSPEKLVEDMEGI-QDYMKAPIFIVGDIRQAGQDYCDRLLKAARE-- 301
                                       689******************999*******************.6665999999999999999999999999999.. PP

                                       CTEEEEEEECSSCHG.HHHHHHHHHTT..-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET.EEEE CS
                                       xxxxxxxxxxxxxxx.xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                       Radical_SAM  76 pgiritvetngtlpd.eeklerllelg..vdrvslgleaaddekvlklmnrghtfeevlealeklreagikr.vvdr 148
                                       +gir++v++  +     e+  +++ +      ++++ +++d+  v+  +++g+t++++ +++ ++  +g+ r   ++
  gi|474933799|ref|YP_007687381.1| 302 SGIRNHVVIELFNGAgGEHFSKIDHAFqgGWSIEFSPDSYDEI-VRLALGKGYTNDAIDKTIPAAFGNGCSRlDLFF 377
                                       8************99*9******9998989************9.9****9**********************999** PP

                                       EEEBTTTSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxx RF
                       Radical_SAM 149 ivglpGendeeleell 164
                                       ++glp +++e   +++
  gi|474933799|ref|YP_007687381.1| 378 MTGLPKQTRESALDTA 393
                                       **********988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (577 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.24s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 3732.22
//
Query:       gi|474933800|ref|YP_007687382.1|  [L=280]
Description: pyrroline-5-carboxylate reductase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-33  114.6   0.8    4.2e-33  113.7   0.8    1.5  1  P5CR_dimer       Pyrroline-5-carboxylate reductase dimerisati
    1.7e-16   60.6   1.0    2.8e-16   59.9   0.1    1.8  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
      0.014   15.5   0.1       0.12   12.5   0.0    2.3  2  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
      0.029   14.6   0.0      0.049   13.9   0.0    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.038   14.8   0.0      0.063   14.1   0.0    1.4  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
      0.075   13.7   1.0       0.37   11.5   0.3    2.4  2  D-ser_dehydrat   Putative serine dehydratase domain


Domain annotation for each model (and alignments):
>> P5CR_dimer  Pyrroline-5-carboxylate reductase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.7   0.8   1.4e-36   4.2e-33       1     103 []     173     277 ..     173     277 .. 0.98

  Alignments for each domain:
  == domain 1  score: 113.7 bits;  conditional E-value: 1.4e-36
                                       CCHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHCHS..HHHHHHHH--TTSHHHH CS
                        P5CR_dimer   1 EkqldavtalsGsgpAyvflliealadagvklGlsreeArelaaqtvaGaaklllese..paelrdkvtspgGtTia 75 
                                       E++ldavt+++Gs+pA++++++  l++ag+k Gl++e++ +laaq+++Ga++++les+   + l+d v+spgGtTi+
  gi|474933800|ref|YP_007687382.1| 173 EQDLDAVTGIAGSSPAFIYMMARGLVEAGMKYGLTEEQSVKLAAQSLIGAGHMVLESGmgLDALIDGVCSPGGTTIE 249
                                       899***************************************************988889***************** PP

                                       HHHHHHHTTHHHHHHHHHHHHHHHHHHH CS
                        P5CR_dimer  76 glkeleegglraavieaveaaakrskel 103
                                       g k+le++g++++v ++v+a+++rs e+
  gi|474933800|ref|YP_007687382.1| 250 GCKVLEQEGFEGTVVRCVDATVARSVEM 277
                                       *************************997 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.9   0.1   9.2e-20   2.8e-16       1      97 []      16     111 ..      16     111 .. 0.98
   2 ?   -2.3   0.1       2.2   6.7e+03      15      23 ..     194     202 ..     191     225 .. 0.46

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 9.2e-20
                                       EEEEETTSHHHHHHHHHHHHTTS.-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHH CS
                     F420_oxidored   1 kigiiGaGnmgealasgllaaga.qpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedvee 76 
                                       +ig+iGaG+m+ a++ gl+a+ + +  eiv a+ +++++++ + ++ g+kv + ++++ a  ad++vla+kp++++ 
  gi|474933800|ref|YP_007687382.1|  16 RIGFIGAGRMAGAMIDGLIAKKVySRDEIV-ACAPTESSRQRMSQKSGIKVYE-KASDIAPLADIIVLACKPKNIAP 90 
                                       79*********************9999999.**********************.*********************** PP

                                       HHHHCGHHHHTTSEEEEESSS CS
                     F420_oxidored  77 vlselakdalkgklvisvlag 97 
                                       + +e    + +++l+is++ag
  gi|474933800|ref|YP_007687382.1|  91 LFNEEGLVLGSNHLLISIAAG 111
                                       *****9999*********997 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.2
                                       HHHHHHTTS CS
                     F420_oxidored  15 asgllaaga 23 
                                       a+gl++ag+
  gi|474933800|ref|YP_007687382.1| 194 ARGLVEAGM 202
                                       445555552 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     4e-05      0.12       1      63 [.      16      83 ..      16     101 .. 0.81
   2 ?   -0.2   0.0      0.34     1e+03     129     153 ..     145     169 ..     139     172 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4e-05
                                      EEEEE--SHHHHHHHHHH....HHTT-EEEEE-SSHHHHHHHHHT.TEEE-SSHHHHHHHCSEEEE-S CS
                     NAD_binding_2  1 kigfiGlGvMGsnmalnl....lkagykvavynrtkekveelvae.gakaaesieelvasldvvitmv 63
                                      +igfiG G M   m+  l    + +  ++++   t+++ +++ ++ g+k++e++++++  +d++++  
  gi|474933800|ref|YP_007687382.1| 16 RIGFIGAGRMAGAMIDGLiakkVYSRDEIVACAPTESSRQRMSQKsGIKVYEKASDIAPLADIIVLAC 83
                                      59**********99999843333345678888888888888877736**************9999865 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.34
                                       EEEEEE-HHHHHHHHHHHHHHEEEE CS
                     NAD_binding_2 129 simvGGseeafervkpvleaigakv 153
                                        + +G+see+ ++v  ++ aig +v
  gi|474933800|ref|YP_007687382.1| 145 VMGPGCSEEDRKTVDTIMAAIGLSV 169
                                       45589**************999765 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.6e-05     0.049       1      68 [.      17      84 ..      17      89 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.6e-05
                                      EEEE--SHHHHHHHHHHHCTCCT-G.EEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHT CS
                   Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvda.eitvadrskeklealaakalgvrfeaialdaenyeavLaallk 68
                                      + +iGaG+++ a+++ l +++ +++ ei+ + +++++ +++ +k +g+++  +a d++  +++++ ++k
  gi|474933800|ref|YP_007687382.1| 17 IGFIGAGRMAGAMIDGLIAKKVYSRdEIVACAPTESSRQRMSQK-SGIKVYEKASDIAPLADIIVLACK 84
                                      678********************999***********9999865.999999999998888877666665 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.1e-05     0.063       1      73 [.      15      86 ..      15     114 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.1e-05
                                      EEEEEETTSHHHHHHHHHHHHTTTTE...EEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GG CS
                      GFO_IDH_MocA  1 lrvaiiGaGkigskhlrplnesqrle...evvalldpdaeraeavaesfgveaysdleelladpeidavivatpng 73
                                      +r+++iGaG+++   +  l ++ + +   e+v ++ p +++ ++++++ g+++y++ ++++    +d+++ a+ ++
  gi|474933800|ref|YP_007687382.1| 15 VRIGFIGAGRMAGAMIDGLIAK-KVYsrdEIV-ACAPTESSRQRMSQKSGIKVYEKASDIAP--LADIIVLACKPK 86
                                      599********88888666666.554575777.5667777777789**************99..999999999884 PP

>> D-ser_dehydrat  Putative serine dehydratase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.3   0.00012      0.37      74      94 ..     125     145 ..      15     146 .. 0.67
   2 ?   -2.3   0.0       2.4   7.2e+03      16      26 ..     217     227 ..     194     265 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                                       -EEEEE-S-HHHHHTT-SEEE CS
                    D-ser_dehydrat  74 dvvrlipnHaCptvnlhdayv 94 
                                        +vr++pnH+C++ ++   yv
  gi|474933800|ref|YP_007687382.1| 125 RIVRVMPNHCCMVLEGAAGYV 145
                                       456*********998776665 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.4
                                       TEEES--HHHH CS
                    D-ser_dehydrat  16 ralvdaGskal 26 
                                       + l+ aG++ l
  gi|474933800|ref|YP_007687382.1| 217 QSLIGAGHMVL 227
                                       33444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1781.98
//
Query:       gi|474933801|ref|YP_007687383.1|  [L=95]
Description: NADH:ubiquinone oxidoreductase subunit 3 (chain A) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      1e-25   89.7   1.2    1.1e-25   89.6   1.2    1.0  1  Oxidored_q4  NADH-ubiquinone/plastoquinone oxidoreductase, ch
  ------ inclusion threshold ------
        1.4    9.1   7.3       0.34   11.1   4.2    1.6  1  MPS-4        MinK-related peptide, potassium channel accessor


Domain annotation for each model (and alignments):
>> Oxidored_q4  NADH-ubiquinone/plastoquinone oxidoreductase, chain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.6   1.2   1.2e-29   1.1e-25       7      95 ..       2      90 ..       1      94 [. 0.96

  Alignments for each domain:
  == domain 1  score: 89.6 bits;  conditional E-value: 1.2e-29
                                      HHCHSS-----HHHHS-SSSS--SS---.--HHCHHHHHHHHHHHHHHHHHHHHHHHHSST..HHHHHHHHHHHHHHHH CS
                       Oxidored_q4  7 lsallgpkkpnkeklspYEcGfepvgearlrfsvkfylvallFliFDvevvflfpwavslkelglfgliemllFllill 85
                                      +s+ll+p+kp+k ++++YEcG  p+g++r++f++++y +al+F++FD+ ++fl+ wav+++ l+  ++i mllFl+i+l
  gi|474933801|ref|YP_007687383.1|  2 FSRLLRPEKPSKWTEETYECGSVPIGDTRIQFRFQYYAFALIFVVFDLITTFLLIWAVAFDGLSRDATIWMLLFLGIML 80
                                      789**********************************************************999999************ PP

                                      HHHHHHHHH- CS
                       Oxidored_q4 86 vglvYewkkg 95
                                      +g+ Y++kk+
  gi|474933801|ref|YP_007687383.1| 81 FGVTYALKKE 90
                                      *******997 PP

>> MPS-4  MinK-related peptide, potassium channel accessory sub-unit protein 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   4.2   3.7e-05      0.34      33      64 ..      29      58 ..      23      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.7e-05
                             MPS-4 33 nrisystkyfdfllvviisvvslglvylllwi 64
                                       ri +  +y+ f l+ +  v+ l   +ll+w+
  gi|474933801|ref|YP_007687383.1| 29 TRIQFRFQYYAFALIFV--VFDLITTFLLIWA 58
                                      59**********99865..79999*******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       821  (0.0457917); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 586.48
//
Query:       gi|474933802|ref|YP_007687384.1|  [L=186]
Description: NADH-quinone oxidoreductase, B subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.1e-22   77.6   0.0    9.2e-22   77.3   0.0    1.1  1  Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit


Domain annotation for each model (and alignments):
>> Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.3   0.0   5.1e-26   9.2e-22       3     129 ..      60     167 ..      59     169 .. 0.91

  Alignments for each domain:
  == domain 1  score: 77.3 bits;  conditional E-value: 5.1e-26
                                       HHHHHHT-TTTTHHHHHHTEEEEEETTT-S--HHHHHHTHTTTSEEEEEESBE...EEEHHHHHHHHGGGSSEEEEE CS
                       Oxidored_q6   3 GcsisllaleedlldllelielryhetlladskeeeieakekeadvlvveGavtrkpkealellkelaekakaviav 79 
                                       +c +++++++ + +d+     +ry++   ++++         + d+l+v+G +++k ++++++l+e ++ +k+ +a+
  gi|474933802|ref|YP_007687384.1|  60 CCALEMAQASAPRFDA-----ERYGMIYRSSPR---------QTDILLVNGWISKKIRPDIRRLWEEMPGPKWAVAM 122
                                       4999999999999999.....999999999999.........9********************************** PP

                                       SHHHHH-TGGGSTT-TEE-HHHHHHHC.S-E.EEE-SSS--HHHHHHHHH CS
                       Oxidored_q6  80 GtCAafGGipaaannpsvgeevgellevvpvdinipGCPphpeailetll 129
                                       G+CA++GG +  ++  s+   v++l++ +pvd++ipGCP++p+a++++++
  gi|474933802|ref|YP_007687384.1| 123 GECAISGGPW--YD--SYN-TVQGLDQIIPVDLYIPGCPARPDAMIDGFM 167
                                       **********..66..333.468**********************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1254.52
//
Query:       gi|474933803|ref|YP_007687385.1|  [L=161]
Description: NADH:ubiquinone oxidoreductase 27 kD subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-34  119.1   0.1    2.2e-34  118.7   0.1    1.1  1  Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd s


Domain annotation for each model (and alignments):
>> Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.7   0.1   1.3e-38   2.2e-34       3     120 ..      43     159 ..      41     160 .. 0.92

  Alignments for each domain:
  == domain 1  score: 118.7 bits;  conditional E-value: 1.3e-38
                                       --HHHHHHHHHHHHH...TT--EEEEEEEEETTSSSEEEEEEEE--S-...-EEEEEE....-S-BEE--TTT-STH CS
                    Complex1_30kDa   3 vepedllevakflkdeeelgfdvlsdltavDekeerfevvyhllslekn..erirvkvevdeeepevpSvtdlfpga 77 
                                        ++e+l++++ fl+d  el+f++++++ +vD   + ++vvyh+l++++     + + v+v++++ +v+Sv+d++ g 
  gi|474933803|ref|YP_007687385.1|  43 AQREALHDICLFLHD--ELNFEHCATVIGVDM-VDYMQVVYHILNYTNYrgTMVEITVDVPNDDLHVQSVSDIWGGS 116
                                       6899***********..59************7.699**********65545667777777999************** PP

                                       HHHHHHHHHHSHHBCTTSSTSS-SSSSTTSSS-TTSTTS---- CS
                    Complex1_30kDa  78 dwyEREayDmfGivfeghpdlrrillpedfeghPLRkdfplsg 120
                                       +w+ERE +++fGivf+ghp l+r+l+p+++e +P+Rk+++l+g
  gi|474933803|ref|YP_007687385.1| 117 NWHEREQWELFGIVFDGHPRLERLLTPKTYEFFPFRKSYKLRG 159
                                       ***************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1066.58
//
Query:       gi|474933804|ref|YP_007687386.1|  [L=428]
Description: NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      5e-83  278.3   1.4    1.5e-80  270.2   1.4    2.2  1  Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd s
      5e-05   22.4   0.0     0.0001   21.4   0.0    1.4  2  NiFeSe_Hases    Nickel-dependent hydrogenase


Domain annotation for each model (and alignments):
>> Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  270.2   1.4   1.6e-84   1.5e-80       1     271 []     181     428 .]     181     428 .] 0.96

  Alignments for each domain:
  == domain 1  score: 270.2 bits;  conditional E-value: 1.6e-84
                                       HTT-HHHHHHHHHHHHHHHHHHHHHHSSSSS-TTBESSBBSS---TTHHHHHHHHHHHHHHHHHHHHHHHHSSSSHH CS
                    Complex1_49kDa   1 DlGaltvflyafreRekildlleevtGaRltasyiriGGvarDlpegllekikeflkelekkldeleklltknrifk 77 
                                       DlG +t fl+a reRe ++d+  +++GaR+t++y riGGv++D pe + ++i +++++++k + e+  l+++n++f+
  gi|474933804|ref|YP_007687386.1| 181 DLGNFTAFLWASREREFWMDMNIRLCGARMTTNYPRIGGVRNDTPEIFDRDIIRLCDRFDKMVWEIFGLIDDNSTFT 257
                                       99*************************************************************************** PP

                                       HHHSSSS-BSHHHHHHHTT-SSSSGGGT-TTTHHHHSS-SSGGGS-------SSBSHHHHHHHHHHHHHHHHHHHHH CS
                    Complex1_49kDa  78 kRtkgvgvlskeealelgltGpvlRasGvkyDlRkaepYeaYdeldfdvpvgeegDvydRylvrveEmrqSlkIieq 154
                                       +R+ g g++++e++ +lg+tGp +R++G+++D+R+++pY+ Yd++dfdvpv+++gD+y+Rylvr eEm qS+kIi+q
  gi|474933804|ref|YP_007687386.1| 258 SRMIGTGIITREQCANLGITGPAARGTGIDFDIRRDDPYDNYDKMDFDVPVSTAGDSYARYLVRNEEMLQSTKIIRQ 334
                                       ***************************************************************************** PP

                                       HHHT--.S-SB---TTTS---GGGGGT-HHHHHHHHHHHHS-----SEEEEEEEEETTEEEEEEEEEESSSS-SEEE CS
                    Complex1_49kDa 155 aleklpegpvlaedkkvalpkkeevkksmealihhfklvtegfkvpkgevyaavEapkGelgvylvsdgsskpyrlk 231
                                       a+ kl+   ++ +d+ +          +++a           +++p+g  ++++E p+Ge  +ylvsdg++kpyrlk
  gi|474933804|ref|YP_007687386.1| 335 AMAKLR---TMGKDEPY----------RIKA----------PMNIPAGRHFMHMEDPRGESLMYLVSDGTDKPYRLK 388
                                       *****8...34444333..........2222..........3469******************************** PP

                                       EE-HHHHTTTTHHHHTTTS-SGGGTHHHHTT---HHHHH- CS
                    Complex1_49kDa 232 irapsfvnlqaleellkgellaDvvailgsldivlgevDR 271
                                       +r+p fvn+++ ++ll+g+++aD+++i++ +d++lge+DR
  gi|474933804|ref|YP_007687386.1| 389 VRSPIFVNVSSSKSLLQGCRIADIPVIMAMIDMCLGETDR 428
                                       ***************************************9 PP

>> NiFeSe_Hases  Nickel-dependent hydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.2e-08    0.0001       1      70 [.     106     175 ..     106     182 .. 0.96
   2 ?   -3.0   0.0      0.28   2.5e+03     370     433 ..     309     370 ..     299     377 .. 0.49

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.2e-08
                                       --HHHHTTTS-GGGHHHHHHTT-SSSTTHHHHHHHHHHHHHHT----HHHHHHHHHHHHHHHHHHHHHHH CS
                      NiFeSe_Hases   1 RGlElilkgrdprdawalvqRiCGVCttvHalasvravedAlgikipknarlirnliaaalllhdhivhF 70 
                                       RG+E+  ++r       +++R C    ++ ++   ++ e+Alg+++p++a++ir +    + l++h++++
  gi|474933804|ref|YP_007687386.1| 106 RGWEKETENRSYPKIIPMADRLCYAASMTYTHLFCMTCEKALGLEVPEKAKYIRIVADEINRLQSHLMWL 175
                                       9*************************999999999********************************985 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.28
                                       SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTB---B--TT-SGGGS-SEEEEEEEEEETTE CS
                      NiFeSe_Hases 370 stlGRtaaRaleakliaellkewldelvenikkgdtetaneekldkkevpkeakGvglveapRG 433
                                       st G   aR l  +  + + ++ +++ +++++++ ++   +   ++ ++p+  + +  +e pRG
  gi|474933804|ref|YP_007687386.1| 309 STAGDSYARYLVRNEEMLQSTKIIRQAMAKLRTMGKDEPYRI-KAPMNIPA-GRHFMHMEDPRG 370
                                       555555555544433333333333333333333322222222.24456666.667777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2860.65
//
Query:       gi|474933805|ref|YP_007687387.1|  [L=391]
Description: NADH:ubiquinone oxidoreductase subunit 1 (chain H) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.2e-89  298.0  22.7    9.4e-89  297.6  22.7    1.1  1  NADHdh       NADH dehydrogenase
  ------ inclusion threshold ------
       0.14   12.7   1.2         26    5.4   0.0    2.8  2  Arc_PepC_II  Archaeal Peptidase A24 C-terminus Type II
       0.64    9.8   4.3       0.25   11.2   0.8    1.9  2  VIT1         VIT family


Domain annotation for each model (and alignments):
>> NADHdh  NADH dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  297.6  22.7   1.6e-92   9.4e-89       4     298 ..      79     382 ..      70     383 .. 0.94

  Alignments for each domain:
  == domain 1  score: 297.6 bits;  conditional E-value: 1.6e-92
                                       HHHHHHHHHHHHHHHHHHHHHHHHHTTS--S-SSTTTTTTHHHHHHHHHCCS-----TTS-HHHHHHHHHHHHHHHH CS
                            NADHdh   4 llllvvlllvvalltlleRkvlAriqdRlGPnrvGplGllqplaDalKlllKediipkkadkllfllapvlalilal 80 
                                       +l+++v ++ +++  + eRkvl+r  dR G  ++G +G+lq +aD++K ++Kedi  k+ dk+ f+++  l++ +++
  gi|474933805|ref|YP_007687387.1|  79 ILMFLVPFTGCLVSLWEERKVLGRAMDRRGT-MIGLMGFLQCVADGFKTFMKEDIKIKEGDKMGFMWTCSLIIGTSV 154
                                       22222334444588999*************9.9******************************************** PP

                                       CTTTTS-SSS..SSS--TTHHHHHHHHHHHCHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH- CS
                            NADHdh  81 lafaviPfge..vladlnvglllilalsslgvygillaGwasnskYallGalRsaaqmisyEvalglsllavvllag 155
                                       l+ ++iP+++   ++++  gll+i+al +l++++il++Gw++n+kYa++G++R++ +m+syEv+l++++ +v+l ag
  gi|474933805|ref|YP_007687387.1| 155 LIAIMIPLSPrwFVVNYGSGLLIIMALYALAPFFILVSGWSQNNKYAMIGGIRATEMMVSYEVPLLIIIATVALQAG 231
                                       *********8789999999********************************************************** PP

                                       SS-HHHHHHCCCTT.-CCCCHHHHHHHHHHHHHHCCTCTTBTTTTSTTSSSSCCCTT-HCHHHHHHHHHHHHHHHHH CS
                            NADHdh 156 slslseiveaqeei.wfillqllafiifliallaetnraPFDlpeaesELvaGfhtEYsgmkfalfflaeyanmvlv 231
                                       ++++  iv+aq ++  +++ q+++fi+f+++++ae +raPFDl+eaesELv+G++tEY+gmk++l++la y++ ++ 
  gi|474933805|ref|YP_007687387.1| 232 TFNIGGIVDAQYDTmPYMIPQFIGFITFFLCATAESERAPFDLAEAESELVEGWQTEYAGMKWGLIMLADYLRGYVS 308
                                       ***********7664467778******************************************************** PP

                                       HHHHHHHCT.SS-HCCS.......HHHHHHHHHHHHHHHHHHHHHC----TCHHHHHHHCCTCHHHHHHHHHHH CS
                            NADHdh 232 salavllFlgGwllpfs.......gllwfllKvllllflfiwiratlpRlRydqlmklgwkvllplalanlllt 298
                                       +a++v++F+gGw+lpf+       + ++fllK++l +f++i++r +  R+R d +++lgwkv++pla++nl+++
  gi|474933805|ref|YP_007687387.1| 309 CAMLVIMFWGGWNLPFIgdyntwiPEIVFLLKCWLAFFFMIIFRCATGRVRTDTILNLGWKVFMPLAILNLMVV 382
                                       ****************9***99998899*******************************************986 PP

>> Arc_PepC_II  Archaeal Peptidase A24 C-terminus Type II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0    0.0043        26      56      80 ..     199     224 ..     193     231 .. 0.78
   2 ?    4.8   0.3    0.0065        39      73      88 ..     246     261 ..     242     263 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0043
                       Arc_PepC_II  56 kykkkglieet.vWvtygvPflipit 80 
                                       ky   g i  t   v+y vP+li i 
  gi|474933805|ref|YP_007687387.1| 199 KYAMIGGIRATeMMVSYEVPLLIIIA 224
                                       55556667776799*********996 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0065
                       Arc_PepC_II  73 vPflipitaGfiialv 88 
                                       +P++ip ++Gfi++++
  gi|474933805|ref|YP_007687387.1| 246 MPYMIPQFIGFITFFL 261
                                       7************986 PP

>> VIT1  VIT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1      0.36   2.1e+03     167     180 ..      71      84 ..      40     126 .. 0.51
   2 ?   11.2   0.8   4.1e-05      0.25     119     180 ..     128     189 ..     120     214 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.36
                              VIT1 167 vvsiavtllalllf 180
                                       +++++v+++ ++l+
  gi|474933805|ref|YP_007687387.1|  71 FFALIVFMILMFLV 84 
                                       22333333333333 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 4.1e-05
                              VIT1 119 lreelgpsaseelasplkaAlssalsfliGgliPllpylfvesvglalvvsiavtllalllf 180
                                       ++e+ ++++ ++    ++  l+++ s li  +iPl p  fv + g +l++ +a+ +la +++
  gi|474933805|ref|YP_007687387.1| 128 MKEDIKIKEGDKMGFMWTCSLIIGTSVLIAIMIPLSPRWFVVNYGSGLLIIMALYALAPFFI 189
                                       555666666555556799********************999989999999988888876643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2486.97
//
Query:       gi|474933806|ref|YP_007687388.1|  [L=248]
Description: Formate hydrogenlyase subunit 6/NADH:ubiquinone oxidoreductase 23 kD subunit (chain I) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-24   82.5  38.3    4.8e-06   26.1   4.2    4.3  4  Fer4      4Fe-4S binding domain
    6.8e-20   71.4  32.7    7.1e-11   42.5  10.6    2.3  2  Fer4_7    4Fe-4S dicluster domain
    1.7e-17   64.1  21.6      3e-05   24.9   1.2    4.3  4  Fer4_16   4Fe-4S double cluster binding domain
    1.7e-14   53.7  27.5    2.1e-09   37.4   6.5    3.1  3  Fer4_9    4Fe-4S dicluster domain
    1.5e-13   50.6  33.0    3.2e-06   27.2   9.7    3.2  3  Fer4_21   4Fe-4S dicluster domain
    6.3e-13   48.6  35.8    5.8e-07   29.5  14.4    3.3  3  Fer4_10   4Fe-4S dicluster domain
    4.4e-11   43.1  28.6    1.5e-05   25.3  10.0    2.8  2  Fer4_8    4Fe-4S dicluster domain
    4.5e-11   42.1  34.2     0.0011   18.9   4.3    4.3  4  Fer4_2    4Fe-4S binding domain
    5.3e-11   42.1  42.4    0.00021   21.2   2.9    4.3  4  Fer4_6    4Fe-4S binding domain
      3e-06   27.7  36.9       0.11   13.0  16.0    4.1  4  Fer4_17   4Fe-4S dicluster domain
    5.1e-06   26.7  21.3      0.025   14.8   0.4    4.1  4  Fer4_18   4Fe-4S dicluster domain
     0.0003   21.1  36.4      0.097   13.2   3.2    4.3  4  Fer4_4    4Fe-4S binding domain
      0.001   19.6  35.6       0.39   11.3   2.0    4.3  4  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
     0.0026   18.6  47.4        0.1   13.6   4.8    4.4  4  Fer4_3    4Fe-4S binding domain
  ------ inclusion threshold ------
       0.11   13.3  27.1       0.56   11.0   1.5    4.9  4  Fer4_15   4Fe-4S single cluster domain
       0.54   11.1  35.6        1.6    9.6   1.3    4.2  6  Fer4_22   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   7.3   8.9e-09     1e-05       3      23 ..      63      83 ..      61      84 .. 0.92
   2 !   24.9   2.1     1e-08   1.2e-05       1      23 [.      99     121 ..      99     122 .. 0.93
   3 !   26.1   4.2   4.3e-09   4.8e-06       7      24 .]     187     204 ..     184     204 .. 0.95
   4 !   24.3   1.7   1.6e-08   1.8e-05       1      23 [.     220     242 ..     220     243 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 8.9e-09
                                      EETTTSSS-THHHHHSTTTEE CS
                              Fer4  3 ideekCigCGaCvevCPvgAI 23
                                       d +kCigCG C+ +CP  AI
  gi|474933806|ref|YP_007687388.1| 63 LDFNKCIGCGMCARMCPCAAI 83
                                      5899***************99 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 1e-08
                                       EEEETTTSSS-THHHHHSTTTEE CS
                              Fer4   1 vvideekCigCGaCvevCPvgAI 23 
                                       +++++ +C +C +C+e CPv+A 
  gi|474933806|ref|YP_007687388.1|  99 PQVNMGRCSFCAYCAEYCPVDAM 121
                                       579*******************7 PP

  == domain 3  score: 26.1 bits;  conditional E-value: 4.3e-09
                                       TSSS-THHHHHSTTTEEE CS
                              Fer4   7 kCigCGaCvevCPvgAIt 24 
                                       kCi C++C +vCPv+AIt
  gi|474933806|ref|YP_007687388.1| 187 KCISCKKCSKVCPVNAIT 204
                                       9****************7 PP

  == domain 4  score: 24.3 bits;  conditional E-value: 1.6e-08
                                       EEEETTTSSS-THHHHHSTTTEE CS
                              Fer4   1 vvideekCigCGaCvevCPvgAI 23 
                                       ++i+ e C+ C +C+++CP  A+
  gi|474933806|ref|YP_007687388.1| 220 PEINSETCVSCSNCIDACPKSAL 242
                                       589****************9997 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8  14.1   1.6e-11   1.8e-08       1      52 []      67     120 ..      67     120 .. 0.90
   2 !   42.5  10.6   6.4e-14   7.1e-11       1      52 []     187     241 ..     187     241 .. 0.86

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 1.6e-11
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgt..ekveidpekClgCgaCvavCPtga 52 
                                       +CigCg C+++Cp  ai l e  +++g+  +++++++ +C++C  C++ CP++a
  gi|474933806|ref|YP_007687388.1|  67 KCIGCGMCARMCPCAAIILVETPDDEGQpvMRPQVNMGRCSFCAYCAEYCPVDA 120
                                       7****************9999988887744666899****************97 PP

  == domain 2  score: 42.5 bits;  conditional E-value: 6.4e-14
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenek.gtekv..eidpekClgCgaCvavCPtga 52 
                                       +Ci C++C ++Cpv+ai++ e+ +++ g++ +  ei++e+C++C +C+++CP+ a
  gi|474933806|ref|YP_007687388.1| 187 KCISCKKCSKVCPVNAITMVEHGVNAkGRPILwpEINSETCVSCSNCIDACPKSA 241
                                       7*******************99665415554367******************976 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.7   8.6e-06    0.0096       1      18 [.      67      84 ..      47      97 .. 0.80
   2 !   15.6   0.1   2.1e-05     0.023       1      20 [.     105     124 ..     105     167 .. 0.84
   3 !   24.9   1.2   2.7e-08     3e-05       1      23 [.     187     209 ..     187     223 .. 0.83
   4 !   19.2   2.2   1.6e-06    0.0017       1      20 [.     226     245 ..     226     248 .] 0.92

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 8.6e-06
                           Fer4_16  1 rCgtCgkCaevCPtnaik 18
                                      +C++Cg Ca +CP +ai 
  gi|474933806|ref|YP_007687388.1| 67 KCIGCGMCARMCPCAAII 84
                                      477777777777777775 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 2.1e-05
                           Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                       rC  C  Cae CP++a++ +
  gi|474933806|ref|YP_007687388.1| 105 RCSFCAYCAEYCPVDAMTVT 124
                                       6999*************977 PP

  == domain 3  score: 24.9 bits;  conditional E-value: 2.7e-08
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkek 23 
                                       +C++C+kC +vCP+nai++ ++ 
  gi|474933806|ref|YP_007687388.1| 187 KCISCKKCSKVCPVNAITMVEHG 209
                                       5*****************98444 PP

  == domain 4  score: 19.2 bits;  conditional E-value: 1.6e-06
                           Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                       +C++C +C+++CP +a+++k
  gi|474933806|ref|YP_007687388.1| 226 TCVSCSNCIDACPKSALSMK 245
                                       5****************988 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   4.6   2.8e-05     0.031      33      51 .]      59      83 ..      27      84 .. 0.76
   2 !   18.4  15.0   1.6e-06    0.0018       1      51 []      67     121 ..      67     121 .. 0.71
   3 !   37.4   6.5   1.9e-12   2.1e-09       1      50 [.     187     241 ..     167     242 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.8e-05
                            Fer4_9 33 e......eaCigCgaCveaCpkgai 51
                                             ++CigCg C+  Cp  ai
  gi|474933806|ref|YP_007687388.1| 59 GrpgldfNKCIGCGMCARMCPCAAI 83
                                      1445556789999999999999876 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 1.6e-06
                            Fer4_9   1 kCtgCgaCveaCpagvv....vedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       kC+gCg C ++Cp  ++    ++d+ ++ +   + ++ +C +C  C+e Cp +a+
  gi|474933806|ref|YP_007687388.1|  67 KCIGCGMCARMCPCAAIilveTPDDEGQPVMRPQVNMGRCSFCAYCAEYCPVDAM 121
                                       7***********988772222333333444444444499************9975 PP

  == domain 3  score: 37.4 bits;  conditional E-value: 1.9e-12
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase.....eaCigCgaCveaCpkga 50 
                                       kC++C++C ++Cp +++++ + +  a+ r   +     e C++C  C++aCpk a
  gi|474933806|ref|YP_007687388.1| 187 KCISCKKCSKVCPVNAITMVEHGVNAKGRPILWpeinsETCVSCSNCIDACPKSA 241
                                       7****************999999999999888899***9*************986 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   9.7   2.8e-09   3.2e-06       4      58 ..      64     122 ..      62     123 .. 0.76
   2 !   20.9   3.9   2.6e-07    0.0003      38      59 .]     185     205 ..     170     205 .. 0.86
   3 !   14.0   4.0   3.8e-05     0.043       2      22 ..     221     241 ..     220     246 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 2.8e-09
                           Fer4_21   4 dedkCigCgkCliaCedtshqaieidaktvl.....kvvedeCvGCnlCssvCPvedcie 58 
                                       d +kCigCg C+ +C+ +++  +e+ +++       +v   +C  C+ C++ CPv d+++
  gi|474933806|ref|YP_007687388.1|  64 DFNKCIGCGMCARMCPCAAIILVETPDDEGQpvmrpQVNMGRCSFCAYCAEYCPV-DAMT 122
                                       668*************8887777655555442223267789*************9.7765 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 2.6e-07
                           Fer4_21  38 edeCvGCnlCssvCPvedciem 59 
                                         +C+ C+ Cs+vCPv ++i+m
  gi|474933806|ref|YP_007687388.1| 185 GAKCISCKKCSKVCPV-NAITM 205
                                       579************9.9**99 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 3.8e-05
                           Fer4_21   2 ridedkCigCgkCliaCedts 22 
                                        i++++C++C +C+ aC++++
  gi|474933806|ref|YP_007687388.1| 221 EINSETCVSCSNCIDACPKSA 241
                                       588889999999999998765 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3  13.8   9.2e-08    0.0001       4      56 .]      63     117 ..      60     117 .. 0.77
   2 !   29.5  14.4   5.2e-10   5.8e-07       5      56 .]     184     238 ..     180     238 .. 0.90
   3 !   16.2   4.0   7.4e-06    0.0083       3      21 ..     221     239 ..     219     246 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 9.2e-08
                           Fer4_10   4 idddtCirCgkCvkaCPadltsvgak..geaseeeavrkkvekCtgcgaCveaCP 56 
                                       +d ++Ci+Cg C ++CP  +   + +  +e  +  + ++++++C +c +C+e CP
  gi|474933806|ref|YP_007687388.1|  63 LDFNKCIGCGMCARMCPCAAIILVETpdDEGQPVMRPQVNMGRCSFCAYCAEYCP 117
                                       6889**************8844444400444555566679**************9 PP

  == domain 2  score: 29.5 bits;  conditional E-value: 5.2e-10
                           Fer4_10   5 dddtCirCgkCvkaCPadl...tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       +  +Ci C+kC k+CP+++    ++g++++  ++   ++++e C  c +C++aCP
  gi|474933806|ref|YP_007687388.1| 184 EGAKCISCKKCSKVCPVNAitmVEHGVNAKGRPILWPEINSETCVSCSNCIDACP 238
                                       6689*************9998888888888999999999***************9 PP

  == domain 3  score: 16.2 bits;  conditional E-value: 7.4e-06
                           Fer4_10   3 vidddtCirCgkCvkaCPa 21 
                                       +i+++tC+ C +C +aCP 
  gi|474933806|ref|YP_007687388.1| 221 EINSETCVSCSNCIDACPK 239
                                       6899**************8 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3  10.0   1.3e-08   1.5e-05       1      64 [.      64     119 ..      64     120 .. 0.79
   2 !   22.8  10.6     8e-08     9e-05       3      64 ..     186     240 ..     184     241 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.3e-08
                            Fer4_8   1 elekCieCgaCqsaCpvlrrtk.khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                       +++kCi+Cg+C  +Cp +     + + d  +     v + qv     ++++C+ c  C+e Cpv+
  gi|474933806|ref|YP_007687388.1|  64 DFNKCIGCGMCARMCPCAAIILvETPDDEGQP----VMRPQV-----NMGRCSFCAYCAEYCPVD 119
                                       589*************9999874444444444....556777.....589*************96 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 8e-08
                            Fer4_8   3 ekCieCgaCqsaCpvlrrtk.khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                        kCi C  C + Cpv   t  +h  +a+g+ +   + e       + ++C++c +C ++Cp++
  gi|474933806|ref|YP_007687388.1| 186 AKCISCKKCSKVCPVNAITMvEHGVNAKGRPIL--WPEI------NSETCVSCSNCIDACPKS 240
                                       59*****************999999*****888..3333......3789************86 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   1.8   3.8e-06    0.0043       2      21 ..      60      79 ..      59      79 .. 0.90
   2 ?    6.3   2.8     0.011        12       2      21 ..      98     117 ..      97     118 .. 0.91
   3 !   17.6   2.4   2.5e-06    0.0028       5      21 ..     183     199 ..     179     200 .. 0.83
   4 !   18.9   4.3   9.9e-07    0.0011       3      21 ..     220     238 ..     220     239 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.8e-06
                            Fer4_2  2 pvvvdtdrCigCgaCvsaCP 21
                                      ++  d ++CigCg C   CP
  gi|474933806|ref|YP_007687388.1| 60 RPGLDFNKCIGCGMCARMCP 79
                                      577899*************9 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.011
                            Fer4_2   2 pvvvdtdrCigCgaCvsaCP 21 
                                       +++v+  rC  C  C   CP
  gi|474933806|ref|YP_007687388.1|  98 RPQVNMGRCSFCAYCAEYCP 117
                                       5899999**99********* PP

  == domain 3  score: 17.6 bits;  conditional E-value: 2.5e-06
                            Fer4_2   5 vdtdrCigCgaCvsaCP 21 
                                        + ++Ci+C++C ++CP
  gi|474933806|ref|YP_007687388.1| 183 LEGAKCISCKKCSKVCP 199
                                       55679************ PP

  == domain 4  score: 18.9 bits;  conditional E-value: 9.9e-07
                            Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                       +++++++C++C+ C++aCP
  gi|474933806|ref|YP_007687388.1| 220 PEINSETCVSCSNCIDACP 238
                                       579***************9 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   8.4   6.8e-05     0.076       7      24 .]      66      83 ..      65      83 .. 0.95
   2 !    6.5   3.0    0.0083       9.4       2      23 ..      99     120 ..      98     121 .. 0.90
   3 !   19.4   4.6   7.2e-07   0.00081       8      24 .]     187     203 ..     186     203 .. 0.95
   4 !   21.2   2.9   1.8e-07   0.00021       2      24 .]     220     242 ..     220     242 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.8e-05
                            Fer4_6  7 dkCigCgdCvrvCPegai 24
                                      +kCigCg C+r CP +ai
  gi|474933806|ref|YP_007687388.1| 66 NKCIGCGMCARMCPCAAI 83
                                      79************9997 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0083
                            Fer4_6   2 veidpdkCigCgdCvrvCPega 23 
                                       ++++  +C  C  C+  CP +a
  gi|474933806|ref|YP_007687388.1|  99 PQVNMGRCSFCAYCAEYCPVDA 120
                                       6789999999*********987 PP

  == domain 3  score: 19.4 bits;  conditional E-value: 7.2e-07
                            Fer4_6   8 kCigCgdCvrvCPegai 24 
                                       kCi+C +C +vCP +ai
  gi|474933806|ref|YP_007687388.1| 187 KCISCKKCSKVCPVNAI 203
                                       9**************98 PP

  == domain 4  score: 21.2 bits;  conditional E-value: 1.8e-07
                            Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                       +ei+ + C++C +C+++CP  a+
  gi|474933806|ref|YP_007687388.1| 220 PEINSETCVSCSNCIDACPKSAL 242
                                       79*****************9886 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   6.7   0.00084      0.94      44      57 ..      66      79 ..      35      81 .. 0.75
   2 !   13.0  16.0    0.0001      0.11       1      58 [.      67     118 ..      67     121 .. 0.73
   3 !   12.8  13.1   0.00012      0.13       1      58 [.     105     200 ..     105     203 .. 0.55
   4 !    9.9  15.0   0.00096       1.1       1      58 [.     187     239 ..     187     241 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00084
                           Fer4_17 44 slCieCgeCerkCP 57
                                      ++Ci+Cg+C+r CP
  gi|474933806|ref|YP_007687388.1| 66 NKCIGCGMCARMCP 79
                                      56666666666665 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.0001
                           Fer4_17   1 rCiqCgyClpeCpsyea....ydnepkkllraaklglleeaekeekaslCieCgeCerkCPq 58 
                                       +Ci+Cg+C+++Cp  ++    +++++ +++ + +           ++++C+ C  C+++CP 
  gi|474933806|ref|YP_007687388.1|  67 KCIGCGMCARMCPCAAIilveTPDDEGQPVMRPQ----------VNMGRCSFCAYCAEYCPV 118
                                       6************987733334444444444422..........379**************6 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 0.00012
                           Fer4_17   1 rCiqCgyClpeCps.............yeaydn....epkkllraakl......................glleeae 38 
                                       rC+ C+yC++ Cp              +  +++     p++l++a +                              
  gi|474933806|ref|YP_007687388.1| 105 RCSFCAYCAEYCPVdamtvtpivelaeF--TRSdliyGPRRLAYAGTTegmkvplketlisdykagnkvmR------ 173
                                       7************854444444333221..11122222334444433355555555555555544432211...... PP

                           Fer4_17  39 ke.......e.kaslCieCgeCerkCPq 58 
                                        +       e +  +Ci+C++C+++CP 
  gi|474933806|ref|YP_007687388.1| 174 -DhasidrpElEGAKCISCKKCSKVCPV 200
                                       .23335554347799************6 PP

  == domain 4  score: 9.9 bits;  conditional E-value: 0.00096
                           Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllraaklglleea.ekeekaslCieCgeCerkCPq 58 
                                       +Ci+C+ C ++Cp ++++  e + + ++      + +   e + ++C++C +C  +CP+
  gi|474933806|ref|YP_007687388.1| 187 KCISCKKCSKVCPVNAITMVE-HGVNAK-----GRPIlWPEINSETCVSCSNCIDACPK 239
                                       6**************998764.434333.....223303345899*************8 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.9    0.0036         4      58      74 ..      65      81 ..      54      86 .. 0.84
   2 ?    6.1   0.6     0.011        12      54      74 ..      99     119 ..      87     123 .. 0.85
   3 !   14.8   0.4   2.2e-05     0.025      54      74 ..     181     201 ..     159     213 .. 0.75
   4 !   11.2   1.2   0.00028      0.31      84      97 ..     226     239 ..     220     247 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0036
                           Fer4_18 58 agdcidcescvkvcPtg 74
                                       ++ci c++c ++cP  
  gi|474933806|ref|YP_007687388.1| 65 FNKCIGCGMCARMCPCA 81
                                      5789**********975 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.011
                           Fer4_18  54 kekgagdcidcescvkvcPtg 74 
                                        + ++g c  c +c + cP++
  gi|474933806|ref|YP_007687388.1|  99 PQVNMGRCSFCAYCAEYCPVD 119
                                       5678999************85 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 2.2e-05
                           Fer4_18  54 kekgagdcidcescvkvcPtg 74 
                                        e + ++ci+c++c kvcP++
  gi|474933806|ref|YP_007687388.1| 181 PELEGAKCISCKKCSKVCPVN 201
                                       3456689************86 PP

  == domain 4  score: 11.2 bits;  conditional E-value: 0.00028
                           Fer4_18  84 eciscllcidacdk 97 
                                        c+sc++cidac k
  gi|474933806|ref|YP_007687388.1| 226 TCVSCSNCIDACPK 239
                                       69999999999976 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   3.2   8.7e-05     0.097       2      15 ..      66      79 ..      65      94 .. 0.89
   2 ?    3.4   2.2      0.12   1.3e+02       3      16 ..     105     118 ..     103     124 .. 0.88
   3 !   10.8   4.7   0.00052      0.59       3      17 .]     187     201 ..     185     201 .. 0.92
   4 !   11.4   3.0   0.00034      0.38       1      15 [.     224     238 ..     224     243 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.7e-05
                            Fer4_4  2 erCigCgsCvaaCP 15
                                      ++CigCg C + CP
  gi|474933806|ref|YP_007687388.1| 66 NKCIGCGMCARMCP 79
                                      79***********9 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.12
                            Fer4_4   3 rCigCgsCvaaCPq 16 
                                       rC  C  C  +CP+
  gi|474933806|ref|YP_007687388.1| 105 RCSFCAYCAEYCPV 118
                                       788899*******6 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00052
                            Fer4_4   3 rCigCgsCvaaCPqg 17 
                                       +Ci C++C  +CP++
  gi|474933806|ref|YP_007687388.1| 187 KCISCKKCSKVCPVN 201
                                       7************75 PP

  == domain 4  score: 11.4 bits;  conditional E-value: 0.00034
                            Fer4_4   1 qerCigCgsCvaaCP 15 
                                       +e+C+ C  C++aCP
  gi|474933806|ref|YP_007687388.1| 224 SETCVSCSNCIDACP 238
                                       589************ PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   4.6   0.00091         1       2      17 ..      64      79 ..      63      81 .. 0.90
   2 ?    5.2   1.7     0.028        32       1      17 [.     101     117 ..     101     119 .. 0.92
   3 !   11.3   2.0   0.00035      0.39       3      17 ..     185     199 ..     183     202 .. 0.90
   4 !   10.8   4.4   0.00048      0.54       1      18 [.     222     239 ..     222     240 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00091
                           Fer4_13  2 DrdtCiacgaCvelaP 17
                                      D ++Ci+cg C+ ++P
  gi|474933806|ref|YP_007687388.1| 64 DFNKCIGCGMCARMCP 79
                                      5689***********9 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.028
                           Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                       V+  +C+ c+ C+e +P
  gi|474933806|ref|YP_007687388.1| 101 VNMGRCSFCAYCAEYCP 117
                                       67889***********9 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00035
                           Fer4_13   3 rdtCiacgaCvelaP 17 
                                         +Ci+c++C +++P
  gi|474933806|ref|YP_007687388.1| 185 GAKCISCKKCSKVCP 199
                                       579***********9 PP

  == domain 4  score: 10.8 bits;  conditional E-value: 0.00048
                           Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                       ++ +tC++c +C +++P+
  gi|474933806|ref|YP_007687388.1| 222 INSETCVSCSNCIDACPK 239
                                       789**************7 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8  10.5      0.12   1.4e+02       1      12 [.      68      79 ..      68      82 .. 0.92
   2 !    8.8   4.1    0.0032       3.6       1      15 []     106     120 ..     106     120 .. 0.95
   3 !   13.6   4.8   8.9e-05       0.1       1      15 []     188     202 ..     188     202 .. 0.98
   4 !   11.0   4.2    0.0006      0.67       1      15 []     227     241 ..     227     241 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.12
                            Fer4_3  1 CtgCgaCvevCP 12
                                      C+gCg C + CP
  gi|474933806|ref|YP_007687388.1| 68 CIGCGMCARMCP 79
                                      ************ PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0032
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C  C  C e CPv+A
  gi|474933806|ref|YP_007687388.1| 106 CSFCAYCAEYCPVDA 120
                                       999*99*******98 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 8.9e-05
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+ C  C +vCPv+A
  gi|474933806|ref|YP_007687388.1| 188 CISCKKCSKVCPVNA 202
                                       *************99 PP

  == domain 4  score: 11.0 bits;  conditional E-value: 0.0006
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+ C+ C ++CP+ A
  gi|474933806|ref|YP_007687388.1| 227 CVSCSNCIDACPKSA 241
                                       99**********977 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.5    0.0005      0.56       3      19 ..      63      79 ..      62      97 .. 0.90
   2 ?    4.4   1.1     0.056        62       7      19 ..     105     117 ..     100     123 .. 0.70
   3 ?    3.7   2.3     0.092     1e+02       6      19 ..     186     199 ..     182     210 .. 0.68
   4 ?    8.4   0.9    0.0032       3.6       3      20 ..     222     239 ..     221     243 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0005
                           Fer4_15  3 vDrdaCigcglCvaeap 19
                                      +D ++Cigcg+C++ +p
  gi|474933806|ref|YP_007687388.1| 63 LDFNKCIGCGMCARMCP 79
                                      68899*********998 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.056
                           Fer4_15   7 aCigcglCvaeap 19 
                                       +C  c+ C++ +p
  gi|474933806|ref|YP_007687388.1| 105 RCSFCAYCAEYCP 117
                                       7888888887776 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.092
                           Fer4_15   6 daCigcglCvaeap 19 
                                        +Ci+c  C +++p
  gi|474933806|ref|YP_007687388.1| 186 AKCISCKKCSKVCP 199
                                       56777777777776 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.0032
                           Fer4_15   3 vDrdaCigcglCvaeape 20 
                                       ++ ++C +c +C++++p+
  gi|474933806|ref|YP_007687388.1| 222 INSETCVSCSNCIDACPK 239
                                       7889************97 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   6.6     0.011        12      78      94 ..      64      80 ..      55      82 .. 0.81
   2 ?    6.0   6.6     0.019        21       1      14 [.      67      80 ..      67     101 .. 0.66
   3 ?    2.6   1.9      0.22   2.4e+02      76      94 ..     100     118 ..      91     121 .. 0.74
   4 ?    7.9   3.4    0.0048       5.3       1      94 [.     187     200 ..     162     203 .. 0.68
   5 ?    8.3   3.4    0.0036         4       1      18 [.     187     204 ..     187     217 .. 0.78
   6 ?    9.6   1.3    0.0015       1.6      76      94 ..     221     239 ..     212     241 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.011
                           Fer4_22 78 gesgCvGCgRCieacpv 94
                                      + ++C+GCg C ++cp 
  gi|474933806|ref|YP_007687388.1| 64 DFNKCIGCGMCARMCPC 80
                                      56789999999999985 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.019
                           Fer4_22  1 rClsCgaCtlvCpt 14
                                      +C++Cg C+ +Cp 
  gi|474933806|ref|YP_007687388.1| 67 KCIGCGMCARMCPC 80
                                      46666666666663 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.22
                           Fer4_22  76 kfgesgCvGCgRCieacpv 94 
                                       ++++  C  C  C e cpv
  gi|474933806|ref|YP_007687388.1| 100 QVNMGRCSFCAYCAEYCPV 118
                                       5666777778888888876 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.0048
                           Fer4_22   1 rClsCgaCtlvCptCsCfdvedetkeeskegervrvwdsClleeftkvaggenvrkekkerlrqrllhklsefkekf 77 
                                       +C+sC +C+ vCp                                                                
  gi|474933806|ref|YP_007687388.1| 187 KCISCKKCSKVCP---------------------------------------------------------------- 199
                                       4555555555555................................................................ PP

                           Fer4_22  78 gesgCvGCgRCieacpv 94 
                                                       v
  gi|474933806|ref|YP_007687388.1| 200 ----------------V 200
                                       ................4 PP

  == domain 5  score: 8.3 bits;  conditional E-value: 0.0036
                           Fer4_22   1 rClsCgaCtlvCptCsCf 18 
                                       +C+sC +C+ vCp    +
  gi|474933806|ref|YP_007687388.1| 187 KCISCKKCSKVCPVNAIT 204
                                       7***********986555 PP

  == domain 6  score: 9.6 bits;  conditional E-value: 0.0015
                           Fer4_22  76 kfgesgCvGCgRCieacpv 94 
                                       ++++++Cv C  Ci+acp+
  gi|474933806|ref|YP_007687388.1| 221 EINSETCVSCSNCIDACPK 239
                                       5678899999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1853.78
//
Query:       gi|474933807|ref|YP_007687389.1|  [L=107]
Description: NADH:ubiquinone oxidoreductase subunit 6 (chain J) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-21   75.5   5.2    3.2e-21   75.5   5.2    1.7  2  Oxidored_q3    NADH-ubiquinone/plastoquinone oxidoreductase c
  ------ inclusion threshold ------
       0.16   12.4   4.9       0.18   12.3   4.9    1.1  1  MerC           MerC mercury resistance protein
        0.2   11.9   1.0        3.5    8.0   0.0    2.7  2  Cm_res_leader  Chloramphenicol resistance gene leader peptide
       0.77   10.1  10.4        1.3    9.4  10.4    1.4  1  DUF4395        Domain of unknown function (DUF4395)
        1.3    9.2   8.4      0.096   12.8   3.2    1.7  2  Cyt_c_ox_IV    Cytochrome c oxidase subunit IV
        5.8    7.4  10.3       0.42   11.0   2.8    2.0  2  DUF983         Protein of unknown function (DUF983)


Domain annotation for each model (and alignments):
>> Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase chain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.4     0.084   2.5e+02      15      30 ..      25      40 ..      23      43 .. 0.80
   2 !   75.5   5.2   1.1e-24   3.2e-21       1      66 [.      37     102 ..      37     107 .] 0.91

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.084
                                      HHHHHHHHHHHHHHHH CS
                       Oxidored_q3 15 alfLilsfvgvaglfi 30
                                      + fLi++ +gvag + 
  gi|474933807|ref|YP_007687389.1| 25 VAFLIVAAIGVAGALW 40
                                      7899999999999775 PP

  == domain 2  score: 75.5 bits;  conditional E-value: 1.1e-24
                                       HHHHHHH-SBHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHIIIIIHHHHHHHHHHHSSTTS-- CS
                       Oxidored_q3   1 gallvitsknpvysalfLilsfvgvaglfillgaeFlallqilvYvGAilvlflFvimllesaeee 66 
                                       gal v+t k+p++sa++L+l+f  va+ +++l+ eFl+++q+lvYvGAi+vlf+F +ml+++  +e
  gi|474933807|ref|YP_007687389.1|  37 GALWVVTDKQPMHSAFYLALVFTTVAVTYFFLETEFLGVIQMLVYVGAITVLFAFCVMLTRKTIME 102
                                       6899*******************************************************8554443 PP

>> MerC  MerC mercury resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   4.9   5.9e-05      0.18      40     113 ..      24      92 ..       3      96 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.9e-05
                              MerC  40 qvllilvvaigllalvvgyrrhrktsvlvlgalGllillvalflgteaeetllfgslwqvltvlGaalLaiahv 113
                                        v++++v+aig+++ ++ ++  + ++  + +al ++ ++v  f+     et  f  ++q+l+++Ga+ +  a +
  gi|474933807|ref|YP_007687389.1|  24 LVAFLIVAAIGVAGALWVVTDKQPMHSAFYLALVFTTVAVTYFFL----ETE-FLGVIQMLVYVGAITVLFAFC 92 
                                       688999*******99999999999999999999999999998888....444.66899********99988766 PP

>> Cm_res_leader  Chloramphenicol resistance gene leader peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0012       3.5       3      13 ..      34      44 ..      32      46 .. 0.89
   2 ?    1.7   0.2      0.14   4.2e+02      10      16 ..      94     100 ..      82     101 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0012
                     Cm_res_leader  3 GvPGALAvvtR 13
                                      Gv GAL vvt 
  gi|474933807|ref|YP_007687389.1| 34 GVAGALWVVTD 44
                                      9********95 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.14
                     Cm_res_leader  10 vvtRRti 16 
                                       + tR+ti
  gi|474933807|ref|YP_007687389.1|  94 MLTRKTI 100
                                       369*999 PP

>> DUF4395  Domain of unknown function (DUF4395)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4  10.4   0.00043       1.3      51     120 ..      29      93 ..       7      94 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00043
                           DUF4395  51 llarrlvaprlgpkpeledaapkrFAqliGlvfllvalvlfllgapvlglvltalllvaafleaafgfCl 120
                                       ++a+  va    +  + +d++p + A  ++lvf++va+  f+l+ ++lg++ +++ + a ++  +f fC+
  gi|474933807|ref|YP_007687389.1|  29 IVAAIGVAG---ALWVVTDKQPMHSAFYLALVFTTVAVTYFFLETEFLGVIQMLVYVGAITV--LFAFCV 93 
                                       444444443...4456789999999***************************9999999999..999997 PP

>> Cyt_c_ox_IV  Cytochrome c oxidase subunit IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.7       0.4   1.2e+03      96     110 ..      30      44 ..      14      58 .. 0.67
   2 ?   12.8   3.2   3.2e-05     0.096      10      65 ..      53     106 ..      45     107 .] 0.87

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.4
                       Cyt_c_ox_IV  96 laalglalgwWllli 110
                                       +aa+g+a ++W+++ 
  gi|474933807|ref|YP_007687389.1|  30 VAAIGVAGALWVVTD 44 
                                       567777778887764 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 3.2e-05
                       Cyt_c_ox_IV  10 llavffllvavvYgvltkieelvGttalvltgglallvgtylafvarridarpedr 65 
                                       +la+ f+ vav Y +l +  e+ G++ +++ +g  ++++++  +++r++ ++ ed+
  gi|474933807|ref|YP_007687389.1|  53 YLALVFTTVAVTYFFLET--EFLGVIQMLVYVGAITVLFAFCVMLTRKTIMEDEDD 106
                                       567888999*******99..*********999999999999999999988888886 PP

>> DUF983  Protein of unknown function (DUF983)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.8   0.00014      0.42      25      72 ..      20      67 ..      13      71 .. 0.77
   2 ?    1.3   4.9      0.15   4.5e+02      29      74 ..      53      97 ..      50     101 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00014
                            DUF983 25 dgPayfvilivghlvvplallvevayepplwvhlliwlpltlllslll 72
                                      d P  + +liv+++ v+ al+v +  +p      l +++ t++++ ++
  gi|474933807|ref|YP_007687389.1| 20 DNPDLVAFLIVAAIGVAGALWVVTDKQPMHSAFYLALVFTTVAVTYFF 67
                                      88999*****************98888766555555555556655555 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.15
                            DUF983 29 yfvilivghlvvplallvevayepplwvhlliwlpltlllsllllr 74
                                      y+ ++++++ v+ ++l +e+   +++ v  +  ++++++++++l r
  gi|474933807|ref|YP_007687389.1| 53 YLALVFTTVAVTYFFLETEFLGVIQMLV-YVGAITVLFAFCVMLTR 97
                                      5666666666666666666666666633.34445555566666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       951  (0.0530426); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 764.46
//
Query:       gi|474933808|ref|YP_007687390.1|  [L=100]
Description: hypothetical protein TALC_00216 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0045   16.7   0.1     0.0053   16.5   0.1    1.1  1  Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase cha
  ------ inclusion threshold ------
      0.058   13.8   0.0        2.5    8.5   0.0    2.1  2  ATP19        ATP synthase subunit K
       0.15   12.2   1.6       0.21   11.7   0.6    1.6  2  DUF3742      Protein of unknown function (DUF3742)


Domain annotation for each model (and alignments):
>> Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase chain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   8.9e-07    0.0053      76     143 ..       5      88 ..       1      89 [. 0.62

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 8.9e-07
                                       HHHHHHHHHHHHHHHTT--..........................--------TT-HHHHHHHHTTTTHHHHHHHHH CS
                       Oxidored_q3  76 alaalligllllallllllles....................sssavdaqvadvsnieaigsllftkyllpfelasl 132
                                       a+a++++++ ll++l +++  +                         ++  +   +  ++ ++lf++y  +++++++
  gi|474933808|ref|YP_007687390.1|   5 AAAGAVLAISLLVVLGAAIYMTswdgfgdspepipydnvveyD----ANGDPVAVTDGSLNETLFEDYGPVLLVLAI 77 
                                       3334445555555555555444577888888887665432210....1112222234466***************** PP

                                       HHHHHHHHHHH CS
                       Oxidored_q3 133 lLLvaligaiv 143
                                       l++ a+ig + 
  gi|474933808|ref|YP_007687390.1|  78 LMFGAMIGGVC 88 
                                       ********986 PP

>> ATP19  ATP synthase subunit K
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0   0.00042       2.5      15      38 ..       9      32 ..       4      63 .. 0.82
   2 ?    3.7   0.0     0.013        79      16      38 ..      74      96 ..      73     100 .] 0.83

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00042
                                      S-SHHHHHHHHH--XXXXXXXXXX CS
                             ATP19 15 hyLAlgtLgttglivylamggskk 38
                                       +LA++ L+ +g+ +y+ ++ +  
  gi|474933808|ref|YP_007687390.1|  9 AVLAISLLVVLGAAIYMTSWDGFG 32
                                      68***************9987655 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.013
                                      -SHHHHHHHHH--XXXXXXXXXX CS
                             ATP19 16 yLAlgtLgttglivylamggskk 38
                                      +LA+ ++g+++++v +a    +k
  gi|474933808|ref|YP_007687390.1| 74 VLAILMFGAMIGGVCIAREEVEK 96
                                      79************998776666 PP

>> DUF3742  Protein of unknown function (DUF3742)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.6   3.5e-05      0.21      42      67 ..       4      29 ..       2      31 .. 0.92
   2 ?   -1.5   0.0      0.42   2.5e+03      55      65 ..      73      83 ..      70      98 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.5e-05
                           DUF3742 42 aavatavlwvvklavlGvllyvafWl 67
                                      +a+a avl +  l+vlG  +y+  W 
  gi|474933808|ref|YP_007687390.1|  4 RAAAGAVLAISLLVVLGAAIYMTSWD 29
                                      68999********************5 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.42
                           DUF3742 55 avlGvllyvaf 65
                                       vl +l++ a+
  gi|474933808|ref|YP_007687390.1| 73 LVLAILMFGAM 83
                                      45555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 605.55
//
Query:       gi|474933809|ref|YP_007687391.1|  [L=100]
Description: NADH:ubiquinone oxidoreductase subunit 11 or 4L (chain K) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-22   79.6   6.6    1.2e-22   79.5   6.6    1.0  1  Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase cha


Domain annotation for each model (and alignments):
>> Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.5   6.6   6.7e-27   1.2e-22       5     103 ..      10      95 ..       6     100 .] 0.91

  Alignments for each domain:
  == domain 1  score: 79.5 bits;  conditional E-value: 6.7e-27
                                       HHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHHHHHHHC.............TTSCGGHHHHHHHHHHHHHH CS
                       Oxidored_q2   5 liallfliGlygvllrrnllkvliglelisnavnlllvlagvftegtlvitnpatefadplpqalvLtaivigaaet 81 
                                         a+lf+iG+ygv+++++ + vl+++el++na+n+++v+++++               dpl+q++v++ i ++aae+
  gi|474933809|ref|YP_007687391.1|  10 FGAILFAIGAYGVFTKKSTIIVLMCIELMLNAANINFVAFSAYG-------------FDPLGQVMVIMTISVAAAEV 73 
                                       5699***************************************9.............******************** PP

                                       HHHHHHHHHHHHHSSS-BCCG- CS
                       Oxidored_q2  82 avgLallvrlyreygtddvqel 103
                                       avg+a+++++y+  +t+ +++l
  gi|474933809|ref|YP_007687391.1|  74 AVGIAIVLNAYKISKTVGTDDL 95 
                                       ******9999888888877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       777  (0.0433376); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 748.26
//
Query:       gi|474933810|ref|YP_007687392.1|  [L=684]
Description: proton-translocating NADH-quinone oxidoreductase, chain L [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.5e-72  242.0  26.9    9.2e-53  179.3  13.5    4.2  5  Proton_antipo_M  Proton-conducting membrane transporter
    3.6e-14   52.6   1.2    3.6e-14   52.6   1.2    3.5  4  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 
      0.004   16.8   0.1      0.004   16.8   0.1    4.5  5  NADH5_C          NADH dehydrogenase subunit 5 C-terminus
  ------ inclusion threshold ------
      0.015   15.6   2.2      0.015   15.6   2.2    6.8  7  DUF4064          Protein of unknown function (DUF4064)
      0.067   12.8   0.3      0.067   12.8   0.3    4.5  4  Oxidored_q2      NADH-ubiquinone/plastoquinone oxidoreductase
       0.19   11.3   7.9      0.065   12.8   3.0    2.6  2  Proton_antipo_C  NADH-dehyrogenase subunit F, TMs, (complex I


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       1.3   3.7e+03      18      51 ..      16      47 ..      11      60 .. 0.71
   2 ?   -2.2   0.3      0.61   1.8e+03     201     223 ..      89     111 ..      74     130 .. 0.59
   3 !  179.3  13.5   3.1e-56   9.2e-53       1     194 [.     138     339 ..     138     346 .. 0.91
   4 !   77.2   5.5   4.1e-25   1.2e-21     189     278 ..     352     440 ..     351     466 .. 0.90
   5 ?   -2.0   2.5      0.55   1.6e+03      44      73 ..     504     551 ..     496     575 .. 0.54

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.3
                   Proton_antipo_M 18 lylLiglwkkkpksleAslklflltllgsliLLl 51
                                      +++++g++++k  + + + ++++ ++++s+i+ l
  gi|474933810|ref|YP_007687392.1| 16 SFVIVGFFGNK--TPQGGGYITVFGAAASFIIAL 47
                                      67788888766..777888888888888887654 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.61
                   Proton_antipo_M 201 aiihllthalfkallFllagsvi 223
                                       a + +l+ ++++ l+F+ +++ +
  gi|474933810|ref|YP_007687392.1|  89 ACLMMLFASFISTLIFVYSLGYM 111
                                       33334444455555555554444 PP

  == domain 3  score: 179.3 bits;  conditional E-value: 3.1e-56
                   Proton_antipo_M   1 andLlllylglElvllplylLiglwk........kkpksleAslklflltllgsliLLlgilllynltgtlefeels 69 
                                       +++++ +++++E+++l++ylLig+w+        +  ++++A+ k+fl+t++g++ L+ g+++l+++ g+l+  +++
  gi|474933810|ref|YP_007687392.1| 138 SSNMVEMFVFWEIMGLCSYLLIGFWSfehpsgddAADNAASAAKKAFLVTRAGDVCLMAGMFVLFQAIGSLDYVDIF 214
                                       6899*********************73333333234578999*********************************** PP

                   Proton_antipo_M  70 kal.elglnslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsall.Aatlvkagvlllirlllllavssn 144
                                       + +  ++++   l+l ++l++ g++ Ksaq+pl  Wlpda +++Pt vsal+ Aat+vkagv++++r ++l+  ++ 
  gi|474933810|ref|YP_007687392.1| 215 NGAnLNAADPGLLSLSAFLIFGGAIGKSAQFPLMDWLPDA-MAGPTTVSALIhAATMVKAGVYIVARCFPLFC-MDI 289
                                       **9555556667789999**********************.********************************.*** PP

                   Proton_antipo_M 145 eisqlllilaiismllgslvalaqtdiKrllAySsishlGymlialavat 194
                                       +++ ++ i++ +++++++++a++ ++iK++lAyS++s+lGym++ l++++
  gi|474933810|ref|YP_007687392.1| 290 NVMLFVGIIGGVTAFFAATMAMNNMNIKKVLAYSTLSQLGYMFLSLGAGG 339
                                       **********************************************9955 PP

  == domain 4  score: 77.2 bits;  conditional E-value: 4.1e-25
                   Proton_antipo_M 189 alavatqygveaaiihllthalfkallFllagsviyerektrdirayggLakkmPilalvllvlllslaGlPptagF 265
                                       al++a++ g++a i+h+  ha+fkallFl++gsvi+++  t+d+r++gg+ kkmPi+++++l++ ls+aG P++agF
  gi|474933810|ref|YP_007687392.1| 352 ALMAAGSLGYTAGILHMANHAFFKALLFLCSGSVIHSC-GTEDMRYMGGMGKKMPITSVTMLIGSLSIAGFPFFAGF 427
                                       7888999******************************9.9************************************* PP

                   Proton_antipo_M 266 lskfliLeaavav 278
                                       +sk+l+L  a+++
  gi|474933810|ref|YP_007687392.1| 428 WSKDLVLDTAMDA 440
                                       *******999975 PP

  == domain 5  score: -2.0 bits;  conditional E-value: 0.55
                   Proton_antipo_M  44 lgsliLLlgilllynltgtlefeelskal..................e 73 
                                       l+ ++ ++g+ ll+++ g  ++++ + +                    
  gi|474933810|ref|YP_007687392.1| 504 LSIFAVVFGFTLLFGFDGLFSITYTAATQvwqignldghtglhfveeL 551
                                       566677777777777777666665555544445444466666555442 PP

>> Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   1.2   1.2e-17   3.6e-14       3      55 ..      70     123 ..      68     126 .. 0.91
   2 ?   -2.6   0.0         2     6e+03      30      37 ..     259     266 ..     255     267 .. 0.89
   3 ?   -4.6   1.1         6   1.8e+04      21      35 ..     559     573 ..     555     575 .. 0.64
   4 ?   -2.0   0.3       1.3     4e+03      26      41 ..     666     681 ..     663     682 .. 0.83

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 1.2e-17
                   Proton_antipo_N   3 tWlsvgglsieigfllDklsalmllvvtfvsllvhlYSigYMadde..gyqRFfa 55 
                                       +W+ +ggl++++g+++D l +lm+l+ +f+s+l+ +YS+gYM  d+  +++R+fa
  gi|474933810|ref|YP_007687392.1|  70 DWFAIGGLQLHFGYYVDALACLMMLFASFISTLIFVYSLGYMG-DQgiKKRRYFA 123
                                       8*****************************************9.54136999998 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2
                   Proton_antipo_N  30 tfvsllvh 37 
                                       t+vs+l+h
  gi|474933810|ref|YP_007687392.1| 259 TTVSALIH 266
                                       89*****9 PP

  == domain 3  score: -4.6 bits;  conditional E-value: 6
                   Proton_antipo_N  21 lsalmllvvtfvsll 35 
                                       l+++ +l+  ++++l
  gi|474933810|ref|YP_007687392.1| 559 LTIVLVLIAIGLAFL 573
                                       666666666666665 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 1.3
                   Proton_antipo_N  26 llvvtfvsllvhlYSi 41 
                                        +++ fv++l + +++
  gi|474933810|ref|YP_007687392.1| 666 GIIILFVAALALCFAF 681
                                       57999*****999987 PP

>> NADH5_C  NADH dehydrogenase subunit 5 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.4       1.2   3.5e+03      71      87 ..      92     108 ..      80     144 .. 0.53
   2 ?    3.6   4.2     0.014        43      57     108 ..     284     331 ..     259     344 .. 0.79
   3 ?   -3.4   0.2       2.1   6.3e+03      97     114 ..     447     464 ..     426     467 .. 0.72
   4 !   16.8   0.1   1.3e-06     0.004       1      47 [.     469     515 ..     469     524 .. 0.97
   5 !    7.0   0.2    0.0014       4.1      66     179 ..     560     672 ..     545     674 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.2
                           NADH5_C  71 vtilGlllglelsklsl 87 
                                       +++   +++  +   sl
  gi|474933810|ref|YP_007687392.1|  92 MMLFASFISTLIFVYSL 108
                                       33333333333333333 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.014
                           NADH5_C  57 vitlplllKllallvtilGlllglelsklslkllkkslklnlssfssslwFl 108
                                       ++++ ++   + l+v i+G ++++  +++++++++ +     +s +s+l+++
  gi|474933810|ref|YP_007687392.1| 284 LFCMDIN---VMLFVGIIGGVTAFFAATMAMNNMNIKKV-LAYSTLSQLGYM 331
                                       4454444...4689****************999998754.899999999998 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 2.1
                           NADH5_C  97 nlssfssslwFlpslshr 114
                                       ++ + +  lwFl  ++ +
  gi|474933810|ref|YP_007687392.1| 447 SSAWIFMVLWFLGVVTAF 464
                                       566777788888766554 PP

  == domain 4  score: 16.8 bits;  conditional E-value: 1.3e-06
                           NADH5_C   1 YSlRliyyvllgsprfsslspineenptllnpilrLalgsiiaGsll 47 
                                       Y +Rl ++++ g+ + ++l++  e+ + ++ p+ +L++++++ G+ l
  gi|474933810|ref|YP_007687392.1| 469 YMFRLWFMTFRGEEHENALHCHGESPNAMTMPLCVLSIFAVVFGFTL 515
                                       88******************************************988 PP

  == domain 5  score: 7.0 bits;  conditional E-value: 0.0014
                           NADH5_C  66 llallvtilGlllglelsklslkllkkslkl.nlssfssslwFlpslshrllsklsLklgqklakqlDqgWlEklgp 141
                                       +++l+++ +Gl + +   k+ +  + +      l+  +   w++p++ +++  kl   + + +++ +D   ++    
  gi|474933810|ref|YP_007687392.1| 560 TIVLVLIAIGLAFLMYCKKSINPGKFSRNGEsALYKTIQNRWYMPEIYNQVSWKLGYGVAK-MVNFFDTQVID-GSV 634
                                       45566677888888877777766555554446999************99987776544433.33347766664.456 PP

                           NADH5_C 142 kglaklllklskliqnlqkglikiyLlsflltllllll 179
                                       +gl+  ++   + ++++q+g++ +y  +++  +++l++
  gi|474933810|ref|YP_007687392.1| 635 NGLSGAVVGGGEAVSKAQDGNVHTYAGVVVAGIIILFV 672
                                       78888888888888888888888888888888888776 PP

>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.9       0.1     3e+02      69     102 ..      11      44 ..       2      45 .. 0.79
   2 ?   -2.6   4.0       2.3   6.9e+03      60      60 ..      88      88 ..      31     161 .. 0.52
   3 ?   -3.8   0.2       5.2   1.5e+04      87     100 ..     191     207 ..     183     208 .. 0.61
   4 ?   -1.0   6.0       0.7   2.1e+03      10      67 ..     294     366 ..     289     391 .. 0.58
   5 ?    2.8   2.1     0.048   1.4e+02      47      83 ..     435     471 ..     403     477 .. 0.74
   6 ?   15.6   2.2     5e-06     0.015      16      85 ..     504     579 ..     500     584 .. 0.86
   7 ?    1.4   0.3      0.13   3.9e+02      62      77 ..     663     678 ..     616     683 .. 0.65

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.1
                           DUF4064  69 liaivlgivgalllkknkkvsGilfiiaailslf 102
                                       li  + +++  ++ +k +  +G++ ++ a++s++
  gi|474933810|ref|YP_007687392.1|  11 LIPVLSFVIVGFFGNKTPQGGGYITVFGAAASFI 44 
                                       5556666777888999999**********99997 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.3
                           DUF4064 60 l 60
                                      l
  gi|474933810|ref|YP_007687392.1| 88 L 88
                                      1 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 5.2
                           DUF4064  87 k...vsGilfiiaails 100
                                           ++G ++++ ai s
  gi|474933810|ref|YP_007687392.1| 191 DvclMAGMFVLFQAIGS 207
                                       44557777777777766 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 0.7
                           DUF4064  10 lIGgilgillglllllflfllssgefsqeltee................qalsgedasavleflstllivlgvi 67 
                                       ++G+i g+ +++++ ++++++++++     t                   al +++ +a+l   ++l++++g++
  gi|474933810|ref|YP_007687392.1| 294 FVGIIGGVTAFFAATMAMNNMNIKKVLAYST-LsqlgymflslgaggylFALGMKNGDAALMAAGSLGYTAGIL 366
                                       4555555555555555555555444322222.235666666777777666666666666666666666666655 PP

  == domain 5  score: 2.8 bits;  conditional E-value: 0.048
                           DUF4064  47 gedasavleflstllivlgvialiaivlgivgalllk 83 
                                       +++ +a+ + l ++ ++++v++++  v  +  a+++ 
  gi|474933810|ref|YP_007687392.1| 435 DTAMDAFHHGLDSSAWIFMVLWFLGVVTAFMTAFYMF 471
                                       6678899999999999999999999999999999885 PP

  == domain 6  score: 15.6 bits;  conditional E-value: 5e-06
                           DUF4064  16 gillglllllflfllssgefsqeltee......qalsgedasavleflstllivlgvialiaivlgivgalllkkn 85 
                                         +++++ +++l++  +g fs ++t+       ++l+g+    ++e l+t ++++++i+l++i++g++++++ kk+
  gi|474933810|ref|YP_007687392.1| 504 LSIFAVVFGFTLLFGFDGLFSITYTAAtqvwqiGNLDGHTGLHFVEELFTNVYTYLTIVLVLIAIGLAFLMYCKKS 579
                                       456666667777888899999999999999989999999999999***************************9975 PP

  == domain 7  score: 1.4 bits;  conditional E-value: 0.13
                           DUF4064  62 ivlgvialiaivlgiv 77 
                                       +v+g+i l+ ++l ++
  gi|474933810|ref|YP_007687392.1| 663 VVAGIIILFVAALALC 678
                                       3444444444444444 PP

>> Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.3   2.2e-05     0.067       7      65 ..     125     176 ..     121     212 .. 0.75
   2 ?    0.1   0.3       0.2   5.9e+02      55      88 ..     483     516 ..     448     531 .. 0.58
   3 ?    0.2   0.5      0.19   5.6e+02       3      19 ..     559     575 ..     553     580 .. 0.59
   4 ?   -3.0   0.2       1.9   5.7e+03      65      79 ..     664     678 ..     641     681 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.2e-05
                                       HHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHHHHHHHC.............TTSC CS
                       Oxidored_q2   7 allfliGlygvllrrnllkvliglelisnavnlllvlagvftegtlvitnpatefadpl 65 
                                       ++lfl G++g+ +++n++ +++  e++++  +ll+  ++  +        + +++ad++
  gi|474933810|ref|YP_007687392.1| 125 VALFLTGMLGLAASSNMVEMFVFWEIMGLCSYLLIGFWSFEH-------PSGDDAADNA 176
                                       689******************************999987766.......3333444444 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.2
                                       .......TTSCGGHHHHHHHHHHHHHHHHHHHHH CS
                       Oxidored_q2  55 tnpatefadplpqalvLtaivigaaetavgLall 88 
                                       +++a + +   p a+++ + v+++  +++g +ll
  gi|474933810|ref|YP_007687392.1| 483 HENALHCHGESPNAMTMPLCVLSIFAVVFGFTLL 516
                                       3344444444555555555555555555555554 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.19
                                       HHHHHHHHHHHHHHHHH CS
                       Oxidored_q2   3 llliallfliGlygvll 19 
                                       l+++++l++iGl  +++
  gi|474933810|ref|YP_007687392.1| 559 LTIVLVLIAIGLAFLMY 575
                                       44555555555555554 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 1.9
                                       CGGHHHHHHHHHHHH CS
                       Oxidored_q2  65 lpqalvLtaivigaa 79 
                                       ++ +++L++ +++++
  gi|474933810|ref|YP_007687392.1| 664 VAGIIILFVAALALC 678
                                       444555555555555 PP

>> Proton_antipo_C  NADH-dehyrogenase subunit F, TMs, (complex I) C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.2         1     3e+03     102     119 ..     282     300 ..     281     322 .. 0.68
   2 ?   12.8   3.0   2.2e-05     0.065      85     225 ..     482     608 ..     467     626 .. 0.61

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1
                   Proton_antipo_C 102 fpllvLvl.ftlfvGliGi 119
                                       fpl+ + + + lfvG+iG 
  gi|474933810|ref|YP_007687392.1| 282 FPLFCMDInVMLFVGIIGG 300
                                       7888776635689999983 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 2.2e-05
                   Proton_antipo_C  85 enkktlsyPhEsdntmlfpllvLvlftlfvGliGip.fnqegidldilskwLtpsinllhknsnesvdwyefltnai 160
                                       e+++ l+   Es+n+m++pl+vL +f ++ G+     f+ + +++ +       +i  l+ ++     + e++tn  
  gi|474933810|ref|YP_007687392.1| 482 EHENALHCHGESPNAMTMPLCVLSIFAVVFGFTLLFgFD-GLFSITYTAATQVWQIGNLDGHTG-LHFVEELFTNVY 556
                                       4455666777*********************96543255.444555555444444445544433.345778889887 PP

                   Proton_antipo_C 161 fSvsia..lfGifiAsllYkpvysslqnldlinsfvkkgpkrilldkiinviynWSynrgYiDvfYe 225
                                       + ++i   l+ i +A+l+Y +  +s+++ ++  + ++  +k+i                 Y+  +Y+
  gi|474933810|ref|YP_007687392.1| 557 TYLTIVlvLIAIGLAFLMYCK--KSINPGKFSRNGESALYKTIQNRW-------------YMPEIYN 608
                                       766665115677789999988..777777666665554444333333.............3333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (684 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       810  (0.0451782); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.74u 0.31s 00:00:01.05 Elapsed: 00:00:00.48
# Mc/sec: 4296.84
//
Query:       gi|474933811|ref|YP_007687393.1|  [L=499]
Description: proton-translocating NADH-quinone oxidoreductase, chain M [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-71  240.7  29.3    1.8e-71  240.7  29.3    1.9  2  Proton_antipo_M  Proton-conducting membrane transporter
    0.00092   19.2   0.4    0.00092   19.2   0.4    3.2  3  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.4      0.27   2.4e+03     237     255 ..      26      45 ..       5      98 .. 0.63
   2 !  240.7  29.3     2e-75   1.8e-71       1     282 [.     128     415 ..     128     431 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.27
                   Proton_antipo_M 237 gLak.kmPilalvllvllls 255
                                       gL+  + +i+a v++++ l+
  gi|474933811|ref|YP_007687393.1|  26 GLRSkYARITAFVFTLVDLA 45 
                                       33322333444444333333 PP

  == domain 2  score: 240.7 bits;  conditional E-value: 2e-75
                   Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgil.llynltg.......tlefeels 69 
                                       a+d +l+y+ +E++l+p+y+Li  +   p++ ++++k+f++t ++sl++L+gi+ l ++ +        + +f+++ 
  gi|474933811|ref|YP_007687393.1| 128 AQDYFLFYIMWEVTLIPMYFLISWY-GGPRRHYSAIKFFIYTHVASLVMLIGIFaLAFESAAvlglgyvDFSFDAVR 203
                                       7899******************866.6669************************45577766444444444444444 PP

                   Proton_antipo_M  70 kalelglnslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla.vssne 145
                                        a   g+++  ++l++ ll++g+lvK+++vp+h+Wlpda+ eaPt +s+llA++++k+g +++ir++l +     ++
  gi|474933811|ref|YP_007687393.1| 204 AA-YGGFSEVFQTLVFGLLFFGFLVKMPAVPFHTWLPDAHTEAPTGGSVLLAGVMLKMGSYGIIRVNLEVLpLGFEN 279
                                       44.999************************************************************99998788899 PP

                   Proton_antipo_M 146 isqlllilaiismllgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFllagsv 222
                                       +++++++++++++++g+ +++aq+d+K+++AySsish+G++++a++++t++gve ai+++++h+l++a+lF++ g +
  gi|474933811|ref|YP_007687393.1| 280 WQYIMIAMGLLAAVYGAYACIAQRDLKKMVAYSSISHMGLVMLAMGLGTAIGVEFAIFQMFAHGLISAMLFMVCGMA 356
                                       **************************************************************************766 PP

                   Proton_antipo_M 223 iyerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslil 282
                                        ++   tr+i  +gg+a kmP++a+ +++++++  GlP++ gF+++f i ++ +++ +  
  gi|474933811|ref|YP_007687393.1| 357 GHN-IGTREIPLLGGMASKMPVYAAFMMFAFMASLGLPGLIGFWGEFGIVYGFYEWAQAN 415
                                       555.59********************************************9999987654 PP

>> Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.4     1e-07   0.00092       3      41 ..      64     102 ..      62     115 .. 0.88
   2 ?   -1.8   0.5      0.38   3.4e+03      22      38 ..     160     176 ..     158     181 .. 0.78
   3 ?   -1.9   0.1      0.41   3.7e+03      19      41 ..     460     479 ..     448     480 .. 0.58

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1e-07
                   Proton_antipo_N   3 tWlsvgglsieigfllDklsalmllvvtfvsllvhlYSi 41 
                                       +W+++++l++ + f++D+ls+lm+++  ++ ++v  +S 
  gi|474933811|ref|YP_007687393.1|  64 SWIDTETLKMGLIFRVDGLSILMVFLTALLEVVVVAFSY 102
                                       7**********************************9995 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.38
                   Proton_antipo_N  22 salmllvvtfvsllvhl 38 
                                       sa+  ++ t v++lv+l
  gi|474933811|ref|YP_007687393.1| 160 SAIKFFIYTHVASLVML 176
                                       77778888888888876 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.41
                   Proton_antipo_N  19 DklsalmllvvtfvsllvhlYSi 41 
                                       D++ a+ l    +++llv +Y +
  gi|474933811|ref|YP_007687393.1| 460 DTIEAICL---GVLALLVAIYGF 479
                                       55555544...346778888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (499 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       889  (0.0495845); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.51
# Mc/sec: 2936.13
//
Query:       gi|474933812|ref|YP_007687394.1|  [L=486]
Description: proton-translocating NADH-quinone oxidoreductase, chain N [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-70  238.2  29.5    1.1e-70  238.2  29.5    2.2  2  Proton_antipo_M  Proton-conducting membrane transporter


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   3.5     0.066   1.2e+03      41      93 ..      24      80 ..      14     112 .. 0.66
   2 !  238.2  29.5   6.1e-75   1.1e-70       1     277 [.     115     396 ..     115     419 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.066
                   Proton_antipo_M 41 ltllgsliLLlgil.llynltg...tlefeelskalelglnslelllllllllvgll 93
                                      lt+++ +i L++i+  +  ltg   +++   ++k + +  + ++l++ll+ ++++++
  gi|474933812|ref|YP_007687394.1| 24 LTAIAMVIVLVSIVlNVMLLTGtvdDVDYAGVFKGMFAYNDFSGLMILLFQIVIAIV 80
                                      566777777777765455566622333344444444555566666666666666655 PP

  == domain 2  score: 238.2 bits;  conditional E-value: 6.1e-75
                   Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelgln 77 
                                       a+dL+++++g E+v++++y+L+++++++p+++eA++k+++++ l+  + ++gi+++y+   tl++ ++  al +   
  gi|474933812|ref|YP_007687394.1| 115 ATDLVAIFVGVEAVSISSYVLVAMKRNDPRAAEAAVKYVVIGGLSTALTIYGISMIYGSLHTLDLADMGAALAMYGY 191
                                       78*********************************************************************999999 PP

                   Proton_antipo_M  78 slelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla......vssneisq 148
                                       s+++ ++l+++++g  +K+a++p+h+W pd+y++a+tpvs++lA    k+g+ ++i+++ll++      v  + +++
  gi|474933812|ref|YP_007687394.1| 192 SWAFIIGLIAMVAGYGFKIAAAPFHMWAPDVYEGASTPVSVMLATGSKKMGIVVFIKVFLLMFiiaqavVNIEPAQY 268
                                       *******************************************88899********999999876555444556899 PP

                   Proton_antipo_M 149 lllilaiismllgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFllagsviye 225
                                       l++++a+ sm +g++va+aq++iKr+lAySsi++ Gy+lia+av+++y++++ ++h++th+++k + Fl++g++i +
  gi|474933812|ref|YP_007687394.1| 269 LFAVIAAFSMTIGNIVAIAQNNIKRMLAYSSIAQAGYILIAMAVMSEYALTGGLFHMFTHVFMKGGAFLIVGALICA 345
                                       **************************************************************************999 PP

                   Proton_antipo_M 226 rektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaava 277
                                        +  ++i +y+gLak+ P+la ++l++l+slaG+Pp+agF skf ++++av 
  gi|474933812|ref|YP_007687394.1| 346 GVG-EKISDYNGLAKRAPLLAFAMLIFLFSLAGVPPLAGFTSKFVLFSGAVY 396
                                       865.679****************************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (486 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1172  (0.065369); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.77u 0.34s 00:00:01.11 Elapsed: 00:00:00.55
# Mc/sec: 2639.83
//
Query:       gi|474933813|ref|YP_007687395.1|  [L=59]
Description: hypothetical protein TALC_00221 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.016   15.2   0.0      0.019   14.9   0.0    1.2  1  HTH_Crp_2    Crp-like helix-turn-helix domain
      0.021   14.8   0.1      0.025   14.6   0.1    1.1  1  HRDC         HRDC domain
      0.026   14.5   0.0      0.031   14.2   0.0    1.2  1  TBPIP        TBPIP/Hop2 winged helix domain
      0.027   14.3   0.0      0.032   14.1   0.0    1.2  1  TrmB         Sugar-specific transcriptional regulator TrmB
      0.028   14.0   0.0      0.031   13.9   0.0    1.1  1  GntR         Bacterial regulatory proteins, gntR family
      0.032   14.2   0.0      0.037   14.0   0.0    1.1  1  HTH_11       HTH domain
      0.083   12.8   0.0      0.095   12.6   0.0    1.1  1  MarR_2       MarR family
       0.13   12.9   0.0       0.14   12.7   0.0    1.2  1  Phage_rep_O  Bacteriophage replication protein O
       0.15   12.2   0.0       0.64   10.1   0.0    1.9  1  HTH_20       Helix-turn-helix domain
       0.17   11.5   0.0       0.19   11.3   0.0    1.1  1  SMC_ScpB     Segregation and condensation complex subunit Scp
       0.18   11.6   0.0       0.22   11.3   0.0    1.2  1  HTH_IclR     IclR helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.2e-05     0.019      21      52 ..      17      48 ..       4      55 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.2e-05
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglis 52
                                      pl+  + A + G+ r  + ++++eLk e+ i 
  gi|474933813|ref|YP_007687395.1| 17 PLSAGDVAKITGIDRAEIDKAFKELKAENAIV 48
                                      89999************************997 PP

>> HRDC  HRDC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   1.5e-05     0.025      27      63 ..       3      40 ..       1      43 [. 0.92

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.5e-05
                                      S-HHHHHHHHHH.---SHHHHHTSTTT-HHHHHHHHHH CS
                              HRDC 27 fpdktLleiAek.lPttleeLlqiegvgkrklekygee 63
                                      ++d++++++ e+ +P +++++++i+g+ ++ ++k  +e
  gi|474933813|ref|YP_007687395.1|  3 VKDEVIKAMKEAgKPLSAGDVAKITGIDRAEIDKAFKE 40
                                      68******************************997666 PP

>> TBPIP  TBPIP/Hop2 winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.9e-05     0.031       4      50 ..       5      49 ..       2      54 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.9e-05
                             TBPIP  4 elvleylqeqnrPfsvqdvvanlqkklgKtavqkaLdeLvdegkiie 50
                                      + v + ++e  +P+s+ dv++ +  ++  + + ka  eL++e+ i++
  gi|474933813|ref|YP_007687395.1|  5 DEVIKAMKEAGKPLSAGDVAKIT--GIDRAEIDKAFKELKAENAIVS 49
                                      568899*************9987..699**************99975 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.9e-05     0.032      21      50 ..      16      45 ..       6      50 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.9e-05
                                      CCCHHCHHCCCTTSSCHCHHHHHHHHHHCT CS
                              TrmB 21 gpatadeiaeelgvprskvYevLrsLedkG 50
                                      +p++a ++a+++g++r+ + ++ ++L+   
  gi|474933813|ref|YP_007687395.1| 16 KPLSAGDVAKITGIDRAEIDKAFKELKAEN 45
                                      6899*********************98765 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.9e-05     0.031       9      55 ..       3      48 ..       1      52 [. 0.89

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.9e-05
                                      HHHHHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              GntR  9 LredIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglve 55
                                      +++++++   ++G +L s  ++a+  g++r  + +A ++L+ae+ ++
  gi|474933813|ref|YP_007687395.1|  3 VKDEVIKAMKEAGKPL-SAGDVAKITGIDRAEIDKAFKELKAENAIV 48
                                      567777777899****.**************************9986 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.3e-05     0.037       5      46 ..       7      48 ..       4      52 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.3e-05
                            HTH_11  5 ilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpI 46
                                      +++  +ea +p+s+ + A+ +++ r+ + +  k+L++  + +
  gi|474933813|ref|YP_007687395.1|  7 VIKAMKEAGKPLSAGDVAKITGIDRAEIDKAFKELKAENAIV 48
                                      6778899999***************************98654 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.8e-05     0.095      18      49 ..      15      45 ..       6      50 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.8e-05
                                      TTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTT CS
                            MarR_2 18 pgrdltvgelarrlglsksavsrilkrLvaaG 49
                                      +  +l++g++a+ +g++++ + ++ k+L a  
  gi|474933813|ref|YP_007687395.1| 15 GK-PLSAGDVAKITGIDRAEIDKAFKELKAEN 45
                                      33.49****************99999998865 PP

>> Phage_rep_O  Bacteriophage replication protein O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   8.8e-05      0.14      47      80 ..      15      48 ..       4      53 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.8e-05
                       Phage_rep_O 47 sdwisnsqlveltgisrtkvskalkeLirekvii 80
                                       +++s ++++++tgi+r+++ ka keL +e+ i+
  gi|474933813|ref|YP_007687395.1| 15 GKPLSAGDVAKITGIDRAEIDKAFKELKAENAIV 48
                                      5689999***********************9886 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0    0.0004      0.64      22      50 ..      15      43 ..       6      52 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0004
                                      CTTB-HHHHHHHHTS-HHHHHHHHHHHHH CS
                            HTH_20 22 aegltaselaerldlskntlsyHLrvLee 50
                                      +++l+a+++a+  +++++++++ +++L  
  gi|474933813|ref|YP_007687395.1| 15 GKPLSAGDVAKITGIDRAEIDKAFKELKA 43
                                      79*************************76 PP

>> SMC_ScpB  Segregation and condensation complex subunit ScpB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00012      0.19      10      40 ..      14      44 ..       7      50 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                          SMC_ScpB 10 ageplsleeLakilelskeeveealeeLkee 40
                                      ag+pls+ ++aki++++++e+++a +eLk+e
  gi|474933813|ref|YP_007687395.1| 14 AGKPLSAGDVAKITGIDRAEIDKAFKELKAE 44
                                      789*************************987 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00014      0.22       8      33 ..       7      32 ..       6      43 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                                      HHCT-CTTBSS-BHHHHHHHHTS-HH CS
                          HTH_IclR  8 iLdalaeapqeltlselArrtglpkS 33
                                      +++a  ea+ +l+  ++A+ tg+ ++
  gi|474933813|ref|YP_007687395.1|  7 VIKAMKEAGKPLSAGDVAKITGIDRA 32
                                      88999******************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.36u 0.29s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 417.93
//
Query:       gi|474933814|ref|YP_007687396.1|  [L=322]
Description: Geranylgeranyl pyrophosphate synthase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-58  197.5   0.0    2.3e-58  197.2   0.0    1.0  1  polyprenyl_synt  Polyprenyl synthetase
  ------ inclusion threshold ------
       0.06   12.6   0.0        0.1   11.9   0.0    1.3  1  ART              NAD:arginine ADP-ribosyltransferase


Domain annotation for each model (and alignments):
>> polyprenyl_synt  Polyprenyl synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.2   0.0   2.6e-62   2.3e-58       2     255 ..      29     273 ..      28     274 .. 0.95

  Alignments for each domain:
  == domain 1  score: 197.2 bits;  conditional E-value: 2.6e-62
                                       HHHHHHHHHHHHSSS--HHHHHHHHHHHHHSCGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEETTEE-HHHCT CS
                   polyprenyl_synt   2 elleealeylveagGKrlRpllvllaaealkeeeeelekaavlawivellhaasLvhDDimDdsetRRGqpcahrlv 78 
                                       ++l+e+++y++ ++GKr+Rp++ +l++ +++ +  +  +a ++++ +el+h+a+L+hDDi D+ e+RRG+++ +r++
  gi|474933814|ref|YP_007687396.1|  29 PELTEMCQYVLANHGKRVRPAFSILSYYVCGGK--DPTRAIDVGCGIELIHNATLIHDDINDQGELRRGAKALYREY 103
                                       6799***************************33..4589************************************** PP

                                       CHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC.SHHHHHHHHHHHTHHHC CS
                   polyprenyl_synt  79 GnklAindgdfllarafellaklfekslellelfsevllqtveGqlldleeekdddlskfsleeyleivkyKTaylf 155
                                          ++i+ gd+l+a+ ++l+ +    s +l++ + e++  ++ G++ + ++e+++ +    ++ey++i+  KTa l+
  gi|474933814|ref|YP_007687396.1| 104 ALGKSIVCGDYLFALGYKLMGSS---SGDLVNFIIEAASGLACGEFSQKKYERNVMVG---EAEYMDIISGKTARLI 174
                                       *********************98...679********************999888888...**************** PP

                                       HHHHHHHHHHTTHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHSS-TSHHHHTT---HHHHHHHHCT-HHH CS
                   polyprenyl_synt 156 alpvalaallagasd.eelealkdiglelGlaFQiqDDylDlfgdpevlgKpagtDiqegkctlpilkalelaspeq 231
                                       +++++++a la+ +d ++++a+ +++ + G aFQi+DD+lD+ gd +++gK++g+Di egk tlp+++a+e  +p+ 
  gi|474933814|ref|YP_007687396.1| 175 ECAAKCGAFLADSTDaQTIDAVGNFAFKAGQAFQIIDDVLDVAGDVSNTGKKLGNDIIEGKPTLPTIYAIE--DPSC 249
                                       ************8886889****************************************************..8899 PP

                                       HHHHHHHTTSSHHHHHHHHHHHHH CS
                   polyprenyl_synt 232 rkvlkeilgkkaekeedvkealel 255
                                        ++++e++++ +++ e+v+ea+el
  gi|474933814|ref|YP_007687396.1| 250 GARIREVFENPESTREEVAEAIEL 273
                                       999*****************9987 PP

>> ART  NAD:arginine ADP-ribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.1e-05       0.1     126     200 ..      92     165 ..      78     173 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.1e-05
                               ART 126 vyRgvkglrfsrakkgksvRfgqFtssslkkkvaeefgqdtllsiktclgvpIkefskfpsedevLIppfevFkv 200
                                       + Rg k   ++    gks+  g +  +   k + + +g+ + ++i++++g   +efs++++e+ v++   e   +
  gi|474933814|ref|YP_007687396.1|  92 LRRGAK-ALYREYALGKSIVCGDYLFALGYKLMGSSSGDLVNFIIEAASGLACGEFSQKKYERNVMVGEAEYMDI 165
                                       567777.445557788899999988888888899999*****************************988876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2238.92
//
Query:       gi|474933815|ref|YP_007687397.1|  [L=366]
Description: geranylgeranyl reductase family [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.7e-14   51.7   1.7    1.3e-07   31.3   0.1    3.2  3  FAD_binding_3   FAD binding domain
    2.6e-08   33.8   0.4    0.00052   19.7   0.3    2.2  2  DAO             FAD dependent oxidoreductase
    3.1e-07   29.6   0.0     0.0022   17.0   0.0    2.8  2  Trp_halogenase  Tryptophan halogenase
    1.1e-06   28.3   0.6    1.1e-06   28.3   0.6    1.9  3  FAD_oxidored    FAD dependent oxidoreductase
    2.4e-06   27.6   0.0      6e-06   26.4   0.0    1.7  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    2.7e-05   23.5   0.0    4.1e-05   22.9   0.0    1.3  1  Thi4            Thi4 family
    2.8e-05   23.4   0.2    4.6e-05   22.7   0.2    1.3  1  FAD_binding_2   FAD binding domain
    3.1e-05   23.4   0.0      4e-05   23.0   0.0    1.4  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    4.1e-05   22.5   0.1    6.4e-05   21.8   0.1    1.2  1  HI0933_like     HI0933-like protein
    6.3e-05   22.2   0.4     0.0072   15.4   0.1    2.2  2  Lycopene_cycl   Lycopene cyclase protein
     0.0015   19.1   1.1     0.0035   17.8   0.2    2.1  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
     0.0016   17.6   0.0     0.0027   16.8   0.0    1.3  1  GIDA            Glucose inhibited division protein A
     0.0088   15.4   0.1      0.014   14.7   0.1    1.3  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
  ------ inclusion threshold ------
       0.12   12.2   0.0       0.33   10.7   0.0    1.7  2  CUE             CUE domain
       0.12   12.1   0.0        0.2   11.4   0.0    1.3  1  DFP             DNA / pantothenate metabolism flavoprotein
       0.21   11.6   0.0       0.39   10.8   0.0    1.4  1  Shikimate_DH    Shikimate / quinate 5-dehydrogenase


Domain annotation for each model (and alignments):
>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.1   1.1e-10   1.3e-07       1      35 [.       8      42 ..       8      55 .. 0.91
   2 !    9.3   0.0   0.00053      0.59     152     187 ..     146     179 ..     106     211 .. 0.82
   3 !    9.1   0.0   0.00061      0.68     283     308 ..     262     287 ..     253     317 .. 0.86

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 1.1e-10
                                      EEEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                     FAD_binding_3  1 etdVlIVGaGpaGlmlallLseaGvrvvlvekrst 35
                                      etdVlIVG+GpaG ++a+  +e+Gvrv+ +e+r +
  gi|474933815|ref|YP_007687397.1|  8 ETDVLIVGSGPAGSLAARAAAEKGVRVTFIERRPE 42
                                      69******************************976 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00053
                                       EEEEEEEEE--GTT-HHHHHHTGGEEEEEEEEEEEE CS
                     FAD_binding_3 152 tvrakYlvGaDGgrStvrktlgiefegeetvyeagv 187
                                       ++r k ++GaDG  S+v++++g++  ++++ y+a +
  gi|474933815|ref|YP_007687397.1| 146 DIRYKVIIGADGPGSRVAQAMGLP--ANRNCYPAVS 179
                                       577788****************77..5555555555 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.00061
                                       ETTEEE-GGGTEEE-STTSHHHHHHH CS
                     FAD_binding_3 283 kgrvflaGDAaHihpPtgGqGlNtai 308
                                        g+ +laGDAa ++ P++G G+  a+
  gi|474933815|ref|YP_007687397.1| 262 TGNCMLAGDAAGVVMPVNGGGIPQAM 287
                                       6899*****************97776 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.3   4.6e-07   0.00052       1      33 [.      10      44 ..      10      50 .. 0.96
   2 !   12.5   0.0   7.2e-05      0.08     137     224 ..      99     175 ..      47     299 .. 0.62

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 4.6e-07
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                      dv+i+G+G +G+ +A+++a++g  Vt +e+++++g
  gi|474933815|ref|YP_007687397.1| 10 DVLIVGSGPAGSLAARAAAEKGvrVTFIERRPEVG 44
                                      8******************************9877 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 7.2e-05
                                       ETTEEEE.EHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEE.EEEEEEEE--GGGHHHH.HTT CS
                               DAO 137 ypdtgqv.dpakltaalaraaealGveilegtevtgleeedgkvwgverttpgen.daadavVnaaGawsdll.gll 210
                                       +p tg   d  ++ ++la++a ++G+e+++++   ++e+      g+  +t      +++ ++ a G++s+ + ++ 
  gi|474933815|ref|YP_007687397.1|  99 FPFTGYTtDRDRFDQYLADQAVSAGAELIRKCAFDRIED------GI-AKT-SLFdIRYKVIIGADGPGSRVAqAMG 167
                                       34444444999**************************43......34.222.22212356699999***98662222 PP

                                       CTTTSEEEEEEEEE CS
                               DAO 211 keldlpispvrgqv 224
                                         l  p  + r ++
  gi|474933815|ref|YP_007687397.1| 168 --L--P--ANRNCY 175
                                       ..2..2..223333 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.9e-06    0.0022       1      56 [.      10      63 ..      10      70 .. 0.83
   2 !    8.8   0.0   0.00058      0.65     148     340 ..     103     287 ..      77     318 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.9e-06
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-.SSS--.-SS-EE--THHHHTHHHH CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlves.eeigt.vgvGeatipsirkllrlL 56
                                      +++ivG G+aG+laA a a+ +   ++vt +e  +e+g+ v+ Ge ++ps++++ +++
  gi|474933815|ref|YP_007687397.1| 10 DVLIVGSGPAGSLAARAAAEKG---VRVTFIERrPEVGVpVRCGE-LVPSVQEIKDMF 63
                                      699*************999998...9*****96368875378888.788888877765 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00058
                                       EEEE-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-T.TS-EEEEEETTS-EEE-SEEEE-SGGG-IIIIIIT---EE CS
                    Trp_halogenase 148 AyhldaalyakfLrrvaearGvtrvegkvvevqlde.dgrveslrledgreveadlfiDcsGfrgllieqaLktgfe 223
                                       +y  d+ +++++L + a ++G + ++ +      d  ++ +++  l     + +  +i + G  +++ +qa   g  
  gi|474933815|ref|YP_007687397.1| 103 GYTTDRDRFDQYLADQAVSAGAELIRKCA----FDRiEDGIAKTSLF---DIRYKVIIGADGPGSRV-AQA--MGLP 169
                                       68899999999999999999999888887....33335556666663...45678888888876665.455..4666 PP

                                       E-TTT----EEEEEEEE--H---SSEEEEE-SSEEEEEEEETTEEEEEEEE-TTTS..-HHHHHHHHHHHCT--TTT CS
                    Trp_halogenase 224 dwsdvLltdrAlavqveseelvepytrataekaGWtWkiPLqhrlgnGyvyssaha..dddeAlaellaeldgklea 298
                                          +  +  +A a +++++++++ + + +a  a   W +P  +r+  G+ +s ++   +    +++++++ ++kl +
  gi|474933815|ref|YP_007687397.1| 170 ANRNCYPAVSAQA-EGDFDPVIQMFFGRIAPGA-YGWIMPKDGRANVGVGFSPKFSsgSLSGYMERFVKDHGLKLIT 244
                                       6677777777766.7777888888877777644.4456899999999999999998444455577788887777555 PP

                                       S-.EEEE---EEES-SEETTEEE-CCCTEE--CCCS-HHHHHH CS
                    Trp_halogenase 299 ep.rkirfttGrrkqawvknvvalGlasgfvePlestsihliq 340
                                           k     G  +++   n+++ G+a+g v P+++ +i  ++
  gi|474933815|ref|YP_007687397.1| 245 PIkGKYVPSEGPISRTVTGNCMLAGDAAGVVMPVNGGGIPQAM 287
                                       4434555567889999999999999999999999999987665 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.6     1e-09   1.1e-06       1      35 [.      10      44 ..      10      45 .. 0.98
   2 ?   -2.7   0.3       2.6   2.9e+03     396     410 ..     261     275 ..     259     276 .. 0.88
   3 ?   -3.0   0.0       3.1   3.5e+03     398     414 ..     284     300 ..     283     308 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 1e-09
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlG 35
                                      Dv++vG+gpaG  AA aAa++G +v  +e+r+ +G
  gi|474933815|ref|YP_007687397.1| 10 DVLIVGSGPAGSLAARAAAEKGVRVTFIERRPEVG 44
                                      9*******************************998 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.6
                      FAD_oxidored 396 vepvcmalGqAaGva 410
                                       v++ cm  G AaGv+
  gi|474933815|ref|YP_007687397.1| 261 VTGNCMLAGDAAGVV 275
                                       6789*********85 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 3.1
                      FAD_oxidored 398 pvcmalGqAaGvaAala 414
                                       p+ m +G  aG aAa  
  gi|474933815|ref|YP_007687397.1| 284 PQAMITGRMAGEAAAEN 300
                                       899**********9965 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   5.3e-09     6e-06       1      34 [.      13      46 ..      13      61 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 5.3e-09
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGG CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGr 34
                                      IvG+G +G++aA+++a++g++v+ +e+r+ +G  
  gi|474933815|ref|YP_007687397.1| 13 IVGSGPAGSLAARAAAEKGVRVTFIERRPEVGVP 46
                                      9******************************965 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   3.7e-08   4.1e-05      12      54 ..       3      44 ..       1      55 [. 0.90

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 3.7e-08
                                      HHHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS-- CS
                              Thi4 12 llkyaesDvvivGaGssGLtaayylakkpdlkvailersvspG 54
                                      ll+ +e+Dv+ivG+G++G  aa+  a+k +++v+ +er+  +G
  gi|474933815|ref|YP_007687397.1|  3 LLDTIETDVLIVGSGPAGSLAARAAAEK-GVRVTFIERRPEVG 44
                                      67899***********************.********987666 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.2   4.1e-08   4.6e-05       1      35 [.      10      44 ..      10      49 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 4.1e-08
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGG CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefg 35
                                      Dv+++GsG AG  AA +aae+G +v+ +e  +e+g
  gi|474933815|ref|YP_007687397.1| 10 DVLIVGSGPAGSLAARAAAEKGVRVTFIERRPEVG 44
                                      9****************************999876 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   3.6e-08     4e-05       2      34 ..      10      41 ..       9     173 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 3.6e-08
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHC CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlvelegt 34
                                      dv+++G+GpAG  aa+ +a++g++vt +e ++ 
  gi|474933815|ref|YP_007687397.1| 10 DVLIVGSGPAGSLAARAAAEKGVRVTFIE-RRP 41
                                      8***************************6.332 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   5.7e-08   6.4e-05       2      36 ..      10      44 ..       9      49 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 5.7e-08
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                      dv+++G G+AG +aA +aa++g rV+ +e+ +++g
  gi|474933815|ref|YP_007687397.1| 10 DVLIVGSGPAGSLAARAAAEKGVRVTFIERRPEVG 44
                                      89****************************99998 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   6.4e-06    0.0072       1      36 [.      10      43 ..      10      49 .. 0.88
   2 ?    4.9   0.0      0.01        11     242     304 ..     250     314 ..     220     348 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.4e-06
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsl 36
                                      Dv+++G+GpAg slAar  +a++g++v+ ie  p++
  gi|474933815|ref|YP_007687397.1| 10 DVLIVGSGPAG-SLAARA-AAEKGVRVTFIERRPEV 43
                                      9**********.678887.79**********98876 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.01
                     Lycopene_cycl 242 viPvtlggslprleqkvlaiGaaaglvhPaTGYsvarslaeapllasaiaaalres...slsaraw 304
                                       ++P  +g+  + +  + + +G aag+v P  G  +++++   ++  +a a+        + ++++w
  gi|474933815|ref|YP_007687397.1| 250 YVPS-EGPISRTVTGNCMLAGDAAGVVMPVNGGGIPQAMITGRMAGEAAAENILDGrplEVYEQEW 314
                                       6777.55555555667899********************999977777665433212444444444 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.2   3.2e-06    0.0035       2      35 ..      11      44 ..      10      53 .. 0.93
   2 ?   -2.3   0.0       5.9   6.7e+03       3      18 ..     151     166 ..     151     171 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.2e-06
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                      v++vG+G  g  +A a+ae g +Vt +er++++ 
  gi|474933815|ref|YP_007687397.1| 11 VLIVGSGPAGSLAARAAAEKGVRVTFIERRPEVG 44
                                      89*****************************987 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.9
                                       EEECSSHHHHHHHHHH CS
                         Pyr_redox   3 vvvGgGyiglElAgal 18 
                                       v++G++  g  +A+a+
  gi|474933815|ref|YP_007687397.1| 151 VIIGADGPGSRVAQAM 166
                                       89****9999999875 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   2.4e-06    0.0027       1      29 [.      10      38 ..      10      62 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.4e-06
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEE CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLit 29
                                      dv ++G G AG+ AA aaa++G++v+ i 
  gi|474933815|ref|YP_007687397.1| 10 DVLIVGSGPAGSLAARAAAEKGVRVTFIE 38
                                      799**********************9984 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   1.3e-05     0.014      24      63 ..       8      43 ..       1      52 [. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.3e-05
                                      TCB---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHH CS
                       AlaDh_PNT_C 24 pgvepakvlviGgGvaGlqAiatakglgakVtvlDvrpar 63
                                      +      vl++G G aG  A+++a++ g +Vt ++ rp++
  gi|474933815|ref|YP_007687397.1|  8 E----TDVLIVGSGPAGSLAARAAAEKGVRVTFIERRPEV 43
                                      4....78******************************986 PP

>> CUE  CUE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0    0.0003      0.33       5      17 ..      56      68 ..      54      70 .. 0.88
   2 ?   -3.7   0.0       9.2     1e+04      27      36 ..     182     191 ..     181     193 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0003
                                      HHHHHHHSTTS-H CS
                               CUE  5 letLkemFPdlde 17
                                      ++++k+mFP+l++
  gi|474933815|ref|YP_007687397.1| 56 VQEIKDMFPNLER 68
                                      89*********97 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 9.2
                                       CTTTHHHHHH CS
                               CUE  27 sngnvEatin 36 
                                         g+ +++i 
  gi|474933815|ref|YP_007687397.1| 182 AEGDFDPVIQ 191
                                       5789999886 PP

>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00018       0.2      28      78 ..      16      68 ..      14      75 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00018
                                      --HHHHHHHHHHHHTT-EEEEEE-S-SS---TT-.E.EEE--SHHHHHHHHHH CS
                               DFP 28 SGkmGyalAeaaaarGaeVtlvsgpvsletpegv.e.vvkvesaeemleavee 78
                                      SG  G   A+aaa++G +Vt++    ++  p ++ e v +v++ ++m  ++e+
  gi|474933815|ref|YP_007687397.1| 16 SGPAGSLAARAAAEKGVRVTFIERRPEVGVPVRCgElVPSVQEIKDMFPNLER 68
                                      999*******************9998877776543414458888888776665 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00035      0.39      12      51 ..       8      46 ..       2      74 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00035
                                      T-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHH CS
                      Shikimate_DH 12 ekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerake 51
                                      e  vl++G G  ++l+a++ ++kgv+ v+ + R  e    
  gi|474933815|ref|YP_007687397.1|  8 ETDVLIVGSGPAGSLAARAAAEKGVR-VTFIERRPEVGVP 46
                                      578***********************.8888887775544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       265  (0.0147805); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 2238.05
//
Query:       gi|474933816|ref|YP_007687398.1|  [L=141]
Description: putative nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-11   45.0   0.0    1.6e-11   44.5   0.0    1.2  1  PIN_6           PIN domain of ribonuclease
     0.0014   19.1   0.0     0.0018   18.8   0.0    1.1  1  PIN             PIN domain
     0.0019   18.3   2.3      0.021   15.0   1.1    2.2  2  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
     0.0055   16.5   1.1      0.011   15.5   1.1    1.5  1  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
     0.0076   15.7   0.0      0.015   14.8   0.0    1.5  2  PIN_5           PINc domain ribonuclease
  ------ inclusion threshold ------
      0.017   15.2   0.1      0.033   14.2   0.1    1.5  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.048   13.7   0.4      0.086   12.8   0.4    1.4  1  zinc-ribbons_6  zinc-ribbons
       0.27   11.1   0.3       0.27   11.1   0.3    2.1  2  Rad50_zn_hook   Rad50 zinc hook motif
        1.9    8.5   4.6       0.39   10.7   1.1    1.8  2  Ogr_Delta       Ogr/Delta-like zinc finger


Domain annotation for each model (and alignments):
>> PIN_6  PIN domain of ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   0.0   8.2e-15   1.6e-11      21      88 ..       7      73 ..       3      74 .. 0.93

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 8.2e-15
                             PIN_6 21 eklyttpeVvaEirdkkarerlellplelevrePspesvkkvtefakktGDlsvLSktDievlALtye 88
                                      e+++  p V++E+ + k  +rl l+   l+v + +++s+kkv+e a+k GDl  LS +D+ vlAL+++
  gi|474933816|ref|YP_007687398.1|  7 EEFCCPPGVIRELEKYKD-RRLGLWGDLLRVSDCTEASLKKVEETARKSGDLGRLSPVDMTVLALALD 73
                                      789999*******98876.589********************************************97 PP

>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   8.8e-07    0.0018      59     120 ..      25      89 ..      13      91 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 8.8e-07
                                       HHHHHHHHTSEEEEBCHHHHHHHHHHHHHHH....SBHHHHHHHHHHHHHT-EEE.ESSTHHHHHH CS
                               PIN  59 velllllsalkilpidaeiaeeaaeialkyg....llpnDaliaAtAkehgikliatfDedfrrva 120
                                       ++l l  + l++ + +++ +++++e a+k g    l+p D+ ++A+A+  g +++ t D  + ++a
  gi|474933816|ref|YP_007687398.1|  25 RRLGLWGDLLRVSDCTEASLKKVEETARKSGdlgrLSPVDMTVLALALDVGGTVL-TDDYSIQNTA 89 
                                       4444457889999999************************************999.***9988876 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0       0.1     2e+02      28      47 ..      38      57 ..      36      66 .. 0.86
   2 !   15.0   1.1     1e-05     0.021       1      32 [.     104     134 ..     104     137 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.1
                      NOB1_Zn_bind 28 kCGnktLkrvavsvdengel 47
                                       C +++Lk+v+ + +++g+l
  gi|474933816|ref|YP_007687398.1| 38 DCTEASLKKVEETARKSGDL 57
                                      7*********9999888765 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1e-05
                      NOB1_Zn_bind   1 ikrvkswvlrChaCfkvtkdmtkkFCpkCGnk 32 
                                       i++v +w ++C +C k +k+ ++  Cp CG++
  gi|474933816|ref|YP_007687398.1| 104 ITKVEKWNYQCIGCGKWYKE-KRDDCPICGSP 134
                                       889*************9987.5677*****86 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   1.1   5.7e-06     0.011      25      48 ..     113     136 ..     109     138 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.7e-06
                                       E-HHHHHHHHHTT-B-TTT--B-- CS
                        zf-C3HC4_3  25 lCeeCaekllkrkkkCpiCrrpie 48 
                                        C  C ++++++++ CpiC +p++
  gi|474933816|ref|YP_007687398.1| 113 QCIGCGKWYKEKRDDCPICGSPMR 136
                                       5********99********99975 PP

>> PIN_5  PINc domain ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.8   3.5e+03      47      61 ..      11      25 ..       8      27 .. 0.79
   2 !   14.8   0.0   7.3e-06     0.015     156     189 ..      61      94 ..      35     101 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.8
                             PIN_5 47 ippsvykElkeflkr 61
                                       pp v +El+++ +r
  gi|474933816|ref|YP_007687398.1| 11 CPPGVIRELEKYKDR 25
                                      689999999998876 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 7.3e-06
                             PIN_5 156 saeDldvllLAkELdaavvssDeGikkwaeklGl 189
                                       s  D+ vl LA ++ ++v+++D  i++ a+ +G+
  gi|474933816|ref|YP_007687398.1|  61 SPVDMTVLALALDVGGTVLTDDYSIQNTARIMGI 94 
                                       67899****************************8 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   1.6e-05     0.033      33      95 ..      57     134 ..      35     139 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.6e-05
                                       EETTCT--HHHHHHHHHHHHCC.T.TTT-EEE..................EEEE--EEEETTTS-EEECHHHHHS-T CS
                              HypA  33 vGelsgvepeaLefafellaegtv.legaeLe..................ieevpvkvrCreCgkefeleekalrCp 90 
                                       +G+ls v+  +L+ a+++   gtv +++ +++                   + ++ +++C  Cgk ++++++   Cp
  gi|474933816|ref|YP_007687398.1|  57 LGRLSPVDMTVLALALDVG--GTVlTDDYSIQntarimgipcrgvgqngiTKVEKWNYQCIGCGKWYKEKRD--DCP 129
                                       5666777777777776653..333233333334444446777777777767778899*******99998866..8** PP

                                       TTSSS CS
                              HypA  91 kCgsa 95 
                                        Cgs 
  gi|474933816|ref|YP_007687398.1| 130 ICGSP 134
                                       ***96 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.4   4.3e-05     0.086      12      43 ..     107     139 ..      94     140 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.3e-05
                                       E-SSEEE-TTT--EEE.EEEE-SSS-S---EEE CS
                    zinc-ribbons_6  12 krgeqyhCeaCqedlk.kealCpeCeqelevlk 43 
                                        ++ +y+C  C + +k k   Cp C++++  ++
  gi|474933816|ref|YP_007687398.1| 107 VEKWNYQCIGCGKWYKeKRDDCPICGSPMRAHR 139
                                       45579********77615679*******98765 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.3      0.68   1.4e+03      17      23 ..       6      12 ..       1      12 [. 0.65
   2 ?   11.1   0.3   0.00014      0.27      16      33 ..     122     139 ..     121     141 .] 0.82

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.68
                                      T-SEE-T CS
                     Rad50_zn_hook 17 eakgcCP 23
                                      +++ cCP
  gi|474933816|ref|YP_007687398.1|  6 DEEFCCP 12
                                      4555**9 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00014
                                       TT-SEE-TTT--EE-HHH CS
                     Rad50_zn_hook  16 keakgcCPlCgReldeeh 33 
                                       ke++++CP Cg+++  ++
  gi|474933816|ref|YP_007687398.1| 122 KEKRDDCPICGSPMRAHR 139
                                       67888********98766 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       3.2   6.3e+03      24      28 ..     110     114 ..     105     119 .. 0.65
   2 ?   10.7   1.1    0.0002      0.39       2      14 ..     128     140 ..     127     141 .] 0.88

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.2
                         Ogr_Delta  24 ryyqC 28 
                                         yqC
  gi|474933816|ref|YP_007687398.1| 110 WNYQC 114
                                       56888 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0002
                         Ogr_Delta   2 CPhCgapaaarts 14 
                                       CP Cg+p++a ++
  gi|474933816|ref|YP_007687398.1| 128 CPICGSPMRAHRK 140
                                       *********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1047.51
//
Query:       gi|474933817|ref|YP_007687399.1|  [L=190]
Description: CDP-diglyceride synthetase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.2e-43  146.2   7.5    1.1e-42  146.0   7.5    1.0  1  CarS-like     CDP-archaeol synthase
    2.8e-06   27.3   2.2    2.8e-06   27.3   2.2    2.0  2  CTP_transf_1  Cytidylyltransferase family
  ------ inclusion threshold ------
        6.2    6.8  10.5       0.31   10.9   2.3    2.7  3  PetG          Cytochrome B6-F complex subunit 5


Domain annotation for each model (and alignments):
>> CarS-like  CDP-archaeol synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.0   7.5   1.8e-46   1.1e-42       2     175 .]       7     190 .]       6     190 .] 0.85

  Alignments for each domain:
  == domain 1  score: 146.0 bits;  conditional E-value: 1.8e-46
                         CarS-like   2 ldlilksiylllpayvanasavlvGGGtpvdlGktlvdGrrliGdGvtyrGtvaGvlvGvlvgliqglleklsi.la 77 
                                       + ++l+  +l+lpa ++n  av++GGGt +d+G+++  G+r+ GdG+++rG+ +G ++G++ gli   +  l +   
  gi|474933817|ref|YP_007687399.1|   7 IVIMLNGFWLFLPAMIPNSAAVVFGGGTKMDFGRSW-RGKRIFGDGKSWRGFFGGAFSGIVLGLILIGISALFGsDD 82 
                                       567899****************************97.7*************************99888877776477 PP

                         CarS-like  78 ldssgsvlefvilalllafGallGdavGsfikrrlkierGkpalildqldfvlgallla........ypvkllpiel 146
                                          +g +   + +   l+fGa+lGd++G+fikrr+++erG +a+ildq dfv+gal ++        y + +   ++
  gi|474933817|ref|YP_007687399.1|  83 YWGYGKFWGCLSVIACLSFGAVLGDLCGAFIKRRYGLERGAKAPILDQYDFVIGALCITalfnpgwvYDIYIEGWHI 159
                                       889*****************************************************998555333222233333345 PP

                         CarS-like 147 iilivlitl..vlhlsaniiayklglkdvwy 175
                                        +li l+ +   +h  +nii yk+glk+ ++
  gi|474933817|ref|YP_007687399.1| 160 AALIFLLVVmfSIHRIVNIIGYKMGLKKEPW 190
                                       5555554441168999***********9887 PP

>> CTP_transf_1  Cytidylyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   2.2   4.6e-10   2.8e-06     170     231 ..      51     118 ..      38     121 .. 0.92
   2 ?   -0.1   0.2      0.11   6.5e+02      23      34 ..     157     169 ..     128     188 .. 0.49

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 4.6e-10
                                       --BHHHHHHHHHHHHHHHHHHHHHHHCTS......---TTSHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                      CTP_transf_1 170 kKTveGfigGlvaavvvglllalvlskal......alsllhllllslllslvavfGDLveSglKRafg 231
                                       +K++ Gf+gG+++ +v+gl+l+ +   +       +  ++  l + + ls+ av+GDL    +KR++g
  gi|474933817|ref|YP_007687399.1|  51 GKSWRGFFGGAFSGIVLGLILIGISALFGsddywgYGKFWGCLSVIACLSFGAVLGDLCGAFIKRRYG 118
                                       6*******************99888876588899999****************************987 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.11
                                       HHHHHHHH.HHHH CS
                      CTP_transf_1  23 lvflllva.vvvi 34 
                                       + +++l++ +vv+
  gi|474933817|ref|YP_007687399.1| 157 WHIAALIFlLVVM 169
                                       2222211101111 PP

>> PetG  Cytochrome B6-F complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.4      0.18   1.1e+03      11      21 ..       4      14 ..       3      20 .. 0.81
   2 ?   10.9   2.3   5.2e-05      0.31       7      22 ..      63      78 ..      61      80 .. 0.92
   3 ?   -1.9   0.0      0.54   3.2e+03       5      12 ..      99     106 ..      96     107 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.18
                              PetG 11 LGLvpVTlaGL 21
                                      LG +++ l G 
  gi|474933817|ref|YP_007687399.1|  4 LGVIVIMLNGF 14
                                      9*****99994 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 5.2e-05
                              PetG  7 lGiVLGLvpVTlaGLF 22
                                      +GiVLGL+ + +  LF
  gi|474933817|ref|YP_007687399.1| 63 SGIVLGLILIGISALF 78
                                      8***********9999 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.54
                              PetG   5 LLlGiVLG 12 
                                       L +G VLG
  gi|474933817|ref|YP_007687399.1|  99 LSFGAVLG 106
                                       779****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1255.45
//
Query:       gi|474933818|ref|YP_007687400.1|  [L=178]
Description: orotate phosphoribosyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.7e-16   58.4   0.9    7.7e-16   58.0   0.9    1.2  1  Pribosyltran  Phosphoribosyl transferase domain
     0.0003   20.3   0.0    0.00041   19.8   0.0    1.2  1  UPRTase       Uracil phosphoribosyltransferase
  ------ inclusion threshold ------
      0.085   12.4   0.0      0.091   12.3   0.0    1.1  1  DUF1403       Protein of unknown function (DUF1403)
       0.11   12.5   1.5         12    5.9   0.0    2.8  3  GA-like       GA-like domain


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.0   0.9   1.7e-19   7.7e-16       8     131 ..      39     153 ..      32     164 .. 0.91

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 1.7e-19
                                       ---EEEEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE--- CS
                      Pribosyltran   8 npaildavarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlled 84 
                                        pa+l+ +a+ +a   +e + +pd v+g+  g++p+a++l+ e ++pl +vrk++++++++  +            +
  gi|474933818|ref|YP_007687400.1|  39 KPAVLALIAKEMAAEMRELGLNPDRVAGVVLGSIPLATALSLETGIPLLMVRKERKDHGTGRLV---------EGDL 106
                                       6899999999999999999*********************************************.........6789 PP

                                       -TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHH CS
                      Pribosyltran  85 pagkkVliVDDildtGgTllaalelLkekgpeevriavlvdkpatee 131
                                        +g  Vl+V+D+++t+g+  +a+ +L+e+g+++ ++  ++d+  + +
  gi|474933818|ref|YP_007687400.1| 107 NKGDDVLVVEDVITTAGSSMKAIAALREEGAKVEKVFSVIDREGGGR 153
                                       9****************9999***********999999988876655 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   9.3e-08   0.00041     120     156 ..     108     144 ..      83     157 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 9.3e-08
                           UPRTase 120 aertvlllDpviaTGgsaaaaiqlLkergvgeekIlv 156
                                       + + vl+++ vi T gs ++ai  L+e+g+++ek++ 
  gi|474933818|ref|YP_007687400.1| 108 KGDDVLVVEDVITTAGSSMKAIAALREEGAKVEKVFS 144
                                       5678*****************************9864 PP

>> DUF1403  Protein of unknown function (DUF1403)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0     2e-05     0.091     139     215 ..      32     105 ..       2     146 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2e-05
                           DUF1403 139 evralaasekaaallaaavaaavaalre.daevlalwladlvLAqrLgWaravPllaaelakpalRkeaggkRvRpg 214
                                       +++++++++   al+a+++aa++ +l     +v++++l  + LA++L  ++ +Pll+ +  +       g+ R   g
  gi|474933818|ref|YP_007687400.1|  32 DIKKASTKPAVLALIAKEMAAEMRELGLnPDRVAGVVLGSIPLATALSLETGIPLLMVRKERK----DHGTGRLVEG 104
                                       456666677777788888888888877756788999********************9987653....4444555555 PP

                           DUF1403 215 e 215
                                       +
  gi|474933818|ref|YP_007687400.1| 105 D 105
                                       4 PP

>> GA-like  GA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       2.1   9.4e+03      14      23 ..       3      12 ..       2      13 .. 0.61
   2 ?    4.9   0.0    0.0057        26      21      45 ..      22      45 ..      21      50 .. 0.86
   3 ?    5.9   0.0    0.0027        12      14      34 ..     127     147 ..     126     148 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.1
                           GA-like 14 aAkaeLkaaG 23
                                      ++k++L++ G
  gi|474933818|ref|YP_007687400.1|  3 DVKKALEECG 12
                                      5677776665 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0057
                           GA-like 21 aaGitsdfyiekIdkAkTvEgVkaL 45
                                      a G++s +yi+ I kA+T+  V aL
  gi|474933818|ref|YP_007687400.1| 22 ASGAKSSYYID-IKKASTKPAVLAL 45
                                      579******98.******9888766 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.0027
                           GA-like  14 aAkaeLkaaGitsdfyiekId 34 
                                       +A+a+L+++G++ ++ ++ Id
  gi|474933818|ref|YP_007687400.1| 127 KAIAALREEGAKVEKVFSVID 147
                                       7**********9999988888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 1161.89
//
Query:       gi|474933819|ref|YP_007687401.1|  [L=180]
Description: uracil-DNA glycosylase, family 4 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-34  117.9   0.0      5e-34  117.5   0.0    1.1  1  UDG       Uracil DNA glycosylase superfamily


Domain annotation for each model (and alignments):
>> UDG  Uracil DNA glycosylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.5   0.0   2.8e-38     5e-34       3     145 ..      26     163 ..      24     172 .. 0.86

  Alignments for each domain:
  == domain 1  score: 117.5 bits;  conditional E-value: 2.8e-38
                                       C-CTT-SEEEEESSTCHHHHHHSSSS.-STT--HHHHHHHCCCCCCCHHGCTEEEEESSS....SECGCTTCCCCTC CS
                               UDG   3 egppdakvvivGeaPgaeedatglpFsgragnllrkllneaglkrdleseqgvyitnvvkcrppgnrdtptsaeika 79 
                                        g+ d++vv+vGeaPg++ed +g+pF+grag++l+k+l+++gl+r      ++ itn+vkcrpp+nr +p ++e++a
  gi|474933819|ref|YP_007687401.1|  26 SGDLDSPVVLVGEAPGENEDLQGKPFVGRAGEILNKILEDVGLDR-----GRLMITNTVKCRPPQNR-EPQPEEMAA 96 
                                       6999*****************************************.....*****************.********* PP

                                       CHHHHHHHHHHHHSSEEEEESHHHHHH....HHHHSCESCCCSCT......SEEEEES-SSTTTTTTTTSHHH CS
                               UDG  80 caplleeeiellkprlivllGktaakall..geklgklrgklleak.....irvlplphPsplnrnffksnpe 145
                                       c+p+l++e++    ++iv lGk a + l+  +  ++ + +++ +++     i ++p++hP +  ++    +p+
  gi|474933819|ref|YP_007687401.1|  97 CRPFLDSELATK--KVIVGLGKSAIRDLMgyEGPMKPIVNTRQHITvggkeILFIPTYHPMACVYQ----KPA 163
                                       ********9976..*************977633444444333333344678**********99999....333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 1122.79
//
Query:       gi|474933820|ref|YP_007687402.1|  [L=265]
Description: putative sugar phosphatases of the HAD superfamily [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-27   96.1   0.0    5.3e-27   93.9   0.0    1.9  2  Hydrolase_6      Haloacid dehalogenase-like hydrolase
    1.7e-21   76.1   0.0    3.1e-21   75.2   0.0    1.5  1  Hydrolase_like   HAD-hyrolase-like
    4.1e-10   40.3   0.3    0.00022   21.6   0.0    3.1  3  Hydrolase        haloacid dehalogenase-like hydrolase
    4.3e-08   33.5   0.0    3.9e-05   23.8   0.0    2.3  2  HAD_2            Haloacid dehalogenase-like hydrolase
    0.00026   20.8   0.0      0.073   12.8   0.0    2.2  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
    0.00036   20.2   0.0    0.00054   19.6   0.0    1.2  1  PGP_phosphatase  Mitochondrial PGP phosphatase
     0.0056   16.3   0.0      0.013   15.1   0.0    1.6  1  Acid_phosphat_B  HAD superfamily, subfamily IIIB (Acid phosph
  ------ inclusion threshold ------
      0.015   15.7   0.0          9    6.6   0.0    2.5  2  HAD              haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.9   0.0   2.4e-30   5.3e-27       1     100 [.       4     103 ..       4     104 .. 0.98
   2 ?   -0.4   0.0      0.56   1.2e+03      54      97 ..     192     235 ..     178     238 .. 0.62

  Alignments for each domain:
  == domain 1  score: 93.9 bits;  conditional E-value: 2.4e-30
                                       EEEESTTTSEETTEE-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHHHHTT----GGGEEEHHHHHHHHHHHH CS
                       Hydrolase_6   1 flfDidGvLwrgdkaipgaaealnalraagkpvvllTNnsskseeeyakkleklgvditeeqvvtsataaaeylkkr 77 
                                       f++D+dG++++gd++ipga+e++  lr++g+p+ +lTNnss ++  +a++l++lg+d+t+++v++s  a+ ++++++
  gi|474933820|ref|YP_007687402.1|   4 FAIDMDGTVYKGDNPIPGAKEFIAELRKRGIPFRFLTNNSSHTRGFFAARLKRLGFDVTDDDVLSSTLATTRFIADK 80 
                                       689************************************************************************** PP

                                       SXXXEEEEESXHHHHHHHHHTTX CS
                       Hydrolase_6  78 kadkkvlvigeeglreelkeagf 100
                                       +++k+v vi ++++++e++  g+
  gi|474933820|ref|YP_007687402.1|  81 RKGKTVRVIATPDVCKEIEVSGI 103
                                       ******************99998 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.56
                                       TT----GGGEEEHHHHHHHHHHHHSXXXEEEEESXHHHHHHHHH CS
                       Hydrolase_6  54 lgvditeeqvvtsataaaeylkkrkadkkvlvigeeglreelke 97 
                                       +g++ ++  ++    ++   +++  + +++lv+ +e +r+++++
  gi|474933820|ref|YP_007687402.1| 192 MGIPPEDVVMIGDRLSTDIRMAELAGTRSILVLSGETDRAIFES 235
                                       44444443444444444444555578899999999999988876 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.2   0.0   1.4e-24   3.1e-21       1      74 [.     176     249 ..     176     250 .. 0.97

  Alignments for each domain:
  == domain 1  score: 75.2 bits;  conditional E-value: 1.4e-24
                                       E.STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTTHHHHHHHHT---SEEES CS
                    Hydrolase_like   1 vlgKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrpedleepehkptyvaddlae 74 
                                       v+gKP++ m+++a +++g++pe+v+miGDrl tDi++A  aG +s+LVl+G t+++  e+   +pt+v+d++a+
  gi|474933820|ref|YP_007687402.1| 176 VIGKPNRLMLEMAGAEMGIPPEDVVMIGDRLSTDIRMAELAGTRSILVLSGETDRAIFESSDSRPTFVLDSVAD 249
                                       68********************************************************9999**********98 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1     0.069   1.5e+02       4      16 ..       4      16 ..       3      19 .. 0.86
   2 !   14.2   0.0   1.8e-05      0.04     115     156 ..      16      55 ..      11      91 .. 0.76
   3 !   21.6   0.0   9.6e-08   0.00022     162     210 .]     168     217 ..     141     217 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.069
                                      EEEESBTTTBCHH CS
                                      xxxxxxxxxxxxx RF
                         Hydrolase  4 vvfDkdGTLttge 16
                                      +++D+dGT+++g 
  gi|474933820|ref|YP_007687402.1|  4 FAIDMDGTVYKGD 16
                                      689*******997 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1.8e-05
                                       HTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 115 dplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG 156
                                       d+  + p+a+e++a+L+++gi+   lt+++++t    a +l 
  gi|474933820|ref|YP_007687402.1|  16 DN--PIPGAKEFIAELRKRGIPFRFLTNNSSHTRGFFAARLK 55 
                                       55..89************************988774444433 PP

  == domain 3  score: 21.6 bits;  conditional E-value: 9.6e-08
                                       EEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHH.HHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                         Hydrolase 162 aviasdietvakpspegkvaaireLqgkpeevamVGDgvn.DaaalaaAg 210
                                          ++d ++++kp+  +++ a  e++++pe+v+m+GD++  D+ +++ Ag
  gi|474933820|ref|YP_007687402.1| 168 SLTGKDATVIGKPNRLMLEMAGAEMGIPPEDVVMIGDRLStDIRMAELAG 217
                                       444555666*************************************9987 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0    0.0018         4      79     119 ..      17      60 ..       7      74 .. 0.76
   2 !   23.8   0.0   1.7e-08   3.9e-05     120     178 .]     164     223 ..     156     223 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0018
                             HAD_2  79 kpydgvkelLeeLkeagyklgivTsk...sreaveekleqlgie 119
                                       +p++g+ke++ eL+++g+     T++   +r  +   l++lg++
  gi|474933820|ref|YP_007687402.1|  17 NPIPGAKEFIAELRKRGIPFRFLTNNsshTRGFFAARLKRLGFD 60 
                                       79*********************999333344556666666655 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 1.7e-08
                             HAD_2 120 syFdvivtsedvekkKPdpeviekaleklklkkeeviyvGDsp.tDieaakkagikviav 178
                                       ++++   +++ +   KP+  ++e a  ++++ +e+v+++GD   tDi  a  ag+++i v
  gi|474933820|ref|YP_007687402.1| 164 RLYESLTGKDATVIGKPNRLMLEMAGAEMGIPPEDVVMIGDRLsTDIRMAELAGTRSILV 223
                                       566777888889999****************************9************9976 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   3.2e-05     0.073       1      39 [.       4      41 ..       4      55 .. 0.88
   2 !    5.9   0.0    0.0042       9.3     197     224 ..     190     218 ..     183     227 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.2e-05
                                      EEEEIIIIIS-TTS---HHHHHHHHHHHHTTSEEEEE-S CS
                       Hydrolase_3  1 ialDlDGTLlnsdkkisektkeaikklkekgikvviATG 39
                                      +a+D+DGT+ + d+ i + +ke i++l+++gi + + T 
  gi|474933820|ref|YP_007687402.1|  4 FAIDMDGTVYKGDNPI-PGAKEFIAELRKRGIPFRFLTN 41
                                      58*******9999998.899************9988775 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0042
                                       HHCT--GGGEEEEESSG.GGHHHHHHSSE CS
                       Hydrolase_3 197 kelnisleeviafGDge.NDieMLeaagl 224
                                        e++i++e+v+ +GD    Di M e ag+
  gi|474933820|ref|YP_007687402.1| 190 AEMGIPPEDVVMIGDRLsTDIRMAELAGT 218
                                       689************9637****999985 PP

>> PGP_phosphatase  Mitochondrial PGP phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   2.4e-07   0.00054     136     164 ..     196     224 ..     190     228 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.4e-07
                   PGP_phosphatase 136 adeiavvgDRllTdvllanmmGslgvwlr 164
                                       +++++++gDRl Td+ +a+  G+ ++++ 
  gi|474933820|ref|YP_007687402.1| 196 PEDVVMIGDRLSTDIRMAELAGTRSILVL 224
                                       799*******************9998875 PP

>> Acid_phosphat_B  HAD superfamily, subfamily IIIB (Acid phosphatase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   5.9e-06     0.013     113     169 ..      14      70 ..      11      90 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.9e-06
                                       TGGCCECCHHHHHHHHHHTTEEEEEEEEEECCCHHHHHHHHHHCT-TTBSCCEEECC CS
                   Acid_phosphat_B 113 geakaipgalelikkvverGvkiffvsgRseeqkaaTvenLkkagfssweklilkgk 169
                                       + +++ipga+e+i+++++rG+   f+++ s + +    + Lk+ gf+ +++ +l ++
  gi|474933820|ref|YP_007687402.1|  14 KGDNPIPGAKEFIAELRKRGIPFRFLTNNSSHTRGFFAARLKRLGFDVTDDDVLSST 70 
                                       56789****************************************998887776665 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.004         9      88     137 ..      20      77 ..      13     106 .. 0.75
   2 ?    6.2   0.0    0.0053        12     153     188 .]     178     214 ..     148     214 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.004
                               HAD  88 pgalellaahraaGdrvvvvSgglrplvepllaelg.......adevlatelevdd.r 137
                                       pga+e++a+ r++G+++  ++++ ++    ++a+l         d+vl++ l++ +  
  gi|474933820|ref|YP_007687402.1|  20 PGAKEFIAELRKRGIPFRFLTNNSSHTRGFFAARLKrlgfdvtDDDVLSSTLATTRfI 77 
                                       8********************9977766666654444447777778888877666553 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0053
                               HAD 153 gkvaalrewlaaegegidleevvayGDsp.sDlpllr 188
                                       gk+++l   +a ++ gi++e+vv +GD   +D+ +++
  gi|474933820|ref|YP_007687402.1| 178 GKPNRLMLEMAGAEMGIPPEDVVMIGDRLsTDIRMAE 214
                                       4788888889999**************9868999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1649.00
//
Query:       gi|474933821|ref|YP_007687403.1|  [L=185]
Description: hypothetical protein TALC_00229 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1187.48
//
Query:       gi|474933822|ref|YP_007687404.1|  [L=163]
Description: hypothetical protein TALC_00230 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0011   18.9   0.3     0.0031   17.4   0.3    1.8  1  Peptidase_S24  Peptidase S24-like
  ------ inclusion threshold ------
        2.3    8.1   5.3        3.5    7.5   5.3    1.2  1  Tmemb_9        TMEM9


Domain annotation for each model (and alignments):
>> Peptidase_S24  Peptidase S24-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.3   3.4e-07    0.0031       2      52 ..      28      86 ..      27      89 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.4e-07
                                      XXSSTT........CCTXXTTXEEEEECTS..---TTSEEEEEETTCE-EEEEEEEEETTE CS
                     Peptidase_S24  2 vpGdSM........eptlldGdlilVdkfs..epkrGdivvfrlpgeeeayiKrviglpgd 52
                                      vp +SM         ++++   l+ V+  +  +++ Gd+vvf  +g    +++r+ig + d
  gi|474933822|ref|YP_007687404.1| 28 VPTGSMdghvteydIDSFPAKTLVTVKDADigDVEIGDVVVFDNNGI--TTVHRCIGIGTD 86
                                      88888887777665588888888999866678**********66666..9******98766 PP

>> Tmemb_9  TMEM9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   5.3   0.00039       3.5      45      72 ..     132     159 ..     130     162 .. 0.94

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00039
                           Tmemb_9  45 RntttikvvviivivvislLviYmlfll 72 
                                       +n+t++ v viiv++v+++ v  m++++
  gi|474933822|ref|YP_007687404.1| 132 KNSTILFVAVIIVLCVMAVTVKDMVVMM 159
                                       799***********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1058  (0.0590105); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1174.06
//
Query:       gi|474933823|ref|YP_007687405.1|  [L=159]
Description: hypothetical protein TALC_00231 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.036   14.1   0.4        3.9    7.6   0.1    2.5  3  DUF5640         Family of unknown function (DUF5640)
      0.082   12.7   0.2       0.14   12.0   0.2    1.4  1  NAGLU_N         Alpha-N-acetylglucosaminidase (NAGLU) N-termi
       0.25   12.3   5.0       0.62   11.0   5.0    1.7  1  Pilin_N         Archaeal Type IV pilin, N-terminal
        2.8    8.1  12.0        5.6    7.1  12.0    1.7  1  Arch_flagellin  Archaebacterial flagellin


Domain annotation for each model (and alignments):
>> DUF5640  Family of unknown function (DUF5640)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.72   3.2e+03      40      52 ..      43      55 ..      35      71 .. 0.72
   2 ?    5.1   0.0    0.0053        24      31      49 ..      67      85 ..      54      89 .. 0.80
   3 ?    7.6   0.1   0.00087       3.9      17      72 ..      89     149 ..      83     158 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.72
                                      E-SSSSEEEEEES CS
                           DUF5640 40 tieedqLkidfea 52
                                      t+++d +++d+++
  gi|474933823|ref|YP_007687405.1| 43 TVSADYISLDIYN 55
                                      6677777777666 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0053
                                      EETTEEEEEE-SSSSEEEE CS
                           DUF5640 31 skaaykftYtieedqLkid 49
                                      ++   +ftYt++++ ++id
  gi|474933823|ref|YP_007687405.1| 67 DSGSLAFTYTTSNGVITID 85
                                      455678***********98 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.00087
                                       EEEE-SSS-EEEEEEETT.EE....EEEE-SSSSEEEEEESS----EEE-EEESSSEEEE- CS
                           DUF5640  17 tYkFdedGtgelelskaa.yk....ftYtieedqLkidfeaekkedceyefsvngntLtLt 72 
                                        ++F + G+++l+ s+++ y+     +Y+++e  ++ d+   +  + ++   ++  tLtLt
  gi|474933823|ref|YP_007687405.1|  89 PLSFIASGSYYLKASSNQnYSvylrASYSLDEAAIQADSLDVATVKENVLAVIKYMTLTLT 149
                                       689************99999999999*******9999766545444456666666677766 PP

>> NAGLU_N  Alpha-N-acetylglucosaminidase (NAGLU) N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2     3e-05      0.14      26      67 ..      67     108 ..      48     116 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3e-05
                                       BTTB-EEEEE-SSS-EEEEESSHHHHHHHHHHHHHHHS--B- CS
                           NAGLU_N  26 ksgkdvFeisskggkilIrGnsgvalasGlnwYLkyycgvhi 67 
                                       +sg+  F+ ++++g i+I G s+ +  +   +YLk   + ++
  gi|474933823|ref|YP_007687405.1|  67 DSGSLAFTYTTSNGVITIDGASPLSFIASGSYYLKASSNQNY 108
                                       678889*******************999999****8776655 PP

>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   5.0   0.00014      0.62       9      65 ..      12      59 ..      11      84 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00014
                           Pilin_N  9 viLmvaitvIlaAviaafvlgl.asneekapqasievkidssastgknavslehkgGd 65
                                      viL+va++ I+aA +++   ++ + ++++ + +s +    s        + + + +Gd
  gi|474933823|ref|YP_007687405.1| 12 VILLVAMIAIAAACVGVALANVvSTVSSTDNTVSADYI--S--------LDIYNVSGD 59
                                      8*****************99996666666666665211..1........333333443 PP

>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1  12.0    0.0012       5.6       7      83 ..      11      85 ..       9     156 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0012
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEEEEE-SSSSSE..EEEEEE--TTS--EE CS
                    Arch_flagellin  7 tlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvgdsatngtine..itiyvklnaGsspid 83
                                      t+I+++Am+ +AA+ +gv++ ++  + ++ ++t++        +l+i ++ gd+a ++++++  ++++ +++ G  +id
  gi|474933823|ref|YP_007687405.1| 11 TVILLVAMIAIAAACVGVALANVVSTVSSTDNTVSADY----ISLDIYNVSGDTAISDSLDSgsLAFTYTTSNGVITID 85
                                      89********************9999999998887654....3466666666555555555555888888777766666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       993  (0.0553851); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1063.07
//
Query:       gi|474933824|ref|YP_007687406.1|  [L=69]
Description: hypothetical protein TALC_00232 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       204  (0.0113782); expected 358.6 (0.02)
Passed bias filter:                      191  (0.0106531); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 446.31
//
Query:       gi|474933825|ref|YP_007687407.1|  [L=1202]
Description: chromosome segregation protein SMC, primarily archaeal type [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.5e-60  202.8   8.1    1.3e-59  201.3   8.1    2.1  1  SMC_N      RecF/RecN/SMC N terminal domain
    1.3e-28   99.7   0.0    3.8e-28   98.1   0.0    1.9  1  SMC_hinge  SMC proteins Flexible Hinge Domain
    6.5e-14   52.9   4.6    6.5e-14   52.9   4.6    6.6  2  AAA_23     AAA domain
    6.8e-11   42.5  15.9    6.8e-11   42.5  15.9    4.0  2  AAA_15     AAA ATPase domain
    1.9e-09   37.8   2.6    0.00059   19.7   0.0    3.4  3  AAA_21     AAA domain, putative AbiEii toxin, Type IV TA syst
    2.7e-09   36.6   0.0    5.7e-09   35.6   0.0    1.5  1  AAA_29     P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.023   15.0   0.5      0.023   15.0   0.5    6.7  9  Tup_N      Tup N-terminal
       0.56   10.3   4.1         28    4.9   0.2    3.8  3  DASH_Dad3  DASH complex subunit Dad3
       0.82   10.2   0.0       0.82   10.2   0.0    5.3  4  ABC_tran   ABC transporter
        7.9    7.0  17.2        1.7    9.1   1.7    5.1  5  DUF4094    Domain of unknown function (DUF4094)
          8    6.3   7.3         10    6.0   0.1    4.7  5  DASH_Duo1  DASH complex subunit Duo1
        8.5    6.9  23.9         25    5.4   0.1    8.5  8  FlaC_arch  Flagella accessory protein C (FlaC)
        8.6    6.4  45.5      0.027   14.5   1.5    7.4 11  DUF1664    Protein of unknown function (DUF1664)


Domain annotation for each model (and alignments):
>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.3   8.1   9.4e-63   1.3e-59       1     218 [.       2    1169 ..       2    1171 .. 0.99

  Alignments for each domain:
  == domain 1  score: 201.3 bits;  conditional E-value: 9.4e-63
                                        EEEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--.BTTCSST CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                             SMC_N    1 vlkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk.skekasv 74  
                                        +lk++e+enFks+   +v++p+ ++  ai+GpNGSGKsn+ dAi+FvLG +s k++r+ ++ dl+++  ++ka++
  gi|474933825|ref|YP_007687407.1|    2 YLKQIELENFKSFG-GKVTIPMMDGYMAITGPNGSGKSNIGDAIMFVLGPKSPKAVRAGRIPDLVFSgGANKAKA 75  
                                        79***********5.99**************************************************98899999 PP

                                        TEEEEEEEEEETTEESSSSSSCEEEEEEEETTSE......EEEEETTEEE-HHHHHHHHHCTT-STT........ CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxx........ RF
                             SMC_N   75 kkaeveitfdnedkklkiekeevsisrrvkrkge......seykingkevtkkevsellesagiske........ 135 
                                        +  + +++fdn+d+ ++ +++ev ++r vk kge      s ++in++++t  +   ll++a+is +        
  gi|474933825|ref|YP_007687407.1|   76 DYMKATLVFDNTDRVMPWNADEVRLTRYVKLKGEdksdytSYFFINDTKATLGDFDTLLSKARISADgynivqqg 150 
                                        9999*************************999988877767789******************************* PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|474933825|ref|YP_007687407.1|  151 dvtnivrmgsverrrildgisgiasfdsdidkaenekeeatanldrisiirgekesqlkslekdreqakiyleqk 225 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|474933825|ref|YP_007687407.1|  226 ekldiakaqlvvrqrdnekatldgintyvarlqndvdelakkkaakrleadendraieakekeiedhtgpeyrqv 300 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|474933825|ref|YP_007687407.1|  301 kndveetkvkvatererkadalleaedqknyrqeladdidanrgqysevaqniadlqsqldsitaekkaaqkqae 375 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|474933825|ref|YP_007687407.1|  376 dlgretashggemtqiqkrieeldraidqfgaedqqakadaasavsvsetaeialanaesaveaakfevkdaeyn 450 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|474933825|ref|YP_007687407.1|  451 laevkraagpddaeelgkqvfafkqkeaslekqeedlraiaekknaefnrlnaekrasdaansgsealsqilaqr 525 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|474933825|ref|YP_007687407.1|  526 dsgqisgiigavselatvdpgyetalsvaagnkmravvvkdddvaatcikflkdnrlgrvtflpinkmmpgkpra 600 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|474933825|ref|YP_007687407.1|  601 kaimvlkqtegyatdflqykpeyenvfwyvlgdtlvdssidharsimggirivtkagelieasgamtggtlstkn 675 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|474933825|ref|YP_007687407.1|  676 ipkfgassqgelsraaeelskanaalegvraelrairdqiretddlmrranssnaenrgkvaaaeaslnaakkal 750 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|474933825|ref|YP_007687407.1|  751 akaeedlarmrkstaeatetvntrqanaaviaeklenmrnertaarerlaaiapadlqeriekarnavyeltqke 825 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|474933825|ref|YP_007687407.1|  826 ndllsqiggaraelsgldkqkealddqvsktdkaiaeaeaeagqhqkamdqldielaakkkilsdmesgvedlks 900 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|474933825|ref|YP_007687407.1|  901 ardalverkyklegevdkaqgdietkngilqsqqaqvlihqqtlqgfeeeikqitveilepipaeetlkrtirtc 975 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|474933825|ref|YP_007687407.1|  976 egtigelgninlraiedydvrraeleellgevarlnkqidelnkltdeltakkkglfmeaytavndnfkriytql 1050
                                        *************************************************************************** PP

                                        ....................................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HH CS
                                        ....................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  136 ....................................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDek 174 
                                                                            +LSgGek+L+al+++fAiq+++p+p+y+lDe+d+ LD+ 
  gi|474933825|ref|YP_007687407.1| 1051 sgggegfmdldnpedpfagglqinakprngkllrleSLSGGEKSLTALSFIFAIQEYQPSPFYVLDEVDMFLDAV 1125
                                        *************************************************************************** PP

                                        HHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEEEEETTE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  175 nvkkvaellkeksknaQfivislreemlekadklvgvtkvengv 218 
                                        n + va+++ke+s +aQfi +slr+  l+ ad+l+gvt   +g+
  gi|474933825|ref|YP_007687407.1| 1126 NSEMVAKRVKESSRKAQFIQVSLRKVALTVADHLIGVTRPPSGI 1169
                                        *************************************9866665 PP

>> SMC_hinge  SMC proteins Flexible Hinge Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.1   0.0   2.8e-31   3.8e-28       2     116 ..     531     646 ..     530     647 .. 0.95

  Alignments for each domain:
  == domain 1  score: 98.1 bits;  conditional E-value: 2.8e-31
                         SMC_hinge   2 kgvlGrladlievdegyekAveaalgnrlqalvvedeetakkiieflkkknagratflpldrikqknkadgandkns 78 
                                       +g++G + +l +vd+gye+A+++a+gn++ a+vv+d+++a  +i+flk++++gr+tflp++++ + +++ +a  + +
  gi|474933825|ref|YP_007687407.1| 531 SGIIGAVSELATVDPGYETALSVAAGNKMRAVVVKDDDVAATCIKFLKDNRLGRVTFLPINKMMPGKPRAKAIMVLK 607
                                       79************************************************************888888888877766 PP

                         SMC_hinge  79 .gavplidlvevddelrkalryllgdtlvvdsldeAeel 116
                                        + ++++d++++++e+++++ y+lgdtlv +s+d+A+ +
  gi|474933825|ref|YP_007687407.1| 608 qTEGYATDFLQYKPEYENVFWYVLGDTLVDSSIDHARSI 646
                                       79**********************************987 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   4.6   4.7e-17   6.5e-14       1     197 [.       5     223 ..       5     293 .. 0.45
   2 ?   -1.0   4.4       1.5   2.1e+03     155     199 ..     701     757 ..     657     802 .. 0.47

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 4.7e-17
                            AAA_23   1 kLkienfrsf.rdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrks.........grgfeksdveies 67 
                                       ++++enf+sf ++++i   +g  +ItGpNG+GK+ i dAi ++L+ ++p+  r           g            
  gi|474933825|ref|YP_007687407.1|   5 QIELENFKSFgGKVTIPMMDGYMAITGPNGSGKSNIGDAIMFVLGPKSPKAVRAGripdlvfsgG-----------A 70 
                                       589*******77789**********************************9999764444444331...........2 PP

                            AAA_23  68 egkvkayveltfenkdgry.......trsiererelskkkgkttkkaklelleideleqfisellgskkiilnlilf 137
                                       ++ ++ y++ t+  +++++        ++++ +  + k++ k+ + + +++ +++++   +++ll++  i+ + + +
  gi|474933825|ref|YP_007687407.1|  71 NKAKADYMKATLVFDNTDRvmpwnadEVRLT-RYVKLKGEDKSDYTSYFFINDTKATLGDFDTLLSKARISADGYNI 146
                                       2334444444433333333345553322221.112222222333444455555555555555555555555555555 PP

                            AAA_23 138 lgqer...................feefelkdkkerleelekeleeledekkllekl.........eqekekekele 186
                                        +q++                               ++++  +++++e+ek++  ++         e ++++ k le
  gi|474933825|ref|YP_007687407.1| 147 VQQGDvtnivrmgsverrrildgiS----------GIASFDSDIDKAENEKEEATANldrisiirgE-KESQLKSLE 212
                                       5555533333333322222222220..........22222222222222222222222222211110.111111111 PP

                            AAA_23 187 eleeeleeilk 197
                                       + +e+ + +l+
  gi|474933825|ref|YP_007687407.1| 213 KDREQAKIYLE 223
                                       11111111111 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.5
                            AAA_23 155 leelekeleeledekkllekl............eqekekek......eleeleeeleeilkel 199
                                       le ++ el+ + d++++ ++l                   k       l++ +++l +++++l
  gi|474933825|ref|YP_007687407.1| 701 LEGVRAELRAIRDQIRETDDLmrranssnaenrG------KvaaaeaSLNAAKKALAKAEEDL 757
                                       3333333333333333333333322222222210......12222223333333333333332 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5  15.9     5e-14   6.8e-11       1     281 [.       1     314 [.       1     522 [. 0.70
   2 ?   -1.2   8.2      0.95   1.3e+03     120     344 ..     877    1130 ..     781    1146 .. 0.50

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 5e-14
                            AAA_15   1 MkIkkikikNFRslkd.veidlseeltvliGkNnsGKSsilealdlFlnnkekkn...................... 54 
                                       M++k+i+++NF+s+   v+i++ + ++ + G+N+sGKS+i +a+ + l  k++k                       
  gi|474933825|ref|YP_007687407.1|   1 MYLKQIELENFKSFGGkVTIPMMDGYMAITGPNGSGKSNIGDAIMFVLGPKSPKAvragripdlvfsggankakady 77 
                                       **************988**********************************88888888777777666654444444 PP

                            AAA_15  55 .......................kkvikiekedleifeniseskdikIdvefaekekakeyektlkskekkkadlll 108
                                                                                                   y+k++ +++++++    
  gi|474933825|ref|YP_007687407.1|  78 mkatlvfdntdrvmpwnadevrlT-----------------------------------RYVKLKGEDKSDYT---S 116
                                       433333333333333333333331...................................33344444444444...3 PP

                            AAA_15 109 kkkesdlkktikdkklklkknelsdekisvekkks...........................kkelpkekeekleke 158
                                        ++++d+k t+ d+++ l+k ++s + +++ ++ +                             +  ++++e+++ +
  gi|474933825|ref|YP_007687407.1| 117 YFFINDTKATLGDFDTLLSKARISADGYNIVQQGDvtnivrmgsverrrildgisgiasfdsDIDKAENEKEEATAN 193
                                       66777777777777777777777777777777777777777777777777777777777665333333333333344 PP

                            AAA_15 159 keelkid...kedlkklikkleeslkkeeelknvlksaiiklllisakRnvsdedsekkssllgklkekileealqe 232
                                        + ++i    ke++ k ++k +e+ k +   +++ k  i k +l   +R++++ + + ++++  +l+++  e a+++
  gi|474933825|ref|YP_007687407.1| 194 LDRISIIrgeKESQLKSLEKDREQAKIYL--EQKEKLDIAKAQLVVRQRDNEKATLDGINTYVARLQNDVDELAKKK 268
                                       44444443356666666666666666666..6666777777777777888888888887777777777776644333 PP

                            AAA_15 233 kl..eeelteklkeiqeklkeidkklaeelkkilkkkidkikkfnykgkkn 281
                                        +  ++e  e+   i+ k kei++  + e+ + +k+++++    ++k++++
  gi|474933825|ref|YP_007687407.1| 269 -AakRLEADENDRAIEAKEKEIEDHTGPEYRQ-VKNDVEET---KVKVATE 314
                                       .3466666667777777777776666666664.44444432...2222222 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.95
                            AAA_15  120 kdkklklkknelsdekisvekkkskkelpkekeeklekekeelkidkedlkklikkleeslkkeeelknvlksai 194 
                                         d +l+ kk+ lsd+   ve+ ks+++  +e+++kle e ++ + d e+++ +++  + ++  +++         
  gi|474933825|ref|YP_007687407.1|  877 LDIELAAKKKILSDMESGVEDLKSARDALVERKYKLEGEVDKAQGDIETKNGILQSQQAQVLIHQQTL------- 944 
                                        22233333444445555555555555555555555555555555555555555553333333333222....... PP

                            AAA_15  195 iklllisakRnvsdedsekkssllgklkekileealqekl...............................eeel 238 
                                                     + ++e+++ +  +++e i  e     l                                eel
  gi|474933825|ref|YP_007687407.1|  945 -------------QGFEEEIKQITVEILEPIPAEET---LkrtirtcegtigelgninlraiedydvrraeLEEL 1003
                                        .............22222222222222222222211...122234444444445555455556655655554444 PP

                            AAA_15  239 teklkeiqeklkeidkklaeelk.......kilkkkidkikkfnykgkkneeieik................... 287 
                                          +  ++++ ++e++k  +e ++       +             y  +++++++i                    
  gi|474933825|ref|YP_007687407.1| 1004 LGEVARLNKQIDELNKLTDELTAkkkglfmE------------AYTAVNDNFKRIYtqlsgggegfmdldnpedp 1066
                                        4555555555555555443333322233331............22222222222222333555555555577777 PP

                            AAA_15  288 ............ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvl 344 
                                                    ++  l l+  + G ++l  l++  +  e +     ++ +++++E +  L   + +++
  gi|474933825|ref|YP_007687407.1| 1067 fagglqinakprNGKLLRLESLSGGEKSLTALSFIFAIQEYQ-----PSPFYVLDEVDMFLDAVNSEMV 1130
                                        778888888898888999999999988888887654444444.....7888888887766655555555 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   4.2e-07   0.00059       2      24 ..      27      49 ..      26      93 .. 0.79
   2 ?    0.3   0.3      0.36   4.9e+02     138     206 ..     240     311 ..     173     362 .. 0.85
   3 !   15.7   0.0   7.1e-06    0.0098     219     293 ..    1045    1144 ..     858    1147 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 4.2e-07
                            AAA_21  2 nvliGpNgsGKSnLLdaldllar 24
                                      ++++GpNgsGKSn+ da+ ++ +
  gi|474933825|ref|YP_007687407.1| 27 MAITGPNGSGKSNIGDAIMFVLG 49
                                      589***************77754 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.36
                            AAA_21 138 lqfgkaltditsrawsllllldglrke...rigllnifadyfgfakekrllqrlvrslklveielsdlgege 206
                                       ++++ka++d +++++  l+++ + + +   +++l  + +d + +akek++ ++  +++++v + ++ +++++
  gi|474933825|ref|YP_007687407.1| 240 RDNEKATLDGINTYVARLQNDVDELAKkkaAKRLEADENDRAIEAKEKEIEDHTGPEYRQVKNDVEETKVKV 311
                                       567889999999999999999888777899999999999999999999999999999999998888887554 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 7.1e-06
                            AAA_21  219 r.........................gvvflengdgqelparelSdGtkrl..lalltallralkkgsllliDEp 266 
                                        r                          ++  ++ +g+ l + +lS G k+l  l ++ a+ +  ++ +++++DE+
  gi|474933825|ref|YP_007687407.1| 1045 RiytqlsgggegfmdldnpedpfaggLQINAKPRNGKLLRLESLSGGEKSLtaLSFIFAIQEYQPS-PFYVLDEV 1118
                                        0444444444444444445555566677888999*****************633777777777777.******** PP

                            AAA_21  267 EngLHPkllrrllellkelsrngaQvi 293 
                                        + +L+    + +++ +ke sr +aQ+i
  gi|474933825|ref|YP_007687407.1| 1119 DMFLDAVNSEMVAKRVKESSR-KAQFI 1144
                                        *****9888888899988888.88887 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.0   4.2e-12   5.7e-09       1      50 [.       3      52 ..       3      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 4.2e-12
                            AAA_29  1 LkrlqlvNWgtfdg.htieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      Lk+++l N  +f g  ti++  +g + +tGp+GsGKS + DAi+++L p++
  gi|474933825|ref|YP_007687407.1|  3 LKQIELENFKSFGGkVTIPMM-DGYMAITGPNGSGKSNIGDAIMFVLGPKS 52
                                      789***********7777775.889**********************9987 PP

>> Tup_N  Tup N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.4       2.6   3.5e+03      11      42 ..     259     290 ..     251     329 .. 0.68
   2 ?   15.0   0.5   1.7e-05     0.023       9      54 ..     356     401 ..     348     407 .. 0.91
   3 ?   -3.3   0.3       8.7   1.2e+04      18      43 ..     475     500 ..     471     504 .. 0.59
   4 ?   -2.6   0.0       5.2   7.2e+03       4      21 ..     699     716 ..     696     731 .. 0.70
   5 ?   -1.5   0.2       2.4   3.3e+03       6      60 ..     743     797 ..     738     815 .. 0.75
   6 ?   -0.9   0.2       1.5   2.1e+03      41      57 ..     811     827 ..     782     832 .. 0.82
   7 ?   -0.7   0.4       1.3   1.8e+03      16      56 ..     863     903 ..     826     927 .. 0.66
   8 ?    0.7   0.1      0.47   6.5e+02      55      73 ..     940     958 ..     927     960 .. 0.87
   9 ?   -0.5   0.1       1.2   1.6e+03      21      44 ..    1008    1020 ..     988    1026 .. 0.56

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.6
                             Tup_N  11 qEfdalsqeasslkaqkdeyelkiqsqiqElq 42 
                                       ++ d+l+++    + + de ++ i+++ +E++
  gi|474933825|ref|YP_007687407.1| 259 NDVDELAKKKAAKRLEADENDRAIEAKEKEIE 290
                                       55566666666666666666666666666654 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.7e-05
                             Tup_N   9 vkqEfdalsqeasslkaqkdeyelkiqsqiqElqqirqtlyeLeea 54 
                                       +++  d+++ e +  ++q +++ +  +s+  E++qi++ + eL++a
  gi|474933825|ref|YP_007687407.1| 356 LQSQLDSITAEKKAAQKQAEDLGRETASHGGEMTQIQKRIEELDRA 401
                                       5677899************************************987 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 8.7
                             Tup_N  18 qeasslkaqkdeyelkiqsqiqElqq 43 
                                       q+  sl++q++++ +  +++ +E+++
  gi|474933825|ref|YP_007687407.1| 475 QKEASLEKQEEDLRAIAEKKNAEFNR 500
                                       44455666666666666666666655 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 5.2
                             Tup_N   4 elLdavkqEfdalsqeas 21 
                                         L+ v++E  a+  ++ 
  gi|474933825|ref|YP_007687407.1| 699 AALEGVRAELRAIRDQIR 716
                                       567777777777766554 PP

  == domain 5  score: -1.5 bits;  conditional E-value: 2.4
                             Tup_N   6 LdavkqEfdalsqeasslkaqkdeyelkiqsqiqElqqirqtlyeLeeahrkikq 60 
                                       L+a k+   ++++++  +++++ e    +++  ++ + i ++l ++ ++ ++ ++
  gi|474933825|ref|YP_007687407.1| 743 LNAAKKALAKAEEDLARMRKSTAEATETVNTRQANAAVIAEKLENMRNERTAARE 797
                                       6666777777777777788877777777887777778888877777777776666 PP

  == domain 6  score: -0.9 bits;  conditional E-value: 1.5
                             Tup_N  41 lqqirqtlyeLeeahrk 57 
                                       +++ r+++yeL ++ ++
  gi|474933825|ref|YP_007687407.1| 811 IEKARNAVYELTQKEND 827
                                       67889999*99998765 PP

  == domain 7  score: -0.7 bits;  conditional E-value: 1.3
                             Tup_N  16 lsqeasslkaqkdeyelkiqsqiqElqqirqtlyeLeeahr 56 
                                       ++ ea + ++  d ++  ++++ + l  + + + +L++a  
  gi|474933825|ref|YP_007687407.1| 863 AEAEAGQHQKAMDQLDIELAAKKKILSDMESGVEDLKSARD 903
                                       34455555555666666666666666666666666666655 PP

  == domain 8  score: 0.7 bits;  conditional E-value: 0.47
                             Tup_N  55 hrkikqqYEeeiarLkaeL 73 
                                       h++  q +Eeei+++  e+
  gi|474933825|ref|YP_007687407.1| 940 HQQTLQGFEEEIKQITVEI 958
                                       899999*******987765 PP

  == domain 9  score: -0.5 bits;  conditional E-value: 1.2
                             Tup_N   21 sslkaqkdeyelkiqsqiqElqqi 44  
                                                     +++qi+El+++
  gi|474933825|ref|YP_007687407.1| 1008 AR-----------LNKQIDELNKL 1020
                                        33...........45555555544 PP

>> DASH_Dad3  DASH complex subunit Dad3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.9     4e+03      18      38 ..     253     273 ..     248     289 .. 0.70
   2 ?    4.3   0.1     0.032        44      11      33 ..     345     372 ..     344     404 .. 0.75
   3 ?    4.9   0.2      0.02        28       7      43 ..    1002    1045 ..     998    1052 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.9
                         DASH_Dad3  18 nlktLaselkeLasnsteeil 38 
                                        + +L++ ++eLa++++++ l
  gi|474933825|ref|YP_007687407.1| 253 YVARLQNDVDELAKKKAAKRL 273
                                       567899999999999665544 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.032
                         DASH_Dad3  11 eYerLaenlktLaselkeLasn.....s 33 
                                       +Y+++a+n+ +L+s+l++++ +     +
  gi|474933825|ref|YP_007687407.1| 345 QYSEVAQNIADLQSQLDSITAEkkaaqK 372
                                       8******************999544440 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.02
                         DASH_Dad3    7 evLdeYerLaenlktLaselkeLasn.......steeildgLRe 43  
                                        e+L e +rL++++++L++  +eL+ +         + + d+++ 
  gi|474933825|ref|YP_007687407.1| 1002 ELLGEVARLNKQIDELNKLTDELTAKkkglfmeAYTAVNDNFKR 1045
                                        7899999****************999555555545555555554 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00059      0.82      14      35 ..      27      48 ..      22      88 .. 0.87
   2 ?   -0.4   2.3       1.1   1.6e+03      57     122 ..     342     433 ..     307     442 .. 0.58
   3 ?   -0.1   1.2      0.88   1.2e+03      52     119 ..     769     849 ..     733     887 .. 0.68
   4 ?    2.8   0.1      0.12   1.6e+02      52     124 ..     998    1103 ..     911    1119 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00059
                                      EEEEESTTSSHHHHHHHHTTSS CS
                                      xxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 14 vaivGenGaGKStLlkllagll 35
                                      +ai+G+nG+GKS +  +++  l
  gi|474933825|ref|YP_007687407.1| 27 MAITGPNGSGKSNIGDAIMFVL 48
                                      79**********9988887655 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.1
                                       CCHCEEEE-SS.--S-TTSB.HHHH..........................HHHTCHHHHHHHSTTGGTTCBGESTT CS
                                       xxxxxxxxxxx.xxxxxxxx.xxxx..........................xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  57 lrkeigvlpqe.pqlfpelt.vren..........................esdeeiekalsklglkelkdtvvkss 105
                                        r + + + q+ + l+++l  +  +                          ++ ee+++a++++g ++   + +k +
  gi|474933825|ref|YP_007687407.1| 342 NRGQYSEVAQNiADLQSQLDsITAEkkaaqkqaedlgretashggemtqiqKRIEELDRAIDQFGAED---QQAKAD 415
                                       44444444444433333322111112344445666666667777777733333333555555555544...554444 PP

                                       S.GGS-HHHHHHHHHHHH CS
                                       x.xxxxxxxxxxxxxxxx RF
                          ABC_tran 106 p.ssLSgGqkqrvalara 122
                                       + s +S  +   +ala+a
  gi|474933825|ref|YP_007687407.1| 416 AaSAVSVSETAEIALANA 433
                                       458999999999998875 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.88
                                       B-HHHCCHCEEEE-SS.--S-TTSB.HHHH.......HHHTCHHHHHHHSTTGG.TTCBGESTTS....GGS-HHHH CS
                                       xxxxxxxxxxxxxxxx.xxxxxxxx.xxxx.......xxxxxxxxxxxxxxxxx.xxxxxxxxxx....xxxxxxxx RF
                          ABC_tran  52 qeleslrkeigvlpqe.pqlfpelt.vren.......esdeeiekalsklglke.lkdtvvkssp....ssLSgGqk 114
                                       ++ +  +++ +v+ ++ +++ +e t +re+       + +e+ieka++ +     ++++ + s+     ++LSg  k
  gi|474933825|ref|YP_007687407.1| 769 ETVNTRQANAAVIAEKlENMRNERTaARERlaaiapaDLQERIEKARNAVYELTqKENDLL-SQIggarAELSGLDK 844
                                       4555566667777777655555555455558888888777777777777644441334444.333366677777777 PP

                                       HHHHH CS
                                       xxxxx RF
                          ABC_tran 115 qrval 119
                                       q+ al
  gi|474933825|ref|YP_007687407.1| 845 QKEAL 849
                                       76555 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.12
                                        B-HHHCCHCEEEE-SS....--S-TTSBHHHH........HHHTCHHHHHHHSTTGG.................. CS
                                        xxxxxxxxxxxxxxxx....xxxxxxxxxxxx........xxxxxxxxxxxxxxxxx.................. RF
                          ABC_tran   52 qeleslrkeigvlpqe....pqlfpeltvren........esdeeiekalsklglke.................. 96  
                                         ele+l  e++ l ++    ++l +elt++++        + +++++++ ++l+  +                  
  gi|474933825|ref|YP_007687407.1|  998 AELEELLGEVARLNKQidelNKLTDELTAKKKglfmeaytAVNDNFKRIYTQLSGGGegfmdldnpedpfagglq 1072
                                        444444444444444433333333444433335555444422222333333333222444555555555555554 PP

                                        .....TTCBGESTTS....GGS-HHHHHHHHHHHHHH CS
                                        .....xxxxxxxxxx....xxxxxxxxxxxxxxxxxx RF
                          ABC_tran   97 .....lkdtvvkssp....ssLSgGqkqrvalarall 124 
                                              +       +    +sLSgG+k+  al  +++
  gi|474933825|ref|YP_007687407.1| 1073 inakpRNG------KllrlESLSGGEKSLTALSFIFA 1103
                                        33221111......12334899999999888866554 PP

>> DUF4094  Domain of unknown function (DUF4094)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.4       1.2   1.6e+03      40      87 ..     322     372 ..     296     373 .. 0.64
   2 ?    2.5   1.2      0.14     2e+02      46      86 ..     369     413 ..     341     415 .. 0.62
   3 ?   -1.7   0.1       2.9   4.1e+03      65      65 ..     774     774 ..     723     838 .. 0.55
   4 ?    9.1   1.7    0.0012       1.7      53      86 ..     844     885 ..     808     887 .. 0.82
   5 ?    2.3   0.1      0.17   2.3e+02      43      78 ..     991    1024 ..     962    1029 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.2
                           DUF4094  40 l.vsedcds.kdaesrskdilg.evskthkaiqtLdktissLemeLaaara 87 
                                       l  +ed ++ +++  ++ d  + ++s+  + i  L+ +++s+  e  aa++
  gi|474933825|ref|YP_007687407.1| 322 LlEAEDQKNyRQELADDIDANRgQYSEVAQNIADLQSQLDSITAEKKAAQK 372
                                       325566665544444444555559999999999999999999998888875 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.14
                           DUF4094  46 dskdaesr...skdilg.evskthkaiqtLdktissLemeLaaar 86 
                                       + +++ ++   +    g e+++ +k i+ Ld++i++   e + a+
  gi|474933825|ref|YP_007687407.1| 369 AAQKQAEDlgrETASHGgEMTQIQKRIEELDRAIDQFGAEDQQAK 413
                                       2222222244444555569***************99877766655 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.9
                           DUF4094  65 h 65 
                                       +
  gi|474933825|ref|YP_007687407.1| 774 R 774
                                       1 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.0012
                           DUF4094  53 rskdilg.evskthkaiqtL.......dktissLemeLaaar 86 
                                       ++k+ l+ +vskt kai          +k++++L +eLaa++
  gi|474933825|ref|YP_007687407.1| 844 KQKEALDdQVSKTDKAIAEAeaeagqhQKAMDQLDIELAAKK 885
                                       37788999**********777778888************998 PP

  == domain 5  score: 2.3 bits;  conditional E-value: 0.17
                           DUF4094   43 edcdskdaesrskdilgevskthkaiqtLdktissL 78  
                                        ed+d ++ae +  ++lgev + +k i  L+k  ++L
  gi|474933825|ref|YP_007687407.1|  991 EDYDVRRAELE--ELLGEVARLNKQIDELNKLTDEL 1024
                                        77776666666..69**************9977666 PP

>> DASH_Duo1  DASH complex subunit Duo1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       4.6   6.4e+03       5      25 ..     243     263 ..     242     268 .. 0.73
   2 ?   -3.1   0.0       4.9   6.8e+03      28      46 ..     386     404 ..     382     410 .. 0.67
   3 ?    6.0   0.1    0.0074        10       2      34 ..     687     719 ..     686     727 .. 0.83
   4 ?   -0.3   0.2      0.69   9.5e+02      16      42 ..     743     769 ..     735     787 .. 0.79
   5 ?   -1.0   0.1       1.2   1.6e+03      22      46 ..     999    1023 ..     984    1026 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 4.6
                         DASH_Duo1   5 EleqLrkinevienviesLkk 25 
                                       E  +L+ in+ +  ++++ ++
  gi|474933825|ref|YP_007687407.1| 243 EKATLDGINTYVARLQNDVDE 263
                                       667888888888888777665 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4.9
                         DASH_Duo1  28 sniervketvestntLLdk 46 
                                       +++ ++++++e+ ++ +d+
  gi|474933825|ref|YP_007687407.1| 386 GEMTQIQKRIEELDRAIDQ 404
                                       5667777777766665555 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0074
                         DASH_Duo1   2 LekEleqLrkinevienviesLkkaksniervk 34 
                                       L +  e+L k n+++e+v+++L++++++i +  
  gi|474933825|ref|YP_007687407.1| 687 LSRAAEELSKANAALEGVRAELRAIRDQIRETD 719
                                       788899*****************9999987765 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 0.69
                         DASH_Duo1  16 ienviesLkkaksniervketvestnt 42 
                                       +++ +++L ka++++ r+ +++ ++ +
  gi|474933825|ref|YP_007687407.1| 743 LNAAKKALAKAEEDLARMRKSTAEATE 769
                                       667778888888888888888877654 PP

  == domain 5  score: -1.0 bits;  conditional E-value: 1.2
                         DASH_Duo1   22 sLkkaksniervketvestntLLdk 46  
                                        +L++  +++ r+++++++ n+L d+
  gi|474933825|ref|YP_007687407.1|  999 ELEELLGEVARLNKQIDELNKLTDE 1023
                                        6788888888999999999888775 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       4.1   5.7e+03      10      33 ..     174     197 ..     172     198 .. 0.82
   2 ?   -0.2   0.1      0.98   1.4e+03       7      33 ..     351     377 ..     345     383 .. 0.61
   3 ?    1.2   0.1      0.36     5e+02      21      37 ..     386     402 ..     373     405 .. 0.63
   4 ?    5.0   0.0     0.024        33       7      35 ..     692     720 ..     687     724 .. 0.88
   5 ?    0.1   0.1      0.81   1.1e+03       2      37 ..     736     771 ..     735     777 .. 0.78
   6 ?    5.4   0.1     0.018        25       4      39 ..     820     855 ..     818     858 .. 0.90
   7 ?    1.7   0.1      0.25   3.4e+02       7      35 ..     872     900 ..     868     907 .. 0.89
   8 ?    1.5   0.2      0.29     4e+02      20      43 ..     997    1020 ..     990    1028 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.1
                         FlaC_arch  10 sklsteletvkkeneelsksveel 33 
                                        ++++ ++ +++e ee   +++++
  gi|474933825|ref|YP_007687407.1| 174 ASFDSDIDKAENEKEEATANLDRI 197
                                       567899999999999999888877 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.98
                         FlaC_arch   7 nklsklsteletvkkeneelsksveel 33 
                                       + + +l+++l+++ +e +  +k+ e+l
  gi|474933825|ref|YP_007687407.1| 351 QNIADLQSQLDSITAEKKAAQKQAEDL 377
                                       556666666666666666655555554 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.36
                         FlaC_arch  21 keneelsksveelkenV 37 
                                        e+ +++k +eel++ +
  gi|474933825|ref|YP_007687407.1| 386 GEMTQIQKRIEELDRAI 402
                                       46667777777777665 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.024
                         FlaC_arch   7 nklsklsteletvkkeneelsksveelke 35 
                                       ++lsk    le v++e+  +++++ e ++
  gi|474933825|ref|YP_007687407.1| 692 EELSKANAALEGVRAELRAIRDQIRETDD 720
                                       6899999****************998766 PP

  == domain 5  score: 0.1 bits;  conditional E-value: 0.81
                         FlaC_arch   2 idelEnklsklsteletvkkeneelsksveelkenV 37 
                                       +   E  l+  +  l+ +++++  ++ks  e  e+V
  gi|474933825|ref|YP_007687407.1| 736 VAAAEASLNAAKKALAKAEEDLARMRKSTAEATETV 771
                                       555678888888888888888888888888888777 PP

  == domain 6  score: 5.4 bits;  conditional E-value: 0.018
                         FlaC_arch   4 elEnklsklsteletvkkeneelsksveelkenVkd 39 
                                       el +k ++l ++++ +++e++ l k+ e l+++V +
  gi|474933825|ref|YP_007687407.1| 820 ELTQKENDLLSQIGGARAELSGLDKQKEALDDQVSK 855
                                       78888899999*********************9964 PP

  == domain 7  score: 1.7 bits;  conditional E-value: 0.25
                         FlaC_arch   7 nklsklsteletvkkeneelsksveelke 35 
                                       + +++l++el+  kk ++++++ ve+lk 
  gi|474933825|ref|YP_007687407.1| 872 KAMDQLDIELAAKKKILSDMESGVEDLKS 900
                                       67999********************9985 PP

  == domain 8  score: 1.5 bits;  conditional E-value: 0.29
                         FlaC_arch   20 kkeneelsksveelkenVkdllsL 43  
                                        ++e+eel  +v +l++++ +l +L
  gi|474933825|ref|YP_007687407.1|  997 RAELEELLGEVARLNKQIDELNKL 1020
                                        567777777777777777776554 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   1.1      0.71   9.7e+02      55      97 ..     226     269 ..     206     299 .. 0.55
   2 ?    0.2   0.9      0.52   7.2e+02      47     103 ..     254     311 ..     242     317 .. 0.69
   3 ?   14.5   1.5     2e-05     0.027      61     120 ..     346     405 ..     328     411 .. 0.89
   4 ?   -0.9   0.0       1.1   1.6e+03      73     100 ..     692     719 ..     683     738 .. 0.53
   5 ?    3.0   1.5     0.072        99      65     121 ..     733     789 ..     695     792 .. 0.72
   6 ?    2.9   1.5     0.074     1e+02      70     121 ..     738     789 ..     722     815 .. 0.60
   7 ?    4.7   1.3     0.021        30      61     121 ..     804     864 ..     781     869 .. 0.85
   8 ?    5.0   1.5     0.018        24      55     113 ..     819     877 ..     800     895 .. 0.53
   9 ?    8.1   2.7    0.0019       2.6      35     107 ..     883     955 ..     871     961 .. 0.84
  10 ?    0.5   0.0      0.41   5.7e+02      63      87 ..    1002    1026 ..     965    1052 .. 0.66
  11 ?   -3.2   0.2         6   8.2e+03      71     110 ..    1118    1155 ..    1115    1157 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.71
                           DUF1664  55 eslaatkrhLssri.drvdkkldeqkeiskeikeevtevredls 97 
                                       e+l  +k +L  r  d+  ++ld  +   + ++++v+e+ ++ +
  gi|474933825|ref|YP_007687407.1| 226 EKLDIAKAQLVVRQrDNEKATLDGINTYVARLQNDVDELAKKKA 269
                                       34444444444332134444555555555555555555555544 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.52
                           DUF1664  47 skqleqvseslaatkrhLssridrvdkklde.qkeiskeikeevtevredlseigedv 103
                                         +l++  ++la+ k     + d+ d+ +++  kei  ++  e  +v++d++e++ +v
  gi|474933825|ref|YP_007687407.1| 254 VARLQNDVDELAKKKAAKRLEADENDRAIEAkEKEIEDHTGPEYRQVKNDVEETKVKV 311
                                       4556666666776666666666778888875246788888888888888888887766 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 2e-05
                           DUF1664  61 krhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                         + +++i+ ++++ld+ ++ +k+ +++ +++ +++++ g +++++++ +e+l+  +++ 
  gi|474933825|ref|YP_007687407.1| 346 YSEVAQNIADLQSQLDSITAEKKAAQKQAEDLGRETASHGGEMTQIQKRIEELDRAIDQF 405
                                       467899*************************************************99976 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 1.1
                           DUF1664  73 kkldeqkeiskeikeevtevredlseig 100
                                       ++l + +++ + +++e+ ++r++++e++
  gi|474933825|ref|YP_007687407.1| 692 EELSKANAALEGVRAELRAIRDQIRETD 719
                                       3333444444444444444444444333 PP

  == domain 5  score: 3.0 bits;  conditional E-value: 0.072
                           DUF1664  65 ssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                         +++  +++l++ k++ ++ +e+++++r+ ++e  e v++ ++    +++kle++ 
  gi|474933825|ref|YP_007687407.1| 733 RGKVAAAEASLNAAKKALAKAEEDLARMRKSTAEATETVNTRQANAAVIAEKLENMR 789
                                       456667777777788888888888888888888888888777777777777777765 PP

  == domain 6  score: 2.9 bits;  conditional E-value: 0.074
                           DUF1664  70 rvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                         +++l++ k++ ++ +e+++++r+ ++e  e v++ ++    +++kle++ 
  gi|474933825|ref|YP_007687407.1| 738 AAEASLNAAKKALAKAEEDLARMRKSTAEATETVNTRQANAAVIAEKLENMR 789
                                       4444455555555555555555555555555555555444444444444443 PP

  == domain 7  score: 4.7 bits;  conditional E-value: 0.021
                           DUF1664  61 krhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                         +L++ri++  + + e ++  +++ +++  +r +ls ++++ e++++ v++ ++ +++ e
  gi|474933825|ref|YP_007687407.1| 804 PADLQERIEKARNAVYELTQKENDLLSQIGGARAELSGLDKQKEALDDQVSKTDKAIAEAE 864
                                       46899***********************************************999998876 PP

  == domain 8  score: 5.0 bits;  conditional E-value: 0.018
                           DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegl 113
                                        +l++  ++L s+i    ++l    + +++++++v++  + ++e + +  + ++a+ +l
  gi|474933825|ref|YP_007687407.1| 819 YELTQKENDLLSQIGGARAELSGLDKQKEALDDQVSKTDKAIAEAEAEAGQHQKAMDQL 877
                                       23344444455555555555555555555555555555555555555555555555554 PP

  == domain 9  score: 8.1 bits;  conditional E-value: 0.0019
                           DUF1664  35 TkrslsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvk 107
                                        k+ + + +es  ++l++  ++l + k +L+ ++d+ +  ++  + i ++ +++v   ++ l+ ++e+++++ 
  gi|474933825|ref|YP_007687407.1| 883 AKKKILSDMESGVEDLKSARDALVERKYKLEGEVDKAQGDIETKNGILQSQQAQVLIHQQTLQGFEEEIKQIT 955
                                       44444444555557899999**************************************************996 PP

  == domain 10  score: 0.5 bits;  conditional E-value: 0.41
                           DUF1664   63 hLssridrvdkkldeqkeiskeike 87  
                                        +L  +++r++k++de ++++ e+++
  gi|474933825|ref|YP_007687407.1| 1002 ELLGEVARLNKQIDELNKLTDELTA 1026
                                        4444455555555555544444333 PP

  == domain 11  score: -3.2 bits;  conditional E-value: 6
                           DUF1664   71 vdkkldeqkeiskeikeevtevredlseigedvesvkeav 110 
                                        vd  ld++   s+ +++ v+e +++ + i+  +++v  +v
  gi|474933825|ref|YP_007687407.1| 1118 VDMFLDAV--NSEMVAKRVKESSRKAQFIQVSLRKVALTV 1155
                                        55555544..367788899999999999999998888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2147  (0.11975); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                       118  (0.00658152); expected 17.9 (0.001)
Passed Fwd filter:                        76  (0.00423894); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 2.31u 0.39s 00:00:02.70 Elapsed: 00:00:00.70
# Mc/sec: 5165.83
//
Query:       gi|474933826|ref|YP_007687408.1|  [L=284]
Description: ScpA/B protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0014   18.6   0.0      0.018   14.9   0.0    2.1  2  SMC_ScpA         Segregation and condensation protein ScpA
  ------ inclusion threshold ------
      0.019   14.4   0.9      0.029   13.8   0.9    1.2  1  DUF3482          Domain of unknown function (DUF3482)
      0.022   14.0   0.0      0.042   13.1   0.0    1.4  1  Rad21_Rec8       Conserved region of Rad21 / Rec8 like protei
      0.097   12.8   2.8          2    8.6   0.1    2.5  2  PEP-utilisers_N  PEP-utilising enzyme, N-terminal


Domain annotation for each model (and alignments):
>> SMC_ScpA  Segregation and condensation protein ScpA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.051   2.3e+02       1      58 [.      60     115 ..      60     138 .. 0.80
   2 !   14.9   0.0   4.1e-06     0.018     142     240 ..     182     269 ..     144     270 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.051
                                       HHHHHHHHHTSSSSXXXXHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHSXXX CS
                          SMC_ScpA   1 LiiakeldvtdvavakvtdqflayiktllnkleleesteylviastlvelKaasLlpl 58 
                                       L+ +  +d++ +++ + +  + + + ++    ++  ++   ++a +++++ +a+  + 
  gi|474933826|ref|YP_007687408.1|  60 LVLDSGMDPWAIDLEEFVKLYSEKVARN--AFDMVVAGRLVLMAWRVLNMQSAEVRDR 115
                                       5677889999999999999999999988..8999999999999999999999877655 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 4.1e-06
                                       XXXXXXXXXXXXXX...HHHHHHHHHHHH...............HHH.....TS-EEGGGSSTT...--HHHHHHHH CS
                          SMC_ScpA 142 lkrakivalaekqiseleisieeqleellaqleqflqarlkevLldl.....rswvdlseLladnkledkkelvgvF 213
                                       + rak++a a+++ +    ++ee  e ++           ++vL ++     +s + ls L  +    d ke +++F
  gi|474933826|ref|YP_007687408.1| 182 IARAKMEAKAPLKFENK--AHEEDDEAVV-----------ERVLEKVrsassGSPIALSSLYTQ----DIKENITIF 241
                                       55666666666655544..6666666666...........455555533222567888888777....99******* PP

                                       HHHHHHHHTT-EEEEESS.TTS-EEEEE CS
                          SMC_ScpA 214 lAlLeLiknqavaleQee.flddLqvsl 240
                                       + +L L+++ + ++ Qe  +++++ vs+
  gi|474933826|ref|YP_007687408.1| 242 VSVLHLVRDGMLDVTQETlPYGEIMVSV 269
                                       ****************975899999987 PP

>> DUF3482  Domain of unknown function (DUF3482)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.9   6.5e-06     0.029      42     115 ..     159     231 ..     153     237 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.5e-06
                           DUF3482  42 aLqrliealeeqrqarreeaaeliaelLidvaayreeadeeaeeaakekllerlqekvRqrEqkcveaLlklYk 115
                                       ++  liea+ee r++   + a+lia++ +++ a  +  +++a e++ e+++er+ ekvR++ +    aL +lY 
  gi|474933826|ref|YP_007687408.1| 159 TMMDLIEAFEEARAESEIRNARLIARAKMEAKAPLKF-ENKAHEEDDEAVVERVLEKVRSASSGSPIALSSLYT 231
                                       56789*********************99988766666.599********************9999999999996 PP

>> Rad21_Rec8  Conserved region of Rad21 / Rec8 like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   9.4e-06     0.042      24      50 ..     241     268 ..     236     273 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.4e-06
                                       HHHHHHHHHHTSEEEEE.SSTT--EEEE CS
                        Rad21_Rec8  24 FyelLvLatkgvIkvkQ.eaPYgdIlit 50 
                                       F ++L L   g+++v+Q + PYg+I ++
  gi|474933826|ref|YP_007687408.1| 241 FVSVLHLVRDGMLDVTQeTLPYGEIMVS 268
                                       7799*************889*****997 PP

>> PEP-utilisers_N  PEP-utilising enzyme, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1   0.00045         2      61      91 ..      12      41 ..       3      57 .. 0.84
   2 ?    4.0   0.4     0.012        53      31      88 ..     162     220 ..     139     254 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00045
                                      HHHHHHHHHHT-HHHHHHHHHHHHHHT--HH CS
                   PEP-utilisers_N 61 aifeahlmlleDpelleeveerIregglnae 91
                                      + +  h++++eDpe l++++  I++ +  ae
  gi|474933826|ref|YP_007687408.1| 12 QHLLFHKAMAEDPETLRKMNGYIETLH-HAE 41
                                      45778******************9655.676 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.012
                                       HHHHHHHHHHHHHHHHHHHHHHHH.T-HHHHH.HHHHHHHHHT-HHHHHHHHHHHHHHT- CS
                   PEP-utilisers_N  31 aelerleeAlekvreelealaeka.lgeeeaa.ifeahlmlleDpelleeveerIreggl 88 
                                       + +e +eeA+++++ + ++l ++a +++ +a   fe  ++  +D++ +e+v e++r++  
  gi|474933826|ref|YP_007687408.1| 162 DLIEAFEEARAESEIRNARLIARAkMEA-KAPlKFENKAHEEDDEAVVERVLEKVRSASS 220
                                       4455566666555555555555554322.2224688888888888888888888886654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2037.13
//
Query:       gi|474933827|ref|YP_007687409.1|  [L=184]
Description: segregation and condensation protein B [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-30  105.7   0.0    2.2e-30  105.4   0.0    1.1  1  SMC_ScpB  Segregation and condensation complex subunit ScpB
    0.00014   21.6   0.2       0.65    9.9   0.0    2.4  2  TrmB      Sugar-specific transcriptional regulator TrmB
    0.00064   19.5   0.0     0.0055   16.5   0.0    2.2  2  HTH_IclR  IclR helix-turn-helix domain
     0.0034   17.2   0.0       0.17   11.8   0.0    2.8  3  MarR_2    MarR family
  ------ inclusion threshold ------
      0.026   14.4   0.0       0.14   12.1   0.0    2.0  2  HTH_5     Bacterial regulatory protein, arsR family
      0.075   13.2   0.1       0.14   12.2   0.1    1.4  1  DprA_WH   DprA winged helix domain
      0.079   12.5   0.0        1.2    8.8   0.0    2.1  2  HTH_24    Winged helix-turn-helix DNA-binding


Domain annotation for each model (and alignments):
>> SMC_ScpB  Segregation and condensation complex subunit ScpB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.4   0.0   8.6e-34   2.2e-30       2     154 ..       6     150 ..       5     157 .. 0.97

  Alignments for each domain:
  == domain 1  score: 105.4 bits;  conditional E-value: 8.6e-34
                          SMC_ScpB   2 iiEAiLfvageplsleeLakilelskeeveealeeLkeeyeeedrglelvevaggyrlvtkpelaevvkklvkekkk 78 
                                       ++EA+Lf+a  pl+++++ + ++l +++v+ al++L+ ey+ +d+++ +  ++g yr++++pe++++   +++    
  gi|474933827|ref|YP_007687409.1|   6 AVEAALFAATAPLTVADIVERTGLPEADVRYALKDLRMEYDMRDSAIIISATGGEYRMMLRPEYQKYTDLFARP--- 79 
                                       79******************************************************************999999... PP

                          SMC_ScpB  79 trLsqaaletLaiIaykqpvtraeieeiRGvnsdsvvrtLlerglieekgrkeepgrpilYgtTekFleyfglksl 154
                                        ++    ++tL+ Iay+qpv ++++ + RG ++++ v +L+e+g + ++     +g ++ ++tT+kF e fg+ s+
  gi|474933827|ref|YP_007687409.1|  80 -EMPPGVMRTLSAIAYNQPVLQSKLVKARGPRAYEDVARLIEMGYVYSRP----SGPTYELTTTKKFSEDFGIGST 150
                                       .9***********************************************9....999999*************985 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0   0.00025      0.65      19      47 ..      14      42 ..       7      44 .. 0.88
   2 !    9.4   0.1   0.00036      0.92      35      60 ..     107     132 ..     101     140 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00025
                                      HHCCCHHCHHCCCTTSSCHCHHHHHHHHH CS
                              TrmB 19 klgpatadeiaeelgvprskvYevLrsLe 47
                                      +  p+t+ +i e++g+p++ v  +L+ L 
  gi|474933827|ref|YP_007687409.1| 14 ATAPLTVADIVERTGLPEADVRYALKDLR 42
                                      5789*********************9985 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00036
                                       SCHCHHHHHHHHHHCTSEEEESSTTT CS
                              TrmB  35 prskvYevLrsLedkGlVerekgrpk 60 
                                         +++Ye + +L+++G+V+ +++ p+
  gi|474933827|ref|YP_007687409.1| 107 RGPRAYEDVARLIEMGYVYSRPSGPT 132
                                       5689*****************99876 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   2.1e-06    0.0055      14      42 ..      13      41 ..       9      44 .. 0.84
   2 ?    0.3   0.0      0.25   6.3e+02      40      50 ..     116     126 ..     109     128 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.1e-06
                                      TTBSS-BHHHHHHHHTS-HHHHHHHHHHH CS
                          HTH_IclR 14 eapqeltlselArrtglpkStvhRlLqtL 42
                                      +a+ +lt++++ +rtglp + v+  L+ L
  gi|474933827|ref|YP_007687409.1| 13 AATAPLTVADIVERTGLPEADVRYALKDL 41
                                      56777*****************9999877 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.25
                                       HHHHHTTSEE. CS
                          HTH_IclR  40 qtLvelGyveq 50 
                                       + L+e+Gyv  
  gi|474933827|ref|YP_007687409.1| 116 ARLIEMGYVYS 126
                                       6799****986 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   6.8e-05      0.17      19      45 ..      17      41 ..       7      42 .. 0.87
   2 ?   -0.4   0.0      0.44   1.1e+03       3      29 ..      81     105 ..      80     108 .. 0.80
   3 ?    1.3   0.0      0.13   3.2e+02      42      56 ..     115     129 ..     114     131 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.8e-05
                                      TSEEEHHHHHHHHTSSHHHHHHHHHHH CS
                            MarR_2 19 grdltvgelarrlglsksavsrilkrL 45
                                      +  ltv+++++r+gl+ + v ++lk+L
  gi|474933827|ref|YP_007687409.1| 17 P--LTVADIVERTGLPEADVRYALKDL 41
                                      3..9********************998 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.44
                                       --HHHHHHHHHHHCTTTSEEEHHHHHH CS
                            MarR_2   3 ltpaqarvLaaLgrrpgrdltvgelar 29 
                                       ++p   r L a++ + +  + ++ l++
  gi|474933827|ref|YP_007687409.1|  81 MPPGVMRTLSAIAYNQP--VLQSKLVK 105
                                       78888999999999999..88877765 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.13
                                       HHHHHHTTSEEEEES CS
                            MarR_2  42 lkrLvaaGLverrpg 56 
                                       ++rL + G+v  rp+
  gi|474933827|ref|YP_007687409.1| 115 VARLIEMGYVYSRPS 129
                                       79********99986 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   5.4e-05      0.14      14      40 ..      16      42 ..      10      44 .. 0.92
   2 ?   -0.5   0.0      0.47   1.2e+03      38      47 .]     117     126 ..     115     126 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.4e-05
                                      SSEEHHHHHHHHTS-HHHHHHHHHHHH CS
                             HTH_5 14 gelcvcelaeelglsqstvShHLkkLr 40
                                       +l+v +++e +gl+++ v++ Lk Lr
  gi|474933827|ref|YP_007687409.1| 16 APLTVADIVERTGLPEADVRYALKDLR 42
                                      79***********************98 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.47
                                       HHHHTTSEEE CS
                             HTH_5  38 kLreaGLVek 47 
                                       +L e+G+V++
  gi|474933827|ref|YP_007687409.1| 117 RLIEMGYVYS 126
                                       799*****85 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   5.6e-05      0.14      15      50 ..       5      42 ..       2      44 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.6e-05
                           DprA_WH 15 rrvLaaL..gpePvhvDqLvrrtglpaaevsaaLleLE 50
                                       +v aaL  + +P++v ++v+rtglp a v  aL  L 
  gi|474933827|ref|YP_007687409.1|  5 TAVEAALfaATAPLTVADIVERTGLPEADVRYALKDLR 42
                                      455566654567**************999999887765 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00045       1.2      14      42 ..      14      42 ..      10      44 .. 0.89
   2 ?    1.6   0.0     0.081   2.1e+02      38      47 ..     115     124 ..     115     125 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00045
                            HTH_24 14 knprisqreLAerlglSpstvnrrlkrLe 42
                                      + + ++ +++ er+gl+ + v++ lk L 
  gi|474933827|ref|YP_007687409.1| 14 ATAPLTVADIVERTGLPEADVRYALKDLR 42
                                      56789*********************995 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.081
                            HTH_24  38 lkrLeeeGlI 47 
                                       + rL+e+G++
  gi|474933827|ref|YP_007687409.1| 115 VARLIEMGYV 124
                                       579******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1123.78
//
Query:       gi|474933828|ref|YP_007687410.1|  [L=540]
Description: ABC-type Fe3+ transport system, permease component [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-32  112.1  30.1    3.4e-19   69.3   3.8    3.7  4  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   4.8     0.013   2.3e+02      12      72 ..      17      77 ..      10      83 .. 0.86
   2 !   56.9  18.4   1.2e-19   2.2e-15       1     182 [.      84     273 ..      80     276 .. 0.80
   3 ?   -1.8   0.6      0.12   2.2e+03     164     177 ..     306     319 ..     296     349 .. 0.53
   4 !   69.3   3.8   1.9e-23   3.4e-19       1     182 [.     354     534 ..     354     537 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.013
                      BPD_transp_1 12 rnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlir 72
                                      r+ +l  ++ +++ ++l   +fv+  l++ +  ++++lg+  ++vi+ +++ ++ +++l++
  gi|474933828|ref|YP_007687410.1| 17 RKAWLGLAVAVFVCIILVPSMFVVTKLFTEWGLVSDVLGSDQMSVILGAVWNSFSLAILVT 77
                                      6777778888888888888888899999999999*********************999987 PP

  == domain 2  score: 56.9 bits;  conditional E-value: 1.2e-19
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf......vilsilghlilp...viillllsaapyv 68 
                                       g+++++++  +r + ++kll++l +++l++P+ vl++ +++ f      v + +lg +i p   +i+l ++++ py+
  gi|474933828|ref|YP_007687410.1|  84 GLPIAWIMV-RRDFGGKKLLDTLLDLPLAFPTAVLGLSVLM-FwgapegVTIPSLGLGIGPyamLILLHFIFTYPYM 158
                                       567777777.99999*******************9999885.559****55555555555520345566677889** PP

                      BPD_transp_1  69 rlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG.lgtlllea 144
                                       ++  +a+l++++++++ aa +lGasr++ +r+++lP+    ++tg+il f ++l ++  +++ +      +t+++ +
  gi|474933828|ref|YP_007687410.1| 159 VRSLSAILEQIDSSYETAAMTLGASRFTAVRTITLPLFRAGLVTGFILCFSRSLSETGGTLIALVLMKvDTTFFTGP 235
                                       *****************************************************977655554441111266666666 PP

                      BPD_transp_1 145 ilgydyseisnggvlalviavlllnlvadilqrlldpr 182
                                       + ++  + + +g+++ + ++++++ l++ ++++ll  +
  gi|474933828|ref|YP_007687410.1| 236 TYISAAHGGDMGPMILISVIMIAIALLLLVVVKLLVTK 273
                                       66666666669999999999999999999999998765 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.12
                      BPD_transp_1 164 avlllnlvadilqr 177
                                       ++l++++ ++ + +
  gi|474933828|ref|YP_007687410.1| 306 LFLVILIPSFYIFA 319
                                       22222222222222 PP

  == domain 4  score: 69.3 bits;  conditional E-value: 1.9e-23
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilp.viillllsaapyvrlirraal 76 
                                       gi++++++a++++ k   ++++l++++l +P+ +l++ l+l+     + g ++ + vi+  + ++ p+v++++ +a+
  gi|474933828|ref|YP_007687410.1| 354 GIPVAMYIARHKKEKAAGIVDTLVNIPLLVPTTALGFSLTLFWGAAHGSGPYAVAlVILGHIAFTYPLVVRNITGAV 430
                                       89**************************************765556666655555578888889999********** PP

                      BPD_transp_1  77 rslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydysei 153
                                       ++++ +++e+a +lGa+++q f+k++lP +++++i+g ilaf+++lg++ ++  ++  p + t+   + +      +
  gi|474933828|ref|YP_007687410.1| 431 EEVDPSYEETAMTLGAKPFQAFYKILLPVIKSSVIAGGILAFTRSLGETGATIAIA--PDVRTVPCYIVELVKAGHT 505
                                       ********************************************************..5555544444444444444 PP

                      BPD_transp_1 154 snggvlalviavlllnlvadilqrlldpr 182
                                        ++ ++++ i+++++++v+ + +r+l + 
  gi|474933828|ref|YP_007687410.1| 506 HYAEAAMCSIVLIAICFVFLVAVRVLTKG 534
                                       45889999999999999999998888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (540 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1053  (0.0587317); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.70u 0.33s 00:00:01.03 Elapsed: 00:00:00.50
# Mc/sec: 3252.94
//
Query:       gi|474933829|ref|YP_007687411.1|  [L=310]
Description: ABC-type spermidine/putrescine transport systems, ATPase component [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.5e-30  104.1   0.0    1.4e-29  103.3   0.0    1.3  1  ABC_tran  ABC transporter
     0.0025   16.9   0.1       0.01   14.9   0.0    1.9  2  T2SSE     Type II/IV secretion system protein
     0.0085   15.9   1.6        1.6    8.4   0.2    2.2  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
  ------ inclusion threshold ------
       0.01   16.2   0.1      0.027   14.9   0.1    1.7  1  AAA_16    AAA ATPase domain
      0.014   15.8   0.6      0.091   13.2   0.6    2.1  1  AAA       ATPase family associated with various cellular acti
      0.023   15.2   0.1      0.031   14.8   0.1    1.4  1  AAA_23    AAA domain
      0.028   14.7   0.6        0.3   11.4   0.1    2.1  2  AAA_22    AAA domain
      0.029   14.4   0.0        0.1   12.6   0.0    1.8  2  AAA_5     AAA domain (dynein-related subfamily)
      0.053   13.5   0.1       0.72    9.9   0.0    2.2  2  TsaE      Threonylcarbamoyl adenosine biosynthesis protein Ts
      0.061   13.0   0.0       0.22   11.2   0.0    1.9  2  AAA_30    AAA domain
       0.07   12.9   0.0       0.14   11.9   0.0    1.5  1  AAA_29    P-loop containing region of AAA domain
      0.078   12.9   0.0       0.18   11.7   0.0    1.6  1  NACHT     NACHT domain
       0.13   12.4   0.3        2.2    8.4   0.1    2.1  2  AAA_33    AAA domain
       0.17   11.6   0.5       0.69    9.7   0.5    2.0  1  DEAD      DEAD/DEAH box helicase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.3   0.0   1.1e-32   1.4e-29       2     136 ..      21     162 ..      20     163 .. 0.90

  Alignments for each domain:
  == domain 1  score: 103.3 bits;  conditional E-value: 1.1e-32
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       +++sl+++ ge + ++G++G+GK+t l+ ++gl+ p++G++l+dg+d+++   +++ ++  +l+q+  lfp++ v+ 
  gi|474933829|ref|YP_007687411.1|  21 DHLSLTVRDGEYLCLLGPTGSGKTTALREICGLTVPDSGRVLFDGRDMSD--VPISVRKATMLSQKYALFPNMDVYG 95 
                                       679***********************************************..999999******************* PP

                                       H.........HHHTCHHHHH.HHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x.........xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.........esdeeiekal.sklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n         +s+++  +++ s +++++   +++++ p +LSgGq+qr alaral +++k+lllDEp 
  gi|474933829|ref|YP_007687411.1|  96 NvvfspvikeWSEKDTRQLAtSMIDMVH-MSKKIHNMPGELSGGQQQRTALARALSSESKILLLDEPL 162
                                       ********99555555555505555555.666667999*****************************6 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   8.2e-06      0.01     105     152 ..       6      53 ..       1      94 [. 0.80
   2 ?   -0.2   0.1      0.34   4.3e+02      93     136 ..     171     217 ..     110     220 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 8.2e-06
                             T2SSE 105 lddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallke 152
                                       l+dl+++   + k ++ l+  vr    + + G+TgsGKtt l  +   
  gi|474933829|ref|YP_007687411.1|   6 LEDLVKTYGGDIKASDHLSLTVRDGEYLCLLGPTGSGKTTALREICGL 53 
                                       66777777777788899999999999999************9766554 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.34
                             T2SSE  93 lviR...kksakeltlddlgaeealkekiaevlrkavrerglilvsG 136
                                       + +R   k+ ++e+ l  + ++++++e+++ + r a+ +rg i+  G
  gi|474933829|ref|YP_007687411.1| 171 IELRkelKSMVQEMGLTSIHVTHDQDEALEVADRIAIIRRGKIVQVG 217
                                       55666666677777888888888888888888888888888777555 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.1    0.0047       6.1       3      17 ..      34      48 ..      33      67 .. 0.90
   2 !    8.4   0.2    0.0013       1.6     236     284 ..     134     179 ..     113     195 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0047
                            AAA_21  3 vliGpNgsGKSnLLd 17
                                      +l Gp gsGK++ L+
  gi|474933829|ref|YP_007687411.1| 34 CLLGPTGSGKTTALR 48
                                      699*********997 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0013
                            AAA_21 236 elSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellke 284
                                       elS G+++  al+ al +     ++ll+DEp   L+ +l  +l + lk+
  gi|474933829|ref|YP_007687411.1| 134 ELSGGQQQRTALARALSSES---KILLLDEPLRALDARLRIELRKELKS 179
                                       67888888844444444444...9***************9999988865 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   2.1e-05     0.027      18      55 ..      26      61 ..      18     184 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.1e-05
                            AAA_16 18 rvrsgrpelvllsGesGvGKsslvrellralekdggif 55
                                      +vr+g  e++ l G+ G+GK++ +re+      d g +
  gi|474933829|ref|YP_007687411.1| 26 TVRDG--EYLCLLGPTGSGKTTALREICGLTVPDSGRV 61
                                      55666..7999***************986444443444 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.6   7.1e-05     0.091       1      66 [.      33     160 ..      33     207 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.1e-05
                                       EEEESSTTSSHHHHHHHHHHHH...............THEEEEEETTTCSSS......................... CS
                               AAA   1 vllyGppGtGKTllakavakel...............gvefleisgsellsk......................... 37 
                                       ++l Gp G GKT++ + ++  +               +v+ +++  +++ls+                         
  gi|474933829|ref|YP_007687411.1|  33 LCLLGPTGSGKTTALREICGLTvpdsgrvlfdgrdmsDVP-ISVRKATMLSQkyalfpnmdvygnvvfspvikewse 108
                                       589****************985444333333322221122.222222222222555555555555555555555555 PP

                                       ......................STTHHHHHHHHHHHHHHHTS.TSEEEEEET CS
                               AAA  38 ......................yvgesekkirelfkeakeka.kpsilfiDE 66 
                                                             + ge +   ++  + a++ + + +il++DE
  gi|474933829|ref|YP_007687411.1| 109 kdtrqlatsmidmvhmskkihnMPGELSGGQQQRTALARALSsESKILLLDE 160
                                       5555555555555555555555666666666666666665555557777777 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   2.4e-05     0.031      23      44 ..      34      55 ..      25     184 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.4e-05
                            AAA_23 23 lItGpNGaGKTTildAiklaLy 44
                                      ++ Gp+G+GKTT l+ i+  + 
  gi|474933829|ref|YP_007687411.1| 34 CLLGPTGSGKTTALREICGLTV 55
                                      689************9997665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00023       0.3       7      25 ..      32      50 ..      27      59 .. 0.87
   2 ?    1.5   0.0      0.26   3.3e+02      71     120 ..     134     183 ..      76     194 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00023
                            AAA_22  7 ilvvtGesGtGKTtllrrl 25
                                       l++ G++G+GKTt lr++
  gi|474933829|ref|YP_007687411.1| 32 YLCLLGPTGSGKTTALREI 50
                                      58899***********985 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.26
                            AAA_22  71 erlsseellealeqalraravielliiDEaqh.lr...seealeeLrsllnlsr 120
                                       e    ++ ++al++al++ ++  +l++DE  + l+   + e+ +eL+s++   +
  gi|474933829|ref|YP_007687411.1| 134 ELSGGQQQRTALARALSSESK--ILLLDEPLRaLDarlRIELRKELKSMVQ--E 183
                                       444556667788888888888..9999997666656444777777777766..4 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   7.9e-05       0.1       2      24 ..      33      56 ..      32      70 .. 0.84
   2 ?   -1.8   0.0       2.2   2.8e+03      58      73 ..     144     160 ..     131     170 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.9e-05
                                      EEEE--SSSSHHHHHHHGGGGB.S CS
                             AAA_5  2 vlLvGppGtgKselaerlaaal.n 24
                                      ++L+Gp+G+gK++  ++++ ++  
  gi|474933829|ref|YP_007687411.1| 33 LCLLGPTGSGKTTALREICGLTvP 56
                                      79****************998863 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.2
                                       -------.G-SEEEEES CS
                             AAA_5  58 plvraar.egeilvlDE 73 
                                       +l ra   e++il+lDE
  gi|474933829|ref|YP_007687411.1| 144 ALARALSsESKILLLDE 160
                                       56666668999999999 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00056      0.72      18      40 ..      27      51 ..       8      58 .. 0.79
   2 ?    1.0   0.0      0.32   4.1e+02       3      40 ..     107     150 ..     103     159 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00056
                                      H..TEEEEEEESTTSSHHHHHHHHH CS
                              TsaE 18 l..gdvilLeGdLGaGKTtlvrgla 40
                                      +  g+ ++L G+ G+GKTt  r+++
  gi|474933829|ref|YP_007687411.1| 27 VrdGEYLCLLGPTGSGKTTALREIC 51
                                      244678***************9987 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.32
                                       SHHHHHHHHHHHHHCH...TEEEEEEESTTSS...HHHHHHHHH CS
                              TsaE   3 seeetealgkklakal...gdvilLeGdLGaG...KTtlvrgla 40 
                                       se++t++l++++ +++   +++  + G+L  G    T+l+r+l 
  gi|474933829|ref|YP_007687411.1| 107 SEKDTRQLATSMIDMVhmsKKIHNMPGELSGGqqqRTALARALS 150
                                       67899999999988777777788999999988444477777665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00017      0.22      17      39 ..      30      51 ..      20      63 .. 0.79
   2 ?   -2.0   0.0         2   2.5e+03       4      22 ..     139     157 ..     136     161 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00017
                            AAA_30 17 gdrvavltGpAGtGKttalkalr 39
                                      g  + +l Gp G+GKttal+++ 
  gi|474933829|ref|YP_007687411.1| 30 G-EYLCLLGPTGSGKTTALREIC 51
                                      3.488999************985 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2
                            AAA_30   4 aeQaaavealltsgdrvav 22 
                                       ++Q++a++++l+s+ ++ +
  gi|474933829|ref|YP_007687411.1| 139 QQQRTALARALSSESKILL 157
                                       6899999999999987655 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00011      0.14      19      49 ..      27      57 ..      18      64 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                            AAA_29 19 idlkg.atlltGpsGsGKSTllDAiqalLvpa 49
                                      ++ +g    l Gp+GsGK+T l  i  l vp+
  gi|474933829|ref|YP_007687411.1| 27 VR-DGeYLCLLGPTGSGKTTALREICGLTVPD 57
                                      44.3458889**********986666666665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00014      0.18       2      21 ..      32      51 ..      31      56 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00014
                                      CEEEEC-TTTCHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqkla 21
                                      +++l G+ GsGKTt l++++
  gi|474933829|ref|YP_007687411.1| 32 YLCLLGPTGSGKTTALREIC 51
                                      689**************997 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1    0.0017       2.2       4      20 ..      35      51 ..      33      62 .. 0.88
   2 ?    2.0   0.0      0.17   2.1e+02      61     109 ..     144     198 ..     106     225 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0017
                            AAA_33  4 lvGlpGsGKstlaerll 20
                                      l G+ GsGK+t +++++
  gi|474933829|ref|YP_007687411.1| 35 LLGPTGSGKTTALREIC 51
                                      67**********99876 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.17
                            AAA_33  61 elarkalsagrn.vildatnlsrrer......arflklarrlgvpvrivvvetdee 109
                                       +la +als++   ++ld +++  ++r      +++ ++++++g     v+ + de+
  gi|474933829|ref|YP_007687411.1| 144 ALA-RALSSESKiLLLDEPLRALDARlrielrKELKSMVQEMGLTSIHVTHDQDEA 198
                                       333.4444444425557776553333334443777777777777777777666666 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.5   0.00054      0.69      13      31 ..      29      47 ..      19     227 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00054
                                      TTCEEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxxxxx RF
                              DEAD 13 gggdvlvaaeTGsGKTlaf 31
                                      +g+ +++ ++TGsGKT+a 
  gi|474933829|ref|YP_007687411.1| 29 DGEYLCLLGPTGSGKTTAL 47
                                      67888999********995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 1892.12
//
Query:       gi|474933830|ref|YP_007687412.1|  [L=64]
Description: TOBE domain protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-06   27.7   0.0    2.6e-06   27.5   0.0    1.1  1  TOBE_2    TOBE domain


Domain annotation for each model (and alignments):
>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   1.4e-10   2.6e-06      28      76 .]       3      50 ..       1      50 [. 0.94

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 1.4e-10
                            TOBE_2 28 ylGsstryvvelaggqlvvvrqpnadrdsalapGdtVelswdpddavvl 76
                                      y G+++ + ve++g  lv +++++++  +a++ Gd V+++w+p++a v+
  gi|474933830|ref|YP_007687412.1|  3 YEGTTITIEVEVEGIGLVSAKRSSRR-YEAYNQGDIVAVTWQPEKASVF 50
                                      89***************999999998.68*****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 427.88
//
Query:       gi|474933831|ref|YP_007687413.1|  [L=361]
Description: ABC-type spermidine/putrescine transport systems, ATPase component [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-33  114.7   0.0    6.6e-33  114.1   0.0    1.3  1  ABC_tran      ABC transporter
    1.5e-06   28.2   0.1    1.2e-05   25.4   0.0    2.4  2  TOBE_2        TOBE domain
    1.7e-06   27.7   0.1    2.6e-05   23.8   0.1    2.1  1  SMC_N         RecF/RecN/SMC N terminal domain
    3.4e-06   27.1   0.2      0.084   12.7   0.0    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    0.00035   21.0   0.0    0.00062   20.2   0.0    1.5  1  AAA_16        AAA ATPase domain
     0.0095   15.4   0.2        0.4   10.0   0.1    2.2  2  TniB          Bacterial TniB protein
  ------ inclusion threshold ------
      0.011   16.2   0.0       0.15   12.5   0.0    2.1  2  AAA           ATPase family associated with various cellular 
      0.011   15.6   0.0      0.026   14.4   0.0    1.6  2  RsgA_GTPase   RsgA GTPase
      0.019   14.9   0.0      0.035   14.0   0.0    1.4  1  Rad17         Rad17 P-loop domain
      0.035   13.8   0.1        0.2   11.4   0.0    2.1  2  AAA_30        AAA domain
      0.073   11.8   0.5       0.82    8.4   0.5    2.1  1  ABC_ATPase    Predicted ATPase of the ABC class
      0.081   12.3   0.0       0.22   10.9   0.0    1.6  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.097   13.0   0.1        6.6    7.1   0.0    2.2  2  AAA_19        AAA domain
        0.1   12.5   0.0        0.2   11.5   0.0    1.4  1  ATPase_2      ATPase domain predominantly from Archaea
       0.12   12.3   0.1       0.34   10.8   0.1    1.7  2  NACHT         NACHT domain
       0.13   12.1   0.3        1.4    8.8   0.0    2.7  3  TrkA_C        TrkA-C domain
       0.13   12.0   0.0       0.27   11.0   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
       0.14   12.5   0.2       0.72   10.1   0.1    2.0  2  AAA_22        AAA domain
       0.14   12.6   0.1       0.29   11.6   0.1    1.4  1  AAA_23        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.1   0.0     7e-36   6.6e-33       2     136 ..      20     161 ..      19     162 .. 0.89

  Alignments for each domain:
  == domain 1  score: 114.1 bits;  conditional E-value: 7e-36
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       +++sl+++ege + i+G++G+GK++L++l++g  +pteG++l+dgkd+++   +  ++ +g+++q+  lfp++++ +
  gi|474933831|ref|YP_007687413.1|  20 RDISLEVQEGEYITILGPSGCGKTSLIRLISGIWTPTEGKVLIDGKDVTH--VPMEDRDVGYVFQNIALFPNMNNLK 94 
                                       689***********************************************..9999******************999 PP

                                       H.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n             e     +ka+  l+l+++  +  +  p +LSgG++q+va+aral++ +k+++lDEp 
  gi|474933831|ref|YP_007687413.1|  95 NvgygprvrgadseE---ADKKARLYLELVNMLGRA-GMFPDELSGGEQQKVAIARALASGSKIIMLDEPL 161
                                       9********984444...445555556666655555.5778*****************************7 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.015        14      34      72 ..     252     284 ..     249     286 .. 0.75
   2 !   25.4   0.0   1.3e-08   1.2e-05       1      73 [.     278     344 ..     278     347 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.015
                            TOBE_2  34 ryvvelaggqlvvvrqpnadrdsalapGdtVelswdpdd 72 
                                       r++v+l gg+    ++   +    +++Gd+V +s++p+ 
  gi|474933831|ref|YP_007687413.1| 252 RTMVRLRGGKV---VRGEKT---EFEEGDAVVISVRPEN 284
                                       56778888844...444555...89***********996 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 1.3e-08
                            TOBE_2   1 laiRPEklrlaaagganglsGtVedveylGsstryvvelaggqlvvvrqpnadrdsalapGdtVelswdpdda 73 
                                       +++RPE++     ++ +g+s++V++ +++G++ r++ + + g  ++   +++    +++ G++V l ++ + +
  gi|474933831|ref|YP_007687413.1| 278 ISVRPENVYT---AT-EGISARVVNSVFMGTYWRVRTSSETGDYIEYNISDNL--VPPENGEEVFLVFNKRMT 344
                                       58********...66.7***************************999888887..5**********9987655 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.1   2.7e-08   2.6e-05      25     212 ..      30     205 ..      10     213 .. 0.72

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 2.7e-08
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--.BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk.skekasvkkaeveitfdnedkklkiekeevsis 100
                                       +   i+Gp G+GK++l+  i+ +   ++         + li     ++  ++  +v  +f+n     +  ++  ++ 
  gi|474933831|ref|YP_007687413.1|  30 EYITILGPSGCGKTSLIRLISGIWTPTEG--------KVLIDGkDVTHVPMEDRDVGYVFQNIALF-PNMNNLKNVG 97 
                                       467899*********99999655554444........45555433344455666677777766664.4444445555 PP

                                       EEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 101 rrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvk 177
                                             g  + + ++k   + e+ ++l +ag+ +++LSgGe++ va+a  +A      + + +lDe  +aLD + ++
  gi|474933831|ref|YP_007687413.1|  98 YGPRVRGADSEEADKKARLYLELVNMLGRAGMFPDELSGGEQQKVAIARALAS----GSKIIMLDEPLSALDTRVRT 170
                                       55555666566789999999**************************9998875....5679**************** PP

                                       HHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 178 kvaellkeksknaQfivislreemlekadklvgvt 212
                                       ++   +++  k+  + v  +++++ e ++   ++ 
  gi|474933831|ref|YP_007687413.1| 171 ELRYEIRRIVKELGITVLHVTHDQEEAMSVSDRIV 205
                                       ***99999999977777666666655555544444 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   8.9e-05     0.084       4      24 ..      34      54 ..      32     117 .. 0.83
   2 !   12.3   0.0   0.00012      0.11     235     298 ..     132     193 ..     118     198 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.9e-05
                            AAA_21  4 liGpNgsGKSnLLdaldllar 24
                                      + Gp g+GK++L++++++++ 
  gi|474933831|ref|YP_007687413.1| 34 ILGPSGCGKTSLIRLISGIWT 54
                                      89**************99953 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00012
                            AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHS 298
                                       +elS G ++  a++ al++     +++ +DEp + L+ ++ ++l   + ++ ++ g+ v+ +TH+
  gi|474933831|ref|YP_007687413.1| 132 DELSGGEQQKVAIARALASGS---KIIMLDEPLSALDTRVRTELRYEIrRIVKELGITVLHVTHD 193
                                       678999999977777777655...9*************9999999666455555799*******8 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   6.6e-07   0.00062      23      69 ..      28      72 ..      18     183 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 6.6e-07
                            AAA_16 23 rpelvllsGesGvGKsslvrellralekdggif.lrgkcdqlesaipy 69
                                      ++e++ + G+sG+GK+sl+r +   ++ ++g + + gk + +   +p+
  gi|474933831|ref|YP_007687413.1| 28 EGEYITILGPSGCGKTSLIRLISGIWTPTEGKVlIDGKDVTH---VPM 72
                                      348999*****************9999998777799988888...665 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.06        57      38      53 ..      32      47 ..      23      54 .. 0.88
   2 !   10.0   0.1   0.00043       0.4      81     160 ..     111     190 ..     100     208 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.06
                              TniB 38 lllvGdsnnGKtmive 53
                                      + ++G+s +GKt++++
  gi|474933831|ref|YP_007687413.1| 32 ITILGPSGCGKTSLIR 47
                                      789**********996 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00043
                              TniB  81 pdekrlyaaiLealgaplkararvskleqqvlrllrel..kvrvLiiDEihnllagsarkqreflnalksLgnelki 155
                                        +++rly ++++ lg      +++s  eqq +++ r+l  + +++++DE  ++l    r + e+   ++++  el i
  gi|474933831|ref|YP_007687413.1| 111 DKKARLYLELVNMLGRAGMFPDELSGGEQQKVAIARALasGSKIIMLDEPLSAL--DTRVRTELRYEIRRIVKELGI 185
                                       46789*********9998888888877777777777652278*******99999..6667789999*********** PP

                              TniB 156 pivlv 160
                                       ++  v
  gi|474933831|ref|YP_007687413.1| 186 TVLHV 190
                                       99876 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00016      0.15       3      22 ..      34      53 ..      32      96 .. 0.78
   2 ?    1.5   0.0      0.39   3.6e+02      52      89 ..     144     183 ..     104     222 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00016
                                      EESSTTSSHHHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavakel 22
                                      + Gp G+GKT+l++ +   +
  gi|474933831|ref|YP_007687413.1| 34 ILGPSGCGKTSLIRLISGIW 53
                                      78************998765 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.39
                                       HHHHTS.TSEEEEEETGGGHHHHH.TTCCCHHHHHHHHHH CS
                               AAA  52 eakeka.kpsilfiDEidalaksr.sgseseeeervvnqL 89 
                                        a++ a + +i+++DE  +   +r +++ + e +r+v++L
  gi|474933831|ref|YP_007687413.1| 144 IARALAsGSKIIMLDEPLSALDTRvRTELRYEIRRIVKEL 183
                                       3344444459999999888778774444445555555555 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.7e-05     0.026      81     121 ..      10      51 ..       1      67 [. 0.78
   2 ?   -3.2   0.0         7   6.6e+03      66      90 ..     174     198 ..     161     202 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.7e-05
                                       E--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  81 lvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                        ++  +  ++++++ ++++ + ++++G+SG GK++Li  + +
  gi|474933831|ref|YP_007687413.1|  10 SMRFGDFYAIRDISLEVQEgEYITILGPSGCGKTSLIRLISG 51 
                                       5555555667778777777799***************98865 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 7
                                       HHHHHHHHHTTSEEEE--TTTHTTH CS
                       RsgA_GTPase  66 eelkeelealgyevllvsaktkegl 90 
                                        e++  +++lg++vl v  +++e++
  gi|474933831|ref|YP_007687413.1| 174 YEIRRIVKELGITVLHVTHDQEEAM 198
                                       5677788899999999887776655 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.7e-05     0.035      39      70 ..      23      54 ..      17      87 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.7e-05
                             Rad17 39 vLesrkkriLLisGPsGCgkstvvkvLskelg 70
                                      +Le ++ + + i GPsGCgk+  ++ +s + +
  gi|474933831|ref|YP_007687413.1| 23 SLEVQEGEYITILGPSGCGKTSLIRLISGIWT 54
                                      78888888999**************9998765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00021       0.2      19      50 ..      30      61 ..      18      70 .. 0.86
   2 ?   -0.5   0.0      0.92   8.6e+02      37      74 ..     175     213 ..     135     224 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00021
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaaggrvi 50
                                       + ++ Gp G GKt +++ +  +w+  +g+v+
  gi|474933831|ref|YP_007687413.1| 30 EYITILGPSGCGKTSLIRLISGIWTPTEGKVL 61
                                      478899*******************9977775 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.92
                            AAA_30  37 alreaweaaggrviglAptgkaAkvLaeelg.ieastia 74 
                                       ++r+++++ g +v+ +++ ++ A  +++ +  ++a ti+
  gi|474933831|ref|YP_007687413.1| 175 EIRRIVKELGITVLHVTHDQEEAMSVSDRIVlMRAGTIH 213
                                       456666666666666666666666666655423666655 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.5   0.00087      0.82     324     413 ..     135     209 ..     129     225 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00087
                                       -HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG--B--HHHCHHHHHHHH--EEEEEESS-GC CS
                        ABC_ATPase 324 SGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskekepitplvdrvrelykklgvstilvvggsgd 400
                                       SG   q ++i++al  g+k++++DE  sA    +r e               l   +r+++k+lg++++ v+   ++
  gi|474933831|ref|YP_007687413.1| 135 SGGEQQKVAIARALASGSKIIMLDEPLSALDTRVRTE---------------LRYEIRRIVKELGITVLHVTHDQEE 196
                                       8999999999999999999999999999965544333...............3445566666666666666666666 PP

                                       CTTT-SEEEEEET CS
                        ABC_ATPase 401 yldvAdtvilmee 413
                                        ++v+d+++lm++
  gi|474933831|ref|YP_007687413.1| 197 AMSVSDRIVLMRA 209
                                       6666666666665 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00024      0.22      22      63 ..      29      70 ..      12      84 .. 0.79
   2 ?   -2.3   0.0       2.5   2.4e+03       5      31 ..     134     160 ..     132     163 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00024
                      Mg_chelatase 22 gHnlllvGppGsGKtmlakrlpsllpplseeealevakiasv 63
                                      g  + ++Gp+G+GKt l++ ++++ +p + +  ++ + ++ v
  gi|474933831|ref|YP_007687413.1| 29 GEYITILGPSGCGKTSLIRLISGIWTPTEGKVLIDGKDVTHV 70
                                      5668899******************99999888887777666 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.5
                      Mg_chelatase   5 vkGqeeakraleiaaaGgHnlllvGpp 31 
                                       + G e++k a+  a a g +++++  p
  gi|474933831|ref|YP_007687413.1| 134 LSGGEQQKVAIARALASGSKIIMLDEP 160
                                       678889999999998888888887655 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0     0.007       6.6      10      33 ..      29      52 ..      21      63 .. 0.81
   2 ?    3.8   0.0     0.068        65      35      78 ..     180     245 ..     166     322 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.007
                            AAA_19 10 ekvllvtaGpGtGKTrvlkhival 33
                                       + + ++++ G+GKT +++ i  +
  gi|474933831|ref|YP_007687413.1| 29 GEYITILGPSGCGKTSLIRLISGI 52
                                      57789*************987655 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.068
                            AAA_19  35 velggvkpeeillvaftgrAakelrerlaalgaeatTiHrlal...........................l 78 
                                       v++ g    ++l v+  +  a+ +++r+  ++++a TiH  +                             
  gi|474933831|ref|YP_007687413.1| 180 VKELG---ITVLHVTHDQEEAMSVSDRI--VLMRAGTIHDSGApidmyrsptsifaayfigetnllegfvT 245
                                       44443...36888888888999999999..99*******98766666666665555555555555544442 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00021       0.2      16      39 ..      25      48 ..      18      51 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00021
                          ATPase_2 16 erepneiyfiYGpegsGKtaLlke 39
                                      e ++ e + i Gp g+GKt+L++ 
  gi|474933831|ref|YP_007687413.1| 25 EVQEGEYITILGPSGCGKTSLIRL 48
                                      556678899*************85 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00036      0.34       2      24 ..      31      53 ..      30      60 .. 0.85
   2 ?   -2.4   0.0       4.2   3.9e+03     123     142 ..     276     295 ..     272     301 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00036
                                      CEEEEC-TTTCHHHHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalaw 24
                                      ++ + G++G+GKT L++ +   w
  gi|474933831|ref|YP_007687413.1| 31 YITILGPSGCGKTSLIRLISGIW 53
                                      6889************9887766 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.2
                                       EEEEEECCCHHHHCTTSSCE CS
                             NACHT 123 llltvrpralrdleeqleea 142
                                       ++++vrp+++  + e+++  
  gi|474933831|ref|YP_007687413.1| 276 VVISVRPENVYTATEGISAR 295
                                       799******98888877665 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.9   1.8e+03      37      59 ..      15      38 ..       8      40 .. 0.78
   2 ?   -1.5   0.1       2.4   2.3e+03      24      44 ..     181     203 ..     171     210 .. 0.71
   3 ?    8.8   0.0    0.0015       1.4      34      65 ..     258     288 ..     234     292 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.9
                                      EEES--T.T-B--TT-EEEEEEEH CS
                            TrkA_C 37 eliipsg.dtvLeeGDvllvvgsp 59
                                      +++  ++ +++ +eG  ++++g++
  gi|474933831|ref|YP_007687413.1| 15 DFYAIRDiSLEVQEGEYITILGPS 38
                                      555566668999********9987 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.4
                                       HH.S-EEEEEE-T.-EEES--TT CS
                            TrkA_C  24 ar.gvlvvairRg.geliipsgd 44 
                                       ++ g++v+ + ++ +e ++ s+ 
  gi|474933831|ref|YP_007687413.1| 181 KElGITVLHVTHDqEEAMSVSDR 203
                                       44699999999987776666655 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0015
                                       -T-EEES--TT-B--TT-EEEEEEEHHHHHHH CS
                            TrkA_C  34 RggeliipsgdtvLeeGDvllvvgspsdlael 65 
                                       Rg   ++ ++ t++eeGD +++ + p+++ ++
  gi|474933831|ref|YP_007687413.1| 258 RG-GKVVRGEKTEFEEGDAVVISVRPENVYTA 288
                                       55.67788889****************98765 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00029      0.27      16      42 ..      23      49 ..      10      60 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00029
                            AAA_29 16 tieidlkgatlltGpsGsGKSTllDAi 42
                                      ++e+++ + + + GpsG GK++l+  i
  gi|474933831|ref|YP_007687413.1| 23 SLEVQEGEYITILGPSGCGKTSLIRLI 49
                                      44555444999************9555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00076      0.72       7      24 ..      31      48 ..      25      51 .. 0.86
   2 ?   -0.8   0.0       1.9   1.8e+03      52      99 ..     112     159 ..      90     191 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00076
                            AAA_22  7 ilvvtGesGtGKTtllrr 24
                                       +++ G+sG+GKT l+r 
  gi|474933831|ref|YP_007687413.1| 31 YITILGPSGCGKTSLIRL 48
                                      5899***********986 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.9
                            AAA_22  52 sskdllrellralglelka..erlsseellealeqalraravielliiDE 99 
                                       + + l+ el++ lg+ +    e    e+   a+++al + ++  ++++DE
  gi|474933831|ref|YP_007687413.1| 112 KKARLYLELVNMLGRAGMFpdELSGGEQQKVAIARALASGSK--IIMLDE 159
                                       556667777777776666643333333333455555555555..888887 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00031      0.29      22      40 ..      32      50 ..      12      66 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00031
                            AAA_23 22 tlItGpNGaGKTTildAik 40
                                        I Gp G+GKT++++ i 
  gi|474933831|ref|YP_007687413.1| 32 ITILGPSGCGKTSLIRLIS 50
                                      569************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 2386.94
//
Query:       gi|474933832|ref|YP_007687414.1|  [L=220]
Description: Phosphate transport regulator [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.5e-17   61.0   5.5    1.1e-16   60.8   5.5    1.0  1  PhoU_div  Protein of unknown function DUF47
  ------ inclusion threshold ------
      0.019   15.1   0.1      0.033   14.4   0.1    1.3  1  RasGAP_C  RasGAP C-terminus


Domain annotation for each model (and alignments):
>> PhoU_div  Protein of unknown function DUF47
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.8   5.5   1.2e-20   1.1e-16       5     213 ..       8     214 ..       3     215 .. 0.89

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 1.2e-20
                          PhoU_div   5 fgsspekslqdhlekvsetvlkliellkallegdyekveellkeiselEreADeikreirlklekglflPvdRedll 81 
                                       +++ +  + + h   v  tv +l+ +l ++ +g+ e + + +++ +  EreAD i       + +g ++  +R dll
  gi|474933832|ref|YP_007687414.1|   8 KEETVSTRARSHGVAVLDTVSELELVLASMAKGEKETALKGVDRLMLSEREADRIEDRLAADISRGDLTVGERGDLL 84 
                                       5555666667777778888889999999999***999**************************************** PP

                          PhoU_div  82 elveslDeildvlediamlvtlr...kvefpeelkdeflallkktveaiealaevieeleklletalskkdiveeie 155
                                       +++ ++D+i++ ++++a  v+l+   +  +p+e+++e+ a ++ ++e ++ l  +ie  + ++   l+    +  i+
  gi|474933832|ref|YP_007687414.1|  85 HFIRQIDSIANWAKEAALHVQLIletDAVVPKEIWEEMAATVNELIEEVKFLVSAIETYNSDIKRTLR---TIDSIN 158
                                       *****************9998863335669**********************9999999999999999...799999 PP

                          PhoU_div 156 slEdeiDqlqrklikklfsredasnplevlllveiieklenvsdraedvadrisiill 213
                                       + E  iD+ +   ik+     + +  +++ll+ e i+ +e  +d+ +  +d+i+i++ 
  gi|474933832|ref|YP_007687414.1| 159 DQERIIDSKYYSSIKHAHM--SDMDAKAILLVTEVINAIEMAADNGKASGDTINILIT 214
                                       9999999998888888776..336899****************************985 PP

>> RasGAP_C  RasGAP C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   3.6e-06     0.033      53     105 ..     120     174 ..     114     186 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.6e-06
                          RasGAP_C  53 esleetlktLseknnylesqlesYkayienvleqlkkkkgk..lpfskqyfkkre 105
                                       e + +t+++L e  ++l s +e+Y++ i+++l ++ + + +  +  sk y++ ++
  gi|474933832|ref|YP_007687414.1| 120 EEMAATVNELIEEVKFLVSAIETYNSDIKRTLRTIDSINDQerIIDSKYYSSIKH 174
                                       56899******************************88763345555554443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1388.17
//
Query:       gi|474933833|ref|YP_007687415.1|  [L=450]
Description: Phosphomannomutase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-40  138.1   0.2    2.9e-40  137.1   0.2    1.5  1  PGM_PMM_I    Phosphoglucomutase/phosphomannomutase, alpha/bet
    2.2e-28   98.9   0.0    5.7e-28   97.6   0.0    1.7  1  PGM_PMM_II   Phosphoglucomutase/phosphomannomutase, alpha/bet
    2.7e-22   79.1   0.0    5.6e-22   78.1   0.0    1.5  1  PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/bet
    5.1e-13   49.0   0.0    1.2e-12   47.9   0.0    1.6  1  PGM_PMM_IV   Phosphoglucomutase/phosphomannomutase, C-termina


Domain annotation for each model (and alignments):
>> PGM_PMM_I  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.1   0.2   6.6e-44   2.9e-40       2     134 ..       3     130 ..       2     133 .. 0.96

  Alignments for each domain:
  == domain 1  score: 137.1 bits;  conditional E-value: 6.6e-44
                                       GGBBTTCEEEECCHCTBSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB- CS
                         PGM_PMM_I   2 qkfgtsGlRgkvgegeltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillgllp 78 
                                       + fgt+G+Rg+v+++ ++ +l++++g+ai+++++       ++++ DtR ss+++++a+++gl+a G++v+++g++p
  gi|474933833|ref|YP_007687415.1|   3 KMFGTNGVRGIVNKD-MNVQLALQMGKAIGSVFTG-----AIAIANDTRLSSDMISSAVCSGLMAVGCDVYDIGMVP 73 
                                       67***********55.9****************97.....7************************************ PP

                                       HHHHHHHHHHCC.ECEEEEE--TTS-TTCCCEEEEETTTCE--CHHHHHHHHHHCCT CS
                         PGM_PMM_I  79 tPavsfairklk.adagimitaSHnppeyngiKvylsnGgpispeveekIeaiieke 134
                                       tPa+++++++++ + ag+mitaSHnppe ngiKv+  +G ++s+e+e ++e+++++e
  gi|474933833|ref|YP_007687415.1|  74 TPALQYYVKTHDdVVAGVMITASHNPPEFNGIKVIEGDGTEASKEKEGEVEEKYDEE 130
                                       **********877***************************************99876 PP

>> PGM_PMM_II  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.6   0.0   1.3e-31   5.7e-28       1     103 []     150     251 ..     150     251 .. 0.99

  Alignments for each domain:
  == domain 1  score: 97.6 bits;  conditional E-value: 1.3e-31
                                       .HHHHHGGGTS-HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TTSS----TT-TTTTHHHH CS
                        PGM_PMM_II   1 eaYiealkekvdseaikksglkvvidplhGaggeilkellkelgvdvvelnaepdpdfptkapnpeekealklliel 77 
                                       eaY++a+++k+d+  i+k+++kvv+d+++Ga+  +++ llk+lgv+ ++ln +p ++fp++ ++p+e e+l +l +l
  gi|474933833|ref|YP_007687415.1| 150 EAYVDAIVSKLDIPMIRKAKFKVVVDCANGAACFTTPLLLKKLGVRCITLNGTPQGEFPGHPSEPTE-ENLGDLKKL 225
                                       58**********99*****************************************************.********* PP

                                       GGGGG-SEEEEE-TTS-BEEEEETTE CS
                        PGM_PMM_II  78 vkkegadlglafDgDaDRlgvvderG 103
                                       vk+++a+lg+a+DgDaDR+++vd++G
  gi|474933833|ref|YP_007687415.1| 226 VKDTKANLGIAHDGDADRCVFVDNKG 251
                                       ***********************998 PP

>> PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.1   0.0   1.3e-25   5.6e-22       1     106 [.     255     358 ..     255     363 .. 0.92

  Alignments for each domain:
  == domain 1  score: 78.1 bits;  conditional E-value: 1.3e-25
                                       HHHHHHHHHHHHHHCHCSTTTCEEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHTTECEEEETTCEEEET CS
                       PGM_PMM_III   1 dgdqllallakylleeklkpgagvvktvmtslalervakklgiklvetkvGdkyvleemkeegavlGgEeSghiifl 77 
                                       +gd +lalla+ +  + ++ g+ +v++v ts+++++ +k++g+++v+t+vG   v ++m e g  +GgEe+g++if+
  gi|474933833|ref|YP_007687415.1| 255 PGDITLALLARSIVMA-NR-GGYIVTPVATSSLIDELVKSAGGEVVRTAVGAPIVSRKMMEIGGKFGGEENGGLIFP 329
                                       69**********9664.44.446****************************************************** PP

                                       TTBSS--HHHHHHHHHHHHHHHTS-HHHH CS
                       PGM_PMM_III  78 deattkDGilaallvleilaetgkslsel 106
                                       d++ ++DG++a+ ++le + ++g  l+++
  gi|474933833|ref|YP_007687415.1| 330 DHQHCRDGAMAIGRMLENICRNGALLKQI 358
                                       *******************9999777766 PP

>> PGM_PMM_IV  Phosphoglucomutase/phosphomannomutase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   0.0   2.6e-16   1.2e-12      16      68 ..     389     438 ..     370     444 .. 0.86

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 2.6e-16
                                       CCCCCTTHHCCCCCCCCGCCEEEE.EEEETTCCEEEEEEEESSHHHHHHHHHH CS
                        PGM_PMM_IV  16 laallkvasikeglkilledGrrlavRpSGTepllrvyvEaksdeelarlaee 68 
                                        +++ k+    +glki + dG++l  RpSGTep  rvy+E+k+++++ +la++
  gi|474933833|ref|YP_007687415.1| 389 TEGVSKN--KTDGLKIMFDDGWVL-ARPSGTEPIFRVYAESKDRDRAVELADQ 438
                                       4566666..99*************.**********************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2739.20
//
Query:       gi|474933834|ref|YP_007687416.1|  [L=219]
Description: hypothetical protein TALC_00242 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.034   14.2  20.1      0.046   13.8  20.1    1.2  1  HC2              Histone H1-like nucleoprotein HC2
       0.33   10.7   5.0        0.4   10.5   5.0    1.1  1  RR_TM4-6         Ryanodine Receptor TM 4-6


Domain annotation for each model (and alignments):
>> HC2  Histone H1-like nucleoprotein HC2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8  20.1   5.1e-06     0.046       7      65 ..     137     197 ..     122     219 .] 0.38

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.1e-06
                               HC2   7 KrsskKtAakkaavrKpa...AkKaaakktvvrKvaaKKtaarKtvakktvakkkvaakkaa 65 
                                       K   kK     + v Kpa     + ++kk+++ K a KK+aa+K +akk+  kk++  k ++
  gi|474933834|ref|YP_007687416.1| 137 KDPEKKGIEEEVRVSKPAeekP-RKTVKKVPAEKSAEKKPAAKKPAAKKAAPKKTPESKPVS 197
                                       3333444444444444443221.122333333333333333333333333333333333322 PP

>> RR_TM4-6  Ryanodine Receptor TM 4-6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   5.0   4.5e-05       0.4      30     139 ..      75     190 ..      52     215 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 4.5e-05
                                       XXXX...XXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXX...XXXXXXXX.....XXXXXXX CS
                          RR_TM4-6  30 dlaeaageeeeedllsdvfgldlkkeggqykvvakkseagLgDlseteaeespt...pelkkkla.....eeeeaee 98 
                                       ++ ++  +e+e     d + +++   +  +k+ + ++e+ L Dl+   a +++       k+k       e ee   
  gi|474933834|ref|YP_007687416.1|  75 EFLTMSPREAERRYADDYLECKMTGSSMVAKLYQMDQEERLADLGIIVAPKKKGllgRLRKQKDPekkgiE-EEVRV 150
                                       444456678888888999999999999999****************9999987555322222222211111.11111 PP

                                       XXXXXXXXXXXX.XXX.XXXXXXXXXXXXX..........XX CS
                          RR_TM4-6  99 ekeeeeepeaeaeeka.daengekeekekekeeeekeseeee 139
                                       +k +ee+p+++  +k   +++ ek+ ++k+  +++k++++++
  gi|474933834|ref|YP_007687416.1| 151 SKPAEEKPRKTV-KKVpAEKSAEKKPAAKK-PAAKKAAPKKT 190
                                       111111111111.11101111111111111.11111111111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       840  (0.0468515); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1592.10
//
Query:       gi|474933835|ref|YP_007687417.1|  [L=287]
Description: agmatinase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-67  227.0   0.0    3.5e-67  226.9   0.0    1.0  1  Arginase  Arginase family


Domain annotation for each model (and alignments):
>> Arginase  Arginase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  226.9   0.0   1.9e-71   3.5e-67       1     277 [.      17     277 ..      17     280 .. 0.93

  Alignments for each domain:
  == domain 1  score: 226.9 bits;  conditional E-value: 1.9e-71
                                       EEEEEEEEE--TTTSSSGGGGGHHHHHHHHHHTSBTHCHEETTTTESCCSE.EEEEEEEE--SSCHHHHHHHHHHHH CS
                          Arginase   1 advallGvPfdaagsgrpGarfGPraireasarleealeynlelgvleelk.ivdlgdvavtpvdneevleqieeav 76 
                                       ad++++G+P+d + s+++Gar++P+a+r+as ++ee   +++e+g  +el+ ++d+g+++  +  +e+++e++  av
  gi|474933835|ref|YP_007687417.1|  17 ADAVIFGIPYDHTASYKAGAREAPTAVRRASYNFEE---FHFEHGLDQELPvVCDYGNCDDFI-LPEDMVEEVRFAV 89 
                                       589********************************8...899999955555278*****9976.9999********* PP

                                       HHHHHTTCEEEEEESSGGGHHHHHHHHHHHHSTTEEEEEESSS----SSCTTTBSSSTTSHHHHHHHHTSECGCEEE CS
                          Arginase  77 aeilkagklpivlGGDHsialgilralaekygkplgvihfDAHaDlrtpetegsgnshGtpfrraaeegllkpkklv 153
                                          +++gk+pi++GG+Hs +++i++++  k    +++i +DAH+D r+++  g+ +sh+++ rraa  +++  ++++
  gi|474933835|ref|YP_007687417.1|  90 GPCIRDGKFPIAIGGEHSGTIPIIQSFEPK---SIALITIDAHLDSRDEY-MGTPLSHACVTRRAA--DVHGIENVC 160
                                       ****************************65...7****************.9**************..566668*** PP

                                       EEEE-STCSHHHHHHHHTTSEEEEHHHHHHHHHHHHHHHHHHHHTCTTSEEEEEEEGGGBBTTTSTSSSS-BSS-B- CS
                          Arginase 154 qiGirsvdneeyelakelgirvitmreidelglkavveeilervgaeedpvylSfDiDvlDpavaPGtGtpepgGlt 230
                                        +G rs+ +ee e ++   + ++t++e+ e+g+++ ++++l+ ++   d vylS+DiD++Dpa+aPGtGtpep Gl 
  gi|474933835|ref|YP_007687417.1| 161 SVGNRSIGREELERDD--VVPHVTAYEVFENGIEWAMKKMLDGLK--ADRVYLSIDIDGIDPAYAPGTGTPEPFGLH 233
                                       **********998887..699***********************7..68**************************** PP

                                       HHHHHHHHHHHHCHSEEEEEEEE-B-GGGSSTTTHHHHHHHHHHHHH CS
                          Arginase 231 lrellallrelaeklnlvgaDvvEvnPaldteaeqtarlaarlvrel 277
                                       +++++++++ + +  +l+g+Dv+E+ P+ d+++ +t++l+arl+ e+
  gi|474933835|ref|YP_007687417.1| 234 PYDVKKAINIVGD--RLAGFDVMEICPPSDPSG-ITSILGARLINEA 277
                                       ***********77..89**************66.**********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       205  (0.011434); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1696.67
//
Query:       gi|474933836|ref|YP_007687418.1|  [L=129]
Description: translation initiation factor 5A (eIF-5A) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-05   25.2   0.1    0.00018   21.5   0.0    2.1  2  EFP_N     Elongation factor P (EF-P) KOW-like domain


Domain annotation for each model (and alignments):
>> EFP_N  Elongation factor P (EF-P) KOW-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0     1e-08   0.00018       4      47 ..      11      55 ..       8      60 .. 0.89
   2 ?    1.6   0.1     0.016   2.9e+02       6      15 ..      74      83 ..      70      94 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1e-08
                                      G--TT-EEEETTEEEEEEEEEEEEETT.S--EEEEEEEETTTS-E CS
                             EFP_N  4 elkkGlvieidgklyvVlefehvkpGk.GqafvrvklknlrtGak 47
                                      elk G  ++id+ +++++++  +kpGk G+a   ++  ++ tGak
  gi|474933836|ref|YP_007687418.1| 11 ELKIGRYVNIDDSPCKIISITTSKPGKhGSAKASIEATDIFTGAK 55
                                      89************************6378889999999999987 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.016
                                      -TT-EEEETT CS
                             EFP_N  6 kkGlvieidg 15
                                      +kG+vi id 
  gi|474933836|ref|YP_007687418.1| 74 RKGQVISIDE 83
                                      9*****9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 866.03
//
Query:       gi|474933837|ref|YP_007687419.1|  [L=363]
Description: Protein implicated in ribosomal biogenesis, Nop56p -like protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-49  167.2   0.0      6e-49  166.6   0.0    1.3  1  Nop       snoRNA binding domain, fibrillarin


Domain annotation for each model (and alignments):
>> Nop  snoRNA binding domain, fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.6   0.0   3.4e-53     6e-49       3     229 ..     125     333 ..     123     334 .. 0.93

  Alignments for each domain:
  == domain 1  score: 166.6 bits;  conditional E-value: 3.4e-53
                                       HHHHHHHHHHHHHHHHHHTTTSTCHHHHS-SHHHHHHHHHHCCCCHCCT.HHTT.HHHHHHHHHHHHCHHHH-SSS- CS
                               Nop   3 deidkeintlhkrvrewYswhFpELeslvkdnleYakvvkligneredlekkeedeelakevimaakvtastsmgae 79 
                                       d++ +  n l++r+ ewY+++FpEL+++ kd  +Ya ++++ g +re++        l+    + +++   +smga+
  gi|474933837|ref|YP_007687419.1| 125 DDLIEVSNLLSERLHEWYGMYFPELADHAKD-KKYAYLIAAKG-DRESI--------LE---ELGLEI---ESMGAD 185
                                       667777899*******************766.69*********.88998........22...245666...589*** PP

                                       S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHCHHHHHHHHHHHHSSHHHHHCS-HHHHTTTT-H CS
                               Nop  80 lseedlknikelcdrvleleelrkelleYlesrmsaiAPNlsaLvGeevaarLishaGgLtnLakmPastiqilGae 156
                                       +++ dl+ ++ l++++ +++e+ ++ +eY++s ++ ++PN++a++G  + arLis aGgL +La++P+st+q+lGae
  gi|474933837|ref|YP_007687419.1| 186 FESADLEAVRGLAENLYNVYEAWETAEEYITSLVQDMCPNMCAILGGPLSARLISLAGGLDRLASLPSSTVQLLGAE 262
                                       ***************************************************************************** PP

                                       HHHCCCHH.T---SSSCHHHCSHHHHHTS-CCCHHHHHHHHHHHHHHHHHHHHTT----SHHHHHHHHHHHHHH CS
                               Nop 157 kalfralk.kkntpkyGliyhselvqkatppklkkkiaRllaaKvalaaRiDafsekdgslGkklreeiekklk 229
                                       ka+fr+l+ +kn pk+G+iy+ + ++ka p ++++ iaR+la Kv +aa+iDa+  + + +G+kl e++ k++ 
  gi|474933837|ref|YP_007687419.1| 263 KAMFRHLRsGKNPPKHGVIYQYPDLRKA-PYWQRGNIARALAGKVLIAAKIDAY--HGEFMGDKLSEDLRKRIA 333
                                       ********888***************77.***********************99..67899********99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.59
# Mc/sec: 1866.34
//
Query:       gi|474933838|ref|YP_007687420.1|  [L=204]
Description: Ribulose-5-phosphate 4-epimerase-related epimerase and aldolase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-49  168.1   0.0    2.3e-49  167.9   0.0    1.0  1  Aldolase_II  Class II Aldolase and Adducin N-terminal domain


Domain annotation for each model (and alignments):
>> Aldolase_II  Class II Aldolase and Adducin N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.9   0.0   1.3e-53   2.3e-49       2     186 .]      10     183 ..       9     183 .. 0.92

  Alignments for each domain:
  == domain 1  score: 167.9 bits;  conditional E-value: 1.3e-53
                                       HHHHHHHHHHHTTSSCTTBCEEEEEETSTTEEEEEBTSS-GGGHTGGGEEEEETTSCEEEECECSSSTB-TTHHHHH CS
                       Aldolase_II   2 elaeasrllarrglvegtgGniSvrvpeedsflitpsgvdfeeltaedlvvvdldsgevvegkekggkpssetplHl 78 
                                       +l+e+++ll++r+l+   gGn+Svr++ ++++litpsg +++ lt +dlv++d++ g+v++    ggkps+e ++Hl
  gi|474933838|ref|YP_007687420.1|  10 RLVECCKLLYQRNLTVSAGGNMSVRLD-DKHILITPSGANKGMLTDDDLVLMDMK-GKVIS----GGKPSIEHRFHL 80 
                                       79************************9.9*************************9.****3....589********* PP

                                       HHHHH-TT-SEEEEE--HHHHHHHTCCSTSCHCC.SSHHHHC.HSSSEEEEES-SSTTCHHHHHHHHHHHHHS-SEE CS
                       Aldolase_II  79 aiykarpdaravvHtHspaavalsalagkeglpp.ltqeaaklllgdevpvipyaapgteelgealaealkedakav 154
                                        +y+a+p+++a+vH+H+ +++a++ +  +e+l++ lt+e+  ll  d+vp ++y++pg+eel +a+ e    da+a+
  gi|474933838|ref|YP_007687420.1|  81 GLYQANPEVNAIVHCHPLYCLAVA-TK-GEPLKStLTPEGVLLL--DQVPTVRYETPGSEELVKAVLECS--DAPAM 151
                                       ************************.65.6999986777777755..99**************66666655..789** PP

                                       EETTTEEEEEESSHHHHHHHHHHHHHHHHHHH CS
                       Aldolase_II 155 llrnHGlltvGetleeAvalaetleeaaeiql 186
                                       l+++HG++t G+tleeA++++e+le+ a++q+
  gi|474933838|ref|YP_007687420.1| 152 LMAKHGAITQGRTLEEAFNRMEELEFQAHLQI 183
                                       ****************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1302.97
//
Query:       gi|474933839|ref|YP_007687421.1|  [L=333]
Description: translation initiation factor 2B subunit I family (IF-2BI) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-68  229.2   0.1      7e-68  228.9   0.1    1.1  1  IF-2B     Initiation factor 2 subunit family


Domain annotation for each model (and alignments):
>> IF-2B  Initiation factor 2 subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  228.9   0.1   3.9e-72     7e-68       4     282 .]      57     325 ..      45     325 .. 0.94

  Alignments for each domain:
  == domain 1  score: 228.9 bits;  conditional E-value: 3.9e-72
                                       SHHHHHHHHHHHHHHHHHHCCCSTHHHHHHHHHHHHHHHHTSSTS-HHHHHHHHHHHHHHHCCTTTSSHHHHHHHHH CS
                             IF-2B   4 GspaiaiaalevllevikdaktskvaeLkeelrkaidlLkkarPtavslgnairrllkeiselksssdvkeakksli 80 
                                       G+p+i+ +a++++  ++ +         k ++ +a++  k+arPta++l+ a +++ k            +a ++ +
  gi|474933839|ref|YP_007687421.1|  57 GAPSIGASAAYAMCLAAIQ---------KADIDEAAKHVKAARPTAFDLFYATDWMVK----------KLKAGADPV 114
                                       5555555555554443333.........45899*************************..........45688999* PP

                                       HHHHHHHHHHHHHHHHHHHHHHTTC-TTEEEEEES--SH........HHHHHHHHHHTTEEEEEEEEEXTTTTHH.H CS
                             IF-2B  81 ekikelikeieeadekigdiaaelikdgdtilTicnskt........vlevlraaakekkkfkVivvEsrPrlqG.r 148
                                       e+++e+++  + +++ ig+++  likdg+ ++T+cn+++        +l+ +r+a++++kkf V++ E+rPrlqG +
  gi|474933839|ref|YP_007687421.1| 115 EAADEYANITVDKCRRIGEFGGALIKDGMKLMTHCNAGAlatvdvgtALAPMRNAHDAGKKFFVYASETRPRLQGmQ 191
                                       ***************************************************************************** PP

                                       THHHHHHHTTXEEEEEEGGGHHHHHHCTESEEEEEXSEEETTSEEEEETTHHHHHHHHHHTTXEEEEEXXGGGBEST CS
                             IF-2B 149 ltakeLvqagipvtlitdsavayvmseevdkvivGAdrilenGaiankiGTsslAvlAkefnipvlvvaeslkfser 225
                                       lta+eL+q+gi+  +i+d ++ay ms+ vd++ivGAdri++nG+ ankiGT+  A++Ak+f ip++v+a+ ++f+  
  gi|474933839|ref|YP_007687421.1| 192 LTAWELNQEGIDHAIIPDGSAAYYMSQGVDMIIVGADRIAANGDFANKIGTYDKAIVAKKFGIPFYVAAPVSTFDFS 268
                                       ***************************************************************************** PP

                                       SSSGGGSSXXBEXTHHHHEETTEESSTTTEEEEEBSEEEEEGGGXSEEEETTEEEXC CS
                             IF-2B 226 vqldedifieerdpeellnitgeriaeeelkvvnpafDvtPpelItliITevGvlpp 282
                                       +++++di+ie r + e++ ++g ria+   k +npafDvt  +l+t++ITe+G+++p
  gi|474933839|ref|YP_007687421.1| 269 TKTGKDIVIEQRSETEMTEVQGIRIAPVGSKALNPAFDVTTSDLVTGFITEKGIFKP 325
                                       *******************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.56
# Mc/sec: 1791.32
//
Query:       gi|474933840|ref|YP_007687422.1|  [L=207]
Description: riboflavin-specific deaminase C-terminal domain protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-43  149.0   0.1    1.7e-43  148.8   0.1    1.0  1  RibD_C       RibD C-terminal domain
  ------ inclusion threshold ------
      0.018   15.4   0.2      0.042   14.2   0.1    1.5  2  Radical_SAM  Radical SAM superfamily
      0.036   14.3   0.0      0.057   13.7   0.0    1.2  1  RIG-I_C-RD   C-terminal domain of RIG-I


Domain annotation for each model (and alignments):
>> RibD_C  RibD C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.8   0.1   2.8e-47   1.7e-43       9     199 ..       1     194 [.       1     195 [. 0.98

  Alignments for each domain:
  == domain 1  score: 148.8 bits;  conditional E-value: 2.8e-47
                                       EETTSBSSCTTSSGCTSS-HHHHHHHHHHHHTSSEEEEEHHHHHHHT--SS--SSCHSCHHHTT.GSS-EEEEEETT CS
                            RibD_C   9 vSlDGklaaaggeskwitgeearadvhelraeadailvGrgtvladnpsltvrwvkkreaeadaearqpvrvVvdst 85 
                                       +S+DGkla +++++ +i+++e+ a+v +lr+   +ilvG+gtv+ d+p+ltv+ + k+        ++pvr+V+d+ 
  gi|474933840|ref|YP_007687422.1|   1 MSADGKLAGPERKQVRISSDEDIARVKDLRKRYRGILVGVGTVISDDPHLTVKGPMKE--------ENPVRIVLDTN 69 
                                       8********************************************************8........99********* PP

                                       S-S-TTSHHHHSSS-EEEEESSCSCHHHHHHCCE......SE-HHHHHHHHHHT.T--EEEEEETHHHHHHHHHTTT CS
                            RibD_C  86 lrvpldakvltddaptlvatteeadkekveklkv......rvdlkelleeLker.girsllveGGatLagsllragl 155
                                        r+p+da+vl+d a+t+++t++e+ k++ ++ +v      ++dl +++e  +e+ gi+s++veGG+ +++s++r++l
  gi|474933840|ref|YP_007687422.1|  70 GRTPDDARVLDDLAETVIVTCRECTKDWGTRATVvragdgKIDLRRAMELIREElGIESVMVEGGGEVIASFFREKL 146
                                       ********99977********************669999************************************** PP

                                       -SEEEEEEESCE--T.TSBCSSSSST-SS...EEEEEEEEEEETTEEE CS
                            RibD_C 156 vDelrlyiaPkllGg.agktlfdgegfka...lklklvksealgegvv 199
                                       v ++ +++ P ++Gg  ++t  dg g  a   ++lk  ++e+lg+g +
  gi|474933840|ref|YP_007687422.1| 147 VGKYTVFVGPQIIGGrTAPTPADGDGRVApegIRLKMESCEQLGNGAL 194
                                       ***************************99****************986 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1     7e-06     0.042      23     100 ..      11      85 ..       7      91 .. 0.72
   2 ?   -1.7   0.0      0.54   3.2e+03      43      46 ..     122     125 ..      89     188 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7e-06
                                       HHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS.TTHHHHHHHHHHTCCCTEEEEEEECSSCHG.HHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                       Radical_SAM  23 egrgrslsveeileevkelkaekgvkevilgggeplly.pdfvellerlaklavpgiritvetngtlpd.eeklerl 97 
                                       e+++  +s +e ++ vk l+ ++  +++++g g+++ + p+++++  +  ++    +ri++ tng +pd  ++l+ l
  gi|474933840|ref|YP_007687422.1|  11 ERKQVRISSDEDIARVKDLR-KR-YRGILVGVGTVISDdPHLTVKGPMKEEN---PVRIVLDTNGRTPDdARVLDDL 82 
                                       55666778888889999996.44.6666666666555416666666666665...************9998888888 PP

                                       HHT CS
                                       xxx RF
                       Radical_SAM  98 lel 100
                                       +e 
  gi|474933840|ref|YP_007687422.1|  83 AET 85 
                                       875 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.54
                                       HHTT CS
                                       xxxx RF
                       Radical_SAM  43 aekg 46 
                                       +e g
  gi|474933840|ref|YP_007687422.1| 122 EELG 125
                                       2222 PP

>> RIG-I_C-RD  C-terminal domain of RIG-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   9.5e-06     0.057      43      72 ..      72     102 ..      57     106 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.5e-06
                        RIG-I_C-RD  43 kkkekkf.edfekkgkikCkkCkkdwGimmk 72 
                                       ++ + ++ +d+ ++  + C++C kdwG+ ++
  gi|474933840|ref|YP_007687422.1|  72 TPDDARVlDDLAETVIVTCRECTKDWGTRAT 102
                                       444455559******************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1364.44
//
Query:       gi|474933841|ref|YP_007687423.1|  [L=345]
Description: RNA 3'-phosphate cyclase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      3e-67  226.1   0.1    3.4e-67  225.9   0.1    1.0  1  RTC         RNA 3'-terminal phosphate cyclase
    1.5e-17   64.0   0.0    2.6e-17   63.2   0.0    1.4  1  RTC_insert  RNA 3'-terminal phosphate cyclase (RTC), insert d


Domain annotation for each model (and alignments):
>> RTC  RNA 3'-terminal phosphate cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.9   0.1   3.8e-71   3.4e-67       2     222 .]      10     327 ..       9     327 .. 0.99

  Alignments for each domain:
  == domain 1  score: 225.9 bits;  conditional E-value: 3.8e-71
                                       TTTSTHHHHHHHHHHHHH---EEEESTTTTSSS-S--HHHHHHHHHHHHHHT-EEE--STT-SEEEEE------SEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               RTC   2 gegGgqiLRtalaLsaltgkpvrIenIRanRkkPGLraqhltavrllakitnaevegaeigsteleFkPgeikagey 78 
                                       gegGgq++Rt++aL++lt++  r+++IR+nR++ GL++qh tav ++ak+t+ +++g++igs+el  +Pg+ +  ++
  gi|474933841|ref|YP_007687423.1|  10 GEGGGQMVRTSVALATLTHTVTRLTRIRENRPTNGLSKQHTTAVAAIAKMTGSKITGNQIGSSELLVEPGNDRVPDI 86 
                                       89********************************************************************77778** PP

                                       EEEEESSEBHHHHHHHHHHHHTTSSS-EEEEEEEBSBBTTS--HHHHHHTHHHHHHHHT.-EEEEEEEE--BTTTB- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               RTC  79 evdigtAGsitlllqtllplllfakkpseltlkGgTnvsaapsvdylktvllpllkrfgvlelelelkkrGfypkGg 155
                                        +digtAGsi+l++q+ l+++   ++p++l+l+GgTnv +ap++d +++vl+pl+kr+g +++++e+ +rGfyp Gg
  gi|474933841|ref|YP_007687423.1|  87 ALDIGTAGSISLVVQATLLAARDYETPFNLDLRGGTNVMWAPPIDSYNMVLFPLMKRMG-IDAHAEIIERGFYPIGG 162
                                       ***********************************************************.7**************** PP

                                       EEEEEEEE-.-S---EB............................................................ CS
                                       xxxxxxxxxxxxxxxxx............................................................ RF
                               RTC 156 Gevelevepskklkpie............................................................ 172
                                       G+v+++ ep  ++kp++                                                            
  gi|474933841|ref|YP_007687423.1| 163 GHVKVTQEPIGTIKPLDldhlgelkgirglcfvqhlsdrigqdmmdacrrvfepeypieieyqkcegtsrgagmvlv 239
                                       *********988***************************************************************** PP

                                       ......................................BSS-HHHHHHHHHHHHHHT.-EEEEESS--HHHHHHHHH CS
                                       ......................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               RTC 173 ......................................acvDehlqdqlilfmaLakgksrirvaeltlhtetairv 211
                                                                             ++vD h++dql+++ma+a+gks++ v+++++h+ +++++
  gi|474933841|ref|YP_007687423.1| 240 aeyengllssnvlsskghsahqsgldaasdllqemrtgSTVDIHTADQLLPYMAMADGKSEFIVSRISKHLLSQMDT 316
                                       ***************************************************************************** PP

                                       HHHHSS-EEEE CS
                                       xxxxxxxxxxx RF
                               RTC 212 ieqflgvkfkv 222
                                       +e+fl+v+f v
  gi|474933841|ref|YP_007687423.1| 317 LESFLDVRFGV 327
                                       ********965 PP

>> RTC_insert  RNA 3'-terminal phosphate cyclase (RTC), insert domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.2   0.0   2.9e-21   2.6e-17       4     102 ..     184     274 ..     181     275 .. 0.90

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 2.9e-21
                                       ---SEEEEEEEEESS-THHHHHHHHHHHHHHTTTSSEEEEEEE.EE-CGGC-SS-EEEEEEEEE-T.TS-EEEEEEE CS
                        RTC_insert   4 GrvkrirGvafaarvspsvanrmveaargvLnkllpdvyiytdvvkegkesgkspGfgisLvaetttegvllgaeal 80 
                                       G++k irG +f+ ++s  +++ m++a+r+v++   + ++i+ +     k +g s+G+g++Lvae++  ++ll++ +l
  gi|474933841|ref|YP_007687423.1| 184 GELKGIRGLCFVQHLSDRIGQDMMDACRRVFEPE-YPIEIEYQ-----KCEGTSRGAGMVLVAEYE--NGLLSSNVL 252
                                       99*****************************887.55664444.....556888***********5..79******* PP

                                       E-TT--HHHHHHHHHHHHHHHH CS
                        RTC_insert  81 gekgvppedvGeeaaeeLleei 102
                                       ++kg ++++ G +aa+ Ll+e+
  gi|474933841|ref|YP_007687423.1| 253 SSKGHSAHQSGLDAASDLLQEM 274
                                       ********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 2128.02
//
Query:       gi|474933842|ref|YP_007687424.1|  [L=484]
Description: putative ATPase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   2.3e-194  646.7   0.0     3e-194  646.3   0.0    1.0  1  DUF853          Bacterial protein of unknown function (DUF853
    4.2e-09   36.8   0.0    4.4e-08   33.5   0.0    2.1  2  DUF87           Helicase HerA, central domain
    8.1e-06   25.0   0.0      0.021   13.7   0.0    2.3  2  AAA_10          AAA-like domain
    8.5e-06   24.9   0.0     0.0086   15.0   0.0    2.4  2  TrwB_AAD_bind   Type IV secretion-system coupling protein DNA
      4e-05   23.1   0.0     0.0013   18.2   0.0    2.4  2  FtsK_SpoIIIE    FtsK/SpoIIIE family
      6e-05   23.3   0.1     0.0058   16.9   0.0    2.5  2  AAA_22          AAA domain
    0.00017   22.0   0.1     0.0098   16.3   0.0    2.7  2  AAA_16          AAA ATPase domain
    0.00021   21.4   0.0       0.24   11.4   0.0    2.5  2  ResIII          Type III restriction enzyme, res subunit
    0.00027   20.7   0.4     0.0045   16.7   0.1    2.7  3  AAA_30          AAA domain
     0.0003   21.2   0.1       0.39   11.1   0.1    2.5  2  AAA             ATPase family associated with various cellula
     0.0079   15.9   0.0       0.03   14.0   0.0    1.9  2  Zot             Zonular occludens toxin (Zot)
  ------ inclusion threshold ------
      0.013   15.7   0.2      0.043   14.0   0.1    1.9  1  AAA_28          AAA domain
      0.025   15.1   0.0       0.14   12.7   0.0    2.2  2  AAA_18          AAA domain
      0.061   13.6   0.2       0.24   11.7   0.0    1.9  2  AAA_19          AAA domain
      0.062   13.4   0.0      0.091   12.8   0.0    1.5  1  CbiA            CobQ/CobB/MinD/ParA nucleotide binding domain
      0.076   12.6   0.1       0.19   11.3   0.0    1.8  2  AAA_25          AAA domain
        0.1   12.1   0.1       0.33   10.5   0.0    1.7  2  AAA_7           P-loop containing dynein motor region
       0.11   12.2   0.0       0.42   10.3   0.0    1.9  2  PRK             Phosphoribulokinase / Uridine kinase family
       0.13   12.2   0.0       0.37   10.8   0.0    1.7  1  DNA_photolyase  DNA photolyase
       0.18   12.3   2.0          4    7.9   0.0    3.2  3  CRISPR_Cse2     CRISPR-associated protein Cse2 (CRISPR_cse2)
        0.2   10.8   5.1        2.2    7.4   0.1    2.6  2  DUF2075         Uncharacterized conserved protein (DUF2075)


Domain annotation for each model (and alignments):
>> DUF853  Bacterial protein of unknown function (DUF853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  646.3   0.0  3.5e-197    3e-194       5     450 ..       9     455 ..       6     479 .. 0.93

  Alignments for each domain:
  == domain 1  score: 646.3 bits;  conditional E-value: 3.5e-197
                            DUF853   5 iakeaeqelalalklanrhGliaGatGtGktvtLqvlaeslseaGvpvfladvkGdLsgiakaGevkdklaarleei 81 
                                       ia++ +++++l +++anrhGli+Ga GtGktvtL+vlaes+s+aG+pvf ad+kGd+  i+++G+++ k+a+r++++
  gi|474933842|ref|YP_007687424.1|   9 IAQSGDKKVFLYPRMANRHGLITGASGTGKTVTLRVLAESFSSAGIPVFFADMKGDVGTIVQPGDPA-KMADRAKKF 84 
                                       5678899**********************************************************96.89******* PP

                            DUF853  82 glddyqlkalPvtlwdvfgekGhpvratiselGPllLarllelndvqegvLnivfriadeeGllLldlkdLrallke 158
                                       g+ +y ++++P ++wdv+g+ G+pvrat+s++G  lL+rl+ l++vq  vLn+vf ia ++ + ++d +dLra+l++
  gi|474933842|ref|YP_007687424.1|  85 GF-EYVPSGFPARFWDVYGDLGTPVRATMSSMGAQLLSRLMGLSEVQADVLNVVFSIARDRKWEIIDTRDLRAVLQY 160
                                       *6.5************************************************************************* PP

                            DUF853 159 vadnakelskqygnvskasvgaiqreLltLeqqGaekffGePaLdledllrtdadGrGvislLaadkllqsPklyat 235
                                       v+d+ +e++++yg++s++s+ga+qr+L ++e+ G++ ffGePa++++d+++ d +GrG+i++L+a+kl ++P+lyat
  gi|474933842|ref|YP_007687424.1| 161 VNDHKDEFTDEYGTMSTQSIGAVQRNLRSMEESGGDVFFGEPAIEIKDWMKCDDEGRGYINVLNAEKLSHNPALYAT 237
                                       ***************************************************************************** PP

                            DUF853 236 fLlWllseLfeeLPevGdldkPklvfffdeahLLfndapkallekveqvvrLirskGvGvyfvtqnPldlPdtvLaq 312
                                       f++Wl+seLf++LPe+Gd++kPklvfffdeah+Lf dapkal++k+eq+v+LirskGvG+yfv+q+P+d+PdtvLaq
  gi|474933842|ref|YP_007687424.1| 238 FMMWLMSELFDKLPEAGDVEKPKLVFFFDEAHMLFSDAPKALVQKIEQMVKLIRSKGVGIYFVSQSPSDIPDTVLAQ 314
                                       ***************************************************************************** PP

                            DUF853 313 LGnrvqhalraftpkdqkavkaaadtfranpefdveeaiteLgvGealvsvLdekGaPsiveralvvpPasrlgpls 389
                                       L nr+qhalra+tp++qkavkaaa++franp+f+++++iteLgvGealvs LdekGaPs+vera++ pP+srlg+l 
  gi|474933842|ref|YP_007687424.1| 315 LSNRIQHALRAYTPAEQKAVKAAATAFRANPAFKTQDVITELGVGEALVSCLDEKGAPSMVERAFILPPQSRLGALD 391
                                       ***************************************************************************** PP

                            DUF853 390 eeeraalvqespvagkydeeidresayevLakkvaeaaeaaeqaaaeeeke...eesgllgalk 450
                                        +  ++++++sp + ky+ + dresaye++++  a++++a+e+ ++e+ k+   ++++ +g+ +
  gi|474933842|ref|YP_007687424.1| 392 RAGYERAISSSPYEEKYRVREDRESAYEKISALNAKDKKAEEKPKKEAVKKepaKKTKSTGQKQ 455
                                       ****************************998877777776666555554432222222222222 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.0   5.2e-11   4.4e-08      10     183 ..      13     200 ..       3     233 .. 0.82
   2 ?    0.5   0.2      0.63   5.4e+02     146     182 ..     417     474 ..     379     480 .. 0.54

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 5.2e-11
                             DUF87  10 sevpvyldlnklvtrHlAilgsTGsGKSntvavLleellekkgatililDpHGEYgkal....ekllsekvkvitps 82 
                                        + +v l   ++ +rH +i g +G+GK+ t +vL e+   + g+++   D+ G+ g++     + ++++++k +  +
  gi|474933842|ref|YP_007687424.1|  13 GDKKVFLYP-RMANRHGLITGASGTGKTVTLRVLAESFS-SAGIPVFFADMKGDVGTIVqpgdPAKMADRAKKFGFE 87 
                                       455778887.999**************************.*******************999989999999999987 PP

                             DUF87  83 psa.............kdkelkinpwsldpeelldlleeddkpaaavqrsvleealdqaka..keekeklssdepve 144
                                         +               ++++  ++s+  + l +l++      ++vq +vl+ +++ a++  +e +   + ++ ++
  gi|474933842|ref|YP_007687424.1|  88 YVPsgfparfwdvygdLGTPVRATMSSMGAQLLSRLMGL-----SEVQADVLNVVFSIARDrkWEIIDTRDLRAVLQ 159
                                       5559999*******99999************99999999.....999**********99965544455555555555 PP

                             DUF87 145 klleelkkekeelrklknqaiarlldkledllrkggsf..s 183
                                       +++++  +  +e+  +++q+i ++++ l+++ ++gg+   +
  gi|474933842|ref|YP_007687424.1| 160 YVNDHKDEFTDEYGTMSTQSIGAVQRNLRSMEESGGDVffG 200
                                       55555556667************************998543 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.63
                             DUF87 146 lleelk.....................kekeelrklknqaiarlldkledllrkggsf 182
                                         e++                        k++ +  ++qa+++  ++l+++ r+ g+f
  gi|474933842|ref|YP_007687424.1| 417 AYEKISalnakdkkaeekpkkeavkkePAKKTKSTGQKQAERAAGNALSSFARSAGTF 474
                                       2222222222222222222222222211244556666777777777777777777776 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0   0.00078      0.66      18      60 ..      22      64 ..       9      79 .. 0.90
   2 !   13.7   0.0   2.5e-05     0.021     221     299 ..     238     323 ..     223     364 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00078
                            AAA_10 18 ktnasasliiGdlGnGKSvlakllvlyisllggkaliiDpkke 60
                                      +  + + li+G  G GK v+ ++l    s +g  +++ D k +
  gi|474933842|ref|YP_007687424.1| 22 RMANRHGLITGASGTGKTVTLRVLAESFSSAGIPVFFADMKGD 64
                                      5678999*************************99999999977 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 2.5e-05
                            AAA_10 221 avlfviaafarefass..dkkefkvvifDEawiftssaeGkkl..lkelvRiGRsynaavylvtqsadDvlkee... 290
                                        ++ +++ +  ++  +   +k   v +fDEa ++ s a  + +  ++++v+  Rs    +y+v+qs++D+ +     
  gi|474933842|ref|YP_007687424.1| 238 FMMWLMSELFDKLPEAgdVEKPKLVFFFDEAHMLFSDAPKALVqkIEQMVKLIRSKGVGIYFVSQSPSDIPDTVlaq 314
                                       5777777777777444313455568899****988765544332356899999*****************7765333 PP

                            AAA_10 291 lknniglkl 299
                                       l+n i ++l
  gi|474933842|ref|YP_007687424.1| 315 LSNRIQHAL 323
                                       555565554 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0     1e-05    0.0086      10      54 ..      20      64 ..      15      69 .. 0.88
   2 !    7.4   0.0    0.0021       1.8     143     282 ..     153     304 ..     128     324 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1e-05
                     TrwB_AAD_bind 10 pkeretqhilivGttGsGKtqalekllrairargdraivlDltGa 54
                                       ++  ++h li+G+ G+GKt++l+ l ++  + g  +  +D++G+
  gi|474933842|ref|YP_007687424.1| 20 YPRMANRHGLITGASGTGKTVTLRVLAESFSSAGIPVFFADMKGD 64
                                      5677899********************999999999999999997 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0021
                     TrwB_AAD_bind 143 dleeLkellagteaaalvaeeaertaasiratlatnlevlelLa....ekgerFSireWleeede.sgwlfltskae 214
                                       dl+ + +++++++ +++++e     ++si a +++nl+++e        ++ +  i++W++ +de +g + +  +ae
  gi|474933842|ref|YP_007687424.1| 153 DLRAVLQYVNDHK-DEFTDEYGTMSTQSIGA-VQRNLRSMEESGgdvfFGEPAIEIKDWMKCDDEgRGYINV-LNAE 226
                                       5555555555544.33444444444455543.344454444333222223335679*******995555544.5566 PP

                     TrwB_AAD_bind 215 qrallrpllsawldlaikalls.lpe...srerrlWfflDElpaL......grleelksllaegRkfGgavvlglqs 281
                                       + + + +l ++ +   +++l + lpe    ++ +l ff+DE + L        +++++++++ +R++G+ +    qs
  gi|474933842|ref|YP_007687424.1| 227 KLSHNPALYATFMMWLMSELFDkLPEagdVEKPKLVFFFDEAHMLfsdapkALVQKIEQMVKLIRSKGVGIYFVSQS 303
                                       666677777777777777776656666658999********999944443334899999999999999877666666 PP

                     TrwB_AAD_bind 282 i 282
                                        
  gi|474933842|ref|YP_007687424.1| 304 P 304
                                       5 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.5e-06    0.0013      27      60 ..      12      46 ..       6      52 .. 0.86
   2 ?    2.2   0.0      0.11        93     147     212 ..     267     329 ..     239     346 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.5e-06
                                      TS-EEEEEGGGS-..SEEEE--TTSSHHHHHHHHH CS
                      FtsK_SpoIIIE 27 sgnplvldlkkma.shllvaGatgsGKStalntLi 60
                                      sg++ v+ ++ ma  h+l+ Ga+g+GK+++l++L 
  gi|474933842|ref|YP_007687424.1| 12 SGDKKVFLYPRMAnRHGLITGASGTGKTVTLRVLA 46
                                      677778888889989*****************995 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.11
                                       --B-TT-......................-----------B-----EEEEEEC-HHHHHHHHHHH. CS
                      FtsK_SpoIIIE 147 gdvflvlDnyddlaaeneritsLsnqgpsygvhvlvtagrelekrpslvvivderieLrlaapkds 212
                                       +  +l++D  ++l ++ e++++L+    s+gv +   +++ + ++ ++++++ +ri+ +l a   +
  gi|474933842|ref|YP_007687424.1| 267 EAHMLFSDAPKALVQKIEQMVKLI---RSKGVGIYFVSQSPSDIPDTVLAQLSNRIQHALRAYTPA 329
                                       345566777777777777666666...4678888888899999*************9877776653 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   6.8e-06    0.0058       5      30 ..      25      50 ..      22      68 .. 0.83
   2 ?    3.9   0.0     0.072        62      92     128 ..     260     300 ..     241     327 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.8e-06
                            AAA_22  5 agilvvtGesGtGKTtllrrlleqld 30
                                       +++++tG sGtGKT++lr l+e++ 
  gi|474933842|ref|YP_007687424.1| 25 NRHGLITGASGTGKTVTLRVLAESFS 50
                                      589******************99985 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.072
                            AAA_22  92 ielliiDEaqhlr...seealeeLrsllnl.srkgvqliLv 128
                                       + ++  DEa+ l+   ++++++++ ++++l ++kgv + +v
  gi|474933842|ref|YP_007687424.1| 260 KLVFFFDEAHMLFsdaPKALVQKIEQMVKLiRSKGVGIYFV 300
                                       579999*****986544777777777777777888888776 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.2e-05    0.0098      26      55 ..      27      57 ..      20     137 .. 0.87
   2 ?    2.4   0.0      0.21   1.8e+02     134     156 ..     257     281 ..     239     300 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.2e-05
                            AAA_16 26 lvllsGesGvGKsslvrellralekdg.gif 55
                                        l++G+sG+GK+  +r l+++++ +g  +f
  gi|474933842|ref|YP_007687424.1| 27 HGLITGASGTGKTVTLRVLAESFSSAGiPVF 57
                                      569********************99964333 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.21
                            AAA_16 134 erp.lvlvlDdlq.wadeaslqlla 156
                                       e+p lv+++D+++  + +a+ +l +
  gi|474933842|ref|YP_007687424.1| 257 EKPkLVFFFDEAHmLFSDAPKALVQ 281
                                       4466*********655556665554 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00028      0.24      24      51 ..      25      52 ..       9      62 .. 0.84
   2 !    7.3   0.0     0.005       4.3     131     160 ..     258     286 ..     156     296 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00028
                                      TSEEEEEESTTSTHHHHHHHHHHHH-S. CS
                            ResIII 24 dkrglikmaTGtGKTlvaaklierllkk 51
                                      +++gli  a GtGKT+++  l+e+++++
  gi|474933842|ref|YP_007687424.1| 25 NRHGLITGASGTGKTVTLRVLAESFSSA 52
                                      789**************99999988776 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.005
                                       TT-SEEEEETGGGTTS.TTTHHHHHT---S CS
                            ResIII 131 drfdviiiDEaHrlgakkswreilekfkea 160
                                       + ++v+++DEaH l + ++ +++++k+++ 
  gi|474933842|ref|YP_007687424.1| 258 KPKLVFFFDEAHMLFS-DAPKALVQKIEQM 286
                                       3344**********99.5444444444433 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   5.3e-06    0.0045      20      52 ..      27      59 ..      21      86 .. 0.87
   2 ?   -1.4   0.0         2   1.7e+03      94     111 ..     169     186 ..     113     199 .. 0.72
   3 ?    0.6   0.0      0.47     4e+02      88     117 ..     259     287 ..     222     344 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.3e-06
                            AAA_30 20 vavltGpAGtGKttalkalreaweaaggrvigl 52
                                        ++tG+ GtGKt +l++l+e + +ag +v+ +
  gi|474933842|ref|YP_007687424.1| 27 HGLITGASGTGKTVTLRVLAESFSSAGIPVFFA 59
                                      5689***********************888765 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2
                            AAA_30  94 vDEagmvdtkqlaallka 111
                                        DE g ++t+++ a+ + 
  gi|474933842|ref|YP_007687424.1| 169 TDEYGTMSTQSIGAVQRN 186
                                       477777777766666555 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.47
                            AAA_30  88 pgtllivDEagmvdtkqlaallkaaekaga 117
                                       p+ ++  DEa m+ ++  +al++++e+  +
  gi|474933842|ref|YP_007687424.1| 259 PKLVFFFDEAHMLFSDAPKALVQKIEQ-MV 287
                                       346677899999988888888888776.33 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.1   0.00046      0.39       2      27 ..      29      57 ..      28      83 .. 0.77
   2 !    7.5   0.0     0.006       5.1      47     119 ..     244     311 ..     218     324 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00046
                                      EEESSTTSSHHHHHHHHHHHHT...HEEE CS
                               AAA  2 llyGppGtGKTllakavakelg...vefl 27
                                      l++G  GtGKT + + +a++++   ++++
  gi|474933842|ref|YP_007687424.1| 29 LITGASGTGKTVTLRVLAESFSsagIPVF 57
                                      789****************9742224444 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.006
                                       HHHHHHHHHTS...TS.EEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS..SSTEEEEEEESSGGGSTH CS
                               AAA  47 relfkeakeka...kp.silfiDEidalaksrsgseseeeervvnqLlteldgvkkk..eskvivigatnrpdkldp 117
                                       +elf+++ e     kp  ++f+DE++ l+++             ++L+++++++ k   ++ v +  ++++p+++++
  gi|474933842|ref|YP_007687424.1| 244 SELFDKLPEAGdveKPkLVFFFDEAHMLFSDA-----------PKALVQKIEQMVKLirSKGVGIYFVSQSPSDIPD 309
                                       566666655556666879***********999...........3333333333333222122445555555555555 PP

                                       HH CS
                               AAA 118 al 119
                                        +
  gi|474933842|ref|YP_007687424.1| 310 TV 311
                                       54 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       2.2   1.9e+03       4      15 ..      29      40 ..      28      58 .. 0.87
   2 !   14.0   0.0   3.5e-05      0.03      83     147 ..     262     324 ..     240     349 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.2
                               Zot  4 lvtGapGsgKts 15
                                      l tGa G+gKt 
  gi|474933842|ref|YP_007687424.1| 29 LITGASGTGKTV 40
                                      579*******96 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 3.5e-05
                               Zot  83 llviDEcqeifpvrakegrkdpevinaftehRhlgwDivlltqdiskihkevralaekavklkrk 147
                                       + ++DE++ +f+   k    ++++++  +  R  g  i ++ q +s i++ v a  +   ++  +
  gi|474933842|ref|YP_007687424.1| 262 VFFFDEAHMLFSDAPKA--LVQKIEQMVKLIRSKGVGIYFVSQSPSDIPDTVLAQLSNRIQHALR 324
                                       5689********99996..679999**************************99988888888655 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   5.1e-05     0.043       4      27 ..      30      57 ..      28      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.1e-05
                            AAA_28  4 itGgestGKTtlleaLaar....gypvv 27
                                      itG+++tGKT +l+ La+     g+pv+
  gi|474933842|ref|YP_007687424.1| 30 ITGASGTGKTVTLRVLAESfssaGIPVF 57
                                      9****************76666788886 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00016      0.14       2      53 ..      29      79 ..      29      84 .. 0.76
   2 ?   -1.9   0.0       5.4   4.6e+03      42      67 ..     166     190 ..     118     214 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00016
                            AAA_18  2 lltGtpGvGKttlakeLskrlgf.gvnlrdvakenglllevdpealdeskrld 53
                                      l+tG++G+GKt   + L+++  + g+ + +   +++  + v+p   d+ k +d
  gi|474933842|ref|YP_007687424.1| 29 LITGASGTGKTVTLRVLAESFSSaGIPVFFADMKGDVGTIVQPG--DPAKMAD 79
                                      69*****************9744788888777777776666666..5555555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.4
                            AAA_18  42 dpealdeskrldedkldklldaleen 67 
                                       d+  +de+  + ++   +++++l+  
  gi|474933842|ref|YP_007687424.1| 166 DE-FTDEYGTMSTQSIGAVQRNLRSM 190
                                       22.36666666666666666666664 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00029      0.24       9      36 ..      24      51 ..      19      57 .. 0.85
   2 ?   -1.7   0.0       3.9   3.3e+03      99     126 ..     255     284 ..     220     290 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00029
                            AAA_19  9 kekvllvtaGpGtGKTrvlkhivallve 36
                                      ++++ l+t+  GtGKT +l+   + + +
  gi|474933842|ref|YP_007687424.1| 24 ANRHGLITGASGTGKTVTLRVLAESFSS 51
                                      67889**************998887765 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.9
                            AAA_19  99 klqeee.llivDEfqdvd.elqyrLlkall 126
                                       ++++ + +++ DE+ ++  +  ++L++++ 
  gi|474933842|ref|YP_007687424.1| 255 DVEKPKlVFFFDEAHMLFsDAPKALVQKIE 284
                                       444555578888988887677777777765 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00011     0.091       5      35 ..      31      61 ..      29     302 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
                                      ESSTTSSHHHHHHHHHHHHHHTT--EEEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  5 stkGGvGKTtlaanLaralarrglrVllvDa 35
                                       + +G+GKT+++  La +++ +g  V+  D+
  gi|474933842|ref|YP_007687424.1| 31 TGASGTGKTVTLRVLAESFSSAGIPVFFADM 61
                                      689************************9996 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00022      0.19      32     107 ..      24     101 ..       8     166 .. 0.76
   2 ?   -3.8   0.0       9.2   7.9e+03      86     116 ..     315     346 ..     313     353 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00022
                            AAA_25  32 agelallaGapgtGKttlaldlalava.tGkpwlg.pvapeqgkVlyvsaEdsedelrrRlravgeal...rddarl 103
                                       a+  +l++Ga+gtGKt+ +  la + +  G p++  ++   +g V  ++  ++ + ++ R+++ g ++    ++ar 
  gi|474933842|ref|YP_007687424.1|  24 ANRHGLITGASGTGKTVTLRVLAESFSsAGIPVFFaDM---KGDVGTIVQPGDPAKMADRAKKFGFEYvpsGFPARF 97 
                                       466789*****************999999***999554...666655555556559999999998877666445554 PP

                            AAA_25 104 lvld 107
                                         ++
  gi|474933842|ref|YP_007687424.1|  98 WDVY 101
                                       4444 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 9.2
                            AAA_25  86 lrrRlravgealrddarllvldlagv.eslpL 116
                                       l +R++ +++a+++ ++ +v  +a+    +p 
  gi|474933842|ref|YP_007687424.1| 315 LSNRIQHALRAYTPAEQKAVKAAATAfRANPA 346
                                       67888888888877766666666665555555 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00038      0.33      32      59 ..      24      51 ..      19      62 .. 0.83
   2 ?   -2.3   0.0       3.1   2.7e+03     100     117 ..     259     276 ..     254     299 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00038
                             AAA_7 32 nkkpvllvGptGtGKtviikdllkkldk 59
                                      ++++ l++G +GtGKtv+++ l +++++
  gi|474933842|ref|YP_007687424.1| 24 ANRHGLITGASGTGKTVTLRVLAESFSS 51
                                      57899*************9998888775 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.1
                             AAA_7 100 kklvvFvDDlnmpakeky 117
                                        klv+F D+ +m   +  
  gi|474933842|ref|YP_007687424.1| 259 PKLVFFFDEAHMLFSDAP 276
                                       6899999*9999887765 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0    0.0005      0.42       4      57 ..      30      84 ..      29     100 .. 0.78
   2 ?   -2.3   0.0       3.6   3.1e+03      73      99 ..     242     268 ..     235     282 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0005
                               PRK  4 vagsSGaGkttvarklekifgrekvkaaeiegds.flrldraekdleleerkrak 57
                                      ++g+SG Gkt + r l ++f  ++++    +++  + ++++  + +++++r++++
  gi|474933842|ref|YP_007687424.1| 30 ITGASGTGKTVTLRVLAESFSSAGIPVFFADMKGdVGTIVQPGDPAKMADRAKKF 84
                                      8********************9999965554443034677888888888888776 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.6
                               PRK  73 llyevlkelkegkkvdkpiYsheteea 99 
                                       l+ e + +l e++ v+kp+ ++  +ea
  gi|474933842|ref|YP_007687424.1| 242 LMSELFDKLPEAGDVEKPKLVFFFDEA 268
                                       788999999999999999888765555 PP

>> DNA_photolyase  DNA photolyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00043      0.37      29     115 ..     261     343 ..     228     363 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00043
                                       EEEEE-HHHHTCGS-CHHHHHHHHHHHHHHHHHHHHTT--EEEEESSHHHHHHHHHHHCTECEEEEE---SHHHHHH CS
                    DNA_photolyase  29 pvfvldpekahklrvgaarvdfllesLadLdeeLrelgirLvvrrgdpadvlpelakelgasavvanreyepderer 105
                                        vf++d++  h l   +   + l + ++++ + +r++g+  ++++ +p d+   ++++l  +  +a r y+p+e++ 
  gi|474933842|ref|YP_007687424.1| 261 LVFFFDEA--HML--FSDAPKALVQKIEQMVKLIRSKGVGIYFVSQSPSDIPDTVLAQLSNRIQHALRAYTPAEQKA 333
                                       68999999..555..66677899***************************99999********************** PP

                                       HHHHHHHHHH CS
                    DNA_photolyase 106 deavkealrk 115
                                        +a ++a+r+
  gi|474933842|ref|YP_007687424.1| 334 VKAAATAFRA 343
                                       *****99996 PP

>> CRISPR_Cse2  CRISPR-associated protein Cse2 (CRISPR_cse2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0047         4      86     115 ..     270     299 ..     268     302 .. 0.89
   2 ?    1.7   0.1      0.41   3.5e+02      28      80 ..     322     376 ..     300     397 .. 0.69
   3 ?   -0.6   0.7       2.1   1.8e+03      30      64 ..     408     453 ..     384     478 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0047
                                       HCT-SSCCCHHHHHHHHHHHHHCTT--B-H CS
                       CRISPR_Cse2  86 lltadtpeelarrLrrlvkllrskevpldy 115
                                       +l +d p++l++ + ++vkl+rsk+v++ +
  gi|474933842|ref|YP_007687424.1| 270 MLFSDAPKALVQKIEQMVKLIRSKGVGIYF 299
                                       7778899*******************9986 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.41
                                       TTT.HHHHHHHHHHHHHHHHHCCHC.S-SB.-TT-CHHHHHHHHHHHTCT.HHHHH CS
                       CRISPR_Cse2  28 eseeekepeeraayavaalyaahqq.ekeh.dsgkslgaalgrlreases.sesie 80 
                                       + +    +e++a+ a+a+++ a++  ++++  ++ ++g+al  + +++++ s+ +e
  gi|474933842|ref|YP_007687424.1| 322 ALRAYTPAEQKAVKAAATAFRANPAfKTQDvITELGVGEALVSCLDEKGApSM-VE 376
                                       44556778999999999999999997444445666799999988877777332.43 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 2.1
                                       T.HHHHHHHHHHHHHHHHHCCHC.................S-SB-TT-CHHH CS
                       CRISPR_Cse2  30 eeekepeeraayavaalyaahqq.................ekehdsgkslga 64 
                                        + +e++e a+  + al a  ++                 +      ks g+
  gi|474933842|ref|YP_007687424.1| 408 YRVREDRESAYEKISALNAKDKKaeekpkkeavkkepakkT------KSTGQ 453
                                       35677888888888888888888777766666644333220......22222 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1    0.0026       2.2       5      22 ..      29      46 ..      26      65 .. 0.84
   2 ?    5.5   0.0    0.0098       8.4      88     131 ..     259     301 ..     234     332 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0026
                           DUF2075  5 lVtGvaGtGKtvvllnll 22
                                      l+tG++GtGKtv l  l+
  gi|474933842|ref|YP_007687424.1| 29 LITGASGTGKTVTLRVLA 46
                                      79**********876555 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0098
                           DUF2075  88 kedvvivDEAhrlltksdqaekqseenqlkelmkrakvvvalvD 131
                                       +  v  +DEAh l +   +++  ++ +q+ +l++ + v +++v 
  gi|474933842|ref|YP_007687424.1| 259 PKLVFFFDEAHMLFS-DAPKALVQKIEQMVKLIRSKGVGIYFVS 301
                                       455889********9.334445556899999999999**99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (484 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1326  (0.0739584); expected 358.6 (0.02)
Passed bias filter:                      756  (0.0421663); expected 358.6 (0.02)
Passed Vit filter:                       111  (0.00619109); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.77u 0.34s 00:00:01.11 Elapsed: 00:00:00.50
# Mc/sec: 2906.38
//
Query:       gi|474933843|ref|YP_007687425.1|  [L=461]
Description: NAD-dependent aldehyde dehydrogenase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-63  213.1   0.0    8.8e-63  212.4   0.0    1.2  1  Aldedh    Aldehyde dehydrogenase family


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.4   0.0   4.9e-67   8.8e-63      19     425 ..      52     443 ..      41     452 .. 0.93

  Alignments for each domain:
  == domain 1  score: 212.4 bits;  conditional E-value: 4.9e-67
                                       EEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH---HHHHHHHHHHHHH CS
                            Aldedh  19 viakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaeletletGkplaearaeveeaid 95 
                                       ++++ ++  + ++++a + A++af+ w+k ++eeR++iL ++ad +e+r  +la+  +l tG   ++a ae e +++
  gi|474933843|ref|YP_007687425.1|  52 IFGRLQDPVPGTMKKAAEDAARAFEMWSKSSPEERSRILSAVADSIEKRLYRLAADVVLSTGMVRKDAFAEAETCLE 128
                                       44677777778899*************************************************************** PP

                                       HHHHHHHHHHHHSEEEEEECTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEEEEE-TTSHHHHHHH CS
                            Aldedh  96 vlryyaelaeklegevlpssegklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvvlKPaeetplsalll 172
                                       v+r + + a +++g               +P Gv+g+I+    Pl+ +++  a+a+aaGNtvv+ P+   p  ++++
  gi|474933843|ref|YP_007687425.1| 129 VVRQASKDAMNVKG---------------KPRGVWGIIALESSPLASVIGYSAAAIAAGNTVVMMPSGHCPRPVYAV 190
                                       ******99999998...............49********************************************** PP

                                       HHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSEEEEEE---EEEEE-TTSH CS
                            Aldedh 173 aelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlkrvtlElGGknplivledaD 249
                                       + lfe+aglP+gvln+v+ + + ++ +l ++++v+ v   G  +   ++   a ++    + E+ G np++v +  D
  gi|474933843|ref|YP_007687425.1| 191 FDLFEQAGLPDGVLNLVCDRTDRFATELSDDENVAGVVASGCGKAMDDMIFLAVDDTLGYINEVKGMNPIVVSQPGD 267
                                       ***********************************************9999999999******************** PP

                                       HHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT-SB---SSHHHHHHHHHHHHH CS
                            Aldedh 250 ldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedtdvGPliseaqlekvekyvee 326
                                       ++ka+++i+ +af n+G   +a+s+++v  +   e+++++ve++k+l+v dp ++++++GPl+++++ +++++++++
  gi|474933843|ref|YP_007687425.1| 268 IKKAADSIIDSAFQNNGKGLYATSKVIVSADDDRELTKAIVERLKDLNVNDPGEKECQMGPLMNKEEEKRLTGLLDS 344
                                       **************************************************************************986 PP

                                       HHHTTSEEEE-TT.E.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEESSHHHHHHHHHSSSEESEEEEE CS
                            Aldedh 327 akeegaklllGge.reeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfkdeeeaieiaNdteyGLaagvf 402
                                       +    a +++Gg+  +++  e+g +++P +l+ v+pd++i   +   P+l++ ++   + +++   +t+ GL+ gv+
  gi|474933843|ref|YP_007687425.1| 345 EA---AYVVMGGKrVKKEYTENGLYYTPILLTSVDPDDDIQYVDSGLPILVIKQAAGADAILQELDQTDCGLSVGVI 418
                                       55...689999998889999********************************************************* PP

                                       -SBHHHHHHHHHHS..-SSEEEESS CS
                            Aldedh 403 tkdleraervaerl..eaGnvyiNd 425
                                       ++d + + ++ e    e  +v +N+
  gi|474933843|ref|YP_007687425.1| 419 SSDSKLISKIKEFAdeENLQVFVNT 443
                                       ***9988888765533444555565 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 3093.39
//
Query:       gi|474933844|ref|YP_007687426.1|  [L=228]
Description: Pyruvate-formate lyase-activating enzyme [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.1e-09   36.7   0.0    7.4e-09   36.2   0.0    1.2  1  Radical_SAM  Radical SAM superfamily
    2.7e-05   24.3   0.0    4.3e-05   23.6   0.0    1.3  1  Fer4_14      4Fe-4S single cluster domain
    0.00014   22.1   0.0     0.0002   21.6   0.0    1.3  1  Fer4_12      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.0   1.2e-12   7.4e-09      10     159 ..      30     169 ..      24     175 .. 0.85

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 1.2e-12
                                       --TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  10 rCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritvetng 86 
                                       rC+f  +p    +++ g sl+++ i++ + + +      e i++ggepl +p + ++l++l+k    ++ i++et+g
  gi|474933844|ref|YP_007687426.1|  30 RCPFFGNPDL--WNEEGPSLDPQPIIDYISARS----SLEGIILGGEPLRDPSLFKFLKELRKT---KVPIRLETSG 97 
                                       6777777775..788888888888888887776....88899999******************8...********** PP

                                       SCHGHHHHHHHHHTT.-SEEEEEEBSSSHH.HHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSH.HH CS
                                       xxxxxxxxxxxxxxx.xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                       Radical_SAM  87 tlpdeeklerllelg.vdrvslgleaadde.kvlklmnrghtfeevlealeklreagikrvvdrivglpGend.ee 159
                                       t+  +e ++ ++ +  vd v + l a+    ++ + + +g + +++ ++l++l +++++ + + iv +pG++  ++
  gi|474933844|ref|YP_007687426.1|  98 TR--PEDVDDFAGAMtVDNVCIVLTAVPGSeRFSEAC-PGADESKIQKTLDLLPDLDVP-SEIQIVAVPGFTNvDD 169
                                       **..69*******9998887777777654456*****.*********************.9*********997344 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   7.2e-09   4.3e-05      17      96 ..      36     104 ..      22     119 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 7.2e-09
                           Fer4_14  17 nketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiwletngtlei 93 
                                       n + w++e    + + +++ i   +       +g  ++GGePL   ++++l+k++k+l++ +  ++i+let+gt   
  gi|474933844|ref|YP_007687426.1|  36 NPDLWNEEGPSLDPQPIIDYIS--ARS-S--LEG-IILGGEPL---RDPSLFKFLKELRKTK--VPIRLETSGTRPE 101
                                       5555555555555555554333..222.2..232.489*****...89************99..*********9887 PP

                           Fer4_14  94 ele 96 
                                       +++
  gi|474933844|ref|YP_007687426.1| 102 DVD 104
                                       766 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   3.3e-08    0.0002      14     102 ..      26     106 ..      15     142 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 3.3e-08
                           Fer4_12  14 gCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdiwl 90 
                                       g +++C+++ n+++w+ ++    ++++++ i ++   +s eg+ +lGGEPl    ++ l +++ke++++k+ +  ++
  gi|474933844|ref|YP_007687426.1|  26 GYDVRCPFFGNPDLWNEEGPSLDPQPIIDYISAR---SSLEGI-ILGGEPLR---DPSLFKFLKELRKTKV-PIRLE 94 
                                       66789***********999999899998888644...567776.68*****9...***************9.7999* PP

                           Fer4_12  91 ytgytleelskk 102
                                       ++g+  e+++++
  gi|474933844|ref|YP_007687426.1|  95 TSGTRPEDVDDF 106
                                       ***999998866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1372.38
//
Query:       gi|474933845|ref|YP_007687427.1|  [L=301]
Description: ACT domain protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0057   16.4   0.2       0.82    9.5   0.0    2.5  2  ACT       ACT domain


Domain annotation for each model (and alignments):
>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.6   0.0    0.0016        29       3      31 ..      65      93 ..      63     105 .. 0.88
   2 !    9.5   0.0   4.6e-05      0.82       3      34 ..     221     252 ..     219     281 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0016
                                      EEEEEESSTTHHHHHHHHHHHTTSEEEEE CS
                               ACT  3 lrvgvpDrPGlLarvfgaladrgiNidsi 31
                                      + v++ D+PG   + +  l+d  i i + 
  gi|474933845|ref|YP_007687427.1| 65 VTVYADDVPGSTVQAAKFLTDQKIRILNS 93
                                      568999******************99765 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 4.6e-05
                                       EEEEEESSTTHHHHHHHHHHHTTSEEEEEEEE CS
                               ACT   3 lrvgvpDrPGlLarvfgaladrgiNidsieqr 34 
                                       + ++vpD  G +   ++ lad+giN++s+ ++
  gi|474933845|ref|YP_007687427.1| 221 IVMDVPDCMGSIDSALSMLADAGINLISVFTK 252
                                       567889999999999************98665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1834.68
//
Query:       gi|474933846|ref|YP_007687428.1|  [L=226]
Description: hypothetical protein TALC_00257 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.045   13.7   0.4      0.082   12.9   0.4    1.4  1  Ogr_Delta  Ogr/Delta-like zinc finger


Domain annotation for each model (and alignments):
>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.4   4.6e-06     0.082       2      37 ..      84     117 ..      83     123 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.6e-06
                         Ogr_Delta   2 CPhCgapaaartsrnlskdvreryyqCsnfeCgatf 37 
                                       CP Cg+++      nl+ +v+e+  +C++  C +++
  gi|474933846|ref|YP_007687428.1|  84 CPVCGNAMSPVMNMNLDGNVTEVKRNCTV--CAFSV 117
                                       ****************************9..88775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       723  (0.0403257); expected 358.6 (0.02)
Passed bias filter:                      601  (0.0335211); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1511.45
//
Query:       gi|474933847|ref|YP_007687429.1|  [L=68]
Description: hypothetical protein TALC_00259 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.014   15.6   2.4      0.017   15.3   2.4    1.1  1  DUF2053   Predicted membrane protein (DUF2053)
        0.2   11.0   2.5       0.21   11.0   2.5    1.0  1  TMEM43    Transmembrane protein 43


Domain annotation for each model (and alignments):
>> DUF2053  Predicted membrane protein (DUF2053)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   2.4   1.9e-06     0.017       5      48 ..      10      53 ..       8      57 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.9e-06
                           DUF2053  5 finclalafiPyyivYkasslseykafskvvlailaylltqlvK 48
                                      +++cla+++iPy++ Y    ls y+ f     +++a++   +++
  gi|474933847|ref|YP_007687429.1| 10 MAACLAMIYIPYLMSYWFDVLSSYTGFVFTTVSFIAFVSLVFLR 53
                                      578***********************999999999999877765 PP

>> TMEM43  Transmembrane protein 43
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.5   2.3e-05      0.21     193     240 ..       5      52 ..       1      57 [. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2.3e-05
                            TMEM43 193 Gfllmflglllllsplsvlvslipllgelvglglalvalllslslsll 240
                                       ++ +m+ ++l ++ + + + +++ +l++++g+++ +v+++  +sl +l
  gi|474933847|ref|YP_007687429.1|   5 SYNIMMAACLAMIYIPYLMSYWFDVLSSYTGFVFTTVSFIAFVSLVFL 52 
                                       566788888888888899999**********************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       745  (0.0415528); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.29s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 466.35
//
Query:       gi|474933848|ref|YP_007687430.1|  [L=1587]
Description: Listeria/Bacterioides repeat protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-19   68.1  37.1    1.2e-07   31.8   0.5    8.4  8  Flg_new   Listeria-Bacteroides repeat domain (List_Bact_rpt)


Domain annotation for each model (and alignments):
>> Flg_new  Listeria-Bacteroides repeat domain (List_Bact_rpt)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.5   6.9e-12   1.2e-07       1      64 [.      28     107 ..      28     108 .. 0.79
   2 !    2.6   1.4    0.0084   1.5e+02       1      42 [.     114     160 ..     113     175 .. 0.71
   3 ?   -3.1   0.3      0.51   9.1e+03       2      35 ..     561     595 ..     561     597 .. 0.66
   4 ?   -0.6   0.0     0.086   1.5e+03      29      39 ..     936     946 ..     921     960 .. 0.79
   5 !   20.6   0.9   2.1e-08   0.00038       1      60 [.     994    1054 ..     994    1059 .. 0.69
   6 ?    0.4   0.1     0.043   7.7e+02      33      54 ..    1111    1130 ..    1095    1136 .. 0.81
   7 !   11.6   0.6   1.4e-05      0.25      15      51 ..    1244    1282 ..    1224    1292 .. 0.56
   8 !   21.4   0.1   1.1e-08    0.0002       1      64 [.    1304    1366 ..    1304    1367 .. 0.89

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 6.9e-12
                                       EEEEEEETTEEEEEE............EETTSB----...B--EETTEEEEEEESSTTC.CSB--TTT-B--SS-EE CS
                           Flg_new   1 YtvtFdanGgtvsqt............vtygetitlp...anptkeGYtFaGWytdsdg.ttaydfgtkvtptgdvt 61 
                                       +t+tFd n g+++++            +  g+++t      + tk+GY F+GW+++++  t+++ +g+ +++ +d+t
  gi|474933848|ref|YP_007687430.1|  28 HTITFDPNTGEAKESriyvaenvigsiYIPGNDFTVDgveYEYTKDGYSFVGWSENPNSlTANIMEGSVWEVHADMT 104
                                       69******99976544444444555555558877776555689**************997899999999******** PP

                                       EEE CS
                           Flg_new  62 LyA 64 
                                       LyA
  gi|474933848|ref|YP_007687430.1| 105 LYA 107
                                       *** PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.0084
                                       EEEEEEETTEEEEEEEETTSB----.....B--EETTEEEEEEESST CS
                           Flg_new   1 YtvtFdanGgtvsqtvtygetitlp.....anptkeGYtFaGWytds 42 
                                       Y vt +  + t++  v+yg+t++++     + p  + Y+ +GW t +
  gi|474933848|ref|YP_007687430.1| 114 YDVTLHYGNTTTTIGVKYGTTTDTThmmflSPPGMSDYVIVGWTTYD 160
                                       5555555444444468888887764445558899*********9964 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 0.51
                                       EEEEEETTEEEEEEE.ETTSB----B--EETTEEE CS
                           Flg_new   2 tvtFdanGgtvsqtv.tygetitlpanptkeGYtF 35 
                                       tv+F  nG+  s+ + +yg  ++ +++   + Y+F
  gi|474933848|ref|YP_007687430.1| 561 TVSFSVNGSLLSEPIgYYGGVYNYSESGGESSYNF 595
                                       89999999987775415566666666666666666 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 0.086
                                       EETTEEEEEEE CS
                           Flg_new  29 tkeGYtFaGWy 39 
                                        k GY+F  W 
  gi|474933848|ref|YP_007687430.1| 936 IKRGYEFGYWD 946
                                       699*******5 PP

  == domain 5  score: 20.6 bits;  conditional E-value: 2.1e-08
                                        EEEEEEETTEEEEE.EEETTSB----B--EETTEEEEEEE.SSTTCC.SB--TTT-B--SS-E CS
                           Flg_new    1 YtvtFdanGgtvsq.tvtygetitlpanptkeGYtFaGWy.tdsdgt.taydfgtkvtptgdv 60  
                                        Y+++Fd++Gg++++   +  ++ t  +npt++GY+F+ W  t  dgt +++ f++++   gd 
  gi|474933848|ref|YP_007687430.1|  994 YSLSFDLQGGEADNpDHYFIDDGTVIQNPTRKGYVFDYWTgTGIDGTaQSIVFDADTY--GDR 1054
                                        99*********765243334555666899**********8344577656777777654..555 PP

  == domain 6  score: 0.4 bits;  conditional E-value: 0.043
                                        EEEEEEESSTTCCSB--TTT-B CS
                           Flg_new   33 YtFaGWytdsdgttaydfgtkv 54  
                                        Y F GW    d +t++d++t v
  gi|474933848|ref|YP_007687430.1| 1111 YIFYGWALP-D-GTKIDSNTRV 1130
                                        99*****95.4.5777877765 PP

  == domain 7  score: 11.6 bits;  conditional E-value: 1.4e-05
                                        EEETTSB----..B--EETTEEEEEEESSTTCCSB--TT CS
                           Flg_new   15 tvtygetitlp..anptkeGYtFaGWytdsdgttaydfg 51  
                                        t+t ++++t +  +  +  GY F+GW+  + g+ a++  
  gi|474933848|ref|YP_007687430.1| 1244 TYTVNDNLTISsaSVTSIPGYAFDGWSLHPGGEVAVTNA 1282
                                        344455444443166678***********9888887654 PP

  == domain 8  score: 21.4 bits;  conditional E-value: 1.1e-08
                                        EEEEEEETTEEEEEEEETTSB----B--EETTEEEEEEESSTTCCSB--TTT-B--SS-EEEEE CS
                           Flg_new    1 YtvtFdanGgtvsqtvtygetitlpanptkeGYtFaGWytdsdgttaydfgtkvtptgdvtLyA 64  
                                        Y +t+d   g +  ++  g++itl +  + +G  FaGW+++++++ +  ++ + t+++d+ +yA
  gi|474933848|ref|YP_007687430.1| 1304 YHITYDPFRGDNVSEFSIGDSITLVP-ISVSGMYFAGWFDNEEYSGDPVESFTATSDHDLFFYA 1366
                                        99******9999999*********99.99***************76555566667789999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1587 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.92u 0.36s 00:00:01.28 Elapsed: 00:00:00.53
# Mc/sec: 8968.86
//
Query:       gi|474933849|ref|YP_007687431.1|  [L=166]
Description: hypothetical protein TALC_00261 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1022.22
//
Query:       gi|474933850|ref|YP_007687432.1|  [L=89]
Description: hypothetical protein TALC_00262 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       172  (0.0095934); expected 358.6 (0.02)
Passed bias filter:                      171  (0.00953762); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.50
# Mc/sec: 537.23
//
Query:       gi|474933851|ref|YP_007687433.1|  [L=145]
Description: hypothetical protein TALC_00263 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 1022.27
//
Query:       gi|474933852|ref|YP_007687434.1|  [L=167]
Description: hypothetical protein TALC_00264 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1118.20
//
Query:       gi|474933853|ref|YP_007687435.1|  [L=398]
Description: conserved hypothetical protein TIGR00299 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     2e-130  435.2   0.0   2.2e-130  435.1   0.0    1.0  1  DUF111    Protein of unknown function DUF111
  ------ inclusion threshold ------
       0.15   12.2   0.0       0.33   11.1   0.0    1.5  1  BET       Bromodomain extra-terminal - transcription regulati


Domain annotation for each model (and alignments):
>> DUF111  Protein of unknown function DUF111
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  435.1   0.0  2.5e-134  2.2e-130       1     372 [.       4     383 ..       4     384 .. 0.98

  Alignments for each domain:
  == domain 1  score: 435.1 bits;  conditional E-value: 2.5e-134
                            DUF111   1 lyldcssGisGDmllgALldlgadkeeleealeklgleeveleiekvkksgisatkvdve.........eeeheheh 68 
                                       lyl+c++G+sGDmllgAL dl  d+ el+  +e lg+ ++ ++++ ++ks+is+++v+++         e+e++h+h
  gi|474933853|ref|YP_007687435.1|   4 LYLECNAGVSGDMLLGALADLLKDPFELKGMIEGLGIPGIVCNVSIDEKSKISGIRVSIScggveegdvENEKKHQH 80 
                                       8********************************************************************8899**** PP

                            DUF111  69 rslaeieeiieaaslsekvkekalaiferlaeAeakvhgvpleevhfhEvGavDaivdivgaalaldeLgvekvvas 145
                                       + + ++ ++i ++++s++vk++a ai++++aeAe++vhg+p++evhfhEvGa+Dai+d+vg+++++++L++ +++as
  gi|474933853|ref|YP_007687435.1|  81 HMVGDVFKLIGSLNVSDRVKSDAAAIYAIIAEAESNVHGKPVNEVHFHEVGALDAIADVVGVCMLIERLAPATIIAS 157
                                       ***************************************************************************** PP

                            DUF111 146 plalGsGtvrcahGilPvPaPAvlellkelklklgevegElvTPTGaAilaalaeefgslpamkvekiGyGaGkrdl 222
                                       pl++G G+v cahG+lPvPaPA++ +l+++++++g++egE++TPTGaAi++++ae+fg+lp m++e++GyG+Gk+d+
  gi|474933853|ref|YP_007687435.1| 158 PLRTGYGEVVCAHGTLPVPAPATAYILQGMSIYAGDAEGEFTTPTGAAIVKHFAESFGQLPLMEFEDMGYGLGKKDM 234
                                       ***************************************************************************** PP

                            DUF111 223 eeipnvlRvlleeeeeelekeevvvletniDDlspevlgyvlerLleaGAlDvfltpilmKKgRpavllsvlckeed 299
                                         i+n++R++++  e + +   v  l++niDD+spe +g+v++ L+eaGAlD+f+t ++mKK+Rp++ll+++c+eed
  gi|474933853|ref|YP_007687435.1| 235 -GIANMVRAFIG--EVDGDLPVVKELSCNIDDMSPEDMGSVIDILMEAGALDAFITGCIMKKSRPGYLLTCICREED 308
                                       .9*********5..5666778999***************************************************** PP

                            DUF111 300 aeeleellfretttlGvReseverlvlereietvetelgevrvKvaee..vvkvkpEyedvkkiAeetglplkev 372
                                       +e+l+ +++++t+t+GvR++ +er+ ++ ++e+ +te+g+vr+Kv+e+   +k kpEyed+ + A + ++p+++v
  gi|474933853|ref|YP_007687435.1| 309 EEDLAMTILAHTSTIGVRTHVCERYEMHSRFESYRTEFGDVRIKVSEGfgYRKWKPEYEDLLRNAIDYDVPVSDV 383
                                       **********************************************66679*********************998 PP

>> BET  Bromodomain extra-terminal - transcription regulation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   3.7e-05      0.33       8      32 ..     255     279 ..     255     285 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.7e-05
                               BET   8 keLseeInkLpgeklgrvveIIqer 32 
                                       keLs +I ++++e++g v++I+ e 
  gi|474933853|ref|YP_007687435.1| 255 KELSCNIDDMSPEDMGSVIDILMEA 279
                                       699******************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2659.03
//
Query:       gi|474933854|ref|YP_007687436.1|  [L=250]
Description: NCAIR mutase (PurE)-related protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-15   55.4   2.7    4.9e-15   55.4   2.7    1.8  2  AIRC      AIR carboxylase
  ------ inclusion threshold ------
      0.096   12.1   0.0       0.23   10.8   0.0    1.6  2  CHAT      CHAT domain


Domain annotation for each model (and alignments):
>> AIRC  AIR carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       0.1     9e+02       4      30 ..      50      76 ..      48     108 .. 0.73
   2 !   55.4   2.7   5.5e-19   4.9e-15       2     126 ..     119     243 ..     118     249 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.1
                                      EEESSGGGHHHHHHHHHHHHHTT-EEE CS
                              AIRC  4 iimGSdsDlevmkkaaeilkelgveye 30
                                      ++ G + D + + ++a++l e g e+ 
  gi|474933854|ref|YP_007687436.1| 50 VVYGESKDAKQCVGIASALMESGAECV 76
                                      788999999999999999999888774 PP

  == domain 2  score: 55.4 bits;  conditional E-value: 5.5e-19
                                       EEEEESSGGGHHHHHHHHHHHHHTT-....EEEEEE--TTTSHHHHHHHHHHCHTTTEEEEEEEEESS--HHHHHHH CS
                              AIRC   2 VgiimGSdsDlevmkkaaeilkelgv....eyevrvvSahrtpeelleyaeeaeerglkviIagAGgaahLpgvvas 74 
                                       V+++++ +sD++v+++aa + ++lg      y+v v   hr  +++  +++       ++++++AG++ +Lp+vv +
  gi|474933854|ref|YP_007687436.1| 119 VCVVTAGTSDIPVAEEAAVTAESLGSrverVYDVGVSGLHRLLSKTDVLLR------ARAVVVVAGMEGALPSVVGG 189
                                       89*********************88744556899***********998887......346899************** PP

                                       HSSS-EEEEEE--...STTCCHHHHHHHHT--TTS--EE-SSTHHHHHHHHHHHH CS
                              AIRC  75 lttlPVigvPvks...kalkgldsllSivqmPsgvpvatvaigkaknAallAaqi 126
                                       l+++PVi+vP++     +++gl +llS+++ +s   v  v+i+++  A+++A  i
  gi|474933854|ref|YP_007687436.1| 190 LVDVPVIAVPTSVgygASFEGLTALLSMMNSCSS-DVSVVNIDNGFGAGYIAGMI 243
                                       ************644468************9984.56677788********9877 PP

>> CHAT  CHAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   2.6e-05      0.23     202     232 ..      52      82 ..      38      98 .. 0.82
   2 ?   -2.3   0.0      0.26   2.3e+03      82     117 ..     105     142 ..      94     170 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 2.6e-05
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CHAT 202 lgevidgegvlgLaralllaGarsviaslwp 232
                                        ge +d+++ +g a+al+++Ga++v++++++
  gi|474933854|ref|YP_007687436.1|  52 YGESKDAKQCVGIASALMESGAECVLITRCS 82 
                                       6888899*********************986 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.26
                                       xxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CHAT  82 lvvgdpkfdaa...ellrklvfpelpgteaEaeaiakll 117
                                       +v+g+p+++      ++ ++ ++++p +e Ea++ a+ l
  gi|474933854|ref|YP_007687436.1| 105 AVIGKPQEPSPnslVCVVTAGTSDIPVAE-EAAVTAESL 142
                                       56666666644444455555555555444.333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1726.81
//
Query:       gi|474933855|ref|YP_007687437.1|  [L=256]
Description: conserved hypothetical protein TIGR00268 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.033   14.0   0.0      0.086   12.6   0.0    1.7  2  ATP_bind_3    PP-loop family
      0.044   12.9   0.0      0.065   12.4   0.0    1.2  1  NAD_synthase  NAD synthase
       0.14   11.8   0.0       0.18   11.4   0.0    1.2  1  Asn_synthase  Asparagine synthase


Domain annotation for each model (and alignments):
>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.4e-05     0.086       1      25 [.      19      43 ..      19      73 .. 0.83
   2 ?   -2.7   0.0      0.73   4.3e+03     152     173 ..     105     126 ..     102     134 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.4e-05
                                      EEEEE--SCHHHHHHHHHHHHHCTT CS
                        ATP_bind_3  1 kvlvAvSgGlDSmaLllllaklkkk 25
                                      kv++A+SgG DS  L++++++   +
  gi|474933855|ref|YP_007687437.1| 19 KVAIAFSGGCDSSYLFYAAVNCDAD 43
                                      589**************99887655 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.73
                                       HHHHHHHTT---B--CGGGCTT CS
                        ATP_bind_3 152 leeylkekkikwveDesNadek 173
                                       + e +k  + + v D +Na+++
  gi|474933855|ref|YP_007687437.1| 105 IIERAKADGYDLVIDGTNASDD 126
                                       6667888899999999999875 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.1e-05     0.065      19      80 ..      18      77 ..       3      93 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.1e-05
                                      SEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--.SSSTTHHHHHHHHHHHHHHTSEEEE-- CS
                      NAD_synthase 19 kgvvlGlSGGvDSslvaalavkalgkenvlalllP.ssvsseedvedalalaenlgievktid 80
                                       +v +  SGG DSs        a++ +  +a+++  s++++e++++dal  a +lg   k+i+
  gi|474933855|ref|YP_007687437.1| 18 PKVAIAFSGGCDSSYLF---YAAVNCDADVAVYFFsSQFQPEHECHDALRTALQLGRPLKVIE 77
                                      4788999******9655...5555566777887776999****************99888776 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0     3e-05      0.18      17      73 ..      17      72 ..      10     123 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3e-05
                      Asn_synthase 17 dvpvGalLSGGlDSSliaalaarqsk.splktFsigfeekgsdeakyakevaehlgte 73
                                        +v++ +SGG DSS++ + a  + +   +  Fs  f  +   e + a ++a +lg +
  gi|474933855|ref|YP_007687437.1| 17 NPKVAIAFSGGCDSSYLFYAAVNCDAdVAVYFFSSQF--QPEHECHDALRTALQLGRP 72
                                      567999****************999855567789999..9999999999999999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1688.79
//
Query:       gi|474933856|ref|YP_007687438.1|  [L=364]
Description: putative transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-19   70.9   0.0    1.6e-19   70.5   0.0    1.2  1  AlbA_2    Putative DNA-binding domain


Domain annotation for each model (and alignments):
>> AlbA_2  Putative DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.5   0.0   8.7e-24   1.6e-19       1     120 [.     206     337 ..     206     339 .. 0.84

  Alignments for each domain:
  == domain 1  score: 70.5 bits;  conditional E-value: 8.7e-24
                            AlbA_2   1 EdellEfKeslgnklkkrers......iakticAfaNsegGtlliGVeDdgkvvGvecsdqeedqlrlelksiikrf 71 
                                       E++ lEfK++l+ +lk+ e++      ++kti+Af+N++gGtlliGV+Ddg++ G+ +++  +  ++++  +++ ++
  gi|474933856|ref|YP_007687438.1| 206 ESSVLEFKSTLRTNLKTGEKDprieraVLKTIVAFLNTKGGTLLIGVSDDGTINGI-DEEAFDGSRDKLTLHLNHLV 281
                                       8999*************9999***********************************.44444444555555566777 PP

                            AlbA_2  72 kpk......vlpdiervelkgkkvlvvkvekskkkp.lyeneegvvyiRrggsskr 120
                                       +++      + + ++ v+++gk v+ v + +s++++ l e+++ ++++R+g ss  
  gi|474933856|ref|YP_007687438.1| 282 ENQigkeyiPYIGYFIVDFDGKGVMRVDCRRSDEPVfLTEKDTYTFFVRSGPSSID 337
                                       7774445655666667********************8889999********99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       820  (0.045736); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2540.01
//
Query:       gi|474933857|ref|YP_007687439.1|  [L=310]
Description: hypothetical protein TALC_00269 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1972.81
//
Query:       gi|474933858|ref|YP_007687440.1|  [L=147]
Description: putative DNA-binding protein with PD1-like DNA-binding motif [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-16   60.7   0.0    1.7e-16   60.5   0.0    1.0  1  DUF296    Plants and Prokaryotes Conserved (PCC) domain


Domain annotation for each model (and alignments):
>> DUF296  Plants and Prokaryotes Conserved (PCC) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.5   0.0   9.3e-21   1.7e-16       1     105 [.       5     125 ..       5     127 .. 0.88

  Alignments for each domain:
  == domain 1  score: 60.5 bits;  conditional E-value: 9.3e-21
                                       TEEEEEE-TTSBHHHHHHHHHHHHT-SSEEEEEEEEEEEEEEEEECTTT...............EE-S-EEEEEEEE CS
                            DUF296   1 rphvlrlepGediveaieefarkrgiraacvlsaiGavsnvtrladgee...............kllgrfeilslsG 62 
                                       r++vl le G+ i +++e+f++++gi+ a++ s++G +++ ++++ g++                ++++ e ++  G
  gi|474933858|ref|YP_007687440.1|   5 RIFVLALESGDPIKATVENFCKDKGISYATF-SVVGGIAEGSTFVAGPAmdggkinepivpivrPITEPSEFTGT-G 79 
                                       689****************************.**********9998888888866555555444444******99.* PP

                                       EEEETT.....EEEEEEEEETTSEEEEEEEEEE.EEEEEEEEEEEEE- CS
                            DUF296  63 tilpdg.....lHlhvslagedgqvvgGhlaegplvaattvevvvaef 105
                                       t++p++     +Hlh+s++++ g+ v G+++ g+++++ t+e+v++e+
  gi|474933858|ref|YP_007687440.1|  80 TVMPSEdgtpvMHLHGSFGRD-GRSVSGCFR-GEAIVWLTMEIVLIEL 125
                                       ****555699**********6.*********.99***********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       203  (0.0113224); expected 358.6 (0.02)
Passed bias filter:                      190  (0.0105974); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 990.05
//
Query:       gi|474933859|ref|YP_007687441.1|  [L=118]
Description: hypothetical protein TALC_00271 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00011   21.5   5.4      0.078   12.4   2.1    2.8  2  zf-ribbon_3     zinc-ribbon domain
    0.00055   19.7   2.4       0.08   12.8   0.1    3.0  3  Rad50_zn_hook   Rad50 zinc hook motif
     0.0011   18.3   3.9     0.0063   15.8   1.0    2.2  2  zf-TFIIB        Transcription factor zinc-finger
     0.0067   16.5   8.3        0.4   10.8   0.1    3.3  3  UPF0547         Uncharacterised protein family UPF0547
     0.0073   16.7  11.1        0.1   13.1   0.5    3.2  3  zf-H2C2_2       Zinc-finger double domain
  ------ inclusion threshold ------
      0.013   15.6  10.7          3    8.0   2.9    3.2  3  zf-CHCC         Zinc-finger domain
      0.025   14.6   0.6      0.025   14.6   0.6    3.0  3  zf-C2H2_6       C2H2-type zinc finger
      0.026   14.2   5.7      0.054   13.2   0.5    2.3  2  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
      0.052   13.2   0.9        2.7    7.7   0.1    2.5  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
      0.056   13.5   8.4       0.26   11.4   8.4    2.2  1  Elf1            Transcription elongation factor Elf1 like
      0.056   13.6   9.8        1.5    9.0   9.8    2.3  1  Zn-ribbon_8     Zinc ribbon domain
      0.066   13.2   6.6       0.35   10.9   6.6    1.9  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.091   13.3  13.2       0.47   11.0   0.5    3.6  3  zf-C2H2         Zinc finger, C2H2 type
       0.17   12.1   6.1        0.4   10.8   6.2    1.6  1  FYVE            FYVE zinc finger
       0.26   12.0   1.7         23    5.9   0.0    2.8  2  zf-WRNIP1_ubi   Werner helicase-interacting protein 1 ubiquit
       0.26   11.6  10.7        1.4    9.2   0.4    2.8  3  zf-Di19         Drought induced 19 protein (Di19), zinc-bindi
       0.28   11.7   0.6       0.28   11.7   0.6    2.4  2  Zn-C2H2_12      Autophagy receptor zinc finger-C2H2 domain
       0.35   11.8   0.7       0.35   11.8   0.7    3.3  3  zf-C2H2_4       C2H2-type zinc finger
       0.38   10.8  10.0        2.5    8.1   3.6    2.5  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
       0.38   10.7   2.6       0.34   10.9   0.8    1.8  2  DUF4428         Domain of unknown function (DUF4428)
       0.41    9.9   2.7        3.3    7.0   2.7    1.9  1  RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
       0.43   10.5   6.7        7.1    6.6   6.7    2.2  1  Prok-RING_1     Prokaryotic RING finger family 1
       0.44   10.4   6.5         10    6.1   0.1    2.3  2  Prok-RING_4     Prokaryotic RING finger family 4
       0.53   10.4   2.0        6.8    6.8   0.3    2.1  2  DUF2614         Zinc-ribbon containing domain
        0.6   10.2   8.1        1.9    8.6   8.1    1.7  1  DZR             Double zinc ribbon
        0.6   10.2   6.9        4.7    7.3   0.7    3.0  3  zf-BED          BED zinc finger
       0.61    9.7   7.6         12    5.5   0.1    3.2  3  Sgf11           Sgf11 (transcriptional regulation protein)
        1.5    9.6   4.0         39    5.0   0.0    2.2  2  FYDLN_acid      Protein of unknown function (FYDLN_acid)
        1.5    8.6   6.4         16    5.4   0.6    2.5  3  zinc_ribbon_5   zinc-ribbon domain
        1.9    8.5   6.8       0.67    9.9   1.8    2.1  2  C1_1            Phorbol esters/diacylglycerol binding domain 
        2.7    7.8   7.0       0.96    9.2   1.8    2.1  2  Ribosomal_S27e  Ribosomal protein S27
        4.6    7.2  11.2        6.1    6.8   0.2    2.2  2  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)


Domain annotation for each model (and alignments):
>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   2.1   0.00014     0.078       4      22 ..      42      63 ..      40      63 .. 0.92
   2 !    9.2   0.1    0.0015      0.82       2      11 ..      72      82 ..      71      85 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                       zf-ribbon_3  4 rCPnCGa.p..lssddnvCpyC 22
                                      +CP CG+     +s++++C+yC
  gi|474933859|ref|YP_007687441.1| 42 KCPVCGKeFslFQSRAVACKYC 63
                                      7*****998877********** PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0015
                       zf-ribbon_3  2 tvrCPnCGa.p 11
                                      +vrCP+C++ +
  gi|474933859|ref|YP_007687441.1| 72 YVRCPYCDSeL 82
                                      79*****9855 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.1   0.00014      0.08      19      30 ..      39      51 ..      33      52 .. 0.78
   2 ?    3.9   0.6     0.084        47      21      30 ..      74      83 ..      66      85 .. 0.90
   3 ?    0.6   0.0      0.89     5e+02      31      46 ..      92     108 ..      90     111 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00014
                                      SE.E-TTT--EE- CS
                     Rad50_zn_hook 19 kg.cCPlCgReld 30
                                      k  +CP+Cg+e++
  gi|474933859|ref|YP_007687441.1| 39 KRfKCPVCGKEFS 51
                                      4459*******96 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.084
                                      E-TTT--EE- CS
                     Rad50_zn_hook 21 cCPlCgReld 30
                                      +CP C++el+
  gi|474933859|ref|YP_007687441.1| 74 RCPYCDSELP 83
                                      8*******96 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.89
                                       HHH.HHHHHHHHHHHHH CS
                     Rad50_zn_hook  31 eeh.rseLikelqskle 46 
                                       +++  ++++++++++  
  gi|474933859|ref|YP_007687441.1|  92 NNKvDQRIMNDYSDEVF 108
                                       5666799******9976 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   1.0   1.1e-05    0.0063       1      24 [.      42      65 ..      42      66 .. 0.97
   2 ?    3.1   0.1       0.1        58       2      12 ..      75      85 ..      74      97 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.1e-05
                          zf-TFIIB  1 kCPkCqdeleeserggveidyCpq 24
                                      kCP+C+ e+  ++++ v ++yCp+
  gi|474933859|ref|YP_007687441.1| 42 KCPVCGKEFSLFQSRAVACKYCPK 65
                                      8*********************97 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.1
                          zf-TFIIB  2 CPkCqdelees 12
                                      CP C +el ++
  gi|474933859|ref|YP_007687441.1| 75 CPYCDSELPIA 85
                                      *****999665 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1     0.015       8.3       9      24 ..      33      50 ..      31      51 .. 0.72
   2 ?    2.2   1.2      0.34   1.9e+02      11      18 ..      57      64 ..      57      73 .. 0.74
   3 !   10.8   0.1   0.00071       0.4       2      13 ..      74      85 ..      74      86 .. 0.94

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.015
                           UPF0547  9 kvPvaaq..fCphCGyvF 24
                                      k++vaa+  +Cp CG +F
  gi|474933859|ref|YP_007687441.1| 33 KLKVAAKrfKCPVCGKEF 50
                                      5677777446****9777 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.34
                           UPF0547 11 PvaaqfCp 18
                                      +va++ Cp
  gi|474933859|ref|YP_007687441.1| 57 AVACKYCP 64
                                      68999996 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00071
                           UPF0547  2 vCPeCeakvPva 13
                                      +CP C++++P+a
  gi|474933859|ref|YP_007687441.1| 74 RCPYCDSELPIA 85
                                      6*********98 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.5   0.00018       0.1      13      25 ..      39      51 ..      36      51 .. 0.91
   2 ?    5.9   0.2     0.033        19      15      25 ..      58      68 ..      54      69 .. 0.81
   3 ?    3.8   0.6      0.15        87      16      21 ..      74      79 ..      71      81 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00018
                         zf-H2C2_2 13 kpyeCplCdkaFk 25
                                      k+++Cp+C+k F+
  gi|474933859|ref|YP_007687441.1| 39 KRFKCPVCGKEFS 51
                                      78********995 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.033
                         zf-H2C2_2 15 yeCplCdkaFk 25
                                      + C++C+ka +
  gi|474933859|ref|YP_007687441.1| 58 VACKYCPKASS 68
                                      67******975 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.15
                         zf-H2C2_2 16 eCplCd 21
                                       Cp+Cd
  gi|474933859|ref|YP_007687441.1| 74 RCPYCD 79
                                      7****8 PP

>> zf-CHCC  Zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.027        15      26      37 .]      39      50 ..      33      50 .. 0.80
   2 ?    5.9   0.1     0.023        13      26      33 ..      56      63 ..      52      66 .. 0.84
   3 ?    8.0   2.9    0.0053         3      26      34 ..      71      79 ..      68      81 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.027
                                      SEEEETTTTEEE CS
                           zf-CHCC 26 gpvdCgYCglrF 37
                                      +  +C+ Cg+ F
  gi|474933859|ref|YP_007687441.1| 39 KRFKCPVCGKEF 50
                                      5669*****998 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.023
                                      SEEEETTT CS
                           zf-CHCC 26 gpvdCgYC 33
                                        v+C+YC
  gi|474933859|ref|YP_007687441.1| 56 RAVACKYC 63
                                      6799**** PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0053
                                      SEEEETTTT CS
                           zf-CHCC 26 gpvdCgYCg 34
                                      ++v+C+YC+
  gi|474933859|ref|YP_007687441.1| 71 EYVRCPYCD 79
                                      69******9 PP

>> zf-C2H2_6  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.6   4.4e-05     0.025       1      15 [.      40      54 ..      40      55 .. 0.86
   2 ?    0.3   0.4       1.3   7.4e+02       4       9 ..      60      65 ..      59      66 .. 0.81
   3 ?    1.6   0.1      0.51   2.9e+02       3       9 ..      74      80 ..      74      83 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.4e-05
                         zf-C2H2_6  1 vheCsvCsksFpslq 15
                                      +++C+vC+k+F+ +q
  gi|474933859|ref|YP_007687441.1| 40 RFKCPVCGKEFSLFQ 54
                                      59*********9776 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.3
                         zf-C2H2_6  4 CsvCsk 9 
                                      C++C k
  gi|474933859|ref|YP_007687441.1| 60 CKYCPK 65
                                      ****55 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.51
                         zf-C2H2_6  3 eCsvCsk 9 
                                      +C++C+ 
  gi|474933859|ref|YP_007687441.1| 74 RCPYCDS 80
                                      7****85 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.5   9.6e-05     0.054       2      23 ..      42      63 ..      41      65 .. 0.95
   2 ?    3.5   0.6       0.1        57      16      23 ..      71      78 ..      66      81 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.6e-05
                                      B-SSS--B----SSS----SSS CS
                    DNA_RNApol_7kD  2 iCgeCgaevslkkgdpiRCkeC 23
                                      +C  Cg+e+sl ++ ++ Ck+C
  gi|474933859|ref|YP_007687441.1| 42 KCPVCGKEFSLFQSRAVACKYC 63
                                      7999****************** PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.1
                                      S----SSS CS
                    DNA_RNApol_7kD 16 dpiRCkeC 23
                                      + +RC +C
  gi|474933859|ref|YP_007687441.1| 71 EYVRCPYC 78
                                      78****** PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1    0.0048       2.7       3      15 ..      41      53 ..      39      56 .. 0.84
   2 ?    3.7   0.1     0.082        46       2      14 ..      72      84 ..      71      87 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0048
                            zf_UBZ  3 ylCerCgkeipes 15
                                      + C+ Cgke++  
  gi|474933859|ref|YP_007687441.1| 41 FKCPVCGKEFSLF 53
                                      89*******9875 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.082
                            zf_UBZ  2 tylCerCgkeipe 14
                                      ++ C+ C++e+p+
  gi|474933859|ref|YP_007687441.1| 72 YVRCPYCDSELPI 84
                                      678*******997 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   8.4   0.00046      0.26      15      75 ..      34     114 ..      24     117 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00046
                              Elf1  15 kkklptkFdCpfCnhe......ksvevkldkkek..iaevsCkvCge......sfetkvnalsepv......DvYsk 71 
                                        k   ++F+Cp+C++e      ++v++k   k +    +v+C +C +      +++ + n++++++      +v+++
  gi|474933859|ref|YP_007687441.1|  34 LKVAAKRFKCPVCGKEfslfqsRAVACKYCPKASsrCEYVRCPYCDSelpiagFITPDNNKVDQRImndysdEVFNR 110
                                       445789********9744444367999986666556999*******9555554222233333333333222236666 PP

                              Elf1  72 wiDa 75 
                                       w D 
  gi|474933859|ref|YP_007687441.1| 111 WADT 114
                                       6665 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   9.8    0.0026       1.5       6      33 ..      41      67 ..      40      83 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0026
                       Zn-ribbon_8  6 YrCeeCghefevlqsisdaplta.CPeCg 33
                                      ++C  Cg+ef  +qs +     + CP+  
  gi|474933859|ref|YP_007687441.1| 41 FKCPVCGKEFSLFQSRA--VACKyCPKAS 67
                                      9*************744..2222255443 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   6.6   0.00062      0.35      64      96 ..      34      67 ..      20      86 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00062
                                      EEEE--EEEETTTS-EEECHHH.HHS-TTTSSS- CS
                              HypA 64 ieevpvkvrCreCgkefeleek.alrCpkCgsad 96
                                      ++    +++C +Cgkef+l ++ a+ C+ C +a+
  gi|474933859|ref|YP_007687441.1| 34 LKVAAKRFKCPVCGKEFSLFQSrAVACKYCPKAS 67
                                      56677899**********7764467566665443 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.5   0.00085      0.47       1      11 [.      41      51 ..      41      52 .. 0.94
   2 ?    5.1   1.5     0.064        36       3      14 ..      60      71 ..      59      74 .. 0.85
   3 ?    4.0   0.3      0.14        79       2       7 ..      74      79 ..      73      95 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00085
                                      EEETTTTEEES CS
                           zf-C2H2  1 ykCpdCgksFk 11
                                      +kCp+Cgk F+
  gi|474933859|ref|YP_007687441.1| 41 FKCPVCGKEFS 51
                                      8********96 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.064
                                      ETTTTEEESSHH CS
                           zf-C2H2  3 CpdCgksFkrks 14
                                      C++C+k  +r +
  gi|474933859|ref|YP_007687441.1| 60 CKYCPKASSRCE 71
                                      ******999876 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.14
                                      EETTTT CS
                           zf-C2H2  2 kCpdCg 7 
                                      +Cp+C+
  gi|474933859|ref|YP_007687441.1| 74 RCPYCD 79
                                      7****9 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   6.2   0.00072       0.4      10      35 ..      41      67 ..      33     104 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00072
                                      SB-TTT--B--SS.S--EE-TTT--EE CS
                              FYVE 10 kkCeiCakkFsll.rrrhhCrlCGkvv 35
                                       kC+ C k+Fsl+ +r   C+ C k+ 
  gi|474933859|ref|YP_007687441.1| 41 FKCPVCGKEFSLFqSRAVACKYCPKAS 67
                                      58********88768999*****8864 PP

>> zf-WRNIP1_ubi  Werner helicase-interacting protein 1 ubiquitin-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.099        55       4       8 ..      42      46 ..      39      49 .. 0.82
   2 ?    5.9   0.0     0.042        23       3      15 ..      73      85 ..      71      88 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.099
                     zf-WRNIP1_ubi  4 qCPvC 8 
                                      +CPvC
  gi|474933859|ref|YP_007687441.1| 42 KCPVC 46
                                      7**** PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.042
                     zf-WRNIP1_ubi  3 vqCPvCqqmmPAA 15
                                      v CP C   +P A
  gi|474933859|ref|YP_007687441.1| 73 VRCPYCDSELPIA 85
                                      99****9999976 PP

>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.4    0.0025       1.4       2      13 ..      40      51 ..      39      56 .. 0.86
   2 ?   -0.7   0.5       3.2   1.8e+03       3      10 ..      58      65 ..      54      73 .. 0.65
   3 ?    8.7   0.2    0.0038       2.1       3      18 ..      73      88 ..      71      90 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0025
                           zf-Di19  2 sftCPyCgkelt 13
                                       f+CP Cgke++
  gi|474933859|ref|YP_007687441.1| 40 RFKCPVCGKEFS 51
                                      69******9986 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 3.2
                           zf-Di19  3 ftCPyCgk 10
                                      ++C yC k
  gi|474933859|ref|YP_007687441.1| 58 VACKYCPK 65
                                      45667765 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0038
                           zf-Di19  3 ftCPyCgkeltvkeLv 18
                                      + CPyC  el  + ++
  gi|474933859|ref|YP_007687441.1| 73 VRCPYCDSELPIAGFI 88
                                      68*****998877776 PP

>> Zn-C2H2_12  Autophagy receptor zinc finger-C2H2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.6    0.0005      0.28       2      12 ..      42      52 ..      42      55 .. 0.90
   2 ?   -0.3   0.2       2.9   1.6e+03       3       7 ..      75      79 ..      74      81 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0005
                        Zn-C2H2_12  2 eCPlCseqFpk 12
                                      +CP+C++ F+ 
  gi|474933859|ref|YP_007687441.1| 42 KCPVCGKEFSL 52
                                      7********95 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 2.9
                        Zn-C2H2_12  3 CPlCs 7 
                                      CP C+
  gi|474933859|ref|YP_007687441.1| 75 CPYCD 79
                                      ****7 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.7   0.00063      0.35       1      11 [.      41      51 ..      41      56 .. 0.87
   2 ?    3.8   1.7      0.24   1.3e+02       2      13 ..      59      70 ..      58      74 .. 0.75
   3 ?    2.7   0.8      0.54     3e+02       2       7 ..      74      79 ..      73      82 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00063
                         zf-C2H2_4  1 fkCpiCgksFs 11
                                      fkCp+Cgk Fs
  gi|474933859|ref|YP_007687441.1| 41 FKCPVCGKEFS 51
                                      8*********6 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.24
                         zf-C2H2_4  2 kCpiCgksFssk 13
                                       C++C+k  s++
  gi|474933859|ref|YP_007687441.1| 59 ACKYCPKASSRC 70
                                      6****9988655 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.54
                         zf-C2H2_4  2 kCpiCg 7 
                                      +Cp+C+
  gi|474933859|ref|YP_007687441.1| 74 RCPYCD 79
                                      7****4 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   3.6    0.0045       2.5      17      43 ..      39      63 ..      37      69 .. 0.74
   2 ?    6.1   0.5     0.019        11      19      27 ..      73      81 ..      67      91 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0045
                     Zn_Tnp_IS1595 17 ngfvCPhCgsr.kayriktrglfqCkeC 43
                                       +f CP Cg++ ++++ +      Ck C
  gi|474933859|ref|YP_007687441.1| 39 KRFKCPVCGKEfSLFQSR---AVACKYC 63
                                      5799*****874444444...5888888 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.019
                     Zn_Tnp_IS1595 19 fvCPhCgsr 27
                                      ++CP+C s+
  gi|474933859|ref|YP_007687441.1| 73 VRCPYCDSE 81
                                      68*****98 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.8   0.00061      0.34       1      16 [.      42      57 ..      42      66 .. 0.84
   2 ?   -1.8   0.0       5.3     3e+03       2      11 ..      75      84 ..      74      94 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00061
                           DUF4428  1 iCaiCgkKigllkrlk 16
                                      +C++Cgk+ +l+ + +
  gi|474933859|ref|YP_007687441.1| 42 KCPVCGKEFSLFQSRA 57
                                      7***********9755 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 5.3
                           DUF4428  2 CaiCgkKigl 11
                                      C+ C+ ++++
  gi|474933859|ref|YP_007687441.1| 75 CPYCDSELPI 84
                                      7777776654 PP

>> RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   2.7    0.0058       3.3      40      66 ..      26      62 ..      19     103 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0058
                                      BSSSSSSSSS-SSSSSTSTTTSSTTT..........T CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxx..........x RF
                    RNA_pol_Rpb1_1 40 egGllDerlgtidkdleCetCgkkkk..........e 66
                                      ++  +D++l + +k+++C +Cgk+++          +
  gi|474933859|ref|YP_007687441.1| 26 RQAGIDPKLKVAAKRFKCPVCGKEFSlfqsravackY 62
                                      456689*****************99877777775552 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   6.7     0.013       7.1       4      27 ..      40      64 ..      37      85 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.013
                       Prok-RING_1  4 gkkCpvCgkelke.edDiVvCpeCg 27
                                        kCpvCgke++  ++ +V C  C 
  gi|474933859|ref|YP_007687441.1| 40 RFKCPVCGKEFSLfQSRAVACKYCP 64
                                      569********96357899999995 PP

>> Prok-RING_4  Prokaryotic RING finger family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1     0.018        10      32      40 ..      42      50 ..      34      54 .. 0.79
   2 ?    5.1   3.4     0.036        20      21      40 ..      60      82 ..      57      85 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.018
                       Prok-RING_4 32 sCPlCqrri 40
                                       CP+C +++
  gi|474933859|ref|YP_007687441.1| 42 KCPVCGKEF 50
                                      7*****997 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.036
                       Prok-RING_4 21 CkeCfdsk...dlssCPlCqrri 40
                                      Ck C +++   ++ +CP C +++
  gi|474933859|ref|YP_007687441.1| 60 CKYCPKASsrcEYVRCPYCDSEL 82
                                      88888777544777*****9986 PP

>> DUF2614  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.3     0.012       6.8      65      90 ..      38      64 ..      32      66 .. 0.81
   2 ?    3.8   0.1      0.11        61      62      81 ..      67      86 ..      64     117 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.012
                           DUF2614 65 avqvvcpeceketkvl.Grvdlcmhcd 90
                                      a + +cp c+ke  ++  r+ +c +c 
  gi|474933859|ref|YP_007687441.1| 38 AKRFKCPVCGKEFSLFqSRAVACKYCP 64
                                      55689******9987637999*****6 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.11
                           DUF2614 62 stkavqvvcpeceketkvlG 81
                                      s+++  v+cp c+ e  + G
  gi|474933859|ref|YP_007687441.1| 67 SSRCEYVRCPYCDSELPIAG 86
                                      889999******99877766 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   8.1    0.0033       1.9       1      38 [.      43      82 ..      37      86 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0033
                               DZR  1 CpqCgee...lppdarfCseCgtklkavaaedrCpsCgekv 38
                                      Cp Cg+e    +++a  C++C ++ +   +  rCp C++++
  gi|474933859|ref|YP_007687441.1| 43 CPVCGKEfslFQSRAVACKYCPKASS-RCEYVRCPYCDSEL 82
                                      88898888878888888888888875.45588999998876 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0      0.09        51      14      27 ..      38      51 ..      32      52 .. 0.85
   2 ?    7.3   0.7    0.0084       4.7      16      28 ..      57      69 ..      53      72 .. 0.86
   3 ?    0.8   0.5      0.91   5.1e+02      17      24 ..      73      80 ..      70      84 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.09
                                      SS--EETTTTEE-- CS
                            zf-BED 14 eqkavCryCgkils 27
                                       ++ +C  Cgk++s
  gi|474933859|ref|YP_007687441.1| 38 AKRFKCPVCGKEFS 51
                                      57899******987 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0084
                                      --EETTTTEE--- CS
                            zf-BED 16 kavCryCgkilsr 28
                                       + C+yC k +sr
  gi|474933859|ref|YP_007687441.1| 57 AVACKYCPKASSR 69
                                      689*******998 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.91
                                      -EETTTTE CS
                            zf-BED 17 avCryCgk 24
                                      ++C yC  
  gi|474933859|ref|YP_007687441.1| 73 VRCPYCDS 80
                                      89****76 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.022        12       4      13 ..      40      49 ..      37      51 .. 0.84
   2 ?    2.1   0.1      0.26   1.4e+02       2      12 ..      55      65 ..      54      68 .. 0.84
   3 ?    5.3   0.5     0.025        14       3      11 ..      71      79 ..      69      87 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.022
                                      EEE-TTTSSE CS
                             Sgf11  4 yvtCpnCgRq 13
                                       ++Cp Cg++
  gi|474933859|ref|YP_007687441.1| 40 RFKCPVCGKE 49
                                      599*****86 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.26
                                      C-EEE-TTTSS CS
                             Sgf11  2 seyvtCpnCgR 12
                                      s+ v C++C +
  gi|474933859|ref|YP_007687441.1| 55 SRAVACKYCPK 65
                                      67899****86 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.025
                                      -EEE-TTTS CS
                             Sgf11  3 eyvtCpnCg 11
                                      eyv+Cp+C+
  gi|474933859|ref|YP_007687441.1| 71 EYVRCPYCD 79
                                      79******7 PP

>> FYDLN_acid  Protein of unknown function (FYDLN_acid)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   2.2     0.084        47       9      34 ..      39      65 ..      32      73 .. 0.79
   2 ?    5.0   0.0     0.069        39      27      44 ..      73      90 ..      68     113 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.084
                        FYDLN_acid  9 Kr.iCpscgakFYDLnkdPivcpkcge 34
                                      Kr  Cp cg+ F  ++ + + c +c +
  gi|474933859|ref|YP_007687441.1| 39 KRfKCPVCGKEFSLFQSRAVACKYCPK 65
                                      663599999999999999999999966 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.069
                        FYDLN_acid 27 ivcpkcgeefepeevlks 44
                                      + cp+c++e +++ + + 
  gi|474933859|ref|YP_007687441.1| 73 VRCPYCDSELPIAGFITP 90
                                      68*********9988433 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.6     0.028        16      18      35 ..      33      50 ..      31      52 .. 0.67
   2 ?    4.1   2.7     0.071        40       3      18 ..      41      56 ..      39      65 .. 0.84
   3 ?    5.0   0.0     0.035        20       3      11 ..      73      81 ..      72      85 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.028
                     zinc_ribbon_5 18 klKksgkkVrCakCaevF 35
                                      klK+  k+ +C  C++ F
  gi|474933859|ref|YP_007687441.1| 33 KLKVAAKRFKCPVCGKEF 50
                                      677777777777777544 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.071
                     zinc_ribbon_5  3 irCpdCdtkFklvdsk 18
                                       +Cp C+  F l +s+
  gi|474933859|ref|YP_007687441.1| 41 FKCPVCGKEFSLFQSR 56
                                      68********998886 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.035
                     zinc_ribbon_5  3 irCpdCdtk 11
                                      +rCp Cd+ 
  gi|474933859|ref|YP_007687441.1| 73 VRCPYCDSE 81
                                      69****985 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.8    0.0012      0.67      12      35 ..      41      64 ..      34      69 .. 0.88
   2 ?    1.3   0.2      0.59   3.3e+02      12      21 ..      73      82 ..      65      92 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0012
                                      -B-TTT-SB--SSSS-EEEETTT- CS
                              C1_1 12 tfCkhCgeflwgkekqglkCswCk 35
                                       +C  Cg+ ++ + +++++C+ C 
  gi|474933859|ref|YP_007687441.1| 41 FKCPVCGKEFSLFQSRAVACKYCP 64
                                      58********77***********6 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.59
                                      -B-TTT-SB- CS
                              C1_1 12 tfCkhCgefl 21
                                       +C +C++ l
  gi|474933859|ref|YP_007687441.1| 73 VRCPYCDSEL 82
                                      6899999887 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   1.8    0.0017      0.96       8      34 ..      41      65 ..      39      68 .. 0.88
   2 ?    1.4   0.3      0.48   2.7e+02       8      15 ..      73      80 ..      66      84 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0017
                                      EE-TTTS-EEEEESS-SS-EEESSSTC CS
                    Ribosomal_S27e  8 vkCpdCenetvvFshaatvvkCisCgk 34
                                       kCp C++e   F++  ++v C  C k
  gi|474933859|ref|YP_007687441.1| 41 FKCPVCGKEFSLFQS--RAVACKYCPK 65
                                      69***********85..889****976 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.48
                                      EE-TTTS- CS
                    Ribosomal_S27e  8 vkCpdCen 15
                                      v+Cp C  
  gi|474933859|ref|YP_007687441.1| 73 VRCPYCDS 80
                                      77888865 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.2     0.011       6.1      35      47 ..      38      50 ..      33      53 .. 0.75
   2 ?    3.2   6.2      0.15        82      24      46 ..      58      81 ..      54      83 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.011
                                      HTT-B-TTT--B- CS
                        zf-C3HC4_3 35 krkkkCpiCrrpi 47
                                      +++ kCp+C ++ 
  gi|474933859|ref|YP_007687441.1| 38 AKRFKCPVCGKEF 50
                                      47789****9876 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.15
                                      EE-HHHHHHHHH.TT-B-TTT--B CS
                        zf-C3HC4_3 24 vlCeeCaekllk.rkkkCpiCrrp 46
                                      v+C+ C +   + +  +Cp+C ++
  gi|474933859|ref|YP_007687441.1| 58 VACKYCPKASSRcEYVRCPYCDSE 81
                                      68999*999988999******876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        38  (0.00211947); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              32  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 756.12
//
Query:       gi|474933860|ref|YP_007687442.1|  [L=246]
Description: geranylgeranylglyceryl phosphate synthase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-57  193.9   0.2    3.1e-57  193.6   0.2    1.0  1  PcrB            PcrB family
    3.4e-08   33.2   0.1      6e-08   32.4   0.1    1.4  1  His_biosynth    Histidine biosynthesis protein
    4.8e-07   29.3   1.8    2.4e-06   27.0   0.6    2.1  2  ThiG            Thiazole biosynthesis protein ThiG
    8.2e-06   24.9   1.2    5.8e-05   22.1   0.6    2.1  2  Trp_syntA       Tryptophan synthase alpha chain
    2.5e-05   23.7   0.1    4.7e-05   22.9   0.1    1.4  1  G3P_antiterm    Glycerol-3-phosphate responsive antiterminato
    3.7e-05   23.0   0.1     0.0002   20.6   0.0    1.9  2  Dus             Dihydrouridine synthase (Dus)
    0.00011   21.5   0.3    0.00028   20.1   0.1    1.8  2  NanE            Putative N-acetylmannosamine-6-phosphate epim
    0.00017   21.0   0.2    0.00042   19.7   0.1    1.7  2  TMP-TENI        Thiamine monophosphate synthase
     0.0007   18.7   0.1       0.01   14.9   0.0    2.0  2  IMPDH           IMP dehydrogenase / GMP reductase domain
    0.00078   18.6   0.1     0.0013   17.9   0.0    1.3  2  FMN_dh          FMN-dependent dehydrogenase
     0.0031   16.8   1.1     0.0085   15.3   0.3    1.8  2  DHO_dh          Dihydroorotate dehydrogenase
     0.0042   16.5   1.1     0.0042   16.5   1.1    2.2  3  NMO             Nitronate monooxygenase
  ------ inclusion threshold ------
      0.082   12.3   0.1       0.22   10.9   0.0    1.7  2  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
       0.11   11.7   0.2       0.22   10.7   0.1    1.5  2  DUF561          Protein of unknown function (DUF561)
       0.17   12.3   0.2       0.79   10.1   0.1    2.0  2  DUF3280         Protein of unknown function (DUF2380)


Domain annotation for each model (and alignments):
>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.6   0.2   2.6e-60   3.1e-57       7     224 ..      16     241 ..       9     243 .. 0.90

  Alignments for each domain:
  == domain 1  score: 193.6 bits;  conditional E-value: 2.6e-60
                                       S.EEEEE-TTSS-CHHHHHHH....HCTT-SEEEEECSTCHHHHH...HHHHHHHHCTSSS-EEEEESSGGG--TTS CS
                              PcrB   7 r.hltklDPeeenpdEiveiv....iesgtDavmigGsqsvtldn...tvrllkkvsriklPivlepsnvegvvrya 75 
                                         h+t+lDPe+  +dE  + +     e gtDa migGs++vt +n   t+r++k+   ++lP + +ps+++++++++
  gi|474933860|ref|YP_007687442.1|  16 TiHITLLDPEKL-TDETTKSIaarlKEAGTDAFMIGGSTGVTSENlgsTARAIKEA--TGLPTIYFPSDPSAISPEV 89 
                                       26*******984.555555543554799***********99888655489999999..******************* PP

                                       SEEEEEEETTBSSTTTTTHHHHHHHHHHHHHHHCTEEEEEEEEEBTTTSHHHHHTTB-.B-TTHHHHHHHHHHHHHH CS
                              PcrB  76 DalFvmsllnsanadWivgahalglkkvkklieseeilaegYlvvePdskvaavteak.vdlnkediaayallaakl 151
                                       D +F+ms++ns+n+ +i+  ha+    + kl   +e + ++Y++veP+ +v++vte k v+++ ++ a   +laa++
  gi|474933860|ref|YP_007687442.1|  90 DGMFYMSIMNSKNPAFITHFHAKVSPYIAKLG--IECISMAYIIVEPGMTVGRVTESKlVKRDDPQEAVGWALAAQY 164
                                       ********************************..**********************************999****** PP

                                       TT-SEEEEE-.TTSSS-H.HHHHHHHHHHSSSEEEEESS--SHHHHHHHHCC.SSEEEE-CHHHHHH.HCHHHHHHH CS
                              PcrB 152 lglrliYlEa.sGaledv.eevialkkklekarlivGGGirsaEkAkevvea.ADvivvGnvveekd.erkidaile 224
                                       +g++liYlEa sGa ++v  e+i+ +k + ++ livGGGi+ +E+A+   ea AD+iv+G+ ve+ +  + ++a+++
  gi|474933860|ref|YP_007687442.1| 165 MGFQLIYLEAgSGADQPVsPEMIKAVKSVIHIPLIVGGGIHTPEQAQAAREAgADAIVTGTFVEKVSdSSILNAVVK 241
                                       ******************9999*999**************************************9883455677766 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.1     5e-11     6e-08      22     106 ..     143     228 ..     128     244 .. 0.79

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 5e-11
                                       TCEEEETTSHHHHHHHHHHHT-SEEEEEEHHHHC.TTHHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-S CS
                      His_biosynth  22 fqelryagdpvelakryeeegadelhvvDldaak.egreanldlveeiaeevfipvqvGGGIrsledveelleagad 97 
                                       +++l+  +dp e++ +  ++++  + ++ l+a + + +++  ++++++ + ++ip+ vGGGI + e+++++ eagad
  gi|474933860|ref|YP_007687442.1| 143 ESKLVKRDDPQEAVGWALAAQYMGFQLIYLEAGSgADQPVSPEMIKAVKSVIHIPLIVGGGIHTPEQAQAAREAGAD 219
                                       667777788888777777777777777778776648899999*********************************** PP

                                       EEEESHHHH CS
                      His_biosynth  98 kviigtaav 106
                                        ++ gt + 
  gi|474933860|ref|YP_007687442.1| 220 AIVTGTFVE 228
                                       ******743 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.18   2.2e+02     136     154 ..      35      53 ..      29      76 .. 0.67
   2 !   27.0   0.6     2e-09   2.4e-06     161     218 ..     181     238 ..     169     245 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.18
                                       HHHHHHHTT-SEBEEBSSS CS
                              ThiG 136 larrleevGcaavmPlaap 154
                                       +a rl+e+G+ a m  ++ 
  gi|474933860|ref|YP_007687442.1|  35 IAARLKEAGTDAFMIGGST 53 
                                       6788888888888865553 PP

  == domain 2  score: 27.0 bits;  conditional E-value: 2e-09
                                       -S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHH CS
                              ThiG 161 llnkealkiiieeakvPvivDAGigspsdaaqamelGadavllntavaeakdpvamAr 218
                                        +++e++k + + +++P+iv  Gi +p++a +a e Gada++  t v + +d   + +
  gi|474933860|ref|YP_007687442.1| 181 PVSPEMIKAVKSVIHIPLIVGGGIHTPEQAQAAREAGADAIVTGTFVEKVSDSSILNA 238
                                       56799******************************************99999766554 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.12   1.5e+02      16      44 ..      19      50 ..       6      74 .. 0.78
   2 !   22.1   0.6   4.8e-08   5.8e-05     187     233 ..     184     230 ..     174     244 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.12
                                      EETTSS-...HHHHHHHHHHHHHCT-SSEEEE CS
                         Trp_syntA 16 vtagdpd...leqsleilkalekagadviElG 44
                                      +t+ dp+    e++ +i   l++ag+d+  +G
  gi|474933860|ref|YP_007687442.1| 19 ITLLDPEkltDETTKSIAARLKEAGTDAFMIG 50
                                      55666654435778888888999999988776 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 4.8e-08
                                       HHHHHHHHHCTSS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHHHHHH CS
                         Trp_syntA 187 delverlkkltavPvavGFGistkeqvkqva.kvadGvivGSalvkki 233
                                        e+++++k++ + P+ vG Gi+t+eq++++  ++ad+++ G   v+k+
  gi|474933860|ref|YP_007687442.1| 184 PEMIKAVKSVIHIPLIVGGGIHTPEQAQAAReAGADAIVTGT-FVEKV 230
                                       579***************************989999999996.45555 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.1   3.9e-08   4.7e-05     127     168 ..     183     224 ..     180     226 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 3.9e-08
                                       GHHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE- CS
                      G3P_antiterm 127 vpkvikeikkelkipiiaGGLietkedveealkaGaiavsts 168
                                        p++ik++k+ ++ip+i GG i+t e+ ++a +aGa+a+ t+
  gi|474933860|ref|YP_007687442.1| 183 SPEMIKAVKSVIHIPLIVGGGIHTPEQAQAAREAGADAIVTG 224
                                       499************************************996 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0       0.3   3.6e+02     195     213 ..      32      50 ..      28      68 .. 0.77
   2 !   20.6   0.0   1.7e-07    0.0002     167     213 ..     179     224 ..     141     229 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.3
                                       HHHHHHHHHHH--SEEEES CS
                               Dus 195 aedaqaileetGadgvmig 213
                                       ++++ a l+e G d+ mig
  gi|474933860|ref|YP_007687442.1|  32 TKSIAARLKEAGTDAFMIG 50 
                                       4566777777788888877 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 1.7e-07
                                       -CG--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEES CS
                               Dus 167 egtadweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmig 213
                                        +++  e Ik+vk  + ip+i+ G+I ++e+aqa+ e  Gad+++ g
  gi|474933860|ref|YP_007687442.1| 179 DQPVSPEMIKAVKSVIHIPLIVGGGIHTPEQAQAAREA-GADAIVTG 224
                                       45677789*************************99888.*****988 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.3   1.5e+03     158     175 ..      35      52 ..      29      74 .. 0.75
   2 !   20.1   0.1   2.3e-07   0.00028     136     178 ..     186     229 ..     157     244 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.3
                                       HHHHHHTT--SEEEE-HH CS
                              NanE 158 kakkaieiGvdavvvGsa 175
                                        a++  e G da ++G++
  gi|474933860|ref|YP_007687442.1|  35 IAARLKEAGTDAFMIGGS 52 
                                       577788888888888876 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 2.3e-07
                                       HHHHHHHT.T--EEEES---SHHHHHHHHTT--SEEEE-HHHH- CS
                              NanE 136 lvkalsea.glkviaeGrintPekakkaieiGvdavvvGsaitr 178
                                       ++ka+++   + +i+ G i+tPe+a+ a e G+da+v G+ + +
  gi|474933860|ref|YP_007687442.1| 186 MIKAVKSViHIPLIVGGGIHTPEQAQAAREAGADAIVTGTFVEK 229
                                       5666655326789**************************87765 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.7   3.2e+03     151     158 ..      44      51 ..      21      65 .. 0.55
   2 !   19.7   0.1   3.5e-07   0.00042     134     176 ..     179     222 ..     127     231 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.7
                          TMP-TENI 151 iPvvaiGG 158
                                          + iGG
  gi|474933860|ref|YP_007687442.1|  44 TDAFMIGG 51 
                                       33333333 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 3.5e-07
                          TMP-TENI 134 aeplgleglkelaealeiPvvaiGGi.tlenvaevleagadgva 176
                                        +p+  e +k++++ ++iP+++ GGi t+e++++++eagad + 
  gi|474933860|ref|YP_007687442.1| 179 DQPVSPEMIKAVKSVIHIPLIVGGGIhTPEQAQAAREAGADAIV 222
                                       46666666666666666666666666335666666666666553 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.091   1.1e+02     105     142 ..      32      70 ..      27      76 .. 0.63
   2 !   14.9   0.0   8.6e-06      0.01     116     173 ..     166     224 ..     152     230 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.091
                                       HHHHHHHHHHTT-SEEEEE-STSS.SHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                             IMPDH 105 alervkalveagvdvlvvdsahgh.sekvleavkeikkk 142
                                       +++ +++l eag d+ ++  + g  se+  ++ ++ik++
  gi|474933860|ref|YP_007687442.1|  32 TKSIAARLKEAGTDAFMIGGSTGVtSENLGSTARAIKEA 70 
                                       445566777777777777777774145555666666665 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 8.6e-06
                                       T-SEEEEE-STSSSHHHH.HHHHHHHHHTTTSEEEEEEE-SHHHHHHHHHTT-SEEEE- CS
                                       xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 116 gvdvlvvdsahghsekvl.eavkeikkkveeveviaGnvataegakaLieagadavkvG 173
                                       g  ++ +++  g  + v  e++k++k+ ++   +++G + t e+a+a  eagada+  G
  gi|474933860|ref|YP_007687442.1| 166 GFQLIYLEAGSGADQPVSpEMIKAVKSVIHIPLIVGGGIHTPEQAQAAREAGADAIVTG 224
                                       556677777777777664389999*999954446799******************9777 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       3.4   4.1e+03     124     142 ..      31      49 ..      28      72 .. 0.67
   2 !   17.9   0.0     1e-06    0.0013     196     242 ..     175     222 ..     130     225 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3.4
                                       HHHHHHHHHHHCTESEEEE CS
                            FMN_dh 124 lteellkraeaagykalvl 142
                                       +t+++ +r ++ag +a+++
  gi|474933860|ref|YP_007687442.1|  31 TTKSIAARLKEAGTDAFMI 49 
                                       5566666666666666554 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 1e-06
                                       CCHB-TC--HHHHHHHHHHHSSEEEEE.EE-SHHHHHHHHHTTESEEE CS
                            FMN_dh 196 gkqldpsltwddikwlreqtklplvvK.GvltaedakraveaGvdgiv 242
                                       g+  d+ ++ + ik +++  ++pl+v  G+ t+e a+ a eaG+d+iv
  gi|474933860|ref|YP_007687442.1| 175 GSGADQPVSPEMIKAVKSVIHIPLIVGgGIHTPEQAQAAREAGADAIV 222
                                       44458889999***************736******************8 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.43   5.2e+02     172     211 ..      26      64 ..       9      73 .. 0.72
   2 !   15.3   0.3   7.1e-06    0.0085     227     277 ..     180     228 ..     168     242 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.43
                                       SSSHHHHHHHHHHHHHHTECEEEE...BSEE--CTTCCGC CS
                            DHO_dh 172 dltdeekkdiadvllelkldgiivtNttvqrlaidlksek 211
                                        ltde+ k ia+ l+e + d+ +++ +t   +  +l s++
  gi|474933860|ref|YP_007687442.1|  26 KLTDETTKSIAARLKEAGTDAFMIGGSTGVTS-ENLGSTA 64 
                                       48999999999999999999988887776655.3444444 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 7.1e-06
                                       HHHHHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHH CS
                            DHO_dh 227 kdialkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalv 277
                                       ++++ ++i +++++++  ip+I  GGi++ e a    eaGA ++  +t + 
  gi|474933860|ref|YP_007687442.1| 180 QPVSPEMIKAVKSVIH--IPLIVGGGIHTPEQAQAAREAGADAIVTGTFVE 228
                                       689999*********9..**************************9999775 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.9   3.4e+03     151     165 ..      38      52 ..      29      69 .. 0.67
   2 ?    0.1   0.0      0.35   4.2e+02       6      29 ..     123     148 ..     119     174 .. 0.78
   3 !   16.5   1.1   3.5e-06    0.0042     183     230 ..     185     232 ..     166     244 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.9
                               NMO 151 kvearGaDalivqGp 165
                                        + ++G Da+ + G+
  gi|474933860|ref|YP_007687442.1|  38 RLKEAGTDAFMIGGS 52 
                                       456667777776665 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.35
                               NMO   6 ellkikppvvqpgmgg..iskarLaa 29 
                                       e + + +++v pgm +  +++ +L+ 
  gi|474933860|ref|YP_007687442.1| 123 ECISMAYIIVEPGMTVgrVTESKLVK 148
                                       6678899******9877799999985 PP

  == domain 3  score: 16.5 bits;  conditional E-value: 3.5e-06
                               NMO 183 aLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtrfLltke 230
                                       ++++ v++++ iP+i  GGi + ++ +aa  +GA ++  gt     ++
  gi|474933860|ref|YP_007687442.1| 185 EMIKAVKSVIHIPLIVGGGIHTPEQAQAAREAGADAIVTGTFVEKVSD 232
                                       35666777777***************************9996555555 PP

>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       3.8   4.6e+03     180     191 ..      36      47 ..      12      51 .. 0.59
   2 ?   10.9   0.0   0.00019      0.22     157     196 ..     191     226 ..     180     227 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.8
                                       CHHHHHHT--EE CS
                    Ribul_P_3_epim 180 ieqiaeagadvl 191
                                       ++++ eag d++
  gi|474933860|ref|YP_007687442.1|  36 AARLKEAGTDAF 47 
                                       333444555554 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00019
                                       HHHHHHHT---EEEEESS--T.TTCHHHHHHT--EEEESHH CS
                    Ribul_P_3_epim 157 rklidekeldlkievDGGvkl.dnieqiaeagadvlVagsa 196
                                       ++       ++ + v GG+++ ++++++ eagad++V+g+ 
  gi|474933860|ref|YP_007687442.1| 191 KS-----VIHIPLIVGGGIHTpEQAQAAREAGADAIVTGTF 226
                                       33.....3557899*****7527888999*********986 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.9   3.5e+03     136     162 ..      34      60 ..      17      77 .. 0.64
   2 ?   10.7   0.1   0.00018      0.22      49      90 ..     183     226 ..     176     241 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.9
                            DUF561 136 kLakkLeslgvdliqteGkitsiskak 162
                                       ++a +L+++g d     G++   s++ 
  gi|474933860|ref|YP_007687442.1|  34 SIAARLKEAGTDAFMIGGSTGVTSENL 60 
                                       567777777777777777666666544 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00018
                            DUF561  49 dpklvkkvksvsniPiCvsa.ve.akllleavkaGadlveiGnf 90 
                                        p+++k vksv++iP+ v + ++ +++   a  aGad +  G f
  gi|474933860|ref|YP_007687442.1| 183 SPEMIKAVKSVIHIPLIVGGgIHtPEQAQAAREAGADAIVTGTF 226
                                       6899***********999743752677777889****9999987 PP

>> DUF3280  Protein of unknown function (DUF2380)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       1.7   2.1e+03      10      32 ..      21      43 ..      16      68 .. 0.63
   2 ?   10.1   0.1   0.00066      0.79      71      93 ..     210     233 ..     206     244 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.7
                           DUF3280 10 liDtsaepadqtaeearRlaavt 32
                                      l D ++ + ++t++ a+Rl+++ 
  gi|474933860|ref|YP_007687442.1| 21 LLDPEKLTDETTKSIAARLKEAG 43
                                      55555555555555555555543 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00066
                           DUF3280  71 adiArklgAdlvlvg.evqKvSnl 93 
                                       a+ Ar++gAd +++g +v+KvS+ 
  gi|474933860|ref|YP_007687442.1| 210 AQAAREAGADAIVTGtFVEKVSDS 233
                                       789***********9569****75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1500.57
//
Query:       gi|474933861|ref|YP_007687443.1|  [L=275]
Description: 4-hydroxybenzoate polyprenyltransferase-related prenyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-37  128.9  14.9    2.5e-37  128.6  14.9    1.1  1  UbiA      UbiA prenyltransferase family
  ------ inclusion threshold ------
        0.5    9.5  17.0      0.038   13.2  11.9    1.7  2  CitMHS    Citrate transporter


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.6  14.9   2.8e-41   2.5e-37       3     251 ..      26     266 ..      21     267 .. 0.87

  Alignments for each domain:
  == domain 1  score: 128.6 bits;  conditional E-value: 2.8e-41
                              UbiA   3 ipalvglalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllil 79 
                                       i++++++ +      ++  ++l+++ +++++a++n lNdy+D+eiD+    +p+RPlv+G++s++++l+ +i+ l++
  gi|474933861|ref|YP_007687443.1|  26 ITCFIAAGW--DVKDSATEVVLAFFVVFAFIAGGNSLNDYIDVEIDKT--AHPERPLVTGELSRRTGLWCGILGLAA 98 
                                       334433333..3444556799999999*********************..9************************** PP

                              UbiA  80 gllllalllnpltallgllalllyvvYtglrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavfllt 156
                                       +++l+ l++n  ++l++++a++l v+Y  + lK+r+++g+v +++  g+++++g a+v  +    +++l+l+ +l++
  gi|474933861|ref|YP_007687443.1|  99 AIVLA-LFINIISVLVVVIAVILMVAYE-VLLKQRGFVGNVDIAVLTGMVFIFGGAVVDDF--SKVWVLGLLAALVS 171
                                       *****.**********************.9****************************987..79999999999*** PP

                              UbiA 157 waialandlrdregDrkagiktlpvvlGrkaaril.lalllavlllallllllalllllylllalllaalallraar 232
                                       ++  +a+d++d e+D ++ +ktlp  +G+++a+ + +a+++a++ l+ ++ l+  + ++++l ++l+ +++++ a+ 
  gi|474933861|ref|YP_007687443.1| 172 IGREIAKDIEDQESD-EGERKTLPMMIGARKAAAVsAAFFVAGPALS-FIPLINDTFGVLYLTVVLADIIFIYCAVT 246
                                       ***************.8899*************99777778888777.77888888888888888888888999888 PP

                              UbiA 233 lvrrrdakkaakff.lflss 251
                                       ++++ +++++ +++ +f ++
  gi|474933861|ref|YP_007687443.1| 247 VFKDAHKAEKFAKVaMFAAL 266
                                       88877766666555688766 PP

>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.2       0.2   1.8e+03     114     114 ..      43      43 ..      14      61 .. 0.43
   2 ?   13.2  11.9   4.2e-06     0.038      77     180 ..      93     254 ..      78     275 .] 0.62

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.2
                                       x RF
                            CitMHS 114 p 114
                                       +
  gi|474933861|ref|YP_007687443.1|  43 V 43 
                                       1 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 4.2e-06
                                       xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS  77 llvlltallsafvsn.dgvvlimipivlslakrlkklppllliplalaaniggaltpiGtpttraaarpglslpnll 152
                                       +l+l++a++ a++ n   v++++i+++l +a ++  +++ ++ ++ +a  +g  + ++G+    +++++ ++++ +l
  gi|474933861|ref|YP_007687443.1|  93 ILGLAAAIVLALFINiISVLVVVIAVILMVAYEVLLKQRGFVGNVDIAVLTGM-VFIFGGA---VVDDFSKVWVLGL 165
                                       4888888888888887999**************9999999******9999987.6667777...69*********** PP

                                       xxxx.............................................................xxxxxxxxxxxx RF
                            CitMHS 153 llal.............................................................llvgllplvllf 168
                                       l al                                                             l v+l+ +++++
  gi|474933861|ref|YP_007687443.1| 166 LAALvsigreiakdiedqesdegerktlpmmigarkaaavsaaffvagpalsfiplindtfgvlyLTVVLADIIFIY 242
                                       *5554445555555555555555555555444444444444444444444444444455444444444456666666 PP

                                       xxxxxxxxxxxx RF
                            CitMHS 169 mfgvalalpvna 180
                                       ++ ++++ + +a
  gi|474933861|ref|YP_007687443.1| 243 CAVTVFKDAHKA 254
                                       444444433333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1222  (0.0681577); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 1968.08
//
Query:       gi|474933862|ref|YP_007687444.1|  [L=330]
Description: putative DNA modification methylase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-29  103.5   0.0    6.8e-29  101.0   0.0    2.0  1  UPF0020          Putative RNA methylase family UPF0020
    4.6e-07   29.8   0.0    4.9e-05   23.1   0.0    2.1  2  N6_N4_Mtase      DNA methylase
    5.3e-07   29.4   0.0    8.5e-07   28.7   0.0    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    1.1e-06   28.4   0.0    3.1e-06   27.0   0.0    1.6  2  Cons_hypoth95    Conserved hypothetical protein 95
    2.4e-06   28.1   0.0    4.7e-06   27.2   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
    2.7e-06   27.3   0.0    5.7e-06   26.2   0.0    1.5  2  Methyltransf_31  Methyltransferase domain
    1.5e-05   25.1   0.0    5.3e-05   23.4   0.0    1.8  2  THUMP            THUMP domain
    2.2e-05   24.1   0.0    3.5e-05   23.4   0.0    1.3  1  MTS              Methyltransferase small domain
     0.0016   17.8   0.0      0.017   14.4   0.0    2.4  1  N6_Mtase         N-6 DNA Methylase
     0.0019   17.7   0.0     0.0028   17.1   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0051   16.3   0.0          2    7.8   0.0    2.2  2  AviRa            RRNA methyltransferase AviRa
  ------ inclusion threshold ------
      0.012   15.4   0.1       0.12   12.0   0.0    2.0  2  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran
      0.033   14.9   0.0      0.077   13.7   0.0    1.7  1  Methyltransf_12  Methyltransferase domain
      0.036   14.7   0.0      0.081   13.6   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
       0.17   11.2   0.0       0.41    9.9   0.0    1.5  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family


Domain annotation for each model (and alignments):
>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.0   0.0   5.7e-32   6.8e-29       4     173 ..     162     305 ..     160     324 .. 0.92

  Alignments for each domain:
  == domain 1  score: 101.0 bits;  conditional E-value: 5.7e-32
                                       S-SS---SS-HHHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EE CS
                           UPF0020   4 RefngpapLketLAaalvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelkly 80 
                                       R+f+ p +L ++ A+al++l+g+k+g + lDP+CG+G++ IEaa +g +++                          
  gi|474933862|ref|YP_007687444.1| 162 RPFFSPISLHPRYARALINLTGVKRGGTVLDPFCGTGGLVIEAAEMGMRAI-------------------------- 212
                                       99************************************************9.......................... PP

                                       EEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE----------HHHH.HHHHHHHHHHHHHH- CS
                           UPF0020  81 gsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGerlgskkal.ekLYseflrelkrvl 156
                                       +sD+d+++v+g+reN   ++++ l +f++ d+ +++ + +e+d+iv++pPYG+++++ +++ +++Y   l+++ +vl
  gi|474933862|ref|YP_007687444.1| 213 ASDFDPEMVAGTRENMDFYCLA-LHDFETIDVGEIPSRFSEIDAIVCDPPYGRSTKTGGENiDRIYARALEAFPKVL 288
                                       9******************997.679**********9999******************99989************** PP

                                       TT..-EEEEEESSHHHH CS
                           UPF0020 157 rgggrlvlltsenkale 173
                                       + gg++ ++++++++  
  gi|474933862|ref|YP_007687444.1| 289 SAGGKAGVVLPHTMDTP 305
                                       ******99999988754 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   4.1e-08   4.9e-05     182     226 ..     176     221 ..     156     226 .. 0.86
   2 ?    4.6   0.0     0.019        22       1      20 [.     253     271 ..     253     295 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 4.1e-08
                                       HHHH.HHHS-TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSHHHH CS
                       N6_N4_Mtase 182 erlI.klstkkgdivlDpFaGSGtTavaakelgrkfiGieieeeyv 226
                                       + lI +   k g++vlDpF+G+G  +++a+e+g ++i  + ++e v
  gi|474933862|ref|YP_007687444.1| 176 RALInLTGVKRGGTVLDPFCGTGGLVIEAAEMGMRAIASDFDPEMV 221
                                       56663345788**************************999999876 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.019
                                       EEEEEE--SSSSSCS..... CS
                       N6_N4_Mtase   1 vdlivtdpPYntgkdyende 20 
                                       +d iv dpPY+ + + + +e
  gi|474933862|ref|YP_007687444.1| 253 IDAIVCDPPYGRSTK-TGGE 271
                                       799********9999.3333 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   7.1e-10   8.5e-07       3      82 ..     189     263 ..     187     275 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 7.1e-10
                   Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvflSp 79 
                                       ++lD+f+G+GG vi+ a+++ + ia++ ++e +a + +N  +Y      ++ + dv e+ ++  +++i  d +++ p
  gi|474933862|ref|YP_007687444.1| 189 TVLDPFCGTGGLVIEAAEMGMRAIASDFDPEMVAGTRENMDFY-CLALHDFETIDVGEIPSR--FSEI--DAIVCDP 260
                                       69*****************************************.666667777777777654..5666..8899999 PP

                   Methyltransf_15  80 PwG 82 
                                       P G
  gi|474933862|ref|YP_007687444.1| 261 PYG 263
                                       998 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       2.3   2.8e+03      97     127 ..     148     178 ..     137     188 .. 0.81
   2 !   27.0   0.0   2.6e-09   3.1e-06      41     127 ..     186     266 ..     175     283 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.3
                                       EES-HHHHCTS--SS-EEEEEEE--SSSTTC CS
                     Cons_hypoth95  97 kedaleallklakkkeefdivflDPPyakel 127
                                       k+da    ++++++ + f  + l P ya+ l
  gi|474933862|ref|YP_007687444.1| 148 KMDADLLRQRKVSERPFFSPISLHPRYARAL 178
                                       6777777788889999999999999999876 PP

  == domain 2  score: 27.0 bits;  conditional E-value: 2.6e-09
                                       CC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEE CS
                     Cons_hypoth95  41 egarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdiv 117
                                       +g +vLD f+G+G+l +EA+  g  +a++ + d+e+v+  +en++   l    + +   ++ +++++    +e+d +
  gi|474933862|ref|YP_007687444.1| 186 RGGTVLDPFCGTGGLVIEAAEMG-MRAIASDFDPEMVAGTRENMDFYCLA--LHDFETIDVGEIPSR---FSEIDAI 256
                                       5778******************9.5799****************998866..577777777788777...5679*** PP

                                       EE--SSSTTC CS
                     Cons_hypoth95 118 flDPPyakel 127
                                         DPPy ++ 
  gi|474933862|ref|YP_007687444.1| 257 VCDPPYGRST 266
                                       ******9874 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0   3.9e-09   4.7e-06       1      70 [.     190     258 ..     190     292 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 3.9e-09
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvs 70 
                                       vLd  cGtG l++++a+ +   + ++ D+++em++ +re+++   l   +f++ d+ ++p   +++D++v+
  gi|474933862|ref|YP_007687444.1| 190 VLDPFCGTGGLVIEAAEMG--MRAIASDFDPEMVAGTRENMDFYCLaLHDFETIDVGEIPSRFSEIDAIVC 258
                                       89**************995..********************765557889**********9999******9 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       3.9   4.7e+03      93     117 ..      76     103 ..      51     124 .. 0.62
   2 !   26.2   0.0   4.7e-09   5.7e-06       3     101 ..     186     288 ..     184     316 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.9
                   Methyltransf_31  93 ileeiervlkpggilliedpr...llae 117
                                        l  +e+v  p+g ++i+ +r    +++
  gi|474933862|ref|YP_007687444.1|  76 DLSPVESVELPEGTFAIRGYRfegRMKD 103
                                       4556778888888888877774433333 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 4.7e-09
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlil 79 
                                       +g +vlD+ CGtG l++e+a e+g+  + +  D+++e++   ren +   l    Fe  d+ e+++ ++   +D i+
  gi|474933862|ref|YP_007687444.1| 186 RGGTVLDPFCGTGGLVIEAA-EMGM--RAIASDFDPEMVAGTRENMDFYCLALHDFETIDVGEIPSRFS--EIDAIV 257
                                       5779****************.8876..789**************99988888899**********6655..4***** PP

                   Methyltransf_31  80 snevl.........naladpdkileeiervl 101
                                       ++ +          n     + +le  ++vl
  gi|474933862|ref|YP_007687444.1| 258 CDPPYgrstktggeNIDRIYARALEAFPKVL 288
                                       *944333333444433333444444445555 PP

>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   4.4e-08   5.3e-05      82     131 ..      86     134 ..      79     146 .. 0.81
   2 ?   -1.4   0.0       1.9   2.2e+03      58      81 ..     267     290 ..     244     293 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 4.4e-08
                                       CT-EEEEEEEESSSTS.SSHHHHHHHHHHHHHHCCTT-EE-SSS-SEEEEE CS
                             THUMP  82 eketFaVrvkrrgkhf.eftsreinrevGkaivektglkVdlenPdivvrv 131
                                       ++ tFa+r  r   +  +++s++i re G+ + +k    V+l++Pd++vr 
  gi|474933862|ref|YP_007687444.1|  86 PEGTFAIRGYRFEGRMkDVDSQKITREAGAVLSRKND--VNLKEPDLTVRM 134
                                       344****9877666666*****************999..**********85 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.9
                                       EEEESSHHHHHHHHHHHHHHHHHH CS
                             THUMP  58 evceadledileaakeivkkkfee 81 
                                        + ++++++i++ a e++ k + +
  gi|474933862|ref|YP_007687444.1| 267 KTGGENIDRIYARALEAFPKVLSA 290
                                       567889999*99999998777655 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0     3e-08   3.5e-05      25     146 ..     180     305 ..     174     325 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 3e-08
                                       HHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTST.TS-EE CS
                               MTS  25 etlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeve.ekkfd 99 
                                       +    ++ g+vlD  cG+G l +++a++  +    + d d + ++ ++en+    l+  ++ + dv e  +   ++d
  gi|474933862|ref|YP_007687444.1| 180 NLTGVKRGGTVLDPFCGTGGLVIEAAEMGMR--AIASDFDPEMVAGTRENMDFYCLAlHDFETIDVGEIPSrFSEID 254
                                       4445558899***************999888..6789999999*********99999766666677665542369** PP

                                       EEEE---STTTCHCHHHHHHHHHHHH....HHHEEEEEEEEEEEETTSCHH CS
                               MTS 100 livsNPPfhagkatelavaeeliaeA....keaLkegGeLliVanrklgye 146
                                       +iv+ PP+ ++++t  + ++++ a A    +++L+ gG+  +V  + ++ +
  gi|474933862|ref|YP_007687444.1| 255 AIVCDPPYGRSTKTGGENIDRIYARAleafPKVLSAGGKAGVVLPHTMDTP 305
                                       ********9988888777777777663323678999999999988777665 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   1.4e-05     0.017      28     105 ..     164     241 ..     154     302 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.4e-05
                          N6_Mtase  28 ffTPrev....sklivellepksgesvyDpacGsggllvqaekvlkeedgktkelsiyGqeknetty.rLakmNlll 99 
                                       ff P ++     + +++l+  k+g +v+Dp cG+ggl ++a+++     g +   s +  e+ + t+ ++    l+l
  gi|474933862|ref|YP_007687444.1| 164 FFSPISLhpryARALINLTGVKRGGTVLDPFCGTGGLVIEAAEM-----GMRAIASDFDPEMVAGTReNMDFYCLAL 235
                                       66666662211355667779999999**************9985.....3333333344444444431233333445 PP

                          N6_Mtase 100 hgieyk 105
                                       h+ e+ 
  gi|474933862|ref|YP_007687444.1| 236 HDFETI 241
                                       555554 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.4e-06    0.0028     159     232 ..     184     258 ..     173     259 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.4e-06
                              PrmA 159 vkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkvea.klevalseellk.eekadviva 232
                                       vk+g +vlD  +G+G L i aa +g + ++a D D+  v  ++eN+++  ++   +e++  +e+++  +++d iv+
  gi|474933862|ref|YP_007687444.1| 184 VKRGGTVLDPFCGTGGLVIEAAEMGMR-AIASDFDPEMVAGTRENMDFYCLALhDFETIDVGEIPSrFSEIDAIVC 258
                                       78899********************86.6799**************998766656666666777753466777777 PP

>> AviRa  RRNA methyltransferase AviRa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0016         2      47     100 ..     180     229 ..     168     234 .. 0.77
   2 !    6.3   0.0    0.0049       5.9     153     201 ..     240     288 ..     233     308 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0016
                             AviRa  47 ekkeegapltlyDpCCGgayLltvlgllhgkkikkvlasDvdeevlelakkNLs 100
                                       + ++ + + t+ Dp CG++ L+   + +      + +asD+d e+++ +++N++
  gi|474933862|ref|YP_007687444.1| 180 NLTGVKRGGTVLDPFCGTGGLVIEAAEMGM----RAIASDFDPEMVAGTRENMD 229
                                       44556667899********99866655544....4569**************97 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0049
                             AviRa 153 kaditekeeeaekevdivitDlPYGelvswqge.seepvkqlleslaavl 201
                                       ++d+  + ++ ++e+d ++ D PYG  ++  ge  ++  ++ le+  +vl
  gi|474933862|ref|YP_007687444.1| 240 TIDVG-EIPSRFSEIDAIVCDPPYGRSTKTGGEnIDRIYARALEAFPKVL 288
                                       55666.44556667**************9998844555666777776666 PP

>> MethyltransfD12  D12 class N6 adenine-specific DNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0    0.0001      0.12      21      55 ..     187     221 ..     180     229 .. 0.89
   2 ?    0.7   0.0      0.28   3.3e+02     179     196 ..     254     267 ..     248     297 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0001
                                       -SEEEETT-TTSCCHHCS...SSCEEEEES-HHHH CS
                   MethyltransfD12  21 gktfvepFaGggaVffeakkqgkkvlinDinedli 55 
                                       g t+ +pF+G+g + +ea + g +++++D+ ++ +
  gi|474933862|ref|YP_007687444.1| 187 GGTVLDPFCGTGGLVIEAAEMGMRAIASDFDPEMV 221
                                       6789*************************998765 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.28
                                       .EEEE--S-T.S...TS- CS
                   MethyltransfD12 179 divYlDPPYnprqytany 196
                                       d++ +DPPY      ++ 
  gi|474933862|ref|YP_007687444.1| 254 DAIVCDPPYGR----STK 267
                                       45669****86....333 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   6.5e-05     0.077       5      72 ..     195     258 ..     191     293 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.5e-05
                   Methyltransf_12   5 cGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvva 72 
                                       cGtG l+ + +e   + + +++D++p++++ ++e + +++   +++ ++++ ++ ++++    D++v+
  gi|474933862|ref|YP_007687444.1| 195 CGTGGLVIEAAEM--GMRAIASDFDPEMVAGTRENMDFYCLALHDFETIDVGEIPSRFS--EIDAIVC 258
                                       *************..*************************9999999999999888876..8999987 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   6.7e-05     0.081       1      67 [.     191     258 ..     191     260 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.7e-05
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEE CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvs 67 
                                       Ld  cGtG l+ + a+ g+r ++ D+++em++  +e+     l   +f   d+ ++p + + +D++v+
  gi|474933862|ref|YP_007687444.1| 191 LDPFCGTGGLVIEAAEMGMRAIASDFDPEMVAGTRENMDFYCLaLHDFETIDVGEIPSRFSEIDAIVC 258
                                       6677***************************7777776665558568899999999988899999987 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00034      0.41      31      90 ..     170     226 ..     166     256 .. 0.83
   2 ?   -2.2   0.0       1.8   2.2e+03     133     170 ..     278     317 ..     268     327 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00034
                                       THHHHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHH CS
                   Ubie_methyltran  31 ihrlWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgek 90 
                                        h  + + +++l++vkrg +vlD  +Gtg l ++ +   +   + +  D++++m+  +++
  gi|474933862|ref|YP_007687444.1| 170 LHPRYARALINLTGVKRGGTVLDPFCGTGGLVIEAA---EMGMRAIASDFDPEMVAGTRE 226
                                       57778888999*******************988654...445566778888888766555 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.8
                                       HHHHHHHHHHEEEEEEEEEEEE----SHHHHH..HHHHHH CS
                   Ubie_methyltran 133 lkaLkeayrvlkpGGrlvvlefskvelpllsq..ayelys 170
                                        +aL+   +vl +GG+  v+    + +p ++    ye+++
  gi|474933862|ref|YP_007687444.1| 278 ARALEAFPKVLSAGGKAGVVLPHTMDTPFMKRecVYEQFV 317
                                       6788888899999999877766666666665311466665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2208.63
//
Query:       gi|474933863|ref|YP_007687445.1|  [L=314]
Description: DNA repair and recombination protein RadA [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-84  282.5   0.0    3.1e-84  282.2   0.0    1.0  1  Rad51            Rad51
    3.2e-11   43.7   0.9    6.8e-11   42.6   0.9    1.6  1  HHH_5            Helix-hairpin-helix domain
    1.6e-09   37.7   0.1    2.4e-09   37.0   0.1    1.2  1  RecA             recA bacterial DNA recombination protein
    5.3e-07   29.2   0.0    8.5e-07   28.6   0.0    1.3  1  ATPase           KaiC
    4.2e-06   26.9   0.0    7.5e-06   26.1   0.0    1.4  1  Cdd1             Pathogenicity locus
    0.00046   19.9   2.6      0.031   14.2   0.2    2.5  2  HHH              Helix-hairpin-helix motif
    0.00062   19.8   0.1     0.0017   18.4   0.1    1.8  1  HHH_2            Helix-hairpin-helix motif
    0.00082   19.1   0.0     0.0096   15.7   0.0    2.4  2  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
     0.0038   17.6   0.5      0.016   15.6   0.0    2.2  3  BAF              Barrier to autointegration factor
  ------ inclusion threshold ------
      0.016   15.5   0.0      0.047   14.0   0.0    1.9  1  IMS_HHH          IMS family HHH motif
      0.037   14.4   0.0       0.11   12.9   0.0    1.8  1  HHH_8            Helix-hairpin-helix domain
       0.14   12.6   0.0       0.27   11.7   0.0    1.5  1  HhH-GPD          HhH-GPD superfamily base excision DNA repair


Domain annotation for each model (and alignments):
>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  282.2   0.0     2e-87   3.1e-84       2     254 ..      65     313 ..      64     314 .] 0.99

  Alignments for each domain:
  == domain 1  score: 282.2 bits;  conditional E-value: 2e-87
                                       S-EBHHHHHHHHHSS-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEE CS
                             Rad51   2 gfvsavellekrsellqlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyid 78 
                                       gf ++ ++l++r+++ +lttGsk++DelLgGGie+++ite +Gef+s ktq+c +l+v + +p + gG ++ ++ id
  gi|474933863|ref|YP_007687445.1|  65 GFETGDSILQRRESVTKLTTGSKAFDELLGGGIESQAITEFYGEFGSCKTQVCFQLAVNATMPEDRGGLDSDVIIID 141
                                       799999*********************************************************************** PP

                                       SSS---GGGGHHHHHHTT--HHHHGGGEEEEE--STTHHHHHHHHTHHHHHHS-EEEEEEETTTGGGCH-------T CS
                             Rad51  79 tegtfrperlveiaerykldkeevlenvayaRaytiehqeellqqaaallaedkfallivDsvtalyRtdfsgrgel 155
                                       +e tfrper+v++a+  ++d++++l+++ +aRa++++hq  l+++a  l ++ k++llivDs+t+++R+++ grg l
  gi|474933863|ref|YP_007687445.1| 142 SENTFRPERIVQMANYLGVDPDATLKRIHVARAFNSQHQVLLVDKANDLAKNLKVRLLIVDSLTSHFRSEYLGRGAL 218
                                       ***************99************************************************************ PP

                                       HHHHHHHHHHHHHHHHHHHHH--EEEEEEE-------.------------HHHHHHHH-SEEEEEEE-STTEEEEEE CS
                             Rad51 156 akRqqklgkllrtLrkladefevavvitnqvvaqvdgqaalfsadpkkPigGlvlahasttRlalrkgkgeeRivkv 232
                                       a+Rqq l+k+++ L  +a   ++a+ +tnqv a++d+    f +dp++PigG +++h+st R++lrkgk  +Ri+++
  gi|474933863|ref|YP_007687445.1| 219 AERQQILNKHMHDLLSFATINNAAIAVTNQVAAKPDA----FFGDPMRPIGGSIVGHTSTFRIYLRKGKAGKRIARL 291
                                       *************************************....99********************************** PP

                                       ES-SSS-S-EEEEEEETTEEE- CS
                             Rad51 233 vdsPnlpeleavfaigeeGied 254
                                       vdsPn+pe eavf+++e+Gi+d
  gi|474933863|ref|YP_007687445.1| 292 VDSPNMPEGEAVFMVTEDGIKD 313
                                       ********************98 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.9   4.6e-14   6.8e-11       2      56 ..       4      58 ..       3      59 .. 0.97

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 4.6e-14
                                      HHHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHH CS
                             HHH_5  2 eeLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilelk 56
                                      + L +++G+Gp++A +l +aG++   ++a a++++La++  iG+k+A+ ii+ +k
  gi|474933863|ref|YP_007687445.1|  4 KTLEDIPGVGPAIAEKLREAGYSDMMKIAVAAPADLAEACEIGEKKAQDIIEGAK 58
                                      6799************************************************987 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.1   1.6e-12   2.4e-09      28     225 ..      76     285 ..      67     294 .. 0.80

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 1.6e-12
                                       -----EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHH...HHTT--...EEEEESS----H... CS
                              RecA  28 klkvetissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaea...qkkggv...aafidaehaldp... 95 
                                       +++v  +++Gs a+d  lG GG+    i+e yG   s kt +++++ ++a   + +gg+   +  id+e ++ p   
  gi|474933863|ref|YP_007687445.1|  76 RESVTKLTTGSKAFDELLG-GGIESQAITEFYGEFGSCKTQVCFQLAVNAtmpEDRGGLdsdVIIIDSENTFRPeri 151
                                       578999*************.*********************998876655223456775444789*******98333 PP

                                       .HHHHHTT--GGG-E....EE--SSHH.HHH..HHHHHHHTTT--SEEEEE-TTT---STT-----------HHHHH CS
                              RecA  96 .kyakklGvdidell....vsqpdtGe.qal..eiadalvrsgaidlivvdsvaalvpkaeieGemgdskvglqarl 164
                                        + a+ lGvd d  l    v++  + + q l  + a+ l +   + l++vds+++   ++e    +g   ++ + ++
  gi|474933863|ref|YP_007687445.1| 152 vQMANYLGVDPDATLkrihVARAFNSQhQVLlvDKANDLAKNLKVRLLIVDSLTSHF-RSEY---LGRGALAERQQI 224
                                       347999***976543222288776554155423557789*************98865.5554...566778888899 PP

                                       HHHHHHHHHHHHTTT--EEEEEEE-----------------HHHHHHH-SEEEEEEEES-- CS
                              RecA 165 msqalrkltgaisksntvvifinqirekiGvmfgnpetttGGralkfyasvrldvrrieei 225
                                       + + +  l +  + +n+++   nq+  k    fg+p    GG  +   ++ r+ +r+ ++ 
  gi|474933863|ref|YP_007687445.1| 225 LNKHMHDLLSFATINNAAIAVTNQVAAKPDAFFGDPMRPIGGSIVGHTSTFRIYLRKGKAG 285
                                       9*********99999*****************************************97765 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   5.7e-10   8.5e-07       2     137 ..      83     211 ..      82     248 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 5.7e-10
                            ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgv.....fvtveepa..edlrenakslG 71 
                                        tg + +De+l gGi +++++  +Ge G+ Kt ++ q +++  +  ++ g+     ++  e +   e + + a+ lG
  gi|474933863|ref|YP_007687445.1|  83 TTGSKAFDELLGGGIESQAITEFYGEFGSCKTQVCFQLAVNATMPEDRGGLdsdviIIDSENTFrpERIVQMANYLG 159
                                       6999*************************************9988766554333105555554377*********** PP

                            ATPase  72 wdlekleeegklaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitglayeeke 137
                                       +d ++  ++  + +  a++s+++            l+++ ++  k++k++ +++Ds+t++    +e
  gi|474933863|ref|YP_007687445.1| 160 VDPDATLKR--IHVARAFNSQHQ----------VLLVDKANDLAKNLKVRLLIVDSLTSH--FRSE 211
                                       ********9..888888888655..........568899999999999999999999998..3344 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   5.1e-09   7.5e-06       6      54 ..       4      52 ..       1      54 [. 0.91

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 5.1e-09
                              Cdd1  6 kelqdiPniGkalaedlvelGirsveelkgedpeelyeklekltgarhD 54
                                      k+l+diP++G+a+ae+l+e G++++ +++   p++l e++e   ++ +D
  gi|474933863|ref|YP_007687445.1|  4 KTLEDIPGVGPAIAEKLREAGYSDMMKIAVAAPADLAEACEIGEKKAQD 52
                                      789**********************************999877776666 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.2   2.1e-05     0.031      11      29 ..       4      22 ..       2      23 .. 0.88
   2 ?    5.6   0.2      0.01        15       8      29 ..      34      55 ..      30      56 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.1e-05
                                      HHHHTSTT-SHHHHHHHHH CS
                               HHH 11 eeLlalPGVGpktAeaIls 29
                                      + L+++PGVGp+ Ae+ ++
  gi|474933863|ref|YP_007687445.1|  4 KTLEDIPGVGPAIAEKLRE 22
                                      679************9875 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.01
                                      SSHHHHHTSTT-SHHHHHHHHH CS
                               HHH  8 asreeLlalPGVGpktAeaIls 29
                                      a +++L++   +G+k+A+ I++
  gi|474933863|ref|YP_007687445.1| 34 AAPADLAEACEIGEKKAQDIIE 55
                                      66667777778*********86 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   1.2e-06    0.0017       8      53 ..       9      55 ..       5      56 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.2e-06
                             HHH_2  8 IrhVGektAklLakr.FksldaLkkasleeLlevddiGeeiAqsive 53
                                      I+ VG + A++L ++ + ++ +++ a   +L+e  +iGe+ Aq+i+e
  gi|474933863|ref|YP_007687445.1|  9 IPGVGPAIAEKLREAgYSDMMKIAVAAPADLAEACEIGEKKAQDIIE 55
                                      9***********9866****************************986 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   6.4e-06    0.0096       2      42 ..       5      46 ..       4      53 .. 0.83
   2 ?    0.4   0.0       0.4     6e+02      32      49 ..     215     232 ..     202     233 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.4e-06
                   DNA_pol_lambd_f  2 lFtkvyGVGpktAkkwyakGirtledlra.krakLtreqqiG 42
                                      ++  + GVGp++A+k+ ++G+ ++  +    +a+L ++  iG
  gi|474933863|ref|YP_007687445.1|  5 TLEDIPGVGPAIAEKLREAGYSDMMKIAVaAPADLAEACEIG 46
                                      6889******************99998876668888888887 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.4
                   DNA_pol_lambd_f  32 rakLtreqqiGlkyyeDl 49 
                                       r  L + qqi  k+ +Dl
  gi|474933863|ref|YP_007687445.1| 215 RGALAERQQILNKHMHDL 232
                                       5678999***9******8 PP

>> BAF  Barrier to autointegration factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.1e-05     0.016      15      42 ..       1      28 [.       1      33 [. 0.91
   2 ?   -2.9   0.0       6.6   9.8e+03      63      79 ..      39      55 ..      38      58 .. 0.75
   3 ?   -1.9   0.0       3.1   4.7e+03      33      60 ..     182     209 ..     167     226 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
                               BAF 15 mgdKevtalaGigevlgkkLeekGfdkA 42
                                      m +K+ ++++G+g+ +++kL+e+G++  
  gi|474933863|ref|YP_007687445.1|  1 MAEKTLEDIPGVGPAIAEKLREAGYSDM 28
                                      89***********************865 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.6
                               BAF 63 lketvganskqakdcye 79
                                      l e++++ +k+a+d++e
  gi|474933863|ref|YP_007687445.1| 39 LAEACEIGEKKAQDIIE 55
                                      56778888888888776 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 3.1
                               BAF  33 kLeekGfdkAyvvlgqfLvlkkdeelFk 60 
                                        L +k  d A+++  + L+++  +++F+
  gi|474933863|ref|YP_007687445.1| 182 LLVDKANDLAKNLKVRLLIVDSLTSHFR 209
                                       5677777888888888888888777775 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.1e-05     0.047      12      31 ..       5      24 ..       1      25 [. 0.86

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.1e-05
                           IMS_HHH 12 pitkipGiGgklgekLeklG 31
                                       + +ipG+G+  +ekL+  G
  gi|474933863|ref|YP_007687445.1|  5 TLEDIPGVGPAIAEKLREAG 24
                                      589*************9887 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.5e-05      0.11      47      65 ..       4      22 ..       1      23 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.5e-05
                                      THCTTSTT--HHHHHHHHH CS
                             HHH_8 47 eeltklpgiGkkiaakiee 65
                                      ++l+++pg+G++ia+k++e
  gi|474933863|ref|YP_007687445.1|  4 KTLEDIPGVGPAIAEKLRE 22
                                      3699*************99 PP

>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00018      0.27      17      67 ..      16     123 ..      13     198 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00018
                                       HHHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH........................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................... RF
                           HhH-GPD  17 iierlferfgfptpedladadeekLrelirelGfyrrKakyikelArilv........................... 66 
                                       i e+l+e+ g  +  ++a a++++L+e+   +  +++Ka+ i+e A+ ++                           
  gi|474933863|ref|YP_007687445.1|  16 IAEKLREA-GYSDMMKIAVAAPADLAEA---CEIGEKKAQDIIEGAKLCAdiggfetgdsilqrresvtklttgska 88 
                                       66777777.6889999************...9***************999888888888888777777776666666 PP

                                       ..................................S CS
                                       ..................................x RF
                           HhH-GPD  67 ..................................g 67 
                                                                         +
  gi|474933863|ref|YP_007687445.1|  89 fdellgggiesqaitefygefgscktqvcfqlavN 123
                                       66666666666666666666666555555555550 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 1863.18
//
Query:       gi|474933864|ref|YP_007687446.1|  [L=123]
Description: hypothetical protein TALC_00276 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1287  (0.0717831); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 744.14
//
Query:       gi|474933865|ref|YP_007687447.1|  [L=442]
Description: CCA-adding enzyme [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.5e-39  132.7   0.0    1.3e-38  131.7   0.0    1.6  1  tRNA_NucTransf2  tRNA nucleotidyltransferase, second domain
      1e-11   45.0   0.1    2.2e-11   43.9   0.1    1.6  1  NTP_transf_2     Nucleotidyltransferase domain


Domain annotation for each model (and alignments):
>> tRNA_NucTransf2  tRNA nucleotidyltransferase, second domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.7   0.0   1.5e-42   1.3e-38       1     113 []     148     258 ..     148     258 .. 0.96

  Alignments for each domain:
  == domain 1  score: 131.7 bits;  conditional E-value: 1.5e-42
                                       HHHHHHHHHHHHTT-BSSSTTT-SB-HHHHHHHHHHHSSHHHHHHHHTT.--TTEEEE......EEE..-SS-EEEE CS
                   tRNA_NucTransf2   1 devrllKkflkgigvYGselkvkGfsGYlaEllvleygsfeevleaaak.wkpkvvidleekeallkkfdeplvviD 76 
                                       d+vrllKkf+kgig+YG+e +++GfsGYl+Ellv+++gsf+ vleaaa  w+++++i++e +      +  plvv+D
  gi|474933865|ref|YP_007687447.1| 148 DQVRLLKKFMKGIGTYGAEPNTRGFSGYLCELLVMKFGSFDGVLEAAAGgWREGTTIEIEARGP---PMIGPLVVYD 221
                                       79*******************************************99877*******9888877...7889****** PP

                                       TTEEEEETTTTS-HHHHHHHHHHHHHHHHS--GGGGS CS
                   tRNA_NucTransf2  77 PvDpkRNvaaalsleklaefilaareflkkpseefff 113
                                       PvD+kRNva+a++l++la fi+aa+++l+ p+ +fff
  gi|474933865|ref|YP_007687447.1| 222 PVDKKRNVASAVHLDTLALFIVAAKDYLRGPDARFFF 258
                                       ***********************************96 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.1   2.5e-15   2.2e-11       6      94 ..      34     133 ..      28     134 .. 0.93

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 2.5e-15
                                       HHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHH...........HHHEHHHHHHHHCCCEEECTTEEE CS
                      NTP_transf_2   6 eelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsre...........kkeegleklaeiikfleellglev 71 
                                       + l +++ +a++  +GS+ ++t+l++ DiDl+ ++p+ ++++           +   g++ ++e+++     +g+ v
  gi|474933865|ref|YP_007687447.1|  34 KYLDDNSIDAELRFVGSFSKDTYLSDPDIDLFMLFPSATPKSeveriglqvgeDLLHGERMYSEHPYTRGVWKGVDV 110
                                       56667777******************************9999***********888999****************** PP

                                       EEECEEECCCCTEEEEEECEEEH CS
                      NTP_transf_2  72 dlvtrekledpllvksileerpl 94 
                                       dlv+ +kl+d+++  s+++++p+
  gi|474933865|ref|YP_007687447.1| 111 DLVPSYKLKDTEKLQSAVDRTPF 133
                                       *****************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 3019.87
//
Query:       gi|474933866|ref|YP_007687448.1|  [L=149]
Description: hypothetical protein TALC_00278 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.2e-08   32.3   0.0    9.9e-08   32.0   0.0    1.1  1  LRR_5     BspA type Leucine rich repeat region (6 copies)


Domain annotation for each model (and alignments):
>> LRR_5  BspA type Leucine rich repeat region (6 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.0   5.5e-12   9.9e-08      22      76 ..      53     106 ..      33     122 .. 0.66

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 5.5e-12
                             LRR_5  22 vtsIgeyaFsnctslksitlpsslteigsyaFsncssltsitipssltsigeyaF 76 
                                       v sI+e+aFs+   l+ +++p s++ ig++aF++cs l+ i i + + s+g+++ 
  gi|474933866|ref|YP_007687448.1|  53 VVSIDESAFSGNLALRCVSIPGSVRDIGDSAFEGCSCLQRIYI-QGIPSFGNRCL 106
                                       4456666666666666666666666666666666655666666.35555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       230  (0.0128284); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1071.52
//
Query:       gi|474933867|ref|YP_007687449.1|  [L=291]
Description: Metal-dependent hydrolases of the beta-lactamase superfamily I [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-24   85.5   0.1    4.5e-24   85.1   0.1    1.2  1  Lactamase_B_2  Beta-lactamase superfamily domain
    9.6e-11   41.8   0.1    1.6e-10   41.1   0.1    1.3  1  Lactamase_B_3  Beta-lactamase superfamily domain
    3.6e-05   23.9   2.6      7e-05   22.9   2.5    1.6  1  Lactamase_B    Metallo-beta-lactamase superfamily


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.1   0.1   7.5e-28   4.5e-24       2     200 ..      35     219 ..      34     220 .. 0.91

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 7.5e-28
                                       EEEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC.....C--EEEEEEEEHHHHHHCCTT CS
                     Lactamase_B_2   2 riLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlre.....lrpkklplyapkgvlavlean 73 
                                        + iD+gp+ ++ ++r++       ++   + V+++h+H DH+ +++++ e     +++k+ ++y+++ v+      
  gi|474933867|ref|YP_007687449.1|  35 YLHIDPGPGALESMKRLR------YDPGLTESVIVSHCHPDHYSDAPSVIEgmthgGWKKRGRVYGSETVMTGTGGL 105
                                       578******999977776......45556688*******************99888888889*************** PP

                                       CGHHHCHTT.TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HH CS
                     Lactamase_B_2  74 fvylaleee.pavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipee 149
                                       ++++   +   +v+ + + +g+ ++++  g+++++t a+h+ ++        ++G+ + +g+  v y+ Dt+y++ e
  gi|474933867|ref|YP_007687449.1| 106 GPAISAYHLqLPVSSEIIRPGDVLDID--GMKVEVTRAKHSDPT--------NMGFKFHTGHGIVSYLSDTEYTE-E 171
                                       999988887899**************8..799************........*******9999*********877.9 PP

                                       HHHHHCT-SEEEEE-S-SSTTHHHHHHT---STSHHHHCTTSSSSEEEEES CS
                     Lactamase_B_2 150 igerlggadllllditayeddemirhmgHltpeeaveaaadlgakrlvliH 200
                                       ige++ g  +l+l++t  + +      +H++ +ea+++a++++++ +++iH
  gi|474933867|ref|YP_007687449.1| 172 IGEQYMGSRVLILPVTTPSRNL---IRWHMNTDEAIKIAKQVRPELVIFIH 219
                                       **************99666655...47************************ PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.1   2.7e-14   1.6e-10      10     163 .]      27     219 ..      24     219 .. 0.88

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 2.7e-14
                     Lactamase_B_3  10 flletagarilvDPf....kanlgyeppaeeaDlvlisqaledHahlet..lkql...................... 58 
                                       +l+e +g  + +DP+    +  + +++++   + v++s+ ++dH+  ++  ++++                      
  gi|474933867|ref|YP_007687449.1|  27 MLIEHDGHYLHIDPGpgalESMKRLRYDPGLTESVIVSHCHPDHYSDAPsvIEGMthggwkkrgrvygsetvmtgtg 103
                                       689************66542267888889999*************8664115555***********99999999999 PP

                     Lactamase_B_3  59 .............aenvkvleegeslevggleiravatshdavggsergenngflleqdgltiyhlGhlahelssee 122
                                                        +++++g+ l+++g++++ ++++h         +n+gf ++ ++  + +l ++ +  ++e 
  gi|474933867|ref|YP_007687449.1| 104 glgpaisayhlqlPVSSEIIRPGDVLDIDGMKVEVTRAKHS------DPTNMGFKFHTGHGIVSYLSDTEY--TEEI 172
                                       99998888888887777888889999999999999999994......4579*******************9..8899 PP

                     Lactamase_B_3 123 lkelgrvDvvltPvgg......pltlgqeealelakrLkpklvlPmh 163
                                        ++     v+++Pv           ++++ea+++ak+++p+lv+ +h
  gi|474933867|ref|YP_007687449.1| 173 GEQYMGSRVLILPVTTpsrnliRWHMNTDEAIKIAKQVRPELVIFIH 219
                                       99999**************999999******************9877 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   2.5   1.2e-08     7e-05      10      66 ..      28      79 ..      26     176 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.2e-08
                                      EEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTT CS
                       Lactamase_B 10 liegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglve 66
                                      lie+dg+ + iD+G ++ +++++     l+++p   + vi++H H+DH+++++ ++e
  gi|474933867|ref|YP_007687449.1| 28 LIEHDGHYLHIDPGPGALESMKR-----LRYDPGLTESVIVSHCHPDHYSDAPSVIE 79
                                      9********************98.....7***********************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1729.72
//
Query:       gi|474933868|ref|YP_007687450.1|  [L=429]
Description: Cytosine deaminase-related metal-dependent hydrolase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-61  209.0   0.1    1.4e-61  208.8   0.1    1.0  1  Amidohydro_1  Amidohydrolase family
    5.3e-19   69.0   0.1    9.8e-16   58.3   0.0    2.1  2  Amidohydro_3  Amidohydrolase family
    1.7e-05   24.3   0.0    3.3e-05   23.4   0.0    1.4  1  A_deaminase   Adenosine/AMP deaminase


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.8   0.1   2.3e-65   1.4e-61       1     344 []      52     401 ..      52     401 .. 0.89

  Alignments for each domain:
  == domain 1  score: 208.8 bits;  conditional E-value: 2.3e-65
                                       EEEE-EEEEEEECETTECSSS....GHHHHH.........STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHH CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrga....tledwl.........vppetaaealesgiktalksGtttvadmgattstgie 64 
                                       +++PGlI++H+H+ + +++g+     + d+l          +++++a++++ g++++  sGttt+ dm++    + +
  gi|474933868|ref|YP_007687450.1|  52 VIMPGLINTHTHIAMEVMKGTlddlLFPDFLnrsfkvdadRTDDDLAVGTKLGCMEMMASGTTTFVDMYY----SED 124
                                       69***************99975555555555*********99999*************************....99* PP

                                       HHHHHHHTSSSEEEEEEESSEGGS...GCCCSHHHHHHHHHHHHHHHHHHCTTTCEE.EEEEECGTCCSHHHHHHHH CS
                      Amidohydro_1  65 alleaaeelplglrilggkvsldr...gsaetskasreklkagaaetikgkadgvvk.valapheapafsdeelkea 137
                                        +++a+ e+  g+r + ++++ld+    +  ++  +++++        +++++++   +++a  + + + +++  ea
  gi|474933868|ref|YP_007687450.1| 125 IIAKATQEA--GIRGVCCWCCLDEdktTQKGNPVQNCKNFY-------QQFKGQRKIiPGVALQGVYCCNEDTCVEA 192
                                       ********8..************755433333444444444.......4445555555******************* PP

                                       HHHHHHHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHHHHHHC CS
                      Amidohydro_1 138 lkeakkrdlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkeag 214
                                           ++ ++p+++H++et+gev +++a+     +   + e++  +g+l++ ++i+ah  +lt++e++l+ e+  + +
  gi|474933868|ref|YP_007687450.1| 193 NAFSEEVNAPLTFHLSETRGEVNNHKAETR---M--RPAEWLSHIGVLND-RCIAAHSAWLTMNEIRLMGEA--GMS 261
                                       **********************99999999...5..5*************.*********************..99* PP

                                       EEHHHHHHHHSEHH.HHHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHHHT CS
                      Amidohydro_1 215 vahcpfsnsilrsg.realrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgllyedeegglslkealrmaT 290
                                       +++cp sn++l++g ++++ +  + Gv+v+lgtDg+  +n+l+++ e+r +++lq+++ + d+++ l++ e+l+++T
  gi|474933868|ref|YP_007687450.1| 262 ISSCPVSNMKLATGgVAPIPEFNKYGVNVSLGTDGNTTNNTLDVIAEMRSLALLQKSSRW-DPTV-LPAQELLDIVT 336
                                       **********887526777777777*******************************8888.7778.*********** PP

                                       HHHHHHTT-TTTSSSS-TTSB--EEEECC...CT........CGGGTTTCTSEEEEEEEETTEEE CS
                      Amidohydro_1 291 ingAkalglddkvGsievGkdADlvvvdl...di........laafvglkkdgnvkkvivkGklv 344
                                        ngAka+ ++dk+Gs+e+Gk AD+vv+d+   +i         + ++++ ++ nvk+v+++G+lv
  gi|474933868|ref|YP_007687450.1| 337 VNGAKAIHMEDKLGSLEPGKFADIVVLDGrmpNIrplvkenlVSVLAYSVSSANVKTVMCQGDLV 401
                                       *****************************87633668888999*******************987 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.1   0.00016      0.93       2      23 ..      45      66 ..      44      76 .. 0.84
   2 !   58.3   0.0   1.6e-19   9.8e-16     310     473 .]     240     402 ..     214     402 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00016
                      Amidohydro_3  2 viDakGrlvlPGFvDsHtHlag 23
                                      +iD++  + +PG++  HtH+a 
  gi|474933868|ref|YP_007687450.1| 45 EIDCSKDVIMPGLINTHTHIAM 66
                                      7999999************765 PP

  == domain 2  score: 58.3 bits;  conditional E-value: 1.6e-19
                      Amidohydro_3 310 rlehaegvtesqiervaalqvaagvqpvfnfedelldsrlgperargstpvkellnagvkvalgsD..apvgpfdpw 384
                                        ++h+ ++t ++i+ + + +  ++ +pv+n           + ++ g++p+ e  + gv+v+lg+D  +  +++d +
  gi|474933868|ref|YP_007687450.1| 240 IAAHSAWLTMNEIRLMGEAGMSISSCPVSNM----------KLATGGVAPIPEFNKYGVNVSLGTDgnTTNNTLDVI 306
                                       67899999*********************99..........4455677******************8888899**** PP

                      Amidohydro_3 385 prigaavmrktrrggevlrpdeelsleealalyTrgpAkalgledrkGtLevGadADlvvld...........adpl 450
                                        +++++  +++      +++   l+ +e+l+ +T ++Aka+++ed+ G+Le+G+ AD+vvld               
  gi|474933868|ref|YP_007687450.1| 307 AEMRSLALLQK----SSRWDPTVLPAQELLDIVTVNGAKAIHMEDKLGSLEPGKFADIVVLDgrmpnirplvkE--- 376
                                       ***********....6789*******************************************999555444444... PP

                      Amidohydro_3 451 dvdppelaear........vrltvvdGrvvy 473
                                            +l++++        v+ ++++G  vy
  gi|474933868|ref|YP_007687450.1| 377 -----NLVSVLaysvssanVKTVMCQGDLVY 402
                                       .....45544455555555999999999997 PP

>> A_deaminase  Adenosine/AMP deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   5.4e-09   3.3e-05     234     291 ..     255     310 ..     249     323 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 5.4e-09
                                       HHHCT-EEEE-HHHHCCCSST-TTTT-CHHHHHHTT-EEEE--BSCCCCT-S.HHHHHH CS
                       A_deaminase 234 lalaqiplevcPlSNvalgafleyaenPlkeflerglnvslntDDPlqfgtt.LieeYa 291
                                       + +a + +  cP+SN++l   ++    P++ef + g+nvsl+tD     +t   i+e+ 
  gi|474933868|ref|YP_007687450.1| 255 MGEAGMSISSCPVSNMKL---ATGGVAPIPEFNKYGVNVSLGTDGNTTNNTLdVIAEMR 310
                                       678899************...99999******************776655544666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2705.87
//
Query:       gi|474933869|ref|YP_007687451.1|  [L=219]
Description: Protein of unknown function (DUF1121) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-45  154.2   0.0    4.1e-45  153.8   0.0    1.2  1  LUD_dom   LUD domain


Domain annotation for each model (and alignments):
>> LUD_dom  LUD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.8   0.0   2.3e-49   4.1e-45       5     189 .]      23     213 ..      19     213 .. 0.93

  Alignments for each domain:
  == domain 1  score: 153.8 bits;  conditional E-value: 2.3e-49
                           LUD_dom   5 ienleangaevyyaktaeealelilellkeksvvseggstdlgeiglapalhsgreevldlfeekltreareelrek 81 
                                       i  +e++++ev++++++eea++l+l+l+++ks+vs+ggs++l++igl +a++sg ++v+d+ e ++ +e+++el +k
  gi|474933869|ref|YP_007687451.1|  23 IPLMEERQFEVHHVNSGEEAVKLALSLMPPKSSVSWGGSMTLDQIGLLNAVRSGPYKVIDRAEGRT-PEEKQELVRK 98 
                                       55689********************************************************99999.********** PP

                           LUD_dom  82 fltadvgitganfaiAetGtlvlvdnegnr.raltflpkvhivvvginkivpdledavkrlkt..aprnatrlqkkt 155
                                       ++++d+++t++n aiA++Gt+v+vd++gnr +a+t++p ++i+vvg+nk++ +   a++r++   a  na+r  k+ 
  gi|474933869|ref|YP_007687451.1|  99 AFSVDFYLTSFN-AIANDGTVVNVDGTGNRvAAITYGPSNVIAVVGMNKVCLSQATAFERAEGeaAQLNAVRFGKED 174
                                       ************.**************************************************99999999977766 PP

                           LUD_dom 156 pyvsfi........sgpsrtadielvlvygvhgpkrihvilv 189
                                       +   f           p r+++   ++    + ++ri+vilv
  gi|474933869|ref|YP_007687451.1| 175 T--LFTdeditvdeIVPGRICNFIEQI-AWCPVKNRIKVILV 213
                                       4..3445688888889******88777.66679********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1431.64
//
Query:       gi|474933870|ref|YP_007687452.1|  [L=54]
Description: hypothetical protein TALC_00282 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      9e-06   26.0   0.8      1e-05   25.8   0.8    1.1  1  FeoB_associated  FeoB-associated Cys-rich membrane protein
  ------ inclusion threshold ------
      0.037   14.5   0.0       0.04   14.4   0.0    1.0  1  DUF2746          Protein of unknown function (DUF2746)
      0.041   14.0   0.4      0.049   13.8   0.4    1.1  1  PARM             PARM
      0.099   12.3   0.8       0.16   11.7   0.8    1.5  1  TGBp3            Triple gene block 3
        0.1   11.2   0.1        0.1   11.2   0.1    1.0  1  Cyt_bd_oxida_I   Cytochrome bd terminal oxidase subunit I


Domain annotation for each model (and alignments):
>> FeoB_associated  FeoB-associated Cys-rich membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.8   2.9e-09     1e-05       2      43 ..       5      46 ..       4      47 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 2.9e-09
                   FeoB_associated  2 tiIVgliiaaavafvirrlikkkkkGsCgggCsgCsssssg....C 43
                                      t  V+++++++++f+ ++  +++++     +C++C ++s++    C
  gi|474933870|ref|YP_007687452.1|  5 TAAVLAVVILVLGFAAWYTLRSARSH----DCASCRNKSCQnpinC 46
                                      66799*****************9999....7****98764477777 PP

>> DUF2746  Protein of unknown function (DUF2746)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.1e-05      0.04      14      60 ..       7      53 ..       3      54 .] 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.1e-05
                           DUF2746 14 tllgvafltfsvpawftgrarkhssdigeikeqvc.nthdtnlrddld 60
                                      ++l v +l +   aw+t r+  +s d    +++ c n  +  +rdd d
  gi|474933870|ref|YP_007687452.1|  7 AVLAVVILVLGFAAWYTLRSA-RSHDCASCRNKSCqNPINCSIRDDDD 53
                                      6899*************9975.46788899999984567999999976 PP

>> PARM  PARM
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.4   1.4e-05     0.049     250     270 ..       5      25 ..       2      31 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.4e-05
                              PARM 250 TvtViAVVLLVFGvAAyLKiR 270
                                       T +V+AVV+LV G AA+  +R
  gi|474933870|ref|YP_007687452.1|   5 TAAVLAVVILVLGFAAWYTLR 25 
                                       889*************99888 PP

>> TGBp3  Triple gene block 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.8   4.4e-05      0.16       3      27 ..       8      32 ..       3      41 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.4e-05
                             TGBp3  3 llaligllvallalyllntsssegC 27
                                      +la++ l++ ++a+y l++ +s++C
  gi|474933870|ref|YP_007687452.1|  8 VLAVVILVLGFAAWYTLRSARSHDC 32
                                      799***************9999999 PP

>> Cyt_bd_oxida_I  Cytochrome bd terminal oxidase subunit I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   2.8e-05       0.1     182     208 ..       4      32 ..       1      44 [. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.8e-05
                    Cyt_bd_oxida_I 182 vlaalltaaffvagvsawyllr..rekef 208
                                        +aa+l+ +++v+g +awy lr  r+++ 
  gi|474933870|ref|YP_007687452.1|   4 ATAAVLAVVILVLGFAAWYTLRsaRSHDC 32 
                                       6899*****************98755543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1085  (0.0605165); expected 358.6 (0.02)
Passed bias filter:                      588  (0.032796); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 379.24
//
Query:       gi|474933871|ref|YP_007687453.1|  [L=721]
Description: ferrous iron transporter FeoB [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-58  196.0   0.0    4.3e-58  195.3   0.0    1.4  1  FeoB_N        Ferrous iron transport protein B
    3.2e-27   95.0  23.8    1.6e-18   67.0   2.8    3.5  3  Gate          Nucleoside recognition
    2.8e-17   62.2   1.0    2.8e-17   62.2   1.0    2.8  2  FeoB_C        Ferrous iron transport protein B C terminus
    1.2e-16   60.8   0.0    2.2e-16   60.0   0.0    1.4  1  MMR_HSR1      50S ribosome-binding GTPase
    8.3e-12   45.5   0.1    1.3e-11   44.8   0.1    1.3  1  FeoB_Cyto     FeoB cytosolic helical domain
    0.00099   19.0   0.5      0.011   15.5   0.0    2.4  3  ATP_bind_1    Conserved hypothetical ATP binding protein
      0.001   18.7   0.3       0.11   12.0   0.1    2.7  2  GTP_EFTU      Elongation factor Tu GTP binding domain
     0.0015   18.4   0.0       0.44   10.4   0.0    2.4  2  RsgA_GTPase   RsgA GTPase
  ------ inclusion threshold ------
       0.06   13.1   0.5       0.33   10.7   0.0    2.2  2  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
       0.18   11.5   1.8       0.31   10.8   0.3    2.2  2  Gemini_mov    Geminivirus putative movement protein
       0.22   10.9   0.0       0.36   10.2   0.0    1.3  1  SRPRB         Signal recognition particle receptor beta subun


Domain annotation for each model (and alignments):
>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.3   0.0   2.6e-61   4.3e-58       2     155 ..       3     160 ..       2     161 .. 0.96

  Alignments for each domain:
  == domain 1  score: 195.3 bits;  conditional E-value: 2.6e-61
                                       EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETT.EEEEEEE----SSSSSSSHHHHHHHHHHH.. CS
                            FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkg.keveivDlPGiYslsayseeekvardfll.. 75 
                                       t al+Gnpn+Gktt+fn+ltg+ q+ gNwpGvtve+k+g ++ +  +++ +vDlPGiYsls+ys ee v+rdfl+  
  gi|474933871|ref|YP_007687453.1|   3 TAALIGNPNAGKTTVFNKLTGSIQQTGNWPGVTVERKQGFIRRSPkDRILVVDLPGIYSLSPYSPEEIVSRDFLIgt 79 
                                       789**************************************98765899*************************988 PP

                                       .CTSSSEEEEEEEGGGHHHHHHHHHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTHHH CS
                            FeoB_N  76 .eeepdvvvnvvdatnlernLyLtlqllelgvpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkegiee 151
                                        +++pdv + vvda+nler LyL+ q+++lg+p+v++lnm+d+aek+g+++d +kLse+Lg++vv++++ +++g+++
  gi|474933871|ref|YP_007687453.1|  80 sDDKPDVAICVVDASNLERGLYLLSQVADLGIPMVIVLNMVDVAEKSGMKVDPSKLSEALGCEVVECVGVRNQGTDD 156
                                       7899************************************************************************9 PP

                                       HHHH CS
                            FeoB_N 152 llka 155
                                       + +a
  gi|474933871|ref|YP_007687453.1| 157 IAEA 160
                                       9887 PP

>> Gate  Nucleoside recognition
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1       1.3   2.2e+03      87     106 ..     291     310 ..     278     313 .. 0.85
   2 !   38.7   5.7     6e-13   9.7e-10       2     109 ..     355     447 ..     354     450 .. 0.93
   3 !   67.0   2.8   9.8e-22   1.6e-18       1     112 []     516     651 ..     516     651 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.3
                              Gate  87 afllfvllytpcvatlaviv 106
                                          ++ l y+++++t+++++
  gi|474933871|ref|YP_007687453.1| 291 FIAIMYLVYFVSIQTIGTMG 310
                                       55688899999999999986 PP

  == domain 2  score: 38.7 bits;  conditional E-value: 6e-13
                              Gate   2 lkagpiillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqg 78 
                                       + ++p i+++++++ +l++ ++++r++ +l+ +f ++g  l++k++++ + g++   ++v++++ ++         +
  gi|474933871|ref|YP_007687453.1| 355 IGFLPQIVVLFLFLAILEEVGYMSRVAYILDRIFCRFG--LSGKTVIPAVIGIG---CGVPAVMGTR---------T 417
                                       67899*********************************..**************...*********9.........* PP

                              Gate  79 fdtpksalafllfvllytpcvatlavivrel 109
                                       +++p ++ +++++++++ pc a l++i  ++
  gi|474933871|ref|YP_007687453.1| 418 IEDPMNRNVAVMTTTFM-PCSAKLPIITVIV 447
                                       ******99999999996.8*****9987666 PP

  == domain 3  score: 67.0 bits;  conditional E-value: 9.8e-22
                              Gate   1 llkagpiillasiliwflss..............ssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgt 63 
                                       ++kag++ill  ++iw+lss               s l+ ig +++++f p g+   w+ +v+ ++g++ake  ++t
  gi|474933871|ref|YP_007687453.1| 516 VKKAGTLILLSAVIIWLLSSytwgfeylgdsetaGSMLADIGHAVTWIFIPNGFGQVWEFSVASISGLMAKENLLAT 592
                                       68*************************************************5555********************** PP

                              Gate  64 lgtly..........tsalgellqgfdtpksalafllfvllytpcvatlavivrelgsk 112
                                       +++l+          + ++   + g ++   a+afl+f+ll+ pc+a+++++++elgs+
  gi|474933871|ref|YP_007687453.1| 593 VAVLFgssvdgegliAADALVDALGPNGAGLAMAFLIFNLLCAPCFAAIGAMRSELGSW 651
                                       ************866333333333555555589************************97 PP

>> FeoB_C  Ferrous iron transport protein B C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.2   1.0   1.7e-20   2.8e-17       2      53 .]     459     511 ..     458     511 .. 0.95
   2 ?   -3.7   2.1       6.1   9.9e+03       2      16 ..     691     705 ..     688     706 .. 0.72

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 1.7e-20
                            FeoB_C   2 fslYllgilvallvalllkktt.lkgepspfvmELPpYrlPslknvliktweR 53 
                                       +s+Yllgi+++l+++++lkk+    g+p+pf+mELP Y+ P++ nv+++++e+
  gi|474933871|ref|YP_007687453.1| 459 LSMYLLGIAMILISGIVLKKFKgVVGKPAPFIMELPVYHAPTPPNVARSVIEK 511
                                       79******************77888*************************997 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 6.1
                            FeoB_C   2 fslYllgilvallva 16 
                                       +++ ++g+lv +++a
  gi|474933871|ref|YP_007687453.1| 691 LAIAFIGLLVYFVAA 705
                                       567788888888777 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.0   0.0   1.3e-19   2.2e-16       2     113 ..       4     118 ..       3     119 .. 0.77

  Alignments for each domain:
  == domain 1  score: 60.0 bits;  conditional E-value: 1.3e-19
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETT.EEEEEEECGGCSS..HHHHHHHHHHHHHH... CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkg.keielvDtpGlie..gaseekglgkafla... 72 
                                       +a++G+pN+GK+t++n+ltg+  +++++pg+T + ++g ++ +  ++i +vD+pG+++    s e+ ++++fl    
  gi|474933871|ref|YP_007687453.1|   4 AALIGNPNAGKTTVFNKLTGSIQQTGNWPGVTVERKQGFIRRSPkDRILVVDLPGIYSlsPYSPEEIVSRDFLIgts 80 
                                       699***********************************999544489********9754334445589999985432 PP

                                       HHCTSEEEEEEETT...TTCSHHHHHHHHHHHHHTTSEEEEEEE CS
                          MMR_HSR1  73 leeadlillvvdas...eeklkpldeeleelleeakkplilvln 113
                                        ++ d+++ vvdas   ++ +  l +++++l    ++p+++vln
  gi|474933871|ref|YP_007687453.1|  81 DDKPDVAICVVDASnleRGLY--LLSQVADL----GIPMVIVLN 118
                                       4457********884321122..33555555....589999988 PP

>> FeoB_Cyto  FeoB cytosolic helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   0.1   8.2e-15   1.3e-11       1      91 []     176     262 ..     176     262 .. 0.97

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 8.2e-15
                         FeoB_Cyto   1 YgeeiEkaiekleellkesnlkaklppRwlAlklLegDeelleelkedpelraeveearkeleaelgedledvIvda 77 
                                       Yg +iE+ ++++++++++    ++   Rw Alkl+e+D+ +++ l    ++ a++ ++++e+e++ g+d  ++I+ a
  gi|474933871|ref|YP_007687453.1| 176 YGSDIEECVDRVSDVIRNC--VRDDVVRWAALKLIERDDMVMQDLDA--DVVAKAFAIIDEMEKRVGDDGVQMIATA 248
                                       9****************97..99999*********************..**************************** PP

                         FeoB_Cyto  78 rykfiegilrevvk 91 
                                       ry+  +++ +++v+
  gi|474933871|ref|YP_007687453.1| 249 RYDSSAAVEKAAVT 262
                                       ***99999998885 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.19   3.1e+02       2      24 ..       7      29 ..       6      35 .. 0.85
   2 !   15.5   0.0   6.9e-06     0.011     131     239 ..      92     195 ..      43     197 .. 0.67
   3 ?   -4.2   0.1         7   1.1e+04     130     163 ..     413     446 ..     409     448 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.19
                        ATP_bind_1  2 vGpaGsGKttfvgalseilelrg 24
                                      +G + +GKtt  ++l+  ++++g
  gi|474933871|ref|YP_007687453.1|  7 IGNPNAGKTTVFNKLTGSIQQTG 29
                                      8999**********998888776 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 6.9e-06
                        ATP_bind_1 131 DsqrltdptkfisgllsalsamlrlelPhvvvlnkfDllkeklekeleffedvealslllekee....ekykklaea 203
                                       D+         +++ l+ ls ++ l++P+v+vln +D+++ k+     +  d+ +ls++l  e     + +++ + +
  gi|474933871|ref|YP_007687453.1|  92 DASN-------LERGLYLLSQVADLGIPMVIVLNMVDVAE-KSG----MKVDPSKLSEALGCEVvecvGVRNQGTDD 156
                                       3333.......4445777777*****************66.332....33344445554444444455555555555 PP

                        ATP_bind_1 204 iaelleefa...lvlrflplssekeesiedllslideal 239
                                       iae+++  +   + +rfl++ s+ ee ++++ ++i++++
  gi|474933871|ref|YP_007687453.1| 157 IAEAVQRAYdgkEAPRFLTYGSDIEECVDRVSDVIRNCV 195
                                       555555433111345999999999999999999999887 PP

  == domain 3  score: -4.2 bits;  conditional E-value: 7
                        ATP_bind_1 130 vDsqrltdptkfisgllsalsamlrlelPhvvvl 163
                                       + +++++dp++   +++++  + ++++lP ++v+
  gi|474933871|ref|YP_007687453.1| 413 MGTRTIEDPMNRNVAVMTTTFMPCSAKLPIITVI 446
                                       5678889999998999999999999999999875 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.1   6.9e-05      0.11      91     153 ..      81     142 ..       1     220 [. 0.70
   2 ?   -2.5   0.0       1.9   3.2e+03     166     182 ..     591     607 ..     572     618 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.9e-05
                                       HHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGST.HHHHHHHHHHHHHHHHHH CS
                          GTP_EFTU  91 lrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrl.kaelkeiveevkqklsrk 153
                                         + D+a+ vvda+    ++   +l ++ ++g+p+++++N +D + k+ +k  ++++++ l  +
  gi|474933871|ref|YP_007687453.1|  81 DDKPDVAICVVDAS--NLERGLYLLSQVADLGIPMVIVLNMVDVAeKSGMKVDPSKLSEALGCE 142
                                       4678*********9..4677788999999****************7778888888888888554 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.9
                                       TTEEEEEEBTTTTBTHH CS
                          GTP_EFTU 166 kevpvvfgSalkgegvk 182
                                        +v v+fgS+++geg+ 
  gi|474933871|ref|YP_007687453.1| 591 ATVAVLFGSSVDGEGLI 607
                                       46899*******99765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.0     0.009        15     101     125 ..       3      27 ..       2      62 .. 0.87
   2 !   10.4   0.0   0.00027      0.44      38      98 ..     102     162 ..      86     166 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.009
                                       EEEEECSTTSSHHHHHHHHCTT--- CS
                       RsgA_GTPase 101 tsvlvGqSGvGKStLinallpelel 125
                                       t++l+G+  +GK+t+ n+l+++ ++
  gi|474933871|ref|YP_007687453.1|   3 TAALIGNPNAGKTTVFNKLTGSIQQ 27 
                                       5789*****************9655 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00027
                                       HHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCT CS
                       RsgA_GTPase  38 fLvlaeekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkellk 98 
                                       +L ++ + gi++vivln +D++e++    + ++  ealg+ev+ +   +++g+++++e+++
  gi|474933871|ref|YP_007687453.1| 102 LLSQVADLGIPMVIVLNMVDVAEKSGMKVDPSKLSEALGCEVVECVGVRNQGTDDIAEAVQ 162
                                       456678899****************966677888899********9999*******99886 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0    0.0002      0.33     106     146 ..     125     169 ..     117     175 .. 0.79
   2 ?   -0.5   0.2      0.57   9.3e+02      28      52 ..     403     429 ..     392     431 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0002
                                       .BS----HHHHHHHTTSEEE...EESSH.HHHHHHHHHHHH.CSS CS
                      TPP_enzyme_C 106 kdlkpvdfaklaealGakga...rvekadveeleealkeal.ekk 146
                                       k +++vd+ kl ealG++++    v+++ +++++ea+++a   k+
  gi|474933871|ref|YP_007687453.1| 125 KSGMKVDPSKLSEALGCEVVecvGVRNQGTDDIAEAVQRAYdGKE 169
                                       35899*************555986778889**********95444 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.57
                                       S-TTTHHHHHHHHHH.HST.TSEEEEE CS
                      TPP_enzyme_C  28 gtmGyglpaAiGakl.akp.drevvai 52 
                                         +G g+pa +G     +p +r+v ++
  gi|474933871|ref|YP_007687453.1| 403 IGIGCGVPAVMGTRTiEDPmNRNVAVM 429
                                       678**********99556766777665 PP

>> Gemini_mov  Geminivirus putative movement protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       5.4   8.7e+03      24      46 ..     432     454 ..     422     467 .. 0.70
   2 ?   10.8   0.3   0.00019      0.31      16      57 ..     495     538 ..     483     541 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 5.4
                        Gemini_mov  24 taapssselpwsrvgeiailtlv 46 
                                       t  p s++lp  +v ++a++   
  gi|474933871|ref|YP_007687453.1| 432 TFMPCSAKLPIITVIVAAFFHES 454
                                       55688889999999888887644 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00019
                        Gemini_mov  16 lyqkPrvptaapssselpwsrvgeiailtlvavlvlYLl..ytl 57 
                                        y++P+ p+ a s  e  ws v  +  l+l++ ++++Ll  yt+
  gi|474933871|ref|YP_007687453.1| 495 VYHAPTPPNVARSVIEKSWSFVKKAGTLILLSAVIIWLLssYTW 538
                                       5799**********************************855666 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00022      0.36       8      62 ..       6      62 ..       2      76 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00022
                                      EE-STTSSHHHHHHHHHHS....S---B---S.S-EEETTG...GGTT-SEEEETT-GCC CS
                             SRPRB  8 lvGlsdsGKTslftrLttd....svkktvtSq.essaalkvksekgskltliDfPGhekl 62
                                      l+G  ++GKT++f++Lt         + vt   ++ +    + + + ++ ++D+PG  +l
  gi|474933871|ref|YP_007687453.1|  6 LIGNPNAGKTTVFNKLTGSiqqtGNWPGVTVErKQGFI---RRSPKDRILVVDLPGIYSL 62
                                      89**************8663221111222222122222...3346667778888887666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (721 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       749  (0.0417759); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.69u 0.29s 00:00:00.98 Elapsed: 00:00:00.46
# Mc/sec: 4668.32
//
Query:       gi|474933872|ref|YP_007687454.1|  [L=83]
Description: Fe2+ transport system protein A [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-13   49.6   0.4    4.2e-13   49.4   0.4    1.1  1  FeoA      FeoA domain


Domain annotation for each model (and alignments):
>> FeoA  FeoA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.4   0.4   2.3e-17   4.2e-13       2      69 ..       2      68 ..       1      72 [. 0.93

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 2.3e-17
                                      EGGG--TT-EEEEEEE-TT.SSHHHHHHHHT--TT-EEEEEEE-TTS-SEEEEETTEEEEE-HHHHTT CS
                              FeoA  2 pLsdlkeGergeiarisdedpellrrLremGlvpGarievvarapfggplvvrvgdtrvaLgreeAqa 69
                                      +  d+  G++++++++  e + l++r +++G++ G  i++v+ ap+g+p+ +++++ r+ +++ eA+ 
  gi|474933872|ref|YP_007687454.1|  2 RFKDMRCGDTATVVNVEGE-GHLRKRILDLGITRGVDIKMVRIAPLGDPIEIELRGYRLTIRKTEADI 68
                                      567999**********777.99********************************************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       165  (0.00920297); expected 358.6 (0.02)
Passed bias filter:                      157  (0.00875676); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 589.24
//
Query:       gi|474933873|ref|YP_007687455.1|  [L=56]
Description: hypothetical protein TALC_00285 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-06   27.8   7.1    3.4e-06   27.4   7.1    1.2  1  FeoB_associated  FeoB-associated Cys-rich membrane protein
  ------ inclusion threshold ------
       0.12   12.2   0.1       0.13   12.2   0.1    1.2  1  ODV-E18          Occlusion-derived virus envelope protein ODV
       0.76   10.7   2.3       0.89   10.5   2.3    1.3  1  EphA2_TM         Ephrin type-A receptor 2 transmembrane domai


Domain annotation for each model (and alignments):
>> FeoB_associated  FeoB-associated Cys-rich membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   7.1   5.6e-10   3.4e-06       2      43 ..       5      47 ..       4      48 .. 0.89

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 5.6e-10
                   FeoB_associated  2 tiIVgliiaaavafvirrlikkkkkG.sCg.ggCsgCsssssgC 43
                                      t +V+++++a+++++i+  ++  +++ +Cg g+C+ C++ ++ C
  gi|474933873|ref|YP_007687455.1|  5 TAVVLVVVIALMILAIIGTRRTMRSEsCCGgGKCCTCQKTQH-C 47
                                      679*******************9999899999*****98666.7 PP

>> ODV-E18  Occlusion-derived virus envelope protein ODV-E18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   2.1e-05      0.13      27      44 ..       3      20 ..       1      41 [. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.1e-05
                           ODV-E18 27 lltilvvlviiillvllv 44
                                      ++t +v++v+i+l++l +
  gi|474933873|ref|YP_007687455.1|  3 FMTAVVLVVVIALMILAI 20
                                      89***********99865 PP

>> EphA2_TM  Ephrin type-A receptor 2 transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   2.3   0.00015      0.89       8      33 ..       6      31 ..       1      55 [. 0.43

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00015
                          EphA2_TM  8 glvllvilvilvlvlvrrrsknrkqk 33
                                      ++vl+v++ +++l ++  r+  r+++
  gi|474933873|ref|YP_007687455.1|  6 AVVLVVVIALMILAIIGTRRTMRSES 31
                                      33333333333333333333333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1671  (0.093201); expected 358.6 (0.02)
Passed bias filter:                      759  (0.0423336); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 367.52
//
Query:       gi|474933874|ref|YP_007687456.1|  [L=200]
Description: Transcriptional regulator [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-17   63.7   0.1    1.5e-16   60.3   0.0    2.0  2  TetR_C_8       Transcriptional regulator C-terminal region
    7.1e-08   32.1   0.0    1.6e-07   31.0   0.0    1.6  1  TetR_N         Bacterial regulatory proteins, tetR family
  ------ inclusion threshold ------
      0.026   14.7   0.1       0.26   11.4   0.0    2.3  2  DNA_ligase_IV  DNA ligase IV
       0.11   12.4   0.0        0.6   10.0   0.0    2.1  2  MarR_2         MarR family
       0.11   12.6   0.0       0.37   11.0   0.0    1.9  2  HTH_AraC       Bacterial regulatory helix-turn-helix proteins
       0.12   12.3   0.1       0.21   11.4   0.1    1.5  1  DIX            DIX domain
       0.15   12.1   0.0       0.86    9.7   0.0    2.0  2  HTH_20         Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> TetR_C_8  Transcriptional regulator C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.2      0.18   4.7e+02      29      69 ..      13      53 ..       8      59 .. 0.66
   2 !   60.3   0.0   5.9e-20   1.5e-16       2     101 ..      80     178 ..      79     179 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.18
                                      .THHHHHHHHHHHHHHHHHHH..HHH-TT--S-HHHHHHHHHH CS
                          TetR_C_8 29 gresfekylkelikelilkvi..eelsegkelseedkefiadf 69
                                       ++++ + +k+l+++  ++ i  +++ eg ++s   + f+++f
  gi|474933874|ref|YP_007687456.1| 13 TKQQLADSFKKLLETKAYDDItvSDITEGCNMS--RQTFYYHF 53
                                      567888888888888888888444444444544..46666665 PP

  == domain 2  score: 60.3 bits;  conditional E-value: 5.9e-20
                                       SHHHHHHHHHHHHHHTHHHHHHHHHH-.THHHHHHHHHHHHHHHHHHHHHH-TT--S-HHHHHHHHHHHHHHHHHHH CS
                          TetR_C_8   2 nwqegllklfeyikenkdfyknllssngresfekylkelikelilkvieelsegkelseedkefiadfysygfvgvi 78 
                                       +w + l+++f y    ++++  +++s + + + +y+ e  k+ i ++++  s+g  l++ d++f+++ +s +fvgv+
  gi|474933874|ref|YP_007687456.1|  80 TWLDKLKQVFAYTVTLRNIIISVYNSRSLQILLDYFLEEGKRRIGDIVDLRSDGI-LNQGDRDFFVNALSFAFVGVM 155
                                       8***********************************************8888776.999****************** PP

                                       HHHHHTTS-S-HHHHHHHHHHHH CS
                          TetR_C_8  79 ldWlengmkespeeiaellskli 101
                                       ++W+++gm ++pe ++++l  +i
  gi|474933874|ref|YP_007687456.1| 156 VKWIDDGMMDTPETMVRRLDAVI 178
                                       ******************98776 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   6.1e-11   1.6e-07       7      43 ..      23      59 ..      17      61 .. 0.92

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 6.1e-11
                                      HHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHH CS
                            TetR_N  7 elfaerGydattvreIAkrAGvskgalYryFpsKeeL 43
                                      +l++ + yd  tv++I + +++s+ ++Y++F+s+ ++
  gi|474933874|ref|YP_007687456.1| 23 KLLETKAYDDITVSDITEGCNMSRQTFYYHFKSMFDI 59
                                      7999*****************************8666 PP

>> DNA_ligase_IV  DNA ligase IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0001      0.26      11      31 ..       2      23 ..       2      25 .. 0.93
   2 ?    0.3   0.0      0.32   8.1e+02      23      30 ..      83      90 ..      80      91 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0001
                     DNA_ligase_IV 11 eYGDS.YtvDtdeeqLKevFnr 31
                                      +YGD  Y  D++ +qL ++F++
  gi|474933874|ref|YP_007687456.1|  2 CYGDGlYMSDATKQQLADSFKK 23
                                      89*98799************98 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.32
                     DNA_ligase_IV 23 eqLKevFn 30
                                      ++LK+vF 
  gi|474933874|ref|YP_007687456.1| 83 DKLKQVFA 90
                                      79*****5 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00023       0.6      11      37 ..      24      48 ..      13      56 .. 0.87
   2 ?   -0.6   0.0      0.48   1.2e+03      35      53 ..     167     185 ..     166     192 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00023
                                      HHHHHCTTTSEEEHHHHHHHHTSSHHH CS
                            MarR_2 11 LaaLgrrpgrdltvgelarrlglsksa 37
                                      L++  + ++  +tv+++++ +++s+++
  gi|474933874|ref|YP_007687456.1| 24 LLETKAYDD--ITVSDITEGCNMSRQT 48
                                      556667776..**************98 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.48
                                       HHHHHHHHHHHHHTTSEEE CS
                            MarR_2  35 ksavsrilkrLvaaGLver 53 
                                       + ++ r+l+    aG+++ 
  gi|474933874|ref|YP_007687456.1| 167 PETMVRRLDAVIGAGYIRN 185
                                       5678899999999999985 PP

>> HTH_AraC  Bacterial regulatory helix-turn-helix proteins, AraC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.7   6.9e+03      20      32 ..       3      16 ..       2      17 .. 0.75
   2 ?   11.0   0.0   0.00014      0.37       8      31 ..      32      55 ..      25      59 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.7
                                      S.SHHHHHHHHHHH CS
                          HTH_AraC 20 f.SrsyFsrlFkke 32
                                      + +  y+s + k++
  gi|474933874|ref|YP_007687456.1|  3 YgDGLYMSDATKQQ 16
                                      44667999999998 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00014
                                      T--HHHHHHHTTSSHHHHHHHHHH CS
                          HTH_AraC  8 nltiediAdelgfSrsyFsrlFkk 31
                                      ++t+ di + +++Sr++F+  Fk+
  gi|474933874|ref|YP_007687456.1| 32 DITVSDITEGCNMSRQTFYYHFKS 55
                                      6899999999*************7 PP

>> DIX  DIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   8.4e-05      0.21      22      68 ..      28      75 ..      14      85 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.4e-05
                               DIX 22 krpdqiTLkdfKellp.kkGnyryffKtldedfegvVkeevtdDsaiL 68
                                      k+ d+iT  d+ e  +  + +++y+fK++ + ++ + + e + D ++L
  gi|474933874|ref|YP_007687456.1| 28 KAYDDITVSDITEGCNmSRQTFYYHFKSMFDIVKWCYFDEAMRDRTNL 75
                                      45599********99988889********9988766677777776665 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.59   1.5e+03      35      50 ..      11      26 ..       5      29 .. 0.84
   2 ?    9.7   0.0   0.00034      0.86      26      47 ..      34      55 ..      29      60 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.59
                                      TS-HHHHHHHHHHHHH CS
                            HTH_20 35 dlskntlsyHLrvLee 50
                                      d +k++l + +++L e
  gi|474933874|ref|YP_007687456.1| 11 DATKQQLADSFKKLLE 26
                                      67999*******9988 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00034
                                      -HHHHHHHHTS-HHHHHHHHHH CS
                            HTH_20 26 taselaerldlskntlsyHLrv 47
                                      t+s++ e + +s++t +yH++ 
  gi|474933874|ref|YP_007687456.1| 34 TVSDITEGCNMSRQTFYYHFKS 55
                                      89*****************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1384.45
//
Query:       gi|474933875|ref|YP_007687457.1|  [L=225]
Description: 4Fe-4S binding domain protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.7e-11   41.5  10.5    7.3e-07   28.7   4.6    3.2  3  Fer4          4Fe-4S binding domain
    1.9e-09   37.2  15.5    4.6e-08   32.8   4.3    3.4  3  Fer4_6        4Fe-4S binding domain
    2.5e-08   33.9   8.0      3e-08   33.6   5.3    2.3  2  Fer4_21       4Fe-4S dicluster domain
    1.1e-07   32.4   7.7    1.1e-07   32.4   7.7    2.5  2  Fer4_7        4Fe-4S dicluster domain
    1.9e-06   28.0   6.4    1.9e-06   28.0   6.4    2.6  2  Fer4_9        4Fe-4S dicluster domain
    7.7e-06   26.6   9.0    0.00011   22.9   2.3    2.7  2  Fer4_15       4Fe-4S single cluster domain
    1.1e-05   26.3   9.5     0.0046   17.9   1.0    2.8  3  Fer4_16       4Fe-4S double cluster binding domain
    4.7e-05   23.2   3.8    4.7e-05   23.2   3.8    3.2  3  Fer4_2        4Fe-4S binding domain
    0.00035   20.6  14.3    0.00041   20.4   9.3    3.0  3  Fer4_10       4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.018   15.6   7.8       0.16   12.5   0.9    2.7  2  Fer4_17       4Fe-4S dicluster domain
      0.049   14.2   4.6      0.049   14.2   4.6    3.8  3  Fer4_4        4Fe-4S binding domain
      0.053   14.5   7.5      0.053   14.5   7.5    3.9  4  Fer4_3        4Fe-4S binding domain
      0.069   13.6  10.8        9.7    6.7  10.7    2.6  1  Fer4_8        4Fe-4S dicluster domain
       0.57   10.8  10.1        8.2    7.1  10.1    2.5  1  Fer4_13       4Fe-4S single cluster domain of Ferredoxin I
       0.91    9.7   6.4       0.45   10.7   1.7    2.5  2  Furin-like_2  Furin-like repeat, cysteine-rich
        5.1    8.0   9.9        1.2   10.0   2.8    2.6  3  Fer4_22       4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   4.6   6.5e-10   7.3e-07       2      23 ..       7      28 ..       6      29 .. 0.91
   2 !   23.3   0.3   3.4e-08   3.8e-05       3      24 .]      38      59 ..      36      59 .. 0.92
   3 ?   -1.4   0.2       2.1   2.4e+03      13      19 ..     152     158 ..     149     159 .. 0.81

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 6.5e-10
                                      EEETTTSSS-THHHHHSTTTEE CS
                              Fer4  2 videekCigCGaCvevCPvgAI 23
                                       id ekC gCGaCve+C  gAI
  gi|474933875|ref|YP_007687457.1|  7 RIDREKCNGCGACVEACAEGAI 28
                                      79***************88888 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 3.4e-08
                                      EETTTSSS-THHHHHSTTTEEE CS
                              Fer4  3 ideekCigCGaCvevCPvgAIt 24
                                      + e+ C g GaC   CP+gAI+
  gi|474933875|ref|YP_007687457.1| 38 VREDYCDGLGACLPECPTGAIS 59
                                      679*****************96 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2.1
                                       HHHHHST CS
                              Fer4  13 aCvevCP 19 
                                        C+  CP
  gi|474933875|ref|YP_007687457.1| 152 VCIIGCP 158
                                       5888898 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   4.3   4.1e-11   4.6e-08       1      24 []       5      28 ..       5      28 .. 0.97
   2 !   10.8   0.4   0.00038      0.43       6      24 .]      40      58 ..      36      58 .. 0.90
   3 ?   -0.6   0.2       1.5   1.7e+03      15      20 ..     153     158 ..     150     160 .. 0.79

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 4.1e-11
                            Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                      vv+id++kC+gCg+Cv +C egai
  gi|474933875|ref|YP_007687457.1|  5 VVRIDREKCNGCGACVEACAEGAI 28
                                      799********************8 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00038
                            Fer4_6  6 pdkCigCgdCvrvCPegai 24
                                      +d C+g g+C   CP+gai
  gi|474933875|ref|YP_007687457.1| 40 EDYCDGLGACLPECPTGAI 58
                                      7899999***********8 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.5
                            Fer4_6  15 CvrvCP 20 
                                       C++ CP
  gi|474933875|ref|YP_007687457.1| 153 CIIGCP 158
                                       999998 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   5.3   2.7e-11     3e-08       2      58 ..       7      59 ..       6      60 .. 0.91
   2 ?   -0.5   0.0       1.2   1.4e+03      12      19 ..     151     158 ..     143     165 .. 0.63

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 2.7e-11
                           Fer4_21  2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58
                                      rid++kC gCg C+ aC +    ai++ + + + v+ed C G   C+  CP+ ++i+
  gi|474933875|ref|YP_007687457.1|  7 RIDREKCNGCGACVEACAE---GAIRMVDGKAMLVREDYCDGLGACLPECPT-GAIS 59
                                      7*****************7...788888888999*****************6.9986 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.2
                           Fer4_21  12 gkCliaCe 19 
                                         C+i C+
  gi|474933875|ref|YP_007687457.1| 151 RVCIIGCP 158
                                       44555554 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   7.7   9.4e-11   1.1e-07       1      52 []      12      57 ..      12      57 .. 0.94
   2 !    8.6   6.3    0.0026       2.9       2      36 ..      43      76 ..      42     160 .. 0.64

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 9.4e-11
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      +C gCgaCv+aC  +ai++ +       + + +++++C g gaC  +CPtga
  gi|474933875|ref|YP_007687457.1| 12 KCNGCGACVEACAEGAIRMVDG------KAMLVREDYCDGLGACLPECPTGA 57
                                      7******************885......568999****************98 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0026
                            Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgtekveidpe 36
                                      C g gaC + Cp++ai+++++ +++++ +++++p+
  gi|474933875|ref|YP_007687457.1| 43 CDGLGACLPECPTGAISIEKR-EAREFSDPKGEPS 76
                                      88889*************987.4555544444333 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   6.4   1.7e-09   1.9e-06       1      51 []      12      58 ..      12      58 .. 0.93
   2 ?    0.2   0.1      0.76   8.5e+02      42      48 ..     153     159 ..     134     175 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.7e-09
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                      kC+gCgaCveaC  g++++ +++ +   + +    C g gaC+  Cp+gai
  gi|474933875|ref|YP_007687457.1| 12 KCNGCGACVEACAEGAIRMVDGKAMLVREDY----CDGLGACLPECPTGAI 58
                                      7****************99999999887665....*************997 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.76
                            Fer4_9  42 CveaCpk 48 
                                       C+  Cpk
  gi|474933875|ref|YP_007687457.1| 153 CIIGCPK 159
                                       6666664 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   2.3   9.7e-08   0.00011       1      34 [.       6      38 ..       6      41 .. 0.81
   2 !    7.6   0.7    0.0057       6.4       5      20 ..      40      55 ..      37      69 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 9.7e-08
                           Fer4_15  1 VvvDrdaCigcglCvaeapevfeldedglasvll 34
                                      V++Dr++C gcg+Cv+++ e      dg+a +l+
  gi|474933875|ref|YP_007687457.1|  6 VRIDREKCNGCGACVEACAEGAIRMVDGKA-MLV 38
                                      89****************776666669999.544 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0057
                           Fer4_15  5 rdaCigcglCvaeape 20
                                      +d C+g g+C+ e+p+
  gi|474933875|ref|YP_007687457.1| 40 EDYCDGLGACLPECPT 55
                                      588***********85 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   1.0   4.1e-06    0.0046       1      20 [.      12      31 ..      12      41 .. 0.86
   2 !   13.4   0.4    0.0001      0.11       2      23 ..      43      64 ..      42      85 .. 0.80
   3 ?   -2.3   0.0       8.3   9.3e+03       7      13 ..     152     158 ..     149     170 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 4.1e-06
                           Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                      +C +Cg+C+e+C ++ai++ 
  gi|474933875|ref|YP_007687457.1| 12 KCNGCGACVEACAEGAIRMV 31
                                      5****************986 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.0001
                           Fer4_16  2 CgtCgkCaevCPtnaikekkek 23
                                      C + g+C+  CPt+ai+ +k++
  gi|474933875|ref|YP_007687457.1| 43 CDGLGACLPECPTGAISIEKRE 64
                                      88889***********977433 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 8.3
                           Fer4_16   7 kCaevCP 13 
                                        C+  CP
  gi|474933875|ref|YP_007687457.1| 152 VCIIGCP 158
                                       4777777 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   3.8   4.2e-08   4.7e-05       3      20 ..       6      23 ..       4      25 .. 0.91
   2 ?    3.1   0.4      0.11   1.2e+02      14      22 .]      47      55 ..      36      55 .. 0.78
   3 ?   -1.7   0.2       3.5     4e+03      15      21 ..     152     158 ..     150     159 .. 0.61

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 4.2e-08
                            Fer4_2  3 vvvdtdrCigCgaCvsaC 20
                                      v +d+++C+gCgaCv aC
  gi|474933875|ref|YP_007687457.1|  6 VRIDREKCNGCGACVEAC 23
                                      679*************** PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.11
                            Fer4_2 14 gaCvsaCPa 22
                                      gaC+  CP+
  gi|474933875|ref|YP_007687457.1| 47 GACLPECPT 55
                                      8*******7 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 3.5
                            Fer4_2  15 aCvsaCP 21 
                                        C+  CP
  gi|474933875|ref|YP_007687457.1| 152 VCIIGCP 158
                                       4655566 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   9.3   3.7e-07   0.00041       2      56 .]       6      54 ..       5      54 .. 0.76
   2 !    8.8   0.3    0.0016       1.8       4      46 ..      38      84 ..      35      94 .. 0.65
   3 ?    0.4   0.1      0.65   7.3e+02      12      21 ..     150     159 ..     148     207 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3.7e-07
                           Fer4_10  2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      v+id+++C +Cg+Cv+aC a     ++     +++a  +  + C+g gaC  +CP
  gi|474933875|ref|YP_007687457.1|  6 VRIDREKCNGCGACVEAC-A-----EGAIRMVDGKAMLVREDYCDGLGACLPECP 54
                                      689***************.5.....233333333444446789***********9 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0016
                           Fer4_10  4 idddtCirCgkCvkaCPadl...tsvgakgeaseeeavrk.kvekCt 46
                                      + +d C + g+C   CP+ +   ++ +a+++ +++++ +  ++ +C+
  gi|474933875|ref|YP_007687457.1| 38 VREDYCDGLGACLPECPTGAisiEKREAREFSDPKGEPSLaVPMACP 84
                                      56789999999999999977666444444444443333333666665 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.65
                           Fer4_10  12 CgkCvkaCPa 21 
                                        + C   CP 
  gi|474933875|ref|YP_007687457.1| 150 GRVCIIGCPK 159
                                       5678888987 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.9   0.00014      0.16       1      15 [.      12      26 ..       9      40 .. 0.68
   2 ?    6.9   0.2    0.0085       9.5       2      17 ..      43      58 ..      41      89 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                           Fer4_17  1 rCiqCgyClpeCpsy 15
                                      +C++Cg+C+++C  +
  gi|474933875|ref|YP_007687457.1| 12 KCNGCGACVEACAEG 26
                                      466666666666654 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0085
                           Fer4_17  2 CiqCgyClpeCpsyea 17
                                      C + g+ClpeCp++++
  gi|474933875|ref|YP_007687457.1| 43 CDGLGACLPECPTGAI 58
                                      7777889999998766 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   4.6   4.3e-05     0.049       2      14 ..      11      23 ..      10      26 .. 0.92
   2 ?    1.2   0.5      0.62   6.9e+02       8      17 .]      47      56 ..      40      56 .. 0.73
   3 ?    3.3   0.1      0.13   1.4e+02       8      15 ..     151     158 ..     148     168 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.3e-05
                            Fer4_4  2 erCigCgsCvaaC 14
                                      e+C+gCg+Cv aC
  gi|474933875|ref|YP_007687457.1| 11 EKCNGCGACVEAC 23
                                      89*********** PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.62
                            Fer4_4  8 gsCvaaCPqg 17
                                      g+C   CP+g
  gi|474933875|ref|YP_007687457.1| 47 GACLPECPTG 56
                                      789999*986 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.13
                            Fer4_4   8 gsCvaaCP 15 
                                       ++C++ CP
  gi|474933875|ref|YP_007687457.1| 151 RVCIIGCP 158
                                       58999999 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   7.5   4.8e-05     0.053       1      15 []      13      27 ..      13      27 .. 0.96
   2 ?    9.2   1.6    0.0022       2.5       1      15 []      43      57 ..      43      57 .. 0.93
   3 ?   -1.9   0.1         8     9e+03      10      13 ..      82      85 ..      82      87 .. 0.73
   4 ?   -0.9   0.0         4   4.4e+03       7      12 ..     153     158 ..     141     160 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.8e-05
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+gCgaCve+C +gA
  gi|474933875|ref|YP_007687457.1| 13 CNGCGACVEACAEGA 27
                                      ***********9998 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0022
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+g gaC+  CP+gA
  gi|474933875|ref|YP_007687457.1| 43 CDGLGACLPECPTGA 57
                                      88889*********9 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 8
                            Fer4_3 10 vCPv 13
                                      +CP 
  gi|474933875|ref|YP_007687457.1| 82 ACPG 85
                                      7*95 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 4
                            Fer4_3   7 CvevCP 12 
                                       C   CP
  gi|474933875|ref|YP_007687457.1| 153 CIIGCP 158
                                       555677 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7  10.7    0.0087       9.7       3      63 ..      11      55 ..       9      97 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0087
                            Fer4_8  3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63
                                      ekC++CgaC +aC         +    g+a+   ++e         ++C + gaC  +Cp+
  gi|474933875|ref|YP_007687457.1| 11 EKCNGCGACVEACA-----EGAIRMVDGKAML--VRE---------DYCDGLGACLPECPT 55
                                      69********9994.....1222233344444..222.........346666666666665 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1  10.1    0.0073       8.2       1      18 [.       8      25 ..       8      60 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0073
                           Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                      +Dr++C +cgaCve++ +
  gi|474933875|ref|YP_007687457.1|  8 IDREKCNGCGACVEACAE 25
                                      8***************87 PP

>> Furin-like_2  Furin-like repeat, cysteine-rich
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.7    0.0004      0.45       1      52 [.      13      66 ..      10      75 .. 0.81
   2 ?   -2.2   0.2         4   4.5e+03      81      90 ..     148     158 ..     123     167 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0004
                      Furin-like_2  1 ckgcalcse..enGclkckkklfllleregirqiGvclascpaGyfgvrnkevn 52
                                      c+gc  c e   +G ++  +   +l++ +     G+cl +cp+G   + ++e  
  gi|474933875|ref|YP_007687457.1| 13 CNGCGACVEacAEGAIRMVDGKAMLVREDYCDGLGACLPECPTGAISIEKREAR 66
                                      678888877224788888888888888888999***********9999888865 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4
                      Furin-like_2  81 hkGk.clescp 90 
                                        kG+ c+  cp
  gi|474933875|ref|YP_007687457.1| 148 IKGRvCIIGCP 158
                                       24433555555 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   2.8    0.0011       1.2      76      94 ..       7      25 ..       2      27 .. 0.87
   2 ?    1.5   0.2      0.48   5.3e+02      78      94 ..      39      55 ..      30      57 .. 0.82
   3 ?   -2.7   0.0       9.9   1.1e+04      41      41 ..     191     191 ..     167     214 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0011
                           Fer4_22 76 kfgesgCvGCgRCieacpv 94
                                      ++++++C GCg C+eac +
  gi|474933875|ref|YP_007687457.1|  7 RIDREKCNGCGACVEACAE 25
                                      67899************86 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.48
                           Fer4_22 78 gesgCvGCgRCieacpv 94
                                       e  C G g C   cp+
  gi|474933875|ref|YP_007687457.1| 39 REDYCDGLGACLPECPT 55
                                      56789999999999996 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 9.9
                           Fer4_22  41 l 41 
                                       +
  gi|474933875|ref|YP_007687457.1| 191 C 191
                                       1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1539.39
//
Query:       gi|474933876|ref|YP_007687458.1|  [L=119]
Description: putative pyrophosphatase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.4e-14   52.0   0.0    8.2e-14   51.6   0.0    1.2  1  MazG-like  MazG-like family
    2.6e-05   24.3   0.0    3.7e-05   23.8   0.0    1.2  1  MazG       MazG nucleotide pyrophosphohydrolase domain
     0.0022   18.4   0.0     0.0027   18.1   0.0    1.3  1  PRA-PH     Phosphoribosyl-ATP pyrophosphohydrolase


Domain annotation for each model (and alignments):
>> MazG-like  MazG-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.6   0.0   1.4e-17   8.2e-14       1      84 [.      34     119 .]      34     119 .] 0.95

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 1.4e-17
                         MazG-like   1 isknlkaiElLkaellksveelfkallk.gseeeildeLAdviiylylLAdrlGidfee.ideklkkklkkypveke 75 
                                       i ++ +a ElL+++  ++ e+ ++ + + ++   + deLAdv+  ++ +A+ +Gid++e  + kl ++ +kypvek 
  gi|474933876|ref|YP_007687458.1|  34 IGISSEAGELLEIFRFQNNEQCQTIINDpQKGGDVRDELADVLYFTLRFAEVCGIDLSEaFESKLRQNREKYPVEKF 110
                                       66899**************9999988867999********************************************* PP

                         MazG-like  76 hglekkygd 84 
                                       +g+++ky++
  gi|474933876|ref|YP_007687458.1| 111 KGVNRKYNE 119
                                       *******86 PP

>> MazG  MazG nucleotide pyrophosphohydrolase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   6.2e-09   3.7e-05       4      67 ..      30     102 ..      27     107 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 6.2e-09
                                       HHHHHHHHHHHHHHHHHHHTT-HH.............HHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHH CS
                              MazG   4 etllaylleEvgEvaeaIkkedrd.............eleeELGDvLlqvlflaniaeeeggidledvaetileKle 67 
                                       + l+ ++  E+gE++e  + ++ +             ++++EL+DvL+  l +a++     gidl++++e+ l+  +
  gi|474933876|ref|YP_007687458.1|  30 KDLAIGISSEAGELLEIFRFQNNEqcqtiindpqkggDVRDELADVLYFTLRFAEV----CGIDLSEAFESKLRQNR 102
                                       567778999******9887644444577777777888******************9....9******9998766554 PP

>> PRA-PH  Phosphoribosyl-ATP pyrophosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   4.5e-07    0.0027      48      78 ..      66      96 ..      24     101 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 4.5e-07
                                      HHHHHHHHHHHHHHHHHHHHCT--CHHHHHH CS
                            PRA-PH 48 aeladelaDllYvtygllvllGidldavfee 78
                                       ++ delaD+lY+t+  +   Gidl + fe+
  gi|474933876|ref|YP_007687458.1| 66 GDVRDELADVLYFTLRFAEVCGIDLSEAFES 96
                                      5688**********************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 835.27
//
Query:       gi|474933877|ref|YP_007687459.1|  [L=269]
Description: hypothetical protein TALC_00289 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0046   17.1   0.1      0.011   15.9   0.1    1.6  1  Mrr_N         Mrr N-terminal domain
     0.0085   14.9   0.1      0.012   14.4   0.1    1.1  1  Cas_Csm6      CRISPR-associated protein (Cas_Csm6)
  ------ inclusion threshold ------
      0.076   11.8   0.0        0.1   11.4   0.0    1.2  1  Cas_Cas02710  CRISPR-associated protein (Cas_Cas02710)


Domain annotation for each model (and alignments):
>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   1.8e-06     0.011      21      85 ..     193     263 ..     178     265 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.8e-06
                             Mrr_N  21 keirervaerf...glseeeraell..psgkqtrfknrvgWartyLkkagllespk.rgvwkiTekGrevl 85 
                                       + +  +v++ +   gl e+e +e    +s kq+++ +  +  ++  +++g++++p+ r+ + +Te+G++v+
  gi|474933877|ref|YP_007687459.1| 193 STVAPAVIKALadaGLWEYEANEGSvkTSPKQKEVMYYQRHFINAWVEQGWIDKPSrRSRFDLTETGKNVI 263
                                       5555555555555589999988866669999999999999999*************8999********996 PP

>> Cas_Csm6  CRISPR-associated protein (Cas_Csm6)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   2.1e-06     0.012       4      75 ..      64     133 ..      62     146 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.1e-06
                          Cas_Csm6   4 eIiereeidnvhefDvFyevFrkilkeiedeneddtiLlNvsSGTPaMksalvllavlgekrlkpvQVsTPe 75 
                                       +Iie ++ d v  f +   +   i+++ ++e ++++iL+N s GT    +a ++  +  ++++++  V T e
  gi|474933877|ref|YP_007687459.1|  64 RIIE-HKEDAVYSFQLMLRDILAIVAQSNKEVPGAEILINASAGTSEFSAAAIIASM-MHPNVTAFTVGTKE 133
                                       7888.777899999999999999999999999**************99877666555.55667776676655 PP

>> Cas_Cas02710  CRISPR-associated protein (Cas_Cas02710)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   1.7e-05       0.1      59     104 ..      81     132 ..      46     143 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.7e-05
                                       HHHHHHS.......TTS-EEEE-SSS-HHHHHHHHHHHHHHTEEEEEEE--B CS
                      Cas_Cas02710  59 kevleka......leeeevivDlTgGtkeMtaglalagillrvklsyVggea 104
                                       +++l+++      ++  e+ ++++ Gt+e +a++++a++++++   +  g++
  gi|474933877|ref|YP_007687459.1|  81 RDILAIVaqsnkeVPGAEILINASAGTSEFSAAAIIASMMHPNVTAFTVGTK 132
                                       44444444445667889************************88877766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1777.76
//
Query:       gi|474933878|ref|YP_007687460.1|  [L=186]
Description: putative membrane protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-48  163.6  13.3    2.7e-48  163.6  13.3    2.0  2  Mntp      Putative manganese efflux pump


Domain annotation for each model (and alignments):
>> Mntp  Putative manganese efflux pump
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   2.9   0.00076        14      75     111 ..       3      40 ..       1      40 [. 0.71
   2 !  163.6  13.3   1.5e-52   2.7e-48       3     152 .]      32     179 ..      30     179 .. 0.98

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.00076
                              Mntp  75 lksllllaiatSiDAlavGls..LallkvnillavlliG 111
                                       + +++llai+  +DA+av +   La+ k+ ++ ++++iG
  gi|474933878|ref|YP_007687460.1|   3 ILTIVLLAIGLAMDAFAVSVCkgLAMGKA-TVRSMVIIG 40 
                                       57899*************99743555544.555555665 PP

  == domain 2  score: 163.6 bits;  conditional E-value: 1.5e-52
                              Mntp   3 klkealkialifGlfqalmpliGwllGkllselieavdhwiafllLlllGlkmivealkeeeeekkekeelslksll 79 
                                        +++++ i+++fG+fq+lmp+iG+++G+ +++ +e++dhwiaf+lLl++Gl+m++e+++ eee+ ++  +l ++ +l
  gi|474933878|ref|YP_007687460.1|  32 TVRSMVIIGAWFGFFQFLMPIIGFYVGRSFKDAVEDYDHWIAFALLLVIGLNMVREGISGEEENVDA--SLGFRIML 106
                                       57899**********************************************************9996..7******* PP

                              Mntp  80 llaiatSiDAlavGlsLallkvnillavlliGlvtlvlsllGlllGrklgsllgkkaeilGGliLiliGlkil 152
                                       +laiatSiDAlavG+sLa+ +  il++ ++iG++t+ +s++G+ +G+ lg++lg++aeilGG+iL+ iG+k+l
  gi|474933878|ref|YP_007687460.1| 107 ILAIATSIDALAVGISLAMDEGTILVPSVIIGVITMGISMTGVKIGSLLGDRLGNRAEILGGIILVTIGFKVL 179
                                       ***********************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1202.42
//
Query:       gi|474933879|ref|YP_007687461.1|  [L=100]
Description: hypothetical protein TALC_00291 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.072   13.5   1.3        8.3    6.9   0.1    2.1  2  Asp23     Asp23 family, cell envelope-related function
       0.15   12.1   0.0       0.27   11.3   0.0    1.3  1  HU-HIG    HU domain fused to wHTH, Ig, or Glycine-rich motif


Domain annotation for each model (and alignments):
>> Asp23  Asp23 family, cell envelope-related function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1   0.00093       8.3      74      97 ..       3      26 ..       1      29 [. 0.89
   2 ?    6.0   0.1    0.0017        15       7      32 ..      45      70 ..      42      96 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00093
                             Asp23 74 ipevaenvqekVkeaveemtglev 97
                                      ++ va+ v + V+++v+emt+ ++
  gi|474933879|ref|YP_007687461.1|  3 VSMVAKGVADDVANRVREMTQSKI 26
                                      6889****************9876 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0017
                             Asp23  7 isdeViakiagiaaeeveGvvgmagk 32
                                      +++eV++ +  +  +ev+Gvv+  ++
  gi|474933879|ref|YP_007687461.1| 45 LNEEVVEILCVVEQSEVDGVVNAISE 70
                                      6799*****************97766 PP

>> HU-HIG  HU domain fused to wHTH, Ig, or Glycine-rich motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0     3e-05      0.27      41      84 ..      50      94 ..      43      98 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3e-05
                            HU-HIG 41 iskrstlsrgdvkavldaledel.keaLadGerVeLgelGyFsls 84
                                      ++  + + +++v++v+ a+++    ++L +G++V ++ +G + +s
  gi|474933879|ref|YP_007687461.1| 50 VEILCVVEQSEVDGVVNAISEIGrMDELGRGYIVTIPSVGVMIPS 94
                                      6667999************99862579*************87665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 636.67
//
Query:       gi|474933880|ref|YP_007687462.1|  [L=490]
Description: Protein of unknown function (DUF1538) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   3.8e-106  353.1  63.9    3.7e-53  180.0  26.6    2.0  2  DUF1538   Protein of unknown function (DUF1538)
  ------ inclusion threshold ------
       0.75   10.1   3.5       0.68   10.3   0.1    2.8  2  KASH      Nuclear envelope localisation domain


Domain annotation for each model (and alignments):
>> DUF1538  Protein of unknown function (DUF1538)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.0  26.6   4.1e-57   3.7e-53       1     210 [.      18     226 ..      18     227 .. 0.98
   2 !  179.4  29.3   6.2e-57   5.5e-53       2     210 ..     270     478 ..     269     479 .. 0.98

  Alignments for each domain:
  == domain 1  score: 180.0 bits;  conditional E-value: 4.1e-57
                           DUF1538   1 ivlvlllfqllvlklslkelaeillGlllvvlGlalFllGvelgllplGeqvgsklakkkklllvllvafllGflvt 77 
                                       i+++ll++ ++++ +++ e++  ++ ++lv+lG++lFl Gv++g++p+G+++g ++ ++k+++ ++++ f++ ++vt
  gi|474933880|ref|YP_007687462.1|  18 ITVLLLVVDTICVGTNPLEFTLEITCVILVLLGFTLFLYGVDVGIIPMGKSIGIEMSRRKSIIPMIAIVFVISIIVT 94 
                                       6789999999999999999999999**************************************************** PP

                           DUF1538  78 lAEPalsvlakqveevsagaikkkvlilavaiGvglaialgvlrillgislkylllpgyllvllltllvpkefvaia 154
                                       +AEP+++ ++++v+ + +  ++ ++l+ ++a+Gvg++++l+ lri+l+islk+l+++gy lvl++ llvpk +++ia
  gi|474933880|ref|YP_007687462.1|  95 VAEPDVTGFSSTVNLLFH-DVDYNMLVASIAVGVGVMLVLAALRIYLDISLKILITIGYSLVLIIGLLVPKYILGIA 170
                                       **************9966.9********************************************************* PP

                           DUF1538 155 fDsgGvttgpitvplilalglGvasalegknalvdgFGlvalaslgPilavlllgl 210
                                       fDsgGvttgpit+p+++a+g+G++ a++++   +++FG+v+las+gP+++v+l+g 
  gi|474933880|ref|YP_007687462.1| 171 FDSGGVTTGPITIPVLMAMGMGIGMATSRNGDPMNSFGMVGLASIGPLITVMLYGQ 226
                                       ******************************************************97 PP

  == domain 2  score: 179.4 bits;  conditional E-value: 6.2e-57
                           DUF1538   2 vlvlllfqllvlklslkelaeillGlllvvlGlalFllGvelgllplGeqvgsklakkkklllvllvafllGflvtl 78 
                                       +++++++  ++l+ s +++  ++lG+ll+v+G+++Fl+Gv  g++p+++++g  l + +  +++ll+++ lGf+v+ 
  gi|474933880|ref|YP_007687462.1| 270 LIIFIIMMKYYLHSSWHDFEMMCLGILLTVVGMIMFLTGVYSGFMPMAQEIGVYLIEDNVGIWILLLGLSLGFMVIA 346
                                       5778888889999**************************************************************** PP

                           DUF1538  79 AEPalsvlakqveevsagaikkkvlilavaiGvglaialgvlrillgislkylllpgyllvllltllvpkefvaiaf 155
                                       AEPa+++l +qve+vs+++i+++++i++v++Gv++++ +g++ +  g+   y++lp+y+l+++l +++++++v+i +
  gi|474933880|ref|YP_007687462.1| 347 AEPAVKILGSQVEAVSKNMITTNTIIIVVGVGVSVFVGIGMYALSQGWMSIYYILPIYALAIALLWFMDNSLVGITY 423
                                       ***************************************************************************** PP

                           DUF1538 156 DsgGvttgpitvplilalglGvasalegknalvdgFGlvalaslgPilavlllgl 210
                                       D+gGv+tgp++v++i+++  ++a++l+g+ a +++FG++al++l+Pi+a+ +lg+
  gi|474933880|ref|YP_007687462.1| 424 DAGGVATGPMSVAIIMSMYAAMAEVLGGEIASENAFGVIALIALAPIIALSVLGI 478
                                       ******************************************************8 PP

>> KASH  Nuclear envelope localisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   7.6e-05      0.68       1      19 [.       7      25 ..       7      32 .. 0.87
   2 ?   -2.4   0.6      0.65   5.9e+03      12      25 ..      41      54 ..      35      59 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 7.6e-05
                              KASH  1 flgRvlraalpLqllLlll 19
                                      +l+ v+r+alp+++lLl++
  gi|474933880|ref|YP_007687462.1|  7 YLWEVCRTALPITVLLLVV 25
                                      6899*********888875 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.65
                              KASH 12 LqllLllllllalL 25
                                      ++ ++l+ll++ l+
  gi|474933880|ref|YP_007687462.1| 41 ITCVILVLLGFTLF 54
                                      55455555555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (490 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1093  (0.0609627); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.75u 0.36s 00:00:01.10 Elapsed: 00:00:00.56
# Mc/sec: 2655.80
//
Query:       gi|474933881|ref|YP_007687463.1|  [L=250]
Description: conserved hypothetical protein TIGR00162 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.8e-41  140.1   0.0    1.1e-40  139.9   0.0    1.0  1  PAC2             PAC2 family
  ------ inclusion threshold ------
      0.057   13.1   0.2      0.097   12.3   0.2    1.3  1  Retrotran_gag_2  gag-polypeptide of LTR copia-type
       0.13   10.6   0.0       0.16   10.4   0.0    1.1  1  Hemagglutinin    Haemagglutinin


Domain annotation for each model (and alignments):
>> PAC2  PAC2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.9   0.0   1.9e-44   1.1e-40       1     209 [.      18     230 ..      18     234 .. 0.93

  Alignments for each domain:
  == domain 1  score: 139.9 bits;  conditional E-value: 1.9e-44
                                       EEEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETT..EEE-SEEE.EEETTT.SEEEEEEE CS
                              PAC2   1 LilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveeg..relepprl.yakdsgsrdllvlqg 74 
                                       +++++pgiGnVg++a d+L+++l+a++++  +s+  +p     p+v+ +++   ++  ++l yak ++++d+++l+g
  gi|474933881|ref|YP_007687463.1|  18 FVEALPGIGNVGKIAGDFLADTLGAKRFAVMYSEN-FP-----PQVIPDQDcvIRMACNELwYAKAPNGKDVIFLRG 88 
                                       689********************************.**.....*********999999***9999889********* PP

                                       ....E-HSCHHHHHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHHH.....CT...- CS
                              PAC2  75 ....repilqyeefakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeelleele.....es...e 139
                                            +p++q + +a+ +++++ ++g +++++Lgg+++g+ +     +p  v+ga+++ +l ++le      +   +
  gi|474933881|ref|YP_007687463.1|  89 dyqgSTPEGQFM-LAEDVMEILLSYGTEKIITLGGYGTGQMT----GEP-HVFGAVSRISLKKNLEkmgvtFNpgqP 159
                                       ************.************************99985....477.9**************64665511667* PP

                                       CEEEEHHHHHHHHHHHHTT-EEEEEEEEEECCC--HHHHHHHHHHHHHHHT--.-HCHHHHHHHHHHHHHH CS
                              PAC2 140 yggivgitglLlsaakergipavgllaevphylpdPkaaaalleflskllgle.vdtedLeedaeeleeql 209
                                       ++gi+g++g+L+++++ +gi++ +l++e+++ + d kaa+a++++l+k++++   d++dL+ ++++++e  
  gi|474933881|ref|YP_007687463.1| 160 QAGIIGAAGALIGLGQLNGIDSFCLMGETSGFFADHKAAIAVINVLKKIFKIRkADMKDLQAMSKQIDELT 230
                                       ***************************************************998*************9865 PP

>> Retrotran_gag_2  gag-polypeptide of LTR copia-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   1.6e-05     0.097      50      96 ..     202     248 ..     191     249 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.6e-05
                   Retrotran_gag_2  50 ltlrkklfslkmkegesvadhinkleelvneLsalgvkiddedkvvl 96 
                                       ++++kk f++++++ ++++ + ++++el  + s++ ++ +d+d + +
  gi|474933881|ref|YP_007687463.1| 202 INVLKKIFKIRKADMKDLQAMSKQIDELTAQVSQAQEQPSDDDSLSY 248
                                       5889**************************************98876 PP

>> Hemagglutinin  Haemagglutinin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   2.6e-05      0.16     355     414 ..     185     242 ..     144     249 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 2.6e-05
                                       EETTEEEEEEXHHHHHHHHHHHHHHHHHHHHHTTTEEEBXSSXXTTTTHHHHHHHHHHHH CS
                     Hemagglutinin 355 sneqGsavaadkkstqeainkitkkvnsliekenkqleavgkelnelekrieeldkkvdd 414
                                        +e  s++ ad+k++   in + kk+ ++ +   k+l+a++k+++el  ++ + +++  d
  gi|474933881|ref|YP_007687463.1| 185 MGE-TSGFFADHKAAIAVIN-VLKKIFKIRKADMKDLQAMSKQIDELTAQVSQAQEQPSD 242
                                       444.58999****9988887.7899**************************999888554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1124  (0.0626917); expected 358.6 (0.02)
Passed bias filter:                      992  (0.0553294); expected 358.6 (0.02)
Passed Vit filter:                       119  (0.00663729); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 1553.42
//
Query:       gi|474933882|ref|YP_007687464.1|  [L=260]
Description: Translation initiation factor 2, alpha subunit (eIF-2alpha) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-23   82.9   0.0    4.6e-23   81.5   0.0    1.7  2  EIF_2_alpha  Eukaryotic translation initiation factor 2 alpha
    1.3e-11   44.7   0.1    2.8e-11   43.6   0.1    1.6  1  S1           S1 RNA binding domain
  ------ inclusion threshold ------
      0.048   13.6   0.0      0.082   12.9   0.0    1.5  1  HNOB         Haem-NO-binding


Domain annotation for each model (and alignments):
>> EIF_2_alpha  Eukaryotic translation initiation factor 2 alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.58   3.5e+03      72      85 ..      50      63 ..      38     115 .. 0.61
   2 !   81.5   0.0   7.7e-27   4.6e-23       1     116 []     120     228 ..     120     228 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.58
                                      HHHHHHHHHHHST. CS
                       EIF_2_alpha 72 veaIkeaLkageea 85
                                      v+ I++ +++g++ 
  gi|474933882|ref|YP_007687464.1| 50 VKYIRDYIREGQKT 63
                                      55666666644442 PP

  == domain 2  score: 81.5 bits;  conditional E-value: 7.7e-27
                                       HHHCTHHHHTTTTS-HHHHHHHHHSTTHHHHHTTS-TTTHHHHHHCTHHHHHHT-EEEEEEEEEEE-STTHHHHHHH CS
                       EIF_2_alpha   1 lyeevgwklyekyghaydaFklaitdeevldkleipeeveeaLveiikkklkpqkvkiradieltcftkdGveaIke 77 
                                       +y+++g+ l e +g++ydaF+ a+ d e + + +++ +++ea+ + +k ++ p++v+i a ie+t+ ++dGve+I++
  gi|474933882|ref|YP_007687464.1| 120 AYDSFGNMLIEDFGTLYDAFEGAVADSESFLS-DYEGDWIEAFCDVAKDNIAPPTVQIDAIIEMTSSAPDGVERIRA 195
                                       599*****************999999996666.6789**************************************** PP

                                       HHHHHST.S..TTSSSEEEEEEEESSSSEEEEEEEES.. CS
                       EIF_2_alpha  78 aLkageeasneeeveeeeevkikliapPeYvltvetldk 116
                                       aL a++++      + + +vki+ +++P+Y++ v+++d+
  gi|474933882|ref|YP_007687464.1| 196 ALLAAQAE------AGDDDVKITSVGSPRYRVVVTSPDY 228
                                       ***76662......34579*****************997 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.1   4.7e-15   2.8e-11       2      75 .]       8      82 ..       8      82 .. 0.96

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 4.7e-15
                                      STTTCEEEEEEEEEETTEEEEEET..TTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEEEEC CS
                                S1  2 pekgevveGeVtsvtkgGafVelg..ngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriilsik 75
                                      pe ge v  +Vtsv ++GafV l+   + egf+++ +++    v+ + + +++G++   kvl+vd +++ i+ls+k
  gi|474933882|ref|YP_007687464.1|  8 PENGELVVCTVTSVKNFGAFVTLDeyDNKEGFIHVRDIATG-WVKYIRDYIREGQKTVCKVLGVDSQKGHIDLSLK 82
                                      678999999****************999************9.99******************************86 PP

>> HNOB  Haem-NO-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.4e-05     0.082      29     121 ..      85     176 ..      51     185 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.4e-05
                                       TSTTSS--TTSBTTHHHHHHHHHHHHHHHTS-HHHHHHHHHHHHHHHHHHHHTHHHHTHTTCSHHHHHHHHHH..HH CS
                              HNOB  29 gleekvftthetYddslllklveaaskvlglsadelleafGeyfvkffsekgydkllrvlgrnlfeFLknldn..lH 103
                                       + ++k   +++  ++++  kl+e ++ +l+ s d+ +  fG+++++ f  + yd++  +   +  +FL+  +   + 
  gi|474933882|ref|YP_007687464.1|  85 NDHQKRERIQQWKNENKAEKLFEIVAGKLKCSPDDAYDSFGNMLIEDFG-TLYDAFEGA-VADSESFLSDYEGdwIE 159
                                       5445555555556778999******************************.***999873.34888888877765333 PP

                                       HHHHHHHSTTSS--EEEE CS
                              HNOB 104 vevlklsypkakpPsfrc 121
                                         ++ ++  ++ pP++++
  gi|474933882|ref|YP_007687464.1| 160 -AFCDVAKDNIAPPTVQI 176
                                       .66666556777776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       876  (0.0488594); expected 358.6 (0.02)
Passed bias filter:                      677  (0.0377601); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1566.64
//
Query:       gi|474933883|ref|YP_007687465.1|  [L=55]
Description: SSU ribosomal protein S27E [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.5e-22   76.5   1.6    9.9e-22   76.4   1.6    1.0  1  Ribosomal_S27e   Ribosomal protein S27
      8e-07   28.5   0.5    1.3e-06   27.8   0.5    1.3  1  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0018   18.3   0.3     0.0021   18.0   0.3    1.1  1  Zn_Tnp_IS91      Transposase zinc-binding domain
     0.0029   17.7   0.4     0.0045   17.1   0.4    1.3  1  Zn-ribbon_8      Zinc ribbon domain
     0.0037   16.8   6.1      0.064   12.9   1.6    2.3  2  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
     0.0056   16.6   0.0     0.0058   16.5   0.0    1.1  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
     0.0062   16.3   1.9        0.3   10.9   0.1    2.1  2  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
  ------ inclusion threshold ------
      0.014   15.8   0.4      0.017   15.5   0.4    1.2  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.016   14.9   2.3       0.78    9.5   0.9    2.2  2  zinc_ribbon_2    zinc-ribbon domain
       0.02   14.5   1.5       0.24   11.1   0.2    2.2  2  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
      0.023   14.6   0.5      0.038   13.9   0.5    1.3  1  Zn_ribbon_SprT   SprT-like zinc ribbon domain
      0.024   14.6   0.5        2.3    8.3   0.0    2.2  2  ADK_lid          Adenylate kinase, active site lid
      0.025   14.3   0.5        5.3    6.8   0.0    2.1  2  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
      0.026   14.6   0.2      0.027   14.5   0.2    1.2  1  HypA             Hydrogenase/urease nickel incorporation, met
      0.036   14.0   0.4      0.043   13.8   0.4    1.2  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.043   13.7   2.0       0.11   12.3   0.6    2.0  2  DUF3797          Domain of unknown function (DUF3797)
        0.1   12.4   0.9       0.37   10.6   1.3    1.7  2  PADR1            PADR1 (NUC008) domain
       0.11   12.3   0.7       0.13   12.2   0.7    1.1  1  eIF-5_eIF-2B     Domain found in IF2B/IF5
       0.14   12.0   2.7       0.66    9.9   2.7    1.9  1  TFIIS_C          Transcription factor S-II (TFIIS)
       0.17   11.3   0.1       0.18   11.2   0.1    1.0  1  Mcm10            Mcm10 replication factor
        0.2   11.6   3.5        2.3    8.2   0.2    2.2  2  zinc_ribbon_4    zinc-ribbon domain
        0.3   11.7   2.1         16    6.1   2.1    2.1  1  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
       0.67    9.7   4.4        2.7    7.8   0.3    2.1  2  A2L_zn_ribbon    A2L zinc ribbon domain
        1.3    9.1   5.5        3.2    7.8   1.1    2.2  2  DUF1610          Domain of unknown function (DUF1610)


Domain annotation for each model (and alignments):
>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.4   1.6   1.3e-24   9.9e-22       3      54 ..       3      54 ..       1      55 [] 0.96

  Alignments for each domain:
  == domain 1  score: 76.4 bits;  conditional E-value: 1.3e-24
                                      --EEEEE-TTTS-EEEEESS-SS-EEESSSTCEEEEECSSSEEESSCEEEEE CS
                    Ribosomal_S27e  3 skFldvkCpdCenetvvFshaatvvkCisCgkvLvePtGGkaklkaqilerl 54
                                       +F+++kCpdC+ne++vF++aat v+C  Cg vLv P+GGk+ lk ++le++
  gi|474933883|ref|YP_007687465.1|  3 NNFVKMKCPDCGNEQIVFQRAATRVLCHVCGAVLVVPKGGKGELKGEVLEVV 54
                                      58***********************************************987 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.5   1.7e-09   1.3e-06       1      29 [.       8      36 ..       8      40 .. 0.97

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1.7e-09
                                      EEETTTTCEECHEETSTTCEEESSSSBEE CS
                      TF_Zn_Ribbon  1 ykCPnCgstnlveDpergelvCtdCGlVl 29
                                      +kCP+Cg++++v+  + + ++C  CG+Vl
  gi|474933883|ref|YP_007687465.1|  8 MKCPDCGNEQIVFQRAATRVLCHVCGAVL 36
                                      89**************************8 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.3   2.8e-06    0.0021      37      65 ..       5      34 ..       2      38 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.8e-06
                       Zn_Tnp_IS91 37 faryeCeeCghekivyfsCksrh.CpsCqk 65
                                      f +++C++Cg+e+iv+++   r  C+ C++
  gi|474933883|ref|YP_007687465.1|  5 FVKMKCPDCGNEQIVFQRAATRVlCHVCGA 34
                                      67899*****************99****97 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.4   6.1e-06    0.0045       7      34 ..       9      34 ..       7      38 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.1e-06
                       Zn-ribbon_8  7 rCeeCghefevlqsisdaplta.CPeCgs 34
                                      +C +Cg+e  v+q+++     + C  Cg+
  gi|474933883|ref|YP_007687465.1|  9 KCPDCGNEQIVFQRAA---TRVlCHVCGA 34
                                      8********9***866...5666*****8 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.2    0.0098       7.3       7      16 ..       8      17 ..       3      25 .. 0.81
   2 !   12.9   1.6   8.6e-05     0.064       9      26 ..      29      46 ..      25      47 .. 0.96

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0098
                                      EE-TTT--EE CS
                   Desulfoferrod_N  7 YkCevCGniV 16
                                       kC  CGn+ 
  gi|474933883|ref|YP_007687465.1|  8 MKCPDCGNEQ 17
                                      59******75 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 8.6e-05
                                      -TTT--EEEECC--SS-E CS
                   Desulfoferrod_N  9 CevCGniVeVleaGgGeL 26
                                      C vCG + +V ++G GeL
  gi|474933883|ref|YP_007687465.1| 29 CHVCGAVLVVPKGGKGEL 46
                                      ****************98 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   7.8e-06    0.0058       5      39 ..       3      37 ..       1      51 [. 0.87

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7.8e-06
                    OrfB_Zn_ribbon  5 keqleykakeyGikveevnpayTSktCseCgsknk 39
                                       ++++ k+ + G + ++ ++a T   C++Cg+++ 
  gi|474933883|ref|YP_007687465.1|  3 NNFVKMKCPDCGNEQIVFQRAATRVLCHVCGAVLV 37
                                      689999*************************9876 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.1    0.0004       0.3       3      15 ..       9      22 ..       7      25 .. 0.84
   2 ?    5.4   0.2     0.021        15       2      19 ..      27      44 ..      26      48 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0004
                                      E-SSS-.-EEEEEE CS
                    zf-C4_Topoisom  3 kCPkCg.gdLvlkr 15
                                      kCP Cg +++v +r
  gi|474933883|ref|YP_007687465.1|  9 KCPDCGnEQIVFQR 22
                                      9*****99999776 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.021
                                      EE-SSS--EEEEEE-SSS CS
                    zf-C4_Topoisom  2 ekCPkCggdLvlkrgkkG 19
                                      + C  Cg+ Lv+ +g kG
  gi|474933883|ref|YP_007687465.1| 27 VLCHVCGAVLVVPKGGKG 44
                                      5799***99999888777 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.4   2.3e-05     0.017       5      37 ..       9      37 ..       8      52 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.3e-05
                   Lar_restr_allev  5 pCPfCggravlersqrvvaeigqcvyCadCga..s 37
                                       CP Cg++++++++  +       v C+ Cga  +
  gi|474933883|ref|YP_007687465.1|  9 KCPDCGNEQIVFQRAAT------RVLCHVCGAvlV 37
                                      5***********99666......599******442 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.9     0.001      0.78       1       8 [.       9      16 ..       9      17 .. 0.92
   2 ?    4.9   0.0     0.031        23      14      22 ..      27      35 ..      23      36 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.001
                     zinc_ribbon_2  1 fCpnCGae 8 
                                      +Cp CG+e
  gi|474933883|ref|YP_007687465.1|  9 KCPDCGNE 16
                                      8*****98 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.031
                     zinc_ribbon_2 14 kFCpyCGtp 22
                                      + C  CG+ 
  gi|474933883|ref|YP_007687465.1| 27 VLCHVCGAV 35
                                      568888875 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   0.00032      0.24      21      31 ..       7      17 ..       6      17 .. 0.92
   2 ?    2.7   0.1      0.13        97      24      29 ..      29      34 ..      23      37 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00032
                     zf-NADH-PPase 21 arvCpaCgleh 31
                                      ++ Cp+Cg+e+
  gi|474933883|ref|YP_007687465.1|  7 KMKCPDCGNEQ 17
                                      79*******97 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.13
                     zf-NADH-PPase 24 CpaCgl 29
                                      C+ Cg+
  gi|474933883|ref|YP_007687465.1| 29 CHVCGA 34
                                      999997 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.5   5.1e-05     0.038       6      35 ..       9      37 ..       9      38 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.1e-05
                    Zn_ribbon_SprT  6 rCtgCgreythhlsirrhn..YrCrrCkgtLr 35
                                      +C++Cg   + +  ++r++    C+ C+ +L+
  gi|474933883|ref|YP_007687465.1|  9 KCPDCG---NEQIVFQRAAtrVLCHVCGAVLV 37
                                      6*****...9999****999999****98875 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0031       2.3      20      31 ..       6      17 ..       4      23 .. 0.77
   2 ?    4.9   0.1     0.036        27      23      32 ..      28      37 ..      24      38 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0031
                                      STTB-TTT--.- CS
                           ADK_lid 20 veglCDkCGepL 31
                                      v+++C +CG + 
  gi|474933883|ref|YP_007687465.1|  6 VKMKCPDCGNEQ 17
                                      689******973 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.036
                                      B-TTT--.-B CS
                           ADK_lid 23 lCDkCGepLv 32
                                      lC +CG  Lv
  gi|474933883|ref|YP_007687465.1| 28 LCHVCGAVLV 37
                                      5666666665 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1      0.01       7.8       5      12 ..       8      15 ..       5      22 .. 0.82
   2 ?    6.8   0.0    0.0071       5.3       5      15 ..      27      37 ..      23      43 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.01
                           zf-RRN7  5 ppCgvCgc 12
                                      + C+ Cg+
  gi|474933883|ref|YP_007687465.1|  8 MKCPDCGN 15
                                      79*****9 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0071
                           zf-RRN7  5 ppCgvCgcrsf 15
                                        C vCg++++
  gi|474933883|ref|YP_007687465.1| 27 VLCHVCGAVLV 37
                                      56******875 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.2   3.6e-05     0.027      69     103 ..       6      43 ..       1      53 [. 0.76

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.6e-05
                                       -EEEETTTS-EEECHH..H.HHS-TTTSSS-EEEEESS CS
                              HypA  69 vkvrCreCgkefelee..k.alrCpkCgsadveivsGe 103
                                       vk++C +Cg+e  + +  + ++ C  Cg+  v  ++G+
  gi|474933883|ref|YP_007687465.1|   6 VKMKCPDCGNEQIVFQraAtRVLCHVCGAVLVVPKGGK 43 
                                       789******99875442325679*****9888777776 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.4   5.8e-05     0.043      19      44 ..       8      33 ..       3      35 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.8e-05
                     Zn_Tnp_IS1595 19 fvCPhCgsrkayriktrglfqCkeCr 44
                                        CP Cg++++ + +++ +  C  C+
  gi|474933883|ref|YP_007687465.1|  8 MKCPDCGNEQIVFQRAATRVLCHVCG 33
                                      57********9999999999999997 PP

>> DUF3797  Domain of unknown function (DUF3797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.6   0.00015      0.11      15      29 ..       9      23 ..       4      30 .. 0.80
   2 ?    1.8   0.0       0.3   2.3e+02      14      29 ..      27      42 ..      19      46 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
                           DUF3797 15 qCPeCgNnkvlNseg 29
                                      +CP+CgN+++    +
  gi|474933883|ref|YP_007687465.1|  9 KCPDCGNEQIVFQRA 23
                                      7********976655 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.3
                           DUF3797 14 vqCPeCgNnkvlNseg 29
                                      v C +Cg   v   +g
  gi|474933883|ref|YP_007687465.1| 27 VLCHVCGAVLVVPKGG 42
                                      67999*9887776666 PP

>> PADR1  PADR1 (NUC008) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.3   0.00049      0.37      15      29 ..       9      23 ..       6      33 .. 0.83
   2 ?   -0.3   0.1       1.2   9.3e+02      16      22 ..      29      34 ..      24      43 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00049
                             PADR1 15 kCpeCkegqlvfdss 29
                                      kCp C++ q+vf++ 
  gi|474933883|ref|YP_007687465.1|  9 KCPDCGNEQIVFQRA 23
                                      8***********986 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.2
                             PADR1 16 CpeCkeg 22
                                      C  C+  
  gi|474933883|ref|YP_007687465.1| 29 CHVCG-A 34
                                      99998.4 PP

>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.7   0.00017      0.13      85     116 ..       3      34 ..       1      35 [. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00017
                                       HHHT..STSSSTSTCEEECC.SSSCEEEEESSSTC CS
                      eIF-5_eIF-2B  85 eeyV..lCkeCkspetelek.eerllvlkCkaCga 116
                                       +++V   C+ C++ ++ +++  +r+l   C+ Cga
  gi|474933883|ref|YP_007687465.1|   3 NNFVkmKCPDCGNEQIVFQRaATRVL---CHVCGA 34 
                                       5565336*********9999557777...999997 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   2.7   0.00088      0.66       2      19 ..       9      26 ..       8      36 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00088
                           TFIIS_C  2 kCpkCgsreayffqlQtR 19
                                      kCp Cg+++++f  + tR
  gi|474933883|ref|YP_007687465.1|  9 KCPDCGNEQIVFQRAATR 26
                                      8**********9876666 PP

>> Mcm10  Mcm10 replication factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00024      0.18     294     335 ..       9      51 ..       4      53 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00024
                             Mcm10 294 kCakCgkRtvsldrlPskh.CsnCgeskwerdgmlkekkGpkl 335
                                       kC++Cg+  + ++r  ++  C+ Cg      +g + e kG +l
  gi|474933883|ref|YP_007687465.1|   9 KCPDCGNEQIVFQRAATRVlCHVCGAVLVVPKGGKGELKGEVL 51 
                                       9*************998844*****987777777777777665 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.2    0.0031       2.3      24      33 ..       6      15 ..       3      18 .. 0.88
   2 ?    4.8   0.3     0.036        27      22      34 ..      23      35 ..      15      37 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0031
                     zinc_ribbon_4 24 vkvrCskCgh 33
                                      vk++C+ Cg+
  gi|474933883|ref|YP_007687465.1|  6 VKMKCPDCGN 15
                                      79******97 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.036
                     zinc_ribbon_4 22 kgvkvrCskCghv 34
                                      ++++v C  Cg+v
  gi|474933883|ref|YP_007687465.1| 23 AATRVLCHVCGAV 35
                                      567899****987 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   2.1     0.022        16       7      17 ..       9      19 ..       6      50 .. 0.54

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.022
                   Zn_ribbon_recom  7 rCgeCGspmtr 17
                                      +C +CG+  ++
  gi|474933883|ref|YP_007687465.1|  9 KCPDCGNEQIV 19
                                      56666654333 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.3    0.0036       2.7      23      31 ..       9      17 ..       7      19 .. 0.83
   2 ?    3.4   0.5     0.086        64       5      10 ..      28      33 ..      24      38 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0036
                     A2L_zn_ribbon 23 vCieCgasf 31
                                       C++Cg+++
  gi|474933883|ref|YP_007687465.1|  9 KCPDCGNEQ 17
                                      6*****987 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.086
                     A2L_zn_ribbon  5 vCsvCg 10
                                       C+vCg
  gi|474933883|ref|YP_007687465.1| 28 LCHVCG 33
                                      699998 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   1.1    0.0042       3.2      15      24 .]       6      15 ..       3      15 .. 0.79
   2 ?    3.6   0.2     0.089        66       1       9 [.      29      37 ..      29      42 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0042
                           DUF1610 15 vvFpCPNCGE 24
                                      v+  CP CG+
  gi|474933883|ref|YP_007687465.1|  6 VKMKCPDCGN 15
                                      5667*****7 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.089
                           DUF1610  1 CtSCGaela 9 
                                      C  CGa+l+
  gi|474933883|ref|YP_007687465.1| 29 CHVCGAVLV 37
                                      667****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                       113  (0.00630264); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.48
# Mc/sec: 344.30
//
Query:       gi|474933884|ref|YP_007687466.1|  [L=92]
Description: LSU ribosomal protein L44E [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.5e-32  109.7   6.5    9.5e-32  109.3   6.5    1.1  1  Ribosomal_L44  Ribosomal protein L44
    0.00074   18.8   1.5       0.13   11.7   0.2    2.2  2  zf-ribbon_3    zinc-ribbon domain
     0.0093   15.9   2.5       0.39   10.7   0.2    2.4  2  Nudix_N_2      Nudix N-terminal
  ------ inclusion threshold ------
      0.021   14.8   1.6      0.044   13.8   1.6    1.5  1  DZR            Double zinc ribbon
      0.055   13.9   5.1      0.083   13.3   0.3    2.4  2  Ribosomal_L33  Ribosomal protein L33
      0.061   13.4   1.8       0.36   11.0   0.1    2.1  2  zf-Mss51       Zinc-finger of mitochondrial splicing suppress
      0.068   13.3   2.7        5.9    7.1   0.1    2.4  2  Zn-ribbon_8    Zinc ribbon domain
       0.12   12.3   0.1       0.12   12.3   0.1    1.5  2  Cys_rich_CPXG  Cysteine-rich CPXCG
       0.13   12.6   3.5       0.62   10.4   0.2    2.1  2  zf-LITAF-like  LITAF-like zinc ribbon domain
       0.13   12.1   1.8       0.13   12.1   1.8    2.0  2  zinc_ribbon_2  zinc-ribbon domain
       0.41   10.6   6.8        3.5    7.7   0.3    2.4  2  Zn_Tnp_IS1595  Transposase zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Ribosomal_L44  Ribosomal protein L44
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.3   6.5   5.8e-35   9.5e-32       1      76 []      16      91 ..      16      91 .. 0.99

  Alignments for each domain:
  == domain 1  score: 109.3 bits;  conditional E-value: 5.8e-35
                                      EEEEEEEEE-------SSSHHHHHHHH.H-SSSGGGGS----.--SSBB--EEEEETTT--EEE----BBS--EEE CS
                     Ribosomal_L44  1 kHtehkveqykkgkdselaqgkRrydrkqsgygGqtkpvfkkkaKttKKivlrleCteCkkkrlkalkRakkfelv 76
                                      +Hteh ve++kk+k+sel++g+Rr+++ +sgygG ++p++++++K+tK+i+lr++C+eCkk++l++++Rakkfel+
  gi|474933884|ref|YP_007687466.1| 16 THTEHAVERVKKKKASELKWGQRRFREVTSGYGGFPRPKPEGREKPTKRINLRYRCNECKKAHLTSCIRAKKFELT 91
                                      6*************************************************************************95 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.2     8e-05      0.13       3      11 ..       9      17 ..       7      21 .. 0.76
   2 !    6.3   0.1     0.004       6.5       3      13 ..      69      80 ..      68      81 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8e-05
                       zf-ribbon_3  3 vrCPnCGap 11
                                      ++CP+CG++
  gi|474933884|ref|YP_007687466.1|  9 TYCPYCGTH 17
                                      789999976 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.004
                       zf-ribbon_3  3 vrCPnCGa.pls 13
                                      +rC++C++ +l+
  gi|474933884|ref|YP_007687466.1| 69 YRCNECKKaHLT 80
                                      69*****98886 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.2   0.00024      0.39       2      15 ..      10      23 ..       9      28 .. 0.90
   2 ?    5.2   0.2     0.012        20      21      31 ..      67      77 ..      57      78 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00024
                                      B-TTT--B-EEE-- CS
                         Nudix_N_2  2 FCsqCGtpvelrip 15
                                      +C+ CGt +e++++
  gi|474933884|ref|YP_007687466.1| 10 YCPYCGTHTEHAVE 23
                                      9*********9986 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.012
                                      -EEEETTTTEE CS
                         Nudix_N_2 21 eRlvCpaCgti 31
                                       R++C+ C   
  gi|474933884|ref|YP_007687466.1| 67 LRYRCNECKKA 77
                                      6*******875 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.6   2.7e-05     0.044      13      37 ..       9      77 ..       3      83 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.7e-05
                               DZR 13 rfCseCgtklkavaa............................................edrCpsCgek 37
                                       +C++Cgt+ + + +                                             +rC +C+++
  gi|474933884|ref|YP_007687466.1|  9 TYCPYCGTHTEHAVErvkkkkaselkwgqrrfrevtsgyggfprpkpegrekptkrinlRYRCNECKKA 77
                                      69*******8765557888999********************************************986 PP

>> Ribosomal_L33  Ribosomal protein L33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   5.1e-05     0.083      30      43 ..       7      20 ..       5      24 .. 0.90
   2 ?    2.4   0.7      0.13   2.2e+02       6      12 ..      70      76 ..      57      90 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.1e-05
                                      EEEEETTTTEEEEE CS
                     Ribosomal_L33 30 lkKYcprcrkhtlh 43
                                      +k Ycp+c  ht h
  gi|474933884|ref|YP_007687466.1|  7 IKTYCPYCGTHTEH 20
                                      788**********9 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.13
                                      EET.... CS
                     Ribosomal_L33  6 eCtecks 12
                                      +C eck+
  gi|474933884|ref|YP_007687466.1| 70 RCNECKK 76
                                      4666665 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00022      0.36      12      49 ..       4      42 ..       1      46 [. 0.79
   2 ?    2.2   0.2      0.12     2e+02       9      22 ..      61      74 ..      53      86 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00022
                          zf-Mss51 12 pkhvdfeCpdCGiptycseehwedDyeahle.icdtLrq 49
                                      p+ ++  Cp CG  t +  e+ ++ + ++l+    + r+
  gi|474933884|ref|YP_007687466.1|  4 PRTIKTYCPYCGTHTEHAVERVKKKKASELKwGQRRFRE 42
                                      6788999***********999999888777744555555 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.12
                          zf-Mss51  9 qtapkhvdfeCpdC 22
                                       t++ + ++ C +C
  gi|474933884|ref|YP_007687466.1| 61 PTKRINLRYRCNEC 74
                                      45666788999999 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1    0.0036       5.9      26      37 ..       8      19 ..       1      25 [. 0.73
   2 ?    6.2   0.5    0.0068        11       6      13 ..      69      76 ..      67      87 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0036
                       Zn-ribbon_8 26 ltaCPeCgsevr 37
                                      +t CP Cg +++
  gi|474933884|ref|YP_007687466.1|  8 KTYCPYCGTHTE 19
                                      456****98665 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0068
                       Zn-ribbon_8  6 YrCeeCgh 13
                                      YrC+eC++
  gi|474933884|ref|YP_007687466.1| 69 YRCNECKK 76
                                      ******96 PP

>> Cys_rich_CPXG  Cysteine-rich CPXCG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   7.3e-05      0.12       2      17 ..      10      25 ..       9      30 .. 0.82
   2 ?   -3.3   0.1       5.4   8.8e+03       3       7 ..      71      75 ..      69      80 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.3e-05
                     Cys_rich_CPXG  2 qCPyCgeeievlvDls 17
                                       CPyCg ++e  v+  
  gi|474933884|ref|YP_007687466.1| 10 YCPYCGTHTEHAVERV 25
                                      5********9998765 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 5.4
                     Cys_rich_CPXG  3 CPyCg 7 
                                      C  C 
  gi|474933884|ref|YP_007687466.1| 71 CNECK 75
                                      66664 PP

>> zf-LITAF-like  LITAF-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   0.00038      0.62       4      27 ..       7      30 ..       4      35 .. 0.83
   2 ?    3.3   0.3     0.063     1e+02       6      19 ..      69      82 ..      66      89 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00038
                     zf-LITAF-like  4 tqvdCpaCqqrvvTsveyksgklt 27
                                       +++Cp+C+++++  ve+ ++k +
  gi|474933884|ref|YP_007687466.1|  7 IKTYCPYCGTHTEHAVERVKKKKA 30
                                      6789*******9999999887765 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.063
                     zf-LITAF-like  6 vdCpaCqqrvvTsv 19
                                        C  C++   Ts 
  gi|474933884|ref|YP_007687466.1| 69 YRCNECKKAHLTSC 82
                                      46888888888775 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.8   7.8e-05      0.13      14      22 ..       9      17 ..       8      18 .. 0.89
   2 ?   -0.7   0.4      0.77   1.3e+03       2       5 ..      71      74 ..      70      79 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.8e-05
                     zinc_ribbon_2 14 kFCpyCGtp 22
                                      ++CpyCGt+
  gi|474933884|ref|YP_007687466.1|  9 TYCPYCGTH 17
                                      79*****96 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.77
                     zinc_ribbon_2  2 CpnC 5 
                                      C +C
  gi|474933884|ref|YP_007687466.1| 71 CNEC 74
                                      8888 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   1.4    0.0075        12      21      33 ..      11      23 ..       5      41 .. 0.74
   2 ?    7.7   0.3    0.0021       3.5      37      45 ..      68      76 ..      57      77 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0075
                     Zn_Tnp_IS1595 21 CPhCgsrkayrik 33
                                      CP+Cg  + + ++
  gi|474933884|ref|YP_007687466.1| 11 CPYCGTHTEHAVE 23
                                      *****88544444 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0021
                     Zn_Tnp_IS1595 37 lfqCkeCrk 45
                                      +++C+eC+k
  gi|474933884|ref|YP_007687466.1| 68 RYRCNECKK 76
                                      8******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 668.75
//
Query:       gi|474933885|ref|YP_007687467.1|  [L=184]
Description: Multimeric flavodoxin WrbA [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.4e-18   65.5   0.0    5.1e-18   65.3   0.0    1.1  1  FMN_red       NADPH-dependent FMN reductase
    9.4e-13   48.3   0.0    1.2e-12   48.0   0.0    1.0  1  Flavodoxin_2  Flavodoxin-like fold


Domain annotation for each model (and alignments):
>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.3   0.0   5.7e-22   5.1e-18       2     143 ..       3     154 ..       2     165 .. 0.78

  Alignments for each domain:
  == domain 1  score: 65.3 bits;  conditional E-value: 5.7e-22
                                       EEEEEES--STT-HHHHHHHHHHCCT-T.T-CEEEEETTTS.--........---HCHGHTCGGSHHHHHHHHHHHH CS
                           FMN_red   2 kilvisGSlrkgsntrklaewaaealkeagaevelidladlilpc......alcdkdlesegqtsddvaellekiaa 72 
                                       ki++i+ S+rkg+n++++++++++ +  +g++++ ++l+ l+  +      a  +++++ e++  d +++ le i  
  gi|474933885|ref|YP_007687467.1|   3 KIVAIVSSPRKGGNSDTIVDAILDGT--MGLTISEVNLHRLNNYQyamdcqACMKCKEDGECHVADSLNKTLEDIYY 77 
                                       9***********************99..7777777776666333334445644455555569*************** PP

                                       -SCEEEEEEECTTCE-HHHHHHHHCHT-......SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHH.HTT-EEE CS
                           FMN_red  73 adaliivtPeYngsysgllKnalDrlsr.....trgkkelrgKpvalvavgggrrgglraeeqlrqvla.elgaivv 143
                                       ad +i++tP Y+  y+g+lK ++Dr+ +     ++   +  +K v++++ g++   ++ ++  l ++l  ++g   v
  gi|474933885|ref|YP_007687467.1|  78 ADSVIVSTPLYFSDYTGVLKCLIDRMFCfvdkdMNVTLPKGKKLVLVITCGSDIESSQMIAKILDNILVkNFGFENV 154
                                       *****************************998555555555777777777777777777777777777766665555 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.0   0.0   1.3e-16   1.2e-12       2     196 ..       3     177 ..       2     180 .. 0.75

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 1.3e-16
                                       EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCCT-----CCCCHCCHHHHTT.C.HHHHHHH.HHHH CS
                      Flavodoxin_2   2 kiLiinahprpeksfssalaqafvealekagphevtvrdLyadflpvlttrdlaaklayeek.p.adveseq.iekl 75 
                                       ki+ i+++pr+ + +s  + +a++++        + +++L+++ +     ++ a+ +  e++ + +    ++ +e++
  gi|474933885|ref|YP_007687467.1|   3 KIVAIVSSPRK-GGNSDTIVDAILDGTMGLT---ISEVNLHRLNNYQYAMDCQACMKCKEDGeChVADSLNKtLEDI 75 
                                       99********9.6999999999999999887...8888888876667766666653455555543444445569*** PP

                                       HCSSEEEEEEE-BTTB--HHHHHHHHHHS-TTTSC.EETTCSSCCCCTTTTSEEEEEEEESS-GGGSSTTSSS-S-H CS
                      Flavodoxin_2  76 laadaivlqfPlwwfgvPailKgwiDrvltagfaf.yteeggegrgggLkgkkalvivttGgpeesyqerglegaam 151
                                         ad +++++Pl++  +  +lK  iDr     f+f +++ +     ++ kgkk+++++t+G++ es q        +
  gi|474933885|ref|YP_007687467.1|  76 YYADSVIVSTPLYFSDYTGVLKCLIDRM----FCFvDKDMN----VTLPKGKKLVLVITCGSDIESSQ-------MI 137
                                       ***************************7....999555444....36666*************87755.......34 PP

                                       HHHHHHHHHHH.HHTT-EEEEEEEEESCTCCCH.HHHHHHHHHHHHH CS
                      Flavodoxin_2 152 dellpplrgil.gfiGikdvepvlvegvagaed.eealaealerlee 196
                                         +l   ++il + +G+++v ++++      +d +e++++ l++++e
  gi|474933885|ref|YP_007687467.1| 138 AKIL---DNILvKNFGFENVGTIIASE----KDmAENREKILAKARE 177
                                       4444...5555499*********9966....3335555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       749  (0.0417759); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1152.04
//
Query:       gi|474933886|ref|YP_007687468.1|  [L=194]
Description: Transcriptional regulator [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.4e-06   25.6   0.0    1.3e-05   25.0   0.0    1.2  1  MarR_2          MarR family
      0.001   18.9   0.0     0.0017   18.3   0.0    1.3  1  MarR            MarR family
     0.0018   18.1   0.0     0.0037   17.1   0.0    1.5  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0067   16.9   0.1      0.011   16.2   0.1    1.4  1  HTH_27          Winged helix DNA-binding domain
  ------ inclusion threshold ------
       0.02   14.5   0.0      0.035   13.7   0.0    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
      0.099   12.8   0.1       0.16   12.1   0.1    1.4  1  Hydrolase_6     Haloacid dehalogenase-like hydrolase
       0.11   12.7   0.1       0.22   11.7   0.1    1.4  1  B-block_TFIIIC  B-block binding subunit of TFIIIC


Domain annotation for each model (and alignments):
>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   4.9e-09   1.3e-05       1      52 [.      35      86 ..      35      94 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 4.9e-09
                                      TT--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSE..E CS
                            MarR_2  1 lgltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLv..e 52
                                      +glt a+a  L+ L  r+g   t   l r l+++ s+++r++k L ++GL+   
  gi|474933886|ref|YP_007687468.1| 35 YGLTSAHATYLMGLTLRDG--QTLVSLSRFLDMDTSNTNRVVKVLREKGLIydD 86
                                      59*****************..9*****************************552 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   6.5e-07    0.0017       1      48 [.      37      84 ..      37      91 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 6.5e-07
                                      --HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR  1 ltltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                      lt ++   L+ l  ++++++  L ++l +++s++ rv++ L +kGli+
  gi|474933886|ref|YP_007687468.1| 37 LTSAHATYLMGLTLRDGQTLVSLSRFLDMDTSNTNRVVKVLREKGLIY 84
                                      6778888899999999******************************97 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.4e-06    0.0037       4      63 ..      35      96 ..      32      99 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.4e-06
                                      CHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST..TTEEE CS
                              TrmB  4 lGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr..pklYr 63
                                      +GL++  a     L  ++  t   +++ l+ + s+ ++v++ L +kGl++  +++   k+Y+
  gi|474933886|ref|YP_007687468.1| 35 YGLTSAHATYLMGLTLRDGQTLVSLSRFLDMDTSNTNRVVKVLREKGLIYDDRETvsSKKYS 96
                                      899999999999999***********************************999887777775 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   4.2e-06     0.011       1      60 [.      37      89 ..      37     103 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.2e-06
                            HTH_27  1 ltrqqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrek 60
                                      lt  +a +L  +   r++++l  l+++l+++ s++  ++k L ekGL+       d+re+
  gi|474933886|ref|YP_007687468.1| 37 LTSAHATYLMGLT-LRDGQTLVSLSRFLDMDTSNTNRVVKVLREKGLI------YDDRET 89
                                      6788999999999.9*********************************......777774 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.4e-05     0.035      18      47 ..      54      83 ..      50      84 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.4e-05
                            HTH_24 18 isqreLAerlglSpstvnrrlkrLeeeGlI 47
                                       +   L++ l++  s++nr +k L e+GlI
  gi|474933886|ref|YP_007687468.1| 54 QTLVSLSRFLDMDTSNTNRVVKVLREKGLI 83
                                      67789************************9 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   6.4e-05      0.16      20      78 ..      71     145 ..      66     171 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.4e-05
                                       HHHHHHHHHTT............-EEEEEE---SS-HHHHHHHH....HHTT----GGGEEEHHHHHHHHHHHHS CS
                       Hydrolase_6  20 aealnalraag............kpvvllTNnsskseeeyakkl....eklgvditeeqvvtsataaaeylkkrk 78 
                                        +++++lr++g            k  ++lTN ++k  e++++      ++l   +t+e+++t+  ++ ++l++++
  gi|474933886|ref|YP_007687468.1|  71 NRVVKVLREKGliyddretvsskKYSIFLTNAGRKLGEHLLEFTnqiyKDLMTGVTKEEILTTRNTLIKMLNNTD 145
                                       67888899999999999999997888*******9998887765500044556669********999999998754 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   8.5e-05      0.22      17      51 ..      52      86 ..      49     101 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.5e-05
                    B-block_TFIIIC 17 sGitqsdLakeskqdprslfyrlksLekkgLIvkq 51
                                      +G t  +L++ +++d ++   ++k+L +kgLI+  
  gi|474933886|ref|YP_007687468.1| 52 DGQTLVSLSRFLDMDTSNTNRVVKVLREKGLIYDD 86
                                      689999**************************964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1381.58
//
Query:       gi|474933887|ref|YP_007687469.1|  [L=213]
Description: dimethylamine corrinoid protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.1e-23   80.6   0.7    1.4e-22   80.0   0.3    1.5  2  B12-binding     B12 binding domain
    3.6e-16   59.4   0.2      8e-16   58.3   0.2    1.5  1  B12-binding_2   B12 binding domain
  ------ inclusion threshold ------
       0.17   11.5   0.0       0.23   11.0   0.0    1.2  1  E3_UFM1_ligase  E3 UFM1-protein ligase 1


Domain annotation for each model (and alignments):
>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       1.4   8.6e+03      65      89 ..      47      71 ..      40      79 .. 0.60
   2 !   80.0   0.3   2.3e-26   1.4e-22       2     118 ..      95     205 ..      94     208 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.4
                       B12-binding 65 leavkelvellkrirprvkvvvGGa 89
                                      +++v  l e+ k   p+v  ++GG 
  gi|474933887|ref|YP_007687469.1| 47 MSDVGVLFERGKLFLPHVLSAAGGM 71
                                      5555556666555666777777774 PP

  == domain 2  score: 80.0 bits;  conditional E-value: 2.3e-26
                       B12-binding   2 kvllatvggdlhplGlavlaaalrdagfeVqllganvenedivaairaekpdvvglSalltsqleavkelvel..lk 76 
                                       +v+++tv+gd+h++G+ +   +l+ agf+V++lg +v+++++++++ ++   +vg+Sal+t+++  +k ++e+    
  gi|474933887|ref|YP_007687469.1|  95 SVVMGTVEGDVHDIGKSICSTMLQCAGFDVHDLGRDVPTPKFLDEVTKNGCTMVGMSALMTTTMVVMKTVIEQlkDL 171
                                       699**********************************************************************8877 PP

                       B12-binding  77 rirprvkvvvGGahpsldpeetleaklgiddvvvgegedale 118
                                       ++r++++v+vGGa+ + ++++   + +g +d    +ge+a e
  gi|474933887|ref|YP_007687469.1| 172 GVRDKTIVMVGGAPITQAYAD---K-IG-AD---IYGESASE 205
                                       999***********9999999...7.**.55...58888765 PP

>> B12-binding_2  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.3   0.2   1.3e-19     8e-16       4      74 ..       9      78 ..       7      79 .. 0.96

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 1.3e-19
                     B12-binding_2  4 rlhwaivhgdkegieelidealaqgsaavdvlndvllpamkeVGdlfgagelflpqvllsaevmkkavahL 74
                                      ++++a+v+ + +gi++++d+ala+g+ + +++n ++ ++m +VG lf++g+lflp+vl +a  m ka++ L
  gi|474933887|ref|YP_007687469.1|  9 AIKDAMVAYKVQGIVDAVDKALAAGMGPTEIIN-AMGDGMSDVGVLFERGKLFLPHVLSAAGGMTKAMEKL 78
                                      789*****************************8.7*********************************987 PP

>> E3_UFM1_ligase  E3 UFM1-protein ligase 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   3.9e-05      0.23      71     135 ..     148     212 ..     133     213 .] 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.9e-05
                    E3_UFM1_ligase  71 vnlvdLakilnvdlshiekkaeeivkedkelqlvqgelitksYldsiaeeineklqeagqvsiae 135
                                       v +  L ++  v ++ + ++++++  +dk++ +v g  it+ Y d+i ++i  +  ++ + ++++
  gi|474933887|ref|YP_007687469.1| 148 VGMSALMTTTMVVMKTVIEQLKDLGVRDKTIVMVGGAPITQAYADKIGADIYGESASETTAKVKD 212
                                       556778889999999999999****************************9998888877777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1499.47
//
Query:       gi|474933888|ref|YP_007687470.1|  [L=459]
Description: dimethylamine:corrinoid methyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   4.8e-251  833.1  12.8   5.4e-251  832.9  12.8    1.0  1  Dimeth_Pyl  Dimethylamine methyltransferase (Dimeth_PyL)


Domain annotation for each model (and alignments):
>> Dimeth_Pyl  Dimethylamine methyltransferase (Dimeth_PyL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  832.9  12.8    3e-255  5.4e-251       7     462 ..       1     456 [.       1     457 [. 1.00

  Alignments for each domain:
  == domain 1  score: 832.9 bits;  conditional E-value: 3e-255
                        Dimeth_Pyl   7 lGdgkrvyltkekiledieaGiadaadlaevpalsedeiekladilvskeklvsveaGkevvltydiGtlklegdqg 83 
                                       +Gdg++vy+t+e++ledi++G+adaad+a+vp+l+e+eie++ad+++s+e+lvsv++G+evv+++d G +k+++d+g
  gi|474933888|ref|YP_007687470.1|   1 MGDGRTVYMTRENVLEDIRKGMADAADAAGVPDLNENEIEQMADVICSDERLVSVPRGHEVVMSEDGGPYKMMIDSG 77 
                                       8**************************************************************************** PP

                        Dimeth_Pyl  84 nsglgieisrlegvliheralgadtlelahidysikpvkpvvaeeaqameviqqnlvvpllyGampnlglyyapdGp 160
                                       +sg+gieisrl+++l+her+lg+d+++lahidysik+vkp++++eaqame+i++ ++vpllyGampn+glyyapdGp
  gi|474933888|ref|YP_007687470.1|  78 SSGNGIEISRLQAILAHERTLGMDSFQLAHIDYSIKAVKPIIGYEAQAMEQINMLSTVPLLYGAMPNMGLYYAPDGP 154
                                       ***************************************************************************** PP

                        Dimeth_Pyl 161 fenpadllrefkieeakesiekaadhlardivyvvskllkagadGvnfdttasaGdadfvatlkavealrkkfpniy 237
                                       f+npadl+refk+eea++++ekaa+++a+di+yv+s +++ag++G+nfdttasaGdadfv+tl++++++rkkfpn+y
  gi|474933888|ref|YP_007687470.1| 155 FGNPADLMREFKMEEAMDQAEKAAAQIAADIDYVFSGMMAAGSEGWNFDTTASAGDADFVGTLNGITEVRKKFPNAY 231
                                       ***************************************************************************** PP

                        Dimeth_Pyl 238 ielGmagelvlGihGeleydGktlaGlyphqqvklvekaGanvfGpvvntntskslawnlaravtlvkeavkasdip 314
                                       ie+Gma+e+vlGihG++eydG+ +aGlyphqqvkl+ekaG+n+fGpvvntnts+s+awn+aravt+vke++k+s+ip
  gi|474933888|ref|YP_007687470.1| 232 IEMGMAAENVLGIHGSIEYDGTPVAGLYPHQQVKLAEKAGVNIFGPVVNTNTSRSFAWNIARAVTMVKECEKVSNIP 308
                                       ***************************************************************************** PP

                        Dimeth_Pyl 315 vhvnlGmGvGGiplletppidavsraskalveiakvdGikvGvGdpvGmaiahvlasGmgGirtaGdlvarmelskn 391
                                       +hvn+GmGvGGip++e+pp+davsra+k++veia+vdGi++G+Gdp+Gm++ahv+asGmgG+rtaGdlvarme+skn
  gi|474933888|ref|YP_007687470.1| 309 CHVNMGMGVGGIPMSECPPLDAVSRANKLMVEIAHVDGIOAGAGDPLGMSNAHVAASGMGGVRTAGDLVARMEFSKN 385
                                       ***************************************************************************** PP

                        Dimeth_Pyl 392 mkideakeyvakklgveeldladevvmrdlreelgiGvvtsvaGaakGiaaklnieklldikinscekfrn 462
                                       mk+++akeyvakklg++e+++ade+vmrdlr++lg+G+vts++GaakG++aklniek+l+i+inscekfr 
  gi|474933888|ref|YP_007687470.1| 386 MKLAKAKEYVAKKLGISEIEIADETVMRDLRYDLGLGNVTSIPGAAKGMEAKLNIEKVLGITINSCEKFRG 456
                                       *********************************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 3516.88
//
Query:       gi|474933889|ref|YP_007687471.1|  [L=349]
Description: hypothetical protein TALC_00302 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.7e-09   35.5  42.8    0.00015   22.0  23.6    2.8  2  EamA      EamA-like transporter family
  ------ inclusion threshold ------
       0.16   12.0   0.6        1.8    8.6   0.1    2.6  2  Ac76      Orf76 (Ac76)
        5.9    6.9  12.9       0.99    9.4   0.3    3.7  3  DUF5510   Family of unknown function (DUF5510)


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0  23.6   2.5e-08   0.00015       2     135 ..      19     173 ..      18     174 .. 0.83
   2 !   18.2  11.2   3.6e-07    0.0021       3     136 ..     190     334 ..     188     335 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.5e-08
                              EamA   2 lgillallaalfwaiyfvlskil..lrkv..............spltltfvrfliagillliiallkegkl....ak 58 
                                       +g ++++l a+fw+i++v +  +  + ++               +l +++++ ++  ++l i+     gkl    + 
  gi|474933889|ref|YP_007687471.1|  19 WGFIWVILIAIFWGIGYVPMATIwcVPEIdgllgmegdkgylgTSLLISALQAIVFMLFLTIVWCGATGKLkeykKT 95 
                                       9*****************99888566666888999998888888888888887655555544433333333666645 PP

                              EamA  59 lslkd.wllllllgllgtvlafllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvll 134
                                       +s k  ++++l+ +++g+ +a +  ++a+ +++a++a+ + +++ +  ++++ +  +ekl+   +lgi++ l+G ++
  gi|474933889|ref|YP_007687471.1|  96 ISNKKiVKWILIGAAFGGPCAIFGSTIAIGYIGAGFAAAMGLMSAITGALFARIMNKEKLSTNAILGIIILLIGGII 172
                                       5555558999***************************************************************9877 PP

                              EamA 135 i 135
                                       i
  gi|474933889|ref|YP_007687471.1| 173 I 173
                                       6 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 3.6e-07
                              EamA   3 gillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegkl...........aklslkdwllll 68 
                                       g++ al + + w++ + ++ + l  +++ + + vr+++ ++l + i+l+  + +           + ++  ++l+  
  gi|474933889|ref|YP_007687471.1| 190 GYIGALMSIIGWGLEGNFAVRSLDVTDSDASLPVRYTLESLLWICIILPISIVIfgpsefidamvDCFTNAPVLFWE 266
                                       8999***************99999999888888888866666533322222222233335788888999999***** PP

                              EamA  69 llgllgtvlafllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                       +++++   +++++++ ++ ++++++   i+s+ + ++li  +++ g+ ++++  +g +++++G ++++
  gi|474933889|ref|YP_007687471.1| 267 FMAAMTLGMCYVCQYRSFATLGVGRTLSIQSFYVPVSLIALYFFMGQEIGIMLAAGSLIAVFGMFVMY 334
                                       *****************************************************************986 PP

>> Ac76  Orf76 (Ac76)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.12   7.2e+02      32      41 ..      72      81 ..      51     103 .. 0.65
   2 ?    8.6   0.1    0.0003       1.8      11      44 ..     144     177 ..     135     189 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.12
                              Ac76 32 llfvlFiill 41
                                      ++f+lF+ ++
  gi|474933889|ref|YP_007687471.1| 72 IVFMLFLTIV 81
                                      4444444433 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0003
                              Ac76  11 ivlafildkneklsellltllllfvlFiillnvy 44 
                                       +++a i++k++ +++ +l +++l++  ii+l+  
  gi|474933889|ref|YP_007687471.1| 144 ALFARIMNKEKLSTNAILGIIILLIGGIIILDPS 177
                                       68999********************999999865 PP

>> DUF5510  Family of unknown function (DUF5510)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   1.0     0.073   4.4e+02      31      52 ..     103     124 ..      96     134 .. 0.75
   2 ?    2.7   0.6      0.02   1.2e+02       5      23 ..     154     174 ..     150     194 .. 0.69
   3 ?    9.4   0.3   0.00017      0.99       6      30 ..     225     249 ..     223     256 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.073
                           DUF5510  31 riiviGtilGlacayftykyii 52 
                                       + i+iG+ +G  ca f     i
  gi|474933889|ref|YP_007687471.1| 103 KWILIGAAFGGPCAIFGSTIAI 124
                                       5699**********99766555 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.02
                           DUF5510   5 syktddiikiviil..Givil 23 
                                          t+ i+ i+i+l  Gi+il
  gi|474933889|ref|YP_007687471.1| 154 KLSTNAILGIIILLigGIIIL 174
                                       556777877777663244444 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.00017
                           DUF5510   6 yktddiikiviilGivilifspakf 30 
                                       y  + ++ i iil i i+if p+ f
  gi|474933889|ref|YP_007687471.1| 225 YTLESLLWICIILPISIVIFGPSEF 249
                                       55667889**************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       803  (0.0447878); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 2402.80
//
Query:       gi|474933890|ref|YP_007687472.1|  [L=95]
Description: hypothetical protein TALC_00303 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 672.19
//
Query:       gi|474933891|ref|YP_007687473.1|  [L=42]
Description: hypothetical protein TALC_00304 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.015   15.5   0.4      0.015   15.5   0.4    1.0  1  IspA      Intracellular septation protein A


Domain annotation for each model (and alignments):
>> IspA  Intracellular septation protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.4   8.5e-07     0.015      70     103 ..       8      41 ..       1      42 [] 0.81

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.5e-07
                              IspA  70 detFikwKptvlyvlfalvLllsllilkknllkr 103
                                       de F    + v+y++fa+vL+++++++++++ k+
  gi|474933891|ref|YP_007687473.1|   8 DEFFAFNNADVVYCVFAVVLTVAAIFIGRTFFKK 41 
                                       5555566788********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       747  (0.0416643); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 293.05
//
Query:       gi|474933892|ref|YP_007687474.1|  [L=474]
Description: Trimethylamine:corrinoid methyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-78  261.8   0.0    8.3e-78  261.6   0.0    1.0  1  MTTB      Trimethylamine methyltransferase (MTTB)


Domain annotation for each model (and alignments):
>> MTTB  Trimethylamine methyltransferase (MTTB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  261.6   0.0   4.6e-82   8.3e-78      47     498 ..       1     458 [.       1     462 [. 0.90

  Alignments for each domain:
  == domain 1  score: 261.6 bits;  conditional E-value: 4.6e-82
                              MTTB  47 lriLeeiGiefldpealellkaaGakv..egervrfdrglvreliakapreftlharnPe.rdveiggknvvfapva 120
                                       +r+Le++G+++   ea++llk++G++v  e+  v+f+r++v+++i++ap++f + +r  +  +++ +g ++ + + +
  gi|474933892|ref|YP_007687474.1|   1 MRVLENVGLRVDYSEARKLLKENGCDVneETRVVKFPRAVVEKAIKSAPEKFNMYGRTGKcVEMVSDGSHTNYLTFG 77 
                                       79*************************8666679***********************97635788889888877765 PP

                              MTTB 121 gaPfvr..Dlerg..rregtledfrnlvkLaqmldvlhhsggtvvepvDvpvnk...rhldvlyakltlsdkvfmgs 190
                                           ++    ++    r +tl+d+ ++ k+++ ld++ +++  +v +vD+ v     r l+  ++  +   k+ m+ 
  gi|474933892|ref|YP_007687474.1|  78 VGTEYTvyKGHNSyeTRGSTLKDIGEICKVTDALDNIDWLC-APVSAVDLAVDEtkcRPLREWKEIFMNLTKPLMA- 152
                                       544444013344335799***********************.6777***987541116788888888888888876. PP

                              MTTB 191 vtekeraedsiemlrivfGaeeeefranpvvttiinvnsPlkfdetmlealeayaragqavivtpfilaGAmaPvtv 267
                                         +++ +ed ++m  ++   +ee+ r+ pv +     +sPl++det    ++a+ + g++++v++  ++ A aP+++
  gi|474933892|ref|YP_007687474.1| 153 DPDPRYIEDYFAMEVALYDGDEEKARKMPVSIMGSCPSSPLQLDETFGRFAMAAPKYGFPMMVLSMAMGAASAPISI 229
                                       578999*******766655555556999*99999999**************************************** PP

                              MTTB 268 agavaqalAEaLagialtqlvrpgapviyGtftssvdlksGApafGtpeaalatlvagqlArrlglPlrssggltas 344
                                       ag+++  +AE+Lagi+l+ql  pgap+ yG+ t+s d  +G+   G+pe al++++++ l++++++P+ ++g+ t++
  gi|474933892|ref|YP_007687474.1| 230 AGTLVTHNAEVLAGITLVQLSCPGAPCFYGSSTTSFDFYTGSAPVGSPELALISAGVSELGQYYKIPTVVAGTOTDA 306
                                       ***************************************************************************** PP

                              MTTB 345 klpDaQaayesanslwaavlaganlvlhaAGwleggLvasyekfilDadvlgmiarllegievseealaldairevg 421
                                       k p  Q ++e++++ +   + ga+ ++   G+l+ g+++s+e++++D+d++gmi+  ++giev++ ++a ++i +vg
  gi|474933892|ref|YP_007687474.1| 307 KRPNEQCGHEKTITGILPGMTGASNIYG-SGMLSLGMSFSLEQLVIDNDIIGMIKYAAKGIEVNDGTMAYQTIVDVG 382
                                       *************************996.5*********************************************** PP

                              MTTB 422 pgghflgtahTlaryetafyepelsdnknfeeWeeeGakdaeerAnekvkkiLaeyeepkldeaideeLrdfiarrk 498
                                        g+ fl+t+ T+a++e+    p ++d++   eWe++G+kd+ + A+ekv +iL++++  ++ +   +  ++ ia  +
  gi|474933892|ref|YP_007687474.1| 383 IGNDFLATPDTMANMENP-SAPTMFDRSMRPEWERAGEKDTGDIAHEKVVDILENHKVEPMSDYAIKRFDEIIAAAE 458
                                       ***************997.59***********************************988888877777888777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 3019.19
//
Query:       gi|474933893|ref|YP_007687475.1|  [L=484]
Description: Trimethylamine:corrinoid methyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.5e-86  287.9   0.1    9.5e-86  287.8   0.1    1.0  1  MTTB      Trimethylamine methyltransferase (MTTB)


Domain annotation for each model (and alignments):
>> MTTB  Trimethylamine methyltransferase (MTTB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  287.8   0.1   5.3e-90   9.5e-86      30     500 ..       5     481 ..       1     483 [. 0.93

  Alignments for each domain:
  == domain 1  score: 287.8 bits;  conditional E-value: 5.3e-90
                              MTTB  30 pyellseeeleaieeaalriLeeiGiefldpealellkaaGakv..egervrfdrglvreliakapreftlharnPe 104
                                       ++e+ls +e+ +i+ea+l++L+ +Gi+++d+ea+++l +aG++v  e+++v++++gl++++++k+p++f lh+r+++
  gi|474933893|ref|YP_007687475.1|   5 RIEILSRDEIRRIHEASLEVLDSVGIAIADEEARRILANAGCSVceESKIVKIPSGLIEDALSKCPKSFVLHGRDRK 81 
                                       689*****************************************999999*************************** PP

                              MTTB 105 rdvei..ggknvvfapvagaPfvrD.lerg.r..regtledfrnlvkLaqmldvlhhsggtvvepvDvpvnk..rhl 173
                                        dv++  +g  + + + +    v++ l rg +  r++tl+d ++++k+ +   +l+++ ++   + D+ ++k  r l
  gi|474933893|ref|YP_007687475.1|  82 YDVKMvsDGSVTNYINLGIGTRVTEyLGRGqYriRDSTLADTADFAKVFDACGNLNWMTQPSS-ALDLMTKKcvRTL 157
                                       ***994445555566666556666524555533489***********************6666.***98875338** PP

                              MTTB 174 dvlyakltlsdkvfmgsvtekeraedsiemlrivfGaeeeefranpvvttiinvnsPlkfdetmlealeayaragqa 250
                                       + + a ++ ++k+++    + + +   +em+++v   +eee r+n++ +    ++sPl++d + ++ +++ a+ g++
  gi|474933893|ref|YP_007687475.1| 158 HEVNALMSNTAKPILPD-PNYQYVDSYFEMMKAVYSGDEEEARKNSFFIIGGTSSSPLQLDVPDCQLMIRGAKLGMP 233
                                       *************9865.456678889******9988888899999999999************************* PP

                              MTTB 251 vivtpfilaGAmaPvtvagavaqalAEaLagialtqlvrpgapviyGtftssvdlksGApafGtpeaalatlvagql 327
                                       ++++   +aG +aPv  ag++++ + EaL  i l+ql  pg++++yGt t++ d       fG+p aal++ +++q+
  gi|474933893|ref|YP_007687475.1| 234 IMTMTMEMAGTTAPVHEAGTLVLHNCEALTNILLAQLCMPGTRCLYGTATTNFDFANNTAPFGSPQAALLSSAIAQI 310
                                       ***************************************************************************** PP

                              MTTB 328 ArrlglPlrssggltasklpDaQaayesanslwaavlaganlvlhaAGwleggLvasyekfilDadvlgmiarlleg 404
                                       A+++glP  ++gg ++s   D+Q+++es+++ + ++l+g+n v+   G+le g+++s+e+++l ++++ + +r+l+g
  gi|474933893|ref|YP_007687475.1| 311 AQYYGLPSITTGGGSDSIHVDVQSGHESTMTALLTALSGSNNVFG-SGLLELGMSFSLEQLVLRNEMIDQEQRILRG 386
                                       ********999999*****************************96.5****************************** PP

                              MTTB 405 ievseealaldairevgpgghflgtahTlaryetafyepelsdnknfeeWeeeGakdaeerAnekvkkiLaeyeepk 481
                                       i+v++e+l+l+ i + g gg f+  + T++ + +      l++++ ++eW+++ +kda erA+++v++iL ++ + +
  gi|474933893|ref|YP_007687475.1| 387 IRVDDETLSLSEIMQAGVGGDFITMPATVSAMSD-VQTDRLFNKSMYDEWADRDSKDALERAHDRVQDILVNHRTTP 462
                                       *******************************976.56889************************************* PP

                              MTTB 482 ldeaideeLrdfiarrkae 500
                                       ++++ ++++++ i +  ++
  gi|474933893|ref|YP_007687475.1| 463 IEPDARKAIDALISKADEK 481
                                       *************997765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (484 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2930.37
//
Query:       gi|474933894|ref|YP_007687476.1|  [L=230]
Description: ribose 5-phosphate isomerase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-62  210.3   0.1    1.8e-62  210.0   0.1    1.1  1  Rib_5-P_isom_A  Ribose 5-phosphate isomerase A (phosphoribois
     0.0026   17.7   0.3     0.0096   15.9   0.1    1.9  2  DeoRC           DeoR C terminal sensor domain
  ------ inclusion threshold ------
      0.014   14.6   0.0      0.022   13.9   0.0    1.3  1  Sugar-bind      Putative sugar-binding domain
       0.06   12.7   0.0       0.09   12.2   0.0    1.3  1  CoA_trans       Coenzyme A transferase


Domain annotation for each model (and alignments):
>> Rib_5-P_isom_A  Ribose 5-phosphate isomerase A (phosphoriboisomerase A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.0   0.1     4e-66   1.8e-62       2     173 .]      55     224 ..      54     224 .. 0.97

  Alignments for each domain:
  == domain 1  score: 210.0 bits;  conditional E-value: 4e-66
                                       EEESSHHHHHHHHHTT--BE-GGCCSSEEEEEE--SEEETTS-EE--TTS-HHHHHHHHHTEEEEEEEEEGGGBESS CS
                    Rib_5-P_isom_A   2 gvptSeqteelaeelgipllsldeveeidlaiDGaDevdedlnliKGgGgallrEKivaaaakkfiviadesKlvek 78 
                                       +v+tS+++e la+e+gi++l+l++v++id++iDGaDevd+ +nliKG GgallrEKivaaa+   i+i+desK vek
  gi|474933894|ref|YP_007687476.1|  55 CVTTSNASEDLAKECGITTLDLNDVDHIDVTIDGADEVDPGMNLIKGLGGALLREKIVAAASVSEIIIVDESKTVEK 131
                                       9**************************************************************************** PP

                                       TT.SS-EEEEE-GGGHHHHHHHHHHTTT-EEEE-TETTTTEE-B-TTS-EEEEEESSSBSSSHHHHHHHHHTSTTEE CS
                    Rib_5-P_isom_A  79 lg.kfpvPveVlpfaleavarelekllggkpelReakgkdgpvvTdngnlilDvkfeekiedpeelekelksipGVv 154
                                       lg k p+PveVl+f++ ++a  l+++ g++p+lR+  ++++p+vTd gn+i D++f e i+ +  l+++l++ipGVv
  gi|474933894|ref|YP_007687476.1| 132 LGtKAPLPVEVLQFGHLKTAYGLKRQ-GCEPVLRM--KDGKPFVTDGGNFIYDCRFPEGIDRAFFLQQALDTIPGVV 205
                                       **77********************76.********..557****************99998888************* PP

                                       EESEE-S--SEEEEEETTC CS
                    Rib_5-P_isom_A 155 etGlFlgladkvlvgkedg 173
                                       e+GlFl+++++v+++k+dg
  gi|474933894|ref|YP_007687476.1| 206 ECGLFLNMVAAVIISKKDG 224
                                       ****************997 PP

>> DeoRC  DeoR C terminal sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   2.1e-06    0.0096       3      50 ..       7      59 ..       5      76 .. 0.78
   2 ?   -0.2   0.0      0.19   8.4e+02     121     139 ..     110     128 ..      69     136 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.1e-06
                             DeoRC  3 aeeKrrIAkaAa.eliedgdtifldaGtTtlelaraLaekk....nltvvTns 50
                                      ++ K++ A++A+ ++++dg+++ l++G+T+++ ++++ e      +l+ vT s
  gi|474933894|ref|YP_007687476.1|  7 QAMKKAAAEKAVnDYVKDGMIVGLGTGSTAYFAIKRVGELVaqgyDLKCVTTS 59
                                      567888888877379****************9999876654444577777765 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.19
                             DeoRC 121 ralieaarrvillaDssKf 139
                                       + +++a+ + i+++D+sK 
  gi|474933894|ref|YP_007687476.1| 110 KIVAAASVSEIIIVDESKT 128
                                       4455556677778888875 PP

>> Sugar-bind  Putative sugar-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.9e-06     0.022      40      83 ..      12      57 ..       2      69 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.9e-06
                                      HHHHHHHHHH--TTEEEEE-SSHHHHHHHHHTHH..CCHTCEEEEE CS
                        Sugar-bind 40 raaaqllesllkdgdvvgvgwGrtlsavaealtp..kslrdvkvvq 83
                                      +aa + +++++kdg++vg+g+G t + +++++ +   +  d+k+v+
  gi|474933894|ref|YP_007687476.1| 12 AAAEKAVNDYVKDGMIVGLGTGSTAYFAIKRVGElvAQGYDLKCVT 57
                                      3567899********************9999998767777777776 PP

>> CoA_trans  Coenzyme A transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     2e-05      0.09       3      50 ..      13      60 ..      11      77 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2e-05
                                      HHHHHHCTT--TTEEEEE-SBTTBT.HHHHHHH...HHHHHTTTSEEEEEST CS
                         CoA_trans  3 taaeavakeikdGmtvavGGFglig.iPealia...alarsgvkdltviise 50
                                       a++av+ ++kdGm+v +G    +g +++ +i+   +l+ +g+  ++v +s+
  gi|474933894|ref|YP_007687476.1| 13 AAEKAVNDYVKDGMIVGLG----TGsTAYFAIKrvgELVAQGYDLKCVTTSN 60
                                      689****************....66455544441114555556555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1487.60
//
Query:       gi|474933895|ref|YP_007687477.1|  [L=219]
Description: putative ATPases of PP-loop superfamily [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-59  200.7   0.0    2.3e-59  200.5   0.0    1.0  1  Diphthami_syn_2  Diphthamide synthase
  ------ inclusion threshold ------
      0.016   15.3   0.0      0.031   14.4   0.0    1.4  1  tRNA_int_endo    tRNA intron endonuclease, catalytic C-termin


Domain annotation for each model (and alignments):
>> Diphthami_syn_2  Diphthamide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.5   0.0   2.6e-63   2.3e-59       1     216 [.       1     217 [.       1     219 [] 0.98

  Alignments for each domain:
  == domain 1  score: 200.5 bits;  conditional E-value: 2.6e-63
                   Diphthami_syn_2   1 mkvavlysGGkDsilaLykalke.sevesLvsvisenkesymfhvvnvhlvellaesvGiplikletaGeeekeved 76 
                                       m+ a l+sGGkDs+++Ly a +  +ev ++v+v++++k+s+ fh++n++ v ++aes+G +li  + +Gee+ + e 
  gi|474933895|ref|YP_007687477.1|   1 MRLASLWSGGKDSAFSLYTAEQMgHEVPYIVNVVPDDKQSWIFHTPNLNNVPAMAESMGKELILGHSTGEEDSDMEG 77 
                                       899******************999***************************************************** PP

                   Diphthami_syn_2  77 LkgtlkkldveavviGaieseyqksriervCrelGlksvaPLWkkdpeelleeiveekfevivvavkaegldeslLG 153
                                       L+  l+ ldv++vv+Ga+ s+yq  r++ vC el lk +aP+W+kd + ll ei++ + ++i+v+ +a g des+LG
  gi|474933895|ref|YP_007687477.1|  78 LRRALEGLDVDGVVSGAVWSDYQWDRMNIVCGELDLKFLAPMWRKDQDLLLDEIIASGTKAIIVGYYADGFDESWLG 154
                                       ***********************************************99999************************* PP

                   Diphthami_syn_2 154 rridkklidelkklsekygidkagegGeaetlvlDaPlfkkrlevkelekkwderrgyldier 216
                                       r+id ++  +lkkl +k+gi   gegGe+e++ +D+Pl+ + l v + ek  +   g l++  
  gi|474933895|ref|YP_007687477.1| 155 RIIDEDCARDLKKLRDKFGISIMGEGGEYESMTVDSPLYSHPLAVRKSEKVVGACSGTLKVTE 217
                                       ***************************************************999999998865 PP

>> tRNA_int_endo  tRNA intron endonuclease, catalytic C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.4e-06     0.031      26      81 ..      13      71 ..       6      75 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.4e-06
                                      SSEEEETSCTTTSSCSEEEEEEETTSEE...EHHHHHHHHHHHHHTTSEEEEEEETTTS CS
                     tRNA_int_endo 26 adFrvYqrrpslehseylVvvvsedeel...dwpdlsaavrlahsvkKklilaivdaeg 81
                                      + F +Y+ ++  ++  y+V vv++d++    + p+l +   +a+s+ K+lil +   e+
  gi|474933895|ref|YP_007687477.1| 13 SAFSLYTAEQMGHEVPYIVNVVPDDKQSwifHTPNLNNVPAMAESMGKELILGHSTGEE 71
                                      78************************9888899*******************9985554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1341.64
//
Query:       gi|474933896|ref|YP_007687478.1|  [L=742]
Description: copper-(or silver)-translocating P-type ATPase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-58  197.1   1.4    1.1e-57  194.5   0.4    2.3  2  E1-E2_ATPase  E1-E2 ATPase
    1.3e-35  123.6   3.4    2.4e-35  122.7   3.4    1.5  1  Hydrolase     haloacid dehalogenase-like hydrolase
    2.4e-16   59.9   1.6    2.7e-16   59.8   0.2    1.9  2  HMA           Heavy-metal-associated domain
    8.7e-07   28.9   0.2    2.8e-06   27.3   0.2    1.8  2  Hydrolase_3   haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
       0.12   12.1   0.2        0.4   10.4   0.0    1.9  2  CT_C_D        Carboxyltransferase domain, subdomain C and D
        1.9    8.9   5.7        3.3    8.1   0.2    2.6  3  DUF2781       Protein of unknown function (DUF2781)


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.092   2.7e+02      77     160 ..      54     135 ..      30     137 .. 0.56
   2 !  194.5   0.4   3.7e-61   1.1e-57       2     180 ..     227     406 ..     226     407 .. 0.98

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.092
                                       EE-EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTT.HHHHHHH CS
                      E1-E2_ATPase  77 vsgeakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgksla.eallral 152
                                       vs   ++++++ +  t ++  ar++eea +++++   k++ + ++++++ l ++  +++ ++ +  + + + l+ a 
  gi|474933896|ref|YP_007687478.1|  54 VSHAQIVKAIEKAGYTVIEGDARATEEADRREARSR-KINLILAIVFAIPLSVY--AMARMFGVDVPFRdDGLVYAS 127
                                       444445677777777778888888888866555544.44444444333333222..222222233333346666677 PP

                                       HHHHHHS- CS
                      E1-E2_ATPase 153 allvaaiP 160
                                       a l+  iP
  gi|474933896|ref|YP_007687478.1| 128 AQLILLIP 135
                                       77776666 PP

  == domain 2  score: 194.5 bits;  conditional E-value: 3.7e-61
                                       SS--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE CS
                      E1-E2_ATPase   2 llpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvs 78 
                                       l+p++a vi dg e ++++++l+ GDi+l+++g++vpaDg+++eg++ v+es+LTGEs+pv k++gd+vfs tv+ +
  gi|474933896|ref|YP_007687478.1| 227 LEPKEASVISDGAEIRVPVEDLKEGDIILVRPGESVPADGKVLEGTSPVNESMLTGESVPVMKSAGDEVFSATVNGE 303
                                       7899************************************************************************* PP

                                       -EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTT.HHHHHHHHH CS
                      E1-E2_ATPase  79 geakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgksla.eallralal 154
                                       g++++++ ++g+dt l +i+ ++e+a+ +k+p+ + +d++++v+vp+v+li+++++l+++llg+  a ++l+ ++++
  gi|474933896|ref|YP_007687478.1| 304 GSLRIRAEHVGKDTVLYRIVGMIESAQGTKAPMARLADRVAGVFVPAVILISVACCLAWFLLGDRSAsFSLTVMISV 380
                                       **************************************************************9999889******** PP

                                       HHHHS-TTHHHHHHHHHHHHHHHHHH CS
                      E1-E2_ATPase 155 lvaaiPcaLplavplalalgarrlak 180
                                       l++a+PcaL+la+pla+++g++++ak
  gi|474933896|ref|YP_007687478.1| 381 LIIACPCALGLATPLAIIMGTGKAAK 406
                                       ************************98 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.7   3.4   8.2e-39   2.4e-35       1     210 []     423     636 ..     423     636 .. 0.92

  Alignments for each domain:
  == domain 1  score: 122.7 bits;  conditional E-value: 8.2e-39
                                       SSEEEEESBTTTBCHHHHHHHHHHHH......CHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTE.... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.... RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsa......alalaaaletgsehpigkalvaaakarsgaltgfatfigrg.... 67 
                                       +++ ++Dk+GT+t+g+p+v+d+++         l  aaa e  s+hp ++a+v+ a  + ++ ++fa ++g+g    
  gi|474933896|ref|YP_007687478.1| 423 VDAAILDKTGTITEGRPEVTDIVAADgsdedtVLNFAAAAEADSQHPVAAAVVRRAGTV-PEHSDFASVTGEGvscl 498
                                       57999*********************66665555555555555*************999.6778************* PP

                                       ....HHHHTHHHHHHHH.HCHHHHHHHHHHHHHHCHHHHHH..TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEE CS
                                       ....xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  68 ....ayaigkpewltal.dippdlgaaigsaqsqgrtvall..qaralavftiadplkvkpeaaeavasLkaagiev 137
                                           ++++g+  +++++    + l  a +++ s+++t +++  ++ a +++++adp  v++ aa av sLk+ gi  
  gi|474933896|ref|YP_007687478.1| 499 scgkRILVGSGSLMKSNgVDVSSLVPAYEKLSSEAKTCMYVaaDGMAIGIIAVADP--VRENAASAVSSLKDLGISP 573
                                       ******************888888899999999999999998899***********..******************* PP

                                       EEEESSEHHHHHHHHHHTTGGGESEEEEHHCES.STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 138 vlltgdnpetaeraanqlGddyfdaviasdiet.vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                        ++tgdn +tae++ + +G           i+   ++++p +k +a++ Lq++ + vam GDg+nDa+al +A+
  gi|474933896|ref|YP_007687478.1| 574 MMVTGDNAQTAEAVGRAVG-----------ITDiRSGAKPGDKIEAVKDLQIRQRTVAMAGDGINDAPALTQAN 636
                                       *******************...........5556************************************9996 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.8   0.2   8.9e-20   2.7e-16       1      62 []       8      69 ..       8      69 .. 0.98
   2 ?   -3.4   0.1       4.8   1.4e+04       5      16 ..     493     504 ..     493     505 .. 0.86

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 8.9e-20
                               HMA  1 tvrvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagyk 62
                                      t+r+ gm+Ca+Ca k+e ++ +lpgV +++ +++++t+tV++d + ++  +i++aiekagy+
  gi|474933896|ref|YP_007687478.1|  8 TLRIGGMTCAACAVKIETSVRRLPGVIDCVSNYGNNTATVTYDSSRVSHAQIVKAIEKAGYT 69
                                      789**********************************************************5 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 4.8
                               HMA   5 sgmhCagCaakv 16 
                                       +g+ C +C +++
  gi|474933896|ref|YP_007687478.1| 493 EGVSCLSCGKRI 504
                                       5899****9998 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.79   2.4e+03      17      55 ..     556     594 ..     553     598 .. 0.84
   2 !   27.3   0.2   9.4e-10   2.8e-06     196     244 ..     609     657 ..     599     664 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.79
                                       -HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCC CS
                       Hydrolase_3  17 sektkeaikklkekgikvviATGRslravlpvleelgld 55 
                                        e++++a+  lk+ gi  +  TG + ++++ v +++g++
  gi|474933896|ref|YP_007687478.1| 556 RENAASAVSSLKDLGISPMMVTGDNAQTAEAVGRAVGIT 594
                                       5778899999999*******9999999998888887765 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 9.4e-10
                                       HHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE- CS
                       Hydrolase_3 196 akelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtk 244
                                       +k l+i +  v+  GDg ND + L++a++gvA+g++++ ++ aAd v  
  gi|474933896|ref|YP_007687478.1| 609 VKDLQIRQRTVAMAGDGINDAPALTQANIGVAVGSGTDIAIGAADVVLM 657
                                       56788****************************************9975 PP

>> CT_C_D  Carboxyltransferase domain, subdomain C and D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00013       0.4      31      76 ..      24      69 ..      14     106 .. 0.73
   2 ?   -2.4   0.0       1.1   3.3e+03     125     149 ..     688     712 ..     681     727 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00013
                                      HHHHHT..STTECEEEE..-SSEEEEEESCCCCHHHHHH.HHHHHHHH CS
                            CT_C_D 31 aaalrakalpgvvelvp..ayrsllvefdpealdaaellaalkallee 76
                                      ++++  ++lpgv+++v   + ++ +v++d  ++++a++++a++++  +
  gi|474933896|ref|YP_007687478.1| 24 ETSV--RRLPGVIDCVSnyGNNTATVTYDSSRVSHAQIVKAIEKAGYT 69
                                      3444..45********73366899******************887555 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.1
                                       EEEEEE-SSTT-EEE----GGG--- CS
                            CT_C_D 125 yrvaflGfapGfaylggldprlavp 149
                                       y  +++  a+G++yl g+ +  ++p
  gi|474933896|ref|YP_007687478.1| 688 YNAVCIPIAAGLPYLLGMGEFDHMP 712
                                       778888999******9997765555 PP

>> DUF2781  Protein of unknown function (DUF2781)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.2    0.0011       3.3      59     107 ..      92     139 ..      83     142 .. 0.89
   2 ?    3.2   0.0     0.036   1.1e+02      70     117 ..     143     189 ..     141     205 .. 0.84
   3 ?   -3.4   0.3         4   1.2e+04     100     127 ..     355     381 ..     346     401 .. 0.51

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0011
                           DUF2781  59 fvllelffqlPlffiavyaLlkkekpwlrllllvYgvhaatttlaciae 107
                                        ++l ++f +Pl+++a+ +++   +  +r+  lvY+ + ++ +++++++
  gi|474933896|ref|YP_007687478.1|  92 NLILAIVFAIPLSVYAMARMFG-VDVPFRDDGLVYASAQLILLIPILWA 139
                                       567899***************4.5899**************99999975 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.036
                           DUF2781  70 lffiavyaLlkkekpwlrllllvYgvhaatttlaciaellsegeavas 117
                                       +f+ ++ aLl+  +p++ +l+ + +  a++ +l c + ++  +   a 
  gi|474933896|ref|YP_007687478.1| 143 FFIRGIPALLR-RSPSMDTLIAMGSGVAVVYSLYCTYRIWMGDAGMAD 189
                                       78899999995.79**************************98876655 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 4
                           DUF2781 100 ttlaciaellsegeavasesekqklkll 127
                                       ++++c+a +l  + ++   s +  +++l
  gi|474933896|ref|YP_007687478.1| 355 SVACCLAWFLLGDRSAS-FSLTVMISVL 381
                                       44455555554443222.1222233333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (742 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.68u 0.27s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 4673.79
//
Query:       gi|474933897|ref|YP_007687479.1|  [L=72]
Description: Copper chaperone [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-08   35.1   0.7    1.7e-08   34.8   0.7    1.1  1  HMA       Heavy-metal-associated domain


Domain annotation for each model (and alignments):
>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.7   9.2e-13   1.7e-08       2      61 ..       7      63 ..       6      64 .. 0.95

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 9.2e-13
                               HMA  2 vrvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagy 61
                                      ++v++m C+ C+a v+k+L  ++gV++ +v  +  ++  ++d+++++ +++i+a+ +ag+
  gi|474933897|ref|YP_007687479.1|  7 LKVDNMMCEVCVANVTKAL-DIDGVSDLSVKIG--SASLSYDEAKVSEEQLIRAVVDAGF 63
                                      68*****************.99**********9..**********999*********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 479.85
//
Query:       gi|474933898|ref|YP_007687480.1|  [L=1244]
Description: HRDC domain protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-28   98.6   0.2    6.5e-28   96.8   0.2    2.1  1  MTES_1575        REase_MTES_1575
    1.1e-22   80.6   0.4    5.3e-22   78.4   0.4    2.0  1  AAA_12           AAA domain
    6.2e-15   55.7   1.9    1.3e-06   28.4   0.0    3.1  3  AAA_11           AAA domain
    6.2e-10   39.2   0.6    7.5e-08   32.5   0.0    3.6  2  DUF4011          Protein of unknown function (DUF4011)
    1.6e-09   37.6   0.0    5.8e-09   35.8   0.0    2.0  1  HRDC             HRDC domain
    1.8e-07   31.1   0.0      5e-05   23.1   0.0    2.4  2  AAA_30           AAA domain
    1.3e-05   24.6   3.5       0.01   15.2   0.2    2.6  2  ALIX_LYPXL_bnd   ALIX V-shaped domain binding to HIV
    3.7e-05   23.5   0.1    0.00023   21.0   0.0    2.4  2  DUF559           Protein of unknown function (DUF559)
    0.00015   21.6   0.0       0.76    9.5   0.0    3.4  3  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    0.00036   20.9   0.0     0.0029   17.9   0.0    2.5  2  AAA_19           AAA domain
     0.0014   18.4   0.0     0.0032   17.2   0.0    1.5  1  IstB_IS21        IstB-like ATP binding protein
  ------ inclusion threshold ------
      0.011   15.1   0.1      0.094   11.9   0.0    2.5  3  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.012   15.3   0.1        1.5    8.5   0.0    2.4  2  DEAD             DEAD/DEAH box helicase
      0.019   14.4   0.1      0.068   12.6   0.1    2.0  2  PhoH             PhoH-like protein
      0.025   13.9   0.0      0.069   12.5   0.0    1.7  1  FtsK_SpoIIIE     FtsK/SpoIIIE family
      0.049   14.0   0.0       0.31   11.4   0.0    2.3  2  AAA_16           AAA ATPase domain
        0.1   12.4   0.0       0.46   10.3   0.0    2.1  2  Helicase_RecD    Helicase
       0.32   10.5   4.5       0.64    9.5   0.0    3.1  3  UvrD-helicase    UvrD/REP helicase N-terminal domain


Domain annotation for each model (and alignments):
>> MTES_1575  REase_MTES_1575
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.8   0.2   6.5e-31   6.5e-28       4      95 .]    1146    1237 ..    1144    1237 .. 0.98

  Alignments for each domain:
  == domain 1  score: 96.8 bits;  conditional E-value: 6.5e-31
                         MTES_1575    4 eVaeaLrergykvkpqvgvggfriDlvvedpgkyllaIecdgdkyhsskeardrdierqevLerlGWkilRiwss 78  
                                        +V++aL+++gy+v+++vg+gg++iDl+v++++k++l+Iecd+  y  s++ r+rd++rq++Le+ GW+i+R+w  
  gi|474933898|ref|YP_007687480.1| 1146 RVYDALIRKGYTVERNVGIGGYNIDLAVKQNDKFILGIECDSRIYALSASTRERDYHRQKYLESRGWHIHRVWTA 1220
                                        79************************************************************************* PP

                         MTES_1575   79 dwyrnpeeeleklveal 95  
                                          y++p+ee++k+v+a+
  gi|474933898|ref|YP_007687480.1| 1221 GMYKDPAEEIAKIVAAI 1237
                                        **************997 PP

>> AAA_12  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.4   0.4   5.3e-25   5.3e-22       4     195 ..     884    1080 ..     881    1083 .. 0.86

  Alignments for each domain:
  == domain 1  score: 78.4 bits;  conditional E-value: 5.3e-25
                            AAA_12    4 SlferllkkekekvvlLdtqYRmh.peIsrfpsklfYkgkLkdaesvkkreleaqealeepleplvfidveksee 77  
                                        Sl++   +++   ++lL+  YR++ +e+  f++  fY+g+L  ++++++   +          p+ +i+v+++ e
  gi|474933898|ref|YP_007687480.1|  884 SLLDLARSRY--DSILLNFHYRSKyEELIAFSNYAFYGGRLYVSPNIASPARP----------PIEMIKVDGKWE 946 
                                        5555444444..899*******97589*********************99999..........999999996655 PP

                            AAA_12   78 ekekkeksyiNeeEaelvvklvekllkkgseeerkkigvitpYraqvellkkklkekeeekseke.......... 142 
                                         +       +N++Ea+ vv+l+++++++ +++  + ig+it+ ++q +l++++++++ +++++ +          
  gi|474933898|ref|YP_007687480.1|  947 DR-------SNSAEADRVVELLKQIFRERQHD--ETIGIITFNSSQRDLINDRIDDACSDDPAFSnliaseekrm 1012
                                        44.......599*******************9..9********************98888877778888888899 PP

                            AAA_12  143 .......ievntvdgfQGrekdviilslVRsnekk.....eigflkd...errlNValTRAkskliiv 195 
                                               + v+ ++++QG e+d+ii+s+  +++++     ++g l+    e+rlNVa++RAk+k++iv
  gi|474933898|ref|YP_007687480.1| 1013 dngedvgLFVKNIESVQGDERDIIIFSIGYAKNEEgrimqRFGWLNThggENRLNVAISRAKKKIYIV 1080
                                        999999**********************999855445554688776533389***************9 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       8.9   8.8e+03     126     140 ..      88     102 ..      35     172 .. 0.61
   2 !   28.4   0.0   1.3e-09   1.3e-06       2      76 ..     380     444 ..     379     481 .. 0.88
   3 !   25.2   0.2   1.3e-08   1.3e-05     189     256 ..     780     856 ..     638     859 .. 0.60

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 8.9
                            AAA_11 126 akeiskeleklakel 140
                                       +k+++++l++l+k+l
  gi|474933898|ref|YP_007687480.1|  88 NKSMDQTLRELQKKL 102
                                       333333333333333 PP

  == domain 2  score: 28.4 bits;  conditional E-value: 1.3e-09
                            AAA_11   2 lndsqreaiksalseseitliqGPPGtgKTktivellsqllsrrkseeeksakpriLvCapSNaAvDellerllr 76 
                                       ln+ q++ ++ + +e+e  ++qGPPGtgK+++i++l+ ++          ++++ +L+ ++  +A D++ +r+ +
  gi|474933898|ref|YP_007687480.1| 380 LNSAQENVLTAVDKEDE-IVVQGPPGTGKSQVITGLICSA---------VAEGKTVLMVSEKKTALDVVYSRMGT 444
                                       78889888888888887.8********************9.........7899*******************877 PP

  == domain 3  score: 25.2 bits;  conditional E-value: 1.3e-08
                            AAA_11 189 e...........eevldeaeivltTlsgagsklleklakkfdvviIDEAaqavEpstliPlrlgakkvvLvGDpkQL 254
                                       +            e+ + ++i l T   +++    ++ + fd+++ DEA+q   ++  iP  ++akkvv +GD+kQL
  gi|474933898|ref|YP_007687480.1| 780 KwslnkfinrygYELFKGVRIWLLTPEVVSEIIPMEM-GLFDLLVFDEASQMY-VERGIPSIYRAKKVVVAGDHKQL 854
                                       0223333334447777778887777777755555555.59***********65.78888888888************ PP

                            AAA_11 255 pa 256
                                       ++
  gi|474933898|ref|YP_007687480.1| 855 RP 856
                                       99 PP

>> DUF4011  Protein of unknown function (DUF4011)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.0   7.5e-11   7.5e-08       4     158 ..     104     234 ..      89     238 .. 0.68
   2 ?    1.3   0.2       0.3     3e+02      57      94 ..     726     767 ..     624     769 .. 0.66

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 7.5e-11
                           DUF4011   4 DlslRnrllnfkeskk.ktleiidedldelfdrLaegekklellppdeeeaakeleteeeekeerkkdkklqtllte 79 
                                       ++s+ nrll +++++  ++++i+d + +++++ L+  +++l+l                             + ++e
  gi|474933898|ref|YP_007687480.1| 104 NISKGNRLLYMPRTSVkNSFDIMDGRDTDVESFLFGRKRSLKLCG-------------------------ASSSKEE 155
                                       444444444444333323344444444444444443333333333.........................1234456 PP

                           DUF4011  80 eelekrlrklyrkartsleEtGvniLYlalgfLewyesdksekpirAPLllvPVeLerksarsnfslkakeeeialN 156
                                       e+  +rl+++ r+  + ++E+G+  LY+ + f+e+    +++ p+r PL l PV+++++ ++ +++l  + + +  N
  gi|474933898|ref|YP_007687480.1| 156 EKKFRRLNNILREVTRDQRERGMYDLYIGYPFIEGSLAGEEDFPLRGPLALFPVTMSKNGREISIELDDSRDTVYNN 232
                                       6666778888888888899****************************************998888888877777666 PP

                           DUF4011 157 ls 158
                                       + 
  gi|474933898|ref|YP_007687480.1| 233 TL 234
                                       54 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.3
                           DUF4011  57 l...e.teeeekeerkkdkklqtllteeelekrlrklyrkar 94 
                                       l   + + ++ +++ ++++++  +l e el+++lr++ ++ r
  gi|474933898|ref|YP_007687480.1| 726 LhdfDsIVADMDRRMEEKRQVTRRLLESELSNSLRYITESKR 767
                                       133322344556667788888889999999999999998877 PP

>> HRDC  HRDC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.0   5.8e-12   5.8e-09      17      67 ..      23      73 ..       6      74 .. 0.93

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 5.8e-12
                                      HHHTS-HHHHS-HHHHHHHHHH---SHHHHHTSTTT-HHHHHHHHHHHHHH CS
                              HRDC 17 reedvppyvvfpdktLleiAeklPttleeLlqiegvgkrklekygeeilea 67
                                      r+++    ++++d++L +++++ P  +++L++i+g+g+r +e yg+++l++
  gi|474933898|ref|YP_007687480.1| 23 RKQNGKEPMICSDEALTQMSQHIPVKEADLSAIDGIGDRFIENYGRDFLAV 73
                                      88999999*****************************************97 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0     5e-08     5e-05       1      68 [.     379     444 ..     379     476 .. 0.85
   2 ?    5.4   0.0     0.013        13      90     130 ..     820     856 ..     783     873 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 5e-08
                            AAA_30   1 elnaeQaaavealltsgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgi 68 
                                       +ln+ Q+++++a+ ++++   v++Gp+GtGK+ ++++l   + a+g++v++++ +++a +v+   +g+
  gi|474933898|ref|YP_007687480.1| 379 TLNSAQENVLTAVDKEDE--IVVQGPPGTGKSQVITGLICSAVAEGKTVLMVSEKKTALDVVYSRMGT 444
                                       58999***9988877775..99****************999999*************99998877775 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.013
                            AAA_30  90 tllivDEagmvdtkqlaallkaaekagakvilvGDerQlas 130
                                       +ll+ DEa+ +  +     + +a     kv+++GD++Ql +
  gi|474933898|ref|YP_007687480.1| 820 DLLVFDEASQMYVERGIPSIYRA----KKVVVAGDHKQLRP 856
                                       78999999988766655555555....56**********76 PP

>> ALIX_LYPXL_bnd  ALIX V-shaped domain binding to HIV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.2     1e-05      0.01      69     156 ..      83     176 ..      71     179 .. 0.86
   2 !    9.5   0.3   0.00055      0.54     182     230 ..     690     745 ..     636     766 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1e-05
                    ALIX_LYPXL_bnd  69 pSseltaelraelqkyreileeAsesDkivrqklqenkedlelLsgpeeeleaalpssssaaa......sesveeqi 139
                                       + s  ++++ + l+++++ l + s+ ++ +    +++k++++++ g + + e++l   +++ +      s+++e+++
  gi|474933898|ref|YP_007687480.1|  83 KGSDINKSMDQTLRELQKKLVNISKGNRLLYMPRTSVKNSFDIMDGRDTDVESFLFGRKRSLKlcgassSKEEEKKF 159
                                       567899************************************************994444422344455899999** PP

                    ALIX_LYPXL_bnd 140 rklrsllekldelkaer 156
                                       r+l ++l ++ + ++er
  gi|474933898|ref|YP_007687480.1| 160 RRLNNILREVTRDQRER 176
                                       *********99988888 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00055
                    ALIX_LYPXL_bnd 182 r.......diaanefealfeeelekydplqeqleqslakqeellkeiqeaneefeq 230
                                       r       + + n+fe +++++l+k+d   ++l q+l++ ++++++ ++ +ee  q
  gi|474933898|ref|YP_007687480.1| 690 RnvktsysNANDNMFEYIMNDHLQKFDATHSELMQELHDFDSIVADMDRRMEEKRQ 745
                                       1222234455668*********************************9866655444 PP

>> DUF559  Protein of unknown function (DUF559)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       6.7   6.6e+03       2      34 ..     684     716 ..     683     730 .. 0.79
   2 !   21.0   0.0   2.3e-07   0.00023      31     108 ..    1154    1237 ..    1146    1238 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 6.7
                                       .XXXXXXXXXXXX-HHHHHHHHHHGGGTTTT-- CS
                            DUF559   2 klkanarklRreqteaekkLWqllrnrrlsglk 34 
                                       +l+a +r+++ + ++a+ ++++++ n++l+ + 
  gi|474933898|ref|YP_007687480.1| 684 NLTALTRNVKTSYSNANDNMFEYIMNDHLQKFD 716
                                       567788999999999999999999999998654 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 2.3e-07
                                        TT--EEEEEEETTEEEEEEETT.TTEE..EEEE-------...----HHHHHHHHHTT-EEEEEEHHHHHH-HHH CS
                            DUF559   31 sglkfrRqkpigsYivDfvclk.akli..velDGaqhdee...eeyDaeRtelLeslGftvlRfkndevlkniee 99  
                                        +g+  +R + ig Y +D + ++  k i  +e D   ++ +   +e+D +R+++Les G+++ R +   + k++ e
  gi|474933898|ref|YP_007687480.1| 1154 KGYTVERNVGIGGYNIDLAVKQnDKFIlgIECDSRIYALSastRERDYHRQKYLESRGWHIHRVWTAGMYKDPAE 1228
                                        578899************887525777557999988765555699****************************99 PP

                                        HHHHHHHHH CS
                            DUF559  100 vleeilkal 108 
                                         +++i++a+
  gi|474933898|ref|YP_007687480.1| 1229 EIAKIVAAI 1237
                                        999998876 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0   0.00077      0.76       1      40 [.     397     435 ..     397     460 .. 0.72
   2 ?    5.2   0.0     0.015        15      63     101 ..     819     855 ..     805     860 .. 0.86
   3 ?    2.6   0.0     0.095        95     215     234 .]    1062    1081 ..     980    1081 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00077
                   Viral_helicase1   1 ivvhGvpGcGKStlirkllrtsliltvnrptaelltegk..p 40 
                                       ivv+G pG GKS++i  l+++   + +++  + +++e k   
  gi|474933898|ref|YP_007687480.1| 397 IVVQGPPGTGKSQVITGLICS--AVAEGKT-VLMVSEKKtaL 435
                                       79*****************99..5444444.77777766554 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.015
                   Viral_helicase1  63 gkililDEylllhaGyill.laalskaklvilfGDplQip 101
                                       +++l++DE+ ++   y++  +  +++ak v++ GD++Q  
  gi|474933898|ref|YP_007687480.1| 819 FDLLVFDEASQM---YVERgIPSIYRAKKVVVAGDHKQLR 855
                                       689******887...599999999**************75 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.095
                   Viral_helicase1  215 srenllvAlTRhrkslvilt 234 
                                        +++ l vA++R++k+++i++
  gi|474933898|ref|YP_007687480.1| 1062 GENRLNVAISRAKKKIYIVN 1081
                                        467788***********985 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   2.9e-06    0.0029       8      76 ..     392     456 ..     384     738 .. 0.76
   2 ?   -0.5   0.0       1.5   1.4e+03     105     142 ..     821     855 ..     814     858 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.9e-06
                            AAA_19   8 lkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgaeatTiHrla 76 
                                        ke+ ++v ++pGtGK++v+++ +  +v++g    +++l+v+  + A + +  r+ +l + a  i   a
  gi|474933898|ref|YP_007687480.1| 392 DKEDEIVVQGPPGTGKSQVITGLICSAVAEG----KTVLMVSEKKTALDVVYSRMGTLSKYALQIDDTA 456
                                       5678899***********************9....789***9999999999999977776666665553 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.5
                            AAA_19 105 llivDEfqdvd.elqyrLlkallgekkklllvGDpdQli 142
                                       ll+ DE+++++ e   r +  ++ ++kk+++ GD++Ql 
  gi|474933898|ref|YP_007687480.1| 821 LLVFDEASQMYvE---RGIPSIY-RAKKVVVAGDHKQLR 855
                                       6777887777632...3356666.55669********86 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   3.2e-06    0.0032      43      83 ..     390     430 ..     371     448 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.2e-06
                         IstB_IS21  43 fiekkenivllGpsGvGKshlaialgveavraglsvlfvrv 83 
                                        ++k++ iv+ Gp+G+GKs + + l  +av++g+ vl v+ 
  gi|474933898|ref|YP_007687480.1| 390 AVDKEDEIVVQGPPGTGKSQVITGLICSAVAEGKTVLMVSE 430
                                       58999*******************************98875 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   9.5e-05     0.094       4      55 ..     397     446 ..     395     477 .. 0.82
   2 ?   -3.4   0.0       4.2   4.2e+03      89     102 ..     819     832 ..     815     845 .. 0.81
   3 ?   -1.3   0.0      0.98   9.7e+02     343     360 ..    1063    1080 ..    1055    1081 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.5e-05
                           DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakke 55 
                                       ++V+G +GtGK+ v   l+  +   +e++t+ ++s  +  ++v+++++   +
  gi|474933898|ref|YP_007687480.1| 397 IVVQGPPGTGKSQVITGLICSA--VAEGKTVLMVSEKKTALDVVYSRMGTLS 446
                                       79******************99..9********************9986555 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 4.2
                           DUF2075  89 edvvivDEAhrllt 102
                                       +d++++DEA  +  
  gi|474933898|ref|YP_007687480.1| 819 FDLLVFDEASQMYV 832
                                       68999999988765 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.98
                           DUF2075  343 kNayrVLLtRGrkGlyiy 360 
                                        +N+++V ++R+ k +yi+
  gi|474933898|ref|YP_007687480.1| 1063 ENRLNVAISRAKKKIYIV 1080
                                        7***************96 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0016       1.5       3      64 ..     383     439 ..     381     472 .. 0.75
   2 ?    4.3   0.0      0.03        30      94     137 ..     794     834 ..     747     854 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0016
                                       HHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   3 iQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtl 64 
                                        Q++++ ++ ++++++v+++ G+GK+ +    ++++v+e     g+ +l+v+  +     ++
  gi|474933898|ref|YP_007687480.1| 383 AQENVLTAVDKEDEIVVQGPPGTGKSQVITGLICSAVAE-----GKTVLMVSEKKTALDVVY 439
                                       799999999999*****************9999999965.....444444444444444444 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.03
                                       HHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  94 ldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqg 137
                                       l +gv+i + tp+ + +++    +++  + +lV+DEa ++  + 
  gi|474933898|ref|YP_007687480.1| 794 LFKGVRIWLLTPEVVSEIIP---MEMGLFDLLVFDEASQMYVER 834
                                       34889************995...5688999*******9998774 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   6.9e-05     0.068       2      46 ..     377     421 ..     376     449 .. 0.84
   2 ?   -3.0   0.0       4.2   4.2e+03     145     158 ..     841     854 ..     822     858 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.9e-05
                                       ----SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHT CS
                              PhoH   2 ikpktkeQkeylealkkndivfaiGpaGtGKtylavalavealkk 46 
                                       i++ +++Q+++l+a++k+d +++ Gp GtGK+ + + l  +a+ +
  gi|474933898|ref|YP_007687480.1| 377 INTLNSAQENVLTAVDKEDEIVVQGPPGTGKSQVITGLICSAVAE 421
                                       78899**************************98766555555555 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.2
                                       TT-EEEEEE----- CS
                              PhoH 145 enskvvvtGdvtqi 158
                                       +  kvvv+Gd +q 
  gi|474933898|ref|YP_007687480.1| 841 RAKKVVVAGDHKQL 854
                                       45799*****9996 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.9e-05     0.069      40      65 ..     395     420 ..     371     435 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.9e-05
                                       .SEEEE--TTSSHHHHHHHHHHHHHT CS
                      FtsK_SpoIIIE  40 shllvaGatgsGKStalntLilSlat 65 
                                         ++v G +g+GKS ++  Li+S+++
  gi|474933898|ref|YP_007687480.1| 395 DEIVVQGPPGTGKSQVITGLICSAVA 420
                                       5799********************97 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00031      0.31      27      96 ..     397     476 ..     376     516 .. 0.64
   2 ?   -1.8   0.0       3.6   3.6e+03     138     159 ..     706     727 ..     635     736 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00031
                            AAA_16  27 vllsGesGvGKsslvrellralekdg..giflrgkcdql.....esa..ipy.salaqalareellrqlldeaesae 93 
                                       +++ G++G+GKs +++ l  ++ ++g  ++ +++k + l     +++    y +++ ++++++++++ql++++++  
  gi|474933898|ref|YP_007687480.1| 397 IVVQGPPGTGKSQVITGLICSAVAEGktVLMVSEKKTALdvvysRMGtlSKYaLQIDDTADKDRFYKQLGNMLRTEP 473
                                       67*************88777777774223336666666633332222444444448888888888888888866544 PP

                            AAA_16  94 lea 96 
                                       +++
  gi|474933898|ref|YP_007687480.1| 474 RAP 476
                                       433 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.6
                            AAA_16 138 vlvlDdlqwadeaslqllaaLl 159
                                       ++  D+lq++d++  +l+++L 
  gi|474933898|ref|YP_007687480.1| 706 YIMNDHLQKFDATHSELMQELH 727
                                       4556888888888888877776 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00046      0.46       1      49 [.     398     445 ..     398     473 .. 0.80
   2 ?   -2.2   0.0       3.2   3.2e+03      92     105 ..     820     833 ..     803     849 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00046
                     Helicase_RecD   1 vltAdRGRGKSaalGlalaaliaegksnilvtapskenvktlfeflakg 49 
                                       v+++ +G+GKS ++  ++ +++aegk ++l+++ +k++++ +++++ + 
  gi|474933898|ref|YP_007687480.1| 398 VVQGPPGTGKSQVITGLICSAVAEGK-TVLMVSEKKTALDVVYSRMGTL 445
                                       68899*********999999999998.8999999**9999999888543 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.2
                     Helicase_RecD  92 dllvvDEAAaiplp 105
                                       dllv DEA+++ ++
  gi|474933898|ref|YP_007687480.1| 820 DLLVFDEASQMYVE 833
                                       99*******98776 PP

>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.75   7.4e+02      88     150 ..      46     106 ..      13     373 .. 0.63
   2 ?    9.5   0.0   0.00065      0.64       2      42 ..     381     423 ..     380     469 .. 0.86
   3 ?   -0.1   1.1      0.54   5.4e+02     212     280 ..     656     727 ..     540     768 .. 0.55

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.75
                                       HCTTSEEEEHHHHHHHHHHHHHGGTT..............................SHTTTEEECHHHHHHCCHHHH CS
                     UvrD-helicase  88 nlseanisTlHsfcqkilkkeanrig..............................ldpnfrildeedeedlkqqel 134
                                        ++ea+ s++++++ ++++++  +                                l                    
  gi|474933898|ref|YP_007687480.1|  46 PVKEADLSAIDGIGDRFIENYGRDFLavtrkyavsaakgsdinksmdqtlrelqkkL-------------------- 102
                                       357888888888888888887776654333333332222222222222222222220.................... PP

                                       HHHHHSCHSHTTTTHH CS
                     UvrD-helicase 135 lkelleksaddslnld 150
                                                   +n++
  gi|474933898|ref|YP_007687480.1| 103 ------------VNIS 106
                                       ............2222 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00065
                                       SHHHHHHHHS..-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSS CS
                     UvrD-helicase   2 npeqreaias..lggpilveAsAGsGKTfvlaerilrlikeee 42 
                                       n  q++ ++    + +i+v   +G+GK++v++ +i   ++e++
  gi|474933898|ref|YP_007687480.1| 381 NSAQENVLTAvdKEDEIVVQGPPGTGKSQVITGLICSAVAEGK 423
                                       6677777777556889********************9999984 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.54
                                       HHHHHHHHHHHHHHHHTCEEHHHHHH.HHHHHHHH..CHHHHHHHHHHSSEEEESSGGG-BHHHHHHHHHHH CS
                     UvrD-helicase 212 kiaeflkeyqeqkkeenalDfsdllh.allellee..neelaealrerykeiliDEyQDTnkiQyrilklla 280
                                       + ++ + ++ ++   ++alD  ++ + + l++l++  + +  +a  + +++i+ D  Q  + +  ++++ l 
  gi|474933898|ref|YP_007687480.1| 656 DSIDDYDRFSRRATLYRALDSTQREYwKNLTALTRnvKTSYSNANDNMFEYIMNDHLQKFDATHSELMQELH 727
                                       223333333333333333443333321222233333444444445555555555555555555555555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       933  (0.0520386); expected 358.6 (0.02)
Passed bias filter:                      669  (0.0373138); expected 358.6 (0.02)
Passed Vit filter:                       112  (0.00624686); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.99u 0.28s 00:00:01.27 Elapsed: 00:00:00.48
# Mc/sec: 7838.25
//
Query:       gi|474933899|ref|YP_007687481.1|  [L=171]
Description: hypothetical protein TALC_00312 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.1e-18   64.4   0.1    1.2e-17   63.8   0.1    1.3  1  bPH_2         Bacterial PH domain
  ------ inclusion threshold ------
      0.029   14.7   1.8       0.04   14.2   1.8    1.2  1  DUF420        Protein of unknown function (DUF420)
       0.06   13.8   1.6        0.1   13.1   1.6    1.3  1  DUF4231       Protein of unknown function (DUF4231)
       0.11   13.3   0.4       0.76   10.5   0.4    2.1  1  Bcl-2         Apoptosis regulator proteins, Bcl-2 family
       0.11   12.2   1.1       0.15   11.7   1.1    1.2  1  DUF4131       Domain of unknown function (DUF4131)
       0.16   11.4   0.0       0.33   10.3   0.0    1.5  1  FAM35_C       Protein family FAM35, C-terminal
       0.21   11.8   4.2        2.6    8.3   4.2    2.2  1  Peptidase_A8  Signal peptidase (SPase) II
       0.47   10.9   3.4          1    9.9   3.4    1.5  1  DUF202        Domain of unknown function (DUF202)


Domain annotation for each model (and alignments):
>> bPH_2  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.8   0.1   5.4e-21   1.2e-17       1      80 []      83     159 ..      83     159 .. 0.97

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 5.4e-21
                             bPH_2   1 yrattytitdrrvvvrsGillrktldiplerIqavsleqsllqrrlglgtivietaggsraevelplrsvpdaeela 77 
                                       yr+++y+i ++ v +r+G++  +   +p+erI+ v+++ +++ r+++l++++i+tagg+   + + ++ + +ae +a
  gi|474933899|ref|YP_007687481.1|  83 YRRYRYRIAEDAVDIRRGVFVITHELVPIERIHQVEVSSGPILRMFNLADVAITTAGGT---AYIQYLEKGEAEGIA 156
                                       8**********************************************************...6************99 PP

                             bPH_2  78 ell 80 
                                       ++l
  gi|474933899|ref|YP_007687481.1| 157 AKL 159
                                       875 PP

>> DUF420  Protein of unknown function (DUF420)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   1.8   1.8e-05      0.04       4      62 ..      33      91 ..      30     112 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.8e-05
                            DUF420  4 lnavlnalaavllllglvaikkgkieaHrklmllafvlsalFlvlYllkhalagetkfg 62
                                      ++ +++a+aa + +++++++k +++++ r + ++af+l+a+F ++Y +  +   + +++
  gi|474933899|ref|YP_007687481.1| 33 VSLIIIAVAAAAAFAAVFFAKGDEYRWERIAAVAAFALVAAFRIVYPVIYYRRYRYRIA 91
                                      578999****************************************7766665555544 PP

>> DUF4231  Protein of unknown function (DUF4231)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.6   4.6e-05       0.1      13      78 ..      26      90 ..      23     104 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.6e-05
                           DUF4231 13 akrrfrllrlitivlgallpilvs.sklgagvsvlkiltallsalvailaaleeffrykerWrryRs 78
                                      +k+  ++++li+i ++a ++++++   +g++ ++  i+++++ alva   ++  +  y++  +ryR 
  gi|474933899|ref|YP_007687481.1| 26 SKKAMYIVSLIIIAVAAAAAFAAVfFAKGDEYRWERIAAVAAFALVAAFRIVYPVIYYRR--YRYRI 90
                                      6888999999999999999999998668999***************99999988887777..66665 PP

>> Bcl-2  Apoptosis regulator proteins, Bcl-2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.4   0.00034      0.76      33      64 ..      43      75 ..      25     171 .] 0.71

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00034
                                      HHHHHHHCCT..TS--SCHHHHHHHHHHHHHHHH CS
                             Bcl-2 33 fakvaeelfs..dgelnWgrvvalfafagalaer 64
                                       a+ a  +f+  d e  W+r++a+ afa + a r
  gi|474933899|ref|YP_007687481.1| 43 AAAFAAVFFAkgD-EYRWERIAAVAAFALVAAFR 75
                                      5566677788534.8*************999887 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.1   6.8e-05      0.15       5      56 ..      33      85 ..      31     106 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.8e-05
                           DUF4131  5 lalvllalllllllllllllrr.rprrrvllllllllllallgfalrapqpna 56
                                      ++l+++a++++++++++++ +   +r+ +++++++++l+a++ +++++ +  +
  gi|474933899|ref|YP_007687481.1| 33 VSLIIIAVAAAAAFAAVFFAKGdEYRWERIAAVAAFALVAAFRIVYPVIYYRR 85
                                      57899999999999999998778888888888888888888887777766655 PP

>> FAM35_C  Protein family FAM35, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00015      0.33      57      90 ..       6      39 ..       3      49 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00015
                           FAM35_C 57 eletDenkiykqCysCLpltavkryyRpalltvk 90
                                        etDen++ ++ y+CL  + +k  y  +l+ ++
  gi|474933899|ref|YP_007687481.1|  6 QFETDENGLTSDGYRCLEPSSKKAMYIVSLIIIA 39
                                      679********************99998887765 PP

>> Peptidase_A8  Signal peptidase (SPase) II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   4.2    0.0012       2.6      55     135 ..      34     142 ..      19     147 .. 0.48

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0012
                      Peptidase_A8  55 llillslvvillliv.lllkkkkkskllria..lalilgGalGNliDrlly.....gkVvDfldfsl.......... 113
                                        li++++++++++++ ++ k   +++++ria   a+ l +a+  ++  ++y         D +d++           
  gi|474933899|ref|YP_007687481.1|  34 SLIIIAVAAAAAFAAvFFAKG-DEYRWERIAavAAFALVAAFRIVYPVIYYrryryRIAEDAVDIRRgvfvithelv 109
                                       344445433333333144333.4466666641223333344433443333344433224444444333344455555 PP

                      Peptidase_A8 114 .....eliefp..........vFNvADvaitvGvill 135
                                            +               +FN+ADvait++    
  gi|474933899|ref|YP_007687481.1| 110 pieriH----QvevssgpilrMFNLADVAITTAGGTA 142
                                       554441....03455666777*********9876554 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   3.4   0.00045         1      18      66 ..      38      87 ..      31      89 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00045
                            DUF202 18 lalialglallrffltgepsalgkilgli.livlgiltllvglvrylrrq 66
                                      +a +a++++ + ff +g++ ++ +i++++ +++++++ +++ ++ y+r +
  gi|474933899|ref|YP_007687481.1| 38 IAVAAAAAFAAVFFAKGDEYRWERIAAVAaFALVAAFRIVYPVIYYRRYR 87
                                      4445555555558889*******999988688888888888777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       821  (0.0457917); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1127.54
//
Query:       gi|474933900|ref|YP_007687482.1|  [L=481]
Description: putative membrane protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-22   79.7   3.5    1.1e-06   28.7   0.1    3.4  3  bPH_2     Bacterial PH domain


Domain annotation for each model (and alignments):
>> bPH_2  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.1   6.1e-11   1.1e-06       1      79 [.      63     143 ..      63     144 .. 0.84
   2 !   27.5   0.0   1.5e-10   2.7e-06      10      69 ..     239     297 ..     230     312 .. 0.79
   3 !   22.5   0.2   5.3e-09   9.5e-05       4      56 ..     389     441 ..     386     462 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 6.1e-11
                             bPH_2   1 yrattytitdrrvvvrsGillrktldiplerIqavsleqsllqrrlglgtivietaggsrae.velpl.rsvpdaee 75 
                                       ++ ttyt+td ++vv +  +++ +++i ++r ++v+++++++  ++g+ t+++ + +   ++ +e  l ++++ a+e
  gi|474933900|ref|YP_007687482.1|  63 WKLTTYTFTDSELVVFKNTVWKAKVEIRYDRMASVQVVRGFWNMIFGTSTLKFNVNSAVNSRnAEATLvLRKDLADE 139
                                       67799***********************************************9999888766744444134556666 PP

                             bPH_2  76 lael 79 
                                       l+e+
  gi|474933900|ref|YP_007687482.1| 140 LRET 143
                                       6665 PP

  == domain 2  score: 27.5 bits;  conditional E-value: 1.5e-10
                             bPH_2  10 drrvvvrsGillrktldiplerIqavsleqsllqrrlglgtivietaggsraevelplrs 69 
                                       +++++v+sG++ +++  ++  ++ +++++ +l++r+lg++t++ e+ g  + ++ +pl++
  gi|474933900|ref|YP_007687482.1| 239 GDTITVHSGLFVTSRKSFKVGKVNSARMRSPLVPRMLGMCTLEAEVVGAMD-DMGIPLIC 297
                                       679*********************************************996.54444433 PP

  == domain 3  score: 22.5 bits;  conditional E-value: 5.3e-09
                             bPH_2   4 ttytitdrrvvvrsGillrktldiplerIqavsleqsllqrrlglgtivieta 56 
                                        t+   ++ +++++G +     ++ ++r+q + ++ +++qrr glgt++i t 
  gi|474933900|ref|YP_007687482.1| 389 RTFSSGEKLFRITRGGFDIADEYLMYDRVQIAGVSSGPIQRRYGLGTLRIMTL 441
                                       556666777899*************************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (481 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       952  (0.0530983); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3216.38
//
Query:       gi|474933901|ref|YP_007687483.1|  [L=128]
Description: putative thioesterase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-06   28.2   0.2    2.5e-06   27.7   0.2    1.2  1  4HBT      Thioesterase superfamily


Domain annotation for each model (and alignments):
>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.2   1.4e-10   2.5e-06       6      77 ..      33     104 ..      29     106 .. 0.94

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.4e-10
                                       HHHHHHHHHHHHHHHHHHTTSTTEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETTSCE CS
                              4HBT   6 gGvylallDeaagaalrslggrgilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrdedgrl 77 
                                        +++ +l+++aa ++l   +++g   v+  + i++++p  +g+e++++++v ++ r+++ + v vrd++g +
  gi|474933901|ref|YP_007687483.1|  33 TPRMIQLIEQAACECLVQFMDGGDTTVGTLMDIRHVSPSPVGSEVVCRVSVCEVDRARVRFAVSVRDSKGDV 104
                                       578889**************************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 924.67
//
Query:       gi|474933902|ref|YP_007687484.1|  [L=468]
Description: Arabinose efflux permease [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-41  141.5  47.9      3e-41  141.5  47.9    2.6  2  MFS_1     Major Facilitator Superfamily
    1.6e-06   27.3  17.5    1.6e-06   27.3  17.5    3.1  3  Sugar_tr  Sugar (and other) transporter
  ------ inclusion threshold ------
       0.37   10.6   0.0       0.37   10.6   0.0    2.5  3  DUF4538   Domain of unknown function (DUF4538)


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.5  47.9   5.1e-45     3e-41       1     352 [.      18     407 ..      18     408 .. 0.93
   2 ?   -0.6   0.6     0.079   4.7e+02     235     270 ..     427     462 ..     406     466 .. 0.45

  Alignments for each domain:
  == domain 1  score: 141.5 bits;  conditional E-value: 5.1e-45
                             MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgll 77 
                                       +++a+f+ +l+ si+g+alp +++e+ g++ ++ ++++ +y  + a + + ++r++  +G r+++++gl++f +g++
  gi|474933902|ref|YP_007687484.1|  18 VFFATFMDGLDGSIVGVALP-TIGESVGVDTATSSWVTITYLMVLAGTLVAFARVASDIGVRKIICVGLAVFTAGSA 93 
                                       69******************.***************9999888877777777999999*****************55 PP

                             MFS_1  78 lllfasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWrav 153
                                       ++ + s  + +l+++rv+qG+ga+++ +a+    ++  p ++ g++++++++g+slG++lgp++gg+++++++W+++
  gi|474933902|ref|YP_007687484.1|  94 VCGL-SADFaMLIAGRVIQGVGAAMMGAAAPMCCTKHLPLSKLGFGMSVVTIGASLGFALGPAIGGAIVEYASWHWC 169
                                       5555.56666******************************************************************* PP

                             MFS_1 154 fyilaivsllafvlfllllpeepperkrkspkeee.......................................... 188
                                       f+i+ ++++ a+    l l + p ++++ s+ ++                                           
  gi|474933902|ref|YP_007687484.1| 170 FLINIPLGIAAAP---LALKAIPASSEPHSGMTLDvsgtvvlcatiilgvfaietlsysgmravsimtglmaialla 243
                                       ***********99...6776777777777777777788*************************************** PP

                             MFS_1 189 .....kgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsglllaglllallalvgail 260
                                            +  +++pl+  +k++++  +  +++i+l l+ ++++g+++l+p+y q  lg +  l++gl+l  +a v+a +
  gi|474933902|ref|YP_007687484.1| 244 lfvriEAGKERPLLH-LKMFRRLDFS-AMFICLMLVNAAYMGMMYLFPFYGQIYLGKP-TLEIGLFLLESATVTALF 317
                                       **9999999999999.9999999944.588888888889999****************.8***************** PP

                             MFS_1 261 allagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfglgfvfpsllalasdlappeeagta 337
                                       ++  +r+sdr gr+++ + a++++++a++++ +++   + + l+++l++ Gf +++v +++++ + ++a    +  a
  gi|474933902|ref|YP_007687484.1| 318 GMPMARWSDRRGRKPFCVAAGVIMTIAFACYGIFGENMTDAELVVILFMKGFVWALVGGPMASRMIEHA--TDRDLA 392
                                       *************************************9*******************************..9***** PP

                             MFS_1 338 sglfntagslggalg 352
                                       s+l+n a+++gga+g
  gi|474933902|ref|YP_007687484.1| 393 SSLTNEAYYIGGAIG 407
                                       **************9 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.079
                             MFS_1 235 qevlglsglllaglllallalvgailallagrls.dr 270
                                       ++v  ++ +l + + +a l++++ ++ l+++ l+ dr
  gi|474933902|ref|YP_007687484.1| 427 MDVARMD-FLDGFIPSAYLCALMGFAILVLSVLIkDR 462
                                       3333444.55555555555555555555666666444 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3  17.5   2.7e-10   1.6e-06       3     183 ..      16     179 ..      13     191 .. 0.82
   2 ?   -1.7   2.3      0.17     1e+03     323     363 ..     203     242 ..     197     248 .. 0.61
   3 !    6.9   9.3   0.00042       2.5     298     414 ..     312     419 ..     247     439 .. 0.74

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 2.7e-10
                                       HHHHHHHHHHHHHHHCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHH CS
                          Sugar_tr   3 lvaalggllfgYdtgvigafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkksl 79 
                                       +++ ++ ++ g d  ++g++l  ++     g+++++s      ++++++  ++l+G ++    +  ++  +G +k++
  gi|474933902|ref|YP_007687484.1|  16 VIVFFATFMDGLDGSIVGVALPTIG--ESVGVDTATS------SWVTITYLMVLAGTLV---AFARVASDIGVRKII 81 
                                       4455566999999999999999999..5555555554......3445666666666665...456677889****** PP

                                       HHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHH CS
                          Sugar_tr  80 liaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaai 156
                                        ++ ++f +g+++++++     + +li+gRv+ G+g+ +  + +Pm + +  p ++ g+ +s+   + ++G+ ++  
  gi|474933902|ref|YP_007687484.1|  82 CVGLAVFTAGSAVCGLSA---DFAMLIAGRVIQGVGAAMMGAAAPMCCTKHLPLSKLGFGMSVVTIGASLGFALGPA 155
                                       ******************...9******************************************************* PP

                                       HHHHHHTSS-TTHHHHHHHCCHHHHHH CS
                          Sugar_tr 157 fglglnktsnadgwrillglqlvpall 183
                                       +g ++ ++ +   w++ + +++ + ++
  gi|474933902|ref|YP_007687484.1| 156 IGGAIVEYAS---WHWCFLINIPLGIA 179
                                       **********...55555555555443 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.17
                                       HHHHHHHHHHHHH..HHHHTTSS....CHHHHHHHHHHHHHH CS
                          Sugar_tr 323 Gaagmaicfvilgivalllvaks.kaasivaivfialfialf 363
                                       ++++ +++++ilg  ++++++ s +++  v+i+  ++ ial 
  gi|474933902|ref|YP_007687484.1| 203 SGTVVLCATIILG--VFAIETLSySGMRAVSIMTGLMAIALL 242
                                       4556666666666..555555555666777666666666654 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.00042
                                       HHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHHHH CS
                          Sugar_tr 298 vvnfvatfvaiflvdrfGRRtllllGaagmaicfvilgivalllvakskaasivaivfialfialfalgwgpvpwvl 374
                                       +v++++ +  +  +dr GR+++ +  +++m+i+f+ +gi    ++++    + v+i f+  f  + al  gp+   +
  gi|474933902|ref|YP_007687484.1| 312 TVTALFGMPMARWSDRRGRKPFCVAAGVIMTIAFACYGIFGENMTDA----ELVVILFMKGF--VWALVGGPMASRM 382
                                       45556666667899***********************9444444444....56666666666..7889999999766 PP

                                       HHHHSHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHH CS
                          Sugar_tr 375 vsElfpqsvRskalaiavavnwlanflisllfpiiteaig 414
                                          +     R++a++++  +  +   + + +f +++   +
  gi|474933902|ref|YP_007687484.1| 383 ---IEHATDRDLASSLTNEAYYIGGAIGTAFFAMTFTLFS 419
                                       ...7788899*************99999999999877665 PP

>> DUF4538  Domain of unknown function (DUF4538)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   0.6       2.4   1.5e+04       7      21 ..     103     117 ..     102     117 .. 0.81
   2 ?   -3.4   0.4       1.4   8.2e+03       3      21 ..     226     244 ..     225     246 .. 0.77
   3 ?   10.6   0.0   6.2e-05      0.37       2      33 ..     328     359 ..     327     360 .. 0.89

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 2.4
                           DUF4538   7 vllvggvvgliglal 21 
                                       +l+ g v+  +g+a+
  gi|474933902|ref|YP_007687484.1| 103 MLIAGRVIQGVGAAM 117
                                       578888999999996 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.4
                           DUF4538   3 glkyvllvggvvgliglal 21 
                                       g + v ++ g+ ++  lal
  gi|474933902|ref|YP_007687484.1| 226 GMRAVSIMTGLMAIALLAL 244
                                       6788888999988877776 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 6.2e-05
                           DUF4538   2 rglkyvllvggvvgliglalYPiiiaPllhpe 33 
                                       rg+k + + +gv+  i+ a+Y i+ + ++++e
  gi|474933902|ref|YP_007687484.1| 328 RGRKPFCVAAGVIMTIAFACYGIFGENMTDAE 359
                                       89999******************977777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.27s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 2914.72
//
Query:       gi|474933903|ref|YP_007687485.1|  [L=470]
Description: Arabinose efflux permease [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.9e-46  158.0  41.1    2.9e-46  158.0  41.1    1.8  2  MFS_1       Major Facilitator Superfamily
    6.8e-08   31.8  13.8    6.8e-08   31.8  13.8    3.3  2  Sugar_tr    Sugar (and other) transporter
    5.7e-07   28.7  21.6    3.2e-05   22.9  10.5    3.1  3  MFS_1_like  MFS_1 like family
  ------ inclusion threshold ------
       0.48    8.8  20.2      0.014   13.8   8.5    2.3  2  MFS_3       Transmembrane secretion effector


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.0  41.1   6.5e-50   2.9e-46       2     352 ..      25     413 ..      24     414 .. 0.91
   2 ?   -3.0   0.4      0.58   2.6e+03     252     267 ..     446     461 ..     415     468 .. 0.51

  Alignments for each domain:
  == domain 1  score: 158.0 bits;  conditional E-value: 6.5e-50
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglll 78 
                                       l+a+f+ +l+ +i+++a+p  ++ dlg++ +++++++ +y+++ a + + ++r+s  +G r+v+ +g+++f++g++l
  gi|474933903|ref|YP_007687485.1|  25 LFATFMDGLDGTIVNVAAP-DIGMDLGVDTATVSWIVIVYMVVLAGTLVAFARISADIGVRKVMAAGIFIFIAGSAL 100
                                       79*****************.9*********************999999999***********************555 PP

                             MFS_1  79 llfasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravf 154
                                       + + s ++ +l+ +r++q++ga+++ +++    +++ p ++ g++++++s+g s+G+++gp +gg++++ + W+++f
  gi|474933903|ref|YP_007687485.1| 101 CGL-SDSFaMLVTFRAVQAIGAAMMGATAPQCCTEYLPLNKLGFGLSIVSIGGSAGFAVGPFIGGAIVEFFDWHWCF 176
                                       555.88888******************************************************************** PP

                             MFS_1 155 yilaivsllafvlfllllpeepperkrkspkeee........................................... 188
                                       +i+ +++l+a+ l  +l   +p++++     + +                                           
  gi|474933903|ref|YP_007687485.1| 177 LINIPIGLVAAPL--VLRALPPRKESGRIRLDYRgavtlcgaiasgtlaietvsypdlrlltavcavlffvmlalfi 251
                                       **********886..666666666666666666689***************************************** PP

                             MFS_1 189 ..kgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsglllaglllallalvgailall 263
                                         +++  +pl++ ++++ k+ +  +++++l ++ ++++g+l+llp++  + l+++  l++g+++++++++++++++ 
  gi|474933903|ref|YP_007687485.1| 252 aaERRTDRPLLN-IRMFAKPDFT-AIFLCLMMMNAAYMGMLYLLPFFGEKCLDMT-SLTVGAFMMISGMAIVVFGMP 325
                                       ************.********66.477777777778888****************.7******************** PP

                             MFS_1 264 agrlsdrlgrrrrlllallllllaalglallavtssavllll..vlvliGfglgfvfpsllalasdlappeeagtas 338
                                       +g++sdr gr  rl+ a+++++++ + ++l+ +  + +++++  +++++Gf++ fv +++++ ++++a+ e + +as
  gi|474933903|ref|YP_007687485.1| 326 IGKWSDRKGR--RLFSACAGISMLIADVILIVLNRDISWAVFavAMFFMGFCWTFVGGPMASRLVEHAG-EDQDMAS 399
                                       *******666..777777777777777777777755555555559999********************8.9****** PP

                             MFS_1 339 glfntagslggalg 352
                                       +l+n  +++g+++g
  gi|474933903|ref|YP_007687485.1| 400 SLTNEGYYIGASVG 413
                                       **********9998 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.58
                             MFS_1 252 llalvgailallagrl 267
                                        +a+v+a++a+l++ l
  gi|474933903|ref|YP_007687485.1| 446 PSAAVCAGMAILVTVL 461
                                       3333333333333333 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8  13.8   1.5e-11   6.8e-08      45     182 ..      53     184 ..      20     197 .. 0.85
   2 !    3.4  16.3    0.0061        27      48     121 ..     304     381 ..     278     467 .. 0.71

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 1.5e-11
                                       ..HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHH CS
                          Sugar_tr  45 svlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasv 121
                                       + ++++iv +++v+ + + + +  ++  +G +k++++++++f++g++l+++++   s+ +l++ R +  ig+ +  +
  gi|474933903|ref|YP_007687485.1|  53 TATVSWIVIVYMVVLAGTLVAFARISADIGVRKVMAAGIFIFIAGSALCGLSD---SFAMLVTFRAVQAIGAAMMGA 126
                                       4457899999999999999999*******************************...********************* PP

                                       HHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHH CS
                          Sugar_tr 122 lvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpal 182
                                       ++P  + E+ p ++ g+  s+   + ++G+ v+ ++g ++ ++ +   w++ + +++ + l
  gi|474933903|ref|YP_007687485.1| 127 TAPQCCTEYLPLNKLGFGLSIVSIGGSAGFAVGPFIGGAIVEFFD---WHWCFLINIPIGL 184
                                       *********************************************...6666666666554 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.0061
                                       HHHHHHTHHHHHHHHHHHH....HHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHH CS
                          Sugar_tr  48 sglivsiflvGaiiGslfa....gllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlas 120
                                       ++l+v++f+ ++ +  +++    g+++dr GR+   ++a++ ++i+ v+ ++ + + s+ v++v+ +++G+++ ++ 
  gi|474933903|ref|YP_007687485.1| 304 TSLTVGAFMMISGMAIVVFgmpiGKWSDRKGRRLFSACAGISMLIADVILIVLNRDISWAVFAVAMFFMGFCWTFVG 380
                                       4555666555555555444112268*****************************9*****************98775 PP

                                       H CS
                          Sugar_tr 121 v 121
                                       +
  gi|474933903|ref|YP_007687485.1| 381 G 381
                                       5 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9  10.5   7.3e-09   3.2e-05     224     384 ..      14     177 ..       7     178 .. 0.85
   2 !    4.8   0.3    0.0024        11      54     121 ..     219     286 ..     206     293 .. 0.78
   3 !    7.6   0.2   0.00033       1.5     180     264 ..     308     400 ..     291     425 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 7.3e-09
                        MFS_1_like 224 npeviifllvalilgmswgiienF...lflYL.kelgasntllGslvalgvvaeiplfffaeklleklGhvklliia 296
                                       ++++ ++++v+l+  ++ g+ ++    +   +  +lg  + +++ +v++ +v    +++   ++   +G++k++ ++
  gi|474933903|ref|YP_007687485.1|  14 KRHLTMLFAVMLFATFMDGLDGTIvnvAAPDIgMDLGVDTATVSWIVIVYMVVLAGTLVAFARISADIGVRKVMAAG 90 
                                       5566666666666655555444442224444445889999999999999999999********************** PP

                        MFS_1_like 297 llayilrfllyaiienawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliGGll 373
                                       ++++i+   l ++ +++ +++ + + ++i  +++ a+a + + +  p +  ++g +++s+   ++G a+G +iGG++
  gi|474933903|ref|YP_007687485.1|  91 IFIFIAGSALCGLSDSFAMLVTFRAVQAIGAAMMGATAPQCCTEYLPLNKLGFGLSIVSIG-GSAGFAVGPFIGGAI 166
                                       *********************************************************9865.899************ PP

                        MFS_1_like 374 wdlksaiflFr 384
                                        + ++ ++ F 
  gi|474933903|ref|YP_007687485.1| 167 VEFFDWHWCFL 177
                                       99999888885 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0024
                        MFS_1_like  54 wgvlaDrfgkrkkvvilslllsavlflsllfippskerqeesklevsvaqdvdaektfwilfllvvla 121
                                        g+la  +  +  + +l++++++++f++l +    ++r +++ l++++  + d++ +f  l+++ + +
  gi|474933903|ref|YP_007687485.1| 219 SGTLAIETVSYPDLRLLTAVCAVLFFVMLALFIAAERRTDRPLLNIRMFAKPDFTAIFLCLMMMNAAY 286
                                       5666666666667778888999999988876666999************9999999999998887665 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.00033
                        MFS_1_like 180 sallyvlaallvisllvvlilnetekesklkvtksl...........qvllnilknpeviifllvalilgmswgiie 245
                                       + +++++ ++ ++++ +    + +++ +  + + +              l+ + ++ + ++f ++++++g++w +++
  gi|474933903|ref|YP_007687485.1| 308 VGAFMMISGMAIVVFGM----PIGKWSDRKGRRLFSacagismliadVILIVLNRDISWAVFAVAMFFMGFCWTFVG 380
                                       45677777777777777....5555555555554445778999997433444446678899*************998 PP

                        MFS_1_like 246 nFlflYL.kelgasntllGs 264
                                         +   L ++ g  + +++s
  gi|474933903|ref|YP_007687485.1| 381 GPMASRLvEHAGEDQDMASS 400
                                       77666666666666655555 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   8.5   3.2e-06     0.014      58     176 ..      61     180 ..      19     204 .. 0.78
   2 ?    0.5   3.8     0.033   1.5e+02      54     157 ..     315     415 ..     276     427 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.2e-06
                             MFS_3  58 ifllsilaGalaDnfdrRkvllavqlllalvs.vlltvlaalgllsp.wlllaltlligiGaalndPaWqAsvgelv 132
                                       i+ + +laG l   f r    + v  ++a++  ++++ +a+ gl +   +l+++  + +iGaa++  +      e +
  gi|474933903|ref|YP_007687485.1|  61 IVYMVVLAGTLV-AFARISADIGVRKVMAAGIfIFIAGSALCGLSDSfAMLVTFRAVQAIGAAMMGATAPQCCTEYL 136
                                       445556666664.355555555555555554413445566677766515788999********************** PP

                             MFS_3 133 krrdvpaAvaLnsvginiaRsvGPAlgGvlvaavGaalafavna 176
                                       + +++     + s+g     +vGP +gG +v ++   + f +n 
  gi|474933903|ref|YP_007687485.1| 137 PLNKLGFGLSIVSIGGSAGFAVGPFIGGAIVEFFDWHWCFLINI 180
                                       ****************************************9985 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.033
                             MFS_3  54 atLPifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalndPaWqAsvge 130
                                       + + i+++ ++ G  +D   rR +   + + ++++ v+l+vl   ++   +  +a+ ++  + + +  P  +  v+ 
  gi|474933903|ref|YP_007687485.1| 315 SGMAIVVFGMPIGKWSDRKGRRLFSACAGISMLIADVILIVLNR-DISWAVFAVAMFFMGFCWTFVGGPMASRLVEH 390
                                       34556666777777777777776666666666666666666654.33333344455555555666666666666655 PP

                             MFS_3 131 lvkrrdvpaAvaLnsvginiaRsvGPA 157
                                         + +d+  A  L+  g+ i  svG A
  gi|474933903|ref|YP_007687485.1| 391 AGEDQDM--ASSLTNEGYYIGASVGTA 415
                                       5544444..445556666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (470 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       824  (0.0459591); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.70u 0.27s 00:00:00.97 Elapsed: 00:00:00.54
# Mc/sec: 2617.02
//
Query:       gi|474933904|ref|YP_007687486.1|  [L=494]
Description: Arabinose efflux permease [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.2e-42  143.6  60.3    9.3e-28   97.2  23.9    3.0  3  MFS_1       Major Facilitator Superfamily
    0.00076   18.4  12.4    0.00076   18.4  12.4    2.2  2  MFS_1_like  MFS_1 like family
  ------ inclusion threshold ------
       0.11   12.4   0.7         13    5.7   0.0    2.6  2  ODV-E18     Occlusion-derived virus envelope protein ODV-E18


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.2  23.9   1.6e-31   9.3e-28       1     173 [.      17     188 ..      17     196 .. 0.88
   2 !   53.7  24.6   2.6e-18   1.5e-14     131     352 ..     202     406 ..     200     407 .. 0.77
   3 ?    0.5   0.1     0.037   2.2e+02     226     277 ..     414     464 ..     404     474 .. 0.49

  Alignments for each domain:
  == domain 1  score: 97.2 bits;  conditional E-value: 1.6e-31
                             MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgll 77 
                                       ++++ f+++l++si+++alp  +++ + ++ ++++++ ++y  + a + ++++ ++   G +rvl +g+++f +g+l
  gi|474933904|ref|YP_007687486.1|  17 VFFTMFMNGLDSSITNVALP-EMGTVFDVDIATVSWVSVIYLMVLACSLMVFAKIAADTGVKRVLPFGIAVFTIGSL 92 
                                       69******************.9******************9998888888888888888****************88 PP

                             MFS_1  78 lllfasslwlllvlrvlqGlgagalfpagaaliadwfpk.eergraigllsagfslGailgpllggllasslgWrav 153
                                       ++++++++w+l+++r++q++g+ a+++a a ++  ++++ ++ g+ +++l++g+++G+++gp +ggl++++  W+++
  gi|474933904|ref|YP_007687486.1|  93 MCAISPTYWFLIFSRAIQAIGG-AALAATAPMVCTIYMPpSRLGFSLSILTVGTGFGYAIGPFVGGLIMEYSTWHLI 168
                                       888779999************6.55555556666666555************************************* PP

                             MFS_1 154 fyilaivsllafvlfllllp 173
                                       f+i+ +v++l++ l +  l+
  gi|474933904|ref|YP_007687486.1| 169 FLINIPVGMLCVPLLMKALR 188
                                       **********9765444444 PP

  == domain 2  score: 53.7 bits;  conditional E-value: 2.6e-18
                             MFS_1 131 slGailgpllggllasslgWravfyilaivsllafv.lfllllpeepperkrkspkeeekgtgpaplvpawkallkd 206
                                       ++G+++++++ g+l+  l  +a ++++a++s +++  l lll+   +                + pl++  k+ll+ 
  gi|474933904|ref|YP_007687486.1| 202 GAGFLCTAIFMGILSLELLPHAGMWVFAVMSGISCSaL-LLLFILAEWGA-------------ENPLLN-MKMLLHF 263
                                       45666666666666644445555555555555553312.13332222222.............224455.6777777 PP

                             MFS_1 207 pvlwillialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllalll 283
                                        ++  l+++l+++ ++++g+++llp++    l++s +l++g +l ++a+v+ il++ ++rlsdr gr+ +   a+ +
  gi|474933904|ref|YP_007687486.1| 264 DFIV-LFLCLAGMNLAYTGATYLLPFFGEVYLDMS-ALEMGEYLLAGAMVTTILGIPIARLSDRRGRKVFCACAGMI 338
                                       7664.999999999*********************.8***************************9998888888888 PP

                             MFS_1 284 lllaalglallavtssavllllvlvliGfglgfvfpsllalasdlappeeagtasglfntagslggalg 352
                                       + l++l++++la   s + ll++l+ iG+g++fv +++ + ++++a  ee+ +as+l+n+a+++gg+ g
  gi|474933904|ref|YP_007687486.1| 339 MGLVFLLYYILADGMSRTTLLILLLGIGLGWAFVGGPMGSRLVEHAR-EERNMASSLTNMAYNIGGVSG 406
                                       88888888888888777777777778********************5.******************977 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.037
                             MFS_1 226 lltllplylqevlgls..glllaglllallalvgailallagrlsdrlgrrrrl 277
                                       ++t++ ++ ++ ++ +  + ++ag  +  ++l+ a  al +g+l+  ++ r+r 
  gi|474933904|ref|YP_007687486.1| 414 FTTFSDSIGMDIFDVPdeN-FIAG--FEPAMLFLALCALAVGALALIVKDRKRK 464
                                       4444444444444444764.5555..3333333333344555555555555554 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4  12.4   1.3e-07   0.00076     275     383 ..      62     169 ..       5     171 .. 0.83
   2 ?   -3.8  15.1       0.7   4.2e+03     165     377 ..     208     417 ..     201     423 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.3e-07
                        MFS_1_like 275 plfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllwaaaveyvskiapksleatgq 351
                                         +++  k+   +G+ ++l +++ ++++  l+ ai    w++++  ++++i  ++l a+a  ++ + +p+s  ++  
  gi|474933904|ref|YP_007687486.1|  62 CSLMVFAKIAADTGVKRVLPFGIAVFTIGSLMCAISPTYWFLIFSRAIQAIGGAALAATAPMVCTIYMPPSRLGFSL 138
                                       2467778999******************************************************************* PP

                        MFS_1_like 352 gllsglyfglGralGsliGGllwdlksaiflF 383
                                       ++l+    g+G a+G ++GGl+ ++++ + +F
  gi|474933904|ref|YP_007687486.1| 139 SILTV-GTGFGYAIGPFVGGLIMEYSTWHLIF 169
                                       **975.69**************9988777777 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 0.7
                        MFS_1_like 165 tGilidhysvnllpysallyvlaallvisllv.vlilnetekesklkvtkslqvllnilknpeviifll.valilgm 239
                                       t i++  +s +llp +a + v+a++  is+   +l +   e++ +  + +    ++ +l +   i+++l  a +  +
  gi|474933904|ref|YP_007687486.1| 208 TAIFMGILSLELLP-HAGMWVFAVMSGISCSAlLLLFILAEWGAENPLLN----MK-MLLHFDFIVLFLcLAGMNLA 278
                                       56667777888888.56777777777666544034556667776666663....33.34444443333303333333 PP

                        MFS_1_like 240 swgiie...nFlflYLkelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaii.en 312
                                         g+ +    F ++YL   + s   +G ++  g++ + +l +   +l ++ G  +    a +++ l flly i+ + 
  gi|474933904|ref|YP_007687486.1| 279 YTGATYllpFFGEVYL---DMSALEMGEYLLAGAMVTTILGIPIARLSDRRGRKVFCACAGMIMGLVFLLYYILaDG 352
                                       3443331112455666...8999999999999999999999999999999999999999999999999999999777 PP

                        MFS_1_like 313 awlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliGGllwdlk 377
                                       ++ + ++ +L gi +g  ++ +   ++ +   + e  + + l+ + + +G+ +G+ ++ l++ ++
  gi|474933904|ref|YP_007687486.1| 353 MSRTTLLILLLGIGLGWAFVGGPMGSRLVEHAREERNMASSLTNMAYNIGGVSGAALASLIFTTF 417
                                       77788888999999999999988888888888888888888888889999999998888877665 PP

>> ODV-E18  Occlusion-derived virus envelope protein ODV-E18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.5    0.0083        50      36      66 ..      11      41 ..       7      50 .. 0.83
   2 ?    5.7   0.0    0.0022        13      12      42 ..     427     457 ..     419     462 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0083
                           ODV-E18 36 iiillvllvqssstGsdssssnannartGfv 66
                                      ii++ v+++ +   G dss +n    ++G v
  gi|474933904|ref|YP_007687486.1| 11 IILVGVVFFTMFMNGLDSSITNVALPEMGTV 41
                                      6666699***************999999876 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0022
                           ODV-E18  12 dagstrrlarlePsllltilvvlviiillvl 42 
                                       d +  +++a++eP++l+  l  l + +l ++
  gi|474933904|ref|YP_007687486.1| 427 DVPDENFIAGFEPAMLFLALCALAVGALALI 457
                                       88999**********9999998888777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (494 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       845  (0.0471303); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3283.90
//
Query:       gi|474933905|ref|YP_007687487.1|  [L=418]
Description: putative membrane protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-58  198.9  39.9    1.3e-58  198.6  39.9    1.0  1  TctA      Tripartite tricarboxylate transporter TctA family


Domain annotation for each model (and alignments):
>> TctA  Tripartite tricarboxylate transporter TctA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.6  39.9   7.5e-63   1.3e-58       1     408 [.      10     406 ..      10     407 .. 0.94

  Alignments for each domain:
  == domain 1  score: 198.6 bits;  conditional E-value: 7.5e-63
                              TctA   1 LllvllGvllGtliGllPGlhatlavalllpltf...........gl.dpeaalilllgiyvgaifggsipaillgv 65 
                                       L+++ lG+l+Gt++Gl+PG+h+++a++++++l +           gl +++++ ++++++ ++++f++++p++++g+
  gi|474933905|ref|YP_007687487.1|  10 LAAAGLGTLVGTFTGLVPGIHVNTAASVMVALHPaavsflgdefgGLdSAVLISCCIMAAATVHSFVDFVPSVFIGA 86 
                                       67889****************************************99556788899********************* PP

                              TctA  66 PGtpssvatvldgyplakqGrageAlrlaaigSfiGglvsvllllllapllakvalkfgpaeyfalillglvliail 142
                                       P +p+ +++vl+g+ l+ qG++  A+r+aaigS++G+ ++v l+++l +++ +       + ++ ++l++l ++++ 
  gi|474933905|ref|YP_007687487.1|  87 P-DPDEALSVLPGHLLVSQGKGMVAVRAAAIGSAVGAACAVALAVPLQWIMLHGGEDLIDPMTLGVLLVALGTVVLT 162
                                       *.***************************************************************999999999988 PP

                              TctA 143 seksllkglialllglllgtvgldpnsgtpRftfgsielldgislvpvliGlFgiselltsleskskiplslkdlk. 218
                                       s +  +++ ++lll++++g+  +d+   +         + +g  l+p+l GlFgi+ ll+++++    p++++d+k 
  gi|474933905|ref|YP_007687487.1| 163 SPG-KIRTAAMLLLSGAVGCAVMDMGIPSH------GLFGEGTLLFPMLAGLFGIPPLLEKSTQ-GLLPPQTDDVKd 231
                                       865.67999***************997444......4778**********************75.444589999995 PP

                              TctA 219 .kslptilrgsliGtivGilPgvGasiaaflayavakrlskkpekfgkgaiegvaapeaannaaaggaliplltlgi 294
                                          + + +rg ++G++ G++Pg++a+++a+++ a++++         k+  +++  + +  +++a++++++l + g 
  gi|474933905|ref|YP_007687487.1| 232 pVGILPGIRGVATGLVAGWFPGITATTGATITAAFSEE---------KDPASFISLTGSIGTVTAIFSVVTLSVSGK 299
                                       5357889************************9999774.........7999************************** PP

                              TctA 295 pgsgvaavllgallihglqpgpeLftenpelvyallasllianvlllvlgllliklfakll.kipkelLlpiilvll 370
                                       ++sg+a+ + ++l     + g + f    e ++++l+s+++a+ + ++++++++k+++ ++ +ip e L  ++lvl+
  gi|474933905|ref|YP_007687487.1| 300 GRSGTAISVGEML-----GDGLQGF--CSEPFVLILLSIALASAAGYAVTVRAGKMMIGIVdRIPAETLGNAVLVLV 369
                                       ******9999975.....8999999..7899****************************999*************** PP

                              TctA 371 vigayalnnslfdvlvmlifgvlGlllrrlgvplaplv 408
                                       +++++++++  ++++v+ ++  +G+++  lg+ +++lv
  gi|474933905|ref|YP_007687487.1| 370 AALVFVFTGP-WGLAVLSVCSGIGMIPPNLGIGRVCLV 406
                                       **********.***********************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2741.11
//
Query:       gi|474933906|ref|YP_007687488.1|  [L=190]
Description: Adenine/guanine phosphoribosyltransferase-related PRPP-binding protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.7e-17   61.7   1.2    7.5e-17   61.3   1.2    1.1  1  Pribosyltran  Phosphoribosyl transferase domain
      9e-05   22.0   0.3    0.00012   21.6   0.3    1.2  1  PRTase_2      Phosphoribosyl transferase
     0.0005   19.6   0.1    0.00065   19.2   0.1    1.1  1  UPRTase       Uracil phosphoribosyltransferase
  ------ inclusion threshold ------
       0.22   11.7   2.5       0.35   11.0   2.4    1.5  1  SH3_12        Xrn1 SH3-like domain


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.3   1.2   1.7e-20   7.5e-17       9     132 ..      36     160 ..      32     177 .. 0.89

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 1.7e-20
                                       --EEEEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE...........EE- CS
                      Pribosyltran   9 paildavarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes...rll 82 
                                       pa+l++v +++++ ++    + dv+++++  G+p+a  ++   ++p+ ++rk+ky  +g  e+ ++   +    +  
  gi|474933906|ref|YP_007687488.1|  36 PAVLKEVISWIEDVSDL---ECDVIAAPEAMGIPLAIPVSLDKGIPYSVIRKKKYGLPGEVEIEQNTGYSKsvmHID 109
                                       77777888888888887...9******************************************8776555599**** PP

                                       ---TTSEEEEE-SEESSSHHHHHHHHHHH.CC-BSEEEEEEEEE-HHHHHH CS
                      Pribosyltran  83 edpagkkVliVDDildtGgTllaalelLk.ekgpeevriavlvdkpateee 132
                                       ++  g +V+i+DD+++tGgTl+a +++L+ e g+e+v ++ +vdk+ ++  
  gi|474933906|ref|YP_007687488.1| 110 GINMGDRVVIIDDVVSTGGTLIALIRALRdEIGAEIVDVVIPVDKKGGADI 160
                                       **************************998356999********99988765 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.3   2.8e-08   0.00012     120     184 ..     113     172 ..     102     177 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.8e-08
                          PRTase_2 120 aakelvLvDDEistGktalnliralqeklprkryvvvslvdwrseedeaafaaleeelgirievv 184
                                         +++v++DD +stG t+++liral++++ ++ + vv  vd +  +     + +e+e+gir++++
  gi|474933906|ref|YP_007687488.1| 113 MGDRVVIIDDVVSTGGTLIALIRALRDEIGAEIVDVVIPVDKKGGA-----DIVERETGIRVKTL 172
                                       5678*************************99999999888887777.....67778888887765 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   1.4e-07   0.00065     121     180 ..     114     171 ..      86     184 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.4e-07
                           UPRTase 121 ertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkrlaeefpkvkvvt 180
                                        ++v+++D v++TGg+++a i+ L++ ++g e + v+  +  + g+  + e+  +++v t
  gi|474933906|ref|YP_007687488.1| 114 GDRVVIIDDVVSTGGTLIALIRALRD-EIGAEIVDVVIPVDKKGGA-DIVERETGIRVKT 171
                                       4679**********************.7887766666655555554.4555555555544 PP

>> SH3_12  Xrn1 SH3-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.4   7.7e-05      0.35       3      54 ..     111     165 ..     109     180 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.7e-05
                            SH3_12   3 frLgdrVvyvrdngksVPlGlrGtVVg........rsdtlleVlfDeeflsgtdlggrcs 54 
                                       ++ gdrVv+++d  + V   + Gt ++           ++++V+   +  +g d+ +r +
  gi|474933906|ref|YP_007687488.1| 111 INMGDRVVIIDD--V-V--STGGTLIAliralrdeIGAEIVDVVIPVDKKGGADIVERET 165
                                       689*********..8.5..6669***9999996652248999998888888877776544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1307.22
//
Query:       gi|474933907|ref|YP_007687489.1|  [L=380]
Description: tyrosyl-tRNA synthetase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      4e-46  157.7   0.0    5.7e-34  117.8   0.0    2.1  2  tRNA-synt_1b  tRNA synthetases class I (W and Y)
  ------ inclusion threshold ------
      0.031   13.7   0.0      0.052   13.0   0.0    1.2  1  CENP_C_N      Kinetochore assembly subunit CENP-C N-terminal


Domain annotation for each model (and alignments):
>> tRNA-synt_1b  tRNA synthetases class I (W and Y)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.8   0.0   6.4e-38   5.7e-34       4     200 ..      31     220 ..      28     221 .. 0.97
   2 !   38.0   0.0   1.3e-13   1.2e-09     198     292 ..     250     352 ..     243     353 .. 0.89

  Alignments for each domain:
  == domain 1  score: 117.8 bits;  conditional E-value: 6.4e-38
                                       S--EEEEEEETSSS-BGGGHHHHHHHHHHHHTTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHHHHHHHHHTC CS
                      tRNA-synt_1b   4 rplrvysGidPTgklHlGylvplkklvelqkaghevffliaDlhAiigdpskaeerklrkreevlenaikaqlakgl 80 
                                       ++  +y G++P+g +HlG+ ++++k+++l++ag +v+++ aD+hA+i+d+   e + +r+ ++++e      +a g+
  gi|474933907|ref|YP_007687489.1|  31 EQPLAYIGFEPSGLVHLGWALVTTKIRDLCEAGFKVIIFWADWHAYINDKLGGEIENIRACARYMEDC---FVALGV 104
                                       56678**********************************************99***************...****** PP

                                       HTTTEEEEETHHHHTTHHHHHHHHHHHTTCBHHHHHHHHHCCHHCSSSC--BHHHHHHHHHHHHHHHHTCHSEEEEE CS
                      tRNA-synt_1b  81 dpekaevvlqsewlehlelaellrdlgklgslnrmlqfksvkkrleegegislgeftYplLqaaDilllkadlvpgG 157
                                       + +k+e+ + se+l+  +++e l ++gk++sl r+ ++ +++ r e + ++  +  +Ypl+qa Di+++  dl   G
  gi|474933907|ref|YP_007687489.1| 105 PRDKVEFRYASEILDDIDYWEKLIKIGKVTSLLRIKRAMTIMGRKEDEADLDSSKVIYPLMQATDIFHMGIDLAYAG 181
                                       ********************************************999779*************************** PP

                                       GGGHHHHHHHHHHHHHHHHHSTTSS-EEEEET-BBSTTSSSBT CS
                      tRNA-synt_1b 158 sDQkqnielgrdlarrfnkkevfkkpegltvplltgldGekKm 200
                                        DQ+    l+rd a++++ k    kp +l +pl++gl+G ++m
  gi|474933907|ref|YP_007687489.1| 182 IDQRRANMLARDAADKLGWK----KPLALHTPLIPGLKGNSRM 220
                                       *****************999....***************9988 PP

  == domain 2  score: 38.0 bits;  conditional E-value: 1.3e-13
                                       SBTTCETTCGC-BTTCCHHHHHHHHHHCHCSTTCSHHHHHHHHHTHHH........CHHHHHHHHCCSEEESSHHHH CS
                      tRNA-synt_1b 198 kKmSKSagnsaIfLddekesvkkkiqkavtdsdeevekllklktelsn........elierleavsgkkpkreaeel 266
                                        KmSKS+++s I + d ++++++ki+ka++ +++e e +++++   +           ier e+++g+    ++e l
  gi|474933907|ref|YP_007687489.1| 250 MKMSKSDPSSSIRIHDTPDEIRQKIKKAFCPPEKEQESVNPILMMSKYiifprigrMDIERPEKYGGNVSFDSYEAL 326
                                       5*********************************777666666544445566999899*********99999***** PP

                                       HHHHHCCCCHHHHHHHHHHHHHHHHH CS
                      tRNA-synt_1b 267 laeevtklvhggdlkkalaealnell 292
                                         ++  +++++ dlk ++a+ l+++l
  gi|474933907|ref|YP_007687489.1| 327 TDAYFGGKLSPVDLKTGAADGLIRCL 352
                                       ********************999988 PP

>> CENP_C_N  Kinetochore assembly subunit CENP-C N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   5.7e-06     0.052     195     257 ..     214     278 ..     210     280 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.7e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXX...XXXXXXXXXXXXXXXXXXXXX CS
                          CENP_C_N 195 lKtkKrLnfeDkdilkkveienkvsevedkvserqqerkqse...tsqkriqdseyeiqpqakksF 257
                                       lK   r+n +  + ++kve+    + +e k se+  e k s+   +s+ ri+d+ +ei+++ kk F
  gi|474933907|ref|YP_007687489.1| 214 LKGNSRMNVDGVKAVEKVEVCRTGEGIE-KQSEGMIEMKMSKsdpSSSIRIHDTPDEIRQKIKKAF 278
                                       678889**************99999998.89999999998873335889****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2271.21
//
Query:       gi|474933908|ref|YP_007687490.1|  [L=330]
Description: Exopolyphosphatase-related protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-11   44.2   0.2    3.5e-11   43.2   0.2    1.5  1  DHH              DHH family
    2.9e-06   27.7   0.7    5.2e-06   26.9   0.7    1.4  1  DHHA1            DHHA1 domain
  ------ inclusion threshold ------
      0.069   13.7   0.1       0.48   11.0   0.0    2.0  2  Ribosomal_S9     Ribosomal protein S9/S16
      0.086   13.3   0.1       0.18   12.3   0.1    1.5  1  Fungal_lectin_2  Alpha-galactosyl-binding fungal lectin


Domain annotation for each model (and alignments):
>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.2   7.7e-15   3.5e-11       4     100 ..      17     150 ..      15     151 .. 0.88

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 7.7e-15
                                       EE-ECSSSHHHHHHHHHHHH........................................CECS--TCGGCGCCHHC CS
                                       xxxxxxxxxxxxxxxxxxxx........................................xxxxxxxxxxxxxxxxx RF
                               DHH   4 ivghknpDtDsigSaialan........................................llvDhneksqavegeak 40 
                                       i+ h+n D+D+igSa+al+                                         ++vD ++++q +++   
  gi|474933908|ref|YP_007687490.1|  17 ILVHGNADMDAIGSAYALRCsfpeadifapagvdriarmvadkmdipildaadlssydlvIVVDSSSPEQLQND-SV 92 
                                       445*****************99999999999999999999999999999999999999999***********88.88 PP

                                       CCSEEEEEEE-S---SS---SS--EEEE-SSS-HHHHHHHHHHHTT----HHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH  41 eeaedviiiDHHrlgeefetlapilflnepvgstaeivaelleekkeeiskeiaellllg 100
                                           d ++iDHH +  + e +   +  + +  s++eiv +++++ ++e+s++   +++ g
  gi|474933908|ref|YP_007687490.1|  93 VLPRDCLVIDHHSPTGKWEGMD--FWCDDSRTSCCEIVLDIIRDAGVELSRQAGLAIIGG 150
                                       8999**********98888884..77789999************9999888776666555 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.7   1.2e-09   5.2e-06      68     121 ..     234     292 ..     195     304 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 1.2e-09
                                       BT.TCEEEEEEEECTEEEEEEEESSH....SS-HHHHHHHHHHHTTCCEEEETCEEEEE CS
                             DHHA1  68 kk.pvivfvakeegdkvkvsarskkd....gvdagelakeaaaklgggGGGHdlAaGag 121
                                        + + +vfv ++++d+ +vs+r++++    gv++ +++ e++++    GGGH  AaG++
  gi|474933908|ref|YP_007687490.1| 234 ASgADVVFVGSQREDEFRVSGRATQEmvrrGVKLDAMMGELSTETDTDGGGHGGAAGMT 292
                                       45589*******************99*******************************86 PP

>> Ribosomal_S9  Ribosomal protein S9/S16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.25   1.1e+03      61     109 ..     149     201 ..     142     210 .. 0.68
   2 ?   11.0   0.0   0.00011      0.48       6      89 ..     227     312 ..     224     323 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.25
                                       S-HHHHHHHHHHHHHHHHHHHHH..HH.HHHHCTCCCTS-B-.-------TTS CS
                      Ribosomal_S9  61 GGlsgqaeAirlgiaraLvalek..ee.kkeLkkaglltrDp.RvvErkKtgk 109
                                       GG+   ++  + + +r+L a+ +  ++   ++++a lltr p  + Er    k
  gi|474933908|ref|YP_007687490.1| 149 GGIITDSGHFQFADSRCLRAFADimDScDIHMDEAMLLTRAPvNMSERMAAMK 201
                                       88888888899999999999987664446677788888887623445544444 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00011
                                       EEEEEEEEESSSEEEETTEECCHHS.TTSCHHHHHCHHHHHTTTSSSEEEEEEEESS-HHHHHHHHHHHHHHHHHHH CS
                      Ribosomal_S9   6 svArvwikegkgkilvngksleeYf.keeaarekvleplkltgllgkfdvfvkvkgGGlsgqaeAirlgiaraLval 81 
                                       +++r+ + +g   + v ++  +e+  + +a +e v + +kl  ++g++ ++  + gGG+ g a+   +g a+a++++
  gi|474933908|ref|YP_007687490.1| 227 ASCRALLASGADVVFVGSQREDEFRvSGRATQEMVRRGVKLDAMMGELSTETDTDGGGHGGAAGMTGVGDAEAMCNM 303
                                       566777777778888888888887667788999999***************************************99 PP

                                       HHHH.HHHH CS
                      Ribosomal_S9  82 ekee.kkeL 89 
                                         ++  +++
  gi|474933908|ref|YP_007687490.1| 304 CMQKtMQQF 312
                                       764434444 PP

>> Fungal_lectin_2  Alpha-galactosyl-binding fungal lectin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1     4e-05      0.18      57      83 ..     155     181 ..     150     188 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4e-05
                   Fungal_lectin_2  57 kgasefdkeecleslkriingCDgnds 83 
                                       +g  +f  ++cl +++ i+++CD + +
  gi|474933908|ref|YP_007687490.1| 155 SGHFQFADSRCLRAFADIMDSCDIHMD 181
                                       5678999****************7654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2651.85
//
Query:       gi|474933909|ref|YP_007687491.1|  [L=124]
Description: prefoldin, beta subunit, archaeal [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-18   65.0  12.2    5.6e-18   64.8  12.2    1.0  1  Prefoldin_2      Prefoldin subunit
    8.8e-05   22.1   2.6    0.00011   21.7   2.6    1.2  1  DUF4527          Protein of unknown function (DUF4527)
    0.00048   20.6   7.5      0.022   15.3   0.1    2.1  2  T3SSipB          Type III cell invasion protein SipB
     0.0027   18.0   8.7      0.014   15.7   8.7    1.9  1  Syntaxin_2       Syntaxin-like protein
      0.003   16.4   1.7     0.0037   16.1   1.7    1.1  1  FbpA             Fibronectin-binding protein A N-terminus (Fb
     0.0041   17.3   8.3       0.44   10.8   8.7    2.6  2  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
     0.0042   17.2   1.8     0.0058   16.7   1.0    1.5  1  UvrA_inter       UvrA interaction domain
     0.0061   16.6  12.3        0.2   11.7   9.2    2.3  2  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
     0.0063   16.1   9.9     0.0083   15.7   9.9    1.1  1  PspA_IM30        PspA/IM30 family
     0.0081   15.5  12.2      0.012   14.9   7.0    2.0  2  GAS              Growth-arrest specific micro-tubule binding
  ------ inclusion threshold ------
       0.01   15.2   5.1      0.012   14.9   5.1    1.0  1  CorA             CorA-like Mg2+ transporter protein
      0.014   15.8   6.4        1.2    9.5   0.2    2.6  2  FlaC_arch        Flagella accessory protein C (FlaC)
      0.018   15.7   3.6      0.018   15.7   3.6    1.7  2  Occludin_ELL     Occludin homology domain
      0.019   15.2   4.7      0.054   13.8   3.8    2.2  2  DUF948           Bacterial protein of unknown function (DUF94
       0.02   14.6   7.6      0.023   14.4   7.6    1.1  1  DUF745           Protein of unknown function (DUF745)
      0.022   14.5   5.5      0.022   14.5   5.5    2.1  2  DivIC            Septum formation initiator
       0.03   14.1   9.6       0.13   12.1   9.6    1.7  1  TACC_C           Transforming acidic coiled-coil-containing p
      0.036   13.5  11.4      0.068   12.6   5.6    2.0  2  DUF4618          Domain of unknown function (DUF4618)
      0.051   12.8   3.0      0.071   12.4   3.0    1.3  1  TMPIT            TMPIT-like protein
      0.055   13.5   8.5       0.11   12.5   1.5    2.0  2  DUF1664          Protein of unknown function (DUF1664)
      0.066   10.7   9.8       0.25    8.8   6.1    1.9  2  DUF3584          Protein of unknown function (DUF3584)
      0.071   13.5  12.5       0.31   11.5  12.5    1.9  1  CENP-H           Centromere protein H (CENP-H)
      0.074   13.3   3.9        2.1    8.6   0.2    2.2  2  XhlA             Haemolysin XhlA
      0.076   11.5   3.4      0.093   11.3   3.4    1.0  1  FUSC             Fusaric acid resistance protein family
      0.077   13.5   7.5       0.23   11.9   1.4    2.5  2  Cep57_MT_bd      Centrosome microtubule-binding domain of Cep
      0.084   12.7   7.6       0.16   11.8   5.1    2.1  2  Phage_GP20       Phage minor structural protein GP20
      0.093   12.8   7.6        1.3    9.1   7.6    2.0  1  Laminin_II       Laminin Domain II
      0.093   11.7  11.6       0.11   11.4   9.9    1.7  1  IFT57            Intra-flagellar transport protein 57
        0.1   10.8   9.8       0.04   12.1   6.2    1.8  1  EzrA             Septation ring formation regulator, EzrA
        0.1   13.4   5.4        0.2   12.5   5.4    1.7  1  DUF4482          Domain of unknown function (DUF4482)
       0.11   13.0   6.0        1.6    9.3   6.0    2.1  1  Syntaxin-6_N     Syntaxin 6, N-terminal
       0.12   12.4   6.4        2.5    8.2   0.2    2.1  2  COG2             COG (conserved oligomeric Golgi) complex com
       0.13   12.5  12.9        0.4   10.9  12.9    1.6  1  ATG16            Autophagy protein 16 (ATG16)
       0.15   10.0   7.0       0.27    9.2   7.0    1.4  1  Prominin         Prominin
       0.18   12.2  16.1      0.096   13.1   7.0    2.2  2  Uso1_p115_C      Uso1 / p115 like vesicle tethering protein, 
        0.2   12.1   0.4        5.3    7.5   0.1    2.3  2  MtrB             Tetrahydromethanopterin S-methyltransferase 
        0.2   11.8   2.5       0.35   11.1   1.1    1.9  2  EIAV_Rev         Rev protein of equine infectious anaemia vir
       0.21   11.9  10.1       0.19   12.0   4.9    2.2  2  BLOC1_2          Biogenesis of lysosome-related organelles co
       0.22   11.4  10.2        1.5    8.7  10.3    1.8  2  Ax_dynein_light  Axonemal dynein light chain
       0.22    9.4   4.0       0.32    8.8   4.0    1.2  1  V_ATPase_I       V-type ATPase 116kDa subunit family
        0.3   10.3   2.9       0.35   10.1   2.9    1.0  1  Peptidase_U57    YabG peptidase U57
        0.3   11.5  10.6        5.6    7.4  10.6    2.2  1  CC2-LZ           Leucine zipper of domain CC2 of NEMO, NF-kap
       0.35   10.8   5.7        2.1    8.3   1.8    2.0  2  Cauli_AT         Aphid transmission protein
       0.37   11.3   7.3        1.2    9.7   2.8    2.3  2  UPF0449          Uncharacterised protein family UPF0449
       0.38   10.9   9.1        4.2    7.5   0.3    2.3  2  bZIP_1           bZIP transcription factor
        0.4   10.5   6.9       0.66    9.8   6.9    1.3  1  PCRF             PCRF domain
       0.41    9.9   9.1        0.2   10.9   4.5    1.9  2  DUF4763          Domain of unknown function (DUF4763)
       0.46    9.7  13.3        1.8    7.8  13.1    1.7  1  HemX             HemX, putative uroporphyrinogen-III C-methyl
       0.49   10.4  10.0        2.8    8.0   0.0    2.9  3  DUF2205          Short coiled-coil protein
       0.51    9.2  12.4       0.94    8.3  12.4    1.4  1  Spc7             Spc7 kinetochore protein
       0.53   10.7   5.1        5.9    7.4   0.1    2.5  2  FAA_hydro_N_2    Fumarylacetoacetase N-terminal domain 2
       0.66    9.8  10.3        5.3    6.8   0.5    2.0  2  DUF724           Protein of unknown function (DUF724)
        0.7    9.8   9.6        2.4    8.0   3.7    2.0  2  Sec34            Sec34-like family
        0.7    9.1  15.6        0.3   10.4   9.5    2.0  2  DUF3450          Protein of unknown function (DUF3450)
        0.8   10.1  11.7        1.5    9.3  11.7    1.4  1  DUF4200          Domain of unknown function (DUF4200)
       0.83    8.2   2.8        1.2    7.7   2.7    1.4  1  DUF3138          Protein of unknown function (DUF3138)
       0.99    9.0  10.7          2    8.0  10.8    1.4  1  DUF4795          Domain of unknown function (DUF4795)
        1.2    9.6  14.1         23    5.5  14.1    2.1  1  ZapB             Cell division protein ZapB
        1.2    9.1   7.7        2.8    7.9   2.0    2.0  2  DUF4446          Protein of unknown function (DUF4446)
        1.5    8.7  11.5      2e+02    1.9  11.5    2.7  1  Prefoldin        Prefoldin subunit
        1.7    7.9  10.1        2.4    7.4  10.1    1.3  1  DUF4407          Domain of unknown function (DUF4407)
        1.7    8.5   5.4         13    5.6   0.2    2.9  3  DASH_Dam1        DASH complex subunit Dam1
        1.9    9.2   9.3         50    4.6   9.3    2.6  1  YabA             Initiation control protein YabA
        2.2    8.7  10.2          7    7.1   0.8    2.8  2  CLZ              C-terminal leucine zipper domain of cyclic n
        2.2    8.5  12.2        5.2    7.4   5.1    2.2  2  Spc24            Spc24 subunit of Ndc80
        2.5    7.7   9.4        5.2    6.7   9.4    1.5  1  GrpE             GrpE
        2.5    8.7  14.7         12    6.6  14.7    2.0  1  Com_YlbF         Control of competence regulator ComK, YlbF/Y
        2.8    6.5   7.3        7.4    5.1   7.3    1.6  1  FapA             Flagellar Assembly Protein A
        2.8    7.6   8.9          5    6.8   8.9    1.4  1  TEX13            Testis-expressed sequence 13 protein family
          3    8.6  10.1         43    4.9  10.1    2.1  1  FliD_N           Flagellar hook-associated protein 2 N-termin
        3.4    8.1   7.7       0.74   10.2   0.4    2.3  2  CCDC-167         Coiled-coil domain-containing protein 167
        3.4    6.3  13.0        1.5    7.5   7.0    2.0  2  DUF773           CDK5 regulatory subunit-associated protein 3
        3.4    8.2  13.8         29    5.2  14.1    1.9  1  APG6_N           Apg6 coiled-coil region
        4.4    7.0   9.2        9.1    6.0   4.5    2.0  2  zf-CpG_bind_C    CpG binding protein zinc finger C terminal d
        4.9    7.8  13.8        4.5    7.9   8.1    2.3  2  BST2             Bone marrow stromal antigen 2
        5.2    7.8   7.7         36    5.1   7.7    2.0  1  DUF2203          Uncharacterized conserved protein (DUF2203)
        6.2    5.8   8.7         15    4.6   8.7    1.6  1  Atg14            Vacuolar sorting 38 and autophagy-related su
        8.4    6.3  10.3        1.8    8.5   0.7    2.1  2  EMP24_GP25L      emp24/gp25L/p24 family/GOLD


Domain annotation for each model (and alignments):
>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.8  12.2   2.5e-20   5.6e-18       1     104 [.       9     111 ..       9     113 .. 0.97

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 2.5e-20
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT--EEEEETTEEEEE.-HHHHHHHHHHHHHHHHH CS
                       Prefoldin_2   1 qelinkfqqlqqqlqqlaqqikqletqlkelelvleelelldedtkvyklvGdvlvkq.dkeevkeeLeerketlek 76 
                                       q++i ++qqlqqqlq   +q+ q+e q+kel+ + eel+++  d  vy++vG +l+k+ dke++ ++ ee++et+e 
  gi|474933909|ref|YP_007687491.1|   9 QNQITQYQQLQQQLQTATAQRIQMESQMKELQRTVEELKKATGD--VYRNVGTLLIKVdDKESLAADMEESLETMEI 83 
                                       89******************************************..************8999*************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHCCTS CS
                       Prefoldin_2  77 eiktlekqleklekeleelkeelqkklq 104
                                       +++  ++q+++l+++ e l ++++ +++
  gi|474933909|ref|YP_007687491.1|  84 RVRGFKNQEDSLRQKAEALSNSINTAMG 111
                                       *********************9998877 PP

>> DUF4527  Protein of unknown function (DUF4527)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   2.6   4.8e-07   0.00011      29     105 ..       6      82 ..       2     113 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 4.8e-07
                           DUF4527  29 cqLRdqasahreLqasreeaerlreelqekleElqkkqhEanlAvtPLkAklAsLvqkCreRnhlithLLqelhrhg 105
                                        qL +q + +++Lq+ ++ a+  r +++++++Elq+  +E + A   +   +  L  k  ++++l + + + l+  +
  gi|474933909|ref|YP_007687491.1|   6 PQLQNQITQYQQLQQQLQTATAQRIQMESQMKELQRTVEELKKATGDVYRNVGTLLIKVDDKESLAADMEESLETME 82 
                                       59**************************************************************9998876665544 PP

>> T3SSipB  Type III cell invasion protein SipB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   5.6     0.019       4.4      22      93 ..       7      81 ..       2      83 .. 0.69
   2 !   15.3   0.1   9.4e-05     0.022      17      63 ..      75     121 ..      69     124 .] 0.91

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.019
                                      HHHHHHHHHHHHHHHTTT...TT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT- CS
                           T3SSipB 22 qLenrlaawkamskaqqe...aasklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeL 93
                                      qL+n+++ +++ ++  q+   + +++  +++++    ++++++  +   ++ ++  ++d+ +  + +  ++l+ +
  gi|474933909|ref|YP_007687491.1|  7 QLQNQITQYQQLQQQLQTataQRIQMESQMKELQRTVEELKKATGDVYRNVGTLLIKVDDKESLAADMEESLETM 81
                                      788888888876655444111456788888888888888888887777777777777777777777777777666 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 9.4e-05
                                       HHCHHHHHHHHHHHHHHHHHTTTTT----STHHHHHHHHHHHHHHHH CS
                           T3SSipB  17 nkSLsqLenrlaawkamskaqqeaasklSdelqtalseakgatddle 63 
                                       + SL+ +e r+  +k +  + +++a++lS+ ++ta+++a +  +d e
  gi|474933909|ref|YP_007687491.1|  75 EESLETMEIRVRGFKNQEDSLRQKAEALSNSINTAMGNAPAPRRDDE 121
                                       68***********************************9988777655 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   8.7   6.2e-05     0.014       7      84 ..       7      79 ..       6     112 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.2e-05
                        Syntaxin_2  7 kinsnvstleklvkqLgtkk.dteelreklhelieeinelikktnellkklsqldnsssdsqqklqkekLkkdfkealq 84
                                      ++++++++ ++l++qL+t++ +  ++ ++++el+  + el k+t +  +++ +l  + +d      ke L+ d++e+l+
  gi|474933909|ref|YP_007687491.1|  7 QLQNQITQYQQLQQQLQTATaQRIQMESQMKELQRTVEELKKATGDVYRNVGTLLIKVDD------KESLAADMEESLE 79
                                      689****************8568999999****************999999999988876......5555555555554 PP

>> FbpA  Fibronectin-binding protein A N-terminus (FbpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   1.7   1.6e-05    0.0037     198     311 ..       2     109 ..       1     114 [. 0.77

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.6e-05
                                       TTXXHHHHHHHHTTXSSSH...............HHHHHHHHTXXX....XXEE.....XSSSEESSXXTTXX.SSX CS
                              FbpA 198 qGlspllaeelleragldketsakelseedlerlyealqelleeleeekfepqlvlkeekpeefsvvplkslselek 274
                                       +G+sp+l +++++  +l+++ ++++++  ++e+ +++lq+ +eel++   +  + +++   ++  ++++  +++l  
  gi|474933909|ref|YP_007687491.1|   2 NGISPQLQNQITQYQQLQQQLQTATAQRIQMESQMKELQRTVEELKK--ATGDV-YRN---VGTLLIKVDDKESLAA 72 
                                       7*********************************************5..44444.333...3444444444445555 PP

                                       XXXSXHHHHHHHHTTTXXX--SHHHHHHHHHHHHHHH CS
                              FbpA 275 esfdslsealdeyYakkaerdrveqkrsdlekrvene 311
                                       +  +sl+++  +  + k ++d ++qk+++l++ ++++
  gi|474933909|ref|YP_007687491.1|  73 DMEESLETMEIRVRGFKNQEDSLRQKAEALSNSINTA 109
                                       6666666666666677999999999999999888765 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   8.7    0.0019      0.44      23     106 ..      21     104 ..       8     104 .. 0.87
   2 ?    7.9   0.3     0.015       3.4      31      66 ..      78     113 ..      71     124 .] 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0019
                                       CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  23 edkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelek 99 
                                       + +   ++ ++++++++elq ++eel++    + +++g +  k +d+e+l a+++e  e ++      k+ e+ l +
  gi|474933909|ref|YP_007687491.1|  21 QLQTATAQRIQMESQMKELQRTVEELKKATGDVYRNVGTLLIKVDDKESLAADMEESLETMEIRVRGFKNQEDSLRQ 97 
                                       5566778889********************************99***********9999999999999999999999 PP

                                       HHCTS-- CS
                      Seryl_tRNA_N 100 lllaiPN 106
                                       ++ a+ N
  gi|474933909|ref|YP_007687491.1|  98 KAEALSN 104
                                       8888887 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.015
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT CS
                      Seryl_tRNA_N  31 lleldekrrelqveleelqaerNelskeIgkakkkk 66 
                                       l  ++ + r  +++ ++l+++  +ls++I  a+ + 
  gi|474933909|ref|YP_007687491.1|  78 LETMEIRVRGFKNQEDSLRQKAEALSNSINTAMGNA 113
                                       556777889999********************9886 PP

>> UvrA_inter  UvrA interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   1.0   2.5e-05    0.0058      23      98 ..       5      80 ..       3      86 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.5e-05
                        UvrA_inter 23 aPvvrerkgefkkllenlkkkGfvrvriDgeiydldedieldknkkhsievvvDrlvvkkeersrlaesvetAlkl 98
                                      +P  +++  ++++l ++l+ +  +r++++ ++ +l+  +e  k+ + ++   v +l +k ++++ la  +e++l+ 
  gi|474933909|ref|YP_007687491.1|  5 SPQLQNQITQYQQLQQQLQTATAQRIQMESQMKELQRTVEELKKATGDVYRNVGTLLIKVDDKESLAADMEESLET 80
                                      8999****************************************************************99999986 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   9.2   0.00087       0.2      61     108 ..       8      55 ..       1      82 [. 0.75
   2 ?    5.2   0.6     0.084        19       7      36 ..      80     109 ..      73     122 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00087
                    CENP-F_leu_zip  61 ieelaeelreleldLvalrsekeeLekelqkkqervseLeslnsslen 108
                                       +++  ++ ++l+++L++ + ++ ++e ++++ q++v+eL+++  ++ +
  gi|474933909|ref|YP_007687491.1|   8 LQNQITQYQQLQQQLQTATAQRIQMESQMKELQRTVEELKKATGDVYR 55 
                                       455556789*******************************99888755 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.084
                    CENP-F_leu_zip   7 hvlekLKeserkadsLkdkvenLerelems 36 
                                        ++ + +  + ++dsL++k+e+L   ++++
  gi|474933909|ref|YP_007687491.1|  80 TMEIRVRGFKNQEDSLRQKAEALSNSINTA 109
                                       455566777888889999988888777665 PP

>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   9.9   3.6e-05    0.0083      33     122 ..      16     107 ..       5     113 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.6e-05
                         PspA_IM30  33 rdmqselakarqalaqviarqkqlerkleeqkeqakklekkAkaALtkg..eeeLArealaeikslekqaealetql 107
                                       + +q++l+ a+ ++ q+  + k+l+r +ee k+   + + ++  +L k   +e+LA+ + ++++++e  +++++ q 
  gi|474933909|ref|YP_007687491.1|  16 QQLQQQLQTATAQRIQMESQMKELQRTVEELKKATGDVYRNVGTLLIKVddKESLAADMEESLETMEIRVRGFKNQE 92 
                                       5577888888888888888888888888888888888888888888887889************************* PP

                         PspA_IM30 108 aqqrsaveqlrkqle 122
                                       + +r+ +e l ++++
  gi|474933909|ref|YP_007687491.1|  93 DSLRQKAEALSNSIN 107
                                       *********999886 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   7.0   5.4e-05     0.012      72     126 ..       7      61 ..       5      71 .. 0.90
   2 ?    6.4   1.1     0.022       5.1      58     123 ..      41     107 ..      40     112 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.4e-05
                               GAS  72 eLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerdely 126
                                       +L++q+ +y++ +q+l+ + a+  ++e+++k+l+   e l++    v +   +l 
  gi|474933909|ref|YP_007687491.1|   7 QLQNQITQYQQLQQQLQTATAQRIQMESQMKELQRTVEELKKATGDVYRNVGTLL 61 
                                       79***************************************99988888776665 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.022
                               GAS  58 rlkepLkkaeeeveeLrkqlknyekdkqslk.nlkarlkelekelkdlkwehevleqrfekvekerd 123
                                       r +e+Lkka+ +v +    l     dk+sl+  +++ l+++e  ++  k + ++l+q+ e+++++++
  gi|474933909|ref|YP_007687491.1|  41 RTVEELKKATGDVYRNVGTLLIKVDDKESLAaDMEESLETMEIRVRGFKNQEDSLRQKAEALSNSIN 107
                                       66788888888888877777778888888862689999*********************99998876 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   5.1   5.2e-05     0.012     125     228 ..       6     112 ..       1     113 [. 0.86

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.2e-05
                              CorA 125 ellekleeeldeledel..edstkkeilrelaqlrrrlvklrralapn.revlkrllakaddkllddedkeylrdll 198
                                       ++l++  ++ ++l+++l   + ++ ++ +++ +l+r++ +l++a  +  r+v + l++ +d++ l ++++e l++++
  gi|474933909|ref|YP_007687491.1|   6 PQLQNQITQYQQLQQQLqtATAQRIQMESQMKELQRTVEELKKATGDVyRNVGTLLIKVDDKESLAADMEESLETME 82 
                                       667777888999999998778888888899999********999998615555556669****************** PP

                              CorA 199 delerllemlealrerleslqdtyssllse 228
                                       ++++   ++ ++lr+++e l++++++ + +
  gi|474933909|ref|YP_007687491.1|  83 IRVRGFKNQEDSLRQKAEALSNSINTAMGN 112
                                       *************************99876 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   1.5     0.011       2.6      18      35 ..      31      48 ..       1      64 [. 0.64
   2 ?    9.5   0.2    0.0054       1.2       4      38 ..      73     107 ..      71     111 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.011
                         FlaC_arch 18 tvkkeneelsksveelke 35
                                       ++++++el+ +veelk+
  gi|474933909|ref|YP_007687491.1| 31 QMESQMKELQRTVEELKK 48
                                      455555555555555554 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0054
                         FlaC_arch   4 elEnklsklsteletvkkeneelsksveelkenVk 38 
                                       ++E+ l+ +++++   k++ ++l+++ e l  +++
  gi|474933909|ref|YP_007687491.1|  73 DMEESLETMEIRVRGFKNQEDSLRQKAEALSNSIN 107
                                       79***************************999986 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   3.6   7.9e-05     0.018      19      67 ..      10      58 ..       6      90 .. 0.80
   2 ?    0.1   0.1       5.8   1.3e+03      30      51 ..      77      98 ..      54     111 .. 0.54

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 7.9e-05
                      Occludin_ELL 19 keYkeYkelhaeleevskkfseLerelkelkegskeykkieeeilqeyk 67
                                      ++ ++Y++l+++l++++++  ++e+++kel+++ +e kk++ +++++  
  gi|474933909|ref|YP_007687491.1| 10 NQITQYQQLQQQLQTATAQRIQMESQMKELQRTVEELKKATGDVYRNVG 58
                                      67789***********************************999888755 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 5.8
                      Occludin_ELL 30 eleevskkfseLerelkelkeg 51
                                      +le+++ +++ ++++ ++l+++
  gi|474933909|ref|YP_007687491.1| 77 SLETMEIRVRGFKNQEDSLRQK 98
                                      3333333333333333333332 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   3.8   0.00024     0.054      23      82 ..      31      93 ..       1     100 [. 0.87
   2 ?    2.5   0.1      0.74   1.7e+02      32      65 ..      75     108 ..      69     113 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00024
                            DUF948 23 klkktldeaaatieelekqvdpilkevedllakvne...lledvneklekvdplteavadlge 82
                                      ++++ ++e+++t+eel+k ++ + ++v +ll kv +   l++d++e le+++  +  +++  +
  gi|474933909|ref|YP_007687491.1| 31 QMESQMKELQRTVEELKKATGDVYRNVGTLLIKVDDkesLAADMEESLETMEIRVRGFKNQED 93
                                      5678899**************************999999999999999998776666666555 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.74
                            DUF948  32 aatieelekqvdpilkevedllakvnelledvne 65 
                                       ++++e++e +v++  ++ + l +k+++l + +n 
  gi|474933909|ref|YP_007687491.1|  75 EESLETMEIRVRGFKNQEDSLRQKAEALSNSINT 108
                                       5556666666666666666666666665555554 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   7.6    0.0001     0.023      77     171 ..       7     101 ..       1     113 [. 0.92

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 0.0001
                            DUF745  77 vvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAkkRveeLkk 153
                                       ++q++ +++q+ ++++++a++ + q+++q++ l++++++ k++  ++ +       ++++k++l ++ ++ +e+++ 
  gi|474933909|ref|YP_007687491.1|   7 QLQNQITQYQQLQQQLQTATAQRIQMESQMKELQRTVEELKKATGDVYRNVGTLLIKVDDKESLAADMEESLETMEI 83 
                                       68999************************************************************************ PP

                            DUF745 154 qlkearkdlektkkaAyk 171
                                       +++  ++  ++ +++A+ 
  gi|474933909|ref|YP_007687491.1|  84 RVRGFKNQEDSLRQKAEA 101
                                       ***999999999999975 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   5.5   9.7e-05     0.022      11      52 ..       7      48 ..       4      55 .. 0.89
   2 ?    1.8   0.2      0.89     2e+02      33      52 ..      85     104 ..      68     110 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 9.7e-05
                                      XXXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XX CS
                             DivIC 11 fgkkgllaykqlkqeiaalqaelaklkaeneeLeaevkdLks 52
                                      ++ +++ +y+ql+q++++ +a+  ++  + +eL++ v++Lk+
  gi|474933909|ref|YP_007687491.1|  7 QLQNQITQYQQLQQQLQTATAQRIQMESQMKELQRTVEELKK 48
                                      68899**********************************986 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.89
                                       HHHHHHHHHHHHHHHCC-XX CS
                             DivIC  33 laklkaeneeLeaevkdLks 52 
                                       +   k+++++L ++ + L++
  gi|474933909|ref|YP_007687491.1|  85 VRGFKNQEDSLRQKAEALSN 104
                                       45555666666666666543 PP

>> TACC_C  Transforming acidic coiled-coil-containing protein (TACC), C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   9.6   0.00055      0.13      26     128 ..       7     108 ..       4     111 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00055
                            TACC_C  26 elkkkveelkkenqemkkivaefektiaqlieekqkqkelakkeiqkvleekeqlladlnsveksfsdlfkryekqk 102
                                       +l++++++ ++ +q+++   a+  ++ +q ++e q++ e+ kk +  v  +   ll ++ + e   +d+ + +e + 
  gi|474933909|ref|YP_007687491.1|   7 QLQNQITQYQQLQQQLQTATAQRIQMESQ-MKELQRTVEELKKATGDVYRNVGTLLIKVDDKESLAADMEESLETME 82 
                                       47888888888888888888877776555.46667777888888888899999999999999999999999999999 PP

                            TACC_C 103 evlegykkneeslkkcaeeylarvkk 128
                                         + g+k++e+sl+++ae + + +++
  gi|474933909|ref|YP_007687491.1|  83 IRVRGFKNQEDSLRQKAEALSNSINT 108
                                       99***************999888876 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   5.6    0.0003     0.068     177     226 ..       4      53 ..       1      59 [. 0.90
   2 ?    5.1   0.3     0.056        13      66     105 ..      68     107 ..      52     112 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0003
                           DUF4618 177 tqeaLlqktlenqvlkkeiekfrefieeleeeipeLkaeveqLqaqaeep 226
                                       ++  L++++ + q+l++++++   +  ++e +++eL+++ve+L++ + ++
  gi|474933909|ref|YP_007687491.1|   4 ISPQLQNQITQYQQLQQQLQTATAQRIQMESQMKELQRTVEELKKATGDV 53 
                                       5678999**************************************99986 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.056
                           DUF4618  66 eqakaeLqeweekeekklekLeqqleqlnakvqklqeeln 105
                                       e++ a+++e  e++e +++  ++q + l +k + l++ +n
  gi|474933909|ref|YP_007687491.1|  68 ESLAADMEESLETMEIRVRGFKNQEDSLRQKAEALSNSIN 107
                                       5567778888888888888888888888888777777666 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   3.0   0.00031     0.071       8      92 ..      12      98 ..       3     119 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00031
                             TMPIT  8 ekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlk... 83
                                       +++++l+++ ++ +++  +++++ +++++++++ kk   ++ +++ +l  +v +++e+ +++++e+l++++  ++   
  gi|474933909|ref|YP_007687491.1| 12 ITQYQQLQQQLQTATAQRIQMESQMKELQRTVEELKKATGDVYRNVGTLLIKV-DDKESLAADMEESLETMEIRVRgfk 89
                                      34566666666666666666666666666666666666666666666666665.5777788888888887776665333 PP

                             TMPIT 84 evesllpkk 92
                                      + e++l +k
  gi|474933909|ref|YP_007687491.1| 90 NQEDSLRQK 98
                                      556666555 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   2.6    0.0033      0.76      71     116 ..       4      49 ..       1      56 [. 0.85
   2 ?   12.5   1.5   0.00048      0.11      48     119 ..      37     108 ..      37     112 .. 0.95

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0033
                           DUF1664  71 vdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesk 116
                                       +  +l++q+   ++++++++++  +  ++++++++++++ve+l++ 
  gi|474933909|ref|YP_007687491.1|   4 ISPQLQNQITQYQQLQQQLQTATAQRIQMESQMKELQRTVEELKKA 49 
                                       5668999999999999999999999999999999999999999865 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00048
                           DUF1664  48 kqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskler 119
                                       k+l++  e+l+++  +  +++ ++  k+d+ + ++++++e +++++  ++ ++++ +s+++  e l +++++
  gi|474933909|ref|YP_007687491.1|  37 KELQRTVEELKKATGDVYRNVGTLLIKVDDKESLAADMEESLETMEIRVRGFKNQEDSLRQKAEALSNSINT 108
                                       6799999************************************************************99975 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   6.1    0.0011      0.25     607     643 ..      14      50 ..       5      59 .. 0.88
   2 ?    3.6   0.1      0.04       9.3     586     619 ..      77     110 ..      63     115 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0011
                           DUF3584 607 rlqaleealqsaeakqkqaeeelkqlnaeleeakrav 643
                                       + q+l+++lq+a+a++ q+e+++k+l+ ++ee+k+a 
  gi|474933909|ref|YP_007687491.1|  14 QYQQLQQQLQTATAQRIQMESQMKELQRTVEELKKAT 50 
                                       5699*****************************9986 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.04
                           DUF3584 586 sLdleridvpdyaaseeeLrerlqaleealqsae 619
                                       sL++ +i v  + ++e+ Lr++++al++ +++a 
  gi|474933909|ref|YP_007687491.1|  77 SLETMEIRVRGFKNQEDSLRQKAEALSNSINTAM 110
                                       6778888888899999999999999998888875 PP

>> CENP-H  Centromere protein H (CENP-H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5  12.5    0.0014      0.31      11      62 ..       4      65 ..       1     111 [. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0014
                            CENP-H 11 lssellklsqelrelqeeltevekenlrlkrknrelaaellelakekesek..........e 62
                                      +s +l+++ +++++lq++l+++++++++++ + +el ++++el+k++              +
  gi|474933909|ref|YP_007687491.1|  4 ISPQLQNQITQYQQLQQQLQTATAQRIQMESQMKELQRTVEELKKATGDVYrnvgtllikvD 65
                                      577899**********************************9999887766556776665552 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.4     0.065        15      21      47 ..      16      42 ..       6      51 .. 0.53
   2 ?    8.6   0.2    0.0093       2.1       8      42 ..      73     107 ..      67     111 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.065
                              XhlA 21 dkleekaaeaeekiknleedlkklesn 47
                                      ++l++   +a ++ +++e ++k+l+ +
  gi|474933909|ref|YP_007687491.1| 16 QQLQQQLQTATAQRIQMESQMKELQRT 42
                                      345555555555555555555555443 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0093
                              XhlA   8 rietkldnleervdkleekaaeaeekiknleedlk 42 
                                        +e+ l+++e rv   ++ ++  ++k++ l + ++
  gi|474933909|ref|YP_007687491.1|  73 DMEESLETMEIRVRGFKNQEDSLRQKAEALSNSIN 107
                                       68999999999999999999999999999999887 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   3.4    0.0004     0.093     212     312 ..       6     111 ..       5     122 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0004
                              FUSC 212 prirararalrrllsrmlallallsslarllarlraeeaaavpelaallaelaal.....eaaaaaealeaalaalr 283
                                       p++++++ ++++l++++++++a+   +++++++l+++ ++  ++  ++ + + +l     +++ +a++ e+ l++++
  gi|474933909|ref|YP_007687491.1|   6 PQLQNQITQYQQLQQQLQTATAQRIQMESQMKELQRTVEELKKATGDVYRNVGTLlikvdDKESLAADMEESLETME 82 
                                       7888999999*************************999999988888888888889999988899************ PP

                              FUSC 284 arlralrraleadadtaalllarlaella 312
                                        r+r  +++++  ++ a++l  +  + ++
  gi|474933909|ref|YP_007687491.1|  83 IRVRGFKNQEDSLRQKAEALSNSINTAMG 111
                                       ******99999888888888888777665 PP

>> Cep57_MT_bd  Centrosome microtubule-binding domain of Cep57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.4   0.00099      0.23      31      67 ..       8      46 ..       1      56 [. 0.73
   2 ?    5.1   0.1      0.13        30      49      67 ..      66      84 ..      59      87 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00099
                       Cep57_MT_bd 31 lqelaaqynaldpsl..gkrkRkdLaeeleelvkrlEaK 67
                                      lq    qy++l++ l    ++R +++++++el++++E+ 
  gi|474933909|ref|YP_007687491.1|  8 LQNQITQYQQLQQQLqtATAQRIQMESQMKELQRTVEEL 46
                                      455555666666665445599************999975 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.13
                       Cep57_MT_bd 49 kRkdLaeeleelvkrlEaK 67
                                       +++La+++ee+++++E +
  gi|474933909|ref|YP_007687491.1| 66 DKESLAADMEESLETMEIR 84
                                      6899*************75 PP

>> Phage_GP20  Phage minor structural protein GP20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   5.1    0.0007      0.16      14      52 ..      11      54 ..       2      84 .. 0.72
   2 ?    2.4   0.3      0.52   1.2e+02     106     137 ..      67      98 ..      55     115 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0007
                        Phage_GP20 14 dit.....kakldeveeerdtlkeqlkdrdkqLedLkkkakdne 52
                                       it     +++l++++++r ++++q+k+ + ++e+Lkk+++d+ 
  gi|474933909|ref|YP_007687491.1| 11 QITqyqqlQQQLQTATAQRIQMESQMKELQRTVEELKKATGDVY 54
                                      454455568999***************************98864 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.52
                        Phage_GP20 106 kdklklkedgelkgLdeqikkLkesdkyLFee 137
                                       k+ l ++ +++l++++  +   k++++ L ++
  gi|474933909|ref|YP_007687491.1|  67 KESLAADMEESLETMEIRVRGFKNQEDSLRQK 98 
                                       44444444444444444444444444333322 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   7.6    0.0055       1.3       9      90 ..      26     104 ..       1     113 [. 0.52

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0055
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH. CS
                        Laminin_II   9 netakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeas 85 
                                         +  + ++q+++l+  +e++k+    + r+v     kv+d+    +d ++s  ++e  +    ++  +l+q+ ea 
  gi|474933909|ref|YP_007687491.1|  26 TAQRIQMESQMKELQRTVEELKKATGDVYRNVGTLLIKVDDKESLAADMEESLETMEIRVRGFKNQEDSLRQKAEA- 101
                                       2222334455555555555555555555555555555555555555555555555555555555554455555444. PP

                                       ..HHH CS
                        Laminin_II  86 sslsd 90 
                                         ls+
  gi|474933909|ref|YP_007687491.1| 102 --LSN 104
                                       ..444 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   9.9   0.00048      0.11     268     321 ..       4      57 ..       2      83 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00048
                             IFT57 268 lnsqleellqeyreaqeelsevkekykqlsegvseltrelaeiseelekvkqem 321
                                       +  ql++++++y+++q++l++++ +  q++++++el+r+ +e+++   +v +++
  gi|474933909|ref|YP_007687491.1|   4 ISPQLQNQITQYQQLQQQLQTATAQRIQMESQMKELQRTVEELKKATGDVYRNV 57 
                                       6679**********************************9999998877776655 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   6.2   0.00017      0.04     348     431 ..       3      86 ..       1      89 [. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00017
                                       HHHHHHHHHHHHHHHHHHHHS-SS---STTGGGTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              EzrA 348 elekelkelekdyeeleekleekkvaYSelqeeleeleekleeieekqeeileslkslrkdEkrAreqldeikkelk 424
                                       +++ +l++  ++y++l+++l++ ++   +++++++el++++ee+++   ++ +++++l  +  + +  ++++++ l+
  gi|474933909|ref|YP_007687491.1|   3 GISPQLQNQITQYQQLQQQLQTATAQRIQMESQMKELQRTVEELKKATGDVYRNVGTLLIKVDDKESLAADMEESLE 79 
                                       577899999************************************************99998888888889999998 PP

                                       HHHHHSS CS
                              EzrA 425 eikrkie 431
                                       +++ +++
  gi|474933909|ref|YP_007687491.1|  80 TMEIRVR 86 
                                       8887775 PP

>> DUF4482  Domain of unknown function (DUF4482)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   5.4   0.00088       0.2      28      51 ..      28      51 ..       7     118 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00088
                           DUF4482 28 ERkewesqwkelqkkieeLqkevk 51
                                       R + esq+kelq+ +eeL+k+  
  gi|474933909|ref|YP_007687491.1| 28 QRIQMESQMKELQRTVEELKKATG 51
                                      6889****************9876 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   6.0     0.007       1.6      18      67 ..       9      60 ..       4     115 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.007
                      Syntaxin-6_N 18 eslyrrwerlledtss..stseeldetrteLrkalrsiewdledLeetvriv 67
                                      ++ ++++++l+++ ++  +++ +++++++eL+++++++++   d  + v+++
  gi|474933909|ref|YP_007687491.1|  9 QNQITQYQQLQQQLQTatAQRIQMESQMKELQRTVEELKKATGDVYRNVGTL 60
                                      3444455444444444323567777777777777777777777777777433 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   2.0     0.028       6.5      57      94 ..      15      52 ..       3      72 .. 0.48
   2 ?    8.2   0.2     0.011       2.5      66     106 ..      73     113 ..      68     121 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.028
                              COG2 57 FvslSghLvglqeeleevesplaaarkkvesvreklse 94
                                      + +l ++L+   ++  ++es+++++++ ve+++++  +
  gi|474933909|ref|YP_007687491.1| 15 YQQLQQQLQTATAQRIQMESQMKELQRTVEELKKATGD 52
                                      33444444444444444444444444444444444433 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.011
                              COG2  66 glqeeleevesplaaarkkvesvreklsereeeveskleea 106
                                       +++e+le++e  +  ++++ +s+r+k ++ ++ ++  + +a
  gi|474933909|ref|YP_007687491.1|  73 DMEESLETMEIRVRGFKNQEDSLRQKAEALSNSINTAMGNA 113
                                       89********************************9988776 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9  12.9    0.0018       0.4      44     145 ..      11     105 ..       4     110 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0018
                             ATG16  44 aaasakssksskksakekeasasqsnskqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklke 120
                                       ++++ ++        ++++++a+++  + ++++++l+ ++ +l++   ++y+  g+l  ++ ++++  ++ ee+l++
  gi|474933909|ref|YP_007687491.1|  11 QITQYQQ-------LQQQLQTATAQRIQMESQMKELQRTVEELKKATGDVYRNVGTLLIKVDDKESLAADMEESLET 80 
                                       3222222.......222222233334456777889999999999999999999999999999999999999999999 PP

                             ATG16 121 deerlaeleaeraaletklkdreee 145
                                       +e r++  +++  +l++k + + + 
  gi|474933909|ref|YP_007687491.1|  81 MEIRVRGFKNQEDSLRQKAEALSNS 105
                                       9999999999999999998877665 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   7.0    0.0012      0.27     232     338 ..       6     113 ..       1     119 [. 0.67

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0012
                          Prominin 232 snvlpaLaelerllenlkeakeqLeqvnklekeLrksgsqLrdglrgvkrdlnqalsnlCqseeCskilssleiekl 308
                                       +++ + +++ ++l ++l++a +q  q+++  keL+ + ++L+++  +v r++ ++l +   ++e   +  +++ e++
  gi|474933909|ref|YP_007687491.1|   6 PQLQNQITQYQQLQQQLQTATAQRIQMESQMKELQRTVEELKKATGDVYRNVGTLLIK-VDDKESLAADMEESLETM 81 
                                       4556668888888888888888888888888888888888888888888888888888.333444444444444445 PP

                          Prominin 309 dtskcl..dqlpnvdevlealeevletnlssi 338
                                       +       +q +++ +  eal + ++t + ++
  gi|474933909|ref|YP_007687491.1|  82 EIRVRGfkNQEDSLRQKAEALSNSINTAMGNA 113
                                       54444345777777777777777777776665 PP

>> Uso1_p115_C  Uso1 / p115 like vesicle tethering protein, C terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   7.0   0.00042     0.096      23      67 ..       7      49 ..       3      56 .. 0.92
   2 ?    5.2   1.4      0.11        26      25      75 ..      65     113 ..      50     124 .] 0.55

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00042
                       Uso1_p115_C 23 elqslskalesleqkeakkaaesqakeleaenkklekeleklrae 67
                                      +lq++ +++++l+q+  ++ a++q  ++e+++k+l++ +e+l+++
  gi|474933909|ref|YP_007687491.1|  7 QLQNQITQYQQLQQQ--LQTATAQRIQMESQMKELQRTVEELKKA 49
                                      899999*********..***********************99986 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.11
                       Uso1_p115_C  25 qslskalesleqkeakkaaesqakeleaenkklekeleklraelkeekeke 75 
                                       +++++ + ++e++  ++  e + +  +++ ++l+++ e+l+  ++++  ++
  gi|474933909|ref|YP_007687491.1|  65 DDKESLAADMEES--LETMEIRVRGFKNQEDSLRQKAEALSNSINTAMGNA 113
                                       4445555555555..444555555555555555555555555555554444 PP

>> MtrB  Tetrahydromethanopterin S-methyltransferase subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.41        95      29      50 ..      34      55 ..      20      60 .. 0.80
   2 ?    7.5   0.1     0.023       5.3      31      70 ..      57      96 ..      49     110 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.41
                              MtrB 29 lsldpvleeidkLekiaddlvn 50
                                       ++++++  +++L+k++ d+++
  gi|474933909|ref|YP_007687491.1| 34 SQMKELQRTVEELKKATGDVYR 55
                                      5799999999999999999876 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.023
                              MtrB 31 ldpvleeidkLekiaddlvnsLdpetallesypgRektlv 70
                                      +  +l ++d+ e++a d+++sL+  +  +  +++ e +l 
  gi|474933909|ref|YP_007687491.1| 57 VGTLLIKVDDKESLAADMEESLETMEIRVRGFKNQEDSLR 96
                                      56677799999***********************998875 PP

>> EIAV_Rev  Rev protein of equine infectious anaemia virus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.1    0.0015      0.35      48      89 ..      16      57 ..       3      77 .. 0.87
   2 ?    0.1   0.0       3.8   8.8e+02      60      78 ..      77      95 ..      69     106 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0015
                          EIAV_Rev 48 rwlreqvlqaevlqerlewrirgvqqaakelekvnkeiwrel 89
                                      + l++q++ a + + ++e +++ +q++  el+k   +++r++
  gi|474933909|ref|YP_007687491.1| 16 QQLQQQLQTATAQRIQMESQMKELQRTVEELKKATGDVYRNV 57
                                      56899**********************************986 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 3.8
                          EIAV_Rev 60 lqerlewrirgvqqaakel 78
                                        e +e r+rg ++    l
  gi|474933909|ref|YP_007687491.1| 77 SLETMEIRVRGFKNQEDSL 95
                                      4578999999998766655 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   4.9   0.00082      0.19      41      88 ..       3      50 ..       1      57 [. 0.83
   2 ?    2.8   0.2      0.64   1.5e+02      41      68 ..      69      96 ..      61     109 .. 0.49

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00082
                           BLOC1_2 41 dvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeys 88
                                       +  +l++++ ++++++++lq    q  q+e q +eL+ +v+eL + +
  gi|474933909|ref|YP_007687491.1|  3 GISPQLQNQITQYQQLQQQLQTATAQRIQMESQMKELQRTVEELKKAT 50
                                      566688999999999999999999999999999999999999997766 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.64
                           BLOC1_2 41 dvaaslekkleklnekyeelqpylqqid 68
                                      + aa++e++le ++ +   ++++ +++ 
  gi|474933909|ref|YP_007687491.1| 69 SLAADMEESLETMEIRVRGFKNQEDSLR 96
                                      4555555555555554444443333332 PP

>> Ax_dynein_light  Axonemal dynein light chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7  10.3    0.0066       1.5      90     184 ..       6      98 ..       2     101 .. 0.84
   2 ?    5.8   0.5     0.051        12     118     158 ..      68     108 ..      62     120 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0066
                   Ax_dynein_light  90 delrmtiaayktlyessvaFgmrkalqaeqgkselekkikeLeeekeelekqvaelkaklealekrekerrqeeekk 166
                                        +l++ i++y++l +  ++ +  + +q e +++el+++++eL++   +  ++v +l  k+++ e+ +++ + e  + 
  gi|474933909|ref|YP_007687491.1|   6 PQLQNQITQYQQLQQ-QLQTATAQRIQMESQMKELQRTVEELKKATGDVYRNVGTLLIKVDDKESLAADME-ESLET 80 
                                       57899*******988.78899999************************************99887766554.45556 PP

                   Ax_dynein_light 167 heeeieflkksnqqlkeq 184
                                        e  +  +k+++ +l+++
  gi|474933909|ref|YP_007687491.1|  81 MEIRVRGFKNQEDSLRQK 98 
                                       677788888888888776 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.051
                   Ax_dynein_light 118 eqgkselekkikeLeeekeelekqvaelkaklealekreke 158
                                       e   +++e+ ++ +e +++ +++q  +l++k+eal ++ + 
  gi|474933909|ref|YP_007687491.1|  68 ESLAADMEESLETMEIRVRGFKNQEDSLRQKAEALSNSINT 108
                                       66678999999999999999999999999999998877665 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   4.0    0.0014      0.32      18     102 ..      15     102 ..       3     115 .. 0.41

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0014
                        V_ATPase_I  18 vnafqrkfvkevrrcdemerklrfleeeieklekavikeeea...eesleapeekeldeleeelekleeelkelnen 91 
                                        +++q++  +   +  +me +++ l++++e+l+ka+    ++      + +++e+   ++ee+le++e +++ ++++
  gi|474933909|ref|YP_007687491.1|  15 YQQLQQQLQTATAQRIQMESQMKELQRTVEELKKATGDVYRNvgtLLIKVDDKESLAADMEESLETMEIRVRGFKNQ 91 
                                       22223332222222223444444444333333333333222233233333344444445555555555555555555 PP

                        V_ATPase_I  92 leklkkelnel 102
                                       +++l+++ + l
  gi|474933909|ref|YP_007687491.1|  92 EDSLRQKAEAL 102
                                       55555544444 PP

>> Peptidase_U57  YabG peptidase U57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   2.9    0.0015      0.35      55     150 ..      10     105 ..       3     110 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0015
                     Peptidase_U57  55 eevkekkkkleekveeslkkllkerkeeeekkkkkekkekekeeafelpgkvL.hlDgdeeYlekclklYkklglea 130
                                       ++++++++ +++ ++ + +++ +e + +e  +++ e+ +k++ ++++  g++L ++D  e+      +  +++++++
  gi|474933909|ref|YP_007687491.1|  10 NQITQYQQLQQQLQTATAQRIQMESQMKE-LQRTVEELKKATGDVYRNVGTLLiKVDDKESLAADMEESLETMEIRV 85 
                                       55666666666666666666644444444.4666666677777777777776548999999999999********** PP

                     Peptidase_U57 131 vgvvvkEkeqpekvkellek 150
                                       +g   +E++  +k ++l ++
  gi|474933909|ref|YP_007687491.1|  86 RGFKNQEDSLRQKAEALSNS 105
                                       *******9999988777665 PP

>> CC2-LZ  Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4  10.6     0.024       5.6      11      49 ..      10      48 ..       3     108 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.024
                            CC2-LZ 11 vkkeeieeLkaqlqaaeealaakqeeidelkeeikkkee 49
                                       +  ++++L++qlq+a  +  +++++++el+ ++++ ++
  gi|474933909|ref|YP_007687491.1| 10 NQITQYQQLQQQLQTATAQRIQMESQMKELQRTVEELKK 48
                                      45899***************************9999888 PP

>> Cauli_AT  Aphid transmission protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   1.8     0.009       2.1     115     157 ..       7      49 ..       3      53 .. 0.90
   2 ?    5.8   0.2     0.051        12      84     135 ..      49     100 ..      46     110 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.009
                          Cauli_AT 115 eaqnrikkleeetkklaekivtekllkeevkdlderlseirds 157
                                       + qn+i++ ++ +++l+  +  + ++++++k+l+++++e+++ 
  gi|474933909|ref|YP_007687491.1|   7 QLQNQITQYQQLQQQLQTATAQRIQMESQMKELQRTVEELKKA 49 
                                       57999********************************999875 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.051
                          Cauli_AT  84 PfgsvfkklkkifkeggedkekktklletLkeaqnrikkleeetkklaekiv 135
                                         g+v++++ + + +++++++ +++  e+L+ ++ r++  +++  +l +k +
  gi|474933909|ref|YP_007687491.1|  49 ATGDVYRNVGTLLIKVDDKESLAADMEESLETMEIRVRGFKNQEDSLRQKAE 100
                                       45899999999999999999999999************99999999999866 PP

>> UPF0449  Uncharacterised protein family UPF0449
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   2.8    0.0051       1.2      62      98 ..      10      49 ..       4      58 .. 0.61
   2 ?    3.9   0.1      0.33        75      79     100 ..      86     107 ..      62     108 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0051
                           UPF0449 62 eqvrtylelnerLeea...keeLkqkceeLktageeLeee 98
                                      +q+++y +l+++L+ a   + +++++++eL++  eeL+++
  gi|474933909|ref|YP_007687491.1| 10 NQITQYQQLQQQLQTAtaqRIQMESQMKELQRTVEELKKA 49
                                      5666666777777665111345666666777777776654 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.33
                           UPF0449  79 eeLkqkceeLktageeLeeeie 100
                                          k++++ L++ +e L+++i+
  gi|474933909|ref|YP_007687491.1|  86 RGFKNQEDSLRQKAEALSNSIN 107
                                       3456677777777777777775 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   3.3     0.039         9      29      61 ..      16      48 ..       9      51 .. 0.78
   2 ?    7.5   0.3     0.018       4.2      26      57 ..      76     107 ..      74     110 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.039
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1 29 eeLerrvkaLekeNksLkseleelkkevekLks 61
                                      ++L+++ ++ +++  ++ s+++el+ +ve+Lk+
  gi|474933909|ref|YP_007687491.1| 16 QQLQQQLQTATAQRIQMESQMKELQRTVEELKK 48
                                      678888888888888888888888888888886 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.018
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  26 aeieeLerrvkaLekeNksLkseleelkkeve 57 
                                       ++ e  e rv  ++++  sL++++e l++ ++
  gi|474933909|ref|YP_007687491.1|  76 ESLETMEIRVRGFKNQEDSLRQKAEALSNSIN 107
                                       678999*********************98875 PP

>> PCRF  PCRF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   6.9    0.0029      0.66       4      90 ..      14     110 ..       8     122 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0029
                                       HHTTTTTST.-GGG..TTTGGGSSSTTHHHHHTHHHH.HHHHHHHHHTTTHHH...HT.....-S-..-GG...... CS
                              PCRF   4 eleelekklsdpev..wedqekakklskelaeleeiv.ealeeleealedleeakelle.edeelaelaee...... 70 
                                       ++++l+++l+  +   ++ ++++k+l+++++el++ + + ++++ ++l ++++ ++l++  +e+l+ ++        
  gi|474933909|ref|YP_007687491.1|  14 QYQQLQQQLQTATAqrIQMESQMKELQRTVEELKKATgDVYRNVGTLLIKVDDKESLAAdMEESLETME-Irvrgfk 89 
                                       677788877655441144566777777777777665425677777777777776666522222233222.1233333 PP

                                       .GTHHHHHHHHHH..HHHHHT CS
                              PCRF  71 .eleelekeleeleeelkklL 90 
                                        + ++l+++ e+l++++++ +
  gi|474933909|ref|YP_007687491.1|  90 nQEDSLRQKAEALSNSINTAM 110
                                       246666666666666666555 PP

>> DUF4763  Domain of unknown function (DUF4763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   4.5   0.00087       0.2      99     146 ..       5      52 ..       1      60 [. 0.86
   2 ?    1.5   0.1      0.66   1.5e+02     117     153 ..      72     108 ..      68     111 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00087
                           DUF4763  99 qpeileLqrnnhkLrqqlaelqqhlkasrkslkelreslcqekkrlrk 146
                                       +p++++   + ++L+qql+ ++ ++ ++++++kel++ + ++kk++  
  gi|474933909|ref|YP_007687491.1|   5 SPQLQNQITQYQQLQQQLQTATAQRIQMESQMKELQRTVEELKKATGD 52 
                                       688888888999*************************99999998765 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.66
                           DUF4763 117 aelqqhlkasrkslkelreslcqekkrlrklqkrlne 153
                                       a+++++l++++  ++ ++++  ++++ +++l+ ++n 
  gi|474933909|ref|YP_007687491.1|  72 ADMEESLETMEIRVRGFKNQEDSLRQKAEALSNSINT 108
                                       5789999999999999999999999999999998875 PP

>> HemX  HemX, putative uroporphyrinogen-III C-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8  13.1    0.0079       1.8      23     104 ..      15     114 ..       9     121 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0079
                              HemX  23 yylgqqqvqeltaevaelqqqlaaleqqlaq..................veaekeqkqeleerlqqlaeklealeke 81 
                                       y+  qqq q++ta+  ++++q+++l+ ++++                  v+ +++  +++ee+l++ + ++   +++
  gi|474933909|ref|YP_007687491.1|  15 YQQLQQQLQTATAQRIQMESQMKELQRTVEElkkatgdvyrnvgtllikVDDKESLAADMEESLETMEIRVRGFKNQ 91 
                                       44445555556666688889999999999999999999999999999888888888899999999999999999999 PP

                              HemX  82 leqlqkqleelqqqlskvsgaer 104
                                        ++l ++ e+l++ +++ +g+ +
  gi|474933909|ref|YP_007687491.1|  92 EDSLRQKAEALSNSINTAMGNAP 114
                                       99999999999999999999855 PP

>> DUF2205  Short coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   2.5       6.3   1.5e+03      22      34 ..      12      24 ..       5      31 .. 0.59
   2 ?    2.3   6.6      0.71   1.6e+02      14      37 ..      25      48 ..      11      56 .. 0.76
   3 ?    8.0   0.0     0.012       2.8      25      65 ..      71     111 ..      62     119 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 6.3
                           DUF2205 22 qqqakeLqssLqa 34
                                      ++q ++Lq+ Lq 
  gi|474933909|ref|YP_007687491.1| 12 ITQYQQLQQQLQT 24
                                      3466778888774 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.71
                           DUF2205 14 erearerLqqqakeLqssLqaLae 37
                                       + +r ++++q+keLq++ ++L +
  gi|474933909|ref|YP_007687491.1| 25 ATAQRIQMESQMKELQRTVEELKK 48
                                      4456777888********999976 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.012
                           DUF2205  25 akeLqssLqaLaervdeVkeehdKLesenrfLqqYIgdLms 65 
                                       a  + +sL+ +  rv   k+ +d L+   + L++ I++ m 
  gi|474933909|ref|YP_007687491.1|  71 AADMEESLETMEIRVRGFKNQEDSLRQKAEALSNSINTAMG 111
                                       667899**************************999998876 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3  12.4    0.0041      0.94     148     238 ..       8     108 ..       1     113 [. 0.68

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0041
                              Spc7 148 legleedkelLekqeeeldellpeleeekaeleeeleklqeaaeeles.........idkeeLee.lreelaelkae 214
                                       l++  +++++L++q + +++   ++e++ +el++++e+l++a  ++            dke+L++ + e+l++ +  
  gi|474933909|ref|YP_007687491.1|   8 LQNQITQYQQLQQQLQTATAQRIQMESQMKELQRTVEELKKATGDVYRnvgtllikvDDKESLAAdMEESLETMEIR 84 
                                       44444556677777777777777777777777777777777333333334446666445888864388999999999 PP

                              Spc7 215 ieekkkelaelqeqleeleekiee 238
                                       ++ +k++ ++l+++ e+l+++i++
  gi|474933909|ref|YP_007687491.1|  85 VRGFKNQEDSLRQKAEALSNSINT 108
                                       999999999999999999999876 PP

>> FAA_hydro_N_2  Fumarylacetoacetase N-terminal domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   1.5      0.15        33      31      55 ..       4      28 ..       1      56 [. 0.71
   2 ?    7.4   0.1     0.026       5.9      18      73 ..      64     112 ..      46     117 .. 0.57

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.15
                     FAA_hydro_N_2 31 iaptlqaaLdnWdevepaLeelyea 55
                                      i p+lq+ + + ++++++L++++++
  gi|474933909|ref|YP_007687491.1|  4 ISPQLQNQITQYQQLQQQLQTATAQ 28
                                      7788888888888888888876543 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.026
                     FAA_hydro_N_2  18 VsrdlkkavdaseiaptlqaaLdnWdevepaLeelyeaLnagtakeafafdpeela 73 
                                       V++  + a+d++e  +t+   +   ++ e +L++++eaL+++       ++++   
  gi|474933909|ref|YP_007687491.1|  64 VDDKESLAADMEESLETMEIRVRGFKNQEDSLRQKAEALSNS-------INTAMGN 112
                                       555555555666666666666666666666666666666554.......4444444 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   7.6     0.058        13     109     169 ..      13      73 ..       4      82 .. 0.56
   2 ?    6.8   0.5     0.023       5.3     117     163 ..      63     109 ..      52     122 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.058
                            DUF724 109 eerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaek 169
                                       ++ ++l+++++++++++ ++e++++el++++ el++    + ++  +   ++ + +s a++
  gi|474933909|ref|YP_007687491.1|  13 TQYQQLQQQLQTATAQRIQMESQMKELQRTVEELKKATGDVYRNVGTLLIKVDDKESLAAD 73 
                                       4455666777777777777777777777777777776655554444444444444444444 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.023
                            DUF724 117 kieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarl 163
                                       k+ ++es  + +ee+++ +e +++ +++q+++l++k ea +++i + 
  gi|474933909|ref|YP_007687491.1|  63 KVDDKESLAADMEESLETMEIRVRGFKNQEDSLRQKAEALSNSINTA 109
                                       677889999999*************************9999998765 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   3.7     0.011       2.4      12      53 ..       8      49 ..       4      58 .. 0.60
   2 ?    5.9   0.2     0.048        11      12      60 ..      57     105 ..      52     110 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.011
                             Sec34 12 cdelleqtdealeqLeeleekfksvsektsslheaceqllee 53
                                      +++ ++q +++++qL++ + +  ++++++++l+++ e+l + 
  gi|474933909|ref|YP_007687491.1|  8 LQNQITQYQQLQQQLQTATAQRIQMESQMKELQRTVEELKKA 49
                                      444455666666666666666666666666666666666543 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.048
                             Sec34  12 cdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleel 60 
                                       + +ll ++d+ +++ +++ee+ ++++ + + ++++ ++l ++ + l++ 
  gi|474933909|ref|YP_007687491.1|  57 VGTLLIKVDDKESLAADMEESLETMEIRVRGFKNQEDSLRQKAEALSNS 105
                                       5678888888888889999999999999999999999998888877764 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   9.5    0.0013       0.3      44      91 ..       6      53 ..       1      61 [. 0.89
   2 ?    2.9   0.3      0.25        57      55      90 ..      73     108 ..      59     113 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0013
                           DUF3450 44 dekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieei 91
                                       + q+   +y++l+++l+ +++++ q+e++++++++++++l++   ++
  gi|474933909|ref|YP_007687491.1|  6 PQLQNQITQYQQLQQQLQTATAQRIQMESQMKELQRTVEELKKATGDV 53
                                      57788899**********************************998776 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.25
                           DUF3450  55 alkeeleslevyneqlerlvasqeqeiasleeqiee 90 
                                       +++e le +e+  +  +++ +s++q+ + l ++i+ 
  gi|474933909|ref|YP_007687491.1|  73 DMEESLETMEIRVRGFKNQEDSLRQKAEALSNSINT 108
                                       566677777777777777777777777777777664 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3  11.7    0.0063       1.5      17     106 ..      13     102 ..       4     105 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0063
                           DUF4200  17 akkeeiqrleealkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeikklkaeietlk 93 
                                       ++ +++q++ ++++ ++ ++e + +el++++++++k   +  ++    l k+++++ l  ++e+ ++ ++  +   k
  gi|474933909|ref|YP_007687491.1|  13 TQYQQLQQQLQTATAQRIQMESQMKELQRTVEELKKATGDVYRNVGTLLIKVDDKESLAADMEESLETMEIRVRGFK 89 
                                       455556666666667778899999***************************************************** PP

                           DUF4200  94 seiekleekleey 106
                                       ++ + l +k e +
  gi|474933909|ref|YP_007687491.1|  90 NQEDSLRQKAEAL 102
                                       *****99998765 PP

>> DUF3138  Protein of unknown function (DUF3138)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   2.7    0.0051       1.2      26     101 ..      21      96 ..       7     111 .. 0.50

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0051
                           DUF3138  26 rikalkaqltalqrqvkelraalaaakaaaGgkissqkaaaaaaaaaeaaaalteddvaqlkeqianaelkvdalq 101
                                       ++++  aq  +++ q+kel+++++  k a+G    ++++     +  e+ aa  e+ ++ +  ++   + + d+l+
  gi|474933909|ref|YP_007687491.1|  21 QLQTATAQRIQMESQMKELQRTVEELKKATGDVYRNVGTLLIKVDDKESLAADMEESLETMEIRVRGFKNQEDSLR 96 
                                       4444444544555555555555555555555544444444444444444444444444444444444444444443 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0  10.8    0.0087         2      12     114 ..       8     109 ..       3     113 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0087
                           DUF4795  12 lqeaieklqeelekleekvkelekrledkekklealkkqieelekvkadkeeveeelaeka.dkeaLatkvsrdq.. 85 
                                       lq++i++ q    +l+++ +    +  + e++++ l+  +eel+k+ +d +     l +k+ dke La+ ++++   
  gi|474933909|ref|YP_007687491.1|   8 LQNQITQYQ----QLQQQLQTATAQRIQMESQMKELQRTVEELKKATGDVYRNVGTLLIKVdDKESLAADMEESLet 80 
                                       555555555....4455666666666778888999999999999999888877777777773478888888766666 PP

                           DUF4795  86 fDeakkeLekmleellekleeqeealkka 114
                                       ++ ++  ++++  +l++k e+ +++++ a
  gi|474933909|ref|YP_007687491.1|  81 MEIRVRGFKNQEDSLRQKAEALSNSINTA 109
                                       55555555555555555555555555544 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5  14.1       0.1        23      14      70 ..       9      65 ..       6     113 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.1
                              ZapB 14 qkaidtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkkLLgkle 70
                                      q+ i+++++Lq++++   ++  +++++++el++ +e+lk+    + + + +LL k +
  gi|474933909|ref|YP_007687491.1|  9 QNQITQYQQLQQQLQTATAQRIQMESQMKELQRTVEELKKATGDVYRNVGTLLIKVD 65
                                      7889****************************9999999666665555555555544 PP

>> DUF4446  Protein of unknown function (DUF4446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   2.0     0.012       2.8      39      83 ..      14      58 ..       5      65 .. 0.80
   2 ?    4.8   0.3      0.11        25      39      79 ..      70     110 ..      60     115 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.012
                           DUF4446 39 dgksleellkekleeveelkeeseelekeieeleeklkkslqkvg 83
                                      + ++l+++l++ +++  +++++++el++++eel++     +++vg
  gi|474933909|ref|YP_007687491.1| 14 QYQQLQQQLQTATAQRIQMESQMKELQRTVEELKKATGDVYRNVG 58
                                      567888888888888889999999999999999998888888887 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.11
                           DUF4446  39 dgksleellkekleeveelkeeseelekeieeleeklkksl 79 
                                        ++++ee l++   +v+ +k+++++l+++ e+l++++++++
  gi|474933909|ref|YP_007687491.1|  70 LAADMEESLETMEIRVRGFKNQEDSLRQKAEALSNSINTAM 110
                                       46788888888888999999999999999999998888765 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9  11.5      0.87     2e+02      14     113 ..       7     112 ..       5     116 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.87
                                       HHHHHHHHHHHHHHHHHHHTT......-TT-EEEEEEETTEEEEEE-.-STTEEEEEEETTEEEEEEHHHHHHHHHH CS
                         Prefoldin  14 qlkeaieelektletlktlkk.....edegkevlvplgaglyvkaev.kdtdkvlvdlGagyyveksleeAiellkk 84 
                                       ql+ +i+ ++++ + l+t  +     e + ke++  +++   + ++v ++   +l+++    ++  ++ee+ e+ + 
  gi|474933909|ref|YP_007687491.1|   7 QLQNQITQYQQLQQQLQTATAqriqmESQMKELQRTVEELKKATGDVyRNVGTLLIKVDDKESLAADMEESLETMEI 83 
                                       67777888888888887777777777777777777777777788888888888999999999999999999999999 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  85 kleelekqlekleeeleklkdqittlean 113
                                       ++   ++q ++l +++e l++ i+t++ n
  gi|474933909|ref|YP_007687491.1|  84 RVRGFKNQEDSLRQKAEALSNSINTAMGN 112
                                       99999999999999999999999988755 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4  10.1     0.011       2.4     124     231 ..       9     115 ..       3     124 .] 0.71

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.011
                           DUF4407 124 keqlaaa..ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqae 198
                                       ++q+++   l+++l++++aq+ +++++++++++++++l+++  + + +  gt   +v  k+  a   ++ l++ + +
  gi|474933909|ref|YP_007687491.1|   9 QNQITQYqqLQQQLQTATAQRIQMESQMKELQRTVEELKKATGDVYRN-VGTLLIKVDDKESLAADMEESLETMEIR 84 
                                       333333344899999999999999999999999999888877766665.6767666788888888888888888888 PP

                           DUF4407 199 laelkakldatarlaalraelaeleaerakera 231
                                       +  +k++  +++ +++++a  +++++++ ++ a
  gi|474933909|ref|YP_007687491.1|  85 VRGFKNQ--EDSLRQKAEALSNSINTAMGNAPA 115
                                       8888888..777777777777777776666555 PP

>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1       2.3   5.3e+02      14      31 ..       7      24 ..       5      28 .. 0.83
   2 ?    3.7   0.3      0.23        54       2      23 ..      33      47 ..      18      55 .. 0.60
   3 ?    5.6   0.2     0.058        13       6      37 ..      72     103 ..      68     111 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 2.3
                         DASH_Dam1 14 tLdknledLqqihesLsd 31
                                      +L++++++ qq++++L++
  gi|474933909|ref|YP_007687491.1|  7 QLQNQITQYQQLQQQLQT 24
                                      588899999999999875 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.23
                         DASH_Dam1  2 epafaeLaDsletLdknledLq 23
                                      e +       +++L++ +e+L+
  gi|474933909|ref|YP_007687491.1| 33 ESQ-------MKELQRTVEELK 47
                                      333.......333333333333 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.058
                         DASH_Dam1   6 aeLaDsletLdknledLqqihesLsdfNeSFa 37 
                                       a++++slet++ +++ +++ ++sL +  e+++
  gi|474933909|ref|YP_007687491.1|  72 ADMEESLETMEIRVRGFKNQEDSLRQKAEALS 103
                                       57788899999999999999999888888776 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   9.3      0.22        50       8      44 ..      27      63 ..       1     122 [. 0.63

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.22
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YabA  8 dkleeleeqleelleeleelkeelaelleenaeLele 44
                                      ++  ++e+q++el++++eelk+++ +++ +  +L + 
  gi|474933909|ref|YP_007687491.1| 27 AQRIQMESQMKELQRTVEELKKATGDVYRNVGTLLIK 63
                                      3445666666666666666666666666666666554 PP

>> CLZ  C-terminal leucine zipper domain of cyclic nucleotide-gated channels
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   3.0      0.12        27      15      46 ..      18      49 ..       7      60 .. 0.82
   2 ?    7.1   0.8     0.031         7      28      60 ..      66      98 ..      59     105 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.12
                               CLZ 15 LDeeaakagaeqkeleekverLessLeaLqtr 46
                                      L ++ + a a++ ++e+++++L+ ++e L++ 
  gi|474933909|ref|YP_007687491.1| 18 LQQQLQTATAQRIQMESQMKELQRTVEELKKA 49
                                      66777888899999999999999999999875 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.031
                               CLZ 28 eleekverLessLeaLqtrlarLlaeyessqrk 60
                                      + e+ +  +e+sLe+++ r++ + ++ +s  +k
  gi|474933909|ref|YP_007687491.1| 66 DKESLAADMEESLETMEIRVRGFKNQEDSLRQK 98
                                      66888899***********98877776666555 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   5.1     0.022       5.2       5      41 ..      14      50 ..       3      72 .. 0.47
   2 ?    5.9   0.9     0.067        15       8      43 ..      73     108 ..      66     124 .] 0.68

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.022
                             Spc24  5 ekfriakelsdleselesleselaelkeeleeleees 41
                                      + ++++++l+ ++++  ++es+ +el++++eel++  
  gi|474933909|ref|YP_007687491.1| 14 QYQQLQQQLQTATAQRIQMESQMKELQRTVEELKKAT 50
                                      2333444444444444444444444444444444333 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.067
                             Spc24   8 riakelsdleselesleselaelkeeleeleeesee 43 
                                       ++ ++l+ +e  +   +++ ++l+++ e l+++ + 
  gi|474933909|ref|YP_007687491.1|  73 DMEESLETMEIRVRGFKNQEDSLRQKAEALSNSINT 108
                                       556677777778888888888888888888887776 PP

>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   9.4     0.023       5.2       8      97 ..       9     101 ..       5     113 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.023
                                       TTTHHHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHH.....HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              GrpE   8 eeeedeeeeleeeleelekevkelkekllrllaefenlrkrt.....ekekeeakkfaiekfakdLLpvlDnleral 79 
                                       +++ ++ ++l+++l+++ ++  ++++++++l+  +e+l+k t     +     +k + +e++a d+ + l+ +e  +
  gi|474933909|ref|YP_007687491.1|   9 QNQITQYQQLQQQLQTATAQRIQMESQMKELQRTVEELKKATgdvyrNVGTLLIKVDDKESLAADMEESLETMEIRV 85 
                                       567789999******************************99944432222335788899999999999999999888 PP

                                       HC..HHH-HHHHHHHHHH CS
                              GrpE  80 ksakeneeekslleGvem 97 
                                         +k  ++e+sl +  e 
  gi|474933909|ref|YP_007687491.1|  86 RGFK--NQEDSLRQKAEA 101
                                       8754..444444554444 PP

>> Com_YlbF  Control of competence regulator ComK, YlbF/YmcA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6  14.7     0.052        12      32      74 ..       6      47 ..       4     111 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.052
                                      HHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHHHHHH CS
                          Com_YlbF 32 eelqklikefkklqkelqekqmkgeelkeeekkelqelkeeld 74
                                      ++lq++i+++++lq++lq++  +  +++ ++k elq+  eel+
  gi|474933909|ref|YP_007687491.1|  6 PQLQNQITQYQQLQQQLQTATAQRIQMESQMK-ELQRTVEELK 47
                                      799***************98877644444444.6666555553 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   7.3     0.032       7.4     336     408 ..      26     106 ..       5     116 .. 0.42

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.032
                              FapA 336 keklkeleeeleeleeeleklkkk........ikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkel 404
                                        +++ ++e +++el++ +e+lkk+         ++l k   ++ l ++++e+l+ ++     +k++  +l+++ ++l
  gi|474933909|ref|YP_007687491.1|  26 TAQRIQMESQMKELQRTVEELKKAtgdvyrnvGTLLIKVDDKESLAADMEESLETMEIRVRGFKNQEDSLRQKAEAL 102
                                       22222223333333333333333233333335333333333444555555555555555555555555555555555 PP

                              FapA 405 keel 408
                                       ++++
  gi|474933909|ref|YP_007687491.1| 103 SNSI 106
                                       5555 PP

>> TEX13  Testis-expressed sequence 13 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   8.9     0.022         5      65     145 ..      15      98 ..       4     104 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.022
                             TEX13  65 wsaLaLgvrvaarqrelqarrvqkLqdqveehksaaqaLaselkrlreq.qemer..keaasqlqlaqaalaevqke 138
                                       ++ L   ++ a+ qr + + +++ Lq  vee k a+  +  ++ +l  + +++e+   +++  l++++ +++  +++
  gi|474933909|ref|YP_007687491.1|  15 YQQLQQQLQTATAQRIQMESQMKELQRTVEELKKATGDVYRNVGTLLIKvDDKESlaADMEESLETMEIRVRGFKNQ 91 
                                       5566667788999999999999*************999999998876431444541155666788899999999999 PP

                             TEX13 139 rdlLrkk 145
                                        d Lr+k
  gi|474933909|ref|YP_007687491.1|  92 EDSLRQK 98 
                                       9999998 PP

>> FliD_N  Flagellar hook-associated protein 2 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9  10.1      0.19        43      17      63 ..       9      56 ..       4     115 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.19
                                      XXXXXXXXXXXXXXXXXHHHHHHHHHHHHHHHHHHHHHXX.GGGGGXE CS
                            FliD_N 17 rakldkleqkktklewkqsayrelnsklsnlksalsalsk.sstfsak 63
                                      ++++++++q +++l++  +   +++s++++l+ ++++l+k ++++  +
  gi|474933909|ref|YP_007687491.1|  9 QNQITQYQQLQQQLQTATAQRIQMESQMKELQRTVEELKKaTGDVYRN 56
                                      457899999999999999999999999999999887887766666543 PP

>> CCDC-167  Coiled-coil domain-containing protein 167
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   1.8       2.3   5.3e+02      31      53 ..      23      45 ..       6      51 .. 0.55
   2 ?   10.2   0.4    0.0032      0.74       5      51 ..      63     110 ..      60     113 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 2.3
                          CCDC-167 31 elseeeResleeEeaslkeqlee 53
                                      +  + +R ++e  +++l+  +ee
  gi|474933909|ref|YP_007687491.1| 23 QTATAQRIQMESQMKELQRTVEE 45
                                      34444566666666666655555 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0032
                          CCDC-167   5 eIdkleeklascrerLeaverrlrkeelseee.ResleeEeaslkeql 51 
                                       ++d+ e   a+++e+Le++e r+r+ + +e+  R+++e   +s+++ +
  gi|474933909|ref|YP_007687491.1|  63 KVDDKESLAADMEESLETMEIRVRGFKNQEDSlRQKAEALSNSINTAM 110
                                       589999999****************99988876888888888887765 PP

>> DUF773  CDK5 regulatory subunit-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   7.0    0.0066       1.5     440     490 ..       6      56 ..       2      64 .. 0.90
   2 ?    3.4   0.3      0.11        25     438     481 ..      60     103 ..      54     109 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0066
                            DUF773 440 asLeqklkqeeklkeklkdleekreelqeelselepkleklvkktrelkkl 490
                                        +L+++ +q ++l+++l++++++r +++++++el+ ++e+l k t ++ ++
  gi|474933909|ref|YP_007687491.1|   6 PQLQNQITQYQQLQQQLQTATAQRIQMESQMKELQRTVEELKKATGDVYRN 56 
                                       589*****************************************9887655 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.11
                            DUF773 438 lvasLeqklkqeeklkeklkdleekreelqeelselepkleklv 481
                                       l  +  +k++ ++ ++e+l+++e + + ++++  +l++k e+l 
  gi|474933909|ref|YP_007687491.1|  60 LLIKVDDKESLAADMEESLETMEIRVRGFKNQEDSLRQKAEALS 103
                                       566778999999**************************999886 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2  14.1      0.13        29      12      95 ..      16      82 ..       7     109 .. 0.38

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.13
                            APG6_N 12 eeldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleee 90
                                      ++l++ql++a+++r ++                 +++++el++ +e+l+k+  +  ++   l  + ++ e+  a+ ee 
  gi|474933909|ref|YP_007687491.1| 16 QQLQQQLQTATAQRIQM-----------------ESQMKELQRTVEELKKATGDVYRNVGTLLIKVDDKESLAADMEES 77
                                      23333333333333333.................333333333333333333333333333333333333333333333 PP

                            APG6_N 91 leale 95
                                      le +e
  gi|474933909|ref|YP_007687491.1| 78 LETME 82
                                      33333 PP

>> zf-CpG_bind_C  CpG binding protein zinc finger C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   4.5      0.04       9.1      26      66 ..      10      50 ..       4      71 .. 0.82
   2 ?    4.2   0.2      0.14        32      25      71 ..      72     118 ..      60     124 .] 0.75

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.04
                     zf-CpG_bind_C 26 enkkklekirkeqeeakkklkelekklkkLeeliekakkls 66
                                      ++ ++ ++++++ ++a+++  ++e+++k+L++ +e+ kk++
  gi|474933909|ref|YP_007687491.1| 10 NQITQYQQLQQQLQTATAQRIQMESQMKELQRTVEELKKAT 50
                                      56678899999999999999999999999999999988875 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.14
                     zf-CpG_bind_C  25 eenkkklekirkeqeeakkklkelekklkkLeeliekakklslkeee 71 
                                       +  +++le+++ +++  k+++ +l +k + L + i++a   +   ++
  gi|474933909|ref|YP_007687491.1|  72 ADMEESLETMEIRVRGFKNQEDSLRQKAEALSNSINTAMGNAPAPRR 118
                                       4556788888889999999****************999876444444 PP

>> BST2  Bone marrow stromal antigen 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   8.1      0.02       4.5      48      81 ..      16      49 ..       7      58 .. 0.85
   2 ?    3.0   0.3      0.65   1.5e+02      48      84 ..      72     108 ..      63     113 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.02
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              BST2 48 vtLkasLekekaqsqkqqakvqelqgeikkLnqk 81
                                      ++L++ L+  +aq  +++++++elq+ +++L++ 
  gi|474933909|ref|YP_007687491.1| 16 QQLQQQLQTATAQRIQMESQMKELQRTVEELKKA 49
                                      5899999999999999999999999999999975 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.65
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              BST2  48 vtLkasLekekaqsqkqqakvqelqgeikkLnqkLqd 84 
                                        ++++sLe ++ + +  +++   l+++ + L ++++ 
  gi|474933909|ref|YP_007687491.1|  72 ADMEESLETMEIRVRGFKNQEDSLRQKAEALSNSINT 108
                                       4566777777777777777777777777777766655 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   7.7      0.15        36      13      89 ..       6      77 ..       2     115 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.15
                           DUF2203 13 pllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkdleaglvDFpak 89
                                      p+l+++++++++l+++l+++ ++  + +++      +el++++eel++   ++ +++  l ++v d e +  D   +
  gi|474933909|ref|YP_007687491.1|  6 PQLQNQITQYQQLQQQLQTATAQRIQMESQ-----MKELQRTVEELKKATGDVYRNVGTLLIKVDDKESLAADMEES 77
                                      566666666666666666654433333333.....566666677777766666666666666666666666665544 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   8.7     0.063        15      19     112 ..      10     107 ..       4     121 .. 0.60

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.063
                             Atg14  19 ngperlyelrerlaklksekeslkkkiekalegke....eaeqledkiknkkakleelksliadlrerlqelkdkls 91 
                                       n+  ++ +l+++l+   +++ +++++++++  + e    ++++  +++ ++  k++++ sl ad +e l++++ +++
  gi|474933909|ref|YP_007687491.1|  10 NQITQYQQLQQQLQTATAQRIQMESQMKELQRTVEelkkATGDVYRNVGTLLIKVDDKESLAADMEESLETMEIRVR 86 
                                       43333334444444444444444444442211111333366777888888888888888888888888888888888 PP

                             Atg14  92 qlkkeieekkkklaklsdklk 112
                                         k + +  ++k ++ls+++ 
  gi|474933909|ref|YP_007687491.1|  87 GFKNQEDSLRQKAEALSNSIN 107
                                       777777777777777777765 PP

>> EMP24_GP25L  emp24/gp25L/p24 family/GOLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   2.9      0.31        70     112     154 ..      14      56 ..       5      62 .. 0.64
   2 ?    8.5   0.7    0.0077       1.8     105     147 ..      63     105 ..      47     110 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.31
                       EMP24_GP25L 112 kletleselkkleekldsikreqkylrereerlrdtnestnsr 154
                                       + ++l+++l++   +  ++++++k l++  e+l+++  +++++
  gi|474933909|ref|YP_007687491.1|  14 QYQQLQQQLQTATAQRIQMESQMKELQRTVEELKKATGDVYRN 56 
                                       5556666777766666666666666666666666666655555 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0077
                       EMP24_GP25L 105 kdsakkekletleselkkleekldsikreqkylrereerlrdt 147
                                       k ++k++   ++e++l+++e +++ +k++ ++lr++ e l + 
  gi|474933909|ref|YP_007687491.1|  63 KVDDKESLAADMEESLETMEIRVRGFKNQEDSLRQKAEALSNS 105
                                       3445555555688888888888888888888888888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3293  (0.183669); expected 358.6 (0.02)
Passed bias filter:                     1418  (0.0790897); expected 358.6 (0.02)
Passed Vit filter:                       239  (0.0133304); expected 17.9 (0.001)
Passed Fwd filter:                        80  (0.00446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              78  [number of targets reported over threshold]
# CPU time: 0.84u 0.31s 00:00:01.14 Elapsed: 00:00:00.50
# Mc/sec: 750.65
//
Query:       gi|474933910|ref|YP_007687492.1|  [L=79]
Description: archaeal conserved hypothetical protein (DUF2144) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-05   23.5   0.2    5.4e-05   23.2   0.2    1.1  1  Pcc1      Transcription factor Pcc1


Domain annotation for each model (and alignments):
>> Pcc1  Transcription factor Pcc1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.2     3e-09   5.4e-05      16      67 ..      15      66 ..       4      71 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 3e-09
                                      HHHHHHHHHCHC-TTECEEEEEEETTEEEEEEEESSHHHHHHHHHHHHHHHH CS
                              Pcc1 16 ialrtLqvDkelsplavkrslslegnvLqveykAttnrmLRvavngfleslg 67
                                      +a+ +L+++     + +k  + +e+ + ++e++A +  ++R+avn+fle + 
  gi|474933910|ref|YP_007687492.1| 15 AAVSALEPEVRRDLPRTKSRIYTEEGDAVLEIEAADTTSMRAAVNSFLECIT 66
                                      677777777444333467777777778999******************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 473.93
//
Query:       gi|474933911|ref|YP_007687493.1|  [L=44]
Description: hypothetical protein TALC_00324 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-06   27.7   2.3      2e-06   27.4   2.3    1.2  1  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
    0.00022   20.7   1.2       0.29   10.8   0.1    2.1  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
    0.00066   19.5   1.6    0.00076   19.3   1.6    1.1  1  C1_1             Phorbol esters/diacylglycerol binding domain
     0.0019   18.0   2.4       0.58   10.0   0.1    2.1  2  ZZ               Zinc finger, ZZ type
     0.0024   17.6   1.0       0.17   11.7   0.2    2.1  2  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
     0.0027   17.4   2.4       0.01   15.5   2.4    1.8  1  zinc_ribbon_2    zinc-ribbon domain
     0.0036   16.8   1.1     0.0047   16.4   1.1    1.3  1  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0037   16.9   1.0     0.0084   15.8   1.0    1.5  1  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
     0.0042   17.0   0.5       0.73    9.8   0.1    2.1  2  zf-dskA_traR     Prokaryotic dksA/traR C4-type zinc finger
     0.0048   16.3   0.8        1.2    8.6   0.1    2.2  2  zf-ribbon_3      zinc-ribbon domain
     0.0051   16.6   1.9       0.84    9.4   0.2    2.2  2  zinc_ribbon_5    zinc-ribbon domain
     0.0055   16.7   0.8     0.0055   16.7   0.8    1.1  1  HypA             Hydrogenase/urease nickel incorporation, met
     0.0084   16.0   2.9        1.5    8.8   0.2    2.2  2  zinc_ribbon_4    zinc-ribbon domain
     0.0088   16.1   2.7      0.018   15.1   2.7    1.5  1  Zn-ribbon_8      Zinc ribbon domain
  ------ inclusion threshold ------
      0.011   15.7   1.4       0.02   14.9   1.4    1.4  1  DZR              Double zinc ribbon
      0.012   15.6   3.0        1.9    8.6   0.2    2.2  2  zf-ACC           Acetyl-coA carboxylase zinc finger domain
      0.016   15.4   1.2      0.016   15.4   1.2    1.0  1  DUF2072          Zn-ribbon containing protein
      0.017   15.1   1.0      0.018   15.0   1.0    1.1  1  zf-C2HC5         Putative zinc finger motif, C2HC5-type
      0.017   15.1   0.7      0.017   15.0   0.7    1.2  1  zinc-ribbons_6   zinc-ribbons
       0.02   14.8   0.2        2.1    8.4   0.0    2.0  2  Ogr_Delta        Ogr/Delta-like zinc finger
      0.022   14.5   1.6       0.34   10.7   0.2    2.1  2  zinc_ribbon_10   Predicted integral membrane zinc-ribbon meta
      0.023   14.3   0.8       0.68    9.7   0.0    2.1  2  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
      0.027   14.4   0.8        2.8    8.0   0.1    2.1  2  ADK_lid          Adenylate kinase, active site lid
      0.029   14.4   0.3       0.03   14.4   0.3    1.1  1  zf-C3HC          C3HC zinc finger-like
       0.03   14.7   1.0          2    8.8   0.0    2.0  2  GFA              Glutathione-dependent formaldehyde-activatin
       0.03   15.0   0.6      0.036   14.8   0.6    1.3  1  zf-3CxxC_2       Zinc-binding domain
      0.036   13.9   1.6        4.7    7.1   0.2    2.1  2  TFIIS_C          Transcription factor S-II (TFIIS)
      0.038   14.1   0.3       0.35   11.0   0.3    2.0  1  YqgC             Uncharacterized YqgC-like
      0.039   14.1   1.6      0.052   13.6   1.6    1.2  1  Ribosomal_L37ae  Ribosomal L37ae protein family
      0.039   13.8   1.0        7.8    6.5   0.0    2.1  2  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
      0.041   13.6   3.5      0.074   12.8   3.4    1.6  1  A2L_zn_ribbon    A2L zinc ribbon domain
      0.041   14.6   0.3      0.048   14.4   0.3    1.2  1  zinc-ribbon_6    zinc-ribbon domain
       0.05   13.5   4.0       0.15   12.0   0.6    2.0  2  DUF951           Bacterial protein of unknown function (DUF95
       0.05   13.8   1.3      0.052   13.7   1.3    1.2  1  NOB1_Zn_bind     Nin one binding (NOB1) Zn-ribbon like
      0.054   13.4   1.3      0.073   13.0   1.3    1.2  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.055   13.2   3.4        1.1    9.0   0.2    2.2  2  Rubredoxin_2     Rubredoxin metal binding domain
      0.077   13.3   1.1      0.083   13.2   1.1    1.1  1  DUF1922          Domain of unknown function (DUF1922)
      0.086   12.9   1.6       0.14   12.2   1.5    1.3  1  DUF1451          Zinc-ribbon containing domain
      0.087   12.8   5.8        2.5    8.2   0.6    2.1  2  YhfH             YhfH-like protein
       0.12   12.9   1.3        8.5    7.1   0.1    2.2  2  zf-C2H2          Zinc finger, C2H2 type
       0.45   11.0   3.6          9    6.9   0.3    2.2  2  Ribosomal_L44    Ribosomal protein L44


Domain annotation for each model (and alignments):
>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   2.3   4.6e-09     2e-06       1      32 []       3      34 ..       3      34 .. 0.99

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 4.6e-09
                                      -B-SSS--B----SSS----SSS-----B--- CS
                    DNA_RNApol_7kD  1 YiCgeCgaevslkkgdpiRCkeCGhRilYKkR 32
                                      Y C++Cg+     ++  ++C +CG++i+ K+R
  gi|474933911|ref|YP_007687493.1|  3 YRCAKCGETIVNTNTMGLQCDKCGSKIFIKER 34
                                      9******************************9 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.1   0.00066      0.29       2      13 ..       2      13 ..       1      18 [. 0.87
   2 !    9.6   0.1    0.0015      0.67       4      17 ..      21      34 ..      19      36 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00066
                            zf_UBZ  2 tylCerCgkeip 13
                                      +y C++Cg++i 
  gi|474933911|ref|YP_007687493.1|  2 QYRCAKCGETIV 13
                                      699******995 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0015
                            zf_UBZ  4 lCerCgkeipesel 17
                                      +C++Cg++i + e+
  gi|474933911|ref|YP_007687493.1| 21 QCDKCGSKIFIKER 34
                                      7*******977766 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   1.6   1.7e-06   0.00076      13      37 ..       4      28 ..       1      32 [. 0.89

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.7e-06
                                      B-TTT-SB--SSSS-EEEETTT--E CS
                              C1_1 13 fCkhCgeflwgkekqglkCswCkll 37
                                      +C++Cge +   ++ gl+C+ C+ +
  gi|474933911|ref|YP_007687493.1|  4 RCAKCGETIVNTNTMGLQCDKCGSK 28
                                      8********88***********865 PP

>> ZZ  Zinc finger, ZZ type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.3    0.0038       1.7       3      16 ..       1      13 [.       1      17 [. 0.74
   2 !   10.0   0.1    0.0013      0.58       3      19 ..      18      34 ..      16      35 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0038
                                      S-EE-TTT-S..EE CS
                                ZZ  3 kkytCdgCseapli 16
                                      ++y C +C+e+ ++
  gi|474933911|ref|YP_007687493.1|  1 MQYRCAKCGET-IV 13
                                      68999999994.33 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0013
                                      S-EE-TTT-S..EESSE CS
                                ZZ  3 kkytCdgCseapligvR 19
                                      ++ +Cd+C++  +i+ R
  gi|474933911|ref|YP_007687493.1| 18 MGLQCDKCGSKIFIKER 34
                                      6789******9888765 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.042        18       3      13 ..       4      14 ..       2      18 .. 0.83
   2 !   11.7   0.2    0.0004      0.17       3      15 ..      21      33 ..      19      38 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.042
                                      E-SSS--EEEE CS
                    zf-C4_Topoisom  3 kCPkCggdLvl 13
                                       C kCg+ +v 
  gi|474933911|ref|YP_007687493.1|  4 RCAKCGETIVN 14
                                      6******9986 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.0004
                                      E-SSS--EEEEEE CS
                    zf-C4_Topoisom  3 kCPkCggdLvlkr 15
                                      +C+kCg+++ +k+
  gi|474933911|ref|YP_007687493.1| 21 QCDKCGSKIFIKE 33
                                      7********9997 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   2.4   2.3e-05      0.01       1      22 [.       4      28 ..       4      29 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.3e-05
                     zinc_ribbon_2  1 fCpnCGaelqdnakF...CpyCGtp 22
                                      +C +CG+++ ++++    C +CG++
  gi|474933911|ref|YP_007687493.1|  4 RCAKCGETIVNTNTMglqCDKCGSK 28
                                      6*************99*******98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   1.1   1.1e-05    0.0047       1      29 [.       3      29 ..       3      36 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.1e-05
                                      EEETTTTCEECHEETSTTCEEESSSSBEE CS
                      TF_Zn_Ribbon  1 ykCPnCgstnlveDpergelvCtdCGlVl 29
                                      y+C +Cg t  ++++++  l C +CG+ +
  gi|474933911|ref|YP_007687493.1|  3 YRCAKCGET--IVNTNTMGLQCDKCGSKI 29
                                      79*****97..9**************986 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   1.0   1.9e-05    0.0084       6      32 .]       5      30 ..       4      30 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.9e-05
                     zf-NADH-PPase  6 CgrCGaptepaeggwarvCpaCglehY 32
                                      C++CG +t+++ + ++++C+ Cg   +
  gi|474933911|ref|YP_007687493.1|  5 CAKCG-ETIVNTNTMGLQCDKCGSKIF 30
                                      9***9.7****************8765 PP

>> zf-dskA_traR  Prokaryotic dksA/traR C4-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.1    0.0017      0.73       6      13 ..       5      12 ..       2      14 .. 0.87
   2 ?    6.0   0.0     0.026        12       4      14 ..      19      30 ..      16      32 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0017
                      zf-dskA_traR  6 CeeCGEpI 13
                                      C++CGE+I
  gi|474933911|ref|YP_007687493.1|  5 CAKCGETI 12
                                      ******99 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.026
                      zf-dskA_traR  4 gs.CeeCGEpIp 14
                                      g  C++CG +I 
  gi|474933911|ref|YP_007687493.1| 19 GLqCDKCGSKIF 30
                                      556*****9985 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1     0.011       4.7       4      11 ..       4      12 ..       1      15 [. 0.67
   2 !    8.6   0.1    0.0028       1.2       4      11 ..      21      29 ..      19      37 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.011
                       zf-ribbon_3  4 rCPnCGa.p 11
                                      rC +CG+ +
  gi|474933911|ref|YP_007687493.1|  4 RCAKCGEtI 12
                                      677777655 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0028
                       zf-ribbon_3  4 rCPnCGa.p 11
                                      +C +CG+ +
  gi|474933911|ref|YP_007687493.1| 21 QCDKCGSkI 29
                                      588888755 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.2    0.0019      0.84      27      33 ..       4      10 ..       2      13 .. 0.87
   2 ?    7.0   0.1     0.011       4.8       3      11 ..      20      28 ..      18      40 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0019
                     zinc_ribbon_5 27 rCakCae 33
                                      rCakC+e
  gi|474933911|ref|YP_007687493.1|  4 RCAKCGE 10
                                      9****98 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.011
                     zinc_ribbon_5  3 irCpdCdtk 11
                                       +C++C++k
  gi|474933911|ref|YP_007687493.1| 20 LQCDKCGSK 28
                                      689999997 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.8   1.3e-05    0.0055      70      95 ..       2      28 ..       1      38 [. 0.84

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.3e-05
                                      EEEETTTS-EEECHHH.HHS-TTTSSS CS
                              HypA 70 kvrCreCgkefeleek.alrCpkCgsa 95
                                      ++rC +Cg+++  +++  l+C kCgs+
  gi|474933911|ref|YP_007687493.1|  2 QYRCAKCGETIVNTNTmGLQCDKCGSK 28
                                      789*****99997765689******96 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.2    0.0052       2.3      27      35 ..       4      12 ..       1      13 [. 0.81
   2 !    8.8   0.2    0.0035       1.5      22      35 ..      16      29 ..      13      31 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0052
                     zinc_ribbon_4 27 rCskCghvF 35
                                      rC+kCg+++
  gi|474933911|ref|YP_007687493.1|  4 RCAKCGETI 12
                                      899999886 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0035
                     zinc_ribbon_4 22 kgvkvrCskCghvF 35
                                      +++ ++C kCg ++
  gi|474933911|ref|YP_007687493.1| 16 NTMGLQCDKCGSKI 29
                                      56668999998765 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   2.7   4.2e-05     0.018       5      35 ..       2      28 ..       2      32 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.2e-05
                       Zn-ribbon_8  5 eYrCeeCghefevlqsisdapltaCPeCgse 35
                                      +YrC +Cg++     ++      +C +Cgs+
  gi|474933911|ref|YP_007687493.1|  2 QYRCAKCGETIVNTNTMG----LQCDKCGSK 28
                                      6*******6666665554....56*****95 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   1.4   4.6e-05      0.02      15      37 ..       5      28 ..       2      35 .. 0.50

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.6e-05
                               DZR 15 CseCgtklkavaa.edrCpsCgek 37
                                      C +Cg+++ ++++   +C++Cg+k
  gi|474933911|ref|YP_007687493.1|  5 CAKCGETIVNTNTmGLQCDKCGSK 28
                                      555555543333334455555544 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.2    0.0043       1.9       3      12 ..       4      13 ..       3      16 .. 0.85
   2 ?    7.9   0.3    0.0072       3.2       3      14 ..      21      32 ..      20      33 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0043
                            zf-ACC  3 KCpsCgemly 12
                                      +C +Cge++ 
  gi|474933911|ref|YP_007687493.1|  4 RCAKCGETIV 13
                                      6******985 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0072
                            zf-ACC  3 KCpsCgemlykk 14
                                      +C++Cg+ ++ k
  gi|474933911|ref|YP_007687493.1| 21 QCDKCGSKIFIK 32
                                      8*****988755 PP

>> DUF2072  Zn-ribbon containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   1.2   3.8e-05     0.016       3      36 ..       4      34 ..       2      44 .] 0.80

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.8e-05
                           DUF2072  3 kCtkCekvfedgskeilkGCpsCGgkkFlyvkee 36
                                      +C+kC++++ + ++ +   C +CG k F   ke+
  gi|474933911|ref|YP_007687493.1|  4 RCAKCGETIVNTNT-MGLQCDKCGSKIFI--KER 34
                                      8**********999.9999*******885..444 PP

>> zf-C2HC5  Putative zinc finger motif, C2HC5-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   1.0   4.2e-05     0.018      19      48 ..       4      33 ..       1      38 [. 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.2e-05
                          zf-C2HC5 19 nClnCGkiiCakeglskpCsfCgspllsse 48
                                       C +CG  i + + +  +C  Cgs+++ +e
  gi|474933911|ref|YP_007687493.1|  4 RCAKCGETIVNTNTMGLQCDKCGSKIFIKE 33
                                      6************999********998765 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.7     4e-05     0.017       2      26 ..       4      29 ..       1      41 [. 0.73

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4e-05
                                      --SSS-S--E.E-SSEEE-TTT--EE CS
                    zinc-ribbons_6  2 kCpeCqqele.krgeqyhCeaCqedl 26
                                       C +C + ++ +++  ++C++C +++
  gi|474933911|ref|YP_007687493.1|  4 RCAKCGETIVnTNTMGLQCDKCGSKI 29
                                      47778777776677777888887654 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1     0.051        22       1      14 [.       4      17 ..       4      21 .. 0.81
   2 ?    8.4   0.0    0.0048       2.1       2      22 ..      22      42 ..      21      43 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.051
                         Ogr_Delta  1 rCPhCgapaaarts 14
                                      rC +Cg+ ++ +++
  gi|474933911|ref|YP_007687493.1|  4 RCAKCGETIVNTNT 17
                                      7*****99888777 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0048
                         Ogr_Delta  2 CPhCgapaaartsrnlskdvr 22
                                      C +Cg+++ +  + n+ k+++
  gi|474933911|ref|YP_007687493.1| 22 CDKCGSKIFIKERPNIKKTLK 42
                                      99**************99987 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   0.00078      0.34      43      53 ..       1      11 [.       1      12 [. 0.87
   2 ?    3.5   0.1      0.13        59      19      30 ..      16      27 ..      13      29 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00078
                    zinc_ribbon_10 43 vkyrCpkCgal 53
                                      ++yrC+kCg++
  gi|474933911|ref|YP_007687493.1|  1 MQYRCAKCGET 11
                                      69*******86 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.13
                    zinc_ribbon_10 19 nryalICskChs 30
                                      n + l C kC s
  gi|474933911|ref|YP_007687493.1| 16 NTMGLQCDKCGS 27
                                      555555666654 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.2      0.13        55       6      13 ..       4      11 ..       4      15 .. 0.80
   2 ?    9.7   0.0    0.0016      0.68       3      15 ..      18      30 ..      16      33 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.13
                           zf-RRN7  6 pCgvCgcr 13
                                      +C+ Cg +
  gi|474933911|ref|YP_007687493.1|  4 RCAKCGET 11
                                      79999986 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0016
                           zf-RRN7  3 kgppCgvCgcrsf 15
                                      +g +C+ Cg++ f
  gi|474933911|ref|YP_007687493.1| 18 MGLQCDKCGSKIF 30
                                      7899*****9988 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1     0.042        18      24      31 ..       5      12 ..       2      14 .. 0.69
   2 ?    8.0   0.1    0.0063       2.8      24      31 ..      22      29 ..      19      33 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.042
                                      -TTT--.- CS
                           ADK_lid 24 CDkCGepL 31
                                      C kCGe+ 
  gi|474933911|ref|YP_007687493.1|  5 CAKCGETI 12
                                      77777765 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0063
                                      -TTT--.- CS
                           ADK_lid 24 CDkCGepL 31
                                      CDkCG++ 
  gi|474933911|ref|YP_007687493.1| 22 CDKCGSKI 29
                                      *****986 PP

>> zf-C3HC  C3HC zinc finger-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.3   6.8e-05      0.03      29      63 ..       3      39 ..       1      44 [] 0.73

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6.8e-05
                           zf-C3HC 29 lkcAkrGWkcvs..kdrlkCevCgaslvlklksseee 63
                                      ++cAk G + v+     l+C+ Cg+++ +k  +++++
  gi|474933911|ref|YP_007687493.1|  3 YRCAKCGETIVNtnTMGLQCDKCGSKIFIKERPNIKK 39
                                      899999987755216679***********96555544 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.2     0.033        15      49      64 ..       2      17 ..       1      21 [. 0.80
   2 ?    8.8   0.0    0.0046         2      51      66 ..      21      36 ..      14      41 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.033
                               GFA 49 rsfCpeCgsplysees 64
                                      ++ C +Cg +++ +++
  gi|474933911|ref|YP_007687493.1|  2 QYRCAKCGETIVNTNT 17
                                      689*******997554 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0046
                               GFA 51 fCpeCgsplyseesaa 66
                                       C++Cgs+++ +e+++
  gi|474933911|ref|YP_007687493.1| 21 QCDKCGSKIFIKERPN 36
                                      6*********986654 PP

>> zf-3CxxC_2  Zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.6   8.2e-05     0.036       7      41 ..       2      33 ..       1      44 [] 0.81

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 8.2e-05
                        zf-3CxxC_2  7 efkCekCgkeWsSanafaneaQeCkkCkekvepyk 41
                                      +++C kCg++ + +n+   ++ +C kC++k+  ++
  gi|474933911|ref|YP_007687493.1|  2 QYRCAKCGETIVNTNT---MGLQCDKCGSKIFIKE 33
                                      7**********99985...8899*****9997554 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.2     0.011       4.7      29      36 ..       3      10 ..       1      12 [. 0.82
   2 ?    6.4   0.1     0.018       7.9       2       9 ..      21      28 ..      16      31 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.011
                           TFIIS_C 29 ykCtkCgh 36
                                      y+C+kCg+
  gi|474933911|ref|YP_007687493.1|  3 YRCAKCGE 10
                                      99999997 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.018
                           TFIIS_C  2 kCpkCgsr 9 
                                      +C kCgs+
  gi|474933911|ref|YP_007687493.1| 21 QCDKCGSK 28
                                      68888775 PP

>> YqgC  Uncharacterized YqgC-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.3   0.00081      0.35       8      24 ..       1      18 [.       1      40 [. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00081
                              YqgC  8 mqsRDaeCGerir.tRtv 24
                                      mq R a CGe i  t t+
  gi|474933911|ref|YP_007687493.1|  1 MQYRCAKCGETIVnTNTM 18
                                      9*********98537777 PP

>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.6   0.00012     0.052      33      61 ..       2      29 ..       1      30 [. 0.92

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00012
                                      -BEESSSSSSEEEEEETTEEEETTTTEEE CS
                   Ribosomal_L37ae 33 kytCpfcgktkvkRkavgiwkCkkcgktv 61
                                      +y+C++cg+t v+ + +g+ +C+kcg ++
  gi|474933911|ref|YP_007687493.1|  2 QYRCAKCGETIVNTNTMGL-QCDKCGSKI 29
                                      7*****************7.8****9875 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.2     0.018       7.9      13      20 ..       4      11 ..       3      13 .. 0.82
   2 ?    6.5   0.0     0.018       7.8      10      19 ..      18      27 ..      17      33 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.018
                           DUF35_N 13 rCpdCGtv 20
                                      rC++CG  
  gi|474933911|ref|YP_007687493.1|  4 RCAKCGET 11
                                      9****986 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.018
                           DUF35_N 10 vgqrCpdCGt 19
                                      +g +C++CG+
  gi|474933911|ref|YP_007687493.1| 18 MGLQCDKCGS 27
                                      7889****96 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   3.4   0.00017     0.074       3      29 ..       2      27 ..       1      29 [. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00017
                     A2L_zn_ribbon  3 lkvCsvCggngilnseqgylvCieCga 29
                                      ++ C +Cg + i+n++  +l+C +Cg+
  gi|474933911|ref|YP_007687493.1|  2 QYRCAKCG-ETIVNTNTMGLQCDKCGS 27
                                      57799995.8999*************7 PP

>> zinc-ribbon_6  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.3   0.00011     0.048       2      25 ..       3      29 ..       2      43 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 0.00011
                     zinc-ribbon_6  2 feCeqCgqllffens...sClkCgaal 25
                                      ++C++Cg+++   n+   +C kCg+++
  gi|474933911|ref|YP_007687493.1|  3 YRCAKCGETIVNTNTmglQCDKCGSKI 29
                                      99**********997444688898887 PP

>> DUF951  Bacterial protein of unknown function (DUF951)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.2      0.16        70      32      41 ..       4      13 ..       1      18 [. 0.83
   2 ?   12.0   0.6   0.00035      0.15      29      52 ..      18      42 ..      16      43 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.16
                            DUF951 32 kClgcgrevm 41
                                      +C +cg+ ++
  gi|474933911|ref|YP_007687493.1|  4 RCAKCGETIV 13
                                      8*****9986 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00035
                            DUF951 29 iklkClgcgrevm.lpRskfekkik 52
                                      + l+C +cg ++   +R +++k +k
  gi|474933911|ref|YP_007687493.1| 18 MGLQCDKCGSKIFiKERPNIKKTLK 42
                                      679*******999347999999988 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.3   0.00012     0.052       9      36 ..       3      32 ..       1      43 [. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00012
                      NOB1_Zn_bind  9 lrChaCfkvt..kdmtkkFCpkCGnktLkr 36
                                      +rC  C +++  +++    C+kCG+k   +
  gi|474933911|ref|YP_007687493.1|  3 YRCAKCGETIvnTNTMGLQCDKCGSKIFIK 32
                                      79*****988545577789*****997766 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.3   0.00017     0.073      30      55 ..       4      28 ..       3      30 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00017
                    OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfe 55
                                      +C++Cg++  +  ++  ++C++Cg +
  gi|474933911|ref|YP_007687493.1|  4 RCAKCGETIVN-TNTMGLQCDKCGSK 28
                                      6**********.9***********86 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.2    0.0026       1.1       1       9 [.       3      11 ..       3      13 .. 0.90
   2 ?    5.2   0.4     0.041        18       2       8 ..      21      27 ..      21      29 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0026
                      Rubredoxin_2  1 YvCsqCGfe 9 
                                      Y+C +CG +
  gi|474933911|ref|YP_007687493.1|  3 YRCAKCGET 11
                                      9******75 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.041
                      Rubredoxin_2  2 vCsqCGf 8 
                                      +C++CG+
  gi|474933911|ref|YP_007687493.1| 21 QCDKCGS 27
                                      6999986 PP

>> DUF1922  Domain of unknown function (DUF1922)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.1   0.00019     0.083       4      40 ..       3      40 ..       1      44 [] 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00019
                                      EEET.TS--EEEETT-SEEEETTTEEEE--SSS-BS-- CS
                           DUF1922  4 fRCd.CGRvlYakegaktrkCvCGktikvkerrilkka 40
                                      +RC  CG ++   +++  +   CG +i +ker  +kk+
  gi|474933911|ref|YP_007687493.1|  3 YRCAkCGETIVNTNTMGLQCDKCGSKIFIKERPNIKKT 40
                                      9**99*****999999888889*********9877776 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.5   0.00033      0.14     115     144 ..       3      31 ..       2      35 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00033
                           DUF1451 115 lvCekCgkelalkkteeippCpkCgateFr 144
                                       ++C+kCg+++  ++t  + +C kCg++ F 
  gi|474933911|ref|YP_007687493.1|   3 YRCAKCGETIVNTNTMGL-QCDKCGSKIFI 31 
                                       68*****99877777776.7******9996 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   5.6     0.016       6.8      16      37 .]       5      25 ..       3      25 .. 0.85
   2 ?    8.2   0.6    0.0057       2.5      15      23 ..      21      29 ..      14      34 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.016
                              YhfH 16 CteCGkeieEqaecYgneCekC 37
                                      C++CG+ i       g +C+kC
  gi|474933911|ref|YP_007687493.1|  5 CAKCGETIVNT-NTMGLQCDKC 25
                                      ********976.5679999999 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0057
                              YhfH 15 kCteCGkei 23
                                      +C +CG++i
  gi|474933911|ref|YP_007687493.1| 21 QCDKCGSKI 29
                                      7*****997 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1     0.019       8.5       1       9 [.       3      11 ..       3      18 .. 0.83
   2 ?    5.4   0.1     0.066        29       2      10 ..      21      30 ..      20      34 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.019
                                      EEETTTTEE CS
                           zf-C2H2  1 ykCpdCgks 9 
                                      y+C +Cg++
  gi|474933911|ref|YP_007687493.1|  3 YRCAKCGET 11
                                      9******87 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.066
                                      EETTTT.EEE CS
                           zf-C2H2  2 kCpdCg.ksF 10
                                      +C++Cg k F
  gi|474933911|ref|YP_007687493.1| 21 QCDKCGsKIF 30
                                      8****98777 PP

>> Ribosomal_L44  Ribosomal protein L44
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.2      0.03        13      53      65 ..       2      14 ..       1      18 [. 0.85
   2 ?    6.9   0.3      0.02         9      53      65 ..      19      31 ..      13      42 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.03
                                      EEEETTT--EEE- CS
                     Ribosomal_L44 53 rleCteCkkkrlk 65
                                      +++C +C++++++
  gi|474933911|ref|YP_007687493.1|  2 QYRCAKCGETIVN 14
                                      79******99886 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.02
                                      EEEETTT--EEE- CS
                     Ribosomal_L44 53 rleCteCkkkrlk 65
                                       l+C +C++k++ 
  gi|474933911|ref|YP_007687493.1| 19 GLQCDKCGSKIFI 31
                                      699******9864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                        41  (0.0022868); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              41  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 282.63
//
Query:       gi|474933912|ref|YP_007687494.1|  [L=92]
Description: LSU ribosomal protein L37AE [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.2e-28   96.3   5.0    9.4e-28   96.1   5.0    1.0  1  Ribosomal_L37ae  Ribosomal L37ae protein family
    1.6e-05   24.7   4.9    2.5e-05   24.2   4.9    1.3  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
     0.0019   18.1   0.9     0.0025   17.7   0.9    1.3  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
     0.0024   17.9   1.8       0.11   12.7   0.2    2.2  2  Zn-ribbon_8      Zinc ribbon domain
     0.0065   16.4   0.4     0.0094   15.9   0.4    1.3  1  zinc-ribbons_6   zinc-ribbons
  ------ inclusion threshold ------
      0.012   15.5   0.7      0.077   12.9   0.1    2.1  2  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
      0.068   13.2   2.1        4.5    7.3   0.4    2.1  2  HypA             Hydrogenase/urease nickel incorporation, met
      0.069   13.6   7.4        1.6    9.3   0.4    2.3  2  zf-H2C2_2        Zinc-finger double domain
       0.23   11.6   7.9        1.7    8.8   7.9    2.0  1  UPF0547          Uncharacterised protein family UPF0547
       0.24   11.8   6.6        1.9    8.9   0.5    2.4  2  DUF4379          Probable Zinc-ribbon domain
          2    8.2   7.9       0.62    9.8   0.6    2.2  2  Rubredoxin_2     Rubredoxin metal binding domain


Domain annotation for each model (and alignments):
>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.1   5.0   5.7e-31   9.4e-28       1      74 [.       4      77 ..       4      90 .. 0.92

  Alignments for each domain:
  == domain 1  score: 96.1 bits;  conditional E-value: 5.7e-31
                                      XXXXXX-GGGGTTSS-HHHHHHHHHHHHHHHS-BEESSSSSSEEEEEETTEEEETTTTEEEE-BSSSSS-HHHH CS
                   Ribosomal_L37ae  1 rtkkvgiaGkygtrYGaslrkrvkkieisqhakytCpfcgktkvkRkavgiwkCkkcgktvaGgAytpettsak 74
                                      rt+k g+aG++g+rYG+ +r+rvk+ie++q+ k++Cp+c++ +v R+++giw+C++cg+++a+ Ay+p+ ++ +
  gi|474933912|ref|YP_007687494.1|  4 RTQKAGTAGRFGARYGVVVRNRVKSIEAHQKMKHECPTCHHASVTRVSAGIWECRHCGYKFAAEAYSPRVKKTT 77
                                      79******************************************************************766554 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   4.9   1.5e-08   2.5e-05      19      45 ..      37      62 ..      31      63 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.5e-08
                     Zn_Tnp_IS1595 19 fvCPhCgsrkayriktrglfqCkeCrk 45
                                      + CP C++++++r+++ g ++C++C++
  gi|474933912|ref|YP_007687494.1| 37 HECPTCHHASVTRVSA-GIWECRHCGY 62
                                      78*************9.********98 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.9   1.5e-06    0.0025      30      58 ..      38      66 ..      17      70 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.5e-06
                    OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfeadr 58
                                      +C+ C + + +++s   ++C++Cg+++ +
  gi|474933912|ref|YP_007687494.1| 38 ECPTCHHASVTRVSAGIWECRHCGYKFAA 66
                                      8************************9876 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.2   6.6e-05      0.11      16      39 ..      30      50 ..      24      51 .. 0.73
   2 ?    4.8   0.1     0.019        32       7      16 ..      56      65 ..      55      76 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.6e-05
                       Zn-ribbon_8 16 evlqsisdaplta.CPeCgs.evrrv 39
                                      e+ q+++     + CP+C++  v+rv
  gi|474933912|ref|YP_007687494.1| 30 EAHQKMK-----HeCPTCHHaSVTRV 50
                                      4555544.....44******999997 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.019
                       Zn-ribbon_8  7 rCeeCghefe 16
                                      +C+ Cg +f 
  gi|474933912|ref|YP_007687494.1| 56 ECRHCGYKFA 65
                                      7999*99996 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.4   5.8e-06    0.0094       2      44 ..      38      82 ..      30      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.8e-06
                                      --SSS-S--EE-S..SEEE-TTT--EEEEEEE-SSS-S---EEEE CS
                    zinc-ribbons_6  2 kCpeCqqelekrg..eqyhCeaCqedlkkealCpeCeqelevlka 44
                                      +Cp+C+++ ++r      +C++C  ++  ea+ p+ ++   v+k 
  gi|474933912|ref|YP_007687494.1| 38 ECPTCHHASVTRVsaGIWECRHCGYKFAAEAYSPRVKKTTGVVKG 82
                                      6******99955534789****************99888777765 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.24   3.9e+02      23      27 ..      38      42 ..      30      45 .. 0.68
   2 ?   12.9   0.1   4.7e-05     0.077      22      34 ..      55      67 ..      46      69 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.24
                                      EESSS CS
                    RNA_POL_M_15KD 23 eCrqC 27
                                      eC +C
  gi|474933912|ref|YP_007687494.1| 38 ECPTC 42
                                      66666 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 4.7e-05
                                      EEESSSS-EEESS CS
                    RNA_POL_M_15KD 22 feCrqCgYeepad 34
                                       eCr CgY++ a+
  gi|474933912|ref|YP_007687494.1| 55 WECRHCGYKFAAE 67
                                      79*******9776 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.4    0.0027       4.5      81     100 ..      30      50 ..      19      53 .. 0.71
   2 ?    6.1   0.1    0.0067        11      71      90 ..      55      71 ..      50      91 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0027
                                       ECHHH.HHS-TTTSSS-EEEE CS
                              HypA  81 eleek.alrCpkCgsadveiv 100
                                       e ++k + +Cp+C++a+v+ v
  gi|474933912|ref|YP_007687494.1|  30 EAHQKmKHECPTCHHASVTRV 50 
                                       333334679*****9998866 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0067
                                      EEETTTS-EEECHHHHHS-T CS
                              HypA 71 vrCreCgkefeleekalrCp 90
                                       +Cr+Cg++f  e++    p
  gi|474933912|ref|YP_007687494.1| 55 WECRHCGYKFAAEAY---SP 71
                                      78********97643...34 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   1.8     0.002       3.3      10      25 ..      32      47 ..      29      48 .. 0.80
   2 ?    9.3   0.4   0.00096       1.6      14      25 ..      54      65 ..      43      66 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.002
                         zf-H2C2_2 10 tgekpyeCplCdkaFk 25
                                      +++ ++eCp C+ a +
  gi|474933912|ref|YP_007687494.1| 32 HQKMKHECPTCHHASV 47
                                      56678******98765 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00096
                         zf-H2C2_2 14 pyeCplCdkaFk 25
                                      ++eC  C+++F+
  gi|474933912|ref|YP_007687494.1| 54 IWECRHCGYKFA 65
                                      58*********6 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   7.9    0.0011       1.7       3      25 ..      39      65 ..      37      66 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0011
                           UPF0547  3 CPeCea....kvPvaaqfCphCGyvFq 25
                                      CP C +     v++   +C+hCGy F 
  gi|474933912|ref|YP_007687494.1| 39 CPTCHHasvtRVSAGIWECRHCGYKFA 65
                                      88887422226888889********96 PP

>> DUF4379  Probable Zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.7     0.007        11      23      43 ..      30      50 ..      24      54 .. 0.78
   2 ?    8.9   0.5    0.0012       1.9      29      44 ..      54      69 ..      46      79 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.007
                           DUF4379 23 gskkkvwWkCakCgheWeasv 43
                                        ++k+   C++C+h   ++v
  gi|474933912|ref|YP_007687494.1| 30 EAHQKMKHECPTCHHASVTRV 50
                                      468899999****99766666 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0012
                           DUF4379 29 wWkCakCgheWeasvs 44
                                       W C++Cg+++ a+ +
  gi|474933912|ref|YP_007687494.1| 54 IWECRHCGYKFAAEAY 69
                                      6*******99988755 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   1.5      0.11   1.8e+02      17      22 ..      39      44 ..      38      44 .. 0.88
   2 ?    9.8   0.6   0.00038      0.62       1      11 [.      55      65 ..      55      66 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.11
                      Rubredoxin_2 17 CpsCgs 22
                                      Cp C++
  gi|474933912|ref|YP_007687494.1| 39 CPTCHH 44
                                      ****96 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00038
                      Rubredoxin_2  1 YvCsqCGfesa 11
                                      ++C++CG+++a
  gi|474933912|ref|YP_007687494.1| 55 WECRHCGYKFA 65
                                      79******976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 588.30
//
Query:       gi|474933913|ref|YP_007687495.1|  [L=260]
Description: RNase PH-related exoribonuclease [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.4e-27   96.8   0.0    5.4e-27   94.9   0.0    1.8  2  RNase_PH    3' exoribonuclease family, domain 1
    4.2e-10   39.5   0.0    1.7e-09   37.5   0.0    2.0  2  RNase_PH_C  3' exoribonuclease family, domain 2


Domain annotation for each model (and alignments):
>> RNase_PH  3' exoribonuclease family, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.9   0.0     6e-31   5.4e-27       1     132 []      31     166 ..      31     166 .. 0.94
   2 ?   -0.7   0.0      0.21   1.9e+03      51      86 ..     215     249 ..     188     251 .. 0.66

  Alignments for each domain:
  == domain 1  score: 94.9 bits;  conditional E-value: 6e-31
                                       EEEEEEEEESSSSTTSEEEEEEECCEEEEEEEEEEEEEE-TCCG.--CCEEEECCCCECCCCEC-C...S...HHHH CS
                          RNase_PH   1 elRslsietgvlsqanGSaylelGdtkvlasvtgpieerpseer.ddaegaldveveyapfasgerrregrpsdeei 76 
                                       e+Rs+++etg++++a+GSa++elGdt v+a+v+    + p +++    +g+l++ +e+ p+a + ++  g p++ +i
  gi|474933913|ref|YP_007687495.1|  31 EFRSIKVETGLIESADGSARVELGDTVVMAGVKIVPGV-PYPDApG--DGTLTTGMELLPMAHPMFEP-GPPDENAI 103
                                       89*******************************99988.6777533..478***************77.9******* PP

                                       HHHHHHHHHHCCTC-C........CGCCTCEEEEEEEEEECCCS-CHHHCHHHHHHHHHCTCEE CS
                          RNase_PH  77 elsrlleralrpsill........ekkpkstididitvlssdggslldalinaaslALadagip 132
                                       e++r+++r +r+s+++        e+++ + + +d++ +++dg +l+da+ +a+ +AL +a ip
  gi|474933913|ref|YP_007687495.1| 104 EMARVVDRGIRESGMIdvkklcikEGESIWMVFLDLYAINHDG-NLFDAATIASVCALRTATIP 166
                                       ***************99999999999999**************.*****************998 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.21
                                       EECCCCECCCCEC-C.........S...HHHHHHHHHHHHHH CS
                          RNase_PH  51 ldveveyapfasger......rregrpsdeeielsrlleral 86 
                                       l+v  +        +      +++gr s +  +ls  l+ra+
  gi|474933913|ref|YP_007687495.1| 215 LTVTTDE-------NgnyramQKGGRGSITRGDLSLCLDRAV 249
                                       4444443.......1333345667999999999999999986 PP

>> RNase_PH_C  3' exoribonuclease family, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.38   3.4e+03      50      64 ..       7      21 ..       6      23 .. 0.83
   2 !   37.5   0.0   1.9e-13   1.7e-09       2      65 ..     186     249 ..     185     251 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.38
                                      SCEEHHHHHHHHHHH CS
                        RNase_PH_C 50 sqldeetlleaielA 64
                                      sq+++++ll+ +  +
  gi|474933913|ref|YP_007687495.1|  7 SQIRRDHLLNLLAEG 21
                                      6799*****999877 PP

  == domain 2  score: 37.5 bits;  conditional E-value: 1.9e-13
                                       --EEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTSEEEEEEEECSSC.EEHHHHHHHHHHHH CS
                        RNase_PH_C   2 pviavtvgkvddqfvlDptkeEedlsegdltlavagtkevvtlmkeggsq.ldeetlleaielAk 65 
                                       ++i+vt  k+++++++Dp+ +Ee++++++lt++ +++++    m+ gg + +++ +l  +++ A 
  gi|474933913|ref|YP_007687495.1| 186 LPISVTEHKIGNDLIVDPNFDEEAIATARLTVTTDENGNY-RAMQKGGRGsITRGDLSLCLDRAV 249
                                       7999999*********************************.5555555555******99999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1701.99
//
Query:       gi|474933914|ref|YP_007687496.1|  [L=247]
Description: ribosomal RNA-processing protein RRP41/SKI6 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-33  116.4   0.1    1.6e-33  116.0   0.1    1.2  1  RNase_PH    3' exoribonuclease family, domain 1
    4.2e-15   55.5   0.1    7.9e-15   54.6   0.1    1.5  1  RNase_PH_C  3' exoribonuclease family, domain 2


Domain annotation for each model (and alignments):
>> RNase_PH  3' exoribonuclease family, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.0   0.1   1.8e-37   1.6e-33       2     132 .]      25     153 ..      24     153 .. 0.94

  Alignments for each domain:
  == domain 1  score: 116.0 bits;  conditional E-value: 1.8e-37
                                       EEEEEEEESSSSTTSEEEEEEECCEEEEEEEEEEEEEE-TCCG--CCEEEECCCCECCCCEC-C...S...HHHHHH CS
                          RNase_PH   2 lRslsietgvlsqanGSaylelGdtkvlasvtgpieerpseerddaegaldveveyapfasgerrregrpsdeeiel 78 
                                        R++++e gvl++a+GS+yle+G++kvl++v+gp+e r +  +d+ + +++v+++++ ++  +r+r   ++++++e+
  gi|474933914|ref|YP_007687496.1|  25 KRNIKVEAGVLKNADGSCYLEVGKNKVLCAVYGPRECRMRHLQDPTKAVITVKYNMQTYSVSDRKR-PGTDRRSVEI 100
                                       59***********************************766665666678***********999977.469******* PP

                                       HHHHHHHHCCTC-CCGCCTCEEEEEEEEEECCCS-CHHHCHHHHHHHHHCTCEE CS
                          RNase_PH  79 srlleralrpsillekkpkstididitvlssdggslldalinaaslALadagip 132
                                       s+l+ +al++++l+e +p+stidi+i++l+++  ++  a  +aas+ALadagip
  gi|474933914|ref|YP_007687496.1| 101 SKLISEALESVVLTELFPRSTIDIYIEILQANA-GTRCAGLTAASVALADAGIP 153
                                       *********************************.*******************9 PP

>> RNase_PH_C  3' exoribonuclease family, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6   0.1   8.8e-19   7.9e-15       2      67 .]     157     221 ..     156     221 .. 0.96

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 8.8e-19
                                       --EEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTSEEEEEEEECSSCEEHHHHHHHHHHHHHH CS
                        RNase_PH_C   2 pviavtvgkvddqfvlDptkeEedlsegdltlavagtkevvtlmkeggsqldeetlleaielAkkg 67 
                                       +v a+++gk d++++lD++keE++++++d++la+  + ++++l++++g+ +++e+l  ++++A k+
  gi|474933914|ref|YP_007687496.1| 157 IVPAIACGKADGHVLLDLNKEEDNYGQADVPLAIIPSTDEIVLLQMDGN-MTREELDYGLDMAFKA 221
                                       6789*********************************************.*************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1681.09
//
Query:       gi|474933915|ref|YP_007687497.1|  [L=240]
Description: RNA-binding protein Rrp4 and related proteins (containing S1 domain and KH domain) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-08   33.9   0.0    4.1e-08   32.9   0.0    1.5  1  ECR1_N    Exosome complex exonuclease RRP4 N-terminal region
    1.2e-07   32.0   0.2      2e-07   31.2   0.2    1.4  1  KH_6      KH domain
    2.8e-07   30.2   2.8    5.5e-07   29.3   2.8    1.5  1  KH_1      KH domain
    3.9e-05   23.9   0.0    8.6e-05   22.8   0.0    1.6  1  S1        S1 RNA binding domain
    0.00016   21.5   2.5    0.00016   21.5   2.5    2.1  2  KH_2      KH domain
  ------ inclusion threshold ------
      0.015   15.2   0.8      0.031   14.1   0.8    1.6  1  KH_4      KH domain


Domain annotation for each model (and alignments):
>> ECR1_N  Exosome complex exonuclease RRP4 N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0   1.4e-11   4.1e-08       2      36 ..      13      47 ..      13      49 .. 0.95

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 1.4e-11
                                      E-TT-EEEETTTSEE-TTEEEETTEEEESSSEEEE CS
                            ECR1_N  2 VtPGevlttdeefmrGhGTYvrggtiyAsvaGtve 36
                                      V+PG+vl++++ef++G++ Y+ +g+i+A v+G+ +
  gi|474933915|ref|YP_007687497.1| 13 VLPGDVLADADEFKAGENAYELDGKIRAEVLGIKT 47
                                      99******************************865 PP

>> KH_6  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.2   6.7e-11     2e-07       1      43 [.     146     191 ..     146     194 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 6.7e-11
                              KH_6   1 GmlfeVslslvrRll...nhvLeeLgkagpfeiavGlNGriWvkse 43 
                                       G+++e+  +++ R++     ++++L+   ++ i+vG+NGriW+++e
  gi|474933915|ref|YP_007687497.1| 146 GQIIEIDHNKISRVIgkgGSMIQMLKNMTDCRITVGQNGRIWIDGE 191
                                       899************777444466766699*************986 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   2.8   1.8e-10   5.5e-07       3      64 ..     148     202 ..     146     207 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 1.8e-10
                                       EEEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEESHHHHHHHHHHH CS
                              KH_1   3 rilvPsslvgriIGkgGsnIkeIreetgakIkvpksedegsderevtisGspeavekAkeli 64 
                                        i++++++++r+IGkgGs+I+ +++ t ++I+v  +      +  + i G+ e+   A+++i
  gi|474933915|ref|YP_007687497.1| 148 IIEIDHNKISRVIGKGGSMIQMLKNMTDCRITVG-Q------NGRIWIDGEGENATVAAAAI 202
                                       579*****************************75.3......34699988666666666655 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   2.9e-08   8.6e-05       2      75 .]      64     136 ..      63     136 .. 0.95

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 2.9e-08
                                       STTTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEEEEC CS
                                S1   2 pekgevveGeVtsvtkgGafVelgngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriilsik 75 
                                       pe+g+ v G++++v + +  +++ ++  + +++se+++++   d +  l+++d v +kvl vd++++ i++++k
  gi|474933915|ref|YP_007687497.1|  64 PETGDTVIGVISDVGPSNWMIDINAPYPAPLHVSEVPWKVEFGDTTSFLTMEDVVLLKVLSVDETKK-ISVTMK 136
                                       799************************************888888889******************9.999876 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   2.5   5.2e-08   0.00016      11      69 ..     134     189 ..     125     193 .. 0.85
   2 ?    0.1   0.1      0.25   7.4e+02      45      56 ..     200     211 ..     198     220 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 5.2e-08
                                       ECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEEE CS
                              KH_2  11 kkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkkVkln 69 
                                       ++++ +  +I   + + ii i  ++  +vIGkgGs+i++++     +i + ++++++++
  gi|474933915|ref|YP_007687497.1| 134 TMKDSGLRKI---EGGQIIEIDHNKISRVIGKGGSMIQMLKNMTDCRITVGQNGRIWID 189
                                       4555666667...6799********************************9999999986 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.25
                                       HHHHHHHHHHHH CS
                              KH_2  45 snikkigkelrk 56 
                                       + ikki++e+r 
  gi|474933915|ref|YP_007687497.1| 200 AAIKKIEEEARS 211
                                       579*****9996 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.8     1e-05     0.031      13      58 ..     126     174 ..     118     186 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1e-05
                              KH_4  13 ddpeevevtee...eeeeeveielnvegedlGrvIGkrGrtldAlqylv 58 
                                       d+ ++++vt++     + e    ++++ +++ rvIGk G +++ l+ ++
  gi|474933915|ref|YP_007687497.1| 126 DETKKISVTMKdsgLRKIEGGQIIEIDHNKISRVIGKGGSMIQMLKNMT 174
                                       55556666666322222334457999****************9888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1508.02
//
Query:       gi|474933916|ref|YP_007687498.1|  [L=232]
Description: conserved hypothetical protein TIGR00291 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-21   74.5   0.0    9.4e-21   73.7   0.0    1.4  1  SBDS      Shwachman-Bodian-Diamond syndrome (SBDS) protein
    3.7e-18   65.6   0.0    6.2e-18   64.9   0.0    1.4  1  SBDS_C    SBDS protein C-terminal domain


Domain annotation for each model (and alignments):
>> SBDS  Shwachman-Bodian-Diamond syndrome (SBDS) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.7   0.0   1.1e-24   9.4e-21       3      88 .]       8      93 ..       6      93 .. 0.97

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 1.1e-24
                                      EEEEEEETTEEEEEEE-HHHHHHHHCTT---HHHHBSSSS-EEETTTTEE--HHHHHHHHS---HHHHHHHHHHHSEEE CS
                              SBDS  3 sivrykkgkkrFeiavyknklleyregkeidLsevlqsekiFtnaskGetaskselekafgteskdeiikeILkkGeiq 81
                                       ++r++++++rFe++ +++++   ++gk++dLs+ l++e++F++a+kG++ + s++ ++f te+  ei+k I++kGe+q
  gi|474933916|ref|YP_007687498.1|  8 IVARLESHGERFEVLLDPKAMDLIKQGKDVDLSDYLAVEDVFKDARKGTRPETSKIMEVFATEDPVEIAKLIIQKGEVQ 86
                                      6799*************************************************************************** PP

                                      --HHHHH CS
                              SBDS 82 vsaeerk 88
                                       +a++rk
  gi|474933916|ref|YP_007687498.1| 87 MTAQQRK 93
                                      ****997 PP

>> SBDS_C  SBDS protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.9   0.0     7e-22   6.2e-18       1     113 [.      99     215 ..      99     218 .. 0.85

  Alignments for each domain:
  == domain 1  score: 64.9 bits;  conditional E-value: 7e-22
                                       HHHHHHHHHHHHEEBTTTTB---HHHHHHHHHHTT----TTS-CCCCHHHHHHHHTTTS--EE-EEEEEEEE-...C CS
                            SBDS_C   1 iekeiieivaeklvnpqtkrpytttmIekalkelgtsvktnksaksQalevikaLiqeipiqrarmrlritcptsik 77 
                                       ++k i+ ++a++++npqtk p+++++Ie al+e +++v++ k+ ++ + e++k L+  +pi++++ r++i ++   +
  gi|474933916|ref|YP_007687498.1|  99 KYKRIVAYIAANAINPQTKLPHPPKRIEIALEEGKFHVDPMKAFDKEVEEAMKILRPLLPIRFEKSRIAIRIK---A 172
                                       5899*********************************************************************...9 PP

                                       CCHHHHHHHH.HH.....S.EE.....EEEE.EEGGGHHHHHH CS
                            SBDS_C  78 dkilklieqv.esqkvaekewe.....vvvl.iePgaykelee 113
                                       d+  +++ ++ +   v  +ew+     +  + i++g+  e+ e
  gi|474933916|ref|YP_007687498.1| 173 DDYGRCFDELcKYGIVDREEWTndgfwIGTMeIPAGLITEITE 215
                                       9999999998454334446666666654444577777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1435.15
//
Query:       gi|474933917|ref|YP_007687499.1|  [L=241]
Description: proteasome endopeptidase complex, archaeal, alpha subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-57  194.1   0.3    1.8e-57  193.9   0.3    1.1  1  Proteasome      Proteasome subunit
    5.9e-14   51.4   0.1    1.1e-13   50.5   0.1    1.5  1  Proteasome_A_N  Proteasome subunit A N-terminal signature


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.9   0.3   2.1e-61   1.8e-57       1     190 []      26     210 ..      26     210 .. 0.98

  Alignments for each domain:
  == domain 1  score: 193.9 bits;  conditional E-value: 2.1e-61
                                       HHHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSS CS
                        Proteasome   1 vkkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygr 77 
                                       vkkG+t++Gik+kdgv+l+adkr++  s l+++++veK++ id+ ig+a++Gl+aDar+lv+ ar++aq ++++yg+
  gi|474933917|ref|YP_007687499.1|  26 VKKGSTTIGIKFKDGVLLVADKRIS--SRLVEPESVEKVYLIDEFIGCATSGLVADARILVDEARKNAQIHKVNYGE 100
                                       79***********************..************************************************** PP

                                       GTCHHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHH CS
                        Proteasome  78 pipverlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekey 154
                                       +i v +l+++v+++ q+ tq +g rpfg ++liag d+ g  +L+++dpsG+++++k a +iG g+ +++ +lekey
  gi|474933917|ref|YP_007687499.1| 101 NIGVAMLTKQVCDYEQNFTQWGGGRPFGTAMLIAGADDLG-VHLFETDPSGAIVAYK-ASCIGVGRAVVMDLLEKEY 175
                                       *************************************888.8**************8.******************* PP

                                       STTBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEEEE CS
                        Proteasome 155 kedltleeavelavkalkealerdklsgknievavi 190
                                       k+ +t + a++l  kal++a+e ++ + + +ev+v+
  gi|474933917|ref|YP_007687499.1| 176 KDGMTCDAALKLGMKALEAAIE-EAPKAESVEVGVV 210
                                       **********************.7799999999986 PP

>> Proteasome_A_N  Proteasome subunit A N-terminal signature
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5   0.1   1.3e-17   1.1e-13       1      23 []       3      25 ..       3      25 .. 0.99

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 1.3e-17
                    Proteasome_A_N  1 YDrslttFSPdGRLfQVEYAmkA 23
                                      YDr +t+FSPdGRLfQVEYA +A
  gi|474933917|ref|YP_007687499.1|  3 YDRGITVFSPDGRLFQVEYAREA 25
                                      *********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.55
# Mc/sec: 1315.11
//
Query:       gi|474933918|ref|YP_007687500.1|  [L=122]
Description: hypothetical protein TALC_00331 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.025   14.8   0.0      0.057   13.7   0.0    1.7  1  RNase_P_Rpp14  Rpp14/Pop5 family
      0.037   14.1   0.5      0.061   13.4   0.5    1.4  1  YqgC           Uncharacterized YqgC-like


Domain annotation for each model (and alignments):
>> RNase_P_Rpp14  Rpp14/Pop5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   6.4e-06     0.057      47     101 ..      36      84 ..      20      86 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.4e-06
                                       EEEEETTTTEEEEEEEGGGHHHHHHHHHT--EETTEEEEEEEEEEESSHHHHHHH CS
                     RNase_P_Rpp14  47 vkyfspatstaiiRcsresyrlvwaaLtlitkiegrpvvfrvvrvsGTikkaeee 101
                                        k ++ a ++a iRcs e+++++ aa++  +         ++vrvsGTi++++ +
  gi|474933918|ref|YP_007687500.1|  36 FKVIQCAGGMAAIRCSPEDVEECAAAMKRADP------SSEMVRVSGTIRTLRDR 84 
                                       566677789999*************9876665......579*********98865 PP

>> YqgC  Uncharacterized YqgC-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.5   6.8e-06     0.061      21      48 ..      75     102 ..      58     105 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.8e-06
                              YqgC  21 tRtvRqvkqqttvhYlvsPPRPPvktnP 48 
                                         t+R ++ +  v    +PPRPP+k  P
  gi|474933918|ref|YP_007687500.1|  75 SGTIRTLRDRYSVLRANAPPRPPRKGTP 102
                                       56999999999999999********877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 718.80
//
Query:       gi|474933919|ref|YP_007687501.1|  [L=1026]
Description: Heterodisulfide reductase, subunit A-related polyferredoxin [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.1e-34  117.6   0.3    4.9e-10   39.1   0.0    3.4  3  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    9.3e-14   51.4   0.1    1.8e-06   28.1   0.0    2.9  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    2.1e-12   47.3   1.3    0.00023   20.9   0.3    4.2  4  DAO            FAD dependent oxidoreductase
    1.4e-08   34.8   0.6       0.35   10.8   0.2    4.3  4  NAD_binding_9  FAD-NAD(P)-binding
    1.5e-08   34.1   2.8     0.0014   17.8   0.1    2.3  2  FAD_binding_2  FAD binding domain
    1.8e-08   34.1   1.4     0.0019   17.6   0.0    2.7  3  FAD_oxidored   FAD dependent oxidoreductase
    4.3e-08   33.6   4.4      0.056   14.0   0.1    4.6  3  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    8.6e-08   31.8   3.0    0.00032   20.0   0.0    3.5  4  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    1.2e-07   32.2  51.0    7.1e-06   26.5  16.7    5.6  5  Fer4_7         4Fe-4S dicluster domain
    7.7e-07   28.5   0.9     0.0032   16.6   0.0    2.5  2  GIDA           Glucose inhibited division protein A
      2e-06   26.8   6.1      0.007   15.1   0.1    3.4  4  HI0933_like    HI0933-like protein
    3.4e-06   27.9  34.0     0.0077   17.1   8.1    5.9  5  Fer4_16        4Fe-4S double cluster binding domain
    5.8e-06   25.9  54.0    0.00014   21.5   7.1    5.6  4  Fer4           4Fe-4S binding domain
    5.3e-05   23.3  24.5    0.00029   21.0  15.7    5.5  5  Fer4_9         4Fe-4S dicluster domain
    0.00016   21.0   0.2       0.27   10.5   0.1    2.4  2  Thi4           Thi4 family
     0.0013   18.7  63.2     0.0056   16.7   5.1    6.3  6  Fer4_6         4Fe-4S binding domain
     0.0025   17.2   0.1        3.7    6.7   0.0    3.9  5  Amino_oxidase  Flavin containing amine oxidoreductase
     0.0029   17.0   0.4        1.1    8.6   0.0    2.5  2  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
     0.0085   16.2  14.1     0.0085   16.2  14.1    5.4  5  Fer4_21        4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.012   15.7  16.3      0.012   15.7  16.3    4.7  5  Fer4_10        4Fe-4S dicluster domain
      0.095   12.4   0.4          1    9.0   0.0    2.3  2  2-Hacid_dh     D-isomer specific 2-hydroxyacid dehydrogenase,
       0.21   10.8   4.1          5    6.3   0.1    2.7  3  FAD_binding_3  FAD binding domain
       0.21   12.1  46.6        0.2   12.3   6.5    5.3  4  Fer4_4         4Fe-4S binding domain
        8.7    6.9  38.8       0.16   12.5   2.2    5.3  5  Fer4_8         4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.0     6e-12   4.5e-09       3     114 ..       6     201 ..       4     227 .. 0.78
   2 !   39.1   0.0   6.6e-13   4.9e-10     152     292 ..     279     434 ..     278     436 .. 0.83
   3 !   38.2   0.3   1.3e-12   9.5e-10       3     293 ..     610     919 ..     608     920 .. 0.70

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 6e-12
                                       EEEE--SHHHHHHHHHHHHHTS-EEEEE...........TTHCHHHCSHHH...HCHHHHHHHHHHHHH........ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxx...xxxxxxxxxxxxxxx........ RF
                       Pyr_redox_2   3 vvviGgGpAGlaaaltlaqagakvtlve...........legtclnggcll...skallgvaedaeias........ 57 
                                        +viGgG+AG++a+l+la  ++ v+l++           l++t+++++c+    s++++ +a++++i +        
  gi|474933919|ref|YP_007687501.1|   6 ALVIGGGIAGIQASLDLADRNIHVYLLDkkptiggtmcmLDKTFPTNDCSAcilSPKMADAAGHPNITLltyhevkk 82 
                                       68*************************88888889999********99765555************999******** PP

                                       ........................................HHHHCHHHHCCCCHC........CT.CEEEEESCEEE CS
                                       ........................................xxxxxxxxxxxxxxx........xx.xxxxxxxxxxx RF
                       Pyr_redox_2  58 ........................................evvkklnqgielllg........ee.vvkidpgkkkv 85 
                                                                               +   +++ g++++++        ++ v  id  k+k+
  gi|474933919|ref|YP_007687501.1|  83 vegkegdfkvtvlkkaryvdpttctacgdcvakcpskgipN---EFEYGLTTRKAiyiphaqaVPrVALIDATKCKM 156
                                       ********************************999996651...455555555556666666644244444444555 PP

                                       EETEEEC.................TCEEEEEESEEEE---EEE-BC CS
                                       xxxxxxx.................xxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  86 klekkke.................gdeekiaydklvlAtGssprdl 114
                                        le  k+                 ++e +++ +++++A G+  +d 
  gi|474933919|ref|YP_007687501.1| 157 LLE-GKCgvcaktcgkgcihyddkDEEITLDIGSIIVAAGFDVFDA 201
                                       553.33446666667777777765777788889*******988876 PP

  == domain 2  score: 39.1 bits;  conditional E-value: 6.6e-13
                                       HHHHHHHHH...HHHHT-EEEEEESSSSSS..TTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE..EEEEEET CS
                                       xxxxxxxxx...xxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxx RF
                       Pyr_redox_2 152 yiGvElAaa...laklgkevtlveardrll..raldkelsaaleealekeGvevklgtsvkeidgnge..klevvle 221
                                       y++++++++   +a + ke   v+    ++  r+++ke++ ++++a ++ G++++ g++v ++++++e  ++ v  +
  gi|474933919|ref|YP_007687501.1| 279 YCSSVCCMYatkQAIITKEHGDVDEDIFFMdiRSYGKEFETYIHRAETEYGIHLHRGARVSNLEEDPEtkQIIVNYT 355
                                       78888888833335555565556665556699***********************************9763336666 PP

                                       TSCE....EEESEEEE-S-EEES-HHCS..HCCT-EEEETTEEE--TTS..BESSTTEEE-GGGCTECCSS--HHHH CS
                                       xxxx....xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 222 dgee....idadlvvvavGvrpstelle..eklglelderggivvdefl..rtnvpgiyaiGDvaggkggpelaqaA 290
                                       d e        d+vv++vG++     +e  ++lg+el+e g+ ++  ++  +t+ +gi + G++a +k++p ++ +A
  gi|474933919|ref|YP_007687501.1| 356 DPENnpqsKVFDMVVLSVGLESPAGAQElaDTLGIELNEYGFAKTSIYQplETSRKGIVVTGAFAAPKDIPTSVAEA 432
                                       6555667699***********987777788*************88877766***********************999 PP

                                       HH CS
                                       xx RF
                       Pyr_redox_2 291 vq 292
                                       + 
  gi|474933919|ref|YP_007687501.1| 433 SG 434
                                       75 PP

  == domain 3  score: 38.2 bits;  conditional E-value: 1.3e-12
                                       EEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHC.SHHH.HCHHHHHHHHHHHHHHHHHCHHHH..CCCCHCCTC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxx RF
                       Pyr_redox_2   3 vvviGgGpAGlaaaltlaqagakvtlvelegtclng.gcll.skallgvaedaeiasevvkklnqg..ielllgeev 75 
                                        ++iGgG+ G++aal++a++++ v+++e++g++ ++ + ++ ++  + v+++ +   e ++k+n++  i++ l++ v
  gi|474933919|ref|YP_007687501.1| 610 AAIIGGGITGMTAALDIAAQNIAVHIFEKDGELGGFaKNFMhKEDGVCVQDFLK---ETINKVNSNdlITVHLNADV 683
                                       58*************************966655333122221333344444443...6677777776799999999* PP

                                       EEEEESC.EEEEETEEECTCEEEEEESEEEE---EEE-BC.TCT.TC.TTBEECCSECHHHHHHCCSS-T......S CS
                                       xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx.xxxxxxxxxxxxxxxxxxxxxxxxx......x RF
                       Pyr_redox_2  76 vkidpgk.kkvklekkkegdeekiaydklvlAtGssprdl.gip.Gvaenvgklvrtldsaealklkllp......k 143
                                       v+i pg  +++ +   k  d+ +   ++++ AtG+   ++     G  ++v +   +++  +++  +  +      +
  gi|474933919|ref|YP_007687501.1| 684 VDI-PGYvGNFAI---KLADGSETPVGAVLFATGAGEYKPvEYNyGSDPKVKT---YVELEKEIAADSSKyagknvA 753
                                       ***.999899999...3467889************999996444566444432...344444444444335564445 PP

                                       EEEEES-SHHHHHHHHHHHHHT-..............EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 144 rivvvGgGyiGvElAaalaklgk..............evtlveardrllraldkelsaaleealekeGvevklgtsv 206
                                        i  +G+ + ++E+++  + +g+              +vt+++   r +      +++ +     k Gv++    + 
  gi|474933919|ref|YP_007687501.1| 754 FIQCIGSRNDSTEYCSRVCCAGAirnaiqlkmndpttNVTIIHKDIRTY-----GFREDMYYMASKLGVRFLRYPTD 825
                                       66789********9999888888888888899999989******98888.....7889989999999***9843333 PP

                                       E...EEEETTE.EEEEEETTSCEEEESEEEE-S-EEES-HHCS...HCCT-EEEETTEE.E--TTSBE...SSTTEE CS
                                       x...xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxx.xxxxxxxx...xxxxxx RF
                       Pyr_redox_2 207 k...eidgnge.klevvledgeeidadlvvvavGvrpstelle...eklglelderggi.vvdeflrt...nvpgiy 272
                                           e dgn    ++  l+++  i++d++v++ G++p +e +e     +++++ ++g++ +  ++lr      +g++
  gi|474933919|ref|YP_007687501.1| 826 GklpEYDGNVVkAYDNGLNEEVAIPVDTLVLSNGITPLREEKEklkIMVKVPTSKDGFFfEAHQKLRPvdfATEGVF 902
                                       31225555554444466666666****************99966433345555777776677777764444789999 PP

                                       E-GGGCTECCSS--HHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 273 aiGDvaggkggpelaqaAvqq 293
                                       ++G+       p+ + + ++q
  gi|474933919|ref|YP_007687501.1| 903 VAGAAH----WPKFMDECIAQ 919
                                       999854....66666555555 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   7.2e-07   0.00054       1      35 [.       8      42 ..       8      51 .. 0.97
   2 !   28.1   0.0   2.3e-09   1.8e-06       1      40 [.     612     651 ..     612     672 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 7.2e-07
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGra 35
                                      ++G+G++G  a   La+++++v ll+k + +GG +
  gi|474933919|ref|YP_007687501.1|  8 VIGGGIAGIQASLDLADRNIHVYLLDKKPTIGGTM 42
                                      8********************************86 PP

  == domain 2  score: 28.1 bits;  conditional E-value: 2.3e-09
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECE CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyev 40 
                                       I+G+G++G++aA  +a +++ v+++ek   lGG a+ + +
  gi|474933919|ref|YP_007687501.1| 612 IIGGGITGMTAALDIAAQNIAVHIFEKDGELGGFAKNFMH 651
                                       9********************************9998866 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   9.9e-06    0.0074       3      36 ..       7      41 ..       5      42 .. 0.93
   2 ?    5.4   0.0     0.016        12     157     208 ..     326     382 ..     313     420 .. 0.70
   3 !   20.9   0.3     3e-07   0.00023       3      33 ..     611     643 ..     609     650 .. 0.91
   4 ?   -0.6   0.0         1   7.6e+02     155     203 ..     811     861 ..     798     897 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9.9e-06
                                      EEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSG CS
                               DAO  3 viiGGGiiGlstAyeLarrg..Vtllekgdiagsga 36
                                      ++iGGGi+G+ + ++La r+  V ll+k++ +g g+
  gi|474933919|ref|YP_007687501.1|  7 LVIGGGIAGIQASLDLADRNihVYLLDKKPTIG-GT 41
                                      8****************99899*******9999.76 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.016
                                       HHTT-EEEESECEEEEEE.EETCEEEEEEECT.EEE.E..EEEEEEE--GGGHH.HHH CS
                               DAO 157 ealGveilegtevtglee.edgkvwgverttp.gen.d..aadavVnaaGawsd.llg 208
                                        + G+++++g++v +lee ++ k   v + t+ ++n +   +d vV++ G+ s   ++
  gi|474933919|ref|YP_007687501.1| 326 TEYGIHLHRGARVSNLEEdPETKQIIV-NYTDpENNpQskVFDMVVLSVGLESPaGAQ 382
                                       56799***********77343554555.4444455543233466*******9984333 PP

  == domain 3  score: 20.9 bits;  conditional E-value: 3e-07
                                       EEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                               DAO   3 viiGGGiiGlstAyeLarrg..Vtllekgdiag 33 
                                       +iiGGGi+G+++A++ a+++  V ++ek+ ++g
  gi|474933919|ref|YP_007687501.1| 611 AIIGGGITGMTAALDIAAQNiaVHIFEKDGELG 643
                                       8****************9999*******98877 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 1
                                       HHHHTT-EEEESECEEE.EEEEETCEEEEE....EECTEEE.EEEEEEEE--GGG CS
                               DAO 155 aaealGveilegtevtg.leeedgkvwgve....rttpgen.daadavVnaaGaw 203
                                        a +lGv++l++ +  g l e+dg v++ +    +   +e+   +d++V+++G+ 
  gi|474933919|ref|YP_007687501.1| 811 MASKLGVRFLRY-PTDGkLPEYDGNVVKAYdnglN---EEVaIPVDTLVLSNGIT 861
                                       68999*******.8888677777887777664322...333347899*****965 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.021        16       2      40 ..       8      41 ..       7      51 .. 0.86
   2 ?    4.3   0.0      0.05        37     104     154 ..     317     374 ..     312     376 .. 0.78
   3 !   10.8   0.2   0.00047      0.35       1      39 [.     611     643 ..     611     652 .. 0.87
   4 !    9.1   0.0    0.0016       1.2     100     155 ..     658     714 ..     655     715 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.021
                     NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfdpsep.gagr 40
                                      ++G+G++G+ +   L++r     ++++ l d++++ g g+
  gi|474933919|ref|YP_007687501.1|  8 VIGGGIAGIQASLDLADR-----NIHVYLLDKKPTiG-GT 41
                                      8***************99.....5********98845.43 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.05
                     NAD_binding_9 104 feellarlpegvtvevhra.evvdleeradgqavll......adgaslaadaVvLAlG 154
                                       fe+ + r++ +  +++hr+ +v +lee++++ +++       ++ +s  +d VvL +G
  gi|474933919|ref|YP_007687501.1| 317 FETYIHRAETEYGIHLHRGaRVSNLEEDPETKQIIVnytdpeNNPQSKVFDMVVLSVG 374
                                       7888999999999****877*********99654443444434447789******999 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00047
                     NAD_binding_9   1 aivGaGprGlavlerLlarakkkspleitlfdpsepgag 39 
                                       ai+G+G++G++++  ++a+     ++ +++f++++   g
  gi|474933919|ref|YP_007687501.1| 611 AIIGGGITGMTAALDIAAQ-----NIAVHIFEKDGEL-G 643
                                       8*****************9.....5********7764.3 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.0016
                     NAD_binding_9 100 lrdlfeellarlpegvtvevh.raevvdleeradgqavlladgaslaadaVvLAlGh 155
                                       ++d+++e +++++++  ++vh +a+vvd+    +++a+ ladg+++ + aV  A+G 
  gi|474933919|ref|YP_007687501.1| 658 VQDFLKETINKVNSNDLITVHlNADVVDIPGYVGNFAIKLADGSETPVGAVLFATGA 714
                                       689999999999777777777699*******************************95 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   1.8e-06    0.0014       2      37 ..       6      41 ..       5      44 .. 0.94
   2 !   16.1   0.7   6.2e-06    0.0046       3      36 ..     611     644 ..     609     649 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.8e-06
                                      EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSG CS
                     FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqefgga 37
                                      ++ViG+G+AG  A+l +a+++  v +++k++  gg+
  gi|474933919|ref|YP_007687501.1|  6 ALVIGGGIAGIQASLDLADRNIHVYLLDKKPTIGGT 41
                                      69*****************************99997 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 6.2e-06
                                       EEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                     FAD_binding_2   3 iViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36 
                                        +iG+G+ G++AAl +a ++  v + ek +e gg
  gi|474933919|ref|YP_007687501.1| 611 AIIGGGITGMTAALDIAAQNIAVHIFEKDGELGG 644
                                       79***************************99887 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   2.6e-06    0.0019       3      38 ..       7      42 ..       6      49 .. 0.96
   2 ?   -3.3   0.0       5.8   4.3e+03     184     222 ..     270     307 ..     242     356 .. 0.60
   3 !   14.4   0.3   2.4e-05     0.018       4      38 ..     612     646 ..     610     656 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.6e-06
                      FAD_oxidored  3 vVvGGgpaGvaAAiaAaraGakvlLveergvlGGll 38
                                      +V+GGg+aG+ A +  a +   v L+++++ +GG++
  gi|474933919|ref|YP_007687501.1|  7 LVIGGGIAGIQASLDLADRNIHVYLLDKKPTIGGTM 42
                                      7*********************************98 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 5.8
                      FAD_oxidored 184 geedekvqaynkrlcltskpenrvpfekkpegydparye 222
                                       +++++++++y++++c   + ++++ + k+ +++d++ + 
  gi|474933919|ref|YP_007687501.1| 270 RSQKSTWKKYCSSVCCMYATKQAIIT-KEHGDVDEDIFF 307
                                       67788888888888776666666655.355555555444 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 2.4e-05
                      FAD_oxidored   4 VvGGgpaGvaAAiaAaraGakvlLveergvlGGll 38 
                                       ++GGg+ G++AA+  a +   v + e++g lGG +
  gi|474933919|ref|YP_007687501.1| 612 IIGGGITGMTAALDIAAQNIAVHIFEKDGELGGFA 646
                                       9********************************76 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.1   7.5e-05     0.056       2      73 ..       6      90 ..       5      97 .. 0.76
   2 ?    6.7   0.0     0.015        11      36      78 ..     311     352 ..     301     358 .. 0.86
   3 !   10.1   0.8    0.0013      0.95       2      35 ..     610     643 ..     609     699 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.5e-05
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS...TTSSHHHHH......HHHHHHHHT....TEEEECSEEEEEEE CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll...rllDeeask......ilqeklekn....gievllntkveeie 67
                                      ++v+GgG  g+ +   la+ + +V++++ ++++     +lD+++ +      il  k+ +     +i++l+ ++v+++e
  gi|474933919|ref|YP_007687501.1|  6 ALVIGGGIAGIQASLDLADRNIHVYLLDKKPTIGgtmCMLDKTFPTndcsacILSPKMADAaghpNITLLTYHEVKKVE 84
                                      79*******************************9877778888755222222455566555677799999999999999 PP

                                      EETTSE CS
                         Pyr_redox 68 gsedgv 73
                                      g+e  +
  gi|474933919|ref|YP_007687501.1| 85 GKEGDF 90
                                      888763 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.015
                                       TTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEEE CS
                         Pyr_redox  36 rllDeeaskilqeklekngievllntkveeiegsedgvesvkl 78 
                                       r +++e+++++++  ++ gi+++ +++v ++e+++++ +++ +
  gi|474933919|ref|YP_007687501.1| 311 RSYGKEFETYIHRAETEYGIHLHRGARVSNLEEDPET-KQIIV 352
                                       789999*******99*****************99984.66655 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.0013
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35 
                                       ++++GgG +g+ +A  +a+ +  V+++e   +l 
  gi|474933919|ref|YP_007687501.1| 610 AAIIGGGITGMTAALDIAAQNIAVHIFEKDGELG 643
                                       69**************************999998 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.1    0.0013      0.94       1      33 [.       7      39 ..       7      52 .. 0.87
   2 ?    0.3   0.0      0.46   3.4e+02      91     121 ..      67      97 ..      62     111 .. 0.79
   3 ?   -2.7   0.0       3.5   2.6e+03      80     116 ..     314     350 ..     302     379 .. 0.75
   4 !   20.0   0.0   4.3e-07   0.00032     164     267 ..     607     714 ..     600     737 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0013
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg.nig 33
                                      ++iG+G aG++a + l + ++ ++  l+k+ +ig
  gi|474933919|ref|YP_007687501.1|  7 LVIGGGIAGIQASLDLADRNI-HVYLLDKKpTIG 39
                                      69*******************.688999986666 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.46
                       Pyr_redox_3  91 aksfelpiklfeeVesvkkedegfevetske 121
                                       a + ++   +++eV++v+ +++ f+v+  k+
  gi|474933919|ref|YP_007687501.1|  67 AGHPNITLLTYHEVKKVEGKEGDFKVTVLKK 97 
                                       556678888999************9997654 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 3.5
                       Pyr_redox_3  80 rkealeYlrevaksfelpiklfeeVesvkkedegfev 116
                                       +ke+  Y  +  +++ ++ +   +V +++++ e+ ++
  gi|474933919|ref|YP_007687501.1| 314 GKEFETYIHRAETEYGIHLHRGARVSNLEEDPETKQI 350
                                       6777788888888888888888888888775444433 PP

  == domain 4  score: 20.0 bits;  conditional E-value: 4.3e-07
                       Pyr_redox_3 164 gqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdp.....syslkpdienrleelvkeekikvlfnaev 235
                                       +q  ++iGg+ +++ aAl++++++  V+++ ++ e+    +++      + ++   ++ ++++ +++ i+v+ na+v
  gi|474933919|ref|YP_007687501.1| 607 TQSAAIIGGGITGMTAALDIAAQNIAVHIFEKDGELGGFAKNFmhkedGVCVQDFLKETINKVNSNDLITVHLNADV 683
                                       57889****************************99976554441000045677777777777777788********* PP

                       Pyr_redox_3 236 keikekeeeykvktedgkkvevkddvvlatGy 267
                                        +i     ++ +k +dg+++ v   v++atG 
  gi|474933919|ref|YP_007687501.1| 684 VDIPGYVGNFAIKLADGSETPV-GAVLFATGA 714
                                       *****************99887.888999*95 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   5.6   4.6e-05     0.035      31      50 ..      92     118 ..      42     120 .. 0.70
   2 !    8.6   0.2    0.0038       2.9       4      23 ..     161     180 ..     133     206 .. 0.84
   3 ?   -0.7   0.2       3.1   2.3e+03       6      19 ..     278     291 ..     266     328 .. 0.76
   4 ?    2.3   0.2      0.36   2.7e+02       5      18 ..     765     778 ..     755     807 .. 0.69
   5 !   26.5  16.7   9.5e-09   7.1e-06       1      52 []     950     999 ..     950     999 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.6e-05
                            Fer4_7  31 v.......eidpekClgCgaCvavCPt 50 
                                       v       ++dp++C+ Cg Cva CP+
  gi|474933919|ref|YP_007687501.1|  92 VtvlkkarYVDPTTCTACGDCVAKCPS 118
                                       13333334789***************8 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0038
                            Fer4_7   4 gCgaCvaaCpvkaieldeee 23 
                                       +Cg C+++C  ++i +d+++
  gi|474933919|ref|YP_007687501.1| 161 KCGVCAKTCGKGCIHYDDKD 180
                                       68888888888888888764 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 3.1
                            Fer4_7   6 gaCvaaCpvkaiel 19 
                                       ++C ++C ++a + 
  gi|474933919|ref|YP_007687501.1| 278 KYCSSVCCMYATKQ 291
                                       58999997666554 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.36
                            Fer4_7   5 CgaCvaaCpvkaie 18 
                                       +++C ++C ++ai+
  gi|474933919|ref|YP_007687501.1| 765 TEYCSRVCCAGAIR 778
                                       35999999888887 PP

  == domain 5  score: 26.5 bits;  conditional E-value: 9.5e-09
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                       +C gCg C+  C ++ai++ e   e+g++   ++p  C gCg Cva+CP+ga
  gi|474933919|ref|YP_007687501.1| 950 SCNGCGTCEGCCEYHAITIVEG--EDGRPISSVNPGLCKGCGCCVAACPSGA 999
                                       5******************886..7899999*******************98 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   4.3e-06    0.0032       3      40 ..       7      43 ..       5      61 .. 0.88
   2 !   10.1   0.3    0.0004       0.3       3      30 ..     611     638 ..     609     716 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.3e-06
                                      EEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--SS CS
                              GIDA  3 iViGgGhAGceAAlaaarlGakvlLithkldtiaelsC 40
                                       ViGgG AG+ A+l +a ++++v L+  k  ti+   C
  gi|474933919|ref|YP_007687501.1|  7 LVIGGGIAGIQASLDLADRNIHVYLL-DKKPTIGGTMC 43
                                      6*************************.66667776666 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0004
                                       EEE-SSHHHHHHHHHHHHTT--EEEEES CS
                              GIDA   3 iViGgGhAGceAAlaaarlGakvlLith 30 
                                        +iGgG  G+ AAl +a  ++ v ++ +
  gi|474933919|ref|YP_007687501.1| 611 AIIGGGITGMTAALDIAAQNIAVHIFEK 638
                                       69*********************99933 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   9.3e-06     0.007       3      36 ..       6      39 ..       4      45 .. 0.92
   2 ?    0.1   0.0      0.34   2.5e+02      99     153 ..      46     100 ..      41     121 .. 0.74
   3 !   11.3   1.3   0.00013     0.098       3      36 ..     610     643 ..     608     647 .. 0.93
   4 ?   -2.4   0.0         2   1.5e+03     372     399 ..     671     698 ..     660     715 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 9.3e-06
                                      EEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                       HI0933_like  3 viviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                       +viGgG AG+ a++ +a+r+ +V ll+k++++g
  gi|474933919|ref|YP_007687501.1|  6 ALVIGGGIAGIQASLDLADRNIHVYLLDKKPTIG 39
                                      68****************************9998 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.34
                                       TEEEETT.-CHHHHH.HHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEE CS
                       HI0933_like  99 grlFpvsdkaedivd.allkelkeagvklrletevksvekeedgkfrvktkseeel 153
                                       ++ Fp++d ++ i++  +  ++ + +++l + +evk+ve +e+  f+v++ ++ ++
  gi|474933919|ref|YP_007687501.1|  46 DKTFPTNDCSACILSpKMADAAGHPNITLLTYHEVKKVEGKEGD-FKVTVLKKARY 100
                                       5789999998888873567778889*************876666.99998344433 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00013
                                       EEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                       HI0933_like   3 viviGgGaAGlmaAisaakrgkrVlllekakklg 36 
                                        ++iGgG  G+ aA+ +a+++  V ++ek  +lg
  gi|474933919|ref|YP_007687501.1| 610 AAIIGGGITGMTAALDIAAQNIAVHIFEKDGELG 643
                                       68***************************98887 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 2
                                       BTTSTTEEE-GGGBSEEE-TTTHHHHHH CS
                       HI0933_like 372 skkvpgLffaGEvlDvegvtGGynlqaA 399
                                       s+ +  +++   v+D+ g++G + ++ A
  gi|474933919|ref|YP_007687501.1| 671 SNDLITVHLNADVVDIPGYVGNFAIKLA 698
                                       5555667777788888888888877766 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   8.1     1e-05    0.0077       1      65 [.     105     170 ..     105     172 .. 0.85
   2 ?    7.0   1.4     0.015        11       3      21 ..     160     179 ..     159     206 .. 0.78
   3 ?    3.6   0.1      0.18   1.3e+02       7      43 ..     767     801 ..     763     814 .. 0.66
   4 ?    5.5   1.2     0.045        34      53      65 ..     950     962 ..     929     975 .. 0.72
   5 !   15.8   2.0   2.6e-05      0.02       2      20 ..     985    1003 ..     984    1020 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1e-05
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiearecisy..ntaekkdlaedeekckkqeaitgCdiCqdvCP 65 
                                       +C+ Cg C+  CP++ i ++ e+ + +r+ i    ++a  + + +d+ kck       C++C+++C 
  gi|474933919|ref|YP_007687501.1| 105 TCTACGDCVAKCPSKGIPNEFEYGLTTRKAIYIphAQAVPRVALIDATKCK-MLLEGKCGVCAKTCG 170
                                       5*******************8888888888777878888899999999999.434589********6 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.015
                           Fer4_16   3 gtCgkCaevCPtnaikek.k 21 
                                       g+Cg Ca++C  ++i+ + k
  gi|474933919|ref|YP_007687501.1| 160 GKCGVCAKTCGKGCIHYDdK 179
                                       68*************98732 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.18
                           Fer4_16   7 kCaevCPtnaikekkekeiearecisyntaekkdlae 43 
                                        C  vC ++ai++    +++ ++ + + t+ +kd+++
  gi|474933919|ref|YP_007687501.1| 767 YCSRVCCAGAIRNA--IQLKMNDPTTNVTIIHKDIRT 801
                                       7***********99..444444444444555555555 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.045
                           Fer4_16  53 aitgCdiCqdvCP 65 
                                        + gC++C+ +C 
  gi|474933919|ref|YP_007687501.1| 950 SCNGCGTCEGCCE 962
                                       4555555555553 PP

  == domain 5  score: 15.8 bits;  conditional E-value: 2.6e-05
                           Fer4_16    2 CgtCgkCaevCPtnaikek 20  
                                        C++Cg C+ +CP++a++++
  gi|474933919|ref|YP_007687501.1|  985 CKGCGCCVAACPSGAMEQR 1003
                                        ****************998 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   3.5   2.8e-06    0.0021       2      20 ..     100     118 ..      99     121 .. 0.91
   2 ?    3.2   4.8      0.11        84      10      23 ..     161     174 ..     160     175 .. 0.91
   3 !    8.4   6.0    0.0026       1.9       4      24 .]     947     967 ..     945     967 .. 0.91
   4 !   21.5   7.1   1.9e-07   0.00014       3      23 ..     980    1000 ..     979    1001 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.8e-06
                                       EEETTTSSS-THHHHHSTT CS
                              Fer4   2 videekCigCGaCvevCPv 20 
                                       ++d+  C++CG Cv  CP 
  gi|474933919|ref|YP_007687501.1| 100 YVDPTTCTACGDCVAKCPS 118
                                       79****************6 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.11
                                       S-THHHHHSTTTEE CS
                              Fer4  10 gCGaCvevCPvgAI 23 
                                       +CG C++ C  g+I
  gi|474933919|ref|YP_007687501.1| 161 KCGVCAKTCGKGCI 174
                                       6********99998 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0026
                                       ETTTSSS-THHHHHSTTTEEE CS
                              Fer4   4 deekCigCGaCvevCPvgAIt 24 
                                       +++ C gCG+C+  C + AIt
  gi|474933919|ref|YP_007687501.1| 947 NPNSCNGCGTCEGCCEYHAIT 967
                                       899*********999999996 PP

  == domain 4  score: 21.5 bits;  conditional E-value: 1.9e-07
                                        EETTTSSS-THHHHHSTTTEE CS
                              Fer4    3 ideekCigCGaCvevCPvgAI 23  
                                        +++ +C gCG Cv +CP gA 
  gi|474933919|ref|YP_007687501.1|  980 VNPGLCKGCGCCVAACPSGAM 1000
                                        89*****************97 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   1.5   7.5e-06    0.0056      33      49 ..      94     119 ..      52     121 .. 0.69
   2 ?    4.3   1.1     0.059        44      38      51 .]     161     174 ..     139     187 .. 0.72
   3 ?   -2.1   0.5       5.9   4.4e+03       7      19 ..     509     521 ..     507     550 .. 0.57
   4 ?   -0.8   0.7       2.3   1.8e+03       6      19 ..     766     779 ..     755     790 .. 0.71
   5 !   21.0  15.7   3.8e-07   0.00029       2      51 .]     951    1000 ..     950    1000 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.5e-06
                            Fer4_9  33 e.........eaCigCgaCveaCpkg 49 
                                                 + C+ Cg+Cv++Cp++
  gi|474933919|ref|YP_007687501.1|  94 VlkkaryvdpTTCTACGDCVAKCPSK 119
                                       034445566678************86 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.059
                            Fer4_9  38 gCgaCveaCpkgai 51 
                                       +Cg C++ C kg+i
  gi|474933919|ref|YP_007687501.1| 161 KCGVCAKTCGKGCI 174
                                       35556666655544 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 5.9
                            Fer4_9   7 aCveaCpagvvve 19 
                                       aC + C +++++ 
  gi|474933919|ref|YP_007687501.1| 509 ACAQDCLQDIAKA 521
                                       4666664444433 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 2.3
                            Fer4_9   6 gaCveaCpagvvve 19 
                                        +C ++C ag++++
  gi|474933919|ref|YP_007687501.1| 766 EYCSRVCCAGAIRN 779
                                       47999999888765 PP

  == domain 5  score: 21.0 bits;  conditional E-value: 3.8e-07
                            Fer4_9    2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51  
                                        C+gCg+C+  C++++++  ++e  + +   +   C gCg Cv+aCp+ga+
  gi|474933919|ref|YP_007687501.1|  951 CNGCGTCEGCCEYHAITIVEGEDGRPISSVNPGLCKGCGCCVAACPSGAM 1000
                                        ***********99999888888888888888889*************975 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0019       1.4      21      58 ..       7      43 ..       2      51 .. 0.89
   2 !   10.5   0.1   0.00036      0.27      20      55 ..     610     644 ..     600     669 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0019
                                      EEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTT CS
                              Thi4 21 vivGaGssGLtaayylakkpdlkvailersvspGGGaw 58
                                      +++G+G +G+ a+  la + +++v +l+++ ++GG + 
  gi|474933919|ref|YP_007687501.1|  7 LVIGGGIAGIQASLDLADR-NIHVYLLDKKPTIGGTMC 43
                                      689****************.***************886 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00036
                                       EEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--T CS
                              Thi4  20 vvivGaGssGLtaayylakkpdlkvailersvspGG 55 
                                        +i+G+G +G+taa  +a + ++ v i+e+   +GG
  gi|474933919|ref|YP_007687501.1| 610 AAIIGGGITGMTAALDIAAQ-NIAVHIFEKDGELGG 644
                                       579*****************.*********998888 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   3.6   1.7e-05     0.012       4      21 ..     101     118 ..     100     122 .. 0.90
   2 !    7.4   2.9    0.0063       4.7       2      23 ..     147     173 ..     146     174 .. 0.85
   3 ?   -2.5   0.9       8.8   6.5e+03      15      23 ..     280     288 ..     278     293 .. 0.77
   4 ?    2.3   1.7      0.26   1.9e+02      14      24 .]     767     777 ..     756     777 .. 0.79
   5 !   13.0   5.0   0.00011     0.084       4      24 .]     946     966 ..     943     966 .. 0.91
   6 !   16.7   5.1   7.5e-06    0.0056       2      23 ..     978     999 ..     977    1000 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.7e-05
                            Fer4_6   4 idpdkCigCgdCvrvCPe 21 
                                       +dp  C+ CgdCv+ CP 
  gi|474933919|ref|YP_007687501.1| 101 VDPTTCTACGDCVAKCPS 118
                                       8****************6 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0063
                            Fer4_6   2 veidpdkCi.....gCgdCvrvCPega 23 
                                       + id+ kC       Cg C++ C  g 
  gi|474933919|ref|YP_007687501.1| 147 ALIDATKCKmllegKCGVCAKTCGKGC 173
                                       679******888877********8775 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 8.8
                            Fer4_6  15 CvrvCPega 23 
                                       C +vC ++a
  gi|474933919|ref|YP_007687501.1| 280 CSSVCCMYA 288
                                       99***9754 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.26
                            Fer4_6  14 dCvrvCPegai 24 
                                        C rvC +gai
  gi|474933919|ref|YP_007687501.1| 767 YCSRVCCAGAI 777
                                       3*********8 PP

  == domain 5  score: 13.0 bits;  conditional E-value: 0.00011
                            Fer4_6   4 idpdkCigCgdCvrvCPegai 24 
                                        +p++C+gCg C+  C + ai
  gi|474933919|ref|YP_007687501.1| 946 SNPNSCNGCGTCEGCCEYHAI 966
                                       69***************9998 PP

  == domain 6  score: 16.7 bits;  conditional E-value: 7.5e-06
                            Fer4_6   2 veidpdkCigCgdCvrvCPega 23 
                                       + ++p +C gCg Cv++CP ga
  gi|474933919|ref|YP_007687501.1| 978 SSVNPGLCKGCGCCVAACPSGA 999
                                       579****************998 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       2.9   2.2e+03       1      29 [.      13      41 ..      13      43 .. 0.95
   2 ?    0.6   0.0      0.35   2.6e+02     222     262 ..     329     375 ..     318     385 .. 0.86
   3 !    6.7   0.0    0.0049       3.7       1      28 [.     617     644 ..     617     659 .. 0.89
   4 ?   -1.5   0.0       1.5   1.1e+03     224     266 ..     676     718 ..     669     756 .. 0.79
   5 ?    3.8   0.0     0.038        28     406     452 .]     887     928 ..     876     928 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.9
                                      HHHHHHHHHHHHTTEEEEEEESSSSSBTT CS
                     Amino_oxidase  1 laGLaaArqLlsaGfdVtvlEardrvGGR 29
                                      +aG+ a   L++++  V +l  ++ +GG 
  gi|474933919|ref|YP_007687501.1| 13 IAGIQASLDLADRNIHVYLLDKKPTIGGT 41
                                      89**************************5 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.35
                                       TEEEETSEEEEEEEEETTC..EEEEETTSTEE....EESEEEE-S-H CS
                     Amino_oxidase 222 gldirlntrVkeikregdg..vtvtledgevv....eaDaVvvTvpl 262
                                       g  ++ ++rV++++ ++++  + v+++d e++     +D Vv+ v l
  gi|474933919|ref|YP_007687501.1| 329 GIHLHRGARVSNLEEDPETkqIIVNYTDPENNpqskVFDMVVLSVGL 375
                                       55688999*******777778*********999999******99876 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0049
                                       HHHHHHHHHHHHTTEEEEEEESSSSSBT CS
                     Amino_oxidase   1 laGLaaArqLlsaGfdVtvlEardrvGG 28 
                                       ++G++aA   ++++  V ++E ++ +GG
  gi|474933919|ref|YP_007687501.1| 617 ITGMTAALDIAAQNIAVHIFEKDGELGG 644
                                       79************************** PP

  == domain 4  score: -1.5 bits;  conditional E-value: 1.5
                                       EEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S-HHHHH CS
                     Amino_oxidase 224 dirlntrVkeikregdgvtvtledgevveaDaVvvTvplgvlk 266
                                       +++ln+ V +i    +  +++l dg+++++ aV+ ++  g  k
  gi|474933919|ref|YP_007687501.1| 676 TVHLNADVVDIPGYVGNFAIKLADGSETPVGAVLFATGAGEYK 718
                                       58999999999998888999999****************9999 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.038
                                       HHHHHHHHHCHHCSTTEEE.SGGGCTTTTTSHHHHHHHHHHHHHHHH CS
                     Amino_oxidase 406 ghedydplakpegdprlffAGehtsreypgtvegAilSGlraAaril 452
                                        h+ ++p+       ++f+AG++ +  +p  ++ +i  G  aA r+l
  gi|474933919|ref|YP_007687501.1| 887 AHQKLRPVDFA--TEGVFVAGAA-H--WPKFMDECIAQGSGAASRML 928
                                       46667777777..88********.7..9***************9986 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0014       1.1      31      62 ..       6      37 ..       2      50 .. 0.88
   2 !    5.9   0.2    0.0094         7      31      62 ..     610     641 ..     582     683 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0014
                                      EEEESTSHHHHHHHHHHHHTT-EEEEEESSHH CS
                       AlaDh_PNT_C 31 vlviGgGvaGlqAiatakglgakVtvlDvrpa 62
                                       lviGgG+aG+qA    +  + +V++lD++p+
  gi|474933919|ref|YP_007687501.1|  6 ALVIGGGIAGIQASLDLADRNIHVYLLDKKPT 37
                                      68***********9999999999999999875 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0094
                                       EEEESTSHHHHHHHHHHHHTT-EEEEEESSHH CS
                       AlaDh_PNT_C  31 vlviGgGvaGlqAiatakglgakVtvlDvrpa 62 
                                         +iGgG+ G+ A+   ++ +  V +++++ +
  gi|474933919|ref|YP_007687501.1| 610 AAIIGGGITGMTAALDIAAQNIAVHIFEKDGE 641
                                       579**********9988888888998887765 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.8    0.0012      0.86       3      53 ..     101     118 ..      88     122 .. 0.64
   2 ?    2.5   2.1      0.21   1.6e+02      10      31 ..     161     179 ..     147     186 .. 0.65
   3 ?   -2.0   0.6       5.3     4e+03      14      41 ..     510     535 ..     507     539 .. 0.52
   4 ?   -1.7   0.2       4.4   3.3e+03      45      57 ..     766     777 ..     744     786 .. 0.74
   5 !   16.2  14.1   1.1e-05    0.0085       4      57 ..     947    1000 ..     944    1002 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0012
                           Fer4_21   3 idedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPv 53 
                                       +d+                                  +C++C  C++ CP 
  gi|474933919|ref|YP_007687501.1| 101 VDP---------------------------------TTCTACGDCVAKCPS 118
                                       344.................................456666666666663 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.21
                           Fer4_21  10 gCgkCliaCedtshqaieidak 31 
                                       +Cg C+++C +    +i++d+k
  gi|474933919|ref|YP_007687501.1| 161 KCGVCAKTCGK---GCIHYDDK 179
                                       69999999985...67776655 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 5.3
                           Fer4_21  14 CliaCedtshqaieidaktvlkvvedeC 41 
                                       C++ C +   +ai+  ++   +vv  +C
  gi|474933919|ref|YP_007687501.1| 510 CAQDCLQDIAKAIQ--EQDLNRVVVASC 535
                                       44445444444443..444555666666 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 4.4
                           Fer4_21  45 nlCssvCPvedci 57 
                                       + Cs vC   ++i
  gi|474933919|ref|YP_007687501.1| 766 EYCSRVCCA-GAI 777
                                       578888863.555 PP

  == domain 5  score: 16.2 bits;  conditional E-value: 1.1e-05
                           Fer4_21    4 dedkCigCgkCliaCedtshqaieidaktvl.kvvedeCvGCnlCssvCPvedci 57  
                                        ++++C gCg C   Ce  +++ +e+++ + +  v    C GC  C++ CP ++++
  gi|474933919|ref|YP_007687501.1|  947 NPNSCNGCGTCEGCCEYHAITIVEGEDGRPIsSVNPGLCKGCGCCVAACP-SGAM 1000
                                        6799************999999998877655166689*************.4665 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5  11.8   7.9e-05     0.059       3      55 ..     100     169 ..      98     170 .. 0.82
   2 ?   -0.3   4.3       1.6   1.2e+03       4      19 ..     149     169 ..     146     188 .. 0.71
   3 ?   -2.5   0.2       7.8   5.8e+03      14      28 ..     279     293 ..     278     305 .. 0.60
   4 ?   -2.7   0.4       9.1   6.8e+03      15      46 ..     510     536 ..     508     548 .. 0.75
   5 ?   15.7  16.3   1.7e-05     0.012       3      56 .]     945     996 ..     943     996 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.9e-05
                           Fer4_10   3 vidddtCirCgkCvkaCPadl............tsvgakgeaseeeavrkkvekCtg.....cgaCveaC 55 
                                       ++d+ tC+ Cg+Cv+ CP++             ++     ++    +  ++  kC +     cg C++ C
  gi|474933919|ref|YP_007687501.1| 100 YVDPTTCTACGDCVAKCPSKGipnefeyglttrKAIYIPHAQAVPRVALIDATKCKMllegkCGVCAKTC 169
                                       5799***************99*********765444455555566666678899999999999****999 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.6
                           Fer4_10   4 idddtC.....irCgkCvkaC 19 
                                       id+ +C      +Cg C k C
  gi|474933919|ref|YP_007687501.1| 149 IDATKCkmlleGKCGVCAKTC 169
                                       677777777767888888888 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 7.8
                           Fer4_10  14 kCvkaCPadltsvga 28 
                                        C ++C +++t++  
  gi|474933919|ref|YP_007687501.1| 279 YCSSVCCMYATKQAI 293
                                       699999675444333 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 9.1
                           Fer4_10  15 CvkaCPadltsvgakgeaseeeavrkkvekCt 46 
                                       C + C      ++  +++ e++ +r++v +Ct
  gi|474933919|ref|YP_007687501.1| 510 CAQDC-----LQDIAKAIQEQDLNRVVVASCT 536
                                       77777.....3677777778888888888887 PP

  == domain 5  score: 15.7 bits;  conditional E-value: 1.7e-05
                           Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       v ++++C +Cg+C   C    ++    + +++    +++++ C gcg Cv+aCP
  gi|474933919|ref|YP_007687501.1| 945 VSNPNSCNGCGTCEGCC--EYHAITIVEGEDGRPISSVNPGLCKGCGCCVAACP 996
                                       6799*************..445555555555555666699*************9 PP

>> 2-Hacid_dh  D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.49   3.7e+02      68      84 ..     192     208 ..     190     215 .. 0.92
   2 ?    9.0   0.0    0.0014         1      81     133 ..     409     531 ..     407     532 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.49
                                       SSSSCTTB-HHHHHHTT CS
                                       xxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh  68 agvGvDnvDldaakerG 84 
                                       +++G+D +D + a+e+G
  gi|474933919|ref|YP_007687501.1| 192 VAAGFDVFDAKKATEYG 208
                                       579************98 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0014
                                       HHTT-EEE...E-TTTTHHHHHHHH.................................................... CS
                                       xxxxxxxx...xxxxxxxxxxxxxx.................................................... RF
                        2-Hacid_dh  81 kerGilVt...nvpgystesvAElt.................................................... 102
                                       +++Gi+Vt    +p+  + svAE                                                      
  gi|474933919|ref|YP_007687501.1| 409 SRKGIVVTgafAAPKDIPTSVAEASgasakagafivndpsfepckpkeypaekdvegkeprigvwvcrcginigsvv 485
                                       5789999733356888899****99**************************************************** PP

                                       ...............T-BHHHHHHHHHHHHHHHHHHHTTCCGTTBC CS
                                       ...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh 103 ...............aaTeeaqeniaeeaaenlvaflkgespanav 133
                                                      +++ee+  + a+ +++ + +++++++++ +v
  gi|474933919|ref|YP_007687501.1| 486 dvpavveyaknlpnvVLSEETKYACAQDCLQDIAKAIQEQDLNRVV 531
                                       ***************************************9999887 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1    0.0066         5       4      34 ..       6      36 ..       3      39 .. 0.92
   2 ?   -2.2   0.0       2.5   1.9e+03     106     143 ..     316     353 ..     288     365 .. 0.76
   3 ?    5.0   0.3     0.017        12       4      33 ..     610     639 ..     607     644 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0066
                                      EEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                     FAD_binding_3  4 VlIVGaGpaGlmlallLseaGvrvvlvekrs 34
                                       l++G+G aG+ ++l L+ + + v l++k  
  gi|474933919|ref|YP_007687501.1|  6 ALVIGGGIAGIQASLDLADRNIHVYLLDKKP 36
                                      69**************************975 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.5
                                       HHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEE CS
                     FAD_binding_3 106 eleriLvehaeerglqvrfktevesleqdeegvtaevr 143
                                       e+e ++  + +e g+ ++++++v +le+d e+ +  v 
  gi|474933919|ref|YP_007687501.1| 316 EFETYIHRAETEYGIHLHRGARVSNLEEDPETKQIIVN 353
                                       67888888888889**********99999987665554 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.017
                                       EEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                     FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvrvvlvekr 33 
                                        +I+G+G +G+++al  + + + v++ ek 
  gi|474933919|ref|YP_007687501.1| 610 AAIIGGGITGMTAALDIAAQNIAVHIFEKD 639
                                       57****************999999999996 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   3.2    0.0013      0.94       3      16 ..     105     118 ..     103     124 .. 0.91
   2 ?    0.7   2.4       1.4     1e+03       7      14 ..     162     169 ..     152     172 .. 0.84
   3 ?    9.4   6.6    0.0021       1.6       1      16 [.     948     963 ..     948     966 .. 0.92
   4 ?   12.3   6.5   0.00026       0.2       3      17 .]     984     998 ..     982    1002 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0013
                            Fer4_4   3 rCigCgsCvaaCPq 16 
                                       +C+ Cg Cva CP+
  gi|474933919|ref|YP_007687501.1| 105 TCTACGDCVAKCPS 118
                                       7************7 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.4
                            Fer4_4   7 CgsCvaaC 14 
                                       Cg+C  +C
  gi|474933919|ref|YP_007687501.1| 162 CGVCAKTC 169
                                       *******9 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0021
                            Fer4_4   1 qerCigCgsCvaaCPq 16 
                                       +++C+gCg C+ +C++
  gi|474933919|ref|YP_007687501.1| 948 PNSCNGCGTCEGCCEY 963
                                       589***********85 PP

  == domain 4  score: 12.3 bits;  conditional E-value: 0.00026
                            Fer4_4   3 rCigCgsCvaaCPqg 17 
                                        C gCg+CvaaCP+g
  gi|474933919|ref|YP_007687501.1| 984 LCKGCGCCVAACPSG 998
                                       5************75 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   2.2   0.00021      0.16      44      64 ..      91     119 ..      39     120 .. 0.60
   2 ?    2.1   0.1      0.37   2.7e+02       7      15 ..     161     169 ..     160     211 .. 0.71
   3 ?   -1.5   0.1       4.8   3.6e+03      10      34 ..     279     303 ..     277     328 .. 0.74
   4 ?    0.2   7.8       1.4   1.1e+03      48      63 ..     948     963 ..     922     965 .. 0.76
   5 ?    4.9   7.0     0.048        36      51      64 ..     985     998 ..     982    1008 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00021
                            Fer4_8  44 e........eealwsCttcgaCtevCpvg 64 
                                       +        +    +Ct+cg C+ +Cp +
  gi|474933919|ref|YP_007687501.1|  91 KvtvlkkarYVDPTTCTACGDCVAKCPSK 119
                                       133333333556789************75 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.37
                            Fer4_8   7 eCgaCqsaC 15 
                                       +Cg C ++C
  gi|474933919|ref|YP_007687501.1| 161 KCGVCAKTC 169
                                       688888887 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 4.8
                            Fer4_8  10 aCqsaCpvlrrtkkhlldargeaae 34 
                                       +C s C ++ +++  + +  g++ e
  gi|474933919|ref|YP_007687501.1| 279 YCSSVCCMYATKQAIITKEHGDVDE 303
                                       7999999888877666666666555 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 1.4
                            Fer4_8  48 lwsCttcgaCtevCpv 63 
                                        +sC++cg C+  C  
  gi|474933919|ref|YP_007687501.1| 948 PNSCNGCGTCEGCCEY 963
                                       5678888888777765 PP

  == domain 5  score: 4.9 bits;  conditional E-value: 0.048
                            Fer4_8  51 CttcgaCtevCpvg 64 
                                       C +cg+C+ +Cp g
  gi|474933919|ref|YP_007687501.1| 985 CKGCGCCVAACPSG 998
                                       66666666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1026 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       807  (0.0450109); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.89u 0.33s 00:00:01.22 Elapsed: 00:00:00.50
# Mc/sec: 6202.25
//
Query:       gi|474933920|ref|YP_007687502.1|  [L=151]
Description: F420-non-reducing hydrogenase subunit D [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.1e-53  177.6   0.0    9.5e-53  177.4   0.0    1.1  1  FlpD      Methyl-viologen-reducing hydrogenase, delta subunit


Domain annotation for each model (and alignments):
>> FlpD  Methyl-viologen-reducing hydrogenase, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.4   0.0   5.3e-57   9.5e-53       1     123 []       9     131 ..       9     131 .. 1.00

  Alignments for each domain:
  == domain 1  score: 177.4 bits;  conditional E-value: 5.3e-57
                              FlpD   1 ilaFlCnwcayaaadlagvsrlqyppnvriirvpCsgrvdpefilkalekGadgVlvlgChpgdChyvkGnekaerr 77 
                                       i+aF+Cnwc+ya+ad+agv r q+ppn+riir++Cs+r+dpef+l+al+kGadgV+vlgChp dChy+ Gn++a+rr
  gi|474933920|ref|YP_007687502.1|   9 IVAFCCNWCSYAGADNAGVGRRQMPPNFRIIRTMCSARIDPEFVLRALSKGADGVIVLGCHPADCHYIGGNYRARRR 85 
                                       9**************************************************************************** PP

                              FlpD  78 veklkelleelgiepeRvrleevsaaegekfaevikefvekikeLG 123
                                       +++l+ +le+ g++p+R+rle+vsa+egekf++v+ +f ++ik+LG
  gi|474933920|ref|YP_007687502.1|  86 IALLRLVLEQYGFDPRRLRLEWVSASEGEKFQTVMVSFIDTIKALG 131
                                       ********************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1188.15
//
Query:       gi|474933921|ref|YP_007687503.1|  [L=411]
Description: Coenzyme F420-reducing hydrogenase, gamma subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.8e-27   94.1   0.1    1.2e-26   93.0   0.1    1.6  1  Oxidored_q6     NADH ubiquinone oxidoreductase, 20 Kd subunit
  ------ inclusion threshold ------
      0.014   15.7   6.6      0.014   15.7   6.6    2.1  2  NiFe_hyd_SSU_C  NiFe/NiFeSe hydrogenase small subunit C-termi
       0.16   12.0   2.0       0.24   11.4   2.0    1.2  1  DUF2076         Uncharacterized protein conserved in bacteria
          3    8.4   4.8        2.5    8.6   3.4    1.5  2  DUF3597         Domain of unknown function (DUF3597)


Domain annotation for each model (and alignments):
>> Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.0   0.1   2.7e-30   1.2e-26       1     130 [.      83     257 ..      83     258 .. 0.91

  Alignments for each domain:
  == domain 1  score: 93.0 bits;  conditional E-value: 2.7e-30
                                       -SHHHHHHT-TTTTHHHHHHTEEEEEETTT-S--HHH.HHHTHTTTSEEEEEESBE...EEEHHHHHHHHGGGSSEE CS
                       Oxidored_q6   1 CtGcsisllaleedlldllelielryhetlladskee.eieakekeadvlvveGavtrkpkealellkelaekakav 76 
                                       C+Gc++s+l+++e++l++++++++++ ++++ d ke+  ++ ++ e+ v +++Ga+  ++ e+ +++k l++k+k+v
  gi|474933921|ref|YP_007687503.1|  83 CGGCDVSILDTNETVLSVADMADIVM-WPIAVDGKEKdIEAMEDGEITVSIINGAI--RNSENEHMVKLLRQKSKLV 156
                                       **************************.99999999886344556799*********..******************* PP

                                       EEESHHHHH-TGGGSTT-TEE..............................................-.HHHHHHHC CS
                       Oxidored_q6  77 iavGtCAafGGipaaannpsv..............................................g.eevgelle 106
                                       +a+G+CA+fGG p++an ++                                               + + v+ l++
  gi|474933921|ref|YP_007687503.1| 157 VAYGSCAVFGGTPSLANLVAGgakeileyvytktptsaqyqkdyhadapcvpqtsfeapegtltlpvVyDTVHSLDQ 233
                                       *****************88445668999**************************9999998887765268899**** PP

                                       .S-E.EEE-SSS--HHHHHHHHHH CS
                       Oxidored_q6 107 vvpvdinipGCPphpeailetlla 130
                                       v++vd++ipGCPp  e i++ ++a
  gi|474933921|ref|YP_007687503.1| 234 VIDVDYFIPGCPPIYESITHLVKA 257
                                       ******************999877 PP

>> NiFe_hyd_SSU_C  NiFe/NiFeSe hydrogenase small subunit C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.2         4   1.8e+04      62      67 ..      81      86 ..      74      89 .. 0.64
   2 ?   15.7   6.6   3.2e-06     0.014       4      71 ..     281     346 ..     279     353 .. 0.88

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 4
                                      S----T CS
                    NiFe_hyd_SSU_C 62 apCigC 67
                                      a+C gC
  gi|474933921|ref|YP_007687503.1| 81 AGCGGC 86
                                      556666 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 3.2e-06
                                       BCGGC-TTHHHHHHT-B-SSTTSH....TSBSGGGT..--GGG-BSSTTTC-BTTTTB-TTTTTS----TTSTT CS
                    NiFe_hyd_SSU_C   4 tihdnCerreyfdagefaeefgde....egClyklG..CkGpvtyadcpkrkwnegvswpvkagapCigCtepg 71 
                                        + d+C+r++ + +  + +e+ +     ++Cl++ G  C Gp t   c+ r        ++++g+pC gC  p+
  gi|474933921|ref|YP_007687503.1| 281 CMCDECPREKTYARITEIKEPYQVnidpDKCLMDQGilCLGPATVGGCNAR--------CTRVGQPCRGCYGPT 346
                                       6779**********99999888777889*****99999**********875........9**********9876 PP

>> DUF2076  Uncharacterized protein conserved in bacteria (DUF2076)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   2.0   5.3e-05      0.24      89     165 ..       2      82 ..       1      88 [. 0.51

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.3e-05
                           DUF2076  89 gFLsglFGggkke.....rpqpspqarpaapagqalgqeeqyaaqpgyaq..qqaqpqygqpaaapq..pggGggFL 156
                                       gF+s+lF++++k+     +++p++++++aapa+ +++++ +++++ g+ +  +    + + p++a+   ++  gg +
  gi|474933921|ref|YP_007687503.1|   2 GFFSNLFKKKEKKteakkEAAPKAAPAKAAPAAAPAKAAPAANGKTGFVEykA----A-DLPKGAAAliGAPPGGKI 73 
                                       9************5554444444444444444444444444444444433221....1.112222222323334677 PP

                           DUF2076 157 ggAlqtAAG 165
                                       + A+  AAG
  gi|474933921|ref|YP_007687503.1|  74 KVAIYWAAG 82 
                                       777777777 PP

>> DUF3597  Domain of unknown function (DUF3597)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   3.4   0.00057       2.5       7      44 ..       5      45 ..       2      58 .. 0.54
   2 ?   -3.6   0.0       3.5   1.6e+04      27      42 ..     192     207 ..     181     234 .. 0.51

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00057
                                      HHHT--.....-SS-TTTT-------SS---S.-------- CS
                           DUF3597  7 skifgk...aaaaaaapaasaapaataaaaaaaaaaPaaaa 44
                                      s++f+k   +++a++++a++aapa++a+aaa a+aaPaa+ 
  gi|474933921|ref|YP_007687503.1|  5 SNLFKKkekKTEAKKEAAPKAAPAKAAPAAAPAKAAPAANG 45
                                      67788722222333333344455555555555556665554 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 3.5
                                       ---SS---S.------ CS
                           DUF3597  27 aataaaaaaaaaaPaa 42 
                                       ++++ ++  +a+aP  
  gi|474933921|ref|YP_007687503.1| 192 TSAQYQKDYHADAPCV 207
                                       2222222223333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       804  (0.0448435); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 3273.41
//
Query:       gi|474933922|ref|YP_007687504.1|  [L=503]
Description: Coenzyme F420-reducing hydrogenase, alpha subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.5e-41  140.8   6.1    1.7e-19   70.1   0.8    3.1  2  NiFeSe_Hases    Nickel-dependent hydrogenase
  ------ inclusion threshold ------
      0.093   11.8   0.0        1.2    8.2   0.0    2.1  2  Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd s


Domain annotation for each model (and alignments):
>> NiFeSe_Hases  Nickel-dependent hydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.1   0.8   1.9e-23   1.7e-19       1      80 [.      53     132 ..      53     144 .. 0.96
   2 !   67.2   0.5   1.4e-22   1.3e-18     154     505 .]     156     477 ..     146     477 .. 0.73

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 1.9e-23
                                       --HHHHTTTS-GGGHHHHHHTT-SSSTTHHHHHHHHHHHHHHT----HHHHHHHHHHHHHHHHHHHHHHHHHTTGGG CS
                      NiFeSe_Hases   1 RGlElilkgrdprdawalvqRiCGVCttvHalasvravedAlgikipknarlirnliaaalllhdhivhFYhLhalD 77 
                                       RG+E +  gr   +  +++ R CGVC+ +H las++a++  +++k+++ a  ir+   +a+++h+hi hFY L+a D
  gi|474933922|ref|YP_007687504.1|  53 RGFERFCIGRRVTELNQITARLCGVCPGAHHLASTKAIDGCFNAKPTEAAFHIRDTFYQAHYVHSHIAHFYALAAGD 129
                                       9**************************************************************************** PP

                                       TS- CS
                      NiFeSe_Hases  78 wvd 80 
                                       +v 
  gi|474933922|ref|YP_007687504.1| 130 FVC 132
                                       *95 PP

  == domain 2  score: 67.2 bits;  conditional E-value: 1.4e-22
                                       HHHHHHHHHHTHHHHHHHSSSSS--.EBTTBESSGBGSBSHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHTGGGG CS
                      NiFeSe_Hases 154 LeaLelqrkaakivaifggknPhpqslvvGGvtcaidllnaerlaevkslikevkefveevylpDvlaiakaYkdwa 230
                                       L  L+++++a++i+ai+ggk  hp   v GGvt ai+  +a++++e+++ +   +e   ++ ++Dv+++ k Y d  
  gi|474933922|ref|YP_007687504.1| 156 LAVLKAREQAQRIQAIIGGKATHPVMGVPGGVTKAISQAEAKEIQEYSENLVAFSELSLKI-FHDVVLANKEYVDII 231
                                       7899*******************************99999999999999999988877665.68**********986 PP

                                       CS--GGGGT-EEEEEEEESSTT-STTGGEEEEEEEES..TTETTSEBEE-TTTEEEE-TTSSBSTS-B-GGG---EB CS
                      NiFeSe_Hases 231 kigkglgkknflsvgefpeekseelkeslllpsGvil..ngdlskveevdeekitEevkhswYkekslhplegetep 305
                                       + +     ++   +  +      + k ++ +++G ++  ++d ++++  d++   ++++++  +             
  gi|474933922|ref|YP_007687504.1| 232 TNKDLYY-HETYHMSIV------NDKGQCDFHDGKVKviDQDGKDFDLYDPNDYLDHIAEASLQ------------W 289
                                       6543332.333333333......22335556666552114444444444444444444444443............3 PP

                                       ---EEE--TTSB-BSS-EEEETTB.......--BESHHHHHHHHHHTT-HHHHHHHHHHHHHHT-HGGGGSSHHHHH CS
                      NiFeSe_Hases 306 kytleeldeegkYswikaPrykgk.......amevGplarvlvayakgkeevkelvdkllkklglkvealfstlGRt 375
                                       +y        +k+ +++ P +kg         + + pl+r+ v+    ++ ++e+++++ + l  + + ++ tl+ +
  gi|474933922|ref|YP_007687504.1| 290 SY--------EKFPYLRNPGFKGLvdgpdsgIYRATPLSRMNVTKDLPTPLANEALKEYRSILAPDGKPVQFTLATH 358
                                       33........35666666666654222222268899*****9999999999999999999999999999******** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHTTB---B--TT-SGGGS-SEEEEEEEEEETTEEEEEEEEE.ETTEEEEEEE CS
                      NiFeSe_Hases 376 aaRaleakliaellkewldelvenikkgdtetaneekldkkevpkeakGvglveapRGaLsHwiki.kdgkienYqa 451
                                        aR +e  ++ae+lke      ++++    ++   +  +++ vp   +Gvg+veapRG+L+H  +  +dg ++  ++
  gi|474933922|ref|YP_007687504.1| 359 WARLIEMLYAAEKLKEDAY--SDKLTDA--NI---K--QTDLVPG-GRGVGCVEAPRGTLTHDYTCdEDGIVTACNL 425
                                       *******999999887542..2322222..11...1..1223565.9***************999867999****** PP

                                       E-HHHHHH--S-TT----HHHHHHTT-B-SSTTS-HHHH.HHHHHT--BHHHHH- CS
                      NiFeSe_Hases 452 vvPsTWnasPrdakgqkgayEaaLigtpvadpekPleil.rtihSfDPClACavH 505
                                       vv +T n +P + +     + +aLi +    p   l+++    +++DPC +Ca+H
  gi|474933922|ref|YP_007687504.1| 426 VVGTTNNNGPICMDVA--KVAKALIKNYDVSPG-LLNMVeMAFRAYDPCNSCATH 477
                                       ************9765..567899976554554.355551468***********9 PP

>> Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0   0.00013       1.2       3      60 ..     151     207 ..     149     235 .. 0.76
   2 ?    1.3   0.0     0.017   1.5e+02     195     223 ..     388     416 ..     354     425 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00013
                                       T-HHHHHHHHHHHHHHHHHHHHHHSSSSS-TTBESSBBSS---TTHHHHHHHHHHHHH CS
                    Complex1_49kDa   3 GaltvflyafreRekildlleevtGaRltasyiriGGvarDlpegllekikeflkele 60 
                                       Ga t  l +++ Re+  ++   + G+  ++ +  +GGv++ +++   ++i+e+ ++l 
  gi|474933922|ref|YP_007687504.1| 151 GAETG-LAVLKAREQAQRIQAIIGGKATHPVMGVPGGVTKAISQAEAKEIQEYSENLV 207
                                       55555.457899********************************88888887766553 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.017
                                       S-----SEEEEEEEEETTEEEEEEEEEES CS
                    Complex1_49kDa 195 egfkvpkgevyaavEapkGelgvylvsdg 223
                                       +   vp g  + +vEap+G+l++  + d+
  gi|474933922|ref|YP_007687504.1| 388 QTDLVPGGRGVGCVEAPRGTLTHDYTCDE 416
                                       4445899999**********998776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (503 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 3144.67
//
Query:       gi|474933923|ref|YP_007687505.1|  [L=268]
Description: putative ICC-like phosphoesterase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-08   36.0   0.8    2.3e-08   34.8   0.8    1.6  1  Metallophos    Calcineurin-like phosphoesterase
      3e-06   27.5   0.2    4.5e-06   27.0   0.2    1.2  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.8   2.6e-12   2.3e-08       4     181 ..      18     167 ..      16     183 .. 0.68

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 2.6e-12
                                       EEEESBTB.......TTCCTHHHHHHHHHHHHHHH..TTESEEEEESTSSSSS.....HHHHHHHHHHHHHHHHTSE CS
                       Metallophos   4 lvigDlHl.......algggqlddllkllddllre..ekpdlvllaGDlvdrg.....dlekellellaalvkypip 66 
                                       lvigDlH+       a+g+   +++++++d + +    +++ ++++GD+ d       +   e+ +++++l++y ++
  gi|474933923|ref|YP_007687505.1|  18 LVIGDLHIgveahlgAKGVHLTSRTDDMFDSIVKAagDDIYRIIVLGDVKDSVpgstkQEYREIPRFFDRLLEYFDQ 94 
                                       8**************99************99944444799********99997778865555566668999999999 PP

                                       EEEEC-TTSCHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTE.....EEEEEEESECEEETHHHHHHHHHH CS
                       Metallophos  67 vylllGNHegfeeellnkygylgifsepwrsdaevfnnlplaslgsgs.....lkvlllhGgspellvsldklgsln 138
                                       v +++GNH+                       ++  ++lp a+ +         +v l+hG+               
  gi|474933923|ref|YP_007687505.1|  95 VNVVRGNHD-----------------------TSIEEFLPGAVRVRPAtgmvvEDVGLVHGH--------------- 133
                                       *********.......................333334444443333333333467777776............... PP

                                       HSCHHHHCCHHHHHHHHHHTTCSEEEEEESSESS....CSSSCSCCH CS
                       Metallophos 139 leleapepgdewlkdlekrekadwvivlgHsply....rgsgylfgd 181
                                                  w ++   r     ++v+gH  ++    +g g ++++
  gi|474933923|ref|YP_007687505.1| 134 ----------TWPSE---RVMECRTLVMGHEHPTvlfrDGVGAHMSE 167
                                       ..........22222...33333555555555555555555555555 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.2     5e-10   4.5e-06       4     135 ..      18     159 ..      16     171 .. 0.67

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 5e-10
                     Metallophos_2   4 aiiSDlH................snldaleavlealkevgvdaiihaGD....leeeep...........evleell 49 
                                       ++i DlH                +  d  + +++a ++ ++ +ii++GD    +    p            + ++ll
  gi|474933923|ref|YP_007687505.1|  18 LVIGDLHigveahlgakgvhltsRTDDMFDSIVKA-AGDDIYRIIVLGDvkdsV----PgstkqeyreipRFFDRLL 89 
                                       78999998888888888886664444444444555.4445899******44441....2333444433325777777 PP

                     Metallophos_2  50 ela.pvlaVrGNnDeevveedvlreaaelgtdlpeeaele.lagek...vlliHgdplgvkdalaellkeaeegsdv 121
                                       e + +v +VrGN+D            + +++ lp + ++  + g+    v+l+Hg+   ++ +    +++       
  gi|474933923|ref|YP_007687505.1|  90 EYFdQVNVVRGNHD------------TSIEEFLPGAVRVRpATGMVvedVGLVHGH--TWPSERVMECRT------- 145
                                       777***********............556666664444442444445569999999..777777766766....... PP

                     Metallophos_2 122 vvcGHtHvpeveke 135
                                       +v+GH H   ++++
  gi|474933923|ref|YP_007687505.1| 146 LVMGHEHPTVLFRD 159
                                       88899987766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1839.75
//
Query:       gi|474933924|ref|YP_007687506.1|  [L=465]
Description: yjeF C-terminal region, hydroxyethylthiazole kinase-related/yjeF N-terminal region [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.1e-50  170.5   0.1    8.1e-50  169.6   0.1    1.4  2  Carb_kinase   Carbohydrate kinase
    2.3e-25   89.4   0.0    5.2e-25   88.3   0.0    1.6  1  YjeF_N        YjeF-related protein N-terminus
    0.00025   20.5   0.3    0.00042   19.8   0.3    1.2  1  HK            Hydroxyethylthiazole kinase family
  ------ inclusion threshold ------
      0.081   12.3   0.0       0.31   10.4   0.0    1.9  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase


Domain annotation for each model (and alignments):
>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       1.3   5.8e+03      88     116 ..      62      90 ..      45      95 .. 0.62
   2 !  169.6   0.1   1.8e-53   8.1e-50       2     240 ..     215     450 ..     214     453 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.3
                                       HHHCCCCS-EEEEGGGGGSGGGG...TTT CS
                       Carb_kinase  88 eevlekdeplviDAdgLnllaqknelser 116
                                        + l++   ++iD+d +   a k+ ls+ 
  gi|474933924|ref|YP_007687506.1|  62 AFYLKNASVFMIDGDDMRSEASKKMLSRL 90 
                                       44455555588999988777776555555 PP

  == domain 2  score: 169.6 bits;  conditional E-value: 1.8e-53
                                       EEEE-BTTCHHHHHHHHHHHHCTT-SEEEEEESSTTTCCCCTTTTTCEECCTT....HTTTS....--SSS-SEEEE CS
                       Carb_kinase   2 lvigGsedytGAallaalaalrlgaglvsvateseaiavlksylpevivhpll....edeqa.kileklerldavvi 73 
                                       l+igG   y GA+ ++a+a +r+ga+ v++at +e   ++   +pe ++h+l+    ++++  ++l + + +davvi
  gi|474933924|ref|YP_007687506.1| 215 LIIGG-GPYFGAPAMSAKASMRAGADYVRIATPEESFDEIAGWCPEFVMHKLQgdvlSQSHLsTVLGICKDVDAVVI 290
                                       78888.9*************************************************97777779999********** PP

                                       -TT-SSSHCHHHHCHHHCCC.CS-EEEEGGGGGSGGGG...TTTTSSEEEE--HHHHHHHCTTTCHHCCSHHHHHHH CS
                       Carb_kinase  74 GpGLgrdekikklleevlek.deplviDAdgLnllaqknelserkaeviLTPhkkEfkrLlkaivkkeddrlelare 149
                                       GpGLgr + + k+++e+ +k   p+viDAdgL+ l  +  +   +  v+ TPh +Ef  L +            + +
  gi|474933924|ref|YP_007687506.1| 291 GPGLGRADDTVKAVREFVTKcPLPMVIDADGLFALGRD--FRIGRDDVVVTPHLGEFRNLGGKDR-----DPGDVMD 360
                                       ******998888777665541677*************8..79999***************99776.....4455678 PP

                                       HHHHHTTEEEEESTTSEEEECTTEEEEE----GGG-STTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHHHHHHC CS
                       Carb_kinase 150 laqklnavvllkgekdvivspegevlinstgssalakGGsGDvLaGligalLaqneasyeaaiaaawlhgaasdeaa 226
                                       la++l+++v+lkg++d++ + ++ + +n tg +a++++G+GDvLaG ig+lL+    +++aa+ +a+l g+a+++a+
  gi|474933924|ref|YP_007687506.1| 361 LADRLGCTVVLKGKEDMVSD-GDRIRLNGTGCAAMTSAGTGDVLAGTIGGLLSKGMGAFDAACLGAYLAGRAGELAF 436
                                       99**************9987.******************************************************** PP

                                       CCT-TS-HCHHHHH CS
                       Carb_kinase 227 ekkgvgmlatelsk 240
                                       +k ++g+ at++++
  gi|474933924|ref|YP_007687506.1| 437 QKFSYGLIATDVAD 450
                                       *****999998876 PP

>> YjeF_N  YjeF-related protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.3   0.0   1.2e-28   5.2e-25       2     169 ..      22     165 ..      21     167 .. 0.81

  Alignments for each domain:
  == domain 1  score: 88.3 bits;  conditional E-value: 1.2e-28
                            YjeF_N   2 eeLmenagravaevlrallgnspaekkvlvlvGsgnnGgdglaaArhLaqegakVtvllleeeekldedaeralell 78 
                                       + Lm nag+ava+++ +++    ++ +v +++G+gnnGgdglaaA +L  ++a+V +  +   ++++++a +++   
  gi|474933924|ref|YP_007687506.1|  22 DTLMDNAGKAVADLILERF----PDSRVAIFCGRGNNGGDGLAAAFYL--KNASVFM--IDG-DDMRSEASKKMLSR 89 
                                       67*****************....999**********************..5555555..655.56666655554444 PP

                            YjeF_N  79 kkaggkvveekpeedleeklsapvdlviDAllGiglrgelreelaeliewlnsseapvlavDiPSGldadtGavsgt 155
                                        ++ ++ +  + +ed         d+++DA lG+g++g lr ++ ++++ +n  e  ++++D+PSG+    G v+  
  gi|474933924|ref|YP_007687506.1|  90 LRCPVSDF--TGKEDG-------FDVLVDAALGTGISGTLRPAYDRYVDFCNGFEGVIVSIDVPSGF----GTVK-- 151
                                       44555555..555544.......89*****************************************9....7788.. PP

                            YjeF_N 156 avkadvtvtfgapk 169
                                        v +d+tv++   k
  gi|474933924|ref|YP_007687506.1| 152 QVVPDITVSMVDSK 165
                                       57789999986655 PP

>> HK  Hydroxyethylthiazole kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.3   9.5e-08   0.00042     144     224 ..     358     437 ..     351     451 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 9.5e-08
                                       HHHHHHHHTSEEEEESSSEEEEESSEEEEEE-S-GGGGGSTTHHHHHHHHHHHHHTTBSSHHHHHHHHHHHHHHHH. CS
                                HK 144 vqkvAqklrvvvvvtGevDvvsdgkkvyklknGtellgkitasGCllgsvvaaflavkkdkllaaveavllykvAgk 220
                                       v  +A +l+++vv+ G+ D+vsdg ++     G   +++  ++G +l+ +++  l+   ++ +aa  +  l   Ag+
  gi|474933924|ref|YP_007687506.1| 358 VMDLADRLGCTVVLKGKEDMVSDGDRIRLNGTGCAAMTS-AGTGDVLAGTIGGLLSKGMGAFDAACLGAYLAGRAGE 433
                                       5679**********************9988889999987.799*************999999999777777788887 PP

                                       HHHH CS
                                HK 221 eaaa 224
                                        a +
  gi|474933924|ref|YP_007687506.1| 434 LAFQ 437
                                       6654 PP

>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   6.9e-05      0.31     122     220 ..     337     420 ..     272     431 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 6.9e-05
                                       EEE-BHHHHHHHHT---SSHHHHHHHHHHHHHTT-SEEEEEEGGS-SSSEEEEEEEETSSEEEEEEEE----S--BT CS
                      Phos_pyr_kin 122 vitPNlpEaeaLlgekikteedmkeaakkllklgakaVlikGghlegeeavvtdvlydgeeveeleaerietknthG 198
                                       v+tP l E + L g k ++  d+ + a++   lg++ V++kG++         d++ ++++ ++l++   +  +  G
  gi|474933924|ref|YP_007687506.1| 337 VVTPHLGEFRNLGG-KDRDPGDVMDLADR---LGCT-VVLKGKE---------DMV-SDGDRIRLNGTGCAAMTSAG 398
                                       89999999999999.33444444444443...5666.5559986.........555.556667888888888***** PP

                                       HHHHHHHHHHHHHHCTSSHHHH CS
                      Phos_pyr_kin 199 tGCtlssaiaaelakgesleeA 220
                                       tG++l+  i + l+kg+   +A
  gi|474933924|ref|YP_007687506.1| 399 TGDVLAGTIGGLLSKGMGAFDA 420
                                       ****************987777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (465 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 3120.94
//
Query:       gi|474933925|ref|YP_007687507.1|  [L=97]
Description: Signal recognition particle 19 kDa protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-20   72.8   0.0    3.9e-20   72.6   0.0    1.1  1  SRP19     SRP19 protein


Domain annotation for each model (and alignments):
>> SRP19  SRP19 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.6   0.0   2.2e-24   3.9e-20       2      85 ..      11      86 ..      10      95 .. 0.85

  Alignments for each domain:
  == domain 1  score: 72.6 bits;  conditional E-value: 2.2e-24
                                      EECCCCBTTS-CCCT--S-CCCSBSS--HHHHHHHHHHCTSCEEEEEEECTTSSTT.CCEEEEEC-..........SS- CS
                             SRP19  2 iYPvYldskktrkeGRrvpkelavenPtaqeiaealkalglevvvepeksyPrdwa.npGrVrvklkedgkevnekikn 79
                                      ++P Y+d+++tr+eGRr+p +l+v++P+++ ia+ +  l l++++ ++k+yP dw+ ++G+Vrv++          + +
  gi|474933925|ref|YP_007687507.1| 11 LWPEYFDAERTRAEGRRLPLSLCVKRPSLDMIAKGAITLDLDYKIYEDKCYPGDWIaKKGCVRVEKG---------KMK 80
                                      8*****************************************************87356******83.........234 PP

                                      CHHHHH CS
                             SRP19 80 kkellk 85
                                      k e+l 
  gi|474933925|ref|YP_007687507.1| 81 KGEILP 86
                                      444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.30s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 647.80
//
Query:       gi|474933926|ref|YP_007687508.1|  [L=128]
Description: SSU ribosomal protein S8E [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-30  106.4   2.4    1.4e-30  106.3   2.4    1.0  1  Ribosomal_S8e  Ribosomal protein S8e


Domain annotation for each model (and alignments):
>> Ribosomal_S8e  Ribosomal protein S8e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.3   2.4   7.8e-35   1.4e-30       4     137 .]       3     128 .]       1     128 [] 0.96

  Alignments for each domain:
  == domain 1  score: 106.3 bits;  conditional E-value: 7.8e-35
                                       BXXCCCSEESSTEEXXXSSXXXCCSBXXXXXXXEE...SSHEEEEEEETTCEEEEEEESESEEEEEETTTTEEEEEE CS
                     Ribosomal_S8e   4 srdskhkrkltGgkakllrkkrkielgrkekatkl...gaervkvvrvrgGkrkkralrlkkanvthpeekvtkklk 77 
                                        +++k+ rk+tGg+  l r krk+e  r+++ t+l   +  + k+ r +gG  k+  l ++ anv +++++++k++k
  gi|474933926|ref|YP_007687508.1|   3 LWQGKSGRKATGGRFILSRGKRKFEISREKQFTRLtkdQPAVRKQYRGMGGSVKVGMLTAQFANVVDKKTNTVKQVK 79 
                                       6899*******************************55448999********************************** PP

                                       EEEEECSSSTCHHHHTTC--TTEEEEEESHHHHHHHHTTEEEEEEESEHHHHSSEEEEEE CS
                     Ribosomal_S8e  78 IlgVkknpsnneyvrlgvltKgaiievdvseLgevtqsgkvvAqvtsrPgqdGcvnavlL 137
                                       Il+V++nps+++yv+++++ Kga ie++++            A vtsrPgq+G +navl+
  gi|474933926|ref|YP_007687508.1|  80 ILNVVENPSDPNYVQRNIINKGAKIETEAGT-----------AIVTSRPGQHGAINAVLI 128
                                       *******************************...........****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 969.43
//
Query:       gi|474933927|ref|YP_007687509.1|  [L=215]
Description: putative phosphoesterase, Icc -like protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-18   67.3   0.0    2.3e-18   67.0   0.0    1.1  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    4.1e-15   56.8   0.0    6.4e-15   56.2   0.0    1.3  1  Metallophos    Calcineurin-like phosphoesterase
    2.8e-10   40.0   0.1    3.4e-09   36.4   0.1    2.5  1  Metallophos_3  Metallophosphoesterase, calcineurin superfamil


Domain annotation for each model (and alignments):
>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.0   0.0   3.8e-22   2.3e-18       1     163 [.       1     200 [.       1     202 [. 0.74

  Alignments for each domain:
  == domain 1  score: 67.0 bits;  conditional E-value: 3.8e-22
                     Metallophos_2   1 MklaiiSDlHsnldaleavlealkevgvdaiihaGDl..eeeepevleellela.pvlaVrGNnD........eevv 66 
                                       Mk+++++DlH++ + l+ + +++++++++ ++++GD+  ++++ +++e + +++ +v+  +GN+D        +e v
  gi|474933927|ref|YP_007687509.1|   1 MKFLVLTDLHQKASNLAWINSIIEKENIENVLFLGDVtdMGTSDDAVEIISSVKaKVYCLPGNCDprdlpariSE-V 76 
                                       ************************************9876666678888888889**********9888865422.4 PP

                     Metallophos_2  67 eedvlreaaelgtdl.................peeaelelagek......vlliHgdpl...........gvkdala 109
                                       + d++ ++ ++g+ +                  +e+e++++ +       +l++H   +            ++ a++
  gi|474933927|ref|YP_007687509.1|  77 AVDMHGKSVQFGDVYvaglggsnvtifgtpfeLSEEEIDAKLRPisrkgmILMTHAPSYgildhipngmsVGSPAIR 153
                                       44444444445444468888888888888665244444432222445566******977999999964432223333 PP

                     Metallophos_2 110 ellkeaeegsd.vvvcGHtHvp.evekeggvlvvnPGsvgeprdgdpetyaildtd 163
                                       + ++   + +  v+++GH+H+  ++++++g+l+vnPG ++e+       +ail++d
  gi|474933927|ref|YP_007687509.1| 154 KIVE---DFRPlVALSGHIHEDiGAQTIDGTLFVNPGPAKEG------YCAILTVD 200
                                       3333...33337**********99***************998......66666666 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.2   0.0   1.1e-18   6.4e-15       1     204 []       1     172 [.       1     172 [. 0.80

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 1.1e-18
                                       EEEEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTSCH CS
                       Metallophos   1 lrilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHegf 77 
                                       +++lv++DlH      q ++ l++++ ++++e++  vl++GD++d g  +   +e ++ + +   +vy+l+GN++  
  gi|474933927|ref|YP_007687509.1|   1 MKFLVLTDLH------QKASNLAWINSIIEKENIENVLFLGDVTDMGTSDD-AVEIISSVKA---KVYCLPGNCD-- 65 
                                       89********......9999999999999999**99******999998888.9999999999...9*********.. PP

                                       HH.HHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEETHHHHHHHHHHHSCHHHHCCHHHHHH CS
                       Metallophos  78 ee.ellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGgspellvsldklgslnleleapepgdewlkd 153
                                          +l+ +  + + + +++   +  f+ +++a+lg+   +v +                             e+ ++
  gi|474933927|ref|YP_007687509.1|  66 -PrDLPARISEVAVDMHGK---SVQFGDVYVAGLGGS--NVTIFGTP------------------------FELSEE 112
                                       .335555555555445555...778999999998888..55444444........................222222 PP

                                       ....HHHHTTCSEEEEEESSESS.....CSSSCSCCHHHHHHHHHHTTESEEEEESSSSE CS
                       Metallophos 154 ....lekrekadwvivlgHsply.....rgsgylfgdealedllkkygvdlvisGHtHvy 204
                                           + ++  ++  i+++H p y       +g + g++a++++ +++++ + +sGH+H++
  gi|474933927|ref|YP_007687509.1| 113 eidaKLRPISRKGMILMTHAPSYgildhIPNGMSVGSPAIRKIVEDFRPLVALSGHIHED 172
                                       23333444566799**********99999999**************************85 PP

>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.1   5.7e-13   3.4e-09      59     253 ..      24     205 ..       1     209 [. 0.77

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 5.7e-13
                                       T----THHHHHHHHHHHHHHHHHHHHHHTT-SEEEEE--TTS--HHHHHHHHHHTTTT-TTEEE-SSEEEEETTTEE CS
                     Metallophos_3  59 rrepdkkeileekneiiklldklfrelgeldvpafvvPGkrDaPlevflreayeaevvfpnlkvvhesfaekeGevl 135
                                       ++e   ++++  +  ++ + d++ +++  ++ +++++PG+ D P +   r     e v   +++       + G+v 
  gi|474933927|ref|YP_007687509.1|  24 EKENIENVLFLGDVTDMGTSDDAVEIISSVKAKVYCLPGNCD-PRDLPAR--IS-E-VAVDMHGK----SVQFGDVY 91 
                                       44555566667778899999*******************999.6664333..22.2.22333333....3445999* PP

                                       EEEE-SEEESS--BSSSS-EEEHHHHHHHGGGGGGS---EEEEEESS--S-SST.BTTBS---S-HHHHHHHHHH-- CS
                     Metallophos_3 136 iaGmGGeivdgekeeefrLkYPaweveyrLkvlkelkdrrkvlllatpPigelv.adkglkekgsevvaelvktlnP 211
                                       +aG+GG  v   ++  f L     e++ +L+ +        +l+ + p  g l+ +++g    gs  + ++v +++P
  gi|474933927|ref|YP_007687509.1|  92 VAGLGGSNVT-IFGTPFELS--EEEIDAKLRPISRK---GMILMTHAPSYGILDhIPNG-MSVGSPAIRKIVEDFRP 161
                                       ******9775.466667665..78888888877654...6788888888999*978888.889************** PP

                                       SEEEE-SS--EE..EEETTEEEEE--BGGGTEEEEEETTTTEEE CS
                     Metallophos_3 212 evvvvghavkeh..eelgktlvvnPGaleeGdfavvdleekkve 253
                                        v++ gh + +    +++ tl vnPG  +eG  a++ +++ k +
  gi|474933927|ref|YP_007687509.1| 162 LVALSGHIHEDIgaQTIDGTLFVNPGPAKEGYCAILTVDNGKAD 205
                                       ********98877799*********************9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:01.26
# Mc/sec: 514.81
//
Query:       gi|474933928|ref|YP_007687510.1|  [L=151]
Description: hypothetical protein TALC_00341 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.7e-07   29.2   0.0    2.9e-06   27.3   0.0    1.8  2  TerB      Tellurite resistance protein TerB


Domain annotation for each model (and alignments):
>> TerB  Tellurite resistance protein TerB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.2   0.00023       4.2      78     129 ..      24      74 ..       2      89 .. 0.76
   2 !   27.3   0.0   1.6e-10   2.9e-06      38     128 ..      56     148 ..      23     151 .] 0.84

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00023
                              TerB  78 eeeavdleqftralkrklspeqrraliealweiAlADGeldeaEdavlrrva 129
                                       +e+++++  + +a+ +  ++  ++ +++++     ADG+l eaE ++++   
  gi|474933928|ref|YP_007687510.1|  24 REKSASVLSALSAITED-EETGAQVFLDFILMSMAADGKLAEAEFNLIKPGL 74 
                                       55677777788888876.67788889999999999*********99997655 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 1.6e-10
                              TerB  38 akaDgqvsesErqafrellksrf..glspeeakallelfeeaeeeavdleqftralkrklspeqrraliealweiAl 112
                                       ++aDg++ e+E + ++  l++ +  +++ eeak ++ + +   +e+  + +f   l  ++sp+ ++++i++++ i  
  gi|474933928|ref|YP_007687510.1|  56 MAADGKLAEAEFNLIKPGLEAFMgqEVPFEEAKRIFNKLQLNTNENKNVVDFMVDLLGQVSPQMKIDIITVCMLICA 132
                                       78*************9888554322577789999999999999999999**************************** PP

                              TerB 113 ADGeldeaEdavlrrv 128
                                        DG+++ +E+a +r+ 
  gi|474933928|ref|YP_007687510.1| 133 VDGRISGKEKAWIRQL 148
                                       **************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1066.25
//
Query:       gi|474933929|ref|YP_007687511.1|  [L=264]
Description: putative hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-20   73.6   0.0    2.7e-15   56.7   0.0    2.1  2  Abhydrolase_1  alpha/beta hydrolase fold
    2.5e-13   49.8   0.0      1e-12   47.8   0.0    1.8  1  Hydrolase_4    Serine aminopeptidase, S33
    1.3e-09   39.0   0.0    1.8e-09   38.6   0.0    1.1  1  Abhydrolase_6  Alpha/beta hydrolase family
     0.0081   14.9   0.0      0.012   14.4   0.0    1.2  1  Ndr            Ndr family
  ------ inclusion threshold ------
      0.022   14.2   0.0       0.63    9.5   0.0    2.5  2  Peptidase_S9   Prolyl oligopeptidase family
       0.18   11.3   0.0       0.24   10.9   0.0    1.2  1  Mak10          Mak10 subunit, NatC N(alpha)-terminal acetyltr


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.7   0.0     9e-19   2.7e-15       2     107 ..      20     118 ..      19     138 .. 0.87
   2 !   15.2   0.0   4.3e-06     0.013     206     252 ..     192     241 ..     150     244 .. 0.84

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 9e-19
                                       EEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEE CS
                     Abhydrolase_1   2 vlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlv 78 
                                       +++++ G ++++  w    ++p L k g++vi+lD rGvg+++   +      +++ +add+  ++d l + k ++v
  gi|474933929|ref|YP_007687511.1|  20 PVILIAGVGANHRFWKT--MVPLL-K-GYRVITLDNRGVGETEYKGEI-----QIDIMADDVIHLMDYLHILKAHIV 87 
                                       89999999999996666..66555.5.***************888874.....7888******************** PP

                                       EETHHHHHHHHHHHHHGGGEEEEEEESE..C CS
                     Abhydrolase_1  79 GhSmGGmialayaaeyperVkalvllga..i 107
                                       G+SmG++i+  +a ++p+r ++l+l+++   
  gi|474933929|ref|YP_007687511.1|  88 GWSMGSQISQSLAIRHPKRLQSLTLVSSyqF 118
                                       ***************************9552 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 4.3e-06
                                       C...THHHHSEEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSSH CS
                     Abhydrolase_1 206 e...lknvlaptlvisgtsDplvppkaledlaqllpkkrlvvisdagHla 252
                                            k+++ap+lvi+g  D +v p  ++ + + +pk +++ ++++gH++
  gi|474933929|ref|YP_007687511.1| 192 TterTKDITAPSLVIHGGMDIMVEPLKGRAIGNSIPKCTYIELPGEGHTI 241
                                       155579999***************************************98 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.0   3.5e-16     1e-12      30     236 ..      42     243 ..      21     245 .. 0.77

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 3.5e-16
                       Hydrolase_4  30 qGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfllGhSmGGliallyllrypdkvaglil 106
                                       +G+ v++lD+rG G++   +g++ ++d + dD+  +++ +      l+  ++G SmG+ i+++++ r+p++++ l l
  gi|474933929|ref|YP_007687511.1|  42 KGYRVITLDNRGVGET-EYKGEI-QIDIMADDVIHLMDYLH----ILKAHIVGWSMGSQISQSLAIRHPKRLQSLTL 112
                                       79**************.666644.79***********9998....88999***********************9999 PP

                       Hydrolase_4 107 saPalkikaklk.appllklllkllgkllpklqvsnnlkadslsrdpevvaayeadplvhgkit....vrlllelld 178
                                       +++  + +++ + a  +++++   +   +   +v  nl+ +s +  ++  aay+++  +   ++     r +++ ++
  gi|474933929|ref|YP_007687511.1| 113 VSSY-QFRPH-RsAYFMYQMTKAAAEGRCTMDEV--NLLLNSFCFPESAFAAYAKKGTIMPVPRhpedPREVYKQMT 185
                                       9887.44433.22555555444444444444444..66666666666666677777666444442122466666666 PP

                       Hydrolase_4 179 amk..rleeraakitlPllllhGeaDkvvdpeasrelyerlgskdktlklypglyHelln 236
                                        m+  +++er+++it+P l++hG+ D  v+p + r++ ++++  ++t+   pg  H +  
  gi|474933929|ref|YP_007687511.1| 186 SMDnfDTTERTKDITAPSLVIHGGMDIMVEPLKGRAIGNSIP--KCTYIELPGEGHTIAP 243
                                       666334689999******************************..6999999999998865 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   0.0   5.9e-13   1.8e-09       1     208 [.      21     240 ..      21     249 .. 0.62

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 5.9e-13
                                       EEEE--GC.....GCHHHHHHHHCCTCEEEEE--TTSTS-GGCS--HHH.......CHHHHHHHCCTT..TTSEEEE CS
                     Abhydrolase_6   1 vlllHGagssassWlvapLaallaagvhvlapDlpGhGrsdpppldled.......ladlaalldelaagggpvvlv 70 
                                       v+l+ G g++++ W    +++ll + ++v+++D +G G+     +++         ++d+ +l d l     ++++v
  gi|474933929|ref|YP_007687511.1|  21 VILIAGVGANHRFWK--TMVPLLKG-YRVITLDNRGVGE-----TEYKGeiqidimADDVIHLMDYLH--ILKAHIV 87 
                                       79************7..55555555.588*********4.....444443322233377788888885..8889*** PP

                                       EETCHHHHHHHHHHCC.......EE.EEES-..----TTTS----TTHHHHHHTT-C.......CCCHCCHS-HSCC CS
                     Abhydrolase_6  71 GHSlGGalalaaapla.....lvvg.vlldppptalpagllaaalelllallallrl.......lawlsreplprlf 134
                                       G+S+G  +++    la     ++ +  l+++       + ++a++ +  +  a++ +       l +        +f
  gi|474933929|ref|YP_007687511.1|  88 GWSMGSQISQS---LAirhpkRLQSlTLVSS---YQFRPHRSAYFMYQMTKAAAEGRctmdevnLLLN-------SF 151
                                       ******97777...44433576666577777...5555554444444444444444445533212222.......22 PP

                                       CCHHH...C..........CCCHCHCCCGHHHHCCHHCHTTCCHHTT-TTGCEEE.CTT-CHHHHCHHCCCH..STT CS
                     Abhydrolase_6 135 laded...a..........daawrarlarlaallaglgllpaaawadlpvpllvl.ggeDplvprllerlla..qag 195
                                       + +e+   a           ++  ++     + ++++ + + ++ +d+++p lv+ gg D +v +l  r+    +++
  gi|474933929|ref|YP_007687511.1| 152 CFPESafaAyakkgtimpvPRHPEDPREVYKQMTSMDNFDTTERTKDITAPSLVIhGGMDIMVEPLKGRAIGnsIPK 228
                                       2222211111222222221233333333333555566677899*********9996789999999988777789999 PP

                                       EEETCE...SSS- CS
                     Abhydrolase_6 196 arlpvvlpgaGHl 208
                                       +++ ++lpg GH 
  gi|474933929|ref|YP_007687511.1| 229 CTY-IELPGEGHT 240
                                       999.********4 PP

>> Ndr  Ndr family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   3.9e-06     0.012      82     148 ..      65     131 ..      59     158 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.9e-06
                                       HHHHHTTHHHHHHHHT---EEEEEETHHHHHHHHHHHHSGGGEEEEEEES---S---HHHHHHHHHH CS
                               Ndr  82 lddladqllavldhfklksviglGvgaGAyilarfalkhperveglvLinitskaagwvewakeKls 148
                                       +d +ad++ +++d++++ ++  +G   G  i    a++hp+r+++l L++     +    ++ + ++
  gi|474933929|ref|YP_007687511.1|  65 IDIMADDVIHLMDYLHILKAHIVGWSMGSQISQSLAIRHPKRLQSLTLVSSYQFRPHRSAYFMYQMT 131
                                       6789*********************************************988777766666666666 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.038   1.1e+02      45      87 ..      69     105 ..      31     114 .. 0.62
   2 ?    9.5   0.0   0.00021      0.63     121     161 ..     174     218 ..     157     251 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.038
                                       HHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHHHHHHH-GG CS
                      Peptidase_S9  45 fdDfiaaaealakegyvdserlaitGgSyGGyltgaalnqrpd 87 
                                       +dD+i  +++l         +  i G+S G + +  ++ ++p+
  gi|474933929|ref|YP_007687511.1|  69 ADDVIHLMDYL------HILKAHIVGWSMGSQISQSLAIRHPK 105
                                       34444444444......44466788888888888877777776 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00021
                                       TTTCHHHHHHHHHH-CGGG--....---EEEEEEETT-SSS-THH CS
                      Peptidase_S9 121 peeneegykelspyspldnvk....aypplLlihGlaDdrvppae 161
                                       pe+ +e yk++ ++++ d  +    +++p L+ihG +D  v p +
  gi|474933929|ref|YP_007687511.1| 174 PEDPREVYKQMTSMDNFDTTErtkdITAPSLVIHGGMDIMVEPLK 218
                                       556789999999999999988999**************9987765 PP

>> Mak10  Mak10 subunit, NatC N(alpha)-terminal acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   8.1e-05      0.24      43     125 ..      62     154 ..      48     194 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8.1e-05
                             Mak10  43 dvsapllpeevlgimdrll...asemaWhsgssLsqTvftclYveklllpspkalkeakfsr........kedeeke 108
                                       +++ ++ +++v+++md l    a+++ W +gs +sq++   ++ ++l++ +  +  + +++r        +++ ++ 
  gi|474933929|ref|YP_007687511.1|  62 EIQIDIMADDVIHLMDYLHilkAHIVGWSMGSQISQSL-AIRHPKRLQSLTLVSSYQFRPHRsayfmyqmTKAAAEG 137
                                       555666799*******875333788************6.78999999998888888888877888888775556666 PP

                             Mak10 109 ktelelvdkvLrayvla 125
                                       +  ++ v+  L+++++ 
  gi|474933929|ref|YP_007687511.1| 138 RCTMDEVNLLLNSFCFP 154
                                       77788888889988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1777.37
//
Query:       gi|474933930|ref|YP_007687512.1|  [L=177]
Description: 2-oxoglutarate ferredoxin oxidoreductase, gamma subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-33  114.3   0.0    7.5e-33  114.1   0.0    1.0  1  POR       Pyruvate ferredoxin/flavodoxin oxidoreductase


Domain annotation for each model (and alignments):
>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.1   0.0   4.2e-37   7.5e-33       1     176 [.      12     175 ..      12     176 .. 0.95

  Alignments for each domain:
  == domain 1  score: 114.1 bits;  conditional E-value: 4.2e-37
                                       CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEE CS
                               POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglk 77 
                                       GGqG++++gk++a+a   +G +v++ ++yg+e rGg  ++ v +sd+ ++ s+ v ++d+lva++  +l+++ +++ 
  gi|474933930|ref|YP_007687512.1|  12 GGQGILFTGKVIAYAGLMEGREVSWLPSYGPEMRGGTANCSVCLSDS-KIGSPLVVNPDVLVAMNLPSLEKFEKDVV 87 
                                       9*********************************************9.8888888********************** PP

                                       EEEEEEEECTCGTT-CCHHHCTS-HHHHHHHT-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHT.S-HHHHHHH CS
                               POR  78 pggiiiynseelkpdelkkakeeerelkerlgvrvygvdatkiakeiggneraaNtvmlGalaallg.lplealeea 153
                                       pgg+ii++s+ + ++++  ++e            v+ ++a++ia+++g  + aaN+v+lG l++ ++   +e l+++
  gi|474933930|ref|YP_007687512.1|  88 PGGLIIVDSSIITKKVERSDVE------------VIYLPASEIAENAGI-KGAANMVILGKLFKETSfCTPENLDKG 151
                                       *********9999988888776............89********88777.*****************9999****** PP

                                       HHCCS-CH..HHHHHHHHHHHHHH CS
                               POR 154 ikkrfpkkk.eviekNlkafragy 176
                                       ++k++p kk ++++kN  ++++g 
  gi|474933930|ref|YP_007687512.1| 152 LQKTIPAKKmDLLDKNRLCIKLGT 175
                                       ******9999********999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 1039.83
//
Query:       gi|474933931|ref|YP_007687513.1|  [L=250]
Description: Pyruvate:ferredoxin oxidoreductase-related 2-oxoacid:ferredoxin oxidoreductase, beta subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.1e-25   88.1   1.6    6.9e-25   87.6   1.6    1.1  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
  ------ inclusion threshold ------
      0.029   13.3   2.3       0.55    9.1   0.3    2.1  2  E1_dh         Dehydrogenase E1 component


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.6   1.6   7.7e-29   6.9e-25       2     153 .]      51     210 ..      50     210 .. 0.87

  Alignments for each domain:
  == domain 1  score: 87.6 bits;  conditional E-value: 7.7e-29
                                       SSHHHHHHHHHHTTSSSSEEEC.ETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEE CS
                      TPP_enzyme_C   2 iGcltlwaarllkvkrprsylt.sgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpit 76 
                                       +Gc+ +           ++y+  + + + +G++ ++A+G+k+a+pd  v+ + GDG+++ i + e+++a+ r+ +i+
  gi|474933931|ref|YP_007687513.1|  51 VGCSVF----------TYNYFGcDMVQAPHGRAPAVATGVKRARPDDVVFTYQGDGDLAAIgMGETVHAAARGENIV 117
                                       677777..........677888677999************************************************* PP

                                       EEEEE-SBCCCHHHH...HHHHTCCTTTTSBB.....BS----HHHHHHHT.TSEEE.EES...SH.HHHHHHHHHH CS
                      TPP_enzyme_C  77 vvvlnNegygmtggq...qepfggkrksgpagk....dlkpvdfaklaeal.Gakga.rve...kadveeleealke 141
                                        + +nN++ygmtggq   ++  g+ ++++p+g+     ++p+++++l  ++ G+  a rv+   +++v+  ++a+k+
  gi|474933931|ref|YP_007687513.1| 118 AIFINNAIYGMTGGQmapTTLPGQVTQTTPYGRdtsvAGNPIRVCELLSSVkGVALAqRVTvdcVKNVKAAKKAIKK 194
                                       ******************99999********99999879***********967775566661124566777999999 PP

                                       HH....CSSSEEEEEE CS
                      TPP_enzyme_C 142 al....ekkgpaliev 153
                                       a+    + kg ++iev
  gi|474933931|ref|YP_007687513.1| 195 AFeyqmAGKGYCIIEV 210
                                       9988888888888876 PP

>> E1_dh  Dehydrogenase E1 component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.3   6.2e-05      0.55     106     167 ..      67     130 ..      56     149 .. 0.82
   2 ?    4.2   0.1    0.0019        17     190     223 ..     177     211 ..     160     213 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 6.2e-05
                                       HHHHHH..HHHHHHHHHTS---EEEEEEGGGTT-HHHHHHHHHHHHTT--EEEEEEEESEETTE CS
                             E1_dh 106 qvplva..GialaakiegkkevailliGDgAanqGdvyealnlaalwklpvifvveNNkygisT 167
                                       q+p++    +a   k +  + v++++ GDg  +   + e+++ aa  +  v  +++N  yg++ 
  gi|474933931|ref|YP_007687513.1|  67 QAPHGRapAVATGVKRARPDDVVFTYQGDGDLAAIGMGETVHAAARGENIVAIFINNAIYGMTG 130
                                       6677774455666789999************5555589****99999999988899999***96 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0019
                                       EEEET.TSHHHHHHHHHHHHHHHHTTT--EEEEEE CS
                             E1_dh 190 lrVdg.nDplavyeAvkfAaeraregkgpllielv 223
                                       ++Vd  + + a ++A k A e+  +gkg  +ie+v
  gi|474933931|ref|YP_007687513.1| 177 VTVDCvKNVKAAKKAIKKAFEYQMAGKGYCIIEVV 211
                                       6666535678999********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1523.96
//
Query:       gi|474933932|ref|YP_007687514.1|  [L=353]
Description: Pyruvate:ferredoxin oxidoreductase-related 2-oxoacid:ferredoxin oxidoreductase, alpha subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.9e-50  169.9   0.0      9e-50  169.6   0.0    1.1  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    3.8e-26   91.4   0.1    7.7e-26   90.4   0.1    1.5  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
    3.6e-07   30.1   0.0    7.5e-07   29.1   0.0    1.5  1  Transketolase_C  Transketolase, C-terminal domain
    0.00024   20.7   0.1    0.00035   20.2   0.1    1.3  1  TPP_enzyme_N     Thiamine pyrophosphate enzyme, N-terminal TP


Domain annotation for each model (and alignments):
>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.6   0.0     2e-53     9e-50       1     189 [.      15     206 ..      15     246 .. 0.83

  Alignments for each domain:
  == domain 1  score: 169.6 bits;  conditional E-value: 2e-53
                                       .HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCC CS
                             POR_N   1 eaaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmie 77 
                                       eaaiaag++ +++YPITP++e+a  +++ ++k +     ++q+esE+++i++v+GA aaG+r++T TS++G++Lm+e
  gi|474933932|ref|YP_007687514.1|  15 EAAIAAGCRHFFGYPITPQTEVAAYMSKRMPKIGG---LYLQAESEVASINMVLGAGAAGVRVMTSTSSPGISLMSE 88 
                                       699*******************************5...9************************************** PP

                                       CHHHHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHH......S---EEEE-SSHHHHHHHHHHHHHHHHHCTSE CS
                             POR_N  78 nlglaageelPvvivvvaRalpstglsirtdqsDlmaar......dtglivlasenvqeafdlalvAfnlAekvrvP 148
                                        + ++ag+ +P++iv+v R++p     i+++qsD ++a       d+ l+v+a+++vqe  dl+  Af l  k+r+P
  gi|474933932|ref|YP_007687514.1|  89 GISYIAGSDVPCLIVNVERGGPGL-GGIQPSQSDYFQATkatghgDFHLLVFAPSTVQETVDLISDAFDLGDKYRMP 164
                                       ************************.89************************************************** PP

                                       EEEEEEHHHH.HEEEEEEC-SGG.GS-----SBX..XXXXXXX CS
                             POR_N 149 vivlfDgfllshevekvelpdeedelklikekle..eyerkey 189
                                        ++l+Dg l+  ++e+v lp+  + ++ ++  ++  + +rk++
  gi|474933932|ref|YP_007687514.1| 165 TMILSDGLLG-QMMEPVVLPEPREPVDNKDWAAKghQGKRKHN 206
                                       **********.********998855544443333003333333 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.4   0.1   1.7e-29   7.7e-26       1     102 []     247     341 ..     247     341 .. 0.99

  Alignments for each domain:
  == domain 1  score: 90.4 bits;  conditional E-value: 1.7e-29
                                       -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHH CS
                           PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaa 77 
                                       Ae+++va+G++++ ++savd++R++gik+Gl+r++tl+P+P + +++ + ++k+++++++n+     Gq+ve+v++ 
  gi|474933932|ref|YP_007687514.1| 247 AEIILVAFGASSRICHSAVDMARAQGIKAGLVRPITLWPYPDKTIRKHIGHAKAFLSVEMNM-----GQMVEDVRTI 318
                                       9*************************************************************.....********** PP

                                       TGGGTSEEEEEE--GGG----HHHH CS
                           PFOR_II  78 lkkskvkvvnfvaglgGrditvedi 102
                                       ++++  k+v f+++ gG ++t++++
  gi|474933932|ref|YP_007687514.1| 319 VEGK--KPVLFFGRTGGVVPTPKEV 341
                                       **99..****************997 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   1.7e-10   7.5e-07       7      71 ..     244     308 ..     240     349 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 1.7e-10
                                       ETTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEE CS
                   Transketolase_C   7 regkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeav 71 
                                        +  +++lva+G+  + +  A+++++++gi+a +v ++t++p   +ti++ + + + ++ ve ++
  gi|474933932|ref|YP_007687514.1| 244 ADDAEIILVAFGASSRICHSAVDMARAQGIKAGLVRPITLWPYPDKTIRKHIGHAKAFLSVEMNM 308
                                       56789********************************************9999999999888654 PP

>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.1   7.7e-08   0.00035       1     106 [.       7     113 ..       7     167 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 7.7e-08
                                       EEHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT....TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHH CS
                      TPP_enzyme_N   1 mtvaealvraLkalgvehvfgvpGsrilplldalseeq...girvvlarhEqgaafaAdgyaratgkpgvvlvtsgp 74 
                                       m++ ea+++a  a+g +h+fg+p +  +++  ++s++    g  +++a +E + +++  g   a   + v   ts p
  gi|474933932|ref|YP_007687514.1|   7 MKGNEAIAEAAIAAGCRHFFGYPITPQTEVAAYMSKRMpkiGGLYLQAESEVASINMVLGAGAAG--VRVMTSTSSP 81 
                                       7899*********************************99888889999999999***99998885..677778889* PP

                                       HHHHCHHHHHHHHHHT--EEEEEEE--CCCHH CS
                      TPP_enzyme_N  75 GatnaltalaeAkvdriPllvlsgdrptslrg 106
                                       G+  +  ++   + + +P+l++  +r+    g
  gi|474933932|ref|YP_007687514.1|  82 GISLMSEGISYIAGSDVPCLIVNVERGGPGLG 113
                                       *********************99888777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2169.01
//
Query:       gi|474933933|ref|YP_007687515.1|  [L=69]
Description: 2-oxoglutarate ferredoxin oxidoreductase, delta subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-11   42.1  18.8    1.5e-05   24.6   4.4    2.2  2  Fer4      4Fe-4S binding domain
    1.3e-08   34.4  13.6    0.00033   20.6   2.5    2.2  2  Fer4_2    4Fe-4S binding domain
    1.4e-08   34.4  18.6    5.4e-06   26.2   3.9    2.2  2  Fer4_6    4Fe-4S binding domain
    2.2e-08   34.6  12.3    3.9e-08   33.8  12.4    1.4  1  Fer4_7    4Fe-4S dicluster domain
    3.5e-08   33.4  16.2    9.7e-05   22.4   2.2    2.0  2  Fer4_10   4Fe-4S dicluster domain
    6.8e-08   32.6  26.6    3.5e-06   27.1  15.3    1.9  2  Fer4_9    4Fe-4S dicluster domain
    3.7e-07   30.2  17.6     0.0017   18.4   6.4    1.9  2  Fer4_21   4Fe-4S dicluster domain
    4.7e-07   29.8  15.2    0.00055   20.2   1.0    2.2  2  Fer4_4    4Fe-4S binding domain
    1.9e-05   25.3  10.8     0.0013   19.4   0.6    2.2  2  Fer4_15   4Fe-4S single cluster domain
    0.00017   22.4  16.3     0.0084   17.0  13.2    2.1  2  Fer4_16   4Fe-4S double cluster binding domain
     0.0002   22.1  12.0      0.006   17.4   3.1    2.1  2  Fer4_22   4Fe-4S dicluster domain
    0.00041   20.8  17.4      0.073   13.6   6.5    2.1  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
     0.0096   16.5  17.4       0.28   11.7   3.7    2.1  2  Fer4_17   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.011   16.1  18.4       0.36   11.3   4.1    2.1  2  Fer4_8    4Fe-4S dicluster domain
      0.079   13.9  20.6        0.1   13.6   4.3    2.3  2  Fer4_3    4Fe-4S binding domain
       0.25   11.6  13.0        1.4    9.1   2.4    2.1  2  Fer4_18   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   4.4   1.3e-08   1.5e-05       1      21 [.       4      24 ..       4      26 .. 0.90
   2 !   23.6   6.5   2.7e-08   3.1e-05       2      20 ..      43      61 ..      42      65 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.3e-08
                                      EEEETTTSSS-THHHHHSTTT CS
                              Fer4  1 vvideekCigCGaCvevCPvg 21
                                      v++d ++C gC  Cv +CP  
  gi|474933933|ref|YP_007687515.1|  4 VIVDNNRCKGCEMCVIACPKK 24
                                      689****************75 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 2.7e-08
                                      EEETTTSSS-THHHHHSTT CS
                              Fer4  2 videekCigCGaCvevCPv 20
                                      v de kCigCG C  +CP 
  gi|474933933|ref|YP_007687515.1| 43 VTDETKCIGCGSCTIMCPD 61
                                      679***************5 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   3.5   5.6e-07   0.00063       2      21 ..       3      22 ..       2      23 .. 0.92
   2 !   20.6   2.5   2.9e-07   0.00033       4      21 ..      43      60 ..      38      61 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 5.6e-07
                            Fer4_2  2 pvvvdtdrCigCgaCvsaCP 21
                                      +v vd +rC gC+ Cv aCP
  gi|474933933|ref|YP_007687515.1|  3 KVIVDNNRCKGCEMCVIACP 22
                                      68899**************9 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 2.9e-07
                            Fer4_2  4 vvdtdrCigCgaCvsaCP 21
                                      v d+ +CigCg+C+  CP
  gi|474933933|ref|YP_007687515.1| 43 VTDETKCIGCGSCTIMCP 60
                                      45677********999*9 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   3.9   4.9e-09   5.4e-06       1      23 [.       3      25 ..       3      27 .. 0.90
   2 !   14.1   6.9   3.2e-05     0.036       5      21 ..      45      61 ..      43      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 4.9e-09
                            Fer4_6  1 vveidpdkCigCgdCvrvCPega 23
                                      +v +d ++C gC+ Cv++CP ++
  gi|474933933|ref|YP_007687515.1|  3 KVIVDNNRCKGCEMCVIACPKKI 25
                                      5889****************765 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 3.2e-05
                            Fer4_6  5 dpdkCigCgdCvrvCPe 21
                                      d+ kCigCg C++ CP 
  gi|474933933|ref|YP_007687515.1| 45 DETKCIGCGSCTIMCPD 61
                                      899*************5 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8  12.4   3.4e-11   3.9e-08       1      49 [.      10      60 ..      10      63 .. 0.82

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 3.4e-11
                            Fer4_7  1 rCigCgaCvaaCpvkaieldee.enekgt.ekveidpekClgCgaCvavCP 49
                                      rC gC+ Cv aCp k + ld + +n kg  +  + d++kC+gCg+C   CP
  gi|474933933|ref|YP_007687515.1| 10 RCKGCEMCVIACPKKILALDHSvTNGKGYhPAHVTDETKCIGCGSCTIMCP 60
                                      8******************9762444555344466899************* PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   2.2   8.7e-08   9.7e-05       1      24 [.       3      30 ..       3      42 .. 0.77
   2 !   17.3   6.4   3.5e-06    0.0039       3      23 ..      43      63 ..      41      69 .] 0.83

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 8.7e-08
                           Fer4_10  1 kvvidddtCirCgkCvkaCPadl....t 24
                                      kv++d ++C +C+ Cv aCP ++    +
  gi|474933933|ref|YP_007687515.1|  3 KVIVDNNRCKGCEMCVIACPKKIlaldH 30
                                      5899****************97666642 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 3.5e-06
                           Fer4_10  3 vidddtCirCgkCvkaCPadl 23
                                      v d+ +Ci+Cg C+ +CP ++
  gi|474933933|ref|YP_007687515.1| 43 VTDETKCIGCGSCTIMCPDCA 63
                                      67999*************855 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   3.4   5.6e-06    0.0063      34      50 ..       9      25 ..       2      26 .. 0.81
   2 !   27.1  15.3   3.1e-09   3.5e-06       1      51 []      10      64 ..      10      64 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.6e-06
                            Fer4_9 34 eaCigCgaCveaCpkga 50
                                      ++C gC+ Cv aCpk++
  gi|474933933|ref|YP_007687515.1|  9 NRCKGCEMCVIACPKKI 25
                                      57************984 PP

  == domain 2  score: 27.1 bits;  conditional E-value: 3.1e-09
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase....eaCigCgaCveaCpkgai 51
                                      +C gC  Cv aCp+++   d++ +  +  +       ++CigCg+C+  Cp  ai
  gi|474933933|ref|YP_007687515.1| 10 RCKGCEMCVIACPKKILALDHSVTNGKGYHPAHvtdeTKCIGCGSCTIMCPDCAI 64
                                      6***************9888877777766655577779*************8665 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   3.8     4e-06    0.0045      36      52 ..       6      22 ..       2      28 .. 0.78
   2 !   18.4   6.4   1.5e-06    0.0017       3      23 ..      44      64 ..      41      68 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4e-06
                           Fer4_21 36 vvedeCvGCnlCssvCP 52
                                      v +++C GC++C++ CP
  gi|474933933|ref|YP_007687515.1|  6 VDNNRCKGCEMCVIACP 22
                                      56789999999999999 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 1.5e-06
                           Fer4_21  3 idedkCigCgkCliaCedtsh 23
                                       de kCigCg+C+i+C+d ++
  gi|474933933|ref|YP_007687515.1| 44 TDETKCIGCGSCTIMCPDCAI 64
                                      478999999999999999765 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   1.0   4.9e-07   0.00055       2      16 ..       9      23 ..       8      34 .. 0.91
   2 !   14.8   7.2   2.8e-05     0.031       3      16 ..      48      61 ..      46      63 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 4.9e-07
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      +rC gC  Cv+aCP 
  gi|474933933|ref|YP_007687515.1|  9 NRCKGCEMCVIACPK 23
                                      79************5 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 2.8e-05
                            Fer4_4  3 rCigCgsCvaaCPq 16
                                      +CigCgsC++ CP+
  gi|474933933|ref|YP_007687515.1| 48 KCIGCGSCTIMCPD 61
                                      8************6 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.6   1.2e-06    0.0013       1      21 [.       4      24 ..       4      36 .. 0.87
   2 !   10.5   3.9   0.00072      0.81       4      20 ..      45      61 ..      43      66 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.2e-06
                           Fer4_15  1 VvvDrdaCigcglCvaeapev 21
                                      V vD ++C gc++Cv ++p+ 
  gi|474933933|ref|YP_007687515.1|  4 VIVDNNRCKGCEMCVIACPKK 24
                                      78****************875 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00072
                           Fer4_15  4 DrdaCigcglCvaeape 20
                                      D+++Cigcg C   +p+
  gi|474933933|ref|YP_007687515.1| 45 DETKCIGCGSCTIMCPD 61
                                      99**********99997 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0  13.2   7.5e-06    0.0084       1      65 [.      10      60 ..      10      61 .. 0.87
   2 !   12.2   6.2   0.00024      0.27       1      20 [.      48      67 ..      48      69 .] 0.90

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 7.5e-06
                           Fer4_16  1 rCgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCP 65
                                      rC++C+ C+ +CP + +  +   +          +++ k++++ + +++  ++++gC+ C+ +CP
  gi|474933933|ref|YP_007687515.1| 10 RCKGCEMCVIACPKKILALD--HS----------VTNGKGYHPAHVTDE--TKCIGCGSCTIMCP 60
                                      6*******************..23..........455688888888887..89***********9 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00024
                           Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                      +C++Cg C+ +CP  aik +
  gi|474933933|ref|YP_007687515.1| 48 KCIGCGSCTIMCPDCAIKVE 67
                                      5****************976 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   1.6   0.00084      0.94      78      96 .]       7      25 ..       2      25 .. 0.87
   2 !   17.4   3.1   5.4e-06     0.006       1      16 [.      48      63 ..      36      68 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00084
                           Fer4_22 78 gesgCvGCgRCieacpvki 96
                                      +++ C GC  C+ acp+ki
  gi|474933933|ref|YP_007687515.1|  7 DNNRCKGCEMCVIACPKKI 25
                                      6789***********9987 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 5.4e-06
                           Fer4_22  1 rClsCgaCtlvCptCs 16
                                      +C++Cg+Ct++Cp C 
  gi|474933933|ref|YP_007687515.1| 48 KCIGCGSCTIMCPDCA 63
                                      6999999999999996 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   3.1   9.1e-05       0.1       1      18 [.       6      23 ..       6      25 .. 0.96
   2 !   13.6   6.5   6.5e-05     0.073       2      18 ..      45      61 ..      43      62 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.1e-05
                           Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                      VD+++C +c+ Cv ++P+
  gi|474933933|ref|YP_007687515.1|  6 VDNNRCKGCEMCVIACPK 23
                                      9****************6 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 6.5e-05
                           Fer4_13  2 DrdtCiacgaCvelaPd 18
                                      D+ +Ci+cg+C  ++Pd
  gi|474933933|ref|YP_007687515.1| 45 DETKCIGCGSCTIMCPD 61
                                      889*************9 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   3.7   0.00025      0.28      44      60 ..       9      25 ..       6      26 .. 0.79
   2 !    9.4   6.5    0.0013       1.5       1      16 [.      48      63 ..      48      67 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00025
                           Fer4_17 44 slCieCgeCerkCPqgl 60
                                      ++C +C++C+ +CP+++
  gi|474933933|ref|YP_007687515.1|  9 NRCKGCEMCVIACPKKI 25
                                      68888888888888765 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0013
                           Fer4_17  1 rCiqCgyClpeCpsye 16
                                      +Ci+Cg C+ +Cp ++
  gi|474933933|ref|YP_007687515.1| 48 KCIGCGSCTIMCPDCA 63
                                      5888888888888776 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   4.1   0.00032      0.36      49      65 .]       9      25 ..       6      25 .. 0.91
   2 ?   10.5   6.5   0.00058      0.65       4      16 ..      48      60 ..      45      67 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00032
                            Fer4_8 49 wsCttcgaCtevCpvgi 65
                                      ++C +c++C+ +Cp++i
  gi|474933933|ref|YP_007687515.1|  9 NRCKGCEMCVIACPKKI 25
                                      68************997 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00058
                            Fer4_8  4 kCieCgaCqsaCp 16
                                      kCi+Cg C+ +Cp
  gi|474933933|ref|YP_007687515.1| 48 KCIGCGSCTIMCP 60
                                      8999999999998 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   4.3   9.3e-05       0.1       1      14 [.      11      24 ..      11      25 .. 0.94
   2 ?    6.3   8.4     0.019        22       1      12 [.      49      60 ..      49      63 .. 0.96

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.3e-05
                            Fer4_3  1 CtgCgaCvevCPvg 14
                                      C gC+ Cv +CP++
  gi|474933933|ref|YP_007687515.1| 11 CKGCEMCVIACPKK 24
                                      9***********98 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.019
                            Fer4_3  1 CtgCgaCvevCP 12
                                      C+gCg C   CP
  gi|474933933|ref|YP_007687515.1| 49 CIGCGSCTIMCP 60
                                      ***********9 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   2.4    0.0013       1.4      58      75 ..       8      25 ..       3      31 .. 0.87
   2 ?    8.7   3.0    0.0017       1.9      53      73 ..      41      61 ..      28      68 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0013
                           Fer4_18 58 agdcidcescvkvcPtgi 75
                                      ++ c  ce+cv  cP +i
  gi|474933933|ref|YP_007687515.1|  8 NNRCKGCEMCVIACPKKI 25
                                      678************987 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0017
                           Fer4_18 53 rkekgagdcidcescvkvcPt 73
                                       + +++++ci c+sc  +cP 
  gi|474933933|ref|YP_007687515.1| 41 AHVTDETKCIGCGSCTIMCPD 61
                                      46678899***********94 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      164  (0.00914719); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 421.87
//
Query:       gi|474933934|ref|YP_007687516.1|  [L=231]
Description: hypothetical protein TALC_00347 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-08   34.5   0.0    5.3e-08   33.0   0.0    1.8  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    1.8e-05   24.3   0.0    2.8e-05   23.7   0.0    1.2  1  ParA         NUBPL iron-transfer P-loop NTPase
    0.00018   21.5   0.0    0.00035   20.5   0.0    1.4  1  AAA_31       AAA domain
    0.00083   18.8   0.0     0.0015   17.9   0.0    1.4  1  ATPase       KaiC
     0.0027   17.3   0.0     0.0058   16.2   0.0    1.5  1  AAA_25       AAA domain
     0.0031   17.2   0.0     0.0068   16.2   0.0    1.5  1  IstB_IS21    IstB-like ATP binding protein
     0.0065   16.1   0.0      0.016   14.9   0.0    1.8  2  SRP54        SRP54-type protein, GTPase domain
     0.0075   16.1   0.1      0.068   13.0   0.0    2.0  2  CLP1_P       mRNA cleavage and polyadenylation factor CLP1 P-
  ------ inclusion threshold ------
      0.011   15.0   0.0      0.015   14.5   0.0    1.3  1  ArsA_ATPase  Anion-transporting ATPase
      0.013   15.6   0.3      0.045   13.9   0.3    2.1  1  AAA_33       AAA domain
      0.019   14.5   0.0      0.028   13.9   0.0    1.3  1  PhoH         PhoH-like protein
      0.027   13.9   0.0      0.048   13.1   0.0    1.3  1  KTI12        Chromatin associated protein KTI12
      0.034   13.4   0.0      0.069   12.4   0.0    1.6  1  MipZ         ATPase MipZ
      0.045   13.0   0.1      0.092   12.0   0.0    1.6  2  Rad51        Rad51


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.0   4.2e-11   5.3e-08       9     104 ..      16     149 ..       8     187 .. 0.78

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 4.2e-11
                                       TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH............................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................... RF
                              CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep............................... 54 
                                       G+GKT l++nLa + a++g +V l+D+D+  +  ++ +  e    +                               
  gi|474933934|ref|YP_007687516.1|  16 GTGKTNLSINLALSCADEGEKVTLIDMDVVNPYFRSSDYAE----Eltargvrvigpnfansnldtpslpaaigdai 88 
                                       9*****************************88887444444....2455599999********************99 PP

                                       ...............CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHC CS
                                       ...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ...............dlkrllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqry 104
                                                      ++  l+  +++l+ +       + +v+nr++++ +   +  ++  +++r+
  gi|474933934|ref|YP_007687516.1|  89 segerviidvggddaGATALGVYARQLSSS----EPDVLYVINRYRSQTTVPGEAVQILSEIERT 149
                                       999999999999888888888888888888....678999*******987777777776666666 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   2.2e-08   2.8e-05       4      45 ..       6      47 ..       4      64 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.2e-08
                              ParA  4 kviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGp 45
                                      + ++v+ g  G GK+ +++nlAl+ a++g kv l+D+D++ p
  gi|474933934|ref|YP_007687516.1|  6 NRVTVICGHYGTGKTNLSINLALSCADEGEKVTLIDMDVVNP 47
                                      6789**********************************9866 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   2.7e-07   0.00035      12      40 ..      16      44 ..       7      56 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.7e-07
                            AAA_31 12 GvGKTTtsvnlaaalaklgkkvLlvDlDp 40
                                      G GKT  s+nla + a +g+kv l+D+D 
  gi|474933934|ref|YP_007687516.1| 16 GTGKTNLSINLALSCADEGEKVTLIDMDV 44
                                      99*************************95 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.2e-06    0.0015      16      58 ..       3      44 ..       1      64 [. 0.89

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.2e-06
                            ATPase 16 ipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtvee 58
                                      +  +rv+ i+G++GtGKt ++ + +++ a + ge++ ++ ++ 
  gi|474933934|ref|YP_007687516.1|  3 FLTNRVTVICGHYGTGKTNLSINLALSCADE-GEKVTLIDMDV 44
                                      6789***********************9999.****9998775 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   4.6e-06    0.0058      33      64 ..       6      38 ..       2      49 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.6e-06
                            AAA_25 33 gelallaGapgtGKttlaldlalava.tGkpwl 64
                                      + +++++G+ gtGKt l ++lal++a +G++++
  gi|474933934|ref|YP_007687516.1|  6 NRVTVICGHYGTGKTNLSINLALSCAdEGEKVT 38
                                      6799**********************9998765 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   5.3e-06    0.0068      49      83 ..       8      42 ..       2      61 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.3e-06
                         IstB_IS21 49 nivllGpsGvGKshlaialgveavraglsvlfvrv 83
                                        v++G+ G+GK+ l+i l+ + + +g +v+ + +
  gi|474933934|ref|YP_007687516.1|  8 VTVICGHYGTGKTNLSINLALSCADEGEKVTLIDM 42
                                      5799*************************998766 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.2e-05     0.016       2      40 ..       7      45 ..       6     109 .. 0.87
   2 ?   -2.6   0.0       2.7   3.4e+03     162     182 ..     182     202 ..     181     207 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.2e-05
                                      EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTS CS
                             SRP54  2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtf 40
                                      +v++++G  G+GKT     La  + +eg+kv l+ +D+ 
  gi|474933934|ref|YP_007687516.1|  7 RVTVICGHYGTGKTNLSINLALSCADEGEKVTLIDMDVV 45
                                      5889********************************974 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.7
                                       HHHHHTS-EEEEE-SSSTTGE CS
                             SRP54 162 iaaelklPikfigvGekiedl 182
                                       +++ ++lP++f++v   ++ l
  gi|474933934|ref|YP_007687516.1| 182 VSRITGLPVRFTTVPAGVDLL 202
                                       678899*****9997777655 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   5.3e-05     0.068       1      33 [.      13      45 ..      13      52 .. 0.91
   2 ?    0.8   0.0      0.28   3.5e+02     102     144 ..      90     134 ..      84     170 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.3e-05
                            CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvG 33
                                      G+  +GK+ l+ +L+  ++ +g+k++++D+Dv 
  gi|474933934|ref|YP_007687516.1| 13 GHYGTGKTNLSINLALSCADEGEKVTLIDMDVV 45
                                      67789**************************96 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.28
                            CLP1_P 102 kasgliIntpGwvkgl.gaellleliealepdvvvvldq.eelln 144
                                       + +++iI+  G   g+ ++ +  + ++  epdv++v+ + + +  
  gi|474933934|ref|YP_007687516.1|  90 EGERVIIDVGGDDAGAtALGVYARQLSSSEPDVLYVINRyRSQTT 134
                                       567788888884444322345577788889999999988433333 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.2e-05     0.015       2      61 ..       7      69 ..       6     104 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.2e-05
                                      EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S...TTTHHHHHHTS--BSS-EEETSS CS
                       ArsA_ATPase  2 kvilvgGKGGVGKttvsaatavklsekgkkvllistD...PAhslsDsfdqklgkeptkvkeN 61
                                      +v ++ G  G GKt +s  +a+ ++++g+kv li  D   P    sD  ++   + ++ +  N
  gi|474933934|ref|YP_007687516.1|  7 RVTVICGHYGTGKTNLSINLALSCADEGEKVTLIDMDvvnPYFRSSDYAEELTARGVRVIGPN 69
                                      677899****************************98844444555555555444555555555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.3   3.5e-05     0.045       1      33 [.       8     111 ..       8     231 .] 0.63

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.5e-05
                            AAA_33   1 lvllvGlpGsGKstlaerllkklg.....avllssdt........................................ 32 
                                       +++++G+ G+GK+ l+ +l+   +     ++l++ d+                                        
  gi|474933934|ref|YP_007687516.1|   8 VTVICGHYGTGKTNLSINLALSCAdegekVTLIDMDVvnpyfrssdyaeeltargvrvigpnfansnldtpslpaai 84 
                                       6899***************6544455588888888887777777776666666665555555555555555555555 PP

                            AAA_33  33 ..........................l 33 
                                                                 +
  gi|474933934|ref|YP_007687516.1|  85 gdaisegerviidvggddagatalgvY 111
                                       555555555555555555555444443 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.2e-05     0.028      18      49 ..       5      36 ..       1      51 [. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.2e-05
                                      H-SEEEEE--TTSSTTHHHHHHHHHHHHTTS- CS
                              PhoH 18 kndivfaiGpaGtGKtylavalavealkkkkv 49
                                      +n ++++ G+ GtGKt l++ la++   +++ 
  gi|474933934|ref|YP_007687516.1|  5 TNRVTVICGHYGTGKTNLSINLALSCADEGEK 36
                                      6889********************99988654 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.7e-05     0.048       5      57 ..      10      64 ..       8      78 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.7e-05
                                      EEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH...TTSSS--GGGHHHHH CS
                             KTI12  5 vltGlPssGKstrakeLakaleeekrsvvviddeslg..iekdsykdsakekalR 57
                                      v++G+  +GK+ ++ +La   ++e+ +v++id + ++  +++++y+++ + + +R
  gi|474933934|ref|YP_007687516.1| 10 VICGHYGTGKTNLSINLALSCADEGEKVTLIDMDVVNpyFRSSDYAEELTARGVR 64
                                      89**********************************9999999999988877776 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   5.4e-05     0.069      10      40 ..      15      45 ..       7     111 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.4e-05
                                      TTSSHHHHHHHHHHHHHTTT--EEEEE--TT CS
                              MipZ 10 GGsGksttavhvavaLlkkGarvaaidldlr 40
                                       G+Gk+  ++ +a + +++G +v+ id+d+ 
  gi|474933934|ref|YP_007687516.1| 15 YGTGKTNLSINLALSCADEGEKVTLIDMDVV 45
                                      59***************************85 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.1e-05     0.092      36      61 ..       5      30 ..       3      63 .. 0.93
   2 ?   -3.8   0.0       4.6   5.9e+03      10      28 ..     157     175 ..     151     176 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.1e-05
                                      SSSEEEEEESTTSSHHHHHHHHHHHT CS
                             Rad51 36 tgsiteifGefrsGktqlchtlcvtv 61
                                      t  +t i+G +++Gkt l+ +l++ +
  gi|474933934|ref|YP_007687516.1|  5 TNRVTVICGHYGTGKTNLSINLALSC 30
                                      6789********************98 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 4.6
                                       HHHHHSS-EE--S-HHHHH CS
                             Rad51  10 lekrsellqlttGskklDe 28 
                                       l + s+l +ltt ++ lD+
  gi|474933934|ref|YP_007687516.1| 157 LVNNSHLQHLTTAETVLDS 175
                                       4567788889999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.53
# Mc/sec: 1313.50
//
Query:       gi|474933935|ref|YP_007687517.1|  [L=184]
Description: Cupin domain protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.6e-13   49.0   0.2    5.9e-13   48.3   0.2    1.3  1  Cupin_2         Cupin domain
    6.3e-09   35.8   0.2    9.6e-09   35.2   0.2    1.2  1  HTH_3           Helix-turn-helix
      1e-08   35.4   0.0    1.5e-08   34.9   0.0    1.2  1  HTH_31          Helix-turn-helix domain
    3.7e-08   33.3   0.1    5.6e-08   32.7   0.1    1.2  1  HTH_19          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.017   15.0   0.0      0.036   13.9   0.0    1.6  1  HTH_25          Helix-turn-helix domain
      0.024   14.7   0.0      0.038   14.1   0.0    1.3  1  MqsA_antitoxin  Antitoxin component of bacterial toxin-antito
       0.07   12.8   0.1       0.14   11.9   0.1    1.4  1  Cupin_3         Protein of unknown function (DUF861)
       0.09   12.7   0.0       0.14   12.0   0.0    1.3  1  AraC_binding    AraC-like ligand binding domain
       0.17   12.3   0.0       0.24   11.9   0.0    1.2  1  HTH_26          Cro/C1-type HTH DNA-binding domain


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.2     3e-16   5.9e-13       6      70 ..     115     179 ..     112     180 .. 0.87

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 3e-16
                                       ETTE.EEEEEC.SSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEEE CS
                           Cupin_2   6 ppGe.sapshr.HpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparllvv 70 
                                         Ge ++p+ + H+ge ef++V++G++ ++++ ee +leaGds+y ++ +pH+++    +pa+++ v
  gi|474933935|ref|YP_007687517.1| 115 RVGEeESPEMSaHEGE-EFIVVVSGKILFIYGKEERILEAGDSAYYNSVVPHYVGAVD-GPAEIYAV 179
                                       567778887777****.*************************************7755.68887765 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.2   4.8e-12   9.6e-09       1      49 [.      11      59 ..      11      63 .. 0.98

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 4.8e-12
                                      HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHT CS
                             HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLg 49
                                      ++++R+q glsqe+LA  +G+   +i  +E G + P +  l++l++aLg
  gi|474933935|ref|YP_007687517.1| 11 IRKYREQMGLSQEDLAINSGIALDSIKEYEEGTSYPPIGSLIRLSRALG 59
                                      8***********************************************9 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.0   7.4e-12   1.5e-08       3      55 ..       8      59 ..       6      65 .. 0.95

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 7.4e-12
                            HTH_31  3 GalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralg 55
                                      G + r +Re+ GLsqe++A  +g+  + +  +E G+   p+ + l +l ralg
  gi|474933935|ref|YP_007687517.1|  8 GKRIRKYREQMGLSQEDLAINSGIALDSIKEYEEGTSY-PPIGSLIRLSRALG 59
                                      899**********************************8.*************9 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.1   2.8e-11   5.6e-08       1      55 [.       8      61 ..       8      67 .. 0.96

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 2.8e-11
                            HTH_19  1 GerLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgid 55
                                      G+r++++Re+ gl+qe+la + gi   +i ++E g + +p+++ l ++++alg+ 
  gi|474933935|ref|YP_007687517.1|  8 GKRIRKYREQMGLSQEDLAINSGIALDSIKEYEEGTS-YPPIGSLIRLSRALGQR 61
                                      99*********************************99.**************985 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.8e-05     0.036       2      34 ..      11      43 ..      10      47 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.8e-05
                                      HHHHHHTTT--HHHHHHHSS--HHHHHHHHCT- CS
                            HTH_25  2 LraaRearglsleevaketkIrkdylealEedd 34
                                       r+ Re++gls e++a    I+ d +++ Ee+ 
  gi|474933935|ref|YP_007687517.1| 11 IRKYREQMGLSQEDLAINSGIALDSIKEYEEGT 43
                                      7999**********************9999985 PP

>> MqsA_antitoxin  Antitoxin component of bacterial toxin-antitoxin system, MqsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.9e-05     0.038      70     120 ..       7      58 ..       1      63 [. 0.87

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.9e-05
                    MqsA_antitoxin  70 dpafiarvrkkleldqreaaeifGgGvnafsryekGkvrppl.alvkllkll 120
                                        ++ i++ r++++l+q+++a   G    +   ye+G + pp+ +l++l + l
  gi|474933935|ref|YP_007687517.1|   7 VGKRIRKYREQMGLSQEDLAINSGIALDSIKEYEEGTSYPPIgSLIRLSRAL 58 
                                       47889**********************************9975788887766 PP

>> Cupin_3  Protein of unknown function (DUF861)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1     7e-05      0.14      24      56 ..     128     159 ..     123     163 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7e-05
                                       SSEEEEEEEECEEEEEETTTEEEEEETTEEEEE CS
                           Cupin_3  24 eedEfcyileGevkvtpeggetvelraGDlvvl 56 
                                       e +Ef+ +++G++ +   g e++ l+aGD++++
  gi|474933935|ref|YP_007687517.1| 128 EGEEFIVVVSGKILFIY-GKEERILEAGDSAYY 159
                                       449**************.9999*********98 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.3e-05      0.14      20      74 ..     126     179 ..     118     183 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.3e-05
                                       TT-SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-TTSEEEEEEE CS
                      AraC_binding  20 vhdeyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesdsedgweyrwl 74 
                                        h+  ++++v++G+  + ++ ++  l++Gd    +  +pH+  + ++ + e + +
  gi|474933935|ref|YP_007687517.1| 126 AHEGEEFIVVVSGKILFIYGKEERILEAGDSAYYNSVVPHYVGAVDG-PAEIYAV 179
                                       69999*************************************99997.6666655 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00012      0.24       1      55 [.      10      63 ..      10      69 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                            HTH_26  1 kLrelmadrgitkseLargtgisaatlsrlvkgkpervsldtLdkiCdaLgctpg 55
                                      ++r+   ++g+++ +La  +gi  ++++ +  g+ +++ ++ L ++ +aLg ++g
  gi|474933935|ref|YP_007687517.1| 10 RIRKYREQMGLSQEDLAINSGIALDSIKEYEEGT-SYPPIGSLIRLSRALGQRVG 63
                                      789999***************************9.7**************98777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1166.47
//
Query:       gi|474933936|ref|YP_007687518.1|  [L=554]
Description: Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.2e-102  343.7   0.1   1.4e-102  343.5   0.1    1.1  1  AMP-binding    AMP-binding enzyme
    5.7e-16   59.3   0.0    1.3e-15   58.1   0.0    1.7  1  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  343.5   0.1  1.6e-106  1.4e-102       5     422 ..      23     452 ..      19     453 .. 0.83

  Alignments for each domain:
  == domain 1  score: 343.5 bits;  conditional E-value: 1.6e-106
                                       HHHSTTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS CS
                       AMP-binding   5 aaktpdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptl 81 
                                        +++pd  a+v+ ++  +l++ +  ++v+r+A+gL+++Gv+kg++Va+++ n p+w+ +++a++k+Ga++ ++n+++
  gi|474933936|ref|YP_007687518.1|  23 IREHPDNDAIVYVDRELRLSWTQWGQEVDRVAKGLMAMGVQKGEKVAVWATNVPDWITLMFATAKIGAILLTINTNY 99 
                                       57899999999988999************************************************************ PP

                                       -HHHHHHHHHHHTESEEE......................ETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHC CS
                       AMP-binding  82 taeelayiledseakvli......................atvdselleklleaaakleavklvivldadellkeee 136
                                       +a+el y+l++s++++l+                      +      l+  +e  +++  + l+ v+  ++  k++ 
  gi|474933936|ref|YP_007687518.1| 100 QAAELDYVLKQSDMETLFlidgvrdtdyvqtvydlvpelkT------LP--RESFHSETYPHLKRVVFLGP-VKHRG 167
                                       ******************88887776555433322211110......11..11222222222222222222.22222 PP

                                       CCHCCCCSCTTS..............-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCC CS
                       AMP-binding 137 lkeeeeseekae..............kpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletrfkl 199
                                       ++++       +              k  ++++++ +d+ +++YTSGTTG PKGVml+h n+++  ++l      + 
  gi|474933936|ref|YP_007687518.1| 168 MYSM-------NevkslavsigddeyKA-RQDTVDVHDVTMMQYTSGTTGFPKGVMLTHFNIANDGYWL--GANMNY 234
                                       3333.......03334455666777644.444899******************************7776..444556 PP

                                       TTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCH CS
                       AMP-binding 200 keddvvlsilplahifglilelllallsGatvvllpkdaaldpklllelieklkvtviagvPrvleallesgalkaa 276
                                       +++d+++  +pl+h+fg++l++++++ +  t+++++ +++ +   ++ +ie++++t ++gvP+++  +l+++ +   
  gi|474933936|ref|YP_007687518.1| 235 GAEDRLCINVPLFHCFGCVLGVMACINHCVTMCFCEVFDPIK---VMTTIEEERCTSVYGVPTMFINILNHKLFP-- 306
                                       789*********************************887744...579**********************65555.. PP

                                       HHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTC.EEEEEEEEGGGSSECEE...CHCTTTCTSTTS-BEE-TTEEEE CS
                       AMP-binding 277 kkakdlsslrlvllggeplspellrffralfge.evlegYGlTEttgvvtv...lpleedkkklgsvGkplpgvevk 349
                                         + d+sslr+ +++g+p++ ++++++ +++   e+  +YGlTE+++ +t    + ++  +kk +svGk lpg++v 
  gi|474933936|ref|YP_007687518.1| 307 --KFDFSSLRTGIMAGSPCPISAMEEVVEKMNMkEITIVYGLTEASPGMTQtryD-EPSIEKKCSSVGKKLPGIDVV 380
                                       ..33***************************9999**************766753.3455567899*********** PP

                                       EE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEETCCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 350 ivDeetgepvpdgeeGellvrgpgvmkgYlkkpeataeafdsegrwlrTGDlgrldedGyleivgRkkdlikl 422
                                       i+D+et ep+pdg++Ge + +g +vmkgY+k pe+ta+++d ++++l++GDlgr+d+dGy++++gR+kd+i++
  gi|474933936|ref|YP_007687518.1| 381 ILDPETYEPCPDGVVGEFCCKGFNVMKGYYKMPEETAKVID-KNGYLHSGDLGRRDPDGYFYVTGRIKDMIIR 452
                                       ****************************************9.757**************************86 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.1   0.0   1.5e-19   1.3e-15       1      76 []     461     537 ..     461     537 .. 0.95

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 1.5e-19
                                       HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE------.HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsea.leeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                       evE  l ++p+V+++ VvGvp ++ Ge + af+v  +g+e+ +e+++++++r +++ +++pk+v fvd++p+++ GK
  gi|474933936|ref|YP_007687518.1| 461 EVEDFLYKCPGVKDVQVVGVPSQKYGEQPGAFIVKFPGYEDmTEQDVMDYCRGKIAWFKTPKYVAFVDDFPMNAAGK 537
                                       8*********************************545975669*********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (554 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 3473.50
//
Query:       gi|474933937|ref|YP_007687519.1|  [L=177]
Description: Cupin domain protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.2e-13   49.2   0.2    7.5e-13   48.0   0.2    1.6  2  Cupin_2       Cupin domain
    8.7e-09   35.3   0.0    1.4e-08   34.6   0.0    1.4  1  HTH_19        Helix-turn-helix domain
    1.1e-07   31.7   0.0    1.6e-07   31.2   0.0    1.2  1  HTH_3         Helix-turn-helix
    1.5e-06   28.2   0.2    2.5e-06   27.5   0.2    1.3  1  AraC_binding  AraC-like ligand binding domain
    8.2e-05   22.2   0.0    0.00018   21.1   0.0    1.7  1  Cupin_3       Protein of unknown function (DUF861)
  ------ inclusion threshold ------
      0.046   14.1   0.0      0.066   13.6   0.0    1.2  1  HTH_31        Helix-turn-helix domain
       0.11   12.3   0.0       0.31   10.8   0.0    1.7  2  EutQ          Ethanolamine utilisation protein EutQ


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       3.1     8e+03      20      30 ..      61      71 ..      58      72 .. 0.76
   2 !   48.0   0.2   2.9e-16   7.5e-13      14      69 ..     115     169 ..     103     171 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.1
                                      EEEEEEEESEE CS
                           Cupin_2 20 deffyVleGeg 30
                                       e+ +V  G+g
  gi|474933937|ref|YP_007687519.1| 61 SECTFVKNGHG 71
                                      48999999986 PP

  == domain 2  score: 48.0 bits;  conditional E-value: 2.9e-16
                                       ECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEE CS
                           Cupin_2  14 hrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparllv 69 
                                        +H+g+ ef yVleG ++++ dg+ ++le+Gdsvy ++g+pH++   ++e ++++ 
  gi|474933937|ref|YP_007687519.1| 115 STHEGN-EFDYVLEGSMRFYHDGHFYDLEPGDSVYYNSGRPHGMYSKSKEGCKFIA 169
                                       46****.********************************************99975 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.0   5.4e-12   1.4e-08       7      63 ..       1      56 [.       1      58 [. 0.96

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 5.4e-12
                            HTH_19  7 aReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgidleyllqge 63
                                      +Re + ++ ee+ae +g ++  +  +E+gk+ ++s   l+kiae +gid  +ll+g+
  gi|474933937|ref|YP_007687519.1|  1 MRELCDISVEEMAEVVGKTPEEYLVYESGKM-DFSFTFLYKIAERCGIDMVELLTGD 56
                                      699999*************************.**********************997 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   6.3e-11   1.6e-07       5      55 .]       2      52 ..       1      52 [. 0.97

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 6.3e-11
                                      HHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHHHH CS
                             HTH_3  5 RkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvsldel 55
                                      R+  ++s ee+Ae++G ++  +  +E+G+   s + l+k+a+ +g+++ el
  gi|474933937|ref|YP_007687519.1|  2 RELCDISVEEMAEVVGKTPEEYLVYESGKMDFSFTFLYKIAERCGIDMVEL 52
                                      999*********************************************987 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.2   9.6e-10   2.5e-06       5      71 ..     101     167 ..      97     176 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 9.6e-10
                                       EEEETTSTT-SEEEETT-SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-TTSEEEE CS
                      AraC_binding   5 egieagypdhsfpphvhdeyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesdsedgwey 71 
                                       +++  g++d +    +h+  ++ yv+eG+ r++++g+ ydl+pGd +  + g pH ++s s +g+++
  gi|474933937|ref|YP_007687519.1| 101 APYIEGDNDTNIHTSTHEGNEFDYVLEGSMRFYHDGHFYDLEPGDSVYYNSGRPHGMYSKSKEGCKF 167
                                       56666777777777899999*****************************************998876 PP

>> Cupin_3  Protein of unknown function (DUF861)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   6.9e-08   0.00018      23      59 ..     117     152 ..      96     173 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 6.9e-08
                                       ESSEEEEEEEECEEEEEETTTEEEEEETTEEEEE-TT CS
                           Cupin_3  23 yeedEfcyileGevkvtpeggetvelraGDlvvlpkg 59 
                                        e +Ef y+leG +++++ +g  + l++GD+v++  g
  gi|474933937|ref|YP_007687519.1| 117 HEGNEFDYVLEGSMRFYH-DGHFYDLEPGDSVYYNSG 152
                                       4459**************.**************9877 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.6e-05     0.066       9      61 ..       1      52 [.       1      54 [. 0.94

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.6e-05
                            HTH_31  9 lReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgldpaer 61
                                      +Re + +s ee+Ae +g ++  +  +E+G+ +  s  +l ++a+ +g d  e+
  gi|474933937|ref|YP_007687519.1|  1 MRELCDISVEEMAEVVGKTPEEYLVYESGKMD-FSFTFLYKIAERCGIDMVEL 52
                                      69*****************************7.**************997765 PP

>> EutQ  Ethanolamine utilisation protein EutQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.57   1.4e+03       6      45 ..      12      54 ..       7      61 .. 0.63
   2 ?   10.8   0.0   0.00012      0.31      93     124 ..     117     148 ..      92     169 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.57
                              EutQ  6 leqlvrkvikeklglekaeqsesf...kkkvdksGilsvklid 45
                                      ++++v k  +e l  e+++++ sf   +k  ++ Gi  v l +
  gi|474933937|ref|YP_007687519.1| 12 MAEVVGKTPEEYLVYESGKMDFSFtflYKIAERCGIDMVELLT 54
                                      5666666667777777777776653334666677777776655 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00012
                              EutQ  93 lnydeidyvieGrldvlidGrkvvaeaGdvil 124
                                        + +e dyv+eG +   +dG+    e+Gd ++
  gi|474933937|ref|YP_007687519.1| 117 HEGNEFDYVLEGSMRFYHDGHFYDLEPGDSVY 148
                                       55689****************99999999776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.56
# Mc/sec: 949.01
//
Query:       gi|474933938|ref|YP_007687520.1|  [L=550]
Description: Acyl-coenzyme A synthetase/AMP-(fatty) acid ligase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-81  273.5   0.0    2.9e-81  273.3   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    6.9e-24   84.6   0.8    1.6e-23   83.4   0.3    1.9  2  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  273.3   0.0   3.2e-85   2.9e-81       2     422 ..      38     447 ..      37     448 .. 0.88

  Alignments for each domain:
  == domain 1  score: 273.3 bits;  conditional E-value: 3.2e-85
                                       HHHHHHSTTSEEEEE...CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEE CS
                       AMP-binding   2 eeqaaktpdkvalvd...sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvv 75 
                                       +e aa  pd++a+v+    g+ +++T+++  + +n++A+++rs+Gvkkgd V+ +l++ +++  + +a+ k+Gav v
  gi|474933938|ref|YP_007687520.1|  38 DEIAAAEPDRTAMVWcnpAGDERRFTFGDISRLSNKAANFFRSMGVKKGDMVLTILKRHYQFWYVSVALHKLGAVMV 114
                                       5778999***********899******************************************************** PP

                                       EEETTS-HHHHHHHHHHHTESEEEETCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TS CS
                       AMP-binding  76 plnptltaeelayiledseakvliatvdsel.leklleaaakleavklvivldadellkeeelkeeeeseekaekpe 151
                                       p    lt+e+++y ++++ +k+ i  + ++  ++++ ++aa+ ++ ++++++ +++     + +++ + ee++e + 
  gi|474933938|ref|YP_007687520.1| 115 PATFMLTKEDVEYRVRAASIKFAI--CTDQSgVPEAVDEAADIPTLEKKMIVNSEREG---WIQFDRGMEEASE-HL 185
                                       ************************..55556677777778888999999999865544...4444444444433.33 PP

                                       CCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHC.SCCTTT-EEEESS-TTSCHHHHHHHHHHHHT CS
                       AMP-binding 152 eeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletr.fklkeddvvlsilplahifglilelllalls 227
                                       + + ++++++ ++ ++SGT G PK V + h +++  ++++k   + +++ +d   lsi++  +  +    +++  + 
  gi|474933938|ref|YP_007687520.1| 186 DRVDTRAEEPTLMYFSSGTSGYPKMVLHNHLYMLGHLSTAK---YwQNVVPDGLHLSIADTGWGKAAWGKIYGQWIM 259
                                       56689******************************999975...42446678889********98877999998888 PP

                                       T-EEEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHH CS
                       AMP-binding 228 GatvvllpkdaaldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffr 304
                                        a v +++ d+ ++p+ +l+ +ek+++t+++++P+++++++++g +      +dlssl ++ ++ge+l+p++ + ++
  gi|474933938|ref|YP_007687520.1| 260 EAGVFVYDYDK-FEPHEILNIVEKYRITTLCCPPTMFRMFINAGLE-----GHDLSSLTYCCIAGEALNPDVFTNWY 330
                                       88788878665.5778899***********************7644.....46************************ PP

                                       HHHTCEEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEET....TS-SE CS
                       AMP-binding 305 alfgeevlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgp....gvmkg 377
                                       + +g +++eg+G+TEtt+ v++++ +++  k++s G+p p  +vk+vD++ g++v++ge+Ge++++ +    g+ ++
  gi|474933938|ref|YP_007687520.1| 331 NATGIKLMEGFGQTETTCTVCNIRGMQP--KPSSMGRPNPQYKVKLVDPD-GNEVANGETGEIVISYEprppGLLMC 404
                                       ***99***************96665555..899****************9.9************98544555***** PP

                                       BTT-HHHHHHHEEETCCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 378 YlkkpeataeafdsegrwlrTGDlgrldedGyleivgRkkdlikl 422
                                       Y++++e+t++ +   ++w++TGD++++dedGy+++vgR +d+ik+
  gi|474933938|ref|YP_007687520.1| 405 YYRDEEKTEKIMH--DGWFHTGDVAWRDEDGYFWYVGRNDDVIKS 447
                                       *********9997..57**************************97 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.87   7.8e+03      52      68 ..     107     123 ..     102     134 .. 0.79
   2 !   83.4   0.3   1.8e-27   1.6e-23       1      76 []     456     534 ..     456     534 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.87
                                       HHT-TTTS-SEEEE-S- CS
                     AMP-binding_C  52 kelgpyavpkkvvfvde 68 
                                       ++lg+++vp ++ +++e
  gi|474933938|ref|YP_007687520.1| 107 HKLGAVMVPATFMLTKE 123
                                       57899999998877754 PP

  == domain 2  score: 83.4 bits;  conditional E-value: 1.8e-27
                                       HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE---..-.--HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TT CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg..s.ealeeeLkahvrkelgpyavpkkvvfvdelpktrs 74 
                                       e+Es+lv+hpaV e+a+ Gvpd+++G+ ++a Vvl+dg  + ++l++eL+ +v+++ +py+ p+ v+fvdelpk  s
  gi|474933938|ref|YP_007687520.1| 456 EIESVLVTHPAVLECAITGVPDPIRGQLVKATVVLRDGfePsDDLKKELQVYVKHKTAPYKYPRVVEFVDELPKSSS 532
                                       8***********************************99743344********************************* PP

                                       S- CS
                     AMP-binding_C  75 GK 76 
                                       GK
  gi|474933938|ref|YP_007687520.1| 533 GK 534
                                       *9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (550 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 3313.48
//
Query:       gi|474933939|ref|YP_007687521.1|  [L=85]
Description: Topoisomerase DNA binding C4 zinc finger [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-09   38.0   6.0    2.2e-09   36.9   6.0    1.6  1  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
      2e-06   28.2   3.5    2.9e-06   27.7   3.5    1.2  1  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
    0.00013   22.0   4.7    0.00022   21.3   4.7    1.4  1  zf-GRF           GRF zinc finger
  ------ inclusion threshold ------
      0.033   14.5   0.6      0.045   14.1   0.6    1.2  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.052   13.1   0.7      0.094   12.3   0.7    1.5  1  TF_Zn_Ribbon     TFIIB zinc-binding
      0.061   13.3   0.9       0.14   12.2   0.9    1.7  1  Ogr_Delta        Ogr/Delta-like zinc finger
       0.14   11.5   0.4       0.22   10.9   0.4    1.3  1  zf-TFIIB         Transcription factor zinc-finger


Domain annotation for each model (and alignments):
>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   6.0   8.5e-13   2.2e-09       3      33 ..      38      71 ..      36      75 .. 0.84

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 8.5e-13
                                      E-SSS--EEEEEE-SSS.EEEEESST.T..---- CS
                    zf-C4_Topoisom  3 kCPkCggdLvlkrgkkG.kFvGCsnYPe..Ckft 33
                                      +CP Cgg +vlk+ k+G kF+GCsnY    Ckft
  gi|474933939|ref|YP_007687521.1| 38 TCPVCGGTMVLKTNKNGhKFYGCSNYRSkgCKFT 71
                                      8*************************42446666 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   3.5   1.2e-09   2.9e-06       7      49 ..      38      76 ..      36      79 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.2e-09
                   Zn_ribbon_recom  7 rCgeCGspmtrrkrkgkrhyYrCstyrrkgkkCsnhsireekl 49
                                       C  CG++m+ +++k++   Y Cs+yr kg  C+    r+ +l
  gi|474933939|ref|YP_007687521.1| 38 TCPVCGGTMVLKTNKNGHKFYGCSNYRSKG--CKF--TRDYEL 76
                                      7*************************7776..875..455555 PP

>> zf-GRF  GRF zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   4.7   8.4e-08   0.00022       2      38 ..      38      70 ..      37      72 .. 0.95

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 8.4e-08
                            zf-GRF  2 lCk.cgrlavlltvrktgpNkGRkFYkCpkgkekqCgF 38
                                      +C+ cg+  vl+t++     +G kFY C++ + k C F
  gi|474933939|ref|YP_007687521.1| 38 TCPvCGGTMVLKTNK-----NGHKFYGCSNYRSKGCKF 70
                                      7*************8.....89**************98 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.6   1.7e-05     0.045       5      36 ..      38      70 ..      36      84 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.7e-05
                   Lar_restr_allev  5 pCPfCggravlersqrvvaeigqcvyCad.....Cga 36
                                       CP Cgg  vl++++++++ +g    C +     C+ 
  gi|474933939|ref|YP_007687521.1| 38 TCPVCGGTMVLKTNKNGHKFYG----CSNyrskgCKF 70
                                      5*****************9655....43322334665 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.7   3.7e-05     0.094       1      18 [.      37      54 ..      37      62 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.7e-05
                                      EEETTTTCEECHEETSTT CS
                      TF_Zn_Ribbon  1 ykCPnCgstnlveDperg 18
                                      ++CP+Cg+t+++  +++g
  gi|474933939|ref|YP_007687521.1| 37 MTCPVCGGTMVLKTNKNG 54
                                      79*******977766665 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.9   5.4e-05      0.14       1      37 [.      38      70 ..      38      79 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.4e-05
                         Ogr_Delta  1 rCPhCgapaaartsrnlskdvreryyqCsnf.e..Cgatf 37
                                      +CP Cg  ++  t  n +k     +y Csn+    C   f
  gi|474933939|ref|YP_007687521.1| 38 TCPVCGGTMVLKTNKNGHK-----FYGCSNYrSkgCK--F 70
                                      6***************999.....8899998444444..3 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.4   8.5e-05      0.22       2      23 ..      39      61 ..      38      68 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8.5e-05
                          zf-TFIIB  2 CPkCqdele.eserggveidyCp 23
                                      CP+C+ +++ +++++g +++ C 
  gi|474933939|ref|YP_007687521.1| 39 CPVCGGTMVlKTNKNGHKFYGCS 61
                                      *******9999999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 607.51
//
Query:       gi|474933940|ref|YP_007687522.1|  [L=344]
Description: Site-specific recombinase XerD [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-11   44.8   0.0    1.6e-11   44.3   0.0    1.2  1  Phage_integrase  Phage integrase family
    8.5e-05   23.0   0.5    0.00024   21.5   0.0    1.9  2  Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
     0.0037   17.6   0.1     0.0089   16.3   0.1    1.6  1  Phage_int_SAM_5  Phage integrase SAM-like domain


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.0   2.6e-15   1.6e-11       2     169 ..     146     323 ..     145     326 .. 0.82

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 2.6e-15
                                       HHHHHHHHHHHHCCGC...HHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSE......EE CS
                   Phage_integrase   2 vltedeverllaalee...slkirdklllellyetGlRisEllsLrvkdldlengvilvheregKgske......ra 69 
                                        lt de++++++a+++    + i  + +++++++t+ R +E++  +  dldl  +++++  r+ Kg+ +      + 
  gi|474933940|ref|YP_007687522.1| 146 ALTIDELRSIFSAADKvpgWNGIMLRGYVAIAFGTACRPKEIILSEERDLDLPAKRFYI--RHPKGEGSwadpqwI- 219
                                       6899************99999**************************************..999999995566432. PP

                                       EECT...HHHHHHHHHHHHHH....CHCCTTTSBSSBETTSSB--HHHHHHHHHHHHHH.CT-SSC--TTHHHHHHH CS
                   Phage_integrase  70 vpls...eealellkellska....leeaeksellfaskrgkplsrqtvrkafkravee.agiekpltpHtlRhsfa 138
                                          +   e +++ l+   +++     e   ks++lf +k ++  ++    +++k++ ee +gi   ++  ++R sf+
  gi|474933940|ref|YP_007687522.1| 220 ---GivrEDMVRKLTLFWEERrrfmEEHGLKSDFLFFNKSTRSHYSLHGFHRMKEILEEkTGIH--FSLKDFRSSFC 291
                                       ...133555555555555554499788899*********7777777777777777777625555..*********** PP

                                       HHHHHHCTS.HHHHHHHHT-SSCCHHHHHHCC CS
                   Phage_integrase 139 taLleagvd.lrvvqkllGHssisttqiYthv 169
                                       + +l   ++ l++v   l Hss++tt+ Y+++
  gi|474933940|ref|YP_007687522.1| 292 SIMLSGDLSrLKAVSLQLRHSSVKTTELYYAK 323
                                       *****998659***************999765 PP

>> Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   4.1e-08   0.00024      14      72 ..      47     113 ..      39     117 .. 0.89
   2 ?   -2.1   0.1      0.91   5.5e+03       9      26 ..     307     324 ..     305     326 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 4.1e-08
                   Phage_int_SAM_4  14 lserTiksYlsaikrflrflkkk..........apeeltkedieaYlnyLanerklsastqknalnals 72 
                                       ++++T + +  +++ f+ f++             p+ +++ +i ++  +L  +r ls+stq  ++++l+
  gi|474933940|ref|YP_007687522.1|  47 FAKTTLYEDEKKLRLFIPFFE-ElkkdgvikttDPRRFDEMHISEFVLWLK-NRGLSVSTQIKYFQVLK 113
                                       799*****************7.22358999999******************.999******99998886 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.91
                   Phage_int_SAM_4   9 lrlaglserTiksYlsai 26 
                                       l+l++ s +T + Y+ +i
  gi|474933940|ref|YP_007687522.1| 307 LQLRHSSVKTTELYYAKI 324
                                       788999999999999887 PP

>> Phage_int_SAM_5  Phage integrase SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   1.5e-06    0.0089      41      80 ..      78     116 ..      34     122 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.5e-06
                                       --TTT--HHHHHHHHHHHHHTS---HHHHHHHHHHHHHHH CS
                   Phage_int_SAM_5  41 itfeeidkefleeFedYLkkkkglsentiskyfkklkavl 80 
                                          + +d+  + eF  +L k++gls +t+ kyf+ lk +l
  gi|474933940|ref|YP_007687522.1|  78 TDPRRFDEMHISEFVLWL-KNRGLSVSTQIKYFQVLKGYL 116
                                       6667789999********.9*****************887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2311.44
//
Query:       gi|474933941|ref|YP_007687523.1|  [L=495]
Description: hypothetical protein TALC_00354 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 3104.22
//
Query:       gi|474933942|ref|YP_007687524.1|  [L=77]
Description: hypothetical protein TALC_00355 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.049   14.0   0.1      0.065   13.6   0.1    1.2  1  Penicillinase_R  Penicillinase repressor
      0.077   13.1   0.0      0.098   12.7   0.0    1.1  1  HTH_20           Helix-turn-helix domain
       0.17   11.8   0.0       0.28   11.1   0.0    1.3  1  TrmB             Sugar-specific transcriptional regulator Trm


Domain annotation for each model (and alignments):
>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.1e-05     0.065       5      70 ..       4      75 ..       2      77 .] 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.1e-05
                                      -SHHHHHHHHHS-.EEHHHHHHT-....-GG.G---HHHHHHHHHHHHHTTS-EEEEETTEEEEE----XXX CS
                   Penicillinase_R  5 Eaevmeilwekge.atvkevveel....eee.kelaysTVktllrrLvkKgllsrekegrafiYsplvseee 70
                                      +++++++++++ + +t++e+v ++    e+      +s +   lr L + +l+   k gr+ ++ ++  +++
  gi|474933942|ref|YP_007687524.1|  4 QLQILRVVRTHPSgITATEIVHQIypgvEDHqIRIRRSRIDKQLRSLARWNLVVVTKRGRENVWKATEGQDN 75
                                      679********999*****999963332333356799*****************************988776 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.6e-05     0.098      13      61 .]       5      63 ..       3      63 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.6e-05
                                      HHHHHHH.STCTTB-HHHHHHHH.........TS-HHHHHHHHHHHHHCTTEEEECTEE CS
                            HTH_20 13 rrilraL.araegltaselaerl.........dlskntlsyHLrvLeeagLvevvregr 61
                                      + ilr   + + g ta+e+ +++         +++++ ++++Lr L++  Lv v++ gr
  gi|474933942|ref|YP_007687524.1|  5 LQILRVVrTHPSGITATEIVHQIypgvedhqiRIRRSRIDKQLRSLARWNLVVVTKRGR 63
                                      6677777889999**********9988766666**********************9997 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   4.6e-05      0.28      31      64 ..      35      69 ..      33      72 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.6e-05
                                      CTTSSCHCHHHHHHHHHHCTSEEEES.STTTEEEE CS
                              TrmB 31 elgvprskvYevLrsLedkGlVerek.grpklYra 64
                                      ++ + rs++ + LrsL +  lV + k gr ++ +a
  gi|474933942|ref|YP_007687524.1| 35 QIRIRRSRIDKQLRSLARWNLVVVTKrGRENVWKA 69
                                      57799*****************9998444556665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 504.00
//
Query:       gi|474933943|ref|YP_007687525.1|  [L=96]
Description: hypothetical protein TALC_00356 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 645.93
//
Query:       gi|474933944|ref|YP_007687526.1|  [L=56]
Description: hypothetical protein TALC_00357 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00032   20.5   0.9    0.00072   19.4   0.9    1.6  1  zf-FPG_IleRS    Zinc finger found in FPG and IleRS
     0.0047   16.4   0.3     0.0064   16.0   0.3    1.2  1  TF_Zn_Ribbon    TFIIB zinc-binding
  ------ inclusion threshold ------
       0.01   15.8   0.5      0.052   13.5   0.1    2.0  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
      0.016   14.9   0.1       0.02   14.6   0.1    1.2  1  TackOD1         Thaumarchaeal output domain 1
      0.034   13.9   2.8          2    8.3   0.1    2.3  2  zinc_ribbon_2   zinc-ribbon domain
      0.045   13.5   2.1        1.3    8.8   0.3    2.2  2  Rubredoxin_2    Rubredoxin metal binding domain
      0.048   13.9   0.2      0.051   13.8   0.2    1.1  1  zf-4CXXC_R1     Zinc-finger domain of monoamine-oxidase A rep
       0.22   11.5   3.1       0.49   10.3   3.1    1.6  1  Zn_ribbon_SprT  SprT-like zinc ribbon domain


Domain annotation for each model (and alignments):
>> zf-FPG_IleRS  Zinc finger found in FPG and IleRS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.9   3.2e-07   0.00072       4      29 ..      12      41 ..      10      42 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 3.2e-07
                                      -TTT--BBEEEEC....TTEEEEE-TTTT. CS
                      zf-FPG_IleRS  4 CpRCwryiervgq....agrstyfCprCqk 29
                                      C  C++y++  ++     g++ ++CprC k
  gi|474933944|ref|YP_007687526.1| 12 CMNCGGYDTQLRIarnyYGNNLWVCPRCEK 41
                                      9***************************87 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.3   2.9e-06    0.0064       3      35 ..      12      49 ..      11      51 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.9e-06
                                      ETTTTCEEC....HEETSTTCE.EESSSSBEEEECCCC CS
                      TF_Zn_Ribbon  3 CPnCgstnl....veDpergel.vCtdCGlVlednsid 35
                                      C nCg++++     +++  ++l vC++C+  l d+  d
  gi|474933944|ref|YP_007687526.1| 12 CMNCGGYDTqlriARNYYGNNLwVCPRCEKNLNDRKLD 49
                                      99****98559999999999999*****9999988777 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.27   6.1e+02       5       9 ..      12      16 ..       8      20 .. 0.66
   2 ?   13.5   0.1   2.3e-05     0.052      13      26 ..      27      40 ..      25      43 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.27
                    PhnA_Zn_Ribbon  5 CplCa 9 
                                      C +C+
  gi|474933944|ref|YP_007687526.1| 12 CMNCG 16
                                      55554 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 2.3e-05
                    PhnA_Zn_Ribbon 13 tYedgallvCpeCa 26
                                      +Y ++ l+vCp C 
  gi|474933944|ref|YP_007687526.1| 27 NYYGNNLWVCPRCE 40
                                      7999*********6 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1     9e-06      0.02     105     140 ..      11      50 ..       2      54 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9e-06
                           TackOD1 105 hhftCgnvgpe....eeflkegkleCpkCktkLrhiGvDY 140
                                        +++Cg  + +    +++  ++  +Cp+C+++L+    DY
  gi|474933944|ref|YP_007687526.1|  11 LCMNCGGYDTQlriaRNYYGNNLWVCPRCEKNLNDRKLDY 50 
                                       599999877662222677888999***********99999 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1   0.00088         2      11      20 ..       7      16 ..       2      18 .. 0.82
   2 ?    6.0   0.5    0.0046        10       2      11 ..      36      45 ..      35      47 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00088
                     zinc_ribbon_2 11 dnakFCpyCG 20
                                      ++a  C +CG
  gi|474933944|ref|YP_007687526.1|  7 PTASLCMNCG 16
                                      78999****8 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0046
                     zinc_ribbon_2  2 CpnCGaelqd 11
                                      Cp+C + l d
  gi|474933944|ref|YP_007687526.1| 36 CPRCEKNLND 45
                                      ****999988 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.012        28      17      25 ..      12      20 ..      11      21 .. 0.82
   2 ?    8.8   0.3   0.00057       1.3      13      21 ..      32      40 ..      27      41 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.012
                      Rubredoxin_2 17 CpsCgsWnt 25
                                      C +Cg ++t
  gi|474933944|ref|YP_007687526.1| 12 CMNCGGYDT 20
                                      888988887 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00057
                      Rubredoxin_2 13 wfGrCpsCg 21
                                       ++ Cp C 
  gi|474933944|ref|YP_007687526.1| 32 NLWVCPRCE 40
                                      68******6 PP

>> zf-4CXXC_R1  Zinc-finger domain of monoamine-oxidase A repressor R1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   2.3e-05     0.051      33      68 ..       9      45 ..       2      54 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.3e-05
                       zf-4CXXC_R1 33 lkfCekClknRygeevee.vaakkeWvCPkCrgiCnc 68
                                       ++C +C     + ++++    ++ WvCP+C +  n 
  gi|474933944|ref|YP_007687526.1|  9 ASLCMNCGGYDTQLRIARnYYGNNLWVCPRCEKNLND 45
                                      6789999877777666550556777******987775 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   3.1   0.00022      0.49       7      34 ..      12      43 ..      11      44 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00022
                    Zn_ribbon_SprT  7 CtgCgreythhlsirrhn.....YrCrrCkgtL 34
                                      C +Cg  y+ +l+i r       + C+rC  +L
  gi|474933944|ref|YP_007687526.1| 12 CMNCG-GYDTQLRIARNYygnnlWVCPRCEKNL 43
                                      999**.899999997744899********8776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.49
# Mc/sec: 340.56
//
Query:       gi|474933945|ref|YP_007687527.1|  [L=40]
Description: hypothetical protein TALC_00358 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       224  (0.0124937); expected 358.6 (0.02)
Passed bias filter:                      194  (0.0108205); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.50
# Mc/sec: 242.36
//
Query:       gi|474933946|ref|YP_007687528.1|  [L=71]
Description: hypothetical protein TALC_00359 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      188  (0.0104858); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.30s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 476.57
//
Query:       gi|474933947|ref|YP_007687529.1|  [L=58]
Description: hypothetical protein TALC_00360 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.062   13.5   1.4      0.091   13.0   1.4    1.3  1  FANCL_C    FANCL C-terminal domain
       0.36   10.6   5.5        5.4    6.8   0.6    2.2  2  zf_C2H2_6  Zinc Finger domain


Domain annotation for each model (and alignments):
>> FANCL_C  FANCL C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.4     1e-05     0.091      39      63 ..      17      42 ..       5      46 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1e-05
                                      HHHHH.HHSSS-TTT--EEE-TTT-S CS
                           FANCL_C 39 eWlrs.lkesrqsfdvlfGeCPyCkk 63
                                      e++r  ++ s + +dv+ G CPyC+ 
  gi|474933947|ref|YP_007687529.1| 17 EFFRDdVQASWNGWDVSRGLCPYCST 42
                                      55654245677889**********96 PP

>> zf_C2H2_6  Zinc Finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.6    0.0006       5.4       4      11 ..       9      16 ..       6      20 .. 0.82
   2 ?    6.4   0.4   0.00082       7.4       4       9 ..      36      41 ..      35      44 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0006
                         zf_C2H2_6  4 VCpYCsLR 11
                                      VC YC  R
  gi|474933947|ref|YP_007687529.1|  9 VCLYCRWR 16
                                      9****877 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.00082
                         zf_C2H2_6  4 VCpYCs 9 
                                       CpYCs
  gi|474933947|ref|YP_007687529.1| 36 LCPYCS 41
                                      5****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 453.25
//
Query:       gi|474933948|ref|YP_007687530.1|  [L=138]
Description: hypothetical protein TALC_00361 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1012.90
//
Query:       gi|474933949|ref|YP_007687531.1|  [L=152]
Description: hypothetical protein TALC_00362 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1112.37
//
Query:       gi|474933950|ref|YP_007687532.1|  [L=65]
Description: hypothetical protein TALC_00363 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 449.84
//
Query:       gi|474933951|ref|YP_007687533.1|  [L=61]
Description: hypothetical protein TALC_00364 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.032   14.5   0.1      0.037   14.3   0.1    1.1  1  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a


Domain annotation for each model (and alignments):
>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   2.1e-06     0.037       9      43 ..      19      51 ..      17      60 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.1e-06
                                      HHHHHCCTTXS-B-HHHHHHHHHHHHHHHHHHHHH CS
                     CBFD_NFYB_HMF  9 kkImksdpdarkiakdAkeliaecveefieelase 43
                                      kkImk++  +  i+++++e+i  c   +++++ +e
  gi|474933951|ref|YP_007687533.1| 19 KKIMKES-RVV-ISQEVREIIGVCPGDYVSFIEDE 51
                                      8*****9.555.************99999999766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 428.87
//
Query:       gi|474933952|ref|YP_007687534.1|  [L=123]
Description: hypothetical protein TALC_00365 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.024   14.6   0.0      0.035   14.1   0.0    1.3  1  HTH_45    Winged helix-turn-helix
      0.058   13.1   0.0      0.082   12.7   0.0    1.2  1  DUF4364   Domain of unknown function (DUF4364)
       0.14   12.1   0.0       0.44   10.5   0.0    1.8  2  MarR_2    MarR family


Domain annotation for each model (and alignments):
>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   5.9e-06     0.035      21      74 ..      31      87 ..      12      89 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.9e-06
                            HTH_45 21 kkTkimykanLsykllnkYLdmLvekgli.......kkskekYvlTekGlelleklkelee 74
                                      + T+i+     +y  +n+ L+ Lve +li       + +   Y+lT  Gle+  +lk+ ++
  gi|474933952|ref|YP_007687534.1| 31 EFTQIVS----NYYSINSILSRLVEAKLIamvpedgRYKIRWYSLTPLGLEVATDLKRAND 87
                                      4444444....7999**************9999998889999************9999775 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.4e-05     0.082      31      73 ..      37      82 ..      30      88 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.4e-05
                           DUF4364 31 tnYfdlqqalseLvesglieeeek...enktlykiTekGketlelf 73
                                       nY +++++ls Lve++li +  +    +   y++T+ G e++  +
  gi|474933952|ref|YP_007687534.1| 37 SNYYSINSILSRLVEAKLIAMVPEdgrYKIRWYSLTPLGLEVATDL 82
                                      69******************9965133455789******9998765 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.55   3.3e+03      39      49 ..       4      14 ..       2      30 .. 0.59
   2 ?   10.5   0.0   7.4e-05      0.44      37      61 ..      41      63 ..      38      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.55
                                      HHHHHHHHHTT CS
                            MarR_2 39 srilkrLvaaG 49
                                      +r l  L+++ 
  gi|474933952|ref|YP_007687534.1|  4 TRNLSILSEKN 14
                                      55555555443 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 7.4e-05
                                      HHHHHHHHHHHTTSEEEEESSSSSS CS
                            MarR_2 37 avsrilkrLvaaGLverrpgpeDkR 61
                                      +++ il rLv+a L+  +  peD+R
  gi|474933952|ref|YP_007687534.1| 41 SINSILSRLVEAKLIAMV--PEDGR 63
                                      7899************99..55999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 840.26
//
Query:       gi|474933953|ref|YP_007687535.1|  [L=275]
Description: hypothetical protein TALC_00366 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0043   17.3   0.0     0.0087   16.3   0.0    1.5  1  ParBc     ParB-like nuclease domain
  ------ inclusion threshold ------
       0.01   16.0   0.0      0.029   14.6   0.0    1.7  2  DUF262    Protein of unknown function DUF262


Domain annotation for each model (and alignments):
>> ParBc  ParB-like nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   9.7e-07    0.0087      19      66 ..      41      97 ..      27     134 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9.7e-07
                             ParBc 19 spekieelvasIkkkGllq...PiivrktrqgryeiiaGerRlrAakrlg.......l 66
                                       p+ki ++++ I k+Gl +   P++   + +g+y + +G rR + +k l        +
  gi|474933953|ref|YP_007687535.1| 41 IPDKILAMARDIAKHGLNPstvPVVFATD-DGKYIVKDGNRRITSLKVLMnpklakdA 97
                                      499**************852326665555.6*************99988756555550 PP

>> DUF262  Protein of unknown function DUF262
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   3.2e-06     0.029      46     100 ..      65     110 ..      42     161 .. 0.71
   2 ?   -1.5   0.0      0.26   2.4e+03      83     120 ..     217     255 ..     186     267 .. 0.53

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.2e-06
                            DUF262  46 ivlwskaadsageleviDGQQRltTltlllaatkeesekriknleaeiekekeee 100
                                       ++     a ++g+++v DG  R+t+l +l++     + ++ +nl +++ek++++ 
  gi|474933953|ref|YP_007687535.1|  65 VF-----ATDDGKYIVKDGNRRITSLKVLMNP----KLAKDANLRKKFEKIQFDR 110
                                       33.....4679*****************9999....6666666666666633222 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.26
                            DUF262  83 ekriknleaeiek.ekeeededrlkrreresdkellqkl 120
                                       ek++ n++ ei k +++ ++ d++++r+ +s+ e +++l
  gi|474933953|ref|YP_007687535.1| 217 EKDFVNCLVEISKdISDANRPDHIDSRIANSSAEVVEYL 255
                                       344444444444446666667777777666666655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2019.18
//
Query:       gi|474933954|ref|YP_007687536.1|  [L=128]
Description: hypothetical protein TALC_00367 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.07   12.9   0.0      0.083   12.6   0.0    1.1  1  PBC       PBC domain


Domain annotation for each model (and alignments):
>> PBC  PBC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.6e-06     0.083      38     119 ..      20      96 ..       7     115 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.6e-06
                               PBC  38 palfsvLveiKektvlslrsaeeeeeekdpqllrldnMLlaeGvagpdksassaaeaaaseensieqsdyrakLaqi 114
                                       +++f  +ve+  k     +++ ++ ++ d+ l  +  +Ll+eG++  d+++s +a  ++    s +  +++++L+q 
  gi|474933954|ref|YP_007687536.1|  20 SVVFRAFVETFTKWFCDRNCT-KNTTKLDKRLTDIADLLLREGLISDDCRKSIKAVLTQ----SDNVLNFNEELNQF 91 
                                       578999999999999999998.99999******************99888865555555....66677899999999 PP

                               PBC 115 rqiye 119
                                        ++ye
  gi|474933954|ref|YP_007687536.1|  92 GHNYE 96 
                                       88887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 946.00
//
Query:       gi|474933955|ref|YP_007687537.1|  [L=280]
Description: Site-specific DNA methylase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-16   59.2   0.0    7.1e-16   58.7   0.0    1.2  1  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran


Domain annotation for each model (and alignments):
>> MethyltransfD12  D12 class N6 adenine-specific DNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.7   0.0     4e-20   7.1e-16      21     244 ..      12     226 ..       2     236 .. 0.82

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 4e-20
                                       -SEEEETT-TTSCCHHCS.....SSCEEEEES-HHHHHHHHHHCCHSHHHHHHHHH.TCTTGGC.TSHHHHHHHHHH CS
                   MethyltransfD12  21 gktfvepFaGggaVffeakk..qgkkvlinDinedlinlykaliknnveelikelekllekeelenereyfyelree 95 
                                       g t+vepFaGg+ V+++++    + k+++nD+ + ++ ++k ++ +  ee+i+++e++ e+     +  +  +++e+
  gi|474933955|ref|YP_007687537.1|  12 GGTYVEPFAGGAGVAINLLLsgFVSKIVLNDVDPSIYWFWKSILDD-NEEFIEKIENT-EL-----TVSEWDRQHEV 81 
                                       679***************988899*****************66665.*********63.33.....45678888877 PP

                                       HH...HHH-HHHHHHHHHHHHCCBGGG---B-TTS-B---B-S-SS-....HHHHHHHHHHHHH....CCEEEC-CH CS
                   MethyltransfD12  96 fnkkidaireaeeaidflylnrllfsglervnkkgnfnvpygaykkpkkvaekelklrseklkn....akiecgdfd 168
                                        ++k ++  +++   + +ylnr+  sg++     g   +  g+yk  +++++ +l +r +++ +     + +c+d+ 
  gi|474933955|ref|YP_007687537.1|  82 QRTKYRQSGFDIG-FSTFYLNRTNRSGIIDGGMIGG-RGQDGMYKLDARFNKGDLIKRIRAIGDlsdsIDLYCSDAS 156
                                       7766777777788.6677*****************5.6667888888899**9**99999999999999*******9 PP

                                       HHHTT-.....-TTE.EEEE--S-T.S...TS--GGGG.CS-HHHHHHHHHHHHHH.HHTT-EEEEEEESEESHHHH CS
                   MethyltransfD12 169 avllka.....kieddivYlDPPYnprqytanytlyetlafsdedevrlaevlkslsskfgvkvllsnsfkdtklfr 240
                                       ++l ++     + e+ +vY DPPY +     +  l++ +     d+v+ a+vl++l+     k++ls++  ++++++
  gi|474933955|ref|YP_007687537.1| 157 YFLDEHlpreyDVENTLVYADPPYYA-----KGGLLYLNHYGHGDHVNIASVLRNLR----FKWILSYD--NVDEIQ 222
                                       9997642111267899*********7.....45555555555555666********8....9*******..999999 PP

                                       HHCT CS
                   MethyltransfD12 241 elyk 244
                                       ++y+
  gi|474933955|ref|YP_007687537.1| 223 QIYS 226
                                       9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1965.29
//
Query:       gi|474933956|ref|YP_007687538.1|  [L=208]
Description: hypothetical protein TALC_00369 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-07   32.2   0.0    1.9e-07   31.7   0.0    1.2  1  DUF3800   Protein of unknown function (DUF3800)


Domain annotation for each model (and alignments):
>> DUF3800  Protein of unknown function (DUF3800)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.0   1.1e-11   1.9e-07       4     119 ..       7     182 ..       4     183 .. 0.58

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 1.1e-11
                           DUF3800   4 iDESGdnklkdgsspyfvlgg.............kkieeikkleekike............lkkky........... 44 
                                       +DESGd  ++ + s+ f++++                                        lk+++           
  gi|474933956|ref|YP_007687538.1|   7 VDESGD-PKRESRSKEFTMTAsinsdprileeivD-------------TkprgtryptkpeLKDELkyfssndrvrt 69 
                                       8****9.6677777888888856666665554440.............33333333333333443344455555565 PP

                           DUF3800  45 ............................krlleriakflkkndlik......sdeesdesilivldk.......... 77 
                                                                   + +++r  ++l      +        + sd  i iv+d+          
  gi|474933956|ref|YP_007687538.1|  70 etlkdilatnpriyavhlnkeeakkessRAVYHRSVRELM-----ElvmgdpMLKTSDAAIDIVFDRhnllgpndaa 141
                                       5555555555665555555555555555444444333333.....13444564456788888889996677665544 PP

                           DUF3800  78 kkkkekakkeleilld.........esvkfvdSkesrglQlADlvagaifr 119
                                       ++ k+                    +++++ +S e+r+lQ+ D++agai++
  gi|474933956|ref|YP_007687538.1| 142 RFAKN----------AakhngimtiDEIRCDRSIENRCLQAHDFLAGAIGA 182
                                       22222..........0222344556************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1242.67
//
Query:       gi|474933957|ref|YP_007687539.1|  [L=506]
Description: hypothetical protein TALC_00370 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   12.6   0.0          1    9.8   0.0    2.2  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   5.9e-05         1       1     120 [.     369     480 ..     369     482 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 5.9e-05
                                       EEE-HHHHHHHH.TTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHH CS
                               PIN   1 ivlDTsvliall.rgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidae 76 
                                       ++lDT+++      g+e + +a ++  + ++ + + +v aEl+            ++e  + ++   +  +l+   +
  gi|474933957|ref|YP_007687539.1| 369 VILDTNIISQGAgQGKEPQVTAIRIAHQKDKYLYTRAVDAELRKTTDP------DKIEGIRKYITQHQKHMLSPPLP 439
                                       589999999999866666666666666669999999999999999999......56666666666444444443555 PP

                                       HHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHHH CS
                               PIN  77 iaeeaaeialkygllpnDaliaAtAkehgikliatfDedfrrva 120
                                         ee ++       l  D +i++ A++++ ++i+t D+ fr+ +
  gi|474933957|ref|YP_007687539.1| 440 TKEELEAMPP---GLNDDRYILSDAIKTKTDIIVTQDKTFRNQG 480
                                       5555544444...4678***********************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (506 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 3183.71
//
Query:       gi|474933958|ref|YP_007687540.1|  [L=118]
Description: hypothetical protein TALC_00371 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.017   15.5   0.0      0.085   13.2   0.0    2.2  2  CitT      Transcriptional regulator
      0.021   15.0   1.1       0.03   14.4   1.1    1.3  1  DUF4337   Domain of unknown function (DUF4337)


Domain annotation for each model (and alignments):
>> CitT  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   9.4e-06     0.085       2      20 ..      18      36 ..      18      48 .. 0.85
   2 ?   -1.5   0.0      0.41   3.6e+03      20      25 ..      72      78 ..      55      78 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.4e-06
                              CitT  2 dQrdVDrLFqraatgqpas 20
                                      +Qr++DrL +r a++++ +
  gi|474933958|ref|YP_007687540.1| 18 EQREIDRLRNRSAREAAKA 36
                                      5**************9975 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.41
                              CitT 20 s.grLPK 25
                                      s + LPK
  gi|474933958|ref|YP_007687540.1| 72 SiEELPK 78
                                      2678998 PP

>> DUF4337  Domain of unknown function (DUF4337)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   1.1   3.4e-06      0.03      74     121 ..      10      57 ..       3      84 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.4e-06
                           DUF4337  74 avdkkiakykkkiarykkekkeikkkAkeleaerdeaneasdkfdlas 121
                                        ++ k+a+ +++i+r +++++  ++kAk++ea++d+  ++++++   +
  gi|474933958|ref|YP_007687540.1|  10 SAELKRAREQREIDRLRNRSAREAAKAKQIEAKADARLARNERYRAVT 57 
                                       455578888999*****************************9976544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1167  (0.0650901); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 788.96
//
Query:       gi|474933959|ref|YP_007687541.1|  [L=385]
Description: hypothetical protein TALC_00372 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0013   18.4   0.0      0.003   17.2   0.0    1.5  1  Zot           Zonular occludens toxin (Zot)
     0.0024   17.2   0.0     0.0041   16.5   0.0    1.2  1  DnaB_C        DnaB-like helicase C terminal domain
     0.0042   17.5   0.0     0.0071   16.8   0.0    1.4  1  AAA           ATPase family associated with various cellular 
     0.0048   16.5   0.0      0.011   15.3   0.0    1.6  2  AAA_25        AAA domain
     0.0061   16.3   1.2      0.046   13.5   0.2    2.3  2  HTH_23        Homeodomain-like domain
  ------ inclusion threshold ------
      0.021   14.5   0.0       0.04   13.6   0.0    1.4  1  Sigma70_r4_2  Sigma-70, region 4
      0.062   12.6   0.0       0.27   10.5   0.0    1.9  2  AIG1          AIG1 family
       0.17   11.0   0.0       0.28   10.3   0.0    1.2  1  TIP49         TIP49 P-loop domain
       0.19   11.4   0.1       0.74    9.5   0.1    1.9  2  IstB_IS21     IstB-like ATP binding protein


Domain annotation for each model (and alignments):
>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.5e-06     0.003       6     135 ..      21     154 ..      17     160 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.5e-06
                               Zot   6 tGapGsgKtsgavkkdllpalk.....egRkiitnidGlrlerieqvlgekvstarliridnpegaetlkefakwat 77 
                                        G  G gKt+ av+   + a+      eg +iitn+  + l+    +  e+ + + + + d    a t+k++ +  +
  gi|474933959|ref|YP_007687541.1|  21 AGRRGHGKTATAVSI-CQHAMNgdyghEGVHIITNVV-FGLKTPSGMPVEAYP-PGVYHED--TLAGTMKRIGDIIK 92 
                                       799**********98.777776655556******987.666555554445555.4565533..33445555544444 PP

                               Zot  78 id..kgallv..iDEcqeifpvrakegrkdpevinaftehRhlgwDivlltqdiskihkevr 135
                                           + al++  +DE+q+   + ++  ++  +  + + ++R++g    +lt+ i+++   vr
  gi|474933959|ref|YP_007687541.1|  93 KCgrRKALIIwlLDEAQNYMMADQNGSKENLALTKYLGNARKFGVCNFFLTPTINNLTPRVR 154
                                       2234999996558****99888888666666666999*******************999888 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0     2e-06    0.0041      16      45 ..      12      41 ..       5      59 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2e-06
                                      BXTTXEEEEEEXTTSSHHHHHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C 16 lqkgdliiiAarpsmGktalalniaenaav 45
                                      lq+g+ i++A+r + Gkta a++i+++a++
  gi|474933959|ref|YP_007687541.1| 12 LQPGETIVLAGRRGHGKTATAVSICQHAMN 41
                                      89***********************99875 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   3.5e-06    0.0071       1      77 [.      18     117 ..      18     148 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.5e-06
                                       EEEESSTTSSHHHHHHHHHHHH........THEEEEEETTTCSSS................STTHHHHHHHHHHHHH CS
                               AAA   1 vllyGppGtGKTllakavakel........gvefleisgsellsk................yvgesekkirelfkea 53 
                                       ++l G  G GKT++a ++++++        gv++++  +  l                   ++  ++k+i +++k++
  gi|474933959|ref|YP_007687541.1|  18 IVLAGRRGHGKTATAVSICQHAmngdygheGVHIITNVVFGLKTPsgmpveayppgvyhedTLAGTMKRIGDIIKKC 94 
                                       5799*****************86665544434433333333331134555667777777779999***********8 PP

                                       HHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA  54 kekakpsilfiDEidalaksrsgs 77 
                                        + ++  i ++DE+ + + +++ +
  gi|474933959|ref|YP_007687541.1|  95 GRRKALIIWLLDEAQNYMMADQ-N 117
                                       55553799999***99988882.2 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   5.4e-06     0.011      24      61 ..       6      43 ..       1      57 [. 0.88
   2 ?   -3.0   0.0       2.3   4.7e+03      82     161 ..      79     118 ..      74     135 .. 0.49

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.4e-06
                            AAA_25 24 wlvkgllpagelallaGapgtGKttlaldlalavatGk 61
                                        +++ll  ge+++laG++g GKt+ a++++ + + G+
  gi|474933959|ref|YP_007687541.1|  6 EFMHELLQPGETIVLAGRRGHGKTATAVSICQHAMNGD 43
                                      56899*************************99988775 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.3
                            AAA_25  82 sedelrrRlravgealrddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralggd 158
                                       + +++ +R+  + ++  +++ l ++ l                                        D  +  + +d
  gi|474933959|ref|YP_007687541.1|  79 TLAGTMKRIGDIIKKCGRRKALIIWLL----------------------------------------DEAQNYMMAD 115
                                       444444444444455444444444433........................................3333333333 PP

                            AAA_25 159 ens 161
                                        n 
  gi|474933959|ref|YP_007687541.1| 116 QNG 118
                                       333 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1       0.2     4e+02       5      16 ..      96     107 ..      95     114 .. 0.85
   2 !   13.5   0.2   2.3e-05     0.046      10      42 ..     307     342 ..     304     351 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.2
                            HTH_23   5 reRlrillllae 16 
                                       r++++i++ll+e
  gi|474933959|ref|YP_007687541.1|  96 RRKALIIWLLDE 107
                                       79********98 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 2.3e-05
                            HTH_23  10 illllae...GlsvreIAreLgvsrrTvyrwlkryr 42 
                                       +  ++++   G++++eIA+e+ ++++T     k+y+
  gi|474933959|ref|YP_007687541.1| 307 AKAMYRRrlrGAPWAEIAEEWEIPESTAKYRFKKYE 342
                                       5567776667******************99999984 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0     2e-05      0.04      15      47 ..     306     338 ..     301     340 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2e-05
                                       HHHHHHHHHTS---HHHHHHHHT--HHHHHHHH CS
                      Sigma70_r4_2  15 qreifllryleglsykEIAellgisegtVksrl 47 
                                       q +++  r+l g + +EIAe+ +i+e+t k+r 
  gi|474933959|ref|YP_007687541.1| 306 QAKAMYRRRLRGAPWAEIAEEWEIPESTAKYRF 338
                                       889999************************986 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00014      0.27       2      22 ..      17      37 ..      16      54 .. 0.89
   2 ?   -0.7   0.0      0.38   7.5e+02     138     160 ..      80     101 ..      70     117 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00014
                                      EEEEESSTTSSHHHHHHHHHT CS
                              AIG1  2 tivlvGktgnGkSaTgNsilg 22
                                      tivl G+ g Gk aT+ si +
  gi|474933959|ref|YP_007687541.1| 17 TIVLAGRRGHGKTATAVSICQ 37
                                      8*****************975 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.38
                                       HHHHH-HHHHHHHHHTTTSEEEE CS
                              AIG1 138 lsksspeaLkevlkecgnRvvlf 160
                                       l+ +  + + +++k+cg+R+ l+
  gi|474933959|ref|YP_007687541.1|  80 LAGT-MKRIGDIIKKCGRRKALI 101
                                       5533.356889********9875 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00014      0.28      49      73 ..      14      38 ..       2      45 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00014
                                      XXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 49 aGravLlaGpsgtGktalaiaiske 73
                                       G +++laG +g Gkta a++i ++
  gi|474933959|ref|YP_007687541.1| 14 PGETIVLAGRRGHGKTATAVSICQH 38
                                      6899******************985 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1   0.00037      0.74      44      75 ..      12      43 ..       5      53 .. 0.88
   2 ?   -2.2   0.0       1.5   2.9e+03     104     125 ..     336     357 ..     331     361 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00037
                         IstB_IS21 44 iekkenivllGpsGvGKshlaialgveavrag 75
                                      ++  e ivl G  G GK+  a+++ ++a++ +
  gi|474933959|ref|YP_007687541.1| 12 LQPGETIVLAGRRGHGKTATAVSICQHAMNGD 43
                                      667899*********************99755 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.5
                         IstB_IS21 104 krllkvdllilDdlgllpldqa 125
                                        r+ k +lli  ++gll+ +q+
  gi|474933959|ref|YP_007687541.1| 336 YRFKKYELLIQRECGLLKNQQQ 357
                                       5788999999999999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2527.33
//
Query:       gi|474933960|ref|YP_007687542.1|  [L=117]
Description: hypothetical protein TALC_00373 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 806.21
//
Query:       gi|474933961|ref|YP_007687543.1|  [L=104]
Description: hypothetical protein TALC_00374 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       231  (0.0128842); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 777.83
//
Query:       gi|474933962|ref|YP_007687544.1|  [L=303]
Description: hypothetical protein TALC_00375 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2162.47
//
Query:       gi|474933963|ref|YP_007687545.1|  [L=77]
Description: hypothetical protein TALC_00376 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.073   12.1   3.8      0.074   12.1   3.8    1.1  1  APG9      Autophagy protein Apg9


Domain annotation for each model (and alignments):
>> APG9  Autophagy protein Apg9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   3.8   4.1e-06     0.074     323     376 ..       4      56 ..       1      68 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.1e-06
                              APG9 323 aiiakfvafvagsiaavlvvlslldeelllefeiegrtvlfyltvlgvilavar 376
                                       +i+  f+ f+a +  ++lv+ + +de +   f+++g+t+l++l v+g+ +a + 
  gi|474933963|ref|YP_007687545.1|   4 VILTLFLGFFAVTASVILVLTGYMDEAVA-FFKVHGQTILIVLQVIGLFWAGMM 56 
                                       56777899999999999999999988876.8*******************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       910  (0.0507558); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 527.58
//
Query:       gi|474933964|ref|YP_007687546.1|  [L=626]
Description: hypothetical protein TALC_00377 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0096   16.2   1.7     0.0096   16.2   1.7    2.7  2  DUF3040   Protein of unknown function (DUF3040)


Domain annotation for each model (and alignments):
>> DUF3040  Protein of unknown function (DUF3040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   1.1      0.15   2.7e+03      44      55 ..      49      60 ..       5      70 .. 0.45
   2 !   16.2   1.7   5.3e-07    0.0096      46      83 ..     573     610 ..     558     611 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.15
                           DUF3040 44 lavlavllfvaG 55
                                       a+++++lf++G
  gi|474933964|ref|YP_007687546.1| 49 DALAPLVLFAVG 60
                                      233333333333 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 5.3e-07
                           DUF3040  46 vlavllfvaGllllvlGvaaaavvlgvvGfvvmlagvv 83 
                                       ++ +l++vaGl++l++G++++ +v++++G++v l gv+
  gi|474933964|ref|YP_007687546.1| 573 WIQILMVVAGLAALIGGIILRRPVMILIGAAVFLCGVF 610
                                       67899************999999*********999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (626 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 4052.49
//
Query:       gi|474933965|ref|YP_007687547.1|  [L=220]
Description: hypothetical protein TALC_00378 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.013   15.5   0.1        3.6    7.6   0.0    2.2  2  Wzt_C     Wzt C-terminal domain
       0.02   15.9   0.1       0.13   13.4   0.0    2.1  2  CopC      CopC domain
      0.038   14.0   0.1         10    6.2   0.0    2.4  2  Y_Y_Y     Y_Y_Y domain
       0.23   11.8   1.2        0.6   10.5   0.3    2.0  2  Big_3     Bacterial Ig-like domain (group 3)


Domain annotation for each model (and alignments):
>> Wzt_C  Wzt C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0008       3.6      77     130 ..      82     137 ..      62     160 .. 0.70
   2 ?    5.8   0.0    0.0028        13      98     121 ..     181     202 ..     178     208 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0008
                             Wzt_C  77 leelkagervevefef.klpLapGeYlltvaledrdgeene..iydwlddalsfeVv 130
                                       ++   a+++ ++ +++ + +L  G+Y+l   + + d++ +   +  +++d lsf+V 
  gi|474933965|ref|YP_007687547.1|  82 YDSHLANGEQTIVLTItE-NLPSGTYTLRWDIFSVDDDCQScsCTVIVRDPLSFSVS 137
                                       344455666678888856.9********99999998885557655666688888875 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0028
                             Wzt_C  98 pGeYlltvaledrdgeeneiydwl 121
                                       pG+Y++tv++++++ +  ++++++
  gi|474933965|ref|YP_007687547.1| 181 PGDYTVTVYCGESHAS--YVIHVV 202
                                       9*********666544..266655 PP

>> CopC  CopC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.8e-05      0.13      51      81 ..      90     117 ..      64     123 .. 0.78
   2 ?   -0.6   0.0      0.62   2.8e+03      61      73 ..     175     187 ..     148     190 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.8e-05
                              CopC  51 aktveaelkvplpelaaGtYtVewrvvsaDG 81 
                                       ++t   +++++lp   +GtYt++w + s D 
  gi|474933965|ref|YP_007687547.1|  90 EQTIVLTITENLP---SGTYTLRWDIFSVDD 117
                                       3444566677777...************995 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.62
                              CopC  61 plpelaaGtYtVe 73 
                                        +++  +G+YtV+
  gi|474933965|ref|YP_007687547.1| 175 GVAPSVPGDYTVT 187
                                       4445778999996 PP

>> Y_Y_Y  Y_Y_Y domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.004        18      34      44 ..      99     109 ..      81     112 .. 0.89
   2 ?    6.2   0.0    0.0023        10      37      47 ..     180     190 ..     168     203 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.004
                                       ES--SEEEEEE CS
                             Y_Y_Y  34 tnlppGdYtlk 44 
                                        nlp+G+Ytl+
  gi|474933965|ref|YP_007687547.1|  99 ENLPSGTYTLR 109
                                       59*******95 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0023
                                       -SEEEEEEEEE CS
                             Y_Y_Y  37 ppGdYtlkVka 47 
                                        pGdYt++V++
  gi|474933965|ref|YP_007687547.1| 180 VPGDYTVTVYC 190
                                       69********9 PP

>> Big_3  Bacterial Ig-like domain (group 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.46   2.1e+03      48      59 ..      88      99 ..      77     108 .. 0.72
   2 ?   10.5   0.3   0.00013       0.6      31      68 .]     162     201 ..     144     201 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.46
                             Big_3 48 aGeytvtvtykg 59
                                       Ge+t+ +t+ +
  gi|474933965|ref|YP_007687547.1| 88 NGEQTIVLTITE 99
                                      499999998876 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00013
                             Big_3  31 e...vpfddvevsgsvdstkaGeytvtvtykgvsatftVtV 68 
                                           ++ ++ +vsg v  + +G ytvtv+  +  a++ ++V
  gi|474933965|ref|YP_007687547.1| 162 GaswLTYSGQTVSG-VAPSVPGDYTVTVYCGESHASYVIHV 201
                                       3445888999****.**************999888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1482.06
//
Query:       gi|474933966|ref|YP_007687548.1|  [L=291]
Description: PKD domain protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-07   31.6   3.2    1.2e-07   31.4   1.1    2.1  2  PKD       PKD domain
  ------ inclusion threshold ------
      0.071   13.0   2.8       0.13   12.1   0.0    2.6  3  FlgD_ig   FlgD Ig-like domain
      0.081   13.1   0.2      0.081   13.1   0.2    3.1  4  Flg_new   Listeria-Bacteroides repeat domain (List_Bact_rpt)
       0.72    9.8   3.8         19    5.2   1.5    2.2  2  DUF3318   Protein of unknown function (DUF3318)


Domain annotation for each model (and alignments):
>> PKD  PKD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   1.1   2.7e-11   1.2e-07      27      70 ..      49      89 ..      39      90 .. 0.92
   2 ?   -1.1   0.0      0.38   1.7e+03      45      62 ..     170     175 ..     129     184 .. 0.62

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 2.7e-11
                                      EEEEE--SS--EEEEETTEEEEEE-SSEEEEEEEEEE-SS-EEE CS
                               PKD 27 tysWdfgdgsvvqvlseptvthtYlspGeYeVtvtasnavgsat 70
                                      t +Wdfgd   + +  ++ v htY+++G Y V+ ta+n++g + 
  gi|474933966|ref|YP_007687548.1| 49 TVEWDFGD---GSTAAGKIVDHTYSETGVYYVKQTATNTIGTSV 89
                                      678*****...99***************************9875 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.38
                                       EEEEEE-SSEEEEEEEEE CS
                               PKD  45 tvthtYlspGeYeVtvta 62 
                                                    Vtvt 
  gi|474933966|ref|YP_007687548.1| 170 Q------------VTVTF 175
                                       3............44444 PP

>> FlgD_ig  FlgD Ig-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.2      0.25   1.1e+03      62      77 ..      68      83 ..      49      84 .. 0.73
   2 ?   -2.3   0.0      0.92   4.1e+03      33      42 ..     107     116 ..     104     125 .. 0.83
   3 ?   12.1   0.0     3e-05      0.13      20      44 ..     166     190 ..     153     194 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.25
                                      -B--SEEEEEEEEEET CS
                           FlgD_ig 62 nkladGaYtvkvtats 77
                                      ++ + G Y vk tat+
  gi|474933966|ref|YP_007687548.1| 68 TYSETGVYYVKQTATN 83
                                      4557899999999987 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.92
                                       S--EEEEEEE CS
                           FlgD_ig  33 sGevVrtidl 42 
                                       +G++V+t++ 
  gi|474933966|ref|YP_007687548.1| 107 NGTLVKTVQQ 116
                                       7999999975 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 3e-05
                                       SSSEEEEEEEE-SS--EEEEEEEEE CS
                           FlgD_ig  20 eaadevtvtikDasGevVrtidlga 44 
                                        a ++vtvt  D++G+vV+t+++ +
  gi|474933966|ref|YP_007687548.1| 166 PAESQVTVTFMDSEGNVVKTVSVDQ 190
                                       455789***************9865 PP

>> Flg_new  Listeria-Bacteroides repeat domain (List_Bact_rpt)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.2       1.2   5.2e+03      15      15 ..      68      68 ..      46      93 .. 0.52
   2 ?   -3.4   0.1       2.5   1.1e+04       3      14 ..     102     113 ..     102     126 .. 0.53
   3 ?    6.5   0.1    0.0021       9.5      38      63 ..     134     157 ..     131     158 .. 0.85
   4 ?   13.1   0.2   1.8e-05     0.081       2      63 ..     172     236 ..     172     238 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.2
                                      E CS
                           Flg_new 15 t 15
                                      t
  gi|474933966|ref|YP_007687548.1| 68 T 68
                                      2 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.5
                                       EEEEETTEEEEE CS
                           Flg_new   3 vtFdanGgtvsq 14 
                                       +++  nG  v++
  gi|474933966|ref|YP_007687548.1| 102 ISYYVNGTLVKT 113
                                       677777744322 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0021
                                       EESSTTCCSB--TTT-B--SS-EEEE CS
                           Flg_new  38 WytdsdgttaydfgtkvtptgdvtLy 63 
                                       Wytd   t+ayd ++ v  t ++ Ly
  gi|474933966|ref|YP_007687548.1| 134 WYTDRGMTSAYDMSSYV--TRSLSLY 157
                                       *****99*****99855..4888887 PP

  == domain 4  score: 13.1 bits;  conditional E-value: 1.8e-05
                                       EEEEEETTEEEEE..EEETTSB----..B--E.ETTEEEEEEESSTTCCSB--TTT-B--SS-EEEE CS
                           Flg_new   2 tvtFdanGgtvsq..tvtygetitlp..anpt.keGYtFaGWytdsdgttaydfgtkvtptgdvtLy 63 
                                       tvtF    g+v +  +v++g+ ++ +  ++ + k+     G ytds++tt ++  +++  ++dvt+y
  gi|474933966|ref|YP_007687548.1| 172 TVTFMDSEGNVVKtvSVDQGSRLSVSdlKDMVgKDKGMILGFYTDSEFTTVFNVAKSI--DSDVTVY 236
                                       8***998888644157999997765544776548889999************999987..5*****9 PP

>> DUF3318  Protein of unknown function (DUF3318)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0    0.0059        27      87     123 ..     105     139 ..      87     150 .. 0.71
   2 ?    5.2   1.5    0.0043        19      82     115 ..     252     285 ..     246     288 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0059
                           DUF3318  87 gklglvvelvqqDavgvllagglaaiaayriwrenks 123
                                        + g++v++vqqDa gv++    ++i ++  w + ++
  gi|474933966|ref|YP_007687548.1| 105 YVNGTLVKTVQQDAYGVAA--KNSGIDGVSAWYTDRG 139
                                       5669999*******99865..4455666666655555 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0043
                           DUF3318  82 vallagklglvvelvqqDavgvllagglaaiaay 115
                                       ++++ag+++l+v +v ++++ +l+a++l a a++
  gi|474933966|ref|YP_007687548.1| 252 GLAVAGIVALIVAAVTRHPIVILAAVALFAAAGI 285
                                       78899*************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       902  (0.0503096); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 1938.05
//
Query:       gi|474933967|ref|YP_007687549.1|  [L=231]
Description: putative Ig domain protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-05   25.5  14.7    4.2e-05   23.6   6.9    3.4  3  He_PIG    Putative Ig domain
  ------ inclusion threshold ------
       0.15   11.7   0.0       0.22   11.1   0.0    1.3  1  DUF4085   Protein of unknown function (DUF4085)


Domain annotation for each model (and alignments):
>> He_PIG  Putative Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.1    0.0021        19      19      47 ..      83     112 ..      54     113 .. 0.85
   2 !   23.6   6.9   4.7e-09   4.2e-05       1      49 []     158     201 ..     148     201 .. 0.91
   3 ?   -2.5   0.0      0.69   6.2e+03      29      29 ..     218     218 ..     204     227 .. 0.44

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0021
                            He_PIG  19 dsstGtitGtpdqtvapG.sytftVtatdg 47 
                                       + s+Gt+ +++ ++ a+G  y + + at++
  gi|474933967|ref|YP_007687549.1|  83 SMSSGTLIVNIPSNAAAGdQYHIVLKATSS 112
                                       6799******888889999********986 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 4.7e-09
                            He_PIG   1 tytlttpgsngLPsGLtLdsstGtitGtpdqtvapGsytftVtatdgsg 49 
                                       t+++   ++++LP GL+L++stG +tG +++    Gs t+ +t t+++g
  gi|474933967|ref|YP_007687549.1| 158 TWSV--KSGTTLPEGLSLNTSTGKVTGIVSSV---GSKTISLTCTSSYG 201
                                       5555..6899**********************...********999876 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.69
                            He_PIG  29 p 29 
                                       p
  gi|474933967|ref|YP_007687549.1| 218 P 218
                                       2 PP

>> DUF4085  Protein of unknown function (DUF4085)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   2.4e-05      0.22     140     178 ..     191     229 ..     178     231 .] 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.4e-05
                           DUF4085 140 vleldcsggfseidkveiTfkdvaklepenletgaywlY 178
                                       ++ l c +++ e+ ++++Tf+ v kl p n  ++   +Y
  gi|474933967|ref|YP_007687549.1| 191 TISLTCTSSYGETSDLTVTFNVVSKLAPTNSPSNGSIIY 229
                                       689************************888777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1467.33
//
Query:       gi|474933968|ref|YP_007687550.1|  [L=410]
Description: MiaB-like tRNA modifying enzyme, archaeal-type [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.2e-22   77.7   0.1    1.1e-21   76.8   0.1    1.5  1  UPF0004      Uncharacterized protein family UPF0004
    7.4e-21   75.2   0.0      2e-20   73.8   0.0    1.7  2  Radical_SAM  Radical SAM superfamily
    1.5e-08   34.5   0.0    3.2e-08   33.4   0.0    1.6  1  TRAM         TRAM domain


Domain annotation for each model (and alignments):
>> UPF0004  Uncharacterized protein family UPF0004
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.8   0.1   1.8e-25   1.1e-21       1      89 [.       2      87 ..       2      94 .. 0.93

  Alignments for each domain:
  == domain 1  score: 76.8 bits;  conditional E-value: 1.8e-25
                                      XEEEE--S-CCCCHHHHHHHHHTTTSSS----SSS--SEEEEEE--SSSSHHHHTHHHHHHHHTTST.--EEEEEEHHH CS
                           UPF0004  1 kvaietlGCqmNevdseelaslLkkegyelvedeeeAdvvlvnTCavrekaekkviqalrelkalkkpekkvvvlGCma 79
                                      k+++e++GC+mN  + eela+++ + g++ v ++++Ad+v++nTC+v+e++ekk+i++++elka+    k+v+v+GCma
  gi|474933968|ref|YP_007687550.1|  2 KFFVESYGCTMNYGEGEELAGRMLDLGFSSVGSADDADIVILNTCTVVETTEKKMIRRMNELKAAG---KEVIVTGCMA 77
                                      789********************************************************9999987...89******** PP

                                      HS-HHHHHHH CS
                           UPF0004 80 qrekeellke 89
                                      + + +++  +
  gi|474933968|ref|YP_007687550.1| 78 KVQASRVNVR 87
                                      *998877655 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.63   3.8e+03     117     145 ..      42      71 ..       7      77 .. 0.54
   2 !   73.8   0.0   3.3e-24     2e-20       1     166 [.     127     298 ..     127     299 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.63
                                       HHHHHT.CTSHHHHHHHHHHHHHHTTSETE CS
                                       xxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 117 vlklmn.rghtfeevlealeklreagikrv 145
                                       +l+ +     t ++ ++ +  l++ag +++
  gi|474933968|ref|YP_007687550.1|  42 ILNTCTvVETTEKKMIRRMNELKAAGKEVI 71 
                                       444444444445555566666666655543 PP

  == domain 2  score: 73.8 bits;  conditional E-value: 3.3e-24
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS.....TTHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxx RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly.....pdfvellerlak 72 
                                       ++v +gC+++C++C++++    +g  +s ++ ++++ ++el ++ gvke++++ ++   y      d+ el++ + +
  gi|474933968|ref|YP_007687550.1| 127 IPVAQGCRGNCTYCITKF---ARGALKSYDPSDLKRRFDEL-VDSGVKEILITAQDTGCYgrdigTDLGELVRSMLA 199
                                       57899*************...8*******************.9**********999999999999999999999999 PP

                                       TCCCTEEEEEEECSSCHG......HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTS CS
                                       xxxxxxxxxxxxxxxxxx......xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  73 lavpgiritvetngtlpd......eeklerllelg.vdrvslgleaaddekvlklmnrghtfeevlealeklreagi 142
                                       ++  ++ri++    +  +      + +le + + +    +++++++++d  vl+ m+r +t ee+  +++++r++  
  gi|474933968|ref|YP_007687550.1| 200 KE-GEYRIRIGMMNP--NslrpvlDSVLEVFEDGRvYRFLHIPVQSGSDS-VLDSMKRHYTSEEFFSLVDTIRAR-Y 271
                                       96.445544433222..2234679*********88***************.************************.9 PP

                                       ET...EEEEEEEBTTTSHHHHHHHHHH CS
                                       xx...xxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 143 kr...vvdrivglpGendeeleellel 166
                                       ++    +d i+g+pGe+d+++ +  el
  gi|474933968|ref|YP_007687550.1| 272 PDmsiATDLITGFPGETDADHAASCEL 298
                                       999*****************9887776 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.0   5.4e-12   3.2e-08       2      60 ..     352     408 ..     351     410 .] 0.97

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 5.4e-12
                                       XXXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT-.-T..TEEEEEEEEEE-SSEEEEE CS
                              TRAM   2 syvGstqeVlveglsksegegiGrtdngkvvfvpgd.lpgIGdfVeVkItkvkrqyLrGe 60 
                                       s+vG t++ lv++ s ++g  i+rt n++++ ++    p  G f ++++t++++ yL G+
  gi|474933968|ref|YP_007687550.1| 352 SMVGGTYRCLVTEIS-PDGSRIARTSNYRPIAIREQvPP--GTFIDAEVTDCHSTYLIGR 408
                                       79*************.********************9**..****************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.51
# Mc/sec: 2405.85
//
Query:       gi|474933969|ref|YP_007687551.1|  [L=208]
Description: putative translation initiation factor aIF-2, beta subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-35  120.6   0.0    4.4e-35  120.1   0.0    1.2  1  eIF-5_eIF-2B    Domain found in IF2B/IF5
    3.8e-07   30.0   0.1    6.9e-07   29.2   0.1    1.4  1  TRAM            TRAM domain
  ------ inclusion threshold ------
      0.019   14.6   0.6        1.8    8.2   0.1    2.5  2  zf_C2H2_13      Zinc finger domain
      0.047   13.6   0.2      0.084   12.8   0.2    1.4  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.12   11.9   6.0        0.4   10.2   0.7    2.4  2  TF_Zn_Ribbon    TFIIB zinc-binding
       0.28   11.0   1.0         19    5.1   0.1    2.3  2  zinc_ribbon_2   zinc-ribbon domain
       0.45   10.2   2.4        1.2    8.9   2.4    1.7  1  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
        0.9    9.5   5.6          2    8.4   2.1    2.6  2  Nudix_N_2       Nudix N-terminal


Domain annotation for each model (and alignments):
>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.1   0.0   1.9e-38   4.4e-35       6     117 .]      21     130 ..      17     130 .. 0.97

  Alignments for each domain:
  == domain 1  score: 120.1 bits;  conditional E-value: 1.9e-38
                                       SSSS--SSTT--EEEETT.EEEETTHHHHHHHHTTSHHHHHHHHHHHHTSEEEESETTEEEESSSSSCCHHHHHHHH CS
                      eIF-5_eIF-2B   6 dkkerykmpklqvkvegkkktvivNfeeiakaLnrdpehvlkyllkelgtqgsidengrlilngkfeakkleklldk 82 
                                       +++er+++p+l++ +egk  t+++Nf++++++++r+peh+l+yllkelgt gsi e++r++++ k + +++++ +++
  gi|474933969|ref|YP_007687551.1|  21 EAHERFELPELDIIQEGK-ITIFRNFMDVCNKIRREPEHLLQYLLKELGTPGSI-EDRRVVFKAKLRVQDIDERVRD 95 
                                       6789**************.***********************************.999******************* PP

                                       HHHHHTSTSSSTSTCEEECCSSSCEEEEESSSTCE CS
                      eIF-5_eIF-2B  83 yieeyVlCkeCkspetelekeerllvlkCkaCgak 117
                                       y e+yV+C+eC++p+t++ek++r++vl C+aCga+
  gi|474933969|ref|YP_007687551.1|  96 YTETYVICSECGRPDTHMEKDGRTFVLVCEACGAR 130
                                       *********************************85 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.1   3.1e-10   6.9e-07       4      61 ..     148     201 ..     146     202 .. 0.96

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 3.1e-10
                                       XXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEE CS
                              TRAM   4 vGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGel 61 
                                       +G  +e++v++++ ++g+g+++    ++v+vpg +   G +V+VkIt     +++G++
  gi|474933969|ref|YP_007687551.1| 148 IGDIIEITVNDVG-KKGDGMAKYM-AYMVIVPGISR--GMRVNVKITNISGTTAFGQV 201
                                       6899*********.**********.***********..******************98 PP

>> zf_C2H2_13  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1   0.00083       1.8      16      26 ..      99     109 ..      89     111 .. 0.85
   2 ?    4.1   0.1     0.016        35      19      27 ..     123     133 ..     119     137 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00083
                        zf_C2H2_13  16 nYRvCnkCGkP 26 
                                        Y +C +CG+P
  gi|474933969|ref|YP_007687551.1|  99 TYVICSECGRP 109
                                       699*******9 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.016
                        zf_C2H2_13  19 vCnkCG..kPi 27 
                                       vC++CG  +Pi
  gi|474933969|ref|YP_007687551.1| 123 VCEACGarRPI 133
                                       9*****55566 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   3.7e-05     0.084      26      54 ..      97     129 ..      76     131 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.7e-05
                    OrfB_Zn_ribbon  26 y.TSktCseCgsknke.alsgrtf..kCpnCgf 54 
                                         T   CseCg+ +++ +++grtf  +C++Cg+
  gi|474933969|ref|YP_007687551.1|  97 TeTYVICSECGRPDTHmEKDGRTFvlVCEACGA 129
                                       347789**********98888887336****97 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.7   0.00018       0.4      11      26 ..      92     107 ..      87     109 .. 0.89
   2 ?    8.3   4.3   0.00071       1.6       2      27 ..     102     129 ..     102     130 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00018
                                       CHEETSTTCEEESSSS CS
                      TF_Zn_Ribbon  11 lveDpergelvCtdCG 26 
                                        v+D+ ++ ++C++CG
  gi|474933969|ref|YP_007687551.1|  92 RVRDYTETYVICSECG 107
                                       59*************9 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00071
                                       EETTTTCEEC..HEETSTTCEEESSSSB CS
                      TF_Zn_Ribbon   2 kCPnCgstnl..veDpergelvCtdCGl 27 
                                       +C +Cg +++  + D  +  lvC++CG+
  gi|474933969|ref|YP_007687551.1| 102 ICSECGRPDThmEKDGRTFVLVCEACGA 129
                                       5******77544888777777*****95 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1    0.0086        19      15      22 ..     102     109 ..      95     109 .. 0.67
   2 ?    4.2   0.1     0.017        37      11      21 ..     116     129 ..     115     130 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0086
                     zinc_ribbon_2  15 FCpyCGtp 22 
                                        C++CG p
  gi|474933969|ref|YP_007687551.1| 102 ICSECGRP 109
                                       47777765 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.017
                     zinc_ribbon_2  11 dnakF...CpyCGt 21 
                                       d+ +F   C+ CG+
  gi|474933969|ref|YP_007687551.1| 116 DGRTFvlvCEACGA 129
                                       56666777999997 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   2.4   0.00052       1.2       5      30 ..     102     130 ..      98     130 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00052
                     zf-NADH-PPase   5 FCgrCGap.tepaeg..gwarvCpaCgle 30 
                                        C+ CG p t+++++   + +vC+aCg++
  gi|474933969|ref|YP_007687551.1| 102 ICSECGRPdTHMEKDgrTFVLVCEACGAR 130
                                       6*****999888888234689******87 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.14   3.1e+02      11      23 ..      83      95 ..      81      96 .. 0.86
   2 ?    8.4   2.1   0.00089         2       3      29 ..     103     128 ..     102     129 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.14
                                      EEE--TT-SS-EE CS
                         Nudix_N_2 11 elripdgDnreRl 23
                                      +lr+ d D+r R 
  gi|474933969|ref|YP_007687551.1| 83 KLRVQDIDERVRD 95
                                      799********96 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00089
                                       -TTT--B-EEE--TT-SS-EEEETTTT CS
                         Nudix_N_2   3 CsqCGtpvelripdgDnreRlvCpaCg 29 
                                       Cs+CG p  +++++++    lvC+aCg
  gi|474933969|ref|YP_007687551.1| 103 CSECGRP-DTHMEKDGRTFVLVCEACG 128
                                       *******.667777888888******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); expected 358.6 (0.02)
Passed bias filter:                      691  (0.0385409); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.55
# Mc/sec: 1135.80
//
Query:       gi|474933970|ref|YP_007687552.1|  [L=132]
Description: SSU ribosomal protein S12P [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.9e-48  160.6   0.6    1.1e-47  160.4   0.6    1.0  1  Ribosom_S12_S23  Ribosomal protein S12/S23


Domain annotation for each model (and alignments):
>> Ribosom_S12_S23  Ribosomal protein S12/S23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.4   0.6     6e-52   1.1e-47       2     113 ..      18     130 ..      17     131 .. 0.97

  Alignments for each domain:
  == domain 1  score: 160.4 bits;  conditional E-value: 6e-52
                                       -------S-TSSTTSSEEEEEEEEEEEE---TT--S-EEEEEEEET.TSEEEEEEE-SSS..----TT-EEEEEE-- CS
                   Ribosom_S12_S23   2 kelrkktksdalegapqkrGvvlekvtveakkPnsAlRkvvrvrLikngkevtafipgegalnfldEhdevlvrGir 78 
                                       + l++++ksd+leg++q rG+vlekv++eak+PnsA+Rk+v+v+Likng+++taf+ g+ga+nf+dEhdevlv+Gi+
  gi|474933970|ref|YP_007687552.1|  18 RVLHLQEKSDPLEGSAQGRGIVLEKVGIEAKQPNSAIRKCVKVQLIKNGRQITAFAVGDGAINFIDEHDEVLVEGIG 94 
                                       677899**********************************************************************9 PP

                                       ......BTTSTTEEEEBETS---TSSSTTTTT---- CS
                   Ribosom_S12_S23  79 rk.gkavkDlpGvrykvvkvagvslkalskykkekp 113
                                       ++ g++ +D+pGvrykv+kv++vsl ++++++ +kp
  gi|474933970|ref|YP_007687552.1|  95 GRmGRSYGDIPGVRYKVIKVNNVSLDEMVRGRVQKP 130
                                       999*****************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 792.74
//
Query:       gi|474933971|ref|YP_007687553.1|  [L=213]
Description: SSU ribosomal protein S7P [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-39  135.0   0.9      2e-39  134.6   0.9    1.1  1  Ribosomal_S7  Ribosomal protein S7p/S5e


Domain annotation for each model (and alignments):
>> Ribosomal_S7  Ribosomal protein S7p/S5e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.6   0.9   1.1e-43     2e-39      18     149 .]      73     213 .]      65     213 .] 0.97

  Alignments for each domain:
  == domain 1  score: 134.6 bits;  conditional E-value: 1.1e-43
                                       TTSBHHHHHHHHHSB....TTBHHHHHHHHHHHHHHHHHHHSS-HHHHHHHHHHHCS-SEEEEEEBSSSSBEEEEEE CS
                      Ribosomal_S7  18 ynselveklinklmk....dGkkslAekivygaldiieektkkdplevleeAlenvkPrvevksrrvGGatyqvpve 90 
                                        n ++ve+lin++m+    +Gkk +A+k+v++a+di++ ktk++p++vl +Al n++Pr+ev+++++GG++++ +v+
  gi|474933971|ref|YP_007687553.1|  73 SNLSIVERLINNIMRtekyTGKKLKAYKTVSSAFDIVAAKTKQNPVQVLCDALCNAAPREEVTRLQFGGISVPKAVD 149
                                       56789************************************************************************ PP

                                       E-HHHHHHHHHHHHHHHH...STSSSS-HHHHHHHHHHHHHTT-..SHHHHHHHHHHHHHHHTG CS
                      Ribosomal_S7  91 vrpkRrqalAlrwiieaa...rkrkeksmaekLaeElidAaege..gaavkkreethrmAeanr 149
                                       ++p+Rr ++Alr++ +++   +++++ks++++La+E++ Aa+g+  + +v k+eet+r+A+++r
  gi|474933971|ref|YP_007687553.1| 150 ISPQRRLDIALRNLSSGVvasSQKNKKSIENCLADEIMLAAKGDmtSFSVAKKEETERVAQSAR 213
                                       ***************99988899999*****************999***************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1489.83
//
Query:       gi|474933972|ref|YP_007687554.1|  [L=735]
Description: translation elongation factor 2 (EF-2/EF-G) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.8e-56  190.2   0.2    4.6e-56  189.4   0.2    1.4  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    9.8e-25   86.7   0.0      3e-24   85.1   0.0    1.9  1  EFG_IV       Elongation factor G, domain IV
    2.9e-22   78.5   0.0    7.3e-22   77.2   0.0    1.7  1  EFG_C        Elongation factor G C-terminus
    1.5e-21   76.3   0.1    2.9e-21   75.3   0.1    1.5  1  EFG_II       Elongation Factor G, domain II
    5.2e-12   46.0   0.3    1.6e-11   44.4   0.3    1.9  1  GTP_EFTU_D2  Elongation factor Tu domain 2
  ------ inclusion threshold ------
       0.02   14.7   0.0      0.045   13.6   0.0    1.6  1  RF3_C        Class II release factor RF3, C-terminal domain


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.4   0.2   1.5e-59   4.6e-56       3     183 ..      21     248 ..      19     301 .. 0.84

  Alignments for each domain:
  == domain 1  score: 189.4 bits;  conditional E-value: 1.5e-59
                                       EEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEET..TCSSEEEEEEEE CS
                          GTP_EFTU   3 irnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaislek..etkkylinliDt 77 
                                       +rnig+++h+DhGKtT++d+L++ +g++s+  e a+++ vlD+ ++E +rgiTi++a +s+ +  e k+ylinliDt
  gi|474933972|ref|YP_007687554.1|  21 VRNIGTAAHIDHGKTTFSDNLIAGAGMMSE--ELAGKQCVLDFDEQEAARGITINAASASMVHhfEDKSYLINLIDT 95 
                                       79***************************9..889999************************5479*********** PP

                                       SSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHH. CS
                          GTP_EFTU  78 PGHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrlkaelkeiveevkqklsrk. 153
                                       PGHvdF  +v+r++r+lDg+ ++++aveG++pqte+v+r+alke+v++++fiNK+Dr++ e + ++e++ +++s+  
  gi|474933972|ref|YP_007687554.1|  96 PGHVDFGGDVTRAMRALDGVFILCCAVEGIMPQTETVIRQALKERVKPMLFINKVDRMIVEQQVTKEMMIERFSKLi 172
                                       **********************************************************9999999999999996666 PP

                                       ...............HHHHHHHHHTTTTTEEEEEEBTTTTBTHH................................. CS
                          GTP_EFTU 154 ...............eeklekygekgekevpvvfgSalkgegvk................................. 182
                                                      ++++++  +    + +v+fgSa+++++++                                 
  gi|474933972|ref|YP_007687554.1| 173 atfnekikanlpaplNKEWQVSIQ----DGTVAFGSAYNNWAISapfmkktgisftdifnycsqedgqkklaklipl 245
                                       666666666665555555555555....557**********998655555555555555555555555555555555 PP

                                       ..H CS
                          GTP_EFTU 183 ..t 183
                                          
  gi|474933972|ref|YP_007687554.1| 246 heV 248
                                       443 PP

>> EFG_IV  Elongation factor G, domain IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.1   0.0     1e-27     3e-24      11     120 ..     516     621 ..     508     622 .. 0.93

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 1e-27
                                       S-CCHCCCCCCCHTSSSHCCCCCEEEECCTTTTSSEEEEE--STCCCHCCCCHHHHCCCCCCTTS-TTTS--EESEE CS
                            EFG_IV  11 kpvkereeklkkqsggdgqyakvileiePleegsgnefvdetkggqvpkeyieavekGfqealkeGplagepvtdvk 87 
                                       k+ k  ++ l++  g++  +ak ++++ +     +n+++d tkg+q+++e++e+v ++f ea+++Gpla+e++ ++k
  gi|474933972|ref|YP_007687554.1| 516 KDPKVLAKQLMD-LGMSDVEAKGVVKFHE-----TNVLIDCTKGIQYLHETMELVADAFDEAMAKGPLANEKCSGLK 586
                                       445557888888.8***************.....8****************************************** PP

                                       EEEEEEE--T..TTC-HHHHHHHHCHHHHHHHHCC CS
                            EFG_IV  88 vtLldgslhe..vdsseaafkpaarralkeallkA 120
                                       ++L+d++lhe  +++++a+++pa+r++++ a+ +A
  gi|474933972|ref|YP_007687554.1| 587 CVLMDAKLHEdtIHRGPAQIIPAVRNGIYGAMCEA 621
                                       ********************************998 PP

>> EFG_C  Elongation factor G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.2   0.0   2.4e-25   7.3e-22       1      88 [.     624     710 ..     624     711 .. 0.96

  Alignments for each domain:
  == domain 1  score: 77.2 bits;  conditional E-value: 2.4e-25
                                       EEEEEEEEEEEEEECCCCCCHHHHHHHCT-EEEEEEEE.TTEEEEEEEEEGGG-TTHHHCHHHCTTTS-EEEEEEEE CS
                             EFG_C   1 vllEPivkveievpeeyvgkvisdlssrrGeiedmeqdasgrviieaeiPlaeligfateLrslTkGegsfsmefsg 77 
                                       vllEP++k+ i+vp +y+g vis++++rrG i+dm qd ++  +++a++P+++++gf  ++r +T+G++ +s+e +g
  gi|474933972|ref|YP_007687554.1| 624 VLLEPMQKIFISVPPDYTGSVISLITQRRGSILDMGQD-GADSTVQAKCPVSDMFGFTADIRGATQGRALWSTENAG 699
                                       59************************************.************************************** PP

                                       EEE--HHHHHH CS
                             EFG_C  78 Yeevpgdklde 88 
                                       +e +  d++++
  gi|474933972|ref|YP_007687554.1| 700 FEVMIPDLQNK 710
                                       **998888765 PP

>> EFG_II  Elongation Factor G, domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.3   0.1   9.7e-25   2.9e-21       1      73 [.     388     460 ..     388     462 .. 0.97

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 9.7e-25
                            EFG_II   1 fPePvislaiepkskadedklskaLarlleEDptlrverdeeTketilsGmGelHleivverlkreykvevel 73 
                                       f+ePv++ aie+k+ +d  kl ++L+++ + Dp+l++e ++eT+e +++GmGelHlei+v r+++e +v + +
  gi|474933972|ref|YP_007687554.1| 388 FSEPVVTEAIEAKDTKDLPKLVEVLRTVGKADPSLSIEINNETGEHLIAGMGELHLEITVYRIENEQGVPIVV 460
                                       79*******************************************************************9876 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   0.3   5.4e-15   1.6e-11       1      73 [.     307     373 ..     307     374 .. 0.93

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 5.4e-15
                                       EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                                       G++a gr++sGt++kG+++++   +    +   r++ +  + +  +++++ a aG+iva+ gl da i+G+t+
  gi|474933972|ref|YP_007687554.1| 307 GEIAVGRLFSGTIQKGQTLYV--AGQ---PAPQRVQTVALMVGADRIPIEDAKAGNIVAVTGLRDA-IAGSTV 373
                                       89*******************..655...55699*******************************8.****98 PP

>> RF3_C  Class II release factor RF3, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.5e-05     0.045      42      83 ..     424     465 ..     382     493 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.5e-05
                                       EEET.TSS-EEEEESSTHHHHHHHHHHHHHH---EEEEE-S- CS
                             RF3_C  42 fkeeeageelilgaVGqLQfeVveeRlknEYgvevrleslpy 83 
                                       ++ ++++ e +++ +G+L +e+  +R++nE gv++ +++  +
  gi|474933972|ref|YP_007687554.1| 424 IEINNETGEHLIAGMGELHLEITVYRIENEQGVPIVVSPPIV 465
                                       344445678999**********************99877554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (735 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.60u 0.24s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 5171.82
//
Query:       gi|474933973|ref|YP_007687555.1|  [L=418]
Description: translation elongation factor 1A (EF-1A/EF-Tu) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-55  188.0   0.2    1.7e-55  187.6   0.2    1.1  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    4.9e-35  120.2   0.2    1.3e-34  118.9   0.1    1.8  2  GTP_EFTU_D3  Elongation factor Tu C-terminal domain
    3.1e-15   56.3   0.5    3.1e-15   56.3   0.5    2.6  3  GTP_EFTU_D2  Elongation factor Tu domain 2
    2.8e-05   23.9   2.5    3.5e-05   23.6   0.8    2.0  2  GTP_EFTU_D4  Elongation factor Tu domain 4
    4.6e-05   23.5   0.1      0.002   18.2   0.1    2.4  1  MMR_HSR1     50S ribosome-binding GTPase
  ------ inclusion threshold ------
      0.068   13.4   0.4       0.24   11.6   0.1    2.1  2  DUF5511      Family of unknown function (DUF5511)
      0.087   12.2   0.0       0.56    9.5   0.0    2.0  2  Gtr1_RagA    Gtr1/RagA G protein conserved region
      0.095   12.2   1.6        1.1    8.8   0.6    2.7  2  FeoB_N       Ferrous iron transport protein B


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.6   0.2   7.8e-59   1.7e-55       1     190 [.       4     212 ..       4     237 .. 0.91

  Alignments for each domain:
  == domain 1  score: 187.6 bits;  conditional E-value: 7.8e-59
                                       TCEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHST.............HCHSHHHHHHTSCSSCEEEEEE CS
                          GTP_EFTU   1 krirnigiighvDhGKtTLtdrLlyktgaiskkgekaeeerv.............lDtlkeErergiTiksaaisle 64 
                                       k+++n++iighvDhGK+TLt+r+l ++gai+ +  ++ ++++             +D lkeErerg+Ti++a+ +++
  gi|474933973|ref|YP_007687555.1|   4 KEHMNLVIIGHVDHGKSTLTGRVLLEAGAIDPHIVEKYKKEAeekgkgsfyfawvMDGLKEERERGVTIDVAHKKFY 80 
                                       689*****************************8777733333467899***************************** PP

                                       TTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTE.EEEEEESCGST...HH CS
                          GTP_EFTU  65 ketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvp.iivfiNKmDrl...ka 137
                                         t+ky +++iD+PGH+dF+k++i+g++++D a++ ++a eG+++qt+e++ la ++gv+ iiv++NKmD +   +a
  gi|474933973|ref|YP_007687555.1|  81 --TDKYYFTVIDAPGHRDFVKNMITGTSQADAAIITCSAIEGPQAQTKEHVFLATTLGVKqIIVAVNKMDAVkyaEA 155
                                       ..************************************************************************9** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHH............HHHHHHHH CS
                          GTP_EFTU 138 elkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvk............tllealve 190
                                       ++k++v+e+++ l       + +g k e ++p++++Sa+ g++vk            tl++al++
  gi|474933973|ref|YP_007687555.1| 156 DYKKCVDEMSKLL-------KMVGNKVE-TIPFIPVSAYCGDNVKeksantpwyngpTLFQALDN 212
                                       **********555.......67777775.9*************9977777777777767777665 PP

>> GTP_EFTU_D3  Elongation factor Tu C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0         4   8.9e+03      56      73 ..     272     289 ..     260     291 .. 0.64
   2 !  118.9   0.1   5.7e-38   1.3e-34       4     111 ..     313     415 ..     310     416 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 4
                                       -BSS-SSCCSTT-CEEEE CS
                       GTP_EFTU_D3  56 vsekkpefvkpGdnvive 73 
                                        ++++ + + pGdnv ++
  gi|474933973|ref|YP_007687555.1| 272 MHHEQMQQALPGDNVGFN 289
                                       334566778888888766 PP

  == domain 2  score: 118.9 bits;  conditional E-value: 5.7e-38
                                       EECCEEEEEEESSS..SS-BSTT-EEEEESSS-EEEEEEEEEEECCSSTTSB-BSS-SSCCSTT-CEEEEEEECCEE CS
                       GTP_EFTU_D3   4 phtkfeAqvyilekerhtpitagYrpvlyirtadvtgkvveLlskldkktekvsekkpefvkpGdnvivevelikpi 80 
                                        +++f+Aq+++l++  ++ it gY+pv++++ta+v+++++e++s   ++ +k+  ++ +f+k+Gdn+iv+++++kp+
  gi|474933973|ref|YP_007687555.1| 313 VAKEFTAQIIVLNH--PSVITVGYTPVFHVHTAQVACQITEIIS--AQRAGKK-LEDLSFLKNGDNAIVKIKPMKPL 384
                                       689***********..**************************44..3345555.6899******************* PP

                                       EE--TTTHCCCCEEEEECTTCEEEEEEEEEE CS
                       GTP_EFTU_D3  81 alekgseypqlGrFaiReggrTvaaGvvtei 111
                                       ++e+ +++p+lGrFaiR++g+TvaaGv +e+
  gi|474933973|ref|YP_007687555.1| 385 VIESAKDFPPLGRFAIRDMGQTVAAGVCVEV 415
                                       ***************************9987 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       2.3   5.1e+03      31      48 ..     111     128 ..      96     177 .. 0.64
   2 !   56.3   0.5   1.4e-18   3.1e-15       1      72 [.     238     303 ..     238     305 .. 0.94
   3 ?   -2.9   0.0       4.2   9.5e+03      43      58 ..     363     378 ..     340     379 .. 0.57

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.3
                                       EEEEEEEEEEETEEESEE CS
                       GTP_EFTU_D2  31 ivtrissletfhededea 48 
                                        + + s++e ++++ +e 
  gi|474933973|ref|YP_007687555.1| 111 AIITCSAIEGPQAQTKEH 128
                                       566677777777777776 PP

  == domain 2  score: 56.3 bits;  conditional E-value: 1.4e-18
                                       EEEEEEEEEESEEETTEEEEEEC.TCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCE CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdt 72 
                                       Gtv  grv++G+lk+  +v++++ +    +   ++++s+e++he++++a +g+n+G++v+++  +d i++Gd+
  gi|474933973|ref|YP_007687555.1| 238 GTVPVGRVETGILKPKTKVVFMPsKA---T---GEVKSIEMHHEQMQQALPGDNVGFNVGGVAKND-IKRGDV 303
                                       99*******************66554...4...*********************************.*****9 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 4.2
                                       EEESEEETTSEEEEEE CS
                       GTP_EFTU_D2  43 ededeavaganaGviv 58 
                                       ed+  + +g+na v++
  gi|474933973|ref|YP_007687555.1| 363 EDLSFLKNGDNAIVKI 378
                                       3333347777777766 PP

>> GTP_EFTU_D4  Elongation factor Tu domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.8   1.6e-08   3.5e-05      21      84 ..     242     303 ..     231     304 .. 0.91
   2 ?   -3.1   0.0       3.3   7.4e+03      47      67 ..     352     375 ..     344     380 .. 0.49

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.6e-08
                                       EEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS-TTTS--TT-E CS
                       GTP_EFTU_D4  21 vGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisiegkivGrqikegdi 84 
                                       vG +v +G++kp+ k++    +  Ge+++i+ +++++++a  G++v+  + g  +  +ik gd+
  gi|474933973|ref|YP_007687555.1| 242 VG-RVETGILKPKTKVVFMPSKATGEVKSIEMHHEQMQQALPGDNVGFNVGGV-AKNDIKRGDV 303
                                       88.9********************************************99775.4888999886 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.3
                                       EEEEEETTEE...ESEEETT-EEE CS
                       GTP_EFTU_D4  47 ilqiqdkgkk...leeakaGqeva 67 
                                       i + q+ gkk   l++ k+G++  
  gi|474933973|ref|YP_007687555.1| 352 IISAQRAGKKledLSFLKNGDNAI 375
                                       444444444400034455555544 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   8.8e-07     0.002       2     114 .]       9     146 ..       8     183 .. 0.59

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 8.8e-07
                                       EEEEESTTSSHHHHHHHHH...................T............STEEESSSTTSSSSEEEEEEEETTEE CS
                          MMR_HSR1   2 vaivGrpNvGKStLinalt...................g............ekaivsdkpgtTrdinegrvklkgke 47 
                                        +i+G+   GKStL  + +                   +            +  + +++ g+T+d+ ++++ +++  
  gi|474933973|ref|YP_007687555.1|   9 LVIIGHVDHGKSTLTGRVLleagaidphivekykkeaeEkgkgsfyfawvmDGLKEERERGVTIDVAHKKFYTDKYY 85 
                                       57999999999999988886666666666655555544045555555544356788999999999999999999999 PP

                                       EEEEECGGC.......SSHHHHHHHHHHHHHHHHCTSEEEEEEETTTTCSHHHH...HHHHHHHHHTTSEEEEEEES CS
                          MMR_HSR1  48 ielvDtpGl.......iegaseekglgkaflaleeadlillvvdaseeklkpld...eeleelleeakkplilvlnk 114
                                       ++++D pG        i                 +ad++++ ++a  e+ +++      l+ +l    k++i+++nk
  gi|474933973|ref|YP_007687555.1|  86 FTVIDAPGHrdfvknmI-------------TGTSQADAAIITCSAI-EGPQAQTkehVFLATTL--GVKQIIVAVNK 146
                                       ********433333330.............3333444444444433.21211110001222222..22333444443 PP

>> DUF5511  Family of unknown function (DUF5511)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       6.5   1.5e+04       5      16 ..       8      19 ..       6      22 .. 0.77
   2 ?   11.6   0.1   0.00011      0.24      14      44 ..     124     154 ..     119     164 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 6.5
                           DUF5511  5 nfymvehvdqvk 16
                                      n+ ++ hvd  k
  gi|474933973|ref|YP_007687555.1|  8 NLVIIGHVDHGK 19
                                      677889999876 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00011
                           DUF5511  14 qvknevhlskylfnkqvivkvsekeaaayae 44 
                                       q k+ v l+  l  kq+iv v + +a  yae
  gi|474933973|ref|YP_007687555.1| 124 QTKEHVFLATTLGVKQIIVAVNKMDAVKYAE 154
                                       899***************************9 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00025      0.56      29      68 ..      66     104 ..      59     118 .. 0.81
   2 ?   -0.2   0.0      0.23   5.1e+02     113     141 ..     139     169 ..     128     187 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00025
                         Gtr1_RagA  29 lrlgatidveksevrflgnltlnlwDcgGqeafveeylss 68 
                                       ++ g+tidv ++++  +++ ++ ++D +G ++fv+++++ 
  gi|474933973|ref|YP_007687555.1|  66 RERGVTIDVAHKKF-YTDKYYFTVIDAPGHRDFVKNMITG 104
                                       55689*********.89*******************7653 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.23
                         Gtr1_RagA 113 kvfvlihKmDliq..edereeifeerkeeir 141
                                       ++ v ++KmD ++  e   +++++e+++ ++
  gi|474933973|ref|YP_007687555.1| 139 QIIVAVNKMDAVKyaEADYKKCVDEMSKLLK 169
                                       578999****998533444444444444444 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.3   2.8e+03       2      17 ..       8      23 ..       7      27 .. 0.83
   2 ?    8.8   0.6   0.00048       1.1      32     124 ..      69     156 ..      67     195 .. 0.59

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.3
                                      EEEEEESTTSSHHHHH CS
                            FeoB_N  2 tvalvGnpnvGkttlf 17
                                      +++++G  + Gk+tl 
  gi|474933973|ref|YP_007687555.1|  8 NLVIIGHVDHGKSTLT 23
                                      57899*********96 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00048
                                       TSSSEEEEEEEEETTEEEEEEE----SSSSSSS.HHHHHHHHHHHCTSSSEEEEEEEGGGHH..HHHHHHHHHHHTT CS
                            FeoB_N  32 GvtvekkegklklkgkeveivDlPGiYslsays.eeekvardflleeepdvvvnvvdatnle..rnLyLtlqllelg 105
                                       Gvt++ ++ k+ ++++ ++++D PG  ++ +   +  + a   ++        + ++  + +   +++L + l    
  gi|474933973|ref|YP_007687555.1|  69 GVTIDVAHKKFYTDKYYFTVIDAPGHRDFVKNMiTGTSQADAAII------TCSAIEGPQAQtkEHVFLATTL--GV 137
                                       9***********999**********97764322022222222222......2233333333300333343333..34 PP

                                       SSEEEEEETHHHHHHTTEE CS
                            FeoB_N 106 vpvvlalnmideaekkgie 124
                                       +++++a+n++d+++ ++ +
  gi|474933973|ref|YP_007687555.1| 138 KQIIVAVNKMDAVKYAEAD 156
                                       6778888888887765544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.73u 0.32s 00:00:01.05 Elapsed: 00:00:00.56
# Mc/sec: 2265.86
//
Query:       gi|474933974|ref|YP_007687556.1|  [L=105]
Description: SSU ribosomal protein S10P [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-25   89.1   0.0    1.8e-25   89.0   0.0    1.0  1  Ribosomal_S10  Ribosomal protein S10p/S20e
     0.0055   17.5   0.0     0.0097   16.7   0.0    1.4  1  PriA_C         Primosomal protein N C-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_S10  Ribosomal protein S10p/S20e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.0   0.0   2.1e-29   1.8e-25       1      97 [.       7     100 ..       7     101 .. 0.99

  Alignments for each domain:
  == domain 1  score: 89.0 bits;  conditional E-value: 2.1e-29
                                       EEEEEESSHHHHHHHHHHHHHHTTSSS-EE---EEEEEEEEEEEEE--SS--.S--EEEEEEEEEEEEEEEE.E-HH CS
                     Ribosomal_S10   1 rirlkSydsklLekavkkivraakelgikvkgpvplPtkrkrvtvlksphvd.kksreqfeirthkRlidisdatke 76 
                                       ri l+++d++++++++++i  + +++g+ ++gpvplPtk+++v  +ksp ++ +++ +++e+r+hkRlid+ da+++
  gi|474933974|ref|YP_007687556.1|   7 RISLSGTDPAQVDDVCNQIRGISQRTGVAIRGPVPLPTKKLKVACRKSPDGEgSETYDRWEMRIHKRLIDL-DADDR 82 
                                       79*********************************************************************.8**** PP

                                       HHHHHS-...S---SS-EEEE CS
                     Ribosomal_S10  77 tidtllkllqlnlpegVsvev 97 
                                        +++l++   +++p+gV++e+
  gi|474933974|ref|YP_007687556.1|  83 ALRQLMR---IQVPDGVNIEI 100
                                       *******...*********97 PP

>> PriA_C  Primosomal protein N C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.1e-06    0.0097       6      53 ..       6      49 ..       3      54 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.1e-06
                            PriA_C  6 alirvsgkdeekveeaaeelaellkealkleeveilgpapapiakikg 53
                                      a+i +sg+d ++v +++++++ + ++    ++v i gp+p p +k+k 
  gi|474933974|ref|YP_007687556.1|  6 ARISLSGTDPAQVDDVCNQIRGISQR----TGVAIRGPVPLPTKKLKV 49
                                      89*******************99998....6799***********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       237  (0.0132188); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 692.39
//
Query:       gi|474933975|ref|YP_007687557.1|  [L=554]
Description: dihydroxyacid dehydratase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.2e-206  687.4   6.1   1.3e-206  687.2   6.1    1.0  1  ILVD_EDD  Dehydratase family


Domain annotation for each model (and alignments):
>> ILVD_EDD  Dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  687.2   6.1  7.4e-211  1.3e-206       1     517 []      31     545 ..      31     545 .. 0.98

  Alignments for each domain:
  == domain 1  score: 687.2 bits;  conditional E-value: 7.4e-211
                          ILVD_EDD   1 kpiigiansyselvpchvhlkelaeavkegveeaggvpaefntigvsDgiamgeegmrysLpsReliadsvetmlea 77 
                                       kp+igians++++vp+h hl++++eavkeg+eeaggv++ f t +v+Dgiamg++gmrysL+sRe+i+d+ e+m+e+
  gi|474933975|ref|YP_007687557.1|  31 KPFIGIANSWNSIVPGHIHLNKVVEAVKEGIEEAGGVAFIFGTPAVCDGIAMGHKGMRYSLISREVISDCCEVMVEG 107
                                       8**************************************************************************** PP

                          ILVD_EDD  78 qllDalvlisgCDKivPgllmaaarlniPaifvsgGpmeagkkk..kldlssvfeavgalaagkiseeeleeleeaa 152
                                       + lD+ v +s+CDK++Pg+lmaa r+++Pa++v+gG meag+++   +d+++vfea+g+++ gk++e+ l+++e+aa
  gi|474933975|ref|YP_007687557.1| 108 HALDGWVGVSNCDKVTPGMLMAAGRMDLPALMVTGGAMEAGSYNgsVIDFQDVFEAIGQVQIGKADEAYLKSIECAA 184
                                       ****************************************99776689***************************** PP

                          ILVD_EDD 153 cpgaGsCsgmgTAntmaclaealGlslpgsasipatsaerkelaeeagkrivelvekdlkprdiltkeafeNAivvl 229
                                       cpg+GsCsg++TAntmacl+e+lG+sl g+++  a+++++ ++a+e+gkrive+v+  ++pr+i+t+e+f NAi+v+
  gi|474933975|ref|YP_007687557.1| 185 CPGPGSCSGLFTANTMACLTETLGMSLTGCGTSLAVDEKKLRIAKESGKRIVEMVRAGITPRSIVTRESFYNAICVD 261
                                       ***************************************************************************** PP

                          ILVD_EDD 230 lalGGStNavlHllAiAreagveltlddfdelsrkvpllaklkPsgkydmedlhraGGvpavlkeLlkagllhgdvl 306
                                       +a+GGStN++lH++Ai + +g+ ++l++fd++sr++p++++l+P+g y++ dl++aGGvpa+lk+L+++  l +d++
  gi|474933975|ref|YP_007687557.1| 262 MAIGGSTNTALHIPAISKDFGCPVDLSEFDRVSRDIPHITSLRPAGAYHIRDLDNAGGVPAILKRLQNK--L-KDAK 335
                                       *******************************************************************66..4.6*** PP

                          ILVD_EDD 307 tvtgktlaenleeaevkeqdvirplekplskegglavLkGnLapeGavvKtsaveeellkfegpArvfdseeeavea 383
                                       t++gkt+ + ++ea+v ++dv+r+le+p++++gg+avLkGn+ap G+v+K++av++++++f+g+A++fdse eav+a
  gi|474933975|ref|YP_007687557.1| 336 TCSGKTIMQIADEAKVLDEDVLRSLENPYHQQGGIAVLKGNIAPMGSVIKQAAVSPKMMVFSGTAKCFDSELEAVAA 412
                                       ***********9***************************************************************** PP

                          ILVD_EDD 384 ilkgkikagdvvviryeGPkGgpGmpEmlkptsallgkglgkkvalitDGRfSGaskglvighvsPEAaegGpialv 460
                                       i++g++kagdvvviryeGPkG+pGmpEml+pts + g+glg++valitDGRfSGa++g +ighvsPEA+e Gpia +
  gi|474933975|ref|YP_007687557.1| 413 IKDGTVKAGDVVVIRYEGPKGAPGMPEMLAPTSIIQGMGLGESVALITDGRFSGATRGGAIGHVSPEAYEFGPIAAL 489
                                       **9************************************************************************** PP

                          ILVD_EDD 461 edGDiieidiekrtlelevseeelaaRraawkp.ekkvktrgllakyaklvssaseGA 517
                                       +dGDii idi++r+l+++++++e+++R +++k  ++ v  +g+++ky++lv++  +GA
  gi|474933975|ref|YP_007687557.1| 490 RDGDIIDIDIPNRKLNARLTDAEIKERLSKVKIvDRPV--TGVQKKYRALVTNGVNGA 545
                                       *****************************999944443..9***********999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (554 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 3460.49
//
Query:       gi|474933976|ref|YP_007687558.1|  [L=105]
Description: hypothetical protein TALC_00392 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.037   13.9   2.4      0.047   13.6   2.4    1.1  1  DUF1686   Protein of unknown function (DUF1686)
      0.072   12.9   2.5      0.061   13.1   1.6    1.3  1  IncD      Inclusion membrane protein D
       0.26   11.2   5.3       0.11   12.4   1.1    1.9  2  DUF1461   Protein of unknown function (DUF1461)
       0.32   10.9   4.1       0.44   10.5   3.0    1.7  1  DUF2678   Protein of unknown function (DUF2678)


Domain annotation for each model (and alignments):
>> DUF1686  Protein of unknown function (DUF1686)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   2.4   1.1e-05     0.047      90     176 ..       8     101 ..       2     104 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.1e-05
                           DUF1686  90 srrqvcvv..vlgnillasaclagdklllpgvedrsslvcvglvvfaallllvsyveeggkkakaeevgevvks... 161
                                       s++q+ ++    g++l+a + +a   +    +++ + ++++ ++ f +l+ ++ y + ++  ++ e      +s   
  gi|474933976|ref|YP_007687558.1|   8 SKKQMLALaiLSGIVLIALTAVAAIGYPEMMSKGLTVYMMAVPIFFTVLAFVLGYLDIEDDLTEGEIRYMKFRSycf 84 
                                       67888765115577777777777446655599************************976655555554444566777 PP

                           DUF1686 162 ..vvlvlsvlvltvvsy 176
                                          ++v+sv+++ v+ +
  gi|474933976|ref|YP_007687558.1|  85 ggAMFVMSVIAVLVLVW 101
                                       77888888888777766 PP

>> IncD  Inclusion membrane protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.6   1.4e-05     0.061      34      92 ..       9      70 ..       3      85 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.4e-05
                              IncD 34 akrlvavav.atilavallvvagllfsgvlcspvsv..laaslffgvgafllggalvggvlt 92
                                       k+++a+a+ + i+ +al  va + +  ++   ++v  +a  +ff v af+lg   +   lt
  gi|474933976|ref|YP_007687558.1|  9 KKQMLALAIlSGIVLIALTAVAAIGYPEMMSKGLTVymMAVPIFFTVLAFVLGYLDIEDDLT 70
                                      577888886367999************999986554228999**********9776666555 PP

>> DUF1461  Protein of unknown function (DUF1461)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.2     0.083   3.7e+02     131     153 ..      11      33 ..       2      39 .. 0.50
   2 ?   12.4   1.1   2.5e-05      0.11      90     150 ..      40     100 ..      37     105 .] 0.81

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.083
                           DUF1461 131 slllavilllliliilgllalid 153
                                       ++l+ +il  ++li+l+++a+i+
  gi|474933976|ref|YP_007687558.1|  11 QMLALAILSGIVLIALTAVAAIG 33 
                                       33333333344444444445555 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 2.5e-05
                           DUF1461  90 kkLfllglivrlvtlillvllllllivlkkkkkkirllkskslllavilllliliilglla 150
                                       k L   +++v +++++l+++l +l i  + ++ +ir++k++s++++ +++++ +i++++l+
  gi|474933976|ref|YP_007687558.1|  40 KGLTVYMMAVPIFFTVLAFVLGYLDIEDDLTEGEIRYMKFRSYCFGGAMFVMSVIAVLVLV 100
                                       56667777888888888877888888888889999**************999998877755 PP

>> DUF2678  Protein of unknown function (DUF2678)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   3.0   9.9e-05      0.44      27      88 ..      10      70 ..       2     100 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 9.9e-05
                           DUF2678 27 driinlvvggltsllvlvtvvssfvfpslppkplniffavcillisssvivlifwyrqgdle 88
                                      ++++ l++ +   +l+  t v+++ +p++  k+l ++++ + ++ ++ + vl +   + dl 
  gi|474933976|ref|YP_007687558.1| 10 KQMLALAILS-GIVLIALTAVAAIGYPEMMSKGLTVYMMAVPIFFTVLAFVLGYLDIEDDLT 70
                                      3444444432.246788999****************99888888888899999988877774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       980  (0.05466); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 751.36
//
Query:       gi|474933977|ref|YP_007687559.1|  [L=97]
Description: Chorismate mutase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.3e-19   67.7   0.3    1.1e-18   67.4   0.3    1.1  1  CM_2      Chorismate mutase type II


Domain annotation for each model (and alignments):
>> CM_2  Chorismate mutase type II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.4   0.3     6e-23   1.1e-18       1      74 [.       9      86 ..       9      87 .. 0.96

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 6e-23
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSGSS-HHHHHHHHHHHHHHH....S-HHHHHHHHHHHHHHHHHHH CS
                              CM_2  1 RkeIdeiDdeileLLaeRaelakevgeyKkeeglpvydpeReaevlerleega....ldeeaierifreiisasralq 74
                                      R+ I +iD eil+LL +R++la e+g+yK+e+g++v++p+  + v++r ++ a    ld++  e i r+++++s+a++
  gi|474933977|ref|YP_007687559.1|  9 RQAIADIDMEILALLRKRLDLAVEIGHYKAEHGMEVLNPGVQDRVIARYRKAAeelgLDPDRCETICRTVMEESIAYE 86
                                      99*************************************************445688*******************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 589.96
//
Query:       gi|474933978|ref|YP_007687560.1|  [L=353]
Description: chorismate synthase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.4e-113  378.9   0.1   1.7e-113  378.6   0.1    1.0  1  Chorismate_synt  Chorismate synthase


Domain annotation for each model (and alignments):
>> Chorismate_synt  Chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  378.6   0.1  9.5e-118  1.7e-113       1     326 [.       8     349 ..       8     349 .. 0.95

  Alignments for each domain:
  == domain 1  score: 378.6 bits;  conditional E-value: 9.5e-118
                                       SEEEEE-SCCSSEEEEEEE---BT-B--HHHHHHHHHHHTCTSSSSSSHHHCS-EEEEESSEETTEE-SS-EEEEEE CS
                   Chorismate_synt   1 lrvttfGeShgkalgavidgvpagleldeediqkeLdrRrpgqsklttqrkEkDeveilsGvfegktlGtpiallie 77 
                                       lr++ fG Sh++ +g++++gvp+g ++d++++ ++++ R+p++  + t rkE+D+v+++ G+ +gk+ G+pi l i 
  gi|474933978|ref|YP_007687560.1|   8 LRFSLFGRSHAPCVGCILEGVPQGTAVDMDSMAADMALRKPSS-GIGTDRKEADRVDVICGIVDGKADGNPIILEIA 83 
                                       6899*************************************95.8******************************** PP

                                       -TTS-..SSSSSTSBE-TTSTCHHHHHHC-S.STHCCCCCTHHCHHHHHHHHHHHHHHHHTTTEEEEEEEEEETTE. CS
                   Chorismate_synt  78 NkdqrskdyeeikevpRpgHADltyalkYgirdlrgggrsSaReTaarvaaGavakklLkelgieivayvssigei. 153
                                       N d++ ++y  ++e+pRpgHADl + lk  + d+ ggg++S+R Ta  vaaG++ak +L+e giei+a++++ig+i 
  gi|474933978|ref|YP_007687560.1|  84 NGDVDDSKYLPFQETPRPGHADLPAILKMPKFDITGGGQFSGRLTAPIVAAGSIAKGMLAEKGIEIAAFCRAIGGIr 160
                                       *****************************666******************************************888 PP

                                       ..........CHHHHH.TT-BS-CCCHHHHHHHHHHHHHTT--B-EEEEEEEES--TT-SBTTTB-HHHHHHHHHHT CS
                   Chorismate_synt 154 ..........ekeaen.pvrcpdeeaaeemeeaieeakkegdslGgvvevvvkgvpaGlGepvfdkldakLakalms 219
                                                 + ++++ p+r++++e ++ m  +i +a+k+gds+Gg+ve++v+g+p+G+G  +f++lda++a a+ +
  gi|474933978|ref|YP_007687560.1| 161 danertikdaK-KSREfPTRAASKELHTFMDGEIMNARKDGDSVGGIVECFVTGLPIGFGGIWFESLDAEIAGAMYG 236
                                       88888877533.344459*********************************************************** PP

                                       STTEEEEEETTGGGGGGSBHHHHS--EE......EESS-TTTTEETTEEBSS-EEEEEEE--SS--SSEEEEEBTTS CS
                   Chorismate_synt 220 ipAvkgveiGsGfeaaelkGseanDeiv......lrktnnaGGieGGisnGepivvrvavKpipsiakeqktvdlet 290
                                       ipA+kgve+G+Gfe ++++Gse nD++       +++tnn+GG+ GG+s+G+p+v+rva+Kp+psiak+q+tv+++t
  gi|474933978|ref|YP_007687560.1| 237 IPACKGVEFGKGFELCQMRGSESNDAYRmkdgkiVTETNNMGGVVGGMSDGQPLVFRVAFKPTPSIAKKQDTVNIKT 313
                                       ***************************965555444***************************************** PP

                                       -E-EEEE--S-S-S-THHHHHHHHHHHHHHHHHHHH CS
                   Chorismate_synt 291 keevelevkgrhDpcvvpravvvveamvalvladal 326
                                        e++ele+kgrhDpc++prav vvea++alv+ad++
  gi|474933978|ref|YP_007687560.1| 314 CENAELEIKGRHDPCIAPRAVAVVEAVTALVIADQM 349
                                       *********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       248  (0.0138323); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 2000.76
//
Query:       gi|474933979|ref|YP_007687561.1|  [L=269]
Description: DNA polymerase III, epsilon subunit-related 3'-5' exonuclease [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-05   25.1   0.4    0.00043   20.9   0.4    2.2  1  RNase_T   Exonuclease
  ------ inclusion threshold ------
      0.014   15.3   0.4      0.093   12.7   0.4    2.0  1  DUF5051   3' exoribonuclease, RNase T-like
        0.2   11.6   0.0       0.45   10.5   0.0    1.5  1  PT-TG     Pre-toxin TG


Domain annotation for each model (and alignments):
>> RNase_T  Exonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.4   7.2e-08   0.00043       1     164 [.       9     179 ..       9     180 .. 0.67

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 7.2e-08
                                       EEEEEEESSSTTCTTS-EEEEEEEEEETTCC......EEEEEEEEE.EEHSSHCSSSHHHHHHHHHCHHHHHTCEBH CS
                           RNase_T   1 vviDlEttgldakekdeiieiaaisidggen......eigetfhfy.vkptelakltdecteftgitqemldeapsf 70 
                                       +viD+Ettgl+  + d+++ i+a+++d g+       e    +  y v   + a+ ++++ + t    e++ + p  
  gi|474933979|ref|YP_007687561.1|   9 LVIDTETTGLSGCPSDHVVDIGAVKVDFGKCtvsdvyE---AIPGYdVSTWDRAHRNAWVFKNTSLCLEDVVTSPLP 82 
                                       69**********99***************998886543...333332344444568899999999999999999999 PP

                                       HH.HHHHHHHHHHHHTCCCETTTCEEEESSHHHHHHHHHHHHH.....HHHHCSEHCECHHHHHHHHHC....HHHH CS
                           RNase_T  71 ke.vleefkellrklallvahnaafdvgflraadkrilkkevp.....krnqfldtlildkatlkelar....tsld 137
                                       +e vl++++++      +  +       +++ +++r+l +e p      + +  +  +l+ a l++ +     + ++
  gi|474933979|ref|YP_007687561.1|  83 QEvVLRDLRRITSDYPFVTSY-------NVDFDFFRFLFNE-PwdlggLQKKLAPDPMLVAAELSGGRWpkldYAYA 151
                                       997788888888744444444.......4445555554442.33444433444555555555555555533334666 PP

                                       HHHHHTTCHSSSS.TSSHHHHHHHHHHH CS
                           RNase_T 138 klaeklgleedgr.aHrAldDaeatakl 164
                                         + + +    gr  HrAl+Da+ +a +
  gi|474933979|ref|YP_007687561.1| 152 RFCPGDPAGIRGRqDHRALSDARVAAHV 179
                                       6666667777777889999999998865 PP

>> DUF5051  3' exoribonuclease, RNase T-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.4   1.6e-05     0.093       3     166 .]       9     184 ..       7     184 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.6e-05
                           DUF5051   3 lmiDiEtlgne..etaelvsIGaVff....petG.eFyaeidlesdeeagidaetieWWlkqskearaellkdtqea 72 
                                       l+iD+Et+g    ++  +v IGaV +    ++    ++a+  ++ +      a+  +W  k  +   + ++++    
  gi|474933979|ref|YP_007687561.1|   9 LVIDTETTGLSgcPSDHVVDIGAVKVdfgkCTVSdVYEAIPGYDVST-W-DRAHRNAWVFKNTSLCLEDVVTSP--- 80 
                                       68*******9999999********99776543335444444443332.1.234455787888887788887555... PP

                           DUF5051  73 kslkdalqaleeFlekslkvwangasfDlviLraafel............................lipwkywndrd 121
                                        + + +l++l++    +  ++  +   D+  +r +f+                             +       d  
  gi|474933979|ref|YP_007687561.1|  81 LPQEVVLRDLRRITS-DYPFVTSYNV-DFDFFRFLFNEpwdlgglqkklapdpmlvaaelsggrwpK------LDYA 149
                                       899999999999875.4445554444.6667777777666778877777777766666655543321......2333 PP

                           DUF5051 122 vrtlvalapelekgeekkreipfegvkHnALaDAkhqakavsail 166
                                       +   + ++p+ ++g           ++H AL DA+  a+++ a++
  gi|474933979|ref|YP_007687561.1| 150 YARFCPGDPAGIRG----------RQDHRALSDARVAAHVILALW 184
                                       44455566664444..........478999999999999888877 PP

>> PT-TG  Pre-toxin TG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   7.5e-05      0.45      17      49 ..      40      66 ..      32      75 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 7.5e-05
                             PT-TG 17 gvkdaieaitGrDpiTGeklsdwdRllaavalv 49
                                      +v d++eai G+D      +s+wdR+ + ++++
  gi|474933979|ref|YP_007687561.1| 40 TVSDVYEAIPGYD------VSTWDRAHRNAWVF 66
                                      689**********......99999998888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       178  (0.00992805); expected 358.6 (0.02)
Passed bias filter:                      157  (0.00875676); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 1508.55
//
Query:       gi|474933980|ref|YP_007687562.1|  [L=68]
Description: hypothetical protein TALC_00397 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       204  (0.0113782); expected 358.6 (0.02)
Passed bias filter:                      196  (0.010932); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.29s 00:00:00.65 Elapsed: 00:00:00.45
# Mc/sec: 457.24
//
Query:       gi|474933981|ref|YP_007687563.1|  [L=76]
Description: hypothetical protein TALC_00398 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 474.18
//
Query:       gi|474933982|ref|YP_007687564.1|  [L=94]
Description: hypothetical protein TALC_00399 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0036   17.3   2.7      0.017   15.1   2.7    1.9  1  HTH_45    Winged helix-turn-helix
  ------ inclusion threshold ------
      0.097   12.5   0.0       0.12   12.2   0.0    1.3  1  DUF1495   Winged helix DNA-binding domain (DUF1495)


Domain annotation for each model (and alignments):
>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   2.7   1.9e-06     0.017       9      75 ..       2      69 ..       1      71 [. 0.67

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.9e-06
                            HTH_45  9 adILeaisegeakkTkimykanLsykllnkYLdm..LvekglikkskekYvlTekGlelleklkeleel 75
                                      a++L+ + ++ +kk++i      + k l   +++  L e +l kk+++  ++TekG ++l+ ++ l+++
  gi|474933982|ref|YP_007687564.1|  2 AEMLRTVLDNPKKKSEIYTGIP-EQKKLALLIEYglLEETKLFKKNTKLISITEKGINVLKAYDVLQKT 69
                                      6677777777777777766654.22223333332226666667********************988876 PP

>> DUF1495  Winged helix DNA-binding domain (DUF1495)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.4e-05      0.12      59      87 ..      31      60 ..      10      63 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.4e-05
                           DUF1495 59 LielGLveeeee.seglklYklteeGieiv 87
                                      Lie GL ee++  ++++kl ++te+Gi++ 
  gi|474933982|ref|YP_007687564.1| 31 LIEYGLLEETKLfKKNTKLISITEKGINVL 60
                                      89*****876658**************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 684.44
//
Query:       gi|474933983|ref|YP_007687565.1|  [L=504]
Description: hypothetical protein TALC_00400 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (504 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 3211.33
//
Query:       gi|474933984|ref|YP_007687566.1|  [L=115]
Description: hypothetical protein TALC_00401 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       231  (0.0128842); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 756.16
//
Query:       gi|474933985|ref|YP_007687567.1|  [L=205]
Description: hypothetical protein TALC_00402 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1238.45
//
Query:       gi|474933986|ref|YP_007687568.1|  [L=161]
Description: Methyltransferase domain protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-06   28.9   0.2    1.4e-05   25.6   0.2    2.0  1  Methyltransf_11  Methyltransferase domain
    6.7e-05   23.5   0.3    0.00061   20.4   0.3    2.1  1  Methyltransf_25  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.2   1.6e-09   1.4e-05       1      96 []       9     115 ..       9     115 .. 0.71

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.6e-09
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES......-C CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvsse......vl 71 
                                       Ldv c++Gr++ ++a+r  ++v +D+ +e + l+  ++   ++    +vad++++pf+d+sf +vv         + 
  gi|474933986|ref|YP_007687568.1|   9 LDV-CCGGRMF-WFADR-DDTVYMDVRDEDILLCDGRTYSVRPD---IVADFREIPFPDSSFSMVVFDPphltrgA- 78 
                                       677.4455554.44433.47888999999998885555555544...9*****************99875544441. PP

                                       CC-C...............CHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  72 hhve...............dpekalkeiaRvLkpgGllvi 96 
                                                          d+++ + e++RvL+ gG+lv+
  gi|474933986|ref|YP_007687568.1|  79 ---GwqvakygrlgknwreDLRRGFGECMRVLRDGGFLVF 115
                                       ...0334455666666666*******************97 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.3   6.8e-08   0.00061       1      97 []       8     111 ..       8     111 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 6.8e-08
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEE.EESBCCGBSSSTTTEEEEEE...... CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvef.vqgdaedlpfedgsfDlvvs...... 70 
                                       +Ld++cG    ++++a+r    + + +D+ +e +  +  r     ++v+  +++d++++pf+d+sf +vv       
  gi|474933986|ref|YP_007687568.1|   8 ILDVCCGG--RMFWFADR---DDTVYMDVRDEDILLCDGRT----YSVRPdIVADFREIPFPDSSFSMVVFdpphlt 75 
                                       89****85..46778877...79999************999....67887789******************777777 PP

                                       ........EST.GGGSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  71 ........sga.lhhlsdedlekalkeiarvLkpgG 97 
                                                ++ l   ++edl++ + e+ rvL++gG
  gi|474933986|ref|YP_007687568.1|  76 rgagwqvaKYGrLGKNWREDLRRGFGECMRVLRDGG 111
                                       7766666534445578999****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1275.57
//
Query:       gi|474933987|ref|YP_007687569.1|  [L=211]
Description: hypothetical protein TALC_00404 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.045   13.6   2.9      0.061   13.2   2.9    1.2  1  Caroten_synth  Carotenoid biosynthesis protein


Domain annotation for each model (and alignments):
>> Caroten_synth  Carotenoid biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   2.9   3.4e-06     0.061       2      61 ..       5      64 ..       4      83 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.4e-06
                     Caroten_synth  2 gvvlillgtaalalyavrllglrralaflllavllslaiEllGvstGfpfGeYsYlsglg 61
                                      +vvli++ ++++ ++a+ + +l  a+a++++ v  ++ + l++v  G+ fG++ Y + + 
  gi|474933987|ref|YP_007687569.1|  5 FVVLIIVVIVVMGAVALYRPDLFSAAAAAVVDVWHTYRMLLVAVPLGWLFGRWLYYRYII 64
                                      57899999999999999999999******************************9987763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       894  (0.0498633); expected 358.6 (0.02)
Passed bias filter:                      640  (0.0356964); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 1569.04
//
Query:       gi|474933988|ref|YP_007687570.1|  [L=36]
Description: hypothetical protein TALC_00405 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (36 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.22s 00:00:00.53 Elapsed: 00:00:00.36
# Mc/sec: 300.34
//
Query:       gi|474933989|ref|YP_007687571.1|  [L=59]
Description: hypothetical protein TALC_00406 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
        1.9    8.5   3.7        2.1    8.4   3.7    1.0  1  Halogen_Hydrol  5-bromo-4-chloroindolyl phosphate hydrolysis 


Domain annotation for each model (and alignments):
>> Halogen_Hydrol  5-bromo-4-chloroindolyl phosphate hydrolysis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   3.7   0.00011       2.1       9      43 ..      14      49 ..       8      58 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00011
                    Halogen_Hydrol  9 liavivalvsffllgfsfflallia.ilggilvyva 43
                                      l++ ++a+++ f++gf+ +l +++  i+g++  +++
  gi|474933989|ref|YP_007687571.1| 14 LASGTIAWFITFMTGFDGVLNIGVTaIVGFVGGIFF 49
                                      34455566666669*******555545544444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.30s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 387.16
//
Query:       gi|474933990|ref|YP_007687572.1|  [L=84]
Description: hypothetical protein TALC_00407 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.1   12.4   0.1        0.1   12.4   0.1    1.6  2  DUF4051   Protein of unknown function (DUF4051)
       0.31   10.9   1.6        9.8    6.1   0.4    2.1  2  PsbN      Photosystem II reaction centre N protein (psbN)


Domain annotation for each model (and alignments):
>> DUF4051  Protein of unknown function (DUF4051)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.5       1.3   1.1e+04       8      12 ..       4       8 ..       2      14 .. 0.49
   2 ?   12.4   0.1   1.1e-05       0.1       2      21 ..      51      70 ..      50      84 .] 0.84

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 1.3
                           DUF4051  8 lllvv 12
                                      +++ v
  gi|474933990|ref|YP_007687572.1|  4 IVVTV 8 
                                      33333 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 1.1e-05
                           DUF4051  2 fIaWywlllvvlvvvgyich 21
                                      f++ +wl++ +l+ v+y+c 
  gi|474933990|ref|YP_007687572.1| 51 FVSECWLIIAFLIGVAYLCL 70
                                      7888**************96 PP

>> PsbN  Photosystem II reaction centre N protein (psbN)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.4    0.0011       9.8       8      24 ..       3      19 ..       1      22 [. 0.86
   2 ?    4.1   0.0    0.0047        42      11      27 ..      58      74 ..      55      80 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0011
                              PsbN  8 sisiaavlvaiTgfsiY 24
                                       i + ++ + iTg++i+
  gi|474933990|ref|YP_007687572.1|  3 GIVVTVIDILITGMAIW 19
                                      578889999*******8 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0047
                              PsbN 11 iaavlvaiTgfsiYtaF 27
                                      i+a+l++++ + +++aF
  gi|474933990|ref|YP_007687572.1| 58 IIAFLIGVAYLCLFIAF 74
                                      78999999999999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 526.38
//
Query:       gi|474933991|ref|YP_007687573.1|  [L=271]
Description: hypothetical protein TALC_00408 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.6e-07   29.1   0.6    1.7e-06   28.1   0.6    1.5  1  Flg_new   Listeria-Bacteroides repeat domain (List_Bact_rpt)


Domain annotation for each model (and alignments):
>> Flg_new  Listeria-Bacteroides repeat domain (List_Bact_rpt)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.6   9.4e-11   1.7e-06       3      61 ..     150     212 ..     148     216 .. 0.64

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 9.4e-11
                                       EEEEETTEE.EEE....EEETTSB----...B--EETTEEEEEEESSTTCCSB--TTT-B--SS-EE CS
                           Flg_new   3 vtFdanGgt.vsq....tvtygetitlp...anptkeGYtFaGWytdsdgttaydfgtkvtptgdvt 61 
                                        tFd++Gg+ +s+    +vt+++ +  +   a+p+++GY FaGW  +    t+++ ++     + vt
  gi|474933991|ref|YP_007687573.1| 150 FTFDTDGGEtMSDivysSVTHTSWLLDLsdvAEPVRDGYRFAGWTWNGATVTSVTCQA----GQTVT 212
                                       69****987456533335777664433345599*************976656555433....23444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1736.24
//
Query:       gi|474933992|ref|YP_007687574.1|  [L=168]
Description: hypothetical protein TALC_00409 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       986  (0.0549947); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1262.68
//
Query:       gi|474933993|ref|YP_007687575.1|  [L=535]
Description: PKD domain protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.3e-10   39.6   1.2    3.3e-10   39.6   1.2    3.8  3  PKD        PKD domain
  ------ inclusion threshold ------
       0.08   12.9   0.3       0.08   12.9   0.3    2.7  2  PGF-CTERM  PGF-CTERM motif


Domain annotation for each model (and alignments):
>> PKD  PKD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.6      0.12   1.1e+03      12      34 ..     197     220 ..     187     275 .. 0.61
   2 ?   -2.0   0.2      0.36   3.2e+03       1       6 [.     360     365 ..     347     378 .. 0.57
   3 !   39.6   1.2   3.7e-14   3.3e-10      27      71 .]     439     480 ..     432     480 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.12
                                       EEEEEEEES..-SS-SEEEEE--S CS
                               PKD  12 atvaftaav.pdganvtysWdfgd 34 
                                       +tv+f  +   +++nvt   + g 
  gi|474933993|ref|YP_007687575.1| 197 QTVTFYVYPkLTASNVTVFYTAGT 220
                                       555555555445555555544444 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.36
                                       EE---S CS
                               PKD   1 vsaspt 6  
                                       v+as+t
  gi|474933993|ref|YP_007687575.1| 360 VAASST 365
                                       233333 PP

  == domain 3  score: 39.6 bits;  conditional E-value: 3.7e-14
                                       EEEEE--SS--EEEEETTEEEEEE-SSEEEEEEEEEE-SS-EEEE CS
                               PKD  27 tysWdfgdgsvvqvlseptvthtYlspGeYeVtvtasnavgsata 71 
                                       t +Wdfgd   ++++ e ++ htY+++G Y+Vt+ta+n+ gs+++
  gi|474933993|ref|YP_007687575.1| 439 TVHWDFGD---GASSDEWCPVHTYAKEGRYTVTLTATNTEGSSST 480
                                       678*****...*******************************986 PP

>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   5.8      0.28   2.5e+03       7      19 ..      10      22 ..       9      23 .. 0.82
   2 ?   12.9   0.3   8.9e-06      0.08       7      23 .]     508     524 ..     507     524 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.28
                         PGF-CTERM  7 vlAlaGLLaaalL 19
                                      + A+++L+aa+++
  gi|474933993|ref|YP_007687575.1| 10 LTAVVALIAAGAF 22
                                      569*******987 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 8.9e-06
                         PGF-CTERM   7 vlAlaGLLaaalLaRRr 23 
                                       v++++G+La+ +L+ R+
  gi|474933993|ref|YP_007687575.1| 508 VVGIIGILAVYFLFMRK 524
                                       99***********9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (535 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       915  (0.0510346); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 3196.34
//
Query:       gi|474933994|ref|YP_007687576.1|  [L=68]
Description: hypothetical protein TALC_00411 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.23s 00:00:00.54 Elapsed: 00:00:00.36
# Mc/sec: 558.34
//
Query:       gi|474933995|ref|YP_007687577.1|  [L=108]
Description: hypothetical protein TALC_00412 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   12.8   0.0        1.9    8.8   0.0    2.4  2  Nif11     Nif11 domain


Domain annotation for each model (and alignments):
>> Nif11  Nif11 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.019   3.4e+02      15      31 ..      39      55 ..      33      74 .. 0.83
   2 ?    8.8   0.0   0.00011       1.9      32      44 ..      90     102 ..      82     104 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.019
                             Nif11 15 qDpalreqlkacsdhee 31
                                       +p++re ++ +sd ++
  gi|474933995|ref|YP_007687577.1| 39 VSPDFREAFAPVSDIDA 55
                                      57999999999998876 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00011
                             Nif11  32 vvalAkeaGyeft 44 
                                       + alA+++Gy++t
  gi|474933995|ref|YP_007687577.1|  90 FTALARANGYDVT 102
                                       689********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.32s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 665.56
//
Query:       gi|474933996|ref|YP_007687578.1|  [L=180]
Description: cob(I)alamin adenosyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-59  201.6   0.0    1.2e-59  201.5   0.0    1.0  1  CobA_CobO_BtuR  ATP:corrinoid adenosyltransferase BtuR/CobO/C
  ------ inclusion threshold ------
      0.046   13.8   0.0       0.05   13.6   0.0    1.3  1  CbiA            CobQ/CobB/MinD/ParA nucleotide binding domain


Domain annotation for each model (and alignments):
>> CobA_CobO_BtuR  ATP:corrinoid adenosyltransferase BtuR/CobO/CobP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.5   0.0   1.3e-63   1.2e-59       3     172 .]      12     180 .]      10     180 .] 0.97

  Alignments for each domain:
  == domain 1  score: 201.5 bits;  conditional E-value: 1.3e-63
                    CobA_CobO_BtuR   3 glihvytGdGKGKttAAlGlalRalgaglkvlvvqFlKgekesgElaalkkl.eielerlgkegfvkmeeeekeeda 78 
                                       gl++vytG+GKGKttAAlGl +Ra+g+gl+vl++qF+K  +++gE+ +++++ +i+++ lg ++fv  +++ +++d 
  gi|474933996|ref|YP_007687578.1|  12 GLVQVYTGNGKGKTTAALGLSFRAAGRGLNVLFLQFMKPPENYGEHIMAERIdNITMMPLGLDHFV--SNSPTDDDV 86 
                                       89*************************************778**********88************..4556999** PP

                    CobA_CobO_BtuR  79 aaakealekakealaseeydlvvlDEinyalklglldeeevlellkkkpeklelvlTGrnapeelleaADlvtemkk 155
                                       + a+eal+ka+e+l s++ydlvvlDE ++a++lgl++ +e+l++l+k+++++e+vlTGr+ p+++ ++ADlvtem+ 
  gi|474933996|ref|YP_007687578.1|  87 RVAHEALAKAEELLISGKYDLVVLDESLNAVRLGLITSAELLDTLRKRHANVEVVLTGRGLPDDIRDYADLVTEMQL 163
                                       ***************************************************************************** PP

                    CobA_CobO_BtuR 156 vkHpydkgikarkGiey 172
                                       vkHp+d+gi+ar Giey
  gi|474933996|ref|YP_007687578.1| 164 VKHPFDEGIDARMGIEY 180
                                       ****************9 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   5.6e-06      0.05       6      34 ..      18      46 ..      13     168 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.6e-06
                                      SSTTSSHHHHHHHHHHHHHHTT--EEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  6 tkGGvGKTtlaanLaralarrglrVllvD 34
                                      t  G GKTt a++L +  a rgl+Vl + 
  gi|474933996|ref|YP_007687578.1| 18 TGNGKGKTTAALGLSFRAAGRGLNVLFLQ 46
                                      56699********************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1195.90
//
Query:       gi|474933997|ref|YP_007687579.1|  [L=191]
Description: hypothetical protein TALC_00414 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.8e-07   30.2   0.1    1.4e-06   28.3   0.1    2.0  2  TetR_C_8   Transcriptional regulator C-terminal region
     0.0006   19.5   0.0     0.0012   18.6   0.0    1.5  1  TetR_N     Bacterial regulatory proteins, tetR family
      0.004   16.9   0.0      0.046   13.5   0.0    2.6  2  HTH_23     Homeodomain-like domain
  ------ inclusion threshold ------
       0.03   14.4   0.0       0.25   11.5   0.0    2.5  2  HTH_AraC   Bacterial regulatory helix-turn-helix proteins, Ar
      0.031   14.4   0.1        0.9    9.7   0.0    2.8  2  HTH_28     Helix-turn-helix domain
      0.057   13.2   0.1       0.11   12.3   0.1    1.5  1  LacI       Bacterial regulatory proteins, lacI family
      0.075   12.8   0.0       0.17   11.7   0.0    1.6  1  HTH_IclR   IclR helix-turn-helix domain
      0.081   12.8   0.0       0.16   11.9   0.0    1.5  1  TrmB       Sugar-specific transcriptional regulator TrmB
        0.1   12.6   0.0       0.21   11.6   0.0    1.6  1  HTH_Crp_2  Crp-like helix-turn-helix domain
       0.12   12.5   0.0       0.27   11.4   0.0    1.6  1  HTH_7      Helix-turn-helix domain of resolvase


Domain annotation for each model (and alignments):
>> TetR_C_8  Transcriptional regulator C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.3   2.3e+03      77      98 ..      84     105 ..      73     110 .. 0.54
   2 !   28.3   0.1     8e-10   1.4e-06      61      96 ..     142     177 ..     102     183 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.3
                                       HHHHHHHTTS-S-HHHHHHHHH CS
                          TetR_C_8  77 vildWlengmkespeeiaells 98 
                                        +++W e++ + +  ++  +++
  gi|474933997|ref|YP_007687579.1|  84 YLQRWTEGDDRSERAYLMSMFT 105
                                       4555555555555555444444 PP

  == domain 2  score: 28.3 bits;  conditional E-value: 8e-10
                                       HHHHHHHHHHHHHHHHHHHHHHHTTS-S-HHHHHHH CS
                          TetR_C_8  61 edkefiadfysygfvgvildWlengmkespeeiael 96 
                                        ++ +  ++ ++g+ g+i++W+e+gm+e+pee++  
  gi|474933997|ref|YP_007687579.1| 142 VQRVYHLAYHAGGVYGIIMHWMEGGMNETPEEMITY 177
                                       56677788999**********************975 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   6.8e-07    0.0012      16      39 ..      45      68 ..      37      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 6.8e-07
                                      T--HHHHHHHHTSSHHHHHHHTSS CS
                            TetR_N 16 attvreIAkrAGvskgalYryFps 39
                                       +t+++IA  AGv+++++Yr F++
  gi|474933997|ref|YP_007687579.1| 45 DVTISDIAGVAGVNRSTVYRSFGD 68
                                      69********************96 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   2.6e-05     0.046      17      36 ..      45      64 ..      20      66 .. 0.74
   2 ?   -0.2   0.0      0.53   9.5e+02      31      44 ..      82      90 ..      68      95 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.6e-05
                            HTH_23 17 GlsvreIAreLgvsrrTvyr 36
                                        ++++IA   gv+r+Tvyr
  gi|474933997|ref|YP_007687579.1| 45 DVTISDIAGVAGVNRSTVYR 64
                                      689****************9 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.53
                            HTH_23 31 rrTvyrwlkryree 44
                                       +     l+r+  e
  gi|474933997|ref|YP_007687579.1| 82 AQY----LQRW-TE 90
                                      444....5555.34 PP

>> HTH_AraC  Bacterial regulatory helix-turn-helix proteins, AraC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0         1   1.8e+03      31      41 ..      16      26 ..      15      27 .. 0.78
   2 ?   11.5   0.0   0.00014      0.25       7      35 ..      44      72 ..      44      73 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1
                                      HHSSS-HHHHH CS
                          HTH_AraC 31 ketGmtPsqyr 41
                                      ++ GmtP  +r
  gi|474933997|ref|YP_007687579.1| 16 RIKGMTPEDTR 26
                                      578****7776 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00014
                                      CT--HHHHHHHTTSSHHHHHHHHHHHSSS CS
                          HTH_AraC  7 tnltiediAdelgfSrsyFsrlFkketGm 35
                                      t+ ti diA  +g++rs+ +r F   +G+
  gi|474933997|ref|YP_007687579.1| 44 TDVTISDIAGVAGVNRSTVYRSFGDLYGI 72
                                      578********************988886 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0    0.0005       0.9      13      31 ..      46      64 ..      25      65 .. 0.82
   2 ?    1.8   0.0      0.15   2.7e+02      16      28 ..     128     140 ..     110     155 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0005
                            HTH_28 13 hsvreaArelgisrrtvyr 31
                                      ++++++A   g++r+tvyr
  gi|474933997|ref|YP_007687579.1| 46 VTISDIAGVAGVNRSTVYR 64
                                      599***************8 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.15
                            HTH_28  16 reaArelgisrrt 28 
                                       + +++++gi+r++
  gi|474933997|ref|YP_007687579.1| 128 DVLMNRFGIHRSH 140
                                       458999***9987 PP

>> LacI  Bacterial regulatory proteins, lacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   6.2e-05      0.11       1      17 [.      47      63 ..      47      75 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.2e-05
                                      -HHHHHHHCTS-HHHHH CS
                              LacI  1 tikDVArlAGVSkaTVS 17
                                      ti D+A  AGV  +TV 
  gi|474933997|ref|YP_007687579.1| 47 TISDIAGVAGVNRSTVY 63
                                      8**************95 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   9.6e-05      0.17      18      37 ..      45      64 ..      32      69 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.6e-05
                                      S-BHHHHHHHHTS-HHHHHH CS
                          HTH_IclR 18 eltlselArrtglpkStvhR 37
                                      ++t+s++A  +g+++Stv+R
  gi|474933997|ref|YP_007687579.1| 45 DVTISDIAGVAGVNRSTVYR 64
                                      489****************9 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   9.1e-05      0.16      12      46 ..      31      69 ..      27      72 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.1e-05
                                      CHCHHHH.HHC...CCHHCHHCCCTTSSCHCHHHHHHHH CS
                              TrmB 12 kvYlaLl.klg...patadeiaeelgvprskvYevLrsL 46
                                      k+++ +l ++g     t+++ia  +gv rs+vY++   L
  gi|474933997|ref|YP_007687579.1| 31 KAFFDILeEKGdvtDVTISDIAGVAGVNRSTVYRSFGDL 69
                                      56666663333111368999999***********98776 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00012      0.21      20      45 ..      44      69 ..      19      71 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
                                      EEHHHHHHHHHTTSSHHHHHHHHHHH CS
                         HTH_Crp_2 20 lpltqeelAsmlGltretvsrilseL 45
                                       ++t  ++A   G++r+tv r +++L
  gi|474933997|ref|YP_007687579.1| 44 TDVTISDIAGVAGVNRSTVYRSFGDL 69
                                      578999****************9987 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00015      0.27      23      41 ..      47      65 ..      46      69 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00015
                                      -STTTSSSS---SSSS--S CS
                             HTH_7 23 siskIAkevnisRsTvYRy 41
                                      +is+IA   ++ RsTvYR 
  gi|474933997|ref|YP_007687579.1| 47 TISDIAGVAGVNRSTVYRS 65
                                      79****************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.51u 0.34s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1133.66
//
Query:       gi|474933998|ref|YP_007687580.1|  [L=175]
Description: hypothetical protein TALC_00415 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-08   34.2   5.0    2.1e-08   33.6   5.0    1.3  1  zinc_ribbon_2   zinc-ribbon domain
    6.1e-07   29.4   0.2    8.7e-07   28.9   0.2    1.3  1  DZR             Double zinc ribbon
    3.5e-06   26.2   3.4    6.3e-06   25.4   3.4    1.3  1  zf-ribbon_3     zinc-ribbon domain
    0.00093   19.9   1.9     0.0016   19.1   1.9    1.4  1  zinc_ribbon_15  zinc-ribbon family
     0.0012   18.7   2.4       0.41   10.6   0.1    2.3  2  Nudix_N_2       Nudix N-terminal
     0.0018   18.4   3.9      0.011   15.8   3.9    2.3  1  DHHC            DHHC palmitoyltransferase
     0.0038   17.5  11.1      0.012   15.9   0.9    2.9  3  DUF4064         Protein of unknown function (DUF4064)
     0.0042   17.0   6.1      0.031   14.3   0.7    2.4  2  YhfH            YhfH-like protein
     0.0079   16.2   4.2      0.014   15.4   4.2    1.4  1  UPF0547         Uncharacterised protein family UPF0547
  ------ inclusion threshold ------
      0.015   14.9   3.2       0.38   10.4   0.4    2.3  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
       0.02   14.4   1.1        4.9    6.7   0.0    2.4  2  TF_Zn_Ribbon    TFIIB zinc-binding
      0.044   13.7   0.3       0.36   10.7   0.0    2.2  2  zf-FPG_IleRS    Zinc finger found in FPG and IleRS
      0.062   13.3   1.1       0.11   12.5   1.1    1.4  1  zinc-ribbons_6  zinc-ribbons
      0.062   13.3   1.0       0.12   12.4   1.0    1.5  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.07   12.3   1.2      0.096   11.9   1.2    1.2  1  CitMHS          Citrate transporter
      0.077   11.7   0.3       0.11   11.3   0.3    1.2  1  DUF2207         Predicted membrane protein (DUF2207)
       0.15   12.4   0.1       0.18   12.0   0.1    1.2  1  DUF2072         Zn-ribbon containing protein
       0.15   12.1   3.7       0.52   10.3   3.7    2.0  1  DUF1610         Domain of unknown function (DUF1610)
       0.33   10.8   7.7      0.088   12.7   1.3    2.3  2  DUF5362         Family of unknown function (DUF5362)
        1.8    8.9   7.9        3.4    8.0   3.0    2.4  2  DUF3040         Protein of unknown function (DUF3040)
        2.5    8.4   9.4        1.6    9.0   0.3    2.6  2  DUF2964         Protein of unknown function (DUF2964)
          3    7.9   6.8          2    8.4   1.1    2.9  3  DUF2116         Uncharacterized protein containing a Zn-ribbo


Domain annotation for each model (and alignments):
>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   5.0   2.6e-11   2.1e-08       1      21 [.       6      26 ..       6      28 .. 0.95

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 2.6e-11
                     zinc_ribbon_2  1 fCpnCGaelqdnakFCpyCGt 21
                                      +C++CGa+++++akFCp+CG 
  gi|474933998|ref|YP_007687580.1|  6 YCTQCGAKISPGAKFCPECGK 26
                                      8*******************6 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.2   1.1e-09   8.7e-07       1      27 [.       7      33 ..       7      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 1.1e-09
                               DZR  1 CpqCgeelppdarfCseCgtklkavaa 27
                                      C qCg++++p+a+fC+eCg+ ++++++
  gi|474933998|ref|YP_007687580.1|  7 CTQCGAKISPGAKFCPECGKYVEEMEQ 33
                                      9*******************9987765 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   3.4   7.8e-09   6.3e-06       4      24 ..       6      26 ..       4      26 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 7.8e-09
                       zf-ribbon_3  4 rCPnCGaplssddnvCpyCGt 24
                                      +C +CGa++s+++++Cp CG+
  gi|474933998|ref|YP_007687580.1|  6 YCTQCGAKISPGAKFCPECGK 26
                                      8******88***********6 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   1.9     2e-06    0.0016      65      86 .]       4      25 ..       1      25 [. 0.93

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2e-06
                    zinc_ribbon_15 65 kkeCknCgkeveeefkyCpkCg 86
                                      +++C +Cg+++++  k+Cp+Cg
  gi|474933998|ref|YP_007687580.1|  4 EMYCTQCGAKISPGAKFCPECG 25
                                      679******************9 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.2    0.0036       2.9       2      11 ..       6      15 ..       5      17 .. 0.87
   2 !   10.6   0.1    0.0005      0.41       1      11 [.      19      29 ..      19      35 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0036
                                      B-TTT--B-E CS
                         Nudix_N_2  2 FCsqCGtpve 11
                                      +C+qCG++++
  gi|474933998|ref|YP_007687580.1|  6 YCTQCGAKIS 15
                                      9*****9875 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0005
                                      -B-TTT--B-E CS
                         Nudix_N_2  1 kFCsqCGtpve 11
                                      kFC++CG+ ve
  gi|474933998|ref|YP_007687580.1| 19 KFCPECGKYVE 29
                                      9******9887 PP

>> DHHC  DHHC palmitoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   3.9   1.4e-05     0.011       4     116 ..       3     129 ..       1     172 [. 0.69

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.4e-05
                              DHHC   4 elkfCstcniykpprskHcrvCnrcvlrfDHhCpwlnnciGerNykyFl.....lfllylllllilalvlllialvk 75 
                                       ++ +C  c     p +k+c +C++ v ++    p++     + N++y        + +y +l++++a+++++ +++ 
  gi|474933998|ref|YP_007687580.1|   3 DEMYCTQCGAKISPGAKFCPECGKYVEEMEQDQPVVSGGTYYANQQYKTinersRLQFYGTLAIVYAILAIISGISC 79 
                                       5789********************************99999999988744555466677777766666666666655 PP

                              DHHC  76 lveeekkseflavtllkk.........llsilllvlsllfllllgllllf 116
                                       + + +   ++ + + ++          ++++l ++  l  ++ l+  +l+
  gi|474933998|ref|YP_007687580.1|  80 IATADMLADAIIEQDIDIgmdveefrdTMVLLGVTSLLSGMCALVGGFLV 129
                                       55555555555444333366666666644443333333333333333333 PP

>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.3    0.0072       5.8      39      76 ..      43      80 ..      29      87 .. 0.73
   2 !   15.9   0.9   1.4e-05     0.012      53     100 ..     100     149 ..      88     152 .. 0.89
   3 ?    1.6   0.4      0.41   3.4e+02      64      82 ..     148     166 ..     146     171 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0072
                           DUF4064 39 lteeqalsgedasavleflstllivlgvialiaivlgi 76
                                      ++++q++ + +  + l f +tl iv++++a+i+++  i
  gi|474933998|ref|YP_007687580.1| 43 YYANQQYKTINERSRLQFYGTLAIVYAILAIISGISCI 80
                                      45556666667777778888888888888888887665 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.4e-05
                           DUF4064  53 vleflstllivlgvialiaivlgivgalllkknkk..vsGilfiiaails 100
                                        +e +  ++++lgv +l+++   +vg +l+ + k   +s +l+i+a +l 
  gi|474933998|ref|YP_007687580.1| 100 DVEEFRDTMVLLGVTSLLSGMCALVGGFLVHGAKQfkLSMVLYIAATVLA 149
                                       56789999***********************888887999***9999986 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.41
                           DUF4064  64 lgvialiaivlgivgalll 82 
                                       l++ ++i +vlg+++++l+
  gi|474933998|ref|YP_007687580.1| 148 LAFESIIPLVLGVIFTYLV 166
                                       5566899999999998887 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.4     0.022        18      15      23 ..       6      14 ..       4      16 .. 0.88
   2 !   14.3   0.7   3.8e-05     0.031      13      27 ..      18      32 ..      15      33 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.022
                              YhfH 15 kCteCGkei 23
                                       Ct+CG +i
  gi|474933998|ref|YP_007687580.1|  6 YCTQCGAKI 14
                                      5*****999 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 3.8e-05
                              YhfH 13 kKkCteCGkeieEqa 27
                                      +K C+eCGk  eE++
  gi|474933998|ref|YP_007687580.1| 18 AKFCPECGKYVEEME 32
                                      799**********97 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   4.2   1.8e-05     0.014       3      21 ..       7      25 ..       6      26 .. 0.96

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.8e-05
                           UPF0547  3 CPeCeakvPvaaqfCphCG 21
                                      C +C ak++  a+fCp+CG
  gi|474933998|ref|YP_007687580.1|  7 CTQCGAKISPGAKFCPECG 25
                                      88****************9 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1     0.015        12       4      14 ..       6      16 ..       3      20 .. 0.83
   2 ?   10.4   0.4   0.00047      0.38       3      17 ..      19      33 ..      17      35 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.015
                            zf_UBZ  4 lCerCgkeipe 14
                                       C +Cg++i++
  gi|474933998|ref|YP_007687580.1|  6 YCTQCGAKISP 16
                                      6********97 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00047
                            zf_UBZ  3 ylCerCgkeipesel 17
                                       +C++Cgk+++e e+
  gi|474933998|ref|YP_007687580.1| 19 KFCPECGKYVEEMEQ 33
                                      58********98765 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0061       4.9      18      29 ..       3      14 ..       1      18 [. 0.83
   2 ?    6.1   0.2    0.0095       7.7      22      31 ..      21      30 ..      19      35 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0061
                                      TCEEESSSSBEE CS
                      TF_Zn_Ribbon 18 gelvCtdCGlVl 29
                                       e++Ct CG+ +
  gi|474933998|ref|YP_007687580.1|  3 DEMYCTQCGAKI 14
                                      599******987 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0095
                                      ESSSSBEEEE CS
                      TF_Zn_Ribbon 22 CtdCGlVled 31
                                      C++CG  +e+
  gi|474933998|ref|YP_007687580.1| 21 CPECGKYVEE 30
                                      6666655555 PP

>> zf-FPG_IleRS  Zinc finger found in FPG and IleRS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       0.8   6.5e+02       4       8 ..       7      11 ..       3      15 .. 0.61
   2 ?   10.7   0.0   0.00044      0.36       3      18 ..      20      35 ..      18      35 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.8
                                      -TTT- CS
                      zf-FPG_IleRS  4 CpRCw 8 
                                      C +C+
  gi|474933998|ref|YP_007687580.1|  7 CTQCG 11
                                      55555 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00044
                                      B-TTT--BBEEEECTT CS
                      zf-FPG_IleRS  3 pCpRCwryiervgqag 18
                                       Cp C+ y+e+++q++
  gi|474933998|ref|YP_007687580.1| 20 FCPECGKYVEEMEQDQ 35
                                      6***********9986 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.1   0.00013      0.11      15      42 ..       3      31 ..       1      38 [. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                                      SEEE-TTT--EEEE.EEE-SSS-S---EE CS
                    zinc-ribbons_6 15 eqyhCeaCqedlkk.ealCpeCeqelevl 42
                                      +++ C +C ++++   ++CpeC++ +e +
  gi|474933998|ref|YP_007687580.1|  3 DEMYCTQCGAKISPgAKFCPECGKYVEEM 31
                                      5789*****998752679******99976 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.0   0.00015      0.12      70     100 ..       4      32 ..       1      38 [. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00015
                                       EEEETTTS-EEECHHHHHS-TTTSSS-EEEE CS
                              HypA  70 kvrCreCgkefeleekalrCpkCgsadveiv 100
                                       +++C++Cg++++  +k   Cp+Cg+   e+ 
  gi|474933998|ref|YP_007687580.1|   4 EMYCTQCGAKISPGAK--FCPECGKYVEEME 32 
                                       689********97744..6*****9866655 PP

>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.2   0.00012     0.096      78     164 ..      67     164 ..      48     174 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS  78 lvlltallsafvsndgvvlimipivlslakrlkklppl...lliplalaaniggaltpiGtpttraaarpglslpnl 151
                                       + ++ a++s++    +++ +++ ++++   ++++++      +++l++ + + g++ ++G+ ++ +a++++ls++  
  gi|474933998|ref|YP_007687580.1|  67 VYAILAIISGIS-CIATADMLADAIIEQDIDIGMDVEEfrdTMVLLGVTSLLSGMCALVGGFLVHGAKQFKLSMVLY 142
                                       333333333333.22234444444444444455555557776788***************************99998 PP

                                       xx.........xxxxxxxxxxx RF
                            CitMHS 152 ll.........lalllvgllpl 164
                                       ++         ++l+l ++++ 
  gi|474933998|ref|YP_007687580.1| 143 IAatvlafesiIPLVLGVIFTY 164
                                       8875555555444444433333 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3   0.00013      0.11     366     425 ..      33     164 ..      18     174 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00013
                           DUF2207 366 k...........kergyfdkkgkkklkklsalglgliilglilillallllvll....................... 408
                                       +           ++++y + +++++l+ +++l+++++il++i ++  ++++ +l                       
  gi|474933998|ref|YP_007687580.1|  33 QdqpvvsggtyyANQQYKTINERSRLQFYGTLAIVYAILAIISGISCIATADMLadaiieqdidigmdveefrdtmv 109
                                       355555555555667777778889999999999999999999999999988888*********************** PP

                           DUF2207 409 ......................................lvfllilllillliaii 425
                                                                             l f +i+ l+l++i+  
  gi|474933998|ref|YP_007687580.1| 110 llgvtsllsgmcalvggflvhgakqfklsmvlyiaatvLAFESIIPLVLGVIFTY 164
                                       *999999999999999999999999999777777666666666666666666544 PP

>> DUF2072  Zn-ribbon containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00023      0.18       4      59 ..       7      54 ..       5      95 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00023
                           DUF2072  4 CtkCekvfedgskeilkGCpsCGgkkFlyvkeeekkedvseekeelvaeaeeeiee 59
                                      Ct+C+  ++ g+k     Cp+CG    +yv+e+e+++ v++  + + +++ ++i+e
  gi|474933998|ref|YP_007687580.1|  7 CTQCGAKISPGAK----FCPECG----KYVEEMEQDQPVVSGGTYYANQQYKTINE 54
                                      ***********99....8*****....69*****9999999888666666666554 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   3.7   0.00064      0.52       1      24 []       7      26 ..       7      26 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00064
                           DUF1610  1 CtSCGaelaprEravvFpCPNCGE 24
                                      Ct CGa + p+    +F CP+CG+
  gi|474933998|ref|YP_007687580.1|  7 CTQCGAKISPGA---KF-CPECGK 26
                                      9*********99...77.*****8 PP

>> DUF5362  Family of unknown function (DUF5362)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.3   0.00011     0.088      27      82 ..      64     118 ..      57     130 .. 0.86
   2 ?    1.5   0.9      0.32   2.6e+02      69      87 ..     132     150 ..     122     167 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                           DUF5362  27 igiiigvllIivglklfkaakaikealrskseeklkealeklakylkillilliie 82 
                                       + i+ ++l Ii+g++ +  a+ +++a+ +++  ++ + +e+ ++ + +l++  +++
  gi|474933998|ref|YP_007687580.1|  64 LAIVYAILAIISGISCIATADMLADAIIEQD-IDIGMDVEEFRDTMVLLGVTSLLS 118
                                       6799**********************98766.689999999999999999988765 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.32
                           DUF5362  69 akylkillilliielvlsi 87 
                                       ak +k+ ++l i + vl  
  gi|474933998|ref|YP_007687580.1| 132 AKQFKLSMVLYIAATVLAF 150
                                       5556666666555555533 PP

>> DUF3040  Protein of unknown function (DUF3040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1      0.11        93      42      64 ..      56      78 ..      42      93 .. 0.63
   2 ?    8.0   3.0    0.0042       3.4      42      79 ..     105     150 ..      86     155 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.11
                           DUF3040 42 rrlavlavllfvaGllllvlGva 64
                                       rl + ++l++v ++l+++ G++
  gi|474933998|ref|YP_007687580.1| 56 SRLQFYGTLAIVYAILAIISGIS 78
                                      44566777777777777777754 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0042
                           DUF3040  42 rrlav.lavllfvaGllllvlGvaaaa.......vvlgvvGfvvml 79 
                                       r+++v l+v  +++G+++lv+G++++        +vl ++ +v+++
  gi|474933998|ref|YP_007687580.1| 105 RDTMVlLGVTSLLSGMCALVGGFLVHGakqfklsMVLYIAATVLAF 150
                                       45555055555666********666665888888888888777766 PP

>> DUF2964  Protein of unknown function (DUF2964)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.3    0.0019       1.6      31      53 ..      60      82 ..      57      88 .. 0.86
   2 ?    2.1   3.7      0.28   2.2e+02       7      51 ..     105     150 ..      99     166 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0019
                           DUF2964 31 fdedavlrygvialliGiaafVv 53
                                      f+ + ++ y+++a+++Gi ++++
  gi|474933998|ref|YP_007687580.1| 60 FYGTLAIVYAILAIISGISCIAT 82
                                      67778899**********99986 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.28
                           DUF2964   7 RvvlAtiavFiaLagiaaaihGlLfdedavlrygvia.lliGiaaf 51 
                                       R  +  + v   L g+ a + G L+  ++ ++ + ++ ++  ++af
  gi|474933998|ref|YP_007687580.1| 105 RDTMVLLGVTSLLSGMCALVGGFLVHGAKQFKLSMVLyIAATVLAF 150
                                       555556666667999*********9999999988654266666666 PP

>> DUF2116  Uncharacterized protein containing a Zn-ribbon (DUF2116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   1.1    0.0025         2       5      26 ..       6      26 ..       2      38 .. 0.80
   2 ?    1.6   0.0      0.33   2.7e+02      36      56 ..      54      74 ..      41      77 .. 0.64
   3 ?   -2.2   0.1       5.1   4.2e+03      39      48 ..     138     147 ..     131     163 .. 0.54

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0025
                           DUF2116  5 HCivCGkaIpldesfCsekCqe 26
                                       C  CG+ I ++ +fC e C +
  gi|474933998|ref|YP_007687580.1|  6 YCTQCGAKISPGAKFCPE-CGK 26
                                      5***************65.665 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.33
                           DUF2116 36 arsqqilfgililllavvlvl 56
                                       rs+  ++g l+++ a+++++
  gi|474933998|ref|YP_007687580.1| 54 ERSRLQFYGTLAIVYAILAII 74
                                      466777888888877777765 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 5.1
                           DUF2116  39 qqilfgilil 48 
                                        ++l+ +  +
  gi|474933998|ref|YP_007687580.1| 138 SMVLYIAATV 147
                                       3333333222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       981  (0.0547158); expected 358.6 (0.02)
Passed bias filter:                      604  (0.0336884); expected 358.6 (0.02)
Passed Vit filter:                       112  (0.00624686); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1226.00
//
Query:       gi|474933999|ref|YP_007687581.1|  [L=590]
Description: alanyl-tRNA synthetase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   5.6e-142  474.1   0.0     7e-142  473.7   0.0    1.0  1  tRNA-synt_2c     tRNA synthetases class II (A)
    2.9e-16   59.3   0.4    6.3e-16   58.2   0.4    1.6  1  tRNA_SAD         Threonyl and Alanyl tRNA synthetase second a
  ------ inclusion threshold ------
       0.11   12.6   0.0       0.26   11.5   0.0    1.5  1  AsnC_trans_reg2  AsnC-like ligand binding domain


Domain annotation for each model (and alignments):
>> tRNA-synt_2c  tRNA synthetases class II (A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  473.7   0.0  1.2e-145    7e-142       1     439 [.       5     442 ..       5     474 .. 0.93

  Alignments for each domain:
  == domain 1  score: 473.7 bits;  conditional E-value: 1.2e-145
                                       HHHHHHHHHHHCTT-EEE----SS-SSSTTCSS--SGGGGGHHHHTTSSCGGSSSEEEEEEEEE-EETTEEGGGGTT CS
                      tRNA-synt_2c   1 eirekFldfFekkgHtvvksssvvpendptllfvnAgmaqfkpiflgkeakpklkravnsQkciRagGkhnDlenVG 77 
                                       e+r+++++fF+++gH++++s+s++pendpt+lf+ Agm ++ p++lg++ +p  +r++  Qkc+R+g    D+++VG
  gi|474933999|ref|YP_007687581.1|   5 ELRDAYINFFKARGHAQIRSASLIPENDPTVLFTTAGMHPLVPYLLGQK-HPAGTRLTDYQKCVRTG----DIDEVG 76 
                                       78***********************************************.*****************....****** PP

                                       TSSS--SEEEEEEEEESSSS-HHHHHHHHHHHHHTTTT--GGGEEEEEETTEH......HHHHHHHHTTTTEGGGEE CS
                      tRNA-synt_2c  78 ktarHhTfFeMlGnfsfgdYfkeeaiefawelltkelgldkerlyvtvfeedd......eaveiweklvgvpeeril 148
                                        +a H+TfFeMlGn+s+gdYfk+e i+++++ll+++l +++e++ vt f +d       e+++iwe+ + +p+eri+
  gi|474933999|ref|YP_007687581.1|  77 -DASHLTFFEMLGNWSLGDYFKKESIAWSYQLLQEVLRIPPEQIAVTAFAGDAdapkdeETAAIWEQQG-IPKERIF 151
                                       .688*********************************************9988889998*********6.******* PP

                                       EE-HHHHEE.ESSSSEEEEEEEEEEE.ECETTSHHCHCCCCTTCTCCHEEEEEEEEEEEEEESTTSHEEEEEEEEEE CS
                      tRNA-synt_2c 149 rfgekdnfw.emgdtgpcgpcseiyy.drgeeigkrkaaseveadddrvleiwnlvfmqfnreedgtlkpLpkksid 223
                                        + ++dn+w  +g+tgpcgp +ei++ d+   +    ++  +   +  + eiwn vfmq+ ++++g+ +pL++k++d
  gi|474933999|ref|YP_007687581.1| 152 FLPKEDNWWgPAGQTGPCGPDTEIFFiDK--TMKPCGPDCRPGCHCGYYTEIWNNVFMQYFKDAEGKFTPLKQKNVD 226
                                       *********669************86266..45555577778889******************************** PP

                                       EEEEHHHHHHHHTTHSSGGGSCCTHHHHHHHHHHHT--TCSTCCHHHHHHHHHHHHHHHHHHHHTT--SSSSHHHHH CS
                      tRNA-synt_2c 224 tGmglerlvavLqevrsnydtdlfvpvieaieeisgatyedkdetdealrviaDHvralafaladGvvpsnegrgYv 300
                                       tGmgler   v+++v++ y+t lf+p+i++iee+sg++y d+   ++a+rviaDH+r+ +f++adGvvp + g gY+
  gi|474933999|ref|YP_007687581.1| 227 TGMGLERALRVVNHVETVYETPLFTPIIAKIEEMSGKKYGDN---KKAFRVIADHLRSSTFLIADGVVPAKIGGGYI 300
                                       ************************************999665...559***************************** PP

                                       HHHHHHHHHHHHHHTT-SSTHHHHHHHHHHHHHTTTGCCHHCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCC CS
                      tRNA-synt_2c 301 lRrllRravrhakkLglkekflaklvavvvevlgdvypelkekeekveeiieeEeerFakTlerGlklleelikklk 377
                                       lRrl+Rra r++++L+++   ++++++v+v+ ++ +y el+e+e+++   +++Eee+F++Tl++Gl+ l+++i++ +
  gi|474933999|ref|YP_007687581.1| 301 LRRLIRRASRYMSQLEIEGVRMKEVAEVIVRDYSAAYSELRENEANIYATLSAEEEKFHNTLRKGLRKLDQVIAAQS 377
                                       ***************************************************************************** PP

                                       CCSEEXHHHHHHHHHCHXXXHHHHHHHHHCTTXEEXHHHHHHHHHHHHHHHCCHHSXSS...XXX CS
                      tRNA-synt_2c 378 kkkelsgedafkLydtyGfPvdltkeiaeekglkvdiegfekameeqrerskkekkekk...lik 439
                                       ++k+l+g+ +f+Lydt+GfP++ltke+aeekg++vd+++f+   ++++ +s+++++++    l++
  gi|474933999|ref|YP_007687581.1| 378 DNKVLDGAAVFQLYDTFGFPIELTKELAEEKGFQVDVDDFNGRFKQHQDTSRSDSSQTFkggLAD 442
                                       **************************************************998887765232222 PP

>> tRNA_SAD  Threonyl and Alanyl tRNA synthetase second additional domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.2   0.4     1e-19   6.3e-16       1      43 [.     540     582 ..     540     583 .. 0.98

  Alignments for each domain:
  == domain 1  score: 58.2 bits;  conditional E-value: 1e-19
                                       EEEEEETT.EEEEESS---SBGGGC-SEEEECCECCCTCEEEE CS
                          tRNA_SAD   1 vrvvsiGdisvelCgGtHvpnTgeIgafkilseesiakglrRI 43 
                                       v v++iGd+s e CgG+Hv++Tge++ fki++e+s+a+g+rRI
  gi|474933999|ref|YP_007687581.1| 540 VKVYTIGDVSCEICGGPHVEHTGELQGFKIQKEQSSAAGVRRI 582
                                       78****************************************9 PP

>> AsnC_trans_reg2  AsnC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   4.3e-05      0.26       9      59 ..     312     362 ..     308     384 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.3e-05
                   AsnC_trans_reg2   9 lvawkvpeerveevaevvaelpevtHcYeRewpynlyfmvharseeeveev 59 
                                       +  ++++  r++evaev+ +    +   +Re++ n+y++++a++e+  ++ 
  gi|474933999|ref|YP_007687581.1| 312 MSQLEIEGVRMKEVAEVIVRDYSAAYSELRENEANIYATLSAEEEKFHNTL 362
                                       5566778889********************************988544443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (590 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.71u 0.31s 00:00:01.02 Elapsed: 00:00:00.50
# Mc/sec: 3527.38
//
Query:       gi|474934000|ref|YP_007687582.1|  [L=344]
Description: radical SAM superfamily protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.2e-14   52.5   0.0    1.2e-13   51.8   0.0    1.3  1  Radical_SAM    Radical SAM superfamily
    8.1e-10   38.9   0.0    1.7e-09   37.9   0.0    1.5  1  Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
     0.0058   16.0   0.0     0.0091   15.4   0.0    1.3  1  AnfO_nitrog    Iron only nitrogenase protein AnfO (AnfO_nitro
  ------ inclusion threshold ------
       0.09   11.8   0.1       0.14   11.2   0.1    1.2  1  Peptidase_M42  M42 glutamyl aminopeptidase


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.8   0.0   2.7e-17   1.2e-13      51     165 ..      13     138 ..       6     140 .. 0.83

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 2.7e-17
                                       EEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHH...........H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........x RF
                       Radical_SAM  51 ilgggepllypdfvellerlaklavpgiritvetngtlpdeeklerllelgvdrvslgleaadde...........k 116
                                       i g g+pl++ +  +++++l++++ p+++++++tng+ + ++ ++rl +lgv  v+++++a+d+e           +
  gi|474934000|ref|YP_007687582.1|  13 IAGPGDPLANEET-FETLALVRERFPDLTLCISTNGLAL-PDSAQRLYDLGVRFVTVTINAPDEEigskiygsvlwD 87 
                                       6789*****8866.56666666667**************.*************************555555555554 PP

                                       HHHHHTCTSHH.............HHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHHH CS
                                       xxxxxxxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 117 vlklmnrghtf.............eevlealeklreagikrvvdrivglpGendeeleelle 165
                                                               e++le+++k++++g+  v+ +iv++p  n + + +l++
  gi|474934000|ref|YP_007687582.1|  88 ----------GrrltgtegarillERQLEGIRKCADLGML-VKANIVMIPEINADAIPDLVK 138
                                       ..........05555555556777****************.*************99988876 PP

>> Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.0   3.7e-13   1.7e-09       2      86 ..     246     333 ..     245     340 .. 0.86

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 3.7e-13
                                       TSCB-STCCC-SEEEEEEESSSCEEEEEEE...E.GCCCTSSCSSTHHHHHHHH.TT-SEEEESSSCHHHHHHHCTT CS
                     Nitro_FeMo-Co   2 gsrvdqhFGrapyFaiyeveegevkivenr...veeaadaegggggklaqllae.egvdvvivgkiGpralakleaa 74 
                                       gs vd  FG a++F++y+v+  ev++v +       +++ ++++ + +++++    ++d++ v++iG  ++  +e++
  gi|474934000|ref|YP_007687582.1| 246 GSSVDRGFGNADRFLVYSVDGPEVNMVREVrpgDLDSSSVGKSHRDHIEAIVNLlDDCDIIAVSEIGDMPRSVIESR 322
                                       789*****************777775555559877778888899999****************************** PP

                                       TSEEEES-SSBH CS
                     Nitro_FeMo-Co  75 gievykgaggtv 86 
                                       + +v++  +g+v
  gi|474934000|ref|YP_007687582.1| 323 KKKVIV-TDGSV 333
                                       ******.55555 PP

>> AnfO_nitrog  Iron only nitrogenase protein AnfO (AnfO_nitrog)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0     2e-06    0.0091      19      93 ..     257     332 ..     239     337 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2e-06
                       AnfO_nitrog  19 givkvyekekgkWkvkrei.efeleeekglaeirekleelveeLgdckifvakevsGilyslLekagfsiweiegk 93 
                                        ++ vy+ ++ + +++re+ + +l++++  +  r+++e++v+ L+dc i+ ++e+ +++ s++e+ + +++  +g+
  gi|474934000|ref|YP_007687582.1| 257 DRFLVYSVDGPEVNMVREVrPGDLDSSSVGKSHRDHIEAIVNLLDDCDIIAVSEIGDMPRSVIESRKKKVIVTDGS 332
                                       5666777777666666665245677777778889******************************999888877776 PP

>> Peptidase_M42  M42 glutamyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1     3e-05      0.14      20      70 ..     288     338 ..     276     342 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3e-05
                                       EE--B-EEEEEEEETTSEEEEEEESS--GGGTTTEEEEEEETTEEEEEEEE CS
                     Peptidase_M42  20 AHmDeiGfmVkeIkedGflrfekvGGvdpkvlegqrvkiltkkgkisGvig 70 
                                       +H D i ++V+ +++   + ++++G +  +v+e+++ k+   +g ++G+++
  gi|474934000|ref|YP_007687582.1| 288 SHRDHIEAIVNLLDDCDIIAVSEIGDMPRSVIESRKKKVIVTDGSVRGTVS 338
                                       7***********************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 2010.44
//
Query:       gi|474934001|ref|YP_007687583.1|  [L=55]
Description: hypothetical protein TALC_00418 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0091   16.4   1.3       0.01   16.2   1.3    1.1  1  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.3   5.7e-07      0.01       1      29 [.      21      53 ..      21      55 .] 0.77

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.7e-07
                                      EEEESEESS--TTTSCCTT....HHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxx....xxxxxxxxxx RF
                       Radical_SAM  1 vvvtrgCnlrCsfCarpet....vrregrgrsl 29
                                      v+v + Cn +C++C+r+++    +r+++++++l
  gi|474934001|ref|YP_007687583.1| 21 VPVAPKCNIQCNYCNRKYDcsneSRPGVTSEVL 53
                                      57899************9987766666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.49
# Mc/sec: 340.33
//
Query:       gi|474934002|ref|YP_007687584.1|  [L=123]
Description: archaeal conserved hypothetical protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-30  105.8   0.0    1.7e-30  105.7   0.0    1.0  1  DUF61     Protein of unknown function DUF61
  ------ inclusion threshold ------
      0.052   12.1   0.0      0.062   11.8   0.0    1.0  1  CATSPERB  Cation channel sperm-associated protein subunit bet


Domain annotation for each model (and alignments):
>> DUF61  Protein of unknown function DUF61
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.7   0.0   1.9e-34   1.7e-30       7     127 .]       1     121 [.       1     121 [. 0.98

  Alignments for each domain:
  == domain 1  score: 105.7 bits;  conditional E-value: 1.9e-34
                                       HHHHHGGGSBSS-EEHHHHHHT--EEEB.TTS-EEE--HHHHHHHHTTS-GGGGGT-EESEEEEE-SSSSE..EEEE CS
                             DUF61   7 eiksinkhlPaerktLkelLeeekptivtkdgsehrfdkeeleklkeilpeelwdklkLPIllemdpelgesvylvr 83 
                                       ++  +n+++P++r++L+++Le+++ t++tk+g++ +f +e +++l++i +++++ +l+LP+++++d + ++s+++++
  gi|474934002|ref|YP_007687584.1|   1 MLAGMNSNIPVDRRSLMDYLENGDLTYRTKSGETVEFGREGIDYLASITNDQEKLTLRLPVFVATDVTAERSAWKIE 77 
                                       5789************************************************************************* PP

                                       S-HHHHHHHHHHT--...-SSEEEHH.HHHHHHHH-ST...TEE CS
                             DUF61  84 gkaevkvvskilgkereeedelviykpevrelrrklptatqliF 127
                                       g++ev+v+s++l+++ ++ed++ +y+p+++e+++ +p ++ ++F
  gi|474934002|ref|YP_007687584.1|  78 GRTEVAVISRALNRRVHSEDRMPVYYPDIAEMKKLIPGLVFTLF 121
                                       **************************************999988 PP

>> CATSPERB  Cation channel sperm-associated protein subunit beta protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0     7e-06     0.062     389     446 ..      46     105 ..      34     114 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7e-06
                          CATSPERB 389 LeiveekekiplesPYlvtvtevnnRknwelkhsesetv..kklkkylesllkssvynPk 446
                                        +i++++ek +l+ P +v+     +R+ w+++  ++  v  + l++ ++s+ +++vy P+
  gi|474934002|ref|YP_007687584.1|  46 ASITNDQEKLTLRLPVFVATDVTAERSAWKIEGRTEVAVisRALNRRVHSEDRMPVYYPD 105
                                       5799***************99999********99888663356889999999*****996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 942.50
//
Query:       gi|474934003|ref|YP_007687585.1|  [L=212]
Description: Zn-dependent hydrolase, including glyoxylase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-30  107.0   0.1    1.5e-30  106.7   0.1    1.1  1  Lactamase_B    Metallo-beta-lactamase superfamily
    8.6e-08   31.9   0.0    1.5e-07   31.1   0.0    1.4  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.014   14.8   0.0      0.021   14.2   0.0    1.2  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.7   0.1   2.6e-34   1.5e-30       6     197 .]      14     192 ..      11     192 .. 0.95

  Alignments for each domain:
  == domain 1  score: 106.7 bits;  conditional E-value: 2.6e-34
                                       SEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCC CS
                       Lactamase_B   6 vnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapal 82 
                                       +n +l+  + ++iLiDtGt+ +++        + l++++++avilTH H+DHiGgl+ + +++++p ++   +a+al
  gi|474934003|ref|YP_007687585.1|  14 SNLWLV-RGRSCILIDTGTGMAENYTN--NIWRALDGLRLSAVILTHCHADHIGGLARIQHEFGCPAYIGFGDAEAL 87 
                                       788999.6********99887777764..467********************************************* PP

                                       HCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCC CS
                       Lactamase_B  83 fmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetgr 159
                                       ++  + + as++ +  ++ ++ ++   + e+d++++g+++l+v+ +pgh+ g+++++++  + lf+GD+++a   gr
  gi|474934003|ref|YP_007687585.1|  88 RTADPVKTASAGLG--IPINPCPDALGLKEGDSFDLGDHRLVVIETPGHTEGSICLYDEVTGALFSGDTVFAQGYGR 162
                                       *****999999885..999999******************************************************* PP

                                       CCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                       Lactamase_B 160 idltlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                       +dl        + ++ ++ ++sl +l + +++ l+pgH
  gi|474934003|ref|YP_007687585.1| 163 VDL--------PSGSMSEMRESLARLNNVNIKALYPGH 192
                                       ***........*************************** PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.0   2.6e-11   1.5e-07       3     111 ..      25     132 ..      24     162 .. 0.63

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 2.6e-11
                                       EEES--TTHHHH.HTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC..C--EEEEEEEE...HHHHHHCCTT CS
                     Lactamase_B_2   3 iLiDagpdlrqq.alralqPvelrdelppidaVllthaHyDHlaglltlre..lrpkklplyap...kgvlavlean 73 
                                       iLiD+g++++++         +++d   ++ aV+lth+H+DH+ gl  +++  ++p  + + ++   +++++ +++ 
  gi|474934003|ref|YP_007687585.1|  25 ILIDTGTGMAENyT-NNI--WRALDG-LRLSAVILTHCHADHIGGLARIQHefGCPAYIGF-GDaeaLRTADPVKTA 96 
                                       9*******998843.333..344554.589*******************997766643222.222234444444444 PP

                                       CGHHHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE- CS
                     Lactamase_B_2  74 fvylaleeepavnvheldwgesfelgdggleitatpar 111
                                       +  l  + +p  ++  l+ g+sf+lgd+   + +++ +
  gi|474934003|ref|YP_007687585.1|  97 SAGLGIPINPCPDALGLKEGDSFDLGDHR--LVVIETP 132
                                       44444444455556666677777777543..5555555 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.6e-06     0.021       8      59 ..      24      73 ..      18      80 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.6e-06
                     Lactamase_B_6  8 kiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallyakf 59
                                      +iL+D G+   + ++++ ++   + + ++++++L+h  ++h+G++a + ++f
  gi|474934003|ref|YP_007687585.1| 24 CILIDTGTGMAE-NYTNNIWRALDGL-RLSAVILTHCHADHIGGLARIQHEF 73
                                      79****999763.4544554444444.69***************98877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1419.89
//
Query:       gi|474934004|ref|YP_007687586.1|  [L=212]
Description: Sua5/YciO/YrdC/YwlC family protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-47  160.9   0.0    2.6e-47  160.6   0.0    1.1  1  Sua5_yciO_yrdC  Telomere recombination
  ------ inclusion threshold ------
      0.084   12.9   0.1       0.15   12.0   0.1    1.4  1  Herpes_UL55     Herpesvirus UL55 protein


Domain annotation for each model (and alignments):
>> Sua5_yciO_yrdC  Telomere recombination
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.6   0.0   2.9e-51   2.6e-47       4     179 .]      28     199 ..      25     199 .. 0.97

  Alignments for each domain:
  == domain 1  score: 160.6 bits;  conditional E-value: 2.9e-51
                                       HTTSEEEEE-SSSEEEEEETTSHHHHHHHHHHHTSHCCC--EEEESSCCCCCCCC-TC--HHHHHHHHCT-SSSCEE CS
                    Sua5_yciO_yrdC   4 rkGgivaiptetvYgLacdatneeaverlreiKgrpsdkplavlvasledlkklaeseveeealkllerfwPGpitl 80 
                                        +G+++++pt+tvYg+++d+ ne av+ l+ +K+rp d  l+v va+ ++++k+a   ++e+a kl+++f+PGp+t+
  gi|474934004|ref|YP_007687586.1|  28 ASGKLIVYPTDTVYGIGADIFNEGAVKALYLAKKRPFDMALSVAVADRKMIEKVAI--LNENAEKLIDAFMPGPLTI 102
                                       68*****************************************************8..******************* PP

                                       EEE..E-TS-HHHHTTTTEEEEEE-SSHHHHHHHHHCTS-EEEEES-STTS-S-SSHHHHHHHC-TTSECB-SS--- CS
                    Sua5_yciO_yrdC  81 llkrskeklpkevapglktvGvrlPdtplarlLlealgeplvaTSanlsgepsitdaeeveeelgeivdlildggei 157
                                       + k++ + +p+ v++ +++vG+r+P++p+a+++++++g p+vaTSan + +p + + + + e +g+ v+ ++d+g+ 
  gi|474934004|ref|YP_007687586.1| 103 IIKKQPD-VPDIVTAMSDKVGIRIPNHPVALEIAKRAG-PIVATSANTHFHPDAVNIDMAVEAFGDAVSTYVDAGQS 177
                                       ***7444.****************************98.************************************** PP

                                       SSS---EEEETTSSTSSECEXX CS
                    Sua5_yciO_yrdC 158 avgvdstVvdltegkpkilRrG 179
                                        +g +st+v + ++ ++i+R+G
  gi|474934004|ref|YP_007687586.1| 178 PIGKPSTIVWIKGSDYEIIRQG 199
                                       ************99******98 PP

>> Herpes_UL55  Herpesvirus UL55 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   1.7e-05      0.15     131     155 ..       5      29 ..       2      34 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.7e-05
                       Herpes_UL55 131 hChCkspfskeCWkgasaaleklav 155
                                        C C +  s eC  +asaa e +a+
  gi|474934004|ref|YP_007687586.1|   5 KCDCSNGLSDECIAAASAAAEDVAS 29 
                                       7********************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1582.21
//
Query:       gi|474934005|ref|YP_007687587.1|  [L=298]
Description: methionine aminopeptidase, type II [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.8e-36  124.1   0.0    7.5e-36  123.8   0.0    1.3  1  Peptidase_M24  Metallopeptidase family M24


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.8   0.0   4.2e-40   7.5e-36       1     191 [.       8     201 ..       8     295 .. 0.87

  Alignments for each domain:
  == domain 1  score: 123.8 bits;  conditional E-value: 4.2e-40
                                       HHHHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBC...SSSB--TT CS
                     Peptidase_M24   1 elirkaariasaaleavleaikpgvterelaaeieattlkrhgarglafppivasgenaavlhytp...ndrvlkeg 74 
                                       e++rka+r++++a++  l++++ g++ +++a+e+e + +++hg+ glafp  + ++ n  ++hytp   +d +l+ g
  gi|474934005|ref|YP_007687587.1|   8 EKLRKAGRVSAEARDLGLSMCQAGTKLYDIAEEVEGY-IRKHGC-GLAFP--CNISLNQVAAHYTPspdDDSKLEIG 80 
                                       689********************************99.666665.89***..9999999999**997655667**** PP

                                       EEEEEEEEEEETTEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSS CS
                     Peptidase_M24  75 dlvlidagaeydgyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffph 151
                                       d+v+id+g+ +dg+++D++ T  vG  t++  +l+ a ++a++++ + v  Gv+lsei+ +++++++++g+ k++ +
  gi|474934005|ref|YP_007687587.1|  81 DIVKIDCGGFLDGFIGDTAGTAEVG--THAFTNLVMASKRARDTVAEFVSDGVPLSEIGSVIEQTVKREGF-KVVEN 154
                                       **********************999..889999***********************************9**.***** PP

                                       CSEEEESS.SSSEEEEEE.SSSTTCSSB--TTBEEEEEE......EEE CS
                     Peptidase_M24 152 glGHgvGl.evhdegpsv.sresndgrkleeGmvftiEp......giy 191
                                       ++GH + + ++h +  s+ +++s+d++++++Gm+f++Ep      g++
  gi|474934005|ref|YP_007687587.1| 155 LCGHQISQwDLHAG-LSIpPYDSGDSTPVRAGMTFAVEPfatngtGYV 201
                                       *******99***98.5542446789**************777766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 1941.81
//
Query:       gi|474934006|ref|YP_007687588.1|  [L=489]
Description: Zn-dependent hydrolase, including glyoxylase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.9e-08   32.3   0.0    0.00088   19.0   0.0    2.5  2  ACT          ACT domain
    4.2e-06   26.9   0.1    8.1e-06   26.0   0.1    1.5  1  Lactamase_B  Metallo-beta-lactamase superfamily
     0.0022   18.6   0.0      0.015   15.9   0.0    2.1  2  ACT_4        ACT domain
  ------ inclusion threshold ------
      0.061   13.2   0.0       0.14   12.0   0.0    1.7  1  ACT_5        ACT domain


Domain annotation for each model (and alignments):
>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   7.8e-05      0.35       6      64 ..      16      72 ..      13      74 .. 0.92
   2 !   19.0   0.0     2e-07   0.00088       4      55 ..      89     140 ..      85     151 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 7.8e-05
                                      EEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHT CS
                               ACT  6 gvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkk 64
                                       +pD  G++ + ++ +a +giNi++++     d   +  f+  ++ ee+l ++ e+l+ 
  gi|474934006|ref|YP_007687588.1| 16 TMPDNIGAFLKASQCFASLGINITRVSYNKAVD--THTLFIDAEGTEEQLLKADEELRG 72
                                      6888899999999********************..7*******************9985 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 2e-07
                                       EEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHH CS
                               ACT   4 rvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedl 55 
                                       ++ ++D+PG   rv+ ++ + g+Ni  i++ +++  + ++ +  +v+d++ +
  gi|474934006|ref|YP_007687588.1|  89 EFILRDEPGSVTRVLELIMEFGFNISYISSQEDGTAYQRFKMGLFVEDTDKV 140
                                       5889*****************************9976666666666665555 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.1   1.8e-09   8.1e-06       3     150 ..     253     421 ..     251     425 .. 0.77

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1.8e-09
                                       CCSSEEEEEEETTCEEEES--SCHHHHHHHH.HHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTH.HCCEETCCEH CS
                       Lactamase_B   3 pdpvnsyliegdggviLiDtGtsteaaraal.elaalglkpkdvdavilTHlHlDHiGglgglvea.tdvpvgavae 77 
                                       p+++n+++i+ dg v+ +DtG+   ++  ++ +   l   +   ++v+++H++lDHiG  + + e  +  +++ +  
  gi|474934006|ref|YP_007687588.1| 253 PCGSNTTIIVSDGQVLFVDTGYACYREETLKvIREILPDFDSMAKRVLISHADLDHIGLCPVFDEVlASENSALCMR 329
                                       799**************************998888888999999***************999999635688888888 PP

                                       HHHCCHCHHHHHHHHHCCHH.....................TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSC CS
                       Lactamase_B  78 eapalfmeeaddaasrkgll.....................lagvsadkpdvdeeeldgnaggrralyvtggpghgh 133
                                       e++++++  +++ + +k+ +                     +a++  d p  +   ld+++++ + ++  gg++ g 
  gi|474934006|ref|YP_007687588.1| 330 EEYEGRDGFRETNPLHKPYIgickiltgyepvptdkvrvmwKARPENDVPLYPVGFLDVGEFSFEVYEGRGGHLKG- 405
                                       8888888888888888888888888888888888888877666555555555555555555555555555555554. PP

                                       CEEEEEETTCCEEEECT CS
                       Lactamase_B 134 ghgvveygggkvlftGD 150
                                         +v+ +   k +ftGD
  gi|474934006|ref|YP_007687588.1| 406 -EIVLIDYRMKAAFTGD 421
                                       .4445555556666666 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.46   2.1e+03      15      41 ..      19      45 ..      15      56 .. 0.80
   2 !   15.9   0.0   3.3e-06     0.015      10      68 ..      89     146 ..      85     155 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.46
                             ACT_4 15 drkglLaditqviseekanivsvnakt 41
                                      d+ g++ + +q +++ ++ni+ v+  +
  gi|474934006|ref|YP_007687588.1| 19 DNIGAFLKASQCFASLGINITRVSYNK 45
                                      7788888899999********998776 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 3.3e-06
                             ACT_4  10 eveaedrkglLaditqviseekanivsvnaktrkkdglaeikitveVkdvehLsrviak 68 
                                       e + +d++g +++++++i e + ni+ ++++++    + ++k+ + V+d++++s+ ia+
  gi|474934006|ref|YP_007687588.1|  89 EFILRDEPGSVTRVLELIMEFGFNISYISSQEDG-TAYQRFKMGLFVEDTDKVSQFIAR 146
                                       56889***************************75.779999************999987 PP

>> ACT_5  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.1e-05      0.14       1      45 [.      94     139 ..      94     154 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.1e-05
                             ACT_5   1 dapgvLeRvlrvvrrrgFevkslnmst.tedggtvrieltVesers 45 
                                       d+pg + Rvl ++   gF+++ +++++  +  +++++ l Ve+ + 
  gi|474934006|ref|YP_007687588.1|  94 DEPGSVTRVLELIMEFGFNISYISSQEdGTAYQRFKMGLFVEDTDK 139
                                       689***********************93333344555556666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (489 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 3154.97
//
Query:       gi|474934007|ref|YP_007687589.1|  [L=178]
Description: archaeal ribosomal protein S13P [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.9e-41  140.1   3.2    5.9e-41  139.8   3.2    1.1  1  Ribosomal_S13  Ribosomal protein S13/S18
      0.008   16.4   0.0      0.014   15.7   0.0    1.4  1  HHH_6          Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.031   14.9   0.4      0.058   14.0   0.4    1.3  1  HHH_5          Helix-hairpin-helix domain
      0.054   13.4   2.2      0.076   12.9   2.2    1.2  1  CagA           CagA exotoxin


Domain annotation for each model (and alignments):
>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.8   3.2   1.3e-44   5.9e-41       1     128 []      41     168 ..      41     168 .. 0.98

  Alignments for each domain:
  == domain 1  score: 139.8 bits;  conditional E-value: 1.3e-44
                     Ribosomal_S13   1 RilgtdidgkkkveialtaikGiGrrkakiilkkadvdedkrigelteeeiekieeivenkaqykipnwinrqkdik 77 
                                       R+++tdidg+k+v+i l++ikG+G+r a+i++kka+vd  ++ig l++e+++k+ee v n ++y + + inrq+d++
  gi|474934007|ref|YP_007687589.1|  41 RMANTDIDGQKHVVIGLQSIKGVGKRVAQIVAKKAGVDPAAKIGSLADEDVKKLEEDVLNYVEYAPVWAINRQNDYE 117
                                       899*********************************************************9999988888******* PP

                     Ribosomal_S13  78 dGkdshvvendlrrklredieRlkkirsyrGlRHkrGlkvRGQrTkttgRt 128
                                       +G+d+h+  +d++  + +di+R+++ir+yrG+RH++  kvRGQrT+++gR+
  gi|474934007|ref|YP_007687589.1| 118 SGEDMHLFGQDVDIIQGDDINRMQMIRCYRGIRHETHHKVRGQRTRSNGRK 168
                                       *************************************************95 PP

>> HHH_6  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0     3e-06     0.014      21      58 ..      49      85 ..      23     102 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3e-06
                             HHH_6 21 edgairlGLaaikglgeaaaerivaeRekegpfksled 58
                                       ++++++GL++ikg+g+++a+ iva+++   p +++  
  gi|474934007|ref|YP_007687589.1| 49 GQKHVVIGLQSIKGVGKRVAQ-IVAKKAGVDPAAKIGS 85
                                      3455*************9986.5665655566655555 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.4   1.3e-05     0.058       4      38 ..      57      95 ..      55      97 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.3e-05
                                      HHTSTT--HHHHHHHHTT.T--SHH...HHHHS-HHHHH CS
                             HHH_5  4 LlsvsGiGpktAlallsa.Giesve...dlaaadveeLa 38
                                      L+s++G+G+++A  ++++ G++  +    la++dv++L 
  gi|474934007|ref|YP_007687589.1| 57 LQSIKGVGKRVAQIVAKKaGVDPAAkigSLADEDVKKLE 95
                                      89****************999965523377999999996 PP

>> CagA  CagA exotoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   2.2   1.7e-05     0.076      23      98 ..       9      87 ..       4     100 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.7e-05
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXBXXXXXXBSXTTXXXXXX CS
                              CagA 23 lknstepiyakvnkkktgqvaspeepiytqvakkvnakidrlnqiasgl...ggvgqaagfplkrhdkvddlskvglsa 98
                                       k+++ p   k  kkk g  a  e+  +  + +  n+ id  +++  gl    gvg+     + ++  vd  +k+g  a
  gi|474934007|ref|YP_007687589.1|  9 QKEAAAPAEKKSGKKKGGASAKTEDENFNYIVRMANTDIDGQKHVVIGLqsiKGVGKRVAQIVAKKAGVDPAAKIGSLA 87
                                      5788899999***********************************9997333599*999999999999***99999655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1156.55
//
Query:       gi|474934008|ref|YP_007687590.1|  [L=220]
Description: SSU ribosomal protein S4P [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-16   60.2   0.1    2.5e-16   59.1   0.1    1.6  1  S4        S4 domain


Domain annotation for each model (and alignments):
>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.1   0.1   1.4e-20   2.5e-16       1      45 [.     107     151 ..     107     153 .. 0.95

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 1.4e-20
                                       EEHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TT CS
                                S4   1 rRLdkvlarlglassrreArqlIehGrVlVNGkvvkdpsyrVkpg 45 
                                       rRL+++++++gla ++r+ArqlI+hG++ VNG +v+ p+y V  +
  gi|474934008|ref|YP_007687590.1| 107 RRLQTIVFQKGLATTIRQARQLINHGHIFVNGHKVTVPGYLVLRS 151
                                       8****************************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.34s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1343.85
//
Query:       gi|474934009|ref|YP_007687591.1|  [L=124]
Description: SSU ribosomal protein S11P [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-42  144.5   2.8    1.9e-42  144.1   2.8    1.1  1  Ribosomal_S11  Ribosomal protein S11


Domain annotation for each model (and alignments):
>> Ribosomal_S11  Ribosomal protein S11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.1   2.8     1e-46   1.9e-42       1     110 []       2     120 ..       2     120 .. 0.99

  Alignments for each domain:
  == domain 1  score: 144.1 bits;  conditional E-value: 1e-46
                     Ribosomal_S11   1 GvahiqasfnntiititdlkGaevlvksaGglgvkasr.kssPyaaqlaaekaaekvldkGikavevkvkg...... 70 
                                       G+a+i+as+nn +it+td++Gae+l k +Gg+ vk+++ +ssPyaaq+aae++ae + +k i+ ++v+v++      
  gi|474934009|ref|YP_007687591.1|   2 GIANIYASYNNIMITLTDITGAETLGKVTGGMIVKQAKdESSPYAAQRAAERIAEIAAEKEITGIHVRVRApggnks 78 
                                       89************************************9************************************** PP

                     Ribosomal_S11  71 ..pGpGreaalralaraGlkigriedvtPiPhdgirrpkkrr 110
                                         pGpG++aa+ralaraGl+igriedvtP+Phdg++++++rr
  gi|474934009|ref|YP_007687591.1|  79 tsPGPGAQAAIRALARAGLRIGRIEDVTPVPHDGTKPKGGRR 120
                                       ***************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 773.99
//
Query:       gi|474934010|ref|YP_007687592.1|  [L=287]
Description: DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.8e-17   61.8   0.0    1.3e-16   60.9   0.0    1.4  1  RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
      2e-15   55.9   0.0    3.8e-15   55.1   0.0    1.5  1  RNA_pol_L      RNA polymerase Rpb3/Rpb11 dimerisation domain
  ------ inclusion threshold ------
       0.14   12.0   0.0       0.22   11.3   0.0    1.3  1  DUF4018        Domain of unknown function (DUF4018)


Domain annotation for each model (and alignments):
>> RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   0.0   2.2e-20   1.3e-16       9     112 .]      65     166 ..      60     166 .. 0.89

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 2.2e-20
                                       SS.HHHHHCHHHCSTCBSSCHHHHHHHHCTT-ETSSSSTTCSEEEEEEEEESSECEEGGGCBES.SSSCEESSTTSE CS
                     RNA_pol_A_bac   9 vlqDEvvaHrlgliplvsedvleillnlkelveeeeegeeeksvelkLnvkgpgevtagdlkle.dadveivnpdil 84 
                                        l DEv+aHr+gl+p+ ++ + +   +  ++ e    g++++s+  +Ln+ gp +v ++dl+   d++  + + +i+
  gi|474934010|ref|YP_007687592.1|  65 PLFDEVIAHRIGLVPIPTDYESF--TFQDQC-ECGGVGCPHCSIMYSLNKTGPATVLSEDLQPLgDKSLAVKDGNIP 138
                                       689**************999888..677777.324689************************9967777777999** PP

                                       EEEEETT-EEEEEEEEEEESSEECTTT- CS
                     RNA_pol_A_bac  85 IakLrkgqeleleakvkkGiGkehakfs 112
                                       I++L+kgq + +  +++ G++++h+k++
  gi|474934010|ref|YP_007687592.1| 139 IVELTKGQAIIVYGTAVMGTARKHVKWQ 166
                                       ***************************6 PP

>> RNA_pol_L  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   0.0   6.4e-19   3.8e-15       3      67 ..      16     274 ..      14     276 .. 0.80

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 6.4e-19
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx................................................. RF
                         RNA_pol_L   3 llrgvdhtlgNaLRrillsevpgvaiea................................................. 30 
                                        lr+++++l+NaLRr++l ++p++ai++                                                 
  gi|474934010|ref|YP_007687592.1|  16 ILRDCTPALANALRRTMLQDIPKMAIDKvefhlgevmsqetdeasesitplfdeviahriglvpiptdyesftfqdq 92 
                                       68999**********************************************************99999999999999 PP

                                       ............................................................................. RF
                         RNA_pol_L  31 ............................................................................. 30 
                                                                                                                    
  gi|474934010|ref|YP_007687592.1|  93 cecggvgcphcsimyslnktgpatvlsedlqplgdkslavkdgnipiveltkgqaiivygtavmgtarkhvkwqaaf 169
                                       99999999999999999999988888888888888888888888877777777777777777777777766666666 PP

                                       .......xx.............................................................xxxxxxx RF
                         RNA_pol_L  31 .......pv.............................................................vkvntdk 39 
                                              pv                                                               v  d+
  gi|474934010|ref|YP_007687592.1| 170 gvgysymPVitvkedkaadpevikaalenypglfeekngklvvadiwkapdfgkgigadlpdtpdvlkdfATVDWDD 246
                                       6666666225556666666666666666666666666666666666666667766676666676666666667799* PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         RNA_pol_L  40 dklilevetdgslkPeealkeAlkiLke 67 
                                       +++ ++ etdgsl+++++l +A++i k+
  gi|474934010|ref|YP_007687592.1| 247 SEFLFKYETDGSLTAQQVLDKAIEIVKA 274
                                       *************************986 PP

>> DUF4018  Domain of unknown function (DUF4018)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   3.7e-05      0.22     125     169 ..     162     206 ..     145     215 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.7e-05
                           DUF4018 125 yilyvvalGfGyalepllkiaelkdaeevveklGygekpkledak 169
                                       ++    a+G+Gy+ +p++ + e k a+  v k    + p l ++k
  gi|474934010|ref|YP_007687592.1| 162 HVKWQAAFGVGYSYMPVITVKEDKAADPEVIKAALENYPGLFEEK 206
                                       5666789******************99888887777777666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1776.42
//
Query:       gi|474934011|ref|YP_007687593.1|  [L=1128]
Description: DNA polymerase, archaeal type II, large subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
          0 1138.6   0.0          0 1133.0   0.0    2.1  2  PolC_DP2        DNA polymerase II large subunit DP2
     0.0074   16.3   6.5       0.25   11.4   0.8    2.9  2  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.018   15.0   0.9        1.4    9.0   0.3    2.8  2  HypA            Hydrogenase/urease nickel incorporation, meta
       0.04   13.9   2.6        1.1    9.3   0.1    2.7  2  zinc-ribbons_6  zinc-ribbons
        0.6   10.1   7.1        3.3    7.7   1.3    2.9  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain


Domain annotation for each model (and alignments):
>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1133.0   0.0         0         0       1     864 []      14     878 ..      14     878 .. 0.97
   2 !    2.5   1.0    0.0074        27     616     674 ..    1042    1104 ..    1015    1124 .. 0.63

  Alignments for each domain:
  == domain 1  score: 1133.0 bits;  conditional E-value: 0
                          PolC_DP2   1 eYfeklekeleeayeiaekarskgldpkeevEiplAkdladRvekllg...ikgvaerirelekel.sreevalkia 73 
                                       +Yfe+l+++++++y+ia+kar++g+dp+ evEip A+dla+Rvekll+   +kg+ae ir+l+ke+ +re va+k a
  gi|474934011|ref|YP_007687593.1|  14 RYFESLNEDTDRLYQIAAKARKEGKDPTLEVEIPRAEDLASRVEKLLEeydVKGLAEIIRRLTKEYgNREVVAIKAA 90 
                                       6*********************************************98888************99945999****** PP

                          PolC_DP2  74 keiaegkvgeaeskeeavdkavrtalalltegvvaAPleGiakvkikknddgteylkvyyaGPiRsaGGtaqalsvL 150
                                       +e+a++ +   es e+a+d+avr++la++teg+++APleGia  +i++nddgt++ ++++aGPiR++GGt qa+svL
  gi|474934011|ref|YP_007687593.1|  91 EEYAKKPA---ESMEKALDRAVRIGLAIVTEGILVAPLEGIACTRIRQNDDGTNFADLVFAGPIRASGGTGQAISVL 164
                                       ****9987...6789************************************************************** PP

                          PolC_DP2 151 vaDyvrkklgldrykpreeeieRyveEielYervaslqyspsdeeirlivknipveidGeatedeevsgyrdlerve 227
                                       ++D+vr+++g+++ykp+e ei R+ eEi lY+++++lq++ps+eeir+iv+++pv++dGe te++e+sg+rdl+r++
  gi|474934011|ref|YP_007687593.1| 165 ICDVVRQAMGIGAYKPTEGEIARFDEEIPLYKQCQHLQFTPSSEEIRTIVSECPVMVDGEGTEQVEISGFRDLPRID 241
                                       ***************************************************************************** PP

                          PolC_DP2 228 tnrvRGGmllvlaeGialkakKikkkvkklklegWewleelikaekeekkeeeeekkevkpkekylrdliaGRpvls 304
                                       tnrvRGG++lv+aeG++lka+Ki+k+vkkl+++gW++++++++ +k+ +++++ +kk v+p++kyl+d++aGRp+++
  gi|474934011|ref|YP_007687593.1| 242 TNRVRGGACLVIAEGMCLKASKIQKHVKKLGIKGWDFIDKYMDLHKAVDTDDKGKKKVVEPATKYLKDMVAGRPIFG 318
                                       ***************************************************************************** PP

                          PolC_DP2 305 hpsrkGGfRLrYGRsrntglatagihPatmelldeflavGtqlkverPgKaaavvpvdsiegPtvklknGdvvridd 381
                                       hp+r+GGfRLrYGR+r++gla+++++Pa+m+ +def+a Gtqlk+erPgKa++v+pvd+iegPtv lknGd+v +d 
  gi|474934011|ref|YP_007687593.1| 319 HPCRMGGFRLRYGRARTSGLASLAYNPASMYAMDEFMALGTQLKIERPGKACVVTPVDTIEGPTVLLKNGDLVYCDR 395
                                       ***************************************************************************** PP

                          PolC_DP2 382 veealeikkeveeildlGeiLvayGeflennhpLvpasyveewwiqelekaaakkeaee..kpsaeealelseeldv 456
                                       +e++l++k++v+e++d GeiLv +Gef+ennh Lvp++y++ew+++e+++a+  +  ++  +p +eea++++++l+v
  gi|474934011|ref|YP_007687593.1| 396 KEDYLAVKEQVAEVVDNGEILVPFGEFCENNHVLVPCGYCTEWHEEEIKAANGGTLPDNwrDPIYEEAVAMCKSLGV 472
                                       *************************************************99887766555699************** PP

                          PolC_DP2 457 pLhPkytylwhdisveelekLaeavaekkkleeeklvleleeevkeiLekllvehkvkeekivi..eealallkslg 531
                                       pLhPk+++ w+d++  +l +L++++ ek++++e++l++++++e+k+iLe+ll  h +++++++i  + +l++l++lg
  gi|474934011|ref|YP_007687593.1| 473 PLHPKFNLNWSDVKLPRLVQLRDFILEKGHISEGNLCMPRDPEIKAILEDLLALHVCRGGSVIIdtKYSLPMLDCLG 549
                                       *****************************9**********************************66667789***** PP

                          PolC_DP2 532 ldleeekleke...eekdalelvnelsglevrekaptrigaRmGRPeKskeRkmkpavhvLfpigeaggkrrsvkea 605
                                       l+++  +++k+   + +++l++v++++g++vr++++tr+g+RmGRPeK+keR   p+v++Lfp+++a ++ r+  +a
  gi|474934011|ref|YP_007687593.1| 550 LSWDGGAMSKRtelTGEESLDAVSAAAGFTVRARSMTRVGTRMGRPEKAKERAGAPMVQSLFPLNDATHTVRDTVSA 626
                                       ****99987775555559*********************************************************** PP

                          PolC_DP2 606 akk...........kgei.eveiarrkCkkCgketlearCeeCgekteeklvCkkceeeveeekcekcekeakavkk 670
                                       +k+           +++i + e+++rkC+ Cgk t  + C++Cge+t +                   +k++  v+ 
  gi|474934011|ref|YP_007687593.1| 627 IKAlgeeptmlnqgRNHIlKPEMSARKCPMCGKITPLVYCHDCGEHTAP------------------FGKTEGGVSP 685
                                       **77899*****995555699***************************9..................56677899** PP

                          PolC_DP2 671 kkidlkellekaleklgereekleelkgvkgltskekipEpleKgilRakhdvsvfkdgtvRyDmtdlplthfrpke 747
                                       +++d+++++++a++ l+e   ++e+lk++++l s++k+pE+leKgilR++hd+s+f+dgtvRyDmtd+plthf+++e
  gi|474934011|ref|YP_007687593.1| 686 IDVDIEKEYNEAMAILHE-PPTKETLKCMDKLKSRTKTPEMLEKGILRRNHDISIFRDGTVRYDMTDIPLTHFKCRE 761
                                       ******************.6799****************************************************** PP

                          PolC_DP2 748 igvsveklrelGYteDieGkplesedqivelkvqDivlsedaaeyllkvakfvDdlLeklyglerfYnvekkedLiG 824
                                       ig+svek ++lGYt+D++Gk+l+++dqivelk+qDi+ s+d+++y+++va fvDd+L+++ygl+rfYn++ +edLiG
  gi|474934011|ref|YP_007687593.1| 762 IGLSVEKAKSLGYTHDWDGKDLTDPDQIVELKCQDIIPSRDCGDYMVRVAGFVDDELQRIYGLPRFYNAKIREDLIG 838
                                       ***************************************************************************** PP

                          PolC_DP2 825 klviglaPHtsagvlgRiiGftkasvgyahPyfHaakRRn 864
                                       ++ +glaPHts+++l+RiiG+++++++y+hP++Ha+kRRn
  gi|474934011|ref|YP_007687593.1| 839 SIAFGLAPHTSGCILCRIIGYSNVRGCYGHPFYHASKRRN 878
                                       ***************************************9 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.0074
                          PolC_DP2  616 iarrkCkkCgke....tlearCeeCgekteeklvCkkcee..eveeekcekcekeakavkkkkid 674 
                                         ++ +C+kCg++     l+  C++Cg++ + +++  ++++  ev+++ cek +      +k++i+
  gi|474934011|ref|YP_007687593.1| 1042 TQTVRCTKCGEKyrrvPLKGVCTKCGHSLNLTVHEASVRKylEVSKNVCEKYDLGYY--TKERIE 1104
                                        456678888765221135567888888877777766666633444555666544333..333333 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.6    0.0022       7.8      11      38 ..     650     673 ..     642     679 .. 0.74
   2 !   11.4   0.8     7e-05      0.25      14      40 ..    1046    1072 ..    1039    1076 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0022
                               DZR  11 darfCseCgtklkavaaedrCpsCgekv 38 
                                       +ar C+ Cg+  +       C  Cge +
  gi|474934011|ref|YP_007687593.1| 650 SARKCPMCGKITP----LVYCHDCGEHT 673
                                       5777888887776....68888888764 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 7e-05
                               DZR   14 fCseCgtklkavaaedrCpsCgekvdp 40  
                                         C +Cg+k ++v+ + +C +Cg+++++
  gi|474934011|ref|YP_007687593.1| 1046 RCTKCGEKYRRVPLKGVCTKCGHSLNL 1072
                                        5*********9999********99765 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.022        77      69      96 ..     650     673 ..     569     682 .. 0.73
   2 ?    9.0   0.3   0.00039       1.4      69      95 ..    1043    1069 ..    1033    1084 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.022
                                       -EEEETTTS-EEECHHHHHS-TTTSSS- CS
                              HypA  69 vkvrCreCgkefeleekalrCpkCgsad 96 
                                          +C  Cgk + l      C +Cg++ 
  gi|474934011|ref|YP_007687593.1| 650 SARKCPMCGKITPLV----YCHDCGEHT 673
                                       344799999887765....599999876 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00039
                                        -EEEETTTS-EEECHHHHHS-TTTSSS CS
                              HypA   69 vkvrCreCgkefeleekalrCpkCgsa 95  
                                         +vrC++Cg++++    +  C kCg++
  gi|474934011|ref|YP_007687593.1| 1043 QTVRCTKCGEKYRRVPLKGVCTKCGHS 1069
                                        5799*****99996654578****986 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.3     0.019        67      12      38 ..     647     672 ..     638     677 .. 0.76
   2 ?    9.3   0.1   0.00031       1.1      14      41 ..    1042    1072 ..    1026    1083 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.019
                                       E-SSEEE-TTT--EEEEEEE-SSS-S- CS
                    zinc-ribbons_6  12 krgeqyhCeaCqedlkkealCpeCeqe 38 
                                        + +  +C  C + ++   +C +C+++
  gi|474934011|ref|YP_007687593.1| 647 PEMSARKCPMCGK-ITPLVYCHDCGEH 672
                                       4556778999986.5677899999985 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00031
                                        SSEEE-TTT--EEEE...EEE-SSS-S---E CS
                    zinc-ribbons_6   14 geqyhCeaCqedlkk...ealCpeCeqelev 41  
                                        +++++C +C e++++   + +C +C+++l+ 
  gi|474934011|ref|YP_007687593.1| 1042 TQTVRCTKCGEKYRRvplKGVCTKCGHSLNL 1072
                                        57899*****97776111567****999875 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.4    0.0099        35      23      55 ..     646     672 ..     641     674 .. 0.83
   2 ?    7.7   1.3   0.00092       3.3      30      57 ..    1046    1071 ..    1040    1074 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0099
                    OrfB_Zn_ribbon  23 npayTSktCseCgsknkealsgrtfkCpnCgfe 55 
                                       +p+ +  +C+ Cg++         ++C +Cg +
  gi|474934011|ref|YP_007687593.1| 646 KPEMSARKCPMCGKITPL------VYCHDCGEH 672
                                       6888999******99877......888888875 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00092
                    OrfB_Zn_ribbon   30 tCseCgsknkealsgrtfkCpnCgfead 57  
                                        +C +Cg+k ++   + + +C++Cg++++
  gi|474934011|ref|YP_007687593.1| 1046 RCTKCGEKYRR--VPLKGVCTKCGHSLN 1071
                                        7*********9..9999*******9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.82u 0.32s 00:00:01.13 Elapsed: 00:00:00.48
# Mc/sec: 7050.03
//
Query:       gi|474934012|ref|YP_007687594.1|  [L=335]
Description: small GTP-binding protein domain protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.7e-33  115.2   0.2    4.8e-33  114.4   0.0    1.5  2  NOG1_N       NOG1 N-terminal helical domain
    3.7e-22   77.9   0.3    8.7e-22   76.7   0.0    1.8  2  NOG1         Nucleolar GTP-binding protein 1 (NOG1)
    3.3e-18   65.8   0.0    7.4e-18   64.7   0.0    1.7  1  MMR_HSR1     50S ribosome-binding GTPase
    8.7e-08   31.8   0.0    1.4e-07   31.2   0.0    1.4  1  FeoB_N       Ferrous iron transport protein B
  ------ inclusion threshold ------
      0.011   15.3   0.0      0.054   13.1   0.0    2.0  1  Ras          Ras family
       0.19   11.6   0.6        1.8    8.4   0.0    2.8  3  RsgA_GTPase  RsgA GTPase


Domain annotation for each model (and alignments):
>> NOG1_N  NOG1 N-terminal helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.4   0.0   1.6e-36   4.8e-33       3     160 .]       7     161 ..       6     161 .. 0.97
   2 ?   -3.8   0.0       3.6   1.1e+04     121     135 ..     307     321 ..     291     326 .. 0.49

  Alignments for each domain:
  == domain 1  score: 114.4 bits;  conditional E-value: 1.6e-36
                            NOG1_N   3 kiptvptseelidkalrrakraakttkkkkneikrlrnlearkvrtasntlsdkLeeivkkfPnldelhpFyrelld 79 
                                       +iptv+++eel+dka+rra++++kt +++   +   ++ + +++++  +++++ L  +++kfP++++ + F+ +l+d
  gi|474934012|ref|YP_007687594.1|   7 QIPTVLSAEELMDKAFRRANKISKTGSDA-LDT--KKKTTLARITASGDIVETTLVGYIQKFPRMEKNDDFFPQLVD 80 
                                       79***********************9887.444..46789999********************************** PP

                            NOG1_N  80 vlvdkdelkksLaqvkwarklirkigkeyvnklkkaddkkeakelrreafgrvasvlkkvdkaldfLedvrkkLrkL 156
                                       +++++d++kksL++++wa+  ++ +++  ++++++ +d++++ ++r++++gr+ s l++++k+l fL+d+++k r+L
  gi|474934012|ref|YP_007687594.1|  81 LVIGIDQYKKSLGALNWAAGQVERLRNGALREVRRYKDPARIDAVRKSFYGRLGSYLNQISKDLLFLQDAKNKFREL 157
                                       ***************************************************************************** PP

                            NOG1_N 157 paiD 160
                                       p+iD
  gi|474934012|ref|YP_007687594.1| 158 PSID 161
                                       ***9 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 3.6
                            NOG1_N 121 akelrreafgrvasv 135
                                       ++el+ e ++ + ++
  gi|474934012|ref|YP_007687594.1| 307 MAELKEELVKMLREI 321
                                       333333333333333 PP

>> NOG1  Nucleolar GTP-binding protein 1 (NOG1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.7   0.0   2.9e-25   8.7e-22       1      58 []     231     288 ..     231     288 .. 0.99
   2 ?   -3.8   0.1       3.8   1.1e+04      36      48 ..     313     325 ..     312     327 .. 0.77

  Alignments for each domain:
  == domain 1  score: 76.7 bits;  conditional E-value: 2.9e-25
                              NOG1   1 eIEkqAiaALkhladavlFllDpseecgysleeQlsLleeikelfankpvivvlnKiD 58 
                                       +IEkqA++AL++l d+++F+lDpse+cgy++ +Q +Lle+i+++f+++p++vv +K+D
  gi|474934012|ref|YP_007687594.1| 231 DIEKQAVLALRYLTDVMVFILDPSETCGYDMGKQTRLLENIRSNFEDVPILVVESKCD 288
                                       6********************************************************9 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 3.8
                              NOG1  36 sLleeikelfank 48 
                                       +L++ ++e f++k
  gi|474934012|ref|YP_007687594.1| 313 ELVKMLREIFRQK 325
                                       6888999999865 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.7   0.0   2.5e-21   7.4e-18       2     111 ..     167     283 ..     166     320 .. 0.79

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 2.5e-21
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETT.EEEEEEECGGCSSHHHHHH..HHHHHHHHHHC CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkg.keielvDtpGliegaseek..glgkaflalee 75 
                                       ++i+G pNvGKS+L+  ++ ++ +v+ +p+tT+ i+ g+++  + +++++vDtpGl++++ e++   +++a+lal+ 
  gi|474934012|ref|YP_007687594.1| 167 AVIAGFPNVGKSSLVTYISSAAPEVAPYPFTTKGITIGHIAD-DwRKFQIVDTPGLLDRDFEDRndIEKQAVLALRY 242
                                       689*************************************94.459*********9973333444567788888777 PP

                                       .TSEEEEEEETT....TTCSHHHHHHHHHHHHH.TTSEEEEE CS
                          MMR_HSR1  76 .adlillvvdas....eeklkpldeeleellee.akkplilv 111
                                        +d++++++d s      ++ ++ + le+++++ ++ p+++v
  gi|474934012|ref|YP_007687594.1| 243 lTDVMVFILDPSetcgY-DMGKQTRLLENIRSNfEDVPILVV 283
                                       78********7754431.233343444444333455565555 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   4.6e-11   1.4e-07       3      88 ..     167     253 ..     165     296 .. 0.83

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 4.6e-11
                                       EEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHH..CT CS
                            FeoB_N   3 valvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardfll..ee 77 
                                        +++G pnvGk++l+  ++ a  +v+ +p +t   + g++  + ++++ivD PG  + + +   + + ++ +l  + 
  gi|474934012|ref|YP_007687594.1| 167 AVIAGFPNVGKSSLVTYISSAAPEVAPYPFTTKGITIGHIADDWRKFQIVDTPGLLDRD-FEDRNDIEKQAVLalRY 242
                                       6799*************************************888**********97743.33334444444441234 PP

                                       SSSEEEEEEEG CS
                            FeoB_N  78 epdvvvnvvda 88 
                                        +dv+v ++d 
  gi|474934012|ref|YP_007687594.1| 243 LTDVMVFILDP 253
                                       46777777775 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.8e-05     0.054       3     133 ..     168     310 ..     166     319 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.8e-05
                                       EEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETT...........SGGGHHHHHHH CS
                               Ras   3 vlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAG...........qeefkslrely 68 
                                       v+ G  +vGK+sl++ ++++  +e         + ++  ++ +   k++i DT G            e+   l+  y
  gi|474934012|ref|YP_007687594.1| 168 VIAGFPNVGKSSLVT-YISSAAPEVAPYPF-TTKGITIGHIADDWRKFQIVDTPGlldrdfedrndIEKQAVLALRY 242
                                       788899999999975.77777777655444.3455555566688899999999995533322111113333344445 PP

                                       HTTESEEEEEEETTBHHHHHTHHHHHHHHHHHSTTTSEEEEEEETTTGGG....G-SS-HHHHHHHHHH CS
                               Ras  69 yrdaegillvyditsresfenvkkwveeikrvaeenvpivLvGnKvDlee....kravsteegeelake 133
                                       ++d+++++l  + t      + ++++e+i++  e +vpi++v  K+D+ +    +r +s  +ge +a+ 
  gi|474934012|ref|YP_007687594.1| 243 LTDVMVFILDPSETCGYDMGKQTRLLENIRSNFE-DVPILVVESKCDVMRtegeTRRISSVSGEGMAEL 310
                                       5555555554444444444455689999999999.6************988888999999999999874 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       1.7   5.2e+03     124     158 ..      22      56 ..      15      56 .. 0.73
   2 ?    8.4   0.0    0.0006       1.8      71     122 ..     136     187 ..     120     227 .. 0.70
   3 ?   -1.2   0.0      0.56   1.7e+03      45      68 ..     276     299 ..     261     319 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.7
                                       ----S--------------SEEEEEETTTEEEESS CS
                       RsgA_GTPase 124 elktgevseklgrGkhTTtavellelaegglliDt 158
                                         + +++s++ +    T ++++l ++ ++g ++ t
  gi|474934012|ref|YP_007687594.1|  22 FRRANKISKTGSDALDTKKKTTLARITASGDIVET 56 
                                       55677788888888888888888888888888766 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0006
                                       HHHHTTSEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  71 elealgyevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                        l+++  ++l+++   k++++el +   +  t+v++G   vGKS+L+  + + 
  gi|474934012|ref|YP_007687594.1| 136 YLNQISKDLLFLQDA-KNKFRELPSIDPKvPTAVIAGFPNVGKSSLVTYISSA 187
                                       566677777777544.66677776665555899**************999876 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.56
                                       TT-EEEEEEE-GGG--HHHHHHHH CS
                       RsgA_GTPase  45 kgiepvivlnKiDlleeeeeleel 68 
                                       +++++++v +K+D++ +e e++++
  gi|474934012|ref|YP_007687594.1| 276 EDVPILVVESKCDVMRTEGETRRI 299
                                       567777777888888777644333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.52
# Mc/sec: 1941.84
//
Query:       gi|474934013|ref|YP_007687595.1|  [L=1316]
Description: hypothetical protein TALC_00432 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-11   43.7   0.0    6.6e-11   42.6   0.0    1.5  1  LTD       Lamin Tail Domain


Domain annotation for each model (and alignments):
>> LTD  Lamin Tail Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.0   3.7e-15   6.6e-11       5     108 ..     975    1064 ..     972    1068 .. 0.87

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 3.7e-15
                               LTD    5 agdvvIsevmedgagnnan.efvelyNtsskavdLsgwkledasgeytfpngtgtlaageyvvvwsgsgttsasn 78  
                                        ++ v I+e+ +++ g++ + e+ e+ N s+++v+L+gw+l+++sg+ ++ +++ +la+ge  vv  ++       
  gi|474934013|ref|YP_007687595.1|  975 KSGVLINEFEPNPEGDDRDnEWAEIINLSGSPVNLEGWTLTNSSGGKKVLDAV-SLAPGERTVVEFSG------- 1041
                                        678**********999988*************************887777776.9*********9984....... PP

                               LTD   79 gskasssavwnnggdavaLydasgevvdsv 108 
                                                 ++n++++++L+da+g v d+ 
  gi|474934013|ref|YP_007687595.1| 1042 -------IFLKNSKERLQLKDAEGAVRDTT 1064
                                        .......45788899999999999998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.78u 0.29s 00:00:01.07 Elapsed: 00:00:00.49
# Mc/sec: 8145.49
//
Query:       gi|474934014|ref|YP_007687596.1|  [L=568]
Description: putative Fe-S oxidoreductase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.3e-17   63.0   0.4    1.4e-16   61.4   0.1    2.0  2  Radical_SAM  Radical SAM superfamily
      2e-09   37.8   0.1    3.9e-09   36.9   0.1    1.5  1  Fer4_12      4Fe-4S single cluster domain
    7.1e-08   32.6   0.7    1.6e-07   31.5   0.1    1.9  2  Fer4_14      4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.012   15.6   0.3      0.029   14.3   0.3    1.6  1  SPOUT_MTase  Predicted SPOUT methyltransferase
      0.019   15.1   0.2      0.073   13.2   0.1    2.0  2  DUF1244      Protein of unknown function (DUF1244)
       0.16   12.2   1.0          5    7.3   0.3    2.5  2  ANAPC9       Anaphase-promoting complex subunit 9
       0.48   10.6   2.9        4.7    7.4   0.0    3.1  3  ExbD         Biopolymer transport protein ExbD/TolR


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.4   0.1   5.3e-20   1.4e-16       3     166 ..     111     278 ..     109     279 .. 0.88
   2 ?   -1.6   0.0       1.2     3e+03      13      67 ..     492     558 ..     484     566 .. 0.50

  Alignments for each domain:
  == domain 1  score: 61.4 bits;  conditional E-value: 5.3e-20
                                       EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHH.HHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelk.aekg.vkevilgggepllypdfvellerlaklavpg 77 
                                        t+ Cn++C+ C  +    + g++++ + e i + ++ l+ +++  +  v ++ggep++yp ++e +++++++  + 
  gi|474934014|ref|YP_007687596.1| 111 LTNRCNMQCPICFASAN--QAGYVYEPDFETICKMLDTLRnEKPIpCTAVQFSGGEPTVYPQLIEVIRAAKER--KF 183
                                       589************96..*********************877779***************************..7* PP

                                       EEEEEEECSSCHG..HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET......EE CS
                                       xxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xx RF
                       Radical_SAM  78 iritvetngtlpd..eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikr......vv 146
                                         + + tng++     +kl++ +e+g+++++l  + +dd+ +  + ++++ ++  ++++ ++ ++  ++      +v
  gi|474934014|ref|YP_007687596.1| 184 AQVQIATNGIVFAkhYDKLKECAEAGLNTIYLQFDGLDDK-IMMRSRGRPMVKVKMDVINNCLKL-KEEtghspsIV 258
                                       ************99999999999999**************.777776666666666666655555.333344489** PP

                                       EEEEEBTTTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 147 drivglpGendeeleellel 166
                                        +++ ++G nd+ + ++l++
  gi|474934014|ref|YP_007687596.1| 259 LVVTTVRGMNDQAIGDILKF 278
                                       **************999998 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.2
                                       TTSCCTT...........HHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHH CS
                                       xxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  13 fCarpet...........vrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvell 67 
                                       fCa ++            + + + ++ + +ee ++++++l + k+     + + ge l   +++e+l
  gi|474934014|ref|YP_007687596.1| 492 FCAYNSGiemrvetekkfSMPIEEWKQKHKEEAKQLAQALIVPKDvPVMQVDSKGETLSSEEMAEDL 558
                                       6666666666333333333333444444444444544444444432222233355555555555555 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.1   1.5e-12   3.9e-09      12     102 ..     112     201 ..      93     219 .. 0.88

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 1.5e-12
                           Fer4_12  12 vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesi...egltllGGEPllpenaeallelvkevkeekpe 85 
                                       +++Cn++C+ Cf  ++ +  +  e ++e++ ++++ l +e+    + + ++GGEP +   +++l+e+++  ke+k+ 
  gi|474934014|ref|YP_007687596.1| 112 TNRCNMQCPICF-ASANQAGYVYEPDFETICKMLDTLRNEKPipcTAVQFSGGEPTV---YPQLIEVIRAAKERKFA 184
                                       679*********.6777788888889***********998877889***********...****************9 PP

                           Fer4_12  86 kdiwlytgytleelskk 102
                                       ++ ++++g  + ++ +k
  gi|474934014|ref|YP_007687596.1| 185 QVQIATNGIVFAKHYDK 201
                                       9**********998754 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.1   6.1e-11   1.6e-07       5     107 ..     112     208 ..     110     219 .. 0.80
   2 ?   -3.5   0.1       4.3   1.1e+04      87      95 ..     505     513 ..     477     532 .. 0.49

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 6.1e-11
                           Fer4_14   5 lsgCnlsCkgCdnketwkselgkpqteelleqilk.dlkkseikiqglvltGGePLhyenkkellklvkrlkeeype 80 
                                       +++Cn++C+ C+ +++++  + +p+ e +  ++l+   +++ i    + ++GGeP  y   ++l+++++  ke++  
  gi|474934014|ref|YP_007687596.1| 112 TNRCNMQCPICFASANQAGYVYEPDFETIC-KMLDtLRNEKPIPCTAVQFSGGEPTVY---PQLIEVIRAAKERK-F 183
                                       69**********999888777777776666.6666356677788899*********99...9********99998.7 PP

                           Fer4_14  81 kkiwletngtleielektpdlkeklea 107
                                        ++++ tng +  +  ++++lke+ ea
  gi|474934014|ref|YP_007687596.1| 184 AQVQIATNGIVFAK--HYDKLKECAEA 208
                                       99*******99855..45778877664 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.3
                           Fer4_14  87 tngtleiel 95 
                                       t  ++ + +
  gi|474934014|ref|YP_007687596.1| 505 TEKKFSMPI 513
                                       222222222 PP

>> SPOUT_MTase  Predicted SPOUT methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.3   1.1e-05     0.029      45      95 ..     513     565 ..     488     568 .] 0.69

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.1e-05
                                       -S-HHHHHHHHHHT--......TT-EEEEE-TTSEE--HHHHHHHHHHHHHHT CS
                       SPOUT_MTase  45 ekeeekakekegerilkk..lkkkayvillderGkelsSeelakkleklaeeg 95 
                                        +e +++ ++e++++ ++  ++k+  v+ +d +G++lsSee+a+ l+ +a + 
  gi|474934014|ref|YP_007687596.1| 513 IEEWKQKHKEEAKQLAQAliVPKDVPVMQVDSKGETLSSEEMAEDLDATAAAE 565
                                       34445666666666764411457778999*****************9876654 PP

>> DUF1244  Protein of unknown function (DUF1244)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       3.4   8.8e+03      24      51 ..     177     204 ..     174     206 .. 0.79
   2 ?   13.2   0.1   2.8e-05     0.073      27      59 ..     496     526 ..     488     531 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.4
                                       HHHHCT----HHHHHHHHHSS-HHHHCH CS
                           DUF1244  24 aaeergvelskdearelvYgmpyeeWka 51 
                                       aa+er ++  + ++  +v++  y++ k+
  gi|474934014|ref|YP_007687596.1| 177 AAKERKFAQVQIATNGIVFAKHYDKLKE 204
                                       7888888888888888999999988775 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 2.8e-05
                                       HCT----HHHHHHHHHSS-HHHHCHCH-----H CS
                           DUF1244  27 ergvelskdearelvYgmpyeeWkakhqkeAtp 59 
                                       ++g+e++ ++ +   + mp+eeWk+kh++eA +
  gi|474934014|ref|YP_007687596.1| 496 NSGIEMRVETEK--KFSMPIEEWKQKHKEEAKQ 526
                                       566667666544..589*************965 PP

>> ANAPC9  Anaphase-promoting complex subunit 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.054   1.4e+02      42      77 ..      37      71 ..      13      73 .. 0.82
   2 ?    7.3   0.3     0.002         5      49      97 ..     495     563 ..     463     568 .] 0.78

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.054
                            ANAPC9 42 DysvftnkktedeesllpaikeSqikawesaEriaq 77
                                      D +vf++k+ + e+  +  i  S  k +++aE+ a+
  gi|474934014|ref|YP_007687596.1| 37 DGKVFMDKECP-EHGKFSDIYWSDAKKYLQAEKYAK 71
                                      889*******7.89999***************9875 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.002
                            ANAPC9  49 kkte......deesllpaikeSqikawesaEriaqnliFdkd.............dsdkevde.dedee 97 
                                       ++ +       e++   +i e + k  e+a + aq li  kd             +s++++++ d+   
  gi|474934014|ref|YP_007687596.1| 495 YNSGiemrveTEKKFSMPIEEWKQKHKEEAKQLAQALIVPKDvpvmqvdskgetlSSEEMAEDlDATAA 563
                                       4444444443899999**************************999999888877777777777555444 PP

>> ExbD  Biopolymer transport protein ExbD/TolR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0018       4.7      83     127 ..     145     190 ..       2     192 .. 0.86
   2 ?   -3.0   0.0       2.9   7.4e+03      58      92 ..     367     401 ..     365     412 .. 0.71
   3 ?    1.5   1.1      0.12   3.1e+02      30      90 ..     501     566 ..     499     568 .] 0.71

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0018
                              ExbD  83 kerkakppdk.ltvaikadkdvsygklvevldtlkkagiekvslvt 127
                                       + +++++p +   v +++ + + y +l+ev+ ++k++++ +v+++t
  gi|474934014|ref|YP_007687596.1| 145 DTLRNEKPIPcTAVQFSGGEPTVYPQLIEVIRAAKERKFAQVQIAT 190
                                       44444444446678889999999*********************98 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.9
                              ExbD  58 isisadgsiyldkkavsveelaqklkerkakppdk 92 
                                       + i++++++y   + ++v+++ + l+e++ak +++
  gi|474934014|ref|YP_007687596.1| 367 LFIDENDNVYPMPEFIDVDKFVAGLEEIAAKAEKA 401
                                       56777777776666668888888888887776665 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.12
                              ExbD  30 lkkpeplevdlPsssstqk.eveekelirisisadgsiyldkka....vsveelaqklkerkakpp 90 
                                       ++++++ ++++P  + +qk + e+k+l +  i  ++   ++ ++    +s ee+a+ l++ +a ++
  gi|474934014|ref|YP_007687596.1| 501 MRVETEKKFSMPIEEWKQKhKEEAKQLAQALIVPKDVPVMQVDSkgetLSSEEMAEDLDATAAAEK 566
                                       778888899999999888877888888888888776644333332243799999999998887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (568 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      572  (0.0319036); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 3571.98
//
Query:       gi|474934015|ref|YP_007687597.1|  [L=65]
Description: 4Fe-4S binding domain protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.7e-16   56.8   7.9    1.6e-07   30.8   1.6    2.1  2  Fer4         4Fe-4S binding domain
    2.7e-12   47.1  34.2      2e-06   28.3  14.0    2.0  3  Fer4_7       4Fe-4S dicluster domain
    2.9e-10   39.8  11.3    3.3e-05   23.8   2.3    2.1  2  Fer4_6       4Fe-4S binding domain
    2.3e-09   36.8  10.5    0.00013   21.9   1.4    2.1  2  Fer4_2       4Fe-4S binding domain
    5.8e-09   36.0   9.1    7.2e-05   22.9   0.9    2.0  2  Fer4_9       4Fe-4S dicluster domain
      6e-09   35.7  15.7    0.00024   21.3   3.8    2.1  2  Fer4_4       4Fe-4S binding domain
    9.7e-09   35.2  13.0    8.3e-05   22.6   2.1    2.0  2  Fer4_10      4Fe-4S dicluster domain
    1.7e-08   34.5   8.6    2.8e-08   33.8   8.6    1.4  1  Fer4_21      4Fe-4S dicluster domain
    4.1e-08   34.0   8.5    0.00033   21.5   2.1    2.1  2  Fer4_16      4Fe-4S double cluster binding domain
    4.6e-06   27.1   8.6     0.0044   17.5   1.1    2.1  2  Fer4_17      4Fe-4S dicluster domain
    0.00024   21.8  20.3      0.052   14.5   5.5    2.2  2  Fer4_3       4Fe-4S binding domain
    0.00026   21.4  14.7      0.033   14.6   3.7    2.1  2  Fer4_8       4Fe-4S dicluster domain
     0.0018   18.8   9.7      0.079   13.5   0.9    2.2  2  Fer4_13      4Fe-4S single cluster domain of Ferredoxin I
     0.0028   17.7   3.4       0.18   11.9   0.1    2.1  2  Fer4_19      Divergent 4Fe-4S mono-cluster
     0.0068   16.2   4.9     0.0097   15.7   4.9    1.3  1  GF_recep_IV  Growth factor receptor domain IV
  ------ inclusion threshold ------
      0.024   14.8  10.7       0.26   11.5   1.9    2.0  2  Fer4_18      4Fe-4S dicluster domain
       0.38   11.5   9.8        3.1    8.6   2.2    2.5  2  Fer4_15      4Fe-4S single cluster domain
        2.2    9.2  14.1        5.6    7.9   3.6    2.1  3  Fer4_22      4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   1.6   1.6e-10   1.6e-07       2      23 ..      10      31 ..       9      32 .. 0.94
   2 !   30.1   0.5   2.7e-10   2.7e-07       5      23 ..      41      59 ..      38      60 .. 0.93

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 1.6e-10
                                      EEETTTSSS-THHHHHSTTTEE CS
                              Fer4  2 videekCigCGaCvevCPvgAI 23
                                      ++d++kC +CG Cv  CP +AI
  gi|474934015|ref|YP_007687597.1| 10 IVDQNKCLHCGGCVGSCPQNAI 31
                                      79*******************9 PP

  == domain 2  score: 30.1 bits;  conditional E-value: 2.7e-10
                                      TTTSSS-THHHHHSTTTEE CS
                              Fer4  5 eekCigCGaCvevCPvgAI 23
                                       +kC +C++Cv+ CPvgA+
  gi|474934015|ref|YP_007687597.1| 41 SDKCNRCKRCVNLCPVGAL 59
                                      59****************8 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   2.6   1.2e-06    0.0011      30      52 .]       8      30 ..       2      30 .. 0.84
   2 !   28.3  14.0     2e-09     2e-06       1      52 []      15      58 ..      15      58 .. 0.93
   3 !   21.3   2.2   3.1e-07   0.00031       1      22 [.      43      64 ..      43      65 .] 0.90

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.2e-06
                            Fer4_7 30 kveidpekClgCgaCvavCPtga 52
                                      ++ +d++kCl+Cg Cv  CP +a
  gi|474934015|ref|YP_007687597.1|  8 DMIVDQNKCLHCGGCVGSCPQNA 30
                                      5668999*************987 PP

  == domain 2  score: 28.3 bits;  conditional E-value: 2e-09
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      +C +Cg Cv  Cp++ai l+++        +   ++kC  C++Cv+ CP+ga
  gi|474934015|ref|YP_007687597.1| 15 KCLHCGGCVGSCPQNAIFLHDF--------YLTFSDKCNRCKRCVNLCPVGA 58
                                      7******************998........56668***************98 PP

  == domain 3  score: 21.3 bits;  conditional E-value: 3.1e-07
                            Fer4_7  1 rCigCgaCvaaCpvkaieldee 22
                                      +C  C++Cv+ Cpv+a++l+e+
  gi|474934015|ref|YP_007687597.1| 43 KCNRCKRCVNLCPVGALSLEEK 64
                                      7***************999876 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   2.3   3.3e-08   3.3e-05       4      24 .]      11      31 ..       9      31 .. 0.95
   2 !   21.5   1.9   1.8e-07   0.00018       6      24 .]      41      59 ..      40      59 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 3.3e-08
                            Fer4_6  4 idpdkCigCgdCvrvCPegai 24
                                      +d++kC++Cg Cv  CP +ai
  gi|474934015|ref|YP_007687597.1| 11 VDQNKCLHCGGCVGSCPQNAI 31
                                      8****************9998 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 1.8e-07
                            Fer4_6  6 pdkCigCgdCvrvCPegai 24
                                       dkC+ C +Cv+ CP ga+
  gi|474934015|ref|YP_007687597.1| 41 SDKCNRCKRCVNLCPVGAL 59
                                      59***************97 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   1.4   1.3e-07   0.00013       4      22 .]      10      28 ..       7      28 .. 0.92
   2 !   20.1   2.2   4.7e-07   0.00047       7      21 ..      41      55 ..      37      56 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.3e-07
                            Fer4_2  4 vvdtdrCigCgaCvsaCPa 22
                                       vd ++C++Cg Cv +CP+
  gi|474934015|ref|YP_007687597.1| 10 IVDQNKCLHCGGCVGSCPQ 28
                                      69****************6 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 4.7e-07
                            Fer4_2  7 tdrCigCgaCvsaCP 21
                                      +d+C++C+ Cv+ CP
  gi|474934015|ref|YP_007687597.1| 41 SDKCNRCKRCVNLCP 55
                                      69************* PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.9   7.2e-08   7.2e-05      32      51 .]      12      31 ..       1      31 [. 0.74
   2 !   18.0   1.7   2.3e-06    0.0023       1      20 [.      43      62 ..      41      65 .] 0.82

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 7.2e-08
                            Fer4_9 32 seeaCigCgaCveaCpkgai 51
                                      ++++C++Cg Cv  Cp++ai
  gi|474934015|ref|YP_007687597.1| 12 DQNKCLHCGGCVGSCPQNAI 31
                                      2258*************997 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 2.3e-06
                            Fer4_9  1 kCtgCgaCveaCpagvvved 20
                                      kC++C++Cv+ Cp g+ + +
  gi|474934015|ref|YP_007687597.1| 43 KCNRCKRCVNLCPVGALSLE 62
                                      79999999999999887665 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   3.8   2.5e-07   0.00024       1      17 []      13      29 ..      13      29 .. 0.94
   2 !   20.4   4.1   5.1e-07    0.0005       1      17 []      41      57 ..      41      57 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.5e-07
                            Fer4_4  1 qerCigCgsCvaaCPqg 17
                                      q++C++Cg Cv +CPq+
  gi|474934015|ref|YP_007687597.1| 13 QNKCLHCGGCVGSCPQN 29
                                      79*************96 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 5.1e-07
                            Fer4_4  1 qerCigCgsCvaaCPqg 17
                                      +++C++C++Cv+ CP+g
  gi|474934015|ref|YP_007687597.1| 41 SDKCNRCKRCVNLCPVG 57
                                      69*************86 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   2.1   8.4e-08   8.3e-05       2      21 ..       9      28 ..       8      35 .. 0.90
   2 !   18.6   3.5   1.5e-06    0.0015       6      21 ..      41      56 ..      36      65 .] 0.84

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 8.4e-08
                           Fer4_10  2 vvidddtCirCgkCvkaCPa 21
                                      +++d+++C++Cg Cv +CP+
  gi|474934015|ref|YP_007687597.1|  9 MIVDQNKCLHCGGCVGSCPQ 28
                                      789****************9 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 1.5e-06
                           Fer4_10  6 ddtCirCgkCvkaCPa 21
                                      +d+C rC++Cv+ CP+
  gi|474934015|ref|YP_007687597.1| 41 SDKCNRCKRCVNLCPV 56
                                      589************9 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   8.6   2.8e-11   2.8e-08       2      57 ..      10      59 ..       9      61 .. 0.85

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 2.8e-11
                           Fer4_21  2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57
                                      ++d++kC++Cg C+ +C++   +ai ++    + + +d+C  C+ C++ CPv +++
  gi|474934015|ref|YP_007687597.1| 10 IVDQNKCLHCGGCVGSCPQ---NAIFLH--DFYLTFSDKCNRCKRCVNLCPV-GAL 59
                                      589***************5...888764..4556789**************9.665 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.5     1e-05      0.01       1      17 [.      15      31 ..      15      38 .. 0.90
   2 !   21.5   2.1   3.3e-07   0.00033       1      21 [.      43      63 ..      43      65 .] 0.89

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1e-05
                           Fer4_16  1 rCgtCgkCaevCPtnai 17
                                      +C  Cg C+ +CP+nai
  gi|474934015|ref|YP_007687597.1| 15 KCLHCGGCVGSCPQNAI 31
                                      59**************9 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 3.3e-07
                           Fer4_16  1 rCgtCgkCaevCPtnaikekk 21
                                      +C +C++C++ CP++a++ ++
  gi|474934015|ref|YP_007687597.1| 43 KCNRCKRCVNLCPVGALSLEE 63
                                      6****************9884 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   1.1   4.5e-06    0.0044      44      59 ..      14      29 ..       3      31 .. 0.86
   2 !   14.3   1.2   4.5e-05     0.045      45      58 ..      43      56 ..      38      65 .] 0.61

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.5e-06
                           Fer4_17 44 slCieCgeCerkCPqg 59
                                      ++C++Cg+C+ +CPq+
  gi|474934015|ref|YP_007687597.1| 14 NKCLHCGGCVGSCPQN 29
                                      7899999999999997 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 4.5e-05
                           Fer4_17 45 lCieCgeCerkCPq 58
                                      +C+ C++C+  CP 
  gi|474934015|ref|YP_007687597.1| 43 KCNRCKRCVNLCPV 56
                                      55555555555553 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   6.9   0.00011      0.11       1      15 []      16      30 ..      16      30 .. 0.97
   2 !   14.5   5.5   5.2e-05     0.052       1      15 []      44      58 ..      44      58 .. 0.97

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00011
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C++Cg Cv +CP +A
  gi|474934015|ref|YP_007687597.1| 16 CLHCGGCVGSCPQNA 30
                                      *************98 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 5.2e-05
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+ C +Cv+ CPvgA
  gi|474934015|ref|YP_007687597.1| 44 CNRCKRCVNLCPVGA 58
                                      999***********9 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   2.9   9.2e-05     0.091       3      63 ..      14      28 ..      12      42 .. 0.65
   2 !   14.6   3.7   3.3e-05     0.033       3      18 ..      42      57 ..      40      64 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.2e-05
                            Fer4_8  3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63
                                      +kC +Cg C  +Cp                                              +
  gi|474934015|ref|YP_007687597.1| 14 NKCLHCGGCVGSCP----------------------------------------------Q 28
                                      56666666666666..............................................3 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 3.3e-05
                            Fer4_8  3 ekCieCgaCqsaCpvl 18
                                      +kC++C +C + Cpv 
  gi|474934015|ref|YP_007687597.1| 42 DKCNRCKRCVNLCPVG 57
                                      4566666666666654 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.9   7.9e-05     0.079       1      18 [.      11      28 ..      11      32 .. 0.95
   2 !    9.9   2.2    0.0011       1.1       4      17 ..      42      55 ..      41      56 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.9e-05
                           Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                      VD+++C  cg Cv  +P+
  gi|474934015|ref|YP_007687597.1| 11 VDQNKCLHCGGCVGSCPQ 28
                                      9****************7 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0011
                           Fer4_13  4 dtCiacgaCvelaP 17
                                      d+C  c+ Cv+l+P
  gi|474934015|ref|YP_007687597.1| 42 DKCNRCKRCVNLCP 55
                                      89***********9 PP

>> Fer4_19  Divergent 4Fe-4S mono-cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.6    0.0064       6.3       4      26 ..       5      27 ..       3      35 .. 0.83
   2 !   11.9   0.1   0.00019      0.18      45      63 ..      45      63 ..      38      64 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0064
                           Fer4_19  4 eeitiednrelCihsgnCvkglp 26
                                        i+   +++ C h g Cv   p
  gi|474934015|ref|YP_007687597.1|  5 RGIDMIVDQNKCLHCGGCVGSCP 27
                                      67899999**********97554 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00019
                           Fer4_19 45 eeiievverCPSGALsyve 63
                                      ++ ++ v+ CP GALs+ e
  gi|474934015|ref|YP_007687597.1| 45 NRCKRCVNLCPVGALSLEE 63
                                      567899*********9876 PP

>> GF_recep_IV  Growth factor receptor domain IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   4.9   9.8e-06    0.0097      85     127 ..      20      62 ..       8      65 .] 0.83

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 9.8e-06
                       GF_recep_IV  85 seCvseCPegvkgekelifkyadaeevCekChenctegctgpe 127
                                         Cv +CP+++   +++   ++d+ + C++C + c  g+ + e
  gi|474934015|ref|YP_007687597.1|  20 GGCVGSCPQNAIFLHDFYLTFSDKCNRCKRCVNLCPVGALSLE 62 
                                       46*********9999999*****************88876655 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   1.6    0.0013       1.3      57      73 ..      12      28 ..       4      39 .. 0.79
   2 ?   11.5   1.9   0.00026      0.26      59      74 ..      42      57 ..      34      62 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0013
                           Fer4_18 57 gagdcidcescvkvcPt 73
                                      ++++c++c+ cv  cP 
  gi|474934015|ref|YP_007687597.1| 12 DQNKCLHCGGCVGSCPQ 28
                                      56788888888888886 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00026
                           Fer4_18 59 gdcidcescvkvcPtg 74
                                       +c  c+ cv++cP+g
  gi|474934015|ref|YP_007687597.1| 42 DKCNRCKRCVNLCPVG 57
                                      67************97 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   2.2    0.0031       3.1       3      20 ..      11      28 ..       9      35 .. 0.89
   2 ?    7.2   0.9    0.0087       8.7       6      19 ..      42      55 ..      41      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0031
                           Fer4_15  3 vDrdaCigcglCvaeape 20
                                      vD+++C  cg Cv  +p+
  gi|474934015|ref|YP_007687597.1| 11 VDQNKCLHCGGCVGSCPQ 28
                                      9*************9985 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0087
                           Fer4_15  6 daCigcglCvaeap 19
                                      d+C  c +Cv ++p
  gi|474934015|ref|YP_007687597.1| 42 DKCNRCKRCVNLCP 55
                                      89********9998 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   3.6    0.0056       5.6      79      94 ..      13      28 ..       5      31 .. 0.66
   2 ?    7.5   3.3    0.0074       7.3       1      14 [.      15      28 ..      15      39 .. 0.84
   3 ?    7.4   2.8    0.0078       7.8      80      94 ..      42      56 ..      30      58 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0056
                           Fer4_22 79 esgCvGCgRCieacpv 94
                                      +++C  Cg C+ +cp+
  gi|474934015|ref|YP_007687597.1| 13 QNKCLHCGGCVGSCPQ 28
                                      5566666666666665 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0074
                           Fer4_22  1 rClsCgaCtlvCpt 14
                                      +Cl+Cg C   Cp 
  gi|474934015|ref|YP_007687597.1| 15 KCLHCGGCVGSCPQ 28
                                      69999999999996 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0078
                           Fer4_22 80 sgCvGCgRCieacpv 94
                                       +C  C RC++ cpv
  gi|474934015|ref|YP_007687597.1| 42 DKCNRCKRCVNLCPV 56
                                      568888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      174  (0.00970495); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 445.43
//
Query:       gi|474934016|ref|YP_007687598.1|  [L=398]
Description: geranylgeranyl reductase family [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-17   63.0   0.0    4.4e-12   45.9   0.0    2.1  2  FAD_binding_3   FAD binding domain
    2.2e-08   33.6   0.8    1.8e-07   30.6   0.5    2.1  2  FAD_binding_2   FAD binding domain
    7.7e-07   28.8   1.8    2.8e-06   26.9   1.7    1.9  2  FAD_oxidored    FAD dependent oxidoreductase
    0.00014   21.2   0.0    0.00037   19.8   0.0    1.7  1  Thi4            Thi4 family
    0.00016   20.5   1.5     0.0003   19.6   0.6    1.8  2  HI0933_like     HI0933-like protein
    0.00022   20.5   0.1    0.00053   19.3   0.1    1.7  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    0.00069   18.6   0.2      0.045   12.6   0.0    2.8  2  Trp_halogenase  Tryptophan halogenase
     0.0013   18.9   0.1     0.0038   17.4   0.1    1.8  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
     0.0039   16.5   1.2      0.007   15.7   1.2    1.4  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
     0.0063   16.1   0.9        0.1   12.1   0.1    2.4  2  DAO             FAD dependent oxidoreductase
     0.0066   15.6   1.3     0.0091   15.1   1.3    1.4  1  GIDA            Glucose inhibited division protein A
     0.0076   15.3   0.1          1    8.3   0.7    2.4  2  Lycopene_cycl   Lycopene cyclase protein
  ------ inclusion threshold ------
      0.021   15.4   0.2       0.22   12.1   0.0    2.7  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
       0.17   10.3   0.5       0.23    9.8   0.5    1.1  1  FMO-like        Flavin-binding monooxygenase-like


Domain annotation for each model (and alignments):
>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.9   0.0   3.4e-15   4.4e-12       1     176 [.       5     172 ..       5     259 .. 0.86
   2 !   15.2   0.0   7.5e-06    0.0096     280     342 ..     274     337 ..     264     343 .. 0.90

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 3.4e-15
                                       EEEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS.--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEE CS
                     FAD_binding_3   1 etdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpr.adglnqrtmellrqlGledrilaegapnelmgeal 76 
                                       ++dVl+VG+GpaG ++++  +e+G +++++ek ++     r a+g++++   +++++G+e r +      ++ g + 
  gi|474934016|ref|YP_007687598.1|   5 KCDVLVVGGGPAGGSAGKSCAERGLDTIIIEKKAEIGAPLRcAEGVSKK---MFKEVGIEPRPEWIC--ADMKGAVI 76 
                                       69******************************99876555527777665...79******9987776..89999999 PP

                                       EEECCCCCEEEEEHH.CHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEE.EECCEECCCCCCCEEEECCTTEEE CS
                     FAD_binding_3  77 ynelsdtpkaradle.lesspervtvypqteleriLvehaeerglqvrfkte.vesleqdeegvtaevrdketgeee 151
                                       + +  d    + +l+  ++++e  +v++ + +++ +   a+e+g+++   t  +  +++d++ v a+ ++   ge+ 
  gi|474934016|ref|YP_007687598.1|  77 KSP--DG--TSFELDeSKAGAEVGYVLNRNLFDKGINILATEAGAKTMLRTWmYDFIRKDGKIVGAKCKQM--GEDI 147
                                       999..33..4445553379999999*******************888887773555677888888887766..7888 PP

                                       EEEEEEEEE--GTT-HHHHHHTGGE CS
                     FAD_binding_3 152 tvrakYlvGaDGgrStvrktlgief 176
                                       ++ ++ +vGaDG+ S+v + +g++ 
  gi|474934016|ref|YP_007687598.1| 148 EIYCDVVVGADGVESQVGRWAGMDT 172
                                       9*****************9999874 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 7.5e-06
                                       SSEETTEEE-GGGTEEE-STTSHHHHHHHHHHHHHHHHHHHH.HTTSS-GGGGHHHHHHHHHHH CS
                     FAD_binding_3 280 kyrkgrvflaGDAaHihpPtgGqGlNtaiqDavnLawkLaav.lkGeAkeelLdtYeeerrava 342
                                        y+ ++v+l+GD+a    P +G G+  a+   ++ +  +a+   kG+ ++e L++Y+++ +a+ 
  gi|474934016|ref|YP_007687598.1| 274 GYSVDNVLLVGDSARLIDPLTGGGIGHALISGMYAGEVIAECkKKGDFSREALKAYDRKIQARM 337
                                       6999************************************87257999********99877765 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.5   1.4e-10   1.8e-07       1      48 [.       7      54 ..       7      83 .. 0.85
   2 ?    0.5   0.0       0.2   2.5e+02     153     198 ..     114     157 ..     105     170 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 1.4e-10
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE-T CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgidav 48
                                      Dv+V+G+G AG +A+ ++ae+Gl+++++ek+ e g  + +++G    +
  gi|474934016|ref|YP_007687598.1|  7 DVLVVGGGPAGGSAGKSCAERGLDTIIIEKKAEIGAPLRCAEGVSKKM 54
                                      9***************************************99976555 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.2
                                       TCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE- CS
                     FAD_binding_2 153 kagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvla 198
                                       +ag + + rt + ++i++dg+++Ga ++  + g++ +i  + vv a
  gi|474934016|ref|YP_007687598.1| 114 EAGAKTMLRTWMYDFIRKDGKIVGAKCK--QMGEDIEIYCDVVVGA 157
                                       45678888999999************99..8788777766655544 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   1.7   2.2e-09   2.8e-06       1     153 [.       7     169 ..       7     175 .. 0.69
   2 ?   -2.9   0.0       2.5   3.1e+03      59     125 ..     307     376 ..     289     379 .. 0.59

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 2.2e-09
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaee......qvvtgiareflerlrqrg 71 
                                       Dv+VvGGgpaG  A  ++a++G  ++++e++  +G  l  + + +  ++k  +      +++  + + +++    +g
  gi|474934016|ref|YP_007687598.1|   7 DVLVVGGGPAGGSAGKSCAERGLDTIIIEKKAEIGAPLRCAEGVSKKMFKEVGieprpeWICADMKGAVIKSP--DG 81 
                                       9**********************************87765555555555534455444344444444444444..22 PP

                      FAD_oxidored  72 ga...rlkkrskwn....tfepevakavleemlaeagvtvllntrlvevekegkriesvtveskegrktirAkvfiD 141
                                       ++   +++k+   +    + + + + + ++ + +eag + +l t++ + ++++++i + ++++  ++++i ++v++ 
  gi|474934016|ref|YP_007687598.1|  82 TSfelDESKAG--AevgyVLNRNLFDKGINILATEAGAKTMLRTWMYDFIRKDGKIVGAKCKQMGEDIEIYCDVVVG 156
                                       33322222222..1234477777777777777799999999999999999999899999997665699999999987 PP

                      FAD_oxidored 142 ATg.dGdlaalaG 153
                                       A g + +++ +aG
  gi|474934016|ref|YP_007687598.1| 157 ADGvESQVGRWAG 169
                                       7553555555555 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.5
                      FAD_oxidored  59 iareflerlrqrggarlk..krskwntfepevakavleemlaeagvtvllntrlvevek..egkriesvtv 125
                                        a+e++++++++g+ +++  k+++ +  + ++   ++ +++a++++  l + ++ + +k  +  +ie+v+v
  gi|474934016|ref|YP_007687598.1| 307 YAGEVIAECKKKGDFSREalKAYD-RKIQARMEDGLYRDWMAKERLATLDDDTINQLVKliSTANIEHVNV 376
                                       456777777776665333222222.3466666666777777777777777777766666443445777766 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   2.9e-07   0.00037      17      55 ..       5      42 ..       1      68 [. 0.90

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2.9e-07
                                      EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--T CS
                              Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailersvspGG 55
                                      + Dv++vG+G++G +a++  a++ +l ++i+e++  +G 
  gi|474934016|ref|YP_007687598.1|  5 KCDVLVVGGGPAGGSAGKSCAER-GLDTIIIEKKAEIGA 42
                                      68*********************.**********99885 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.6   2.3e-07    0.0003       2      40 ..       7      45 ..       6      49 .. 0.92
   2 ?   -1.6   0.0      0.66   8.5e+02     296     344 ..     328     373 ..     302     382 .. 0.64

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.3e-07
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHH CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrKil 40
                                      dv+v+GgG+AG  a  s+a+rg +++++ek+ ++g  ++
  gi|474934016|ref|YP_007687598.1|  7 DVLVVGGGPAGGSAGKSCAERGLDTIIIEKKAEIGAPLR 45
                                      8*********************************98766 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.66
                                       HHTTTS-HHHHHHHHHC..TTT-TTBGGG--HHHHHHHHHHHHSEEE-- CS
                       HI0933_like 296 alaellpkrlvevlleealieeedkklaqlskkelkklaealkaltvkv 344
                                       a  + ++ r+ + l+ +     ++++la+l ++++++l++++ +++++ 
  gi|474934016|ref|YP_007687598.1| 328 AYDRKIQARMEDGLYRD-W--MAKERLATLDDDTINQLVKLISTANIEH 373
                                       34555566666666665.2..3566788888888888888888877765 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   4.2e-07   0.00053       2     119 ..       7     170 ..       6     189 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4.2e-07
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEE...............TTHCHHHCSHHHHCHHHHHHHHHHHHH...... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxx...... RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlve...............legtclnggcllskallgvaedaeias...... 57 
                                       dv+v+GgGpAG +a +  a+ g++++++e               +           +k + +v+ +++ +       
  gi|474934016|ref|YP_007687598.1|   7 DVLVVGGGPAGGSAGKSCAERGLDTIIIEkkaeigaplrcaegvS-----------KKMFKEVGIEPRPEWicadmk 72 
                                       89**************************76555333333333444...........444444444444333455555 PP

                                       ....................................HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEEC.TCEEE CS
                                       ....................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                       Pyr_redox_2  58 ....................................evvkklnqgielllgeevvkidpgkkkvklekkke.gdeek 97 
                                                                           + +   ++g +++l++   +++++ +k++  k k+ g+  +
  gi|474934016|ref|YP_007687598.1|  73 gavikspdgtsfeldeskagaevgyvlnrnlfdkgiN-ILATEAGAKTMLRTWMYDFIRKDGKIVGAKCKQmGEDIE 148
                                       5555588888888888888888888888888887752.445566778888866777777777777766555677778 PP

                                       EEESEEEE---EEE-BCTCTTC CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  98 iaydklvlAtGssprdlgipGv 119
                                       i +d +v A G ++      G+
  gi|474934016|ref|YP_007687598.1| 149 IYCDVVVGADGVESQVGRWAGM 170
                                       8888888888877766666666 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.3     0.067        86       1      32 [.       7      35 ..       7      43 .. 0.74
   2 !   12.6   0.0   3.5e-05     0.045     145     373 ..      93     339 ..      70     358 .. 0.68

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.067
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlve 32
                                      ++++vGGG+aG  a   +a+ +   l+  ++e
  gi|474934016|ref|YP_007687598.1|  7 DVLVVGGGPAGGSAGKSCAERG---LDTIIIE 35
                                      699********98888777766...5555555 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 3.5e-05
                                       S--EEEE-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETT...S-EEE-SEEEE-SGGG-IIIIIIT CS
                    Trp_halogenase 145 lsyAyhldaalyakfLrrvaearGvtrvegkvvevqldedgrveslrled...greveadlfiDcsGfrgllieqaL 218
                                        + +y l+++l++k ++  a+++G + +  +     +++dg++ + + ++   + e+  d ++ + G ++ +   a 
  gi|474934016|ref|YP_007687598.1|  93 AEVGYVLNRNLFDKGINILATEAGAKTMLRTWMYDFIRKDGKIVGAKCKQmgeDIEIYCDVVVGADGVESQVGRWA- 168
                                       5666777777777777777777777777777777777777777777766663233444577777777777766665. PP

                                       ---EEE-TTT----EEEEEEEE--H---SSEE....EEE-SSEEEEEEEETTEEEE.EEEE-TTTS-HHHHHHHHHH CS
                    Trp_halogenase 219 ktgfedwsdvLltdrAlavqveseelvepytr....ataekaGWtWkiPLqhrlgn.GyvyssahadddeAlaella 290
                                         g+++  +   ++  l   + + +    + +          G  W  P  + + n G+  +  +a++    +++l 
  gi|474934016|ref|YP_007687598.1| 169 --GMDTNLKLADIEPCLQYRMSNCDCSMEFCEfilgLSVAPGGYLWIFPKGNGIANvGIGIAGTFAKNGVRPKQFLD 243
                                       ..333333333334444444444443333333333334445777777777777777777777777755554444444 PP

                                       H.CT--TTTS-.EEEE---EE.......ES-SEETTEEE-CCCTEE--CCCS-HHHHHHH....HHHHHHHT--BTT CS
                    Trp_halogenase 291 e.ldgkleaep.rkirfttGr.......rkqawvknvvalGlasgfvePlestsihliqa....alrrLlallpdks 354
                                       + +  +++ ++ + i++++G        +  + v nv+++G+++  ++Pl + +i ++      a + ++++  ++ 
  gi|474934016|ref|YP_007687598.1| 244 KfIAEDPRFKNaQIIEIDAGFdstcpglEDGYSVDNVLLVGDSARLIDPLTGGGIGHALIsgmyAGEVIAECKKKGD 320
                                       4134455555556777887777777777888999*********************7776545557788999999999 PP

                                       --HHHHHHHHHHHHHHHHH CS
                    Trp_halogenase 355 depaaiaefnrevareler 373
                                       ++  a++ ++r++++ +e+
  gi|474934016|ref|YP_007687598.1| 321 FSREALKAYDRKIQARMED 339
                                       99***********999986 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1     3e-06    0.0038       1      36 [.      10      47 ..      10      69 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3e-06
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSS..GGG- CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlG..Graa 36
                                      +vG+G +G +a   +a++g+d  ++ek   +G   r+a
  gi|474934016|ref|YP_007687598.1| 10 VVGGGPAGGSAGKSCAERGLDTIIIEKKAEIGapLRCA 47
                                      8*******************************444444 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   1.2   5.4e-06     0.007       1      34 [.       9      42 ..       9      46 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.4e-06
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg.nign 34
                                      +++G+GPaG +a+  + + gl d +i+Ek+ +ig+
  gi|474934016|ref|YP_007687598.1|  9 LVVGGGPAGGSAGKSCAERGL-DTIIIEKKaEIGA 42
                                      69*******************.689***9977776 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.1   8.2e-05       0.1       1      33 [.       7      41 ..       7      57 .. 0.92
   2 ?    2.4   0.0     0.073        93     150     213 ..     106     174 ..      93     315 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.2e-05
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                      dv+++GGG +G s+    a+rg  ++++ek+ ++g
  gi|474934016|ref|YP_007687598.1|  7 DVLVVGGGPAGGSAGKSCAERGldTIIIEKKAEIG 41
                                      8*****************************98877 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.073
                                       HHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEE.E.EEEEEEE--GGGHH..HH.HTTCTT CS
                               DAO 150 aalaraaealGveilegtevtgleeedgkvwgverttp.gen.d.aadavVnaaGawsd..ll.gllkel 213
                                       +++   a ++G++  ++t   ++ ++dgk++g  + ++ ge  +  +d vV a G+ s+   + g++ +l
  gi|474934016|ref|YP_007687598.1| 106 KGINILATEAGAKTMLRTWMYDFIRKDGKIVGA-KCKQmGEDiEiYCDVVVGADGVESQvgRWaGMDTNL 174
                                       666677889999999999999988889999999.666667764344577999999998866555555333 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   1.3   7.1e-06    0.0091       1      44 [.       7      50 ..       7     177 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 7.1e-06
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--SSSSEE CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkldtiaelsCnpsi 44
                                      dv V+GgG AG  A   +a++G+++++i +k +  a l C + +
  gi|474934016|ref|YP_007687598.1|  7 DVLVVGGGPAGGSAGKSCAERGLDTIIIEKKAEIGAPLRCAEGV 50
                                      79**************************8888777777777655 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.7   0.00082         1       1      36 [.       7      40 ..       7     176 .. 0.83
   2 ?    4.4   0.0     0.013        16     256     339 ..     278     363 ..     257     372 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00082
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsl 36
                                      Dv+v+G+GpAg s  +    a+ gl  ++ie  +++
  gi|474934016|ref|YP_007687598.1|  7 DVLVVGGGPAGGSAGKSC--AERGLDTIIIEKKAEI 40
                                      9************99888..9999*99999987765 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.013
                     Lycopene_cycl 256 qkvlaiGaaaglvhPaTGYsvarslaeapllasaiaaalresslsarawatlw.prerkrqreffr.llglalllkl 330
                                        +vl +G  a l+ P TG  +  +l       ++ia+  ++ + s++a ++   + +++++ +++r  +  + l +l
  gi|474934016|ref|YP_007687598.1| 278 DNVLLVGDSARLIDPLTGGGIGHALISGMYAGEVIAECKKKGDFSREALKAYDrKIQARMEDGLYRdWMAKERLATL 354
                                       56899********************9999888999999998777777666544145677888888844566667777 PP

                     Lycopene_cycl 331 diegrrrfl 339
                                       d + +++++
  gi|474934016|ref|YP_007687598.1| 355 DDDTINQLV 363
                                       776666665 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00017      0.22       2      56 ..       8      61 ..       7      73 .. 0.90
   2 ?   -1.1   0.0       2.3   2.9e+03      39      59 ..      92     112 ..      86     118 .. 0.79
   3 ?   -2.7   0.0       7.3   9.3e+03      33      49 ..     324     340 ..     321     343 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00017
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHT.TEE CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekn.gie 56
                                      v+vvGgG  g  +++  ae g ++ ++e + ++    +  +++ + +k+ k+ gie
  gi|474934016|ref|YP_007687598.1|  8 VLVVGGGPAGGSAGKSCAERGLDTIIIEKKAEIG--APLRCAEGVSKKMFKEvGIE 61
                                      89********************************..88888888888887776886 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.3
                                       SHHHHHHHHHHHHHTTEEEEC CS
                         Pyr_redox  39 Deeaskilqeklekngievll 59 
                                       ++e++ +l ++l ++gi++l 
  gi|474934016|ref|YP_007687598.1|  92 GAEVGYVLNRNLFDKGINILA 112
                                       577888899999999999985 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 7.3
                                       SSSTTSSHHHHHHHHHH CS
                         Pyr_redox  33 kllrllDeeaskilqek 49 
                                       + l+++D+++++++++ 
  gi|474934016|ref|YP_007687598.1| 324 EALKAYDRKIQARMEDG 340
                                       56789999999999875 PP

>> FMO-like  Flavin-binding monooxygenase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.5   0.00018      0.23       4      46 ..       8      50 ..       5      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00018
                          FMO-like  4 vaviGaGvsGlasikccleegleptcfersddiGGlwrfkenv 46
                                      v v+G+G +G ++ k+c e gl+ +  e+ ++iG   r  e v
  gi|474934016|ref|YP_007687598.1|  8 VLVVGGGPAGGSAGKSCAERGLDTIIIEKKAEIGAPLRCAEGV 50
                                      789*******************************988877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 2512.75
//
Query:       gi|474934017|ref|YP_007687599.1|  [L=326]
Description: mevalonate kinase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.5e-14   51.9   0.8    1.4e-13   50.8   0.4    1.8  2  GHMP_kinases_N   GHMP kinases N terminal domain
    1.7e-13   50.7   2.0    1.9e-13   50.6   0.1    1.9  2  GHMP_kinases_C   GHMP kinases C terminal
  ------ inclusion threshold ------
       0.13   11.9   0.0       0.26   10.9   0.0    1.5  1  GalKase_gal_bdg  Galactokinase galactose-binding signature


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   0.4   2.4e-17   1.4e-13       2      66 .]      73     139 ..      72     139 .. 0.92
   2 ?   -2.5   0.0       1.1   6.4e+03      30      50 ..     241     263 ..     238     277 .. 0.55

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 2.4e-17
                                       EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHH.HH..HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                    GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglsl.ee..aklaleaerlaqggngsggDvaasvyGg 66 
                                       i i+s++P+g+GLGSSAAl++a   A+  + +l+  +e  a+ a+eae  aq g+gs++D ++sv Gg
  gi|474934017|ref|YP_007687599.1|  73 IFIDSRVPTGSGLGSSAALSAAYSGAVRMMKNLPYdNEsvAREAYEAEYDAQ-GRGSPMDTSTSVNGG 139
                                       89*************************9999999643368************.************998 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.1
                                       HHTTEHH.HHHHHHHHHH.HHHH CS
                    GHMP_kinases_N  30 allglsl.eeaklaleae.rlaq 50 
                                       + lg+s  e++kl+   e   ++
  gi|474934017|ref|YP_007687599.1| 241 SILGVSCpELNKLCESVEpFSFG 263
                                       55666653447777777744443 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.4      0.68   4.1e+03      54      63 ..      81      90 ..      80     101 .. 0.85
   2 !   50.6   0.1   3.2e-17   1.9e-13       2      77 ..     218     290 ..     218     294 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.68
                    GHMP_kinases_C 54 sGaGgGptvf 63
                                      +G+G+G++ +
  gi|474934017|ref|YP_007687599.1| 81 TGSGLGSSAA 90
                                      7999999875 PP

  == domain 2  score: 50.6 bits;  conditional E-value: 3.2e-17
                    GHMP_kinases_C   2 lealergdlellgellnlsqrselkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvar 77 
                                       l+a++++dle+lg l++  +   l+  +g+++pel +l+e+ +    +gakl+G+GgG++ +al+++++++++v+ 
  gi|474934017|ref|YP_007687599.1| 218 LKAIKENDLEELGALMTYDHK--LLSILGVSCPELNKLCESVEPFS-FGAKLTGSGGGGCMVALTDKPEKVAEVIA 290
                                       689**************9999..899****************9999.******************88888887775 PP

>> GalKase_gal_bdg  Galactokinase galactose-binding signature
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   4.3e-05      0.26      14      45 ..       4      35 ..       2      39 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.3e-05
                                      EEEEEEEEEE--S-TTTT-EEEEEEEEEEEEE CS
                   GalKase_gal_bdg 14 asAPGRvnLiGEHtDYngGfVlpmAieqdiyi 45
                                      asAPG   ++GEH    g   l  Ai+++ ++
  gi|474934017|ref|YP_007687599.1|  4 ASAPGKFVILGEHAVVYGKPALTLAIDMRFSM 35
                                      89************************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2185.17
//
Query:       gi|474934018|ref|YP_007687600.1|  [L=174]
Description: hypothetical protein TALC_00437 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1226.24
//
Query:       gi|474934019|ref|YP_007687601.1|  [L=380]
Description: Aspartate/tyrosine/aromatic aminotransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-59  201.1   0.0    3.3e-59  200.9   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    6.3e-08   32.3   0.0    9.6e-08   31.7   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    2.7e-06   26.2   0.0    4.1e-06   25.6   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    0.00049   19.5   0.0    0.00083   18.7   0.0    1.3  1  Beta_elim_lyase  Beta-eliminating lyase
     0.0012   17.9   0.0      0.006   15.6   0.0    1.9  1  Aminotran_5      Aminotransferase class-V


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.9   0.0   9.1e-63   3.3e-59       2     358 ..      29     366 ..      28     371 .. 0.94

  Alignments for each domain:
  == domain 1  score: 200.9 bits;  conditional E-value: 9.1e-63
                                       EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHH CS
                     Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGag 78 
                                       d +nLg +e++ +    +++e+++ ++   +a  + n+y+p+ g pel+ a+a+ +  +++ +lk  +  v+ sG++
  gi|474934019|ref|YP_007687601.1|  29 DSVNLGLGEPDLE----PPKEAIEGMNA--AALAGKNKYSPTAGIPELRDAIAQRFA-RYNPDLKGADVMVTPSGST 98 
                                       569**********....********986..9999999*******************9.8999999998899999999 PP

                                       HHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEE CS
                     Aminotran_1_2  79 aliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilve 155
                                       al+e+   +++  pgde+lvp+p +  y + ++l+gg  v+y+l+ e df+ d++ ++e ++       +tk+i+v+
  gi|474934019|ref|YP_007687601.1|  99 ALLEITQSFID--PGDEVLVPSPGFVIYAPHAKLAGGVPVEYRLT-EGDFQPDIDYILERVTP------RTKMIVVN 166
                                       99999999997..******************************88.****************9......******** PP

                                       SS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTT.EEEEEESSSTTSSGGG-EE CS
                     Aminotran_1_2 156 sphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepn.llivgslsKafGlaGeRvG 231
                                       +p+NPtG v+t+e   +l+d+ak +++++++De+Y+ f ++ +     ++ + ++ +  +i++++sK ++++G+R+G
  gi|474934019|ref|YP_007687601.1| 167 TPSNPTGGVLTEESRNALADIAKDKGIMILSDEVYESFIYEGK-----HSSFLPYLDrAVIASGFSKMMAVTGWRMG 238
                                       *****************************************65.....88888888889****************** PP

                                       EEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS.TEEEECCSCSSE CS
                     Aminotran_1_2 232 yilgnaavvsqlrklsrpflsssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael.glkvlasqsgmf 307
                                       ++++n++  ++l k++ +++  s++ +a   +l++ + ++ +le++r+++++rr+ +  +++e+ g ++++++++++
  gi|474934019|ref|YP_007687601.1| 239 FTIANEEATQALIKMQYHVCA-SPGMPAMYGILKALPSIDPYLENARKTFKARRDLISRRINEIpGMSIVPPKGAFY 314
                                       ****************99886.5777888899999999999************************************ PP

                                       EEEEETHH.CHHHHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHH CS
                     Aminotran_1_2 308 lltdlsae.takelskkLleevgvyvtpgtsftv..pgrlRitvAglteeelee 358
                                        +  ++   + ++l+ +L++  g+++tpg+ f++  +g+lR+++ + +ee++++
  gi|474934019|ref|YP_007687601.1| 315 AFPSYDLDiKSQDLANELVKA-GLICTPGSAFGTfgEGHLRFSY-AANEEKINR 366
                                       ******9999***********.**********************.777777766 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.0   2.7e-11   9.6e-08      38     144 ..      87     198 ..      67     200 .. 0.76

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 2.7e-11
                                       -SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEE CS
                   DegT_DnrJ_EryC1  38 vkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaieaaitertka 114
                                        + +  + sG++Al+  ++   ++pgdeV+vps +Fv  a  +  +g +pv    ++ ++++d + i + +t+rtk 
  gi|474934019|ref|YP_007687601.1|  87 GADVMVTPSGSTALL-EITQSFIDPGDEVLVPSPGFVIYAPHAKLAGGVPVEYRLTEGDFQPDIDYILERVTPRTKM 162
                                       344556678888874.55666799***************************************************** PP

                                       EEEB-....GGGB--..-HHHHHHHHHHCT-EEEEE CS
                   DegT_DnrJ_EryC1 115 IlpVh....lyGqva..dmdalkaiaakhglkvieD 144
                                       I++      + G       +al +ia+++g+++++D
  gi|474934019|ref|YP_007687601.1| 163 IVVNTpsnpTGGVLTeeSRNALADIAKDKGIMILSD 198
                                       985321122444444434578999999999999988 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   1.2e-09   4.1e-06      66     178 ..      86     203 ..      71     207 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.2e-09
                                       T-SEEEEESSHHHHHHHHHHTTS-TTEEEEEEST...SSHHHHHHHHHTHHHTTCEEEEESTTSHHHHHHHCCTTEE CS
                   Cys_Met_Meta_PP  66 ggeaalavssGmaAiaaailallkaGdeivvsdd...lYggtqrllkkvlkklgievkfvdtsdleelekaikentk 139
                                       +g+ +++++sG +A+  + ++++  Gde++v +    +Y +  +l   v  +  ++   +++ d++ + + ++++tk
  gi|474934019|ref|YP_007687601.1|  86 KGADVMVTPSGSTALLEITQSFIDPGDEVLVPSPgfvIYAPHAKLAGGVPVEYRLTEGDFQP-DIDYILERVTPRTK 161
                                       578899*************************9963336777777777666666666555555.678888999***** PP

                                       EEEEESS-TTTT----...HHHHHHHHHHTT-EEEEEGTTTH CS
                   Cys_Met_Meta_PP 140 lvylEtptnpllkvvD...iekiaklakkagvlvvvDntfas 178
                                       ++ + tp+np+  v+     +++a++ak++g++++ D ++ s
  gi|474934019|ref|YP_007687601.1| 162 MIVVNTPSNPTGGVLTeesRNALADIAKDKGIMILSDEVYES 203
                                       **********988875111567999********999988765 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   2.3e-07   0.00083      12     167 ..      44     198 ..      40     200 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.3e-07
                                       HHHHHHH.HCS----CCCT--HHHHHHHHHHHH........HTT-SEEEEES-HHHHHHHHHHHH--TTEEEEEETT CS
                   Beta_elim_lyase  12 eamsdaq.aaamlGdesYgedktvnrLedavae........lfgkeaalfvpqGtaAnsillkillqrgeevivtep 79 
                                       ++ ++ + aaa +G + Y    ++ +L da+a+        l g++ ++ +p+G  A     + ++ +g+ev+v +p
  gi|474934019|ref|YP_007687601.1|  44 KEAIEGMnAAALAGKNKYSPTAGIPELRDAIAQrfarynpdLKGAD-VMVTPSGSTALLEITQSFIDPGDEVLVPSP 119
                                       577888999***********************97777766555544.5569******99999*************** PP

                                       -HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHH CS
                   Beta_elim_lyase  80 ahihfdetgaiaelagvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaai 156
                                       + ++      +a lag  +++ +  e G+++++ +  ++++     +++k+i++ +  n   G v++ e+ +++a+i
  gi|474934019|ref|YP_007687601.1| 120 GFVIY---APHAKLAGGVPVEYRLTE-GDFQPD-IDYILER---VTPRTKMIVVNTPSNP-TGGVLTEESRNALADI 187
                                       98876...5678888888********.***985.8888888...358******9988885.7889************ PP

                                       HHHCT-EEEEE CS
                   Beta_elim_lyase 157 akkygiplhlD 167
                                       ak++gi ++ D
  gi|474934019|ref|YP_007687601.1| 188 AKDKGIMILSD 198
                                       ******99887 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.7e-06     0.006      65     177 ..      91     200 ..      84     361 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.7e-06
                                       EEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEE CS
                       Aminotran_5  65 iftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektk 141
                                       ++t ++++a+  + +s+   ++pgde++v + +      p ++la   g+ v++   + + + d+d + + ++++tk
  gi|474934019|ref|YP_007687601.1|  91 MVTPSGSTALLEITQSF---IDPGDEVLVPSPGFVIYA-PHAKLA--GGVPVEYRLTEGDFQPDIDYILERVTPRTK 161
                                       45555555777777777...9********999876555.666665..9***************************** PP

                                       EEEEESBETTTTEB...--HHHHHHHHHHTT-EEEEE-T CS
                       Aminotran_5 142 lvaithvsnvtGti...qpveeigklakkkgalvlvDaa 177
                                       ++ ++  sn tG +   +  ++++++ak+kg+++l D +
  gi|474934019|ref|YP_007687601.1| 162 MIVVNTPSNPTGGVlteESRNALADIAKDKGIMILSDEV 200
                                       ***********97511144568999**********9977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2681.38
//
Query:       gi|474934020|ref|YP_007687602.1|  [L=106]
Description: hypothetical protein TALC_00439 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.01   15.6   0.0       0.01   15.6   0.0    1.0  1  BacA             Bacitracin resistance protein BacA
      0.023   14.7   4.0      0.028   14.5   4.0    1.1  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
      0.063   13.2   0.6       0.58   10.1   0.0    2.0  2  DUF2854          Protein of unknown function (DUF2854)
       0.95    9.0   4.3        3.4    7.2   1.0    2.1  2  Saf_2TM          SAVED-fused 2TM effector domain
        1.4    7.9   6.9        1.8    7.6   6.9    1.1  1  DUF973           Protein of unknown function (DUF973)


Domain annotation for each model (and alignments):
>> BacA  Bacitracin resistance protein BacA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.0   2.8e-06      0.01      81     131 ..       7      58 ..       2      99 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.8e-06
                              BacA  81 rlllliivatipaailglll.kdlieellrsplvvaialivtglllllaekl 131
                                       ++ l +++a ip++i+g+l+  +++   l+ + +v++a+i+ g +l +++ +
  gi|474934020|ref|YP_007687602.1|   7 EIGLIVLLAGIPVIIAGFLCfTEIVGLGLAALFYVGVAMIIIGAALCYIDVK 58 
                                       667789***********995378888888999**************999943 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   4.0   7.7e-06     0.028      43      86 ..       9      55 ..       2      66 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.7e-06
                   Phage_holin_3_6 43 agvlallalllllvalalala.a.lwlaali.vaavllvlagvlalv 86
                                      +++++l ++++++++++ + + + l laal  v++++++++++l ++
  gi|474934020|ref|YP_007687602.1|  9 GLIVLLAGIPVIIAGFLCFTEiVgLGLAALFyVGVAMIIIGAALCYI 55
                                      45555555555555555444433556688888*********999876 PP

>> DUF2854  Protein of unknown function (DUF2854)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.3     0.037   1.3e+02      10      29 ..       5      24 ..       2      31 .. 0.85
   2 ?   10.1   0.0   0.00016      0.58       9      54 ..      29      75 ..      22      92 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.037
                           DUF2854 10 natlnllglfygipillgGl 29
                                      n ++ l++l+ gip++++G+
  gi|474934020|ref|YP_007687602.1|  5 NGEIGLIVLLAGIPVIIAGF 24
                                      56788999*********997 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00016
                           DUF2854  9 dnatlnllglfy.gipillgGlaLkaaelkPvpllketsaevlalre 54
                                      +   l l+ lfy g+ ++++G aL + ++k    + e+++++ alr+
  gi|474934020|ref|YP_007687602.1| 29 EIVGLGLAALFYvGVAMIIIGAALCYIDVKGSDGVFEQYDSLCALRK 75
                                      55677787777769****************99999889999888887 PP

>> Saf_2TM  SAVED-fused 2TM effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.2     0.015        55      16      39 ..       3      26 ..       1      38 [. 0.81
   2 ?    7.2   1.0   0.00096       3.4      69      90 ..      36      57 ..      28      61 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.015
                           Saf_2TM 16 fRkrsaelllftigvalllailgt 39
                                      +R  +++l+++  g+ +++a++  
  gi|474934020|ref|YP_007687602.1|  3 LRNGEIGLIVLLAGIPVIIAGFLC 26
                                      577889999999999999999874 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00096
                           Saf_2TM 69 aiilvigvllivvGavllilry 90
                                      a ++ +gv++i++Ga l +++ 
  gi|474934020|ref|YP_007687602.1| 36 AALFYVGVAMIIIGAALCYIDV 57
                                      56899**************997 PP

>> DUF973  Protein of unknown function (DUF973)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   6.9    0.0005       1.8      93     146 ..       2      55 ..       1      58 [. 0.75

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0005
                            DUF973  93 dvgiGitgltliligaiiiiigvilaivsllslilslillgviilligiilali 146
                                       ++++G++gl+++l+g+ +ii g++    ++      l  +gv++++ig+ l  i
  gi|474934020|ref|YP_007687602.1|   2 ELRNGEIGLIVLLAGIPVIIAGFLCFTEIVGLGLAALFYVGVAMIIIGAALCYI 55 
                                       5789**************999998555334344556667788888888776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 816.78
//
Query:       gi|474934021|ref|YP_007687603.1|  [L=383]
Description: putative hydrolases of HD superfamily [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-20   72.9   0.0    1.9e-18   67.0   0.0    2.6  2  HD_3      HD domain
    1.2e-18   67.5   0.0    5.6e-15   55.6   0.0    2.1  2  HD_2      HD containing hydrolase-like enzyme


Domain annotation for each model (and alignments):
>> HD_3  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.26   2.3e+03      73      97 ..      85     109 ..      40     144 .. 0.60
   2 !   67.0   0.0   2.1e-22   1.9e-18       1     158 [.     198     349 ..     198     355 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.26
                              HD_3  73 lakeekeeeekeaaerilkllpeel 97 
                                       + + + ee+  ++ +++l+  +e++
  gi|474934021|ref|YP_007687603.1|  85 IFHRIVEEKSDDVSRYVLAQFDENI 109
                                       3444555555555555555555553 PP

  == domain 2  score: 67.0 bits;  conditional E-value: 2.1e-22
                              HD_3   1 vekLKfqkRqgwlqtgrvreesvaeHmwrvalmalllseelkekvdiarvikmf...LiHDlvEiltgDiispd... 71 
                                       v++L+fq+R  w +t+r+++++v++H+++va m +l   + +  v  ++v   f   L+HDl+E+lt D+i+p+   
  gi|474934021|ref|YP_007687603.1| 198 VGQLRFQQR--WARTPRIPKTTVLGHSLMVANMVYLSDCDRQ--VRGEQVYYDFftaLFHDLPEVLTKDVITPVkts 270
                                       69*******..*************************977666..******99999*******************9*9 PP

                              HD_3  72 ..elakeekeeeekeaaerilkllpeelaeellalweEFeeretkeakfakdlDklepllqalekegdslaaf.eak 145
                                         +l +  +  e + +++ i++l+pe+++++l  +   ++  ++ e+ +          +++++k +d laa  ea+
  gi|474934021|ref|YP_007687603.1| 271 vnGLPDLLEGIEHELVENTIMPLIPESWRKDLGFM--AYDPFSDSESPV---------RDGHAIKACDWLAAWmEAH 336
                                       966***************************99865..344444444433.........6677777777777777777 PP

                              HD_3 146 lsqvygvsskela 158
                                       +s+vygvssk l+
  gi|474934021|ref|YP_007687603.1| 337 ISIVYGVSSKALR 349
                                       7777777776665 PP

>> HD_2  HD containing hydrolase-like enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.2   6.9e-05      0.62      10     136 ..      18     143 ..      10     173 .. 0.81
   2 !   55.6   0.0   6.3e-19   5.6e-15       1     142 [.     193     336 ..     193     355 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 6.9e-05
                              HD_2  10 kyieRwalmrntreenvaeHslevaliahalalienkkfggkldaerlallalyHDasEiitGDlptpvKyanpeir 86 
                                        +++Rw+    t + +  +   + a ia +l+  e++  g+++d++ l++  l+  ++ i   Dl+ ++ ++   ++
  gi|474934021|ref|YP_007687603.1|  18 ANMHRWNDHLRTLDLTELDKQAHKAAIAWMLGKAEEDA-GNRVDWHVLIEHMLFSFLQRIALTDLKPQIFHR--IVE 91 
                                       67888888888877777778888899********9988.99**************************99665..456 PP

                              HD_2  87 eaykevEeeaeekllelLpe...elreeyeelladeeaeeeekklvkaaDkls 136
                                       e+ ++v +    ++ e +pe   ++r ++e++l++e+ +++e  +v aa  l 
  gi|474934021|ref|YP_007687603.1|  92 EKSDDVSRYVLAQFDENIPEtdaDFRGRFESYLFSEK-DSREDAIVRAAHYLA 143
                                       666666666666666666643338*********6554.578999***998776 PP

  == domain 2  score: 55.6 bits;  conditional E-value: 6.3e-19
                              HD_2   1 eFfallsrlkyieRwalmrntreenvaeHslevaliahalalienkkfggkldaerlallalyHDasEiitGDlptp 77 
                                       +F+ ++ +l++ +Rwa      + +v  Hsl va + ++    +++  g+++  +  +  al+HD++E++t D+ tp
  gi|474934021|ref|YP_007687603.1| 193 KFIDIVGQLRFQQRWARTPRIPKTTVLGHSLMVANMVYLS-DCDRQVRGEQVYYD--FFTALFHDLPEVLTKDVITP 266
                                       6999******************************998755.55555546666555..678***************** PP

                              HD_2  78 vKyanpeireaykevEee.aeekllelLpeelreeyeell...a.deeaeeeekklvkaaDklsalikcl 142
                                       vK + + + + ++ +E+e  e++++ l+pe++r++   +    + d+e   + ++ +ka+D l a +++ 
  gi|474934021|ref|YP_007687603.1| 267 VKTSVNGLPDLLEGIEHElVENTIMPLIPESWRKDLGFMAydpFsDSESPVRDGHAIKACDWLAAWMEAH 336
                                       ******************99**************98766654432555555699***********99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2656.12
//
Query:       gi|474934022|ref|YP_007687604.1|  [L=338]
Description: tRNA-dihydrouridine synthase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.9e-66  222.1   0.0    1.1e-65  221.7   0.0    1.0  1  Dus           Dihydrouridine synthase (Dus)
    0.00059   19.4   0.0     0.0011   18.5   0.0    1.3  1  PEP_mutase    Phosphoenolpyruvate phosphomutase
  ------ inclusion threshold ------
      0.026   14.0   0.0      0.045   13.2   0.0    1.3  1  His_biosynth  Histidine biosynthesis protein
      0.074   12.8   0.5       0.69    9.7   0.1    2.2  2  SOR_SNZ       SOR/SNZ family
      0.091   12.1   0.1       0.18   11.1   0.1    1.4  1  ThiG          Thiazole biosynthesis protein ThiG


Domain annotation for each model (and alignments):
>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.7   0.0   3.2e-69   1.1e-65       2     295 ..      15     309 ..      14     323 .. 0.95

  Alignments for each domain:
  == domain 1  score: 221.7 bits;  conditional E-value: 3.2e-69
                                       E---TTTS-HHHHHHHHHTT-SSEEEEEEEE-SSS---HHHHHHH-GGGGGTSCEEEEEE-S-HHHHHHHHHHHHH. CS
                               Dus   2 laPmagvtdlpfRelvrefgataLvvtemvtakaivreekvrirmlseeeeetplavQlggsdpallaeaAklvad. 77 
                                       l Pm+g t +++R +++ fga+   +tem +a+ +++   ++   + +e +  p+ vQl+g dp++la aA+++ + 
  gi|474934022|ref|YP_007687604.1|  15 LGPMSGFTSRAYRDFMKPFGAA-VSITEMASATGVLHGMGKTGPYIRFEGNY-PTGVQLFGGDPDTLASAAEKALEv 89 
                                       67********************.***************88888888888888.********************9884 PP

                                       .TT-SCEEEEESSTTEEETTEEEGGGGGGSHHHHHHHHHHHHCCSSS-EEEEEESESSTTTC.HHHHHHHHHHCT-S CS
                               Dus  78 .lgadeIdlNvGCPskkvtrggaGaaLlrkpdlvaqivkavvkaveiPvtvkirigiddeeenalelakiveaaGaq 153
                                         +    d+N+GCP+ kv r++aG++L+++p   a+iv++++++v++Pvt+kir+g+     n  e++  +e+aGa+
  gi|474934022|ref|YP_007687604.1|  90 nPEIAFFDVNMGCPVAKVVRNQAGSFLMKEPGRCAEIVRKMKSKVDVPVTAKIRLGWSAGTVNFREIIPLLEEAGAD 166
                                       4567778********************************************************************** PP

                                       EEEEESSECCCTT-CG--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHHH.HHHH CS
                               Dus 154 altvHgRtraqnyegtadweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfae.stav 229
                                       a+++H+Rtr+++y g+  ++ ++ +++++s+p+++ G+I++++da ++ e tGa+g+m++rga gnP+l+ +   ++
  gi|474934022|ref|YP_007687604.1| 167 AVMLHARTREERYAGEPHYDMVEGLRKEMSVPLVISGNIYSLNDAIRAAEITGAEGIMAARGAVGNPYLITQiDRYF 243
                                       ***************************************************************************** PP

                                       HHSC------HHHHHHHHHHHHHHCHHTTCCCCCCHHHHHHHHHHHHHHTTTTCHHHHHHHHHHHH CS
                               Dus 230 ktgeaepapplaeeaeiveehlkkleeelgedkglrkirkhlawylkglkkaaelrreleevsdke 295
                                       +tge  p+p++ +++e +++  +++ ee+g ++g+r  r      + g+++ +e+r+ l++ +  +
  gi|474934022|ref|YP_007687604.1| 244 RTGERLPNPTVSQQVEWCKRFSDAIIEESGDEVGIRRLRTYAPRFIAGCHGCREYRKRLATETYSR 309
                                       ****************************************************99999887766555 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   2.9e-07    0.0011      58     121 ..     124     189 ..     118     201 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.9e-07
                        PEP_mutase  58 laavraiaevvslPlivDledGygespeevaetvrrliaaGvvgvniEDkkkn.d.aerqlldiee 121
                                        ++vr++ + v++P+++ ++ G+++   +++e ++ l++aG+ +v++  ++++ + a+++ +d+ e
  gi|474934022|ref|YP_007687604.1| 124 AEIVRKMKSKVDVPVTAKIRLGWSAGTVNFREIIPLLEEAGADAVMLHARTREeRyAGEPHYDMVE 189
                                       689********************************************9994443346666666544 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.3e-05     0.045     102     221 ..     113     227 ..     103     239 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.3e-05
                                       SHHHHH-THHHHHHHHHHCGGGEEEEEEEEECEEEEETTTTEEEEEEHHHHHHHHHHTT-SEEEEEETTTTTTSS-. CS
                      His_biosynth 102 gtaavknpelikelaekfgsqkivvaiDarrgykvaikgwreetgldavelakkleelgageilltdidrdGtlsG. 177
                                       g+  +k+p  + e+++k+ s k+ v + a+        gw    ++++ e++  lee+ga +++l+   r+   +G 
  gi|474934022|ref|YP_007687604.1| 113 GSFLMKEPGRCAEIVRKMKS-KVDVPVTAKIR-----LGWSAG-TVNFREIIPLLEEAGADAVMLHARTREERYAGe 182
                                       66677778888888888777.66666665544.....567666.8999999***********999999998888884 PP

                                       --HHHHHHHHHHHSSEEEEESS--SHHHHHHHH.HTTCSEEEESH CS
                      His_biosynth 178 pdleltkelaeavkipviasGGvgsledlkelk.segvdavivgs 221
                                       p +++++ l++++++p+++sG + sl+d  +++  +g++++++++
  gi|474934022|ref|YP_007687604.1| 183 PHYDMVEGLRKEMSVPLVISGNIYSLNDAIRAAeITGAEGIMAAR 227
                                       677************************976666477889999886 PP

>> SOR_SNZ  SOR/SNZ family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   0.00019      0.69      45      82 ..     106     147 ..      98     156 .. 0.76
   2 ?    0.9   0.0      0.09   3.2e+02      28      73 ..     159     199 ..     149     211 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00019
                                       HHHHHH-S------H....HHHHHHHHH-SS-EEEEEETT-H CS
                           SOR_SNZ  45 adirkeggvarmsdp....klikeikeavsipvmakvriGhf 82 
                                       + +r+++g   m +p    ++++++k++v++pv ak+r+G  
  gi|474934022|ref|YP_007687604.1| 106 KVVRNQAGSFLMKEPgrcaEIVRKMKSKVDVPVTAKIRLGWS 147
                                       5567777777777763333578888999***********976 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.09
                                       HHHHHT-SEEEE-SS-HHHHHHH-S------HHHHHHHHHH-SS-E CS
                           SOR_SNZ  28 iaeeaGavavmalervpadirkeggvarmsdpklikeikeavsipv 73 
                                       + eeaGa avm   r  ++ r     a   + ++++ + + +s+p+
  gi|474934022|ref|YP_007687604.1| 159 LLEEAGADAVMLHARTREE-RY----AGEPHYDMVEGLRKEMSVPL 199
                                       5699*******76665443.33....33455566666666666665 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1     5e-05      0.18     140     204 ..     160     226 ..     155     238 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5e-05
                                       HHHTT-SEBEEBSSSTT.S----S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHT.T-SEEEES CS
                              ThiG 140 leevGcaavmPlaapiG.sglGllnkealkiiieeakvPvivDAGigspsdaaqamel.Gadavlln 204
                                       lee+G+ avm  a        G  +  +++ +++e++vP+++   i s +da+ a e+ Ga++++ +
  gi|474934022|ref|YP_007687604.1| 160 LEEAGADAVMLHARTREeRYAGEPHYDMVEGLRKEMSVPLVISGNIYSLNDAIRAAEItGAEGIMAA 226
                                       899*******88876651457999999*****************************96699999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.55
# Mc/sec: 1864.89
//
Query:       gi|474934023|ref|YP_007687605.1|  [L=429]
Description: seryl-tRNA synthetase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-30  105.3   0.0    7.4e-30  104.2   0.0    1.5  1  tRNA-synt_2b     tRNA synthetase class II core domain (G, H, 
    8.8e-24   83.8   6.4    1.4e-23   83.2   6.4    1.3  1  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
  ------ inclusion threshold ------
       0.22   11.7   0.7       0.67   10.1   0.7    1.8  1  DUF2387          Probable metal-binding protein (DUF2387)
       0.24   10.6   0.0        0.5    9.6   0.0    1.4  1  Pneumo_matrix    Pneumovirus matrix protein
       0.27   10.2   1.7       0.42    9.5   1.7    1.2  1  L_lactis_ph-MCP  Lactococcus lactis bacteriophage major capsi
       0.29   11.0   1.0         19    5.2   0.2    2.5  2  zinc_ribbon_12   Probable zinc-ribbon domain
       0.42   10.3   3.4       0.37   10.5   0.2    2.7  3  Nbl1_Borealin_N  Nbl1 / Borealin N terminal


Domain annotation for each model (and alignments):
>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.2   0.0   2.9e-33   7.4e-30       8     179 .]     221     397 ..     217     397 .. 0.96

  Alignments for each domain:
  == domain 1  score: 104.2 bits;  conditional E-value: 2.9e-33
                                       SEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEEEBTTTS...TBCTTTB-SEEEEEEEEEEESGGGHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b   8 dreyiLkPtneetfvelirdevlrskrLPlklyqiqtkyRdEks...dsrGLlRvreFhqkdgyvfhaeaslddslr 81 
                                        +++ L Pt+e ++++l +  +l +++LP+kl+++ + +R+E     d+ G++Rv+eF++ + + f  +++++d l+
  gi|474934023|ref|YP_007687605.1| 221 RDDMWLNPTAEVPVTNLLQGDILAKEDLPIKLTAYLPSFRREVGkhaDTAGIIRVHEFNKVEMVRFEEPSKSWDALE 297
                                       4789*****************9999******************6689999*************************** PP

                                       HHHHHHHHHHHHTT.SCEEEEEEGTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTS.SEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                      tRNA-synt_2b  82 dlikaisriferlglefraiielmsaksadykdkkefeavsesltkgieigtiqklgtrlserlgatvldenn.rek 157
                                       ++   ++++++ lgl++++++++++++s++ ++ +++e++ +  ++++e+++++++ + +++r  +++  e   +++
  gi|474934023|ref|YP_007687605.1| 298 EMKGNAEELLQLLGLPYHVLLLCTGDQSFSCSKCYDIEVWAPGEDRYLECSSCSNDLDFQARRAMIKYRPEPHlKSE 374
                                       ********************************************************************999888*** PP

                                       EEEEEEEE.EEHHHHHHHHHHHH CS
                                       xxxxxxxx.xxxxxxxxxxxxxx RF
                      tRNA-synt_2b 158 svimicaa.igveRllsaileqn 179
                                       +v++++ + +++ R++ a+le++
  gi|474934023|ref|YP_007687605.1| 375 FVHTLNGSgLALPRTMVAVLENY 397
                                       ******999************96 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.2   6.4   5.5e-27   1.4e-23       1     108 []       1     107 [.       1     107 [. 0.98

  Alignments for each domain:
  == domain 1  score: 83.2 bits;  conditional E-value: 5.5e-27
                                       ---HHHHHH-HHHHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCH CS
                      Seryl_tRNA_N   1 MLDiklirenpeavkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevk 77 
                                       MLDi+ ir +pe++++ l kR++ ++ +d++le+d ++r+l +e + l++ rN++s eI+k+ k ++++++ i e++
  gi|474934023|ref|YP_007687605.1|   1 MLDIDVIRADPEKIRDMLIKRNKTTERLDKFLEVDGRWRQLTAENNLLRKTRNAVSMEISKMPK-GAEKDAKIREMR 76 
                                       ***********************************************************98775.78********** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHCTS---- CS
                      Seryl_tRNA_N  78 elkeelkaleaelkeleaeleklllaiPNip 108
                                       e+++++ka ++e+++le+  ++ ll+iPNip
  gi|474934023|ref|YP_007687605.1|  77 EVGDKIKANDDEMAQLEEIRKDCLLNIPNIP 107
                                       ******************************8 PP

>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.7   0.00026      0.67      14      37 ..     328     351 ..     324     366 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00026
                           DUF2387  14 CsemDkirmweedeveyrECvsCg 37 
                                       Cs+   i +w++ e++y EC sC+
  gi|474934023|ref|YP_007687605.1| 328 CSKCYDIEVWAPGEDRYLECSSCS 351
                                       889999*****************7 PP

>> Pneumo_matrix  Pneumovirus matrix protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0    0.0002       0.5      12      43 ..     232     263 ..     224     273 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0002
                     Pneumo_matrix  12 vtytaavqtdllekdddparltvwvplfqssv 43 
                                       v+ t  +q d+l k+d+p +lt ++p f+ +v
  gi|474934023|ref|YP_007687605.1| 232 VPVTNLLQGDILAKEDLPIKLTAYLPSFRREV 263
                                       788999**********************9876 PP

>> L_lactis_ph-MCP  Lactococcus lactis bacteriophage major capsid protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   1.7   0.00017      0.42       4      86 ..      22     104 ..      19     108 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00017
                   L_lactis_ph-MCP   4 netqeimkqaieagvkvreleakveelnkereelkkereasipsekpedverkfmrelgdkm.aempeqgflrefan 79 
                                       n+t e + + +e   + r+l a  + l k r+ +  e  +++p    +d++ + mre+gdk+ a+  e   l e+ +
  gi|474934023|ref|YP_007687605.1|  22 NKTTERLDKFLEVDGRWRQLTAENNLLRKTRNAVSMEI-SKMPKGAEKDAKIREMREVGDKIkANDDEMAQLEEIRK 97 
                                       88999999999999999999999999999999999886.6899999***************8345667788888888 PP

                   L_lactis_ph-MCP  80 aadlnvv 86 
                                        + ln+ 
  gi|474934023|ref|YP_007687605.1|  98 DCLLNIP 104
                                       8877775 PP

>> zinc_ribbon_12  Probable zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.2    0.0073        19      14      39 ..     308     333 ..     305     335 .. 0.90
   2 ?    3.7   0.0     0.021        54      32      44 ..     345     357 ..     340     358 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0073
                    zinc_ribbon_12  14 elLqlPkkflllkkkqqklrCGaCse 39 
                                       +lL lP  +lll    q + C++C  
  gi|474934023|ref|YP_007687605.1| 308 QLLGLPYHVLLLCTGDQSFSCSKCYD 333
                                       8999**9999999999********75 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.021
                    zinc_ribbon_12  32 lrCGaCsevlsfs 44 
                                       l C++Cs+ l+f+
  gi|474934023|ref|YP_007687605.1| 345 LECSSCSNDLDFQ 357
                                       8999999988875 PP

>> Nbl1_Borealin_N  Nbl1 / Borealin N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.63   1.6e+03      43      52 ..      11      20 ..       2      23 .. 0.81
   2 ?   10.5   0.2   0.00014      0.37      11      44 ..      32      64 ..      20      76 .. 0.85
   3 ?   -3.4   0.1       3.2   8.2e+03      18      29 ..     297     308 ..     296     310 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.63
                   Nbl1_Borealin_N 43 PkavRkmtmk 52
                                      P+++R+m +k
  gi|474934023|ref|YP_007687605.1| 11 PEKIRDMLIK 20
                                      999****987 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00014
                   Nbl1_Borealin_N 11 lEveeRirrlraelelllktlrnrfelellriPk 44
                                      lEv+ R r+l ae ++ll + rn+  +e+ ++Pk
  gi|474934023|ref|YP_007687605.1| 32 LEVDGRWRQLTAE-NNLLRKTRNAVSMEISKMPK 64
                                      69**********9.5666777************8 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 3.2
                   Nbl1_Borealin_N  18 rrlraelelllk 29 
                                       ++++ ++e ll+
  gi|474934023|ref|YP_007687605.1| 297 EEMKGNAEELLQ 308
                                       789999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 2598.20
//
Query:       gi|474934024|ref|YP_007687606.1|  [L=98]
Description: putative RNA-binding protein containing KH domain, possibly ribosomal protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.2e-15   56.0   1.1    4.3e-15   55.6   1.1    1.1  1  CRS1_YhbY  CRS1 / YhbY (CRM) domain
  ------ inclusion threshold ------
      0.027   14.9   0.4      0.031   14.7   0.4    1.1  1  CelTOS     Cell-traversal protein for ookinetes and sporozoit


Domain annotation for each model (and alignments):
>> CRS1_YhbY  CRS1 / YhbY (CRM) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.6   1.1   4.8e-19   4.3e-15       4      82 ..       5      83 ..       2      83 .. 0.94

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 4.8e-19
                         CRS1_YhbY  4 kelrrLrhlairlkpkvkiGkaGvtkevvdeiheklkteelvkvkcegppalnmkrmaeiLeektgglviqrsgtsivL 82
                                      + +++L ++a +++++v++Gk+G+ +++ +ei  +lk++ l+kvk+ +  +++  ++ae+++e+tg++v++++g +i+L
  gi|474934024|ref|YP_007687606.1|  5 EAKKELMRRAKDIDATVRVGKDGIDENLNNEIVAQLKKRRLIKVKVLRNADSETSDVAEQIAEATGSVVVDVRGGVILL 83
                                      67899*****************************************6667777**********************9987 PP

>> CelTOS  Cell-traversal protein for ookinetes and sporozoites
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.4   3.5e-06     0.031      10      77 ..       7      77 ..       2      93 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.5e-06
                            CelTOS 10 qkslssklseiiradldskgdelvdliandlekelqknslvaasfLq....sgfdvkkkaKeiiKkvllevl 77
                                      +k+l+ + ++ i a++    d + +++ n+++ +l+k  l+++  L     ++ dv++++ e   +v+++v 
  gi|474934024|ref|YP_007687606.1|  7 KKELMRRAKD-IDATVRVGKDGIDENLNNEIVAQLKKRRLIKVKVLRnadsETSDVAEQIAEATGSVVVDVR 77
                                      5666677777.888888899**************************94444345888999888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       980  (0.05466); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.34s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 563.50
//
Query:       gi|474934025|ref|YP_007687607.1|  [L=105]
Description: RNase P subunit RPR2 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-09   37.9   2.3      3e-09   37.0   2.4    1.4  1  Rpr2            RNAse P Rpr2/Rpp21/SNM1 subunit domain
     0.0086   16.1   1.8      0.016   15.2   1.8    1.5  1  DZR             Double zinc ribbon
     0.0099   15.6   0.2     0.0099   15.6   0.2    2.1  2  zf-RRN7         Zinc-finger of RNA-polymerase I-specific TFII
  ------ inclusion threshold ------
       0.02   15.6   2.2       0.25   12.1   0.0    2.1  2  zinc_ribbon_15  zinc-ribbon family
       0.14   11.9   0.1       0.69    9.6   0.3    1.9  2  COX5B           Cytochrome c oxidase subunit Vb


Domain annotation for each model (and alignments):
>> Rpr2  RNAse P Rpr2/Rpp21/SNM1 subunit domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   2.4   8.5e-13     3e-09       1      90 []      17      92 ..      17      92 .. 0.92

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 8.5e-13
                                      HHHHHHHHHH.HHHHH-HHHHHHHHHHHHHHHHHCT---SSTCCCTB-TTT--B--CTTTEEEEEE-SSS-E....... CS
                              Rpr2  1 rlnfLyqaahlqlaeaspalsrylakqlrevskkaqlrlppsvkrtvCkkCgsvlipgvtcsvrvenkskkkkkkkkka 79
                                      r+++L++++  + +e   + +r++++  r+++ k+++ +p+ +  ++CkkC   l+pg +c+vr+     ++k      
  gi|474934025|ref|YP_007687607.1| 17 RVSILTDLSVKAAKEGKDERARRYVELSRAICGKTRVDMPDGF--RYCKKCYLPLVPGTNCTVRLT----GHK------ 83
                                      7899999999999999*************************98..79******************5....444...... PP

                                      ..EEEEETTTT CS
                              Rpr2 80 dvlvvtClaCg 90
                                        +v +C+ Cg
  gi|474934025|ref|YP_007687607.1| 84 --IVSRCKCCG 92
                                      ..789999996 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   1.8   4.6e-06     0.016       6      37 ..      53      94 ..      46      98 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.6e-06
                               DZR  6 eelppdarfCseCgtklkavaa..........edrCpsCgek 37
                                       ++p++ r+C++C  +l + ++            rC  Cg+ 
  gi|474934025|ref|YP_007687607.1| 53 VDMPDGFRYCKKCYLPLVPGTNctvrltghkiVSRCKCCGTV 94
                                      459**************86555999999999999*****986 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.2   2.8e-06    0.0099       9      28 ..      47      66 ..      46      67 .. 0.92
   2 ?   -1.7   1.8      0.66   2.4e+03      24      31 ..      88      95 ..      88      95 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.8e-06
                           zf-RRN7  9 vCgcrsftlddGfyyCrrCh 28
                                      +Cg ++++  dGf+yC+ C+
  gi|474934025|ref|YP_007687607.1| 47 ICGKTRVDMPDGFRYCKKCY 66
                                      7999999999*********7 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.66
                           zf-RRN7 24 CrrChtqe 31
                                      C+ C+t++
  gi|474934025|ref|YP_007687607.1| 88 CKCCGTVW 95
                                      88899985 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   6.9e-05      0.25      54      85 ..      34      65 ..      13      66 .. 0.73
   2 ?    3.5   0.6     0.035   1.3e+02      35      48 ..      83      96 ..      73     105 .] 0.60

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.9e-05
                    zinc_ribbon_15 54 gkeiekkesse........kkeCknCgkeveeefkyCpkC 85
                                       +        +          +C + +  + + f+yC kC
  gi|474934025|ref|YP_007687607.1| 34 DE--------RarryvelsRAICGKTRVDMPDGFRYCKKC 65
                                      22........13334456699******************* PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.035
                    zinc_ribbon_15 35 kpylacskCkslle 48
                                      k +  c++C+++  
  gi|474934025|ref|YP_007687607.1| 83 KIVSRCKCCGTVWR 96
                                      55556666666544 PP

>> COX5B  Cytochrome c oxidase subunit Vb
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.21   7.4e+02      29      49 ..       4      24 ..       2      33 .. 0.84
   2 ?    9.6   0.3   0.00019      0.69     103     124 ..      82     104 ..      71     105 .] 0.82

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.21
                             COX5B 29 tvPtdleqatGleRlellgkl 49
                                      ++P ++  + G eR+ +l++l
  gi|474934025|ref|YP_007687607.1|  4 HIPKNVVRNIGSERVSILTDL 24
                                      588999999999999999876 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00019
                             COX5B 103 ek.vaRcaecGsvyklkllgeee 124
                                       +k v+Rc+ cG+v+++ +l e++
  gi|474934025|ref|YP_007687607.1|  82 HKiVSRCKCCGTVWRMPYLKEQR 104
                                       45589************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 657.40
//
Query:       gi|474934026|ref|YP_007687608.1|  [L=151]
Description: LSU ribosomal protein L10AE [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-25   90.0   0.0    1.5e-25   89.7   0.0    1.0  1  Ribosomal_L16  Ribosomal protein L16p/L10e


Domain annotation for each model (and alignments):
>> Ribosomal_L16  Ribosomal protein L16p/L10e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.7   0.0   8.6e-30   1.5e-25      15     131 ..       2     141 ..       1     141 [. 0.92

  Alignments for each domain:
  == domain 1  score: 89.7 bits;  conditional E-value: 8.6e-30
                                       TSXX.XSXXXXXESX..........EEEEESSXEEEEHHHHHHHHHHHCTCCCCTSXC...EEXXSXXXXEEEEE-. CS
                     Ribosomal_L16  15 rgvs.tkgtklefgd..........ygLvalekgqltaealeaariainrylkkkrgk...klwirvfphhpvtkk. 76 
                                        gv+  +++++++g+          + L+++++ q++++a+ea+ria+nr l+        ++++r++ph +++++ 
  gi|474934026|ref|YP_007687608.1|   2 GGVPaVRISQFDMGTlnrddsfpvvLTLKVKNRVQVRHTAIEAGRIAANRVLSGIG-VdnyHFKVRAYPHVVLRENk 77 
                                       689999*****************9999**************************333.2467**************** PP

                                       ....SS-TTTSSSS....XEEEEEEEEEXSSCEEEEE.TTXXXSHHHHHHHHHHHHTSSSXEEE CS
                     Ribosomal_L16  77 ....agedRmgkGk....Gkpegwvarvkigqiifei.kagvneeiakealrraasKlpiktki 131
                                           ag+dR+++G+    Gk  g++ar + +q i+++     ++ ++keal ra++Klp ++ i
  gi|474934026|ref|YP_007687608.1|  78 latgAGADRVSSGMrrafGKTVGTAARLECNQAIYTVyTTAEKATQVKEALWRASMKLPSPCYI 141
                                       *************************************744358889*************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1005.05
//
Query:       gi|474934027|ref|YP_007687609.1|  [L=326]
Description: diphthamide biosynthesis protein 2-related domain protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-76  257.1   0.0    2.9e-76  256.8   0.0    1.0  1  Diphthamide_syn  Putative diphthamide synthesis protein


Domain annotation for each model (and alignments):
>> Diphthamide_syn  Putative diphthamide synthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  256.8   0.0   1.6e-80   2.9e-76       1     302 [.      26     321 ..      26     322 .. 0.95

  Alignments for each domain:
  == domain 1  score: 256.8 bits;  conditional E-value: 1.6e-80
                   Diphthamide_syn   1 fPegllpdsaeiadil.eefgaevvilgDttYGaCcvdevaaehlgadllvHyGhsclspvd.rlpvlYvfveield 75 
                                       +Pegl++ ++e++d++ +++g +vvilg ++YGaC++     +   a+ lvH+Ghs++++   + +vlYv ++ ++d
  gi|474934027|ref|YP_007687609.1|  26 LPEGLKIRATELSDRIfKDTGSKVVILGYPCYGACDLFVDYKRY--AQGLVHFGHSPIPNLPrDDDVLYVEARADVD 100
                                       6************************************7766666..9************866699************ PP

                   Diphthamide_syn  76 vehlvetlkknfkekkkivlvstiqyahaleevkeeleeegyevv.kvpqsekplspgevlgctspklkeeeeevda 151
                                       +++l++++ +     +ki+l++++qy+h l+e+k++lee+g + v  +++  ++ +pg+vlgc+ +++ + +e+v+a
  gi|474934027|ref|YP_007687609.1| 101 ISSLADSISELP---SKIGLLASVQYVHLLPEAKRILEESGRTAViGKGDD-RIFYPGQVLGCNCSSAISVQEDVEA 173
                                       ********9987...78*********************9988666366666.9***************999****** PP

                   Diphthamide_syn 152 ilyigdgrfhllslmlsnpklpvyrydpyskklteesydakkllrrRyaaiekakdakkvGiivgtlgvqgrlelve 228
                                       +l++g+g+fh+l + +   k +v+ y+p++k++++ +   +++lrrR+aaie+a++a+++ +iv+ + +q r++ ++
  gi|474934027|ref|YP_007687609.1| 174 FLFLGEGDFHPLAATFGVAK-HVFIYNPVTKEMRSVDDVKDRILRRRFAAIESARSAQSFLVIVCGKIGQCRMDAAD 249
                                       ******************77.9******************************************************* PP

                   Diphthamide_syn 229 rlkkllkeagkksylvlvgelnpakLanfaeidafVlvaCprlsiddgkeFekPvltpyElevalgerewteey 302
                                       r++++l++agk++y ++ +e++p+ L  f ++da+V +aCpr+++dd+ +++ P+lt  E+e +lg r+w+ +y
  gi|474934027|ref|YP_007687609.1| 250 RIEQQLRDAGKTVYRLVTDEITPNALIPF-KVDAYVSTACPRVAMDDQAKYQHPMLTIPEAETVLGLRTWD-DY 321
                                       *****************************.9***************************************5.44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2094.27
//
Query:       gi|474934028|ref|YP_007687610.1|  [L=242]
Description: putative methanogen marker protein 4 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.1e-06   26.3   0.1    0.00011   21.7   0.1    2.0  1  PTA_PTB       Phosphate acetyl/butaryl transferase
  ------ inclusion threshold ------
      0.016   14.3   0.2      0.036   13.1   0.1    1.5  1  FA_synthesis  Fatty acid synthesis protein


Domain annotation for each model (and alignments):
>> PTA_PTB  Phosphate acetyl/butaryl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   1.2e-08   0.00011     113     306 ..      47     224 ..      34     235 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.2e-08
                                       HTTSSSEEEE-TTS-HHHHHHHHHHCT-B-TT----EEEEEEEETTEEEEEESSSS-SS--HHHHHHHHHHHHHHHH CS
                           PTA_PTB 113 klgeaDglvsGavnttadtlrpalqiiktkpgvklvSsvfimlledrlllfaDcavnvnPtaeelaeialesaktak 189
                                       ++g+ D+ v G +++++      l +ik++     +  +++  ++d+++l a + + +  t+e++a +a  s+   k
  gi|474934028|ref|YP_007687610.1|  47 ASGKIDAAVRGDMSSSKL-----LPLIKQALNLDHLDRIVMYGIRDKVVLSAPVGIDEGWTVEDKAYMARASVALLK 118
                                       678888888888877654.....6788888888899999999999******************************** PP

                                       HCCSS--EEEEE-SSSTTSS-SHHHHHHHHHHHHHHHH-TTSEEEEEE-HHHHH-HHHHHHH-TTSTTTT--SEEE- CS
                           PTA_PTB 190 algeeeprvAlLSyStkgsakgesvekvrealkivkekapdlvvdGelqlDaAlseevaekkapesevaGkAnvlvf 266
                                       +lg + pr+A++S     s ++ + e+v   ++ ++e    lv +G   +Da   +++    + e +   +A+v++ 
  gi|474934028|ref|YP_007687610.1| 119 KLGVDSPRIAVMS--GGRSEDMGRNENVDRTIRDAEEVTGLLVSEG---YDAY-HAQI----LIE-DAVDDADVIIA 184
                                       **********986..6889999999999999999999999999999...4532.2222....222.23358****** PP

                                       SSHHHHHHHHHHHHHCCTEEEEEEEEESBSS-EEE--TT- CS
                           PTA_PTB 267 PdLeagnigykivqrlakaeaiGPilqGlakPvndlSrga 306
                                       Pd  +gni +++++ ++++ a G  ++ ++k + d+Sr  
  gi|474934028|ref|YP_007687610.1| 185 PDGISGNIIFRVLHFIGDVPAFGAPVINTDKVFVDTSRVK 224
                                       *************************************965 PP

>> FA_synthesis  Fatty acid synthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1     4e-06     0.036     168     236 ..     120     196 ..     102     203 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4e-06
                                       S--SS-EEEEEESSSSTT-SSH........HHHHHHHHHHT-TTSEEEEEEEGGGCCCTS-SEEE--HHHHHHHHHH CS
                      FA_synthesis 168 lgvdsprvglLniGeeevkgnd........lvkqtfellkaiesieflGnvegrdildgkvdvivcdgftgNvilkt 236
                                       lgvdspr++++++G  e +g +         + ++  ll + ++ ++   +  +d +d+   +i  dg+ gN+i + 
  gi|474934028|ref|YP_007687610.1| 120 LGVDSPRIAVMSGGRSEDMGRNenvdrtirDAEEVTGLLVSEGYDAYHAQILIEDAVDDADVIIAPDGISGNIIFRV 196
                                       599*****************9988888766667777788888888888888889988887777788*******9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1609.09
//
Query:       gi|474934029|ref|YP_007687611.1|  [L=158]
Description: 6-pyruvoyl-tetrahydropterin synthase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-24   85.2   0.1    4.1e-24   84.9   0.1    1.1  1  PTPS      6-pyruvoyl tetrahydropterin synthase


Domain annotation for each model (and alignments):
>> PTPS  6-pyruvoyl tetrahydropterin synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.9   0.1   2.3e-28   4.1e-24       6     121 ..      13     155 ..      10     157 .. 0.93

  Alignments for each domain:
  == domain 1  score: 84.9 bits;  conditional E-value: 2.3e-28
                                       EEEEEEE--TTTTGGGGSTEEEEEEEEEEEEEC-STCTTBSS-HHHHHHHHHHHHHCTTTEEC.CCC-CCHHCCS.. CS
                              PTPS   6 feFdaaHrlrkhegkcrnlHGHnykvevtvegeeldetgmvvdfgelkealkeileelDhkfl.naddpeleell.. 79 
                                       ++++a+H++++he kc++lHGH+y +++ +eg+   e+gmv+df elk+ lk+i+ee+Dh++l   ++ ++  ++  
  gi|474934029|ref|YP_007687611.1|  13 IRYSACHFIPNHE-KCSRLHGHSYIIHLRLEGD-IGENGMVMDFVELKRELKKIVEEMDHAVLlP-AKSDVVHITee 86 
                                       589*******999.*******************.9****************************76.66666666679 PP

                                       ...........................--HHHHHHHHHHHHHHHH.GCCCGCEEEEEEEEETTEEEEEE CS
                              PTPS  80 ..........................spTaEnlaklifeelkerl.qekevklskvrvwEtpnswaeyr 121
                                                                 ++TaE++ k+++e++ +++  +++v+  ++ + E+++++a y+
  gi|474934029|ref|YP_007687611.1|  87 ggdvhveclgkrymfpkcdvrmldvpTTTAEEMTKMMAERMVREVnIPSNVRSLSIGLDEERGQTAWYT 155
                                       9***********************9988*****************98999**********999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      590  (0.0329076); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1077.70
//
Query:       gi|474934030|ref|YP_007687612.1|  [L=227]
Description: preQ(0) biosynthesis protein QueC [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.9e-73  245.1   0.0    5.5e-73  244.9   0.0    1.0  1  QueC           Queuosine biosynthesis protein QueC
    3.3e-05   23.7   0.2    4.7e-05   23.2   0.2    1.2  1  Asn_synthase   Asparagine synthase
    0.00023   20.1   0.0    0.00031   19.6   0.0    1.2  1  tRNA_Me_trans  tRNA methyl transferase
      0.008   15.3   0.0      0.033   13.3   0.0    1.8  2  NAD_synthase   NAD synthase
     0.0097   15.7   0.0       0.18   11.6   0.0    2.1  2  ATP_bind_3     PP-loop family
  ------ inclusion threshold ------
      0.048   13.2   0.0       0.19   11.3   0.0    1.8  2  ThiI           Thiamine biosynthesis protein (ThiI)


Domain annotation for each model (and alignments):
>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  244.9   0.0   1.8e-76   5.5e-73       1     209 [.       3     213 ..       3     214 .. 0.95

  Alignments for each domain:
  == domain 1  score: 244.9 bits;  conditional E-value: 1.8e-76
                                       EEEEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-GGGGGGSCGGG----- CS
                              QueC   1 kavvllSGGlDSttvlalakkegkevealtfdYgqrhkkeleaakkiakelgveehkildldllkelggsaLtdeei 77 
                                       kavvllSGGlDStt la+a ++g+ ++a++f+Ygq+h++ele+a+++++++g+ +h ++dld l+++ +saLt+++ 
  gi|474934030|ref|YP_007687612.1|   3 KAVVLLSGGLDSTTTLAQAIDDGYSCTAISFRYGQKHTRELESADRVCRHYGI-AHAVIDLD-LSSF-RSALTRDDL 76 
                                       79***************************************************.********.7776.79******* PP

                                       ----..--...--------TTHHHHHHHHHHHHHHHHT-SEEEE---S-STT--GGGSHHHHHHHHHHHHHH..... CS
                              QueC  78 evpk..eeleeeelpntfVpaRNliflslaasyaealgaeaiiiGvneedfsgYPDcrdefvkalnkalnlg..... 147
                                       evp   e    ee+p t+VpaRN++fls+aa++ae+++ae+i++G+n++d+sgYPD r++f++a++k+l  g     
  gi|474934030|ref|YP_007687612.1|  77 EVPMdrEGDLAEEIPITYVPARNIVFLSIAAGLAESIDAERIYLGANAVDYSGYPDDRPDFLEAFQKMLDKGtkagv 153
                                       *9984344445*************************************************************99999 PP

                                       HTS--EEE-TTTT--HHHHHHHHHHTTHHHHH-B-STTS.-BTTTTSSSHHHHHHHHHHHHH CS
                              QueC 148 edkkieieaPlidlsKaeivklgkelgvpleetlsCYegeeegkaCgeCdaCalRkkgfeea 209
                                       e+++++++aPl+ l+Ka+iv+lg++l++ple+t+sCY+g+e+  aCg+Cd+C+lR +gf++a
  gi|474934030|ref|YP_007687612.1| 154 EGHTVQVTAPLLYLTKAQIVELGMKLKAPLELTWSCYNGGER--ACGHCDSCRLRLEGFRKA 213
                                       999************************************777..***************987 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.2   1.6e-08   4.7e-05      22      80 ..       6      63 ..       2      76 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.6e-08
                      Asn_synthase 22 alLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtelvlt 80
                                      +lLSGGlDS++  a a      + ++ s  + +k+  e++ a +v++h+g+ h  + l+
  gi|474934030|ref|YP_007687612.1|  6 VLLSGGLDSTTTLAQAIDDGY-SCTAISFRYGQKHTRELESADRVCRHYGIAHAVIDLD 63
                                      89********99888888775.78888888888********************888765 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0     1e-07   0.00031       2      71 ..       3      63 ..       2      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1e-07
                     tRNA_Me_trans  2 kvvvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfe 71
                                      k vv+lSgG DS+ ++a   + gy+++++ ++  ++         ++++l+ a rv+++ gi + v+d+ 
  gi|474934030|ref|YP_007687612.1|  3 KAVVLLSGGLDSTTTLAQAIDDGYSCTAISFRYGQK---------HTRELESADRVCRHYGIAHAVIDLD 63
                                      679**************************9998665.........457899**************99986 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   1.1e-05     0.033      19      82 ..       2      63 ..       1      80 [. 0.88
   2 ?   -0.5   0.0      0.18   5.3e+02     149     171 ..     162     184 ..     149     187 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.1e-05
                                      SEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE---H CS
                      NAD_synthase 19 kgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidik 82
                                      k++v+ lSGG+DS++  +la+ + +    +a+ +   +++ +++e a  ++ ++gi   +id++
  gi|474934030|ref|YP_007687612.1|  2 KKAVVLLSGGLDSTT--TLAQAIDDGYSCTAISFRYGQKHTRELESADRVCRHYGIAHAVIDLD 63
                                      789999*******97..5888888889999999999999*****************99999875 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.18
                                       ETTTTS-HHHHHHHHHHTT--HH CS
                      NAD_synthase 149 apiaellKtevkeLakelnvPer 171
                                       ap+  l+K ++ eL  +l +P +
  gi|474934030|ref|YP_007687612.1| 162 APLLYLTKAQIVELGMKLKAPLE 184
                                       79999***********9999976 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   5.9e-05      0.18       2      68 ..       4      64 ..       3      76 .. 0.77
   2 ?    1.9   0.0     0.054   1.6e+02     134     155 ..     154     175 ..     133     182 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.9e-05
                                      EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H CS
                        ATP_bind_3  2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvdv 68
                                      ++v +SgGlDS++ l  + +     g +++ai + +g  ++  +e e   ++c++++i++ + ++d+
  gi|474934030|ref|YP_007687612.1|  4 AVVLLSGGLDSTTTLAQAIDD----GYSCTAISFRYG--QKHTRELESADRVCRHYGIAHAVIDLDL 64
                                      57889*******988777666....446677776666..566778888999*****99999888776 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.054
                                       EETTCCEE-CCCT--HHHHHHH CS
                        ATP_bind_3 134 eiasirlvRPlLkvskeeleey 155
                                       e +++++  PlL ++k+++ e+
  gi|474934030|ref|YP_007687612.1| 154 EGHTVQVTAPLLYLTKAQIVEL 175
                                       335689999*********9875 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   6.4e-05      0.19       5      53 ..       3      47 ..       1      76 [. 0.74
   2 ?   -0.7   0.0       0.3   8.9e+02     137     158 ..     157     178 ..     150     182 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.4e-05
                              ThiI  5 kvlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekvekla 53
                                      k+++LlSgG+DS  +   ++  G    ++ +     +    +  +e++ 
  gi|474934030|ref|YP_007687612.1|  3 KAVVLLSGGLDSTTTLAQAIDDGYSCTAISFRYGQKH----TRELESAD 47
                                      899****************************633322....22334444 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.3
                              ThiI 137 nllilrPLigldKeeiiklAke 158
                                        + +  PL+ l K +i++l  +
  gi|474934030|ref|YP_007687612.1| 157 TVQVTAPLLYLTKAQIVELGMK 178
                                       567899***********98766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1476.47
//
Query:       gi|474934031|ref|YP_007687613.1|  [L=209]
Description: Organic radical activating enzyme [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-14   53.9   0.0    2.6e-14   53.4   0.0    1.3  1  Fer4_14      4Fe-4S single cluster domain
    1.1e-13   51.9   0.0    1.5e-13   51.5   0.0    1.2  1  Radical_SAM  Radical SAM superfamily
    1.1e-08   35.5   0.0    1.5e-08   35.0   0.0    1.2  1  Fer4_12      4Fe-4S single cluster domain
  ------ inclusion threshold ------
       0.12   12.5   0.0       0.22   11.6   0.0    1.6  1  Hydrolase_6  Haloacid dehalogenase-like hydrolase
       0.14   11.3   0.0        0.2   10.8   0.0    1.2  1  DUF561       Protein of unknown function (DUF561)


Domain annotation for each model (and alignments):
>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   0.0   7.3e-18   2.6e-14       1     109 [.      22     116 ..      22     124 .. 0.81

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 7.3e-18
                           Fer4_14   1 lfvrlsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkee 77 
                                       +f+r++gC+l C +Cd+  + +++ g++ +   ++qil  +  +++  +++ +tGGePL   +++e+ kl++ l + 
  gi|474934031|ref|YP_007687613.1|  22 YFIRTAGCSLRCAWCDTAWSRRFDQGEEMS---VSQIL--ALVKDV--RNVCVTGGEPL---EQEEMPKLLQALADA 88 
                                       8***************98766666665544...44556..444555..449********...789************ PP

                           Fer4_14  78 ypekkiwletngtleielektpdlkekleals 109
                                       +  k + letng+++i++   p++++++ +++
  gi|474934031|ref|YP_007687613.1|  89 G--KTVVLETNGSMDISVV--PHSENIIISMD 116
                                       *..************8866..88888888876 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.5   0.0   4.1e-17   1.5e-13       2      89 ..      24     101 ..      23     129 .. 0.91

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 4.1e-17
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgi 78 
                                       + t gC+lrC +C++ ++ rr + g+++sv +il++vk +      ++v ++ggepl + ++ +ll +la     g 
  gi|474934031|ref|YP_007687613.1|  24 IRTAGCSLRCAWCDTAWS-RRFDQGEEMSVSQILALVKDV------RNVCVTGGEPLEQEEMPKLLQALADA---GK 90 
                                       5799*************7.******************666......59***********************7...** PP

                                       EEEEEECSSCH CS
                                       xxxxxxxxxxx RF
                       Radical_SAM  79 ritvetngtlp 89 
                                       ++++etng ++
  gi|474934031|ref|YP_007687613.1|  91 TVVLETNGSMD 101
                                       ********874 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.0   4.3e-12   1.5e-08       1      95 [.      10     100 ..      10     119 .. 0.81

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 4.3e-12
                           Fer4_12   1 lnGeG...vrl..slfvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeal 72 
                                       l+GeG   +rl  +++++gC+l+C+ C     ++f++g+e++   +  +++d+     + + ++GGEPl+   +e++
  gi|474934031|ref|YP_007687613.1|  10 LQGEGlmiGRLtyFIRTAGCSLRCAWCDTAWSRRFDQGEEMSVSQILALVKDV-----RNVCVTGGEPLE---QEEM 78 
                                       5899966544333777**************************88777777776.....99**********...7788 PP

                           Fer4_12  73 lelvkevkeekpekdiwlytgyt 95 
                                        +l++ +  ++   ++++++g++
  gi|474934031|ref|YP_007687613.1|  79 PKLLQALADAGK-TVVLETNGSM 100
                                       888888888777.4788888875 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   6.2e-05      0.22       7      41 ..      64     100 ..      58     158 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.2e-05
                                       TTSEETTEE-T..THHHHHHHHHHTT-EEEEEE---S CS
                       Hydrolase_6   7 GvLwrgdkaip..gaaealnalraagkpvvllTNnss 41 
                                        v + g+++++  + +++l+al +agk+vvl TN+s 
  gi|474934031|ref|YP_007687613.1|  64 NVCVTGGEPLEqeEMPKLLQALADAGKTVVLETNGSM 100
                                       5666667776422689******************986 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   5.6e-05       0.2      94     159 ..      44     103 ..      39     124 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.6e-05
                            DUF561  94 YeqgrklsseeilalvkevrkLlPktdlsvtiPyiLkleeqvkLakkLeslgvd.liqteGkitsis 159
                                       ++qg  +s+++ilalvk+vr+      ++vt    L++ee  kL ++L ++g   ++ t+G++ +is
  gi|474934031|ref|YP_007687613.1|  44 FDQGEEMSVSQILALVKDVRN------VCVTGGEPLEQEEMPKLLQALADAGKTvVLETNGSM-DIS 103
                                       689*****************7......589999999999999999999998866156788854.444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1415.46
//
Query:       gi|474934032|ref|YP_007687614.1|  [L=112]
Description: hypothetical protein TALC_00451 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-18   67.2   0.1    1.5e-18   66.9   0.1    1.1  1  Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor


Domain annotation for each model (and alignments):
>> Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.9   0.1   8.2e-23   1.5e-18       2      91 ..      13      99 ..      12     103 .. 0.94

  Alignments for each domain:
  == domain 1  score: 66.9 bits;  conditional E-value: 8.2e-23
                                      TSCB-STCCC-SEEEEEEESSSCEEEEEEEE.GCCCTSSCSSTHHHHHHHHTT-SEEEESSSCHHHHHHHCTTTSEEEE CS
                     Nitro_FeMo-Co  2 gsrvdqhFGrapyFaiyeveegevkivenrveeaadaegggggklaqllaeegvdvvivgkiGpralakleaagievyk 80
                                      +s v + FG+ap+F+i++ e+ ++++ven+    +++++g+g+k+a+++   gv+ vi+g+iG + ++ l++agi+v  
  gi|474934032|ref|YP_007687614.1| 13 ESLVAEDFGHAPFFLIVDSENLDYTVVENE----YASGEGAGYKVANSIVPLGVEHVICGGIGTHGIKILQDAGIRVWY 87
                                      7899**************************....666779**************************************9 PP

                                      S.-SSBHHHHHH CS
                     Nitro_FeMo-Co 81 g.aggtveealk 91
                                         + tv+ea +
  gi|474934032|ref|YP_007687614.1| 88 DmDEYTVQEAAE 99
                                      99*******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 746.45
//
Query:       gi|474934033|ref|YP_007687615.1|  [L=288]
Description: ATPases involved in chromosome partitioning [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   7.8e-102  339.9   1.5   9.1e-102  339.7   1.5    1.0  1  ParA             NUBPL iron-transfer P-loop NTPase
    1.6e-13   50.8   0.0    1.8e-12   47.5   0.0    2.3  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    1.3e-09   38.2   1.9    5.7e-08   32.9   1.5    2.5  1  AAA_31           AAA domain
      2e-09   37.1   0.5    5.1e-08   32.5   0.1    2.7  3  ArsA_ATPase      Anion-transporting ATPase
    7.4e-08   32.0   0.0    1.1e-07   31.4   0.0    1.3  1  MipZ             ATPase MipZ
    8.1e-08   32.0   0.1      0.001   18.6   0.1    2.2  2  Fer4_NifH        4Fe-4S iron sulfur cluster binding proteins,
     0.0008   18.5   0.1     0.0017   17.4   0.1    1.4  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
     0.0019   17.7   0.1       0.22   11.0   0.0    2.5  3  CBP_BcsQ         Cellulose biosynthesis protein BcsQ
     0.0037   17.1   1.1       0.89    9.3   0.3    2.2  2  AAA_26           AAA domain
     0.0042   16.7   0.5     0.0083   15.7   0.5    1.4  1  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
     0.0051   16.0   0.1     0.0088   15.2   0.1    1.3  1  NB-ARC           NB-ARC domain
      0.006   16.2   0.0      0.014   15.0   0.0    1.6  1  AAA_25           AAA domain
     0.0066   16.4   0.2      0.013   15.5   0.2    1.5  1  RsgA_GTPase      RsgA GTPase
     0.0082   16.7   0.0      0.014   16.0   0.0    1.5  1  AAA_18           AAA domain
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.016   15.1   0.0    1.3  1  APS_kinase       Adenylylsulphate kinase
      0.016   15.0   0.0       0.09   12.5   0.0    2.0  2  Cytidylate_kin   Cytidylate kinase
      0.022   14.6   0.0      0.046   13.5   0.0    1.5  1  CLP1_P           mRNA cleavage and polyadenylation factor CLP
      0.023   14.6   0.2       0.07   13.0   0.2    1.8  1  NTPase_1         NTPase
      0.027   14.1   0.1       0.05   13.2   0.1    1.4  1  SRP54            SRP54-type protein, GTPase domain
      0.029   13.6   0.0      0.035   13.4   0.0    1.1  1  KAP_NTPase       KAP family P-loop domain
      0.031   13.7   0.0      0.057   12.9   0.0    1.4  1  KTI12            Chromatin associated protein KTI12
      0.031   14.7   0.1       0.13   12.6   0.1    1.9  2  AAA_16           AAA ATPase domain
      0.067   13.6   0.0       0.15   12.5   0.0    1.6  1  RNA_helicase     RNA helicase
      0.068   13.0   0.0       0.11   12.4   0.0    1.4  1  zf-ZPR1          ZPR1 zinc-finger domain
        0.1   12.5   0.0       0.18   11.7   0.0    1.4  1  Rad17            Rad17 P-loop domain
        0.1   11.9   0.0        0.2   10.9   0.0    1.4  1  Zeta_toxin       Zeta toxin
       0.11   12.0   0.0       0.19   11.2   0.0    1.3  1  AAA_7            P-loop containing dynein motor region
       0.16   12.0   0.2       0.41   10.6   0.1    1.7  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain


Domain annotation for each model (and alignments):
>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  339.7   1.5  1.4e-104  9.1e-102       1     245 [.      19     265 ..      19     266 .. 0.99

  Alignments for each domain:
  == domain 1  score: 339.7 bits;  conditional E-value: 1.4e-104
                              ParA   1 kvkkviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqsekkliPvea.kgikvm 76 
                                       ++k+vi+v+SgKGGVGKStv++nlA+aL+k+g+++g++D+Di+Gp+ip+++ ve+ek  ++++kliPv+   ++k+m
  gi|474934033|ref|YP_007687615.1|  19 NIKHVIIVISGKGGVGKSTVSSNLAVALSKEGYQTGIMDIDITGPNIPKMFHVEDEKLLVENDKLIPVMYpPSLKIM 95 
                                       69***********************************************************99******999***** PP

                              ParA  77 SigfllesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqkl.plagaviVttpqevalad 152
                                       S++fll+++d+a++wrGp+k++a++q+++dv+wg+lDyL+iD+PPGtgDe+l+++q + + +ga++Vttpq+va+ d
  gi|474934033|ref|YP_007687615.1|  96 SMAFLLPDKDSAIMWRGPVKMGAVRQFIEDVQWGNLDYLVIDMPPGTGDEALSIVQLIpKADGAIVVTTPQDVAILD 172
                                       **********************************************************8889*************** PP

                              ParA 153 vkkaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkplvlke 229
                                        +k+++++ +++++v+G++eNmsgfvcp+cge ++if++ggge++a+++gv++lg++p++ +++e++d+g p+v+++
  gi|474934033|ref|YP_007687615.1| 173 SRKSVTFALQTHIPVIGIIENMSGFVCPHCGEVVNIFKSGGGEAAAKDMGVQFLGRVPMEAAVAESGDSGLPIVEAD 249
                                       ***************************************************************************** PP

                              ParA 230 peseaakaleeiaekv 245
                                       p s+ ak+++ei++kv
  gi|474934033|ref|YP_007687615.1| 250 PASASAKSFREIVNKV 265
                                       **************98 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   0.0   2.7e-15   1.8e-12       1     128 []      24     245 ..      24     245 .. 0.77

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 2.7e-15
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep....................... 54 
                                       i+++s+kGGvGK+t++ nLa+al+++g+++   D D  ++n    +  ++d++                        
  gi|474934033|ref|YP_007687615.1|  24 IIVISGKGGVGKSTVSSNLAVALSKEGYQTGIMDIDITGPNIPK-MFHVEDEKLlvendklipvmyppslkimsmaf 99 
                                       79***************************************983.33333333368888899*************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|474934033|ref|YP_007687615.1| 100 llpdkdsaimwrgpvkmgavrqfiedvqwgnldylvidmppgtgdealsivqlipkadgaivvttpqdvaildsrks 176
                                       *********************************************99999999999999999999999987765554 PP

                                       ......CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHT CS
                                       ......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ......dlkrllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeaparg 125
                                             + + +++++e++++ +       g v+n +++         + e   +++gv++lg +p   avae+  +g
  gi|474934033|ref|YP_007687615.1| 177 vtfalqTHIPVIGIIENMSGFV---CPHCGEVVNIFKSG--------GGEAAAKDMGVQFLGRVPMEAAVAESGDSG 242
                                       4444442223333333333221...33445555555554........222222233999999999999999999999 PP

                                       S-H CS
                                       xxx RF
                              CbiA 126 epv 128
                                       +p+
  gi|474934033|ref|YP_007687615.1| 243 LPI 245
                                       886 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   1.5   8.9e-11   5.7e-08       2     153 ..      22     169 ..      21     183 .. 0.70

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 8.9e-11
                            AAA_31   2 kvIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQa.nattglgiekneiektlyevlieeknikeaiiktk 77 
                                       +vI ++  KGGvGK+T s nla+al+k+g+++ ++D+D  + n    +++e ++       +l+e+ ++  +++   
  gi|474934033|ref|YP_007687615.1|  22 HVIIVISGKGGVGKSTVSSNLAVALSKEGYQTGIMDIDITGpNIPKMFHVEDEK-------LLVENDKLIPVMY--- 88 
                                       5899**********************************8763555555543333.......3334444444555... PP

                            AAA_31  78 venldlipssidLaeaeielvelekk.eeilkellekvk.deYDyiiiDcpPsLg...lltenaLvasdsviipvqa 149
                                         +l+++     L + +  ++        ++++++e+v+  + Dy +iD+pP  g   l  ++ +  +d  i+++ +
  gi|474934033|ref|YP_007687615.1|  89 PPSLKIMSMAFLLPDKDSAIMWRGPVkMGAVRQFIEDVQwGNLDYLVIDMPPGTGdeaLSIVQLIPKADGAIVVTTP 165
                                       45566666667777777766655554244568888888745789999999998763323333444578888888888 PP

                            AAA_31 150 eaya 153
                                       ++ a
  gi|474934033|ref|YP_007687615.1| 166 QDVA 169
                                       7766 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.1   7.9e-11   5.1e-08       3      38 ..      24      59 ..      22      84 .. 0.83
   2 ?    1.6   0.0       0.2   1.3e+02     114     144 ..     120     152 ..     114     193 .. 0.82
   3 ?   -1.2   0.0       1.4   8.7e+02      34      61 ..     245     272 ..     233     287 .. 0.63

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 7.9e-11
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                       ArsA_ATPase  3 vilvgGKGGVGKttvsaatavklsekgkkvllistD 38
                                      +i+++GKGGVGK+tvs+ +av ls++g+++ ++  D
  gi|474934033|ref|YP_007687615.1| 24 IIVISGKGGVGKSTVSSNLAVALSKEGYQTGIMDID 59
                                      799**************************9998887 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.2
                                       HHHHHHHHCSSSSEEEEESBS.CC.HTCGGGGH CS
                       ArsA_ATPase 114 eellkyvkeeeydvvvlDtaP.TG.htlrllsl 144
                                        ++++ v+  + d++v+D +P TG ++l +++l
  gi|474934033|ref|YP_007687615.1| 120 RQFIEDVQWGNLDYLVIDMPPgTGdEALSIVQL 152
                                       567777888999*******99777447777776 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.4
                                       EEE-STTTHHHHHHTS--BSS-EEETSS CS
                       ArsA_ATPase  34 listDPAhslsDsfdqklgkeptkvkeN 61 
                                       ++  DPA   + sf + ++k  + +++ 
  gi|474934033|ref|YP_007687615.1| 245 IVEADPASASAKSFREIVNKVIRTIENE 272
                                       5667777777777777666666666543 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.0   1.8e-10   1.1e-07       1     110 [.      22     142 ..      22     173 .. 0.66

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 1.8e-10
                                       EEEEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHH..HHHHHHHHHHT-.......-----EEE CS
                              MipZ   1 hvivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlaryl..enraataerkgl.......sLplpeal 68 
                                       hvi++   kGG Gkst++  +avaL+k+G + + +d+d+    + + +  e+ +  +e+ +l       sL++ ++ 
  gi|474934033|ref|YP_007687615.1|  22 HVIIVISGKGGVGKSTVSSNLAVALSKEGYQTGIMDIDITGPNIPKMFhvEDEKLLVENDKLipvmyppSLKIMSMA 98 
                                       899999*********************************99888776522444444555444232222233333333 PP

                                       -SSS-HHHHTTS-HHHHHHHHHHHHHHHH.HH-SEEEEE--.SS CS
                              MipZ  69 alseaeeaeveeeeeaevaeleelvadle.aeldfividtP.Gs 110
                                        l   + + +      ++ ++++ ++d++  +ld++vid P G+
  gi|474934033|ref|YP_007687615.1|  99 FLLPDKDSAIMWRGPVKMGAVRQFIEDVQwGNLDYLVIDMPpGT 142
                                       33333445555555566677778888776357899999986343 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   1.6e-06     0.001       3      30 ..      25      52 ..      23      74 .. 0.88
   2 !   11.6   0.0   0.00022      0.14     194     246 ..     215     267 ..     149     277 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.6e-06
                         Fer4_NifH  3 iaiyGkGGiGksttsqnlsaalaemgkk 30
                                      i i GkGG+Gkst s+nl+ al++ g +
  gi|474934033|ref|YP_007687615.1| 25 IVISGKGGVGKSTVSSNLAVALSKEGYQ 52
                                      8899*******************99965 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00022
                         Fer4_NifH 194 ekfaeelgtkvlevvPrdeivrkaelrkktvieyapeseqakeyrelarkile 246
                                       e+ a+++g++ l  vP++  v ++      ++e +p s  ak +re+ +k++ 
  gi|474934033|ref|YP_007687615.1| 215 EAAAKDMGVQFLGRVPMEAAVAESGDSGLPIVEADPASASAKSFREIVNKVIR 267
                                       567999********************************************975 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   2.6e-06    0.0017      31      69 ..      24      62 ..       7      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.6e-06
                                      EEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE---- CS
                              MeaB 31 vvGltGvPGaGkstlvealglelrrrGkrvavlavDPss 69
                                       + + G  G+Gkst+ ++l++ l ++G++ +++ +D + 
  gi|474934033|ref|YP_007687615.1| 24 IIVISGKGGVGKSTVSSNLAVALSKEGYQTGIMDIDITG 62
                                      56789******************************9765 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   0.00034      0.22       4      43 ..      25      65 ..      22      76 .. 0.75
   2 ?    3.9   0.0     0.049        31     103     148 ..     117     166 ..      90     181 .. 0.82
   3 ?   -1.9   0.0       2.9   1.9e+03     201     232 ..     233     264 ..     229     266 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00034
                          CBP_BcsQ  4 lalqGvRGGvGttsllaaLawalhelges..vlviDlspdnl 43
                                      ++++G +GGvG++++++ La al + g++  ++ iD++  n+
  gi|474934033|ref|YP_007687615.1| 25 IVISG-KGGVGKSTVSSNLAVALSKEGYQtgIMDIDITGPNI 65
                                      56666.8*****************999872245566666665 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.049
                          CBP_BcsQ 103 eallaalkelk.eqyrwillDlpagasalt...rellaladlvllvvepd 148
                                       +a+ ++++ ++ ++ +++++D+p g+ + +    +l+ +ad  + v++p+
  gi|474934033|ref|YP_007687615.1| 117 GAVRQFIEDVQwGNLDYLVIDMPPGTGDEAlsiVQLIPKADGAIVVTTPQ 166
                                       567778888888999*********7776551115677799******9996 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 2.9
                          CBP_BcsQ 201 ealaEalaakqPlgeyrpdslaaeevktLanw 232
                                       +a+aE+  + +P+ e  p s+ a+  + ++n 
  gi|474934033|ref|YP_007687615.1| 233 AAVAESGDSGLPIVEADPASASAKSFREIVNK 264
                                       68899999999999999999999988887765 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.3    0.0014      0.89       2      34 ..      23      55 ..      22      62 .. 0.92
   2 ?    6.5   0.0      0.01       6.6     132     194 ..     160     235 ..     145     238 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0014
                            AAA_26  2 tifvtgtdtgvGKTvvslgLvralkrkgvkvgy 34
                                       i+v++   gvGK++vs  L+ al+++g+++g 
  gi|474934033|ref|YP_007687615.1| 23 VIIVISGKGGVGKSTVSSNLAVALSKEGYQTGI 55
                                      58999999*******************999886 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.01
                            AAA_26 132 ilVargglgtinqllltiealrqknvrvlGvilNk....vrnpenvetlekksg.........ipvlGvvPylpdl 194
                                       i+V+++++ +i +   ++ ++ q++++v+G+i N     +++  +v +++k++g         ++ lG+vP+++ +
  gi|474934033|ref|YP_007687615.1| 160 IVVTTPQDVAILDSRKSVTFALQTHIPVIGIIENMsgfvCPHCGEVVNIFKSGGgeaaakdmgVQFLGRVPMEAAV 235
                                       667777777788888889999999********99866543444577777777766777777779*******98765 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.5   1.3e-05    0.0083       7      25 ..     197     215 ..     192     217 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.3e-05
                                       EE-TTT--EEEECC--SS- CS
                   Desulfoferrod_N   7 YkCevCGniVeVleaGgGe 25 
                                       + C +CG++V++ + GgGe
  gi|474934033|ref|YP_007687615.1| 197 FVCPHCGEVVNIFKSGGGE 215
                                       77****************7 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   1.4e-05    0.0088       8      40 ..      13      42 ..       7      55 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.4e-05
                                      HHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHH CS
                            NB-ARC  8 viekLlekdelqslvvalvGmgGvGKttlakqi 40
                                      + e+L+   +++ +++ ++G+gGvGK+t++++ 
  gi|474934033|ref|YP_007687615.1| 13 LRETLS---NIKHVIIVISGKGGVGKSTVSSNL 42
                                      455555...89999***************9886 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.1e-05     0.014      32      59 ..      21      49 ..       3      61 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.1e-05
                            AAA_25 32 agelallaGapgtGKttlaldlalava.t 59
                                      ++ ++++ G +g+GK+t+ ++la+a++ +
  gi|474934033|ref|YP_007687615.1| 21 KHVIIVISGKGGVGKSTVSSNLAVALSkE 49
                                      78899*******************99844 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2     2e-05     0.013      85     121 ..       8      44 ..       1      55 [. 0.77

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2e-05
                                       TTHTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  85 ktkegleelkellkdktsvlvGqSGvGKStLinallp 121
                                       +++++l+e  +++k+ ++v+ G+ GvGKSt+  +l+ 
  gi|474934033|ref|YP_007687615.1|   8 EEETKLRETLSNIKHVIIVISGKGGVGKSTVSSNLAV 44 
                                       4556667777778888999***********9888865 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.1e-05     0.014       1      25 [.      25      62 ..      25     137 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.1e-05
                            AAA_18  1 IlltGtpGvGKttlakeL....skrlgf..........g 25
                                      I+++G+ GvGK+t++ +L    sk+ g+          g
  gi|474934033|ref|YP_007687615.1| 25 IVISGKGGVGKSTVSSNLavalSKE-GYqtgimdiditG 62
                                      89****************5544444.3455444444442 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   2.5e-05     0.016       3      39 ..      23      59 ..      21      75 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.5e-05
                                      EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHH CS
                        APS_kinase  3 vvvwltGlsgsGKstianalekkLvekgisvylLdGd 39
                                      v++ ++G  g GKst++ +l+ +L ++g+++ ++d d
  gi|474934033|ref|YP_007687615.1| 23 VIIVISGKGGVGKSTVSSNLAVALSKEGYQTGIMDID 59
                                      7899**************************9999866 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00014      0.09       1      55 [.      25      79 ..      25     106 .. 0.82
   2 ?   -0.3   0.0       1.2   7.4e+02     193     210 ..     253     270 ..     246     277 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                                      EEEE-STTSSHHHHHHHHHHHHT-EEEEHHHHHHHHHHHHHHTT--TT-HHHHHH CS
                    Cytidylate_kin  1 iaiDGPagsGKssvaralaeklglkyldtgalYRalalaalrrkvdlldeaalve 55
                                      i i G  g GKs+v+  la  l+ +  +tg +   ++   + +   + de+ lve
  gi|474934033|ref|YP_007687615.1| 25 IVISGKGGVGKSTVSSNLAVALSKEGYQTGIMDIDITGPNIPKMFHVEDEKLLVE 79
                                      6789999************************987777777777666666666665 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.2
                                       TTTS-HHHHHHHHHHHHH CS
                    Cytidylate_kin 193 tskltieevvekilelik 210
                                       +s ++++e+v+k++++i+
  gi|474934033|ref|YP_007687615.1| 253 ASAKSFREIVNKVIRTIE 270
                                       455666666666666554 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   7.1e-05     0.046       1      35 [.      29      63 ..      29      66 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.1e-05
                            CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGqs 35
                                      G+  +GKST++ +L+  + ++g+++ ++D+D+  +
  gi|474934033|ref|YP_007687615.1| 29 GKGGVGKSTVSSNLAVALSKEGYQTGIMDIDITGP 63
                                      66789**************************9655 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   0.00011      0.07       2      30 ..      25      53 ..      24      64 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
                                      EEEE--TTSSHHHHHHHHHHHH...GGGE CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkv 30
                                      ++i+G+ GvGK+T+ ++++ +l+++g++ 
  gi|474934033|ref|YP_007687615.1| 25 IVISGKGGVGKSTVSSNLAVALSKEGYQT 53
                                      79***********************9985 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   7.8e-05      0.05       3      39 ..      24      60 ..      22      64 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.8e-05
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDt 39
                                      +i++ G  G+GK t  + La  l+keg+++ ++  D+
  gi|474934033|ref|YP_007687615.1| 24 IIVISGKGGVGKSTVSSNLAVALSKEGYQTGIMDIDI 60
                                      78999*************************9998886 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   5.4e-05     0.035      18      91 ..      20     279 ..      10     288 .] 0.91

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.4e-05
                        KAP_NTPase  18 atpivvgLygkWGsGKssllnkledelkefa.............................................. 48 
                                        + ++++++gk G+GKs++  +l  +l+++                                               
  gi|474934033|ref|YP_007687615.1|  20 IKHVIIVISGKGGVGKSTVSSNLAVALSKEGyqtgimdiditgpnipkmfhvedekllvendklipvmyppslkims 96 
                                       35789*************************99********************************************* PP

                        KAP_NTPase  49 ............................................................................. 48 
                                                                                                                    
  gi|474934033|ref|YP_007687615.1|  97 mafllpdkdsaimwrgpvkmgavrqfiedvqwgnldylvidmppgtgdealsivqlipkadgaivvttpqdvailds 173
                                       ***************************************************************************** PP

                        KAP_NTPase  49 .................................................................kpvrflfaefna 60 
                                                                                                            + ++e+++
  gi|474934033|ref|YP_007687615.1| 174 rksvtfalqthipvigiienmsgfvcphcgevvnifksgggeaaakdmgvqflgrvpmeaavaesGDSGLPIVEADP 250
                                       *************************************************************9999888999****** PP

                        KAP_NTPase  61 wsfkggddavaellaaLadaleeeygqlatk 91 
                                       +s++   ++++e+++  ++++e e   l+ +
  gi|474934033|ref|YP_007687615.1| 251 ASAS--AKSFREIVNKVIRTIENEQAYLEAQ 279
                                       *998..5999999999999999887666554 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   8.9e-05     0.057       3      39 ..      24      60 ..      23      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.9e-05
                                      EEEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THH CS
                             KTI12  3 LvvltGlPssGKstrakeLakaleeekrsvvviddes 39
                                      ++v++G   +GKst++++La al++e+++  ++d + 
  gi|474934033|ref|YP_007687615.1| 24 IIVISGKGGVGKSTVSSNLAVALSKEGYQTGIMDIDI 60
                                      599**************************99998665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00021      0.13      25      52 ..      23      50 ..       8      62 .. 0.77
   2 ?   -1.2   0.0       3.5   2.2e+03     107     133 ..     244     272 ..     207     277 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00021
                            AAA_16 25 elvllsGesGvGKsslvrellralekdg 52
                                       ++++sG  GvGKs++   l+ al+k+g
  gi|474934033|ref|YP_007687615.1| 23 VIIVISGKGGVGKSTVSSNLAVALSKEG 50
                                      699**************99999998884 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.5
                            AAA_16 107 avpelagaea..srllellkrllallsrd 133
                                       ++ e+++a+a  ++++e +++ ++ ++++
  gi|474934033|ref|YP_007687615.1| 244 PIVEADPASAsaKSFREIVNKVIRTIENE 272
                                       33444444444688999888888887774 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00023      0.15       1      26 [.      25      50 ..      25      75 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00023
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkkl 26
                                      i+++G+ g+GKSt++ +La al+k+ 
  gi|474934033|ref|YP_007687615.1| 25 IVISGKGGVGKSTVSSNLAVALSKEG 50
                                      789******************99764 PP

>> zf-ZPR1  ZPR1 zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00017      0.11      10      94 ..     175     257 ..     172     288 .] 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00017
                           zf-ZPR1  10 ngetrllltkiPyfkeviims.feCehCgyknnevksageieekGkritlkveseedlnrqvlkSetatveipelel 85 
                                       +++t  l+t+iP ++ +  ms f+C+hCg   n +ks+g   + +k + ++   +  ++  v  S  + + i e + 
  gi|474934033|ref|YP_007687615.1| 175 KSVTFALQTHIPVIGIIENMSgFVCPHCGEVVNIFKSGGGEAA-AKDMGVQFLGRVPMEAAVAESGDSGLPIVEADP 250
                                       56788999********9988879**********9999998665.888888888888899999998888888888774 PP

                           zf-ZPR1  86 eippgtleg 94 
                                          +   ++
  gi|474934033|ref|YP_007687615.1| 251 ASAS--AKS 257
                                       4433..444 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00027      0.18      37      70 ..      14      47 ..       3      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00027
                             Rad17 37 advLesrkkriLLisGPsGCgkstvvkvLskelg 70
                                       ++L + k+ i++isG  G gkstv   L+  l+
  gi|474934033|ref|YP_007687615.1| 14 RETLSNIKHVIIVISGKGGVGKSTVSSNLAVALS 47
                                      5789999******************998886655 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00031       0.2      10      42 ..      16      48 ..       8      60 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00031
                        Zeta_toxin 10 ypsqerPklillgGqpGAGKselaellkdeler 42
                                      + s+ + ++i+++G  G GKs++++ l+ +l +
  gi|474934033|ref|YP_007687615.1| 16 TLSNIKHVIIVISGKGGVGKSTVSSNLAVALSK 48
                                      45677889******************9999864 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00029      0.19      29      68 ..      16      57 ..       3      61 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00029
                             AAA_7 29 llknkkpvllv..GptGtGKtviikdllkkldkekylsltin 68
                                       l+n k+v++v  G+ G+GK+++ ++l  +l+ke y++ ++ 
  gi|474934033|ref|YP_007687615.1| 16 TLSNIKHVIIVisGKGGVGKSTVSSNLAVALSKEGYQTGIMD 57
                                      4445555543334***********************987765 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00065      0.41      17      26 ..     195     204 ..     194     212 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00065
                     Zn_Tnp_IS1595  17 ngfvCPhCgs 26 
                                       +gfvCPhCg 
  gi|474934033|ref|YP_007687615.1| 195 SGFVCPHCGE 204
                                       58******95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       764  (0.0426125); expected 358.6 (0.02)
Passed bias filter:                      673  (0.037537); expected 358.6 (0.02)
Passed Vit filter:                       137  (0.00764125); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 1717.44
//
Query:       gi|474934034|ref|YP_007687616.1|  [L=143]
Description: Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    0.00019   21.6   0.0       0.18   12.0   0.0    2.1  2  Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygena


Domain annotation for each model (and alignments):
>> Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0   0.00019       3.5       5      32 ..      25      52 ..      23      75 .. 0.82
   2 !   12.0   0.0     1e-05      0.18      82     125 ..      80     121 ..      76     124 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00019
                                      EEEEESHHHHHHHHHHHHHTSEEEEEEE CS
                        Glyoxalase  5 vallvgdleksldFYtkvLGfklvkktd 32
                                      ++++++d+ +++ FY++ L +k++   +
  gi|474934034|ref|YP_007687616.1| 25 CSVPTPDPLRAVGFYRDTLMMKVLYSGP 52
                                      56899**************999987665 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 1e-05
                                       EEHCHHHHHHHHHHHTTGEEEEEEECHHCTEEEEEEEEETTSEE CS
                        Glyoxalase  82 ldvedvgkaldrlkeagvkvvaepgrhyfgalysfyfrDpdGil 125
                                         v+d +++++r+ ++gv++ + p r ++g   s  f+D dG+ 
  gi|474934034|ref|YP_007687616.1|  80 IGVDDPYDFHRRMIDEGVRFKMDPRRLPMGVATS--FFDCDGNI 121
                                       5689**************************9998..99999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       181  (0.0100954); expected 358.6 (0.02)
Passed bias filter:                      174  (0.00970495); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.50
# Mc/sec: 855.52
//
Query:       gi|474934035|ref|YP_007687617.1|  [L=191]
Description: Multimeric flavodoxin WrbA [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.3e-24   84.5   0.0    7.9e-24   84.2   0.0    1.1  1  FMN_red       NADPH-dependent FMN reductase
    5.3e-08   32.8   0.0    7.5e-08   32.3   0.0    1.2  1  Flavodoxin_2  Flavodoxin-like fold
  ------ inclusion threshold ------
      0.018   14.8   0.0      0.031   14.0   0.0    1.3  1  DUF2284       Predicted metal-binding protein (DUF2284)


Domain annotation for each model (and alignments):
>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.2   0.0   1.3e-27   7.9e-24       1     145 [.       1     151 [.       1     159 [. 0.88

  Alignments for each domain:
  == domain 1  score: 84.2 bits;  conditional E-value: 1.3e-27
                                       -EEEEEES--STT-HHHHHHHHHHCCT-T.T-CEEEEETTTS..--...---HCHGHT.......CGGSHHHHHHHH CS
                           FMN_red   1 mkilvisGSlrkgsntrklaewaaealkeagaevelidladl.ilpc.alcdkdlese.......gqtsddvaelle 68 
                                       mk++++ GS+++ +nt  ++  +a++l+++g+e+e+i+l  +    c +  ++    e         + d ++++l+
  gi|474934035|ref|YP_007687617.1|   1 MKVILLDGSAKPIGNTSNILADFADELEREGIETEHIQLYAYdFTSCnDCRTC----EvrgdgrcIDEADGFNDILD 73 
                                       9*****************************************77776633333....334457767888899***** PP

                                       HHHH-SCEEEEEEECTTCE-HHHHHHHHCHT-...SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHHHTT-EEE CS
                           FMN_red  69 kiaaadaliivtPeYngsysgllKnalDrlsr..trgkkelrgKpvalvavgggrrgglraeeqlrqvlaelgaivv 143
                                        +++ad++++++P Y gs+sg + ++l+r+    ++g++ lrgK++a++av+   +g++ +  ql  ++   +++vv
  gi|474934035|ref|YP_007687617.1|  74 VMREADGIVLASPGYAGSASGRMRTFLERAALvlEKGDRGLRGKVGAAIAVS-EHDGAESTYMQLVWWMLKSEMHVV 149
                                       ******************************98*****************999.558888888888888889999999 PP

                                       EC CS
                           FMN_red 144 pr 145
                                       ++
  gi|474934035|ref|YP_007687617.1| 150 GT 151
                                       87 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.0   1.3e-11   7.5e-08       1     193 [.       1     175 [.       1     183 [. 0.71

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 1.3e-11
                                       -EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCC.T-----CCCCHCC.HHHHTT.C.HHHHHHH.H CS
                      Flavodoxin_2   1 mkiLiinahprpeksfssalaqafvealekagphevtvrdLyad.flpvlttrdlaak.layeek.p.adveseq.i 72 
                                       mk+ +++++ +p   ++s++++ f+++le +g  e + + Lya  f    +  + +++ + + +    ad   +  +
  gi|474934035|ref|YP_007687617.1|   1 MKVILLDGSAKP-IGNTSNILADFADELEREG-IETEHIQLYAYdFTSCND--CRTCEvRGDGRCiDeAD-GFNDiL 72 
                                       9***********.5999***************.9*********74422222..22222333322122133.345558 PP

                                       HHHHCSSEEEEEEE-BTTB--HHHHHHHHHHS-TTTSCEETTCSSCCCCTTTTSEEEEEEEESS-GGGSSTTSSS-S CS
                      Flavodoxin_2  73 ekllaadaivlqfPlwwfgvPailKgwiDrvltagfafyteeggegrgggLkgkkalvivttGgpeesyqerglega 149
                                       + +++ad ivl++P +  + +  +  +++r +        e    ++++gL+gk    i+ +  +       g e  
  gi|474934035|ref|YP_007687617.1|  73 DVMREADGIVLASPGYAGSASGRMRTFLERAA---LVL--E----KGDRGLRGKVGAAIAVSEHD-------GAEST 133
                                       99****************************62...233..2....34799****55555555444.......23445 PP

                                       -HHHHHHHHHHHHHHTT-EEEEEEEEESCTCCCHHHHHHHHHHH CS
                      Flavodoxin_2 150 amdellpplrgilgfiGikdvepvlvegvagaedeealaealer 193
                                        m+ +++ l++ ++ +G  + +++++ g    ed+ +  + l+r
  gi|474934035|ref|YP_007687617.1| 134 YMQLVWWMLKSEMHVVGTCPMPIFHALGQY--EDDTKAMKGLKR 175
                                       78888888*****************99954..332223333333 PP

>> DUF2284  Predicted metal-binding protein (DUF2284)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   5.1e-06     0.031      73     120 ..      16      63 ..       7      81 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.1e-06
                           DUF2284  73 vkeelekillelekeafeagypkalalsagsCtlCetCayeegepCrh 120
                                       +++ l + + ele+e +e+++ + +a+  +sC+ C+tC++  +  C  
  gi|474934035|ref|YP_007687617.1|  16 TSNILADFADELEREGIETEHIQLYAYDFTSCNDCRTCEVRGDGRCID 63 
                                       5666788899*******************************9999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1339.45
//
Query:       gi|474934036|ref|YP_007687618.1|  [L=350]
Description: ABC-type Fe3+-hydroxamate transport system, periplasmic component [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.9e-24   84.4   0.2    1.4e-23   83.7   0.2    1.3  1  Peripla_BP_2  Periplasmic binding protein
  ------ inclusion threshold ------
        0.1   12.0   0.0        1.8    7.9   0.0    2.2  2  AroM          AroM protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.7   0.2   1.6e-27   1.4e-23       1     236 [.      49     298 ..      49     300 .. 0.87

  Alignments for each domain:
  == domain 1  score: 83.7 bits;  conditional E-value: 1.6e-27
                                       EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT............TS-BSBESSSB-H......HHHHHH--S CS
                      Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadklee..........aivevgadgeidv......EklaalkPD 61 
                                       ias++   te++  lG+  ++vg  +++        +             ++++++++ + +      E++aa  PD
  gi|474934036|ref|YP_007687618.1|  49 IASTTAVGTEVVCDLGLRANIVGATNSAHIYDMTTHVSGvalefdypstMKADIDSGKIAKFkwnwssETVAATNPD 125
                                       89999999999999999999999999887666666555555666666663344444444444779999********* PP

                                       EEEE-GGG.....GGGHHHHHHHS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT. CS
                      Peripla_BP_2  62 lvilskgl..gltdedeellksgiptvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidsek 136
                                       lv+l+++    + +++++l+++gi +++    n  e++ ++ ++lg++l++ d+a+++v+  +++ a+++++ + + 
  gi|474934036|ref|YP_007687618.1| 126 LVLLDPSSvaTDDSKMKQLQALGITCFVLWDENNWEDIGKNYKVLGKVLDKYDRAKEIVKAGEKADAKIMEKFKDQP 202
                                       *********9***************9887665555*****************************************8 PP

                                       -EEEEEEEETTE..EEEE-TTSTTTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEH.HHHT-S--HH CS
                      Peripla_BP_2 137 pkpvlvfggadeggyvvagsnsyigdlldalgieniaaeskkseyeeisaEqilasdpdvifvsgr.aeadnktgle 212
                                        k+++++ + ++  +++++++s+  d +  lg  n+ a+   +  ++i aEqil+++pd i+++++  + d +++ +
  gi|474934036|ref|YP_007687618.1| 203 SKKIAYVCYCYG--TYYIYDSSGLMDAALKLGCTNAMAS---DKTSTITAEQILSANPDFIIFDDMgTSLDWNAVIA 274
                                       889999987777..8888888888888888******777...5899********************99********* PP

                                       HHT-SHHHHTSHHHHTT-EEEE-H CS
                      Peripla_BP_2 213 flkenpllaelpAvkngrVyalds 236
                                       + k++p+ +++pA++n+++y++ +
  gi|474934036|ref|YP_007687618.1| 275 EWKADPVMNSIPAIANNKFYCMEA 298
                                       *********************976 PP

>> AroM  AroM protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.019   1.7e+02     141     173 ..     157     191 ..     151     196 .. 0.88
   2 ?    7.9   0.0    0.0002       1.8     157     211 ..     235     289 ..     224     291 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.019
                              AroM 141 ekkweelak..evvvavaspygseeelaeaarela 173
                                       e++we+++k  +v  +v + y++++e+ +a+++  
  gi|474934036|ref|YP_007687618.1| 157 ENNWEDIGKnyKVLGKVLDKYDRAKEIVKAGEKAD 191
                                       689****997788899***************9876 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0002
                              AroM 157 spygseeelaeaarelaeqgadlivldciGYteemkaavaealgkpVllarslva 211
                                       + ++s++  + +a+++ +++ d+i+ d +G +    a++ae    pV+++   +a
  gi|474934036|ref|YP_007687618.1| 235 NAMASDKTSTITAEQILSANPDFIIFDDMGTSLDWNAVIAEWKADPVMNSIPAIA 289
                                       566666777778999999*****************************99987776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2372.14
//
Query:       gi|474934037|ref|YP_007687619.1|  [L=361]
Description: ABC-type Fe3+-siderophore transport system, permease component [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-82  274.9  31.7    9.1e-82  274.5  31.7    1.1  1  FecCD     FecCD transport family
    3.2e-08   33.4  22.3    3.2e-08   33.4  22.3    2.3  2  ABC-3     ABC 3 transport family


Domain annotation for each model (and alignments):
>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  274.5  31.7     1e-85   9.1e-82       2     312 .]      37     354 ..      36     354 .. 0.97

  Alignments for each domain:
  == domain 1  score: 274.5 bits;  conditional E-value: 1e-85
                             FecCD   2 lllllllslllgavkispsevfeallgka......dsleaeivlelrlprvlaallvGaaLavaGallQtvtrNpLa 72 
                                       +++l ++sl++ga++i + e f+ + +        ++ + ++++ lr+pr +a+llvG++LavaGa++Q++++NpL+
  gi|474934037|ref|YP_007687619.1|  37 IVVLYIFSLTMGAYHIGFFEAFDQMKEVItswgkpEDVSGKVIYHLRMPRSIAVLLVGGGLAVAGAVMQALIHNPLV 113
                                       68999******************977655888888788888************************************ PP

                             FecCD  73 dPsilGissgaalgavlallll....lgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsalls 145
                                       dP++ G+ssga++g+v+++l +     + ++++ +p+ a++ga+ a+ll++ +a + +g + ++ +L G ++++ ls
  gi|474934037|ref|YP_007687619.1| 114 DPYVTGVSSGASFGVVVMTLGGaitvGSLATMWLIPVGAIIGAVGAFLLTMSVA-EAAGGKAMSYVLGGTIMASGLS 189
                                       *****************999889998899999**********************.9999****************** PP

                             FecCD 146 altsllllllneealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrl 222
                                       a t+l++++ n+++++ i+ w++Gs+s+++w++v+++ + ++++++++++ ar+l+++ lg+++A+ lG+n ++++ 
  gi|474934037|ref|YP_007687619.1| 190 AGTTLIMYY-NADKIQHITAWMFGSFSSIQWDDVYVMTIPIVAIIAFIIYQARNLNVMLLGETQAQYLGMNARTYKR 265
                                       *********.******************************************************************* PP

                             FecCD 223 lllllvalltavavalvGpigFvGLivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivta 299
                                        +l+l+a+lta +va++G+igF+GLi+Ph++r++vg dhr l+p s+++G+l+ll+ad++++  +   elp+g++++
  gi|474934037|ref|YP_007687619.1| 266 NMLILTAILTAFCVAYCGVIGFLGLIIPHLCRMVVGGDHRVLIPTSVVVGGLVLLVADIVCKSNT-GGELPIGAIIS 341
                                       **************************************************************996.8********** PP

                             FecCD 300 liGapffiylllr 312
                                       +iG+pffi+l+++
  gi|474934037|ref|YP_007687619.1| 342 VIGVPFFIFLMVK 354
                                       ***********97 PP

>> ABC-3  ABC 3 transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   1.4      0.13   1.2e+03     179     229 ..      27      77 ..      22     105 .. 0.62
   2 !   33.4  22.3   3.6e-12   3.2e-08      63     256 ..     154     353 ..     118     355 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.13
                             ABC-3 179 avvvalqavGviLvialliiPaatArrltrslesllivAillglvsvvaGl 229
                                       +v v+l +vG++++     + +a  + + + ++++  v +  g    v+G 
  gi|474934037|ref|YP_007687619.1|  27 TVIVVLGIVGIVVLYIFSLTMGAYHIGFFEAFDQMKEVITSWGKPEDVSGK 77 
                                       677777777777666666666666666666666666655555555555555 PP

  == domain 2  score: 33.4 bits;  conditional E-value: 3.6e-12
                             ABC-3  63 vgliaavalel.lkrkt..klkedtaigivlsvflalglvlvslikk.skvdldsyLfGniltisqedliliaiiea 135
                                       +g ++a+ l++ +++++  k  + ++ g +++++l+ g  l+ + +    +++++++fG+  +i+ +d+++++i  +
  gi|474934037|ref|YP_007687619.1| 154 IGAVGAFLLTMsVAEAAggKAMSYVLGGTIMASGLSAGTTLIMYYNAdKIQHITAWMFGSFSSIQWDDVYVMTIPIV 230
                                       33333333322133332225556677799*********9999988876889************************** PP

                             ABC-3 136 vvllllllfwkelllitfdeelAkveglsvkllkllllalialavvvalqavGviLvialliiPaatArrltrsles 212
                                        +++ ++++ ++l ++ + e++A+  g++ +++k  +l+l+a+  +  +   Gvi     liiP    + ++ + + 
  gi|474934037|ref|YP_007687619.1| 231 AIIAFIIYQARNLNVMLLGETQAQYLGMNARTYKRNMLILTAILTAFCVAYCGVIGFLG-LIIPHLCRMVVGGDHRV 306
                                       *******************************************************9888.589************** PP

                             ABC-3 213 llivAillglvsvvaGlll..Syyld.latGavivlvatllfllall 256
                                       l+ +++++g + +++  ++  S +   l+ Ga+i ++ + +f++ ++
  gi|474934037|ref|YP_007687619.1| 307 LIPTSVVVGGLVLLVADIVckSNTGGeLPIGAIISVIGVPFFIFLMV 353
                                       ********998887776651233333599999999999999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       900  (0.050198); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 2224.93
//
Query:       gi|474934038|ref|YP_007687620.1|  [L=260]
Description: ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase component [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.4e-28   98.5   0.0      7e-28   97.8   0.0    1.3  1  ABC_tran      ABC transporter
      5e-08   33.1   0.0      0.002   18.0   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    1.1e-05   25.0   0.3     0.0062   16.0   0.1    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
      3e-05   23.9   0.0    0.00062   19.6   0.0    1.9  2  AAA_15        AAA ATPase domain
    7.9e-05   23.2   0.1    0.00012   22.6   0.1    1.2  1  AAA_23        AAA domain
    0.00012   22.4   0.1    0.00045   20.5   0.1    1.8  1  AAA_22        AAA domain
    0.00064   19.4   0.0     0.0014   18.4   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
    0.00083   19.3   0.0     0.0016   18.4   0.0    1.5  1  RsgA_GTPase   RsgA GTPase
     0.0024   17.6   0.2      0.015   15.1   0.2    2.1  1  AAA_30        AAA domain
     0.0045   17.4   0.0     0.0074   16.7   0.0    1.4  1  AAA_16        AAA ATPase domain
     0.0098   16.2   0.2      0.024   15.0   0.2    1.6  1  AAA_19        AAA domain
  ------ inclusion threshold ------
      0.011   15.7   0.1       0.03   14.2   0.1    1.7  1  NACHT         NACHT domain
      0.021   14.0   0.0      0.033   13.4   0.0    1.2  1  NB-ARC        NB-ARC domain
      0.031   11.8   0.0      0.042   11.4   0.0    1.1  1  DUF3584       Protein of unknown function (DUF3584)
      0.035   13.8   0.0      0.048   13.4   0.0    1.2  1  PRK           Phosphoribulokinase / Uridine kinase family
      0.039   13.2   0.0      0.057   12.7   0.0    1.2  1  Zeta_toxin    Zeta toxin
       0.05   13.6   0.0       0.11   12.5   0.0    1.5  1  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
      0.075   12.8   0.1       0.17   11.6   0.1    1.5  1  CobS_N        Cobaltochelatase CobS subunit N terminal
      0.076   13.6   0.1       0.38   11.3   0.0    2.0  2  AAA_18        AAA domain
      0.086   12.4   0.0       0.44   10.1   0.0    2.0  2  AAA_25        AAA domain
      0.094   12.3   0.0       0.16   11.5   0.0    1.3  1  AAA_27        AAA domain
       0.11   11.1   0.0       0.15   10.7   0.0    1.1  1  AAA_13        AAA domain
       0.12   12.6   0.0       0.17   12.0   0.0    1.4  1  AAA_33        AAA domain
       0.13   12.0   0.0        0.2   11.3   0.0    1.3  1  AAA_24        AAA domain
       0.14   11.6   0.0       0.27   10.6   0.0    1.4  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
       0.16   11.2   0.0       0.27   10.4   0.0    1.3  1  NTPase_P4     ATPase P4 of dsRNA bacteriophage phi-12


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.8   0.0     1e-30     7e-28       1     137 []      11     160 ..      11     160 .. 0.96

  Alignments for each domain:
  == domain 1  score: 97.8 bits;  conditional E-value: 1e-30
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l+++++++++ge va++G+nG+GK+tL++++ + lk  +Geil+d++++k+ ++e+  +   ++p +++l+  ltvr
  gi|474934038|ref|YP_007687620.1|  11 LEDITFDISPGEFVAVMGQNGSGKTTLMRCINKILKIRSGEILVDDNSVKTMTMEEIARLCTTVPADTSLDFSLTVR 87 
                                       689************************************************************************** PP

                                       HH.................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xx.................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       +                  e+++ i++al  +g+++ + +++    ++LS G++ rv la+ +++ pkl+l+DEp+a
  gi|474934038|ref|YP_007687620.1|  88 DFvslgrspflksvwwedaEDERIIDQALWDFGITQYAGRRL----HELSSGERARVLLAKGVVQTPKLMLVDEPSA 160
                                       ***************887666666******************....*****************************75 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.9e-06     0.002       2     109 ..      24     108 ..      23     116 .. 0.62
   2 !   13.8   0.0   5.5e-05     0.038     220     302 ..     115     194 ..     104     195 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.9e-06
                            AAA_21   2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrl 78 
                                        ++ G NgsGK++L++++             ++ + ++g+i +++++  +   e+ +++ ++  +  ++  +++l++
  gi|474934038|ref|YP_007687620.1|  24 VAVMGQNGSGKTTLMRCIN------------KILKIRSGEILVDDNSVKTMTMEEIARLCTT--VPADTSLDFSLTV 86 
                                       6788**************3............3344444444444444444444444444444..7777777777777 PP

                            AAA_21  79 ersqveeklssvetllesgllldkrsleeed 109
                                        ++           l++s++l+  ++++ ed
  gi|474934038|ref|YP_007687620.1|  87 RDFVS---------LGRSPFLKSVWWEDAED 108
                                       77777.........66666666666665555 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 5.5e-05
                            AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltT 296
                                        ++ +  +++  + ++elS+G +    l+  + +++   +l l+DEp ++L+ k    ++ell+ l+++g  ++++ 
  gi|474934038|ref|YP_007687620.1| 115 ALWDFGITQYAGRRLHELSSGERARVLLAKGVVQTP---KLMLVDEPSAHLDIKYKVQVMELLRMLADKGMAILMAN 188
                                       66666777778889999*****99989999999888...9***************************9999999999 PP

                            AAA_21 297 HSplll 302
                                       H+  ll
  gi|474934038|ref|YP_007687620.1| 189 HDINLL 194
                                       987765 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1     9e-06    0.0062      21      52 ..      17      49 ..       7      60 .. 0.77
   2 !    6.8   0.0     0.006       4.1     136     190 ..     131     181 ..      99     202 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 9e-06
                                      ETTS.SEEEEEESTTSSHHHHHHHHHHHCTT.T CS
                                      xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 21 pfsk.sftaivGpNGSGKsnlldAilFvLGers 52
                                      ++s+ +f a++G+NGSGK+ l+  i  +L  rs
  gi|474934038|ref|YP_007687620.1| 17 DISPgEFVAVMGQNGSGKTTLMRCINKILKIRS 49
                                      44442599**************99987776655 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.006
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskna 190
                                       +LS Ge++     +l+A   v+   l+l+De  a+LD k+  +v ell+   ++ 
  gi|474934038|ref|YP_007687620.1| 131 ELSSGERA----RVLLAKGVVQTPKLMLVDEPSAHLDIKYKVQVMELLRMLADKG 181
                                       56777765....45677777888889**********************9877664 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   8.9e-07   0.00062      14      83 ..      11      88 ..       9     119 .. 0.76
   2 ?    2.5   0.0      0.14        97     322     355 ..     148     181 ..     119     194 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 8.9e-07
                            AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekkn..........kkvikiekedleifeniseskdikIdv 81
                                      l+d++ d+s+  +  + G N+sGK+++++ ++++l+     +          k  + +e   l ++   ++s d+ ++v
  gi|474934038|ref|YP_007687620.1| 11 LEDITFDISPGeFVAVMGQNGSGKTTLMRCINKILKIR---SgeilvddnsvKTMTMEEIARLCTTVPADTSLDFSLTV 86
                                      56777777777899**********************77...23357777777666777777788888888888888887 PP

                            AAA_15 82 ef 83
                                        
  gi|474934038|ref|YP_007687620.1| 87 RD 88
                                      66 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.14
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandn 355
                                       +++++ l++EP ahL ++ + ++++ll+ la+++
  gi|474934038|ref|YP_007687620.1| 148 QTPKLMLVDEPSAHLDIKYKVQVMELLRMLADKG 181
                                       678899**********************999987 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.1   1.8e-07   0.00012      11      40 ..      12      42 ..       4      59 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.8e-07
                            AAA_23 11 rdqeidFskg.ltlItGpNGaGKTTildAik 40
                                      +d ++d s+g ++++ G+NG+GKTT++++i 
  gi|474934038|ref|YP_007687620.1| 12 EDITFDISPGeFVAVMGQNGSGKTTLMRCIN 42
                                      55667778853789****************7 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   6.5e-07   0.00045       6     124 ..      22     183 ..      18     198 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 6.5e-07
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee.........erpevv....fvtlpsst.sskdllrellralglel 68 
                                        +++v+G+ G+GKTtl+r + + l++++                  +    + + +++  +s d+   +  ++ l++
  gi|474934038|ref|YP_007687620.1|  22 EFVAVMGQNGSGKTTLMRCINKILKIRSGEILvddnsvktmT----MeeiaRLCTTVPAdTSLDFSLTVRDFVSLGR 94 
                                       6899********************877665558886665552....0333444444444457888778877777777 PP

                            AAA_22  69 ka............................erlsseell.ealeqalrarav...ielliiDEaqh.lr...seeal 109
                                       +                             ++ +++el     ++ l a++v   ++l+++DE    l+   + +++
  gi|474934038|ref|YP_007687620.1|  95 SPflksvwwedaederiidqalwdfgitqyAGRRLHELSsGERARVLLAKGVvqtPKLMLVDEPSAhLDikyKVQVM 171
                                       779999999999999999999999999999677777777666666666666668888*****965558775558888 PP

                            AAA_22 110 eeLrsllnlsrkgvq 124
                                       e Lr+l++   kg++
  gi|474934038|ref|YP_007687620.1| 172 ELLRMLAD---KGMA 183
                                       88888888...4444 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0     2e-06    0.0014      16      46 ..      15      45 ..       9      49 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2e-06
                            AAA_29 16 tieidlkgatlltGpsGsGKSTllDAiqalL 46
                                      t++i++ +++ ++G++GsGK+Tl+  i+ +L
  gi|474934038|ref|YP_007687620.1| 15 TFDISPGEFVAVMGQNGSGKTTLMRCINKIL 45
                                      78899888***************97777665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   2.3e-06    0.0016      85     136 ..       6      58 ..       1      78 [. 0.82

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.3e-06
                                       TTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S-------- CS
                       RsgA_GTPase  85 ktkegleelkellkd.ktsvlvGqSGvGKStLinallpelelktgevseklgr 136
                                        +k++le+++  ++  ++++++Gq G GK+tL+  ++  l+++ ge+  ++++
  gi|474934038|ref|YP_007687620.1|   6 AKKNNLEDITFDISPgEFVAVMGQNGSGKTTLMRCINKILKIRSGEILVDDNS 58 
                                       4678999***999988***********************9***9999876655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.2   2.1e-05     0.015      18      50 ..      21      53 ..      15     190 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.1e-05
                            AAA_30 18 drvavltGpAGtGKttalkalreaweaaggrvi 50
                                        ++++ G  G+GKtt+++ ++++++ + g+++
  gi|474934038|ref|YP_007687620.1| 21 GEFVAVMGQNGSGKTTLMRCINKILKIRSGEIL 53
                                      568899******************998854443 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.1e-05    0.0074      24      51 ..      20      48 ..       9     116 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.1e-05
                            AAA_16 24 p.elvllsGesGvGKsslvrellralekd 51
                                      p e v + G+ G+GK++l+r++ + l+ +
  gi|474934038|ref|YP_007687620.1| 20 PgEFVAVMGQNGSGKTTLMRCINKILKIR 48
                                      3489******************9987765 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   3.5e-05     0.024       8     132 ..      19     184 ..      12     192 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.5e-05
                            AAA_19   8 lkekvllvtaGpGtGKTrvlkhivallvelggv.kpeeillvaftgrAakelrerlaalgaeatTiHrlal...... 77 
                                       ++ + ++v++  G+GKT+++++i ++l+ + g+  +++  + ++t     +l       +++a+T   ++l      
  gi|474934038|ref|YP_007687620.1|  19 SPGEFVAVMGQNGSGKTTLMRCINKILKIRSGEiLVDDNSVKTMTMEEIARLC-----TTVPADTSLDFSLtvrdfv 90 
                                       5678999****************999976654404455555555544444444.....3457777776666667777 PP

                            AAA_19  78 .......................................ldfddlltealelleeaeeekklqeeellivDEfq... 112
                                                                               ++ + +  a  ll     +  +q  +l++vDE +   
  gi|474934038|ref|YP_007687620.1|  91 slgrspflksvwwedaederiidqalwdfgitqyagrrlHELSSGE-RARVLL----AKGVVQTPKLMLVDEPSahl 162
                                       7777777777777777777777777777666555554432222222.222222....24455556688888876444 PP

                            AAA_19 113 dvd..elqyrLlkallgekkkl 132
                                       d++   + ++Ll+ l+++++ +
  gi|474934038|ref|YP_007687620.1| 163 DIKykVQVMELLRMLADKGMAI 184
                                       4554334457777777666544 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   4.4e-05      0.03       3      24 ..      24      45 ..      22      53 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.4e-05
                                      EEEEC-TTTCHHHHHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqklalaw 24
                                      v++ G++GsGKTtL++ +   +
  gi|474934038|ref|YP_007687620.1| 24 VAVMGQNGSGKTTLMRCINKIL 45
                                      899************9886655 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.8e-05     0.033      21      43 ..      22      44 ..       8      52 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.8e-05
                                      EEEEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC 21 lvvalvGmgGvGKttlakqilnk 43
                                       +va++G  G+GKttl++ i++ 
  gi|474934038|ref|YP_007687620.1| 22 EFVAVMGQNGSGKTTLMRCINKI 44
                                      589***************99875 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0     6e-05     0.042      17      37 ..      21      41 ..      14      42 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6e-05
                           DUF3584 17 dghtnieGtNaaGKTtLlrLi 37
                                       + + + G N++GKTtL+r i
  gi|474934038|ref|YP_007687620.1| 21 GEFVAVMGQNGSGKTTLMRCI 41
                                      566899*************86 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     7e-05     0.048       2      27 ..      24      49 ..      23      90 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7e-05
                               PRK  2 IgvagsSGaGkttvarklekifgrek 27
                                      ++v g+ G+Gktt++r ++ki++  +
  gi|474934038|ref|YP_007687620.1| 24 VAVMGQNGSGKTTLMRCINKILKIRS 49
                                      79********************9443 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   8.3e-05     0.057      19      57 ..      24      62 ..      11      90 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.3e-05
                        Zeta_toxin 19 illgGqpGAGKselaellkdelerqgnvvrldpDdlRel 57
                                      + + Gq G+GK++l++ +++ l+ +++ + +d  +++++
  gi|474934038|ref|YP_007687620.1| 24 VAVMGQNGSGKTTLMRCINKILKIRSGEILVDDNSVKTM 62
                                      5678*****************998888888888888876 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00016      0.11      14      46 ..      18      48 ..       5      54 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00016
                                      HHHCHTEEEEEEESTTSSHHHHHHHHHHHTT-- CS
                              TsaE 14 lakalgdvilLeGdLGaGKTtlvrglakalgve 46
                                      +    g++++  G+ G+GKTtl+r + k l+++
  gi|474934038|ref|YP_007687620.1| 18 ISP--GEFVAVMGQNGSGKTTLMRCINKILKIR 48
                                      333..7889*****************9999875 PP

>> CobS_N  Cobaltochelatase CobS subunit N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00024      0.17      12      22 ..     224     234 ..     221     235 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00024
                            CobS_N  12 vRevFGIDsDm 22 
                                        R+vFGI++Dm
  gi|474934038|ref|YP_007687620.1| 224 IRKVFGIEVDM 234
                                       7********** PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00056      0.38       1      38 [.      24      59 ..      24      89 .. 0.77
   2 ?   -0.1   0.0       1.8   1.2e+03      55      93 ..     179     225 ..     122     237 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00056
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakengll 38
                                      ++++G  G+GKttl + ++k l   +++++++ +++++
  gi|474934038|ref|YP_007687620.1| 24 VAVMGQNGSGKTTLMRCINKIL--KIRSGEILVDDNSV 59
                                      6899**************9999..55555544444444 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.8
                            AAA_18  55 dkldklldaleenss........aleegknlvidghlaeleseaakd 93 
                                       dk +++l a++ ++          l ++++++ dg + e + e++++
  gi|474934038|ref|YP_007687620.1| 179 DKGMAILMANHDINLltrfcdriLLLHEGHIIGDGTPREVINEENIR 225
                                       22222222222222245555555455555556666666666666655 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00063      0.44      31      50 ..      19      38 ..       6      65 .. 0.88
   2 ?    0.1   0.0      0.74   5.1e+02      73     107 ..     100     144 ..      72     193 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00063
                            AAA_25 31 pagelallaGapgtGKttla 50
                                        ge+++++G+ g+GKttl 
  gi|474934038|ref|YP_007687620.1| 19 SPGEFVAVMGQNGSGKTTLM 38
                                      569***************95 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.74
                            AAA_25  73 kVlyvsaEdsedelrrRlravg.eal..........rddarllvld 107
                                        V++ +aEd +  + + l+  g +++           ++ar+l+ +
  gi|474934038|ref|YP_007687620.1| 100 SVWWEDAEDER-IIDQALWDFGiTQYagrrlhelssGERARVLLAK 144
                                       68888888888.8888888887444456555555443333333333 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00023      0.16      18      50 ..      13      45 ..       3      46 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00023
                            AAA_27 18 sldfsaeeadlhliyGpNEAGKstalrAisdll 50
                                       ++f+ +  ++  ++G N +GK+t++r i+++l
  gi|474934038|ref|YP_007687620.1| 13 DITFDISPGEFVAVMGQNGSGKTTLMRCINKIL 45
                                      4566667899******************99876 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00022      0.15      21      39 ..      26      44 ..      19      68 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00022
                            AAA_13 21 iYGwNGaGKTtLSrllrsl 39
                                      + G+NG+GKTtL r ++++
  gi|474934038|ref|YP_007687620.1| 26 VMGQNGSGKTTLMRCINKI 44
                                      569************9986 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00025      0.17       2      41 ..      24      66 ..      23     173 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00025
                            AAA_33  2 vllvGlpGsGKstlaerllkklg...avllssdtlrrrlfgtd 41
                                      v + G +GsGK+tl + + k l+   +++l  d+  ++++ ++
  gi|474934038|ref|YP_007687620.1| 24 VAVMGQNGSGKTTLMRCINKILKirsGEILVDDNSVKTMTMEE 66
                                      5688************997777777799999999777777643 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00029       0.2       5      29 ..      24      47 ..      22      90 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00029
                            AAA_24  5 iliyGpsgiGKTtlakelgpkplfi 29
                                      ++++G++g+GKTtl++ + +k+l i
  gi|474934038|ref|YP_007687620.1| 24 VAVMGQNGSGKTTLMRCI-NKILKI 47
                                      689************999.777655 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0    0.0004      0.27      25      65 ..      24      64 ..      13      81 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0004
                      Mg_chelatase 25 lllvGppGsGKtmlakrlpsllpplseeealevakiasvag 65
                                      + ++G  GsGKt l ++++++l   s e  ++ +++++++ 
  gi|474934038|ref|YP_007687620.1| 24 VAVMGQNGSGKTTLMRCINKILKIRSGEILVDDNSVKTMTM 64
                                      5679******************8887777777777776665 PP

>> NTPase_P4  ATPase P4 of dsRNA bacteriophage phi-12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0    0.0004      0.27     114     163 ..      24      72 ..      18      92 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0004
                                       EEEEESTTSSHHHHHHTTS-SEEEEBSSSSTGGGGSTTEEEHHCHHHHHH CS
                         NTPase_P4 114 vvvvGktgsGkskaLnekdpdvtiRfGepaeaydeedsavavddlaemli 163
                                       v+v+G+ gsGk+  +   ++   iR Ge +   +    ++ ++++a++  
  gi|474934038|ref|YP_007687620.1|  24 VAVMGQNGSGKTTLMRCINKILKIRSGEILVDDNS-VKTMTMEEIARLCT 72 
                                       79**************************9976555.44455666666433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      587  (0.0327403); expected 358.6 (0.02)
Passed Vit filter:                       114  (0.00635841); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 1729.66
//
Query:       gi|474934039|ref|YP_007687621.1|  [L=239]
Description: hypothetical protein TALC_00458 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1647.33
//
Query:       gi|474934040|ref|YP_007687622.1|  [L=163]
Description: putative RNA-binding protein (contains PUA domain) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-14   53.4   0.0    2.7e-14   52.9   0.0    1.3  1  PUA       PUA domain
  ------ inclusion threshold ------
       0.05   13.9   0.0        0.1   12.9   0.0    1.5  1  UPF0113   UPF0113 PUA domain


Domain annotation for each model (and alignments):
>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.0   3.1e-18   2.7e-14       3      70 ..      82     150 ..      80     154 .. 0.95

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 3.1e-18
                                       EEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETT.SCEEEEEEESS-HHHHHHHCTSEEEEE CS
                               PUA   3 vvvddgAvkallsgasLlapGvvevegdfeegdvVaivded.gelvavGlanysseelakikggksvei 70 
                                       v+vd gAv ++++ga+ + pG+v+++ +++egd V i d +  +++avG++  s+ el + k gk++++
  gi|474934040|ref|YP_007687622.1|  82 VTVDMGAVPFIANGADCMGPGIVDADPEIKEGDFVWIRDIKnLRPLAVGISSRSGTELLEKKTGKAIKT 150
                                       89*************************************9857***********************996 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.1e-05       0.1      15      71 ..      95     155 ..      82     158 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.1e-05
                           UPF0113  15 GrdvlkesilkitesvkenqvvvVln.engeplGiGkirkdt..k.aspgkivvknlaDiG 71 
                                       G d ++ +i+  ++++ke+++v + + +n +pl++G++++++     +++++ +k+l  +G
  gi|474934040|ref|YP_007687622.1|  95 GADCMGPGIVDADPEIKEGDFVWIRDiKNLRPLAVGISSRSGteLlEKKTGKAIKTLNSVG 155
                                       77889999****************6648899*********999856899999999998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1067.53
//
Query:       gi|474934041|ref|YP_007687623.1|  [L=441]
Description: HD superfamily phosphohydrolase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-12   46.6   0.2    8.9e-12   45.3   0.2    1.7  1  HD        HD domain


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.2     5e-16   8.9e-12       1      67 [.      56     122 ..      56     132 .. 0.87

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 5e-16
                                       HHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHH CS
                                HD   1 rleHsleVaklarrlaedlge.eedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeil 67 
                                       r+eH+l++++la+++a+ +g+ e+d+ ++++aaL+HDi + pf+++ e  +e   + l+H++ ++ ++
  gi|474934041|ref|YP_007687623.1|  56 RFEHCLGTYHLAGKMAKAIGLtECDSMVVRTAALMHDICHAPFSHTLEGLME-ESTGLDHMELARNLI 122
                                       79******************************************96665444.445578888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2913.36
//
Query:       gi|474934042|ref|YP_007687624.1|  [L=483]
Description: hypothetical protein TALC_00461 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     7e-160  532.7   0.0   7.9e-160  532.5   0.0    1.0  1  RtcB      tRNA-splicing ligase RtcB


Domain annotation for each model (and alignments):
>> RtcB  tRNA-splicing ligase RtcB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  532.5   0.0  4.4e-164  7.9e-160       1     412 []      49     483 .]      49     483 .] 0.99

  Alignments for each domain:
  == domain 1  score: 532.5 bits;  conditional E-value: 4.4e-164
                                       HHHHHTTSTTB-S-EEEEEEEE--SSS-EEEEEEE-...-EE-HHHC-SST.-EEEEEEEEEEHHHHGGGHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB   1 qlknvaslpgivkhvaamPDvHlGkgapiGsViatk...gviiPaaVGvDI.CGvrllktnltaeeleeklkelvke 73 
                                       q++nva+lp iv +++amPD+H+G+g+piG+V+a++   g i+P+++G+DI CGvrl+kt++t  ++ ++++ l+++
  gi|474934042|ref|YP_007687624.1|  49 QAANVACLPEIVGNSMAMPDIHWGYGFPIGGVAAVDvneGSISPGGIGFDInCGVRLIKTDITLGDIGDRIRPLMDA 125
                                       89*************************************************************************** PP

                                       HHHHS-------------HHHHHHHHHHTHHHHHHTTSS-GGGGGGBGGGG--TT--GGGS-HHHHHHHGGGTT--- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB  74 lekavpvglgskkkvklskkeleevleegakwaveeglgeeedlekieeegalkeadlekvskkakerarkqlGtlG 150
                                       l ++vp+glgsk+ +++++k+l+++l+ g++wa+e+g+g+eedl+ +eeeg++kead++ v +k ++r+ ++lG+lG
  gi|474934042|ref|YP_007687624.1| 126 LYRNVPSGLGSKGLTRVTQKDLSDILDIGSRWAIENGYGWEEDLKATEEEGCMKEADQTGVGEKSRKRGLPELGSLG 202
                                       ***************************************************************************** PP

                                       STT-EEEEEEEEEES-HHHHHHHT--TTEEEEEEEE--HHHHHHHHHHHHHHHHCCHHHCT---SSGGG--EETTSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB 151 sGNHFiEvqlveeildeeaakalgleegqvvvmlHsGSRglGhqiaedylkiakkalkkkgiklpdrdLaylpagse 227
                                       sGNHF+E+ +v+e++de++aka+gl++g+v++++H+GSRg+Ghqia+dyl+++++ +k+  ++lpdr+La++p++ +
  gi|474934042|ref|YP_007687624.1| 203 SGNHFLELDVVDEVFDEATAKAYGLKKGTVTITIHCGSRGVGHQIATDYLQKMEHYIKTRSVDLPDRQLACAPLKDR 279
                                       **********************************************************999**************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT.T--HHHH--EEEEEEESEEEEEEEE..T...EEEEEEEES-E CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x...xxxxxxxxxxx RF
                              RtcB 228 egqaYlkamqaaanyAkaNRqvitervreilekvlkkekedlelelvvdvaHNiakkEehe.d...ekvlVhRKGAt 300
                                        g++Y+ am+++anyA++NRq+it+++re++e+vl++++edl++++v+dvaHNiakkE+h+ +    +vlVhRKGAt
  gi|474934042|ref|YP_007687624.1| 280 LGEEYFGAMCCGANYAWTNRQMITHWARESFEQVLGESAEDLGMDVVYDVAHNIAKKERHDyEghsVDVLVHRKGAT 356
                                       *************************************99*********************9845889********** PP

                                       E-.............TT--EEEE--STTS-EEEEE--HHHH..SSSEE---S-----------------TTTTTCCC CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB 301 rA.............kvgqpviipGsmgtkSyivkGkgnae..sfgStsHGAGRlmsRakakkkfkleevkkdleeq 362
                                       rA             + gqpv+ipG+m t+ y+++G++ a+  +fgSt+HGAGR+msR++a ++++++ ++k++++q
  gi|474934042|ref|YP_007687624.1| 357 RAfapgrseitqkyrDYGQPVLIPGDMSTGTYVLAGRKGAMqeTFGSTCHGAGRQMSRKAAIENLNVDAIRKKMSDQ 433
                                       **************************************99999********************************** PP

                                       T-EEEE------------------HHHHHHHHCTS-EEEEEEEEEEEEE- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB 363 gigvearkkegvleEapeaYKdideVveaqaeaglvevvarlkpvlvvkg 412
                                       gi++++ ++eg+leEap+aYKd++++++++ +agl+ +va+l p++vvkg
  gi|474934042|ref|YP_007687624.1| 434 GIYLRSGSDEGILEEAPDAYKDVNQIIDVVCNAGLTAKVAKLVPFGVVKG 483
                                       *************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (483 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 3043.95
//
Query:       gi|474934043|ref|YP_007687625.1|  [L=337]
Description: methyltransferase, MtaA/CmuA family [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.5e-65  219.0   0.4    1.1e-64  218.8   0.4    1.0  1  URO-D     Uroporphyrinogen decarboxylase (URO-D)
  ------ inclusion threshold ------
      0.035   14.2   0.1       0.14   12.3   0.1    2.1  1  DD_K      Dermaseptin


Domain annotation for each model (and alignments):
>> URO-D  Uroporphyrinogen decarboxylase (URO-D)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.8   0.4   1.2e-68   1.1e-64      10     345 ..       1     334 [.       1     335 [. 0.92

  Alignments for each domain:
  == domain 1  score: 218.8 bits;  conditional E-value: 1.2e-68
                                       HTT---SS--B--TT-SSTTSHHHHHHHTSSSHHHHHH-HHHHHHHHHHHHHHH--S-EE-S--TTGGGGGGT-EEE CS
                             URO-D  10 lrgekvdrvPvwlmRqaGrylpeyraeragvsflelcknpelaaevtlqpvrrfglDaailfsdilveaealGleve 86 
                                       +++e+ dr+P  +    +++++  ++ ++g+ ++e++k+++ +a+++ +    fg++++   ++++ eae lG++v 
  gi|474934043|ref|YP_007687625.1|   1 MNKENLDRPPAAI---FTQSATLGQMDKTGAAWPEAHKDAKIMAKLAAAQATVFGFECVRTSFCLTAEAERLGCTVA 74 
                                       67899********...888********************************************************** PP

                                       EETTTE.EEEE--S-....GGGS.......----GGG........G..HHHHHHHHHHHHH.--SS-EEEEEE-HHH CS
                             URO-D  87 feegeg.Pvvekpvrtaedvekl.......evpddvee.......grlpyvleaikllkkelggevpligfvgaPft 148
                                         + +  P +++++++ + +e +                      gr+++v++++++lk ++g++  +++++++Pft
  gi|474934043|ref|YP_007687625.1|  75 VDKRDAaPMIKSHPFKFDCMEGVyddpsamM------SvdeflkgGRVAEVIKSCEILKNDMGKDYCVVAGTTGPFT 145
                                       *995555********9888885533332222......234455678******************************* PP

                                       HHHHHHCTT-SS-HHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEE..TTGGGS-HHHHHHHTHHH CS
                             URO-D 149 lasylveGgskgfekllkllykdpeevhklldkltdvvieylkaqieagAdaiqifD..swagllspedfeefvlpy 223
                                       la ++v      +e+l+  +++ pe v+k++d +t ++++y +a i+agAd+iq+ +  ++ ++l p++f+e + ++
  gi|474934043|ref|YP_007687625.1| 146 LAGHMV-----STENLIFGMMMAPEMVDKWVDAVTPICKAYGQAVIDAGADIIQMSEpsASTDMLAPDMFQEAAGKA 217
                                       ******.....************************************************9***************99 PP

                                       HHHHHHHHHH.H--S-EEEEESSHH.HHHHHHTTS-..-SEEE--TTS-HHHHHHSS....EEE--B-G.GGGG.S- CS
                             URO-D 224 lkrivdevkaegpkvpvilfikgagaeiledlaelg..advlsldwtvdlkeaarevgdkvalqGnldPialLl.gs 297
                                       +   +   k+       il+i+g++++il+++a +g  ++++s++++vd  ea+++vgdk++l+Gn+  ++ L+ g+
  gi|474934043|ref|YP_007687625.1| 218 VLGSLGSTKGG---LGNILHICGDTTPILDQMAVVGgsVKGISIEEKVDSYEAVKAVGDKCVLVGNVGSVKPLFqGT 291
                                       98888888885...579****************98856788************************************ PP

                                       HHHHHHHHHHHHT.T---SSSEEB-BSS---TTS-HHHHHHHHHHHHT CS
                             URO-D 298 peeiekevkeilekgaggkkgyilnlGhgippetppenvkalveavke 345
                                       pee+++ v + +++     + +i+++G+gi+p t  en++a+v+avk+
  gi|474934043|ref|YP_007687625.1| 292 PEEVKEGVFRSCDA-----GFHIISSGCGIAPATADENMQAFVDAVKA 334
                                       *************4.....489************************97 PP

>> DD_K  Dermaseptin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   1.6e-05      0.14      12      22 ..     212     222 ..     208     223 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.6e-05
                              DD_K  12 kAAGKAALnAv 22 
                                       +AAGKA+L++ 
  gi|474934043|ref|YP_007687625.1| 212 EAAGKAVLGSL 222
                                       69*******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 2130.69
//
Query:       gi|474934044|ref|YP_007687626.1|  [L=242]
Description: putative phosphoesterase, SbcD/Mre11-related protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      5e-06   27.2   0.8      1e-05   26.1   0.1    1.6  2  Metallophos    Calcineurin-like phosphoesterase
     0.0002   21.6   0.1    0.00028   21.1   0.1    1.2  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.1   1.1e-09     1e-05       2      82 ..      26     117 ..      25     148 .. 0.68
   2 ?   -1.2   0.4      0.28   2.5e+03     191     203 ..     146     158 ..     129     159 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1.1e-09
                                       EEEEEESBTB...........TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS.........HHHHHHHHHHH CS
                       Metallophos   2 rilvigDlHl...........algggqlddllkllddllreekpdlvllaGDlvdrg.........dlekellella 58 
                                       + +vigDlHl                + d++++ l+++l+  +p  ++l+GD+ ++          ++ + +++l++
  gi|474934044|ref|YP_007687626.1|  26 PTAVIGDLHLgyesaleadgmFIPRINTDSVRDSLNRILDTYEPSRIVLLGDIKHDFrrssygareEVRS-IMKLVS 101
                                       679******99999999999944456666666666777777799999999**999987666655533333.555555 PP

                                       HHHHHTSEEEEEC-TTSCHHHHHH CS
                       Metallophos  59 alvkypipvylllGNHegfeeell 82 
                                          +     ++++GNH+    ++l
  gi|474934044|ref|YP_007687626.1| 102 DAAE----TVVIRGNHD----NYL 117
                                       5555....6********....222 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.28
                                       TTESEEEEESSSS CS
                       Metallophos 191 ygvdlvisGHtHv 203
                                        g+  vi GH+H+
  gi|474934044|ref|YP_007687626.1| 146 SGIRPVIIGHEHP 158
                                       55666899***97 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.1   3.1e-08   0.00028       4     103 ..      28     165 ..      27     186 .. 0.63

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.1e-08
                     Metallophos_2   4 aiiSDlH....................snldaleavlealkevgvdaiihaGDleeeep............evleel 48 
                                       a+i DlH                    s +d l+++l   +  ++ +i+++GD+ + ++            ++++ +
  gi|474934044|ref|YP_007687626.1|  28 AVIGDLHlgyesaleadgmfiprintdSVRDSLNRIL---DTYEPSRIVLLGDI-KHDFrrssygareevrSIMKLV 100
                                       6889999888888887777777764444444444444...445667*******5.2222334445553332244444 PP

                     Metallophos_2  49 lela.pvlaVrGNnD...eev..veedvlreaaelgtdlpeeaelelagekvlliHgdpl.....g 103
                                        + a + +++rGN+D   +++   +   + e+ ++g+++ e+  ++ + + v + H++p+     +
  gi|474934044|ref|YP_007687626.1| 101 SD-AaETVVIRGNHDnylQNIlaDVGLTAMESIDIGGYHLEHGHVDSGIRPVIIGHEHPSvkipgE 165
                                       44.36**********776444444445555666777777788888866666888888876655551 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1497.58
//
Query:       gi|474934045|ref|YP_007687627.1|  [L=467]
Description: Single-stranded DNA-specific exonuclease [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-19   70.7   0.3    3.3e-19   69.7   0.3    1.5  1  DHHA1     DHHA1 domain
  ------ inclusion threshold ------
      0.044   14.0   0.0      0.086   13.1   0.0    1.5  1  DHH       DHH family


Domain annotation for each model (and alignments):
>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.7   0.3   3.7e-23   3.3e-19      19     138 .]     341     461 ..     324     461 .. 0.81

  Alignments for each domain:
  == domain 1  score: 69.7 bits;  conditional E-value: 3.7e-23
                                       HHHHHHHHHHHHHHTCEEECTCEEEEEECHCCHHHHHHHHHHHHHHTHG...BT.TCEEEEEEEECTEEEEEEEESS CS
                             DHHA1  19 kealaklkaeellekaeevkgvkvlvaevgeewdagalgiaadklkskl...kk.pvivfvakeegdkvkvsarskk 91 
                                       + al+++k + l+ +    +++  ++ +  ++++ +++gi+a++++s     +  p+i+f+a+++g  +kvsar+++
  gi|474934045|ref|YP_007687627.1| 341 SVALQMVKDNHLIRR----RKYLQYFDAG-TDIRETVVGIVAGMVLSSDeadPYlPIIAFAAADDG--IKVSARASR 410
                                       445555555555544....2444444444.89999************66778888*********98..********9 PP

                                       H....SS-HHHHHHHHHHHTTCCEEEETCEEEEEEEHCHHHHHHHHHHHHH CS
                             DHHA1  92 d....gvdagelakeaaaklgggGGGHdlAaGagipaekleealealeeai 138
                                            g+d++ ++k+aa+++gg GGGH  AaGa+ip++  e +l+++e+++
  gi|474934045|ref|YP_007687627.1| 411 PliskGLDLSQIMKDAAEAVGGLGGGHSVAAGATIPEGTQERFLDEVEKLV 461
                                       9**********************************************9975 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   9.6e-06     0.086       2      84 ..      22     145 ..      21     161 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.6e-06
                                       EEEE-ECSSSHHHHHH.HHHHHH....................C............ECS--TCGGCGCCHHCCCSEE CS
                                       xxxxxxxxxxxxxxxx.xxxxxx....................x............xxxxxxxxxxxxxxxxxxxxx RF
                               DHH   2 ilivghknpDtDsigS.aialan....................l............lvDhneksqavegeakeeaed 45 
                                       + iv   + D+D+i + +ia  +                    +            ++D +++  ++     ++ + 
  gi|474934045|ref|YP_007687627.1|  22 VRIV--THIDADGISAgSIAALAvqrlgiphtlvfekkitdpvIeginscpedvvwICDLGSAYMSQ-----FTRNG 91 
                                       5674..5556666655555544425566665555555555555055555555555599999888777.....56999 PP

                                       EEEEE-S---S..............S---SS--EEEE-SS.S-HHHHHHHHHHH CS
                                       xxxxxxxxxxx..............xxxxxxxxxxxxxxx.xxxxxxxxxxxxx RF
                               DHH  46 viiiDHHrlge..............efetlapilflnepv.gstaeivaellee 84 
                                       ++++DHH +                +++ + +++ ln ++  ++a++ + l++e
  gi|474934045|ref|YP_007687627.1|  92 IVVTDHHVPDGkwrsgqsfldsfraSYQMNPHLYGLNGSYeVCGAGMTYLLAKE 145
                                       ********9889999999999999755555555555544426888888888655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (467 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 2602.52
//
Query:       gi|474934046|ref|YP_007687628.1|  [L=305]
Description: ornithine carbamoyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.5e-55  185.1   0.0    1.2e-54  184.7   0.0    1.2  1  OTCace    Aspartate/ornithine carbamoyltransferase, Asp/Orn b
    1.5e-44  151.6   0.0    2.3e-44  151.0   0.0    1.3  1  OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl


Domain annotation for each model (and alignments):
>> OTCace  Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.7   0.0   1.3e-58   1.2e-54       2     156 ..     148     301 ..     147     302 .. 0.98

  Alignments for each domain:
  == domain 1  score: 184.7 bits;  conditional E-value: 1.3e-58
                                       C.EEEEESSTTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE- CS
                            OTCace   2 glkiafvGdkknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvytd 78 
                                       g+k++++Gd+ nnv+nsl++++a+lg+d+v+++P +  p+ e++  a+ +a+++g++i  +++++ea+ +aDv+ytd
  gi|474934046|ref|YP_007687628.1| 148 GKKLVYLGDG-NNVCNSLLYACAILGVDMVACCPATRMPNAEIMLGAARIADANGSKIIASHEPTEACVDADVLYTD 223
                                       89********.*************************777799999******************************** PP

                                       -SSETTCCGGHHHHHHHHCCCSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHHHHHHHH CS
                            OTCace  79 vwvsmgeekereerlkklkdyqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlhtikAllv 155
                                       +w+smg+++  e+ +k +++yq++++ll+ ak+d+iv+HcLPa+rg+E+t+eV+++p+svvf+qaeNrlh++kA+l+
  gi|474934046|ref|YP_007687628.1| 224 TWISMGDNTPVEAAVKLFHKYQINDDLLSIAKPDCIVMHCLPAHRGQEITNEVIEGPHSVVFDQAENRLHAQKAVLY 300
                                       ****************************************************************************9 PP

                                       H CS
                            OTCace 156 l 156
                                       +
  gi|474934046|ref|YP_007687628.1| 301 T 301
                                       7 PP

>> OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.0   0.0   2.6e-48   2.3e-44       1     148 []       4     141 ..       4     141 .. 0.96

  Alignments for each domain:
  == domain 1  score: 151.0 bits;  conditional E-value: 2.6e-48
                                       S-BSSGGGS-HHHHHHHHHHHHHHHHHHHTTT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTS CS
                          OTCace_N   1 rhllsledlskeeieelldlaaelkekvkkekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaedi 77 
                                       r+l+s+ d++ +e+ +l+dla +lk+ +   ++ + l+gktla++Fe+pStRTr+Sf+vA+++lGg++l+l+  +++
  gi|474934046|ref|YP_007687628.1|   4 RNLISVLDMK-DEWPALVDLAIKLKKGRG--HHGDPLAGKTLAMMFEKPSTRTRTSFDVAITELGGHALYLD-VTKM 76 
                                       799*****97.9*************9975..99999************************************.7689 PP

                                       CTTTGGSTTSSCHHHHHHHHHHHTSEEEEEESSHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHHH CS
                          OTCace_N  78 qlssvskgrkEsleDtarvlsryvdaiviRhpgaeeleelakyasvpviNagdgdgeHPtQaLaDlltire 148
                                       q++     ++E++eDtarvlsr+v++i++R+++ + +++l ++ +vpvi+++  d eHP+QaLaD++ti+e
  gi|474934046|ref|YP_007687628.1|  77 QMG-----HGETVEDTARVLSRFVHGIMYRAFDYKMMDKLGEWTTVPVISGL-DDLEHPCQALADMVTIKE 141
                                       999.....67**********************9999****************.9***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2118.87
//
Query:       gi|474934047|ref|YP_007687629.1|  [L=1431]
Description: hypothetical protein TALC_00467 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-17   64.1   3.9    1.4e-17   64.1   3.9   12.7 13  MBG_2         MBG domain (YGX type)
    1.4e-07   31.6   1.5    1.4e-07   31.6   1.5    5.8  7  Flg_new       Listeria-Bacteroides repeat domain (List_Bact_r
  ------ inclusion threshold ------
        0.1   12.9   0.1        6.3    7.2   0.0    2.8  2  PHA_gran_rgn  Putative polyhydroxyalkanoic acid system protei
        1.1    9.3   9.5         12    6.0   1.4    3.4  2  BmKX          BmKX
        4.3    7.5   8.3         13    6.0   0.1    5.0  5  bMG10         Bacterial Alpha-2-macroglobulin MG10 domain


Domain annotation for each model (and alignments):
>> MBG_2  MBG domain (YGX type)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -9.5  13.8         5   1.8e+04      13      63 ..      57     104 ..      18     116 .. 0.54
   2 ?  -10.5  15.2         5   1.8e+04      13      62 ..     146     192 ..     105     205 .. 0.46
   3 ?    2.5   7.5     0.063   2.3e+02      14      66 ..     218     268 ..     194     272 .. 0.62
   4 !    5.3   5.1    0.0089        32      14      66 ..     301     351 ..     282     355 .. 0.61
   5 ?   -3.4   0.0       4.4   1.6e+04      52      62 ..     433     443 ..     396     454 .. 0.53
   6 ?   -2.8   3.6       2.8     1e+04      27      59 ..     486     522 ..     454     526 .. 0.56
   7 !   64.1   3.9   3.9e-21   1.4e-17       1      71 [.     542     611 ..     542     612 .. 0.94
   8 !    6.7   0.8    0.0031        11      38      65 ..     660     687 ..     627     692 .. 0.81
   9 ?   -0.7   0.7      0.63   2.3e+03      35      62 ..     755     786 ..     712     788 .. 0.71
  10 ?   -0.4   2.0      0.52   1.8e+03      37      65 ..     847     875 ..     811     882 .. 0.70
  11 !   11.8   3.5   8.2e-05      0.29       2      64 ..     892     952 ..     890     958 .. 0.77
  12 ?   -4.3   5.6         5   1.8e+04      11      54 ..    1087    1132 ..    1058    1152 .. 0.57
  13 ?   -2.1   0.3       1.8   6.4e+03      34      71 ..    1243    1280 ..    1227    1281 .. 0.63

  Alignments for each domain:
  == domain 1  score: -9.5 bits;  conditional E-value: 5
                             MBG_2  13 GdadPeltytvsGlvngDtlssltgtlsrtagenvG.tY..aitasglsssNYt 63 
                                       G++  + t+t+  + +g+      +t+s  ++ n+G tY   +t + ++++NY+
  gi|474934047|ref|YP_007687629.1|  57 GSNTTAGTFTYCATSDGE------YTTSLVSAVNAGnTYtaYYTFTPTDTTNYN 104
                                       333333334433333333......333333444443344222444444444565 PP

  == domain 2  score: -10.5 bits;  conditional E-value: 5
                             MBG_2  13 GdadPeltytvsGlvngDtlssltgtlsrtagenvG.tY..aitasglsssNY 62 
                                       G++  + t+t+  + +g+      +t+s  ++ n+G tY   +t + ++++NY
  gi|474934047|ref|YP_007687629.1| 146 GSNTTAGTFTYCATSDGE------YTTSLVSAVNAGnTYtaYYTFTPTDTTNY 192
                                       222222233332222222......33333333333333322233333333355 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.063
                             MBG_2  14 dadPeltytvsGlvn.gDtlssltgtlsrtagenvGtYaitasglsss.NYtity 66 
                                       +a P+++++ + lv  g ++    g+ ++ + +  G+Y+ ++  ++++ NYt+ y
  gi|474934047|ref|YP_007687629.1| 218 AATPTYSGSAQDLVTaGSSEH---GSFTYST-TESGDYDASVPQGTNAgNYTVWY 268
                                       355666666666666333333...6666555.66899*55555555555***976 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.0089
                             MBG_2  14 dadPeltytvsGlvn.gDtlssltgtlsrtagenvGtYaitasglsss.NYtity 66 
                                       +a P+++++ + lv  g ++    g+ ++ + +  G+Y+ ++  ++++ NYt+ y
  gi|474934047|ref|YP_007687629.1| 301 AATPTYSGSAQDLVTaGSSEH---GSFTYST-TESGDYDASVPQGTNAgNYTVWY 351
                                       456667777777777333333...6666555.66899*55555555555***976 PP

  == domain 5  score: -3.4 bits;  conditional E-value: 4.4
                             MBG_2  52 itasglsssNY 62 
                                       +++++ +s+NY
  gi|474934047|ref|YP_007687629.1| 433 VKVTTEASDNY 443
                                       44445555555 PP

  == domain 6  score: -2.8 bits;  conditional E-value: 2.8
                             MBG_2  27 vngDtlssltgtlsrta.......genvGtYaitasglss 59 
                                           tl+   ++l   +       ++n+G+Y++    l +
  gi|474934047|ref|YP_007687629.1| 486 TTAGTLQ---YSLDNSSwdaalptATNAGSYTVYYRVLGN 522
                                       3323322...333333344455558999999887666555 PP

  == domain 7  score: 64.1 bits;  conditional E-value: 3.9e-21
                             MBG_2   1 LtVtaddkskvyGdadPeltytvsGlvn.gDtlssltgtlsrtagenvGtYaitasglsss.NYtityvngtl 71 
                                       +tV addk + yGdadPelt+tv+G ++ g t+    + +sr+ag nvG+Y+it++g +++ NY++ty++gt+
  gi|474934047|ref|YP_007687629.1| 542 VTVAADDKDRPYGDADPELTATVTGKLDdGSTIV---YEVSREAGDNVGSYDITPTGEENQgNYHVTYTPGTF 611
                                       69***********************999566666...***********************************8 PP

  == domain 8  score: 6.7 bits;  conditional E-value: 0.0031
                             MBG_2  38 tlsrtagenvGtYaitasglsssNYtit 65 
                                       ++ + ++  vG+Y  +as++ss NY+  
  gi|474934047|ref|YP_007687629.1| 660 SVPVITSAPVGNYWAKASTASSGNYSTV 687
                                       4555568899***************865 PP

  == domain 9  score: -0.7 bits;  conditional E-value: 0.63
                             MBG_2  35 lt...gtlsrtagenvGtYa..itasglsssNY 62 
                                       +t   +++++ta  n+G Y+  + +++ +  NY
  gi|474934047|ref|YP_007687629.1| 755 VTgftWNTEATA-VNAGAYTvfYYIDASAEGNY 786
                                       334446666666.88899963334444444477 PP

  == domain 10  score: -0.4 bits;  conditional E-value: 0.52
                             MBG_2  37 gtlsrtagenvGtYaitasglsssNYtit 65 
                                       +++    ++nvGt   +a+ ++s+NY+  
  gi|474934047|ref|YP_007687629.1| 847 VAIDNILTQNVGTVYAKATVAESANYNAL 875
                                       3444444899**998999999999**965 PP

  == domain 11  score: 11.8 bits;  conditional E-value: 8.2e-05
                             MBG_2   2 tVtaddkskvyGdadPeltyt.vsGlvngDtlssltgtlsrtagenvGtYaitasglsssNYti 64 
                                       tV a d+   y   dP+ +y+  +G v     ss++++++  a ++ G+Y+++++ ++s+NY+ 
  gi|474934047|ref|YP_007687629.1| 892 TVAA-DQVLSYTGVDPVIEYSgNTGAVSFAWFSSAEVSIA--APTDPGSYKVKVTVAESTNYNA 952
                                       5555.555555558***99998899999888887655555..566*****************96 PP

  == domain 12  score: -4.3 bits;  conditional E-value: 5
                             MBG_2   11 vyGdadPeltytvsGlvngDtlssltgtlsrtagenvGtY.....aita 54  
                                         yG++  ++ ++ +G v++ t +++   ++++  e vGtY     +it 
  gi|474934047|ref|YP_007687629.1| 1087 DYGTTLTAVIADKTGYVKSVTPAEV--VVAAN-VEFVGTYtpaayTITF 1132
                                        3344444444446666666665532..33322.2556777333112333 PP

  == domain 13  score: -2.1 bits;  conditional E-value: 1.8
                             MBG_2   34 sltgtlsrtagenvGtYaitasglsssNYtityvngtl 71  
                                        +++++ s+t +  + + ai+a + ++ N +i+++ngt+
  gi|474934047|ref|YP_007687629.1| 1243 TVDISASKTDSVSIKSDAIKAASDANLNVNIETKNGTM 1280
                                        33344444444444444788888888899999999986 PP

>> Flg_new  Listeria-Bacteroides repeat domain (List_Bact_rpt)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.3   2.3         5   1.8e+04      14      29 ..      81      96 ..      64     105 .. 0.50
   2 ?   -3.7   1.8       4.1   1.5e+04      15      29 ..     171     185 ..     153     198 .. 0.53
   3 ?   -2.1   0.3       1.2   4.5e+03       2      32 ..     265     308 ..     264     309 .. 0.41
   4 ?   -3.8   0.0       4.4   1.6e+04      39      53 ..    1018    1033 ..    1015    1043 .. 0.72
   5 ?   -1.9   0.5       1.1   3.8e+03       9      33 ..    1076    1102 ..    1059    1103 .. 0.44
   6 !   31.6   1.5   3.9e-11   1.4e-07       1      63 [.    1128    1201 ..    1128    1202 .. 0.77
   7 ?   -3.3   0.2         3   1.1e+04       3      19 ..    1356    1375 ..    1355    1383 .. 0.62

  Alignments for each domain:
  == domain 1  score: -4.3 bits;  conditional E-value: 5
                                      EEEETTSB----B--E CS
                           Flg_new 14 qtvtygetitlpanpt 29
                                        v++g+t+t   ++t
  gi|474934047|ref|YP_007687629.1| 81 SAVNAGNTYTAYYTFT 96
                                      2477777777664444 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 4.1
                                       EEETTSB----B--E CS
                           Flg_new  15 tvtygetitlpanpt 29 
                                        v++g+t+t   ++t
  gi|474934047|ref|YP_007687629.1| 171 AVNAGNTYTAYYTFT 185
                                       366677766654443 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.2
                                       EEEEEETTEE.....E.....EEE.EETTSB----..B--EETT CS
                           Flg_new   2 tvtFdanGgt.....v.....sqt.vtygetitlp..anptkeG 32 
                                       tv ++  G       +     s t ++++ tit p  a+pt +G
  gi|474934047|ref|YP_007687629.1| 265 TVWYKFTGDAnhndiAatqvaSVTiAKANPTITAPvaATPTYSG 308
                                       55555544331111211111122324456677777656676655 PP

  == domain 4  score: -3.8 bits;  conditional E-value: 4.4
                                        ESSTTC.CSB--TTT- CS
                           Flg_new   39 ytdsdg.ttaydfgtk 53  
                                        +t++dg +ta++f++ 
  gi|474934047|ref|YP_007687629.1| 1018 NTAADGsGTAFAFEQV 1033
                                        7999995699999874 PP

  == domain 5  score: -1.9 bits;  conditional E-value: 1.1
                                        TEEEEEE.......EETTSB----B--EETTE CS
                           Flg_new    9 Ggtvsqt.......vtygetitlpanptkeGY 33  
                                        G     t       v+yg+t+t      k+GY
  gi|474934047|ref|YP_007687629.1| 1076 GQ----TviasgslVDYGTTLTAVI-ADKTGY 1102
                                        22....2222233577777776653.566666 PP

  == domain 6  score: 31.6 bits;  conditional E-value: 3.9e-11
                                        EEEEEEETT....EEEEE.EEETTSB----.B--EETTEEEEEEESSTTCCSB--TTT-.....B--SS-EEEE CS
                           Flg_new    1 YtvtFdanG....gtvsq.tvtygetitlp.anptkeGYtFaGWytdsdgttaydfgtk.....vtptgdvtLy 63  
                                        Yt+tF+ n     g +   ++ty+ ++ l+ ++++++G++F GW t++dg + y+ +++      t  g+v+Ly
  gi|474934047|ref|YP_007687629.1| 1128 YTITFNKNAdaatGDMAVlNATYDVDVILTeNAFVRTGFVFGGWATAADGAAVYNDKATvknliATDGGNVNLY 1201
                                        *******974433344445899998888885679******************9999988555554555677776 PP

  == domain 7  score: -3.3 bits;  conditional E-value: 3
                                        EEEEETTEEEEE...EEETT CS
                           Flg_new    3 vtFdanGgtvsq...tvtyg 19  
                                        v + an+gt ++   +++++
  gi|474934047|ref|YP_007687629.1| 1356 VAYLANDGTLQKmegSYYEN 1375
                                        78999999965422254443 PP

>> PHA_gran_rgn  Putative polyhydroxyalkanoic acid system protein (PHA_gran_rgn)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0017       6.3      36      58 ..     876     898 ..     850     900 .. 0.85
   2 ?    2.3   0.0     0.056     2e+02      20      50 ..    1041    1071 ..    1034    1082 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0017
                      PHA_gran_rgn  36 egdtlkfkrsgvdGqlevepdkv 58 
                                        +d l+f+ +++dG+++v++d+v
  gi|474934047|ref|YP_007687629.1| 876 VNDALSFTIAKADGSVTVAADQV 898
                                       38*******************98 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.056
                      PHA_gran_rgn   20 elaekleeefglelewegdtlkfkrsgvdGq 50  
                                        ++a++ +  +++ ++w++ t++++++g+ G 
  gi|474934047|ref|YP_007687629.1| 1041 AVAQNHHVTLHMIWAWDQYTVTISGTGAAGV 1071
                                        567777777899**************99994 PP

>> BmKX  BmKX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   1.4    0.0033        12      14      30 .]      53      69 ..      48      69 .. 0.90
   2 ?    6.0   1.4    0.0033        12      14      30 .]     142     158 ..     137     158 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0033
                              BmKX 14 mCTaGtddkaGTCTaCt 30
                                      + TaG +  aGT T C+
  gi|474934047|ref|YP_007687629.1| 53 LITAGSNTTAGTFTYCA 69
                                      67**************7 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0033
                              BmKX  14 mCTaGtddkaGTCTaCt 30 
                                       + TaG +  aGT T C+
  gi|474934047|ref|YP_007687629.1| 142 LITAGSNTTAGTFTYCA 158
                                       67**************7 PP

>> bMG10  Bacterial Alpha-2-macroglobulin MG10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       1.5   5.3e+03      23      27 ..      83      87 ..      58     121 .. 0.52
   2 ?   -2.3   0.1       1.3   4.7e+03      23      23 ..     172     172 ..     143     211 .. 0.54
   3 ?   -1.1   0.0      0.55     2e+03       5      39 ..     407     441 ..     405     448 .. 0.76
   4 ?    6.0   0.1    0.0036        13      94     120 ..     764     790 ..     758     795 .. 0.88
   5 ?    1.8   0.1      0.07   2.5e+02      21      59 ..    1260    1300 ..    1244    1330 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.5
                             bMG10 23 lkvGd 27
                                      +++G+
  gi|474934047|ref|YP_007687629.1| 83 VNAGN 87
                                      33333 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.3
                             bMG10  23 l 23 
                                       +
  gi|474934047|ref|YP_007687629.1| 172 V 172
                                       3 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.55
                             bMG10   5 eReyeklegkevsksdaklkvGdkvrvrltvttpr 39 
                                        R y++ e++e  ++ + +++G++v v++t ++++
  gi|474934047|ref|YP_007687629.1| 407 FRYYTTGERDEEIPNWEWATAGSTVYVKVTTEASD 441
                                       67777777777777777899********9998655 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.0036
                             bMG10  94 adylpkgtytfeylvravtpGtfsvpp 120
                                       a+ +++g+yt+ y + a+++G++s+ +
  gi|474934047|ref|YP_007687629.1| 764 ATAVNAGAYTVFYYIDASAEGNYSHLA 790
                                       77899******************9875 PP

  == domain 5  score: 1.8 bits;  conditional E-value: 0.07
                             bMG10   21 a.klkvGdkvrvrltvttpr.dleyvaledplPAGlepvnp 59  
                                        a k+++   + v+++ +  + +    al+d+++AG+++  +
  gi|474934047|ref|YP_007687629.1| 1260 AiKAASDANLNVNIETKNGTmEFPSAALKDKVAAGTTVKSE 1300
                                        256666667777777775555778999********987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.84u 0.30s 00:00:01.13 Elapsed: 00:00:00.48
# Mc/sec: 9026.40
//
Query:       gi|474934048|ref|YP_007687630.1|  [L=236]
Description: archaeal conserved hypothetical protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.7e-47  159.7   6.0    9.9e-47  159.5   6.0    1.0  1  DUF169    Uncharacterised ArCR, COG2043


Domain annotation for each model (and alignments):
>> DUF169  Uncharacterised ArCR, COG2043
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.5   6.0   5.5e-51   9.9e-47       1     204 [.      14     219 ..      14     221 .. 0.96

  Alignments for each domain:
  == domain 1  score: 159.5 bits;  conditional E-value: 5.5e-51
                            DUF169   1 kLaealrlktePVavkfsdekpelpekkekieekkrlCqmvalarakgktvvftaetlgCpgGaaalGfkelpeklk 77 
                                       kL+ ++r  +ePVa+k+++e +e+p+  +++ e++++Cq+v  a  +g+ + + ae+++C+ G++alG+ e+pek+ 
  gi|474934048|ref|YP_007687630.1|  14 KLKSTVRFAREPVAIKLIREGEEFPACCKRPAEQMSHCQAVFAAS-RGECLNMYAEDQACHVGSSALGMAETPEKVA 89 
                                       7999************************9999999**********.******************************* PP

                            DUF169  78 sg.....egylkspeaakkfveslprleagevkyvvvapLekaefePdvvvffanpeqlmrLvqlalydrgggrlnv 149
                                       +g     +g+++s eaa+k++++  +++ ++  + +v+pL++a+f Pdvv f+  pe+ +++v l + ++gg r ++
  gi|474934048|ref|YP_007687630.1|  90 TGefhskMGMHDSAEAAAKMISDRAVVPFKT-LGEAVCPLKDADFVPDVVAFIDIPERCYWFVPLETAETGG-RAQF 164
                                       ***********************99886555.9*************************************99.8888 PP

                            DUF169 150 sfpgngaaCadivaypykegepniglgdpgarkfaklkddelafgiPyelleemv 204
                                       s++ ++ aC+d++a+p+ +g+pni++g+ g+rk +++k++e+a+giPy++++ +v
  gi|474934048|ref|YP_007687630.1| 165 STSPFQCACEDVTAQPVCTGKPNISMGCFGCRKKTDMKPEEMAVGIPYARIPAYV 219
                                       88888*********************************************99877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1509.70
//
Query:       gi|474934049|ref|YP_007687631.1|  [L=443]
Description: methyl-coenzyme M reductase, beta subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   2.8e-131  436.6   6.1   4.4e-131  436.0   6.1    1.3  1  MCR_beta    Methyl-coenzyme M reductase beta subunit, C-termi
    6.2e-76  254.1   4.1    6.2e-76  254.1   4.1    1.5  2  MCR_beta_N  Methyl-coenzyme M reductase beta subunit, N-termi


Domain annotation for each model (and alignments):
>> MCR_beta  Methyl-coenzyme M reductase beta subunit, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  436.0   6.1  4.9e-135  4.4e-131       1     248 [.     188     435 ..     188     436 .. 0.99

  Alignments for each domain:
  == domain 1  score: 436.0 bits;  conditional E-value: 4.9e-135
                          MCR_beta   1 GyalrnikanhvvaitkknalnaaalssileqtavfemGdavGaferahllglayqGlnannlvydlvkengkegtv 77 
                                       G+alrni++nhvva++++na++++als+i+e++a++emGdavG+fer+hll+layqGlnann+vy+lvk+ngk+gtv
  gi|474934049|ref|YP_007687631.1| 188 GFALRNIMSNHVVALVQRNAMQGTALSAIFETCAAYEMGDAVGPFERQHLLSLAYQGLNANNVVYSLVKKNGKTGTV 264
                                       8**************************************************************************** PP

                          MCR_beta  78 GtvveslveraiedkvikvekklpsgyklyetkdvalwnayaaaGllaavivnvgaaraaqavsstllyyndlleke 154
                                       Gtvvesl+ raied+vi+v+++lpsgyk+y+t+d++lwnayaaaG +aav+vnvgaaraaq+v+st+lyyndlle+e
  gi|474934049|ref|YP_007687631.1| 265 GTVVESLMARAIEDGVIRVKETLPSGYKVYTTDDLPLWNAYAAAGEVAAVMVNVGAARAAQGVPSTVLYYNDLLEHE 341
                                       ***************************************************************************** PP

                          MCR_beta 155 tglpGvdfGrveGtavGfsffshsiyGGGGpGifnGnhvvtrhskGfaipcvaaavaldaGtqlfspeatsglvgev 231
                                       +glpG+d+Gr+eG++vG+sffshsiyGGGGpG+f+Gnhvvtrh+kG+ ip+v+a+ +ld+Gtq+fs+eatsg++++ 
  gi|474934049|ref|YP_007687631.1| 342 SGLPGTDYGRAEGVGVGMSFFSHSIYGGGGPGLFHGNHVVTRHAKGTLIPAVTAGNCLDGGTQTFSAEATSGVFNTA 418
                                       ***************************************************************************** PP

                          MCR_beta 232 fgeidefreplkavaea 248
                                       fg ++ef+ p+++v  +
  gi|474934049|ref|YP_007687631.1| 419 FGGMPEFNAPMQFVGAE 435
                                       *************9876 PP

>> MCR_beta_N  Methyl-coenzyme M reductase beta subunit, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  254.1   4.1   6.9e-80   6.2e-76       1     182 []       6     186 ..       6     186 .. 0.99
   2 ?   -3.5   0.0      0.74   6.6e+03      49      78 ..     256     285 ..     249     292 .. 0.72

  Alignments for each domain:
  == domain 1  score: 254.1 bits;  conditional E-value: 6.9e-80
                        MCR_beta_N   1 DkidlyddkGkllesdvpleaisPlknpaikkivkdvkrtvavnlagiekalktgkvggkaskilGreldldivena 77 
                                       D idlydd Gk ++++vpleaisPl+n+ai+ki +++krtv v+lagiekalktg+vgg ++ i+G+e+d +iv++a
  gi|474934049|ref|YP_007687631.1|   6 DVIDLYDDYGKRIAKGVPLEAISPLRNKAIQKIASLTKRTVVVSLAGIEKALKTGAVGG-NNWIAGKEIDAPIVADA 81 
                                       89********************************************************9.79*************** PP

                        MCR_beta_N  78 daiaekikelvqveedddtkvkllngGkqllvqvPskRleaaaeysvallataaavveaiidefdvdmfdasvvkaa 154
                                       +++a++ik +vqv+edd t+v + +gGk+l v vP++R++a+ ey+++++++aaa++eaiid+++v m++a++vkaa
  gi|474934049|ref|YP_007687631.1|  82 EKLAKDIKAMVQVTEDDGTQVIVKDGGKSLTVIVPEARTDAGIEYTTGFTTVAAATTEAIIDRYKVPMYKANMVKAA 158
                                       ***************************************************************************** PP

                        MCR_beta_N 155 vlGryPqtvdlaggnvasilsipqkneG 182
                                       v+GryPqt+++ g+n++sil++pq+neG
  gi|474934049|ref|YP_007687631.1| 159 VWGRYPQTINFVGSNIKSILEVPQNNEG 186
                                       ***************************9 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 0.74
                        MCR_beta_N  49 ekalktgkvggkaskilGreldldivenad 78 
                                       +k  ktg+vg+  ++++ r ++  ++  ++
  gi|474934049|ref|YP_007687631.1| 256 KKNGKTGTVGTVVESLMARAIEDGVIRVKE 285
                                       556678888888888888888777776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 3118.34
//
Query:       gi|474934050|ref|YP_007687632.1|  [L=123]
Description: Methyl coenzyme M reductase, subunit D [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-30  103.7   0.0    8.6e-30  103.5   0.0    1.0  1  MCR_D     Methyl-coenzyme M reductase operon protein D


Domain annotation for each model (and alignments):
>> MCR_D  Methyl-coenzyme M reductase operon protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.5   0.0   4.8e-34   8.6e-30       6     118 ..       2     120 ..       1     122 [. 0.96

  Alignments for each domain:
  == domain 1  score: 103.5 bits;  conditional E-value: 4.8e-34
                             MCR_D   6 peRlLkpetteklLnelvelegikrvvihGprLPkkvpygpakGkevehkerkvievkgeeveLkvkvGrillele. 81 
                                       ++RlL+++ te +Ln + ++e i++v + G++LP++++ gpakG++++h+er++i+v+++eveL+  vG + +ele 
  gi|474934050|ref|YP_007687632.1|   2 TNRLLSAQSTEAVLNAIDDIEHIRQVNMSGENLPATINSGPAKGMSNNHTERQIIHVGQQEVELHCLVGAFYIELEv 78 
                                       68************************************************************************999 PP

                             MCR_D  82 .....deeviekieeiceevlpfsyeikegkfirkkktvsDy 118
                                             e +++ki+++c+e+++ +y+++ g++ + +++++Dy
  gi|474934050|ref|YP_007687632.1|  79 ddkdmLEATVDKIKAACDEHIKDGYSLEIGRYSKYRPSLTDY 120
                                       88777788999******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 785.41
//
Query:       gi|474934051|ref|YP_007687633.1|  [L=259]
Description: methyl-coenzyme M reductase, gamma subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   2.4e-125  416.7   0.1   2.7e-125  416.6   0.1    1.0  1  MCR_gamma  Methyl-coenzyme M reductase gamma subunit


Domain annotation for each model (and alignments):
>> MCR_gamma  Methyl-coenzyme M reductase gamma subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  416.6   0.1  1.5e-129  2.7e-125       1     246 []       7     252 ..       7     252 .. 0.99

  Alignments for each domain:
  == domain 1  score: 416.6 bits;  conditional E-value: 1.5e-129
                         MCR_gamma   1 aqyyPGeskvaenrrkfmdpeaeleklreisdedvvkilghraPGeeyksvhPPleemdepedpirelvePieGaka 77 
                                       +q+yPG+s  a+nrr+++dp+++l+klr+++++dvv+++ghraPGe+yks+hPP+ee +ep++pirelv PieGak+
  gi|474934051|ref|YP_007687633.1|   7 RQFYPGQSIPAQNRRRYLDPKVKLKKLRDVPMDDVVRLMGHRAPGEAYKSIHPPIEEGKEPKCPIRELVVPIEGAKH 83 
                                       59*************************************************************************** PP

                         MCR_gamma  78 GdrvryiqfadsmyfaPaqPyqrarlellryrgvdtGtlsGrqiievrerdlekiskelletelfdpartgirGatv 154
                                       Gdrvryiqf+ds+yfaP++Pyqra+++++r+rgvdtGtlsGrqiievrerdle ++kel+++e+fdpa tgirG+tv
  gi|474934051|ref|YP_007687633.1|  84 GDRVRYIQFTDSVYFAPISPYQRAWMYMSRWRGVDTGTLSGRQIIEVRERDLEVYAKELIDDETFDPALTGIRGSTV 160
                                       ***************************************************************************** PP

                         MCR_gamma 155 hGhslrldenGlmfdalqrlvldeedgevkyvkdqvgvpldkkvdvGkpldedelkkkttiyrldgvalrddkevve 231
                                       hGh++rldenGlmfd +qr+v+d +++ev+y kdqv+ pldk++ vGkp ++++lkk+tti+r+dgv++rddkev +
  gi|474934051|ref|YP_007687633.1| 161 HGHACRLDENGLMFDGWQRYVWDAKKKEVVYKKDQVALPLDKDIYVGKPASMENLKKRTTIFRADGVDMRDDKEVTD 237
                                       ***************************************************************************** PP

                         MCR_gamma 232 vvkrihelrtklgfk 246
                                       ++ r+h lrt +g++
  gi|474934051|ref|YP_007687633.1| 238 FYIRVHWLRTLGGYR 252
                                       *************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.52
# Mc/sec: 1509.58
//
Query:       gi|474934052|ref|YP_007687634.1|  [L=552]
Description: methyl-coenzyme M reductase, alpha subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   6.7e-140  465.1   0.2     1e-139  464.5   0.2    1.3  1  MCR_alpha_N  Methyl-coenzyme M reductase alpha subunit, N-ter
    9.7e-62  207.1   4.5    2.5e-61  205.7   4.5    1.7  1  MCR_alpha    Methyl-coenzyme M reductase alpha subunit, C-ter
  ------ inclusion threshold ------
       0.26   11.2   1.1        8.4    6.3   0.4    3.0  2  XH           XH domain


Domain annotation for each model (and alignments):
>> MCR_alpha_N  Methyl-coenzyme M reductase alpha subunit, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  464.5   0.2  1.7e-143    1e-139       1     270 []       5     269 ..       5     269 .. 0.99

  Alignments for each domain:
  == domain 1  score: 464.5 bits;  conditional E-value: 1.7e-143
                                       XX--HHHHHHH-S.S-TT--B---S-S-GGGG-HHHHHHHHHHHHHHHHH-S----TTS...S--S-SS---EEEBT CS
                       MCR_alpha_N   1 eklflkalkkkfkkedpeekktkfykfeGlkqserkrefveaakkiakkrgislynpdilhlGvplGqrklmpykvs 77 
                                       eklfl+a+kkkfk e+p++++tk+y+++G+kqs++k ef+++a++iakkrg++++n+d+   GvplGqr++mpy++s
  gi|474934052|ref|YP_007687634.1|   5 EKLFLEACKKKFK-EEPTSMETKYYCYGGWKQSKSKVEFQKEAMEIAKKRGFPMMNEDV---GVPLGQRSWMPYQLS 77 
                                       699**********.99*****************************************98...*************** PP

                                       TS--EEEGGGSSGGG-HHHHHHHHHHHTEEEEE-HHHHHHHHHTT-----HHHHHHHHHHHHHHTTT--SS-TT--- CS
                       MCR_alpha_N  78 gtdvlvegddlhfvnnaalqqlwddirrtvivgldtahevlekrlGkevtPetineylevlnhalPGgavvqehmve 154
                                       +td++ve+ddlh++nn+a+qq+wddirrtv+vgld+ h+++ekrlGkevtPetin yle +nh++PGga+vqehm+e
  gi|474934052|ref|YP_007687634.1|  78 HTDIFVEPDDLHCINNPAIQQAWDDIRRTVLVGLDSPHQTIEKRLGKEVTPETINAYLEAVNHTIPGGAIVQEHMAE 154
                                       ***************************************************************************** PP

                                       --TTT-TT-EEEEEES-HHHHTTS-GGGB--HHHHS-HHHHHHHHHHH-S-EEEEEE--HHHHHHS-HHHHHHHHHH CS
                       MCR_alpha_N 155 thPalvedcyvkvftGddeladeidkqflidinkefpeeqaeqlkkaiGkklyqvvriPtivsrtcdGgttsrwsam 231
                                       ++Palv d+yvkvf+G+del+deid++f+idink+fp++qae+lkka+Gk+++q+vr+Pt+v+r++dG+t+sr++am
  gi|474934052|ref|YP_007687634.1| 155 CNPALVYDSYVKVFSGNDELIDEIDPRFVIDINKNFPKDQAEKLKKAMGKTVMQAVRVPTMVGRVMDGATVSRHAAM 231
                                       ***************************************************************************** PP

                                       HHHHHHHHHHT--SS-TTHHHHHHHHHTTSEEES---B- CS
                       MCR_alpha_N 232 qigmsfisayklcaGeaavadlayaakhaeviemgellP 270
                                       qi+msfis+ykl+aGeaa+ad+ay+akh + i+mg+++P
  gi|474934052|ref|YP_007687634.1| 232 QISMSFISSYKLAAGEAAIADFAYSAKHLS-INMGTMMP 269
                                       *****************************9.9******9 PP

>> MCR_alpha  Methyl-coenzyme M reductase alpha subunit, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.7   4.5   4.2e-65   2.5e-61       1     127 []     317     444 ..     317     444 .. 0.99

  Alignments for each domain:
  == domain 1  score: 205.7 bits;  conditional E-value: 4.2e-65
                         MCR_alpha   1 dqiwlGsymsGGvGftqyataaytdnilddfvyygvdyvkdkygglakvka.tlevvkdiatevtlyaleqyekypt 76 
                                       dqi+lG+ymsGGvGftqyataaytdnil+d+vy++vd++kdkygg++ vka +++++ ++++e++ yale+ye+yp+
  gi|474934052|ref|YP_007687634.1| 317 DQIYLGGYMSGGVGFTQYATAAYTDNILEDYVYHAVDIIKDKYGGFCGVKAdDYKKQLQLGDEISSYALEMYERYPA 393
                                       9*************************************************9678999******************** PP

                         MCR_alpha  77 lledhfGGsqraavlaaaagistalatgnsnaGlngwylsmllhkeahsrl 127
                                       ++e+hfGGsqra+v+aa++gi+ a+atg++++Gln wy+sml+hke+++rl
  gi|474934052|ref|YP_007687634.1| 394 VMETHFGGSQRATVTAASTGIAGAMATGVADNGLNLWYQSMLQHKERTGRL 444
                                       *************************************************98 PP

>> XH  XH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.4    0.0014       8.4       8      48 ..       5      75 ..       3     152 .. 0.59
   2 ?    0.9   0.0     0.066   3.9e+02      67      83 ..     195     211 ..     186     217 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0014
                                XH  8 ekpFleackkklseeeaeekaaelc.slWqeeikdp.............................kwhPfk 48
                                      ek Fleackkk++ee ++++++  c   W+++ +++                             +w+P++
  gi|474934052|ref|YP_007687634.1|  5 EKLFLEACKKKFKEEPTSMETKYYCyGGWKQSKSKVefqkeameiakkrgfpmmnedvgvplgqrSWMPYQ 75
                                      688*********98887666665551567766555544445555555555555555555555555555555 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.066
                                XH  67 LkeLkeeyGeevykaVt 83 
                                        ++Lk+ +G+ v++aV+
  gi|474934052|ref|YP_007687634.1| 195 AEKLKKAMGKTVMQAVR 211
                                       579************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (552 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 3477.85
//
Query:       gi|474934053|ref|YP_007687635.1|  [L=96]
Description: archaeal conserved hypothetical protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.8e-25   87.0   0.8    8.8e-25   86.9   0.8    1.0  1  DUF2098   Uncharacterized protein conserved in archaea (DUF20


Domain annotation for each model (and alignments):
>> DUF2098  Uncharacterized protein conserved in archaea (DUF2098)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.9   0.8   4.9e-29   8.8e-25       2      94 .]       5      96 .]       4      96 .] 0.95

  Alignments for each domain:
  == domain 1  score: 86.9 bits;  conditional E-value: 4.9e-29
                           DUF2098  2 ievGsvVrYinTgTvGkVvdikkeedgevwvkLdstdLyYrvdtLevideke.......kkkekeekekedleelekke 73
                                      +e G++V+Y+ T+TvGk+vd++ eedg+vwvkLd ++LyYr++t+e++d++e       ++k+ke  +++d+e+l++++
  gi|474934053|ref|YP_007687635.1|  5 MEKGEIVKYMPTSTVGKIVDVR-EEDGSVWVKLDVSNLYYRASTVEPCDASEykatsfkERKAKEYGSAQDIEDLKRMQ 82
                                      899*******************.****************************9******99999999************* PP

                           DUF2098 74 keleeevdeeketdesceGGG 94
                                      ke++        td+s +GGG
  gi|474934053|ref|YP_007687635.1| 83 KEVD-------ITDMSPTGGG 96
                                      ***9.......6789999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 585.31
//
Query:       gi|474934054|ref|YP_007687636.1|  [L=408]
Description: putative methanogenesis marker protein 1 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-83  280.9   0.0    1.7e-83  280.6   0.0    1.1  1  YcaO           YcaO cyclodehydratase, ATP-ad Mg2+-binding
  ------ inclusion threshold ------
      0.031   14.3   0.0       0.05   13.7   0.0    1.3  1  TPK_catalytic  Thiamin pyrophosphokinase, catalytic domain


Domain annotation for each model (and alignments):
>> YcaO  YcaO cyclodehydratase, ATP-ad Mg2+-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  280.6   0.0   1.9e-87   1.7e-83       1     323 []      71     386 ..      71     386 .. 0.90

  Alignments for each domain:
  == domain 1  score: 280.6 bits;  conditional E-value: 1.9e-87
                              YcaO   1 nGkGateeaArasalgEalErysaegffrgdekrvrasyrel.egegaldpeelglyseeekdaadfvlepfdpdrp 76 
                                       nGkG t+e+A+as+++Ea+Ery+ae   r+d++  +++y++  + +  ++pe+l l+ +          +  + +++
  gi|474934054|ref|YP_007687636.1|  71 NGKGPTPEQAEASGIMEAMERYAAE--PREDDEIAYGTYEQAsDIGLTVNPESLILPMP---------HRGAWMGQQ 136
                                       8*********************977..566666666******999************66.........7999***** PP

                              YcaO  77 idwvpgwsltdgeevlvPanlvyl.yeppegearlfletsnGlAaGntleeAilhGllEliERdafalawyerlplp 152
                                       i w++g+++++g++v+vPa +vy+ y+p+e+  +lf++ +nG AaGnt+eeAilh+llE iERda ++a y++ +  
  gi|474934054|ref|YP_007687636.1| 137 IAWCEGYEMFRGCPVWVPACAVYHvYKPDEDF-QLFRSHTNGIAAGNTMEEAILHALLEDIERDAWSIAEYNETANA 212
                                       ************************87777765.9***************************************9999 PP

                              YcaO 153 ridlasd.peirellerlreagievrlldatldlgipvvaavlvd...pk.lllvagaGahldpevAlerAltElaq 224
                                       ++ + ++ +   +ll+++r+ag+ev+l+d+t+d+gi++++a ++d   ++  +l++g+G+hldp++A +rAltE+aq
  gi|474934054|ref|YP_007687636.1| 213 DVIIGDEnSVPGKLLKKFRDAGVEVHLKDITTDIGITTIGAAADDvetKDpEMLTIGVGTHLDPQIACIRALTEVAQ 289
                                       88777445999**********************************9652268899********************** PP

                              YcaO 225 srltlisgaredpdfdeeladvatleradreallwl.peaaakrldfllfaewassgdleedletllerlkaagld. 299
                                       sr+t+++g + +++   + + + ++e  ++++ lw+ +++++ +l +++  ++ +++ + +d+e +l++l +ag+d 
  gi|474934054|ref|YP_007687636.1| 290 SRATHKDGTKINAQL-VKKNLELGYEGVKKQNPLWYrKSNKS-KLLEDM--PNLATDYVLDDIEVVLQHLMDAGFDm 362
                                       ********8866666.45678888886677799999677777.888888..666679*******************9 PP

                              YcaO 300 vlvvdltrpdlglpvvkvivPgle 323
                                       v+  dltrp++g+pvv++ vPgle
  gi|474934054|ref|YP_007687636.1| 363 VVCNDLTRPETGVPVVRMTVPGLE 386
                                       9999******************97 PP

>> TPK_catalytic  Thiamin pyrophosphokinase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.6e-06      0.05      28     116 ..     207     292 ..     179     295 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.6e-06
                     TPK_catalytic  28 rlellpdvivGDlDSirpevkefyeskgteivkkpdqdstDlekaialvlekekedknksivvlgalggRfDhtlan 104
                                       ++    dvi+GD  S+  + ++++++ g+e+  k+   +tD+  +   ++ +  e k  + +++ ++g+ +D  +a+
  gi|474934054|ref|YP_007687636.1| 207 NETANADVIIGDENSVPGKLLKKFRDAGVEVHLKD--ITTDIGITTIGAAADDVETKDPE-MLTIGVGTHLDPQIAC 280
                                       456678**********************9997655..57888776655555554454444.5556799********* PP

                     TPK_catalytic 105 invllklkkkki 116
                                       i  l +++++++
  gi|474934054|ref|YP_007687636.1| 281 IRALTEVAQSRA 292
                                       ****99877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 2360.28
//
Query:       gi|474934055|ref|YP_007687637.1|  [L=219]
Description: putative membrane protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       778  (0.0433934); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 1254.27
//
Query:       gi|474934056|ref|YP_007687638.1|  [L=212]
Description: hypothetical protein TALC_00476 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1267.88
//
Query:       gi|474934057|ref|YP_007687639.1|  [L=321]
Description: archaeal conserved hypothetical protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-32  110.5   1.5    6.3e-32  109.5   1.5    1.5  1  DUF2111   Uncharacterized protein conserved in archaea (DUF21
    1.5e-05   25.2   0.0    4.2e-05   23.7   0.0    1.7  2  DUF4443   Domain of unknown function (DUF4443)


Domain annotation for each model (and alignments):
>> DUF2111  Uncharacterized protein conserved in archaea (DUF2111)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.5   1.5     7e-36   6.3e-32       1      82 [.     223     303 ..     223     304 .. 0.99

  Alignments for each domain:
  == domain 1  score: 109.5 bits;  conditional E-value: 7e-36
                           DUF2111   1 vhelvgklPvtirsknkkGvriekgkvvdedYtgpvLeevleegkvikkvpkeGaYkGvpvvvaPikekegkviaai 77 
                                       vh+lvg lPv+++s+++ G+rie+gkv+d++Ytg vLeevl+ g++i++++++G+YkG++v+v+P++  +++viaai
  gi|474934057|ref|YP_007687639.1| 223 VHDLVGGLPVCAKSRDNLGIRIEDGKVIDNAYTGAVLEEVLKVGTTIRRIATSGPYKGIRVIVTPLEM-NNSVIAAI 298
                                       8*******************************************************************.******** PP

                           DUF2111  78 GvVDi 82 
                                       GvVDi
  gi|474934057|ref|YP_007687639.1| 299 GVVDI 303
                                       ****8 PP

>> DUF4443  Domain of unknown function (DUF4443)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.66   5.9e+03      41      60 ..      60      79 ..      54      89 .. 0.77
   2 !   23.7   0.0   4.7e-09   4.2e-05      28     105 ..     117     191 ..      95     195 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.66
                           DUF4443 41 kgamilivkngepvfpeder 60
                                      +  +i + kng  + pe ++
  gi|474934057|ref|YP_007687639.1| 60 ESNLISVKKNGVTLTPEGKK 79
                                      56678889999999998765 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 4.7e-09
                           DUF4443  28 sielrdeairffakgamilivkngepvfpederplrdtmeelamnieevlnfsdgdlivvtwaenpsdamksayhva 104
                                         e rd ai+  a ga  li  ng  +fp +e p+    e+    i + + + + d+i++  a+ p +a + a    
  gi|474934057|ref|YP_007687639.1| 117 GCEERDSAIKSGATGATTLICSNGMLMFPGNEYPVSAKAEK---AIRNAFSLNNEDVIIIGTADTPEQAEEGAVTAG 190
                                       4689*******************************998876...46677888899************9988887665 PP

                           DUF4443 105 l 105
                                       l
  gi|474934057|ref|YP_007687639.1| 191 L 191
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2374.93
//
Query:       gi|474934058|ref|YP_007687640.1|  [L=546]
Description: methyl coenzyme M reductase system, component A2 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.9e-50  170.3   0.0    4.3e-25   88.8   0.0    2.3  2  ABC_tran     ABC transporter
    1.6e-05   24.9   1.0        1.9    8.2   0.1    3.8  4  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
      2e-05   24.2   1.9       0.17   11.6   0.5    2.4  2  AAA_29       P-loop containing region of AAA domain
    2.1e-05   24.5   0.3      0.094   12.6   0.1    2.4  2  RsgA_GTPase  RsgA GTPase
    2.1e-05   24.8   0.6        0.2   11.9   0.1    2.8  2  AAA_22       AAA domain
    4.3e-05   23.9   0.0       0.17   12.2   0.0    2.7  2  AAA_16       AAA ATPase domain
     0.0013   18.5   0.9       0.54   10.0   0.1    3.0  3  AAA_30       AAA domain
     0.0018   18.4   0.3       0.31   11.2   0.1    2.8  3  AAA_33       AAA domain
     0.0024   17.1   2.0       0.73    9.0   0.2    2.4  2  NB-ARC       NB-ARC domain
     0.0033   17.1   0.3        1.7    8.3   0.0    2.5  2  ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-bindi
     0.0081   16.7   0.1          2    9.0   0.1    2.8  2  AAA_18       AAA domain
  ------ inclusion threshold ------
      0.011   16.2   1.3        0.3   11.6   0.0    2.3  2  AAA_23       AAA domain
      0.012   15.7   1.5        4.6    7.4   0.0    2.9  3  MMR_HSR1     50S ribosome-binding GTPase
      0.014   15.1   0.2        2.4    7.9   0.2    2.3  2  PRK          Phosphoribulokinase / Uridine kinase family
      0.032   13.2   0.0      0.053   12.4   0.0    1.3  1  mTERF        mTERF
       0.05   13.1   0.5         13    5.2   0.0    3.0  3  PhoH         PhoH-like protein
       0.07   11.8   0.0      0.096   11.3   0.0    1.3  1  PEPCK_ATP    Phosphoenolpyruvate carboxykinase
      0.099   12.5   0.7         14    5.6   0.1    2.7  2  MobB         Molybdopterin guanine dinucleotide synthesis pro
        0.1   12.5   0.2          4    7.3   0.0    2.3  2  NACHT        NACHT domain
       0.11   12.2   0.6         12    5.6   0.1    2.9  3  AAA_24       AAA domain
       0.11   11.7   0.1        9.5    5.4   0.0    2.3  2  Zeta_toxin   Zeta toxin
       0.12   12.7   0.0         13    6.1   0.0    2.7  2  SbcCD_C      Putative exonuclease SbcCD, C subunit
       0.13   12.0   0.0         23    4.7   0.0    2.4  2  PduV-EutP    Ethanolamine utilisation - propanediol utilisati
       0.14   12.0   0.0        5.2    6.9   0.0    2.9  3  APS_kinase   Adenylylsulphate kinase
        0.2   10.3   0.0       0.43    9.2   0.0    1.5  1  AAA_13       AAA domain
       0.64   10.0   2.1         10    6.1   0.1    2.7  3  TsaE         Threonylcarbamoyl adenosine biosynthesis protein
        1.1    8.8   3.0         30    4.1   0.0    3.4  4  AAA_25       AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.5   0.0   4.9e-25   3.3e-22       1     136 [.      23     201 ..      23     202 .. 0.87
   2 !   88.8   0.0   6.5e-28   4.3e-25       2     136 ..     306     460 ..     305     461 .. 0.91

  Alignments for each domain:
  == domain 1  score: 79.5 bits;  conditional E-value: 4.9e-25
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTS..S--SEEEE.............................EETT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx.............................xxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagl..lkpteGei.............................lldg 46 
                                       lk+ s ++k ge+++++G++G+GKS Ll +l g+  +kp++G++                             +   
  gi|474934058|ref|YP_007687640.1|  23 LKDFSTTIKTGEIIGLIGRSGSGKSVLLHMLRGNadYKPDKGRViyhvnrccscgnldvpiegqpctkcggdtQ--V 97 
                                       7899***************************99733677********************888888887777442..2 PP

                                       CEGGG..........B-HHHCCHCEEEE-SS.--S-TTSBHHHH.......HHHTCHHHHHHHSTTGGTTCBGESTT CS
                                       xxxxx..........xxxxxxxxxxxxxxxx.xxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  47 kdlke..........qeleslrkeigvlpqe.pqlfpeltvren.......esdeeiekalsklglkelkdtvvkss 105
                                       +   +            +e++r +i+++ q    lf + +v en       +  ++ie+a s l+ ++++++++ + 
  gi|474934058|ref|YP_007687640.1|  98 Q---NidywalgqhdPVREEVRDRIAIMLQRtFALFGDNSVIENvmealpdNTPKKIEAAFSLLEFVNMTHRTM-HI 170
                                       2...133366777878899********9999889999999****9*99999888899***99999999999998.56 PP

                                       SGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 106 pssLSgGqkqrvalarallkkpkllllDEpt 136
                                       ++ LSgG+kqrv++ar l+k+p ++l+DEpt
  gi|474934058|ref|YP_007687640.1| 171 ARDLSGGEKQRVVMARQLAKNPLFFLADEPT 201
                                       6*****************************9 PP

  == domain 2  score: 88.8 bits;  conditional E-value: 6.5e-28
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET.TCEGGG......B-HHHCCHCEEEE-SS--S- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx......xxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilld.gkdlke......qeleslrkeigvlpqepqlf 71 
                                       + v++++ e e+ ai+G +GaGK+t+ +++agl++ teG+++++ g+d+ +      + + ++   ig+l+qe +l 
  gi|474934058|ref|YP_007687640.1| 306 DGVTFDIGEREVFAIIGLSGAGKTTVSRMIAGLSSATEGKVEVRiGDDWVDmgkegvEGRGRATPYIGILHQEYTLY 382
                                       789*****************************************9999999999999999999************** PP

                                       TTSBHHHH............HHHTCHHHHHHHSTTGGTT.CBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEEST CS
                                       xxxxxxxx............xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  72 peltvren............esdeeiekalsklglkelk.dtvvksspssLSgGqkqrvalarallkkpkllllDEp 135
                                       p  tv en             ++ ++ ++l ++g ++++ +++++  p +LS G+ qr+a a++l+k+p+l++lDEp
  gi|474934058|ref|YP_007687640.1| 383 PFDTVLENlttcigvnmpaeLARMKAIQVLMSVGFDKKEvNRILEAYPDTLSVGECQRIAFAQVLIKEPRLVILDEP 459
                                       ***************998765556688889999887755167777777***************************** PP

                                       T CS
                                       x RF
                          ABC_tran 136 t 136
                                       t
  gi|474934058|ref|YP_007687640.1| 460 T 460
                                       9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0     0.005       3.3       2      20 ..      36      54 ..      35      70 .. 0.84
   2 ?   -0.6   0.0       1.4   9.1e+02     253     300 ..     186     235 ..     135     238 .. 0.74
   3 !    8.2   0.1    0.0029       1.9       2      25 ..     318     341 ..     317     383 .. 0.78
   4 ?    4.8   0.0     0.031        21     233     301 ..     429     496 ..     406     498 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.005
                            AAA_21  2 nvliGpNgsGKSnLLdald 20
                                       +liG+ gsGKS LL  l+
  gi|474934058|ref|YP_007687640.1| 36 IGLIGRSGSGKSVLLHMLR 54
                                      68************97775 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.4
                            AAA_21 253 ralkkgsllli.DEpEngLHPkllrrll..ellkelsrngaQviltTHSpl 300
                                       r+l k++l+++ DEp   L+P  +++++  +l+k+ +++++  i+++H p+
  gi|474934058|ref|YP_007687640.1| 186 RQLAKNPLFFLaDEPTGTLDP-YTAEIIhtKLVKYVKEHNICMIFASHWPE 235
                                       333344555555999999999.66666668888888888888899999665 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0029
                            AAA_21   2 nvliGpNgsGKSnLLdaldllarl 25 
                                        ++iG  g+GK+++ + + +l+++
  gi|474934058|ref|YP_007687640.1| 318 FAIIGLSGAGKTTVSRMIAGLSSA 341
                                       68******************9764 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.031
                            AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrll.ellkelsr.ngaQviltTHS.pll 301
                                        ++ lS G  + +a++  l+  +   +l+++DEp   ++P +++ ++ + + ++++  g  +++++H+  ++
  gi|474934058|ref|YP_007687640.1| 429 YPDTLSVGECQRIAFAQVLIKEP---RLVILDEPTGTMDP-ITKAIVaKSVLRARDtLGETFVVVSHDmDFI 496
                                       55667777777778888888877...**************.8888888666444445789999999995555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.5   0.00026      0.17      18      39 ..      29      50 ..      22      53 .. 0.81
   2 !   11.4   0.0   0.00031      0.21      12      38 ..     305     331 ..     303     335 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00026
                            AAA_29 18 eidlkgatlltGpsGsGKSTll 39
                                      +i++ +++ l+G+sGsGKS ll
  gi|474934058|ref|YP_007687640.1| 29 TIKTGEIIGLIGRSGSGKSVLL 50
                                      5565558889*********998 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00031
                            AAA_29  12 fdghtieidlkgatlltGpsGsGKSTl 38 
                                        dg t++i +++++ ++G sG+GK+T+
  gi|474934058|ref|YP_007687640.1| 305 VDGVTFDIGEREVFAIIGLSGAGKTTV 331
                                       578899999999*************96 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1   0.00014     0.094      93     125 ..      26      59 ..      11      67 .. 0.83
   2 !    9.5   0.0    0.0013      0.84      88     130 ..     303     346 ..     272     352 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                                       HHHHCTT.SEEEEECSTTSSHHHHHHHHCTT--- CS
                       RsgA_GTPase  93 lkellkd.ktsvlvGqSGvGKStLinallpelel 125
                                        ++ +k  +++ l+G SG GKS L+ +l+++++ 
  gi|474934058|ref|YP_007687640.1|  26 FSTTIKTgEIIGLIGRSGSGKSVLLHMLRGNADY 59 
                                       555666658999*****************99875 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0013
                                       TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                       RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinallpelelktgev 130
                                       ++++ ++  + + ++ +++G SG+GK+t+  ++++  ++  g+v
  gi|474934058|ref|YP_007687640.1| 303 KAVDGVTFDIGErEVFAIIGLSGAGKTTVSRMIAGLSSATEGKV 346
                                       56666666676668999************999988666655555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.1   0.00031       0.2       4      30 ..      32      58 ..      28      81 .. 0.82
   2 !   10.2   0.1     0.001      0.67       5      26 ..     315     336 ..     311     348 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00031
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleqld 30
                                      t  i+ ++G sG+GK++ll +l+ ++d
  gi|474934058|ref|YP_007687640.1| 32 TGEIIGLIGRSGSGKSVLLHMLRGNAD 58
                                      677899***************998875 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.001
                            AAA_22   5 agilvvtGesGtGKTtllrrll 26 
                                       + + +++G sG+GKTt+ r+++
  gi|474934058|ref|YP_007687640.1| 315 REVFAIIGLSGAGKTTVSRMIA 336
                                       66789************99876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00026      0.17      23      57 ..      32      68 ..      22     137 .. 0.79
   2 !    8.8   0.0    0.0029       1.9      22      51 ..     313     342 ..     304     395 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00026
                            AAA_16 23 rpelvllsGesGvGKsslvrellralekd..ggiflr 57
                                      ++e++ l+G sG+GKs l+ +l+  +  +  +g +++
  gi|474934058|ref|YP_007687640.1| 32 TGEIIGLIGRSGSGKSVLLHMLRGNADYKpdKGRVIY 68
                                      348999***************9976665554444444 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0029
                            AAA_16  22 grpelvllsGesGvGKsslvrellralekd 51 
                                       g+ e+  ++G sG GK+++ r+++   +++
  gi|474934058|ref|YP_007687640.1| 313 GEREVFAIIGLSGAGKTTVSRMIAGLSSAT 342
                                       5557889**************999533333 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.032        21      17      41 ..      33      56 ..      25      69 .. 0.75
   2 !   10.0   0.1   0.00081      0.54      17      49 ..     314     346 ..     308     350 .. 0.85
   3 ?    0.0   0.0      0.88   5.9e+02      60      97 ..     410     459 ..     400     483 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.032
                            AAA_30 17 gdrvavltGpAGtGKttalkalrea 41
                                      g  +  l G+ G+GK+ +l  lr  
  gi|474934058|ref|YP_007687640.1| 33 G-EIIGLIGRSGSGKSVLLHMLRGN 56
                                      4.377899***********999754 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00081
                            AAA_30  17 gdrvavltGpAGtGKttalkalreaweaaggrv 49 
                                       ++ v ++ G  G+GKtt+ + ++ +  a +g+v
  gi|474934058|ref|YP_007687640.1| 314 EREVFAIIGLSGAGKTTVSRMIAGLSSATEGKV 346
                                       567999***************999998887666 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.88
                            AAA_30  60 kvLaeelgieastiakllkrlk.............grarlepgtllivDEa 97 
                                       +vL  ++g++ + ++++l+++              +++ +++ +l+i DE 
  gi|474934058|ref|YP_007687640.1| 410 QVLM-SVGFDKKEVNRILEAYPdtlsvgecqriafAQVLIKEPRLVILDEP 459
                                       4444.7888888888888777788888888888886677888899999993 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.064        42       4      19 ..      38      53 ..      35      67 .. 0.85
   2 !   11.2   0.1   0.00047      0.31       2      19 ..     318     335 ..     317     381 .. 0.86
   3 ?   -2.4   0.0       7.1   4.7e+03      59      78 ..     441     459 ..     385     491 .. 0.57

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.064
                            AAA_33  4 lvGlpGsGKstlaerl 19
                                      l+G +GsGKs l++ l
  gi|474934058|ref|YP_007687640.1| 38 LIGRSGSGKSVLLHML 53
                                      79*********98765 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00047
                            AAA_33   2 vllvGlpGsGKstlaerl 19 
                                       + ++Gl+G+GK+t+++ +
  gi|474934058|ref|YP_007687640.1| 318 FAIIGLSGAGKTTVSRMI 335
                                       6789**********9976 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 7.1
                            AAA_33  59 lnelarkalsagrnvildat 78 
                                       + ++a+   ++ r vild +
  gi|474934058|ref|YP_007687640.1| 441 I-AFAQVLIKEPRLVILDEP 459
                                       3.455556666666666655 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.1     0.004       2.7      21      38 ..      34      51 ..      21      59 .. 0.86
   2 !    9.0   0.2    0.0011      0.73      17      61 ..     314     359 ..     301     370 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.004
                                      EEEEEEESTTSSHHHHHH CS
                            NB-ARC 21 lvvalvGmgGvGKttlak 38
                                       +++l G+ G+GK++l++
  gi|474934058|ref|YP_007687640.1| 34 EIIGLIGRSGSGKSVLLH 51
                                      499************986 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0011
                                       TSCSEEEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEE...EEEEES CS
                            NB-ARC  17 elqslvvalvGmgGvGKttlakqilnksdevegrFdsva...wvvvsk 61 
                                       e +  v a+ G  G GKtt+++ i   s+ +eg+ ++ +   wv ++k
  gi|474934058|ref|YP_007687640.1| 314 ERE--VFAIIGLSGAGKTTVSRMIAGLSSATEGKVEVRIgddWVDMGK 359
                                       555..99*****************999999999988776555777766 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0025       1.7       6      46 ..      25      68 ..      20     274 .. 0.85
   2 !    6.7   0.2    0.0075         5       9      50 ..     310     351 ..     301     442 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0025
                                      HHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTS..S.EEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..x.xxxx RF
                       ATP-synt_ab  6 DalfpivqGqrtlipgafgvGktvisqslskqsnsd..d.aiiy 46
                                      D  ++i  G+ ++++g +g Gk+v++++l  +++ +  +  +iy
  gi|474934058|ref|YP_007687640.1| 25 DFSTTIKTGEIIGLIGRSGSGKSVLLHMLRGNADYKpdKgRVIY 68
                                      67789999********************9888765554345555 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0075
                                       S-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEEES CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab   9 fpivqGqrtlipgafgvGktvisqslskqsnsddaiiyvgiG 50 
                                       f i++ +  +i+g +g Gkt++s++++  s++++  + v iG
  gi|474934058|ref|YP_007687640.1| 310 FDIGEREVFAIIGLSGAGKTTVSRMIAGLSSATEGKVEVRIG 351
                                       5566666779****************9998666555555544 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.066        44       1      21 [.      36      56 ..      36     145 .. 0.82
   2 !    9.0   0.1    0.0029         2       3      19 ..     320     336 ..     319     361 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.066
                            AAA_18  1 IlltGtpGvGKttlakeLskr 21
                                      I+l G +G+GK+ l + L+  
  gi|474934058|ref|YP_007687640.1| 36 IGLIGRSGSGKSVLLHMLRGN 56
                                      899***********9999654 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0029
                            AAA_18   3 ltGtpGvGKttlakeLs 19 
                                       + G +G+GKtt+++ ++
  gi|474934058|ref|YP_007687640.1| 320 IIGLSGAGKTTVSRMIA 336
                                       89***********9885 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.4      0.18   1.2e+02      16      39 ..      25      53 ..       8      55 .. 0.67
   2 ?   11.6   0.0   0.00045       0.3      11      36 ..     306     332 ..     298     338 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.18
                            AAA_23 16 dF.....skgltlItGpNGaGKTTildAi 39
                                      dF        +  ++G  G+GK+ +l  +
  gi|474934058|ref|YP_007687640.1| 25 DFsttikTGEIIGLIGRSGSGKSVLLHML 53
                                      55555555568899*********998655 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00045
                            AAA_23  11 rdqeidF.skgltlItGpNGaGKTTil 36 
                                       +++++d  ++ +++I+G  GaGKTT+ 
  gi|474934058|ref|YP_007687640.1| 306 DGVTFDIgEREVFAIIGLSGAGKTTVS 332
                                       56778887889**************85 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0069       4.6       2      22 ..      36      56 ..      35      68 .. 0.86
   2 ?    6.1   0.2     0.017        11       2      22 ..     318     338 ..     317     351 .. 0.79
   3 ?   -2.5   0.0       8.1   5.4e+03      28      55 ..     457     483 ..     440     514 .. 0.57

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0069
                                      EEEEESTTSSHHHHHHHHHTS CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltge 22
                                      ++++Gr+ +GKS L+  l g+
  gi|474934058|ref|YP_007687640.1| 36 IGLIGRSGSGKSVLLHMLRGN 56
                                      89*************999775 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.017
                                       EEEEESTTSSHHHHHHHHHTS CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltge 22 
                                       +ai+G + +GK+t+ + + g 
  gi|474934058|ref|YP_007687640.1| 318 FAIIGLSGAGKTTVSRMIAGL 338
                                       59************9999874 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 8.1
                                       SSTTSSSSEEEEEEEETTEEEEEEECGG CS
                          MMR_HSR1  28 dkpgtTrdinegrvklkgkeielvDtpG 55 
                                       d+p  T d++++ +   ++ ++  Dt G
  gi|474934058|ref|YP_007687640.1| 457 DEPTGTMDPITKAIV-AKSVLRARDTLG 483
                                       455555555544443.223344444443 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.028        19       1      20 [.      35      54 ..      35      73 .. 0.87
   2 ?    7.9   0.2    0.0035       2.4       2      20 ..     318     336 ..     317     355 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.028
                               PRK  1 vIgvagsSGaGkttvarkle 20
                                      +Ig+ g SG+Gk+ + + l+
  gi|474934058|ref|YP_007687640.1| 35 IIGLIGRSGSGKSVLLHMLR 54
                                      8************9887765 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0035
                               PRK   2 IgvagsSGaGkttvarkle 20 
                                        ++ g SGaGkttv+r + 
  gi|474934058|ref|YP_007687640.1| 318 FAIIGLSGAGKTTVSRMIA 336
                                       6899***********9986 PP

>> mTERF  mTERF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     8e-05     0.053     201     246 ..     387     435 ..     378     449 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8e-05
                             mTERF 201 vikkyPqilsls...eekilksvetLlglGfskeevakmvkrfpqllgl 246
                                       v++++  +++++   e + +k ++ L+++Gf k+ev ++  ++p+ l +
  gi|474934058|ref|YP_007687640.1| 387 VLENLTTCIGVNmpaELARMKAIQVLMSVGFDKKEVNRILEAYPDTLSV 435
                                       6777777777777666666777788888888888888888888877754 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.019        13      12      35 ..      26      49 ..      20      71 .. 0.85
   2 ?   -1.7   0.0       2.4   1.6e+03     177     201 ..      96     120 ..      94     124 .. 0.86
   3 ?    4.7   0.0     0.027        18      17      50 ..     313     347 ..     303     412 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.019
                                      HHHHHHH-SEEEEE--TTSSTTHH CS
                              PhoH 12 ylealkkndivfaiGpaGtGKtyl 35
                                      + +++k+ +i+  iG++G+GK+ l
  gi|474934058|ref|YP_007687640.1| 26 FSTTIKTGEIIGLIGRSGSGKSVL 49
                                      67789999*************987 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.4
                                       T-TTEEEEE--GGG----HHHHHHH CS
                              PhoH 177 nvegieivelkkkdvvRhplvkkiv 201
                                       +v++i+  +l ++d vR+++  +i 
  gi|474934058|ref|YP_007687640.1|  96 QVQNIDYWALGQHDPVREEVRDRIA 120
                                       67899999***********999886 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.027
                                       HH-SEEEEE--TTSSTTHHH.HHHHHHHHHTTS-S CS
                              PhoH  17 kkndivfaiGpaGtGKtyla.valavealkkkkvk 50 
                                        + ++  +iG +G+GKt ++ + ++++  +++kv+
  gi|474934058|ref|YP_007687640.1| 313 GEREVFAIIGLSGAGKTTVSrMIAGLSSATEGKVE 347
                                       5788999**********998345567777777665 PP

>> PEPCK_ATP  Phosphoenolpyruvate carboxykinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00015     0.096     205     247 ..     312     362 ..     181     394 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
                                       E-T.TS-EEEEEE-TTSSHHHHH..........-BTTB-EEESSEEEE-SS-E CS
                         PEPCK_ATP 205 vgekkgdvalfFGLSGtGKTtLs..........adperkligdDehgwsdegv 247
                                       +g  + +v    GLSG+GKTt+s          + + ++ igdD + + +egv
  gi|474934058|ref|YP_007687640.1| 312 IG--EREVFAIIGLSGAGKTTVSrmiaglssatEGKVEVRIGDDWVDMGKEGV 362
                                       45..23577779***********999999987545556679999777777666 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.046        31       1      19 [.      35      53 ..      35      59 .. 0.91
   2 ?    5.6   0.1      0.02        14       1      23 [.     317     338 ..     317     349 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.046
                              MobB  1 vlgivgksgsGKTtLlekl 19
                                      ++g++g+sgsGK  Ll+ l
  gi|474934058|ref|YP_007687640.1| 35 IIGLIGRSGSGKSVLLHML 53
                                      799************9866 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.02
                              MobB   1 vlgivgksgsGKTtLleklipel 23 
                                       v++i+g sg+GKTt  +++i+ l
  gi|474934058|ref|YP_007687640.1| 317 VFAIIGLSGAGKTTV-SRMIAGL 338
                                       689**********95.5666555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0061         4       4      20 ..      37      53 ..      34      80 .. 0.74
   2 ?    2.8   0.2      0.15        97       2      21 ..     317     336 ..     316     346 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0061
                                      EEEC-TTTCHHHHHHHH CS
                             NACHT  4 ilqGeaGsGKTtLlqkl 20
                                       l G++GsGK++Ll+ l
  gi|474934058|ref|YP_007687640.1| 37 GLIGRSGSGKSVLLHML 53
                                      589***********976 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.15
                                       CEEEEC-TTTCHHHHHHHHH CS
                             NACHT   2 lvilqGeaGsGKTtLlqkla 21 
                                       + ++ G +G GKTt  + +a
  gi|474934058|ref|YP_007687640.1| 317 VFAIIGLSGAGKTTVSRMIA 336
                                       56899*********887776 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.087        58       5      22 ..      36      53 ..      32      64 .. 0.84
   2 ?   -1.4   0.0       2.5   1.7e+03     152     184 ..     143     184 ..     120     206 .. 0.80
   3 ?    5.6   0.1     0.018        12       5      22 ..     318     335 ..     315     348 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.087
                            AAA_24  5 iliyGpsgiGKTtlakel 22
                                      i ++G sg+GK+ l+ +l
  gi|474934058|ref|YP_007687640.1| 36 IGLIGRSGSGKSVLLHML 53
                                      789*********999887 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.5
                            AAA_24 152 lgkktanelkeevDlvlranlkred.........kvgervlk 184
                                       l++ t ++++  + l+ ++n++  +         ++ +rv++
  gi|474934058|ref|YP_007687640.1| 143 LPDNTPKKIEAAFSLLEFVNMTHRTmhiardlsgGEKQRVVM 184
                                       678889999999999999999766677777777666666655 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.018
                            AAA_24   5 iliyGpsgiGKTtlakel 22 
                                       ++i+G sg+GKTt+ +++
  gi|474934058|ref|YP_007687640.1| 318 FAIIGLSGAGKTTVSRMI 335
                                       68***********98876 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.045        30      18      40 ..      35      57 ..      22      69 .. 0.79
   2 ?    5.4   0.0     0.014       9.5      23      47 ..     322     346 ..     313     354 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.045
                        Zeta_toxin 18 lillgGqpGAGKselaellkdel 40
                                      +i l G +G+GKs l+++l+ + 
  gi|474934058|ref|YP_007687640.1| 35 IIGLIGRSGSGKSVLLHMLRGNA 57
                                      5667899***********98775 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.014
                        Zeta_toxin  23 GqpGAGKselaellkdelerqgnvv 47 
                                       G +GAGK++++++++    ++++ v
  gi|474934058|ref|YP_007687640.1| 322 GLSGAGKTTVSRMIAGLSSATEGKV 346
                                       789**********998766444444 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.12        82      26      43 ..     167     184 ..     153     189 .. 0.78
   2 ?    6.1   0.0      0.02        13      62      78 ..     449     465 ..     436     474 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.12
                           SbcCD_C  26 lsrssgtlSGGekqflay 43 
                                       + + ++ lSGGekq +++
  gi|474934058|ref|YP_007687640.1| 167 TMHIARDLSGGEKQRVVM 184
                                       5667789******98875 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.02
                           SbcCD_C  62 palrlvfLDEAFsklDe 78 
                                       + +rlv+LDE  +++D+
  gi|474934058|ref|YP_007687640.1| 449 KEPRLVILDEPTGTMDP 465
                                       469*************7 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.035        23       4      24 ..      36      56 ..      33      73 .. 0.84
   2 ?    4.6   0.0     0.036        24       6      25 ..     320     339 ..     315     365 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.035
                         PduV-EutP  4 illiGkvgsGKttLtqalkge 24
                                      i liG++gsGK  L + l+g+
  gi|474934058|ref|YP_007687640.1| 36 IGLIGRSGSGKSVLLHMLRGN 56
                                      569*************99985 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.036
                         PduV-EutP   6 liGkvgsGKttLtqalkgee 25 
                                       +iG +g+GKtt+++ + g +
  gi|474934058|ref|YP_007687640.1| 320 IIGLSGAGKTTVSRMIAGLS 339
                                       79***********9998865 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.44     3e+02       3      22 ..      34      53 ..      32      62 .. 0.84
   2 ?   -3.1   0.0       9.6   6.4e+03      26      44 ..     237     255 ..     230     276 .. 0.80
   3 ?    6.9   0.0    0.0079       5.2       6      33 ..     319     346 ..     315     355 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.44
                                      EEEEEESSTTSSHHHHHHHH CS
                        APS_kinase  3 vvvwltGlsgsGKstianal 22
                                       ++ l G sgsGKs + ++l
  gi|474934058|ref|YP_007687640.1| 34 EIIGLIGRSGSGKSVLLHML 53
                                      578899********997776 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 9.6
                                       HHHTT--EEEEEHHHHTTT CS
                        APS_kinase  26 LvekgisvylLdGdnvRhg 44 
                                       ++++  ++y LdG +v+++
  gi|474934058|ref|YP_007687640.1| 237 IESMADRAYWLDGGEVKME 255
                                       6677788999999998865 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0079
                                       EEESSTTSSHHHHHHHHHHHHHHTT--E CS
                        APS_kinase   6 wltGlsgsGKstianalekkLvekgisv 33 
                                        + Glsg+GK+t++++++    ++  +v
  gi|474934058|ref|YP_007687640.1| 319 AIIGLSGAGKTTVSRMIAGLSSATEGKV 346
                                       578***********99875555544555 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00065      0.43      21      42 ..     320     341 ..     315     360 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00065
                            AAA_13  21 iYGwNGaGKTtLSrllrslelg 42 
                                       i G  GaGKTt+Sr+++ l++ 
  gi|474934058|ref|YP_007687640.1| 320 IIGLSGAGKTTVSRMIAGLSSA 341
                                       66889*************9653 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.21   1.4e+02      12      39 ..      28      53 ..      19      63 .. 0.76
   2 ?   -2.5   0.1       7.3   4.9e+03      79     107 ..     210     241 ..     207     255 .. 0.68
   3 ?    6.1   0.1     0.016        10      19      41 ..     315     337 ..     295     347 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.21
                                      HHHHHCHTEEEEEEESTTSSHHHHHHHH CS
                              TsaE 12 kklakalgdvilLeGdLGaGKTtlvrgl 39
                                      +++++  g++i L G  G+GK++l + l
  gi|474934058|ref|YP_007687640.1| 28 TTIKT--GEIIGLIGRSGSGKSVLLHML 53
                                      33433..889*************98776 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 7.3
                                       HHHHCTTCCCCSTSCEEEE...ETGGGGCCCS CS
                              TsaE  79 eleelgleeyleeeavvlv...EWpekleell 107
                                       e+ +++l +y++e++++++    Wpe +e++ 
  gi|474934058|ref|YP_007687640.1| 210 EIIHTKLVKYVKEHNICMIfasHWPEAIESMA 241
                                       55667777888766666664447998877664 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.016
                                       TEEEEEEESTTSSHHHHHHHHHH CS
                              TsaE  19 gdvilLeGdLGaGKTtlvrglak 41 
                                       ++v+++ G  GaGKTt +r +a 
  gi|474934058|ref|YP_007687640.1| 315 REVFAIIGLSGAGKTTVSRMIAG 337
                                       5678999999*********9875 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       2.2   1.5e+03     143     158 ..       5      20 ..       2      22 .. 0.86
   2 ?    4.1   0.0     0.045        30      30      50 ..      30      50 ..      26      70 .. 0.82
   3 ?    2.8   0.1      0.11        76      31      49 ..     313     331 ..     305     342 .. 0.89
   4 ?   -3.5   0.0       9.6   6.4e+03     141     150 ..     449     458 ..     439     464 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.2
                            AAA_25 143 vrlvviDplsralggd 158
                                       v+l+ iD++s++++g+
  gi|474934058|ref|YP_007687640.1|   5 VELITIDNVSKVFDGN 20 
                                       89*********99986 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.045
                            AAA_25 30 lpagelallaGapgtGKttla 50
                                      +  ge++ l+G++g+GK++l+
  gi|474934058|ref|YP_007687640.1| 30 IKTGEIIGLIGRSGSGKSVLL 50
                                      56789999**********986 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.11
                            AAA_25  31 pagelallaGapgtGKttl 49 
                                        + e+ +++G +g+GKtt+
  gi|474934058|ref|YP_007687640.1| 313 GEREVFAIIGLSGAGKTTV 331
                                       6789999**********98 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 9.6
                            AAA_25 141 egvrlvviDp 150
                                       +++rlv++D 
  gi|474934058|ref|YP_007687640.1| 449 KEPRLVILDE 458
                                       579*****95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (546 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.70u 0.29s 00:00:00.99 Elapsed: 00:00:00.47
# Mc/sec: 3487.24
//
Query:       gi|474934059|ref|YP_007687641.1|  [L=206]
Description: methyl-coenzyme M reductase I operon protein C [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-05   23.5   0.4    5.2e-05   22.5   0.3    1.6  1  MCR_C            Methyl-coenzyme M reductase operon protein C
  ------ inclusion threshold ------
      0.012   15.5   0.2       0.21   11.5   0.0    2.2  2  Transketolase_C  Transketolase, C-terminal domain


Domain annotation for each model (and alignments):
>> MCR_C  Methyl-coenzyme M reductase operon protein C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.3   5.8e-09   5.2e-05      68     169 ..      35     145 ..      25     179 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 5.8e-09
                             MCR_C  68 agteiavvsptLarhhlPhsaCDvaeylrraGaktnmiGlarGvgkriaq..........ikeeekrlinehDlavf 134
                                        g ++ v+++   r+h+  ++C+++  lr+ G    ++ +  G g  +            ++  e + i  + +++ 
  gi|474934059|ref|YP_007687641.1|  35 SGRDVCVIAMGPGRRHITKPVCEITYALREDGIDASVLVVNAGSGVPTDApdvttgtrfgLDPIEVERIRQYKVILI 111
                                       58899******************************999999998864432111111122245568899********* PP

                             MCR_C 135 vlGnfkdCikkkkeklfedievPvvvtggPeelkl 169
                                        lGn ++ i  k + +++++++P vv++    ++ 
  gi|474934059|ref|YP_007687641.1| 112 HLGNVRNHIIYKARLILRNVDLPAVVVSQC-PVDF 145
                                       ***********************9887654.3444 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.4e-05      0.21       3      41 ..      30      72 ..      28      90 .. 0.71
   2 ?    2.0   0.1     0.019   1.7e+02      40      86 ..     137     180 ..      99     195 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.4e-05
                                      EEEEETTSSEEEEEETTHHHH....HHHHHHHHHTTTTCEEEE CS
                   Transketolase_C  3 aeilregkdvtlvayGsmvee....aleAaeeLekegisaeVv 41
                                      a i  +g+dv+++a+G   ++    + e+  +L+++gi+a+V+
  gi|474934059|ref|YP_007687641.1| 30 ATISESGRDVCVIAMGPGRRHitkpVCEITYALREDGIDASVL 72
                                      667788**********8765511116789999****9999864 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.019
                                       EEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHHHHHHHHHHH CS
                   Transketolase_C  40 VvdlrtvkplDketilesvkktgrlvvveeavkrgGigsevaaalae 86 
                                       Vv+     p+D+e+++++  kt+ ++   e+  + G   e+++ + +
  gi|474934059|ref|YP_007687641.1| 137 VVSQ---CPVDFEDFAAIGVKTRDVMPAPEDIGTKGTIMEIVTGVVR 180
                                       4433...4888888888889999998888887777777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1486.56
//
Query:       gi|474934060|ref|YP_007687642.1|  [L=504]
Description: putative peptidyl-prolyl cis-trans isomerase (rotamase), cyclophilin family [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (504 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3496.66
//
Query:       gi|474934061|ref|YP_007687643.1|  [L=141]
Description: putative methanogenesis marker protein 6 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-38  129.5   0.0    4.3e-38  129.2   0.0    1.1  1  DUF2102   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2102  Uncharacterized protein conserved in archaea (DUF2102)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.2   0.0   2.4e-42   4.3e-38       2     103 .]      10     110 ..       9     110 .. 0.98

  Alignments for each domain:
  == domain 1  score: 129.2 bits;  conditional E-value: 2.4e-42
                           DUF2102   2 vvieseaevtpselvrkvyeleedvtiketCfGllvegeeeevekvveevrkldpnkifvkeRgfppgderrCRakr 78 
                                       ++i++++++tp+ l+r+v++++e++++ketC+G+lve++ e +++++++vr+  +n++f+k+Rg+p+gd+rrCRa++
  gi|474934061|ref|YP_007687643.1|  10 LMISPDSNITPDVLARAVHTMAENLSVKETCYGCLVEADAEVMKTIISKVRADYRNEVFTKRRGYPAGDPRRCRAQH 86 
                                       79**************************************************************************9 PP

                           DUF2102  79 ggaRpGfhqlekEvelleliskaLe 103
                                        g+RpGf+qle+E+e+l+li++aL+
  gi|474934061|ref|YP_007687643.1|  87 -GTRPGFAQLEAEWECLPLIQHALD 110
                                       .9*********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 827.25
//
Query:       gi|474934062|ref|YP_007687644.1|  [L=149]
Description: putative methanogenesis marker protein 5 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.1e-61  205.2   0.0    4.6e-61  205.1   0.0    1.0  1  DUF2112     Uncharacterized protein conserved in archaea (DUF
  ------ inclusion threshold ------
       0.16   12.2   0.0       0.28   11.3   0.0    1.4  1  FtsK_alpha  FtsK alpha domain


Domain annotation for each model (and alignments):
>> DUF2112  Uncharacterized protein conserved in archaea (DUF2112)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.1   0.0   5.1e-65   4.6e-61       1     143 []       1     143 [.       1     143 [. 0.99

  Alignments for each domain:
  == domain 1  score: 205.1 bits;  conditional E-value: 5.1e-65
                           DUF2112   1 mkvaviPdnsliladlverfgheplslakeikekvktaeldspplniteedpkkGlkyaavevPsGvrGRlsligpl 77 
                                       mkv++ P+ns+il dlverfghepls++  i+ekv++ e+d pp+n+t ed+ kGlkya++evPsG+rGRl+l+gp+
  gi|474934062|ref|YP_007687644.1|   1 MKVFIDPPNSMILFDLVERFGHEPLSSMAVIQEKVDNIEVDMPPMNVTLEDVIKGLKYAGIEVPSGIRGRLALWGPM 77 
                                       8**************************************************************************** PP

                           DUF2112  78 ieeaeaaiiveeadilfgcvGCartnelvkalirkkdiPileleyPkseeeaielvkkineFLksl 143
                                       i+ a+aai++e+++++fgcvGC+r+nel+k+l+++++iP+l ++yP++ e a+++v +i+eFL++l
  gi|474934062|ref|YP_007687644.1|  78 IDAADAAIVIENPPFSFGCVGCDRSNELTKYLLQRRGIPMLTVAYPNDAEGAKSMVGQIKEFLDNL 143
                                       ***************************************************************997 PP

>> FtsK_alpha  FtsK alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   3.2e-05      0.28      64     100 ..      28      64 ..      15      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.2e-05
                        FtsK_alpha  64 vskiaaleddlalaLaaksirieapipGksvvGievP 100
                                       ++ i++  d++ + +   ++ +e +i+G ++ GievP
  gi|474934062|ref|YP_007687644.1|  28 MAVIQEKVDNIEVDMPPMNVTLEDVIKGLKYAGIEVP 64 
                                       566888899***************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 990.13
//
Query:       gi|474934063|ref|YP_007687645.1|  [L=409]
Description: putative methanogenesis marker protein 15 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.2e-57  193.7   6.1    5.7e-57  193.2   6.1    1.2  1  BcrAD_BadFG    BadF/BadG/BcrA/BcrD ATPase family
     0.0027   18.1   0.8      0.054   13.9   0.8    2.6  1  FtsA           Cell division protein FtsA
     0.0048   16.5   0.5       0.31   10.6   0.0    2.4  2  FGGY_N         FGGY family of carbohydrate kinases, N-termina
     0.0078   15.9   0.0       0.92    9.2   0.0    2.4  2  Peptidase_M22  Glycoprotease family
  ------ inclusion threshold ------
       0.16   12.1   0.3       0.38   10.8   0.1    1.8  2  UPF0004        Uncharacterized protein family UPF0004


Domain annotation for each model (and alignments):
>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.2   6.1   1.6e-60   5.7e-57       2     266 ..     150     402 ..     149     403 .. 0.95

  Alignments for each domain:
  == domain 1  score: 193.2 bits;  conditional E-value: 1.6e-60
                                       EEEE-SSEEEEEEEETTTEEEEEEEE--TTS-HHH.........HHHHHHHHHHT--GGGECEE..EEESTTCCCTC CS
                       BcrAD_BadFG   2 GiDgGsTttkavlmdekgevlgrgitnsanlesvrfeaaekvleealtealerageeeadieetylvgtgyGratlp 78 
                                       G+D+Gs+ttkav+m++++ + + + + ++ ++s+          ++l+ea+++ag e +die +  ++tgyGr tl+
  gi|474934063|ref|YP_007687645.1| 150 GLDSGSSTTKAVVMQDNKIIGKSWTASGDVVQSAT---------QVLEEAMKQAGVELKDIEAI--GTTGYGRFTLG 215
                                       9****************988888888888888776.........9*****************88..*********** PP

                                       TTBSEEE-..HHHHHHHHHHHH-TT--...EEEEEETTEEEEEEEETTEEEEEEEESS--TTSHHHHHHHHHHHT-- CS
                       BcrAD_BadFG  79 ekfekeiirseilvhgdGavalypgtr...tvldigGqdskgiqidkgkvenfqmndrcaageGrylgiiadelnmg 152
                                       ++f+++ +++e++v+++Gav l++ +r   t++digG+d+k+i++++g ++nf+m++ ca+ +Gr+l+++a++l+++
  gi|474934063|ref|YP_007687645.1| 216 KHFNAKLVQEELTVNSKGAVWLADRQRgeaTIIDIGGMDNKAITVRDGVPDNFTMGGICAGASGRFLEMTARRLKVE 292
                                       ***************************************************************************** PP

                                       TTTHHHHHTT--.S-------SHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHHTT---SS.EEEESGGGG CS
                       BcrAD_BadFG 153 lreldglaekat.kkarinstcavfaeaelrdalsggekaedIlaglhraialrvialisrsggvtdevtltGGvak 228
                                       + el++ a +++ ++a++ns+c vf  ++l++ l  g++ ed+ a ++r++a++v +++ ++ +v+  ++ +GG++ 
  gi|474934063|ref|YP_007687645.1| 293 IGELGDYAVRGDwRNAKMNSYCSVFGIQDLVTNLGAGKVFEDVAAAACRSVAEQVYEQQLQEIDVRHPIIQVGGTSL 369
                                       ************8889************************************************************* PP

                                       -HHHHHHH.....HHHH-S-EE--GGGGGHHHHHHHHH CS
                       BcrAD_BadFG 229 neaavkelrklvkenygevkininpdsiytgalGAalf 266
                                       n+++vk++      ++++++  +++ds+y ga+G al+
  gi|474934063|ref|YP_007687645.1| 370 NKGLVKAV-----GEVLGEEPIVPKDSQYIGAVGGALL 402
                                       *9999988.....34444445689**********9987 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.8   1.5e-05     0.054       1      87 [.     149     384 ..     149     398 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.5e-05
                                       EEEEE-SSSEEEEEEETTEEEEEEEES-...-HHHHHHHHHHHHT--HHHH.HHHHHHH--S--............. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx............. RF
                              FtsA   1 alvDiGagktdvavaedgalvhlrvigv...ggngitkdiakalrtaveeA.erikikyGsala............. 60 
                                       a++D G+++t+++v++d++++     g    ++  + +++ ++l +a+++A  ++k                     
  gi|474934063|ref|YP_007687645.1| 149 AGLDSGSSTTKAVVMQDNKII-----GKswtASGDVVQSATQVLEEAMKQAgVELKD------Ieaigttgygrftl 214
                                       789**************7555.....4444466666666677777777777434441......01122333344445 PP

                                       .....EEEEEHHHHH.............................................................. CS
                                       .....xxxxxxxxxx.............................................................. RF
                              FtsA  61 .....ekeigrkels.............................................................. 70 
                                                  k ++                                                              
  gi|474934063|ref|YP_007687645.1| 215 gkhfnA-----KLVQeeltvnskgavwladrqrgeatiidiggmdnkaitvrdgvpdnftmggicagasgrflemta 286
                                       444431.....222244446777777777777777778888888888888888888888888888888888888888 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              FtsA  71 ............................................................................. 70 
                                                                                                                    
  gi|474934063|ref|YP_007687645.1| 287 rrlkveigelgdyavrgdwrnakmnsycsvfgiqdlvtnlgagkvfedvaaaacrsvaeqvyeqqlqeidvrhpiiq 363
                                       88888888998999999999999999999999999999999999998888888888888888888888888888888 PP

                                       ..GGGGSTTHHHHHHHHH..T CS
                                       ..xxxxxxxxxxxxxxxx..x RF
                              FtsA  71 ..ggsalpnleelaeral..s 87 
                                         g+s  ++l++++ ++l  +
  gi|474934063|ref|YP_007687645.1| 364 vgGTSLNKGLVKAVGEVLgeE 384
                                       888888888888888887552 PP

>> FGGY_N  FGGY family of carbohydrate kinases, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.011        40       3      21 ..     149     167 ..     147     175 .. 0.80
   2 !   10.6   0.0   8.7e-05      0.31      48      79 ..     179     210 ..     171     224 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.011
                                       EEEEEESSEEEEEEEETTS CS
                            FGGY_N   3 lglDcGttstkaivldekg 21 
                                        glD G + tka+v+  ++
  gi|474934063|ref|YP_007687645.1| 149 AGLDSGSSTTKAVVMQDNK 167
                                       69************98664 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 8.7e-05
                                       HHHHHHHHHHHHHHHCT.-GCCEEEEEEEE-S CS
                            FGGY_N  48 iwqalaeairkvleqagisekqikaIgisgqr 79 
                                       + q+ +++++++++qag++ k+i+aIg +g +
  gi|474934063|ref|YP_007687645.1| 179 VVQSATQVLEEAMKQAGVELKDIEAIGTTGYG 210
                                       57999**********************99976 PP

>> Peptidase_M22  Glycoprotease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0   0.00026      0.92      31      57 ..     181     207 ..     174     209 .. 0.87
   2 !    4.2   0.0    0.0082        29     176     249 ..     311     383 ..     271     398 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00026
                                       HHHHHHHHHHHHHHTSTGGGEEEEEEE CS
                     Peptidase_M22  31 erllplieealaeaglsledldaIavt 57 
                                       +  ++++eea+++ag++l+d++aI  t
  gi|474934063|ref|YP_007687645.1| 181 QSATQVLEEAMKQAGVELKDIEAIGTT 207
                                       678899******************877 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0082
                                       TTEEE.CHHHHHHHHHHSTT.HHHHHHHHHHHHHHHHHHHHHHHHHHCTBSE.EEEESGGGGXHHHHHCHCCHHHH CS
                     Peptidase_M22 176 gldfsfsGlktavlkeleke.vedlaasfqeavvdhlvekteralklpkake.lvilGGvaankrLrealeeeaee 249
                                       +  +s  G++  v+++   + +ed+aa+  ++v++++ e     l++ ++++ ++ +GG + nk+L +a+ e+  e
  gi|474934063|ref|YP_007687645.1| 311 NSYCSVFGIQDLVTNLGAGKvFEDVAAAACRSVAEQVYEQ---QLQEIDVRHpIIQVGGTSLNKGLVKAVGEVLGE 383
                                       44467777777777766334799***99999988885555...45555555526889*********9998765544 PP

>> UPF0004  Uncharacterized protein family UPF0004
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00011      0.38      21      66 ..      59     103 ..      53     133 .. 0.74
   2 ?   -3.5   0.0       3.2   1.2e+04      16      31 ..     184     199 ..     179     203 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00011
                                       HHTTTSSS----SSS--SEEEEEE--SSSSHHHHTHHHHHHHHTTS CS
                           UPF0004  21 slLkkegyelvedeeeAdvvlvnTCavrekaekkviqalrelkalk 66 
                                       +l+ ++ ++l++++ +Ad+v++ TC   ++a   v+++lr++ +++
  gi|474934063|ref|YP_007687645.1|  59 QLMIARAVSLADEKYDADAVFITTCFRCAEA-ALVRNELRRFIQEH 103
                                       556677799999*************655554.57888888888776 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.2
                                       HHHHHHHTTTSSS--- CS
                           UPF0004  16 seelaslLkkegyelv 31 
                                       +++l +++k++g+el 
  gi|474934063|ref|YP_007687645.1| 184 TQVLEEAMKQAGVELK 199
                                       5677788888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 2820.45
//
Query:       gi|474934064|ref|YP_007687646.1|  [L=193]
Description: putative methanogenesis marker protein 17 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-54  184.6   0.2    1.3e-54  184.4   0.2    1.0  1  DUF2113   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2113  Uncharacterized protein conserved in archaea (DUF2113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.4   0.2     7e-59   1.3e-54       2     184 ..       6     185 ..       5     186 .. 0.98

  Alignments for each domain:
  == domain 1  score: 184.4 bits;  conditional E-value: 7e-59
                           DUF2113   2 evectdeegaeaYeeiirdilqDlnllrsierlkvyidpeeplFiiavllrktsspiklgdvaeveedkeegkvkik 78 
                                        v++td+ g++aY+ ++++i++D++ l+s+er +++++pe+plFii v++++++s+ k+gd+a +++  e+g v+++
  gi|474934064|ref|YP_007687646.1|   6 GVTGTDQFGNDAYKLLYQEIMYDIGKLASVERSTIVLKPEVPLFIISVKMKARPSARKIGDIAATRA--EKGVVYVS 80 
                                       6999***************************************************************..******** PP

                           DUF2113  79 iedEtylpelLkkLwekygrenveqpdRfeiiiesdedleeleelvVaDpkeelkkkvidaliriaPEGfrvrkeal 155
                                       i+dE+y+p +L +Lwe+ygr+nv+q+dR++i+++++++++e+++l V +++e+ +++++ al+r++PEG+rvr+e+ 
  gi|474934064|ref|YP_007687646.1|  81 ISDEMYAPGTLARLWEEYGRDNVQQTDRLDITVRGADTSAEVDSLEV-ESSEQPVREILGALWRVLPEGIRVRREFE 156
                                       *************************************99********.99*************************** PP

                           DUF2113 156 ednsfvfvAseetlkeewieeakelkeel 184
                                       ++  +++vA+ee++++e++ee k++++++
  gi|474934064|ref|YP_007687646.1| 157 NQGVITVVATEEIMRSEFLEEGKKVEDAM 185
                                       ***********************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1334.18
//
Query:       gi|474934065|ref|YP_007687647.1|  [L=314]
Description: putative methanogenesis marker protein 7 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   8.5e-103  343.1   0.3     1e-102  342.9   0.3    1.0  1  MCR_C     Methyl-coenzyme M reductase operon protein C
  ------ inclusion threshold ------
       0.17   12.1   0.0       0.31   11.2   0.0    1.4  1  DUF1798   Bacterial domain of unknown function (DUF1798)


Domain annotation for each model (and alignments):
>> MCR_C  Methyl-coenzyme M reductase operon protein C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  342.9   0.3  1.1e-106    1e-102       1     271 []       2     269 ..       2     269 .. 0.98

  Alignments for each domain:
  == domain 1  score: 342.9 bits;  conditional E-value: 1.1e-106
                             MCR_C   1 lepltyeGGvykhdellelieDlGGyilqknvialevvltllvPkedvelieelakellgklteaPlagteiavvsp 77 
                                       +e+++y+GG+y++del elieD+GG +l kn +++ +++t+ +P+ed +++e+ +ke+ g+++++Plagteiav+ p
  gi|474934065|ref|YP_007687647.1|   2 YEVIMYDGGIYRSDELFELIEDVGGVVLLKNRSSQMLTVTMSIPEEDRPMVEAFCKEIGGQVRDVPLAGTEIAVIGP 78 
                                       799************************************************************************** PP

                             MCR_C  78 tLarhhlPhsaCDvaeylrraGaktnmiGlarGvgkriaqikeeekrlinehDlavfvlGnfkdCikkkkeklfedi 154
                                       tL rhh+Ph+ CD+aeylrr Ga t+++GlarG gk+++qi+ ee+++i+e+D++vf+lGnfk C+++k e l+++i
  gi|474934065|ref|YP_007687647.1|  79 TLGRHHMPHPICDIAEYLRRCGAVTVVMGLARGRGKHTSQISLEETKIIDEYDACVFMLGNFKPCVETKAELLLSNI 155
                                       ***************************************************************************** PP

                             MCR_C 155 evPvvvtggPeelkleevpgaeayvgglGriahrlrkeeeiealdelveeveevldkkreelakDpllvsparvkke 231
                                       ++P v+++gP  + +e   +++a+v+g+Gr+a r+r+  + ++l+e+ ++veevld+k++++++Dp++v+p+++k+ 
  gi|474934065|ref|YP_007687647.1| 156 NIPTVLVCGPVPEGIEG--TCDAIVTGVGRKASRMREPGDRAKLEEVGDRVEEVLDDKKKAIEEDPPFVHPSEIKAL 230
                                       **********8888887..5*******************************************************99 PP

                             MCR_C 232 ieeqveeieevlsPapitlqldglrvklpydeyaekieev 271
                                       +e ++e i+++l+Pap++++ldglr k++ydey+e+ie++
  gi|474934065|ref|YP_007687647.1| 231 LE-NFEPIDMCLRPAPLVMHLDGLRAKISYDEYHEQIENM 269
                                       98.9*********************************986 PP

>> DUF1798  Bacterial domain of unknown function (DUF1798)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.5e-05      0.31      36      76 ..     198     237 ..     194     240 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.5e-05
                                       HHHHHHHHHHHHHHHHHHHHS--SSS-HHHHHHHHHHHHHH CS
                           DUF1798  36 devkelldewkelalewvkkerpkylheeqieataenlekl 76 
                                       +ev ++++e  +++++ +++  p+ +h++ i+a+ en+e +
  gi|474934065|ref|YP_007687647.1| 198 EEVGDRVEEVLDDKKKAIEE-DPPFVHPSEIKALLENFEPI 237
                                       889999**************.*****************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2013.85
//
Query:       gi|474934066|ref|YP_007687648.1|  [L=138]
Description: hypothetical protein TALC_00486 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.5e-21   74.3   0.1    1.1e-20   73.9   0.1    1.2  1  DUF123    Domain of unknown function DUF123
  ------ inclusion threshold ------
       0.12   12.6   0.0       0.18   12.1   0.0    1.2  1  GIY-YIG   GIY-YIG catalytic domain


Domain annotation for each model (and alignments):
>> DUF123  Domain of unknown function DUF123
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.9   0.1   1.2e-24   1.1e-20       3      93 ..      30     116 ..      28     117 .. 0.81

  Alignments for each domain:
  == domain 1  score: 73.9 bits;  conditional E-value: 1.2e-24
                            DUF123   3 lkkgvylYvGsalgsgglasRvkrHaslskkkekklhWhiDyLleseeaelaevvv.aseerlEcalaeal.eaea. 76 
                                       +++g+y+YvGsa+g  gl +R++rH+++     kk +WhiD+L++  +   a+++    ++  Ec la+   e  + 
  gi|474934066|ref|YP_007687648.1|  30 FHAGTYVYVGSAMG--GLDQRLSRHLAHV----KKIRWHIDHLTTVCDS--ARAWEsYPDSIPECGLARMAeE--Cg 96 
                                       789***********..9********5544....58*********65544..444442389999*******933..22 PP

                            DUF123  77 ...pvagfGasDckcesHLl 93 
                                          +++gfG+sDc+c++HL+
  gi|474934066|ref|YP_007687648.1|  97 mvpEMDGFGCSDCSCRTHLF 116
                                       356889*************9 PP

>> GIY-YIG  GIY-YIG catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     2e-05      0.18      12      35 ..      33      57 ..      27      77 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2e-05
                                      T--EEEEEE.SSHHHHHHHHHHHHH CS
                           GIY-YIG 12 nkliYvGst.knlekRlkqHnagkk 35
                                      + ++YvGs+   l++Rl++H+a+ k
  gi|474934066|ref|YP_007687648.1| 33 GTYVYVGSAmGGLDQRLSRHLAHVK 57
                                      6789*****88*********88754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.54
# Mc/sec: 762.60
//
Query:       gi|474934067|ref|YP_007687649.1|  [L=538]
Description: FAD/FMN-containing dehydrogenase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-38  130.6   0.1    5.6e-38  129.8   0.1    1.4  1  FAD_binding_4  FAD binding domain
    6.3e-12   45.7   0.0      1e-11   45.0   0.0    1.3  1  FAD-oxidase_C  FAD linked oxidases, C-terminal domain


Domain annotation for each model (and alignments):
>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.8   0.1   6.2e-42   5.6e-38       1     139 []      56     196 ..      56     196 .. 0.97

  Alignments for each domain:
  == domain 1  score: 129.8 bits;  conditional E-value: 6.2e-42
                                       EEEEEEESSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTC.SCCEEEEEETT.S--EEEEETTTTEEEEETTSBHH CS
                     FAD_binding_4   1 paavvrpeseeevaaalrlaneaglpvlvrGgGssllgqav.atggvvldlsr.lnrileideeegtatveaGvtlg 75 
                                       p++vvrp+ +e+vaa++r+a e+g+ v++rG+ +  lg+++  + g+v+d+s  +n+i+++d+e+  ++v+aG+t++
  gi|474934067|ref|YP_007687649.1|  56 PDVVVRPTCTEDVAAVMRIAYENGVAVTPRGNSTWGLGGCQpVFAGIVVDFSSkMNKIIKLDPEHLCVKVQAGITFK 132
                                       89******************************99999999889********977*********************** PP

                                       HHHHHHHHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETTSEEEEEE CS
                     FAD_binding_4  76 dlvealaakglllglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvladGevvrls 139
                                       ++  a+ akg+++g +p+s+  +t+GG+  tn++G g  k G+++dnvl++evvl+dG+v++++
  gi|474934067|ref|YP_007687649.1| 133 EVLDACMAKGFIIGSYPSSFPAATIGGWYGTNGMGIGTYKFGSVKDNVLNMEVVLPDGSVIETG 196
                                       ************************************************************9985 PP

>> FAD-oxidase_C  FAD linked oxidases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.0   1.1e-15     1e-11      11     250 .]     242     473 ..     235     473 .. 0.84

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 1.1e-15
                                       EESSHHHHHHHHHHHHHH.T---SEEEEE-HHHHHHHHHTS-SS..TTS-TTT-EEEEEEEEE-HHHHHHHHHHHHH CS
                     FAD-oxidase_C  11 afpsfeaavkavreiaqa.giipaalelmdkkaldlveatkgak..kglpdeeealllvefegddeeeaeeelealv 84 
                                       +f+++++a  a+++ia++  i+p+ ++  d + +   ++  + +    + +e++ ++lv ++gd++ ++ e+   +v
  gi|474934067|ref|YP_007687649.1| 242 NFENLADADPAIQAIAKHpSIKPLHVSWADFNHFANQARAAKEEpsIHVHSECKNTVLVVLQGDERFVDLEDE--AV 316
                                       799999999*********9999999999996655444444444448899****************65555555..5* PP

                                       HHTTT-EEEEE..........E.TGGGGGGGGHHHHHHHHHCTTEEEEEEEEEEEHHHHHHHHHHHHHHHHHHHEEE CS
                     FAD-oxidase_C  85 eaileatgaadvlvaqdeaeae.alwkaRkaalpylrdallkagvavlseDtsvPvsrladlvrdikalldkyglev 160
                                       e+i+ ++g+++      ++e++ + w+ R + ++     +++ gv  +  ++ vP +   ++v +  + + k ++e+
  gi|474934067|ref|YP_007687649.1| 317 EEIMVKAGGQK-----LPNEIAdHEWDERCYEFR-----ARAVGVGEIPAEVIVPSNSWGQFVGECYEGFSKMKMET 383
                                       **********9.....455555599*********.....899********************************655 PP

                                       .EEEEEEETTEEEEEEEEEEE..--TT--THHHHHH..HHHHHHTT-----------------------THHHHHHH CS
                     FAD-oxidase_C 161 .vlfgHagdgnlhlyilfdladeaeeeraeklvdev..vdlavelgGsisgEHGvGldkkaylerekgeeglalmrr 234
                                         ++g++ d    l + + + d + +  + +++ ++   d+a ++gG  +g    G+  +  l +  + +++++mr+
  gi|474934067|ref|YP_007687649.1| 384 gGIIGQMVDPQTVLFMPYYFMDNEGMLGMTAFSFNFylGDVATRYGGRTTG---LGVFFAWNLDNIHDANTVEYMRE 457
                                       167899988777777777788889999999**9999999**********96...55555555*************** PP

                                       HHHHH-TT--BSTT-- CS
                     FAD-oxidase_C 235 iKaalDPkgiLNPgkv 250
                                       +K +lDP++++NPg v
  gi|474934067|ref|YP_007687649.1| 458 LKTYLDPRDVMNPGHV 473
                                       **************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (538 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:00.53
# Mc/sec: 3049.13
//
Query:       gi|474934068|ref|YP_007687650.1|  [L=293]
Description: hypothetical protein TALC_00488 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.2e-21   77.0   0.0    1.7e-21   76.6   0.0    1.2  1  DUF4143    Domain of unknown function (DUF4143)
  ------ inclusion threshold ------
       0.19   11.6   0.0       0.27   11.1   0.0    1.3  1  Herpes_gI  Alphaherpesvirus glycoprotein I


Domain annotation for each model (and alignments):
>> DUF4143  Domain of unknown function (DUF4143)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.6   0.0   1.9e-25   1.7e-21       2     122 .]      70     236 ..      69     236 .. 0.89

  Alignments for each domain:
  == domain 1  score: 76.6 bits;  conditional E-value: 1.9e-25
                                       xxxxxxxxx.xxxxxxxx.............................................xxxxxxxxxxxxxx RF
                           DUF4143   2 rDirklagv.rdpeelrk.............................................glverlppwsespn 32 
                                       +D +k +g+ rd+++l++                                              ++   p++s++ +
  gi|474934068|ref|YP_007687650.1|  70 EDAQKTDGKrRDVAKLKRlfhslarnestiatkkklstditqyedegldndtvtdyldvfgklHIIGDQPAYSPNYR 146
                                       56666666634466666677777778888888999999999999999999999999*99999**********66667 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DUF4143  33 skkrlrkspKlyfvDtGLlvallgldkeelledsenkGallEnlVaqeLlkysekegaklyyyrdkngaEvDfviel 109
                                       s  r+ k+pK +++D++L++a+lgld+++l++d  ++G+l+E l+ ++L  y+++ g+++++yrd++++E+D+v+el
  gi|474934068|ref|YP_007687650.1| 147 SPVRVGKNPKRHLADPSLAAAALGLDRKTLMNDTRTLGFLFEALCERDLTIYADTFGGEVFHYRDHSNREIDAVVEL 223
                                       777899*********************************************************************** PP

                                       xxxxxxxxxxxxx RF
                           DUF4143 110 kggkivpiEvKss 122
                                       k++ + ++E+K++
  gi|474934068|ref|YP_007687650.1| 224 KNEGWGAFEIKLG 236
                                       ***********85 PP

>> Herpes_gI  Alphaherpesvirus glycoprotein I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   3.1e-05      0.27      37      75 ..     119     158 ..      87     199 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.1e-05
                         Herpes_gI  37 ldkvvee.dvkgeLvFlGdqvpkttsYdGtvellkadeea 75 
                                        d v++  dv+g+L+ +Gdq   + +Y   v++ k ++ +
  gi|474934068|ref|YP_007687650.1| 119 NDTVTDYlDVFGKLHIIGDQPAYSPNYRSPVRVGKNPKRH 158
                                       344444226**********************999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1811.86
//
Query:       gi|474934069|ref|YP_007687651.1|  [L=146]
Description: hypothetical protein TALC_00489 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       180  (0.0100396); expected 358.6 (0.02)
Passed bias filter:                      176  (0.0098165); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1103.50
//
Query:       gi|474934070|ref|YP_007687652.1|  [L=92]
Description: Acetyltransferase (GNAT) family [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-09   38.5   0.0    1.4e-09   38.2   0.0    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    7.7e-09   35.6   0.0    9.3e-09   35.3   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    3.3e-08   33.8   0.0      8e-08   32.6   0.0    1.5  2  Acetyltransf_7   Acetyltransferase (GNAT) domain
    0.00014   21.9   0.0    0.00019   21.5   0.0    1.4  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
      0.001   19.0   0.0     0.0016   18.3   0.0    1.3  1  Rubredoxin_C     Rubredoxin NAD+ reductase C-terminal domain
     0.0038   17.4   0.1     0.0081   16.3   0.0    1.6  2  Acetyltransf_6   Acetyltransferase (GNAT) domain
     0.0092   15.7   0.0     0.0096   15.6   0.0    1.1  1  PanZ             Acetyltransferase (GNAT) domain, PanZ
  ------ inclusion threshold ------
      0.011   15.2   0.0      0.016   14.7   0.0    1.2  1  Acetyltransf_15  Putative acetyl-transferase
       0.18   11.8   0.0       0.26   11.3   0.0    1.3  1  FR47             FR47-like protein


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.0     7e-13   1.4e-09       3      84 ..      15      91 ..      13      92 .] 0.79

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 7e-13
                                      HHHHHHHHHTHHHHHHHHHHHHHHHHHSTTC.EEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHH CS
                    Acetyltransf_1  3 dlvellvesffppnedaseeefeesfsleae.gllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsa 80
                                      ++ el+ ++ +  +ed++e +   sf   ++ +++ a  dg+++G + +  +       a i+ l+V+p++r++G++ +
  gi|474934070|ref|YP_007687652.1| 15 EILELWSADRPVSREDSEEGI--SSFLSRNGkYCFTAVSDGKVVGAVLCGSDGR----SARIYHLVVDPDFRRQGIAHT 87
                                      566777777777677777777..4444467736666***********8888877....8******************** PP

                                      HHHH CS
                    Acetyltransf_1 81 Llea 84
                                      L+++
  gi|474934070|ref|YP_007687652.1| 88 LIKH 91
                                      *987 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.0   4.7e-12   9.3e-09      20      75 ..      33      91 ..      22      92 .] 0.84

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 4.7e-12
                   Acetyltransf_10 20 ealrerieegealllvaeeggkivGviel.rdgs..hisllfVdpeyrgqGigkaLlea 75
                                      e +++ ++ + ++++ a  +gk+vG++   +dg+  +i++l+Vdp++r+qGi++ L+++
  gi|474934070|ref|YP_007687652.1| 33 EGISSFLSRNGKYCFTAVSDGKVVGAVLCgSDGRsaRIYHLVVDPDFRRQGIAHTLIKH 91
                                      5556666677888999999********887777689********************986 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.9   3.8e+03      35      45 ..       4      14 ..       2      35 .. 0.72
   2 !   32.6   0.0     4e-11     8e-08       3      48 ..      44      91 ..      42      92 .] 0.88

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.9
                                      GGTTSSHHHHH CS
                    Acetyltransf_7 35 eyrgkGiGraL 45
                                      eyrg  iG  L
  gi|474934070|ref|YP_007687652.1|  4 EYRGTVIGDYL 14
                                      57776666544 PP

  == domain 2  score: 32.6 bits;  conditional E-value: 4e-11
                                      EEEEEEEETTEEEEEEEEEEES..TCTEEEEE-GGGTTSSHHHHHHHH CS
                    Acetyltransf_7  3 gevfVaeddgkivGfialslld..aeitrlaVdpeyrgkGiGraLlea 48
                                      +++f a  dgk+vG + +  ++  a i +l+Vdp++r++Gi++ L+++
  gi|474934070|ref|YP_007687652.1| 44 KYCFTAVSDGKVVGAVLCGSDGrsARIYHLVVDPDFRRQGIAHTLIKH 91
                                      5789999*******887777779999999*****************97 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   9.3e-08   0.00019      11      48 ..      55      91 ..      30      92 .] 0.82

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 9.3e-08
                   Acetyltransf_CG 11 evafleYevrkegvldfthTeVpeelrGkGiAkkLvka 48
                                       v+ +    +++    ++h +V++ +r++GiA  L+k+
  gi|474934070|ref|YP_007687652.1| 55 VVGAVLCG-SDGRSARIYHLVVDPDFRRQGIAHTLIKH 91
                                      55555554.5667899*******************985 PP

>> Rubredoxin_C  Rubredoxin NAD+ reductase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0     8e-07    0.0016      21      66 ..      29      74 ..      24      76 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 8e-07
                                      ---SEEEEEE-SS-..EEEEEEETTEEEEEEEES-HHHHHHHHHHH CS
                      Rubredoxin_C 21 eekaeelveedkekgkYkklfikngklvGAiliGDtkesaklkkli 66
                                      e++ e ++   +++gkY    + +gk+vGA+l G   +sa++  l+
  gi|474934070|ref|YP_007687652.1| 29 EDSEEGISSFLSRNGKYCFTAVSDGKVVGAVLCGSDGRSARIYHLV 74
                                      555677777788999*******************999999988775 PP

>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.96   1.9e+03      69      84 ..      12      27 ..       8      29 .. 0.85
   2 !   16.3   0.0   4.1e-06    0.0081      73     116 ..      46      89 ..      19      92 .] 0.87

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.96
                    Acetyltransf_6 69 galrlyvlrldgrpvA 84
                                      + l++++l+  +rpv+
  gi|474934070|ref|YP_007687652.1| 12 DYLEILELWSADRPVS 27
                                      6789999999999996 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 4.1e-06
                    Acetyltransf_6  73 lyvlrldgrpvAvalglrsgdrlyywlggydpelaklspgllll 116
                                       ++++  dg++v+++l+  +g+ +  +   +dp++++ ++   l+
  gi|474934070|ref|YP_007687652.1|  46 CFTAVSDGKVVGAVLCGSDGRSARIYHLVVDPDFRRQGIAHTLI 89 
                                       688899******************************99887776 PP

>> PanZ  Acetyltransferase (GNAT) domain, PanZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   4.8e-06    0.0096      36      84 ..      42      90 ..      12      92 .] 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.8e-06
                              PanZ 36 eegalfaarFNdRlLgAvkveledkeaelsdlcVRevTRrRGVgsyLle 84
                                      +++  f a    +  gAv    ++++a++ +l+V    Rr G+++ L++
  gi|474934070|ref|YP_007687652.1| 42 NGKYCFTAVSDGKVVGAVLCGSDGRSARIYHLVVDPDFRRQGIAHTLIK 90
                                      33445677788899*********************************97 PP

>> Acetyltransf_15  Putative acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0     8e-06     0.016      74      96 ..      69      91 ..      62      92 .] 0.91

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 8e-06
                   Acetyltransf_15 74 eiYtlyvsekyrgkGlakklLee 96
                                       iY+l+v++++r++G+a  l+++
  gi|474934070|ref|YP_007687652.1| 69 RIYHLVVDPDFRRQGIAHTLIKH 91
                                      69*****************9986 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00013      0.26      22      44 ..      68      90 ..      53      91 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00013
                                      SSEEEEEE-GGG-SSSHHHHHHH CS
                              FR47 22 gelgalqvlpehrrrGlgsrlvk 44
                                        ++ l v+p++rr+G +  l+k
  gi|474934070|ref|YP_007687652.1| 68 ARIYHLVVDPDFRRQGIAHTLIK 90
                                      6799**************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 633.87
//
Query:       gi|474934071|ref|YP_007687653.1|  [L=46]
Description: hypothetical protein TALC_00491 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       194  (0.0108205); expected 358.6 (0.02)
Passed bias filter:                      173  (0.00964917); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 314.28
//
Query:       gi|474934072|ref|YP_007687654.1|  [L=230]
Description: putative phosphatase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-22   79.9   0.0      3e-22   79.6   0.0    1.1  1  HAD_2           Haloacid dehalogenase-like hydrolase
      1e-16   61.8   0.7      2e-16   60.9   0.7    1.5  1  Hydrolase       haloacid dehalogenase-like hydrolase
    2.1e-09   38.1   0.1    2.6e-09   37.7   0.1    1.2  1  HAD             haloacid dehalogenase-like hydrolase
    1.5e-07   31.3   0.0    2.8e-07   30.5   0.0    1.5  1  Hydrolase_like  HAD-hyrolase-like
  ------ inclusion threshold ------
      0.015   15.4   0.0      0.064   13.4   0.0    2.3  1  Hydrolase_6     Haloacid dehalogenase-like hydrolase
      0.017   14.1   1.4        2.2    7.1   0.2    2.3  2  5_nucleotid     5' nucleotidase family


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.6   0.0   9.9e-26     3e-22       3     178 .]      14     197 ..      12     197 .. 0.86

  Alignments for each domain:
  == domain 1  score: 79.6 bits;  conditional E-value: 9.9e-26
                             HAD_2   3 FDlDgTlldteeliiqafnelleey.............glselseeelrkliglslrellrklgeseeeeekieell 66 
                                       FD+DgT +dt+  +++ +n + + y             g+ +l+ e++++ i+ +    l+k ++    ++ i+e  
  gi|474934072|ref|YP_007687654.1|  14 FDMDGTFMDTRVDYVKLANVVTDAYskygvpadvlkadGY-KLTMENCDRWIEENG---LQKHKPA--IDNEIQENA 84 
                                       *********************9999777777766665333.666666666666666...4444443..223777777 PP

                             HAD_2  67 rkyneekkkkevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekk..KPdpevi 141
                                        +++ e+ +   ++++g+ elL+ +k++g+k gi T + r+ +e  l + g+ + Fd  v  +d  ++  KP+p  +
  gi|474934072|ref|YP_007687654.1|  85 TEIEMENAN-VARIFPGAVELLDAMKAKGLKAGILTRGGRRYAEYVLGNAGVLDRFDALVARDDYPENeaKPSPLAM 160
                                       777777777.89****************************************************988778******* PP

                             HAD_2 142 ekaleklklkkeeviyvGDsptDieaakkagikviav 178
                                       e + +++++k +e++yvGD   D  +a + g ++i+v
  gi|474934072|ref|YP_007687654.1| 161 EHLAKEFGVKCDEILYVGDGLVDYLTAYNSGARFIGV 197
                                       ***********************************87 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   0.7   6.7e-20     2e-16       1     205 [.       9     186 ..       9     191 .. 0.79

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 6.7e-20
                                       SSEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrgayaigkpewl 77 
                                       ik++ fD+dGT  +++   +d ++ a                 + ++ a+ + + +  ++ +  g    +++  +w+
  gi|474934072|ref|YP_007687654.1|   9 IKAIGFDMDGTFMDTR---VDYVKLA-----------------NVVTDAYSKYGVPA-DVLKADGYKLTMENCDRWI 64 
                                       89***********999...5555555.................55566666664444.3333355559********* PP

                                       HHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHH.HTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  78 taldippdlgaaigsaqsqgrtvallqaralavftia.dplkvkpeaaeavasLkaagievvlltgdnpetaeraan 153
                                       +++          +++  +   ++ ++a + ++  +     +++p+a+e++ + ka+g++ ++lt + ++ ae ++ 
  gi|474934072|ref|YP_007687654.1|  65 EEN--------GLQKHKPAIDNEIQENATEIEMENANvA--RIFPGAVELLDAMKAKGLKAGILTRGGRRYAEYVLG 131
                                       ***........4444444444444444444554444424..59********************************** PP

                                       HTT.GGGESEEEEHHCES..STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHH CS
                                       xxx.xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 154 qlG.ddyfdaviasdiet..vakpspegkvaaireLqgkpeevamVGDgvnDaaa 205
                                       ++G  d fda +a+d+     akpsp +++++++e+++k  e++ VGDg+ D   
  gi|474934072|ref|YP_007687654.1| 132 NAGvLDRFDALVARDDYPenEAKPSPLAMEHLAKEFGVKCDEILYVGDGLVDYLT 186
                                       ********999999999999******************************99765 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.1   8.9e-13   2.6e-09       2     185 ..      13     185 ..      12     188 .. 0.71

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 8.9e-13
                               HAD   2 lfDfDgTLldgdsle.....lllrfllrrgaprlwralreklllalfrellrldraglaelleallagls.eelaae 72 
                                        fD+DgT +d+  ++     + ++      a + +   +  l+++ ++  +++ +++++e+    +++    e+ + 
  gi|474934072|ref|YP_007687654.1|  13 GFDMDGTFMDTRVDYvklanVVTD------AYSKYGVPADVLKADGYKLTMENCDRWIEENGLQKHKPAIdNEIQEN 83 
                                       6**********6666444444444......33334444444444445555555555566666555555554444444 PP

                               HAD  73 lerfv.aevirpklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkp 148
                                       + ++  + +   +++ pga+ell+a +a+G +  +++ g r+++e +l + g    +        r+++ +  ++ p
  gi|474934072|ref|YP_007687654.1|  84 ATEIEmENANVARIF-PGAVELLDAMKAKGLKAGILTRGGRRYAEYVLGNAG----VLD------RFDALVARDDYP 149
                                       444446666666678.********************************9999....555......599998888888 PP

                               HAD 149 vrgegkvaalrewlaaegegidleevvayGDspsDlp 185
                                        ++ +k++ l+    a++ g + +e+ ++GD+  D+ 
  gi|474934072|ref|YP_007687654.1| 150 ENE-AKPSPLAMEHLAKEFGVKCDEILYVGDGLVDYL 185
                                       888.999999997788888999999********9985 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   9.5e-11   2.8e-07       4      57 ..     154     206 ..     152     226 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 9.5e-11
                                       TTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTT CS
                    Hydrolase_like   4 KPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrped 57 
                                       KP+p +++  ++++g++ +e+l++GD    D + A n G++++ V +G  ++++
  gi|474934072|ref|YP_007687654.1| 154 KPSPLAMEHLAKEFGVKCDEILYVGDG-LVDYLTAYNSGARFIGVMSGHDNRTR 206
                                       ***************************.********************977754 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.1e-05     0.064      11      45 ..      93     127 ..      12     201 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.1e-05
                                       ETTEE-TTHHHHHHHHHHTT-EEEEEE---SS-HH CS
                       Hydrolase_6  11 rgdkaipgaaealnalraagkpvvllTNnssksee 45 
                                       +  +++pga+e+l+a++a+g +  +lT ++++  e
  gi|474934072|ref|YP_007687654.1|  93 NVARIFPGAVELLDAMKAKGLKAGILTRGGRRYAE 127
                                       567899*********************99988755 PP

>> 5_nucleotid  5' nucleotidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.2   0.00075       2.2      10      27 ..       7      24 ..       1      57 [. 0.70
   2 ?    6.1   0.1    0.0015       4.5     290     311 ..     160     181 ..     159     190 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00075
                                      TT--EEEE-TBTTTBEE- CS
                       5_nucleotid 10 kkIkvvGFDmDYTLaqYk 27
                                      +kIk++GFDmD T +  +
  gi|474934072|ref|YP_007687654.1|  7 AKIKAIGFDMDGTFMDTR 24
                                      48*********9987655 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0015
                                       HHHHHHHTT--GGGEEEEESS- CS
                       5_nucleotid 290 lkelekllgvkgkevLYvGDhi 311
                                       +++l k +gvk +e+LYvGD +
  gi|474934072|ref|YP_007687654.1| 160 MEHLAKEFGVKCDEILYVGDGL 181
                                       68999***************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1567.35
//
Query:       gi|474934073|ref|YP_007687655.1|  [L=69]
Description: hypothetical protein TALC_00493 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       149  (0.00831056); expected 358.6 (0.02)
Passed bias filter:                      122  (0.00680462); expected 358.6 (0.02)
Passed Vit filter:                         4  (0.000223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.29u 0.23s 00:00:00.52 Elapsed: 00:00:00.37
# Mc/sec: 563.60
//
Query:       gi|474934074|ref|YP_007687656.1|  [L=392]
Description: putative ATPase (AAA+ superfamily) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-22   79.3   0.0    5.3e-22   78.2   0.0    1.6  1  AAA_14    AAA domain
    7.7e-05   22.7   0.4       0.02   14.8   0.0    2.8  3  ATPase_2  ATPase domain predominantly from Archaea
    0.00078   18.5   0.0     0.0021   17.1   0.0    1.6  2  MeaB      Methylmalonyl Co-A mutase-associated GTPase MeaB
     0.0059   16.3   0.0      0.015   15.0   0.0    1.6  1  AAA_29    P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.013   15.2   0.0      0.024   14.4   0.0    1.3  1  AAA_30    AAA domain
      0.035   14.5   0.0      0.066   13.6   0.0    1.5  1  AAA_16    AAA ATPase domain
       0.04   14.2   0.0        2.5    8.4   0.0    2.6  2  AAA_22    AAA domain
       0.12   11.9   0.0       0.21   11.1   0.0    1.3  1  FBP_C     FBP C-terminal treble-clef zinc-finger
       0.14   12.3   0.0       0.33   11.1   0.0    1.6  1  DUF150_C  RimP C-terminal SH3 domain


Domain annotation for each model (and alignments):
>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.2   0.0   2.7e-25   5.3e-22       2     131 .]      23     153 ..      22     153 .. 0.92

  Alignments for each domain:
  == domain 1  score: 78.2 bits;  conditional E-value: 2.7e-25
                            AAA_14   2 rkilvitGaRrvGKTtllkqlikell...vkkesilyinldderdkkladpekllelileklkeekktylflDEiqe 75 
                                       r ++v+tG+R vGK+t++ q+i++ +    ++++i+ +++d+ ++ +++  e+l  l+ ++++++ + ++++DE+q+
  gi|474934074|ref|YP_007687656.1|  23 RAVKVLTGLRGVGKSTIMDQFIQRMIdngKNPDDIIRFDFDSVDLFDIRYAEDLKILVTKSVEGKTDPFVIMDEVQK 99 
                                       5799******************9999***9***************99997776666666668778999********* PP

                            AAA_14  76 vpewekalkslvdegknldvivtGSnskllskeiatslagrvaeielyplsfaEfl 131
                                       +p+w++al  l++++   ++++t S  ++     +t+l     ei+++pls+ Ef+
  gi|474934074|ref|YP_007687656.1| 100 IPGWSEALWALMQQN-FAEYFLTSSDDSVTAP-RKTDLKPCLREIRVMPLSIYEFM 153
                                       *************99.889********99988.59*******************96 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   9.9e-06      0.02       4      49 ..       8      52 ..       5      60 .. 0.82
   2 !    5.1   0.0     0.009        18     116     147 ..      85     113 ..      60     177 .. 0.60
   3 ?   -2.4   0.0       1.8   3.6e+03      81      81 ..     302     302 ..     262     363 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 9.9e-06
                          ATPase_2  4 RekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdk 49
                                      R++ l++le +    ++ + +++G +g+GK++++ ++i++  d +k
  gi|474934074|ref|YP_007687656.1|  8 RNMYLDRLEDLTGD-RRAVKVLTGLRGVGKSTIMDQFIQRMIDNGK 52
                                      66667777776554.899*********************9977665 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.009
                          ATPase_2 116 kgkk.iiiiiDelqklidlglngaellvkeLln 147
                                       +gk  + +i+De+qk+   g    e l + +++
  gi|474934074|ref|YP_007687656.1|  85 EGKTdPFVIMDEVQKIP--GWS--EALWALMQQ 113
                                       22336***********9..666..444444443 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.8
                          ATPase_2  81 a 81 
                                       a
  gi|474934074|ref|YP_007687656.1| 302 A 302
                                       2 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.1e-06    0.0021      19      58 ..      12      52 ..       8      63 .. 0.85
   2 ?   -2.7   0.0       1.2   2.3e+03      41      62 ..     295     316 ..     283     320 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.1e-06
                                      HHHHGGG-S-SEEE.EEEE-TTSSHHHHHHHHHHHHHCTT- CS
                              MeaB 19 lerllakaGraqvv.GltGvPGaGkstlvealglelrrrGk 58
                                      l+rl + +G  + v  ltG+ G+Gkst++++++++++++Gk
  gi|474934074|ref|YP_007687656.1| 12 LDRLEDLTGDRRAVkVLTGLRGVGKSTIMDQFIQRMIDNGK 52
                                      77888888866655148**********************98 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.2
                                       SHHHHHHHHHHHHHCTT--EEE CS
                              MeaB  41 GkstlvealglelrrrGkrvav 62 
                                        +s + +a+ +el+rrG +v v
  gi|474934074|ref|YP_007687656.1| 295 VQSETENAVFIELKRRGCKVKV 316
                                       5666778889999999999977 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   7.7e-06     0.015      17      42 ..      18      43 ..       9      52 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.7e-06
                            AAA_29 17 ieidlkgatlltGpsGsGKSTllDAi 42
                                      ++ d++ + +ltG  G+GKST++D +
  gi|474934074|ref|YP_007687656.1| 18 LTGDRRAVKVLTGLRGVGKSTIMDQF 43
                                      5556666889**************65 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.2e-05     0.024      10      42 ..      15      47 ..      12      58 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.2e-05
                            AAA_30 10 vealltsgdrvavltGpAGtGKttalkalreaw 42
                                      +e l+++++ v+vltG  G GK+t++ +  + +
  gi|474934074|ref|YP_007687656.1| 15 LEDLTGDRRAVKVLTGLRGVGKSTIMDQFIQRM 47
                                      5789999*******************9885544 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.3e-05     0.066      25      51 ..      24      50 ..       7     143 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.3e-05
                            AAA_16 25 elvllsGesGvGKsslvrellralekd 51
                                       + +l+G +GvGKs++++++ +++ ++
  gi|474934074|ref|YP_007687656.1| 24 AVKVLTGLRGVGKSTIMDQFIQRMIDN 50
                                      45589***************9988777 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0012       2.5       7      28 ..      25      46 ..      19      65 .. 0.83
   2 ?    2.7   0.0     0.073   1.5e+02      81     112 ..      79     107 ..      69     128 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0012
                            AAA_22  7 ilvvtGesGtGKTtllrrlleq 28
                                      + v+tG  G+GK+t + ++ ++
  gi|474934074|ref|YP_007687656.1| 25 VKVLTGLRGVGKSTIMDQFIQR 46
                                      5689************999876 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.073
                            AAA_22  81 aleqalraravielliiDEaqhlrs..eealeeL 112
                                       ++++ ++ + + +++i DE+q++ +      e L
  gi|474934074|ref|YP_007687656.1|  79 LVTKSVEGKTD-PFVIMDEVQKI-PgwS---EAL 107
                                       56677777777.9*********9.4332...333 PP

>> FBP_C  FBP C-terminal treble-clef zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0    0.0001      0.21      84     150 ..     230     297 ..     216     301 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0001
                             FBP_C  84 assevsLftarragaagrkgnt.vGtyiCadlaCslnvrgkkksaearaeeeltveerierlrerlaa 150
                                        s+ev+ ++ ++ g ++r+ ++ vGty+  + +  +++ + kks++  + ++l +++ i+ +++++++
  gi|474934074|ref|YP_007687656.1| 230 DSDEVMSMSGKKFGYTSRALDSlVGTYLVMENEGRSYINKLKKSQMIYYAADLGIRNSIKGVTRNVQS 297
                                       5789****************9878***************************************99975 PP

>> DUF150_C  RimP C-terminal SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00017      0.33      18      56 ..     342     380 ..     340     383 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00017
                          DUF150_C  18 klklpvegrkkftGkivevdeetitlevdgkkrkketti 56 
                                       +l  p+  +k f Gk++e+  et+ +++dg ++k+ +t+
  gi|474934074|ref|YP_007687656.1| 342 ELTAPEPPKKSFFGKVKEALTETVRISIDGSSGKNHVTF 380
                                       667778889***********************9998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 2347.31
//
Query:       gi|474934075|ref|YP_007687657.1|  [L=103]
Description: hypothetical protein TALC_00496 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   12.9   0.1       0.13   12.6   0.1    1.2  1  DUF2865   Protein of unknown function (DUF2865)
       0.12   12.5   0.0       0.15   12.1   0.0    1.3  1  Sel_put   Selenoprotein, putative


Domain annotation for each model (and alignments):
>> DUF2865  Protein of unknown function (DUF2865)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   1.5e-05      0.13      27      58 ..      23      54 ..       9      73 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.5e-05
                           DUF2865 27 addaetCqalCpaseaklytlrdpgkdieqav 58
                                        ++e C ++C+a ++kly  +d g +i++ +
  gi|474934075|ref|YP_007687657.1| 23 RLTQEDCVRICEAVQVKLYNAKDVGGSISTLI 54
                                      44789***************999998887765 PP

>> Sel_put  Selenoprotein, putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.7e-05      0.15       4      39 ..      45      81 ..      42      99 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.7e-05
                           Sel_put  4 ralrrvrqylrllvGepdYerYv.ehmrrhHpdkppm 39
                                      +++  ++  +  ++  pdY + v e mr  Hpdk+ +
  gi|474934075|ref|YP_007687657.1| 45 DVGGSISTLIDCVMDNPDYAKRVsEEMRSAHPDKELP 81
                                      56667788889999*********99*********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 664.35
//
Query:       gi|474934076|ref|YP_007687658.1|  [L=355]
Description: Biotin synthase-related enzyme [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-14   54.9   0.0    2.5e-14   54.0   0.0    1.4  1  Radical_SAM  Radical SAM superfamily
    0.00027   21.2   0.0    0.00049   20.4   0.0    1.4  1  Fer4_12      4Fe-4S single cluster domain
  ------ inclusion threshold ------
       0.02   15.0   0.0      0.057   13.6   0.0    1.7  2  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   0.0   4.1e-18   2.5e-14       3     163 ..      60     215 ..      58     217 .. 0.86

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 4.1e-18
                                       EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGG.GSTTHHHHHHHHHHTCCCTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepl.lypdfvellerlaklavpgi 78 
                                       ++  C+++C+fC+ ++t  +  + + ++++ei++++  l +e g++ v l++ge + +y+d + +l  ++ +  + +
  gi|474934076|ref|YP_007687658.1|  60 FSTYCHNNCTFCYYRRT--NQIDRYRKTPDEIVDLAMDL-KEEGIDLVDLTMGEDDhMYADNYSELIDIVSRV-SSL 132
                                       7889************8..********************.588888888886665426777777777777775.555 PP

                                       EEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  79 ritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGe 155
                                        i v ++++ +  e   +l+e+g d +++  e+ + e   ++++ +++f+ +++  e +++ag+    d+++++ Ge
  gi|474934076|ref|YP_007687658.1| 133 GINVMVSPGAVKQEAFPKLKEAGADFFAVYQETHNRE-LYDRLRLQQDFDFRYNQREWAHDAGML-AEDGLLVGVGE 207
                                       555555555555*************************.99999999*******************.9********** PP

                                       SHHHHHHH CS
                                       xxxxxxxx RF
                       Radical_SAM 156 ndeeleel 163
                                       + +++ + 
  gi|474934076|ref|YP_007687658.1| 208 TISDIADS 215
                                       **998775 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   8.1e-08   0.00049       9      93 ..      58     141 ..      49     166 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 8.1e-08
                           Fer4_12   9 slfvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEP..llpenaeallelvkevkeek 83 
                                       + f + C  +C +C+ + t + ++ +++++e+ + ++ dlk+e i+ + l+ GE   +   n+++l+++v +v + +
  gi|474934076|ref|YP_007687658.1|  58 VYFSTYCHNNCTFCYYRRTNQIDRYRKTPDEIVDLAM-DLKEEGIDLVDLTMGEDdhMYADNYSELIDIVSRVSSLG 133
                                       556789*************************998887.789************9622566789**********9999 PP

                           Fer4_12  84 pekdiwlytg 93 
                                       +  +++++ g
  gi|474934076|ref|YP_007687658.1| 134 I--NVMVSPG 141
                                       8..4565555 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   9.5e-06     0.057       6      97 ..      62     150 ..      57     167 .. 0.68
   2 ?   -2.2   0.0      0.74   4.4e+03      25      48 ..     328     351 ..     323     355 .] 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.5e-06
                           Fer4_14   6 sgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGe..PLhyenkkellklvkrlkeeype 80 
                                         C+ +C++C+ + t + +   +  +e+++  + dlk++ i+   + lt Ge   +   n +el+++v+r+   +  
  gi|474934076|ref|YP_007687658.1|  62 TYCHNNCTFCYYRRTNQIDRYRKTPDEIVDLAM-DLKEEGIDL--VDLTMGEddHMYADNYSELIDIVSRVSSLG-- 133
                                       56*********7665555544444555555555.889998854..555555511677788999999999999888.. PP

                           Fer4_14  81 kkiwletngtleielek 97 
                                       +++ +  +++ +  + k
  gi|474934076|ref|YP_007687658.1| 134 INVMVSPGAVKQEAFPK 150
                                       88888888887755544 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.74
                           Fer4_14  25 lgkpqteelleqilkdlkkseiki 48 
                                        +k+ t+++ ++i++dl+++  + 
  gi|474934076|ref|YP_007687658.1| 328 GKKIATQNEFSHIIADLEAKLARS 351
                                       578889999999999998887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2718.34
//
Query:       gi|474934077|ref|YP_007687659.1|  [L=112]
Description: Membrane transporter of cations and cationic drugs [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-15   57.2  10.0    2.5e-15   56.9  10.0    1.1  1  Multi_Drug_Res  Small Multidrug Resistance protein
    0.00011   22.2   2.6    0.00015   21.8   2.6    1.2  1  TMEM234         Putative transmembrane family 234
    0.00035   20.7  11.8    0.00047   20.3  11.8    1.2  1  EamA            EamA-like transporter family


Domain annotation for each model (and alignments):
>> Multi_Drug_Res  Small Multidrug Resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.9  10.0   4.2e-19   2.5e-15       1      93 []       3      98 ..       3      98 .. 0.91

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 4.2e-19
                                      XX-HHHHHHHHHHHHHHHH---...-----------HHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHH CS
                    Multi_Drug_Res  1 mnwvllvlAillevvgailLkl...segftkltpsllvivgygisfllLskalkslpvsvAYavwsGiGtvlivlvgil 76
                                      m +v++++ +++e  +++ L     + g t+ ++++l+ ++ + s+++L + ++ ++++vAYa+w+++G+ ++++v+ +
  gi|474934077|ref|YP_007687659.1|  3 MGMVWIFIGGIFETLWVTCLTKssmTTGWTRRIWFVLFFICSVGSIFFLGLGMDGMNIGVAYAIWTAVGATITLVVSRV 81
                                      7889**************9977355667778888888888889999********************************* PP

                                      HH--------HHHHHHH CS
                    Multi_Drug_Res 77 lfgeslslkkliglali 93
                                      lf+e+l+  k++ + li
  gi|474934077|ref|YP_007687659.1| 82 LFKEQLNKGKILAVFLI 98
                                      *************9997 PP

>> TMEM234  Putative transmembrane family 234
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   2.6   2.5e-08   0.00015      38     113 ..      27     103 ..      15     105 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 2.5e-08
                           TMEM234  38 lkflllrlkyliplllNqsgSvlff.lllgkadlslavpiaNslafvfTvltelllgekvlkkktvlgmllvvvgia 113
                                       + + ++r  +++ + +  +gS++f  l +  +++ +a +i  ++   +T++++++l +++l+k ++l ++l+++gi+
  gi|474934077|ref|YP_007687659.1|  27 MTTGWTRRIWFVLFFICSVGSIFFLgLGMDGMNIGVAYAIWTAVGATITLVVSRVLFKEQLNKGKILAVFLILTGII 103
                                       5556788888999999******997467999*******************************************985 PP

>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3  11.8   7.9e-08   0.00047      36     135 ..       6     105 ..       1     107 [. 0.82

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 7.9e-08
                              EamA  36 vrfliagillliiallkegkl..aklslkdwllllllgllgtvlafllffyalkktsasnaslitslePvftlilsv 110
                                       v ++i+gi+  ++  +  ++     ++++ w+ l++++ +g++++ +l + +++ + a   ++ t++   +tl+ s 
  gi|474934077|ref|YP_007687659.1|   6 VWIFIGGIFETLWVTCLTKSSmtTGWTRRIWFVLFFICSVGSIFFLGLGMDGMNIGVAY--AIWTAVGATITLVVSR 80 
                                       5567889988776655555555899*************999999999888888776554..456999999******* PP

                              EamA 111 lllgekltlkqllgivlillGvlli 135
                                       +l++e+l++ ++l+++lil G++ +
  gi|474934077|ref|YP_007687659.1|  81 VLFKEQLNKGKILAVFLILTGIIGL 105
                                       **********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       819  (0.0456802); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.53
# Mc/sec: 641.80
//
Query:       gi|474934078|ref|YP_007687660.1|  [L=114]
Description: Membrane transporter of cations and cationic drugs [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-16   61.2   5.1    1.6e-16   60.7   5.1    1.1  1  Multi_Drug_Res  Small Multidrug Resistance protein
  ------ inclusion threshold ------
       0.02   15.1   6.1       0.02   15.1   6.1    2.0  2  EamA            EamA-like transporter family


Domain annotation for each model (and alignments):
>> Multi_Drug_Res  Small Multidrug Resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.7   5.1   1.8e-20   1.6e-16       3      92 ..       4      94 ..       2      95 .. 0.97

  Alignments for each domain:
  == domain 1  score: 60.7 bits;  conditional E-value: 1.8e-20
                                      -HHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHHH--.-----HHHHHHHHHHHHHHHHHHHHH-- CS
                    Multi_Drug_Res  3 wvllvlAillevvgailLklsegftkltpsllvivgygisfllLskalks.lpvsvAYavwsGiGtvlivlvgillfge 80
                                      w++++l +++e ++a+ L +s  ft   +++++i++  +s+++L k lk+ ++ + +Yavw+G Gt++ +++gil+f+e
  gi|474934078|ref|YP_007687660.1|  4 WIWIALGGIFEATWAVTLSMSGHFTVPLWTATTITVNFVSIWFLNKGLKQgTKPGSSYAVWTGCGTIFSTIAGILIFDE 82
                                      ************************************************9989*************************** PP

                                      ------HHHHHH CS
                    Multi_Drug_Res 81 slslkkliglal 92
                                      ++sl ++++l++
  gi|474934078|ref|YP_007687660.1| 83 TMSLTEVLFLGI 94
                                      ********9987 PP

>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   4.4    0.0041        37       2      46 ..       2      47 ..       1      66 [. 0.73
   2 ?   15.1   6.1   2.2e-06      0.02      71     135 ..      36     102 ..      26     104 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0041
                              EamA  2 lgillallaalfwaiyfvlskillrkvspl.tltfvrfliagilll 46
                                      ++++++ l+ +f a+++v+  +  +++ pl t+t+++  + +i +l
  gi|474934078|ref|YP_007687660.1|  2 SPWIWIALGGIFEATWAVTLSMSGHFTVPLwTATTITVNFVSIWFL 47
                                      6899********9999999999988887773444455556666555 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 2.2e-06
                              EamA  71 gllgtvlafllffyalkktsas..naslitslePvftlilsvlllgekltlkqllgivlillGvlli 135
                                        +  +++  ++++++lk ++      ++ t    +f++i ++l++ e+++l+++l +++ l Gvl++
  gi|474934078|ref|YP_007687660.1|  36 TITVNFVSIWFLNKGLKQGTKPgsSYAVWTGCGTIFSTIAGILIFDETMSLTEVLFLGILLTGVLMM 102
                                       45567888899*****99987522666669999*******************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 784.29
//
Query:       gi|474934079|ref|YP_007687661.1|  [L=348]
Description: Uroporphyrinogen-III decarboxylase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-50  171.6   0.2      3e-50  171.3   0.2    1.0  1  URO-D     Uroporphyrinogen decarboxylase (URO-D)


Domain annotation for each model (and alignments):
>> URO-D  Uroporphyrinogen decarboxylase (URO-D)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.3   0.2   1.7e-54     3e-50       4     344 ..       8     342 ..       6     344 .. 0.94

  Alignments for each domain:
  == domain 1  score: 171.3 bits;  conditional E-value: 1.7e-54
                                       -HHHHHHTT---SS--B--TT-SSTTSHHHHHHHTSSSHHHHHH-HHHHHHHHHHHHHHH--S-EE-S--TTGGGGG CS
                             URO-D   4 erllralrgekvdrvPvwlmRqaGrylpeyraeragvsflelcknpelaaevtlqpvrrfglDaailfsdilveaea 80 
                                       + + +al+ ek dr+Pv        ++  ++ + ag+ +++   npe+ a v++    + + D +    d  ++++ 
  gi|474934079|ref|YP_007687661.1|   8 SAVEAALKFEKQDRTPVNN------FALVTASRSAGYLVKDTRFNPEMSARVSVDYAMKTKSDFVKPILDSQMVFAD 78 
                                       56789**************......9999999999****************************************** PP

                                       GT-EEEEETTTEEEEE--S-.....GGGS----GGG....G..H.HHHHHHHHHHHH.--SS-EEEEEE-HHHHHHH CS
                             URO-D  81 lGlevefeegegPvvekpvr.taedveklevpddvee...grlp.yvleaikllkkelggevpligfvgaPftlasy 152
                                       lG++v f ++++ +v++ ++ +ae++++l   d+ +    ++++  +++a++ + + +++++ + g + +P+t+a y
  gi|474934079|ref|YP_007687661.1|  79 LGMDVSFADDDYGRVRSVLVhDAEEIDDLAFFDPNAAkecPNFDlCIMQALRETARIIPEDLHICGLAWGPITTAGY 155
                                       ***************************9988887555445334324799999999999******************* PP

                                       HHCTT-SS-HHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEE..TTGGGS-HHHHHHHTHHHHHHH CS
                             URO-D 153 lveGgskgfekllkllykdpeevhklldkltdvvieylkaqieagAdaiqifD..swagllspedfeefvlpylkri 227
                                       l+     g+e+l+++l+++ +++ kl+dk +++v e   a+ +ag  ++ ++D  ++ +++ p++f+ f++  +k +
  gi|474934079|ref|YP_007687661.1| 156 LL-----GVENLIMDLLMEGDLAPKLIDKSARFVGEQQVAMGRAGQTLMWMADptASEDIIAPDMFH-FAADGVKTA 226
                                       **.....***********************************************************6.********* PP

                                       HHHHHH.H--S-EEEEESSHH.HHHHHHTTS--SEEE--TTS-HHHHHHSS....EEE--B-G.GGGG.S-HHHHHH CS
                             URO-D 228 vdevkaegpkvpvilfikgagaeiledlaelgadvlsldwtvdlkeaarevgdkvalqGnldPialLl.gspeeiek 303
                                       v+  k+e  + p  l+i+g+++ +++ +ae+gad+ls+d++vd++ a+++   k+al+Gn+dP++ L+ g+pe++ +
  gi|474934079|ref|YP_007687661.1| 227 VSMYKKEFAN-PAFLHICGNTKDVIPMVAETGADCLSFDHAVDPAVAKAQADGKIALMGNIDPVKYLMmGTPEQVTE 302
                                       *******976.**********99*********************55555777************************* PP

                                       HHHHHHT.T---SSSEEB-BSS---TTS-HHHHHHHHHHHH CS
                             URO-D 304 evkeilekgaggkkgyilnlGhgippetppenvkalveavk 344
                                       +  ++++ + g  +g il++G+++p  +p +nv a+ +a +
  gi|474934079|ref|YP_007687661.1| 303 QSYRVIR-ECGMDSGLILAPGCETPISSPDANVIAMGDAGR 342
                                       *******.69999***********************99866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2407.67
//
Query:       gi|474934080|ref|YP_007687662.1|  [L=351]
Description: Isocitrate/isopropylmalate dehydrogenase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-20   71.7   0.0    1.2e-19   70.7   0.0    1.4  1  Iso_dh    Isocitrate/isopropylmalate dehydrogenase


Domain annotation for each model (and alignments):
>> Iso_dh  Isocitrate/isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.7   0.0   6.6e-24   1.2e-19       1     317 [.       5     295 ..       5     298 .. 0.87

  Alignments for each domain:
  == domain 1  score: 70.7 bits;  conditional E-value: 6.6e-24
                                       EEEEEEESTTHHHHHHHHHHHHHHHHHHHT-EEEEEE---THHHHHHHSSSS-HHHHHHHHHSSEEEEEE---CSSS CS
                            Iso_dh   1 kiallegdgiGpevveaalkvlkaakekaglelefeevdvGgaaidetgeplpeetleaikeadvvllgavgtpkek 77 
                                       k+ +l+gdg+Gp v++aa +v++aa+  +   +++ + ++G +a+++t + lp et ++i + d +l g v      
  gi|474934080|ref|YP_007687662.1|   5 KVLILPGDGCGPAVIQAAERVINAAA--P--MVDLIHGEIGRSAYEHTADVLPVETEDMIADCDSILCGHVDVSG-- 75 
                                       6889********************99..3..488***********************************998655.. PP

                                       SSSHHHHHHHHHHHTTEEEEEEEEE-BCCTTCCSSBTHHHHCT-EEEEEEE-SSCGGCSSEEEEETTG.GGGEEEEE CS
                            Iso_dh  78 evrpengLlaLrkeldlfanlrpvkvfeklkvksplkrevveevdlvivReltggiYfgeekekkgsifteevavdt 154
                                        +++  ++l++ ++ +++a +    ++     ks   r    ++d+ i+  +t    +  e        ++ ++vd 
  gi|474934080|ref|YP_007687662.1|  76 -MNVRDPVLSILRHTNMYAEMSE--FY--PLSKSVGNR----NMDIAIIGPNTRVNQMVSEM-------ESLEGVDA 136
                                       .888888999*9*******9865..44..335555554....79*****9999643333322.......23356777 PP

                                       EEE.EHHHHHHHHHHHHHHHHHTTTSEEEEEESTTTTHHHH.HHHHHHHHHHCCTTTTSEEEEEEHHHHHHHHHHSG CS
                            Iso_dh 155 kly.seeeieriaraafelAlkrgkkkvtlvdKanvlksse.lwrkiveevaeeeypdielehqlvDsaamqlvksp 229
                                         + s +++e++ + ++ l ++++k+kv lv+ +  l ++  ++r+i+++v++  + + + + +   +a+  l ++p
  gi|474934080|ref|YP_007687662.1| 137 DYFtSSDDTEKFFEKSVTLCEAKKKSKVALVTDSELLPTTIeMYRNIFQKVFA--ATEFQTSMMQSTDATCLLAEHP 211
                                       66515666*****************************99988**********9..7788888887788888999*** PP

                                       GGGSEEEE-HHHHHHHHHHHHHHTTSGCC-EEEEEETSS-EEEEESS---CCCTTSS-S-THHHHHHHHHHHHHTTT CS
                            Iso_dh 230 kqfdVivtkNlfGDilSDeaaalvGslGllpSaslgekkvaifEavHGsapdiagkdkaNpiavilSaalmLryslg 306
                                        + +++++  + G  l  ea+ + G+ Gl++ a +g + +a++ +   + p      + Np+++il+ al+L   lg
  gi|474934080|ref|YP_007687662.1| 212 GEVEILIAGPFSGPFLRGEASGMNGGRGLMARAFIG-EDMAMYMP--DTCPMRTDNRIENPTSAILASALLLLN-LG 284
                                       ************************************.57999988..59*********************9998.99 PP

                                       -HHHHHHHHHH CS
                            Iso_dh 307 leeaAdkiekA 317
                                        e+a d+i  A
  gi|474934080|ref|YP_007687662.1| 285 FEQAHDNIVMA 295
                                       99998888655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2241.46
//
Query:       gi|474934081|ref|YP_007687663.1|  [L=336]
Description: Deoxyhypusine synthase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-97  324.2   0.1      8e-97  324.0   0.1    1.0  1  DS        Deoxyhypusine synthase


Domain annotation for each model (and alignments):
>> DS  Deoxyhypusine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  324.0   0.1  4.5e-101     8e-97       1     286 [.      32     329 ..      32     331 .. 0.96

  Alignments for each domain:
  == domain 1  score: 324.0 bits;  conditional E-value: 4.5e-101
                                DS   1 ellesyeki.gfqatslgeaidilnkmrkdekctiflgltsnlissGlreiiadlvkeklvdvivtTaggieeDlik 76 
                                       e+l++++++ gf+a++l++a+di++km kd+kc  +l++ + ++++G+r++++d+vk+k+vdvi+tT+g +++Dl +
  gi|474934081|ref|YP_007687663.1|  32 EMLKAMGRAgGFTAQKLSDATDIVEKMAKDKKCLRILSFPACIMATGTRGVLVDMVKNKMVDVIITTCGCLDHDLSR 108
                                       6899*****9******************************************************************* PP

                                DS  77 algkktylgdfelddeeLrekginRignllvpneny.ckfedwvreildkleeeqk........vwspselikelGk 144
                                        ++  +y+gdf +dd++Lr +++ R+gn+lvp++ y   +ed + +++d++ + ++        ++s+se+i+++G+
  gi|474934081|ref|YP_007687663.1| 109 LYAA-YYKGDFMMDDAMLRANEVSRLGNVLVPDSCYgAVLEDNLLPMFDEIFACEEarkydkviSLSTSEIIDKVGE 184
                                       **99.*******************************999************997666788887666*********** PP

                                DS 145 ein....deeSilywAykndipvfcpaltDgslGdqlllfhsvkekkklkldivkDirelndial.kakktgaiilG 216
                                       +i+    +e+S+lywA+ n++ v +p++tDgs+G ql+ ++++  +++l++d++ D + ln+++  +a++tgaii+G
  gi|474934081|ref|YP_007687663.1| 185 QIAnvpgHEDSLLYWAHVNGVKVVVPGITDGSFGCQLWQYYQF--HRNLRIDLFGDEQMLNEMITnEAEHTGAIIIG 259
                                       ***9*99**********************************76..5579*************98836799******* PP

                                DS 217 GGvpKhhilnanlmrngadyavyittaqefdGslsgatldEavSwgkikaeaksvkvyaDaTivlPLlva 286
                                       GG++Khh++++n++r g+dy++y+tta+e+dGslsga+++EavSwgk+k++ak+++v +DaTi+lPL+ a
  gi|474934081|ref|YP_007687663.1| 260 GGISKHHVIWWNQFRGGLDYCIYLTTAEEYDGSLSGARIREAVSWGKVKKNAKKMTVEGDATITLPLIWA 329
                                       ********************************************************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      630  (0.0351386); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2162.63
//
Query:       gi|474934082|ref|YP_007687664.1|  [L=190]
Description: DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.8e-13   49.3   0.0      1e-12   48.2   0.0    1.6  1  S1           S1 RNA binding domain
      9e-09   35.6   0.0    1.6e-08   34.8   0.0    1.4  1  SHS2_Rpb7-N  SHS2 domain found in N terminus of Rpb7p/Rpc25p/


Domain annotation for each model (and alignments):
>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.2   0.0   1.2e-16     1e-12       1      70 [.      79     157 ..      79     161 .. 0.95

  Alignments for each domain:
  == domain 1  score: 48.2 bits;  conditional E-value: 1.2e-16
                                       HSTTTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSS..........CEESCHHHCEETTEEEEEEEEEEETTT CS
                                S1   1 kpekgevveGeVtsvtkgGafVelgngvegfvpaselsrd..........arvedpdevlkvGdevkvkvlkvdkdr 67 
                                       kp+++e +eG+V+++  +GafV++g + ++++++s++++d            ++d ++ l vGd+v+++++ ++ ++
  gi|474934082|ref|YP_007687664.1|  79 KPKENELIEGTVVEILSFGAFVRFG-PLDALLHVSQIMNDrvdadlanqrLIGKDTGRYLAVGDRVRARITSIELNE 154
                                       799**********************.***********************99999*******************9998 PP

                                       TEE CS
                                S1  68 rri 70 
                                       +++
  gi|474934082|ref|YP_007687664.1| 155 KNP 157
                                       875 PP

>> SHS2_Rpb7-N  SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.0   1.7e-12   1.6e-08       2      70 .]       9      78 ..       8      78 .. 0.97

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 1.7e-12
                                      EEEEE-GGGTTSTHHHHHHHHHHHHHTTBEETTTEEEEEEEEEEEECC.EEE-TTTSSEEEEEEEEEEEE CS
                       SHS2_Rpb7-N  2 dtvrlePsylgstledallerllekyegkvvpslGvivavldiaeyse.gkvlggsGsvyvrVtfralvF 70
                                      ++vr++Ps lg+++++ +  +  e +egk+ ++  + v v+d+  +++ g++++g+G+vy+ Vtf+ lvF
  gi|474934082|ref|YP_007687664.1|  9 RIVRIPPSRLGENIDEVVGPIACETFEGKLGEDKSIAVLVSDVRTDGApGRIVHGDGAVYQPVTFKQLVF 78
                                      79*****************************************999999********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       265  (0.0147805); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1307.23
//
Query:       gi|474934083|ref|YP_007687665.1|  [L=65]
Description: DNA-directed RNA polymerase, subunit E'' [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-13   49.5   2.7      7e-13   48.5   2.7    1.5  1  Spt4           Spt4/RpoE2 zinc finger
    9.3e-05   21.9   0.6    0.00012   21.5   0.6    1.2  1  RecR           RecR protein
  ------ inclusion threshold ------
       0.01   13.7   0.2       0.01   13.7   0.2    1.0  1  PolC_DP2       DNA polymerase II large subunit DP2
      0.041   13.3   0.4      0.067   12.6   0.4    1.4  1  NMD3           NMD3 family
       0.06   13.2   2.7       0.17   11.8   2.7    1.7  1  DUF35_N        Rubredoxin-like zinc ribbon domain (DUF35_N)
      0.091   12.8   1.2       0.13   12.3   0.5    1.6  2  Nop10p         Nucleolar RNA-binding protein, Nop10p family
      0.091   12.8   0.3       0.11   12.6   0.3    1.2  1  HypA           Hydrogenase/urease nickel incorporation, metal
       0.12   12.1   0.3       0.12   12.1   0.3    1.7  2  zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
       0.38   10.9   5.1        1.7    8.9   5.1    2.0  1  Zn-ribbon_8    Zinc ribbon domain


Domain annotation for each model (and alignments):
>> Spt4  Spt4/RpoE2 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   2.7   3.5e-16     7e-13       2      77 .]       9      65 .]       8      65 .] 0.96

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 3.5e-16
                              Spt4  2 rACllCklvktedqFeeegCpnCeilelkgdkekvsectseefeGlvaildpekSwvAkwqrldkkvpglYAlkve 77
                                      +AC++C++++++d      Cp C               ts++++G+vai+d ekS++Ak+  ++ ++ g+YAlkv+
  gi|474934083|ref|YP_007687665.1|  9 KACKDCQFITEDDV-----CPRC------------GGATSKDWQGMVAIADFEKSEIAKK--MGITANGTYALKVR 65
                                      9*********9999.....****............889**********************..************96 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.6   6.2e-08   0.00012      16      34 ..       8      26 ..       1      29 [. 0.85

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 6.2e-08
                                      -EE-TTT--EESSSS-CCC CS
                              RecR 16 vrhCsrCgnlteedlCaIC 34
                                       + C+ C+ +te+d+C+ C
  gi|474934083|ref|YP_007687665.1|  8 YKACKDCQFITEDDVCPRC 26
                                      688***************9 PP

>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   5.2e-06      0.01     614     663 ..       4      54 ..       1      65 [] 0.75

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.2e-06
                          PolC_DP2 614 veiarrkCkkCgketlearCeeCgekteeklvCkkceeeve.eekcekcek 663
                                       ++i  + Ck+C+  t    C++Cg  t++ ++ + + ++ e +e ++k++ 
  gi|474934083|ref|YP_007687665.1|   4 ARIVYKACKDCQFITEDDVCPRCGGATSKDWQGMVAIADFEkSEIAKKMGI 54 
                                       5788899*********************99988776666653444555554 PP

>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.4   3.4e-05     0.067     120     154 ..       9      43 ..       2      59 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.4e-05
                              NMD3 120 qqevevevkvkrqqCprCsriaggyyeaivQvRqk 154
                                       +  +++++ ++  +CprC   +++ ++++v +   
  gi|474934083|ref|YP_007687665.1|   9 KACKDCQFITEDDVCPRCGGATSKDWQGMVAIADF 43 
                                       556678899999******************88655 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   2.7   8.5e-05      0.17       8      34 ..       5      29 ..       2      34 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.5e-05
                           DUF35_N  8 rLvgqrCpdCGtvqfPPravCphCgsd 34
                                      r+v+  C+dC+        vCp+Cg+ 
  gi|474934083|ref|YP_007687665.1|  5 RIVYKACKDCQFIT--EDDVCPRCGGA 29
                                      789999***99996..66******875 PP

>> Nop10p  Nucleolar RNA-binding protein, Nop10p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.5   6.6e-05      0.13       6      28 ..       9      31 ..       5      33 .. 0.89
   2 ?   -2.1   0.0       2.1   4.1e+03       9      17 ..      56      63 ..      50      64 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.6e-05
                                      EE-TTT--EESSSB-TTT-SB-B CS
                            Nop10p  6 rkcgkcrvYTLkkvcpecggptk 28
                                      + c++c+  T  +vcp+cgg+t 
  gi|474934083|ref|YP_007687665.1|  9 KACKDCQFITEDDVCPRCGGATS 31
                                      6899****************996 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.1
                                      TTT--EESS CS
                            Nop10p  9 gkcrvYTLk 17
                                       + ++Y Lk
  gi|474934083|ref|YP_007687665.1| 56 AN-GTYALK 63
                                      44.789987 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.3   5.3e-05      0.11      72     102 ..      10      36 ..       3      45 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.3e-05
                                       EETTTS-EEECHHHHHS-TTTSSS-EEEEES CS
                              HypA  72 rCreCgkefeleekalrCpkCgsadveivsG 102
                                        C++C+  +e +     Cp+Cg+a  +  +G
  gi|474934083|ref|YP_007687665.1|  10 ACKDCQFITEDD----VCPRCGGATSKDWQG 36 
                                       7*****666644....7*****997766555 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.5       2.2   4.5e+03      24      28 ..      11      15 ..       9      15 .. 0.77
   2 ?   12.1   0.3   5.9e-05      0.12       6      15 ..      23      32 ..      22      38 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.2
                     zf-NADH-PPase 24 CpaCg 28
                                      C +C+
  gi|474934083|ref|YP_007687665.1| 11 CKDCQ 15
                                      88896 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 5.9e-05
                     zf-NADH-PPase  6 CgrCGaptep 15
                                      C+rCG++t +
  gi|474934083|ref|YP_007687665.1| 23 CPRCGGATSK 32
                                      ********75 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   5.1   0.00083       1.7       8      38 ..      11      32 ..       7      34 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00083
                       Zn-ribbon_8  8 CeeCghefevlqsisdapltaCPeCgsevrr 38
                                      C++C+   e         + +CP+Cg+++ +
  gi|474934083|ref|YP_007687665.1| 11 CKDCQFITE---------DDVCPRCGGATSK 32
                                      777775555.........567******8776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 423.80
//
Query:       gi|474934084|ref|YP_007687666.1|  [L=168]
Description: archaeal conserved hypothetical protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-30  104.9   0.0    2.7e-30  104.6   0.0    1.1  1  DUF359    Protein of unknown function (DUF359)


Domain annotation for each model (and alignments):
>> DUF359  Protein of unknown function (DUF359)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.6   0.0   1.5e-34   2.7e-30       1     126 []      43     165 ..      43     165 .. 0.92

  Alignments for each domain:
  == domain 1  score: 104.6 bits;  conditional E-value: 1.5e-34
                            DUF359   1 vtknllkagikPdlaivDgktkReevee.eekeeekekekekevievkNpaGtiteelieaikealeseekvlilVd 76 
                                       v+ +++++gi+P l+++Dg t+R+e++   +     +++++ e++ v+NpaGt+t++l +a+++al+ ++  +i V+
  gi|474934084|ref|YP_007687666.1|  43 VSLTMRENGIVPLLSVYDGYTERRELTGfAD----LVRNTGLEETVVSNPAGTVTSQLEDAVENALAGRSAGIIRVE 115
                                       677899******************6655333....3456999*********************************** PP

                            DUF359  77 GEEDLavlpaillapegsvvvYGqpdeGvvlvkvteeakeeaeellekfe 126
                                       GEEDLa lp++l apeg+vvvYG p++G+ +v ++ ++++ aee+l ++e
  gi|474934084|ref|YP_007687666.1| 116 GEEDLALLPCVLHAPEGAVVVYGWPGRGMKAVATDGSSRKWAEEMLGRME 165
                                       **********************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1080.94
//
Query:       gi|474934085|ref|YP_007687667.1|  [L=103]
Description: Ribosomal protein S24E [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-24   85.2   0.4    2.9e-24   84.8   0.4    1.2  1  Ribosomal_S24e  Ribosomal protein S24e
  ------ inclusion threshold ------
      0.039   14.0   0.1      0.044   13.8   0.1    1.3  1  SLIDE           SLIDE
       0.12   12.0   0.0       0.13   11.8   0.0    1.2  1  AAA_25          AAA domain


Domain annotation for each model (and alignments):
>> Ribosomal_S24e  Ribosomal protein S24e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.8   0.4   4.8e-28   2.9e-24       2      77 ..      21      96 ..      20      98 .. 0.96

  Alignments for each domain:
  == domain 1  score: 84.8 bits;  conditional E-value: 4.8e-28
                                      EEEE-SSS-S--HHHHHHHHHHHHTS-CTTEEEEEEEE-SSSSEEEEEEEEES-HHHHHHHS-HHHHHHTTSS--- CS
                    Ribosomal_S24e  2 vdvlHpgkatpskteireklakmykvdpdlvvvfgfrthfGggkttGfakiYdsleaakkfEpkhrlaRnglaekk 77
                                      + v H++++tp +  ++e+lak+++++ +lv+++++++ +G gkt G+akiY+++++akkfE++++l+Rng + k 
  gi|474934085|ref|YP_007687667.1| 21 FLVDHDKESTPGRHAVAEELAKKFNTKRELVIIDSLDSMYGVGKTLGYAKIYKDVATAKKFENDYLLKRNGYQDKP 96
                                      6699*******************************************************************99886 PP

>> SLIDE  SLIDE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   7.3e-06     0.044      49      93 ..      41      89 ..       2      94 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.3e-06
                             SLIDE 49 kkeyteeeDrfllvllak.yGygn...yekikkeiresplFrfDwflks 93
                                       k+++++ + +++  l+  yG+g+   y ki k++ ++++F+ D+ lk 
  gi|474934085|ref|YP_007687667.1| 41 AKKFNTKRELVIIDSLDSmYGVGKtlgYAKIYKDVATAKKFENDYLLKR 89
                                      34599999999999997626***9*********************9986 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.3e-05      0.13     113     158 ..      19      63 ..       5      83 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.3e-05
                            AAA_25 113 slpLfakdrggtl.ltadvdaleaaieevegvrlvviDplsralggd 158
                                          L++ d+++t  + a+ ++l+++ +  +  +lv+iD+l++++g +
  gi|474934085|ref|YP_007687667.1|  19 VHFLVDHDKESTPgRHAVAEELAKKFNT-K-RELVIIDSLDSMYGVG 63 
                                       3344544544444778888888888888.3.7************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 649.45
//
Query:       gi|474934086|ref|YP_007687668.1|  [L=57]
Description: SSU ribosomal protein S27AE [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-15   56.3   1.5    3.7e-15   55.8   1.5    1.2  1  Ribosomal_S27   Ribosomal protein S27a
    0.00036   20.4   2.4     0.0008   19.3   2.4    1.6  1  Nudix_N_2       Nudix N-terminal
     0.0033   17.3   3.9     0.0089   15.9   3.9    1.7  1  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
     0.0035   17.0   6.6      0.024   14.4   1.6    2.3  2  zinc_ribbon_2   zinc-ribbon domain
     0.0046   16.6   0.3        2.4    8.0   0.0    2.2  2  A2L_zn_ribbon   A2L zinc ribbon domain
     0.0075   16.4   1.0      0.011   15.9   1.0    1.3  1  Ribosomal_L37e  Ribosomal protein L37e
     0.0096   15.3   5.5      0.083   12.3   1.4    2.2  2  zf-ribbon_3     zinc-ribbon domain
  ------ inclusion threshold ------
      0.025   14.6   1.8      0.053   13.6   1.8    1.6  1  DZR             Double zinc ribbon
      0.042   13.8   1.3      0.067   13.2   1.3    1.3  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
       0.23   11.4   5.3          4    7.4   5.3    2.4  1  DUF1936         Domain of unknown function (DUF1936)
       0.33   10.7   3.1        2.2    8.1   0.4    2.2  2  zf-HYPF         HypF finger
       0.72   10.1   5.8       0.38   11.0   0.8    2.1  2  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
        1.3    8.7   5.9        8.8    6.0   0.1    2.2  2  zf_C2H2_10      C2H2 type zinc-finger
        1.5    8.6   6.9        1.2    8.9   0.5    2.3  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain


Domain annotation for each model (and alignments):
>> Ribosomal_S27  Ribosomal protein S27a
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8   1.5   2.9e-18   3.7e-15       9      45 .]      18      53 ..      15      53 .. 0.94

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 2.9e-18
                                      SSSSEEESS-B-SS-S-TTSBEEECTTEEEESSTTTE CS
                     Ribosomal_S27  9 dsgkverlrkeCpreCGaGvfMAehkdRkyCGkCglT 45
                                      ++gk +  rk Cp+ CG+Gvf+A h dR +CGkCg+T
  gi|474934086|ref|YP_007687668.1| 18 EDGKPKDGRKFCPK-CGPGVFLAVHSDRLSCGKCGYT 53
                                      57899999******.*********************9 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   2.4   6.3e-07    0.0008       1      31 [.      27      53 ..      27      54 .. 0.95

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 6.3e-07
                                      -B-TTT--B-EEE--TT-SS-EEEETTTTEE CS
                         Nudix_N_2  1 kFCsqCGtpvelripdgDnreRlvCpaCgti 31
                                      kFC++CG  v l++    +  Rl C +Cg++
  gi|474934086|ref|YP_007687668.1| 27 KFCPKCGPGVFLAV----HSDRLSCGKCGYT 53
                                      9*************....899********96 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   3.9   6.9e-06    0.0089       2      31 ..      27      54 ..      27      57 .] 0.87

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6.9e-06
                                      EBESTTTS..BEEEEECSCCCEEEESSSS-EE CS
                    RNA_POL_M_15KD  2 kFCpkCgN..lLlpkedkegknfeCrqCgYee 31
                                      kFCpkCg    L + +d++     C +CgY e
  gi|474934086|ref|YP_007687668.1| 27 KFCPKCGPgvFLAVHSDRLS----CGKCGYTE 54
                                      7*****85449*********....******87 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   1.6   1.8e-05     0.024      10      20 ..      23      33 ..      20      33 .. 0.91
   2 ?    5.5   0.3     0.011        15      16      21 ..      47      52 ..      42      53 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.8e-05
                     zinc_ribbon_2 10 qdnakFCpyCG 20
                                      +d+ kFCp+CG
  gi|474934086|ref|YP_007687668.1| 23 KDGRKFCPKCG 33
                                      5999******9 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.011
                     zinc_ribbon_2 16 CpyCGt 21
                                      C +CG+
  gi|474934086|ref|YP_007687668.1| 47 CGKCGY 52
                                      888886 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.1    0.0033       4.3      19      28 ..      24      33 ..      22      34 .. 0.86
   2 !    8.0   0.0    0.0019       2.4      20      31 ..      43      54 ..      35      56 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0033
                     A2L_zn_ribbon 19 qgylvCieCg 28
                                      +g  +C++Cg
  gi|474934086|ref|YP_007687668.1| 24 DGRKFCPKCG 33
                                      7788*****9 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0019
                     A2L_zn_ribbon 20 gylvCieCgasf 31
                                      + l+C +Cg+++
  gi|474934086|ref|YP_007687668.1| 43 DRLSCGKCGYTE 54
                                      6799******97 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   1.0   8.3e-06     0.011      17      43 ..      27      56 ..      18      57 .] 0.82

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 8.3e-06
                    Ribosomal_L37e 17 ilCrrCgkrsy...hvqkktCascGypsak 43
                                       +C +Cg   +   h  + +C++cGy ++k
  gi|474934086|ref|YP_007687668.1| 27 KFCPKCGPGVFlavHSDRLSCGKCGYTEKK 56
                                      58*****9998766888899******9887 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   1.4   6.5e-05     0.083       9      23 ..      20      33 ..      20      34 .. 0.91
   2 ?    5.1   0.1     0.012        16      17      24 ..      45      52 ..      39      53 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.5e-05
                       zf-ribbon_3  9 GaplssddnvCpyCG 23
                                      G+p +++ ++Cp+CG
  gi|474934086|ref|YP_007687668.1| 20 GKP-KDGRKFCPKCG 33
                                      778.99********9 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.012
                       zf-ribbon_3 17 nvCpyCGt 24
                                        C +CG+
  gi|474934086|ref|YP_007687668.1| 45 LSCGKCGY 52
                                      579***97 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.8   4.1e-05     0.053       9      37 ..      23      53 ..      19      57 .] 0.75

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.1e-05
                               DZR  9 ppdarfCseCgtklkavaa..edrCpsCgek 37
                                      +++ +fC++Cg  +  + +     C +Cg+ 
  gi|474934086|ref|YP_007687668.1| 23 KDGRKFCPKCGPGVFLAVHsdRLSCGKCGYT 53
                                      57889*****999544444559999999986 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.3   5.3e-05     0.067      18      46 .]      25      53 ..      22      53 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.3e-05
                     Zn_Tnp_IS1595 18 gfv.CPhCgsrkayriktrglfqCkeCrkq 46
                                      g+  CP+Cg   +  + +  ++ C +C+++
  gi|474934086|ref|YP_007687668.1| 25 GRKfCPKCGPGVFLAVHS-DRLSCGKCGYT 53
                                      5555*****999999998.9*******985 PP

>> DUF1936  Domain of unknown function (DUF1936)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   5.3    0.0031         4       2      16 ..      29      43 ..      28      54 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0031
                                      -TTTSSSBEEEEE-T CS
                           DUF1936  2 CPKCnvGkLEPVYNe 16
                                      CPKC+ G+   V  +
  gi|474934086|ref|YP_007687668.1| 29 CPKCGPGVFLAVHSD 43
                                      *******98777766 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.4    0.0017       2.2      24      32 ..      29      37 ..      28      39 .. 0.85
   2 ?    3.4   0.1     0.053        68      22      28 ..      45      51 ..      40      53 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0017
                                      -TTTS--EE CS
                           zf-HYPF 24 CtnCGPrls 32
                                      C++CGP + 
  gi|474934086|ref|YP_007687668.1| 29 CPKCGPGVF 37
                                      ******876 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.053
                                      ---TTTS CS
                           zf-HYPF 22 isCtnCG 28
                                       sC +CG
  gi|474934086|ref|YP_007687668.1| 45 LSCGKCG 51
                                      69****9 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.8   0.00029      0.38      20      31 ..      23      34 ..      18      41 .. 0.83
   2 ?    2.1   0.3      0.17   2.2e+02      21      31 ..      42      52 ..      36      56 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00029
                      NOB1_Zn_bind 20 dmtkkFCpkCGn 31
                                      +  +kFCpkCG 
  gi|474934086|ref|YP_007687668.1| 23 KDGRKFCPKCGP 34
                                      5679******95 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.17
                      NOB1_Zn_bind 21 mtkkFCpkCGn 31
                                      +++  C kCG 
  gi|474934086|ref|YP_007687668.1| 42 SDRLSCGKCGY 52
                                      56777999996 PP

>> zf_C2H2_10  C2H2 type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   2.4     0.026        34       5       9 ..      29      33 ..      27      35 .. 0.88
   2 ?    6.0   0.1    0.0068       8.8       4      10 ..      46      52 ..      44      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.026
                        zf_C2H2_10  5 CPKCq 9 
                                      CPKC+
  gi|474934086|ref|YP_007687668.1| 29 CPKCG 33
                                      ****6 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0068
                        zf_C2H2_10  4 sCPKCqe 10
                                      sC KC++
  gi|474934086|ref|YP_007687668.1| 46 SCGKCGY 52
                                      9*****9 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.5   0.00091       1.2       4      10 ..      27      33 ..      26      40 .. 0.87
   2 ?    3.0   1.1     0.065        83       6      10 ..      47      51 ..      46      53 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00091
                     zf-NADH-PPase  4 rFCgrCG 10
                                      +FC++CG
  gi|474934086|ref|YP_007687668.1| 27 KFCPKCG 33
                                      5*****9 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.065
                     zf-NADH-PPase  6 CgrCG 10
                                      Cg+CG
  gi|474934086|ref|YP_007687668.1| 47 CGKCG 51
                                      99999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.32u 0.25s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 449.44
//
Query:       gi|474934088|ref|YP_007687670.1|  [L=50]
Description: hypothetical protein TALC_00510 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.2    8.0   8.9        1.1    8.1   8.9    1.0  1  VESA1_N   Variant erythrocyte surface antigen-1


Domain annotation for each model (and alignments):
>> VESA1_N  Variant erythrocyte surface antigen-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   8.9   6.3e-05       1.1     148     191 ..       2      44 ..       1      50 [] 0.76

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 6.3e-05
                           VESA1_N 148 ckcstgesecsageeckcakaGkcckccckkcekckekcscvke 191
                                       c+ s  + +c+ + + kc ++Gkcc c+  + ek ++   c ++
  gi|474934088|ref|YP_007687670.1|   2 CEHSPITRDCKCP-NEKCPRHGKCCECVAFHREKRNKPPFCLRN 44 
                                       5556666899995.559***********9988888877777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      153  (0.00853366); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 356.78
//
Query:       gi|474934089|ref|YP_007687671.1|  [L=394]
Description: hypothetical protein TALC_00511 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   3.9e-147  490.1   0.3   4.4e-147  490.0   0.3    1.0  1  DUF521    Protein of unknown function (DUF521)


Domain annotation for each model (and alignments):
>> DUF521  Protein of unknown function (DUF521)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  490.0   0.3  2.5e-151  4.4e-147       1     400 [.       1     390 [.       1     391 [. 0.97

  Alignments for each domain:
  == domain 1  score: 490.0 bits;  conditional E-value: 2.5e-151
                            DUF521   1 mkLtkeeeamlnGeeGealqkameilvalGeilgAerLvpvtsahvsgvsyktigdaglefleelaekgakvrvptt 77 
                                       m+Lt+ee+a+l+Ge+G ++qkame+++al++++gA++Lv++tsah+sg+syktig++gl++l+++++ gakv+vp+t
  gi|474934089|ref|YP_007687671.1|   1 MYLTNEEQAILDGEKGAGAQKAMELVTALAKVYGADSLVDITSAHLSGASYKTIGEGGLKYLSDMVAGGAKVSVPST 77 
                                       9**************************************************************************** PP

                            DUF521  78 lnpigvdlerweelgvdeefaekqeriieayeklGveltftCtpyllgnapkkGehlawsESsavvyaNSvlGarTn 154
                                       lnp+g+d+erw e++++e+fa+kq +ii+ y k+G++ t++Ctpy   n+pk+G+h+aw+ESsa + aNS +GarTn
  gi|474934089|ref|YP_007687671.1|  78 LNPVGMDRERWAEMHITEDFAKKQIEIIDLYGKMGIQKTCSCTPYTGANVPKFGDHIAWAESSALSVANSFFGARTN 154
                                       ***************************************************************************** PP

                            DUF521 155 reggpsalaaAitGrtpeyGlhldenRkptvlveveaesedeadygalGylvGkkvgeriPvlkglekpsedelKal 231
                                       reggp alaaAi G+t++yGlhld nRkptv+++v++  ++ +dy++lG +vG+k+g+++P+++gl++ + +++K l
  gi|474934089|ref|YP_007687671.1| 155 REGGPGALAAAILGKTANYGLHLDGNRKPTVVIDVQDMGSSVFDYSVLGQAVGMKMGKGVPYFRGLHDITLEDAKTL 231
                                       ************************************99*************************************** PP

                            DUF521 232 gAalaasgavalfhiegvTPeaetleealg.ekekaekititkedleevleelskakeekvdlvalGcPhlsleElr 307
                                       +Aa+aa+g+val h eg+TPea+      g + +  e+iti +++ e++ ++l  ++ ++v+l+alGcPhl+++E++
  gi|474934089|ref|YP_007687671.1| 232 SAAMAAAGSVALWHAEGCTPEAK-----NGlDVSGLETITIGRKEREDACQKL--NTVDDVQLIALGCPHLTVKEMK 301
                                       *********************33.....3326667******************..99999***************** PP

                            DUF521 308 elaellkgkkkkv.kvelwvttsrevkeeaerlglveklekaGvkvlsdtCmvvsplikkkevkkvatnSgKaahYl 383
                                       ++a+ll+gk+k++ +ve+w++ts+ev++++ ++  v+++e++G  vl+dtCmvv+p++   ++++ atnS+Ka +Yl
  gi|474934089|ref|YP_007687671.1| 302 DIAALLRGKEKRNrDVEIWFCTSEEVRAKCPDE--VKEMERFGP-VLADTCMVVAPIEG--TFQRTATNSAKAGNYL 373
                                       ******888776659****************99..********7.9***********98..49************** PP

                            DUF521 384 pgltgvkvalgsleecv 400
                                       p l+++kv+++++++++
  gi|474934089|ref|YP_007687671.1| 374 PTLCSQKVKFAEISDLL 390
                                       *************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.63
# Mc/sec: 1872.60
//
Query:       gi|474934090|ref|YP_007687672.1|  [L=253]
Description: hypothetical protein TALC_00512 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-23   81.9   0.6    3.7e-23   81.1   0.1    1.7  2  DUF126    Aconitase X swivel domain
    2.2e-19   69.8   0.2      3e-19   69.4   0.2    1.2  1  NUDIX     NUDIX domain
     0.0025   17.8   0.0     0.0043   17.0   0.0    1.4  1  NUDIX_4   NUDIX domain


Domain annotation for each model (and alignments):
>> DUF126  Aconitase X swivel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.1   0.1   6.2e-27   3.7e-23       1      80 []      24      98 ..      24      98 .. 0.96
   2 ?   -3.8   0.0         2   1.2e+04       7      19 ..     114     126 ..     112     129 .. 0.71

  Alignments for each domain:
  == domain 1  score: 81.1 bits;  conditional E-value: 6.2e-27
                                      --TTS-B-TTT-BB-S.-SSSTT-B-TTSEEEES--S--SS-TTHHHHHHHHT-S-SEEEESS--HHHHHHHHHHT--E CS
                            DUF126  1 lSflggvdpetGkvidkghplegqsiagkiLvlpsgkGStvgsyvllelakngtaPaAlilreadpilalGaivadiPl 79
                                      +Sflggvd +tG++       ++ +i gk++++p+gkGStvgsyv+++l+ +g+ PaAli+r+a++i+++Ga+++++P+
  gi|474934090|ref|YP_007687672.1| 24 FSFLGGVDGRTGNFNV-----RDGNIGGKVFIFPNGKGSTVGSYVVYDLKVQGHPPAALINRSAETIVTTGAVISSVPM 97
                                      79***********975.....7789*****************************************************9 PP

                                      E CS
                            DUF126 80 v 80
                                      v
  gi|474934090|ref|YP_007687672.1| 98 V 98
                                      8 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2
                                       B-TTT-BB-S.-S CS
                            DUF126   7 vdpetGkvidkgh 19 
                                       v+ +tG+v  k+ 
  gi|474934090|ref|YP_007687672.1| 114 VNGSTGEVEIKNV 126
                                       6778888887765 PP

>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.4   0.2     5e-23     3e-19       4     130 ..     130     252 ..     127     253 .] 0.82

  Alignments for each domain:
  == domain 1  score: 69.4 bits;  conditional E-value: 5e-23
                                       EEEEEE.EEETTSEEEEEEES..SSSTTT.EESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEE CS
                             NUDIX   4 ravgvv.llnekgevLlvrrs..kkpfpg.WelPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydg 76 
                                       +av+   + n+k  vLl+rr    + fpg W+l+ G++e+gEtpeeAArRE+eEEtG+++   + +++  +++ +++
  gi|474934090|ref|YP_007687672.1| 130 PAVSSAlVHNGK--VLLLRRPddARSFPGkWSLVSGHIEEGETPEEAARREIEEETGVKVSSPRNVQDAFCVREGNT 204
                                       555555377777..*********999999****************************98888888887766666665 PP

                                       EEEEEEEEEEEEEEEECSGCSSTSTTTEEEEEEEEHHHHHHHHTHCTHHHHHHH CS
                             NUDIX  77 pygdeheilyvfleevegelepndenevsevrwvpleellkeklaaesrkllpw 130
                                       +++     ++ fl +v++e+    ++e  ++ wv+ +++  +kl+++ +k++++
  gi|474934090|ref|YP_007687672.1| 205 VWE-----IHPFLFAVDSEMIDL-SPENVDFAWVECAKVGCDKLVDGVEKIVRE 252
                                       555.....788888899998887.88888888****999887777777777766 PP

>> NUDIX_4  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   7.1e-07    0.0043       5      71 ..     136     209 ..     133     252 .. 0.58

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 7.1e-07
                                       EEECTEEEEEE--TTS.SSTT-EE-SEEE.-TTS-HHHHHH...HHHHS-EEEEEEEEEEEEEETTE....EEEEE CS
                           NUDIX_4   5 irddgrvllekRpekg.llggLwefPgge.eegeeleeala...reelgieveelepgtvkHvftHf....rltlt 71 
                                       ++++g+vll +Rp++     g w++ +g+ eege++eea+    +ee+g++v   +p  v+  f  +     ++++
  gi|474934090|ref|YP_007687672.1| 136 LVHNGKVLLLRRPDDArSFPGKWSLVSGHiEEGETPEEAARreiEEETGVKVS--SPRNVQDAFCVRegntVWEIH 209
                                       55669*********866**********99999999888764455667775433..233333344333222245555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1626.84
//
Query:       gi|474934091|ref|YP_007687673.1|  [L=234]
Description: Mg-dependent DNase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.9e-33  115.9   0.0    2.6e-33  115.5   0.0    1.2  1  TatD_DNase  TatD related DNase


Domain annotation for each model (and alignments):
>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.5   0.0   1.4e-37   2.6e-33       2     254 ..       7     233 ..       6     234 .] 0.88

  Alignments for each domain:
  == domain 1  score: 115.5 bits;  conditional E-value: 1.4e-37
                                       EEEE-TTSCCCTTTHHHHHHHHHHTTEEEEEEE-SSGGGHHHHHHHHTT.TTTEEEEE---GGGGGCC.CCHHHHHH CS
                        TatD_DNase   2 DaHcHldskefeedreeileraeeagvaavvvvgtsskdskavlelakkypnkvyavlGiHPnevdeasedlleelk 78 
                                       D+H H+ ++      +++    +  ++++ v+++ s+ d++a  ++ k+++n  + + G+HP+ + e++ d+ e l+
  gi|474934091|ref|YP_007687673.1|   7 DSHLHIADEG----FPGTYGDYQ--SLQRAVSCTASVSDWDA--QSGKSADN-TVQCYGVHPWFCGEWNGDVAERLR 74 
                                       8888888866....466665554..77788777777777764..56666676.999********************* PP

                                       HHHHCCCTSEEEEEEEEEET-CCCCCGHHHHHHHHHHHHHHHHHTTEEEEEEEES-HHHHHHHHHHCGGCCSEEEET CS
                        TatD_DNase  79 elanvkhskvvaiGeiGLDyysreestkeaqeevFeeqlrlAkelklplviHlrkaeedlleilkeaaeakakvvlH 155
                                       ++  ++ +    +GeiGLD    ++++ ++q  +F +ql++Ake++++  iH  ++e+++l+++++a   ++k vlH
  gi|474934091|ref|YP_007687673.1|  75 SI--LASDGRFHVGEIGLDA---KKGDISEQMPAFIAQLEIAKETGRVATIHITDSEKEVLDAVRRA---GCKAVLH 143
                                       **..8777788*********...6799***************************************7...5789*** PP

                                       T--S-HHHHHHHHHTTEEEEE-GGGGTTTTHHHHHHHHHS-GGGEEE---TTSSEECCCTTSE--GGGHHHHHHHHH CS
                        TatD_DNase 156 sfsgsaeeakkflklgyyislsglltfknakelrelvkavpldrlLiETDaPyltpkpyrgkrnepanvayvvekla 232
                                       sfs  +  ak f++ g+++s+s  +  +++ ++++l+ ++p+drlL+E+DaP                + + +  +a
  gi|474934091|ref|YP_007687673.1| 144 SFSA-ESYAKPFAEAGCFFSISPRILSRSDARIIRLLGSIPDDRLLLESDAPHQGR--------NFTSMGEFASRIA 211
                                       *985.689999***************************************865555........56788999***** PP

                                       HHHTS-HHHHHHHHHHHHHHHH CS
                        TatD_DNase 233 elkaltleelaeitaeNakrlf 254
                                         k++++eel +++a+N+ r+f
  gi|474934091|ref|YP_007687673.1| 212 GFKGVPPEELLRTVADNFTRVF 233
                                       *********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1741.58
//
Query:       gi|474934092|ref|YP_007687674.1|  [L=234]
Description: Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-38  132.3   0.6    2.2e-38  132.0   0.6    1.0  1  ThiF           ThiF family
  ------ inclusion threshold ------
       0.03   14.8   0.1      0.068   13.6   0.1    1.6  1  NAD_binding_7  Putative NAD(P)-binding
       0.27   11.5   4.1       0.39   11.0   0.4    2.6  3  TrkA_N         TrkA-N domain


Domain annotation for each model (and alignments):
>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.0   0.6   3.7e-42   2.2e-38       5     208 ..       9     231 ..       5     234 .] 0.79

  Alignments for each domain:
  == domain 1  score: 132.0 bits;  conditional E-value: 3.7e-42
                                       HHHHHHHHHHHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEEESSB--GGGGGTBTTS-GGGTTSBHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF   5 lallgedgqekLrdskvllvGaGglGsellknLalsGvgkltlvDnDkielsNlnRqflfreediGkpKaevaaeal 81 
                                         ++gedg+e+Lr+++ +l G+G++G ++l+ L+++Gvg+++++D D+ + sN nRq+l++++ +G+ K+eva e++
  gi|474934092|ref|YP_007687674.1|   9 AIIVGEDGLERLRNARAVLCGCGAVGGYALEGLVRAGVGHIRVIDKDVFSESNINRQILATTDTVGRVKVEVACERA 85 
                                       344777*********************************************************************** PP

                                       HHT-TTSEEEEEES-CCGCCS-HHHHTT-SEEEEESSSHHHHHHHHHHHHHHT-EEEEEEEETTEEEEEEE..EE.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xx.. RF
                              ThiF  82 qeinpdveveavteritdetvleellesvDlVvdalDniearrlvnracvkkgiplieagtlgfegqvvvi..ip.. 154
                                       ++inpd+++e +   ++det+   l  ++D+ vda+D++  +  + +++++ gip  +++ +++++++ ++  ++  
  gi|474934092|ref|YP_007687674.1|  86 RSINPDIDIEGLDILVSDETIPSILEGDFDVLVDAIDTVGMKTKLLEKACEIGIPTFSSMGAALHTDAAAVriANir 162
                                       ******************9988777789******************************7666666666666423233 PP

                                       CCS-ECTSS-.....................TGGS.EECCCCEEHHHHHHCTE-B-HHHHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxx.....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF 155 gktgcyeCld.....................psstedptekkvplctsiagnipaiatttavvaglaalellkll 208
                                       +++ c    +                     p   + pte+ ++   si g   ++ t++a++++ +a+e++ ++
  gi|474934092|ref|YP_007687674.1| 163 DTSVCPIAAKvrralrdldsskitcvysletP--VTVPTERDECGK-SILG---SLPTIPAIFGMSLANEAIAYI 231
                                       55555555554444443334333332222221..344444444444.6666...999**************9876 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.1e-05     0.068       5      81 ..      20     133 ..      18     144 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.1e-05
                     NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleag.akvtvvapevkeele.....................elvklaeee..... 54 
                                       l++ + ++ G G v+   ++ l++ag  ++ v++++v++e++                     e             
  gi|474934092|ref|YP_007687674.1|  20 LRNARAVLCGCGAVGGYALEGLVRAGvGHIRVIDKDVFSESNinrqilattdtvgrvkvevacE-------Rarsin 89 
                                       7899**********************78********9665556665555555554433333330.......122222 PP

                     NAD_binding_7  55 ................lekdleg.adlviaatddrelneriaea 81 
                                                       +++ leg +d+++ a+d   +++++ e+
  gi|474934092|ref|YP_007687674.1|  90 pdidiegldilvsdetIPSILEGdFDVLVDAIDTVGMKTKLLEK 133
                                       22222222222222223333443356666666666666665555 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.4   6.6e-05      0.39       2      30 ..      26      55 ..      25      68 .. 0.87
   2 ?   -1.5   0.0      0.48   2.9e+03      78      91 ..      80      93 ..      60     110 .. 0.76
   3 ?    0.9   0.2      0.09   5.4e+02      57      98 ..     136     175 ..     115     182 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.6e-05
                                      EEES-SHHHHHHHHHHHHTT.EEEEEEESS CS
                            TrkA_N  2 iiiGlGrvGrslaeeLsegg.kdvvvidkd 30
                                      +++G+G vG   +e L ++g  ++ vidkd
  gi|474934092|ref|YP_007687674.1| 26 VLCGCGAVGGYALEGLVRAGvGHIRVIDKD 55
                                      89****************55555*****98 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.48
                                      HHHHHHHHHTSSSE CS
                            TrkA_N 78 lavllakelnpkkk 91
                                      +a++ a+++np++ 
  gi|474934092|ref|YP_007687674.1| 80 VACERARSINPDID 93
                                      57888888888765 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.09
                                       HTTGGGESEEEE-SSSHHHHHHHHHHHHHHTSSSEEEEEESS CS
                            TrkA_N  57 eagiekadaviaatgddeanilavllakelnpkkkiiaraqd 98 
                                       e+gi +++++ aa+  d+a + ++ + ++  + ++i a++++
  gi|474934092|ref|YP_007687674.1| 136 EIGIPTFSSMGAALHTDAAAVRIANI-RDT-SVCPIAAKVRR 175
                                       56999999999999999999998554.443.44778888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1379.68
//
Query:       gi|474934093|ref|YP_007687675.1|  [L=970]
Description: isoleucyl-tRNA synthetase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   2.9e-190  633.5   4.3   3.7e-190  633.2   4.3    1.1  1  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)
    4.2e-26   91.6   7.0    3.3e-10   39.3   0.6    4.4  3  tRNA-synt_1g  tRNA synthetases class I (M)
    2.6e-25   89.1   1.7    5.5e-25   88.1   1.7    1.5  1  Anticodon_1   Anticodon-binding domain of tRNA
    9.6e-09   35.0   0.0    5.6e-06   25.9   0.0    2.4  2  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
    5.6e-05   22.2   0.0     0.0014   17.6   0.0    2.9  3  tRNA-synt_1f  tRNA synthetases class I (K)
  ------ inclusion threshold ------
      0.079   13.0   0.2         22    5.1   0.0    2.9  3  CpXC          CpXC protein
        0.1   13.0   0.7          3    8.3   0.1    2.9  2  zf-IS66       zinc-finger binding domain of transposase IS66
       0.22   11.5   0.7       0.79    9.7   0.7    2.0  1  DUF1610       Domain of unknown function (DUF1610)
       0.34   11.1   1.4         11    6.2   0.1    2.7  2  Zn-ribbon_8   Zinc ribbon domain
        0.5   10.5   4.6         16    5.7   0.1    3.6  3  zf-ACC        Acetyl-coA carboxylase zinc finger domain
        4.3    6.9   4.9         11    5.5   0.2    3.1  3  zf-ribbon_3   zinc-ribbon domain
        5.7    6.6   6.9        1.3    8.7   0.2    2.8  3  zf_UBZ        Ubiquitin-Binding Zinc Finger


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  633.2   4.3  2.5e-193  3.7e-190       2     597 ..       5     619 ..       4     624 .. 0.94

  Alignments for each domain:
  == domain 1  score: 633.2 bits;  conditional E-value: 2.5e-193
                       tRNA-synt_1   2 lyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaiea 78 
                                       ++e+W+ e +++k++e +++ ++f +vdgPPy tG++H+G al+kt+kdi+iry rm+G++v+ +pG+D++Gl+ie 
  gi|474934093|ref|YP_007687675.1|   5 IQEFWKSEHAYEKTKELREKGEKFYFVDGPPYTTGAIHLGTALNKTVKDILIRYWRMNGYNVRDQPGFDMHGLPIEV 81 
                                       789************************************************************************** PP

                       tRNA-synt_1  79 kvekklgakekke.rkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkg 154
                                       kvek +g + kk+  +++g ++f+  ++e++   ++++++q+k+lG+++D+dr+y Tl  +++e+ +++  + ++kg
  gi|474934093|ref|YP_007687675.1|  82 KVEKSIGVHSKKQiEEEIGIDKFVRTCQEFALGLHASMTEQFKQLGAWLDWDRPYQTLRLDYMESAWWTCQQAFKKG 158
                                       *******9877661678************************************************************ PP

                       tRNA-synt_1 155 liyrgkklvnwstklktalselEveykdkkdalihvafpladkeevklviaTTtPeTllgdtavavnpeldyv.... 227
                                       l+  ++++v w+++++tal+e+E++y d++d++++v+fpl+d+++++l i+TTtP+Tl++++avav+p++ y+    
  gi|474934093|ref|YP_007687675.1| 159 LLKDSSRVVTWCPRCETALAEAEIDYSDETDPSVMVRFPLKDDASTSLLIWTTTPWTLPSNMAVAVHPDETYAkvkf 235
                                       *************************************************************************9999 PP

                       tRNA-synt_1 228 ...itkeklilaeallkslvkke.sek.kiledergkeLegkevelpl........vnrkipiiaddyvdkeaGtGv 291
                                             e++i+++++++ ++++   ++ +il++++gk+L+g  + +p+        ++ + +++   yv+k++ tG+
  gi|474934093|ref|YP_007687675.1| 236 sgdSGSENVIIMKSQIEYVMNAGgYSSfEILQEYNGKDLIGTAYMPPFeigdglqrTDYTYKVVDAPYVEKDN-TGL 311
                                       9988899***************985556**************************999999**********997.*** PP

                       tRNA-synt_1 292 VkiaPahdedDyevgkkynlevinildedgtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcers 368
                                       V++aP++++dD+ +gk+y+l + +++de g++t++ +  +g kv   ++ v+++lke++ll++++ki+h +++c+r 
  gi|474934093|ref|YP_007687675.1| 312 VHTAPGFGPDDFDTGKRYGLVPFCPVDEAGRFTDDFPLMAGKKVRTVNEDVISYLKERNLLFSTSKIKHRYGHCWRC 388
                                       ***************************************************************************** PP

                       tRNA-synt_1 369 kkpiiyrateqWfvrvkeladaalkavekvqfvpks.kekryaswleniqdWciSRqrwWGhriplfvsketeevvv 444
                                       k+pii+r t qWf++v ++++++l++v++v+++p++ + +r ++w+en++dWc+SRqr+WG ++p++  +  e+ vv
  gi|474934093|ref|YP_007687675.1| 389 KTPIIFRNTRQWFIEVPKVKEKMLSEVDRVKWTPDWaGSSREKNWVENARDWCVSRQRYWGIPLPIWECECGEKKVV 465
                                       ************************************9999****************************999776666 PP

                       tRNA-synt_1 445 reelkelvagreeeeaekkalekeakdkl....kkekgelekdedvlDvWFsSgswpfstlgypeedteelkkffpa 517
                                         + +e+ +g+  +e+   ++++  +dk+     k  +++++++dv+DvWF+Sg  p + lgyp++ ++e++k +p 
  gi|474934093|ref|YP_007687675.1| 466 -GQYDEMREGQGYTEG--MDTHRPWIDKVtftcPKCGKTMHRIPDVMDVWFDSGVAPWADLGYPHK-KDEFEKWWPP 538
                                       .666666664444443..344455566655555455579***************************.********** PP

                       tRNA-synt_1 518 dmlleGlDiirgWvarlillslaltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltli.ls 593
                                        +++e  D++rgW+++ +  ++  ++++P+ e+++h+ ++d++GrKmSKslgNv++pl+vi++ygadalR++l+ ++
  gi|474934093|ref|YP_007687675.1| 539 KFIVEAHDQTRGWFYTTLASGVVSFDRAPYDEIMMHAWMLDSKGRKMSKSLGNVVEPLEVISQYGADALRFYLVmNN 615
                                       *************************************************************************9666 PP

                       tRNA-synt_1 594 dvgr 597
                                          +
  gi|474934093|ref|YP_007687675.1| 616 APWE 619
                                       5555 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.0   3.7e-11   5.5e-08       8      67 ..      35      95 ..      29     185 .. 0.73
   2 !   20.1   0.4   1.5e-07   0.00023     168     239 ..     384     456 ..     374     465 .. 0.83
   3 !   39.3   0.6   2.2e-13   3.3e-10     244     369 ..     508     626 ..     490     644 .. 0.82

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 3.7e-11
                                      B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHT.TS-HHHHH CS
                      tRNA-synt_1g  8 pYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAeke.gvtpeelv 67
                                      pY++g++HlG +l+    Di++Ry r++g++v    g D+hG pie+k ek+ gv+ ++ +
  gi|474934093|ref|YP_007687675.1| 35 PYTTGAIHLGTALNKTVKDILIRYWRMNGYNVRDQPGFDMHGLPIEVKVEKSiGVHSKKQI 95
                                      9************99999*****************************99875355444433 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 1.5e-07
                                       .........EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EET..T CS
                      tRNA-synt_1g 168 ksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvP..g 239
                                       ++  +++  ++++t+++f +++k+++k+ + +++ + +     ++  k+w+++  +d+++sr+  wGip+P  +
  gi|474934093|ref|YP_007687675.1| 384 HCWRCKTPIIFRNTRQWFIEVPKVKEKMLSEVDRVKWTPDWAGSSREKNWVEN-ARDWCVSRQRYWGIPLPiwE 456
                                       688899999********************99966665555555667789**99.9***************9651 PP

  == domain 3  score: 39.3 bits;  conditional E-value: 2.2e-13
                                       EE-HHHHHHHHHHHTTTTT-...TTSGGGG.G--S......EEEEEGGGHHHHHTHHHHHHHH...TT----S-EEE CS
                      tRNA-synt_1g 244 vlYVWldAligYisatkelakkkgeeekwkeyWakdkevelvhfigkdiikFHtifwPaillg...aelklpkkvva 317
                                       v+ VW+d  +   + +++      ++++++++W         +fi     +    f++++  g    +    ++++ 
  gi|474934093|ref|YP_007687675.1| 508 VMDVWFDSGVAPWADLGYPH----KKDEFEKWWPP-------KFIVEAHDQTRGWFYTTLASGvvsFDRAPYDEIMM 573
                                       67899999999999999987....4579*****33.......56655555555667766666665456667789999 PP

                                       E--E.EE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HH CS
                      tRNA-synt_1g 318 heyl.tvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswe 369
                                       h ++   +g+K+SkS g+vv + e++ ++ ad+lR+yl++++   +D+ f+ +
  gi|474934093|ref|YP_007687675.1| 574 HAWMlDSKGRKMSKSLGNVVEPLEVISQYGADALRFYLVMNNAPWEDTCFQKN 626
                                       99962689**********************************99999999865 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.1   1.7   3.7e-28   5.5e-25       1     151 [.     672     820 ..     672     821 .. 0.90

  Alignments for each domain:
  == domain 1  score: 88.1 bits;  conditional E-value: 3.7e-28
                       Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkra.aqevllevletllrl 76 
                                       d w+ls+++k  + vt+++e  +++k+a+al + +++dl++wyl lv++r ++e++++++   + +l+ ++ + ++ 
  gi|474934093|ref|YP_007687675.1| 672 DLWMLSRTEKMKAAVTASLETKELQKVARALSDYILEDLSRWYLHLVRDRSWDEESSEDKMaSYFMLHRAIMSATIA 748
                                       78**************************************************9998777665779************ PP

                       Anticodon_1  77 laPfmPfitEelwqreeeel.gkkesimlaewpe.kaeel.ekeleeeevellkeivkairklrselkikpsselkv 150
                                       laP +P+itE+++      + gk  s+++++w   ++  l +++l e+++ l+++i+++i + r++++ k +++lk+
  gi|474934093|ref|YP_007687675.1| 749 LAPLCPHITEKIY----SAMgGKLLSVHMEDWQVaDE-RLyNEDL-EHSMRLIQNIIEIIANERAKMGSKLRWPLKA 819
                                       *************....7773555*********8444.4445555.88**********************9999876 PP

                       Anticodon_1 151 v 151
                                       v
  gi|474934093|ref|YP_007687675.1| 820 V 820
                                       5 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0    0.0033         5      19      49 ..      37      67 ..      18      69 .. 0.82
   2 !   25.9   0.0   3.7e-09   5.6e-06     231     282 ..     561     613 ..     554     621 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0033
                                      TTS--BHHHHHHHHHHHHHHHHHHHTT-EEE CS
                      tRNA-synt_1e 19 vydashlGhaRslvafDilrrilqalgYdvq 49
                                         a+hlG a +  + Dil r+ ++ gY+v+
  gi|474934093|ref|YP_007687675.1| 37 TTGAIHLGTALNKTVKDILIRYWRMNGYNVR 67
                                      45789************************95 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 3.7e-09
                                       HHSS.S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHS CS
                      tRNA-synt_1e 231 aafd.kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRlllls 282
                                         fd  ++ ++ +h+ +l  +g+kmsksL+n++   +v+ ++ + +lR++l+ 
  gi|474934093|ref|YP_007687675.1| 561 VSFDrAPYDEIMMHAWMLDSKGRKMSKSLGNVVEPLEVISQYGADALRFYLVM 613
                                       567767788999**************************************986 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.36   5.3e+02       3      59 ..       9      63 ..       7      68 .. 0.71
   2 !   17.6   0.0   9.3e-07    0.0014     268     312 ..     571     615 ..     555     627 .. 0.87
   3 ?   -0.2   0.0      0.25   3.7e+02     136     178 ..     780     822 ..     770     840 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.36
                      tRNA-synt_1f  3 WadklaeklieerkkkkaekdevvvesGispSGliHiGnlrevltadlvaralrkrg 59
                                      W ++ a + ++e ++k  +++ + v+    + G iH+G++ +    d++ r  r  g
  gi|474934093|ref|YP_007687675.1|  9 WKSEHAYEKTKELREK--GEKFYFVDGPPYTTGAIHLGTALNKTVKDILIRYWRMNG 63
                                      7778887777666554..55677777778899*******988777777777666665 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 9.3e-07
                      tRNA-synt_1f 268 kvvYelillkggekmssSkGnvltledwlevaepevlrflilrrk 312
                                        ++ +++l+++g+kms+S Gnv+ + ++++ +  + lrf+++ ++
  gi|474934093|ref|YP_007687675.1| 571 IMMHAWMLDSKGRKMSKSLGNVVEPLEVISQYGADALRFYLVMNN 615
                                       58999*********************************9987644 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.25
                      tRNA-synt_1f 136 ksglydeaikealenrekikeilekyrgeereetyspylpvce 178
                                        ++ly+e +++ ++  ++i ei+++ r +  ++  +p+++v  
  gi|474934093|ref|YP_007687675.1| 780 DERLYNEDLEHSMRLIQNIIEIIANERAKMGSKLRWPLKAVYV 822
                                       5789**********************99999999999987654 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       5.1   7.7e+03      11      35 ..      80     104 ..      78     109 .. 0.81
   2 ?    4.6   0.0     0.022        33      24      76 ..     153     205 ..     139     255 .. 0.71
   3 ?    5.1   0.0     0.015        22      37      48 ..     492     503 ..     489     512 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 5.1
                              CpXC  11 eaeiwtsidadedpelkeklldgsl 35 
                                       e+++++si + ++++++e++  +++
  gi|474934093|ref|YP_007687675.1|  80 EVKVEKSIGVHSKKQIEEEIGIDKF 104
                                       789999999*******999976665 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.022
                              CpXC  24 pelkeklldgslfeat.CpkCgatakleapllyhdpekellillvpeserseee 76 
                                       + +k+ ll++s + +t Cp+C++ a +ea++ y d+++  +++ +p +++ +++
  gi|474934093|ref|YP_007687675.1| 153 QAFKKGLLKDSSRVVTwCPRCET-ALAEAEIDYSDETDPSVMVRFPLKDDASTS 205
                                       56677777776666555****86.568999*****9999999999988887666 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.015
                              CpXC  37 eatCpkCgatak 48 
                                       ++tCpkCg+t +
  gi|474934093|ref|YP_007687675.1| 492 TFTCPKCGKTMH 503
                                       799*****9865 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0       0.3   4.4e+02       4      22 ..     170     187 ..     166     191 .. 0.75
   2 ?    8.3   0.1     0.002         3       3      16 ..     494     507 ..     494     510 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.3
                           zf-IS66   4 CpcCGgllkpigedrvree 22 
                                       Cp C ++l +++ d  + e
  gi|474934093|ref|YP_007687675.1| 170 CPRCETALAEAEID-YSDE 187
                                       99999977888777.5555 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.002
                           zf-IS66   3 tCpcCGgllkpige 16 
                                       tCp+CG+++++i++
  gi|474934093|ref|YP_007687675.1| 494 TCPKCGKTMHRIPD 507
                                       7***********87 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.7   0.00053      0.79      15      24 .]     491     500 ..     490     500 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00053
                           DUF1610  15 vvFpCPNCGE 24 
                                       v F CP+CG+
  gi|474934093|ref|YP_007687675.1| 491 VTFTCPKCGK 500
                                       78*******8 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.2     0.085   1.3e+02      11      35 ..     151     176 ..     150     180 .. 0.59
   2 ?    6.2   0.1    0.0076        11      28      39 ..     494     505 ..     482     506 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.085
                       Zn-ribbon_8  11 Cghefe..vlqsisdaplta.CPeCgse 35 
                                       C++ f    l  +s    ++ CP+C  +
  gi|474934093|ref|YP_007687675.1| 151 CQQAFKkgLLKDSS--RVVTwCPRCETA 176
                                       66666643333333..35566****875 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0076
                       Zn-ribbon_8  28 aCPeCgsevrrv 39 
                                       +CP+Cg++++r+
  gi|474934093|ref|YP_007687675.1| 494 TCPKCGKTMHRI 505
                                       4*****999985 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1     0.055        83       4      16 ..     170     182 ..     168     184 .. 0.86
   2 ?    5.7   0.1     0.011        16       3      13 ..     494     504 ..     493     505 .. 0.85
   3 ?    1.0   0.1      0.31   4.6e+02      11      20 ..     783     792 ..     780     793 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.055
                            zf-ACC   4 CpsCgemlykkeL 16 
                                       Cp+C++ l   e+
  gi|474934093|ref|YP_007687675.1| 170 CPRCETALAEAEI 182
                                       ******9988876 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.011
                            zf-ACC   3 KCpsCgemlyk 13 
                                        Cp+Cg ++++
  gi|474934093|ref|YP_007687675.1| 494 TCPKCGKTMHR 504
                                       6*****99997 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.31
                            zf-ACC  11 lykkeLernl 20 
                                       ly+++Le+++
  gi|474934093|ref|YP_007687675.1| 783 LYNEDLEHSM 792
                                       8******987 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       1.3     2e+03       5       8 ..     170     173 ..     168     179 .. 0.68
   2 ?    1.7   0.1      0.12   1.8e+02       4      12 ..     384     392 ..     382     395 .. 0.86
   3 ?    5.5   0.2    0.0076        11       3      10 ..     493     500 ..     491     502 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.3
                       zf-ribbon_3   5 CPnC 8  
                                       CP+C
  gi|474934093|ref|YP_007687675.1| 170 CPRC 173
                                       7777 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.12
                       zf-ribbon_3   4 rCPnCGapl 12 
                                       +C++C++p+
  gi|474934093|ref|YP_007687675.1| 384 HCWRCKTPI 392
                                       8*****964 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.0076
                       zf-ribbon_3   3 vrCPnCGa 10 
                                        +CP+CG+
  gi|474934093|ref|YP_007687675.1| 493 FTCPKCGK 500
                                       67888886 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.23   3.5e+02       5      17 ..     170     182 ..     169     183 .. 0.86
   2 ?   -3.1   0.2       4.3   6.4e+03       5      12 ..     385     392 ..     384     393 .. 0.86
   3 ?    8.7   0.2   0.00085       1.3       2      12 ..     492     502 ..     491     505 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.23
                            zf_UBZ   5 CerCgkeipesel 17 
                                       C+rC + + e+e 
  gi|474934093|ref|YP_007687675.1| 170 CPRCETALAEAEI 182
                                       *****99998875 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4.3
                            zf_UBZ   5 CerCgkei 12 
                                       C rC+++i
  gi|474934093|ref|YP_007687675.1| 385 CWRCKTPI 392
                                       99***987 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.00085
                            zf_UBZ   2 tylCerCgkei 12 
                                       t++C++Cgk++
  gi|474934093|ref|YP_007687675.1| 492 TFTCPKCGKTM 502
                                       8********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (970 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.84u 0.33s 00:00:01.17 Elapsed: 00:00:00.52
# Mc/sec: 5581.62
//
Query:       gi|474934094|ref|YP_007687676.1|  [L=386]
Description: hypothetical protein TALC_00516 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-13   50.7   1.8    9.1e-13   48.2   0.9    2.0  2  Arylsulfotran_2  Arylsulfotransferase (ASST)
    1.1e-11   44.3   8.0    4.6e-10   38.9   8.0    2.7  1  Arylsulfotrans   Arylsulfotransferase (ASST)


Domain annotation for each model (and alignments):
>> Arylsulfotran_2  Arylsulfotransferase (ASST)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.019   1.7e+02     154     182 ..      36      63 ..      28      86 .. 0.88
   2 !   48.2   0.9     1e-16   9.1e-13      80     251 ..     159     321 ..      96     349 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.019
                   Arylsulfotran_2 154 dgdyLiSlrelsslflirpkegkvlWqlq 182
                                       +g+++iS+ + + ++++    g+v+W ++
  gi|474934094|ref|YP_007687676.1|  36 PGNFFISFVYSKNIMMLD-GHGNVVWSKH 63 
                                       58999***********99.8999999886 PP

  == domain 2  score: 48.2 bits;  conditional E-value: 1e-16
                   Arylsulfotran_2  80 adltsvggekdgwvldsliyeidietnevlfrwSalehvdeiple..eskaplgdfgrdeskpedyfHlNsvekfed 154
                                         +t v g +++ v+ s ++e+d   + v+ +w + +  +   ++  e+  + +dfg+ ++ + dy+H+N     +d
  gi|474934094|ref|YP_007687676.1| 159 DTVTNVPGYAQSTVIYSYLQEVD--HGTVVWEWKSIDYPELYGMVctEATPNANDFGNVTTAAPDYVHFNAMRVNDD 233
                                       55555556666666666666666..56899999999988888888445668999*********************** PP

                   Arylsulfotran_2 155 gdyLiSlrelsslflirpke..gkvlWqlqGpkggdfel.dnstfsrQHdariveetedkivislfnNentdtnere 228
                                       g+++ S+r+l++++++  ++  ++++W+l+Gp   +f+l d+ ++s QH ++++     +  i +f+N+n d    +
  gi|474934094|ref|YP_007687676.1| 234 GNLVCSFRHLDTILFLDRSKstDQIIWRLSGP-HDEFHLaDDQKTSGQHYVTVS-----GNQIMVFDNHNID----K 300
                                       *************9997432449*********.899*****************6.....89999****6433....3 PP

                   Arylsulfotran_2 229 pttglildvdlqnkevtllrklk 251
                                       +t    +d+d+    +t+ ++l+
  gi|474934094|ref|YP_007687676.1| 301 HTHIHTFDLDTG--GMTAASTLY 321
                                       333333444444..333333333 PP

>> Arylsulfotrans  Arylsulfotransferase (ASST)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   8.0   5.2e-14   4.6e-10      25     325 ..      44     334 ..      27     381 .. 0.72

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 5.2e-14
                    Arylsulfotrans  25 dekknnlivDtkGevrWyldqdkisdnk......lkrlkng.kllilsg....................qklaefdl 74 
                                        ++kn +++D  G+v W    d+  dn       +k+   g k ++  +                            
  gi|474934094|ref|YP_007687676.1|  44 VYSKNIMMLDGHGNVVWSKHEDQKDDNVhagfwdFKKHTVGgKTYYSYHdqdsscdkfglegfapgdrvI------- 113
                                       5778899999999999999999999988999888554443303333333445333333333333333220....... PP

                    Arylsulfotrans  75 lGrvikeyrlpggy..................idlhHdivelpngnllvlvaeenykrk..dgkkvktveDtiievd 131
                                                l++++                      Hd +  + +++++ +  +++ ++     +++++   + evd
  gi|474934094|ref|YP_007687676.1| 114 ---------LDENFnevkrirfeqssvvekghPLDGHDFFLFDLDHYIMSGYIRDTVTNvpGYAQSTVIYSYLQEVD 181
                                       .........33333333444444444444443444599999999999999999999888655577778888888888 PP

                    Arylsulfotrans 132 ktGkvvkewdlakiLdpyrdallkaakapfgdiagvgagrdWlHiNsveydekddsiivSsRhqsavvkid..yrtk 206
                                         G vv+ew+  +  + y + +++a++++ +  + + a+ d +H N++ ++  d+++++S+Rh ++++ +d  ++t+
  gi|474934094|ref|YP_007687676.1| 182 -HGTVVWEWKSIDYPELYGMVCTEATPNANDFGNVTTAAPDYVHFNAMRVND-DGNLVCSFRHLDTILFLDrsKSTD 256
                                       .7**********************98888888888889************99.******************888999 PP

                    Arylsulfotrans 207 kvkWilgdke.gwekelqkklLtpvdskGkkidleegdfdwtwgqHtavlipngstiiellvFDNgdgrskeqpall 282
                                       ++ W l+ +   +  +                     d + t gqH +++  n+     ++vFDN++  ++++    
  gi|474934094|ref|YP_007687676.1| 257 QIIWRLSGPHdEFHLA---------------------DDQKTSGQHYVTVSGNQ-----IMVFDNHNIDKHTH---- 303
                                       ****998765144433.....................56778999999999998.....99999999888774.... PP

                    Arylsulfotrans 283 spkdnySraveYkideknmTveqvweygkerGaefYSsivssv 325
                                               +  + +d+  mT++ +    +++    +Ss+++sv
  gi|474934094|ref|YP_007687676.1| 304 --------IHTFDLDTGGMTAASTLYTVDGK----FSSACGSV 334
                                       ........44555666666655555444443....56666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2441.42
//
Query:       gi|474934095|ref|YP_007687677.1|  [L=324]
Description: hypothetical protein TALC_00517 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-05   25.1   0.1    2.8e-05   24.1   0.0    1.4  1  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
  ------ inclusion threshold ------
      0.026   15.0   0.0      0.047   14.2   0.0    1.4  1  AAA_23    AAA domain
      0.051   13.0   0.3      0.078   12.4   0.3    1.7  1  SMC_N     RecF/RecN/SMC N terminal domain
        0.1   13.1   0.0       0.21   12.1   0.0    1.4  1  ABC_tran  ABC transporter


Domain annotation for each model (and alignments):
>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   6.1e-09   2.8e-05       3     100 ..      45     130 ..      44     159 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 6.1e-09
                            AAA_21   3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrle 79 
                                       v+ GpNgsGK++L  a   ++++                 +  +  +++++ +++++f+ e f + ++r++y++   
  gi|474934095|ref|YP_007687677.1|  45 VVLGPNGSGKTSLGLAVTDIRDM---------------VRGRREQPSRPDQSKYESVFHYE-FTDGDSRIEYEYART 105
                                       899**************998886...............99999999***************.**********99988 PP

                            AAA_21  80 rsqv....eeklssvetllesglll 100
                                        ++     + ++s+ et+ + gl +
  gi|474934095|ref|YP_007687677.1| 106 GRRTlsreSLSISDGETVSRNGLSD 130
                                       8888666555555555555555544 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0     1e-05     0.047       5      42 ..      10      64 ..       9     138 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1e-05
                            AAA_23  5 enfrsf.rdqeidF.............skglt...lItGpNGaGKTTildAikla 42
                                      en+r+f +++e+d+             ++g +   ++ GpNG+GKT++  A++ +
  gi|474934095|ref|YP_007687677.1| 10 ENYRCFgGRFELDLslvrdyrfsqecvESGTVmkgVVLGPNGSGKTSLGLAVTDI 64
                                      7999996678999988988888777776665578899**********96666654 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   1.7e-05     0.078      27      44 ..      44      61 ..      20     281 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.7e-05
                                      EEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxx RF
                             SMC_N 27 taivGpNGSGKsnlldAi 44
                                       +++GpNGSGK++l  A+
  gi|474934095|ref|YP_007687677.1| 44 GVVLGPNGSGKTSLGLAV 61
                                      5789*********98776 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   4.7e-05      0.21      15      42 ..      45      72 ..      35     169 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.7e-05
                                      EEEESTTSSHHHHHHHHTTSS--SEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 15 aivGenGaGKStLlkllagllkpteGei 42
                                      +++G+nG+GK++L  +++   +   G+ 
  gi|474934095|ref|YP_007687677.1| 45 VVLGPNGSGKTSLGLAVTDIRDMVRGRR 72
                                      689**********999988888777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 2135.91
//
Query:       gi|474934096|ref|YP_007687678.1|  [L=342]
Description: flap structure-specific endonuclease [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-25   89.0   0.0      4e-25   88.0   0.0    1.6  1  XPG_I         XPG I-region
    7.1e-20   71.4   0.0    1.3e-19   70.6   0.0    1.4  1  XPG_N         XPG N-terminal domain
    1.3e-05   25.7   0.0    3.6e-05   24.3   0.0    1.8  1  5_3_exonuc    5'-3' exonuclease, C-terminal SAM fold


Domain annotation for each model (and alignments):
>> XPG_I  XPG I-region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.0   0.0   6.6e-29     4e-25       2      94 .]     141     236 ..     140     236 .. 0.93

  Alignments for each domain:
  == domain 1  score: 88.0 bits;  conditional E-value: 6.6e-29
                                       HHT--EEE-SS-HHHHHHHHHHTTSSSEEE-SSSHHHHTT-SEEEESTT..ECECTT......EEECEEEEEEHHHH CS
                             XPG_I   2 lmgipyvvApgEAEAqcayLqkkglvdaviseDsDlllFGapkvlrnls.kkkskkk....kekekkkvevidlekv 73 
                                        mg+p+v+Ap+++E q++y++++g+v++++s+D D+llFG+p+++rnl+ ++++  k    + +++ k evid  + 
  gi|474934096|ref|YP_007687678.1| 141 YMGFPMVQAPSDGEQQASYMCRRGDVYGAASQDFDSLLFGTPVLIRNLTmNGRR--KvpgkQLYKEIKTEVIDSAEF 215
                                       59**********************************************954444..24588889999********** PP

                                       HHHHT--HHHHHHHHHHHCET CS
                             XPG_I  74 lkelgltreqlidlaillgcD 94 
                                       l +lg+treql+d+++l+g+D
  gi|474934096|ref|YP_007687678.1| 216 LGNLGITREQLVDMCMLIGTD 236
                                       *******************99 PP

>> XPG_N  XPG N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.6   0.0   2.1e-23   1.3e-19       6     101 .]       5     101 ..       1     101 [. 0.92

  Alignments for each domain:
  == domain 1  score: 70.6 bits;  conditional E-value: 2.1e-23
                                       HHHHHHHH-GEEEEEGGGGTTEEEEEEHHHHHHHHHHHSE.ETTEE-BS.....-HHHHHHHHHHHHHHHTTEEEEE CS
                             XPG_N   6 LlkllkevaairsvsiealegkklaiDaslwlyrfliavreqlgnalen.....tshlmglfsrllrlldfgikPif 77 
                                       L +l++++    +v++ +l+gkk+a+D +   y+f+ a+r+++g+ l       tshl+gl++r+  l++ gi+P f
  gi|474934096|ref|YP_007687678.1|   5 LSDLVEPR----NVELSELSGKKVAVDTYNIAYQFMSAIRQPDGQPLCDhdgriTSHLTGLLYRTANLVEAGIEPTF 77 
                                       55555554....599******************************9988899************************* PP

                                       EE--S--GGGHHHHHHHHHHHHHH CS
                             XPG_N  78 VFdgkapdlkkeelekrserrqea 101
                                       VFdgk+ dlk+ +l+ r err++a
  gi|474934096|ref|YP_007687678.1|  78 VFDGKPHDLKSRTLRERDERREKA 101
                                       *********************975 PP

>> 5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0     6e-09   3.6e-05       3      52 ..     223     271 ..     221     305 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 6e-09
                        5_3_exonuc   3 PeqiidlkaLvGDssDnipGvpgiGektAakLlkeygsleeilenld.elk 52 
                                        eq++d+  L+G   D  +G++giG+k+A k ++  g+le+ l+++  ++ 
  gi|474934096|ref|YP_007687678.1| 223 REQLVDMCMLIGT--DFNEGIRGIGPKKALKYIRDNGTLENALSKIGtDIP 271
                                       589*********6..5668*************************9953443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1015  (0.0566122); expected 358.6 (0.02)
Passed bias filter:                      650  (0.0362541); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2469.60
//
Query:       gi|474934097|ref|YP_007687679.1|  [L=220]
Description: ribulose-5-phosphate 3-epimerase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-72  243.3   0.0    1.6e-72  243.1   0.0    1.0  1  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
    0.00071   19.1   0.0      0.016   14.7   0.0    2.3  2  His_biosynth    Histidine biosynthesis protein
  ------ inclusion threshold ------
       0.02   14.1   0.0      0.062   12.5   0.0    1.8  1  NanE            Putative N-acetylmannosamine-6-phosphate epim
      0.094   13.5   0.0         32    5.4   0.1    2.6  3  Glyoxalase_6    Glyoxalase-like domain
       0.18   11.5   0.0       0.43   10.3   0.0    1.6  1  PYNP_C          Pyrimidine nucleoside phosphorylase C-termina


Domain annotation for each model (and alignments):
>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  243.1   0.0   4.4e-76   1.6e-72       2     198 .]       4     200 ..       3     200 .. 0.99

  Alignments for each domain:
  == domain 1  score: 243.1 bits;  conditional E-value: 4.4e-76
                                       EEEBGGGS-GGGHHHHHHHHHHTT-SEEEEEEEBSSSSS-B-B-HHHHHHHGGGE-S-EEEEEESSSHHHCHHHHHH CS
                    Ribul_P_3_epim   2 iapSllsadfarlgeevkaveeagadllHvDvmDghfvpNltigplvvealrkltelpldvHLmveevdrivpefae 78 
                                       iapS+ls df+rlgeev++v++ gad++H+DvmDg fvpNlt+g  v++ +r+ t+ p+dvHLm+e++ r++++f++
  gi|474934097|ref|YP_007687679.1|   4 IAPSMLSCDFSRLGEEVERVDRSGADWIHLDVMDGMFVPNLTFGAPVIKTVRDRTKKPFDVHLMIEDPLRYIDDFVR 80 
                                       9**************************************************************************** PP

                                       CT-SEEEEE-ST-TTHHHHHHHHHHTTSEEEEEE-TT--GGGGTTTCCC-SEEEEESS-TT-SS----CCHHHHHHH CS
                    Ribul_P_3_epim  79 agasiisvHaEalehlkrtiqeikeaGakaglvlnpatplealeyllekldlvllmsvePgfgGQkFipevlekikk 155
                                       aga++i+vHaEa   +    ++i+++G+k+g+ +np tp++ +e+ l++ dlvl+m+v+ gfgGQkF pe+l+ki+ 
  gi|474934097|ref|YP_007687679.1|  81 AGADLITVHAEAEGDIPAAFAKIRDCGCKTGITINPGTPVSEIERYLPDADLVLIMTVNAGFGGQKFHPECLPKIEF 157
                                       ***************************************************************************** PP

                                       HHHHHHHHT---EEEEESS--TTTCHHHHHHT--EEEESHHHH CS
                    Ribul_P_3_epim 156 vrklidekeldlkievDGGvkldnieqiaeagadvlVagsavf 198
                                       v ++ +e++ +++i vDGG++ ++ +q ++aga vlVags +f
  gi|474934097|ref|YP_007687679.1| 158 VSRYREENNPHMEISVDGGINRETGKQCVDAGATVLVAGSSLF 200
                                       ****************************************998 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.029     1e+02      14      47 ..      54      87 ..      16      95 .. 0.51
   2 !   14.7   0.0   4.4e-06     0.016      62     116 ..     155     210 ..     107     219 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.029
                                      EEECTTCSTCEEEETTSHHHHHHHHHHHT-SEEE CS
                      His_biosynth 14 VrlvkGdrfqelryagdpvelakryeeegadelh 47
                                      Vr +  + f+ + + +dp+ ++ ++ ++gad ++
  gi|474934097|ref|YP_007687679.1| 54 VRDRTKKPFDVHLMIEDPLRYIDDFVRAGADLIT 87
                                      2222223344444555555555555555555554 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 4.4e-06
                                       HHHHHHHHHH-S..SEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHH CS
                      His_biosynth  62 ldlveeiaeevf..ipvqvGGGIrsledveelleagadkviigtaavknpelikela 116
                                       ++ v++ +ee +  +++ v+GGI++    ++ ++aga  ++ g++ ++ p++ +e+a
  gi|474934097|ref|YP_007687679.1| 155 IEFVSRYREENNphMEISVDGGINRET-GKQCVDAGATVLVAGSSLFRLPDMTDEIA 210
                                       5677788877666699*******9877.9************************9986 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.7e-05     0.062      45     184 ..      63     207 ..      23     212 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.7e-05
                                       TS---BS-SHHHHHHHHTTT-SEEEEE--SS--T--HHHHHHHHHHH--EEE......EE-SSHHHHHHHHHTT-SE CS
                              NanE  45 dsevritatlkdideLaaagadiialDatdrerpvtieelikkikekyqllm......aDistleeglvakklGvdi 115
                                       d +++i   l+ id+++ agad+i + a     + +i + ++ki++ ++         + +s +e   +  ++ + +
  gi|474934097|ref|YP_007687679.1|  63 DVHLMIEDPLRYIDDFVRAGADLITVHAEA---EGDIPAAFAKIRDCGCKTGitinpgTPVSEIER--YLPDADLVL 134
                                       445567777888999999999999887754...456777777777777433200011133444443..445566667 PP

                                       EE-TTTTSSTTS-...SS--HHHHHHHHHTT...--EEEES---SHHHHHHHHTT--SEEEE-HHHH-HHHHHH CS
                              NanE 116 vGttlsGytkeeek..aepDfalvkalseag...lkviaeGrintPekakkaieiGvdavvvGsaitrleeiak 184
                                       + t   G+ +++ +    p +++v  + e++   +++ ++G in  e  k++++ G++++v Gs++ rl ++++
  gi|474934097|ref|YP_007687679.1| 135 IMTVNAGFGGQKFHpeCLPKIEFVSRYREENnphMEISVDGGINR-ETGKQCVDAGATVLVAGSSLFRLPDMTD 207
                                       888888998887664467999999999887722255889****96.899*******************988775 PP

>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.4   5.1e+03      70      82 ..      17      29 ..       9      37 .. 0.63
   2 ?    5.4   0.1    0.0089        32      50      91 ..      52      93 ..      15     102 .. 0.78
   3 ?    5.4   0.0    0.0089        32      55      84 ..     162     193 ..     123     200 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.4
                      Glyoxalase_6 70 daevarlvalGAr 82
                                       +ev+r+ + GA 
  gi|474934097|ref|YP_007687679.1| 17 GEEVERVDRSGAD 29
                                      4666666666664 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0089
                      Glyoxalase_6 50 qrvpepaknrvHldlavedldaevarlvalGArvlreprdgt 91
                                      ++v+++ k+++ ++l  ed+ + ++  v++GA  ++ + + +
  gi|474934097|ref|YP_007687679.1| 52 KTVRDRTKKPFDVHLMIEDPLRYIDDFVRAGADLITVHAEAE 93
                                      44455667778888888***************9998887764 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.0089
                      Glyoxalase_6  55 paknrvHldlavedl..daevarlvalGArvl 84 
                                       +++n  H++++v+    +++ +++v++GA+vl
  gi|474934097|ref|YP_007687679.1| 162 REENNPHMEISVDGGinRETGKQCVDAGATVL 193
                                       467889******7776689***********97 PP

>> PYNP_C  Pyrimidine nucleoside phosphorylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00012      0.43      40      70 ..      75     105 ..      69     107 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00012
                                       TT-EEBTTSEEEEEEESSSCHHHHHHHHHHH CS
                            PYNP_C  40 lGdkVkkGeplatiYankeekleeavkklkk 70 
                                       + d V +G  l+t++a+ e ++++a +k+++
  gi|474934097|ref|YP_007687679.1|  75 IDDFVRAGADLITVHAEAEGDIPAAFAKIRD 105
                                       6899**********************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1327.12
//
Query:       gi|474934098|ref|YP_007687680.1|  [L=72]
Description: hypothetical protein TALC_00520 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.23   11.8   4.7       0.42   10.9   0.8    2.1  2  CxC6      CxC6 like cysteine cluster associated with KDZ tran


Domain annotation for each model (and alignments):
>> CxC6  CxC6 like cysteine cluster associated with KDZ transposases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.8   2.3e-05      0.42      31      57 ..       6      37 ..       4      46 .. 0.75
   2 ?    4.2   0.9     0.003        54      14      35 ..      32      56 ..      28      63 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 2.3e-05
                              CxC6 31 eHeelekiCavqgCenpve.....kgsktcsd 57
                                       H  + +iC v+gC+n++e     k+   cs+
  gi|474934098|ref|YP_007687680.1|  6 GHGTKTEICDVDGCNNEAErslnmKQVAKCSL 37
                                      5888899**********995554444556665 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.003
                              CxC6 14 vhdCtepLen..nr.drFCaeHeel 35
                                      v +C  +L+   +r  + C+eH ++
  gi|474934098|ref|YP_007687680.1| 32 VAKCSLKLKGgeHRsVHLCKEHYKQ 56
                                      6778888887434434899999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 489.36
//
Query:       gi|474934099|ref|YP_007687681.1|  [L=302]
Description: ribonuclease Z [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-19   70.2   0.0    2.5e-18   66.3   0.0    2.0  1  Lactamase_B_2  Beta-lactamase superfamily domain
    3.3e-11   43.6   0.0    1.4e-10   41.5   0.0    1.9  2  Lactamase_B    Metallo-beta-lactamase superfamily
    2.9e-05   23.7   0.0    5.4e-05   22.8   0.0    1.4  1  Lactamase_B_4  tRNase Z endonuclease


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.3   0.0   4.3e-22   2.5e-18       3     200 ..      32     261 ..      31     262 .. 0.85

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 4.3e-22
                                       EEES--TTHHHHHTCGG.S--SSS--..SEEEEE-SS--HHHHGGGGCCCC.....C--EEEEEEEEHHHHHHCCTT CS
                     Lactamase_B_2   3 iLiDagpdlrqqalral.qPvelrdelppidaVllthaHyDHlaglltlre.....lrpkklplyapkgvlavlean 73 
                                       iL+D+g +   q l  + +P +    + +i a+++th H DH+ gl+ l +     +r++kl l +pkg ++ l+ +
  gi|474934099|ref|YP_007687681.1|  32 ILFDCGEGSQRQ-L--MvSPFS----FMKIRAIFVTHLHGDHFYGLPGLVQtmgmmGREEKLILRGPKGFSDALRIS 101
                                       8*******4333.3..335664....99***********************99954444445555************ PP

                                       CGHHHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--C.....................TCCE-TT...... CS
                     Lactamase_B_2  74 fvylaleeepavnvheldwgesfelgdggleitatparhksgr.....................rldrnag...... 123
                                       ++ +  +  +++++ ++++ge  ++   +l++ ++  +h+ +                      +     g      
  gi|474934099|ref|YP_007687681.1| 102 LSLCEGDIGFETDIADIAPGEVQDVC--DLRVSVFRTEHGIESqgyvvrepdirgkidtkkarkM-----Giqgsdy 171
                                       *****9999****************6..6899999999999989999999999988876444440.....2555666 PP

                                       .......TSEEEEEE......CTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SSTTHHHH.HHT---STSHHH CS
                     Lactamase_B_2 124 .......dtlGlrie......gggkrvyyigDtgyipeeigerlggadllllditayeddemir.hmgHltpeeave 186
                                              ++ G+ ++      + g +v+y+gDt +++  ++e l+++++++++ t++e+d+  + +++H+t   a+e
  gi|474934099|ref|YP_007687681.1| 172 saleageTVNGVTLAdicsepRRGSSVAYTGDTMRCQ-TVDEALKDVEVIIHESTYLEKDKRLAaEHFHSTAASAAE 247
                                       66666668889999989888888999**********9.7799*******************8889************ PP

                                       HCTTSSSSEEEEES CS
                     Lactamase_B_2 187 aaadlgakrlvliH 200
                                        a+ ++a+ l+liH
  gi|474934099|ref|YP_007687681.1| 248 TAKNCNARALFLIH 261
                                       ************** PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   0.0   2.4e-14   1.4e-10       8      87 ..      22      96 ..      20     140 .. 0.87
   2 ?   -0.7   0.0      0.21   1.2e+03     142     176 ..     195     226 ..     191     252 .. 0.57

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 2.4e-14
                                      EEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHH CS
                       Lactamase_B  8 syliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmee 86
                                      ++ ++ +g+ iL+D+G ++++++++       +   +++a+++THlH DH+ gl+glv++ +   ++++++++ ++++ 
  gi|474934099|ref|YP_007687681.1| 22 CVAVRRGGDIILFDCGEGSQRQLMV-----SPFSFMKIRAIFVTHLHGDHFYGLPGLVQTMGMMGREEKLILRGPKGFS 95
                                      899**********************.....6****************************99988888888888887776 PP

                                      H CS
                       Lactamase_B 87 a 87
                                       
  gi|474934099|ref|YP_007687681.1| 96 D 96
                                      6 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.21
                                       TCCEEEECTTTS..SHHCCCCCC.TTCEEE-SHCHHH CS
                       Lactamase_B 142 ggkvlftGDall..agetgridltlrgaevrdpsdae 176
                                       g +v++tGD+    + ++++ d      ev+ + +  
  gi|474934099|ref|YP_007687681.1| 195 GSSVAYTGDTMRcqTVDEALKDV-----EVIIHESTY 226
                                       56799999998733333333333.....444444433 PP

>> Lactamase_B_4  tRNase Z endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0     9e-09   5.4e-05      12      56 ..      20      63 ..      10      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 9e-09
                     Lactamase_B_4 12 gPlllLqldskrYlfGkvgEgtQRavneqkvrlsklesiFLtgkv 56
                                       P+++++   +  lf ++gEg+QR ++ + +++ k+  iF+t+ +
  gi|474934099|ref|YP_007687681.1| 20 LPCVAVRRGGDIILF-DCGEGSQRQLMVSPFSFMKIRAIFVTHLH 63
                                      4899999999999**.**************************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.34s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 1752.92
//
Query:       gi|474934100|ref|YP_007687682.1|  [L=187]
Description: putative transcriptional regulator with C-terminal CBS domains [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-19   69.7   0.6    1.7e-08   34.8   0.2    2.5  2  CBS             CBS domain
    7.1e-12   45.2   0.2    1.3e-11   44.4   0.2    1.4  1  HTH_3           Helix-turn-helix
    3.2e-09   37.0   0.0    6.6e-09   36.0   0.0    1.5  1  HTH_31          Helix-turn-helix domain
    5.6e-07   29.5   0.0    1.1e-06   28.5   0.0    1.5  1  HTH_19          Helix-turn-helix domain
    7.1e-05   22.7   0.1    0.00015   21.7   0.1    1.6  1  HTH_37          Helix-turn-helix domain
    0.00087   19.7   0.3     0.0029   18.0   0.1    2.0  2  HTH_26          Cro/C1-type HTH DNA-binding domain
     0.0015   18.3   0.1     0.0032   17.3   0.1    1.6  1  HTH_25          Helix-turn-helix domain
     0.0053   16.9   0.0       0.01   15.9   0.0    1.4  1  MqsA_antitoxin  Antitoxin component of bacterial toxin-antito
     0.0059   16.1   0.3      0.016   14.7   0.1    1.8  2  Sigma70_r4      Sigma-70, region 4
  ------ inclusion threshold ------
      0.024   14.2   0.0      0.054   13.1   0.0    1.7  1  HTH_24          Winged helix-turn-helix DNA-binding
      0.035   14.2   0.1      0.075   13.1   0.1    1.6  1  Phage_CI_repr   Bacteriophage CI repressor helix-turn-helix d
      0.039   13.9   0.7       0.28   11.2   0.2    2.6  4  HTH_6           Helix-turn-helix domain, rpiR family
        0.1   12.5   0.1        0.8    9.6   0.1    2.3  2  MarR_2          MarR family
       0.14   12.2   0.4       0.71    9.9   0.1    1.9  2  DUF3071         Protein of unknown function (DUF3071)
       0.14   12.3   0.1        0.7   10.1   0.1    2.2  2  HTH_28          Helix-turn-helix domain
       0.15   12.1   0.1       0.48   10.4   0.1    1.8  1  Pou             Pou domain - N-terminal to homeobox domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0   5.7e-11   6.4e-08       2      55 ..      70     122 ..      69     124 .. 0.90
   2 !   34.8   0.2   1.5e-11   1.7e-08       2      55 ..     137     187 .]     136     187 .] 0.91

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 5.7e-11
                                       HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       +d+ ++d+vtv  ++ ++ a+elm  +g+s+lPV+ +d  +vG +++r +++ +
  gi|474934100|ref|YP_007687682.1|  70 ADVASHDLVTVQSSDKVRVAAELMQTAGFSQLPVLKGDT-PVGSISERAIFERI 122
                                       6999********************6666*******7777.**********9876 PP

  == domain 2  score: 34.8 bits;  conditional E-value: 1.5e-11
                                       HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       +dim + +++v ++t+++ +  +m +  +++++V    gklvG++t+ D+l+++
  gi|474934100|ref|YP_007687682.1| 137 ADIMDDSFPMVAENTPMSSVTAMMSD--YNAVLV-ARKGKLVGVITKADILKLI 187
                                       79**********************55..****55.59**************975 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   0.2   1.1e-14   1.3e-11       1      49 [.       9      57 ..       9      59 .. 0.97

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 1.1e-14
                                      HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHT CS
                             HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLg 49
                                      ++++Rk+ + +q+eLA ++G+s+sti++iE+++ + s  t++kl ++L+
  gi|474934100|ref|YP_007687682.1|  9 IRRMRKAMDVTQAELANASGISQSTIAKIERDRISASYATVVKLFETLD 57
                                      89******************************************99986 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.0   5.9e-12   6.6e-09       6      55 ..       9      57 ..       6      62 .. 0.94

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 5.9e-12
                            HTH_31  6 LralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralg 55
                                       r++R++  ++q+e+A ++g+s+st+ ++E+ r+   s a++ +l + l+
  gi|474934100|ref|YP_007687682.1|  9 IRRMRKAMDVTQAELANASGISQSTIAKIERDRI-SASYATVVKLFETLD 57
                                      59********************************.6*******9998876 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0     1e-09   1.1e-06       4      55 ..       9      59 ..       7      66 .. 0.94

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1e-09
                            HTH_19  4 LkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgid 55
                                      ++++R+    tq+ela+  gis+s i++iE +++  +s+ ++ k+ e+l++ 
  gi|474934100|ref|YP_007687682.1|  9 IRRMRKAMDVTQAELANASGISQSTIAKIERDRI-SASYATVVKLFETLDQL 59
                                      79********************************.**********9999875 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   1.3e-07   0.00015      19      69 ..       5      57 ..       1      62 [. 0.80

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.3e-07
                                      HHHHHHHHHHHCT--HHHHHHHHT--HHHHHHHHTT--TT..--HHHHHHHHH CS
                            HTH_37 19 lalaiaeliekrelsqseaaqllgiaqPkvsrllrgklsr..fsldkLlnllt 69
                                       a+ i++++++++ +q+e+a++ gi+q+ + +++r ++s    ++ kL + l+
  gi|474934100|ref|YP_007687682.1|  5 PASDIRRMRKAMDVTQAELANASGISQSTIAKIERDRISAsyATVVKLFETLD 57
                                      5788*******************************999862234555555555 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   2.6e-06    0.0029       2      43 ..       9      49 ..       8      61 .. 0.79
   2 ?   -2.7   0.0       7.7   8.6e+03      51      58 ..     133     140 ..     117     142 .. 0.62

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.6e-06
                            HTH_26  2 LrelmadrgitkseLargtgisaatlsrlvkgkpervsldtL 43
                                      +r++ +++++t++eLa ++gis++t++++  +++ + s  t 
  gi|474934100|ref|YP_007687682.1|  9 IRRMRKAMDVTQAELANASGISQSTIAKIERDRI-SASYATV 49
                                      79999************************99997.4444444 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7.7
                            HTH_26  51 gctpgDLl 58 
                                       + t++D++
  gi|474934100|ref|YP_007687682.1| 133 ELTIADIM 140
                                       34555554 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   2.8e-06    0.0032       3      37 ..      10      44 ..       8      53 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.8e-06
                                      HHHHHTTT--HHHHHHHSS--HHHHHHHHCT--TT CS
                            HTH_25  3 raaRearglsleevaketkIrkdylealEeddfda 37
                                      r+ R+a+  +  e+a+   I+++++ ++E+d+++a
  gi|474934100|ref|YP_007687682.1| 10 RRMRKAMDVTQAELANASGISQSTIAKIERDRISA 44
                                      899****************************9886 PP

>> MqsA_antitoxin  Antitoxin component of bacterial toxin-antitoxin system, MqsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   9.4e-06      0.01      72     122 ..       7      58 ..       2      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9.4e-06
                    MqsA_antitoxin  72 afiarvrkkleldqreaaeifGgGvnafsryekGkvrppla.lvkllklldr 122
                                       ++i+r+rk+++++q+e+a+  G    + ++ e+ ++ ++ a +vkl++ ld+
  gi|474934100|ref|YP_007687682.1|   7 SDIRRMRKAMDVTQAELANASGISQSTIAKIERDRISASYAtVVKLFETLDQ 58 
                                       689********************************988755289****9996 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   1.4e-05     0.016      14      42 ..      11      39 ..       8      43 .. 0.91
   2 ?   -2.6   0.0       3.6     4e+03      10      23 ..     116     136 ..     115     139 .. 0.47

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.4e-05
                                      HHHHTTT--HHHHHHHHTS-HHHHHHHHH CS
                        Sigma70_r4 14 elrfgeglTleEIgerlgiSrerVrqiek 42
                                      ++r   + T++E+++  giS++++  ie+
  gi|474934100|ref|YP_007687682.1| 11 RMRKAMDVTQAELANASGISQSTIAKIER 39
                                      5788899********************98 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.6
                                       HHHHHHHH.......TTT--H CS
                        Sigma70_r4  10 revlelrf.......geglTl 23 
                                       r ++e  +        ++lT 
  gi|474934100|ref|YP_007687682.1| 116 RAIFERIRsgqtmndIKELTI 136
                                       555555444444444555555 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.9e-05     0.054      18      35 ..      18      35 ..      10      37 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.9e-05
                            HTH_24 18 isqreLAerlglSpstvn 35
                                       +q+eLA ++g+S+st+ 
  gi|474934100|ref|YP_007687682.1| 18 VTQAELANASGISQSTIA 35
                                      79**************86 PP

>> Phage_CI_repr  Bacteriophage CI repressor helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   6.7e-05     0.075       3      40 ..       9      44 ..       8      79 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.7e-05
                                      HHHHHHHHT-SSCHHHHCCTT--HHHHHHHHHSSS--H CS
                     Phage_CI_repr  3 leRlmsaygvkmqkeLAdlLgiakssvstwvrRdffPg 40
                                      ++R+ +a+ v +  eLA+  gi++s+++  ++Rd++++
  gi|474934100|ref|YP_007687682.1|  9 IRRMRKAMDVTQA-ELANASGISQSTIA-KIERDRISA 44
                                      799*******988.*************8.578888774 PP

>> HTH_6  Helix-turn-helix domain, rpiR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00025      0.28      30      54 ..      13      37 ..       9      41 .. 0.87
   2 ?   -0.9   0.0       1.5   1.7e+03      45      59 ..      43      57 ..      40      59 .. 0.80
   3 ?   -2.3   0.0         4   4.5e+03      52      66 ..      86     101 ..      68     103 .. 0.64
   4 ?   -2.9   0.0       6.3     7e+03      19      39 ..     116     138 ..     114     142 .. 0.46

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00025
                                      ---TT--HHHHHHHTT--HHHHHHH CS
                             HTH_6 30 dkaielsikalAkaaavSeativrf 54
                                       ka+ ++ ++lA+a+++S++ti ++
  gi|474934100|ref|YP_007687682.1| 13 RKAMDVTQAELANASGISQSTIAKI 37
                                      57889999**************997 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.5
                                      T--HHHHHHHH---S CS
                             HTH_6 45 avSeativrfakkLG 59
                                      + S at+v++  +L+
  gi|474934100|ref|YP_007687682.1| 43 SASYATVVKLFETLD 57
                                      56899****988775 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 4
                                       HHHH.---S-SSHHHH CS
                             HTH_6  52 vrfa.kkLGfkGFsel 66 
                                       vr+a   + + GFs+l
  gi|474934100|ref|YP_007687682.1|  86 VRVAaELMQTAGFSQL 101
                                       4443134566777765 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 6.3
                                       HHHHHHHHH..-S---TT--HHH CS
                             HTH_6  19 kkiaeyila..spdkaielsika 39 
                                       + i e i++    + + el+i++
  gi|474934100|ref|YP_007687682.1| 116 RAIFERIRSgqTMNDIKELTIAD 138
                                       55555554311334444455544 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00072       0.8      20      41 ..      14      37 ..       4      51 .. 0.80
   2 ?   -0.3   0.0      0.91     1e+03      11      29 ..      56      74 ..      53      83 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00072
                                      S..EEEHHHHHHHHTSSHHHHHHH CS
                            MarR_2 20 r..dltvgelarrlglsksavsri 41
                                      +  d+t++ela + g+s+s++ +i
  gi|474934100|ref|YP_007687682.1| 14 KamDVTQAELANASGISQSTIAKI 37
                                      14689***************9887 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.91
                                      HHHHHCTTTSEEEHHHHHH CS
                            MarR_2 11 LaaLgrrpgrdltvgelar 29
                                      L  L+ ++  d+t++++a 
  gi|474934100|ref|YP_007687682.1| 56 LDQLAKGGKHDVTAADVAS 74
                                      6777777777999999986 PP

>> DUF3071  Protein of unknown function (DUF3071)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.2      0.14   1.6e+02      68     129 ..      19      81 ..       9      97 .. 0.79
   2 ?    9.9   0.1   0.00064      0.71      22      76 ..      74     135 ..      55     161 .. 0.66

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.14
                           DUF3071  68 sveevaeeagvsververyah.PvlaERariaelarkahvvredgpakltLgevlaealaarg 129
                                       + +e+a+++g+s + + + +   + a  a +++l+++     + g+++ t ++v ++ l + +
  gi|474934100|ref|YP_007687682.1|  19 TQAELANASGISQSTIAKIERdRISASYATVVKLFETLDQLAKGGKHDVTAADVASHDLVTVQ 81 
                                       557899999999999999886258888888999999998888888888898888888887655 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00064
                           DUF3071  22 egeefflavddeLraalreeser.......qaeaeeesslrpreIQariRaGasveevaeea 76 
                                       +++  +++ +d++r a++  ++         +  +   s++ r I +riR+G++++++ e +
  gi|474934100|ref|YP_007687682.1|  74 SHDLVTVQSSDKVRVAAELMQTAgfsqlpvLKGDTPVGSISERAIFERIRSGQTMNDIKELT 135
                                       5555566667777765555332233322322233444559****************998754 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00063       0.7      10      32 ..      15      37 ..       9      42 .. 0.83
   2 ?   -2.4   0.0       4.7   5.3e+03      15      27 ..      86      99 ..      82     106 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00063
                            HTH_28 10 aaGhsvreaArelgisrrtvyrW 32
                                      a  ++++e+A++ gis++t+ + 
  gi|474934100|ref|YP_007687682.1| 15 AMDVTQAELANASGISQSTIAKI 37
                                      4578****************875 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.7
                            HTH_28 15 vreaArelgi.srr 27
                                      vr aA+++++ + +
  gi|474934100|ref|YP_007687682.1| 86 VRVAAELMQTaGFS 99
                                      67888888775555 PP

>> Pou  Pou domain - N-terminal to homeobox domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00043      0.48      11      60 ..       7      50 ..       5      58 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00043
                               Pou 11 kefkqkRiklgltQadvglaLgklygkefSqttIcrFEkLdlslknmlkl 60
                                      +  ++ R ++ +tQa++++a      + +Sq+tI ++E+  +s + +  +
  gi|474934100|ref|YP_007687682.1|  7 SDIRRMRKAMDVTQAELANA------SGISQSTIAKIERDRISASYATVV 50
                                      66788899999999999988......789*********999888766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1174.18
//
Query:       gi|474934101|ref|YP_007687683.1|  [L=412]
Description: Archaeal S-adenosylmethionine synthetase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     5e-155  516.2   5.1   5.7e-155  516.0   5.1    1.0  1  AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synt
    0.00055   20.6   2.6       0.15   12.8   0.1    3.0  3  S-AdoMet_synt_N  S-adenosylmethionine synthetase, N-terminal 


Domain annotation for each model (and alignments):
>> AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synthetase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  516.0   5.1  6.4e-159  5.7e-155       1     396 []       5     408 ..       5     408 .. 0.96

  Alignments for each domain:
  == domain 1  score: 516.0 bits;  conditional E-value: 6.4e-159
                                       --EEEEE-TTS-GTTSSEEEEEEE-TTSHHHHHHHHHHHHHHHHHHHHHHHHSS---EEEEEEEEE--EEEEETTEE CS
                   AdoMet_Synthase   1 rnivveelkkkpveeqevEivErKGiGHPDsiaDgiaeavsralskeylekfgailhhniDkvllvaGesepkfgGG 77 
                                       +ni v+ +++ pv  +++EivErKGiGHPDs+aD+iae+vs+al+k+y +++g++lhhn+D++++vaG+s+++fgGG
  gi|474934101|ref|YP_007687683.1|   5 KNIYVNGINQVPVPMRQIEIVERKGIGHPDSVADNIAETVSEALCKMYKDEIGHVLHHNTDQTEVVAGRSKSQFGGG 81 
                                       69*************************************************************************** PP

                                       EEEE-EEEEEEEEEEEEE.....EEE--HHHHHHHHHHHHHHHH-SS--TTTSEEEEEEEEEEEEHHHHHHCH-SS. CS
                   AdoMet_Synthase  78 eviepieillsgratkev....egekipveeialeaakeylkenlraldlekdvivdvklgkgsadLkdvferkkke 150
                                       ++i+p+++l+ grat+ +    e+  +pve+ al+ +  +lk+ ++ ldle+d+i+d+klg gs+dL++v+++++  
  gi|474934101|ref|YP_007687683.1|  82 KIIKPVYVLMDGRATTVInkkgEEILLPVESTALKGVTAMLKRDYPLLDLESDIILDTKLGMGSDDLTGVYKASNY- 157
                                       ****************99553334448**********************************************665. PP

                                       .-BESSSEEEEEEES--HHHHHHHHHHHHHTSHHHHHH-TTEEEEEEEEEEEETTEEEEEEEEEEEGGG--SHHHHH CS
                   AdoMet_Synthase 151 vplaNDtSfgvgyaplseleklvleterllnskelkkklpevGeDiKvmglRekkkielTvavalvdrlvkdleeYl 227
                                         l+NDtSfgvgyap+s +++l ++te+++n k++kkklpe+G+D+Kvm+ R ++ki++T+a+a+vdr+++d+++Y+
  gi|474934101|ref|YP_007687683.1| 158 --LSNDTSFGVGYAPFSITDTLTFQTEQFINGKAYKKKLPEAGQDVKVMCSRVGDKITMTIACAMVDRFIEDKTAYK 232
                                       ..9************************************************************************** PP

                                       HHHHHHHHHHHHHHH....HHSTTSEEEEEE-TT-BGGGTB--EESSSSGGGTT--EETTSS--TTSSB-TTS---- CS
                   AdoMet_Synthase 228 evkeeikeeveelak....kltkerevevevNtaDkkeeesvyltvtGtsaEegDdGsvGRGNRvnGlitpnrpmsl 300
                                       ++ e+++++v+e+a     k  ++ +++vevNt D+++++++y tvtG s+E+gDdGsvGRGNR+nGlitp+rpms+
  gi|474934101|ref|YP_007687683.1| 233 SAVEQLTKDVTENALdiidKAGSKVKLKVEVNTGDDYKRNVLYTTVTGLSQENGDDGSVGRGNRCNGLITPYRPMSM 309
                                       **********988764444667778999************************************************* PP

                                       S--TTS-TTT-HHHHHHHHHHHHHHHHHHH-TTEEEEEEEEEE-TTSBTTS-SEEEEEEEE...SSS---HHSHHHH CS
                   AdoMet_Synthase 301 EAaaGKNPvsHvGKiYnvlaneiakeiveevegvkevyvrllsqiGkpidePlvasvqvil...ekgvsleevekev 374
                                       EA++GKNP++HvGKiYnvl+n+ia++++++++  +e++vrllsqiG++i++Pl+a++++i+   +++ +l ++++e+
  gi|474934101|ref|YP_007687683.1| 310 EATSGKNPITHVGKIYNVLSNKIAQDVAKKIKADAEIHVRLLSQIGHTISDPLNAAIDIIApgaDANPKLPKWQQEA 386
                                       ***********************************************************987667788999****** PP

                                       HHHHHHHHT-HHHHHHHHTTT- CS
                   AdoMet_Synthase 375 eeiideelekieeiteeliegk 396
                                        +i++e+l++i+++ e++i+gk
  gi|474934101|ref|YP_007687683.1| 387 YSIAAEWLDNIDKVSEDIINGK 408
                                       *******************996 PP

>> S-AdoMet_synt_N  S-adenosylmethionine synthetase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.1   1.6e-05      0.15      11      32 ..      30      51 ..      22      87 .. 0.74
   2 !    6.5   0.3    0.0015        13      15      46 ..     210     241 ..     208     276 .. 0.84
   3 ?   -2.0   0.0      0.66   5.9e+03      41      74 ..     310     340 ..     303     357 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.6e-05
                   S-AdoMet_synt_N 11 eGHPDkvadqisdaildailke 32
                                       GHPD vad+i++++ +a+ k 
  gi|474934101|ref|YP_007687683.1| 30 IGHPDSVADNIAETVSEALCKM 51
                                      6************998887654 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0015
                   S-AdoMet_synt_N  15 Dkvadqisdaildailkedpkarvacetlvtt 46 
                                       Dk++ +i+ a++d+++++ +  + a+e l+++
  gi|474934101|ref|YP_007687683.1| 210 DKITMTIACAMVDRFIEDKTAYKSAVEQLTKD 241
                                       9*****************9999*****99764 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.66
                   S-AdoMet_synt_N  41 etlvttglvvvageittkakvdiekivrevikei 74 
                                       e++  ++ ++ +g+i +      +ki+++v k+i
  gi|474934101|ref|YP_007687683.1| 310 EATSGKNPITHVGKIYNV---LSNKIAQDVAKKI 340
                                       555556666666666333...3344444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       800  (0.0446204); expected 358.6 (0.02)
Passed bias filter:                      619  (0.0345251); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 2526.25
//
Query:       gi|474934102|ref|YP_007687684.1|  [L=194]
Description: hypothetical protein TALC_00524 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.027   14.7   0.0      0.036   14.3   0.0    1.2  1  DUF4443         Domain of unknown function (DUF4443)
       0.14   11.9   0.0       0.21   11.3   0.0    1.2  1  Ribosomal_S19e  Ribosomal protein S19e


Domain annotation for each model (and alignments):
>> DUF4443  Domain of unknown function (DUF4443)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     4e-06     0.036      27     105 ..     114     191 ..      93     194 .] 0.85

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4e-06
                           DUF4443  27 ksielrdeairffakgamilivkngepvfpederplrdtmeelamnieevlnfsdgdlivvtwaenpsdamksayhv 103
                                       + ++ rd  i+  a g+  ++++ng  ++p d   + +   ela +i +   +   d+i+v  a+    a++++   
  gi|474934102|ref|YP_007687684.1| 114 NGMQQRDAGIKAGASGCTTIVIRNGALMIPPDWN-MDEQTPELAAKIRKETGIGPEDVIIVGSADSQISAVEASLNA 189
                                       56788*************************9976.6666789**********************9999998887766 PP

                           DUF4443 104 al 105
                                       a+
  gi|474934102|ref|YP_007687684.1| 190 AF 191
                                       65 PP

>> Ribosomal_S19e  Ribosomal protein S19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.3e-05      0.21      93     130 ..      46      82 ..      28      88 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.3e-05
                                       HHTTSSS--SSS---SS-HHHHHTHHHHH--SS--S-- CS
                    Ribosomal_S19e  93 gsvirkilqqLeklglvkkekkkgrrltkkGqrlldri 130
                                       +  +r+il+++ + ++v   k++g  ++k+G+++l++i
  gi|474934102|ref|YP_007687684.1|  46 EGSMRRILEKFREWNFVD-IKQTGISISKQGMTFLEQI 82 
                                       4578*************4.4467*************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1232.81
//
Query:       gi|474934103|ref|YP_007687685.1|  [L=318]
Description: hypothetical protein TALC_00525 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-07   31.5   0.1    3.5e-07   29.9   0.1    1.9  2  AP_endonuc_2  Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.13   2.4e+03       4      16 ..      26      38 ..      24      40 .. 0.87
   2 !   29.9   0.1   1.9e-11   3.5e-07      64     188 ..      85     234 ..      52     280 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.13
                                      HHHCT-SEEEEEC CS
                      AP_endonuc_2  4 aaeaGfdgvElfg 16
                                       a++G+dg Elf+
  gi|474934103|ref|YP_007687685.1| 26 TASLGIDGYELFT 38
                                      699********96 PP

  == domain 2  score: 29.9 bits;  conditional E-value: 1.9e-11
                                       S..HHHHHHHHHHHHHHHHHHTBSEEEEEBCC......GBCTTTSGHHHHHHHHHHHHHHHHHHHHHHT...SEEEE CS
                      AP_endonuc_2  64 r..reesvdalkraielaaaLGapllvlhpGt......agagpkgseeeawerlaeslneladyaekeg...vklal 129
                                          ree v +l+++i +aa++   + vlh+G+       ++++++++   + ++a+ +n+ +      g    klal
  gi|474934103|ref|YP_007687685.1|  85 GhdREEMVGNLRDCINYAAKVRPAYGVLHAGNtdirqvLHRRHESDDLKVLGLFADFINQTVSGMP-GGeppFKLAL 160
                                       1336777*************************9*98875566666777889999999999988864.33677***** PP

                                       E--TTTTSSSTC.HHHHHHHHHHTTTTEEEEEEHHHHHHH......TTTHHHHHHHHHGG........EEEEEE CS
                      AP_endonuc_2 130 Etlagsgvelgd.eelarlldavdspnvgvclDtgHllia......eedvddalraladr........ikhvHi 188
                                       E+l+++g  l+  ee++ l ++++ +n g++lDtgHl+        e+  +d++ a+ dr        i+ +H+
  gi|474934103|ref|YP_007687685.1| 161 ENLWWEGLKLRSpEEWRLLERKLEFDNWGFTLDTGHLMNTcdgaydEDSAIDEVMAVIDRyprdmrdrIGTIHL 234
                                       *******99999999999999*******************9999996666666666666656667777888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1988.32
//
Query:       gi|474934104|ref|YP_007687686.1|  [L=49]
Description: LSU ribosomal protein L40E [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.1e-09   35.6   4.6    7.5e-09   35.3   4.4    1.3  1  Ribosomal_L40e  Ribosomal L40e family
    0.00063   19.7   0.8    0.00066   19.7   0.8    1.2  1  DZR             Double zinc ribbon
     0.0011   18.6   2.9     0.0016   18.1   2.9    1.3  1  zinc_ribbon_2   zinc-ribbon domain
     0.0026   18.2   3.8     0.0033   17.8   3.8    1.2  1  Toxin_5         Scorpion short toxin
  ------ inclusion threshold ------
      0.051   13.1   1.1      0.049   13.1   1.1    1.0  1  QueC            Queuosine biosynthesis protein QueC


Domain annotation for each model (and alignments):
>> Ribosomal_L40e  Ribosomal L40e family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   4.4   2.1e-12   7.5e-09       9      49 ..       7      44 ..       5      45 .. 0.87

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 2.1e-12
                    Ribosomal_L40e  9 AqKyncdKmiCrkCYArlpprAtnCrkkkCghsnnlrpKKk 49
                                      A++   dK++C  CYA  pp+At+Cr  kCg s  lrpK k
  gi|474934104|ref|YP_007687686.1|  7 AERRLLDKSVCMSCYATNPPKATKCR--KCGDS-HLRPKAK 44
                                      5666789*******************..9**87.5888855 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.8   1.8e-07   0.00066      28      49 .]      14      35 ..       2      45 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.8e-07
                               DZR 28 edrCpsCgekvdpearfCpeCG 49
                                      + +C+sC + ++p+a+ C +CG
  gi|474934104|ref|YP_007687686.1| 14 KSVCMSCYATNPPKATKCRKCG 35
                                      6788888888888888888887 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   2.9   4.4e-07    0.0016       2      20 ..      17      35 ..      16      37 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 4.4e-07
                     zinc_ribbon_2  2 CpnCGaelqdnakFCpyCG 20
                                      C +C a+++++a+ C +CG
  gi|474934104|ref|YP_007687686.1| 17 CMSCYATNPPKATKCRKCG 35
                                      ******************9 PP

>> Toxin_5  Scorpion short toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   3.8   9.3e-07    0.0033       1      18 [.      17      34 ..      17      40 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 9.3e-07
                           Toxin_5  1 CgPCFTTdpqmeakCreC 18
                                      C+ C+ T+p  + kCr+C
  gi|474934104|ref|YP_007687686.1| 17 CMSCYATNPPKATKCRKC 34
                                      9***************** PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.1   1.4e-05     0.049     175     206 ..      12      44 ..       2      48 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.4e-05
                                       HHHHH-B-STTS..-BTTTTSSSHHHHHHHHHH CS
                              QueC 175 vpleetlsCYege.eegkaCgeCdaCalRkkgf 206
                                       ++ +  +sCY+ +  ++++C++C   +lR k+ 
  gi|474934104|ref|YP_007687686.1|  12 LDKSVCMSCYATNpPKATKCRKCGDSHLRPKAK 44 
                                       6667789****9987789***********9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       723  (0.0403257); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 287.62
//
Query:       gi|474934105|ref|YP_007687687.1|  [L=301]
Description: Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.1e-08   33.1   0.0    4.6e-07   30.0   0.1    2.4  2  Response_reg  Response regulator receiver domain
  ------ inclusion threshold ------
      0.011   15.4   0.7      0.041   13.6   0.1    2.2  3  DUF835        Protein of unknown function (DUF835)


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.1   5.2e-11   4.6e-07       2      66 ..       4      67 ..       3      74 .. 0.95
   2 ?   -0.4   0.0      0.14   1.3e+03      77     100 ..     114     137 ..     110     143 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 5.2e-11
                                      EEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHH CS
                      Response_reg  2 livdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeir 66
                                      li++D   +  ++ ++le+ g+ e+ ++++ ++ le ++++++d+++lD + ++  G++++ ei 
  gi|474934105|ref|YP_007687687.1|  4 LIIEDRDSMTGVICSILEKGGI-ETNVVRNIRAGLEEYNTNRYDIVILDTEVDDFRGMQFILEIT 67
                                      8*********************.*************************************99986 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.14
                                       EESSTSHHHHHHHHHCTESEEEES CS
                      Response_reg  77 ltahseeedavealkagaddflsK 100
                                       +t+++ ee + +a+  +ad fl K
  gi|474934105|ref|YP_007687687.1| 114 FTSKELEEAVAKAIPREADRFLEK 137
                                       68888899999999999**99999 PP

>> DUF835  Protein of unknown function (DUF835)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.37   3.3e+03      48      83 ..      17      51 ..      10      52 .. 0.73
   2 ?   -1.7   0.0      0.25   2.3e+03      21      56 ..      87     123 ..      80     146 .. 0.60
   3 ?   13.6   0.1   4.6e-06     0.041       4     134 ..     168     292 ..     165     294 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.37
                            DUF835 48 tkveeentvsPtnlekltetivkflkeaekgvvliD 83
                                      +++ e++ ++ + + ++++ ++++ +++++ +v++D
  gi|474934105|ref|YP_007687687.1| 17 CSILEKGGIETNVVRNIRAGLEEYNTNRYD-IVILD 51
                                      555566777777777888888888888886.88887 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.25
                            DUF835  21 kvlaitRenpkkirekv.kienvkviwltkveeentv 56 
                                       ++++++R+ ++ + +    ++   v  +t++e e++v
  gi|474934105|ref|YP_007687687.1|  87 PGVIVIRTVSERVPSDCpRVKAELVRPFTSKELEEAV 123
                                       6667777777766666655555555555555544443 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 4.6e-06
                            DUF835   4 kkekakeilsdlvkegvkvlaitRenpkkirekv.kienvkviwltkveeentvsPtnlekltetivkflkeaekgv 79 
                                       k+++ +ei+ ++ k g+++++it ++pk  r+++     ++v+ l+ +e        +l  + e+++ f+ + e+ v
  gi|474934105|ref|YP_007687687.1| 168 KNDFIQEIMGTFAKAGYDMFLITASRPKVARDRFgLDRDAEVFTLSGNEY-------KLGSMIESVKLFIARTEHPV 237
                                       7788999999************************6677889999999997.......8******************* PP

                            DUF835  80 vliDgleyLvlengFesvlkflltlkDavllkngtlilvidkealeekelalLkr 134
                                       v +D l+  + +++ ++++  l+++ ++   ++ t++ ++d e l ++  ++L+ 
  gi|474934105|ref|YP_007687687.1| 238 VAMDDLDNVIEHSSMDRTVTALSEILSTKKKTGFTFLTSVDGELLTQNIKNILRD 292
                                       *************************999999999999999999999888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1882.59
//
Query:       gi|474934106|ref|YP_007687688.1|  [L=424]
Description: enolase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   1.8e-122  408.3   0.0   2.3e-122  407.9   0.0    1.1  1  Enolase_C  Enolase, C-terminal TIM barrel domain
    9.9e-49  164.9   0.2    1.6e-48  164.2   0.2    1.3  1  Enolase_N  Enolase, N-terminal domain
    1.9e-06   27.6   0.0    1.2e-05   25.0   0.0    2.0  2  MR_MLE_C   Enolase C-terminal domain-like


Domain annotation for each model (and alignments):
>> Enolase_C  Enolase, C-terminal TIM barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  407.9   0.0  3.9e-126  2.3e-122       2     293 ..     137     422 ..     136     424 .] 0.98

  Alignments for each domain:
  == domain 1  score: 407.9 bits;  conditional E-value: 3.9e-126
                                       -EE-EE-EEEEE-GGGSSSS--SSEEEEE-TT-SSHHHHHHHHHHHHHHHHHHHHHCC.GGGG-B-TTS-B----SS CS
                         Enolase_C   2 lvlPvPalnvinGGshagnklalqefmilPvgassfkealrlGaevyhklksvlkkkygksatnvGdeGGfaPnlqs 78 
                                       ++lPvP++n+inGG+hag++l++qe mi+P+ga+sf+e lr+ ae+y++lks+lkkkyg sa nvGdeGGfaP +++
  gi|474934106|ref|YP_007687688.1| 137 VTLPVPMYNIINGGKHAGGDLKVQECMIIPAGAKSFSECLRMAAETYQSLKSLLKKKYGVSAINVGDEGGFAPPVNT 213
                                       68*************************************************************************** PP

                                       HHHHHHHHHHHHHHCT-TC..TBEEEEE--GGGCEETCTTEEECTTTTTT..GGCEEEHHHHHHHHHHHHHHS-EEE CS
                         Enolase_C  79 nkealdliveaiekaGykg..kvkialdvassefykekdkkydldfkeeesdkskkltseqladlykelvkkyPivs 153
                                        +eal +iv+ai++aGy +  +v +++d+assef++e  +kyd+d+ +        l+  +l d+y++++k++P++s
  gi|474934106|ref|YP_007687688.1| 214 VSEALSTIVDAISDAGYAPgkDVYLGIDCASSEFFDEASQKYDVDGMK--------LSPGELLDHYVDITKEFPLIS 282
                                       *****************9888***********************9987........9******************** PP

                                       EES-S-TT-HHHHHHHHHHHTTTSEEEESTTTTT-HHHHHHHHHCT--SEEEE-HHHH-SHHHHHHHHHHHHHTT-E CS
                         Enolase_C 154 iedpldeddweawkklteelgdkvqivGddltvtnpkrlkeaiekkaanalllkvnqiGsltesleavklakeagyg 230
                                       iedp++e+d+e+ + +t+++g++vqivGddl+vtn+krlk++i+ +aanalllkvnqiG+lte+ +a +++ ++gy 
  gi|474934106|ref|YP_007687688.1| 283 IEDPFQENDFETTTAFTKKVGEHVQIVGDDLFVTNSKRLKTGIDCGAANALLLKVNQIGTLTEAQDAQEMSAANGYR 359
                                       ***************************************************************************** PP

                                       EEEE--SC--S--HHHHHHHHCT-SEEE---S-SHHHHHHHHHHHHHHHHHGCC-EE-GGGCT CS
                         Enolase_C 231 vvvshrsGetedttiadlavglsaGqiktGaparserlakynqllrieeelgekakyaGkkvr 293
                                       vvvshrsGe+edtti+dl+vg  +GqiktGap+r er akyn+llrie+ lg+ka++ Gkk+ 
  gi|474934106|ref|YP_007687688.1| 360 VVVSHRSGESEDTTISDLSVGWGTGQIKTGAPCRGERTAKYNRLLRIEDRLGSKAVFPGKKAL 422
                                       ***********************************************************9875 PP

>> Enolase_N  Enolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.2   0.2   2.7e-52   1.6e-48       1     131 []       4     132 ..       4     132 .. 0.98

  Alignments for each domain:
  == domain 1  score: 164.2 bits;  conditional E-value: 2.7e-52
                                       EEEEEEEEEE-TTS-EEEEEEEEETTC-EEEEE--B-BSSSSSS-B----SSTTSGGGT--HHHHHHHHHTHHHHHT CS
                         Enolase_N   1 IkkvkareildSrGnpTvevevttedgalgraavpsGaStgekealelrDgdkkrylgkgvekavenvnekiapali 77 
                                       I+kv are+ldSrGnpTve+ vt++ g   +a++psGaStg  ea elrDg + r++gkgv+kavenv++ ia+a++
  gi|474934106|ref|YP_007687688.1|   4 IEKVWAREVLDSRGNPTVEAVVTVN-GREISAIAPSGASTGMWEANELRDG-DGRFHGKGVQKAVENVRTAIAKAIV 78 
                                       89**********************7.6677********************9.79*********************** PP

                                       TSBTT-HHHHHHHHHHHH-STT-TTT-HHHHHHHHHHHHHHHHHHHTS-HHHHH CS
                         Enolase_N  78 gldvtdqeeiDkllielDgtenksklGaNailavSlAvakaaAkakelplyryl 131
                                       g+d+tdq+ iD++++++Dgt+nk+ lG+Na++avS+Ava+a+A  ++++ly+y+
  gi|474934106|ref|YP_007687688.1|  79 GMDPTDQKGIDEAMLRADGTDNKKVLGGNATTAVSFAVAHAGAFVSNQELYEYV 132
                                       *****************************************************7 PP

>> MR_MLE_C  Enolase C-terminal domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0     0.086   5.2e+02     124     186 ..      77     136 ..      63     160 .. 0.70
   2 !   25.0   0.0     2e-09   1.2e-05      70     156 ..     276     364 ..     220     388 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.086
                                       EEEEBHHHHTSHHHHHHHHHHHHHTT-EEEEBSCSSHHHHHHHHHHHHTTTTBEEEEEEGGGG CS
                          MR_MLE_C 124 ivqpdvsrvgGitearkvaalaeafgvpvapHsgsgglglaaslhlaaaipnllileyfldae 186
                                       iv +d++   Gi+ea+  a+  +   v    ++ ++++++ a +h  a ++n   +ey   ++
  gi|474934106|ref|YP_007687688.1|  77 IVGMDPTDQKGIDEAMLRADGTDNKKVL--GGNATTAVSF-AVAHAGAFVSNQELYEYVGKDH 136
                                       6777777777777777777666666666..2222346666.5689999999999999987765 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 2e-09
                                       GGGTESEEESSSSTTTHHHHHHHHHH.HH.SSEEEESTTSSS.HHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHH CS
                          MR_MLE_C  70 eeldllwlEEPvppeddleglaelra.ra.sipiaagEslys.radfrelleagavdivqpdvsrvgGitearkvaa 143
                                       +e+ l  +E+P++  +d e   + ++    +++i+++    +  ++++  +++ga+ ++ ++v+++g +tea++  +
  gi|474934106|ref|YP_007687688.1| 276 KEFPLISIEDPFQE-NDFETTTAFTKkVGeHVQIVGDDLFVTnSKRLKTGIDCGAANALLLKVNQIGTLTEAQDAQE 351
                                       5577889******9.88********863379******9876669********************************* PP

                                       HHHHTT-EEEEBS CS
                          MR_MLE_C 144 laeafgvpvapHs 156
                                       + +a+g++v++ +
  gi|474934106|ref|YP_007687688.1| 352 MSAANGYRVVVSH 364
                                       ********88655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2796.82
//
Query:       gi|474934107|ref|YP_007687689.1|  [L=397]
Description: Nicotinic acid phosphoribosyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-22   80.4   0.0    1.7e-22   80.0   0.0    1.2  1  QRPTase_C       Quinolinate phosphoribosyl transferase, C-ter
  ------ inclusion threshold ------
      0.051   13.3   3.5       0.11   12.2   3.5    1.6  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
      0.081   13.3   0.0        3.7    8.0   0.0    2.3  2  NAPRTase_N      Nicotinate phosphoribosyltransferase (NAPRTas
        0.1   12.8   0.3       0.25   11.5   0.3    1.6  1  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like


Domain annotation for each model (and alignments):
>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.0   0.0   3.8e-26   1.7e-22       1     169 []     123     311 ..     123     311 .. 0.95

  Alignments for each domain:
  == domain 1  score: 80.0 bits;  conditional E-value: 3.8e-26
                                       HHHHHHHHHHHHHCTSSEEEE-S---TTTHHHHHHHHHHTTSB.......--TSSTTTSEEE-HHHHHHHSSHHHHH CS
                         QRPTase_C   1 iAtltarmveaaksakvrildTRkttPglrllekyAvliGGgd.......nhrlgLsdmvlikdnhiaaagsiveav 70 
                                       iAt++ar++ a k+++v  ++ R+++Pg++ +  ++ +iGG+d           g + + +++++ + ++gs + a 
  gi|474934107|ref|YP_007687689.1| 123 IATASARVKIASKGKTVLAFGNRRMHPGIAGVIDRSCYIGGCDgvaspfgADLCGTEAVGTVPHALMLVMGSNEAAF 199
                                       9**********************************************9999999*********************** PP

                                       HHHHHHHTTTSE..EEEEESSHHHHHHHHHHT....-SEEEEES--H..HHHHHHHHHH.HHHSTT....SEEEEES CS
                         QRPTase_C  71 ksvreavdkevk..ievevesleeleevleae....adiimLDnfsv..eelkkaveel.keknkr....vlievSG 134
                                       k+++e++d +v   + +++  +e   +v++a+      +++LD++s+   ++k+ ++e+ +e + +    v i +SG
  gi|474934107|ref|YP_007687689.1| 200 KAFDEVIDPKVGrvMLIDTFEDERKAAVAAAGlikdLKGVRLDTPSSrrGNFKELINEVrWELDVNgyrdVDIIASG 276
                                       *******88887799****99999999999888877899******997799*****99989988878899******* PP

                                       S--TTTHHHHHCTT-SEEEECHHCHTB----EEEE CS
                         QRPTase_C 135 gvtlenveeyaksgvdvisvgalthsvkalDislk 169
                                       g+ +++++++ +s v  ++vg+ + ++++lD+ ++
  gi|474934107|ref|YP_007687689.1| 277 GLDENTISAIVDSAVAGFGVGTSIANAPTLDMGMD 311
                                       ********************************996 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   3.5   2.5e-05      0.11       1      24 [.     333     357 ..     333     359 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.5e-05
                                       -B-SSS--.B----SSS----SSS- CS
                    DNA_RNApol_7kD   1 YiCgeCga.evslkkgdpiRCkeCG 24 
                                       Y C  C a  vsl++ d iRC +CG
  gi|474934107|ref|YP_007687689.1| 333 YRCPCCFAmGVSLRPDDTIRCPDCG 357
                                       788888652588************9 PP

>> NAPRTase_N  Nicotinate phosphoribosyltransferase (NAPRTase) N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0   0.00082       3.7       4      53 ..      20      70 ..      17      75 .. 0.81
   2 ?    3.3   0.0     0.023     1e+02      90     124 ..      77     117 ..      71     118 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00082
                        NAPRTase_N  4 DlYkltmaqavfkkgp.dvevvfelffRkkpfkgeyaivagleevieylen 53
                                      D+Y     q++  kg  d++vv e+++   p k + a++ gleev++ +e 
  gi|474934107|ref|YP_007687689.1| 20 DVYFQRTKQILEAKGFkDTKVVAEFTCGGLPNKWPWAVFCGLEEVVRLMEG 70
                                      66655556666556655**************999*************9986 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.023
                        NAPRTase_N  90 aveeeev......vfpgepeirveGpwieaillEtplLaiv 124
                                       av+e++v      +  + p ++v G  ++  ++Et++L +v
  gi|474934107|ref|YP_007687689.1|  77 AVPEGTVfrardsASVRVPLMNVAGAYADFGIYETAMLGMV 117
                                       555555544444466789********************887 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.3   5.6e-05      0.25       5      42 ..     329     368 ..     327     381 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.6e-05
                      NOB1_Zn_bind   5 kswvlrChaCfkvt...kdmtkkFCpkCGnktLkrvavsvd 42 
                                       +++ +rC +Cf +    +  +   Cp CG++ ++ ++v v 
  gi|474934107|ref|YP_007687689.1| 329 RKFAYRCPCCFAMGvslRPDDTIRCPDCGKA-MEMIEVPVL 368
                                       899*********764445588899*****85.444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.56
# Mc/sec: 2136.60
//
Query:       gi|474934108|ref|YP_007687690.1|  [L=62]
Description: hypothetical protein TALC_00530 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 399.13
//
Query:       gi|474934109|ref|YP_007687691.1|  [L=137]
Description: hypothetical protein TALC_00531 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       233  (0.0129957); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 891.29
//
Query:       gi|474934110|ref|YP_007687692.1|  [L=228]
Description: NaMN:DMB phosphoribosyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-05   23.7   0.1    3.3e-05   23.3   0.1    1.1  1  DBI_PRT   Phosphoribosyltransferase


Domain annotation for each model (and alignments):
>> DBI_PRT  Phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.1   1.9e-09   3.3e-05     118     175 ..     126     182 ..      99     195 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.9e-09
                                       SB--TTTS-SS-HHHHHHHHHHHHHHHHHHHCTTECEEEEEEE-TTCHHHHHHHHHHH CS
                           DBI_PRT 118 gtaniakepAmtreeaeaaleaGieladeladagadllalGemGigNttaaaallaal 175
                                         ++i+++ Am++e++++++e+G  l ++l ++ +d ++l e   g tt+a a+l a+
  gi|474934110|ref|YP_007687692.1| 126 AGEKITTGHAMSAEQVKKSFEYGKILGEQL-ASTYDFVVLSESCAGGTTTALAVLLAM 182
                                       567899*****************9988887.567*******************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1521.99
//
Query:       gi|474934111|ref|YP_007687693.1|  [L=334]
Description: putative phosphoglycerate mutase, AP superfamily [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.2e-06   26.0   0.3    2.3e-05   23.9   0.5    1.8  2  Metalloenzyme  Metalloenzyme superfamily
    0.00061   19.7   0.0     0.0016   18.3   0.0    1.7  2  PhosphMutase   2,3-bisphosphoglycerate-independent phosphogly


Domain annotation for each model (and alignments):
>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0     0.091   8.1e+02       4      30 ..       5      34 ..       2      49 .. 0.87
   2 !   23.9   0.5   2.6e-09   2.3e-05     121     209 ..     234     307 ..     199     323 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.091
                                      EEEEETTBB----GGGTT...HHHS--HHH CS
                                      xxxxxxxxxxxxxxxxxx...xxxxxxxxx RF
                     Metalloenzyme  4 vlvvlDGlGeapadelna...ihvAktPtl 30
                                      + v+lDG+ + p+  l++    +vA++P +
  gi|474934111|ref|YP_007687693.1|  5 LFVLLDGMEDDPNPALGGrkpYEVARMPFI 34
                                      6799*********99999999999999976 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 2.6e-09
                                       HHHHHHH.CC.-SEEEEEE-HHHHHHHTT-HHHHHHHHHHHHHHHHHHHTTS-TTTEEEEEE-SSB--TTTSS.... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 121 ekaldailsgkfdlvvvniknaDmvGHtgdleatiaaieaaDeavkeildaieqvdgilvvtADHgnaedmvkrdkq 197
                                        +a++a+++g    v++++ + D+++H++d +++i+ +e++D+++++ +++++ v        DHg+     +    
  gi|474934111|ref|YP_007687693.1| 234 PAAAEALKEG---NVFLHMDEVDEYSHEKDHNKKIRILEHIDSMMEKYFSDVRRVV----FFVDHGTSCVTGT---- 299
                                       5677888665...8********************************9998887765....556***9987777.... PP

                                       ....-----EEE CS
                                       xxxxxxxxxxxx RF
                     Metalloenzyme 198 plTsHtlepVPi 209
                                           H l  VP+
  gi|474934111|ref|YP_007687693.1| 300 ----HILMDVPF 307
                                       ....77766665 PP

>> PhosphMutase  2,3-bisphosphoglycerate-independent phosphoglycerate mutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.8e-07    0.0016      39      73 ..      67      99 ..      62     174 .. 0.75
   2 ?   -2.7   0.0      0.52   4.7e+03      55      72 ..     304     320 ..     303     325 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.8e-07
                                      HHHHHHHHTT----TT-EEEEEEEEEEC..TTCEE CS
                      PhosphMutase 39 RGplEAlgiGlelkpgdvafRcnlvtvdeedgiii 73
                                      RG+lEA g+G+++++g  afR+  + ++  dg++ 
  gi|474934111|ref|YP_007687693.1| 67 RGALEAQGLGMRMGNGRTAFRMSPAYIE--DGMVR 99
                                      9*************************95..44443 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.52
                                       -EEEEEEEEEEC..TTCE CS
                      PhosphMutase  55 dvafRcnlvtvdeedgii 72 
                                       dv fR+nl ++++ ++ i
  gi|474934111|ref|YP_007687693.1| 304 DVPFRTNLNCFKDGEH-I 320
                                       789******9986533.2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2089.95
//
Query:       gi|474934112|ref|YP_007687694.1|  [L=724]
Description: [NiFe] hydrogenase maturation protein HypF [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-31  109.2   0.0    2.6e-31  108.5   0.0    1.4  1  Sua5_yciO_yrdC   Telomere recombination
    1.4e-22   80.3   0.1    2.6e-22   79.4   0.1    1.4  1  HypF_C           HypF Kae1-like domain
    9.6e-21   73.3  18.0    1.8e-13   50.0   6.9    3.2  3  zf-HYPF          HypF finger
    4.1e-16   59.2   0.0    7.6e-16   58.3   0.0    1.5  1  Acylphosphatase  Acylphosphatase
  ------ inclusion threshold ------
      0.052   13.7   0.6      0.052   13.7   0.6    3.0  3  Zn-ribbon_8      Zinc ribbon domain
       0.11   12.8   4.6       0.22   12.0   2.0    2.6  2  Lar_restr_allev  Restriction alleviation protein Lar
        2.7    7.8   7.6        1.2    9.0   0.1    3.0  3  zinc_ribbon_5    zinc-ribbon domain
        3.8    8.6  10.2        2.4    9.2   0.5    3.9  3  zf-C2H2_4        C2H2-type zinc finger
        5.2    6.7  10.4        4.9    6.8   3.3    3.4  3  TF_Zn_Ribbon     TFIIB zinc-binding
        7.1    7.3  11.8         14    6.4   0.5    3.7  3  zf-C2H2          Zinc finger, C2H2 type
        8.1    5.9  11.9       0.58    9.5   0.9    3.0  3  zf-TFIIB         Transcription factor zinc-finger


Domain annotation for each model (and alignments):
>> Sua5_yciO_yrdC  Telomere recombination
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.5   0.0   1.6e-34   2.6e-31       2     178 ..     200     367 ..     199     368 .. 0.92

  Alignments for each domain:
  == domain 1  score: 108.5 bits;  conditional E-value: 1.6e-34
                                       HHHTTSEEEEE-SSSEEEEEETTSHHHHHHHHHHHTSHCCC--EEEESSCCCCCCCC-.TC--HHHHHHHHCT-SSS CS
                    Sua5_yciO_yrdC   2 alrkGgivaiptetvYgLacdatneeaverlreiKgrpsdkplavlvasledlkklae.seveeealkllerfwPGp 77 
                                       +l++G++ + +  ++ +++c ++      rlre  +r  +kp+a++v++++ ++++ae +++eee l +++r    p
  gi|474934112|ref|YP_007687694.1| 200 FLEEGKLGIAKSWGGMHICCTLE---QTGRLREWYRRG-EKPFAIMVRDMDAVRRYAEpTPEEEERLLSPHR----P 268
                                       689*****************876...7789********.*********************************....* PP

                                       CEEEEE..E-TS-HHHHTTTTEEEEEE-SSHHHHHHHHHCTS-.EEEEES-STTS-S-SSHHHHHHHC-TTSECB-S CS
                    Sua5_yciO_yrdC  78 itlllkrskeklpkevapglktvGvrlPdtplarlLlealgep.lvaTSanlsgepsitdaeeveeelgeivdlild 153
                                       i+l++k +++ l ++v+pgl+++G++lP+t +  lL++al++  l++TSan++gep+++d   + +     +d++l 
  gi|474934112|ref|YP_007687694.1| 269 IVLVKKVPSD-LTDAVSPGLDNIGIFLPYTGMQILLFDALNADaLIMTSANVPGEPMVLDDGRILDL---GADVYLL 341
                                       ******8555.*****************************8656********************664...6788999 PP

                                       S-.--SSS---EEEETTSSTSSECEX CS
                    Sua5_yciO_yrdC 154 gg.eiavgvdstVvdltegkpkilRr 178
                                       ++ ei +++d++V+++ ++   ++R+
  gi|474934112|ref|YP_007687694.1| 342 HNqEIVNRADDSVLRVCGSDTFFIRK 367
                                       998*************9888888886 PP

>> HypF_C  HypF Kae1-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.4   0.1   1.6e-25   2.6e-22       5     102 .]     383     480 ..     380     480 .. 0.98

  Alignments for each domain:
  == domain 1  score: 79.4 bits;  conditional E-value: 1.6e-25
                            HypF_C   5 evLAlGaelkntfalakggqallsqhlGdlenletleayeealeeleklleikpevivcDlhpdylstklaeelaek 81 
                                       +++A+G + + t a+a+gg+++ +qh+G+ e++   e +eea++   +ll+++p +++ D+hp yl++++a+ lae+
  gi|474934112|ref|YP_007687694.1| 383 DAVAVGPQENITGAVASGGRIYPTQHIGNGEHIGVPEYLEEAVRFQMSLLGCRPGIVAEDMHPAYLNRRFAHALAEE 459
                                       579************************************************************************** PP

                            HypF_C  82 eklelievqHHhAHllavlae 102
                                        ++e+i+vqHHhAH+++++++
  gi|474934112|ref|YP_007687694.1| 460 CGAEIIDVQHHHAHVASLMVD 480
                                       *******************86 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   2.1   5.1e-10   8.4e-07       1      34 []     101     132 ..     101     132 .. 0.93
   2 !   50.0   6.9   1.1e-16   1.8e-13       2      34 .]     150     182 ..     149     182 .. 0.98
   3 ?   -2.5   0.0       2.7   4.5e+03       3      17 ..     458     472 ..     458     475 .. 0.74

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 5.1e-10
                                       --HHHHHHHC-TTSTTTT-TT---TTTS--EEEE CS
                           zf-HYPF   1 lCedClrEykdpldRRfhaqfisCtnCGPrlsli 34 
                                       +C +C  +++    RR  + f++Ct+CGPr++l+
  gi|474934112|ref|YP_007687694.1| 101 ICARCIDDMRS--GRRTGYLFTTCTDCGPRFTLL 132
                                       79*****9998..69*****************95 PP

  == domain 2  score: 50.0 bits;  conditional E-value: 1.1e-16
                                       -HHHHHHHC-TTSTTTT-TT---TTTS--EEEE CS
                           zf-HYPF   2 CedClrEykdpldRRfhaqfisCtnCGPrlsli 34 
                                       C+ C +Ey +p+dRRfh+q+++C++CGP+++l+
  gi|474934112|ref|YP_007687694.1| 150 CPVCGKEYSEPSDRRFHHQTVCCPDCGPQYRLV 182
                                       ******************************996 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 2.7
                                       HHHHHHHC-TTSTTT CS
                           zf-HYPF   3 edClrEykdpldRRf 17 
                                       e+C +E+ d + +  
  gi|474934112|ref|YP_007687694.1| 458 EECGAEIIDVQHHHA 472
                                       689999999876555 PP

>> Acylphosphatase  Acylphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.3   0.0   4.6e-19   7.6e-16       2      85 .]       3      82 ..       2      82 .. 0.93

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 4.6e-19
                   Acylphosphatase  2 rllvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdgsVeivaegeeekvekfleelksgppkarvdeveveeleeeeef 80
                                      r++++G VQgvgFR+ v+r A +lgl+G+v+N+  + V + +   ++ +++f++ l   pp arvd+ve e+++ + + 
  gi|474934112|ref|YP_007687694.1|  3 RIVIRGVVQGVGFRPAVYRTAASLGLRGTVCNHGSH-VTVDVDDGDAFLDSFMKNL---PPLARVDSVEKEDYDIPADV 77
                                      799*********************************.9999999999999998777...588***************** PP

                   Acylphosphatase 81 kdFei 85
                                      k+F+i
  gi|474934112|ref|YP_007687694.1| 78 KGFSI 82
                                      ***98 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1       7.8   1.3e+04      24      32 ..      96     105 ..      93     109 .. 0.77
   2 ?   13.7   0.6   3.2e-05     0.052       8      35 ..     122     156 ..     117     159 .. 0.82
   3 ?    4.3   8.0     0.028        45       7      33 ..     149     176 ..     146     181 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 7.8
                       Zn-ribbon_8  24 aplta.CPeC 32 
                                       + +ta C +C
  gi|474934112|ref|YP_007687694.1|  96 PTDTAiCARC 105
                                       5578889998 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 3.2e-05
                       Zn-ribbon_8   8 CeeCghefevlqsis.dap......ltaCPeCgse 35 
                                       C++Cg +f+ l+s   d++       + CP Cg+e
  gi|474934112|ref|YP_007687694.1| 122 CTDCGPRFTLLRSLPyDRErtamseFPRCPVCGKE 156
                                       *********8888888777788886777*****85 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.028
                       Zn-ribbon_8   7 rCeeCghefevlqsisdaplta.CPeCg 33 
                                       rC  Cg+e+ +        +t+ CP+Cg
  gi|474934112|ref|YP_007687694.1| 149 RCPVCGKEYSEPSDRRFHHQTVcCPDCG 176
                                       8********95544443346777****9 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.89   1.4e+03      28      36 ..     119     127 ..      81     141 .. 0.78
   2 ?   12.0   2.0   0.00013      0.22       3      36 ..     147     177 ..     145     196 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.89
                   Lar_restr_allev  28 cvyCadCga 36 
                                       + +C+dCg 
  gi|474934112|ref|YP_007687694.1| 119 FTTCTDCGP 127
                                       778999996 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00013
                   Lar_restr_allev   3 LkpCPfCggravlersqrvvaeigqcvyCadCga 36 
                                          CP Cg++     + r + +   +v+C dCg 
  gi|474934112|ref|YP_007687694.1| 147 FPRCPVCGKEYSEPSDRRFHHQ---TVCCPDCGP 177
                                       678*************999987...*******97 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.4     0.087   1.4e+02       1      15 [.     118     132 ..     118     135 .. 0.83
   2 ?   -2.3   0.2       2.4   3.9e+03       4       9 ..     149     154 ..     149     157 .. 0.80
   3 ?    9.0   0.1   0.00071       1.2       4      17 ..     171     184 ..     169     187 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.087
                     zinc_ribbon_5   1 LiirCpdCdtkFklv 15 
                                       L + C dC+  F l 
  gi|474934112|ref|YP_007687694.1| 118 LFTTCTDCGPRFTLL 132
                                       5689*******9885 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.4
                     zinc_ribbon_5   4 rCpdCd 9  
                                       rCp C+
  gi|474934112|ref|YP_007687694.1| 149 RCPVCG 154
                                       799997 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00071
                     zinc_ribbon_5   4 rCpdCdtkFklvds 17 
                                        CpdC+ +++lvds
  gi|474934112|ref|YP_007687694.1| 171 CCPDCGPQYRLVDS 184
                                       5************9 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1      0.23   3.7e+02       2      11 ..     121     130 ..     120     136 .. 0.81
   2 ?    9.2   0.5    0.0015       2.4       2      21 ..     149     168 ..     148     170 .. 0.81
   3 ?    1.0   0.6      0.66   1.1e+03       2      11 ..     171     180 ..     170     184 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.23
                         zf-C2H2_4   2 kCpiCgksFs 11 
                                       +C+ Cg +F+
  gi|474934112|ref|YP_007687694.1| 121 TCTDCGPRFT 130
                                       6********6 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0015
                         zf-C2H2_4   2 kCpiCgksFsskkaLlr.Hlk 21 
                                       +Cp+Cgk +s +++ +r H +
  gi|474934112|ref|YP_007687694.1| 149 RCPVCGKEYSEPSD-RRfHHQ 168
                                       7***********99.444866 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.66
                         zf-C2H2_4   2 kCpiCgksFs 11 
                                       +Cp Cg  ++
  gi|474934112|ref|YP_007687694.1| 171 CCPDCGPQYR 180
                                       8****99885 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.2     0.066   1.1e+02      20      27 ..     120     127 ..     114     129 .. 0.87
   2 ?    6.8   3.3     0.003       4.9       2      27 ..     149     177 ..     148     184 .. 0.86
   3 ?   -2.4   0.0       2.1   3.5e+03       5      14 ..     357     366 ..     356     371 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.066
                                       EEESSSSB CS
                      TF_Zn_Ribbon  20 lvCtdCGl 27 
                                       ++CtdCG+
  gi|474934112|ref|YP_007687694.1| 120 TTCTDCGP 127
                                       69****96 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.003
                                       EETTTTCEEC...HEETSTTCEEESSSSB CS
                      TF_Zn_Ribbon   2 kCPnCgstnl...veDpergelvCtdCGl 27 
                                       +CP+Cg ++     + + + ++ C+dCG+
  gi|474934112|ref|YP_007687694.1| 149 RCPVCGKEYSepsDRRFHHQTVCCPDCGP 177
                                       6*****9885566666999*********7 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2.1
                                       TTTCEECHEE CS
                      TF_Zn_Ribbon   5 nCgstnlveD 14 
                                       +Cgs+++   
  gi|474934112|ref|YP_007687694.1| 357 VCGSDTFFIR 366
                                       7***885444 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1     0.016        25       2      11 ..     121     130 ..     120     135 .. 0.85
   2 ?    6.4   0.5    0.0086        14       2      15 ..     149     162 ..     149     169 .. 0.83
   3 ?    1.0   1.1      0.45   7.3e+02       3      10 ..     172     179 ..     170     181 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.016
                                       EETTTTEEES CS
                           zf-C2H2   2 kCpdCgksFk 11 
                                       +C+dCg +F+
  gi|474934112|ref|YP_007687694.1| 121 TCTDCGPRFT 130
                                       8********7 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0086
                                       EETTTTEEESSHHH CS
                           zf-C2H2   2 kCpdCgksFkrksn 15 
                                       +Cp+Cgk ++ +s+
  gi|474934112|ref|YP_007687694.1| 149 RCPVCGKEYSEPSD 162
                                       7********99987 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.45
                                       ETTTTEEE CS
                           zf-C2H2   3 CpdCgksF 10 
                                       CpdCg  +
  gi|474934112|ref|YP_007687694.1| 172 CPDCGPQY 179
                                       99***876 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.9   0.00036      0.58       2      26 ..     102     126 ..     101     126 .. 0.97
   2 ?   -2.1   6.1       1.5   2.4e+03       2      26 ..     150     176 ..     149     176 .. 0.67
   3 ?   -3.6   0.0       4.5   7.3e+03      30      39 ..     479     488 ..     478     489 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00036
                          zf-TFIIB   2 CPkCqdeleeserggveidyCpqCr 26 
                                       C +C d+++  +r g+++ +C++C+
  gi|474934112|ref|YP_007687694.1| 102 CARCIDDMRSGRRTGYLFTTCTDCG 126
                                       ************************7 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.5
                          zf-TFIIB   2 CPkCqde.leeser..ggveidyCpqCr 26 
                                       CP+C+ e  e+s+r  ++ +++ Cp+C+
  gi|474934112|ref|YP_007687694.1| 150 CPVCGKEySEPSDRrfHHQTVC-CPDCG 176
                                       ****986466777754554444.88886 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 4.5
                          zf-TFIIB  30 ldrgelekll 39 
                                       +drg le+++
  gi|474934112|ref|YP_007687694.1| 479 VDRGNLEHMT 488
                                       79****9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (724 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.69u 0.28s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 4481.40
//
Query:       gi|474934113|ref|YP_007687695.1|  [L=264]
Description: methylthioadenosine phosphorylase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      8e-49  166.0   0.0    9.7e-49  165.7   0.0    1.0  1  PNP_UDP_1  Phosphorylase superfamily


Domain annotation for each model (and alignments):
>> PNP_UDP_1  Phosphorylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.7   0.0   5.4e-53   9.7e-49       1     231 [.       3     236 ..       3     238 .. 0.96

  Alignments for each domain:
  == domain 1  score: 165.7 bits;  conditional E-value: 5.4e-53
                                       CEEEEESSH....HHHHHHHHHEEEEEEEEEE.TTEEEEEEEETTEEE.EEEE--...SSHHHHH.HHHHHHHHHHC CS
                         PNP_UDP_1   1 kiaiivgsp....gevellaespleetpfgregrgfkfvtGtlkgkpv.vivstG...iGkpnaa.vvaeirllkef 68 
                                       kiaii+gs+    + +el+ e  + +tpfg++  +  + +G+++g++v +++++G     +p++  ++a++ +lk +
  gi|474934113|ref|YP_007687695.1|   3 KIAIIGGSGiynpDSFELIEEV-FPDTPFGKP--SDPIMIGKINGVEVaFLFRHGkqhQHPPSSVpYRANMYALKKL 76 
                                       69**********9999999999.*********..*********8888879*******988888888*********** PP

                                       --SEEEEEEEEEESSTTT-TT-EEEEEEEEESSSCCGCCTHHCCTCCCCTTSSEE--HHHHHHHHHCHHTTTTTEEE CS
                         PNP_UDP_1  69 gvkaiiriGtaGglnpdlkvGDvvipddainfdgrsplygpkeegqyfpdsydapadpelrallkeaaealgikvhr 145
                                       g++ +i+  ++G+l++++++GD+vi+d++i+f+  +++ ++ ++   ++ ++d+  +p l  +  e+ae++ i++h 
  gi|474934113|ref|YP_007687695.1|  77 GCEYVISACAVGSLREEFRPGDLVITDQFIDFTKKRDYSFFMDQ-TVHISMPDP-CCPYLNGIFGEVAEDMKIPYHI 151
                                       ******************************************99.*********.********************** PP

                                       .EEEEEESESS-CHHHHHHHHHHTC-CEEESSHHHHHHHHHHTT--EEEEEEEEETTTBETTCTCH.HCCCHHHHHH CS
                         PNP_UDP_1 146 .GvvatadgfyaeteaelrllrrlgadaveMEtaavaqlArelgipfaairvvsdlaaggadaeatheeveefaqea 221
                                        G++++ +g++++t+ae++++r++g d+++M+ ++++qlArelg++++++++v+d ++ + d+  t e v+++++e+
  gi|474934113|ref|YP_007687695.1| 152 gGTYVCIEGPRFSTRAESNMFRQFG-DIIGMTIVPECQLARELGMCYCSLATVTD-YDCWKDEDVTIEMVMKTMAEC 226
                                       *************************.*****************************.9******************** PP

                                       HHHHHHHHHH CS
                         PNP_UDP_1 222 aknaaallla 231
                                        +++ +ll++
  gi|474934113|ref|YP_007687695.1| 227 LDKVLRLLEK 236
                                       ***9999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1680.42
//
Query:       gi|474934114|ref|YP_007687696.1|  [L=56]
Description: hypothetical protein TALC_00536 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-06   28.0  14.7    2.7e-06   27.6  14.7    1.1  1  FeoB_associated  FeoB-associated Cys-rich membrane protein
  ------ inclusion threshold ------
       0.16   12.1   0.3        0.2   11.9   0.3    1.1  1  DUF2749          Protein of unknown function (DUF2749)


Domain annotation for each model (and alignments):
>> FeoB_associated  FeoB-associated Cys-rich membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6  14.7   3.1e-10   2.7e-06       2      43 ..       5      45 ..       4      47 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 3.1e-10
                   FeoB_associated  2 tiIVgliiaaavafvirrlikkkkkG..sCg.ggCsgCsssssgC 43
                                       iIV++++a+a+a ++ +li ++++G  sCg g+C++C++    C
  gi|474934114|ref|YP_007687696.1|  5 SIIVLAVVAVAIACAVGSLIYNHRSGksSCGcGDCCSCKN----C 45
                                      69*************9999999888888777578999987....5 PP

>> DUF2749  Protein of unknown function (DUF2749)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3   2.2e-05       0.2       5      35 ..       5      35 ..       1      39 [. 0.69

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.2e-05
                           DUF2749  5 ilIvlvia.vaagagtilwlvvqpragtsgsg 35
                                       +Ivl+++ va++ + +  l+ + r+g s+ g
  gi|474934114|ref|YP_007687696.1|  5 SIIVLAVVaVAIACA-VGSLIYNHRSGKSSCG 35
                                      466665553877665.5677899999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1383  (0.0771376); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 363.67
//
Query:       gi|474934115|ref|YP_007687697.1|  [L=721]
Description: ferrous iron transporter FeoB [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-64  216.5   0.0      2e-64  215.9   0.0    1.3  1  FeoB_N           Ferrous iron transport protein B
    2.9e-42  143.5   8.0    3.3e-29  101.4   0.2    2.8  2  Gate             Nucleoside recognition
      1e-19   70.7   0.1    1.9e-19   69.9   0.1    1.4  1  MMR_HSR1         50S ribosome-binding GTPase
      4e-18   64.8   5.8    4.2e-18   64.8   1.0    3.1  2  FeoB_C           Ferrous iron transport protein B C terminus
    2.8e-12   47.0   0.2    4.9e-12   46.2   0.2    1.4  1  FeoB_Cyto        FeoB cytosolic helical domain
    1.2e-05   24.9   0.2     0.0029   17.2   0.1    3.0  2  GTP_EFTU         Elongation factor Tu GTP binding domain
    6.4e-05   22.9   0.9       0.21   11.5   0.0    2.5  2  RsgA_GTPase      RsgA GTPase
    0.00019   20.9   0.0    0.00032   20.2   0.0    1.3  1  SRPRB            Signal recognition particle receptor beta su
     0.0088   16.1   0.1        3.5    7.6   0.1    2.4  2  Dynamin_N        Dynamin family
  ------ inclusion threshold ------
      0.014   15.1   0.0      0.091   12.5   0.0    2.1  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
      0.049   13.4   0.0       0.72    9.6   0.0    2.1  2  ATP_bind_1       Conserved hypothetical ATP binding protein


Domain annotation for each model (and alignments):
>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.9   0.0   1.2e-67     2e-64       2     154 ..       4     155 ..       3     157 .. 0.98

  Alignments for each domain:
  == domain 1  score: 215.9 bits;  conditional E-value: 1.2e-67
                                       EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHHCTS CS
                            FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardflleee 78 
                                       t+al+Gnpn+Gkttlfn+ltga+q+vgNwpGvt+++k+gk++  ++ ve+vD PGiYsls+ys ee v+r+fl+e +
  gi|474934115|ref|YP_007687697.1|   4 TIALAGNPNSGKTTLFNKLTGASQRVGNWPGVTIDRKTGKIR-GTNGVELVDTPGIYSLSPYSPEEVVTRNFLMEGN 79 
                                       79****************************************.889******************************* PP

                                       SSEEEEEEEGGGHHHHHHHHHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTHHHHHH CS
                            FeoB_N  79 pdvvvnvvdatnlernLyLtlqllelgvpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkegieellk 154
                                        d+v+n+vdatn+ernL+Ltlq+l++g+p+v+alnm+d++ek+g ++d++kL+e+Lg+pvv++sa k++gi+el++
  gi|474934115|ref|YP_007687697.1|  80 HDAVINIVDATNIERNLFLTLQILDTGIPTVVALNMMDAVEKEGGSLDAEKLAERLGCPVVPISALKSDGIRELVE 155
                                       *************************************************************************987 PP

>> Gate  Nucleoside recognition
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   3.2   1.5e-14   2.4e-11       2     111 ..     355     449 ..     354     450 .. 0.96
   2 !  101.4   0.2     2e-32   3.3e-29       1     112 []     516     649 ..     516     649 .. 0.99

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 1.5e-14
                              Gate   2 lkagpiillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqg 78 
                                       + ++p +l++++++ +l++ ++++r++++++ vf+ +g  l++k++++ ++g +   ++v+ ++ ++         +
  gi|474934115|ref|YP_007687697.1| 355 IGFLPQMLVLFLVLCILEDIGYMARAAFVMDRVFRFFG--LSGKSFIPVIVGTG---CGVPGIMATR---------T 417
                                       678999********************************..**************...*********9.........* PP

                              Gate  79 fdtpksalafllfvllytpcvatlavivrelgs 111
                                       +++ +++ ++ ++v+++ pc+a l++i+ ++g+
  gi|474934115|ref|YP_007687697.1| 418 IENDRDRRITAMTVTFM-PCGAKLPIIALIAGA 449
                                       ****************6.8********999986 PP

  == domain 2  score: 101.4 bits;  conditional E-value: 2e-32
                              Gate   1 llkagpiillasiliwflss..............ssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgt 63 
                                       ++kag+iillas++iwfl s              +s+l+ +g ++  +f+plg e++w++tv+ +tg++ake  vgt
  gi|474934115|ref|YP_007687697.1| 516 VKKAGTIILLASVFIWFLASfdtsfsylgadatsDSILQTVGEAVCGIFQPLGWEDHWELTVGSVTGLIAKENLVGT 592
                                       68*************************************************************************** PP

                              Gate  64 lgtly........tsalgellqgfdtpksalafllfvllytpcvatlavivrelgsk 112
                                       lgtl+        +++++++l+   tp++ l+fl+f+ll+ pc+a++++i relgs+
  gi|474934115|ref|YP_007687697.1| 593 LGTLFsldevgesGEEYWDILAAYLTPAAGLSFLVFNLLCAPCFAAIGAIHRELGSW 649
                                       *******************************************************97 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.9   0.1   1.1e-22   1.9e-19       2     113 ..       5     114 ..       4     115 .. 0.79

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 1.1e-22
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETT.EEEEEEECGGCSS..HHHHHHHHHHHHHHHHC CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkg.keielvDtpGlie..gaseekglgkaflalee 75 
                                       +a++G+pN+GK+tL+n+ltg+  +v+++pg+T+d ++g+++  g + +elvDtpG+++    s e+ ++++fl   +
  gi|474934115|ref|YP_007687697.1|   5 IALAGNPNSGKTTLFNKLTGASQRVGNWPGVTIDRKTGKIR--GtNGVELVDTPGIYSlsPYSPEEVVTRNFLMEGN 79 
                                       89**************************************9..5489********975534455669******9999 PP

                                       TSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEE CS
                          MMR_HSR1  76 adlillvvdaseeklkpldeeleelleeakkplilvln 113
                                        d+++ +vda+ + ++++     ++l ++++p++++ln
  gi|474934115|ref|YP_007687697.1|  80 HDAVINIVDAT-N-IERNLFLTLQIL-DTGIPTVVALN 114
                                       9********77.3.444432222332.24566666665 PP

>> FeoB_C  Ferrous iron transport protein B C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.8   1.0   2.6e-21   4.2e-18       2      53 .]     459     511 ..     458     511 .. 0.95
   2 ?    0.7   0.3      0.27   4.4e+02       6      33 ..     684     710 ..     684     711 .. 0.82

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 2.6e-21
                            FeoB_C   2 fslYllgilvallvalllkktt.lkgepspfvmELPpYrlPslknvliktweR 53 
                                       ++ Y+lgi+v+l+++++lkk   l g+p+pf+mELPpY+lP++ nv++ t +R
  gi|474934115|ref|YP_007687697.1| 459 LFSYVLGIVVILMSGIILKKWKsLAGKPAPFIMELPPYHLPTVLNVVKGTLDR 511
                                       567*****************889***************************998 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.27
                            FeoB_C   6 llgilvallvalllkkttlkgepspfvm 33 
                                       ++gi++a ++  +l  + l  ++++fv+
  gi|474934115|ref|YP_007687697.1| 684 VTGIAIAAVSVVVLAYL-LVSKNPFFVI 710
                                       57999999999999887.8888888887 PP

>> FeoB_Cyto  FeoB cytosolic helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.2     3e-15   4.9e-12       3      91 .]     174     257 ..     172     257 .. 0.95

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 3e-15
                         FeoB_Cyto   3 eeiEkaiekleellkesnlkaklppRwlAlklLegDeelleelkedpelraeveearkeleaelgedledvIvdary 79 
                                       + iE  i++  e+l++    ++  +Rw+++kl+e+D+ l e+  e   +++e++e ++ +e+e+g++++++I dary
  gi|474934115|ref|YP_007687697.1| 174 DSIESLISEAGEKLADA--VPEERKRWYSVKLIEKDQGLSEKFPE---IAEEMKERCAPVEEEYGDEMDSIISDARY 245
                                       689************98..99********************9999...***************************** PP

                         FeoB_Cyto  80 kfiegilrevvk 91 
                                       + i ++++ +v+
  gi|474934115|ref|YP_007687697.1| 246 EIIGRLVSGAVT 257
                                       ******999885 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   1.8e-06    0.0029      52     192 ..      33     161 ..       2     163 .. 0.70
   2 ?   -3.0   0.0       2.8   4.5e+03      38      57 ..     183     202 ..     171     205 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.8e-06
                                       HTSCSSCEEEEEETTCSSEEEEEEEESSSGG...GHHH.HHHH....HHT-SEEEEEEETTTBSTHHHHHHHHHHHH CS
                          GTP_EFTU  52 rgiTiksaaisleketkkylinliDtPGHvd...Fske.virg....lrvlDgavlvvdaveGvepqteevlrlalk 120
                                        g+Ti+ ++ ++     +  + l+DtPG  +   +s e v +         D ++ +vda+  + ++   +  ++l+
  gi|474934115|ref|YP_007687697.1|  33 PGVTIDRKTGKIR---GTNGVELVDTPGIYSlspYSPEeVVTRnflmEGNHDAVINIVDAT-NI-ERNLFLTLQILD 104
                                       4788888888888...677899999**9876445775524444243233467788888888.34.444567789999 PP

                                       TTTEEEEEEESCGST.HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHS CS
                          GTP_EFTU 121 egvpiivfiNKmDrl.kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvell 192
                                        g+p++v++N mD + k+  +  +e++ ++l             g   +pvv++Salk +g+++l+e  v+ +
  gi|474934115|ref|YP_007687697.1| 105 TGIPTVVALNMMDAVeKEGGSLDAEKLAERL-------------G---CPVVPISALKSDGIRELVERTVSVA 161
                                       ***************5555667778888888.............3...8*****************9888765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.8
                                       HHHSTHCHSHHHHHHTSCSS CS
                          GTP_EFTU  38 eeervlDtlkeErergiTik 57 
                                        +e+  D  +eEr+r  ++k
  gi|474934115|ref|YP_007687697.1| 183 AGEKLADAVPEERKRWYSVK 202
                                       346789********998887 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.4   0.00073       1.2     101     164 ..       4      61 ..       2      63 .. 0.72
   2 !   11.5   0.0   0.00013      0.21      35      96 ..      92     156 ..      82     162 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00073
                                       EEEEECSTTSSHHHHHHHHCTT-----S--------------SEEEEEETTTEEEESS-SSSS- CS
                       RsgA_GTPase 101 tsvlvGqSGvGKStLinallpelelktgevseklgrGkhTTtavellelaegglliDtPGfrel 164
                                       t++l+G+   GK+tL n+l++  ++++g+            +++  ++  +g  l+DtPG+ +l
  gi|474934115|ref|YP_007687697.1|   4 TIALAGNPNSGKTTLFNKLTGA-SQRVGNWPG-----VTIDRKTGKIRGTNGVELVDTPGIYSL 61 
                                       678999999************8.788887654.....333333444445556669999998765 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00013
                                       HHHHHH...HHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHH CS
                       RsgA_GTPase  35 ldrfLv...laeekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkel 96 
                                       ++r L+   ++ ++gi+ v++ln +D +e+e    + ++  e+lg++v+ +sa +++g++el e+
  gi|474934115|ref|YP_007687697.1|  92 IERNLFltlQILDTGIPTVVALNMMDAVEKEGGSLDAEKLAERLGCPVVPISALKSDGIRELVER 156
                                       55555411145679******************99999999*******************999875 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0     2e-07   0.00032       5      92 ..       4      96 ..       1     114 [. 0.71

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2e-07
                                      EEEEE-STTSSHHHHHHHHHHSS---B---S..S-EEETTG...GGTT-SEEEETT-GCCS....HH.HHHHHHHHGGE CS
                             SRPRB  5 avllvGlsdsGKTslftrLttdsvkktvtSq..essaalkvksekgskltliDfPGheklr....qk.lleklkakssl 76
                                      ++ l+G  +sGKT+lf++Lt  s +            + k+  +  + ++l+D PG  +l      + ++ +++ + + 
  gi|474934115|ref|YP_007687697.1|  4 TIALAGNPNSGKTTLFNKLTGASQRVGNWPGvtIDRKTGKI--RGTNGVELVDTPGIYSLSpyspEEvVTRNFLMEGNH 80
                                      6889****************987665554321355556666..566789********9997222223123334444556 PP

                                      EEEEEEEETTS-HHHH CS
                             SRPRB 77 kglvfvvDStidpkev 92
                                       +++ +vD+t  ++++
  gi|474934115|ref|YP_007687697.1| 81 DAVINIVDATNIERNL 96
                                      7888888888777776 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.0    0.0069        11       1      21 [.       5      25 ..       5      33 .. 0.91
   2 !    7.6   0.1    0.0022       3.5     101     163 ..      48     111 ..      43     116 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0069
                                      EEEEEBTTTTHHHHHHHHHTS CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLlge 21
                                      ia+ G+ +sGK+++ n+L+g+
  gi|474934115|ref|YP_007687697.1|  5 IALAGNPNSGKTTLFNKLTGA 25
                                      7999***************97 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0022
                                       -SEEEEE---B-S..SSGTTSHHHHHHH..STTEEEEEEEETTS-CCC-CHHHHHHHHSTTBTTEEE CS
                         Dynamin_N 101 kgltlvDlPGlds..vnkrdqelvkeyi..kkadiilavtsanhdlsnsealflarevdpkgkrtiv 163
                                       +g++lvD+PG+ s      ++ ++++++   ++d+++ +++a +     ++lfl  ++ + g  t+v
  gi|474934115|ref|YP_007687697.1|  48 NGVELVDTPGIYSlsPYSPEEVVTRNFLmeGNHDAVINIVDATN---IERNLFLTLQILDTGIPTVV 111
                                       689********995333334467777776667788888888876...34566666666666666655 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.6e-05     0.091       4     139 ..       5     155 ..       2     158 .. 0.74
   2 ?   -0.8   0.0      0.72   1.2e+03      75     105 ..     235     265 ..     232     277 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.6e-05
                         PduV-EutP   4 illiGkvgsGKttLtqalkg.........eelkYkktqaiefsdev..iDtPGeylenr.....klysalivtsaea 64 
                                       i l G+ +sGKttL ++l+g            + +kt  i  ++ v  +DtPG y  +       + + + +     
  gi|474934115|ref|YP_007687697.1|   5 IALAGNPNSGKTTLFNKLTGasqrvgnwpGVTIDRKTGKIRGTNGVelVDTPGIYSLSPyspeeVVTRNFLMEGNHD 81 
                                       7799***************98877777764456799****99998777*****998765111113444455555555 PP

                         PduV-EutP  65 dvialvqdateeesvfppgfasvfnkeviGiitkidlaedeenieaveelLksaGaekifevsavekegieellk 139
                                        vi +v +++ e+++f          +++  +  +d +e+e     +e+l +  G+  +  +sa++++gi el++
  gi|474934115|ref|YP_007687697.1|  82 AVINIVDATNIERNLFLTLQILDTGIPTVVALNMMDAVEKEGGSLDAEKLAERLGCP-VVPISALKSDGIRELVE 155
                                       688888888888888877666666667777778889888888777888888888885.67899999999999875 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.72
                         PduV-EutP  75 eeesvfppgfasvfnkeviGiitkidlaede 105
                                       e++s+++++  +++ + v G +tk+++ +++
  gi|474934115|ref|YP_007687697.1| 235 EMDSIISDARYEIIGRLVSGAVTKAEVDKST 265
                                       678899999999************9988665 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.13   2.1e+02       2      20 ..       8      26 ..       7      35 .. 0.82
   2 ?    9.6   0.0   0.00044      0.72      95     172 ..      52     122 ..      36     157 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.13
                        ATP_bind_1  2 vGpaGsGKttfvgalseil 20
                                      +G + sGKtt+ ++l+   
  gi|474934115|ref|YP_007687697.1|  8 AGNPNSGKTTLFNKLTGAS 26
                                      69999*******9997655 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00044
                        ATP_bind_1  95 lfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltdptkfisgllsalsamlrlelPhvvvlnkfDllke 171
                                       l+DtPG   l  +s++ +   + L++     v+++vD++ ++         l+    +l +++P+vv+ln +D +++
  gi|474934115|ref|YP_007687697.1|  52 LVDTPGIYSLSPYSPEEVVTRNFLMEGNHDAVINIVDATNIERN-------LFLTLQILDTGIPTVVALNMMDAVEK 121
                                       89999999999999999944455555666678899999888873.......333346899*************9886 PP

                        ATP_bind_1 172 k 172
                                       +
  gi|474934115|ref|YP_007687697.1| 122 E 122
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (721 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       680  (0.0379274); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.75u 0.29s 00:00:01.04 Elapsed: 00:00:00.52
# Mc/sec: 4160.54
//
Query:       gi|474934116|ref|YP_007687698.1|  [L=43]
Description: Fe2+ transport system protein A [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-09   36.4   0.0      5e-09   36.3   0.0    1.0  1  FeoA      FeoA domain


Domain annotation for each model (and alignments):
>> FeoA  FeoA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.0   2.8e-13     5e-09      31      73 ..       1      43 []       1      43 [] 0.98

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 2.8e-13
                                      HT--TT-EEEEEEE-TTS-SEEEEETTEEEEE-HHHHTTEEEE CS
                              FeoA 31 mGlvpGarievvarapfggplvvrvgdtrvaLgreeAqaIlVe 73
                                      mG+++G++i v + ap+g+p+ + v++ ++ L+r+eA+ + Ve
  gi|474934116|ref|YP_007687698.1|  1 MGITKGCEIYVRKVAPLGDPVEITVRGYELTLRRSEAEIVEVE 43
                                      9*************************************99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       172  (0.0095934); expected 358.6 (0.02)
Passed bias filter:                      151  (0.00842211); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.50
# Mc/sec: 257.01
//
Query:       gi|474934117|ref|YP_007687699.1|  [L=84]
Description: FeoA domain protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-12   47.7   0.1    1.5e-12   47.6   0.1    1.0  1  FeoA      FeoA domain


Domain annotation for each model (and alignments):
>> FeoA  FeoA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   0.1   8.3e-17   1.5e-12       2      73 ..      14      82 ..      13      83 .. 0.92

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 8.3e-17
                                      EGGG--TT-EEEEEEE-TT.SSHHHHHHHHT--TT-EEEEEEE-TTS-SEEEEETTEEEEE-HHHHTTEEEE CS
                              FeoA  2 pLsdlkeGergeiarisdedpellrrLremGlvpGarievvarapfggplvvrvgdtrvaLgreeAqaIlVe 73
                                      p s +k Ge g+++ri   d+ +++ L ++G+++Ga+++ v   + +g  +++v+++r+a+++++A++I+ +
  gi|474934117|ref|YP_007687699.1| 14 PISLAKAGECGTVVRITG-DAGTRKFLTDLGFTVGAQVQAVT--DVKGSKILAVRGSRIAVDSRMASKIYFR 82
                                      78999***********75.699*******************5..7899*********************865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       241  (0.0134419); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 594.37
//
Query:       gi|474934118|ref|YP_007687700.1|  [L=56]
Description: hypothetical protein TALC_00540 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 400.83
//
Query:       gi|474934119|ref|YP_007687701.1|  [L=377]
Description: Alcohol dehydrogenase, class IV [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.1e-96  321.0   2.7    9.2e-96  320.8   2.7    1.0  1  Fe-ADH         Iron-containing alcohol dehydrogenase
    4.4e-19   69.2   6.2      3e-16   59.9   6.2    2.2  1  Fe-ADH_2       Iron-containing alcohol dehydrogenase
  ------ inclusion threshold ------
       0.09   12.6   0.2       0.18   11.7   0.1    1.6  2  Helicase_RecD  Helicase
        0.1   11.2   0.2       0.14   10.8   0.2    1.2  1  GvpD           GvpD gas vesicle protein
       0.51    9.4   3.2        1.9    7.6   0.2    2.6  2  DHQ_synthase   3-dehydroquinate synthase


Domain annotation for each model (and alignments):
>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  320.8   2.7   2.6e-99   9.2e-96       1     364 []       8     369 ..       8     369 .. 0.96

  Alignments for each domain:
  == domain 1  score: 320.8 bits;  conditional E-value: 2.6e-99
                                       -SEEEEETTGGGGHHHHHTTT-..EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTTS CS
                            Fe-ADH   1 Ptrivfgkgaleelgellkklgakralivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaala 77 
                                       Pt++vfg+g+ + +ge ++++g kralivt+k+++ ++gll+ ++ +le+a +e++v+dgv+ npt++ v+++++ a
  gi|474934119|ref|YP_007687701.1|   8 PTNLVFGRGKSKAVGESVARFG-KRALIVTGKSTA-STGLLESAKGQLEDAHVEFAVYDGVSRNPTTDVVMKGVEEA 82 
                                       99********************.9*********88.***************************************** PP

                                       -TT.--EEEEEESHHHHHHHHHHHHHTT....................--EEEEESS-S-S-TT-SEEEEE.-TTSE CS
                            Fe-ADH  78 reegadvviavGGGsviDtAKaialllanpe.vedyl.gegkakkkkalpliaiPTtaGtGsevtplavitdeeege 152
                                       + +gad+++a+GGGs+iD+AKaia+++a ++ + dy+ g+      kalp +a+PTt+GtGsev++++v+td+++  
  gi|474934119|ref|YP_007687701.1|  83 KYHGADCILALGGGSSIDAAKAIAAMVATGGnILDYMrGNPGGVDVKALPTVAVPTTCGTGSEVNGVSVLTDPATCD 159
                                       ****************************9856*****64444667788***************************** PP

                                       EEEE-..SS--SEEEEEHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHT---TTSSB--HHHHHHHHHHHHHHHHHHH CS
                            Fe-ADH 153 klsifdpellPdlaivDpeltltlPkrvtaatglDalahalEayvskkanplsdalaleairliaknleravadged 229
                                       k++++  +++P+++ivDpel+ t+Pk+v+ a   Da++h +E+yv  ka+plsdal+++a+  + kn+  + +d +d
  gi|474934119|ref|YP_007687701.1| 160 KIAMRYVSMVPKASIVDPELMETMPKEVLSAVTYDAMCHIVESYVHLKATPLSDALCEKALDCLSKNIVAVNDDIHD 236
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHSS---HHHHHHHHHHC.CGGGGGS-HHHHHHHHH..........HHHHHHT....... CS
                            Fe-ADH 230 leareqmllastlaglafsnaglgavHalahalgalfgiphglanaillpavlrfnaeaaperlaqlaralggesde 306
                                       +ea  q++ ast+agl + + g+   Hal+h+l+++ +i hg+++a + pa +   a+ +p ++a++ +algg+   
  gi|474934119|ref|YP_007687701.1| 237 AEALDQVCFASTIAGLTIFSNGTISPHALEHPLSGMKNIVHGRGLAAVAPACFMKCARGSPFKFARVSHALGGK--- 310
                                       ****************99999**************99****************88888889**********997... PP

                                       T--HHHHHHHHHHHHHTT---SHHHHT-TT-HHHHHHHHHT-T..SGGGGSSS---HHHH CS
                            Fe-ADH 307 eaaeeliealrellkelglptsLselgvdeedldklaeaalkd..rslannpreltaedv 364
                                          +++ + +rel  ++g  t+Ls  g++++d+++l+++++++  + l  np++lt++d+
  gi|474934119|ref|YP_007687701.1| 311 -DEHDVDDMMRELAVNIGTFTTLSIEGFSKSDIPELTANVMRTggSKLTYNPVKLTEKDI 369
                                       .5566668899**********************************9***********996 PP

>> Fe-ADH_2  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.9   6.2   8.3e-20     3e-16       5     247 ..      16     279 ..      12     282 .. 0.83

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 8.3e-20
                          Fe-ADH_2   5 galeklgellkelelkkvllvadentkka.agekveeslkeagikvevveeveeeadleeveklvealreketdlvv 80 
                                       g  + +ge +++ + k++l+v+++ t ++ + e+ + +l++a+++ +v++ v+ +++ + v+k ve+++ +++d+++
  gi|474934119|ref|YP_007687701.1|  16 GKSKAVGESVARFG-KRALIVTGKSTASTgLLESAKGQLEDAHVEFAVYDGVSRNPTTDVVMKGVEEAKYHGADCIL 91 
                                       55566666666654.78899999999988799********************************************* PP

                          Fe-ADH_2  81 avGgGtiiDiakyvsak....................lnvpyvsvpTaaS....vDGfaspgaslvvdgkkrtv.ak 132
                                       a+GgG+ iD+ak ++a                     + +p v+vpT+      v+G +  + + + d+  + + + 
  gi|474934119|ref|YP_007687701.1|  92 ALGGGSSIDAAKAIAAMvatggnildymrgnpggvdvKALPTVAVPTTCGtgseVNGVSVLTDPATCDK--IAMrYV 166
                                       *************99862222222222222222222234789999998752222566666666666665..555568 PP

                          Fe-ADH_2 133 aaaPlaviaDldvlaeAPrrllasGvGDllgkytaladwklanevseplaklsaamvqeaaeklvedkketealeel 209
                                         +P a i+D +++++ P++ l + + D++  ++  + +  a+ +s+ l++++ + +++++ ++ +d ++ eal ++
  gi|474934119|ref|YP_007687701.1| 167 SMVPKASIVDPELMETMPKEVLSAVTYDAMCHIVESYVHLKATPLSDALCEKALDCLSKNIVAVNDDIHDAEALDQV 243
                                       99*************************************************************************** PP

                          Fe-ADH_2 210 lealalsgigisrpaSGsEHliSHaldmlalkqalHGe 247
                                       + a++++g++i + +  s H + H l  ++  + +HG 
  gi|474934119|ref|YP_007687701.1| 244 CFASTIAGLTIFSNGTISPHALEHPLSGMK--NIVHGR 279
                                       **************************9998..899995 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1     5e-05      0.18       7      58 ..      14      64 ..      13     111 .. 0.72
   2 ?   -4.1   0.0       3.4   1.2e+04     115     125 ..     241     251 ..     238     251 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5e-05
                     Helicase_RecD  7 GRGKSaalGlalaaliaegksnilvtapskenvktlfeflakglealglke...e 58
                                      GRGKS a+G  +a++ ++    ++vt  s  + + l+e+++ +le+ +++     
  gi|474934119|ref|YP_007687701.1| 14 GRGKSKAVGESVARFGKR---ALIVTGKST-ASTGLLESAKGQLEDAHVEFavyD 64
                                      9***********999888...457776665.566789999999998887765553 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 3.4
                     Helicase_RecD 115 krvvlatTvhG 125
                                       ++v++a+T+ G
  gi|474934119|ref|YP_007687701.1| 241 DQVCFASTIAG 251
                                       6899****987 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   3.8e-05      0.14     271     368 ..     146     251 ..     100     261 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.8e-05
                              GvpD 271 rdawsvlvlaairdflsqemgvavvppke.gspgllkndlnivlskavidvtasvfetyagllksl........aek 338
                                        +  svl+ +a  d ++    v++vp      p l+++  + vls   +d ++++ e y  l            a +
  gi|474934119|ref|YP_007687701.1| 146 VNGVSVLTDPATCDKIA-MRYVSMVPKASiVDPELMETMPKEVLSAVTYDAMCHIVESYVHLKATPlsdalcekALD 221
                                       45789***********9.445777776542689**************************765443333346544444 PP

                              GvpD 339 ylenaittskddaidPdrltgsdyvisleg 368
                                        l + i + +dd+ d + l    + +++ g
  gi|474934119|ref|YP_007687701.1| 222 CLSKNIVAVNDDIHDAEALDQVCFASTIAG 251
                                       556677777888877777766667766666 PP

>> DHQ_synthase  3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.2   0.00054       1.9      19      56 ..      75     112 ..      66     121 .. 0.85
   2 ?    1.6   0.3     0.035   1.2e+02      95     116 ..     170     191 ..     164     323 .. 0.58

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00054
                                       HHHHHHHTT--TT-EEEEEESHHHHHHHHHHHHHBTT- CS
                      DHQ_synthase  19 ildalleakleRksllialGGGvvgDlaGfvAatylRG 56 
                                       +++ + eak++  ++++alGGG   D a  +Aa++  G
  gi|474934119|ref|YP_007687701.1|  75 VMKGVEEAKYHGADCILALGGGSSIDAAKAIAAMVATG 112
                                       6677788899999********************98777 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.035
                                       -SEEEEEGGGGGGS-HHHHHHH CS
                      DHQ_synthase  95 PkavlidlevLktLperelraG 116
                                       Pka ++d+e+++t+p++ l+a 
  gi|474934119|ref|YP_007687701.1| 170 PKASIVDPELMETMPKEVLSAV 191
                                       6666666666666666555432 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2521.96
//
Query:       gi|474934120|ref|YP_007687702.1|  [L=215]
Description: Histidinol phosphatase and related hydrolases of the PHP family [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      8e-09   36.0   0.0    8.4e-09   35.9   0.0    1.3  1  PHP          PHP domain
    9.2e-06   25.3   0.0    1.7e-05   24.4   0.0    1.4  1  RNase_P_p30  RNase P subunit p30


Domain annotation for each model (and alignments):
>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.0   9.4e-13   8.4e-09       1      72 [.       4      76 ..       4     202 .. 0.76

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 9.4e-13
                                      EEEE--CCC--.S-H..HHHHHHHHHCT-SEEEEEEEEBTT.......HHHHHHHHHHHHTTTTSEEEEEEE....... CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               PHP  1 dlHvHteyslldgalsieelvkkakelglkaiaiTDhgnlf.......gyvefykaakkkykagikpiiGleayvadds 72
                                      dlH+H+ +s   + + + elv++a + g++ iaiTDh+++        +    +ka+ + +++ i++i G+e++ ++ +
  gi|474934120|ref|YP_007687702.1|  4 DLHTHSIFSDG-ELI-PAELVRRAMDCGHDLIAITDHVDMTnvefvvrN---VVKAC-ELREDYIRVIPGVEITHVPPR 76
                                      79******954.233.6************************88754422...33333.455567********8776655 PP

>> RNase_P_p30  RNase P subunit p30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   1.9e-09   1.7e-05      14     145 ..      17     145 ..       5     148 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.9e-09
                                       ....HHHHHHHHH-SEEEEEEEEEESS---HHHHH.......HHHHHHHH....HHSSEEEEEEES-...H..HHHH CS
                       RNase_P_p30  14 kksrtiktlaelgytgvainftveaekekkpnasepikeelkelkkelsg..lkllsRvtlvvsdps...kl.qrls 84 
                                        ++++++++++ g + +ai+ +v+  ++++   +      + ++     +  +++  +v+++   p+   ++ ++ +
  gi|474934120|ref|YP_007687702.1|  17 IPAELVRRAMDCGHDLIAITDHVDMTNVEFVVRNV----VKACELR---EdyIRVIPGVEITHVPPRliaQVaKQAR 86 
                                       556789999***************99999999999....2233333...2339**************5443356666 PP

                                       HHHHH--EEEEE--SHHH....HHHHHHT.T-SEEE-TTTTSSS-S--HHHHHHHHHHT-EEEEE CS
                       RNase_P_p30  85 kvrqkfdllavrPtteka....lraacenldvDiisidltsrlpfglkhktiraAvergvafEin 145
                                       ++  k+ ++  + +te +    +ra +en+d+Di+ ++       +++ +++++A ++gva+Ei+
  gi|474934120|ref|YP_007687702.1|  87 QYGAKWVVVHGETVTEPVmkgtNRASVENPDIDILAHPG------FITLEEAQLAKDNGVALEIT 145
                                       666666677554444443222299*************99......7999**************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 1260.38
//
Query:       gi|474934121|ref|YP_007687703.1|  [L=203]
Description: phosphoribosyl-ATP pyrophosphohydrolase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-34  116.8   1.1    4.8e-34  116.0   1.1    1.4  1  PRA-CH         Phosphoribosyl-AMP cyclohydrolase
    2.2e-18   66.5   0.2    3.4e-18   65.8   0.2    1.3  1  PRA-PH         Phosphoribosyl-ATP pyrophosphohydrolase
    6.6e-06   26.2   2.5    1.2e-05   25.4   2.5    1.4  1  MazG           MazG nucleotide pyrophosphohydrolase domain
  ------ inclusion threshold ------
      0.015   15.0   0.0      0.023   14.3   0.0    1.4  1  ApbA           Ketopantoate reductase PanE/ApbA
      0.041   13.5   0.1      0.063   12.9   0.1    1.3  1  Peptidase_C71  Pseudomurein endo-isopeptidase Pei


Domain annotation for each model (and alignments):
>> PRA-CH  Phosphoribosyl-AMP cyclohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.0   1.1   1.3e-37   4.8e-34       1      73 [.      29     101 ..      29     102 .. 0.99

  Alignments for each domain:
  == domain 1  score: 116.0 bits;  conditional E-value: 1.3e-37
                                       EEEEE-HHHHHHHHHHSB-EEEETTTTEEEETTTTTS--EEEEEEEE-TTSSEEEEEEEESS-SSTTSBSSS- CS
                            PRA-CH   1 mlaymnkealektletgkavyySrsrkklWkKGetSgnvqkvkeirlDcDqDalllkveqkgaaCHtgkesCF 73 
                                       m+ay+n+ea+++  etg+++++Srsr+klWkKGe+Sg+vqk+k+i+ DcD+D+ll++veq+g+aCHtg++sCF
  gi|474934121|ref|YP_007687703.1|  29 MMAYSNEEAVRRMYETGYTCFWSRSRQKLWKKGEESGHVQKIKSIQADCDDDTLLVRVEQTGVACHTGTPSCF 101
                                       9************************************************************************ PP

>> PRA-PH  Phosphoribosyl-ATP pyrophosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.8   0.2   9.6e-22   3.4e-18       1      82 [.     116     201 ..     116     202 .. 0.94

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 9.6e-22
                                       HHHHHHHCT----SS----.-HHHHHH...HHHHHHHHHHHHHHHT-SCHHHHHHHHHHHHHHHHHHHHHHCT--CH CS
                            PRA-PH   1 vkefhrligerkpetPeas.taelasl...raaligEEavElleaasegdlaeladelaDllYvtygllvllGidld 73 
                                       v ++ r+i++rk++   +s t +l+     ++++++EEa+E++ a++++d +ela e+aDllY+t++l+v+ G+dl+
  gi|474934121|ref|YP_007687703.1| 116 VPDLVRTIKDRKENPCDESyTCKLLGNetkMCKKVVEEAAEVILACKDHDNEELAGEVADLLYHTLVLIVKEGLDLE 192
                                       56899*********999999****998899*********************************************** PP

                                       HHHHHHHHH CS
                            PRA-PH  74 avfeevhra 82 
                                       +v++e+ ++
  gi|474934121|ref|YP_007687703.1| 193 KVYAELWER 201
                                       *****9776 PP

>> MazG  MazG nucleotide pyrophosphohydrolase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   2.5   3.3e-09   1.2e-05       4      64 ..     144     200 ..     142     203 .] 0.91

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 3.3e-09
                                       HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHH CS
                              MazG   4 etllaylleEvgEvaeaIkkedrdeleeELGDvLlqvlflaniaeeeggidledvaetile 64 
                                       + + + ++eE+ Ev+ a k +d +el+ E++D+L++ l l+       g+dle+v +++ e
  gi|474934121|ref|YP_007687703.1| 144 TKMCKKVVEEAAEVILACKDHDNEELAGEVADLLYHTLVLIVK----EGLDLEKVYAELWE 200
                                       5678999*********************************995....9*******988765 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   6.4e-06     0.023      64     113 ..     149     197 ..     120     203 .] 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.4e-06
                                       CCCS-ESEEEE-SSGGGHHHHHHHHGGGECTCEEEEEESSSSCHHHHHTT CS
                              ApbA  64 selepidlvivtvKayqteealeeikplldpntvvlllqNGlgheeelre 113
                                       +  e++  vi+++K  ++ee + e+++ll + t vl++ +Gl+ e+  +e
  gi|474934121|ref|YP_007687703.1| 149 KVVEEAAEVILACKDHDNEELAGEVADLLYH-TLVLIVKEGLDLEKVYAE 197
                                       456788889*********************9.5**********9988766 PP

>> Peptidase_C71  Pseudomurein endo-isopeptidase Pei
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   1.8e-05     0.063      40      98 ..      31      87 ..      10     107 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.8e-05
                     Peptidase_C71 40 kvpnreaikkivtdGinc..tdasqlfkkvlealGyevkiehvrvrcndgkwyGhyllrvk 98
                                       ++n+ea++++++ G  c  + + q + k +e+ G+  ki+ ++  c+d++    +l+rv+
  gi|474934121|ref|YP_007687703.1| 31 AYSNEEAVRRMYETGYTCfwSRSRQKLWKKGEESGHVQKIKSIQADCDDDT----LLVRVE 87
                                      689***************444678999999*******************99....555655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       737  (0.0411066); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 1104.61
//
Query:       gi|474934122|ref|YP_007687704.1|  [L=252]
Description: imidazole glycerol phosphate synthase subunit hisF [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-89  298.2   0.4    3.9e-89  298.0   0.4    1.0  1  His_biosynth  Histidine biosynthesis protein
    1.1e-08   34.9   0.4     0.0028   17.1   0.0    2.1  2  NMO           Nitronate monooxygenase
    5.7e-08   32.2   0.0     0.0028   16.8   0.0    2.1  2  Dus           Dihydrouridine synthase (Dus)
    5.7e-06   25.8   0.0     0.0038   16.5   0.0    2.2  2  DHO_dh        Dihydroorotate dehydrogenase
    6.2e-06   25.4   0.4     0.0023   17.0   0.1    2.1  2  IMPDH         IMP dehydrogenase / GMP reductase domain
    6.7e-06   25.6   0.1     0.0018   17.7   0.1    2.2  2  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
    7.3e-06   25.5   0.1    0.00095   18.5   0.0    2.1  2  ThiG          Thiazole biosynthesis protein ThiG
      2e-05   24.0   0.1      0.016   14.6   0.0    2.2  2  TMP-TENI      Thiamine monophosphate synthase
    0.00066   18.9   0.0    0.00099   18.3   0.0    1.2  1  Glu_synthase  Conserved region in glutamate synthase
     0.0013   17.8   0.6     0.0032   16.5   0.2    1.7  2  FMN_dh        FMN-dependent dehydrogenase
     0.0075   15.1   0.2      0.011   14.6   0.2    1.2  1  Trp_syntA     Tryptophan synthase alpha chain
  ------ inclusion threshold ------
       0.11   11.9   0.1       0.32   10.4   0.0    1.7  2  PcrB          PcrB family


Domain annotation for each model (and alignments):
>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  298.0   0.4   2.6e-92   3.9e-89       1     228 [.       6     235 ..       6     236 .. 0.98

  Alignments for each domain:
  == domain 1  score: 298.0 bits;  conditional E-value: 2.6e-92
                                       EEEEEEEEETTEEEEECTTCSTCEEEETTSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEE CS
                      His_biosynth   1 riipalDlkdGkvVrlvkGdrfqelryagdpvelakryeeegadelhvvDldaakegreanldlveeiaeevfipvq 77 
                                       r+ip+lD+k+GkvV   kG++f +lr+ g p +lakry+++gade++++D+ a+ke+r++ ldlv+e+ae+vf+p++
  gi|474934122|ref|YP_007687704.1|   6 RVIPCLDVKNGKVV---KGTEFVNLRDVGYPPDLAKRYSDQGADEITFLDIAASKESRGTTLDLVRETAEKVFVPLT 79 
                                       79************...************************************************************ PP

                                       EESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEE.C...EEEEETTTTEEEEEEHH CS
                      His_biosynth  78 vGGGIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarr.g...ykvaikgwreetgldav 150
                                       vGGGIr+ edv+++l agadkv+i++aav +pe+i+e +e+fg+q++vvaiDa+r g   ++v++kg+ e tg+da+
  gi|474934122|ref|YP_007687704.1|  80 VGGGIRTAEDVHQALLAGADKVSINSAAVAHPEVISESSERFGRQCVVVAIDAKRvGddkWEVYVKGGSEPTGIDAL 156
                                       *******************************************************84678***************** PP

                                       HHHHHHHHTT-SEEEEEETTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHHHTTC.SEEEESHHHHTT CS
                      His_biosynth 151 elakkleelgageilltdidrdGtlsGpdleltkelaeavkipviasGGvgsledlkelksegv.davivgsalyeg 226
                                       e+a ++e++gageillt+id+dGt++G+d++lt+++ e+++ipviasGG+g++ed++e+++++  +a++++s+++++
  gi|474934122|ref|YP_007687704.1| 157 EWAGEAEDRGAGEILLTSIDADGTKNGYDIPLTRAVVEQTNIPVIASGGCGKMEDIYEVFAQTDcSAALAASIFHYN 233
                                       ************************************************************66666***********9 PP

                                       SS CS
                      His_biosynth 227 el 228
                                       e 
  gi|474934122|ref|YP_007687704.1| 234 EC 235
                                       86 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   3.7e-06    0.0056     180     225 ..      62     107 ..      43     119 .. 0.85
   2 !   17.1   0.0   1.9e-06    0.0028     149     238 ..     159     242 ..     149     249 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.7e-06
                               NMO 180 glfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtrf 225
                                        ++ Lv + ++ v +P+   GGi ++++v  aL +GA  v i ++ 
  gi|474934122|ref|YP_007687704.1|  62 TTLDLVRETAEKVFVPLTVGGGIRTAEDVHQALLAGADKVSINSAA 107
                                       46778888888888**************************999875 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 1.9e-06
                               NMO 149 arkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtrf 225
                                       a ++e rGa  + ++  +a G +    +     + L   v++  +iPviA GG  + +++  ++a     +++++  
  gi|474934122|ref|YP_007687704.1| 159 AGEAEDRGAGEILLTSIDADGTKN--GY----DIPLTRAVVEQTNIPVIASGGCGKMEDIYEVFAQTDCSAALAASI 229
                                       566666666666666666655554..23....3568888999999*******************************9 PP

                               NMO 226 Lltkesdakdahk 238
                                          +e++  ++h+
  gi|474934122|ref|YP_007687704.1| 230 FHYNECTPDQVHE 242
                                       9999999888886 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.9e-06    0.0028     143     227 ..      36     119 ..      33     134 .. 0.78
   2 !   13.7   0.0   1.7e-05     0.025     135     213 ..     150     227 ..     125     247 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.9e-06
                                       HHHHHHHCT-SEEEEESSECCCTT-CG--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCS CS
                               Dus 143 lakiveaaGaqaltvHgRtraqnyegtadweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgn 219
                                       lak+ +++Ga+++t     + ++++g   ++ ++e  ++v +p+ + G+I++aed++++l   Gad v i  +a   
  gi|474934122|ref|YP_007687704.1|  36 LAKRYSDQGADEITFLDIAASKESRG-TTLDLVRETAEKVFVPLTVGGGIRTAEDVHQALLA-GADKVSINSAAVAH 110
                                       56666666666666554444444444.4567799999***********************99.************** PP

                                       TTHHHH.HH CS
                               Dus 220 Pwlfae.st 227
                                       P ++ e s+
  gi|474934122|ref|YP_007687704.1| 111 PEVISEsSE 119
                                       ***997444 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1.7e-05
                                       TTTC.HHHHHHHHHHCT-SEEEEESSECCCTT-CG--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEE CS
                               Dus 135 deeenalelakiveaaGaqaltvHgRtraqnyegtadweaIkevkqavsipviaNGdIkdaedaqaileetGadgvm 211
                                        +  +ale a  +e+ Ga ++ +     a++ +   d+   ++v ++ +ipvia G++ ++ed+ ++ ++t + + +
  gi|474934122|ref|YP_007687704.1| 150 PTGIDALEWAGEAEDRGAGEILLTS-IDADGTKNGYDIPLTRAVVEQTNIPVIASGGCGKMEDIYEVFAQTDCSAAL 225
                                       5556677777777777777776643.45555555677788899*****************************99987 PP

                                       ES CS
                               Dus 212 ig 213
                                       ++
  gi|474934122|ref|YP_007687704.1| 226 AA 227
                                       65 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   2.5e-06    0.0038     229     278 ..      62     109 ..      56     120 .. 0.86
   2 !    7.2   0.0    0.0017       2.5     235     264 ..     190     217 ..     184     246 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.5e-06
                                       HHHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHH CS
                            DHO_dh 229 ialkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvf 278
                                       + l ++re ++++   +p+   GGi ++eD+   + aGA  v + +a v 
  gi|474934122|ref|YP_007687704.1|  62 TTLDLVRETAEKVF--VPLTVGGGIRTAEDVHQALLAGADKVSINSAAVA 109
                                       67788999999999..9**99************************99854 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0017
                                       HHHHHHTTT.S-EEEESS--SHHHHHHHHH CS
                            DHO_dh 235 relykrlkkeipiIgvGGiesgeDalekie 264
                                       r++ ++++  ip+I++GG    eD +e + 
  gi|474934122|ref|YP_007687704.1| 190 RAVVEQTN--IPVIASGGCGKMEDIYEVFA 217
                                       67777888..**************999753 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   1.5e-06    0.0023     193     250 ..      61     118 ..      48     146 .. 0.85
   2 !    7.0   0.0    0.0017       2.6     196     228 ..     186     218 ..     165     243 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.5e-06
                                       HHHHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCCTTBTTSSSEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 193 ltAvaevaeaakkagvpviaDGGikysgdivkAlaaGadavmlGsllagteEspgevi 250
                                        t +  v e+a+k  vp+   GGi++ +d+ +Al aGad v + s   +  E  +e  
  gi|474934122|ref|YP_007687704.1|  61 GTTLDLVRETAEKVFVPLTVGGGIRTAEDVHQALLAGADKVSINSAAVAHPEVISESS 118
                                       566777889999*****************************99888777777666655 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0017
                                       HHHHHHHHCTCT-EEEEES---SHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 196 vaevaeaakkagvpviaDGGikysgdivkAlaa 228
                                       +  + ++++++++pvia GG  + +di   +a 
  gi|474934122|ref|YP_007687704.1| 186 IPLTRAVVEQTNIPVIASGGCGKMEDIYEVFAQ 218
                                       555667899******************988775 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   1.2e-06    0.0018     128     169 ..      64     105 ..      61     108 .. 0.89
   2 !    5.8   0.0    0.0056       8.4     131     160 ..     189     218 ..     184     228 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.2e-06
                                       HHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE-- CS
                      G3P_antiterm 128 pkvikeikkelkipiiaGGLietkedveealkaGaiavstsn 169
                                        ++++e+ +++ +p+  GG i+t edv++al aGa+ vs  +
  gi|474934122|ref|YP_007687704.1|  64 LDLVRETAEKVFVPLTVGGGIRTAEDVHQALLAGADKVSINS 105
                                       57889999******************************9865 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0056
                                       HCTSTTS...EEEEESS--SHHHHHHHCTT CS
                      G3P_antiterm 131 ikeikkelkipiiaGGLietkedveealka 160
                                       ++++ ++++ip+ia+G   + ed+ e++++
  gi|474934122|ref|YP_007687704.1| 189 TRAVVEQTNIPVIASGGCGKMEDIYEVFAQ 218
                                       5778999*****************998765 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   6.4e-07   0.00095     137     209 ..      37     110 ..      16     136 .. 0.76
   2 !    5.2   0.0    0.0078        12     167     194 ..     189     216 ..     163     232 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 6.4e-07
                                       HHHHHHTT-SEBEEBSSSTTS----S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHH.HHT CS
                              ThiG 137 arrleevGcaavmPlaapiGsglGllnkealkiiieeakvPvivDAGigspsdaaqamelGadavllnta.vae 209
                                       a+r  + G+  +  l  +       ++   ++   e++ vP+ v  Gi++++d+ qa+  Gad v +n+a va+
  gi|474934122|ref|YP_007687704.1|  37 AKRYSDQGADEITFLDIAASKESRGTTLDLVRETAEKVFVPLTVGGGIRTAEDVHQALLAGADKVSINSAaVAH 110
                                       666666666655544333333333345566777888999*****************************972444 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0078
                                       HHHHHHH-SS-BEEES---SHHHHHHHH CS
                              ThiG 167 lkiiieeakvPvivDAGigspsdaaqam 194
                                        + ++e++++Pvi   G g+ +d+ +++
  gi|474934122|ref|YP_007687704.1| 189 TRAVVEQTNIPVIASGGCGKMEDIYEVF 216
                                       47899******************99886 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.1e-05     0.016     131     180 ..      57     106 ..      33     107 .. 0.76
   2 !    7.6   0.0    0.0015       2.2     122     168 ..     167     216 ..     151     229 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.1e-05
                          TMP-TENI 131 KkdaeplgleglkelaealeiPvvaiGGi.tlenvaevleagadgvavvsa 180
                                       K++ +   l++++e+ae++ +P+ + GGi t+e+v+++l agad v++ sa
  gi|474934122|ref|YP_007687704.1|  57 KES-RGTTLDLVRETAEKVFVPLTVGGGIrTAEDVHQALLAGADKVSINSA 106
                                       433.4678999******************44689************99887 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0015
                          TMP-TENI 122 vGpifpTdtKkda..eplgleglkelaealeiPvvaiGGit.lenvaevl 168
                                       +G i  T+   d   +  ++ + ++++e+++iPv+a GG   +e++ ev+
  gi|474934122|ref|YP_007687704.1| 167 AGEILLTSIDADGtkNGYDIPLTRAVVEQTNIPVIASGGCGkMEDIYEVF 216
                                       455555555555422344677899***************85156666666 PP

>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   6.7e-07   0.00099     272     307 ..      73     108 ..      62     113 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 6.7e-07
                                       GGG-EEEEESS--SHHHHHHHHHHT-SEEE-SHHHH CS
                      Glu_synthase 272 rdrvsliadGglktgadvvkalalGAdavgigtaal 307
                                       +  v l++ Gg++t++dv  al+ GAd+v+i +aa+
  gi|474934122|ref|YP_007687704.1|  73 KVFVPLTVGGGIRTAEDVHQALLAGADKVSINSAAV 108
                                       455889*************************99875 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.2   2.2e-06    0.0032     256     299 ..      62     103 ..      54     110 .. 0.84
   2 ?   -2.7   0.0       1.5   2.3e+03     266     287 ..     191     213 ..     184     217 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.2e-06
                                       -HHHCHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEE CS
                            FMN_dh 256 atidvLpeiveavggrievlvDgGirrGsDvlkAlalGAdavll 299
                                       +t+d   e +e+v   +++ v gGir+ +Dv +Al  GAd v +
  gi|474934122|ref|YP_007687704.1|  62 TTLDLVRETAEKVF--VPLTVGGGIRTAEDVHQALLAGADKVSI 103
                                       56666777777775..9***********************9987 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.5
                                       HHH...SS-EEEESS--SHHHHH CS
                            FMN_dh 266 eavgg.rievlvDgGirrGsDvl 287
                                       + v++ +i+v+++gG  + +D+ 
  gi|474934122|ref|YP_007687704.1| 191 AVVEQtNIPVIASGGCGKMEDIY 213
                                       44444359999999988888876 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.2   7.5e-06     0.011     188     234 ..      65     112 ..      53     133 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 7.5e-06
                                       HHHHHHHHCTSS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHHHHHHH CS
                         Trp_syntA 188 elverlkkltavPvavGFGistkeqvkqva.kvadGvivGSalvkkie 234
                                       +lv++  +   vP+ vG Gi+t+e+v+q+  ++ad v + Sa v + e
  gi|474934122|ref|YP_007687704.1|  65 DLVRETAEKVFVPLTVGGGIRTAEDVHQALlAGADKVSINSAAVAHPE 112
                                       677777777889*****************99***********998655 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00021      0.32     182     207 ..      77     103 ..      48     119 .. 0.80
   2 ?   -1.6   0.0         1   1.5e+03     179     203 ..     196     220 ..     173     224 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00021
                                       EEEEESS--SHHHHHHHHCC.SSEEEE CS
                              PcrB 182 rlivGGGirsaEkAkevvea.ADvivv 207
                                        l vGGGir aE+ ++ + a AD + +
  gi|474934122|ref|YP_007687704.1|  77 PLTVGGGIRTAEDVHQALLAgADKVSI 103
                                       588*****************9**8855 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1
                                       SSSEEEEESS--SHHHHHHHHCCSS CS
                              PcrB 179 ekarlivGGGirsaEkAkevveaAD 203
                                       +++ +i  GG  + E+ +ev  + D
  gi|474934122|ref|YP_007687704.1| 196 TNIPVIASGGCGKMEDIYEVFAQTD 220
                                       4455678888888888888877666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1604.62
//
Query:       gi|474934123|ref|YP_007687705.1|  [L=182]
Description: Imidazoleglycerol-phosphate dehydratase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-39  135.7   2.0    3.3e-39  134.5   1.1    2.0  2  IGPD      Imidazoleglycerol-phosphate dehydratase


Domain annotation for each model (and alignments):
>> IGPD  Imidazoleglycerol-phosphate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.42   7.5e+03      70      82 ..      14      26 ..       8      32 .. 0.66
   2 !  134.5   1.1   1.9e-43   3.3e-39       2     144 .]      34     162 ..      33     162 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.42
                                      TEEEEEEEE--SS CS
                              IGPD 70 ealaevaldlsgr 82
                                      e+ ++v ld+ g 
  gi|474934123|ref|YP_007687705.1| 14 ETKVSVDLDIDGS 26
                                      5666677776665 PP

  == domain 2  score: 134.5 bits;  conditional E-value: 1.9e-43
                                       ...HHHHHHHHHHHHHT--EEEEEEESSH...HHHHHHHHHHHHHHHHHHS..-SSB--EEEEEEEETTEEEEEEEE CS
                              IGPD   2 gigfldhmLdqlakhggfdlkvkvkgdlevddHhtvedvgialGqalkealgdkrgikRfgsallpmDealaevald 78 
                                       +i+fl hm+++la+++gfdlk+k+ gd    dHh++edv+i+lG a+k+a+g+   ++R++s++lpmD+al+ va+d
  gi|474934123|ref|YP_007687705.1|  34 DIQFLKHMVESLARYAGFDLKMKACGDN---DHHIIEDVAITLGDAFKKAVGEG-PVERTASCVLPMDDALVMVAVD 106
                                       599************************5...6*******************976.57******************** PP

                                       --SS-EEE--..-SB--TT.--HHHHHHHHHHHHHHHT-EEEEEEEE--BHHHHHHHHHHHHHHHH CS
                              IGPD  79 lsgrpylvleaelkrekigeldtelveeffeslaeaagitlhvkvlrgenahhivealfKafaraL 144
                                       l  rpy+  +          +   l e+ff+s+a++agitlhv  +rg ++hhi+ea+fKa++++L
  gi|474934123|ref|YP_007687705.1| 107 LVDRPYCDAD----------CPDPLYEHFFRSFAMSAGITLHVAEIRGFDDHHIIEASFKALGKCL 162
                                       *******988..........56679****************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 1192.60
//
Query:       gi|474934124|ref|YP_007687706.1|  [L=165]
Description: putative regulator of amino acid metabolism, contains ACT domain [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-05   25.1   0.9    4.3e-05   23.2   0.1    2.4  3  ACT       ACT domain
    0.00077   19.2   0.8     0.0021   17.8   0.1    2.2  3  ACT_7     ACT domain
     0.0031   17.3   0.0     0.0063   16.3   0.0    1.5  1  ACT_5     ACT domain
     0.0035   17.9   0.1      0.026   15.1   0.1    2.2  1  ACT_4     ACT domain


Domain annotation for each model (and alignments):
>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.52   2.3e+03      17      28 ..      18      29 ..      17      31 .. 0.81
   2 ?   -2.3   0.0       0.9     4e+03      47      53 ..      58      64 ..      39      77 .. 0.55
   3 !   23.2   0.1   9.6e-09   4.3e-05      10      50 ..     104     143 ..     103     161 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.52
                                      HHHHHHHTTSEE CS
                               ACT 17 vfgaladrgiNi 28
                                      v+ ++ ++gi++
  gi|474934124|ref|YP_007687706.1| 18 VAELMLKHGISV 29
                                      7788889***99 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.9
                                      EEEEEHH CS
                               ACT 47 vivvdee 53
                                        ++++ 
  gi|474934124|ref|YP_007687706.1| 58 RSTIEDI 64
                                      3333333 PP

  == domain 3  score: 23.2 bits;  conditional E-value: 9.6e-09
                                       STTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEE CS
                               ACT  10 rPGlLarvfgaladrgiNidsieqrssedkvagivfvvivv 50 
                                       rPG++a + ++l+++giNi+ + ++  e + ++  ++++ +
  gi|474934124|ref|YP_007687706.1| 104 RPGVMAGIMNVLSRAGINIRQAVVTGEENE-VSHLIITVDG 143
                                       8**************************998.5555555544 PP

>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.31   1.4e+03      10      38 ..      71      97 ..      69      99 .. 0.69
   2 !   17.8   0.1   4.7e-07    0.0021       5      40 ..      91     124 ..      87     128 .. 0.88
   3 ?   -1.7   0.1      0.59   2.6e+03      12      27 ..     142     163 ..     137     165 .] 0.53

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.31
                                      EE-S-.---SS--HHHHHHHHHHTTT--- CS
                             ACT_7 10 svvgsglpfdvtGivaklaspLaeagIsi 38
                                      s  +s+l  d+  ++a  as L    I++
  gi|474934124|ref|YP_007687706.1| 71 SALFSKL--DSMVVLADAASLLGCSAIEV 97
                                      5566666..77888888888887666665 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 4.7e-07
                                       EEEEEEE-S-.---SS--HHHHHHHHHHTTT---EE CS
                             ACT_7   5 gwiklsvvgsglpfdvtGivaklaspLaeagIsifq 40 
                                       g++++ vv ++     +G++a++ ++L++agI+i q
  gi|474934124|ref|YP_007687706.1|  91 GCSAIEVVPDDA--RRPGVMAGIMNVLSRAGINIRQ 124
                                       688899999966..88*****************965 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.59
                                       -S-........---SS--HHHHH CS
                             ACT_7  12 vgs.......glpfdvtGivakl 27 
                                       +g+        +++ ++G+++ +
  gi|474934124|ref|YP_007687706.1| 142 DGDipgyvmtEIRG-SPGVASVI 163
                                       55544444444555.77777665 PP

>> ACT_5  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.4e-06    0.0063       2      43 ..     104     144 ..     103     147 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.4e-06
                             ACT_5   2 apgvLeRvlrvvrrrgFevkslnmsttedggtvrieltVese 43 
                                       +pgv   +++v++r g ++++ +++  e+++ +++ +tV+++
  gi|474934124|ref|YP_007687706.1| 104 RPGVMAGIMNVLSRAGINIRQAVVTG-EENEVSHLIITVDGD 144
                                       89***********************9.9999********985 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   5.8e-06     0.026      16      78 ..     104     162 ..      95     163 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.8e-06
                             ACT_4  16 rkglLaditqviseekanivsvnaktrkkdglaeikitveVkdvehLsrviakLraipgVisV 78 
                                       r+g++a i++v+s +++ni+   ++ ++ +++ ++ itv   d +    v++ +r  pgV sV
  gi|474934124|ref|YP_007687706.1| 104 RPGVMAGIMNVLSRAGINIRQAVVTGEE-NEVSHLIITV---DGDIPGYVMTEIRGSPGVASV 162
                                       89******************99998875.7798888888...455556777777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1103.13
//
Query:       gi|474934125|ref|YP_007687707.1|  [L=100]
Description: Chorismate mutase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-14   52.1   3.9    7.4e-14   51.9   3.9    1.1  1  CM_2      Chorismate mutase type II
  ------ inclusion threshold ------
      0.019   15.4   0.5      0.022   15.2   0.5    1.3  1  Sld5      GINS complex protein
      0.049   14.4   0.3      0.091   13.5   0.2    1.5  1  DUF5327   Family of unknown function (DUF5327)


Domain annotation for each model (and alignments):
>> CM_2  Chorismate mutase type II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.9   3.9   1.2e-17   7.4e-14       1      75 []      15      93 ..      15      93 .. 0.96

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 1.2e-17
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSGSS-HHHHHHHHHHHHH..HH..S-HHHHHHHHHHHHHHHHHHHH CS
                              CM_2  1 RkeIdeiDdeileLLaeRaelakevgeyKkeeglpvydpeReaevlerlee..ga..ldeeaierifreiisasralqk 75
                                      R+eI +iD++i++L+a R ++++e +++K+++g++  d + ea ++er  e  ++  l+++ +e+i + i+++sr++qk
  gi|474934125|ref|YP_007687707.1| 15 RDEIADIDSQIIDLIATRVDITDELAKAKRRSGQDYWDSATEAHIIERYCElcQEvsLSKDDAEKIAKLILAISRERQK 93
                                      99*************************************************873367********************96 PP

>> Sld5  GINS complex protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.5   3.7e-06     0.022      48      86 ..      61      99 ..       7     100 .] 0.72

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.7e-06
                                      TTHHHHHHHHHHHHT..HCHHHHHHHHHHHHHHHHHHHTH CS
                              Sld5 48 phflelavkllelard.ldelkrllrdllevRlakirkfa 86
                                      + ++el+ +  +l++d ++++++l++++ + R +ki++++
  gi|474934125|ref|YP_007687707.1| 61 ERYCELC-QEVSLSKDdAEKIAKLILAISRERQKKIYDST 99
                                      3455555.444555559*******************9876 PP

>> DUF5327  Family of unknown function (DUF5327)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   1.5e-05     0.091      12      57 ..      35      82 ..      33      99 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.5e-05
                           DUF5327 12 meeelekak..kaeseakvrehiaaikalceLlleeeaeekapvpskp 57
                                      + +el+kak  + ++    + +++ i+ +ceL  e + +++ +++ ++
  gi|474934125|ref|YP_007687707.1| 35 ITDELAKAKrrSGQDYWDSATEAHIIERYCELCQEVSLSKDDAEKIAK 82
                                      6789*****7555577788999************97765544444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1073  (0.0598472); expected 358.6 (0.02)
Passed bias filter:                      646  (0.036031); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 808.05
//
Query:       gi|474934126|ref|YP_007687708.1|  [L=354]
Description: aspartate-semialdehyde dehydrogenase (non-peptidoglycan organisms) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-35  122.1   0.0    4.1e-35  121.5   0.0    1.3  1  Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation dom
      1e-29  103.4   0.0    1.9e-29  102.6   0.0    1.4  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
    7.7e-05   23.5   0.0    0.00014   22.7   0.0    1.4  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
    0.00019   21.1   0.0     0.0014   18.2   0.0    2.3  3  Gp_dh_C          Glyceraldehyde 3-phosphate dehydrogenase, C-
    0.00034   20.7   0.0    0.00059   20.0   0.0    1.4  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
     0.0012   18.9   0.0     0.0021   18.2   0.0    1.3  1  Ldh_1_N          lactate/malate dehydrogenase, NAD binding do
     0.0023   18.7   0.0     0.0057   17.4   0.0    1.7  1  DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomer
  ------ inclusion threshold ------
      0.087   12.3   0.0       0.14   11.6   0.0    1.3  1  Epimerase        NAD dependent epimerase/dehydratase family
       0.14   12.4   0.0       0.42   10.9   0.0    1.8  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma


Domain annotation for each model (and alignments):
>> Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.5   0.0   2.1e-38   4.1e-35       1     183 [.     159     334 ..     159     335 .. 0.92

  Alignments for each domain:
  == domain 1  score: 121.5 bits;  conditional E-value: 2.1e-38
                                       HHHHHHCTT.EEEEEEEEEEEGGGCHHHHHHHHHHHHHHHHHSTTS.CTTTSSHHTTSEESTCSTBTTTTCHCBHHH CS
                   Semialdhyde_dhC   1 LkPLldalgelervivatyqavSGaGkkgvreLlkqvaelqrsdeakpgvfgvpiagNlipyidkeedkgepetree 77 
                                       Lk+L da ++le+v v+tyqa+SGaG+                    pgv++++i gN+ip+i  ee+k+e+e ++ 
  gi|474934126|ref|YP_007687708.1| 159 LKALDDA-YGLEEVFVSTYQAISGAGY--------------------PGVPSLDIVGNVIPFISHEEEKMETELAKM 214
                                       89999*8.89*****************....................9***************************** PP

                                       HHHHHHHHHHCTESCSEEEEEEEESBSSEEEEEEEEEES..SSHHHHHHHHHHHHCS.........TTEEEEESSHC CS
                   Semialdhyde_dhC  78 lkavaetkkileftekvsatcvrVPvlrGhseavtiklk..lkdveveeveellaaa.........pevkvvvneee 143
                                        + +a+ + ++++++ v+a c rVPv++Gh+e++ i+lk  ++ +e+++ ++ ++ +         pe+ ++v++e+
  gi|474934126|ref|YP_007687708.1| 215 IGTYADGEFRFADFK-VMANCARVPVIDGHTESLVIRLKknPSVEEIAKTLADFRGEaqklglpsaPEAPIIVRPEP 290
                                       **************8.**********************9666666666666677666******************** PP

                                       HHSSHHHHTTC.......SSSEEEEEEEEETTCTTEEEEEEEEETTT CS
                   Semialdhyde_dhC 144 drPtpaavagg.......tnsvsVGRirkdemgdeglklvvvgDNll 183
                                       +rP+p  ++         +++ +VGRir+ +    + k++vv++N+l
  gi|474934126|ref|YP_007687708.1| 291 NRPQPIFDVFAgsperarGMASTVGRIRQGN---GYYKMWVVSHNTL 334
                                       *****99875556888889**********99...3689*******98 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.6   0.0   9.3e-33   1.9e-29       1     119 [.       6     130 ..       6     132 .. 0.94

  Alignments for each domain:
  == domain 1  score: 102.6 bits;  conditional E-value: 9.3e-33
                                       EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSG.....GGTTTECEBEEEGGGGGC.TT-SEEE CS
                    Semialdhyde_dh   1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavk.....aleegkdlkvedvdeeel.kevdivf 71 
                                       kva++GatG++Gq+++++Le+hp++e+  l++s+rs+Gk++ +  k       +e+ d k++++d + + k++ i+f
  gi|474934126|ref|YP_007687708.1|   6 KVAVLGATGMIGQRFVQMLEDHPYFEVEGLYASERSDGKRFGDTLKvrdynYKQETLDTKISKMDLDHIaKNCRIAF 82 
                                       7*********************************************998876677788888999999999******* PP

                                       E-SCHHHHHHHHHHHHHTTSEEEESSSTTTTSTTSEBE-HHHHGGGGG CS
                    Semialdhyde_dh  72 lalpagvskelapklaeagvkviDlssdfRlkddavyvlpevnreaik 119
                                       +  p++ + e + +la++gv v+ +++++R++ ++++++pevn ++ +
  gi|474934126|ref|YP_007687708.1|  83 SGIPSDLAGETETELAKKGVAVFTNAGAHRMDRHVPIIVPEVNVDQFE 130
                                       *******************************************98865 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0     7e-08   0.00014       1      91 [.       5     106 ..       5     107 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 7e-08
                                       EEEEEETT.SHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESS.............HHHHHTCTTE CS
                      GFO_IDH_MocA   1 lrvaiiGa.Gkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysd.............leelladpei 63 
                                       ++va+ Ga G+ig+++++ l ++ +  ev +l+ ++ +  +++ ++++v  y+              l+++++  ++
  gi|474934126|ref|YP_007687708.1|   5 VKVAVLGAtGMIGQRFVQMLEDH-PYFEVEGLYASERSDGKRFGDTLKVRDYNYkqetldtkiskmdLDHIAK--NC 78 
                                       589*****9999*****777777.999***********************77765588888855555555555..8* PP

                                       SEEEE-S-GGGHHHHHHHHHHTT-EEEE CS
                      GFO_IDH_MocA  64 davivatpngtheelakaaleagkhvll 91 
                                       ++++ ++p+++  e + +++++g++v+ 
  gi|474934126|ref|YP_007687708.1|  79 RIAFSGIPSDLAGETETELAKKGVAVFT 106
                                       **************************95 PP

>> Gp_dh_C  Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.5     5e+03      22      36 ..      52      66 ..      50      80 .. 0.79
   2 ?   -0.8   0.0      0.52     1e+03       5      23 ..     159     177 ..     155     181 .. 0.84
   3 !   18.2   0.0   7.1e-07    0.0014      71     108 ..     229     266 ..     222     284 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.5
                                      EEECTTTSBSSSS-- CS
                           Gp_dh_C 22 vhaytndQkllDgps 36
                                      v++y  +Q++lD++ 
  gi|474934126|ref|YP_007687708.1| 52 VRDYNYKQETLDTKI 66
                                      889999999999765 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.52
                                       HHHHHHHHEEEEEEEEEEE CS
                           Gp_dh_C   5 akvlndkfgikkglmttvh 23 
                                       +k+l+d++g++++++ t  
  gi|474934126|ref|YP_007687708.1| 159 LKALDDAYGLEEVFVSTYQ 177
                                       799**********999865 PP

  == domain 3  score: 18.2 bits;  conditional E-value: 7.1e-07
                                       TEEEEEEEESSSSEEEEEEEEEESSTS-HHHHHHHHHH CS
                           Gp_dh_C  71 kldglAvrVPtpnvsvvdlvvelekevtveevnaalke 108
                                       k+ +   rVP+++++  +lv++l+k+ +vee+ ++l +
  gi|474934126|ref|YP_007687708.1| 229 KVMANCARVPVIDGHTESLVIRLKKNPSVEEIAKTLAD 266
                                       5566778**************************99976 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   2.9e-07   0.00059       1      57 [.       5      59 ..       5     115 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.9e-07
                                      EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BE CS
                            DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvav 57
                                      +kvav+Ga+G +G++ v+++e+++ +e+ + + +++   +gk +g+ l+++  +++ 
  gi|474934126|ref|YP_007687708.1|  5 VKVAVLGATGMIGQRFVQMLEDHPYFEVEGLYASER--SDGKRFGDTLKVRDYNYKQ 59
                                      69*****************************99987..6899999888877655544 PP

>> Ldh_1_N  lactate/malate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0     1e-06    0.0021       1     103 [.       5     110 ..       5     121 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1e-06
                                       EEEEEETTTSHHHHHHHHHHHHTTSSSEEEEE-SSHH..HHHHHHHHHHHCHCCSTS.-EEEEE.SSGGGGTTESEE CS
                           Ldh_1_N   1 vkvavvGaaGgiGqslalllankkladelaLlDiake..kleGvaldlshistflsv.kvkvse.keeealkdadvv 73 
                                       vkvav+Ga+G+iGq +  +l  +++ +   L+  +++  k  G++l + + ++  ++ ++k+s+ +  ++ k++ ++
  gi|474934126|ref|YP_007687708.1|   5 VKVAVLGATGMIGQRFVQMLEDHPYFEVEGLYASERSdgKRFGDTLKVRDYNYKQETlDTKISKmDLDHIAKNCRIA 81 
                                       69*********************999988899888877788999****99998775425666666778888888765 PP

                                       EE--S-SS-.TTTTHHHHHHHHHHHHHHHHH CS
                           Ldh_1_N  74 vitagvprk.pGetRddLlkvNakIvkeive 103
                                          +g+p    Get  +L k+ ++++++ ++
  gi|474934126|ref|YP_007687708.1|  82 --FSGIPSDlAGETETELAKKGVAVFTNAGA 110
                                       ..67887654899999999999999987765 PP

>> DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   2.9e-06    0.0057       1      36 [.       7      41 ..       7      52 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.9e-06
                                      EEEESTTSHHHHHHHHHHHHCTTTEEEEEEEESSTH CS
                   DXP_reductoisom  1 vviLGsTGSIGtqtLdvieenpdkfevvalaagsnv 36
                                      v++LG+TG IG+  ++++e++p  fev++l+a+++ 
  gi|474934126|ref|YP_007687708.1|  7 VAVLGATGMIGQRFVQMLEDHP-YFEVEGLYASERS 41
                                      78********************.9*******97765 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   6.8e-05      0.14       2      37 ..       8      44 ..       7      82 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.8e-05
                                      EEETTTSHHHHHHHHHHHHCTSE.EEEEES-STTTTC CS
                         Epimerase  2 lVtGatGfiGsalvkallekgye.vigldrlssasnt 37
                                       V+GatG+iG+ +v+ l+++ y  v gl   ++++ +
  gi|474934126|ref|YP_007687708.1|  8 AVLGATGMIGQRFVQMLEDHPYFeVEGLYASERSDGK 44
                                      69*******************6448777766554444 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00021      0.42       1      60 [.       7      68 ..       7      91 .. 0.70
   2 ?   -2.6   0.0       3.1   6.2e+03      35      78 ..     205     253 ..     195     266 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00021
                                      EEEE--.SHHHHHHHHHHHCTCCT-G.EEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHH CS
                   Sacchrp_dh_NADP  1 vliiGa.GsvGqavaellarhfdvda.eitvadrskeklealaakalgvrfeaialdaenye 60
                                      v ++Ga G++Gq ++++l++h  ++   +   +rs+ k      k++  + ++++ld +  +
  gi|474934126|ref|YP_007687708.1|  7 VAVLGAtGMIGQRFVQMLEDHPYFEVeGLYASERSDGKRFGDTLKVRDYNYKQETLDTKISK 68
                                      679******************88765555555555555333333446666666666665555 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.1
                                       HHHHHHHCHH....TTTCEEEEE--TTTHHHHHHHHHTTS..SEEEE-SS CS
                   Sacchrp_dh_NADP  35 eklealaaka....lgvrfeaialdaenyeavLaallkeg..dlvvnlsp 78 
                                       ek+e ++ak+    +  +f ++ + ++   a  ++++ ++   lv+ l  
  gi|474934126|ref|YP_007687708.1| 205 EKMETELAKMigtyADGEFRFADFKVMANCA-RVPVIDGHteSLVIRLKK 253
                                       5555555444444455555555555555555.555555555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2465.88
//
Query:       gi|474934127|ref|YP_007687709.1|  [L=289]
Description: ATP phosphoribosyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-48  162.5   0.4    1.1e-47  162.0   0.4    1.2  1  HisG      ATP phosphoribosyltransferase
    8.3e-22   77.1   0.1      2e-21   75.9   0.1    1.7  1  HisG_C    HisG, C-terminal domain


Domain annotation for each model (and alignments):
>> HisG  ATP phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.0   0.4   1.2e-51   1.1e-47       1     159 [.      51     208 ..      51     209 .. 0.93

  Alignments for each domain:
  == domain 1  score: 162.0 bits;  conditional E-value: 1.2e-51
                                       -GGGHHHHHHTTSSSEEEEEHHHHHHCT...TEEEEEEESESEEEEEEEEETTSS--SGCGG.TT-.EEEEES-HHH CS
                              HisG   1 raadiptyVeegavdlGitGkDvveEskeeeeveelldLgfgkcklvvavpeesevkslkdlvedkgkriaTsypnl 77 
                                       ra+dip+++ +gavd+GitG+Dv +E++  ++++ +ldL+fg+c+l++a+p++se+ ++ ++ +  g r+aTs+p+l
  gi|474934127|ref|YP_007687709.1|  51 RAQDIPVFIDSGAVDFGITGQDVEAEAG--KKLTDILDLNFGQCRLAIAAPDDSEIAKTGKM-K-DGIRVATSFPKL 123
                                       89************************75..57**********************99988876.3.457********* PP

                                       HHHHHHHTT-EEEEEE-SS-CTHHHHTTS-SEEEEEESSSHHHHHTTEEEEEEEEEEEEEEEEEHHHHHS...HHHH CS
                              HisG  78 akkyfeekglkveiiklsGsvEaapalglaDaIvDlvetGeTLrangLkaietilessavLiankkslkk...keki 151
                                       +kk+f++kg+k++i+ ++G+ E++p lg++D+I+Dlv tG TLr n+L ++ ti+es+a ++++k+++k+   k++i
  gi|474934127|ref|YP_007687709.1| 124 TKKFFDAKGIKADIVFVQGAAEIMPLLGVSDCIADLVATGGTLRMNHLVEVVTIIESQASVFTSKAAMKDaekKRRI 200
                                       ********************************************************************954544499 PP

                                       HHHHHHHH CS
                              HisG 152 eellerlr 159
                                       +e+++ +r
  gi|474934127|ref|YP_007687709.1| 201 TEIVDAIR 208
                                       99999987 PP

>> HisG_C  HisG, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.9   0.1   2.2e-25     2e-21       1      73 []     213     286 ..     213     286 .. 0.98

  Alignments for each domain:
  == domain 1  score: 75.9 bits;  conditional E-value: 2.2e-25
                                       TTTEEEEEEEEEGGGHHHHHHH---SSS-EEEE-..SS-EEEEEEEEECCCHHHHHHHHHCTT-EEEEEEE-S- CS
                            HisG_C   1 ArkyvllmynvpkesleevlkilPGlrsPTvspla.degwvaVsavveekevaevideLkaaGAsdIlvlpiek 73 
                                       A+++++lm++vpk++l+ev +i+PG+ +PTv +la +++ va+++v+  ++ ++++ eLk++GA++Il +pie+
  gi|474934127|ref|YP_007687709.1| 213 AEGKKYLMADVPKKRLKEVERIVPGIGGPTVIDLAgNDDCVAIQVVIAAEDSYRIVAELKKIGAKGILTIPIER 286
                                       899********************************999**********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2073.70
//
Query:       gi|474934128|ref|YP_007687710.1|  [L=354]
Description: histidinol-phosphate aminotransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-46  158.7   0.0    2.6e-46  158.5   0.0    1.0  1  Aminotran_1_2   Aminotransferase class I and II
    0.00016   20.7   0.0    0.00024   20.1   0.0    1.2  1  Alliinase_C     Allinase
  ------ inclusion threshold ------
      0.052   12.5   0.0      0.091   11.7   0.0    1.3  1  Aminotran_5     Aminotransferase class-V
      0.062   13.0   0.0        0.1   12.2   0.0    1.3  1  Toxin_R_bind_C  Clostridium neurotoxin, C-terminal receptor b


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.5   0.0   5.8e-50   2.6e-46      36     363 .]      50     345 ..      27     345 .. 0.93

  Alignments for each domain:
  == domain 1  score: 158.5 bits;  conditional E-value: 5.8e-50
                                       STTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEE.EESS-THHHHHHH CS
                     Aminotran_1_2  36 tlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilv.pdptyasyknilr 111
                                       ++n+y+++  ++ l+  la+f+g      + r+ ++v g+G++++++++ + + + pg+ +   p p+y+ y+  + 
  gi|474934128|ref|YP_007687710.1|  50 DTNSYPNTY-SDGLRDVLAEFYG------ISRD-NLVAGNGSDEMLNTVYTTF-VTPGKTVCTqPCPSYSLYSYFAD 117
                                       578999999.*************......8888.*******************.888888876378*********** PP

                                       HTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEE CS
                     Aminotran_1_2 112 lsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDe 188
                                       ls g+v+++ l+  +df+ld++a++ + +e       + +i+  sp+NPtG  + +++le++     k++ ++++De
  gi|474934128|ref|YP_007687710.1| 118 LSSGAVREVDLT--DDFQLDVDAMIGKGEE------NRGIIIMPSPNNPTGNCFRKKDLEEI---LAKHEGIVILDE 183
                                       **********99..************9999......889***********************...999********* PP

                                       TTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHH CS
                     Aminotran_1_2 189 aYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsrpflsssllqaavaaals 265
                                       aY++ +  ++     + +v+e  nl+++ ++sKa+++a +R+Gy ++n +v++ l++++ p+    +   a+ aa++
  gi|474934128|ref|YP_007687710.1| 184 AYSEYARFTM-----IDKVDEFENLIVCKTFSKAYAMAAFRIGYMASNLKVADMLNSVKVPYSLNKISEGAAIAAVK 255
                                       ******9844.....9************************************************************* PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEEEEETHHCHHHHHHHHHHTCTEEEEEGGGGTS.T CS
                     Aminotran_1_2 266 dallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmflltdlsaetakelskkLleevgvyvtpgtsftv.p 341
                                       d++    ++e +++ ++++r +l ++L++lg++ ++s+s+++l      +   +l + L ++ g++++ + s +  +
  gi|474934128|ref|YP_007687710.1| 256 DQD----FVERSVRLVEEQRPKLAAKLRQLGFEPYPSDSNFILAKSPIDH--AKLVQGLKDR-GILIRDFGSKRRtE 325
                                       *99....89*********************************99765555..79********.*****96555558* PP

                                       TEEEEECTTS-HHHHHHHHHHH CS
                     Aminotran_1_2 342 grlRitvAglteeeleelveal 363
                                       +++R tv  +tee +++  +a+
  gi|474934128|ref|YP_007687710.1| 326 NCVRPTV--GTEELNKRMTDAI 345
                                       *******..****999988776 PP

>> Alliinase_C  Allinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   5.2e-08   0.00024      69     205 ..      77     222 ..      72     250 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 5.2e-08
                                       EEEECHHHHHHHHHHHHHHHH...SSSSSEEEEE-SS--THHHHHTTTT-BTTEEEEEESTT-.--S..S-EEEEEE CS
                       Alliinase_C  69 ivvGtGstqLlqalvyalspe.asseskpvkvvaavPyysvykeqtslldsklykweGdaaayvkkknpeefielvt 144
                                       +v G+Gs ++l+++  ++ +  ++ +++p    +   y++   + +      +  ++ d  a + k + +  i ++ 
  gi|474934128|ref|YP_007687710.1|  77 LVAGNGSDEMLNTVYTTFVTPgKTVCTQPCPSYSLYSYFADLSSGAVREVDLTDDFQLDVDAMIGKGEENRGIIIMP 153
                                       788999999999887775544266677777777777777766665554444445566666667777778888999** PP

                                       SS-TTT---.-....-----TT-EEEEEE-TT-.STTTS---S-B-.-S.EEEEEHHHHHS-GGG-EEE CS
                       Alliinase_C 145 sPnnPdgll.r....eavvkgseakviyDlayY.WPhytpitskad.ed.imLftlskltGhaGsrlGW 205
                                       sPnnP g+  r    e++++++e++vi D ay  + ++t i +  + e+ i+  t+sk    a  r+G+
  gi|474934128|ref|YP_007687710.1| 154 SPNNPTGNCfRkkdlEEILAKHEGIVILDEAYSeYARFTMIDKVDEfENlIVCKTFSKAYAMAAFRIGY 222
                                       ******9853522334799************95489*****87554244256679*************8 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0     2e-05     0.091      48     177 ..      62     184 ..      51     198 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2e-05
                                       HHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETT CS
                       Aminotran_5  48 arekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldee 124
                                        r+ +ae+++++  ++++   G+ e +n+v  ++   + pg+++ ++     +     ++l+      v+ + l+++
  gi|474934128|ref|YP_007687710.1|  62 LRDVLAEFYGISR-DNLVAGNGSDEMLNTVYTTF---VTPGKTVCTQPCPSYSLYSYFADLS---SGAVREVDLTDD 131
                                       689999*****96.99999999999*********...99********999999996666666...568********* PP

                                       SCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-T CS
                       Aminotran_5 125 geldldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaa 177
                                        +ld+d++  + +e+  ++++   +n tG+++  +++ +++ k++ +v++D a
  gi|474934128|ref|YP_007687710.1| 132 FQLDVDAMIGKGEENRGIIIMPSPNNPTGNCFRKKDLEEILAKHEGIVILDEA 184
                                       *******************************************9999999987 PP

>> Toxin_R_bind_C  Clostridium neurotoxin, C-terminal receptor binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.3e-05       0.1      98     154 ..     213     269 ..     186     287 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.3e-05
                                       ETTEEEEEEEETTSSECTCCEEEEECCG.-TTSBEEEEEECE-TTSTCSSBBEEEEE CS
                    Toxin_R_bind_C  98 vknkeyilaypkdqaavekldrilevgdnvgnlslvkkmkakklrdlktkskqlkld 154
                                       +    ++++y  ++  v ++++ ++v+++   +s    + a+k++d+ ++s++l  +
  gi|474934128|ref|YP_007687710.1| 213 YAMAAFRIGYMASNLKVADMLNSVKVPYSLNKISEGAAIAAVKDQDFVERSVRLVEE 269
                                       55667999******************************************9988655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2326.40
//
Query:       gi|474934129|ref|YP_007687711.1|  [L=198]
Description: imidazole glycerol phosphate synthase, glutamine amidotransferase subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-16   60.9   0.0    1.5e-16   60.7   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
  ------ inclusion threshold ------
      0.018   14.8   0.0        0.3   10.8   0.0    2.1  2  Peptidase_C26  Peptidase C26
      0.019   14.5   0.0      0.027   14.1   0.0    1.2  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
      0.041   13.7   0.0      0.079   12.8   0.0    1.4  1  DJ-1_PfpI      DJ-1/PfpI family


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.7   0.0   3.4e-20   1.5e-16       2     187 ..       5     191 ..       4     194 .. 0.82

  Alignments for each domain:
  == domain 1  score: 60.7 bits;  conditional E-value: 3.4e-20
                                       EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT..TTTHHHHHHHHCT...STS- CS
                            GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg..vegkieaikeare...nkiP 73 
                                       l D++ ++++++++al  +g++v+ v   ++ +          ++++ +G+g+    +e  + + +++re   +++P
  gi|474934129|ref|YP_007687711.1|   5 LADYGVGNIHSITKALEMAGFQVDTVTDMSKLL--------DAKCIMFPGVGAFDstMERLLPVREQVRErleAGVP 73 
                                       6799******************99999443333........3579999******99999999999999988889*** PP

                                       EEEETHHHHHHHHHTTT..............EEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGC CS
                            GATase  74 iLGICLGmQllaiefgr..............kvvkekekehhggtmrlgddetallyglknevierhrHryevnpke 136
                                        L IC G Q+++ ++ +              k+   k+ +h+g++   ++d   +l++ + + + ++ H+y ++   
  gi|474934129|ref|YP_007687711.1|  74 TLSICIGAQIMFSASDEgkgpgigvyegrvrKL-GSKTVPHMGWNTLNTED--PILEDIG-SRHFYFAHSYYCDA-- 144
                                       ***************999999996666644444.44559******999995..5999995.5599*********9.. PP

                                       HHHTTEEEEEEEETTEEEEEEEEETTTEEEESSBTTSTTSTTHHHHHHHHH CS
                            GATase 137 lepaglevtakseddeelmeiiekknpfvgvQFHPEststpegpellfnfl 187
                                        +p+   v +++e ++ +     +k+++v++QFHPE++s   g+++l+nf+
  gi|474934129|ref|YP_007687711.1| 145 -VPDI--VKGTTEYEGFIFPTLMRKYNIVSTQFHPEKSSV-SGQKFLKNFY 191
                                       .9995..55666666677777777777*********8765.5599999986 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   6.6e-05       0.3      98     120 ..      64      86 ..      54      90 .. 0.89
   2 ?    1.7   0.0      0.04   1.8e+02     204     216 .]     165     177 ..     156     177 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.6e-05
                     Peptidase_C26  98 iraalergvPilgiCrGlqllnv 120
                                       +r+ le+gvP l+iC G q++  
  gi|474934129|ref|YP_007687711.1|  64 VRERLEAGVPTLSICIGAQIMFS 86 
                                       68999***************965 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.04
                     Peptidase_C26 204 akafvlgvQwHPE 216
                                       +k+ +++ Q+HPE
  gi|474934129|ref|YP_007687711.1| 165 RKYNIVSTQFHPE 177
                                       578899******9 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0     6e-06     0.027      25      90 ..      25      86 ..       3     113 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6e-06
                          GATase_3 25 vrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGe 90
                                       +v  v+   ++l  da  +++pG    ++d  ++r   ++e+++e +eag+p l iC G q++ +
  gi|474934129|ref|YP_007687711.1| 25 FQVDTVT-DMSKL-LDAKCIMFPGVG--AFDSTMERLLPVREQVRERLEAGVPTLSICIGAQIMFS 86
                                      4455555.55555.459999999975..67889999999***********************9865 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.8e-05     0.079      48     110 ..      25      87 ..      12     110 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.8e-05
                                       EE-SEEGGGCTCCG-SEEEE--BHHHHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHHT CS
                         DJ-1_PfpI  48 vtvdaslddvkaaeyDalvlpGGragperlrenekvvelvkefaekgklvaaICagpqlLaaa 110
                                       + vd++ d  k  +  +++ pG  a   ++++   v+e v+e +e+g +  +IC g+q++ +a
  gi|474934129|ref|YP_007687711.1|  25 FQVDTVTDMSKLLDAKCIMFPGVGAFDSTMERLLPVREQVRERLEAGVPTLSICIGAQIMFSA 87 
                                       6677776666666899999999888889999999***********************998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1429.35
//
Query:       gi|474934130|ref|YP_007687712.1|  [L=237]
Description: Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.3e-61  205.4   1.0    9.4e-61  205.2   1.0    1.0  1  His_biosynth     Histidine biosynthesis protein
    0.00012   21.6   0.8      0.056   12.9   0.1    2.2  2  PcrB             PcrB family
    0.00018   21.2   0.3       0.58    9.7   0.1    2.2  2  DeoC             DeoC/LacD family aldolase
     0.0083   15.3   0.3        2.9    7.1   0.1    2.2  2  NanE             Putative N-acetylmannosamine-6-phosphate epi
  ------ inclusion threshold ------
      0.011   14.7   1.1       0.83    8.6   0.1    2.1  2  IMPDH            IMP dehydrogenase / GMP reductase domain
      0.012   14.5   0.7      0.023   13.6   0.0    1.7  2  Trp_syntA        Tryptophan synthase alpha chain
       0.02   14.2   0.0       0.98    8.7   0.0    2.5  3  ThiG             Thiazole biosynthesis protein ThiG
      0.026   14.7   0.1       0.99    9.7   0.0    2.5  2  DUF1611_N        Domain of unknown function (DUF1611_N) Rossm
      0.027   13.7   0.1       0.12   11.6   0.0    1.9  2  DHO_dh           Dihydroorotate dehydrogenase
      0.056   12.6   0.1        3.5    6.7   0.0    2.3  3  IGPS             Indole-3-glycerol phosphate synthase
      0.086   13.3   0.0       0.21   12.1   0.0    1.6  1  GDPD_2           Glycerophosphoryl diester phosphodiesterase 
       0.11   12.4   0.0       0.19   11.7   0.0    1.3  1  Methyltransf_17  S-adenosyl-L-methionine methyltransferase


Domain annotation for each model (and alignments):
>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.2   1.0   6.3e-64   9.4e-61       2     228 ..       3     226 ..       2     227 .. 0.99

  Alignments for each domain:
  == domain 1  score: 205.2 bits;  conditional E-value: 6.3e-64
                                       EEEEEEEETTEEEEECTTCSTCEEEETTSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEEE CS
                      His_biosynth   2 iipalDlkdGkvVrlvkGdrfqelryagdpvelakryeeegadelhvvDldaakegreanldlveeiaeevfipvqv 78 
                                       iipa+D+ d kvV+lv G+  +++++  d++e+a+++ ++ga++lh+vDldaa+ g+e n d+  ++++e+ +p++v
  gi|474934130|ref|YP_007687712.1|   3 IIPAVDVLDHKVVQLVGGVPGSQQVVLPDVMETARDWVSKGAKYLHLVDLDAAF-GKEDNSDIFCRVIRECGVPCEV 78 
                                       9****************************************************8.999******************* PP

                                       ESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEECEEEEETTTTEEEEEEHHHHHHH CS
                      His_biosynth  79 GGGIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarrgykvaikgwreetgldavelakk 155
                                       GGG+rs  ++++++eag+d++i+gt+avk+pe+++e+aek+++ k+v+++D++ g ++ ikgw+ee++ +++++  +
  gi|474934130|ref|YP_007687712.1|  79 GGGVRSEAQIKKYVEAGVDRIIVGTKAVKEPEWLEEMAEKYPG-KLVLGLDMKGG-RISIKGWQEEVDTSLESVFDR 153
                                       *******************************************.***********.********************* PP

                                       HHHTT-SEEEEEETTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHHHTTCSEEEESHHHHTTSS CS
                      His_biosynth 156 leelgageilltdidrdGtlsGpdleltkelaeavkipviasGGvgsledlkelksegvdavivgsalyegel 228
                                       + +l ++ +l t+id +G  +G+d+e+  ++ + + ++vi+sGGv++ ed  ++ ++g++a++vg a y+g +
  gi|474934130|ref|YP_007687712.1| 154 IRSLPLAGVLNTNIDVEGQGKGVDVEFNTRFIKGCPHRVIVSGGVTTFEDSVTMSDAGAYAAVVGMAVYKGMM 226
                                       **********************************************************************976 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.1   3.7e-05     0.056     185     215 ..      78     109 ..      33     119 .. 0.81
   2 !    7.4   0.1    0.0017       2.6     174     213 ..     184     223 ..     164     228 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.7e-05
                                       EESS--SHHHHHHHHCC.SSEEEE-CHHHHHH CS
                              PcrB 185 vGGGirsaEkAkevvea.ADvivvGnvveekd 215
                                       vGGG+rs+ + k++vea  D i+vG+   +++
  gi|474934130|ref|YP_007687712.1|  78 VGGGVRSEAQIKKYVEAgVDRIIVGTKAVKEP 109
                                       8************************8654444 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0017
                                       HHHHHSSSEEEEESS--SHHHHHHHHCC.SSEEEE-CHHHH CS
                              PcrB 174 lkkklekarlivGGGirsaEkAkevvea.ADvivvGnvvee 213
                                         k +   r+iv GG+   E+   +  a A + vvG +v++
  gi|474934130|ref|YP_007687712.1| 184 FIKGCP-HRVIVSGGVTTFEDSVTMSDAgAYAAVVGMAVYK 223
                                       555554.57899***************************97 PP

>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0   0.00046      0.69     179     216 ..      57      94 ..      50     103 .. 0.87
   2 !    9.7   0.1   0.00039      0.58     183     234 ..     177     223 ..     165     224 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00046
                                       .HHHHHHHHHHHHHCHSSTEEEEETTS.SHHHHHHHHHH CS
                              DeoC 179 ateedaevfkdvikaapvpgvvlsGGv.seedfletved 216
                                        +e+  ++f++vi+++ vp   + GGv se+++++ ve 
  gi|474934130|ref|YP_007687712.1|  57 GKEDNSDIFCRVIRECGVP-CEVGGGVrSEAQIKKYVEA 94 
                                       578899*************.999****999999999986 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00039
                                       HHHHHHHHHHCHSSTEEEEETTSSHHHHHHHHHHHHHHHTHCEEEESHHHHT CS
                              DeoC 183 daevfkdvikaapvpgvvlsGGvseedfletvedAvkeagasGvlsGRaifq 234
                                       d+e+ ++ ik++p   v++sGGv  ++f + v ++   aga  +++G a+++
  gi|474934130|ref|YP_007687712.1| 177 DVEFNTRFIKGCPHR-VIVSGGV--TTFEDSVTMSD--AGAYAAVVGMAVYK 223
                                       567778999999888.*******..89999888776..88877777777765 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0    0.0029       4.4     136     177 ..      65     106 ..      54     123 .. 0.76
   2 !    7.1   0.1    0.0019       2.9     144     176 ..     189     221 ..     161     226 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0029
                                       HHHHHHHTT--EEEES---SHHHHHHHHTT--SEEEE-HHHH CS
                              NanE 136 lvkalseaglkviaeGrintPekakkaieiGvdavvvGsait 177
                                       + + + e g+   + G + + ++ kk +e Gvd ++vG+   
  gi|474934130|ref|YP_007687712.1|  65 FCRVIRECGVPCEVGGGVRSEAQIKKYVEAGVDRIIVGTKAV 106
                                       567777888888899999********************7433 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0019
                                       T--EEEES---SHHHHHHHHTT--SEEEE-HHH CS
                              NanE 144 glkviaeGrintPekakkaieiGvdavvvGsai 176
                                         +vi+ G + t e + ++ + G++a vvG a+
  gi|474934130|ref|YP_007687712.1| 189 PHRVIVSGGVTTFEDSVTMSDAGAYAAVVGMAV 221
                                       346***************************998 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1   0.00055      0.83     135     236 ..      65     102 ..      18     110 .. 0.63
   2 ?    5.2   0.1     0.006         9     105     174 ..     150     219 ..     143     221 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00055
                                       HHHHHHHHTTTSEEEEEEE-SHHHHHHHHHTT-SEEEE-SS-STTBHHHHHCSB---HHHHHHHHHHHHCTCT-EEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 135 avkeikkkveeveviaGnvataegakaLieagadavkvGiGpGsiCttrvvagvGvpqltAvaevaeaakkagvpvi 211
                                         + i                                                                ++ gvp+ 
  gi|474934130|ref|YP_007687712.1|  65 FCRVI----------------------------------------------------------------RECGVPCE 77 
                                       44444................................................................45555555 PP

                                       EES---SHHHHHHHHHTT-SEEEES CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 212 aDGGikysgdivkAlaaGadavmlG 236
                                         GG++++ +i k + aG d +++G
  gi|474934130|ref|YP_007687712.1|  78 VGGGVRSEAQIKKYVEAGVDRIIVG 102
                                       5555555555555555555555555 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.006
                                       HHHHHHHHHHTT-SEEEEE-.STSSSHHHHHHHHHHHHHTTTSEEEEEEE-SHHHHHHHHHTT-SEEEE-S CS
                                       xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 105 alervkalveagvdvlvvds.ahghsekvleavkeikkkveeveviaGnvataegakaLieagadavkvGi 174
                                        ++r++ l  agv    +d+  +g+   v    + ik   ++v +++G v+t e   ++ +aga a  vG+
  gi|474934130|ref|YP_007687712.1| 150 VFDRIRSLPLAGVLNTNIDVeGQGKGVDVEFNTRFIKGCPHRV-IVSGGVTTFEDSVTMSDAGAYAAVVGM 219
                                       5677777777777777777624667777777777788666445.99*******************999998 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.5e-05     0.023     193     234 ..      68     110 ..      54     124 .. 0.82
   2 ?   -2.2   0.2      0.96   1.4e+03     206     230 ..     197     222 ..     190     227 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.5e-05
                                       HHHCTSS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHHHHHHH CS
                         Trp_syntA 193 lkkltavPvavGFGistkeqvkqva.kvadGvivGSalvkkie 234
                                       + +   vP  vG G+++++q+k+ + ++ d +ivG + vk+ e
  gi|474934130|ref|YP_007687712.1|  68 VIRECGVPCEVGGGVRSEAQIKKYVeAGVDRIIVGTKAVKEPE 110
                                       4455569****************9989************9866 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.96
                                       SS-SHHHHHHHH.TT-SEEEE-HHHH CS
                         Trp_syntA 206 Gistkeqvkqva.kvadGvivGSalv 230
                                       G+ t e+  ++  ++a +++vG a+ 
  gi|474934130|ref|YP_007687712.1| 197 GVTTFEDSVTMSdAGAYAAVVGMAVY 222
                                       77777777777778899999998775 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.83   1.2e+03      98     114 ..      21      37 ..       6      55 .. 0.77
   2 ?    8.7   0.0   0.00066      0.98     168     218 ..      66     117 ..      55     135 .. 0.85
   3 ?    2.3   0.0     0.059        88     201     232 ..     192     223 ..     170     231 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.83
                                       -BCETTTTEB-HHHHHH CS
                              ThiG  98 viadektLlPdvvetlk 114
                                       v ++++++lPdv+et +
  gi|474934130|ref|YP_007687712.1|  21 VPGSQQVVLPDVMETAR 37 
                                       67789999999999865 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00066
                                       HHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESH.HHHTSSSHHHHHH CS
                              ThiG 168 kiiieeakvPvivDAGigspsdaaqamelGadavllnt.avaeakdpvamAr 218
                                         +i+e+ vP  v  G++s  ++ + +e G+d +++ t av e +   +mA+
  gi|474934130|ref|YP_007687712.1|  66 CRVIRECGVPCEVGGGVRSEAQIKKYVEAGVDRIIVGTkAVKEPEWLEEMAE 117
                                       5578899*****************************9857777766677776 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.059
                                       EEESHHHHTSSSHHHHHHHHHHHHHHHHHHHH CS
                              ThiG 201 vllntavaeakdpvamArafklaveaGrlayl 232
                                       v++   v++ +d v+m  a ++a   G   y+
  gi|474934130|ref|YP_007687712.1| 192 VIVSGGVTTFEDSVTMSDAGAYAAVVGMAVYK 223
                                       66666677777777777776666666655554 PP

>> DUF1611_N  Domain of unknown function (DUF1611_N) Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00066      0.99      15      58 ..     104     148 ..      91     154 .. 0.83
   2 ?    2.3   0.0      0.13     2e+02      23      46 ..     205     227 ..     187     233 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00066
                         DUF1611_N  15 rgipvvssleealaagaevlviGiapeggklp.eswreavkeAle 58 
                                       +++++ + lee +++ +  lv+G+  +gg+++ + w+e+v++ le
  gi|474934130|ref|YP_007687712.1| 104 KAVKEPEWLEEMAEKYPGKLVLGLDMKGGRISiKGWQEEVDTSLE 148
                                       667777777777899999**************889******9987 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.13
                         DUF1611_N  23 leealaagaevlviGiapeggklp 46 
                                       + + ++aga + v+G+a+  g+++
  gi|474934130|ref|YP_007687712.1| 205 VTM-SDAGAYAAVVGMAVYKGMMK 227
                                       333.5899*********9999885 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.43   6.5e+02     251     284 ..      80     112 ..      66     122 .. 0.78
   2 ?   11.6   0.0   8.1e-05      0.12     247     282 ..     192     226 ..     178     230 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.43
                                       SS--SHHHHHHHHHHTECEEEESHHHHHHGTCHH CS
                            DHO_dh 251 GGiesgeDalekieaGAslvqvytalvfegpkia 284
                                       GG+ s      ++eaG   + v+t  v ++p + 
  gi|474934130|ref|YP_007687712.1|  80 GGVRSEAQIKKYVEAGVDRIIVGTKAV-KEPEWL 112
                                       899999999999999999999999884.445554 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 8.1e-05
                                       EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTC CS
                            DHO_dh 247 iIgvGGiesgeDalekieaGAslvqvytalvfegpk 282
                                       +I +GG+++ eD + +  aGA +  v+ a+ ++g++
  gi|474934130|ref|YP_007687712.1| 192 VIVSGGVTTFEDSVTMSDAGAYAAVVGMAV-YKGMM 226
                                       899************************999.88875 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.5   2.3e+03       3      43 ..      31      71 ..      29      78 .. 0.77
   2 ?    6.7   0.0    0.0023       3.5     217     246 ..      81     110 ..      73     117 .. 0.88
   3 ?    3.2   0.0     0.027        40     195     242 ..     177     222 ..     168     227 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.5
                                      HCHHHHHHHHHHHHCCS-GGCCCCG..-SS-SS-HHHHCHC CS
                              IGPS  3 kivaekkeevaeakkrqsladleaavklakpkrsfaeaLre 43
                                      +++++ + +v++  k  +l dl+aa  ++++   f + +re
  gi|474934130|ref|YP_007687712.1| 31 DVMETARDWVSKGAKYLHLVDLDAAFGKEDNSDIFCRVIRE 71
                                      56778888888888888899999888887777777777765 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0023
                                       SS-SHHHHHHHCCTT-SEEEESHHHHC-TT CS
                              IGPS 217 GiktredveklkeegvnafLvGeslmrqed 246
                                       G++++++++k+ e+gv+ ++vG+  +++++
  gi|474934130|ref|YP_007687712.1|  81 GVRSEAQIKKYVEAGVDRIIVGTKAVKEPE 110
                                       9*********************99888766 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.027
                                       -CHHHHHHCHCC-TTSEEEEESSS-SHHHHHHHCCTT-SEEEESHHHH CS
                              IGPS 195 dlntteeLaklvpkdvllvaeSGiktredveklkeegvnafLvGeslm 242
                                       d++  ++ +k  p    ++   G++t ed  +++++g+ a  vG ++ 
  gi|474934130|ref|YP_007687712.1| 177 DVEFNTRFIKGCP--HRVIVSGGVTTFEDSVTMSDAGAYAAVVGMAVY 222
                                       5555556666666..4566678**********************9875 PP

>> GDPD_2  Glycerophosphoryl diester phosphodiesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00014      0.21      10      25 ..      85     100 ..      78     100 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                            GDPD_2  10 eavwrelvgaGVdgIn 25 
                                       ea+++ +v+aGVd+I+
  gi|474934130|ref|YP_007687712.1|  85 EAQIKKYVEAGVDRII 100
                                       799************8 PP

>> Methyltransf_17  S-adenosyl-L-methionine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00013      0.19      57     128 ..       9      81 ..       5      94 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                                       EEESS--S-GGG---GGGEEES-HHHHHHHHHHH-S-.EEEEEE----S-HHHHHHHHHHHHHHHGGGEEEEE CS
                   Methyltransf_17  57 vfdralaahpssvPeeedlllGeieetlealakigak.aalvhaDlGtgykekdavtatrlsdliagllapgG 128
                                       v+d+++      vP +++++l ++ et+++    gak + lv  D  +g++++ + + + + +  ++  + gG
  gi|474934130|ref|YP_007687712.1|   9 VLDHKVVQLVGGVPGSQQVVLPDVMETARDWVSKGAKyLHLVDLDAAFGKEDNSDIFCRVIRECGVPCEVGGG 81 
                                       788888899999******************6666665379*************99999998877666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1571.06
//
Query:       gi|474934131|ref|YP_007687713.1|  [L=1071]
Description: carbamoyl-phosphate synthase large subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   8.7e-111  368.5   0.0    3.6e-72  242.3   0.0    2.3  2  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
      7e-42  142.6   0.5    1.6e-41  141.4   0.5    1.7  1  CPSase_L_D3      Carbamoyl-phosphate synthetase large chain, 
    7.2e-19   67.8   0.4    4.7e-18   65.2   0.1    2.7  3  MGS              MGS-like domain
    2.6e-15   56.5   0.0    5.7e-09   35.8   0.0    2.7  2  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    5.5e-13   48.8   0.0    8.6e-09   35.2   0.0    2.3  2  ATP-grasp        ATP-grasp domain
    2.1e-12   46.9   0.0    2.8e-06   27.1   0.0    2.8  3  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
    1.6e-07   31.5   0.1    0.00032   20.8   0.0    2.7  2  ATP-grasp_3      ATP-grasp domain
    7.8e-05   22.5   0.0     0.0017   18.1   0.0    2.6  2  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
    0.00026   20.7   0.0     0.0055   16.3   0.0    2.5  2  RimK             RimK-like ATP-grasp domain
  ------ inclusion threshold ------
      0.013   15.1   0.0       0.17   11.5   0.0    2.6  2  ATP-grasp_2      ATP-grasp domain
      0.026   14.8   0.2        9.1    6.6   0.1    2.9  3  TrkA_N           TrkA-N domain
       0.03   13.8   0.0        0.2   11.1   0.0    2.2  2  ATP-grasp_5      ATP-grasp domain
      0.031   14.3   0.0        4.6    7.4   0.0    2.8  2  DUF4176          Domain of unknown function (DUF4176)


Domain annotation for each model (and alignments):
>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  242.3   0.0   2.6e-75   3.6e-72       1     210 [.     126     333 ..     126     334 .. 0.98
   2 !  124.1   0.0   3.7e-39   5.2e-36       1     209 [.     669     870 ..     669     872 .. 0.94

  Alignments for each domain:
  == domain 1  score: 242.3 bits;  conditional E-value: 2.6e-75
                                       SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH..-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2   1 Dkesakealkkinvpvvpssaapvetleealaiakei..gyPviikaafglGGkGmrvarneeelaelvkkalaeak 75 
                                       D+e +ke+++ i++pv  s +a  +++eeal++++++   yPv+i++af+lGG+G+++a+neeel+++++++la ++
  gi|474934131|ref|YP_007687713.1| 126 DRELFKETMETIGEPVPLSRPA--NSIEEALDAVNNVigRYPVLIRPAFTLGGTGGGIAYNEEELRDICARGLAYSR 200
                                       9*******************99..*********9997555************************************7 PP

                                       HHHSTS-EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCEC..TCCCCEEEES-SS--HHHHHHHHHHHHHHHH CS
                       CPSase_L_D2  76 aafgnkqvlvekslkgpkeiEvevlrDakgnvitvcerenslql..rtqkvievAPsqtLtdeerqalreaavkvvr 150
                                            +qvl+e+s+ g+keiE+ev+rDa++n++++c++en++++  +t+++i+ AP  tL+d++ q+ r+a++k+++
  gi|474934131|ref|YP_007687713.1| 201 ----IHQVLIEESVLGWKEIEYEVMRDANDNCVIICNMENLDAMgiHTGESIVCAPCLTLSDRDLQTFRTASIKIIH 273
                                       ....9************************************************************************ PP

                                       HHT-EEEEEEEEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT--GCG CS
                       CPSase_L_D2 151 evgvvgagtveflldpkskeyyviEvNtRlsvesalaekaTGldlvkeaakialgekLee 210
                                       +++++g+++v+f++dp +++y viEvN+R+s++sala+kaTG++++ +a kia+g++L+e
  gi|474934131|ref|YP_007687713.1| 274 ALQIEGGCNVQFAFDPVTHDYRVIEVNPRVSRSSALASKATGYPIARVATKIAVGYTLDE 333
                                       **********************************************************97 PP

  == domain 2  score: 124.1 bits;  conditional E-value: 3.7e-39
                                       SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaa 77 
                                       D+++++++++k+n++  ps +a   + eea++ia+ei yPv++++++ lGG+Gm ++++ +el+  +++a++ ++  
  gi|474934131|ref|YP_007687713.1| 669 DRKRFTDLMRKLNIKQPPSGTA--YSFEEAVKIAEEIEYPVLVRPSYVLGGRGMEIVYSADELKTYMETAVKVSR-- 741
                                       9*******************99..9*************************************************7.. PP

                                       HSTS-EEEEE--SSSEEEEEEEEEETTS-EEE.EEEEEECCECTCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT CS
                       CPSase_L_D2  78 fgnkqvlvekslkgpkeiEvevlrDakgnvit.vcerenslqlrtqkvievAPsqtLtdeerqalreaavkvvrevg 153
                                         n+ vl++k+l++  ei+v+ ++D ++  +  + e       + ++   v P  tL ++  +++ e   +v+ +++
  gi|474934131|ref|YP_007687713.1| 742 --NHPVLIDKYLTEAIEIDVDSVSDGEDVYVGgILEHVEYAGCHSGDATMVMPPYTLPKDIIDQIVEINRQVALNLK 816
                                       ..9**********************999777423344444455********************************** PP

                                       -EEEEEEEEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT--GC CS
                       CPSase_L_D2 154 vvgagtveflldpkskeyyviEvNtRlsvesalaekaTGldlvkeaakialgekLe 209
                                       + g  +++ +++  ++e+ +iE N+R s+  +  +kaTG++l+k+ +k+ lg+kL+
  gi|474934131|ref|YP_007687713.1| 817 ILGLMNLQLAYK--DGEIWMIEANPRASRTVPFISKATGIPLAKIGVKVMLGKKLK 870
                                       ***********9..6***************************************97 PP

>> CPSase_L_D3  Carbamoyl-phosphate synthetase large chain, oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.4   0.5   1.2e-44   1.6e-41       3     122 .]     421     538 ..     419     538 .. 0.97

  Alignments for each domain:
  == domain 1  score: 141.4 bits;  conditional E-value: 1.2e-44
                       CPSase_L_D3   3 lkeptdeRifaiaealrrglsveeiheltkidpwFLekleelvelekelkkkkkeldeellreakklGfsDkqiael 79 
                                        k++td+Rifa+ ealrrg++ve++++ +  d +F++kl+++v++e+++k+++  l+++ll+eak +GfsD++ia+l
  gi|474934131|ref|YP_007687713.1| 421 FKDATDRRIFAMGEALRRGWTVEQVAKECAWDIFFVQKLKNIVDMENRIKSED--LTDDLLKEAKYMGFSDETIATL 495
                                       6889*********************************************9996..9********************* PP

                       CPSase_L_D3  80 leeeeeeevrelrkklgilpvykrvDtcAaeFeaetpYlYstY 122
                                       l+ ++e +vr+ r+klg+ p yk+vDtcAaeF+aetpY+YstY
  gi|474934131|ref|YP_007687713.1| 496 LKGKTEWDVRAQREKLGVFPYYKMVDTCAAEFSAETPYFYSTY 538
                                       *99***************************************9 PP

>> MGS  MGS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       4.9   6.8e+03      77      93 ..     313     329 ..     303     330 .. 0.80
   2 ?   -3.3   0.0       7.9   1.1e+04      56      70 ..     580     594 ..     575     606 .. 0.60
   3 !   65.2   0.1   3.4e-21   4.7e-18       3      95 .]     953    1039 ..     951    1039 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4.9
                                       CHHHHHHHHHHHTTSHE CS
                               MGS  77 kdgykirraaenidIpl 93 
                                         gy i+r+a++i +++
  gi|474934131|ref|YP_007687713.1| 313 ATGYPIARVATKIAVGY 329
                                       379999*******9997 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 7.9
                                       HHTTSCCEEEEE--T CS
                               MGS  56 ikngeidlvintlyp 70 
                                       +++++i++v ++ +p
  gi|474934131|ref|YP_007687713.1| 580 LQEEGIEAVMINNNP 594
                                       566666644444444 PP

  == domain 3  score: 65.2 bits;  conditional E-value: 3.4e-21
                                        HHHHHHHHHTTCEEEEEHHHHHHHHHTT--EEECCCCHSTGSGGTHCHHHHHHHHTTSCCEEEEE--THHHHHHC CS
                               MGS    3 velakklkelgfellATgGTakllkeagipvtevvektgegerlggrveildaikngeidlvintlypfkatvak 77  
                                         e+ak+l+++gf+++AT+GT  +l+e+g++ t v +  +   +++       ++++g i+l+int++ ++ +v+ 
  gi|474934131|ref|YP_007687713.1|  953 TEVAKQLVQMGFKIYATKGTSTYLREHGVENTAVFKNSENM-KPN----AISLMRDGAINLIINTPSLHSGAVR- 1021
                                        689***************************66666666666.888....9***********************9. PP

                                        HHHHHHHHHHHTTSHEES CS
                               MGS   78 dgykirraaenidIplpt 95  
                                        dg+++rr+a++ +Ip +t
  gi|474934131|ref|YP_007687713.1| 1022 DGHRMRRLAVELEIPFIT 1039
                                        ***************998 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.6e-06    0.0023      26     173 ..     152     300 ..     141     303 .. 0.74
   2 !   35.8   0.0   4.1e-12   5.7e-09      28     174 ..     696     839 ..     684     849 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.6e-06
                                       HHHHHHHHHC-.SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT-..SCEEEEE--.ESEEEEEEEEETSSCEE CS
                   Dala_Dala_lig_C  26 ellekveeelg.ypvfVKpareGSSvGvskveseeelkeaieeafkyd..ekvlvEeai.egreievavlgneklev 98 
                                       e l++v + +g ypv+++pa +    G   + +eeel++  ++ + y   ++vl+Ee +   +eie  v+ + + ++
  gi|474934131|ref|YP_007687713.1| 152 EALDAVNNVIGrYPVLIRPAFTLGGTGGGIAYNEEELRDICARGLAYSriHQVLIEESVlGWKEIEYEVMRDANDNC 228
                                       455666666544********98778888999********9998776653379******9899*********555444 PP

                                       EEEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEE.ETTTEEEEEEEE CS
                   Dala_Dala_lig_C  99 sevgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDffl.teegeivlnEvN 173
                                         +     + +  d    ++++++ +    +l++   ++ +++++k+ +al+++G + v f     + +  + EvN
  gi|474934131|ref|YP_007687713.1| 229 VIIC----NMENLDAMGIHTGESIVCAPCLTLSDRDLQTFRTASIKIIHALQIEGGCNVQFAFdPVTHDYRVIEVN 300
                                       4333....33334444445566677777778899999999999999999999999999999884456667777777 PP

  == domain 2  score: 35.8 bits;  conditional E-value: 4.1e-12
                                       HHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT..-SCEEEEE--.ESEEEEE.EEEETSSCEEEE CS
                   Dala_Dala_lig_C  28 lekveeelgypvfVKpareGSSvGvskveseeelkeaieeafky..dekvlvEeai.egreiev.avlgneklevse 100
                                         k+ ee+ ypv+V+p+      G++ v s++elk ++e+a+k   ++ vl+++++ e+ ei+v +v + e++ v  
  gi|474934131|ref|YP_007687713.1| 696 AVKIAEEIEYPVLVRPSYVLGGRGMEIVYSADELKTYMETAVKVsrNHPVLIDKYLtEAIEIDVdSVSDGEDVYVGG 772
                                       56899************999999******************98622667*******9*******6677888899998 PP

                                       EEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEES CS
                   Dala_Dala_lig_C 101 vgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvNt 174
                                       + e+v      +y+  +s+d+++++ p +l+k++ ++i e+  ++  +l++ Gl  + + ++ +gei++ E N+
  gi|474934131|ref|YP_007687713.1| 773 ILEHV------EYAGCHSGDATMVMPPYTLPKDIIDQIVEINRQVALNLKILGLMNLQLAYK-DGEIWMIEANP 839
                                       88886......68888899**************************99999999999998887.9********97 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   0.00015      0.21       5     160 ..     138     303 ..     134     311 .. 0.80
   2 !   35.2   0.0   6.2e-12   8.6e-09       2     160 ..     678     841 ..     677     844 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00015
                                       T--B-EEEEECCHHHHHHHHHHH..-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC....GTTCEEEEE----S CS
                         ATP-grasp   5 glpvprflaveskeeleeaaeel..glpvvvKarrlgydGkGqsvvrseedleqaleal....keekvivEefvpfe 75 
                                       g pvp    ++s ee+ +a++++  ++pv+++ +     G G  +  +ee+l+++ +      + ++v++Ee v   
  gi|474934131|ref|YP_007687713.1| 138 GEPVPLSRPANSIEEALDAVNNVigRYPVLIR-PAFTLGGTGGGIAYNEEELRDICARGlaysRIHQVLIEESVLGW 213
                                       56778888888888777777776666888887.999****************99877655777889*********** PP

                                       EEEEEEEEEETTC-EEE--EEEEEEETTEEE...EEEECEE-SCH.HHHHHHHHHHHHHHHHTSSEEEEEEE.EEET CS
                         ATP-grasp  76 kElsvlvvrsaeGetafypvvetvqedgilr...lsvapaevsek.aqkkaeeiakkiveeLggvGvfavEl.Fvle 147
                                       kE+   v+r+a+ + +++  +e++   gi     +++ap+   ++ ++++ ++   ki+++L++ G   v + F   
  gi|474934131|ref|YP_007687713.1| 214 KEIEYEVMRDANDNCVIICNMENLDAMGIHTgesIVCAPCLTLSDrDLQTFRTASIKIIHALQIEGGCNVQFaFDPV 290
                                       ****************************9853336788876555516666666666**********99998745555 PP

                                       TCTEEEEEEESS- CS
                         ATP-grasp 148 dgellvnElapRp 160
                                       + +  v E+ pR+
  gi|474934131|ref|YP_007687713.1| 291 THDYRVIEVNPRV 303
                                       6667888888887 PP

  == domain 2  score: 35.2 bits;  conditional E-value: 6.2e-12
                                       HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC....GTTCEEEEE---- CS
                         ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal....keekvivEefvpf 74 
                                       +kl+++ p+  ++ s ee+ ++aee+++pv+v+ +     G+G  +v s+++l++ +e++    ++++v++ ++   
  gi|474934131|ref|YP_007687713.1| 678 RKLNIKQPPSGTAYSFEEAVKIAEEIEYPVLVR-PSYVLGGRGMEIVYSADELKTYMETAvkvsRNHPVLIDKYLTE 753
                                       6899999**************************.99999**************999999989989************ PP

                                       SEEEEEEEEEETTC-EEE--EEEEEE....ETTEEEEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEET CS
                         ATP-grasp  75 ekElsvlvvrsaeGetafypvvetvq....edgilrlsvapaevsekaqkkaeeiakkiveeLggvGvfavElFvle 147
                                         E+ v  v + e  +++  + e+v+    ++g+  +++ p+++++++  ++ ei ++++ +L ++G++ + l ++ 
  gi|474934131|ref|YP_007687713.1| 754 AIEIDVDSVSDGED-VYVGGILEHVEyagcHSGDATMVMPPYTLPKDIIDQIVEINRQVALNLKILGLMNLQLAYK- 828
                                       *****999987776.777777777763333678999*************************************999. PP

                                       TCTEEEEEEESS- CS
                         ATP-grasp 148 dgellvnElapRp 160
                                       dge+++ E  pR 
  gi|474934131|ref|YP_007687713.1| 829 DGEIWMIEANPRA 841
                                       ***********96 PP

>> ATPgrasp_Ter  ATP-grasp in the biosynthetic pathway with Ter operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   3.7e-06    0.0051      52     126 ..     267     344 ..     258     349 .. 0.81
   2 !   27.1   0.0     2e-09   2.8e-06      47     114 ..     802     870 ..     799     878 .. 0.91
   3 ?   -3.7   0.0       6.8   9.3e+03      10      22 ..    1040    1052 ..    1038    1058 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.7e-06
                      ATPgrasp_Ter  52 laerlaeefgldglvnvQvrededg..pkLLEiNpRasGGlg.ysalaGvnlpylalklllgleteeveepeeglrv 125
                                       ++ +++++++++g  nvQ+  d  +  ++++E+NpR+s      s ++G  ++++a k + g   +e++++ +g ++
  gi|474934131|ref|YP_007687713.1| 267 ASIKIIHALQIEGGCNVQFAFDPVThdYRVIEVNPRVSRSSAlASKATGYPIARVATKIAVGYTLDEIPNHITGKTY 343
                                       67899**************999765569*********96555156677************99988888888777666 PP

                      ATPgrasp_Ter 126 r 126
                                       +
  gi|474934131|ref|YP_007687713.1| 344 A 344
                                       5 PP

  == domain 2  score: 27.1 bits;  conditional E-value: 2e-09
                      ATPgrasp_Ter  47 eelielaerlaeefgldglvnvQvrededgpkLLEiNpRasGGlg.ysalaGvnlpylalklllglete 114
                                       ++++e+ +++a ++++ gl+n+Q+ +++++  ++E NpRas ++  +s ++G+ l+++ +k +lg++ +
  gi|474934131|ref|YP_007687713.1| 802 DQIVEINRQVALNLKILGLMNLQLAYKDGEIWMIEANPRASRTVPfISKATGIPLAKIGVKVMLGKKLK 870
                                       5789****************************************8357888**************7554 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 6.8
                      ATPgrasp_Ter   10 yLegpEySvDvla 22  
                                        +L+g+E+Sv  +a
  gi|474934131|ref|YP_007687713.1| 1040 TLNGAEISVGAIA 1052
                                        799*****97766 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0022       3.1      30     158 ..     157     303 ..     125     306 .. 0.63
   2 !   20.8   0.0   2.3e-07   0.00032       2     158 ..     668     841 ..     667     844 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0022
                                       -.....SSSEEEEESS-------B--SS--TTE...............EEEE---S.EEEEEEEEE.SSSEEEEEEE CS
                       ATP-grasp_3  30 e.....ekklvvKprdGaggesvrvveekeeaeaaieeve........lvqefieG.kplSvsllsdgekvlvlavn 92 
                                       +      +++ + p+   gg++  ++ ++ee+  +++           l+ e + G k++  +++ d++++ v+ +n
  gi|474934131|ref|YP_007687713.1| 157 VnnvigRYPVLIRPAFTLGGTGGGIAYNEEELRDICARGLaysrihqvLIEESVLGwKEIEYEVMRDANDNCVIICN 233
                                       13444488888999999999888888888777755544335666555544444445567788899999999999999 PP

                                       EEEEET........TEEEEEEES----HHHHHHHHHHHHHTTSTT--EEEEEEEEESS...SEEEEEEESS- CS
                       ATP-grasp_3  93 rqliekaeke....fvyaGnvtpietelkeevvelaeevvekleglaGyvGvDlvlkd..eepyviEvNPRl 158
                                        + ++  + +    +v a ++t ++ ++ + ++++  +++++l ++ G   v +      ++  viEvNPR+
  gi|474934131|ref|YP_007687713.1| 234 MENLDAMGIHtgesIVCAPCLTLSD-RDLQTFRTASIKIIHAL-QIEGGCNVQFAFDPvtHDYRVIEVNPRV 303
                                       9988875544555455555555555.55667888888999999.56665555555433334589*******8 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 2.3e-07
                                       TSHHHHHHHHTTT.S---.......-EESS--....SSSEEEEESS-------B--SS--TTE.............. CS
                       ATP-grasp_3   2 sdKlktykkLkeagvkvP...tkleaeeleee....ekklvvKprdGaggesvrvveekeeaeaaieeve....... 64 
                                       +d  ++++ +++ ++k P   t ++ ee+ +     e+++ v p++  gg ++ +v   +e+++ +e+         
  gi|474934131|ref|YP_007687713.1| 668 EDRKRFTDLMRKLNIKQPpsgTAYSFEEAVKIaeeiEYPVLVRPSYVLGGRGMEIVYSADELKTYMETAVkvsrnhp 744
                                       566677788888899999999777777766556666***************************9999887899**** PP

                                       .EEEE--.-SEEEEEEEEE.SSSEEEEEEEEEEEET....TEEEEEEE....S----H..HHHHHHHHHHHHTTSTT CS
                       ATP-grasp_3  65 .lvqefi.eGkplSvsllsdgekvlvlavnrqliekaekefvyaGnvt....pietel..keevvelaeevvekleg 133
                                        l+ +++ e  ++ v+ +sdge+v+v  + + +        + +G  t    p+   +   +++ve+ ++v  +l +
  gi|474934131|ref|YP_007687713.1| 745 vLIDKYLtEAIEIDVDSVSDGEDVYVGGILEHVEYA----GCHSGDATmvmpPYTLPKdiIDQIVEINRQVALNL-K 816
                                       *777776489************99998877665544....67777655222255555545678899999999999.* PP

                                       --EEEEEEEEESS.SEEEEEEESS- CS
                       ATP-grasp_3 134 laGyvGvDlvlkdeepyviEvNPRl 158
                                       ++G++   l +kd+e+ +iE NPR 
  gi|474934131|ref|YP_007687713.1| 817 ILGLMNLQLAYKDGEIWMIEANPRA 841
                                       ************************6 PP

>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0       0.2   2.8e+02       5     104 ..     129     226 ..     125     274 .. 0.80
   2 !   18.1   0.0   1.2e-06    0.0017       7     106 ..     674     769 ..     669     801 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.2
                                       HHHHHHHHTT--B--EEEESSHHHHHHHHHHHSSSE.EEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TTCCCC CS
                            GARS_A   5 fakdllkkagiptaeyeaftdpeeakeyieeataka.lVvKadglaagKgvivakseeealkavkeilekkkfGeag 80 
                                         k+ ++ +g p +  +  ++ eea + ++++  +  + ++++   +g g  +a +eee  ++ +  l      +  
  gi|474934131|ref|YP_007687713.1| 129 LFKETMETIGEPVPLSRPANSIEEALDAVNNVIGRYpVLIRPAFTLGGTGGGIAYNEEELRDICARGLA----YSRI 201
                                       567888888888888888899999999998887666456788877888999999999987666665554....4567 PP

                                       SSEEEEE---S.EEEEEEEEECTTE CS
                            GARS_A  81 ekvviEelleG.eEvsllalvdgkt 104
                                       ++v+iEe + G +E+   ++ d ++
  gi|474934131|ref|YP_007687713.1| 202 HQVLIEESVLGwKEIEYEVMRDAND 226
                                       8999999888856888888887655 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 1.2e-06
                                       HHHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TTCCCCSSE CS
                            GARS_A   7 kdllkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeilekkkfGeagekv 83 
                                        dl++k +i+ +   +  + eea ++ ee + ++  v+++ + +g+g+ ++ s++e  ++++  ++     + ++ v
  gi|474934131|ref|YP_007687713.1| 674 TDLMRKLNIKQPPSGTAYSFEEAVKIAEEIEYPV-LVRPSYVLGGRGMEIVYSADELKTYMETAVK----VSRNHPV 745
                                       489*******************************.9********************9999988887....45789** PP

                                       EEEE--.-SEEEEEEEEECTTEEE CS
                            GARS_A  84 viEell.eGeEvsllalvdgktvk 106
                                       +i+++l e +E+ + +++dg++v+
  gi|474934131|ref|YP_007687713.1| 746 LIDKYLtEAIEIDVDSVSDGEDVY 769
                                       ****995689***********986 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.17   2.4e+02      19      84 ..     142     208 ..     129     216 .. 0.77
   2 !   16.3   0.0     4e-06    0.0055       1     181 [.     667     857 ..     667     863 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.17
                                       --EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH.GGG--EEEEE--S CS
                              RimK  19 pntalardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlea.lkeailvqeyiee 84 
                                       p ++ a++ e+a + ++++  r Pv+++  ++  G +  +a +e++l+++    l  + + q  iee
  gi|474934131|ref|YP_007687713.1| 142 PLSRPANSIEEALDAVNNVIGRYPVLIRPAFTLGGTGGGIAYNEEELRDICARgLAYSRIHQVLIEE 208
                                       44555666777777777776799*****999999999999999999999965457777777777666 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 4e-06
                                       HH-HHHHHHHHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH.....G CS
                              RimK   1 ardKlkslklLakakikvpntalardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlea.....l 72 
                                       a+d+ +   l+ k +ik p +  a + e+a+k+ e+i  + Pv+v+ ++   G ++ +    ++lk  +e+      
  gi|474934131|ref|YP_007687713.1| 667 AEDRKRFTDLMRKLNIKQPPSGTAYSFEEAVKIAEEI--EYPVLVRPSYVLGGRGMEIVYSADELKTYMETavkvsR 741
                                       6788899999***************************..6********999999999999999******99888767 PP

                                       GG--EEEEE--SS-SEEEEEEEETTEE.EEEEEEE--SSS----TTTT-EEE...E----HHHHHHHHHHHH..HCT CS
                              RimK  73 keailvqeyieeaenediRvlvvddev.vaalrrvskeGdFRsnlhrGgvae...klqlseeekelAikaak..ame 143
                                       ++ +l+ +y+ ea + d+  +  +++v v+++     e    + +h G ++    +++l ++  +  +++ +  a++
  gi|474934131|ref|YP_007687713.1| 742 NHPVLIDKYLTEAIEIDVDSVSDGEDVyVGGILEHV-E---YAGCHSGDATMvmpPYTLPKDIIDQIVEINRqvALN 814
                                       7789**********9999988877777577776653.3...367777776541114566665444333333311455 PP

                                       -SEEEEE...EEEETTEEEEEEEE..SS--SHHHHHHHT--HH CS
                              RimK 144 lvvaGvD...llrakrgllvlEvn..sspglekiektlgidia 181
                                       l ++G+    l  ++ ++ ++E n  +s  +  i+k +gi +a
  gi|474934131|ref|YP_007687713.1| 815 LKILGLMnlqLAYKDGEIWMIEANprASRTVPFISKATGIPLA 857
                                       6666654331333333445566664445555566666666655 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.39   5.3e+02       8      67 ..     131     187 ..     129     232 .. 0.77
   2 ?   11.5   0.0   0.00012      0.17       9      72 ..     675     733 ..     672     741 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.39
                                       HHHHHCTT----SEEEESSHHHHHHHHHH.HTSSSEEEEE--SSSTCCCTTCEEEESSHHH CS
                       ATP-grasp_2   8 keilakygvkvpegevaesaeeaeeaakk.lgekelvvKaQvlaGGRGKagGvklvkskee 67 
                                       ke ++  g +vp ++ a+s eea +a+++ +g+  + ++     GG G  gG+ +  ++ee
  gi|474934131|ref|YP_007687713.1| 131 KETMETIGEPVPLSRPANSIEEALDAVNNvIGRYPVLIRPAFTLGGTG--GGIAY--NEEE 187
                                       677888889999999999999998776652677888899999999866..77654..3444 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00012
                                       HHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTCCCTTCEEEESSHHHHHHHH CS
                       ATP-grasp_2   9 eilakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGRGKagGvklvkskeeakeaa 72 
                                       ++++k ++k p +  a s eea ++a++++  +  v+     GGRG    +++v+s++e+k+++
  gi|474934131|ref|YP_007687713.1| 675 DLMRKLNIKQPPSGTAYSFEEAVKIAEEIEYPV-LVRPSYVLGGRG----MEIVYSADELKTYM 733
                                       799****************************99.77878888***7....67777777777665 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.023        31      10      71 ..      28      89 ..      24     109 .. 0.84
   2 ?    6.6   0.1    0.0066       9.1      16      77 ..     579     641 ..     575     669 .. 0.83
   3 ?   -3.5   0.0       8.7   1.2e+04      32      62 ..     954     983 ..     938     987 .. 0.49

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.023
                                      HHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SS CS
                            TrkA_N 10 GrslaeeLse.ggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatg 71
                                      G++ ++ L+e g+ + v++ ++++++++  +   +v++   t e++ + ++ e +d+v+  +g
  gi|474934131|ref|YP_007687713.1| 28 GSQACRSLREeGY-KTVLVNSNPATIQTDPDTADRVYIEPMTAESIAKIIEKEGVDGVLSGMG 89
                                      8999******777.5*************98888999999999999988888888888877665 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0066
                                       HHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSH.HHHH CS
                            TrkA_N  16 eLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgdd.eani 77 
                                        L+e+g++ v i +++e+v +  +   + +      e+vL  + +e+ad+vi+  g    +n+
  gi|474934131|ref|YP_007687713.1| 579 ALQEEGIEAVMINNNPETVSTDYDISDRLYFEPLELEDVLNVIRAEDADGVICQYGGQtSVNL 641
                                       577877779************9999999*************************9876634444 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 8.7
                                       HHHHHHHHTTSEEEES-TTSHHHHHHTTGGG CS
                            TrkA_N  32 erveelreeglevvvgdatdeevLeeagiek 62 
                                       e++++l + g++++   +t    L+e g+e+
  gi|474934131|ref|YP_007687713.1| 954 EVAKQLVQMGFKIYATKGT-STYLREHGVEN 983
                                       2333333444445544444.44566666655 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.71   9.8e+02      16      51 ..     131     168 ..     121     170 .. 0.85
   2 ?   11.1   0.0   0.00015       0.2      16      51 ..     674     709 ..     665     712 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.71
                       ATP-grasp_5  16 kelleaygipvvetrlassaeeaveaaeei..gypvvl 51 
                                       ke +e +g pv+ +r a+s eea++a++++   ypv +
  gi|474934131|ref|YP_007687713.1| 131 KETMETIGEPVPLSRPANSIEEALDAVNNVigRYPVLI 168
                                       677899999*****************999877777765 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00015
                       ATP-grasp_5  16 kelleaygipvvetrlassaeeaveaaeeigypvvl 51 
                                        +l++ ++i+ +++  a s eeav++aeei+ypv +
  gi|474934131|ref|YP_007687713.1| 674 TDLMRKLNIKQPPSGTAYSFEEAVKIAEEIEYPVLV 709
                                       578999***************************976 PP

>> DUF4176  Domain of unknown function (DUF4176)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.042        58      12      37 ..       3      28 ..       1      39 [. 0.91
   2 ?    7.4   0.0    0.0033       4.6      12      38 ..     548     574 ..     544     589 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.042
                           DUF4176 12 ggtkkvmiigrrqieeeekkiydYvg 37
                                      ++ kk+m+ig  +i+ ++ + +d++g
  gi|474934131|ref|YP_007687713.1|  3 KDYKKLMVIGSGPIVIGQAAEFDFSG 28
                                      5679************9999***998 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0033
                           DUF4176  12 ggtkkvmiigrrqieeeekkiydYvgc 38 
                                       +++kkv+iig  +i+ +++  +dY+ +
  gi|474934131|ref|YP_007687713.1| 548 DSKKKVVIIGGGPIRIGQGIEFDYCCV 574
                                       6899********************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1071 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      643  (0.0358637); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.89u 0.36s 00:00:01.25 Elapsed: 00:00:00.51
# Mc/sec: 6266.06
//
Query:       gi|474934132|ref|YP_007687714.1|  [L=214]
Description: Carbamoylphosphate synthase small subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-35  122.1   0.0    2.9e-35  121.8   0.0    1.1  1  GATase         Glutamine amidotransferase class-I
    3.2e-06   27.0   0.4    0.00045   20.0   0.1    2.5  3  Peptidase_C26  Peptidase C26


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.8   0.0   3.3e-39   2.9e-35       4     189 ..      22     207 ..      20     208 .. 0.92

  Alignments for each domain:
  == domain 1  score: 121.8 bits;  conditional E-value: 3.3e-39
                                       ESSTSTHHHHHHHHHHTT........-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT....TTTHHHHHHHHC CS
                            GATase   4 Dnydsvtenlvhalvelg........vkvevvpidasaeeilellknpdgilvsgGpgspg....vegkieaikear 68 
                                       Dn++++t  l++++ +l+        ++v ++p+d++a+ i   ++ +dgilvs+Gpg+p     v g  +++  ++
  gi|474934132|ref|YP_007687714.1|  22 DNGKQYTVGLLDCGEKLRilhdlsqhFNVIMYPYDTPADVIT--EDRIDGILVSNGPGDPMhkaiVAGPAKTVGILA 96 
                                       7777777777777777777777777799*********99995..799**************9999999999999999 PP

                                       TSTS-EEEETHHHHHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEE CS
                            GATase  69 enkiPiLGICLGmQllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevt 145
                                       e ++P++GIC+G+Q++ai +g+k++k+k ++h+g ++++          +++++i++++H++ v++++l  +gl+  
  gi|474934132|ref|YP_007687714.1|  97 E-QVPLFGICFGNQVTAIGLGGKTYKMK-FGHRGCNQPVMY--------NGKVYITSQNHGFSVDEDSLKGTGLIAD 163
                                       9.**************************.**********99........457**************99999****** PP

                                       EEEETTEEEEEEEEETTTEEEESSBTTSTTSTTHHHHHHHHHHH CS
                            GATase 146 akseddeelmeiiekknpfvgvQFHPEststpegpellfnflik 189
                                         + +d++++++  k+ p++  Q+HPE+ ++p+++++lf+ + k
  gi|474934132|ref|YP_007687714.1| 164 QFNINDKTVEGMKYKDLPVFTSQYHPEANPGPMDTSFLFERFAK 207
                                       ***************************************99876 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.35   3.1e+03      50      72 ..      60      79 ..      49      84 .. 0.65
   2 !   20.0   0.1     5e-08   0.00045     101     130 ..      94     123 ..      89     168 .. 0.71
   3 !    5.5   0.0    0.0014        12     174     216 .]     146     190 ..     131     190 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.35
                     Peptidase_C26 50 edvkaildkldgllltGgq.dveP 72
                                      +++++  d++dg+l++ g+ d  P
  gi|474934132|ref|YP_007687714.1| 60 DVITE--DRIDGILVSNGPgD--P 79
                                      44443..899***99988733..5 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 5e-08
                     Peptidase_C26 101 alergvPilgiCrGlqllnvalGGtlyqdi 130
                                       +l+++vP++giC G q+ ++ lGG++y+  
  gi|474934132|ref|YP_007687714.1|  94 ILAEQVPLFGICFGNQVTAIGLGGKTYKMK 123
                                       5789**********************9754 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.0014
                     Peptidase_C26 174 Hhqaike...laeelrveAvae.DgviEaieseeakafvlgvQwHPE 216
                                       H ++++e    +++l        D ++E ++ ++   +v+  Q+HPE
  gi|474934132|ref|YP_007687714.1| 146 HGFSVDEdslKGTGLIADQFNInDKTVEGMKYKD--LPVFTSQYHPE 190
                                       666666655423333333333239******9999..569999****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.32s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1356.45
//
Query:       gi|474934133|ref|YP_007687715.1|  [L=142]
Description: Carbamoylphosphate synthase small subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      9e-51  171.0   0.0      1e-50  170.9   0.0    1.0  1  CPSase_sm_chain  Carbamoyl-phosphate synthase small chain, CP
  ------ inclusion threshold ------
      0.048   13.9   0.0       0.33   11.2   0.0    2.2  2  MGS              MGS-like domain


Domain annotation for each model (and alignments):
>> CPSase_sm_chain  Carbamoyl-phosphate synthase small chain, CPSase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.9   0.0   1.1e-54     1e-50       2     127 ..       4     130 ..       3     131 .. 0.97

  Alignments for each domain:
  == domain 1  score: 170.9 bits;  conditional E-value: 1.1e-54
                   CPSase_sm_chain   2 avLvLedGtvfeGksfg.akeavGEvvfnTgmtGYqeiltDpsYagqilvltypliGnyGvneedvesekikvaglv 77 
                                        +LvLedGtv+eG+sfg   ea+GEvvf Tgm+GYqe++tDpsY+gqi+v+t+pliGnyG++++ ++se i+++++v
  gi|474934133|ref|YP_007687715.1|   4 SYLVLEDGTVYEGESFGyPAEASGEVVFATGMSGYQESFTDPSYKGQIIVMTFPLIGNYGTTADFFQSEGIHCRAVV 80 
                                       59***************6699******************************************************** PP

                   CPSase_sm_chain  78 vrelseepsnwraeesLsewlkeekipgisgvDTRaLtkklrekgamkgv 127
                                       vre++++p +  + ++++e+lk++kipgi+g+DTR L+ k+re+g++kg+
  gi|474934133|ref|YP_007687715.1|  81 VREYTKNPTDSYHGKTIDEFLKDYKIPGIAGIDTRDLVIKIREHGTLKGA 130
                                       ***********************************************997 PP

>> MGS  MGS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.7e-05      0.33      51      94 ..      64     109 ..      29     110 .. 0.74
   2 ?   -1.1   0.0      0.24   2.2e+03      29      50 ..     110     131 ..     109     140 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.7e-05
                                       HHHHHHHTTSCC..EEEEE--THHHHHHCHHHHHHHHHHHTTSHEE CS
                               MGS  51 eildaikngeid..lvintlypfkatvakdgykirraaenidIplp 94 
                                          d  ++++i+  +v++  y+++ t + +g++i++   +++Ip++
  gi|474934133|ref|YP_007687715.1|  64 TTADFFQSEGIHcrAVVVREYTKNPTDSYHGKTIDEFLKDYKIPGI 109
                                       4455566667777777788888888877788888888888888876 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.24
                                       TT--EEECCCCHSTGSGGTHCH CS
                               MGS  29 agipvtevvektgegerlggrv 50 
                                       agi+ +++v k+ e+  l+g v
  gi|474934133|ref|YP_007687715.1| 110 AGIDTRDLVIKIREHGTLKGAV 131
                                       5888888888998888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 952.99
//
Query:       gi|474934134|ref|YP_007687716.1|  [L=343]
Description: putative translation factor pelota [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-30  106.2   0.0    2.2e-30  105.3   0.0    1.4  1  eRF1_1    eRF1 domain 1
    1.8e-20   73.5   0.1    5.7e-20   71.9   0.1    1.9  1  eRF1_3    eRF1 domain 3


Domain annotation for each model (and alignments):
>> eRF1_1  eRF1 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.3   0.0   2.4e-34   2.2e-30      12     128 ..       6     121 ..       3     122 .. 0.94

  Alignments for each domain:
  == domain 1  score: 105.3 bits;  conditional E-value: 2.4e-34
                                       SCCEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH........--CEEEEEEEEEEEEEEECTTSSEEEEEEEE CS
                            eRF1_1  12 gsgsvtLipeddedlwhlynliapgdsvrastvrkvqr.esstgsreservklkLtikvekvdfdkdagvlrisGkv 87 
                                       g+g ++++pe+d+d+whl+n+i+ gd v ast+r+ ++ + +      e+++++L +++ek+++d da ++r+ G +
  gi|474934134|ref|YP_007687716.1|   6 GTGEIKVMPETDDDIWHLFNVIQVGDIVTASTTRRDEKaDDKLRAERAEKIRMTLGVRIEKIEYDDDALRMRLLGVI 82 
                                       89*********************************9884455566669***************************** PP

                                       EEGGGG--TTSEEEEEE-TTSEEEEEECEESHHHHHHHHHH CS
                            eRF1_1  88 ieenehvklgafhtldlelkrpftiikeewdsfalerLkea 128
                                        ++ +   +g++htl +e++ p+t+ k++w++ +++rL+ a
  gi|474934134|ref|YP_007687716.1|  83 ETGPQ--DIGQHHTLMIEPGSPLTVGKYKWKKTQIDRLESA 121
                                       *****..6******************************987 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.9   0.1   6.3e-24   5.7e-20       4     112 ..     253     341 ..     250     342 .. 0.96

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 6.3e-24
                                       HHHHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSHHHHHS-HHH-HHHHHHHHHHHHHHHHH CS
                            eRF1_3   4 ekklleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdtlkekvketgeelelvelieelvenvee 80 
                                       e +++e+++e+++kd g+a+YG ++v +a++ gAvetLLv++++ r+rd                  ++++++ ve+
  gi|474934134|ref|YP_007687716.1| 253 EMEAVEQLMERISKD-GLATYGPQQVFDAANAGAVETLLVLDSVIRERD------------------LDDIIRAVET 310
                                       8899***********.******************************983..................89******** PP

                                       TT-EEEEE-TTSHHHHHHHHHTTTEEEEESS- CS
                            eRF1_3  81 sgakveiisseseeGeqlvkafgGiaaiLRyk 112
                                       +++kv+++s +++ G ql +a+gG++a+LRyk
  gi|474934134|ref|YP_007687716.1| 311 QRGKVVVVSGDHDGGRQL-AALGGMGALLRYK 341
                                       ******************.************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2234.46
//
Query:       gi|474934135|ref|YP_007687717.1|  [L=391]
Description: homocitrate synthase NifV [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      2e-72  244.0   0.6    2.4e-72  243.7   0.6    1.1  1  HMGL-like  HMGL-like


Domain annotation for each model (and alignments):
>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  243.7   0.6   1.3e-76   2.4e-72       2     253 ..      16     262 ..      15     273 .. 0.96

  Alignments for each domain:
  == domain 1  score: 243.7 bits;  conditional E-value: 1.3e-76
                                       -EEEE-TTTHHHHTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHH CS
                         HMGL-like   2 vkivdttLRDGeqalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkarilalvrarekdi 78 
                                       v ++dttLRDGeq++++ +s  ek +iak L++agv++iE+g+p ++ d+  +v+ ia+ + +a+il++ ra+++di
  gi|474934135|ref|YP_007687717.1|  16 VVVCDTTLRDGEQTAGVVFSNIEKYRIAKYLSDAGVQQIEAGIPTMGADEKTAVKHIAHMGLDASILGWNRADIHDI 92 
                                       568************************************************************************** PP

                                       HHHHH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--HHHHHHHHHHH CS
                         HMGL-like  79 kaavealkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkdvelsledasrtdleflaevveaa 155
                                       +  ++    + +++v + ++ s++h++ kl+kdr++v++k++e +++a+ +g  v+   edasr+d++fl+e v++a
  gi|474934135|ref|YP_007687717.1|  93 ETSID----CDVDSVAISMSSSDIHIQNKLRKDRQWVLDKITESIEFAKAHGLYVSCNGEDASRADMDFLLEFVKTA 165
                                       *****....******************************************************************** PP

                                       HHHT-SEEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--EEEEBTTS--SSBB CS
                         HMGL-like 156 eeaGatriniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadrvdgtvnGlGeraG 232
                                       ++aGa+r++  Dt+G   P++ +++++++ +++   +++++H Hnd+G+A+an+la+veaGa+ +++t+ GlGeraG
  gi|474934135|ref|YP_007687717.1| 166 KAAGADRFRYCDTIGREYPSNCYKRVKRIIDETG--MEVEMHMHNDFGMATANALAGVEAGARFLSCTITGLGERAG 240
                                       **********************************..***************************************** PP

                                       B-BHHHHHHHHHHTT.-B---- CS
                         HMGL-like 233 naaleelvaalealg.vdtgld 253
                                       n +lee+v+    l   +tg++
  gi|474934135|ref|YP_007687717.1| 241 NEPLEEVVMGCDELLgKKTGIN 262
                                       *********8765433666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2931.35
//
Query:       gi|474934136|ref|YP_007687718.1|  [L=568]
Description: Kef-type K+ transport systems, membrane components [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.3e-56  189.4  49.6    8.3e-56  189.4  49.6    2.3  2  Na_H_Exchanger  Sodium/hydrogen exchanger family


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.4  49.6   4.6e-60   8.3e-56       6     372 ..       3     365 ..       1     368 [. 0.95
   2 ?   -1.3   2.1      0.04   7.1e+02      25      68 ..     425     484 ..     406     499 .. 0.70

  Alignments for each domain:
  == domain 1  score: 189.4 bits;  conditional E-value: 4.6e-60
                                       HHHHHHHH..H.HHHTTSXHHHHHHHHHHHHTTTTTS......HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHHH CS
                    Na_H_Exchanger   6 llallvgl..l.arrlklpeivgliiaGlllGpsglg.liepseedlevlselglilllFlaGleldlrelrknlks 78 
                                       ll+ll+gl  + +++lklp i+g++++G+++G++  g ++e +  ++e+ls  gl+l +F +G el+l++++k +  
  gi|474934136|ref|YP_007687718.1|   3 LLLLLGGLcsViFKKLKLPAIIGYLVCGIVIGNYWDGrSLETD-AIIELLSSMGLVLMMFTIGTELNLNKMKKAGSF 78 
                                       557777778855**********************999446666.********************************* PP

                                       HHHHHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHHHHHC CS
                    Na_H_Exchanger  79 illlallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvlnDava 155
                                       + ++ ++ v i +++ G+l + +++lg++ ++a+ +gai+sa++++vv+ il++++r++     +++ + v++D++ 
  gi|474934136|ref|YP_007687718.1|  79 ASMVVMINVPIIMIG-GVLGG-TMLLGLTSIQAITLGAIISASSTAVVTVILTDQNRLDHGDCETIILIMVVEDVAQ 153
                                       ***************.99999.5899*************************************************** PP

                                       CCCCHHHHHHTX.XXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTHHHHHHHHHHHHHHHHHHHHH CS
                    Na_H_Exchanger 156 vvllavllalak.eeaggetslllllliflvvavgglllglvigwllrlitrftdddrelevllvlllallaallae 231
                                       v++l+ +  +++ e++  ++ +++l+ i++++++ ++++  +++ ll  i ++    +e+ ++++l l++++++l++
  gi|474934136|ref|YP_007687718.1| 154 VIILSAISPMLNgEGMEIGSMIFMLITIAVFIVASAVVGMMLVPRLLDWIGKR--MPDEILLIVALGLCFMLSWLST 228
                                       ****9999999889999999999999999999999999999999999999999..6********************* PP

                                       TSXXXHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHSXHHHHHXXHHHHHHHHHHHHHHHTHHH CS
                    Na_H_Exchanger 232 llgvsgilgaflaGlvlseyefsnklseklesfreglfnplfFvlvGlsldlkvlnnhlsvlilvllilvaillgri 308
                                       ++g+s ++gaf++G+v+s+ + s+ +++++ ++  ++f  +fF+++Gl + +k+l    +++i +l+i+ ++ +  +
  gi|474934136|ref|YP_007687718.1| 229 VVGLSEAIGAFIMGVVVSQAKASKAITHDVIPMK-NIFMMMFFISIGLVISPKAL---ADNIIPILIIYGLFAILMF 301
                                       **********************************.9*******************...9****************** PP

                                       HHHHHHTTTXSSXHHHHHHCCCCSS.BHHHHHHHHHHHHHHXHHHHTTSSTTTCSTSXHHHHHH CS
                    Na_H_Exchanger 309 lavflllrllglslrealiigfgglqrgavalalaalgpalgllarelyallivvvlftvlvqG 372
                                       +a+++   + +++lr +++ ++++l  g++a+++  ++ ++g+++++ly+ +i+++l++++v +
  gi|474934136|ref|YP_007687718.1| 302 VATMISFFIGNKPLRKSFFSAVSLLAMGEFAFIISKVAFDSGAIDEALYTSIIGAALISIIVLP 365
                                       *****998889**************************************************654 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.04
                                       HHHHHHHHHTTTTTS.....................HHHCHCCHHHHCHHCCHHHHCTCG CS
                    Na_H_Exchanger  25 gliiaGlllGpsglg......lieps..........eedlevlselglilllFlaGleld 68 
                                       +li++Gl+  ++ lg      +i+++          ++++ ++  l+l ++lF + ++l+
  gi|474934136|ref|YP_007687718.1| 425 LLILMGLVEILFWLGspflsdFINENtpesvsyymtTIIVMTVNFLLLLPILFRLVYNLK 484
                                       566666665555555444334444446777777777777777778888888887777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (568 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1079  (0.0601818); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.70u 0.30s 00:00:01.00 Elapsed: 00:00:00.47
# Mc/sec: 3610.87
//
Query:       gi|474934137|ref|YP_007687719.1|  [L=134]
Description: Sel1 repeat protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-15   55.2   2.4    6.9e-05   23.4   0.5    3.7  3  Sel1      Sel1 repeat
  ------ inclusion threshold ------
       0.59   10.9   3.4         46    4.9   0.0    3.4  3  TPR_6     Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> Sel1  Sel1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0     0.001       9.2       6      31 ..      25      48 ..      21      50 .. 0.83
   2 !   23.4   0.5   7.7e-09   6.9e-05       7      38 .]      62      91 ..      59      91 .. 0.91
   3 !   22.3   0.0   1.7e-08   0.00015       1      37 [.      92     126 ..      92     127 .. 0.95

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.001
                              Sel1  6 rLGmfylylnGlgvpkDpekAiewye 31
                                       LG   ly++G+ v k +++A+ +y 
  gi|474934137|ref|YP_007687719.1| 25 TLG--RLYFEGTNVQKSVRLAHSLYY 48
                                      599..777*************99985 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 7.7e-09
                              Sel1  7 LGmfylylnGlgvpkDpekAiewyekAAeqGd 38
                                      LG   +ylnG+  + D +kA ++++kAA+++d
  gi|474934137|ref|YP_007687719.1| 62 LG--AMYLNGDCAEEDASKAAYLFRKAAQKDD 91
                                      89..566***99****************9986 PP

  == domain 3  score: 22.3 bits;  conditional E-value: 1.7e-08
                              Sel1   1 aeAmyrLGmfylylnGlgvpkDpekAiewyekAAeqG 37 
                                       + A+y  G  ++y +G gv+  p+kA  w+ +AA++G
  gi|474934137|ref|YP_007687719.1|  92 PLAQYYIG--QMYREGIGVEISPSKADLWLSRAARNG 126
                                       57******..988*********************998 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0    0.0051        46       6      25 ..      26      45 ..      25      51 .. 0.88
   2 ?    1.3   0.1     0.073   6.6e+02      13      29 ..      74      89 ..      61      91 .. 0.67
   3 ?    3.8   0.2     0.012   1.1e+02       2      13 ..      94     105 ..      93     132 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0051
                                      HHHHHHHHHHHHHHHHHHHH CS
                             TPR_6  6 lalsyrklgdtdkAlealer 25
                                      l+++y+++++ +k++++  +
  gi|474934137|ref|YP_007687719.1| 26 LGRLYFEGTNVQKSVRLAHS 45
                                      79*****99****9998665 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.073
                                      HHHHHHHHHHHHHHHHH CS
                             TPR_6 13 lgdtdkAlealerlike 29
                                        d++kA  ++++  ++
  gi|474934137|ref|YP_007687719.1| 74 E-DASKAAYLFRKAAQK 89
                                      3.788888888887665 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.012
                                       HHHHHHHHHHHH CS
                             TPR_6   2 Alyklalsyrkl 13 
                                       A+y++++ yr++
  gi|474934137|ref|YP_007687719.1|  94 AQYYIGQMYREG 105
                                       89*******995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       195  (0.0108762); expected 358.6 (0.02)
Passed bias filter:                      179  (0.00998383); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.54
# Mc/sec: 747.20
//
Query:       gi|474934138|ref|YP_007687720.1|  [L=263]
Description: putative phospho-2-dehydro-3-deoxyheptonate aldolase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-56  191.1   0.1    2.7e-56  190.8   0.1    1.1  1  DeoC      DeoC/LacD family aldolase
  ------ inclusion threshold ------
      0.021   14.1   0.0      0.048   13.0   0.0    1.5  1  TMP-TENI  Thiamine monophosphate synthase


Domain annotation for each model (and alignments):
>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.8   0.1     3e-60   2.7e-56       2     234 ..      20     233 ..      19     234 .. 0.98

  Alignments for each domain:
  == domain 1  score: 190.8 bits;  conditional E-value: 3e-60
                                       EEEEECCSHHHHHHHHCTSSHHHHHHHHHHHHHHGGGSSEEEEETTTHHHHHHCSCTTSEEEEETECSSCCTTSTTE CS
                              DeoC   2 vilavDqrvankddtasaqneqledlkalvkealtpgasavlldpgviasaskeyakdiallvkldkgtyllkskqr 78 
                                       vi+++D++++n+++++       +d+ka+v++++++ga av +++g+i+   ++ +kd++l+++l+++t+   s+++
  gi|474934138|ref|YP_007687720.1|  20 VIIPMDHGISNGPLEGL------IDMKATVDAVTNGGATAVIMHKGLIRYSYRGAGKDVGLILHLSASTDVGVSANH 90 
                                       89***************......9***************************************************** PP

                                       EEETTCHHHHHHHTT-SEEEEEEEEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEEEEE-CTTBSSTTCHHHHHHH CS
                              DeoC  79 dvdevasveeakalGAdavkvvvyyradgseeeqqklaeikrvkeacheeglplilelylrdeaikdekvdpdlvae 155
                                       +v+ va+veea++ GAdav+++++y   g+e+e ++l+  ++v+  c+e+g+pl++++y+r+ ++ + + dp+l+++
  gi|474934138|ref|YP_007687720.1|  91 KVL-VANVEEAIKIGADAVSIHINY---GDEYEPEMLEAAGEVSRICNEWGMPLLVMAYPRGHDV-NSY-DPKLIGH 161
                                       ***.*********************...************************************5.666.9****** PP

                                       HHHHHTCCT-SEEEE--SSCC.B.HHHHHHHHHHHHHCHSSTEEEEETTS...SHHHHHHHHHHHHHHHTHCEEEES CS
                              DeoC 156 AarvsaelGaDiiKvevpkevvnateedaevfkdvikaapvpgvvlsGGv...seedfletvedAvkeagasGvlsG 229
                                        ar+saelGaD++Kv+++        +d+++f++v+++a  p ++++GG+   ++ d+l++v+d++ eag+ Gv++G
  gi|474934138|ref|YP_007687720.1| 162 VARASAELGADLVKVNYT--------GDIDSFREVTRGALAP-ILIAGGPkmnTDLDVLNMVHDSL-EAGGCGVSIG 228
                                       ******************........****************.********999999*********.********** PP

                                       HHHHT CS
                              DeoC 230 Raifq 234
                                       R++fq
  gi|474934138|ref|YP_007687720.1| 229 RNVFQ 233
                                       ****9 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   5.4e-06     0.048      12      63 ..      90     143 ..      80     147 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.4e-06
                          TMP-TENI  12 neellevveealkggvtlvqlRek..eldarellelaeklaalcrkygvpliin 63 
                                       ++ l++ veea+k g+++v +     +  + e+le a ++ ++c++ g+pl++ 
  gi|474934138|ref|YP_007687720.1|  90 HKVLVANVEEAIKIGADAVSIHINygDEYEPEMLEAAGEVSRICNEWGMPLLVM 143
                                       456999*********9999999987788999********************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1720.23
//
Query:       gi|474934139|ref|YP_007687721.1|  [L=340]
Description: putative alternative 3-dehydroquinate synthase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   8.4e-126  419.6   0.2   9.8e-126  419.4   0.2    1.0  1  DHQS           3-dehydroquinate synthase II
      0.005   16.4   0.1      0.009   15.5   0.1    1.4  1  Peptidase_S31  Pestivirus NS3 polyprotein peptidase S31
  ------ inclusion threshold ------
      0.014   16.0   0.0      0.027   15.0   0.0    1.4  1  TNT            Tuberculosis necrotizing toxin
      0.083   12.4   0.1        1.1    8.7   0.0    2.5  3  Hint           Hint module


Domain annotation for each model (and alignments):
>> DHQS  3-dehydroquinate synthase II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  419.4   0.2  2.2e-129  9.8e-126       1     352 []       4     340 .]       4     340 .] 0.96

  Alignments for each domain:
  == domain 1  score: 419.4 bits;  conditional E-value: 2.2e-129
                              DHQS   1 kevwikade.eeweerkelvtaaleagvdavlveeedaekvkelgkikviakeeddavlvgkddleklkkakkvaal 76 
                                       k+v+++ad  +++++rk+lvt++leagv  ++++ + +e ++ lgk++ +  +ed     g++       a+  +a+
  gi|474934139|ref|YP_007687721.1|   4 KKVFVRADGpSDTDDRKDLVTNGLEAGVVSFVLR-KGDEAFEGLGKMEDVVYTED-----GQA-------ADPDWAC 67 
                                       899*****999**********************9.88999*******96666656.....222.......345699* PP

                              DHQS  77 veikskeeeeeaaeaakeadyvivelkdwtvIPlEnliAalqgeetkiiaavksaeeAklaletLEkGadgvllkte 153
                                       ++i++++++e+a ++a +++ vi+++ dw vIPlEnliA+++++ tki+a+++++e+A+l+l+t+EkG+dg++++t+
  gi|474934139|ref|YP_007687721.1|  68 IRIDTPDDQEKALSLAGKKKAVIIDTGDWAVIPLENLIAKFRTSGTKIYAVASKKEDAELYLKTMEKGVDGIVIRTD 144
                                       ***************************************************************************** PP

                              DHQS 154 dveeikelaelleeaeeekleLkeaevtkveevgmgdRvcvDtcslmkegeGmLvGsssrglfLvhsEtlespYvas 230
                                       d+ +i ++++ll+ +  e ++L+e+ev++v++++mgdRvcvDtcs+m++geGmLvGs+s++lfL++sE++e+ Yva+
  gi|474934139|ref|YP_007687721.1| 145 DPLSIGKFKDLLTVS--EPVSLQEVEVVSVRPIEMGDRVCVDTCSMMNPGEGMLVGSYSNCLFLIQSESEENGYVAT 219
                                       ************665..589********************************************************* PP

                              DHQS 231 RPFRVNAGavhaYvlvpggkTkYLseLkaGdevlvvdkkGktreavvGRvKiEkRPlllveaeaegkkvstilQnae 307
                                       RPFRVNAGavh Y ++pgg T+YLse++aGd+vlv+d++G+tr + vGR+K+E RP+l+vea+  +k++++ilQnae
  gi|474934139|ref|YP_007687721.1| 220 RPFRVNAGAVHEYAMMPGGGTRYLSEVSAGDSVLVCDREGNTRIVSVGRCKVEVRPMLIVEATDGKKTYNVILQNAE 296
                                       ***************************************************************************** PP

                              DHQS 308 tirlvtedgkaisvteLkeGdevlvyleekaRHfGikieEtiiEk 352
                                       ti++vt+ g + svt+Lk+Gd++l+++++++RHfG+++eEti+Ek
  gi|474934139|ref|YP_007687721.1| 297 TIKVVTPAG-SESVTRLKKGDKILAHIATGGRHFGMAVEETITEK 340
                                       *********.99********************************8 PP

>> Peptidase_S31  Pestivirus NS3 polyprotein peptidase S31
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1     2e-06     0.009      46     104 ..     222     280 ..     214     331 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                     Peptidase_S31  46 lkvrrgletawaythqggissvdhvtagkdllvcdsmgrtrvvcqsnnrltdeteygvk 104
                                       ++v  g    +a    gg   +  v+ag  +lvcd  g tr+v     ++       v+
  gi|474934139|ref|YP_007687721.1| 222 FRVNAGAVHEYAMMPGGGTRYLSEVSAGDSVLVCDREGNTRIVSVGRCKVEVRPMLIVE 280
                                       5677788888999999**************************97666555444444443 PP

>> TNT  Tuberculosis necrotizing toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   5.9e-06     0.027      38      71 ..     211     244 ..     200     261 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.9e-06
                                       S-EEEEEE.----EEEEEB--BTTB----EEEEE CS
                               TNT  38 knyhvYevlkpleveaGeiapwfgqpGgGvqyel 71 
                                       ++ + Y  ++p++v+aG + +    pGgG++y  
  gi|474934139|ref|YP_007687721.1| 211 SEENGYVATRPFRVNAGAVHEYAMMPGGGTRYLS 244
                                       56678***************************76 PP

>> Hint  Hint module
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.34   1.5e+03      19      39 ..     162     182 ..     155     196 .. 0.76
   2 ?    8.7   0.0   0.00025       1.1      19      50 ..     233     264 ..     229     286 .. 0.89
   3 ?   -0.1   0.0      0.12   5.5e+02      25      42 ..     305     322 ..     294     330 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.34
                                       XXXXXXXXXXXXXXXXXXXXX CS
                              Hint  19 vtvedgeqkslseLepGdkVl 39 
                                       v++++ e +s++ +e+Gd+V 
  gi|474934139|ref|YP_007687721.1| 162 VSLQEVEVVSVRPIEMGDRVC 182
                                       666777777788888888875 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00025
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              Hint  19 vtvedgeqkslseLepGdkVlavdesgevvfs 50 
                                       +++ +g+++ lse++ Gd Vl +d +g++ + 
  gi|474934139|ref|YP_007687721.1| 233 AMMPGGGTRYLSEVSAGDSVLVCDREGNTRIV 264
                                       57899*******************99987655 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.12
                                       XXXXXXXXXXXXXXXXXX CS
                              Hint  25 eqkslseLepGdkVlavd 42 
                                       +  s+  L+ Gdk+la  
  gi|474934139|ref|YP_007687721.1| 305 GSESVTRLKKGDKILAHI 322
                                       4678999********965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2137.75
//
Query:       gi|474934140|ref|YP_007687722.1|  [L=433]
Description: shikimate 5-dehydrogenase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.6e-23   81.6   0.0    6.3e-23   80.8   0.0    1.4  1  Shikimate_dh_N  Shikimate dehydrogenase substrate binding dom
      4e-20   73.0   0.1    1.2e-18   68.2   0.0    2.2  2  DHquinase_I     Type I 3-dehydroquinase
    8.4e-15   54.2   0.1    1.7e-14   53.3   0.1    1.5  1  SDH_C           Shikimate 5'-dehydrogenase C-terminal domain
    0.00064   19.8   0.0     0.0026   17.8   0.0    2.0  2  Shikimate_DH    Shikimate / quinate 5-dehydrogenase


Domain annotation for each model (and alignments):
>> Shikimate_dh_N  Shikimate dehydrogenase substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.8   0.0   1.4e-26   6.3e-23       1      83 []     182     262 ..     182     262 .. 0.99

  Alignments for each domain:
  == domain 1  score: 80.8 bits;  conditional E-value: 1.4e-26
                                       EEESS-TT-SHHHHHHHHHHHCTSSEEEEEEE-SCCTHHHHHHHHHHTTESEEEE-TTSCCHHHGGSSEE-HHHHHH CS
                    Shikimate_dh_N   1 viGnpikhSlSPaihnaafkalglngsyeafeveedelekaveelralglaGlnvTiPfKeaviplldelseeAkai 77 
                                       +iGnp+ h +SPa++naa++++g+ng y  fe +   l+ka + +r+ ++aG+nvTiP+K+ ++++ld++++ A  i
  gi|474934140|ref|YP_007687722.1| 182 IIGNPLGHTKSPAMQNAAMERAGVNGIYLKFESP--TLDKAGDVIREYDIAGVNVTIPHKQGIMEHLDSVEKCAGDI 256
                                       79********************************..***************************************** PP

                                       T--SEE CS
                    Shikimate_dh_N  78 gAvNti 83 
                                       gAvNti
  gi|474934140|ref|YP_007687722.1| 257 GAVNTI 262
                                       *****8 PP

>> DHquinase_I  Type I 3-dehydroquinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.039   1.7e+02      22      36 ..      18      32 ..       5      53 .. 0.71
   2 !   68.2   0.0   2.6e-22   1.2e-18     119     228 ..      74     173 ..      66     173 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.039
                                      S-SEEEEEGGG-.TT CS
                       DHquinase_I 22 kaDlvElRlDllket 36
                                      +aD+ E+R+D +++ 
  gi|474934140|ref|YP_007687722.1| 18 EADMQEIRMDVFDSV 32
                                      79*********9543 PP

  == domain 2  score: 68.2 bits;  conditional E-value: 2.6e-22
                                       EEEEEEESS----HHHHHHHHHHHHHTT-SEEEEEE--SSHHHHHHHHHHHHHHHHHT-SS-EEEEE-TTTTGHHHC CS
                       DHquinase_I 119 vIvSyhdfegtpsaeelkallekmqalgaDivKiavmaksieDvlrllsltseakeekdeaplIamamGelGkiSRi 195
                                        I+S h+fe+tp+    ++++ ++ + +  i K avm+ks++D  ++ ++ +     + ++  I++ mGelG+i+Ri
  gi|474934140|ref|YP_007687722.1|  74 KIRSVHNFERTPTY---VEMMFSLGSGDQWISKYAVMPKSFSDLHTIYRAAN-----SCDRRHIVLGMGELGQITRI 142
                                       59**********76...55555555566679*******************85.....345789************** PP

                                       HHHHHTB-EEEEESSS-..SSTT-EEHHHHHHH CS
                       DHquinase_I 196 lgevfGspvtfasleeakasapGqltarelrei 228
                                         +++G ++tfas+++a  +a Gqlt++e+r++
  gi|474934140|ref|YP_007687722.1| 143 RQNALGNYLTFASAGKA--TAKGQLTIEEMRKL 173
                                       *************7777..************85 PP

>> SDH_C  Shikimate 5'-dehydrogenase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.3   0.1   3.7e-18   1.7e-14       1      31 []     403     433 .]     403     433 .] 0.98

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 3.7e-18
                                       HHHHHHHHHHHHHHHHHS----HHHHHHHHH CS
                             SDH_C   1 GLgMLveQgaeqFelWTGrepPvevMreall 31 
                                       G++ML++Qgae+F++W+G ep+++vMr+a++
  gi|474934140|ref|YP_007687722.1| 403 GTEMLIGQGAESFRRWFGTEPDTDVMRKAVQ 433
                                       9****************************96 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       1.9   8.5e+03      12      25 ..     125     138 ..     120     140 .. 0.79
   2 !   17.8   0.0   5.8e-07    0.0026      11      74 ..     292     353 ..     285     357 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.9
                                       T-EEEEES-SHHHH CS
                      Shikimate_DH  12 ekkvlliGaGemae 25 
                                       +++ +++G Ge+++
  gi|474934140|ref|YP_007687722.1| 125 DRRHIVLGMGELGQ 138
                                       5678999****997 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 5.8e-07
                                       TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHH CS
                      Shikimate_DH  11 kekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkella 74 
                                       + +kvl+ G+G  a+ ++ + +++g++   v++Rt e+++e++++++ e +  +++++++++++
  gi|474934140|ref|YP_007687722.1| 292 DCSKVLVFGTGGAARAAVYAAMDSGCE-TYVLGRTPEHVSEICRDFGCE-AGSRRIQDYDAVIN 353
                                       4589**********************9.99****************544.77888888777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 3040.61
//
Query:       gi|474934141|ref|YP_007687723.1|  [L=270]
Description: shikimate kinase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-10   41.2   0.0      3e-10   40.2   0.0    1.5  1  GHMP_kinases_N  GHMP kinases N terminal domain
    7.4e-07   29.5   0.2      3e-06   27.5   0.1    2.1  2  GHMP_kinases_C  GHMP kinases C terminal


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.0   3.4e-14     3e-10       2      61 ..      77     139 ..      76     141 .. 0.92

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 3.4e-14
                                       EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHH...HHHHHHHHHHHHHHHHHSHHHHH CS
                    GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglslee...aklaleaerlaqggngsggDvaa 61 
                                       ++ikseiP+++GL SS++++ a+++A+l+    s+e+    kl++e  ++a ++ ++ +D+a+
  gi|474934141|ref|YP_007687723.1|  77 LTIKSEIPPSRGLKSSSSVCNAIIRAVLDEHHESMETmdiIKLGVECAKEAKVTITGSFDDAC 139
                                       68***************************99777755678***********9999*****987 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.94   8.5e+03      40      56 ..     121     134 ..      99     135 .. 0.58
   2 !   27.5   0.1   3.3e-10     3e-06      15      78 ..     204     259 ..     191     265 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.94
                    GHMP_kinases_C  40 lealselGalgaklsGa 56 
                                       +e+++e+    + ++G+
  gi|474934141|ref|YP_007687723.1| 121 VECAKEAK---VTITGS 134
                                       45555555...555555 PP

  == domain 2  score: 27.5 bits;  conditional E-value: 3.3e-10
                    GHMP_kinases_C  15 ellnlsqrselkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvara 78 
                                       ++++ + r      ++ +  e  +l++a++e Gal+a++sG+  Gp++++++ d+   e +a++
  gi|474934141|ref|YP_007687723.1| 204 KAMTMNGR-----LIADIVGEPSDLIDAAMESGALAAGISGT--GPAIAIIC-DPGTGEWMAEK 259
                                       66666667.....57777778889******************..********.87776665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1795.94
//
Query:       gi|474934142|ref|YP_007687724.1|  [L=421]
Description: 3-phosphoshikimate 1-carboxyvinyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   5.5e-106  354.7   0.0   6.9e-106  354.4   0.0    1.0  1  EPSP_synthase  EPSP synthase (3-phosphoshikimate 1-carboxyvin
  ------ inclusion threshold ------
      0.088   13.1   0.0       0.51   10.7   0.0    2.2  2  B5             tRNA synthetase B5 domain


Domain annotation for each model (and alignments):
>> EPSP_synthase  EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  354.4   0.0  7.7e-110  6.9e-106       5     417 .]      11     411 ..       9     411 .. 0.94

  Alignments for each domain:
  == domain 1  score: 354.4 bits;  conditional E-value: 7.7e-110
                                       S--EEEEE--B-HHHHHHHHHHHGGGBSSEEEES---SHHHHHHHHHHHHTT.EEEEEECTSEEEEEGTT..--EE- CS
                     EPSP_synthase   5 krlegevkvpGsksisnralllAaLaegestitnlLdseDvrsmlealreLgaeiikldeekevviveglggsfeap 81 
                                       + l+g+v +p+sks ++ra++l+aL+eg+++i+ +L s D+r++++a+r++gae++ +   ++ + v    g + ap
  gi|474934142|ref|YP_007687724.1|  11 GTLDGKVSPPPSKSHTHRAIILSALSEGKCRIDSPLISFDTRATMDAVRSMGAEVSVV---GDHIEVDC--GGIHAP 82 
                                       5799************************************************887666...45555544..568999 PP

                                       HHHHTT-GGGGGGHHHHHHHHSEESSEEEEE-SBTTCGS--HHHHHHHHHTT-EEEEETTEEEEEESEET.SS-BEE CS
                     EPSP_synthase  82 eelvldlgnsgtalrlLtallalasgevvLtGdesirkRPidrlldaLrqlGaeieveegenkaplkvkg.lklkgv 157
                                        +  +d+ nsgt++rl+t+++++ +++++LtGd+si+kRP+ +lldaL + G+++   ++ +k+p++v+g   + ++
  gi|474934142|ref|YP_007687724.1|  83 -DREIDVLNSGTTMRLMTGIVSTFPSKTSLTGDDSIKKRPMGPLLDALSACGVRCS--SNGGKPPVTVEGpISGDEM 156
                                       .799**************************************************99..5558*************** PP

                                       EEETSSTTHHHHHHHHHHHTTSBS.EEEEES.-TTHHHHHHHHHHHHHTT-EEEETTSSEEEEEE--SSB--EEEE- CS
                     EPSP_synthase 158 eikaevsSqqvtsllllaallaeg.ttelee.lasepsiddtlkmlkkfgikietsgteesitvkGkeklpgteyvv 232
                                        i+++vsSq+++sll++a+l+    t+++++  +s+p+id+t++++++fg+++e+  +++  ++ G+ +    +y+v
  gi|474934142|ref|YP_007687724.1| 157 VIDGSVSSQFISSLLMSAPLVGRPmTVKVTGrEVSKPYIDITVSIMRRFGANVEE--EGTAYRISGNYSPA--DYRV 229
                                       *******************9988899*****************************..55667999966555..5*** PP

                                       -B-HHHHHHHHHHHHHTT-EEEEES--GGGGHHH..HHHHHHHHTTEEEEEESTSEEEEEETTS--BEEEEEBGSTT CS
                     EPSP_synthase 233 egDassAayflvaAaitggevtvenvginslqGdiealdeilekmgaeitqeedasivvgpsglklkdvdietlpde 309
                                       ++D ss a++lva+a+ g +vt ++++++  qGd +++d il+++g++i+   d+++  +p ++k  ++d+ ++pd+
  gi|474934142|ref|YP_007687724.1| 230 PADFSSSAFPLVAGALGG-RVTARGMDLSDAQGDSRIID-ILREVGCQIDVDGDEITCTRPAEIKAAEIDVGDIPDL 304
                                       ***************977.*****************999.*************999999999*************** PP

                                       SBHGGGHHHHHHHHHTSBSEEEEEGSSSTTCCHHHHHHHTTT-EEEEETTEEEEEEEEE.EB-EEEE-TTSTTTTHH CS
                     EPSP_synthase 310 aptlavlaafaegttviegiaelrvketdrlaamateLrklGaeveeeedgliiipaekqlkgaevesydDhRiama 386
                                       +p+lavl   a+g++++ g+ +lr ke+dr+a + ++Lr lGa+++ ++dg+ii+++  +l+g+++e  +DhR+ ma
  gi|474934142|ref|YP_007687724.1| 305 FPILAVLLSTAKGRSRLYGAPHLRFKESDRIALTEKMLRTLGADITATDDGCIINGVP-KLHGGRIEHNGDHRMFMA 380
                                       ****************************************************987776.5***************** PP

                                       HHHHHHHSBSEEEEETTHHHHHHSSSHHHHH CS
                     EPSP_synthase 387 lalaglvaegeveiddiectdksfpefeekL 417
                                        ++a+lv++g+v  ++ +c ++s+p+f e++
  gi|474934142|ref|YP_007687724.1| 381 AVVASLVSDGPVSMENDACWNVSYPGFPEQM 411
                                       ***************************9986 PP

>> B5  tRNA synthetase B5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   5.7e-05      0.51      13      46 ..     253     289 ..     245     299 .. 0.84
   2 ?   -2.1   0.0      0.57   5.1e+03      22      36 ..     339     353 ..     335     376 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 5.7e-05
                                       TS---H....HHHHHHHHHTT-E.EESSTTCEEEE--T CS
                                       xxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                B5  13 Gidlse....eeiikiLkrlgceriekdkdlllVtvPs 46 
                                       G+dls+    ++ii+iL+++gc+ i  d+d++++t P+
  gi|474934142|ref|YP_007687724.1| 253 GMDLSDaqgdSRIIDILREVGCQ-IDVDGDEITCTRPA 289
                                       666766444469**********9.6********99986 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.57
                                       HHHHHHTT-E.EESS CS
                                       xxxxxxxxxxxxxxx RF
                                B5  22 ikiLkrlgceriekd 36 
                                       +k+L+ lg +++ +d
  gi|474934142|ref|YP_007687724.1| 339 EKMLRTLGADITATD 353
                                       566666666543333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2806.72
//
Query:       gi|474934143|ref|YP_007687725.1|  [L=197]
Description: Thiamine monophosphate synthase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-36  124.7   0.0      3e-36  124.5   0.0    1.0  1  TMP-TENI      Thiamine monophosphate synthase
    1.2e-05   24.9   0.0    1.3e-05   24.7   0.0    1.2  1  NMO           Nitronate monooxygenase
    8.5e-05   21.8   0.0    0.00039   19.7   0.0    1.9  1  NanE          Putative N-acetylmannosamine-6-phosphate epimer
     0.0013   18.1   0.0     0.0019   17.6   0.0    1.3  1  ThiG          Thiazole biosynthesis protein ThiG
     0.0013   18.2   0.0      0.062   12.8   0.0    2.0  2  His_biosynth  Histidine biosynthesis protein
  ------ inclusion threshold ------
      0.058   13.2   0.0       0.25   11.1   0.0    1.9  2  QRPTase_C     Quinolinate phosphoribosyl transferase, C-termi
       0.11   11.5   0.0       0.18   10.8   0.0    1.4  1  FMN_dh        FMN-dependent dehydrogenase


Domain annotation for each model (and alignments):
>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.5   0.0   1.2e-39     3e-36       2     180 ..       4     178 ..       3     179 .. 0.92

  Alignments for each domain:
  == domain 1  score: 124.5 bits;  conditional E-value: 1.2e-39
                          TMP-TENI   2 ylvtdskldkneellevveealkggvtlvqlRekeldarellelaeklaalcrkygvpliindrvdlalavgadgvH 78 
                                        ++td+kl+ +  ++e+v+++++++ +++ lRek+ +   ++ la  + + c+k +v l++n  +++a+++++    
  gi|474934143|ref|YP_007687725.1|   4 IAITDRKLV-DGPFMECVNKVAEAKPDAIILREKDVNVGVFKMLAHGAMDSCAKNRVTLVLNTFFNVAKELKV---- 75 
                                       689*****9.9*************************************************************9.... PP

                          TMP-TENI  79 lgqddlpvaearellg..pdliiGlSvhsleeaeeaealgadYigvGpifpTdtKkdaeplgleglkelaealeiPv 153
                                        g+ +lp++ +re  +  ++l +G+S+hsl+e++eae+ g+d + +G +f+T++K++++++gl++lk+++e++++Pv
  gi|474934143|ref|YP_007687725.1|  76 -GKCQLPMDVLREYSKelKGLKVGASIHSLDELREAEQYGVDWVLFGNVFETSCKPGQPAAGLDLLKKVCEESKVPV 151
                                       .55555555555544422589******************************************************** PP

                          TMP-TENI 154 vaiGGitlenvaevleagadgvavvsa 180
                                       +a+GGit+en+ +++eaga+gv+  s+
  gi|474934143|ref|YP_007687725.1| 152 YAVGGITPENARSCMEAGAAGVCARSS 178
                                       ***********************9875 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   5.2e-09   1.3e-05     131     233 ..      89     187 ..       8     196 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 5.2e-09
                               NMO 131 rlkeagvvliptissvkearkvearGaDalivqGpeaGGhqG.tpevgdkglfaLvpqvldavdiPviAaGGiidrr 206
                                       +++  g+ +  +i s +e+r++e+ G D +      +   ++ +p+      + L+++v +  ++Pv A GGi   +
  gi|474934143|ref|YP_007687725.1|  89 SKELKGLKVGASIHSLDELREAEQYGVDWVLFGNVFETSCKPgQPAA----GLDLLKKVCEESKVPVYAVGGITP-E 160
                                       455567888899****************9888766555555525555....59*******************975.6 PP

                               NMO 207 gvaaaLalGAsgvqigtrfLltkesda 233
                                       +    + +GA+gv   + f+ +++ +a
  gi|474934143|ref|YP_007687725.1| 161 NARSCMEAGAAGVCARSSFMTCEDPKA 187
                                       78999*****************99876 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.5e-07   0.00039      93     176 ..      95     179 ..       4     197 .] 0.82

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.5e-07
                                       -EEEEE-SSHHHHHHHHHTT-SEE..E-TTTTSSTTS-.SS--HHHHHHHHH.TT--EEEES---SHHHHHHHHTT- CS
                              NanE  93 qllmaDistleeglvakklGvdiv..GttlsGytkeeekaepDfalvkalse.aglkviaeGrintPekakkaieiG 166
                                       + + a i +l+e   a++ Gvd v  G  +    k  ++    ++l+k+++e +++ v a G i tPe+a++++e G
  gi|474934143|ref|YP_007687725.1|  95 LKVGASIHSLDELREAEQYGVDWVlfGNVFETSCKPGQP-AAGLDLLKKVCEeSKVPVYAVGGI-TPENARSCMEAG 169
                                       55668999**************87445555555555444.45689999998626789*****99.9*********** PP

                                       -SEEEE-HHH CS
                              NanE 167 vdavvvGsai 176
                                       ++ v   s+ 
  gi|474934143|ref|YP_007687725.1| 170 AAGVCARSSF 179
                                       ***9987764 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   7.2e-07    0.0019     166     223 ..     139     195 ..     128     197 .] 0.92

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 7.2e-07
                                       HHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHH CS
                              ThiG 166 alkiiieeakvPvivDAGigspsdaaqamelGadavllntavaeakdpvamArafkla 223
                                        lk ++ee kvPv    Gi +p++a   me Ga +v   ++  + +dp a+ + f++a
  gi|474934143|ref|YP_007687725.1| 139 LLKKVCEESKVPVYAVGGI-TPENARSCMEAGAAGVCARSSFMTCEDPKALVEEFRKA 195
                                       68999********999998.7********************************99998 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.02        52     200     223 ..     101     124 ..      74     130 .. 0.71
   2 !   12.8   0.0   2.4e-05     0.062      62     106 ..     137     180 ..     129     195 .. 0.65

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.02
                                       --SHHHHHHHHHTTCSEEEESHHH CS
                      His_biosynth 200 vgsledlkelksegvdavivgsal 223
                                       ++sl++l+e+++ gvd v+ g+++
  gi|474934143|ref|YP_007687725.1| 101 IHSLDELREAEQYGVDWVLFGNVF 124
                                       677888888888888888888876 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 2.4e-05
                                       HHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHH CS
                      His_biosynth  62 ldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaav 106
                                       ldl+++++ee ++pv   GGI   + +++ +eaga  v+  ++ +
  gi|474934143|ref|YP_007687725.1| 137 LDLLKKVCEESKVPVYAVGGITPEN-ARSCMEAGAAGVCARSSFM 180
                                       5667777777777777777775444.7777777777766666544 PP

>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.23     6e+02      85     108 ..      12      35 ..       6      69 .. 0.81
   2 ?   11.1   0.0   9.9e-05      0.25      73     148 ..      85     169 ..      54     184 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.23
                                       EEESSHHHHHHHHHHT-SEEEEES CS
                         QRPTase_C  85 vevesleeleevleaeadiimLDn 108
                                       v+  ++e +++v+ea++d i L +
  gi|474934143|ref|YP_007687725.1|  12 VDGPFMECVNKVAEAKPDAIILRE 35 
                                       666778899999999999999855 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 9.9e-05
                                       HHHHHTTTSE...EEEEESSHHHHHHHHHHT-SEEEEES-.....-HHHHHHHHHHHHHHSTT..SEEEEESS--TT CS
                         QRPTase_C  73 vreavdkevk...ievevesleeleevleaeadiimLDnf.....sveelkkaveelkeknkr..vlievSGgvtle 139
                                       +re+ ++  k   +   ++sl+el+e+ + ++d +++ n+     ++ + +  +++lk+  ++  v + + Gg+t e
  gi|474934143|ref|YP_007687725.1|  85 LREYSKEL-KglkVGASIHSLDELREAEQYGVDWVLFGNVfetscKPGQPAAGLDLLKKVCEEskVPVYAVGGITPE 160
                                       44444333.3322667889********************988888667777777777665544459*********** PP

                                       THHHHHCTT CS
                         QRPTase_C 140 nveeyaksg 148
                                       n +   + g
  gi|474934143|ref|YP_007687725.1| 161 NARSCMEAG 169
                                       *99877766 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   6.9e-05      0.18     200     241 ..     132     173 ..      80     175 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.9e-05
                                       -TC--HHHHHHHHHHHSSEEEEEEE-SHHHHHHHHHTTESEE CS
                            FMN_dh 200 dpsltwddikwlreqtklplvvKGvltaedakraveaGvdgi 241
                                       +p+   d +k++ e+ k+p+   G +t+e+a+ ++eaG+ g+
  gi|474934143|ref|YP_007687725.1| 132 QPAAGLDLLKKVCEESKVPVYAVGGITPENARSCMEAGAAGV 173
                                       566778889********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.56
# Mc/sec: 1064.88
//
Query:       gi|474934144|ref|YP_007687726.1|  [L=383]
Description: tyrosine lyase ThiH [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.5e-20   71.3   0.0      1e-19   70.4   0.0    1.5  1  BATS         Biotin and Thiamin Synthesis associated domain
    3.8e-08   33.9   0.1    7.4e-08   32.9   0.1    1.5  1  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> BATS  Biotin and Thiamin Synthesis associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.4   0.0   1.2e-23     1e-19       1      86 []     272     374 ..     272     374 .. 0.97

  Alignments for each domain:
  == domain 1  score: 70.4 bits;  conditional E-value: 1.2e-23
                                       E--B----..........TCCCCHHHHHHHHHHSTTSECCCTCHH-HHHHHHHHHCCT--EEE-C---TTTGGG... CS
                              BATS   1 siprlrpi..........kdtpllkiiaalRlllPkagillsgResaefrdqlllklGansisagsktevggya... 64 
                                       s+prlrp+          ++++ll++ +a+Rl+lP agi++s+Re  +frd+++ +++a++isa s++++gg a   
  gi|474934144|ref|YP_007687726.1| 272 SLPRLRPClthasdtnpvHERQLLQVAMAYRLFLPFAGITISTREVGKFRDNIV-QICATKISADSHVGIGGRAeee 347
                                       789*********9999999999********************************.********************** PP

                                       .....SESSTT-TCCCCHHHHHHTT-E CS
                              BATS  65 .....flttdgrsleedvkmleelGle 86 
                                            f+++d r++ e+ k+le+ G++
  gi|474934144|ref|YP_007687726.1| 348 kgdeqFEVSDARTVLEVKKALEKNGMQ 374
                                       *************************86 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.1   8.3e-12   7.4e-08       3     121 ..      95     208 ..      93     235 .. 0.78

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 8.3e-12
                                       EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgir 79 
                                       ++++C +rC +C+++    ++   + ls ee+ +e++ + a  g  e++++ ge    +  v+++ +++k a + +r
  gi|474934144|ref|YP_007687726.1|  95 TSNWCGNRCAYCTFNAG--NRIARAKLSEEEVDAEMRNI-AATGLTEILILTGESRE-KSGVDYIGMCVKTATKYFR 167
                                       789************96..********************.899*6666666665444.3455555555555444444 PP

                                       EEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  80 itvetngtlpdeeklerllelgvdrvslgleaaddekvlklm 121
                                          +  ++l   +  + l++ g d+v++  e++d+e++ +l+
  gi|474934144|ref|YP_007687726.1| 168 SIGIEVYPLN-HDEYRYLRDCGADYVTVFQETYDPERYGELH 208
                                       4444444443.899**********************888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2543.03
//
Query:       gi|474934145|ref|YP_007687727.1|  [L=256]
Description: thiazole-phosphate synthase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-96  321.3   3.2    3.9e-96  321.1   3.2    1.0  1  ThiG          Thiazole biosynthesis protein ThiG
    0.00031   20.3   0.0    0.00053   19.5   0.0    1.5  1  His_biosynth  Histidine biosynthesis protein
  ------ inclusion threshold ------
      0.028   13.4   0.3      0.053   12.5   0.3    1.4  1  IMPDH         IMP dehydrogenase / GMP reductase domain
      0.036   13.5   1.3      0.047   13.1   1.3    1.2  1  NMO           Nitronate monooxygenase
       0.16   11.0   0.2       0.78    8.8   0.1    1.9  2  Dus           Dihydrouridine synthase (Dus)


Domain annotation for each model (and alignments):
>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  321.1   3.2   1.1e-99   3.9e-96       2     247 .]       7     248 ..       6     248 .. 0.97

  Alignments for each domain:
  == domain 1  score: 321.1 bits;  conditional E-value: 1.1e-99
                                       ETTEEES--EEEE-STSSSHHHHHHHHHHHT-SEEEEECCGSTTTS.TTS--CCCCCHCCTSEEEEE-TT-SSHHHH CS
                              ThiG   2 iagkefksrlllGtgkykslevlkeaveasgaeivtvalrRvnleekaseeellelleekevtllPntaGaktaeeA 78 
                                       i+g++fksr++lG+gk+ sle+++ ++++ g ei t+a+rR+n++    +e++l++++ +++tllPnt+Ga++aeeA
  gi|474934145|ref|YP_007687727.1|   7 IGGRKFKSRFILGSGKF-SLEMTDAVIRNGGVEIATLAIRRANAGG---QENILDYMP-EGITLLPNTSGARNAEEA 78 
                                       899**************.9*************************99...79******9.9***************** PP

                                       HHHHHHHHHTTS-SEEEE--BCETTTTEB-HHHHHHHHHHHHHTT-EEEEEE-S-HHHHHHHHHTT-SEBEEBSSST CS
                              ThiG  79 vriarlarevletdliklEviadektLlPdvvetlkaaeiLvkeGFevlpYvsdDlvlarrleevGcaavmPlaapi 155
                                       vria lare+ + d++k+E++ d+k+LlPd+vet+ka ++L +eGF+v+pY+ +Dl +ar ++ +G+aa+mPl+api
  gi|474934145|ref|YP_007687727.1|  79 VRIALLARELGCGDMVKVEIVRDSKYLLPDNVETIKAVKMLSDEGFIVMPYMMPDLSAARDMQAAGAAAIMPLGAPI 155
                                       ***************************************************************************** PP

                                       TS----S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHHHHHHHHHH CS
                              ThiG 156 GsglGllnkealkiiieeakvPvivDAGigspsdaaqamelGadavllntavaeakdpvamArafklaveaGrlayl 232
                                       Gs++Gll++ ++kii++e++vPvivDAGig+ps+a++amelG+ av+ ntava+a+d+ +mA+af++a+eaGrlayl
  gi|474934145|ref|YP_007687727.1| 156 GSNKGLLTRDFVKIIVDELDVPVIVDAGIGRPSQACEAMELGCAAVMANTAVATARDIPKMATAFRMAIEAGRLAYL 232
                                       ***************************************************************************** PP

                                       H------S.S-XTTST CS
                              ThiG 233 agriekre.vasassp 247
                                       ag  +  +  ++assp
  gi|474934145|ref|YP_007687727.1| 233 AGLGRVLDrGGEASSP 248
                                       **99886625688887 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.5e-07   0.00053      61     111 ..     163     213 ..     111     227 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.5e-07
                                       HHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THH CS
                      His_biosynth  61 nldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpel 111
                                         d v+ i++e+++pv v+ GI + +++ e++e+g+  v+ +ta+++  ++
  gi|474934145|ref|YP_007687727.1| 163 TRDFVKIIVDELDVPVIVDAGIGRPSQACEAMELGCAAVMANTAVATARDI 213
                                       56899**************************************99887765 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.3   1.5e-05     0.053     203     246 ..     171     214 ..     160     226 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.5e-05
                                       HCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCCTTBTTSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 203 akkagvpviaDGGikysgdivkAlaaGadavmlGsllagteEsp 246
                                       +++ +vpvi D Gi    + + A+ +G  avm    +a  ++ p
  gi|474934145|ref|YP_007687727.1| 171 VDELDVPVIVDAGIGRPSQACEAMELGCAAVMANTAVATARDIP 214
                                       67889****************************99999988766 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.3   1.3e-05     0.047     124     230 ..     111     212 ..      64     228 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.3e-05
                               NMO 124 pteevvarlkeagvvlipti.ssvkearkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavdiPviAa 199
                                       +t ++v+ l++ g +++p +     +ar ++a+Ga a+   G   G  +G        +   v+ ++d +d+Pvi  
  gi|474934145|ref|YP_007687727.1| 111 ETIKAVKMLSDEGFIVMPYMmPDLSAARDMQAAGAAAIMPLGAPIGSNKGLL------TRDFVKIIVDELDVPVIVD 181
                                       55678889999999999865167999**********************9933......55799************** PP

                               NMO 200 GGiidrrgvaaaLalGAsgvqigtrfLltke 230
                                        Gi +  +   a+ lG ++v   t+   + +
  gi|474934145|ref|YP_007687727.1| 182 AGIGRPSQACEAMELGCAAVMANTAVATARD 212
                                       ********************99999876666 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.12   4.3e+02      16      44 ..      84     112 ..      76     128 .. 0.76
   2 ?    8.8   0.1   0.00022      0.78     173     215 ..     165     206 ..     133     230 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.12
                                       HHHHTT-SSEEEEEEEE-SSS---HHHHH CS
                               Dus  16 lvrefgataLvvtemvtakaivreekvri 44 
                                       l re+g++++v  e+v+  +++ +++v+ 
  gi|474934145|ref|YP_007687727.1|  84 LARELGCGDMVKVEIVRDSKYLLPDNVET 112
                                       78999999999999999999888776543 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00022
                                       HHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCH CS
                               Dus 173 eaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrg 215
                                       + +k + +++ +pvi+  +I  +++a +++e  G+ +vm+  +
  gi|474934145|ref|YP_007687727.1| 165 DFVKIIVDELDVPVIVDAGIGRPSQACEAMEL-GCAAVMANTA 206
                                       678889999*********************99.******8544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1681.84
//
Query:       gi|474934146|ref|YP_007687728.1|  [L=266]
Description: thiamine biosynthesis protein ThiF, family 2 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.8e-29  101.7   0.1    4.8e-29  101.4   0.1    1.2  1  ThiF          ThiF family
    4.6e-15   55.4   0.0    7.7e-15   54.7   0.0    1.4  1  ThiS-like     ThiS-like ubiquitin
  ------ inclusion threshold ------
      0.014   14.7   0.0      0.027   13.8   0.0    1.5  1  2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, 


Domain annotation for each model (and alignments):
>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.4   0.1     8e-33   4.8e-29      13     140 ..      76     202 ..      64     255 .. 0.87

  Alignments for each domain:
  == domain 1  score: 101.4 bits;  conditional E-value: 8e-33
                                       HHHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEEESSB--GGGGGTBTTS-GGGTTSBHHHHHHHHHHHT-TTSE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  13 qekLrdskvllvGaGglGsellknLalsGvgkltlvDnDkielsNlnRqflfreediGkpKaevaaealqeinpdve 89 
                                       + + rd+kv + G+GglGs+++ +L ++G+g++ ++D+D+++++NlnRq +  ++diGk K+e+ a++ + inp+v+
  gi|474934146|ref|YP_007687728.1|  76 YTRFRDAKVGIAGLGGLGSNIAIMLTRLGIGHFVIADFDTVDITNLNRQNY-DRDDIGKRKTEATARHMRLINPYVD 151
                                       6789*********************************************87.************************* PP

                                       EEEEES-CCGCCS-HHHHTT-SEEEEESSSHHHHHHHHHHHH.HHT-EEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                              ThiF  90 veavteritdetvleellesvDlVvdalDniearrlvnracv.kkgipliea 140
                                       ve + +++++++v   +++++ +Vv a D+ + ++++ +    + ++ ++++
  gi|474934146|ref|YP_007687728.1| 152 VECFDGKLDESNV-CGVFRNCGIVVEAFDEASQKVMLVNTILgNTDKWVVSG 202
                                       **********884.389*************8887665555552555444443 PP

>> ThiS-like  ThiS-like ubiquitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.7   0.0   1.3e-18   7.7e-15       1      56 [.       1      54 [.       1      55 [. 0.98

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 1.3e-18
                         ThiS-like  1 MkIklNekeveveegttlealkekikpdaDvvIlNGFpikeDteLkegDevflIkK 56
                                      M+I+lN+ke++v++ t ++al+++i p+  +v+++GF+++eD++L+eg++vf+++K
  gi|474934146|ref|YP_007687728.1|  1 MRIVLNGKETDVSD-TAAFALRDRILPGG-YVVIDGFSASEDVPLREGMQVFVFEK 54
                                      9*************.99************.************************99 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.6e-06     0.027      28      67 ..      73     112 ..      51     138 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.6e-06
                                       CGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESS CS
                      2-Hacid_dh_C  28 allgkelsgktvGiiGlGrIGqavakrlkafgmkviaydr 67 
                                         l ++ ++ +vGi GlG +G+++a +l+ +g+  +++  
  gi|474934146|ref|YP_007687728.1|  73 PGLYTRFRDAKVGIAGLGGLGSNIAIMLTRLGIGHFVIAD 112
                                       455678999********************99995444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1709.81
//
Query:       gi|474934147|ref|YP_007687729.1|  [L=57]
Description: thiamine biosynthesis protein ThiS [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-11   44.5   0.0    1.8e-11   44.5   0.0    1.0  1  ThiS           ThiS family
  ------ inclusion threshold ------
      0.026   14.9   0.0      0.026   14.9   0.0    1.1  1  Lambda_tail_I  Bacteriophage lambda tail assembly protein I


Domain annotation for each model (and alignments):
>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   0.0     2e-15   1.8e-11      19      77 .]       4      57 .]       1      57 [] 0.96

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 2e-15
                                      SSTSBHHHHHHHHHHHTCHHGTTTTEEEEETTEEEGC.CTTTSB--TTCEEEEEESTTC- CS
                              ThiS 19 aegstvaelleaLgerypelalerrvavavNgeivpr.lwldtelkdgDevailppVaGG 77
                                      ++  t++e+l + g+ +       r+av++Ng+ivpr ++++t + d D+++++  V+GG
  gi|474934147|ref|YP_007687729.1|  4 SSSVTLSEVLSEQGFSD------SRIAVELNGRIVPRaKYAETMVCDSDTLEVVSMVGGG 57
                                      6789*************......**************99********************9 PP

>> Lambda_tail_I  Bacteriophage lambda tail assembly protein I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   2.9e-06     0.026      44      86 .]      13      57 .]       1      57 [] 0.72

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.9e-06
                     Lambda_tail_I 44 lq.rskfavrvag.vdVgesvpvdryaetlkd.gkvvtivpvpaGg 86
                                      l+ ++ ++ r+a   + g  vp+++yaet+++   +  +v ++ Gg
  gi|474934147|ref|YP_007687729.1| 13 LSeQGFSDSRIAVeLN-GRIVPRAKYAETMVCdSDTLEVVSMVGGG 57
                                      3446777777776245.999*******9988736789999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       244  (0.0136092); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 357.88
//
Query:       gi|474934148|ref|YP_007687730.1|  [L=35]
Description: hypothetical protein TALC_00570 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (35 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       875  (0.0488036); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.46
# Mc/sec: 230.81
//
Query:       gi|474934149|ref|YP_007687731.1|  [L=189]
Description: Prephenate dehydratase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.6e-35  120.4   0.0    8.5e-35  120.2   0.0    1.0  1  PDT             Prephenate dehydratase
     0.0043   16.2   0.0     0.0074   15.4   0.0    1.5  1  Lipoprotein_9   NLPA lipoprotein
     0.0076   15.9   0.0      0.009   15.6   0.0    1.2  1  Phosphonate-bd  ABC transporter, phosphonate, periplasmic sub
  ------ inclusion threshold ------
      0.042   13.8   0.1       0.06   13.3   0.1    1.3  1  NMT1            NMT1/THI5 like
       0.06   12.9   0.1       0.11   12.0   0.1    1.3  1  OpuAC           Substrate binding domain of ABC-type glycine 


Domain annotation for each model (and alignments):
>> PDT  Prephenate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.2   0.0   2.4e-38   8.5e-35       1     179 [.       6     184 ..       6     188 .. 0.94

  Alignments for each domain:
  == domain 1  score: 120.2 bits;  conditional E-value: 2.4e-38
                                       EEEES-TTSHHHHHHCCCS.......EEEEES-HHHHHHHHCTTS-SEEEEEEEESSS-B-HHHHHHHHH.SSEEEE CS
                               PDT   1 vaylGpegtyshqAalkvf..kaedvelipvasieevfeavekgeadyavvPiENsteGsVnetlDlLlkesdlkiv 75 
                                       v+y+G + + + + a+ ++   + d+el+p  s ++ +ea+e +e+d++v ++ N t+G+V+et D + + + l+++
  gi|474934149|ref|YP_007687731.1|   6 VGYMGIPYSNTWEMAKIFAeeAGLDAELVPLVSASKTMEAMEAKEVDFGVFAFRNATAGQVVETRDAIKG-HVLEVF 81 
                                       789***********99777878899*********************************************.77**** PP

                                       EEEEEE---EEEE-TT--TTT--EEEE-HHHHHHTHHHHHH-.TTSEEEE-S-HHHHHHHHHHCT-TT.EEEEE-HH CS
                               PDT  76 gEvvlpiehcLlakpktkleeikkvyShpqalgQcrkfLeehlpqvervavestaeAakkveassdkd.aaaiasev 151
                                       +   l+i+hc ++k++    ++k v Sh qalgQc+k L++ +p+++ +++++ta +a+++++ +  d +a+i+++ 
  gi|474934149|ref|YP_007687731.1|  82 RKGHLQIHHCVFTKNAD--TRVKAVSSHIQALGQCKKNLARLYPDARLMESADTALSAQMLAEGKLPDdTAVICKQA 156
                                       ************99999..99***************************************888665543999***** PP

                                       HHHHTT-EEEECS-SS-S--EEEEEEEE CS
                               PDT 152 aaelyglkvleeniedkknntTRFlvla 179
                                       a e+ gl++ + nied+k+n+T F++l+
  gi|474934149|ref|YP_007687731.1| 157 AGEHWGLHLAHINIEDRKDNITDFVMLR 184
                                       *************************997 PP

>> Lipoprotein_9  NLPA lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   2.1e-06    0.0074       1      53 [.       4      56 ..       4      81 .. 0.96

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.1e-06
                                      EEEEEETTTHHHHHHHHHHHHHTTTEEEEEEEESSSSHHHHHHHTTSSSEEEE CS
                     Lipoprotein_9  1 lkvGvlsgpeaevlekvkkllkkkgldleiveFtdyvqpNkaladgeiDanaF 53
                                      +kvG + +p ++ +e +k ++++ gld e+v + ++++  +a++++e+D  +F
  gi|474934149|ref|YP_007687731.1|  4 VKVGYMGIPYSNTWEMAKIFAEEAGLDAELVPLVSASKTMEAMEAKEVDFGVF 56
                                      79***********************************************9998 PP

>> Phosphonate-bd  ABC transporter, phosphonate, periplasmic substrate-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.5e-06     0.009      18      95 ..      18      98 ..      13     152 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.5e-06
                                      HHHHHHHHHHSSEEEEE--SSHHHHHHHHHTTS-SEEE-...-HHHHHHHHHHS-EEEEEEEEETT--SEEEEEEEEET CS
                    Phosphonate-bd 18 pladyLseelGvevelvvatdyaavvealragqvDiafl...gplayvqardqagveplatrvrsdGsasyrsviivra 93
                                      ++a+++ ee G + elv+  + + ++ea++a +vD++ +   ++ a+ +++ +++++  + +v ++G  +++  +++++
  gi|474934149|ref|YP_007687731.1| 18 EMAKIFAEEAGLDAELVPLVSASKTMEAMEAKEVDFGVFafrNATAGQVVETRDAIKGHVLEVFRKGHLQIHHCVFTKN 96
                                      7999*******************************97662225555555666677666555555577655555544444 PP

                                      TS CS
                    Phosphonate-bd 94 ds 95
                                       +
  gi|474934149|ref|YP_007687731.1| 97 AD 98
                                      33 PP

>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   1.7e-05      0.06      96     157 ..       6      67 ..       4     113 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.7e-05
                                       EEE-S-TTHH..HHHHHHHHHTT--GGG-EEEE-.TT-HHHHHHCTSSSEEECEETTTHHHHHH CS
                              NMT1  96 igyvgspfek..allkallakdggdpsdvtlvnvggtslakalltgkvDaaiggyenwegvele 157
                                       +gy+g p ++   + k + +++g+d++ v lv++  +++++a+ +++vD+++ +++n  + ++ 
  gi|474934149|ref|YP_007687731.1|   6 VGYMGIPYSNtwEMAKIFAEEAGLDAELVPLVSA--SKTMEAMEAKEVDFGVFAFRNATAGQVV 67 
                                       6666666544115777788889999999999888..5556799999999999999998766643 PP

>> OpuAC  Substrate binding domain of ABC-type glycine betaine transport system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   3.1e-05      0.11       3      68 ..       4      68 ..       2      85 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.1e-05
                                      EEEEEESSHHHHHHHHHHHHHHHHTTEEEEEEEEESHHHHHHHHHTTSSSEEEEEEHHHHHHHHHH CS
                             OpuAC  3 ivigsknwteqevlaeilkqllekkGykveltnlgstavlfaalasGdiDvypeewtgtayeaykk 68
                                      +++g+++++ +  + e++k + e++G+++el++l s   +++a++ +++D+ + ++ ++++ ++ +
  gi|474934149|ref|YP_007687731.1|  4 VKVGYMGIPYSN-TWEMAKIFAEEAGLDAELVPLVSASKTMEAMEAKEVDFGVFAFRNATAGQVVE 68
                                      666666666655.45899999***************999**************9999999877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1218.12
//
Query:       gi|474934150|ref|YP_007687732.1|  [L=605]
Description: ATPase component of ABC transporters with duplicated ATPase domains [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-47  161.1   1.1    7.1e-24   84.9   0.0    2.8  3  ABC_tran       ABC transporter
    4.4e-16   59.6   1.4    0.00029   20.8   0.0    4.2  4  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 
    1.6e-15   57.2   0.3    6.3e-09   35.6   0.0    3.3  3  SMC_N          RecF/RecN/SMC N terminal domain
    6.4e-13   48.5  14.3      1e-11   44.7  12.3    2.7  2  ABC_tran_Xtn   ABC transporter
    7.7e-08   32.4   0.0    0.00066   19.7   0.0    3.0  2  MMR_HSR1       50S ribosome-binding GTPase
    6.3e-07   29.6   0.0     0.0011   19.0   0.0    3.0  2  Dynamin_N      Dynamin family
    7.1e-06   25.7   0.7      0.084   12.6   0.1    2.6  2  AAA_29         P-loop containing region of AAA domain
      3e-05   24.0   0.1       0.14   12.1   0.0    2.7  2  RsgA_GTPase    RsgA GTPase
    0.00032   19.8   0.2       0.74    8.7   0.0    2.4  2  MeaB           Methylmalonyl Co-A mutase-associated GTPase Me
    0.00089   19.4   0.2        3.6    7.7   0.0    3.3  3  AAA_33         AAA domain
     0.0013   19.0   1.6       0.25   11.6   0.1    3.5  3  AAA_22         AAA domain
     0.0015   18.3   0.9        1.5    8.5   0.2    3.2  3  AAA_24         AAA domain
     0.0027   18.0   4.2       0.24   11.6   0.0    4.0  3  AAA_28         AAA domain
      0.003   17.6   0.4        1.2    9.1   0.0    3.0  3  TsaE           Threonylcarbamoyl adenosine biosynthesis prote
     0.0044   17.6   4.9        2.2    8.8   0.0    3.7  3  AAA_18         AAA domain
  ------ inclusion threshold ------
      0.011   15.7   0.0       0.58   10.0   0.0    2.9  2  MobB           Molybdopterin guanine dinucleotide synthesis p
      0.013   15.9   0.1       0.49   10.8   0.0    2.9  2  AAA            ATPase family associated with various cellular
      0.021   15.2   0.9       0.71   10.3   0.0    2.8  2  RNA_helicase   RNA helicase
      0.025   15.1  20.3      0.074   13.5   0.2    3.2  2  AAA_23         AAA domain
      0.025   13.6   0.0       0.13   11.3   0.0    2.0  2  T2SSE          Type II/IV secretion system protein
      0.025   13.7   0.0        1.5    7.9   0.0    2.3  2  DUF815         Protein of unknown function (DUF815)
      0.028   14.8   0.0       0.52   10.7   0.0    2.5  2  AAA_16         AAA ATPase domain
       0.04   14.0  10.2       0.11   12.5   0.1    3.3  3  DUF87          Helicase HerA, central domain
      0.058   13.8   1.5        7.5    7.0   0.0    3.1  3  AAA_17         AAA domain
      0.063   13.0   1.4         11    5.7   0.0    3.3  4  IstB_IS21      IstB-like ATP binding protein
      0.086   12.4   3.0         11    5.6   0.1    3.6  4  cobW           CobW/HypB/UreG, nucleotide-binding domain
        0.1   12.2   0.0       0.25   11.0   0.0    1.6  1  ATP-synt_ab    ATP synthase alpha/beta family, nucleotide-bin
       0.13   12.1   6.1        2.5    8.0   0.1    4.3  4  NTPase_1       NTPase
       0.15   12.0   2.2       0.66    9.9   0.1    2.4  2  NACHT          NACHT domain
       0.15   11.8   9.5       0.51   10.0   0.9    3.1  3  AAA_15         AAA ATPase domain
       0.92    8.3   6.2       0.93    8.3   0.1    3.0  3  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
       0.93    8.1   7.6        2.5    6.6   0.0    3.3  4  AAA_13         AAA domain
        1.5    8.4   4.5        9.8    5.7   0.0    3.0  3  AAA_27         AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.3   0.0   2.5e-23   1.3e-20       1     137 []      18     191 ..      18     191 .. 0.90
   2 ?   -2.1   0.2       9.3     5e+03      55      94 ..     256     281 ..     224     322 .. 0.49
   3 !   84.9   0.0   1.3e-26   7.1e-24       1     137 []     343     473 ..     343     473 .. 0.89

  Alignments for each domain:
  == domain 1  score: 74.3 bits;  conditional E-value: 2.5e-23
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l + s++++e   ++++G nGaGKSt++k+l+g +  + Gei            ++  ++ig+l+q ++  +e tvr
  gi|474934150|ref|YP_007687732.1|  18 LTDASIQINEHDAIGLIGINGAGKSTFIKILLGIEPCDTGEI------------TRRTRRIGYLEQFAESSREFTVR 82 
                                       568899************************************............678999***************** PP

                                       HH..................................................HHHTCHHHHHHHSTTGGTTCBGEST CS
                                       xx..................................................xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en..................................................esdeeiekalsklglkelkdtvvks 104
                                       +                                                   ++++++   l+++gl+    + +++
  gi|474934150|ref|YP_007687732.1|  83 DVlgrpyghienirrrmaeidelmasgkdnidwnglateyadleqklancdiADEKKLIFCLEEVGLSR---DLMDR 156
                                       ***************************999999999999988888888888777788888888888877...55555 PP

                                       TSGGS-HHHHHHHHHHHHHHH..TSSEEEEESTTT CS
                                       xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx RF
                          ABC_tran 105 spssLSgGqkqrvalarallk..kpkllllDEpta 137
                                        + +LSgG++ +v+lar++++  + ++l++DEpt+
  gi|474934150|ref|YP_007687732.1| 157 TMDTLSGGERTKVMLARIVVQaeECDILIMDEPTS 191
                                       68****************98622568*******96 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 9.3
                                       HHCCHCEEEE-SS--S-TTSBHHHHHHHTCHHHHHHHSTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  55 eslrkeigvlpqepqlfpeltvrenesdeeiekalsklgl 94 
                                       ++ ++e++ + q ++ ++               ++++l+ 
  gi|474934150|ref|YP_007687732.1| 256 QRQEREWEKYNQAKRTQEA--------------IAERLRH 281
                                       3333333333333222222..............2222222 PP

  == domain 3  score: 84.9 bits;  conditional E-value: 1.3e-26
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltv 76 
                                       l++v+l++++g k++i+G nG GK+tL+k+l+++   t+Ge+           ++   +++g+++q+ ++l+ +l++
  gi|474934150|ref|YP_007687732.1| 343 LEHVNLDIRKGDKIGIFGANGQGKTTLVKALLEEIPVTAGEL-----------WTAPGNKVGYYSQHhENLDLRLSA 408
                                       679***************************************...........889***********999*****99 PP

                                       HHH.......HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  77 ren.......esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       +e+       e ++e+ ++l ++ l +   + v++ +s+LSgGq+ rvala +l+++ ++l+lDEpt+
  gi|474934150|ref|YP_007687732.1| 409 EEQllvymgkEHRAEARQMLGRFLLFG---DAVERPMSTLSGGQRCRVALAVLLMRETNVLVLDEPTN 473
                                       999***865555555555555555555...7777778******************************8 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.8e-05    0.0097       3      22 ..      32      51 ..      31     113 .. 0.80
   2 !   11.0   0.0   0.00051      0.28     235     303 .]     159     223 ..     147     223 .. 0.77
   3 !    8.1   0.1    0.0038       2.1       3      19 ..     357     373 ..     356     381 .. 0.93
   4 !   20.8   0.0   5.3e-07   0.00029     219     303 .]     420     505 ..     386     505 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.8e-05
                            AAA_21  3 vliGpNgsGKSnLLdaldll 22
                                      +liG Ng+GKS+++++l ++
  gi|474934150|ref|YP_007687732.1| 32 GLIGINGAGKSTFIKILLGI 51
                                      69***************877 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00051
                            AAA_21 235 relSdGtkrl..lalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpllld 303
                                       + lS G +    la ++  ++ +   ++l+ DEp ++L+   ++ l ++l ++sr    v++++H+ ++ld
  gi|474934150|ref|YP_007687732.1| 159 DTLSGGERTKvmLARIVVQAEEC---DILIMDEPTSHLDIDTIEWLEDFL-LKSR--CAVLVVSHDRYFLD 223
                                       55666655551146666666666...9*************9999999999.6666..99******988876 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0038
                            AAA_21   3 vliGpNgsGKSnLLdal 19 
                                       ++ G+Ng GK++L +al
  gi|474934150|ref|YP_007687732.1| 357 GIFGANGQGKTTLVKAL 373
                                       699*************9 PP

  == domain 4  score: 20.8 bits;  conditional E-value: 5.3e-07
                            AAA_21 219 r.......gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrn 288
                                                 +fl  gd  e+p++ lS G++   al+++l r      +l++DEp n L+  + + + e l e    
  gi|474934150|ref|YP_007687732.1| 420 HraearqmLGRFLLFGDAVERPMSTLSGGQRCRVALAVLLMRET---NVLVLDEPTNYLDIPARHAIEEALTEY--- 490
                                       0334444577999****************874446666666644...8********************888554... PP

                            AAA_21 289 gaQviltTHSpllld 303
                                       ++ +i +TH+ ++ld
  gi|474934150|ref|YP_007687732.1| 491 DGTIITVTHDRYFLD 505
                                       779******988876 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.0   1.2e-11   6.3e-09      25     211 ..      29     232 ..      17     239 .. 0.84
   2 ?    5.6   0.1     0.017       9.5      28      44 ..     357     373 ..     341     376 .. 0.83
   3 !   11.7   0.0   0.00023      0.13     136     205 ..     444     507 ..     401     519 .. 0.85

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 1.2e-11
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--.BTTCSSTTEEEEEEEE.EETTEESSSSSSCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk.skekasvkkaeveitf.dnedkklkiekeevsi 99 
                                           ++G NG+GKs ++  +   LG +   +   ++ ++ i + ++  +s+ + +v  ++ +  ++ ++i++   +i
  gi|474934150|ref|YP_007687732.1|  29 DAIGLIGINGAGKSTFIKIL---LGIEPCDTGEITRRTRRIGYlEQFAESSREFTVRDVLgRPYGHIENIRRRMAEI 102
                                       456789**********9877...999887777777777777775555666667777777734556667888888888 PP

                                       EEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT......................CS-HHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................xxxxxxxxxxxxxxxxxxx RF
                             SMC_N 100 srrvkrkgeseykingkevtkkevsellesagiske......................lLSgGektLvalaLlfAiq 154
                                          + ++++ ++  ng   +++++++ l++ +i  e                      +LSgGe+t v+la +  + 
  gi|474934150|ref|YP_007687732.1| 103 DELMASGKD-NIDWNGLATEYADLEQKLANCDIADEkklifcleevglsrdlmdrtmdTLSGGERTKVMLARI--VV 176
                                       877766665.9************************9***********************************99..78 PP

                                       CCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-.SCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                             SMC_N 155 kvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemleka.dklvgv 211
                                       +++   + ++De  ++LD   ++ + ++l +++  + ++v+s+++ +l k+  k+v +
  gi|474934150|ref|YP_007687732.1| 177 QAEECDILIMDEPTSHLDIDTIEWLEDFLLKSR--CAVLVVSHDRYFLDKMaVKMVEI 232
                                       889999***********************9999..9************9984556655 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.017
                                       EEEESTTSSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxx RF
                             SMC_N  28 aivGpNGSGKsnlldAi 44 
                                        i G+NG GK+ l+ A+
  gi|474934150|ref|YP_007687732.1| 357 GIFGANGQGKTTLVKAL 373
                                       699************98 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00023
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemleka 205
                                       +LSgG++  vala+l     ++ + + +lDe    LD   ++++ e l e      +i +++++ +l  +
  gi|474934150|ref|YP_007687732.1| 444 TLSGGQRCRVALAVL----LMRETNVLVLDEPTNYLDIPARHAIEEALTEYD--GTIITVTHDRYFLDSV 507
                                       7******99888887....5899999***********************999..7899999998888765 PP

>> ABC_tran_Xtn  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7  12.3   1.9e-14     1e-11       1      79 [.     230     308 ..     230     315 .. 0.93
   2 ?    2.7   0.0      0.23   1.3e+02       1      17 [.     512     528 ..     512     531 .. 0.92

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 1.9e-14
                      ABC_tran_Xtn   1 velengklteYkGnYseyleekeerleqqqkayekqqkeikkleefIerfrakakkakqaqsrekaLeklekiekpe 77 
                                       ve+engk +eY+GnYs+++ +k  +l++q+++ ek  +  + +e++ er+r     a+  + rek++ k+e  +kpe
  gi|474934150|ref|YP_007687732.1| 230 VEIENGKTREYRGNYSQFVMKKMLDLQRQEREWEKYNQAKRTQEAIAERLRHDQWYAATYKTREKMIAKMEVKQKPE 306
                                       79**************************************************************************5 PP

                      ABC_tran_Xtn  78 ek 79 
                                       e 
  gi|474934150|ref|YP_007687732.1| 307 EF 308
                                       53 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.23
                      ABC_tran_Xtn   1 velengklteYkGnYse 17 
                                       +e+++gk+  Y G Yse
  gi|474934150|ref|YP_007687732.1| 512 IEVKDGKAIPYAGTYSE 528
                                       6999***********97 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.2e-06   0.00066       2     111 ..      31     143 ..      30     146 .. 0.68
   2 !    9.3   0.1    0.0021       1.1       1      23 [.     355     377 ..     355     393 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.2e-06
                                       EEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSE.EEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHC. CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltge.kaivsdkpgtTrdi.negrvklkgkeielvDtpGliegaseekglgkaflalee. 75 
                                       ++++G   +GKSt+i+ l+g   + ++++   Tr i   ++++++ +e+++ D+ G     + e ++++++++++e 
  gi|474934150|ref|YP_007687732.1|  31 IGLIGINGAGKSTFIKILLGIePCDTGEITRRTRRIgYLEQFAESSREFTVRDVLGRPY-GHIE-NIRRRMAEIDEl 105
                                       89******************7589************55556777779*********432.1222.456666655553 PP

                                       TSEEEEEEETT..TTCSHHHHHHHHHHHHHTTSEEEEE CS
                          MMR_HSR1  76 adlillvvdas..eeklkpldeeleelleeakkplilv 111
                                       +      +d +   +++++l+++l+++   ++k+li++
  gi|474934150|ref|YP_007687732.1| 106 MASGKDNIDWNglATEYADLEQKLANCDIADEKKLIFC 143
                                       33333444433543346666666666665566666665 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0021
                                       EEEEEESTTSSHHHHHHHHHTST CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltgek 23 
                                       +++i+G    GK+tL++al++e 
  gi|474934150|ref|YP_007687732.1| 355 KIGIFGANGQGKTTLVKALLEEI 377
                                       699****************9973 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   2.1e-06    0.0011       1      90 [.      31     169 ..      31     331 .. 0.71
   2 !    7.3   0.0    0.0081       4.4       1      40 [.     356     394 ..     356     464 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.1e-06
                                       EEEEEBTTTTHHHHHHHHHTS--S---SSS---S-EEEEE.....................CCT---C.CS...SSE CS
                         Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrrplelql.....................geeeeas.eravkeel 55 
                                       i ++G   +GKS+++  Llg +  p +++ +Trr+  + +                     g+ e+++  +a+++el
  gi|474934150|ref|YP_007687732.1|  31 IGLIGINGAGKSTFIKILLGIE--PCDTGEITRRTRRIGYleqfaessreftvrdvlgrpyGHIENIRrRMAEIDEL 105
                                       67899999**************..****************5555555555555555555552222222333344444 PP

                                       EEET-EB--CHHHHHHHHHHHHHHHTSSSS--SS...............................- CS
                         Dynamin_N  56 kekekkledfsevreeieketekiagankgiskk...............................v 90 
                                           k+  d++ +++e+ + ++k+a  n +i ++                               v
  gi|474934150|ref|YP_007687732.1| 106 MASGKDNIDWNGLATEYADLEQKLA--NCDIADEkklifcleevglsrdlmdrtmdtlsggertkV 169
                                       4445555555555555555555555..222222233444444444444444444444444444443 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0081
                                       EEEEEBTTTTHHHHHHHHHTS--S---SSS---S-EEEEE CS
                         Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrrplelql 40 
                                       i ++G+  +GK++++ aLl+e   ++  ++ T+  +++ +
  gi|474934150|ref|YP_007687732.1| 356 IGIFGANGQGKTTLVKALLEEI-PVTAGELWTAPGNKVGY 394
                                       789****************874.55555566666666655 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1   0.00015     0.084      14      39 ..      20      45 ..      16      50 .. 0.86
   2 !   10.7   0.0   0.00063      0.34      17      42 ..     348     373 ..     342     375 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00015
                            AAA_29 14 ghtieidlkgatlltGpsGsGKSTll 39
                                      + +i+i++++a+ l+G +G+GKST++
  gi|474934150|ref|YP_007687732.1| 20 DASIQINEHDAIGLIGINGAGKSTFI 45
                                      5678999999999***********98 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00063
                            AAA_29  17 ieidlkgatlltGpsGsGKSTllDAi 42 
                                       ++i+  + + + G++G GK+Tl+ A+
  gi|474934150|ref|YP_007687732.1| 348 LDIRKGDKIGIFGANGQGKTTLVKAL 373
                                       5666444888************9886 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   0.00025      0.14     101     135 ..      30      64 ..      18      67 .. 0.87
   2 !    9.0   0.0    0.0023       1.2      84     129 ..     337     383 ..     290     392 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00025
                                       EEEEECSTTSSHHHHHHHHCTT-----S------- CS
                       RsgA_GTPase 101 tsvlvGqSGvGKStLinallpelelktgevseklg 135
                                        + l+G  G+GKSt+i+ ll+ +   tge+ ++++
  gi|474934150|ref|YP_007687732.1|  30 AIGLIGINGAGKSTFIKILLGIEPCDTGEITRRTR 64 
                                       56699****************99*******98875 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0023
                                       TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S- CS
                       RsgA_GTPase  84 aktkegleelkellkd.ktsvlvGqSGvGKStLinallpelelktge 129
                                       + + + le+++  +++ + + + G  G GK+tL++all+e  +  ge
  gi|474934150|ref|YP_007687732.1| 337 KGKPNILEHVNLDIRKgDKIGIFGANGQGKTTLVKALLEEIPVTAGE 383
                                       33445566777677666778899**************9997766665 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0014      0.74      24      49 ..      23      48 ..      11      60 .. 0.80
   2 !    8.5   0.0    0.0016      0.86      17      53 ..     341     377 ..     333     384 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0014
                                      GG-S-SEEEEEEE-TTSSHHHHHHHH CS
                              MeaB 24 akaGraqvvGltGvPGaGkstlveal 49
                                       +  +   +Gl G+ GaGkst+++ l
  gi|474934150|ref|YP_007687732.1| 23 IQINEHDAIGLIGINGAGKSTFIKIL 48
                                      55566678**************9865 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0016
                                       HHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHH CS
                              MeaB  17 ellerllakaGraqvvGltGvPGaGkstlvealglel 53 
                                       ++le++  +  +  ++G+ G  G Gk tlv+al +e+
  gi|474934150|ref|YP_007687732.1| 341 NILEHVNLDIRKGDKIGIFGANGQGKTTLVKALLEEI 377
                                       57777888888899******************98876 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0    0.0099       5.4       4      20 ..      33      49 ..      31     116 .. 0.91
   2 ?    0.1   0.1       1.5   8.2e+02      24      72 ..     272     324 ..     235     331 .. 0.67
   3 !    7.7   0.0    0.0067       3.6       5      24 ..     359     378 ..     356     413 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0099
                            AAA_33  4 lvGlpGsGKstlaerll 20
                                      l+G +G+GKst+++ ll
  gi|474934150|ref|YP_007687732.1| 33 LIGINGAGKSTFIKILL 49
                                      79**********99776 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.5
                            AAA_33  24 g...avllssdtlrrrlfgtdqqsktdytrvldr..lyqilnelarkalsagrn 72 
                                       +   a++l+ d+++ + ++t ++ + +  +v+++    + ++  ++ a ++g+n
  gi|474934150|ref|YP_007687732.1| 272 QeaiAERLRHDQWYAATYKTREKMIAK-MEVKQKpeEFREIRVQIQAAHKSGKN 324
                                       344688888888888887765554432.33333322333344555555566655 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0067
                            AAA_33   5 vGlpGsGKstlaerllkklg 24 
                                        G++G GK+tl++ ll++ +
  gi|474934150|ref|YP_007687732.1| 359 FGANGQGKTTLVKALLEEIP 378
                                       69*************99866 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0      0.11        58       8      26 ..      31      49 ..      25      87 .. 0.77
   2 ?   -0.7   0.1       2.9   1.6e+03      69     117 ..     162     206 ..     121     218 .. 0.69
   3 !   11.6   0.1   0.00045      0.25      10     100 ..     358     471 ..     350     494 .. 0.56

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.11
                            AAA_22  8 lvvtGesGtGKTtllrrll 26
                                      + ++G  G+GK+t ++ ll
  gi|474934150|ref|YP_007687732.1| 31 IGLIGINGAGKSTFIKILL 49
                                      5589**********99876 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.9
                            AAA_22  69 kaerlsseellealeqalraravielliiDEaqh.lrseealeeLrslln 117
                                       ++ + +++ +l+++  ++++++    li DE    l   + +e+L ++l 
  gi|474934150|ref|YP_007687732.1| 162 SG-GERTKVMLARIVVQAEECDI---LIMDEPTShL-DIDTIEWLEDFLL 206
                                       34.56777777888888888866...9999976668.5666666655544 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00045
                            AAA_22  10 vtGesGtGKTtllrrlleqldeeakaee.......................erpevvfvtlpsstsskdllrellra 63 
                                       ++G  G GKTtl++ lle+ +  a   +                       e+  +v++   +  + +++l ++l  
  gi|474934150|ref|YP_007687732.1| 358 IFGANGQGKTTLVKALLEEIPVTAGELWtapgnkvgyysqhhenldlrlsaEEQLLVYMGKEHRAEARQMLGRFLL- 433
                                       89****************9976544444765555555555555555554322222223333333344444333332. PP

                            AAA_22  64 lglelka.........erlsseellealeqalraravielliiDEa 100
                                                            ++++ al+  l +     +l++DE 
  gi|474934150|ref|YP_007687732.1| 434 ------FgdaverpmsTLSGGQRCRVALAVLLMRETN--VLVLDEP 471
                                       ......0222332343355555555666555555555..7777775 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.014       7.8       5      22 ..      31      48 ..      28     133 .. 0.86
   2 ?   -0.5   0.0       1.6   8.5e+02      71      87 ..     195     211 ..     179     222 .. 0.85
   3 !    8.5   0.2    0.0028       1.5       3      22 ..     354     373 ..     352     382 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.014
                            AAA_24  5 iliyGpsgiGKTtlakel 22
                                      i ++G +g+GK+t++k l
  gi|474934150|ref|YP_007687732.1| 31 IGLIGINGAGKSTFIKIL 48
                                      789************977 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.6
                            AAA_24  71 iDtideleelclaevir 87 
                                       iDti++le++ l+  + 
  gi|474934150|ref|YP_007687732.1| 195 IDTIEWLEDFLLKSRCA 211
                                       9********99888775 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0028
                            AAA_24   3 lkiliyGpsgiGKTtlakel 22 
                                        ki i+G +g GKTtl+k l
  gi|474934150|ref|YP_007687732.1| 354 DKIGIFGANGQGKTTLVKAL 373
                                       699**************988 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.2      0.12        66       4      55 ..      33     102 ..      30     147 .. 0.56
   2 ?    0.5   0.2       1.2   6.5e+02     118     148 ..     262     292 ..     214     323 .. 0.73
   3 !   11.6   0.0   0.00045      0.24       1      22 [.     355     376 ..     355     428 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.12
                            AAA_28   4 itGgestGKTtlleaLa...........ar....gyp.vvpEaareileekl.akgedalpwv.edllaf 55 
                                       ++G  ++GK+t ++ L            +r    gy   ++E+ re++      +  ++++   +++ ++
  gi|474934150|ref|YP_007687732.1|  33 LIGINGAGKSTFIKILLgiepcdtgeitRRtrriGYLeQFAESSREFTVRDVlGRPYGHIENIrRRMAEI 102
                                       6777888888888777666666555554112335333245666666655444455555555554433333 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.2
                            AAA_28 118 apeidddgeR.redleereaiderlrealrel 148
                                       ++++ + + R +e  +er + d++  ++++++
  gi|474934150|ref|YP_007687732.1| 262 WEKY-NQAKRtQEAIAERLRHDQWYAATYKTR 292
                                       4444.333441467777777777777777765 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00045
                            AAA_28   1 kivitGgestGKTtlleaLaar 22 
                                       ki i+G+ + GKTtl++aL ++
  gi|474934150|ref|YP_007687732.1| 355 KIGIFGANGQGKTTLVKALLEE 376
                                       5789***************876 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.038        21      19      40 ..      28      49 ..       9      59 .. 0.82
   2 ?   -2.4   0.0       8.2   4.5e+03      78     103 ..     179     204 ..     173     221 .. 0.62
   3 !    9.1   0.0    0.0023       1.2      19      45 ..     353     379 ..     336     398 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.038
                                      TEEEEEEESTTSSHHHHHHHHH CS
                              TsaE 19 gdvilLeGdLGaGKTtlvrgla 40
                                      +d+i L G  GaGK+t+++ l+
  gi|474934150|ref|YP_007687732.1| 28 HDAIGLIGINGAGKSTFIKILL 49
                                      678999************9875 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 8.2
                                       HHHHHCTTCCCCSTSCEEEEETGGGG CS
                              TsaE  78 eeleelgleeyleeeavvlvEWpekl 103
                                       ee++ l ++e +++  +  +EW e +
  gi|474934150|ref|YP_007687732.1| 179 EECDILIMDEPTSHLDIDTIEWLEDF 204
                                       55555555555544468899999983 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0023
                                       TEEEEEEESTTSSHHHHHHHHHHHTT- CS
                              TsaE  19 gdvilLeGdLGaGKTtlvrglakalgv 45 
                                       gd i + G  G GKTtlv++l++++ v
  gi|474934150|ref|YP_007687732.1| 353 GDKIGIFGANGQGKTTLVKALLEEIPV 379
                                       5668889999************99866 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.7    0.0061       3.3       1      18 [.      31      48 ..      31     196 .. 0.73
   2 ?   -1.4   0.2       5.9   3.2e+03      30      30 ..     284     284 ..     231     351 .. 0.55
   3 !    8.8   0.0     0.004       2.2       1      25 [.     356     392 ..     356     434 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0061
                            AAA_18  1 IlltGtpGvGKttlakeL 18
                                      I+l G+ G+GK+t+ k L
  gi|474934150|ref|YP_007687732.1| 31 IGLIGINGAGKSTFIKIL 48
                                      899*************99 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 5.9
                            AAA_18  30 d 30 
                                        
  gi|474934150|ref|YP_007687732.1| 284 W 284
                                       1 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.004
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf............g 25 
                                       I++ G+ G GKttl k+L ++  +            +
  gi|474934150|ref|YP_007687732.1| 356 IGIFGANGQGKTTLVKALLEEIPVtagelwtapgnkV 392
                                       89****************8875334555555554443 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.24   1.3e+02       2      20 ..      31      49 ..      30      84 .. 0.90
   2 ?   10.0   0.0    0.0011      0.58       2      23 ..     356     377 ..     355     405 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.24
                              MobB  2 lgivgksgsGKTtLlekli 20
                                      +g++g +g+GK t+++ l+
  gi|474934150|ref|YP_007687732.1| 31 IGLIGINGAGKSTFIKILL 49
                                      799************9887 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0011
                              MobB   2 lgivgksgsGKTtLleklipel 23 
                                       +gi g +g+GKTtL++ l++e+
  gi|474934150|ref|YP_007687732.1| 356 IGIFGANGQGKTTLVKALLEEI 377
                                       7899**************9876 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.62   3.4e+02       3      19 ..      33      49 ..      31      87 .. 0.90
   2 ?   10.8   0.0    0.0009      0.49       3      24 ..     358     379 ..     356     422 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.62
                                      EESSTTSSHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakava 19
                                      l+G  G GK++++k + 
  gi|474934150|ref|YP_007687732.1| 33 LIGINGAGKSTFIKILL 49
                                      89***********9886 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0009
                                       EESSTTSSHHHHHHHHHHHHTH CS
                               AAA   3 lyGppGtGKTllakavakelgv 24 
                                       ++G  G GKT+l+ka+ +e+ v
  gi|474934150|ref|YP_007687732.1| 358 IFGANGQGKTTLVKALLEEIPV 379
                                       689***************9744 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.35   1.9e+02       3      18 ..      33      48 ..      31      61 .. 0.88
   2 ?   10.3   0.0    0.0013      0.71       3      23 ..     358     378 ..     356     401 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.35
                      RNA_helicase  3 lyGpsgeGKStlakeL 18
                                      l G +g GKSt++k L
  gi|474934150|ref|YP_007687732.1| 33 LIGINGAGKSTFIKIL 48
                                      67999*******9986 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0013
                      RNA_helicase   3 lyGpsgeGKStlakeLakall 23 
                                       ++G++g+GK+tl+k L +++ 
  gi|474934150|ref|YP_007687732.1| 358 IFGANGQGKTTLVKALLEEIP 378
                                       89*************988875 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1  15.4       1.9     1e+03      15     195 ..      23     318 ..      10     321 .. 0.53
   2 ?   13.5   0.2   0.00014     0.074      22      39 ..     356     373 ..     341     374 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.9
                            AAA_23  15 idF.skgltlItGpNGaGKTTildAikla...Lygetprlsrksgrgfeksdveiese..............gkvka 73 
                                       i+  ++    ++G NGaGK+T++  +  +    +ge +r  r+ g  + ++  e + e              ++ ++
  gi|474934150|ref|YP_007687732.1|  23 IQInEHDAIGLIGINGAGKSTFIKILLGIepcDTGEITRRTRRIG--YLEQFAESSREftvrdvlgrpyghiENIRR 97 
                                       5555556677899********998777652215787777777553..333333333331122333333322211111 PP

                            AAA_23  74 y.veltfenkdgrytrsiererelskkkgkttkkaklelleideleqfise..llgskki..ilnlilflgqer... 142
                                         +e++    +g+  ++i+++   ++    ++k a+ ++ ++++l   i    ++g + +    ++  + g er   
  gi|474934150|ref|YP_007687732.1|  98 RmAEIDELMASGK--DNIDWNGLATEYADLEQKLANCDIADEKKL---IFCleEVGLSRDlmDRTMDTLSGGERtkv 169
                                       1233332223332..344444444444333333333333322222...11111222222211112222223333444 PP

                            AAA_23 143 ............................................................................. 142
                                                                                                                    
  gi|474934150|ref|YP_007687732.1| 170 mlarivvqaeecdilimdeptshldidtiewledfllksrcavlvvshdryfldkmavkmveiengktreyrgnysq 246
                                       44444444444556655556666666666555555555555555555555555555555555555555555555555 PP

                            AAA_23 143 ...feefelkdkkerleelekeleeledekkllekl................eqekekekeleeleeeleei 195
                                          +++++l++++ ++e+++++++++e++++ l++                  + k+k +e+ e++ +++ +
  gi|474934150|ref|YP_007687732.1| 247 fvmKKMLDLQRQEREWEKYNQAKRTQEAIAERLRHDqwyaatyktrekmiakMEVKQKPEEFREIRVQIQAA 318
                                       55555555555556**************99999999999999999999988657788888999999999876 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00014
                            AAA_23  22 tlItGpNGaGKTTildAi 39 
                                         I+G NG GKTT++ A+
  gi|474934150|ref|YP_007687732.1| 356 IGIFGANGQGKTTLVKAL 373
                                       57*************997 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.97   5.3e+02     126     152 ..      25      51 ..      18      74 .. 0.82
   2 ?   11.3   0.0   0.00025      0.13     106     160 ..     330     384 ..     245     401 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.97
                             T2SSE 126 vrerglilvsGgTgsGKttllyallke 152
                                       ++e+  i + G  g GK+t++ +ll +
  gi|474934150|ref|YP_007687732.1|  25 INEHDAIGLIGINGAGKSTFIKILLGI 51 
                                       5567777788999********999875 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00025
                             T2SSE 106 ddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderi 160
                                       d  +a e+ k++i e ++  +r+   i + G+ g GKttl+ all+ei+ +  ++
  gi|474934150|ref|YP_007687732.1| 330 DCAVAYEKGKPNILEHVNLDIRKGDKIGIFGANGQGKTTLVKALLEEIPVTAGEL 384
                                       334566777899999999******************************9876665 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.078        42      56      74 ..      31      49 ..      18      54 .. 0.84
   2 ?    7.9   0.0    0.0028       1.5      54      77 ..     354     377 ..     329     384 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.078
                            DUF815 56 vLLwGarGtGKSslvkall 74
                                      + L+G  G+GKS+ +k ll
  gi|474934150|ref|YP_007687732.1| 31 IGLIGINGAGKSTFIKILL 49
                                      5599************886 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0028
                            DUF815  54 nnvLLwGarGtGKSslvkallney 77 
                                        ++ ++Ga G GK +lvkall+e+
  gi|474934150|ref|YP_007687732.1| 354 DKIGIFGANGQGKTTLVKALLEEI 377
                                       566689**************9986 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.74     4e+02      27      49 ..      31      52 ..      18     167 .. 0.63
   2 ?   10.7   0.0   0.00096      0.52      29      63 ..     358     394 ..     343     476 .. 0.59

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.74
                            AAA_16 27 vllsGesGvGKsslvrellrale 49
                                      + l+G  G GKs+ ++ ll  +e
  gi|474934150|ref|YP_007687732.1| 31 IGLIGINGAGKSTFIKILL-GIE 52
                                      5688999*****9998777.344 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00096
                            AAA_16  29 lsGesGvGKsslvrellralekd..ggiflrgkcdql 63 
                                       + G+ G GK++lv++ll+++  +  + +++ g+ + +
  gi|474934150|ref|YP_007687732.1| 358 IFGANGQGKTTLVKALLEEIPVTagELWTAPGNKVGY 394
                                       779***************8887765355555555554 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.048        26      22      44 ..      25      49 ..       9      50 .. 0.75
   2 ?    0.2   2.2       1.2   6.7e+02     130     182 ..     257     315 ..     226     347 .. 0.72
   3 ?   12.5   0.1   0.00021      0.11      24      47 ..     354     377 ..     344     382 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.048
                             DUF87 22 vtrH..lAilgsTGsGKSntvavLl 44
                                      +++H  ++ +g  G+GKS+++++Ll
  gi|474934150|ref|YP_007687732.1| 25 INEHdaIGLIGINGAGKSTFIKILL 49
                                      5555225669************997 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.2
                             DUF87 130 a......keekeklssdepveklleelkkekeelrklknqaiarlldkledllrkggsf 182
                                       +      k ++ k + +++ e+l+++ ++ +++  ++k+ a++++++k e++ + + ++
  gi|474934150|ref|YP_007687732.1| 257 RqereweKYNQAKRTQEAIAERLRHDQWYAATYKTREKMIAKMEVKQKPEEFREIRVQI 315
                                       13444435677777777777777777788888999999999999999999998887777 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 0.00021
                             DUF87  24 rHlAilgsTGsGKSntvavLleel 47 
                                         ++i+g  G GK+++v+ Llee+
  gi|474934150|ref|YP_007687732.1| 354 DKIGIFGANGQGKTTLVKALLEEI 377
                                       579*******************98 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.014       7.5       1      67 [.      34      97 ..      34     163 .. 0.64
   2 ?   -1.1   0.2       4.3   2.4e+03      43      78 ..     292     330 ..     250     351 .. 0.59
   3 ?    4.5   0.0     0.083        45       1      29 [.     359     384 ..     359     449 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.014
                                      EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHH CS
                            AAA_17  1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrklpleekkelqkeaaekiae 67
                                      +G+ G+GK+t ++ l   +g++   +G++ r + + g l++  +  r+   ++        +e+i++
  gi|474934150|ref|YP_007687732.1| 34 IGINGAGKSTFIKIL---LGIEPCDTGEITRRTRRIGYLEQFAESSREFTVRDVLGRPYGHIENIRR 97
                                      59**********554...8999999999999999888888877777776666655544444444444 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 4.3
                                       HHHHC...TSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE CS
                            AAA_17  43 rdemr...klpleekkelqkeaaekiaeeakkkgvlvdg 78 
                                       r++m    ++++++++    +++ + a++++k+ +l++ 
  gi|474934150|ref|YP_007687732.1| 292 REKMIakmEVKQKPEEFREIRVQIQAAHKSGKNVFLMKD 330
                                       333332212222222222223344445555555555555 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.083
                                       EE-TTSSHHHHHHHHHHHHTEEEEEHHHH CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdl 29 
                                       +G  G GK+t+++ l e++ +t   aG+l
  gi|474934150|ref|YP_007687732.1| 359 FGANGQGKTTLVKALLEEIPVT---AGEL 384
                                       6999************998754...4555 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.021        11      44      79 ..      25      61 ..      15      85 .. 0.81
   2 ?   -2.2   0.0       5.4   2.9e+03      95     117 ..     167     189 ..     158     197 .. 0.80
   3 ?   -2.1   0.0         5   2.7e+03     153     174 ..     261     282 ..     252     304 .. 0.71
   4 ?    4.3   0.0     0.054        29      44      68 ..     350     374 ..     309     395 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.021
                         IstB_IS21 44 iekkenivllGpsGvGKs.hlaialgveavraglsvl 79
                                      i+++++i l+G  G+GKs ++ i lg e + +g  ++
  gi|474934150|ref|YP_007687732.1| 25 INEHDAIGLIGINGAGKStFIKILLGIEPCDTGEITR 61
                                      7899*************63778999999999886655 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.4
                         IstB_IS21  95 rdgklaralkrllkvdllilDdl 117
                                       ++  lar++ +  ++d+li+D+ 
  gi|474934150|ref|YP_007687732.1| 167 TKVMLARIVVQAEECDILIMDEP 189
                                       5566788899999999****995 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 5
                         IstB_IS21 153 ewdevlgdatlatAilDRlvHh 174
                                       ew++  + +   +Ai  Rl H+
  gi|474934150|ref|YP_007687732.1| 261 EWEKYNQAKRTQEAIAERLRHD 282
                                       5666666666666666666664 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.054
                         IstB_IS21  44 iekkenivllGpsGvGKshlaialg 68 
                                       i+k + i ++G  G GK+ l  al 
  gi|474934150|ref|YP_007687732.1| 350 IRKGDKIGIFGANGQGKTTLVKALL 374
                                       78899999************99985 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1      0.13        72       3      21 ..      31      49 ..      29      60 .. 0.83
   2 ?    1.6   0.0      0.33   1.8e+02      39      61 ..     215     237 ..     208     261 .. 0.88
   3 ?    5.6   0.1      0.02        11       4      22 ..     357     375 ..     355     384 .. 0.86
   4 ?   -3.1   0.0         9   4.9e+03      38      60 ..     496     518 ..     493     520 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.13
                                      EEEEESTTCCHHHHHHHHH CS
                              cobW  3 tvltGflGsGKTtLlnhll 21
                                      ++l G  G+GK+t+++ ll
  gi|474934150|ref|YP_007687732.1| 31 IGLIGINGAGKSTFIKILL 49
                                      67899**********9887 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.33
                                       CHCCCCCCHCCCT.EEEETTTTE CS
                              cobW  39 vsiDaellretgveivelenGci 61 
                                       vs+D+ +l++ +v++ve+enG+ 
  gi|474934150|ref|YP_007687732.1| 215 VSHDRYFLDKMAVKMVEIENGKT 237
                                       789******************85 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.02
                                       EEEESTTCCHHHHHHHHHC CS
                              cobW   4 vltGflGsGKTtLlnhlle 22 
                                       ++ G  G GKTtL+++lle
  gi|474934150|ref|YP_007687732.1| 357 GIFGANGQGKTTLVKALLE 375
                                       678999**********996 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 9
                                       SCHCCCCCCHCCCT.EEEETTTT CS
                              cobW  38 evsiDaellretgveivelenGc 60 
                                       +v +D+ +l++ +++++e+++G+
  gi|474934150|ref|YP_007687732.1| 496 TVTHDRYFLDSVCTSVIEVKDGK 518
                                       578999999999999****9997 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00046      0.25      11      37 ..     350     376 ..     346     426 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00046
                                       EBTT-EEEEEESTTSSHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  11 ivqGqrtlipgafgvGktvisqslskq 37 
                                       i +G +++i+ga+g Gkt+++++l+++
  gi|474934150|ref|YP_007687732.1| 350 IRKGDKIGIFGANGQGKTTLVKALLEE 376
                                       679******************999876 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.71   3.9e+02       3      19 ..      32      48 ..      30     101 .. 0.86
   2 ?    2.5   0.3      0.23   1.2e+02      83     135 ..     168     219 ..     132     241 .. 0.67
   3 ?    8.0   0.1    0.0046       2.5       2      23 ..     356     377 ..     355     391 .. 0.89
   4 ?   -0.8   0.0       2.3   1.2e+03      94     137 ..     461     504 ..     443     521 .. 0.64

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.71
                                      EEE--TTSSHHHHHHHH CS
                          NTPase_1  3 fiTGppGvGKtTlvkkv 19
                                       + G  G GK+T++k +
  gi|474934150|ref|YP_007687732.1| 32 GLIGINGAGKSTFIKIL 48
                                      5678899*****99754 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.23
                                       HHHHHHHHHHHHHH-EEEE---STTGGG-HHHHHHHHHHHTTTSEEEEE--SS CS
                          NTPase_1  83 elalealrkalseadviviDEiGkmElkskkfkeaveevLksekpvlavihrr 135
                                       +++l+ +  + +e+d++++DE  +  l + +++   + +Lks   vl+v h r
  gi|474934150|ref|YP_007687732.1| 168 KVMLARIVVQAEECDILIMDEPTS-HLDIDTIEWLEDFLLKSRCAVLVVSHDR 219
                                       566666666779********9422.2333333222233455666666666666 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0046
                                       EEEE--TTSSHHHHHHHHHHHH CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlell 23 
                                       + i G  G+GKtTlvk +le++
  gi|474934150|ref|YP_007687732.1| 356 IGIFGANGQGKTTLVKALLEEI 377
                                       7789*************99987 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 2.3
                                       HHH-EEEE---STTGGG-HHHHHHHHHHHT.TTSEEEEE--SS-.- CS
                          NTPase_1  94 seadviviDEiGkmElkskkfkeaveevLk.sekpvlavihrrk.d 137
                                       +e++v+v+DE  +  +     ++a+ee+L+  +  +++v h r   
  gi|474934150|ref|YP_007687732.1| 461 RETNVLVLDE--PTNYLDIPARHAIEEALTeYDGTIITVTHDRYfL 504
                                       6677777777..5555555667888888886666666666666442 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.3      0.54   2.9e+02       5      18 ..      33      46 ..      29      51 .. 0.83
   2 ?    9.9   0.1    0.0012      0.66       5      23 ..     358     376 ..     354     382 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.54
                                      EEC-TTTCHHHHHH CS
                             NACHT  5 lqGeaGsGKTtLlq 18
                                      l G +G GK+t+++
  gi|474934150|ref|YP_007687732.1| 33 LIGINGAGKSTFIK 46
                                      7899********87 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0012
                                       EEC-TTTCHHHHHHHHHHH CS
                             NACHT   5 lqGeaGsGKTtLlqklala 23 
                                       + G++G+GKTtL++ l ++
  gi|474934150|ref|YP_007687732.1| 358 IFGANGQGKTTLVKALLEE 376
                                       77************99876 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.9   0.00094      0.51      15      43 ..      19      48 ..      17      51 .. 0.89
   2 ?   -0.3   0.2       1.2   6.7e+02     235     287 ..     254     312 ..     197     338 .. 0.63
   3 ?    5.7   0.1      0.02        11      16      43 ..     345     373 ..     342     377 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00094
                            AAA_15 15 kdveidlsee.ltvliGkNnsGKSsileal 43
                                       d++i+++e     liG N++GKS+++++l
  gi|474934150|ref|YP_007687732.1| 19 TDASIQINEHdAIGLIGINGAGKSTFIKIL 48
                                      57889999888999**************98 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.2
                            AAA_15 235 eeelteklkeiqeklkeidkklaeelk......kilkkkidkikkfnykgkkneeieik 287
                                       +++ +e   e  +  k +++ +ae+l        ++k   + i k+++k+k++e++ei+
  gi|474934150|ref|YP_007687732.1| 254 DLQRQEREWEKYNQAKRTQEAIAERLRhdqwyaATYKTREKMIAKMEVKQKPEEFREIR 312
                                       34444444444444444555555555555555544444444444555555555555554 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.02
                            AAA_15  16 dveidlsee.ltvliGkNnsGKSsileal 43 
                                       +v +d+ +     + G+N+ GK+++++al
  gi|474934150|ref|YP_007687732.1| 345 HVNLDIRKGdKIGIFGANGQGKTTLVKAL 373
                                       556666665677788*************9 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.28   1.5e+02      13      36 ..      26      49 ..      21      51 .. 0.87
   2 ?   -0.5   0.7       0.8   4.4e+02      91     170 ..     223     298 ..     215     317 .. 0.74
   3 ?    8.3   0.1    0.0017      0.93      17      39 ..     355     377 ..     346     383 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.28
                     TrwB_AAD_bind 13 retqhilivGttGsGKtqalekll 36
                                      +e+  i ++G  G+GK++ ++ ll
  gi|474934150|ref|YP_007687732.1| 26 NEHDAIGLIGINGAGKSTFIKILL 49
                                      5778899***********999887 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.8
                     TrwB_AAD_bind  91 aeiAaalipedggssdpfWaeaartvlaetlrelvrekkksnaallralltadleeLkellagteaaalvaeeaert 167
                                       +++A +++  ++g+ +++  ++++ v++++l  l+r+ ++ ++++ +  +++  e ++e l+  + +a + ++ e++
  gi|474934150|ref|YP_007687732.1| 223 DKMAVKMVEIENGKTREYRGNYSQFVMKKMLD-LQRQ-EREWEKYNQ--AKRTQEAIAERLRHDQWYAATYKTREKM 295
                                       78999999998888888888999999988875.5554.455544444..5677777888888888777777777777 PP

                     TrwB_AAD_bind 168 aas 170
                                        a 
  gi|474934150|ref|YP_007687732.1| 296 IAK 298
                                       665 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0017
                     TrwB_AAD_bind  17 hilivGttGsGKtqalekllrai 39 
                                       +i i+G+ G GKt+ +++ll++i
  gi|474934150|ref|YP_007687732.1| 355 KIGIFGANGQGKTTLVKALLEEI 377
                                       689*****************998 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.087        47      23      38 ..      35      50 ..      19      67 .. 0.84
   2 ?   -1.8   0.3       1.7   9.1e+02     498     578 ..     159     226 ..     151     272 .. 0.59
   3 ?   -1.1   2.8         1   5.6e+02     307     374 ..     250     318 ..     218     324 .. 0.59
   4 ?    6.6   0.0    0.0047       2.5      21      36 ..     358     373 ..     357     415 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.087
                            AAA_13 23 GwNGaGKTtLSrllrs 38
                                      G NGaGK+t+ ++l  
  gi|474934150|ref|YP_007687732.1| 35 GINGAGKSTFIKILLG 50
                                      9********9988865 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.7
                            AAA_13 498 etLSeGEktaIaflYFlkslkeddseigkdkivviDDPvSSLDsnslfivfs.liksrllkkkkakQlfiLTHnlef 573
                                       +tLS GE+t + +     ++  + +   +  i ++D P S LD + +      l+ksr+        +++  H  +f
  gi|474934150|ref|YP_007687732.1| 159 DTLSGGERTKVMLA----RIVVQAE---ECDILIMDEPTSHLDIDTIEWLEDfLLKSRC-------AVLVVSHDRYF 221
                                       68888888888654....4442222...3478888888888887766443331344444.......45555555555 PP

                            AAA_13 574 fkevk 578
                                       + ++ 
  gi|474934150|ref|YP_007687732.1| 222 LDKMA 226
                                       55555 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1
                            AAA_13 307 kavsdeasensafeedkeelkaeaealeeqLkg..lqraleaKrkepfksvelesvkakiesikklvaei 374
                                       k++ d ++ +++  e+++++k+  ea++e+L+   ++ a  + r+++ +++e+++  ++  +i  +++++
  gi|474934150|ref|YP_007687732.1| 250 KKMLDLQR-QEREWEKYNQAKRTQEAIAERLRHdqWYAATYKTREKMIAKMEVKQKPEEFREIRVQIQAA 318
                                       33333333.3334555777777777777777654466666666677777777777777776666666665 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.0047
                            AAA_13  21 iYGwNGaGKTtLSrll 36 
                                       i+G+NG GKTtL ++l
  gi|474934150|ref|YP_007687732.1| 358 IFGANGQGKTTLVKAL 373
                                       9***********8876 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.018       9.8      10      44 ..      11      46 ..       8     128 .. 0.84
   2 ?   -2.4   0.8       5.6     3e+03     181     203 ..     263     285 ..     249     315 .. 0.65
   3 ?    3.4   0.0     0.089        48      31      47 ..     358     374 ..     344     382 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.018
                            AAA_27 10 ryGk...ftdrsldfsaeeadlhliyGpNEAGKstalr 44
                                      ++G+   +td s++++  e+d   ++G N AGKst ++
  gi|474934150|ref|YP_007687732.1| 11 AFGPvhvLTDASIQIN--EHDAIGLIGINGAGKSTFIK 46
                                      5665333589999998..55555567*********876 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.6
                            AAA_27 181 rainealeeleeakkelreaqvr 203
                                       +++n+a+++ e+  ++lr++q  
  gi|474934150|ref|YP_007687732.1| 263 EKYNQAKRTQEAIAERLRHDQWY 285
                                       46666666666666666655544 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.089
                            AAA_27  31 iyGpNEAGKstalrAis 47 
                                       i+G+N  GK+t+++A+ 
  gi|474934150|ref|YP_007687732.1| 358 IFGANGQGKTTLVKALL 374
                                       89************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (605 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       963  (0.0537119); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                        33  (0.00184059); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              33  [number of targets reported over threshold]
# CPU time: 0.81u 0.34s 00:00:01.15 Elapsed: 00:00:00.52
# Mc/sec: 3475.09
//
Query:       gi|474934151|ref|YP_007687733.1|  [L=406]
Description: Isocitrate/isopropylmalate dehydrogenase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-65  220.1   0.1    1.1e-64  218.8   0.1    1.5  1  Iso_dh    Isocitrate/isopropylmalate dehydrogenase


Domain annotation for each model (and alignments):
>> Iso_dh  Isocitrate/isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.8   0.1     6e-69   1.1e-64       2     324 ..      45     359 ..      44     379 .. 0.90

  Alignments for each domain:
  == domain 1  score: 218.8 bits;  conditional E-value: 6e-69
                                       EEEEEESTTHHHHHHHHHHHHHHHHHHHT-EEEEEE---THHHHHHHS...SSS-HHHHHHHHHSSEEEEEE---CS CS
                            Iso_dh   2 iallegdgiGpevveaalkvlkaakekaglelefeevdvGgaaidetg...eplpeetleaikeadvvllgavgtpk 75 
                                       + +  gdgiGp +++ a kvl+ + + + +  ++e +++ g +i++     +++p++t+e +k+ +v+l+g+++tpk
  gi|474934151|ref|YP_007687733.1|  45 VGVCGGDGIGPYICNDARKVLEFMLADKIAAGKVEVRNIDGLTIERRAavmKAIPDDTMEELKKCHVILKGPTTTPK 121
                                       66889*******************9999988888999988888887665669************************* PP

                                       ....SSSSSHHHHHHHHHHHTTEEEEEEEEE-BCCTTCCSSBTHHHHCT-EEEEEEE-SSCGGCSSEEEEETTG.GG CS
                            Iso_dh  76 ....ekevrpengLlaLrkeldlfanlrpvkvfeklkvksplkrevveevdlvivReltggiYfgeekekkgsifte 148
                                             ++++ n  +a+rkeldlfan+rpv v  +             +++   +Re+t+g Y+   + ++    t+
  gi|474934151|ref|YP_007687733.1| 122 kgdqWPNIESAN--VAMRKELDLFANVRPVSVP-A------------LGINWRFFRENTEGSYAVGSNGINV---TD 180
                                       655445566666..****************998.1............1344568**********99998887...58 PP

                                       GEEEEEEEEEHHHHHHHHHHHHHHHHHTTTSEEEEEESTTTTHHHH.HHHHHHHHHHCCTTTTSEEEEEEHHHHHHH CS
                            Iso_dh 149 evavdtklyseeeieriaraafelAlkrgkkkvtlvdKanvlksse.lwrkiveevaeeeypdielehqlvDsaamq 224
                                       + a+d  + +++++eri ra+fe+A+k g + v +++Kan++k+++  + +i+e+va+ +yp+++ ++ ++D ++++
  gi|474934151|ref|YP_007687733.1| 181 DLAIDYCVATTQGTERILRAGFEYAKKTGANYVSVITKANIIKTTDgKFLNIAERVAK-DYPEVRWDDWFIDITTAK 256
                                       9*********************************************999999999999.****************** PP

                                       HHHSG..GGGSEEEE-HHHHHHHHHHHHHHTTSGCC-EEEEEETSS-EEEEESS---CCCTTSS-...S-THHHHHH CS
                            Iso_dh 225 lvksp..kqfdVivtkNlfGDilSDeaaalvGslGllpSaslgekkvaifEavHGsapdiagkdk...aNpiavilS 296
                                       l+     ++f V v +Nl+GDi+ Deaa++ G++G + Sa++g kk a+fEa+HGsap++   +    a p ++i +
  gi|474934151|ref|YP_007687733.1| 257 LLDPArrSAFRVFVLPNLYGDIITDEAAQIQGGVGTAGSANIG-KKYAMFEAIHGSAPRMVDEGRakfADPCSMIKA 332
                                       **755448999********************************.79************99866665569******** PP

                                       HHHHHHHTTT-HHHHHHHHHHHHHHHHH CS
                            Iso_dh 297 aalmLryslgleeaAdkiekAvekvlea 324
                                       +a+mL + +g+ e+A+k++ A++  ++ 
  gi|474934151|ref|YP_007687733.1| 333 VAMMLDH-IGEAEKARKLDMALDVCVQF 359
                                       *******.*************9887764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 2639.51
//
Query:       gi|474934152|ref|YP_007687734.1|  [L=222]
Description: putative DNA binding protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-17   62.0   0.0    4.7e-17   61.5   0.0    1.3  1  HTH_10    HTH DNA binding domain
  ------ inclusion threshold ------
      0.093   12.8   0.0       0.19   11.8   0.0    1.5  1  HTH_Mga   M protein trans-acting positive regulator (MGA) HTH


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.5   0.0   5.3e-21   4.7e-17       1      53 []     156     208 ..     156     208 .. 0.98

  Alignments for each domain:
  == domain 1  score: 61.5 bits;  conditional E-value: 5.3e-21
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaesklie 53 
                                       LT+k+ +++k Ay++GY+d+PRr++l+ L ++lG skstl   Lr ae+kli+
  gi|474934152|ref|YP_007687734.1| 156 LTPKEERYVKSAYDKGYYDVPRRIDLDGLCEALGCSKSTLNVALRTAERKLIA 208
                                       9**************************************************95 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.2e-05      0.19      19      38 ..     177     196 ..     173     201 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.2e-05
                           HTH_Mga  19 ksltldelakeLglseltlq 38 
                                       +++ ld l+++Lg+s +tl+
  gi|474934152|ref|YP_007687734.1| 177 RRIDLDGLCEALGCSKSTLN 196
                                       7999**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.38s 00:00:00.96 Elapsed: 00:00:00.57
# Mc/sec: 1170.77
//
Query:       gi|474934153|ref|YP_007687735.1|  [L=221]
Description: hypothetical protein TALC_00575 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-05   23.9   0.0    0.00012   22.1   0.0    1.8  1  CYTH      CYTH domain


Domain annotation for each model (and alignments):
>> CYTH  CYTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   6.5e-09   0.00012      32      95 ..      45     112 ..      21     216 .. 0.65

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 6.5e-09
                                       EEEEEEEEEE-TTTHHHHTTEEEEEEEETTTEEEEEEEEECSSST....EEEEEEEECCCEEECCCC.H CS
                              CYTH  32 tveqrdtYydtpdrdlartdeaLRiRraegdgeeltlKgpgvdge....reevegevsreEyeepls.d 95 
                                        v+++d Y+d     l ++   LR R + gd++++t+K+p v +     r+e+e+e+ +    +++  +
  gi|474934153|ref|YP_007687735.1|  45 MVRYHDEYFDDAAGTLTSRGVILRYRDK-GDSAFVTIKQPYVKDGlglsRRETETELFKARNLNIIGaV 112
                                       47899*********************88.99999*******9999999999999998844444444352 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1721.44
//
Query:       gi|474934154|ref|YP_007687736.1|  [L=206]
Description: Multimeric flavodoxin WrbA [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.4e-22   77.6   0.0    1.1e-21   77.3   0.0    1.1  1  FMN_red       NADPH-dependent FMN reductase
    2.6e-05   24.0   0.0    4.3e-05   23.3   0.0    1.5  1  Flavodoxin_2  Flavodoxin-like fold
  ------ inclusion threshold ------
      0.016   15.4   0.0      0.079   13.2   0.0    2.0  2  Flavodoxin_5  Flavodoxin domain
        0.1   12.4   0.4        0.1   12.4   0.4    2.1  3  DUF1450       Protein of unknown function (DUF1450)


Domain annotation for each model (and alignments):
>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.3   0.0   2.3e-25   1.1e-21       1     152 [.       1     152 [.       1     155 [. 0.87

  Alignments for each domain:
  == domain 1  score: 77.3 bits;  conditional E-value: 2.3e-25
                                       -EEEEEES--STT-HHHHHHHHHHCCT-T.T-CEEEEETTTS.--.....---HCHGHT.CGGSHHHHHHHHHHHH- CS
                           FMN_red   1 mkilvisGSlrkgsntrklaewaaealkeagaevelidladlilpc...alcdkdlese.gqtsddvaellekiaaa 73 
                                       mk+++i+GS++++++t++ ++++a+al+e++++ e++ +++   +c     c +++  +   ++d v++l ++  + 
  gi|474934154|ref|YP_007687736.1|   1 MKVALINGSPHEKGCTYTDMQEIAKALREQDVDSEIFWIGKEVYGCracGSCREKH--RcVIDGDLVNDLAARFDEF 75 
                                       9**************************************99999997533333333..337889999********** PP

                                       SCEEEEEEECTTCE-HHHHHHHHCHT-.SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHH.HTT-EEEECSEEE CS
                           FMN_red  74 daliivtPeYngsysgllKnalDrlsrtrgkkelrgKpvalvavgggrrgglraeeqlrqvla.elgaivvpraava 149
                                       d+++++ P+Y  ++ + + +++Dr+ +  +   ++gK+ a v  +  rrgg  a  +  + +a + +a+vv++ +++
  gi|474934154|ref|YP_007687736.1|  76 DGFVFGAPVYYSGAAASMCAFMDRFFY-VNASKMAGKVTASV--VNARRGGNSASFERLNQYAlISNAVVVGSQYWN 149
                                       *************************86.88889999999999..456899999998888888879********8888 PP

                                       ETS CS
                           FMN_red 150 vgk 152
                                       + +
  gi|474934154|ref|YP_007687736.1| 150 FTH 152
                                       766 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   9.5e-09   4.3e-05       1     143 [.       1     130 [.       1     171 [. 0.77

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 9.5e-09
                                       -EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCC.T-----CCCCHCCHHHHTT....C.HHHHHHH CS
                      Flavodoxin_2   1 mkiLiinahprpeksfssalaqafvealekagphevtvrdLyad.flpvlttrdlaaklayeek....p.adveseq 71 
                                       mk+ +in++p++ k  ++   q++++al++++  + +++ + ++ +  + +       +  e++        v   +
  gi|474934154|ref|YP_007687736.1|   1 MKVALINGSPHE-KGCTYTDMQEIAKALREQD-VDSEIFWIGKEvYGCRACG------SCREKHrcviDgDLVNDLA 69 
                                       9*********99.7999***************.8999999999733222222......2223334335445566666 PP

                                       HHHHHCSSEEEEEEE-BTTB--HHHHHHHHHHS-TTTSCEETTCSSCCCCTTTTS.EEEEEEEE.SS-GGGSST CS
                      Flavodoxin_2  72 iekllaadaivlqfPlwwfgvPailKgwiDrvltagfafyteeggegrgggLkgk.kalvivtt.Ggpeesyqe 143
                                        +++ + d  v+++P+++ g  a + +++Dr     f+         +  +++gk +a v++++ Gg+ +s+++
  gi|474934154|ref|YP_007687736.1|  70 -ARFDEFDGFVFGAPVYYSGAAASMCAFMDRF----FYV--------NASKMAGKvTASVVNARrGGNSASFER 130
                                       .******************************7....333........346788888888888886777666663 PP

>> Flavodoxin_5  Flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.45     2e+03       8      26 ..      13      32 ..      12      39 .. 0.77
   2 ?   13.2   0.0   1.8e-05     0.079      38      89 ..      69     120 ..      52     137 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.45
                      Flavodoxin_5  8 dGqTkkiaeriaeelree.g 26
                                      +G T + +++ia++lre+ +
  gi|474934154|ref|YP_007687736.1| 13 KGCTYTDMQEIAKALREQdV 32
                                      57788889999999998833 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.8e-05
                      Flavodoxin_5  38 sedlesydavvigasvyygkllpelakFvekhreaLstkpvalfsvsltark 89 
                                       + +++++d +v+ga+vyy++   ++ +F ++     ++k+   ++ s+++ +
  gi|474934154|ref|YP_007687736.1|  69 AARFDEFDGFVFGAPVYYSGAAASMCAFMDRFFYVNASKMAGKVTASVVNAR 120
                                       467899***********************99888888888887777777555 PP

>> DUF1450  Protein of unknown function (DUF1450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.4   2.3e-05       0.1      16      57 ..      20      66 ..      13      74 .. 0.70
   2 ?   -3.4   0.0         2   8.9e+03      45      60 ..      97     112 ..      92     118 .. 0.62
   3 ?   -2.9   0.0       1.3     6e+03      46      59 ..     132     145 ..     130     147 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.3e-05
                           DUF1450 16 tqevleklekd.pdvdvi.....eygClsnCglCakspfAlVnGeiva 57
                                      +qe+ + l+++  d ++       ygC  +Cg C++++ ++++G++v+
  gi|474934154|ref|YP_007687736.1| 20 MQEIAKALREQdVDSEIFwigkeVYGC-RACGSCREKHRCVIDGDLVN 66
                                      555555554332555554223335999.79***************996 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2
                           DUF1450  45 kspfAlVnGeivaaet 60 
                                       ++ f +Vn + +a++ 
  gi|474934154|ref|YP_007687736.1|  97 MDRFFYVNASKMAGKV 112
                                       4567788877766665 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.3
                           DUF1450  46 spfAlVnGeivaae 59 
                                       +++Al+  ++v ++
  gi|474934154|ref|YP_007687736.1| 132 NQYALISNAVVVGS 145
                                       67999998888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       812  (0.0452898); expected 358.6 (0.02)
Passed bias filter:                      637  (0.035529); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1505.45
//
Query:       gi|474934155|ref|YP_007687737.1|  [L=181]
Description: Multimeric flavodoxin WrbA [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.7e-21   75.2   0.0    5.4e-21   74.9   0.0    1.1  1  FMN_red       NADPH-dependent FMN reductase
    4.6e-14   52.6   0.0      6e-14   52.2   0.0    1.2  1  Flavodoxin_2  Flavodoxin-like fold
  ------ inclusion threshold ------
       0.13   12.3   0.0       0.17   11.9   0.0    1.1  1  Ncstrn_small  Nicastrin small lobe


Domain annotation for each model (and alignments):
>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.9   0.0   9.1e-25   5.4e-21       2     120 ..       3     126 ..       2     159 .. 0.79

  Alignments for each domain:
  == domain 1  score: 74.9 bits;  conditional E-value: 9.1e-25
                                       EEEEEES--STT-HHHHHHHHHHCCT-T.T-CEEEEETTTS..--.....---HCHGHTCGGSHHHHHHHHHHHH-S CS
                           FMN_red   2 kilvisGSlrkgsntrklaewaaealkeagaevelidladl.ilpc...alcdkdlesegqtsddvaellekiaaad 74 
                                        i+v+sGS+r ++nt +l+ ++++ ++  g +v++ d+a     +c   + c   ++ ++++ d  + +   i++ad
  gi|474934155|ref|YP_007687737.1|   3 DIVVLSGSPRVKGNTSALVAAFKASAESLGHTVKVYDVAANaLRGCracNGCYRSEDRPCVQTDGWNPIAHDIRNAD 79 
                                       59************************999********99999999966544444444449***************** PP

                                       CEEEEEEECTTCE-HHHHHHHHCHT-..SSCHCCTT-EEEEEEE-SS CS
                           FMN_red  75 aliivtPeYngsysgllKnalDrlsr.trgkkelrgKpvalvavggg 120
                                       +++++ P+Y++++sg++K alDr+ + ++ +     K + l++ +++
  gi|474934155|ref|YP_007687737.1|  80 GVVFAFPIYFYGMSGQMKVALDRMYCfHKLGFDTGEKKASLISCVAD 126
                                       ************************99955555555555555554444 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   0.0     1e-17     6e-14       3     178 ..       4     159 ..       2     178 .. 0.71

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 1e-17
                                       EEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCCT-----CCCCHC.C..HHHHTTC.HHHHHHH..HH CS
                      Flavodoxin_2   3 iLiinahprpeksfssalaqafvealekagphevtvrdLyadflpvlttrdlaa.k..layeekp.adveseq..ie 73 
                                       i+++ ++pr  k ++sal +af +++e+ g h+v+v d++a  l  +++    + +  +++++ p + ++  +   +
  gi|474934155|ref|YP_007687737.1|   4 IVVLSGSPRV-KGNTSALVAAFKASAESLG-HTVKVYDVAANALRGCRA----CnGcyRSEDR-PcVQTDGWNpiAH 73 
                                       899*******.7******************.**********63333332....2325344444.5566666666779 PP

                                       HHHCSSEEEEEEE-BTTB--HHHHHHHHHHS-TTT.SCEETTCSSCCCCTTT.TSEEEEEEEESS-GGGSSTTSSS- CS
                      Flavodoxin_2  74 kllaadaivlqfPlwwfgvPailKgwiDrvltagf.afyteeggegrgggLk.gkkalvivttGgpeesyqergleg 148
                                       ++++ad +v++fP++++g++ ++K  +Dr +  ++  f             +  kka +i+ +  +  s +      
  gi|474934155|ref|YP_007687737.1|  74 DIRNADGVVFAFPIYFYGMSGQMKVALDRMYCFHKlGF------------DTgEKKASLISCVADD--SDD------ 130
                                       *****************************844433222............2324445444444333..322...... PP

                                       S-HHHHHHHHHHHHHHTT-EEEEEEEEESC CS
                      Flavodoxin_2 149 aamdellpplrgilgfiGikdvepvlvegv 178
                                        a+d +   ++++l ++G +dv  vl+ gv
  gi|474934155|ref|YP_007687737.1| 131 -AFDGVKATFDHTLAMLGWEDVGDVLLGGV 159
                                       .56666666777777777777777777665 PP

>> Ncstrn_small  Nicastrin small lobe
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.8e-05      0.17      98     159 ..      58     124 ..      31     128 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.8e-05
                                       ...-TT----SSTT---GGGSE...ESS-EEEE-HHH.HHHHHHH..HHHT.......TS--SS-EE CS
                      Ncstrn_small  98 eeaycnasyeWNpaGsgllfed...fnfPiflleneteiekirek..cyekfnakkekskksyplca 159
                                       e++ c ++  WNp + ++++ d   f fPi++   + +++++ ++  c++k   ++ ++k+s   c+
  gi|474934155|ref|YP_007687737.1|  58 EDRPCVQTDGWNPIAHDIRNADgvvFAFPIYFYGMSGQMKVALDRmyCFHKLGFDTGEKKASLISCV 124
                                       5777999999******9999887779******99988888877651166665566666666655565 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1178.46
//
Query:       gi|474934156|ref|YP_007687738.1|  [L=162]
Description: CBS-domain-containing membrane protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-32  112.9  10.2      1e-32  112.9  10.2    1.5  2  HPP            HPP family
  ------ inclusion threshold ------
       0.34   11.2   0.2       0.34   11.2   0.2    4.0  5  LHC            Antenna complex alpha/beta subunit
       0.53   10.4   6.8        2.9    8.0   0.8    2.2  2  DUF3671        Protein of unknown function
        1.6    9.1   7.1         34    4.8   0.1    3.0  3  DUF1430        Protein of unknown function (DUF1430)


Domain annotation for each model (and alignments):
>> HPP  HPP family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.79   3.6e+03       3      13 ..      21      31 ..      11      38 .. 0.50
   2 !  112.9  10.2   2.3e-36     1e-32       1     121 [.      41     153 ..      41     154 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.79
                               HPP  3 aslGAsavllf 13
                                      a+++A  ++ f
  gi|474934156|ref|YP_007687738.1| 21 AAFAAIGIVAF 31
                                      33333333333 PP

  == domain 2  score: 112.9 bits;  conditional E-value: 2.3e-36
                               HPP   1 liaslGAsavllfavpesplaqPrnvvgGhlisalvGvaiaklfglsllwlaaalavalaialmlltrtlhPPagAt 77 
                                       l+as+GA+avl +avpe pl+qP+n+++Ghl+sa++Gv+i+ l+g    w+a+alava ai++m+lt+t+hPP+gAt
  gi|474934156|ref|YP_007687738.1|  41 LVASFGATAVLAYAVPEGPLSQPKNIFFGHLFSAVIGVTIYILLG--DPWFAIALAVASAIVVMVLTGTTHPPGGAT 115
                                       79******************************************9..7899************************** PP

                               HPP  78 aliavlgkeikelgwafllvpvllgslllvlvalllnnlserrY 121
                                       al++v+g +     ++ +l  vl++s+++v + l+ n+  +r+Y
  gi|474934156|ref|YP_007687738.1| 116 ALSCVYGCYD---TYEAVLWIVLFASVMIV-IMLIANK--GRQY 153
                                       *******983...67777774555555544.4455555..3555 PP

>> LHC  Antenna complex alpha/beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   7.6e-05      0.34       9      28 ..      11      30 ..      10      30 .. 0.96
   2 ?    2.1   1.1      0.05   2.2e+02      12      25 ..      39      52 ..      38      55 .. 0.83
   3 ?   -1.7   0.3      0.81   3.6e+03      22      28 ..      74      80 ..      69      89 .. 0.54
   4 ?   -2.8   2.3       1.7   7.6e+03      24      27 ..      91      94 ..      79     105 .. 0.63
   5 ?   -1.6   1.0      0.73   3.3e+03      13      24 ..     132     143 ..     128     148 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.6e-05
                                      ..HHHHHHHHHHHHHHHHHH CS
                               LHC  9 dPhrglvallgffavlAlli 28
                                      dP++ l++++ +fa++++++
  gi|474934156|ref|YP_007687738.1| 11 DPRKLLITFFAAFAAIGIVA 30
                                      9*****************97 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.05
                                      HHHHHHHHHHHHHH CS
                               LHC 12 rglvallgffavlA 25
                                      + lva++g+ avlA
  gi|474934156|ref|YP_007687738.1| 39 VFLVASFGATAVLA 52
                                      57999999999999 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.81
                                      HHHHHHH CS
                               LHC 22 avlAlli 28
                                      av+++ i
  gi|474934156|ref|YP_007687738.1| 74 AVIGVTI 80
                                      5666555 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 1.7
                                      HHHH CS
                               LHC 24 lAll 27
                                      +Al+
  gi|474934156|ref|YP_007687738.1| 91 IALA 94
                                      3332 PP

  == domain 5  score: -1.6 bits;  conditional E-value: 0.73
                                       HHHHHHHHHHHH CS
                               LHC  13 glvallgffavl 24 
                                       ++v+++++++v+
  gi|474934156|ref|YP_007687738.1| 132 WIVLFASVMIVI 143
                                       344555555554 PP

>> DUF3671  Protein of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.8   0.00064       2.9      46     109 ..      15      84 ..      10      86 .. 0.71
   2 ?    5.8   0.6    0.0031        14      49     109 ..      89     148 ..      84     153 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00064
                           DUF3671  46 lllilpvllpliglivpilfeaksk..........kslkkkelevlatsieklytiffiilvviillvliYili 109
                                       ll+ +++ + +ig++ ++  e  ++                +  v +  + + ++iff  l + ++ v iYil+
  gi|474934156|ref|YP_007687738.1|  15 LLITFFAAFAAIGIVAFVQTE--VRnvflvasfgaT--AVLAYAVPEGPLSQPKNIFFGHLFSAVIGVTIYILL 84 
                                       567789999999955555433..3336888666432..223334666678899*******************95 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0031
                           DUF3671  49 ilpvllpliglivpilfeakskkslkkkelevlatsieklytiffiilvviillvliYili 109
                                       + ++l ++ +++v++l ++ ++    +++l+ +    + ++ +++i+l   +++v++ i  
  gi|474934156|ref|YP_007687738.1|  89 FAIALAVASAIVVMVLTGTTHP-PGGATALSCVYGCYDTYEAVLWIVLFASVMIVIMLIAN 148
                                       5566677777777777666665.44444444434444455566666666666667776655 PP

>> DUF1430  Protein of unknown function (DUF1430)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1     0.033   1.5e+02      41      73 ..      13      45 ..       8      55 .. 0.69
   2 ?    4.5   0.3    0.0091        41      41      81 ..      64     104 ..      59     109 .. 0.70
   3 ?    4.8   0.1    0.0076        34      36      62 ..     123     149 ..     120     155 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.033
                           DUF1430 41 keyliiqlivllillvlifiltkekiillvvlv 73
                                      +++li  ++ +  + +++f++t+  +++lv+ +
  gi|474934156|ref|YP_007687738.1| 13 RKLLITFFAAFAAIGIVAFVQTEVRNVFLVASF 45
                                      567777777777788888888887777766554 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0091
                           DUF1430  41 keyliiqlivllillvlifiltkekiillvvlvlllielll 81 
                                       k+ ++  l++ +i++++ ++l + ++++ ++++ +++ ++l
  gi|474934156|ref|YP_007687738.1|  64 KNIFFGHLFSAVIGVTIYILLGDPWFAIALAVASAIVVMVL 104
                                       77888889999998888888887666666666655555544 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.0076
                           DUF1430  36 lfkrhkeyliiqlivllillvlifilt 62 
                                        +++++ +l+i+l+ +++++++++  +
  gi|474934156|ref|YP_007687738.1| 123 CYDTYEAVLWIVLFASVMIVIMLIANK 149
                                       578999999999999999988877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1058  (0.0590105); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1041.57
//
Query:       gi|474934157|ref|YP_007687739.1|  [L=172]
Description: isochorismatase family protein Amidases nicotinamidase -like protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-17   64.2   0.0      2e-17   63.9   0.0    1.0  1  Isochorismatase  Isochorismatase family


Domain annotation for each model (and alignments):
>> Isochorismatase  Isochorismatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.9   0.0   1.1e-21     2e-17       2     163 ..       4     153 ..       3     159 .. 0.87

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 1.1e-21
                   Isochorismatase   2 alvviDmqndfveegvkeseeisavveninkllkaarkagipviftrdvheleevkgdlderkaaphfkpgttgael 78 
                                       +l+viD+q +f+      +e+ +++++ i++l + + + ++ + +t++v+       d +   ++++ +  t++++ 
  gi|474934157|ref|YP_007687739.1|   4 CLLVIDLQYGFI------TEKTKDILPGIKELTEVWPEEDY-IAATKFVNA-----DDSPFTTDMGWEGLKTPDEQE 68 
                                       79**********......**********************9.*********.....444444455555555555555 PP

                   Isochorismatase  79 vpelaplegdvvvdKtrfsafagtdldeiLkelgiktivlaGiatdvCVeatardaldlGyevvvvsDAvaalspel 155
                                       +  +     d v +Kt++sa  + ++  +++e+gi+++ ++G+ +d+C++ ta d+++ G+   v+++ va+    +
  gi|474934157|ref|YP_007687739.1|  69 LAGFLRANADLVYEKTGYSAV-TDEFLSFIEENGIDEVDVCGVDADCCILRTAFDLFEMGMPFLVLKKYVASNGGKG 144
                                       55555556*************.99************************************************99999 PP

                   Isochorismatase 156 .hdaalkrl 163
                                         daa+k +
  gi|474934157|ref|YP_007687739.1| 145 sTDAAFKVM 153
                                       899999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1077.99
//
Query:       gi|474934158|ref|YP_007687740.1|  [L=172]
Description: hypothetical protein TALC_00580 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      4091  (0.228178); expected 358.6 (0.02)
Passed bias filter:                     1010  (0.0563333); expected 358.6 (0.02)
Passed Vit filter:                       778  (0.0433934); expected 17.9 (0.001)
Passed Fwd filter:                       338  (0.0188521); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 2.89u 0.39s 00:00:03.28 Elapsed: 00:00:00.67
# Mc/sec: 775.16
//
Query:       gi|474934159|ref|YP_007687741.1|  [L=279]
Description: hypothetical protein TALC_00581 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.94    8.1  34.5        1.3    7.6  34.5    1.2  1  Med15          ARC105 or Med15 subunit of Mediator complex no


Domain annotation for each model (and alignments):
>> Med15  ARC105 or Med15 subunit of Mediator complex non-fungal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6  34.5   7.4e-05       1.3     222     469 ..      10     267 ..       2     277 .. 0.39

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 7.4e-05
                             Med15 222 pngqgggaggnnqqnplvqtrlqaqlqnqq.kqqldqvrgpadaqaqmqqqaqanagmnpqqmagaqa..qv.arqq 294
                                       +++++++a  ++q ++   ++++a+      kq  ++ + +a+a+a+++ qa+ +a+m+ qq+a+ +a   + a ++
  gi|474934159|ref|YP_007687741.1|  10 KEQAKQEAAAKKQAEKE--AQMKAKEEAAArKQAEKEAQAKAKAEADAKRQAEKEAQMKEQQKAKEEAaaRKaAEKE 84 
                                       34445555555555544..3333333222213333334456666666666666666666666544332002213333 PP

                             Med15 295 qqaqqqaqqsqlgalanqmqqmaqGdrqaagqgapgqpmgpvsqqpgalvaq..sqqsvlsiedqnvkl.qqqtrqq 368
                                       +qa+++a+ + ++ +a++  qm++ ++ aa ++a  q   ++ q     +aq  +qq++ + +    k+ +++ r++
  gi|474934159|ref|YP_007687741.1|  85 AQAKAKAE-ADAKRQAEKEAQMKAKEEAAARKQAEKQ---AHAQADSDKTAQreAQQKAKA-DAAAKKQaEKEARAK 156
                                       33333333.5556666666666333333222222111...222222111111112232222.111111111111111 PP

                             Med15 369 qqqqggnqeaaqkqqvnlsvgqggqvvale..............lnnagnigglginpmqrgqPemmsspspvdgsa 431
                                        qq+ +++ aa kq    + +++++  a++              l + +++    i+   + + +   s s  + + 
  gi|474934159|ref|YP_007687741.1| 157 EQQKAKEEAAARKQAEKEAKQKAKEEAAAKkaadksepapkkekLSKRRKRSLPRIPRRPQPK-NTTRSTSSTPRKL 232
                                       111111111122222222222222222222333344444444433366666666666554422.2333444455677 PP

                             Med15 432 vrqvttnqslrqspqpsvpspqgPgsqppqsvsggmiP 469
                                        r  t n+ + + p+ +      P+ +  + ++ +  P
  gi|474934159|ref|YP_007687741.1| 233 TRPATRNRRMLSRPSTRRS---RPTTKSRPRKTRKSSP 267
                                       7777777777777777733...4554444444444445 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3992  (0.222656); expected 358.6 (0.02)
Passed bias filter:                     1024  (0.0571142); expected 358.6 (0.02)
Passed Vit filter:                       808  (0.0450667); expected 17.9 (0.001)
Passed Fwd filter:                       326  (0.0181828); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 3.85u 0.45s 00:00:04.30 Elapsed: 00:00:00.83
# Mc/sec: 1018.80
//
Query:       gi|474934160|ref|YP_007687742.1|  [L=221]
Description: putative phosphatase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-23   82.9   0.0    3.6e-23   82.6   0.0    1.1  1  HAD_2           Haloacid dehalogenase-like hydrolase
    5.1e-14   53.1   0.0    3.2e-12   47.2   0.0    2.1  1  Hydrolase       haloacid dehalogenase-like hydrolase
    7.2e-07   29.8   0.0    1.6e-06   28.6   0.0    1.6  1  HAD             haloacid dehalogenase-like hydrolase
     0.0015   18.4   0.0     0.0095   15.7   0.0    1.9  1  NIF             NLI interacting factor-like phosphatase
     0.0085   16.1   0.2      0.022   14.8   0.1    1.7  2  Hydrolase_like  HAD-hyrolase-like
  ------ inclusion threshold ------
      0.033   13.9   0.0        6.8    6.3   0.0    2.1  2  Hydrolase_3     haloacid dehalogenase-like hydrolase
      0.093   12.8   0.0         12    6.0   0.0    2.6  3  Hydrolase_6     Haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.6   0.0   1.4e-26   3.6e-23       1     177 [.      14     188 ..      14     189 .. 0.93

  Alignments for each domain:
  == domain 1  score: 82.6 bits;  conditional E-value: 1.4e-26
                             HAD_2   1 iiFDlDgTlldteeliiqafnelleeyglselseeelrkliglslrellrklgeseeeee..kieellrkyneekkk 75 
                                       +iFDlDgTl  +++ i++a+++++e++gl+ +s+e l+ ++  +l + +r l+    e e   i  +++ky e    
  gi|474934160|ref|YP_007687742.1|  14 VIFDLDGTLTQSKPSIFAAYRYAAEKMGLPVPSDEMLEGHLCGDLPNNIRTLFGVSGETErlGIGLYREKYTEICMG 90 
                                       7************************************999988888888888877776667899************9 PP

                             HAD_2  76 kevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekk.KPdpeviekaleklklk 151
                                        +v +++gv+++L++L+e+g+ + ++T k +e++  ++e lg+ ++F+++ +++  +   K  +++i++++     +
  gi|474934160|ref|YP_007687742.1|  91 -NVPLFPGVEQALDSLSEMGVDMYVATMKIEEVAIPFIESLGLSKFFEKVRGASADGSVtK--ADMILECIGDD--D 162
                                       .***************************************************998888735..9****999865..8 PP

                             HAD_2 152 keeviyvGDsptDieaakkagikvia 177
                                       k+++++vGD p+D+ a+ +ag+++ia
  gi|474934160|ref|YP_007687742.1| 163 KSRAVMVGDCPQDLRASAEAGVDFIA 188
                                       99**********************98 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.2   0.0   1.2e-15   3.2e-12       2     210 .]      12     183 ..      11     183 .. 0.85

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 1.2e-15
                                       SEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   2 ktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrgayaigkpewlt 78 
                                       + v+fD+dGTLt+++ps+  ++++a                     a+  +++ + +++ +    g+++   p  ++
  gi|474934160|ref|YP_007687742.1|  12 DIVIFDLDGTLTQSKPSIFAAYRYA---------------------AEKMGLPVPSDEMLE----GHLCGDLPNNIR 63 
                                       679**********************.....................777777888877777....577777777777 PP

                                       HHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  79 aldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanql 155
                                        l          g+ ++ g   + +  ++ ++     p  ++p++++a+ sL ++g++++++t   +e a   ++ l
  gi|474934160|ref|YP_007687742.1|  64 TL------FGVSGETERLGIGLYRE--KYTEICMGNVP--LFPGVEQALDSLSEMGVDMYVATMKIEEVAIPFIESL 130
                                       77......77778888888888888..88888888888..************************************* PP

                                       TGGGESEEEEHHCESSTTTSHHHHHHHHHHHT.....STGGGEEEEESSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 156 GddyfdaviasdietvakpspegkvaaireLq.....gkpeevamVGDgvnDaaalaaAg 210
                                       G       +++  e+v ++s +g v +++ +       ++++ +mVGD + D+ a a+Ag
  gi|474934160|ref|YP_007687742.1| 131 G-------LSKFFEKVRGASADGSVTKADMILecigdDDKSRAVMVGDCPQDLRASAEAG 183
                                       *.......5555788888888888888888833444577*******************98 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   6.4e-10   1.6e-06       1     186 [.      14     178 ..      14     180 .. 0.74

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 6.4e-10
                               HAD   1 alfDfDgTLldg.dslelllrfllrrgaprlwralreklllalfrellrldraglaelleallaglseelaaelerf 76 
                                       ++fD+DgTL+++  s+++  r+ +++ +   +     + l+ +   +++l       +  ++l g s+e ++    +
  gi|474934160|ref|YP_007687742.1|  14 VIFDLDGTLTQSkPSIFAAYRYAAEKMG---LPVPSDEMLEGH--LCGDL------PNNIRTLFGVSGETERLGIGL 79 
                                       79**********5555544443333322...344444455555..34444......45678999***9999999999 PP

                               HAD  77 vaevirpk......lldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegk 147
                                       ++e++++       l+ pg+ ++l+   + G+  +v +  +++++ p+ + lg    l+        ++ +  ++g 
  gi|474934160|ref|YP_007687742.1|  80 YREKYTEIcmgnvpLF-PGVEQALDSLSEMGVDMYVATMKIEEVAIPFIESLG----LSK-------FFEK--VRGA 142
                                       9999999999998878.99999999888*************************....999.......5555..5666 PP

                               HAD 148 pvrgegkvaalrewlaaegegidlee.vvayGDspsDlpl 186
                                       +  g    ++ ++ +  e+ g+d ++  v +GD p+Dl +
  gi|474934160|ref|YP_007687742.1| 143 SADG----SVTKADMILECIGDDDKSrAVMVGDCPQDLRA 178
                                       6666....55555445556655555549999******986 PP

>> NIF  NLI interacting factor-like phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   3.7e-06    0.0095       2     125 ..      13     184 ..      12     193 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.7e-06
                               NIF   2 tLVLDLDetLvhsk...leksk............................................klkve...... 25 
                                       ++++DLD+tL  sk   +   +                                               +       
  gi|474934160|ref|YP_007687742.1|  13 IVIFDLDGTLTQSKpsiF---AayryaaekmglpvpsdemleghlcgdlpnnirtlfgvsgeterlG--IGlyreky 84 
                                       589999999998883330...1344555566677777788888888877776666555555444331..11322222 PP

                               NIF  26 gekvevsvlkRpgldefLkelskl.yevvifTasseeyaeavidildpekkllshr..lyrescvkkkgeyvKdLsl 99 
                                       +e + + v + pg+++ L++ls++ +++++ T++ ee a + i++l   k  ++++   + + +  +k + +  L+ 
  gi|474934160|ref|YP_007687742.1|  85 TEICMGNVPLFPGVEQALDSLSEMgVDMYVATMKIEEVAIPFIESLGLSKF-FEKVrgASADGS-VTKADMI--LEC 157
                                       33355666666***********************************99986.665522222222.2244555..777 PP

                               NIF 100 lgr.dlsrvvivDdspdsfelqpengi 125
                                       +g  d sr v+v d p+  +++ e g+
  gi|474934160|ref|YP_007687742.1| 158 IGDdDKSRAVMVGDCPQDLRASAEAGV 184
                                       766599999999999999888877665 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.5   3.9e+03       9      20 ..      32      43 ..      25      50 .. 0.71
   2 !   14.8   0.1   8.6e-06     0.022      19      57 ..     161     198 ..     132     214 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.5
                                      HHHHHHHHH--- CS
                    Hydrolase_like  9 mydfalevlgsd 20
                                      +y++a+e++g++
  gi|474934160|ref|YP_007687742.1| 32 AYRYAAEKMGLP 43
                                      689999998766 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 8.6e-06
                                       --GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTT CS
                    Hydrolase_like  19 sdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrped 57 
                                        d+++ +m+GD   +D+++  +aG+++++   G   p +
  gi|474934160|ref|YP_007687742.1| 161 DDKSRAVMVGDC-PQDLRASAEAGVDFIAASYGYGLPVE 198
                                       5699********.9**************99988766644 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0027       6.8       1      17 [.      14      30 ..      14      40 .. 0.78
   2 ?    5.6   0.0    0.0046        12      21      66 ..      99     144 ..      93     163 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0027
                                      EEEEIIIIIS-TTS--- CS
                       Hydrolase_3  1 ialDlDGTLlnsdkkis 17
                                      +++DlDGTL +s+ +i 
  gi|474934160|ref|YP_007687742.1| 14 VIFDLDGTLTQSKPSIF 30
                                      69*******99998775 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0046
                                       HHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGTEE CS
                       Hydrolase_3  21 keaikklkekgikvviATGRslravlpvleelgldlpvialNGali 66 
                                        +a+  l+e g+   +AT    + ++p++e+lgl+ ++  + Ga  
  gi|474934160|ref|YP_007687742.1|  99 EQALDSLSEMGVDMYVATMKIEEVAIPFIESLGLSKFFEKVRGASA 144
                                       689********************************99999999877 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.018        46       1      16 [.      14      29 ..      14      44 .. 0.83
   2 ?   -1.9   0.0       1.4   3.6e+03      51      67 ..      37      53 ..      30      55 .. 0.79
   3 ?    6.0   0.0    0.0049        12      15      37 ..      94     116 ..      87     184 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.018
                                      EEEESTTTSEETTEE- CS
                       Hydrolase_6  1 flfDidGvLwrgdkai 16
                                      ++fD+dG+L + +  i
  gi|474934160|ref|YP_007687742.1| 14 VIFDLDGTLTQSKPSI 29
                                      69*******9987655 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.4
                                      HHHTT----GGGEEEHH CS
                       Hydrolase_6 51 leklgvditeeqvvtsa 67
                                       ek+g+++  ++++  +
  gi|474934160|ref|YP_007687742.1| 37 AEKMGLPVPSDEMLEGH 53
                                      5899***9999998765 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0049
                                       E-TTHHHHHHHHHHTT-EEEEEE CS
                       Hydrolase_6  15 aipgaaealnalraagkpvvllT 37 
                                       ++pg+++al+ l ++g+++++ T
  gi|474934160|ref|YP_007687742.1|  94 LFPGVEQALDSLSEMGVDMYVAT 116
                                       68*****************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 1287.11
//
Query:       gi|474934161|ref|YP_007687743.1|  [L=290]
Description: Glucose-1-phosphate thymidylyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-60  203.5   0.0    4.5e-60  203.3   0.0    1.0  1  NTP_transferase  Nucleotidyl transferase
    2.5e-15   57.2   0.0    5.9e-15   56.0   0.0    1.6  2  NTP_transf_3     MobA-like NTP transferase domain
    4.7e-05   23.2   0.0    8.9e-05   22.3   0.0    1.5  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.3   0.0   7.5e-64   4.5e-60       1     246 [.       2     238 ..       2     240 .. 0.98

  Alignments for each domain:
  == domain 1  score: 203.3 bits;  conditional E-value: 7.5e-64
                                       EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEE CS
                   NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevli 77 
                                       k++ILa G+GtRL+P ++ ++k l+p+++k ++i+++ls+l+++gi++i+v++++++++ +++ l++g++fg+++++
  gi|474934161|ref|YP_007687743.1|   2 KGIILAAGKGTRLYPASSHISKILLPIYDK-PMIYYPLSTLMSAGIRDILVIVNKDDRAYFKKLLGDGKQFGISIKY 77 
                                       79****************************.********************************************** PP

                                       EEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEEC CS
                   NTP_transferase  78 alepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGviead 154
                                       a+++ +kg+AdA+++++++++ ++   ++l Lg+++++++++ e++++a++      ++++  +ve+a+++Gv+e++
  gi|474934161|ref|YP_007687743.1|  78 AVQKVQKGIADALIIGEKFADGDN---VALALGDNVFYGEEMYELLAEAMSITD--GACVFCHEVEDARAFGVAEFG 149
                                       *********************999...5**************************..9******************** PP

                                       TTSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEE CS
                   NTP_transferase 155 eegrverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsD 231
                                        +g++ +++EKPk +k s+ ++ G+Y++++e  + + k l++++rge eitd+++ ++++gk ++ +   d+  W D
  gi|474934161|ref|YP_007687743.1| 150 PDGNIVDIEEKPKDPK-SNAVVVGLYFYDKECSKLA-KTLKPSARGEIEITDLNKLYIKQGKLKALVTGPDT-IWAD 223
                                       ****************.***************9998.89********************************7.7*** PP

                                       XSSHHHHHHHHHHHH CS
                   NTP_transferase 232 vGtldslleanekla 246
                                       +Gt++sll+a+++++
  gi|474934161|ref|YP_007687743.1| 224 TGTFESLLDASNRVH 238
                                       ***********9876 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.0   0.0   9.8e-19   5.9e-15       1     125 [.       3     138 ..       3     211 .. 0.75
   2 ?   -1.6   0.0      0.53   3.2e+03      89     112 ..     212     235 ..     198     253 .. 0.74

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 9.8e-19
                                       EEEEEESS-TTT..TT...THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSHCHHHH......HHTTCTS-E..EE CS
                      NTP_transf_3   1 aviLAGGrSsRm..gg...dKallplggkpllervldalraagvdevvvvggdeevla......alarlgvrv..ve 64 
                                       ++iLA+G+++R+   +    K llp+ +kp++ + l +l +ag+++++v+++ ++ +       + +++g+++  ++
  gi|474934161|ref|YP_007687743.1|   3 GIILAAGKGTRLypASshiSKILLPIYDKPMIYYPLSTLMSAGIRDILVIVNKDDRAYfkkllgDGKQFGISIkyAV 79 
                                       79**********55224789*******************************99854422222224466675551155 PP

                                       -TTSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSS CS
                      NTP_transf_3  65 dedpgkgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvptyeg 125
                                       ++  +kg++ +l  + + a d d v+++++D +++ +e++e l++a+  +++++v++   +
  gi|474934161|ref|YP_007687743.1|  80 QK-VQKGIADALIIGEKFA-DGDNVALALGDNVFYGEEMYELLAEAMSITDGACVFCHEVE 138
                                       54.489**********998.***************************86666555444333 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.53
                                       EEEEETT-TT--HHHHHHHHHCHH CS
                      NTP_transf_3  89 vlvlacDmPlltpelverllaaaa 112
                                       +lv+  D+++ ++ + e ll+a  
  gi|474934161|ref|YP_007687743.1| 212 ALVTGPDTIWADTGTFESLLDASN 235
                                       577777888888888888888763 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   1.5e-08   8.9e-05       4      66 ..       4      69 ..       1      88 [. 0.88

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.5e-08
                                      EEECTTSSCTT...-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGG.C CS
                              IspD  4 vipAAGsGkRm...kaglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllld.k 66
                                      +i AAG+G+R+    +   K +l + +++++   +++l++   +  i+v+v++dd+ +f++ll+d k
  gi|474934161|ref|YP_007687743.1|  4 IILAAGKGTRLypaSSHISKILLPIYDKPMIYYPLSTLMS-AGIRDILVIVNKDDRAYFKKLLGDgK 69
                                      89********844357889******************999.889*******************9853 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1710.80
//
Query:       gi|474934162|ref|YP_007687744.1|  [L=340]
Description: Glucose-6-phosphate isomerase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-43  148.7   0.0      2e-43  148.0   0.0    1.3  1  bact-PGI_C  Bacterial phospho-glucose isomerase C-terminal SI
    6.5e-06   26.0   0.1    0.00069   19.5   0.0    2.5  2  SIS         SIS domain
     0.0099   15.9   0.1      0.062   13.3   0.0    2.1  2  SIS_2       SIS domain


Domain annotation for each model (and alignments):
>> bact-PGI_C  Bacterial phospho-glucose isomerase C-terminal SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.0   0.0   3.4e-47     2e-43       2     152 .]     186     333 ..     185     333 .. 0.97

  Alignments for each domain:
  == domain 1  score: 148.0 bits;  conditional E-value: 3.4e-47
                                       G-HHHHHHHHHTTSEEEEE-..TT-THHHHHHHHHHHHTT----B---.SSHHHHHHHTTSS-GGGGTTEEEEEESS CS
                        bact-PGI_C   2 knpakqlAlelagklpviygssellevaArRfknqlnenAKipafagvlpeanhneivgleaeeelkkrlrlvllrd 78 
                                       +++a+ +A++++g++pv+yg s+ l++ A+R+knqlnen+Ki+af+g++pe+nhne+vg+ +e++l+k++  ++++d
  gi|474934162|ref|YP_007687744.1| 186 DSYARYVAKRIVGYVPVVYG-SPDLSATAVRMKNQLNENSKIVAFSGTMPEFNHNEVVGW-YEDPLRKNFLPIIIND 260
                                       678999**************.***************************************.89*************7 PP

                                       HH........HHHHHHHHTTTSSEEEEE---SSSHHHHHHHHHHHHHHHHHHHHHHCT---S-TTTTHHHHH.. CS
                        bact-PGI_C  79 eeehprvkkraeivkelaeergvrvtevkaegesplerlaslillgDfvSvylAllrgvDPtpvpaIdelKeel 152
                                       ++  ++v+k+++++ + +++rg + + v+ +ges+ er++++i++gD+vS+ lA  r+vDP +v++I ++K+++
  gi|474934162|ref|YP_007687744.1| 261 DD-LTDVRKIVKATISTLKSRGLDPIIVDVKGESVSERIIYAIMFGDYVSLFLAANRKVDPCNVDPIVDIKTRM 333
                                       77.49******************************************************************986 PP

>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.2e-07   0.00069       6      89 ..      37     117 ..      34     133 .. 0.85
   2 !    3.9   0.0    0.0075        45      10      84 ..     203     285 ..     201     303 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.2e-07
                                       SEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTTSE CS
                               SIS   6 kriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelakergak 82 
                                       k++++ G+G+s+  ++ +a     ++++ v+v +a +    ++ + +ed+l+++ s+sg+t+++v+  +la e g  
  gi|474934162|ref|YP_007687744.1|  37 KNVLICGMGASAIGGAVFADSTYYTSKVYVDVTKALS---IPVWVTKEDTLFVACSYSGNTFETVKMYKLAVESGLD 110
                                       6788889999988888888777777777777777777...788999******************************* PP

                                       EEEEESS CS
                               SIS  83 iiaITds 89 
                                       +ia+T+ 
  gi|474934162|ref|YP_007687744.1| 111 VIAVTHG 117
                                       *****74 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0075
                                       EEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGG.....GG-STTCEEEEEE...SSSHHHHHHHHHHHHHH CS
                               SIS  10 vlGaGtsyaiakelalkleeiggivvevedaselkhgvl.....alideddlvilis...fsgetkdlvaaaelake 78 
                                       v+G+    a+a  ++ +l+e ++iv++    +e+ h+ +     ++++++ l i+i     ++  k ++a++  +k+
  gi|474934162|ref|YP_007687744.1| 203 VYGSPDLSATAVRMKNQLNENSKIVAFSGTMPEFNHNEVvgwyeDPLRKNFLPIIINdddLTDVRKIVKATISTLKS 279
                                       788888899999*********************99984322222455555555555545555555556666666666 PP

                                       TTSEEE CS
                               SIS  79 rgakii 84 
                                       rg  +i
  gi|474934162|ref|YP_007687744.1| 280 RGLDPI 285
                                       666665 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.16   9.5e+02      36      48 ..      37      49 ..      20      59 .. 0.82
   2 !   13.3   0.0     1e-05     0.062     101     137 ..      78     115 ..      55     116 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.16
                                      --EEEEESGGGHH CS
                             SIS_2 36 gkvlvfGsGhSaa 48
                                      + vl++G G Sa+
  gi|474934162|ref|YP_007687744.1| 37 KNVLICGMGASAI 49
                                      6799*******98 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 1e-05
                                       --TT-EEEEE.-SS--SHHHHHHHHHHHHHT-EEEEEE CS
                             SIS_2 101 lkpgDvLlvi.SnsGnnavvveaaeaakergmkviAlt 137
                                       + ++D+L+v+ S sGn    v++ + a e g+ viA+t
  gi|474934162|ref|YP_007687744.1|  78 VTKEDTLFVAcSYSGNTFETVKMYKLAVESGLDVIAVT 115
                                       5788888775499************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.53
# Mc/sec: 1919.48
//
Query:       gi|474934163|ref|YP_007687745.1|  [L=333]
Description: Galactose mutarotase-related enzyme [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.3e-87  292.6   0.0    3.7e-87  292.4   0.0    1.0  1  Aldose_epim  Aldose 1-epimerase


Domain annotation for each model (and alignments):
>> Aldose_epim  Aldose 1-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  292.4   0.0   2.1e-91   3.7e-87       6     299 ..      20     325 ..      15     327 .. 0.97

  Alignments for each domain:
  == domain 1  score: 292.4 bits;  conditional E-value: 2.1e-91
                                       EETTEEEEEECTCTTEEEEEEETT.S..TEESB-B-STHHHHHHSC.CSSCEECSS-SEEETTEEEETTEEEECCCC CS
                       Aldose_epim   6 kngaglsakislyGAtllslkvpdke..qrevllgsddaeeylkds.yfgatlgrvanRianGeFeldGkpyqlpqn 79 
                                       + g +ls+ i +yGA l+ l vpd++   ++v+lg++++ +y++ s  +ga++gr+anRian++Fel G++y l+ n
  gi|474934163|ref|YP_007687745.1|  20 ECG-NLSCGILTYGAVLQNLLVPDSDgfDTDVVLGYENVNSYEELSgRMGAVIGRYANRIANARFELGGRTYELSRN 95 
                                       555.59999***************99*********************99**************************** PP

                                       BTTTCEETBSGGG...SB-EEEEEEETTEEEEEEEEEEETCHCSTSEEEEEEEEEEETTEEEEEEEEEEESSS-EEE CS
                       Aldose_epim  80 eegknplHGgarg...reWeveevkeddgvtvslvlkpdgeegypgdlevrvtytLnednelkieyeatndgkptpf 153
                                         g+ ++HGg+ g   ++W+v++v+   +vt+sl++ pdg+egypg+++v+vtytL++d+ l+i y+a++d ++t+ 
  gi|474934163|ref|YP_007687745.1|  96 R-GPDHIHGGFSGfdrKIWDVKSVS-GRSVTLSLSS-PDGDEGYPGNIDVEVTYTLDGDS-LSIGYTARSD-EDTVC 167
                                       *.***********************.6*********.***********************.**********.8**** PP

                                       EEEEEEEEETSSC...TCTGGEEEEEEEEEEEECTTSGEEEEEEECTTCCCCCCSSEEHCSSET...EEEEEEEESS CS
                       Aldose_epim 154 nltnHtYFnlsge...sidshelqieadeylevdeeliptgelkdvkgtpfdfrqpkaigedlk...glDhayllks 224
                                       nltnH+YFnl+g+   +++++ ++i++++++ + ++++ptge+++v+gtp+d+rq++++g++l+   g+D++yll++
  gi|474934163|ref|YP_007687745.1| 168 NLTNHSYFNLNGHnrgTVEDNYVSINSSRHTVLGDRSLPTGEIAPVDGTPLDLRQARSLGTRLRkygGFDNNYLLDG 244
                                       ****************************************************************************9 PP

                                       CSEEEEEETTTTEEEEEEEETTSSEEEEEECTTTT........SEECCEEESSECTCETCCCECHHHT-EEEHTTTE CS
                       Aldose_epim 225 klkaviidpdkksgiklevsttepalvvytgnflk........kylsreglaletqmlpdepnhpefpsivlkpGes 293
                                         +++++++ +ksgi++ev+t+ pa+++yt+n+lk        +y +++gl+letq +pd+pn+pefp  vl++Ge+
  gi|474934163|ref|YP_007687745.1| 245 --RKAATVYAPKSGITMEVETDSPAVQFYTANGLKnvdgkygsRYGKWSGLCLETQECPDAPNRPEFPPAVLRKGET 319
                                       ..9999*********************************************************************** PP

                                       EEEEEE CS
                       Aldose_epim 294 ysaets 299
                                       y+  t+
  gi|474934163|ref|YP_007687745.1| 320 YRRLTR 325
                                       *97666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.56
# Mc/sec: 1787.72
//
Query:       gi|474934164|ref|YP_007687746.1|  [L=151]
Description: Protein-tyrosine-phosphatase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.9e-34  116.9   0.0      1e-33  116.7   0.0    1.0  1  LMWPc     Low molecular weight phosphotyrosine protein phosph


Domain annotation for each model (and alignments):
>> LMWPc  Low molecular weight phosphotyrosine protein phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.7   0.0   5.6e-38     1e-33       1     142 []       5     146 ..       5     146 .. 0.98

  Alignments for each domain:
  == domain 1  score: 116.7 bits;  conditional E-value: 5.6e-38
                                       EEEEESSSSSHHHHHHHHHHHHHHHTT-CCCEEEEEEESTST.TT-B--HHHHHHHHHTTS--TT-BB-BS-HHHHH CS
                             LMWPc   1 vlfvClgNicRSpmAealfrkelekagleekvevdSaGtgal.vgkradpravevlkekgislsghvarqlskeela 76 
                                       +lfvC gNicRSpmAe +++++++kag+e+++ + S++t++  +g+ +++ + ++l ++g++++++ ar l+ +e++
  gi|474934164|ref|YP_007687746.1|   5 ILFVCHGNICRSPMAEFVMKDIVRKAGAEDDFVIASCATSNEeIGNGVHYGTRNILSQNGVPFEQRSARRLKSDEYD 81 
                                       89*************************************************************************** PP

                                       HSSEEEESSHHHHHHHHHHCCTTGGGGEEEGGGG.SSTSS---HTTSSHHHHHHHHHHHHHHHHHHH CS
                             LMWPc  77 elDlilamdeenkreleslapekekakvkllgey.teqldieDPyygeieafeevldeieeavkkll 142
                                       + D+i+ mdeen+r +  +  +  ++kv ll ++ +e+ ++eDP+y++  +f +v+ +i++ +++l+
  gi|474934164|ref|YP_007687746.1|  82 KWDYIIGMDEENIRGIMGIIGKDPENKVSLLMSHaGEDRAVEDPWYTG--GFGKVYLDITKGCNALF 146
                                       *******************9999999********9************9..*************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 984.29
//
Query:       gi|474934165|ref|YP_007687747.1|  [L=335]
Description: hypothetical protein TALC_00588 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.018   15.2   0.0        6.2    7.1   0.0    2.6  2  FYRC            F/Y rich C-terminus
       0.34   10.4   4.1        1.1    8.7   4.1    1.8  1  zf-ribbon_3     zinc-ribbon domain
        7.9    6.3   6.5         21    5.0   6.5    1.7  1  zinc_ribbon_2   zinc-ribbon domain


Domain annotation for each model (and alignments):
>> FYRC  F/Y rich C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0     0.001       6.2      57      81 ..      98     122 ..      95     125 .. 0.91
   2 ?    5.2   0.0    0.0041        24      66      83 ..     147     164 ..     143     165 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.001
                              FYRC  57 GLsepaivrlieslpgaekctnYkf 81 
                                       G   pa+ + +e+lp ++++++Y f
  gi|474934165|ref|YP_007687747.1|  98 GYLPPAVEKWLEALPRIREIERYDF 122
                                       67789******************87 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0041
                              FYRC  66 lieslpgaekctnYkfry 83 
                                        +eslp +e++++Y f++
  gi|474934165|ref|YP_007687747.1| 147 EMESLPRIEELVRYAFDF 164
                                       58************9987 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   4.1   0.00019       1.1       2      22 ..       5      29 ..       4      31 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00019
                       zf-ribbon_3  2 tvrCPnCGa.plssddn....vCpyC 22
                                      +++CP+CG+ +   dd+    +C yC
  gi|474934165|ref|YP_007687747.1|  5 YIKCPKCGNkL-FIDDSvgggMCFYC 29
                                      589*****955.44444113356666 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   6.5    0.0036        21       1       9 [.       7      15 ..       7      29 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0036
                     zinc_ribbon_2  1 fCpnCGael 9 
                                      +Cp+CG++l
  gi|474934165|ref|YP_007687747.1|  7 KCPKCGNKL 15
                                      7******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       731  (0.0407719); expected 358.6 (0.02)
Passed bias filter:                      613  (0.0341904); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2234.03
//
Query:       gi|474934166|ref|YP_007687748.1|  [L=878]
Description: aconitase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   5.3e-168  559.8   0.0   7.1e-168  559.4   0.0    1.1  1  Aconitase    Aconitase family (aconitate hydratase)
    2.4e-42  144.4   0.0    1.8e-41  141.5   0.0    2.1  2  Aconitase_C  Aconitase C-terminal domain


Domain annotation for each model (and alignments):
>> Aconitase  Aconitase family (aconitate hydratase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  559.4   0.0  7.9e-172  7.1e-168      12     461 .]      75     551 ..      56     551 .. 0.94

  Alignments for each domain:
  == domain 1  score: 559.4 bits;  conditional E-value: 7.9e-172
                         Aconitase  12 egiayvpdrvllqdvtgvqalvdlaaareavrrlggtlatidhlvpvdlvidhsv.....gaeealeknledefern 83 
                                        +i+ +p+rvllqd tg  a+ dla++r+av+r+g+++++i++ +pv+lvidhs+     g ++a+++n e  f+rn
  gi|474934166|ref|YP_007687748.1|  75 ADIPWIPARVLLQDLTGGAAVTDLASMRDAVARMGKDPQSINPIIPVNLVIDHSIqtdvaGCDKAMQENEEIDFSRN 151
                                       23999**************************************************9999999999************ PP

                         Aconitase  84 keryefLksaakaf.girvvppgqGIvHqvnlEy.............glalpgktvvgtDSHTtmigglGvlaiGvG 146
                                       kery+ +k+a+k+f ++++vpp +GI+Hqvn+E               +a+p+ ++ gtDSHTt i+glGv ++GvG
  gi|474934166|ref|YP_007687748.1| 152 KERYALFKWAQKSFrNFTAVPPWNGICHQVNIEFlsplvhvkdvdgkKIAYPD-SCFGTDSHTTQIDGLGVAGWGVG 227
                                       ******************************************999766*****.*********************** PP

                         Aconitase 147 gieaeavllgqplelkipkvvgvkltGklkegvtakDlvlavigklrkkgvvgkvvEffGegvesLsledraTiaNM 223
                                       gieaeav++gqp ++++p+vvg+kl Gkl++gvta+Dlvl+v+++lr+kgvvgk+vEffG+g +sL + dr T+aNM
  gi|474934166|ref|YP_007687748.1| 228 GIEAEAVMVGQPSYMSLPDVVGFKLVGKLSPGVTATDLVLTVVQMLREKGVVGKFVEFFGPGYQSLDVSDRSTVANM 304
                                       ***************************************************************************** PP

                         Aconitase 224 aaEvGAttglfpvdektleYLkatgreeaav.lveaydkaqalfelaadedaeydkvleldlstlepsvagpkrPqd 299
                                       a+E+GAt+g++p+d kt++YL++t+r++ ++ ++eay+k+q l+  + ++ +ey+++leldlst+epsvag krPqd
  gi|474934166|ref|YP_007687748.1| 305 APEYGATMGYCPIDAKTMDYLRLTNRDDRHIaAIEAYEKEQMLW-YDPENIPEYTDTLELDLSTVEPSVAGHKRPQD 380
                                       ******************************9999**********.5666789************************* PP

                         Aconitase 300 avplselvkkefkeelekeaaekaley...klkegtklkdgkvdiaaigSCTNssnedvraaaglla.kavekglkv 372
                                       ++pl++++ ++f+++l       al +   + +eg ++ dg+v ia i+SCTN+ n++v++aagl+a ka e g ++
  gi|474934166|ref|YP_007687748.1| 381 RIPLRNMK-AQFSKTLG------ALGVpqqRMGEGERMGDGSVAIASITSCTNTANPSVMIAAGLVAkKAFELGIRP 450
                                       ****5555.57999883......333332357889****************************************** PP

                         Aconitase 373 kpgvktsvaPGSevvkayleaeGlleiLekaGfevvgagCstCignsdrle........ege...aivsssNRNFeg 438
                                       k++vkts+aPGS++v++yl+++Gl+++L++ Gf+  g+gC+tCigns++l+        +g+   a+v ssNRNFeg
  gi|474934166|ref|YP_007687748.1| 451 KKYVKTSLAPGSKAVTDYLTKSGLQKYLDAEGFQNCGYGCMTCIGNSGPLSddvskqikDGDlavAAVASSNRNFEG 527
                                       **************************************************978866655444999************ PP

                         Aconitase 439 Rqgpntra.yLaSPelvvaaAlaG 461
                                       R++p ++a yL+SP+lvv +AlaG
  gi|474934166|ref|YP_007687748.1| 528 RIHPLVKAnYLMSPPLVVCFALAG 551
                                       ***********************9 PP

>> Aconitase_C  Aconitase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.11   9.6e+02      15      70 ..     101     156 ..      92     161 .. 0.85
   2 !  141.5   0.0     2e-45   1.8e-41       3     130 ..     679     806 ..     677     807 .. 0.98

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.11
                                       HHSTGGGCCGHCCHHHCCCGGTTTCCCCTTTSBBSEEEETTTTEEEEHHHHHHHHH CS
                       Aconitase_C  15 eksnvdtdlkipkqfegtianiglgnelveekrankttdlddgekedvvdaaeryk 70 
                                       ++++v++ +k+p+ ++ +i    +  + +++  a++++ ++++e+ d+  ++ery 
  gi|474934166|ref|YP_007687748.1| 101 MRDAVARMGKDPQSINPIIPVNLVIDHSIQTDVAGCDKAMQENEEIDFSRNKERYA 156
                                       67889999999999999998777777788888999999999999*********996 PP

  == domain 2  score: 141.5 bits;  conditional E-value: 2e-45
                                       CCCCCTT--CHHHHSTGGGCCGHCCHHHCCCGGTTTCCCCTTTSBBSEEEETTTTEEEEHHHHHHHHHHTT--EEEE CS
                       Aconitase_C   3 kllklkGlttedeksnvdtdlkipkqfegtianiglgnelveekrankttdlddgekedvvdaaerykkegaklvvi 79 
                                       k+l + G++++d++s+++++++++ +++gt+an++l+n ++++ + +  ++++dg    ++++ e+y++++++l+vi
  gi|474934166|ref|YP_007687748.1| 679 KYLISLGVQKKDFNSYGSRRANHEIMVRGTFANVRLRNMIAPGTEGGYSKYVPDGSVDYMYETSEKYRRDDTPLIVI 755
                                       789999*********************************************************************** PP

                                       --SSBTBS---THHHHHHHHTTEEEEEES-B-HHHHHHHHHTT-EEEEEST CS
                       Aconitase_C  80 agknfGeGSSRehAAkalrllGikaviaeSFerIfennliknglLplefke 130
                                       agk++G GSSR++AAk+++llG+kaviaeSFerI+++nl+++g++pl+f+e
  gi|474934166|ref|YP_007687748.1| 756 AGKDYGMGSSRDWAAKGPLLLGVKAVIAESFERIHRSNLVGMGIIPLQFEE 806
                                       *************************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (878 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.72u 0.34s 00:00:01.06 Elapsed: 00:00:00.52
# Mc/sec: 5070.41
//
Query:       gi|474934167|ref|YP_007687749.1|  [L=42]
Description: hypothetical protein TALC_00590 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.32s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 266.67
//
Query:       gi|474934168|ref|YP_007687750.1|  [L=225]
Description: hypothetical protein TALC_00591 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-16   59.7   0.0    4.1e-16   59.2   0.0    1.2  1  PPK2      Polyphosphate kinase 2 (PPK2)


Domain annotation for each model (and alignments):
>> PPK2  Polyphosphate kinase 2 (PPK2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.2   0.0   2.3e-20   4.1e-16      15     201 ..      10     187 ..       5     208 .. 0.82

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 2.3e-20
                                       HHHHHHHHHSGGGGG-EEEEEEEESTTS-HHHHHHHHHTTS-GGG-EEEE--S--HHHHTS-TTHHHHTT---TT-E CS
                              PPK2  15 qielvklqekvkaegkklvvifegrDaAGKgGaikrvtealnprvarvvalkaPteeEksqwylqRyvehlPakgei 91 
                                       + +l ++q ++++++  ++++feg  +     +++++   l+pr ++   ++       +   l  +ve  P kgei
  gi|474934168|ref|YP_007687750.1|  10 EKRLNRAQMELAQRDVPVLIVFEGGSGRVISRVVNEIARSLEPRCVTYHHFDVMK---SGPRALANMVEATPGKGEI 83 
                                       5689999*****************8888788888888888999988888887655...556668999********** PP

                                       EEEES-GGGGGTHHHHHTSS-HHHHHHHHHHHHHHHHHHHHTTEEEEEEEEE--HHHHHHHHHH.HHHSS-CCC--- CS
                              PPK2  92 vlFdRswYnragvervmgfctdkeaerflreipefErmlvesgillvKfwlsiskeeqleRfke.RredPlkqwKls 167
                                       +lFdRswY     e+  g+       + l+ i++fE+ l+++g+ l+K  ls+++e  +   ++ R  +Pl    ls
  gi|474934168|ref|YP_007687750.1|  84 ALFDRSWYS-MFLEKFNGVK--GGLAEGLKVIRAFEEYLQDNGTYLIKIDLSVTPEAMKDYAEQyRPFTPLSGTFLS 157
                                       ********7.5789999985..568899***************************9877765432666777665554 PP

                                       CCCCCHHHCHHHHHHHHHHHHHHH--SSS-EEEE CS
                              PPK2 168 plDlksrekWddytkakeemlartdteeaPWivv 201
                                        +D  +r    +y +  +em+  tdt+ aPW  +
  gi|474934168|ref|YP_007687750.1| 158 -VDRIDRV---KYWAMADEMISGTDTDRAPWDRI 187
                                       .3444443...466789**************765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1633.04
//
Query:       gi|474934169|ref|YP_007687751.1|  [L=217]
Description: hypothetical protein TALC_00592 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-80  270.1   0.1    1.6e-80  269.9   0.1    1.0  1  PPK2      Polyphosphate kinase 2 (PPK2)
  ------ inclusion threshold ------
      0.013   15.3   0.0      0.024   14.4   0.0    1.4  1  Coa1      Cytochrome oxidase complex assembly protein 1


Domain annotation for each model (and alignments):
>> PPK2  Polyphosphate kinase 2 (PPK2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  269.9   0.1   1.8e-84   1.6e-80      13     223 ..       3     213 ..       1     216 [. 0.98

  Alignments for each domain:
  == domain 1  score: 269.9 bits;  conditional E-value: 1.8e-84
                                       HHHHHHHHHHHSGGGGG-EEEEEEEESTTS-HHHHHHHHHTTS-GGG-EEEE--S--HHHHTS-TTHHHHTT---TT CS
                              PPK2  13 klqielvklqekvkaegkklvvifegrDaAGKgGaikrvtealnprvarvvalkaPteeEksqwylqRyvehlPakg 89 
                                       +l ++l  lq  +  +g ++v++feg+DaAGKgG ik++ +alnpr++ +  +k+Pt+++ ++ yl+R+ + +P  g
  gi|474934169|ref|YP_007687751.1|   3 RLSTDLEGLQILLSLSGMSVVLVFEGWDAAGKGGCIKHIAHALNPRGYLIDRVKKPTATDLAHTYLWRFASYMPRPG 79 
                                       577889999999***************************************************************** PP

                                       -EEEEES-GGGGGTHHHHHTSS-HHHHHHHHHHHHHHHHHHHHTTEEEEEEEEE--HHHHHHHHHHHHHSS-CCC-- CS
                              PPK2  90 eivlFdRswYnragvervmgfctdkeaerflreipefErmlvesgillvKfwlsiskeeqleRfkeRredPlkqwKl 166
                                       +i++FdRswY+r +ve ++gfct++e+ r  +ei+++E+ml++sg +++Kfwl+i+k+eq+ Rf++R+edPlk+wKl
  gi|474934169|ref|YP_007687751.1|  80 HISIFDRSWYGRMMVEPIEGFCTPEEYSRSADEINTMEHMLADSGAIVIKFWLDITKDEQEVRFNARKEDPLKSWKL 156
                                       ***************************************************************************** PP

                                       -CCCCCHHHCHHHHHHHHHHHHHHH--SSS-EEEEE-SSHHHHHHHHHHHHHHHHHH CS
                              PPK2 167 splDlksrekWddytkakeemlartdteeaPWivveaddKkrarlnvirtllkalky 223
                                       +++D+++rekWd y++ ++ m+a t+t+ aPW+vv+a++Kk+a+++v++ ++++lk+
  gi|474934169|ref|YP_007687751.1| 157 TDEDWRNREKWDVYEEYVDRMIASTNTPYAPWVVVPANNKKAAQMQVMSAVVSELKK 213
                                       ****************************************************99986 PP

>> Coa1  Cytochrome oxidase complex assembly protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.7e-06     0.024      60     101 ..     110     157 ..     102     162 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.7e-06
                              Coa1  60 sGelntv......kGkidlsfpvkGskgeGtvyltaeResktepfeil 101
                                        +e+nt+      +G i ++f++  +k e +v+++a++e++ + ++++
  gi|474934169|ref|YP_007687751.1| 110 ADEINTMehmladSGAIVIKFWLDITKDEQEVRFNARKEDPLKSWKLT 157
                                       67777777777889*******************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1395.20
//
Query:       gi|474934170|ref|YP_007687752.1|  [L=230]
Description: putative transcriptional regulator [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.5e-13   49.1   0.0    9.3e-13   48.0   0.0    1.5  1  HTH_3           Helix-turn-helix
    4.5e-09   36.5   0.0    8.1e-09   35.7   0.0    1.3  1  HTH_31          Helix-turn-helix domain
    2.7e-07   30.5   0.0    7.4e-07   29.1   0.0    1.8  1  HTH_19          Helix-turn-helix domain
     0.0025   17.9   0.0     0.0049   17.0   0.0    1.4  1  MqsA_antitoxin  Antitoxin component of bacterial toxin-antito
      0.007   16.3   0.0      0.014   15.3   0.0    1.5  1  HTH_37          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.034   13.9   0.0      0.088   12.6   0.0    1.6  1  HTH_38          Helix-turn-helix domain
        0.1   12.4   0.0       0.41   10.5   0.0    2.0  2  HTH_23          Homeodomain-like domain


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.0   0.0   3.6e-16   9.3e-13       1      48 [.      23      71 ..      23      72 .. 0.96

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 3.6e-16
                                      HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTT.SSCSBHHHHHHHHHHH CS
                             HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnG.ernPsletlkklakaL 48
                                      ++++R++ g+sq eLA+++Gvs s is++E+G + +P + ++kk+ +++
  gi|474934170|ref|YP_007687752.1| 23 IRKWREEFGISQYELADAMGVSHSVISDYESGrRKSPGVAVVKKMVDTF 71
                                      89*******************************999********98765 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.0   3.2e-12   8.1e-09       3      53 ..      20      70 ..      20      77 .. 0.92

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 3.2e-12
                            HTH_31  3 GalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealara 53
                                      G   r +Re+ G+sq e+A++ gvs s +s++E+Grr  p  av+ ++++ 
  gi|474934170|ref|YP_007687752.1| 20 GKAIRKWREEFGISQYELADAMGVSHSVISDYESGRRKSPGVAVVKKMVDT 70
                                      566899****************************************99876 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   2.9e-10   7.4e-07       1      48 [.      20      67 ..      20      75 .. 0.92

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 2.9e-10
                            HTH_19  1 GerLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllki 48
                                      G+ +++ Ree+g++q ela+  g+s s is +E+g+++ p+  +++k 
  gi|474934170|ref|YP_007687752.1| 20 GKAIRKWREEFGISQYELADAMGVSHSVISDYESGRRKSPGVAVVKKM 67
                                      899********************************999**98887765 PP

>> MqsA_antitoxin  Antitoxin component of bacterial toxin-antitoxin system, MqsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.9e-06    0.0049      67     115 ..      16      65 ..       2      72 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.9e-06
                    MqsA_antitoxin  67 elvdpafiarvrkkleldqreaaeifGgGvnafsryekGkvrpp.lalvk 115
                                       ++  ++ i++ r++++++q e+a+ +G+     s ye+G+ ++p +a+vk
  gi|474934170|ref|YP_007687752.1|  16 SSEPGKAIRKWREEFGISQYELADAMGVSHSVISDYESGRRKSPgVAVVK 65 
                                       4456789********************************98865377877 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   5.5e-06     0.014      10      55 ..      10      55 ..       2      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.5e-06
                                      HHHHHHHHHHHHHHHHHHHHCT--HHHHHHHHT--HHHHHHHHTT- CS
                            HTH_37 10 aeelkaKaqlalaiaeliekrelsqseaaqllgiaqPkvsrllrgk 55
                                      a e+ + ++  +ai++ +e+ ++sq e+a ++g++++ +s+ + g+
  gi|474934170|ref|YP_007687752.1| 10 AGEITLSSEPGKAIRKWREEFGISQYELADAMGVSHSVISDYESGR 55
                                      5667777888899***************************999877 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.4e-05     0.088      13      38 ..      23      49 ..      21      49 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.4e-05
                            HTH_38 13 Ierlla.eGlslreIArrLgrspsTIs 38
                                      I ++++  G s++e A  +g+s+s Is
  gi|474934170|ref|YP_007687752.1| 23 IRKWREeFGISQYELADAMGVSHSVIS 49
                                      788886258*****************8 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00016      0.41      10      37 ..      22      51 ..      20      57 .. 0.87
   2 ?   -1.7   0.0       1.1   2.9e+03      16      24 ..     151     161 ..     140     168 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00016
                            HTH_23 10 illllae..GlsvreIAreLgvsrrTvyrw 37
                                      +++  +e  G+s+ e A+++gvs++ ++ +
  gi|474934170|ref|YP_007687752.1| 22 AIRKWREefGISQYELADAMGVSHSVISDY 51
                                      89999999****************987765 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.1
                            HTH_23  16 e..GlsvreIA 24 
                                       +  G+s++++ 
  gi|474934170|ref|YP_007687752.1| 151 KiyGWSIERAL 161
                                       36799998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1619.95
//
Query:       gi|474934171|ref|YP_007687753.1|  [L=350]
Description: putative hydroxymethylglutaryl-CoA synthase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-11   43.9   0.0    5.8e-11   42.4   0.0    1.8  1  ACP_syn_III_C   3-Oxoacyl-[acyl-carrier-protein (ACP)] syntha
    8.3e-07   28.9   0.0     0.0002   21.1   0.0    2.2  2  HMG_CoA_synt_C  Hydroxymethylglutaryl-coenzyme A synthase C t
  ------ inclusion threshold ------
      0.011   15.5   0.8       0.03   14.1   0.8    1.8  1  ACP_syn_III     3-Oxoacyl-[acyl-carrier-protein (ACP)] syntha
      0.028   13.8   0.4      0.046   13.1   0.4    1.3  1  Thiolase_N      Thiolase, N-terminal domain


Domain annotation for each model (and alignments):
>> ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.0   1.3e-14   5.8e-11       2      81 ..     220     299 ..     219     305 .. 0.92

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 1.3e-14
                                       HHTT--GGG-SEEEE-SSSHHHHHHHHHHHT--GGGB--TH..HHH-B-GGGHHHHHHHHHHHTTSS-TT-EEEEEE CS
                     ACP_syn_III_C   2 ekagltpedidalvphqanlriidavakklglpeekvvvnl..deyGntsaasiplaLdeaveegklkpgdlvllvg 76 
                                       e+ g tp+d +++v+hq n ++   va +lg+++e+v   l   ++Gn+ +  +p+ L++ ++    k+gd++l+++
  gi|474934171|ref|YP_007687753.1| 220 EAMGTTPADYNYCVFHQPNGKFPTRVAAQLGFTPEQVECGLvtPNIGNCYSGAVPIGLAHVLD--HAKAGDRILVTS 294
                                       77899******************************8876665599******************..99********** PP

                                       EETTT CS
                     ACP_syn_III_C  77 fGaGl 81 
                                        G G 
  gi|474934171|ref|YP_007687753.1| 295 YGSGA 299
                                       **996 PP

>> HMG_CoA_synt_C  Hydroxymethylglutaryl-coenzyme A synthase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0    0.0016       7.1      39      93 ..     207     252 ..     174     258 .. 0.67
   2 !   21.1   0.0   4.5e-08    0.0002     149     211 ..     260     318 ..     251     346 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0016
                                       HHHHHHHHHHHHHHHHHHHHHH------GGG-SEEEE--SSHHHHHHHHHHHHHH CS
                    HMG_CoA_synt_C  39 YlkaldrcYksyskkvkkitkdadkeftlddfdyvifhsPfcklvqkslarllyn 93 
                                       Y + + ++ k +++            +t  d++y++fh P  k+ ++  a+l ++
  gi|474934171|ref|YP_007687753.1| 207 YFRHVSTAAKMMME---------AMGTTPADYNYCVFHQPNGKFPTRVAAQLGFT 252
                                       44444444333332.........3345667899***********99999999887 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 4.5e-08
                                       HHHHHH---GGGHHHHHHHHHHHHS-HHHHTT-EEEEEEEETTTEEEEEEEEE-S--STTSHH CS
                    HMG_CoA_synt_C 149 lvptevGnmYtaslyaalasllskvsadelagkriglfsYGsGlaaslfslrvkqdvsedsil 211
                                       lv+ ++Gn Y  ++   la +l ++     ag ri++ sYGsG  +  f ++v++++++ +  
  gi|474934171|ref|YP_007687753.1| 260 LVTPNIGNCYSGAVPIGLAHVLDHA----KAGDRILVTSYGSGAGSDAFDITVTDEMTNYRKE 318
                                       45668*****************554....5799**********************99885544 PP

>> ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.8   6.8e-06      0.03       2      64 ..     108     167 ..     107     184 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.8e-06
                                       EEE-GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEGGGCS-TTTHHHHTTB-EEEEEEEEEEE CS
                       ACP_syn_III   2 DlnaaCsgfvyalsvAdaliesgaakrvLvigaetlskilDwkdrstavlfGDGAgAvvleas 64 
                                       Dl+ aC++ +++++   +l++s+++k+++ iga+t s+       +  +  + G++A +l+++
  gi|474934171|ref|YP_007687753.1| 108 DLEFACKAGTAGIQAGLGLVKSDMVKYAVAIGADT-SQGA--PGDALEYSAAAGGAAYLLGKE 167
                                       8999******************************9.5533..234555556777777777775 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.4     1e-05     0.046      24     113 ..      51     141 ..      39     159 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1e-05
                                       HHHHHHHHHHHHHHHT.S-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSEEEEEEHGGGHHHHHHHHHHHHH CS
                        Thiolase_N  24 eeLlaealkallekag.vdpeevdevivGnvlqagegqniarqaalkagipeevpavtvnkvcsSglkavalaaqsi 99 
                                       + ++++a++ ++++++ v+p+++  v++G   +  + +  +  +a ++g   +++a  ++ +c  g +++ ++ + +
  gi|474934171|ref|YP_007687753.1|  51 VTIATAAARFMMARVPeVNPADIGAVYIGSESHPYAVKPSSAIVATAIGATPNMTAADLEFACKAGTAGIQAGLGLV 127
                                       56777888889999999************************************************************ PP

                                       HTTSHSEEEEEEEE CS
                        Thiolase_N 100 aageadvvvagGvE 113
                                       ++  ++ +va+G+ 
  gi|474934171|ref|YP_007687753.1| 128 KSDMVKYAVAIGAD 141
                                       ************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 2100.56
//
Query:       gi|474934172|ref|YP_007687754.1|  [L=389]
Description: Acetyl-CoA acetyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-25   89.0   1.3      8e-25   87.7   1.3    1.6  1  Thiolase_N     Thiolase, N-terminal domain
    1.6e-06   27.7   1.5    1.2e-05   24.9   0.5    2.5  2  Thiolase_C     Thiolase, C-terminal domain
    1.8e-05   24.4   2.8     0.0043   16.7   0.8    3.4  3  ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
  ------ inclusion threshold ------
        3.1    8.0   9.1          2    8.6   0.7    2.8  2  YadA_anchor    YadA-like membrane anchor domain


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.7   1.3   1.8e-28     8e-25       1     258 [.       4     224 ..       4     226 .. 0.92

  Alignments for each domain:
  == domain 1  score: 87.7 bits;  conditional E-value: 1.8e-28
                                       EEEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCT..TSTSCHHHHHHHHTTS-.T CS
                        Thiolase_N   1 vvivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqa..gegqniarqaalkagip.e 74 
                                       v+i++a  t++g+    l  +s + L+ ea+ +++++ag++ +e+d v++Gn +++   + qni   +a  +g++ +
  gi|474934172|ref|YP_007687754.1|   4 VAIIGAGSTKFGE----LWGASFRALGIEAGAKAIADAGLSGDEIDAVYIGNLASGnfIKQQNIDALVADYTGMAtR 76 
                                       79***********....88889999******************************98778999*9999999999636 PP

                                       TSEEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGSSSSEEEEEHHHHHHTEETTT CS
                        Thiolase_N  75 evpavtvnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvrsglklgdekakdllipdgladafn 151
                                       +vpa++ +   +Sg  a  +++q++a+g +d+v++gG+E+m++ + +     + +++l++e   ++ i++       
  gi|474934172|ref|YP_007687754.1|  77 HVPAIRTEAGGASGGVAFRQGVQAVASGMSDIVIVGGAEKMTDMDDDRV-GQVLNATLDAEWEAGVGITE------- 145
                                       8*******************************************99886.55688888999888888888....... PP

                                       TSEHHHHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHT CS
                        Thiolase_N 152 eehmGltaenlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLak 228
                                           ++ a++l k+  ++Ree ++ Av+sh ++a +++a  F++ei              + d+ +r++ t ++L  
  gi|474934172|ref|YP_007687754.1| 146 TSIYAMIARRLIKEGIATREEIASCAVNSHFHGARNPEAE-FRKEI--------------KLDTVLRAGPTCDPLTM 207
                                       67889**********************************9.*****..............78999999999999999 PP

                                       S-BSSSTTSS-BTTSB--BEEEEEEEEEEE CS
                        Thiolase_N 229 lkpaFkkeGtvtAgnasqisDGaaavllms 258
                                                     +  + sDGa+av+l++
  gi|474934172|ref|YP_007687754.1| 208 F-------------DGAPFSDGASAVILCP 224
                                       9.............8899999999999985 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0     0.082   3.7e+02      26      48 ..      28      50 ..      20      69 .. 0.80
   2 !   24.9   0.5   2.7e-09   1.2e-05      25     117 ..     263     381 ..     231     387 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.082
                                      HHHHHHHHHHT--GGGESEEEE- CS
                        Thiolase_C 26 yaikkvlkkagltvedidlfEin 48
                                       a  k++ +agl+ ++id++ i 
  gi|474934172|ref|YP_007687754.1| 28 EAGAKAIADAGLSGDEIDAVYIG 50
                                      577899************98775 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 2.7e-09
                                       HHHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--G...................GGBSTT--HHHH-B-T CS
                        Thiolase_C  25 ayaikkvlkkagltvedidlfEinEAFaaqaLavakaldldl...................ekvNvnGGaialGHPl 82 
                                         a++++  +a +t +di++ E+++A ++  + ++++l+l                       vN  GG  + G P+
  gi|474934172|ref|YP_007687754.1| 263 SVAAQQAYRDAHITAADIQVAEVHDAQTVGGVLALQDLGLYGngeagkaflegqthfdagkVAVNTSGGLKSKGYPV 339
                                       57899999*******************************99899***************88889************* PP

                                       TTHHHHHHHHHHHHHHH.......CTTSEEEEEEEETTTEEE CS
                        Thiolase_C  83 GasGaRivvtllselkk.......eggklgvaalCigggqgv 117
                                       Ga+G+ ++v l ++l+        +++k g+a    g+g +v
  gi|474934172|ref|YP_007687754.1| 340 GAAGVSQIVELYQQLTGtagdrqvKDAKHGLAQSVGGTGSAV 381
                                       **************9751111111445556665555555554 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.7   0.0    0.0089        40      90     120 ..      24      54 ..      20      79 .. 0.75
   2 !   16.7   0.8   9.6e-07    0.0043     167     207 ..      79     119 ..      76     131 .. 0.91
   3 ?    1.6   0.0     0.039   1.8e+02     234     253 .]     209     228 ..     196     228 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.0089
                                       HHHHHHHHHHHHHHTS-HHTCTTGGEEEEEE CS
                     ketoacyl-synt  90 rllleaawealedagltpeeldgsrvgvfiG 120
                                        l +ea ++a++dagl+ +e+d   +g+++ 
  gi|474934172|ref|YP_007687754.1|  24 ALGIEAGAKAIADAGLSGDEIDAVYIGNLAS 54 
                                       6899****************99876666554 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 9.6e-07
                                       SEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---S CS
                     ketoacyl-synt 167 psvtvdtACsSslvavhaavqslrsgeadvalaGGvelllt 207
                                       p++ +++  +S+ va  + vq++ sg +d++++GG+e ++ 
  gi|474934172|ref|YP_007687754.1|  79 PAIRTEAGGASGGVAFRQGVQAVASGMSDIVIVGGAEKMTD 119
                                       778889999****************************9875 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.039
                                       -SB-BB-EEEEEEEEECHHH CS
                     ketoacyl-synt 234 dGfvlGEGvGavvLkrleda 253
                                       dG  +++G+ av+L +leda
  gi|474934172|ref|YP_007687754.1| 209 DGAPFSDGASAVILCPLEDA 228
                                       8999*************998 PP

>> YadA_anchor  YadA-like membrane anchor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   2.0     0.037   1.6e+02      11      32 ..      88     109 ..      82     112 .. 0.86
   2 ?    8.6   0.7   0.00044         2      32      57 ..     319     345 ..     315     346 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.037
                       YadA_anchor  11 vgaGvGgYkgqsAvAvGasars 32 
                                        + Gv++ +g +AvA G+s ++
  gi|474934172|ref|YP_007687754.1|  88 ASGGVAFRQGVQAVASGMSDIV 109
                                       57899999**********9765 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00044
                       YadA_anchor  32 s.ngnlvvklgvavssggsvgggvGvg 57 
                                       + +g+++v+++++ +s+g   g++Gv+
  gi|474934172|ref|YP_007687754.1| 319 FdAGKVAVNTSGGLKSKGYPVGAAGVS 345
                                       5689*********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2540.79
//
Query:       gi|474934173|ref|YP_007687755.1|  [L=135]
Description: putative nucleic-acid-binding protein containing a Zn-ribbon [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-16   60.1   0.0    2.4e-16   59.5   0.0    1.4  1  OB_aCoA_assoc   DUF35 OB-fold domain, acyl-CoA-associated
    2.6e-09   36.8   2.4    3.6e-09   36.3   2.4    1.2  1  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
     0.0021   18.2   1.6      0.004   17.3   1.6    1.4  1  C5HCH           NSD Cys-His rich domain
     0.0067   16.4   0.4       0.01   15.8   0.4    1.2  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.022   15.5   0.4      0.036   14.8   0.4    1.3  1  zinc_ribbon_15  zinc-ribbon family
      0.045   14.0   0.4       0.22   11.8   0.0    2.1  2  zf-LITAF-like   LITAF-like zinc ribbon domain
      0.054   13.2   0.8       0.13   12.0   0.8    1.6  1  WCCH            WCCH motif
          1    9.6   6.4        4.5    7.5   0.1    2.6  2  zf-RING_7       C4-type zinc ribbon domain
        1.1    9.1   7.8         15    5.4   7.8    2.3  1  zinc_ribbon_2   zinc-ribbon domain


Domain annotation for each model (and alignments):
>> OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.5   0.0   1.2e-19   2.4e-16       3      65 .]      52     114 ..      50     114 .. 0.95

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 1.2e-19
                                       EE-GG-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT...-EE-EEEEEEES..TT-B-EEE-S CS
                     OB_aCoA_assoc   3 elsgrGtvysftvvhrappgfaeeaPyvvgvVeLdegvrimarlvgvdpdevriGmrVravfr 65 
                                       +lsg+G+vys++++h +  +++   Py+v++V+ d+gv + ++lv+vd + ++iGmrVrav+r
  gi|474934173|ref|YP_007687755.1|  52 RLSGKGEVYSYSIIHDNSGFNGCMMPYAVAMVKDDDGVMVEGQLVDVDLEKIEIGMRVRAVMR 114
                                       79****************7777899***********************************986 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   2.4   1.8e-12   3.6e-09       2      34 ..      11      43 ..      10      46 .. 0.89

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 1.8e-12
                           DUF35_N  2 daaaegrLvgqrCpdCGtvqfPPravCphCgsd 34
                                      +   ++ L g++C+ CG+ +fP r +Cp+C++ 
  gi|474934173|ref|YP_007687755.1| 11 EIPGRYNLEGSKCTECGRIFFPERSFCPYCRRH 43
                                      666799************************976 PP

>> C5HCH  NSD Cys-His rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   1.6     2e-06     0.004       3      39 ..      22      56 ..      21      59 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2e-06
                             C5HCH  3 qCsvCgkaatsfCefCPssFCkeHekGalvasalegr 39
                                      +C++Cg+       fCP  +C++H  G++  + l g+
  gi|474934173|ref|YP_007687755.1| 22 KCTECGRIFFPERSFCP--YCRRHSMGKMEKHRLSGK 56
                                      7****************..9************99986 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.4   5.2e-06      0.01      29      48 ..      21      40 ..       7      41 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.2e-06
                               DZR 29 drCpsCgekvdpearfCpeC 48
                                       +C +Cg+   pe +fCp+C
  gi|474934173|ref|YP_007687755.1| 21 SKCTECGRIFFPERSFCPYC 40
                                      68****************** PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.4   1.8e-05     0.036      62      85 ..      17      40 ..       4      41 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.8e-05
                    zinc_ribbon_15 62 ssekkeCknCgkeveeefkyCpkC 85
                                      + e  +C +Cg+   +e ++Cp+C
  gi|474934173|ref|YP_007687755.1| 17 NLEGSKCTECGRIFFPERSFCPYC 40
                                      455789****************** PP

>> zf-LITAF-like  LITAF-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.81   1.6e+03      58      64 ..      22      28 ..      20      30 .. 0.76
   2 ?   11.8   0.0   0.00011      0.22       3      54 ..      32      85 ..      31      87 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.81
                     zf-LITAF-like 58 yCpnCga 64
                                      +C++Cg+
  gi|474934173|ref|YP_007687755.1| 22 KCTECGR 28
                                      6888886 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00011
                     zf-LITAF-like  3 ptqvdCpaCqqrvvTsveyks..gkltwlla.lllclfgcllccliPfcvdslkd 54
                                      p++  Cp+C+++++ ++e++   gk+      ++    g + +c++P+ v + kd
  gi|474934173|ref|YP_007687755.1| 32 PERSFCPYCRRHSMGKMEKHRlsGKGEVYSYsIIHDNSG-FNGCMMPYAVAMVKD 85
                                      78889*************996114444444435555555.467888888888877 PP

>> WCCH  WCCH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.8   6.3e-05      0.13       7      14 ..      36      43 ..      36      47 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.3e-05
                              WCCH  7 cCPhCPRH 14
                                      +CP+C+RH
  gi|474934173|ref|YP_007687755.1| 36 FCPYCRRH 43
                                      7******* PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1    0.0023       4.5      25      32 ..      22      29 ..       9      30 .. 0.91
   2 ?    3.6   2.0     0.039        78      25      31 ..      36      42 ..      34      42 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0023
                                      E-TTT--E CS
                         zf-RING_7 25 tCpeCGRI 32
                                      +C eCGRI
  gi|474934173|ref|YP_007687755.1| 22 KCTECGRI 29
                                      7******9 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.039
                                      E-TTT-- CS
                         zf-RING_7 25 tCpeCGR 31
                                      +Cp+C R
  gi|474934173|ref|YP_007687755.1| 36 FCPYCRR 42
                                      8****98 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   7.8    0.0077        15       1      21 [.      22      42 ..      22      44 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0077
                     zinc_ribbon_2  1 fCpnCGaelqdnakFCpyCGt 21
                                      +C++CG+   ++  FCpyC+ 
  gi|474934173|ref|YP_007687755.1| 22 KCTECGRIFFPERSFCPYCRR 42
                                      7999999999999******75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 945.31
//
Query:       gi|474934174|ref|YP_007687756.1|  [L=155]
Description: hypothetical protein TALC_00597 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-10   41.9   0.0    1.2e-10   41.7   0.0    1.2  1  CGI-121   Kinase binding protein CGI-121
  ------ inclusion threshold ------
      0.013   15.7   0.1      0.022   15.0   0.1    1.4  1  SMBP      Small metal-binding protein


Domain annotation for each model (and alignments):
>> CGI-121  Kinase binding protein CGI-121
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   0.0   1.3e-14   1.2e-10      22      96 ..      28     102 ..      16     147 .. 0.87

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 1.3e-14
                                       T-EEE-GGG---HHHHHHHHHHHHHHHHHS---SSSHHHHHHHHHSSSS-HHHHHHHHB--TT-S-EEEEEEESS CS
                           CGI-121  22 dfafldaslilskehllsAvlrallaaargklktktlhsEilfsLspnnnIgealkrfgisdkttsllvvkvsss 96 
                                       ++ +l++s+++ k h++sAv++a  a a+g+ + ktl +Ei+++   +++Ig+alk++  +d t+ ++++ ++ +
  gi|474934174|ref|YP_007687756.1|  28 EVVLLEPSVVCGKDHVVSAVMHAERAFAEGRNRAKTLLTEIVLYAACERQIGKALKKMKPTDGTAGMVAAVLNYP 102
                                       679***********************************************************9998888887766 PP

>> SMBP  Small metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   2.5e-06     0.022      13      51 ..      29      66 ..      17      87 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.5e-06
                                      XXXXXXXXXXX--HHHHHHHHHHHHHHHHHTT-HHHHHH CS
                              SMBP 13 lalfsssavaaeehlaeAiehaeaAvahgkaghakalve 51
                                      ++l+  s v +++h+  A+ hae+A a+g +  ak l++
  gi|474934174|ref|YP_007687756.1| 29 VVLLEPSVVCGKDHVVSAVMHAERAFAEGRN-RAKTLLT 66
                                      3455677888999*****************7.8888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1034.11
//
Query:       gi|474934175|ref|YP_007687757.1|  [L=310]
Description: homoserine kinase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-06   28.6   0.0    3.2e-06   27.4   0.0    1.6  1  GHMP_kinases_C  GHMP kinases C terminal
    5.1e-06   26.6   2.8    9.5e-06   25.8   2.8    1.5  1  GHMP_kinases_N  GHMP kinases N terminal domain


Domain annotation for each model (and alignments):
>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   3.6e-10   3.2e-06       8      71 ..     218     276 ..     211     290 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 3.6e-10
                    GHMP_kinases_C   8 gdlellgellnlsqrs...elkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkde 71 
                                        dl+l+g+ +     +   e+   ++ l p+l+e+ +a++e+Ga+ ++l G+  Gp+v a++++  +
  gi|474934175|ref|YP_007687757.1| 218 DDLPLIGRSVA----DmvfEP--ARAHLIPNLKEAEKAAMEHGAIVSFLGGS--GPCVMAFYDKSTH 276
                                       67888888888....455589..*****************************..********55444 PP

>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   2.8   1.1e-09   9.5e-06       2      66 .]      85     151 ..      84     151 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 1.1e-09
                                       EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHH..HHHHH.HHHHHHHHHHHHHHSHHHHHHHHSS CS
                    GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglsl..eeakl.aleaerlaqggngsggDvaasvyGg 66 
                                       ++i++ i + +G+GSS+A a+++++ +    g +l  +e+ l a+ ae +   g+ + ++va++++Gg
  gi|474934175|ref|YP_007687757.1|  85 VKIHKGIRPCSGIGSSGASAAGGAYLAHLISGEKLsiNEVILcAAYAEGYTS-GSIHADNVAPCILGG 151
                                       7899****************99999976666777754445553777777776.999***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2198.69
//
Query:       gi|474934176|ref|YP_007687758.1|  [L=414]
Description: L-threonine synthase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.8e-75  252.7   1.1    5.6e-75  252.5   1.1    1.0  1  PALP            Pyridoxal-phosphate dependent enzyme
    2.1e-05   24.1   2.1    4.7e-05   22.9   2.1    1.6  1  zinc_ribbon_2   zinc-ribbon domain
      4e-05   22.9   1.9    7.6e-05   22.0   1.9    1.5  1  zf-ribbon_3     zinc-ribbon domain
     0.0054   16.7   0.3      0.013   15.5   0.3    1.6  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.077   13.0   0.1       0.16   12.0   0.1    1.5  1  HypA            Hydrogenase/urease nickel incorporation, meta
        0.4   10.5   2.0       0.39   10.5   0.2    1.8  2  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  252.5   1.1   1.9e-78   5.6e-75       2     294 .]      77     380 ..      76     380 .. 0.97

  Alignments for each domain:
  == domain 1  score: 252.5 bits;  conditional E-value: 1.9e-78
                                       GGCSSS--EEEECCTCCCCCCE.EEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHH CS
                              PALP   2 tlgigpTPlvrlprlskelgvp.lflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaall 77 
                                       + ++g+TPl + ++l +e+gvp  ++K E+lnptgSfKdRg++  ++++ke  gak+v +as+GN+ ++l+a+a+++
  gi|474934176|ref|YP_007687758.1|  77 SIQEGGTPLYKTEALGAEVGVPdAYVKFEGLNPTGSFKDRGMTIGVSHAKEL-GAKVVGCASTGNTSASLSAYASKA 152
                                       5689************************************************.************************ PP

                                       T-EEEEEEETTS-H.HHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHH CS
                              PALP  78 Glkvtivvpadasp.ekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileq 153
                                       G+k+ +++p+++ + +k+a+   +Ga+v  ++g++d+a+a+a+++a+e ++ yl+++  np++ eg++++ +Ei++q
  gi|474934176|ref|YP_007687758.1| 153 GMKCAVFLPSGKVAmGKLAQALFFGAKVLSIDGNFDDALALARKMAEE-RKLYLLNSI-NPYRPEGQKSVLFEIMDQ 227
                                       *************87*********************************.*********.9***************** PP

                                       TT.TTEEEEEEE-SSSHHHHHHHHHHHH....HSTT..-EEEEEEECTTCGGTTCCS..S.SS..B...SSS.CCST CS
                              PALP 154 lg.gkpdavvvpvGgGgliaGiaaglke....rrpd..vrvigvepegsdalarslragrrvtvpvs..dtiadgla 221
                                       l+ ++pd +++pvG++++i +++++ ke    ++ d  + + g++++gs+++ar+++ag+ + + ++  +tia++++
  gi|474934176|ref|YP_007687758.1| 228 LKyDVPDRIILPVGNAANIWAVYKACKEleevGWIDriPMLTGIQAAGSAPVARAFEAGSNDFMAEPnpETIATAIR 304
                                       ****************************98887777978888*****************9999988888******** PP

                                       CS..CGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH.HHHHHHCCTTCEEEEEEE-B CS
                              PALP 222 vg..spselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaal.klreagelkegdrvvviltg 294
                                       +g  +++++a++++ ++ + + tv+d+e+++a++ll rreg+ vep+saa++a+l klre g ++++++vv+i tg
  gi|474934176|ref|YP_007687758.1| 305 IGnpVSGVKALKAIYDTKGFCTTVTDDEIVAAQQLLGRREGVCVEPASAASVAGLkKLREEGVIDKSEKVVCICTG 380
                                       ***9*********************************************************************998 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   2.1   1.6e-08   4.7e-05       2      20 ..      15      34 ..      14      35 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.6e-08
                     zinc_ribbon_2  2 CpnCGaelqd.nakFCpyCG 20
                                      C++CGae++d  ++ Cp+CG
  gi|474934176|ref|YP_007687758.1| 15 CWKCGAEVSDpYVNLCPKCG 34
                                      ********755********9 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   1.9   2.5e-08   7.6e-05       3      25 ..      13      36 ..      11      37 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.5e-08
                       zf-ribbon_3  3 vrCPnCGa.plssddnvCpyCGtk 25
                                      v C++CGa + ++ +n Cp+CG+ 
  gi|474934176|ref|YP_007687758.1| 13 VVCWKCGAeVSDPYVNLCPKCGGL 36
                                      78********************86 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.3   4.4e-06     0.013      27      49 .]      11      34 ..       3      34 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.4e-06
                               DZR 27 aedrCpsCgek.vdpearfCpeCG 49
                                      ++ +C++Cg++  dp  + Cp+CG
  gi|474934176|ref|YP_007687758.1| 11 HKVVCWKCGAEvSDPYVNLCPKCG 34
                                      4789******98899********9 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   5.5e-05      0.16      67      95 ..       9      36 ..       3      50 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.5e-05
                                      E--EEEETTTS-EEECHHHHHS-TTTSSS CS
                              HypA 67 vpvkvrCreCgkefeleekalrCpkCgsa 95
                                       + kv C +Cg+e++       CpkCg+ 
  gi|474934176|ref|YP_007687758.1|  9 ANHKVVCWKCGAEVSDPYV-NLCPKCGGL 36
                                      56789*********96643.46****985 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       1.2   3.7e+03       2      10 ..      13      21 ..      12      22 .. 0.78
   2 ?   10.5   0.2   0.00013      0.39       2      15 ..      28      41 ..      27      42 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.2
                                      EE-SSS--E CS
                    zf-C4_Topoisom  2 ekCPkCggd 10
                                      + C kCg++
  gi|474934176|ref|YP_007687758.1| 13 VVCWKCGAE 21
                                      5699***86 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00013
                                      EE-SSS--EEEEEE CS
                    zf-C4_Topoisom  2 ekCPkCggdLvlkr 15
                                      + CPkCgg L +k+
  gi|474934176|ref|YP_007687758.1| 28 NLCPKCGGLLTVKM 41
                                      68********9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      572  (0.0319036); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2705.76
//
Query:       gi|474934177|ref|YP_007687759.1|  [L=404]
Description: hypothetical protein TALC_00600 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-05   23.5   0.0     0.0003   20.8   0.0    2.4  1  AAA_14    AAA domain


Domain annotation for each model (and alignments):
>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   1.7e-08    0.0003       4      99 ..      22     131 ..      19     153 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.7e-08
                            AAA_14   4 ilvitGaRrvGKTtllkqlikell................vkkesilyinldderdkkladpekllelilek.lkee 63 
                                       + v++G+ r+GKT llk  + +                    + ++l +++    ++ l+d   +l+ + +  +++ 
  gi|474934177|ref|YP_007687759.1|  22 VTVVRGVHRSGKTSLLKFHVCRDVdisteadgrlvygcgsDGDTNVLALDVGLAGNYHLRDV-GILSGFVKGrIEDG 97 
                                       789*************7666666668975455555554433334444444444444555555.46666666557668 PP

                            AAA_14  64 kktylflDEiqevpewekalkslvdegknldvivtG 99 
                                       k++++++D i +v++we +  +l + g   d++vtG
  gi|474934177|ref|YP_007687759.1|  98 KHNVVLIDGIEHVKGWEPFATDLARGG--ADIYVTG 131
                                       99***********************88..79****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2668.58
//
Query:       gi|474934178|ref|YP_007687760.1|  [L=760]
Description: Superfamily II helicase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-26   91.9   0.0    1.4e-24   86.9   0.0    2.9  3  DEAD             DEAD/DEAH box helicase
    5.6e-10   39.6   0.2    1.5e-08   34.9   0.1    2.6  2  Helicase_C       Helicase conserved C-terminal domain
    3.4e-09   37.2   0.1    1.2e-08   35.5   0.1    1.9  1  HHH_5            Helix-hairpin-helix domain
    9.6e-07   29.0   0.0    2.2e-06   27.8   0.0    1.6  1  ResIII           Type III restriction enzyme, res subunit
    0.00053   20.0   0.1     0.0029   17.7   0.0    2.2  2  HHH_2            Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.022   14.7   0.2      0.097   12.6   0.0    2.1  2  DUF438           Family of unknown function (DUF438)
      0.076   12.9   0.0       0.25   11.2   0.0    1.9  1  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.9   0.0   5.3e-28   1.4e-24       2     172 ..      30     186 ..      29     190 .. 0.89
   2 ?   -0.4   0.0      0.33   8.6e+02      44      76 ..     248     283 ..     239     315 .. 0.71
   3 ?    0.5   0.0      0.18   4.5e+02      78     145 ..     518     585 ..     505     596 .. 0.72

  Alignments for each domain:
  == domain 1  score: 86.9 bits;  conditional E-value: 5.3e-28
                                       HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrv 78 
                                       + Qaeaip +l+g+++++a +T+sGK+++ ++p+l+ v+    ++g+k+l+++P+++La +  ++l+kf + ++++v
  gi|474934178|ref|YP_007687760.1|  30 PPQAEAIPKALTGRSLVAAVPTASGKSMIGFVPALSMVL----SSGKKVLYIVPLKALASEKRDDLNKFAH-LGIKV 101
                                       67************************************5....6999***********************9.78999 PP

                                       EEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  79 lliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcd 155
                                       ++++g+ +++d++s+     div++t ++ d++++ g+  ++++ +++ DE++++ d g++++++  ++++    ++
  gi|474934178|ref|YP_007687760.1| 102 VMTTGDPDRDDDVSDA----DIVIATSEKADSMIRHGNRWTEDLGMVIADEVHMIADPGRGPTLEIAMTKFM---HR 171
                                       9888877777777766....**************988888**************************999993...33 PP

                                       ST.TTSEEEEEESSBSHH CS
                                       xx.xxxxxxxxxxxxxxx RF
                              DEAD 156 gk.lqrqvivlSATlpkd 172
                                        + lq  vi+lSAT++ +
  gi|474934178|ref|YP_007687760.1| 172 NRfLQ--VIALSATIS-N 186
                                       33366..*******98.4 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.33
                                       TSTS-EEEEEESSHHHHHHHHHHHHHHTTTST...S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...x RF
                              DEAD  44 gktgpkalivePtreLaeqtlnnlkkfkkyid...l 76 
                                        ++g +a+i + tr  +e  +++++k +k+++   +
  gi|474934178|ref|YP_007687760.1| 248 IEEGGQAMIFVNTRRSTEALAKKFSKPMKELTgssI 283
                                       467889999999999999999999999996332331 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.18
                                       EEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHH.HHHCTSSHCTTEEEEEEETHHHHHHT.TTHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                              DEAD  78 vlliiggvaardqlskldngvdivvgtpgrldd.llstgklnlsqvrflVlDEadrlldq.gfsdfinri 145
                                       vl i++ v+  + l ++++++d++ + p++ d+  l+  +++ +   f  +DE d+ +d+ +  + ++  
  gi|474934178|ref|YP_007687760.1| 518 VLRITEAVDDLQILHAVSCTPDVMGMYPKKTDQnELE--SVDAEYSDFWLVDEKDESMDSpDWDNSYEIH 585
                                       4455666667777777778899999999999984444..456899999********99985555544444 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       4.4   1.1e+04      54      74 ..      86     106 ..      64     124 .. 0.48
   2 !   34.9   0.1   5.9e-12   1.5e-08      13     111 .]     248     389 ..     240     389 .. 0.71

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4.4
                                       HHHHHHHHHHTTSSSEEEESG CS
                        Helicase_C  54 ereeileqfnkgesdvLiatd 74 
                                       e+++ l++f +  ++v+++t 
  gi|474934178|ref|YP_007687760.1|  86 EKRDDLNKFAHLGIKVVMTTG 106
                                       233333333333333333333 PP

  == domain 2  score: 34.9 bits;  conditional E-value: 5.9e-12
                                       TTTTSEEEEEESSHHHHHH.HHHH.....................HHHT..............TSTEEEESTTSTHH CS
                        Helicase_C  13 eeeggkilifvntidrlek.vkll.....................lekk..............gikvavlhgelpqn 53 
                                        eegg+++ifvnt+++ e  +k +                                       +  +a +h+ l  +
  gi|474934178|ref|YP_007687760.1| 248 IEEGGQAMIFVNTRRSTEAlAKKFskpmkeltgssiteaeqalleG--GdestavgkilagcvACGIAFHHAGLDYK 322
                                       48999**********6644423333333443555555544444440..1444456666777777889999999**** PP

                                       HHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEE..ESSSS.......SSHHHHHHHHTTSSSTT CS
                        Helicase_C  54 ereeileqfnkgesdvLiatdvaerGidipkvnlVi..nfdlp.......rnvtsyiqriGRtgRag 111
                                       +r+ + + f++ ++++++at  ++ Gi++p  ++++   + +         +v +++q+ GR+gR g
  gi|474934178|ref|YP_007687760.1| 323 QRRFVEDGFRNRTIKCIVATPTLAAGINLPARRVIVrdTYRFEsnagnvpISVMEVQQMCGRAGRPG 389
                                       ******************************88888844333334443333446************75 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.1   4.5e-12   1.2e-08       6      54 ..     667     715 ..     661     717 .. 0.94

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 4.5e-12
                                       TSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHH CS
                             HHH_5   6 svsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriile 54 
                                       +  G+G+ +A++l  aG+++ +dlaaadv+ +a +p iGk +A++i+++
  gi|474934178|ref|YP_007687760.1| 667 TFRGVGRNRARTLFTAGFKTRQDLAAADVNVIAGLPKIGKALARSIKEQ 715
                                       567*******************************************997 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   8.7e-10   2.2e-06       5     169 ..      29     184 ..      25     186 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 8.7e-10
                                       -HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG. CS
                            ResIII   5 reyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflsea 81 
                                       ++ Q+eai + l        + ++ + +T +GK+++ +  + ++  + + +k+l +vp k+l +  +++++kf++  
  gi|474934178|ref|YP_007687760.1|  29 YPPQAEAIPKALT------GRSLVAAVPTASGKSMIGFVPALSMVLSSG-KKVLYIVPLKALASEKRDDLNKFAHLG 98 
                                       5666666666663......44688999**********998888888766.5************************99 PP

                                       ...GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS....T....TTH CS
                            ResIII  82 ykeigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak...k....swr 151
                                        k +++  + d+++      ++++i+++t +++d+ ++++++       +   ++i DE+H +++         +++
  gi|474934178|ref|YP_007687760.1|  99 IKVVMTTGDPDRDDD----VSDADIVIATSEKADSMIRHGNR-----WTEDLGMVIADEVHMIADPgrgPtleiAMT 166
                                       877777777777777....99****************33333.....3334459**********9755423444555 PP

                                       HHHHT---SEEEEEESS- CS
                            ResIII 152 eilekfkeavllglTATp 169
                                       + +  ++   +++l+AT+
  gi|474934178|ref|YP_007687760.1| 167 KFMHRNRFLQVIALSATI 184
                                       555555557889999997 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.7   4.5e+03      41      52 ..     139     150 ..     138     152 .. 0.87
   2 !   17.7   0.0   1.1e-06    0.0029       9      53 ..     669     714 ..     663     722 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.7
                             HHH_2  41 ddiGeeiAqsiv 52 
                                       +d G +iA++++
  gi|474934178|ref|YP_007687760.1| 139 EDLGMVIADEVH 150
                                       799*******98 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 1.1e-06
                             HHH_2   9 rhVGektAklLakr.FksldaLkkasleeLlevddiGeeiAqsive 53 
                                       r VG + A++L ++ Fk+ + L++a+++ ++ ++ iG+  A+si+e
  gi|474934178|ref|YP_007687760.1| 669 RGVGRNRARTLFTAgFKTRQDLAAADVNVIAGLPKIGKALARSIKE 714
                                       99*********8655*****************************87 PP

>> DUF438  Family of unknown function (DUF438)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.8e-05     0.097      11      48 ..     261     298 ..     257     304 .. 0.86
   2 ?   -2.1   0.0       1.5   3.9e+03      45      54 ..     373     382 ..     372     383 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.8e-05
                            DUF438  11 gesleevkeefkellkevsaeEIsqaEqeLieeGipve 48 
                                        +s+e++ ++f++ +ke++ + I++aEq+L+e G + +
  gi|474934178|ref|YP_007687760.1| 261 RRSTEALAKKFSKPMKELTGSSITEAEQALLEGGDEST 298
                                       67899***************************996655 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.5
                            DUF438  45 ipveeiqkLC 54 
                                       i+v e+q++C
  gi|474934178|ref|YP_007687760.1| 373 ISVMEVQQMC 382
                                       67899****9 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   9.8e-05      0.25       8      30 ..     670     692 ..     668     705 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9.8e-05
                   DNA_pol_lambd_f   8 GVGpktAkkwyakGirtledlra 30 
                                       GVG+ +A+ ++ +G++t +dl a
  gi|474934178|ref|YP_007687760.1| 670 GVGRNRARTLFTAGFKTRQDLAA 692
                                       9********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (760 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.47
# Mc/sec: 4900.72
//
Query:       gi|474934179|ref|YP_007687761.1|  [L=375]
Description: hypothetical protein TALC_00602 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00036   21.0   0.0    0.00074   19.9   0.0    1.5  1  Transglut_core  Transglutaminase-like superfamily
  ------ inclusion threshold ------
      0.053   13.4   0.1      0.093   12.6   0.1    1.4  1  HMG_CoA_synt_N  Hydroxymethylglutaryl-coenzyme A synthase N t
      0.066   13.8   0.0       0.12   12.9   0.0    1.6  1  SUA5            Putative GTP-binding controlling metal-bindin


Domain annotation for each model (and alignments):
>> Transglut_core  Transglutaminase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   1.2e-07   0.00074       6     104 ..     164     258 ..     159     272 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.2e-07
                    Transglut_core   6 eltagakdplekakaiyewvr.knveys.aprrtpgsrdaeavle...tgkGncedfaslfvallRalGipaRvvtg 77 
                                       +++ g k++ ek+ +++++++ k++ey+ +++++++ + a  +       +  ce+++sl  a +    ip+  v+g
  gi|474934179|ref|YP_007687761.1| 164 SFDLGSKSDAEKLDKLNDYICgKSIEYDaEAEYSSSIYGALVAADdkgVHRILCEGYSSLVQAFCIQEHIPCISVFG 240
                                       5566889999***********999****7667777777666665532222358************************ PP

                    Transglut_core  78 ylsgeeekeqsvasedaHawvevyleg 104
                                       +           + +d+Haw+ v + g
  gi|474934179|ref|YP_007687761.1| 241 MSA--------QSENDYHAWNVVVI-G 258
                                       *98........56899*****9988.4 PP

>> HMG_CoA_synt_N  Hydroxymethylglutaryl-coenzyme A synthase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   1.5e-05     0.093      74     136 ..     139     201 ..     107     215 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.5e-05
                    HMG_CoA_synt_N  74 aigrlevgtetiidksksvksvlmqlfeesgntdiegidtlnacyggtaalfnavnwiessaw 136
                                       ++  ++ g +t++d+sk+  + l+  f+  +++d e +d ln    g +  ++a     ss +
  gi|474934179|ref|YP_007687761.1| 139 SLPEVKTGLQTMVDQSKAKLTELIASFDLGSKSDAEKLDKLNDYICGKSIEYDAEAEYSSSIY 201
                                       556678899*********************************999998888887666655554 PP

>> SUA5  Putative GTP-binding controlling metal-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     2e-05      0.12      82     116 ..     164     220 ..      12     228 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2e-05
                                       ........................E-TT-HHHHHHHHHHHHHHHHHS--SEEEEE-- CS
                              SUA5  82 s......................lgsrsdleeaarnLFaaLrelDeegvdlilvegv 116
                                       s                        + + ++e+++ ++ aL ++D++gv+ il+eg 
  gi|474934179|ref|YP_007687761.1| 164 SfdlgsksdaekldklndyicgkSIEYDAEAEYSSSIYGALVAADDKGVHRILCEGY 220
                                       0333333333334444555555544568899**************99********76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.35s 00:00:01.00 Elapsed: 00:00:00.54
# Mc/sec: 2099.90
//
Query:       gi|474934180|ref|YP_007687762.1|  [L=719]
Description: lon-related putative ATP-dependent protease [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-30  106.3   0.0    3.6e-20   72.2   0.0    2.3  2  AAA_32           AAA domain
    1.3e-26   93.4   2.2    2.3e-26   92.6   2.2    1.4  1  Lon_C            Lon protease (S16) C-terminal proteolytic do
    7.3e-15   54.9   0.1    7.1e-09   35.3   0.1    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    2.2e-14   53.5   0.4    2.2e-07   30.8   0.0    2.9  3  Sigma54_activat  Sigma-54 interaction domain
    4.2e-09   36.5   0.0     0.0025   17.8   0.0    2.5  2  AAA_5            AAA domain (dynein-related subfamily)
    4.8e-08   32.4   0.0     0.0012   18.0   0.0    2.8  3  MCM              MCM P-loop domain
    2.8e-06   27.8   0.0      0.021   15.2   0.0    2.5  2  AAA              ATPase family associated with various cellul
    5.8e-06   26.6   0.0    0.00025   21.4   0.0    2.5  2  AAA_22           AAA domain
    1.6e-05   24.5   0.4      6e-05   22.6   0.0    2.2  2  AAA_7            P-loop containing dynein motor region
    1.8e-05   25.1   0.5    0.00013   22.3   0.5    2.3  1  AAA_19           AAA domain
    6.1e-05   22.8   0.0       0.43   10.3   0.0    2.5  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    6.5e-05   23.1   0.0       0.42   10.7   0.0    2.4  2  Sigma54_activ_2  Sigma-54 interaction domain
    7.8e-05   22.5   0.1      0.017   14.9   0.0    2.8  3  AAA_3            ATPase family associated with various cellul
    7.9e-05   22.5   0.3    0.00018   21.3   0.3    1.7  1  ChlI             Subunit ChlI of Mg-chelatase
     0.0044   17.4   0.0      0.024   15.0   0.0    2.2  2  AAA_16           AAA ATPase domain
     0.0077   15.5   0.1        2.8    7.1   0.0    2.4  2  TIP49            TIP49 P-loop domain
     0.0082   15.6   0.9      0.018   14.5   0.0    2.0  2  PhoH             PhoH-like protein
  ------ inclusion threshold ------
       0.01   15.6   0.1       0.11   12.2   0.0    2.3  2  AAA_30           AAA domain
      0.022   13.7   0.0        1.4    7.7   0.0    2.2  2  AAA_PrkA         PrkA AAA domain
      0.022   13.7   0.0       0.05   12.5   0.0    1.6  1  AAA_10           AAA-like domain
      0.023   13.8   0.0       0.19   10.8   0.0    2.1  2  T2SSE            Type II/IV secretion system protein
      0.026   14.4   0.0      0.059   13.3   0.0    1.6  1  NACHT            NACHT domain
       0.03   14.7   0.0       0.19   12.1   0.0    2.3  2  RNA_helicase     RNA helicase
      0.041   13.1   0.0      0.078   12.2   0.0    1.5  1  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.046   14.2   0.2       0.25   11.8   0.0    2.3  2  ABC_tran         ABC transporter
      0.057   12.8   0.0       0.12   11.7   0.0    1.5  1  FtsK_SpoIIIE     FtsK/SpoIIIE family
      0.074   13.6   0.0       0.37   11.3   0.0    2.2  1  AAA_18           AAA domain
      0.085   12.6   0.0       0.19   11.4   0.0    1.6  1  AAA_24           AAA domain
      0.085   12.8   0.0       0.22   11.4   0.0    1.7  1  RsgA_GTPase      RsgA GTPase
       0.11   11.4   0.1       0.19   10.6   0.1    1.3  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
       0.11   11.9   0.0       0.24   10.8   0.0    1.5  1  SMC_N            RecF/RecN/SMC N terminal domain
       0.11   12.6   0.0       0.39   10.9   0.0    1.9  1  AAA_33           AAA domain
       0.12   12.2   0.0       0.24   11.1   0.0    1.5  1  IstB_IS21        IstB-like ATP binding protein
        0.2   11.8   1.4       0.76    9.9   0.0    2.7  2  MMR_HSR1         50S ribosome-binding GTPase


Domain annotation for each model (and alignments):
>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.1   1.5e-10     8e-08       8      96 ..      61     144 ..      56     156 .. 0.85
   2 !   72.2   0.0   6.9e-23   3.6e-20     276     508 ..     204     435 ..     194     440 .. 0.90

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 1.5e-10
                            AAA_32   8 eeiigqeRAvealefglkikkkgYNifvlGesgtGrttlvkrlleeiakkeptpdDwcYvnnfdnpeePkalsLpaG 84 
                                       +++igq+RAve ++ + +    + ++ ++Ge+gtG+++l+++++e+  k     +D++   n ++++eP++  +paG
  gi|474934180|ref|YP_007687762.1|  61 DRVIGQDRAVEVMKKAAAQ---KRHMMLIGEPGTGKSMLANSMVEHLPKG--EMQDIVAYSNPEDENEPRVRVFPAG 132
                                       789***********98765...55999*****************998655..468999999**************** PP

                            AAA_32  85 kGkelkkdmeel 96 
                                       kGk+  ++ + +
  gi|474934180|ref|YP_007687762.1| 133 KGKAVVQQQKMI 144
                                       ***998876655 PP

  == domain 2  score: 72.2 bits;  conditional E-value: 6.9e-23
                            AAA_32 276 krYkvnvlvdnsetegaPVvvednptyanLfGkieyesemg.alvt.dftlIkaGaLhkAnGGyLildaedlLeepl 350
                                       + Y  ++lv ++  +  P v  +  +   L+G + ++ ++   l t  +++++aG +h+An G+L +d  + L+   
  gi|474934180|ref|YP_007687762.1| 204 TSYVPKLLVGHDVGDMPPFVDATGTHSGALLGDVRHDPYQSgGLETpAHQRLEAGDIHRANKGVLYIDEINTLRI-E 279
                                       67999*******************************98765455553899*********************9986.5 PP

                            AAA_32 351 aWeaLkraLrskeikiesleeqlglistvsLkPepipldvKViLiGsrelYylLseyDpdfkklFkvkadFddemer 427
                                       + ++L  a++++++ i       + +s    k ep+p+d   +  G+ +  + ++ +     + +  +  + ++m+ 
  gi|474934180|ref|YP_007687762.1| 280 SQQSLLTAMQEHKMAITGQ---SERSSGALVKSEPVPCDFVLVCAGNLDAMKGMHPALRSRIRGYGYEIYMRSTMPD 353
                                       6799*************53...446788999****************99999888888888888999********** PP

                            AAA_32 428 teenekkyarfiasivkk.ekllpfdrsavarlieyssrlaedqeklstrfseiadllrEAdywakkegaevveaeh 503
                                       t+++ ++++rf+a+ vkk +k+++fdr av ++i+++ r a+++ kl++rf+e+  l+r A  +a  ++a +v++++
  gi|474934180|ref|YP_007687762.1| 354 TDQHRNDVVRFVAQEVKKdKKIPHFDRFAVGEIIKEAQRRAGRKGKLTLRFRELGGLIRVAGDLAVARSAPYVTRDD 430
                                       *************988752689******************************************************* PP

                            AAA_32 504 VekAl 508
                                       V +A+
  gi|474934180|ref|YP_007687762.1| 431 VLAAM 435
                                       *9997 PP

>> Lon_C  Lon protease (S16) C-terminal proteolytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.6   2.2   4.4e-29   2.3e-26      19     204 ..     462     647 ..     443     648 .. 0.80

  Alignments for each domain:
  == domain 1  score: 92.6 bits;  conditional E-value: 4.4e-29
                                       SSSSS--BSSEEEEEE.......EETTEEEEEEEEEEEES....S-S-EEEEES--HHHHHHHHHHHHHHTSS-GGG CS
                             Lon_C  19 eeaekedqvGvvtGla.......wtevGGdlltieavllp....gkgklkltGklgdvmkesaqaalsyvrsraeel 84 
                                       e a     vG+v Gla       ++e+ G +l i a +++      gk++ tGklg++ ke+++   ++++ + + +
  gi|474934180|ref|YP_007687762.1| 462 EGA----LVGQVNGLAaldpgtgMAEYSGIMLPIVAEVTSphaeKGGKIIATGKLGEIAKEAVENISAVLK-KYSAV 533
                                       433....56777776622222224677899999877665422324579*************9997655554.33333 PP

                                       SS-SS-TTT-EEEEEE-S-B-GGGGGGGHHHHHHHHHHHHTS--B-TTBEE--EE-TT-BEE--S-HHHHHHHHHHT CS
                             Lon_C  85 gidkevfekkdihihvPeGavPkdGPsaGvtlatalvslltgkkvrkdvamtGeitLrGrvlpiGGlkekllaakra 161
                                       +     +++ d+h+         +G sa +t+++ ++s+l g+++r+dvamtG + +rG+vlp+G +  kl aa  a
  gi|474934180|ref|YP_007687762.1| 534 D-----LSTVDVHLEYIGTYDGVEGDSASITMTAVILSALEGIPIRQDVAMTGSLNVRGKVLPVGAVTAKLEAAASA 605
                                       3.....45789999888777889****************************************************** PP

                                       T-SBEEEEGGGGGGTTTS-HHHHTS-B--EESBHHHHHHHHB- CS
                             Lon_C 162 gikkvilPkenekdlediPeevreeleiilveevdevlkaalv 204
                                       gik  ++P +n kd+  + ++  + ++i +v+++ +v++ a+v
  gi|474934180|ref|YP_007687762.1| 606 GIKLALVPADNGKDVM-VRNKYYDTMDIYTVSTIRDVIEYAFV 647
                                       **************96.89999*****************9986 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.1   1.3e-11   7.1e-09       4      56 ..      62     114 ..      59     123 .. 0.93
   2 !   17.0   0.0   5.6e-06    0.0029      96     157 ..     254     323 ..     245     337 .. 0.78

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 1.3e-11
                      Mg_chelatase   4 dvkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeeale 56 
                                        v+Gq++a ++++ aaa + +++l+G pG+GK+mla+ + + lp+ ++++++ 
  gi|474934180|ref|YP_007687762.1|  62 RVIGQDRAVEVMKKAAAQKRHMMLIGEPGTGKSMLANSMVEHLPKGEMQDIVA 114
                                       699*****************************************999998765 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 5.6e-06
                      Mg_chelatase  96 kpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakak....v....efparfqlvaamN 157
                                       + + G+i +a++GvL++DE+  ++ +  ++L + +++++++i+ ++++    +      p++f lv+a N
  gi|474934180|ref|YP_007687762.1| 254 RLEAGDIHRANKGVLYIDEINTLRIESQQSLLTAMQEHKMAITGQSERssgaLvksePVPCDFVLVCAGN 323
                                       6789************************************997544331111211114678888888877 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.1e-06    0.0006      10      48 ..      68     106 ..      63     120 .. 0.86
   2 ?   -1.6   0.0       3.6   1.9e+03      31      61 ..     131     163 ..     129     175 .. 0.70
   3 !   30.8   0.0   4.1e-10   2.2e-07      81     130 ..     251     301 ..     242     328 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.1e-06
                                       HHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTT CS
                   Sigma54_activat  10 elleqikkvaktdlsvlitGesGtGKellaraiheaskr 48 
                                       +++e +kk+a+++ ++++ Ge GtGK++la+++ e+ ++
  gi|474934180|ref|YP_007687762.1|  68 RAVEVMKKAAAQKRHMMLIGEPGTGKSMLANSMVEHLPK 106
                                       678999**************************9886654 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.6
                                       TTSSHHHHHHH..HHHHSTTTTS-EEEEETTTS CS
                   Sigma54_activat  31 sGtGKellara..iheaskrkekpfvavncaai 61 
                                        G GK ++ ++  i ++s+ ++++     caai
  gi|474934180|ref|YP_007687762.1| 131 AGKGKAVVQQQkmIAAQSRSNKSSTYMYACAAI 163
                                       589999987542155567777778888899987 PP

  == domain 3  score: 30.8 bits;  conditional E-value: 4.1e-10
                                       TSS-BE.HHHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSE CS
                   Sigma54_activat  81 Aekekk.GlfekadgGtlfLDeigelplelQekLlrvlqegevervGsske 130
                                       A+++ + G +++a++G+l++Dei++l +e Q+ Ll+++qe+++   G+s+ 
  gi|474934180|ref|YP_007687762.1| 251 AHQRLEaGDIHRANKGVLYIDEINTLRIESQQSLLTAMQEHKMAITGQSER 301
                                       5554444************************************99998765 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   4.7e-06    0.0025       1      27 [.      82     109 ..      82     154 .. 0.83
   2 !   16.2   0.0   1.5e-05    0.0077      65     137 ..     264     337 ..     231     338 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.7e-06
                                       EEEEE--SSSSHHHHHHHGGGGB.S--E CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaal.nrev 27 
                                       +++L+G+pGtgKs+la ++ + l + e+
  gi|474934180|ref|YP_007687762.1|  82 HMMLIGEPGTGKSMLANSMVEHLpKGEM 109
                                       689****************999974444 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.5e-05
                                       G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---............-EEEEEESS--.-TT-TTHHHH CS
                             AAA_5  65 egeilvlDEveraesevlnsLlslleerrllleeggelvkaknddller......frviatanpldrslnelspalr 135
                                       ++ +l++DE+++++ e ++sLl+ + e ++ +    e+ + +             f ++ ++n      + + palr
  gi|474934180|ref|YP_007687762.1| 264 NKGVLYIDEINTLRIESQQSLLTAMQEHKMAITGQSERSSGALV--K-SepvpcdFVLVCAGNLDA--MKGMHPALR 335
                                       789****************************8877777777763..2.246899999999999887..778889*** PP

                                       TT CS
                             AAA_5 136 sR 137
                                       sR
  gi|474934180|ref|YP_007687762.1| 336 SR 337
                                       99 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   0.00027      0.14      54      87 ..      77     110 ..      62     119 .. 0.79
   2 !   18.0   0.0   2.3e-06    0.0012     110     153 ..     253     296 ..     221     299 .. 0.87
   3 ?   -3.4   0.0       7.7   4.1e+03     109     129 ..     457     477 ..     447     494 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00027
                                       BCSS-EEEEEESSTSTHHHHHHHHHHHSSSEEEE CS
                               MCM  54 lrgdinvllvgdpgtaKsqlLkyveklapravyt 87 
                                          + +++l+g+pgt+Ks l +++ + +p++ + 
  gi|474934180|ref|YP_007687762.1|  77 AAQKRHMMLIGEPGTGKSMLANSMVEHLPKGEMQ 110
                                       55678****************9999999988765 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 2.3e-06
                                       EEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEE CS
                               MCM 110 fvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisia 153
                                         leaG +  a+kGv++iDe++  + e +++l+ am + ++ i+
  gi|474934180|ref|YP_007687762.1| 253 QRLEAGDIHRANKGVLYIDEINTLRIESQQSLLTAMQEHKMAIT 296
                                       569*********************************99998875 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 7.7
                                       SEEEEETHHHHTTTSEEEEES CS
                               MCM 109 efvleaGalvladkGvcciDe 129
                                       +++   Galv   +G++++D 
  gi|474934180|ref|YP_007687762.1| 457 QLFSTEGALVGQVNGLAALDP 477
                                       455567888888888888885 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0     4e-05     0.021       1      32 [.      83     118 ..      83     172 .. 0.75
   2 !   10.0   0.0    0.0017      0.89      55     124 ..     262     338 ..     245     343 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4e-05
                                       EEEESSTTSSHHHHHHHHHHHH..T..HEEEEEETT CS
                               AAA   1 vllyGppGtGKTllakavakel..g..vefleisgs 32 
                                       ++l+G pGtGK++la++++++l  g  ++++  s +
  gi|474934180|ref|YP_007687762.1|  83 MMLIGEPGTGKSMLANSMVEHLpkGemQDIVAYSNP 118
                                       79****************999853133555555555 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0017
                                       HTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS..................SSTEEEEEEESS.. CS
                               AAA  55 ekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk..................eskvivigatnr.. 111
                                       +  ++ +l iDEi  l  ++           ++ Llt++++ k                      ++++++a+n   
  gi|474934180|ref|YP_007687762.1| 262 RA-NKGVLYIDEINTLRIES-----------QQSLLTAMQEHKMAitgqserssgalvksepvPCDFVLVCAGNLda 326
                                       33.379**********7666...........99999999999999999999999********9667********999 PP

                                       GGGSTHHHHSTTS CS
                               AAA 112 pdkldpallrgRf 124
                                       ++ + pal+ +R+
  gi|474934180|ref|YP_007687762.1| 327 MKGMHPALR-SRI 338
                                       999*****9.887 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   4.7e-07   0.00025       4      38 ..      79     121 ..      75     154 .. 0.79
   2 ?    2.4   0.0      0.33   1.8e+02      86     108 ..     260     283 ..     233     301 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 4.7e-07
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee........e 38 
                                       ++++++++Ge+GtGK++l++ ++e l++ + ++         e
  gi|474934180|ref|YP_007687762.1|  79 QKRHMMLIGEPGTGKSMLANSMVEHLPKGEMQDIvaysnpedE 121
                                       6899**********************87765544544444332 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.33
                            AAA_22  86 lraravielliiDEaqhlr..seea 108
                                       ++++ + ++l iDE+  lr  s++ 
  gi|474934180|ref|YP_007687762.1| 260 IHRANK-GVLYIDEINTLRieSQQS 283
                                       455555.***********7653332 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   1.1e-07     6e-05      25      64 ..      72     111 ..      65     119 .. 0.89
   2 ?   -3.0   0.0       8.6   4.5e+03      40      58 ..     129     148 ..     120     158 .. 0.67

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.1e-07
                             AAA_7  25 llelllknkkpvllvGptGtGKtviikdllkkldkekyls 64 
                                       ++++  ++k++++l+G+ GtGK++++++++++l+k +++ 
  gi|474934180|ref|YP_007687762.1|  72 VMKKAAAQKRHMMLIGEPGTGKSMLANSMVEHLPKGEMQD 111
                                       789999****************************988765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 8.6
                             AAA_7  40 GptGtGKtviikd.llkkld 58 
                                        p+G GK v+ ++ ++ + +
  gi|474934180|ref|YP_007687762.1| 129 FPAGKGKAVVQQQkMIAAQS 148
                                       58899999999995444444 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.5   2.5e-07   0.00013       7     131 ..      77     294 ..      68     302 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.5e-07
                            AAA_19   7 alkekvllvtaGpGtGKTrvlkhivallvelggvkp..........eeillvaftgrAakelrerlaalgae..... 68 
                                       a++++++++++ pGtGK+ + + +v++l + + ++           e+ + v ++g+    ++++  ++ a+     
  gi|474934180|ref|YP_007687762.1|  77 AAQKRHMMLIGEPGTGKSMLANSMVEHLPKGEMQDIvaysnpedenEPRVRVFPAGKGKAVVQQQK-MIAAQsrsnk 152
                                       6899*************************9998888999*****9977777777777666666654.3333335677 PP

                            AAA_19  69 atTiHrlal.................................................................... 77 
                                        +T+ +                                                                       
  gi|474934180|ref|YP_007687762.1| 153 SSTYMYACAaivilgligalftgsyyvlfiamfavmiilifarnpmmtrndtsyvpkllvghdvgdmppfvdatgth 229
                                       44444332246667777888888888888888888888888889999999999999999999999999988888888 PP

                            AAA_19  78 ............ldfddlltealelleeaeeekklqeee.llivDEfqdvd.elqyrLlkallgekkk 131
                                                    +  +l+t a + le     +  ++++ +l +DE+  +  e q++Ll a+ ++k+ 
  gi|474934180|ref|YP_007687762.1| 230 sgallgdvrhdpYQSGGLETPAHQRLEA---GDIHRANKgVLYIDEINTLRiESQQSLLTAMQEHKMA 294
                                       8888888777665555555555555553...223334456**********************965553 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00081      0.43      15      56 ..      69     103 ..      56     114 .. 0.71
   2 !    9.6   0.0    0.0014      0.71      84     119 ..     264     299 ..     253     338 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00081
                            RuvB_N  15 vkeklkifieaakkreealdhvllyGpPGlGkttlakiiake 56 
                                         e         kk   +  h++l+G PG Gk+ la+ + + 
  gi|474934180|ref|YP_007687762.1|  69 AVE-------VMKKAAAQKRHMMLIGEPGTGKSMLANSMVEH 103
                                       333.......33444445569***************977665 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0014
                            RuvB_N  84 ekdvlfideihrlsraveevlysamedfrldivigk 119
                                       +k vl+idei  l+ + ++ l +am+++++ i+ ++
  gi|474934180|ref|YP_007687762.1| 264 NKGVLYIDEINTLRIESQQSLLTAMQEHKMAITGQS 299
                                       678**************************9987433 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0    0.0016      0.84      14      53 ..      73     114 ..      67     131 .. 0.78
   2 !   10.7   0.0    0.0008      0.42      66     111 ..     261     324 ..     241     334 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0016
                                       HHHHHT-SS-EEEEEETT--HHHHHHCC..--TTS-EE--SS CS
                   Sigma54_activ_2  14 LeqaaqsklpvfltGekGsgkelvArlL..hknsgpwleifv 53 
                                       +++aa++k  + l+Ge+G+gk++ A+ +  h ++g+ ++i+ 
  gi|474934180|ref|YP_007687762.1|  73 MKKAAAQKRHMMLIGEPGTGKSMLANSMveHLPKGEMQDIVA 114
                                       7899999******************98833334555555555 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0008
                                       HHTTTSEEEEEE-TT--HHHHHHHHHHHHH..................HTTTT-EEEEEEEE-T CS
                   Sigma54_activ_2  66 eqakggtLylkdiadlskaeqkeLlellak..................aeksslrlVstsskdl 111
                                        +a+ g+Ly+ +i+ l  + q+ Ll ++++                  +e+  + +V +++ +l
  gi|474934180|ref|YP_007687762.1| 261 HRANKGVLYIDEINTLRIESQQSLLTAMQEhkmaitgqserssgalvkSEPVPCDFVLVCAGNL 324
                                       5799*************************97777777766666666665655565555555555 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.065        34       1      23 [.      82     104 ..      82     113 .. 0.89
   2 !   14.9   0.0   3.3e-05     0.017      64      98 ..     266     300 ..     249     312 .. 0.86
   3 ?   -2.5   0.0       8.4   4.4e+03      75     130 ..     604     660 ..     597     660 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.065
                             AAA_3   1 hvllegvPGlaktllvkalakal 23 
                                       h++l g PG++k +l++++ ++l
  gi|474934180|ref|YP_007687762.1|  82 HMMLIGEPGTGKSMLANSMVEHL 104
                                       99***************998876 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 3.3e-05
                             AAA_3  64 nllladeinrappktqsalleameerqvtvegeth 98 
                                        +l  dein     +q +ll am+e++++++g++ 
  gi|474934180|ref|YP_007687762.1| 266 GVLYIDEINTLRIESQQSLLTAMQEHKMAITGQSE 300
                                       58899*************************99876 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 8.4
                             AAA_3  75 ppktqsalleameerqvtvegethklpepflvlatqnPieqeGt.yplpeaqldrfl 130
                                       ++ ++ al+ a + ++v v+++ ++  + ++v + ++ ie+  +  p  +  ldrfl
  gi|474934180|ref|YP_007687762.1| 604 SAGIKLALVPADNGKDVMVRNKYYDTMDIYTVSTIRDVIEYAFVdCPKKQEYLDRFL 660
                                       556677888888999999999999999999998888888876441344444577775 PP

>> ChlI  Subunit ChlI of Mg-chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.3   3.5e-07   0.00018      16     121 .]     510     616 ..     495     616 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 3.5e-07
                              ChlI  16 Glpdtavkeskervrsalkn.sgfefpakkitvnLaPadlkkeGsafDLpiAigilaaleqieaeeetlflGeLsld 91 
                                       G + +  ke+ e + + lk+ s +++ +  + ++        eG + ++++   il+ale i+ ++++ + G L+  
  gi|474934180|ref|YP_007687762.1| 510 GKLGEIAKEAVENISAVLKKySAVDLSTVDVHLEYIGTYDGVEGDSASITMTAVILSALEGIPIRQDVAMTGSLNVR 586
                                       56666677777777777777566666666666666666667799999999*************************** PP

                              ChlI  92 Gslrpvkgvlpialaakkegikkvivpken 121
                                       G++ pv  v++ + aa+++gik ++vp++n
  gi|474934180|ref|YP_007687762.1| 587 GKVLPVGAVTAKLEAAASAGIKLALVPADN 616
                                       ***************************998 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   4.6e-05     0.024      20      51 ..      77     107 ..      63     154 .. 0.78
   2 ?   -1.9   0.0       7.1   3.7e+03      64      91 ..     420     451 ..     386     500 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.6e-05
                            AAA_16  20 rsgrpelvllsGesGvGKsslvrellralekd 51 
                                       ++ + + ++l+Ge+G+GKs l+++  ++l k 
  gi|474934180|ref|YP_007687762.1|  77 AA-QKRHMMLIGEPGTGKSMLANSMVEHLPKG 107
                                       33.34899****************99998876 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 7.1
                            AAA_16  64 esaipy....salaqalareellrqlldeaes 91 
                                        +++py    ++la ++ +++l +q++d++ +
  gi|474934180|ref|YP_007687762.1| 420 ARSAPYvtrdDVLAAMINARSLEQQIADRQIE 451
                                       36677777755588888888888888877444 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0052       2.8      19      75 ..      56     105 ..      47     116 .. 0.77
   2 ?    5.7   0.0     0.014       7.3     279     304 ..     265     290 ..     255     296 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0052
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  19 aekeeeglvGqkkareaagvivelikekklaGravLlaGpsgtGktalaiaiskelg 75 
                                       +ek ++ ++Gq +a       ve++k+     r ++l G++gtGk+ la ++ ++l 
  gi|474934180|ref|YP_007687762.1|  56 PEKMSDRVIGQDRA-------VEVMKKAAAQKRHMMLIGEPGTGKSMLANSMVEHLP 105
                                       55666667777665.......55667777777899**************99888775 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.014
                                       XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 279 pGvlfiDevhmlDiecfsylnrales 304
                                       +Gvl+iDe++ l ie+   l  a+ +
  gi|474934180|ref|YP_007687762.1| 265 KGVLYIDEINTLRIESQQSLLTAMQE 290
                                       6**************98877777754 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   3.4e-05     0.018       7      56 ..      64     116 ..      58     145 .. 0.81
   2 ?   -2.8   0.0       6.8   3.6e+03      85     106 ..     430     451 ..     421     455 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.4e-05
                                       HHHHHHHHHHH....H-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE CS
                              PhoH   7 keQkeylealk....kndivfaiGpaGtGKtylavalavealkkkkvkriiltr 56 
                                        +Q++++e++k    ++  ++ iG+ GtGK++la ++ ve l k++++ i+   
  gi|474934180|ref|YP_007687762.1|  64 IGQDRAVEVMKkaaaQKRHMMLIGEPGTGKSMLANSM-VEHLPKGEMQDIVAYS 116
                                       57888888888766677799**************998.8999999999999654 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6.8
                                       HHHTTTS-TTCHHHHHHTTSEE CS
                              PhoH  85 daLkdllgaekvekllekgkie 106
                                       d L  +++a+++e+ + +++ie
  gi|474934180|ref|YP_007687762.1| 430 DVLAAMINARSLEQQIADRQIE 451
                                       8899999999999999999998 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00021      0.11       9      45 ..      72     107 ..      65     148 .. 0.81
   2 ?    0.4   0.0      0.89   4.7e+02      87     119 ..     263     295 ..     233     298 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00021
                            AAA_30   9 avealltsgdrvavltGpAGtGKttalkalreaweaa 45 
                                       +++++++++ r ++l G +GtGK+++ ++++e++ + 
  gi|474934180|ref|YP_007687762.1|  72 VMKKAAAQK-RHMMLIGEPGTGKSMLANSMVEHLPKG 107
                                       456666666.599***************999988766 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.89
                            AAA_30  87 epgtllivDEagmvdtkqlaallkaaekagakv 119
                                       +++ +l +DE+  + +++ ++ll+a++++++ +
  gi|474934180|ref|YP_007687762.1| 263 ANKGVLYIDEINTLRIESQQSLLTAMQEHKMAI 295
                                       4558999******************99977655 PP

>> AAA_PrkA  PrkA AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.048        25      82     113 ..      74     105 ..      28     141 .. 0.82
   2 ?    7.7   0.0    0.0027       1.4     226     267 ..     257     298 ..     219     305 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.048
                          AAA_PrkA  82 qrleerkqilyllGPvggGksslverlkklle 113
                                       ++   +k+ ++l+G  g+Gks l++++ + l 
  gi|474934180|ref|YP_007687762.1|  74 KKAAAQKRHMMLIGEPGTGKSMLANSMVEHLP 105
                                       44456789999**********99998876664 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0027
                          AAA_PrkA 226 sGalnranrGllefvemfkadikvlhplltatqegnykstek 267
                                        G++ ran+G+l   e+    i+   +llta qe ++  t++
  gi|474934180|ref|YP_007687762.1| 257 AGDIHRANKGVLYIDEINTLRIESQQSLLTAMQEHKMAITGQ 298
                                       5999******************************99988775 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   9.5e-05      0.05      15      70 ..      74     131 ..      66     155 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.5e-05
                            AAA_10  15 kgsktnasasliiGdlGnGKSvlakllvlyisllg..gkaliiDpkkerekfketlpe 70 
                                       k +  +  ++++iG++G GKS+la+ +v  +   +  + + +  p  e+e  ++ +p+
  gi|474934180|ref|YP_007687762.1|  74 KKAAAQKRHMMLIGEPGTGKSMLANSMVEHLPKGEmqDIVAYSNPEDENEPRVRVFPA 131
                                       5556677899*****************9887654421334455666666666666654 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00036      0.19     116     158 ..      67     110 ..      30     140 .. 0.79
   2 ?    0.1   0.0      0.64   3.4e+02      50     107 ..     573     634 ..     526     645 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00036
                             T2SSE 116 ekiaevlrkavrerglilvsGgTgsGKttllyallkeinks.de 158
                                       ++  ev++ka +++  +++ G  g+GK+ l++++++ ++k   +
  gi|474934180|ref|YP_007687762.1|  67 DRAVEVMKKAAAQKRHMMLIGEPGTGKSMLANSMVEHLPKGeMQ 110
                                       66678899998999999999******************998334 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.64
                             T2SSE  50 lisriaalakldiseerplqdarlp....ekgvrlrvvllPvvagealviRkksakeltldd 107
                                       + + +a++ +l++  + +++ a         ++ ++++l+P+ +g+ + +R+k    +++ +
  gi|474934180|ref|YP_007687762.1| 573 IRQDVAMTGSLNVRGKVLPVGAVTAkleaAASAGIKLALVPADNGKDVMVRNKYYDTMDIYT 634
                                       5667777777777777777655444444777888999**************99888887765 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   0.00011     0.059       2      29 ..      82     109 ..      81     117 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00011
                                       CEEEEC-TTTCHHHHHHHHHHHHCTS-S CS
                             NACHT   2 lvilqGeaGsGKTtLlqklalawaegkl 29 
                                        ++l Ge+G GK++L+ ++++ + +g+ 
  gi|474934180|ref|YP_007687762.1|  82 HMMLIGEPGTGKSMLANSMVEHLPKGEM 109
                                       6899****************99988875 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00036      0.19       2      29 ..      84     107 ..      83     125 .. 0.69
   2 ?   -1.9   0.0       8.2   4.3e+03       6      36 ..     130     157 ..     128     164 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00036
                      RNA_helicase   2 wlyGpsgeGKStlakeLakallkklklk 29 
                                       +l G++g+GKS+la++++++l     + 
  gi|474934180|ref|YP_007687762.1|  84 MLIGEPGTGKSMLANSMVEHLP----KG 107
                                       789*************887776....22 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 8.2
                      RNA_helicase   6 psgeGKStlakeLakallkklklkkkdsvys 36 
                                       p+g GK ++ ++  k ++ ++ + +k+s+y+
  gi|474934180|ref|YP_007687762.1| 130 PAGKGKAVVQQQ--KMIAAQSRS-NKSSTYM 157
                                       568899888888..666666644.4466665 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00015     0.078       6      37 ..      85     130 ..      80     164 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                           DUF2075   6 VtGvaGtGKtvvllnllael..............eddeeertavyl 37 
                                         G++GtGK++++++++  l              ed++e r +v+ 
  gi|474934180|ref|YP_007687762.1|  85 LIGEPGTGKSMLANSMVEHLpkgemqdivaysnpEDENEPRVRVFP 130
                                       45******************55555555555444444444444444 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.31   1.6e+02      71     135 ..      17      89 ..       8      89 .. 0.72
   2 ?   11.8   0.0   0.00048      0.25      10      41 ..      79     108 ..      71     164 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.31
                                       -TTSBHHHH..HHHTC.......HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHH.HHHHTSSEEEEEST CS
                                       xxxxxxxxx..xxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                          ABC_tran  71 fpeltvren..esdee.......iekalsklglkelkdtvvksspssLSgGqkqrvalar.allkkpkllllDEp 135
                                         ++tv+en  e  ++       +e+++++ + k +kd  v +++s    Gq + v++++ a ++k+ ++l+ Ep
  gi|474934180|ref|YP_007687762.1|  17 EGKTTVQENtdE--NDavltdvpVEEWVKNQQFKSTKDVDVPEKMSDRVIGQDRAVEVMKkAAAQKRHMMLIGEP 89 
                                       456779999551..334455555999999999999888888777777778****999885277888889998887 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00048
                                       TTSEEEEEESTTSSHHHHHHHHTTSS--SEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  10 egekvaivGenGaGKStLlkllagllkpteGe 41 
                                       + + + ++Ge G+GKS L++ + ++l +  Ge
  gi|474934180|ref|YP_007687762.1|  79 QKRHMMLIGEPGTGKSMLANSMVEHLPK--GE 108
                                       567789**************99988765..33 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00023      0.12      20      60 ..      53     101 ..      40     104 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00023
                                       EEEEEETTS-EEEEEGGGS-.........SEEEE--TTSSHHHHHHHHH CS
                      FtsK_SpoIIIE  20 valgkeisgnplvldlkkma........shllvaGatgsGKStalntLi 60 
                                       v++++++s++++  d ++           h++++G +g+GKS   n+++
  gi|474934180|ref|YP_007687762.1|  53 VDVPEKMSDRVIGQDRAVEVmkkaaaqkRHMMLIGEPGTGKSMLANSMV 101
                                       55555555555554443333334456899**************999997 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0007      0.37       2      87 ..      84     173 ..      83     197 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0007
                            AAA_18   2 lltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpe.....aldeskrldedkldklldaleenssalee 73 
                                       +l G pG+GK+ la+   ++l    + +d+++ +++++e++p      a + + +++++k+ ++++  +++s  +  
  gi|474934180|ref|YP_007687762.1|  84 MLIGEPGTGKSMLANSMVEHL-PKGEMQDIVAYSNPEDENEPRvrvfpAGKGKAVVQQQKMIAAQSRSNKSSTYMYA 159
                                       689****************95.3778899999999999999998888778888888888888888888887778888 PP

                            AAA_18  74 gknlvidghlaele 87 
                                       +  +vi g+++ l+
  gi|474934180|ref|YP_007687762.1| 160 CAAIVILGLIGALF 173
                                       88888888777776 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00036      0.19       2      22 ..      80     100 ..      79     125 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00036
                            AAA_24   2 klkiliyGpsgiGKTtlakel 22 
                                       k+ ++++G++g+GK++la+++
  gi|474934180|ref|YP_007687762.1|  80 KRHMMLIGEPGTGKSMLANSM 100
                                       6789***************99 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00042      0.22      88     123 ..      68     104 ..      35     138 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00042
                                       TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT- CS
                       RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinallpel 123
                                       +++e +k++ ++ + ++l+G+ G GKS L n+++++l
  gi|474934180|ref|YP_007687762.1|  68 RAVEVMKKAAAQkRHMMLIGEPGTGKSMLANSMVEHL 104
                                       5666777766665999****************99874 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00037      0.19      13      48 ..      78     113 ..      70     116 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00037
                     TrwB_AAD_bind  13 retqhilivGttGsGKtqalekllrairargdraiv 48 
                                       + ++h++++G  G+GK+  ++++++++ + + + iv
  gi|474934180|ref|YP_007687762.1|  78 AQKRHMMLIGEPGTGKSMLANSMVEHLPKGEMQDIV 113
                                       6789*******************9998777666655 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00046      0.24      21     112 ..      77     157 ..      70     162 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00046
                                       ETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  21 pfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeev 97 
                                         +k++ +++G+ G GKs l +++         ++l + +++d++ + ++ +  ++ +v ++   ++k+  + +++ 
  gi|474934180|ref|YP_007687762.1|  77 AAQKRHMMLIGEPGTGKSMLANSM--------VEHLPKGEMQDIVAY-SNPEDENEPRVRVFPAGKGKA--VVQQQK 142
                                       5688999***************99........458999********9.99999********64555554..444555 PP

                                       EEEEEEETTSEEEEE CS
                                       xxxxxxxxxxxxxxx RF
                             SMC_N  98 sisrrvkrkgeseyk 112
                                        i  +  ++++s+y+
  gi|474934180|ref|YP_007687762.1| 143 MIAAQSRSNKSSTYM 157
                                       666777777777775 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00074      0.39       3      25 ..      84     107 ..      83     156 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00074
                            AAA_33   3 llvGlpGsGKstlaerllkklg.a 25 
                                       +l+G pG+GKs la +++++l+ +
  gi|474934180|ref|YP_007687762.1|  84 MLIGEPGTGKSMLANSMVEHLPkG 107
                                       89****************999862 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00045      0.24      45      68 ..      78     101 ..      37     115 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00045
                         IstB_IS21  45 ekkenivllGpsGvGKshlaialg 68 
                                       ++k  ++l+G +G+GKs la ++ 
  gi|474934180|ref|YP_007687762.1|  78 AQKRHMMLIGEPGTGKSMLANSMV 101
                                       4677899*************9986 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.2       5.7     3e+03      35      78 ..      14      55 ..       5      79 .. 0.62
   2 ?    9.9   0.0    0.0014      0.76       2      22 ..      83     103 ..      82     117 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 5.7
                                      SEEEEEEE....ETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHCTSE CS
                          MMR_HSR1 35 dinegrvk....lkgkeielvDtpGliegaseekglgkaflaleeadl 78
                                      + +eg+ +    +++++ +l+D+p   e    e+  +++f++ +++d+
  gi|474934180|ref|YP_007687762.1| 14 EKEEGKTTvqenTDENDAVLTDVPV--E----EWVKNQQFKSTKDVDV 55
                                      4444444433333356788888886..5....6666666666666665 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0014
                                       EEEEESTTSSHHHHHHHHHTS CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltge 22 
                                       ++++G p +GKS L n++++ 
  gi|474934180|ref|YP_007687762.1|  83 MMLIGEPGTGKSMLANSMVEH 103
                                       689***************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (719 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       932  (0.0519828); expected 358.6 (0.02)
Passed bias filter:                      663  (0.0369792); expected 358.6 (0.02)
Passed Vit filter:                       127  (0.0070835); expected 17.9 (0.001)
Passed Fwd filter:                        34  (0.00189637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              34  [number of targets reported over threshold]
# CPU time: 0.77u 0.35s 00:00:01.12 Elapsed: 00:00:00.52
# Mc/sec: 4172.99
//
Query:       gi|474934181|ref|YP_007687763.1|  [L=177]
Description: nicotinamide-nucleotide adenylyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-14   53.2   0.0    7.3e-14   52.2   0.0    1.5  1  CTP_transf_like  Cytidylyltransferase-like
     0.0083   15.8   0.0        2.3    7.9   0.0    2.7  3  Citrate_ly_lig   Citrate lyase ligase C-terminal domain
  ------ inclusion threshold ------
      0.024   14.5   0.0      0.032   14.1   0.0    1.2  1  FAD_syn          FAD synthetase
       0.19   10.9   0.0       0.81    8.8   0.1    1.8  2  HIGH_NTase1      HIGH Nucleotidyl Transferase
        0.2   11.1   0.1         21    4.5   0.1    2.6  3  ATP-sulfurylase  ATP-sulfurylase


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   0.0     2e-17   7.3e-14       1     143 []      10     139 ..      10     139 .. 0.87

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 2e-17
                                       EEEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHH.HH CS
                   CTP_transf_like   1 lagGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRlemlelakevdevisvdpweltr.ev 76 
                                       l+ G+F+p+H+GH++++++ +++ +  l +g+ s++ +++   ++++a eR+ m+e+a + +    +d + +++ e 
  gi|474934181|ref|YP_007687763.1|  10 LVIGRFQPLHNGHMEVIRKCAAESDH-LTIGIGSAQYSHQV-DNPFTAGERYLMIEQALKGEG---IDNYSIVPiED 81 
                                       578***********************.************99.****************65555...88888888566 PP

                                       HHHTTTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHHHH CS
                   CTP_transf_like  77 lkklkpdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkirer 143
                                       l+++      +v    +++       + ++++n+++  + ++e  + v+  + +++  +S+t++r+r
  gi|474934181|ref|YP_007687763.1|  82 LNRY--S--TWVSHVASMCP-----PFTRVYTNNPFTKRLFSEAGYIVKDSPLYNRDLYSGTEVRRR 139
                                       6666..3..46666656665.....58***************9999999999*************97 PP

>> Citrate_ly_lig  Citrate lyase ligase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.8   0.0    0.0055        20       8      35 ..      15      42 ..       8      50 .. 0.82
   2 !    7.9   0.0   0.00063       2.3       9      24 ..      51      67 ..      48      81 .. 0.86
   3 ?   -1.1   0.0      0.37   1.3e+03     148     175 ..     126     151 ..      99     155 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0055
                    Citrate_ly_lig  8 anPftlGhryLvekaakendvvhlfvvk 35
                                        P  +Gh  ++ k a+e+d++ + + +
  gi|474934181|ref|YP_007687763.1| 15 FQPLHNGHMEVIRKCAAESDHLTIGIGS 42
                                      57999****************9987655 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00063
                    Citrate_ly_lig  9 nPftlGhryL.vekaak 24
                                      nPft G ryL +e+a k
  gi|474934181|ref|YP_007687763.1| 51 NPFTAGERYLmIEQALK 67
                                      9********85799876 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.37
                    Citrate_ly_lig 148 keeelisaskvrkllkeknleklaelvP 175
                                       ++ +l s ++vr+ + e++  + ++lvP
  gi|474934181|ref|YP_007687763.1| 126 YNRDLYSGTEVRRRMVEGE--DWRSLVP 151
                                       4556667777777666543..3455555 PP

>> FAD_syn  FAD synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0     9e-06     0.032       8      48 ..       8      48 ..       2      77 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9e-06
                           FAD_syn  8 avvtlGnFDGvHlGHqallkkaveaakekglpsvvvtFeph 48
                                        +++G F  +H GH ++++k  +++++  + +    ++++
  gi|474934181|ref|YP_007687763.1|  8 YSLVIGRFQPLHNGHMEVIRKCAAESDHLTIGIGSAQYSHQ 48
                                      6789*****************99998877766665555555 PP

>> HIGH_NTase1  HIGH Nucleotidyl Transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1   0.00023      0.81       7      40 ..      12      44 ..       9      48 .. 0.78
   2 ?   -0.8   0.0      0.19   6.8e+02     201     233 ..     128     157 ..     115     169 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00023
                       HIGH_NTase1  7 IaEYNPfHnGHlyhlekakeltgadvviavmSGn 40
                                      I  + P+HnGH+  ++k+  + +++++i + S +
  gi|474934181|ref|YP_007687763.1| 12 IGRFQPLHNGHMEVIRKCAAE-SDHLTIGIGSAQ 44
                                      66689************9997.556666666665 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.19
                       HIGH_NTase1 201 eeiaSAtaiRkalkeekkleelkklvPestlei 233
                                       +++ S t +R+ + e    e+ ++lvPe+++ +
  gi|474934181|ref|YP_007687763.1| 128 RDLYSGTEVRRRMVEG---EDWRSLVPEAAALV 157
                                       5789********9666...68999999987655 PP

>> ATP-sulfurylase  ATP-sulfurylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1    0.0058        21      29      50 ..      16      36 ..      12      51 .. 0.79
   2 ?   -0.5   0.0       0.2   7.1e+02      25      44 ..      47      66 ..      43      79 .. 0.82
   3 ?    3.1   0.0     0.016        56     177     195 ..     127     145 ..     108     157 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0058
                                      S---HHHHHHHHHHHHHTSEEE CS
                   ATP-sulfurylase 29 nplHraHeellkraleeeadgl 50
                                      +plH++H e++++ +  e d l
  gi|474934181|ref|YP_007687763.1| 16 QPLHNGHMEVIRKCAA-ESDHL 36
                                      7*********999888.45534 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.2
                                      EEESS---HHHHHHHHHHHH CS
                   ATP-sulfurylase 25 fqtrnplHraHeellkrale 44
                                      +q +np+  + ++l+ + + 
  gi|474934181|ref|YP_007687763.1| 47 HQVDNPFTAGERYLMIEQAL 66
                                      899*********99987665 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.016
                                       GEEE--HHHHHCCHHTT-- CS
                   ATP-sulfurylase 177 evesisgtelrkllregee 195
                                       ++  +sgte+r+++ ege+
  gi|474934181|ref|YP_007687763.1| 127 NRDLYSGTEVRRRMVEGED 145
                                       56779***********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       232  (0.0129399); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 1004.28
//
Query:       gi|474934182|ref|YP_007687764.1|  [L=160]
Description: competence/damage-inducible protein CinA C-terminal domain protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-54  182.6   0.4    3.7e-54  182.5   0.4    1.0  1  CinA      Competence-damaged protein
     0.0047   16.7   1.1       0.12   12.1   0.4    2.1  2  UPF0254   Uncharacterised protein family (UPF0254)


Domain annotation for each model (and alignments):
>> CinA  Competence-damaged protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.5   0.4   4.2e-58   3.7e-54       3     153 ..       5     155 ..       3     157 .. 0.97

  Alignments for each domain:
  == domain 1  score: 182.5 bits;  conditional E-value: 4.2e-58
                              CinA   3 slaeevvkllkkkgltlatAEScTGGllaaaltsvpGaSavfeggvvtYsneaKeelLgvseetleehgavSeevae 79 
                                       ++ ++++++l +k+lt+++AES+TGGl+++a+t++pG+Sa+f g++vtYsne+Kee+Lg++  ++ e+gavSe+va 
  gi|474934182|ref|YP_007687764.1|   5 DMCRKLADALVSKHLTISCAESLTGGLIGSAITALPGSSAYFMGSAVTYSNESKEEILGIPLGLVWEYGAVSEAVAI 81 
                                       56678999********************************************************************* PP

                              CinA  80 emaegarerlgadiavavtGiAGpsggteekpvGtvyialagkggveveklefegdreeireaavkaALellre 153
                                       +ma+ ar+ +++diav++tGiAGp+g+te+kpvG+vyi++++++g+++ ++ feg+r+++re++v++AL++ +e
  gi|474934182|ref|YP_007687764.1|  82 QMARSARRIYSSDIAVSCTGIAGPGGATETKPVGLVYIGVSSSKGERAFRYVFEGSRDDVRERTVEEALRIALE 155
                                       *********************************************************************99876 PP

>> UPF0254  Uncharacterised protein family (UPF0254)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.4   0.0    0.0066        59       2      27 ..      19      46 ..      18      64 .. 0.73
   2 !   12.1   0.4   1.3e-05      0.12      86     116 ..      77     107 ..      73     127 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.0066
                                      EEEEEEESTTTTHHHHHHHHH..HCT-S CS
                           UPF0254  2 irvataECFthgkigreiHal..asgYe 27
                                      ++++ aE  t g ig  i al  +s Y 
  gi|474934182|ref|YP_007687764.1| 19 LTISCAESLTGGLIGSAITALpgSSAYF 46
                                      689***************9973344454 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 1.3e-05
                                       HHHHHHHHHHHHHHHT-SEEEEEE-SEES-E CS
                           UPF0254  86 kevallmakavkkitnadigigttAGiGrGa 116
                                       + va+ ma++ ++i ++di+++ t   G G+
  gi|474934182|ref|YP_007687764.1|  77 EAVAIQMARSARRIYSSDIAVSCTGIAGPGG 107
                                       579*******************998788887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1023.21
//
Query:       gi|474934183|ref|YP_007687765.1|  [L=300]
Description: phosphoribosylaminoimidazole-succinocarboxamide synthase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-45  156.0   1.8    1.8e-45  155.5   1.8    1.2  1  SAICAR_synt  SAICAR synthetase
  ------ inclusion threshold ------
       0.11   12.0   0.0       0.21   11.1   0.0    1.4  1  KNOX2        KNOX2 domain
       0.51   10.4   7.0         40    4.4   0.0    4.5  5  Phage_XkdX   Phage uncharacterised protein (Phage_XkdX)


Domain annotation for each model (and alignments):
>> SAICAR_synt  SAICAR synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.5   1.8   3.1e-49   1.8e-45       2     247 ..       4     258 ..       3     262 .. 0.85

  Alignments for each domain:
  == domain 1  score: 155.5 bits;  conditional E-value: 3.1e-49
                                       EEE-SSEEEEE-SSTTEEEEEEESEEEECCCTEEEEETTHHHHHHHHHHHHHHHHHH..--BSEEEE.......... CS
                       SAICAR_synt   2 lyeGKvrdvYeledddklllvakDrisAfdvvlkeeipgKGkvltqlsafwfeklek..ipnhliksldpe...... 70 
                                       + +GKv++vY++ ddd+l + ++D+is+fd + ++ +p+KG+ l+++++fwf  l+k  i+nh+i++++ +      
  gi|474934183|ref|YP_007687765.1|   4 IMTGKVKEVYAI-DDDTLEFAYTDHISVFDKIIPSMVPHKGETLCRTAKFWFGILTKegINNHYISEPSKDrmdvkr 79 
                                       789*********.888****************************************668******775422333445 PP

                                       ...-SSSEEEEE-EE..EESEEEEEEEE--HHH........HH....HH....T--TT-EEEEEEEEEEE--CCCT. CS
                       SAICAR_synt  71 ..qlegrsmlvkklk..mlpvEvvvRgyltGslwkeykks.gkvcgirlpe..glkegeklpepiftpstKaeegeh 140
                                          +++ s +  k++  ++p+E+++R y++Gsl+   k++  +   + +p+  ++k geklp+p ++ +tK ee   
  gi|474934183|ref|YP_007687765.1|  80 vqVIRDYSKIDGKTTnyLIPLEIICRHYAAGSLLDRVKAGkITAEQLGFPKghEVKYGEKLPRPFVEATTKLEET-- 154
                                       543344444433332225778************888887754445555666236899****************95.. PP

                                       S-EE-HHHHH.HTT.-HHHHHHHHHHHHHHHHHHHHHHHHTTEEEEEEEEEEEEETTTTEEEEES--.STTTEEEEE CS
                       SAICAR_synt 141 Deniseeevvealg.teeeaeeieelalavyekaaelaaergiilvDtKlEFGldeedgelvLaDevltpDssRfwd 216
                                       D n++ +e+ e++g t++e++ei +++l++ e++a+ aa+r++i  D K E+  d+ + +l+++D + t D  R wd
  gi|474934183|ref|YP_007687765.1| 155 DRNLTTAEAKEMAGlTDAEYDEIVKTTLKIDEIIAREAAKRNLIHCDGKKEYAYDK-QRKLMVVDTFGTLDEDRWWD 230
                                       9***********99*****************************************5.9******************* PP

                                       TTT.....GGGB-STHHHHTT-STHHHHHHH CS
                       SAICAR_synt 217 aetyeegkeqeslDKqfvRdwleeveekwke 247
                                       ae+y++g+   +l K+fvR++ +e  +++++
  gi|474934183|ref|YP_007687765.1| 231 AEEYAKGN-IVELSKEFVRQYYRE--TGYHK 258
                                       *****876.5689********998..77766 PP

>> KNOX2  KNOX2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   3.5e-05      0.21      20      45 ..     134     159 ..     134     160 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.5e-05
                             KNOX2  20 vkYkeeLtrpveEAteFlreieqqLq 45 
                                       vkY e L rp+ EAt+ l+e   +L+
  gi|474934183|ref|YP_007687765.1| 134 VKYGEKLPRPFVEATTKLEETDRNLT 159
                                       79*****************9999886 PP

>> Phage_XkdX  Phage uncharacterised protein (Phage_XkdX)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0    0.0066        40      22      31 ..     116     125 ..     107     126 .. 0.88
   2 ?    3.5   0.2     0.012        74      27      37 ..     169     179 ..     158     181 .. 0.88
   3 ?   -3.1   0.1       1.4   8.3e+03      28      33 ..     230     235 ..     227     236 .. 0.71
   4 ?   -2.7   0.1       1.1   6.5e+03       3      15 ..     246     258 ..     245     259 .. 0.72
   5 ?    3.5   0.1     0.012        74      32      40 .]     292     300 .]     285     300 .] 0.87

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0066
                        Phage_XkdX  22 VgkgkITkee 31 
                                       V++gkIT+e+
  gi|474934183|ref|YP_007687765.1| 116 VKAGKITAEQ 125
                                       99*******9 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.012
                        Phage_XkdX  27 ITkeeYeeITG 37 
                                       +T +eY eI+ 
  gi|474934183|ref|YP_007687765.1| 169 LTDAEYDEIVK 179
                                       89*******96 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 1.4
                        Phage_XkdX  28 TkeeYe 33 
                                       ++eeY 
  gi|474934183|ref|YP_007687765.1| 230 DAEEYA 235
                                       689997 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 1.1
                        Phage_XkdX   3 diKeyYdwglwtk 15 
                                        + +yY +  + k
  gi|474934183|ref|YP_007687765.1| 246 FVRQYYRETGYHK 258
                                       5889998877765 PP

  == domain 5  score: 3.5 bits;  conditional E-value: 0.012
                        Phage_XkdX  32 YeeITGeeY 40 
                                       Ye ITGe++
  gi|474934183|ref|YP_007687765.1| 292 YERITGEKF 300
                                       9******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 1943.31
//
Query:       gi|474934184|ref|YP_007687766.1|  [L=183]
Description: hypothetical protein TALC_00607 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.051   12.6   7.4      0.024   13.7   5.2    1.5  1  DuoxA         Dual oxidase maturation factor
       0.14   12.4   4.1          4    7.7   0.3    2.4  2  SepZ          SepZ
        9.2    6.0   7.4         52    3.6   0.9    2.5  2  Trp_oprn_chp  Tryptophan-associated transmembrane protein (Tr


Domain annotation for each model (and alignments):
>> DuoxA  Dual oxidase maturation factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   5.2     4e-06     0.024     192     260 ..      98     175 ..      78     180 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4e-06
                             DuoxA 192 lvvirygaymllltgallllalliyslvlpkcelvipl.........eaavletefgwsfwlvlatGllclllglii 259
                                          i+yg+ ++++ g++ ++ ++++ + +   ++  +           ++++  ++g  f+++++ G+l+l++gli 
  gi|474934184|ref|YP_007687766.1|  98 PGCIKYGSFAIIAFGVIGIVCCVLFYTWTFDVTFDATAfgmgiidlgIDEHVGDDIGIGFYVTVIGGVLVLVAGLID 174
                                       4579*********************999888888876578899999767889**********************985 PP

                             DuoxA 260 l 260
                                       +
  gi|474934184|ref|YP_007687766.1| 175 A 175
                                       4 PP

>> SepZ  SepZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.4    0.0026        15      45      88 ..      79     118 ..      54     123 .. 0.63
   2 ?    7.7   0.3   0.00067         4      56      94 ..     134     172 ..     126     176 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0026
                              SepZ  45 laGvalattalaalGaGiaalcvenssqkklglGiaaGvlGglt 88 
                                       l+Gv  a +a+ a+ a +   c++  s       ia Gv+G + 
  gi|474934184|ref|YP_007687766.1|  79 LGGVFAALGAIIAVLAIVKPGCIKYGSFAI----IAFGVIGIVC 118
                                       455555555555555555555555555444....3456666554 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00067
                              SepZ  56 aalGaGiaalcvenssqkklglGiaaGvlGgltalGgal 94 
                                       +a G Gi  l +++   + +g+G    v+Gg+  l ++l
  gi|474934184|ref|YP_007687766.1| 134 TAFGMGIIDLGIDEHVGDDIGIGFYVTVIGGVLVLVAGL 172
                                       689*****************************9988776 PP

>> Trp_oprn_chp  Tryptophan-associated transmembrane protein (Trp_oprn_chp)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.9    0.0087        52     121     139 ..      76      94 ..      11     105 .. 0.60
   2 ?    1.0   6.9     0.054   3.2e+02     117     135 ..     151     173 ..      77     181 .. 0.60

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0087
                      Trp_oprn_chp 121 lalaggvllllagvllllr 139
                                         ++ggv ++l++++++l+
  gi|474934184|ref|YP_007687766.1|  76 CPVLGGVFAALGAIIAVLA 94 
                                       3344555555554444433 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.054
                      Trp_oprn_chp 117 a....wpvlalaggvllllagvl 135
                                       +    + +++++ggvl+l+ag++
  gi|474934184|ref|YP_007687766.1| 151 DdigiGFYVTVIGGVLVLVAGLI 173
                                       1344488999**********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       782  (0.0436165); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1182.77
//
Query:       gi|474934185|ref|YP_007687767.1|  [L=130]
Description: archaeal conserved hypothetical protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-33  115.6   6.1    1.7e-33  115.5   6.1    1.0  1  UPF0179   Uncharacterised protein family (UPF0179)
     0.0085   15.7   0.5      0.016   14.9   0.2    1.6  2  TMEM95    TMEM95 family


Domain annotation for each model (and alignments):
>> UPF0179  Uncharacterised protein family (UPF0179)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.5   6.1   1.9e-37   1.7e-33      12     139 ..       2     128 ..       1     129 [. 0.94

  Alignments for each domain:
  == domain 1  score: 115.5 bits;  conditional E-value: 1.9e-37
                           UPF0179  12 eGteFiylgeaeeCekCklkkvClnLekgrkYrivevrekteheCavheegvvaveveeapiealieskkavegski 88 
                                       +G++F+ylg+ +eC+ C+lk +C+nLekg++Yr++++r++ +h+C  +e+ v++veve+++ ea++e+k a+egs++
  gi|474934185|ref|YP_007687767.1|   2 VGKSFVYLGPDRECKFCQLKGICFNLEKGSMYRVKSLRKT-THQCEATEGTVHVVEVEKVSREAAVEKKYAIEGSTV 77 
                                       699*************************************.************************************ PP

                           UPF0179  89 tleseeCdevecesyelcepeglkege.kvkivevlgeieeckkgrslkkve 139
                                       t++ + C ++ c+s++lc+peg++++e +v+  +v ++i+ c+ g+s ++v+
  gi|474934185|ref|YP_007687767.1|  78 TFACSGCGNIGCPSFKLCNPEGMEDEEiRVELLKVGEKID-CPIGESRNRVT 128
                                       **********************987654778888888888.***99988876 PP

>> TMEM95  TMEM95 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1     0.083   7.4e+02       1      44 [.      15      61 ..      15      71 .. 0.41
   2 !   14.9   0.2   1.8e-06     0.016      91     135 ..      70     112 ..      33     117 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.083
                            TMEM95  1 cvfcrlkak..dlsgrlarlcsqleakkkeceast.dfsafaldevs 44
                                      c fc+lk    +l++      + l++  ++cea+  + + + +++vs
  gi|474934185|ref|YP_007687767.1| 15 CKFCQLKGIcfNLEKGSMYRVKSLRKTTHQCEATEgTVHVVEVEKVS 61
                                      55666654211333322223334444455555332133344444444 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.8e-06
                            TMEM95  91 PacrGstilyncstcegkevscwprkrcfPgshdlrearilllsv 135
                                        a +Gst+++ cs c   ++ c ++k c P+  +  e r+ ll v
  gi|474934185|ref|YP_007687767.1|  70 YAIEGSTVTFACSGCG--NIGCPSFKLCNPEGMEDEEIRVELLKV 112
                                       4679***********7..578****************99999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       874  (0.0487478); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 881.76
//
Query:       gi|474934186|ref|YP_007687768.1|  [L=354]
Description: Glycerol dehydrogenase-related enzyme [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.5e-63  212.8   0.5    8.3e-63  212.4   0.5    1.1  1  Fe-ADH_2      Iron-containing alcohol dehydrogenase
    6.9e-28   97.5   0.9    1.8e-26   92.8   0.9    2.0  1  Fe-ADH        Iron-containing alcohol dehydrogenase
    5.5e-09   35.6   0.0    3.3e-08   33.0   0.0    1.9  1  DHQ_synthase  3-dehydroquinate synthase


Domain annotation for each model (and alignments):
>> Fe-ADH_2  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.4   0.5   1.4e-66   8.3e-63       2     250 .]      19     276 ..      18     276 .. 0.85

  Alignments for each domain:
  == domain 1  score: 212.4 bits;  conditional E-value: 1.4e-66
                          Fe-ADH_2   2 igegaleklgellkelel.kkvllvadentkkaagekveeslkeagikvevveeveeeadleeveklvealreketd 77 
                                       +g+g++++++e++ +l + k+ ++v++e+t +aag+ v + ++e+ ++++ v  + +++d++++ek  +a++  +++
  gi|474934186|ref|YP_007687768.1|  19 MGHGVIDQTREICDSLLFgKNGIIVTGEKTFDAAGKTVYDLMSEK-YEMTKV--FVGNSDHDDIEKATAAAKDCDAK 92 
                                       789*************86489*******************99888.888755..689******************** PP

                          Fe-ADH_2  78 lvvavGgGtiiDiakyvsaklnvpyvsvpTaaSvDGfaspgaslvvd.gkkrtvakaaaPlaviaDldvlaeAPrrl 153
                                       +v+avGgG+ iDi+k+vs +l++p+vs+pT+ ++DG++s  as++ + g+  t+ +a  P+aviaD++vl +AP r+
  gi|474934186|ref|YP_007687768.1|  93 FVLAVGGGSKIDISKIVSNNLRIPFVSIPTSVAHDGICSDRASVKDEkGAPMTI-QAMPPMAVIADTEVLLKAPYRF 168
                                       *********************************************999999999.********************** PP

                          Fe-ADH_2 154 lasGvGDllgkytaladwklanevse........plaklsaamvqeaaeklvedkke...tealee.llealalsgi 218
                                       lasG++D+++++tal dw  a+++++         la+ sa+++++ a+ +   ++e     al+  ++++  ++++
  gi|474934186|ref|YP_007687768.1| 169 LASGCADVISNLTALWDWDFARRMKDeefstsayTLAHYSAQSLVDYADFIKP-GMEesiWLALKPiIASGTSMCIA 244
                                       *********************95544322223334555555555555554433.2221223344440445569**** PP

                          Fe-ADH_2 219 gisrpaSGsEHliSHaldmlalkqalHGeqVG 250
                                       g+srp SGsEH++SHald l++++a+HGeq+G
  gi|474934186|ref|YP_007687768.1| 245 GSSRPTSGSEHMFSHALDILHPSSAMHGEQCG 276
                                       *******************************9 PP

>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.8   0.9   3.1e-30   1.8e-26       1     344 [.      14     322 ..      14     340 .. 0.78

  Alignments for each domain:
  == domain 1  score: 92.8 bits;  conditional E-value: 3.1e-30
                                       -SEEEEETTGGGGHHHHHTTT..-..EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHT CS
                            Fe-ADH   1 Ptrivfgkgaleelgellkkl..gakralivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaa 75 
                                       P+ +v+g g+++++ e +++l  g k+ +ivt+++++   +++ k +  l +++ e+t  + + +n + +++e+a+a
  gi|474934186|ref|YP_007687768.1|  14 PRSVVMGHGVIDQTREICDSLlfG-KNGIIVTGEKTF---DAAGKTVYDLMSEKYEMT--KVFVGNSDHDDIEKATA 84 
                                       889*****************9767.9*********88...788888888855555555..7889************* PP

                                       TS-TT.--EEEEEESHHHHHHHHHHHHHTT..................--EEEEESS-S-S-TT-SEEEEE.-TTSE CS
                            Fe-ADH  76 lareegadvviavGGGsviDtAKaialllanpevedylgegkakkkkalpliaiPTtaGtGsevtplavitdeeege 152
                                       +a++ +a +v+avGGGs iD+ K+++  l+                  +p++ iPT  + +  ++  a +  +e+g+
  gi|474934186|ref|YP_007687768.1|  85 AAKDCDAKFVLAVGGGSKIDISKIVSNNLR------------------IPFVSIPTSVAHDGICSDRASVK-DEKGA 142
                                       ******************************..................***********************.88889 PP

                                       EEEE-..SS--SEEEEEHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHT---TTSS.B--HHHHHHHHHHHHHHHHHH CS
                            Fe-ADH 153 klsifdpellPdlaivDpeltltlPkrvtaatglDalahalEayvskkanplsda.laleairliaknleravadge 228
                                        ++i    + P ++i D+e++l++P r++a++ +D+++          a  + d  ++ +a  l+  + + +v+ ++
  gi|474934186|ref|YP_007687768.1| 143 PMTIQ--AMPPMAVIADTEVLLKAPYRFLASGCADVISNLTALWDWDFARRMKDEeFSTSAYTLAHYSAQSLVDYAD 217
                                       9*999..9******************************988666669******985777777777777777776664 PP

                                       HH...........HHHHHHHHHHHHHHHHHHSS---HHHHHHHHHHC.CGGG..GGS-HHHHHHHHH.......... CS
                            Fe-ADH 229 dl...........eareqmllastlaglafsnaglgavHalahalgalfgip..hglanaillpavlrfnaeaaper 292
                                                    +    ++ +  +   + s    g  H+++hal  l+  +  hg+ +++    ++          
  gi|474934186|ref|YP_007687768.1| 218 -FikpgmeesiwlALKPIIASGTSMCIAGSSRPTSGSEHMFSHALDILHPSSamHGEQCGV--GCIM---------- 281
                                       .334455455554444444444444444555555556666666666644222235555554..2233.......... PP

                                       HHHHHHT.......T--HHHHHHHHHHHHHTT---SHHHHT-TT-HH.HHHHH CS
                            Fe-ADH 293 laqlaralggesdeeaaeeliealrellkelglptsLselgvdeedl.dklae 344
                                       +             + +    + +r+ lk++g+pt+ selg++eed+ d+l++
  gi|474934186|ref|YP_007687768.1| 282 M------------TQLQSGNWKVIRDALKKIGAPTTASELGLSEEDIvDALVA 322
                                       2............24455567889999*****************988655443 PP

>> DHQ_synthase  3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.0   5.5e-12   3.3e-08      23     256 ..      83     321 ..      73     330 .. 0.77

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 5.5e-12
                                       HHHTT--TT-EEEEEESHHHHHHHHHHHHHBTT--EEEEEE-SHHHHHTTTSSSEEEEEETTEEEEEEEE---SEEE CS
                      DHQ_synthase  23 lleakleRksllialGGGvvgDlaGfvAatylRGvrfvqvPttllaqvDssvGgKtainlplgKNliGafaqPkavl 99 
                                        ++ak    + ++a+GGG   D+   v+  ++  + fv +Pt++ a  D     + ++  ++g  +    + P av+
  gi|474934186|ref|YP_007687768.1|  83 TAAAKDCDAKFVLAVGGGSKIDISKIVSNNLR--IPFVSIPTSV-A-HDGICSDRASVKDEKGAPMTIQAMPPMAVI 155
                                       555554556789************99987765..********97.4.48888999********************** PP

                                       EEGGGGGGS-HHHHHHHHHHHHH.HHHHT-HHHHHHHHHHHHHHHC...........TTTHHHHHHHHHHHHHHHHH CS
                      DHQ_synthase 100 idlevLktLperelraGlaEviK.yalikdeelfelleenaeallk...........eeeeealeeliarsievkae 164
                                       +d+evL   p r l++G+a+vi   ++++d ++ +++++++ ++ +              ++ ++  +++si +  +
  gi|474934186|ref|YP_007687768.1| 156 ADTEVLLKAPYRFLASGCADVISnLTALWDWDFARRMKDEEFSTSAytlahysaqslVDYADFIKPGMEESIWLALK 232
                                       *********************9626899***********99999888888877666522334444444777776665 PP

                                       HHHHCCTT....TTGGGGGGTTHHHHHHHHHHHTTTTS-HHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHTT CS
                      DHQ_synthase 165 vveeDeke....kglralLnlGHtigHaiEallgyekllHGeaVaiGmvlaaelseklgllkkeeverllkllkklg 237
                                        + +  +      + r +    H ++Ha++ l+   + +HGe   +G ++ ++l +          + +++ lkk+g
  gi|474934186|ref|YP_007687768.1| 233 PIIASGTSmciaGSSRPTSGSEHMFSHALDILHPS-SAMHGEQCGVGCIMMTQLQSGN-------WKVIRDALKKIG 301
                                       4444333213337789999999*******988877.**************99998333.......356778888888 PP

                                       ---STTTT..-HHHHHHHHT CS
                      DHQ_synthase 238 lpvslkel.leveellealk 256
                                        p++ +el l+ e++++al 
  gi|474934186|ref|YP_007687768.1| 302 APTTASELgLSEEDIVDALV 321
                                       88877776555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2570.90
//
Query:       gi|474934187|ref|YP_007687769.1|  [L=182]
Description: Multimeric flavodoxin WrbA [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.5e-21   74.3   0.0    1.1e-20   74.0   0.0    1.2  1  FMN_red          NADPH-dependent FMN reductase
    6.6e-10   39.0   0.0      9e-10   38.6   0.0    1.2  1  Flavodoxin_2     Flavodoxin-like fold
     0.0079   15.7   0.5      0.013   15.0   0.5    1.3  1  NADH-G_4Fe-4S_3  NADH-ubiquinone oxidoreductase-G iron-sulfur


Domain annotation for each model (and alignments):
>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.0   0.0   1.8e-24   1.1e-20       1     114 [.       1     138 [.       1     154 [. 0.78

  Alignments for each domain:
  == domain 1  score: 74.0 bits;  conditional E-value: 1.8e-24
                                       -EEEEEES--STT-HHHHHHHHHHCCT-T.T-CEEEEETTTS..--...---HCHGHTCGGSHHHHHHHHHHHH-SC CS
                           FMN_red   1 mkilvisGSlrkgsntrklaewaaealkeagaevelidladl.ilpc.alcdkdlesegqtsddvaellekiaaada 75 
                                       mk lv+ GS +++++t  ++++a + l+ ag+e ++++l++  i +c   + + +  ++  +d + + ++++ + d 
  gi|474934187|ref|YP_007687769.1|   1 MKALVLDGSGNPNGFTSEMCQAASSVLEGAGIECSVVQLGKVwIEHCnGCLSCRKGGKCTIDDGMTAYYDALGEIDL 77 
                                       99*********************************************744444554569****************** PP

                                       EEEEEEECTTCE-HHHHHHHHCHT-.......................SSCHCCTT-EEEE CS
                           FMN_red  76 liivtPeYngsysgllKnalDrlsr......................trgkkelrgKpval 114
                                       l+++tP+ + ++s++lK+++Drl++                      +r +++l+ + ++ 
  gi|474934187|ref|YP_007687769.1|  78 LVFATPIRFSGPSSILKTFMDRLNPffysnlkhprfaaammcggadaPRFSNALSEMKALS 138
                                       ***********************97555555444444444444444444444444444444 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   0.0   1.5e-13     9e-10       1     189 [.       1     165 [.       1     173 [. 0.79

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 1.5e-13
                                       -EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCCT-----CCCCHCCHHHHTT..C.HHHHHHH.HH CS
                      Flavodoxin_2   1 mkiLiinahprpeksfssalaqafvealekagphevtvrdLyadflpvlttrdlaaklayeek..p.adveseq.ie 73 
                                       mk L+++++ +p + f+s++ qa+ + le ag  e  v+ L + ++ +++  +l+     +++  + +d  + +  +
  gi|474934187|ref|YP_007687769.1|   1 MKALVLDGSGNP-NGFTSEMCQAASSVLEGAG-IECSVVQLGKVWIEHCNG-CLS----CRKGgkCtIDDGMTAyYD 70 
                                       9***********.6******************.9*********99999987.444....3333466699999999** PP

                                       HHHCSSEEEEEEE-BTTB--HHHHHHHHHHS-TTTSCEETTCSSCCCCTTTTSEEEEEEEESS-GGGSSTTSSS-S- CS
                      Flavodoxin_2  74 kllaadaivlqfPlwwfgvPailKgwiDrvltagfafyteeggegrgggLkgkkalvivttGgpeesyqerglegaa 150
                                       +l + d++v+++P+ + g ++ilK ++Dr   + f +            Lk+ +   ++ +Gg  ++          
  gi|474934187|ref|YP_007687769.1|  71 ALGEIDLLVFATPIRFSGPSSILKTFMDRL--NPFFY----------SNLKHPRFAAAMMCGGA-DAP--------R 126
                                       *****************************7..66655..........45777777777777777.332........3 PP

                                       HHHHHHHHHHHHHHTT-EEEEEEEEESCTCCCHHHHHHH CS
                      Flavodoxin_2 151 mdellpplrgilgfiGikdvepvlvegvagaedeealae 189
                                       +  +l+ +++    +G+++   + v g++++++ee  ae
  gi|474934187|ref|YP_007687769.1| 127 FSNALSEMKALSITVGAEWAGELEVSGTDSKSREEVAAE 165
                                       566677777777777777777777777765555554433 PP

>> NADH-G_4Fe-4S_3  NADH-ubiquinone oxidoreductase-G iron-sulfur binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.5   2.3e-06     0.013      10      26 ..      44      60 ..      39      68 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.3e-06
                   NADH-G_4Fe-4S_3 10 anHpldCltCdknGnCe 26
                                      ++H++ Cl+C k+G+C+
  gi|474934187|ref|YP_007687769.1| 44 IEHCNGCLSCRKGGKCT 60
                                      68**************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1193.42
//
Query:       gi|474934188|ref|YP_007687770.1|  [L=201]
Description: hypothetical protein TALC_00611 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.037   13.5   0.0        3.1    7.2   0.0    2.0  2  His_biosynth  Histidine biosynthesis protein


Domain annotation for each model (and alignments):
>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0   0.00077        14      56     117 ..      54     114 ..      29     123 .. 0.83
   2 ?    7.2   0.0   0.00017       3.1      12      56 ..     118     162 ..     115     165 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.00077
                                       TTHHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHH CS
                      His_biosynth  56 egreanldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpelikelae 117
                                       + r+ n + ve+++ +   ++++   +r+l dv++++ a +++++i   +v++ +++++++ 
  gi|474934188|ref|YP_007687770.1|  54 STRSFNAKFVEKVRIT-GSEIWLVETVRDLADVADAFLANISRLVIPVHTVDSYDVLEDAMA 114
                                       5667777788877766.778888888*******************************99886 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00017
                                       EEEEECTTCSTCEEEETTSHHHHHHHHHHHT-SEEEEEEHHHHCT CS
                      His_biosynth  12 kvVrlvkGdrfqelryagdpvelakryeeegadelhvvDldaake 56 
                                        +V l+  +  +++ +++d   ++ r+ ++g++ ++v+Dld+ ++
  gi|474934188|ref|YP_007687770.1| 118 DCVPLIVTESGTAQGEERDTTRILDRLVKTGFRNVVVMDLDGYMD 162
                                       688888888899999999***********************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1333.63
//
Query:       gi|474934189|ref|YP_007687771.1|  [L=164]
Description: hypothetical protein TALC_00612 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.072   12.4   3.9      0.085   12.2   3.9    1.1  1  EXS              EXS family
       0.24   11.7   5.6        0.5   10.6   5.6    1.5  1  DUF4293          Domain of unknown function (DUF4293)
       0.33   11.2  16.7       0.57   10.5   0.1    2.8  2  DUF996           Protein of unknown function (DUF996)
          1    9.0   9.0       0.32   10.6   1.9    2.6  3  DUF3341          Protein of unknown function (DUF3341)
        3.4    8.1  19.1          5    7.5   4.9    3.4  3  Phage_holin_5_2  Phage holin family Hol44, in holin superfami


Domain annotation for each model (and alignments):
>> EXS  EXS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   3.9   2.4e-05     0.085       3     100 ..      15     115 ..      13     134 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.4e-05
                               EXS   3 lpyrvlllvvlglllwalnlhvlsklginyalifeldprsslsyrqlyelaa.lllllllllllllll.saevd.al 76 
                                         +  +l++v +++ wa  + +++++ + ++ i   d     ++++++ ++  ++ ++++++ ll+++ +   d  +
  gi|474934189|ref|YP_007687771.1|  15 TFIGAILMIVAYFVDWASITSYVANHSVGTVNIDAGDIADADDWQKYIPMLGlVFGIIIVVIELLNFFvPGALDkLA 91 
                                       5677899999999***********************************86661455555556666666544444256 PP

                               EXS  77 ellplllllllllllllplnilyr 100
                                       +++p++++++ +l++++ + ++ +
  gi|474934189|ref|YP_007687771.1|  92 TIIPIIVFVFGILAVVFAIMFMTW 115
                                       699998888888888877665555 PP

>> DUF4293  Domain of unknown function (DUF4293)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   5.6   0.00014       0.5       7     135 ..      13     147 ..      12     152 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00014
                           DUF4293   7 lyLllaailmaaflflplasivtedellsfyalgvs...taeaetsvnvsvwvlvilllliailaliaIflyknRkl 80 
                                       l+ ++ ailm++  f+  asi++   ++s+ ++ +     a+a+  +++  +  +++ ++i+++ l++ f       
  gi|474934189|ref|YP_007687771.1|  13 LFTFIGAILMIVAYFVDWASITSYVANHSVGTVNIDagdIADADDWQKYIPMLGLVFGIIIVVIELLNFFVPGALDK 89 
                                       788999**************998888877776666644444666666777777788888888888888887666555 PP

                           DUF4293  81 Qlrlc.linllllvllyvllal..lllvnkanaaaeslgesslkiglilplialilnl 135
                                        ++++ +i  ++ +l +v++++  ++ v ++ + a++ ++ss+++g++l l+  i++l
  gi|474934189|ref|YP_007687771.1|  90 LATIIpIIVFVFGILAVVFAIMfmTWDVWDSHMVAGNGTKSSMGLGFYLLLAGGIVTL 147
                                       5554433333333333333222212333445556666678999***999988766654 PP

>> DUF996  Protein of unknown function (DUF996)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00016      0.57     104     124 ..       5      25 ..       1      28 [. 0.85
   2 ?    2.4  12.1     0.051   1.8e+02      30      94 ..      96     160 ..      33     163 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00016
                            DUF996 104 vklFetagllyfiGaiLtivl 124
                                       +k  +t gl+ fiGaiL+iv+
  gi|474934189|ref|YP_007687771.1|   5 IKDPKTIGLFTFIGAILMIVA 25 
                                       6666899************95 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.051
                            DUF996  30 liafilsiialvvailalllvlgalatalelpgleeaaslilllllvliiayvlliisavflkks 94 
                                       +i f+++i a+v+ai+ +   +  + ++ +++  + +  ++ lll+  i+++++ i +a+   k+
  gi|474934189|ref|YP_007687771.1|  96 IIVFVFGILAVVFAIMFMTWDVWDSHMVAGNGTKSSMGLGFYLLLAGGIVTLIFSIGQAIPAIKA 160
                                       55666666666666666666666666666666556655588888888899999998877766665 PP

>> DUF3341  Protein of unknown function (DUF3341)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1     0.031   1.1e+02      47      77 ..       8      36 ..       3      42 .. 0.64
   2 ?   -1.5   0.0      0.47   1.7e+03      48      66 ..      60      78 ..      55      89 .. 0.74
   3 ?   10.6   1.9   8.8e-05      0.32      43      71 ..      87     115 ..      83     143 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.031
                                      SS-STHHHHHHHHHHHHHHHHHHHIIIIISS CS
                           DUF3341 47 ksrlpliallgGllGlalalllqvytsvvdy 77
                                      ++ ++l++++g++l + +a+++  ++s+ +y
  gi|474934189|ref|YP_007687771.1|  8 PKTIGLFTFIGAILMI-VAYFVD-WASITSY 36
                                      5678889999888854.455543.4444445 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.47
                                      S-STHHHHHHHHHHHHHHH CS
                           DUF3341 48 srlpliallgGllGlalal 66
                                      +++p++ l++G++ +++ l
  gi|474934189|ref|YP_007687771.1| 60 KYIPMLGLVFGIIIVVIEL 78
                                      5688888888888666655 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 8.8e-05
                                       SS--SS-STHHHHHHHHHHHHHHHHHHHI CS
                           DUF3341  43 lglkksrlpliallgGllGlalalllqvy 71 
                                       l+   + +p+i++++G+l++++a++++++
  gi|474934189|ref|YP_007687771.1|  87 LDKLATIIPIIVFVFGILAVVFAIMFMTW 115
                                       5566799*******************998 PP

>> Phage_holin_5_2  Phage holin family Hol44, in holin superfamily V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.5      0.07   2.5e+02      22      43 ..      10      32 ..       2      50 .. 0.65
   2 ?    7.4   1.4    0.0016       5.6      20      37 ..      57      76 ..      42      93 .. 0.81
   3 ?    7.5   4.9    0.0014         5      21      64 ..      92     149 ..      85     159 .. 0.61

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.07
                   Phage_holin_5_2 22 yIPlilgiiGiilgvvivfta..d 43
                                      +I  + ++iG+il +v++f++  +
  gi|474934189|ref|YP_007687771.1| 10 TIG-LFTFIGAILMIVAYFVDwaS 32
                                      443.45678888888888875441 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0016
                   Phage_holin_5_2 20 d..kyIPlilgiiGiilgvv 37
                                      d  kyIP++ +++Gii+ v+
  gi|474934189|ref|YP_007687771.1| 57 DwqKYIPMLGLVFGIIIVVI 76
                                      366*************9855 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0014
                   Phage_holin_5_2  21 kyIPlilgiiGiilgvvivftadfqaedilifg..............aiiqGilsgga 64 
                                         IP+i+ ++Gi+  v ++++++++ +d  + +               ++ Gi++  +
  gi|474934189|ref|YP_007687771.1|  92 TIIPIIVFVFGILAVVFAIMFMTWDVWDSHMVAgngtkssmglgfylLLAGGIVTLIF 149
                                       6799999999998875555545333333322222346666666566555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1251  (0.0697752); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 1038.30
//
Query:       gi|474934190|ref|YP_007687772.1|  [L=127]
Description: desulfoferrodoxin ferrous iron-binding domain protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-18   66.9   0.0    2.4e-18   66.5   0.0    1.2  1  Desulfoferrodox  Desulfoferrodoxin
    8.4e-06   25.3   1.4    1.5e-05   24.5   1.4    1.4  1  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain


Domain annotation for each model (and alignments):
>> Desulfoferrodox  Desulfoferrodoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.5   0.0   2.7e-22   2.4e-18       4      96 .]      45     127 .]      42     127 .] 0.90

  Alignments for each domain:
  == domain 1  score: 66.5 bits;  conditional E-value: 2.7e-22
                                       TTTHTTSEEEEEESEEEETTEEEEEEEESS.SS--BSSSS-EEEEEEEEEETTSSEEEE-TBSESEEEEEEEESSSE CS
                   Desulfoferrodox   4 ekeekHvPvieadevvkagelfevkvkvgk.ipHpneeeHyIewielyleeegekrvelsaedepevtftvklkkek 79 
                                         e+kHvP+ie   ++++     + vkvgk  +Hp+e++HyI +ie+   +    r+ l+++d+pe+ f vk++k  
  gi|474934190|ref|YP_007687772.1|  45 PDENKHVPFIE---KQAD----GILVKVGKaSAHPMESDHYIIYIEICA-DGILMRKYLKPGDKPEAFFPVKADK-- 111
                                       5689*******...3334....599*****99***************99.7888899****************87.. PP

                                       EEEEEEEETTTEEEEEE CS
                   Desulfoferrodox  80 klvalsyCnlHGlWese 96 
                                        +va + Cn HGlW+se
  gi|474934190|ref|YP_007687772.1| 112 -VVAWELCNKHGLWKSE 127
                                       .9************985 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   1.4   1.6e-09   1.5e-05       5      35 ..       6      37 ..       2      38 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.6e-09
                                      -EEE-TTT--EEEEC.C--SS-EEETTEE-EE CS
                   Desulfoferrod_N  5 evYkCevCGniVeVl.eaGgGeLVCCgepMkl 35
                                       v++Ce CGn+ e +  +Gg + VCC +p k 
  gi|474934190|ref|YP_007687772.1|  6 AVFQCEKCGNVYEKTyAKGGCTPVCCAQPAKQ 37
                                      69*********9865278***********875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 872.96
//
Query:       gi|474934191|ref|YP_007687773.1|  [L=165]
Description: hypothetical protein TALC_00614 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.73    7.3  10.7       0.86    7.0  10.7    1.0  1  DUF3584   Protein of unknown function (DUF3584)
        1.4    9.0  10.0        2.1    8.4  10.0    1.3  1  UPF0242   Uncharacterised protein family (UPF0242) N-terminus
        2.4    7.5  11.9        3.3    7.0  11.2    1.5  1  DUF4407   Domain of unknown function (DUF4407)


Domain annotation for each model (and alignments):
>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0  10.7   0.00014      0.86     669     757 ..      11      99 ..       2     113 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00014
                           DUF3584 669 dklekaiaerkqqaeeqlqkldaqlkqleeqqkaaleelkedlseerlekkakwqevvgeldeqlaelkkaieaart 745
                                       ++ ek   ++kq++e+  +k+  ++ +l + +++  ++ k+  +eer ++ka  + +v++++e +a+lk +   +++
  gi|474934191|ref|YP_007687773.1|  11 KRHEKLARSKKQEVENLEVKISMEQSALRHFKDDRAQQCKKLPREERAAFKADTRREVAKRKETIAKLKSEYRTKKA 87 
                                       44444555566666666689*****************************************************9999 PP

                           DUF3584 746 qakarlkeleea 757
                                       + k++ +e  ++
  gi|474934191|ref|YP_007687773.1|  88 ALKKKPEEPRKE 99 
                                       999987776555 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4  10.0   0.00035       2.1      81     170 ..       6      94 ..       1     100 [. 0.84

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00035
                           UPF0242  81 deglktkeealeelqeee.eeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeqLaekqellqeyqe 156
                                       +++ ++ +e+l  ++++e e+L+ +++  +++l++ k + +q  +kl    e+ +++k +   ++a+++e + +++ 
  gi|474934191|ref|YP_007687773.1|   6 SPKATKRHEKLARSKKQEvENLEVKISMEQSALRHFKDDRAQQCKKLPR--EERAAFKADTRREVAKRKETIAKLKS 80 
                                       5566677778877666543889999**999*****99999988888888..9999********************** PP

                           UPF0242 157 tieeqrsvlekrqd 170
                                       +   +++ l+k+ +
  gi|474934191|ref|YP_007687773.1|  81 EYRTKKAALKKKPE 94 
                                       **********9976 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0  11.2   0.00056       3.3     101     211 ..      38     139 ..      14     158 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00056
                           DUF4407 101 LkiFekeIdaelaeeqqeeakelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttg 177
                                       L+ F+++ +++ ++  +ee +++k+      + e+a+ ++ ia+l++e+++++a+l+++ +e +ke++ ++ ++   
  gi|474934191|ref|YP_007687773.1|  38 LRHFKDDRAQQCKKLPREERAAFKAD----TRREVAKRKETIAKLKSEYRTKKAALKKKPEEPRKEAKSAPAKE--- 107
                                       44555555555555555555555444....789***********************************988555... PP

                           DUF4407 178 vaGkgpaakekkaqldaaqaelaelkakldatar 211
                                        +  +p+ + k + + +a ae   ++++l+  ++
  gi|474934191|ref|YP_007687773.1| 108 APKAEPVPEPKAEPAGEAPAEEVPAEETLS--EE 139
                                       566666666666666666666666666633..22 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2161  (0.120531); expected 358.6 (0.02)
Passed bias filter:                      644  (0.0359195); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.47
# Mc/sec: 1049.81
//
Query:       gi|474934192|ref|YP_007687774.1|  [L=526]
Description: Isopropylmalate/homocitrate/citramalate synthase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.5e-87  291.9   0.4    4.5e-87  291.9   0.4    1.7  2  HMGL-like   HMGL-like
    8.5e-26   90.4   5.2    1.5e-25   89.6   5.2    1.4  1  LeuA_dimer  LeuA allosteric (dimerisation) domain


Domain annotation for each model (and alignments):
>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  291.9   0.4     5e-91   4.5e-87       2     264 .]      30     286 ..      29     286 .. 0.99
   2 ?   -1.8   0.2       0.2   1.8e+03      34      46 ..     456     468 ..     424     516 .. 0.49

  Alignments for each domain:
  == domain 1  score: 291.9 bits;  conditional E-value: 5e-91
                                       -EEEE-TTTHHHHTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHH CS
                         HMGL-like   2 vkivdttLRDGeqalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkarilalvrarekdi 78 
                                       v+i+dttLRDGeqa++ als ++k++iakaLd++g d iE+gf+++s  +++ +r+i +   + ++++l+r+++kdi
  gi|474934192|ref|YP_007687774.1|  30 VRIFDTTLRDGEQAPGIALSPDDKVRIAKALDNLGTDIIEAGFAVSSDIERDTIRQIRDLNLDCKVCSLARSVKKDI 106
                                       89*************************************************************************** PP

                                       HHHHH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--HHHHHHHHHHH CS
                         HMGL-like  79 kaavealkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkdvelsledasrtdleflaevveaa 155
                                       +a ++    +g + vh+fiats+lh+k+klk++ e+v+++a+eav++ar++g +v +s+eda+r+  ef+ +++  +
  gi|474934192|ref|YP_007687774.1| 107 DAVID----TGLDFVHTFIATSDLHMKYKLKMSPEDVRNSAVEAVEYARDHGLEVMFSCEDATRSRYEFMRDILLDV 179
                                       *****....******************************************************************** PP

                                       HHHT-SEEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--EEEEBTTS--SSBB CS
                         HMGL-like 156 eeaGatriniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadrvdgtvnGlGeraG 232
                                       ++aGa ++ni+DtvGv+ P +++++i+ l++++k  v++svHcHnd+GlA+antlaAve+Ga+ v g++nG+GeraG
  gi|474934192|ref|YP_007687774.1| 180 QDAGASCVNIPDTVGVILPAAFGKMIADLRSELK--VPISVHCHNDMGLALANTLAAVENGATIVQGCLNGIGERAG 254
                                       **********************************..***************************************** PP

                                       B-BHHHHHHHHHHTT-B----HHHHHHHHHHH CS
                         HMGL-like 233 naaleelvaalealgvdtgldlqklrsiaalv 264
                                       n+alee++++l a      ldl k+ s++alv
  gi|474934192|ref|YP_007687774.1| 255 NVALEEVAVNLLANYGVRTLDLPKIASTSALV 286
                                       ***********99998999*********9997 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.2
                                       HHT-SEE--TSGG CS
                         HMGL-like  34 eagvdeiEvgfpa 46 
                                       ++ ++ +E   +a
  gi|474934192|ref|YP_007687774.1| 456 NVNMSMVEFKSSA 468
                                       2222233332222 PP

>> LeuA_dimer  LeuA allosteric (dimerisation) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.6   5.2   1.7e-29   1.5e-25       1     131 [.     381     516 ..     381     518 .. 0.91

  Alignments for each domain:
  == domain 1  score: 89.6 bits;  conditional E-value: 1.7e-29
                                       XXXXXXXXXXXXXXXXX...XX--EEEEEEEEEEETTCEEEEEEEEEE.TTEEEEEEEE-SSHHHHHHHHHHHHHHH CS
                        LeuA_dimer   1 evtdedlealvkdelle...aeerlkleklqvssgedelstatvklevkdgeekeasaeGnGpvdAllnAlrkalgv 74 
                                       ev+d ++ a+++d + +    +++  le+l+v++g+++++tatvk++  dg+ ++++ +G+Gpv+A++nA+rka++v
  gi|474934192|ref|YP_007687774.1| 381 EVADVEVGAIAEDIMWNkatLRRECILEELTVTTGKSTTPTATVKIRRSDGSAVTVADVGVGPVNAAVNAIRKAVNV 457
                                       56777777777777766443347788*************************************************** PP

                                       T-EEEEEEEE--TT-TT--EEEEEEEE-..-GGGEEEEEEEESSHHHHHHHHHHHHHHH CS
                        LeuA_dimer  75 dikLldYsvhaitegtdaqaevrVelev..ddgkkvsgvGvdsdiveASlkAlisalnr 131
                                       ++++ +++  a+t+++d   +v V++++  +dg+   g++v+ diveAS++A++ a+nr
  gi|474934192|ref|YP_007687774.1| 458 NMSMVEFKSSAVTGQSDSICTVAVTVKNvqNDGNLSFGRAVSVDIVEASVEATMAAINR 516
                                       **************************988788998***********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (526 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       699  (0.0389871); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 3597.54
//
Query:       gi|474934193|ref|YP_007687775.1|  [L=87]
Description: hypothetical protein TALC_00616 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-05   23.5   0.0    5.8e-05   23.1   0.0    1.2  1  Pcc1      Transcription factor Pcc1


Domain annotation for each model (and alignments):
>> Pcc1  Transcription factor Pcc1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   3.2e-09   5.8e-05       1      69 [.       5      68 ..       5      72 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 3.2e-09
                                      EEEEEEE-SSHHHHHHHHHHHHHHCHC-TTECEEEEEEETTEEEEEEEESSHHHHHHHHHHHHHHHHHH CS
                              Pcc1  1 sltisvpfpterlAsialrtLqvDkelsplavkrslslegnvLqveykAttnrmLRvavngfleslglv 69
                                      +l+ ++p+ +e+ A +++ ++++++   +    ++ +leg+v+  + kA+t+ +LR + + +l  ++ +
  gi|474934193|ref|YP_007687775.1|  5 TLEMRFPYADEKTANAVFSAVAPEN---SG--FVESRLEGPVIIYNLKAETAGSLRNTADDLLACIKAA 68
                                      5889********************5...33..35568*********************99999877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       202  (0.0112667); expected 358.6 (0.02)
Passed bias filter:                      184  (0.0102627); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 612.76
//
Query:       gi|474934194|ref|YP_007687776.1|  [L=646]
Description: tRNA-guanine transglycosylase, archaeosine-15-forming [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-69  235.2   0.0    1.6e-69  234.7   0.0    1.1  1  TGT       Queuine tRNA-ribosyltransferase
    1.1e-21   76.7   0.0    2.7e-21   75.4   0.0    1.6  1  TGT_C2    Patch-forming domain C2 of tRNA-guanine transglycos
    1.8e-11   43.8   0.2    5.2e-11   42.3   0.2    1.8  1  PUA       PUA domain
    2.2e-06   27.6   0.0    5.6e-06   26.3   0.0    1.7  1  DUF5591   Domain of unknown function (DUF5591)
  ------ inclusion threshold ------
       0.16   11.5   0.0       0.34   10.5   0.0    1.5  1  PGM1_C    PGM1 C-terminal domain
       0.21   12.3   0.9         29    5.4   0.1    2.5  2  DUF2769   Protein of unknown function (DUF2769)


Domain annotation for each model (and alignments):
>> TGT  Queuine tRNA-ribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.7   0.0   5.4e-73   1.6e-69       3     349 ..      11     335 ..       8     336 .. 0.95

  Alignments for each domain:
  == domain 1  score: 234.7 bits;  conditional E-value: 5.4e-73
                                       EEEEEEEETT.EEEEESEEEEBETTSSBTTB-HHHHH.HTTES-EEEEHHHHHHTTTHHHHHHTTHHHHHHT--S-E CS
                               TGT   3 aRlGklelph.gtietPafmpvgtqgtvkgltpdelkeelgaqiilsntyhlelrpgeelvakagglhkflgwdkpi 78 
                                       aR+Gk+++   +++etPa++pv  ++++k+++p+el +++g ++i++n+y+++++p  +  a+ +glh++l++++ i
  gi|474934194|ref|YP_007687776.1|  11 ARMGKFTTTSgRVLETPALLPV-INPKIKTVSPRELYDDFGFRAIITNSYIIKNNPDLKEEAQSKGLHEMLDFPGVI 86 
                                       9*******88569*********.999**********999*********************9**************** PP

                                       EEE-SHHHHHHHEEEESSEEEEE-TTTS-EEEE-HHHHHHHHHHHT-SEEE-------SS--HHHHHHHHHHHHHHH CS
                               TGT  79 ltdsggfqvfslkkiteegvsfqsridGskvlltpeesieiqeklgsDiimalddvvpspaskkrveksverTlrwl 155
                                       +tdsg+fq               s++ G  v lt+ e++e+q+++g Di + ld  ++++ ++++ +k+v+ Tl+++
  gi|474934194|ref|YP_007687776.1|  87 MTDSGTFQ---------------SHMYGT-VPLTNPEIVEFQKSIGTDIGTVLDIFTEPDWDEEKTRKAVDITLERT 147
                                       ********...............455599.*********************************************** PP

                                       HHHHHHH.SE.EEEEE--TT-HHHHHHHHHHHHHH--SEEEE-S.SSSSS..HHHHHHHHHHHHGGGS-TTS-EEET CS
                               TGT 156 drcleah.qa.lfgivqGglyedlreesaeelakrdfdgyaigG.lsvge..ekeellevveavtellpedkprylm 227
                                       +++++ + ++ + g++qG++y+dlr+ +a++ a +d+d+ +igG ++++e  ++ el++v+ +++  ++ ++p++l+
  gi|474934194|ref|YP_007687776.1| 148 EEAVAMKgEMmINGVIQGSVYNDLRTYCARKEAVMDIDVHPIGGvVPLMEqyRYVELVDVIMSSKMGMNPNRPVHLF 224
                                       ****9889555*********************************888***88889********************** PP

                                       TB-SHHHHHHHHHTT--EEEESHHHHHHHTTEEEETTEEEETTSGGGTT--SBSSSS--SHHHHH-BHHHHHHHHHT CS
                               TGT 228 GvgtPedlleavalGvDmfdcvyptrtarngraltsegelnlknakyaedfspldegCsCytCknytraylhhllkt 304
                                       G+g+P+ l+ a  +G+D+fd++ +++ a+++r+++ +g+ +l++       + l  +C+C++C+  t + l+ + k 
  gi|474934194|ref|YP_007687776.1| 225 GAGHPMILAFATLMGCDLFDSASYAKFAKDDRMMFIDGTSRLQDM------QSL--DCDCPACRGITLEGLRAMEKG 293
                                       **************************************9999744......442..5******************99 PP

                                       T-HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHT CS
                               TGT 305 kemlgaiLltiHNlhyylelfkriReaIkegtfeefveefarkye 349
                                        +   ++L++ HNl+ ++ ++  +R+ + eg+++e++e+++r+++
  gi|474934194|ref|YP_007687776.1| 294 AR---SKLIARHNLYQIKSELGLVRRYLLEGRLWELAEQRCRAHP 335
                                       99...*************************************987 PP

>> TGT_C2  Patch-forming domain C2 of tRNA-guanine transglycosylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.4   0.0   9.2e-25   2.7e-21       3      71 .]     496     565 ..     495     565 .. 0.97

  Alignments for each domain:
  == domain 1  score: 75.4 bits;  conditional E-value: 9.2e-25
                            TGT_C2   3 lraiadYqFGagagdaLfpedvtitrs.atgrirqvlvdgerlatlraqdgrltLsleGarrlheslppP 71 
                                        +a+  YqFG +a daLf++++++++s +tg+ir+v+ dge+++++ra dg+ tL +eGa+r+ e+ p P
  gi|474934194|ref|YP_007687776.1| 496 AKAVSRYQFGIEATDALFRGKIELKISrKTGKIRNVISDGEHVLSMRAGDGFYTLRMEGAKRIIEACPSP 565
                                       68999*************************************************************9987 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.2   1.8e-14   5.2e-11       3      72 ..     569     638 ..     567     639 .. 0.96

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 1.8e-14
                                       EEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEE CS
                               PUA   3 vvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveier 72 
                                         v d Av +  +g++++a +v  ++g++ ++d+V +vd++++++a G +++ ++e++ +k+g++v+++ 
  gi|474934194|ref|YP_007687776.1| 569 CMVQDDAVPFCEKGRNVFAQFVDMADGELVPKDEVIVVDRNDRPIATGQMLLVADEIRCMKKGIAVKVRS 638
                                       5799******999******************************************************985 PP

>> DUF5591  Domain of unknown function (DUF5591)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   1.9e-09   5.6e-06       2      76 ..     377     444 ..     376     454 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.9e-09
                                       -HHHHHHHHH---S..SSEEEEEE--SSSSGGGSHHHHHHHHHS---...SEEEEE-SS-.EEEGGGTT------ CS
                           DUF5591   2 krfrervlerYeppeekkvlvLlPcsakkPyseskshrkfaeaikkrkakvheviltsPlGvvPreleevYPaaq 76 
                                       kr+ +r++erY  p+  k   ++  ++ kPys+  +  +f +a +         ++ sP+G vP el+e+YP+aq
  gi|474934194|ref|YP_007687776.1| 377 KRYFDRMMERYVAPT--KKAAIFDATEGKPYSRAMQD-QFWSAWRLG----YTPVVISPFGPVPAELDEMYPLAQ 444
                                       79************6..5566789*********9875.566665555....345566***************986 PP

>> PGM1_C  PGM1 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00011      0.34      13      30 ..     354     371 ..     353     376 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00011
                            PGM1_C  13 YdpetreGVVlytgtlpg 30 
                                       Ydp +reG+++ytg+ + 
  gi|474934194|ref|YP_007687776.1| 354 YDPISREGAIFYTGAETR 371
                                       9************88555 PP

>> DUF2769  Protein of unknown function (DUF2769)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1    0.0098        29      19      47 ..     256     283 ..     240     291 .. 0.68
   2 ?    4.8   0.1     0.015        45       5      28 ..     561     584 ..     558     588 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0098
                           DUF2769  19 ellFCargksekcieeekgClCpeCevyk 47 
                                        ++F + g+s+ + ++  +C Cp+C+  +
  gi|474934194|ref|YP_007687776.1| 256 RMMF-IDGTSRLQDMQSLDCDCPACRGIT 283
                                       3555.6788878888889*******8655 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.015
                           DUF2769   5 kCpsytaeckkkelellFCargks 28 
                                        Cps +++c+ +     FC +g++
  gi|474934194|ref|YP_007687776.1| 561 ACPSPHMRCMVQDDAVPFCEKGRN 584
                                       7************9*****99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (646 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 3980.96
//
Query:       gi|474934195|ref|YP_007687777.1|  [L=133]
Description: hypothetical protein TALC_00618 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.056   13.5   0.0       0.12   12.4   0.0    1.5  1  DUF1192   Protein of unknown function (DUF1192)


Domain annotation for each model (and alignments):
>> DUF1192  Protein of unknown function (DUF1192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.7e-06      0.12       7      35 ..      12      40 ..       9      44 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.7e-06
                           DUF1192  7 kkptheigqDLslLSveELeerIalLeaE 35
                                      k+p+ + g++L + Sv+E++++I++L  E
  gi|474934195|ref|YP_007687777.1| 12 KEPECLPGKELRHKSVQEMNDYIEHLVFE 40
                                      4557899******************9766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 859.12
//
Query:       gi|474934196|ref|YP_007687778.1|  [L=445]
Description: TPR repeat protein, SEL1 subfamily [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-48  161.4  27.1    1.4e-06   28.7   0.0   11.1 11  Sel1      Sel1 repeat
    0.00078   19.7   1.1        3.5    8.2   0.0    5.0  5  TPR_17    Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.033   15.0  15.9          1   10.3   2.7    5.1  5  TPR_14    Tetratricopeptide repeat
      0.099   12.7   3.7         12    6.0   0.1    4.2  4  MIT       MIT (microtubule interacting and transport) domain
       0.38   11.1  12.1         16    5.9   2.2    4.9  5  TPR_12    Tetratricopeptide repeat
        1.2    8.8   5.2        9.6    6.0   0.2    4.5  4  TPR_11    TPR repeat
        8.9    6.3  10.0         32    4.6   0.0    4.8  6  TPR_10    Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> Sel1  Sel1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1     2e-05     0.051       2      37 ..      14      47 ..      13      48 .. 0.77
   2 !   19.8   0.8   3.5e-07   0.00091       3      38 .]      51      84 ..      50      84 .. 0.90
   3 !   21.7   0.1   9.2e-08   0.00024       3      38 .]      87     120 ..      85     120 .. 0.92
   4 ?    5.0   0.0     0.017        44       1      18 [.     121     136 ..     121     151 .. 0.76
   5 !   12.0   0.0    0.0001      0.27       2      38 .]     158     192 ..     157     192 .. 0.89
   6 ?    3.2   0.0     0.062   1.6e+02       7      30 ..     199     220 ..     199     225 .. 0.85
   7 ?    3.5   0.0      0.05   1.3e+02       1      38 []     255     290 ..     255     290 .. 0.89
   8 !   24.2   0.1   1.5e-08   3.8e-05       3      38 .]     293     326 ..     291     326 .. 0.93
   9 !   28.7   0.0   5.6e-10   1.4e-06       3      36 ..     329     360 ..     328     361 .. 0.90
  10 !   23.0   0.0   3.5e-08   9.1e-05       1      38 []     368     403 ..     368     403 .. 0.95
  11 !   14.4   2.0   1.8e-05     0.047      14      38 .]     409     435 ..     404     435 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2e-05
                              Sel1  2 eAmyrLGmfylylnGlgvpkDpekAiewyekAAeqG 37
                                      +A++r +    +  G+  ++  e+A+++y+kAA++G
  gi|474934196|ref|YP_007687778.1| 14 DALMRRA--DELRLGTAGEQSFEEAFRLYKKAASKG 47
                                      6788888..633555546789*************99 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 3.5e-07
                              Sel1  3 AmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38
                                      A++ LG+++  ++G+g+ + ++ A++wy + A+++d
  gi|474934196|ref|YP_007687778.1| 51 AYFLLGCMC--EAGQGTSQSYKVAYQWYDRGAQRND 84
                                      99****555..*********************9875 PP

  == domain 3  score: 21.7 bits;  conditional E-value: 9.2e-08
                              Sel1   3 AmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                       +++ LG   ly++Glg+++ +e+Aie++e AA++G+
  gi|474934196|ref|YP_007687778.1|  87 CQASLG--FLYEAGLGTKRSRELAIEHLENAANAGN 120
                                       6888**..777**********************997 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.017
                              Sel1   1 aeAmyrLGmfylylnGlg 18 
                                       + A+++LG  ++yl++ g
  gi|474934196|ref|YP_007687778.1| 121 PRAQNNLG--LIYLDRSG 136
                                       57******..66699875 PP

  == domain 5  score: 12.0 bits;  conditional E-value: 0.0001
                              Sel1   2 eAmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                        A ++L+   +y++G g ++  + A  +++ AA+ G+
  gi|474934196|ref|YP_007687778.1| 158 PATANLA--RMYEKGIGMERKCDTAANLFKTAAKGGS 192
                                       57899**..666*****9999************9986 PP

  == domain 6  score: 3.2 bits;  conditional E-value: 0.062
                              Sel1   7 LGmfylylnGlgvpkDpekAiewy 30 
                                       L+  ++y +G g+p+ +  A++ y
  gi|474934196|ref|YP_007687778.1| 199 LA--EMYKFGIGIPASEVYARHIY 220
                                       78..888********999998866 PP

  == domain 7  score: 3.5 bits;  conditional E-value: 0.05
                              Sel1   1 aeAmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                       + A+  LG  + +l+G  + + +  A+ ++e +A+ G+
  gi|474934196|ref|YP_007687778.1| 255 PKAQLSLG--LSFLDGGFTLQSVPTAMFLLEASARGGN 290
                                       579999**..77799977***************99986 PP

  == domain 8  score: 24.2 bits;  conditional E-value: 1.5e-08
                              Sel1   3 AmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                       Amy LG  ++y++Gl +++ + +A++wy+  A++G+
  gi|474934196|ref|YP_007687778.1| 293 AMYVLG--QIYETGLFTERSKFLAMKWYKWGADKGN 326
                                       9*****..999******************9999886 PP

  == domain 9  score: 28.7 bits;  conditional E-value: 5.6e-10
                              Sel1   3 AmyrLGmfylylnGlgvpkDpekAiewyekAAeq 36 
                                       ++y+LG  ++y++G gv  DpekA+e y++++e 
  gi|474934196|ref|YP_007687778.1| 329 CAYNLG--CMYEDGVGVQHDPEKAFEMYKRSCEC 360
                                       58****..666********************985 PP

  == domain 10  score: 23.0 bits;  conditional E-value: 3.5e-08
                              Sel1   1 aeAmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                       ++A+y+L+   l+  Glg +kD+++A+e++ ++ ++G+
  gi|474934196|ref|YP_007687778.1| 368 SDALYALA--SLLRSGLGCEKDEDRALELFVRSSDLGH 403
                                       68******..877************************8 PP

  == domain 11  score: 14.4 bits;  conditional E-value: 1.8e-05
                              Sel1  14 lnGlg.vpk.DpekAiewyekAAeqGd 38 
                                        +G++  ++ D+ +A++++e+AAeqGd
  gi|474934196|ref|YP_007687778.1| 409 AAGKMfADRgDRASARKYLEMAAEQGD 435
                                       45664445559***************7 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1     0.047   1.2e+02       9      27 ..     117     135 ..     111     141 .. 0.82
   2 ?   -1.7   0.0         2   5.2e+03      13      24 ..     157     168 ..     154     197 .. 0.61
   3 ?   -0.4   0.0      0.78     2e+03      12      24 ..     290     302 ..     288     311 .. 0.87
   4 ?    1.2   0.0      0.24   6.2e+02       9      32 ..     323     350 ..     322     352 .. 0.75
   5 !    8.2   0.0    0.0014       3.5       1      24 [.     353     379 ..     353     393 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.047
                            TPR_17   9 dPnnadaynnLAelllknG 27 
                                       +  n+ a nnL+ ++l + 
  gi|474934196|ref|YP_007687778.1| 117 NAGNPRAQNNLGLIYLDRS 135
                                       778999*********9764 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2
                            TPR_17  13 adaynnLAelll 24 
                                       ++a  nLA+ ++
  gi|474934196|ref|YP_007687778.1| 157 PPATANLARMYE 168
                                       556678888776 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.78
                            TPR_17  12 nadaynnLAelll 24 
                                       n  a++ L+++++
  gi|474934196|ref|YP_007687778.1| 290 NTTAMYVLGQIYE 302
                                       7789*******96 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.24
                            TPR_17   9 dPnnadaynnLAelll....knGdlmtA 32 
                                       d+ n +  +nL+  ++     ++d+++A
  gi|474934196|ref|YP_007687778.1| 323 DKGNGPCAYNLGCMYEdgvgVQHDPEKA 350
                                       6789999******998666666666655 PP

  == domain 5  score: 8.2 bits;  conditional E-value: 0.0014
                            TPR_17   1 lylkaleldPnn...adaynnLAelll 24 
                                       +y+++ e+d +    +da++ LA ll+
  gi|474934196|ref|YP_007687778.1| 353 MYKRSCECDQDEdaeSDALYALASLLR 379
                                       69*******99669***********97 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.2     0.019        49       2      39 ..      14      53 ..      13      56 .. 0.63
   2 ?   -2.5   0.0       5.2   1.3e+04      20      38 ..     108     124 ..      93     129 .. 0.66
   3 ?    5.5   0.1     0.014        37      15      43 ..     345     376 ..     344     377 .. 0.72
   4 ?    0.2   0.1      0.75   1.9e+03       2      24 ..     369     395 ..     368     400 .. 0.67
   5 ?   10.3   2.7   0.00041         1       2      35 ..     405     438 ..     404     445 .] 0.87

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.019
                            TPR_14  2 eallalaeall..alGd..pdeAiallrralalaPddaeawl 39
                                      +al+++a+ l+  ++G+  ++eA +l+++a +++   ++a++
  gi|474934196|ref|YP_007687778.1| 14 DALMRRADELRlgTAGEqsFEEAFRLYKKAASKGV--ERAYF 53
                                      56666666655333444459**********88554..44544 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.2
                            TPR_14  20 AiallrralalaPddaeaw 38 
                                       Ai++l+ a  ++ ++++a+
  gi|474934196|ref|YP_007687778.1| 108 AIEHLENA--ANAGNPRAQ 124
                                       77777776..345555555 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.014
                            TPR_14  15 GdpdeAiallrrala..laPdda.eawlllaq 43 
                                        dp++A ++++r ++  ++ d + +a+++la 
  gi|474934196|ref|YP_007687778.1| 345 HDPEKAFEMYKRSCEcdQDEDAEsDALYALAS 376
                                       69***********9964444433368888775 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 0.75
                            TPR_14   2 eallalaealla....lGdpdeAiall 24 
                                       +al+ala++l+       d d+A++l+
  gi|474934196|ref|YP_007687778.1| 369 DALYALASLLRSglgcEKDEDRALELF 395
                                       689999999986322235777777776 PP

  == domain 5  score: 10.3 bits;  conditional E-value: 0.00041
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPdda 35 
                                        a++a+++ ++ +Gd + A+++l+ a +++ d a
  gi|474934196|ref|YP_007687778.1| 405 GAQYAAGKMFADRGDRASARKYLEMAAEQGDDRA 438
                                       589***********************99887654 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1    0.0047        12      18      31 ..      31      44 ..      29      46 .. 0.87
   2 ?    0.3   0.1       0.3   7.7e+02      18      31 ..      67      80 ..      65      82 .. 0.85
   3 ?    3.5   0.0      0.03        77      18      32 ..     345     359 ..     343     363 .. 0.86
   4 ?   -3.5   0.0       4.4   1.1e+04      31      47 ..     424     440 ..     421     443 .. 0.46

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0047
                               MIT 18 gnyeeAlelYkeal 31
                                      + +eeA++lYk+a 
  gi|474934196|ref|YP_007687778.1| 31 QSFEEAFRLYKKAA 44
                                      789*********96 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.3
                               MIT 18 gnyeeAlelYkeal 31
                                      + y+ A+++Y  + 
  gi|474934196|ref|YP_007687778.1| 67 QSYKVAYQWYDRGA 80
                                      78********9986 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.03
                               MIT  18 gnyeeAlelYkeale 32 
                                       ++ e+A+e+Yk ++e
  gi|474934196|ref|YP_007687778.1| 345 HDPEKAFEMYKRSCE 359
                                       56799*******998 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 4.4
                               MIT  31 lelLlqalkekneerre 47 
                                        ++L +a  + +++  e
  gi|474934196|ref|YP_007687778.1| 424 RKYLEMAAEQGDDRASE 440
                                       44555555433334444 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.09   2.3e+02      24      55 ..      31      59 ..      23      65 .. 0.62
   2 ?    1.2   0.1      0.17   4.4e+02      28      57 ..     103     133 ..      87     141 .. 0.71
   3 ?   -3.0   0.0       3.8   9.6e+03      46      56 ..     292     302 ..     282     306 .. 0.80
   4 ?    4.4   0.1     0.017        45      17      33 ..     345     361 ..     343     383 .. 0.53
   5 ?    5.9   2.2    0.0063        16      27      72 ..     389     431 ..     368     433 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.09
                            TPR_12 24 ellekaleiarrllGpdhpltattlrnLgrly 55
                                      + +e+a ++++++    + ++ ++++ Lg ++
  gi|474934196|ref|YP_007687778.1| 31 QSFEEAFRLYKKA--ASK-GVERAYFLLGCMC 59
                                      5566666666555..322.4666666666665 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.17
                            TPR_12  28 kaleia.rrllGpdhpltattlrnLgrlyra 57 
                                       +++e+a + l +  +++  ++++nLg +y+ 
  gi|474934196|ref|YP_007687778.1| 103 RSRELAiEHLENAANAGNPRAQNNLGLIYLD 133
                                       5556665666666677777888999999864 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 3.8
                            TPR_12  46 ttlrnLgrlyr 56 
                                       t+++ Lg++y+
  gi|474934196|ref|YP_007687778.1| 292 TAMYVLGQIYE 302
                                       68999999984 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.017
                            TPR_12  17 grydeAlellekaleia 33 
                                        + ++A+e+++++ e  
  gi|474934196|ref|YP_007687778.1| 345 HDPEKAFEMYKRSCECD 361
                                       45555555555555555 PP

  == domain 5  score: 5.9 bits;  conditional E-value: 0.0063
                            TPR_12  27 ekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeal 72 
                                       ++ale++ r+   d ++ a ++++ g ++  +g+ + A+++le a 
  gi|474934196|ref|YP_007687778.1| 389 DRALELFVRS--SD-LGHAGAQYAAGKMFADRGDRASARKYLEMAA 431
                                       6899999776..54.58899***********************986 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.22   5.7e+02       9      20 ..      32      43 ..      30      45 .. 0.87
   2 ?    6.0   0.2    0.0038       9.6      25      39 ..     118     132 ..     106     134 .. 0.77
   3 ?   -0.3   0.0      0.35     9e+02      26      39 ..     253     266 ..     252     269 .. 0.86
   4 ?   -1.1   0.1      0.62   1.6e+03      11      26 ..     348     363 ..     347     376 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.22
                            TPR_11  9 kyeeAieaYkkA 20
                                       +eeA   YkkA
  gi|474934196|ref|YP_007687778.1| 32 SFEEAFRLYKKA 43
                                      68*********9 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0038
                            TPR_11  25 PdnaeayynLGlayy 39 
                                         n++a +nLGl+y+
  gi|474934196|ref|YP_007687778.1| 118 AGNPRAQNNLGLIYL 132
                                       569**********97 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.35
                            TPR_11  26 dnaeayynLGlayy 39 
                                       +n+ a + LGl ++
  gi|474934196|ref|YP_007687778.1| 253 ENPKAQLSLGLSFL 266
                                       79********9876 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 0.62
                            TPR_11  11 eeAieaYkkAlkldPd 26 
                                       e+A e Yk+ ++ d+d
  gi|474934196|ref|YP_007687778.1| 348 EKAFEMYKRSCECDQD 363
                                       6888999999999987 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.26   6.6e+02      18      28 ..      33      43 ..      28      47 .. 0.63
   2 ?    4.6   0.0     0.012        32       4      15 ..     123     134 ..     122     141 .. 0.87
   3 ?   -3.5   0.1       4.3   1.1e+04       7      12 ..     162     167 ..     161     168 .. 0.88
   4 ?   -2.2   0.0       1.7   4.5e+03       4      12 ..     329     337 ..     329     339 .. 0.82
   5 ?   -1.5   0.0         1   2.6e+03      26      35 ..     348     357 ..     345     363 .. 0.68
   6 ?    3.2   0.6     0.034        86       9      28 ..     411     430 ..     404     432 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.26
                            TPR_10 18 ydeAealleea 28
                                      ++eA +l+++a
  gi|474934196|ref|YP_007687778.1| 33 FEEAFRLYKKA 43
                                      45555555555 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.012
                            TPR_10   4 slnNLanalrqr 15 
                                       ++nNL+ ++ +r
  gi|474934196|ref|YP_007687778.1| 123 AQNNLGLIYLDR 134
                                       89*******987 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 4.3
                            TPR_10   7 NLanal 12 
                                       NLa+++
  gi|474934196|ref|YP_007687778.1| 162 NLARMY 167
                                       9**999 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 1.7
                            TPR_10   4 slnNLanal 12 
                                       +  NL++++
  gi|474934196|ref|YP_007687778.1| 329 CAYNLGCMY 337
                                       567****99 PP

  == domain 5  score: -1.5 bits;  conditional E-value: 1
                            TPR_10  26 eealairrrl 35 
                                       e+a ++++r 
  gi|474934196|ref|YP_007687778.1| 348 EKAFEMYKRS 357
                                       6677777765 PP

  == domain 6  score: 3.2 bits;  conditional E-value: 0.034
                            TPR_10   9 analrqrgrydeAealleea 28 
                                       + +  +rg+++ A+++le a
  gi|474934196|ref|YP_007687778.1| 411 GKMFADRGDRASARKYLEMA 430
                                       566789***********977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2995.88
//
Query:       gi|474934197|ref|YP_007687779.1|  [L=125]
Description: conserved hypothetical protein TIGR00283 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-38  130.6   0.2    3.7e-38  130.4   0.2    1.0  1  PTH2      Peptidyl-tRNA hydrolase PTH2


Domain annotation for each model (and alignments):
>> PTH2  Peptidyl-tRNA hydrolase PTH2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.4   0.2   2.1e-42   3.7e-38       1     117 []      10     125 .]      10     125 .] 0.97

  Alignments for each domain:
  == domain 1  score: 130.4 bits;  conditional E-value: 2.1e-42
                                       EEEEEEEESSSSS-HHHHHHHHHHHHHHHHHHHHHH.CHHHHHHHHHHT.TTSEEEEEESSHHHHHHHHHHHHHTT- CS
                              PTH2   1 lkmvlvvrkDLkmskGkiaaqcahAavalvkkllkesnekellkeWeee.gqkkivlkveseeeLlelaakakalgl 76 
                                       +k+v++vr+D+kmskGk aaq++hAava++ +++k+ ++ + ++ We + gqk ++lkv s +eL e +a a+++g+
  gi|474934197|ref|YP_007687779.1|  10 YKVVILVRQDVKMSKGKTAAQASHAAVACALAAKKN-HP-REFSGWETSgGQKIVALKVASLKELFEFKAIADQQGI 84 
                                       699*****************************9998.77.789****9999999*********************** PP

                                       SEEEEEETSSSSSSTTCEEEEEEEEEEHHHHHHHHTTSEB- CS
                              PTH2  77 paalirDagrtqiepgtkTvlaigPapksivdkvtgkLkll 117
                                       ++a++ Dagrt+i+pgt T+l+igP ++s++dk+tg+L +l
  gi|474934197|ref|YP_007687779.1|  85 TNAVVCDAGRTEIDPGTITCLGIGPEKQSVIDKITGDLSML 125
                                       **************************************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 775.65
//
Query:       gi|474934198|ref|YP_007687780.1|  [L=213]
Description: thiamine-phosphate pyrophosphorylase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.9e-58  196.2   2.1    3.4e-58  195.9   2.1    1.0  1  TMP-TENI        Thiamine monophosphate synthase
    1.1e-05   25.0   4.5    1.5e-05   24.6   4.2    1.3  1  NMO             Nitronate monooxygenase
    0.00033   20.5   0.3     0.0011   18.7   0.1    1.9  2  QRPTase_C       Quinolinate phosphoribosyl transferase, C-ter
     0.0013   18.1   0.8     0.0029   16.9   0.2    1.6  1  DHO_dh          Dihydroorotate dehydrogenase
      0.005   16.3   0.2     0.0066   15.9   0.2    1.3  1  CutC            CutC family
  ------ inclusion threshold ------
      0.041   13.3   1.9       0.61    9.4   0.4    2.2  2  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
      0.049   12.7   6.3      0.019   14.0   4.1    1.5  2  FMN_dh          FMN-dependent dehydrogenase
      0.068   12.4   1.3       0.46    9.6   0.2    2.0  2  PEP_hydrolase   Phosphoenolpyruvate hydrolase-like


Domain annotation for each model (and alignments):
>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.9   2.1   1.5e-61   3.4e-58       1     181 []       4     187 ..       4     187 .. 0.99

  Alignments for each domain:
  == domain 1  score: 195.9 bits;  conditional E-value: 1.5e-61
                          TMP-TENI   1 lylvtdskldkneellevveealkggvtlvqlRekeldarellelaeklaalcrkygvpliindrvdlalavgadgv 77 
                                       ly++td+++  +++ +e+++ + +gg+++vqlR+k++d  e+l++a++++a++++y+  +i+ndrvd+a+   adgv
  gi|474934198|ref|YP_007687780.1|   4 LYAITDREMLGKTTEAEAARLCYEGGADIVQLRMKDADGGEMLRVAKEMQAVADEYSKFFIVNDRVDIAILSSADGV 80 
                                       7*********9999*************************************************************** PP

                          TMP-TENI  78 HlgqddlpvaearellgpdliiGlSvhsleeaeeaealgadYigvGpifpTdtKkda.eplgleglkelaeale..i 151
                                       Hlgq+d+p++ear+l+g+++iiG+S+ + e+a++a ++gadY+++G+if T tKkda + +gl+ + ++++a+e  +
  gi|474934198|ref|YP_007687780.1|  81 HLGQSDIPLKEARRLCGEEMIIGISCDNAEQARQAVEDGADYVAIGSIFTTGTKKDAkQGVGLDAIMDVRNAIEdaV 157
                                       ***************************************************************************** PP

                          TMP-TENI 152 PvvaiGGitlenvaevleagadgvavvsai 181
                                       P+vaiGGi+  n+ +vl+agad  avvsai
  gi|474934198|ref|YP_007687780.1| 158 PIVAIGGINRGNILDVLAAGADCPAVVSAI 187
                                       *****************************8 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   4.2   6.5e-09   1.5e-05      78     235 ..      44     197 ..      32     210 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 6.5e-09
                               NMO  78 draekykkeleeaalelnieegvrfyrkvevvldekvevvsfgfglpteevvarlkeagvvliptissvkearkvea 154
                                       +   + +ke++ +a e+  +  v+   +v++     ++ v +g  + + +   rl   ++++ ++   +++ar++ +
  gi|474934198|ref|YP_007687780.1|  44 EM-LRVAKEMQAVADEYSKFFIVN--DRVDIAILSSADGVHLGQSDIPLKEARRLCGEEMIIGISCDNAEQARQAVE 117
                                       44.456677777888888888888..88888888888888888888888899999999999999999********** PP

                               NMO 155 rGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavd..iPviAaGGiidrrgvaaaLalGAsgvqigtrfLltk 229
                                        GaD + +      G + + + g +gl a++  v++a++  +P++A GGi+++ ++  +La+GA   ++ ++ ++  
  gi|474934198|ref|YP_007687780.1| 118 DGADYVAIGSIFTTGTKKDAKQG-VGLDAIM-DVRNAIEdaVPIVAIGGINRG-NILDVLAAGADCPAVVSAIMAQP 191
                                       *****999888888888866665.5555544.4677777779********876.57779*******99999999887 PP

                               NMO 230 esdakd 235
                                       +  a +
  gi|474934198|ref|YP_007687780.1| 192 DIRAAA 197
                                       766654 PP

>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.44   9.8e+02      90     120 ..      19      51 ..       9      66 .. 0.60
   2 !   18.7   0.1   5.1e-07    0.0011      63     156 ..      82     185 ..      67     193 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.44
                                       HHHHHHHHHHT-SEEEEES--H..HHHHHHHHH CS
                         QRPTase_C  90 leeleevleaeadiimLDnfsv..eelkkavee 120
                                        e ++  +e +adi++L   ++   e+ ++++e
  gi|474934198|ref|YP_007687780.1|  19 AEAARLCYEGGADIVQLRMKDAdgGEMLRVAKE 51 
                                       445555667779999885443322344444444 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 5.1e-07
                                       HSSHHHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHT-SEEEEES-..........-HHHHHHHHHHHHHHSTTSE CS
                         QRPTase_C  63 agsiveavksvreavdkevkievevesleeleevleaeadiimLDnf..........sveelkkaveelkeknkrvl 129
                                       +g+    +k++r  +++e+ i + +++ e++++++e +ad + +  +          +   l  +++++++++  v 
  gi|474934198|ref|YP_007687780.1|  82 LGQSDIPLKEARRLCGEEMIIGISCDNAEQARQAVEDGADYVAIGSIfttgtkkdakQGVGLDAIMDVRNAIEDAVP 158
                                       56556668999****99999************************9997888777664446677777777778888** PP

                                       EEEESS--TTTHHHHHCTT-SEEEECH CS
                         QRPTase_C 130 ievSGgvtlenveeyaksgvdvisvga 156
                                       i + Gg++  n+ ++   g d+ +v +
  gi|474934198|ref|YP_007687780.1| 159 IVAIGGINRGNILDVLAAGADCPAVVS 185
                                       *************99999888766554 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.2   1.3e-06    0.0029     229     277 ..     141     188 ..     135     203 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.3e-06
                                       HHHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHH CS
                            DHO_dh 229 ialkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalv 277
                                       ++l  i+++++ +++ +pi+++GGi+ g+  l+ + aGA   +v +a++
  gi|474934198|ref|YP_007687780.1| 141 VGLDAIMDVRNAIEDAVPIVAIGGINRGN-ILDVLAAGADCPAVVSAIM 188
                                       67899**********************96.9********9999998874 PP

>> CutC  CutC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.2   2.9e-06    0.0066     122     189 ..     105     175 ..      32     182 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.9e-06
                              CutC 122 AfDvvadpeealeqliel.gvervLtsGqkssaleg..leklaeLveqaaerieimagaGvnaenvaelak 189
                                         D  ++  +a+e+  ++  +  + t G+k++a +g  l+ ++++ +  ++ + i+a +G+n +n+ ++  
  gi|474934198|ref|YP_007687780.1| 105 SCDNAEQARQAVEDGADYvAIGSIFTTGTKKDAKQGvgLDAIMDVRNAIEDAVPIVAIGGINRGNILDVLA 175
                                       56788888999999887637899*******99998622689***99999*****************98865 PP

>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.02        45     154     196 ..      90     128 ..      49     130 .. 0.70
   2 ?    9.4   0.4   0.00027      0.61     151     197 ..     144     187 ..     139     188 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.02
                                       HHHHHHHHHHT---EEEEESS--TTTCHHHHHHT--EEEESHH CS
                    Ribul_P_3_epim 154 kkvrklidekeldlkievDGGvkldnieqiaeagadvlVagsa 196
                                       k++r+l+ e e+ + i  D   ++++++q++e+gad + +gs 
  gi|474934198|ref|YP_007687780.1|  90 KEARRLCGE-EMIIGISCD---NAEQARQAVEDGADYVAIGSI 128
                                       555555555.444444444...56667788999*****99996 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00027
                                       HHHHHHHHHHHHHT---EEEEESS--TTTCHHHHHHT--EEEESHHH CS
                    Ribul_P_3_epim 151 ekikkvrklidekeldlkievDGGvkldnieqiaeagadvlVagsav 197
                                       + i +vr++i++    + i + GG++  ni  + +agad+  + sa+
  gi|474934198|ref|YP_007687780.1| 144 DAIMDVRNAIED---AVPIVAIGGINRGNILDVLAAGADCPAVVSAI 187
                                       667888888887...7788888*****************98777776 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.2   2.6e+03     227     242 ..      19      34 ..       8      61 .. 0.81
   2 ?   14.0   4.1   8.3e-06     0.019     226     297 ..     108     181 ..      69     197 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.2
                                       HHHHHHHHHTTESEEE CS
                            FMN_dh 227 aedakraveaGvdgiv 242
                                       ae a++++e G+d++ 
  gi|474934198|ref|YP_007687780.1|  19 AEAARLCYEGGADIVQ 34 
                                       6677777777777765 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 8.3e-06
                                       SHHHHHHHHHTTESEEEE--...GGGTSSTT---HHHCHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEE CS
                            FMN_dh 226 taedakraveaGvdgivvSN...HGGRqldgapatidvLpeiveavggrievlvDgGirrGsDvlkAlalGAdav 297
                                       +ae a++ave G+d + +      G ++  +    +d++ ++++a+++ +++++ gGi rG+ +l  la GAd+ 
  gi|474934198|ref|YP_007687780.1| 108 NAEQARQAVEDGADYVAIGSiftTGTKKDAKQGVGLDAIMDVRNAIEDAVPIVAIGGINRGN-ILDVLAAGADCP 181
                                       6899************9975442677777777789**************************6.9999*****975 PP

>> PEP_hydrolase  Phosphoenolpyruvate hydrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.06   1.3e+02     158     207 ..      18      66 ..      13      84 .. 0.71
   2 ?    9.6   0.2   0.00021      0.46     158     207 ..     108     157 ..      98     167 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.06
                     PEP_hydrolase 158 neeearamaeaGadvivahlGlttggsigaktalsleeavelvqeiadaa 207
                                       ++e ar   e Gad++ + +    gg++  + a+++++++++ ++++ + 
  gi|474934198|ref|YP_007687780.1|  18 EAEAARLCYEGGADIVQLRMKDADGGEML-RVAKEMQAVADEYSKFFIVN 66 
                                       456677778999***99999988888874.45566666666666655555 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00021
                     PEP_hydrolase 158 neeearamaeaGadvivahlGlttggsigaktalsleeavelvqeiadaa 207
                                       n+e+ar+ +e Gad + +   +ttg +  ak+ + l++ ++  ++i da+
  gi|474934198|ref|YP_007687780.1| 108 NAEQARQAVEDGADYVAIGSIFTTGTKKDAKQGVGLDAIMDVRNAIEDAV 157
                                       899************************************99999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1331.91
//
Query:       gi|474934199|ref|YP_007687781.1|  [L=260]
Description: Hydroxyethylthiazole kinase, sugar kinase family [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-65  221.2   0.9    1.5e-65  221.0   0.9    1.0  1  HK            Hydroxyethylthiazole kinase family
    6.5e-07   29.0   0.1    7.8e-07   28.7   0.1    1.2  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
      2e-05   24.2   0.4    2.7e-05   23.8   0.4    1.1  1  Carb_kinase   Carbohydrate kinase
  ------ inclusion threshold ------
       0.18   10.7   0.9       0.29   10.1   0.9    1.2  1  E1_dh         Dehydrogenase E1 component


Domain annotation for each model (and alignments):
>> HK  Hydroxyethylthiazole kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.0   0.9   3.4e-69   1.5e-65       2     246 .]       9     258 ..       8     258 .. 0.94

  Alignments for each domain:
  == domain 1  score: 221.0 bits;  conditional E-value: 3.4e-69
                                       HHHHHH--EEEEE--TTTHHHHHHHHHHHT-EEEE--STTTHHHHHHTSSEEEEE-TT--HHHH.HHHHHHHHHHHH CS
                                HK   2 kklreksPlvhhiTNkVaqnfsANvllAlgaSPimseaeeEvselakianaLllNiGtleekai.ealkaAvksake 77 
                                       +++rek+P v h+TN V+ n+ ANv +A+g+SP ms+ +++v +la++ +a+++N+Gtl+ +a+ +al  A+ +a +
  gi|474934199|ref|YP_007687781.1|   9 RQVREKHPFVVHVTNIVTVNDCANVCIAMGGSPCMSMYNDDVLDLAAACDAVVVNMGTLDGQAVgDALWSAAVKATN 85 
                                       689*********************************************************9887479999999999* PP

                                       TT--EEEE-TTBTTBHHHHHHHHHHHHHS.....--SEEEEEHHHHHHHHTSSCCSCSSSSSS-SHHHHHHHHHHHH CS
                                HK  78 vnrPvvlDPVgvgAtelRrelalellkev.....klavikGNasEilslaglelkvkGvDskeaataavaavqkvAq 149
                                       +++Pvv+DP g+gA+++R+  + + +++      +  vikGN +Ei  l+gl +kv+GvDs  a+    aa++k+A+
  gi|474934199|ref|YP_007687781.1|  86 LHKPVVFDPTGAGASKFRNMWSGSFIQYLipkapESVVIKGNYGEIGYLSGLGGKVQGVDSAGADD-PKAAAEKLAK 161
                                       *******************9888888776222124568**********************987665.89******** PP

                                       HHTSEEEEESSSEEEEESSEEEEEE-S-GGGGGSTTHHHHHHHHHHHHHTTBSSHHHHHHHHHHHHHHHH.HHHHHH CS
                                HK 150 klrvvvvvtGevDvvsdgkkvyklknGtellgkitasGCllgsvvaaflavkkdkllaaveavllykvAgkeaaars 226
                                         +++v++tG vD+vsdg+++++l+ Gt++   + ++GC+l+svv+ f++ +  +l+++++a+ ++++A+++aa+ s
  gi|474934199|ref|YP_007687781.1| 162 DNHCIVAATGPVDYVSDGETTLELRHGTPMQNLVSGTGCMLSSVVGCFVGANGVSLESVAAAIDAFNIAAENAAKVS 238
                                       ***************************************************************************** PP

                                       HTTHHHHHHHHHHHHH--HH CS
                                HK 227 egsgsFqvelldalsqltee 246
                                       +g+g+F+++l+da+++l+ee
  gi|474934199|ref|YP_007687781.1| 239 KGPGTFHMNLMDAVYNLKEE 258
                                       *****************987 PP

>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.1   1.7e-10   7.8e-07      63     244 ..      61     243 ..      21     245 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1.7e-10
                                       EEEE-S--SHHHHHHHHHHH.HHTTS..SEEEE---SSCTS.SSBSSHHHHHHHHHHTGGG-SEEE-BHHHHHHHHT CS
                      Phos_pyr_kin  63 avKiGmlasaeiievvaekl.kkykv..pvVlDPVmvaksg.selleeeavealkeeLlplatvitPNlpEaeaLlg 135
                                       +v +G l  +++ +++ ++  k  ++  pvV+DP  +  s  +++ + + ++ l    +p++ vi  N  E+  L+g
  gi|474934199|ref|YP_007687781.1|  61 VVNMGTLDGQAVGDALWSAAvKATNLhkPVVFDPTGAGASKfRNMWSGSFIQYLIP-KAPESVVIKGNYGEIGYLSG 136
                                       56677777777777775555455444459*****9776555145556666666665.578889************99 PP

                                       ..---S.....SHHHHHHHHHHHHHTT-SEEEEEEGGS-SSSEEEEEEEETSSEEEEEEEE----S--BTHHHHHHH CS
                      Phos_pyr_kin 136 ..ekik.....teedmkeaakkllklgakaVlikGghlegeeavvtdvlydgeeveeleaerietknthGtGCtlss 205
                                          k++      ++d k+aa+kl+k +   V  +G        v  d++ dge++ el++    ++   GtGC lss
  gi|474934199|ref|YP_007687781.1| 137 lgGKVQgvdsaGADDPKAAAEKLAKDNHCIVAATGP-------V--DYVSDGETTLELRHGTPMQNLVSGTGCMLSS 204
                                       884444333436679999999999987776665554.......3..99****************9************ PP

                                       HHHHHHHCTSSHHHHHHHHHHHHHHHHHCG-BSTSSS-B CS
                      Phos_pyr_kin 206 aiaaelakgesleeAvkkAkeyvteaikealelgkgagp 244
                                       ++ + +  +    e+v+ A +  + a ++a ++ kg g+
  gi|474934199|ref|YP_007687781.1| 205 VVGCFVGANGVSLESVAAAIDAFNIAAENAAKVSKGPGT 243
                                       ******99999999**************99999999876 PP

>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.4   6.1e-09   2.7e-05      59     227 ..      47     236 ..      17     255 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 6.1e-09
                                       S....--SSS-SEEEE-TT.-SSSHCHHH...HCHHHCCCCS-EEEEGGGGGSGGGG............TTTTSSEE CS
                       Carb_kinase  59 a.kileklerldavviGpG.Lgrdekikk...lleevlekdeplviDAdgLnllaqkne.........lserkaevi 121
                                          +l+++ + davv+ +G L+ +  +++   +  ++ + ++p+v D  g    +  n          +++  + v+
  gi|474934199|ref|YP_007687781.1|  47 NdDVLDLAAACDAVVVNMGtLDGQAVGDAlwsAAVKATNLHKPVVFDPTGAGASKFRNMwsgsfiqylIPKAPESVV 123
                                       2256899999********96555555444555777888999******555444444433445888899999****** PP

                                       EE--HHHHHHHCTTTCH.......HCCSHHHHHHHHHHHHTTEEEEESTTSEEEECTTEEEEE----GGG-.STTHH CS
                       Carb_kinase 122 LTPhkkEfkrLlkaivk.......keddrlelarelaqklnavvllkgekdvivspegevlinstgssala.kGGsG 190
                                       +  + +E  +L+++ +k         dd   +a++la+  +++v   g +d + + ++ +l +  g++++  + G+G
  gi|474934199|ref|YP_007687781.1| 124 IKGNYGEIGYLSGLGGKvqgvdsaGADDPKAAAEKLAKDNHCIVAATGPVDYVSD-GETTLELRHGTPMQNlVSGTG 199
                                       **************9999999998889999999*******************988.888889999999876489*** PP

                                       HHHHHHHHHHHHCTSSHHHHHHHHHHHHHHHHHHHCC CS
                       Carb_kinase 191 DvLaGligalLaqneasyeaaiaaawlhgaasdeaae 227
                                         L+ ++g++   n  s+e+++aa  +   a+++aa+
  gi|474934199|ref|YP_007687781.1| 200 CMLSSVVGCFVGANGVSLESVAAAIDAFNIAAENAAK 236
                                       *************996666666666665555555544 PP

>> E1_dh  Dehydrogenase E1 component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.9   6.4e-05      0.29     150     221 ..      22      93 ..      18      96 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 6.4e-05
                                       TT--EEEEEEEESEETTEEHHHH-S---GGG..TTTTS-EEEEETTSHHHHHHHHHHHHHHHHTTT--EEEE CS
                             E1_dh 150 wklpvifvveNNkygisTeaekasaskeladrargvgipglrVdgnDplavyeAvkfAaeraregkgpllie 221
                                        ++ ++  ++N  ++++ ++ ++   +++ d a+++ +  ++    D  av  A   Aa  a + ++p++ +
  gi|474934199|ref|YP_007687781.1|  22 TNIVTVNDCANVCIAMGGSPCMSMYNDDVLDLAAACDAVVVNMGTLDGQAVGDALWSAAVKATNLHKPVVFD 93 
                                       55666888*************************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1619.44
//
Query:       gi|474934200|ref|YP_007687782.1|  [L=407]
Description: hypothetical protein TALC_00623 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00038   19.1  17.7    0.00041   19.0  17.7    1.1  1  Borrelia_P83   Borrelia P83/100 protein
  ------ inclusion threshold ------
      0.018   15.4   0.0      0.063   13.6   0.0    2.0  2  FKBP_C         FKBP-type peptidyl-prolyl cis-trans isomerase
       0.12   11.4  13.1       0.18   10.9  13.1    1.2  1  LAP1C          Lamina-associated polypeptide 1C (LAP1C)
       0.13   12.6   8.2       0.17   12.1   8.2    1.2  1  MMR1           Mitochondrial Myo2 receptor-related protein
       0.22   10.2  16.0       0.31    9.8  16.0    1.2  1  Presenilin     Presenilin
       0.22   10.5  12.2       0.25   10.4  12.2    1.1  1  BAF1_ABF1      BAF1 / ABF1 chromatin reorganising factor
       0.64    7.1  12.2       0.75    6.8  12.2    1.0  1  GREB1          Gene regulated by oestrogen in breast cancer
        1.1    9.2  23.4        1.6    8.8  23.4    1.2  1  Asp-B-Hydro_N  Aspartyl beta-hydroxylase N-terminal region
        1.6    7.5   6.9          2    7.2   6.9    1.1  1  Apt1           Golgi-body localisation protein domain
        2.6    6.1  13.6        3.2    5.8  13.6    1.1  1  Hid1           High-temperature-induced dauer-formation prote
          5    5.7   8.5         12    4.5   7.0    2.2  2  ResB           ResB-like family
        8.9    5.0  13.2         16    4.2  13.2    1.3  1  ALMT           Aluminium activated malate transporter
        9.6    4.4  20.1         14    3.9  20.1    1.2  1  CDC45          CDC45-like protein


Domain annotation for each model (and alignments):
>> Borrelia_P83  Borrelia P83/100 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0  17.7     3e-07   0.00041     229     334 ..       7     112 ..       1     243 [. 0.63

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 3e-07
                      Borrelia_P83 229 adkakkkadtaednadk.....qrkevreklqeaknlpepadvsskkedkkvaeekkreieka..qkeikkkdee.. 296
                                       a+++ k+   a+++a+k      + e++ k+q++k+++ +a+          + + kr++ek    ke +k++ee  
  gi|474934200|ref|YP_007687782.1|   7 AAQKAKEEAAAKKAAEKeaqaqAKAEANAKRQAEKEAQAQAKA---------EANAKRQAEKEarMKEQQKAKEEaa 74 
                                       1111111111111111100000222233333333322222222.........1233333333211234444444311 PP

                      Borrelia_P83 297 akkakdakaedlkkeskaeekeaedkeleakkereeva 334
                                       a+ka +++a   +ke  a +k ae  e   +kere++a
  gi|474934200|ref|YP_007687782.1|  75 AQKAAQKEARAKAKEEAAAKKAAEAPERKVRKEREPIA 112
                                       56666666777777777777788888888899999987 PP

>> FKBP_C  FKBP-type peptidyl-prolyl cis-trans isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   4.6e-05     0.063       9      73 ..     148     233 ..     141     291 .. 0.77
   2 ?   -2.2   0.0         4   5.5e+03      82      93 ..     392     403 ..     357     404 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.6e-05
                                       CEEEEEEEEEE............TTSSEEEEH........CC.HTSEEEEETTSSSSCHHHHHHHTTSBTT-EEEEE CS
                            FKBP_C   9 dtVtvhykgkl............edgkvfdss........rs.rakplefkvGsgqvikGfeealegmkvGekrtlt 64 
                                       + V+v y++ +            ++ +++d+s        ++  +  +++ + + + ++Gf +al g ++G++ ++ 
  gi|474934200|ref|YP_007687782.1| 148 SSVEVYYTLSFydfyenggpiyqTNYEKVDKSdkwvhadgYTySEDVYKVSMANSNALQGFRDALLGHSAGDTVKIR 224
                                       56667777766666633333332233444444666666664457888999999999********************* PP

                                       EEGGGTTTT CS
                            FKBP_C  65 ippelaYge 73 
                                       i  + +Y  
  gi|474934200|ref|YP_007687782.1| 225 IAAKDGYNV 233
                                       *******75 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4
                                       .TTSEEEEEEEE CS
                            FKBP_C  82 ppnatLvFeveL 93 
                                       + n++L+F++++
  gi|474934200|ref|YP_007687782.1| 392 QDNQDLYFTIKI 403
                                       456788888876 PP

>> LAP1C  Lamina-associated polypeptide 1C (LAP1C)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9  13.1   0.00013      0.18     104     221 ..       8     127 ..       1     153 [. 0.41

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00013
                                       XXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXX......XXXXXXXXXXX.XXXXXXXXXX..XXXX..XXX CS
                             LAP1C 104 svsssdktgradaqleessaalseeasdrtaasqepsaadsqeaqssghskaeqe.eqdtlrrtrllvpeaeshqqe 179
                                         + +++++  +a  +e +a+ + ea+ + +a++e +a+ + ea+ ++++++e   +++++ +   ++++a   q+e
  gi|474934200|ref|YP_007687782.1|   8 AQKAKEEAAAKKAAEKEAQAQAKAEANAKRQAEKEAQAQAKAEANAKRQAEKEARmKEQQKAKEEAAAQKAA--QKE 82 
                                       334444444445555555555555555555555555553333333322222222111111222122222222..222 PP

                                       XXXXXXXXX.XXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXX CS
                             LAP1C 180 telleeske.saqdtlrkskkksfvkyksil...llllvvavllls 221
                                       ++  + ++e  a+++++ +++k   + + i+    ++l+va+++++
  gi|474934200|ref|YP_007687782.1|  83 AR-AKAKEEaAAKKAAEAPERKVRKEREPIAffcSIILLVACVAVA 127
                                       22.2222232344444433333333333333000333344444444 PP

>> MMR1  Mitochondrial Myo2 receptor-related protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   8.2   0.00012      0.17      89     174 ..      12      96 ..       1     163 [. 0.38

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00012
                              MMR1  89 vekskiskltiketleqlreeksqqksksaekekqkrsvaakseqesekveelekskser.eisetssaiSestlle 164
                                        e++   k  +ke+  q+++ + + k++  ++++ + +++a+ + + ek+ +++++++++ e+  ++ a  e+ +  
  gi|474934200|ref|YP_007687782.1|  12 KEEAAAKKAAEKEAQAQAKA-EANAKRQAEKEAQAQAKAEANAKRQAEKEARMKEQQKAKeEAAAQKAAQKEARAKA 87 
                                       22222234444444444422.11111121122222222222222222222222222222201111111111111111 PP

                              MMR1 165 ledle.tteae 174
                                       +e  e   +++
  gi|474934200|ref|YP_007687782.1|  88 KE--EaAAKKA 96 
                                       11..1112222 PP

>> Presenilin  Presenilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8  16.0   0.00022      0.31     235     311 ..      17      93 ..       1     144 [. 0.37

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00022
                        Presenilin 235 seeeeeaekkkeeasesskeeeseeesseksaqsseseeeseeesseaessaeesseeke.seessesseeeeeeee 310
                                       +++++e+e+++++++e+++++++e+e++ + + ++ + +++ e+++++++++++++e ++ +++++e++++ +ee+ 
  gi|474934200|ref|YP_007687782.1|  17 AKKAAEKEAQAQAKAEANAKRQAEKEAQAQAKAEA-NAKRQAEKEARMKEQQKAKEEAAAqKAAQKEARAKAKEEAA 92 
                                       11111111111111111111111111111111111.11111111111111111111111101111111111111111 PP

                        Presenilin 311 e 311
                                       +
  gi|474934200|ref|YP_007687782.1|  93 A 93 
                                       1 PP

>> BAF1_ABF1  BAF1 / ABF1 chromatin reorganising factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4  12.2   0.00018      0.25     354     447 ..       7     100 ..       1     203 [. 0.60

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00018
                         BAF1_ABF1 354 eslesteaaliskeektrpssalsiesnskaasskkskskkekeinanddkeelseeskdkeeetnseree.rqkel 429
                                       + ++++e+a ++k  +++++ ++++e+n+k++++k+ + + + e na++++e+++  +++++ +++++ ++ +qke+
  gi|474934200|ref|YP_007687782.1|   7 AAQKAKEEAAAKKAAEKEAQAQAKAEANAKRQAEKEAQAQAKAEANAKRQAEKEARMKEQQKAKEEAAAQKaAQKEA 83 
                                       33444444444444445555555555555555555555555555555555555555444444444444444344444 PP

                         BAF1_ABF1 430 eseakeaqaaAqaaines 447
                                       +++ake++a A++a ++ 
  gi|474934200|ref|YP_007687782.1|  84 RAKAKEEAA-AKKAAEAP 100
                                       444444333.33333322 PP

>> GREB1  Gene regulated by oestrogen in breast cancer
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8  12.2   0.00054      0.75    1152    1261 ..       4     112 ..       1     149 [. 0.69

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.00054
                             GREB1 1152 skdavesglsskasakselseasaaaasaseeakspkasvtseeeeseeskekekeslsketesqlsleaseqke 1226
                                        +kda++++++  a++k++ +ea+a+a+++ +++++ +++++++ ++ +++k++ +++++ ++ +q  +e++ +++
  gi|474934200|ref|YP_007687782.1|    4 EKDAAQKAKEEAAAKKAAEKEAQAQAKAEANAKRQAEKEAQAQAKAEANAKRQAEKEARMKE-QQKAKEEAAAQK 77  
                                        55666666666666666666666677777777777766666666666655555555555444.444566667777 PP

                             GREB1 1227 aldakasskssssssssssassPssscslakavkr 1261
                                        a++++a++k ++ ++ +  a++P+++++  +   +
  gi|474934200|ref|YP_007687782.1|   78 AAQKEARAKAKEEAAAKKAAEAPERKVRKEREPIA 112 
                                        77778899999999999999999999988776544 PP

>> Asp-B-Hydro_N  Aspartyl beta-hydroxylase N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8  23.4    0.0011       1.6     117     212 ..       7     105 ..       1     139 [. 0.51

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0011
                     Asp-B-Hydro_N 117 vvkeeeeegieee.pqleeekkllkedsderqeeleagk.vkeevEeslkveetvseeakkdmkekaseeenekske 191
                                        +++ +ee  +++  ++e + + ++e++ +rq+e+ea++ +k e++++ + e+ ++ ++++++ke+a+ +++++++ 
  gi|474934200|ref|YP_007687782.1|   7 AAQKAKEEAAAKKaAEKEAQAQAKAEANAKRQAEKEAQAqAKAEANAKRQAEKEARMKEQQKAKEEAAAQKAAQKEA 83 
                                       22332222222220333333444444444454444444313445555556666666666666666666666555443 PP

                     Asp-B-Hydro_N 192 pve.eaekekaeakeveeedke 212
                                         + ++e   ++a e  e++  
  gi|474934200|ref|YP_007687782.1|  84 RAKaKEEAAAKKAAEAPERKVR 105
                                       3332333333333333333322 PP

>> Apt1  Golgi-body localisation protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   6.9    0.0014         2     313     405 ..      16     144 ..       1     160 [. 0.35

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0014
                              Apt1 313 s....seeddesdeesessssss.ssssssassssssssrssslelrlkptsstssssssessssssskkrsseess 384
                                       +    +e++ + + + e++ +++ +++ + +++++ + +r+ ++e r+k++++++++ + ++ ++   ++++++e++
  gi|474934200|ref|YP_007687782.1|  16 AakkaAEKEAQAQAKAEANAKRQaEKEAQAQAKAEANAKRQAEKEARMKEQQKAKEEAAAQKAAQ-KEARAKAKEEA 91 
                                       11111111111111111111111233333333333333333333333332222222211111111.11122222223 PP

                              Apt1 385 lessaserv..kssr................................asddleem 405
                                       + ++a e++  k                                   a+d+ +++
  gi|474934200|ref|YP_007687782.1|  92 AAKKAAEAPerK--VrkerepiaffcsiillvacvavagswiydeaiADDSGDKV 144
                                       333333333221..12334555555555555555555555555555555555555 PP

>> Hid1  High-temperature-induced dauer-formation protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8  13.6    0.0023       3.2     589     680 ..      13      98 ..       1     138 [. 0.45

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0023
                              Hid1 589 sarldsideeeeenssessrieesrsesrspslsevpelksslaitddeskaereksatessssqavsqlremseka 665
                                       +++ ++++ e+e + + + +++ +r+ +++++ +++ e++++ +++++   +e++k ++e+++++a++      ++a
  gi|474934200|ref|YP_007687782.1|  13 EEAAAKKAAEKEAQAQAKAEANAKRQAEKEAQAQAKAEANAKRQAEKEARMKEQQKAKEEAAAQKAAQ------KEA 83 
                                       22223333333333333333333334444444444444444333333333333333333333333333......222 PP

                              Hid1 666 rakesaesteesrqe 680
                                       rak ++e  +++++e
  gi|474934200|ref|YP_007687782.1|  84 RAKAKEEAAAKKAAE 98 
                                       222222222222222 PP

>> ResB  ResB-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   7.0    0.0086        12      89     179 ..      45     136 ..       7     174 .. 0.74
   2 ?    0.5   0.0      0.14   1.9e+02     257     357 ..     167     272 ..     161     365 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0086
                              ResB  89 rpkraekslkrlphsaelelaeapeeaveraaavLkkrgyrvrv..eeedgavslaAekGrlsrlGnlvfHialvli 163
                                        + +ae+++kr+ ++ e++++e++++ +e+aa+  +++  r +   e ++++ + a e+   ++  +++f  +++l+
  gi|474934200|ref|YP_007687782.1|  45 AQAKAEANAKRQAEK-EARMKEQQKAKEEAAAQKAAQKEARAKAkeEAAAKKAAEAPERKVRKEREPIAFFCSIILL 120
                                       445677777777777.466755554434555555555555555521447777788999999**************** PP

                              ResB 164 ligallgslfgfrgnv 179
                                       ++ +++ + + +++ +
  gi|474934200|ref|YP_007687782.1| 121 VACVAVAGSWIYDEAI 136
                                       ******9999998654 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.14
                              ResB 257 riYqssfgdggklelklvllkgksaqelelpgtvslslra.lelane.elrnvgpavqfkvrdpd.gevan.mepv. 328
                                        iYq+ +++   ++   ++ +++ + + ++ +++ ++ +a + +++    +  g  v++++  +d  +v+  m ++ 
  gi|474934200|ref|YP_007687782.1| 167 PIYQTNYEKV--DKSDKWVHADGYTYSEDVYKVSMANSNAlQGFRDAlLGHSAGDTVKIRIAAKDgYNVECdMDKIa 241
                                       5788888333..44444444433333333444443333333333333445677778888888888667777888886 PP

                              ResB 329 pqdg.nvlssgvrk.pqlafqglflPtaees 357
                                       +  + ++ s+ v++  + + ++ f+P+ + +
  gi|474934200|ref|YP_007687782.1| 242 DITNiSMDSTSVMTsAEFEAEYGFVPAGNVT 272
                                       5566689999999988999999999998765 PP

>> ALMT  Aluminium activated malate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2  13.2     0.012        16     351     455 ..      26     124 ..       2     131 .. 0.31

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.012
                              ALMT 351 lvnsekweaakkkekaeeveekkeeekeseskkeeaeaveeaeseseksllkeskrslklskkesapaeesleekql 427
                                       + +++ +++ak+++++e++ + k+e++ ++      +a++ea++++++++++e   ++  +k+  a+a+e+   k+ 
  gi|474934200|ref|YP_007687782.1|  26 QAQAKAEANAKRQAEKEAQAQAKAEANAKR------QAEKEARMKEQQKAKEEAAAQKAAQKEARAKAKEEAAAKKA 96 
                                       111111111111111111111111111111......11111111111111111122222222222222223333444 PP

                              ALMT 428 skeeelkelelaealslatfaslLielv 455
                                       +++ e k  +  e + +  ++ lL++ v
  gi|474934200|ref|YP_007687782.1|  97 AEAPERKVRKEREPIAFFCSIILLVACV 124
                                       4444444444455555555555555555 PP

>> CDC45  CDC45-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9  20.1    0.0098        14     109     209 ..       4     105 ..       1     125 [. 0.35

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0098
                             CDC45 109 Dgdieeeleeereayealeeeeesdeedeeeeeeddddeeeeeeeeedeedeeedeeeskkkrk.sksdeeee...s 181
                                       ++d +++ +ee  a +a e+e +++     + e + ++++e+e + +++ + +++ + +k+ r+ ++++++ee   +
  gi|474934200|ref|YP_007687782.1|   4 EKDAAQKAKEEAAAKKAAEKEAQAQA----KAEANAKRQAEKEAQAQAKAEANAKRQAEKEARMkEQQKAKEEaaaQ 76 
                                       33433333333333333333333321....11122222222222222222222222222222221222222222333 PP

                             CDC45 182 ddddersrkrrrsepsakklrrq.lkker 209
                                       + +++++r + ++e++akk+ +  ++k r
  gi|474934200|ref|YP_007687782.1|  77 KAAQKEARAKAKEEAAAKKAAEApERKVR 105
                                       33334444444444333333333222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3674  (0.204919); expected 358.6 (0.02)
Passed bias filter:                     1243  (0.069329); expected 358.6 (0.02)
Passed Vit filter:                       494  (0.0275531); expected 17.9 (0.001)
Passed Fwd filter:                       143  (0.0079759); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 1.44u 0.42s 00:00:01.86 Elapsed: 00:00:00.56
# Mc/sec: 2182.52
//
Query:       gi|474934201|ref|YP_007687783.1|  [L=432]
Description: phosphomethylpyrimidine kinase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.9e-82  274.0   2.2    3.3e-81  272.3   1.1    2.0  2  Phos_pyr_kin  Phosphomethylpyrimidine kinase
    2.1e-34  118.5   0.3    2.6e-33  115.0   0.2    2.2  2  ThiP_synth    Thiamine-phosphate synthase
    0.00016   21.1   0.0    0.00038   19.8   0.0    1.6  1  PfkB          pfkB family carbohydrate kinase
    0.00043   19.8   0.8     0.0011   18.5   0.8    1.7  1  Carb_kinase   Carbohydrate kinase


Domain annotation for each model (and alignments):
>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  272.3   1.1   7.3e-85   3.3e-81       1     245 [.      11     252 ..      11     253 .. 0.98
   2 ?    0.2   0.0     0.089     4e+02     139     166 ..     385     412 ..     374     425 .. 0.80

  Alignments for each domain:
  == domain 1  score: 272.3 bits;  conditional E-value: 7.3e-85
                                       ETTSSSHHHHHHHHHHHTTEEEEEEEEEEEEEETTCEEEEEE--HHHHHHHHHHHHHTS--SEEEE-S--SHHHHHH CS
                      Phos_pyr_kin   1 DssGGAGiqADlktfsalgvygmsvitaltaqntkgvkevhplpaelveaqleavledvkvdavKiGmlasaeiiev 77 
                                       Ds GGAGiqAD+k++++ gv+++svita+taqnt++v++++p+pa++v+aql+avl+d++++a+K+Gml++aei+ v
  gi|474934201|ref|YP_007687783.1|  11 DSVGGAGIQADIKAMASVGVHATSVITAVTAQNTCSVSSIFPMPADVVQAQLDAVLKDCEIKAIKTGMLYNAEIVGV 87 
                                       99*************************************************************************** PP

                                       HHHHHHHTTSSEEEE---SSCTSSSBSSHHHHHHHHHHTGGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHHT CS
                      Phos_pyr_kin  78 vaeklkkykvpvVlDPVmvaksgselleeeavealkeeLlplatvitPNlpEaeaLlgekikteedmkeaakkllkl 154
                                       v+++l+ +++p+++DPVmva+ g++l +e++++alk++Llp+++++tPN +Eae+L+g ki++e+d+  a++ + k 
  gi|474934201|ref|YP_007687783.1|  88 VVDALEDHNIPLIVDPVMVATVGDRLYDESYIKALKRKLLPICELVTPNRQEAEVLSGIKIRNEDDVTYACEVIGKE 164
                                       **************************************************************************998 PP

                                       T-SEEEEEEGGS-SSSEEEEEEEETSSEEEEEEEE----S--BTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHH CS
                      Phos_pyr_kin 155 gakaVlikGghlegeeavvtdvlydgeeveeleaerietknthGtGCtlssaiaaelakgesleeAvkkAkeyvtea 231
                                       g ++Vl+kGgh   +++vvtd+ly ++++++++++r+  ++ hG+GC++s+ i+a++a+g +l ++v ++++ ++++
  gi|474934201|ref|YP_007687783.1| 165 G-SSVLLKGGHF--DSKVVTDYLYLSSGITRIRNPRTRGESGHGSGCAFSAFITANMANGLDLVTSVLESRKMIQKS 238
                                       6.67999****7..88999********************************************************** PP

                                       HHCG-BSTSSS-B- CS
                      Phos_pyr_kin 232 ikealelgkgagpv 245
                                       i+ ++++gkg+  v
  gi|474934201|ref|YP_007687783.1| 239 IETQYSVGKGVDVV 252
                                       *********98766 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.089
                                       SSHHHHHHHHHHHHHTT-SEEEEEEGGS CS
                      Phos_pyr_kin 139 kteedmkeaakkllklgakaVlikGghl 166
                                       ++ ++  + a +l+k   +aV+ikG++ 
  gi|474934201|ref|YP_007687783.1| 385 ESIAETTRNALSLSKKFPDAVIIKGKRN 412
                                       46677888899999999********973 PP

>> ThiP_synth  Thiamine-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.053   2.4e+02      89     148 ..     114     166 ..     107     173 .. 0.60
   2 !  115.0   0.2   5.8e-37   2.6e-33       1     164 [.     272     429 ..     272     430 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.053
                                       --HHHHHHHCCTTSEEEE--CCCS-CCCT-HHHHHHHHHHHCCS-ECEEEE--BCTB--E CS
                        ThiP_synth  89 ydekilealeelglkvvefdreeepeevgstmewgvaeaieelevpdviydeGgvGkEpm 148
                                       yde +++al+++ l ++e    +++e+       +v + i+ ++  dv y    +GkE  
  gi|474934201|ref|YP_007687783.1| 114 YDESYIKALKRKLLPICELVTPNRQEA-------EVLSGIKIRNEDDVTYACEVIGKEGS 166
                                       777777777777777777766666666.......22222222222256666666666655 PP

  == domain 2  score: 115.0 bits;  conditional E-value: 5.8e-37
                                       HHHHHHHHHHCC--.GCC--TT-B-EEEE-ST--SGGGEEEETT-EEE-TSSEEE-S-EEETS-CHHHHHHHHHHCC CS
                        ThiP_synth   1 eleralelleeeeefakliPevgsNiayalpdAksieDvaavpGRIvrvkgrvkvvgepefgasshvarvllaamkf 77 
                                       ++++a+ ++++++   +l+P+ g+Niaya ++Ak++e++a+++ RI++++g +k  g+++fga +h++ vl+++mk 
  gi|474934201|ref|YP_007687783.1| 272 DMDTAVAKIMRIMP-LDLVPKDGMNIAYAVKNAKGPEEIAGIEKRIYVHNGSLKKGGNVKFGAGEHLSYVLMECMKT 347
                                       5899*********6.9************************************************************* PP

                                       -TT--EEEEEE--HHHHHHHCCTTSEEEE--CCCS-CCCT-HHHHHHHHHHHCC.S-ECEEEE--BCTB--EEEEEE CS
                        ThiP_synth  78 dpevraainirydekilealeelglkvvefdreeepeevgstmewgvaeaieel.evpdviydeGgvGkEpmiyvlg 153
                                       +pe+r++++++ d+++++ ++++gl+vv +++++ + e   ++++ +++a++ + ++pd+++ +G   k  ++ ++g
  gi|474934201|ref|YP_007687783.1| 348 NPEMRCVMTFEADSALESDMKDAGLDVVIVKEKDVNGE---SIAETTRNALSLSkKFPDAVIIKG---KRNTVDLFG 418
                                       *******************************9999999...899999999988888*******98...7999***** PP

                                       SSHHHHHHHHH CS
                        ThiP_synth 154 kdaeevvekvl 164
                                       k ++++++k++
  gi|474934201|ref|YP_007687783.1| 419 KGPRDIMSKLE 429
                                       ********986 PP

>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   8.6e-08   0.00038     172     279 ..     112     228 ..      85     231 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 8.6e-08
                                       H......HHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEGGGEEEEEE.....T CS
                              PfkB 172 q......fkeallellaladllkpneeElealtgekledieealaalhklkakgaktvvvtlGkeGalvve.....k 237
                                               k   ++ll+ + l++pn+ E+e l+g k+ ++++++ a++ + ++g + v+ + G   + vv+     +
  gi|474934201|ref|YP_007687783.1| 112 RlydesyIKALKRKLLPICELVTPNRQEAEVLSGIKIRNEDDVTYACEVIGKEG-SSVLLKGGHFDSKVVTdylylS 187
                                       3433454556668899*********************99999999998755444.7888899988888888888877 PP

                                       TEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHH CS
                              PfkB 238 dgelkvpavpkvkvvDttGAGDsfvggflaallegksleeal 279
                                       +g  ++   p +   +  G G +f + ++a+ ++g +l +++
  gi|474934201|ref|YP_007687783.1| 188 SGITRIRN-PRTRGESGHGSGCAFSAFITANMANGLDLVTSV 228
                                       77777777.888888888888888888888888888888776 PP

>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.8   2.4e-07    0.0011       2     164 ..       5     174 ..       4     182 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.4e-07
                                       EEEE-BTTCHHHHHHHHHHHHCT.T-SEEEEEESSTTTCCCCTTTTTCEECCTTHTTTS...--SSS-SEEEE-TT- CS
                       Carb_kinase   2 lvigGsedytGAallaalaalrl.gaglvsvateseaiavlksylpevivhplledeqakileklerldavviGpGL 77 
                                       l i+Gs+   GA++ a + a+++ g+  +sv+t  +a +   + +   +  ++ + +q   + k   ++a+  G+ L
  gi|474934201|ref|YP_007687783.1|   5 LTIAGSDSVGGAGIQADIKAMASvGVHATSVITAVTAQNTCSVSSIFPMPADVVQ-AQLDAVLKDCEIKAIKTGM-L 79 
                                       679*************998886526999***998888887777666666666663.3332334444666666666.6 PP

                                       SSSHCHHHHCHHHCCCCS-EEEEGGGGGSGGGG.............TTTTSSEEEE--HHHHHHHCTTTCHHCCSHH CS
                       Carb_kinase  78 grdekikklleevlekdeplviDAdgLnllaqkne..........lserkaeviLTPhkkEfkrLlkaivkkeddrl 144
                                        + e +  +++  ++++ pl++D    + + +             +  + +e   TP+ +E + L++  +  ++d +
  gi|474934201|ref|YP_007687783.1|  80 YNAEIVGVVVDALEDHNIPLIVDPVMVATVGDRLYdesyikalkrKLLPICE-LVTPNRQEAEVLSGIKI-RNEDDV 154
                                       7777777789999999999999965555554432234454323322223333.57************999.777778 PP

                                       HHHHHHHHHHTTEEEEESTT CS
                       Carb_kinase 145 elarelaqklnavvllkgek 164
                                       ++a e++ k ++ vllkg +
  gi|474934201|ref|YP_007687783.1| 155 TYACEVIGKEGSSVLLKGGH 174
                                       88889999999999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 3074.42
//
Query:       gi|474934202|ref|YP_007687784.1|  [L=127]
Description: hypothetical protein TALC_00625 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 856.19
//
Query:       gi|474934203|ref|YP_007687785.1|  [L=440]
Description: O-acetylhomoserine sulfhydrolase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.5e-134  448.4   0.0   1.7e-134  448.2   0.0    1.0  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    1.6e-10   40.9   0.1    3.7e-10   39.7   0.2    1.5  2  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    3.3e-10   39.7   0.0    7.8e-10   38.5   0.0    1.6  2  Aminotran_1_2    Aminotransferase class I and II
    1.9e-06   27.1   0.0    4.6e-06   25.8   0.0    1.6  1  Aminotran_5      Aminotransferase class-V
    0.00082   18.7   0.1     0.0015   17.9   0.1    1.3  1  Beta_elim_lyase  Beta-eliminating lyase
     0.0016   17.4   0.0     0.0023   16.8   0.0    1.2  1  GDC-P            Glycine cleavage system P-protein
  ------ inclusion threshold ------
      0.076   12.8   0.2       0.14   11.9   0.2    1.4  1  Stealth_CR1      Stealth protein CR1, conserved region 1
        0.3   11.0   2.2        5.4    7.0   0.3    2.5  2  YqbF             YqbF, hypothetical protein domain
       0.33    9.9   1.6        3.9    6.4   1.5    2.2  1  SelA             L-seryl-tRNA selenium transferase
       0.51    9.7   0.9        8.3    5.7   0.0    2.2  2  Nop53            Nop53 (60S ribosomal biogenesis)


Domain annotation for each model (and alignments):
>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  448.2   0.0  9.3e-138  1.7e-134       1     382 []      20     438 ..      20     438 .. 0.98

  Alignments for each domain:
  == domain 1  score: 448.2 bits;  conditional E-value: 9.3e-138
                                       HHHHHHTTTTCHT.TTTBSS--B---SBBBESSHHHH...CTTCSSS-SBTTT--HHHHHHHHHHHHHHT-SEEEEE CS
                   Cys_Met_Meta_PP   1 eTllvhagqekde.qtgavavpiyltstykfkdvdea...fageekgyeYsRsgnptrsvleeriaaLeggeaalav 73 
                                       +T+++h+gqe+ + +t+a++vpiylts+y+fkd+++a   fa +e g++Y+R++n t+  +e+riaaLegg +alav
  gi|474934203|ref|YP_007687785.1|  20 DTIQIHKGQEQADpATDARNVPIYLTSSYVFKDSKQAadrFALKEGGNIYGRLTNTTQAIFEDRIAALEGGVSALAV 96 
                                       799*****987655********************999999************************************* PP

                                       SSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHH.TTCEEEEESTTSHHHHHHHCCTTEEEEEEESS-TT CS
                   Cys_Met_Meta_PP  74 ssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkk.lgievkfvdtsdleelekaikentklvylEtptnp 149
                                       ssG aA++ ai al+++Gd+iv+ +++Yggt++l++++++   gi++++vd+sd++++ekai+++t++++ Et +np
  gi|474934203|ref|YP_007687785.1|  97 SSGAAAVTYAINALCRSGDNIVSANNIYGGTYNLFEHTFPSfNGITTTWVDPSDPANFEKAITDRTRVIFAETFGNP 173
                                       ****************************************9679********************************* PP

                                       TT----HHHHHHHHHHTT-EEEEEGTTTHTTTS-GGGGT-SEEEEETTTTTTCSSS--EEEEEESSCHHHHHHHHHH CS
                   Cys_Met_Meta_PP 150 llkvvDiekiaklakkagvlvvvDntfaspllqrplklgaDivvhSaTKylgGhsdvvaGvivvkgkeelkkelkfl 226
                                         +++D+e+ia++a+ +++++v+Dntfa+p+l+rpl++gaDivv+SaTK+++Gh++v+aGviv+ gk+++  + +  
  gi|474934203|ref|YP_007687785.1| 174 NADITDVEAIAEIAHRHNIVLVIDNTFATPYLFRPLEHGADIVVESATKFISGHGNVIAGVIVEGGKFDWFAKPELY 250
                                       ***********************************************************************999988 PP

                                       H...............................HHHT-B--HHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHTSTT CS
                   Cys_Met_Meta_PP 227 q...............................nalGavlspfdawlllrGlkTLslRlerhqenAlkvAefLekhpk 272
                                       +                               +++Ga +spf+aw+ll+ ++TLslR+e++ +nAlk+  +L+++pk
  gi|474934203|ref|YP_007687785.1| 251 PqfteedpsyhgtvfakfgpgafttwircillRDTGACISPFTAWVLLQSVETLSLRVEKQVSNALKIVDYLKNNPK 327
                                       7899************************************************************************* PP

                                       EEEEE-TTSTTSTTHHHHHHHSSSG-S.EEEEEESSHHHHHHHHHHC-SSSEECSS-SSSS-EEEETTTTTTTTSCH CS
                   Cys_Met_Meta_PP 273 vekvyYpglpshpqhelakkqlkgagg.vlsFelkseeekakkfvdnlklfslaeslGgveslielpasmthasipk 348
                                       v +v++p+l+s +q el  +++ ++g+ +++F++k+++e+a+k+ +nlklfsl++++ +v+sli++pas+th ++++
  gi|474934203|ref|YP_007687785.1| 328 VASVSHPSLSSGKQKELYDRYFPNGGAsIFTFDVKGTKEQAQKLTENLKLFSLLANIADVKSLIIHPASTTHSQLTE 404
                                       **********************999988************************************************* PP

                                       HHHHHTTS-TTEEEEE--SS-HHHHHHHHHHHHH CS
                   Cys_Met_Meta_PP 349 eereaagvtddliRlsvGiEdvdDliaDlkqale 382
                                       ee e   + ++ iR+s+G E+ dDliaDl+++++
  gi|474934203|ref|YP_007687785.1| 405 EELEGVHIRPTTIRISIGAENPDDLIADLEEGFK 438
                                       *******************************996 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.2   2.1e-13   3.7e-10      22     146 ..      74     199 ..      52     209 .. 0.83
   2 ?   -3.5   0.0       2.6   4.7e+03     221     265 ..     288     332 ..     286     341 .. 0.78

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 2.1e-13
                                       SHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSS CS
                   DegT_DnrJ_EryC1  22 gpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtyn 98 
                                       + + + FE ++aa  g   a+avssG aA+  a++al  + gd ++ + + + +t n   ++   p f  ++ + + 
  gi|474934203|ref|YP_007687785.1|  74 NTTQAIFEDRIAALEGGVSALAVSSGAAAVTYAINALCRS-GDNIVSANNIYGGTYNLFEHT--FPSFNGITTTWVD 147
                                       567778******************************8766.9***************99885..5777777744444 PP

                                       B.-GGGCGGG--TTEEEEEEB-GGGB--....-HHHHHHHHHHCT-EEEEE-T CS
                   DegT_DnrJ_EryC1  99 i.dpaaieaaitertkaIlpVhlyGqva....dmdalkaiaakhglkvieDaA 146
                                       + dpa+ e+ait rt+ I+ ++++G+++    d++a+ +ia++h+++++ D  
  gi|474934203|ref|YP_007687785.1| 148 PsDPANFEKAITDRTRVIF-AETFGNPNaditDVEAIAEIAHRHNIVLVIDNT 199
                                       339*************886.6888876544448999************99965 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.6
                                       B-BHHHHHHHHHHHCTHHHHHHHHHHHHHHHHHHHHTCCCCEESC CS
                   DegT_DnrJ_EryC1 221 rlteiqAAiglaqLerldelvarRreiaelykeeLaelegtaelt 265
                                       +++ + A ++l+  e l+  v+++  +a  + + L++ +++a + 
  gi|474934203|ref|YP_007687785.1| 288 CISPFTAWVLLQSVETLSLRVEKQVSNALKIVDYLKNNPKVASVS 332
                                       677788889999999999999999888888888888888766554 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.0   4.4e-13   7.8e-10      10     192 ..      40     202 ..      37     231 .. 0.85
   2 ?   -2.7   0.0       1.4   2.6e+03     282     349 ..     365     423 ..     357     431 .. 0.55

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 4.4e-13
                                       STTSTTSSHHHHHHHHHHHH.HHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHH CS
                     Aminotran_1_2  10 eylgdsgkptlpevakaeke.galaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagalieali 85 
                                        + ++++++++++ ++a+ +  + +gg++   ++++ ++ +e ++a + g          +a+ v+sGa a+  a++
  gi|474934203|ref|YP_007687785.1|  40 VPIYLTSSYVFKDSKQAADRfALKEGGNIYGRLTNTTQAIFEDRIAALEG--------GVSALAVSSGAAAVTYAIN 108
                                       5556666788999999999966666666666677788999**********........777**************** PP

                                       HHHHHTTT-EEEEEESS-THHHHHHHH.....TTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS CS
                     Aminotran_1_2  86 fllklnpgdeilvpdptyasyknilrl.....sggevvryplyseedfhldlealeealkeapegnkktkvilvesp 157
                                       +l++   gd+i++ +  y+   n +++     +g++   +          d  ++e+a+++      +t+vi+ e+ 
  gi|474934203|ref|YP_007687785.1| 109 ALCR--SGDNIVSANNIYGGTYNLFEHtfpsfNGITTTWVD-------PSDPANFEKAITD------RTRVIFAETF 170
                                       ***9..*******************9833222344444444.......67999********......********** PP

                                       -TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTT CS
                     Aminotran_1_2 158 hNPtGtvatleeleklldlakkynlllfvDeaYag 192
                                        NP  ++ + e + ++   a+++n++l++D ++a+
  gi|474934203|ref|YP_007687785.1| 171 GNPNADITDVEAIAEI---AHRHNIVLVIDNTFAT 202
                                       *********9999999...************9986 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHHHHSTEEEECCSCSSEEEEEETHHCHHHHHHHHHHT..CTEEEEEGGGGTSTTEEEEEC.T CS
                     Aminotran_1_2 282 qkrrkelrdeLaelglkvlasqsgmflltdlsaetakelskkLlee..vgvyvtpgtsftvpgrlRitv.A 349
                                       ++++++l+++L  + ++ la+ + + +l   +a+       +L+ee  +gv+++p       + +Ri++ A
  gi|474934203|ref|YP_007687785.1| 365 KEQAQKLTENL--KLFSLLANIADVKSLIIHPAS---TTHSQLTEEelEGVHIRP-------TTIRISIgA 423
                                       55555555555..234444444444444444444...334456666566777777.......668888744 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   2.5e-09   4.6e-06      67     207 ..      96     228 ..      71     270 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 2.5e-09
                                       ESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEE CS
                       Aminotran_5  67 tsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklv 143
                                       +s+++ a++ ++++l    + gd+iv  ++ + ++     +l + t    + i+ ++    d+ ++ek+++++t+++
  gi|474934203|ref|YP_007687785.1|  96 VSSGAAAVTYAINAL---CRSGDNIVSANNIYGGTY----NLFEHTFPSFNGITTTWVDPSDPANFEKAITDRTRVI 165
                                       555666666666666...777777766555555555....4444555666667777778899*************** PP

                                       EEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTTTTSSTT CS
                       Aminotran_5 144 aithvsnvtGtiqpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghKllgPtG 207
                                       +     n    i +ve+i+++a+++++++++D + a +       + g+D+++ s+ K++   G
  gi|474934203|ref|YP_007687785.1| 166 FAETFGNPNADITDVEAIAEIAHRHNIVLVIDNTFATPYLF-RPLEHGADIVVESATKFISGHG 228
                                       ********************************998887664.445789*********9988777 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   8.3e-07    0.0015      20     168 ..      61     198 ..      52     201 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 8.3e-07
                                       CS----CCCT--HHHHH..HHHHHHHHTT-SEEEEES-HHHHHHHHHHHH--TTEEEEEETT..-HHHHSSTTHHHH CS
                   Beta_elim_lyase  20 aamlGdesYgedktvnr..LedavaelfgkeaalfvpqGtaAnsillkillqrgeevivtep..ahihfdetgaiae 92 
                                       a+  G + Yg+ +++ +  +ed++a+l g   al v +G aA   ++++l+++g++++  ++  + +++        
  gi|474934203|ref|YP_007687785.1|  61 ALKEGGNIYGRLTNTTQaiFEDRIAALEGGVSALAVSSGAAAVTYAINALCRSGDNIVSANNiyGGTYNLFEHTFPS 137
                                       566677778875544432289***********************************998888553333333344445 PP

                                       CC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEE CS
                   Beta_elim_lyase  93 lagvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDg 168
                                       ++g++ + ++ +     d++++e+ai++      ++++i  ++  n        +  ++++a+ia++++i l++D 
  gi|474934203|ref|YP_007687785.1| 138 FNGITTTWVDPS-----DPANFEKAITD------RTRVIFAETFGN----PNADITDVEAIAEIAHRHNIVLVIDN 198
                                       788855555544.....6*********9......478888877666....5789********************95 PP

>> GDC-P  Glycine cleavage system P-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.3e-06    0.0023     140     260 ..     100     223 ..      90     233 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.3e-06
                                       HHHHHHHHHH-SSS--EEEEETTS-HHHHHHH.HHHHGGGT-EEEEE-GGG--S-........S-EEEEEEEES-TT CS
                             GDC-P 140 aEAvllaaraskkkakkvvvdkkvhpqtlevl.ktrakglgieivevdlteekvtd.....kekevagvlvqypnte 210
                                       a Av+ a +a  +  +++v +++++  t +   +t  +  gi +  vd ++    +     +++ +++  +  pn  
  gi|474934203|ref|YP_007687785.1| 100 AAAVTYAINALCRSGDNIVSANNIYGGTYNLFeHTFPSFNGITTTWVDPSDPANFEkaitdRTRVIFAETFGNPN-- 174
                                       456666666666667777777777777777663566666677776666544333322211144445555555554.. PP

                                       SB----HHHHHHHHHTT-EEEEEE-TTGGGTB--HHHHT-SEEEEE-TTT CS
                             GDC-P 211 GriedlkelvekakkkkslvvvaadllaLtllkpPgelgaDivvGsaqrf 260
                                         i+d+++++e a+++++++v   + +a   l  P e gaDivv sa +f
  gi|474934203|ref|YP_007687785.1| 175 ADITDVEAIAEIAHRHNIVLV-IDNTFATPYLFRPLEHGADIVVESATKF 223
                                       57*************998665.568999999999************9988 PP

>> Stealth_CR1  Stealth protein CR1, conserved region 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2     8e-05      0.14       8      19 ..     144     155 ..     144     156 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8e-05
                       Stealth_CR1   8 TWVNGSDPewqa 19 
                                       TWV+ SDP+  +
  gi|474934203|ref|YP_007687785.1| 144 TWVDPSDPANFE 155
                                       9*******9776 PP

>> YqbF  YqbF, hypothetical protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.3     0.003       5.4       2      13 ..     124     135 ..     123     142 .. 0.89
   2 ?    3.1   0.1     0.047        84      17      33 ..     308     326 ..     305     327 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.003
                                       S-SEEEETTEEE CS
                              YqbF   2 kGktYtalGhtF 13 
                                        G+tY+++ htF
  gi|474934203|ref|YP_007687785.1| 124 YGGTYNLFEHTF 135
                                       5*********** PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.047
                                       -EEEE-H..HHHHHHHHST CS
                              YqbF  17 veedVek..eiynYLqdne 33 
                                       ve++V +  +i++YL+ n+
  gi|474934203|ref|YP_007687785.1| 308 VEKQVSNalKIVDYLKNNP 326
                                       67777765589*****996 PP

>> SelA  L-seryl-tRNA selenium transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   1.5    0.0022       3.9      51     102 ..      79     128 ..      69     248 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0022
                                       HHHHHHHHHHT-SEEEEES-HHHHHHHHHHHHHBTSEEEEETTSGTEETTTE CS
                              SelA  51 lveellkeltgaedalvvnnnaaavllvLntlaagkeviisrGeLveiGGsf 102
                                         e+ +  l g  +al v   aaav  ++n+l++  + i+s  ++   GG++
  gi|474934203|ref|YP_007687785.1|  79 IFEDRIAALEGGVSALAVSSGAAAVTYAINALCRSGDNIVSANNI--YGGTY 128
                                       5678899999999***************************98765..35555 PP

>> Nop53  Nop53 (60S ribosomal biogenesis)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.2     0.053        96      57      90 ..     307     340 ..     297     347 .. 0.77
   2 ?    5.7   0.0    0.0046       8.3      42      86 ..     355     396 ..     353     415 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.053
                             Nop53  57 karkkkkkpLksdeiLaqrsavpavsakrkrkka 90 
                                       +++k+ +  Lk+  +L+++ +v +vs++  ++++
  gi|474934203|ref|YP_007687785.1| 307 RVEKQVSNALKIVDYLKNNPKVASVSHPSLSSGK 340
                                       44788999**************999988755544 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0046
                             Nop53  42 eLFvvDtkgdeelkkkarkkkkkpLksdeiLaqrsavpa.vsakrk 86 
                                       ++F+ D+kg++e     ++k +++Lk  + La+   v++ ++++ +
  gi|474934203|ref|YP_007687785.1| 355 SIFTFDVKGTKEQ----AQKLTENLKLFSLLANIADVKSlIIHPAS 396
                                       68********995....45779***********9999884444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2908.09
//
Query:       gi|474934204|ref|YP_007687786.1|  [L=482]
Description: argininosuccinate lyase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.5e-64  215.9   0.0    1.3e-63  215.3   0.0    1.3  1  Lyase_1   Lyase
    2.2e-26   92.4   0.0    9.5e-26   90.4   0.0    2.2  2  ASL_C2    Argininosuccinate lyase C-terminal


Domain annotation for each model (and alignments):
>> Lyase_1  Lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.3   0.0   1.4e-67   1.3e-63       1     312 []       9     303 ..       9     303 .. 0.97

  Alignments for each domain:
  == domain 1  score: 215.3 bits;  conditional E-value: 1.4e-67
                                       CEEEEETCHHHHHHHHHHHHHGGGHHHHHCHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHCHCHHCGGHHHBSSSS CS
                           Lyase_1   1 grftvkadklmgiftersrenfrlseedikalaalkkaaakanvdlkeeaaaiikaldevleegklddqfvlkviqe 77 
                                       grf+   d    +ft ++  +  + ++d+ ++ a  + +    ++++e a+ i ++l+++ ++++++ +f+ ++  e
  gi|474934204|ref|YP_007687786.1|   9 GRFSEGMDDSTLAFTSSLDVDSAMAVYDVLGSLAHVRMLKACRIIPAEDADRITEGLKKIEKQLEKG-EFKWDSKLE 84 
                                       788889999999*****************9********************************99999.********* PP

                                       SHHHHHHHHHHHHHHHHTTHSSGIIIIITTT--HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHTTT-EE CS
                           Lyase_1  78 gsgtavnmnlnevigellgekvepndkvhtgqSsnDqvpTalrlalkkalsekLlpaleqLidalkekakefkdvvk 154
                                       + +t+v+  l+ +ig        + +k+htg+S+nDqv+T++++ l++      ++a+++Li++l++ a+e++d+++
  gi|474934204|ref|YP_007687786.1|  85 DVHTNVENTLTAMIG-------PAGGKLHTGRSRNDQVATDFKMYLRDGALG-AVEAVDRLISSLQNVAQEHRDTIL 153
                                       ***************.......99************************8855.89********************** PP

                                       EEEETTEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHTCEETTTTTTTSSTTTSCCTHHHHHHHHHHHHHCSTEE CS
                           Lyase_1 155 iGrThlqdAtPvtlgqelsayaealerdrerlkellkrllvellgggtavgtglnadpefaelvakelakvtglpvk 231
                                       +G+Th q+A+P+tl+q l a+a  + rd  r++++ +r+ + +lg+++++gt + +d++   + a+ l+ ++    +
  gi|474934204|ref|YP_007687786.1| 154 PGFTHMQHAQPITLAQHLLAHAFRFGRDADRFMDAIERMDKCPLGSAALAGTTYPIDRK---MTAELLG-FKD---P 223
                                       ***********************************************************...9999999.888...* PP

                                       SSSHHHHHHC-HHHHHHHHHHHHHHHHHHHHHHHHHHHTSTTTSSEEEEGCCTSSC-TTSTTTEBTHHHHHHHHHHH CS
                           Lyase_1 232 apnsfeavsdrDavvellgalkllatsLskfaeDlrllssgeaglvelslaesepGSSiMPgKvNPvqlElltgvag 308
                                       ++ns+++v +rD+v+el++ ++++a++ s ++e+l++ ss e+++ve+++ +s+ GSSiMP+K+NP+ +El +g+ g
  gi|474934204|ref|YP_007687786.1| 224 TENSMDSVGSRDFVAELSFDAAMTAIDVSSLCEELIYWSSQEFRFVEMDDKYST-GSSIMPQKKNPDIAELSRGKTG 299
                                       ******************************************************.********************99 PP

                                       HHHH CS
                           Lyase_1 309 rvvG 312
                                        +vG
  gi|474934204|ref|YP_007687786.1| 300 GIVG 303
                                       9988 PP

>> ASL_C2  Argininosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.82   7.3e+03       4      10 ..     337     343 ..     301     346 .. 0.61
   2 !   90.4   0.0   1.1e-29   9.5e-26       1      68 [.     366     433 ..     366     434 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.82
                                       HHHHHHH CS
                            ASL_C2   4 ATdlADy 10 
                                       +Td+A++
  gi|474934204|ref|YP_007687786.1| 337 VTDIAEM 343
                                       4556655 PP

  == domain 2  score: 90.4 bits;  conditional E-value: 1.1e-29
                                       STTHHHHHHHHHHCTS-HHHHHHHHHHHHHHHHHTT--GGG--HHHHHHH-TT--GGGGGGSSHHHHT CS
                            ASL_C2   1 FstATdlADyLvrkGlpFReAHeivgravrlaeekgkeleeltleelkeisplleedveeaLdpeasV 68 
                                       F++ATdlADyLv kG+pFReAH ivg+ vr +++++++l++ltl++++++spl+eedv++a++++++V
  gi|474934204|ref|YP_007687786.1| 366 FINATDLADYLVTKGVPFREAHGIVGETVRFCIDNKVTLDNLTLDQFRKFSPLIEEDVFQAISVKNCV 433
                                       99*****************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (482 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.74u 0.36s 00:00:01.10 Elapsed: 00:00:00.58
# Mc/sec: 2511.01
//
Query:       gi|474934205|ref|YP_007687787.1|  [L=425]
Description: argininosuccinate synthase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   5.7e-164  546.0   0.0   6.7e-164  545.8   0.0    1.0  1  Arginosuc_synth  Arginosuccinate synthase
  ------ inclusion threshold ------
      0.065   12.7   0.0       0.13   11.8   0.0    1.5  1  QueC             Queuosine biosynthesis protein QueC


Domain annotation for each model (and alignments):
>> Arginosuc_synth  Arginosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  545.8   0.0  7.5e-168  6.7e-164       1     384 [.      19     404 ..      19     408 .. 0.99

  Alignments for each domain:
  == domain 1  score: 545.8 bits;  conditional E-value: 7.5e-168
                   Arginosuc_synth   1 vLaysGGlDtsviikllkeklgeeviavavdvGqeeedldevkekalklgavksvvvDakeefvedyifpaikanal 77 
                                       vLaysGGlDtsv i +l+e+++ +v+a++vdvGq+e d +e+ ++a + ga+++   D+++efve+y++p +kan++
  gi|474934205|ref|YP_007687787.1|  19 VLAYSGGLDTSVDIRWLQENYDVDVVAISVDVGQPETDGEEIVSRAYRNGAIRADFFDVRKEFVEEYVWPLVKANGM 95 
                                       8**************************************************************************** PP

                   Arginosuc_synth  78 YedrYllgtalaRPliakklvevakkegaeavahGctGkGnDqvRfevsirslaPdlkviaPvReleltReeeieya 154
                                       Y+d Y+l+ta+aRPl+ak+lv +a++ega+++ahGctGkGnDqvRf+++i +++P lk+iaP Re+  tR+eei+ya
  gi|474934205|ref|YP_007687787.1|  96 YQDVYPLSTAIARPLMAKTLVRIAHEEGAKYIAHGCTGKGNDQVRFDAGIIAQDPSLKIIAPQREWVATRDEEIDYA 172
                                       ***************************************************************************** PP

                   Arginosuc_synth 155 kekgipvevtkkkpysiDenllgrsieagiLedpknappediyeltkdpakapdepeeveiefekGvPvaldgeels 231
                                       ++kg+++++t+++p+s Denl+g s+e+g Led +++ppe++++ t dp+kapd++ ++ei+fekGvPv+ldg++++
  gi|474934205|ref|YP_007687787.1| 173 EAKGVEIKATREHPFSRDENLWGASCECGALEDAWAEPPEGVWAHTVDPEKAPDKATVIEIGFEKGVPVSLDGKKMD 249
                                       ***************************************************************************** PP

                   Arginosuc_synth 232 vlelieklneiagkhGvGRiDivedRlvglksReiYeapaalvLikahkdlekltlerevakfkkiveekyaelvYk 308
                                        ++li kln+iagk+GvGRiD+vedRlvg+ksRe+Ye+paa+v+i+ahk++e++ l+rev+ fkk +e+k+ ++vY+
  gi|474934205|ref|YP_007687787.1| 250 GVALIDKLNDIAGKNGVGRIDHVEDRLVGIKSRETYECPAAVVIIAAHKAMESMCLQREVLDFKKDIEKKFCRMVYD 326
                                       ***************************************************************************** PP

                   Arginosuc_synth 309 GlwfsPlkealdafiektqervtGtvrvklfkGsvvvlgReseeslYdeelasy..deedefdqkeaeGfikihglq 383
                                       G wf  l+e ++afi++tq+ vtGtvrvkl+kGs +v+gR+s++slYd+ la+y  d+ d+fd+++a Gfi+++gl 
  gi|474934205|ref|YP_007687787.1| 327 GQWFGGLREPINAFIDETQKFVTGTVRVKLYKGSYTVIGRKSPYSLYDTGLATYskDTVDTFDHHAAMGFIYVWGLP 403
                                       *****************************************************93345689**************97 PP

                   Arginosuc_synth 384 a 384
                                        
  gi|474934205|ref|YP_007687787.1| 404 D 404
                                       5 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.4e-05      0.13       1      57 [.      17      73 ..      17      99 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.4e-05
                                      EEEEE--SSHHHHHHHHHHHHH-S.EEEEEEEESS-TTSHHHHHHHHHHHHT--.-EE CS
                              QueC  1 kavvllSGGlDSttvlalakkegk.evealtfdYgqrhkkeleaakkiakelgveehk 57
                                      k+v+  SGGlD ++ + + +++++  v a+++d gq ++   e++++  ++  + +  
  gi|474934205|ref|YP_007687787.1| 17 KVVLAYSGGLDTSVDIRWLQENYDvDVVAISVDVGQPETDGEEIVSRAYRNGAI-RAD 73
                                      568889****************9548**********988888887777776666.544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2560.49
//
Query:       gi|474934206|ref|YP_007687788.1|  [L=340]
Description: N-acetyl-gamma-glutamyl-phosphate reductase, common form [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-33  114.8   0.0    5.1e-33  114.1   0.0    1.4  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
    6.7e-19   68.7   0.0      9e-19   68.3   0.0    1.2  1  Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation dom
     0.0051   16.9   0.0     0.0097   16.0   0.0    1.4  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
     0.0057   17.5   0.0      0.011   16.5   0.0    1.5  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
  ------ inclusion threshold ------
      0.083   12.3   0.0       0.13   11.7   0.0    1.3  1  Epimerase        NAD dependent epimerase/dehydratase family


Domain annotation for each model (and alignments):
>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.1   0.0   1.4e-36   5.1e-33       1     120 [.       4     140 ..       4     141 .. 0.99

  Alignments for each domain:
  == domain 1  score: 114.1 bits;  conditional E-value: 1.4e-36
                                       EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SCHH CS
                    Semialdhyde_dh   1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeelkevdivflalpag 77 
                                       +v+i+G+tGy+G+el r+L+ hp++el++l+s+++ aGk++++++  l++++d+ +++ ++ ++k++d+v+ a+p g
  gi|474934206|ref|YP_007687788.1|   4 RVGIIGGTGYTGSELSRILSVHPDIELAALTSRAN-AGKRVSDVHTFLKGYTDICFTE-KISDTKDLDLVMVATPFG 78 
                                       7**********************************.**********************.999*************** PP

                                       HHHHHHHHHHHTTSEEEESSSTTTTST...................TSEBE-HHHHGGGGGG CS
                    Semialdhyde_dh  78 vskelapklaeagvkviDlssdfRlkd...................davyvlpevnreaikk 120
                                       v+++ +p+l e+g+k iDls+d+R+kd                   dav++lpe+ r++ik 
  gi|474934206|ref|YP_007687788.1|  79 VAMDEVPALHEQGIKSIDLSGDYRMKDpavyqkwygkehtdpeglkDAVFGLPELFRDRIKG 140
                                       ***********************************************************986 PP

>> Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.3   0.0   2.5e-22     9e-19       2     184 .]     159     311 ..     158     311 .. 0.94

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 2.5e-22
                                       HHHHHC.TT.EEEEEEEEEEEGGGCHHHHHHHHHHHHHHHHHSTTS.CTTTSSHHTTSEESTCSTBTTTTCHCBHHH CS
                   Semialdhyde_dhC   2 kPLlda.lgelervivatyqavSGaGkkgvreLlkqvaelqrsdeakpgvfgvpiagNlipyidkeedkgepetree 77 
                                       +PL++  l+ ++ v v+ ++++SGaG k                 ++++ ++  +  ++ipy+ +  ++++pe++  
  gi|474934206|ref|YP_007687788.1| 159 APLMKSgLVYPD-VFVDGKSGTSGAGMK-----------------PSERLHHPTCGESVIPYKIG-SHRHQPEIDMA 216
                                       799999666555.**************9.................********************.9********** PP

                                       HHHHHHHHHHCTESCSEEEEEEEESBSSEEEEEEEEEES..SSHHHHHHHHHHHHCSTTEEEEESSHCHHSSHHHHT CS
                   Semialdhyde_dhC  78 lkavaetkkileftekvsatcvrVPvlrGhseavtiklk..lkdveveeveellaaapevkvvvneeedrPtpaava 152
                                        ++ a  +  ++f +      +++P++rG+  ++++++k  ++++ev++v+e+ + a e +v+  +   +P  +av+
  gi|474934206|ref|YP_007687788.1| 217 VGMFAGVTPDVAFVP------HLIPIVRGIISSCYFRTKkeVTQEEVDAVYEKQYGA-ERFVHYVP---EPSIRAVV 283
                                       ***************......8*****************999***************.*******8...9******* PP

                                       TCSSSEEEEEEEEETTCTTEEEEEEEEETTTT CS
                   Semialdhyde_dhC 153 ggtnsvsVGRirkdemgdeglklvvvgDNllk 184
                                         +n+++VG   +   g++ ++ + v+DNl+k
  gi|474934206|ref|YP_007687788.1| 284 A-SNHAQVG---STVLGKDRVVSFGVIDNLVK 311
                                       8.9******...55555666**********97 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.7e-06    0.0097       2      92 ..       4      92 ..       3      95 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.7e-06
                                      EEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH-SEEEE-S-HHHH CS
                            DapB_N  2 kvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavtddleevlekadvliDFTtpeav 80
                                      +v+++G +G  G+e+ + ++ ++d+el+a  +r +   + +d+ ++l+ g +++ +t++++++++  d +   T   ++
  gi|474934206|ref|YP_007687788.1|  4 RVGIIGGTGYTGSELSRILSVHPDIELAALTSRANAGKRVSDVHTFLK-GYTDICFTEKISDTKD-LDLVMVATPFGVA 80
                                      89*********************************8888888877765.5888888888888776.4444445656666 PP

                                      HHHHHHHHHTT- CS
                            DapB_N 81 lenlklalekgv 92
                                      ++ + ++ e+g+
  gi|474934206|ref|YP_007687788.1| 81 MDEVPALHEQGI 92
                                      666666666655 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   3.2e-06     0.011       2      80 ..       4      85 ..       3      95 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.2e-06
                                      EEEEETT.SHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESS...HHHHHTCTTESEEEE-S-GGGHH CS
                      GFO_IDH_MocA  2 rvaiiGa.Gkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysd...leelladpeidavivatpngthe 76
                                      rv+iiG+ G+ gs+  r l  + ++ e++al ++ ++  +    ++ ++ y+d    e++++ ++ d+v+vatp g  +
  gi|474934206|ref|YP_007687788.1|  4 RVGIIGGtGYTGSELSRILSVH-PDIELAALTSRANAGKRVSDVHTFLKGYTDicfTEKISDTKDLDLVMVATPFGVAM 81
                                      899**99788899998666666.***********999988888899999999999788888888**********75554 PP

                                      HHHH CS
                      GFO_IDH_MocA 77 elak 80
                                      + + 
  gi|474934206|ref|YP_007687788.1| 82 DEVP 85
                                      4444 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.7e-05      0.13       3      69 ..       7      72 ..       5      83 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.7e-05
                                      EETTTSHHHHHHHHHHHHCT.SEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEE CS
                         Epimerase  3 VtGatGfiGsalvkallekg.yevigldrlssasntarledlelveldltdrsalerlfkeeqpdavi 69
                                      ++G+tG+ Gs l + l  +  +e+ +l+++ +a+++ ++ +       +td   +e++ ++++ d v+
  gi|474934206|ref|YP_007687788.1|  7 IIGGTGYTGSELSRILSVHPdIELAALTSRANAGKRVSDVH--TFLKGYTDICFTEKISDTKDLDLVM 72
                                      89*****************9999*******99888777665..4444456666666666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 2096.64
//
Query:       gi|474934207|ref|YP_007687789.1|  [L=408]
Description: glutamate N-acetyltransferase/amino-acid acetyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   6.6e-124  413.5   3.4   7.4e-124  413.3   3.4    1.0  1  ArgJ      ArgJ family


Domain annotation for each model (and alignments):
>> ArgJ  ArgJ family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  413.3   3.4  4.1e-128  7.4e-124       1     376 []      16     408 .]      16     408 .] 0.92

  Alignments for each domain:
  == domain 1  score: 413.3 bits;  conditional E-value: 4.1e-128
                                       EEEEEXXSSS..SXXEEEEEEEEEEEEEEEEEXXSSXXHHHHHHHHHHH.HHSEEEEEEEEEEXXXSXHHHHHHHHH CS
                              ArgJ   1 kaagvaagikkkkkdlalivseepasaaavfTknkvkAapvkvsrevlkkkkgaravvvnsgnANavtgeqGledae 77 
                                       kaagv+ g+k ++ dl l++se+pa+a   fT+nkvkAapv+++ ++ +   +++avvvnsgnANa+tg++G+eda 
  gi|474934207|ref|YP_007687789.1|  16 KAAGVHSGVKYRSLDLGLLYSEVPATAFKAFTSNKVKAAPVQLMIAQDS--PTLSAVVVNSGNANALTGRRGYEDAM 90 
                                       5899******99******************************9877663..459*********************** PP

                                       HHHHHHHHHHTSXGGGEEEEEEEESSXXXXHHHHHHHHHHX....X......HHHHHHHXSSXSSXXEEEEEEEE.. CS
                              ArgJ  78 emaeavaealgikeeevlvasTGviGerlpmekieagieklvekle......eeaaeAimTTDtvpKlaavevel.. 146
                                       +m++ava+ l++++e+v v+sTG+iG+ ++m+k++ gi+k+v++l+      ++++eAimTTDtv+K++av+v+l  
  gi|474934207|ref|YP_007687789.1|  91 TMQKAVAASLNLPPETVGVMSTGLIGRFMDMHKVQYGISKAVKDLDvgreadADITEAIMTTDTVKKECAVRVRLtd 167
                                       ********************************************9777888889*******************9986 PP

                                       TEEEEEEEEEEXSSSXXXXE....E--EEEEEE-----HHHHHHHHHHHHHHTGGGB-SSS---SS-EEEEEE--TT CS
                              ArgJ 147 gkevtiagiaKGaGmihPnm....aTmLafittDaavsaealqellkeavdksFnsisvDgdtSTnDtvlllAngaa 219
                                       g+ v i  i+KG+Gmi+P++    +T+L++ittDa ++++ ++ ++++  d++ n++svD+d+STnDt+l+lAng a
  gi|474934207|ref|YP_007687789.1| 168 GTLVYISMISKGSGMISPHLrtlhGTTLSMITTDAVLTPK-FEPTFQKLLDNTMNMVSVDSDQSTNDTCLMLANGLA 243
                                       689*****************999999*********99886.79999******************************9 PP

                                       TT..STTHHHHHHHHHHHHHHHHHHHHHTSTT-S-EEEEEEEEESSHHHHHHHHHHHHT-HHHHHHHHTT---HHHH CS
                              ArgJ 220 eee.eedleefeealtevlqeLakqivrDGEGatklveveVkgakseeeAkkvaksvanssLvKtAlfGeDanwGRi 295
                                         +  ++  +f eal+ vl+++a+ i++DGEGatkl++ve++gak+eeeA+ +ak++++s+LvKtA+fG+D+n+GR+
  gi|474934207|ref|YP_007687789.1| 244 GGKpADEDPKFIEALDMVLHKIARTIASDGEGATKLITVEINGAKDEEEARIAAKAIIDSPLVKTAIFGSDPNYGRV 320
                                       4333778899******************************************************************* PP

                                       HHHHHHSSS---TTS-EE..TT....EEEEETTEE----HHHHH....HHHH-SSEEEEEE--SSSEEEEEEEE--- CS
                              ArgJ 296 laavGyagaeldpekvsvllge....vkvlekgepeevdeerak....eilkeeeveievdlgegeeeatvwtcDLs 364
                                       ++a+G++g+e++ e+v++++++    v +l++g+p+ ++eer        ++++ev +++dlg g+++at+w+cDL+
  gi|474934207|ref|YP_007687789.1| 321 MMALGKCGVEFNLEEVHLTIKGgdmeVPILDSGAPV-FQEERSVevvrMAMDNKEVILQLDLGVGDGSATAWGCDLT 396
                                       ******************665445559******976.45554441221556799*********************** PP

                                       HHHHHHHTT-XX CS
                              ArgJ 365 yeYvkiNadYrt 376
                                       y+Yv+iNa+Y++
  gi|474934207|ref|YP_007687789.1| 397 YDYVRINAEYTS 408
                                       **********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2513.30
//
Query:       gi|474934208|ref|YP_007687790.1|  [L=274]
Description: acetylglutamate kinase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.4e-44  152.6   3.2    1.5e-44  152.4   3.2    1.0  1  AA_kinase  Amino acid kinase family


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.4   3.2   8.6e-49   1.5e-44       3     237 ..       8     246 ..       6     250 .. 0.96

  Alignments for each domain:
  == domain 1  score: 152.4 bits;  conditional E-value: 8.6e-49
                                       EEEEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC....E..HHHHHHHHH CS
                         AA_kinase   3 vVvKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaaglrstleeagevatr 79 
                                       + +K+GG+ l+++++  ++rla++ia+l+++g+ ++vVhGgg+ + + +++ +gl++ +   g+r t+e+a+e+++ 
  gi|474934208|ref|YP_007687790.1|   8 FLIKFGGNTLSEPDN--VKRLAKEIADLQKAGKSVIVVHGGGPSISEEMKR-RGLNPVMVG-GQRITDEAALECVE- 79 
                                       68***********99..**********************************.*********.**************. PP

                                       HHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE...............HHHTTTCEEECCHHHHHHHTT-EEEE CS
                         AA_kinase  80 dalaslgerlvaallaaglpavglsaaaldateagr.............degsdgnvesvdaeaieelleagvvpvl 143
                                       d l  ++e  v+al+++g   vgl a+ ++++e++              d g +gnv sv+ae++ +ll++gv+pv+
  gi|474934208|ref|YP_007687790.1|  80 DTLRGINEMFVRALQDEGATVVGLGAFLFTLSEKKPpyhvlvdgkeevvDLGLVGNVVSVNAETVTDLLADGVLPVV 156
                                       ********************************9999***************************************** PP

                                       ESEEEEETTTEEEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH.CSSS.TTTHH CS
                         AA_kinase 144 tgfigldeegelgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaee.saselatgGm 219
                                        +  g d + +l ++++Dt+aa +A+ ++A+++i +tdV+G++ +  +      ++++++  +++  +a++ ++gGm
  gi|474934208|ref|YP_007687790.1| 157 YPV-GTDGKHHL-NVNADTMAAGIAAGVKAEEMIAVTDVPGILRDVHDLS---SKIDRVNLADIDRlIADGTISGGM 228
                                       **6.58888886.********************************99999...************************ PP

                                       HHCHHHHHHHHHCTT-EE CS
                         AA_kinase 220 kvkhpaalaaarrggipv 237
                                       ++k++a+ +a++ g   v
  gi|474934208|ref|YP_007687790.1| 229 IPKVEACSKAVKAGASAV 246
                                       ************996555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1681.91
//
Query:       gi|474934209|ref|YP_007687791.1|  [L=394]
Description: acetylornithine and succinylornithine aminotransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   5.3e-116  387.6   0.2   6.4e-116  387.3   0.2    1.1  1  Aminotran_3  Aminotransferase class-III
  ------ inclusion threshold ------
      0.024   13.6   0.2      0.039   12.9   0.0    1.5  2  Aminotran_5  Aminotransferase class-V


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  387.3   0.2  7.2e-120  6.4e-116       6     406 .]      18     390 ..      13     390 .. 0.96

  Alignments for each domain:
  == domain 1  score: 387.3 bits;  conditional E-value: 7.2e-120
                                       B--SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHH CS
                       Aminotran_3   6 ednlllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllkl 82 
                                       +  + ++ + +eG+yl+d dg++ylD vs+iav  lG++hP+ vka+++q+ +l+hvs +++  ++++ la+ l+ +
  gi|474934209|ref|YP_007687791.1|  18 YGRMDVCFESGEGCYLYDLDGNKYLDSVSGIAVCSLGYSHPDWVKAMRDQVSHLVHVS-NLYYVQEQALLAQRLNTI 93 
                                       556679999*************************************************.****************** PP

                                       CT-..SEEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEE CS
                       Aminotran_3  83 apkgldkvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvr 159
                                       +p  + ++++ansG+eA+e+AlK+a k      +t++ k++a  ++fHGrt ++l++tg+ kky+t+f+p++ + ++
  gi|474934209|ref|YP_007687791.1|  94 TPDAITRTLFANSGAEANEGALKTAVK------YTQRGKVLAALNGFHGRTSASLGATGQ-KKYQTGFEPLISNAYQ 163
                                       ***************************......9**************************.**********877664 PP

                                       .E-TTBGGGTB-HHHHHHHHHHHHHHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TT CS
                       Aminotran_3 160 .lkypdeevlkeneeeeaalleelealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvq 235
                                         +y+        +         le++++ ++ ++aA+i+E iqgegGvv a+pefl+++r+lc+++++l++vDEvq
  gi|474934209|ref|YP_007687791.1| 164 yYEYN--------N---------LENVKNLIDRDTAALIIEGIQGEGGVVCATPEFLKGVRDLCTDNGALMVVDEVQ 223
                                       03444........3.........89999999********************************************** PP

                                       TTTTTTSSSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHHHHHHHHHHHHTT CS
                       Aminotran_3 236 tGfGrTGklfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgshgsTfgGnplacavalavleiieeek 312
                                       tG+GrTGk+++++h+g+ pD++t+aK+l++G+p+ a+++t+e+++++ pg hg+TfgGnpl  a   av++ii++e 
  gi|474934209|ref|YP_007687791.1| 224 TGVGRTGKWWCMDHFGIVPDIITTAKGLGAGMPIGAIMTTDEIAKVMVPGTHGTTFGGNPLVTASGCAVIDIINRER 300
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTCHHHHHHHHHCTEE-EEETTTEEEE---TT CS
                       Aminotran_3 313 llenaqelgaalkegLeelqkkyevikevRgkGlmiaielkeeaevkekeilkkakekGvlilsaGdnvirllppli 389
                                       ll+n+ ++g++ ke +++++    +ik+vRg+G++i++e+  ++++   ++ k + ++G+++  ++ +v+r++ppli
  gi|474934209|ref|YP_007687791.1| 301 LLDNVTAVGNKWKEDMKAVKCP--MIKDVRGLGFLIGVEMDTDDHAA--AVKKYMFKHGIIVNVCHGHVVRIIPPLI 373
                                       ******************9944..9******************9955..8888999********************* PP

                                       --HHHHHHHHHHHHHHH CS
                       Aminotran_3 390 itdeeidelleilkkal 406
                                       +t e+ +e ++ +k+al
  gi|474934209|ref|YP_007687791.1| 374 FTIEQEKEWMTVFKQAL 390
                                       **************997 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   4.4e-06     0.039      64     180 ..     101     225 ..      53     232 .. 0.71
   2 ?   -4.1   0.1      0.66   5.9e+03     320     339 ..     343     364 ..     336     368 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.4e-06
                                       EEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEE..EEBETTSCBE...GGGHHHH CS
                       Aminotran_5  64 iiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkv..ipldeegeld...ldelekl 135
                                       ++f  +++ea++ +++++ +   ++ +++   ++ h+ + +   +  +++++  +  +  ++ + ++   l+++++l
  gi|474934209|ref|YP_007687791.1| 101 TLFANSGAEANEGALKTAVK-YTQRGKVLAALNGFHGRTSASLGATGQKKYQTGFepLISNAYQYYEynnLENVKNL 176
                                       57777777777777777744.666667777777777777666555555555543300334555555555689999** PP

                                       --TTEEEEEEESBETTTTEB--HHHHHH....HHHHTT-EEEEE-TTTT CS
                       Aminotran_5 136 lnektklvaithvsnvtGtiqpveeigk....lakkkgalvlvDaaqav 180
                                       ++ +t++++i  ++ + G++  ++e+ k    l+ ++gal++vD +q+ 
  gi|474934209|ref|YP_007687791.1| 177 IDRDTAALIIEGIQGEGGVVCATPEFLKgvrdLCTDNGALMVVDEVQTG 225
                                       *******************977776655111167779**********85 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 0.66
                                       SHHHHHHHHHHTTEEEEE..E- CS
                       Aminotran_5 320 haedvatlLdeegIavrs..Gh 339
                                       ha+ v++++ ++gI v    Gh
  gi|474934209|ref|YP_007687791.1| 343 HAAAVKKYMFKHGIIVNVchGH 364
                                       7888999999999999885555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 2399.33
//
Query:       gi|474934210|ref|YP_007687792.1|  [L=244]
Description: hypothetical protein TALC_00633 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      7e-08   32.2   0.1    1.4e-07   31.2   0.1    1.6  1  ACT_7        ACT domain
  ------ inclusion threshold ------
      0.036   14.2   0.1      0.077   13.2   0.1    1.5  1  FrhB_FdhB_N  Coenzyme F420 hydrogenase/dehydrogenase, beta su


Domain annotation for each model (and alignments):
>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.1   1.6e-11   1.4e-07       4      64 ..     169     230 ..     166     231 .. 0.87

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 1.6e-11
                                       EEEEEEEE-S-.---SS--HHHHHHHHHHTTT---E.EEE-SS-EEEEEEGGGHHHHHHHHH CS
                             ACT_7   4 dgwiklsvvgsglpfdvtGivaklaspLaeagIsif.qiStyrtdyiLVpeedlekAveaLh 64 
                                       ++ + + v ++   +d++G++a l++ L++agI+i   +S++++ +++V+e d+ +A+ +L+
  gi|474934210|ref|YP_007687792.1| 169 EDLVEIVVKSPEGIVDTPGVIAYLITNLSDAGINIEeTVSCHTDTIFIVKEPDMINAYTVLT 230
                                       6667788888867799*******************73677******************9997 PP

>> FrhB_FdhB_N  Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   8.6e-06     0.077       8      74 ..     130     196 ..     128     199 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.6e-06
                       FrhB_FdhB_N   8 dkeirkkaqsGGivtallkylLeegiidgvivvapskdpwrpkpviattkeellaaaGskYtlspnl 74 
                                       +++i +  qs  +vt +++++L+  i d v   +  k + + + ++++++e ++++ G++ +l+ nl
  gi|474934210|ref|YP_007687792.1| 130 ENSIMQCVQSASAVTIIAEKMLKDRIMDTVGRFNIIKVREDLVEIVVKSPEGIVDTPGVIAYLITNL 196
                                       56799999**********************999977666689************9999887765554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1615.19
//
Query:       gi|474934211|ref|YP_007687793.1|  [L=504]
Description: Superfamily II DNA and RNA helicase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.2e-46  156.4   0.0    1.1e-44  152.2   0.0    2.1  2  DEAD          DEAD/DEAH box helicase
    3.6e-29  101.3   0.0    1.1e-28   99.8   0.0    1.8  2  Helicase_C    Helicase conserved C-terminal domain
    6.6e-15   54.9   5.1    6.6e-15   54.9   1.7    2.7  3  DbpA          DbpA RNA binding domain
    1.3e-06   28.5   0.0    3.8e-06   27.0   0.0    1.7  2  ResIII        Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
       0.01   15.2   1.0      0.035   13.4   0.0    2.2  2  CMS1          U3-containing 90S pre-ribosomal complex subunit
        0.1   12.9   1.3       0.65   10.3   1.3    2.2  1  AAA_22        AAA domain
       0.16   11.0   0.0       0.24   10.5   0.0    1.3  1  ANF_receptor  Receptor family ligand binding region


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.2   0.0   4.5e-48   1.1e-44       1     174 [.      26     190 ..      26     192 .. 0.95
   2 ?    2.0   0.0     0.059   1.5e+02      43      72 ..     235     264 ..     215     312 .. 0.76

  Alignments for each domain:
  == domain 1  score: 152.2 bits;  conditional E-value: 4.5e-48
                                       -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlr 77 
                                       t++Q +aip+ ++g+d++++a+TG+GKT+a+++ v++++ +  gk+ p a++++PtreLa q+  +++k+    +  
  gi|474934211|ref|YP_007687793.1|  26 TPVQVQAIPEGIRGRDIIARAQTGTGKTGAYSMIVMSRIPS--GKKSPSAIVIAPTRELALQVDGEMRKLSRLSGHF 100
                                       79*************************************76..*****************************87755 PP

                                       EEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  78 vlliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitc 154
                                        + i+gg + r+q+ +l++g+divvgtpgr+ d+++++ l+ls++++ V+DEadr+ d+gf++++n il +l     
  gi|474934211|ref|YP_007687793.1| 101 SVPIYGGAEVRKQVFQLNRGADIVVGTPGRIRDMVTREVLDLSHIEIAVIDEADRMFDMGFEEDLNFILDAL----- 172
                                       5689*************999****************************************************..... PP

                                       TSTTTSEEEEEESSBSHHHH CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                              DEAD 155 dgklqrqvivlSATlpkdvk 174
                                         ++ rq++++SAT+++dv+
  gi|474934211|ref|YP_007687793.1| 173 --PERRQTLMFSATMTDDVQ 190
                                       ..67788*********9997 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.059
                                       TTSTS-EEEEEESSHHHHHHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  43 kgktgpkalivePtreLaeqtlnnlkkfkk 72 
                                        gk +pk+++ + t+ ++e+ +++++  + 
  gi|474934211|ref|YP_007687793.1| 235 LGKGTPKTIVFVATKTMVEELFTEMRADGM 264
                                       48999**************99999876555 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       5.5   1.4e+04      18      48 ..      72     106 ..      66     125 .. 0.56
   2 !   99.8   0.0   4.3e-32   1.1e-28       2     111 .]     227     334 ..     226     334 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 5.5
                                       EEEEEESSHH...HHHH.HHHHHHHTTSTEEEEST CS
                        Helicase_C  18 kilifvntid...rlek.vklllekkgikvavlhg 48 
                                        ++++++t++   +++  ++ l + +g  +++++g
  gi|474934211|ref|YP_007687793.1|  72 SAIVIAPTRElalQVDGeMRKLSRLSGHFSVPIYG 106
                                       56777777775433332545554444555556666 PP

  == domain 2  score: 99.8 bits;  conditional E-value: 4.3e-32
                                       HHHHHHHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHT..TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGG CS
                        Helicase_C   2 kleallellkleeeggkilifvntidrlekvklllekk..gikvavlhgelpqnereeileqfnkgesdvLiatdva 76 
                                       k ++l e+l   + + k+++fv t++++e  +l++e +  g+kv +lhg++pq+ re+i+  f+++++  L+atdva
  gi|474934211|ref|YP_007687793.1| 227 KRDILREIL--GKGTPKTIVFVATKTMVE--ELFTEMRadGMKVGTLHGDMPQDLREKIIGMFRDNRILTLLATDVA 299
                                       566777776..88999************9..999777788*************************9*99******** PP

                                       TSSSTSTTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                        Helicase_C  77 erGidipkvnlVinfdlprnvtsyiqriGRtgRag 111
                                       +rG+di +v+lV+nfd+p  +++y +riGRtgRag
  gi|474934211|ref|YP_007687793.1| 300 ARGLDISDVDLVVNFDVPSRPETYLHRIGRTGRAG 334
                                       *********************************97 PP

>> DbpA  DbpA RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.94   2.4e+03      13      37 ..     127     152 ..     127     156 .. 0.86
   2 ?   -1.3   0.0       0.9   2.3e+03      13      38 ..     286     311 ..     284     314 .. 0.86
   3 !   54.9   1.7   2.6e-18   6.6e-15       2      71 ..     421     490 ..     420     491 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.94
                                       -HHHHHHHHHTCT.TB-GGGEEEEEE CS
                              DbpA  13 rpgdivgaiakea.glsgkdIGkIdi 37 
                                       +pg i +++++e  +ls  +I  Id 
  gi|474934211|ref|YP_007687793.1| 127 TPGRIRDMVTREVlDLSHIEIAVIDE 152
                                       5999999****999999999999985 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.9
                                       -HHHHHHHHHTCTTB-GGGEEEEEE- CS
                              DbpA  13 rpgdivgaiakeaglsgkdIGkIdil 38 
                                       r + i+ ++a +   +g dI ++d+ 
  gi|474934211|ref|YP_007687793.1| 286 RDNRILTLLATDVAARGLDISDVDLV 311
                                       678999***************99985 PP

  == domain 3  score: 54.9 bits;  conditional E-value: 2.6e-18
                                       EEES-SGGGT--HHHHHHHHHTCTTB-GGGEEEEEE-SS-EEEEE-TT-HHHHHHHHTT--SSS----EE CS
                              DbpA   2 lfinvGkkdklrpgdivgaiakeaglsgkdIGkIdildkfSfvevpkekaeevlkalkkkkikGrkvrve 71 
                                       ++i++Gk d+++  +i ++i k+a+++ + +Gk+ ++d+ Sfvev++++++ v+++l + ++ +++v+v+
  gi|474934211|ref|YP_007687793.1| 421 IQIGIGKGDGFNRTQIADFIRKRANIDDDAVGKVGLKDSVSFVEVSEDVSDYVIQQLDGCRVGNKTVNVT 490
                                       689*****************************************************************97 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   1.5e-09   3.8e-06      24     169 ..      39     185 ..      23     187 .. 0.80
   2 ?   -2.4   0.0       1.6     4e+03      51      73 ..     237     258 ..     218     265 .. 0.69

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 1.5e-09
                                       TSEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.......GEEEESSS-B-- CS
                            ResIII  24 dkrglikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkflseayke...igkkvsgdkkka 96 
                                        + ++  + TGtGKT  + + ++ r+ + +k   +++++p+++l  q   e++k++    ++   i +  + +k+ +
  gi|474934211|ref|YP_007687793.1|  39 GRDIIARAQTGTGKTGAYsMIVMSRIPSGKKSPSAIVIAPTRELALQVDGEMRKLSRLSGHFsvpIYGGAEVRKQVF 115
                                       456888999*******99677777777776777*******************9999998888555333344444444 PP

                                       .......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS....TTTHHHHHT---.SEEEEEESS- CS
                            ResIII  97 kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak...kswreilekfke.avllglTATp 169
                                         + +  ++i+v t  ++         ++e l+ +++++ +iDEa r+ ++   +  + il++++e    l ++AT+
  gi|474934211|ref|YP_007687793.1| 116 --QLNRGADIVVGTPGRIRDMV-----TREVLDLSHIEIAVIDEADRMFDMgfeEDLNFILDALPErRQTLMFSATM 185
                                       ..668899***********999.....9999999****************9665577778999976477899***97 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.6
                                       .....-EEEEESSHHHHHHHHHH CS
                            ResIII  51 kgkeekflflvprkslleqtlee 73 
                                       kg   k++++v +k+++e + +e
  gi|474934211|ref|YP_007687793.1| 237 KGT-PKTIVFVATKTMVEELFTE 258
                                       333.4777777888887777665 PP

>> CMS1  U3-containing 90S pre-ribosomal complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.4e-05     0.035     179     209 ..     122     152 ..     109     180 .. 0.88
   2 ?   -0.5   0.3      0.25   6.3e+02      26      47 ..     383     404 ..     376     473 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.4e-05
                              CMS1 179 giavGtpgRildLleeeslsvdeLkrivlDa 209
                                        i vGtpgRi d+++ e+l +++++  v+D 
  gi|474934211|ref|YP_007687793.1| 122 DIVVGTPGRIRDMVTREVLDLSHIEIAVIDE 152
                                       589***********************99996 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.25
                              CMS1  26 skkkerkkgklketqDvkaglt 47 
                                       +k +++++   k+  D+k    
  gi|474934211|ref|YP_007687793.1| 383 EKADRKERERKKKALDPKEAER 404
                                       3222222222222224333322 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.3   0.00026      0.65      74     114 ..     127     170 ..      42     189 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00026
                            AAA_22  74 sseellealeqalraravielliiDEaqhlr..s.eealeeLrs 114
                                       +  ++++++++ + + + ie+ +iDEa++++    ee l+++ +
  gi|474934211|ref|YP_007687793.1| 127 TPGRIRDMVTREVLDLSHIEIAVIDEADRMFdmGfEEDLNFILD 170
                                       5667788999999999999**********874436777776643 PP

>> ANF_receptor  Receptor family ligand binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   9.4e-05      0.24     158     206 ..     211     269 ..     186     382 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 9.4e-05
                                       T............CHHHCHHHHHHHHHHTT.T--EEEEEE-HHHHHHHHHHHHHTTS-STTE CS
                      ANF_receptor 158 e............ssnddevvrkllkeiks.karvivlfcssedarellkaarrlgltgeey 206
                                                    ++++ +++r++l   ++ +++ iv+++  ++++el+ ++r  g+  ++ 
  gi|474934211|ref|YP_007687793.1| 211 VtgltkqfivkcqRNEKRDILREIL---GKgTPKTIVFVATKTMVEELFTEMRADGMKVGTL 269
                                       5555555555574445669999999...99899************************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (504 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 3503.97
//
Query:       gi|474934212|ref|YP_007687794.1|  [L=287]
Description: hypothetical protein TALC_00635 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.4   0.0       0.29   11.2   0.0    1.6  1  DUF1327   Protein of unknown function (DUF1327)


Domain annotation for each model (and alignments):
>> DUF1327  Protein of unknown function (DUF1327)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   1.6e-05      0.29      11      53 ..      39      84 ..      33     101 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.6e-05
                           DUF1327 11 Gvrnyedk.vtvtva..leikerfdlllfdvavaldrveGaalefy 53
                                      G+r  +d  v  +va  ++  +rfd+   d++ a dr+ Ga++e+ 
  gi|474934212|ref|YP_007687794.1| 39 GIRVLKDGdVVTSVAhlIQFVDRFDGDAKDLSRAYDRITGATIELI 84
                                      5565555413334552246779*********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1891.95
//
Query:       gi|474934213|ref|YP_007687795.1|  [L=54]
Description: hypothetical protein TALC_00636 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1486  (0.0828825); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.26s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 412.80
//
Query:       gi|474934214|ref|YP_007687796.1|  [L=208]
Description: hypothetical protein TALC_00637 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1567.71
//
Query:       gi|474934215|ref|YP_007687797.1|  [L=323]
Description: hypothetical protein TALC_00638 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.016   15.2   4.8      0.036   14.0   4.8    1.6  1  Zn_Tnp_IS1595  Transposase zinc-ribbon domain
      0.075   12.6   2.2       0.25   10.9   2.2    1.9  1  TF_Zn_Ribbon   TFIIB zinc-binding
       0.11   12.4   3.0       0.25   11.3   3.0    1.6  1  C1_1           Phorbol esters/diacylglycerol binding domain (
       0.16   12.0   2.2       0.43   10.6   2.2    1.7  1  DZR            Double zinc ribbon
       0.32   10.5   2.3        1.5    8.3   0.4    2.6  2  zf-ribbon_3    zinc-ribbon domain
       0.44   10.5   4.0        6.8    6.7   0.1    3.0  2  zf-C2HC_2      zinc-finger of a C2HC-type


Domain annotation for each model (and alignments):
>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   4.8   1.2e-05     0.036      20      45 ..       7      31 ..       5      32 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.2e-05
                     Zn_Tnp_IS1595 20 vCPhCgsrkayriktrglfqCkeCrk 45
                                      vCP+Cg +++y ++ r+   C +Cr+
  gi|474934215|ref|YP_007687797.1|  7 VCPYCG-KEFYAYSERQTVVCTHCRR 31
                                      8*****.99***************98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   2.2   8.4e-05      0.25       2      25 ..       7      29 ..       6      29 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8.4e-05
                                      EETTTTCEECHEETSTTCEEESSS CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdC 25
                                      +CP+Cg ++ +   er ++vCt C
  gi|474934215|ref|YP_007687797.1|  7 VCPYCGKEF-YAYSERQTVVCTHC 29
                                      8*****886.566699******99 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   3.0   8.2e-05      0.25      13      38 ..       7      33 ..       4      37 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.2e-05
                                      B-TTT-SB--S.SSS-EEEETTT--EE CS
                              C1_1 13 fCkhCgeflwg.kekqglkCswCkllv 38
                                       C +Cg+ ++   e+q + C+ C++++
  gi|474934215|ref|YP_007687797.1|  7 VCPYCGKEFYAySERQTVVCTHCRRKC 33
                                      6********99*************988 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   2.2   0.00014      0.43      14      40 ..       7      35 ..       4      40 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00014
                               DZR 14 fCseCgtklkavaa..edrCpsCgekvdp 40
                                      +C++Cg++  a+++    +C +C +k+  
  gi|474934215|ref|YP_007687797.1|  7 VCPYCGKEFYAYSErqTVVCTHCRRKCAH 35
                                      6*******9999889999******99765 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.4   0.00051       1.5      18      25 ..       7      14 ..       6      15 .. 0.78
   2 ?    0.7   0.1      0.13   3.7e+02      17      22 ..      24      29 ..      19      30 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00051
                       zf-ribbon_3 18 vCpyCGtk 25
                                      vCpyCG++
  gi|474934215|ref|YP_007687797.1|  7 VCPYCGKE 14
                                      79999976 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.13
                       zf-ribbon_3 17 nvCpyC 22
                                      +vC++C
  gi|474934215|ref|YP_007687797.1| 24 VVCTHC 29
                                      689999 PP

>> zf-C2HC_2  zinc-finger of a C2HC-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1    0.0023       6.8       5      12 ..       8      15 ..       6      19 .. 0.89
   2 ?    3.5   0.8     0.022        67       1      11 [.      22      32 ..      22      32 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0023
                         zf-C2HC_2  5 CpkCgRsF 12
                                      Cp+Cg  F
  gi|474934215|ref|YP_007687797.1|  8 CPYCGKEF 15
                                      ******99 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.022
                         zf-C2HC_2  1 elvpCpkCgRs 11
                                      ++v C +C R+
  gi|474934215|ref|YP_007687797.1| 22 QTVVCTHCRRK 32
                                      6999*****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1977.98
//
Query:       gi|474934216|ref|YP_007687798.1|  [L=572]
Description: Arabinose efflux permease [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-51  175.6  42.4    1.3e-51  175.6  42.4    1.9  2  MFS_1     Major Facilitator Superfamily
    8.5e-11   41.4  43.6    3.6e-09   36.0  11.1    2.9  2  Sugar_tr  Sugar (and other) transporter
    6.2e-05   21.6  25.6    0.00084   17.9  25.6    2.1  1  TRI12     Fungal trichothecene efflux pump (TRI12)


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.6  42.4   2.1e-55   1.3e-51       1     352 [.      23     418 ..      23     419 .. 0.85
   2 ?   -0.6   0.2     0.081   4.9e+02     152     178 ..     500     524 ..     486     547 .. 0.66

  Alignments for each domain:
  == domain 1  score: 175.6 bits;  conditional E-value: 2.1e-55
                             MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgll 77 
                                       l++a ++++l+ +i+g+  p  +a dl    s + +++t+y l   v++++ G lsd +Gr++++l+gl++f++g++
  gi|474934216|ref|YP_007687798.1|  23 LIFAMLIACLDGTIVGVCGP-KIAADLE-GNSLYAWMITAYLLCETVMIPLSGKLSDLYGRKPLFLIGLTIFVFGSF 97 
                                       679999**************.*******.**********************************************55 PP

                             MFS_1  78 lllfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgglla..sslgWra 152
                                       ++  ++s+++++v+r++qG+g+g+l+p++ a++ad++++ er+++ g l+a f++G+ +gpl+ggll+  + lgWr+
  gi|474934216|ref|YP_007687798.1|  98 AAGASTSMTMFIVCRAVQGVGGGILIPVATAAVADLYSPVERPKMQGALGAVFGIGSGIGPLIGGLLTesDMLGWRW 174
                                       555436666***********************************************************878899*** PP

                             MFS_1 153 vfyilaivsllafvlfllllpeepperkrkspkeee......................................... 188
                                       +fyi+ +++++a vl l  +p+++ ++k+  +++                                           
  gi|474934216|ref|YP_007687798.1| 175 AFYINIPLAIVAYVLTLKKFPAPEIDSKPIIDVKGMtvlsvmlldlvlffefagdeiawisiesgamiglfialmvv 251
                                       **************9999999999999999999999*******************************9999999999 PP

                             MFS_1 189 ....kgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlgls......glllaglllallal 255
                                           ++ +  p++    +ll ++     ++++++++++f ++++ + +y  + + ++      + ++ag l++l+++
  gi|474934216|ref|YP_007687798.1| 252 fvkiEQGALEPVLA--PHLLQNR----PIVIACIMMLIFGIAMMGSMTY-ASLFAITiliedhSTITAG-LYSLFMV 320
                                       97764444444444..6777777....5555555555666666666666.6666666666666434444.4555555 PP

                             MFS_1 256 vgail.allagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfglgfvfpsllalasdlapp 331
                                       +g+++   l+g+++ ++g r+ ++++ ++++++ l++  + + +s   +++ l+l+G glg++++++++ ++++ ++
  gi|474934216|ref|YP_007687798.1| 321 AGMVItVNLSGKFLEKTGYRFWIIIGTVITAASMLLMSKMTMDTSLNYYAVCLFLLGAGLGCMMATIMVGVQNSSSE 397
                                       44444488**********9666666666666666666666666777777779999********************** PP

                             MFS_1 332 eeagtasglfntagslggalg 352
                                       +e+g+ ++++n+++s+g+ +g
  gi|474934216|ref|YP_007687798.1| 398 KEMGMSTSAVNLLRSIGATVG 418
                                       ******************998 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.081
                             MFS_1 152 avfyilaivsllafvlfllllpeeppe 178
                                         f++ a+++l+ +v   ++++ ++  
  gi|474934216|ref|YP_007687798.1| 500 FGFVAGAVITLVIIV--PAFFFKPKFY 524
                                       456666677777644..5666666555 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0  11.1   6.1e-13   3.6e-09      45     187 ..      51     189 ..      39     193 .. 0.83
   2 !   12.8  21.3   6.7e-06      0.04      10     161 ..     280     425 ..     270     437 .. 0.86

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 6.1e-13
                                       ..HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHH CS
                          Sugar_tr  45 svlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasv 121
                                       ++l+ ++  ++l+ +++   ++g+l+d +GRk+ +li+ ++fv g++  +a++   s+ ++iv+R + G+g G+   
  gi|474934216|ref|YP_007687798.1|  51 NSLYAWMITAYLLCETVMIPLSGKLSDLYGRKPLFLIGLTIFVFGSFAAGAST---SMTMFIVCRAVQGVGGGILIP 124
                                       56788999999999999999*********************************...********************* PP

                                       HHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHH CS
                          Sugar_tr 122 lvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllil 187
                                       +++  ++ +  +  R ++ +       +G  ++  +g  l +++   gwr+ +++++ +a++  +l
  gi|474934216|ref|YP_007687798.1| 125 VATAAVADLYSPVERPKMQGALGAVFGIGSGIGPLIGGLLTESDM-LGWRWAFYINIPLAIVAYVL 189
                                       ***999998766666555555555555666666666666666666.89************765554 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 6.7e-06
                                       HHHHHHHHCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHH CS
                          Sugar_tr  10 llfgYdtgvigafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlf 86 
                                       ++  + ++++g++++ + fa     + +++      ++ gl   ++++G +i+  ++g++ ++ G++  ++i++v++
  gi|474934216|ref|YP_007687798.1| 280 MMLIFGIAMMGSMTYASLFAITILIEDHST------ITAGLYSLFMVAGMVITVNLSGKFLEKTGYRFWIIIGTVIT 350
                                       677777888888888888666666666665......44699999********************************* PP

                                       HHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Sugar_tr  87 vigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglgl 161
                                        ++ +l+   + ++s+  ++v+ +l+G g+G+  +++ + ++  + +k  g+ +s  +l  ++G  v++ + + +
  gi|474934216|ref|YP_007687798.1| 351 AASMLLMSKMTMDTSLNYYAVCLFLLGAGLGCMMATIMVGVQNSSSEKEMGMSTSAVNLLRSIGATVGTAIFAMV 425
                                       *****************************************************************9987665544 PP

>> TRI12  Fungal trichothecene efflux pump (TRI12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9  25.6   1.4e-07   0.00084      72     479 ..      46     440 ..      35     453 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.4e-07
                             TRI12  72 qdvgqsensslfstlwttgqavsilvmgrltdrfgrrpfvilthilglvgaivgctatkfntllaamtllgvaagpa 148
                                        d+      + + t + + ++v i + g+l+d +gr+p+ ++   + + g+    ++t +  ++ + ++ gv  g  
  gi|474934216|ref|YP_007687798.1|  46 ADLEGNSLYAWMITAYLLCETVMIPLSGKLSDLYGRKPLFLIGLTIFVFGSFAAGASTSMTMFIVCRAVQGVGGGIL 122
                                       55544444455567788899*******************999999999****99999999999*********99964 PP

                             TRI12 149 .gasplfvgelms..nktkflgllivsipvvvtsglspylgqrlaiqg..swrwifyiyiitsaiavllivvwyypp 220
                                          +   v +l s  ++ k+ g l       + sg++p +g  l+      wrw fyi i ++ +a +l +  +  p
  gi|474934216|ref|YP_007687798.1| 123 iPVATAAVADLYSpvERPKMQGALGA--VFGIGSGIGPLIGGLLTESDmlGWRWAFYINIPLAIVAYVLTLKKFPAP 197
                                       14567789999984457788887754..4456799*******997654227*********99999998887776666 PP

                             TRI12 221 sfaqlhgkkvrkreelakldwigiilvivgvslfllgvswggkpnspwnsakviglissglgslvvfalyevygkpv 297
                                        +     k          +d  g+ +++v    ++l   + g+    w s     +i   +  +vvf   e      
  gi|474934216|ref|YP_007687798.1| 198 EI---DSK--------PIIDVKGMTVLSVMLLDLVLFFEFAGDE-IAWISIESGAMIGLFIALMVVFVKIEQ--GAL 260
                                       54...333........4567777777777666667777888864.457665544444444566777776663..457 PP

                             TRI12 298 rpivppalfkdtrgfv..cilli...ssimgamnlslviiypqqvvnifgsslknweetawmsatasfgtgagvvvl 369
                                       +p++ p l+++   +v  ci+++    ++mg+m              +f  ++   + ++  +   s+   ag+v+ 
  gi|474934216|ref|YP_007687798.1| 261 EPVLAPHLLQNR-PIViaCIMMLifgIAMMGSMTY----------ASLFAITILIEDHSTITAGLYSLFMVAGMVIT 326
                                       799999998764.4441254432111133444433..........34444444444444444455666677777776 PP

                             TRI12 370 gsl...fhlvrhirwqilvgalwltaflgamssvnrdnknaaials.vlsgfvvawaqditmllvqfittdedlgva 442
                                        +l   f      r+ i++g++  +a +  ms +  d      a+  +l g  ++      m+ vq  ++++++g++
  gi|474934216|ref|YP_007687798.1| 327 VNLsgkFLEKTGYRFWIIIGTVITAASMLLMSKMTMDTSLNYYAVClFLLGAGLGCMMATIMVGVQNSSSEKEMGMS 403
                                       6552214444567999*********************987766665256788999999999**************** PP

                             TRI12 443 favvaaarpfagsiftaafislysnrypkelashlss 479
                                        + v   r +  ++ ta f  + sn+   el   l +
  gi|474934216|ref|YP_007687798.1| 404 TSAVNLLRSIGATVGTAIFAMVISNKIGSELDKNLPA 440
                                       ****************************999988764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (572 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       890  (0.0496402); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.47
# Mc/sec: 3663.14
//
Query:       gi|474934217|ref|YP_007687799.1|  [L=291]
Description: Transcriptional regulator [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-06   28.3   0.0    9.7e-06   25.6   0.0    2.1  2  HTH_28        Helix-turn-helix domain
    2.3e-05   24.2   0.0    0.00033   20.5   0.0    2.2  2  TrmB          Sugar-specific transcriptional regulator TrmB
    6.8e-05   22.7   0.0      0.014   15.3   0.0    2.4  2  MarR          MarR family
    8.3e-05   22.3   0.0    0.00021   21.0   0.0    1.6  1  HTH_23        Homeodomain-like domain
    0.00012   21.8   0.0     0.0042   16.9   0.0    2.3  2  MarR_2        MarR family
    0.00028   20.5   0.5     0.0009   18.9   0.0    2.0  2  Sigma70_r4_2  Sigma-70, region 4
    0.00093   19.2   0.2      0.043   13.8   0.1    2.3  2  HTH_29        Winged helix-turn helix
    0.00095   18.9   0.0       0.74    9.7   0.0    2.6  2  HTH_IclR      IclR helix-turn-helix domain
     0.0014   19.1   0.0     0.0026   18.2   0.0    1.4  1  HTH_27        Winged helix DNA-binding domain
     0.0019   17.7   0.0       0.35   10.5   0.0    2.5  2  HTH_24        Winged helix-turn-helix DNA-binding
     0.0023   17.0   0.1      0.024   13.6   0.1    2.1  2  TnsD          Tn7-like transposition protein D
     0.0025   17.2   0.0     0.0057   16.1   0.0    1.5  1  HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family I
     0.0028   17.4   0.0     0.0053   16.5   0.0    1.5  1  DUF4364       Domain of unknown function (DUF4364)
     0.0037   17.5   0.0     0.0079   16.5   0.0    1.5  1  HTH_Tnp_1     Transposase
     0.0068   16.4   0.0      0.014   15.4   0.0    1.4  1  HTH_45        Winged helix-turn-helix
     0.0078   16.2   0.1      0.014   15.3   0.1    1.4  1  DUF3137       Protein of unknown function (DUF3137)
  ------ inclusion threshold ------
      0.012   15.1   0.0       0.03   13.9   0.0    1.6  1  GerE          Bacterial regulatory proteins, luxR family
      0.014   15.4   0.0      0.051   13.6   0.0    1.9  1  HTH_7         Helix-turn-helix domain of resolvase
      0.018   15.0   0.1        1.2    9.1   0.0    2.5  2  HTH_Crp_2     Crp-like helix-turn-helix domain
      0.025   14.1   0.1       0.68    9.5   0.0    2.9  3  Sigma70_r4    Sigma-70, region 4
      0.027   14.9   0.0       0.22   12.0   0.0    2.2  2  HTH_40        Helix-turn-helix domain
      0.028   14.6   0.0       0.35   11.1   0.0    2.4  2  HTH_17        Helix-turn-helix domain
      0.037   13.9   0.0        3.3    7.6   0.0    2.4  2  HTH_5         Bacterial regulatory protein, arsR family
      0.047   13.4   0.0      0.082   12.7   0.0    1.4  1  HTH_psq       helix-turn-helix, Psq domain
      0.053   14.0   0.1         27    5.3   0.0    2.8  3  PCI           PCI domain
      0.088   12.9   0.0       0.29   11.2   0.0    1.9  1  HemN_C        HemN C-terminal domain
       0.11   13.0   0.1       0.27   11.7   0.1    1.6  1  HTH_26        Cro/C1-type HTH DNA-binding domain
       0.12   12.2   0.0       0.68    9.8   0.0    2.1  2  DUF1495       Winged helix DNA-binding domain (DUF1495)
       0.12   12.2   0.4       0.24   11.3   0.0    1.6  1  Sigma70_ECF   ECF sigma factor
       0.12   12.4   0.0       0.37   10.9   0.0    1.8  1  HTH_3         Helix-turn-helix
       0.14   12.3   0.3        1.1    9.4   0.1    2.3  2  DUF2802       Protein of unknown function (DUF2802)
       0.19   11.5   0.7       0.65    9.8   0.0    2.3  2  HTH_38        Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   1.7e-08   9.7e-06       4      33 ..      76     105 ..      76     110 .. 0.94
   2 ?   -0.3   0.0       2.2   1.2e+03      13      34 ..     188     209 ..     178     218 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.7e-08
                            HTH_28   4 eiikllaaGhsvreaArelgisrrtvyrWi 33 
                                       e++++l++G+sv+e+A +lg+s+ tv+rW 
  gi|474934217|ref|YP_007687799.1|  76 EAMECLQSGMSVSETASKLGLSSATVRRWY 105
                                       6899*************************6 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 2.2
                            HTH_28  13 hsvreaArelgisrrtvyrWik 34 
                                       ++ re A+ l  +r++++  +k
  gi|474934217|ref|YP_007687799.1| 188 MTLREFANVLPFDRSRISFVLK 209
                                       589999****9****9998887 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.68   3.8e+02      22      45 ..      84     107 ..      81     111 .. 0.81
   2 !   20.5   0.0   5.9e-07   0.00033      17      66 ..     182     232 ..     167     233 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.68
                                       CCHHCHHCCCTTSSCHCHHHHHHH CS
                              TrmB  22 patadeiaeelgvprskvYevLrs 45 
                                        ++++e a++lg++ ++v +  ++
  gi|474934217|ref|YP_007687799.1|  84 GMSVSETASKLGLSSATVRRWYSN 107
                                       68899***********99876555 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 5.9e-07
                                       HHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.TTEEEE-- CS
                              TrmB  17 LlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.pklYravd 66 
                                       L ++ ++t +e a+ l  +rs++  vL++++d G+V+ e  + p +Y+ ++
  gi|474934217|ref|YP_007687799.1| 182 LGAQPRMTLREFANVLPFDRSRISFVLKEMIDQGFVTQENDQkPAKYSLTP 232
                                       5577899*******************************9955599**8765 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.048        27      17      37 ..      84     104 ..      81     109 .. 0.88
   2 !   15.3   0.0   2.4e-05     0.014      10      50 ..     180     220 ..     172     224 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.048
                                       TEEHHHHHHHHTS-HHHHHHH CS
                              MarR  17 plsvseLakklgvskstvtrv 37 
                                       ++svse a+klg+s++tv r+
  gi|474934217|ref|YP_007687799.1|  84 GMSVSETASKLGLSSATVRRW 104
                                       799**************9876 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2.4e-05
                                       HHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR  10 rilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50 
                                        +l  q+ +++ e a+ l  ++s ++ vl++++++G+++ +
  gi|474934217|ref|YP_007687799.1| 180 LKLGAQPRMTLREFANVLPFDRSRISFVLKEMIDQGFVTQE 220
                                       67899*********************************866 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   3.7e-07   0.00021      13      39 ..      80     106 ..      76     115 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3.7e-07
                            HTH_23  13 llaeGlsvreIAreLgvsrrTvyrwlk 39 
                                        l+ G+sv+e A +Lg s  Tv+rw +
  gi|474934217|ref|YP_007687799.1|  80 CLQSGMSVSETASKLGLSSATVRRWYS 106
                                       4455*********************76 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.28   1.5e+02      19      40 ..      84     103 ..      76     106 .. 0.87
   2 !   16.9   0.0   7.5e-06    0.0042      14      56 ..     182     222 ..     168     227 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.28
                                       TSEEEHHHHHHHHTSSHHHHHH CS
                            MarR_2  19 grdltvgelarrlglsksavsr 40 
                                       g  ++v+e a +lgls ++v r
  gi|474934217|ref|YP_007687799.1|  84 G--MSVSETASKLGLSSATVRR 103
                                       3..899*************976 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 7.5e-06
                                       HHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2  14 LgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56 
                                       Lg+ p  ++t +e a  l  ++s++s +lk++ ++G+v+++ +
  gi|474934217|ref|YP_007687799.1| 182 LGAQP--RMTLREFANVLPFDRSRISFVLKEMIDQGFVTQEND 222
                                       45555..5******************************99865 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.6e-06    0.0009      26      48 ..      84     106 ..      80     107 .. 0.94
   2 ?   -1.8   0.1       4.5   2.5e+03       9      24 ..     239     253 ..     236     260 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.6e-06
                                       ---HHHHHHHHT--HHHHHHHHH CS
                      Sigma70_r4_2  26 glsykEIAellgisegtVksrls 48 
                                       g+s  E+A++lg+s++tV++++s
  gi|474934217|ref|YP_007687799.1|  84 GMSVSETASKLGLSSATVRRWYS 106
                                       9********************97 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.5
                                       TTS-HHHHHHHHHHHT CS
                      Sigma70_r4_2   9 aeLperqreifllryl 24 
                                       ++L e  r +f +  +
  gi|474934217|ref|YP_007687799.1| 239 ERLRELSRNVFRMV-F 253
                                       67888899999984.4 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   7.7e-05     0.043       9      32 ..      82     104 ..      76     106 .. 0.92
   2 ?    2.9   0.0      0.21   1.2e+02      29      59 ..     249     277 ..     242     277 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.7e-05
                            HTH_29   9 aeGvstvsqiAkllglsrrtvyrw 32 
                                         G+s vs+ A  lgls  tv+rw
  gi|474934217|ref|YP_007687799.1|  82 QSGMS-VSETASKLGLSSATVRRW 104
                                       67998.****************** PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.21
                            HTH_29  29 vyrwlkrfeegGlaalld.rrrsgrprnrlse 59 
                                       ++ +  +f e++    +  r++ gr++nrl+e
  gi|474934217|ref|YP_007687799.1| 249 FRMVFAAFSEEE---SMQiRKGIGRLNNRLDE 277
                                       555556677777...77889**********97 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0    0.0013      0.74      17      37 ..      83     103 ..      76     110 .. 0.89
   2 ?    6.5   0.0     0.013       7.3      15      51 ..     184     220 ..     182     221 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0013
                                       SS-BHHHHHHHHTS-HHHHHH CS
                          HTH_IclR  17 qeltlselArrtglpkStvhR 37 
                                        ++++se A ++gl+ +tv+R
  gi|474934217|ref|YP_007687799.1|  83 SGMSVSETASKLGLSSATVRR 103
                                       689*****************9 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.013
                                       TBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR  15 apqeltlselArrtglpkStvhRlLqtLvelGyveqd 51 
                                       a++++tl+e A+ +   +S  +  L+ ++ +G+v+q+
  gi|474934217|ref|YP_007687799.1| 184 AQPRMTLREFANVLPFDRSRISFVLKEMIDQGFVTQE 220
                                       45569******************************96 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   4.7e-06    0.0026      14      68 .]     183     234 ..     174     234 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4.7e-06
                            HTH_27  14 hrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68 
                                       + + r++l++ + +l ++ s is +lk+++ +G+v   + e d+++  ++lT+ G
  gi|474934217|ref|YP_007687799.1| 183 GAQPRMTLREFANVLPFDRSRISFVLKEMIDQGFV---TQENDQKPAKYSLTPQG 234
                                       56789999***************************...777999*********98 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   0.00062      0.35      16      36 ..      83     103 ..      78     108 .. 0.92
   2 ?    4.6   0.0     0.043        24      14      48 .]     184     218 ..     181     218 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00062
                            HTH_24  16 prisqreLAerlglSpstvnr 36 
                                       +++s +e A +lglS++tv+r
  gi|474934217|ref|YP_007687799.1|  83 SGMSVSETASKLGLSSATVRR 103
                                       699****************97 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.043
                            HTH_24  14 knprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                       ++pr++ re A  l   +s ++  lk+++++G+++
  gi|474934217|ref|YP_007687799.1| 184 AQPRMTLREFANVLPFDRSRISFVLKEMIDQGFVT 218
                                       68999999999999999***************996 PP

>> TnsD  Tn7-like transposition protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.1   4.3e-05     0.024     122     224 ..      14     109 ..       7     142 .. 0.77
   2 ?    0.9   0.0      0.32   1.8e+02     196     267 ..     184     265 ..     169     275 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.3e-05
                              TnsD 122 pClNpaadhylkpvikevkikynkdtk.kpigtfsC.scGfsytrsgedlseedayrisrikkfGivweerlkeLve 196
                                       +C+N+ ++ y ++   ++  +  ++ + +++ +f C  cG ++  +   + e  ++++++       ++e+++ L +
  gi|474934217|ref|YP_007687799.1|  14 ACPNRDCEKYGQTGQGNIVGNGTYKASgEVVRKFLCrCCGHTFNSRTGTVYEGIRTNVDK-------MDEAMECLQS 83 
                                       8**********999888877666665568*******999999988866666654555554.......5677777776 PP

                              TnsD 197 eeglslkeiAkelgvdiktVlryakklg 224
                                         g+s+ e+A+ lg++  tV+r  ++  
  gi|474934217|ref|YP_007687799.1|  84 --GMSVSETASKLGLSSATVRRWYSNMA 109
                                       ..*******************9876655 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.32
                              TnsD 196 eeeglslkeiAkelgvdiktVlryakklgllkekkkqkkesrelsskd............rekkrkewleliksypd 260
                                       ++  ++l+e A+ l +d +++  ++k+ +++   ++ ++++  +   +            re +r+ ++ + +++++
  gi|474934217|ref|YP_007687799.1| 184 AQPRMTLREFANVLPFDRSRISFVLKEMIDQGFVTQENDQKPAKY--SltpqgmeqyerlRELSRNVFRMVFAAFSE 258
                                       556799999999999999999999998877765444444444333..233556666666666666666666666666 PP

                              TnsD 261 lgktelr 267
                                           ++r
  gi|474934217|ref|YP_007687799.1| 259 EESMQIR 265
                                       6555555 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0     1e-05    0.0057      22      48 ..      78     105 ..      77     107 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1e-05
                      HTH_Tnp_ISL3  22 ellles.rsvkavArqlgvSwtTVwril 48 
                                       +++l+s +sv++ A  lg+S  TV+r++
  gi|474934217|ref|YP_007687799.1|  78 MECLQSgMSVSETASKLGLSSATVRRWY 105
                                       5677888*******************97 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   9.5e-06    0.0053      39      81 ..     207     248 ..     202     269 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 9.5e-06
                           DUF4364  39 alseLvesglieeeekenktlykiTekGketlelfenripksi 81 
                                       +l+e++++g++++e++++   y++T++G e  e + +  + ++
  gi|474934217|ref|YP_007687799.1| 207 VLKEMIDQGFVTQENDQKPAKYSLTPQGMEQYERLREL-SRNV 248
                                       79****************************99988654.3333 PP

>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.4e-05    0.0079      18      47 ..      79     108 ..      73     129 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.4e-05
                         HTH_Tnp_1  18 eslepgksvsevArrhgvspnqLykWrrqy 47 
                                       e l++g svse+A ++g+s ++ ++W +  
  gi|474934217|ref|YP_007687799.1|  79 ECLQSGMSVSETASKLGLSSATVRRWYSNM 108
                                       6799**********************8766 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   2.5e-05     0.014      39      74 ..     207     246 ..     198     248 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.5e-05
                            HTH_45  39 YLdmLvekgli....kkskekYvlTekGlelleklkelee 74 
                                        L+ ++++g++    +++  kY+lT +G+e +e+l+el +
  gi|474934217|ref|YP_007687799.1| 207 VLKEMIDQGFVtqenDQKPAKYSLTPQGMEQYERLRELSR 246
                                       599********8866667789***************9876 PP

>> DUF3137  Protein of unknown function (DUF3137)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   2.5e-05     0.014      48      88 ..     212     255 ..     190     265 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.5e-05
                           DUF3137  48 FekkFeVysndqvearyiLtpalmerllelrekfkg...kikas 88 
                                        ++ F +  ndq  a+y Ltp+ me+  +lre +++    ++a+
  gi|474934217|ref|YP_007687799.1| 212 IDQGFVTQENDQKPAKYSLTPQGMEQYERLRELSRNvfrMVFAA 255
                                       678899******************99888887777733244455 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   5.4e-05      0.03      10      41 ..      77     108 ..      75     110 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.4e-05
                                       HHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHH CS
                              GerE  10 vLrllaeGksnkeIAeelniSekTVkvhksni 41 
                                        +++l +G+s+ e A++l++S  TV+   sn+
  gi|474934217|ref|YP_007687799.1|  77 AMECLQSGMSVSETASKLGLSSATVRRWYSNM 108
                                       6999*********************9777776 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   9.2e-05     0.051      10      40 ..      73     103 ..      67     106 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.2e-05
                                       HHGGGGSSTTTT--STTTSSSS---SSSS-- CS
                             HTH_7  10 dinrvvkLleeGisiskIAkevnisRsTvYR 40 
                                       +++++ + l++G+s+s++A  +++s +Tv R
  gi|474934217|ref|YP_007687799.1|  73 KMDEAMECLQSGMSVSETASKLGLSSATVRR 103
                                       69**************************977 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.15        83      18      45 ..      81     108 ..      46     114 .. 0.82
   2 ?    9.1   0.0    0.0022       1.2      20      53 ..     182     219 ..     152     225 .. 0.65

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.15
                                       EEEEHHHHHHHHHTTSSHHHHHHHHHHH CS
                         HTH_Crp_2  18 ielpltqeelAsmlGltretvsrilseL 45 
                                       ++  ++  e As lGl+  tv r  s +
  gi|474934217|ref|YP_007687799.1|  81 LQSGMSVSETASKLGLSSATVRRWYSNM 108
                                       5567899999***********9977766 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0022
                                       E....EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEE CS
                         HTH_Crp_2  20 l....pltqeelAsmlGltretvsrilseLkreglisr 53 
                                       l    ++t +e A+ l   r+ +s +l+e+ ++g +++
  gi|474934217|ref|YP_007687799.1| 182 LgaqpRMTLREFANVLPFDRSRISFVLKEMIDQGFVTQ 219
                                       233339****************************9984 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0    0.0012      0.68      20      39 ..      84     103 ..      80     107 .. 0.92
   2 ?   -0.7   0.0       1.9     1e+03      20      38 ..     187     205 ..     178     213 .. 0.82
   3 ?   -0.1   0.1       1.2   6.9e+02       4      18 ..     240     258 ..     239     263 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0012
                                       T--HHHHHHHHTS-HHHHHH CS
                        Sigma70_r4  20 glTleEIgerlgiSrerVrq 39 
                                       g++ +E++ +lg+S  +Vr+
  gi|474934217|ref|YP_007687799.1|  84 GMSVSETASKLGLSSATVRR 103
                                       799****************8 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.9
                                       T--HHHHHHHHTS-HHHHH CS
                        Sigma70_r4  20 glTleEIgerlgiSrerVr 38 
                                        +Tl E +++l   r+r++
  gi|474934217|ref|YP_007687799.1| 187 RMTLREFANVLPFDRSRIS 205
                                       5899999999999999998 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 1.2
                                       HS-HHHHHHHHHHH....T CS
                        Sigma70_r4   4 sLpererevlelrf....g 18 
                                       +L e  r+v++++f    +
  gi|474934217|ref|YP_007687799.1| 240 RLRELSRNVFRMVFaafsE 258
                                       688889******9977643 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00039      0.22       3      32 ..      75     104 ..      73     135 .. 0.80
   2 ?    0.0   0.0       2.2   1.2e+03      49      77 ..     256     283 ..     236     289 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00039
                            HTH_40   3 eetlelleeglsieeIAkerglkesTIegH 32 
                                       +e++e l++g+s+ e A + gl+ +T+ + 
  gi|474934217|ref|YP_007687799.1|  75 DEAMECLQSGMSVSETASKLGLSSATVRRW 104
                                       68899**********************765 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 2.2
                            HTH_40  49 vseeeekeIeeaiekvgseklkpikealp 77 
                                       +seee  +I++ i +++ ++l +i ++  
  gi|474934217|ref|YP_007687799.1| 256 FSEEESMQIRKGIGRLN-NRLDEISDQIS 283
                                       47888888888888877.77888877764 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00062      0.35       2      21 ..      85     104 ..      85     107 .. 0.95
   2 ?    0.5   0.0       1.3   7.2e+02       2      18 ..     188     204 ..     187     213 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00062
                            HTH_17   2 ltveEaAelLgvsrstvyrl 21 
                                       ++v+E A  Lg+s +tv+r+
  gi|474934217|ref|YP_007687799.1|  85 MSVSETASKLGLSSATVRRW 104
                                       89*****************9 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.3
                            HTH_17   2 ltveEaAelLgvsrstv 18 
                                       +t  E+A+ L   rs +
  gi|474934217|ref|YP_007687799.1| 188 MTLREFANVLPFDRSRI 204
                                       899*******9998876 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0     0.006       3.3      16      34 ..      85     103 ..      78     104 .. 0.89
   2 ?    3.8   0.0     0.097        55      16      46 ..     188     218 ..     178     219 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.006
                                       EEHHHHHHHHTS-HHHHHH CS
                             HTH_5  16 lcvcelaeelglsqstvSh 34 
                                       ++v+e a +lgls +tv++
  gi|474934217|ref|YP_007687799.1|  85 MSVSETASKLGLSSATVRR 103
                                       99***************86 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.097
                                       EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  16 lcvcelaeelglsqstvShHLkkLreaGLVe 46 
                                       ++  e a+ l   +s +S  Lk + ++G+V+
  gi|474934217|ref|YP_007687799.1| 188 MTLREFANVLPFDRSRISFVLKEMIDQGFVT 218
                                       77888888999999***************96 PP

>> HTH_psq  helix-turn-helix, Psq domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00015     0.082       3      39 ..      72     107 ..      71     113 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00015
                           HTH_psq   3 ealaaAleavvnGkmSirkAArkYgiPrsTLwrrkrg 39 
                                       +++++A e  ++G mS+++ A+k g +  T +r ++ 
  gi|474934217|ref|YP_007687799.1|  72 DKMDEAMECLQSG-MSVSETASKLGLSSATVRRWYSN 107
                                       89***********.*************9998887765 PP

>> PCI  PCI domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.058        32      61      97 ..      85     121 ..      67     124 .. 0.87
   2 ?    5.3   0.0     0.048        27      48      91 ..     173     218 ..     152     226 .. 0.83
   3 ?   -0.7   0.0       3.7   2.1e+03      37      56 ..     237     258 ..     219     267 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.058
                                       EEHHHHHHHHTSSHHHHHHHHHHHHHTTSSSEEEETT CS
                               PCI  61 islerlaklldlsvdevEkilvklIrdgeirakidqe 97 
                                        s+++ a++l+ls+  v ++ +++ +  +++  +d++
  gi|474934217|ref|YP_007687799.1|  85 MSVSETASKLGLSSATVRRWYSNMASVSRLQPMMDST 121
                                       578999********************99998777765 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.048
                                       HHHHHHHHH..CESEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSSS CS
                               PCI  48 erllrqvsk..iyssislerlaklldlsvdevEkilvklIrdgeir 91 
                                       ++ +  v k   + + +l ++a+ l+++ + +  +l ++I +g++ 
  gi|474934217|ref|YP_007687799.1| 173 RHHIAFVLKlgAQPRMTLREFANVLPFDRSRISFVLKEMIDQGFVT 218
                                       5555555556667788999************************987 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 3.7
                                       H..HHHHHHHHHHHHHHHHHHH CS
                               PCI  37 q..llesLekkvrerllrqvsk 56 
                                       q   l +L ++v ++++  +s+
  gi|474934217|ref|YP_007687799.1| 237 QyeRLRELSRNVFRMVFAAFSE 258
                                       4447889999999999877776 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00052      0.29      23      65 ..     190     235 ..     185     236 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00052
                            HemN_C  23 laafeqrfgldleellaaaleklqeqGLLeldg....grlrltprGr 65 
                                       l++f+   + d   +  ++l+++++qG++++++     +++ltp+G+
  gi|474934217|ref|YP_007687799.1| 190 LREFANVLPFDR-SRISFVLKEMIDQGFVTQENdqkpAKYSLTPQGM 235
                                       677778888884.44599***************99999999999997 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00049      0.27       8      38 ..      82     111 ..      77     118 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00049
                            HTH_26   8 drgitkseLargtgisaatlsrlvkgkperv 38 
                                       + g+++se a ++g+s+at+ r++++ + +v
  gi|474934217|ref|YP_007687799.1|  82 QSGMSVSETASKLGLSSATVRRWYSNMA-SV 111
                                       5799*********************975.44 PP

>> DUF1495  Winged helix DNA-binding domain (DUF1495)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       2.2   1.3e+03      16      66 ..      46      98 ..      42     109 .. 0.68
   2 ?    9.8   0.0    0.0012      0.68      59      89 ..     211     240 ..     207     241 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2.2
                           DUF1495 16 lyLysiypeksn..lqeisrrvrskpsnvkGaleGmgkrynsessLielGLve 66
                                       +L++ + ++ n  +  + + +r+++ ++  a+e  +  ++ ++   +lGL +
  gi|474934217|ref|YP_007687799.1| 46 KFLCRCCGHTFNsrTGTVYEGIRTNVDKMDEAMECLQSGMSVSETASKLGLSS 98
                                      56777666654411445677788888888888888888888887777777764 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0012
                           DUF1495  59 LielGLveeeeeseglklYklteeGieivev 89 
                                       +i +G v+ +e+++  + Y+lt++G+e  e+
  gi|474934217|ref|YP_007687799.1| 211 MIDQGFVT-QENDQKPAKYSLTPQGMEQYER 240
                                       799****6.68899999********997765 PP

>> Sigma70_ECF  ECF sigma factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00043      0.24     150     171 ..      83     104 ..      68     113 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00043
                       Sigma70_ECF 150 eGlsveEiAeklgvskrtverr 171
                                       +G+sv E+A klg+s +tv+r 
  gi|474934217|ref|YP_007687799.1|  83 SGMSVSETASKLGLSSATVRRW 104
                                       7******************885 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00067      0.37       6      30 ..      81     105 ..      76     114 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00067
                                       HHTTHHHHHHHHHHTSSHHHHHHHH CS
                             HTH_3   6 kqlglsqeeLAeklGvsrstisriE 30 
                                       +q g+s  e A klG+s +t++r+ 
  gi|474934217|ref|YP_007687799.1|  81 LQSGMSVSETASKLGLSSATVRRWY 105
                                       599********************95 PP

>> DUF2802  Protein of unknown function (DUF2802)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.1     0.002       1.1      34      58 ..      75      99 ..      67     100 .. 0.92
   2 ?   -0.5   0.0       2.4   1.4e+03       5      23 ..     267     285 ..     263     289 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.002
                           DUF2802 34 sqAiklvrqGasveelaeecgLsra 58
                                      ++A++ +++G+sv+e a++ gLs a
  gi|474934217|ref|YP_007687799.1| 75 DEAMECLQSGMSVSETASKLGLSSA 99
                                      78********************976 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2.4
                           DUF2802   5 rlaelekrlkqleerleel 23 
                                        + +l++rl+++++++++ 
  gi|474934217|ref|YP_007687799.1| 267 GIGRLNNRLDEISDQISSR 285
                                       5677888888888888765 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0    0.0012      0.65      17      39 ..      81     103 ..      76     104 .. 0.92
   2 ?   -2.7   0.0       9.1   5.1e+03      24      37 ..     191     204 ..     187     215 .. 0.53

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0012
                            HTH_38  17 laeGlslreIArrLgrspsTIsR 39 
                                       l+ G+s++e A +Lg s  T+ R
  gi|474934217|ref|YP_007687799.1|  81 LQSGMSVSETASKLGLSSATVRR 103
                                       789******************98 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 9.1
                            HTH_38  24 reIArrLgrspsTI 37 
                                       re A  L  ++s I
  gi|474934217|ref|YP_007687799.1| 191 REFANVLPFDRSRI 204
                                       55555554444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       802  (0.044732); expected 358.6 (0.02)
Passed bias filter:                      667  (0.0372023); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); expected 17.9 (0.001)
Passed Fwd filter:                        32  (0.00178482); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              32  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 1946.35
//
Query:       gi|474934218|ref|YP_007687800.1|  [L=232]
Description: FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-10   40.0   0.1    6.5e-10   39.0   0.1    1.6  1  FKBP26_C  FKBP26_C-terminal
    1.5e-08   34.9   0.0    5.8e-08   32.9   0.0    2.1  2  FKBP_C    FKBP-type peptidyl-prolyl cis-trans isomerase


Domain annotation for each model (and alignments):
>> FKBP26_C  FKBP26_C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.1   7.2e-14   6.5e-10       8      70 ..     161     220 ..     154     222 .. 0.87

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 7.2e-14
                                       HHHHH-TT--..--EEEEETTEEEEE--TTGGGSTTHHHHHHHHHHHHHHH-TTEEEEEEEEE CS
                          FKBP26_C   8 lIkryiPnidlekfkieiedktvtIelpeeakFieniqlaklrIAkdilkrieevekVkFvde 70 
                                       +++     +  ++fk+ + +++vt++lpe +kF+++  +a++r++ d+++ + +v++V+Fv++
  gi|474934218|ref|YP_007687800.1| 161 IVEADFGPA--DEFKFDFPGEKVTVTLPEITKFHQEWPVARFRVVSDLREAF-GVDTVEFVEI 220
                                       555554444..59***************************************.********97 PP

>> FKBP_C  FKBP-type peptidyl-prolyl cis-trans isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0   6.5e-12   5.8e-08       7      73 ..       4      84 ..       1     150 [. 0.88
   2 ?   -1.3   0.0      0.31   2.8e+03      58      73 ..     178     193 ..     177     212 .. 0.87

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 6.5e-12
                                      TTCEEEEEEEEEET.TSSEEEEH..........CC...HTSEEEEETTSSSSCHHHHHHHTTSBTT-EEEEEEEGGGTT CS
                            FKBP_C  7 egdtVtvhykgkle.dgkvfdss..........rs...rakplefkvGsgqvikGfeealegmkvGekrtltippelaY 71
                                       +++++++yk++l+  +k  d++          ++    +kp+   vGs+++ +++++a+   kvGe+ t++ip e++ 
  gi|474934218|ref|YP_007687800.1|  4 AKKVIRLNYKAYLAdSEKMYDTTdeaaakdagiYNekvSYKPMAYIVGSNKLFPALDKAIADAKVGEEFTVEIPCEEGA 82
                                      567899********445555666999999999854668*************************************9986 PP

                                      TT CS
                            FKBP_C 72 ge 73
                                      g 
  gi|474934218|ref|YP_007687800.1| 83 GV 84
                                      65 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.31
                                       T-EEEEEEEGGGTTTT CS
                            FKBP_C  58 GekrtltippelaYge 73 
                                       Gek t+t p   ++++
  gi|474934218|ref|YP_007687800.1| 178 GEKVTVTLPEITKFHQ 193
                                       9999999998888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1683.83
//
Query:       gi|474934219|ref|YP_007687801.1|  [L=150]
Description: hypothetical protein TALC_00644 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0052   16.9  10.2       0.02   15.0   0.2    2.8  2  Zn-ribbon_8      Zinc ribbon domain
     0.0054   16.5   0.3     0.0054   16.5   0.3    2.4  2  DUF3039          Protein of unknown function (DUF3039)
     0.0076   16.3  11.3        0.3   11.1   3.0    2.2  2  HypA             Hydrogenase/urease nickel incorporation, met
  ------ inclusion threshold ------
      0.016   15.3  19.2       0.73   10.0   0.2    4.3  4  UPF0547          Uncharacterised protein family UPF0547
      0.021   14.7  12.9       0.23   11.4   1.0    2.4  2  zf-C3HC4_3       Zinc finger, C3HC4 type (RING finger)
      0.025   14.7   0.0      0.044   13.9   0.0    1.4  1  HTH_7            Helix-turn-helix domain of resolvase
      0.082   12.6   0.0       0.11   12.2   0.0    1.2  1  CT_C_D           Carboxyltransferase domain, subdomain C and 
       0.12   12.3  12.1       0.11   12.4   8.7    2.5  3  C1_1             Phorbol esters/diacylglycerol binding domain
       0.15   11.8   0.0       0.31   10.8   0.0    1.5  1  HTH_38           Helix-turn-helix domain
       0.66    9.8   8.7        3.4    7.5   1.7    2.2  2  MCM_OB           MCM OB domain
       0.69    9.9   8.3        0.7    9.9   0.2    2.2  2  DUF1451          Zinc-ribbon containing domain
        3.4    8.4   6.7        1.2    9.8   0.6    2.2  2  FYDLN_acid       Protein of unknown function (FYDLN_acid)
          5    7.3  10.1       0.13   12.4   1.3    2.4  3  Ribosomal_L37ae  Ribosomal L37ae protein family
        5.8    6.9  20.0        1.8    8.5   0.2    4.1  4  TFIIS_C          Transcription factor S-II (TFIIS)


Domain annotation for each model (and alignments):
>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   1.5e-05      0.02       6      36 ..      20      48 ..      19      50 .. 0.78
   2 ?    3.6   5.2     0.056        72       7      34 ..      57      80 ..      52      83 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.5e-05
                       Zn-ribbon_8  6 YrCeeCghefevlqsisdaplta.CPeCgsev 36
                                      Y C  Cgh      s +d+  ++ CP+C s+v
  gi|474934219|ref|YP_007687801.1| 20 YTCALCGHNWV---SRKDNGVPKsCPKCRSTV 48
                                      99*****7665...4456777777****9975 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.056
                       Zn-ribbon_8  7 rCeeCghefevlqsisdapltaCPeCgs 34
                                      +C +Cg    ++ s +++p   CP C+ 
  gi|474934219|ref|YP_007687801.1| 57 ECVRCGY---KWGSTHERP-SRCPGCHT 80
                                      4999994...455555544.56****96 PP

>> DUF3039  Protein of unknown function (DUF3039)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.3   4.2e-06    0.0054      27      51 ..      22      46 ..       7      51 .. 0.82
   2 ?    0.2   3.2      0.51   6.5e+02      30      48 ..      61      80 ..      58      83 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.2e-06
                           DUF3039 27 vALCGkvwvptrdpkkfPvCpeCke 51
                                       ALCG+ wv  +d      Cp+C+ 
  gi|474934219|ref|YP_007687801.1| 22 CALCGHNWVSRKDNGVPKSCPKCRS 46
                                      6*******98888776668****86 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.51
                           DUF3039 30 CGkvwvptrd.pkkfPvCpe 48
                                      CG  w  t++ p++ P C +
  gi|474934219|ref|YP_007687801.1| 61 CGYKWGSTHErPSRCPGCHT 80
                                      *****988762669888865 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   1.1   0.00042      0.53      70      95 ..      19      47 ..      14      52 .. 0.79
   2 !   11.1   3.0   0.00023       0.3      70      99 ..      55      85 ..      48      90 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00042
                                      EEEETTTS-EEECHHH...HHS-TTTSSS CS
                              HypA 70 kvrCreCgkefeleek...alrCpkCgsa 95
                                      +++C  Cg+++ ++++     +CpkC s+
  gi|474934219|ref|YP_007687801.1| 19 VYTCALCGHNWVSRKDngvPKSCPKCRST 47
                                      578*********8774345559****986 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00023
                                      EEEETTTS-EEECHHH.HHS-TTTSSS-EEE CS
                              HypA 70 kvrCreCgkefeleek.alrCpkCgsadvei 99
                                      +++C +Cg+++ ++++   rCp C++++ ++
  gi|474934219|ref|YP_007687801.1| 55 VCECVRCGYKWGSTHErPSRCPGCHTTKWDV 85
                                      689*********77644789*****998765 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.2   0.00057      0.73      16      25 ..      21      30 ..      18      31 .. 0.85
   2 ?    7.9   0.4    0.0025       3.3       1      10 [.      39      48 ..      39      49 .. 0.93
   3 ?    3.3   2.9     0.071        90      16      24 ..      57      65 ..      53      67 .. 0.83
   4 ?    4.5   0.2      0.03        39       2       9 ..      74      81 ..      74      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00057
                           UPF0547 16 fCphCGyvFq 25
                                       C++CG+ + 
  gi|474934219|ref|YP_007687801.1| 21 TCALCGHNWV 30
                                      6********7 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0025
                           UPF0547  1 KvCPeCeakv 10
                                      K CP C+++v
  gi|474934219|ref|YP_007687801.1| 39 KSCPKCRSTV 48
                                      99*****998 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.071
                           UPF0547 16 fCphCGyvF 24
                                      +C  CGy +
  gi|474934219|ref|YP_007687801.1| 57 ECVRCGYKW 65
                                      6877****9 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.03
                           UPF0547  2 vCPeCeak 9 
                                      +CP+C ++
  gi|474934219|ref|YP_007687801.1| 74 RCPGCHTT 81
                                      6****875 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.0   0.00018      0.23      22      47 ..      18      48 ..      11      51 .. 0.87
   2 ?    9.0   4.4     0.001       1.3      22      45 ..      54      80 ..      46      85 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00018
                                      EEEE-HHHHHHHHH.....TT-B-TTT--B- CS
                        zf-C3HC4_3 22 HlvlCeeCaekllk.....rkkkCpiCrrpi 47
                                       +++C  C  ++ +       k+Cp Cr+ +
  gi|474934219|ref|YP_007687801.1| 18 SVYTCALCGHNWVSrkdngVPKSCPKCRSTV 48
                                      5789********988999999*******976 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.001
                                      EEEE-HHHHHHHHH...TT-B-TTT-- CS
                        zf-C3HC4_3 22 HlvlCeeCaekllk...rkkkCpiCrr 45
                                      H++ C +C  k+ +   r  +Cp C++
  gi|474934219|ref|YP_007687801.1| 54 HVCECVRCGYKWGStheRPSRCPGCHT 80
                                      ************99999********87 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.4e-05     0.044      10      34 ..     102     131 ..      91     132 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.4e-05
                                       H.....HGGGGSSTTTT--STTTSSSS--- CS
                             HTH_7  10 d.....inrvvkLleeGisiskIAkevnis 34 
                                       +      +++  L+++G+ i++IA+ +++s
  gi|474934219|ref|YP_007687801.1| 102 SvtpdkAEEINCLYDAGENITAIARHTGLS 131
                                       04444499999****************998 PP

>> CT_C_D  Carboxyltransferase domain, subdomain C and D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   8.6e-05      0.11      83     122 ..     104     141 ..      83     144 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.6e-05
                                       ----EEEEEEEESTTT-TTHHHHHHHHTS-HHHHHHHHHH CS
                            CT_C_D  83 eesrlveipvcYdgevgpDLeevaelnglsveevirlhta 122
                                       ++ +  ei ++Yd  +g+++ ++a+++gls  +v +++++
  gi|474934219|ref|YP_007687801.1| 104 TPDKAEEINCLYD--AGENITAIARHTGLSFCKVFSVISD 141
                                       3344589******..9**************9999988776 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       1.1   1.4e+03      28      34 ..      19      25 ..      10      26 .. 0.67
   2 ?   12.4   8.7   8.5e-05      0.11       1      37 [.      27      64 ..      27      79 .. 0.91
   3 ?   -0.5   0.3      0.95   1.2e+03       3      18 ..      65      79 ..      63      84 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.1
                                      EEEETTT CS
                              C1_1 28 glkCswC 34
                                       ++C+ C
  gi|474934219|ref|YP_007687801.1| 19 VYTCALC 25
                                      5667777 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 8.5e-05
                                      --EEEE.--SS--B-TTT-SB--SSSS-EEEETTT--E CS
                              C1_1  1 Hhwvhr.nfkqptfCkhCgeflwgkekqglkCswCkll 37
                                      H+wv r     p+ C +C++ +w k ++ + C  C+++
  gi|474934219|ref|YP_007687801.1| 27 HNWVSRkDNGVPKSCPKCRSTVWNKDYHVCECVRCGYK 64
                                      *****953489************************996 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.95
                                      EEEE--SS--B-TTT- CS
                              C1_1  3 wvhrnfkqptfCkhCg 18
                                      w  ++ ++p++C  C 
  gi|474934219|ref|YP_007687801.1| 65 WGSTH-ERPSRCPGCH 79
                                      55566.7888888886 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00024      0.31      10      31 ..     108     129 ..     103     132 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00024
                            HTH_38  10 ReeIerllaeGlslreIArrLg 31 
                                        eeI  l+++G+++ +IAr+ g
  gi|474934219|ref|YP_007687801.1| 108 AEEINCLYDAGENITAIARHTG 129
                                       589999*************866 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   1.8    0.0089        11      33      61 ..      18      46 ..      11      56 .. 0.73
   2 ?    7.5   1.7    0.0027       3.4      33      67 ..      54      85 ..      49      98 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0089
                                      EEEEETTT-.-EEES---...-SB-..TTT-H CS
                            MCM_OB 33 avfeckkcgktvevelee...PrkCeekeCes 61
                                      +v++c  cg++   +  +   P++C  ++C+s
  gi|474934219|ref|YP_007687801.1| 18 SVYTCALCGHNWVSRK-DngvPKSC--PKCRS 46
                                      789******9655322.2356****..99*95 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0027
                                      EEEEETTT-.-EEES----SB-..TTT-HHH-EEE CS
                            MCM_OB 33 avfeckkcgktveveleePrkCeekeCeskdpfkl 67
                                       v ec +cg++ + + e+P++C  + C+ ++++ +
  gi|474934219|ref|YP_007687801.1| 54 HVCECVRCGYKWGSTHERPSRC--PGCH-TTKWDV 85
                                      5789*****998888999****..99*9.555554 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.2   0.00055       0.7     113     143 ..      18      49 ..       5      52 .. 0.81
   2 ?    2.5   3.4       0.1   1.3e+02     116     143 ..      57      83 ..      54      84 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00055
                           DUF1451 113 GtlvCekCgkelalkkteeip.pCpkCgateF 143
                                        +++C+ Cg++   +k + +p  CpkC++t +
  gi|474934219|ref|YP_007687801.1|  18 SVYTCALCGHNWVSRKDNGVPkSCPKCRSTVW 49 
                                       5689*******988887777626*****9976 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.1
                           DUF1451 116 vCekCgkelalkkteeippCpkCgateF 143
                                       +C +Cg +   ++ e+ ++Cp C+ t++
  gi|474934219|ref|YP_007687801.1|  57 ECVRCGYKWGSTH-ERPSRCPGCHTTKW 83 
                                       799****998766.56699*****9975 PP

>> FYDLN_acid  Protein of unknown function (FYDLN_acid)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   1.0      0.33   4.2e+02      25      36 ..      37      48 ..      17      57 .. 0.72
   2 ?    9.8   0.6   0.00096       1.2      12      53 ..      58     100 ..      54     121 .. 0.65

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.33
                        FYDLN_acid 25 dPivcpkcgeef 36
                                       P  cpkc +++
  gi|474934219|ref|YP_007687801.1| 37 VPKSCPKCRSTV 48
                                      477788877654 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00096
                        FYDLN_acid  12 CpscgakFYDLnkdPivcpkcgee.fepeevlksraaaaeaee 53 
                                       C  cg k+     +P  cp c+++ +++ e  + r++ ++ ++
  gi|474934219|ref|YP_007687801.1|  58 CVRCGYKWGSTHERPSRCPGCHTTkWDVPEDSAGRKKHRRPAR 100
                                       99*******************9752555444233333222222 PP

>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.3    0.0001      0.13      32      61 ..      18      48 ..      12      54 .. 0.87
   2 ?    2.6   3.1      0.11   1.4e+02      35      62 ..      40      66 ..      38      73 .. 0.86
   3 ?   -1.9   0.1       2.9   3.7e+03      33      43 ..      72      82 ..      63      84 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0001
                                      S-BEESSSSSSEEEEEETTE.EEETTTTEEE CS
                   Ribosomal_L37ae 32 akytCpfcgktkvkRkavgi.wkCkkcgktv 61
                                      + ytC+ cg++ v+Rk  g+  +C kc+ tv
  gi|474934219|ref|YP_007687801.1| 18 SVYTCALCGHNWVSRKDNGVpKSCPKCRSTV 48
                                      56******************4469***9987 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.11
                                      EESSSSSSEEEEEETTEEEETTTTEEEE CS
                   Ribosomal_L37ae 35 tCpfcgktkvkRkavgiwkCkkcgktva 62
                                       Cp+c +++v  k   + +C +cg+++ 
  gi|474934219|ref|YP_007687801.1| 40 SCPKC-RSTVWNKDYHVCECVRCGYKWG 66
                                      69999.567889999**********985 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 2.9
                                      -BEESSSSSSE CS
                   Ribosomal_L37ae 33 kytCpfcgktk 43
                                        +Cp c++tk
  gi|474934219|ref|YP_007687801.1| 72 PSRCPGCHTTK 82
                                      45799998876 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.2    0.0014       1.8      28      38 ..      19      29 ..      17      30 .. 0.92
   2 ?    3.2   0.3     0.064        81       2       9 ..      40      47 ..      39      49 .. 0.82
   3 ?    4.7   3.2     0.021        27      29      38 ..      56      65 ..      53      66 .. 0.90
   4 ?    1.1   0.3      0.29   3.7e+02       2      10 ..      74      82 ..      73      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0014
                           TFIIS_C 28 fykCtkCghrW 38
                                       y+C+ Cgh+W
  gi|474934219|ref|YP_007687801.1| 19 VYTCALCGHNW 29
                                      59********* PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.064
                           TFIIS_C  2 kCpkCgsr 9 
                                       CpkC+s+
  gi|474934219|ref|YP_007687801.1| 40 SCPKCRST 47
                                      6****975 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.021
                           TFIIS_C 29 ykCtkCghrW 38
                                      ++C+ Cg++W
  gi|474934219|ref|YP_007687801.1| 56 CECVRCGYKW 65
                                      89******** PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.29
                           TFIIS_C  2 kCpkCgsre 10
                                      +Cp C+ ++
  gi|474934219|ref|YP_007687801.1| 74 RCPGCHTTK 82
                                      6****9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 887.85
//
Query:       gi|474934220|ref|YP_007687802.1|  [L=85]
Description: hypothetical protein TALC_00645 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.27   11.1  12.6        1.1    9.2   0.1    3.2  3  ZZ        Zinc finger, ZZ type


Domain annotation for each model (and alignments):
>> ZZ  Zinc finger, ZZ type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   2.6    0.0026        46       6      24 ..       8      26 ..       4      30 .. 0.87
   2 ?    9.2   0.1     6e-05       1.1       6      22 ..      44      60 ..      42      68 .. 0.88
   3 ?    3.9   0.4    0.0026        46      24      31 ..      72      79 ..      70      81 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0026
                                      E-TTT-S..EESSEEEESS CS
                                ZZ  6 tCdgCseapligvRyhclr 24
                                      +Cd+C  + + g  + c++
  gi|474934220|ref|YP_007687802.1|  8 KCDVCRYCVHDGDDWACMI 26
                                      7******999999999975 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 6e-05
                                      E-TTT-S..EESSEEEE CS
                                ZZ  6 tCdgCseapligvRyhc 22
                                      tC+ Cs+a+++  +++c
  gi|474934220|ref|YP_007687802.1| 44 TCENCSHAEIVFGVVKC 60
                                      8**********999999 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.0026
                                      SSSS-EE- CS
                                ZZ 24 rcsdYDLC 31
                                      +csdYD C
  gi|474934220|ref|YP_007687802.1| 72 VCSDYDPC 79
                                      6*****99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      170  (0.00948185); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.49
# Mc/sec: 524.42
//
Query:       gi|474934221|ref|YP_007687803.1|  [L=304]
Description: hypothetical protein TALC_00646 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.095   12.8   0.6       0.44   10.7   0.2    2.1  2  DUF5595   Domain of unknown function (DUF5595)


Domain annotation for each model (and alignments):
>> DUF5595  Domain of unknown function (DUF5595)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0     0.078   1.4e+03      28      49 ..     127     148 ..     123     154 .. 0.80
   2 ?   10.7   0.2   2.4e-05      0.44      15      65 ..     205     255 ..     198     261 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.078
                           DUF5595  28 eDtFeeedaeleskLkelynvd 49 
                                       e  F+e+d  +   + +l +  
  gi|474934221|ref|YP_007687803.1| 127 EERFPEYDRTVGEGFARLRELE 148
                                       6789*****9999999987765 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 2.4e-05
                           DUF5595  15 dYtvkcYekFmqgeDtFeeedaeleskLkelynvdeaqlesleeeekrLee 65 
                                       dYt  +++ F+   D F + ++ +++ + ++ +  ++ ++sl+  + r  +
  gi|474934221|ref|YP_007687803.1| 205 DYTDGTFNPFLVSCDRFVNRKEYMDANMYQIAETVKQSMASLQDSYARVRK 255
                                       9******************************************99988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:00.54
# Mc/sec: 1704.83
//
Query:       gi|474934222|ref|YP_007687804.1|  [L=97]
Description: hypothetical protein TALC_00647 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       864  (0.0481901); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 631.02
//
Query:       gi|474934223|ref|YP_007687805.1|  [L=379]
Description: Arylsulfatase regulator (Fe-S oxidoreductase) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.6e-08   32.6   0.1    1.5e-07   31.9   0.1    1.3  1  Radical_SAM  Radical SAM superfamily
     0.0061   16.7   0.1      0.014   15.6   0.1    1.6  1  Fer4_14      4Fe-4S single cluster domain
     0.0062   16.8   0.1      0.012   15.9   0.1    1.4  1  Fer4_12      4Fe-4S single cluster domain
     0.0074   16.8   3.0      0.025   15.1   3.0    1.9  1  SPASM        Iron-sulfur cluster-binding domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.1   3.4e-11   1.5e-07       2     141 ..      10     143 ..       9     170 .. 0.76

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 3.4e-11
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTC... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlakla... 74 
                                        +t +Cn++C++C+ +     +  +  +s e++++++++++ ++     +i++ggepl  p    +++++++l+   
  gi|474934223|ref|YP_007687805.1|  10 KPTLACNMACRHCYHSPE--ERSSEGRISFERLEKLFRIAS-RDYeSVWFIWHGGEPLELP--LSFWKKAIELQeky 81 
                                       6899************95..999999999999999999996.65559999999*****987..46666666666688 PP

                                       ..CCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTT CS
                                       ..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  75 ..vpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreag 141
                                         +    +t+ tng+ +d+++le  ++     + ++ e + d+    l+ r  + ++v ++++k+ ++g
  gi|474934223|ref|YP_007687805.1|  82 fgNHTCGNTIQTNGLNIDRKFLEFCRK-KQINIGVSHEGPYDD----LL-R-TDCSKVEDTIRKMSDKG 143
                                       99999************8888888888.435555555555555....55.4.55667777777777774 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1     3e-06     0.014       7      77 ..      14      80 ..      11     119 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3e-06
                           Fer4_14  7 gCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkee 77
                                       Cn++C+ C+++ + +s+ g ++ e+l+ + ++ ++ ++         GGePL+     ++ k   +l+e+
  gi|474934223|ref|YP_007687805.1| 14 ACNMACRHCYHSPEERSSEGRISFERLE-KLFRIASRDYE-SVWFIWHGGEPLEL--PLSFWKKAIELQEK 80
                                      5***********9999999999988887.66644444444.4457889*****53..33444444444444 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   2.6e-06     0.012      15      93 ..      15      95 ..       7     124 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.6e-06
                           Fer4_12 15 CnlsCkgCfnketwsfksgkeftkelleeiiedlkk.esiegltllGGEPllpena..eallelvkevkeekpekdiwl 90
                                      Cn++C+ C+  +  + +s+  +++e le++++ ++  ++   ++  GGEPl+      ++ +el ++   +   ++ + 
  gi|474934223|ref|YP_007687805.1| 15 CNMACRHCY-HSPEERSSEGRISFERLEKLFRIASRdYESVWFIWHGGEPLELPLSfwKKAIELQEKYFGNHTCGNTIQ 92
                                      *********.55566666667788888899988876155588999******8322224555555555544444444555 PP

                           Fer4_12 91 ytg 93
                                      ++g
  gi|474934223|ref|YP_007687805.1| 93 TNG 95
                                      555 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   3.0   5.5e-06     0.025       4      68 .]     244     305 ..     238     305 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.5e-06
                             SPASM   4 psrslfInsdGdVvpCcvdkktyveelklGni.reesleeIwnseeyqefrkskkfplielCrnCp 68 
                                        +r +++ ++Gd +pC    k   + +kl ni + + + e  + e + e+  +   ++ e C++C+
  gi|474934223|ref|YP_007687805.1| 244 LTRWVCLYPNGDLYPC---AKACPSSMKLCNIdSVNAVPEAFRTEGFAEIL-KGTIARREKCQKCD 305
                                       6788999*********...4555556999999778889***********88.333444566****6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2412.09
//
Query:       gi|474934224|ref|YP_007687806.1|  [L=129]
Description: endoribonuclease L-PSP [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-34  118.8   0.1    1.6e-34  118.5   0.1    1.0  1  Ribonuc_L-PSP  Endoribonuclease L-PSP


Domain annotation for each model (and alignments):
>> Ribonuc_L-PSP  Endoribonuclease L-PSP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.5   0.1     9e-39   1.6e-34       2     118 ..      11     124 ..      10     126 .. 0.97

  Alignments for each domain:
  == domain 1  score: 118.5 bits;  conditional E-value: 9e-39
                                       TTSTTTSSS-BSEEEETTEEEEEEE-SB-TTTSCB.-SSHHHHHHHHHHHHHHHHHHTT--GGGEEEEEEEESSGGG CS
                     Ribonuc_L-PSP   2 eaapaaaapYsqavkagnlvyvsGqlpldpetgelvegdveeqtrqalenlkavLaaagaslsdvVkvtvFladied 78 
                                       e+ap a++pYsq++ agnlv+++G +p+dp+tg +  +++eeq++qal+n+ avL+a +++++ +V vtv+l+died
  gi|474934224|ref|YP_007687806.1|  11 EEAPLAVGPYSQGISAGNLVFTAGEIPVDPHTGAV-GETIEEQANQALKNVIAVLEAGHVAKDGIVSVTVYLTDIED 86 
                                       6899******************************8.99*************************************** PP

                                       HHHHHHHHHHHSSSSTS--EEEEEE-SBSGGG-SEEEEEE CS
                     Ribonuc_L-PSP  79 faevnevyaeafdelkeaParsaveVaaLpkgakvEIeai 118
                                       f++vn +y+++f e++  Pars+veV++Lpkg+k+ + ai
  gi|474934224|ref|YP_007687806.1|  87 FQTVNLIYKDYFGEPY--PARSCVEVSNLPKGVKIMVSAI 124
                                       ***************7..****************988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 791.29
//
Query:       gi|474934225|ref|YP_007687807.1|  [L=307]
Description: homoserine O-succinyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   5.2e-135  449.1   0.0   5.8e-135  449.0   0.0    1.0  1  HTS       Homoserine O-succinyltransferase


Domain annotation for each model (and alignments):
>> HTS  Homoserine O-succinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  449.0   0.0  3.3e-139  5.8e-135       1     298 []       2     299 ..       2     299 .. 1.00

  Alignments for each domain:
  == domain 1  score: 449.0 bits;  conditional E-value: 3.3e-139
                                       -EE--TT-HHHHHHHTTT---B------------EEEEEE---SSHHHHHHHHHHHHHSSSS-EEEEEE--S----- CS
                               HTS   1 pikipkdlpaveiLekenifvmeeeraakqdirplkililNlmpkkietEtqllrllgntplqvelellrleshesk 77 
                                       pik+p+dlpa+++Le+en+fvm+++ra +qdirpl+i++lNlmp+k+etE q++rll+ntplq++++ll++++h sk
  gi|474934225|ref|YP_007687807.1|   2 PIKVPNDLPAATVLEEENLFVMRQDRADTQDIRPLEIIVLNLMPTKVETEIQIMRLLSNTPLQINVTLLQMSTHVSK 78 
                                       8**************************************************************************** PP

                                       SS-HHHHHHH-B-GGGTTT--EEEEEE---S-TTS-GGGSTTHHHHHHHHHHHHHHEEEEEEETHHHHHHHHHHH-- CS
                               HTS  78 ntskehlekfYktfeeikdekfDgliiTGApveqlefeevkYWeelteildwakenvtstlfiCwaaqaalyylygv 154
                                       n s+e+l+kfY tf+e+kd+k+DgliiTGApve+++f+ev+YW+el+ei+dw+ +nv st++iCw+aqa+ly++ygv
  gi|474934225|ref|YP_007687807.1|  79 NISQEYLDKFYATFDEVKDRKWDGLIITGAPVENIDFSEVDYWDELCEIMDWSVKNVFSTMHICWGAQAGLYHHYGV 155
                                       ***************************************************************************** PP

                                       --EEEEEEEEEEEEEEES.S--GGGTT--SEEEEEEEEEEE--HHHHTT-TTEEEEEEETTTEEEEEEESSSSEEEE CS
                               HTS 155 ekkklpeKlfGvfehkvlkekspllrgfddeflvphsRytevkeedieekkelevLaeseeaGvsllaskdkrevfv 231
                                       +k+ l+eK++Gvf+h+ l  ++pllrg dd f +phsR+tev+  di ++++l+++a s+eaGv ++ s+++++vf+
  gi|474934225|ref|YP_007687807.1| 156 DKYPLEEKMSGVFPHRALVGDDPLLRGCDDVFWFPHSRHTEVRARDILKNPHLHIIAVSDEAGVGIVISEKANQVFI 232
                                       ***************************************************************************** PP

                                       -S-TT--TTHHHHHHHHHHHTT------BTTSGGG-TTS-----SHHHHHHHHHHHHHHTTTTT-XX CS
                               HTS 232 lgHpEYdaetLkkEyeRDlekgleielPknYfpeddpkkepkarWrshanllfsnWlnylvyqetpy 298
                                       +gH+EYda+tL+ Ey RDl +g+++++P +Yfp+ddp+++p ++Wrs+anl+f nWlny++yq+tp+
  gi|474934225|ref|YP_007687807.1| 233 TGHMEYDAKTLSYEYYRDLGRGMNPHVPYHYFPDDDPSRDPLMTWRSTANLIFGNWLNYYIYQNTPF 299
                                       *****************************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1898.63
//
Query:       gi|474934226|ref|YP_007687808.1|  [L=302]
Description: cysteine synthase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.7e-67  226.8   3.2    4.1e-67  226.6   3.2    1.0  1  PALP        Pyridoxal-phosphate dependent enzyme
    0.00099   19.1   0.1     0.0022   18.0   0.1    1.5  1  QRPTase_N   Quinolinate phosphoribosyl transferase, N-termina
  ------ inclusion threshold ------
      0.021   14.8   0.4      0.062   13.3   0.1    1.9  2  ADH_zinc_N  Zinc-binding dehydrogenase
       0.14   12.0   0.3       0.34   10.7   0.1    1.7  2  DFP         DNA / pantothenate metabolism flavoprotein
       0.14   12.8   0.0        0.4   11.3   0.0    1.7  1  PepSY       Peptidase propeptide and YPEB domain


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  226.6   3.2   1.2e-70   4.1e-67       1     294 []       7     290 ..       7     290 .. 0.93

  Alignments for each domain:
  == domain 1  score: 226.6 bits;  conditional E-value: 1.2e-70
                                       GGGCSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTT...TTTSEEEEEBSSHHHHHHHHHH CS
                              PALP   1 ltlgigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkeg...tgaktvveassGNhgralAaaa 74 
                                       +t  ig+TPlvrl r+s   g  +++K E  np+gS+KdR++ +++ +++ +    ++ t++e +sGN+g+a+A++a
  gi|474934226|ref|YP_007687808.1|   7 ITETIGNTPLVRLGRMS-PAGSSVYVKIERGNPGGSIKDRAVLSIINDAEAKgrlSPGGTIIEPTSGNTGIAIAMIA 82 
                                       5789************9.78999*************************777779*********************** PP

                                       HHHT-EEEEEEETTS-HHHHHHHHHTT-EEEEECCH..HHHHHHHHHHHHHHSTTCEE--TTTSHHHHHH.HHTHHH CS
                              PALP  75 allGlkvtivvpadaspekvallrllGaevvevggd..ydeavaaaaelaaegegaylvsqfdnptvieg.ygtigl 148
                                       a+ G+k++ v+p+++++e++al++++Gaevv+++g    + +v++a+el+a +++ +++ qfdnp++i++  +t+g 
  gi|474934226|ref|YP_007687808.1|  83 AARGYKAVMVMPDTMTKERIALMKAYGAEVVLTPGKlgMQGSVDKANELCACTPNSIIAGQFDNPANILAhRTTTGR 159
                                       *********************************998667777777******************************** PP

                                       HHHHHTTTTEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCS.C CS
                              PALP 149 EileqlggkpdavvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvsdtiadglavg.s 224
                                       Eil++l +++d vv++ G+Gg+++Gia +lk++++d +vi+vep++s+ + ++           +++ ++g++++ +
  gi|474934226|ref|YP_007687808.1| 160 EILADL-PDVDFVVAGFGTGGTASGIAWALKDAGSDGKVIAVEPAESALVSSGS---------AGPHKIQGIGANfV 226
                                       ******.6*************************************999999999.........5599********66 PP

                                       GTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTCEEEEEEE-B CS
                              PALP 225 pselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaalklreagelkegdrvvviltg 294
                                       p++l+     + v++i tv+ ++a++++r+lar+egi+++ s++a++  +  + a++ +++ +vv+il++
  gi|474934226|ref|YP_007687808.1| 227 PGNLDR----DVVGTIETVKGDDAVATARRLAREEGIFCGISAGANVFKA-IEIAQRHPGS-KVVAILPD 290
                                       666655....66689999***********************999999999.7788887777.9***9986 PP

>> QRPTase_N  Quinolinate phosphoribosyl transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1     6e-07    0.0022      11      55 ..     241     291 ..     235     296 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 6e-07
                                       HGCTTSEEEEEEEESSSEEE-SHHHHHHHHHHH......TTTEEEESS-TT CS
                         QRPTase_N  11 lipeekkakaeiiakeegvvaGlevaeevfell......pglevellvkDG 55 
                                       +  +++ a+a+ +a+eeg+++G+++ ++vf+ +      pg +v +  +DG
  gi|474934226|ref|YP_007687808.1| 241 VKGDDAVATARRLAREEGIFCGISAGANVFKAIeiaqrhPGSKVVAILPDG 291
                                       56678899***********************99777777777777777776 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   1.7e-05     0.062       3      43 ..      75     118 ..      74     156 .. 0.75
   2 ?   -2.4   0.0       1.2   4.3e+03      64      92 ..     239     265 ..     228     279 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.7e-05
                                       HHHHHHHHHHTT-EEEEE...ESSHHHHHHHHHTTESEEEETTT CS
                        ADH_zinc_N   3 GlaavqlAkalGaeviav...dsseeklelakklGadevinyke 43 
                                       G+a  ++A+a G + ++v     ++e+++l+k +Ga++v+++ +
  gi|474934226|ref|YP_007687808.1|  75 GIAIAMIAAARGYKAVMVmpdTMTKERIALMKAYGAEVVLTPGK 118
                                       67777777777775555511156789**************9933 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.2
                                       ESSCSHHHHHHHHHCEEEEEEEEECSCTS CS
                        ADH_zinc_N  64 ecvGsgatleaalkllkpgGrlvvvGggk 92 
                                       e+v   +++ +a +l+++ G +  +G++ 
  gi|474934226|ref|YP_007687808.1| 239 ETVKGDDAVATARRLAREEGIF--CGISA 265
                                       5554466777777777777744..33333 PP

>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   9.3e-05      0.34      25      56 ..      68      99 ..      62     130 .. 0.80
   2 ?   -3.4   0.0       2.1   7.4e+03     116     153 ..     238     277 ..     233     283 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 9.3e-05
                                      E----HHHHHHHHHHHHTT-EEEEEE-S-SS- CS
                               DFP 25 NrSSGkmGyalAeaaaarGaeVtlvsgpvsle 56
                                       + SG +G+a+A  aaarG +  +v   + ++
  gi|474934226|ref|YP_007687808.1| 68 EPTSGNTGIAIAMIAAARGYKAVMVMPDTMTK 99
                                      578******************99998775433 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.1
                                       --EEE---HHHHHHHC-S.S-EEEEEEE-SS..-HHHHHH CS
                               DFP 116 leleknpdilaelaekkkkkqllvGFaaete..ellenar 153
                                       +e +k  d +a++++ ++++ +++G +a  +  +++e a+
  gi|474934226|ref|YP_007687808.1| 238 IETVKGDDAVATARRLAREEGIFCGISAGANvfKAIEIAQ 277
                                       5666777777777766666667777777765455666555 PP

>> PepSY  Peptidase propeptide and YPEB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00011       0.4       6      33 ..     271     296 ..     271     299 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHSTTEEEEEEEEEEETTEEE CS
                             PepSY   6 qAlaiAlaavpgkiieielededdgrlv 33 
                                       +A++iA+++ pg++++++l+d+ ++++v
  gi|474934226|ref|YP_007687808.1| 271 KAIEIAQRH-PGSKVVAILPDG-GDKYV 296
                                       79*******.************.99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1919.38
//
Query:       gi|474934227|ref|YP_007687809.1|  [L=465]
Description: Arabinose efflux permease [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.6e-47  159.8  52.6    9.6e-46  156.3  49.6    2.7  2  MFS_1           Major Facilitator Superfamily
    3.1e-07   29.6  18.1    3.1e-07   29.6  18.1    3.7  4  Sugar_tr        Sugar (and other) transporter
     0.0012   17.8  30.3     0.0015   17.5   6.6    3.1  3  MFS_1_like      MFS_1 like family
  ------ inclusion threshold ------
        1.6    9.0   4.0        3.8    7.7   0.3    2.8  3  Shisa           Wnt and FGF inhibitory regulator
        2.3    6.4   4.5        3.8    5.6   4.5    1.2  1  TcdA_TcdB_pore  TcdA/TcdB pore forming domain


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.3  49.6   2.7e-49   9.6e-46       2     352 ..      19     405 ..      18     406 .. 0.92
   2 !    8.1   0.1   0.00031       1.1     127     176 ..     399     458 ..     397     465 .] 0.81

  Alignments for each domain:
  == domain 1  score: 156.3 bits;  conditional E-value: 2.7e-49
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglll 78 
                                        +a+f++ l++++l+++l   ++e++ +  + +g + t++ lg++++++p++ ++  +G r+v+l g+l++ +++l+
  gi|474934227|ref|YP_007687809.1|  19 TIATFVTPLMSTMLNLSLL-DIGEEFDVGSHDLGYVNTMFILGSVIGMVPAAKIASIYGMRKVFLSGILGSMASALI 94 
                                       589***************9.******************************************************555 PP

                             MFS_1  79 llfa.sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravf 154
                                       ++ + +++++l+vlr+l+G++a+ ++ +++a+i   fp e+rg aig+ ++g+ +G  lgp +ggll++ +gWr++f
  gi|474934227|ref|YP_007687809.1|  95 IM-SsPNFPFLIVLRLLTGIFASQILVTSVAMIGLSFPVENRGWAIGVNTTGVYIGLSLGPTIGGLLSDTFGWRSLF 170
                                       55.648888******************************************************************** PP

                             MFS_1 155 yilaivsllafvlfllllpeepperkrkspkeee.......................................kgtg 192
                                       +++ +++++af +   +  e +p+++r  +++                                           ++
  gi|474934227|ref|YP_007687809.1| 171 VLIVALFMVAFAVCTRYKGEMKPQEGRMMDWKGAvmwgisifvlmygvvnmsegwalvmiavggvltaatiwyLLRA 247
                                       **********998889999999999999999999***************************9999999999988888 PP

                             MFS_1 193 paplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsd 269
                                       ++p+++  k+++ + +   + +a++++  + +++ ++l lylq+  +++ + +ag+++ l  l+ + l   ag++sd
  gi|474934227|ref|YP_007687809.1| 248 ESPVLN-VKLFRDPTFA-KAALASFMNYGACYSIAFFLALYLQSIGKMT-ATEAGIFMLLQPLIQVLLTAKAGAVSD 321
                                       888888.6666666633.355555555556666****************.8************************** PP

                             MFS_1 270 rlgrrrrlllallllllaalglallavtssavllll.vlvliGfglgfvfpsllalasdlappeeagtasglfntag 345
                                       r+  +r   ++ ++++++ ++++++  t++++++++ ++v++G+glg++ +++++++ + ap + +g asg++ +++
  gi|474934227|ref|YP_007687809.1| 322 RMRDKRVVPVFASATTAVGIAMFIMLGTDTSMFYVAvMMVILGVGLGCFGAPVNTILLNEAPVQFRGDASGVVALVR 398
                                       *9999999999999999999999999997777777779999************************************ PP

                             MFS_1 346 slggalg 352
                                       + g++++
  gi|474934227|ref|YP_007687809.1| 399 QTGMMVS 405
                                       ***9987 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00031
                             MFS_1 127 sagfslGailgpllggllasslg.............Wravfyilaivsllafvlfllllpeep 176
                                       ++g+ +++ +g++  ++++ s                r++f i+ ++++la+++    l+ +p
  gi|474934227|ref|YP_007687809.1| 399 QTGMMVSMGFGMACISFIMGSTDnlgpdtydlfidvIRLAFSICLVMCILALIC---CLTLKP 458
                                       78889999999999999996666999*************************995...333333 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6  18.1   8.7e-11   3.1e-07      47     187 ..      49     181 ..      28     187 .. 0.92
   2 !    5.8   3.0    0.0015       5.4     306     364 ..     156     217 ..     150     232 .. 0.63
   3 ?    0.3   1.0     0.069   2.5e+02     345     371 ..     268     294 ..     228     298 .. 0.83
   4 !    8.9   9.8   0.00017      0.61      74     187 ..     325     452 ..     296     458 .. 0.75

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 8.7e-11
                                       HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHH CS
                          Sugar_tr  47 lsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlv 123
                                       ++g +  +f++G++iG + a +++ ++G +k++l +++ ++++a++++ ++   ++  liv R+l+Gi++  + v++
  gi|474934227|ref|YP_007687809.1|  49 DLGYVNTMFILGSVIGMVPAAKIASIYGMRKVFLSGILGSMASALIIMSSP---NFPFLIVLRLLTGIFASQILVTS 122
                                       56788899*******************************************...*********************** PP

                                       HHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHH CS
                          Sugar_tr 124 PmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllil 187
                                          i+   p + Rg  ++++ +++ +G  ++ ++g  l++t +   wr l+ l +  al+++++
  gi|474934227|ref|YP_007687809.1| 123 VAMIGLSFPVENRGWAIGVNTTGVYIGLSLGPTIGGLLSDTFG---WRSLFVLIV--ALFMVAF 181
                                       ******************************************9...999998755..4455544 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0015
                                       HHHHHHHHS-SHHHHHHHHHHHHHHHHHHH...HHHHTTSS.....CHHHHHHHHHHHHHHH CS
                          Sugar_tr 306 vaiflvdrfGRRtllllGaagmaicfvilg.ivalllvaks..kaasivaivfialfialfa 364
                                       ++ +l+d fG R l++l +a  +++f++ + +   + +++     ++++++ +i +f+ +++
  gi|474934227|ref|YP_007687809.1| 156 IGGLLSDTFGWRSLFVLIVALFMVAFAVCTrYKGEMKPQEGrmMDWKGAVMWGISIFVLMYG 217
                                       44578888888888888888888888888853333333333664444555556666666665 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.069
                                       S...CHHHHHHHHHHHHHHHTTTTHHH CS
                          Sugar_tr 345 skaasivaivfialfialfalgwgpvp 371
                                        + ++++a   ia+f+al+  ++g + 
  gi|474934227|ref|YP_007687809.1| 268 ASFMNYGACYSIAFFLALYLQSIGKMT 294
                                       3679999************99999875 PP

  == domain 4  score: 8.9 bits;  conditional E-value: 0.00017
                                       THHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHH CS
                          Sugar_tr  74 GRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfG 150
                                       +++ + ++a++ + +g+++ ++   ++s+  ++v+ v++G+g+G++ + v + +   Ap + Rg   ++  l  ++G
  gi|474934227|ref|YP_007687809.1| 325 DKRVVPVFASATTAVGIAMFIMLGTDTSMFYVAVMMVILGVGLGCFGAPVNTILLNEAPVQFRGDASGVVALVRQTG 401
                                       455555678888888888877777667788888999*********988888877778******************** PP

                                       HHHHHHHHHHH.HTSS-.............TTHHHHHHHCCHHHHHHHHHH CS
                          Sugar_tr 151 ilvaaifglgl.nktsn.............adgwrillglqlvpallllil 187
                                       ++v+ +fg++  + + +              d  r+ + ++lv+ +l li+
  gi|474934227|ref|YP_007687809.1| 402 MMVSMGFGMACiSFIMGstdnlgpdtydlfIDVIRLAFSICLVMCILALIC 452
                                       *****9999885655556666776665555555555566666655555555 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   8.5   2.1e-05     0.076     258     384 ..      46     171 ..       5     172 .. 0.82
   2 ?   -2.6   0.7      0.51   1.8e+03     157     329 ..     206     240 ..     175     246 .. 0.57
   3 !   17.5   6.6   4.1e-07    0.0015       9      84 ..     270     346 ..     263     461 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.1e-05
                        MFS_1_like 258 sntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllwaaa 334
                                        +  lG + ++  +++++  + a k+  ++G++k+ + ++l  ++  l++ +  n+ +++++ +L gi    + ++ 
  gi|474934227|ref|YP_007687809.1|  46 GSHDLGYVNTMFILGSVIGMVPAAKIASIYGMRKVFLSGILGSMASALIIMSSPNFPFLIVLRLLTGIFASQILVTS 122
                                       4556889999999999999*********************998888888888899********************** PP

                        MFS_1_like 335 veyvskiapksleatgqglls.glyfglGralGsliGGllwdlksaiflFr 384
                                       v  +   +p + ++  +g+ + g+y  +G  lG  iGGll d+++ + lF 
  gi|474934227|ref|YP_007687809.1| 123 VAMIGLSFPVENRGWAIGVNTtGVY--IGLSLGPTIGGLLSDTFGWRSLFV 171
                                       ******************9751455..5567999****9999999999985 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.51
                        MFS_1_like 157 GyaifafitGilidhysvnllpysallyvlaallvisllvvlilnetekesklkvtkslqvllnilknpeviifllv 233
                                        +                                                                           
  gi|474934227|ref|YP_007687809.1| 206 MW--------------------------------------------------------------------------- 207
                                       33........................................................................... PP

                        MFS_1_like 234 alilgmswgiienFlflYLkelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaii 310
                                                                                                     ++++++l + ++++ 
  gi|474934227|ref|YP_007687809.1| 208 --------------------------------------------------------------GISIFVLMYGVVNM- 221
                                       ..............................................................33333333333332. PP

                        MFS_1_like 311 enawlvlpievLhgisfgl 329
                                       ++ w +++i v   ++ ++
  gi|474934227|ref|YP_007687809.1| 222 SEGWALVMIAVGGVLTAAT 240
                                       3344444444444444444 PP

  == domain 3  score: 17.5 bits;  conditional E-value: 4.1e-07
                        MFS_1_like   9 FfffaalgsllPYltiylkskg.lkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlflsllf 84 
                                       F+ ++a  s+  +l +yl+s+g ++a e gi +l+ pl+++l     g+++Dr++ +  v ++++   av  +++++
  gi|474934227|ref|YP_007687809.1| 270 FMNYGACYSIAFFLALYLQSIGkMTATEAGIFMLLQPLIQVLLTAKAGAVSDRMRDKRVVPVFASATTAVGIAMFIM 346
                                       999*****************98799***********************************9**99999998885544 PP

>> Shisa  Wnt and FGF inhibitory regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.14   4.9e+02      92     125 ..     169     198 ..     165     211 .. 0.55
   2 ?   -1.6   0.2      0.78   2.8e+03      81     111 ..     337     370 ..     315     373 .. 0.69
   3 ?    7.7   0.3    0.0011       3.8      91     114 ..     434     457 ..     420     464 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.14
                             Shisa  92 ifivfvivgvvvivcccgclkkkqrekrpgrenl 125
                                       +f+++v + +v++ +c +  +k + +++  +  +
  gi|474934227|ref|YP_007687809.1| 169 LFVLIVALFMVAFAVCTR--YKGEMKPQ--EGRM 198
                                       566666665555544433..34444433..4444 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.78
                             Shisa  81 d...iyvpvlivktifivfvivgvvvivcccgcl 111
                                           i++++++++    ++v v +v++ +  gc+
  gi|474934227|ref|YP_007687809.1| 337 TavgIAMFIMLGTDTSMFYVAVMMVILGVGLGCF 370
                                       0333788899998888888888888877777776 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0011
                             Shisa  91 tifivfvivgvvvivcccgclkkk 114
                                        i  +f i+ v++i+++++cl+ k
  gi|474934227|ref|YP_007687809.1| 434 VIRLAFSICLVMCILALICCLTLK 457
                                       5778999*************9855 PP

>> TcdA_TcdB_pore  TcdA/TcdB pore forming domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   4.5    0.0011       3.8     211     267 ..     347     403 ..     334     406 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0011
                    TcdA_TcdB_pore 211 lgvqlafdsaalvtsavGigaglvGasivaavlsillvplaGlsvGftaLaeafgav 267
                                       lg++ ++   a++  ++G+g g +Ga++ + +l  + v + G + G+ aL+   g++
  gi|474934227|ref|YP_007687809.1| 347 LGTDTSMFYVAVMMVILGVGLGCFGAPVNTILLNEAPVQFRGDASGVVALVRQTGMM 403
                                       678888888899999************************************998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (465 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       900  (0.050198); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.69u 0.29s 00:00:00.98 Elapsed: 00:00:00.49
# Mc/sec: 2858.80
//
Query:       gi|474934228|ref|YP_007687810.1|  [L=347]
Description: cation diffusion facilitator family transporter [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.8e-40  137.4  13.0    5.9e-40  137.1  13.0    1.1  1  Cation_efflux  Cation efflux family
    6.3e-09   35.8   1.4    1.1e-08   35.0   1.4    1.4  1  ZT_dimer       Dimerisation domain of Zinc Transporter
  ------ inclusion threshold ------
        3.9    7.0  10.1         45    3.5  10.1    2.5  1  BaxI_1         Bax inhibitor 1 like


Domain annotation for each model (and alignments):
>> Cation_efflux  Cation efflux family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.1  13.0   9.9e-44   5.9e-40       7     196 ..      22     212 ..      17     215 .. 0.96

  Alignments for each domain:
  == domain 1  score: 137.1 bits;  conditional E-value: 9.9e-44
                     Cation_efflux   7 anlilalvelivglltnSlalladafhslsdlvsllllllalklsrkppderfpfGygrlevlgalvsgllllglav 83 
                                       + ++l+l +++++llt+S+a+l da+ s++++v+  ++l al+ls +p+d+ +p+G+g++e + + v g +++++++
  gi|474934228|ref|YP_007687810.1|  22 VGTVLMLGKFFAYLLTGSVAILTDALESIVNVVAGCIGLYALWLSMQPADRSHPYGHGKVELISSSVEGTMIVIAGL 98 
                                       45689************************************************************************ PP

                     Cation_efflux  84 fllleaiqklikegereihaglalvvalvslvvnlalllilrragrklrsaalkaaalhvlgDaltslgvlvsalvi 160
                                        +++e++ +l+ ++e+  + ++ +v+++++++ n+a+    +r g+k +s+al+a+  h  +D+++s+g+++++ ++
  gi|474934228|ref|YP_007687810.1|  99 LIIYESVMRLL-NPEDIRELDVGIVIVALAAIANFAMGATAIRMGKKSNSIALEASGRHLCTDTYSSVGIIIGLTIV 174
                                       ***********.***************************************************************** PP

                     Cation_efflux 161 llfnlksg..plaDpvaslligliilysalkllkesls 196
                                       l  + ++    ++Dp+++l++g++i++++++++  s+ 
  gi|474934228|ref|YP_007687810.1| 175 LAADWAGYdcAWIDPIMALMFGAFIVVTGVRVIYRSFN 212
                                       **988866************************998876 PP

>> ZT_dimer  Dimerisation domain of Zinc Transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   1.4   1.9e-12   1.1e-08       8      77 ..     225     296 ..     219     298 .. 0.87

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 1.9e-12
                                       HHHHHHTT..-SS-EEEEEEEEE-S----EEEEEEEE-TTS-HHHHHHHHHHHHHHHHHH-TT--EEEEEEE CS
                          ZT_dimer   8 eireiiks..vpgvkgvhdlrtrksGskifvdlhievdgdlsvkeaHeiadevekrikeefpgvadvliHve 77 
                                       e+ +++++  +p++++vh+lr+ ++G+ +++d h++v++dls+++  ++     + i++ + +  d++   e
  gi|474934228|ref|YP_007687810.1| 225 EVIRCLNKvrTPEIIDVHHLRVVRYGTAVHIDAHMVVPQDLSIEQVWNLQVTMSDTIMRMIGENVDITFQAE 296
                                       555566544599***********************************************9999999987766 PP

>> BaxI_1  Bax inhibitor 1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5  10.1    0.0075        45     101     181 ..      71     177 ..       6     220 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.0075
                            BaxI_1 101 a.........pgivvqAvlgTlgvfavmlvlYktgairvtpkftkivvaaligilllylvnlvlslf.......... 158
                                                   ++  +v gT++v+a++l++Y++ +   +p   + + + ++ ++l +++n+ +  +          
  gi|474934228|ref|YP_007687810.1|  71 DrshpyghgkVELISSSVEGTMIVIAGLLIIYESVMRLLNPEDIRELDVGIVIVALAAIANFAMGATairmgkksns 147
                                       3444444466679999*****************99999999998888888888888888888888777788888888 PP

                            BaxI_1 159 .....gvgeglrdgg..lgilfslvvivlA 181
                                            ++++ ++d+   +gi+++l +++ A
  gi|474934228|ref|YP_007687810.1| 148 ialeaSGRHLCTDTYssVGIIIGLTIVLAA 177
                                       776642222334442369999988877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2417.24
//
Query:       gi|474934229|ref|YP_007687811.1|  [L=198]
Description: hypothetical protein TALC_00654 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1421.52
//
Query:       gi|474934230|ref|YP_007687812.1|  [L=114]
Description: Uncharacterized protein conserved in bacteria [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      0.005   16.7   0.0     0.0083   16.0   0.0    1.3  1  CutA1     CutA1 divalent ion tolerance protein


Domain annotation for each model (and alignments):
>> CutA1  CutA1 divalent ion tolerance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   4.6e-07    0.0083      43      84 ..      64     105 ..      62     111 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.6e-07
                                       TEEEEEEEEEEEEEEEGGGHHHHHHHHHHHSSSSS-EEEEEE CS
                             CutA1  43 gkieedkEvllliktreekveelekrvkelhpyevpeiialp 84 
                                       g+i  ++E+++ + +re+ +e++ k + ++hpye p++ ++p
  gi|474934230|ref|YP_007687812.1|  64 GEITVADEIRIKFVCREKDLENVLKIIDRVHPYEEPAVDVVP 105
                                       789999******************************997665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 904.01
//
Query:       gi|474934231|ref|YP_007687813.1|  [L=159]
Description: hypothetical protein TALC_00656 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-06   25.9   0.0    1.3e-05   24.8   0.0    1.5  1  PHP_C     PHP-associated


Domain annotation for each model (and alignments):
>> PHP_C  PHP-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   7.3e-10   1.3e-05      18      56 .]      10      46 ..       8      46 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 7.3e-10
                             PHP_C 18 gtgGSDAHrleeVGrayTefeepiatpdelleairegrt 56
                                      ++ GSDAH+l + G  +Tef+  +a  +e+ +ai  ++t
  gi|474934231|ref|YP_007687813.1| 10 ALSGSDAHSLYTAGYNWTEFPGTTA--EEFRQAILHRKT 46
                                      578*****************77766..*******99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      624  (0.0348039); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1081.56
//
Query:       gi|474934232|ref|YP_007687814.1|  [L=155]
Description: putative metal-dependent phosphoesterases (PHP family) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-07   30.5   0.0    4.8e-07   30.2   0.0    1.3  1  PHP       PHP domain


Domain annotation for each model (and alignments):
>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   2.6e-11   4.8e-07       1      72 [.       9      87 ..       9     143 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 2.6e-11
                                      EEEE--CCC...--.S-H..HH.......HHHHHHHCT-SEEEEEEEEBTTHHHHHHHHHHHHTTTTSEEEEEEE.... CS
                                      xxxxxxxxx...xxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               PHP  1 dlHvHteys...lldgalsiee.......lvkkakelglkaiaiTDhgnlfgyvefykaakkkykagikpiiGleayva 69
                                      d HvHt+ys   +l g+l+  e        v+ a+++gl  ++iTDh++  g + + k+a++ +  +i++++G e+   
  gi|474934232|ref|YP_007687814.1|  9 DTHVHTNYSgfnSL-GILRFPEsviepsvQVDDARRRGLNVLCITDHNDTRGGFIAQKYARQFD--DIEIVVGDEVMTN 84
                                      68*******99744.5555444444444499*********************999999**7544..7********6555 PP

                                      ... CS
                                      xxx RF
                               PHP 70 dds 72
                                      +++
  gi|474934232|ref|YP_007687814.1| 85 QGE 87
                                      544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 993.23
//
Query:       gi|474934233|ref|YP_007687815.1|  [L=596]
Description: putative ATPase, RNase L inhibitor (RLI) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-39  134.9   0.0    1.7e-18   67.4   0.0    2.5  2  ABC_tran      ABC transporter
    1.1e-12   48.3   0.5     0.0064   16.3   1.0    4.2  4  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    4.8e-10   39.1   2.3    1.1e-09   37.9   2.3    1.7  1  RLI           Possible Fer4-like domain in RNase L inhibitor,
    1.4e-09   37.7   6.3     0.0017   17.8   0.0    4.6  5  SMC_N         RecF/RecN/SMC N terminal domain
    1.1e-06   28.2   3.1    1.1e-06   28.2   3.1    2.3  2  Fer4          4Fe-4S binding domain
    1.7e-05   25.4   0.3      0.015   15.9   0.0    2.7  2  AAA_23        AAA domain
    3.6e-05   23.7   0.0        1.5    8.4   0.0    3.7  4  AAA_15        AAA ATPase domain
    0.00013   22.0   0.0      0.017   15.0   0.0    2.4  2  Rad17         Rad17 P-loop domain
    0.00023   21.6   0.1       0.13   12.7   0.0    2.7  2  AAA           ATPase family associated with various cellular 
     0.0007   20.0   0.5       0.19   12.1   0.0    2.9  2  AAA_16        AAA ATPase domain
     0.0007   19.6   2.2     0.0007   19.6   2.2    2.4  2  Fer4_6        4Fe-4S binding domain
    0.00095   19.2   9.2      0.013   15.6   1.5    2.3  2  Fer4_10       4Fe-4S dicluster domain
      0.001   18.8   0.2       0.12   12.2   0.0    2.4  2  AAA_29        P-loop containing region of AAA domain
     0.0026   17.8   6.2     0.0053   16.9   6.2    1.5  1  Fer4_21       4Fe-4S dicluster domain
     0.0041   16.9   1.8        1.7    8.3   0.2    2.5  2  AAA_24        AAA domain
      0.005   17.4   9.1      0.013   16.1   1.9    2.2  3  Fer4_7        4Fe-4S dicluster domain
     0.0057   16.8   7.5      0.014   15.6   7.5    1.7  1  Fer4_9        4Fe-4S dicluster domain
     0.0076   16.6   0.0        6.2    7.3   0.0    2.9  2  RNA_helicase  RNA helicase
       0.01   16.8   0.1       0.01   16.8   0.1    2.6  2  Fer4_16       4Fe-4S double cluster binding domain
  ------ inclusion threshold ------
       0.02   15.1   0.4         11    6.2   0.0    2.9  3  AAA_28        AAA domain
      0.022   14.7   0.7        2.7    7.9   0.0    2.4  2  RsgA_GTPase   RsgA GTPase
      0.027   15.0   0.5        7.9    7.0   0.1    3.3  3  AAA_18        AAA domain
      0.027   14.5   1.1        2.1    8.4   0.1    2.7  2  MMR_HSR1      50S ribosome-binding GTPase
      0.049   13.8   0.4        0.9    9.7   0.0    2.5  2  AAA_33        AAA domain
      0.052   13.6   0.1         12    6.0   0.0    3.2  3  AAA_14        AAA domain
      0.052   13.5   2.6        1.4    8.8   0.3    2.8  2  NTPase_1      NTPase
      0.086   13.4  12.6       0.36   11.5   3.3    2.4  2  Fer4_4        4Fe-4S binding domain
       0.13   12.5   0.1         22    5.4   0.0    3.1  2  SbcCD_C       Putative exonuclease SbcCD, C subunit
       0.19   11.9   9.1      0.077   13.1   1.6    2.5  2  Fer4_2        4Fe-4S binding domain
       0.29   10.2   0.4         14    4.6   0.1    2.2  2  T2SSE         Type II/IV secretion system protein
       0.42   10.2   2.0         11    5.6   0.1    2.3  2  SRP54         SRP54-type protein, GTPase domain
        8.5    7.6  14.0          2    9.5   5.0    2.4  2  Fer4_3        4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.4   0.0   3.1e-21   1.7e-18       9     137 .]      99     243 ..      98     243 .. 0.79
   2 !   64.9   0.0   1.9e-20   1.1e-17       5     137 .]     362     486 ..     358     486 .. 0.79

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 3.1e-21
                                       ETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE...........EETTCEGGG..B-HHHCCHCEE..EE-SS--S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxx..xxxxxxxxxxx..xxxxxxxx RF
                          ABC_tran   9 kegekvaivGenGaGKStLlkllagllkpteGei...........lldgkdlke..qeleslrkeig..vlpqepql 70 
                                       k+g +++i+G+nG GK+t +++l+gl+ p+ G+            +++g+d++e     ++++  i+  v pq    
  gi|474934233|ref|YP_007687815.1|  99 KKGAITGILGPNGIGKTTAINILSGLVIPNLGNYenppskeevlaHFKGTDIHEyfS--NVYSGGIRtaVKPQYVDK 173
                                       6899*************************9999988999999999999999999553..444444430033444222 PP

                                       -TTSBHHHH..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  71 fpeltvren..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                        p+  v  n          +++  +e+a+ ++gl+e+ d+ +    ++LSgG+ qrva+a++ +k+++++++DEpt+
  gi|474934233|ref|YP_007687815.1| 174 IPKA-V--NgvvrdmlskvQERMTLEEAAGTFGLTEILDRDL----TKLSGGELQRVAMAATCMKDADIYFFDEPTS 243
                                       2222.1..1223445665577777************999999....*****************************96 PP

  == domain 2  score: 64.9 bits;  conditional E-value: 1.9e-20
                                       EEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx RF
                          ABC_tran   5 slklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvrene 80 
                                       s  ++ ge v++vG+n +GK+t++k+lag+ kp+ G++         +   ++  + ++++qe +   +++  ++n+
  gi|474934233|ref|YP_007687815.1| 362 SGAVRIGESVGVVGPNATGKTTFVKMLAGEIKPDTGSV---------NGVMKVAYKPQYISQEyEGTVQDYLYAKNY 429
                                       667889********************************.........345566777778888864444444466666 PP

                                       HHTC....HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  81 sdee....iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       +++      +++++ l +k l d+++    ++LSgG+ qrva+a +l+++++++llDEp+a
  gi|474934233|ref|YP_007687815.1| 430 DTVTsgffETQVINPLAIKFLFDKPM----KNLSGGELQRVAIAGCLAEDADIYLLDEPSA 486
                                       66664554566677777777777776....*****************************75 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   1.0   1.1e-05    0.0064       1      60 [.     103     141 ..     103     163 .. 0.73
   2 !   10.6   0.0   0.00062      0.35     233     287 ..     211     262 ..     204     278 .. 0.81
   3 !   11.8   0.0   0.00028      0.16       3      33 ..     372     396 ..     370     459 .. 0.68
   4 ?    3.7   0.0     0.083        47     234     285 ..     455     507 ..     445     514 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.1e-05
                            AAA_21   1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfef 60 
                                       ++++ GpNg GK++ + +l++l                     +ip+l +  +p ++ e 
  gi|474934233|ref|YP_007687815.1| 103 ITGILGPNGIGKTTAINILSGL---------------------VIPNLGNYENPPSKEEV 141
                                       799****************999.....................45555555555555444 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00062
                            AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr 287
                                       ++++lS G ++  a+++ +  ++   +++++DEp + L+     + ++++k+l++
  gi|474934233|ref|YP_007687815.1| 211 DLTKLSGGELQRVAMAATCMKDA---DIYFFDEPTSYLDIYQRVKMARIIKSLAS 262
                                       6778999999999*******999...9*************888888888887776 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.00028
                            AAA_21   3 vliGpNgsGKSnLLdaldllarldrdveglt 33 
                                       +++GpN++GK+++ + l      +++++++t
  gi|474934233|ref|YP_007687815.1| 372 GVVGPNATGKTTFVKML------AGEIKPDT 396
                                       69************999......33333333 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.083
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHP....kllrrllellkel 285
                                       + +lS G ++  a++  l++++   +++l+DEp + L+     ++ +++ ++++++
  gi|474934233|ref|YP_007687815.1| 455 MKNLSGGELQRVAIAGCLAEDA---DIYLLDEPSAYLDSnqrmEAAKCISGMMEKT 507
                                       5678888888889999999999...9**********99866555556666666555 PP

>> RLI  Possible Fer4-like domain in RNase L inhibitor, RLI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   2.3     2e-12   1.1e-09       1      33 [.       5      34 ..       5      36 .. 0.97

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 2e-12
                                      --EEEES---------TTHHHHHTTSEEEESS- CS
                               RLI  1 mrlAivdadqCdPKKCtgkkcarfcpvrlvrtg 33
                                      mr+A v +d+C+ KKC+  +c++fcp   +rtg
  gi|474934233|ref|YP_007687815.1|  5 MRIAAVLFDRCQNKKCNK-ECEKFCPL--IRTG 34
                                      9*****************.********..***9 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.018        10      21      41 ..      98     118 ..      85     124 .. 0.80
   2 !   17.8   0.0   3.1e-06    0.0017     136     195 ..     214     269 ..     135     291 .. 0.80
   3 ?    1.0   0.0      0.41   2.3e+02      28      42 ..     372     386 ..     351     392 .. 0.86
   4 !   12.0   0.0   0.00018       0.1     135     186 ..     456     503 ..     431     530 .. 0.85
   5 ?   -0.5   0.0       1.2   6.7e+02      78     113 ..     557     593 ..     546     596 .] 0.74

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.018
                                       ETTSSEEEEEESTTSSHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  21 pfsksftaivGpNGSGKsnll 41 
                                       p +  +t i+GpNG GK+  +
  gi|474934233|ref|YP_007687815.1|  98 PKKGAITGILGPNGIGKTTAI 118
                                       5566799**********9765 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 3.1e-06
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivi 195
                                        LSgGe + va+a       +k a +y++De  + LD  ++ k+a+++k+  ++  f+v+
  gi|474934233|ref|YP_007687815.1| 214 KLSGGELQRVAMA----ATCMKDADIYFFDEPTSYLDIYQRVKMARIIKSLASDDKFVVV 269
                                       79****9988765....55889999************************99988887765 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.41
                                       EEEESTTSSHHHHHH CS
                                       xxxxxxxxxxxxxxx RF
                             SMC_N  28 aivGpNGSGKsnlld 42 
                                        +vGpN  GK+ ++ 
  gi|474934233|ref|YP_007687815.1| 372 GVVGPNATGKTTFVK 386
                                       69*********9876 PP

  == domain 4  score: 12.0 bits;  conditional E-value: 0.00018
                                       TCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 135 elLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkek 186
                                       ++LSgGe + va+a  +A    + a +yllDe  a LD +++ + a+ +   
  gi|474934233|ref|YP_007687815.1| 456 KNLSGGELQRVAIAGCLA----EDADIYLLDEPSAYLDSNQRMEAAKCISGM 503
                                       58**********999987....7789******************99999744 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 1.2
                                       EEEEEE..EETTEESSSSSSCEEEEEEEETTSEEEEEE CS
                                       xxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  78 eveitf..dnedkklkiekeevsisrrvkrkgeseyki 113
                                       +v+itf  d + ++ +i+ke+ ++ r+ k+kge  y+ 
  gi|474934233|ref|YP_007687815.1| 557 SVDITFrrDADTHRPRINKEDSNLDRTQKSKGE-YYYA 593
                                       567777446666778999*********999999.4444 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.2       1.4   7.6e+02      13      19 ..      23      29 ..      22      30 .. 0.90
   2 !   28.2   3.1   1.9e-09   1.1e-06       1      24 []      46      69 ..      46      69 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.4
                                      HHHHHST CS
                              Fer4 13 aCvevCP 19
                                      +C++ CP
  gi|474934233|ref|YP_007687815.1| 23 ECEKFCP 29
                                      7*****9 PP

  == domain 2  score: 28.2 bits;  conditional E-value: 1.9e-09
                                      EEEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  1 vvideekCigCGaCvevCPvgAIt 24
                                      ++i e +C gCG+Cv+ CP+ AI+
  gi|474934233|ref|YP_007687815.1| 46 PIISETLCQGCGICVNKCPFKAIK 69
                                      5899******************96 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.6e-05     0.015       9      40 ..      84     122 ..      77     211 .. 0.83
   2 ?    6.8   0.1     0.016       8.7      23      37 ..     372     386 ..     346     390 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.6e-05
                            AAA_23   9 sfrdqeidF.......skgltlItGpNGaGKTTildAik 40 
                                       ++++ ++ +       +  +t I GpNG GKTT ++ + 
  gi|474934233|ref|YP_007687815.1|  84 QYGENTFRLfrlpvpkKGAITGILGPNGIGKTTAINILS 122
                                       56666666666677744569**************99775 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.016
                            AAA_23  23 lItGpNGaGKTTild 37 
                                        ++GpN +GKTT++ 
  gi|474934233|ref|YP_007687815.1| 372 GVVGPNATGKTTFVK 386
                                       689*********986 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0046       2.6      21      44 ..      97     122 ..      88     153 .. 0.84
   2 ?    2.6   0.0      0.16        89     322     356 ..     231     265 ..     222     276 .. 0.88
   3 !    8.4   0.0    0.0027       1.5      27      43 ..     372     388 ..     351     429 .. 0.87
   4 ?   -1.8   0.0       3.4   1.9e+03     322     343 ..     474     495 ..     471     509 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0046
                            AAA_15  21 lsee..ltvliGkNnsGKSsileald 44 
                                       + ++  +t + G+N++GK++++++l 
  gi|474934233|ref|YP_007687815.1|  97 VPKKgaITGILGPNGIGKTTAINILS 122
                                       4455568999*************996 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.16
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnk 356
                                       ++ +i++++EP  +L + +   +++ +k+la+d+k
  gi|474934233|ref|YP_007687815.1| 231 KDADIYFFDEPTSYLDIYQRVKMARIIKSLASDDK 265
                                       4689****************************997 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0027
                            AAA_15  27 vliGkNnsGKSsileal 43 
                                        ++G+N++GK++++++l
  gi|474934233|ref|YP_007687815.1| 372 GVVGPNATGKTTFVKML 388
                                       58*************98 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 3.4
                            AAA_15 322 eknvilliEEPEahLHpqaqkv 343
                                       e+ +i+l++EP a+L  ++ ++
  gi|474934233|ref|YP_007687815.1| 474 EDADIYLLDEPSAYLDSNQRME 495
                                       6789**********96666655 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   3.1e-05     0.017      47      84 ..     103     140 ..      89     159 .. 0.78
   2 ?    4.4   0.0     0.058        32      50      73 ..     373     396 ..     369     423 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.1e-05
                             Rad17  47 iLLisGPsGCgkstvvkvLskelgiklrewlnpvslke 84 
                                       i  i GP G gk+t++++Ls    ++l ++ np s  e
  gi|474934233|ref|YP_007687815.1| 103 ITGILGPNGIGKTTAINILSGLVIPNLGNYENPPSKEE 140
                                       77799***************************988333 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.058
                             Rad17  50 isGPsGCgkstvvkvLskelgikl 73 
                                       + GP   gk+t vk+L+ e  ++ 
  gi|474934233|ref|YP_007687815.1| 373 VVGPNATGKTTFVKMLAGEIKPDT 396
                                       67***************9987765 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.027        15       4      21 ..     107     124 ..     105     193 .. 0.71
   2 !   12.7   0.0   0.00023      0.13       3      32 ..     373     402 ..     371     432 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.027
                                       ESSTTSSHHHHHHHHHHH CS
                               AAA   4 yGppGtGKTllakavake 21 
                                        Gp G+GKT++++ +   
  gi|474934233|ref|YP_007687815.1| 107 LGPNGIGKTTAINILSGL 124
                                       7**********9988665 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00023
                                       EESSTTSSHHHHHHHHHHHHTHEEEEEETT CS
                               AAA   3 lyGppGtGKTllakavakelgvefleisgs 32 
                                       ++Gp  tGKT+++k +a e++ +  +++g 
  gi|474934233|ref|YP_007687815.1| 373 VVGPNATGKTTFVKMLAGEIKPDTGSVNGV 402
                                       79*****************98766666654 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.3     0.055        31      26      43 ..     103     120 ..      90     287 .. 0.86
   2 !   12.1   0.0   0.00034      0.19      24      52 ..     365     400 ..     356     477 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.055
                            AAA_16  26 lvllsGesGvGKsslvre 43 
                                       ++ + G+ G+GK++ ++ 
  gi|474934233|ref|YP_007687815.1| 103 ITGILGPNGIGKTTAINI 120
                                       56689********98875 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00034
                            AAA_16  24 p...elvllsGesGvGKsslvrellralekd....g 52 
                                           e+v ++G+ ++GK++ v++l+ +++ d    +
  gi|474934233|ref|YP_007687815.1| 365 VrigESVGVVGPNATGKTTFVKMLAGEIKPDtgsvN 400
                                       34448999*****************99999954441 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   1.5     0.084        47       7      20 ..      13      29 ..      13      38 .. 0.75
   2 !   19.6   2.2   1.3e-06    0.0007       2      24 .]      46      68 ..      45      68 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.084
                            Fer4_6  7 dkCi..gCgd.CvrvCP 20
                                      d+C    C++ C++ CP
  gi|474934233|ref|YP_007687815.1| 13 DRCQnkKCNKeCEKFCP 29
                                      7898667*666****** PP

  == domain 2  score: 19.6 bits;  conditional E-value: 1.3e-06
                            Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                      + i + +C gCg Cv+ CP++ai
  gi|474934233|ref|YP_007687815.1| 46 PIISETLCQGCGICVNKCPFKAI 68
                                      678899**************998 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7  11.1   8.8e-05     0.049       7      56 .]      13      64 ..       9      64 .. 0.82
   2 !   15.6   1.5   2.3e-05     0.013       2      24 ..      46      72 ..      45      92 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.8e-05
                           Fer4_10  7 dtC..irCg.kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      d+C   +C+ +C k+CP   t+v+++++ ++++++      C+gcg Cv +CP
  gi|474934233|ref|YP_007687815.1| 13 DRCqnKKCNkECEKFCPLIRTGVNVIEFGERGKPIIS-ETLCQGCGICVNKCP 64
                                      57755589989*******7788888888888877765.566***********9 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 2.3e-05
                           Fer4_10  2 vvidddtCirCgkCvkaCPadl....t 24
                                      ++i +  C +Cg Cv+ CP+++     
  gi|474934233|ref|YP_007687815.1| 46 PIISETLCQGCGICVNKCPFKAikliG 72
                                      6788999*************5544330 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00021      0.12      11      49 ..      89     128 ..      81     139 .. 0.83
   2 ?    3.9   0.1     0.079        44      24      39 ..     370     385 ..     358     390 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00021
                            AAA_29  11 tfdghtieidlkg.atlltGpsGsGKSTllDAiqalLvpa 49 
                                       tf+  ++++  kg +t + Gp+G GK+T +  ++ l +p+
  gi|474934233|ref|YP_007687815.1|  89 TFRLFRLPVPKKGaITGILGPNGIGKTTAINILSGLVIPN 128
                                       66666788999999***************98888888877 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.079
                            AAA_29  24 atlltGpsGsGKSTll 39 
                                       ++ ++Gp+ +GK+T++
  gi|474934233|ref|YP_007687815.1| 370 SVGVVGPNATGKTTFV 385
                                       46689*********97 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   6.2   9.4e-06    0.0053      10      58 ..      19      69 ..       8      70 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 9.4e-06
                           Fer4_21 10 gCgk.CliaCe..dtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58
                                      +C+k C + C+   t+++ ie+ ++ +  + e  C GC +C++ CP  ++i+
  gi|474934233|ref|YP_007687815.1| 19 KCNKeCEKFCPliRTGVNVIEFGERGKPIISETLCQGCGICVNKCPF-KAIK 69
                                      57755999998556999****9877776666899************7.7776 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.1    0.0059       3.3       5      22 ..     104     121 ..     100     134 .. 0.83
   2 !    8.3   0.2     0.003       1.7       4      22 ..     370     388 ..     368     401 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0059
                            AAA_24   5 iliyGpsgiGKTtlakel 22 
                                         i Gp+giGKTt ++ l
  gi|474934233|ref|YP_007687815.1| 104 TGILGPNGIGKTTAINIL 121
                                       5799*********99866 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.003
                            AAA_24   4 kiliyGpsgiGKTtlakel 22 
                                       ++ ++Gp+ +GKTt++k+l
  gi|474934233|ref|YP_007687815.1| 370 SVGVVGPNATGKTTFVKML 388
                                       5789*************99 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   1.9      0.34   1.9e+02      32      49 ..       9      29 ..       3      35 .. 0.78
   2 !   13.2  10.9   0.00019       0.1       4      52 .]      19      67 ..      13      67 .. 0.84
   3 !   16.1   1.9   2.2e-05     0.013       2      20 ..      53      71 ..      52      88 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.34
                            Fer4_7 32 eidpekClg..Cga.CvavCP 49
                                      ++  ++C++  C++ C++ CP
  gi|474934233|ref|YP_007687815.1|  9 AVLFDRCQNkkCNKeCEKFCP 29
                                      556789986558888999999 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00019
                            Fer4_7  4 gCg.aCvaaCp.....vkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      +C+  C++ Cp     v++ie+ e+       k+ i+++ C+gCg Cv+ CP++a
  gi|474934233|ref|YP_007687815.1| 19 KCNkECEKFCPlirtgVNVIEFGER------GKPIISETLCQGCGICVNKCPFKA 67
                                      57549*****988878888888776......58899****************986 PP

  == domain 3  score: 16.1 bits;  conditional E-value: 2.2e-05
                            Fer4_7  2 CigCgaCvaaCpvkaield 20
                                      C gCg Cv+ Cp kai+l 
  gi|474934233|ref|YP_007687815.1| 53 CQGCGICVNKCPFKAIKLI 71
                                      9**************9975 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   7.5   2.5e-05     0.014       4      51 .]      19      68 ..      13      68 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.5e-05
                            Fer4_9  4 gCga.CveaCpagvvvedaaerkarlra.aseeaCigCgaCveaCpkgai 51
                                      +C++ C++ Cp   +     e   r +   se+ C gCg Cv++Cp +ai
  gi|474934233|ref|YP_007687815.1| 19 KCNKeCEKFCPLIRTGVNVIEFGERGKPiISETLCQGCGICVNKCPFKAI 68
                                      3653488888544443333333222222023379************9887 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.026        15       3      23 ..     106     126 ..     105     157 .. 0.71
   2 ?    7.3   0.0     0.011       6.2       3      25 ..     373     395 ..     371     457 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.026
                      RNA_helicase   3 lyGpsgeGKStlakeLakall 23 
                                       + Gp+g+GK+t+++ L+  + 
  gi|474934233|ref|YP_007687815.1| 106 ILGPNGIGKTTAINILSGLVI 126
                                       67***********99765554 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.011
                      RNA_helicase   3 lyGpsgeGKStlakeLakallkk 25 
                                       ++Gp+ +GK+t++k La ++  +
  gi|474934233|ref|YP_007687815.1| 373 VVGPNATGKTTFVKMLAGEIKPD 395
                                       78*************99888733 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   1.9       2.8   1.6e+03       4      13 ..      19      29 ..      14      37 .. 0.79
   2 !   16.8   0.1   1.8e-05      0.01       2      20 ..      53      71 ..      52      95 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 2.8
                           Fer4_16  4 tCgk.CaevCP 13
                                      +C+k C + CP
  gi|474934233|ref|YP_007687815.1| 19 KCNKeCEKFCP 29
                                      68777888888 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 1.8e-05
                           Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                      C++Cg C++ CP +aik  
  gi|474934233|ref|YP_007687815.1| 53 CQGCGICVNKCPFKAIKLI 71
                                      ****************965 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.028        16       4      20 ..     106     122 ..     104     164 .. 0.89
   2 ?   -1.5   0.0       4.6   2.6e+03      51      94 ..     211     254 ..     180     266 .. 0.64
   3 ?    6.2   0.0      0.02        11       4      21 ..     373     390 ..     370     438 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.028
                            AAA_28   4 itGgestGKTtlleaLa 20 
                                       i+G+ + GKTt ++ L+
  gi|474934233|ref|YP_007687815.1| 106 ILGPNGIGKTTAINILS 122
                                       89************998 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.6
                            AAA_28  51 dllafaervleeqleeeaaa..aankvlfcDrglldtlaYaraygg 94 
                                       dl ++  + l+  + ++  +  ++ +++f+D  +    +Y r+ + 
  gi|474934233|ref|YP_007687815.1| 211 DLTKLSGGELQRVAMAA--TcmKDADIYFFDEPTSYLDIYQRVKMA 254
                                       55555555444333333..235999999999877777777776665 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.02
                            AAA_28   4 itGgestGKTtlleaLaa 21 
                                       ++G+  tGKTt ++ La 
  gi|474934233|ref|YP_007687815.1| 373 VVGPNATGKTTFVKMLAG 390
                                       78**************93 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0048       2.7      99     121 ..     101     123 ..      87     134 .. 0.88
   2 ?    4.7   0.1     0.047        26     103     131 ..     372     400 ..     364     405 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0048
                                       TSEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  99 dktsvlvGqSGvGKStLinallp 121
                                       + ++ ++G+ G+GK+t in l +
  gi|474934233|ref|YP_007687815.1| 101 GAITGILGPNGIGKTTAINILSG 123
                                       578889*************9976 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.047
                                       EEECSTTSSHHHHHHHHCTT-----S--- CS
                       RsgA_GTPase 103 vlvGqSGvGKStLinallpelelktgevs 131
                                        +vG+   GK+t++++l++e +  tg+v 
  gi|474934233|ref|YP_007687815.1| 372 GVVGPNATGKTTFVKMLAGEIKPDTGSVN 400
                                       5799999***************9999986 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0      0.12        67       3      21 ..     106     124 ..     105     192 .. 0.74
   2 ?    7.0   0.1     0.014       7.9       1      21 [.     371     391 ..     371     443 .. 0.75
   3 ?   -0.3   0.0       2.5   1.4e+03      28      67 ..     469     503 ..     419     591 .. 0.60

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.12
                            AAA_18   3 ltGtpGvGKttlakeLskr 21 
                                       + G+ G GKtt  + Ls +
  gi|474934233|ref|YP_007687815.1| 106 ILGPNGIGKTTAINILSGL 124
                                       89*************9765 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.014
                            AAA_18   1 IlltGtpGvGKttlakeLskr 21 
                                       +++ G+ ++GKtt+ k L+ +
  gi|474934233|ref|YP_007687815.1| 371 VGVVGPNATGKTTFVKMLAGE 391
                                       6899************99765 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 2.5
                            AAA_18  28 lrdvakenglllevdpe.aldeskrldedkldklldaleen 67 
                                        +++a + +++l ++p         ld ++++++ +++ + 
  gi|474934233|ref|YP_007687815.1| 469 AGCLAEDADIYLLDEPSaY------LDSNQRMEAAKCISGM 503
                                       5555666666666555533......3333333333333333 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.074        42       3      21 ..     105     123 ..     103     167 .. 0.80
   2 ?    8.4   0.1    0.0038       2.1       2      31 ..     371     401 ..     370     529 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.074
                                       EEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1   3 aivGrpNvGKStLinaltg 21 
                                       +i+G    GK+t in l+g
  gi|474934233|ref|YP_007687815.1| 105 GILGPNGIGKTTAINILSG 123
                                       799*************997 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0038
                                       EEEEESTTSSHHHHHHHHHTS.TEEESSSTT CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltge.kaivsdkpg 31 
                                       v++vG   +GK+t+++ l ge k  +++ +g
  gi|474934233|ref|YP_007687815.1| 371 VGVVGPNATGKTTFVKMLAGEiKPDTGSVNG 401
                                       89*****************976444444443 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.58   3.3e+02       5      16 ..     107     118 ..     104     123 .. 0.86
   2 ?    9.7   0.0    0.0016       0.9       4      22 ..     373     391 ..     371     433 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.58
                            AAA_33   5 vGlpGsGKstla 16 
                                        G++G GK+t +
  gi|474934233|ref|YP_007687815.1| 107 LGPNGIGKTTAI 118
                                       59********76 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0016
                            AAA_33   4 lvGlpGsGKstlaerllkk 22 
                                       +vG++++GK+t+++ l+ +
  gi|474934233|ref|YP_007687815.1| 373 VVGPNATGKTTFVKMLAGE 391
                                       79************99865 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.12        69       3      20 ..     102     119 ..     100     158 .. 0.87
   2 ?   -0.9   0.0       2.8   1.6e+03      53      84 ..     221     252 ..     198     270 .. 0.62
   3 ?    6.0   0.0     0.021        12       5      27 ..     371     393 ..     368     437 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.12
                            AAA_14   3 kilvitGaRrvGKTtllk 20 
                                        i  i G+  +GKTt ++
  gi|474934233|ref|YP_007687815.1| 102 AITGILGPNGIGKTTAIN 119
                                       57889**********986 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.8
                            AAA_14  53 lelilek.lkeekktylflDEiqevpewekalk 84 
                                        ++ ++   ++ +  + f+DE   + ++++ +k
  gi|474934233|ref|YP_007687815.1| 221 QRVAMAAtCMK-DADIYFFDEPTSYLDIYQRVK 252
                                       44445543333.677899999988855555444 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.021
                            AAA_14   5 lvitGaRrvGKTtllkqlikell 27 
                                       + ++G+  +GKTt++k l+ e  
  gi|474934233|ref|YP_007687815.1| 371 VGVVGPNATGKTTFVKMLAGEIK 393
                                       6799************9987654 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.2      0.11        61       4      19 ..     106     121 ..     103     128 .. 0.82
   2 ?    8.8   0.3    0.0025       1.4       2      34 ..     371     403 ..     370     410 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.11
                                       EE--TTSSHHHHHHHH CS
                          NTPase_1   4 iTGppGvGKtTlvkkv 19 
                                       i Gp G+GKtT ++ +
  gi|474934233|ref|YP_007687815.1| 106 ILGPNGIGKTTAINIL 121
                                       669********99765 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0025
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEEEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfy 34 
                                       v + Gp  +GKtT+vk ++ ++k +  +v+G++
  gi|474934233|ref|YP_007687815.1| 371 VGVVGPNATGKTTFVKMLAGEIKPDTGSVNGVM 403
                                       6788***************************97 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   1.9      0.02        11       2      15 ..      13      29 ..      12      37 .. 0.81
   2 ?   11.5   3.3   0.00064      0.36       4      16 ..      53      65 ..      49      66 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.02
                            Fer4_4  2 erCigCgs...CvaaCP 15
                                      +rC++ ++   C+ +CP
  gi|474934233|ref|YP_007687815.1| 13 DRCQNKKCnkeCEKFCP 29
                                      89997775557****** PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00064
                            Fer4_4  4 CigCgsCvaaCPq 16
                                      C+gCg Cv+ CP+
  gi|474934233|ref|YP_007687815.1| 53 CQGCGICVNKCPF 65
                                      ************7 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.039        22      24      47 ..     206     229 ..     188     258 .. 0.83
   2 ?    3.4   0.0      0.16        92      26      42 ..     451     467 ..     427     501 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.039
                           SbcCD_C  24 kelsrssgtlSGGekqflaylala 47 
                                       + l+r+ ++lSGGe q +a+ a +
  gi|474934233|ref|YP_007687815.1| 206 EILDRDLTKLSGGELQRVAMAATC 229
                                       448999*********998887765 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.16
                           SbcCD_C  26 lsrssgtlSGGekqfla 42 
                                       +++ +++lSGGe q +a
  gi|474934233|ref|YP_007687815.1| 451 FDKPMKNLSGGELQRVA 467
                                       67889999999997654 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   1.0      0.28   1.6e+02       5      21 ..      10      29 ..       6      30 .. 0.77
   2 ?   13.1   1.6   0.00014     0.077       4      21 ..      47      64 ..      44      65 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.28
                            Fer4_2  5 vdtdrCig..Cg.aCvsaCP 21
                                      v  drC +  C+  C + CP
  gi|474934233|ref|YP_007687815.1| 10 VLFDRCQNkkCNkECEKFCP 29
                                      56789977779669*****9 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00014
                            Fer4_2  4 vvdtdrCigCgaCvsaCP 21
                                       + +  C gCg+Cv+ CP
  gi|474934233|ref|YP_007687815.1| 47 IISETLCQGCGICVNKCP 64
                                      566778************ PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.061        34     117     153 ..      88     125 ..      68     131 .. 0.80
   2 ?    4.6   0.1     0.025        14     126     156 ..     365     395 ..     349     402 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.061
                             T2SSE 117 kiaevlrkavrerglil.vsGgTgsGKttllyallkei 153
                                       +  ++ r +v ++g i  + G+ g GKtt +++l   +
  gi|474934233|ref|YP_007687815.1|  88 NTFRLFRLPVPKKGAITgILGPNGIGKTTAINILSGLV 125
                                       55567788888888886688************998765 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.025
                             T2SSE 126 vrerglilvsGgTgsGKttllyallkeinks 156
                                       vr   ++ v G+  +GKtt++ +l  ei+ +
  gi|474934233|ref|YP_007687815.1| 365 VRIGESVGVVGPNATGKTTFVKMLAGEIKPD 395
                                       5555666799*************99999876 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1     0.019        11       6      22 ..     106     122 ..     102     129 .. 0.84
   2 ?    3.7   0.2     0.073        41       6      26 ..     373     393 ..     369     404 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.019
                                       EEESTTSSHHHHHHHHH CS
                             SRP54   6 lvGlqGaGKTttlaKLa 22 
                                       ++G++G+GKTt++  L+
  gi|474934233|ref|YP_007687815.1| 106 ILGPNGIGKTTAINILS 122
                                       78*********998765 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.073
                                       EEESTTSSHHHHHHHHHHHHH CS
                             SRP54   6 lvGlqGaGKTttlaKLaallk 26 
                                       +vG++ +GKTt +  La  +k
  gi|474934233|ref|YP_007687815.1| 373 VVGPNATGKTTFVKMLAGEIK 393
                                       79***********99998776 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   1.6      0.47   2.6e+02       3      12 ..      19      29 ..      15      34 .. 0.76
   2 ?    9.5   5.0    0.0036         2       1      15 []      53      67 ..      53      67 .. 0.97

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.47
                            Fer4_3  3 gCg.aCvevCP 12
                                       C+  C++ CP
  gi|474934233|ref|YP_007687815.1| 19 KCNkECEKFCP 29
                                      38767*****9 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0036
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+gCg Cv+ CP +A
  gi|474934233|ref|YP_007687815.1| 53 CQGCGICVNKCPFKA 67
                                      ************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (596 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        33  (0.00184059); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              32  [number of targets reported over threshold]
# CPU time: 0.69u 0.31s 00:00:01.00 Elapsed: 00:00:00.47
# Mc/sec: 3784.99
//
Query:       gi|474934234|ref|YP_007687816.1|  [L=60]
Description: hypothetical protein TALC_00659 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.24   11.7   4.3       0.52   10.6   4.3    1.7  1  DUF4134   Domain of unknown function (DUF4134)


Domain annotation for each model (and alignments):
>> DUF4134  Domain of unknown function (DUF4134)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   4.3   2.9e-05      0.52      37      64 ..       4      30 ..       1      53 [. 0.78

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 2.9e-05
                           DUF4134 37 pvtkliyaiaavvglvgalkvYikwnsg 64
                                      ++t+l+yai+++v+lv a++v++ +   
  gi|474934234|ref|YP_007687816.1|  4 SITNLLYAIIGIVALV-AFNVFNGLGVA 30
                                      689************9.79999876554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 390.02
//
Query:       gi|474934235|ref|YP_007687817.1|  [L=454]
Description: putative efflux protein, MATE family [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-30  105.6  37.3      2e-21   76.3  10.7    2.7  3  MatE             MatE
    4.3e-07   30.1   9.8    4.3e-07   30.1   9.8    5.0  5  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai


Domain annotation for each model (and alignments):
>> MatE  MatE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.3  10.7   2.2e-25     2e-21       1     161 []      24     183 ..      24     183 .. 0.97
   2 !   38.4  14.6     1e-13   9.1e-10       2     156 ..     245     403 ..     244     408 .. 0.90
   3 ?   -2.3   0.1      0.34     3e+03      77     102 ..     421     446 ..     414     450 .. 0.74

  Alignments for each domain:
  == domain 1  score: 76.3 bits;  conditional E-value: 2.2e-25
                              MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgli 77 
                                       P+a++ ++++l + +d +++++lg++al+++++a ++   ++ ++ gl++++++  ++a+G +++++a+ ++ q++ 
  gi|474934235|ref|YP_007687817.1|  24 PLAVAIFVQNLNGVTDAMWAAWLGADALGGLGLAYPLYASIVGIGSGLAIGVAAAEARAVGLGDREGASGYAAQSFT 100
                                       99*************************************************************************** PP

                              MatE  78 lllllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislll 154
                                       ++l++s+++a+ +++f+ +++  f++ +  +  a +y    + + ++++ + v sgilrg g +k +++i +i++  
  gi|474934235|ref|YP_007687817.1| 101 ISLVISVALAIPLVIFAVPLMDAFGSGA-ASREAVDYGMPFFSFGFFIIASAVMSGILRGEGAAKESMAIQVIGAAT 176
                                       ************************8777.59999999999999999999**************************** PP

                              MatE 155 niplnyl 161
                                       ni+l+++
  gi|474934235|ref|YP_007687817.1| 177 NIVLDPV 183
                                       ****985 PP

  == domain 2  score: 38.4 bits;  conditional E-value: 1e-13
                              MatE   2 ialenllesllslidtllvgrl.gskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgli 77 
                                        a e +++sl+++ +++++ ++ g++a++ ++ a++i+ l+ +++ ++s a+ ++++ ++  ++ + +++a+  g+ 
  gi|474934235|ref|YP_007687817.1| 245 EAAELATMSLINIPMNFIIVGVgGASAVGFYTSAWRIAYLVLIPAQAISGAIVSVCSTEFARGRGDLVQRAFSFGTR 321
                                       578899*********************************************************************** PP

                              MatE  78 lllllsliiallvllfseqilslftqdeevlelakr...ylrililgipalalqlvlsgilrgagktkvplyislis 151
                                       ++l    i+a+++ ++s +++ +ft++  + ++  +   ++ +l+l +p+++  +v s++l++ + +++++  s+i+
  gi|474934235|ref|YP_007687817.1| 322 ISLKQTTIFAVVMAVLSYPLAMVFTASSSMDPYRGEmciLIILLALMLPVMSQVFVGSAYLQALKHSEIGFLSSFIR 398
                                       *****************************66554441114555667889999999********************** PP

                              MatE 152 lllni 156
                                       +l+ +
  gi|474934235|ref|YP_007687817.1| 399 NLIMV 403
                                       98765 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.34
                              MatE  77 illlllsliiallvllfseqilslft 102
                                       ++  ++ ++   +++lf++  ++ f 
  gi|474934235|ref|YP_007687817.1| 421 VACSAIEIFGGTMMWLFARRYVRAFV 446
                                       44457788888899999988888875 PP

>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   1.0      0.62   5.6e+03      43      53 ..      54      64 ..      22      82 .. 0.52
   2 !    4.7   0.2    0.0032        28      31      61 ..      99     129 ..      90     132 .. 0.65
   3 !   30.1   9.8   4.8e-11   4.3e-07      10      85 ..     145     223 ..     138     281 .. 0.69
   4 !    4.0   1.7    0.0052        46      47     113 ..     284     346 ..     281     362 .. 0.72
   5 !   10.6   7.5     5e-05      0.45       2      82 ..     362     443 ..     360     449 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.62
                   Polysacc_synt_C 43 lilnllliplf 53
                                      l+l ++l  ++
  gi|474934235|ref|YP_007687817.1| 54 LGLAYPLYASI 64
                                      33333333222 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0032
                   Polysacc_synt_C  31 alkalvigalvklilnllliplfgivGaaia 61 
                                       ++++lvi++++ + l ++ +pl+ + G  +a
  gi|474934235|ref|YP_007687817.1|  99 FTISLVISVALAIPLVIFAVPLMDAFGSGAA 129
                                       4566666666666666666688888886555 PP

  == domain 3  score: 30.1 bits;  conditional E-value: 4.8e-11
                   Polysacc_synt_C  10 iflslstvlssiLqglgrqkialkalvigalvklilnllli..plfgivGaaiatvlallvvavln.lyalrrllgi 83 
                                       +f+  s v+s+iL g g +k+ + + viga+ +++l  +l+    +g+ Ga +atv+a +v+++l   +++r+++ i
  gi|474934235|ref|YP_007687817.1| 145 FFIIASAVMSGILRGEGAAKESMAIQVIGAATNIVLDPVLMygLDMGVAGAGWATVIAGAVSLLLGlSFYARKKMFI 221
                                       788888***********************************655779****************99945666666655 PP

                   Polysacc_synt_C  84 kl 85 
                                        l
  gi|474934235|ref|YP_007687817.1| 222 VL 223
                                       55 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.0052
                   Polysacc_synt_C  47 llliplfgivGaaiatvlallvvavlnlyalrrllgiklellrrllkpllaalvmgivvylllllll 113
                                       l+lip   i Ga+++ + ++++     l+     +g ++  l+++    ++a+vm+++ y l++++ 
  gi|474934235|ref|YP_007687817.1| 284 LVLIPAQAISGAIVSVCSTEFARGRGDLVQRAFSFGTRI-SLKQT---TIFAVVMAVLSYPLAMVFT 346
                                       678888889999999999998888888777777777777.45555...5788888888665544443 PP

  == domain 5  score: 10.6 bits;  conditional E-value: 5e-05
                   Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfg.ivGaaiatvlallvvavlnlyal 77 
                                       + +lal+++++s   v+s++Lq+l++  i +++++i  l+ +   ++   lfg ++G+ +a  + ++++  +++ ++
  gi|474934235|ref|YP_007687817.1| 362 IILLALMLPVMSQVFVGSAYLQALKHSEIGFLSSFIRNLIMVSGYFVAAELFGvTMGIWVACSAIEIFGGTMMWLFA 438
                                       56899999999999***************************************56********************** PP

                   Polysacc_synt_C  78 rrllg 82 
                                       rr+++
  gi|474934235|ref|YP_007687817.1| 439 RRYVR 443
                                       **986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2842.82
//
Query:       gi|474934236|ref|YP_007687818.1|  [L=773]
Description: methionyl-tRNA synthetase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   1.8e-142  474.7   0.0   2.3e-142  474.4   0.0    1.1  1  tRNA-synt_1g    tRNA synthetases class I (M)
    7.1e-27   93.4   0.0    1.3e-26   92.5   0.0    1.5  1  tRNA_bind       Putative tRNA binding domain
    2.7e-17   62.3   0.2    2.2e-09   36.1   0.1    3.2  3  tRNA-synt_1     tRNA synthetases class I (I, L, M and V)
    4.8e-07   29.9   0.0    8.1e-07   29.1   0.0    1.4  1  Anticodon_1     Anticodon-binding domain of tRNA
    9.7e-06   25.1   0.0     0.0024   17.3   0.0    2.4  2  tRNA-synt_1e    tRNA synthetases class I (C) catalytic domain
     0.0011   19.0   3.8       0.24   11.4   0.1    2.7  2  HypA            Hydrogenase/urease nickel incorporation, meta
     0.0018   18.2  10.9      0.017   15.1   6.8    2.6  2  DZR             Double zinc ribbon
      0.005   16.5   3.2      0.036   13.7   3.4    2.0  2  TackOD1         Thaumarchaeal output domain 1
  ------ inclusion threshold ------
       0.15   12.3   0.0       0.32   11.2   0.0    1.6  1  CH              Calponin homology (CH) domain
       0.15    9.9   0.6       0.23    9.3   0.6    1.1  1  PolC_DP2        DNA polymerase II large subunit DP2
       0.17   12.0  14.2        1.2    9.3   2.8    3.1  2  Zn-ribbon_8     Zinc ribbon domain
       0.23   10.9  16.1       0.81    9.2   5.2    4.1  3  zf-ribbon_3     zinc-ribbon domain
       0.36   10.9   6.6        1.3    9.1   6.5    1.9  1  zinc-ribbons_6  zinc-ribbons
       0.96    9.4  10.5        3.7    7.6   3.0    2.5  2  Prok-RING_1     Prokaryotic RING finger family 1
        2.4    7.8   5.2       0.63    9.6   1.0    2.1  2  zf_C2H2_10      C2H2 type zinc-finger


Domain annotation for each model (and alignments):
>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  474.4   0.0  1.9e-145  2.3e-142       1     391 []       4     408 ..       4     408 .. 0.96

  Alignments for each domain:
  == domain 1  score: 474.4 bits;  conditional E-value: 1.9e-145
                                       EEEEE--B--SS---HHHHH.HHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHH CS
                      tRNA-synt_1g   1 vlvttalpYangklHlGhll.evisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvheeike 76 
                                       +lv+ a+pY+ng++HlGh++ + ++ Dif+Ry+rl g+ev+ v+g+D+hGtpi+++Aekegvtpe++++++h+++k+
  gi|474934236|ref|YP_007687818.1|   4 ILVNIAWPYSNGPIHLGHVAgSLLPPDIFSRYNRLLGNEVMVVGGSDQHGTPITVTAEKEGVTPEQVADRYHAMNKK 80 
                                       689************************************************************************** PP

                                       HHHHTT---SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-EE........-TTS-EE- CS
                      tRNA-synt_1g  77 lfkklnisfdkygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdryvegtCPkckseeargdqce 153
                                         ++l+i+++ y++t++  h e++q++f+kl ++g+iy+k+ + +ycpk+ +flpdryvegtCP+c++ + r+dqc+
  gi|474934236|ref|YP_007687818.1|  81 AIEDLGIEYSLYSKTHNPVHFEVTQKLFTKLLDNGYIYTKDENEYYCPKCRKFLPDRYVEGTCPNCGATDVRSDQCD 157
                                       ***************************************************************************** PP

                                       TTSSB-E................EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS CS
                      tRNA-synt_1g 154 ecgkkleptelinpksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrd 230
                                       +cg+++ep ++i+p+++ +g++pevk ++++f+kls+fek l +++  +++ ++ nv+ +++++lk gLkd+ai+rd
  gi|474934236|ref|YP_007687818.1| 158 SCGTTFEPGDVIDPHCTRCGTRPEVKASTQFFLKLSAFEKPLLDFL-ADKTYWRANVRAYTQNFLKGGLKDRAITRD 233
                                       **********************************************.77779************************* PP

                                       -SSS-EET....TECCEEE-HHHHHHHHHHHTTTTT-...TTSGGGG.G--S......EEEEEGGGHHHHHTHHHHH CS
                      tRNA-synt_1g 231 ldwGipvP....gaekkvlYVWldAligYisatkelakkkgeeekwkeyWakdkevelvhfigkdiikFHtifwPai 303
                                       ++wG+p+P    + ++kv+YVW+dA+igY+s + e++++ g+++ wk +W  d++++ ++figkd+i+FH+i+wPai
  gi|474934236|ref|YP_007687818.1| 234 MSWGVPIPvegdEWKEKVIYVWFDAVIGYLSDSIEYCRSIGKPDMWKDFW-LDRDCKHYYFIGKDNIPFHSIIWPAI 309
                                       *********988889***********************************.88************************ PP

                                       HHH..TT----S-EEEE--EEE--------------HH.........HHHHHH-HHHHHHHHHHHS-TTS-EEE-HH CS
                      tRNA-synt_1g 304 llg..aelklpkkvvaheyltvegkKlSkSrgvvvkak.........ealerldadllRYylaaeapekkDldfswe 369
                                       l+g  ++++lp  + a+eyl+++g+KlSkSr+ +v+           ++le++d++ +RYyl+   p ++D++fsw+
  gi|474934236|ref|YP_007687818.1| 310 LMGqeEGFNLPYDIPANEYLMFNGGKLSKSRKGAVTDAesliprdmpHVLEKFDPEEIRYYLSIIMPDTHDAEFSWS 386
                                       ***9999************************998864411222222257899************************* PP

                                       HHHHHHHHHCCCHHHHHHHHH. CS
                      tRNA-synt_1g 370 dfvervNseLadklgnlvnRvl 391
                                       d+ ++vNseL+++lgn+ +R+l
  gi|474934236|ref|YP_007687818.1| 387 DMEQKVNSELVAALGNFYHRTL 408
                                       ********************85 PP

>> tRNA_bind  Putative tRNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.5   0.0   1.1e-29   1.3e-26       1      95 [.     592     689 ..     592     690 .. 0.92

  Alignments for each domain:
  == domain 1  score: 92.5 bits;  conditional E-value: 1.1e-29
                                       EEEEEEEEEEEETTSSTEEEEEEEESSSSEEEEEESCTTTSTHHHHTTEEEEEETTSESEEETTEEESSEE-EEEC. CS
                         tRNA_bind   1 lrvGkvleaeehpnadkLlvlkvdvGeeeprqivsgaknvyepeelvakkvvvvanlkpkklrGveSeGMilsaee. 76 
                                       lrvG+v+ +e+hpnadkL++l+vd+Ge +pr+i++g+k +y+ +e++++k +vv nl p+ lrG+eS GM+l+a++ 
  gi|474934236|ref|YP_007687818.1| 592 LRVGQVIRVEDHPNADKLFKLTVDIGEDKPRTICAGLKAFYSADEMLNRKAIVVSNLAPRPLRGIESCGMLLAADDe 668
                                       79*************************************************************************98 PP

                                       .CESSCEEEEEE.SST--TTC CS
                         tRNA_bind  77 .ldekevgilel.padveaGe 95 
                                        l +++v +l++ + d+++G+
  gi|474934236|ref|YP_007687818.1| 669 eLGGNSVLLLKPsDPDIPVGT 689
                                       888888888887345777776 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.1   1.9e-12   2.2e-09      28     175 ..       7     136 ..       2     145 .. 0.89
   2 !   21.2   0.0   6.1e-08   7.3e-05     363     443 ..     171     252 ..     161     261 .. 0.86
   3 ?   -4.2   0.0         3   3.6e+03     561     592 ..     333     374 ..     332     383 .. 0.70

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 1.9e-12
                       tRNA-synt_1  28 vdgPPyvtGslHiGhalaktl.kdivirykrmkGkevlyvpGwDhaGlaieakvekklgakekkerkklgreefrek 103
                                        +  Py +G +H+Gh+  + l  di  ry+r+ G+ev  v G D +G +i  + ek+ g + +              
  gi|474934236|ref|YP_007687818.1|   7 NIAWPYSNGPIHLGHVAGSLLpPDIFSRYNRLLGNEVMVVGGSDQHGTPITVTAEKE-GVTPE-------------- 68 
                                       5677*************999945****************************999999.44443.............. PP

                       tRNA-synt_1 104 vrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgliyrgkklvnwstklktalse 175
                                         + +++y++  +k++++lG+   ++   +T ++   e +++ f++l d+g iy      ++++k++  l +
  gi|474934236|ref|YP_007687818.1|  69 --QVADRYHAMNKKAIEDLGI--EYSLYSKTHNPVHFEVTQKLFTKLLDNGYIYTKDENEYYCPKCRKFLPD 136
                                       ..57899*************5..7899999************************************988766 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 6.1e-08
                       tRNA-synt_1 363 pfcerskkpiiyrateqWfvrvkeladaalkave.kvqfvpkskekryaswleniqdWciSRqrwWGhriplfvske 438
                                       p+c r ++  +++a++q f +++++++ +l+ +  k+++  + +  + + +    +d +i R+  WG++ip+  ++ 
  gi|474934236|ref|YP_007687818.1| 171 PHCTRCGTRPEVKASTQFFLKLSAFEKPLLDFLAdKTYWRANVRAYTQNFLKGGLKDRAITRDMSWGVPIPVEGDEW 247
                                       9******************************999788888888766655555689****************977777 PP

                       tRNA-synt_1 439 teevv 443
                                       +e+v+
  gi|474934236|ref|YP_007687818.1| 248 KEKVI 252
                                       66665 PP

  == domain 3  score: -4.2 bits;  conditional E-value: 3
                       tRNA-synt_1 561 GrKmSKs.lgNvidpldvik........kygadalRltli.l 592
                                       G K+SKs +g v d +++i         k   + +R++l   
  gi|474934236|ref|YP_007687818.1| 333 GGKLSKSrKGAVTDAESLIPrdmphvleKFDPEEIRYYLSiI 374
                                       889999845678888888776777777788888888887644 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   6.8e-10   8.1e-07       1     100 [.     425     519 ..     425     578 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 6.8e-10
                       Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedk.raaqevllevletllrl 76 
                                       dr +   +n++ ++++++++ ++f+ka+++++ +    +++ y+++  p+   +++ +k  aa +  l ++++l  l
  gi|474934236|ref|YP_007687818.1| 425 DRKVTDAINSAMEDAKANLQVCNFKKALQDVMGL--AHFANEYFNSCMPWKLIKEDREKcGAALYENLRLVKALAVL 499
                                       7888999**************************8..88***************999888655668888899****** PP

                       Anticodon_1  77 laPfmPfitEelwqreeeelgkke 100
                                         P +P  +E++w++    +g + 
  gi|474934236|ref|YP_007687818.1| 500 AWPYLPRSSEKIWEY----MGLPG 519
                                       *************44....44333 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0     2e-06    0.0024      23     130 ..      17     126 ..       8     136 .. 0.85
   2 !    5.2   0.0    0.0094        11     244     282 ..     326     373 ..     323     393 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2e-06
                                       -BHHH.HHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHTT----SB. CS
                      tRNA-synt_1e  23 shlGh.aRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeksvkelaekfieefkkdleaLnvlkptl. 97 
                                       +hlGh a sl+  Di+ r+ + lg +v+ v         i   a++e+ + +++a+++ +  kk++e+L++  + + 
  gi|474934236|ref|YP_007687818.1|  17 IHLGHvAGSLLPPDIFSRYNRLLGNEVMVVGGSDQHGTPITVTAEKEGVTPEQVADRYHAMNKKAIEDLGIEYSLYs 93 
                                       7****44578889******************99999999********************************986541 PP

                                       --BGGGGHHHHHHHHHHHHHTTSEEE-TTS-EE CS
                      tRNA-synt_1e  98 eprvsekvdeiielvekliekgyaYavsdgdvy 130
                                       +++   + +   +l  kl+++gy Y+ ++++ y
  gi|474934236|ref|YP_007687818.1|  94 KTHNPVHFEVTQKLFTKLLDNGYIYTKDENEYY 126
                                       34444566777899************9965544 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0094
                                       E--EEETTBE--TTTT---B.........HHHHHTTS-HHHHHHHHHS CS
                      tRNA-synt_1e 244 nghlkiegekmsksLknfit.........ikdvlkkfdprqlRlllls 282
                                       n++l+++g k+sks k  +t         + +vl+kfdp+++R++l  
  gi|474934236|ref|YP_007687818.1| 326 NEYLMFNGGKLSKSRKGAVTdaesliprdMPHVLEKFDPEEIRYYLSI 373
                                       67999*********99888644444444456799**********9964 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.1    0.0002      0.24      63      98 ..     108     152 ..      56     155 .. 0.62
   2 !    8.2   0.6    0.0021       2.5      72     100 ..     155     183 ..     152     195 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0002
                                       E.........EEEE--EEEETTTS-EEECHHH.HHS-TTTSSS-EE CS
                              HypA  63 e.........ieevpvkvrCreCgkefeleek.alrCpkCgsadve 98 
                                                 +++ + +++C +C+k    + + + +Cp+Cg++dv+
  gi|474934236|ref|YP_007687818.1| 108 FtklldngyiYTKDENEYYCPKCRKFLPDR-YvEGTCPNCGATDVR 152
                                       044444555467788999******777755.44789******9986 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0021
                                       EETTTS-EEECHHH.HHS-TTTSSS-EEEE CS
                              HypA  72 rCreCgkefeleek.alrCpkCgsadveiv 100
                                       +C++Cg++fe  +  + +C +Cg++  e++
  gi|474934236|ref|YP_007687818.1| 155 QCDSCGTTFEPGDViDPHCTRCGTR-PEVK 183
                                       7*********87656889****986.3444 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   6.8   1.4e-05     0.017      10      49 .]     122     160 ..     118     160 .. 0.84
   2 !   11.3   7.5   0.00023      0.27       1      39 [.     143     181 ..     143     188 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.4e-05
                               DZR  10 pdarfCseCgtklkavaaedrCpsCgekvdpearfCpeCG 49 
                                       ++  +C++C++ l+    e +Cp+Cg+  d ++  C++CG
  gi|474934236|ref|YP_007687818.1| 122 ENEYYCPKCRKFLPDRYVEGTCPNCGAT-DVRSDQCDSCG 160
                                       5677*********98888********86.555568****9 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00023
                               DZR   1 CpqCgeelppdarfCseCgtklkavaa..edrCpsCgekvd 39 
                                       Cp+Cg+  + ++  C+ Cgt+ + + +    +C +Cg+  +
  gi|474934236|ref|YP_007687818.1| 143 CPNCGAT-DVRSDQCDSCGTTFE-PGDviDPHCTRCGTRPE 181
                                       9***987.999999*******97.34468899****99743 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   3.4     3e-05     0.036      34     122 ..      84     172 ..      68     179 .. 0.74
   2 ?    4.8   0.4     0.016        19     147     175 ..     154     183 ..     151     187 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3e-05
                           TackOD1  34 kelysypllealsk..ekeeseelleelvkrglleeelvdrirlCpsCksgh..lnvrevCpkCkSidieeqelihh 106
                                       + +++y+l +++++  + e +++l+++l ++g++ ++  ++   Cp+C+       v  +Cp+C+++d+++++   +
  gi|474934236|ref|YP_007687818.1|  84 DLGIEYSLYSKTHNpvHFEVTQKLFTKLLDNGYIYTKD-ENEYYCPKCRKFLpdRYVEGTCPNCGATDVRSDQ---C 156
                                       447888888888875444578899999*******9776.55679*****97511457889*********9985...9 PP

                           TackOD1 107 ftCgnvgpeeeflkeg 122
                                        +Cg++ +  +  + +
  gi|474934236|ref|YP_007687818.1| 157 DSCGTTFEPGDVIDPH 172
                                       9999887666655555 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.016
                           TackOD1 147 ykCnsCkslfsepev.karClsCekesesd 175
                                        +C+sC+++f   +v   +C++C+++ e++
  gi|474934236|ref|YP_007687818.1| 154 DQCDSCGTTFEPGDViDPHCTRCGTRPEVK 183
                                       68********988762689*****987765 PP

>> CH  Calponin homology (CH) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00027      0.32       7      61 ..     428     482 ..     422     498 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00027
                                       HHHHHHHHHTTSTTSSTTSCHHHHHTTSHHHHHHHHHHSTTTSSGGGSTTTHHHH CS
                                CH   7 llrWinshleeagpkvkvedfeedlrDGvlLckLlnklapglvdkkklnksefkk 61 
                                       +++ ins +e+a+ + +v +f+++l+D + L++++n    ++ ++k ++ +++k+
  gi|474934236|ref|YP_007687818.1| 428 VTDAINSAMEDAKANLQVCNFKKALQDVMGLAHFANEYFNSCMPWKLIKEDREKC 482
                                       5666999***************************************998775554 PP

>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.6   0.00019      0.23     617     672 ..     123     187 ..     101     200 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00019
                          PolC_DP2 617 arrkCkkCgk....etlearCeeCgekteeklvCkkceeeve.eek....cekcekeakavkkkk 672
                                       ++++C+kC k    + +e +C++Cg++   + +C +c+++ e  +     c +c+++ + +++++
  gi|474934236|ref|YP_007687818.1| 123 NEYYCPKCRKflpdRYVEGTCPNCGATDVRSDQCDSCGTTFEpGDVidphCTRCGTRPEVKASTQ 187
                                       67899999973332457889******************977743335666999998877766655 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   3.6    0.0059         7       5      37 ..     124     152 ..     123     153 .. 0.78
   2 ?    9.3   2.8     0.001       1.2       7      34 ..     155     178 ..     155     184 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0059
                       Zn-ribbon_8   5 eYrCeeCghefevlqsisdapltaCPeCgs.evr 37 
                                       eY C +C  +f + +      + +CP+Cg+ +vr
  gi|474934236|ref|YP_007687818.1| 124 EYYCPKCR-KFLPDRY-V---EGTCPNCGAtDVR 152
                                       899****9.8886653.2...566******8876 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.001
                       Zn-ribbon_8   7 rCeeCghefevlqsisdapltaCPeCgs 34 
                                       +C++Cg++fe+   +    +++C +Cg 
  gi|474934236|ref|YP_007687818.1| 155 QCDSCGTTFEPGD-VI---DPHCTRCGT 178
                                       6*********776.44...567****98 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.2     0.049        58       2       8 ..     124     130 ..     123     137 .. 0.77
   2 ?    9.2   5.2   0.00068      0.81       4      24 ..     142     161 ..     139     163 .. 0.86
   3 ?    5.6   4.1    0.0092        11       4      24 ..     155     178 ..     154     179 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.049
                       zf-ribbon_3   2 tvrCPnC 8  
                                       +++CP+C
  gi|474934236|ref|YP_007687818.1| 124 EYYCPKC 130
                                       789**** PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00068
                       zf-ribbon_3   4 rCPnCGaplssddnvCpyCGt 24 
                                       +CPnCGa  + +   C +CGt
  gi|474934236|ref|YP_007687818.1| 142 TCPNCGAT-DVRSDQCDSCGT 161
                                       6******8.777777*****8 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.0092
                       zf-ribbon_3   4 rCPnCGa.plssddn...vCpyCGt 24 
                                       +C +CG+   +++d+   +C+ CGt
  gi|474934236|ref|YP_007687818.1| 155 QCDSCGTtF-EPGDVidpHCTRCGT 178
                                       6******99.***862226888876 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   6.5    0.0011       1.3       2      40 ..     126     164 ..     125     178 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0011
                                       --SSS-S--EE-SSEEE-TTT--EEEEEEE-SSS-S--- CS
                    zinc-ribbons_6   2 kCpeCqqelekrgeqyhCeaCqedlkkealCpeCeqele 40 
                                       +Cp+C + l  r  + +C +C +   +   C+ C+   e
  gi|474934236|ref|YP_007687818.1| 126 YCPKCRKFLPDRYVEGTCPNCGATDVRSDQCDSCGTTFE 164
                                       7*********************************98765 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.8    0.0079       9.5       3      29 ..     123     149 ..     121     153 .. 0.83
   2 ?    7.6   3.0    0.0031       3.7       4      28 ..     153     178 ..     150     180 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0079
                       Prok-RING_1   3 tgkkCpvCgkelkeedDiVvCpeCgtp 29 
                                       ++  Cp C+k l +     +Cp+Cg+ 
  gi|474934236|ref|YP_007687818.1| 123 NEYYCPKCRKFLPDRYVEGTCPNCGAT 149
                                       6788*****99999977779*****96 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0031
                       Prok-RING_1   4 gkkCpvCgkelkeedDiV..vCpeCgt 28 
                                        ++C  Cg +++++ D++   C+ Cgt
  gi|474934236|ref|YP_007687818.1| 153 SDQCDSCGTTFEPG-DVIdpHCTRCGT 178
                                       679***********.666457*****9 PP

>> zf_C2H2_10  C2H2 type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.0   0.00053      0.63       3      14 ..     125     136 ..     124     137 .. 0.91
   2 ?   -1.8   0.2       1.9   2.3e+03       5       9 ..     143     147 ..     141     149 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00053
                        zf_C2H2_10   3 fsCPKCqeklPD 14 
                                       + CPKC   lPD
  gi|474934236|ref|YP_007687818.1| 125 YYCPKCRKFLPD 136
                                       77*********9 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.9
                        zf_C2H2_10   5 CPKCq 9  
                                       CP C+
  gi|474934236|ref|YP_007687818.1| 143 CPNCG 147
                                       ****7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (773 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                        31  (0.00172904); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.81u 0.35s 00:00:01.16 Elapsed: 00:00:00.55
# Mc/sec: 4265.66
//
Query:       gi|474934237|ref|YP_007687819.1|  [L=193]
Description: EMAP domain protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.8e-30  104.9   0.0    9.3e-30  102.6   0.0    1.9  2  tRNA_bind  Putative tRNA binding domain


Domain annotation for each model (and alignments):
>> tRNA_bind  Putative tRNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.6   0.0   5.2e-34   9.3e-30       1      95 [.      16     112 ..      16     113 .. 0.96
   2 ?   -0.1   0.0     0.056     1e+03      35      65 ..     116     148 ..     114     173 .. 0.60

  Alignments for each domain:
  == domain 1  score: 102.6 bits;  conditional E-value: 5.2e-34
                                       EEEEEEEEEEEETTSSTEEEEEEEESSSSEEEEEESCTTTSTHHHHTTEEEEEETTSESEEETTEEESSEE-EEEC. CS
                         tRNA_bind   1 lrvGkvleaeehpnadkLlvlkvdvGeeeprqivsgaknvyepeelvakkvvvvanlkpkklrGveSeGMilsaee. 76 
                                       lr+G+v+++e+hp+a+kL++lkvd+Geeepr++v+++k++y+pe+++++k+ +vanlkp+++rGv+S GM+++a++ 
  gi|474934237|ref|YP_007687819.1|  16 LRIGTVVSVEDHPDAEKLYILKVDLGEEEPRTVVTNIKSFYPPEKMMGRKLLLVANLKPANFRGVKSFGMLCAADDm 92 
                                       79**************************************************************************8 PP

                                       .CESSCEEEEEESST--TTC CS
                         tRNA_bind  77 .ldekevgilelpadveaGe 95 
                                        + +++  +l++  dv++G+
  gi|474934237|ref|YP_007687819.1|  93 eMGGNSLLLLDPSVDVPNGT 112
                                       88888999999999999996 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.056
                                       ESCTTTSTHHHH..TTEEEEEETTSESEEETTE CS
                         tRNA_bind  35 sgaknvyepeel..vakkvvvvanlkpkklrGv 65 
                                       +g++n  +  e+  ++k+ + va+l   k++G+
  gi|474934237|ref|YP_007687819.1| 116 CGLENSQSRVEMkhIEKVTMKVAKLSGGKFMGM 148
                                       666666663333003333333333333355553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 1395.75
//
Query:       gi|474934238|ref|YP_007687820.1|  [L=218]
Description: putative metal-dependent phosphoesterases (PHP family) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.7e-12   44.6   0.0    1.6e-11   43.8   0.0    1.4  1  PHP_C     PHP-associated
    2.7e-08   34.3   0.0    3.5e-08   33.9   0.0    1.2  1  PHP       PHP domain


Domain annotation for each model (and alignments):
>> PHP_C  PHP-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.0   1.7e-15   1.6e-11       2      53 ..     133     184 ..     132     187 .. 0.95

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 1.7e-15
                             PHP_C   2 eaNrrArrfAeklglpgtgGSDAHrleeVGrayTefeepiatpdelleaire 53 
                                       +aNr++ ++A++ g+p t+GSDAH++  VG + + +++   t++e++++i +
  gi|474934238|ref|YP_007687820.1| 133 SANRKSMKLAKRIGKPITAGSDAHSPHRVGWGNVTLPDGLTTWEEVVASIMR 184
                                       79***********************************************986 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0   3.9e-12   3.5e-08       1      46 [.       4      48 ..       4     100 .. 0.92

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 3.9e-12
                                      EEEE--CCC--.S-H..HHHHHHHHHCT-SEEEEEEEEBTTHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               PHP  1 dlHvHteyslldgalsieelvkkakelglkaiaiTDhgnlfgyvef 46
                                      dlHvHt ys   g  +++++++ ++e+g+  +aiTDh+ +++y++ 
  gi|474934238|ref|YP_007687820.1|  4 DLHVHTCYSKD-GKSTPQQVIDMCIEKGIGCVAITDHNSFQAYFDV 48
                                      89*******88.89999************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1350.24
//
Query:       gi|474934239|ref|YP_007687821.1|  [L=52]
Description: hypothetical protein TALC_00664 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 373.64
//
Query:       gi|474934240|ref|YP_007687822.1|  [L=397]
Description: putative ATPase (AAA+ superfamily) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-38  130.1   0.1    1.3e-37  128.7   0.1    1.7  2  AAA_14    AAA domain
      9e-07   29.0   0.1    1.3e-05   25.2   0.0    2.4  2  ATPase_2  ATPase domain predominantly from Archaea
    6.7e-05   23.0   0.0    0.00012   22.2   0.0    1.4  1  DUF4143   Domain of unknown function (DUF4143)
    0.00053   20.4   0.0      0.012   16.0   0.0    2.7  3  AAA_16    AAA ATPase domain
    0.00058   19.4   0.0     0.0017   17.9   0.0    1.8  1  HTH_24    Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.024   14.6   0.0    1.6  1  HTH_11    HTH domain
      0.013   15.8   0.0      0.092   13.0   0.0    2.0  2  AAA_22    AAA domain
      0.044   12.6   0.0      0.071   11.9   0.0    1.2  1  AAA_35    AAA-like domain
      0.044   13.7   0.0        1.1    9.3   0.0    2.3  2  MarR      MarR family
      0.067   13.2   0.0       0.19   11.8   0.0    1.7  1  DUF2089   Protein of unknown function (DUF2089)
       0.11   13.1   0.0       0.29   11.7   0.0    1.8  1  AAA_18    AAA domain
       0.11   12.3   0.0       0.26   11.1   0.0    1.6  1  HTH_10    HTH DNA binding domain
       0.12   12.3   0.0       0.37   10.7   0.0    1.8  2  NTPase_1  NTPase
       0.16   11.7   0.0       0.41   10.4   0.0    1.6  1  AAA_29    P-loop containing region of AAA domain


Domain annotation for each model (and alignments):
>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.7   0.1     1e-40   1.3e-37       4     131 .]      22     151 ..      19     151 .. 0.94
   2 ?   -3.0   0.0       5.4   6.9e+03      92     125 ..     324     357 ..     318     358 .. 0.75

  Alignments for each domain:
  == domain 1  score: 128.7 bits;  conditional E-value: 1e-40
                            AAA_14   4 ilvitGaRrvGKTtllkqlikell...vkkesilyinldderdkkladpekllelileklkeekktylflDEiqevp 77 
                                       i+vitG+Rr+GK+tll+q++ +l    ++++si+ in++d + + ++d + l+e i +++ ++++ y+flDE+q+v+
  gi|474934240|ref|YP_007687822.1|  22 IKVITGMRRSGKSTLLEQYAARLKeqgISDNSIFMINFEDTEWQYITDHTILNEWISDNIPKKGQCYVFLDEVQNVD 98 
                                       89******************999999*****************99999876777777777778************** PP

                            AAA_14  78 ewekalkslvdegknldvivtGSnskllskeiatslagrvaeielyplsfaEfl 131
                                       +we+ + +l +++ n+dv++tGSnsk+ls+e+at+ +gr++ei+++plsf+E+l
  gi|474934240|ref|YP_007687822.1|  99 GWERSVSGLQNKK-NCDVYITGSNSKMLSSELATHISGRYTEIKVMPLSFSEYL 151
                                       ***********99.**************************************97 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.4
                            AAA_14  92 nldvivtGSnskllskeiatslagrvaeielypl 125
                                       ++d+ ++ S      +  +t +a+ + e e+ p+
  gi|474934240|ref|YP_007687822.1| 324 EVDFTASDSEGTEYFQVCQTMMAEDTYEREMRPF 357
                                       5677777777777778888888888889999887 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0     1e-08   1.3e-05      15      68 ..      15      70 ..       6      98 .. 0.80
   2 ?    0.7   0.0      0.31     4e+02     151     200 ..     105     153 ..      83     162 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1e-08
                          ATPase_2 15 lerepneiyfiYGpegsGKtaLlkeiienledkdk..yviyyialreesiskldef 68
                                       +  ++ i +i+G ++sGK++Ll + + +l++++   + i++i++++ + +++++ 
  gi|474934240|ref|YP_007687822.1| 15 GRDRNDVIKVITGMRRSGKSTLLEQYAARLKEQGIsdNSIFMINFEDTEWQYITDH 70
                                      455678999*********************98877669********9999988876 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.31
                          ATPase_2 151 sltkekhlcvviclsSeglfiervyneselegrhkyilvddldketalnf 200
                                       s +++k+ c v ++ S++ ++   +      gr + i+v +l + + l++
  gi|474934240|ref|YP_007687822.1| 105 SGLQNKKNCDVYITGSNSKMLS-SELATHISGRYTEIKVMPLSFSEYLKL 153
                                       5567889999988888888888.445556778888899999988888877 PP

>> DUF4143  Domain of unknown function (DUF4143)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   9.7e-08   0.00012      18     111 ..     220     333 ..     163     341 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 9.7e-08
                                       x.................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DUF4143  18 k.................................glverlppwsespnskkrlrkspKlyfvDtGLlvallgldkee 61 
                                                                         +l++ ++++      kk l+++ K+y  D G+ + +lg  ++ 
  gi|474934240|ref|YP_007687822.1| 220 YsnignttnidsiaeatgisnptvskyvdemckaFLFYHAERY--DVVGKKILKTNGKYYASDLGMRNVMLGGPSAG 294
                                       1444555556666668888888888889999999*********..9999999**********************999 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DUF4143  62 lledsenkGallEnlVaqeLlkysekegaklyyyrdkngaEvDfvielkg 111
                                       +++++      lEn+V+ eLl+ +++ ++++  yrd    EvDf  ++++
  gi|474934240|ref|YP_007687822.1| 295 DISRP------LENVVYLELLR-RGY-EVRVGSYRD---CEVDFTASDSE 333
                                       88877......***********.555.678999998...7****887644 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   9.1e-06     0.012      14      52 ..      10      52 ..       5      82 .. 0.77
   2 ?   -0.1   0.0       0.8     1e+03     125     148 ..      75      98 ..      70     107 .. 0.74
   3 ?   -0.2   0.0      0.86   1.1e+03      64      95 ..     178     210 ..     148     261 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 9.1e-06
                            AAA_16 14 salervrsgrpelvllsGesGvGKsslvrellralekd....g 52
                                      s+le+ r+    + +++G++ +GKs+l+++ + +l+++    +
  gi|474934240|ref|YP_007687822.1| 10 SLLEAGRDRNDVIKVITGMRRSGKSTLLEQYAARLKEQgisdN 52
                                      566666666668889*********************9944442 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.8
                            AAA_16 125 rll.allsrderplvlvlDdlqwad 148
                                       + + + ++++++  +++lD++q +d
  gi|474934240|ref|YP_007687822.1|  75 EWIsDNIPKKGQ-CYVFLDEVQNVD 98 
                                       556566677555.9********877 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.86
                            AAA_16  64 esaipysa.laqalareellrqlldeaesaele 95 
                                       ++++++s  l++ +++  l++++l+++++++++
  gi|474934240|ref|YP_007687822.1| 178 DADRRFSGgLLEGIFNTVLVKDILSRLKTDDVS 210
                                       333556777888888889999999885554443 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.3e-06    0.0017      19      44 ..     228     253 ..     224     253 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.3e-06
                            HTH_24  19 sqreLAerlglSpstvnrrlkrLeee 44 
                                       ++  +Ae++g+S +tv++++++++++
  gi|474934240|ref|YP_007687822.1| 228 NIDSIAEATGISNPTVSKYVDEMCKA 253
                                       5678*******************985 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.9e-05     0.024       2      46 ..     212     269 ..     211     278 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.9e-05
                            HTH_11   2 llqilelLleargp.isgeeLAeeLnvSrrtvrrdIkaLeelg............vpI 46 
                                       l++i ++L+++ g+  +++ +Ae +++S  tv ++++++ ++              +I
  gi|474934240|ref|YP_007687822.1| 212 LTAIARFLYSNIGNtTNIDSIAEATGISNPTVSKYVDEMCKAFlfyhaerydvvgKKI 269
                                       6789999*******************************96665577777755555555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   7.2e-05     0.092       7      62 ..      22      74 ..      16      91 .. 0.76
   2 ?    1.0   0.0      0.36   4.6e+02      80     109 ..      75     101 ..      66     126 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.2e-05
                            AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdl.lrellr 62
                                      i v+tG   +GK+tll++++ +l+e+      ++  +f+   ++t+++ +  + +l+
  gi|474934240|ref|YP_007687822.1| 22 IKVITGMRRSGKSTLLEQYAARLKEQGI----SDNSIFMINFEDTEWQYItDHTILN 74
                                      5589*******************76654....6666677777777777765666665 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.36
                            AAA_22  80 ealeqalraravielliiDEaqhlrseeal 109
                                       e + +++ +++    + +DE+q+++     
  gi|474934240|ref|YP_007687822.1|  75 EWISDNIPKKGQ-CYVFLDEVQNVD--GWE 101
                                       667777778888.9999******95..222 PP

>> AAA_35  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   5.5e-05     0.071      36     117 ..      25     117 ..      10     127 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.5e-05
                            AAA_35  36 ikapkkmGKtSLlarilakakqq...gyktvsldlqladkeilsdldkflrwfcanvsrqLklenkl.....deyWd 104
                                       i + ++ GK+ Ll++  a+ k+q   +++ ++++++ ++ + ++d   + +w++ n+ ++ +    l      + W+
  gi|474934240|ref|YP_007687822.1|  25 ITGMRRSGKSTLLEQYAARLKEQgisDNSIFMINFEDTEWQYITDHTILNEWISDNIPKKGQCYVFLdevqnVDGWE 101
                                       78899*****************95545678899************************99876654331112246687 PP

                            AAA_35 105 ...eelgskvsctayl 117
                                          + l++k +c+ y+
  gi|474934240|ref|YP_007687822.1| 102 rsvSGLQNKKNCDVYI 117
                                       3223356778888886 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.027        35       8      37 ..     200     229 ..     199     230 .. 0.90
   2 ?    9.3   0.0   0.00084       1.1      18      43 ..     227     252 ..     222     253 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.027
                                       HHHHHHHSTTEEHHHHHHHHTS-HHHHHHH CS
                              MarR   8 iLrilyeqgplsvseLakklgvskstvtrv 37 
                                       iL  l++ +  +++ +a++l+ +++++t++
  gi|474934240|ref|YP_007687822.1| 200 ILSRLKTDDVSKLTAIARFLYSNIGNTTNI 229
                                       7888888888999***************86 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00084
                                       EEHHHHHHHHTS-HHHHHHHHHHHHH CS
                              MarR  18 lsvseLakklgvskstvtrvldrLek 43 
                                        ++  +a++ g+s++tv++ +d++ k
  gi|474934240|ref|YP_007687822.1| 227 TNIDSIAEATGISNPTVSKYVDEMCK 252
                                       56669*****************9977 PP

>> DUF2089  Protein of unknown function (DUF2089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00015      0.19      39      82 ..     216     259 ..     188     275 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                           DUF2089  39 lefvelfikarGnlkevekelgisYpTvrnrldeileaLgyeee 82 
                                        +f+   i +  n+ +++++ gis pTv + +de+++a+ + + 
  gi|474934240|ref|YP_007687822.1| 216 ARFLYSNIGNTTNIDSIAEATGISNPTVSKYVDEMCKAFLFYHA 259
                                       467778888999***********************999765554 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00023      0.29       2      70 ..      24     108 ..      24     143 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00023
                            AAA_18   2 lltGtpGvGKttlakeLskrl.gf..gvnlrdvakenglllevdpe.....aldeskrldedkldklldaleenss. 69 
                                       ++tG+ ++GK+tl +  + rl +   ++n+++++  +++++ +  +     ++ + ++ +++++ + ld++++ +  
  gi|474934240|ref|YP_007687822.1|  24 VITGMRRSGKSTLLEQYAARLkEQgiSDNSIFMINFEDTEWQYITDhtilnEWISDNIPKKGQCYVFLDEVQNVDGw 100
                                       59*************99888744477555555555444444444443333323344444444443334443333333 PP

                            AAA_18  70 .......a 70 
                                               
  gi|474934240|ref|YP_007687822.1| 101 ersvsglQ 108
                                       33444552 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0    0.0002      0.26      24      44 ..     227     247 ..     220     252 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0002
                            HTH_10  24 vtlkeLAkelGIskstlsehL 44 
                                       ++++++A++ GIs++t+s+++
  gi|474934240|ref|YP_007687822.1| 227 TNIDSIAEATGISNPTVSKYV 247
                                       7899**************997 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00029      0.37       3      29 ..      24      50 ..      23      60 .. 0.93
   2 ?   -3.1   0.0         5   6.4e+03      67      84 ..      80      97 ..      69     117 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00029
                                      EEE--TTSSHHHHHHHHHHHH...GGG CS
                          NTPase_1  3 fiTGppGvGKtTlvkkvlellkssgvk 29
                                      +iTG+  +GK+Tl+++ +  lk++g++
  gi|474934240|ref|YP_007687822.1| 24 VITGMRRSGKSTLLEQYAARLKEQGIS 50
                                      69*********************9975 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5
                                      -SSEETTEEE-HHHHHHH CS
                          NTPase_1 67 reprvgkyvvdvesfeel 84
                                      + p+ g+ +v++++++++
  gi|474934240|ref|YP_007687822.1| 80 NIPKKGQCYVFLDEVQNV 97
                                      557778888888886654 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00032      0.41      22      40 ..      19      38 ..      13      47 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00032
                            AAA_29 22 kg.atlltGpsGsGKSTllD 40
                                      ++ + ++tG   sGKSTll 
  gi|474934240|ref|YP_007687822.1| 19 NDvIKVITGMRRSGKSTLLE 38
                                      455679************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      667  (0.0372023); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 2743.59
//
Query:       gi|474934241|ref|YP_007687823.1|  [L=40]
Description: hypothetical protein TALC_00666 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-05   25.0   0.0    1.1e-05   25.0   0.0    1.1  1  HTH_23          Homeodomain-like domain
    6.5e-05   22.6   0.0    6.8e-05   22.5   0.0    1.1  1  HTH_Tnp_4       Helix-turn-helix of DDE superfamily endonucle
    0.00038   19.8   0.0    0.00039   19.8   0.0    1.1  1  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
    0.00076   19.5   0.0    0.00082   19.4   0.0    1.0  1  HTH_3           Helix-turn-helix
     0.0012   18.9   0.0     0.0014   18.7   0.0    1.1  1  HTH_28          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.011   15.8   0.0      0.012   15.6   0.0    1.1  1  HTH_29          Winged helix-turn helix
      0.025   14.7   0.0      0.032   14.4   0.0    1.1  1  HTH_17          Helix-turn-helix domain
      0.047   13.5   0.0      0.047   13.5   0.0    1.1  1  DUF746          Domain of Unknown Function (DUF746)
      0.063   13.6   0.0      0.063   13.6   0.0    1.1  1  HTH_31          Helix-turn-helix domain
       0.11   12.4   0.0       0.13   12.2   0.0    1.1  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox


Domain annotation for each model (and alignments):
>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   6.2e-09   1.1e-05      17      43 ..       6      32 ..       1      37 [. 0.85

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 6.2e-09
                            HTH_23 17 GlsvreIAreLgvsrrTvyrwlkryre 43
                                        +++++A+++gvs+ T+ +w++++++
  gi|474934241|ref|YP_007687823.1|  6 DVPRETVAALFGVSEDTITNWVNAWKK 32
                                      46899********************54 PP

>> HTH_Tnp_4  Helix-turn-helix of DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   3.8e-08   6.8e-05      20      43 ..       7      30 ..       1      32 [. 0.87

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 3.8e-08
                         HTH_Tnp_4 20 ltyqdLayrFgvsestvsrifhkw 43
                                      ++ + +a++Fgvse t+++++++w
  gi|474934241|ref|YP_007687823.1|  7 VPRETVAALFGVSEDTITNWVNAW 30
                                      677889*****************9 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   2.2e-07   0.00039      29      50 ..       8      29 ..       1      31 [. 0.88

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2.2e-07
                      HTH_Tnp_ISL3 29 svkavArqlgvSwtTVwrildr 50
                                      ++ +vA+++gvS++T+ +++++
  gi|474934241|ref|YP_007687823.1|  8 PRETVAALFGVSEDTITNWVNA 29
                                      7889***************987 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   4.6e-07   0.00082       5      40 ..       2      39 ..       1      39 [. 0.94

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 4.6e-07
                                      HHHTTHHHHHHHHHHTSSHHHHHHHHTT..SSCSBHHH CS
                             HTH_3  5 RkqlglsqeeLAeklGvsrstisriEnG..ernPslet 40
                                      R++ +  +e +A++ Gvs  ti+++ n   +++Ps et
  gi|474934241|ref|YP_007687823.1|  2 RLEYDVPRETVAALFGVSEDTITNWVNAwkKSHPSDET 39
                                      88899999***************************987 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0     8e-07    0.0014      18      38 ..      12      32 ..       4      33 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 8e-07
                            HTH_28 18 aArelgisrrtvyrWikryee 38
                                      +A+++g+s++t+  W++++ +
  gi|474934241|ref|YP_007687823.1| 12 VAALFGVSEDTITNWVNAWKK 32
                                      8*****************975 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.0   6.7e-06     0.012      17      37 ..      11      31 ..       6      35 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 6.7e-06
                            HTH_29 17 qiAkllglsrrtvyrwlkrfe 37
                                       +A+l g+s++t+ +w++++ 
  gi|474934241|ref|YP_007687823.1| 11 TVAALFGVSEDTITNWVNAWK 31
                                      5899**************996 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.8e-05     0.032       7      24 ..      12      29 ..       9      33 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.8e-05
                            HTH_17  7 aAelLgvsrstvyrlirr 24
                                      +A+l+gvs+ t+ +++++
  gi|474934241|ref|YP_007687823.1| 12 VAALFGVSEDTITNWVNA 29
                                      9***************86 PP

>> DUF746  Domain of Unknown Function (DUF746)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.6e-05     0.047      15      37 ..       9      31 ..       1      34 [. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.6e-05
                            DUF746 15 laeaadllgtdegiiakwvreFr 37
                                       + +a l g++e++i +wv+ ++
  gi|474934241|ref|YP_007687823.1|  9 RETVAALFGVSEDTITNWVNAWK 31
                                      567999**************997 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.5e-05     0.063      17      36 ..       9      28 ..       1      39 [. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.5e-05
                            HTH_31 17 qeevAerlgvsestlsrlEq 36
                                      +e vA++ gvse+t++ + +
  gi|474934241|ref|YP_007687823.1|  9 RETVAALFGVSEDTITNWVN 28
                                      899*************9987 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     7e-05      0.13      13      31 ..      11      29 ..       8      37 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7e-05
                    YdaS_antitoxin 13 aLAealgvsqqaVsqWlkg 31
                                       +A + gvs+ ++ +W++ 
  gi|474934241|ref|YP_007687823.1| 11 TVAALFGVSEDTITNWVNA 29
                                      6899*************94 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.42u 0.31s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 257.49
//
Query:       gi|474934242|ref|YP_007687824.1|  [L=73]
Description: hypothetical protein TALC_00667 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 531.55
//
Query:       gi|474934243|ref|YP_007687825.1|  [L=50]
Description: hypothetical protein TALC_00668 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.50
# Mc/sec: 301.81
//
Query:       gi|474934244|ref|YP_007687826.1|  [L=73]
Description: hypothetical protein TALC_00669 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.15   12.3   0.0       0.21   11.8   0.0    1.3  1  DUF4143   Domain of unknown function (DUF4143)


Domain annotation for each model (and alignments):
>> DUF4143  Domain of unknown function (DUF4143)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.2e-05      0.21      97     120 ..       2      24 ..       1      26 [. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.2e-05
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                           DUF4143  97 dkngaEvDfvielkggkivpiEvK 120
                                       dkn+ Ev f+++ +g+ki p+EvK
  gi|474934244|ref|YP_007687826.1|   2 DKNRCEVNFLVR-NGKKIDPVEVK 24 
                                       56789******8.699*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 513.14
//
Query:       gi|474934245|ref|YP_007687827.1|  [L=265]
Description: putative phospho-2-dehydro-3-deoxyheptonate aldolase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-58  198.4   0.1    1.5e-58  198.2   0.1    1.0  1  DeoC      DeoC/LacD family aldolase


Domain annotation for each model (and alignments):
>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.2   0.1   8.6e-63   1.5e-58       1     235 []      19     235 ..      19     235 .. 0.99

  Alignments for each domain:
  == domain 1  score: 198.2 bits;  conditional E-value: 8.6e-63
                                       EEEEEECCSHHHHHHHHCTSSHHHHHHHHHHHHHHGGGSSEEEEETTTHHHHHHCSCTTSEEEEETECSSCCTTSTT CS
                              DeoC   1 ivilavDqrvankddtasaqneqledlkalvkealtpgasavlldpgviasaskeyakdiallvkldkgtyllkskq 77 
                                       +vi+++D++++ +++ ++       d+k++v++++ +ga avl+++g+i++++++ ++d++l+++l+++t++  ++q
  gi|474934245|ref|YP_007687827.1|  19 CVIVPLDHGISVGPIPGI------VDFKKTVSDVTIGGATAVLMHKGMIPHGHRTSGHDVGLILHLSASTDIGVNSQ 89 
                                       79****************......9**************************************************** PP

                                       EEEETTCHHHHHHHTT-SEEEEEEEEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEEEEE-CTTBSSTTCHHHHHH CS
                              DeoC  78 rdvdevasveeakalGAdavkvvvyyradgseeeqqklaeikrvkeacheeglplilelylrdeaikdekvdpdlva 154
                                        +v+ va+ve  ++lGAda+++++++   g++ee q+la+ +rv++ c e+g+pli++ y r+++ikd + dp +va
  gi|474934245|ref|YP_007687827.1|  90 SKVL-VATVEDGLKLGADAISIHINV---GAQEEPQMLADAGRVSSSCMEWGMPLIAMTYARGPSIKDSF-DPAAVA 161
                                       ***9.*********************...*****************************************.****** PP

                                       HHHHHHTCCT-SEEEE--SSCC.B.HHHHHHHHHHHHHCHSSTEEEEETTS...SHHHHHHHHHHHHHHHTHCEEEE CS
                              DeoC 155 eAarvsaelGaDiiKvevpkevvnateedaevfkdvikaapvpgvvlsGGv...seedfletvedAvkeagasGvls 228
                                       +Aarv+aelGaDi+K +++        +d+++f++v ++a+vp vv++GG+   s+ d+l++v d++ +ag+ Gv++
  gi|474934245|ref|YP_007687827.1| 162 HAARVGAELGADIVKCSYT--------GDIDSFSKVCDGAQVP-VVIAGGPkmdSDMDILNMVADSL-QAGGHGVSI 228
                                       *******************........****************.***********************.********* PP

                                       SHHHHTT CS
                              DeoC 229 GRaifqk 235
                                       GR++fq+
  gi|474934245|ref|YP_007687827.1| 229 GRNVFQH 235
                                       *****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1733.81
//
Query:       gi|474934246|ref|YP_007687828.1|  [L=87]
Description: Regulator of competence-specific genes [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-10   39.8   0.0    3.9e-10   39.8   0.0    1.1  1  TfoX_N    TfoX N-terminal domain


Domain annotation for each model (and alignments):
>> TfoX_N  TfoX N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   0.0   2.2e-14   3.9e-10       6      58 ..       5      56 ..       1      82 [. 0.86

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 2.2e-14
                                      GS-EEEEEETTEEEEEETTEEEEEEETTEEEEE--HHHHHHHHHTT----EEE CS
                            TfoX_N  6 lgevtsrrmFGgyglfvdglmfalvsdgelylradeetreefeaaglepftya 58
                                      l e+tsrrm+G y l++dg++f+ + d++l+l+ ++ ++  + + +++ f y+
  gi|474934246|ref|YP_007687828.1|  5 LPEITSRRMMGEYLLYLDGTLFGGIYDDRLLLKITKVSATLLHDCESA-FPYE 56
                                      689***********************************9999977776.4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       200  (0.0111551); expected 358.6 (0.02)
Passed bias filter:                      195  (0.0108762); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 563.72
//
Query:       gi|474934247|ref|YP_007687829.1|  [L=270]
Description: hypothetical protein TALC_00672 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.11   12.4   0.1       0.74    9.7   0.0    2.0  2  GyrB_insert  DNA gyrase B subunit insert domain
       0.11   12.6   0.2       0.38   10.9   0.0    2.0  2  NHL          NHL repeat
       0.58   10.5   8.9       0.13   12.6   1.3    3.0  3  Myco_19_kDa  Mycobacterium 19 kDa lipoprotein antigen


Domain annotation for each model (and alignments):
>> GyrB_insert  DNA gyrase B subunit insert domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0     0.077   4.6e+02      99     131 ..      53      85 ..      22      87 .. 0.71
   2 ?    9.7   0.0   0.00012      0.74      80     127 ..     156     205 ..     121     215 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.077
                       GyrB_insert  99 levertqhGnekesvldadffesadYralaela 131
                                         v+  + G  + s+ +++ fes d+ +lae+a
  gi|474934247|ref|YP_007687829.1|  53 SVVDSVADGKVTYSYKSETTFESDDFFELAEFA 85 
                                       45777788899999999999*****99999986 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00012
                       GyrB_insert  80 kgeryeveveedeeeekallevertqhGnekesvldadffes..adYral 127
                                       +g++ ++ +++d e++  +l v+  + Gn +e+vl adf +s  +dY  +
  gi|474934247|ref|YP_007687829.1| 156 TGSDSSFITKYDVETDGNKLDVKYDHKGNGTETVLIADFYDSvlTDYDPV 205
                                       56777888999*****************************9955577665 PP

>> NHL  NHL repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   6.4e-05      0.38       3      17 ..     101     115 ..     100     119 .. 0.91
   2 ?   -2.4   0.0       1.1   6.4e+03      15      21 ..     189     195 ..     187     197 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6.4e-05
                                       SEEEEEEETTTEEEE CS
                               NHL   3 yPhGvavdsnGdiyV 17 
                                       yP+Gv+v+++G++y 
  gi|474934247|ref|YP_007687829.1| 101 YPEGVTVSKDGNVYT 115
                                       9************96 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.1
                                       EEEEECC CS
                               NHL  15 iyVaDse 21 
                                       +++aD++
  gi|474934247|ref|YP_007687829.1| 189 VLIADFY 195
                                       89***76 PP

>> Myco_19_kDa  Mycobacterium 19 kDa lipoprotein antigen
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.3   2.1e-05      0.13      68      95 ..      95     121 ..      18     141 .. 0.87
   2 ?    0.8   0.5     0.095   5.7e+02      77     101 ..     134     158 ..     120     189 .. 0.57
   3 ?    0.8   1.0     0.093   5.6e+02      50      91 ..     202     230 ..     144     248 .. 0.44

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.1e-05
                       Myco_19_kDa  68 ltyaegtgggsaevtkdgntYtitGtae 95 
                                        t a+g ++g ++v+kdgn Yti+Gt +
  gi|474934247|ref|YP_007687829.1|  95 YTAASGYPEG-VTVSKDGNVYTINGTQT 121
                                       4455566677.**************976 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.095
                       Myco_19_kDa  77 gsaevtkdgntYtitGtaegadsan 101
                                       +s+++t dg    ++G+a+   ++ 
  gi|474934247|ref|YP_007687829.1| 134 NSVKITYDGAVKAVSGKATVDFTGS 158
                                       4455555555555555554433333 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.093
                       Myco_19_kDa  50 gdeptvesvgigdvdGftltyaegtgggsaevtkdgntYtit 91 
                                        d+++++        G +++ +e++ gg +++t+     + t
  gi|474934247|ref|YP_007687829.1| 202 YDPVMLT--------GLSVETSEKEIGG-VNATVY----HGT 230
                                       3333333........3334444444333.333222....222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1707.27
//
Query:       gi|474934248|ref|YP_007687830.1|  [L=636]
Description: Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase-related enzyme [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-36  125.3   0.0    5.4e-21   74.9   0.0    2.2  2  PLDc_2    PLD-like domain
    2.4e-11   44.0   0.0    1.7e-10   41.3   0.0    2.5  3  LTD       Lamin Tail Domain
     0.0016   18.3   0.1     0.0083   15.9   0.1    2.3  1  PKD       PKD domain
  ------ inclusion threshold ------
       0.53   10.6   7.8        6.9    7.0   0.1    3.3  3  PLDc      Phospholipase D Active site motif


Domain annotation for each model (and alignments):
>> PLDc_2  PLD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.9   0.0   1.2e-24   5.4e-21       1     132 [.     174     308 ..     174     309 .. 0.90
   2 !   48.4   0.0   1.8e-16   8.2e-13      29     131 ..     396     495 ..     377     497 .. 0.77

  Alignments for each domain:
  == domain 1  score: 74.9 bits;  conditional E-value: 1.2e-24
                            PLDc_2   1 liqliksAkksidiatyyfvsdreildallkaakrgvkvrilldskkddagavdeaslkelkellleagvevrvfet 77 
                                       +i++i sA+++idi++y + ++r++ + l++  +rgv+vrill     ++ + d  +   +++ ++  g ev+++++
  gi|474934248|ref|YP_007687830.1| 174 IIDAIGSAQSRIDISIYLL-TSRNLCALLCDVLQRGVEVRILLEG---SPLGTDISNELSMMKNITGLGGEVHLINS 246
                                       799****************.*************************...66666666666666666*********994 PP

                            PLDc_2  78 .....llgslHaKlylidgktvivGSsNltkrgl..dlnlElnvviedkelakeleeeFerl 132
                                            +++ lH+K+++idg+ vi++S N+t++++  ++n+ ++  +e+++ a+++e+ Fe++
  gi|474934248|ref|YP_007687830.1| 247 gsgnpRFTYLHNKYAVIDGDKVIITSENWTNSNFgeEGNRGWGALVESPDYASYMEAVFEND 308
                                       444444489*************************99***********************986 PP

  == domain 2  score: 48.4 bits;  conditional E-value: 1.8e-16
                            PLDc_2  29 llkaakrgvkvrilldskkddagavdeaslkelkellleagvevrvfet..ll..gslHaKlylidgktvivGSsNl 101
                                       ++ aa+rg +vr +ld++++++g+      + + +l ++++  ++      ++  +++H+K++++d + v +GS+N+
  gi|474934248|ref|YP_007687830.1| 396 MASAASRGADVRFILDASQSTSGD-----HRAYVNL-INGTTGIQALAVdgREgfDTIHNKGIIMD-SSVWLGSVNW 465
                                       5679*************6554333.....3344444.44444433433223235689********7.6899****** PP

                            PLDc_2 102 tkrgldlnlElnvviedkelakeleeeFer 131
                                       t  +l+ n+E++v i ++e+ +++ ++F +
  gi|474934248|ref|YP_007687830.1| 466 TSTSLKNNRETAVLINSAEVSQYFSRYFLS 495
                                       ***************************965 PP

>> LTD  Lamin Tail Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.0   3.7e-14   1.7e-10      10     111 ..       3     105 ..       1     106 [. 0.89
   2 ?   -2.9   0.0         2   8.9e+03      16      33 ..     412     431 ..     400     437 .. 0.72
   3 ?   -2.6   0.0       1.6     7e+03      84     100 ..     466     482 ..     450     493 .. 0.70

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 3.7e-14
                               LTD  10 IsevmedgagnnanefvelyNtsskavdLsgwkledasgeytfpngtgtlaageyvvvwsgsgtt.........sas 77 
                                       I+ev+++       e + ++N s + v+L+gw+l+d+ g+  f++   tl +g +++v+   g +         ++ 
  gi|474934248|ref|YP_007687830.1|   3 ITEVDPAC------EGITITNVSFSWVNLEGWYLTDSEGKLFFHSR--TLSPGCSLTVVKTRGDDwfssredvvEFG 71 
                                       89999988......************************99***999..5************9999*********444 PP

                               LTD  78 ngskas.ssavwnnggdavaLydasgevvdsvgyg 111
                                        g + + +s+v+ nggd ++Ly    +++dsv yg
  gi|474934248|ref|YP_007687830.1|  72 MGGTTKsGSLVLANGGDDISLYS-GSTLIDSVCYG 105
                                       44444449*************98.8899****987 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2
                               LTD  16 dgagnnan..efvelyNtss 33 
                                       ++++++++   +v l N ++
  gi|474934248|ref|YP_007687830.1| 412 ASQSTSGDhrAYVNLINGTT 431
                                       44444444679999999886 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.6
                               LTD  84 ssavwnnggdavaLyda 100
                                       +s++++n+ ++++L+++
  gi|474934248|ref|YP_007687830.1| 466 TSTSLKNNRETAVLINS 482
                                       66677778888888874 PP

>> PKD  PKD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   1.9e-06    0.0083      18      63 ..     528     570 ..     509     573 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.9e-06
                                       EES.-SS-SEEEEE--SS--EEEEETTEEEEEE-SSEEEEEEEEEE CS
                               PKD  18 aavpdganvtysWdfgdgsvvqvlseptvthtYlspGeYeVtvtas 63 
                                       a  + +++ ty W+fgd ++  ++  p v    +spG+Y ++vt +
  gi|474934248|ref|YP_007687830.1| 528 A--DGPSDCTYVWEFGD-GTRRITGVPDVVFDAPSPGKYIAKVTIQ 570
                                       2..45899*********.99999999999999999****9999965 PP

>> PLDc  Phospholipase D Active site motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1    0.0015       6.9       5      26 ..     256     277 ..     253     278 .. 0.93
   2 ?    6.7   0.7     0.002         9       4      27 ..     446     468 ..     443     469 .. 0.89
   3 ?   -2.2   0.1       1.2   5.5e+03      18      24 ..     593     599 ..     590     599 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0015
                                       E---EEEETTTEEEEE---SSH CS
                              PLDc   5 hHqKivivDdrvafvGgaNLcd 26 
                                       +H K  ++D++ +++++ N+++
  gi|474934248|ref|YP_007687830.1| 256 LHNKYAVIDGDKVIITSENWTN 277
                                       8*******************97 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.002
                                       EE---EEEETTTEEEEE---SSHH CS
                              PLDc   4 thHqKivivDdrvafvGgaNLcdg 27 
                                       t H K++i D   + +G+ N++  
  gi|474934248|ref|YP_007687830.1| 446 TIHNKGIIMDSS-VWLGSVNWTST 468
                                       77**********.********975 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.2
                                       EEE---S CS
                              PLDc  18 fvGgaNL 24 
                                       f+G+a+L
  gi|474934248|ref|YP_007687830.1| 593 FYGSASL 599
                                       9****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (636 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.68u 0.33s 00:00:01.01 Elapsed: 00:00:00.54
# Mc/sec: 3577.85
//
Query:       gi|474934249|ref|YP_007687831.1|  [L=147]
Description: Acetyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-17   62.7   0.1    4.2e-17   62.4   0.1    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    7.4e-17   61.5   0.0    8.3e-17   61.3   0.0    1.0  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    2.1e-11   44.1   0.0    2.8e-11   43.7   0.0    1.1  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    2.4e-10   40.8   0.0    2.7e-10   40.6   0.0    1.1  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    1.3e-08   34.7   0.1    1.7e-08   34.3   0.1    1.2  1  FR47             FR47-like protein
    4.2e-05   23.3   0.1    4.9e-05   23.1   0.1    1.1  1  PanZ             Acetyltransferase (GNAT) domain, PanZ
    0.00018   21.2   0.0    0.00022   21.0   0.0    1.1  1  Acetyltransf_8   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.012   15.5   0.0      0.025   14.4   0.0    1.4  1  Acetyltransf_18  Acetyltransferase (GNAT) domain
      0.028   14.5   0.1      0.034   14.2   0.1    1.3  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
      0.043   14.5   0.0       0.05   14.3   0.0    1.2  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
       0.16   12.1   0.1       0.38   10.9   0.0    1.7  2  Acetyltransf_CG  GCN5-related N-acetyl-transferase


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.4   0.1   2.6e-20   4.2e-17      16     117 .]      21     117 ..       7     117 .. 0.85

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 2.6e-20
                                       HHHHHHHH.HHHHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHH CS
                    Acetyltransf_1  16 nedaseee.feesfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerare 91 
                                       + ++ +++ + ++   +a++++++ + g++ G+i ++  ++   g+a++  l V+   rg+G+G  Ll +l + ar 
  gi|474934249|ref|YP_007687831.1|  21 FAREVLDYfMMQW---PAGSFVAVDYAGRIMGYIAGSRLQN---GRAAVSLLCVNQLVRGRGVGESLLAHLRQAARM 91 
                                       3344444444455...6667777******************...********************************* PP

                                       TTESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  92 egikkivlaveedndaairlYeklGF 117
                                       egi+ i l+v+ +n+ air+Ye+ GF
  gi|474934249|ref|YP_007687831.1|  92 EGIRTIQLEVRTTNTEAIRFYERRGF 117
                                       *************************9 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.3   0.0   5.1e-20   8.3e-17      18     123 ..      22     136 ..       8     140 .. 0.85

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 5.1e-20
                   Acetyltransf_10  18 spealreri.eegealllvaeeggkivGvi...elrdgs.hisllfVdpeyrgqGigkaLleaveeeaekdgikl.e 88 
                                       ++e l+  + + ++  +++++  g+i+G+i   +l++g+  +sll+V++  rg+G+g++Ll +++++a+ +gi++ +
  gi|474934249|ref|YP_007687831.1|  22 AREVLDYFMmQWPAGSFVAVDYAGRIMGYIagsRLQNGRaAVSLLCVNQLVRGRGVGESLLAHLRQAARMEGIRTiQ 98 
                                       55555555535667778999999*******8777766668************************************* PP

                   Acetyltransf_10  89 ltvnasp.yavpfYeklGFkav..geeqeenGirfvpM 123
                                       l+v+ ++ +a++fYe+ GFk+v   + ++ +G   ++M
  gi|474934249|ref|YP_007687831.1|  99 LEVRTTNtEAIRFYERRGFKPVesLPRFYNDGGDGIRM 136
                                       **********************7667899999988888 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   0.0   1.7e-14   2.8e-11       4      76 .]      37     119 ..      33     119 .. 0.73

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 1.7e-14
                                       EEEEEEETTEEEEEEEEEEES...TCTEEEEE-GGGTTSSHHHHHHHH...TT..SEEEEE.EEEE..THHHHHHHH CS
                    Acetyltransf_7   4 evfVaeddgkivGfialslld...aeitrlaVdpeyrgkGiGraLlea...ae..kgiile.qlel..naekaikfY 69 
                                       ++  ++  g+i+G+ia s+l+   a    l+V++  rg+G+G  Ll++   a+  +gi+ + qle+  ++++ai+fY
  gi|474934249|ref|YP_007687831.1|  37 SFVAVDYAGRIMGYIAGSRLQngrAAVSLLCVNQLVRGRGVGESLLAHlrqAArmEGIR-TiQLEVrtTNTEAIRFY 112
                                       555566669999***99999765444444*****************9865411577855.334444323349***** PP

                                       HHTTEEE CS
                    Acetyltransf_7  70 eklGFee 76 
                                       e+ GF++
  gi|474934249|ref|YP_007687831.1| 113 ERRGFKP 119
                                       *****95 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.0   1.6e-13   2.7e-10      52     154 ..      39     137 ..      16     138 .. 0.89

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 1.6e-13
                    Acetyltransf_4  52 flvaesdrivGyaylgqfkkrakdwkaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqf 128
                                         v++++ri+Gy +++ +    +++ a +s + ++++ + +g+g  l+++l q +++ +i+++  e+  +n+++i f
  gi|474934249|ref|YP_007687831.1|  39 VAVDYAGRIMGYIAGSRL----QNGRAAVSLLCVNQLVRGRGVGESLLAHLRQAARMEGIRTIQLEVRTTNTEAIRF 111
                                       45777**********944....669999999999899**************************************** PP

                    Acetyltransf_4 129 hkalGFelvgifkkcikkngrwiDmi 154
                                       +++ GF+ v  + ++++++g  i mi
  gi|474934249|ref|YP_007687831.1| 112 YERRGFKPVESLPRFYNDGGDGIRMI 137
                                       ******************99888775 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.1   1.1e-11   1.7e-08      11      79 ..      50     119 ..      43     125 .. 0.90

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 1.1e-11
                                       -EEEEEEE-TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S.-EEEEEETT-HHHHHHHHHHT-EE CS
                              FR47  11 elaawilrkdggelgalqvlpehrrrGlgsrlvkalakeiaergk.tvllvvvasNtpsirlyeklGfek 79 
                                        +a+ +l++   +++ l+v++ +r+rG g +l + l ++ + +g+ t+ l v+++Nt++ir+ye+ Gf+ 
  gi|474934249|ref|YP_007687831.1|  50 YIAGSRLQNGRAAVSLLCVNQLVRGRGVGESLLAHLRQAARMEGIrTIQLEVRTTNTEAIRFYERRGFKP 119
                                       578889999999******************************997367899*****************85 PP

>> PanZ  Acetyltransferase (GNAT) domain, PanZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.1     3e-08   4.9e-05      39     120 ..      37     117 ..      25     125 .. 0.72

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 3e-08
                              PanZ  39 alfaarFNdRlLgAvkv.eledkeaelsdlcVRevTRrRGVgsyLleearrqaPevkswvlaeedvkeldlavlqaf 114
                                       +++a  +  R +g ++  +l+++ a++s lcV ++ R RGVg+ Ll + r+ a +++  +  + +v++++   + +f
  gi|474934249|ref|YP_007687831.1|  37 SFVAVDYAGRIMGYIAGsRLQNGRAAVSLLCVNQLVRGRGVGESLLAHLRQAA-RMEGIRTIQLEVRTTN-TEAIRF 111
                                       566667777777776641568889**********************9887766.6665555555555433.333456 PP

                              PanZ 115 lealgf 120
                                        e+ gf
  gi|474934249|ref|YP_007687831.1| 112 YERRGF 117
                                       666666 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.3e-07   0.00022      74     141 ..      55     121 ..      21     124 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.3e-07
                                       ---TT-EEEEEEESSHHHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EEEE CS
                    Acetyltransf_8  74 daepgdrGiHlligeaeargkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfekek 141
                                       + ++g   + ll+ ++  rg+g++ +ll +l + + + +++r + +E + +N++air++e+ Gf++++
  gi|474934249|ref|YP_007687831.1|  55 RLQNGRAAVSLLCVNQLVRGRGVGESLLAHLRQ-AARMEGIRTIQLEVRTTNTEAIRFYERRGFKPVE 121
                                       567777888889999999*******99988755.55566*************************9876 PP

>> Acetyltransf_18  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.5e-05     0.025      20     110 ..      30     128 ..      22     133 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.5e-05
                   Acetyltransf_18  20 rlkqaeqklvvveedgeivGyglarktrkglkiGPlvAene.....eiAeaLlkalvanaeg...kkvridvpeenk 88 
                                       +++ +  + v+v+ +g+i Gy    + ++g +   l++ n+      + e+Ll++l + a+    + + + v ++n+
  gi|474934249|ref|YP_007687831.1|  30 MMQWPAGSFVAVDYAGRIMGYIAGSRLQNGRAAVSLLCVNQlvrgrGVGESLLAHLRQAARMegiRTIQLEVRTTNT 106
                                       466688889999999999999999999999999999998872222246899**9998776652256788******** PP

                   Acetyltransf_18  89 alielleklgfkevfecarmvk 110
                                       ++i++ e+ gfk v + +r + 
  gi|474934249|ref|YP_007687831.1| 107 EAIRFYERRGFKPVESLPRFYN 128
                                       ****************999887 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   2.1e-05     0.034      74     127 ..      61     119 ..      24     120 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.1e-05
                                       EEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--.....SSHHHHHTTT-EE CS
                    Acetyltransf_9  74 agvtgVavapehrgrgvlskLlaraleemreegqplsllfP.....ssipiYrrfGyei 127
                                       a+v+  +v+   rgrgv ++Lla++ + +r eg++ + l        +i++Y+r G+++
  gi|474934249|ref|YP_007687831.1|  61 AAVSLLCVNQLVRGRGVGESLLAHLRQAARMEGIRTIQLEVrttntEAIRFYERRGFKP 119
                                       678999********************************99988775558********87 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.1e-05      0.05      60     138 .]      42     118 ..      12     118 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.1e-05
                    Acetyltransf_3  60 lkdtgviGsvglrdleeedeeaelgymlaps.fwgkGyateavralleyafeelglerlvavidkeNeaSirvlekl 135
                                       + +++++G++   +l++ +  a ++++   + ++g+G++   ++ l ++a + +g++++  ++ ++N+  ir +e+ 
  gi|474934249|ref|YP_007687831.1|  42 DYAGRIMGYIAGSRLQNGR--AAVSLLCVNQlVRGRGVGESLLAHLRQAA-RMEGIRTIQLEVRTTNTEAIRFYERR 115
                                       4444468888555555544..666655554449******99999999998.8999********************** PP

                    Acetyltransf_3 136 Gfe 138
                                       Gf+
  gi|474934249|ref|YP_007687831.1| 116 GFK 118
                                       *97 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       3.3   5.4e+03      62      73 ..      12      23 ..      11      28 .. 0.75
   2 ?   10.9   0.0   0.00023      0.38      20      59 ..      56      95 ..      38      99 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3.3
                   Acetyltransf_CG 62 ptCsyvaaylek 73
                                      ++Cs + +y+ +
  gi|474934249|ref|YP_007687831.1| 12 VLCSSLDEYFAR 23
                                      578888888876 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00023
                   Acetyltransf_CG 20 rkegvldfthTeVpeelrGkGiAkkLvkaalddareeglk 59
                                       ++g+ ++    V++ +rG+G+++ L  +  + ar eg +
  gi|474934249|ref|YP_007687831.1| 56 LQNGRAAVSLLCVNQLVRGRGVGESLLAHLRQAARMEGIR 95
                                      5566667777789999*******************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 886.75
//
Query:       gi|474934250|ref|YP_007687832.1|  [L=216]
Description: Sel1 repeat protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-39  133.4  28.7    4.1e-10   40.0   0.5    5.5  6  Sel1      Sel1 repeat


Domain annotation for each model (and alignments):
>> Sel1  Sel1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.43   7.8e+03      25      38 .]       3      16 ..       2      16 .. 0.87
   2 !   26.7   1.2   3.4e-10     6e-06       1      37 [.      17      51 ..      17      52 .. 0.97
   3 !   40.0   0.5   2.3e-14   4.1e-10       1      38 []      53      88 ..      53      88 .. 0.96
   4 !   23.7   0.1   3.2e-09   5.7e-05       2      38 .]      90     124 ..      89     124 .. 0.92
   5 !   24.8   1.0   1.4e-09   2.4e-05       1      38 []     125     160 ..     125     160 .. 0.93
   6 !   36.0   1.4   4.2e-13   7.5e-09       1      38 []     161     196 ..     161     196 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.43
                              Sel1 25 kAiewyekAAeqGd 38
                                      kA++ +  A + Gd
  gi|474934250|ref|YP_007687832.1|  3 KAFQIFAEASDSGD 16
                                      89999999999986 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 3.4e-10
                              Sel1  1 aeAmyrLGmfylylnGlgvpkDpekAiewyekAAeqG 37
                                      aeA+yr G  ++++ G g  ++p+ A+++y +AA+qG
  gi|474934250|ref|YP_007687832.1| 17 AEALYRFG--QMFDRGYGCTQNPKVAMKYYAMAADQG 51
                                      79******..999***********************9 PP

  == domain 3  score: 40.0 bits;  conditional E-value: 2.3e-14
                              Sel1  1 aeAmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38
                                      a+A+++ G   l+++G+g+p+D+++A+ew+ kAAeq++
  gi|474934250|ref|YP_007687832.1| 53 ADAQFAIG--ILHFYGRGTPQDYSLAREWFAKAAEQDY 88
                                      68******..999***********************85 PP

  == domain 4  score: 23.7 bits;  conditional E-value: 3.2e-09
                              Sel1   2 eAmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                        A ++LG   + +nG g + D   A+ewy kA e+G+
  gi|474934250|ref|YP_007687832.1|  90 KAVFNLG--VMAENGMGCEVDFGTAREWYLKASELGS 124
                                       6889***..666***********************96 PP

  == domain 5  score: 24.8 bits;  conditional E-value: 1.4e-09
                              Sel1   1 aeAmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                       a A y+L+   +y +G gv+kDp k +ewy k+A++G+
  gi|474934250|ref|YP_007687832.1| 125 AKAEYNLA--VMYGKGNGVEKDPAKQFEWYMKSARRGY 160
                                       68******..777*********************9996 PP

  == domain 6  score: 36.0 bits;  conditional E-value: 4.2e-13
                              Sel1   1 aeAmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                       a A+y +G   +y++Glgv++   +A++w+++ A+qG+
  gi|474934250|ref|YP_007687832.1| 161 AKAQYGVG--FCYYKGLGVDQSDFEAMKWFQLGAAQGH 196
                                       68******..999************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 1312.21
//
Query:       gi|474934251|ref|YP_007687833.1|  [L=509]
Description: putative ATP-dependent protease [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-17   62.3   0.1    3.1e-10   39.8   0.1    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    1.6e-15   56.9   0.1    3.5e-07   29.4   0.1    3.0  3  AAA_32           AAA domain
    2.6e-11   43.5   0.0    0.00015   21.5   0.0    2.4  2  Sigma54_activat  Sigma-54 interaction domain
    9.1e-08   32.2   0.0     0.0011   18.9   0.0    2.5  2  AAA_5            AAA domain (dynein-related subfamily)
    3.4e-07   30.8   0.0    0.00036   21.0   0.0    2.6  2  AAA              ATPase family associated with various cellul
    2.1e-06   27.6   0.0      0.064   13.0   0.0    2.4  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    2.3e-05   23.6   0.0       0.12   11.4   0.0    2.4  2  MCM              MCM P-loop domain
    3.6e-05   24.0   0.0    0.00098   19.4   0.0    2.3  2  AAA_22           AAA domain
    0.00013   22.4   0.0     0.0003   21.2   0.0    1.6  1  AAA_16           AAA ATPase domain
    0.00019   21.0   0.0    0.00036   20.1   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
    0.00035   20.4   0.0    0.00067   19.4   0.0    1.4  1  IstB_IS21        IstB-like ATP binding protein
    0.00065   20.1   0.0       0.11   12.8   0.0    2.4  2  AAA_19           AAA domain
    0.00074   19.3   0.0     0.0025   17.5   0.0    1.8  2  AAA_30           AAA domain
    0.00087   19.4   0.0       0.04   14.0   0.0    2.5  2  Sigma54_activ_2  Sigma-54 interaction domain
     0.0015   18.6   0.0       0.78    9.8   0.0    3.1  3  AAA_14           AAA domain
     0.0023   18.4   0.0     0.0061   17.1   0.0    1.8  1  ABC_tran         ABC transporter
     0.0035   16.6   0.1      0.039   13.2   0.0    2.3  2  TIP49            TIP49 P-loop domain
     0.0048   16.3   0.0       0.03   13.7   0.0    2.0  2  TniB             Bacterial TniB protein
  ------ inclusion threshold ------
      0.023   13.8   0.0      0.041   13.0   0.0    1.3  1  Parvo_NS1        Parvovirus non-structural protein NS1
      0.032   13.6   2.8      0.065   12.7   2.8    1.4  1  zf-ribbon_3      zinc-ribbon domain
      0.033   13.2   0.0      0.065   12.3   0.0    1.5  1  T2SSE            Type II/IV secretion system protein
      0.037   13.9   0.0       0.16   11.8   0.0    2.0  2  Rad17            Rad17 P-loop domain
       0.04   13.9   0.0       0.16   11.9   0.0    2.0  2  ResIII           Type III restriction enzyme, res subunit
      0.074   13.6   0.0       0.19   12.3   0.0    1.7  1  AAA_18           AAA domain
      0.096   12.0   0.0        1.7    7.9   0.0    2.5  2  Zeta_toxin       Zeta toxin
      0.096   12.8   0.0        0.5   10.5   0.0    2.1  2  AAA_33           AAA domain
        0.1   11.5   0.0       0.23   10.4   0.0    1.5  1  AAA_10           AAA-like domain
       0.11   12.3   0.1        0.3   10.8   0.0    1.7  1  AAA_11           AAA domain
       0.15   12.5   0.0       0.32   11.4   0.0    1.6  1  RNA_helicase     RNA helicase
       0.15   11.9   0.0       0.27   11.2   0.0    1.3  1  NACHT            NACHT domain
       0.17   11.6   0.0       0.43   10.4   0.0    1.6  1  AAA_29           P-loop containing region of AAA domain
       0.29   11.0   1.3        0.5   10.3   1.3    1.4  1  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)


Domain annotation for each model (and alignments):
>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   0.1   5.5e-13   3.1e-10       2      52 ..      33      83 ..      32      89 .. 0.93
   2 !   19.9   0.0   6.6e-07   0.00037      95     158 ..     277     347 ..     262     358 .. 0.78

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 5.5e-13
                      Mg_chelatase  2 lkdvkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllpplsee 52
                                      l  v Gqeea    +iaa+ + nlllvGppG+GK+m+a++++  lp+ ++e
  gi|474934251|ref|YP_007687833.1| 33 LDRVLGQEEAIALAKIAATQRRNLLLVGPPGTGKSMIARAISMNLPKAHQE 83
                                      6789******************************************98765 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 6.6e-07
                      Mg_chelatase  95 skpkpGeislahnGvLfLDElpe...fkrkvlevLRe...Pledgevtisrakakv.efparfqlvaamNp 158
                                       +++ pG+i  ah+GvLf+DE+++   ++r +l ++ +   P+  ++ + s a+ +v + p++f lvaa N 
  gi|474934251|ref|YP_007687833.1| 277 QRVIPGAIHEAHEGVLFIDEISHlgnLQRFILTAMQDkkfPITGRNPQSSGASVRVdNVPCDFILVAACNM 347
                                       5789****************987222466677666433348888888888888777468999999999996 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00028      0.15       5      77 ..      31      97 ..      29     105 .. 0.81
   2 !   13.3   0.0   4.7e-05     0.026     290     342 ..     241     296 ..     208     356 .. 0.87
   3 !   29.4   0.1   6.3e-10   3.5e-07     422     509 ..     371     462 ..     360     465 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00028
                            AAA_32  5 epleeiigqeRAvealefglkikkkgYNifvlGesgtGrttlvkrlleeiakkeptpdDwcYvnnfdnpeePk 77
                                      +pl++++gqe A++  +++     +  N+ ++G++gtG++++++ +  +     ++ +++   nn +npe+P 
  gi|474934251|ref|YP_007687833.1| 31 DPLDRVLGQEEAIALAKIAAT---QRRNLLLVGPPGTGKSMIARAISMNLP---KAHQEIRVANNPENPERPF 97
                                      5789999**999888888765...556*************99999887764...4556788899999999986 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 4.7e-05
                            AAA_32 290 egaPVvvednptyanLfGkieyesemg...alvtdftlIkaGaLhkAnGGyLilda 342
                                       +  P v+ +  + ++L+G + ++ + g   + v  ++++ +Ga+h+A+ G+L +d 
  gi|474934251|ref|YP_007687833.1| 241 DRDPFVMATGASETELLGDVRHDPYGGhekIGVPTYQRVIPGAIHEAHEGVLFIDE 296
                                       56799999**************9987744467899*****************9985 PP

  == domain 3  score: 29.4 bits;  conditional E-value: 6.3e-10
                            AAA_32 422 ddemerteenekkyarfias.ivkkekllpfdrsavarlieyssrlaedqek...lstrfseiadllrEAdywakke 494
                                       d  m+ t++n  kya+f+a+ i+ + ++++ + +av+++i ++ r a   ++   l++r++e+  l+r A  +a  e
  gi|474934251|ref|YP_007687833.1| 371 DVAMPDTSHNRAKYAQFVAQeIAMDGHIPDATIEAVEEIIAEGKRRAKADNQlnsLTLRLRELGGLIRAAGDIAVIE 447
                                       788***************973667778999***************9987765222689******************* PP

                            AAA_32 495 gaevveaehVekAle 509
                                       g++++++ehV  A +
  gi|474934251|ref|YP_007687833.1| 448 GSKLITREHVIMAKK 462
                                       **********99865 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.2e-06    0.0007      10      60 ..      41      91 ..      37     100 .. 0.84
   2 !   21.5   0.0   2.7e-07   0.00015      86     136 ..     281     331 ..     266     350 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.2e-06
                                      HHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTT CS
                   Sigma54_activat 10 elleqikkvaktdlsvlitGesGtGKellaraiheaskrkekpfvavncaa 60
                                      e+++ +k +a+++ ++l++G  GtGK+++arai  + +++++++   n  +
  gi|474934251|ref|YP_007687833.1| 41 EAIALAKIAATQRRNLLLVGPPGTGKSMIARAISMNLPKAHQEIRVANNPE 91
                                      6677888899999********************999999888877666555 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 2.7e-07
                                       EHHHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSEEESBTSS.SEEE--EE CS
                   Sigma54_activat  86 kGlfekadgGtlfLDeigelplelQekLlrvlqegevervGss.keikvdvr 136
                                        G++++a++G+lf+Dei++l  +lQ  +l+++q++++   G + ++  ++vr
  gi|474934251|ref|YP_007687833.1| 281 PGAIHEAHEGVLFIDEISHLG-NLQRFILTAMQDKKFPITGRNpQSSGASVR 331
                                       59*****************97.79*************999987344556666 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0     2e-06    0.0011       1      24 [.      55      78 ..      55      95 .. 0.80
   2 !   10.8   0.0   0.00066      0.37      65     137 ..     288     360 ..     243     361 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2e-06
                                      EEEEE--SSSSHHHHHHHGGGGBS CS
                             AAA_5  1 dvlLvGppGtgKselaerlaaaln 24
                                      ++lLvGppGtgKs++a+ ++  l 
  gi|474934251|ref|YP_007687833.1| 55 NLLLVGPPGTGKSMIARAISMNLP 78
                                      69****************998883 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00066
                                       G-SEEEEESGGG--.HHHHHHHHHHHHSSEEE..-SSSEEE---...........-EEEEEESS--.-TT-TTHHHH CS
                             AAA_5  65 egeilvlDEverae.sevlnsLlslleerrllleeggelvkaknddller.....frviatanpldrslnelspalr 135
                                       +  +l++DE+   +  + +   l+ + ++++++  ++ + + ++     +     f ++a++n +d  l+++ ++lr
  gi|474934251|ref|YP_007687833.1| 288 HEGVLFIDEIS--HlGNLQRFILTAMQDKKFPITGRNPQSSGASVRV--DnvpcdFILVAACNMQD--LQNILSPLR 358
                                       5679*******..4489999999*********776666666665323..2469*************..9999***** PP

                                       TT CS
                             AAA_5 136 sR 137
                                       sR
  gi|474934251|ref|YP_007687833.1| 359 SR 360
                                       *9 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   6.5e-07   0.00036       1      22 [.      56      77 ..      56     106 .. 0.82
   2 ?    7.0   0.0     0.013       7.5      57     123 ..     287     360 ..     274     364 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 6.5e-07
                                      EEEESSTTSSHHHHHHHHHHHH CS
                               AAA  1 vllyGppGtGKTllakavakel 22
                                      +ll+GppGtGK+++a+a+  +l
  gi|474934251|ref|YP_007687833.1| 56 LLLVGPPGTGKSMIARAISMNL 77
                                      69****************9887 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.013
                                       STSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS..................SSTEEEEEEESS..GG CS
                               AAA  57 akpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk..................eskvivigatnr..pd 113
                                       a+  +lfiDEi  l++ +              +lt++++ k                      ++i+++a+n    +
  gi|474934251|ref|YP_007687833.1| 287 AHEGVLFIDEISHLGNLQ------------RFILTAMQDKKFPitgrnpqssgasvrvdnvPCDFILVAACNMqdLQ 351
                                       3249**********7665............77777777777777777888888888888885568899999886667 PP

                                       GSTHHHHSTT CS
                               AAA 114 kldpallrgR 123
                                       ++ ++l+ +R
  gi|474934251|ref|YP_007687833.1| 352 NILSPLR-SR 360
                                       7777777.66 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00025      0.14      26      59 ..      46      79 ..      31      97 .. 0.73
   2 !   13.0   0.0   0.00012     0.064      84     153 ..     288     361 ..     282     364 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00025
                            RuvB_N 26 akkreealdhvllyGpPGlGkttlakiiakelgv 59
                                      ak   ++   +ll+GpPG Gk+ +a+ i+ +l  
  gi|474934251|ref|YP_007687833.1| 46 AKIAATQRRNLLLVGPPGTGKSMIARAISMNLPK 79
                                      444444445689****************998753 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00012
                            RuvB_N  84 ekdvlfideihrlsraveevlysamedfrldivigkGps.arsikldlp..kftlvgattragl..lssPlrdrf 153
                                       ++ vlfidei  l +  + ++ +am+d ++ i+  + +s   s+++d     f lv+a   + l  + sPlr+r+
  gi|474934251|ref|YP_007687833.1| 288 HEGVLFIDEISHLGNL-QRFILTAMQDKKFPITGRNPQSsGASVRVDNVpcDFILVAACNMQDLqnILSPLRSRI 361
                                       4679*********875.677789********98544333134556653313599***998776533779999995 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0   0.00079      0.44      52      84 ..      48      80 ..      33      88 .. 0.82
   2 !   11.4   0.0   0.00022      0.12      81     150 ..     240     316 ..     226     321 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00079
                                      SBBCSS-EEEEEESSTSTHHHHHHHHHHHSSSE CS
                               MCM 52 tklrgdinvllvgdpgtaKsqlLkyveklapra 84
                                      +    + n+llvg pgt+Ks + ++++ ++p+a
  gi|474934251|ref|YP_007687833.1| 48 IAATQRRNLLLVGPPGTGKSMIARAISMNLPKA 80
                                      45566789******************9999987 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00022
                                       SSSEEEEESSSSSSSHSSSEEEEESSSSS........EEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSE CS
                               MCM  81 apravytsgkgssaagLtaavvrdeetge........fvleaGalvladkGvcciDefdkmkeedrsalhEamEqqt 149
                                       ++r  ++ ++g+s+++L   v++d+  g+          +  Ga+  a++Gv+ iDe+ +  +  +  ++ am +++
  gi|474934251|ref|YP_007687833.1| 240 LDRDPFVMATGASETELLGDVRHDPYGGHekigvptyQRVIPGAIHEAHEGVLFIDEISHLGN-LQRFILTAMQDKK 315
                                       567778889999999999999999887665666654445679*******************99.8889999998876 PP

                                       E CS
                               MCM 150 i 150
                                        
  gi|474934251|ref|YP_007687833.1| 316 F 316
                                       5 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.8e-06   0.00098       4      38 ..      52      91 ..      49     121 .. 0.76
   2 ?    2.0   0.0      0.43   2.4e+02      86     104 ..     284     301 ..     265     321 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.8e-06
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeeakaee.....e 38
                                      +++ l+++G++GtGK++ +r + ++l+++ +  +     e
  gi|474934251|ref|YP_007687833.1| 52 QRRNLLLVGPPGTGKSMIARAISMNLPKAHQEIRvannpE 91
                                      68899********************985433333655542 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.43
                            AAA_22  86 lraravielliiDEaqhlr 104
                                       +++++  ++l iDE+ hl 
  gi|474934251|ref|YP_007687833.1| 284 IHEAHE-GVLFIDEISHLG 301
                                       566666.9*********93 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   5.4e-07    0.0003      15      86 ..      44     110 ..      35     173 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 5.4e-07
                            AAA_16  15 alervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqll 86 
                                       al ++++ + +++ll+G++G+GKs ++r++   l k++    + +   ++++ p  +++++l++ + ++ + 
  gi|474934251|ref|YP_007687833.1|  44 ALAKIAATQRRNLLLVGPPGTGKSMIARAISMNLPKAH---QEIRVANNPEN-PERPFLEVLDE-KDVNLES 110
                                       5667777888********************99999984...22222222112.22457777755.4444443 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   6.4e-07   0.00036      25      62 ..      45      82 ..      39     102 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 6.4e-07
                             AAA_7 25 llelllknkkpvllvGptGtGKtviikdllkkldkeky 62
                                      l +   ++++++llvGp GtGK++i++ +  +l+k + 
  gi|474934251|ref|YP_007687833.1| 45 LAKIAATQRRNLLLVGPPGTGKSMIARAISMNLPKAHQ 82
                                      6778899*********************9999996554 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.2e-06   0.00067      45      75 ..      51      81 ..      35      90 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.2e-06
                         IstB_IS21 45 ekkenivllGpsGvGKshlaialgveavrag 75
                                      +++ n++l+Gp+G+GKs +a a++++  +a 
  gi|474934251|ref|YP_007687833.1| 51 TQRRNLLLVGPPGTGKSMIARAISMNLPKAH 81
                                      4678*******************99876654 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0    0.0002      0.11       5      38 ..      49      81 ..      39      88 .. 0.80
   2 ?    4.9   0.0     0.053        30     103     129 ..     288     314 ..     208     327 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0002
                            AAA_19  5 vealkekvllvtaGpGtGKTrvlkhivallvelg 38
                                      + a+++++ll++++pGtGK+ + ++i   l +++
  gi|474934251|ref|YP_007687833.1| 49 A-ATQRRNLLLVGPPGTGKSMIARAISMNLPKAH 81
                                      2.7899**************99998877766655 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.053
                            AAA_19 103 ee.llivDEfqdvdelqyrLlkallgek 129
                                       +e +l++DE++ +  lq  +l a+  +k
  gi|474934251|ref|YP_007687833.1| 288 HEgVLFIDEISHLGNLQRFILTAMQ-DK 314
                                       3459*****************9998.33 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   4.6e-06    0.0025       6      49 ..      41      84 ..      36      91 .. 0.79
   2 ?   -2.0   0.0       4.5   2.5e+03      89     104 ..     289     304 ..     262     315 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.6e-06
                            AAA_30  6 QaaavealltsgdrvavltGpAGtGKttalkalreaweaaggrv 49
                                       a a+++++++++r  +l+Gp+GtGK+++ +a+   + +a +++
  gi|474934251|ref|YP_007687833.1| 41 EAIALAKIAATQRRNLLLVGPPGTGKSMIARAISMNLPKAHQEI 84
                                      4456789999999*******************987766665555 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.5
                            AAA_30  89 gtllivDEagmvdtkq 104
                                       + +l +DE++ +++ q
  gi|474934251|ref|YP_007687833.1| 289 EGVLFIDEISHLGNLQ 304
                                       47899****9998765 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   7.1e-05      0.04      17      49 ..      49      81 ..      40     106 .. 0.73
   2 ?    2.6   0.0      0.24   1.3e+02      66      89 ..     285     308 ..     245     331 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.1e-05
                                      HHT-SS-EEEEEETT--HHHHHHCC--TTS-EE CS
                   Sigma54_activ_2 17 aaqsklpvfltGekGsgkelvArlLhknsgpwl 49
                                      aa +  +++l+G++G+gk+++Ar+++ n  +  
  gi|474934251|ref|YP_007687833.1| 49 AATQRRNLLLVGPPGTGKSMIARAISMNLPKAH 81
                                      457889*******************87654443 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.24
                                       HHTTTSEEEEEE-TT--HHHHHHH CS
                   Sigma54_activ_2  66 eqakggtLylkdiadlskaeqkeL 89 
                                        +a++g+L++ +i +l++ +   L
  gi|474934251|ref|YP_007687833.1| 285 HEAHEGVLFIDEISHLGNLQRFIL 308
                                       5689************98766555 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.083        46       2      35 ..      53      83 ..      52     117 .. 0.69
   2 ?    0.4   0.0       1.1     6e+02      84     122 ..     235     273 ..     228     278 .. 0.81
   3 !    9.8   0.0    0.0014      0.78      63      99 ..     287     320 ..     274     331 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.083
                            AAA_14  2 rkilvitGaRrvGKTtllkqlikellvkkesily 35
                                      r+ l+++G+  +GK+++++ +  +l    +   +
  gi|474934251|ref|YP_007687833.1| 53 RRNLLLVGPPGTGKSMIARAISMNLP---KAHQE 83
                                      57789************988765555...33333 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.1
                            AAA_14  84 kslvdegknldvivtGSnskllskeiatslagrvaeiel 122
                                       k +v+ +++  v++tG +   l+ ++++++ g +++i +
  gi|474934251|ref|YP_007687833.1| 235 KTIVKLDRDPFVMATGASETELLGDVRHDPYGGHEKIGV 273
                                       566666666789***************999998888765 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.0014
                            AAA_14  63 ekktylflDEiqevpewekalkslvdegknldvivtG 99 
                                        ++ +lf+DEi+++ ++++++   ++++   ++ +tG
  gi|474934251|ref|YP_007687833.1| 287 AHEGVLFIDEISHLGNLQRFILTAMQDK---KFPITG 320
                                       46789********************999...677777 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.1e-05    0.0061      12      50 ..      54      92 ..      42     162 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.1e-05
                                      SEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGG CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 12 ekvaivGenGaGKStLlkllagllkpteGeilldgkdlk 50
                                      + + +vG+ G+GKS ++++++ +l ++  ei++ +++ +
  gi|474934251|ref|YP_007687833.1| 54 RNLLLVGPPGTGKSMIARAISMNLPKAHQEIRVANNPEN 92
                                      66889**************************87766544 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0     7e-05     0.039      48      76 ..      51      79 ..      12      88 .. 0.80
   2 ?    0.7   0.0      0.44   2.4e+02     279     290 ..     289     300 ..     278     319 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7e-05
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 48 laGravLlaGpsgtGktalaiaiskelge 76
                                         r +Ll+Gp+gtGk+ +a ais +l +
  gi|474934251|ref|YP_007687833.1| 51 TQRRNLLLVGPPGTGKSMIARAISMNLPK 79
                                      34589*******************99865 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.44
                                       XXXXXXXXXXXX CS
                             TIP49 279 pGvlfiDevhml 290
                                        GvlfiDe+  l
  gi|474934251|ref|YP_007687833.1| 289 EGVLFIDEISHL 300
                                       7*******8554 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   5.3e-05      0.03      26      63 ..      45      81 ..      37     100 .. 0.79
   2 ?   -0.6   0.0       1.3   7.2e+02     115     131 ..     284     300 ..     272     306 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.3e-05
                              TniB 26 LleypkrkrmpnlllvGdsnnGKtmivekFarlhppek 63
                                      L + +  +r +nlllvG++ +GK+mi++  + + p+++
  gi|474934251|ref|YP_007687833.1| 45 LAKIAATQR-RNLLLVGPPGTGKSMIARAISMNLPKAH 81
                                      555556666.9****************98877766554 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.3
                              TniB 115 lrelkvrvLiiDEihnl 131
                                       ++e +  vL iDEi +l
  gi|474934251|ref|YP_007687833.1| 284 IHEAHEGVLFIDEISHL 300
                                       56777889******998 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   7.2e-05     0.041     112     141 ..      51      80 ..      30     103 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.2e-05
                         Parvo_NS1 112 gkrntvwfyGpantGktnlaeaIakavply 141
                                       ++r  ++++Gp+ tGk+++a+aI   +p+ 
  gi|474934251|ref|YP_007687833.1|  51 TQRRNLLLVGPPGTGKSMIARAISMNLPKA 80 
                                       557778999**************9888764 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   2.8   0.00012     0.065       3      22 ..     136     155 ..     135     156 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                       zf-ribbon_3   3 vrCPnCGa.plssddnvCpyC 22 
                                       +rC +CGa   +++d  Cp+C
  gi|474934251|ref|YP_007687833.1| 136 YRCKYCGAfS-TPEDLSCPSC 155
                                       69******88.********** PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00012     0.065     124     164 ..      48      88 ..       2     102 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00012
                             T2SSE 124 kavrerglilvsGgTgsGKttllyallkeinksderivtvE 164
                                        a ++r ++l+ G+ g+GK+ ++ a+   ++k +++i ++ 
  gi|474934251|ref|YP_007687833.1|  48 IAATQRRNLLLVGPPGTGKSMIARAISMNLPKAHQEIRVAN 88 
                                       3346799************************9988887665 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00029      0.16      38      77 ..      46      85 ..      10     115 .. 0.74
   2 ?   -1.3   0.0       3.2   1.8e+03     105     147 ..     299     341 ..     289     360 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00029
                             Rad17 38 dvLesrkkriLLisGPsGCgkstvvkvLskelgiklrewl 77
                                        +   ++r LL+ GP+G gks + + +s +l    +e  
  gi|474934251|ref|YP_007687833.1| 46 AKIAATQRRNLLLVGPPGTGKSMIARAISMNLPKAHQEIR 85
                                      4445556789999**************9998866655543 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.2
                             Rad17 105 qiesfkeleLkdakylklqklGddlrtdkklilvedlPnkfyr 147
                                        +   + + L + + +k+   G + ++    + v+++P  f  
  gi|474934251|ref|YP_007687833.1| 299 HLGNLQRFILTAMQDKKFPITGRNPQSSGASVRVDNVPCDFIL 341
                                       5556678899999999999999999999999999999988854 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00029      0.16       8      55 ..      39      84 ..      33     116 .. 0.79
   2 ?   -2.8   0.0       9.8   5.5e+03     131     146 ..     287     302 ..     270     314 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00029
                                      HHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S..... CS
                            ResIII  8 QeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkee 55
                                      Qeeai     k+ +++++++l++ + GtGK+++a ++  +l k+++e 
  gi|474934251|ref|YP_007687833.1| 39 QEEAIALA--KIAATQRRNLLLVGPPGTGKSMIARAISMNLPKAHQEI 84
                                      67777544..56658999999*************99999999887654 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 9.8
                                       TT-SEEEEETGGGTTS CS
                            ResIII 131 drfdviiiDEaHrlga 146
                                        ++ v++iDE  +lg 
  gi|474934251|ref|YP_007687833.1| 287 AHEGVLFIDEISHLGN 302
                                       4566999999877765 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00033      0.19       2      22 ..      57      77 ..      56     126 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00033
                            AAA_18  2 lltGtpGvGKttlakeLskrl 22
                                      ll G+pG+GK+ +a+++s  l
  gi|474934251|ref|YP_007687833.1| 57 LLVGPPGTGKSMIARAISMNL 77
                                      689**************7665 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0     0.003       1.7      19      49 ..      56      86 ..      44      91 .. 0.83
   2 ?    0.8   0.0      0.45   2.5e+02      80     111 ..     350     381 ..     342     424 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.003
                        Zeta_toxin 19 illgGqpGAGKselaellkdelerqgnvvrl 49
                                      +ll+G pG GKs +a+++  +l ++ + +r+
  gi|474934251|ref|YP_007687833.1| 56 LLLVGPPGTGKSMIARAISMNLPKAHQEIRV 86
                                      699***************9999877666665 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.45
                        Zeta_toxin  80 aselvekllqeaiengyniivegtlrspdvvk 111
                                        + +   l+  +i ngy+++v+ ++ +++  +
  gi|474934251|ref|YP_007687833.1| 350 LQNILSPLRSRIIGNGYEVLVDVAMPDTSHNR 381
                                       55666678889999********9997765544 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00089       0.5       3      23 ..      57      77 ..      56     104 .. 0.84
   2 ?   -1.1   0.0       3.5   1.9e+03      53      99 ..     348     391 ..     342     421 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00089
                            AAA_33  3 llvGlpGsGKstlaerllkkl 23
                                      llvG+pG+GKs  a+ +  +l
  gi|474934251|ref|YP_007687833.1| 57 LLVGPPGTGKSMIARAISMNL 77
                                      79************9876555 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 3.5
                            AAA_33  53 drlyqilnelarkalsagrnvildatnlsr.rerarflklarrlgvpv 99 
                                       ++l +il+ l  +    g+ v++d  + +  ++ra++ +++     ++
  gi|474934251|ref|YP_007687833.1| 348 QDLQNILSPLRSRIIGNGYEVLVDVAMPDTsHNRAKYAQFVA----QE 391
                                       567788888888888899999999999887788888888864....33 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0    0.0004      0.23      15      70 ..      49     103 ..      40     125 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0004
                            AAA_10  15 kgsktnasasliiGdlGnGKSvlakllvlyisllggkaliiDpkke.rekfketlpe 70 
                                         ++ +++  l++G++G GKS++a+ + +++  + + + +    ++ ++ f e l e
  gi|474934251|ref|YP_007687833.1|  49 AATQRRNL--LLVGPPGTGKSMIARAISMNLPKAHQEIRVANNPENpERPFLEVLDE 103
                                       44444555..******************99987777665544333325556666655 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00054       0.3       6      42 ..      39      78 ..      37     117 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00054
                            AAA_11  6 qreai...ksalseseitliqGPPGtgKTktivellsqll 42
                                      q+eai   k a +++   l+ GPPGtgK+    ++ ++l 
  gi|474934251|ref|YP_007687833.1| 39 QEEAIalaKIAATQRRNLLLVGPPGTGKSMIARAISMNLP 78
                                      5666655555556666689**********88877777773 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00057      0.32       2      28 ..      57      83 ..      56     108 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00057
                      RNA_helicase  2 wlyGpsgeGKStlakeLakallkklkl 28
                                      +l+Gp+g+GKS++a+ ++ +l k+ ++
  gi|474934251|ref|YP_007687833.1| 57 LLVGPPGTGKSMIARAISMNLPKAHQE 83
                                      799*************99999866533 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00048      0.27       2      29 ..      55      82 ..      54      86 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00048
                                      CEEEEC-TTTCHHHHHHHHHHHHCTS-S CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalawaegkl 29
                                       ++l G++G GK++ ++ + + + + ++
  gi|474934251|ref|YP_007687833.1| 55 NLLLVGPPGTGKSMIARAISMNLPKAHQ 82
                                      5799****************99988775 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00077      0.43      21      44 ..      52      75 ..      44      86 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00077
                            AAA_29 21 lkgatlltGpsGsGKSTllDAiqa 44
                                      ++ + ll+Gp G+GKS +  Ai++
  gi|474934251|ref|YP_007687833.1| 52 QRRNLLLVGPPGTGKSMIARAISM 75
                                      33479***********99888765 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.3   0.00089       0.5      11      34 ..     135     158 ..     134     161 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00089
                           DUF35_N  11 gqrCpdCGtvqfPPravCphCgsd 34 
                                       g rC+ CG++  P   +Cp C  +
  gi|474934251|ref|YP_007687833.1| 135 GYRCKYCGAFSTPEDLSCPSCAKS 158
                                       88*********9999******755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (509 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      650  (0.0362541); expected 358.6 (0.02)
Passed Vit filter:                       130  (0.00725082); expected 17.9 (0.001)
Passed Fwd filter:                        32  (0.00178482); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              32  [number of targets reported over threshold]
# CPU time: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.48
# Mc/sec: 3166.44
//
Query:       gi|474934252|ref|YP_007687834.1|  [L=570]
Description: DNA primase (bacterial type) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-11   42.7   0.1    1.8e-10   41.2   0.1    2.0  1  Toprim_4  Toprim domain
    0.00012   22.5   0.0    0.00043   20.7   0.0    2.1  1  Toprim_2  Toprim-like
  ------ inclusion threshold ------
      0.051   13.8   0.1       0.27   11.5   0.1    2.3  1  Toprim    Toprim domain


Domain annotation for each model (and alignments):
>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.1     3e-14   1.8e-10       2      57 ..     163     222 ..     162     253 .. 0.79

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 3e-14
                          Toprim_4   2 eiiiVEgyaDvlalekagiknvvavlggalspldgirpeklkt.enlve....aekkvkev 57 
                                       +iiiVEg+ Dvl+l +agikn+vav g+++ p++  +++k +  +++v+    +e +++e+
  gi|474934252|ref|YP_007687834.1| 163 AIIIVEGRSDVLNLLRAGIKNAVAVEGTNI-PKSVQELSKERVtTAFVDgdrgGELILREL 222
                                       69****************************.666666555555467777666655555555 PP

>> Toprim_2  Toprim-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   7.2e-08   0.00043       1      66 [.     165     224 ..     165     264 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 7.2e-08
                          Toprim_2   1 vvfEgaiDalSlaqlgikektnvvalgGtalteaalkllerypekkvvlalDnDkaGrkaakrlae 66 
                                       +++Eg  D+l l+++gik   n+va+ Gt + ++ +++l+++  +     +D D+ G+   ++l +
  gi|474934252|ref|YP_007687834.1| 165 IIVEGRSDVLNLLRAGIK---NAVAVEGT-NIPKSVQELSKE--RVTTAFVDGDRGGELILRELFQ 224
                                       69***************9...********.777778888877..4345559*******99887755 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   4.6e-05      0.27       2      88 ..     164     227 ..     163     243 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.6e-05
                                       EEEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHSTTEEEEEECTTTHHHHHHHHHHHHHHSEEEEE.CSSSHHHH CS
                            Toprim   2 lvivEgpsdaktiakalgsgfqavtaslGhildletefkpvyeeiedkkkvlkalkelakradeiila.tDpDreGe 77 
                                       ++ivEg sd+ ++ +a   g ++++a+ G+ +                       +el+   +++  a  D+Dr Ge
  gi|474934252|ref|YP_007687834.1| 164 IIIVEGRSDVLNLLRA---GIKNAVAVEGTNIPKSV-------------------QELS--KERVTTAfVDGDRGGE 216
                                       89**************...9*********9887665...................5554..2334444389999999 PP

                                       HHHHHHHHHHT CS
                            Toprim  78 aiawellevlk 88 
                                        i  el++  +
  gi|474934252|ref|YP_007687834.1| 217 LILRELFQTSE 227
                                       99999997655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (570 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1092  (0.0609069); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.71u 0.33s 00:00:01.04 Elapsed: 00:00:00.51
# Mc/sec: 3383.20
//
Query:       gi|474934253|ref|YP_007687835.1|  [L=708]
Description: hypothetical protein TALC_00678 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-10   41.5   5.7    2.1e-10   41.5   5.7    2.7  2  AAA_23         AAA domain
    1.5e-09   37.8   0.3    1.6e-08   34.4   0.1    2.7  1  AAA_27         AAA domain
    0.00032   20.2   0.1       0.51    9.7   0.0    2.6  2  SMC_N          RecF/RecN/SMC N terminal domain
    0.00083   19.2   2.2     0.0025   17.6   0.4    2.5  2  AAA_15         AAA ATPase domain
  ------ inclusion threshold ------
      0.037   13.8   0.0       0.11   12.2   0.0    1.8  2  AAA_29         P-loop containing region of AAA domain
       0.09   12.9   0.1       0.19   11.9   0.1    1.4  1  Herpes_UL49_5  Herpesvirus UL49.5 envelope/tegument protein
       0.65   10.3   5.6       0.41   11.0   1.8    2.2  2  DUF3040        Protein of unknown function (DUF3040)
        3.6    7.1   7.9        2.6    7.5   4.2    2.2  2  Exonuc_VII_L   Exonuclease VII, large subunit
        8.3    6.7  13.7       0.33   11.2   2.2    3.3  3  Cnn_1N         Centrosomin N-terminal motif 1
        9.1    6.2   7.8        3.4    7.6   0.6    3.5  3  PKcGMP_CC      Coiled-coil N-terminus of cGMP-dependent prote


Domain annotation for each model (and alignments):
>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   5.7   1.1e-13   2.1e-10       6     197 ..      10     282 ..       5     310 .. 0.51
   2 ?   -1.2   1.3       1.4   2.5e+03      90     114 ..     512     536 ..     376     555 .. 0.59

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 1.1e-13
                            AAA_23   6 nfrsfrdqeidFskgltlItGpNGaGKTTildAiklaLyget.prlsrksgrgfeksdveiesegkvkayveltfen 81 
                                        f+ +rd e++Fs+gl++++G+N+ GK+T+  +i+  L+  +  r +  +++++ + dve++++ + +  +e++ ++
  gi|474934253|ref|YP_007687835.1|  10 SFGNLRDREVEFSPGLNVVYGENEVGKSTLRTFITNTLFPASkLRYPAPKQSDSGTLDVELSDG-Q-RMRFERDGKK 84 
                                       455559*********************************8552444555577888999998775.3.3334444333 PP

                            AAA_23  82 kdgry................................................................trsierer 94 
                                           +                                                                        
  gi|474934253|ref|YP_007687835.1|  85 ----SngsaegicgitsaeyisiysispdelrdtdsisggnirnrfltipggrdlpqayaeldrerreyL------- 150
                                       ....333346788877777777666665555555555555555555555555555544222222221110....... PP

                            AAA_23  95 elskkkgkttkka..klelleideleqfisellgskkiilnlilflgqerfeefelkdkke................ 153
                                            + k  +k+  + +l + ++  ++++el ++++   ++  +l++++          +                
  gi|474934253|ref|YP_007687835.1| 151 ----PDQKWSSKSiiADSLAKSRAASERVRELKSRTDGDDHYAELLHEKE----------Nlesrlrqadeefgsaq 213
                                       ....1111111111122222222223333322222222222222222222..........01122222223334444 PP

                            AAA_23 154 .................rleelekeleeledekkllekl...............eqekekekeleeleeeleeilk 197
                                                        r+       +ele++++ll+                  ++++  k+l +  e+l+++++
  gi|474934253|ref|YP_007687835.1| 214 taavnsarreviskdieRI-------RELEAQAELLKYAeradddarntyielqVKAENSSKTLRDRSEALTDAKQ 282
                                       4433334222222222222.......22233333333334444444444544434556666666666666666665 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.4
                            AAA_23  90 iererelskkkgkttkkaklellei 114
                                       +  +r +  +k+ ++++a++++l++
  gi|474934253|ref|YP_007687835.1| 512 VASSRDTLIEKKTRVDEAIKSILND 536
                                       1222222222233333333333333 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.1   8.7e-12   1.6e-08       1      53 [.       1      50 [.       1     185 [. 0.88

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 8.7e-12
                            AAA_27  1 MrlerLdLeryGkftdrsldfsaeeadlhliyGpNEAGKstalrAisdllfGi 53
                                      Mr+ r ++  +G++ dr+++fs   ++l ++yG NE GKst+++ i++ lf  
  gi|474934253|ref|YP_007687835.1|  1 MRILRARIGSFGNLRDREVEFS---PGLNVVYGENEVGKSTLRTFITNTLFPA 50
                                      9********************9...9**********************99964 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0     0.001       1.8       7      43 ..       8      42 ..       2      55 .. 0.78
   2 !    9.7   0.0   0.00028      0.51     135     200 ..     485     693 ..     208     706 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.001
                                      EESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  7 ienFksyagktvilpfsksftaivGpNGSGKsnlldA 43
                                      i  F ++  +  +++fs+++++++G+N  GKs l   
  gi|474934253|ref|YP_007687835.1|  8 IGSFGNL--RDREVEFSPGLNVVYGENEVGKSTLRTF 42
                                      5566666..467889*****************98655 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00028
                                       T............................................................................ CS
                                       x............................................................................ RF
                             SMC_N 135 e............................................................................ 135
                                       +                                                                            
  gi|474934253|ref|YP_007687835.1| 485 Ntlnelknrlpedayeevpevtvqvndvassrdtliekktrvdeaiksilndteveeaitaasdaegdvynavlgwa 561
                                       05555555555555555555555555555555555555555555555555555555559999999999999999999 PP

                                       .................................................................CS-HHHHHHHHH CS
                                       .................................................................xxxxxxxxxxxx RF
                             SMC_N 136 .................................................................lLSgGektLval 147
                                                                                                        + S G    v l
  gi|474934253|ref|YP_007687835.1| 562 rlylterilddacekaysahrpsviqdtdaflssmtggrygmnldpkeqditvvdrttgeikgekEWSTGLGDQVKL 638
                                       99999999999999999999999999999999999999999999999999999999999999999777776666677 PP

                                       HHHHH..HHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHH CS
                                       xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 148 aLlfA..iqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislree 200
                                       ++++A  +   k  p ++lD++    D  + +  ae ++  s++ Q+i  + ++e
  gi|474934253|ref|YP_007687835.1| 639 SIRMAvsLSLSKEMPPVILDDVLLTSDSGRKRGAAEAIRLLSDRIQVIYFTCDRE 693
                                       777764488899************************************9998776 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.4   1.4e-06    0.0025       1      43 [.       1      43 [.       1     315 [. 0.85
   2 ?   -0.7   0.1      0.51   9.1e+02     213     254 ..     482     535 ..     376     568 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.4e-06
                            AAA_15  1 MkIkkikikNFRslkdveidlseeltvliGkNnsGKSsileal 43
                                      M+I + +i  F+ l+d e+++s+ l+v+ G+N +GKS++  ++
  gi|474934253|ref|YP_007687835.1|  1 MRILRARIGSFGNLRDREVEFSPGLNVVYGENEVGKSTLRTFI 43
                                      899999999*****************************86666 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.51
                            AAA_15 213 kkssllgklkekileealqekl.............eeelteklkeiqeklkeidk 254
                                       ++ ++l++lk+++ e+a++e               ++ l+ek  +++e++k i +
  gi|474934253|ref|YP_007687835.1| 482 ETVNTLNELKNRLPEDAYEE-VpevtvqvndvassRDTLIEKKTRVDEAIKSILN 535
                                       22334444444444443222.1233334333333333333333333333333322 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   6.4e-05      0.11      11      54 ..      13      55 ..       5      58 .. 0.84
   2 ?   -3.3   0.1       4.3   7.7e+03      53      60 ..     442     449 ..     439     450 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.4e-05
                            AAA_29 11 tfdghtieidlkgatlltGpsGsGKSTllDAiqalLvpakkvrf 54
                                       ++++++e+++    ++ G++++GKSTl   i+  L pa+k+r+
  gi|474934253|ref|YP_007687835.1| 13 NLRDREVEFSPG-LNVVYGENEVGKSTLRTFITNTLFPASKLRY 55
                                      566678888855.699************9999999999998887 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.3
                            AAA_29  53 rfNkaane 60 
                                       ++N+aa+e
  gi|474934253|ref|YP_007687835.1| 442 AYNEAADE 449
                                       7*****86 PP

>> Herpes_UL49_5  Herpesvirus UL49.5 envelope/tegument protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1    0.0001      0.19      13      55 ..     363     415 ..     355     419 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0001
                     Herpes_UL49_5  13 lavvvllllalvraasgd..........galdiareeeredFwhaaCsarGvs 55 
                                       +av  ++++a+v  +s++          +++ +a+  e e+ w ++Csa+G+ 
  gi|474934253|ref|YP_007687835.1| 363 VAVAGAAIFAVVYQKSSKtverapavrrNREAEAELSEIEELWMSTCSAVGIK 415
                                       6666777777777777777888888887666666667899***********85 PP

>> DUF3040  Protein of unknown function (DUF3040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.1       0.6   1.1e+03      12      35 ..     196     217 ..     194     227 .. 0.71
   2 ?   11.0   1.8   0.00023      0.41      35      79 ..     327     372 ..     314     375 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.6
                           DUF3040  12 eeiEraLaaeDPklaaalrggaar 35 
                                       e +E++L++ D ++ +a   +aa 
  gi|474934253|ref|YP_007687835.1| 196 ENLESRLRQADEEFGSAQ--TAAV 217
                                       579***********9998..3332 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00023
                           DUF3040  35 rarrrslrrlavlavllfvaGllllvlGvaaaa.vvlgvvGfvvml 79 
                                       ++++ +++ l  +++l+++aGl++  lG+++   v+++v+G+++ +
  gi|474934253|ref|YP_007687835.1| 327 TEKHMRMKPLSAVGLLIMAAGLAIAGLGISLYGgVAVAVAGAAIFA 372
                                       2555567777788888888888888888666667999999998865 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   4.2    0.0015       2.6     138     266 ..     192     294 ..     134     347 .. 0.49
   2 ?    0.4   0.1      0.21   3.8e+02     196     250 ..     467     527 ..     368     544 .. 0.43

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0015
                      Exonuc_VII_L 138 vvpdkaeleeqleelerrlekaikrlleekkqrleklasrlkspeellerkrqrldeleerleralkkqlkkkrerl 214
                                       +  +k++le++l+++++++ +a + ++                                   ++a ++ ++k  er+
  gi|474934253|ref|YP_007687835.1| 192 LH-EKENLESRLRQADEEFGSAQTAAV-----------------------------------NSARREVISKDIERI 232
                                       11.222222222222222222221111...................................111111133333333 PP

                      Exonuc_VII_L 215 eelkerlk.....ekleekkerlkklkerle...................lleekkerleeleeklealsplkvLk 266
                                       +el+++ +     e+               +                   +l++++e+l+ ++++l  l+ +++L+
  gi|474934253|ref|YP_007687835.1| 233 RELEAQAEllkyaERA--------------DddarntyielqvkaensskTLRDRSEALTDAKQRLGGLDADRILA 294
                                       3333222122222111..............1111111111112222333356666666666666666666666654 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.21
                      Exonuc_VII_L 196 eerleralkkq..lkkkrerleelkerl.k...ekleekkerlkklkerlelleekkerle 250
                                       ++r+e+al+    +++  ++l+elk+rl +   e++ e + ++++++++ ++l ekk+r++
  gi|474934253|ref|YP_007687835.1| 467 KDRFEKALEDCrsYNETVNTLNELKNRLpEdayEEVPEVTVQVNDVASSRDTLIEKKTRVD 527
                                       2222222221122444555555555555443333333333333333333334444444444 PP

>> Cnn_1N  Centrosomin N-terminal motif 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.4      0.18   3.2e+02      42      71 ..     178     207 ..     162     209 .. 0.78
   2 ?   11.2   2.2   0.00018      0.33      23      72 ..     232     283 ..     231     284 .. 0.87
   3 ?   -0.3   0.2       0.7   1.3e+03      30      69 ..     487     529 ..     481     533 .. 0.53

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.18
                            Cnn_1N  42 lkenielkveveslqkelkekkkllreaek 71 
                                       lk++++  ++ ++l +e+++++ +lr+a +
  gi|474934253|ref|YP_007687835.1| 178 LKSRTDGDDHYAELLHEKENLESRLRQADE 207
                                       56688889999999************9986 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00018
                            Cnn_1N  23 iyfLeer..leklseeqkeellkenielkveveslqkelkekkkllreaeka 72 
                                       i +Le +  l k +e+  +++ ++ iel+v+ e+  k+l  + + l++a+++
  gi|474934253|ref|YP_007687835.1| 232 IRELEAQaeLLKYAERADDDARNTYIELQVKAENSSKTLRDRSEALTDAKQR 283
                                       666666544888889*********************************9875 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.7
                            Cnn_1N  30 leklseeqkeellkenielkve...veslqkelkekkkllrea 69 
                                       l++l+++  e++ +e  e+ v+   v+s +++l ekk +++ea
  gi|474934253|ref|YP_007687835.1| 487 LNELKNRLPEDAYEEVPEVTVQvndVASSRDTLIEKKTRVDEA 529
                                       4444555555555555555555111455556666666666665 PP

>> PKcGMP_CC  Coiled-coil N-terminus of cGMP-dependent protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       0.5   8.9e+02       8      16 ..     173     181 ..     170     186 .. 0.79
   2 ?   -0.8   0.6       0.8   1.4e+03      12      23 ..     197     208 ..     191     209 .. 0.88
   3 ?    7.6   0.6    0.0019       3.4       5      16 ..     226     238 ..     224     241 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.5
                         PKcGMP_CC   8 ERIRELEkr 16 
                                       ER+REL  r
  gi|474934253|ref|YP_007687835.1| 173 ERVRELKSR 181
                                       788888654 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.8
                         PKcGMP_CC  12 ELEkrlaekdeE 23 
                                        LE rl++ deE
  gi|474934253|ref|YP_007687835.1| 197 NLESRLRQADEE 208
                                       59******9998 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0019
                         PKcGMP_CC   5 lKD.ERIRELEkr 16 
                                       +KD ERIRELE++
  gi|474934253|ref|YP_007687835.1| 226 SKDiERIRELEAQ 238
                                       56659******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (708 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1013  (0.0565006); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.84u 0.39s 00:00:01.23 Elapsed: 00:00:00.54
# Mc/sec: 3957.09
//
Query:       gi|474934254|ref|YP_007687836.1|  [L=399]
Description: DNA repair exonuclease [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.8e-12   46.0   0.0    2.9e-11   44.2   0.0    1.8  1  Metallophos    Calcineurin-like phosphoesterase
    3.9e-10   40.2   0.0      6e-10   39.6   0.0    1.3  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.0   3.3e-15   2.9e-11       1     203 [.       5     197 ..       5     198 .. 0.60

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 3.3e-15
                                       EEEEEEESBTB...................TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS....HHHHHHH CS
                       Metallophos   1 lrilvigDlHl...................algggqlddllkllddllreekpdlvllaGDlvdrg....dlekell 54 
                                       +++++ +DlHl                   +     ++++++++d +  +ek+d++++ GD +d++        +  
  gi|474934254|ref|YP_007687836.1|   5 FTFVHAADLHLgsrfwgislkdpdlgkrlfE---STFESFRRIIDLT--KEKADFLVISGDAFDEStmtlRTKLR-- 74 
                                       789*****************99966663333...3344444444222..359**************664444444.. PP

                                       HHHHHHHHH..TSEEEEEC-TTSCHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEETH CS
                       Metallophos  55 ellaalvky..pipvylllGNHegfeeellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGgspellv 129
                                         +++ +k+   +pv+l++GNH+ f +++  + ++  +   +  s+++   n+         ++++ +  g+++   
  gi|474934254|ref|YP_007687836.1|  75 --FCEEIKRlgTKPVFLVKGNHD-FGDSWADSIPFPSNVHLLRDSPQSMTLNFRNET-----VEIVGMSYGTQHT-- 141
                                       ..44444444559**********.888888888877776555555422222222222.....1222222221111.. PP

                                       HHHHHHHHHHSCHHHHCCHHHHHHHHHHTTCSEEEEEESSESS..CSSSCSCCHHHHHHHHHHTTESEEEEESSSS CS
                       Metallophos 130 sldklgslnleleapepgdewlkdlekrekadwvivlgHsply..rgsgylfgdealedllkkygvdlvisGHtHv 203
                                                         +++ + +   +++ ++i++ H  ++    sg++ +  + +     +++d++  GH+H+
  gi|474934254|ref|YP_007687836.1| 142 -----------S------ENIAS-KLSGNPDAFTIAVLHCSVSdvAESGDYAPCSVSD--MLGKNIDYWALGHIHK 197
                                       ...........1......22222.3555788888888888888553333333333333..6788899999999996 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.0   6.7e-14     6e-10       3     162 ..       7     232 ..       5     235 .. 0.72

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 6.7e-14
                     Metallophos_2   3 laiiSDlH.....................snldaleavlealkevgvdaiihaGDl.eeeep......evleellel 51 
                                       +++ +DlH                     s ++  +++++  ke  +d ++ +GD+  e++        ++ee+++l
  gi|474934254|ref|YP_007687836.1|   7 FVHAADLHlgsrfwgislkdpdlgkrlfeSTFESFRRIIDLTKEK-ADFLVISGDAfDESTMtlrtklRFCEEIKRL 82 
                                       678899999999999999999999999989999999999998888.9********7533333333322467777776 PP

                     Metallophos_2  52 a..pvlaVrGNnD............eevveedvlreaaelgtdlpeeaelelagekvlliHgdpl............ 102
                                          pv  V+GN+D            +   ++ + ++++ ++ ++   +++e+ g++ +  H +++            
  gi|474934254|ref|YP_007687836.1|  83 GtkPVFLVKGNHDfgdswadsipfpS--NVHLLRDSPQSMTLNF-RNETVEIVGMSYGTQHTSENiasklsgnpdaf 156
                                       69************999986554331..5566666666666666.66666666666666666655666666666666 PP

                     Metallophos_2 103 ............gvkdalaellkeaeegsd..vvvcGHtHvpevekeggvlvvnPGsvgeprdgdpe..tyaildt 162
                                                   + + ++a+   + + g++  + ++GH+H++ v +e +  +v+PG +++++ ++++  ++ ++++
  gi|474934254|ref|YP_007687836.1| 157 tiavlhcsvsdvAESGDYAPCSVSDMLGKNidYWALGHIHKRMVLRESSPCIVYPGNIQGRSPKETGekGCYLVSV 232
                                       66666666668844444444444444444455****************************9998887775555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 2370.07
//
Query:       gi|474934255|ref|YP_007687837.1|  [L=225]
Description: triosephosphate isomerase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-07   30.9   0.0    2.5e-07   30.3   0.0    1.3  1  TIM           Triosephosphate isomerase
    2.6e-05   23.6   2.4    2.6e-05   23.6   2.4    1.8  2  ThiG          Thiazole biosynthesis protein ThiG
    6.7e-05   22.4   2.0    6.7e-05   22.4   2.0    2.1  3  NMO           Nitronate monooxygenase
    8.2e-05   21.8   2.2    8.2e-05   21.8   2.2    2.0  2  FMN_dh        FMN-dependent dehydrogenase
  ------ inclusion threshold ------
      0.027   13.9   0.1       0.04   13.4   0.1    1.3  1  His_biosynth  Histidine biosynthesis protein


Domain annotation for each model (and alignments):
>> TIM  Triosephosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0     7e-11   2.5e-07       3     108 ..       9     109 ..       7     131 .. 0.79

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 7e-11
                                       EEEE-TBTS-H..HHHHHHHHHHHHHCHGCTSEEEEE--GGGHHHHHHHHTTSSECEEES--BSSSSBS-TT--BHH CS
                               TIM   3 iagNwKmnktl..eeakellkklkaklkeekvevviappflylekvkklleesklklgaqnvsaeksGafTGevsae 77 
                                       i+ N+K + +   e a +l++++++   e+ v++++app+++l +v+++++   + + +q ++ ++ G+ TG v+a+
  gi|474934255|ref|YP_007687837.1|   9 IVVNFKAYPQVhgEGAIALAQTCEQVALESGVSIAVAPPMVSLAAVAAAVD---IPVFSQSIDPRTPGSQTGWVTAD 82 
                                       778999987541145667777777777778***************999996...*********************** PP

                                       HHHHTT-SEEEES-HHHHHHST--HHHHHHH CS
                               TIM  78 mlkdlgvkyviiGHsErrqlfkEtdelvakK 108
                                       m++ + +  ++i HsE +   +     v k 
  gi|474934255|ref|YP_007687837.1|  83 MIAATAAAGTLINHSEHKYDAE----AVSKC 109
                                       ****************876543....33333 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.4      0.65   2.3e+03     191     218 ..      24      51 ..       3      63 .. 0.63
   2 !   23.6   2.4   7.4e-09   2.6e-05     175     221 ..     176     222 ..     161     225 .] 0.88

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.65
                                       HHHHHTT-SEEEESHHHHTSSSHHHHHH CS
                              ThiG 191 aqamelGadavllntavaeakdpvamAr 218
                                       a a+   ++ v l++ v+ a  p ++  
  gi|474934255|ref|YP_007687837.1|  24 AIALAQTCEQVALESGVSIAVAPPMVSL 51 
                                       5566666666666666666655554443 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 7.4e-09
                                       SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHHH CS
                              ThiG 175 kvPvivDAGigspsdaaqamelGadavllntavaeakdpvamArafk 221
                                       k+ v+  AG+ + +d+a+a++lGa++vll++ v +a+dp a+ r ++
  gi|474934255|ref|YP_007687837.1| 176 KIAVLCGAGVKNGKDVAAAIKLGAEGVLLASGVVKAADPLAVMRDLA 222
                                       78999**********************************99877666 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.5       1.4   4.9e+03     185     196 ..      51      62 ..      44      64 .. 0.81
   2 ?   -0.2   0.1      0.15   5.3e+02      19      37 ..      76      93 ..      66      94 .. 0.80
   3 !   22.4   2.0   1.9e-08   6.7e-05     133     226 ..     114     209 ..     101     217 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.4
                               NMO 185 vpqvldavdiPv 196
                                       ++ v+ avdiPv
  gi|474934255|ref|YP_007687837.1|  51 LAAVAAAVDIPV 62 
                                       567899999998 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.15
                               NMO 19 mggiskarLaaavsnaGgL 37
                                       g+++ a+++aa++ aG L
  gi|474934255|ref|YP_007687837.1| 76 TGWVT-ADMIAATAAAGTL 93
                                      68887.5688999999987 PP

  == domain 3  score: 22.4 bits;  conditional E-value: 1.9e-08
                               NMO 133 keagvvliptissvkearkvearGaDalivqGpe.aGGhqGtpevgdkglfaLvpqvldavd....iPviAaGGiid 204
                                       k  ++v  + + +v+ ar +++  +D + v+ pe  GG +  + ++  +   + ++v+ +++    i v+   G+ +
  gi|474934255|ref|YP_007687837.1| 114 KGCELVTCVCADTVDIARDLARFSPDFIAVEPPElIGGDIS-VTTA--DPKVVSDTVAAVHSvdrkIAVLCGAGVKN 187
                                       556778889999*******************9983588777.4444..455555666666667789*********** PP

                               NMO 205 rrgvaaaLalGAsgvqigtrfL 226
                                       +++vaaa+ lGA+gv +++  +
  gi|474934255|ref|YP_007687837.1| 188 GKDVAAAIKLGAEGVLLASGVV 209
                                       ****************998665 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.2     0.068   2.4e+02      72     107 ..      19      54 ..       3     107 .. 0.72
   2 !   21.8   2.2   2.3e-08   8.2e-05     263     304 ..     168     209 ..     152     214 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.068
                                       TSTTHHHHHHHHHHHHTS-EEEETT-SS-HHHHHHH CS
                            FMN_dh  72 ahpdgelalaraaakagipfvlstvastsleevaaa 107
                                       +h +g +ala+++++  +  ++s +   ++  +aa 
  gi|474934255|ref|YP_007687837.1|  19 VHGEGAIALAQTCEQVALESGVSIAVAPPMVSLAAV 54 
                                       688899999999999999888888776665555552 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 2.3e-08
                                       HHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHH CS
                            FMN_dh 263 eiveavggrievlvDgGirrGsDvlkAlalGAdavllGRpfl 304
                                       + v+ v+++i vl+  G+++G+Dv+ A+ lGA++vll+  ++
  gi|474934255|ref|YP_007687837.1| 168 AAVHSVDRKIAVLCGAGVKNGKDVAAAIKLGAEGVLLASGVV 209
                                       335566679***************************987665 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   1.1e-05      0.04      29     110 ..     131     213 ..     105     223 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.1e-05
                                       TSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-S..SEEEEESSSSSHHHHHHHHHCT-SEEEESH CS
                      His_biosynth  29 gdpvelakryeeegadelhvvDldaakegreanldlveeiaeevf..ipvqvGGGIrsledveelleagadkviigt 103
                                       +d + +  ++ + +  el+  D++ + +  ++  d v+++ +  +  i v  G G+++ +dv++++++ga+ v +++
  gi|474934255|ref|YP_007687837.1| 131 RDLARFSPDFIAVEPPELIGGDISVTTADPKVVSDTVAAVHSV-DrkIAVLCGAGVKNGKDVAAAIKLGAEGVLLAS 206
                                       4444444455555555555556655555555555555444332.12399999************************* PP

                                       HHHH-TH CS
                      His_biosynth 104 aavknpe 110
                                        +vk  +
  gi|474934255|ref|YP_007687837.1| 207 GVVKAAD 213
                                       9998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 1312.88
//
Query:       gi|474934256|ref|YP_007687838.1|  [L=394]
Description: D-fructose 1,6-bisphosphatase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.8e-160  533.4   0.0   3.1e-160  533.2   0.0    1.0  1  FBPase_3  Fructose-1,6-bisphosphatase


Domain annotation for each model (and alignments):
>> FBPase_3  Fructose-1,6-bisphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  533.2   0.0  1.8e-164  3.1e-160       1     360 [.       4     376 ..       4     377 .. 0.99

  Alignments for each domain:
  == domain 1  score: 533.2 bits;  conditional E-value: 1.8e-164
                          FBPase_3   1 kvtlsvikaDvGslaGhtkvheellekveevleeakkkgllidfyvtkvGDDielimthtkgvdneevhklawdafk 77 
                                       kvt+s+ikaD+Gs+aGh+++h++++++++++l++++k+g+++dfyvt+vGDDi+l+mth kg++n evh+ awd+f+
  gi|474934256|ref|YP_007687838.1|   4 KVTVSIIKADIGSIAGHMTPHPSMMQAAKDILADKQKQGVIEDFYVTRVGDDINLYMTHYKGENNAEVHGAAWDCFQ 80 
                                       89*************************************************************************** PP

                          FBPase_3  78 eatevakelklygaGqDlLkdafsGnvkGlGPgvaelefeeRksepvvvfaaDktepgafnlplykifadpfntaGl 154
                                       eat+++++++ly+aGqDlL+d+fsGnvkG+GPg ae++feeR++ep+v+f+aDktep+a++  l +if dpf+t+Gl
  gi|474934256|ref|YP_007687838.1|  81 EATKISRRMHLYAAGQDLLTDSFSGNVKGAGPGSAEMTFEERPAEPLVFFMADKTEPSAYSPILSRIFLDPFTTTGL 157
                                       ***************************************************************************** PP

                          FBPase_3 155 vidpklheGfkfevlDvieekkillsapeelydllallgakeryvikrvyskkdeeiaavvsterlsliaGkYvGkD 231
                                       vid++ ++Gf+fe+ Dv+++kk+++s+pee+ ++l+llg+++ry+ikrv+s++   +aavvst++l+++aG+YvGkD
  gi|474934256|ref|YP_007687838.1| 158 VIDKRAKQGFDFEIRDVMDNKKVVMSSPEETLSILSLLGDTSRYAIKRVCSRAGLGPAAVVSTDKLNMTAGRYVGKD 234
                                       ***************************************************************************** PP

                          FBPase_3 232 DPvaivRaqsglPavgevlepfa.lphlvaGwmrGshngplmPvslkdakptrfdgpprvvalgfqlkegklvg... 304
                                       DPv+i+Raqsg+P+vge++++fa  ++lvaGwmrGsh g+++P+s ++++p+++dgppr+++lgfql +g+l+g   
  gi|474934256|ref|YP_007687838.1| 235 DPVCICRAQSGFPSVGEYTQVFAqYTWLVAGWMRGSHIGAFYPCSPENSDPVYYDGPPRICCLGFQLVNGHLQGlep 311
                                       **********************95699************************************************** PP

                          FBPase_3 305 .........pvDlfddpafdeaRekaaeiadelRrqGpfephrlpeeeleYttlpevleklkerf 360
                                                pvD+f   ++d+aR+ a ++++ +R+qGpf+p++l +ee+eYt+ pevl++lk+rf
  gi|474934256|ref|YP_007687838.1| 312 egakngehiPVDIFGSDTWDKARADAIRASKLMRSQGPFQPSILGAEEMEYTSRPEVLKDLKTRF 376
                                       ****************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.54
# Mc/sec: 2182.78
//
Query:       gi|474934257|ref|YP_007687839.1|  [L=436]
Description: aspartyl-tRNA synthetase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-87  293.7   0.0    1.8e-87  293.4   0.0    1.0  1  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    6.6e-14   51.6   0.0    1.3e-13   50.8   0.0    1.4  1  tRNA_anti-codon  OB-fold nucleic acid binding domain


Domain annotation for each model (and alignments):
>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  293.4   0.0     2e-91   1.8e-87       2     313 ..     116     430 ..     115     431 .. 0.95

  Alignments for each domain:
  == domain 1  score: 293.4 bits;  conditional E-value: 2e-91
                                       CCHHHHTHHHHCCSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE....- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....x RF
                       tRNA-synt_2   2 eelrlknryldlrtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeff....a 74 
                                       +++rl+ r++dlr++++++v+++rs++t+++++y++++gf+++ tP +  s  e+ga+lF +       ++f    +
  gi|474934257|ref|YP_007687839.1| 116 MDTRLNSRFMDLRKPEIRAVFEIRSEATRLIHEYMTSQGFVNVATPKINASGAEGGATLFHI-------DYFgkpaF 185
                                       689***********************************************************.......77778889 PP

                                       E-S-SHHHHHHHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEEEEEET-SCHH.HHHHHHHHHHHHHHHHHHCSC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  75 LtqspqlylellivagidrvfqiaraFRaEdsrtdrhlaEFtqieaemsfieeed.imqvleelikslvkevlessa 150
                                       L+qspqly+++l++ g+drv++i++aFRaE s+t+rh +EFt+ + e+s+i +e+ +m+++e+ ++++++ + e+++
  gi|474934257|ref|YP_007687839.1| 186 LAQSPQLYKQMLMSTGLDRVYEIGPAFRAEHSNTTRHVTEFTSWDGEFSWIANEEeVMDFIEGAVRYVIRGINENCR 262
                                       **************************************************999999********************* PP

                                       CCCCHTTTTTSEE-SSS-EEEEHHHHHHHHHTS......-SS--HHHHHHHHH...HS--SEEEEEEEBGGGSTTCB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 151 kdiefvirrnskdlkkpfkrltykeaieklnei......gkdldkaderalvk...keknepvfvtdfPaelkpFya 218
                                       k++e   ++  +   +pf++lty+e ++++++       g+dl ++ e+a  +    ++++ +f++++P+e kpFy 
  gi|474934257|ref|YP_007687839.1| 263 KQMELLGKESIEVSDQPFPKLTYSECLKIAQDAgldlkdGDDLGTDGEKAVGEymgAKGFVLYFICEYPEEEKPFYI 339
                                       **999999988777778************888899999977888888888776666799****************** PP

                                       BBSTTSTTBBSEEEEEETTEEEEEEEEB--SHHHHHHHHHHCCHHSSSGGGGHHHHHHHHCT--SEEEEEEEHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 219 rkeeddkkltesyDllingvElvgGslRiedpeeleeklkskgldeeaeekfswylealeyGapphgGlglGldRlv 295
                                        +++  +  + s+Dl ++g E+ +G +R++++++l +++++kgl+   ++ f++yl a+++G+pphgG+g+G+dR++
  gi|474934257|ref|YP_007687839.1| 340 MEKDG-THYSFSFDLDYKGQEISSGGQREHRYDVLVARMEKKGLK---PADFEDYLAAFRFGMPPHGGFGIGIDRFI 412
                                       99998.89*************************************...***************************** PP

                                       HHHCT-SSGGGCSSS-XX CS
                                       xxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 296 mlllgsesIrdviaFPkl 313
                                         +l+++++r++i+FP+ 
  gi|474934257|ref|YP_007687839.1| 413 EKMLDLPNVREAILFPRD 430
                                       ****************95 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   0.0   1.4e-17   1.3e-13       2      68 ..      19      89 ..      18      97 .. 0.89

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 1.4e-17
                                      EEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET....HHHHHHHTTS-TTSEEEEEEEEEECTTS..SEEE CS
                   tRNA_anti-codon  2 tvaGrvtsisdrsggkvifidlrDgtgriqvvlfr....eeatklaenlkeGdvvrvtGrvkrrpgg..elel 68
                                      tv+G+v+++  r+ g+++f++lrD+ g+iq++l +     + ++++ +l++++vv vtG+vk++++    +el
  gi|474934257|ref|YP_007687839.1| 19 TVKGWVQDT--RNLGGISFVTLRDRFGTIQITLPKkkiePALFDTLTKLPRESVVAVTGEVKESNQTalGVEL 89
                                      8********..****************************************************9776553444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 2467.79
//
Query:       gi|474934258|ref|YP_007687840.1|  [L=194]
Description: Archaeal holliday junction resolvase (hjc) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-16   58.4   0.0      7e-16   58.0   0.0    1.2  1  Hjc       Archaeal holliday junction resolvase (hjc)


Domain annotation for each model (and alignments):
>> Hjc  Archaeal holliday junction resolvase (hjc)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.0   0.0   3.9e-20     7e-16       1      91 [.       7     125 ..       7     127 .. 0.95

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 3.9e-20
                                       HHHHHHHHHHHHTT.........................-EEEEBSCSSSSSSSS-SEEEEETTEEEEEEEEEESSS CS
                               Hjc   1 tyERelvkiLrerg.........................favvRsagSggatkplpDviAirgdvvlviEvKsskke 52 
                                       tyERel+ +L + +                         f  +R+agS g+     D++A+r d++  iEvKss k+
  gi|474934258|ref|YP_007687840.1|   7 TYERELKYLLSGDEktirkmvktcseeetvaytsmfdhpFLMIRAAGSLGV-----DLVALRWDFSFPIEVKSSEKD 78 
                                       69*************************************************.....********************* PP

                                       EEEE.....EHHHHHHHHHHHHHHTCEEEEEEEE...TTTEEEEEEG CS
                               Hjc  53 riyl.....kkeqvekllefarkaggelllavkl...qgkewkllvv 91 
                                       ++y+       +q++++l+ ++k+ + +++a++l   +g++w+++ +
  gi|474934258|ref|YP_007687840.1|  79 TLYMskserLGDQADEMLSTCNKSHIIPIYAYRLkgvRGDPWRIFTI 125
                                       ****776665689*********************99999****9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1362.02
//
Query:       gi|474934259|ref|YP_007687841.1|  [L=300]
Description: quinolinate synthetase complex, A subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   3.3e-117  390.9   0.8   3.8e-117  390.7   0.8    1.0  1  NadA      Quinolinate synthetase A protein


Domain annotation for each model (and alignments):
>> NadA  Quinolinate synthetase A protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  390.7   0.8  2.1e-121  3.8e-117       1     298 [.       6     296 ..       6     297 .. 0.98

  Alignments for each domain:
  == domain 1  score: 390.7 bits;  conditional E-value: 2.1e-121
                                       HHHHHHHHHHTEEEEEETTS-HHHHHH-SEEE-HHHHHHHCCC-SSSEEEEES-HHHHHHHHHHSTTSEEE-SSTT- CS
                              NadA   1 eeikelkkeknavilaHnYqedeiqeiadfvGDSleLarkaaeteaevivfcGVhFMaetakiLspekkvllpdlea 77 
                                       e+i++lkkeknavilaHnY+++e+q++ad+vGDSl L++kaa+t+a++ivf+GV+FM+etakiLsp kkvllp++ea
  gi|474934259|ref|YP_007687841.1|   6 ERIAALKKEKNAVILAHNYTSPEVQDLADYVGDSLGLSKKAAATDADIIVFAGVSFMGETAKILSPAKKVLLPEPEA 82 
                                       58*************************************************************************** PP

                                       --HHHCT--HHHHHHHHHHSTTS-EEEESSS-HHHHTT-SEEE-TTTHHHHHHHSS-SEEEEES-HHHHHHHHHHH. CS
                              NadA  78 gCsladmitaeeveelkeelpdaavvtYvNssaevKalsdivcTSsnavkvvealkekkilflPDqnLgryvakklg 154
                                       +C +a m++ e+++++++++p+a+vv YvN++a++K+++d++cTSsna +vv+a+ +++i+f+PD nLgryv++k g
  gi|474934259|ref|YP_007687841.1|  83 KCAMAAMCSPEQIRQVRAQHPGAVVVGYVNTDAATKTEMDYCCTSSNALNVVKAIGSDDIIFVPDVNLGRYVREKSG 159
                                       ***************************************************************************98 PP

                                       SEEEEESSSS-GCGGG--CHHHHHHHHCSTT-EEEE-TTS-HHHHHCSSEE--HHHHCCCCGTTSSSCEEEES-THH CS
                              NadA 155 ekkiilwkgaCsvHeefkaeeveelkeehpdakvlvHPEckeevveaadvvgSTsqiikavkeseakefiigTelgl 231
                                       + +++lw+g+C+vH+ +++++veelk++hp+a v +HPEc+ +v++++d++gST++i+++++es+a+efii Te+g+
  gi|474934259|ref|YP_007687841.1| 160 K-NVVLWNGFCPVHQCVTVRQVEELKAQHPGAVVAAHPECRLDVLNMSDYIGSTENILNYCRESPAQEFIILTEMGM 235
                                       7.7************************************************************************** PP

                                       HHHHHHH-TTSEEE.....ECSSSSSTTGGG--HHHHHHHHHHT-S.B----HHHHHHHHHHHHHHH CS
                              NadA 232 verlkkeapekefialsaeaaeeavCetMkkitleklleaLeeleeeeikvdeevaekAkkalerml 298
                                        +rl++++p+k+f+      +++  C tMk+i++e++le+Le+++  ei ++++vaekA ++++rm 
  gi|474934259|ref|YP_007687841.1| 236 GHRLERACPGKKFY-----FTNQSLCMTMKMISPESVLECLEKETG-EIVLPDDVAEKAYVPVNRMT 296
                                       **************.....456678*******************99.*******************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2007.18
//
Query:       gi|474934260|ref|YP_007687842.1|  [L=127]
Description: archaeal conserved hypothetical protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.2e-37  126.2   0.1    8.3e-37  126.0   0.1    1.0  1  DHNA       Dihydroneopterin aldolase
  ------ inclusion threshold ------
      0.091   12.4   0.0        0.1   12.3   0.0    1.3  1  YscJ_FliF  Secretory protein of YscJ/FliF family


Domain annotation for each model (and alignments):
>> DHNA  Dihydroneopterin aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.0   0.1   9.3e-41   8.3e-37       1     107 [.      16     121 ..      16     122 .. 0.96

  Alignments for each domain:
  == domain 1  score: 126.0 bits;  conditional E-value: 9.3e-41
                                       -HHHHHHHHHHHHHHHHHHHHTT-EESTTTHHHHHHHHHHHHHTSTTEEEEEEEE-S-..GGCC-STS-EE--TTTE CS
                              DHNA   1 tdrerAvFEagiklgalyHqfvGtPvseesaeslekaieesielQPfvedvkvkidrekleekleefgYteLtgeml 77 
                                       t++erA FEagik++++yHqfvGtP+se++++ le++ie++i++QP+ve+++vki+ +   +k ++++Yt+Ltg+m+
  gi|474934260|ref|YP_007687842.1|  16 TESERASFEAGIKMATVYHQFVGTPFSEKNKADLERSIEKCIMAQPYVESARVKISVNG-GDKGDQYTYTSLTGDMI 91 
                                       789****************************************************9986.555568*********** PP

                                       EEEEEEEETTEEEEEEEEEETTTTEEEEEE CS
                              DHNA  78 dveitvkyeeaevkarleyieeldYplmkv 107
                                       d+ +++ +++++v+a+++y++ l+Yplm+v
  gi|474934260|ref|YP_007687842.1|  92 DAIVVILLGKTRVTAEMRYDNVLRYPLMYV 121
                                       *****************************9 PP

>> YscJ_FliF  Secretory protein of YscJ/FliF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.1e-05       0.1      93     131 ..      36      72 ..      14     107 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.1e-05
                         YscJ_FliF  93 fgtTdfeeqvkyqralegeLartiesldgVesArVhlal 131
                                       f  T f e+   +  le ++++ i++   VesArV++++
  gi|474934260|ref|YP_007687842.1|  36 FVGTPFSEK--NKADLERSIEKCIMAQPYVESARVKISV 72 
                                       555666554..56789********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 810.99
//
Query:       gi|474934261|ref|YP_007687843.1|  [L=184]
Description: putative nucleotide kinase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-40  137.9   2.0    3.3e-40  137.7   2.0    1.0  1  NTPase_1         NTPase
    3.5e-06   26.7   0.2    6.2e-06   25.9   0.2    1.4  1  DUF2478          Protein of unknown function (DUF2478)
    2.6e-05   24.0   0.9    5.9e-05   22.9   0.7    1.7  1  AAA_30           AAA domain
    3.9e-05   24.0   3.5    0.00081   19.8   2.8    2.6  2  AAA_19           AAA domain
     0.0011   19.6   0.1     0.0017   18.9   0.1    1.4  1  AAA_18           AAA domain
     0.0026   18.2   1.8     0.0068   16.8   1.8    1.8  1  AAA              ATPase family associated with various cellul
     0.0038   17.0   0.7       0.16   11.7   0.3    2.2  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
     0.0041   16.9   3.0      0.014   15.2   3.1    1.9  1  AAA_24           AAA domain
     0.0047   16.9   1.8       0.33   11.0   1.8    2.1  1  AAA_14           AAA domain
     0.0065   16.5   1.0       0.36   10.8   1.0    2.3  1  AAA_5            AAA domain (dynein-related subfamily)
      0.007   15.4   2.8      0.011   14.7   2.7    1.6  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
     0.0089   15.0   0.1      0.013   14.4   0.1    1.2  1  DUF463           YcjX-like family, DUF463
  ------ inclusion threshold ------
      0.022   15.3   0.3      0.039   14.5   0.3    1.4  1  ABC_tran         ABC transporter
      0.034   14.4   0.8       0.11   12.8   0.8    2.0  1  AAA_22           AAA domain
      0.083   13.3   3.4       0.97    9.9   3.4    2.0  1  AAA_17           AAA domain
        0.1   12.5   1.0       0.22   11.4   0.2    1.9  2  MobB             Molybdopterin guanine dinucleotide synthesis
       0.13   12.2   0.0       0.19   11.6   0.0    1.4  1  Helicase_RecD    Helicase
       0.13   11.8   4.2        1.6    8.3   4.2    2.1  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
       0.15   11.8   2.8        1.7    8.3   0.1    2.3  2  AAA_11           AAA domain
       0.26   10.5   0.9       0.63    9.2   0.9    1.6  1  DUF2075          Uncharacterized conserved protein (DUF2075)
       0.27   10.8   4.4        4.6    6.8   0.1    2.3  2  SRP54            SRP54-type protein, GTPase domain


Domain annotation for each model (and alignments):
>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.7   2.0   3.9e-43   3.3e-40       1     167 [.       6     175 ..       6     176 .. 0.96

  Alignments for each domain:
  == domain 1  score: 137.7 bits;  conditional E-value: 3.9e-43
                                       EEEEE--TTSSHHHHHHHHHHHH...G.GGEEEEEEEEE-..------EEEEEET.T--EEEEEETT---SSEETTE CS
                          NTPase_1   1 kvfiTGppGvGKtTlvkkvlellkssg.vkvgGfyteevr..eggrrigFkivdlasgeegiLarveakreprvgky 74 
                                       k+ iTG pG+GKt  +k v+++l s+g v+vgG++ e++    g ++ig ++ ++ ++e   +a+ e+++++ vg+ 
  gi|474934261|ref|YP_007687843.1|   6 KIGITGLPGSGKTYTLKSVIKMLTSDGkVTVGGMIDEKINdgTGRHKIGIQVRNILTDESVVFANPETESKIMVGNL 82 
                                       589********************999549***********6666789****************************** PP

                                       EE-HHHHHHHHHHHHHHHHHHH-EEEE---STTGGG-HHHHHHHHHHHTTTSEEEEE--SS--SHHHHHHHT-TT-E CS
                          NTPase_1  75 vvdvesfeelalealrkalseadviviDEiGkmElkskkfkeaveevLksekpvlavihrrkdlalveeirerkdvk 151
                                        vd+  fe++ +ea+++a +++d++viDE+Gk E++s+ f +av+e+L+ +kp+++++h++++++l+++ir+r dv+
  gi|474934261|ref|YP_007687843.1|  83 GVDLALFESVSIEAIKTACEQCDIVVIDEVGKVEVESQAFVDAVKEALDVDKPMIITLHKKSRNPLLQDIRRRDDVR 159
                                       ***************************************************************************** PP

                                       EEE--TTTTTTHHHHH CS
                          NTPase_1 152 vfevteenrdalleei 167
                                       ++evt+ nr+ l+ +i
  gi|474934261|ref|YP_007687843.1| 160 ILEVTPTNRKLLPYKI 175
                                       ************9998 PP

>> DUF2478  Protein of unknown function (DUF2478)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.2   7.2e-09   6.2e-06      14     134 ..      19     144 ..       8     150 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 7.2e-09
                           DUF2478  14 alLaafaerlraeG.lrvaGvvqenaeeaegkkc.dmeledlatgeririsqdlgsgs.q..gCrLdpeaLaeaaaa 85 
                                        +L+++ + l+++G + v+G++ e+ ++++g+++  ++++++ t+e++   +   +         +d + ++ ++  
  gi|474934261|ref|YP_007687843.1|  19 YTLKSVIKMLTSDGkVTVGGMIDEKINDGTGRHKiGIQVRNILTDESVVFANPETESKiMvgNLGVDLALFESVSIE 95 
                                       56888888888887589***********9999999********9999988775544331311345688888888876 PP

                           DUF2478  86 veralaegadlvivnkFGkqEaeGrGlreeiaaalaagiPvltaVsekl 134
                                         ++  e++d+v++   Gk E e + + +++++al  + P+++++++k 
  gi|474934261|ref|YP_007687843.1|  96 AIKTACEQCDIVVIDEVGKVEVESQAFVDAVKEALDVDKPMIITLHKKS 144
                                       6666669************************************999876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.7   6.9e-08   5.9e-05      23     104 ..       9     119 ..       3     140 .. 0.66

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 6.9e-08
                            AAA_30  23 ltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLa.eelgieasti...akllkrlk.............. 81 
                                       +tG +G+GKt++lk++ ++++++g+  +g    +k  +  + +++gi+ ++i   ++++ ++               
  gi|474934261|ref|YP_007687843.1|   9 ITGLPGSGKTYTLKSVIKMLTSDGKVTVGGMIDEKINDGTGrHKIGIQVRNIltdESVVFANPeteskimvgnlgvd 85 
                                       89*********************955555555555555533145666444431113333333366666777777777 PP

                            AAA_30  82 ............grarlepgtllivDEagmvdtkq 104
                                                   + +++e+ +++++DE+g v  ++
  gi|474934261|ref|YP_007687843.1|  86 lalfesvsieaiK-TACEQCDIVVIDEVGKVEVES 119
                                       7777777777532.455666*********997654 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   2.8   9.4e-07   0.00081      12     126 ..       6     127 ..       1     139 [. 0.66
   2 ?   -1.0   0.0       2.3     2e+03      33      53 ..     148     168 ..     138     170 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 9.4e-07
                            AAA_19  12 vllvtaGpGtGKTrvlkhivallvelggvkp.....eeillvaftgrAakelrerlaalgae......atTiHrlal 77 
                                        + +t+ pG+GKT++lk ++++l + g+v +     e+i   +  ++   ++r+ l   + e       +T  ++ +
  gi|474934261|ref|YP_007687843.1|   6 KIGITGLPGSGKTYTLKSVIKMLTSDGKVTVggmidEKINDGTGRHKIGIQVRNIL---TDEsvvfanPETESKI-M 78 
                                       5779***********************99887776555555555555444444433...2222333335555555.3 PP

                            AAA_19  78 ...ldfddlltealelleeaeeekklqeeellivDEfqdvdelqyrLlkall 126
                                          l++d  l e +++   ++ ++  ++++++++DE+  v+   +++++a++
  gi|474934261|ref|YP_007687843.1|  79 vgnLGVDLALFESVSI---EAIKTACEQCDIVVIDEVGKVEVESQAFVDAVK 127
                                       2334444444333333...456677767779999999999999999999887 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.3
                            AAA_19  33 llvelggvkpeeillvaftgr 53 
                                       ll+++++++  +il v++t+r
  gi|474934261|ref|YP_007687843.1| 148 LLQDIRRRDDVRILEVTPTNR 168
                                       566777777789999999998 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1     2e-06    0.0017       1      96 [.       7     127 ..       7     157 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2e-06
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.......................gvnlrdvakenglllevdpealdeskrlde 54 
                                       I++tG pG+GKt   k + k+l +                       g+++r +++++  ++ + +    esk+++ 
  gi|474934261|ref|YP_007687843.1|   7 IGITGLPGSGKTYTLKSVIKMLTSdgkvtvggmidekindgtgrhkiGIQVRNILTDESVVFANPET---ESKIMVG 80 
                                       89****************9998667888889999999999999999999999999999998888777...5655555 PP

                            AAA_18  55 dkldklldaleenss.....aleegknlvidghlaele.seaakdikk 96 
                                       +   + l ++e  s      a e+++ +vid +    + s a++d++k
  gi|474934261|ref|YP_007687843.1|  81 NL-GVDLALFESVSIeaiktACEQCDIVVIDEVGKVEVeSQAFVDAVK 127
                                       54.777777777666888999999999999998765552555555555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   1.8     8e-06    0.0068       3      74 ..       9     119 ..       7     177 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 8e-06
                                       EESSTTSSHHHHHHHHHHHHTHE....................EEEEETTTCSSS...................... CS
                               AAA   3 lyGppGtGKTllakavakelgve....................fleisgsellsk...................... 37 
                                       ++G pG GKT++ k+v+k l ++                                                      
  gi|474934261|ref|YP_007687843.1|   9 ITGLPGSGKTYTLKSVIKMLTSDgkvtvggmidekindgtgrhK----------Igiqvrniltdesvvfanpetes 75 
                                       689****************9555222233333333333333332..........03333333334566666666767 PP

                                       .....STTHHHHHHHHHHHHHHHTS..TSEEEEEETGGGHHHHH CS
                               AAA  38 .....yvgesekkirelfkeakeka..kpsilfiDEidalaksr 74 
                                             +g   + ++ +  ea + a  ++ i++iDE+ ++  ++
  gi|474934261|ref|YP_007687843.1|  76 kimvgNLGVDLALFESVSIEAIKTAceQCDIVVIDEVGKVEVES 119
                                       787776666666666666666555675569******99985544 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.3   0.00019      0.16       3      25 ..       9      28 ..       7      51 .. 0.85
   2 ?    4.1   0.0      0.04        34      53      75 ..      97     116 ..      57     130 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00019
                   Viral_helicase1  3 vhGvpGcGKStlirkllrtslil 25
                                      + G pG+GK+  +++++++   l
  gi|474934261|ref|YP_007687843.1|  9 ITGLPGSGKTYTLKSVIKM---L 28
                                      79***************99...3 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.04
                   Viral_helicase1  53 flmalvkstkgkililDEylllh 75 
                                       +  a+    +++i+++DE ++++
  gi|474934261|ref|YP_007687843.1|  97 IKTACE---QCDIVVIDEVGKVE 116
                                       444443...59*********987 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   3.1   1.6e-05     0.014       2      91 ..       4     129 ..       3     146 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.6e-05
                            AAA_24   2 klkiliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie..........swedfldevvel......... 59 
                                       ++ki i+G +g+GKT+++k+   k l  d    +  + + k++d +          +          +         
  gi|474934261|ref|YP_007687843.1|   4 SVKIGITGLPGSGKTYTLKSV-IKMLTSDGKVTVGGMIDEKINDGTgrhkigiqvrN----------Iltdesvvfa 69 
                                       689******************.88888877777777777777777665555443320..........2233344456 PP

                            AAA_24  60 ............................aaeladyktlviDtideleelclaevirqnek 91 
                                                                   +++ ++++++viD ++++e    a v+  +e+
  gi|474934261|ref|YP_007687843.1|  70 npeteskimvgnlgvdlalfesvsieaiKTACEQCDIVVIDEVGKVEVESQAFVDAVKEA 129
                                       77777778888888888999999999999999***********99987777777666655 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   1.8   0.00038      0.33       5      92 ..       7     135 ..       3     166 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00038
                            AAA_14   5 lvitGaRrvGKTtllkqlikell...............................vkkesilyinldderdkkladpe 50 
                                       + itG+  +GKT+ lk +ik l                                 ++es+++ n ++e++ +  +  
  gi|474934261|ref|YP_007687843.1|   7 IGITGLPGSGKTYTLKSVIKMLTsdgkvtvggmidekindgtgrhkigiqvrniLTDESVVFANPETESKIMVGNLG 83 
                                       5699999999**99999999888666666666666666665555555555555545555555555555554433332 PP

                            AAA_14  51 kllelileklke.........ekktylflDEiqev....pewekalkslvdegkn 92 
                                        ++ +++e+            e+  ++++DE+ +v    + + +a+k+ +d +k 
  gi|474934261|ref|YP_007687843.1|  84 -VDLALFES--VsieaiktacEQCDIVVIDEVGKVevesQAFVDAVKEALDVDKP 135
                                       .22222222..01122334566778888888888877667788888888876644 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   1.0   0.00042      0.36       6      79 ..      11     117 ..       7     180 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00042
                                       --SSSSHHHHHHHGGGGB.S--EEEEE--TT--HHHHH--B--..........--------................ CS
                             AAA_5   6 GppGtgKselaerlaaal.nreveyvqltrdtteedlkgrreik.ngttslvdsplvraar................ 64 
                                       G pG+gK+   +++ ++l  +  ++v +  d + +d +gr +i  + +  l+d ++v  a+                
  gi|474934261|ref|YP_007687843.1|  11 GLPGSGKTYTLKSVIKMLtSDGKVTVGGMIDEKINDGTGRHKIGiQVRNILTDESVV-FANpeteskimvgnlgvdl 86 
                                       556666666666666666544455555555555555555555555555555555555.3334555555555555555 PP

                                       ................G-SEEEEESGGG--H CS
                             AAA_5  65 ................egeilvlDEveraes 79 
                                                       + +i+v+DEv ++e 
  gi|474934261|ref|YP_007687843.1|  87 alfesvsieaiktaceQCDIVVIDEVGKVEV 117
                                       5555555555555555999******999873 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   2.7   1.3e-05     0.011      29      60 ..       4      34 ..       2     132 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.3e-05
                                      SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--E CS
                              MeaB 29 aqvvGltGvPGaGkstlvealglelrrrGkrv 60
                                      + ++G+tG+PG+Gk  +++ ++  l++ Gk v
  gi|474934261|ref|YP_007687843.1|  4 SVKIGITGLPGSGKTYTLKSVIKMLTSDGK-V 34
                                      679***********************9996.3 PP

>> DUF463  YcjX-like family, DUF463
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   1.5e-05     0.013       1      27 [.       5      31 ..       5      46 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.5e-05
                            DUF463  1 lrlavTGLsraGKtvfitsLvnqLlaa 27
                                      +++++TGL ++GKt  + s+++ L++ 
  gi|474934261|ref|YP_007687843.1|  5 VKIGITGLPGSGKTYTLKSVIKMLTSD 31
                                      79*********************9854 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.3   4.6e-05     0.039      13      64 ..       6      56 ..       2     134 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.6e-05
                                      EEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 13 kvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvl 64
                                      k++i+G  G+GK+  lk ++++l+   G++++ g   ++++    r++ig+ 
  gi|474934261|ref|YP_007687843.1|  6 KIGITGLPGSGKTYTLKSVIKMLT-SDGKVTVGGMIDEKINDGTGRHKIGIQ 56
                                      79****************999998.689997664333333333333333332 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.8   0.00013      0.11      10      32 ..       9      31 ..       7     161 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                            AAA_22 10 vtGesGtGKTtllrrlleqldee 32
                                      +tG +G+GKT++l+ + + l+ +
  gi|474934261|ref|YP_007687843.1|  9 ITGLPGSGKTYTLKSVIKMLTSD 31
                                      89**************9999755 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   3.4    0.0011      0.97       1      39 [.      10      49 ..      10     162 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0011
                                      EE-TTSSHHHHHHHHHHHH.TEEEEEHHHHHHHHHHTTTS CS
                            AAA_17  1 lGgPGsGKgtqceklveky.gfthlsaGdllreeakrggl 39
                                      +G+PGsGK+  ++ + + +     ++ G ++ e +++g  
  gi|474934261|ref|YP_007687843.1| 10 TGLPGSGKTYTLKSVIKMLtSDGKVTVGGMIDEKINDGTG 49
                                      7************999977434456667777777666642 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   0.00026      0.22       2      27 ..       7      32 ..       6      47 .. 0.89
   2 ?   -0.7   0.0       1.5   1.3e+03      80      96 ..      93     109 ..      72     139 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00026
                              MobB  2 lgivgksgsGKTtLleklipelkarg 27
                                      +gi+g  gsGKT  l+ +i++l++ g
  gi|474934261|ref|YP_007687843.1|  7 IGITGLPGSGKTYTLKSVIKMLTSDG 32
                                      789*******************9987 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.5
                              MobB  80 sleellarlsevDlvlv 96 
                                       s+e + + ++++D+v++
  gi|474934261|ref|YP_007687843.1|  93 SIEAIKTACEQCDIVVI 109
                                       44455555566777765 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00022      0.19       2     104 ..       9     117 ..       8     133 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00022
                     Helicase_RecD   2 ltAdRGRGKSaalGlalaaliaegksnilvtapskenvktlfeflakglealglke.......eekkkka.ekaelr 70 
                                       +t+ +G GK+ +l  +++ l+++gk  + v     e+++  + + + g++  ++ +       +++++++    +l 
  gi|474934261|ref|YP_007687843.1|   9 ITGLPGSGKTYTLKSVIKMLTSDGK--VTVGGMIDEKINDGTGRHKIGIQVRNILTdesvvfaNPETESKiMVGNLG 83 
                                       7888999******999999999987..88888888888888777777776666555568877633333330334455 PP

                     Helicase_RecD  71 vrkqrieyiapdellklkeqadllvvDEAAaipl 104
                                       v+   +e ++ +++++++eq+d++v+DE   +++
  gi|474934261|ref|YP_007687843.1|  84 VDLALFESVSIEAIKTACEQCDIVVIDEVGKVEV 117
                                       5588888899999999999*********988776 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   4.2    0.0018       1.6       3      23 ..       7      27 ..       5     146 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0018
                                      EEEEESTTCCHHHHHHHHHCT CS
                              cobW  3 tvltGflGsGKTtLlnhllen 23
                                      +++tG +GsGKT  l+++++ 
  gi|474934261|ref|YP_007687843.1|  7 IGITGLPGSGKTYTLKSVIKM 27
                                      689**************9943 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1     0.002       1.7      22      44 ..       9      31 ..       2      70 .. 0.77
   2 ?    3.5   0.6     0.062        53     210     228 ..      96     114 ..      87     124 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.002
                            AAA_11 22 iqGPPGtgKTktivellsqllsr 44
                                      i G PG+gKT t+ +++++l+s 
  gi|474934261|ref|YP_007687843.1|  9 ITGLPGSGKTYTLKSVIKMLTSD 31
                                      8899***************9643 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.062
                            AAA_11 210 lleklakkfdvviIDEAaq 228
                                       +++++ ++ d+v+IDE ++
  gi|474934261|ref|YP_007687843.1|  96 AIKTACEQCDIVVIDEVGK 114
                                       455555699*******987 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.9   0.00073      0.63       6     102 ..       9     117 ..       5     161 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00073
                           DUF2075   6 VtGvaGtGKtvvllnllael............eddeeertavylsvNhplvlvlrealakkeekkkkkeafeklssf 70 
                                       +tG +G+GKt+ l +++  l                  ++ +  ++ h+    +r+ l+ +  +  + +  ++++ +
  gi|474934261|ref|YP_007687843.1|   9 ITGLPGSGKTYTLKSVIKMLtsdgkvtvggmiD-----EKINDGTGRHKIGIQVRNILTDE--SVVFANPETESKIM 78 
                                       99***********99999993222222222210.....11222222222222333333222..24444444444444 PP

                           DUF2075  71 innlsef.......kkaeekkeepkedvvivDEAhrllt 102
                                       + nl          + ++ k + +++d+v++DE  ++  
  gi|474934261|ref|YP_007687843.1|  79 VGNLGVDlalfesvSIEAIKTACEQCDIVVIDEVGKVEV 117
                                       444442244445444455556777777777777666655 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.6     0.015        13       5      31 ..       8      34 ..       4      43 .. 0.84
   2 ?    6.8   0.1    0.0054       4.6      71     104 ..      92     124 ..      87     145 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.015
                                      EEEESTTSSHHHHHHHHHHHHHHTTS- CS
                             SRP54  5 llvGlqGaGKTttlaKLaallkkegkk 31
                                       + Gl G+GKT tl  + ++l+++gk 
  gi|474934261|ref|YP_007687843.1|  8 GITGLPGSGKTYTLKSVIKMLTSDGKV 34
                                      578************999999988764 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0054
                                       HHHHHHHHHHHTTSSEEEEEE--SSTTHHHHHHH CS
                             SRP54  71 vakeavekakeekidvvlvDTaGrlqndkelmee 104
                                       v  ea+++a e ++d+v++D  G+ + +++ + +
  gi|474934261|ref|YP_007687843.1|  92 VSIEAIKTACE-QCDIVVIDEVGKVEVESQAFVD 124
                                       56678888777.89***********999876643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.65u 0.37s 00:00:01.02 Elapsed: 00:00:00.56
# Mc/sec: 992.19
//
Query:       gi|474934262|ref|YP_007687844.1|  [L=372]
Description: N2,N2-dimethylguanosine tRNA methyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-80  270.0   0.0    4.2e-80  269.7   0.0    1.1  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
    1.2e-05   25.2   0.0    1.7e-05   24.6   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
      4e-05   23.5   0.0    5.9e-05   22.9   0.0    1.2  1  Met_10           Met-10+ like-protein
    0.00052   19.6   0.1    0.00083   18.9   0.1    1.2  1  MTS              Methyltransferase small domain
     0.0082   16.8   0.0      0.018   15.7   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
  ------ inclusion threshold ------
       0.14   11.5   0.1       0.22   10.9   0.1    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm


Domain annotation for each model (and alignments):
>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  269.7   0.0   1.4e-83   4.2e-80       1     376 []      11     363 ..      11     363 .. 0.91

  Alignments for each domain:
  == domain 1  score: 269.7 bits;  conditional E-value: 1.4e-83
                                       TTEEEEE----SS....--TT--SS--GGGHHHHHHHHHH...HHHHHHHH-S-EEEEESS-TTSHHHHHHHHH-S- CS
                               TRM   1 Geakikvedkevt....vskkeeVFYNPvqefnRDlsvlvirqlellkkklgekikvldaLsasGlRaiRfalEvpg 73 
                                       G+++i v++++++      ++  VF+N  ++fnRD+s+++   l +l++     ++v+da++a+G Ra+R a Evpg
  gi|474934262|ref|YP_007687844.1|  11 GSTRILVPETHSVsgpgKINAGSVFFNEQMAFNRDVSIML---LRALGRP---SMTVADAMTATGSRAVRIANEVPG 81 
                                       66777777776555776456699*****************...5555555...478******************998 PP

                                       EEEEEEE-S-HHHHHHHHHHHHHTT--GGEEEE-S-HHHHHC--SS-EEEEEE--SS--GGGHHHHHHHEEEEEEEE CS
                               TRM  74 vkevlaNDisekAvelikeNvklneveeivvineddAnvllaekkkrfdviDlDPfGspapfldsavqsvkekglLl 150
                                       +  vlaND+ e+A+  i+ N++ln+  +   +n+   n++    ++ fd++DlDPfGsp+ f++sa++  +++g+++
  gi|474934262|ref|YP_007687844.1|  82 T-DVLANDFDENAMPYIQANIDLNNLTNC-RANH--QNMISLFADNSFDYVDLDPFGSPSLFIQSAIRGTRKRGIVA 154
                                       6.6999*********************94.4444..366666799******************************** PP

                                       EEE--HHHHTTSSHHHHHHHHSSB---STTHHHHHHHHHHHHHHHHHHTTTEEEEEEEEEEETTEEEEEEEEEE-HH CS
                               TRM 151 vTaTDtavLaGaspekclrkYgavalkselcHEvalRillkavareaakYekavepllslsadfYvrvfvkvktgaa 227
                                       +TaTDta+LaGa+  kc r+Y+  +++  +cHE +lRil+  +are  k++  + plls++ad+Y+r ++++  g++
  gi|474934262|ref|YP_007687844.1| 155 ITATDTAPLAGAQAPKCRRRYQCEPIRGYMCHEGGLRILMCNIAREVGKFDMGMRPLLSFYADHYYRTYIELVPGTK 231
                                       ***************************************************************************** PP

                                       HHHHHHTTEEEEEEETTT--EEEE--GGG--SB-TTT-SBEEEEEEEE-S-S--HHHHHHHHHHHCT..-TTS-HHH CS
                               TRM 228 kvkkvleklglvlhCsgClseekvkglakfkaecehcgaklhlaGPlwlgplkdkefveevleeaekekeeelkkrv 304
                                         +++l++lg++ +           ++++++++ +    + h  GP+wlgpl dk ++ ++  e  +      +k+ 
  gi|474934262|ref|YP_007687844.1| 232 ACDDMLDQLGYMRY-----------DMKTLERDTSRTYDRDHRLGPFWLGPLFDKGLLAKMSPEGMA-----KEKKC 292
                                       ************99...........55556667778888999******************9987766.....47999 PP

                                       HHHHHHHHHHHS--SS-EEHHHHHHHHT-SS---HHHHHHH....TT-EE-TTSTTEEE-SS-HHHHHHHHH CS
                               TRM 305 kklLklikeElldaplyydlsqlasvlklsvpplkkvvsalkelgfevsrtHakpkaikTnapleavvevlr 376
                                        ++L++ ++E   +p++yd+++l++  k+s p+l+ ++++l+e+g  +s+tH++p+++ T++ple++++v+r
  gi|474934262|ref|YP_007687844.1| 293 TNVLDVWRNEIDSTPFVYDMNELSRFTKISPPNLEVFIEKLNEIG-PASKTHFCPTSFVTELPLETILDVYR 363
                                       **********999********************************.79*********************986 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   5.8e-09   1.7e-05       4     113 ..      58     159 ..      56     201 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 5.8e-09
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlils 80 
                                        ++v D+ ++tG  + ++a +  p+ +v   D++e+a  + ++n + ++l+n++  ++++ +l    +d++fD++  
  gi|474934262|ref|YP_007687844.1|  58 SMTVADAMTATGSRAVRIA-NEVPGTDVLANDFDENAMPYIQANIDLNNLTNCRANHQNMISLF---ADNSFDYVD- 129
                                       6899***************.66899*************************************65...58*****54. PP

                   Methyltransf_31  81 nevlnaladpdkileeiervlkpggilliedpr 113
                                          l+ + +p  ++++++r  ++ gi++i+  +
  gi|474934262|ref|YP_007687844.1| 130 ---LDPFGSPSLFIQSAIRGTRKRGIVAITATD 159
                                       ...579*********************999877 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0     2e-08   5.9e-05      80     197 ..      33     153 ..      19     155 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 2e-08
                                       TS---GGGHHHHHH....HHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTC CS
                            Met_10  80 kvyfsskleaErer....laklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekv 152
                                        v+f+++ +  r      l +l ++  +V d +   G  a+ ia    +  vla+d + +++ y++ ni lN++ + 
  gi|474934262|ref|YP_007687844.1|  33 SVFFNEQMAFNRDVsimlLRALGRPSMTVADAMTATGSRAVRIANEVPGTDVLANDFDENAMPYIQANIDLNNLTNC 109
                                       5667766666664311112234578889**********************************************997 PP

                                       EEEEES-GGG---TT-EEEEEE--TTTGGGGHHHHHHHEEEEEEE CS
                            Met_10 153 vkpileDgrevireqladrvvmnlpksaieFldkvlaalkdggvi 197
                                         +  +    +  ++ +d v ++   s   F++++++  +++g++
  gi|474934262|ref|YP_007687844.1| 110 R-ANHQNMISLFADNSFDYVDLDPFGSPSLFIQSAIRGTRKRGIV 153
                                       6.5555555555688899998998999999999999998888876 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   2.8e-07   0.00083      20     101 ..      47     128 ..      30     133 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.8e-07
                                       HHHHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTSTT CS
                               MTS  20 sklLletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleevee 95 
                                       s +Ll++l    s +v+D  + +G  ++ +a+e p ++v + d d +A+   ++n+  n+l  +++ ++++++ +++
  gi|474934262|ref|YP_007687844.1|  47 SIMLLRALGR-PSMTVADAMTATGSRAVRIANEVPGTDVLANDFDENAMPYIQANIDLNNLTnCRANHQNMISLFAD 122
                                       5578888888.7788**********************************************99************** PP

                                       S-EEEE CS
                               MTS  96 kkfdli 101
                                       ++fd++
  gi|474934262|ref|YP_007687844.1| 123 NSFDYV 128
                                       ****98 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   6.1e-06     0.018       1      68 [.      61     128 ..      61     133 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.1e-06
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlv 68 
                                       v d+ + tG  + ++a++++  +v++ D++e+++ +++++++ ++l n++  ++++ +l f+d+sfD+v
  gi|474934262|ref|YP_007687844.1|  61 VADAMTATGSRAVRIANEVPGTDVLANDFDENAMPYIQANIDLNNLtNCRANHQNMISL-FADNSFDYV 128
                                       6788899************55********************888777888888888777.99*****98 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   7.2e-05      0.22     151     215 ..      47     113 ..      44     128 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 7.2e-05
                              PrmA 151 clealeklvkegeevlDv..GtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkvea.klev 215
                                       ++ +l +l ++  +v D    tGS    ia       +v+a D De A+   ++N++lN++++ + + 
  gi|474934262|ref|YP_007687844.1|  47 SIMLLRALGRPSMTVADAmtATGSRAVRIANEV-PGTDVLANDFDENAMPYIQANIDLNNLTNcRANH 113
                                       566777777888888886225677777776655.5568*********************999855533 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 2207.27
//
Query:       gi|474934263|ref|YP_007687845.1|  [L=268]
Description: hypothetical protein TALC_00688 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1937.63
//
Query:       gi|474934264|ref|YP_007687846.1|  [L=434]
Description: adenylosuccinate synthase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.8e-168  560.8   0.4     2e-168  560.7   0.4    1.0  1  Adenylsucc_synt  Adenylosuccinate synthetase


Domain annotation for each model (and alignments):
>> Adenylsucc_synt  Adenylosuccinate synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  560.7   0.4  1.1e-172    2e-168       2     419 .]       5     426 ..       4     426 .. 0.97

  Alignments for each domain:
  == domain 1  score: 560.7 bits;  conditional E-value: 1.1e-172
                                       EEEE-SSS-S-HHHHHHHHHTT-SEEEE-SB-TTSSEEEEETTEEEEESSS-GGGGSTT-EEEE-TTBEE-HHHHHH CS
                   Adenylsucc_synt   2 vvvGaqwGDEGKGkivDllaeeadvvvRfqGGanAGHtvvvdgkkyklhllpSGilnpgvvnviGngvvvdpealle 78 
                                       +v+G+qwGDEGKGki+D+l e+ad+++RfqGG+nAGHt+vv+++ +klh lpSG+++pg+ +viGng+vv++e+ll+
  gi|474934264|ref|YP_007687846.1|   5 AVIGSQWGDEGKGKIIDYLDENADIICRFQGGNNAGHTIVVGDRVFKLHGLPSGVVRPGKLAVIGNGTVVNIEELLD 81 
                                       79*************************************************************************** PP

                                       HHTTSS-TT......TEEEETTSEE--HHHHHHHHHHHHH----------TTHHHHHHHHHTT---BGGGGGSHHHH CS
                   Adenylsucc_synt  79 EieeleakgvelskerllisdrahlvlpyhkalDkleeaakgkkkiGtTkkGiGpayadkvarrgirvgdlldeeel 155
                                       Ei+++e++g ++  + l+isdra l+++yhk+lD++ee+ kgkk++GtT+kGiGpay+dk++r g+r+gdll++++l
  gi|474934264|ref|YP_007687846.1|  82 EIKQVEDNGGSI--DGLRISDRAALIMNYHKKLDGAEEKYKGKKQVGTTGKGIGPAYQDKISRIGFRAGDLLEDDTL 156
                                       *********988..7************************************************************** PP

                                       HHHHHHHHHHTHHHHHHT.....T-----HHHHHHHHHHHHGGGEE-HHHHHHHHHHTT--EEEE--S-GGG-TTTS CS
                   Adenylsucc_synt 156 eeklekllelknkllekldk..eeleveelleellkyaerlkpyvvdtvallnealkegkkvLfEGaqgtllDidhG 230
                                       +ek++ ll +k++l++ l +   +++ e+l+e+++ + e+l +++vdt+ l+ne l++gk+v+fEGaqg++lDid+G
  gi|474934264|ref|YP_007687846.1| 157 REKIAMLLPYKKDLMKMLGAevCSCTEESLFEKMHGWGEKLGKHIVDTSVLINEYLDQGKNVMFEGAQGAMLDIDYG 233
                                       **************99987644333337799**999***************************************** PP

                                       STTSS-SS--SHHHHHHHTT--GGGEEEEEEEEESSEEESSSS--TTB--SHHHHHHHHHTT-B-TTT--B-EEE-E CS
                   Adenylsucc_synt 231 tYPfvTsSnttaggaltglglapkkidevlgvvKAyttrvGeGpfptelkdevgeklrekGkEfgtttgrpRrcGwl 307
                                       tYP+vTsS+t+ gg++tg+g+ap+++d+v+gvvKAyttrvGeGpf tel+++++ +l+++G+Efg+ttgr RrcGwl
  gi|474934264|ref|YP_007687846.1| 234 TYPYVTSSATLGGGICTGSGIAPNRLDHVMGVVKAYTTRVGEGPFVTELHGDAEAELQKRGGEFGVTTGRGRRCGWL 310
                                       ***************************************************************************** PP

                                       EHHHHHHHHHHHT-SEEEEE-GGGGTT-SEEEEEEEEEETTEEESS--S.....-GEEEEEEEEE--...S--TT-. CS
                   Adenylsucc_synt 308 DlvllryavrvngvtelaltklDvldgldeikvcvaYkldgkeldefpasleelekvepvyeelpgWk..edisgv. 381
                                       Dlv++++a r+ g++++a+tk+Dvl++++e+ vc+aY++dg+++++fp s+++le+++pvy++++gWk  +d+++v 
  gi|474934264|ref|YP_007687846.1| 311 DLVVVNHAKRLCGFDSMAITKIDVLNDYEELPVCTAYEIDGEKTKYFPGSIRKLERAKPVYTTFKGWKgwNDTEAVv 387
                                       *******************************************************************9878899998 PP

                                       .--GGGS-HHHHHHHHHHHHHHTS-EEEEE-SSSTT-EE CS
                   Adenylsucc_synt 382 .rsfedlpenakkyvefieellgvpvkiisvGpereqti 419
                                          +++lp+++k+y+efie+++g+p +++svGper++ti
  gi|474934264|ref|YP_007687846.1| 388 kAGYDALPKEMKTYIEFIEKETGIPADLVSVGPERDATI 426
                                       889*********************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.34s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2611.14
//
Query:       gi|474934265|ref|YP_007687847.1|  [L=114]
Description: hypothetical protein TALC_00690 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-17   63.3   0.1    2.5e-17   63.0   0.1    1.1  1  Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor


Domain annotation for each model (and alignments):
>> Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.0   0.1   1.4e-21   2.5e-17       3      93 ..      10      95 ..       9      97 .. 0.93

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 1.4e-21
                                      SCB-STCCC-SEEEEEEESSSCEEEEEEEE.GCCCTSSCSSTHHHHHHHHTT-SEEEESSSCHHHHHHHCTTTSEEEES CS
                     Nitro_FeMo-Co  3 srvdqhFGrapyFaiyeveegevkivenrveeaadaegggggklaqllaeegvdvvivgkiGpralakleaagievykg 81
                                      +++ qhFG++p F iy ve+   kiv+ +     d++g  +g+l   l+++g+d++++g+iG +a+ kl + gi +y+g
  gi|474934265|ref|YP_007687847.1| 10 GQIFQHFGQSPGFKIYTVED--GKIVSSE---VIDNGGNSHGTLIGYLSQAGIDALVCGGIGNGAVDKLTSMGISMYTG 83
                                      6899***************5..5799999...99********************************************* PP

                                      -SSBHHHHHHHH CS
                     Nitro_FeMo-Co 82 aggtveealkev 93
                                       +g+ +++ +++
  gi|474934265|ref|YP_007687847.1| 84 FSGDADAVAARI 95
                                      999999998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 726.13
//
Query:       gi|474934266|ref|YP_007687848.1|  [L=420]
Description: UbiD family decarboxylase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-93  312.0   0.1    7.1e-93  311.7   0.1    1.0  1  UbiD      3-octaprenyl-4-hydroxybenzoate carboxy-lyase


Domain annotation for each model (and alignments):
>> UbiD  3-octaprenyl-4-hydroxybenzoate carboxy-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  311.7   0.1   3.9e-97   7.1e-93      12     397 ..      10     373 ..       4     380 .. 0.90

  Alignments for each domain:
  == domain 1  score: 311.7 bits;  conditional E-value: 3.9e-97
                                       EEESEB-TBTHHHHHHHHHHHHT--EEEEEEBTTB.TT-EEEE-TTS-HCHHHHHHTS-GHHHHHHHHHHHHHS..- CS
                              UbiD  12 rikeevdpelEiaeiarrvleeggpallFenvkgkgskfpvltnlfgtrervalalglssleeileklaellepkpp 88 
                                        i+ee+dp+      +r +   ++   lFe+ +g     ++++n+++tre++a+a+g++  ++i+ ++ ++++   p
  gi|474934266|ref|YP_007687848.1|  10 VISEEIDPDN--YDATRYMQDDQQATFLFERLNG----GKAAGNVYSTREKIAKAMGIE-RDQIVMHVMDAIAA--P 77 
                                       6788888843..33445555556889******53....489****************86.59999999999996..3 PP

                                       ---EE--GCG-GGGSEEECCCCC--HHHS---BSSTTSSS-EEECEEEEEE-TTTT-EEEEEEEEEEEETTEEEE-- CS
                              UbiD  89 ippkvvesekapcqeevvlegddvdLskLPvltlwpgDgGpyitlglvitrdpetgkrnlgiyRmqvldknklglhw 165
                                       +p ++   +  p  ++    +  +dL+kLP+++++p+D+G+yi++g+v+++   +gkrn++++Rm + +k+++g+++
  gi|474934266|ref|YP_007687848.1|  78 VPTEE---DAEPLFKQQ---ELPLDLTKLPIVKYFPEDAGRYISAGIVVSE--FGGKRNVSFHRMLIRGKDEIGIRL 146
                                       44333...344555344...457***************************9..59********************** PP

                                       TTTHCHHHHHHHHHHCCT--EEEEEEES--HHHHHHCTS--TTT-TCHHHHHHHH....TS--EEEE-SSSSSEEET CS
                              UbiD 166 qihkggaehlrkakkkggeplpvavaiGvdPaltlaAvaplPeglsElefaGalr....gepvelvkcetvdlevpa 238
                                       ++++     +++akk+g ++l+++++iG++  ++++A+ ++  g++El++a+a+     g+p++++kc+ ++l+vpa
  gi|474934266|ref|YP_007687848.1| 147 VPRHTFTL-FNEAKKAG-QDLKISICIGAPVEAMVSAALSVDFGVDELTIASAMHtkghGTPLKVAKCD-NGLYVPA 220
                                       **999888.********.9***********************************9999999*******5.59***** PP

                                       T-SEEEEEEEECCEEEECTTTC-TTSCEEC--CCEEEEEEEEEEE-TT-EEEE-SSSCCSHHHHCHHHHHHHHHHHH CS
                              UbiD 239 dAEivleGeidpgetapEGPfgdhtGyysevrdefpvfkVtaithRkdpiypttvvgkppeedallgkalealflpl 315
                                       ++E+vleG+i+  eta EGPf+d+ G+y+ vrd +pv+k+++i+ +kdp+++ +++g   e+ +l+g+++e+++++ 
  gi|474934266|ref|YP_007687848.1| 221 ECEYVLEGRITS-ETASEGPFVDIAGTYDAVRD-QPVVKIDRIWAKKDPVFQILLPGGF-EHFLLMGVPREPVIFRT 294
                                       ***********9.79****************99.5*****************9989999.***************** PP

                                       HHCCSTTEEEEEE-GGGTTTCEEEEECHHHTCCHHHHHHHHHHCCTTGGC-SEEEEEEETTS-TTSHHHHHHHHHHC CS
                              UbiD 316 lkkqvpevkdvhlpeeggfhllavvsikkrypghakkvmealwalkqqlsltKlvivvDedvdvrdlkevlwaiatr 392
                                       ++++vp+vk+v+l+e g+++l  vvsi+k+ +g+  ++++a+++ ++  s+ K vi+vD+d+d++d +ev+wa+atr
  gi|474934266|ref|YP_007687848.1| 295 VRQAVPKVKNVRLTEGGCCWLNGVVSISKNKEGDGVNAIMAAFTGHP--SM-KNVIIVDDDIDIFDDREVEWAVATR 368
                                       *******************************************9999..77.************************* PP

                                       --CCC CS
                              UbiD 393 vdpdr 397
                                       +++dr
  gi|474934266|ref|YP_007687848.1| 369 MQADR 373
                                       ***99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2647.64
//
Query:       gi|474934267|ref|YP_007687849.1|  [L=233]
Description: Transcriptional regulator [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.5e-16   59.2   0.0      5e-16   58.2   0.0    1.5  1  TetR_N       Bacterial regulatory proteins, tetR family
  ------ inclusion threshold ------
      0.019   15.1   0.0       0.03   14.5   0.0    1.4  1  HTH_Tnp_1_2  Helix-turn-helix of insertion element transposas
      0.072   13.5   0.2       0.48   10.8   0.1    2.1  2  Herpes_UL20  Herpesvirus egress protein UL20


Domain annotation for each model (and alignments):
>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.2   0.0   8.4e-20     5e-16       1      46 [.      23      68 ..      23      69 .. 0.97

  Alignments for each domain:
  == domain 1  score: 58.2 bits;  conditional E-value: 8.4e-20
                                      HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHH CS
                            TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLlea 46
                                      Il aA+ lf e+Gyd+tt+reI  rAG+  g+lY +F+sKe++l+ 
  gi|474934267|ref|YP_007687849.1| 23 ILNAAMDLFFEQGYDKTTTREIIYRAGILNGTLYNRFKSKEDILLS 68
                                      9******************************************986 PP

>> HTH_Tnp_1_2  Helix-turn-helix of insertion element transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0     5e-06      0.03      15      76 ..      27      89 ..      14     121 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5e-06
                                      HHHHHHHHHH--S-HHHHHHHHTS-HHHHH.HHHH-HH.HHHHHHHHHHHHHHTTHHHHHHHHH CS
                       HTH_Tnp_1_2 15 aaellvendyekltldeiaeevgvsrsTly.kWkkkke.FieyvnelaeefleeeraevykaLl 76
                                      a+ l  e+ y+k+t++ei    g+ + Tly + k+k++   + v+   +ef++e  ++v+k  +
  gi|474934267|ref|YP_007687849.1| 27 AMDLFFEQGYDKTTTREIIYRAGILNGTLYnRFKSKEDiLLSLVSDGQSEFMKE-AETVFKDSK 89
                                      567889************************456766552567889999999986.467777655 PP

>> Herpes_UL20  Herpesvirus egress protein UL20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   8.1e-05      0.48     114     158 ..      69     119 ..      42     132 .. 0.81
   2 ?    0.7   0.0     0.098   5.8e+02     115     158 ..     129     171 ..     119     188 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 8.1e-05
                       Herpes_UL20 114 lfkDsevyFlat..alfpdakskiLpvstslktaiylvl....aasvvyaa 158
                                       l  D++  F+++  ++f d+k+ i+++  + + +iy++     aa ++yaa
  gi|474934267|ref|YP_007687849.1|  69 LVSDGQSEFMKEaeTVFKDSKNPIVAFVLPSALEIYIASrsakAADLIYAA 119
                                       7899******999999**********9999999999875111144455555 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.098
                       Herpes_UL20 115 fkDsevyFlatalfpdakskiLpvstslktaiylvlaasvvyaa 158
                                       ++Ds + + a a++p+   kiL+ +   k  i++v a   ++a+
  gi|474934267|ref|YP_007687849.1| 129 YTDSYLEW-ASAIMPENSGKILSDELLRKKVIAMVGATGNIAAM 171
                                       66777777.66899********9888777766666555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1396.27
//
Query:       gi|474934268|ref|YP_007687850.1|  [L=863]
Description: putative drug exporters of the RND superfamily [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-85  286.4  22.6    8.6e-46  156.4   8.4    2.3  2  MMPL            MMPL family
    7.6e-05   21.0   7.2    7.6e-05   21.0   7.2    2.1  2  Patched         Patched family
      0.001   19.0   3.9      0.001   19.0   3.9    3.1  3  Sterol-sensing  Sterol-sensing domain of SREBP cleavage-activ
     0.0062   16.5   0.2      0.014   15.3   0.2    1.6  1  RIFIN           Rifin
  ------ inclusion threshold ------
       0.13   12.3   0.3       0.81    9.7   0.1    2.1  2  Erp_C           Erp protein C-terminus


Domain annotation for each model (and alignments):
>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.4   8.4   2.4e-49   8.6e-46     103     310 ..     137     345 ..     114     392 .. 0.87
   2 !  135.6   6.2     5e-43   1.8e-39      84     310 ..     606     846 ..     560     856 .. 0.86

  Alignments for each domain:
  == domain 1  score: 156.4 bits;  conditional E-value: 2.4e-49
                              MMPL 103 adesvaairaaveear..pleglkvevtGpaatladlrdasdrdlklievvtlvvilviLlivyrSlvaallplltv 177
                                         ++  +ir+ v++a+    ++l+ +vtG  a+  d++++s++d++ +  +++++i+++L++ + +lv+a++p ++v
  gi|474934268|ref|YP_007687850.1| 137 VSDQTGDIRHLVSQAKanVGADLTSYVTGNDAISYDTEKSSMQDVARVDPISVALIFILLALFFYALVTAFVPPAVV 213
                                       4577889999999999777999******************************************************* PP

                              MMPL 178 vvsllaalglvlilalllglelstfvlgllvvlliavGtDYallLvsRyreelaagedreeaviravastgkvvtaa 254
                                       ++ +++ l+l  i+ l + ++++  + +l  v ++++G DY +++++Ryr+e+++g d + a+ +a++  g++v+ +
  gi|474934268|ref|YP_007687850.1| 214 GMAYGVVLSL--IWGLGQLMGIYYITSTLILVSMLGAGCDYSIFIIARYRDERKKGLDHDVALKEAIMWGGEAVFTS 288
                                       **********..***************************************************************** PP

                              MMPL 255 GltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTllPAllvllGraa.lakp 310
                                       G+ v+i +++L++ ++++++++G+ +alG+l+++l++lT++PA+l ++G +  ++++
  gi|474934268|ref|YP_007687850.1| 289 GVSVMIGFAALALCDFSMVQTMGICLALGILMALLAALTFIPAMLNIVGDRIfWPSS 345
                                       ***************************************************666633 PP

  == domain 2  score: 135.6 bits;  conditional E-value: 5e-43
                              MMPL  84 Dgkaaralvtlegdpgsteadesvaairaaveear......pleglkv......evtGpaatladlrdasdrdlkli 148
                                       D + + ++v ++ +p s+ +++ ++++++  +         + +g +v      +v+G++a+++ ++ +++ +  +i
  gi|474934268|ref|YP_007687850.1| 606 DSHYVNMMVITTEKPMSENTMAFMKDLQKEFHGENgydtyvTVSGSNVdvigasYVSGSSAVMDQITGVVEDQFSMI 682
                                       555555555555566666666666666666666666666663333333224444899******************** PP

                              MMPL 149 evvtlvvilviLlivyrSlvaallplltvvvsllaalgl.vlilalllglelstfvlgllvvlliavGtDYallLvs 224
                                        +v +v+++++L+++++  ++++  ++t+++s++ +++l   ++  l    + + ++  l+v+l++ G DY ++L++
  gi|474934268|ref|YP_007687850.1| 683 RIVVIVLLIILLFLILGCYLTPIRAIITIMLSVVWTVALtRFVFDGLMDTPVIWLIPIVLFVVLLGLGMDYEIFLTT 759
                                       ***************************************9999********************************** PP

                              MMPL 225 RyreelaagedreeaviravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTll.PAllv 300
                                       ++re + +g d ++a+ +av+++g+v+   +l + +++l+L++a+ ++l+++G+a+++G+l+d l ++ ++ P+l+ 
  gi|474934268|ref|YP_007687850.1| 760 KIRENRVKGMDNDTAIEEAVKQAGGVISLCALLMGGTFLSLTLANSSMLQEFGFALGVGILIDGLFMVGFIsPSLMH 836
                                       ***************************************************************************** PP

                              MMPL 301 llGraalakp 310
                                       l+G++ ++ p
  gi|474934268|ref|YP_007687850.1| 837 LMGEWSWKGP 846
                                       *****99865 PP

>> Patched  Patched family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   7.2   2.1e-08   7.6e-05     665     809 ..     187     336 ..      86     338 .. 0.88
   2 ?   -3.6   7.0      0.57     2e+03     196     387 ..     645     842 ..     588     859 .. 0.66

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.1e-08
                           Patched 665 lallcmfvvallfipelitvlvitlsivsidigviGflslWgv.dLDpismit...iims.iGfsvdlsaHiayafv 736
                                       ++++++f+  +lf + l+t++v   ++v + +gv+  l +Wg  +L  i  it   i++s  G   d+s  i+ ++ 
  gi|474934268|ref|YP_007687850.1| 187 ISVALIFILLALFFYALVTAFV-PPAVVGMAYGVVLSL-IWGLgQLMGIYYITstlILVSmLGAGCDYSIFIIARYR 261
                                       78899999999***99999875.6899*******8444.59975798887775444555646*************** PP

                           Patched 737 rsekd..dakeRvvealealgwPvvqgalSTilgvlvLlfvdsymvqvFfktvvLvvvigllHgLlilPillslf 809
                                        ++k+  d +  ++ea+   g  v+ +++S ++g   L++ d +mvq+   ++ L +++ ll +L ++P +l ++
  gi|474934268|ref|YP_007687850.1| 262 DERKKglDHDVALKEAIMWGGEAVFTSGVSVMIGFAALALCDFSMVQTMGICLALGILMALLAALTFIPAMLNIV 336
                                       ***9999999999**********************************************************9876 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 0.57
                           Patched 196 hievsilhsqiledelqrnaktllpflvvtiaiLlvfsiivsvvlssd...alkidwvrskpilailgvlspvlAiv 269
                                       +++vs     ++    +  + +++ +++    +   fs+i +vv        + i      pi ai+ ++ +v+ +v
  gi|474934268|ref|YP_007687850.1| 645 YVTVSGSNVDVIGASYVSGSSAVMDQITGV--VEDQFSMIRIVVIVLLiilLFLILGCYLTPIRAIITIMLSVVWTV 719
                                       566666666666666666665555554432..222333333322222111134444556789999999999999998 PP

                           Patched 270 sslGlll..wlGfrfnsivtvtPFLv.LaiGvD.dmflmvaawkrteaklsvkkrigealseagvaitiTslTdvls 342
                                       +   +++  ++  + +    ++ F+v L++G+D ++fl  +  ++  +  +    i+ea+ +ag  i++  l    +
  gi|474934268|ref|YP_007687850.1| 720 ALTRFVFdgLMDTPVIWLIPIVLFVVlLGLGMDyEIFLTTKIRENRVKGMDNDTAIEEAVKQAGGVISLCALLMGGT 796
                                       76666653344444444445555776369999977899999999999999999999999999999999999999999 PP

                           Patched 343 FgiGaittlpaiqlFciytavailfdfiYqitffaa.vlaiaakae 387
                                       F   ++++   +q F    +v il+d ++ + f ++ ++ ++++  
  gi|474934268|ref|YP_007687850.1| 797 FLSLTLANSSMLQEFGFALGVGILIDGLFMVGFISPsLMHLMGEWS 842
                                       9999999999999999999999999999999999973566666655 PP

>> Sterol-sensing  Sterol-sensing domain of SREBP cleavage-activation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.6      0.56     2e+03     116     134 ..     187     205 ..     168     209 .. 0.80
   2 !    5.3   4.7    0.0046        17      47     135 ..     246     335 ..     203     341 .. 0.68
   3 !   19.0   3.9   2.8e-07     0.001      11     127 ..     706     828 ..     701     837 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.56
                                       HHHHHHHHHHHTHHHHHHH CS
                    Sterol-sensing 116 vavlvdFllqitfFvavLs 134
                                       ++v++ F+l ++fF a+ +
  gi|474934268|ref|YP_007687850.1| 187 ISVALIFILLALFFYALVT 205
                                       7888999999999999875 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0046
                                       HHHCHH.CCHHCHHHHHHHHTTTCHHHHHHHHHHHHCCCCHHCCCHHHHHHH.HHHHCCHHHHHHHHHHHHHHHHHH CS
                    Sterol-sensing  47 lavgvd.nifvlvkavqrtsrsldeseriaealgevgpsilltsltellall.lgaltdvpavqeFclfaavavlvd 121
                                       l  g d  if++ +  ++ ++ ld +  ++ea+   g +++ + ++ ++ ++ l+ l d++ vq+  +  a+++l+ 
  gi|474934268|ref|YP_007687850.1| 246 LGAGCDySIFIIARYRDERKKGLDHDVALKEAIMWGGEAVFTSGVSVMIGFAaLA-LCDFSMVQTMGICLALGILMA 321
                                       5566663355666655666666777888888888888888888888888888555.888999999999999999998 PP

                                       HHHHHTHHHHHHHH CS
                    Sterol-sensing 122 FllqitfFvavLsl 135
                                        l  +tf  a+L +
  gi|474934268|ref|YP_007687850.1| 322 LLAALTFIPAMLNI 335
                                       88888888888866 PP

  == domain 3  score: 19.0 bits;  conditional E-value: 2.8e-07
                                       HHHHHHHCCHHHHCCHHHHH..HHHHHHHHH..HHHHHHH.HHHCHH.CCHHCHHHHHHHHTTTCHHHHHHHHHHHH CS
                    Sterol-sensing  11 agviivllsvasslgllayl..gltltliil..evlPflv.lavgvd.nifvlvkavqrtsrsldeseriaealgev 81 
                                        ++i+++lsv+ ++ l  ++  gl  t++i+   ++ f+v l  g+d +if+ +k  ++  +  d++  i ea++++
  gi|474934268|ref|YP_007687850.1| 706 RAIITIMLSVVWTVALTRFVfdGLMDTPVIWliPIVLFVVlLGLGMDyEIFLTTKIRENRVKGMDNDTAIEEAVKQA 782
                                       579999****9999997765458888887772244557762579***5566666666677777788*********** PP

                                       CCCCHHCCCHHHHHHH.HHHHCCHHHHHHHHHHHHHHHHHHHHHHHT CS
                    Sterol-sensing  82 gpsilltsltellall.lgaltdvpavqeFclfaavavlvdFllqit 127
                                       g  i l++l    ++l l +l + + +qeF +   v++l+d l+ + 
  gi|474934268|ref|YP_007687850.1| 783 GGVISLCALLMGGTFLsL-TLANSSMLQEFGFALGVGILIDGLFMVG 828
                                       **********99999955.599******************9777654 PP

>> RIFIN  Rifin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2     4e-06     0.014     123     301 ..     510     698 ..     485     701 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4e-06
                             RIFIN 123 vGllggiavaawkkaalaaaieaaie.ageaagikaviellkkllk...lselkekklesli.tatnyknvt...sl 191
                                        G ++g+  + +  + + aa+  a++ + +aa+i++  +++k+ ++   ++ l+++   + i t+t+y ++    s+
  gi|474934268|ref|YP_007687850.1| 510 AGTISGLNSYDIICNNVRAAMPGATTaQVNAAAISMLPDMVKTPIQslfYNPLDQQYHYE-IdTTTTYLSADplvSI 585
                                       566777777776666666666666662223555555544444433322223333333334.4488888887611144 PP

                             RIFIN 192 vkaikeeyeescllklkkskaaltsakekekkeasskekikkkvekivekaekkaaaaaa.eaaaeataeaekaeta 267
                                       +++i    + s+ +  ++ +  + ++++  ++e+  +e+++  ++++++++  ++  ++  +++ ++ + + ++ ++
  gi|474934268|ref|YP_007687850.1| 586 SNVIDGILNVSTGILPANVADSHYVNMMVITTEKPMSENTMAFMKDLQKEFHGENGYDTYvTVSGSNVDVIGASYVS 662
                                       45555555555555555555555666666666777777777777777777777776666624444445555554455 PP

                             RIFIN 268 aveattaslqtai..iasivaivvIvLimvIIYLiL 301
                                         +a++ +++  +    s++ ivvIvL ++  +LiL
  gi|474934268|ref|YP_007687850.1| 663 GSSAVMDQITGVVedQFSMIRIVVIVLLIILLFLIL 698
                                       44444444444432258******************9 PP

>> Erp_C  Erp protein C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.31   1.1e+03      95     116 ..     129     150 ..     115     166 .. 0.83
   2 ?    9.7   0.1   0.00023      0.81      13      42 ..     651     680 ..     646     684 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.31
                             Erp_C  95 pklkenvnvseikedleklksk 116
                                        k+ en++vs+   d+ +l s+
  gi|474934268|ref|YP_007687850.1| 129 AKVDENIDVSDQTGDIRHLVSQ 150
                                       5788999999999999888776 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00023
                             Erp_C  13 knidvikeqtsvgakevidkitgpvyddft 42 
                                        n+dvi    + g+ +v+d+itg v d+f+
  gi|474934268|ref|YP_007687850.1| 651 SNVDVIGASYVSGSSAVMDQITGVVEDQFS 680
                                       69**************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (863 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       910  (0.0507558); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.86u 0.32s 00:00:01.18 Elapsed: 00:00:00.54
# Mc/sec: 4843.04
//
Query:       gi|474934269|ref|YP_007687851.1|  [L=557]
Description: glutamyl-tRNA synthetase, archaeal and eukaryotic family [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.1e-71  238.3   0.0    1.2e-70  237.9   0.0    1.2  1  tRNA-synt_1c    tRNA synthetases class I (E and Q), catalytic
    7.9e-20   71.4   0.0    1.8e-19   70.3   0.0    1.6  1  tRNA-synt_1c_C  tRNA synthetases class I (E and Q), anti-codo


Domain annotation for each model (and alignments):
>> tRNA-synt_1c  tRNA synthetases class I (E and Q), catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.9   0.0   1.4e-74   1.2e-70       3     310 ..     100     399 ..      98     403 .. 0.91

  Alignments for each domain:
  == domain 1  score: 237.9 bits;  conditional E-value: 1.4e-74
                                       EEEE---SSSS-BHHHHHHHHHHHHHHHHTT-EEEEEE--SSCCC--HHHHHHHHHHHHHTT---SSEEEEGGGGHH CS
                      tRNA-synt_1c   3 rtRfaPePtGyLHiGhakaallnylfAknnnGkfilRieDTdperekeeaeesiledlkwlgikwdekptyqsdrfd 79 
                                       + R+aP P+G LHiGh +  +ln  + k+++G+++lR+eDT+pe+ +++a + i edl+wlg+   ++   qs+rf+
  gi|474934269|ref|YP_007687851.1| 100 VMRIAPGPSGPLHIGHTRVSVLNDEYTKRYEGQLVLRFEDTNPEKIDPDAYDMIPEDLDWLGVRI-HQKFIQSERFE 175
                                       67***************************************************************.77889****** PP

                                       HHHHHHHHHHHTTSEEEE-STHHHHHHHHCCSSHSS-TTTTS-HHHHHHHHHHHHHTTHSTTTS-..EEEESSBTTS CS
                      tRNA-synt_1c  80 elkkyaeeLikkGkAYvcectkeeleeereeqeklgskerdrydeenlklfeeemkkgkaegeka..vvRlkidees 154
                                       +++++  +Li++G+AYvc c ++  ++++e+  k +++ r+ +++e+++ f+  m +g +e +ka  vv+  id+ +
  gi|474934269|ref|YP_007687851.1| 176 TYYDITRRLIEEGHAYVCTCDPDDWRAKKER--KEACPCRNLPVNEQMERFD-RMMEGGYEPGKAiaVVKTAIDHPN 249
                                       *****************************99..777789************5.566677777666114555566665 PP

                                       SGGGSSTEEEEEEESGGGSBTTTBTSTSEEE-HHHHHHHHHHHTT-SEEEEEGGGGCCHHHHHHHHHHTT-S.-EEE CS
                      tRNA-synt_1c 155 svefrDlvrgriklepqeihdlvivksdiyPtYdfavvidDaleeithvlrteefldntpkyiwllealglevppfi 231
                                         ++rD v+ ri  +p   h+++++k+++yP+ ++ v+idD+l+++thv+r++++l+nt+++  ++ ++g++  p +
  gi|474934269|ref|YP_007687851.1| 250 -PAVRDFVALRIVDAP---HPRTGSKYRVYPMMNLSVAIDDHLMGMTHVIRGKDHLNNTERQKYIFGYMGWK-MPTY 321
                                       .5**************...*****************************************************.5566 PP

                                       EEE--EEETTSB-SHHHHHHHHHTTSSSSTT-TTSCBHHHHHHCTB-HHHHHHHHHHHCCCSSS.EEEEHHHHHHHH CS
                      tRNA-synt_1c 232 heylrlnlekkklSKRklsllvdekqvkewddlreallnflrrlGwtpekerelftreeliksfdlnresksleafd 308
                                       + y ++n+ +++l    ++++++  ++++wdd r  ++++l r+G+ pe++r    + ++   + ++ ++++l  ++
  gi|474934269|ref|YP_007687851.1| 322 YHYGLVNIPDTVLKTSLIKQSIKAGEYTGWDDVRTGTVRALERRGIRPEAIRRYWVESGIKSVD-IEFSWDNLYGMN 397
                                       6799*********99999***********************************99999876655.999998887777 PP

                                       HH CS
                      tRNA-synt_1c 309 rk 310
                                       r+
  gi|474934269|ref|YP_007687851.1| 398 RN 399
                                       76 PP

>> tRNA-synt_1c_C  tRNA synthetases class I (E and Q), anti-codon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.3   0.0     2e-23   1.8e-19       2     173 ..     406     542 ..     405     543 .. 0.88

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 2e-23
                    tRNA-synt_1c_C   2 pRymaVldpvkvtienlpegkeeelevplhpknpelgtrkvpfs..keiyiereDakrlkpgeevrLkelynikvee 76 
                                       +Ry++V+dpv+  i+++   +++e ++plhp+n ++g r++ ++  k+++++++D   ++++++vrLk+l+n+ ++ 
  gi|474934269|ref|YP_007687851.1| 406 DRYFFVQDPVRYDISGT---DVIEGKAPLHPDNADKGFREYRLEgpKTVFLSEKDSSLFAQERKVRLKDLCNLDYNT 479
                                       7**************54...589*********************767****************************76 PP

                    tRNA-synt_1c_C  77 vekdesgevtelkleydgesleearkkkg.iihWvsaeeaveaevrlYdrLfkeeededfllnpdslkvleeglaep 152
                                                  + + yd       +k  +  ++Wvs ++++++                +++ pd++  + egl+e+
  gi|474934269|ref|YP_007687851.1| 480 P---------AIFAGYDV------KKGGMkAVQWVS-RDSTPC----------------KVYMPDGS--IAEGLVEN 522
                                       5.........35555554......2444459*****.599***................9******9..48****** PP

                    tRNA-synt_1c_C 153 alanlkkgdivQfeRiGyfrv 173
                                       a+ + +k d vQfeR+G++r+
  gi|474934269|ref|YP_007687851.1| 523 AILK-EKADTVQFERFGFVRI 542
                                       ***9.88999*********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (557 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 3736.40
//
Query:       gi|474934270|ref|YP_007687852.1|  [L=221]
Description: Mn-dependent transcriptional regulator [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-22   79.7   0.3    4.6e-22   78.0   0.3    1.9  2  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
    3.5e-19   68.6   0.5    7.4e-19   67.6   0.5    1.5  1  Fe_dep_repr_C    Iron dependent repressor, metal binding and 
    4.3e-12   46.1   0.0    9.1e-12   45.1   0.0    1.6  1  FeoA             FeoA domain
    1.4e-06   28.2   0.1    1.2e-05   25.1   0.1    2.2  2  MarR             MarR family
      3e-05   23.9   0.0    7.6e-05   22.6   0.0    1.8  1  HTH_Crp_2        Crp-like helix-turn-helix domain
    3.5e-05   23.6   0.0    0.00012   21.9   0.0    2.0  1  MarR_2           MarR family
    6.4e-05   23.0   0.3    0.00013   22.0   0.2    1.6  1  DUF2250          Uncharacterized protein conserved in archaea
    6.9e-05   23.3   0.1    0.00082   19.8   0.0    2.5  2  HTH_27           Winged helix DNA-binding domain
    0.00013   21.7   0.0    0.00043   20.1   0.0    1.9  1  HTH_5            Bacterial regulatory protein, arsR family
    0.00019   21.7   0.1    0.00034   20.9   0.1    1.5  1  Rrf2             Transcriptional regulator
    0.00025   20.6   0.0    0.00097   18.7   0.0    2.0  2  HTH_24           Winged helix-turn-helix DNA-binding
     0.0014   18.2   0.0     0.0027   17.3   0.0    1.5  1  GntR             Bacterial regulatory proteins, gntR family
  ------ inclusion threshold ------
      0.011   15.8   0.1      0.017   15.1   0.1    1.3  1  HTH_45           Winged helix-turn-helix
       0.02   14.8   0.2      0.076   12.9   0.0    1.9  2  TrmB             Sugar-specific transcriptional regulator Trm
      0.023   14.7   0.0      0.041   13.8   0.0    1.5  1  HTH_12           Ribonuclease R winged-helix domain
      0.024   14.3   0.1       0.04   13.6   0.1    1.3  1  DUF4423          Domain of unknown function (DUF4423)
       0.04   14.0   0.1       0.14   12.2   0.0    1.9  2  Sigma70_r3       Sigma-70 region 3
       0.04   14.0   0.2       0.14   12.2   0.0    2.0  2  HTH_20           Helix-turn-helix domain
      0.057   13.6   0.1       0.21   11.9   0.0    1.9  2  Rio2_N           Rio2, N-terminal
      0.061   12.8   0.0      0.095   12.2   0.0    1.3  1  Glu_syn_central  Glutamate synthase central domain
      0.069   13.1   0.0       0.12   12.4   0.0    1.4  1  HTH_11           HTH domain
       0.11   12.3   0.0        0.2   11.5   0.0    1.4  1  HTH_IclR         IclR helix-turn-helix domain
       0.13   12.0   0.0       0.26   11.1   0.0    1.5  1  LexA_DNA_bind    LexA DNA binding domain


Domain annotation for each model (and alignments):
>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.0   0.3   5.9e-25   4.6e-22       1      60 []       1      60 [.       1      60 [. 0.98
   2 ?   -1.9   0.0       5.2     4e+03      42      52 ..     168     178 ..     166     179 .. 0.84

  Alignments for each domain:
  == domain 1  score: 78.0 bits;  conditional E-value: 5.9e-25
                                      X--HHHHHHHHHHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTTEE CS
                    Fe_dep_repress  1 dLvestEdYLetIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyveyekykgl 60
                                      +++++ EdYL +I++l e++ v+kt++la+++nvsp+sVsemlk L+kdG+vey+ky+g+
  gi|474934270|ref|YP_007687852.1|  1 MTTSNREDYLLAILKLTEDGTVAKTTELAQFMNVSPASVSEMLKILSKDGLVEYAKYRGV 60
                                      7899******************************************************97 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.2
                                       HHHHHHHTTSE CS
                    Fe_dep_repress  42 mlkkLekdGyv 52 
                                        +kkL  +G+v
  gi|474934270|ref|YP_007687852.1| 168 QVKKLLTMGFV 178
                                       599******98 PP

>> Fe_dep_repr_C  Iron dependent repressor, metal binding and dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.6   0.5   9.5e-22   7.4e-19       1      63 [.      63     125 ..      63     130 .. 0.97

  Alignments for each domain:
  == domain 1  score: 67.6 bits;  conditional E-value: 9.5e-22
                                       -HHHHHHHHHHHHHHHHHHHHHHHHCT--CCCHHHHCCCCGGGS-HHHHHHHHHHCT-.SB-T CS
                     Fe_dep_repr_C   1 TekGrelAkrlvrrhrllerfLvdvlgvdweeaheeAerlEhalseelierldellgfpeecP 63 
                                       Te G  +A+ + +rh ++erfL dvl++d e aheeA+r+Eh +s+e++ +++++lg+p  c 
  gi|474934270|ref|YP_007687852.1|  63 TEAGLTEARLTRKRHHVVERFLIDVLDMDHEAAHEEASRIEHSISDEAAVNMCNMLGNPPDCD 125
                                       9**********************************************************9996 PP

>> FeoA  FeoA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   0.0   1.2e-14   9.1e-12       1      73 [.     145     217 ..     145     218 .. 0.95

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 1.2e-14
                                       EEGGG--TT-EEEEEEE-TT.SSHHHHHHHHT--TT-EEEEEEE-TTS-SEEEEETTEEEEE-HHHHTTEEEE CS
                              FeoA   1 vpLsdlkeGergeiarisdedpellrrLremGlvpGarievvarapfggplvvrvgdtrvaLgreeAqaIlVe 73 
                                       ++L+d+  G++g+++ +++ed++  ++L+ mG+vpG ++ + +      plv+ +g++ v+L+r +A a++V 
  gi|474934270|ref|YP_007687852.1| 145 MNLTDMRSGDKGKVSHLKSEDTAQVKKLLTMGFVPGREVVMDSCEGEDSPLVIIIGNQSVVLDRTMACAVFVD 217
                                       89****************************************966669********999************96 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.1   1.5e-08   1.2e-05      18      48 ..      23      53 ..      10      56 .. 0.84
   2 ?    0.3   0.0      0.89     7e+02      35      47 ..     166     178 ..     162     179 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.5e-08
                                      EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR 18 lsvseLakklgvskstvtrvldrLekkGlie 48
                                      ++ +eLa +++vs+++v+++l+ L k+Gl+e
  gi|474934270|ref|YP_007687852.1| 23 AKTTELAQFMNVSPASVSEMLKILSKDGLVE 53
                                      6778*************************97 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.89
                                       HHHHHHHHHTTSE CS
                              MarR  35 trvldrLekkGli 47 
                                       t ++++L   G++
  gi|474934270|ref|YP_007687852.1| 166 TAQVKKLLTMGFV 178
                                       7789********8 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   9.7e-08   7.6e-05      24      59 ..      25      62 ..       9      70 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 9.7e-08
                                      HHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETEE.EEE CS
                         HTH_Crp_2 24 qeelAsmlGltretvsrilseLkreglis.rgrr.iri 59
                                       +elA+++++++ +vs +l+ L+++gl++  ++r +++
  gi|474934270|ref|YP_007687852.1| 25 TTELAQFMNVSPASVSEMLKILSKDGLVEyAKYRgVKL 62
                                      579**************************634333665 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   1.5e-07   0.00012      24      54 ..      25      55 ..       9      76 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.5e-07
                                      HHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 24 vgelarrlglsksavsrilkrLvaaGLverr 54
                                       +ela+ +++s+++vs +lk L++ GLve+ 
  gi|474934270|ref|YP_007687852.1| 25 TTELAQFMNVSPASVSEMLKILSKDGLVEYA 55
                                      689*************************975 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.2   1.7e-07   0.00013       6      77 ..       6      77 ..       1      79 [. 0.92

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.7e-07
                           DUF2250  6 edelalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlervegktikrteaklKkksevhkhH 77
                                      +++  l++lk  +   v     +a+ ++++   v+e+lk L + GL+e+ + + +k tea l ++  ++k+H
  gi|474934270|ref|YP_007687852.1|  6 REDYLLAILKLTEDGTVAKTTELAQFMNVSPASVSEMLKILSKDGLVEYAKYRGVKLTEAGLTEARLTRKRH 77
                                      5566799999999999*9999************************************************988 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0     1e-06   0.00082      13      68 .]      15      66 ..       4      66 .. 0.81
   2 ?    0.1   0.0       1.5   1.2e+03      39      58 ..     169     181 ..     167     187 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1e-06
                            HTH_27 13 r.hrrrrkkl.adlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      +  +++++++ ++l++++nv+ +++s++lk L + GLv      +  +++ v+lT++G
  gi|474934270|ref|YP_007687852.1| 15 KlTEDGTVAKtTELAQFMNVSPASVSEMLKILSKDGLV------EYAKYRGVKLTEAG 66
                                      33357777888***************************......55588899999998 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.5
                            HTH_27  39 lkkLtekGLvertgdeadrr 58 
                                       +kkL  +G+v       ++r
  gi|474934270|ref|YP_007687852.1| 169 VKKLLTMGFV-------PGR 181
                                       89*******9.......344 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   5.5e-07   0.00043       7      47 .]      13      54 ..      11      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 5.5e-07
                                      HHHHHTTSS.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5  7 ILklLaege.lcvcelaeelglsqstvShHLkkLreaGLVek 47
                                      ILkl ++g  ++ +ela  +++s++ vS+ Lk+L + GLVe+
  gi|474934270|ref|YP_007687852.1| 13 ILKLTEDGTvAKTTELAQFMNVSPASVSEMLKILSKDGLVEY 54
                                      6777777666899***************************96 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.1   4.4e-07   0.00034      13      57 ..      10      54 ..       1      68 [. 0.88

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 4.4e-07
                                      HHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              Rrf2 13 allyLakeeeeepvsseeiaerqnispsylekilakLrkaglvks 57
                                      +l++L++ e+++ ++++e+a+ +n+sp  ++ +l+ L+k glv+ 
  gi|474934270|ref|YP_007687852.1| 10 LLAILKLTEDGTVAKTTELAQFMNVSPASVSEMLKILSKDGLVEY 54
                                      5778899999999******************************85 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.2e-06   0.00097      12      48 .]      17      53 ..       6      53 .. 0.82
   2 ?   -1.2   0.0         2   1.5e+03      36      47 ..     167     178 ..     166     178 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.2e-06
                            HTH_24 12 Lqknpr.isqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                       + ++     +eLA+  ++Sp+ v++ lk L ++Gl++
  gi|474934270|ref|YP_007687852.1| 17 TE-DGTvAKTTELAQFMNVSPASVSEMLKILSKDGLVE 53
                                      33.44447889*************************96 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2
                            HTH_24  36 rrlkrLeeeGlI 47 
                                       +++k+L  +G++
  gi|474934270|ref|YP_007687852.1| 167 AQVKKLLTMGFV 178
                                       689******987 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   3.5e-06    0.0027      28      62 ..      26      60 ..      14      62 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.5e-06
                                      HHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTCEE CS
                              GntR 28 reLaaefgVsrttvReALrrLeaeglverrqgrGt 62
                                       eLa+ ++Vs  +v e L+ L+ +glve  + rG+
  gi|474934270|ref|YP_007687852.1| 26 TELAQFMNVSPASVSEMLKILSKDGLVEYAKYRGV 60
                                      69**************************9999887 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.1   2.2e-05     0.017       9      69 ..      11      73 ..       6      81 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.2e-05
                            HTH_45  9 adILeaisege.akkTkimykanLsykllnkYLdmLvekglikk.skekYvlTekGlellekl 69
                                      ++IL+ +++g  ak T++    n s   ++++L++L + gl++  +    +lTe Gl   +  
  gi|474934270|ref|YP_007687852.1| 11 LAILKLTEDGTvAKTTELAQFMNVSPASVSEMLKILSKDGLVEYaKYRGVKLTEAGLTEARLT 73
                                      68999999655278889*************************885667789999998765555 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   9.8e-05     0.076      23      56 ..      23      56 ..      10      72 .. 0.89
   2 ?   -1.2   0.0       2.5   1.9e+03      43      52 ..     169     178 ..     167     183 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.8e-05
                                      CHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB 23 atadeiaeelgvprskvYevLrsLedkGlVerek 56
                                      a+++e+a+  +v+ ++v e+L+ L++ GlVe  k
  gi|474934270|ref|YP_007687852.1| 23 AKTTELAQFMNVSPASVSEMLKILSKDGLVEYAK 56
                                      7899**************************9765 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.5
                                       HHHHHHCTSE CS
                              TrmB  43 LrsLedkGlV 52 
                                       +++L+ +G+V
  gi|474934270|ref|YP_007687852.1| 169 VKKLLTMGFV 178
                                       789******9 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   5.3e-05     0.041      34      65 ..      38      69 ..      13      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.3e-05
                            HTH_12 34 avRyrLrkleergltrrvgyagreltEkGlee 65
                                      +v   L++l ++gl++   y g +ltE Gl+e
  gi|474934270|ref|YP_007687852.1| 38 SVSEMLKILSKDGLVEYAKYRGVKLTEAGLTE 69
                                      566679***********************997 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   5.1e-05      0.04      20      84 ..       7      68 ..       4      82 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.1e-05
                           DUF4423 20 sWyypvirellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqtekslt 84
                                      + y ++i++l +  ++ a++ ela+ ++  +s + v++ l++L k gl++  +   ++ te+ lt
  gi|474934270|ref|YP_007687852.1|  7 EDYLLAILKLTEDGTV-AKTTELAQFMN--VSPASVSEMLKILSKDGLVEYAKYRGVKLTEAGLT 68
                                      6799999999999999.***********..********************999988988888887 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00018      0.14      18      43 ..      20      45 ..       8      52 .. 0.87
   2 ?   -1.9   0.0       4.8   3.7e+03      50      72 ..      90     112 ..      87     117 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00018
                                      SSXXXHHHHHHHHTXXHHHHHHHHHH CS
                        Sigma70_r3 18 grePtpeEiAeeLglseekVrevlea 43
                                      g  ++++E+A+++++s++ V e+l++
  gi|474934270|ref|YP_007687852.1| 20 GTVAKTTELAQFMNVSPASVSEMLKI 45
                                      567899******************96 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.8
                                       TTXBSSSSTTXBSTTTXBXSSSX CS
                        Sigma70_r3  50 ldlpvgeeedtelgdlleddeae 72 
                                       +d+++ +ee ++++  + d+ a+
  gi|474934270|ref|YP_007687852.1|  90 MDHEAAHEEASRIEHSISDEAAV 112
                                       57778888888888888888655 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00018      0.14      15      56 ..      13      54 ..      10      58 .. 0.83
   2 ?   -1.5   0.1       3.4   2.6e+03      47      57 ..      61      71 ..      60      75 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00018
                                      HHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20 15 ilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                      il++  ++  +  +ela+ + +s++++s  L++L++ gLve 
  gi|474934270|ref|YP_007687852.1| 13 ILKLTEDGTVAKTTELAQFMNVSPASVSEMLKILSKDGLVEY 54
                                      55555556666679**************************96 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.4
                                      HHHHCTTEEEE CS
                            HTH_20 47 vLeeagLvevv 57
                                      +L eagL e +
  gi|474934270|ref|YP_007687852.1| 61 KLTEAGLTEAR 71
                                      79999998765 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00026      0.21      26      71 ..      24      67 ..      10      72 .. 0.89
   2 ?   -1.9   0.0       5.3   4.1e+03      18      43 ..      73      97 ..      67     106 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00026
                            Rio2_N 26 ptelieeisrlkeeevkkrlsrllkaklisrktakydGYkLtyeGy 71
                                       t++++++ +++  +v++ l+ l k +l+++   ky G kLt +G+
  gi|474934270|ref|YP_007687852.1| 24 KTTELAQFMNVSPASVSEMLKILSKDGLVEYA--KYRGVKLTEAGL 67
                                      56789999999*******************97..7*******9985 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.3
                            Rio2_N 18 gmrnhevVptelieeisrlkeeevkk 43
                                      + ++h vV + li  +  +++e  ++
  gi|474934270|ref|YP_007687852.1| 73 TRKRHHVVERFLID-VLDMDHEAAHE 97
                                      56777777655553.44555555555 PP

>> Glu_syn_central  Glutamate synthase central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00012     0.095     228     275 ..      15      65 ..       8      68 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                                       HHHTTTS-...----HH...HHHHHHHHHHHHHHHHHTT--BHHHHHHS--EEE CS
                   Glu_syn_central 228 klveegal...aeeele...knyrkavekGllKimskmGistlqSYkgaqifea 275
                                       kl+e+g++   +e        n+  a  + +lKi+sk G+ + + Y+g ++ ea
  gi|474934270|ref|YP_007687852.1|  15 KLTEDGTVaktTE---LaqfMNVSPASVSEMLKILSKDGLVEYAKYRGVKLTEA 65 
                                       6677776632223...234599999*************************9998 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00015      0.12       6      45 ..      11      51 ..       6      61 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00015
                            HTH_11  6 lelLl.eargp.isgeeLAeeLnvSrrtvrrdIkaLeelgvp 45
                                      l +L+  ++g+     eLA+ +nvS + v   +k+L++ g  
  gi|474934270|ref|YP_007687852.1| 11 LAILKlTEDGTvAKTTELAQFMNVSPASVSEMLKILSKDG-L 51
                                      4554303445568899**********************99.3 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00025       0.2      19      50 ..      23      54 ..      10      56 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00025
                                      -BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 19 ltlselArrtglpkStvhRlLqtLvelGyveq 50
                                       + +elA+   +++++v+ +L+ L + G+ve+
  gi|474934270|ref|YP_007687852.1| 23 AKTTELAQFMNVSPASVSEMLKILSKDGLVEY 54
                                      489***************************96 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00034      0.26      28      59 ..      25      55 ..       5      59 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00034
                                      HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE-G CS
                     LexA_DNA_bind 28 ireiaralglkSpsaveehLkaLerKGyierd 59
                                        e+a+ ++++ p++v e Lk L++ G++e  
  gi|474934270|ref|YP_007687852.1| 25 TTELAQFMNVS-PASVSEMLKILSKDGLVEYA 55
                                      57999999986.*****************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1450.73
//
Query:       gi|474934271|ref|YP_007687853.1|  [L=280]
Description: Protein of unknown function (DUF1638) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      8e-25   87.8   0.0    2.9e-24   86.0   0.0    1.7  1  DUF1638   Protein of unknown function (DUF1638)


Domain annotation for each model (and alignments):
>> DUF1638  Protein of unknown function (DUF1638)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.0   0.0   1.6e-28   2.9e-24       4     150 ..      81     256 ..      78     265 .. 0.83

  Alignments for each domain:
  == domain 1  score: 86.0 bits;  conditional E-value: 1.6e-28
                           DUF1638   4 aglHnrpeeLrealqeeidrakadydqIllgYGlCggalagl.....rsdecpveilkg......ddCislllgsee 69 
                                        glH++p+ Lre+++e+++r+++ +d I l YGlCg+   ++     +    p e+ ++      ddCi++++g+ +
  gi|474934271|ref|YP_007687853.1|  81 LGLHADPKALREKVEEQVRRISPRVDSIALYYGLCGNFGWDMtqwarDNGLKPTEMFRDsagricDDCIGAAIGGGA 157
                                       59*********************************998888888887777789999999****************** PP

                           DUF1638  70 ayaeelkdekgtffltpgwvkewdrlv.....leky.g.eelarmifgk...........llkgYkrlvyidtgltd 128
                                       +y e +k++ g+f++ p ++ +w++++     ++   + +++ ++ ++             ++gY+++v++dtgl d
  gi|474934271|ref|YP_007687853.1| 158 RYLELQKTYFGMFYVIPAIAHNWKDFLddgsaTDAArNlPDDLKDELDIhsdedyirwmfRTCGYTNMVKMDTGLAD 234
                                       ********************888888766443222222333333333337777777777777*************** PP

                           DUF1638 129 dpeleeraeefaarlglelevi 150
                                       ++ +e+++e++++r++l+ + i
  gi|474934271|ref|YP_007687853.1| 235 KELFEKEFEALCERMELKPITI 256
                                       ****************997765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1654.32
//
Query:       gi|474934272|ref|YP_007687854.1|  [L=427]
Description: serine hydroxymethyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-70  237.5   0.0    2.2e-70  237.3   0.0    1.0  1  SHMT             Serine hydroxymethyltransferase
    1.5e-05   24.3   0.0    0.00016   21.0   0.0    2.0  1  Aminotran_1_2    Aminotransferase class I and II
    2.8e-05   23.5   0.0      0.037   13.3   0.0    2.4  2  Beta_elim_lyase  Beta-eliminating lyase
     0.0056   15.7   0.0     0.0084   15.1   0.0    1.3  1  SelA             L-seryl-tRNA selenium transferase
  ------ inclusion threshold ------
       0.12   12.7   0.0       0.53   10.6   0.0    1.9  2  DDE_Tnp_IS1      IS1 transposase


Domain annotation for each model (and alignments):
>> SHMT  Serine hydroxymethyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.3   0.0     6e-74   2.2e-70      16     399 .]      17     382 ..       1     382 [. 0.93

  Alignments for each domain:
  == domain 1  score: 237.3 bits;  conditional E-value: 6e-74
                                       HHHHHHSEE-STT-----HHHHHHHTSGGGG----EETTEESSST-HHHHHHHHHHHHHHHHHCT-STTTEEEE--- CS
                              SHMT  16 kerqkeeieliasenftskavlealGsvltnkyaeGyPGkryyGGcefvdeveelaqdrakelfkldpakwgvnvqp 92 
                                       ++  ++ i +iasen++s+ + e+l s + ++yaeG+PGkryy G+ +vd+ve+ a + ak++f++d    +++v+p
  gi|474934272|ref|YP_007687854.1|  17 NKWFEDCIPMIASENLMSPLAKEMLISDFADRYAEGLPGKRYYQGNIYVDKVETRAVELAKKVFNCD----FADVRP 89 
                                       455567799**********************************************************....****** PP

                                       SSHHHHHHHHHHHHT-TT-EEEEESCTTTSTGGGT-BTSS-B-SHHHHHSEEEEE-B-TTTSSB-HHHHHHHHHHH- CS
                              SHMT  93 lsGsqanlavytallepgdrilgldladGGhlthGakveskkisassklfesveykvdketglidydelekkakefk 169
                                        sG+ an++v  a+ +pgd+i    l +G h++      +          +sv+y  + e+  +d+d   k  k++k
  gi|474934272|ref|YP_007687854.1|  90 ISGTVANMSVLFAFAQPGDTITCSALDQGAHISTCEFGAF-----GQRGVKSVNYPWRIEDMNLDIDGTAKLIKQVK 161
                                       ********************************98766666.....455678888888888***************** PP

                                       -SEEEEE-SST-S---HHHHHHHHHHTT-EEEEE-GGGHHHHHTTSS--GCCT.SSEEEEESSSTT-S-S-EEEEEC CS
                              SHMT 170 PklivaGtsaysrlidyarlreiadevgayllvdmahiaGlvaagvipsPfey.advvtttthktlrGprgglillr 245
                                       Pk+   G s +      + l +  +evg  +  d ah+ Gl+a+g +  Pfe   ++v++ thkt+ Gp  g++l +
  gi|474934272|ref|YP_007687854.1| 162 PKVAQFGLSVFLFPPPIKELEDTFNEVGCLVWEDCAHVLGLIAGGQFQKPFEDgVNLVSASTHKTFPGPNHGIVLGN 238
                                       ***************************************************97369*******************99 PP

                                       -SEEEEETTTEEEEHHHHHHHHHHHTTTT-SS--HHHHHHHHHHHHHCTSHHHHHHHHHHHHHHHHHHHHHHHTT-E CS
                              SHMT 246 kgvksvdktgkevleelekkinsavfPglqGGPlnhviaakavalkealepefkvyqkqvlknakalaealkekgyk 322
                                                  + +ee  kk+++a+fPg+    + h++aa+a++l e ++   k+y+ q  kna+al +al e+g+ 
  gi|474934272|ref|YP_007687854.1| 239 -----------NLTEEQVKKMQHAIFPGVTSSHHLHAMAALAITLAE-MDVFGKEYAAQACKNARALGQALYERGIP 303
                                       ...........7889999***************************87.55666************************ PP

                                       EGGGS...-SSSEEEEEGGGGTS-HHHHHHHHHHTTEE-EEE--TTSSTTTT-SEEEEESHHHHHTT--HHHHHHHH CS
                              SHMT 323 lvsgG...tdnhlvlvdlrekgldGkraekvlekvnitankntvPgdksalvtsGlrlGtpaltsrgfkeedlekva 396
                                       ++ +    t +h + +d+++ g +Gk++ k le +ni +nkn +P+d s++ +sGlrlG   +t+ g+ke+++  va
  gi|474934272|ref|YP_007687854.1| 304 VLCENlgfTRSHAIALDVTQFG-KGKQCAKDLEDANIICNKNMLPTDTSSVNPSGLRLGVQEMTRLGMKEKEMVDVA 379
                                       *986333499********9887.8***************************************************** PP

                                       HHH CS
                              SHMT 397 kfi 399
                                       +fi
  gi|474934272|ref|YP_007687854.1| 380 EFI 382
                                       997 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   4.5e-08   0.00016      64     307 ..      81     312 ..      55     372 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 4.5e-08
                                       HTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHH.....HTTSEEEEEEBEETTTTEE-HHHH CS
                     Aminotran_1_2  64 klkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilr.....lsggevvryplyseedfhldleal 135
                                       + +    v  +sG+ a+ ++l+++++  pgd i  +++  + ++  ++      +g++ v yp +  ed++ld+++ 
  gi|474934272|ref|YP_007687854.1|  81 NCDFA-DVRPISGTVANMSVLFAFAQ--PGDTITCSALDQGAHISTCEfgafgQRGVKSVNYP-WRIEDMNLDIDGT 153
                                       44444.67788**************9..****************9887332224677777777.447********** PP

                                       HHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTT CS
                     Aminotran_1_2 136 eealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepn 212
                                        +++k+ +++ +      +        + + ++ +++l d+ ++ ++l+  D a+  +     ++      +e+++n
  gi|474934272|ref|YP_007687854.1| 154 AKLIKQVKPKVA-----QF-----GLSVFLFPPPIKELEDTFNEVGCLVWEDCAHVLGLIAGGQF---QKPFEDGVN 217
                                       *****9655554.....22.....23344555556666666***************999997777...558899999 PP

                                       EEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTS...SHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHH CS
                     Aminotran_1_2 213 llivgslsKafGlaGeRvGyilgnaavvsqlrklsrpfls...ssllqaavaaalsdallkqs.eleemrqrlqkrr 285
                                        l+  s  K f  ++   G++lgn    +q++k++ ++     ss+  +a aa + +  ++ + + +e +++  k++
  gi|474934272|ref|YP_007687854.1| 218 -LVSASTHKTFPGPN--HGIVLGNNLTEEQVKKMQHAIFPgvtSSHHLHAMAALAITLAEM-DvFGKEYAAQACKNA 290
                                       .88888888886666..9*******999999998887555775565555555555555544.45************* PP

                                       HHHHHHHHHSTEEEECCSCSSE CS
                     Aminotran_1_2 286 kelrdeLaelglkvlasqsgmf 307
                                       + l ++L e g++vl ++ g+ 
  gi|474934272|ref|YP_007687854.1| 291 RALGQALYERGIPVLCENLGFT 312
                                       ************9998887765 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0     1e-05     0.037      24     122 ..      55     161 ..      43     167 .. 0.72
   2 !    8.0   0.0   0.00043       1.6     189     242 ..     216     335 ..     189     404 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1e-05
                                       --CCCT--HHHHHHHHHHHHHTT-SEEEE........ES-HHHHHHHHHHHH--TTEEEEEETT...-HHHHSSTTH CS
                   Beta_elim_lyase  24 GdesYgedktvnrLedavaelfgkeaalf........vpqGtaAnsillkillqrgeevivtep...ahihfdetga 89 
                                       G   Y+++  v ++e ++ el+ k   +f          +Gt An   l +++q+g+ + ++     ahi + e ga
  gi|474934272|ref|YP_007687854.1|  55 GKRYYQGNIYVDKVETRAVELAKK---VFncdfadvrPISGTVANMSVLFAFAQPGDTITCSALdqgAHISTCEFGA 128
                                       555666666666666666554432...222223443367**********************987888********** PP

                                       HHHCC--EEEEE-..EBTTTBE-HHHHHHHS--S- CS
                   Beta_elim_lyase  90 iaelagvklrdlk..nkeaGkmdlekleaaikevg 122
                                         +  gvk ++ +  +++  ++d++  +++ik+v+
  gi|474934272|ref|YP_007687854.1| 129 FGQR-GVKSVNYPwrIED-MNLDIDGTAKLIKQVK 161
                                       *997.4444444421444.9999999999999854 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00043
                                       SSEEEEESSSTT--SS-EEEEE-HH.........................................HHHHHHHHHHH CS
                   Beta_elim_lyase 189 vDsvtmslkKdllanvGgvlafrddel.....................................edylaerveqrky 228
                                       v  v++s  K    +  g++++++  +                                     ++y a++++ +++
  gi|474934272|ref|YP_007687854.1| 216 VNLVSASTHKTFPGPNHGIVLGNNLTEeqvkkmqhaifpgvtsshhlhamaalaitlaemdvfgKEYAAQACKNARA 292
                                       556677777777777777888777755778888888888888888888888888888888999999*********** PP

                                       HT---SSTHHHHH.............................. CS
                   Beta_elim_lyase 229 lggglrqagvlaa.............................l 242
                                       lg+ l++ g+++                              +
  gi|474934272|ref|YP_007687854.1| 293 LGQALYERGIPVLcenlgftrshaialdvtqfgkgkqcakdlE 335
                                       **********998666665555555555544444444444440 PP

>> SelA  L-seryl-tRNA selenium transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.3e-06    0.0084     188     237 ..     200     249 ..     165     292 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.3e-06
                                       GT-----BHHHHHHTT-SEEEEETTSTT-SSS-EEEEE-HHHHHHHHHST CS
                              SelA 188 yglskePtvqealaeGvdlvsfsGDkllGgpqaGiivGkkelieklkknp 237
                                        gl    ++q+ +++Gv+lvs s  k + gp  Gi++G+    e++kk +
  gi|474934272|ref|YP_007687854.1| 200 LGLIAGGQFQKPFEDGVNLVSASTHKTFPGPNHGIVLGNNLTEEQVKKMQ 249
                                       4777788999****************************987766666644 PP

>> DDE_Tnp_IS1  IS1 transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00015      0.53      52     100 ..      31      79 ..       9      84 .. 0.89
   2 ?   -1.4   0.0      0.76   2.7e+03      77      98 ..     131     152 ..      96     175 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00015
                       DDE_Tnp_IS1  52 allspfdvviltsddwglyerelkkdkhliskiytqriernnltlrtrl 100
                                        l+sp+   +l+sd    y + l+++++  + iy +++e + ++l +++
  gi|474934272|ref|YP_007687854.1|  31 NLMSPLAKEMLISDFADRYAEGLPGKRYYQGNIYVDKVETRAVELAKKV 79 
                                       5899************************************999998876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.76
                       DDE_Tnp_IS1  77 dkhliskiytqriernnltlrt 98 
                                       ++ + s  y  rie  nl++  
  gi|474934272|ref|YP_007687854.1| 131 QRGVKSVNYPWRIEDMNLDIDG 152
                                       5567788899999999998753 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 2720.42
//
Query:       gi|474934273|ref|YP_007687855.1|  [L=174]
Description: Protein of unknown function (DUF998) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-11   44.5  14.6    1.6e-10   40.9  14.6    1.9  1  DUF998    Protein of unknown function (DUF998)


Domain annotation for each model (and alignments):
>> DUF998  Protein of unknown function (DUF998)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9  14.6   8.8e-15   1.6e-10       3     184 ..       6     168 ..       4     169 .. 0.85

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 8.8e-15
                            DUF998   3 aallalavilaaallrpgydplrhaiSeLgaeg.gpggwlfnaglvllgllvlalavgllraargragragrlllav 78 
                                       a++++ ++++++a  + ++ + ++ +S  g  +    + lfn+g+v +g++ + +++g+++  + +++++ +++  +
  gi|474934273|ref|YP_007687855.1|   6 APIVFSVLWVLSATIDGDWTFGEDSLSRMGISEnRIAAALFNGGCVFVGAMGFIVGIGIMS-GKDPLSKPEGIAYSA 81 
                                       78899999***********************7777788899******************99.*************** PP

                            DUF998  79 aglglvlagvfptdpgggspslsglvHglasavaflalavavlllasaarrrawallrlvggvallllvaalvwlla 155
                                       + ++l+l+gvfp+d g         +H+ +++++++ +++a+ll++      a  ++++      ++ +a++v +la
  gi|474934273|ref|YP_007687855.1|  82 GMVFLMLVGVFPMDLGT--------IHNTVATTFGVFVFIAILLAS------AVDYRNRDHPEIDVIVLAFTVIMLA 144
                                       **************996........*********************......4444444444444444455555555 PP

                            DUF998 156 aaldgslllGlaerllvlaitawllalal 184
                                       +     +++ ++e llv+a ++w ++l+l
  gi|474934273|ref|YP_007687855.1| 145 T-----QRFEVWEPLLVIATMVWTAVLGL 168
                                       5.....67778999999999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1210.08
//
Query:       gi|474934274|ref|YP_007687856.1|  [L=140]
Description: hypothetical protein TALC_00699 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.6   0.0       0.23   11.6   0.0    1.5  1  AbiEi_4   Transcriptional regulator, AbiEi antitoxin


Domain annotation for each model (and alignments):
>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   1.3e-05      0.23      20      45 ..      42      71 ..      29      73 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.3e-05
                           AbiEi_4 20 eaaGispsa....lrrLvrkGwLvrlrrGv 45
                                      e++ +++s+    l rLv+ G+ +r+ rG+
  gi|474934274|ref|YP_007687856.1| 42 EESSKDYSNpsckLGRLVKDGKYHRIIRGL 71
                                      45778888888999***************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 851.21
//
Query:       gi|474934275|ref|YP_007687857.1|  [L=100]
Description: hypothetical protein TALC_00700 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.21s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 835.54
//
Query:       gi|474934276|ref|YP_007687858.1|  [L=237]
Description: 3,4-dihydroxy-2-butanone 4-phosphate synthase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.8e-57  192.1   0.0    7.9e-57  191.9   0.0    1.0  1  DHBP_synthase  3,4-dihydroxy-2-butanone 4-phosphate synthase


Domain annotation for each model (and alignments):
>> DHBP_synthase  3,4-dihydroxy-2-butanone 4-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.9   0.0   4.4e-61   7.9e-57       1     191 [.       4     223 ..       4     224 .. 0.95

  Alignments for each domain:
  == domain 1  score: 191.9 bits;  conditional E-value: 4.4e-61
                                       HHHHHHHHTT--EEEESSTTTT-BEEEEEEGGG--HHHHHHHHHHB-S--EEEEEHHHHHHTT--BSSSS-S..... CS
                     DHBP_synthase   1 eeaiealkaGkfvivvDdedrenegdLiiaAekvtpekvafmirhasGlicvalteeradeLeLplmveene..... 72 
                                       +ea+ea+++Gk+++++D +dre+e d+  a+e+vt e+v+ m+++a+Gl+c++++ ++a++++Lp+++  +      
  gi|474934276|ref|YP_007687858.1|   4 QEALEAIRNGKVILIYDFDDREKESDMTAASEFVTYETVRQMRKDAGGLLCTTTPYRVAKAVGLPYLS--DVfwdar 78 
                                       68*****************************************************************9..4456667 PP

                                       ................STT---BB--EEESST-SSS-SHHHHHHHHHHHH-T...........T--GGGEEEEEEEE CS
                     DHBP_synthase  73 ................dkhktaftvsvdaaegttTGIsaaDRalTirkladp...........kakpedfrrPGhvf 122
                                                       d+ k++f v+++++ +t TGI ++DRalTi+++a++           k   +dfr+PGhv+
  gi|474934276|ref|YP_007687858.1|  79 ekypvlglmaptdipyDNTKSSFGVTINHR-ETYTGIPDRDRALTISEFAKTifqdkpageiaKDLGRDFRAPGHVH 154
                                       889*************99************.9*******************88889999998755669********* PP

                                       EEEE-TTGGGTS-SHHHHHHHHHHHTTS-SBEEEEEBB-TTSCB-BHHHHHHHHHHHT-EEEEHHHHHH CS
                     DHBP_synthase 123 plrareggvleRrghTEaavdLarlaglkpaavicellnddgtmarrdeleefakkhglkiitiedlie 191
                                       +l ++e+ + +R+ghTE+a +++ +ag+kp a+ice++ ddg++ r+++++e+++k+g++++t++++i+
  gi|474934276|ref|YP_007687858.1| 155 LLTSSEHILSNRHGHTELASAMMYMAGVKPSATICEMMGDDGNSERKENCIEYSEKNGIPFVTGDEVIA 223
                                       ******************************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1543.03
//
Query:       gi|474934277|ref|YP_007687859.1|  [L=140]
Description: cytidyltransferase-related domain protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-17   64.3   0.0    1.4e-17   64.2   0.0    1.1  1  CTP_transf_like  Cytidylyltransferase-like
  ------ inclusion threshold ------
      0.041   13.8   0.2       0.41   10.5   0.2    2.3  1  FAD_syn          FAD synthetase


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.2   0.0   1.5e-21   1.4e-17       1     103 [.       2      99 ..       2     135 .. 0.87

  Alignments for each domain:
  == domain 1  score: 64.2 bits;  conditional E-value: 1.5e-21
                                       EEEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-.SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHH CS
                   CTP_transf_like   1 lagGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkk.kplasaeeRlemlelakevdevisvdpweltrev 76 
                                       +a G+FD+iH GH+ +l+qak+ ++e liv ++sd+++++kk +p+++ + R + +e +k vd++i+  +  +  ++
  gi|474934277|ref|YP_007687859.1|   2 IASGVFDIIHPGHISYLQQAKSFGDE-LIVVIASDNTVRRKKhEPITPDYMRARIVENLKPVDRAIVGHDSGSIFDI 77 
                                       578***********************.**************88********************************** PP

                                       HHHTTTTEEEEEEEHHHHHHHHCHHHH CS
                   CTP_transf_like  77 lkklkpdklylvigadvledfsewkel 103
                                       +++++pd  ++v+g d+  d   + el
  gi|474934277|ref|YP_007687859.1|  78 VREIRPD--VIVLGFDQNFD---DAEL 99 
                                       *******..****9886444...3344 PP

>> FAD_syn  FAD synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2   4.5e-05      0.41      10      36 ..       2      28 ..       1     127 [. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 4.5e-05
                           FAD_syn 10 vtlGnFDGvHlGHqallkkaveaakek 36
                                      ++ G FD +H GH + l++a++  +e 
  gi|474934277|ref|YP_007687859.1|  2 IASGVFDIIHPGHISYLQQAKSFGDEL 28
                                      677*****************9988654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1019.87
//
Query:       gi|474934278|ref|YP_007687860.1|  [L=155]
Description: riboflavin synthase alpha chain [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-14   54.3   0.0    1.6e-14   53.9   0.0    1.1  1  DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase


Domain annotation for each model (and alignments):
>> DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   0.0     9e-19   1.6e-14       8     137 ..       8     129 ..       2     132 .. 0.83

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 9e-19
                                       EESTTHHHHHHHHHHHHHHHHHCTTSSCCEEEEEESSCCCHHHHHHHHCTSTT-.SEEEEEEEEE--SSCHHHHHHH CS
                     DMRL_synthase   8 varfneeitdkllegaldelkeagvaeenidvvtVPGafElplaakklaesskyldavialGvvirGetphfeyvae 84 
                                        ++f      ++ ++a+del++ g    ++ +vtVPG  +lp+a+kkl+e+ +++d v+alG  + G  ++++++a+
  gi|474934278|ref|YP_007687860.1|   8 DTTF---ARYDMGKAAMDELERTGTG-FRFIRVTVPGMKDLPVACKKLIEE-QHCDIVMALG--MPGPMQKDKMCAH 77 
                                       5555...677899***********75.89*********************5.446*******..9************ PP

                                       HHHHHHHHHHHHCTS-EEEEEEEESSHHCCHHCCTSTCCCHHHHHHHHHHHHH CS
                     DMRL_synthase  85 avskglmrvsldtgvPvifgvltvdteeqaleraggkagnkGeeaaeaalema 137
                                       ++s gl ++ l t++ +i   +  d+ ++ +e a   a  +++e+a ++ +m+
  gi|474934278|ref|YP_007687860.1|  78 EASMGLQHAMLMTNTHIIEVFVHEDEAKDDKELA-WLADRRAREHAVNVYDML 129
                                       **************88777666655555555555.335899999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 1070.58
//
Query:       gi|474934279|ref|YP_007687861.1|  [L=145]
Description: 6,7-dimethyl-8-ribityllumazine synthase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-34  119.0   0.3    1.5e-34  118.9   0.3    1.0  1  DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase


Domain annotation for each model (and alignments):
>> DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.9   0.3   8.2e-39   1.5e-34       2     139 ..      11     141 ..      10     143 .. 0.96

  Alignments for each domain:
  == domain 1  score: 118.9 bits;  conditional E-value: 8.2e-39
                                       EEEEEEEESTTHHHHHHHHHHHHHHHHHCTTSSCCEEEEEESSCCCHHHHHHHHCTSTT-.SEEEEEEEEE--SSCH CS
                     DMRL_synthase   2 lriaiVvarfneeitdkllegaldelkeagvaeenidvvtVPGafElplaakklaesskyldavialGvvirGetph 78 
                                        +i+ V a+fn e+t  ++e+a++e++ +gv+   +++++VPG+f++pla+kkl+e +  +davi+lG+vi G+t+h
  gi|474934279|ref|YP_007687861.1|  11 YKIGAVLAEFNYEVTMLMMERAKAEAEFLGVE--ITKTIKVPGVFDMPLAIKKLLECK-DIDAVITLGAVITGATKH 84 
                                       5899**************************96..9*********************64.47**************** PP

                                       HHHHHHHHHHHHHHHHHHCTS-EEEEEEEES.SHHCCHHCCTSTCCCHHHHHHHHHHHHHHH CS
                     DMRL_synthase  79 feyvaeavskglmrvsldtgvPvifgvltvd.teeqaleraggkagnkGeeaaeaalemanl 139
                                       +e++++++s+++m+++l++++Pv+fgv  +  te +a +r+     +kG++a+++++++++ 
  gi|474934279|ref|YP_007687861.1|  85 DEVIMAQASRQIMDLALSYDKPVAFGVNGPGmTELEAVDRI-----EKGRDAVDSVVKLLQR 141
                                       *******************************9*********.....9***********9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 912.32
//
Query:       gi|474934280|ref|YP_007687862.1|  [L=212]
Description: Formate/nitrite family of transporters [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.1e-28   97.5  18.6    1.2e-27   96.8  18.6    1.2  1  Form_Nir_trans  Formate/nitrite transporter


Domain annotation for each model (and alignments):
>> Form_Nir_trans  Formate/nitrite transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.8  18.6   6.8e-32   1.2e-27      18     231 ..       6     197 ..       3     202 .. 0.83

  Alignments for each domain:
  == domain 1  score: 96.8 bits;  conditional E-value: 6.8e-32
                                       HHHHHHHHHHHHHHHHHHHHHHHHHCCCHCCTTCHHHHHHHHHCCCHHHHHHHHHT---CCCCCCHHHHHHCTTSSS CS
                    Form_Nir_trans  18 ldklfllgilAGafigfgvllalvvaaalaesnpglakllgglvFpvGlilvvllgaeLfTgntllltlavlkkkvs 94 
                                       + k++l++ilAG+ ig+g+++ + + ++    +    + +g+++F++Gl+ v+ +g +L+Tg++      +++   +
  gi|474934280|ref|YP_007687862.1|   6 YSKCLLRAILAGMAIGMGGCVFMALVNT----D---YRWVGAVLFSIGLFAVFTFGFDLYTGKVG----YAVE---N 68 
                                       6799**************9998888775....2...5789************************9....2333...3 PP

                                       CHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTGGHHHHHHHHHCCC..SS-HHHHHHHHHHHHHHHHHHHHHHCC-SS CS
                    Form_Nir_trans  95 lkkllknwlvvllgNliGsllvalllvvlsgllaekllsiaeakl..slsfleaflrGilCNwlVclavwlalaakd 169
                                         +++  ++v++lgN++G+l+   +++    +  + ++si++a+l  + +f+++f++G++C++l+ +a     + k 
  gi|474934280|ref|YP_007687862.1|  69 PPSYIVDLVVIILGNFVGALITG-YMIP---MSDASVVSIVDARLtdDIDFFRVFCKGVFCGILMFIAADYYKTRK- 140
                                       678999999*************8.4443...446899*******9444569************9877766555555. PP

                                       HHHHHHHHHHHHHHHHHCT---HHHHHHHHHHHHHHSHHHHHHHCHHHHHHHHHHHHHCCHH CS
                    Form_Nir_trans 170 vigkilaiflpifafvasgfeHsvanmfliplgllltvadfilknlipvtlGNivGGallvg 231
                                          + la+f+++ +f+++gfeHs+a+mf++  +  + + d++   +++v+lGN vGG+l++ 
  gi|474934280|ref|YP_007687862.1| 141 ---QYLATFICVPVFILAGFEHSIADMFYFCSAQAF-TFDAL-LFILVVILGNAVGGILIPL 197
                                       ...599**********************99999988.34443.46799*********99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       922  (0.0514251); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1259.25
//
Query:       gi|474934281|ref|YP_007687863.1|  [L=427]
Description: Nucleotidyltransferase/DNA polymerase involved in DNA repair [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.7e-45  152.6   0.0    1.9e-44  151.3   0.0    1.7  2  IMS              impB/mucB/samB family
    3.5e-14   53.5   0.2    6.7e-14   52.6   0.2    1.4  1  IMS_C            impB/mucB/samB family C-terminal domain
  ------ inclusion threshold ------
      0.084   13.2   0.0       0.33   11.3   0.0    2.0  1  DUF1805          Domain of unknown function (DUF1805)
       0.12   13.0   0.0       0.35   11.5   0.0    1.8  1  HHH_5            Helix-hairpin-helix domain
       0.14   12.4   0.0       0.34   11.2   0.0    1.6  1  Cdd1             Pathogenicity locus
       0.16   11.8   0.0        5.8    6.7   0.0    2.8  3  Methyltransf_23  Methyltransferase domain
       0.16   12.4   0.0       0.48   10.9   0.0    1.9  1  IMS_HHH          IMS family HHH motif


Domain annotation for each model (and alignments):
>> IMS  impB/mucB/samB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.3   0.0   7.4e-48   1.9e-44       1     150 []       8     155 ..       8     155 .. 0.98
   2 ?   -3.3   0.0         3   7.8e+03      46      66 ..     392     413 ..     391     421 .. 0.72

  Alignments for each domain:
  == domain 1  score: 151.3 bits;  conditional E-value: 7.4e-48
                                       EEETTHHHHHHHHHT.T-TTS-EEEEET....TEEEEE-HHHHTTT--TTSBHHHHHTTHTT-EEEEEE-HHHHHHH CS
                               IMS   1 iDmdaFyasverardpeLkgkPvvvaqgsekrgiviavsyeArayGvkrgmrikeakklcpdlivvkvdlekyrras 77 
                                       +DmdaFyasve +++p+L+g+P+++++  ++rg+v ++syeAr++Gv++gm+ikea++lcpd ++  +d+ ky+++s
  gi|474934281|ref|YP_007687863.1|   8 VDMDAFYASVEIRDNPSLRGRPLIIGSMPDERGVVSTCSYEAREFGVRSGMNIKEAYRLCPDGVYKHPDFYKYMEVS 84 
                                       7**************************************************************************** PP

                                       HHHHHHHHHH-S..EEEEETTEEEEE-HHHHHHHH-SHHHHHHHHHHHHHHHH---EEEEEESSHHHHHHHHH CS
                               IMS  78 kkileilkrfispkvekasiDEayldltgleelaesegaalakelrkaikeelgltvsiGiasnkllAKlase 150
                                       +k++ei   + +   e++ +D  yld+t+++  +e+  +++a+ ++++ ++e+glt+s+G+a +k +AK+ase
  gi|474934281|ref|YP_007687863.1|  85 RKLHEIWDPY-ASSSEPVALDDTYLDVTETAGTFEKA-REIARLIKERTFKEMGLTCSVGLAYSKAAAKIASE 155
                                       **********.559*********************96.*********************************96 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3
                                       T--TTSBHHHHHTTHT.T-EEE CS
                               IMS  46 Gvkrgmrikeakklcp.dlivv 66 
                                       G+ ++mri+++++  + +++ v
  gi|474934281|ref|YP_007687863.1| 392 GIVEHMRIQSVRRRQSvKVVAV 413
                                       8889999999988765335554 PP

>> IMS_C  impB/mucB/samB family C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   0.2   2.6e-17   6.7e-14       5     115 ..     240     348 ..     237     351 .. 0.85

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 2.6e-17
                             IMS_C   5 rpepksissektfpepydesk.lkkelreLaeelarrLrdkglvartitlklrysdfh.asrsatLprpt.sdtrei 78 
                                       ++e ks+s e tf++++++   +  ++  La ++ +r r++gl +  +++k+ +sd + ++rs+t+  p+  ++ ei
  gi|474934281|ref|YP_007687863.1| 240 PREAKSVSREMTFQKDVSDTRlIADVMLLLAMSVEERARRHGLHGTGVSIKVTFSDMKsITRSRTV--PScETAVEI 314
                                       6899***********4443223555555************************99988889999977..5669999** PP

                             IMS_C  79 leaalkLlrrlidepglpirligvsasnlvekaesqa 115
                                         +a+kLl+ +   +++p+rligv+  nl+ek+  q+
  gi|474934281|ref|YP_007687863.1| 315 HSEAVKLLDGV---KKRPVRLIGVGIFNLSEKRVRQS 348
                                       ********444...78**************9887775 PP

>> DUF1805  Domain of unknown function (DUF1805)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00013      0.33      38      60 ..      42      64 ..      39      66 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00013
                                      -SEE-HHHHHTT--TT-BHHHHG CS
                           DUF1805 38 vesvteaAeelGikeGmtgkeaL 60
                                      v   + +A+e G++ Gm+ kea 
  gi|474934281|ref|YP_007687863.1| 42 VSTCSYEAREFGVRSGMNIKEAY 64
                                      667899***************95 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00014      0.35      10      40 ..     186     218 ..     182     235 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00014
                                       --HHHHHHHHTTT--SHHHHHHS..-HHHHHTS CS
                             HHH_5  10 iGpktAlallsaGiesvedlaaa..dveeLaki 40 
                                       +GpktA +l s  i++v dl +   dve L  +
  gi|474934281|ref|YP_007687863.1| 186 VGPKTAERLNSIDIFTVGDLRERadDVESLLGA 218
                                       9*******************8754478877655 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00013      0.34       8      36 ..     180     208 ..     176     215 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00013
                              Cdd1   8 lqdiPniGkalaedlvelGirsveelkge 36 
                                        + + ++G+++ae l +++i +v +l+++
  gi|474934281|ref|YP_007687863.1| 180 VRVLFSVGPKTAERLNSIDIFTVGDLRER 208
                                       677899********************987 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.28   7.1e+02     125     158 ..      98     130 ..      80     135 .. 0.71
   2 ?    6.7   0.0    0.0023       5.8      97     124 ..     145     172 ..     134     221 .. 0.75
   3 ?    0.1   0.0      0.24   6.2e+02      62     105 ..     342     397 ..     290     399 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.28
                   Methyltransf_23 125 kedrllldwlylvpagrhisffsarslkelleea 158
                                       +e  +l d +yl+  ++ + f  ar++++l +e 
  gi|474934281|ref|YP_007687863.1|  98 SEPVAL-DDTYLDVTETAGTFEKAREIARLIKER 130
                                       444444.455555555*************99986 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0023
                   Methyltransf_23  97 dppellrqiatllkpgGylllseplasl 124
                                       +  ++ + + + +kp+Gy+++++p+++ 
  gi|474934281|ref|YP_007687863.1| 145 YSKAAAKIASEEMKPDGYFEILTPGEYV 172
                                       566788888999************9876 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.24
                   Methyltransf_23  62 kakkaqkdqfdeqeaaepqg............kfdlIvlrevlehvpdppellrqi 105
                                       +++  q++  d  + +e +g            +fd++  ++ +++v++++  + ++
  gi|474934281|ref|YP_007687863.1| 342 EKRVRQSTLDDLGDSEEGNGlreklkrmhsryRFDFVKHMDKIYRVDSLHGIVEHM 397
                                       344455555544455555557777778888889****9999999999999988886 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00019      0.48       5      32 .]     172     199 ..     168     199 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00019
                           IMS_HHH   5 kefLwplpitkipGiGgklgekLeklGi 32 
                                        +++++++++ +  +G+k++e+L++++i
  gi|474934281|ref|YP_007687863.1| 172 VDLISSRDVRVLFSVGPKTAERLNSIDI 199
                                       57899999999*************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 2400.18
//
Query:       gi|474934283|ref|YP_007687865.1|  [L=375]
Description: Small-conductance mechanosensitive channel [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.9e-32  111.9   2.4    2.9e-32  111.9   2.4    1.5  2  MS_channel   Mechanosensitive ion channel
  ------ inclusion threshold ------
      0.041   14.0   2.3          5    7.3   0.0    3.1  3  DUF872       Eukaryotic protein of unknown function (DUF872)
       0.06   12.8   0.8       0.23   10.9   0.0    2.0  2  DUF1129      Protein of unknown function (DUF1129)
        1.1    9.6   0.0        1.1    9.6   0.0    2.6  3  Sigma_reg_N  Sigma factor regulator N-terminal


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -5.9   2.7         4   1.8e+04       6      22 ..      44      60 ..      42      62 .. 0.69
   2 !  111.9   2.4   6.4e-36   2.9e-32       4     206 .]     134     329 ..     132     329 .. 0.93

  Alignments for each domain:
  == domain 1  score: -5.9 bits;  conditional E-value: 4
                                      HHHHHHHHHHHHHTTT- CS
                        MS_channel  6 iliivvgilivlsllgv 22
                                      il+i++++l+v++ +g+
  gi|474934283|ref|YP_007687865.1| 44 ILAIFLTFLAVMTIIGI 60
                                      67777777777777775 PP

  == domain 2  score: 111.9 bits;  conditional E-value: 6.4e-36
                                       HHHHHHHHHHHHHHHTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEEE- CS
                        MS_channel   4 lkiliivvgilivlsllgvnvsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVedig 80 
                                       +++ i++++il +l+ +g ++ +ll+++G+lgl +gl++++li++++aG++++f+  +k+GD++ ++  +GtVe+ig
  gi|474934283|ref|YP_007687865.1| 134 TRYAIFIIAILFILTAWGADTRTLLVSAGILGLIIGLGAQSLIADIIAGMFIVFDGEYKVGDVIVVNSWRGTVEEIG 210
                                       799************************************************************************** PP

                                       SSEEEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-TTS-EE CS
                        MS_channel  81 lrttkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlkdkell 157
                                       +rttki +  g+i +i ns ++  +++N s+  + + +  + +++y+++  + e  ++e    +++ + +  + +  
  gi|474934283|ref|YP_007687865.1| 211 IRTTKIVDTGGNIKYINNSHIS--EVINKSQ--DLSLVSSTLCIPYEANLIETELKIKEYIPKIMQREPIFVEGPFY 283
                                       **********************..*******..****************8777766666655555555566689999 PP

                                       EEEEEE-SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHHHHHHT--- CS
                        MS_channel 158 vvldefgdsslnfevrvfvktvvpeeylsvqseinlrikkileeegiei 206
                                       + ++++++ss+++   ++ k+   e+y+  ++++n+++  + +e gi+i
  gi|474934283|ref|YP_007687865.1| 284 KGVEAMSASSVDLMFHALCKE---EDYFPARRALNREVYIMANEIGINI 329
                                       *********************...*************999888888875 PP

>> DUF872  Eukaryotic protein of unknown function (DUF872)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0011         5      33      67 ..      23      57 ..       3      62 .. 0.77
   2 ?    0.8   0.0      0.12   5.4e+02       9      59 ..      63     112 ..      60     119 .. 0.74
   3 ?    2.6   1.3     0.032   1.4e+02      49     104 ..     144     205 ..     134     207 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0011
                            DUF872 33 wlkhPkvkknrkvvlaallLlllGlvLlllgvvil 67
                                        k+P+ kk+rk ++++  L++l + L +l+v+  
  gi|474934283|ref|YP_007687865.1| 23 KQKQPRPKKERKPIVLSHELIILAIFLTFLAVMTI 57
                                      67889999999999999999999999999888755 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.12
                            DUF872   9 eddlianssqysfsslssvtqrsywlkhPkvkknrkvvlaallLlllGlvL 59 
                                       +d+ ++ ++ y ++s++++    +  + P++ +  + ++ a + l++Gl  
  gi|474934283|ref|YP_007687865.1|  63 DDEFFGAATDYDPGSIDNKYLDWTNQQIPHIIRSCQILFVAAI-LFIGLKF 112
                                       5677777888999999998865566778998888887777765.4667665 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.032
                            DUF872  49 allLlllGl...vLlllgvvilvepseGvssavf.lvlGlllfiPGvYhv..vyiylavrGa 104
                                        ++L++ G+   +Ll+ + ++ +    G +s +  +++G+ ++  G Y+v  v+++ ++rG+
  gi|474934283|ref|YP_007687865.1| 144 LFILTAWGAdtrTLLVSAGILGLIIGLGAQSLIAdIIAGMFIVFDGEYKVgdVIVVNSWRGT 205
                                       45566666422223333333445556788888888**************9666888899995 PP

>> DUF1129  Protein of unknown function (DUF1129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   5.1e-05      0.23      58     103 ..      10      59 ..       1      68 [. 0.71
   2 ?   -0.5   0.6      0.17   7.4e+02     122     168 ..     105     149 ..      88     172 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.1e-05
                           DUF1129  58 kaeellekkkkakkesk....enpwlmalDnsLlllalfallfgilalfs 103
                                        a+e  + +  ++k+++    ++ + ++l   L++la+f  + +++++++
  gi|474934283|ref|YP_007687865.1|  10 EAQEGAQAPPREPKQKQprpkKERKPIVLSHELIILAIFLTFLAVMTIIG 59 
                                       44444444444444444455589999********************9886 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.17
                           DUF1129 122 vgGlamvlvyrlltre..kkkkkrpplwkrllilllllvvwlvlftlva 168
                                       +  + +    ++l+r   +k++ r+ +  ++ ++  +++++ +lf+l+a
  gi|474934283|ref|YP_007687865.1| 105 ILFIGL----KFLQRFigDKTSFRTAAKLMISFTRYAIFIIAILFILTA 149
                                       333333....444444434555566665566666666666666666554 PP

>> Sigma_reg_N  Sigma factor regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00025       1.1       5      38 ..      30      64 ..      30      87 .. 0.89
   2 ?   -1.6   0.1      0.75   3.4e+03      24      45 ..     100     121 ..      92     135 .. 0.52
   3 ?   -2.5   2.1       1.4   6.3e+03      19      29 ..     137     147 ..     124     154 .. 0.50

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00025
                       Sigma_reg_N  5 kkakrksilrivlislivlllifvil.vvtllyla 38
                                      kk ++ + l+  li+l+++l++++++ +++++y++
  gi|474934283|ref|YP_007687865.1| 30 KKERKPIVLSHELIILAIFLTFLAVMtIIGIAYDD 64
                                      788999999999**************999999974 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.75
                       Sigma_reg_N  24 llifvilvvtllylaekegnkl 45 
                                       l++ +il+++l++l+   g+k+
  gi|474934283|ref|YP_007687865.1| 100 LFVAAILFIGLKFLQRFIGDKT 121
                                       3333344555555544444444 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.4
                       Sigma_reg_N  19 slivlllifvi 29 
                                       +++++ ++f++
  gi|474934283|ref|YP_007687865.1| 137 AIFIIAILFIL 147
                                       33333333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       961  (0.0536003); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.68u 0.34s 00:00:01.02 Elapsed: 00:00:00.55
# Mc/sec: 2062.97
//
Query:       gi|474934284|ref|YP_007687866.1|  [L=766]
Description: hypothetical protein TALC_00709 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.4e-10   39.5  13.0       0.24   11.8   0.0    6.8  6  fn3              Fibronectin type III domain
     0.0005   20.6  28.4       0.87   10.2   1.0    7.0  6  Pur_ac_phosph_N  Purple acid Phosphatase, N-terminal domain
  ------ inclusion threshold ------
      0.059   13.0   0.4        1.2    8.8   0.1    2.6  2  OB_RNB           Ribonuclease B OB domain
       0.68    9.8   3.1        1.1    9.1   3.1    1.2  1  RIFIN            Rifin
        1.7    6.7  10.1        3.6    5.6  10.1    1.5  1  FSA_C            Fragile site-associated protein C-terminus
        6.6    7.4  17.0       0.74   10.4   1.2    4.0  4  DUF1735          Domain of unknown function (DUF1735)
        8.8    6.7   7.9         17    5.8   7.9    1.4  1  DUF1180          Protein of unknown function (DUF1180)


Domain annotation for each model (and alignments):
>> fn3  Fibronectin type III domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   9.3e-05      0.24       9      75 ..     136     211 ..     129     214 .. 0.82
   2 ?    1.4   0.0      0.16     4e+02      37      73 ..     265     300 ..     255     305 .. 0.69
   3 !    6.7   0.1    0.0036       9.2      45      79 ..     359     395 ..     338     398 .. 0.72
   4 ?    3.2   0.1     0.043   1.1e+02      30      72 ..     420     466 ..     405     469 .. 0.85
   5 !    8.8   0.8   0.00076         2      51      76 ..     542     567 ..     489     574 .. 0.68
   6 !    9.3   0.1   0.00055       1.4      33      74 ..     601     650 ..     591     660 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.3e-05
                                       EEESSSEEEEEEE-CSSSSSTEEEEEEEEEETTSTS..........TEEEEEECSTSSEEEEESSSTTEEEEEEEEE CS
                               fn3   9 sevtstsltvsWeppkdgggpitgYeveyrekgsee..........ewneftvprtttsvtltgLkpgteYevrVqa 75 
                                        +vt+  ++v +++    g+++ gYe+ +++ ++e+          e  ++ + + ++s  + +Lkpg  Y+++V++
  gi|474934284|ref|YP_007687866.1| 136 PAVTDADVSVDFSKL-VSGSDFIGYEIYISDFEGENirivlmdglnEVYSVEAMNGENSGSIDNLKPGNSYVLEVRS 211
                                       566777788888888.799********99999999999**9998875555556666888****************85 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.16
                                       EEETTSTSTEEEEEECSTSSEEEEESSSTTEEEEEEE CS
                               fn3  37 yrekgseeewneftvprtttsvtltgLkpgteYevrV 73 
                                         +++++e   +   +++t+s ++tgL pg++  +++
  gi|474934284|ref|YP_007687866.1| 265 AFSENGTE-LLNEAMTEPTSSGQITGLAPGSKCYFSI 300
                                       55566666.44555555666**********9866665 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0036
                                       TEEEEEECSTSS.EEEEESSSTTEEEEEEEE.EEETS CS
                               fn3  45 ewneftvprttt.svtltgLkpgteYevrVq.avngg 79 
                                       +  ef+v   +     ++gL p t Y++ V  +vng 
  gi|474934284|ref|YP_007687866.1| 359 VIDEFSVVTAEIeKKIVSGLSPETGYRLYVVcTVNGT 395
                                       4667776666655889*************99888886 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.043
                                       EEEEEEEEEETTSTS.....TEEEEEECSTSSEEEEESSSTTEEEEEE CS
                               fn3  30 itgYeveyrekgsee.....ewneftvprtttsvtltgLkpgteYevr 72 
                                         +Y+++y ++g+++       +++  +++  +  + +L+p+ +Y+++
  gi|474934284|ref|YP_007687866.1| 420 TINYRLDYVPDGETSvsvssMGQTVFSSGDL-NGWIYDLEPSGTYTFT 466
                                       568********99999998777777788888.8899999999999996 PP

  == domain 5  score: 8.8 bits;  conditional E-value: 0.00076
                                       ECSTSSEEEEESSSTTEEEEEEEEEE CS
                               fn3  51 vprtttsvtltgLkpgteYevrVqav 76 
                                       +++t t++t  gL+pgt+Y++ V   
  gi|474934284|ref|YP_007687866.1| 542 NSPTVTNHTAVGLNPGTTYRLHVVYE 567
                                       455566***************99755 PP

  == domain 6  score: 9.3 bits;  conditional E-value: 0.00055
                                       EEEEEEETTSTS........TEEEEEECSTSSEEEEESSSTTEEEEEEEE CS
                               fn3  33 Yeveyrekgsee........ewneftvprtttsvtltgLkpgteYevrVq 74 
                                       Y++ y +++  +        +++  t p++ +  t+tgL+p t Y++ ++
  gi|474934284|ref|YP_007687866.1| 601 YSLSYTPTSAASvvvtngngDPVDATMPSNVYGGTVTGLEPITSYTFHLY 650
                                       56666555555555555555789999999999***************876 PP

>> Pur_ac_phosph_N  Purple acid Phosphatase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.7     0.018        45      58      83 ..     188     213 ..      73     225 .. 0.67
   2 !    7.5   0.0    0.0024       6.2      59      91 ..     280     313 ..     247     315 .. 0.82
   3 ?    1.5   0.1      0.18   4.5e+02      54      83 ..     363     393 ..     324     409 .. 0.68
   4 ?    2.1   1.0      0.12     3e+02      66      84 ..     454     472 ..     401     484 .. 0.73
   5 !   10.2   1.0   0.00034      0.87       4      82 ..     489     567 ..     484     591 .. 0.68
   6 !    9.5   0.6   0.00055       1.4      28      86 ..     600     659 ..     578     667 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.018
                   Pur_ac_phosph_N  58 sgyshkatltgLepgttYyYrvgdde 83 
                                        +  ++  +++L+pg  Y+  v++++
  gi|474934284|ref|YP_007687866.1| 188 MNGENSGSIDNLKPGNSYVLEVRSGT 213
                                       455678899*************9986 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0024
                   Pur_ac_phosph_N  59 gyshkatltgLepgttYyYrvgddeg.gwSevys 91 
                                       + + + ++tgL+pg + y+++ d+++  wSe  s
  gi|474934284|ref|YP_007687866.1| 280 EPTSSGQITGLAPGSKCYFSITDGTDtLWSEMVS 313
                                       5566778*****************777***9876 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.18
                   Pur_ac_phosph_N  54 tnyksgyshkatltgLepgttYy.Yrvgdde 83 
                                        + ++  + k  ++gL p t Y  Y v++ +
  gi|474934284|ref|YP_007687866.1| 363 FSVVTAEIEKKIVSGLSPETGYRlYVVCTVN 393
                                       44556667777899********845555444 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.12
                   Pur_ac_phosph_N  66 ltgLepgttYyYrvgddeg 84 
                                       + +Lep+ tY + + d+++
  gi|474934284|ref|YP_007687866.1| 454 IYDLEPSGTYTFTFTDGGN 472
                                       568************9974 PP

  == domain 5  score: 10.2 bits;  conditional E-value: 0.00034
                   Pur_ac_phosph_N   4 vhlsltedtstsmtvsWitpektkksvvrygtssdalestaeatsstyet......tnyksgyshkatltgLepgtt 74 
                                       v+l+++++ts+s+t s + p+  +  +v++  ++        ++ stye+       n +s  +++ t+ gL pgtt
  gi|474934284|ref|YP_007687866.1| 489 VTLTVSGHTSSSITYSVNAPDYLAGDNVQVLVNELI------GSVSTYEQtvesciFNLNSPTVTNHTAVGLNPGTT 559
                                       566666655555555555555555555555555433......333333333333558999***************** PP

                   Pur_ac_phosph_N  75 YyYrvgdd 82 
                                       Y   v  +
  gi|474934284|ref|YP_007687866.1| 560 YRLHVVYE 567
                                       *9988654 PP

  == domain 6  score: 9.5 bits;  conditional E-value: 0.00055
                   Pur_ac_phosph_N  28 ksvvrygtssdalestaeatsstyettnyksgyshkatltgLepgttYyYrvgddeg...gw 86 
                                       ++++ y ++s a+   ++++   +    +   +++  t+tgLep t Y +   d+ +   +w
  gi|474934284|ref|YP_007687866.1| 600 NYSLSYTPTSAASVVVTNGNGDPV--DATMPSNVYGGTVTGLEPITSYTFHLYDGADevgQW 659
                                       555666666666666666666555..467899999*****************9886645555 PP

>> OB_RNB  Ribonuclease B OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.12     3e+02      30      44 ..     340     354 ..     333     359 .. 0.82
   2 ?    8.8   0.1   0.00048       1.2      15      52 ..     677     713 ..     675     718 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.12
                                       TTS-TT-EEEEEEEE CS
                            OB_RNB  30 kkamhGDrVlvritk 44 
                                       ++   GD V+vr+t 
  gi|474934284|ref|YP_007687866.1| 340 NGFYTGDNVTVRVTD 354
                                       56667********96 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00048
                                       ECT.TEEEEE-HHHHTTS-TT-EEEEEEEESSSEEEEE CS
                            OB_RNB  15 pdegkeDifippeqmkkamhGDrVlvritkgdrrgrre 52 
                                        ++g++D+ i    +++ m+GD V v+i ++++   +e
  gi|474934284|ref|YP_007687866.1| 677 YEGGSDDVTIG-GTVNGFMDGDVVRVKIFSYSDTTGQE 713
                                       56777888886.4699************9954444444 PP

>> RIFIN  Rifin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   3.1   0.00044       1.1     181     290 ..      27     130 ..       4     137 .. 0.37

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00044
                             RIFIN 181 tatnyknvtslvkaikeeyeescllklkkskaaltsakekekkeasskekikkkvekivekaekkaaaaaaeaaaea 257
                                       ++ +y+n   +    ++e  +++   +++++ +   ++++ +++++ +   ++ v+++ ++a + a++ a+++aa++
  gi|474934284|ref|YP_007687866.1|  27 QSAEYNNLRDFRADSYTED-QIAGRPMRSTT-V---SSSSPQRNMEPEVDGNDIVNSMSSSASTGATTGASTTAATT 98 
                                       4455555555554444442.22221222222.2...22222222222222333333333333333333333333333 PP

                             RIFIN 258 taeaekaetaaveattaslqtaiiasivaivvI 290
                                       ta++ +a t+a+ a+ta +  ++  ++va+vv+
  gi|474934284|ref|YP_007687866.1|  99 TAATSTAATTAA-ASTAATVGTVATTFVALVVV 130
                                       333333322222.22233333344444444444 PP

>> FSA_C  Fragile site-associated protein C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6  10.1    0.0014       3.6     549     597 ..      76     124 ..      27     161 .. 0.63

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0014
                             FSA_C 549 kssleslqgsqdsiaiattasavelndatsstiasaatasslsstkstv 597
                                        +s++s   +  ++  +tta+++++ ++t++t+a+a+ta+++ +  +t 
  gi|474934284|ref|YP_007687866.1|  76 VNSMSSSASTGATTGASTTAATTTAATSTAATTAAASTAATVGTVATTF 124
                                       2445555444455555666666666666666666666666555444443 PP

>> DUF1735  Domain of unknown function (DUF1735)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.4       1.9   4.9e+03      19      19 ..     146     146 ..      76     211 .. 0.61
   2 ?   -1.5   0.1       1.5   3.7e+03      54      76 ..     185     208 ..     129     239 .. 0.52
   3 ?   10.4   1.2   0.00029      0.74      25      88 ..     346     419 ..     323     439 .. 0.64
   4 ?    5.3   2.0     0.011        28       9      55 ..     467     512 ..     451     550 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.9
                                       E CS
                           DUF1735  19 t 19 
                                       +
  gi|474934284|ref|YP_007687866.1| 146 D 146
                                       2 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.5
                                       HCCHCCCCT--.EE--GGG.EEE. CS
                           DUF1735  54 ldeyNaangtnykllPeey.ytlp 76 
                                       ++++N +n  +   l +++ y l+
  gi|474934284|ref|YP_007687866.1| 185 VEAMNGENSGSIDNLKPGNsYVLE 208
                                       556664444444444443335553 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00029
                                       SECEEEEEEE.ECC--T.T-EEEEEEE-CHHHCCHC...........CCCT--.EE--GGGEEE.GCGCEEECCGGT CS
                           DUF1735  25 eektieltvy.lsgsnp.kdvtvtlevdeslldeyN...........aangtnykllPeeyytlpsstvtikaGees 88 
                                       +++t  + v+ lsg+   +   vt e+++++++ +            + ngt+y ll+++y+++++s +   +G ++
  gi|474934284|ref|YP_007687866.1| 346 DNVT--VRVTdLSGTVIdEFSVVTAEIEKKIVSGLSpetgyrlyvvcTVNGTDYSLLDSDYVEFETSGMESQSG-YT 419
                                       3333..44444555333233444445555555544455555566666677**************9888888888.33 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.011
                                       CCCCCCEECEEECEESSECEEEEEEEECC--TT-EEEEEEE-CHHHC CS
                           DUF1735   9 gannsgelsltlddlgeektieltvylsgsnpkdvtvtlevdeslld 55 
                                       ++++ +++ +t  d+ +  + e+t+++sg++++ +t+++ + +++l+
  gi|474934284|ref|YP_007687866.1| 467 FTDGGNTVYTTDVDTVNLEESEVTLTVSGHTSSSITYSVNA-PDYLA 512
                                       44555566666666777777789999999888888888744.66655 PP

>> DUF1180  Protein of unknown function (DUF1180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   7.9    0.0068        17      37     114 ..      50     135 ..      25     139 .. 0.56

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0068
                           DUF1180  37 pPlppgataaespgkataieaksaqaaeggngss.....pragsaad.......aggslavvpelssntdkpmtlqr 101
                                       +P++ +++++ sp++    e  ++   ++ + s      ++a            a++s a  +  +s      t++ 
  gi|474934284|ref|YP_007687866.1|  50 RPMRSTTVSSSSPQRNMEPEVDGNDIVNSMSSSAstgatTGA----SttaatttAATSTAATTAAASTAATVGTVAT 122
                                       566665555555666555444333332222222211211111....1223333356666666667888888899888 PP

                           DUF1180 102 allvlvvvsaavi 114
                                       +++ lvvvs++++
  gi|474934284|ref|YP_007687866.1| 123 TFVALVVVSSVIV 135
                                       8888888877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (766 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1163  (0.064867); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.79u 0.34s 00:00:01.13 Elapsed: 00:00:00.51
# Mc/sec: 4536.92
//
Query:       gi|474934285|ref|YP_007687867.1|  [L=80]
Description: hypothetical protein TALC_00710 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 543.14
//
Query:       gi|474934286|ref|YP_007687868.1|  [L=402]
Description: L-alanine aminotransferase apoenzyme [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-53  181.7   0.0    2.8e-53  181.4   0.0    1.1  1  Aminotran_1_2    Aminotransferase class I and II
    2.9e-09   36.7   0.0      5e-09   35.9   0.0    1.3  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    0.00057   19.2   0.0    0.00089   18.6   0.0    1.3  1  Beta_elim_lyase  Beta-eliminating lyase
     0.0014   17.7   0.0      0.021   13.8   0.0    2.1  2  Aminotran_5      Aminotransferase class-V
     0.0078   14.8   0.0      0.012   14.2   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
  ------ inclusion threshold ------
      0.084   13.1   0.0       0.16   12.2   0.0    1.5  1  MGS              MGS-like domain


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.4   0.0   9.5e-57   2.8e-53       4     344 ..      36     375 ..      33     387 .. 0.91

  Alignments for each domain:
  == domain 1  score: 181.4 bits;  conditional E-value: 9.5e-57
                                       EESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHH CS
                     Aminotran_1_2   4 inLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagal 80 
                                        n++++++   +  +t++   k++ +  +  +t n yg+++g  +l+e + +  ++++++ ++++  v v+ G +++
  gi|474934286|ref|YP_007687868.1|  36 YNFNIGDPNK-WDFETPEY-FKETLR-QAVDNTDNGYGDSQGNLDLRESIVDREFEKNGIRIDTK-DVYVTAGVSEC 108
                                       5777777755.34455555.555555.5999**********************************.*********** PP

                                       HHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS CS
                     Aminotran_1_2  81 iealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesp 157
                                       i+  + ++ ++pgde+lvp p y++y+++++ + g++v+y++ +eed+  d++ + + +++      +tk i+v +p
  gi|474934286|ref|YP_007687868.1| 109 INFMMGAM-IEPGDEVLVPGPGYPNYEQYINFYEGKCVPYRMIEEEDWAPDVDMIRDRITN------RTKAIVVINP 178
                                       ********.****************************************************......********** PP

                                       -TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEE CS
                     Aminotran_1_2 158 hNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyil 234
                                       +NPtG+v+t+++l+++ d+a +y + +++De+Y + vf+  ++ +  + + +++  +i++++sK   ++G+R Gy++
  gi|474934286|ref|YP_007687868.1| 179 NNPTGAVYTEKDLRAIGDIAAEYDIPVISDEIYDKIVFDG-KFFS-MSRLPDDIPRVILNGFSKVNLMPGWRQGYCY 253
                                       **************************************95.5777.888888888********************** PP

                                       EEH......HHHHH.HHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS.TEEEECCS CS
                     Aminotran_1_2 235 gna......avvsq.lrklsrpflsssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael.glkvlasq 303
                                         +      ++++  +r++ ++++   + q+a+  +l+ +++   ++ em ++l++r+++ +++++e+ gl+  +++
  gi|474934286|ref|YP_007687868.1| 254 FMDrnglmdEIREGmMRQFRARICANVPCQEAARVSLQGPQD---YIVEMNRKLKERAEYTYKRFNEIpGLSSNKPH 327
                                       *777*****8877626888999999****************7...8******************************* PP

                                       CSSEEEEEETHH....CHHHHHHHHHHTCTEEEEEGGGGTS...TTEE CS
                     Aminotran_1_2 304 sgmflltdlsae....takelskkLleevgvyvtpgtsftv...pgrl 344
                                       ++++ +  ++      ++ke+   Ll+  gv++++g+ f     ++++
  gi|474934286|ref|YP_007687868.1| 328 GALYAFPKVDLGkvwkNDKEFVLDLLDTTGVVMVQGSGFCQefgQSHF 375
                                       ******999977889999999999***********9988655555555 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.0   1.7e-12     5e-09      54     144 ..     111     208 ..      90     209 .. 0.84

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 1.7e-12
                                       HHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE.-B-TTTSSB-GGGCGGG--TTEEEEEEB-...GGGB--. CS
                   DegT_DnrJ_EryC1  54 aLralgvgpgdeVIvpsltFvatanavlelgakpvfv.DvdpdtynidpaaieaaitertkaIlpVh...lyGqva. 125
                                        ++   ++pgdeV+vp  ++    + +     k v+   ++++++ +d+++i+  it+rtkaI++++     G+v  
  gi|474934286|ref|YP_007687868.1| 111 FMMGAMIEPGDEVLVPGPGYPNYEQYINFYEGKCVPYrMIEEEDWAPDVDMIRDRITNRTKAIVVINpnnPTGAVYt 187
                                       45567799*******************988888776516899**********************9973224677766 PP

                                       ..-HHHHHHHHHHCT-EEEEE CS
                   DegT_DnrJ_EryC1 126 ..dmdalkaiaakhglkvieD 144
                                         d+ a+ +iaa+++++vi+D
  gi|474934286|ref|YP_007687868.1| 188 ekDLRAIGDIAAEYDIPVISD 208
                                       67*****************99 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0     3e-07   0.00089      64     167 ..     113     208 ..      50     209 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 3e-07
                                       HHHH--TTEEEEEETT-HHHHSSTTHHHHC.C--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTT CS
                   Beta_elim_lyase  64 lkillqrgeevivtepahihfdetgaiael.agvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnnt 139
                                       + +++++g+ev+v  p+  +    + i+++ +   +  +  +e+   d++ +++ i++      ++k+i++ + nn 
  gi|474934286|ref|YP_007687868.1| 113 MGAMIEPGDEVLVPGPG--YPNYEQYINFYeGKCVPYRMIEEEDWAPDVDMIRDRITN------RTKAIVVINPNNP 181
                                       45666666666665554..333334455554555566777777788888888888888......6899999999995 PP

                                       TTTB---HHHHHHHHHHHHHCT-EEEEE CS
                   Beta_elim_lyase 140 agGqvvsleelrevaaiakkygiplhlD 167
                                         G v++ + lr++ +ia +y+ip++ D
  gi|474934286|ref|YP_007687868.1| 182 -TGAVYTEKDLRAIGDIAAEYDIPVISD 208
                                       .9***********************998 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0     7e-06     0.021      59     175 ..      95     208 ..      87     210 .. 0.83
   2 ?    1.4   0.0     0.041   1.2e+02     275     339 ..     299     364 ..     279     373 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7e-06
                                       STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEB.ETTSCBEGGGHHH CS
                       Aminotran_5  59 eseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipl.deegeldldelek 134
                                       + ++++++t G +e in ++ ++   ++pgde++v   ++       q ++  +g  v +  + +e++  d+d +++
  gi|474934286|ref|YP_007687868.1|  95 D-TKDVYVTAGVSECINFMMGAM---IEPGDEVLVPGPGYPNYE---QYINFYEGKCVPYRMIeEEDWAPDVDMIRD 164
                                       4.488999***********9999...9************99777...666666666665544415789********* PP

                                       H--TTEEEEEEESBETTTTE...B--HHHHHHHHHHTT-EEEEE CS
                       Aminotran_5 135 llnektklvaithvsnvtGt...iqpveeigklakkkgalvlvD 175
                                        ++++tk++ +   +n tG     +++ +ig++a ++++ v+ D
  gi|474934286|ref|YP_007687868.1| 165 RITNRTKAIVVINPNNPTGAvytEKDLRAIGDIAAEYDIPVISD 208
                                       *******************8333478999999999999888776 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.041
                                       HHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEETTCSH...HHHHHHHHHTTEEEEEE- CS
                       Aminotran_5 275 aiekhekelaeyllerlkslpgvrlygpdkaerrasivsfnfkgvha...edvatlLdeegIavrsGh 339
                                       +++++ ke aey+++r +++pg+  ++  ++ +  +   + + +v     e v  lLd++g+ + +G+
  gi|474934286|ref|YP_007687868.1| 299 EMNRKLKERAEYTYKRFNEIPGLSSNK--PHGALYAFPKVDLGKVWKndkEFVLDLLDTTGVVMVQGS 364
                                       678899999**************9944..577777777777776655222446667777777777765 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   4.1e-06     0.012      75     174 ..     103     209 ..      92     215 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.1e-06
                                       SHHH.HHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEEST....TSHHHHHHHCCTTEEEEEEESS CS
                   Cys_Met_Meta_PP  75 sGma.AiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdt....sdleelekaikentklvylEtp 146
                                       +G++  i+ ++ a+++ Gde++v    Y   +++++ +  k ++ +++++      d++ ++  i+++tk++ +  p
  gi|474934286|ref|YP_007687868.1| 103 AGVSeCINFMMGAMIEPGDEVLVPGPGYPNYEQYINFYEGK-CVPYRMIEEedwaPDVDMIRDRITNRTKAIVVINP 178
                                       444414556777999*************9999999877666.4778887773333468899**************** PP

                                       -TTTT--...--HHHHHHHHHHTT-EEEEEG CS
                   Cys_Met_Meta_PP 147 tnpllkv...vDiekiaklakkagvlvvvDn 174
                                        np+  v    D+++i ++a + +++v+ D 
  gi|474934286|ref|YP_007687868.1| 179 NNPTGAVyteKDLRAIGDIAAEYDIPVISDE 209
                                       ***96663227****************9986 PP

>> MGS  MGS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   5.2e-05      0.16      50      94 ..     159     206 ..      96     207 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.2e-05
                                       H.HHHHHHHTTSCCEEEEE--THHHHHH..CHHHHHHHHHHHTTSHEE CS
                               MGS  50 v.eildaikngeidlvintlypfkatva..kdgykirraaenidIplp 94 
                                       v  i d+i n    +v++++++ + +v   kd  +i ++a ++dIp++
  gi|474934286|ref|YP_007687868.1| 159 VdMIRDRITNRTKAIVVINPNNPTGAVYteKDLRAIGDIAAEYDIPVI 206
                                       356999999999999999999999998888999*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2660.19
//
Query:       gi|474934287|ref|YP_007687869.1|  [L=651]
Description: 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase-related enzyme [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.1e-33  115.3   0.0    6.3e-33  114.2   0.0    1.5  1  PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
    5.4e-18   64.7   0.0    1.8e-17   63.0   0.0    1.9  1  PUA          PUA domain
    2.8e-06   27.4   9.1    2.8e-06   27.4   9.1    2.4  2  Fer4_21      4Fe-4S dicluster domain
    7.8e-05   22.7   0.0    0.00014   21.9   0.0    1.5  1  TGT_C2       Patch-forming domain C2 of tRNA-guanine transgly
     0.0027   17.8  12.8      0.076   13.2   2.2    2.9  2  Fer4_9       4Fe-4S dicluster domain
     0.0031   17.3  16.7       0.29   11.0   3.7    3.0  2  Fer4         4Fe-4S binding domain
  ------ inclusion threshold ------
      0.014   16.0  13.2      0.065   13.8  13.3    2.2  1  Fer4_7       4Fe-4S dicluster domain
       0.03   14.4   2.3       0.03   14.4   2.3    2.7  4  Fer4_10      4Fe-4S dicluster domain
      0.034   14.7   0.2      0.034   14.7   0.2    3.3  3  Fer4_17      4Fe-4S dicluster domain
      0.042   14.0   0.2       0.37   11.0   0.0    2.5  2  Trp_ring     Trimeric autotransporter adhesin Trp ring domain


Domain annotation for each model (and alignments):
>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.2   0.0   3.5e-36   6.3e-33       2     173 ..     249     422 ..     248     423 .. 0.98

  Alignments for each domain:
  == domain 1  score: 114.2 bits;  conditional E-value: 3.5e-36
                                       EEEE--SSCTCHHHHHHHHHHCTTHEEEEEE-STB-HHHHHHHHHHHHHTT-E.EEEEE-SCHHHHHHHHHH-S-TH CS
                       PAPS_reduct   2 lvvsvsgGkdslVllhLalkafkpvpvvfvdtghefpetiefvdeleeryglr.lkvyepeeevaekinaekhgssl 77 
                                        vvs+sgGkdsl+++  ++ a  + + +f++tg e +et+++v ++++r +l  l+   p++ +  +++ ++ + ++
  gi|474934287|ref|YP_007687869.1| 249 AVVSFSGGKDSLATMLVTMDAGLNLRPMFLNTGLELDETVQYVHDFAKRHDLAlLEEDAPNDAFFGNLVYFGPPAKD 325
                                       59***************************************************999999****************** PP

                                       HHCHHHHHHTHHHHHHHHHCT..TECEEE----CCCTTTTTTSSSEEECTTT-SCEEE-CCCT--HHHHHHHHHHCT CS
                       PAPS_reduct  78 yeeaaeriaKveplkkaLekl..dedalltGaRrdesksraklpiveidedfekslrvfPllnWteedvwqyilren 152
                                       y++ +++  K+ p    ++ +  d ++ ++G+R++es++r ++p ++ + + + ++   P+ nW+  +vw yi +++
  gi|474934287|ref|YP_007687869.1| 326 YRW-CCKTNKLGPTVHMISSNfpDGVLSFIGQRKYESEARNAKPRIWQNPWTPGQIGASPIQNWSAMHVWLYIFYKK 401
                                       ***.***************999999**************************************************** PP

                                       --B-CCCCTT-SS--BCTTB- CS
                       PAPS_reduct 153 ipynpLydqgfrsiGcvpctg 173
                                        pyn  y +g ++iGc++c++
  gi|474934287|ref|YP_007687869.1| 402 EPYNVWYARGLDRIGCFMCPA 422
                                       *******************85 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.0   0.0     1e-20   1.8e-17       1      71 [.     130     200 ..     130     202 .. 0.98

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 1e-20
                                       CEEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEE CS
                               PUA   1 grvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveie 71 
                                       grv +d +Avk++ + ++L+apGvv+++++++++d+V  +  d ++++ G a++s++e+++ ++g++v+++
  gi|474934287|ref|YP_007687869.1| 130 GRVFLDPSAVKFVQENKNLMAPGVVDADESIRPDDEVIMMLADHTVIGTGTAKMSGKEMKESDHGMAVKTR 200
                                       799*****************************************************************986 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   1.0       1.7     3e+03      40      53 ..      13      29 ..       5      32 .. 0.70
   2 !   27.4   9.1   1.5e-09   2.8e-06       7      55 ..     590     637 ..     585     641 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.7
                           Fer4_21 40 eCvGCnlCs...svCPv 53
                                       C +Cnl +   + CPv
  gi|474934287|ref|YP_007687869.1| 13 WCSACNLPVmekKECPV 29
                                      58999987622246887 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 1.5e-09
                           Fer4_21   7 kCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPved 55 
                                       +C+gCg+C+  C++ + +++ +++ + +k+  d+C+ C  C+ +CP  d
  gi|474934287|ref|YP_007687869.1| 590 NCVGCGLCAARCQKDGGKCMYMEDGK-VKINGDDCIFCRKCYGPCPAVD 637
                                       7*******************997655.59*****************876 PP

>> TGT_C2  Patch-forming domain C2 of tRNA-guanine transglycosylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   8.1e-08   0.00014       2      68 ..      55     127 ..      54     129 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 8.1e-08
                            TGT_C2   2 rlraiadYqFGagagdaLfped..vtitrs.atgrirqvlvdgerlatlraqdg...rltLsleGarrlhesl 68 
                                       ++r++ad  FG g+g aL+pe   + + +  +  r+++v+ dg  + t+r + g   r+++  +Ga r+ +++
  gi|474934287|ref|YP_007687869.1|  55 KIRDMADRTFGPGCGLALIPEGhiAIMNKCpSVDRMEEVFCDGAVVTTMRFDMGagwRFIIRTQGAFRIRDAM 127
                                       79******************98755555558*******************88776669********9999875 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   2.2   4.2e-05     0.076      33      49 ..     580     604 ..     561     606 .. 0.69
   2 !   11.8  14.0   0.00012      0.21       1      48 [.     590     635 ..     590     638 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.2e-05
                            Fer4_9  33 e........eaCigCgaCveaCpkg 49 
                                       e         +C+gCg C+++C+k+
  gi|474934287|ref|YP_007687869.1| 580 EasqliaraFNCVGCGLCAARCQKD 604
                                       13445555589***********986 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00012
                            Fer4_9   1 kCtgCgaCveaC...pagvvvedaaerkarlraaseeaCigCgaCveaCpk 48 
                                       +C+gCg C + C     + + +++++ k++      ++Ci+C++C+  Cp 
  gi|474934287|ref|YP_007687869.1| 590 NCVGCGLCAARCqkdGGKCMYMEDGKVKING-----DDCIFCRKCYGPCPA 635
                                       6***********4432223333333333333.....26***********95 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   3.7   0.00016      0.29       8      19 ..     591     602 ..     589     604 .. 0.88
   2 !   10.7   5.1   0.00021      0.37       1      20 [.     616     635 ..     616     636 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00016
                                       SSS-THHHHHST CS
                              Fer4   8 CigCGaCvevCP 19 
                                       C+gCG+C+  C 
  gi|474934287|ref|YP_007687869.1| 591 CVGCGLCAARCQ 602
                                       ***********6 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00021
                                       EEEETTTSSS-THHHHHSTT CS
                              Fer4   1 vvideekCigCGaCvevCPv 20 
                                       v+i+ ++Ci+C +C+  CP 
  gi|474934287|ref|YP_007687869.1| 616 VKINGDDCIFCRKCYGPCPA 635
                                       57999**************5 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8  13.3   3.6e-05     0.065       2      50 ..     591     635 ..     590     636 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.6e-05
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPt 50 
                                       C+gCg C+a C  +  +  +     +  kv+i+ ++C++C++C   CP+
  gi|474934287|ref|YP_007687869.1| 591 CVGCGLCAARCQKDGGKCMYM----EDGKVKINGDDCIFCRKCYGPCPA 635
                                       ***********9666666555....23489*****************95 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.3   1.2        10   1.8e+04      17      21 ..      25      29 ..      14      36 .. 0.60
   2 ?   -4.6   0.1        10   1.8e+04      18      21 ..     419     422 ..     417     429 .. 0.72
   3 ?   13.8  14.8   2.5e-05     0.046       6      56 .]     588     634 ..     583     634 .. 0.93
   4 ?   14.4   2.3   1.7e-05      0.03       1      21 [.     615     635 ..     615     648 .. 0.81

  Alignments for each domain:
  == domain 1  score: -4.3 bits;  conditional E-value: 10
                           Fer4_10 17 kaCPa 21
                                      k CP+
  gi|474934287|ref|YP_007687869.1| 25 KECPV 29
                                      24444 PP

  == domain 2  score: -4.6 bits;  conditional E-value: 10
                           Fer4_10  18 aCPa 21 
                                       +CPa
  gi|474934287|ref|YP_007687869.1| 419 MCPA 422
                                       5887 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 2.5e-05
                           Fer4_10   6 ddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       +  C++Cg C + C    +++g+k  ++e+++v+++ ++C++c +C+  CP
  gi|474934287|ref|YP_007687869.1| 588 AFNCVGCGLCAARC----QKDGGKCMYMEDGKVKINGDDCIFCRKCYGPCP 634
                                       568***********....69******************************9 PP

  == domain 4  score: 14.4 bits;  conditional E-value: 1.7e-05
                           Fer4_10   1 kvvidddtCirCgkCvkaCPa 21 
                                       kv+i+ d Ci C+kC   CPa
  gi|474934287|ref|YP_007687869.1| 615 KVKINGDDCIFCRKCYGPCPA 635
                                       5899****************9 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.7        10   1.8e+04      10      14 ..      22      29 ..      13      41 .. 0.55
   2 ?   14.7   0.2   1.9e-05     0.034      33      58 ..     578     603 ..     550     604 .. 0.70
   3 ?    4.7   2.8     0.025        44      43      58 ..     620     635 ..     607     637 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 10
                           Fer4_17 10 p...eCps 14
                                          eCp 
  gi|474934287|ref|YP_007687869.1| 22 MekkECPV 29
                                      13335555 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.9e-05
                           Fer4_17  33 lleeaeke.....ekaslCieCgeCerkCPq 58 
                                       +      e      +a +C++Cg+C+++C +
  gi|474934287|ref|YP_007687869.1| 578 MG-----EasqliARAFNCVGCGLCAARCQK 603
                                       22.....123344799*************76 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.025
                           Fer4_17  43 aslCieCgeCerkCPq 58 
                                        ++Ci C++C   CP+
  gi|474934287|ref|YP_007687869.1| 620 GDDCIFCRKCYGPCPA 635
                                       589***********95 PP

>> Trp_ring  Trimeric autotransporter adhesin Trp ring domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.79   1.4e+03      26      39 ..     177     190 ..     176     199 .. 0.77
   2 ?   11.0   0.0   0.00021      0.37       1      41 [.     538     575 ..     538     578 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.79
                          Trp_ring  26 GeggakVsGktded 39 
                                       G+g+ak sGk  ++
  gi|474934287|ref|YP_007687869.1| 177 GTGTAKMSGKEMKE 190
                                       99*******98665 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00021
                          Trp_ring   1 mGWVVsadgnaYsaaVkNAneVkFvGeggakVsGktdedgv 41 
                                       +GWV++  +++       An V F G g ++V++ t+ d  
  gi|474934287|ref|YP_007687869.1| 538 LGWVIKL-DEE--NDALYANYVTFYGAGSITVKAYTERDAQ 575
                                       6888884.333..333579****************976655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (651 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.68u 0.27s 00:00:00.95 Elapsed: 00:00:00.47
# Mc/sec: 4125.88
//
Query:       gi|474934288|ref|YP_007687870.1|  [L=220]
Description: serine O-acetyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.5e-14   50.8  11.9    1.3e-07   31.0   5.4    2.7  2  Hexapep         Bacterial transferase hexapeptide (six repeat
    4.6e-06   26.3  14.4    3.9e-05   23.3   6.1    2.9  2  Hexapep_2       Hexapeptide repeat of succinyl-transferase
    0.00087   19.6   0.1      0.003   17.9   0.0    1.7  2  SATase_N        Serine acetyltransferase, N-terminal
     0.0021   17.9   1.0     0.0035   17.1   1.0    1.3  1  HSBP1           Heat shock factor binding protein 1
      0.003   18.0   2.1     0.0048   17.3   2.1    1.3  1  ZapB            Cell division protein ZapB
     0.0052   16.6   0.9     0.0083   16.0   0.9    1.3  1  GIT_CC          GIT coiled-coil Rho guanine nucleotide exchan
     0.0064   16.6   1.0      0.011   15.8   1.0    1.3  1  TolA_bind_tri   TolA binding protein trimerisation
  ------ inclusion threshold ------
      0.012   15.9   2.2      0.018   15.4   2.2    1.3  1  TSC22           TSC-22/dip/bun family
      0.015   15.4   0.9      0.024   14.8   0.9    1.3  1  K-box           K-box region
       0.04   14.5   0.0      0.087   13.4   0.0    1.5  1  RNA_pol_Rpb2_5  RNA polymerase Rpb2, domain 5
      0.046   14.4   0.3        0.1   13.3   0.3    1.6  1  YabA            Initiation control protein YabA
      0.072   13.5   1.9       0.12   12.8   1.9    1.3  1  UPF0184         Uncharacterised protein family (UPF0184)
      0.079   13.0   0.2       0.12   12.4   0.2    1.3  1  FlxA            FlxA-like protein
      0.088   12.6   2.8       0.17   11.7   2.8    1.4  1  DivIC           Septum formation initiator
       0.11   13.0   0.2       0.18   12.3   0.2    1.3  1  NPV_P10         Nucleopolyhedrovirus P10 protein
       0.11   13.0   0.9       0.25   11.8   0.9    1.8  1  DUF4140         N-terminal domain of unknown function (DUF414
       0.15   12.3   1.1       0.38   11.0   0.4    1.8  1  HALZ            Homeobox associated leucine zipper
       0.39   10.6   3.3       0.15   12.0   0.6    1.6  2  Prefoldin       Prefoldin subunit
       0.71    9.8   3.9        1.6    8.7   1.8    2.2  2  RBD-FIP         FIP domain


Domain annotation for each model (and alignments):
>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.4   4.3e-08     4e-05       1      36 []      70     107 ..      61     107 .. 0.94
   2 !   31.0   5.4   1.4e-10   1.3e-07       1      34 [.     116     149 ..     116     151 .. 0.95

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 4.3e-08
                                       TEEEETTEEE-T..TEEEETTEEE-TTEEEETTEEEES CS
                           Hexapep   1 stvIGsnvlIgp..faviggnVkIGdnvkIgagvvigg 36 
                                       +++IG+  +I++  ++vig+ ++IGd+v++  gv++gg
  gi|474934288|ref|YP_007687870.1|  70 GAQIGERFFIDHatGVVIGETAIIGDDVTLYQGVTLGG 107
                                       578999999999***********************997 PP

  == domain 2  score: 31.0 bits;  conditional E-value: 1.4e-10
                                       TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                           Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34 
                                       ++++G+ v+ g++a+++gn++IGd+v+Igag+v+
  gi|474934288|ref|YP_007687870.1| 116 HPTVGNRVVFGAGAIVLGNITIGDDVRIGAGSVV 149
                                       5799*****************************9 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   1.2    0.0047       4.5      15      32 ..      86     105 ..      64     106 .. 0.77
   2 !   23.3   6.1   4.2e-08   3.9e-05       3      32 ..     118     149 ..     118     151 .. 0.94

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0047
                                       EES..EEE-TT-EE-TT-EE CS
                         Hexapep_2  15 giG..vslGdncvvgaGvvi 32 
                                       +iG   ++Gd+++++ Gv++
  gi|474934288|ref|YP_007687870.1|  86 VIGetAIIGDDVTLYQGVTL 105
                                       35666789999999999876 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 4.2e-08
                                       EE-TT-EE-TT-EE.S.EEE-TT-EE-TT-EE CS
                         Hexapep_2   3 iIGdnCliGanagi.G.vslGdncvvgaGvvi 32 
                                       ++G+++++Ga a++ G +++Gd++ +gaG+v+
  gi|474934288|ref|YP_007687870.1| 118 TVGNRVVFGAGAIVlGnITIGDDVRIGAGSVV 149
                                       58***********9999**************9 PP

>> SATase_N  Serine acetyltransferase, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   3.2e-06     0.003      76     103 ..       7      34 ..       5      35 .. 0.96
   2 ?   -1.4   0.0       3.2     3e+03      38      62 ..     186     210 ..     176     219 .. 0.56

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.2e-06
                                       HHHHHHHH-TT---THHHHHH-HHHHHH CS
                          SATase_N  76 DlkAvlerDpAcksylepllyfKGFhAl 103
                                       Dl+Av+erDpA+ +  +++ y+ GF A+
  gi|474934288|ref|YP_007687870.1|   7 DLQAVMERDPAVIDENDAINYHTGFRAV 34 
                                       9*************************97 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.2
                                       HHHHHHHH-BSSS-HHHHHHHHHHH CS
                          SATase_N  38 aflLanklasstlsaeqlrelfeea 62 
                                         ++a+k++s + + ++l++ ++e 
  gi|474934288|ref|YP_007687870.1| 186 PDVIADKIDSMQKQIDELQTEVREL 210
                                       4455666666555555555554444 PP

>> HSBP1  Heat shock factor binding protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   1.0   3.7e-06    0.0035      23      50 ..     187     214 ..     183     215 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.7e-06
                             HSBP1  23 dqilsriDdMssriDdLEksiadlmtqa 50 
                                       d i ++iD M++ iD+L++ + +l +++
  gi|474934288|ref|YP_007687870.1| 187 DVIADKIDSMQKQIDELQTEVRELREEN 214
                                       67999******************98875 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   2.1   5.1e-06    0.0048      18      47 ..     191     220 .]     187     220 .] 0.88

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.1e-06
                              ZapB  18 dtitlLqmeieeLkeeneelkeenreleee 47 
                                       d+i+++q++i+eL+ e++el eenr+l++e
  gi|474934288|ref|YP_007687870.1| 191 DKIDSMQKQIDELQTEVRELREENRRLRKE 220
                                       899999999999999999999999999865 PP

>> GIT_CC  GIT coiled-coil Rho guanine nucleotide exchange factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.9   8.8e-06    0.0083      41      65 ..     195     219 ..     189     220 .] 0.93

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 8.8e-06
                            GIT_CC  41 slsdelrlLQskvqkLqaeNaqlrd 65 
                                       s+++++ +LQ +v +L +eN  lr+
  gi|474934288|ref|YP_007687870.1| 195 SMQKQIDELQTEVRELREENRRLRK 219
                                       89*********************97 PP

>> TolA_bind_tri  TolA binding protein trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   1.0   1.1e-05     0.011      22      43 ..     195     216 ..     189     220 .] 0.87

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.1e-05
                     TolA_bind_tri  22 elqqqlealqqelreLRGqiEe 43 
                                        +q+q+++lq+e+reLR ++ +
  gi|474934288|ref|YP_007687870.1| 195 SMQKQIDELQTEVRELREENRR 216
                                       5****************88765 PP

>> TSC22  TSC-22/dip/bun family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   2.2   1.9e-05     0.018      14      42 ..     191     219 ..     188     220 .] 0.92

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.9e-05
                             TSC22  14 EeVevLkekIkeLeernseleeENslLka 42 
                                       + ++ ++++I eL+ +++el+eEN+ L++
  gi|474934288|ref|YP_007687870.1| 191 DKIDSMQKQIDELQTEVRELREENRRLRK 219
                                       678999*********************96 PP

>> K-box  K-box region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.9   2.5e-05     0.024      61      90 ..     190     219 ..     177     220 .] 0.88

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.5e-05
                             K-box  61 srKeqllleeieelkkkekqleeenkeLre 90 
                                       + K + ++++i+el+ + ++l+een++Lr+
  gi|474934288|ref|YP_007687870.1| 190 ADKIDSMQKQIDELQTEVRELREENRRLRK 219
                                       5678899*********************98 PP

>> RNA_pol_Rpb2_5  RNA polymerase Rpb2, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   9.2e-05     0.087      23      58 .]      34      69 ..      31      69 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.2e-05
                                      EESSTTTCSST-SSTTTSS--TTSSSST-SEEES-G CS
                    RNA_pol_Rpb2_5 23 IamtpedleksreekealeekenskshtyTHcEIhP 58
                                      ++m+ e  + + e k+++++k n ++ht T c+IhP
  gi|474934288|ref|YP_007687870.1| 34 VCMYRESHKLWVEGKKEQARKINYDAHTLTGCDIHP 69
                                      89999999999777778888***************9 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   0.00011       0.1      14      44 ..     190     220 .]     180     220 .] 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YabA  14 eeqleelleeleelkeelaelleenaeLele 44 
                                        +++++++++++el++e+ el een++L+ e
  gi|474934288|ref|YP_007687870.1| 190 ADKIDSMQKQIDELQTEVRELREENRRLRKE 220
                                       5688999999999999999999999999876 PP

>> UPF0184  Uncharacterised protein family (UPF0184)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.9   0.00013      0.12      31      69 ..     182     220 .]     173     220 .] 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                           UPF0184  31 insmLDqinsaLDalEernDdlnskLrELlesnRqiRle 69 
                                        n   D i   +D + ++ D+l++ +rEL e nR+ R+e
  gi|474934288|ref|YP_007687870.1| 182 HNRLPDVIADKIDSMQKQIDELQTEVRELREENRRLRKE 220
                                       56677999999*************************986 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   0.00013      0.12      15      39 ..     189     213 ..     184     220 .] 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                              FlxA  15 sasqiasLqkQiknlqkqLkelses 39 
                                       +a++i s+qkQi++lq +++el e+
  gi|474934288|ref|YP_007687870.1| 189 IADKIDSMQKQIDELQTEVRELREE 213
                                       5789999999999999999999887 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   2.8   0.00018      0.17      20      46 ..     194     220 .]     190     220 .] 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00018
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             DivIC  20 kqlkqeiaalqaelaklkaeneeLeae 46 
                                        +++++i++lq e+ +l++en++L +e
  gi|474934288|ref|YP_007687870.1| 194 DSMQKQIDELQTEVRELREENRRLRKE 220
                                       578899999999999999999999876 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   0.00019      0.18      16      39 ..     189     212 ..     176     219 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00019
                           NPV_P10  16 vddkVdalqqqvddvqenlpdvte 39 
                                       + dk+d++q+q+d++q++++++ e
  gi|474934288|ref|YP_007687870.1| 189 IADKIDSMQKQIDELQTEVRELRE 212
                                       335555555555555555554444 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.9   0.00026      0.25      57      93 ..     183     219 ..      97     220 .] 0.73

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00026
                           DUF4140  57 vpnreaeeeelkalraeleeledelaaledelaaaea 93 
                                       +  ++  ++++++++++++el++e ++l++e +++++
  gi|474934288|ref|YP_007687870.1| 183 NRLPDVIADKIDSMQKQIDELQTEVRELREENRRLRK 219
                                       3333333337*********************999987 PP

>> HALZ  Homeobox associated leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.4    0.0004      0.38      18      41 ..     190     213 ..     187     215 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0004
                              HALZ  18 ksdydsLkkenekLkaelqeLkek 41 
                                       + + ds++k+ ++L++e++eL+e 
  gi|474934288|ref|YP_007687870.1| 190 ADKIDSMQKQIDELQTEVRELREE 213
                                       5578******************95 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       6.5   6.1e+03      45      66 ..     125     146 ..     121     153 .. 0.70
   2 ?   12.0   0.6   0.00015      0.15      81     108 ..     188     215 ..     186     220 .] 0.86

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 6.5
                                       EETTEEEEEE--STTEEEEEEE CS
                         Prefoldin  45 lgaglyvkaevkdtdkvlvdlG 66 
                                       +gag++v +++++ d+v +  G
  gi|474934288|ref|YP_007687870.1| 125 FGAGAIVLGNITIGDDVRIGAG 146
                                       6788888888888888755444 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00015
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  81 llkkkleelekqlekleeeleklkdqit 108
                                       ++ +k+++++kq+++l+ e+++l+++  
  gi|474934288|ref|YP_007687870.1| 188 VIADKIDSMQKQIDELQTEVRELREENR 215
                                       6899*******************99865 PP

>> RBD-FIP  FIP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.59   5.6e+02      27      35 ..       8      16 ..       8      19 .. 0.87
   2 ?    8.7   1.8    0.0017       1.6       3      20 ..     201     218 ..     200     219 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.59
                                      HHHHHHC-G CS
                           RBD-FIP 27 LlrvmEhnP 35
                                      L++vmE  P
  gi|474934288|ref|YP_007687870.1|  8 LQAVMERDP 16
                                      89****999 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0017
                                       HHHHHHHHHHHHHHHHHH CS
                           RBD-FIP   3 deLiqalqkqEeenrrLe 20 
                                       deL+ ++++  eenrrL+
  gi|474934288|ref|YP_007687870.1| 201 DELQTEVRELREENRRLR 218
                                       8****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1079  (0.0601818); expected 358.6 (0.02)
Passed bias filter:                      866  (0.0483016); expected 358.6 (0.02)
Passed Vit filter:                       215  (0.0119917); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 1432.40
//
Query:       gi|474934289|ref|YP_007687871.1|  [L=474]
Description: cysteinyl-tRNA synthetase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   6.4e-124  413.2   0.1   8.9e-124  412.7   0.1    1.2  1  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
    2.8e-14   53.3   1.2    9.1e-14   51.7   0.7    2.1  2  DALR_2        DALR domain
    1.3e-13   50.5   0.3    4.9e-09   35.4   0.1    2.3  2  tRNA-synt_1g  tRNA synthetases class I (M)
    6.3e-07   28.0   0.0     0.0036   15.6   0.0    2.1  2  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)
    2.6e-05   23.3   0.1      0.071   12.0   0.0    2.2  2  tRNA-synt_1f  tRNA synthetases class I (K)
    0.00011   21.3   0.1    0.00027   20.0   0.0    1.6  2  tRNA-synt_1d  tRNA synthetases class I (R)
  ------ inclusion threshold ------
      0.072   13.2   0.0       0.14   12.2   0.0    1.4  1  Mut7-C        Mut7-C RNAse domain


Domain annotation for each model (and alignments):
>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  412.7   0.1  3.5e-127  8.9e-124       2     300 ..      16     319 ..      15     320 .. 0.97

  Alignments for each domain:
  == domain 1  score: 412.7 bits;  conditional E-value: 3.5e-127
                                       ---SBTTEEEEEEEEEBTTS--BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-HHHHHHH CS
                      tRNA-synt_1e   2 vkpleekkvtlYvCGptvydashlGhaRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeksvkelaek 78 
                                       ++p+e++kv++YvCG+tvyd++h+GhaRs+++fD++ r+l++lgYdv+fv n+tD+dDkii+ra+e++ +  +l+++
  gi|474934289|ref|YP_007687871.1|  16 FVPIEKGKVKMYVCGVTVYDDIHMGHARSIIVFDVVSRYLRYLGYDVTFVTNFTDVDDKIINRANERGIEALALSKE 92 
                                       678999*********************************************************************** PP

                                       HHHHHHHHHHHTT----SB--BGGGGHHHHHHHHHHHHHTTSEEE-TTS-EEE-GGG-TTTTTTTT--HHHHHHT-- CS
                      tRNA-synt_1e  79 fieefkkdleaLnvlkptleprvsekvdeiielvekliekgyaYavsdgdvyfdvskkeeYgklskqnleelelgae 155
                                       +ie++++d+e+L+v+++++ p++s  ++ ii++v  +i+kgy Ya++dg vyf v+k ++Yg+ls+++l+e+++  +
  gi|474934289|ref|YP_007687871.1|  93 YIEKYFRDIESLGVRRADIYPQASTSMPYIIDMVRDIIDKGYGYATKDGSVYFRVRKIPDYGQLSNRTLDEMRSSGR 169
                                       ***************************************************************************** PP

                                       --S--S-SSTT-EEEEEE--TTS--B--TTSSEEE-SSHHHHHHHHHHH-SSEEEEEEEGGGTTTHHHHHHHHHHHH CS
                      tRNA-synt_1e 156 gevseekkdkkDfaLWkaskegepswdsPwgkGRPGWhieCsvmaskllgseidihsGGiDLafPhhenelaqseaa 232
                                       ++   +k+d++Dfa+Wk  k+ge+sw+sPwg+GRPGWhieCs+m++++lg+ idih+GG+DL+fPhhene+ q+ea+
  gi|474934289|ref|YP_007687871.1| 170 VDLDPDKEDPMDFAVWKGVKPGEVSWESPWGEGRPGWHIECSAMIRHYLGDVIDIHGGGNDLIFPHHENEILQTEAV 246
                                       ***************************************************************************** PP

                                       SSS--EEEEEEE--EEETTB.....E--TTTT---BHHHHHTTS-HHHHHHHHHSS-TTS-EEE-HHHHHHHH CS
                      tRNA-synt_1e 233 fdkqlvkyflhnghlkiege.....kmsksLknfitikdvlkkfdprqlRllllsahyrsqldfkeelleeak 300
                                       ++++l++y++hng+l+ +g      kmsksLknf++++dv kkfd  ++R++ l++hyrs+l + ee++ ea+
  gi|474934289|ref|YP_007687871.1| 247 TGTHLANYWMHNGMLETKGAdgkavKMSKSLKNFFKVEDVAKKFDKYTIRFYYLNTHYRSPLTYGEENMLEAQ 319
                                       ****************9864444559******************************************98875 PP

>> DALR_2  DALR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.7   0.7   3.6e-17   9.1e-14       2      57 ..     358     415 ..     357     420 .. 0.94
   2 ?   -2.0   0.0         2   5.1e+03      18      32 ..     431     444 ..     427     461 .. 0.61

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 3.6e-17
                                       HHHHHTBT--HHHHHHHHHHHHHHHHH..HHHTT-HHHHHHHHHHHHHHHGGGT-S-S CS
                            DALR_2   2 FeeaMdDDFNTaeAiavlFelakeiNr..alkeedkaaasalkallrelaevLGllqe 57 
                                       F+e+MdDDFNT +Ai +lF  a++ Nr  ++k+ +k+ a+a+ a++ e+ +vLG+l e
  gi|474934289|ref|YP_007687871.1| 358 FRESMDDDFNTRAAIEALFAFARTTNRmmGEKTLTKEGAQAAIAFMDEINDVLGILPE 415
                                       9**************************999999999999**9*************976 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2
                                       HHHHHHHHHHHHHHT CS
                            DALR_2  18 vlFelakeiNralke 32 
                                        l +l ke+++ +k+
  gi|474934289|ref|YP_007687871.1| 431 ILIDLRKELRT-KKQ 444
                                       57788888888.222 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.1   1.9e-12   4.9e-09      12      93 ..      35     117 ..      28     150 .. 0.81
   2 !   12.9   0.0   1.3e-05     0.033     325     357 ..     270     302 ..     206     319 .. 0.77

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 1.9e-12
                                       S---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHTT--.-SE CS
                      tRNA-synt_1g  12 gklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvheeikelfkklnis.fdk 87 
                                       +++H+Gh++++i  D+++Ry r  g++v+fv+       +i  +A+++g+++ +l +++ e++ ++ ++l++   d 
  gi|474934289|ref|YP_007687871.1|  35 DDIHMGHARSIIVFDVVSRYLRYLGYDVTFVTNFTDVDDKIINRANERGIEALALSKEYIEKYFRDIESLGVRrADI 111
                                       579******************************99999*********************************972466 PP

                                       EEETTS CS
                      tRNA-synt_1g  88 ygrtts 93 
                                       y ++++
  gi|474934289|ref|YP_007687871.1| 112 YPQAST 117
                                       655443 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 1.3e-05
                                       -------------HHHHHHHH-HHHHHHHHHHH CS
                      tRNA-synt_1g 325 gkKlSkSrgvvvkakealerldadllRYylaae 357
                                         K+SkS +++ k++++++++d+ ++R+y++ +
  gi|474934289|ref|YP_007687871.1| 270 AVKMSKSLKNFFKVEDVAKKFDKYTIRFYYLNT 302
                                       349*************************99864 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   5.6e-05      0.14      37      67 ..      36      66 ..      20     101 .. 0.92
   2 !   15.6   0.0   1.4e-06    0.0036     523     596 ..     228     305 ..     216     310 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 5.6e-05
                       tRNA-synt_1 37 slHiGhalaktlkdivirykrmkGkevlyvp 67
                                       +H+Gha   ++ d+v ry r  G++v++v+
  gi|474934289|ref|YP_007687871.1| 36 DIHMGHARSIIVFDVVSRYLRYLGYDVTFVT 66
                                      69**************************986 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.4e-06
                       tRNA-synt_1 523 GlDiirgWvarlillslaltgsePfkevlvhglvr..deeGr..KmSKslgNvidpldvikkygadalRltlilsdv 595
                                       G D i+   ++ il++ a+tg +  +  + +g++    ++G+  KmSKsl+N  + +dv+kk     +R++ +++++
  gi|474934289|ref|YP_007687871.1| 228 GNDLIFPHHENEILQTEAVTGTHLANYWMHNGMLEtkGADGKavKMSKSLKNFFKVEDVAKKFDKYTIRFYYLNTHY 304
                                       66666666666666666666666555566666643113445444****************************99987 PP

                       tRNA-synt_1 596 g 596
                                        
  gi|474934289|ref|YP_007687871.1| 305 R 305
                                       5 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   2.8e-05     0.071      21      73 ..      20      73 ..       3     101 .. 0.74
   2 !    9.2   0.0    0.0002      0.51     277     338 ..     267     335 ..     258     351 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.8e-05
                      tRNA-synt_1f 21 ekdev.vvesGispSGliHiGnlrevltadlvaralrkrgeevrlilisDdmDg 73
                                      ek++v +   G+++   iH+G +r ++  d+v r lr +g +v +++   d+D 
  gi|474934289|ref|YP_007687871.1| 20 EKGKVkMYVCGVTVYDDIHMGHARSIIVFDVVSRYLRYLGYDVTFVTNFTDVDD 73
                                      55544134579999999*******************************999995 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0002
                      tRNA-synt_1f 277 kgge.kmssSkGnvltledwlevaepevlrflilrrkPkk......akkldldleilrlvdeYdklerk 338
                                       +g++ kms+S  n++ +ed+ +   + ++rf++l+++ ++      +  l+ +  + rl ++Y +l+++
  gi|474934289|ref|YP_007687871.1| 267 DGKAvKMSKSLKNFFKVEDVAKKFDKYTIRFYYLNTHYRSpltygeENMLEAQAALRRLWNNYRDLQAA 335
                                       44446****************************997654411111144556666666666666666655 PP

>> tRNA-synt_1d  tRNA synthetases class I (R)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0     1e-07   0.00027       2      64 ..       5      66 ..       4      74 .. 0.83
   2 ?   -3.2   0.0       1.2   3.1e+03      82     123 ..     360     401 ..     357     412 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1e-07
                                      HHHHHCCTTTT.---SST-EEEEE----BTTS--BHHHHHHHHHHHHHHHHHHHCT-EEEEEE CS
                      tRNA-synt_1d  2 vssiLvqkrklqkksrekkkvvvdfssPniakemhvGhLrstiiGdavsrlleflGydvirln 64
                                      +++ L++k++      ek kv +      +  ++h+Gh rs i+ d+vsr l +lGydv+ + 
  gi|474934289|ref|YP_007687871.1|  5 IQNTLTNKKEE-FVPIEKGKVKMYVCGVTVYDDIHMGHARSIIVFDVVSRYLRYLGYDVTFVT 66
                                      67777777774.66777888888888889999***************************9664 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.2
                                       HHTTTTTTS-----SCCCHHHHHHHHCCCSHCCCHHHHHHHH CS
                      tRNA-synt_1d  82 kkqdekllqeqelqdLeafykeakkdydeeeifaerarnyvv 123
                                       +  d+   ++  ++ L+af + +++ + e    +e a+  + 
  gi|474934289|ref|YP_007687871.1| 360 ESMDDDFNTRAAIEALFAFARTTNRMMGEKTLTKEGAQAAIA 401
                                       556666677788888888888888877777776666665554 PP

>> Mut7-C  Mut7-C RNAse domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   5.6e-05      0.14      11      51 ..      50      92 ..      46     114 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.6e-05
                            Mut7-C 11 klakyLRllGydalyasdv..edeellalaakekrillTrdre 51
                                       +++yLR lGyd+ + +++   d++++++a++++   l  ++e
  gi|474934289|ref|YP_007687871.1| 50 VVSRYLRYLGYDVTFVTNFtdVDDKIINRANERGIEALALSKE 92
                                      589*********9976655337899****99987655555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.63u 0.26s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 3137.05
//
Query:       gi|474934290|ref|YP_007687872.1|  [L=308]
Description: conserved hypothetical protein TIGR00269 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-13   50.8   0.0    3.4e-13   49.7   0.0    1.5  1  ATP_bind_3      PP-loop family
     0.0094   14.8   0.0       0.03   13.1   0.0    1.7  1  tRNA_Me_trans   tRNA methyl transferase
  ------ inclusion threshold ------
      0.049   13.6   0.3      0.093   12.7   0.3    1.4  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an


Domain annotation for each model (and alignments):
>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   0.0   5.7e-17   3.4e-13       3     122 ..      51     181 ..      49     200 .. 0.88

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 5.7e-17
                                       EEE--SCHHHHHHHHHHHHH.CTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H.......... CS
                        ATP_bind_3   3 lvAvSgGlDSmaLllllakl.kkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvdv.......... 68 
                                        vAvSgG DSm+ l +l++l ++k+gi+lv+i +d g+        ++v+++c+ ++i+++  +++           
  gi|474934290|ref|YP_007687872.1|  51 GVAVSGGKDSMVVLSILNSLfNTKNGIRLVCIAIDEGIEGYRPPSLDIVRKFCSDHGIEYRQRSFSElggltmdsia 127
                                       69************9999872567888***************************************99999988774 PP

                                       HHCT.TSTCCCHHHHHHHHHHHHCHHCCT.CEEE---BHHHHHHHHHHHHCCT-- CS
                        ATP_bind_3  69 akkk.gknleeaARelRYevlkealkkegievlllAhhadDqaEtfllrlargsg 122
                                          +  ++  +    +R ++++  ++k g+++l+++h+ dD a  +++++ rg  
  gi|474934290|ref|YP_007687872.1| 128 P-VSgDSSPCTYCGVFRRKLMNDEARKVGAKYLATGHNLDDLAQSVMMNFVRGDV 181
                                       2.33144455778899************************************976 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0     5e-06      0.03       3     124 ..      50     163 ..      48     173 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5e-06
                     tRNA_Me_trans   3 vvvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfekeykekvf 79 
                                       v va+SgG DS v++ +l++ +    g+ l +++  de   e      l  +++ ++  gi++++ +f++     + 
  gi|474934290|ref|YP_007687872.1|  50 VGVAVSGGKDSMVVLSILNSLFNTKNGIRLVCIAI-DEGI-EGYRPPSLDIVRKFCSDHGIEYRQRSFSEL--GGLT 122
                                       78****************************99998.3333.46667778899*************999875..3344 PP

                     tRNA_Me_trans  80 eefleeyeeGrTPnPdvlCNkeiKfgallekakeelgadalatGH 124
                                        + +   + G   +P+  C    + +++ ++a +  ga++latGH
  gi|474934290|ref|YP_007687872.1| 123 MDSIAPVS-GD-SSPCTYCGVF-RRKLMNDEARK-VGAKYLATGH 163
                                       44454443.44.3789999643.44556666665.8999999998 PP

>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.3   1.6e-05     0.093      13      37 ..      36      61 ..      36      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.6e-05
                                      CCCHHHCCEECTCEEEEEECTT.CCC CS
                    MazE_antitoxin 13 kevrfelgireGdevelevdgd.kii 37
                                      ke+r+e ++r+Gd v + v g+ +++
  gi|474934290|ref|YP_007687872.1| 36 KEIRKEVDLRRGDVVGVAVSGGkDSM 61
                                      8******************9996554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2165.82
//
Query:       gi|474934291|ref|YP_007687873.1|  [L=395]
Description: orc1/cdc6 family replication initiation protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-12   47.9   0.0    3.9e-12   46.6   0.0    1.6  1  AAA_22        AAA domain
    7.1e-09   36.3   0.2    1.2e-06   29.0   0.0    3.2  3  AAA_16        AAA ATPase domain
    2.3e-07   31.3   0.0    4.5e-07   30.3   0.0    1.5  1  AAA           ATPase family associated with various cellular 
    6.2e-07   29.3   0.0    1.5e-06   28.1   0.0    1.6  1  Cdc6_C        CDC6, C terminal winged helix domain
    7.5e-05   22.2   0.0    0.00014   21.4   0.0    1.4  1  TniB          Bacterial TniB protein
     0.0001   22.3   0.9    0.00094   19.2   0.9    2.2  1  ATPase_2      ATPase domain predominantly from Archaea
     0.0012   18.2   0.0     0.0016   17.7   0.0    1.3  1  DUF2075       Uncharacterized conserved protein (DUF2075)
     0.0038   16.6   0.2        1.5    8.1   0.0    2.3  2  ATPase        KaiC
     0.0041   17.0   0.0     0.0074   16.2   0.0    1.3  1  NACHT         NACHT domain
      0.005   17.1   0.0      0.012   16.0   0.0    1.6  1  AAA_assoc_2   AAA C-terminal domain
  ------ inclusion threshold ------
      0.028   13.2   0.0       0.26   10.0   0.0    2.0  2  AAA_32        AAA domain
      0.045   13.8   0.0       0.14   12.2   0.0    1.9  2  AAA_14        AAA domain
      0.052   13.7   0.0       0.25   11.5   0.0    2.2  2  TIP49_C       TIP49 AAA-lid domain
      0.099   11.5   0.0       0.14   10.9   0.0    1.3  1  AAA_35        AAA-like domain
       0.13   12.7   0.0       0.29   11.6   0.0    1.6  1  RNA_helicase  RNA helicase
       0.16   11.4   0.0       0.29   10.6   0.0    1.4  1  AAA_7         P-loop containing dynein motor region


Domain annotation for each model (and alignments):
>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   0.0   3.4e-15   3.9e-12       9     134 ..      51     181 ..      49     183 .. 0.92

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 3.4e-15
                            AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellealeqa 85 
                                       +vtG +GtGKT+++r++ +    e +   ++ ++++v++  ++s   ++ el+r +++  ++++ s +++++ l q+
  gi|474934291|ref|YP_007687873.1|  51 YVTGSVGTGKTVTVRKFCSDMRGEFSVSGKSLDIIYVNCRLKNSEYGVMLELVRHYDRLFSDRGFSVDQMISSLKQH 127
                                       89*****************9988888888****************************87777999************ PP

                            AAA_22  86 lraravielliiDEaqh.lr.s.eealeeLrsllnl..srkgvqliLvGtpelr 134
                                       +++ ++++++i+DEa+  lr s ++++ +L +++++  +  +v+liL+ +++l+
  gi|474934291|ref|YP_007687873.1| 128 INSEKTPVVIILDEADViLRsSaKNVVYQLTRFSEDatAGIPVSLILISQYSLQ 181
                                       *****************776647*******9**999999999999999999886 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   1.1e-09   1.2e-06       1     160 [.      23     159 ..      23     175 .. 0.65
   2 ?   -0.0   0.1      0.89     1e+03      57     144 ..     157     271 ..     142     306 .. 0.46
   3 ?   -0.5   0.0       1.2   1.4e+03      57      91 ..     331     359 ..     300     391 .. 0.62

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 1.1e-09
                            AAA_16   1 rlvGReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellralekdggif.lrgkcdqlesaipysalaqa 75 
                                       +lv+R++++ +L++a++++  +   +  +++G  G+GK+  vr++   ++++   f ++gk  +        +++++
  gi|474934291|ref|YP_007687873.1|  23 KLVCRDAQMTELENAFRPLFFNNVpCTAYVTGSVGTGKTVTVRKFCSDMRGE---FsVSGKSLDI-------IYVNC 89 
                                       69***************8887777699*******************988877...4455555555.......34444 PP

                            AAA_16  76 lareellrqlldeaesaeleawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlqwadeasl 152
                                         +++ +  +l+      + ++r + ++ ++           ++   lk+++    +++ p+v++lD+++ +  +s+
  gi|474934291|ref|YP_007687873.1|  90 RLKNSEYGVMLEL----VRHYDRLFSDRGFS---------VDQMISSLKQHI---NSEKTPVVIILDEADVILRSSA 150
                                       4444443333333....34444444444433.........344555555555...4446789999999986666555 PP

                            AAA_16 153 ql.laaLlr 160
                                       +   ++L r
  gi|474934291|ref|YP_007687873.1| 151 KNvVYQLTR 159
                                       443666555 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.89
                            AAA_16  57 rgkcdql.esaipysa.laqalareellrqlldeaesaeleawrekleeala...................avpela 112
                                        +++ +  +++ip s  l+++ +   l   l+++++s+  +    k+++  +                   +     
  gi|474934291|ref|YP_007687873.1| 157 LTRFSEDaTAGIPVSLiLISQYSLQALA--LDQASQSSFGRSGTVKFDKYNEdqlrdivklradlalgpgsI----- 226
                                       4444444455566633344444221111..111111211222222222222233332222333333334331..... PP

                            AAA_16 113 gaea................srllellkrll.allsrderplvlvlDdl 144
                                                            rl+ ++ + + +l+++ +   ++ lD++
  gi|474934291|ref|YP_007687873.1| 227 ---TddgigmiakisapygdARLAMEILEKAaNLAET-KGARYIDLDHI 271
                                       ...0333333334444444566666666666355555.44466666655 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1.2
                            AAA_16  57 rgkcdqlesaipysalaqalareellrqlldeaes 91 
                                       + k+      + y+++++ l++++l++ +l+++ +
  gi|474934291|ref|YP_007687873.1| 331 AKKY------TQYYTYVKDLEARSLIKTELRPEPA 359
                                       2233......5568888888899999999888433 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0     4e-10   4.5e-07       2     111 ..      51     178 ..      50     196 .. 0.73

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 4e-10
                                       EEESSTTSSHHHHHHHHHHHH.........THEEEEEETTTCSSS.............STTHHHHHHHHHHHHHHHT CS
                               AAA   2 llyGppGtGKTllakavakel.........gvefleisgsellsk.............yvgesekkirelfkeakek 56 
                                       +++G  GtGKT +++  ++++         + +++ +++    s+             +++++  ++ ++++++k++
  gi|474934291|ref|YP_007687873.1|  51 YVTGSVGTGKTVTVRKFCSDMrgefsvsgkSLDIIYVNCRLKNSEygvmlelvrhydrLFSDRGFSVDQMISSLKQH 127
                                       689*****************944433333223344444443333388888888888886666666666666666655 PP

                                       S....TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS CS
                               AAA  57 a....kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnr 111
                                            +p+++++DE+d + +s+       +++vv qL ++ ++ +    +v +i+++++
  gi|474934291|ref|YP_007687873.1| 128 InsekTPVVIILDEADVILRSS-------AKNVVYQLTRFSEDATAG-IPVSLILISQY 178
                                       5566679**************9.......999999999999999885.44777777765 PP

>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   1.3e-09   1.5e-06       1      75 [.     298     369 ..     298     378 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 1.3e-09
                                       HHHHHHHHCHCSSS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEES CS
                            Cdc6_C   1 LcalvlllrksgkeevttgevyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtrkisLn 75 
                                       L+++++ l   +++evtt  ++ +Y   Ce+ gv + + ++++ ++++Le++ ++++e + +   +gr ++i+++
  gi|474934291|ref|YP_007687873.1| 298 LLSIARSLF--KNPEVTTLHAQGTYAAACEEFGVPAKKYTQYYTYVKDLEARSLIKTELRPEPA-GGRATYITIT 369
                                       667777655..799********************************************997765.6999999884 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.2e-07   0.00014      38     138 ..      50     152 ..      28     172 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.2e-07
                              TniB  38 lllvGdsnnGKtmivekFarlhppekdedaekvpvlvvqappkpdekrlyaaiLealgaplkara.rvskleqqvlr 113
                                       +++ G   +GKt+ v+kF+++ + e + + +++++++v+++ k +e +   +++++    ++ r  +v+++ +   +
  gi|474934291|ref|YP_007687873.1|  50 AYVTGSVGTGKTVTVRKFCSDMRGEFSVSGKSLDIIYVNCRLKNSEYGVMLELVRHYDRLFSDRGfSVDQMISSLKQ 126
                                       57899**************************************************9999998876566666666666 PP

                              TniB 114 llrel.kvrvLiiDEihnllagsark 138
                                        +++   + v+i+DE + +l+ sa++
  gi|474934291|ref|YP_007687873.1| 127 HINSEkTPVVIILDEADVILRSSAKN 152
                                       6655405567889*******988765 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.9   8.3e-07   0.00094      24     157 ..      51     169 ..      44     217 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 8.3e-07
                          ATPase_2  24 fiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekalgiavpkaeleeilkeksk 100
                                       +++G+ g GKt  ++++ +  +       +  + ++ +i +++  +    ++++   + ++ v+    +++++++  
  gi|474934291|ref|YP_007687873.1|  51 YVTGSVGTGKTVTVRKFCSDMRG-----EFSVSGKSLDIIYVNCRL----KNSEYGVM-LELVR--HYDRLFSDRGF 115
                                       56666666666666666665522.....344455555555554442....12211111.22222..35567888889 PP

                          ATPase_2 101 lvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLlnliesltkekh 157
                                        v++ i++l++ i+ +++ ++ii+De+  +      +a+++v++L ++ e+ t+   
  gi|474934291|ref|YP_007687873.1| 116 SVDQMISSLKQHINSEKTPVVIILDEADVIL--R-SSAKNVVYQLTRFSEDATAGIP 169
                                       ****************************999..5.5599*********999776544 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.4e-06    0.0016       5     109 ..      51     154 ..      47     214 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.4e-06
                           DUF2075   5 lVtGvaGtGKtvvllnllael..eddeeertavylsvNhplvl...vlrealakkeekkkkkeafeklssfinnlse 76 
                                        VtG  GtGKtv   ++  ++  e + ++++  +++vN +l +    +  +l ++  ++ ++++   ++++i +l+ 
  gi|474934291|ref|YP_007687873.1|  51 YVTGSVGTGKTVTVRKFCSDMrgEFSVSGKSLDIIYVNCRLKNseyGVMLELVRHY-DRLFSDRGFSVDQMISSLK- 125
                                       69*******************999999*************9993333334555666.7888888889999999999. PP

                           DUF2075  77 fkkaeekkeepkedvvivDEAhrlltksdqaek 109
                                           ++ ++e++  v+i DEA  +l +s ++  
  gi|474934291|ref|YP_007687873.1| 126 ----QHINSEKTPVVIILDEADVILRSSAKNVV 154
                                       ....7777888888999****999986665444 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.1     0.005       5.6      23      40 ..      51      68 ..      47      77 .. 0.88
   2 !    8.1   0.0    0.0013       1.5      84     194 ..      98     208 ..      89     235 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.005
                            ATPase 23 litGepGtGKtifalqFl 40
                                       +tG+ GtGKt+ + +F 
  gi|474934291|ref|YP_007687873.1| 51 YVTGSVGTGKTVTVRKFC 68
                                      69************9996 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0013
                            ATPase  84 aiidasesaeesaeekdkedleelieelaeaikeika.krvviDsitglayeekeavaReilrqlvrvl.kklgvTa 158
                                       ++++++++ ++  + ++ ++++++i++l++ i++ k    +++D  +++  +++++ +  +l ++ +   +++ v  
  gi|474934291|ref|YP_007687873.1|  98 VMLELVRHYDRLFS-DRGFSVDQMISSLKQHINSEKTpVVIILDEADVI-LRSSAKNVVYQLTRFSEDAtAGIPVSL 172
                                       55666666555333.77899************99888466778******.88888888889999998877999**** PP

                            ATPase 159 ilvsekssseeaaggygveefivdgvivLdlkeiee 194
                                       il+s+ s ++ a  +   + f  +g+++ d+  +++
  gi|474934291|ref|YP_007687873.1| 173 ILISQYSLQALALDQASQSSFGRSGTVKFDKYNEDQ 208
                                       *****9999999999999999999999998554443 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   6.6e-06    0.0074       4      95 ..      51     147 ..      49     168 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6.6e-06
                                       EEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-........-HCHHHCCCCTS--SSS-CCHHH CS
                             NACHT   4 ilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgna.....rsladllfsqlpepaapvsevwav 75 
                                        ++G  G GKT+ ++k++++++ +   +g+   ++++++r  + +  +     r+ ++l  + +    + +s   ++
  gi|474934291|ref|YP_007687873.1|  51 YVTGSVGTGKTVTVRKFCSDMRGEFSVSGKSLDIIYVNCRLKNSEYGVmlelvRHYDRLFSDRGFSVDQMISSLKQH 127
                                       689*********************9999999999*****9998887778999999999999999999********** PP

                                       HCCSCCCEEEEEE-STT-SS CS
                             NACHT  76 llelperlLlilDglDelvt 95 
                                       + + ++ +++ilD +D + +
  gi|474934291|ref|YP_007687873.1| 128 INSEKTPVVIILDEADVILR 147
                                       ***************98765 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.1e-05     0.012       7      54 ..     226     274 ..     222     285 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.1e-05
                                       XXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXX CS
                       AAA_assoc_2   7 leddalealaelad..GDaRkaLnlLElaaeaaeakegkieitledleea 54 
                                       ++dd + ++a+++   GDaR a+ +LE aa+ ae+ +g + i+l+++++a
  gi|474934291|ref|YP_007687873.1| 226 ITDDGIGMIAKISApyGDARLAMEILEKAANLAET-KGARYIDLDHIRTA 274
                                       7788888888888555***********99999987.999******99876 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00023      0.26      34     105 ..      51     129 ..      48     134 .. 0.80
   2 ?    0.6   0.0      0.16   1.8e+02     480     507 ..     247     274 ..     241     278 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00023
                            AAA_32  34 fvlGesgtGrttlvkrlleeiakkeptpd...DwcYvn.nfdnpeePkalsLpaGkGkelkkd...meelveelkke 103
                                       +v+G+ gtG+t +v+++ +++  + ++     D++Yvn   +n e  ++l+L     + ++++   +++++++lk+ 
  gi|474934291|ref|YP_007687873.1|  51 YVTGSVGTGKTVTVRKFCSDMRGEFSVSGkslDIIYVNcRLKNSEYGVMLELVRHYDRLFSDRgfsVDQMISSLKQH 127
                                       9*******************988877663445*****8568999999999999998888887433377777777777 PP

                            AAA_32 104 ip 105
                                       i+
  gi|474934291|ref|YP_007687873.1| 128 IN 129
                                       65 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.16
                            AAA_32 480 iadllrEAdywakkegaevveaehVekA 507
                                        +++l+ A+ +a+++ga++++ +h+++A
  gi|474934291|ref|YP_007687873.1| 247 AMEILEKAANLAETKGARYIDLDHIRTA 274
                                       6799*********************998 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00013      0.14       6      76 ..      51     145 ..      48     201 .. 0.74
   2 ?   -2.2   0.0       3.5     4e+03      28      50 ..     258     280 ..     246     298 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                            AAA_14   6 vitGaRrvGKTtllkqlikell......vkkesilyinldderd...............kkladpe.......klle 54 
                                        +tG   +GKT+ ++++ ++         k+ +i+y+n+  ++                      +       ++++
  gi|474934291|ref|YP_007687873.1|  51 YVTGSVGTGKTVTVRKFCSDMRgefsvsGKSLDIIYVNCRLKNSeygvmlelvrhydrlF-----SdrgfsvdQMIS 122
                                       5899999**********99988999*988999*******998887888887776544331.....134452334444 PP

                            AAA_14  55 lileklke.ekktylflDEiqev 76 
                                        +++++++ +   +++lDE+  +
  gi|474934291|ref|YP_007687873.1| 123 SLKQHINSeKTPVVIILDEADVI 145
                                       44444433456677999*98765 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.5
                            AAA_14  28 vkkesilyinldderdkkladpe 50 
                                       ++ +   yi+ld+ r++ ++ ++
  gi|474934291|ref|YP_007687873.1| 258 AETKGARYIDLDHIRTAGASVYS 280
                                       45666778888888776655444 PP

>> TIP49_C  TIP49 AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       4.5   5.1e+03      49      66 .]      95     112 ..      84     112 .. 0.76
   2 ?   11.5   0.0   0.00023      0.25      13      60 ..     226     274 ..     212     279 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4.5
                           TIP49_C  49 kkevevedveeveeLFlD 66 
                                       +  v +e v+  ++LF D
  gi|474934291|ref|YP_007687873.1|  95 EYGVMLELVRHYDRLFSD 112
                                       44588899999999*998 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00023
                           TIP49_C  13 ldeeAldlLakigtetS.LRYaiqLltpasilakkrkkkevevedveev 60 
                                       ++++++ ++aki+   +  R a++ l+ a  la++++++ +++++++ +
  gi|474934291|ref|YP_007687873.1| 226 ITDDGIGMIAKISAPYGdARLAMEILEKAANLAETKGARYIDLDHIRTA 274
                                       8899999999999887647***************************976 PP

>> AAA_35  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00013      0.14     117     211 ..     124     214 ..      94     255 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00013
                            AAA_35 117 leeylLkeidkplvLaldevdrlfeypeiakdflslLRswheeaknkeiwqkLrLvvvhstevyipldinqSpfnvG 193
                                       l++++ ++ ++p+v++lde d ++   + ak+++  L  ++e+a    i   L L+  +s ++    + +qS f   
  gi|474934291|ref|YP_007687873.1| 124 LKQHI-NSEKTPVVIILDEADVILR--SSAKNVVYQLTRFSEDATA-GIPVSLILISQYSLQALALDQASQSSFGRS 196
                                       55555.34479*************9..5567888888888888765.556689*********************999 PP

                            AAA_35 194 lpieLpeFtkeqvqeLaq 211
                                        +++  +++++q +++ +
  gi|474934291|ref|YP_007687873.1| 197 GTVKFDKYNEDQLRDIVK 214
                                       999*********999876 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00026      0.29       2      85 ..      51     136 ..      50     152 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00026
                      RNA_helicase   2 wlyGpsgeGKStlakeLakallkkl..klkkkdsvysrnpeddfwdgYtgqevvvidDfgqvkdeenpsdlaelirl 76 
                                       +++G+ g+GK+++++++++++ +++    k+ d +y++   ++  +g   + v  +d + +++  + +++++ l + 
  gi|474934291|ref|YP_007687873.1|  51 YVTGSVGTGKTVTVRKFCSDMRGEFsvSGKSLDIIYVNCRLKNSEYGVMLELVRHYDRLFSDRGFSVDQMISSLKQH 127
                                       899*******************9985433333445554444555577777777777777777655456677777777 PP

                      RNA_helicase  77 vsstpypln 85 
                                       ++s + p+ 
  gi|474934291|ref|YP_007687873.1| 128 INSEKTPVV 136
                                       777776665 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00026      0.29      37      58 ..      51      72 ..      30      83 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00026
                             AAA_7 37 llvGptGtGKtviikdllkkld 58
                                       ++G++GtGKtv+++++++ + 
  gi|474934291|ref|YP_007687873.1| 51 YVTGSVGTGKTVTVRKFCSDMR 72
                                      689*************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.47
# Mc/sec: 2514.10
//
Query:       gi|474934292|ref|YP_007687874.1|  [L=320]
Description: hypothetical protein TALC_00717 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      576  (0.0321267); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 2268.57
//
Query:       gi|474934293|ref|YP_007687875.1|  [L=318]
Description: replication factor C small subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-20   73.7   0.1    2.7e-20   72.6   0.1    1.6  1  Rep_fac_C        Replication factor C C-terminal domain
    2.6e-16   60.2   0.0    5.3e-16   59.2   0.0    1.6  1  AAA              ATPase family associated with various cellul
    1.2e-12   47.9   0.0    4.4e-09   36.3   0.0    2.9  3  DNA_pol3_delta2  DNA polymerase III, delta subunit
    2.3e-09   37.2   0.0    3.4e-08   33.4   0.0    2.2  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    7.6e-07   29.1   0.0    1.4e-06   28.2   0.0    1.4  1  DNA_pol3_delta   DNA polymerase III, delta subunit
    3.7e-05   24.0   1.6    5.3e-05   23.5   0.3    2.2  1  AAA_assoc_2      AAA C-terminal domain
    0.00023   21.2   0.0     0.0015   18.6   0.0    2.2  2  AAA_14           AAA domain
    0.00035   20.0   0.0      0.049   13.0   0.0    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00043   20.2   0.0    0.00099   19.1   0.0    1.5  1  Rad17            Rad17 P-loop domain
    0.00058   20.4   0.0    0.00098   19.7   0.0    1.5  1  AAA_18           AAA domain
     0.0011   18.6   0.0     0.0018   17.9   0.0    1.4  1  AAA_25           AAA domain
     0.0011   19.0   0.0     0.0037   17.3   0.0    1.9  1  ResIII           Type III restriction enzyme, res subunit
     0.0016   18.2   0.0     0.0032   17.2   0.0    1.5  1  AAA_24           AAA domain
      0.004   16.5   0.0      0.066   12.6   0.0    2.3  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
  ------ inclusion threshold ------
      0.013   15.0   0.0       0.02   14.4   0.0    1.3  1  AAA_7            P-loop containing dynein motor region
      0.014   15.4   0.0       0.11   12.4   0.0    2.4  1  AAA_5            AAA domain (dynein-related subfamily)
      0.016   15.6   0.0      0.058   13.8   0.0    1.9  1  AAA_16           AAA ATPase domain
      0.016   14.4   0.0       0.04   13.1   0.0    1.7  1  TIP49            TIP49 P-loop domain
      0.017   15.4   0.4        1.8    8.9   0.1    2.5  2  AAA_22           AAA domain
      0.028   14.7   0.0      0.052   13.8   0.0    1.5  1  AAA_28           AAA domain
      0.033   14.3   0.0       0.17   12.0   0.0    2.1  1  Sigma54_activ_2  Sigma-54 interaction domain
      0.037   13.9   0.0      0.068   13.0   0.0    1.4  1  AAA_3            ATPase family associated with various cellul
      0.052   12.5   0.0       0.12   11.3   0.0    1.5  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
      0.056   12.7   0.0       0.12   11.6   0.0    1.6  1  Zeta_toxin       Zeta toxin
      0.064   13.0   0.0        0.1   12.3   0.0    1.3  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.077   13.1   0.0       0.16   12.0   0.0    1.5  1  Torsin           Torsin
        0.1   12.3   0.0       0.17   11.6   0.0    1.4  1  IstB_IS21        IstB-like ATP binding protein
       0.17   11.6   0.1        4.4    7.0   0.0    2.5  2  DEAD             DEAD/DEAH box helicase
       0.17   11.6   0.0       0.22   11.3   0.0    1.3  1  AAA_11           AAA domain
       0.28   10.2   0.0       0.42    9.6   0.0    1.1  1  BAF1_ABF1        BAF1 / ABF1 chromatin reorganising factor


Domain annotation for each model (and alignments):
>> Rep_fac_C  Replication factor C C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.6   0.1   4.5e-23   2.7e-20       1      87 [.     224     309 ..     224     310 .. 0.96

  Alignments for each domain:
  == domain 1  score: 72.6 bits;  conditional E-value: 4.5e-23
                                       --HHHHHHHHHHHHHT-HHHHHHHHHHHHHHC---HHHHHHHHHHHGCCS..S-HHHHHHHHHHHHHHHHHHHCTH- CS
                         Rep_fac_C   1 phpteieeileaclngdfeeaykklrellvekGysaediltqlhrvvkeqeelpeaqkleilellgeiekrlveGas 77 
                                       p++++i  ++ a+l g+f ea++ l++ ++e+G+s++d+++q+h  +++   l+ + k++++++ ge+e+r++eG++
  gi|474934293|ref|YP_007687875.1| 224 PNEEDILGVMTAALDGKFVEASNLLDKVMIEYGLSGQDVIKQMHSEIFKL-PLETRDKVRLIDKTGEVEFRIIEGSN 299
                                       789999999****99*********************************96.6999********************** PP

                                       HHHHHHHHHH CS
                         Rep_fac_C  78 ehlqlsalla 87 
                                       e++ql+al+a
  gi|474934293|ref|YP_007687875.1| 300 EKIQLEALIA 309
                                       *********8 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.2   0.0   8.9e-19   5.3e-16       2     130 ..      40     157 ..      39     159 .. 0.91

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 8.9e-19
                                       EEESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHH CS
                               AAA   2 llyGppGtGKTllakavakel.....gvefleisgsellskyvgesekkirelfkeakeka.kpsilfiDEidalak 72 
                                       ++ G+pGtGKT++  a+a+e+     + +fle+++s+ +   +     +i+++ k+a     + +i+f+DE+dal++
  gi|474934293|ref|YP_007687875.1|  40 MFAGTPGTGKTTCSLALAREMygdswKGNFLELNASDER--GIDVVRGRIKDFAKTAPIDGaEFKIIFLDEADALTN 114
                                       799*****************866555799**********..999**********9997777566***********98 PP

                                       HHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEEEET CS
                               AAA  73 srsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrkiei 130
                                       +            + +L + ++ +++   ++ +i+ +n+ +k+ +++  +R+ +  + 
  gi|474934293|ref|YP_007687875.1| 115 DA-----------QGALRRTMEMYSR---TCRFIISCNYSSKIIDPIQ-SRCAVFRFR 157
                                       88...........*************...69*****************.9**987765 PP

>> DNA_pol3_delta2  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0042       2.5       1      45 [.      19      62 ..      19      75 .. 0.90
   2 !   36.3   0.0   7.4e-12   4.4e-09      84     162 ..      79     159 ..      69     160 .. 0.89
   3 ?   -0.2   0.0       1.2   7.4e+02      85     112 ..     260     287 ..     186     293 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0042
                   DNA_pol3_delta2  1 gqeealkilskalksgrlahayLfeGdegigkkelalnlakallc 45
                                      gq+++ + l++ ++  +++h ++f+G+ g+gk ++ l+la+++  
  gi|474934293|ref|YP_007687875.1| 19 GQKNVTERLKGYVEARNMSH-LMFAGTPGTGKTTCSLALAREMYG 62
                                      69999*************99.79*****************99875 PP

  == domain 2  score: 36.3 bits;  conditional E-value: 7.4e-12
                   DNA_pol3_delta2  84 kldqir.elieelsrkpre.skkkiiiiedaekmtksAaNalLktlEEPsenaifiLitsdtnklLktirSRcqelk 158
                                        +d +r +++++++  p+  ++ kii +++a+ +t+ A+ al +t+E  s+   fi+  + ++k++++i+SRc +++
  gi|474934293|ref|YP_007687875.1|  79 GIDVVRgRIKDFAKTAPIDgAEFKIIFLDEADALTNDAQGALRRTMEMYSRTCRFIISCNYSSKIIDPIQSRCAVFR 155
                                       68999966666667777777789****************************************************** PP

                   DNA_pol3_delta2 159 fspl 162
                                       f+pl
  gi|474934293|ref|YP_007687875.1| 156 FRPL 159
                                       **98 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 1.2
                   DNA_pol3_delta2  85 ldqirelieelsrkpreskkkiiiieda 112
                                        d i+++ +e+ + p e + k+ +i++ 
  gi|474934293|ref|YP_007687875.1| 260 QDVIKQMHSEIFKLPLETRDKVRLIDKT 287
                                       5788999999999999999999999875 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.0   5.8e-11   3.4e-08       2      58 ..      10      61 ..       9      75 .. 0.93
   2 ?    1.2   0.0      0.45   2.7e+02      85     111 ..     101     127 ..      85     144 .. 0.88

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 5.8e-11
                            RuvB_N  2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelg 58
                                      rPk+l+e igq++v+e+lk ++ea      ++ h++++G PG Gktt +  +a+e+ 
  gi|474934293|ref|YP_007687875.1| 10 RPKKLDEVIGQKNVTERLKGYVEAR-----NMSHLMFAGTPGTGKTTCSLALAREMY 61
                                      9*********************984.....578**********************96 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.45
                            RuvB_N  85 kdvlfideihrlsraveevlysamedf 111
                                        +++f+de   l++ ++  l  +me +
  gi|474934293|ref|YP_007687875.1| 101 FKIIFLDEADALTNDAQGALRRTMEMY 127
                                       579*******************99987 PP

>> DNA_pol3_delta  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   2.3e-09   1.4e-06      58     170 ..     101     203 ..      69     205 .. 0.92

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 2.3e-09
                                       EEEEEEE--.....TT-S-TTHHHHHHHHTTT--SSEEEEEEES.S--HHHHHHHHHTTTEEEEEE----TTTHHHH CS
                    DNA_pol3_delta  58 krivvlknpklltkesklnekllkeLeeylsnlpedtlLiliapkklderkklvklLkkkatvveaktlkeeelkkw 134
                                        +i++l+ +      + l+ + + +L ++++ ++ ++ +i+ ++       k+++ ++++  v+++ +l++++++++
  gi|474934293|ref|YP_007687875.1| 101 FKIIFLDEA------DALTNDAQGALRRTMEMYSRTCRFIISCN----YSSKIIDPIQSRCAVFRFRPLNNDDIREY 167
                                       577777777......66899999*********************....5578************************* PP

                                       HHHHHHHTT-EE-HHHHHHHHHHHTT-HHHHHHHHH CS
                    DNA_pol3_delta 135 iqkraqelglkiekealelLlelvennlsaikqele 170
                                       +++++++++l++e+ a++ L++  +++++ + + l+
  gi|474934293|ref|YP_007687875.1| 168 LERIVAAENLDMEEGAMDALVYIASGDMRKAVNTLQ 203
                                       *****************************9999886 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.3   8.8e-08   5.3e-05       3      38 ..     175     210 ..     173     295 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 8.8e-08
                                       X.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       AAA_assoc_2   3 kklkleddalealaeladGDaRkaLnlLElaaeaae 38 
                                       ++l++e+ a++al+ +a+GD+Rka n+L++aa+  +
  gi|474934293|ref|YP_007687875.1| 175 ENLDMEEGAMDALVYIASGDMRKAVNTLQTAASLGA 210
                                       57899************************9987654 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.88   5.2e+02      70      98 ..      14      42 ..       2      45 .. 0.69
   2 !   18.6   0.0   2.5e-06    0.0015       8      99 ..      42     137 ..      35     167 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.88
                            AAA_14 70 lDEiqevpewekalkslvdegknldvivt 98
                                      lDE+   +++ + lk++v+ ++  +++++
  gi|474934293|ref|YP_007687875.1| 14 LDEVIGQKNVTERLKGYVEARNMSHLMFA 42
                                      67777777777777777777655555555 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 2.5e-06
                            AAA_14   8 tGaRrvGKTtllkqlikell..vkkesilyinldderdkkladpekllelilek.lkeekktylflDEiqev.pewe 80 
                                        G   +GKTt    l++e +    k ++l++n  der  +     ++ ++ +   + + + +++flDE+  + ++++
  gi|474934293|ref|YP_007687875.1|  42 AGTPGTGKTTCSLALAREMYgdSWKGNFLELNASDERGIDVVRG-RIKDFAKTApIDGAEFKIIFLDEADALtNDAQ 117
                                       677789**************998899999999999999775544.355555555666678999******9873679* PP

                            AAA_14  81 kalkslvdeg.knldvivtG 99 
                                        al++ ++ + + +++i++ 
  gi|474934293|ref|YP_007687875.1| 118 GALRRTMEMYsRTCRFIISC 137
                                       ********886789999864 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   8.2e-05     0.049       2      42 ..      14      56 ..      13      75 .. 0.85
   2 ?    4.7   0.0     0.029        17     105     133 ..      99     127 ..      85     153 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.2e-05
                      Mg_chelatase  2 lkdvkGqeeakrale..iaaaGgHnlllvGppGsGKtmlakrl 42
                                      l +v+Gq++  + l+  + a    +l+++G+pG+GKt    +l
  gi|474934293|ref|YP_007687875.1| 14 LDEVIGQKNVTERLKgyVEARNMSHLMFAGTPGTGKTTCSLAL 56
                                      7899****9999997668999999*************876555 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.029
                      Mg_chelatase 105 ahnGvLfLDElpefkrkvlevLRePledg 133
                                       a+  ++fLDE+  +++++  +LR+ +e  
  gi|474934293|ref|YP_007687875.1|  99 AEFKIIFLDEADALTNDAQGALRRTMEMY 127
                                       566699*******************9965 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.6e-06   0.00099       6      69 ..       2      60 ..       1      78 [. 0.82

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.6e-06
                             Rad17  6 nelWfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskel 69
                                      ne W eky+P+k++e+   k+  e +k +++a  +       L+ +G +G gk+t    L++e+
  gi|474934293|ref|YP_007687875.1|  2 NEIWTEKYRPKKLDEVIGQKNVTERLKGYVEARNM-----SHLMFAGTPGTGKTTCSLALAREM 60
                                      799*************9888766666666666554.....4589***********999999875 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.6e-06   0.00098       3      65 ..      41     125 ..      39     177 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.6e-06
                            AAA_18   3 ltGtpGvGKttlakeLskrlgf......................gvnlrdvakenglllevdpe.aldeskrldedk 56 
                                        +GtpG+GKtt + +L++++ +                        +++d ak   +   +++   lde + l  d 
  gi|474934293|ref|YP_007687875.1|  41 FAGTPGTGKTTCSLALAREM-YgdswkgnflelnasdergidvvRGRIKDFAKTAPIDGAEFKIiFLDEADALTNDA 116
                                       79**************9996.44566666677777755555555555555555555555555556666666666666 PP

                            AAA_18  57 ldklldale 65 
                                       + +l +++e
  gi|474934293|ref|YP_007687875.1| 117 QGALRRTME 125
                                       666666665 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   2.9e-06    0.0018      33     153 ..      36     149 ..       8     177 .. 0.61

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.9e-06
                            AAA_25  33 gelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEds..edelrrRlravgeal...rddarll 104
                                        +  ++aG pgtGKtt  l la ++  G++w g       + l ++a d    d +r R++   +++    +  +  
  gi|474934293|ref|YP_007687875.1|  36 MSHLMFAGTPGTGKTTCSLALAREMY-GDSWKG-------NFLELNASDErgIDVVRGRIKDFAKTApidGAEFKII 104
                                       566789********************.888977.......5555555444115677777777777774443344444 PP

                            AAA_25 105 vldlagveslpLfakdrggtl.ltadvdaleaaieevegvrlvviDplsr 153
                                       +ld a+     L+ + +g  + + + + +  + i + +++   +iDp+++
  gi|474934293|ref|YP_007687875.1| 105 FLDEADA----LTNDAQGALRrTMEMYSRTCRFIIS-CNYSSKIIDPIQS 149
                                       5554443....3333333333444455555555555.4566666666666 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   6.2e-06    0.0037       7      60 ..      19      72 ..      13     142 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 6.2e-06
                                      HHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEE CS
                            ResIII  7 yQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflfl 60
                                       Q+++ e+l+  +++++  +++++ + GtGKT ++++l+++++   ++ +fl l
  gi|474934293|ref|YP_007687875.1| 19 GQKNVTERLKGYVEARNMSHLMFAGTPGTGKTTCSLALAREMYGDSWKGNFLEL 72
                                      5888888888888878888************************99999999866 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   5.4e-06    0.0032       6      87 ..      40     122 ..      36     130 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.4e-06
                            AAA_24   6 liyGpsgiGKTtlakel.........gpkplfidtekGlksldadkfpdieswedfldevvelaaeladyktlviDt 73 
                                       +  G +g+GKTt+ + l         + ++l ++  +  + +d+ ++        ++d++++ + + a++k++++D 
  gi|474934293|ref|YP_007687875.1|  40 MFAGTPGTGKTTCSLALaremygdswKGNFLELNASD-ERGIDVVRGR-------IKDFAKTAPIDGAEFKIIFLDE 108
                                       678**********999999999999999999998755.3455666654.......58899999************** PP

                            AAA_24  74 ideleelclaevir 87 
                                       +d l + +   ++r
  gi|474934293|ref|YP_007687875.1| 109 ADALTNDAQGALRR 122
                                       ****9998877765 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   0.00011     0.066      31      56 ..      29      53 ..       4      57 .. 0.81
   2 ?    1.2   0.0      0.33     2e+02     125     172 ..      77     129 ..      73     142 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                                      EEEEGGGS-.SEEEE--TTSSHHHHH CS
                      FtsK_SpoIIIE 31 lvldlkkmashllvaGatgsGKStal 56
                                       ++++++m  hl+ aG++g+GK+t+ 
  gi|474934293|ref|YP_007687875.1| 29 GYVEARNMS-HLMFAGTPGTGKTTCS 53
                                      467778888.**************95 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.33
                                       HTT-SSHHH.HHHHHHHHHHTT---B-TT-....................... CS
                      FtsK_SpoIIIE 125 eagvrsiaa.ydgeiaedpldifgdvflvlDnyddlaaene....ritsLsnq 172
                                       e+g++ +++  ++ ++++p d+ ++  ++lD+ d+l +  +    r +++ ++
  gi|474934293|ref|YP_007687875.1|  77 ERGIDVVRGrIKDFAKTAPIDGAEFKIIFLDEADALTNDAQgalrRTMEMYSR 129
                                       67778888788899999******************998777667666666665 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.3e-05      0.02      31      72 ..      34      75 ..      21     118 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.3e-05
                             AAA_7 31 knkkpvllvGptGtGKtviikdllkkldkekylsltinfsaq 72
                                      +n  ++++ G+ GtGKt++   l +++  ++++ ++++++a+
  gi|474934293|ref|YP_007687875.1| 34 RNMSHLMFAGTPGTGKTTCSLALAREMYGDSWKGNFLELNAS 75
                                      56789***************************9999999885 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00019      0.11       1      90 [.      38     125 ..      38     132 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00019
                                       EEEEE--SSSSHHHHHHHGGGGB.....S--EEEEE--TT--HHHHH--B--.........--------G-SEEEEE CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaal.....nreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlD 72 
                                       +++  G pGtgK++ +  la+ +     + ++++ + ++    + ++gr++       + + +    + e +i++lD
  gi|474934293|ref|YP_007687875.1|  38 HLMFAGTPGTGKTTCSLALAREMygdswKGNFLELNASDERGIDVVRGRIK------DFAKTAPI-DGAEFKIIFLD 107
                                       68999***************9999886666666666666666666666666......34444444.45588999999 PP

                                       SGGG--HHHHHHHHHHHH CS
                             AAA_5  73 EveraesevlnsLlslle 90 
                                       E + +  +++++L + +e
  gi|474934293|ref|YP_007687875.1| 108 EADALTNDAQGALRRTME 125
                                       999999999999977665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   9.8e-05     0.058       2      68 ..      17      95 ..      16     177 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.8e-05
                            AAA_16  2 lvGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekd...............ggiflrgkcdqles 65
                                      ++G ++ +e+L+ ++e+ ++   + +++ G +G+GK++   +l+r++ +d               g+ ++rg+ +++ +
  gi|474934293|ref|YP_007687875.1| 17 VIGQKNVTERLKGYVEARNM---SHLMFAGTPGTGKTTCSLALAREMYGDswkgnflelnasderGIDVVRGRIKDFAK 92
                                      57888889999999996665...5899*************999998888877666666666666445556666666644 PP

                            AAA_16 66 aip 68
                                       +p
  gi|474934293|ref|YP_007687875.1| 93 TAP 95
                                      444 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   6.7e-05      0.04      26      87 ..      17      76 ..       6      87 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.7e-05
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXX CS
                             TIP49 26 lvGqkkareaagvivelikekklaGravLlaGpsgtGktalaiaiskelg...edvpfvalsgse 87
                                      ++Gqk+  e    +   +++++++   +++aG +gtGkt  ++a+++e+     +  f  l++s+
  gi|474934293|ref|YP_007687875.1| 17 VIGQKNVTER---LKGYVEARNMS--HLMFAGTPGTGKTTCSLALAREMYgdsWKGNFLELNASD 76
                                      5666555443...34557788888..899*******************95222345677777775 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1    0.0029       1.8       6      27 ..      37      58 ..      32      64 .. 0.85
   2 ?    4.2   0.0     0.084        50      92     118 ..     101     126 ..      67     140 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0029
                            AAA_22  6 gilvvtGesGtGKTtllrrlle 27
                                      ++l+  G +GtGKTt+   l++
  gi|474934293|ref|YP_007687875.1| 37 SHLMFAGTPGTGKTTCSLALAR 58
                                      789999*********9888776 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.084
                            AAA_22  92 ielliiDEaqhlrseealeeLrsllnl 118
                                        +++ +DEa+ l +++a   Lr+ ++ 
  gi|474934293|ref|YP_007687875.1| 101 FKIIFLDEADAL-TNDAQGALRRTMEM 126
                                       4799********.76666666555554 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   8.7e-05     0.052       3      23 ..      40      62 ..      38     120 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.7e-05
                            AAA_28  3 vitGgestGKTtlleaLaar..g 23
                                      ++ G+++tGKTt + aLa++  g
  gi|474934293|ref|YP_007687875.1| 40 MFAGTPGTGKTTCSLALAREmyG 62
                                      588***************76452 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00028      0.17      12     110 ..      25     140 ..      19     145 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00028
                                       HHHHHHH..T-SS-EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH-H...........HHHHHH.....TTT CS
                   Sigma54_activ_2  12 erLeqaa..qsklpvfltGekGsgkelvArlLhknsgpwleifvverlaklp...........ldlleq.....akg 70 
                                       erL+  +  ++++ +  +G +G+gk++++ +L+ +  +++   ++ +l ++            +d+ ++     a+ 
  gi|474934293|ref|YP_007687875.1|  25 ERLKGYVeaRNMSHLMFAGTPGTGKTTCSLALAREMYGDSWKGNFLELNASDergidvvrgriKDFAKTapidgAEF 101
                                       55554433378999999****************99877665555555554334466777777755555544333688 PP

                                       SEEEEEE-TT--HHHHHHHHHHHHHHTTTT-EEEEEEEE- CS
                   Sigma54_activ_2  71 gtLylkdiadlskaeqkeLlellakaeksslrlVstsskd 110
                                        +++l + + l +++q  L   ++      +r++ ++ ++
  gi|474934293|ref|YP_007687875.1| 102 KIIFLDEADALTNDAQGALRRTMEMY-SRTCRFIISCNYS 140
                                       89999999999999999999999998.8899999998765 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00011     0.068       1      88 [.      38     126 ..      38     134 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
                             AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkk...Gpvfanllladeinra 74 
                                       h+++ g+PG++kt+   ala+ +  +  +  f  +l  sd  G++v++ + k+f  ++   G+ f ++++ de +  
  gi|474934293|ref|YP_007687875.1|  38 HLMFAGTPGTGKTTCSLALAREMYGDSWKGNFL-ELNASDERGIDVVRGRIKDFAKTApidGAEF-KIIFLDEADAL 112
                                       9999*********************99999996.7999**********99999975431114444.688889**999 PP

                             AAA_3  75 ppktqsalleamee 88 
                                       +  +q al  +me 
  gi|474934293|ref|YP_007687875.1| 113 TNDAQGALRRTMEM 126
                                       999****9999985 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00019      0.12      12      38 ..      33      59 ..      28      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00019
                     TrwB_AAD_bind 12 eretqhilivGttGsGKtqalekllra 38
                                       r  +h++++Gt G+GKt++  +l r+
  gi|474934293|ref|YP_007687875.1| 33 ARNMSHLMFAGTPGTGKTTCSLALARE 59
                                      57789**************99988776 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0002      0.12       4      52 ..      23      75 ..      20      82 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0002
                        Zeta_toxin  4 llkdkk.ypsqerPklillgGqpGAGKselaellkdele...rqgnvvrldpD 52
                                      ++++ k y++ ++   ++ +G pG GK++ + +l++e+     +gn+++l++ 
  gi|474934293|ref|YP_007687875.1| 23 VTERLKgYVEARNMSHLMFAGTPGTGKTTCSLALAREMYgdsWKGNFLELNAS 75
                                      5666666777777777889*******************766667777777765 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00017       0.1       2      74 ..      40     112 ..      39     120 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00017
                   Viral_helicase1   2 vvhGvpGcGKStlirkllrtsliltvnrptaelltegkpklpnlsvrtvdsflmalvks.tkgkililDEylll 74 
                                       + +G pG GK+t+   l+r+ +   + + ++  l+++ ++  +    ++++f +++  +  ++ki++lDE+ +l
  gi|474934293|ref|YP_007687875.1|  40 MFAGTPGTGKTTCSLALARE-MYGDSWKGNFLELNASDERGIDVVRGRIKDFAKTAPIDgAEFKIIFLDEADAL 112
                                       5689****************.77777888888888888777777777899999988888899********8665 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00027      0.16      34      88 ..      20      71 ..      12      77 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00027
                                      HHHHHHHHHHHHT-SS-SS-EEEEEEE-TTSSHHHHHHHHHHHHSTTGGGSTTEE CS
                            Torsin 34 kklvvksvkaylenekpkkpLvlsfhGwtGtGknfvaeiiaenlyrdGlrsdyvk 88
                                      +k v + +k+y+e  + +    l f G++GtGk   +  +a ++y d  + ++ +
  gi|474934293|ref|YP_007687875.1| 20 QKNVTERLKGYVEARNMS---HLMFAGTPGTGKTTCSLALAREMYGDSWKGNFLE 71
                                      677888999999987766...588*********************9999888865 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00028      0.17      45      84 ..      34      73 ..      13     140 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00028
                         IstB_IS21 45 ekkenivllGpsGvGKshlaialgveavraglsvlfvrve 84
                                      ++   +++ G +G+GK+  + al++e   + ++  f+ ++
  gi|474934293|ref|YP_007687875.1| 34 RNMSHLMFAGTPGTGKTTCSLALAREMYGDSWKGNFLELN 73
                                      45567899******************99999998887765 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1      0.37   2.2e+02      16      35 ..      38      56 ..      19      68 .. 0.73
   2 ?    7.0   0.0    0.0074       4.4     105     149 ..      84     127 ..      70     138 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.37
                                      EEEEEESTTSSHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxx RF
                              DEAD 16 dvlvaaeTGsGKTlaflipv 35
                                      +++ a+  G+GKT++ l ++
  gi|474934293|ref|YP_007687875.1| 38 HLMFAGTPGTGKTTCSL-AL 56
                                      55677788******954.43 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0074
                                       HHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 105 pgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnql 149
                                        gr+ d+ +t  ++  +++++ lDEad l ++  +  ++r ++  
  gi|474934293|ref|YP_007687875.1|  84 RGRIKDFAKTAPIDGAEFKIIFLDEADALTND-AQGALRRTMEMY 127
                                       58889988999999999************998.666666655554 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00037      0.22      16      43 ..      36      99 ..      21     228 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00037
                            AAA_11 16 eseitliqGPPGtgKTktivellsqll.....................................s 43
                                       s+  ++ G PGtgKT+  ++l ++++                                      
  gi|474934293|ref|YP_007687875.1| 36 MSH-LMFAGTPGTGKTTCSLALAREMYgdswkgnflelnasdergidvvrgrikdfaktapidgA 99
                                      444.6899******************766666666665555555555555555555444444440 PP

>> BAF1_ABF1  BAF1 / ABF1 chromatin reorganising factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00071      0.42     283     313 ..     240     270 ..     238     276 .. 0.95

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00071
                         BAF1_ABF1 283 qyVeeSgildilkerYgLtdedldKkllsqi 313
                                       ++Ve S +ld ++  YgL+ +d+ K++ s+i
  gi|474934293|ref|YP_007687875.1| 240 KFVEASNLLDKVMIEYGLSGQDVIKQMHSEI 270
                                       7****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 2087.11
//
Query:       gi|474934294|ref|YP_007687876.1|  [L=349]
Description: phenylacetate-CoA ligase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-18   66.6   0.0    5.1e-18   65.2   0.0    1.8  2  AMP-binding_C_2  AMP-binding enzyme C-terminal domain
    2.3e-12   46.3   0.1    2.3e-12   46.3   0.1    1.8  2  AMP-binding      AMP-binding enzyme
    8.3e-07   28.2   0.0     0.0049   15.8   0.0    2.1  2  GH3              GH3 auxin-responsive promoter
    0.00092   18.3   0.0     0.0015   17.7   0.0    1.2  1  LuxE             Acyl-protein synthetase, LuxE


Domain annotation for each model (and alignments):
>> AMP-binding_C_2  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.2   5.6e+03      54      71 ..     135     152 ..     120     154 .. 0.77
   2 !   65.2   0.0   1.1e-21   5.1e-18       1      96 []     257     348 ..     257     348 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHHHHSS- CS
                   AMP-binding_C_2  54 ealekkiakklksklgvs 71 
                                       e+  ++++++++++lgv+
  gi|474934294|ref|YP_007687876.1| 135 ERWGDRMRQRIADELGVE 152
                                       666788899999999886 PP

  == domain 2  score: 65.2 bits;  conditional E-value: 1.1e-21
                                       TEEE-HHHHHHHHHT-TTEEEEEEEEEEEETTEEEEEEEEEE-TT----HHHHHHHHHHHHHHHHHHHSS--EEEEE CS
                   AMP-binding_C_2   1 GvnvfPsqieevlkeieevepeYqivvtregelDelevkvEvkegfsdelkelealekkiakklksklgvsvkvelv 77 
                                       Gvn+fP q eevl++++++++eYq+++++ +++D l++  E+ e      ++  ale++++ k+++ +g +++ + v
  gi|474934294|ref|YP_007687876.1| 257 GVNMFPAQFEEVLSKVPGTSSEYQVMIDHLEGKDILTLFFETGEPK----EKWPALEEAVTGKFREIVGPTISPKAV 329
                                       9*******************************************85....579************************ PP

                                       -TT-S---------EEE-S CS
                   AMP-binding_C_2  78 epgtlprsegKakrviDkR 96 
                                       + g lprse+K+ r++D+R
  gi|474934294|ref|YP_007687876.1| 330 KIGDLPRSEKKTSRIFDNR 348
                                       ******************9 PP

>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   0.1     5e-16   2.3e-12     158     370 ..       5     208 ..       2     210 .. 0.79
   2 ?   -0.6   0.4     0.084   3.7e+02     412     422 ..     245     255 ..     242     256 .. 0.91

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 5e-16
                                       TTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHH.HHHCSCCTTT-EEEES.S-TTSCHHHHHHHHHHHHTT-EEE CS
                       AMP-binding 158 pddlayiiYTSGTTGkPKGVmlshrnlvanvaslk.letrfklkeddvvlsi.lplahifglilelllallsGatvv 232
                                       +++++ i  +SGTTG+P  + ++ + +   ++ ++ +++  ++++ d++  +     + +g+  +  +a   Ga vv
  gi|474934294|ref|YP_007687876.1|   5 EEQIVRIHSSSGTTGTPVVIPYTAKDVEDWATMFErCYKMAGCTNLDRIHITpGYGLWTAGI-GFQAGAEKLGAMVV 80 
                                       5677778889**************99955555544555555565657764441444577775.************** PP

                                       E-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTC CS
                       AMP-binding 233 llpkdaaldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffralfge 309
                                        + + ++   k+ l+++++lk tv++++ + +  l+e+  ++ a+  kd  +lr  ++g e+    + +++ + +g 
  gi|474934294|ref|YP_007687876.1|  81 PMGPGNTE--KQ-LKMMQDLKSTVLCATSSYALLLAEQ--IT-ARGIKDSIRLRKGIIGSERWGDRMRQRIADELGV 151
                                       99999983..33.69***************99999886..33.345567677***9********************* PP

                                       EEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEE CS
                       AMP-binding 310 evlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvr 370
                                       e++++YGlTE  g  + + ++ +      +      v  +++D+ t++ vpdg++Gel++ 
  gi|474934294|ref|YP_007687876.1| 152 ELYDIYGLTEIYGPGIGISCSYK----DGIHMWDDYVYFEVIDPVTLKNVPDGTVGELVIT 208
                                       **************983333333....3244444599999******************995 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.084
                                       EEEECCCEEEE CS
                       AMP-binding 412 ivgRkkdlikl 422
                                       i+gR++d++k+
  gi|474934294|ref|YP_007687876.1| 245 ITGRTDDMVKV 255
                                       89********8 PP

>> GH3  GH3 auxin-responsive promoter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.1e-06    0.0049      74     115 ..       6      45 ..       2     106 .. 0.85
   2 !   10.7   0.0   3.9e-05      0.17     334     453 ..     186     298 ..     163     318 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.1e-06
                                       SS-SEEEEECCEETTEEEEEEESHHHHHHHHHH.HHHHHHHH CS
                               GH3  74 epiklfalsSGTtsgksKliPvteeslkelallvlallaall 115
                                       e+i+++  sSGTt g + +iP+t++ ++++a + ++ ++++ 
  gi|474934294|ref|YP_007687876.1|   6 EQIVRIHSSSGTT-GTPVVIPYTAKDVEDWATM-FERCYKMA 45 
                                       78999********.***************9987.77766665 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 3.9e-05
                                       EEEEESSTT.TSSSSEECCCS-TTSEEEEEEES..TTS..-SSEEECEEEEE.EEEE...TTEEEEEE.EECCTEEE CS
                               GH3 334 fEFipveedeeepetvdleevevGkeYelvvTt..faG..LyRYrigDvvrv.tgfy...nkaPrleF.vgRknvvl 401
                                       fE i         ++v+l++v  G   elv+Tt    G  L RYr++D+ r+ tg++    + Pr+ + +gR++ ++
  gi|474934294|ref|YP_007687876.1| 186 FEVI---------DPVTLKNVPDGTVGELVITTlvKEGapLIRYRTHDLTRImTGTCpcgSRYPRIDIiTGRTDDMV 253
                                       4444.........4799****************6634555***********83455433368999986268****** PP

                                       -SSSS-CCHHHHHHHHH.HHHHHTT-EEEEEEEEE.ESS.SSSEEEEEEEEE CS
                               GH3 402 sidgeklteeelqkaveeaakeltglelvdftsfapdtsesepghyvlflEl 453
                                       +++g  +   ++++++ +          +++ +++ d   + +   +lf E 
  gi|474934294|ref|YP_007687876.1| 254 KVKGVNMFPAQFEEVLSKVPGT-----SSEYQVMI-DHL-EGKDILTLFFET 298
                                       ***9999999999999854433.....35666655.333.555555566665 PP

>> LuxE  Acyl-protein synthetase, LuxE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   3.3e-07    0.0015     256     358 ..     146     249 ..     137     263 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.3e-07
                              LuxE 256 advlnlsiddvvdiygfteqveln...tpdfkdelkrkrvysdviirdeetlkvvgdGkvGlleyvdalstsyPafv 329
                                       ad l++   ++ diyg+te  +      + +kd+++    y +  + d+ tlk v+dG vG l     + +  P   
  gi|474934294|ref|YP_007687876.1| 146 ADELGV---ELYDIYGLTEIYGPGigiSCSYKDGIHMWDDYVYFEVIDPVTLKNVPDGTVGELVITTLVKEGAPLIR 219
                                       555555...4679999999876542226999**99999988888888******************9999*****999 PP

                              LuxE 330 vltddlGvieeslcegqkaGklvkvl.rrv 358
                                         t dl  i    c ++    +++++ +r+
  gi|474934294|ref|YP_007687876.1| 220 YRTHDLTRIMTGTCPCGSRYPRIDIItGRT 249
                                       99****998889*****9999999983344 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2450.42
//
Query:       gi|474934296|ref|YP_007687878.1|  [L=240]
Description: TPR repeat protein, SEL1 subfamily [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-42  142.9  12.2    8.1e-11   42.2   0.0    6.1  6  Sel1      Sel1 repeat
    1.9e-06   27.5   0.2      0.001   18.9   0.0    3.4  3  TPR_7     Tetratricopeptide repeat
    3.7e-05   24.1   4.9        1.4    9.7   0.0    5.2  5  TPR_6     Tetratricopeptide repeat
    4.8e-05   23.0   4.1       0.61   10.0   0.0    6.5  8  TPR_1     Tetratricopeptide repeat
     0.0023   18.5   0.5        1.3    9.7   0.1    3.4  4  TPR_16    Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.042   13.9   0.7         17    5.5   0.0    3.9  4  MIT       MIT (microtubule interacting and transport) domain
      0.049   13.8   8.5        1.7    9.0   0.0    6.2  8  TPR_2     Tetratricopeptide repeat
       0.27   11.0   2.2         12    5.7   0.0    3.6  4  TPR_11    TPR repeat
          2    8.8   4.3        7.8    6.9   0.1    3.7  5  TPR_12    Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> Sel1  Sel1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.0     4e-14   8.1e-11       1      38 []      15      50 ..      15      50 .. 0.94
   2 !    9.3   0.0   0.00098       1.9       2      37 ..      52      85 ..      51      86 .. 0.85
   3 !   28.3   0.1     1e-09     2e-06       2      37 ..      88     121 ..      87     122 .. 0.92
   4 !   33.0   0.1   3.4e-11   6.7e-08       2      35 ..     124     155 ..     123     158 .. 0.89
   5 !   19.0   0.0   8.3e-07    0.0017       6      38 .]     164     194 ..     160     194 .. 0.88
   6 !   15.4   0.1   1.1e-05     0.022       1      34 [.     195     226 ..     195     230 .. 0.93

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 4e-14
                              Sel1  1 aeAmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38
                                      + A+++LG  ++y++G+g+p+D ++A+ w+ +AAeqGd
  gi|474934296|ref|YP_007687878.1| 15 PRAQCALG--LIYYTGDGTPQDLNRAFIWFNMAAEQGD 50
                                      57******..777************************7 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00098
                              Sel1  2 eAmyrLGmfylylnGlgvpkDpekAiewyekAAeqG 37
                                      e  +  +  y+y + lg+ +++++A+++y  +Ae+G
  gi|474934296|ref|YP_007687878.1| 52 EGEFYTA--YMYVHALGTNANIDEAVRFYTDSAEKG 85
                                      6788899..777888889***********9999998 PP

  == domain 3  score: 28.3 bits;  conditional E-value: 1e-09
                              Sel1   2 eAmyrLGmfylylnGlgvpkDpekAiewyekAAeqG 37 
                                        +m++L+   +y +Glgv++D +kAi +y++A e G
  gi|474934296|ref|YP_007687878.1|  88 RSMFNLA--HMYSDGLGVKQDWSKAIDYYQRAMEGG 121
                                       59*****..***********************7766 PP

  == domain 4  score: 33.0 bits;  conditional E-value: 3.4e-11
                              Sel1   2 eAmyrLGmfylylnGlgvpkDpekAiewyekAAe 35 
                                        A+yrLG   +y++G gv+kDpekA+ +y + Ae
  gi|474934296|ref|YP_007687878.1| 124 PACYRLG--VIYDEGYGVEKDPEKAFGYYSRCAE 155
                                       59*****..777*****************99776 PP

  == domain 5  score: 19.0 bits;  conditional E-value: 8.3e-07
                              Sel1   6 rLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                       r +m+y  l+G+gv k+p+ A++++  AA +Gd
  gi|474934296|ref|YP_007687878.1| 164 RIAMLY--LEGRGVQKNPNAAVKHLNAAAGNGD 194
                                       889777..********************98776 PP

  == domain 6  score: 15.4 bits;  conditional E-value: 1.1e-05
                              Sel1   1 aeAmyrLGmfylylnGlgvpkDpekAiewyekAA 34 
                                       a+Am  LG   l l G g  k ++ A +w++kA 
  gi|474934296|ref|YP_007687878.1| 195 ADAMLWLG--KLSLSGEGMAKSVNNAKKWLQKAS 226
                                       68******..999********************6 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.54   1.1e+03      16      24 ..      72      80 ..      69      84 .. 0.81
   2 !   18.9   0.0   5.2e-07     0.001       2      28 ..      90     118 ..      89     122 .. 0.90
   3 ?    3.9   0.0     0.033        65       1      31 [.     125     159 ..     125     164 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.54
                             TPR_7 16 eeAielyeq 24
                                      +eA+++y+ 
  gi|474934296|ref|YP_007687878.1| 72 DEAVRFYTD 80
                                      89*****96 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 5.2e-07
                             TPR_7   2 LlnLarlysr....lGdyeeAielyeqsLal 28 
                                        +nLa++ys+     +d+++Ai++y++  a+
  gi|474934296|ref|YP_007687878.1|  90 MFNLAHMYSDglgvKQDWSKAIDYYQR--AM 118
                                       68*************************..55 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.033
                             TPR_7   1 aLlnLarlysr....lGdyeeAielyeqsLaltkd 31 
                                       a+++L+++y +    + d e+A ++y ++ ++ +d
  gi|474934296|ref|YP_007687878.1| 125 ACYRLGVIYDEgygvEKDPEKAFGYYSRCAEVGYD 159
                                       799*******9999999999999999887776666 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       1.4   2.7e+03       4      24 ..      55      79 ..      52      81 .. 0.66
   2 !    9.7   0.0   0.00068       1.4       2      26 ..      89     117 ..      88     119 .. 0.84
   3 ?    5.9   0.0     0.012        23       4      27 ..     127     154 ..     125     156 .. 0.92
   4 ?    3.8   0.0     0.053   1.1e+02       2      24 ..     161     187 ..     160     191 .. 0.80
   5 ?    1.9   0.1      0.22   4.4e+02       1      13 [.     196     208 ..     196     240 .] 0.72

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.4
                                      HHHHHHHHHH....HHHHHHHHHHH CS
                             TPR_6  4 yklalsyrkl....gdtdkAleale 24
                                      ++ a+ y  +     + d+A++ + 
  gi|474934296|ref|YP_007687878.1| 55 FYTAYMYVHAlgtnANIDEAVRFYT 79
                                      5566666653355448899999885 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00068
                                       HHHHHHHHHHHH....HHHHHHHHHHHHH CS
                             TPR_6   2 Alyklalsyrkl....gdtdkAlealerl 26 
                                       ++++la  y  +    +d++kA+++++r 
  gi|474934296|ref|YP_007687878.1|  89 SMFNLAHMYSDGlgvkQDWSKAIDYYQRA 117
                                       58888888888569988**********96 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.012
                                       HHHHHHHHHH....HHHHHHHHHHHHHH CS
                             TPR_6   4 yklalsyrkl....gdtdkAlealerli 27 
                                       y+l+  y ++    +d++kA  ++ r+ 
  gi|474934296|ref|YP_007687878.1| 127 YRLGVIYDEGygveKDPEKAFGYYSRCA 154
                                       99*******99*************9975 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.053
                                       HHHHHHHHHHHH....HHHHHHHHHHH CS
                             TPR_6   2 Alyklalsyrkl....gdtdkAleale 24 
                                       A  ++a++y+++    +++ +A++ l+
  gi|474934296|ref|YP_007687878.1| 161 ASVRIAMLYLEGrgvqKNPNAAVKHLN 187
                                       6679*******8788778888887765 PP

  == domain 5  score: 1.9 bits;  conditional E-value: 0.22
                                       HHHHHHHHHHHHH CS
                             TPR_6   1 dAlyklalsyrkl 13 
                                       dA+++l+++ +++
  gi|474934296|ref|YP_007687878.1| 196 DAMLWLGKLSLSG 208
                                       79****9887775 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.27   5.4e+02       2      12 ..      16      26 ..      15      27 .. 0.87
   2 ?   -2.4   0.0       2.5     5e+03       2       9 ..      39      46 ..      38      48 .. 0.77
   3 ?   -1.6   0.0       1.4   2.8e+03      16      24 ..      70      78 ..      64      80 .. 0.86
   4 ?   -1.3   0.0       1.1   2.3e+03       3      12 ..      89      98 ..      87      99 .. 0.80
   5 !   10.0   0.0   0.00031      0.61      15      28 ..     105     118 ..     102     119 .. 0.87
   6 ?    3.5   0.0     0.034        69       2      12 ..     124     134 ..     123     135 .. 0.86
   7 ?    1.7   0.0      0.13   2.5e+02      14      29 ..     140     155 ..     137     156 .. 0.83
   8 ?   -0.3   0.0      0.54   1.1e+03      14      27 ..     176     189 ..     175     190 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.27
                                      HHHHHHHHHHH CS
                             TPR_1  2 kalynlGnayf 12
                                      +a + lG++y+
  gi|474934296|ref|YP_007687878.1| 16 RAQCALGLIYY 26
                                      78999*****8 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.5
                                      HHHHHHHH CS
                             TPR_1  2 kalynlGn 9 
                                       +++n+++
  gi|474934296|ref|YP_007687878.1| 39 FIWFNMAA 46
                                      68999996 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.4
                                      -HHHHHHHH CS
                             TPR_1 16 kydeAleyy 24
                                      + deA+ +y
  gi|474934296|ref|YP_007687878.1| 70 NIDEAVRFY 78
                                      789***999 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 1.1
                                      HHHHHHHHHH CS
                             TPR_1  3 alynlGnayf 12
                                      + +nl+++y 
  gi|474934296|ref|YP_007687878.1| 89 SMFNLAHMYS 98
                                      568****996 PP

  == domain 5  score: 10.0 bits;  conditional E-value: 0.00031
                                       T-HHHHHHHHHHHH CS
                             TPR_1  15 gkydeAleyyekAL 28 
                                       +++ +A++yy++A 
  gi|474934296|ref|YP_007687878.1| 105 QDWSKAIDYYQRAM 118
                                       6899********96 PP

  == domain 6  score: 3.5 bits;  conditional E-value: 0.034
                                       HHHHHHHHHHH CS
                             TPR_1   2 kalynlGnayf 12 
                                        a+y+lG++y 
  gi|474934296|ref|YP_007687878.1| 124 PACYRLGVIYD 134
                                       599*******5 PP

  == domain 7  score: 1.7 bits;  conditional E-value: 0.13
                                       TT-HHHHHHHHHHHHH CS
                             TPR_1  14 lgkydeAleyyekALe 29 
                                        +++++A  yy+++ e
  gi|474934296|ref|YP_007687878.1| 140 EKDPEKAFGYYSRCAE 155
                                       689*********9866 PP

  == domain 8  score: -0.3 bits;  conditional E-value: 0.54
                                       TT-HHHHHHHHHHH CS
                             TPR_1  14 lgkydeAleyyekA 27 
                                       +++++ A+++ + A
  gi|474934296|ref|YP_007687878.1| 176 QKNPNAAVKHLNAA 189
                                       8999*****99876 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.25     5e+02      30      64 ..      11      49 ..       5      53 .. 0.78
   2 ?    2.9   0.0     0.092   1.8e+02       7      60 ..      65     117 ..      59     122 .. 0.72
   3 ?    2.1   0.0      0.16   3.2e+02      11      42 ..     105     131 ..      99     152 .. 0.67
   4 !    9.7   0.1   0.00067       1.3      10      43 ..     176     204 ..     173     209 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.25
                            TPR_16 30 sPdaaeAllllgdaalrq....grlaeAaalyraalraa 64
                                      s+ +++A+ +lg++++      ++l +A  +++ a++++
  gi|474934296|ref|YP_007687878.1| 11 SSGDPRAQCALGLIYYTGdgtpQDLNRAFIWFNMAAEQG 49
                                      466788999999999988888888888888888888654 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.092
                            TPR_16   7 alragdyddAaaaleaalkrdpssPdaaeAllllgdaalrq....grlaeAaalyraa 60 
                                       +  + + d+A++ ++   +++      ++++++l+ ++       +++ +A+++y++a
  gi|474934296|ref|YP_007687878.1|  65 LGTNANIDEAVRFYTDSAEKG-----FVRSMFNLAHMYSDGlgvkQDWSKAIDYYQRA 117
                                       555666677776666666666.....77777777777777777778999999999887 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.16
                            TPR_16  11 gdyddAaaaleaalkrdpssPdaaeAllllgd 42 
                                       +d+ +A+ ++++a + +      + A + lg+
  gi|474934296|ref|YP_007687878.1| 105 QDWSKAIDYYQRAMEGG-----SVPACYRLGV 131
                                       56677777777776666.....4455555555 PP

  == domain 4  score: 9.7 bits;  conditional E-value: 0.00067
                            TPR_16  10 agdyddAaaaleaalkrdpssPdaaeAllllgda 43 
                                       ++++ +A++ l+aa  ++     +a+A+l+lg +
  gi|474934296|ref|YP_007687878.1| 176 QKNPNAAVKHLNAAAGNG-----DADAMLWLGKL 204
                                       899***************.....********975 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.89   1.8e+03       3      27 ..      37      61 ..      35      67 .. 0.69
   2 ?    2.6   0.0     0.074   1.5e+02      17      32 ..      68      83 ..      64      84 .. 0.86
   3 ?    5.5   0.0    0.0088        17      17      32 ..     104     119 ..     102     120 .. 0.90
   4 ?    0.5   0.0      0.33   6.6e+02      17      32 ..     140     155 ..     138     156 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.89
                               MIT  3 kAlelvkkA.veeDnagnyeeAlelY 27
                                      +A+  +++A  + D +g++ +A+ +Y
  gi|474934296|ref|YP_007687878.1| 37 RAFIWFNMAaEQGDPEGEFYTAY-MY 61
                                      56666666647789999999998.45 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.074
                               MIT 17 agnyeeAlelYkeale 32
                                      + n++eA++ Y+++ e
  gi|474934296|ref|YP_007687878.1| 68 NANIDEAVRFYTDSAE 83
                                      5699********9976 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.0088
                               MIT  17 agnyeeAlelYkeale 32 
                                       ++++++A+++Y+ a+e
  gi|474934296|ref|YP_007687878.1| 104 KQDWSKAIDYYQRAME 119
                                       6899*********986 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.33
                               MIT  17 agnyeeAlelYkeale 32 
                                       +++ e+A+ +Y+ + e
  gi|474934296|ref|YP_007687878.1| 140 EKDPEKAFGYYSRCAE 155
                                       57889*******9987 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       0.6   1.2e+03       2      12 ..      16      26 ..      15      28 .. 0.86
   2 ?   -3.5   0.0         8   1.6e+04       1       8 [.      38      45 ..      38      47 .. 0.77
   3 ?   -1.0   0.0       1.4   2.7e+03      16      26 ..      70      80 ..      68      84 .. 0.80
   4 ?    9.0   0.0   0.00085       1.7      14      29 ..     104     119 ..      90     119 .. 0.90
   5 ?    1.2   0.0      0.25     5e+02       3      11 ..     125     133 ..     123     136 .. 0.86
   6 ?    0.3   0.0       0.5   9.9e+02      15      29 ..     141     155 ..     137     156 .. 0.85
   7 ?   -0.0   0.0      0.63   1.3e+03      14      27 ..     176     189 ..     175     190 .. 0.88
   8 ?   -2.3   0.0       3.5   7.1e+03      19      27 ..     217     225 ..     215     225 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.6
                             TPR_2  2 ealynlGlayy 12
                                      +a ++lGl+yy
  gi|474934296|ref|YP_007687878.1| 16 RAQCALGLIYY 26
                                      68899*****9 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 8
                             TPR_2  1 aealynlG 8 
                                      a +++n++
  gi|474934296|ref|YP_007687878.1| 38 AFIWFNMA 45
                                      57899987 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.4
                             TPR_2 16 dyeeAleafek 26
                                      + +eA++++  
  gi|474934296|ref|YP_007687878.1| 70 NIDEAVRFYTD 80
                                      679***99975 PP

  == domain 4  score: 9.0 bits;  conditional E-value: 0.00085
                             TPR_2  14 lgdyeeAleafekAle 29 
                                       ++d+ +A++++++A e
  gi|474934296|ref|YP_007687878.1| 104 KQDWSKAIDYYQRAME 119
                                       589***********75 PP

  == domain 5  score: 1.2 bits;  conditional E-value: 0.25
                             TPR_2   3 alynlGlay 11 
                                       a+y+lG +y
  gi|474934296|ref|YP_007687878.1| 125 ACYRLGVIY 133
                                       89*****99 PP

  == domain 6  score: 0.3 bits;  conditional E-value: 0.5
                             TPR_2  15 gdyeeAleafekAle 29 
                                       +d+e+A  ++ ++ e
  gi|474934296|ref|YP_007687878.1| 141 KDPEKAFGYYSRCAE 155
                                       799*******99875 PP

  == domain 7  score: -0.0 bits;  conditional E-value: 0.63
                             TPR_2  14 lgdyeeAleafekA 27 
                                       +++++ A++++++A
  gi|474934296|ref|YP_007687878.1| 176 QKNPNAAVKHLNAA 189
                                       789999****9998 PP

  == domain 8  score: -2.3 bits;  conditional E-value: 3.5
                             TPR_2  19 eAleafekA 27 
                                        A+++++kA
  gi|474934296|ref|YP_007687878.1| 217 NAKKWLQKA 225
                                       599999998 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0    0.0061        12      27      39 ..      14      26 ..      11      28 .. 0.91
   2 ?    2.8   0.1     0.048        95       8      21 ..     105     118 ..     104     119 .. 0.86
   3 ?   -2.8   0.1       2.7   5.3e+03      11      20 ..     180     189 ..     177     190 .. 0.80
   4 ?   -3.0   0.0         3     6e+03      27      36 ..     194     203 ..     194     204 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0061
                            TPR_11 27 naeayynLGlayy 39
                                      +++a ++LGl+yy
  gi|474934296|ref|YP_007687878.1| 14 DPRAQCALGLIYY 26
                                      79**********9 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.048
                            TPR_11   8 GkyeeAieaYkkAl 21 
                                       +++ +Ai  Y++A 
  gi|474934296|ref|YP_007687878.1| 105 QDWSKAIDYYQRAM 118
                                       7899********95 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 2.7
                            TPR_11  11 eeAieaYkkA 20 
                                       ++A++++++A
  gi|474934296|ref|YP_007687878.1| 180 NAAVKHLNAA 189
                                       5789998887 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 3
                            TPR_11  27 naeayynLGl 36 
                                       +a+a ++LG+
  gi|474934296|ref|YP_007687878.1| 194 DADAMLWLGK 203
                                       6899999998 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.1         8   1.6e+04      47      56 ..      17      26 ..      16      29 .. 0.67
   2 ?   -1.1   0.0       1.2   2.5e+03      60      71 ..      70      81 ..      59      83 .. 0.67
   3 ?    6.9   0.1    0.0039       7.8      17      73 ..     105     119 ..      87     122 .. 0.63
   4 ?    0.5   0.0      0.37   7.5e+02      17      32 ..     141     156 ..     137     170 .. 0.83
   5 ?   -3.6   0.0       7.2   1.4e+04      17      29 ..     177     189 ..     176     190 .. 0.51

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 8
                            TPR_12 47 tlrnLgrlyr 56
                                      ++++Lg +y+
  gi|474934296|ref|YP_007687878.1| 17 AQCALGLIYY 26
                                      5677888875 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.2
                            TPR_12 60 ryeeAlelleea 71
                                      + +eA+++++++
  gi|474934296|ref|YP_007687878.1| 70 NIDEAVRFYTDS 81
                                      556677766665 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0039
                            TPR_12  17 grydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                       +                                          ++ +A++++++a++
  gi|474934296|ref|YP_007687878.1| 105 Q------------------------------------------DWSKAIDYYQRAME 119
                                       3..........................................66666666666665 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.37
                            TPR_12  17 grydeAlellekalei 32 
                                       ++ ++A+ ++ ++ e+
  gi|474934296|ref|YP_007687878.1| 141 KDPEKAFGYYSRCAEV 156
                                       7889999999999886 PP

  == domain 5  score: -3.6 bits;  conditional E-value: 7.2
                            TPR_12  17 grydeAlelleka 29 
                                       ++   A ++l++a
  gi|474934296|ref|YP_007687878.1| 177 KNPNAAVKHLNAA 189
                                       4555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.34
# Mc/sec: 2087.12
//
Query:       gi|474934297|ref|YP_007687879.1|  [L=495]
Description: TPR repeat protein, SEL1 subfamily [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-58  194.4  58.7    6.6e-11   42.5   1.6   10.6 11  Sel1      Sel1 repeat
  ------ inclusion threshold ------
        0.4   11.4  25.2       0.21   12.2   1.3    5.8  4  TPR_16    Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> Sel1  Sel1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.2   1.1e+04       3      18 ..      46      61 ..      44      69 .. 0.61
   2 ?    1.0   0.0     0.086   7.7e+02      14      30 ..     123     146 ..     121     146 .. 0.76
   3 !   26.8   0.0   6.5e-10   5.8e-06       2      37 ..     156     189 ..     155     190 .. 0.94
   4 !   41.1   4.3     2e-14   1.8e-10       1      38 []     191     227 ..     191     227 .. 0.94
   5 !   10.8   0.1   7.3e-05      0.65      10      38 .]     232     263 ..     230     263 .. 0.81
   6 !   18.3   1.0     3e-07    0.0027       2      38 .]     265     300 ..     264     300 .. 0.91
   7 !   25.9   1.1   1.3e-09   1.2e-05       3      35 ..     303     333 ..     301     336 .. 0.91
   8 !   29.9   4.8   7.1e-11   6.4e-07       2      37 ..     338     371 ..     337     372 .. 0.93
   9 !   42.5   1.6   7.4e-15   6.6e-11       2      38 .]     374     408 ..     373     408 .. 0.95
  10 !    6.1   0.0    0.0021        19       3      38 .]     411     444 ..     409     444 .. 0.92
  11 !   22.4   0.5   1.5e-08   0.00014       2      38 .]     446     480 ..     445     480 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.2
                              Sel1  3 AmyrLGmfylylnGl..g 18
                                      + y +++f   ++G+   
  gi|474934297|ref|YP_007687879.1| 46 CRYLYALFR--YTGTctK 61
                                      568888777..8888442 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.086
                              Sel1  14 lnGl......g.vpkDpekAiewy 30 
                                       ++G+      g v k+  +A+++y
  gi|474934297|ref|YP_007687879.1| 123 DTGKnpdgtkGpVRKNHAEAVRFY 146
                                       556666555888999******998 PP

  == domain 3  score: 26.8 bits;  conditional E-value: 6.5e-10
                              Sel1   2 eAmyrLGmfylylnGlgvpkDpekAiewyekAAeqG 37 
                                       eA++  G  y+yl G+gv+k++e Ai+++  AA++G
  gi|474934297|ref|YP_007687879.1| 156 EAQNTIG--YMYLCGKGVEKNKEIAIRLLSEAADHG 189
                                       789999*..999***********************9 PP

  == domain 4  score: 41.1 bits;  conditional E-value: 2e-14
                              Sel1   1 aeAmyrLGmfylylnGlg.vpkDpekAiewyekAAeqGd 38 
                                       a A+yr G  y+y++G+  v++D +kA+ewy+kAA++G+
  gi|474934297|ref|YP_007687879.1| 191 AQAAYRIG--YMYDAGQCyVDQDLDKAVEWYQKAADLGY 227
                                       68******..999****66******************96 PP

  == domain 5  score: 10.8 bits;  conditional E-value: 7.3e-05
                              Sel1  10 fylylnGlg.vpk....DpekAiewyekAAeqGd 38 
                                       ++  l+G +  ++    Dp+kA +++ kAA+ G+
  gi|474934297|ref|YP_007687879.1| 232 YQ--LTGIMfMKQgkwfDPSKAQKHLIKAADGGN 263
                                       45..8888556666689**************997 PP

  == domain 6  score: 18.3 bits;  conditional E-value: 3e-07
                              Sel1   2 eAmyrLGmfylylnGlg.vpkDpekAiewyekAAeqGd 38 
                                       +Am  LG++y   +G     +Dp+kA  ++ kA+e+Gd
  gi|474934297|ref|YP_007687879.1| 265 DAMRELGTMY--AYGYNnFRRDPKKADAYLLKACEAGD 300
                                       69*****999..****75788***************97 PP

  == domain 7  score: 25.9 bits;  conditional E-value: 1.3e-09
                              Sel1   3 AmyrLGmfylylnGlgvpkDpekAiewyekAAe 35 
                                       Am +++   l ++G+ +p++ +kA +w+ekAA+
  gi|474934297|ref|YP_007687879.1| 303 AMINYA--NLCFEGQALPRNLQKAAYWFEKAAK 333
                                       9*****..666*********************8 PP

  == domain 8  score: 29.9 bits;  conditional E-value: 7.1e-11
                              Sel1   2 eAmyrLGmfylylnGlgvpkDpekAiewyekAAeqG 37 
                                        A+y+LG+fy   nG   ++D  kA +w++ AAe G
  gi|474934297|ref|YP_007687879.1| 338 QAQYALGCFY--GNGYYYEQDNTKAAYWFQEAAEGG 371
                                       59*****777..**********************88 PP

  == domain 9  score: 42.5 bits;  conditional E-value: 7.4e-15
                              Sel1   2 eAmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                        A+y+L++fy  ++G+gv+kD +kA  w++ AAeqG+
  gi|474934297|ref|YP_007687879.1| 374 NAQYALACFY--YEGRGVEKDNKKAAAWFQEAAEQGH 408
                                       69*****777..************************9 PP

  == domain 10  score: 6.1 bits;  conditional E-value: 0.0021
                              Sel1   3 AmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                       Am+  Gmf    +G++v++D+e +++ ++ AA++G+
  gi|474934297|ref|YP_007687879.1| 411 AMAFFGMFK--VTGKDVEQDIEGGVQMLKDAADNGY 444
                                       888889999..**********************996 PP

  == domain 11  score: 22.4 bits;  conditional E-value: 1.5e-08
                              Sel1   2 eAmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                       +A++ LG   ly +G  v+k++  A + + +AA+qGd
  gi|474934297|ref|YP_007687879.1| 446 DAQFYLG--KLYAEGEYVEKNIPYAKKMLSMAAKQGD 480
                                       7******..999************************7 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.3   2.4e-05      0.21      14      63 ..     176     225 ..     172     230 .. 0.91
   2 ?    3.6   1.9     0.012   1.1e+02      27      66 ..     299     337 ..     280     339 .. 0.78
   3 ?    2.5   4.4     0.026   2.3e+02       7      63 ..     351     406 ..     348     411 .. 0.80
   4 ?    2.7   0.0     0.023   2.1e+02      18      51 ..     434     462 ..     427     483 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.4e-05
                            TPR_16  14 ddAaaaleaalkrdpssPdaaeAllllgdaalrq.....grlaeAaalyraalra 63 
                                       + A+++l +a + +     +a+A++  g ++ +      ++l++A+++y++a++ 
  gi|474934297|ref|YP_007687879.1| 176 EIAIRLLSEAADHG-----CAQAAYRIGYMYDAGqcyvdQDLDKAVEWYQKAADL 225
                                       77999*********.....************9999****************9975 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.012
                            TPR_16  27 dpssPdaaeAllllgdaalrq....grlaeAaalyraalraapd 66 
                                       +     + +A+ ++++++++      +l++Aa ++++a++++ +
  gi|474934297|ref|YP_007687879.1| 299 G-----DQQAMINYANLCFEGqalpRNLQKAAYWFEKAAKEYNG 337
                                       4.....678888999999988899999***********999876 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.026
                            TPR_16   7 alragdyddAaaaleaalkrdpssPdaaeAllllgdaalrq....grlaeAaalyraalra 63 
                                       +++ +d ++Aa  +++a + +      + A+++l+  +++     ++ ++Aaa++++a+++
  gi|474934297|ref|YP_007687879.1| 351 YYYEQDNTKAAYWFQEAAEGG-----EPNAQYALACFYYEGrgveKDNKKAAAWFQEAAEQ 406
                                       667777777777778888888.....7889999999999999999************9954 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.023
                            TPR_16  18 aaleaalkrdpssPdaaeAllllgdaalrqgrla 51 
                                        +l+ a +++      ++A+++lg ++++   ++
  gi|474934297|ref|YP_007687879.1| 434 QMLKDAADNG-----YVDAQFYLGKLYAEGEYVE 462
                                       5677777778.....899******9998865555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 3030.97
//
Query:       gi|474934298|ref|YP_007687880.1|  [L=165]
Description: hypothetical protein TALC_00723 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-11   44.0   0.0    2.9e-11   43.6   0.0    1.2  1  DUF4143   Domain of unknown function (DUF4143)


Domain annotation for each model (and alignments):
>> DUF4143  Domain of unknown function (DUF4143)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.0   1.6e-15   2.9e-11      35     121 ..      18     102 ..       2     103 .. 0.92

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 1.6e-15
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DUF4143  35 krlrkspKlyfvDtGLlvallgldkeelleds...enkGallEnlVaqeLlkysekegaklyyyrdkngaEvDfvie 108
                                       +++   +++y++DtG++v+  ++ +++++ ++   ++ G ++E +Va eL++    ++  l+y++ k+++ + f ++
  gi|474934298|ref|YP_007687880.1|  18 EEDSGLFRYYLADTGMFVHQSRIPRSDFMVKDkrrTLSGTFYEKYVADELRA----KEIALFYWTGKKSNGMEFAVQ 90 
                                       4577789*******************999988999*****************....79******************9 PP

                                       xxxxxxxxxxxxx RF
                           DUF4143 109 lkggkivpiEvKs 121
                                        +g   vpi vK 
  gi|474934298|ref|YP_007687880.1|  91 -NGPYAVPIDVKK 102
                                       .699********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1101.48
//
Query:       gi|474934299|ref|YP_007687881.1|  [L=222]
Description: Sel1 repeat protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-36  123.4   7.8      2e-09   37.8   0.2    5.1  5  Sel1      Sel1 repeat
  ------ inclusion threshold ------
       0.34   11.6   7.6       0.48   11.1   1.6    3.5  4  TPR_16    Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> Sel1  Sel1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.2   2.3e-13     2e-09       1      38 []      43      78 ..      43      78 .. 0.95
   2 !   21.3   0.0   3.6e-08   0.00032       3      32 ..      81     108 ..      79     114 .. 0.89
   3 !   23.4   0.1   7.9e-09   7.1e-05       2      38 .]     116     150 ..     115     150 .. 0.94
   4 !   22.1   0.0   1.9e-08   0.00017       2      38 .]     152     186 ..     151     186 .. 0.92
   5 !   19.9   0.1     1e-07   0.00089       3      33 ..     189     217 ..     188     217 .. 0.93

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 2.3e-13
                              Sel1  1 aeAmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38
                                      aeA++ LG++y    G+g+p+D ++A+ w+++A +qG+
  gi|474934299|ref|YP_007687881.1| 43 AEAQFYLGLVY--ARGQGIPRDFRLARDWLQRASDQGN 78
                                      79******777..************************7 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 3.6e-08
                              Sel1   3 AmyrLGmfylylnGlgvpkDpekAiewyek 32 
                                       Amy LG   +y  G g+++Dp +A e++ k
  gi|474934299|ref|YP_007687881.1|  81 AMYFLG--KIYVRGYGTEPDPVRAAELFTK 108
                                       9*****..999*****************98 PP

  == domain 3  score: 23.4 bits;  conditional E-value: 7.9e-09
                              Sel1   2 eAmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                        Amy+L+  +ly++G gv +D +k + +++ AAe G+
  gi|474934299|ref|YP_007687881.1| 116 RAMYALA--LLYMDGNGVGRDLSKTFSLMRDAAEGGN 150
                                       69*****..777**********************997 PP

  == domain 4  score: 22.1 bits;  conditional E-value: 1.9e-08
                              Sel1   2 eAmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                       eA++ LG  +ly +G g ++D ++ ++w+  AA +G+
  gi|474934299|ref|YP_007687881.1| 152 EAQFVLG--QLYKTGAGCETDLNQSVRWLSSAAVNGH 186
                                       8******..999********************96665 PP

  == domain 5  score: 19.9 bits;  conditional E-value: 1e-07
                              Sel1   3 AmyrLGmfylylnGlgvpkDpekAiewyekA 33 
                                       A+  LG   +y +G+gv  Dp++A +wy +A
  gi|474934299|ref|YP_007687881.1| 189 AQILLG--DMYTAGDGVQEDPDEAGRWYNMA 217
                                       899***..666*****************998 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.6   5.4e-05      0.48      12      60 ..      26      73 ..      26      81 .. 0.87
   2 ?    3.6   0.2     0.012   1.1e+02      11      57 ..      61     106 ..      61     110 .. 0.82
   3 ?    0.5   0.1      0.11     1e+03      30      44 ..     111     125 ..      87     131 .. 0.69
   4 ?   -0.4   0.0      0.22   1.9e+03      38      60 ..     191     217 ..     181     220 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.4e-05
                            TPR_16 12 dyddAaaaleaalkrdpssPdaaeAllllgdaalrq....grlaeAaalyraa 60
                                      dy dA  +l  + +++     +aeA+++lg++++r      ++ +A++++++a
  gi|474934299|ref|YP_007687881.1| 26 DYSDAFSVLSSYADKG-----NAEAQFYLGLVYARGqgipRDFRLARDWLQRA 73
                                      6778888888888888.....*************9999999999999999997 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.012
                            TPR_16  11 gdyddAaaaleaalkrdpssPdaaeAllllgdaalrq....grlaeAaaly 57 
                                       +d++ A+  l++a +++     +  A+++lg ++ r     ++  +Aa+l+
  gi|474934299|ref|YP_007687881.1|  61 RDFRLARDWLQRASDQG-----NLGAMYFLGKIYVRGygtePDPVRAAELF 106
                                       57888888889999999.....999******99988887778888888777 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.11
                            TPR_16  30 sPdaaeAllllgdaa 44 
                                       +  + +A+++l++++
  gi|474934299|ref|YP_007687881.1| 111 EAGDTRAMYALALLY 125
                                       333777888888776 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 0.22
                            TPR_16  38 lllgdaalrq....grlaeAaalyraa 60 
                                        llgd++ +      + +eA  +y+ a
  gi|474934299|ref|YP_007687881.1| 191 ILLGDMYTAGdgvqEDPDEAGRWYNMA 217
                                       556666665555558888888999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       201  (0.0112109); expected 358.6 (0.02)
Passed bias filter:                      190  (0.0105974); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1854.17
//
Query:       gi|474934300|ref|YP_007687882.1|  [L=560]
Description: Formate-tetrahydrofolate ligase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     9e-239  793.3   3.3     1e-238  793.1   3.3    1.0  1  FTHFS     Formate--tetrahydrofolate ligase
  ------ inclusion threshold ------
       0.02   14.9   1.5       0.16   12.0   1.5    2.4  3  CbiA      CobQ/CobB/MinD/ParA nucleotide binding domain


Domain annotation for each model (and alignments):
>> FTHFS  Formate--tetrahydrofolate ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  793.1   3.3  1.1e-242    1e-238       1     553 [.       2     559 ..       2     560 .] 0.99

  Alignments for each domain:
  == domain 1  score: 793.1 bits;  conditional E-value: 1.1e-242
                                       --HHHHHHCS----HHHHHHCTT--CCCEEEBSTTEEEE-CHHCCTCTTTS-.-EEEEEEESS--TT--SHHHHHHH CS
                             FTHFS   1 ksdieiaqeaklkpieeiaeklglkeeelelyGkykakvslkvlerllkekkkgklilvtaitPtplGeGKttttig 77 
                                       ++dieia++ak+k+i+eia+++gl+++++e++Gky akv l+vle+++++k +gkl+lvta+tPt++GeGKt+tti+
  gi|474934300|ref|YP_007687882.1|   2 MTDIEIAENAKVKKITEIAKTIGLDADDIEQFGKYIAKVPLDVLEKAEAKKGQGKLVLVTAVTPTQAGEGKTVTTIS 78 
                                       68********************************************99999************************** PP

                                       HHHHHHHTT--EEEEE----SHHHHCST--SCEETTEEEESHHHHHTTTTSHHHHHHHHHHHHHHHHHHHHHTTTTT CS
                             FTHFS  78 LaqalnklgkkavaalRepslGPvfgiKGgAaGGGysqvvPmedinLhltGDihaitaannllaalidnrifhenel 154
                                       L q+l+ lgk++v alReps+GP+fgiKGgA+GGG++q+ Pm +i+L++tGDiha+++a+nll+a+++n++ ++n l
  gi|474934300|ref|YP_007687882.1|  79 LIQGLAALGKNVVGALREPSIGPTFGIKGGATGGGHAQIYPMWKIDLEFTGDIHAVASAHNLLSAVLENNLVRDNPL 155
                                       ***************************************************************************** PP

                                       -EECCCE---EEESS--GGGSSEEES-SSTT..S---EEE-EEEGGGSHHHHHHHH-SSHHHHHHHHHC-EEEEETT CS
                             FTHFS 155 didpkkitwkrvlDvndraLRkivvglggke..kgvpretgfditvasEimailaLakdledlkerlgrivvaytkd 229
                                       +idp++i+wk+++D+n r+LR+ivvg+g+++   gv++e+gf it asEi ailaLa +++dl+erl+rivvayt d
  gi|474934300|ref|YP_007687882.1| 156 NIDPSRIVWKKTVDMNMRELRRIVVGIGDTKvsGGVTHESGFLITSASEISAILALAVSYKDLRERLERIVVAYTFD 232
                                       ***************************98864478****************************************** PP

                                       S-EEECCCCT-HHHHHHHTTTTTS-EEEEETT--EEEE-----SSSS--B--HHHHHHHHHH-SEEEEEBSSSTTTH CS
                             FTHFS 230 gepvtaedlkvagalavllkdaikPnlvqtlegtpalvHggPFAniahGcnsviatklalkladyvvtEaGFgadlg 306
                                       ++pvta +l++ g+++vll++a+ Pnlvqtleg+p++vHg PFAniahG+nsviatk+a+ + d++vtE GF+adlg
  gi|474934300|ref|YP_007687882.1| 233 NKPVTAGQLGCVGSMMVLLREALMPNLVQTLEGQPVFVHGFPFANIAHGNNSVIATKAAMAFGDIAVTEGGFAADLG 309
                                       ***************************************************************************** PP

                                       HHHHHHTHHHHHT---SEEEEEEEHHHHHHHTT--CCCTTS--HHHHHHHHHHHHHHHHHHCTTT--EEEEEE--TT CS
                             FTHFS 307 aekfldikcrasglkpdavvlvatvraLklhggvekeelkeenlealekGlanlekhienvkkfgvpvvvainkfkt 383
                                        +kf+di +r+sg++p+avv+vatvraL +hgg++ ++ ++  ++al++G+anl+kh+en+k++gvpv+v+in+f t
  gi|474934300|ref|YP_007687882.1| 310 GQKFMDIVARQSGIRPSAVVIVATVRALMMHGGADVKDPESFTTAALQRGFANLDKHVENMKSYGVPVIVSINHFYT 386
                                       ***************************************************************************** PP

                                       --HHHHHHHHHHHHCTTSEEEEE-HHHHGGGGGHHHHHHHHHHCC..--.---SS-TTS-HHHHHHHHHHHTT--SE CS
                             FTHFS 384 DteaelelvkelaeakavevalsevwakGgeGalelaeavveale..ekefkflYdlelsieekietiakeiYgadg 458
                                       D+e++++l+++++++ ++e+++s+ + +Gg+Ga+elae+vve+l   + efkf Y++elsi+ekiet+a++iYgadg
  gi|474934300|ref|YP_007687882.1| 387 DSESDIKLIRDHCREIGAECVMSDGYLEGGKGAKELAEKVVEVLGstKPEFKFSYPDELSIQEKIETVATKIYGADG 463
                                       ********************************************954477*************************** PP

                                       EEE-HHHHHHHHHHHHTTCTTS-EEEE--SSSSSSSTT--SS--S-EEEEEEEEEETTTTEEEEESST--SS----S CS
                             FTHFS 459 velseeakkklkklekqgldklpvciaKtqySlsddpklkgapegftltvrevrlsaGagfivalageimtmPGlpk 535
                                       v++s+ a+k+++ +++qg++klp+ciaKtqyS+sd+p+lkgap g+tl+vrev lsaGagf+v+++g+im mPGl+k
  gi|474934300|ref|YP_007687882.1| 464 VRFSKLAEKQIQAINDQGYGKLPICIAKTQYSISDNPDLKGAPIGWTLSVREVLLSAGAGFVVPVCGNIMLMPGLSK 540
                                       ***************************************************************************** PP

                                       S-GGGC-EE-TT.SEEES- CS
                             FTHFS 536 kpaaekidvdee.gkieGl 553
                                       +paa +id++e+ +ki Gl
  gi|474934300|ref|YP_007687882.1| 541 EPAALRIDLSEDgKKIIGL 559
                                       ************7789998 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.5   1.8e-05      0.16       2      31 ..      62      91 ..      61      93 .. 0.91
   2 ?   -2.2   0.0      0.44     4e+03      76      96 ..     179     197 ..     140     234 .. 0.74
   3 ?   -1.3   0.0      0.23   2.1e+03     117     117 ..     386     386 ..     343     488 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.8e-05
                                      EEEESSTTSSHHHHHHHHHHHHHHTT--EE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  2 aiastkGGvGKTtlaanLaralarrglrVl 31
                                      a++ t  G+GKT+++++L++ la  g++V+
  gi|474934300|ref|YP_007687882.1| 62 AVTPTQAGEGKTVTTISLIQGLAALGKNVV 91
                                      6778899*********************97 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.44
                                       EEEEEEEEESS...-TTCHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  76 iagvvlnrvdgeneetllkea 96 
                                       ++g+++++v g    t+++ +
  gi|474934300|ref|YP_007687882.1| 179 VVGIGDTKVSGG--VTHESGF 197
                                       677778888777..4444444 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.23
                                       C CS
                                       x RF
                              CbiA 117 a 117
                                        
  gi|474934300|ref|YP_007687882.1| 386 T 386
                                       0 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (560 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.45
# Mc/sec: 3698.88
//
Query:       gi|474934301|ref|YP_007687883.1|  [L=26]
Description: hypothetical protein TALC_00726 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (26 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       156  (0.00870099); expected 358.6 (0.02)
Passed bias filter:                      141  (0.00786435); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 193.29
//
Query:       gi|474934302|ref|YP_007687884.1|  [L=181]
Description: putative phosphatase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-18   66.0   0.0    4.8e-18   65.9   0.0    1.0  1  HAD_2           Haloacid dehalogenase-like hydrolase
    3.1e-06   27.2   0.0    4.6e-06   26.6   0.0    1.3  1  Hydrolase_like  HAD-hyrolase-like
    0.00013   22.3   0.0    0.00016   22.0   0.0    1.1  1  Hydrolase       haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.9   0.0     8e-22   4.8e-18      31     177 ..       8     155 ..       1     156 [. 0.91

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 8e-22
                             HAD_2  31 elseeelrkliglslrellrklgeseeeee..kieellrkyneekkkkevkpydgvkelLeeLkeagyklgivTsks 105
                                        ++++   ++ +++l++l+++  +  ++e    ++  +  y+ ++k  e +++++v  +L  L++++ +lgiv+ + 
  gi|474934302|ref|YP_007687884.1|   8 AYDPNMDYEYAEMPLDQLFSQHHKGCTCEYrdFVTMTIAAYERNMKS-EANIFPDVPLTLGILRSNNRRLGIVSRSY 83 
                                       55555566888899999999999887777787889999999999999.***************************** PP

                             HAD_2 106 reaveekleqlgiesyFdvivtsedvekkKPdpeviekaleklklkkeeviyvGDsptDieaakkagikvia 177
                                       +  +++ l+ + +e+ Fd iv+ e +  + P+p ++  +++++++++++++ v  +p Die++++ag+k++ 
  gi|474934302|ref|YP_007687884.1|  84 EHHIRMILSDFSMEDAFDSIVGLERAVLQRPNPYTVDLCMREMGADRNNTLLVSSNPLDIETGHNAGVKTAL 155
                                       *********************************************************************985 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   7.8e-10   4.6e-06       3      74 ..     112     177 ..     110     178 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 7.8e-10
                                       STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTTHHHHHHHHT---SEEES CS
                    Hydrolase_like   3 gKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrpedleepehkptyvaddlae 74 
                                         P+p ++d  ++++g+d++++l++  +   Di+ ++naG+k++L  +  ++  d     ++pty++ +++e
  gi|474934302|ref|YP_007687884.1| 112 QRPNPYTVDLCMREMGADRNNTLLVSSN-PLDIETGHNAGVKTALLDRSGHTGPD-----CGPTYYISSFDE 177
                                       67**************************.99************998775544434.....778888887776 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   2.7e-08   0.00016     117     210 .]      56     150 ..      37     150 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.7e-08
                                       HHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT.GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 117 lkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG.ddyfdaviasdietvakpspegkvaaireLqgkpee 192
                                         ++p++  ++  L++++ ++++++ + +++ + +++ +  +d+fd +++ +  +   p+p  +   +re++++ ++
  gi|474934302|ref|YP_007687884.1|  56 ANIFPDVPLTLGILRSNNRRLGIVSRSYEHHIRMILSDFSmEDAFDSIVGLERAVLQRPNPYTVDLCMREMGADRNN 132
                                       4499**********************************999************************************ PP

                                       EEEEESSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxx RF
                         Hydrolase 193 vamVGDgvnDaaalaaAg 210
                                       ++ V  ++ D++ + +Ag
  gi|474934302|ref|YP_007687884.1| 133 TLLVSSNPLDIETGHNAG 150
                                       *************99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 1048.15
//
Query:       gi|474934303|ref|YP_007687885.1|  [L=318]
Description: TPR repeat protein, SEL1 subfamily [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-30  102.9  18.4    0.00016   22.2   0.1    7.6  7  Sel1      Sel1 repeat


Domain annotation for each model (and alignments):
>> Sel1  Sel1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0     1e-08   0.00018       3      38 .]      45      78 ..      43      78 .. 0.94
   2 !    6.5   0.0    0.0008        14       3      37 ..      81     112 ..      79     113 .. 0.75
   3 !   12.1   0.6   1.4e-05      0.25       7      36 ..     120     148 ..     120     150 .. 0.82
   4 !   15.5   0.0   1.2e-06     0.022       3      25 ..     152     172 ..     151     178 .. 0.90
   5 !    9.8   0.1   7.3e-05       1.3       1      30 [.     186     212 ..     186     214 .. 0.87
   6 !   22.2   0.1   9.2e-09   0.00016       2      38 .]     221     255 ..     220     255 .. 0.91
   7 !   21.9   0.4   1.1e-08    0.0002       2      38 .]     257     291 ..     256     291 .. 0.95

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1e-08
                              Sel1  3 AmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38
                                       m+ L+  +l + G+ vp+D e Ai +y kAAeqG+
  gi|474934303|ref|YP_007687885.1| 45 GMFGLA--ELKMSGRWVPQDTEGAISLYTKAAEQGN 78
                                      699***..888************************7 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0008
                              Sel1   3 AmyrLGmfylylnGlgvpk.DpekAiewyekAAeqG 37 
                                       Am+rLG   ++ + ++    Dp kA+ ++ k A++G
  gi|474934303|ref|YP_007687885.1|  81 AMFRLG--NIFVTDKD--HeDPAKAFDYLTKCADAG 112
                                       788888..54456653..249*********999988 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 1.4e-05
                              Sel1   7 LGmfylylnGlgvpkDpek.AiewyekAAeq 36 
                                       LG   ++++G g +kDp + A+e+++ A + 
  gi|474934303|ref|YP_007687885.1| 120 LG--DMHYYGIGRDKDPARaAEEYMRAASKG 148
                                       89..899*********999788888777664 PP

  == domain 4  score: 15.5 bits;  conditional E-value: 1.2e-06
                              Sel1   3 AmyrLGmfylylnGlgvpkDpek 25 
                                       +m++LG  +++++G gv+kDp++
  gi|474934303|ref|YP_007687885.1| 152 SMFKLG--CMFEAGIGVEKDPKR 172
                                       8*****..888*********987 PP

  == domain 5  score: 9.8 bits;  conditional E-value: 7.3e-05
                              Sel1   1 aeAmyrLGmfylylnGlgvpkDpekAiewy 30 
                                       aeA+++++   + ++G   p   e+A +wy
  gi|474934303|ref|YP_007687885.1| 186 AEAQFKVA--SMVYDGE-MPGGHEEAAKWY 212
                                       79******..5558**9.8889*******9 PP

  == domain 6  score: 22.2 bits;  conditional E-value: 9.2e-09
                              Sel1   2 eAmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                        A ++L+++y  l G+gv kD +kA+ +y+  A++Gd
  gi|474934303|ref|YP_007687885.1| 221 VAKFNLATMY--LQGDGVAKDAKKAFSLYRDLADLGD 255
                                       6889***999..*****************99999886 PP

  == domain 7  score: 21.9 bits;  conditional E-value: 1.1e-08
                              Sel1   2 eAmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                       +A++++G   +yl+G gv+++ e+++++   AA++Gd
  gi|474934303|ref|YP_007687885.1| 257 DAAMQVG--KMYLDGEGVEQNAEEGFRYIGIAAKAGD 291
                                       699****..999**********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1937.58
//
Query:       gi|474934304|ref|YP_007687886.1|  [L=105]
Description: transcriptional regulator, ArsR family [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-12   47.0   0.1    5.9e-12   45.5   0.0    1.7  2  HTH_20         Helix-turn-helix domain
    7.2e-12   45.0   0.1    1.6e-11   43.9   0.0    1.6  2  HTH_5          Bacterial regulatory protein, arsR family
    2.2e-05   23.9   0.0    3.8e-05   23.2   0.0    1.4  1  HTH_24         Winged helix-turn-helix DNA-binding
    0.00016   21.5   0.0    0.00023   21.0   0.0    1.2  1  MarR_2         MarR family
    0.00017   21.4   0.0    0.00024   20.9   0.0    1.2  1  TrmB           Sugar-specific transcriptional regulator TrmB
      0.003   17.3   0.0     0.0057   16.4   0.0    1.3  1  LexA_DNA_bind  LexA DNA binding domain
     0.0034   17.5   0.0     0.0048   17.1   0.0    1.2  1  HTH_34         Winged helix DNA-binding domain
     0.0075   16.2   0.1     0.0098   15.9   0.1    1.5  1  HTH_Crp_2      Crp-like helix-turn-helix domain
     0.0077   16.6   0.0       0.01   16.2   0.0    1.2  1  Rrf2           Transcriptional regulator
  ------ inclusion threshold ------
      0.011   15.5   0.1      0.016   15.0   0.1    1.3  1  HTH_23         Homeodomain-like domain
      0.051   13.8   0.0      0.074   13.3   0.0    1.2  1  pXO2-72        Uncharacterized protein pXO2-72
      0.083   13.1   0.1       0.12   12.6   0.1    1.5  1  PaaX           PaaX-like protein
      0.091   12.3   0.0       0.13   11.8   0.0    1.2  1  HTH_CodY       CodY helix-turn-helix domain
       0.13   12.0   0.0       0.22   11.3   0.0    1.3  1  HTH_IclR       IclR helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.0   4.6e-15   5.9e-12       2      61 .]      22      80 ..      21      80 .. 0.96
   2 ?   -1.0   0.1       1.5   1.9e+03      43      53 ..      89      99 ..      87     105 .] 0.80

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 4.6e-15
                                      HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                            HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvregr 61
                                      + ++++++ +R ril  L  +++l++ ++ ++l++s++ +s++L++L+  g+ve +r g+
  gi|474934304|ref|YP_007687886.1| 22 DFFSIFSDSTRIRILWVL-YGRELCVRDISDTLGISMSACSHQLKTLRNSGAVEARRDGK 80
                                      78999*************.**************************************985 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.5
                                      HHHHHHHHCTT CS
                            HTH_20 43 yHLrvLeeagL 53
                                       H+++L + gL
  gi|474934304|ref|YP_007687886.1| 89 EHVEILLRTGL 99
                                      69999*99998 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       6.8   8.7e+03      16      23 ..      15      22 ..      14      23 .. 0.81
   2 !   43.9   0.0   1.2e-14   1.6e-11       1      46 [.      29      74 ..      29      75 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 6.8
                                      EEHHHHHH CS
                             HTH_5 16 lcvcelae 23
                                       cv +la+
  gi|474934304|ref|YP_007687886.1| 15 ECVMDLAD 22
                                      69999985 PP

  == domain 2  score: 43.9 bits;  conditional E-value: 1.2e-14
                                      SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  1 dptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      d+tR++IL  L  +elcv ++++ lg+s s+ Sh+Lk Lr++G Ve
  gi|474934304|ref|YP_007687886.1| 29 DSTRIRILWVLYGRELCVRDISDTLGISMSACSHQLKTLRNSGAVE 74
                                      89*****************************************876 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   2.9e-08   3.8e-05       2      47 ..      29      73 ..      28      74 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 2.9e-08
                            HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      d t+++IL +L+    ++ r++++ lg+S s+++ +lk L ++G +
  gi|474934304|ref|YP_007687886.1| 29 DSTRIRILWVLYG-RELCVRDISDTLGISMSACSHQLKTLRNSGAV 73
                                      7799999999999.88***************************976 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.8e-07   0.00023       6      56 ..      31      78 ..      27      80 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.8e-07
                                      HHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2  6 aqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                      +  r+L +L+ r+   l v+++ ++lg+s sa s  lk L   G ve r++
  gi|474934304|ref|YP_007687886.1| 31 TRIRILWVLYGRE---LCVRDISDTLGISMSACSHQLKTLRNSGAVEARRD 78
                                      7789********9...9******************************9976 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.9e-07   0.00024      22      63 ..      43      84 ..      36      89 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.9e-07
                                      CCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEE CS
                              TrmB 22 patadeiaeelgvprskvYevLrsLedkGlVerekgrpklYr 63
                                      ++ +++i+  lg++ s +   L+ L + G Ve ++  +++Y 
  gi|474934304|ref|YP_007687886.1| 43 ELCVRDISDTLGISMSACSHQLKTLRNSGAVEARRDGKMIYY 84
                                      6779*******************************9888764 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   4.4e-06    0.0057      28      58 ..      46      75 ..      45      80 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.4e-06
                                      HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE- CS
                     LexA_DNA_bind 28 ireiaralglkSpsaveehLkaLerKGyier 58
                                      +r+i++ lg++  sa  ++Lk+L++ G++e 
  gi|474934304|ref|YP_007687886.1| 46 VRDISDTLGIS-MSACSHQLKTLRNSGAVEA 75
                                      89********7.9****************95 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   3.7e-06    0.0048       2      48 ..      32      77 ..      31      83 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.7e-06
                            HTH_34  2 RlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdk 48
                                      R+ +l++L+  +e + ++++++l+++ ++ s +lk+L + g +e + 
  gi|474934304|ref|YP_007687886.1| 32 RIRILWVLYG-RELCVRDISDTLGISMSACSHQLKTLRNSGAVEARR 77
                                      8999****97.6799**************************998775 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   7.6e-06    0.0098      25      54 ..      47      77 ..      20     102 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.6e-06
                                      HHHHHHTTSSHHHHHHHHHHHHHTTSEE.ET CS
                         HTH_Crp_2 25 eelAsmlGltretvsrilseLkreglis.rg 54
                                      +++++ lG++ + +s  l+ L++ g ++ r+
  gi|474934304|ref|YP_007687886.1| 47 RDISDTLGISMSACSHQLKTLRNSGAVEaRR 77
                                      79**************************765 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   7.9e-06      0.01      24      76 ..      43      95 ..      31     101 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.9e-06
                                      C-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET.TT-TCEEESSHCCCSBH CS
                              Rrf2 24 epvsseeiaerqnispsylekilakLrkaglvksvr.GkgGGyrLakppeeItl 76
                                      e + +++i++  +is s +++ l++Lr++g v+++r Gk   y+La +  eI l
  gi|474934304|ref|YP_007687886.1| 43 E-LCVRDISDTLGISMSACSHQLKTLRNSGAVEARRdGKMIYYKLADEHVEILL 95
                                      3.7789****************************98799999999998888865 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   1.2e-05     0.016       4      46 ..      31      73 ..      28      77 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.2e-05
                            HTH_23  4 ereRlrillllaeGlsvreIAreLgvsrrTvyrwlkryreeG.l 46
                                       r+R++ +l  +e l+vr+I++ Lg+s +  ++ lk+ r++G +
  gi|474934304|ref|YP_007687886.1| 31 TRIRILWVLYGRE-LCVRDISDTLGISMSACSHQLKTLRNSGaV 73
                                      5566666666665.9*********************99988845 PP

>> pXO2-72  Uncharacterized protein pXO2-72
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   5.8e-05     0.074      11      52 ..      46      86 ..      37      92 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.8e-05
                           pXO2-72 11 treaCdrWeitleaLrmkLkrlkdselldkLikeGklkyykP 52
                                       r+  d  +i + a   +Lk l++s  ++   ++Gk+ yyk 
  gi|474934304|ref|YP_007687886.1| 46 VRDISDTLGISMSACSHQLKTLRNSGAVEA-RRDGKMIYYKL 86
                                      57888999********************97.6********95 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   9.5e-05      0.12      30      69 ..      50      89 ..      23      90 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.5e-05
                              PaaX 30 laelGiseslvRaalsRlakaGwlvrekegrrsfYrLsdk 69
                                         lGis s+    l  l + G + + ++g+  +Y+L+d+
  gi|474934304|ref|YP_007687886.1| 50 SDTLGISMSACSHQLKTLRNSGAVEARRDGKMIYYKLADE 89
                                      56789999999999999*********************97 PP

>> HTH_CodY  CodY helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0    0.0001      0.13       5      48 ..      44      86 ..      41      95 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0001
                          HTH_CodY  5 LtaskiaDriGitrsvivnaLrkLesaGiiesrsLGmkGtYlkv 48
                                      L    i+D +Gi  s     L+ L  +G +e+r  G k  Y k 
  gi|474934304|ref|YP_007687886.1| 44 LCVRDISDTLGISMSACSHQLKTLRNSGAVEARRDG-KMIYYKL 86
                                      566789***************************887.5566665 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00017      0.22      17      49 ..      42      74 ..      40      77 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                                      SS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR 17 qeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      +el ++++++ +g++ S+ ++ L+tL + G ve
  gi|474934304|ref|YP_007687886.1| 42 RELCVRDISDTLGISMSACSHQLKTLRNSGAVE 74
                                      678899************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 744.15
//
Query:       gi|474934305|ref|YP_007687887.1|  [L=769]
Description: heavy metal-(Cd/Co/Hg/Pb/Zn)-translocating P-type ATPase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-43  148.4   0.1    1.5e-43  148.4   0.1    1.7  2  E1-E2_ATPase  E1-E2 ATPase
      3e-32  112.6   0.1    5.1e-32  111.9   0.1    1.4  1  Hydrolase     haloacid dehalogenase-like hydrolase
    4.4e-07   30.3   0.0      1e-06   29.1   0.0    1.6  1  HMA           Heavy-metal-associated domain
  ------ inclusion threshold ------
      0.014   15.2   0.6      0.064   13.0   0.4    2.0  2  Hydrolase_3   haloacid dehalogenase-like hydrolase
        6.7    5.8   8.3         12    5.0   8.3    1.4  1  Zip           ZIP Zinc transporter


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.4   0.1   4.1e-47   1.5e-43       3     181 .]     199     378 ..     197     378 .. 0.95
   2 ?   -4.8   1.3       4.4   1.6e+04     117     157 ..     645     685 ..     637     687 .. 0.47

  Alignments for each domain:
  == domain 1  score: 148.4 bits;  conditional E-value: 4.1e-47
                                       S--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE- CS
                      E1-E2_ATPase   3 lpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvsg 79 
                                       + + a+v+r+g+ +++  +++++G  v++ +g+ vp+Dg ++eg   vd+ aLTGEs+p +++ +d+v sG ++++ 
  gi|474934305|ref|YP_007687887.1| 199 KVSYATVVRGGKAVKVSPQDVNVGEAVIVGPGEMVPVDGTVLEGDGFVDTKALTGESVPRHVSPEDQVLSGYINTEI 275
                                       6689************************************************************************* PP

                                       EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-ST.TTSSTTHHHHHHHHHH CS
                      E1-E2_ATPase  80 eakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvfliall.lgkslaeallralall 155
                                       e+++++ +  +d+ +++i rl+ee+++ k++ +k+++k+++v++p+v+++a++v++i  + + +s+ +++lr l +l
  gi|474934305|ref|YP_007687887.1| 276 ELVIRADRPYSDSAVKRIFRLIEESSAVKSESEKFITKFARVYTPAVVICAIAVAIIPSIiWPDSWEDWVLRCLIFL 352
                                       *******************************************************998661555555********** PP

                                       HHHS-TTHHHHHHHHHHHHHHHHHHT CS
                      E1-E2_ATPase 156 vaaiPcaLplavplalalgarrlakk 181
                                       v+++PcaL++ vpl+++ g+++++++
  gi|474934305|ref|YP_007687887.1| 353 VVSCPCALVISVPLSYFCGIGAASRR 378
                                       *********************99985 PP

  == domain 2  score: -4.8 bits;  conditional E-value: 4.4
                                       HHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHH CS
                      E1-E2_ATPase 117 klgkvlvpvvlliallvflialllgkslaeallralallva 157
                                       +++ + ++++l++ ++++ ++l+   + + a++  +++lv+
  gi|474934305|ref|YP_007687887.1| 645 RIVMQNIAMALIVKFIILELTLMGLVNMWLAIFGDVGVLVI 685
                                       44444444444444444444444444444566666666665 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.9   0.1   1.4e-35   5.1e-32       1     210 []     394     604 ..     394     604 .. 0.85

  Alignments for each domain:
  == domain 1  score: 111.9 bits;  conditional E-value: 1.4e-35
                                       SSEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHH......HHCHHHHHHHHHHHHH..HHHHHHHHHETTTE.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx.. RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsaalalaaaletg......sehpigkalvaaakar..sgaltgfatfigrg.. 67 
                                       i+ v+fDk+GTLt+g  sv+ v++s    + ++  ++      s+hpig+ + ++a     +  +++    +g+g  
  gi|474934305|ref|YP_007687887.1| 394 IRNVAFDKTGTLTKGDFSVVSVTPSEGFTEEEVVDLAfcaeaySNHPIGRSIREYAGRDvdPSRIQNSINTPGKGvg 470
                                       5779**********************77777777777779999*********7777777664444566666999999 PP

                                       ......HHHHTHHHHHHHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEE CS
                                       ......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  68 ......ayaigkpewltaldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievv 138
                                             a+++g+  ++t++    + + +  +      + + +++r  + + i+d+  +k eaa+a+ sL+  gi+++
  gi|474934305|ref|YP_007687887.1| 471 aqvderAVLVGSYSFMTEN----QIQCQHREIGMGVDIYVAVDGRHAGNILISDS--LKAEAAHAIGSLRTDGIRTF 541
                                       *******************....44444444444444444449************..******************** PP

                                       EEESSEHHHHHHHHHHTTGGGESEEEEHHCES.STTTSHHHHHHHHHHH.TSTGGGEEEEESSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 139 lltgdnpetaeraanqlGddyfdaviasdiet.vakpspegkvaaireL.qgkpeevamVGDgvnDaaalaaAg 210
                                       +ltgd ++ a ++a  lG           +++  a+ +pe+k ++++ + +     +a+VGDgvnDa+ l +A+
  gi|474934305|ref|YP_007687887.1| 542 MLTGDTQASAAEIAGTLG-----------VDEfRAGMLPEDKTRVLDGIiRSADGTTAFVGDGVNDAPSLMRAD 604
                                       ******************...........7777****************4344668*************99887 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   2.9e-10     1e-06       1      38 [.       4      40 ..       4      57 .. 0.91

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 2.9e-10
                               HMA  1 tvrvsgmhCagCaakvekvLselpgVesvkvdlatktv 38
                                      ++++ +++C +Ca+ ve+++s+++gVes+++++ +k++
  gi|474934305|ref|YP_007687887.1|  4 VFAI-DIDCPNCAREVEEAISRIDGVESATLSFMEKRM 40
                                      5778.9***************************99886 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.33   1.2e+03      16      56 ..     522     562 ..     519     567 .. 0.86
   2 ?   13.0   0.4   1.8e-05     0.064     205     245 ..     586     627 ..     580     635 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.33
                                       --HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCS CS
                       Hydrolase_3  16 isektkeaikklkekgikvviATGRslravlpvleelgldl 56 
                                       ++ ++++ai  l+  gi  +  TG    ++ +++  lg+d 
  gi|474934305|ref|YP_007687887.1| 522 LKAEAAHAIGSLRTDGIRTFMLTGDTQASAAEIAGTLGVDE 562
                                       56788999999*************99999999999999885 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 1.8e-05
                                       GEEEEESSGGGHHHHHHSSEEEEETT.S-HHHHHHSSEEE-- CS
                       Hydrolase_3 205 eviafGDgeNDieMLeaaglgvAmgn.aseevkkaAdyvtks 245
                                        ++ +GDg ND + L +a++g+Amg  +s+ +++aAd v+ +
  gi|474934305|ref|YP_007687887.1| 586 TTAFVGDGVNDAPSLMRADVGIAMGGiGSDAAIEAADVVILD 627
                                       57789*******************7549**********9876 PP

>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   8.3    0.0033        12     115     168 ..     707     759 ..     670     769 .] 0.53

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0033
                               Zip 115 sssssesaakksvsndkveeseekedhvaeadtdadskeelrngkqekseseke 168
                                       +++ +e+a ++ ++++  ++  e++ h  ++ +d+  +e +++++++ ++++ +
  gi|474934305|ref|YP_007687887.1| 707 EADGEECACGHDHHEHHDHGHGECHCH-DHESHDHGDEECQHHEHEHRHDHGRC 759
                                       222334444444444444444444332.22223344444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (769 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       808  (0.0450667); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.48
# Mc/sec: 4836.52
//
Query:       gi|474934306|ref|YP_007687888.1|  [L=675]
Description: Molecular chaperone [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   3.2e-107  359.2   1.7    5.8e-93  312.1   0.5    2.0  2  HSP70     Hsp70 protein
    3.2e-17   63.3   0.0    6.8e-17   62.3   0.0    1.5  1  VWA       von Willebrand factor type A domain
    4.3e-14   52.1   0.4    2.7e-13   49.5   0.1    2.2  2  MreB_Mbl  MreB/Mbl protein
    3.9e-13   50.0   0.0    1.2e-12   48.5   0.0    1.8  1  VWA_2     von Willebrand factor type A domain
    5.3e-05   23.2   0.0    9.5e-05   22.4   0.0    1.4  1  VWA_3     von Willebrand factor type A domain
  ------ inclusion threshold ------
       0.13   11.4   0.0       0.26   10.5   0.0    1.4  1  StbA      StbA protein


Domain annotation for each model (and alignments):
>> HSP70  Hsp70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.0   5.4e-16   1.6e-12       2      71 ..       3      74 ..       2      79 .. 0.93
   2 !  312.1   0.5   1.9e-96   5.8e-93     103     487 ..      81     465 ..      74     480 .. 0.93

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 5.4e-16
                                      EEEEEXSSEEEEEEEE..TTEEEEEXXTTSXSSEESEEEEXTTSEEETHHHHHCTTTTGGGEEEXGGGTTTX CS
                             HSP70  2 iGiDLGttnsvvavme..ggkievianeegnrttPsvvaFtkkerlvGeaAkrqavtnpkntvfsvKrliGr 71
                                      +GiDLGtt+svva  +    ++++i n eg+  tPsv+ F + + l+G+ Akr ++  + +    +Kr iG+
  gi|474934306|ref|YP_007687888.1|  3 VGIDLGTTYSVVARYNpaTSSADIIPNGEGKDLTPSVICFMDGDVLIGDDAKRMQMGGAGEIASTFKRGIGN 74
                                      8************9873256799***********************************************96 PP

  == domain 2  score: 312.1 bits;  conditional E-value: 1.9e-96
                                       ETTEEEEHHHHHHHHHHHHHHHHHHHHTSBEEEEEEEEXTTXXHHHHHHHHHHHHHTTXEEEEEEEHHHHHHHHHHT CS
                             HSP70 103 aagekftpeqisamvLkklketaeaylgkkvtdavitvPaYfndaqRqatkdAgkiAGLnvlRivNepTAaalaYGl 179
                                        + e++++e++sa + ++l e ae+  g+k++ a+itvPaYfnd qR+at +A++ AG++vl+i+NepTAaa+ YG 
  gi|474934306|ref|YP_007687888.1|  81 CNSEHYSAEDLSAIMYRHLAESAEESAGEKIDGAIITVPAYFNDIQRKATISAAQTAGIKVLKIMNEPTAAAIYYGY 157
                                       34789***********************************************************************9 PP

                                       CCSSSCEEEEEEEEXSSXEEEEEEEEETTEEEEEEEEEETTXSHHHHHHHHHHHHHHHHHHHHSXXGGGSHHHHHHH CS
                             HSP70 180 dkkdkernvlvyDlGggtfdvSilelekGvfevkaTagDthlGGedfDealvehlveefkkkegidlskdkkalqrl 256
                                         +  +++++vyDlGggtfdv i+++ +G ++v++Tag++ lGG+d+De+l++ ++++f  + g d ++d+ a +++
  gi|474934306|ref|YP_007687888.1| 158 RHSA-DKTLMVYDLGGGTFDVTIVKVTEGRIDVLGTAGNHILGGKDWDEVLMNMVCDRFADEFGADPRNDTVAREEI 233
                                       9998.************************************************************************ PP

                                       HHHHHHHHHHTTTSSCSEEEEEEEEEETTTEEEEEEEEHHHHHHHHHHHHHHTHHHHHHHHHHCTEEGGGCSEEEEE CS
                             HSP70 257 keaaekaKkeLSsskqteinleietvdedgkdlseklsRakfeelvedllertlepvekalkdaklkkeeidevvlv 333
                                       + ++e  Kk LS+  +  i++++  + +d    + +++R+++e  ++ l+  t  +v ++l d +l    +dev+lv
  gi|474934306|ref|YP_007687888.1| 234 LAQCESFKKLLST--SGVIRIPVSFAGND---GEYSVTREEYEAKTAYLITATDAVVDSVLDDLHLAPAAVDEVLLV 305
                                       *************..78899998887775...5899***************************************** PP

                                       SGGGGSHHHHHHHHHHTTCHHBSSSHTTTHHHHHHHHHHHHHCTC.GCSHCCEEEEBESS-EEEEETT.....TEEE CS
                             HSP70 334 GGstRiPkvqelvkelfgkepsktvnpDeavaiGAAvqagvlsge.eevkdllllDvtpLslgietlg.....gvmt 404
                                       GGstR+P+v++ ++     + ++  + D ava+GAA+ a+++sg+ +  +d+++ Dvt+ slg+   g      v +
  gi|474934306|ref|YP_007687888.1| 306 GGSTRMPQVEHHLRRQGFTNIKSHRDTDLAVAKGAALSAELFSGSaTGLRDIVVNDVTSHSLGMLSIGpdhrsYVNE 382
                                       *************998889999999*******************86789*********9888875544111115678 PP

                                       EEESTTCBSSEEEEEEEEESSTTSS.SEEEEEEESSSSBGGGSEEEEEEEEECESSCSTTCSEEEEEEEEETTSCEE CS
                             HSP70 405 kliernttiptkksqvfstaadnqt.aveievlqgerelvkdnkllgsfeldgippaprGvpqieVtfdidanGilt 480
                                        +iern  +p +k++ + + +dn t  +e+ +lqge ++ +d++ +g+  ++g +   rG  +i +tf+ d+nG+++
  gi|474934306|ref|YP_007687888.1| 383 IMIERNSPVPVSKTKAYRIEEDNLTdIIEVFILQGESTVPADCTVIGKEVITGFENNGRGL-NISITFSYDENGVVH 458
                                       89***********************778***************************999997.6************** PP

                                       EEEEETT CS
                             HSP70 481 vsakdke 487
                                       vsa++ +
  gi|474934306|ref|YP_007687888.1| 459 VSARNGN 465
                                       **98765 PP

>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.3   0.0   2.3e-20   6.8e-17       1     167 [.     498     653 ..     498     661 .. 0.92

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 2.3e-20
                                       EEEEEEE-STTSCHHHHHHHHHHHHHHHHHHTBTTTTEEEEEEEESSSEEEEEETTSHCHHHHHHHHHHTGSGGGGS CS
                               VWA   1 DivfvlDgSgsmgeenfekvkefikklveklevgpegtrvglvqfssevktefslndysskeellsalnnlkysggg 77 
                                       +i++ +D S sm +en+e vk++i ++v +l    + t+++l+ f++ ++++ +l+++   +++ +a+++lk    g
  gi|474934306|ref|YP_007687888.1| 498 NIAICVDLSRSM-GENLEGVKDAIRNFVLSLA--GDFTKFALIGFGDRTHVISPLSSDP--DDIRNAVERLKLNRMG 569
                                       79**********.9******************..9**********************66..9*********888888 PP

                                       SC-HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CS.SHTHHHHHHHHGCTEEEEEEEESSSHHHHHHHHHSS CS
                               VWA  78 ttntgkalkyaleklfkssagaRenakkviilltdGksnd.gdpkeaaneakeqgikvfavGvgnadekelLnkias 153
                                          t+++   ++++++++++g      +v ++ltdG   + ++  e a+e+++++i+++av +g+ad    L++ia+
  gi|474934306|ref|YP_007687888.1| 570 RG-TDANPVDTIREILSGEKG-----ARVGVILTDGIWGSrDEAVESARECRAEKINLVAVWFGDADYSF-LKQIAT 639
                                       88.88888889999*******.....9***********7756************************9999.****** PP

                                       SSCHHCEEEESSHH CS
                               VWA 154 epgeghvftvtdfe 167
                                        +++  + t+++  
  gi|474934306|ref|YP_007687888.1| 640 IEENAMYTTLSNLG 653
                                       **988888888876 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.12   3.7e+02       3      16 ..       2      15 ..       1      65 [. 0.85
   2 !   49.5   0.1     9e-17   2.7e-13      75     320 ..      93     345 ..      87     350 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.12
                                      EEEEEE-SSEEEEE CS
                          MreB_Mbl  3 dlgiDLGtantlvy 16
                                      ++giDLGt+  +v 
  gi|474934306|ref|YP_007687888.1|  2 KVGIDLGTTYSVVA 15
                                      689*****999984 PP

  == domain 2  score: 49.5 bits;  conditional E-value: 9e-17
                                       HHHHHHHHHHHHTSS-SS--EEEEEE-SS--HHHHHHHHHHHHHTT-SEEEEEEHHHHHHHHTT--TTSSS-EEEEE CS
                          MreB_Mbl  75 eellkyfikkvkkkkslskprvvicvPsgiteverrAvkeaakkaGarevllieeplaAAiGaglpveepsgnmvvd 151
                                       + + +++ + ++++   + +  +i+vP   ++++r+A + aa++aG +  ++++ep aAAi  g   ++ +  mv d
  gi|474934306|ref|YP_007687888.1|  93 AIMYRHLAESAEESAGEKIDGAIITVPAYFNDIQRKATISAAQTAGIKVLKIMNEPTAAAIYYGYRHSADKTLMVYD 169
                                       558889999999999999999******************************************************** PP

                                       E-SS-EEEEEEETTE..E..E.EEEEES-SHHHHHHHHHHHHHHHHSEE--HHHHHH..HHHHH-BSS--HHHH... CS
                          MreB_Mbl 152 iGggttevavislgg..i..v.tsksvrvaGdeldeaiikyirkkynlliGertaek..ikieigsavkeeeee... 218
                                       +Gggt +v+++ + +  i    t+    ++G+++de +++ +  ++    G    ++   + ei + +++ ++    
  gi|474934306|ref|YP_007687888.1| 170 LGGGTFDVTIVKVTEgrIdvLgTAGNHILGGKDWDEVLMNMVCDRFADEFGADPRNDtvAREEILAQCESFKKLlst 246
                                       **********97643224212144556689*******************9986554411566776666655554543 PP

                                       EEEEEEEETTTTCEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHHH-EEEESGGGGSBTHHHHHHH CS
                          MreB_Mbl 219 kmeikGrdlvtglpkevevsseevrealkepvsaiveavkevLektppeLaadivdrgivltGGgallkgldkllse 295
                                       +  i+      g   e +v+ ee +   +  ++a    v +vL++    La   vd+ ++l+GG++ + ++++ l++
  gi|474934306|ref|YP_007687888.1| 247 SGVIRIPVSFAGNDGEYSVTREEYEAKTAYLITATDAVVDSVLDDL--HLAPAAVDE-VLLVGGSTRMPQVEHHLRR 320
                                       445666677899999******9999988888888888889999987..577777776.7788*************** PP

                                       HHSS-EEE-SSTTTHHHHHHHHTTC CS
                          MreB_Mbl 296 etglpvkvaedpltcvakGtgkvle 320
                                       +   ++k   d+  +vakG++  +e
  gi|474934306|ref|YP_007687888.1| 321 QGFTNIKSHRDTDLAVAKGAALSAE 345
                                       **9****************987665 PP

>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   0.0   3.9e-16   1.2e-12       2     106 ..     500     599 ..     499     600 .. 0.92

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 3.9e-16
                             VWA_2   2 vfvlDtSgSmrngdygptrleaakdaveallkslpgd..rvglvtfsdgpevlipltkdkakilnalrnleak..gg 74 
                                        +++D S Sm+++      le +kda+++++ sl+gd  +++l+ f+d+ +v++pl++d+++i+na+++l+    g 
  gi|474934306|ref|YP_007687888.1| 500 AICVDLSRSMGEN------LEGVKDAIRNFVLSLAGDftKFALIGFGDRTHVISPLSSDPDDIRNAVERLKLNrmGR 570
                                       79**********8......***************99999********************************889555 PP

                             VWA_2  75 gtnlaaaLqlarkalkkrrkgekrvivlitDg 106
                                       gt+ a+ +++ r++l+ ++    rv v++tDg
  gi|474934306|ref|YP_007687888.1| 571 GTD-ANPVDTIREILSGEK--GARVGVILTDG 599
                                       555.7899*******9886..9999999**98 PP

>> VWA_3  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   3.2e-08   9.5e-05       2     147 ..     498     639 ..     497     642 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 3.2e-08
                             VWA_3   2 evvivvDvsssmsaenklvkdaLsvalrqLptnd.kiavllfgtkprplfpgsravsaaelqealqkikelelslga 77 
                                       +++i vD s sm  + + vkda+++++ +L     k+a+++fg+++   +p s     ++ ++++ +++ l+l++ +
  gi|474934306|ref|YP_007687888.1| 498 NIAICVDLSRSMGENLEGVKDAIRNFVLSLAGDFtKFALIGFGDRTHVISPLS-----SDPDDIRNAVERLKLNRMG 569
                                       799*********9766*************965544**********77555554.....4555777777777777665 PP

                             VWA_3  78 snlegaLkealrqp.akpgevrsvilltDgssaqgeervsdlisrar.ekirfhalglgsslsaamlqaLAe 147
                                         + +   +++r   +  + +r  ++ltDg    + ++++++ +++r eki ++a+ +g+ ++   l+++A 
  gi|474934306|ref|YP_007687888.1| 570 RGTDANPVDTIREIlSGEKGARVGVILTDGI-WGSRDEAVESARECRaEKINLVAVWFGD-ADYSFLKQIAT 639
                                       55554444444433334567888899*****.556689999999999899**********.99999999996 PP

>> StbA  StbA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   8.7e-05      0.26     124     181 ..     124     181 ..     121     194 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 8.7e-05
                              StbA 124 nvmrevelqggesftikkvkvlPeslPagfealkeldeleslLiiDlGGttLDvakvr 181
                                       +++r+ ++   ++  ik  k++ e   a++    + +    l++ DlGG t Dv+ v+
  gi|474934306|ref|YP_007687888.1| 124 DIQRKATISAAQTAGIKVLKIMNEPTAAAIYYGYRHSADKTLMVYDLGGGTFDVTIVK 181
                                       57889999999999**************9999999999999*************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (675 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.74u 0.32s 00:00:01.06 Elapsed: 00:00:00.51
# Mc/sec: 3977.17
//
Query:       gi|474934307|ref|YP_007687889.1|  [L=1001]
Description: hypothetical protein TALC_00732 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-06   27.1  10.3    8.6e-06   25.7  10.3    1.8  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.031   13.7  17.2      0.059   12.8   4.4    3.8  3  zf-ribbon_3     zinc-ribbon domain
      0.061   13.1   0.3      0.061   13.1   0.3    3.2  3  zinc_ribbon_2   zinc-ribbon domain
        1.3    9.1   5.4        4.5    7.3   5.4    1.9  1  zinc-ribbons_6  zinc-ribbons
        2.9    7.9   9.5       0.43   10.6   2.7    2.7  2  Prok-RING_1     Prokaryotic RING finger family 1
        8.4    6.5  10.6        1.3    9.1   1.7    2.6  2  zf-C2HC5        Putative zinc finger motif, C2HC5-type


Domain annotation for each model (and alignments):
>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7  10.3   2.9e-09   8.6e-06       1      49 []     312     357 ..     312     357 .. 0.97

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 2.9e-09
                               DZR   1 CpqCgeelppdar..fCseCgtklkavaaedrCpsCgekvdpearfCpeCG 49 
                                       Cp+C + +p+++   fC+ Cg++++     ++Cp Cg+   ++ r C  CG
  gi|474934307|ref|YP_007687889.1| 312 CPSCTAMIPSSDSlfFCPVCGSPVR-----TMCPVCGKIQAAGNRNCSGCG 357
                                       *********999889*********8.....********************9 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   5.5     0.039   1.2e+02       4      25 ..     311     334 ..     308     334 .. 0.73
   2 ?    6.3   0.5    0.0022       6.6       4      13 ..     327     336 ..     324     338 .. 0.83
   3 ?   12.8   4.4     2e-05     0.059       5      26 .]     339     360 ..     337     360 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.039
                       zf-ribbon_3   4 rCPnCGa.plssddn.vCpyCGtk 25 
                                        CP+C a ++ssd   +Cp CG++
  gi|474934307|ref|YP_007687889.1| 311 VCPSCTAmIPSSDSLfFCPVCGSP 334
                                       599999977555555569999975 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0022
                       zf-ribbon_3   4 rCPnCGapls 13 
                                       +CP CG+p++
  gi|474934307|ref|YP_007687889.1| 327 FCPVCGSPVR 336
                                       8******876 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 2e-05
                       zf-ribbon_3   5 CPnCGa.plssddnvCpyCGtkl 26 
                                       CP CG+ + +++ ++C  CG+ l
  gi|474934307|ref|YP_007687889.1| 339 CPVCGKiQ-AAGNRNCSGCGSNL 360
                                       ******88.***********976 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.3       2.4   7.2e+03      10      16 ..       4      10 ..       4      10 .. 0.88
   2 ?   13.1   0.3   2.1e-05     0.061       2      23 .]     312     335 ..     311     335 .. 0.85
   3 ?    4.8   3.2    0.0083        25       2      23 .]     339     360 ..     338     360 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.4
                     zinc_ribbon_2 10 qdnakFC 16
                                      q++++FC
  gi|474934307|ref|YP_007687889.1|  4 QNRDNFC 10
                                      6899*** PP

  == domain 2  score: 13.1 bits;  conditional E-value: 2.1e-05
                     zinc_ribbon_2   2 CpnCGaelqd.nakF.CpyCGtpl 23 
                                       Cp+C a ++  ++ F Cp CG+p+
  gi|474934307|ref|YP_007687889.1| 312 CPSCTAMIPSsDSLFfCPVCGSPV 335
                                       ********8537777******995 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.0083
                     zinc_ribbon_2   2 CpnCGaelqdnakFCpyCGtpl 23 
                                       Cp CG+    +++ C+ CG++l
  gi|474934307|ref|YP_007687889.1| 339 CPVCGKIQAAGNRNCSGCGSNL 360
                                       ******9999*********986 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   5.4    0.0015       4.5       2      38 ..     311     345 ..     310     368 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0015
                                       --SSS-S--EE-SSEEE-TTT--EEEEEEE-SSS-S- CS
                    zinc-ribbons_6   2 kCpeCqqelekrgeqyhCeaCqedlkkealCpeCeqe 38 
                                        Cp+C + + ++++ ++C  C + ++  ++Cp C++ 
  gi|474934307|ref|YP_007687889.1| 311 VCPSCTAMIPSSDSLFFCPVCGSPVR--TMCPVCGKI 345
                                       59999999999999999999998764..678888752 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   2.7   0.00014      0.43       6      34 ..     311     339 ..     309     341 .. 0.91
   2 ?   -0.7   0.1      0.47   1.4e+03       4      16 ..     350     362 ..     347     364 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00014
                       Prok-RING_1   6 kCpvCgkelkeedDiVvCpeCgtpyHraC 34 
                                        Cp C   + + d +  Cp+Cg+p    C
  gi|474934307|ref|YP_007687889.1| 311 VCPSCTAMIPSSDSLFFCPVCGSPVRTMC 339
                                       5**********************976666 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.47
                       Prok-RING_1   4 gkkCpvCgkelke 16 
                                       + +C+ Cg +l+e
  gi|474934307|ref|YP_007687889.1| 350 NRNCSGCGSNLSE 362
                                       678*****99986 PP

>> zf-C2HC5  Putative zinc finger motif, C2HC5-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   1.5     0.026        79      19      44 ..     311     335 ..     307     338 .. 0.89
   2 ?    9.1   1.7   0.00043       1.3      16      49 ..     335     365 ..     333     370 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.026
                          zf-C2HC5  19 nClnCGkiiCakeglskpCsfCgspl 44 
                                        C +C   i + + l   C+ Cgsp+
  gi|474934307|ref|YP_007687889.1| 311 VCPSCTAMIPSSDSL-FFCPVCGSPV 335
                                       799************.9******996 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00043
                          zf-C2HC5  16 aapnClnCGkiiCakeglskpCsfCgspllssee 49 
                                       + ++C  CGki     g   +Cs Cgs+l +s +
  gi|474934307|ref|YP_007687889.1| 335 VRTMCPVCGKIQA--AGN-RNCSGCGSNLSESRT 365
                                       5689*******54..444.77*******987654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1001 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.79u 0.29s 00:00:01.08 Elapsed: 00:00:00.49
# Mc/sec: 6108.73
//
Query:       gi|474934308|ref|YP_007687890.1|  [L=413]
Description: hypothetical protein TALC_00733 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.17   11.8   0.0        0.3   11.0   0.0    1.4  1  ATPase_2      ATPase domain predominantly from Archaea
        1.2    8.7   7.1      0.087   12.4   1.8    1.8  2  RecR          RecR protein
        1.5    8.4   0.0        1.5    8.4   0.0    2.7  3  TF_Zn_Ribbon  TFIIB zinc-binding
        5.4    7.1   5.9       0.86    9.7   0.5    2.1  2  DZR           Double zinc ribbon


Domain annotation for each model (and alignments):
>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   6.6e-05       0.3      15      68 ..     113     165 ..     109     224 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.6e-05
                          ATPase_2  15 lerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldef 68 
                                       +e++ ++iy++ G+ + GK+  l  +++ l + ++   + ++l+  s+ +++++
  gi|474934308|ref|YP_007687890.1| 113 AEENGSSIYVVLGSARTGKSHYLAVLVNTLMH-SFSAEFGTELKPASQRTVSKY 165
                                       688999*********************99944.666777777666666655554 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.3      0.98   4.4e+03      31      34 ..      10      13 ..       8      29 .. 0.59
   2 ?   12.4   1.8   1.9e-05     0.087      18      37 ..      89     108 ..      86     109 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.98
                                      -CCC CS
                              RecR 31 CaIC 34
                                      C++C
  gi|474934308|ref|YP_007687890.1| 10 CPFC 13
                                      4444 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 1.9e-05
                                       E-TTT--EESSSS-CCCCST CS
                              RecR  18 hCsrCgnlteedlCaICsdp 37 
                                       +C++Cg  +   lC+IC +p
  gi|474934308|ref|YP_007687890.1|  89 RCEICGQPAYLRLCPICHNP 108
                                       7****************998 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0   0.00033       1.5      19      33 ..       7      22 ..       5      23 .. 0.89
   2 ?   -4.0   0.4       2.5   1.1e+04       3       7 ..      90      94 ..      89      96 .. 0.54
   3 ?    0.3   0.4      0.11   5.1e+02       3       9 ..     102     108 ..     100     116 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00033
                                      CEEESSS.SBEEEECC CS
                      TF_Zn_Ribbon 19 elvCtdC.GlVledns 33
                                       ++C++C G+V  d++
  gi|474934308|ref|YP_007687890.1|  7 KYICPFCfGTVSMDRI 22
                                      59**********9986 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 2.5
                                      ETTTT CS
                      TF_Zn_Ribbon  3 CPnCg 7 
                                      C +Cg
  gi|474934308|ref|YP_007687890.1| 90 CEICG 94
                                      55555 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.11
                                       ETTTTCE CS
                      TF_Zn_Ribbon   3 CPnCgst 9  
                                       CP+C+++
  gi|474934308|ref|YP_007687890.1| 102 CPICHNP 108
                                       ****975 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.6       0.4   1.8e+03      13      23 ..       8      18 ..       2      33 .. 0.56
   2 ?    9.7   0.5   0.00019      0.86      10      42 ..      85     113 ..      78     115 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.4
                               DZR 13 rfCseCgtklk 23
                                        C+ C  +++
  gi|474934308|ref|YP_007687890.1|  8 YICPFCFGTVS 18
                                      45555555554 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00019
                               DZR  10 pdarfCseCgtklkavaaedrCpsCgekvdpea 42 
                                       +++  C+ Cg++       + Cp C+ +++p+a
  gi|474934308|ref|YP_007687890.1|  85 SRDGRCEICGQPAY----LRLCPICHNPIPPDA 113
                                       45558*******87....79********99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      608  (0.0339115); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2789.97
//
Query:       gi|474934309|ref|YP_007687891.1|  [L=197]
Description: hypothetical protein TALC_00734 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.6e-06   25.4   0.0    1.3e-05   25.0   0.0    1.1  1  GrpE      GrpE
  ------ inclusion threshold ------
      0.083   12.1   0.0       0.11   11.7   0.0    1.1  1  ERO1      Endoplasmic Reticulum Oxidoreductin 1 (ERO1)


Domain annotation for each model (and alignments):
>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   1.4e-09   1.3e-05      33     164 ..      50     187 ..      42     189 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.4e-09
                                       CCCCTTTTTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC.....HHH-HHHHHHHHHHHHHHHHHHH CS
                              GrpE  33 ekllrllaefenlrkrtekekeeakkfaiekfakdLLpvlDnleralksak...eneeekslleGvemtlkqllkiL 106
                                        +++ ++++fe ++k  +++  e ++++   ++++L  +++++ +  + ++   ++ + +++l  ++     ++++L
  gi|474934309|ref|YP_007687891.1|  50 TQYMTSREQFESYQKVINRRDGEFAEKQFMHLLEQLCLLREDFLKLCSGMQtkiDTFSASDVLASFRAYGVDIENML 126
                                       589999*************************************99999987644555555***************** PP

                                       HHTT-E..E---TTSB--TTTEEEEEEECSSC....TBEEEEEE--EEETTEEEE-EEEEE CS
                              GrpE 107 ekhgve..kiepkgepFDpnlheavstvedde.keegtvvevvqkGYklkdrvlRpAmVkV 164
                                          gv+   + + g++ D n + +vs+v++++   +g v + +++GY++++r +   +V+V
  gi|474934309|ref|YP_007687891.1| 127 TDAGVKfgTFGNPGSQVDTNNQRIVSVVPTSDpSRNGVVAQRLSSGYQYQGRTIVKEKVTV 187
                                       *****85456666******************99999******************9999998 PP

>> ERO1  Endoplasmic Reticulum Oxidoreductin 1 (ERO1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.2e-05      0.11     144     179 ..      79     114 ..      47     136 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.2e-05
                              ERO1 144 ekeleelclekrvfyrliSGlhasisihlaaeylnq 179
                                        + le+lcl ++ f +l SG+++ i ++ a++ l +
  gi|474934309|ref|YP_007687891.1|  79 MHLLEQLCLLREDFLKLCSGMQTKIDTFSASDVLAS 114
                                       567899************************998874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1360.54
//
Query:       gi|474934310|ref|YP_007687892.1|  [L=548]
Description: Molecular chaperone [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-86  290.3   6.9    6.2e-79  265.8   1.3    3.0  2  HSP70     Hsp70 protein
    1.1e-18   67.1   0.9    2.1e-18   66.3   0.9    1.4  1  MreB_Mbl  MreB/Mbl protein


Domain annotation for each model (and alignments):
>> HSP70  Hsp70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  265.8   1.3     7e-83   6.2e-79       2     373 ..       7     353 ..       6     363 .. 0.92
   2 !   18.6   0.4   4.7e-08   0.00042     382     509 ..     401     537 ..     391     547 .. 0.77

  Alignments for each domain:
  == domain 1  score: 265.8 bits;  conditional E-value: 7e-83
                                       EEEEEXSSEEEEEEEETTEEEEE.XXTTSXSSEESEEEEXTT.SEEETHHHHHCTTTT.GGGEEEXGGGTTTXBTTS CS
                             HSP70   2 iGiDLGttnsvvavmeggkievi.aneegnrttPsvvaFtkk.erlvGeaAkrqavtn.pkntvfsvKrliGrkfsd 75 
                                       +GiDLGtt+s++a +++++  v+ +n e + ttPsv+ F+++ e +vG++Ak  + +  p++ +  vKr +G++++ 
  gi|474934310|ref|YP_007687892.1|   7 VGIDLGTTYSCIAFIDENGDAVVdKNYEQEDTTPSVILFNENgESIVGSPAKDMVLMYpPDRIIRGVKRRMGTDYT- 82 
                                       8************88766555552799999***********************9987516889999*******655. PP

                                       HHHHHHHTTXSSEEEEETTSBEEEEEEETTEEEEHHHHHHHHHHHHHHHHHHHHTSBEEEEEEEEXTTXXHHHHHHH CS
                             HSP70  76 pevqkeikelpykvvkkengkavveveaagekftpeqisamvLkklketaeaylgkkvtdavitvPaYfndaqRqat 152
                                                    v+ +            +  ++p  +s+m+L+k+ ++ ++  g ++++avit+PaYf  ++R at
  gi|474934310|ref|YP_007687892.1|  83 -------------VTID------------DVVYNPVTLSGMILRKMITDFNENHGVELKKAVITCPAYFGQKERDAT 134
                                       .............4444............4479******************************************** PP

                                       HHHHHHTTXEEEEEEEHHHHHHHHHHTCCSSSCEEEEEEEEXSSXEEEEEEEEETTEEEEEEEEEETTXSHHHHHHH CS
                             HSP70 153 kdAgkiAGLnvlRivNepTAaalaYGldkkdkernvlvyDlGggtfdvSilelekGvfevkaTagDthlGGedfDea 229
                                       kdAgk+AGL+ + i+NepTAaa+++G  ++++ + + vyDlGggtfdv ile+e   f  + T g+ +lGG ++Dea
  gi|474934310|ref|YP_007687892.1| 135 KDAGKVAGLDEVTIINEPTAAAISFGYGNTETRKRIFVYDLGGGTFDVTILEIEGKGFTAVTTDGERELGGLNWDEA 211
                                       ******************************************************999******************** PP

                                       HHHHHHHHHHHHHSXX...GGGSHHHHHHHHHHHHHHHHHTTTSSCSEEEEEEEEEETTTEEEEEEEEHHHHHHHHH CS
                             HSP70 230 lvehlveefkkkegid...lskdkkalqrlkeaaekaKkeLSsskqteinleietvdedgkdlseklsRakfeelve 303
                                       l+  +++++ +++g+d   +  d+++ + l+ + e++Kk LS +++t+ ++ i      gk++  k++R++fe+ ++
  gi|474934310|ref|YP_007687892.1| 212 LTGIIIRKIAEQTGMDdseIDADDEVRSSLSIDSENIKKRLSPAESTKGTITI-----GGKKIVYKVTRDEFEDATR 283
                                       **************9733356799999****************8888877655.....46999************** PP

                                       HHHHHTHHHHHHHHHHCTEEGGGCSEEEEESGGGGSHHHHHHHHHHTTCHHBSSSHTTTHHHHHHHHHHH CS
                             HSP70 304 dllertlepvekalkdaklkkeeidevvlvGGstRiPkvqelvkelfgkepsktvnpDeavaiGAAvqag 373
                                       +l+ert++ v++al   +++  +id+ +lvGGs+++P+v +++   f     +  +p + va+GAA+ a 
  gi|474934310|ref|YP_007687892.1| 284 PLIERTMDIVQRALDVKGFTPRDIDAFLLVGGSSKMPMVSDSMIARFPDAKIQVFDPNQSVAKGAAIFAR 353
                                       ************************************************999****************885 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 4.7e-08
                                       HCCEEEEBESS-EEEEETTTE....EEEEESTTCBSSEEEEEEEEESSTTSSSEEEEEEESS........SSBGGGS CS
                             HSP70 382 kdllllDvtpLslgietlggv....mtkliernttiptkksqvfstaadnqtaveievlqge........relvkdn 446
                                       + +++  v + s+gi++++++    + ++i rn+t+p  +++ +s + d+q ++++e+++ +        r+ v+  
  gi|474934310|ref|YP_007687892.1| 401 ESIVVHNVLSKSFGIKVTDESgreyISNIIFRNKTLPITRTKQYSPMVDGQISIKVEIYENNaqddedglRSDVAAS 477
                                       568899999999***99987633336677889**************************9865222222226667778 PP

                                       EEEEEEEEECESSCSTTCSEEEEEEEEETTSCEEEEEEETTTCCEEEEEEECCSSSBHHHHHH CS
                             HSP70 447 kllgsfeldgippaprGvpqieVtfdidanGiltvsakdketgkeeeitieaseglseeeiek 509
                                       + +g+fe++ +p +      + V f    +Gil+ +a+ ++++k+ +  i+++  +++++i+k
  gi|474934310|ref|YP_007687892.1| 478 NPVGEFEME-LPEMVTKDTPVSVRFIASDEGILSATAECMNQRKDYR--IQNNIAMDADAIAK 537
                                       99*****96.6778888889**************9999998877655..55555566666655 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.3   0.9   2.3e-22   2.1e-18       3     326 ..       6     359 ..       4     360 .. 0.75

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 2.3e-22
                                       EEEEEE-SSEEEE.EETTTEE.EEEE........ES-EEEETTT--EEEESHHHHTTTTS-GTTEEEE-SEE..... CS
                          MreB_Mbl   3 dlgiDLGtantlv.yvkgkgi.vlne........psvvAikkktkkvlavGeeAkkmlgktpgnikavrPlk..... 64 
                                       ++giDLGt+   + ++ ++g  v+++        psv+ ++++ +++  vG+ Ak+m+   p + +++r +k     
  gi|474934310|ref|YP_007687892.1|   6 SVGIDLGTTYSCIaFIDENGDaVVDKnyeqedttPSVILFNENGESI--VGSPAKDMVLMYPPD-RIIRGVKrrmgt 79 
                                       589****9987664777777523321233344449****99998887..8*******9876654.334444311111 PP

                                       .......TTEESSHHHHHHHHHHHHHHHHTSS-SS--EEEEEE-SS--HHHHHHHHHHHHHTT-SEEEEEEHHHHHH CS
                          MreB_Mbl  65 .......dGviadlevaeellkyfikkvkkkkslskprvvicvPsgiteverrAvkeaakkaGarevllieeplaAA 134
                                              d v   +++   +l+++i++ ++++ ++ ++ vi++P    + er A k+a k aG +ev++i+ep aAA
  gi|474934310|ref|YP_007687892.1|  80 dytvtidDVVYNPVTLSGMILRKMITDFNENHGVELKKAVITCPAYFGQKERDATKDAGKVAGLDEVTIINEPTAAA 156
                                       111111022333355666789******************************************************** PP

                                       HHTT--TTSS.S-EEEEEE-SS-EEEEEEETTE.....EEEEEEES-SHHHHHHHHHHHHHHHHSEE--HHHHH... CS
                          MreB_Mbl 135 iGaglpveep.sgnmvvdiGggttevavislgg.....ivtsksvrvaGdeldeaiikyirkkynlliGertae... 202
                                       i  g   +e+ +  +v d+Gggt +v+++ + g     ++t     ++G ++dea++  i +k     G   +e   
  gi|474934310|ref|YP_007687892.1| 157 ISFGYGNTETrKRIFVYDLGGGTFDVTILEIEGkgftaVTTDGERELGGLNWDEALTGIIIRKIAEQTGMDDSEida 233
                                       **999666651566799************987644443556667789********8888888877777766554333 PP

                                       ..HHHHHH-BSS--HHHH...EEEEEEEETTTTCEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHH CS
                          MreB_Mbl 203 ..kikieigsavkeeeee...kmeikGrdlvtglpkevevsseevrealkepvsaiveavkevLektppeLaadivd 274
                                         +++ +++   ++ +++     + kG+  + g     +v+ +e ++a +  +++ ++ v+++L+        di  
  gi|474934310|ref|YP_007687892.1| 234 ddEVRSSLSIDSENIKKRlspAESTKGTITIGGKKIVYKVTRDEFEDATRPLIERTMDIVQRALDVK-GFTPRDI-- 307
                                       3367777766665555555567889***************************************853.3345666.. PP

                                       H-EEEESGGGGSBTHHHHHHHHH.SS-EEE-SSTTTHHHHHHHHTTC-HHHHT CS
                          MreB_Mbl 275 rgivltGGgallkgldkllseet.glpvkvaedpltcvakGtgkvleklkklk 326
                                        + +l+GG++++  + + +  ++ + +++v  dp ++vakG+++++ + +++k
  gi|474934310|ref|YP_007687892.1| 308 DAFLLVGGSSKMPMVSDSMIARFpDAKIQV-FDPNQSVAKGAAIFARSNNAMK 359
                                       468999*******99766555551566665.68**********9998887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (548 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 3313.98
//
Query:       gi|474934311|ref|YP_007687893.1|  [L=244]
Description: ribosomal large subunit pseudouridine synthase F [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-17   63.4   0.1    3.6e-16   59.7   0.1    2.1  1  PseudoU_synth_2  RNA pseudouridylate synthase
    1.3e-10   40.8   4.8    3.2e-10   39.6   0.2    2.8  3  S4               S4 domain
  ------ inclusion threshold ------
      0.045   13.6   0.2       0.24   11.2   0.2    2.2  1  S4_2             S4 domain


Domain annotation for each model (and alignments):
>> PseudoU_synth_2  RNA pseudouridylate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7   0.1     6e-20   3.6e-16       2     160 .]      67     194 ..      66     194 .. 0.80

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 6e-20
                   PseudoU_synth_2   2 lvvvnKPagvpvqpeakdgsekekettatssraeeekkelklvhRLDkatsGllllAksseaanklakafeerkvrK 78 
                                       ++v+nKP g+++++++        +   +  +  + ++++ +++RLDk+++Gllll++++++ank ++  ++++++K
  gi|474934311|ref|YP_007687893.1|  67 ILVFNKPRGLTCTSDK--------GDGTNVIDYIGYPRRIFTIGRLDKDSEGLLLLTNDGDLANKIMR--SRYGHEK 133
                                       589*************........8888999999**********************************..9****** PP

                   PseudoU_synth_2  79 kYlalvfgapeeeegaikkkiskdtekqegarrkaeeldgkkavtylk.vlksgsseksakvslveleletGrkhQi 154
                                       +Y+++v+        +i++++ +               + +k v++   v+ ++++++  +    +++l++G ++Qi
  gi|474934311|ref|YP_007687893.1| 134 EYVVTVD-------REIDESFLR---------------GMEKGVEIEDgVVTRKCRTEMVDLFTFRIVLKQGLNRQI 188
                                       ******6.......444444444...............222222222212222226667888899************ PP

                   PseudoU_synth_2 155 Rvhlaa 160
                                       R+++++
  gi|474934311|ref|YP_007687893.1| 189 RRMCEH 194
                                       ****86 PP

>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.2   5.3e-14   3.2e-10       1      46 [.       6      49 ..       6      51 .. 0.85
   2 ?    3.4   0.1      0.01        62      27      36 ..      50      59 ..      44      61 .. 0.88
   3 ?   -2.4   0.1      0.67     4e+03      17      25 ..     186     194 ..     185     194 .. 0.91

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 5.3e-14
                                      EEHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTC CS
                                S4  1 rRLdkvlarlglassrreArqlIehGrVlVNGkvvkdpsyrVkpgD 46
                                      +RL k++a++g as rr A ++Ie+GrV+VNG++    ++r+++ D
  gi|474934311|ref|YP_007687893.1|  6 VRLNKFIAEAGVAS-RRAADRMIEEGRVTVNGRKGV-LGDRITSDD 49
                                      6************9.*****************9855.555555555 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.01
                                      TEEETTEEE- CS
                                S4 27 rVlVNGkvvk 36
                                       V+V+G+v++
  gi|474934311|ref|YP_007687893.1| 50 EVRVDGRVIT 59
                                      6*******98 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.67
                                       HHHHHHHHT CS
                                S4  17 reArqlIeh 25 
                                       r++r+++eh
  gi|474934311|ref|YP_007687893.1| 186 RQIRRMCEH 194
                                       89****998 PP

>> S4_2  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2     4e-05      0.24       7      62 ..       5      58 ..       1      59 [. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4e-05
                              S4_2  7 yItLgqlLKlaglvesGgeaKafiaegeVkvNGevetrRgkKlraGdvVeidgeti 62
                                       ++L++++ +ag+++   +a  +i+eg V+vNG +    g ++ ++d V +dg  i
  gi|474934311|ref|YP_007687893.1|  5 GVRLNKFIAEAGVASR-RAADRMIEEGRVTVNGRKGV-LGDRITSDDEVRVDGRVI 58
                                      5788888888887776.77889***********8754.588888888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.56
# Mc/sec: 1308.45
//
Query:       gi|474934312|ref|YP_007687894.1|  [L=356]
Description: Pirin-related protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-14   52.7   0.0    6.4e-14   51.8   0.0    1.5  1  Pirin     Pirin
    1.3e-06   28.7   0.0    4.1e-06   27.1   0.0    1.8  2  Pirin_C   Pirin C-terminal cupin domain


Domain annotation for each model (and alignments):
>> Pirin  Pirin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.8   0.0   7.1e-18   6.4e-14      37      97 ..      74     134 ..      45     149 .. 0.84

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 7.1e-18
                                       EEET-EEEEEEEBSEEEEEEEECSEEEEEETTS-EEEEETT-EEEEE-TT-EEEEEEE-SS CS
                             Pirin  37 dvigagfpphphrgletvtylleGevehrDslGnkgvirpGdvqwmtAgsGivhsEmneee 97 
                                        +++ gfp h+h g et+ty+ +G v+h Ds+Gn g+   Gd+qw+tA s   h+Em + +
  gi|474934312|ref|YP_007687894.1|  74 GKVSPGFPLHTHWGYETLTYVSQGYVDHFDSEGNCGRFGFGDLQWVTASSRYRHDEMYPLA 134
                                       35789****************************************************8876 PP

>> Pirin_C  Pirin C-terminal cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.2   1.1e+04      16      32 ..      84     100 ..      77     123 .. 0.71
   2 !   27.1   0.0   4.6e-10   4.1e-06       3      93 ..     212     301 ..     210     305 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.2
                                       --TT-EEEEEEEES-EE CS
                           Pirin_C  16 lpegleaavyvleGele 32 
                                       +  g+e++ yv +G + 
  gi|474934312|ref|YP_007687894.1|  84 THWGYETLTYVSQGYVD 100
                                       55678888899888764 PP

  == domain 2  score: 27.1 bits;  conditional E-value: 4.6e-10
                                       EEEE-TT-EEEEE--TT-EEEEEEEES-EEESSTTEEE-TTEEEEE-SSSEEEEE--S.S-EEEEEEEE----S--E CS
                           Pirin_C   3 dltleagaelelplpegleaavyvleGelevggerseieeeqlavlgdgdslvvkaee.kgarvlLlaGePlgepvv 78 
                                        l ++ +ae+e+p +e  ++ +y ++ +++v g++   ++++ + +++  ++ ++ +e ++ ++ Ll+G P+ge+ +
  gi|474934312|ref|YP_007687894.1| 212 RLVMDRDAEIEIPASEAGTRNLYLIDAKVTVFGRE--YHADTRLKIRPDVTVPIRMGEgNRPEIWLLEGDPIGEKQA 286
                                       5678999***************************6..9999999999*********9888889************** PP

                                       EETTEEESSHHHHHH CS
                           Pirin_C  79 qyGpfVmntkeeieq 93 
                                       +yGp +  t +e++ 
  gi|474934312|ref|YP_007687894.1| 287 SYGPVILGTDKEVRS 301
                                       *********999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       229  (0.0127726); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2362.21
//
Query:       gi|474934313|ref|YP_007687895.1|  [L=93]
Description: Parvulin-like peptidyl-prolyl isomerase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.5e-24   86.8   0.0    1.8e-24   86.5   0.0    1.1  1  Rotamase    PPIC-type PPIASE domain
    6.6e-24   84.7   0.0    8.6e-24   84.3   0.0    1.2  1  Rotamase_3  PPIC-type PPIASE domain
    3.5e-07   31.1   0.0    4.2e-07   30.8   0.0    1.1  1  Rotamase_2  PPIC-type PPIASE domain


Domain annotation for each model (and alignments):
>> Rotamase  PPIC-type PPIASE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.5   0.0   2.9e-28   1.8e-24      17      95 ..      13      89 ..       4      91 .. 0.96

  Alignments for each domain:
  == domain 1  score: 86.5 bits;  conditional E-value: 2.9e-28
                                      HHHHHHHHHHCCTCCCHHHHHHHHCCC-.-CHHHCCTTEEECEETTTS-CCCHHHHCCS-CT-B-S-EEETTEEEEEEE CS
                          Rotamase 17 eakakaeeileqlksgedtFeelArkySddknsakngGdlgwvekgqlppefekaafslkkGeisepvetkfGfhiikl 95
                                      +++++a+++++++ sge+ F +lA+k+S +++s k+gGdl wv++g ++++f+ka+f+ kkG++++pv+tkfG+h+ik+
  gi|474934313|ref|YP_007687895.1| 13 ATEKEAKSLKDRIASGEN-FGQLAKKFS-QCPSGKEGGDLHWVRPGMMVEQFDKAIFAGKKGDLIGPVKTKFGWHVIKI 89
                                      6789**************.*********.************************************************97 PP

>> Rotamase_3  PPIC-type PPIASE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.3   0.0   1.4e-27   8.6e-24      15     115 ..       4      92 ..       1      93 [] 0.92

  Alignments for each domain:
  == domain 1  score: 84.3 bits;  conditional E-value: 1.4e-27
                        Rotamase_3  15 svkvshIlistkgkesrseeeakakadsllaalkegadFaalAkeySdDpaskenGGelgwftkgqmvkeFedavfs 91 
                                       +v+v+hIl++t           ++ a sl  ++  g++F +lAk++S+ p+ +++GG+l w+ +g+mv++F++a+f+
  gi|474934313|ref|YP_007687895.1|   4 EVHVAHILVAT-----------EKEAKSLKDRIASGENFGQLAKKFSQCPS-GKEGGDLHWVRPGMMVEQFDKAIFA 68 
                                       67888888875...........567889999999**************886.************************* PP

                        Rotamase_3  92 lkkgeiskvvktdfGyHiikvtdk 115
                                        kkg+++++vkt+fG+H+ik++++
  gi|474934313|ref|YP_007687895.1|  69 GKKGDLIGPVKTKFGWHVIKILEE 92 
                                       *********************986 PP

>> Rotamase_2  PPIC-type PPIASE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   7.1e-11   4.2e-07      26     107 ..       9      91 ..       2      93 .] 0.67

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 7.1e-11
                        Rotamase_2  26 elavvkdqvaaeaalalakagaekdfaalakgnskkaadlg.....ifesasnlpeelakaafalkpgevsgpvetd 97 
                                       +++v+++++a+ ++++ a ++   +f +lak+ s +++ ++     +++    + e++ ka+fa k+g++ gpv+t 
  gi|474934313|ref|YP_007687895.1|   9 HILVATEKEAKSLKDRIASGE---NFGQLAKKFSQCPSGKEggdlhWVRPG-MMVEQFDKAIFAGKKGDLIGPVKTK 81 
                                       455555555555555555555...555666665555444443334477654.5778********************* PP

                        Rotamase_2  98 ngyyivkvte 107
                                       +g++++k+ e
  gi|474934313|ref|YP_007687895.1|  82 FGWHVIKILE 91 
                                       *******965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 670.12
//
Query:       gi|474934314|ref|YP_007687896.1|  [L=155]
Description: hypothetical protein TALC_00739 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.8e-10   39.7   1.1    3.8e-10   39.7   1.1    2.6  2  DUF2188     Uncharacterized protein conserved in bacteria (DU
      0.002   18.2  70.5      0.065   13.3  70.5    2.0  1  HC2         Histone H1-like nucleoprotein HC2


Domain annotation for each model (and alignments):
>> DUF2188  Uncharacterized protein conserved in bacteria (DUF2188)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   1.1   4.3e-14   3.8e-10       1      58 [.      25      83 ..      25      86 .. 0.92
   2 ?   -3.4   5.1       1.3   1.1e+04      14      39 ..      96     121 ..      89     133 .. 0.73

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 4.3e-14
                           DUF2188  1 yhVvP.kddggWavkreGgsrasktfdTqeeAieaArelAkeqggselvihgrdGqire 58
                                      y V + k++++W vk  G++ra  +++T++eAi++ + l  +++ +   ++++dG++++
  gi|474934314|ref|YP_007687896.1| 25 YKVEKdKEKNKWVVKAVGAQRAIGYYNTKDEAIAKVNSLTSKNTNATATVRKTDGTFQK 83
                                      668888999*******************************6668************996 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.3
                           DUF2188  14 kreGgsrasktfdTqeeAieaArelA 39 
                                       k+e+++++++++  ++ A + A + A
  gi|474934314|ref|YP_007687896.1|  96 KKEPAKKPAAKPAAKKTAAKPAAKKA 121
                                       78888888777777777766666666 PP

>> HC2  Histone H1-like nucleoprotein HC2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3  70.5   7.2e-06     0.065       1     144 [.       4     155 .]       3     155 .] 0.44

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.2e-06
                               HC2   1 mlgvqKKrsskKtAakkaavrKpa.....AkKaaakktvvrKvaaKKtaarKtv.....akktvakkkvaakkaaak 67 
                                       m+ ++KK+++kK+ a       p       k          K ++K + a++++     + +++ak +    k +  
  gi|474934314|ref|YP_007687896.1|   4 MAEAAKKPAAKKASA-----DGPKknykvEKDKEK-----NKWVVKAVGAQRAIgyyntKDEAIAKVNSLTSKNTNA 70 
                                       555555555555555.....444211122122222.....3333333333333311110333333333333333333 PP

                               HC2  68 kaavkk..........avakkvva.kkkvakKavAKKaaakKvvakkvvakKtvakkaaaakKpaakkavakkaaar 133
                                        a+v+k          a+ kk++a kk++akK +A K+aakK++ak  +akK++akk  + kKpaakk + kk +a+
  gi|474934314|ref|YP_007687896.1|  71 TATVRKtdgtfqkhenAAVKKAAApKKEPAKKPAA-KPAAKKTAAK-PAAKKAPAKK-ETEKKPAAKKPAPKKEPAK 144
                                       33333311111111213344444423355555544.4666777665.4558888777.6778888888888888888 PP

                               HC2 134 KaaakKavaKk 144
                                       K+aakKa aKk
  gi|474934314|ref|YP_007687896.1| 145 KPAAKKAPAKK 155
                                       88888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1833  (0.102237); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.49
# Mc/sec: 948.67
//
Query:       gi|474934315|ref|YP_007687897.1|  [L=125]
Description: putative transcriptional regulator [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.3e-23   81.8   0.0    2.8e-23   81.6   0.0    1.1  1  HxlR       HxlR-like helix-turn-helix
  ------ inclusion threshold ------
      0.032   14.3   0.0      0.067   13.3   0.0    1.5  1  HTH_20     Helix-turn-helix domain
       0.04   13.9   0.0      0.066   13.2   0.0    1.3  1  HTH_Crp_2  Crp-like helix-turn-helix domain
      0.089   12.8   0.0       0.17   11.9   0.0    1.4  1  PadR       Transcriptional regulator PadR-like family


Domain annotation for each model (and alignments):
>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.6   0.0   6.3e-27   2.8e-23       2      88 ..      18     106 ..      17     109 .. 0.95

  Alignments for each domain:
  == domain 1  score: 81.6 bits;  conditional E-value: 6.3e-27
                                       HHSTTHHHHHHHHTT..S-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHH CS
                              HxlR   2 iggkWkllilvellk..gkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvl 76 
                                       i+g+Wk++il+ l +   ++Rf++l ++lp+is ++ + +L+eLe+dgl+ rev +e P+ v Ysl+++G sl p+l
  gi|474934315|ref|YP_007687897.1|  18 IEGRWKTVILCRLANagVPMRFNQLMAELPGISPRIFSLQLKELEKDGLLVREVRSESPKCVVYSLSDRGLSLIPIL 94 
                                       889***********984489********************************************************* PP

                                       HHHHHHHHHHHH CS
                              HxlR  77 qelkkwgeeyle 88 
                                       + l+ wg+++ +
  gi|474934315|ref|YP_007687897.1|  95 DLLAVWGMQNFS 106
                                       ********9876 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.5e-05     0.067      20      59 ..      32      73 ..      24      75 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.5e-05
                                      STCTTB-HHHHHHHH.TS-HHHHHHHHHHHHHCTT.EEEECT CS
                            HTH_20 20 araegltaselaerl.dlskntlsyHLrvLeeagL.vevvre 59
                                      + + ++ +++l+++l ++s+   s +L++Le+ gL v+ vr+
  gi|474934315|ref|YP_007687897.1| 32 NAGVPMRFNQLMAELpGISPRIFSLQLKELEKDGLlVREVRS 73
                                      567789999******99***************9996777765 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.5e-05     0.066      24      54 ..      40      70 ..      25      78 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.5e-05
                                      HHHHHHHTTSSHHHHHHHHHHHHHTTSEEET CS
                         HTH_Crp_2 24 qeelAsmlGltretvsrilseLkreglisrg 54
                                      ++ +A++ G+++  +s  l+eL+++gl+ r+
  gi|474934315|ref|YP_007687897.1| 40 NQLMAELPGISPRIFSLQLKELEKDGLLVRE 70
                                      5789***********************9864 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.8e-05      0.17      37      69 ..      57      87 ..      56      91 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.8e-05
                                      HHHHHHHTTSEEEEEE-STSSS-EEEEEESHCC CS
                              PadR 37 aLkrLekeglveseweesgegpprkyYrlTdaG 69
                                      +Lk+Lek+gl+++e +   e+p+  +Y l d+G
  gi|474934315|ref|YP_007687897.1| 57 QLKELEKDGLLVREVRS--ESPKCVVYSLSDRG 87
                                      59************886..69**********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 847.74
//
Query:       gi|474934316|ref|YP_007687898.1|  [L=336]
Description: Uroporphyrinogen-III decarboxylase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.7e-42  143.3   0.0    1.1e-41  143.2   0.0    1.0  1  URO-D     Uroporphyrinogen decarboxylase (URO-D)


Domain annotation for each model (and alignments):
>> URO-D  Uroporphyrinogen decarboxylase (URO-D)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.2   0.0   6.1e-46   1.1e-41       3     343 ..       4     334 ..       2     336 .] 0.93

  Alignments for each domain:
  == domain 1  score: 143.2 bits;  conditional E-value: 6.1e-46
                                       --HHHHHHTT---SS--B--TT-SSTTSHHHHHHHTSSSHHHHHH-HHHHHHHHHHHHHHH--S-EE-S--TTGGGG CS
                             URO-D   3 nerllralrgekvdrvPvwlmRqaGrylpeyraeragvsflelcknpelaaevtlqpvrrfglDaailfsdilveae 79 
                                       ++++++a+ g+  d +P  +    +++ +  ++   g  ++e+   + +++e++lq+++rfg+ ++ +++di+v ae
  gi|474934316|ref|YP_007687898.1|   4 RDQIIDAMDGKGGDCPPAAV---FTQTGTVSQMDACGSYWPEANFVASKMVELALQAHKRFGFGTIRIPFDITVQAE 77 
                                       799*****************...77799999********************************************** PP

                                       GGT-EEEEETTTE.EEEE--S-....GGGS----GGG.........G..HHHHHHHHHHHHH.--SS-EEEEEE-HH CS
                             URO-D  80 alGlevefeegeg.Pvvekpvrtaedveklevpddvee........grlpyvleaikllkkelggevpligfvgaPf 147
                                       a+G++v+ ++++  P+v + +++   +e  +vp+d+          +r++++lea +l+     + +  ++++++P+
  gi|474934316|ref|YP_007687898.1|  78 AFGCSVDKGRKNSqPAVMSSPFNDGSMEIPPVPEDF-IpveefmknPRIRTMLEAAELASG---HGLFSTAAMTGPL 150
                                       *********97766********98888877777775.235456655688888888888877...46999******** PP

                                       HHHHHHHCTT-SS-HHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEETTGGGS-HHHHHHHTHHHH CS
                             URO-D 148 tlasylveGgskgfekllkllykdpeevhklldkltdvvieylkaqieagAdaiqifDswagllspedfeefvlpyl 224
                                         a  ++     g+e++++ l++d  +v++++  l    ++y++a+     ++++i + + +l++ e fe + + +l
  gi|474934316|ref|YP_007687898.1| 151 GSANDIL-----GMENVMMALMMDESVVKSWVAALKPHAMAYAEALSSRCDNVLIIEEITTDLIPAEYFESITASPL 222
                                       *******.....**********************************999888999999******************* PP

                                       HHHHHHHHH.H--S-EEEEESSHH.HHHHHHTTS--SEEE--TTS-HHHHHHSS....EEE--B-G.GGGG.S-HHH CS
                             URO-D 225 krivdevkaegpkvpvilfikgagaeiledlaelgadvlsldwtvdlkeaarevgdkvalqGnldPialLl.gspee 300
                                       k +++  ++     +  ++++g++ e+ +++ +lg d+ls   +  ++e +  v+ ++ l+G ++P+++Ll g+p++
  gi|474934316|ref|YP_007687898.1| 223 KDVIKSARSD---SYCSIHCCGSTIEVADKVSSLGEDALSPQASDCMEEYVDLVNGRTRLLGSVNPVDTLLmGTPAD 296
                                       ********94...49*********99*********************88888999********************** PP

                                       HHHHHHHHHT.T---SSSEEB-BSS---TTS-HHHHHHHHHHH CS
                             URO-D 301 iekevkeilekgaggkkgyilnlGhgippetppenvkalveav 343
                                       + +++k+  e+g +      + + +gippetp en+ al e +
  gi|474934316|ref|YP_007687898.1| 297 VVAQAKKSAEAGFD-----LITPECGIPPETPDENMLALSEYA 334
                                       **********9899.....*******************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2322.34
//
Query:       gi|474934317|ref|YP_007687899.1|  [L=296]
Description: putative permease [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-52  177.9  31.3    9.4e-29  100.3  12.0    2.0  2  EamA            EamA-like transporter family
    5.5e-07   29.2   9.6    8.3e-07   28.6   9.6    1.4  1  TPT             Triose-phosphate Transporter family
  ------ inclusion threshold ------
      0.094   13.4  14.1       0.27   11.9   3.2    3.2  3  Multi_Drug_Res  Small Multidrug Resistance protein
          6    5.0  22.7        3.5    5.8   9.0    2.0  2  DUF2070         Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.9  11.3   2.4e-27   1.1e-23       4     135 ..       9     141 ..       6     143 .. 0.95
   2 !  100.3  12.0   2.1e-32   9.4e-29       2     136 ..     154     289 ..     153     290 .. 0.98

  Alignments for each domain:
  == domain 1  score: 83.9 bits;  conditional E-value: 2.4e-27
                              EamA   4 illallaalfwaiyfvlskil.lrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlaf 79 
                                       + l+++aa++w++  ++++ l  + +sp++ tfvr l+ + ++ +i+++ +++l ++ +kd+  +l +g+l++v+++
  gi|474934317|ref|YP_007687899.1|   9 AALVITAAVLWGVICLFTRSLnDEGLSPVQCTFVRALVTAPIVGAILAVADRRLFRIEPKDIWMFLGTGILSIVMFN 85 
                                       5799**************98867788*****************999999999998********************** PP

                              EamA  80 llffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvlli 135
                                       +++f+a ++++ s a+++++++Pvf++++sv+l+ge+lt  ++++++l+++G++l+
  gi|474934317|ref|YP_007687899.1|  86 ICYFSAAEEVTMSMAAVLLYTAPVFVMLMSVILFGERLTNVKMIALALAFAGCVLT 141
                                       ******************************************************97 PP

  == domain 2  score: 100.3 bits;  conditional E-value: 2.1e-32
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegkl.aklslkdwllllllgllgtvl 77 
                                       +g+l+ l a + +a+y +++k +lrk++p+t+tf++flia+++ll++a l+e+ + a+ s k++l +l lg+++t++
  gi|474934317|ref|YP_007687899.1| 154 RGLLFGLGAGIGYAFYSIFAKFALRKYHPFTITFYTFLIAALALLPFAGLWEIADvASGSGKHLLEMLALGTVCTAA 230
                                       699****************************************************99999999************** PP

                              EamA  78 afllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                        ++l++++l+ ++a++as++ + eP+ +++ +++++ e+l++ ++lgi+lil++++l++
  gi|474934317|ref|YP_007687899.1| 231 PYFLYTKGLEGMEAGKASVLAFAEPMTATVAGFVVYDETLGIVEILGILLILVSIFLLS 289
                                       *********************************************************97 PP

>> TPT  Triose-phosphate Transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   9.6   1.9e-10   8.3e-07      30     232 ..      35     235 ..      17     289 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.9e-10
                               TPT  30 yPltvsavqllvgsvlilvlwalglkkrpkisseflkailplalvktlghvlavvs.lskvaVSfthtvKasePiFt 105
                                        P+  + v+ lv+  ++ +++a+  ++  +i+ + +++ l  +++ ++      +s  ++v+ S + ++  ++P+F 
  gi|474934317|ref|YP_007687899.1|  35 SPVQCTFVRALVTAPIVGAILAVADRRLFRIEPKDIWMFLGTGILSIVMFNICYFSaAEEVTMSMAAVLLYTAPVFV 111
                                       58888999999999999999999999999*************999887666666551679***************** PP

                               TPT 106 vilsrlllgeklsllvylsLlpivgGvalas.vt..ElsFnligfisAlisnltfslrnifsKkllkklkdldalnl 179
                                        ++s +l+ge+l+  ++++L    +G++l++ +       n+ g++  l + ++ ++ +if+K +l+k    +  ++
  gi|474934317|ref|YP_007687899.1| 112 MLMSVILFGERLTNVKMIALALAFAGCVLTAgLIggSQGVNVRGLLFGLGAGIGYAFYSIFAKFALRK---YHPFTI 185
                                       **************************99966344124568****************************...689999 PP

                               TPT 180 faiitilslllllPvallvegvlktpsllkstkvslkevllllllsgvlfhly 232
                                        +++ ++++l llP+a l e + +     k+    l+ + l  ++ +  ++ly
  gi|474934317|ref|YP_007687899.1| 186 TFYTFLIAALALLPFAGLWEIADVASGSGKH---LLEMLALGTVCTAAPYFLY 235
                                       99999999999***99998882222222222...2444445555555555555 PP

>> Multi_Drug_Res  Small Multidrug Resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   3.2   5.9e-05      0.27      33      92 ..      76     133 ..      45     134 .. 0.78
   2 ?   -1.5   0.1      0.91   4.1e+03      24      45 ..     181     197 ..     164     207 .. 0.51
   3 ?    7.1   1.7     0.002       8.9      24      93 .]     213     281 ..     192     281 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.9e-05
                                       -HHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHH--------HHHHHH CS
                    Multi_Drug_Res  33 llvivgygisfllLskalkslpvsvAYavwsGiGtvlivlvgillfgeslslkkliglal 92 
                                        +++ +++++++ +s a +++ +s+A av+     v+++l++++lfge+l   k+i lal
  gi|474934317|ref|YP_007687899.1|  76 TGILSIVMFNICYFS-AAEEVTMSMA-AVLLYTAPVFVMLMSVILFGERLTNVKMIALAL 133
                                       344445555555555.6688999999.777777899*********************998 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.91
                                       ----------HHHHHHHHHHHH CS
                    Multi_Drug_Res  24 egftkltpsllvivgygisfll 45 
                                       + ft ++ +     +++++++l
  gi|474934317|ref|YP_007687899.1| 181 HPFTITFYT-----FLIAALAL 197
                                       333333333.....33333333 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.002
                                       ----------HHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHH--------HHHHHHH CS
                    Multi_Drug_Res  24 egftkltpsllvivgygisfllLskalkslpvsvAYavwsGiGtvlivlvgillfgeslslkkliglali 93 
                                       +g + l + +l  v+ ++ ++l +k l+ ++++ A  v++    +  +++g+++++e+l + +++g+ li
  gi|474934317|ref|YP_007687899.1| 213 SGKHLLEMLALGTVCTAAPYFLYTKGLEGMEAGKA-SVLAFAEPMTATVAGFVVYDETLGIVEILGILLI 281
                                       45555566666666788889999999999999999.788888889999*******************998 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9  11.1    0.0029        13      19     174 ..      14     172 ..       4     179 .. 0.59
   2 ?    5.8   9.0   0.00078       3.5      28     170 ..     142     286 ..     128     293 .. 0.60

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0029
                           DUF2070  19 lliillalligllaflssk...lfgillfglpalvaflltlpvlrilggr.ltykrslflalltelivviisllail 91 
                                       ++++l +++  +  +l  +   l  + + ++ alv++ ++  +l ++ +r + ++ + + ++l + i++i+++  + 
  gi|474934317|ref|YP_007687899.1|  14 TAAVLWGVICLFTRSL--NdegLSPVQCTFVRALVTAPIVGAILAVADRRlFRIEPKDIWMFLGTGILSIVMFNICY 88 
                                       3333333333333222..24577888888888888888888888888888888888877777777777776666666 PP

                           DUF2070  92 lsall.qalvllalvlslalvfalrllvlvavsdesllkavlpaliqpllailllvlyfspesfllllllslifala 167
                                       +sa    ++++ a++l  a vf++ + v+++  + +  k++++al+    ++ + ++  s+   ++ ll+ l  +++
  gi|474934317|ref|YP_007687899.1|  89 FSAAEeVTMSMAAVLLYTAPVFVMLMSVILFGERLTNVKMIALALAFAGCVLTAGLIGGSQGVNVRGLLFGLGAGIG 165
                                       66555555555555555555555555555555555555666655555555555555555555566666666666655 PP

                           DUF2070 168 vylfivv 174
                                        +++ ++
  gi|474934317|ref|YP_007687899.1| 166 YAFYSIF 172
                                       5555555 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.00078
                           DUF2070  28 igllaflssk.......lfgillfglpalvaflltlpvlrilggr...ltykrslflalltelivvi.isllaills 93 
                                       +g                 + llfgl a +  ++++ + +++ ++   +t+       +l++ ++++ +  l  ++ 
  gi|474934317|ref|YP_007687899.1| 142 AG-------LiggsqgvNVRGLLFGLGAGIGYAFYSIFAKFALRKyhpFTITFY---TFLIAALALLpFAGLWEIAD 208
                                       22.......112223345678899999999999999999999888544333333...33332222220112222222 PP

                           DUF2070  94 all...qalvllalvlslalvfalrllvlvavsdesllkavlpaliqpllailllvlyfspesfllllllslifala 167
                                       +      +++l +l+l+ + ++a  +l +  + + + +ka+++a++ p++a ++ +++ +++  + + +l ++++l+
  gi|474934317|ref|YP_007687899.1| 209 V-AsgsGKHLLEMLALGTVCTAAPYFLYTKGLEGMEAGKASVLAFAEPMTATVAGFVVYDETLGI-VEILGILLILV 283
                                       2.135599***************9*******************************9993222222.22222222222 PP

                           DUF2070 168 vyl 170
                                       +++
  gi|474934317|ref|YP_007687899.1| 284 SIF 286
                                       222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       878  (0.0489709); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1822.61
//
Query:       gi|474934318|ref|YP_007687900.1|  [L=318]
Description: Asparagine synthase (glutamine-hydrolyzing) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.5e-27   95.4   0.0      4e-23   82.6   0.1    2.1  2  Asn_synthase   Asparagine synthase
    0.00033   19.8   0.0    0.00053   19.2   0.0    1.3  1  NAD_synthase   NAD synthase
  ------ inclusion threshold ------
      0.067   12.7   0.0       0.11   12.0   0.0    1.3  1  QueC           Queuosine biosynthesis protein QueC
      0.077   11.8   0.5       0.15   10.8   0.1    1.6  2  tRNA_Me_trans  tRNA methyl transferase


Domain annotation for each model (and alignments):
>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.6   0.1     9e-27     4e-23       2     135 ..       7     135 ..       6     162 .. 0.91
   2 !   11.0   0.0   5.3e-05      0.24     238     297 ..     177     238 ..     140     275 .. 0.84

  Alignments for each domain:
  == domain 1  score: 82.6 bits;  conditional E-value: 9e-27
                      Asn_synthase   2 lrelLedaVkrrlradvpvGalLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtelv 78 
                                       l +++e++V++  ++  +v++ +SGG+DS+l+aala+++++ +++++++g+  ++s ++++ +e+a +l+++ ++ +
  gi|474934318|ref|YP_007687900.1|   7 LGRAIEESVRKASMG-KEVAVAFSGGMDSGLVAALAKKYAR-SVTCYTCGT--DDSFDVQAGRELAGKLELPWVHCR 79 
                                       5678999**977665.69*********************98.9********..************************ PP

                      Asn_synthase  79 lteeelldalpdviyhlee..pfadrsaiplyllsrlakrkgvkvvLsGeGaDElfgGY 135
                                       + e+ ++  ++++i+++    pf+++ ++ l+ ++r+a++    vvLsG+G+DE fgG 
  gi|474934318|ref|YP_007687900.1|  80 IGEDTIEGDIRELIQATKVsdPFTISYELQLFTVCRKAHEP---VVLSGQGSDEYFGGC 135
                                       ***************988888*****************888...*************96 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 5.3e-05
                      Asn_synthase 238 RvPflDhrlvevalrlppelklrg..gieKyiLRealegylPeeileRpKegfsapvgewkl 297
                                        +P+lD  ++  + +++pe+   +  g+ K++ ++++e +  +++++R+K++ ++++g+ +l
  gi|474934318|ref|YP_007687900.1| 177 LYPYLDGSVLGEVGKIDPEELRPRslGERKSVVKQVAEELGFPALAHRTKKASQYGSGTTEL 238
                                       58****************99888789**************999**********999988854 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.2e-07   0.00053       3      74 ..       5      73 ..       3      96 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.2e-07
                                      HHHHHHHHHHHHHCTT.SEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTS CS
                      NAD_synthase  3 eelvdflkeyvkkaga.kgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgi 74
                                      eel   ++e v+ka + k+v +  SGG+DS lvaala+k     + ++ +    + +  dv++ ++la +l++
  gi|474934318|ref|YP_007687900.1|  5 EELGRAIEESVRKASMgKEVAVAFSGGMDSGLVAALAKKYA---RSVTCYT-CGTDDSFDVQAGRELAGKLEL 73
                                      66778899*****99989999*****************976...3333333.244555566666666666555 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.4e-05      0.11       4      30 ..      26      52 ..      23      78 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.4e-05
                                      EE--SSHHHHHHHHHHHHH-SEEEEEE CS
                              QueC  4 vllSGGlDSttvlalakkegkevealt 30
                                      v +SGG+DS  v+alakk    v++ t
  gi|474934318|ref|YP_007687900.1| 26 VAFSGGMDSGLVAALAKKYARSVTCYT 52
                                      78****************999998755 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   3.4e-05      0.15       2      30 ..      23      51 ..      22      70 .. 0.83
   2 ?   -2.1   0.0      0.29   1.3e+03     172     193 ..     205     229 ..     202     230 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.4e-05
                     tRNA_Me_trans  2 kvvvalSgGVDSsvaaallkeqgyevigv 30
                                      +v+va+SgG DS ++aal k+  ++v+  
  gi|474934318|ref|YP_007687900.1| 23 EVAVAFSGGMDSGLVAALAKKYARSVTCY 51
                                      79***************999988888765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.29
                     tRNA_Me_trans 172 tKeevrkiAkeagla...vaekkdS 193
                                        K+ v+++A+e g++     +kk S
  gi|474934318|ref|YP_007687900.1| 205 RKSVVKQVAEELGFPalaHRTKKAS 229
                                       5899999999999885334556665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1863.93
//
Query:       gi|474934320|ref|YP_007687902.1|  [L=110]
Description: hypothetical protein TALC_00746 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0018   18.4   0.0     0.0024   18.0   0.0    1.2  1  DUF4143   Domain of unknown function (DUF4143)


Domain annotation for each model (and alignments):
>> DUF4143  Domain of unknown function (DUF4143)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.3e-07    0.0024      73     120 ..       1      54 [.       1      56 [. 0.78

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.3e-07
                                       xxxxxxxxxxxx.xxxxxxxxxxxxxx......x.xxxxxxxxxxxxxxxxxxxxx RF
                           DUF4143  73 lEnlVaqeLlky.sekegaklyyyrdk......n.gaEvDfvielkggkivpiEvK 120
                                       +En++++eL+ + ++++ +++y  + +      + g EvDfv ++ g++ ++i+  
  gi|474934320|ref|YP_007687902.1|   1 MENVIYNELRCRgYDVDVGTIYRTK-SedgkrkRiGSEVDFVANR-GNTRIYIQSA 54 
                                       7**********98777555555444.369**9978********96.8888899865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 700.75
//
Query:       gi|474934321|ref|YP_007687903.1|  [L=104]
Description: hypothetical protein TALC_00747 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.3e-05   24.0   0.0    4.4e-05   23.6   0.0    1.2  1  DUF4143    Domain of unknown function (DUF4143)
  ------ inclusion threshold ------
       0.05   13.2   0.0      0.061   12.9   0.0    1.1  1  AA_kinase  Amino acid kinase family


Domain annotation for each model (and alignments):
>> DUF4143  Domain of unknown function (DUF4143)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   4.9e-09   4.4e-05      76     121 ..       1      46 [.       1      47 [. 0.94

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 4.9e-09
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DUF4143  76 lVaqeLlkysekegaklyyyrdkngaEvDfvielkggkivpiEvKs 121
                                       +V+++L+ y+++ ++++y yrd+ g+E+D+v++l++g++ ++ +K+
  gi|474934321|ref|YP_007687903.1|   1 MVIRDLRVYAQSLDGDVYRYRDNLGNECDAVVHLRNGRYGLVAIKL 46 
                                       79*******9999*********77*****************99997 PP

>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.8e-06     0.061       3      47 ..      42      87 ..      40      90 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.8e-06
                                      EEEEE-TT.CCCCTCCHHHHHHHHHHHHHHHHT....TEEEEEE--HHHH CS
                         AA_kinase  3 vVvKlGGs.sltdkeeaslrrlaeqiaalkesg....nklvvVhGggsft 47
                                      v +KlGG  +++d+    +++l++ +++l +++     +++vV+G g+++
  gi|474934321|ref|YP_007687903.1| 42 VAIKLGGEnLISDG----VKSLCRVLKRLDTQKmgepSFMAVVTGVGGYA 87
                                      779*****999966....78*********8777999*********99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 709.72
//
Query:       gi|474934322|ref|YP_007687904.1|  [L=649]
Description: hypothetical protein TALC_00748 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.9e-74  249.8   0.0    6.1e-74  249.4   0.0    1.1  1  DUF2075     Uncharacterized conserved protein (DUF2075)
    6.8e-07   29.6   0.0    1.6e-05   25.2   0.1    2.9  2  AAA_22      AAA domain
    0.00063   19.8   0.0        0.7    9.9   0.0    2.4  2  ResIII      Type III restriction enzyme, res subunit
    0.00091   19.7   0.0     0.0023   18.4   0.0    1.7  1  AAA         ATPase family associated with various cellular ac
     0.0063   16.8   0.0      0.015   15.6   0.0    1.6  1  AAA_19      AAA domain
  ------ inclusion threshold ------
      0.042   13.2   0.0      0.091   12.1   0.0    1.6  1  ATPase      KaiC
      0.042   13.6   0.0      0.089   12.5   0.0    1.5  1  AAA_30      AAA domain
       0.05   14.0   0.1       0.12   12.8   0.1    1.6  1  AAA_16      AAA ATPase domain
      0.073   12.3   0.0        0.2   10.9   0.0    1.7  2  Zeta_toxin  Zeta toxin
      0.077   12.8   0.3       0.18   11.7   0.3    1.6  1  DUF2527     Protein of unknown function (DUF2627)
      0.091   12.3   0.0       0.19   11.3   0.0    1.5  1  AAA_25      AAA domain
       0.14   11.9   0.0       0.34   10.6   0.0    1.6  2  IstB_IS21   IstB-like ATP binding protein
       0.18   12.2   0.7         39    4.7   0.2    3.3  3  AAA_17      AAA domain
       0.31   11.6   1.6         33    5.0   0.6    3.5  2  AAA_18      AAA domain


Domain annotation for each model (and alignments):
>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  249.4   0.0   4.8e-77   6.1e-74       1     363 []     288     633 ..     288     633 .. 0.85

  Alignments for each domain:
  == domain 1  score: 249.4 bits;  conditional E-value: 4.8e-77
                           DUF2075   1 kavvlVtGvaGtGKtvvllnllael........eddeeertavylsvNhplvlvlrealakkeekkkkkeafeklss 69 
                                       k+v++V+G++GtGK+v++l+llael        + +     + y+++  + ++++ ++l+  +++   +  f++ ss
  gi|474934322|ref|YP_007687904.1| 288 KRVYIVRGGPGTGKSVLALKLLAELiggyedkfTGNHIMIPTLYVTKTSAPREIYSKELKTLSKEVGVEYLFKGASS 364
                                       689**********************5555332222222233455555555555555555555555555555555555 PP

                           DUF2075  70 finnlsefkkaeekkeepkedvvivDEAhrlltksdqaekqseenqlkelmkrakvvvalvDegQelntgeigteee 146
                                       f+ + +           ++   ++vDEAhrl+t+s+q+ k  ++nq+ e++++a  +v+++De+Q +++++igt++e
  gi|474934322|ref|YP_007687904.1| 365 FVDAER-----------NEYPAILVDEAHRLTTRSSQYVKG-GKNQVMEIINAALASVFFIDEDQNVSMQDIGTIDE 429
                                       555555...........****************99998885.9********************************** PP

                           DUF2075 147 lkklakkleveleekv.hLksqfRvaaseaviewvdalldgkkekakplssqenfdirvfddleelkkalkeknkes 222
                                       ++++a++ ++e++ +   L++qfR+++s  +i+w+d++l  +k ++ +l  +  +di v+d+++el + +++k  e+
  gi|474934322|ref|YP_007687904.1| 430 IEHWANEFGAEIVTNGlVLQTQFRCSGSGLYIAWLDDMLGIRKSENLNLLGKLPYDISVADSPKELMERIEKKRAEG 506
                                       **********99765349*******************************99************************** PP

                           DUF2075 223 grsrlvatydakrlaekkkkkskekdvkieegdfklpWnleekelkkpwaessdtleevgseytiQGleldyvgvii 299
                                         sr++a+y+++++ +++k+ ++ +   ie+     +Wn +       wa++++  +e+g+++t QG+e+ y+gvii
  gi|474934322|ref|YP_007687904.1| 507 YDSRILAGYCWDWRSHNTKDGKDFDLDGIEA----QRWNTDYT-----WANNNNLRDEIGCVHTGQGMEFQYAGVII 574
                                       **************99999999999999988....89**9999.....***************************** PP

                           DUF2075 300 Gpdlvyrkeedrikfrgkksedk.eakskrkkkkeseekaqkllkNayrVLLtRGrkGlyiyaed 363
                                       G d+vyr  +++i++ +++  dk + ++ r    ++  +a+++++N yr+L+tRG++G+++y++d
  gi|474934322|ref|YP_007687904.1| 575 GGDMVYR--NGHIETCPEENHDKgALGGWR----KDPARADRIIRNIYRTLMTRGMDGCIVYCVD 633
                                       *******..666666666666651555566....78999************************98 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       2.3     3e+03      51      85 ..      36      81 ..      17      91 .. 0.75
   2 !   25.2   0.1   1.3e-08   1.6e-05       3     111 ..     286     401 ..     283     446 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.3
                            AAA_22 51 t...sskdllrellralglelka........erlsseellealeqa 85
                                          ss+ +l ++ +a+++++ +        ++++s ++++ + + 
  gi|474934322|ref|YP_007687904.1| 36 FddvSSRRILDKIESAMDVRHIGydkiseerAWKDSTRCMKEVLET 81
                                      2556899999999999999999888888777777777777766655 PP

  == domain 2  score: 25.2 bits;  conditional E-value: 1.3e-08
                            AAA_22   3 ktagilvvtGesGtGKTtllrrlleqldeeakaeeerpevv..fvtlpsstsskdllrellralglelkaerlssee 77 
                                       +t+++ +v G +GtGK++l+ +ll +l   ++ +  + +++  + ++++ + +++++++ l+ l       +   e 
  gi|474934322|ref|YP_007687904.1| 286 RTKRVYIVRGGPGTGKSVLALKLLAELIGGYEDKFTGNHIMipTLYVTKTSAPREIYSKELKTLSK-----EVGVEY 357
                                       48999*********************955544444444444579999999999*****99999994.....456799 PP

                            AAA_22  78 llealeqalrarav.ielliiDEaqhlr..s.......eealee 111
                                       l++     ++a +   +++++DEa++l+  s       ++++ e
  gi|474934322|ref|YP_007687904.1| 358 LFKGASSFVDAERNeYPAILVDEAHRLTtrSsqyvkggKNQVME 401
                                       99999999999999999*********977624566566333333 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0    0.0045       5.8       6      55 ..     266     318 ..     261     332 .. 0.75
   2 !    9.9   0.0   0.00055       0.7     128     149 ..     368     395 ..     341     413 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0045
                                       HHHHHHHHHHT.........TTS.EEEEEESTTSTHHHHHHHHHHHH-S..... CS
                            ResIII   6 eyQeeaienlleklks...krdk.rglikmaTGtGKTlvaaklierllkkgkee 55 
                                       + Q  +  +ll+ + +   +r k  +++    GtGK+++a+kl ++l    +e+
  gi|474934322|ref|YP_007687904.1| 266 DNQVAVYHKLLNGIRNchrTRTKrVYIVRGGPGTGKSVLALKLLAELIGG-YED 318
                                       66777778888777777774555155588999*************99874.444 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00055
                                       HHTTT-SEEEEETGGGTTS.T......T CS
                            ResIII 128 llrdrfdviiiDEaHrlgakk......s 149
                                       ++r++++ i++DEaHrl+  +       
  gi|474934322|ref|YP_007687904.1| 368 AERNEYPAILVDEAHRLTTRSsqyvkgG 395
                                       5678889**********99733333332 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.8e-06    0.0023       2      90 ..     292     404 ..     291     423 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.8e-06
                                       EEESSTTSSHHHHHHHHHHHH................THEEEEEETTTCS.SS..STTHHHHHHHHHHHHHHHTS.. CS
                               AAA   2 llyGppGtGKTllakavakel................gvefleisgsell.sk..yvgesekkirelfkeakeka.. 57 
                                       ++ G pGtGK+ la  +  el                  ++ ++s+++ + sk      +e  ++ lfk a++    
  gi|474934322|ref|YP_007687904.1| 292 IVRGGPGTGKSVLALKLLAELiggyedkftgnhimipTLYVTKTSAPREIySKelKTLSKEVGVEYLFKGASSFVda 368
                                       56799***************877666554443333332447777777776566553344555566677766333344 PP

                                       ...TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHH CS
                               AAA  58 ...kpsilfiDEidalaksrsgseseeeervvnqLl 90 
                                          +   +++DE+++l++++s+  ++ +++v++ + 
  gi|474934322|ref|YP_007687904.1| 369 ernEYPAILVDEAHRLTTRSSQYVKGGKNQVMEIIN 404
                                       4534699*********99885555555555554443 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.2e-05     0.015       7     126 ..     285     396 ..     280     434 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.2e-05
                            AAA_19   7 alkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgaeatTiHrlalldfddl 83 
                                       + +++v +v +GpGtGK+ +  + +a+l+   + k     ++ +t   +k  + r   + +e +T+ +   ++++ l
  gi|474934322|ref|YP_007687904.1| 285 TRTKRVYIVRGGPGTGKSVLALKLLAELIGGYEDKFTGNHIMIPTLYVTKTSAPRE-IYSKELKTLSKE--VGVEYL 358
                                       567899**********************9999888855555555555555444444.456667777766..666666 PP

                            AAA_19  84 ltealelleeaeeekklqeee.llivDEfqdvdelqyrLlkall 126
                                        + a ++++   e    ++e+ +++vDE+  ++    + +k  +
  gi|474934322|ref|YP_007687904.1| 359 FKGASSFVDA--E----RNEYpAILVDEAHRLTTRSSQYVKGGK 396
                                       6666666332..1....344446666666666555444444333 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   7.1e-05     0.091      18      48 ..     287     317 ..     274     423 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.1e-05
                            ATPase  18 egrvvlitGepGtGKtifalqFlikgaekyg 48 
                                        +rv+ + G+pGtGK+++al+ l + +  y+
  gi|474934322|ref|YP_007687904.1| 287 TKRVYIVRGGPGTGKSVLALKLLAELIGGYE 317
                                       6899****************99887665554 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     7e-05     0.089      15     104 ..     285     388 ..     280     451 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7e-05
                            AAA_30  15 tsgdrvavltGpAGtGKtt.alkalreaweaag.............grviglAptgkaAkvLa...eelgi..east 72 
                                       t ++rv ++ G++GtGK+  alk l+e++   +             +     Ap +  +k+L+   +e+g+      
  gi|474934322|ref|YP_007687904.1| 285 TRTKRVYIVRGGPGTGKSVlALKLLAELIGGYEdkftgnhimiptlYVTKTSAPREIYSKELKtlsKEVGVeyL--- 358
                                       45667*************73577778888766456777777766666666666666666666633323222111... PP

                            AAA_30  73 iakllkrlk......grarlepgtllivDEagmvdtkq 104
                                               k      + a+ ++   ++vDEa  + t++
  gi|474934322|ref|YP_007687904.1| 359 ----F---KgassfvD-AERNEYPAILVDEAHRLTTRS 388
                                       ....1...01122211.222223444455554444433 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   9.3e-05      0.12      12      62 ..     275     322 ..     268     394 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.3e-05
                            AAA_16  12 Llsalervrsgrp.elvllsGesGvGKsslvrellralekdggiflrgkcdq 62 
                                       Ll+ +++ ++ r+ ++ +++G +G+GKs l+ +ll +l +      + k++ 
  gi|474934322|ref|YP_007687904.1| 275 LLNGIRNCHRTRTkRVYIVRGGPGTGKSVLALKLLAELIGG----YEDKFTG 322
                                       5555666667777799***************9999877665....4555554 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00015       0.2       7      40 ..     278     312 ..     273     321 .. 0.86
   2 ?   -4.2   0.0       6.5   8.4e+03     106     128 ..     491     513 ..     489     516 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00015
                        Zeta_toxin   7 dkk.ypsqerPklillgGqpGAGKselaellkdel 40 
                                        ++ +++ +++ ++++ G+pG GKs la +l +el
  gi|474934322|ref|YP_007687904.1| 278 GIRnCHRTRTKRVYIVRGGPGTGKSVLALKLLAEL 312
                                       55669999********************9999987 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 6.5
                        Zeta_toxin 106 spdvvkklaealkkaGYevevvv 128
                                       sp ++ + +e+ +++GY+ ++++
  gi|474934322|ref|YP_007687904.1| 491 SPKELMERIEKKRAEGYDSRILA 513
                                       55666667777788899988875 PP

>> DUF2527  Protein of unknown function (DUF2627)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   0.00014      0.18       4      20 ..     341     359 ..     340     368 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00014
                           DUF2527   4 IFSKEV..LSKdVdVEYRF 20 
                                       I+SKE   LSK+V VEY F
  gi|474934322|ref|YP_007687904.1| 341 IYSKELktLSKEVGVEYLF 359
                                       99**9666*********99 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00015      0.19      33      78 ..     288     333 ..     281     443 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
                            AAA_25  33 gelallaGapgtGKttlaldlalava..tGkpwlgpvapeqgkVlyvs 78 
                                       + + ++ G pgtGK++lal l +++     ++++g+  +  +++lyv 
  gi|474934322|ref|YP_007687904.1| 288 KRVYIVRGGPGTGKSVLALKLLAELIggYEDKFTGN--HIMIPTLYVT 333
                                       5678999*****************995533557773..2567777775 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00027      0.34      26      72 ..     267     313 ..     243     347 .. 0.78
   2 ?   -3.4   0.0       5.3   6.8e+03      36      52 ..     405     421 ..     396     445 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00027
                         IstB_IS21  26 aarsldkrkvkeLatlsfiekkenivllGpsGvGKshlaialgveav 72 
                                       ++  + ++ ++ +++++ +++k   ++ G++G+GKs la  l  e +
  gi|474934322|ref|YP_007687904.1| 267 NQVAVYHKLLNGIRNCHRTRTKRVYIVRGGPGTGKSVLALKLLAELI 313
                                       3445667788889999999********************98876655 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 5.3
                         IstB_IS21  36 keLatlsfiekkenivl 52 
                                       ++La+  fi++ +n+ +
  gi|474934322|ref|YP_007687904.1| 405 AALASVFFIDEDQNVSM 421
                                       47888899999999865 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.089   1.1e+02      23      69 ..     214     260 ..     200     274 .. 0.80
   2 ?    4.7   0.2      0.03        39       2      27 ..     295     322 ..     294     423 .. 0.54
   3 ?    0.1   0.0      0.79     1e+03     108     128 ..     488     508 ..     471     526 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.089
                                       EEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHH CS
                            AAA_17  23 hlsaGdllreeakrgglakardemrklpleekkelqkeaaekiaeea 69 
                                       + s++d +  ++ +    ++ +++++++l +   lqk +++ + e++
  gi|474934322|ref|YP_007687904.1| 214 IKSFSDFIKRNIVKPDNLETLEKIENGKLTVSSSLQKSLKRVLHEKD 260
                                       5589999998888887669*******************998777764 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.03
                                       E-TTSSHHHHHHHHHHHH..TEEEEEHH CS
                            AAA_17   2 GgPGsGKgtqceklveky..gfthlsaG 27 
                                       GgPG GK+ ++ kl  ++  g++   +G
  gi|474934322|ref|YP_007687904.1| 295 GGPGTGKSVLALKLLAELigGYEDKFTG 322
                                       9*********999988876655544444 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.79
                                       EE--HHHHHHHHHHHTTST-T CS
                            AAA_17 108 leadpeeilerrlkdrtrgrd 128
                                       + ++p+e++er  k+r +g d
  gi|474934322|ref|YP_007687904.1| 488 VADSPKELMERIEKKRAEGYD 508
                                       567788888888887766654 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.46   5.9e+02      10      44 ..     240     268 ..     239     290 .. 0.63
   2 ?    5.0   0.6     0.026        33       3      25 ..     293     322 ..     292     518 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.46
                            AAA_18  10 GKttlakeLskrlgfgvnlrdvakenglllevdpe 44 
                                       GK t++  L+k+l      + v+ e++   + d++
  gi|474934322|ref|YP_007687904.1| 240 GKLTVSSSLQKSL------KRVLHEKDFFAPMDNQ 268
                                       9**********97......5555555444444444 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.026
                            AAA_18   3 ltGtpGvGKttlakeL.skrl.gf.....g 25 
                                       + G pG+GK+ la  L +++  g+     g
  gi|474934322|ref|YP_007687904.1| 293 VRGGPGTGKSVLALKLlAELIgGYedkftG 322
                                       668889999998876634443333443331 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (649 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.47
# Mc/sec: 4181.59
//
Query:       gi|474934323|ref|YP_007687905.1|  [L=497]
Description: Transglutaminase-like superfamily [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-08   34.5   0.0    3.9e-08   33.7   0.0    1.4  1  Transglut_core  Transglutaminase-like superfamily


Domain annotation for each model (and alignments):
>> Transglut_core  Transglutaminase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.0   2.2e-12   3.9e-08       5     111 ..     135     230 ..     131     231 .. 0.89

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 2.2e-12
                    Transglut_core   5 eeltagakdplekakaiyewvrknveysaprrtpgsrdaeavletgkGncedfaslfvallRalGipaRvvtgylsg 81 
                                       ++l ++ + ++ek+ +i++ + + ++y+  +    s+++  +l +g+ +ce++a ++  l+  +Gi + vv+g+  +
  gi|474934323|ref|YP_007687905.1| 135 KKL-ESCTYDYEKVLTIHDSLVSGIKYT--KDRANSHNIYGALVEGQCVCEGYARAMQYLCQINGIDCPVVSGTGIN 208
                                       555.778899******************..666666679***********************************997 PP

                    Transglut_core  82 eeekeqsvasedaHawvevylegygWvplD 111
                                               ++++ H+w+ + +  + W+ lD
  gi|474934323|ref|YP_007687905.1| 209 -------SSGSEGHMWNIIRI-SGSWYCLD 230
                                       .......689999********.99999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (497 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       910  (0.0507558); expected 358.6 (0.02)
Passed bias filter:                      750  (0.0418317); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.71u 0.33s 00:00:01.04 Elapsed: 00:00:00.52
# Mc/sec: 2887.65
//
Query:       gi|474934324|ref|YP_007687906.1|  [L=456]
Description: Permease [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-32  110.8  39.4      8e-32  110.4  39.4    1.2  1  Xan_ur_permease  Permease family
  ------ inclusion threshold ------
        6.1    6.3   8.0        6.1    6.3   0.6    2.6  2  DUF3959          Protein of unknown function (DUF3959)


Domain annotation for each model (and alignments):
>> Xan_ur_permease  Permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.4  39.4   8.9e-36     8e-32       4     384 ..      25     411 ..      22     443 .. 0.93

  Alignments for each domain:
  == domain 1  score: 110.4 bits;  conditional E-value: 8.9e-36
                                       HHHHHHHHHHHHHHHHHHHHTTTS-.........H.HHHHHHHHHHHHHHHHHTTT-----EEE-GGGHHHHHGGG- CS
                   Xan_ur_permease   4 lllglQhllamfaalvvvPllvgdalglaeelrqlisatllasGiatllqllifgirlpillgssfafvtalmialG 80 
                                       +  gl ++l m + l v+Pl+++ a+++  ++++l++at la+ ia+ll+ l++  +++++ g++++++ +++i++ 
  gi|474934324|ref|YP_007687906.1|  25 IKGGLITFLSMSYILAVNPLILSPAAEG-YTFDELFTATALAACIACLLMGLYARFPVALAPGMGLNAFLSYTICQS 100
                                       668999*******************666.8999*************************************9999999 PP

                                       ....HHHHHHHHHHHHHHHHHHHHHHHTT-SH.HHHHH--HHHHHHHHHHHHHHHHHHHHHHTTSS-..BTT.B--- CS
                   Xan_ur_permease  81 saedieialagllgallvagvlfilisltglrgrlarlipPvvtgpvvlliGlslaqiavkkvgggwaavegltvvs 157
                                       +    + +++  l+ ++++g +f+l+ + g+r   ++ ip     ++  +iG+++a i + + g++    ++  +v 
  gi|474934324|ref|YP_007687906.1| 101 M----GFTYEQGLMVVFISGTMFFLVTVSGIRRGMVESIPKSLKIAIAAGIGFFIAIIDLYNTGIIVHGTSS-ALVP 172
                                       5....99***************************************************99999999766555.7*** PP

                                       HHHHHHHHHHHHHHHHHHHSSSTTTTTHHHHHHHHHHHHHHHHHHHTTSSHH...............HHS-SS---- CS
                   Xan_ur_permease 158 lkllllavvvllvilllsvflkglfsqlpiLigiiagwllalfmgivnlspe...............vseapwfqlp 219
                                       ++    +v + l+ ++++v+l    + ++i +giia+w++ + +    l++e               ++   ++++ 
  gi|474934324|ref|YP_007687906.1| 173 GDMSDPGVLLALFCIIVTVCLWYRRKWYAIILGIIATWAIGALLFRYGLESEigtlpdaglvtgisaPDFGLFAKVF 249
                                       ****************************************************9**********98884445556666 PP

                                       -------HH..H.HHHHTHHH.HHHHHHHHHHHHHHHHHHTS-TII..IIIHHHHHHHHHHHHHHHHHHT---EEE- CS
                   Xan_ur_permease 220 splkfgtplfnlgliltvlavalvavvesvGdiravakvvgrslkp..kpdlrralladGlatllsgllGalpvtty 294
                                       ++++++++++  + i +++++++v +++++G+++ v++++g s  +     +  a++ad  a+l ++++G++ +t+y
  gi|474934324|ref|YP_007687906.1| 250 TGFEMFPSSMWVAFIGALVSMFIVDMFDTTGTLISVSSMSGMSEGRdeFDTIDVAMRADAAASLSGAMVGTSTTTSY 326
                                       6778888888899999************************97666566788999*********************** PP

                                       HHHHHHHHHHTB--HHHHHHHHHHHHHHT--HHHHHHHTTS-HHHHHHHHHHHHHHHHHHHHHHHHHTTS-SHHHHH CS
                   Xan_ur_permease 295 aeniGvvaltkvasrrvmvtagvilillglipklaallssIPepvlgGvllvvfgmiaasgvsnlqtvdldsarnll 371
                                       +e+  +++ +     r++++a v  +l+++ + ++ l++s+ ++  ++ +l+++g+i++ +++ ++++d    ++ +
  gi|474934324|ref|YP_007687906.1| 327 IESFTGIESG----ARTGILALVCGLLFAFAMVFSGLFASVTAAC-TAGALILVGLIMVRNIRDIEWKDPVLCFSSI 398
                                       **********....***************************9888.77778899*****************999999 PP

                                       HHHHHHHHHHH-- CS
                   Xan_ur_permease 372 ivavslvlGlgva 384
                                       i+ ++++l+ +++
  gi|474934324|ref|YP_007687906.1| 399 ITVFMMGLAGSIT 411
                                       9999999987665 PP

>> DUF3959  Protein of unknown function (DUF3959)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.6   0.00068       6.1      65     141 ..      52     128 ..      12     138 .. 0.76
   2 ?    3.1   1.5    0.0063        56      80     107 ..     186     216 ..     143     221 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.00068
                           DUF3959  65 yvtassllanakiaaciaviplilrfrtyaitlgllalwgallwdikevqslavlgrlmnlltteklyllllvagfl 141
                                         t   l++ + +aacia + + l  r        + l   l + i +   ++  + lm ++ +  +++l+ v+g+ 
  gi|474934324|ref|YP_007687906.1|  52 GYTFDELFTATALAACIACLLMGLYARFPVALAPGMGLNAFLSYTICQSMGFTYEQGLMVVFISGTMFFLVTVSGIR 128
                                       457788999999******9877666554333333467888999******************************9975 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.0063
                           DUF3959  80 ciav.iplilrfrtyaitlgllalw..gall 107
                                       ci v + l +r + yai lg++a w  gall
  gi|474934324|ref|YP_007687906.1| 186 CIIVtVCLWYRRKWYAIILGIIATWaiGALL 216
                                       44431566778889***********555666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       865  (0.0482459); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.51
# Mc/sec: 2693.91
//
Query:       gi|474934325|ref|YP_007687907.1|  [L=331]
Description: hypothetical protein TALC_00751 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-18   65.5   0.0    1.2e-17   64.6   0.0    1.5  1  Fic       Fic/DOC family
  ------ inclusion threshold ------
       0.05   13.7   0.0       0.24   11.5   0.0    2.0  2  Fic_N     Fic/DOC family N-terminal
      0.069   13.0   0.0       0.15   12.0   0.0    1.6  1  HHH       Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> Fic  Fic/DOC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.6   0.0     2e-21   1.2e-17       2      97 .]      91     196 ..      90     196 .. 0.94

  Alignments for each domain:
  == domain 1  score: 64.6 bits;  conditional E-value: 2e-21
                                       -SHHHHHHHHCHS-S------TS--SS-S........T..EEEE---SCCCHHHHHHHHHHHHC..HHT-S-HHHHH CS
                               Fic   2 ltledllelhrlllqdigeeagefrdeev........segklesalappeevpaeleelleyln..elekeepleka 68 
                                       ++++++l+lhr+ll +++ ++g+++++++        +++++++ + p++++p+++e+++  +   e+e +epl ++
  gi|474934325|ref|YP_007687907.1|  91 FDETTILDLHRILLSHTDRKGGSYKTSDNiimeidgsGNRRIHFKPLPARDTPHAMEQMVLAYIdaEQEGIEPLLLI 167
                                       6899***************99****9999********99*****************888766666************ PP

                                       HHHHHHHHHH--SSS-HHHHHHHHHHHHH CS
                               Fic  69 aalhyefekiHPFaDGNgRtarlllnllL 97 
                                        +++  f + HPF DGNgR++rll+ llL
  gi|474934325|ref|YP_007687907.1| 168 PCFILDFLSVHPFDDGNGRMSRLLTLLLL 196
                                       *************************9987 PP

>> Fic_N  Fic/DOC family N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0     4e-05      0.24      38      78 ..      40      80 ..      38      81 .. 0.92
   2 ?   -1.3   0.0      0.39   2.3e+03      68      82 .]     148     162 ..     137     162 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4e-05
                             Fic_N 38 lSSeIEgtqttlddlleaeadeeeekskdvkEVlnYvkAle 78
                                       S +IEg+ t+ + l +   ++ e   +d +E+  Y++Al+
  gi|474934325|ref|YP_007687907.1| 40 GSNAIEGIFTSDQRLTSLMDRSVEPVGHDEQEIAGYRDALT 80
                                      5899*****************9999778***********96 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.39
                             Fic_N  68 kEVlnYvkAleyGle 82 
                                       + Vl Y++A ++G+e
  gi|474934325|ref|YP_007687907.1| 148 QMVLAYIDAEQEGIE 162
                                       56999****999986 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.6e-05      0.15       2      28 ..     279     306 ..     279     307 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.6e-05
                                       HHHHHTSSHHHHHT.STT-SHHHHHHHH CS
                               HHH   2 leglipasreeLla.lPGVGpktAeaIl 28 
                                       l+++ip s +e+l+ lP V + t ea l
  gi|474934325|ref|YP_007687907.1| 279 LDSIIPISKAEILSaLPDVSRTTVEACL 306
                                       6899*********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1971.26
//
Query:       gi|474934326|ref|YP_007687908.1|  [L=433]
Description: histidinol dehydrogenase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   1.3e-160  534.9   0.1   1.5e-160  534.7   0.1    1.0  1  Histidinol_dh   Histidinol dehydrogenase
  ------ inclusion threshold ------
       0.06   13.8   0.0       0.12   12.8   0.0    1.4  1  DUF3486         Protein of unknown function (DUF3486)
        0.1   13.3   0.0       0.27   11.9   0.0    1.7  1  Tn7_Tnp_TnsA_C  TnsA endonuclease C terminal


Domain annotation for each model (and alignments):
>> Histidinol_dh  Histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  534.7   0.1  2.6e-164  1.5e-160       4     408 ..      28     427 ..      25     428 .. 0.98

  Alignments for each domain:
  == domain 1  score: 534.7 bits;  conditional E-value: 2.6e-164
                                       -----HHHHHHHHHHHHHHHHHCHHHHHHHHHHCCSSSSGGCCEE-HHHHHHHHHCS-HHHHHHHHHHHHHHHHHHH CS
                     Histidinol_dh   4 seedseeveetvkeiledvreeGdealleytekFDkvkkleslrvseeeieealekldeelkealeeaaenirkfhe 80 
                                       ++++++ev+e v+ i+e+vr+ Gd+al+e+tekFDk+k l++++vs++ei++a+ek+d+++++ le+aa ni++fh+
  gi|474934326|ref|YP_007687908.1|  28 RQSKTDEVKEIVEGIIEQVRTGGDKALKELTEKFDKTK-LTRISVSRDEIDKAYEKVDPDIVDELENAAYNIQRFHR 103
                                       678899*****************************664.689*********************************** PP

                                       CC----EEEEEECTTEEEEEEEEE-SEEEEE---STT--CHHHHHHHHHHHHHT-SEEEEEE-SSGG.--HHHHHHH CS
                     Histidinol_dh  81 aqkeseeevketepgvvlgqkvrpiervGlYvPgGkaaypStvlmnavpAkvAgvkeivvvtPpqdgkvnpavlaaa 157
                                        q++ +++++e epg++lg k +p+ervG+Y+PgG a+ypSt+lm++v Ak Agv+e++++tP+    vnp +l+a+
  gi|474934326|ref|YP_007687908.1| 104 MQLPPDMWTSEVEPGITLGVKSTPLERVGCYIPGGLASYPSTALMTVVAAKTAGVDEVICCTPA---PVNPITLVAL 177
                                       ****99*********************************************************5...7********* PP

                                       HHCT-SEEEE--HHHHHHHHHH--SSS---SEEE---SHHHHHHHHHHCTTBEES----S-EEEEEE-TTS-HHHHH CS
                     Histidinol_dh 158 klagvdeiykvGGaqAiaalAyGtesipkvdkivGPGniyVaaAKrlvsgevgiDmiaGPsEvlviaDetadpefvA 234
                                       ++ag deiy+vGGaqAiaa+A Gtesi++v+kivGPGn++V++AK l+++ +giD++aGPsE +v+aD++a pefvA
  gi|474934326|ref|YP_007687908.1| 178 DIAGCDEIYTVGGAQAIAAMALGTESIEPVQKIVGPGNRFVTEAKILLQNICGIDFPAGPSEAAVLADSSAVPEFVA 254
                                       ***************************************************************************** PP

                                       HHHHHHHTT-TT-EEEEEES-HHHHHHHHHHHHHHHCC-TTHHHHHHHHCCH-EEEE-SSHHHHHHHHHHH--SEEE CS
                     Histidinol_dh 235 aDLlsqaEHdedaqavlvttseelaeaveeevekqleelprkeiaekslekqsaiilvedleeaielaneyApEHle 311
                                       aDL++q EH+++++ vlvt++e+l ++v + +e+q++e+pr++i+ +s+++ s +i+++d+e aie++ne+ApEHl 
  gi|474934326|ref|YP_007687908.1| 255 ADLVAQGEHGPSSAFVLVTDDETLPDKVWKCMEEQVAEAPRRDIIVQSFQN-SGYIVCKDMELAIETMNEVAPEHLC 330
                                       ***************************************************.9999********************* PP

                                       EESTTHHHHGGG--S-SEEEESTT--HHHHHHTSSS------TTGGGT---S-GGGGEEEEEEEEE-HHHHHHHHHH CS
                     Histidinol_dh 312 lqvedpeellekiknaGaiflGeyspeslgDYaaGtnhvLPTsgtArfssglsvedFlkkisvqelskealkelaea 388
                                       +qv+dp+++l+ki+naG+if+G+y+p ++gDYa+GtnhvLPTsg+A + sgl+v+ F k+++vq l+k++l+ela++
  gi|474934326|ref|YP_007687908.1| 331 IQVRDPMDVLSKIRNAGSIFVGPYTPIAAGDYASGTNHVLPTSGYATMCSGLTVSMFRKTSTVQILTKDGLRELAPT 407
                                       ***************************************************************************** PP

                                       HHHHHHHTT-HHHHHHHHHH CS
                     Histidinol_dh 389 vetlAeaEgLeaHaeavkvR 408
                                       ++tlA+aEgL+aHa++v++R
  gi|474934326|ref|YP_007687908.1| 408 ITTLADAEGLNAHAASVDIR 427
                                       ******************99 PP

>> DUF3486  Protein of unknown function (DUF3486)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     2e-05      0.12      62     146 ..      27     116 ..      22     131 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2e-05
                           DUF3486  62 evaeklresreiaealveelgdeedddvtealiellqtllfellmalee..eeeeeidpkeakeL...akalakler 133
                                       ++  k +e++ei e ++e++    d+ ++e++ ++ +t+l++++++ +e  +  e++dp+ + eL   a ++++  r
  gi|474934326|ref|YP_007687908.1|  27 NRQSKTDEVKEIVEGIIEQVRTGGDKALKELTEKFDKTKLTRISVSRDEidKAYEKVDPDIVDELenaAYNIQRFHR 103
                                       5678999***************************************9999988888999999999777888888888 PP

                           DUF3486 134 asvaskkrraeir 146
                                       ++     + +e++
  gi|474934326|ref|YP_007687908.1| 104 MQLPPDMWTSEVE 116
                                       8877777777766 PP

>> Tn7_Tnp_TnsA_C  TnsA endonuclease C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   4.6e-05      0.27      24      59 ..      30      65 ..      19      72 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.6e-05
                    Tn7_Tnp_TnsA_C 24 lseeeleelaelllerlrenpdttlrellkelDkey 59
                                       +++e +e++e ++e++r+ +d+ l+el++++Dk+ 
  gi|474934326|ref|YP_007687908.1| 30 SKTDEVKEIVEGIIEQVRTGGDKALKELTEKFDKTK 65
                                      345666**************************8865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.34s 00:00:01.01 Elapsed: 00:00:00.56
# Mc/sec: 2347.27
//
Query:       gi|474934327|ref|YP_007687909.1|  [L=696]
Description: Polyphosphate kinase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.7e-67  224.1   0.0      3e-66  222.1   0.0    1.9  2  PP_kinase_C    Polyphosphate kinase C-terminal domain 2
    1.1e-65  220.3   0.1    2.7e-65  219.0   0.0    1.7  2  PP_kinase_C_1  Polyphosphate kinase C-terminal domain 1
    9.2e-62  208.2   0.7    2.2e-61  207.0   0.0    1.9  2  PP_kinase      Polyphosphate kinase middle domain
    5.1e-29  100.7   0.0    1.7e-28   99.1   0.0    1.9  2  PP_kinase_N    Polyphosphate kinase N-terminal domain
      8e-09   35.5   0.0    3.7e-05   23.6   0.2    3.0  2  PLDc_2         PLD-like domain


Domain annotation for each model (and alignments):
>> PP_kinase_C  Polyphosphate kinase C-terminal domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       0.4   1.4e+03      40      60 ..     381     401 ..     363     413 .. 0.81
   2 !  222.1   0.0   8.3e-70     3e-66       1     172 []     505     678 ..     505     678 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.4
                       PP_kinase_C  40 dkeiidkLyeAsqaGVkikli 60 
                                       ++e+i++L++A + G  ++++
  gi|474934327|ref|YP_007687909.1| 381 NSEVIRQLMRAKENGKAVSVL 401
                                       678999999999999777665 PP

  == domain 2  score: 222.1 bits;  conditional E-value: 8.3e-70
                       PP_kinase_C   1 LlvaplnlrekllelidreieaakagkkakiilklNsledkeiidkLyeAsqaGVkiklivrgicclrpgvkglsen 77 
                                       Llvapl+l+++l+eli++e+e+++ag ka+i +k N l d++ii++Ly+As aGVki+l +rg+cclrpg+kg+sen
  gi|474934327|ref|YP_007687909.1| 505 LLVAPLTLKSTLIELIRSEAENKRAGGKAYIAMKANGLIDSDIIAELYRASMAGVKIDLNIRGLCCLRPGMKGISEN 581
                                       89*************************************************************************** PP

                       PP_kinase_C  78 ikvisivdrfLEhaRiyifenggeeevyisSaDlmtRnldrRvevlvpvedeklkkel.keilelqlkDnvkareld 153
                                       i+v+sivdrfLEhaRiy+fengg++++y++S+D+m+Rnl  Rve+l+pv d+++  e+ ++il+ +l+Dnvkar+l+
  gi|474934327|ref|YP_007687909.1| 582 ITVTSIVDRFLEHARIYYFENGGDPKMYMGSSDMMPRNLLARVETLFPVPDKEILMEIrENILKPCLQDNVKARVLQ 658
                                       **********************************************************6679*************** PP

                       PP_kinase_C 154 edgeykkvke.keekkvraQ 172
                                       +dg+y   ++ k+ kk+r+Q
  gi|474934327|ref|YP_007687909.1| 659 SDGTYVLRRPkKGVKKMRSQ 678
                                       ******99998999999998 PP

>> PP_kinase_C_1  Polyphosphate kinase C-terminal domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.0   0.0   7.4e-69   2.7e-65       1     163 [.     333     495 ..     333     499 .. 0.99
   2 ?   -2.4   0.0      0.87   3.1e+03      14      66 ..     507     561 ..     501     565 .. 0.57

  Alignments for each domain:
  == domain 1  score: 219.0 bits;  conditional E-value: 7.4e-69
                                       SHHHHHHHS-EEEECTTB-SCHHHHHHHHHHC-TTEEEEEEEES-S-S--HHHHHHHHHHHTT-EEEEEES--SSS- CS
                     PP_kinase_C_1   1 sifeairkkdillhhPyesfesvvelleeAaedpkvlaikitlYrvakdskivkaLieAaengkqvtvlvElkArfd 77 
                                       s+f++ir++d++ +hPye f+ v+++l+e+a+dp+v++iki+lYr++k+s+++++L++A+engk v+vl+El+A+fd
  gi|474934327|ref|YP_007687909.1| 333 SMFDVIRERDWIAYHPYEPFDIVIRFLRESADDPNVQSIKISLYRLGKNSEVIRQLMRAKENGKAVSVLMELRAKFD 409
                                       58*************************************************************************** PP

                                       -HHHHHHHHHHHHHT-EEEE--TT--B--EEEEEEE---S---EEEEEESS-SS---SS-EEEEEEEE--HHHHHHH CS
                     PP_kinase_C_1  78 eenNiewakkleeagvkvvygvvglkvhaklllvvrreeeklrryvhlgtGnynektaklYtDlslltadeelgedv 154
                                       e nNi++a++le+ gv+vvyg v+lkvh+kll vvr e+++l ry+h+++Gnyn+++ak Y+D+s++ta++e+gedv
  gi|474934327|ref|YP_007687909.1| 410 EVNNISLARQLEKIGVHVVYGPVNLKVHSKLLQVVRLEKDHLVRYTHMSSGNYNANSAKSYADISYFTANQEIGEDV 486
                                       ***************************************************************************** PP

                                       HHHHHHHTT CS
                     PP_kinase_C_1 155 eklfnvltg 163
                                        +lfn+ltg
  gi|474934327|ref|YP_007687909.1| 487 GELFNALTG 495
                                       *******97 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.87
                                       ECTTB-SCHHHHHHHHHHC-TTEEEEEEEES-S-S..--HHHHHHHHHHHTT-EE CS
                     PP_kinase_C_1  14 hhPyesfesvvelleeAaedpkvlaikitlYrvak..dskivkaLieAaengkqv 66 
                                         P    ++++el+++ ae+++         + +   ds+i++ L +A  +g ++
  gi|474934327|ref|YP_007687909.1| 507 VAPLTLKSTLIELIRSEAENKRAGGKAYIAMKANGliDSDIIAELYRASMAGVKI 561
                                       5555555666666666666555433333333332222788888888888887665 PP

>> PP_kinase  Polyphosphate kinase middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.0   0.0   6.2e-65   2.2e-61       1     201 [.     126     325 ..     126     326 .. 0.96
   2 ?   -1.4   0.2      0.42   1.5e+03     128     185 ..     385     442 ..     382     457 .. 0.68

  Alignments for each domain:
  == domain 1  score: 207.0 bits;  conditional E-value: 6.2e-65
                                       HHHHHHHHHHHHTTGGG---EE--TTTS-----TT-EEEEEEEESST-SS-..EEEEEE--.TTS-SEEEE-T.TSS CS
                         PP_kinase   1 eqkefleeyFeeevfpvLtplavdpshpfpflsnkslnlavelrkkekeekekefalvkvP.svlpRfielppeeeg 76 
                                       +qk ++++y++e++ p+Ltpla+d shpfpf+sn+slnlav+lrkk+++  e  +a++kvP   lpRf+++p+ e++
  gi|474934327|ref|YP_007687909.1| 126 KQKMWVDDYYDERIHPLLTPLALDISHPFPFISNNSLNLAVKLRKKDEG--EVLYARIKVPvGILPRFLKVPS-EGK 199
                                       5999*****************************************8544..459*****************55.788 PP

                                       -.EEEEHHHHHHCCHHHH-TTSEEEEEEEEEEE-SSS----.---.-------------------EEEEETT--HHH CS
                         PP_kinase  77 kerfilledvIeanldelFpgyevleaylfrvtRnadleidedeaedlleeiekeLkkRrrgevvRLeveaempeel 153
                                       k +f+lle+vI+ ++ +lFpg +vl++y fr+tRnad++++ dea dl++++e++L +R  g +vR++ve++mp++l
  gi|474934327|ref|YP_007687909.1| 200 KLEFVLLENVIKDHAASLFPGLDVLGVYKFRITRNADVKVTIDEAVDLMSAVESALDSRDLGFPVRMVVEDTMPADL 276
                                       88*************************************************************************** PP

                                       HCCHTTTT---TTT.EEEE-.S--GGGGGCS...--TTTSSS----B-- CS
                         PP_kinase 154 lkfLlkeleldeedvyeidg.pldltdlmklvgkdrpeLkyppftpqtp 201
                                        ++ +k+l+l++++v   +   + ltdl+++ g + p Lky+pftp+ p
  gi|474934327|ref|YP_007687909.1| 277 AAVFAKNLKLKDNQVTSASDkGMMLTDLWEINGLNLPALKYKPFTPKLP 325
                                       ****************99988**********88999**********976 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.42
                                       --------------EEEEETT--HHHHCCHTTTT---TTT.EEEE-S--GGGGGCS.. CS
                         PP_kinase 128 iekeLkkRrrgevvRLeveaempeellkfLlkeleldeedvyeidgpldltdlmklvg 185
                                       i++ ++ ++ g++v + +e +++ + ++ +  + +l++  v+++ gp++l+  +kl +
  gi|474934327|ref|YP_007687909.1| 385 IRQLMRAKENGKAVSVLMELRAKFDEVNNISLARQLEKIGVHVVYGPVNLKVHSKLLQ 442
                                       5666677777777777777666666666666666778888899999999988888764 PP

>> PP_kinase_N  Polyphosphate kinase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.1   0.0   4.8e-32   1.7e-28       1     106 [.      12     117 ..      12     118 .. 0.91
   2 ?   -2.2   0.0       1.4   5.1e+03      79     106 ..     400     427 ..     377     428 .. 0.70

  Alignments for each domain:
  == domain 1  score: 99.1 bits;  conditional E-value: 4.8e-32
                                       XXXHHHHHHHHHHHHHHHHH-TTS-HHHHHHHHHHHHHHHHHHHHHCCHHHHH.HTT-..-----------HHHHH. CS
                       PP_kinase_N   1 ylnRelSwLkFneRVLeeAedervplleRlkFlaIfssNlDEFfmvRvaslkrqleakvekksedgltpeeqlkai. 76 
                                       y+nRe+SwL+Fn+R LeeA d++vp+leR+kFlaI+  N+DEFfm+R+ +l  + ++++ +  +d  + e++l +i 
  gi|474934327|ref|YP_007687909.1|  12 YINREISWLAFNKRCLEEALDPSVPVLERVKFLAICYGNMDEFFMIRMPGLLGAEKDRLVNLGPDAYSDENELINIl 88 
                                       99***************************************************777778888899666666665555 PP

                                       HHHHHHHHHHHHHHHHHTHHHHHHHTTEEE CS
                       PP_kinase_N  77 seeveelveeqekileeellpeLaeegikl 106
                                       +++v+el++  e+++ +e+ +eLa++g+++
  gi|474934327|ref|YP_007687909.1|  89 NDKVNELIDGYEDCW-AEIEKELATKGVSV 117
                                       9**************.***********986 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHHHHHHTHHHHHHHTTEEE CS
                       PP_kinase_N  79 eveelveeqekileeellpeLaeegikl 106
                                        + el ++++++ + +l ++L++ g+++
  gi|474934327|ref|YP_007687909.1| 400 VLMELRAKFDEVNNISLARQLEKIGVHV 427
                                       4556777888888888888998888886 PP

>> PLDc_2  PLD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.2     1e-08   3.7e-05      10     132 ..     369     493 ..     361     494 .. 0.80
   2 !    8.2   0.0   0.00061       2.2      21     128 ..     543     642 ..     527     645 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1e-08
                            PLDc_2  10 ksidiatyyfvsdreildallkaakrgvkvrilldskkddagavdeaslkelkellleagvevrvfetllgslHaKl 86 
                                       +si i+ y +  ++e++++l++a+++g+ v +l+  +++ + +    ++  l+++l + gv v    + +  +H+Kl
  gi|474934327|ref|YP_007687909.1| 369 QSIKISLYRLGKNSEVIRQLMRAKENGKAVSVLMELRAKFDEV----NNISLARQLEKIGVHVVY-GPVNLKVHSKL 440
                                       799********************************94443333....344444444555888554.3456789**** PP

                            PLDc_2  87 ylid..gk.....tvivGSsNltkrgldlnlElnvviedkelakeleeeFerl 132
                                       + +   +k     ++ + S N+++++ ++  ++  ++ ++e+ + + e F++l
  gi|474934327|ref|YP_007687909.1| 441 LQVVrlEKdhlvrYTHMSSGNYNANSAKSYADISYFTANQEIGEDVGELFNAL 493
                                       *9964722456668999*****************************9999875 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00061
                            PLDc_2  21 sdreildallkaakrgvkvrilldskkddagavdeaslkelkellleagvevrvfetllgslHaKlylid...gktv 94 
                                        d++i+++l++a+  gvk+ + ++       +  ++  k ++e ++ + +    f  l+   Ha +y ++   +  +
  gi|474934327|ref|YP_007687909.1| 543 IDSDIIAELYRASMAGVKIDLNIRG-----LCCLRPGMKGISENITVTSIV-DRF--LE---HARIYYFEnggDPKM 608
                                       4777888888888888888887776.....455556666666664444444.222..34...*******966555** PP

                            PLDc_2  95 ivGSsNltkrgldlnlElnvviedkelakeleee 128
                                       ++GSs + +r+l ++ E+++ + dke+  e++e+
  gi|474934327|ref|YP_007687909.1| 609 YMGSSDMMPRNLLARVETLFPVPDKEILMEIREN 642
                                       *************************999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (696 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.72u 0.33s 00:00:01.05 Elapsed: 00:00:00.53
# Mc/sec: 3985.82
//
Query:       gi|474934328|ref|YP_007687910.1|  [L=507]
Description: Exopolyphosphatase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-52  177.5   0.0    4.9e-52  177.1   0.0    1.1  1  Ppx-GppA  Ppx/GppA phosphatase family
    1.3e-12   48.0   0.1    2.7e-12   47.0   0.1    1.6  1  HD        HD domain
  ------ inclusion threshold ------
       0.13   12.7   0.0        0.9   10.0   0.0    2.3  2  FtsA      Cell division protein FtsA


Domain annotation for each model (and alignments):
>> Ppx-GppA  Ppx/GppA phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.1   0.0   8.2e-56   4.9e-52       7     285 .]      24     304 ..      18     304 .. 0.95

  Alignments for each domain:
  == domain 1  score: 177.1 bits;  conditional E-value: 8.2e-56
                                       TTE.EEEEEEEEEE--CCCCCHCCSSC-HHHHHHHHHHHHHHHHHCCCTTGCCEEEEEEHHHHHSTTHHHHHHHHCC CS
                          Ppx-GppA   7 agl.lqivarekrkvrLaeglnesgrlqeeaiertisaLkefaellqkfkvenvrvVATsalRdavNadeFlarvkk 82 
                                       +g+  +++ ++k+ vrL++ l  +g++ +e ie+t+ +L++f+ ++++++ve++ + AT a+R+a+Na e l +++k
  gi|474934328|ref|YP_007687910.1|  24 EGSlGTPIYQDKEAVRLGKSLYGQGKFDPETIEKTRVVLSKFKDIAEGMGVEEIVAYATCAAREAPNASELLDAARK 100
                                       555457899***************************************************************98876 PP

                                       CCSS-EEEE-HHHHHHHHHHHHHHHT---SSEEEEEEETTEEEEEEEETTEEEEEEEES--CCHHH..HHHSGCCC- CS
                          Ppx-GppA  83 evglkveiisgeeEarliylgvvssllekgrglviDiGGGStElvlgeekevsklvSlplGavrlt..erfltddpl 157
                                         g+++ iisg eEarl+ lgvv     + r l  DiGGGStE+ ++e+++   + S++lGavr++  e f +++ +
  gi|474934328|ref|YP_007687910.1| 101 -AGVDLRIISGLEEARLTRLGVVGPD-CARRTLLMDIGGGSTEVTIAEGRNNLYMDSMSLGAVRFAygEGFDPSQRI 175
                                       .6**********************99.88999*********************************9667899999** PP

                                       -HHHHHHHHHHHHHHCTTTHHHHCCCEHHCCCCCCCHCCHHCHHHHHHCT.S..SCEEEHHHHHHHHHHHCTSSCHH CS
                          Ppx-GppA 158 tkeeveaarkavekeleevkdevkkegewtrlvgtsgtisalaeltelhgek..gyeitaeeleeliekllqlkkee 232
                                       t ++ +++r+ v+    + +  ++  g    ++g+sgt+ ala + +++      + i+++el+el++ l ++++ee
  gi|474934328|ref|YP_007687910.1| 176 TPKQYDFLRRQVDTASYRSVGRIRDLG-FEEAIGSSGTLMALAAILAAKRGDddASYIDYNELKELMKDLCRMTAEE 251
                                       ***************************.*****************999986677999******************** PP

                                       HHHSTTS-CCHHCTHHHHHHHHHHHHHHCT-SEEEEES--HHHHHHHHHHHHH CS
                          Ppx-GppA 233 elklagvsdeRadvivagalilsavlealeieaviisegalrEGvlyslllke 285
                                       + ++ ++s +Ra++i +g++++++++  + i+ ++is+ +lrEG++ + ll++
  gi|474934328|ref|YP_007687910.1| 252 RSRVPKLSSNRAEIIIGGGAVAEELMFLFGISRLEISPNGLREGMRTEYLLEH 304
                                       **********************************************9998876 PP

>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   0.1   4.6e-16   2.7e-12       3     121 ..     328     447 ..     327     448 .. 0.93

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 4.6e-16
                                       HHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHH CS
                                HD   3 eHsleVaklarrlaedlge.......eedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevek 72 
                                       eHs +Va++a+r++++l         +  r ll  aa lHD+G+  +++             +H+++++ i+r++ +
  gi|474934328|ref|YP_007687910.1| 328 EHSEAVAEYAARIYDSLCTegvfarnDRWRSLLGYAAQLHDVGEFISYE-------------DHADFSYLIIRNAYL 391
                                       8***************988*****99999*****************886.............8************99 PP

                                       HHHHH..HHHHHHHHHTTCCHHHHHHHH..H...HHHCCTSCHHHHHHHHHHHHHH CS
                                HD  73 rlgld..ledvaklirehheswegkkrp..r...glaerqlslearivklaDrlaa 121
                                         +++  le++a+++r hh s++g+     +   ++++ +l   a+i+k+aD l++
  gi|474934328|ref|YP_007687910.1| 392 AGFDNeeLEAIAQIARMHHSSMPGQSGKglSripREDIPPLVQCALILKVADILDR 447
                                       99888******************77555661578********************98 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.25   1.5e+03       3      17 ..       8      22 ..       7      34 .. 0.87
   2 ?   10.0   0.0   0.00015       0.9       2      29 ..     132     159 ..     131     278 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.25
                                      EEE-SSSEEEEEEET CS
                                      xxxxxxxxxxxxxxx RF
                              FtsA  3 vDiGagktdvavaed 17
                                      +D+G++++ ++v++ 
  gi|474934328|ref|YP_007687910.1|  8 IDVGTNSVHMLVVRF 22
                                      9**********9986 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00015
                                       EEEE-SSSEEEEEEETTEEEEEEEES-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              FtsA   2 lvDiGagktdvavaedgalvhlrvigvg 29 
                                       l DiG+g+t+v++ae+ +  ++++  +g
  gi|474934328|ref|YP_007687910.1| 132 LMDIGGGSTEVTIAEGRNNLYMDSMSLG 159
                                       78**************999997777763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (507 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 3351.69
//
Query:       gi|474934329|ref|YP_007687911.1|  [L=416]
Description: putative ATPase (AAA+ superfamily) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-19   70.0   0.0    5.6e-19   68.5   0.0    1.7  2  DUF4143   Domain of unknown function (DUF4143)
    4.5e-12   46.1   0.0    2.6e-11   43.7   0.0    2.1  1  AAA_14    AAA domain


Domain annotation for each model (and alignments):
>> DUF4143  Domain of unknown function (DUF4143)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.34   3.1e+03      95     113 ..      52      70 ..      39      75 .. 0.71
   2 !   68.5   0.0   6.3e-23   5.6e-19       1     122 []     197     364 ..     197     364 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.34
                                       xxxxxxxxxxxxxxxxxxx RF
                           DUF4143  95 yrdkngaEvDfvielkggk 113
                                       +r+k+ aE+D+ i+lkg++
  gi|474934329|ref|YP_007687911.1|  52 HRNKKIAEIDVNIALKGEE 70 
                                       5677799999988887766 PP

  == domain 2  score: 68.5 bits;  conditional E-value: 6.3e-23
                                       xxxxxxxxxxxxxxxxxx..............................................xxxxxxxxxxxxx RF
                           DUF4143   1 erDirklagvrdpeelrk..............................................glverlppwsesp 31 
                                       e+D+ +++gv++ ++  k                                              +++ + +++s++ 
  gi|474934329|ref|YP_007687911.1| 197 EDDVVRIDGVKRDSRKMKmllrslarnessvvsdsrimadmgindnetmssptlndylgvlrrlNILCEQEAFSANV 273
                                       67888888884333333357779999999999999999999999999999999999999999898888999997788 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DUF4143  32 nskkrlrkspKlyfvDtGLlvallgldkeelledsenkGallEnlVaqeLlkysekegaklyyyrdkngaEvDfvie 108
                                       +s+  + kspK ++vD++L +a+l++d ++ ++d e++G+++E ++ ++L  ys++ g++ly+yrd++g+E+D+vi+
  gi|474934329|ref|YP_007687911.1| 274 RSSVSVGKSPKRHLVDPSLSIAALNMDVKSCIRDLETYGFMFEAMCERDLDIYSQAIGGNLYHYRDNKGNEIDAVIT 350
                                       88888************************************************9999*********99********* PP

                                       xxxxxxxxxxxxxx RF
                           DUF4143 109 lkggkivpiEvKss 122
                                         g+++ ++E+K++
  gi|474934329|ref|YP_007687911.1| 351 IPGREWGAFEIKLG 364
                                       ************85 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   0.0   2.8e-15   2.6e-11       4     129 ..      25     133 ..      23     135 .. 0.80

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 2.8e-15
                            AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevpewe 80 
                                       ++ i+G++ +GKT+ ++ + ++++        +n  ++   k+a+ +   ++ l+      ++  ++DE+qevpe++
  gi|474934329|ref|YP_007687911.1|  25 AVSIEGPKNCGKTWTARAFSESEF-------QLNHRNK---KIAEID--VNIALKG-----EEPHLIDEWQEVPEIW 84 
                                       688************999976555.......4444443...444332..3455553.....34489*********** PP

                            AAA_14  81 kalkslvdeg.knldvivtGSnskllskeiatslagrvaeielyplsfaE 129
                                       + ++  vd++ k++++i+  S+ +      ++s agr+ ++++ p+s+ E
  gi|474934329|ref|YP_007687911.1|  85 DEVRFEVDRStKKGRFILCASSTLATGV-KNHSGAGRIGVLKMRPMSLYE 133
                                       ********88799********9999966.589***************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2661.84
//
Query:       gi|474934330|ref|YP_007687912.1|  [L=290]
Description: hypothetical protein TALC_00756 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.24   11.7   0.3        3.4    8.0   0.1    2.6  3  C2        C2 domain


Domain annotation for each model (and alignments):
>> C2  C2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1   0.00019       3.4      44      59 ..       3      17 ..       1      35 [. 0.82
   2 ?   -1.6   0.0      0.19   3.3e+03      19      30 ..     206     217 ..     187     224 .. 0.65
   3 ?    0.1   0.0     0.056     1e+03      76      90 ..     243     257 ..     232     269 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00019
                                      SSSSEEEEEEEEEESC CS
                                C2 44 slnPvWnekftfevae 59
                                      + +P+Wne+++f++++
  gi|474934330|ref|YP_007687912.1|  3 N-HPEWNESYYFNLHD 17
                                      4.6**********999 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.19
                                       TSSCEEEEEEEE CS
                                C2  19 kgssdpyvkvsl 30 
                                       ++s dp vk+++
  gi|474934330|ref|YP_007687912.1| 206 ENSNDPVVKIDI 217
                                       567899999998 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.056
                                       STEEEEEEEEEEGHH CS
                                C2  76 skddfiGkveiplst 90 
                                        k ++iG++++p++ 
  gi|474934330|ref|YP_007687912.1| 243 VKAKVIGHATLPMQG 257
                                       57889*******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1937.60
//
Query:       gi|474934331|ref|YP_007687913.1|  [L=872]
Description: Phosphoenolpyruvate synthase/pyruvate phosphate dikinase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.9e-92  309.0   0.0    5.5e-92  308.5   0.0    1.1  1  PPDK_N         Pyruvate phosphate dikinase, PEP/pyruvate bind
    3.7e-22   77.8   0.5    1.4e-21   76.0   0.5    2.0  2  PEP-utilizers  PEP-utilising enzyme, mobile domain


Domain annotation for each model (and alignments):
>> PPDK_N  Pyruvate phosphate dikinase, PEP/pyruvate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  308.5   0.0   6.1e-96   5.5e-92       2     319 ..      20     322 ..      19     325 .. 0.96

  Alignments for each domain:
  == domain 1  score: 308.5 bits;  conditional E-value: 6.1e-96
                            PPDK_N   2 elvGGKganLaellneagipvPpgfaitadafrefleengleekideelkeldvddvdelrkaskeirelilsaelP 78 
                                       elvGGKg+n+a++++ +g +vPp fa+t da++ fl++n+l+++i ++l+++d+dd ++l+  s+eir+l+l+a++ 
  gi|474934331|ref|YP_007687913.1|  20 ELVGGKGVNIAKMIA-NGFSVPPAFAVTVDAYEMFLNRNNLRDDIAAILERTDFDDDASLNSSSEEIRSLFLNANIE 95 
                                       79***********66.9***********************************************************9 PP

                            PPDK_N  79 eeleeaikeayeelgkkfgdeelpvaVRSSataEDlpkasfaGqqdtyLnvggeeevleaikavfaSlfnerAilYr 155
                                       ++   ++k+   +l+       + +aVRSSa+aEDl++asfaGqqdtyLnv+ +e+v++ i  ++aS +n+rA+ Yr
  gi|474934331|ref|YP_007687913.1|  96 DDELIDLKKQRGALEG------EYFAVRSSAVAEDLADASFAGQQDTYLNVR-RENVVRMILTCWASYWNARAMKYR 165
                                       9866666666666654......79***************************6.999********************* PP

                            PPDK_N 156 kekgldheevalavvvqkmvnsdlgasGVafsldpetGfkdevlinasyGlGeaVVaGrvtpdefvvekstrkilek 232
                                       ++++ dh + ++avvvq+mvns+  +sGV+f++dp tG +d+v+++as+GlGe++V+G vtpd++v++k+  ++ e 
  gi|474934331|ref|YP_007687913.1| 166 HDASKDHLSQGMAVVVQRMVNSE--ISGVMFTADPVTG-DDRVIVEASWGLGESIVSGLVTPDHYVLSKPGLEVGEF 239
                                       ***********************..*************.************************************** PP

                            PPDK_N 233 kigekeikivydekeegtkevevpeeereklaLsdeeveeLaeiakkiekhygtpmdiEfaideeegklyllQaRpe 309
                                       +++ ke  ++  + e++    ++p+e++e+ + +d+ ++ +ae + ++e+h+g+p+diE+a++   g++y+lQ+R++
  gi|474934331|ref|YP_007687913.1| 240 TVNVKEHGYYLADGEDV--MLDIPKEKAEARCADDRILKLIAEQGIALENHFGCPQDIEWAVE--AGRVYILQSRNI 312
                                       *************9977..999*****************************************..************ PP

                            PPDK_N 310 trtsekkekk 319
                                       t+  +k+ek+
  gi|474934331|ref|YP_007687913.1| 313 TTLPDKSEKD 322
                                       ***9999875 PP

>> PEP-utilizers  PEP-utilising enzyme, mobile domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.47   4.2e+03      15      37 ..     703     725 ..     702     728 .. 0.84
   2 !   76.0   0.5   1.6e-25   1.4e-21       2      73 .]     792     863 ..     791     863 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.47
                                       HHHHTTS-GEEEEEES--TTHHH CS
                     PEP-utilizers  15 psdiagldkaaGivterGGmtSH 37 
                                       ++di  l+  ++i + rGG  S 
  gi|474934331|ref|YP_007687913.1| 703 NEDIFFLEDTEAIAILRGGDASS 725
                                       67888899999********9886 PP

  == domain 2  score: 76.0 bits;  conditional E-value: 1.6e-25
                                       --S-EEEEES---HHHHTTS-GEEEEEES--TTHHHHHHHHHHTT--EEE--SSHH.HH--TEEEEEETTTT CS
                     PEP-utilizers   2 leegvILvaeetspsdiagldkaaGivterGGmtSHaAivArelgiPaVvgvgeatielkegdlitvDgstG 73 
                                       +e+g+ILv+++t+p +++ ++k+ G++te+GG  +H A+++re+ iPaV  v++at++l++gdl++vDgs+G
  gi|474934331|ref|YP_007687913.1| 792 VEKGEILVTSNTDPGWTVVFSKLGGLITETGGILCHGAVISREYRIPAVTAVKSATTVLHTGDLVSVDGSKG 863
                                       799*******************************************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (872 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.71u 0.32s 00:00:01.03 Elapsed: 00:00:00.52
# Mc/sec: 5039.84
//
Query:       gi|474934332|ref|YP_007687914.1|  [L=171]
Description: Nitroreductase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-29  103.3   0.0    8.4e-15   55.2   0.0    2.0  2  Nitroreductase  Nitroreductase family
    9.3e-14   51.5   0.0      3e-06   27.0   0.0    3.0  3  TM1586_NiRdase  Putative TM nitroreductase


Domain annotation for each model (and alignments):
>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.2   0.0   9.4e-19   8.4e-15       2      57 ..       8      63 ..       7      67 .. 0.94
   2 !   46.8   0.0   3.6e-16   3.2e-12      87     170 .]      66     147 ..      61     147 .. 0.97

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 9.4e-19
                                      HH--B---B-S----HHHHHHHHHHHHTS--GGG---EEEEEE.-CCCHHHHHHHH CS
                    Nitroreductase  2 rkRrSiRkFddepvpkeelekileaarraPsagnlqpwrfvvvqdkelryklaeaa 57
                                      +kR+S+R+++d++v+ke+l+ ileaar aP+++  qp+r++v+q++e ++k++ ++
  gi|474934332|ref|YP_007687914.1|  8 KKRYSVRQYSDRKVEKEKLDLILEAARVAPTGCDYQPVRIYVIQSGEGLEKMRSLS 63
                                      89***********************************************9998765 PP

  == domain 2  score: 46.8 bits;  conditional E-value: 3.6e-16
                                       HHHSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHHHHHHHHT-S..SEEE CS
                    Nitroreductase  87 lagapvlivivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfdeaaeevrkllglpdeeeiv 163
                                        +ga+++++++++ d+ ++++ e + +   +d++++a+  +++A++lGlg+c+ ++f + +  v k + lp+ e++v
  gi|474934332|ref|YP_007687914.1|  66 TFGANTILLFTYDRDEEWNNPLENGVHSGDQDVSIVATHAMMEAEDLGLGTCWCNYFANSE--VEKAFSLPPCERVV 140
                                       579**********************************************************..************** PP

                                       EEEEEE- CS
                    Nitroreductase 164 vliavGy 170
                                       +++++Gy
  gi|474934332|ref|YP_007687914.1| 141 LFMTLGY 147
                                       ******9 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.4   6.1e-06     0.055       3      27 ..       4      28 ..       2      29 .. 0.87
   2 !   10.2   0.0   4.6e-05      0.41     158     185 ..      24      51 ..      23      69 .. 0.82
   3 !   27.0   0.0   3.3e-10     3e-06      90     151 ..     104     170 ..      96     171 .] 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.1e-06
                                      HHHHHH--B---B--S---HHHHHH CS
                    TM1586_NiRdase  3 yeaiekRhsvRkYkdealeeellee 27
                                      +e  +kR svR+Y+d+++e+e+l+ 
  gi|474934332|ref|YP_007687914.1|  4 LELAKKRYSVRQYSDRKVEKEKLDL 28
                                      67789***************99875 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 4.6e-05
                                       HHHHHHHHHHHTS--GGG----EEE.E- CS
                    TM1586_NiRdase 158 ewfkeileaarlAPsAlNqqpwrfelkd 185
                                       e+++ ileaar+AP+  + qp+r+ + +
  gi|474934332|ref|YP_007687914.1|  24 EKLDLILEAARVAPTGCDYQPVRIYVIQ 51 
                                       677889****************997655 PP

  == domain 3  score: 27.0 bits;  conditional E-value: 3.3e-10
                                       HHHHHHHHTT-EEEEES--SST............T-S-EEEEE-BS----.....-----HHHHBSS CS
                    TM1586_NiRdase  90 qlvLkltalGlgtcWvggtykk.kkakvelkkgeklvivIalGyaktklv....eakrkpleelcev 151
                                       + ++++  lGlgtcW     ++ ++++++l+  e++v++++lGy++++      + +rkp+e+++++
  gi|474934332|ref|YP_007687914.1| 104 HAMMEAEDLGLGTCWCNYFANSeVEKAFSLPPCERVVLFMTLGYPADDAQplnlHFRRKPVEDIVRY 170
                                       678999**********98766558999*********************965666********99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.33s 00:00:00.85 Elapsed: 00:00:00.53
# Mc/sec: 976.45
//
Query:       gi|474934333|ref|YP_007687915.1|  [L=83]
Description: hypothetical protein TALC_00759 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.05   13.6   0.0        2.5    8.1   0.0    2.2  2  TFIID_30kDa  Transcription initiation factor TFIID 23-30kDa s


Domain annotation for each model (and alignments):
>> TFIID_30kDa  Transcription initiation factor TFIID 23-30kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0   0.00014       2.5      25      47 ..      17      39 ..       3      42 .. 0.85
   2 ?    3.7   0.0    0.0032        58      36      49 ..      51      64 ..      50      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00014
                       TFIID_30kDa 25 arlvsLaaqKFisdiaadAyqys 47
                                       rl s+ +q+F+   +++A +y 
  gi|474934333|ref|YP_007687915.1| 17 QRLCSVDTQRFLVSFLRNAGDYT 39
                                      599*********99999998775 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0032
                       TFIID_30kDa 36 isdiaadAyqyski 49
                                      + d++++A +y+k 
  gi|474934333|ref|YP_007687915.1| 51 VEDVLREASEYCKA 64
                                      68**********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 546.97
//
Query:       gi|474934334|ref|YP_007687916.1|  [L=264]
Description: DNA repair photolyase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-09   38.3   0.1    5.2e-09   36.7   0.1    1.7  2  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
      0.023   15.0   0.0       0.29   11.4   0.0    2.3  3  GGDEF_2      GGDEF-like domain
       0.11   12.2   3.3       0.96    9.1   3.9    2.0  3  DUF1848      Domain of unknown function (DUF1848)


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.1   8.7e-13   5.2e-09       2     164 ..      48     211 ..      47     214 .. 0.83
   2 ?    0.9   0.0     0.088   5.2e+02      90     143 ..     205     262 ..     193     263 .. 0.78

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 8.7e-13
                                       EEESEESS--TTTSCCTT...HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC. CS
                                       xxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpet...vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla. 74 
                                       +++ gC ++C++C+ pe    + +++r+  + +  + ++ +el     +   ++g g++++ +  +e+ +rl ++  
  gi|474934334|ref|YP_007687916.1|  48 NPYGGCEHGCVYCYAPEVthqQWDGWRVVKVKTNVVSRLSRELP----GLSGTIGIGTVTDPYQGAEKRFRLTRKCl 120
                                       6789***************9877777777777788888888885....66667777777777777777777777667 PP

                                       ....CCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEE CS
                                       ....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  75 ....vpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvv 146
                                           ++ + + + t   l+  +  ++l+ ++  +v +++ ++d++ + k+++ + + ++ +l++l klr+ gi+   
  gi|474934334|ref|YP_007687916.1| 121 eilsSKSFGVEIYTKSDLV-LRDTDLLKSMR-CTVGVTVTTLDER-ISKITEpGAPMPSVRLDTLCKLRSEGIDCFA 194
                                       7899999999999999999.***********.*************.******99999*****************666 PP

                                       EEEEEBTTTSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 147 drivglpGendeeleell 164
                                        + ++l   +d+e +e++
  gi|474934334|ref|YP_007687916.1| 195 MVAPVLDHLSDHE-DEFA 211
                                       6666666666666.6655 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.088
                                       G..HHHHHHHHHTT-SEEEEEEBSSSHH..HHHHHHTCTSHHHHHHHHHHHHHHTTSE CS
                                       x..xxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  90 d..eeklerllelgvdrvslgleaadde..kvlklmnrghtfeevlealeklreagik 143
                                       d  +e++e+l+  gv r  ++     +   + l++m+ g ++++   + + lr++gi+
  gi|474934334|ref|YP_007687916.1| 205 DheDEFAEALASTGVERAMVDPLNRRPQlmQRLERMGFGCSPSQAAVVADSLRAHGIR 262
                                       155999******9999999999888888887778888888888887777777777776 PP

>> GGDEF_2  GGDEF-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   4.9e-05      0.29      61     116 .]      58     122 ..      28     122 .. 0.84
   2 ?   -3.9   0.0       2.8   1.6e+04      93     110 ..     196     213 ..     184     216 .. 0.49
   3 ?    0.8   0.0     0.095   5.7e+02       6      29 ..     231     254 ..     226     261 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.9e-05
                           GGDEF_2  61 lvlllpaedeedae.........allerlarrlgglsvriGiGspveglaglrrSyreArrAlrl 116
                                       +++  p  + ++++          +++rl+r+l+gls +iGiG++ +  +g+ + +r  r++l++
  gi|474934334|ref|YP_007687916.1|  58 VYCYAPEVTHQQWDgwrvvkvktNVVSRLSRELPGLSGTIGIGTVTDPYQGAEKRFRLTRKCLEI 122
                                       5566666666666667777788899*********************9999999999999999986 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 2.8
                           GGDEF_2  93 iGspveglaglrrSyreA 110
                                       + ++ ++l++  + + eA
  gi|474934334|ref|YP_007687916.1| 196 VAPVLDHLSDHEDEFAEA 213
                                       344444444444444444 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.095
                           GGDEF_2   6 eellerarrlgldldgpyvvvvie 29 
                                       ++l +r +r+g+  + ++++vv++
  gi|474934334|ref|YP_007687916.1| 231 PQLMQRLERMGFGCSPSQAAVVAD 254
                                       5899********999999999987 PP

>> DUF1848  Domain of unknown function (DUF1848)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   3.9   0.00016      0.96     253     265 .]      50      62 ..      46      62 .. 0.93
   2 ?   -2.8   0.0      0.67     4e+03     134     167 ..      81     115 ..      76     142 .. 0.66
   3 ?   -0.5   0.0      0.14   8.1e+02      61     106 ..     139     186 ..      98     189 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00016
                           DUF1848 253 yntClhgCvYCYA 265
                                       y  C+hgCvYCYA
  gi|474934334|ref|YP_007687916.1|  50 YGGCEHGCVYCYA 62 
                                       899*********9 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.67
                           DUF1848 134 ekfeklaeelkgytekvviSfv.dlykkvkrnlkk 167
                                       + +++l++el g   ++ i  v d+y+ ++++++ 
  gi|474934334|ref|YP_007687916.1|  81 NVVSRLSRELPGLSGTIGIGTVtDPYQGAEKRFRL 115
                                       55667777777777777665441558888777743 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.14
                           DUF1848  61 llkkleelkergiklyfqfTltdyeke....lepnvpsleerietfkels 106
                                       +l+ ++ lk+  +++++ +T+t+ ++      ep+ p  + r++t+ +l 
  gi|474934334|ref|YP_007687916.1| 139 VLRDTDLLKS--MRCTVGVTVTTLDERiskiTEPGAPMPSVRLDTLCKLR 186
                                       4556666664..56666666666554411125777787777888877775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1725.93
//
Query:       gi|474934335|ref|YP_007687917.1|  [L=546]
Description: thermosome subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   1.5e-169  564.8  18.5   1.7e-169  564.6  18.5    1.0  1  Cpn60_TCP1      TCP-1/cpn60 chaperonin family
  ------ inclusion threshold ------
        0.9   10.0   5.4        8.1    6.9   0.1    3.4  3  Saccharop_dh_N  LOR/SDH bifunctional enzyme conserved region


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  564.6  18.5  1.8e-173  1.7e-169       1     490 [.      35     525 ..      35     526 .. 0.98

  Alignments for each domain:
  == domain 1  score: 564.6 bits;  conditional E-value: 1.8e-173
                                       HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHH CS
                        Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleea 77 
                                       +ad v++tlGPkGmdKmlvn++g+vv+TnDG+tilkel+++hPaak++ve+a++qd+e+GDGTtt v+LageLl+++
  gi|474934335|ref|YP_007687917.1|  35 VADSVRSTLGPKGMDKMLVNSIGDVVITNDGVTILKELDVQHPAAKMVVEVAKTQDTECGDGTTTSVVLAGELLKQS 111
                                       6899************************************************************************* PP

                                       HHHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTS..SXXSTHHHHHHHHHHHHHC CS
                        Cpn60_TCP1  78 ekliaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslssk..ltskeaeelsklvvdAvkl 152
                                       e+li+a+vhpt+i++g+++a+eka  +L++i  +i+ +  ++++L++va tsl++k    ++++++l++lvv+A k 
  gi|474934335|ref|YP_007687917.1| 112 EELINANVHPTVITNGFNMAAEKAQAILDSI--AIPAN--NDKILATVADTSLTGKdvGEEDDKKKLADLVVKAAKF 184
                                       *******************************..77765..569*************7666777899*********** PP

                                       HCCCSEECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCCH CS
                        Cpn60_TCP1 153 ieenekeldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdaee 229
                                       + ++++++d ++i++ k+ gg + d+ +v+G+v+dk+++++ mp+ ++nak++l++++Le +kte++++++++d+++
  gi|474934335|ref|YP_007687917.1| 185 VADDNGRVDTKNIRMTKKVGGVIADTYMVQGVVVDKELVHARMPQVMKNAKIALFNCGLEVKKTEIDAQIQITDPSR 261
                                       *9999************************************************************************ PP

                                       HHHHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGGC CS
                        Cpn60_TCP1 230 leklekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledltp 306
                                       +++++ +ee+ ++ +++ i+k g+nvv+++k+ d+l++h+l k+gi++ rr+k++dle lakatG+ +v +++++t+
  gi|474934335|ref|YP_007687917.1| 262 MNDFLAQEEASMKAMVDHIKKIGANVVFTTKALDELIQHYLSKAGIMGYRRLKESDLEALAKATGGVIVGDPMEITE 338
                                       ***************************************************************************** PP

                                       GC-EEEEEEEECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHH CS
                        Cpn60_TCP1 307 eelGtakkveeekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelel 383
                                       ++lG a++ve++k+g++ +++++++k++k++t+ +rg t++v++e+era+ dA++ v  ++ed+kvv+G+Ga e+el
  gi|474934335|ref|YP_007687917.1| 339 KDLGFAGEVEQKKVGDDGMCFVTGCKNPKAVTLFIRGGTEHVIEEVERALTDAIRTVGITLEDGKVVAGAGAPEIEL 415
                                       ***************************************************************************** PP

                                       HHHHHCCCCTSXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTX...TTEEEETTTTCEEECCCC CS
                        Cpn60_TCP1 384 akklkeyaksvsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkge...kelgidvesgeiidlvea 457
                                         +l+++a sv g+eqlaie+fakA+e ip tLaeNaGldpi+v+ k+++ah++++   k +gid++sge++d++++
  gi|474934335|ref|YP_007687917.1| 416 DIQLQKFAASVGGREQLAIEKFAKAMECIPWTLAENAGLDPIDVIIKMKSAHENNKaagKYFGIDLDSGEPVDMKKR 492
                                       ****************************************************888878889**************** PP

                                       TXEEEHHHHHHHHHHHHHHHHHHHCEEEEEXXX CS
                        Cpn60_TCP1 458 gvvDplkvkrqalksAteaastiLrideiikak 490
                                       +v++pl++k+qa++sAte+a++iLrid++i a+
  gi|474934335|ref|YP_007687917.1| 493 NVIEPLRIKKQAVSSATEVANMILRIDDVIAAR 525
                                       ******************************987 PP

>> Saccharop_dh_N  LOR/SDH bifunctional enzyme conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1      0.17   1.5e+03      11      37 ..      48      74 ..      46      89 .. 0.86
   2 ?    6.9   0.1    0.0009       8.1      10      54 ..     138     182 ..     135     186 .. 0.95
   3 ?    3.1   0.2     0.014   1.2e+02       7      74 ..     214     288 ..     209     301 .. 0.58

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.17
                                      TTSSHHHHHHHHHHHTTXEEEEEEEEX CS
                    Saccharop_dh_N 11 iDsgilnkvldlileaggsfevlefev 37
                                      +D++++n + d++++++g   ++e++v
  gi|474934335|ref|YP_007687917.1| 48 MDKMLVNSIGDVVITNDGVTILKELDV 74
                                      799************999888888877 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0009
                                       XTTSSHHHHHHHHHHHTTXEEEEEEEEXXSSTTSXEEEEEEEEES CS
                    Saccharop_dh_N  10 liDsgilnkvldlileaggsfevlefevGkkkkdtSyaelevsae 54 
                                       ++Ds  ++   d+il++ ++ +++  +vG++ +++  a+l v+a 
  gi|474934335|ref|YP_007687917.1| 138 ILDSIAIPANNDKILATVADTSLTGKDVGEEDDKKKLADLVVKAA 182
                                       89****************************************996 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.014
                                       EEXXTTSSHHHHHHHHHHHT......TXEEEEEEEEXXSSTTSXEEEEEE.EEESSHHHHHHHHHHHHHHHHHSC CS
                    Saccharop_dh_N   7 eGhliDsgilnkvldlilea......ggsfevlefevGkkkkdtSyaele.vsaedeevLeeileeltelgaelv 74 
                                       +G ++D+ +++  + +++++      +   ev++ e+ ++ + t  ++++   a++e+ +++++++++++ga++v
  gi|474934335|ref|YP_007687917.1| 214 QGVVVDKELVHARMPQVMKNakialfNCGLEVKKTEIDAQIQITDPSRMNdFLAQEEASMKAMVDHIKKIGANVV 288
                                       566666666666555555531111113334455555555444444444432568888999999999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (546 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.51
# Mc/sec: 3247.88
//
Query:       gi|474934336|ref|YP_007687918.1|  [L=232]
Description: Dolichol kinase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       933  (0.0520386); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.36s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 1361.72
//
Query:       gi|474934337|ref|YP_007687919.1|  [L=190]
Description: Thymidylate kinase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-28   98.7   0.0    3.5e-28   98.5   0.0    1.0  1  Thymidylate_kin  Thymidylate kinase
    7.7e-06   25.9   0.1      0.024   14.5   0.1    2.1  2  dNK              Deoxynucleoside kinase
    3.3e-05   24.5   0.2    0.00099   19.7   0.2    2.4  1  AAA_18           AAA domain
    0.00056   20.1   0.1     0.0059   16.8   0.1    2.4  1  AAA_33           AAA domain
     0.0023   17.4   0.1      0.011   15.2   0.0    1.8  2  KTI12            Chromatin associated protein KTI12
     0.0033   16.5   0.1      0.013   14.5   0.0    1.8  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
     0.0085   15.8   0.0      0.011   15.4   0.0    1.3  1  AAA_30           AAA domain
     0.0089   16.3   0.0      0.024   14.9   0.0    1.7  2  AAA_22           AAA domain
  ------ inclusion threshold ------
      0.019   14.9   0.0      0.034   14.0   0.0    1.4  1  APS_kinase       Adenylylsulphate kinase
      0.027   13.8   0.0      0.067   12.5   0.0    1.6  2  Zeta_toxin       Zeta toxin
      0.027   14.4   0.1       0.13   12.2   0.0    2.1  3  NTPase_1         NTPase
       0.03   14.7   0.2       0.81   10.1   0.0    2.4  2  AAA_17           AAA domain
      0.041   13.9   0.0         12    6.0   0.0    2.2  2  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
      0.043   13.1   0.0       0.06   12.6   0.0    1.2  1  DUF5050          Domain of unknown function (DUF5050)
      0.076   13.4   0.0       0.11   12.9   0.0    1.3  1  AAA_16           AAA ATPase domain
       0.11   12.4   0.0        1.4    8.8   0.0    2.2  2  AAA_31           AAA domain
       0.12   12.2   0.0       0.26   11.0   0.0    1.5  2  ATP_bind_1       Conserved hypothetical ATP binding protein
       0.15   11.7   0.0       0.66    9.6   0.0    1.8  2  SRP54            SRP54-type protein, GTPase domain


Domain annotation for each model (and alignments):
>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.5   0.0   3.5e-31   3.5e-28       1     185 []       6     182 ..       6     182 .. 0.93

  Alignments for each domain:
  == domain 1  score: 98.5 bits;  conditional E-value: 3.5e-31
                                       EEESTTSSHHHHHHHHHHHHHHTTE..EEEESSSTTSHHHHHHHHHHHTCS---HHHHHHHHHHHHHHTTHHHHHHH CS
                   Thymidylate_kin   1 iEGlDGaGKttqaellkerlkeegik.vvltrepggteiGekirelllkeeeleeqteallfaadriehleekikpa 76 
                                       ++G+DG+GK+t ae+l+e l+++g+k  ++t+++ ++ +G++  + l+ e + + +   + + ad+ ++l+  + + 
  gi|474934337|ref|YP_007687919.1|   6 VDGMDGSGKSTAAEMLREELESRGRKvFLVTHPNVSCVVGRMEAKFLTIEGKPAMMLSTMCYIADVLRSLT-IMRAR 81 
                                       79************************999*******************999999999999******66665.99999 PP

                                       HHTT-EEEEES-HHHHHHHHHTTTTTTCHHHHHHGGGTTSE-SEEEEEESSHHHHHTSCCTTSSTTTSHHHHHHHHH CS
                   Thymidylate_kin  77 lkqgktvivdRylfSslaYqgakegvdldlvlslnedvllkPdltflldvdpevalkRlakrdeldeeeeeqldflr 153
                                       l + +  ++ Ry+++++++++ k    +  v+++ e +l++Pd  +l+dvdp++al R+ +r+e ++e++e +d+l+
  gi|474934337|ref|YP_007687919.1|  82 LRKYDDFVFVRYIMGVAYLPESK----VPKVYRMVERILPMPDTKYLIDVDPDTALSRIDTRGE-EKEVFETRDKLE 153
                                       ****************9999964....5788888888888************************.9*********** PP

                                       HHHHHHHHHHHTTSTEEEEETTS-HHHHHHHH CS
                   Thymidylate_kin 154 kvrerylelakederiliidasksieevheeI 185
                                       ++r++++++    + ++i+d +k +e+++++I
  gi|474934337|ref|YP_007687919.1| 154 ETRRKMMSVS---DGWIIVDNTKDMEDTRRQI 182
                                       *********9...5788899999999999887 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0   0.00076      0.76       2      23 ..       5      26 ..       4      34 .. 0.91
   2 !   14.5   0.1   2.4e-05     0.024      85     153 ..      85     149 ..      72     174 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00076
                                      EEEESTTSSHHHHHHHHHCCST CS
                               dNK  2 vveGnIgaGKstlvklLskklg 23
                                      vv+G  g+GKst +++L+++l+
  gi|474934337|ref|YP_007687919.1|  5 VVDGMDGSGKSTAAEMLREELE 26
                                      79****************9987 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 2.4e-05
                                       HHHHHTHHHHHHHTTSS-HHHHHHHHHHHHHHHHHCCH-SEEEEEE--HHHHHHHHHHCTTCCCTTS-H CS
                               dNK  85 ysdryiFakalaekgtlseeelkiykelldnlleelakpdlliYLkasletclerikkRgreeekkiel 153
                                       y d+ +F+   +   +l+e+++ + + + +++l   + pd    ++++++t l ri  Rg+e+e    +
  gi|474934337|ref|YP_007687919.1|  85 YDDF-VFVRYIMGVAYLPESKVPKVYRMVERIL---PMPDTKYLIDVDPDTALSRIDTRGEEKEVFETR 149
                                       7788.**************************99...668888889*****************9974444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.2     1e-06   0.00099       3     117 ..       6     143 ..       5     156 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1e-06
                            AAA_18   3 ltGtpGvGKttlakeLskrlgf.........gvnlrdvakenglllevdpealdeskrldedkldklldaleenss. 69 
                                       + G+ G+GK+t a+ L+++l++         + n+++v+   +  +   +   ++   l ++   ++ d l+     
  gi|474934337|ref|YP_007687919.1|   6 VDGMDGSGKSTAAEMLREELESrgrkvflvtHPNVSCVVGRMEAKFLTIEG--KPAMMLSTM--CYIADVLRSLTIm 78 
                                       669****************97778888888888888888777777777777..444444433..3444444433334 PP

                            AAA_18  70 ..aleegknl....vidghlaeleseaakdikk...........vvLtaspeelleRlekRgyee 117
                                         +l++ ++     +i g+   +es   k + +           + ++++p++ l R+ +Rg+e+
  gi|474934337|ref|YP_007687919.1|  79 raRLRKYDDFvfvrYIMGVAYLPESKVPKVYRMverilpmpdtkYLIDVDPDTALSRIDTRGEEK 143
                                       44777888775444444444444444444444499999999999999999999999999999665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   5.9e-06    0.0059       4     124 ..       6     145 ..       4     189 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.9e-06
                            AAA_33   4 lvGlpGsGKstlaerllkklg.....avllssdt...lrrrlfg.....tdqqsktdytr.vldrlyqilnelarka 66 
                                       + G+ GsGKst ae l ++l      ++l++ ++   +  r+++     ++++    +t     ++ + l  + r +
  gi|474934337|ref|YP_007687919.1|   6 VDGMDGSGKSTAAEMLREELEsrgrkVFLVTHPNvscVVGRMEAkfltiEGKPAMMLSTMcYIADVLRSL-TIMRAR 81 
                                       569*************88888888*9999**999666444555555554444444443433445566666.677777 PP

                            AAA_33  67 lsagrnvil.....datnlsrrerarflklar.rlgvpvrivvvetdeetlkeRlakRaangdd 124
                                       l++  ++++        +l +++  ++ ++++  l +p++   +++d++t+ +R+  R +++++
  gi|474934337|ref|YP_007687919.1|  82 LRKYDDFVFvryimGVAYLPESKVPKVYRMVErILPMPDTKYLIDVDPDTALSRIDTRGEEKEV 145
                                       7777777773332233355577776555555514678888888888888888888888888643 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.1e-05     0.011       1      39 [.       1      39 [.       1      51 [. 0.87
   2 ?   -0.1   0.1      0.53   5.3e+02      53      89 ..     145     182 ..     120     185 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.1e-05
                                      E.EEEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THH CS
                             KTI12  1 MpLvvltGlPssGKstrakeLakaleeekrsvvviddes 39
                                      M+  v+ G+  sGKst+a+ L+++le+++r+v ++    
  gi|474934337|ref|YP_007687919.1|  1 MAWYVVDGMDGSGKSTAAEMLREELESRGRKVFLVTHPN 39
                                      6667899999**********************9987655 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.53
                                       HHHHHHHHHHHHHHHHTT.S.EEEE-S---SHHHHHHH CS
                             KTI12  53 ekalRsslrsavkrdLskek.vVIvDslnyikgfRYeL 89 
                                         ++R++l +  ++ +s ++ ++IvD++  +   R+++
  gi|474934337|ref|YP_007687919.1| 145 VFETRDKLEETRRKMMSVSDgWIIVDNTKDMEDTRRQI 182
                                       34556666666666666443378888887777777765 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   1.3e-05     0.013      34      64 ..       6      36 ..       4      46 .. 0.87
   2 ?   -1.0   0.0      0.68   6.7e+02     153     185 ..     147     181 ..     144     187 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.3e-05
                                      EEE-TTSSHHHHHHHHHHHHHCTT--EEEEE CS
                              MeaB 34 ltGvPGaGkstlvealglelrrrGkrvavla 64
                                      + G+ G+Gkst+ e l +el +rG++v ++ 
  gi|474934337|ref|YP_007687919.1|  6 VDGMDGSGKSTAAEMLREELESRGRKVFLVT 36
                                      5699***********************8765 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.68
                                       STTTTTTT--CCCHHH-S..EEEEE---HHHHHHH CS
                              MeaB 153 eaGDelqgikkGileiaD..iivvnkaDkkeaeka 185
                                       e+ D+l   ++ ++ ++D  iiv n  D +++++ 
  gi|474934337|ref|YP_007687919.1| 147 ETRDKLEETRRKMMSVSDgwIIVDNTKDMEDTRRQ 181
                                       67799999999999999966667677777666554 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.1e-05     0.011      21      54 ..       4      37 ..       1      81 [. 0.90

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.1e-05
                            AAA_30 21 avltGpAGtGKttalkalreaweaaggrviglAp 54
                                       v+ G  G+GK+ta + lre +e++g++v+++++
  gi|474934337|ref|YP_007687919.1|  4 YVVDGMDGSGKSTAAEMLREELESRGRKVFLVTH 37
                                      5899*************************99876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.4e-05     0.024       9      49 ..       5      39 ..       3      85 .. 0.84
   2 ?   -1.3   0.0       2.5   2.5e+03      82      99 ..     152     171 ..      97     184 .. 0.56

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.4e-05
                            AAA_22  9 vvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlps 49
                                      vv G  G+GK+t +++l+e+l+ +      +++v++vt p+
  gi|474934337|ref|YP_007687919.1|  5 VVDGMDGSGKSTAAEMLREELESR------GRKVFLVTHPN 39
                                      799******************876......77777777665 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.5
                            AAA_22  82 leqalrarav...ielliiDE 99 
                                       le+  r+  +    + +i+D+
  gi|474934337|ref|YP_007687919.1| 152 LEETRRKM-MsvsDGWIIVDN 171
                                       22222222.135556777776 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.4e-05     0.034       7      37 ..       6      36 ..       2      45 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.4e-05
                                      EESSTTSSHHHHHHHHHHHHHHTT--EEEEE CS
                        APS_kinase  7 ltGlsgsGKstianalekkLvekgisvylLd 37
                                      + G+ gsGKst a++l ++L+++g++v l+ 
  gi|474934337|ref|YP_007687919.1|  6 VDGMDGSGKSTAAEMLREELESRGRKVFLVT 36
                                      5699*********************998776 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.7e-05     0.067      19      48 ..       4      33 ..       2      37 .. 0.85
   2 ?   -2.6   0.0       2.7   2.7e+03     129     148 ..     125     145 ..     123     161 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.7e-05
                        Zeta_toxin 19 illgGqpGAGKselaellkdelerqgnvvr 48
                                      +++ G  G+GKs++ae+l++ele++g+ v 
  gi|474934337|ref|YP_007687919.1|  4 YVVDGMDGSGKSTAAEMLREELESRGRKVF 33
                                      6778999***************98887765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.7
                        Zeta_toxin 129 vavkkelSrlgvldRyeee.v 148
                                       + v++ ++ +++  R ee+ v
  gi|474934337|ref|YP_007687919.1| 125 IDVDPDTALSRIDTRGEEKeV 145
                                       567777777888888777643 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00013      0.13       3      52 ..       5      54 ..       4      86 .. 0.81
   2 ?   -1.4   0.0       1.9   1.9e+03     108     135 ..     102     130 ..     102     162 .. 0.62
   3 ?   -1.5   0.0       2.1   2.1e+03      90     114 ..     157     182 ..     123     187 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                                      EEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE-------EEEEEET CS
                          NTPase_1  3 fiTGppGvGKtTlvkkvlellkssgvkvgGfyteevreggrrigFkivdl 52
                                      ++ G+ G+GK+T  + + e+l+s+g kv  +  ++v     r+  k  ++
  gi|474934337|ref|YP_007687919.1|  5 VVDGMDGSGKSTAAEMLREELESRGRKVFLVTHPNVSCVVGRMEAKFLTI 54
                                      5789***********************98777777776666666666666 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.9
                                       GGG-HHHHHHHHHHHT.TTSEEEEE--SS CS
                          NTPase_1 108 ElkskkfkeaveevLk.sekpvlavihrr 135
                                       E k++k+ ++ve++L  +++  l+ +   
  gi|474934337|ref|YP_007687919.1| 102 ESKVPKVYRMVERILPmPDTKYLIDVDPD 130
                                       66777888888888877666666544433 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2.1
                                       HHHHHHH-.EEEE---STTGGG-HHH CS
                          NTPase_1  90 rkalsead.viviDEiGkmElkskkf 114
                                       rk++s +d  i++D    mE + +++
  gi|474934337|ref|YP_007687919.1| 157 RKMMSVSDgWIIVDNTKDMEDTRRQI 182
                                       23333333367777777777666555 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00081      0.81       2      19 ..       8      25 ..       8      44 .. 0.91
   2 ?    2.1   0.1      0.25   2.5e+02      95     124 ..     111     141 ..      94     156 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00081
                                      E-TTSSHHHHHHHHHHHH CS
                            AAA_17  2 GgPGsGKgtqceklveky 19
                                      G+ GsGK+t++e l e++
  gi|474934337|ref|YP_007687919.1|  8 GMDGSGKSTAAEMLREEL 25
                                      899************998 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.25
                                       HHHHHH...SEEEEEE--HHHHHHHHHHHTT CS
                            AAA_17  95 evleel.kpdaiilleadpeeilerrlkdrt 124
                                        v++ l  pd+  l+++dp++ l+r   + +
  gi|474934337|ref|YP_007687919.1| 111 MVERILpMPDTKYLIDVDPDTALSRIDTRGE 141
                                       45555534699999******99999866533 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.012        12       7      33 ..       9      35 ..       4      39 .. 0.89
   2 ?    5.6   0.0     0.015        15      32      85 ..     124     174 ..     121     189 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.012
                                      STTSSHHHHHHHHHHHHHHTT--EEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  7 kGGvGKTtlaanLaralarrglrVllv 33
                                        G+GK+t a  L   l  rg++V+lv
  gi|474934337|ref|YP_007687919.1|  9 MDGSGKSTAAEMLREELESRGRKVFLV 35
                                      569*********************987 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.015
                                       EEEEEESSCCCCH.HTTEB-HHHHCCHCCCHHHHHHCHCHHHH..EEEEEEEEES CS
                                       xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  32 lvDaDpqannlai.leglendiepdlkrllellealgkkkalllkiagvvlnrvd 85 
                                       l+D+Dp++ +++i   g e+++ +++++l+e+ +++  +     +   +v+n  d
  gi|474934337|ref|YP_007687919.1| 124 LIDVDPDTALSRIdTRGEEKEVFETRDKLEETRRKMMSV----SDGWIIVDNTKD 174
                                       89**********876666666666777777776666655....344444444444 PP

>> DUF5050  Domain of unknown function (DUF5050)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0     6e-05      0.06     186     237 ..     120     177 ..     107     187 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6e-05
                                       TTEEEEEGGGTT-EEEE-SSS---EE-......S-S-EEEEEEETTEEEEEE-SSS-E CS
                           DUF5050 186 dyiYyidlsknyaLyrvklsgsekevl......tedkvdnyNvtgnwiYyqkesdeek 237
                                       d+ Y id++ ++aL r+++ g+ekev       +e++ +++ v++ wi + + +d e 
  gi|474934337|ref|YP_007687919.1| 120 DTKYLIDVDPDTALSRIDTRGEEKEVFetrdklEETRRKMMSVSDGWIIVDNTKDMED 177
                                       778**********************997666666677889********9999988776 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00011      0.11      28      59 ..       5      37 ..       3      84 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                            AAA_16 28 llsGesGvGKsslvrellralekdg.giflrgk 59
                                      ++ G+ G+GKs+ +++l+++le +g  +fl ++
  gi|474934337|ref|YP_007687919.1|  5 VVDGMDGSGKSTAAEMLREELESRGrKVFLVTH 37
                                      5779*******************9634443333 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0014       1.4      12      36 ..      11      35 ..       5      82 .. 0.92
   2 ?    1.4   0.0      0.26   2.6e+02      35      62 ..     124     148 ..     110     182 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0014
                            AAA_31 12 GvGKTTtsvnlaaalaklgkkvLlv 36
                                      G GK+T + +l + l ++g kv lv
  gi|474934337|ref|YP_007687919.1| 11 GSGKSTAAEMLREELESRGRKVFLV 35
                                      99*********************99 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.26
                            AAA_31  35 lvDlDpQanattglgiekneiektlyev 62 
                                       l+D+Dp ++++    i+++  ek+++e+
  gi|474934337|ref|YP_007687919.1| 124 LIDVDPDTALSR---IDTRGEEKEVFET 148
                                       689999999887...4444444555544 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00026      0.26       2      30 ..       7      35 ..       6      37 .. 0.92
   2 ?   -2.7   0.0       4.1   4.1e+03     181     181 ..     147     147 ..     102     182 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00026
                        ATP_bind_1  2 vGpaGsGKttfvgalseilelrgrsvavv 30
                                       G+ GsGK+t  + l e le+rgr+v +v
  gi|474934337|ref|YP_007687919.1|  7 DGMDGSGKSTAAEMLREELESRGRKVFLV 35
                                      59**********************99876 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.1
                        ATP_bind_1 181 e 181
                                       e
  gi|474934337|ref|YP_007687919.1| 147 E 147
                                       2 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00066      0.66       5      36 ..       5      36 ..       1      40 [. 0.91
   2 ?   -0.5   0.1      0.79   7.9e+02      89     128 ..     136     176 ..     131     184 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00066
                                      EEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE CS
                             SRP54  5 llvGlqGaGKTttlaKLaallkkegkkvllva 36
                                      ++ G+ G+GK t++  L + l+++g+kv lv+
  gi|474934337|ref|YP_007687919.1|  5 VVDGMDGSGKSTAAEMLREELESRGRKVFLVT 36
                                      677***************************97 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.79
                                       EEE--SSTTHHHHHHHHHHHHHHH.SSSEEEEEEETTBHTH CS
                             SRP54  89 vDTaGrlqndkelmeelkkikkvv.kpdevllvldattgqe 128
                                       +DT G  ++  e  + l+++++ + +  +  +++d t   e
  gi|474934337|ref|YP_007687919.1| 136 IDTRGEEKEVFETRDKLEETRRKMmSVSDGWIIVDNTKDME 176
                                       79999999999999999999876635566667777666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.60u 0.39s 00:00:00.99 Elapsed: 00:00:00.55
# Mc/sec: 1039.04
//
Query:       gi|474934338|ref|YP_007687920.1|  [L=206]
Description: hypothetical protein TALC_00764 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.017   14.8   0.3      0.017   14.8   0.3    2.9  4  DUF3149          Protein of unknown function (DUF3149)
        0.5   10.1  11.8       0.19   11.5   4.3    2.6  2  PAP2             PAP2 superfamily
        1.4    8.2   5.4          9    5.6   0.0    2.3  2  DUF4191          Domain of unknown function (DUF4191)
        1.8    8.8   7.0         15    5.9   1.4    2.6  2  Pox_EPC_I2-L1    Poxvirus entry protein complex L1 and I2
        4.9    6.8   7.9       0.96    9.1   0.2    2.1  2  DUF1673          Protein of unknown function (DUF1673)


Domain annotation for each model (and alignments):
>> DUF3149  Protein of unknown function (DUF3149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.3   4.6e-06     0.017      12      34 ..      54      76 ..      52      81 .. 0.87
   2 ?   -2.4   0.3       1.1   3.9e+03      16      27 ..     127     138 ..     125     139 .. 0.55
   3 ?   -2.7   0.1       1.3   4.7e+03       9      14 ..     145     152 ..     144     161 .. 0.59
   4 ?   -2.4   0.1       1.1   3.9e+03      27      34 ..     174     181 ..     172     182 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.6e-06
                           DUF3149 12 lSliVIvftigmgaffiryFirK 34
                                      + li Ivf+i++  +fi+yF ++
  gi|474934338|ref|YP_007687920.1| 54 YTLICIVFAIVLPMVFISYFAKR 76
                                      5799****************876 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.1
                           DUF3149  16 VIvftigmgaff 27 
                                       V v+++++  ++
  gi|474934338|ref|YP_007687920.1| 127 VTVAVLLITFYW 138
                                       556666665554 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 1.3
                           DUF3149   9 vGLl..Sl 14 
                                       +GL+  S+
  gi|474934338|ref|YP_007687920.1| 145 IGLMgpSM 152
                                       56664444 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 1.1
                           DUF3149  27 firyFirK 34 
                                       ++ry+++K
  gi|474934338|ref|YP_007687920.1| 174 WARYYLKK 181
                                       89***998 PP

>> PAP2  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   3.2     0.059   2.1e+02      64      99 ..      99     132 ..      57     139 .. 0.76
   2 ?   11.5   4.3   5.3e-05      0.19      66     130 ..     129     204 ..     125     206 .] 0.74

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.059
                              PAP2  64 afalalllalllrrkrkkiglvllalillllavlva 99 
                                       +f+l+ +++l+l+++ +   +++l+l++l+++v v 
  gi|474934338|ref|YP_007687920.1|  99 VFYLLGTVCLYLADAPEI--TTVLMLCYLVVTVAVL 132
                                       577888888888888888..5666666666665554 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 5.3e-05
                              PAP2  66 alalllalllrrkrkkig...........lvllalillllavlvalsRlylgvHflsDvlaGlliGialaalayrl 130
                                       +++ll++++++   + ig             l  l llll   v ++R+yl  H++ ++  + ++G+a++++++ l
  gi|474934338|ref|YP_007687920.1| 129 VAVLLITFYWKISLHSIGlmgpsmalfvtFGLPGLALLLLYPPVLWARYYLKKHTPLQLALAPAVGFAITYAIFLL 204
                                       55555566666666666666666665555445556688888889***************************99875 PP

>> DUF4191  Domain of unknown function (DUF4191)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0    0.0025         9      34      75 ..      32      76 ..      15      81 .. 0.68
   2 ?    3.4   2.5     0.012        42      23      53 ..     114     142 ..      83     161 .. 0.48

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0025
                           DUF4191 34 lvvvvvfvvlglll...gslilllilgillgllvalivltrraek 75
                                      ++ + vf++l   +   g+++l++++ i++++++ +++++  a++
  gi|474934338|ref|YP_007687920.1| 32 VISIPVFMLLNTEAaglGGWLLYTLICIVFAIVLPMVFISYFAKR 76
                                      4444455555444332247*****************999988876 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.012
                           DUF4191  23 kkllwlllaaflvvvvvfvvlglllgslill 53 
                                       ++++ +l++  lvv+v+++++++ +   i l
  gi|474934338|ref|YP_007687920.1| 114 PEITTVLMLCYLVVTVAVLLITFYW--KISL 142
                                       3333333333333333333444443..3444 PP

>> Pox_EPC_I2-L1  Poxvirus entry protein complex L1 and I2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.4    0.0049        18      43      68 ..      48      73 ..      40      76 .. 0.68
   2 ?    5.9   1.4    0.0043        15      48      71 ..     117     140 ..     109     141 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0049
                     Pox_EPC_I2-L1 43 sgtklwltlliiliavlilvlllfly 68
                                       g +l +tl+ i++a+++ ++++ ++
  gi|474934338|ref|YP_007687920.1| 48 LGGWLLYTLICIVFAIVLPMVFISYF 73
                                      45566666888888888888887554 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0043
                     Pox_EPC_I2-L1  48 wltlliiliavlilvlllflylKv 71 
                                        ++l++  ++v ++vll+++y K+
  gi|474934338|ref|YP_007687920.1| 117 TTVLMLCYLVVTVAVLLITFYWKI 140
                                       344778888999*********996 PP

>> DUF1673  Protein of unknown function (DUF1673)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.2   0.00027      0.96     146     202 ..      52     110 ..      17     113 .. 0.72
   2 ?    0.9   2.8     0.088   3.1e+02     150     201 ..     119     169 ..     110     189 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00027
                           DUF1673 146 vlrwllrllllviflliavllillsyvesiagelqlge..vvssfis.gllllllwliyl 202
                                        l+ l+ ++++++++++ +++++   + +  g++++ e   v++ ++  + ll ++  yl
  gi|474934338|ref|YP_007687920.1|  52 LLYTLICIVFAIVLPMV-FISYFAKRYGNDDGDIVRREdrYVMLALGaVFYLLGTVCLYL 110
                                       45556778888888888.9999*999*********9997744444440444555566666 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.088
                           DUF1673 150 llrllllviflliavllillsyvesiagelqlge.vvssfisgllllllwliy 201
                                       +l+l +lv+ +++ +l+++   ++ ++  l+  + +++ ++++ +l+ l+l y
  gi|474934338|ref|YP_007687920.1| 119 VLMLCYLVVTVAV-LLITFYWKISLHSIGLMGPSmALFVTFGLPGLA-LLLLY 169
                                       5666666655555.566666667777777754435555555554443.33333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1091  (0.0608511); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.64u 0.35s 00:00:00.99 Elapsed: 00:00:00.54
# Mc/sec: 1148.05
//
Query:       gi|474934339|ref|YP_007687921.1|  [L=296]
Description: hypothetical protein TALC_00765 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.11   12.4   0.0        1.2    9.1   0.0    2.2  2  TrkA_C       TrkA-C domain
       0.39   11.0   3.7        0.7   10.2   0.0    3.0  4  Myco_19_kDa  Mycobacterium 19 kDa lipoprotein antigen


Domain annotation for each model (and alignments):
>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00013       1.2      30      67 ..      25      64 ..      20      66 .. 0.89
   2 ?    0.5   0.0      0.06   5.4e+02      40      61 ..     118     139 ..     115     144 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00013
                                      EEEE-T..-EEES--TT-B--TT-EEEEEEEHHHHHHHHH CS
                            TrkA_C 30 vairRg..geliipsgdtvLeeGDvllvvgspsdlaelre 67
                                      +a  R+   ++++ ++++ +eeG ++++ g+++++++ ++
  gi|474934339|ref|YP_007687921.1| 25 IAMERNasSDYTLLDDSLNIEEGMKITLKGTSDGVSTTEK 64
                                      466788899999***********************99876 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.06
                                       S--TT-B--TT-EEEEEEEHHH CS
                            TrkA_C  40 ipsgdtvLeeGDvllvvgspsd 61 
                                       +psg tv +eGD+ ++ g+ ++
  gi|474934339|ref|YP_007687921.1| 118 VPSGYTVKREGDTYIISGTHDE 139
                                       5888888899999999998775 PP

>> Myco_19_kDa  Mycobacterium 19 kDa lipoprotein antigen
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.14   1.3e+03      88     101 ..      50      63 ..      32      88 .. 0.58
   2 ?   10.2   0.0   7.8e-05       0.7      66      97 ..     111     140 ..     103     159 .. 0.66
   3 ?   -3.0   0.0      0.96   8.6e+03      89      99 ..     169     179 ..     160     190 .. 0.59
   4 ?   -0.8   0.2       0.2   1.8e+03      84      94 ..     243     253 ..     179     265 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.14
                       Myco_19_kDa  88 YtitGtaegadsan 101
                                        t++Gt +g+ +++
  gi|474934339|ref|YP_007687921.1|  50 ITLKGTSDGVSTTE 63 
                                       34444444443332 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 7.8e-05
                       Myco_19_kDa  66 ftltyaegtgggsaevtkdgntYtitGtaega 97 
                                       f+   +++++ +  +v+++g+tY i+Gt + +
  gi|474934339|ref|YP_007687921.1| 111 FNY--TSEDVPSGYTVKREGDTYIISGTHDES 140
                                       444..444433339**************8765 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 0.96
                       Myco_19_kDa  89 titGtaegads 99 
                                       +i+G+ +g+  
  gi|474934339|ref|YP_007687921.1| 169 EIEGESSGFGD 179
                                       46666666633 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 0.2
                       Myco_19_kDa  84 dgntYtitGta 94 
                                       + + Y itGt 
  gi|474934339|ref|YP_007687921.1| 243 TATVYSITGTS 253
                                       23457777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2030.76
//
Query:       gi|474934340|ref|YP_007687922.1|  [L=258]
Description: Site-specific recombinase, DNA invertase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-35  122.9   1.9    1.3e-35  122.6   1.3    1.4  2  Resolvase    Resolvase, N terminal domain
    7.1e-20   71.4   0.0    1.5e-19   70.3   0.0    1.6  1  Recombinase  Recombinase
     0.0024   17.9   0.0     0.0054   16.7   0.0    1.6  1  SPOUT_MTase  Predicted SPOUT methyltransferase


Domain annotation for each model (and alignments):
>> Resolvase  Resolvase, N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.6   1.3   2.2e-39   1.3e-35       1     142 [.       6     148 ..       6     151 .. 0.96
   2 ?   -3.2   0.0       1.4   8.4e+03      30      49 ..     174     193 ..     168     204 .. 0.68

  Alignments for each domain:
  == domain 1  score: 122.6 bits;  conditional E-value: 2.2e-39
                                       EEEEEEES-----T...HHHHHHHHHHHH-S--..SE...EEEE.S-TT-TT-HHHHHHHHHHTT-EE.EEEESSCC CS
                         Resolvase   1 aigYaRvSteeqdd...slerQkealrayakenglkivkefeDkgvSGakleRpglkrllaalregkgdvlvvekld 74 
                                       +++Y+RvSte+q     sl++Q+++lr y+k +g+++++++ D+g SG++  Rp+++r+ a++ +   d+++v k+d
  gi|474934340|ref|YP_007687922.1|   6 VAIYVRVSTEDQARvgySLDAQEKRLRDYCKFRGVEVADVYRDEGYSGTSPARPEYQRMFAEIDR--WDAVLVLKMD 80 
                                       689********655555************************************************..********** PP

                                       CC-S...S-HHHHHHHHHTT-EEEESS..SS----HHHHHHHHHHHHHHHHHHHHHCT-TTHHHHHHH CS
                         Resolvase  75 RLaRsvrdlltlleelrekgvslvsldegidtstpmgrlllqilaalaeferelirertkeglaaaka 142
                                       R+ R+  ++++++ +l++ g +++s++e++d st+mgr+ ++i+  +a++e+e+i er+k g++++++
  gi|474934340|ref|YP_007687922.1|  81 RIHRNSVHFAEMIAMLNDSGKQFISVSEKYDSSTAMGRFAMDIIERIAQLESEQIGERVKIGMKRKAE 148
                                       *****************************************************************997 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.4
                                       -..SE...EEEE.S-TT-TT CS
                         Resolvase  30 nglkivkefeDkgvSGakle 49 
                                       ++ ++v+++ D  +SG ++e
  gi|474934340|ref|YP_007687922.1| 174 QEAEVVRDIFDMYISGMTME 193
                                       44567777777778887755 PP

>> Recombinase  Recombinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.3   0.0   2.5e-23   1.5e-19       1      98 [.     173     254 ..     173     257 .. 0.96

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 2.5e-23
                       Recombinase   1 peeaeivrrifelylegkslksiaryLneegiktprgkekWskstvkriLtnpvyiGilvynktkgkkkkkrkddse 77 
                                       ++eae+vr+if++y++g+++++ia+ L   +i+t++g++ Wsk+tv++iL+npvy G+l ++               
  gi|474934340|ref|YP_007687922.1| 173 EQEAEVVRDIFDMYISGMTMENIATSLAMSDIPTKNGGR-WSKATVHKILHNPVYAGYLQWDDVL------------ 236
                                       589************************************.**********************999............ PP

                       Recombinase  78 wivieathepiiseelfeavq 98 
                                           +++h pi+s +++++v+
  gi|474934340|ref|YP_007687922.1| 237 ---RPGNHSPIVSLNTYQEVN 254
                                       ...999999999999999987 PP

>> SPOUT_MTase  Predicted SPOUT methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0     9e-07    0.0054      18      97 ..      22     102 ..       6     107 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 9e-07
                                       HHHHHHHHHHTTT-EEEEEEE.....---S-HHHHHHHHHHT--....TT-EEEEE-TTSEE--HHHHHHHHHHHHH CS
                       SPOUT_MTase  18 elieeYlkrlkkyakleiielk.kekksekeeekakekegerilkklkkkayvillderGkelsSeelakkleklae 93 
                                         ++  +krl+ y+k++ +e++   +++  + ++  + e +r+ +++++ + v++l+++  + +S+++a++++ l++
  gi|474934340|ref|YP_007687922.1|  22 YSLDAQEKRLRDYCKFRGVEVAdVYRDEGYSGTSPARPEYQRMFAEIDRWDAVLVLKMDRIHRNSVHFAEMIAMLND 98 
                                       5567789**************6333344777888999999***********************************99 PP

                                       HT-. CS
                       SPOUT_MTase  94 egks 97 
                                       +gk+
  gi|474934340|ref|YP_007687922.1|  99 SGKQ 102
                                       9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 1456.60
//
Query:       gi|474934341|ref|YP_007687923.1|  [L=292]
Description: Site-specific recombinase, DNA invertase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.4e-34  117.7   0.4    6.6e-34  117.1   0.4    1.2  1  Resolvase    Resolvase, N terminal domain
    3.7e-14   53.0   0.1    2.6e-13   50.3   0.0    2.3  2  Recombinase  Recombinase
     0.0036   16.8   0.0     0.0072   15.8   0.0    1.5  1  GerE         Bacterial regulatory proteins, luxR family
  ------ inclusion threshold ------
      0.019   15.1   0.1        1.2    9.3   0.0    2.8  3  AsiA         Anti-Sigma Factor A


Domain annotation for each model (and alignments):
>> Resolvase  Resolvase, N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.1   0.4   1.5e-37   6.6e-34       1     141 [.       5     153 ..       5     155 .. 0.96

  Alignments for each domain:
  == domain 1  score: 117.1 bits;  conditional E-value: 1.5e-37
                                       EEEEEEES---...--THHHHHHHHHHHH-S--.........SE...EEEE.S-TT-TT-HHHHHHHHHHTT-EE.E CS
                         Resolvase   1 aigYaRvStee...qddslerQkealrayaken.......glkivkefeDkgvSGakleRpglkrllaalregkgdv 67 
                                       a++Y+RvStee   +++s+++Qke+l a++           + i ++++D+g SG++++Rpg++++++++ e   d 
  gi|474934341|ref|YP_007687923.1|   5 AALYCRVSTEEqaiEGYSIDAQKERLAAFCSFSmddqgndAYSIYQFYVDDGYSGRNTNRPGYRKMMEDIDE--WDS 79 
                                       689********888889*************8888888887888999**************************..*** PP

                                       EEESSCCCC-S...S-HHHHHHHHHTT-EEEESS..SS----HHHHHHHHHHHHHHHHHHHHHCT-TTHHHHHH CS
                         Resolvase  68 lvvekldRLaRsvrdlltlleelrekgvslvsldegidtstpmgrlllqilaalaeferelirertkeglaaak 141
                                       ++v k+dR+ R++ ++l+++++l+++g ++vs++e++d +t+mgr++   ++ +a++e+e+i ert  g+++++
  gi|474934341|ref|YP_007687923.1|  80 VIVLKMDRIHRNTYNFLKMMDDLSRRGKEFVSATENLDNTTAMGRFVTSTIQNIAQLESEQIGERTYMGMREKA 153
                                       **********************************************************************9987 PP

>> Recombinase  Recombinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.24   1.1e+03      39      65 ..     117     150 ..      36     171 .. 0.61
   2 !   50.3   0.0   5.7e-17   2.6e-13       5      64 ..     189     247 ..     186     272 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.24
                       Recombinase  39 e......kWskstvkriLtnpvy.iGilvynktk 65 
                                       +      ++ +st+++i + +   iG+++y   +
  gi|474934341|ref|YP_007687923.1| 117 DnttamgRFVTSTIQNIAQLESEqIGERTYMGMR 150
                                       0333333366666666644333224555555555 PP

  == domain 2  score: 50.3 bits;  conditional E-value: 5.7e-17
                       Recombinase   5 eivrrifelylegkslksiaryLneegiktprgkekWskstvkriLtnpvyiGilvynkt 64 
                                        +v+++fe+ l g s+ +ia++ n++gi+t rg++ ++k +v+ iL+np+y G++++++ 
  gi|474934341|ref|YP_007687923.1| 189 DVVKQMFEWCLGGESMHDIAEDVNRNGIRTHRGNK-FTKFSVSDILHNPIYAGYIRWEEL 247
                                       69*********************************.*********************875 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.6e-06    0.0072       8      50 ..     192     232 ..     192     239 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.6e-06
                                       HHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHHHT-SSH CS
                              GerE   8 revLrllaeGksnkeIAeelniSekTVkvhksnimkKLnvksr 50 
                                       +++++++  G+s+ +IAe+ n   + +++h++n ++K+ v + 
  gi|474934341|ref|YP_007687923.1| 192 KQMFEWCLGGESMHDIAEDVN--RNGIRTHRGNKFTKFSVSDI 232
                                       5899*************9877..699************99875 PP

>> AsiA  Anti-Sigma Factor A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.48   2.1e+03      45      60 ..      58      73 ..      35      79 .. 0.79
   2 ?    2.4   0.0     0.038   1.7e+02      12      48 ..      76     108 ..      68     115 .. 0.72
   3 ?    9.3   0.0   0.00028       1.2      34      58 ..     209     233 ..     191     236 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.48
                                      SSSE--HHHHHHHHHT CS
                              AsiA 45 eGkkltqnsfrkivar 60
                                       G++ ++  +rk++ +
  gi|474934341|ref|YP_007687923.1| 58 SGRNTNRPGYRKMMED 73
                                      7999999999999876 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.038
                                       HHHHHHHHTTTHHHHTSHHHHHHHHHHHT-.ESSSSE CS
                              AsiA  12 avaslLvklsrdeivenrklfvellneiGvrtteGkk 48 
                                          s++v l  d i  n  +f++++++       Gk+
  gi|474934341|ref|YP_007687923.1|  76 EWDSVIV-LKMDRIHRNTYNFLKMMDDLSR---RGKE 108
                                       5555544.5668899**********99876...4555 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00028
                                       HHHHHHT-.ESSSSE--HHHHHHHH CS
                              AsiA  34 ellneiGvrtteGkkltqnsfrkiv 58 
                                       e +n  G+rt+ G k+t+ s   i+
  gi|474934341|ref|YP_007687923.1| 209 EDVNRNGIRTHRGNKFTKFSVSDIL 233
                                       558999************9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1858.20
//
Query:       gi|474934342|ref|YP_007687924.1|  [L=189]
Description: Conserved protein/domain typically associated with flavoprotein oxygenase, DIM6/NTAB family [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.4e-10   39.5   0.0    7.1e-10   39.1   0.0    1.1  1  Flavin_Reduct  Flavin reductase like domain


Domain annotation for each model (and alignments):
>> Flavin_Reduct  Flavin reductase like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.0   3.9e-14   7.1e-10       4     139 ..      12     147 ..      10     169 .. 0.88

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 3.9e-14
                                       S-EE-EEEEE.EETTEEEEEEESSEEEEETTTTEEEEEEETTSHHHHHHHHHSEEEEEEEBCCGHHHHHHTCS...S CS
                     Flavin_Reduct   4 vaqpvavvttsvpptsplgatlssftslsldPplvafslrlpsstadalkeagefvinllsesqealadafsqksgp 80 
                                       ++ pv ++ t ++ + p+++ + +   +s d + +++sl+++++t ++l  ++ f++    es+ a  d f+ + g 
  gi|474934342|ref|YP_007687924.1|  12 YPMPVLIIGTYDENGVPNAMNAAWG-GISDD-NQITISLGKERKTVQNLTVKKCFTVFPATESNVAESDYFGIQHG- 85 
                                       689*******999999988888775.68888.9******************************************9. PP

                                       CCCCCCCCCCCEEECT.CCCSEEETTCSEEEEEEEEE..EECCTTEEEEEEEEEEEEESTTE CS
                     Flavin_Reduct  81 rtddksifagltwees.ptgapallgalasleCqvvg..svelgdhelfigeVvavkvgdda 139
                                        +++k++ +g + +++ ++ ap++++ +++leCq ++  + e++    +ig++v+v+ +++ 
  gi|474934342|ref|YP_007687924.1|  86 FDVNKIERVGFHVRKAeNVDAPIIEEYPMALECQMLSmsEEEIDGGYRLIGRIVNVSADESV 147
                                       *****9999****99989999****************6434445578899******988874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 1168.61
//
Query:       gi|474934343|ref|YP_007687925.1|  [L=31]
Description: hypothetical protein TALC_00769 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (31 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1075  (0.0599587); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 205.83
//
Query:       gi|474934344|ref|YP_007687926.1|  [L=421]
Description: Na+/H+ antiporter NhaD-related arsenite permease [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-36  124.6  34.4    4.5e-36  124.6  34.4    1.9  2  CitMHS           Citrate transporter
    8.8e-16   58.2  32.9    1.2e-15   57.8  32.9    1.0  1  ArsB             Arsenical pump membrane protein
  ------ inclusion threshold ------
        6.1    6.9   5.7        1.1    9.3   0.6    2.5  2  TMEMspv1-c74-12  Plectrovirus spv1-c74 ORF 12 transmembrane p


Domain annotation for each model (and alignments):
>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.6  34.4   7.6e-40   4.5e-36       8     285 ..      23     354 ..      16     366 .. 0.71
   2 ?    1.5   0.9     0.023   1.4e+02     118     166 ..     356     416 ..     351     420 .. 0.70

  Alignments for each domain:
  == domain 1  score: 124.6 bits;  conditional E-value: 7.6e-40
                                       x.....xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS   8 k.....lrldvvallvlvll....vltieealsgiaspiillllgamiigaaleetGlfdrlaakllrlaggkrdll 75 
                                       k     + + +++l +++++    +l ++++   + +++i+lllg+m + a le +G+fd +++kl+r+  +  + +
  gi|474934344|ref|YP_007687926.1|  23 KigkyrIKSYMASLAGAAIMlllgILPLDKVADSVEWSVIFLLLGMMALNASLEYCGFFDLVVEKLMRKYSNTMQFF 99 
                                       445555666677777777777789***********************************************854477 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS  76 vllvlltallsafvsndgvvlimipivlslakrlkklppllliplalaaniggaltpiGtpttraaarpglslpnll 152
                                        +++++ta+lsa++ nd+vvli++piv++ +++l+ +p+ +li+l ++anig a+t +G p             n +
  gi|474934344|ref|YP_007687926.1| 100 GAIMVITAVLSAIALNDAVVLIFCPIVIKCCQKLHANPIPFLIALFISANIGCAATFVGAP------------HNAV 164
                                       78*******************************9999999*********************............7777 PP

                                       x....................................................xxx........xxxxxxxxxxxxx RF
                            CitMHS 153 l....................................................lal........llvgllplvllfm 169
                                       +                                                    + +        ++++l++ v++f+
  gi|474934344|ref|YP_007687926.1| 165 VetyagmsfldysirsiplvaiclpitifmmkrlyakdlskeftdfnepyierI-VvktpkmyaCMAVLVATVVFFA 240
                                       777777777776666622211132222222222222222222222222222220.0222222223333444444443 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........................xxxxxxxxxxxxxx RF
                            CitMHS 170 fgvalalpvnapkvkkqkaiieaiarsllpvatillla.........................ykkveWsvlllfaG 221
                                       +++ + l +                            +                          k++eWs+ll+f+G
  gi|474934344|ref|YP_007687926.1| 241 ISNYIGLEI----------------------------YqialvsgaiatliimtdrpvnclyvAKHIEWSLLLFFIG 289
                                       333333333............................02222233333334556999999999************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 222 vfllvgaleqtGilealadllga..ggplvalalvlgliallsafisnvavaalmapialgmapal 285
                                       +f++v +  ++Gi+e la+++g   g    +++ v++++a+ls++i nv++ +l+  ++++ +p +
  gi|474934344|ref|YP_007687926.1| 290 LFIVVRGAVEVGIIEDLASVMGLgeG-STPSILTVTVFSAVLSNLICNVPACVLLGEMIVSSDPMI 354
                                       *********************65552.33344678999***********************99832 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.023
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................xxxxxxxxxxxxx RF
                            CitMHS 118 iplalaaniggaltpiGtpttraaarpglslpnlll........................lalllvgllplvl 166
                                       +++a++a+    +t+iG              +nl++                        ++ +lv+l +++l
  gi|474934344|ref|YP_007687926.1| 356 VAVAVSASFACNATLIGAA------------TNLICadigerrghqinfwefmkigvpisVVTILVALGYMYL 416
                                       567777777777999****............999998888888888888888888875554444444444444 PP

>> ArsB  Arsenical pump membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.8  32.9     2e-19   1.2e-15       1     421 [.       9     416 ..       8     417 .. 0.80

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 2e-19
                              ArsB   1 lavfiflltlvlviwqpknlsigw.sacggavlaliagvvnfhdvltvtgivwnatlafvaiilislildnigffew 76 
                                       la+fi+   l+ +    k     + ++  ga + l+ g++ +  v     + w   + ++ ++ ++  l+  gff+ 
  gi|474934344|ref|YP_007687926.1|   9 LAIFIVTYGLIAIRKIGKYRIKSYmASLAGAAIMLLLGILPLDKVA--DSVEWSVIFLLLGMMALNASLEYCGFFDL 83 
                                       4566666666555444454333331456788889999****99886..5789***********************98 PP

                              ArsB  77 aalhmakaakgygvrmfvyvsllgaivaalfandgaaliltpivlamvralhfneklvfpfiiasgfiadttslpfv 153
                                          ++ +      +++f  + ++ a+++a+  nd   li+ piv+   + lh n    +pf+ia  + a+       
  gi|474934344|ref|YP_007687926.1|  84 VVEKLMRK-YSNTMQFFGAIMVITAVLSAIALNDAVVLIFCPIVIKCCQKLHANP---IPFLIALFISANIGCAATF 156
                                       76554443.23356778889999******************************96...8*****9999999999989 PP

                              ArsB 154 vsnlvnivsadyfhitfidyasrmvvpylfsllasiivlylffrksipkry.dltevkkpveaikdqnmfrlswyil 229
                                       v    n v   y  ++f+dy+ r +    + l  +i ++  ++ k + k + d+ e       +k  +m+     +l
  gi|474934344|ref|YP_007687926.1| 157 VGAPHNAVVETYAGMSFLDYSIRSIPLVAICLPITIFMMKRLYAKDLSKEFtDFNEPYIERIVVKTPKMYACMA-VL 232
                                       99999******************98888899999999***********98645666655556778888987554.44 PP

                              ArsB 230 gllligyfaseffsipv...svvagsiaiifliaaqkspavhtkkvvkeapwaivffsigmyvvvygvrnagltdvl 303
                                          ++ +  s+++ + +   ++v+g+ia +++++    p v    v k   w++++f ig+++vv g  + g+ + l
  gi|474934344|ref|YP_007687926.1| 233 VATVVFFAISNYIGLEIyqiALVSGAIATLIIMT--DRP-VNCLYVAKHIEWSLLLFFIGLFIVVRGAVEVGIIEDL 306
                                       4444445557776665411156777777655544..444.77888999***************************** PP

                              ArsB 304 sdviqaaadqglfagtigmgfiaailssimnnlptvmidalaiagtdthgmmrealiyanvigsdlgpkitpigsla 380
                                       + v+     +g     + + + +a+ls+++ n+p+ ++    i  +d   m+      a  + + +  + t ig+ +
  gi|474934344|ref|YP_007687926.1| 307 ASVMGL--GEGSTPSILTVTVFSAVLSNLICNVPACVLLGEMIVSSDP--MIW----VAVAVSASFACNATLIGAAT 375
                                       *99865..5788889999999*************99988888888775..433....344567789999******** PP

                              ArsB 381 tllwlhvlshkgmkiswgtyfktgiiltiptllitlvglyi 421
                                        l+   +  ++g +i++  ++k g+ +++ t+l++l  +y+
  gi|474934344|ref|YP_007687926.1| 376 NLICADIGERRGHQINFWEFMKIGVPISVVTILVALGYMYL 416
                                       ***********************************988875 PP

>> TMEMspv1-c74-12  Plectrovirus spv1-c74 ORF 12 transmembrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.4       2.4   1.4e+04      15      28 ..       9      23 ..       6      29 .. 0.62
   2 ?    9.3   0.6   0.00018       1.1       8      27 ..     232     251 ..     225     254 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 2.4
                   TMEMspv1-c74-12 15 LgiFly.iGLsiyqK 28
                                      L+iF+   GL    K
  gi|474934344|ref|YP_007687926.1|  9 LAIFIVtYGLIAIRK 23
                                      788864256655555 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00018
                   TMEMspv1-c74-12   8 iFSvvivLgiFlyiGLsiyq 27 
                                       + + v+  +i  yiGL iyq
  gi|474934344|ref|YP_007687926.1| 232 LVATVVFFAISNYIGLEIYQ 251
                                       55678999***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1095  (0.0610742); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 2538.78
//
Query:       gi|474934345|ref|YP_007687927.1|  [L=398]
Description: Arabinose efflux permease [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.9e-44  150.7  41.9      7e-33  114.0  24.9    2.0  2  MFS_1       Major Facilitator Superfamily
    1.1e-11   44.3  27.0    1.2e-08   34.3  10.2    3.1  3  Sugar_tr    Sugar (and other) transporter
      1e-06   27.9  30.1    3.3e-05   22.9  15.2    2.5  3  MFS_1_like  MFS_1 like family
    1.1e-06   28.2  15.4    1.6e-06   27.7  15.4    1.1  1  MFS_4       Uncharacterised MFS-type transporter YbfB
     0.0044   15.9   0.1     0.0044   15.9   0.1    2.6  3  PTR2        POT family
     0.0087   14.5  11.0       0.26    9.6   3.9    2.1  2  TRI12       Fungal trichothecene efflux pump (TRI12)


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.0  24.9   2.3e-36     7e-33       2     290 ..      15     290 ..      14     292 .. 0.83
   2 !   50.5   9.1   4.9e-17   1.5e-13      38     183 ..     250     395 ..     244     398 .] 0.89

  Alignments for each domain:
  == domain 1  score: 114.0 bits;  conditional E-value: 2.3e-36
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalgll 77 
                                        la f+++++++++++ ++++ +e+lg s   +g++++++ lg +++ +++Gr ++ +G +r ++ + +++++++  
  gi|474934345|ref|YP_007687927.1|  15 TLASFFYTIMFFMFYTGMSSYTTEELGCSTIIAGMAASTFVLGDLLSRIIFGRRMELYGKKRvCVTFLAAGTFVC-- 89 
                                       5899999***********99******************************************5555555555555.. PP

                             MFS_1  78 lllfa.sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWrav 153
                                       l+ f  + +++ll++r+l Gl++ga+++a++++ia+  p ++rg ++g++++++slG+++gp l  +l +++ +  +
  gi|474934345|ref|YP_007687927.1|  90 LFYFQaHDFYTLLFVRFLHGLTYGAMTAAINTIIAHALPASRRGEGMGYFMLSISLGSAIGPFLCMWLEQNGTYDDI 166
                                       4444426666******************************************************************* PP

                             MFS_1 154 fyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvl.....willialllfffgfsg 225
                                       f i +++s+la++   ++l+ ++++ +  +++e             ++ ++ ++ +       + +++l+fff +sg
  gi|474934345|ref|YP_007687927.1| 167 FTIGTAASMLALL---CVLFLKDSRMRFTPEEEA----D-------IRRFRLSNIIerssiP-ISLVCLVFFFSYSG 228
                                       ***********99...555566666666656555....2.......4444444433322213.9999999999**** PP

                             MFS_1 226 lltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalg 290
                                       +lt++  y     gl+    +++++ +++++++ ++ll+gr+ dr g   +l+ +++l++++ ++
  gi|474934345|ref|YP_007687927.1| 229 VLTFISPY-GREIGLA--EASTYFFVFISIATLTARLLGGRVYDRHGENVALIPFFILFFIGMVM 290
                                       ********.*******..88888999999999999**********77766666666666665554 PP

  == domain 2  score: 50.5 bits;  conditional E-value: 4.9e-17
                             MFS_1  38 ltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslw.lllvlrvlqGlgagalfpagaaliadw 113
                                       +++ +++++ a l++Gr+ dr+G    l+  ++lf++g+++l+  +  + +ll + +l+G+  + ++++g++l+++ 
  gi|474934345|ref|YP_007687927.1| 250 FVFISIATLTARLLGGRVYDRHGENVALIPFFILFFIGMVMLSR-ADNPyVLLTAGLLMGFNVAQMVSVGQSLVVKR 325
                                       45567899******************************555554.66677*************************** PP

                             MFS_1 114 fpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeepperkrks 183
                                       +++ + + ai+ ++ +  +++ +gp++ g++++ +g+r  f+++ +vs+ +++l l+    +++++++++
  gi|474934345|ref|YP_007687927.1| 326 ASRARYSVAISTFNNFLDFAYCIGPIVFGFVVEGIGYRDGFLAFSFVSVASLLLYLAIHGIPEHRHPTPE 395
                                       ***************************************************9976666677777776654 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3  10.2   3.9e-12   1.2e-08      17     194 ..      14     187 ..       6     200 .. 0.89
   2 !   10.9   3.0   4.9e-05      0.15      47     117 ..     245     312 ..     222     342 .. 0.82
   3 !    9.0   1.2   0.00019      0.56      42      97 ..     329     384 ..     313     390 .. 0.85

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 3.9e-12
                                       HCGGGTHHHHHHHHTSTT--SHHHHHH.....HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHH CS
                          Sugar_tr  17 gvigafltllkfaknfglsksksskee..ssvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigav 91 
                                        ++++f + + f+++++  +s++++e   s++  g+ +s f++G +++ +++g  ++ +G+k +   +++++ +g++
  gi|474934345|ref|YP_007687927.1|  14 CTLASFFYTIMFFMFYTGMSSYTTEELgcSTIIAGMAASTFVLGDLLSRIIFGRRMELYGKKRV---CVTFLAAGTF 87 
                                       56777888888888888888887666699*********************************96...5567788999 PP

                                       HHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TT CS
                          Sugar_tr  92 lqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnad 168
                                       ++ +  ++  ++ l++ R+l G+  G+ ++ + + i+   p++ Rg  ++++ l+i++G  ++ ++ + l++++   
  gi|474934345|ref|YP_007687927.1|  88 VCLFYFQAHDFYTLLFVRFLHGLTYGAMTAAINTIIAHALPASRRGEGMGYFMLSISLGSAIGPFLCMWLEQNGT-- 162
                                       9999888899**********************************************************9988888.. PP

                                       HHHHHHHCCHHHHHHHHHHGGGS--- CS
                          Sugar_tr 169 gwrillglqlvpallllilllflPES 194
                                        +   + +  + ++l l+++lfl +S
  gi|474934345|ref|YP_007687927.1| 163 -YDDIFTIGTAASMLALLCVLFLKDS 187
                                       .8889999999999999999999999 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 4.9e-05
                                       HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHH CS
                          Sugar_tr  47 lsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvG 117
                                        s+ ++ + ++  +   l++g + dr G   +l+ + +lf+ig v+   a+   + +vl+++ +l+G+ v 
  gi|474934345|ref|YP_007687927.1| 245 ASTYFFVFISIATLTARLLGGRVYDRHGENVALIPFFILFFIGMVMLSRAD---NPYVLLTAGLLMGFNVA 312
                                       5788999999*****************************************...9*************986 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00019
                                       HH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TT CS
                          Sugar_tr  42 eessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaak 97 
                                       ++ sv ++ + +++ +   iG +++g++++ +G+++++l++++++v++ +l  a++
  gi|474934345|ref|YP_007687927.1| 329 ARYSVAISTFNNFLDFAYCIGPIVFGFVVEGIGYRDGFLAFSFVSVASLLLYLAIH 384
                                       345688888889999999*****************************999988887 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9  15.2   1.1e-08   3.3e-05     231     379 ..      15     162 ..       3     169 .. 0.85
   2 !   11.2   6.6     4e-05      0.12     190     383 ..     174     366 ..     159     374 .. 0.75
   3 ?    2.0   0.1     0.025        74      44      89 ..     343     390 ..     332     396 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.1e-08
                        MFS_1_like 231 llvalilgmswgiienFlflYL.kelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfll 306
                                        l+ ++  +++ ++++ ++ Y  +elg s++++G++    v++ +   ++  + +e +G  ++ ++ l a ++  l 
  gi|474934345|ref|YP_007687927.1|  15 TLASFFYTIMFFMFYTGMSSYTtEELGCSTIIAGMAASTFVLGDLLSRIIFGRRMELYGKKRVCVTFLAAGTFVCLF 91 
                                       4556666777777777799**99*************************************99877766666555555 PP

                        MFS_1_like 307 yaiienawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliGGllw.dlksa 379
                                       y   +++  +l++ +Lhg+++g++ aa+ + ++++ p s ++ g+g   +l+++lG+a+G +++  +w +++++
  gi|474934345|ref|YP_007687927.1|  92 YFQAHDFYTLLFVRFLHGLTYGAMTAAINTIIAHALPASRRGEGMGY-FMLSISLGSAIGPFLC--MWlEQNGT 162
                                       55559*****************************************5.5899************..88676665 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 4e-05
                        MFS_1_like 190 lvisllvvlilnetek..esklkvtksl.qvllnilknpeviifllvalilgmswgiienFlflYLkelgasntllG 263
                                        +++ll+vl l++ +    ++ +   ++   l ni++ ++ i + lv+l+  +s++ + +F++ Y  e g  +    
  gi|474934345|ref|YP_007687927.1| 174 SMLALLCVLFLKDSRMrfTPEEEAD-IRrFRLSNIIE-RSSIPISLVCLVFFFSYSGVLTFISPYGREIGLAEAST- 247
                                       3444444444433322002222222.22134555555.566777888889999999999***********998765. PP

                        MFS_1_like 264 slvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllwaaaveyvsk 340
                                        + ++  +a+++  +++ ++ ++ G  + li  ++++++  ++++  +n+ ++l + +L g+ ++ + +++ + v k
  gi|474934345|ref|YP_007687927.1| 248 YFFVFISIATLTARLLGGRVYDRHGENVALIPFFILFFIGMVMLSRADNPYVLLTAGLLMGFNVAQMVSVGQSLVVK 324
                                       666777899******************************************************************** PP

                        MFS_1_like 341 iapksleatgqgllsglyfglGralGsliGGllwdlksaiflF 383
                                        a++   +  ++ ++ +   +  ++G ++ G++ +  + ++ F
  gi|474934345|ref|YP_007687927.1| 325 RASRARYSVAISTFNNF-LDFAYCIGPIVFGFVVEGIGYRDGF 366
                                       *****999999999887.5566777777777776555555444 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.025
                        MFS_1_like  44 pltsilsppiwgvlaDrfgkrkkvvils..lllsavlflsllfippsk 89 
                                        +   ++p ++g++++ +g r   +++s  +++s++l+l++  ip+++
  gi|474934345|ref|YP_007687927.1| 343 DFAYCIGPIVFGFVVEGIGYRDGFLAFSfvSVASLLLYLAIHGIPEHR 390
                                       5667799****************8877611456677777777788554 PP

>> MFS_4  Uncharacterised MFS-type transporter YbfB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7  15.4   5.2e-10   1.6e-06      21     357 ..      38     379 ..      25     384 .. 0.73

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 5.2e-10
                             MFS_4  21 aegqlslsqagllaaaNylGYLvGallaafalsa.gaeRlrllagllatvllllamaltesfaaflliRflaGvasA 96 
                                       +e++ s   ag+ a+   lG L+  +++  +++  g++R+     l a + + l    ++ f ++l +Rfl G++ +
  gi|474934345|ref|YP_007687927.1|  38 EELGCSTIIAGMAASTFVLGDLLSRIIFGRRMELyGKKRV-CVTFLAAGTFVCLFYFQAHDFYTLLFVRFLHGLTYG 113
                                       6667777778999999999999999988666554145555.455555555666666777899*************** PP

                             MFS_4  97 vvlvfgsslvlahaaaarrervgallfaGvGlGiavsgllvllllqlglsasslWlalavlsavllllvalllp... 170
                                       ++  ++ +++ + + a+rr++ ++ +   + lG a++  l + l q g+    +  + ++ s+++ll v+ l     
  gi|474934345|ref|YP_007687927.1| 114 AMTAAINTIIAHALPASRRGEGMGYFMLSISLGSAIGPFLCMWLEQNGTYDD-IFTIGTAASMLALLCVLFLKDsrm 189
                                       ****************************************999999998888.667777777777777776665433 PP

                             MFS_4 171 .raalreasaaaeaakaeqkslpllalllaYglaGfGYiitatFlvaiardgaggalleallWllvGlaaivgvlvw 246
                                         ++++ea    + +  +  +++ + + l+  ++ f Y  + tF++ + r+  g a +   + + + +a +++ l+ 
  gi|474934345|ref|YP_007687927.1| 190 rFTPEEEADIR-RFRLSNIIERSSIPISLVCLVFFFSYSGVLTFISPYGRE-IGLAEASTYFFVFISIATLTARLLG 264
                                       22223333332.3334444556666667777777789999***********.666667788999999********** PP

                             MFS_4 247 lrvakrsglrralaaallieavgvllsllspsplglivssvllGltflaitalvlqlarelappat.rrllglmTas 322
                                        rv +r+g + al   +++  +g+++    + p++l+ +++l+G     +++++  l+ + a  a+   +++     
  gi|474934345|ref|YP_007687927.1| 265 GRVYDRHGENVALIPFFILFFIGMVMLSRADNPYVLLTAGLLMGFNVAQMVSVGQSLVVKRASRARySVAISTFNNF 341
                                       ***********************99888889**************99999998888777777766654444444444 PP

                             MFS_4 323 fgigQilGpllasllaeatg...slalallvaaaalvl 357
                                             +Gp++++ + e  g   ++ + ++v+ a+l+l
  gi|474934345|ref|YP_007687927.1| 342 LDFAYCIGPIVFGFVVEGIGyrdGFLAFSFVSVASLLL 379
                                       44455556666666555544222333333444444433 PP

>> PTR2  POT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.7       0.3   9.1e+02     211     229 ..      18      36 ..      11      50 .. 0.84
   2 !   15.9   0.1   1.5e-06    0.0044      48     124 ..     110     183 ..      97     207 .. 0.79
   3 ?   -1.5   0.3      0.28   8.3e+02      11      26 ..     284     299 ..     276     382 .. 0.63

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.3
                                       HHHHHHHHHHHHHHHHCHH CS
                              PTR2 211 lflpliifwalyaQmgttl 229
                                        f+ +i+f+++y  m+++ 
  gi|474934345|ref|YP_007687927.1|  18 SFFYTIMFFMFYTGMSSYT 36 
                                       5888999999999999875 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.5e-06
                                       HHHHHHHHHHHHHHCTTT-SSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHC CS
                              PTR2  48 lGtGgiKpnvSafgadqfeekdprersrfFsiFyfsiNvGSLlsliitpylqenvgyplgFgipavlmiiallvFll 124
                                       l +G + + + +++a+ ++ +   e  +   +F++si++GS + ++++ +l++n  y   F i ++  ++all  l+
  gi|474934345|ref|YP_007687927.1| 110 LTYGAMTAAINTIIAHALPASRRGEGMG---YFMLSISLGSAIGPFLCMWLEQNGTYDDIFTIGTAASMLALLCVLF 183
                                       6667777777777777777766666666...99******************************99988888875443 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.28
                                       HHHHHHHCCCCTTTTS CS
                              PTR2  11 yaiGhvvlalsaipsl 26 
                                        +iG+v+l+ +++p +
  gi|474934345|ref|YP_007687927.1| 284 FFIGMVMLSRADNPYV 299
                                       5555555554444433 PP

>> TRI12  Fungal trichothecene efflux pump (TRI12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   3.9   8.8e-05      0.26      81     214 ..      48     182 ..       7     192 .. 0.81
   2 !    9.1   0.8   0.00013      0.38      65     145 ..     231     311 ..     202     326 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 8.8e-05
                             TRI12  81 slfstlwttgqavsilvmgrltdrfgrrpfvilthilglvgaivgctatkfntllaamtllgvaagpagas.plfvg 156
                                       ++ ++ + +g+ +s +++gr  + +g++ + +     g   ++    a  f tll    l g++ g   a+   ++ 
  gi|474934345|ref|YP_007687927.1|  48 GMAASTFVLGDLLSRIIFGRRMELYGKKRVCVTFLAAGTFVCLFYFQAHDFYTLLFVRFLHGLTYGAMTAAiNTIIA 124
                                       566677899999***************99998888899999999*******************99987655244555 PP

                             TRI12 157 elm..snktkflgllivsipvvvtsglspylgqrlaiqgswrwifyiyiitsaiavlliv 214
                                         +  s +   +g +++si     s+++p+l   l  +g++  if i    s +a+l ++
  gi|474934345|ref|YP_007687927.1| 125 HALpaSRRGEGMGYFMLSISL--GSAIGPFLCMWLEQNGTYDDIFTIGTAASMLALLCVL 182
                                       554226677788888888764..5678*********************999999977654 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00013
                             TRI12  65 salpnilqdvgqsensslfstlwttgqavsilvmgrltdrfgrrpfvilthilglvgaivgctatkfntllaamtll 141
                                       + +    +++g +e s+ f  + ++    + l+ gr+ dr g    +i   il ++g ++   a++   ll+a  l+
  gi|474934345|ref|YP_007687927.1| 231 TFISPYGREIGLAEASTYFFVFISIATLTARLLGGRVYDRHGENVALIPFFILFFIGMVMLSRADNPYVLLTAGLLM 307
                                       445555689********************************************************9999*9999999 PP

                             TRI12 142 gvaa 145
                                       g   
  gi|474934345|ref|YP_007687927.1| 308 GFNV 311
                                       8654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 2565.54
//
Query:       gi|474934346|ref|YP_007687928.1|  [L=293]
Description: putative hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-15   57.1   0.0      5e-14   52.6   0.0    2.1  1  Abhydrolase_1  alpha/beta hydrolase fold
    3.3e-11   44.2   0.0    4.4e-11   43.8   0.0    1.1  1  Abhydrolase_6  Alpha/beta hydrolase family
    1.3e-10   41.0   0.0    3.6e-07   29.7   0.0    2.5  3  Hydrolase_4    Serine aminopeptidase, S33
  ------ inclusion threshold ------
      0.052   12.3   0.0      0.089   11.5   0.0    1.3  1  Ndr            Ndr family
       0.21   11.6   0.0       0.26   11.3   0.0    1.3  1  PAC2           PAC2 family


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   0.0   1.4e-17     5e-14       2     255 ..      32     275 ..      31     277 .. 0.75

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 1.4e-17
                                       EEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEE CS
                     Abhydrolase_1   2 vlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlv 78 
                                       ++v++hG+pg + ++ +   ++     g+ v+++D++G+g+S+p p+     +g++ +   l+ + d  g dk++l+
  gi|474934346|ref|YP_007687928.1|  32 PIVMVHGGPGDGCSPDK---GEKMTV-GHPVYMYDQLGCGESDPIPDI--GKWGLDEYTSELREFIDGMGFDKVILI 102
                                       89********8877666...666666.********************9..99************************* PP

                                       EETHHHHHHHHHHHHH.GGGEEEEEEESE.....CSSCCHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHHCCSC CS
                     Abhydrolase_1  79 GhSmGGmialayaaey.perVkalvllga.....idpaaslieaqrqqaksfpdffdgyaadcarnpagplladela 149
                                       G S+G++++  ya +    ++ a+vl ++     i    s+    +++   +   ++   a ++  +   ++ d++a
  gi|474934346|ref|YP_007687928.1| 103 GASWGSALCVSYAKLTsCAKIVAMVLPSPylsaeIWKDDSIKNVSEMSHTAYLQLMECLDAGDFGERYRAIMKDYYA 179
                                       ***************77777777777777776665555555555566666666667777777777777777777777 PP

                                       HHHHHHHHHHHHHHHCHHHCCHHHHHHHCHHHHHHHHHHHHHHHHCCHHHHHHHHHCTHHHHSEEEEEEETTCSSSC CS
                     Abhydrolase_1 150 aleqrhrlvdalkfpdkskrfpssgsdnasslatgalksieqwpttdsaklllrlrelknvlaptlvisgtsDplvp 226
                                        +++  ++      ++   ++  + + n +  a ++ +++e   t+    l + l    ++ +p+l+++g+sD +  
  gi|474934346|ref|YP_007687928.1| 180 KYLFTREV------NRPIADAVAEAPLNDVFRALCGENDFECTGTLKGLDLTDYLP---EIDVPVLFMCGDSDEVR- 246
                                       77777766......555555555566666666666666665555555544444422...35559999999999975. PP

                                       HHHHHHHHHCHTSEEEEEEETCSSSHHHH CS
                     Abhydrolase_1 227 pkaledlaqllpkkrlvvisdagHlafle 255
                                        + +  +++  p++rl v++ agH + +e
  gi|474934346|ref|YP_007687928.1| 247 MDTMQMYREYVPGSRLAVVPFAGHALSFE 275
                                       57788888889999999999999998887 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.0   1.2e-14   4.4e-11       1     212 [.      33     275 ..      33     280 .. 0.48

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 1.2e-14
                                       EEEE--GC.....G...CHHHHHHHHCCTCEEEEE--TTSTS-GGCS..--HHHCHHH....HHHHCCTT..TTSEE CS
                     Abhydrolase_6   1 vlllHGagssassW...lvapLaallaagvhvlapDlpGhGrsdppp..ldledladl....aalldelaagggpvv 68 
                                       ++++HG+++++ s      + +      g+ v+++D  G+G+sdp p    +   +++    ++++d+   g ++v+
  gi|474934346|ref|YP_007687928.1|  33 IVMVHGGPGDGCSPdkgEKMTV------GHPVYMYDQLGCGESDPIPdiGKWGL-DEYtselREFIDGM--GFDKVI 100
                                       7999999988666643322355......6666*********4433334433333.55531126677777..6***** PP

                                       EEEETCHHHHHHHHHHCC.....EE.EEES-..----TTT...............S----TTHHHHHHTT-C..... CS
                     Abhydrolase_6  69 lvGHSlGGalalaaapla...lvvg.vlldppptalpagl...............laaalelllallallrl..... 121
                                       l+G S+G al   +a+l+    +v+ vl +p      ++                  a+l+l+              
  gi|474934346|ref|YP_007687928.1| 101 LIGASWGSALCVSYAKLTscaKIVAmVLPSP-----YLSAeiwkddsiknvsemsHTAYLQLM--------Ecldag 164
                                       *************555556653333355555.....222211222222222122211111111........111111 PP

                                       ...CCCHCCH..S-HS.CCCCHHH.....C..CCCHCHCCCGHH........HHCCHHC...HTTCCHHTT-TTGCE CS
                     Abhydrolase_6 122 ...lawlsre..plpr.lfladed.....a..daawrarlarla........allaglg...llpaaawadlpvpll 174
                                           ++++ +  ++++ lf +++      a  +a+ ++ +++l+                  l   + ++ + vp+l
  gi|474934346|ref|YP_007687928.1| 165 dfgERYRAIMkdYYAKyLFTREVNrpiadAvaEAPLNDVFRALCgendfectG-----TlkgLDLTDYLPEIDVPVL 236
                                       11122221112222221222222221111111233333333333443332221.....1222334667777777777 PP

                                       EECTT-CHHH.HCHHCCCH.STTEEETCE...SSS-HHHH CS
                     Abhydrolase_6 175 vlggeDplvp.rllerlla.qagarlpvvlpgaGHlphle 212
                                        ++g+ + v+ ++++ +   ++g rl  v+p aGH++ +e
  gi|474934346|ref|YP_007687928.1| 237 FMCGDSDEVRmDTMQMYREyVPGSRL-AVVPFAGHALSFE 275
                                       7786666555233444444779****.********76663 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.53   1.9e+03     189     212 ..      28      51 ..      25      56 .. 0.76
   2 !   29.7   0.0   9.9e-11   3.6e-07      31     114 ..      55     136 ..      33     196 .. 0.80
   3 !    8.8   0.0   0.00025      0.89     183     237 ..     224     275 ..     216     276 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.53
                       Hydrolase_4 189 kitlPllllhGeaDkvvdpeasre 212
                                       + t+P+ ++hG+    ++p++ ++
  gi|474934346|ref|YP_007687928.1|  28 EQTVPIVMVHGGPGDGCSPDKGEK 51 
                                       567999999999777777777665 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 9.9e-11
                       Hydrolase_4  31 GfavyalDhrGhGrse..gkrghvpsfddyvdDlaafvekvkeehpelplfllGhSmGGliallyl.lrypdkvagl 104
                                       G  vy++D+ G G+s+  +  g++  +d+y+  l++f++ +       +++l+G S+G+++ ++y+ l+  +k+ ++
  gi|474934346|ref|YP_007687928.1|  55 GHPVYMYDQLGCGESDpiPDIGKW-GLDEYTSELREFIDGMG----FDKVILIGASWGSALCVSYAkLTSCAKIVAM 126
                                       677*************98666655.69***********9888....678*****************655555899** PP

                       Hydrolase_4 105 ilsaPalkik 114
                                       +l +P l+ +
  gi|474934346|ref|YP_007687928.1| 127 VLPSPYLSAE 136
                                       *****99765 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.00025
                       Hydrolase_4 183 leeraakitlPllllhGeaDkvvdpeasrelyerlgskdktlklypglyHellnE 237
                                       l++  ++i++P+l+++G++D+v    ++ ++y++      +l++ p + H l +E
  gi|474934346|ref|YP_007687928.1| 224 LTDYLPEIDVPVLFMCGDSDEVRM--DTMQMYREYVP-GSRLAVVPFAGHALSFE 275
                                       56667899**************77..77889999886.89999999999999888 PP

>> Ndr  Ndr family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.5e-05     0.089      82     237 ..      80     250 ..      70     259 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.5e-05
                                       HHHHHTTHHHHHHHHT---EEEEEETHHHHHHHHHH.HHSGGGEEEEEEES---S---HHHHHHHHHH.......TT CS
                               Ndr  82 lddladqllavldhfklksviglGvgaGAyilarfa.lkhperveglvLinitskaagwvewakeKlsskllkkvgl 157
                                       ld+ + +l + +d + +++vi +G+  G  + + +a l+   +++++vL ++  +a+ w +   + +s +   +   
  gi|474934346|ref|YP_007687928.1|  80 LDEYTSELREFIDGMGFDKVILIGASWGSALCVSYAkLTSCAKIVAMVLPSPYLSAEIWKDDSIKNVSEM--SH-TA 153
                                       7788899999*********************99999678889*******************999999953..22.33 PP

                                       TS-HHHHHHHHHS-HHHHHHT-H......HHHHHHHHHHT-TTHHHHHHHHHHHHT-------TTSSS......... CS
                               Ndr 158 tdllkdlllahkFgkeeksensd......lvreyrkllkerlnsknlelyleaynkRrdleierkkle......... 219
                                         +l ++l a  Fg+ ++   +d        re  + +++++ ++ l+  ++a+   +d+e + + +          
  gi|474934346|ref|YP_007687928.1| 154 YLQLMECLDAGDFGERYRAIMKDyyakylFTREVNRPIADAVAEAPLNDVFRALCGENDFECTGTLKGldltdylpe 230
                                       34567899999999999998777333333444445566666666667777777776666666655554556666666 PP

                                       ..S-EEEEEETTSTTHHHHH CS
                               Ndr 220 ..vkvllvvGdkspfvdevv 237
                                         v+vl + Gd+     +++
  gi|474934346|ref|YP_007687928.1| 231 idVPVLFMCGDSDEVRMDTM 250
                                       66666666666666555555 PP

>> PAC2  PAC2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   7.3e-05      0.26      65     106 ..      49     105 ..      10     199 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.3e-05
                                       T......SEEEEEEE........E-HSCHHH..HHHHHHHHHHHHTTESEEEEEEEE CS
                              PAC2  65 g.....srdllvlqg........repilqye..efakalldwaeelgvkevvvLggl 106
                                       g     +++++   +        +  i+++   e++++l ++++ +g+++v+++g+ 
  gi|474934346|ref|YP_007687928.1|  49 GekmtvGHPVYMYDQlgcgesdpIPDIGKWGldEYTSELREFIDGMGFDKVILIGAS 105
                                       1445556777777778888888667788999***********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 1637.56
//
Query:       gi|474934347|ref|YP_007687929.1|  [L=47]
Description: hypothetical protein TALC_00773 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-06   27.2   0.0    3.8e-06   27.0   0.0    1.1  1  AAA_14    AAA domain
     0.0079   16.1   0.0     0.0079   16.1   0.0    1.0  1  ATPase_2  ATPase domain predominantly from Archaea
  ------ inclusion threshold ------
      0.015   14.7   0.0      0.015   14.7   0.0    1.0  1  TniB      Bacterial TniB protein


Domain annotation for each model (and alignments):
>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   6.4e-10   3.8e-06       2      27 ..      19      44 ..      18      47 .] 0.91

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 6.4e-10
                            AAA_14  2 rkilvitGaRrvGKTtllkqlikell 27
                                      rk+lv+ G+R++GKT++l ++ ke+ 
  gi|474934347|ref|YP_007687929.1| 19 RKPLVLLGIRQCGKTFILTEFGKEHH 44
                                      799******************99986 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.3e-06    0.0079       9      43 ..       8      42 ..       3      47 .] 0.89

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.3e-06
                          ATPase_2  9 keleeilerepneiyfiYGpegsGKtaLlkeiien 43
                                      ++l+++ e  +++++++ G +++GKt +l e+ ++
  gi|474934347|ref|YP_007687929.1|  8 EKLLSWKEFAKRKPLVLLGIRQCGKTFILTEFGKE 42
                                      5899*************************998666 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   2.6e-06     0.015      24      60 ..       8      44 ..       3      47 .] 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.6e-06
                              TniB 24 eeLleypkrkrmpnlllvGdsnnGKtmivekFarlhp 60
                                      e+Ll++ +  + + l+l+G  ++GKt i+ +F ++h+
  gi|474934347|ref|YP_007687929.1|  8 EKLLSWKEFAKRKPLVLLGIRQCGKTFILTEFGKEHH 44
                                      689999998888999******************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 295.04
//
Query:       gi|474934348|ref|YP_007687930.1|  [L=349]
Description: Dehydrogenases (flavoproteins) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-12   47.0   0.1    6.5e-11   42.1   0.1    2.3  1  FAD_binding_3   FAD binding domain
    2.2e-07   30.4   0.0      3e-07   30.0   0.0    1.1  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    3.6e-06   26.3   0.0     0.0011   18.0   0.0    2.4  2  Lycopene_cycl   Lycopene cyclase protein
      3e-05   23.4   0.1      6e-05   22.4   0.1    1.5  1  Thi4            Thi4 family
    0.00011   22.3   0.1     0.0003   20.9   0.0    1.8  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    0.00013   21.6   0.0       0.26   10.8   0.0    2.2  2  DAO             FAD dependent oxidoreductase
     0.0004   19.6   0.0    0.00053   19.2   0.0    1.2  1  GIDA            Glucose inhibited division protein A
     0.0012   18.0   0.0     0.0029   16.8   0.0    1.6  2  FAD_binding_2   FAD binding domain
  ------ inclusion threshold ------
      0.012   14.5   0.0        9.1    5.0   0.0    3.0  3  Trp_halogenase  Tryptophan halogenase
      0.016   13.9   0.0       0.16   10.6   0.1    2.0  2  HI0933_like     HI0933-like protein
      0.018   14.1   0.0        0.5    9.4   0.0    2.1  2  SE              Squalene epoxidase
      0.023   13.9   0.0       0.16   11.2   0.0    2.0  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
      0.064   12.6   0.0       0.09   12.1   0.0    1.1  1  FAD_oxidored    FAD dependent oxidoreductase


Domain annotation for each model (and alignments):
>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.1   4.7e-14   6.5e-11       1     172 [.       2     155 ..       2     169 .. 0.82

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 4.7e-14
                                       EEEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSS.S--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEE CS
                     FAD_binding_3   1 etdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlp.radglnqrtmellrqlGledrilaegapnelmgeal 76 
                                       e+dV+I+G+Gp+G  ++ +Ls+ G +vv++e+ + + +    +   ++ +   +r++G+ d+ +++    + + + +
  gi|474934348|ref|YP_007687930.1|   2 EADVAIIGSGPSGSAASFFLSKSGLKVVCIERLTGDRYRRyHSLCGECISRKGIRTVGIRDNEIRNR--IDSIYIDW 76 
                                       579*****************************998776666********************998888..44444555 PP

                                       EEECCCCCEEEEEHHCHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEE CS
                     FAD_binding_3  77 ynelsdtpkaradlelesspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetv 153
                                        ++    +  r+ ++        +++  ++++  L+ +a + g+ +  +  ++ + +++e     +r +  g   ++
  gi|474934348|ref|YP_007687930.1|  77 AGR----RTLRIGIK-------GYIIDRNMVLDRLRTEAHQNGAMFVNGSVLR-IIRNGER--YIIRLH--GGS-EI 136
                                       555....34455555.......67899****************9999998887.5555554..555555..444.79 PP

                                       EEEEEEE--GTT-HHHHHH CS
                     FAD_binding_3 154 rakYlvGaDGgrStvrktl 172
                                        +kY++GaDG+ S vr++l
  gi|474934348|ref|YP_007687930.1| 137 VSKYIIGADGAFSVVRRDL 155
                                       ****************987 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   2.2e-10     3e-07       2     111 ..       4     149 ..       3     177 .. 0.87

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 2.2e-10
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEE.......TTHCHHHCSHHHHCHHHHHHHHHHHHH.............. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxx.............. RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlve.......legtclnggcllskallgvaedaeias.............. 57 
                                       dv++iG+Gp G aa+ +l+++g+kv+++e       ++ + l g c+  k ++ v+ + ++++              
  gi|474934348|ref|YP_007687930.1|   4 DVAIIGSGPSGSAASFFLSKSGLKVVCIErltgdryRRYHSLCGECISRKGIRTVGIRDNEIRnridsiyidwagrr 80 
                                       8***************************9999999988999999***********999999999************* PP

                                       ...................HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE CS
                                       ...................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  58 ...................evvkklnqgielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssp 111
                                                            ++  ++g ++++g +v++i+++ +++ ++ +    + +i  ++++ A G+ +
  gi|474934348|ref|YP_007687930.1|  81 tlrigikgyiidrnmvldrLRTEAHQNGAMFVNG-SVLRIIRNGERYIIR-L--HGGSEIVSKYIIGADGAFS 149
                                       *****************98444556788999999.9****9888777772.3..4567999999999999844 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   8.3e-07    0.0011       1     145 [.       4     151 ..       4     164 .. 0.83
   2 !    5.8   0.0    0.0045       6.2     240     295 ..     223     276 ..     210     326 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 8.3e-07
                     Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnnyvWsdefedlga........leecvehsWsgtivyl 69 
                                       Dv++iG+Gp g +    l  +k glkvv+ie   +  +   ++ + e   +++         ++ +  +     +  
  gi|474934348|ref|YP_007687930.1|   4 DVAIIGSGPSGSAASFFL--SKSGLKVVCIERLTGDRYRRYHSLCGEC--ISRkgirtvgiRDNEIRNRIDSIYIDW 76 
                                       9**********9888888..**********976666444444554443..333334557767788888888999999 PP

                     Lycopene_cycl  70 ddgkkillgraYgrvsskrlkeellerlvengvklleakvesveeeeageslvvleggrkirarlvvdarglaslk 145
                                       ++ ++  +g +   + ++    +l  +  +ng+ ++++ v ++  + + +  + l+gg +i ++ ++ a g++s  
  gi|474934348|ref|YP_007687930.1|  77 AGRRTLRIGIKGYIIDRNMVLDRLRTEAHQNGAMFVNGSVLRIIRNGE-RYIIRLHGGSEIVSKYIIGADGAFSVV 151
                                       999999999888899****************************99988.88999*****************99876 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0045
                     Lycopene_cycl 240 qgviPvtlggslprleqkvlaiGaaaglvhPaTGYsvarslaeapllasaiaaalr 295
                                       + +iP+  gg    ++ + + iG a+ +v P T   +  +l  a ++++ +++   
  gi|474934348|ref|YP_007687930.1| 223 TRYIPI--GGLEHIVNGNAALIGDAGAMVNPLTFGGLRIALDSAAKMSECLVKGDL 276
                                       569***..9988888899999************88888888888877777766533 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.1   4.3e-08     6e-05      16      49 ..       1      33 [.       1      36 [. 0.95

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 4.3e-08
                                      TEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                              Thi4 16 aesDvvivGaGssGLtaayylakkpdlkvailer 49
                                      +e+Dv+i+G+G+sG +a++ l+k+ +lkv+ +er
  gi|474934348|ref|YP_007687930.1|  1 MEADVAIIGSGPSGSAASFFLSKS-GLKVVCIER 33
                                      699*********************.********8 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   2.2e-07    0.0003       1      27 [.       7      33 ..       7      42 .. 0.95

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.2e-07
                                      EE--SHHHHHHHHHHHCCTEEEEEE-S CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllek 27
                                      I+G+G sG++a  +L+k g++v+++e+
  gi|474934348|ref|YP_007687930.1|  7 IIGSGPSGSAASFFLSKSGLKVVCIER 33
                                      9************************98 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00019      0.26       1      28 [.       4      33 ..       4      36 .. 0.95
   2 !    8.9   0.0   0.00072      0.99     141     209 ..      89     154 ..      41     210 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00019
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEES CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllek 28
                                      dv+iiG+G  G+++ ++L++ g  V+ +e+
  gi|474934348|ref|YP_007687930.1|  4 DVAIIGSGPSGSAASFFLSKSGlkVVCIER 33
                                      9***********************999997 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00072
                                       EEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEE.EEEEEEEE--GGGHHHH..HT CS
                               DAO 141 gqvdpakltaalaraaealGveilegtevtgleeedgkvwgverttpgen.daadavVnaaGawsdll..gl 209
                                        ++d   ++  l+ +a ++G+ +++g  v ++ +++   + + r   g++ ++ ++++ a Ga+s  +  + 
  gi|474934348|ref|YP_007687930.1|  89 YIIDRNMVLDRLRTEAHQNGAMFVNG-SVLRIIRNG-ERYII-RLHGGSEiVS-KYIIGADGAFS--VvrRD 154
                                       4668889999****************.777764533.33555.3333555355.88******998..32322 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   3.8e-07   0.00053       1     152 [.       4     149 ..       4     185 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3.8e-07
                                       CEEEE-SSHHHHHHHHHHHHTT--EEEE........ES-GGGTT--SSSSEEE-TTHHHHHHHHHH.HT-SHHHHHH CS
                              GIDA   1 dviViGgGhAGceAAlaaarlGakvlLi........thkldtiaelsCnpsiggiakgllvrEida.lggliikaad 68 
                                       dv +iG G +G++A++ ++++G+kv+ i            + ++e  C    g   +g+  +Ei++ ++++ i +a 
  gi|474934348|ref|YP_007687930.1|   4 DVAIIGSGPSGSAASFFLSKSGLKVVCIerltgdryRRYHSLCGE--CISRKGIRTVGIRDNEIRNrIDSIYIDWAG 78 
                                       799*************************98887763333333333..55555555999******95388*******9 PP

                                       HHEEEEEEESTTS-CCC-EEEEEE-HHHHHHHHHHHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEE CS
                              GIDA  69 kagiqfrilNrskGpavralraqvdrelyskevteklenepnleiieeeveeliveekkvkgvvtedgetikakavv 145
                                       + ++  ri        +++    +dr+ +  +++ + ++ +    ++++v ++ +++++   ++++ g++i +k ++
  gi|474934348|ref|YP_007687930.1|  79 RRTL--RI-------GIKGY--IIDRNMVLDRLRTEAHQ-NGAMFVNGSVLRI-IRNGERYIIRLHGGSEIVSKYII 142
                                       9999..33.......34444..68999999999988777.6666778999999.55888899999999999999999 PP

                                       E--TT-B CS
                              GIDA 146 iatGtfl 152
                                        a G+f+
  gi|474934348|ref|YP_007687930.1| 143 GADGAFS 149
                                       9999986 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   2.1e-06    0.0029       1      32 [.       4      35 ..       4      65 .. 0.91
   2 ?   -2.3   0.0       1.3   1.8e+03     172     205 ..     108     154 ..      78     188 .. 0.58

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.1e-06
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSS CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeq 32
                                      Dv +iGsG +G aA+  +++ Glkv+++e   
  gi|474934348|ref|YP_007687930.1|  4 DVAIIGSGPSGSAASFFLSKSGLKVVCIERLT 35
                                      9***************************9865 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.3
                                       T..EEEEEEEEETTTTCEE........EEEESEEEE-----GG.... CS
                     FAD_binding_2 172 g..rvtGavvenpesgrev........rirakavvlatgGfgr...a 205
                                       g   v+G v++  ++g++         +i++k ++ a g+f+    +
  gi|474934348|ref|YP_007687930.1| 108 GamFVNGSVLRIIRNGERYiirlhggsEIVSKYIIGADGAFSVvrrD 154
                                       25556666666666666555555555566666666666666654443 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.015        21       1      32 [.       4      32 ..       4      41 .. 0.87
   2 ?    2.3   0.0     0.044        61     148     208 ..      88     146 ..      56     159 .. 0.83
   3 ?    5.0   0.0    0.0066       9.1     308     362 ..     229     278 ..     182     320 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.015
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlve 32
                                      ++ i+G G++G+ a   l+k +   l+v  +e
  gi|474934348|ref|YP_007687930.1|  4 DVAIIGSGPSGSAASFFLSKSG---LKVVCIE 32
                                      699****************998...7777777 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.044
                                       EEEE-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SG CS
                    Trp_halogenase 148 AyhldaalyakfLrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsG 208
                                       +y +d++ + + Lr+ a+++G   v+g v  +  + + ++ +l  + g e+    +i + G
  gi|474934348|ref|YP_007687930.1|  88 GYIIDRNMVLDRLRTEAHQNGAMFVNGSVLRIIRNGERYIIRL--HGGSEIVSKYIIGADG 146
                                       6899*************************88877777776544..5577777777776666 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.0066
                                       EEES-SEETTEEE-CCCTEE--CCCS-HHHHHHHHHHHHHHT--BTT--HHHHHH CS
                    Trp_halogenase 308 GrrkqawvknvvalGlasgfvePlestsihliqaalrrLlallpdksdepaaiae 362
                                       G  +++ + n  ++G+a + v+Pl   ++ ++  ++ ++ ++l ++       a+
  gi|474934348|ref|YP_007687930.1| 229 GGLEHIVNGNAALIGDAGAMVNPLTFGGLRIALDSAAKMSECLVKGDL-----AR 278
                                       556778899*******************************99987743.....33 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00012      0.16       2      31 ..       4      33 ..       3      37 .. 0.94
   2 ?    1.0   0.0       0.1   1.4e+02     111     167 ..      96     150 ..      92     163 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00012
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-S CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllek 31
                                      dv++iG G++G  a+  ++k g +V+ +e+
  gi|474934348|ref|YP_007687930.1|  4 DVAIIGSGPSGSAASFFLSKSGLKVVCIER 33
                                      89************************9997 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.1
                                       HHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS- CS
                       HI0933_like 111 ivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGlSi 167
                                       ++d l +e++++g    ++ +v ++ ++ ++ + +++++++e+ +++++ A G  S+
  gi|474934348|ref|YP_007687930.1|  96 VLDRLRTEAHQNGAM-FVNGSVLRIIRNGER-YIIRLHGGSEIVSKYIIGADGAFSV 150
                                       788888888887765.566778888675555.9999999************999987 PP

>> SE  Squalene epoxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.043        59       5      25 ..     141     161 ..     137     171 .. 0.78
   2 ?    9.4   0.0   0.00036       0.5     132     166 ..     239     273 ..     216     288 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.043
                                SE   5 tvvcDGifsklRkelsdnkve 25 
                                        + +DG fs +R++l   k++
  gi|474934348|ref|YP_007687930.1| 141 IIGADGAFSVVRRDLFGTKPK 161
                                       5789***********955554 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00036
                                SE 132 lillGDalnmRHPltggGmtvalnDivllskllkp 166
                                       + l+GDa  m  Plt gG+ +al  ++ +s+ l +
  gi|474934348|ref|YP_007687930.1| 239 AALIGDAGAMVNPLTFGGLRIALDSAAKMSECLVK 273
                                       569********************998888777755 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00012      0.16       2     136 ..       7     149 ..       6     168 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                       Pyr_redox_3   2 IiGaGPaGlaaaielkkagledylilEkgnignsiyrypk.emtfispsftsekleipdlnaiseets......... 68 
                                       IiG GP G aa   l k+gl +++ +E+   g+ ++ry       is +   + ++i d n i +            
  gi|474934348|ref|YP_007687930.1|   7 IIGSGPSGSAASFFLSKSGL-KVVCIERL-TGDRYRRYHSlCGECISRK-GIRTVGIRD-NEIRNRIDsiyidwagr 79 
                                       9*******************.7999*996.5777777765145666643.445556655.34433332244555555 PP

                       Pyr_redox_3  69 ..pafslkeeklsrkealeYlrevaksfelpiklfeeVesvkkedegfevetske.tyeAkkviiAtGefd 136
                                          ++ +k   + r+ +l+ lr+ a+++      + +V ++ +++e ++++   + ++ +k++i A G f+
  gi|474934348|ref|YP_007687930.1|  80 rtLRIGIKGYIIDRNMVLDRLRTEAHQNGA-MFVNGSVLRIIRNGERYIIRLHGGsEIVSKYIIGADGAFS 149
                                       444445556666677777777666555444.6667777777777777777777766777777777777776 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   6.5e-05      0.09       1      30 [.       4      33 ..       4      35 .. 0.96

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.5e-05
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLvee 30
                                      Dv ++G+gp+G aA     ++G kv+ +e+
  gi|474934348|ref|YP_007687930.1|  4 DVAIIGSGPSGSAASFFLSKSGLKVVCIER 33
                                      9*************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 2241.89
//
Query:       gi|474934349|ref|YP_007687931.1|  [L=285]
Description: hypothetical protein TALC_00775 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-14   54.8   0.0    2.7e-14   54.3   0.0    1.2  1  Trypsin_2     Trypsin-like peptidase domain
    0.00023   21.0   0.0    0.00049   20.0   0.0    1.5  1  Trypsin       Trypsin
  ------ inclusion threshold ------
      0.058   13.2   0.0       0.12   12.2   0.0    1.5  1  Peptidase_S3  Alphavirus core protein


Domain annotation for each model (and alignments):
>> Trypsin_2  Trypsin-like peptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3   0.0   4.5e-18   2.7e-14       2     150 .]      33     221 ..      32     221 .. 0.78

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 4.5e-18
                         Trypsin_2   2 sGflvgsdglilTnaHvvdsadgaavkaikkkveeagadgrevpakvvaadp........................e 54 
                                       + f+++s+g+  T+ Hv+ds ++ +   +++k +ea++ + ++p +++++dp                        +
  gi|474934349|ref|YP_007687931.1|  33 TMFIINSEGWAFTAGHVFDSFHKFQG--DQNKIKEAEEINAKRPDNPIQKDPkwitnhsfwfgqdgvrmskvyvnrQ 107
                                       569***********************..9999999999999999999999999999999999999999999999877 PP

                         Trypsin_2  55 lDlAllkvssderaglpplp....lgpsealkggepvyvvGyp........lggeksg.svssGivsgvve...... 112
                                        DlAllk+      g+ppl     +++ e++++g++++ +G+p        +     + + ++ i +gv +      
  gi|474934349|ref|YP_007687931.1| 108 VDLALLKL-----EGIPPLSnypvFRDPESIVPGTSLCRLGFPfvkaateyN-----EtTNAFTIKNGVLPlpffpn 174
                                       7*******.....5555555555588999999999*******9776644331.....03333333344444555577 PP

                         Trypsin_2 113 ........sesaasgegesfl.qtdaatspGsSGGplfdsdGrvvGl 150
                                               s+++++   e+f  +t+++   G+SGGp+fds+Gr+ ++
  gi|474934349|ref|YP_007687931.1| 175 dgihtrniSSGMSNDGLERFYvETSTPGLKGQSGGPIFDSRGRICAM 221
                                       7777776533333333333336*********************9887 PP

>> Trypsin  Trypsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   8.3e-08   0.00049      25     199 ..      30     229 ..       9     241 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 8.3e-08
                                       EEEEEEEEETT.EEEEEGGGTTTGGGEEE...EESE.SBTTSCTTTEEEEEEEE....EEEETTEBTTTT....... CS
                           Trypsin  25 hlCgGslisen.wvlTAaHCvsnasdvkv...vlge.hnlkksegkeqklkvek....vivhpnynpstl....... 85 
                                        +++ ++i+++ w  TA+H++++ ++++     ++e ++++ ++++    +++k    ++ h+ +  ++        
  gi|474934349|ref|YP_007687931.1|  30 AVATMFIINSEgWAFTAGHVFDSFHKFQGdqnKIKEaEEINAKRPD---NPIQKdpkwITNHSFWFGQDGvrmskvy 103
                                       456678888888***********44444421122222333333333...233332234666665555442599999* PP

                                       ...TTTEEEEEESSSSTSBSSBHCCBBCSTTHTTSTTTEEEEEESSB....SSTSS....BSSBEEEEEEEEEEHHH CS
                           Trypsin  86 ...dnDiallklkepvklgdtvrpiclpaassslpvgttclvsGwgr....tkekg....ksdtlqevevpvvsret 151
                                          + D+allkl+    + ++   ++ p+   s+ +gt+ +  G++     t+ ++    ++ +   + +p  +++ 
  gi|474934349|ref|YP_007687931.1| 104 vnrQVDLALLKLEGI-PPLSNYPVFRDPE---SIVPGTSLCRLGFPFvkaaTEYNEttnaFTIKNGVLPLPFFPNDG 176
                                       ***9**********7.6666777888888...568999999999988544422222452444444555567789997 PP

                                       HHHH.TTTTSTTTEEEEESTTSSSBCTTTTTTSEEEETTT....EEEEEEEEE CS
                           Trypsin 152 cksa.ykgkvtenmlcagakeggkdacqGDSGGPlvcsdg....elvGivswg 199
                                       + ++ ++  ++++ l   + e++    +G SGGP++ s g    +++G +s +
  gi|474934349|ref|YP_007687931.1| 177 IHTRnISSGMSNDGLERFYVETSTPGLKGQSGGPIFDSRGricaMQQGTNSIS 229
                                       77766666677777888888999999************999999999999876 PP

>> Peptidase_S3  Alphavirus core protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     2e-05      0.12      96     126 ..     193     224 ..     178     230 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2e-05
                                       EEEEETTS.--TT-TT-EEE-TTS-EEEEEEE CS
                      Peptidase_S3  96 rftiprgv.gkrgdsgrpildnkgrvvaivlg 126
                                       rf + + + g +g+sg pi+d +gr+ a+  g
  gi|474934349|ref|YP_007687931.1| 193 RFYVETSTpGLKGQSGGPIFDSRGRICAMQQG 224
                                       777766543889***************98766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1940.35
//
Query:       gi|474934350|ref|YP_007687932.1|  [L=151]
Description: hypothetical protein TALC_00776 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.52
# Mc/sec: 875.97
//
Query:       gi|474934351|ref|YP_007687933.1|  [L=64]
Description: hypothetical protein TALC_00777 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 435.65
//
Query:       gi|474934352|ref|YP_007687934.1|  [L=211]
Description: Sel1 repeat protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-17   62.6   3.5    1.7e-05   25.4   0.7    3.3  3  Sel1      Sel1 repeat
  ------ inclusion threshold ------
       0.12   12.3   0.1       0.36   10.7   0.2    1.9  2  DUF2024   Domain of unknown function (DUF2024)


Domain annotation for each model (and alignments):
>> Sel1  Sel1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0     2e-06     0.018       4      38 .]      11      43 ..       8      43 .. 0.91
   2 !   20.8   0.1   5.1e-08   0.00046       3      35 ..      46      76 ..      44      77 .. 0.91
   3 !   25.4   0.7   1.9e-09   1.7e-05       2      33 ..      81     110 ..      80     112 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2e-06
                              Sel1  4 myrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38
                                      my +G    y +G+g p++ e++ ++  +AAe+G+
  gi|474934352|ref|YP_007687934.1| 11 MYEVG--VSYITGTGRPQNSEEGAKYISMAAEKGY 43
                                      9****..556999999*****************96 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 5.1e-08
                              Sel1  3 AmyrLGmfylylnGlgvpkDpekAiewyekAAe 35
                                      A  +LG   lyl G gv++D+++A+  ++kAA+
  gi|474934352|ref|YP_007687934.1| 46 AIRDLG--VLYLSGNGVERDYRRAYDNLKKAAD 76
                                      6678**..778*********************7 PP

  == domain 3  score: 25.4 bits;  conditional E-value: 1.9e-09
                              Sel1   2 eAmyrLGmfylylnGlgvpkDpekAiewyekA 33 
                                        Amy L+  ++y+nGlgv+kD  +A++++  A
  gi|474934352|ref|YP_007687934.1|  81 NAMYHLA--LMYENGLGVEKDLYEALRLMGFA 110
                                       6******..777**************998655 PP

>> DUF2024  Domain of unknown function (DUF2024)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       0.6   5.4e+03      28      47 ..       7      26 ..       3      30 .. 0.80
   2 ?   10.7   0.2     4e-05      0.36      27      66 ..     167     206 ..     145     211 .] 0.83

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.6
                                      -HHHHHHHHHHHHHHHT--- CS
                           DUF2024 28 deekaleyakeyLkskgeee 47
                                      d e+++e + +y++++g  +
  gi|474934352|ref|YP_007687934.1|  7 DPEHMYEVGVSYITGTGRPQ 26
                                      67888999999999988765 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 4e-05
                                       --HHHHHHHHHHHHHHHT---S---TTTEEEEEEEE--HH CS
                           DUF2024  27 kdeekaleyakeyLkskgeeeakvtskeCkfCHseeaeee 66 
                                       kd   + +y    L s  ee+ +   +eC fCH ++++ +
  gi|474934352|ref|YP_007687934.1| 167 KDYYVVDTYQGPMLVSEDEEGYETPITECPFCHKKAVRVQ 206
                                       566677788889999999***************9988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1396.10
//
Query:       gi|474934353|ref|YP_007687935.1|  [L=301]
Description: TPR repeat protein, SEL1 subfamily [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-47  158.5  25.7    2.1e-10   40.9   0.2    7.1  7  Sel1      Sel1 repeat
  ------ inclusion threshold ------
      0.096   12.5   0.6          9    6.2   0.1    2.4  2  DUF1289   Protein of unknown function (DUF1289)
       0.69   10.5  10.2        3.1    8.4   1.6    4.5  5  TPR_19    Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> Sel1  Sel1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   1.0   8.6e-09   5.1e-05       1      38 []      36      71 ..      36      71 .. 0.91
   2 ?    0.7   0.0      0.17   9.9e+02      21      37 ..      89     106 ..      79     107 .. 0.76
   3 !   22.5   1.6   2.2e-08   0.00013       1      38 []     108     143 ..     108     143 .. 0.92
   4 !   25.5   0.1   2.5e-09   1.5e-05       2      38 .]     145     179 ..     144     179 .. 0.93
   5 !   40.9   0.2   3.5e-14   2.1e-10       3      38 .]     182     215 ..     180     215 .. 0.96
   6 !   30.4   0.1   7.4e-11   4.4e-07       2      37 ..     217     251 ..     216     252 .. 0.88
   7 !   27.9   0.1   4.5e-10   2.7e-06       2      38 .]     254     288 ..     253     288 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 8.6e-09
                              Sel1  1 aeAmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38
                                      ++ my+LG  y+yl+G   + D+ +++ ++ekAAe+G+
  gi|474934353|ref|YP_007687935.1| 36 PAGMYALG--YAYLFGVCKDIDKGRGYDLLEKAAEKGN 71
                                      578*****..******8777799*************97 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.17
                              Sel1  21 k.DpekAiewyekAAeqG 37 
                                         D ek++++ + AA+ G
  gi|474934353|ref|YP_007687935.1|  89 GlDTEKCVQYSKDAADEG 106
                                       34899*****99999987 PP

  == domain 3  score: 22.5 bits;  conditional E-value: 2.2e-08
                              Sel1   1 aeAmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                       ae +  +G   ++++G gv++Dp  A e ++kAA+qG+
  gi|474934353|ref|YP_007687935.1| 108 AEGQLYYG--VALMDGEGVEADPAAAAEMFRKAAMQGN 143
                                       57888999..888************************7 PP

  == domain 4  score: 25.5 bits;  conditional E-value: 2.5e-09
                              Sel1   2 eAmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                       eA + L+  y+yl+G gv++D  kA+  ++ AA++G+
  gi|474934353|ref|YP_007687935.1| 145 EARNSLA--YMYLEGNGVEQDTGKAFTMFRTAAKAGN 179
                                       677889*..999***********************97 PP

  == domain 5  score: 40.9 bits;  conditional E-value: 3.5e-14
                              Sel1   3 AmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                       ++y++G   +y++G+g +k + +A++wy+kAA+qGd
  gi|474934353|ref|YP_007687935.1| 182 SQYQMG--VCYETGTGCEKSYAEALRWYRKAADQGD 215
                                       8*****..999************************7 PP

  == domain 6  score: 30.4 bits;  conditional E-value: 7.4e-11
                              Sel1   2 eAmyrLGmfylylnGlg.vpkDpekAiewyekAAeqG 37 
                                       +A  r G   +y+nG+  +++Dp+k +ew+ +AA++G
  gi|474934353|ref|YP_007687935.1| 217 YAEDRIG--IMYYNGDStLKADPKKSFEWFLRAASNG 251
                                       678899*..666****87888**************98 PP

  == domain 7  score: 27.9 bits;  conditional E-value: 4.5e-10
                              Sel1   2 eAmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                       ++my +G++y   +G g +kD+++A++w+ +A ++G+
  gi|474934353|ref|YP_007687935.1| 254 DSMYSVGCYY--ADGFGCEKDISEARKWLNMAKDNGH 288
                                       79*****666..***********************98 PP

>> DUF1289  Protein of unknown function (DUF1289)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1    0.0066        39      17      36 ..     194     213 ..     183     220 .. 0.79
   2 ?    6.2   0.1    0.0015         9      18      36 ..     268     286 ..     267     297 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0066
                           DUF1289  17 lGCgRtldEiaaWssmsdee 36 
                                       +GC  +  E  +W +   ++
  gi|474934353|ref|YP_007687935.1| 194 TGCEKSYAEALRWYRKAADQ 213
                                       5************9876665 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0015
                           DUF1289  18 GCgRtldEiaaWssmsdee 36 
                                       GC   + E ++W +m ++ 
  gi|474934353|ref|YP_007687935.1| 268 GCEKDISEARKWLNMAKDN 286
                                       9**************9875 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.13     8e+02      13      33 ..      62      80 ..      59      84 .. 0.81
   2 ?    8.4   1.6   0.00051       3.1       6      40 ..     127     159 ..     117     162 .. 0.84
   3 ?   -0.5   0.0       0.3   1.8e+03       4      35 ..     161     190 ..     161     192 .. 0.82
   4 ?    2.5   0.1     0.035   2.1e+02       5      24 ..     198     217 ..     197     225 .. 0.78
   5 ?   -0.7   0.0      0.34   2.1e+03      40      54 ..     272     286 ..     270     300 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.13
                            TPR_19 13 lleqalqedpknaearllLAe 33
                                      lle+a  ++ +n+ea+ lL++
  gi|474934353|ref|YP_007687935.1| 62 LLEKA--AEKGNPEAKVLLVR 80
                                      67886..6779*****99987 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00051
                            TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgq 40 
                                       d+a+A++++++a  +  +n+ear  LA  +l+ + 
  gi|474934353|ref|YP_007687935.1| 127 DPAAAAEMFRKA--AMQGNQEARNSLAYMYLEGNG 159
                                       9**********8..6779************98775 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.3
                            TPR_19   4 egdyaeAlalleqalqedpknaearllLAeal 35 
                                       e+d   A  +++ a  ++++n + ++++  ++
  gi|474934353|ref|YP_007687935.1| 161 EQDTGKAFTMFRTA--AKAGNVNSQYQMGVCY 190
                                       57888888888887..6779999999999998 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.035
                            TPR_19   5 gdyaeAlalleqalqedpkn 24 
                                       + yaeAl+ +++a ++   +
  gi|474934353|ref|YP_007687935.1| 198 KSYAEALRWYRKAADQGDAY 217
                                       68**********97665444 PP

  == domain 5  score: -0.7 bits;  conditional E-value: 0.34
                            TPR_19  40 qldeAealLdalpee 54 
                                       ++ eA++ L+ + + 
  gi|474934353|ref|YP_007687935.1| 272 DISEARKWLNMAKDN 286
                                       567777777776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1912.50
//
Query:       gi|474934354|ref|YP_007687936.1|  [L=233]
Description: Protein of unknown function DUF45 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    0.00018   21.7   0.0    0.00027   21.0   0.0    1.3  1  DUF45      Protein of unknown function DUF45
  ------ inclusion threshold ------
       0.01   15.7   0.0      0.018   14.9   0.0    1.4  1  SprT-like  SprT-like family


Domain annotation for each model (and alignments):
>> DUF45  Protein of unknown function DUF45
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0     3e-08   0.00027     134     205 ..     144     224 ..     134     226 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3e-08
                             DUF45 134 vsikdmktrWGscss.kgkirlnwrL..vkappevidYVvvHElaHlle.......knHskrFwalvekllPdwkea 200
                                       +++k   tr G+cs+  + +  +  L    ++++ +dYVv HE++Hl++       + H ++F ++++k+ P+ kea
  gi|474934354|ref|YP_007687936.1| 144 WTVKPNYTRLGYCSPlMRVVAVSSALdrPDISEHALDYVVYHECMHLRQgyrpfdrRPHDAAFHREMAKF-PGLKEA 219
                                       6677777777778441455556666622357899*************97554444478*********996.999999 PP

                             DUF45 201 kkeLk 205
                                       +ke +
  gi|474934354|ref|YP_007687936.1| 220 EKEIN 224
                                       98877 PP

>> SprT-like  SprT-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   2.1e-06     0.018      58     102 ..     172     216 ..     122     226 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.1e-06
                         SprT-like  58 s.rsedrllntLaHElcHlalfvisgvrnnpHGaeFkawaakveka 102
                                          se++l  ++ HE+ Hl    ++  +++pH+a F++ +ak   +
  gi|474934354|ref|YP_007687936.1| 172 PdISEHALDYVVYHECMHLRQG-YRPFDRRPHDAAFHREMAKFPGL 216
                                       4457899************993.34446************997554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1513.39
//
Query:       gi|474934355|ref|YP_007687937.1|  [L=381]
Description: putative oxidoreductases of the aldo/keto reductase family [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-26   92.5   0.0    3.9e-25   88.6   0.0    2.1  1  Aldo_ket_red  Aldo/keto reductase family
    3.3e-08   33.5   7.1    1.1e-07   31.9   7.1    1.9  1  Fer4_9        4Fe-4S dicluster domain
      1e-07   32.4   6.7    2.2e-07   31.3   6.7    1.6  1  Fer4_17       4Fe-4S dicluster domain
    1.2e-06   28.6   5.7    0.00035   20.6   1.0    2.6  2  Fer4_10       4Fe-4S dicluster domain
    2.4e-06   28.0   7.5      1e-05   26.0   7.5    2.1  1  Fer4_7        4Fe-4S dicluster domain
      8e-06   26.0   3.9      0.045   13.9   0.3    2.4  2  Fer4_18       4Fe-4S dicluster domain
    2.6e-05   23.8  13.3    0.00018   21.2   3.1    2.5  2  Fer4          4Fe-4S binding domain
    4.2e-05   23.4  16.6    0.00044   20.2   5.2    2.7  2  Fer4_6        4Fe-4S binding domain
     0.0012   19.2  11.3     0.0065   16.9  11.2    2.1  2  Fer4_8        4Fe-4S dicluster domain
     0.0051   17.6   5.1       0.06   14.2   0.3    2.7  2  Fer4_22       4Fe-4S dicluster domain
      0.007   16.8   6.1      0.007   16.8   6.1    3.1  3  Fer4_4        4Fe-4S binding domain
  ------ inclusion threshold ------
       0.01   15.9   5.5       0.01   15.9   5.5    2.7  2  Fer4_2        4Fe-4S binding domain
      0.024   14.8  13.8        1.8    8.8  14.5    2.4  2  Fer4_21       4Fe-4S dicluster domain
      0.025   15.5  11.2      0.041   14.8   1.4    2.5  2  Fer4_16       4Fe-4S double cluster binding domain
      0.049   13.4   9.1        1.7    8.5   2.9    2.5  2  Fer4_20       Dihydroprymidine dehydrogenase domain II, 4Fe-4
          3    9.0  18.0       0.36   11.9   5.0    2.8  2  Fer4_3        4Fe-4S binding domain
        7.7    7.2   9.7        3.1    8.4   1.1    2.8  2  Fer4_13       4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> Aldo_ket_red  Aldo/keto reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.6   0.0   3.7e-28   3.9e-25       4     198 ..      16     215 ..      13     287 .. 0.81

  Alignments for each domain:
  == domain 1  score: 88.6 bits;  conditional E-value: 3.7e-28
                                       EE-SSS-ST.....TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE--SSST CS
                      Aldo_ket_red   4 lGtwqlgsk....eeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKvdlrdae 76 
                                       +G ++l       ++ ++e+  el+++a+e+Gin++DtA+ Y+ g se+++Geal++   +r+++ +a K +++d +
  gi|474934355|ref|YP_007687937.1|  16 FGCMRLPCIcgddSKPDPEKTKELVKYAMEHGINYYDTAWGYHAGNSETVIGEALSA--YPRDSFYLADKFPGYDVS 90 
                                       56666554344457889999*************************************..************444444 PP

                                       TSSSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-......HHHHHHHHHHHHHTTSEEEEEEES--.HHHHH CS
                      Aldo_ket_red  77 iksglskeniresleeslkrLgtdyvDllllHrpdpslp.....sieevldaleelvkeGkiraiGvSnfs.veqle 147
                                       +++       +e +e++lk+++tdy+D +l+H++              + d++++ vk G i+++G+S +   + l 
  gi|474934355|ref|YP_007687937.1|  91 NMP-----KAEEIFEQQLKKCRTDYFDFYLIHNVCELNIrqyldPQFGIKDYFVKQVKNGRIKHLGFSVHGeMDCLN 162
                                       444.....5799********************98544434433244455599999999**********999777777 PP

                                       HH..HHTTT--EEEEE-B-BTT-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTG CS
                      Aldo_ket_red 148 ka..kkkkkvkivavqveynllreleeegllelckkkgvpliaysplggGllt 198
                                       +        +++  +q++y +++ +++++ +e + ++g+p+ +++pl gG l 
  gi|474934355|ref|YP_007687937.1| 163 AFleVYGDAMEFCQIQINYFDWNFQHAKEKVERVSELGIPVWVMEPLRGGKLA 215
                                       6699999999************999999999*******************998 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   7.1     1e-10   1.1e-07       2      49 ..     297     361 ..     296     363 .. 0.88

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 1e-10
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase.................eaCigCgaCveaCpkg 49 
                                       Ct+C++Cv+ C++++ ++   +r++++  ++                  +aC+gC++C+++Cp++
  gi|474934355|ref|YP_007687937.1| 297 CTSCRYCVTHCQKNLDIPLLIARYNQHLVTEVdfitpmamggtpkeqwpDACVGCRKCEKVCPQQ 361
                                       ***********9999988888888887666558888999999999999999*************9 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   6.7   2.1e-10   2.2e-07       2      60 ..     297     362 ..     296     363 .. 0.80

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 2.1e-10
                           Fer4_17   2 CiqCgyClpeCpsyea....ydnepkkllraakl...glleeaekeekaslCieCgeCerkCPqgl 60 
                                       C++C+yC+ +C  + +    +  +++ l+ ++ +     ++++ ke+  + C++C++Ce++CPq++
  gi|474934355|ref|YP_007687937.1| 297 CTSCRYCVTHCQKNLDipllIARYNQHLVTEVDFitpMAMGGTPKEQWPDACVGCRKCEKVCPQQI 362
                                       *************999454444478888888877665456666777899***************97 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.3   0.00095         1       8      19 ..     296     307 ..     284     329 .. 0.77
   2 !   20.6   1.0   3.3e-07   0.00035       6      23 ..     345     362 ..     341     378 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00095
                           Fer4_10   8 tCirCgkCvkaC 19 
                                        C+ C+ Cv+ C
  gi|474934355|ref|YP_007687937.1| 296 PCTSCRYCVTHC 307
                                       366666666666 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 3.3e-07
                           Fer4_10   6 ddtCirCgkCvkaCPadl 23 
                                       +d C++C+kC k+CP+++
  gi|474934355|ref|YP_007687937.1| 345 PDACVGCRKCEKVCPQQI 362
                                       699*************54 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   7.5   9.7e-09     1e-05       2      51 ..     297     361 ..     296     362 .. 0.62

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 9.7e-09
                            Fer4_7   2 CigCgaCvaaC.............pvkaieldeeenek..............gtekveid.pekClgCgaCvavCPt 50 
                                       C+ C++Cv  C                          +              g  +++ + p+ C+gC++C++vCP 
  gi|474934355|ref|YP_007687937.1| 297 CTSCRYCVTHCqknldiplliaryN------------QhlvtevdfitpmamG-GTPKEQwPDACVGCRKCEKVCPQ 360
                                       ***********66666644444331............1122223333333321.45555559**************8 PP

                            Fer4_7  51 g 51 
                                       +
  gi|474934355|ref|YP_007687937.1| 361 Q 361
                                       7 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.3   4.3e-05     0.045      21      77 ..     257     313 ..     249     316 .. 0.81
   2 !   12.7   0.3   0.00011      0.11      58      79 ..     345     366 ..     332     371 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.3e-05
                           Fer4_18  21 deetllvvydakrGekiagrkkekkalkekeerkekgagdcidcescvkvcPtgidi 77 
                                       d e  +v  d    ek    k+ ++ ++  +e +++g+  c++c++cv+ c  ++di
  gi|474934355|ref|YP_007687937.1| 257 DFEQQKVKIDCYGEEKPLTGKEFETIVRIGDEMAASGTVPCTSCRYCVTHCQKNLDI 313
                                       55666666666666666777777888888999999********************98 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00011
                           Fer4_18  58 agdcidcescvkvcPtgidirk 79 
                                          c+ c++c kvcP +i i +
  gi|474934355|ref|YP_007687937.1| 345 PDACVGCRKCEKVCPQQIKISE 366
                                       467***************9976 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   2.6    0.0032       3.4       8      19 ..     297     308 ..     296     310 .. 0.91
   2 !   21.2   3.1   1.7e-07   0.00018       5      20 ..     345     360 ..     342     363 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0032
                                       SSS-THHHHHST CS
                              Fer4   8 CigCGaCvevCP 19 
                                       C+ C +Cv  C 
  gi|474934355|ref|YP_007687937.1| 297 CTSCRYCVTHCQ 308
                                       ***********6 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 1.7e-07
                                       TTTSSS-THHHHHSTT CS
                              Fer4   5 eekCigCGaCvevCPv 20 
                                       ++ C+gC +C++vCP 
  gi|474934355|ref|YP_007687937.1| 345 PDACVGCRKCEKVCPQ 360
                                       89*************7 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   3.5    0.0029         3       8      19 ..     296     307 ..     295     310 .. 0.94
   2 !   20.2   5.2   4.1e-07   0.00044       6      22 ..     345     361 ..     345     362 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0029
                            Fer4_6   8 kCigCgdCvrvC 19 
                                       +C++C+ Cv++C
  gi|474934355|ref|YP_007687937.1| 296 PCTSCRYCVTHC 307
                                       6*********** PP

  == domain 2  score: 20.2 bits;  conditional E-value: 4.1e-07
                            Fer4_6   6 pdkCigCgdCvrvCPeg 22 
                                       pd+C+gC++C++vCP +
  gi|474934355|ref|YP_007687937.1| 345 PDACVGCRKCEKVCPQQ 361
                                       79*************66 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   3.6    0.0081       8.5      45      64 ..     291     310 ..     259     313 .. 0.77
   2 !   16.9  11.2   6.1e-06    0.0065       5      65 .]     297     362 ..     294     362 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0081
                            Fer4_8  45 eealwsCttcgaCtevCpvg 64 
                                       + +   Ct+c+ C++ C ++
  gi|474934355|ref|YP_007687937.1| 291 ASGTVPCTSCRYCVTHCQKN 310
                                       667778***********987 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 6.1e-06
                            Fer4_8   5 CieCgaCqsaC......pvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvgi 65 
                                       C+ C +C ++C      p+l ++ + +l ++ + +       ++ +e+  ++C++c++C++vCp++i
  gi|474934355|ref|YP_007687937.1| 297 CTSCRYCVTHCqknldiPLLIARYNQHLVTEVDFIT-PMAMGGTPKEQWPDACVGCRKCEKVCPQQI 362
                                       ***********6666666666666666666666666.34444444478899*************986 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.7     0.048        50      70      95 ..     285     310 ..     255     311 .. 0.81
   2 !   14.2   0.3   5.7e-05      0.06      80      96 .]     346     362 ..     320     362 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.048
                           Fer4_22  70 lsefkekfgesgCvGCgRCieacpvk 95 
                                       + + ++  g+  C+ C  C+++c+++
  gi|474934355|ref|YP_007687937.1| 285 IGDEMAASGTVPCTSCRYCVTHCQKN 310
                                       55556667889999999999999986 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 5.7e-05
                           Fer4_22  80 sgCvGCgRCieacpvki 96 
                                        +CvGC +C+++cp++i
  gi|474934355|ref|YP_007687937.1| 346 DACVGCRKCEKVCPQQI 362
                                       68************987 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       6.2   6.6e+03       5       9 ..      16      20 ..      12      24 .. 0.69
   2 ?    2.9   3.8      0.19     2e+02       4      14 ..     297     307 ..     292     310 .. 0.91
   3 !   16.8   6.1   6.6e-06     0.007       1      17 []     345     361 ..     345     361 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 6.2
                            Fer4_4  5 igCgs 9 
                                      +gC++
  gi|474934355|ref|YP_007687937.1| 16 FGCMR 20
                                      89997 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.19
                            Fer4_4   4 CigCgsCvaaC 14 
                                       C+ C+ Cv  C
  gi|474934355|ref|YP_007687937.1| 297 CTSCRYCVTHC 307
                                       ********999 PP

  == domain 3  score: 16.8 bits;  conditional E-value: 6.6e-06
                            Fer4_4   1 qerCigCgsCvaaCPqg 17 
                                       ++ C+gC++C+ +CPq+
  gi|474934355|ref|YP_007687937.1| 345 PDACVGCRKCEKVCPQQ 361
                                       689************96 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   5.7     0.051        53      10      20 ..     297     307 ..     295     308 .. 0.95
   2 ?   15.9   5.5   9.5e-06      0.01       7      22 .]     345     360 ..     345     360 .. 0.94

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.051
                            Fer4_2  10 CigCgaCvsaC 20 
                                       C++C+ Cv+ C
  gi|474934355|ref|YP_007687937.1| 297 CTSCRYCVTHC 307
                                       *********99 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 9.5e-06
                            Fer4_2   7 tdrCigCgaCvsaCPa 22 
                                       +d+C+gC++C ++CP+
  gi|474934355|ref|YP_007687937.1| 345 PDACVGCRKCEKVCPQ 360
                                       699************6 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   2.9     0.057        61      31      51 ..     287     307 ..     277     313 .. 0.70
   2 ?    8.8  14.5    0.0017       1.8       8      53 ..     297     360 ..     294     365 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.057
                           Fer4_21  31 ktvlkvvedeCvGCnlCssvC 51 
                                       +++++  +  C+ C  C++ C
  gi|474934355|ref|YP_007687937.1| 287 DEMAASGTVPCTSCRYCVTHC 307
                                       555556666788888888887 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0017
                           Fer4_21   8 CigCgkCliaCedtshqaieidaktvl..................kvvedeCvGCnlCssvCPv 53 
                                       C +C  C++ C+++    + i+  +++                  +   d CvGC  C +vCP 
  gi|474934355|ref|YP_007687937.1| 297 CTSCRYCVTHCQKNLDIPLLIARYNQHlvtevdfitpmamggtpkEQWPDACVGCRKCEKVCPQ 360
                                       9999999999998665545333332222556666777777777656678**************4 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   2.6     0.048        51       2      14 ..     297     309 ..     296     315 .. 0.87
   2 ?   14.8   1.4   3.9e-05     0.041       2      16 ..     348     362 ..     340     373 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.048
                           Fer4_16   2 CgtCgkCaevCPt 14 
                                       C++C+ C+  C  
  gi|474934355|ref|YP_007687937.1| 297 CTSCRYCVTHCQK 309
                                       9********9965 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 3.9e-05
                           Fer4_16   2 CgtCgkCaevCPtna 16 
                                       C++C+kC +vCP++ 
  gi|474934355|ref|YP_007687937.1| 348 CVGCRKCEKVCPQQI 362
                                       888999999998875 PP

>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.4    0.0022       2.4      13      52 ..     286     323 ..     276     332 .. 0.80
   2 ?    8.5   2.9    0.0016       1.7      23      50 ..     347     372 ..     334     377 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0022
                                       -HHHHHHHHTT----TT-HHHHCSTT---HHHHHHHHHTT CS
                           Fer4_20  13 teeealeeAsRClqCkkapcvkgCPveidipefikkiaeg 52 
                                        +e+a++    C +C  ++cv++C  ++dip  i + +++
  gi|474934355|ref|YP_007687937.1| 286 GDEMAASGTVPCTSC--RYCVTHCQKNLDIPLLIARYNQH 323
                                       56777788888999*..89************999877665 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0016
                                       T----TT-HHHHCSTT---HHHHHHHHH CS
                           Fer4_20  23 RClqCkkapcvkgCPveidipefikkia 50 
                                        C+ C  ++c+k CP +i+i e +kk +
  gi|474934355|ref|YP_007687937.1| 347 ACVGC--RKCEKVCPQQIKISEIMKKFS 372
                                       59999..89************9999865 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   5.1      0.46   4.8e+02       1      14 [.     297     310 ..     297     310 .. 0.91
   2 ?   11.9   5.0   0.00034      0.36       1      13 [.     348     360 ..     348     362 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.46
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       Ct C+ Cv  C ++
  gi|474934355|ref|YP_007687937.1| 297 CTSCRYCVTHCQKN 310
                                       ****99*****875 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00034
                            Fer4_3   1 CtgCgaCvevCPv 13 
                                       C+gC+ C++vCP 
  gi|474934355|ref|YP_007687937.1| 348 CVGCRKCEKVCPQ 360
                                       ************5 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   2.0      0.25   2.7e+02       6      18 ..     297     309 ..     295     313 .. 0.86
   2 ?    8.4   1.1     0.003       3.1       4      18 ..     346     360 ..     345     371 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.25
                           Fer4_13   6 CiacgaCvelaPd 18 
                                       C++c  Cv  + +
  gi|474934355|ref|YP_007687937.1| 297 CTSCRYCVTHCQK 309
                                       ********99965 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.003
                           Fer4_13   4 dtCiacgaCvelaPd 18 
                                       d C++c +C +++P+
  gi|474934355|ref|YP_007687937.1| 346 DACVGCRKCEKVCPQ 360
                                       78************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 2583.11
//
Query:       gi|474934356|ref|YP_007687938.1|  [L=573]
Description: Fe-S oxidoreductase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   5.6e-111  370.5   0.0   7.4e-111  370.2   0.0    1.1  1  Radical_SAM_N  Radical SAM N-terminal
    3.7e-13   50.2   0.4    7.4e-13   49.2   0.4    1.5  1  Radical_SAM    Radical SAM superfamily
      3e-06   27.6   0.4    4.8e-06   27.0   0.4    1.3  1  DUF3362        Domain of unknown function (DUF3362)
  ------ inclusion threshold ------
      0.096   12.3   0.0       0.19   11.4   0.0    1.4  1  RecG_wedge     RecG wedge domain


Domain annotation for each model (and alignments):
>> Radical_SAM_N  Radical SAM N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  370.2   0.0  1.6e-114  7.4e-111       1     298 []       2     293 ..       2     293 .. 0.98

  Alignments for each domain:
  == domain 1  score: 370.2 bits;  conditional E-value: 1.6e-114
                     Radical_SAM_N   1 flpvsrkemeergwdelDvilvsgDaYvDhpsfgaaligrlLeaeGfrvgiiaqPdwksaedfkklGkPrlffgvsa 77 
                                       f+p++++em+e+gwd+lD+ilvsgD+Y+D+p  gaa+ig++L ++Gfrvgii+qP  ++a+d+++lG Prlf+ v+a
  gi|474934356|ref|YP_007687938.1|   2 FIPTTKEEMKEKGWDSLDIILVSGDTYIDSPYNGAAMIGHYLIDRGFRVGIICQPVTDDASDISRLGSPRLFWSVTA 78 
                                       99*************************************************************************** PP

                     Radical_SAM_N  78 GnlDsmvnkytaekklrsdDaytpggkagkRPdravivYsnlireaykdvpvvlGgiEaSLRriahYDywsdkvrrs 154
                                       G++Dsmv++yt + k r+dD++tpgg +++RPdra+i Ysnli++++k+ p+vlGgiEaSLRr+ hYD wsd++rrs
  gi|474934356|ref|YP_007687938.1|  79 GCVDSMVANYTPTGKFRKDDDFTPGGVNDRRPDRACIAYSNLIKRFCKGKPIVLGGIEASLRRVVHYDAWSDSLRRS 155
                                       ***************************************************************************** PP

                     Radical_SAM_N 155 illdskadllvyGmgeraiveiakrlakgeeveelkdirgtavllkkeakakekevielpsyeevkedkklyaeafr 231
                                       +++d+kad ++yGm+e + +e+a+ +a+g++   ++++rg++++ k    + ++ ++e+psyee+ +d+k++ +afr
  gi|474934356|ref|YP_007687938.1| 156 VIFDAKADAITYGMAELSNLELARCMAEGRD---WHSVRGICYIGK----EVPEGYLEIPSYEECLSDPKEFSRAFR 225
                                       *****************************99...889******666....34578********************** PP

                     Radical_SAM_N 232 lleeetnplnakalvqkhgdravvlnppalplsteelDevyelpyarkahpsy.kkkkipalemikfS 298
                                        ++e+ +p++a  l+q+hgdr++v+npp++ l+ eelD+vy   y+ ++hp y k++ ++a+++ik S
  gi|474934356|ref|YP_007687938.1| 226 GFYENCDPVTAVGLAQRHGDRYMVQNPPQRLLTPEELDSVYMSGYEYAVHPFYaKDGPVKAMDTIKNS 293
                                       *****************************************************7788*********87 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.4   1.6e-16   7.4e-13       2     166 ..     295     502 ..     294     503 .. 0.79

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 1.6e-16
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGS...............TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx...............xx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggeplly...............pd 62 
                                       +  rgC + CsfCa+  +  +++++ s++ ++i++e++++ + +g  + +  +gg p+++               + 
  gi|474934356|ref|YP_007687938.1| 295 TSHRGCYGECSFCAIAVH--QGRTVVSRTADSIVKEAERITKLPGfNGIIYDVGG-PTADmwgfeckkklrdgacR- 367
                                       6779************97..********************988886666667777.99976665555555555551. PP

                                       HHHHHHHHHHTC............................CCTEEEEEEECSSCHG.........HHHHHHHHHTT. CS
                                       xxxxxxxxxxxx............................xxxxxxxxxxxxxxxx.........xxxxxxxxxxx. RF
                       Radical_SAM  63 fvellerlakla............................vpgiritvetngtlpd.........eeklerllelg. 101
                                                  +                            vpg++ +++t+g++ d         +++++ +++ + 
  gi|474934356|ref|YP_007687938.1| 368 -----------DrkclyprpcrllpidhgcqidllnrissVPGVKKVFVTSGIRYDmvvfddghgRDYVDCIVKDHv 433
                                       ...........055555555555566666667777777789************************999999999778 PP

                                       -SEEEEEEBSSSHHHHHHHHTCTSHH.......HHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 102 vdrvslgleaaddekvlklmnrghtf.......eevlealeklreagikrvvdrivglpGendeeleellel 166
                                         ++ +  e+++ e vl lm+ ++++       + + ++ +++ ++++  ++++i  +pG   + +eel ++
  gi|474934356|ref|YP_007687938.1| 434 SGQLKIAPEHVNRE-VLALMG-KPEPnvlldfkDMFDKSNRRFGKRQFL-TYYFIAAHPGCGNRSMEELSHF 502
                                       99************.*****6.455545766666666666666666666.**********999999998766 PP

>> DUF3362  Domain of unknown function (DUF3362)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.4   1.1e-09   4.8e-06       1      42 [.     512     553 ..     512     559 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 1.1e-09
                           DUF3362   1 dqVqtFyPsPmatattmYhtgknpltkvkreeesvdvvrgek 42 
                                       +qVq F P+P++++t mY+t+++   + +  +e+v   ++++
  gi|474934356|ref|YP_007687938.1| 512 EQVQIFTPTPSTVSTLMYYTRRDYADRRNVWSEHVPQLKQKQ 553
                                       7**********************9996666688887766654 PP

>> RecG_wedge  RecG wedge domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   4.2e-05      0.19      22      52 ..     522     554 ..     518     566 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.2e-05
                        RecG_wedge  22 etiedllyyfPrdyedrrkiv..piseikedek 52 
                                       +t+  l+yy  rdy drr++    + ++k+++k
  gi|474934356|ref|YP_007687938.1| 522 STVSTLMYYTRRDYADRRNVWseHVPQLKQKQK 554
                                       58999**************96224666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (573 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.51
# Mc/sec: 3354.81
//
Query:       gi|474934357|ref|YP_007687939.1|  [L=164]
Description: Acetyltransferase (GNAT) family [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-14   53.3   0.1    3.3e-14   53.1   0.1    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    7.5e-12   45.3   0.2    1.1e-11   44.8   0.2    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    6.9e-08   32.8   0.4    8.9e-08   32.5   0.4    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    4.3e-05   23.4   0.0    6.5e-05   22.8   0.0    1.2  1  FR47             FR47-like protein
    0.00011   22.3   0.1    0.00014   22.0   0.1    1.2  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    0.00083   20.0   0.1    0.00099   19.8   0.1    1.2  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.027   14.2   0.0       0.09   12.5   0.0    1.8  2  Acetyltransf_8   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.1   0.1   1.3e-17   3.3e-14      28     117 .]      52     139 ..      12     139 .. 0.82

  Alignments for each domain:
  == domain 1  score: 53.1 bits;  conditional E-value: 1.3e-17
                                       HHSTTC.EEEE.EEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEE CS
                    Acetyltransf_1  28 fsleae.gllv.aeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlave 102
                                       + + ++ +l+  a ++g+ iG+ +l++  +     ++i  ++ ++++r+kG GsaL + ++++ re+g+ + +l+v 
  gi|474934357|ref|YP_007687939.1|  52 LKDMEDgFLYGfAFDGGKKIGYFCLRIEGE----SMFISKCYLHRDARHKGFGSALQQFMIQYGREHGCSRAYLHVN 124
                                       2333442566688999************99....8**********************************888***** PP

                                       TTEHHHHHHHHHTTE CS
                    Acetyltransf_1 103 edndaairlYeklGF 117
                                       + n+ air Y++ GF
  gi|474934357|ref|YP_007687939.1| 125 VRNVDAIRSYKRNGF 139
                                       **********88*99 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   0.2   4.3e-15   1.1e-11       7     117 ..      36     150 ..      32     154 .. 0.85

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 4.3e-15
                   Acetyltransf_10   7 eegietfkefispealrerieegealllvaeeggkivGvielrdgs...hisllfVdpeyrgqGigkaLleaveeea 80 
                                       ee++  f++  s++a+ + + e   l+  a++ggk +G+  lr ++    is ++ ++++r++G g+aL ++++++ 
  gi|474934357|ref|YP_007687939.1|  36 EEAMYLFNTWQSKDAVLKDM-EDGFLYGFAFDGGKKIGYFCLRIEGesmFISKCYLHRDARHKGFGSALQQFMIQYG 111
                                       66777787777788888888.7778888999********9663333356**************************** PP

                   Acetyltransf_10  81 ekdgikl.eltvnasp.yavpfYeklGFkavgeeqeenG 117
                                       +++g +   l+vn  +  a++ Y++ GF+ +  e ++ G
  gi|474934357|ref|YP_007687939.1| 112 REHGCSRaYLHVNVRNvDAIRSYKRNGFQITLHEVTDRG 150
                                       *****************************9966666665 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.4   3.5e-11   8.9e-08       8      75 ..      64     140 ..      37     141 .. 0.78

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 3.5e-11
                                       EEETTEEEEEEEEEEES..TCTEEEEE-GGGTTSSHHHHHHHH.TT....SEEE.EE.EEEETHHHHHHHHHHTTEE CS
                    Acetyltransf_7   8 aeddgkivGfialslld..aeitrlaVdpeyrgkGiGraLlea.ae....kgii.le.qlelnaekaikfYeklGFe 75 
                                       a d+gk +G+ +l +++    i + + + ++r kG G+aL ++ ++    +g+   + ++++++  ai+ Y+++GF+
  gi|474934357|ref|YP_007687939.1|  64 AFDGGKKIGYFCLRIEGesMFISKCYLHRDARHKGFGSALQQFmIQygreHGCSrAYlHVNVRNVDAIRSYKRNGFQ 140
                                       77889*****99999987777777999*************99851244457876312333333348**********8 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   2.6e-08   6.5e-05      22      82 ..      83     144 ..      67     147 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 2.6e-08
                                       SSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-.S-EEEEEETT-HHHHHHHHHHT-EEEEE CS
                              FR47  22 gelgalqvlpehrrrGlgsrlvkalakeiaerg.ktvllvvvasNtpsirlyeklGfekiee 82 
                                        +++  +++ ++r +G+gs l + +++  +e g   + l+v+  N  +ir y++ Gf+   +
  gi|474934357|ref|YP_007687939.1|  83 MFISKCYLHRDARHKGFGSALQQFMIQYGREHGcSRAYLHVNVRNVDAIRSYKRNGFQITLH 144
                                       5788999************************8846799*******************98765 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.1   5.5e-08   0.00014      41     139 ..      52     144 ..      31     160 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 5.5e-08
                    Acetyltransf_4  41 lealdsekeyvflvae.sdrivGyaylgqfkkrakdwkaelsvylaerdnnkeglgrelidaleqvlkeqnienlla 116
                                       l+++  e  ++++ a   ++ +Gy+ l+ ++    +   + + yl +rd++++g g++l ++++q+ +e +  + + 
  gi|474934357|ref|YP_007687939.1|  52 LKDM--EDGFLYGFAFdGGKKIGYFCLR-IEG---ESMFISKCYL-HRDARHKGFGSALQQFMIQYGREHGCSRAYL 121
                                       4554..6677887766588999999999.888...8889999***.69***************************** PP

                    Acetyltransf_4 117 eiaspnensiqfhkalGFelvgi 139
                                        + + n  +i  +k+ GF+++  
  gi|474934357|ref|YP_007687939.1| 122 HVNVRNVDAIRSYKRNGFQITLH 144
                                       *******************9754 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1   3.9e-07   0.00099      47     138 .]      52     140 ..       9     140 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3.9e-07
                    Acetyltransf_3  47 eeseeeg..ygwaivlkdtgviGsvglrdleeedeeaelgymlapsfwgkGyateavralleyafeelglerlvavi 121
                                        ++ e+g  yg+a    +++ iG+  lr +e+e+  +    +l+++++ kG+++   + +++y  +e+g +r + ++
  gi|474934357|ref|YP_007687939.1|  52 LKDMEDGflYGFAF--DGGKKIGYFCLR-IEGESM-FISKCYLHRDARHKGFGSALQQFMIQYG-REHGCSRAYLHV 123
                                       23334554466666..44446****887.666654.777899**********************.8888******** PP

                    Acetyltransf_3 122 dkeNeaSirvleklGfe 138
                                       + +N   ir +++ Gf+
  gi|474934357|ref|YP_007687939.1| 124 NVRNVDAIRSYKRNGFQ 140
                                       ****************6 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.52   1.3e+03      46      68 ..      29      51 ..       8      60 .. 0.56
   2 ?   12.5   0.0   3.5e-05      0.09      90     139 ..      93     141 ..      75     146 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.52
                                      EEEEEETTEEEEEEEEEEGGGCG CS
                    Acetyltransf_8 46 pliglldgepvgyfeiYwakede 68
                                      p+++  ++e + +f + + k+  
  gi|474934357|ref|YP_007687939.1| 29 PMLIGGEEEAMYLFNTWQSKDAV 51
                                      55555555555555555554443 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 3.5e-05
                                       HHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EE CS
                    Acetyltransf_8  90 eargkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfek 139
                                       +ar kg+++al + +++y  ++ +++r  +   vrN  air +++ Gf+ 
  gi|474934357|ref|YP_007687939.1|  93 DARHKGFGSALQQFMIQYGREH-GCSRAYLHVNVRNVDAIRSYKRNGFQI 141
                                       5788999998877777776655.*************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.52
# Mc/sec: 941.92
//
Query:       gi|474934358|ref|YP_007687940.1|  [L=163]
Description: Acetyltransferase (GNAT) family [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.1e-11   42.0   0.1    1.1e-10   41.6   0.1    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    4.3e-09   36.6   0.2    5.2e-09   36.4   0.2    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    3.4e-06   27.4   0.2      5e-06   26.9   0.2    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.1   1.8e-14   1.1e-10       8     116 ..      36     149 ..      24     154 .. 0.91

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 1.8e-14
                   Acetyltransf_10   8 egietf.kefispealrerieegealllvaeeggkivGvielrdgs...hisllfVdpeyrgqGigkaLleaveeea 80 
                                       e +e+f ++f  ++a+ + + +  + ++   ++g+++G+i+ + ++    is l++  +yr++G++++ le++    
  gi|474934358|ref|YP_007687940.1|  36 ESAEKFfHRFTGKDAVLAAF-DRGCRYWEIVVDGEVAGIIAAEVTGdslFISKLYILGKYRHTGLAQETLEFLFGIG 111
                                       5668888999999*******.999****************775555478***************************9 PP

                   Acetyltransf_10  81 ekdgikl.eltvnasp.yavpfYeklGFkavgeeqeen 116
                                       +k g     l+vn+ +  a++ Y k GF+  ++eq+ +
  gi|474934358|ref|YP_007687940.1| 112 RKSGCTSaYLKVNSENrMAKKAYAKAGFVYESSEQNVD 149
                                       99999999**********************99998765 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.2   8.7e-13   5.2e-09      13     117 .]      41     139 ..      13     139 .. 0.86

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 8.7e-13
                                       HHHHHHHHHHHHHHHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHH CS
                    Acetyltransf_1  13 fppnedaseeefeesfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeera 89 
                                       f+++ +   ++ + +  +  ++++ +  dge++G i +    d      +i  l++  +yr+ Gl+++ le l  + 
  gi|474934358|ref|YP_007687940.1|  41 FFHRFTGKDAVLAAF--DRGCRYWEIVVDGEVAGIIAAEVTGD----SLFISKLYILGKYRHTGLAQETLEFLFGIG 111
                                       344444555554455..45669999***********9999999....8***************************** PP

                                       HHTTESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  90 reegikkivlaveedndaairlYeklGF 117
                                       r+ g++  +l v + n+ a + Y k GF
  gi|474934358|ref|YP_007687940.1| 112 RKSGCTSAYLKVNSENRMAKKAYAKAGF 139
                                       *****888***************99**9 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.2   8.3e-10     5e-06       4      75 ..      60     140 ..      48     141 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 8.3e-10
                                       EEEEEEETTEEEEEEEEEEES..TCTEEEEE-GGGTTSSHHHHHHHH.....TTSEEEEEEEEE..THH..HHHHHH CS
                    Acetyltransf_7   4 evfVaeddgkivGfialslld..aeitrlaVdpeyrgkGiGraLlea.....aekgiileqlel..nae..kaikfY 69 
                                       +++ +  dg++ G ia+++++    i +l+++ +yr  G++++ le+     +++g++ + ++l  n+e   a k Y
  gi|474934358|ref|YP_007687940.1|  60 RYWEIVVDGEVAGIIAAEVTGdsLFISKLYILGKYRHTGLAQETLEFlfgigRKSGCT-S-AYLkvNSEnrMAKKAY 134
                                       4564555799999999999887777777******************866654338886.3.34443332458999** PP

                                       HHTTEE CS
                    Acetyltransf_7  70 eklGFe 75 
                                       +k GF+
  gi|474934358|ref|YP_007687940.1| 135 AKAGFV 140
                                       *****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 998.00
//
Query:       gi|474934359|ref|YP_007687941.1|  [L=282]
Description: Pyridoxal/pyridoxine/pyridoxamine kinase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-20   73.2   0.0    2.5e-20   72.9   0.0    1.0  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
    2.9e-06   26.8   0.0    3.8e-06   26.4   0.0    1.2  1  PfkB          pfkB family carbohydrate kinase


Domain annotation for each model (and alignments):
>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.9   0.0   2.8e-24   2.5e-20      22     240 ..      34     259 ..      24     264 .. 0.80

  Alignments for each domain:
  == domain 1  score: 72.9 bits;  conditional E-value: 2.8e-24
                                       EEEEEEEEEEEETTCEEEEE..E--HHHHHHHHHHHHHTS--SEEEE-S--SHHHHHHHHHHHHHTTS..SEEEE-- CS
                      Phos_pyr_kin  22 gmsvitaltaqntkgvkevh..plpaelveaqleavledvkvdavKiGmlasaeiievvaeklkkykv..pvVlDPV 94 
                                       +  + ta+    t g ++++  +l ++lv    +  + dvk d + +G l+s e i++v + ++ ++    v +DPV
  gi|474934359|ref|YP_007687941.1|  34 CSGMPTAVLSTHTGGFTGFTyrDLTSDLVPIADHWKTLDVKFDGIYTGFLGSFEQIDIVSQLIDDFGKdaLVAVDPV 110
                                       555556666666666665431155566665555556679************************88655526669*** PP

                                       -SSCTSSSBSSHHHHHHHHHHTGGG-SEEE-BHHHHHHHHT---S....SHHHHHHHHHHHHHTT-SEEEEEEGGS- CS
                      Phos_pyr_kin  95 mvaksgselleeeavealkeeLlplatvitPNlpEaeaLlgekik....teedmkeaakkllklgakaVlikGghle 167
                                       m+ +++   + ++++ a  ++L+ +a++i PN+ Ea  +lge+        + ++   k+l+ +g ++++++G   +
  gi|474934359|ref|YP_007687941.1| 111 MADNGQLYSIFDRTFPAGMRKLCSKADLILPNFTEATLMLGEEYVpgpyGRDYVEGLLKRLSGIGPSKIVLTGVFFD 187
                                       **9999888888888888888********************77765666788999999****************875 PP

                                       SSSEEEEEEEE..TSSEEEEEEEE----S--BTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHHHHCG-BSTS CS
                      Phos_pyr_kin 168 geeavvtdvly..dgeeveeleaerietknthGtGCtlssaiaaelakgesleeAvkkAkeyvteaikealelgk 240
                                       ++e       y  +++e+    ae i+   +hGtG+ +ss++ + l +g sl  + + A ++++++i ++ e g+
  gi|474934359|ref|YP_007687941.1| 188 DSEV--GAASYdaETGEIDYAFAETIP-GYYHGTGDIFSSVVVSGLMNGLSLARSTAIAVDFTQRSIVRTHEAGT 259
                                       5444..455554377778888888999.***************************************99888875 PP

>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   4.3e-10   3.8e-06     162     284 ..     117     245 ..      65     259 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 4.3e-10
                                       EEEECESSSHHHHHHHHHHHCTESEEEEEHHHHHHHHTSCT.......HSHHHHHHHHHHHHHTTS..SEEEEEEGG CS
                              PfkB 162 dpnlldplgaqfkeallellaladllkpneeElealtgekl.......edieealaalhklkakga..ktvvvtlGk 229
                                        + + d++ +     +++l ++adl+ pn +E+  ++ge+        + +e +l++l  + ++ +  + v++  ++
  gi|474934359|ref|YP_007687941.1| 117 LYSIFDRTFP---AGMRKLCSKADLILPNFTEATLMLGEEYvpgpygrDYVEGLLKRLSGIGPSKIvlTGVFFDDSE 190
                                       4444444443...689999*****************************************88888888899999*** PP

                                       GEEEEEETTEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHH CS
                              PfkB 230 eGalvvekdgelkvpavpkvkvvDttGAGDsfvggflaallegksleealrfana 284
                                        Ga+ ++ ++  +  a+ ++ +    G+GD f + ++++l++g sl+++ ++a+ 
  gi|474934359|ref|YP_007687941.1| 191 VGAASYDAETGEIDYAFAETIPGYYHGTGDIFSSVVVSGLMNGLSLARSTAIAVD 245
                                       ******98888888888999999**************************999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 2295.02
//
Query:       gi|474934360|ref|YP_007687942.1|  [L=305]
Description: hypothetical protein TALC_00786 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-05   24.9   0.0        1.6    9.1   0.0    4.7  5  TPR_2      Tetratricopeptide repeat
    2.5e-05   23.9   0.0        2.5    8.1   0.1    4.4  4  TPR_1      Tetratricopeptide repeat
    0.00013   21.9   1.0     0.0091   16.1   0.2    4.2  6  TPR_8      Tetratricopeptide repeat
    0.00047   20.4   0.1        0.2   11.9   0.0    2.8  3  TPR_12     Tetratricopeptide repeat
     0.0047   16.9   0.2       0.67   10.1   0.0    3.9  4  TPR_7      Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.021   15.3   0.3        3.1    8.4   0.1    3.8  5  TPR_19     Tetratricopeptide repeat
      0.081   12.7   0.1       0.16   11.7   0.1    1.5  1  DUF410     Protein of unknown function (DUF410)
      0.096   12.8   0.1        1.2    9.2   0.0    2.5  2  DEP        Domain found in Dishevelled, Egl-10, and Pleckstri
       0.19   11.8   0.1       0.35   10.9   0.1    1.4  1  TACI-CRD2  TACI, cysteine-rich domain


Domain annotation for each model (and alignments):
>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1      0.21   4.3e+02      16      28 ..       7      19 ..       4      24 .. 0.77
   2 ?    5.1   0.0     0.014        29       2      30 ..      33      61 ..      32      64 .. 0.92
   3 ?   -4.0   0.0         9   1.8e+04      24      30 ..     146     152 ..     142     152 .. 0.74
   4 ?    2.7   0.0     0.088   1.8e+02       2      28 ..     167     193 ..     166     197 .. 0.89
   5 !    9.1   0.0   0.00078       1.6       2      26 ..     259     283 ..     258     288 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.21
                             TPR_2 16 dyeeAleafekAl 28
                                      ++e+Al  +++A+
  gi|474934360|ref|YP_007687942.1|  7 HLERALSEYNEAV 19
                                      5788888888886 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.014
                             TPR_2  2 ealynlGlayyklgdyeeAleafekAlel 30
                                      +al n+G+++  ++ +  A e+f+ A+ +
  gi|474934360|ref|YP_007687942.1| 33 DALINRGRILSMMDSWVTAMEDFNDAVDI 61
                                      689*********************99875 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 9
                             TPR_2  24 fekAlel 30 
                                        ekAl+l
  gi|474934360|ref|YP_007687942.1| 146 IEKALSL 152
                                       5888876 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.088
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAl 28 
                                       ea  ++G+ ++ + d   A++af++ +
  gi|474934360|ref|YP_007687942.1| 167 EAMSARGQTLMLNSDNVPAIKAFDETI 193
                                       78999******************9866 PP

  == domain 5  score: 9.1 bits;  conditional E-value: 0.00078
                             TPR_2   2 ealynlGlayyklgdyeeAleafek 26 
                                       e++ ++++ay+++gd ++A+ ++ k
  gi|474934360|ref|YP_007687942.1| 259 ELHGEIAKAYMEKGDMKKAESHLLK 283
                                       678899**************99876 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.7   3.3e+03      13      20 ..      11      18 ..       6      19 .. 0.48
   2 !    6.8   0.0    0.0032       6.4       2      30 ..      33      61 ..      32      63 .. 0.93
   3 ?    3.2   0.0     0.044        89       3      29 ..     168     194 ..     166     197 .. 0.87
   4 !    8.1   0.1    0.0012       2.5       3      24 ..     260     281 ..     258     283 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.7
                                      HTT-HHHH CS
                             TPR_1 13 klgkydeA 20
                                       l +y+eA
  gi|474934360|ref|YP_007687942.1| 11 ALSEYNEA 18
                                      34455555 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0032
                                      HHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1  2 kalynlGnayfklgkydeAleyyekALel 30
                                      +al n+G ++  +  +  A e+++ A+ +
  gi|474934360|ref|YP_007687942.1| 33 DALINRGRILSMMDSWVTAMEDFNDAVDI 61
                                      799*********************99875 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.044
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALe 29 
                                       a   +G++++ + +   A++++++ ++
  gi|474934360|ref|YP_007687942.1| 168 AMSARGQTLMLNSDNVPAIKAFDETIR 194
                                       66779*****************99775 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.0012
                                       HHHHHHHHHHHTT-HHHHHHHH CS
                             TPR_1   3 alynlGnayfklgkydeAleyy 24 
                                        +  ++ ay+++g+ ++A+ + 
  gi|474934360|ref|YP_007687942.1| 260 LHGEIAKAYMEKGDMKKAESHL 281
                                       67889*************9875 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.6   3.3e+03      17      28 ..       8      19 ..       3      21 .. 0.71
   2 ?   -3.7   0.0         9   1.8e+04       2      11 ..      33      42 ..      32      43 .. 0.78
   3 ?   -2.3   0.0       3.7   7.4e+03      20      30 ..      51      61 ..      50      62 .. 0.84
   4 ?   -0.7   0.0       1.2   2.3e+03      20      30 ..     142     152 ..     138     152 .. 0.84
   5 ?   -1.0   0.0       1.4   2.8e+03       6      18 ..     210     222 ..     209     226 .. 0.84
   6 !   16.1   0.2   4.6e-06    0.0091       3      31 ..     260     288 ..     258     290 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.6
                                      HHHHHHHHHHHH CS
                             TPR_8 17 yeeAkeyyekal 28
                                      +e A + y++a+
  gi|474934360|ref|YP_007687942.1|  8 LERALSEYNEAV 19
                                      677777787776 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 9
                                      CHHHHHHHHH CS
                             TPR_8  2 eayynlgsiy 11
                                      +a+ n g+i+
  gi|474934360|ref|YP_007687942.1| 33 DALINRGRIL 42
                                      6888999987 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 3.7
                                      HHHHHHHHHHH CS
                             TPR_8 20 Akeyyekalel 30
                                      A+e ++ a+++
  gi|474934360|ref|YP_007687942.1| 51 AMEDFNDAVDI 61
                                      89999999876 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHH CS
                             TPR_8  20 Akeyyekalel 30 
                                       A  ++ekal+l
  gi|474934360|ref|YP_007687942.1| 142 ADPFIEKALSL 152
                                       78899****97 PP

  == domain 5  score: -1.0 bits;  conditional E-value: 1.4
                                       HHHHHHHHTT-HH CS
                             TPR_8   6 nlgsiylklgdye 18 
                                       +l ++y + gd+e
  gi|474934360|ref|YP_007687942.1| 210 LLVYAYVSRGDME 222
                                       57799*****998 PP

  == domain 6  score: 16.1 bits;  conditional E-value: 4.6e-06
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleld 31 
                                       ++  ++++y+++gd+++A++ + k ++l+
  gi|474934360|ref|YP_007687942.1| 260 LHGEIAKAYMEKGDMKKAESHLLKQVSLN 288
                                       66789*********************998 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0    0.0001       0.2      20      74 ..       9      61 ..       5      63 .. 0.90
   2 ?   -2.9   0.0       4.5   8.9e+03      16      35 ..     179     198 ..     166     205 .. 0.50
   3 ?    5.2   0.1     0.013        26       5      29 ..     260     284 ..     256     293 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0001
                            TPR_12 20 deAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74
                                      + Al+ +++a+++ ++  Gp + +++ +l+n gr++++++ +  A e +++a++i
  gi|474934360|ref|YP_007687942.1|  9 ERALSEYNEAVNRLEAD-GP-STELLDALINRGRILSMMDSWVTAMEDFNDAVDI 61
                                      6799**********765.77.669***************************9987 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.5
                            TPR_12  16 lgrydeAlellekaleiarr 35 
                                         +   A++ +++ +++ ++
  gi|474934360|ref|YP_007687942.1| 179 NSDNVPAIKAFDETIRVGEE 198
                                       33333355555555555544 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.013
                            TPR_12   5 alnnlaavlrrlgrydeAlelleka 29 
                                       ++ ++a ++++ g++ +A+++l k 
  gi|474934360|ref|YP_007687942.1| 260 LHGEIAKAYMEKGDMKKAESHLLKQ 284
                                       5567999**************9875 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.41   8.2e+02      11      24 ..      11      24 ..       7      38 .. 0.82
   2 ?   -1.8   0.0       2.2   4.4e+03       5      16 ..     211     222 ..     209     223 .. 0.81
   3 ?    0.0   0.0      0.56   1.1e+03      14      28 ..     234     246 ..     233     254 .. 0.80
   4 !   10.1   0.0   0.00034      0.67       3      25 ..     262     284 ..     260     293 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.41
                             TPR_7 11 rlGdyeeAielyeq 24
                                      +l +y eA+  +e+
  gi|474934360|ref|YP_007687942.1| 11 ALSEYNEAVNRLEA 24
                                      589999**999987 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.2
                             TPR_7   5 LarlysrlGdye 16 
                                       L  +y+++Gd+e
  gi|474934360|ref|YP_007687942.1| 211 LVYAYVSRGDME 222
                                       66799*****97 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.56
                             TPR_7  14 dyeeAielyeqsLal 28 
                                       d+e+Ai+l ++   +
  gi|474934360|ref|YP_007687942.1| 234 DRERAIGLMKE--MM 246
                                       89*****9998..44 PP

  == domain 4  score: 10.1 bits;  conditional E-value: 0.00034
                             TPR_7   3 lnLarlysrlGdyeeAielyeqs 25 
                                         +a +y + Gd+++A++++ ++
  gi|474934360|ref|YP_007687942.1| 262 GEIAKAYMEKGDMKKAESHLLKQ 284
                                       5699**************99984 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.92   1.8e+03      17      48 ..      11      22 ..       6      41 .. 0.57
   2 ?    1.0   0.0       0.3     6e+02      37      57 ..      51      71 ..      50      83 .. 0.76
   3 ?   -1.6   0.0       2.1   4.2e+03      23      40 ..     157     174 ..     140     175 .. 0.71
   4 ?   -2.5   0.0       3.8   7.6e+03      29      41 ..     209     221 ..     189     223 .. 0.70
   5 ?    8.4   0.1    0.0015       3.1       8      48 ..     236     281 ..     233     288 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.92
                            TPR_19 17 alqedpknaearllLAeallalgqldeAealL 48
                                      al+e                    ++eA + L
  gi|474934360|ref|YP_007687942.1| 11 ALSE--------------------YNEAVNRL 22
                                      4444....................33333333 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.3
                            TPR_19 37 algqldeAealLdalpeedpd 57
                                      a+ ++++A +++d+l +e ++
  gi|474934360|ref|YP_007687942.1| 51 AMEDFNDAVDIIDTLSREGKK 71
                                      567888999999988887665 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2.1
                            TPR_19  23 knaearllLAeallalgq 40 
                                       ++++ r ++ ea+ a gq
  gi|474934360|ref|YP_007687942.1| 157 DDPWSRNRYFEAMSARGQ 174
                                       588888899999999888 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 3.8
                            TPR_19  29 llLAeallalgql 41 
                                       llL+ a+++ g+ 
  gi|474934360|ref|YP_007687942.1| 209 LLLVYAYVSRGDM 221
                                       4557777777775 PP

  == domain 5  score: 8.4 bits;  conditional E-value: 0.0015
                            TPR_19   8 aeAlalleqalqedpk.naearllL....AeallalgqldeAealL 48 
                                       ++A+ l++++++ ++  + e++  L    A+a+++ g+ ++Ae  L
  gi|474934360|ref|YP_007687942.1| 236 ERAIGLMKEMMDNNALeDVELLSELhgeiAKAYMEKGDMKKAESHL 281
                                       67888888875554436555555445555*************9765 PP

>> DUF410  Protein of unknown function (DUF410)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   8.3e-05      0.16      89     113 ..     258     282 ..     241     289 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.3e-05
                            DUF410  89 peLhhllaklllkegeleeAerhll 113
                                        eLh  +ak+++++g++++Ae+hll
  gi|474934360|ref|YP_007687942.1| 258 SELHGEIAKAYMEKGDMKKAESHLL 282
                                       59*********************98 PP

>> DEP  Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.44   8.9e+02      32      50 ..     181     203 ..     173     207 .. 0.77
   2 ?    9.2   0.0   0.00061       1.2      33      56 ..     232     255 ..     225     262 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.44
                                       S....SSSHHHHHHHHHHHHHCT CS
                               DEP  32 d....iedreeAvalgqlLldqg 50 
                                       d    i+  +e++++g++Ll+ g
  gi|474934360|ref|YP_007687942.1| 181 DnvpaIKAFDETIRVGEELLSDG 203
                                       4445888899*********9876 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00061
                                       SSSHHHHHHHHHHHHHCTSCECSS CS
                               DEP  33 iedreeAvalgqlLldqgliehve 56 
                                        +dre A+ l+++++d++ +e+ve
  gi|474934360|ref|YP_007687942.1| 232 FTDRERAIGLMKEMMDNNALEDVE 255
                                       68*******************996 PP

>> TACI-CRD2  TACI, cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00018      0.35       6      22 ..     112     130 ..     110     131 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00018
                         TACI-CRD2   6 eqGrYYDe..LlrdCisCs 22 
                                       e+ r+YD+  L+++Ci+C+
  gi|474934360|ref|YP_007687942.1| 112 EKSRFYDRksLIKECIDCA 130
                                       56799**555********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2148.60
//
Query:       gi|474934361|ref|YP_007687943.1|  [L=655]
Description: Rad3-related DNA helicase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-52  178.2   0.0    5.3e-52  176.3   0.0    1.9  2  HBB           Helical and beta-bridge domain
    1.5e-33  116.4   0.0    3.2e-33  115.3   0.0    1.5  1  Helicase_C_2  Helicase C-terminal domain
    6.3e-32  110.6   0.1    9.5e-32  110.0   0.1    1.3  1  DEAD_2        DEAD_2
      2e-10   40.9   0.0    9.6e-10   38.7   0.0    1.9  1  ResIII        Type III restriction enzyme, res subunit
    2.8e-06   27.2   0.3    0.00095   19.0   0.1    2.3  2  DEAD          DEAD/DEAH box helicase
     0.0035   16.7   0.0     0.0065   15.8   0.0    1.4  1  ATPase        KaiC
     0.0088   16.4   0.0      0.027   14.8   0.0    1.8  2  AAA_19        AAA domain
  ------ inclusion threshold ------
      0.017   14.4   0.3        3.3    6.8   0.1    2.2  2  DUF2075       Uncharacterized conserved protein (DUF2075)
      0.028   14.1   0.3      0.097   12.4   0.1    1.9  2  AAA_30        AAA domain
      0.076   12.1   0.1       0.35    9.9   0.1    1.9  2  T2SSE         Type II/IV secretion system protein
      0.093   12.2   0.7       0.24   10.8   0.1    1.9  2  PhoH          PhoH-like protein
        0.2   12.0   0.9        2.5    8.4   0.1    2.5  2  AAA_22        AAA domain


Domain annotation for each model (and alignments):
>> HBB  Helical and beta-bridge domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.2   1.7e+03      46      79 ..     218     251 ..     196     255 .. 0.81
   2 !  176.3   0.0   3.6e-55   5.3e-52       1     189 [.     264     459 ..     264     460 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.2
                                       HHHHCHCHHHCHHHHHHHHHHHHHHHHHHHCCHH CS
                               HBB  46 eileeavpglirsaehflsllkrlveygkarree 79 
                                       +i ++ ++ l++++++++ ++ + +++++a+re+
  gi|474934361|ref|YP_007687943.1| 218 AIRDNFFQNLGMDEKDIVLIVDEAHNLMDAVREQ 251
                                       5667778889999999999999999999999876 PP

  == domain 2  score: 176.3 bits;  conditional E-value: 3.6e-55
                                       HCHCHCCCCHHCCCCCCCH..HHHHHHHHCCCCHHHHSTTTE...CCHCHHHHHCHCHHHCHHHHHHHHHHHHHHHH CS
                               HBB   1 aikeaketdepklqdeysr..LvegLreaeeereeeyvleee...pilpdeileeavpglirsaehflsllkrlvey 72 
                                       a++e++++++p ++++++   +v+++r++ +  +++++   e   +++p+e+++ +++ ++++ ++++s++++l+e+
  gi|474934361|ref|YP_007687943.1| 264 ALDECMAFNKPPVSSTMTLddFVRAVRRVVKGLASKKIPLGEkeaMLEPREFETALASESGTDVTGLRSIVEKLTEL 340
                                       579****************************99977776555579******************************** PP

                                       HHHCCHHCCCTCC-SHHHHHHHHHHHHHHHTS.TTTEEEEEE.STT..EECCCCS-TCCHHHHHHHCHCCCCCCTS- CS
                               HBB  73 gkarreekieksesPrsflsrlaefllawlssdeedYvrlvskeeg.esLeavcldPskalrflkerlssllmsgtl 148
                                       g++r +e+i++++sP+s+l ++a +l +w++s+e++Y+++v+++e+ e+++a+c+dP+++  fl++++ +++msgtl
  gi|474934361|ref|YP_007687943.1| 341 GEKR-QEAIADTDSPDSPLLDFAILLGKWVKSPEDRYIKVVRTNEEgEFIQASCIDPADVPAFLRKLPGAVHMSGTL 416
                                       ****.9************************************99988****************************** PP

                                       SSHHHHHHHHT......EEE.S..S.GGHCCCCCCCCCSHTCC CS
                               HBB 149 tpleeysdiiGle..aklkkfpspfpkEnlivlfatdVsTkyk 189
                                       +pl++y++++Gl+  + ++k+pspfpkEn++v++atdV++++k
  gi|474934361|ref|YP_007687943.1| 417 QPLAQYARVMGLPdnTLPRKYPSPFPKENKKVVYATDVTSEFK 459
                                       ***************************************9987 PP

>> Helicase_C_2  Helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.3   0.0   2.1e-36   3.2e-33       2     158 ..     476     629 ..     475     636 .. 0.87

  Alignments for each domain:
  == domain 1  score: 115.3 bits;  conditional E-value: 2.1e-36
                      Helicase_C_2   2 lellevvpggvlvffpSyklleevverlkeeleskkieifvee..keesrekvleeykekkkkgaillavcrGklsE 76 
                                       ++l++++ g++lvf+pSy++l+ +  +l++     ++++++e    ++++ k l+ +++  +++ ++++v++G++ E
  gi|474934361|ref|YP_007687943.1| 476 IRLCNSIDGNTLVFMPSYRVLKLMQPALEDGI---DKPLYWELsgRQRQTMKNLDAFRS--GRNGVFVCVMGGSIAE 547
                                       689*************************9977...578888843344455555666666..**************** PP

                      Helicase_C_2  77 GidfsddllraviivglPfpnpkdpeveakreyldekgk.knsgkewylpealravnQaiGRliRhkdDygaivllD 152
                                       G+df++d+l   +ivg+P+++p + e++a ++++d++ +   ++k+  + +a+r+++QaiGRliR+++D+g+ v+lD
  gi|474934361|ref|YP_007687943.1| 548 GMDFPGDQLCFAVIVGMPYAPP-SLEIKAMKDMFDKRYGpGTGWKYTGEIPAVRKIRQAIGRLIRTETDRGMAVILD 623
                                       *********************9.8999********999834446667799*************************** PP

                      Helicase_C_2 153 eRfake 158
                                       +R a++
  gi|474934361|ref|YP_007687943.1| 624 SRAARN 629
                                       **9875 PP

>> DEAD_2  DEAD_2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.0   0.1   6.4e-35   9.5e-32       1     174 [.      83     259 ..      83     261 .. 0.91

  Alignments for each domain:
  == domain 1  score: 110.0 bits;  conditional E-value: 6.4e-35
                                       EEESSHHHHHHHHHHHHHHHHHCHHHS---EEEE--CCCC-....SCHHCCCHHCCCCHHHHHHHHHCCHHCCHTTT CS
                            DEAD_2   1 ycsRThsqleqvvkelkklesykkkkekvkvviLgSRknlC....ineevkkekkekavneaCkelkkkkaeekeek 73 
                                       y +RT sq +qv+kel+ ++++k     v  ++L++R++ C     ++++++  + +a++++C+++k+k ++++   
  gi|474934361|ref|YP_007687943.1|  83 YITRTISQSDQVMKELRAINTIKP----VSGITLTGRSKSCpllmARPDFEN-LSPSALSTLCSDRKQKSQQNRAGG 154
                                       89*****************98887....*************43322344444.4478899**********9999*** PP

                                       TTT-SCC.CCHHHHHHHHHHC---CHHHHHHHHHCT--HHHHHHHHHCCTSEEEEEHHHHTSCCCHHHHH...T..G CS
                            DEAD_2  74 Csffenl.eelkklkkllleevvdiedlvelgeklklCPYylsrelledadiiilpYqyLldekireslk...gisl 146
                                       C++f+++  ++++ ++  ++e    ++l  ++++ ++CPY + +++++d d+i++pY  ++d+ ir+++    g++ 
  gi|474934361|ref|YP_007687943.1| 155 CPYFDKTlPQIDNIERYCKKEFPRSDELDIYCKNSGACPYEAKKAMMKDFDVIVAPYIHMIDPAIRDNFFqnlGMDE 231
                                       ****9998999999****************************************************9876678899* PP

                                       CGCEEEECTCCCHHHHHHHCC-EEEECH CS
                            DEAD_2 147 knsivilDEAhNiedvceeaasveisee 174
                                       k+ ++i+DEAhN+ d ++e  s+ is++
  gi|474934361|ref|YP_007687943.1| 232 KDIVLIVDEAHNLMDAVREQESFTISSR 259
                                       *************************976 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.0   6.4e-13   9.6e-10       2     146 ..      29     246 ..      28     271 .. 0.73

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 6.4e-13
                                       -EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHG.... CS
                            ResIII   2 lelreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleef.... 74 
                                       +e+re Q+++i +++++l+  + ++++i+  TGtGKT+v+++   + +k    +k++ +  ++s  +q ++e+    
  gi|474934361|ref|YP_007687943.1|  29 YEPRELQIDIISDIRSALD--QSRHIVIESGTGTGKTIVSLAGSLEHAKRT-GKKVVYITRTISQSDQVMKELrain 102
                                       589***************5..*******************77777776654.46*******************9999 PP

                                       ..................................................................GGGTGG....G CS
                            ResIII  75 ..................................................................kkflseaykei 85 
                                                                                                         +          
  gi|474934361|ref|YP_007687943.1| 103 tikpvsgitltgrskscpllmarpdfenlspsalstlcsdrkqksqqnraggcpyfdktlpqidniE---------- 169
                                       ******************9999999977777777776666655555544444444444333333331.......... PP

                                       EEEESSS-B--.................................-SEEEEEH.HHHHHTH........HHHTTT-SE CS
                            ResIII  86 gkkvsgdkkka..........................kekdstnkkilvtti.qsldadseeeeeeseellrdrfdv 135
                                                 +                          k+   ++ +++v+ + +++d ++ +++  ++   +++  v
  gi|474934361|ref|YP_007687943.1| 170 ----------RyckkefprsdeldiycknsgacpyeaKKAMMKDFDVIVAPYiHMIDPAI-RDNFFQNLGMDEKDIV 235
                                       ..........03322234444444466666666666566777788888876515555555.667777777777777* PP

                                       EEEETGGGTTS CS
                            ResIII 136 iiiDEaHrlga 146
                                       +i+DEaH+l +
  gi|474934361|ref|YP_007687943.1| 236 LIVDEAHNLMD 246
                                       *******9987 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   6.3e-07   0.00095      11     116 ..      42     144 ..      32     152 .. 0.74
   2 !    6.3   0.0    0.0048       7.2     124     149 ..     235     260 ..     166     285 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 6.3e-07
                                       HH....TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEET CS
                                       xx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  11 il....gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliig 83 
                                       i     + ++++++  TG+GKT + l   l++     ++tg+k+++++ t +   q++++l+ +     ++ ++ i+
  gi|474934361|ref|YP_007687943.1|  42 IRsaldQSRHIVIESGTGTGKTIVSLAGSLEHA----KRTGKKVVYITRTISQSDQVMKELRAINT---IKPVSGIT 111
                                       4433357799********************888....799*********************99888...44555555 PP

                                       TSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  84 gvaardqlskldngvdivvgtpgrlddllstgk 116
                                        + +++    l +++d+    p+ l  l+s++k
  gi|474934361|ref|YP_007687943.1| 112 LTGRSKSCPLLMARPDFENLSPSALSTLCSDRK 144
                                       555555666666667777777777777776555 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0048
                                       EEEEETHHHHHHTTTHHHHHHHHHHS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 124 flVlDEadrlldqgfsdfinrilnql 149
                                       +l++DEa++l+d  ++++  +i ++l
  gi|474934361|ref|YP_007687943.1| 235 VLIVDEAHNLMDAVREQESFTISSRL 260
                                       69**********98877777666666 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   4.4e-06    0.0065      17      59 ..      47      89 ..      36     103 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.4e-06
                            ATPase 17 pegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveep 59
                                       + r + i  ++GtGKti++l   ++ a+++g+++v++t   +
  gi|474934361|ref|YP_007687943.1| 47 DQSRHIVIESGTGTGKTIVSLAGSLEHAKRTGKKVVYITRTIS 89
                                      57788999999***************************96544 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.8e-05     0.027       9     112 ..      48     242 ..      42     251 .. 0.67
   2 ?   -3.1   0.0       5.8   8.7e+03      27      60 ..     602     632 ..     585     636 .. 0.51

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.8e-05
                            AAA_19   9 kekvllvtaGpGtGKTrv.lkhivallvelggvkpeeillvaftgrAakelrerlaalgaeatTiHrlal....... 77 
                                       +++++++  G GtGKT v l + +++++++g    ++++ ++ t    +++ ++l    ++++Ti  ++        
  gi|474934361|ref|YP_007687943.1|  48 QSRHIVIESGTGTGKTIVsLAGSLEHAKRTG----KKVVYITRTISQSDQVMKEL----RAINTIKPVSGitltgrs 116
                                       67899***********875889999999999....78999999977777766667....566677666555667777 PP

                            AAA_19  78 ............................................................................. 77 
                                                                                                                    
  gi|474934361|ref|YP_007687943.1| 117 kscpllmarpdfenlspsalstlcsdrkqksqqnraggcpyfdktlpqidnieryckkefprsdeldiycknsgacp 193
                                       78888888888888888888888888888888888888888888888888888888888877777666666666666 PP

                            AAA_19  78 ........ldfddlltealelle.......eaeeekklqeee.llivDEfq 112
                                                dfd ++    ++++          ++  + e++ +livDE+ 
  gi|474934361|ref|YP_007687943.1| 194 yeakkammKDFDVIVAPYIHMIDpairdnfF--QNLGMDEKDiVLIVDEAH 242
                                       6655555522332222222222233333210..112223333466666655 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.8
                            AAA_19  27 lkhivallvelggvkpeeillvaftgrAakelre 60 
                                       +++++  l+   + + ++ ++v + +rAa++ re
  gi|474934361|ref|YP_007687943.1| 602 IRQAIGRLI---RTETDRGMAVILDSRAARNARE 632
                                       223333333...3334667777777777777665 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0022       3.3       3      52 ..      51      99 ..      49     108 .. 0.84
   2 ?    5.6   0.0    0.0054         8      85     111 ..     229     255 ..     191     276 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0022
                           DUF2075  3 vvlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlreala 52
                                       ++++ ++GtGKt+v l+   e+  ++ ++++vy+++  ++ + + ++l+
  gi|474934361|ref|YP_007687943.1| 51 HIVIESGTGTGKTIVSLAGSLEH-AKRTGKKVVYITRTISQSDQVMKELR 99
                                      589999***********999999.88899999999988877777777665 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0054
                           DUF2075  85 eepkedvvivDEAhrlltksdqaekqs 111
                                       +++k  v+ivDEAh l++  + +e+++
  gi|474934361|ref|YP_007687943.1| 229 MDEKDIVLIVDEAHNLMDAVREQESFT 255
                                       55666799*********9544444443 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   6.5e-05     0.097      12      66 ..      44      98 ..      34     113 .. 0.81
   2 ?   -1.8   0.0       1.5   2.2e+03      85      98 ..     228     242 ..     196     250 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.5e-05
                            AAA_30 12 alltsgdrvavltGpAGtGKtta.lkalreaweaaggrviglAptgkaAkvLaeel 66
                                      ++l ++ r  v++ + GtGKt + l++  e++++ g++v+ ++ t  +++++ +el
  gi|474934361|ref|YP_007687943.1| 44 SALDQS-RHIVIESGTGTGKTIVsLAGSLEHAKRTGKKVVYITRTISQSDQVMKEL 98
                                      555555.48999*********85388889999999**********99999976665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.5
                            AAA_30  85 rlepg.tllivDEag 98 
                                        ++++  +livDEa 
  gi|474934361|ref|YP_007687943.1| 228 GMDEKdIVLIVDEAH 242
                                       456665799****95 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00023      0.35     121     163 ..      41      84 ..      17     104 .. 0.77
   2 ?   -1.0   0.0      0.49   7.3e+02      78     112 ..     202     236 ..     191     259 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00023
                             T2SSE 121 vlrkavrerglilvsGgTgsGKttllyal.lkeinksderivtv 163
                                        +r+a+ +   i++  gTg+GKt++  a  l+  + + +++v +
  gi|474934361|ref|YP_007687943.1|  41 DIRSALDQSRHIVIESGTGTGKTIVSLAGsLEHAKRTGKKVVYI 84 
                                       46777888899999999******876554044444446666655 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.49
                             T2SSE  78 vrlrvvllPvvagealviRkksakeltlddlgaee 112
                                        ++ v+++P ++    +iR++  ++l +d+  +  
  gi|474934361|ref|YP_007687943.1| 202 KDFDVIVAPYIHMIDPAIRDNFFQNLGMDEKDIVL 236
                                       6899***************9999988777654444 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00016      0.24      14      61 ..      44      91 ..      34     102 .. 0.78
   2 ?   -1.9   0.1       1.2   1.8e+03     120     133 ..     233     246 ..     231     253 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00016
                                      HHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--T CS
                              PhoH 14 ealkkndivfaiGpaGtGKtylavalavealkkkkvkriiltrpavea 61
                                      +al+++  +++   +GtGKt +++a  +e  k+   k + +tr + ++
  gi|474934361|ref|YP_007687943.1| 44 SALDQSRHIVIESGTGTGKTIVSLAGSLEHAKRTGKKVVYITRTISQS 91
                                      567777777788889**************9988776666667766555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.2
                                       SEEEEE-SGGG--H CS
                              PhoH 120 dafvilDEAQnttk 133
                                       d ++i+DEA n+  
  gi|474934361|ref|YP_007687943.1| 233 DIVLIVDEAHNLMD 246
                                       6789******9865 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1      0.25   3.7e+02       5      28 ..      49      72 ..      44     124 .. 0.75
   2 ?    8.4   0.1    0.0017       2.5      89     107 ..     231     252 ..     218     271 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.25
                            AAA_22  5 agilvvtGesGtGKTtllrrlleq 28
                                       +++v+   +GtGKT +      +
  gi|474934361|ref|YP_007687943.1| 49 SRHIVIESGTGTGKTIVSLAGSLE 72
                                      6788888899*****876544444 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0017
                            AAA_22  89 ravielliiDEaqhlr....see 107
                                        ++  +li+DEa++l+    ++e
  gi|474934361|ref|YP_007687943.1| 231 EKD-IVLIVDEAHNLMdavrEQE 252
                                       445.7*********965543233 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (655 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.76u 0.33s 00:00:01.09 Elapsed: 00:00:00.54
# Mc/sec: 3655.87
//
Query:       gi|474934362|ref|YP_007687944.1|  [L=309]
Description: putative Na+-dependent transporter [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-08   33.1  14.5    4.1e-08   33.1  14.5    1.7  1  SBF       Sodium Bile acid symporter family


Domain annotation for each model (and alignments):
>> SBF  Sodium Bile acid symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1  14.5   2.3e-12   4.1e-08       2     164 ..      34     189 ..      33     209 .. 0.89

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 2.3e-12
                               SBF   2 ilLilmmfpmglkveveklk..ellkrpkalllglvlqwvikPllmfilakillrdlklepelavGlilvglapgga 76 
                                       ++++ +m++m++ +e  +++  +  k+ k+++ ++v+ + +  l + ++  ++++ +    ++  G ++++++p + 
  gi|474934362|ref|YP_007687944.1|  34 LVIVALMLQMIASMEGLSFRgeDFRKESKPIVWSFVCCFGVCTLATLAIGSLFIGPY---RTVWYGWVMLAAVPSAV 107
                                       788899********9999973246777**************9999999999998888...99*************** PP

                               SBF  77 msnvwtylakGdlelsvvlvalstllailltPlllyllaksleqttlkvpieeivksvlivviiPliaGillryill 153
                                       +++ ++ +++G++ +sv   +++ ++a++ltPl++ +l+++       ++  ei+k vl+++ iPl+a i lr++ +
  gi|474934362|ref|YP_007687944.1| 108 SVISLSLMMRGNRVMSVLALTATYVVALGLTPLITTVLIGDA------ISPLEIFKYVLLFIAIPLLANIPLRRVPI 178
                                       ******************************************......********************999998877 PP

                               SBF 154 khkGrewfesk 164
                                       +++ +  f+++
  gi|474934362|ref|YP_007687944.1| 179 NRRAKLVFINV 189
                                       75555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       805  (0.0448993); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2084.92
//
Query:       gi|474934363|ref|YP_007687945.1|  [L=120]
Description: hypothetical protein TALC_00790 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0005   20.2   0.1     0.0009   19.4   0.1    1.3  1  PaaX      PaaX-like protein


Domain annotation for each model (and alignments):
>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1     5e-08    0.0009      32      64 ..      59      92 ..      57      94 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 5e-08
                              PaaX 32 elGiseslvRaalsRlakaGwlvrekegr.rsfY 64
                                      ++G++e+ v aa+ R+++aG++ + ++   + +Y
  gi|474934363|ref|YP_007687945.1| 59 AFGMEEKRVNAAVLRMKAAGLICSRRVDEvHEYY 92
                                      69***********************999844444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 797.97
//
Query:       gi|474934364|ref|YP_007687946.1|  [L=216]
Description: Sel1 repeat protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-32  110.4   7.0    4.4e-08   33.5   0.0    5.1  5  Sel1      Sel1 repeat


Domain annotation for each model (and alignments):
>> Sel1  Sel1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   5.6e-09    0.0001       7      38 .]      24      53 ..      21      53 .. 0.87
   2 !   33.5   0.0   2.5e-12   4.4e-08       2      38 .]      55      89 ..      54      89 .. 0.94
   3 !   21.2   0.1   1.9e-08   0.00034       1      37 [.      90     124 ..      90     125 .. 0.93
   4 !   13.1   0.2   6.7e-06      0.12       3      36 ..     128     160 ..     126     162 .. 0.88
   5 !   20.2   0.0   3.8e-08   0.00069       1      33 [.     163     193 ..     163     195 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 5.6e-09
                              Sel1  7 LGmfylylnGlgvpkDpekAiewyekAAeqGd 38
                                      ++   +y+ G  vp D+ekA+++y+++Ae+G+
  gi|474934364|ref|YP_007687946.1| 24 YA--GMYFQGITVPVDKEKAVRLYRMSAEKGN 53
                                      56..355***********************97 PP

  == domain 2  score: 33.5 bits;  conditional E-value: 2.5e-12
                              Sel1  2 eAmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38
                                      +A+ rLG   +y++G+g +kD+++ ++w+++A ++G+
  gi|474934364|ref|YP_007687946.1| 55 DAQVRLG--IIYMTGDGAEKDYSESFKWFKLASDRGN 89
                                      79*****..777***********************97 PP

  == domain 3  score: 21.2 bits;  conditional E-value: 1.9e-08
                              Sel1   1 aeAmyrLGmfylylnGlgvpkDpekAiewyekAAeqG 37 
                                       ++A y     ++y  G g++k+p++A+++  +AA+ G
  gi|474934364|ref|YP_007687946.1|  90 PDAEYFAS--LMYSRGWGTEKNPSEAVRLCYLAADSG 124
                                       689*****..677**********************98 PP

  == domain 4  score: 13.1 bits;  conditional E-value: 6.7e-06
                              Sel1   3 AmyrLGmfylylnGlg.vpkDpekAiewyekAAeq 36 
                                       Am   +   +y +G   + k  ++++ w+++AA++
  gi|474934364|ref|YP_007687946.1| 128 AMVEIA--KWYRDGENlLAKSTDLCLAWLRRAADR 160
                                       899999..888****65888*************96 PP

  == domain 5  score: 20.2 bits;  conditional E-value: 3.8e-08
                              Sel1   1 aeAmyrLGmfylylnGlgvpkDpekAiewyekA 33 
                                       ++A+y LG  ++y +G gv+kD++ ++ ++e A
  gi|474934364|ref|YP_007687946.1| 163 PDALYELG--CMYSFGEGVEKDVKTGRILLEYA 193
                                       68******..666**********9999999866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       241  (0.0134419); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1404.38
//
Query:       gi|474934365|ref|YP_007687947.1|  [L=65]
Description: hypothetical protein TALC_00792 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.49
# Mc/sec: 402.33
//
Query:       gi|474934366|ref|YP_007687948.1|  [L=180]
Description: CDP-alcohol phosphatidyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-10   40.1   0.4    4.6e-10   40.1   0.4    2.7  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
  ------ inclusion threshold ------
      0.039   13.6   0.0        2.6    7.7   0.0    2.2  2  DUF4222          Domain of unknown function (DUF4222)
        6.9    6.6   9.0        1.1    9.2   4.6    2.0  2  DUF2970          Protein of unknown function (DUF2970)


Domain annotation for each model (and alignments):
>> CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.4   7.6e-14   4.6e-10       2      66 .]       5      66 ..       4      66 .. 0.85
   2 ?   -3.9   6.2         3   1.8e+04      47      47 ..     107     107 ..      67     168 .. 0.55

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 7.6e-14
                                      -HHHHHHHHHHHHHHHHHGGGS-H..HHHHHHHH.HHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
                   CDP-OH_P_transf  2 lPnaiTllrlllsvlailllltyyplvlaillll.iasltDalDGklARrlnqvstlGkllDslaD 66
                                      +P+ ++ +r++l    +l+l+ ++pl + +l++  +a++tD+lDG+lAR ++++++ G +lDs aD
  gi|474934366|ref|YP_007687948.1|  5 APDCLSASRIAL----ALVLFLTEPLSWQFLIIYaAAGTTDILDGRLARMTGKTTRHGPYLDSTAD 66
                                      7999*******9....445557788777777776588****************888********99 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 3
                                       H CS
                   CDP-OH_P_transf  47 l 47 
                                       l
  gi|474934366|ref|YP_007687948.1| 107 L 107
                                       0 PP

>> DUF4222  Domain of unknown function (DUF4222)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0   0.00043       2.6      16      41 ..      96     121 ..      95     123 .. 0.91
   2 ?    3.7   0.0    0.0078        47      31      43 ..     163     176 ..     147     177 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00043
                           DUF4222  16 vVkvisvdenrVtFrRdGYehpcvap 41 
                                       vV+v++ ++    +rR+ + h+++ +
  gi|474934366|ref|YP_007687948.1|  96 VVRVTGFAAGSLRYRRPAFVHTNMSK 121
                                       8********************99865 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0078
                           DUF4222  31 R.dGYehpcvaple 43 
                                       R dGY+ +c+  ++
  gi|474934366|ref|YP_007687948.1| 163 RsDGYDPDCASAIS 176
                                       55*******98776 PP

>> DUF2970  Protein of unknown function (DUF2970)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1      0.86   5.2e+03      30      39 ..      88      97 ..      82     104 .. 0.51
   2 ?    9.2   4.6   0.00018       1.1      28      52 ..     129     153 ..     127     155 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.86
                           DUF2970 30 plhviivGli 39
                                      ++ + +++++
  gi|474934366|ref|YP_007687948.1| 88 LVWIAAIAVV 97
                                      3444444444 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00018
                           DUF2970  28 lsplhviivGlilaalfvllLillV 52 
                                       lsp  +ii+G++ ++l+v+++ ++ 
  gi|474934366|ref|YP_007687948.1| 129 LSPFLIIIIGIVPTVLLVGAVATVS 153
                                       79******************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1266.34
//
Query:       gi|474934367|ref|YP_007687949.1|  [L=284]
Description: hypothetical protein TALC_00794 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.7e-10   39.3   0.0    1.3e-09   38.1   0.0    1.6  1  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
  ------ inclusion threshold ------
      0.025   15.0   0.2       0.45   11.0   0.1    2.7  3  OAM_dimer       Dimerisation domain of d-ornithine 4,5-aminom
      0.043   13.8   0.3       0.24   11.3   0.1    2.3  2  TerB            Tellurite resistance protein TerB
      0.046   14.3   0.1        2.1    8.9   0.0    2.2  2  FliG_N          FliG N-terminal domain


Domain annotation for each model (and alignments):
>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.0   2.9e-13   1.3e-09       5      84 ..     159     234 ..     156     238 .. 0.87

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 2.9e-13
                                       HHHHHHHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETTGSEEEEEEEEE CS
                    Putative_PNPOx   5 lreflaeskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallflddelgrgvrieGta 81 
                                       + +fl+e+k++vlAT+d d  P +++++lk   +  +++fa+ +  + +++l++npr+ +l  +    + +r +G+a
  gi|474934367|ref|YP_007687949.1| 159 IDAFLNEAKTFVLATADGDQ-PRMRVLGLKLKLDG-KLYFAVGTFKDVYKQLQANPRCEILASSGM--EFLRWDGKA 231
                                       679*************9999.*********77776.9***********************987777..777777777 PP

                                       EEE CS
                    Putative_PNPOx  82 elv 84 
                                        + 
  gi|474934367|ref|YP_007687949.1| 232 VFT 234
                                       665 PP

>> OAM_dimer  Dimerisation domain of d-ornithine 4,5-aminomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.047   2.1e+02       2      14 ..      69      81 ..      68      84 .. 0.89
   2 ?   11.0   0.1    0.0001      0.45      25      48 ..      79     102 ..      75     108 .. 0.86
   3 ?   -3.4   0.0       3.1   1.4e+04      37      63 ..     255     268 ..     248     278 .. 0.53

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.047
                                      E---SSSTT--EE CS
                         OAM_dimer  2 ikPygdtlnDGvv 14
                                      +kP  dt++DG v
  gi|474934367|ref|YP_007687949.1| 69 LKPMFDTMADGDV 81
                                      89*********87 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0001
                                       CHHHHHHHHHHHHCTTSEEEEEEE CS
                         OAM_dimer  25 eeeAeeAAlelakkmGledpeVvh 48 
                                       ++++ e A+e+ ++mGl++peV +
  gi|474934367|ref|YP_007687949.1|  79 GDVGYEKAKEMFNQMGLSEPEVYQ 102
                                       6778899**************975 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 3.1
                                       HCTTSEEEEEEEEEEEETTEEEEEEEE CS
                         OAM_dimer  37 kkmGledpeVvhkeelheeftffvvyG 63 
                                       +             +++ +  ff + G
  gi|474934367|ref|YP_007687949.1| 255 N-------------QMGWKLGFFTLEG 268
                                       3.............4444444555555 PP

>> TerB  Tellurite resistance protein TerB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   5.5e-05      0.24      37     128 ..      55     148 ..      15     162 .. 0.75
   2 ?    7.5   0.0   0.00081       3.6      27      56 ..     120     149 ..     114     178 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.5e-05
                              TerB  37 vakaDgqvsesErqafrellksrfglspeeakallelfeeaeeeavdleqftr....alkrklspeqrraliealwe 109
                                       v +aDg ++e+E   ++ ++ ++++  +   +++ e f++   ++++++q +      +  ++s+e++ +++ ++  
  gi|474934367|ref|YP_007687949.1|  55 V-AADGVLTEEEFLMLKPMF-DTMADGDVGYEKAKEMFNQMGLSEPEVYQEIVdtmvDIIGMVSEETKDDIVMLCLM 129
                                       4.489999999999999999.55555777778889999999988888887653111133444558888888888888 PP

                              TerB 110 iAlADGeldeaEdavlrrv 128
                                           DG+++e+E++ +++ 
  gi|474934367|ref|YP_007687949.1| 130 TCAMDGHISEKEKDWIKQL 148
                                       8888999999999999876 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00081
                              TerB  27 alalaallaevakaDgqvsesErqafrell 56 
                                       ++ ++ l++   ++Dg +se+E++ +++l+
  gi|474934367|ref|YP_007687949.1| 120 KDDIVMLCLMTCAMDGHISEKEKDWIKQLV 149
                                       567788999999999999999999999887 PP

>> FliG_N  FliG N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.03   1.4e+02      42      93 ..      11      62 ..       8      66 .. 0.89
   2 ?    8.9   0.0   0.00048       2.1      16      80 ..      82     150 ..      80     165 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.03
                                      HTTXXHHHHHHHHHHHHHHHHCCCCHHCHHHHHHHHHHHHHHSHHHHHHHCH CS
                            FliG_N 42 lksvskeeveaVleefleeleaqeylseggeeyarelLekalgeekaeelle 93
                                      l+ ++k++ +aV+++  +++ ++ ++ +gg +++ + L+  l +  a+ +l 
  gi|474934367|ref|YP_007687949.1| 11 LEGLDKQTFAAVMNKKSADVLNALTALSGGTSAINTYLHFILASVAADGVLT 62
                                      788999**************99999999*******99999998888888875 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00048
                                       XHHHHHHHHTTS...XHHHHHHHHHHHHC.HTTXXHHHHHHHHHHHHHHHHCCCCHHCHHHHHHHHHHH CS
                            FliG_N  16 geeeaaevlkhL...deeeiekltkeias.lksvskeeveaVleefleeleaqeylseggeeyarelLe 80 
                                       g e+a+e++ ++   ++e  ++++ +++  ++ vs+e++++++   l +++    +se+ ++ +++l  
  gi|474934367|ref|YP_007687949.1|  82 GYEKAKEMFNQMglsEPEVYQEIVDTMVDiIGMVSEETKDDIVMLCLMTCAMDGHISEKEKDWIKQLVA 150
                                       779999999998444577789******873699*****************************9998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 1738.36
//
Query:       gi|474934368|ref|YP_007687950.1|  [L=177]
Description: hypothetical protein TALC_00795 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.012   15.6   2.1      0.012   15.6   2.1    3.0  2  DUF2798   Protein of unknown function (DUF2798)
        3.8    7.4   5.6        3.1    7.7   0.9    2.4  2  Flp_Fap   Flp/Fap pilin component


Domain annotation for each model (and alignments):
>> DUF2798  Protein of unknown function (DUF2798)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   2.1   1.4e-06     0.012       2      52 ..      18      68 ..      17      76 .. 0.88
   2 ?    2.5  12.4     0.017   1.5e+02       1      55 [.     100     161 ..      91     165 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.4e-06
                           DUF2798  2 lmsllmslimSgiitllnlGfsddflsaWlkawllAwpvAfpivllvaPlv 52
                                      +++++ sl++ g+  +  +G++ d +  +l  +ll wpv+f+i++++a +v
  gi|474934368|ref|YP_007687950.1| 18 IIAGISSLLIGGYNAYDSMGYGIDSFGDFLMDYLLIWPVMFLIAFFLANFV 68
                                      789****************************************88877554 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.017
                           DUF2798   1 llmsllmsli...mSgiitllnlGfs...ddflsaWlkawllAwpvAfpi.vllvaPlvrkl 55 
                                       l+ms++++++   + g i ++  G +    + +++W + w   +++Af +  l++ P +r  
  gi|474934368|ref|YP_007687950.1| 100 LMMSAILTFVgglVGGSIGAMLGGQTvevVEVVRNWPRIWPRNFCIAFWVeMLIAQPAARMA 161
                                       678888888888888888888888777778999*****************889999988855 PP

>> Flp_Fap  Flp/Fap pilin component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.9   0.00034       3.1      13      29 ..      15      31 ..      12      37 .. 0.86
   2 ?    1.5   0.3     0.031   2.8e+02      18      39 ..     100     121 ..      97     125 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00034
                           Flp_Fap 13 YgLIaaliAvviiayvt 29
                                      Yg I a i+ ++i++ +
  gi|474934368|ref|YP_007687950.1| 15 YGMIIAGISSLLIGGYN 31
                                      *************7655 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.031
                           Flp_Fap  18 aliAvviiayvttlgtaLktkF 39 
                                        +++ ++ ++++ +g+++ +++
  gi|474934368|ref|YP_007687950.1| 100 LMMSAILTFVGGLVGGSIGAML 121
                                       46777777********998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1260.87
//
Query:       gi|474934369|ref|YP_007687951.1|  [L=901]
Description: hypothetical protein TALC_00796 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.5e-85  281.0   7.7    4.2e-29  101.1   0.1    6.1  5  LRR_5     BspA type Leucine rich repeat region (6 copies)
    1.6e-17   63.0   0.0      0.003   17.3   0.0    7.8  9  LRR_8     Leucine rich repeat
  ------ inclusion threshold ------
        0.1   12.5   3.2       0.35   10.8   3.2    1.9  1  PsbJ      PsbJ


Domain annotation for each model (and alignments):
>> LRR_5  BspA type Leucine rich repeat region (6 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.8   0.3   6.4e-31   3.8e-27      11     109 ..      94     193 ..      92     194 .. 0.96
   2 !   93.7   0.4   1.4e-30   8.2e-27       3     117 ..     131     249 ..     131     259 .. 0.92
   3 !  101.1   0.1     7e-33   4.2e-29       3     110 ..     284     393 ..     270     406 .. 0.77
   4 !   19.1   0.0   1.6e-07   0.00095      63     113 ..     433     484 ..     426     501 .. 0.59
   5 !    4.3   0.1     0.006        36      39      88 ..     514     558 ..     510     585 .. 0.62

  Alignments for each domain:
  == domain 1  score: 94.8 bits;  conditional E-value: 6.4e-31
                             LRR_5  11 cnltsitipssvtsIgeyaFsnctslksitlpsslteigsyaFsncssltsitipssltsigeyaFsncsslkeitl 87 
                                       +++t+i+i+s +tsIg++aF +  +l+s+t+p+++t ig ++F++c+sl+ +t+p+sl++i++yaF+nc+sl+ i++
  gi|474934369|ref|YP_007687951.1|  94 KDITTIVIQSGITSIGKFAFFDLPNLTSVTIPEGVTLIGYESFYGCRSLSALTLPDSLETIKNYAFQNCTSLTGISI 170
                                       6799************************************************************************* PP

                             LRR_5  88 psnlttigssaFsnc.slesiti 109
                                       p  +tt++s +F +c sl+si +
  gi|474934369|ref|YP_007687951.1| 171 PDGVTTLESGVFTGCsSLQSIDL 193
                                       ***************99**9975 PP

  == domain 2  score: 93.7 bits;  conditional E-value: 1.4e-30
                             LRR_5   3 IgsyaFync.nltsitipssvtsIgeyaFsnctslksitlpsslteigsyaFsncssltsitipssltsigeyaFsn 78 
                                       Ig ++Fy+c +l+ +t+p+s+++I++yaF+nctsl+ i++p+++t+++s +F +cssl+si++  s++ ++ +a  +
  gi|474934369|ref|YP_007687951.1| 131 IGYESFYGCrSLSALTLPDSLETIKNYAFQNCTSLTGISIPDGVTTLESGVFTGCSSLQSIDL-GSIEDLNGNALDG 206
                                       8899***********************************************************.59*********** PP

                             LRR_5  79 csslkeitlpsnlttigs...saFsnc.slesitipssvtkig 117
                                       c+sl++it+p ++t+i s    +F  + sl+sit+++  tk++
  gi|474934369|ref|YP_007687951.1| 207 CNSLTSITIPATVTNIYSadyGCFGRTpSLTSITVEAGSTKFK 249
                                       **********9888776533379************99888776 PP

  == domain 3  score: 101.1 bits;  conditional E-value: 7e-33
                             LRR_5   3 IgsyaFync.nltsitipssvtsIgeyaFsnctslksitlpsslteigsyaFsncssltsitipssltsigeyaFsn 78 
                                       I++ aF+nc +l+++t+p++++ I ++aF+nc sl+s+++p ++t+i++++F +c+sl+s++ pss+t+ig+yaF +
  gi|474934369|ref|YP_007687951.1| 284 IRHAAFSNCpSLQTVTFPDTLKVIYNNAFRNCPSLTSVSIPAGITTINDNSFRECTSLESFSAPSSVTHIGDYAFFG 360
                                       67778888888888888888888888888888888888888888888888888888888888888888888888888 PP

                             LRR_5  79 csslkeitlpsnlttigssaFsnc.slesitip 110
                                       c+sl e+++   +   g+  F++c sl+sit+ 
  gi|474934369|ref|YP_007687951.1| 361 CTSLAEVQIHGVIGAEGQGTFKGCtSLTSITVD 393
                                       888888888777888888888887788888775 PP

  == domain 4  score: 19.1 bits;  conditional E-value: 1.6e-07
                             LRR_5  63 tipssltsigeyaFsncsslkeitlpsnlttigssaFsnc.slesitipssv 113
                                       +ip+ +t +g+ a s + +l+++++p ++t+i+  aF ++  l s+t++++ 
  gi|474934369|ref|YP_007687951.1| 433 SIPEGITAVGDGAISFNAHLRSLSIPDSVTSINGGAFDGTdGLGSVTVSANN 484
                                       4555555555555555555555555555555555555555555555555444 PP

  == domain 5  score: 4.3 bits;  conditional E-value: 0.006
                             LRR_5  39 itlpsslteigsyaFsncssltsitipssltsigeyaFsncsslkeitlp 88 
                                       +t+p+++ +++ +  s+  +ltsit+p+s+   ++ +F +c +l +++ +
  gi|474934369|ref|YP_007687951.1| 514 FTIPDGVATVSGQ-LSSI-HLTSITVPDSF---ENPSFFDCPNLVSVNGN 558
                                       5555555555443.3444.67777777555...45555557777666653 PP

>> LRR_8  Leucine rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   3.2e-05      0.19      11      56 ..     103     147 ..      98     151 .. 0.91
   2 !    6.7   0.0     0.001       6.2      17      52 ..     132     166 ..     128     172 .. 0.87
   3 !    9.5   0.0   0.00013       0.8      13      56 ..     151     193 ..     149     193 .. 0.92
   4 !   17.3   0.0     5e-07     0.003      14      56 ..     175     215 ..     171     218 .. 0.92
   5 ?   -3.7   0.0       1.8   1.1e+04      42      55 ..     227     240 ..     221     242 .. 0.61
   6 !    9.3   0.0   0.00016      0.94      15      53 ..     283     320 ..     280     324 .. 0.92
   7 ?    1.6   0.0      0.04   2.4e+02      37      53 ..     327     343 ..     326     348 .. 0.84
   8 ?    3.0   0.0     0.015        88      13      57 ..     350     393 ..     346     396 .. 0.73
   9 !    7.3   0.0   0.00063       3.8      13      60 ..     438     484 ..     436     484 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.2e-05
                                       S--SEE-TTSSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE- CS
                             LRR_8  11 NrltslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdL 56 
                                       + +ts+++ aF++l+nL++  + +   t +  ++f g++sL  L+L
  gi|474934369|ref|YP_007687951.1| 103 SGITSIGKFAFFDLPNLTSVTIPEG-VTLIGYESFYGCRSLSALTL 147
                                       569*********************9.8888889***********99 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.001
                                       -TTSSTT-TT--EEE--SS---GGGGGGGTT--S-. CS
                             LRR_8  17 ddeaFkglsnLkvLdLsnNllttlspgafsgLpsLr 52 
                                       + e+F+g+++L  L L +  l+t+ + af++++sL+
  gi|474934369|ref|YP_007687951.1| 132 GYESFYGCRSLSALTLPDS-LETIKNYAFQNCTSLT 166
                                       5689************999.999999******9998 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00013
                                       -SEE-TTSSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE- CS
                             LRR_8  13 ltslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdL 56 
                                       l+ ++  aF+++++L+ +++ +   ttl+ g+f g++sL+s+dL
  gi|474934369|ref|YP_007687951.1| 151 LETIKNYAFQNCTSLTGISIPDG-VTTLESGVFTGCSSLQSIDL 193
                                       788999999**********9999.999**************998 PP

  == domain 4  score: 17.3 bits;  conditional E-value: 5e-07
                                       SEE-TTSSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE- CS
                             LRR_8  14 tslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdL 56 
                                       t l+ ++F+g+s+L+++dL++  ++ l+ +a++g++sL+s+++
  gi|474934369|ref|YP_007687951.1| 175 TTLESGVFTGCSSLQSIDLGS--IEDLNGNALDGCNSLTSITI 215
                                       7899****************6..9***************9976 PP

  == domain 5  score: -3.7 bits;  conditional E-value: 1.8
                                       GGGGTT--S-.EEE CS
                             LRR_8  42 pgafsgLpsLrsLd 55 
                                        g+f   psL+s++
  gi|474934369|ref|YP_007687951.1| 227 YGCFGRTPSLTSIT 240
                                       45666666666665 PP

  == domain 6  score: 9.3 bits;  conditional E-value: 0.00016
                                       EE-TTSSTT-TT--EEE--SS---GGGGGGGTT--S-.E CS
                             LRR_8  15 slddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrs 53 
                                       +++  aF+++++L++    +  l+++ ++af+++psL+s
  gi|474934369|ref|YP_007687951.1| 283 DIRHAAFSNCPSLQTVTFPDT-LKVIYNNAFRNCPSLTS 320
                                       7999****************9.999999*********97 PP

  == domain 7  score: 1.6 bits;  conditional E-value: 0.04
                                       --GGGGGGGTT--S-.E CS
                             LRR_8  37 lttlspgafsgLpsLrs 53 
                                       +tt++ ++f+ ++sL+s
  gi|474934369|ref|YP_007687951.1| 327 ITTINDNSFRECTSLES 343
                                       78999999999999986 PP

  == domain 8  score: 3.0 bits;  conditional E-value: 0.015
                                       -SEE-TTSSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE-- CS
                             LRR_8  13 ltslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLs 57 
                                        t+++d aF+g+++L + ++    +    +g+f g++sL+s++++
  gi|474934369|ref|YP_007687951.1| 350 VTHIGDYAFFGCTSLAEVQIHGV-IGAEGQGTFKGCTSLTSITVD 393
                                       67888888888888888877665.666667777777777777665 PP

  == domain 9  score: 7.3 bits;  conditional E-value: 0.00063
                                       -SEE-TTSSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE--SS- CS
                             LRR_8  13 ltslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNr 60 
                                       +t+++d+a + + +L++L++ +   t+++ gaf+g   L s ++s N+
  gi|474934369|ref|YP_007687951.1| 438 ITAVGDGAISFNAHLRSLSIPDS-VTSINGGAFDGTDGLGSVTVSANN 484
                                       899*******************9.9**********9999999988885 PP

>> PsbJ  PsbJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   3.2   5.8e-05      0.35       7      29 ..     874     896 ..     868     896 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.8e-05
                                       S-HHHHHHHHHHHHHHHHHHHHH CS
                              PsbJ   7 IPLWlVatvaGlgvitvvglFfY 29 
                                        P W+Va++a   +++ vg+Ff+
  gi|474934369|ref|YP_007687951.1| 874 FPIWIVAVIAIAVAVAAVGTFFF 896
                                       6*********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (901 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.72u 0.32s 00:00:01.04 Elapsed: 00:00:00.48
# Mc/sec: 5599.35
//
Query:       gi|474934370|ref|YP_007687952.1|  [L=70]
Description: hypothetical protein TALC_00797 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 504.85
//
Query:       gi|474934371|ref|YP_007687953.1|  [L=106]
Description: hypothetical protein TALC_00798 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 734.33
//
Query:       gi|474934372|ref|YP_007687954.1|  [L=410]
Description: hypothetical protein TALC_00799 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-26   92.7   0.2    3.7e-26   91.7   0.2    1.5  1  HEPN_LA2681  LA2681-like HEPN
  ------ inclusion threshold ------
      0.092   12.9   0.0       0.27   11.4   0.0    1.8  1  LZ3wCH       Leucine zipper with capping helix domain


Domain annotation for each model (and alignments):
>> HEPN_LA2681  LA2681-like HEPN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.7   0.2   4.1e-30   3.7e-26       5     209 ..     203     405 ..     199     406 .. 0.88

  Alignments for each domain:
  == domain 1  score: 91.7 bits;  conditional E-value: 4.1e-30
                       HEPN_LA2681   5 eeepelfglfnqlKqeYisaRyllyeglelkdkehfsdkdvkl.vdtldyelyslrteklklafrsaYsllDKiaff 80 
                                        + pel+ +++++ + ++++R+ +y +++      + ++  ++ +++ ++++  +++e+l   +  +Ys+lDKi+++
  gi|474934372|ref|YP_007687954.1| 203 FRVPELNIMMEDVMETFAHCRFQVYTATS------YVSSIAEVaYSFSPMAKRIFNQELLLDIYPRLYSVLDKISHI 273
                                       5789999**********************......666666666999****************************** PP

                       HEPN_LA2681  81 ineyfelgikek..kvsfrsiWykkkkkkke.......lnekleeseNlaLrgLywlskDlvelkekliepeakelk 148
                                       +++ + ++ +++   +  +  +++  k+ ++       l + +e +++++ r++y+  kD    +  ++ pea++++
  gi|474934372|ref|YP_007687954.1| 274 VMKSCGITLSPNkdGYLPQPSYNQIVKEIRShsdgnpyLLTLCEIFDEINPRYIYYKKKD---QPFYAMLPEAEDMD 347
                                       *******9999988555555666555555555666999**********************...33338********* PP

                       HEPN_LA2681 149 eiRnaleHrylkiteegaskesessdelaytisreeleektlkllklvRsaliylslavel 209
                                       +iR+++ H+ +++t e++ k+s   ++  ++i+++e+ +++++ll lv++a+++++lave+
  gi|474934372|ref|YP_007687954.1| 348 RIRHHIVHSSISLTVEDSGKKS---NKDICYITEREFAQRCHDLLCLVKEAIMNTCLAVEY 405
                                       **************96666555...9********************************987 PP

>> LZ3wCH  Leucine zipper with capping helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0     3e-05      0.27       4      44 ..      83     126 ..      73     130 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3e-05
                            LZ3wCH   4 eekkkatkkakeaanrWtd....nifdikswikekfpkskkelne 44 
                                       ++++  +k++ke  nr++d     i++++ + + ++  +kk ++ 
  gi|474934372|ref|YP_007687954.1|  83 KKLRILYKVYKEVPNRYRDlfagYIYNLLAYFLDRYKDDKK-FFY 126
                                       5778889***************************9996665.444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       758  (0.0422779); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 3085.19
//
Query:       gi|474934373|ref|YP_007687955.1|  [L=232]
Description: hypothetical protein TALC_00800 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-05   24.3   0.1    5.2e-05   22.7   0.0    1.9  2  HTH_24          Winged helix-turn-helix DNA-binding
    6.7e-05   22.9   0.1    0.00012   22.1   0.1    1.3  1  HTH_20          Helix-turn-helix domain
     0.0001   22.1   0.0    0.00024   20.9   0.0    1.7  1  MarR_2          MarR family
    0.00072   18.5   0.0    0.00093   18.1   0.0    1.1  1  Cas_Cas02710    CRISPR-associated protein (Cas_Cas02710)
     0.0021   17.5   0.0     0.0033   16.9   0.0    1.3  1  RtcR            Regulator of RNA terminal phosphate cyclase
     0.0023   17.6   0.2     0.0027   17.4   0.2    1.1  1  Cas_DxTHG       CRISPR-associated (Cas) DxTHG family
     0.0064   16.2   0.0       0.01   15.5   0.0    1.3  1  RP-C            Replication protein C N-terminal domain
  ------ inclusion threshold ------
      0.013   15.4   0.1      0.049   13.5   0.0    2.0  3  HTH_5           Bacterial regulatory protein, arsR family
      0.029   14.9   0.2        0.5   10.9   0.1    2.8  3  HTH_27          Winged helix DNA-binding domain
      0.097   12.8   0.0       0.22   11.7   0.0    1.6  2  B-block_TFIIIC  B-block binding subunit of TFIIIC
       0.12   12.6   0.6        5.5    7.3   0.0    2.9  3  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       2.5     4e+03      38      47 ..      49      58 ..      48      58 .. 0.86
   2 !   22.7   0.0   3.2e-08   5.2e-05      18      48 .]     171     201 ..     153     201 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.5
                            HTH_24 38 lkrLeeeGlI 47
                                      +++L e+G++
  gi|474934373|ref|YP_007687955.1| 49 MEKLGEMGYV 58
                                      7899999*97 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 3.2e-08
                            HTH_24  18 isqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                        ++ ++A+r ++ p++v ++++rL ++G+I+
  gi|474934373|ref|YP_007687955.1| 171 VCNVDVARRFDMKPQAVMYHINRLLDAGVIE 201
                                       6899**************************7 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.1   7.3e-08   0.00012      16      57 ..     158     203 ..     152     205 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 7.3e-08
                                       HHHH....STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20  16 lraL....araegltaselaerldlskntlsyHLrvLeeagLvevv 57 
                                       lr +     r+++++  ++a+r+d++++ + yH++ L +ag +e +
  gi|474934373|ref|YP_007687955.1| 158 LRFIaeeqDRRREVCNVDVARRFDMKPQAVMYHINRLLDAGVIEME 203
                                       444466667788888899*************************987 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.4e-07   0.00024      26      55 ..     175     204 ..     155     216 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.4e-07
                                       HHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2  26 elarrlglsksavsrilkrLvaaGLverrp 55 
                                       ++arr++++++av ++++rL +aG +e ++
  gi|474934373|ref|YP_007687955.1| 175 DVARRFDMKPQAVMYHINRLLDAGVIEMED 204
                                       89************************9884 PP

>> Cas_Cas02710  CRISPR-associated protein (Cas_Cas02710)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   5.7e-07   0.00093      14     103 ..      28     124 ..      17     132 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 5.7e-07
                                       EEEEEE-TGGGGGHHHHHHHH-S-.....EEEEE..--TT-HHHHHHHHHHHHHHS....TTS-EEEE-SSS-HHHH CS
                      Cas_Cas02710  14 rVvflasekSekkleevkealgkklkq..evlld..edandllelykkikevleka...leeeevivDlTgGtkeMt 83 
                                       r+++l+s    k  e+  e l +kl +  +v+    + + d+l++ ++i++++e++    ++ +  vD+T Gt  M+
  gi|474934373|ref|YP_007687955.1|  28 RIILLYSISEDKIYEKTTEILMEKLGEmgYVCESkvIKPFDFLNIVDTIYNIYEQYseeDRRAKFSVDITNGTNLMS 104
                                       66666666555555555555555555555444431145668999999999999999776788899************ PP

                                       HHHHHHHHHHTEEEEEEE-- CS
                      Cas_Cas02710  84 aglalagillrvklsyVgge 103
                                       a++   ++++   + y   +
  gi|474934373|ref|YP_007687955.1| 105 AAACNTAFFMNSDVYYMMDQ 124
                                       ************99998664 PP

>> RtcR  Regulator of RNA terminal phosphate cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0     2e-06    0.0033      28     118 ..      14     103 ..      10     120 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2e-06
                              RtcR  28 PtvslvqqedllvdrleLlyekresklaeevaediaevspetevrlkevelkdpWdfeevyaalldfakaykfdtek 104
                                       Pt++ ++     +dr+ Lly+ +e k+ e+ +e + e   e+     e ++ +p+df ++  +++++ ++y+ +  +
  gi|474934373|ref|YP_007687955.1|  14 PTLNTIKAIPNAIDRIILLYSISEDKIYEKTTEILMEKLGEMGYVC-ESKVIKPFDFLNIVDTIYNIYEQYSEEDRR 89 
                                       777777777889*****************99998777666666544.456778************************ PP

                              RtcR 105 edYlvhittGthva 118
                                        ++ v+it Gt ++
  gi|474934373|ref|YP_007687955.1|  90 AKFSVDITNGTNLM 103
                                       ***********886 PP

>> Cas_DxTHG  CRISPR-associated (Cas) DxTHG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.2   1.6e-06    0.0027      44     129 ..      25     107 ..      14     174 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.6e-06
                         Cas_DxTHG  44 dpdkvvilltdtladkeaeek..eeaak.lkeeleelleiekvdveiipgggteeelweifekllekleende...i 114
                                         d++++l         +e+k  e++ + l e+l e+  + + +   +    ++ ++++ +++++e++ e+d+   +
  gi|474934373|ref|YP_007687955.1|  25 AIDRIILLYSI------SEDKiyEKTTEiLMEKLGEMGYVCESK---VIKPFDFLNIVDTIYNIYEQYSEEDRrakF 92 
                                       33466555555......555556778888999998887744455...44478888899999999999999977888* PP

                         Cas_DxTHG 115 ilDiThGfrylPvla 129
                                        +DiT+G++ +   a
  gi|474934373|ref|YP_007687955.1|  93 SVDITNGTNLMSAAA 107
                                       ***********3333 PP

>> RP-C  Replication protein C N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   6.2e-06      0.01      74     109 ..     173     208 ..     170     223 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.2e-06
                              RP-C  74 NaqLsralglsestlrrhlaaLveaGliirrDspng 109
                                       N + +r++++ ++++ +h+ +L +aG+i + D  + 
  gi|474934373|ref|YP_007687955.1| 173 NVDVARRFDMKPQAVMYHINRLLDAGVIEMEDAYTP 208
                                       77889***************************7544 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       2.4   3.9e+03       4      22 ..      28      49 ..      27      54 .. 0.61
   2 ?   -2.5   0.0         3     5e+03      38      45 ..      51      58 ..      49      58 .. 0.87
   3 ?   13.5   0.0     3e-05     0.049      13      46 ..     163     201 ..     154     202 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.4
                                      HHHHHHHHTT...SSEEHHHHH CS
                             HTH_5  4 RlkILklLae...gelcvcela 22
                                      R+ +L++ +e    e++   l+
  gi|474934373|ref|YP_007687955.1| 28 RIILLYSISEdkiYEKTTEILM 49
                                      7778888888544445554455 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3
                                      HHHHTTSE CS
                             HTH_5 38 kLreaGLV 45
                                      kL e+G+V
  gi|474934373|ref|YP_007687955.1| 51 KLGEMGYV 58
                                      899***98 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 3e-05
                                       T.....SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  13 e.....gelcvcelaeelglsqstvShHLkkLreaGLVe 46 
                                       e     +e c  + a+ +++ + +v +H ++L +aG++e
  gi|474934373|ref|YP_007687955.1| 163 EeqdrrREVCNVDVARRFDMKPQAVMYHINRLLDAGVIE 201
                                       544545888999************************996 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.53   8.6e+02      39      48 ..      49      58 ..      12      63 .. 0.85
   2 ?   -1.7   0.0       2.6   4.2e+03      51      61 ..      82      92 ..      79      97 .. 0.80
   3 ?   10.9   0.1   0.00031       0.5       9      56 ..     158     208 ..     150     218 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.53
                            HTH_27 39 lkkLtekGLv 48
                                      ++kL e+G+v
  gi|474934373|ref|YP_007687955.1| 49 MEKLGEMGYV 58
                                      6899999999 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.6
                            HTH_27 51 tgdeadrrekr 61
                                      + +e+drr+k+
  gi|474934373|ref|YP_007687955.1| 82 QYSEEDRRAKF 92
                                      66899***986 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00031
                            HTH_27   9 Lhlir...hrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdead 56 
                                       L+ i+    rrr++   d+++r ++  ++++y +++L  +G++e++   ++
  gi|474934373|ref|YP_007687955.1| 158 LRFIAeeqDRRREVCNVDVARRFDMKPQAVMYHINRLLDAGVIEMEDAYTP 208
                                       67777754455555569**************************88765555 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       6.6   1.1e+04      40      54 ..      50      64 ..      48      88 .. 0.66
   2 ?   11.7   0.0   0.00013      0.22      21      53 ..     173     205 ..     154     223 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 6.6
                    B-block_TFIIIC 40 ksLekkgLIvkqsii 54
                                       +L + g++   ++i
  gi|474934373|ref|YP_007687955.1| 50 EKLGEMGYVCESKVI 64
                                      567777777766664 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00013
                    B-block_TFIIIC  21 qsdLakeskqdprslfyrlksLekkgLIvkqsi 53 
                                         d+a+ ++++p  + y+++ L + g I++  +
  gi|474934373|ref|YP_007687955.1| 173 NVDVARRFDMKPQAVMYHINRLLDAGVIEMEDA 205
                                       5799999**********************9987 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.3   2.1e+03      13      28 ..      32      47 ..      30      48 .. 0.90
   2 ?    1.9   0.1      0.16   2.6e+02      43      53 ..      49      59 ..      44      63 .. 0.83
   3 ?    7.3   0.0    0.0034       5.5      10      55 ..     158     203 ..     153     206 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.3
                                      HHHHHHHHSSB-HHHH CS
                    Fe_dep_repress 13 IYtlseekkvvktkdl 28
                                      +Y++se+k + kt+++
  gi|474934373|ref|YP_007687955.1| 32 LYSISEDKIYEKTTEI 47
                                      699*****99999987 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.16
                                      HHHHHHTTSEE CS
                    Fe_dep_repress 43 lkkLekdGyve 53
                                      ++kL ++Gyv 
  gi|474934373|ref|YP_007687955.1| 49 MEKLGEMGYVC 59
                                      589******95 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0034
                                       HHHHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                    Fe_dep_repress  10 LetIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyveye 55 
                                       L+ I + ++ +  v + d+a+r + +p  V   +++L ++G +e e
  gi|474934373|ref|YP_007687955.1| 158 LRFIAEEQDRRREVCNVDVARRFDMKPQAVMYHINRLLDAGVIEME 203
                                       56666667777888999***********************988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 1285.80
//
Query:       gi|474934374|ref|YP_007687956.1|  [L=379]
Description: hypothetical protein TALC_00801 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.4e-06   26.8   0.2    3.2e-05   24.3   0.0    2.2  2  HEPN_Apea  Apea-like HEPN


Domain annotation for each model (and alignments):
>> HEPN_Apea  Apea-like HEPN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0     0.076   1.4e+03      53      76 ..     159     182 ..     108     195 .. 0.70
   2 !   24.3   0.0   1.8e-09   3.2e-05       6      93 ..     204     300 ..     200     347 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.076
                         HEPN_Apea  53 kislrsnaylke.dkeerkelkkki 76 
                                       ++slr+   +++ d++e+k+++k+ 
  gi|474934374|ref|YP_007687956.1| 159 NMSLRA-LPIFTlDDDEKKDFQKFY 182
                                       455566.555555677888877654 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 1.8e-09
                         HEPN_Apea   6 fekrlkralewfgeaireeddedaildlvialEaldll.....ldkkeeitekislrsn...ayl.ke....dkeer 69 
                                       + + +k  l+ ++ a+r +d e+a++ +  + E    +     +     i e +s+r++   ++   +    + +++
  gi|474934374|ref|YP_007687956.1| 204 KDQLTKKMLDLYRNAYRCNDVETAFIAISGIWELFAQQfpeegS---P-IGEGVSERIRqsvSRMvRNggvvKGKKQ 276
                                       44589999*********7777999***********544764331...2.6666665554444555533579889999 PP

                         HEPN_Apea  70 kelkkkikklYdlRSkivHggkik 93 
                                        +l+kk+  lY  RS ivH +k +
  gi|474934374|ref|YP_007687956.1| 277 ANLYKKVGYLYRQRSIIVHKDKDE 300
                                       *******************98654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2379.09
//
Query:       gi|474934375|ref|YP_007687957.1|  [L=276]
Description: Molybdenum cofactor biosynthesis enzyme [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.9e-18   66.8   0.2    5.2e-18   66.0   0.2    1.4  1  Radical_SAM  Radical SAM superfamily
    2.9e-05   24.2   0.1    6.6e-05   23.0   0.1    1.6  1  Fer4_14      4Fe-4S single cluster domain
    0.00012   22.4   0.1    0.00027   21.2   0.0    1.6  2  Fer4_12      4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.084   13.0   0.0       0.22   11.6   0.0    1.7  2  DUF1959      Domain of unknown function (DUF1959)


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.0   0.2   1.2e-21   5.2e-18       4     164 ..      19     169 ..      16     172 .. 0.88

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 1.2e-21
                                       ESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   4 trgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiri 80 
                                       +  Cn+rC +C  +       +  ++ + + ++ +  l +e gv+ + l ggep+lyp + +     +     g+++
  gi|474934375|ref|YP_007687957.1|  19 YGKCNYRCEHCFDR-----CLTKNYMRPADWVDTLTFL-KEYGVEKINLAGGEPTLYPFLDQMCYLVKGM---GFKL 86 
                                       568***********.....589****************.6889*************99666666666665...**** PP

                                       EEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHH.HHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  81 tvetngtlpdeeklerllelgvdrvslgleaadde.kvlklmnrghtfeevlealeklreagikrvvdrivglpGen 156
                                       ++++ng l +e+++er+     d++ l+++++d+e ++l   +rg+ +e ++++ +++r++gik v+ +i++++   
  gi|474934375|ref|YP_007687957.1|  87 SIVSNGSLMTEDWMERMEGVV-DWIGLSIDSVDEEdEILIGRGRGGHLENIVQVAQMARRHGIK-VKLNITVVRRSW 161
                                       *******************55.*************86666666*********************.*******99777 PP

                                       HHHHHHHH CS
                                       xxxxxxxx RF
                       Radical_SAM 157 deeleell 164
                                       +++++ ++
  gi|474934375|ref|YP_007687957.1| 162 MKDFKPFI 169
                                       77776665 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.1   1.5e-08   6.6e-05       5      94 ..      19      97 ..      16     116 .. 0.72

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.5e-08
                           Fer4_14  5 lsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekki 83
                                       ++Cn  C  C+++    +++  p +  +  + l   k++ +  +++ l GGeP +y   + l++++  +k  +  +k 
  gi|474934375|ref|YP_007687957.1| 19 YGKCNYRCEHCFDRC-LTKNYMRPADWVDTLTFL---KEYGV--EKINLAGGEPTLY---PFLDQMCYLVKGMG--FKL 86
                                      689***********9.555555555444443444...55555..6799*******99...89999999999999..888 PP

                           Fer4_14 84 wletngtleie 94
                                       + +ng+l+ e
  gi|474934375|ref|YP_007687957.1| 87 SIVSNGSLMTE 97
                                      99999999843 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0     6e-08   0.00027      12     111 ..      19     110 ..       9     136 .. 0.77
   2 ?   -3.6   0.0       2.8   1.2e+04      86     102 ..     193     209 ..     181     216 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 6e-08
                           Fer4_12  12 vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdi 88 
                                        + Cn +C+ Cf       ++ ++ +       ++ lk++ +e++ l GGEP l   ++ l ++++ vk  ++ k  
  gi|474934375|ref|YP_007687957.1|  19 YGKCNYRCEHCFD-RCLTKNYMRPAD---WVDTLTFLKEYGVEKINLAGGEPTL---YPFLDQMCYLVKGMGF-KLS 87 
                                       678*********4.344444444443...45556899999**************...99999********999.789 PP

                           Fer4_12  89 wlytgytleelskkekeellkei 111
                                       ++++g+ + e   ++ e +++ i
  gi|474934375|ref|YP_007687957.1|  88 IVSNGSLMTEDWMERMEGVVDWI 110
                                       99999988776555555555555 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.8
                           Fer4_12  86 kdiwlytgytleelskk 102
                                       +d w+ t  ++++++++
  gi|474934375|ref|YP_007687957.1| 193 PDTWSITDEQFDDFRRR 209
                                       46788888888888754 PP

>> DUF1959  Domain of unknown function (DUF1959)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0     5e-05      0.22      25      86 ..     116     178 ..      99     188 .. 0.88
   2 ?   -3.7   0.0       2.9   1.3e+04      48      64 ..     249     265 ..     241     266 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5e-05
                                       THHHHHHHHHHHS-HHHHHHHHHHHHTTHHHHHHHHHHHH.TTHHHHTTTS--S-HHHHHHHH CS
                           DUF1959  25 sveeledilvkklDmasleelhatvesakkeclkrkldiD.LrlcWlsDvleliskedadeik 86 
                                       sv+e  +il+ +  +  le++   +  a+++ +k kl+i  +r  W+ D+  +i + + d++k
  gi|474934375|ref|YP_007687957.1| 116 SVDEEDEILIGRGRGGHLENIVQVAQMARRHGIKVKLNITvVRRSWMKDFKPFIERVNPDRVK 178
                                       4688899*******************************983599******9999998888776 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2.9
                                       HHHTTHHHHHHHHHHHH CS
                           DUF1959  48 tvesakkeclkrkldiD 64 
                                        +e  ++e l r +d+D
  gi|474934375|ref|YP_007687957.1| 249 SFEVVRREGLDREVDVD 265
                                       67888899999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1971.99
//
Query:       gi|474934376|ref|YP_007687958.1|  [L=106]
Description: hypothetical protein TALC_00803 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       244  (0.0136092); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 721.08
//
Query:       gi|474934377|ref|YP_007687959.1|  [L=216]
Description: hypothetical protein TALC_00804 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00056   20.3   0.0     0.0075   16.7   0.0    2.1  1  AAA_17    AAA domain


Domain annotation for each model (and alignments):
>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   4.2e-07    0.0075       4     118 ..      18     154 ..      15     173 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.2e-07
                                       TTSSHHHHHHHHHH.....HHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEE CS
                            AAA_17   4 PGsGKgtqceklve.....kygfthlsaGdllreeakrgglakardemrklpleekkelqkeaaekiaeeakkkgvl 75 
                                         sGK   ++   e      ++f hls  d++r+    + l       r++++ ek++l +e+ ++i   a++++v+
  gi|474934377|ref|YP_007687959.1|  18 SRSGKNYTIDDFIElaksnGVEFVHLSPMDMIRARLDGCRL-------RDMSEAEKQALVDEVRDEIDTVAENHNVI 87 
                                       55666666666654222224589999999****99877777.......66688899999*********999****** PP

                                       EEE-SEE.......EETTEEE.ESSHHHH................HHHH..SEEEEEE--HHHHHHH CS
                            AAA_17  76 vdghpri.......keqagfl.dglpkev................leelkpdaiilleadpeeiler 118
                                       vd h++        k ++g++ ++lp ++                +e+lk+d++ ++++dp  i+er
  gi|474934377|ref|YP_007687959.1|  88 VDEHFCYpatfggkKLENGYYdEKLPHDIlhlpgcvtdyevvfprFESLKYDLFAVMSIDPSIIVER 154
                                       ****976222222222233332455555533333333333333333566777777777777766666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1383.27
//
Query:       gi|474934378|ref|YP_007687960.1|  [L=170]
Description: 5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-07   30.6   0.0    5.6e-06   26.3   0.0    2.2  1  NT5C      5' nucleotidase, deoxy (Pyrimidine), cytosolic type


Domain annotation for each model (and alignments):
>> NT5C  5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   3.1e-10   5.6e-06       4     158 ..       6     157 ..       2     163 .. 0.73

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 3.1e-10
                              NT5C   4 vlvDlDgvladlygkmlevankrf.eatllpeevsswdleefvkPeqreslyrf.ltepglFadlepipgarevLee 78 
                                       +++D+D+vl d+ g  +e    +  +++   ++v    ++ +       +l  f +  + +  +le  ++ re  + 
  gi|474934378|ref|YP_007687960.1|   6 IYFDMDDVLVDFTGGAREFCGIEIrGKNAVGDDVL---FDSI------RELGDFyMRVKPILGSLELFNDVREWYGD 73 
                                       67888888888888888777654414556666666...3444......33444414445677788888888888887 PP

                              NT5C  79 ladegrlvvitaallqfydavkekveWldehlplipyrnlvlvkekd.lv..rgDvlidDapknleklrgrs...il 149
                                        +++  l  + +  +  +   ++k+eW++++l +    n+vl +ek   v  rg vlidD++ n++ ++  +   +l
  gi|474934378|ref|YP_007687960.1|  74 KVEI--LTAVPKPSRNLPTLGEDKIEWVKRYLGGDVVVNIVLRREKVgFVrnRGSVLIDDNAGNIKAWNEAGgtgVL 148
                                       7777..7777777888888999************************63344489***********98875444459* PP

                              NT5C 150 fdsptnrhi 158
                                       f+ p    +
  gi|474934378|ref|YP_007687960.1| 149 FTDPVSAKM 157
                                       *99987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       199  (0.0110993); expected 358.6 (0.02)
Passed bias filter:                      190  (0.0105974); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 1318.14
//
Query:       gi|474934379|ref|YP_007687961.1|  [L=63]
Description: hypothetical protein TALC_00806 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.035   13.9   0.0      0.042   13.7   0.0    1.2  1  DUF3954   Protein of unknown function (DUF3954)


Domain annotation for each model (and alignments):
>> DUF3954  Protein of unknown function (DUF3954)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.3e-06     0.042      22      41 ..      32      51 ..      15      57 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.3e-06
                           DUF3954 22 LnPPvtGfGeqvitWqGGkv 41
                                      + P  tG  e ++tW  Gkv
  gi|474934379|ref|YP_007687961.1| 32 MCPKTTGLAEEMLTWLDGKV 51
                                      35999**************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 387.88
//
Query:       gi|474934380|ref|YP_007687962.1|  [L=132]
Description: hypothetical protein TALC_00807 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 939.61
//
Query:       gi|474934381|ref|YP_007687963.1|  [L=380]
Description: hypothetical protein TALC_00808 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.013   15.4   0.0      0.028   14.3   0.0    1.5  1  TrmB         Sugar-specific transcriptional regulator TrmB
      0.018   15.2   0.1      0.028   14.5   0.1    1.3  1  sCache_like  Single Cache-like
       0.14   11.6   0.1       0.22   11.0   0.1    1.2  1  Mce4_CUP1    Cholesterol uptake porter CUP1 of Mce4, putative


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   4.7e-06     0.028      20      64 ..      17      63 ..      10      64 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.7e-06
                                      HCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST..TTEEEE CS
                              TrmB 20 lgpatadeiaeelgvprskvYevLrsLedkGlVerekgr..pklYra 64
                                      l+  +a+  ++elg+p  ++Y+++ +L    +++ ++g+  p +Y++
  gi|474934381|ref|YP_007687963.1| 17 LKGRSAYAASSELGIPARSAYNIVAKLCHLHYIRAIPGTdnPIIYEP 63
                                      556789999****************************9999999987 PP

>> sCache_like  Single Cache-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   4.6e-06     0.028      35     106 ..     304     371 ..     289     379 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.6e-06
                                       HHHHHHHHHT-EEEEEETTS-EEEETTS...S---HHHHHHHHTT--.....EE-----S-EEEEEEEEETT CS
                       sCache_like  35 vleeasekldaritivdadgkvlydtgqeieeaeseavikellskeerskevviteeeedlyyyavpikkeg 106
                                       + ee++  l+    i+d    v+ +t+   + +++++ i +l++++   + v++ +++++  yya pi +  
  gi|474934381|ref|YP_007687963.1| 304 TSEEVKARLETVFGILDLVTGVQERTAD--ALMRESENIANLVKNNT--EIVSVLTQHQAQMYYASPIEDPQ 371
                                       4577888888888899999999999999..9*************999..999999*************9844 PP

>> Mce4_CUP1  Cholesterol uptake porter CUP1 of Mce4, putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   3.7e-05      0.22      67     141 ..     283     360 ..     271     363 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.7e-05
                         Mce4_CUP1  67 vYadaapdlldaLdnavttsrTiveqqaeLdal...llaavglsntgadllerngdnLirlaadlrptlelLakYsp 140
                                       v+a   + +l+aLd+++    T +e +a+L+++   l  ++g+ +++ad l r ++n+++l+++  + +++L +++ 
  gi|474934381|ref|YP_007687963.1| 283 VFARTPQYVLKALDESSSARCTSEEVKARLETVfgiLDLVTGVQERTADALMRESENIANLVKNNTEIVSVLTQHQA 359
                                       5666677789999998877777666666666642227889********************************99876 PP

                         Mce4_CUP1 141 e 141
                                       +
  gi|474934381|ref|YP_007687963.1| 360 Q 360
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2825.40
//
Query:       gi|474934382|ref|YP_007687964.1|  [L=71]
Description: hypothetical protein TALC_00809 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.04   13.5   0.0       0.28   10.8   0.0    1.9  2  FlbD      Flagellar and Swarming motility proteins
      0.075   13.1   0.0      0.095   12.8   0.0    1.1  1  DUF4366   Domain of unknown function (DUF4366)


Domain annotation for each model (and alignments):
>> FlbD  Flagellar and Swarming motility proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   3.1e-05      0.28      30      53 ..      10      33 ..       8      39 .. 0.90
   2 ?    0.9   0.0     0.039   3.5e+02       2      24 ..      39      61 ..      38      65 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.1e-05
                              FlbD 30 ItLtnGkkyvVkEsvdeviervie 53
                                      I LtnGk + V   + +v++++ +
  gi|474934382|ref|YP_007687964.1| 10 IFLTNGKSFYVDSGARKVMDEILN 33
                                      99******************9986 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.039
                              FlbD  2 IkltrlngeefvlNadlIetiee 24
                                      I+++  +g + ++N d I  ++e
  gi|474934382|ref|YP_007687964.1| 39 IEMQCTDGCHHYMNIDRIIDVKE 61
                                      66666788888999999988776 PP

>> DUF4366  Domain of unknown function (DUF4366)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.1e-05     0.095       4      40 ..      21      56 ..      18      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.1e-05
                           DUF4366  4 peGnltlvddleeesnkqfitvttksgntFYivIDrd 40
                                      ++G+ +++d++  +++ qfi ++  +g   Y+ IDr 
  gi|474934382|ref|YP_007687964.1| 21 DSGARKVMDEI-LNGKGQFIEMQCTDGCHHYMNIDRI 56
                                      78999******.67788******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 463.67
//
Query:       gi|474934383|ref|YP_007687965.1|  [L=52]
Description: hypothetical protein TALC_00810 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.076   12.9   2.7        1.4    8.8   0.2    2.2  2  TFIIS_C        Transcription factor S-II (TFIIS)
        1.1    9.1   6.4        1.1    9.1   1.6    2.3  2  zf-HYPF        HypF finger
        5.2    7.3   7.7    3.9e+02    1.3   7.7    2.6  1  Zn-ribbon_8    Zinc ribbon domain


Domain annotation for each model (and alignments):
>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.2    0.0052        31       2       9 ..       3      10 ..       2      14 .. 0.67
   2 ?    8.8   0.2   0.00024       1.4      26      38 ..      28      40 ..      22      41 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0052
                           TFIIS_C  2 kCpkCgsr 9 
                                      +C kCg +
  gi|474934383|ref|YP_007687965.1|  3 ECAKCGRT 10
                                      67777754 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00024
                           TFIIS_C 26 tvfykCtkCghrW 38
                                       +f+ C +C+h++
  gi|474934383|ref|YP_007687965.1| 28 FLFHLCEECQHEY 40
                                      58999*****986 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.2     0.022   1.3e+02      22      28 ..       2       8 ..       1      12 [. 0.85
   2 ?    9.1   1.6   0.00018       1.1       1       9 [.      32      40 ..      32      43 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.022
                                      ---TTTS CS
                           zf-HYPF 22 isCtnCG 28
                                      + C +CG
  gi|474934383|ref|YP_007687965.1|  2 TECAKCG 8 
                                      5699999 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00018
                                      --HHHHHHH CS
                           zf-HYPF  1 lCedClrEy 9 
                                      lCe+C++Ey
  gi|474934383|ref|YP_007687965.1| 32 LCEECQHEY 40
                                      7*******9 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   7.7     0.065   3.9e+02      28      34 ..      31      38 ..       2      51 .. 0.52

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.065
                       Zn-ribbon_8 28 a.CPeCgs 34
                                      + C eC++
  gi|474934383|ref|YP_007687965.1| 31 HlCEECQH 38
                                      33555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 373.99
//
Query:       gi|474934384|ref|YP_007687966.1|  [L=61]
Description: hypothetical protein TALC_00811 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.14   11.0   0.0       0.14   11.0   0.0    1.0  1  Arylsulfotrans  Arylsulfotransferase (ASST)


Domain annotation for each model (and alignments):
>> Arylsulfotrans  Arylsulfotransferase (ASST)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0     8e-06      0.14      21      55 ..      17      51 ..       3      58 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8e-06
                    Arylsulfotrans 21 nlewdekknnlivDtkGevrWyldqdkisdnklkr 55
                                      n ++  +++++i+D+kG+ rW l++    d+ +++
  gi|474934384|ref|YP_007687966.1| 17 NETKVHASYFVILDEKGNPRWALENLPDPDDFFRE 51
                                      456778899***************99888775554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 464.99
//
Query:       gi|474934385|ref|YP_007687967.1|  [L=327]
Description: Site-specific recombinase, DNA invertase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.5e-20   73.1   0.3    7.6e-20   71.5   0.0    1.9  2  Resolvase  Resolvase, N terminal domain
    0.00088   18.8   0.0     0.0013   18.2   0.0    1.2  1  Pox_F16    Poxvirus F16 protein
  ------ inclusion threshold ------
      0.058   13.4   0.1       0.11   12.5   0.1    1.4  1  Slx4       Slx4 endonuclease


Domain annotation for each model (and alignments):
>> Resolvase  Resolvase, N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.5   0.0   1.3e-23   7.6e-20       1     140 [.      10     154 ..      10     160 .. 0.86
   2 ?   -1.5   0.2       0.4   2.4e+03     118     142 ..     274     298 ..     270     303 .. 0.71

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 1.3e-23
                                       EEEEEEES-----T...HHHHHHHHHHHH-S--..SE...EEEE.S-TT-TT-HHHHHHHHHHTT-EE.EEEESSCC CS
                         Resolvase   1 aigYaRvSteeqdd...slerQkealrayakenglkivkefeDkgvSGakleRpglkrllaalregkgdvlvvekld 74 
                                       a++YaRvSt+ q d   s+e Q++ +r++++++g+++v+ef D+gvSG++++R+++ +++a + +++ d lv ++ +
  gi|474934385|ref|YP_007687967.1|  10 AVIYARVSTKGQADsgvSIETQLKVCRQWCDSQGVTVVAEFHDDGVSGTTTDRDEFAAMIATIISKEPDFLVLYDTS 86 
                                       69*********877777********************************************9999888********* PP

                                       CC-S....S-HHHHHHHHHTT-EEEESS...SS----HHHHHHHHHHHHHHHHHHHHHCT-TTHHHHH CS
                         Resolvase  75 RLaRs.vrdlltlleelrekgvslvslde.gidtstpmgrlllqilaalaeferelirertkeglaaa 140
                                       R++R+   ++ +l++ l+  ++ +v     gi+ ++++ r+++ +  +   +  +    +t+e +++ 
  gi|474934385|ref|YP_007687967.1|  87 RITREgNDKYNKLVQALEGFKCGVVYPGMgGITADSQAARFVVPFKTTTDSILVKESTSKTRESVDRL 154
                                       *****778889999999999999999985257777777888888877777777777777776666665 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.4
                                       HHHHHHHHHHHHHCT-TTHHHHHHH CS
                         Resolvase 118 laalaeferelirertkeglaaaka 142
                                       + ++ e  r++ir+r ++ +++ ++
  gi|474934385|ref|YP_007687967.1| 274 YDSMFEPYRKNIRDRARKEREQCRK 298
                                       5566677888899998887776554 PP

>> Pox_F16  Poxvirus F16 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   2.2e-07    0.0013      14      86 ..      26     101 ..      10     108 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.2e-07
                           Pox_F16  14 aslefqlkvCrdyCeslslqvvkeikefG...yinektLetekWediinndidllvfyqvkqlsisveklYnllik 86 
                                       +s+e qlkvCr++C+s  ++vv e+++ G   + +++        +ii+++ d lv y   +++   +  Yn+l++
  gi|474934385|ref|YP_007687967.1|  26 VSIETQLKVCRQWCDSQGVTVVAEFHDDGvsgTTTDRDEFAAMIATIISKEPDFLVLYDTSRITREGNDKYNKLVQ 101
                                       69***********************986511155555566667778888999999999999999999999998876 PP

>> Slx4  Slx4 endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   1.8e-05      0.11      42      59 ..      29      46 ..      11      48 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.8e-05
                                      GS-HHHHHHHHHHHT--E CS
                              Slx4 42 evdpaelrewcdskgIcc 59
                                      e   +  r+wcds+g+++
  gi|474934385|ref|YP_007687967.1| 29 ETQLKVCRQWCDSQGVTV 46
                                      6778899*********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2010.95
//
Query:       gi|474934386|ref|YP_007687968.1|  [L=299]
Description: hypothetical protein TALC_00813 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.18   11.2   0.6       0.36   10.2   0.6    1.4  1  NMD3      NMD3 family


Domain annotation for each model (and alignments):
>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.6     2e-05      0.36       1      26 [.       4      28 ..       4      37 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 2e-05
                              NMD3  1 CcrCGkeieelinglCedCllkevdi 26
                                      C+ CG+++  + +g+C+dC+ ++  +
  gi|474934386|ref|YP_007687968.1|  4 CIYCGNPSG-RKDGICDDCMGEQRVL 28
                                      9*******9.55*******9888655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.36s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 1628.34
//
Query:       gi|474934387|ref|YP_007687969.1|  [L=301]
Description: hypothetical protein TALC_00814 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 1781.80
//
Query:       gi|474934388|ref|YP_007687970.1|  [L=83]
Description: hypothetical protein TALC_00815 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       248  (0.0138323); expected 358.6 (0.02)
Passed bias filter:                      195  (0.0108762); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 587.50
//
Query:       gi|474934389|ref|YP_007687971.1|  [L=60]
Description: hypothetical protein TALC_00816 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.016   15.3   1.7        2.2    8.4   0.0    2.2  2  Zn-ribbon_8     Zinc ribbon domain
      0.022   14.7   5.5      0.034   14.1   5.5    1.4  1  Zn_ribbon_SprT  SprT-like zinc ribbon domain
      0.026   14.5   3.9      0.048   13.6   3.9    1.5  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
      0.029   13.9   2.9      0.059   12.9   2.9    1.5  1  TF_Zn_Ribbon    TFIIB zinc-binding
        1.9    9.1   7.9         10    6.8   3.5    2.3  2  zf-C2H2         Zinc finger, C2H2 type


Domain annotation for each model (and alignments):
>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0   0.00062       2.2      29      40 .]       3      14 ..       1      14 [. 0.84
   2 ?    6.4   0.4    0.0026       9.4       6      20 ..      25      39 ..      24      47 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00062
                       Zn-ribbon_8 29 CPeCgsevrrvi 40
                                      CP+Cg +  r++
  gi|474934389|ref|YP_007687971.1|  3 CPTCGNRYARLF 14
                                      *****9999975 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0026
                       Zn-ribbon_8  6 YrCeeCghefevlqs 20
                                      YrC+ C   f v+++
  gi|474934389|ref|YP_007687971.1| 25 YRCTHCTCSFIVIRE 39
                                      9*****988887775 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   5.5   9.4e-06     0.034       7      35 ..       3      36 ..       2      39 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.4e-06
                    Zn_ribbon_SprT  7 CtgCgreythhlsi.rrhn...YrCrrCk.gtLr 35
                                      C+ Cg++y + +   +  +   YrC +C  ++++
  gi|474934389|ref|YP_007687971.1|  3 CPTCGNRYARLFFRdDLTKaagYRCTHCTcSFIV 36
                                      **************77777*********877766 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   3.9   1.3e-05     0.048      20      43 ..       2      30 ..       1      33 [. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.3e-05
                     Zn_Tnp_IS1595 20 vCPhCgsr.kayrikt....rglfqCkeC 43
                                      +CP Cg+r    ++++    +  ++C +C
  gi|474934389|ref|YP_007687971.1|  2 ICPTCGNRyARLFFRDdltkAAGYRCTHC 30
                                      6*******966677767999999*****9 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   2.9   1.6e-05     0.059       1      27 [.       1      32 [.       1      34 [. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.6e-05
                                      EEETTTTCEE.C..HEE..TSTTCEEESSSSB CS
                      TF_Zn_Ribbon  1 ykCPnCgstn.l..veD..pergelvCtdCGl 27
                                      ++CP Cg+++     +D  ++ + ++Ct C++
  gi|474934389|ref|YP_007687971.1|  1 MICPTCGNRYaRlfFRDdlTKAAGYRCTHCTC 32
                                      79******9965777779************86 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.014        49       3      12 ..       3      12 ..       1      17 [. 0.82
   2 ?    6.8   3.5    0.0029        10       1      10 [.      25      34 ..      25      36 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.014
                                      ETTTTEEESS CS
                           zf-C2H2  3 CpdCgksFkr 12
                                      Cp Cg ++ r
  gi|474934389|ref|YP_007687971.1|  3 CPTCGNRYAR 12
                                      *****88766 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0029
                                      EEETTTTEEE CS
                           zf-C2H2  1 ykCpdCgksF 10
                                      y+C++C+ sF
  gi|474934389|ref|YP_007687971.1| 25 YRCTHCTCSF 34
                                      9********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.49
# Mc/sec: 370.70
//
Query:       gi|474934390|ref|YP_007687972.1|  [L=210]
Description: Exonuclease [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.6e-07   30.9   0.3    7.1e-06   26.7   0.3    2.2  1  RNase_T    Exonuclease
     0.0032   17.5   0.0       0.02   14.9   0.0    1.9  1  DUF5051    3' exoribonuclease, RNase T-like
  ------ inclusion threshold ------
      0.044   13.8   0.3        1.2    9.1   0.3    2.1  1  RNase_H_2  RNase_H superfamily


Domain annotation for each model (and alignments):
>> RNase_T  Exonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.3   1.2e-09   7.1e-06       1     134 [.       3     171 ..       3     202 .. 0.71

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 1.2e-09
                                       EEEEEEESSSTTCTTS-EEEEEEEEEETTCC.............EEEEEEEEEEEHSSHCSSSHHHHHHHHHCHHHH CS
                           RNase_T   1 vviDlEttgldakekdeiieiaaisidggen.............eigetfhfyvkptelakltdecteftgitqeml 64 
                                       ++iD+Ettgl  ++ d+++ei+  + d                 +i e+ ++yv+p+ +     ++ + +  + e+ 
  gi|474934390|ref|YP_007687972.1|   3 LIIDTETTGLRGIPEDRVLEIGIAEYDEVSGkispvysemirydDIVEFDSKYVNPDGS--RRIWIYRNSDMRVEDT 77 
                                       59***********************999888889*********99999999********..8899999999998886 PP

                                       HTCEBHHH.HHHHHHHHHHHHTCCCETTTCEEEE.SSHHHHHHHHHHHHHHHHHCSEHCECHHHHHHHHHC...... CS
                           RNase_T  65 deapsfke.vleefkellrklallvahnaafdvg.flraadkrilkkevpkrnqfldtlildkatlkelar...... 133
                                        +ap+  + v++e++e++  ++++  +n+ fd g fl ++ + i  + v      +d ++l++ ++ ela+      
  gi|474934390|ref|YP_007687972.1|  78 LNAPKDLDtVVKEVREIVS-GKEVTSYNVGFDFGkFLYQEPWNI-RNMV---TRKIDIMKLATTKVYELADsdsied 149
                                       666665555**********.999999**9999973666666665.5523...3456666666655555555544444 PP

                                       .....................H CS
                           RNase_T 134 .....................t 134
                                                            +
  gi|474934390|ref|YP_007687972.1| 150 kglqerllreredscypekwvR 171
                                       4444444455555555555552 PP

>> DUF5051  3' exoribonuclease, RNase T-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   3.3e-06      0.02       3     162 ..       3     205 ..       1     209 [. 0.70

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.3e-06
                           DUF5051   3 lmiDiEtlgne..etaelvsIGaVff.petG..........eFyaeidlesdeeagidaetieWWlkqskearaell 66 
                                       l+iD+Et+g +  ++  +++IG+  +    G           +  +++++s+   ++d++   W  + s+   +  l
  gi|474934390|ref|YP_007687972.1|   3 LIIDTETTGLRgiPEDRVLEIGIAEYdEVSGkispvysemiRYDDIVEFDSK-YVNPDGSRRIWIYRNSDMRVEDTL 78 
                                       78*******99999**********9976667999956666666666666444.344555555555555555545555 PP

                           DUF5051  67 kdtqeakslkdalqaleeFlekslkvwangasfDlviLraafel................................. 110
                                       +     k l++++++++e +    +v  ++  fD+  + +   +                                 
  gi|474934390|ref|YP_007687972.1|  79 NA---PKDLDTVVKEVREIV-SGKEVTSYNVGFDFGKFLYQEPWnirnmvtrkidimklattkvyeladsdsiedkg 151
                                       44...48899**********.47789999999999877777566888888888888888888888888888888888 PP

                           DUF5051 111 ...........lipwkywndrdvrtlvala...pelekgeekkreipfegvkHnALaDAkhqakav 162
                                                  +     + ++ vr++ a +   p        +  +  eg +H A++DA    +++
  gi|474934390|ref|YP_007687972.1| 152 lqerllreredS----CYPEKWVRSIDAYRvlcP--------EDPMGLEGMRHRAIDDAVMEGWIL 205
                                       888777765431....344666666666662222........344556788999999998777766 PP

>> RNase_H_2  RNase_H superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.3    0.0002       1.2       1      38 [.       3      40 ..       3     178 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0002
                         RNase_H_2  1 lffDiEttGlspkknl.iyliGvldvdekeiekltqlla 38
                                      l +D+EttGl + ++  +  iG++++de + + ++ +  
  gi|474934390|ref|YP_007687972.1|  3 LIIDTETTGLRGIPEDrVLEIGIAEYDEVSGK-ISPVYS 40
                                      5789******9877664899999999996655.333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1341.15
//
Query:       gi|474934391|ref|YP_007687973.1|  [L=78]
Description: hypothetical protein TALC_00818 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.026   15.0   5.0      0.031   14.7   5.0    1.2  1  DUF4491   Domain of unknown function (DUF4491)
       0.45   11.0   7.8       0.27   11.7   6.0    1.5  2  FtsX      FtsX-like permease family
       0.79    9.8   8.2       0.24   11.5   1.6    2.2  2  DUF2892   Protein of unknown function (DUF2892)
        2.8    8.3  16.1         36    4.8  16.1    2.2  1  DUF308    Short repeat of unknown function (DUF308)


Domain annotation for each model (and alignments):
>> DUF4491  Domain of unknown function (DUF4491)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   5.0   6.9e-06     0.031      10      71 ..      10      74 ..       4      78 .] 0.80

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.9e-06
                           DUF4491 10 atfliiglfhpivikaeyy...lgkkiwwvflvagillivaslfvenvllsavlgvlgfsllWsi 71
                                      ++f i g++  ++ika ++   +g+++ w+f+++gi+liv s++ + +++ a  g +++  l +i
  gi|474934391|ref|YP_007687973.1| 10 LVFAIAGFVSDVLIKAFFFsgdFGTEYGWLFILIGIILIVGSVIEAITVCDAKGGWFAVGYLLGI 74
                                      4678888888888888877444789******************9999988888888887776665 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   6.0   6.1e-05      0.27      38      84 ..       9      54 ..       6      72 .. 0.90
   2 ?   -1.5   0.1      0.83   3.7e+03      30      42 ..      67      75 ..      63      77 .. 0.47

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.1e-05
                              FtsX 38 glgllaaqllsdvllssvfsselkisidlitvliiivlllllallag 84
                                      gl +++a ++sdvl + +f ++ ++ + + +++i+i+++l++ +++ 
  gi|474934391|ref|YP_007687973.1|  9 GLVFAIAGFVSDVLIKAFF-FSGDFGTEYGWLFILIGIILIVGSVIE 54
                                      57789999***********.***********************9984 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.83
                              FtsX 30 lvalviGlglgll 42
                                      +v++++G+    l
  gi|474934391|ref|YP_007687973.1| 67 AVGYLLGI----L 75
                                      34444443....2 PP

>> DUF2892  Protein of unknown function (DUF2892)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.6   5.3e-05      0.24       4      48 ..       3      52 ..       1      54 [. 0.64
   2 ?    6.2   1.7    0.0024        11      14      43 ..      47      76 ..      45      78 .] 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.3e-05
                           DUF2892  4 NvgtldRilrivvGlvllllallglsggw.....gwllglvGavllltgl 48
                                      N + ++ ++ +++G+v  +l  ++  +g      gwl++l+G++l++ ++
  gi|474934391|ref|YP_007687973.1|  3 NTQLVEGLVFAIAGFVSDVLIKAFFFSGDfgteyGWLFILIGIILIVGSV 52
                                      666666677777777643333222222224789************99776 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0024
                           DUF2892 14 ivvGlvllllallglsggwgwllglvGavl 43
                                      ++vG+v+ ++ ++   ggw+ + +l+G+ l
  gi|474934391|ref|YP_007687973.1| 47 LIVGSVIEAITVCDAKGGWFAVGYLLGILL 76
                                      79*****************77777888776 PP

>> DUF308  Short repeat of unknown function (DUF308)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8  16.1    0.0081        36      23      65 ..      38      77 ..       7      78 .] 0.57

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0081
                            DUF308 23 alvllfGilllvsGivqiiaafaarkknrggrwlglllGilyl 65
                                      +l +l+Gi+l+v+++++ i   +  + ++g + +g llGil++
  gi|474934391|ref|YP_007687973.1| 38 WLFILIGIILIVGSVIEAI---TVCDAKGGWFAVGYLLGILLI 77
                                      4555555555555555555...556666666778889999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       779  (0.0434492); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.31s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 492.67
//
Query:       gi|474934392|ref|YP_007687974.1|  [L=851]
Description: type I restriction system adenine methylase (hsdM) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.1e-92  308.2   1.5    6.2e-92  308.2   0.0    1.7  2  N6_Mtase       N-6 DNA Methylase
    8.1e-15   55.7   1.9    8.1e-15   55.7   1.9    2.6  3  HsdM_N         HsdM N-terminal domain
    9.9e-05   22.8   0.0    0.00035   21.1   0.0    2.0  1  Eco57I         Eco57I restriction-modification methylase
  ------ inclusion threshold ------
      0.012   15.1   0.1      0.032   13.7   0.1    1.6  1  DIT1_PvcA      Pyoverdine/dityrosine biosynthesis protein
      0.065   12.7   0.6       0.16   11.4   0.0    1.9  2  AviRa          RRNA methyltransferase AviRa
      0.094   12.8   0.0        0.4   10.7   0.0    2.1  1  DUF1266        Protein of unknown function (DUF1266)
       0.13   11.7   0.0       0.23   10.8   0.0    1.4  1  Peptidase_C54  Peptidase family C54
       0.13   11.9   0.0       0.73    9.5   0.0    2.2  1  UPF0020        Putative RNA methylase family UPF0020
       0.62    8.5   5.2       0.46    9.0   3.2    1.6  2  RRN3           RNA polymerase I specific transcription initia


Domain annotation for each model (and alignments):
>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  308.2   0.0   3.1e-95   6.2e-92       2     308 ..     164     471 ..     163     475 .. 0.95
   2 ?   -3.3   0.3       2.1   4.3e+03     246     271 ..     731     758 ..     712     770 .. 0.74

  Alignments for each domain:
  == domain 1  score: 308.2 bits;  conditional E-value: 3.1e-95
                          N6_Mtase   2 skdllGdvYEyllrkfaeeegksgGeffTPrevsklivell....epksgesvyDpacGsggllvqaekvlkeedgk 74 
                                       + d+lG vYEyll++fa+++gk++Gef+TP evs+l+  ++    +++++ ++ Dp +Gsg+ll++  k l++e+ +
  gi|474934392|ref|YP_007687974.1| 164 DYDVLGFVYEYLLEQFASNSGKKAGEFYTPTEVSELMSVIVadhlKNREKITICDPTSGSGSLLLHIGK-LSSETID 239
                                       68***********************************9999887777777889**************99.7899*** PP

                          N6_Mtase  75 tkelsiyGqeknettyrLakmNlllhgieykkvkirlgdtlekpkfe.....kdkkfdvvvaNppfnqkewkektle 146
                                         ++++y q+  e +y+L++mNl+++g++  ++ +r++dtl +++           +d+vv+Npp+++k w   t +
  gi|474934392|ref|YP_007687974.1| 240 WDNIKYYAQDYSEDAYNLTRMNLIMKGVNHWNIFARNKDTLGDDWPLdleqgGPLFVDAVVSNPPYSHK-W---TPK 312
                                       ********************************************9985555555569************.9...889 PP

                          N6_Mtase 147 kderfrea.vapksnadlafllhiieslkpkGraavvlangvLfrggkegkIrkalvekdlveavialpeklFynts 222
                                       +d+rf+++ +apks+ad+afllh ++++k++G +a+vl++gvLfrg+ke++Ir++lve +++e++i lp+++Fynts
  gi|474934392|ref|YP_007687974.1| 313 EDSRFSDYgLAPKSAADYAFLLHDLYHIKHDGIVAIVLPHGVLFRGNKEKDIRQQLVELNQIETIIGLPPNIFYNTS 389
                                       9*****999******************************************************************** PP

                          N6_Mtase 223 iptcilvlkkekaerkgkvlfidaseefkkkdrkknklteediekildtykekskevdkfskvveleeiaendynln 299
                                       i t+i++lkk++   +g++lf++as+ f+k  +kknkl++ di++i d++ ++  e++kfs+ v+ eei++ +y+ln
  gi|474934392|ref|YP_007687974.1| 390 IETIIVILKKGR--SDGSILFVNASKCFTKA-SKKNKLRAMDIKRISDAVLNR-AEIPKFSRIVSKEEIQKAEYDLN 462
                                       ************..8****************.7********************.*********************** PP

                          N6_Mtase 300 vgryvetee 308
                                       + ryv+ +e
  gi|474934392|ref|YP_007687974.1| 463 IARYVDVSE 471
                                       *****9876 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.1
                          N6_Mtase 246 aseefkkkd..rkknklteediekildt 271
                                        s+  +kk   +k++kl++e+++k +++
  gi|474934392|ref|YP_007687974.1| 731 VSKLLEKKAalSKQTKLKKEELDKAVKV 758
                                       5555556555689999999999998876 PP

>> HsdM_N  HsdM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   1.9     4e-18   8.1e-15       1     135 [.       8     152 ..       8     154 .. 0.68
   2 ?   -2.2   1.3       2.9   5.8e+03      83     116 ..     668     701 ..     638     758 .. 0.53
   3 ?   -1.5   1.0       1.9   3.7e+03      73      98 ..     739     763 ..     695     823 .. 0.55

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 4e-18
                                       HHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHHHHHHH..HHCC..............--..--------.... CS
                            HsdM_N   1 lesklwkaadiLRgkvdaseykeyilgLlFlKrlddveeer..eekllee.......ykenaleeleeklksk.... 64 
                                       l++++ + ad+LRgk+daseyk+y+lg lF+K+l+d+e++   +     e       +  ++l+e+ +++  +    
  gi|474934392|ref|YP_007687974.1|   8 LARTIYSTADELRGKIDASEYKNYVLGVLFYKFLSDKEKRDlcK-----EgwteeimK--QDLNESDKETVIDcqvk 77 
                                       6789**********************************777542.....332223432..22222222222224444 PP

                                       ....S-CCCSHHHHHHS--HHHHHHHHHHCHHHHCT--S...T..HHHHHHHS.......S-----SSHHHHHHHHH CS
                            HsdM_N  65 eafyipeelrWkelakkkdddelgenlnkafpaleelnk...s..lkgvfmkd.dfnafalgeitkkspalLskvie 135
                                       ++++i  +  ++ + ++ +dd   +n+++a++a+e+l +   s  +k++f k       +lg + ++++++ +k++e
  gi|474934392|ref|YP_007687974.1|  78 NGYFISYDNLYSTWLAN-KDDFDISNVRDALNAFERLIDhnhSelFKDLF-KTlRDGLGKLGSDSTEQTNNMRKLLE 152
                                       78999999999999998.33346788999888888886653324455555.35566677777777788887777776 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.9
                                       -HHHHHHHHHHCHHHHCT--STHHHHHHHS.... CS
                            HsdM_N  83 dddelgenlnkafpaleelnkslkgvfmkddfna 116
                                       +++e+  +++ +f++l e+  ++  ++++dd  +
  gi|474934392|ref|YP_007687974.1| 668 EAEEIDVQIESIFEELDESWIEANPELFNDDCTK 701
                                       4455555555555555554332222222222222 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.9
                                       CSHHHHHHS--HHHHHHHHHHCHHHH CS
                            HsdM_N  73 lrWkelakkkdddelgenlnkafpal 98 
                                       + +++  k+ +++el ++++ a+++l
  gi|474934392|ref|YP_007687974.1| 739 AALSKQTKL-KKEELDKAVKVAVEGL 763
                                       333332222.2223333333333333 PP

>> Eco57I  Eco57I restriction-modification methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   1.7e-07   0.00035       3     102 ..     296     399 ..     294     403 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.7e-07
                            Eco57I   3 fdviiGNPPYqeseakkelkaleek.....akdiyqkFvekalkle.dkylaliiparflasgkglkefrekllkdk 73 
                                       +d+++ NPPY ++ + ke +  +       +++ y   ++  ++++ d+++a+++p+  l +g+  k++r++l++ +
  gi|474934392|ref|YP_007687974.1| 296 VDAVVSNPPYSHKWTPKEDSRFSDYglapkSAADYAFLLHDLYHIKhDGIVAIVLPHGVLFRGNKEKDIRQQLVELN 372
                                       599********99877777644443677768888999999*****9999*********999**************** PP

                            Eco57I  74 klkklvefedskevFkdveikggilvflk 102
                                       ++++++ ++ +  +F +++i++ i+++ k
  gi|474934392|ref|YP_007687974.1| 373 QIETIIGLPPN--IFYNTSIETIIVILKK 399
                                       ******99874..7********9998877 PP

>> DIT1_PvcA  Pyoverdine/dityrosine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   1.6e-05     0.032      50     135 ..     675     759 ..     667     784 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.6e-05
                                       HHHHHSTT-EEEEEE--HHHHG.GGTT--HHHHHHHHHHHHHHHHHCT-TTEEEE-GGG-GGGGGG........... CS
                         DIT1_PvcA  50 eieevYepGakltiisDghvfs.DligvddeevdaYgeeLrelakekglediefvrlkdlleseeeaeeeseellse 125
                                       +ie+++e   + +i +    f+ D+ + d++ v++Yg+++++   e+   + +++++++lle++++   +++++l++
  gi|474934392|ref|YP_007687974.1| 675 QIESIFEELDESWIEANPELFNdDCTKFDNASVKKYGNQMKKESLEEDSPEYQVREVSKLLEKKAA--LSKQTKLKK 749
                                       799999999999*********945************************99***********76554..444556777 PP

                                       ...TT-HHHH CS
                         DIT1_PvcA 126 eeyleeaekl 135
                                       ee+ + ++  
  gi|474934392|ref|YP_007687974.1| 750 EELDKAVKVA 759
                                       7777666555 PP

>> AviRa  RRNA methyltransferase AviRa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   7.8e-05      0.16      43     100 ..     205     263 ..     191     275 .. 0.81
   2 ?   -3.0   0.3         2     4e+03     108     150 ..     713     754 ..     707     784 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.8e-05
                             AviRa  43 lellekkeegapltlyDpCCGgayLltvlgllhgkkik....kvlasDvdeevlelakkNLs 100
                                       + +l+++e    +t+ Dp  G++ Ll  +g l +++i     k +a D +e++ +l++ NL 
  gi|474934392|ref|YP_007687974.1| 205 ADHLKNRE---KITICDPTSGSGSLLLHIGKLSSETIDwdniKYYAQDYSEDAYNLTRMNLI 263
                                       34554444...5************************965544679*************9995 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2
                             AviRa 108 akreeelrelaeeyekeshaealesaerleellakkgeekeie 150
                                       + ++e+l+e++ ey+ +   + le  + l+++++ k+ee++ +
  gi|474934392|ref|YP_007687974.1| 713 QMKKESLEEDSPEYQVREVSKLLEKKAALSKQTKLKKEELD-K 754
                                       56777788888888877777777777777777644444433.2 PP

>> DUF1266  Protein of unknown function (DUF1266)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0    0.0002       0.4       4      70 ..      96     195 ..      95     271 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0002
                           DUF1266   4 esWgItdresalatlerLleeghrpefdeflkrlraadeaelreeldeleedekeladalgtdesa........... 69 
                                       ++++I++  +al+  erL++++h++ f+++ k lr    +  ++ +    e+++++ + l+  ++            
  gi|474934392|ref|YP_007687974.1|  96 DDFDISNVRDALNAFERLIDHNHSELFKDLFKTLRDGLGKLGSDST----EQTNNMRKLLEVLNDVptdskqdydvl 168
                                       799********************************96664444444....444444444443333344345566666 PP

                           DUF1266  70 ..........................k 70 
                                                                 +
  gi|474934392|ref|YP_007687974.1| 169 gfvyeylleqfasnsgkkagefytptE 195
                                       655555555555555555555555551 PP

>> Peptidase_C54  Peptidase family C54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00012      0.23      66     125 ..     141     209 ..      97     264 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00012
                     Peptidase_C54  66 kkeeetyrkilslFlDkps...apfSihrlv......kigkslgkkvgeWfgPstvaqilkklvekake 125
                                       +++++++rk+l++  D p+   + + +  +v      + ++++gkk+ge+++P++v+++++ +v+++ +
  gi|474934392|ref|YP_007687974.1| 141 TEQTNNMRKLLEVLNDVPTdskQDYDVLGFVyeylleQFASNSGKKAGEFYTPTEVSELMSVIVADHLK 209
                                       377888899999999997766666666666655554444569*******************99985433 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00037      0.73      28     136 ..     212     310 ..     190     316 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00037
                                       TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHHHHHHHHHHT.T-GG CS
                           UPF0020  28 pgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDldrrvvqgareNaeka.gvgd 103
                                       +  ++ DP +GsG++l+  + l+++ +       + ++k  a+   ++ ++l  ++l+ + v+  +  a++  ++gd
  gi|474934392|ref|YP_007687974.1| 212 EKITICDPTSGSGSLLLHIGKLSSETI------DWDNIKYYAQDYSEDAYNLTRMNLIMKGVNHWNIFARNKdTLGD 282
                                       556899****************99999......56667777777777777777777777777776666665414555 PP

                                       GEEEEE--GGG--STTS---EEEE--------- CS
                           UPF0020 104 liefsqadaakLrlkegevdvivtnpPYGerlg 136
                                        + +   +   L      vd++v+npPY  + +
  gi|474934392|ref|YP_007687974.1| 283 DWPLDLEQGGPLF-----VDAVVSNPPYSHKWT 310
                                       5555555555444.....99********87655 PP

>> RRN3  RNA polymerase I specific transcription initiation factor RRN3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.52     1e+03      11      58 ..     102     156 ..      96     160 .. 0.65
   2 ?    9.0   3.2   0.00023      0.46     208     298 ..     671     768 ..     665     816 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.52
                              RRN3  11 fVrnALeekek....gdseqydeLleqfsekk......eeseapslaelkqllkalss 58 
                                        Vr+AL+++e+    ++se +++L + +   +       ++++++++++++ll++l  
  gi|474934392|ref|YP_007687974.1| 102 NVRDALNAFERlidhNHSELFKDLFKTL---RdglgklGSDSTEQTNNMRKLLEVLND 156
                                       5788888876521114455555555555...244577788888889999999988865 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00023
                              RRN3 208 kiDVeiqveledlddeedeeleeelee.....deddedddedd..........eesdlddlssdeeaeedee.kdee 268
                                       +iDV+i+   e+ld++  e++ e +++     d         +          ++++l+++s + + +e ++  +++
  gi|474934392|ref|YP_007687974.1| 671 EIDVQIESIFEELDESWIEANPELFNDdctkfD---------NasvkkygnqmKKESLEEDSPEYQVREVSKlLEKK 738
                                       8***************99999888766443321.........12233445334334444444444445555544444 PP

                              RRN3 269 eeslkkikelvekLDailtllfehlekkfs 298
                                       ++  k++k   e+LD+ +++ +e l+++ +
  gi|474934392|ref|YP_007687974.1| 739 AALSKQTKLKKEELDKAVKVAVEGLTPEKE 768
                                       455589999999*********999998333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (851 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1153  (0.0643092); expected 358.6 (0.02)
Passed bias filter:                      667  (0.0372023); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.94u 0.38s 00:00:01.31 Elapsed: 00:00:00.61
# Mc/sec: 4221.30
//
Query:       gi|474934393|ref|YP_007687975.1|  [L=381]
Description: Restriction endonuclease S subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.5e-34  118.9   2.1    1.3e-20   74.3   0.0    2.1  2  Methylase_S  Type I restriction modification DNA specificity 
  ------ inclusion threshold ------
      0.061   13.9   0.8        1.8    9.2   0.0    2.4  2  MCM_N        MCM N-terminal domain


Domain annotation for each model (and alignments):
>> Methylase_S  Type I restriction modification DNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.5   2.8e-15   2.5e-11       2     158 ..      16     178 ..      15     184 .. 0.76
   2 !   74.3   0.0   1.4e-24   1.3e-20       3     164 ..     200     365 ..     199     367 .. 0.88

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 2.8e-15
                                       TT-EEEEHHHHEEEEE-----TTGGTTT--EEEE-HHHCCT..EE-HHHHCCTT---B-.TT-EEEE-S..SSTT-E CS
                       Methylase_S   2 edwevvkLgdvfeikkgktpkkkelkengkypyiragilnn..kvvkdglgykkkyilp.kgdilissr..atiGkv 73 
                                       +dwe+v+ +d+     +k++ k ++  +g+ ++i++  ++   +  +   +y k+y+++  gdi ++ +   ++ + 
  gi|474934393|ref|YP_007687975.1|  16 KDWEEVRFSDLY----KKAIQK-NDLSYGNRDIISVAKMYYapNPLITNSEYLKTYNIFlRGDIAFEGNrsKHFAYG 87 
                                       79**********....445555.888888888888885555588888899*****************8888555555 PP

                                       EEESS...-BEE-TTEEEEEESTTT--HHHHHHHHHHCHH......HHHHH.....CCSSTTT---HHHHCC-EEEE CS
                       Methylase_S  74 ayrdk...kyylnqsvivlipknkkkineflylylllklk......klksl.....svgstqpkltkenlkkikIpl 136
                                        + ++   + ++++ ++v++p++      +++ y +++ +      +         + ++ +++l+++++ + kI++
  gi|474934393|ref|YP_007687975.1|  88 RFVENtigDGIVSHVFKVFRPIK-----DYDIQYWKYAINeekvmrS---RlavstKSSTMMKELRDQDFLNEKIMI 156
                                       5555533344***********86.....4445555544442223340...155556889999*************** PP

                                       --HHHHHHHHHHHHHHHHHHHH CS
                       Methylase_S 137 PpleeQkkIakiLsqldntiel 158
                                       Pp +eQ +I + Ls+ld++ie 
  gi|474934393|ref|YP_007687975.1| 157 PPVDEQRRIGQLLSTLDQLIEY 178
                                       ******************8775 PP

  == domain 2  score: 74.3 bits;  conditional E-value: 1.4e-24
                                       T-EEEEHHHHEEEEE-----TT.GGTTT--EEEE-HH.HCCT.EE-HHHHCCTT---B-TT-EEEE-SSSTT-EEEE CS
                       Methylase_S   3 dwevvkLgdvfeikkgktpkkk.elkengkypyirag.ilnn.kvvkdglgykkkyilpkgdilissratiGkvayr 76 
                                       d e+v L ++++i++g +p ++  + ++ ++p++  +    + +v  ++   ++k++ +  dil s ra++G v++ 
  gi|474934393|ref|YP_007687975.1| 200 DHEKVPLTELATINMGQSPESStYNDQGIGMPFYQGKtEFTDtFVEVKTYCSDPKKVAKPMDILMSVRAPVGAVNLT 276
                                       67999*****************444555578****99777775666666666677788899**************** PP

                                       SS-BEE-TTEEEEEEST.TT--HHHHHHHHHHCHHHHHHHCCSSTTT---HHHHCC-EEEE--HHHHHHHHHHHHHH CS
                       Methylase_S  77 dkkyylnqsvivlipkn.kkkineflylylllklkklkslsvgstqpkltkenlkkikIplPpleeQkkIakiLsql 152
                                       +++++ + ++  ++pkn    +  fl++ l+++ +++++l vgst++ ++ke++kkikIpl pl+ Q +  ++  q+
  gi|474934393|ref|YP_007687975.1| 277 SQECCIGRGLAAITPKNgL-ADVWFLFNALKTMEQQISDLGVGSTFKAINKEDMKKIKIPLAPLDLQTQFSSFVNQV 352
                                       ****************844.446****************************************************** PP

                                       HH.HHHHHHHHHH CS
                       Methylase_S 153 dn.tielekkikn 164
                                       d+ ++ +++k++n
  gi|474934393|ref|YP_007687975.1| 353 DKsKFMFMTKLQN 365
                                       **88888777765 PP

>> MCM_N  MCM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0    0.0002       1.8      55      85 ..     173     203 ..     169     232 .. 0.80
   2 ?    2.2   0.5     0.029   2.6e+02       1      39 [.     342     374 ..     342     376 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0002
                             MCM_N  55 eailenpkeylplleealkevvkklepsykd 85 
                                       ++++e++++ +p++++ +k  + +++ + ++
  gi|474934393|ref|YP_007687975.1| 173 DQLIEYYERAIPIFDRLVKSRFIEMFSDHEK 203
                                       79*****************999999886544 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.029
                             MCM_N   1 qekFedFLeefkddsededgekkYrdqlqemaerekttL 39 
                                       q++F +F ++       +++++ ++ +lq++++ +++ +
  gi|474934393|ref|YP_007687975.1| 342 QTQFSSFVNQV------DKSKFMFMTKLQNLRNIKESMI 374
                                       67899999988......5679***********9999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.35s 00:00:01.00 Elapsed: 00:00:00.57
# Mc/sec: 2023.96
//
Query:       gi|474934394|ref|YP_007687976.1|  [L=1007]
Description: type I site-specific deoxyribonuclease, HsdR family [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.9e-43  148.1   0.0    6.6e-43  147.0   0.0    1.6  1  SWI2_SNF2   SWI2/SNF2 ATPase
    8.7e-26   90.9   1.3    1.9e-25   89.9   0.0    2.3  3  ResIII      Type III restriction enzyme, res subunit
    2.2e-15   57.1   1.4      8e-15   55.3   0.1    2.6  3  HSDR_N      Type I restriction enzyme R protein N terminus (H
    3.7e-05   23.6   0.0    8.9e-05   22.3   0.0    1.6  1  DEAD        DEAD/DEAH box helicase
  ------ inclusion threshold ------
        1.2    9.1   5.7        4.1    7.4   0.3    3.5  4  Tudor_FRX1  Fragile X mental retardation Tudor domain


Domain annotation for each model (and alignments):
>> SWI2_SNF2  SWI2/SNF2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.0   0.0   1.8e-46   6.6e-43       1     192 [.     246     453 ..     246     487 .. 0.84

  Alignments for each domain:
  == domain 1  score: 147.0 bits;  conditional E-value: 1.8e-46
                         SWI2_SNF2   1 qQyravekavervke.....gdrkgGviWHtqGSGKsltmvflakklleeelknpkvvvvtDRkdLdkQlsktfaka 72 
                                       +Q++avek+ +++        +r+gG+++Ht+GSGK+lt++++a+ +++ + k  k +++ DRk+L  Q+ ++++++
  gi|474934394|ref|YP_007687976.1| 246 YQIFAVEKISSALDVahwtrAERRGGYVFHTTGSGKTLTSFKAASLVAS-DGKVDKSLFLADRKELGFQTLNEYQNF 321
                                       7********9999877788888***********************9999.9999*********************98 PP

                         SWI2_SNF2  73 ..geekpkqaesrkeLkell.eke.sekiifttiqKfe...ee..ekeklevlsereniivlvDEaHRsqygelakk 140
                                         g  +++ +e++ eL ++l +++ ++k+i+t iqK++   ++  ++ +++++s+++ i ++vDE+HRs +g++ + 
  gi|474934394|ref|YP_007687976.1| 322 asGMIAVQDTEDTVELYTKLkSNNiEDKLIVTSIQKMAllsNDygHNPEFSTISSKR-IAIIVDECHRSTFGKMLRD 397
                                       44555678999999******534479***********98862233445678888777.******************* PP

                         SWI2_SNF2 141 lrkalpnaafigFTGTPilkkd....kktkevFgeyidkYtikeaveDgavvpilY 192
                                       +++alp a+++gF GTPi  ++     +t++ Fge + kYti++  +Dg+v+    
  gi|474934394|ref|YP_007687976.1| 398 IEDALPVAKYFGFSGTPIYDENnkdgGTTSDLFGEELCKYTITDGLRDGNVLAFDL 453
                                       ******************98664444569**********************87433 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.9   0.0   5.2e-29   1.9e-25       3     169 ..     242     414 ..     240     416 .. 0.86
   2 ?   -3.0   0.1       1.8   6.4e+03      76      96 ..     579     599 ..     558     643 .. 0.52
   3 ?   -3.3   0.0       2.1   7.7e+03      92     118 ..     782     808 ..     749     822 .. 0.52

  Alignments for each domain:
  == domain 1  score: 89.9 bits;  conditional E-value: 5.2e-29
                                       EE-HHHHHHHHHHT...........TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHG CS
                            ResIII   3 elreyQeeaienlleklks.....krdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleef 74 
                                        lr+yQ+ a+e++ ++l+       +++ g++ ++TG+GKTl+++k++  +++ gk +k lfl++rk+l  qtl+e+
  gi|474934394|ref|YP_007687976.1| 242 VLRSYQIFAVEKISSALDVahwtrAERRGGYVFHTTGSGKTLTSFKAASLVASDGKVDKSLFLADRKELGFQTLNEY 318
                                       69************99988889878888999********************************************** PP

                                       GGGTGG....GEEEESSS-B--.......-SEEEEEHHHHHHTH.........HHHTTT-SEEEEETGGGTTS.TTT CS
                            ResIII  75 kkflseaykeigkkvsgdkkkakekdstnkkilvttiqsldadseee.eeeseellrdrfdviiiDEaHrlgakksw 150
                                       ++f+s   + + ++ + + +++ ++++ + k++vt+iq++   s+    + + +  +++   ii+DE+Hr++  k  
  gi|474934394|ref|YP_007687976.1| 319 QNFASGMIAVQDTEDTVELYTKLKSNNIEDKLIVTSIQKMALLSNDYgHNPEFSTISSKRIAIIVDECHRSTFGKML 395
                                       *****9987744444444444445667899**********999933355555566666777**************** PP

                                       HHHHHT---SEEEEEESS- CS
                            ResIII 151 reilekfkeavllglTATp 169
                                       r i ++++ a+ +g+++Tp
  gi|474934394|ref|YP_007687976.1| 396 RDIEDALPVAKYFGFSGTP 414
                                       ******************9 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.8
                                       GGTGG....GEEEESSS-B-- CS
                            ResIII  76 kflseaykeigkkvsgdkkka 96 
                                       +f+++++k+i++++++ ++++
  gi|474934394|ref|YP_007687976.1| 579 QFSPTKVKAIKEILEDYNDTF 599
                                       455555554544444444444 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 2.1
                                       S-B--.......-SEEEEEHHHHHHTH CS
                            ResIII  92 dkkkakekdstnkkilvttiqsldads 118
                                       dkk++k  +++ k i+v  ++++++++
  gi|474934394|ref|YP_007687976.1| 782 DKKDRKYVFENGKIIIVDLTEEIYKIL 808
                                       334443444555555555555555555 PP

>> HSDR_N  Type I restriction enzyme R protein N terminus (HSDR_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.3   0.1   2.2e-18     8e-15      41     189 ..      10     186 ..       2     190 .. 0.73
   2 ?   -1.6   0.0      0.63   2.3e+03      12      86 ..     303     347 ..     294     379 .. 0.53
   3 ?   -3.6   0.0       2.6   9.3e+03      40      62 ..     710     737 ..     692     760 .. 0.48

  Alignments for each domain:
  == domain 1  score: 55.3 bits;  conditional E-value: 2.2e-18
                                       --SHHHHHHHHHHHHHHHH...........-HHHHHHHH...TT--HHHHHHHHHTS.-EEEE.........TS-EE CS
                            HSDR_N  41 skaevaleknlreqlgaln...........ikkltkrla...lsdgnkefyellkeg.kvkfk.........egrkk 93 
                                        k+e++l +n  + l + n           ++ ++k+l     s+g    +++l +g +  ++          g++ 
  gi|474934394|ref|YP_007687976.1|  10 YKDEKQLIDNWATILFENNrdidrlndcplTEGEKKQLMqmvKSKGSPFLLNKLVNGrTLSIQrdnekdklhYGKTV 86 
                                       55555555555555555555555555777766666666667667777777788888877775553333222222222 PP

                                       EEES..S-SSSGGG..S-EEEEE----S....SSS---EEEEEEETTEEEEEEEE--TT.-HHHHHHHHTSS---.- CS
                            HSDR_N  94 nikL..iDkknlen..NrfqvvnQvtvt....gnqkrrpDivlfvnglplvviElKrpg.tieeAinQikryrkeks 161
                                          L   D ++++    r+q+++Q  +      ++krr D++l++ng p+++iElK++g  +++A+nQi++yr+e  
  gi|474934394|ref|YP_007687976.1|  87 S--LsiYDRNQIAGgkSRYQIAQQPLFIpeseMDRKRRGDLTLLINGMPVIHIELKKSGiPVNQAVNQIRKYRDEG- 160
                                       2..2436666554244********999889999*************************99*************886. PP

                                       --SSSGGGGG--EEEEE-SS-EEEEE-- CS
                            HSDR_N 162 dvsipqlfrYlqfgvisngketrfyakt 189
                                         + + lf  +q++v+   +++ ++a++
  gi|474934394|ref|YP_007687976.1| 161 --KFEGLFSLIQVFVAMTPEDHLYFANP 186
                                       ..57*************99999999986 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.63
                                       HHHHHHHTT-EE................----SHHHHHHHHHHHHHHHH-HHHHHHHHTT--HHHHHHHHHTS-EE CS
                            HSDR_N  12 idellrelGyqvlskkdveiegrrpe.vrkskaevaleknlreqlgalnikkltkrlalsdgnkefyellkegkvk 86 
                                        ++  +elG+q l++ + +++g     v + ++                              +e y++lk+++++
  gi|474934394|ref|YP_007687976.1| 303 FLADRKELGFQTLNEYQNFASG--MIaVQDTED-----------------------------TVELYTKLKSNNIE 347
                                       5555666677766666666555..222333333.............................34444444444444 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 2.6
                                       ---SHHHHHHHHHHHHHHHH.....-HH CS
                            HSDR_N  40 kskaevaleknlreqlgaln.....ikk 62 
                                       ++ a++   ++l e l+++n     ik+
  gi|474934394|ref|YP_007687976.1| 710 GERASEMFVSKLPERLESINnyykmIKS 737
                                       2234455555566666666655333222 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   2.5e-08   8.9e-05      22     142 ..     276     398 ..     250     418 .. 0.69

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.5e-08
                                       STTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHHHTT. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                              DEAD  22 eTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardqlskldng. 97 
                                        TGsGKTl  + ++   v++  + +  k l+++  +eL  qtln++++f + +     ++   +++ + ++kl+++ 
  gi|474934394|ref|YP_007687976.1| 276 TTGSGKTLTSFKAAS-LVAS--DGKVDKSLFLADRKELGFQTLNEYQNFASGM----IAVQDTEDTVELYTKLKSNn 345
                                       7*******9555554.6655..455559***********************73....23344455555566665333 PP

                                       ..CSEEEEEHHHHHHHH.....HCTSSH.CTTEEE.EEEETHHHHHHTTTHHHH CS
                                       ..xxxxxxxxxxxxxxx.....xxxxxx.xxxxxx.xxxxxxxxxxxxxxxxxx RF
                              DEAD  98 ..vdivvgtpgrlddll.....stgkln.lsqvrf.lVlDEadrlldqgfsdfi 142
                                          +++v+  ++++ ll     ++ +++ +s+ r+ +++DE++r    ++ ++i
  gi|474934394|ref|YP_007687976.1| 346 ieDKLIVTSIQKMA-LLsndygHNPEFStISSKRIaIIVDECHRSTFGKMLRDI 398
                                       52445555555555.45466663333334555555599*****98765555555 PP

>> Tudor_FRX1  Fragile X mental retardation Tudor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.49   1.8e+03      22      35 ..      18      31 ..      14      34 .. 0.74
   2 ?    7.4   0.3    0.0011       4.1      12      33 ..     518     539 ..     514     541 .. 0.92
   3 ?   -2.8   0.0       1.7   6.1e+03      12      35 ..     554     577 ..     553     580 .. 0.83
   4 ?    2.0   0.0     0.054   1.9e+02      12      41 ..     731     760 ..     727     763 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.49
                        Tudor_FRX1 22 edsltvaFennWqp 35
                                      ++  t+ Fenn   
  gi|474934394|ref|YP_007687976.1| 18 DNWATILFENNRDI 31
                                      56679*****9765 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0011
                        Tudor_FRX1  12 fykafvkdvhedsltvaFennW 33 
                                       +y ++v +v+ d ++++F n+ 
  gi|474934394|ref|YP_007687976.1| 518 YYESVVDNVLKDWISISFANKF 539
                                       9******************986 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.7
                        Tudor_FRX1  12 fykafvkdvhedsltvaFennWqp 35 
                                       +y+ f k+  +  +t+ F++   +
  gi|474934394|ref|YP_007687976.1| 554 YYRLFKKNAPQLKITALFDEHDGN 577
                                       999999999999999999976555 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.054
                        Tudor_FRX1  12 fykafvkdvhedsltvaFennWqper.qvpf 41 
                                       +yk ++k  ++ + +  Fe  +++e+ ++ f
  gi|474934394|ref|YP_007687976.1| 731 YYK-MIKSLFDSENITYFERLPKSEQsKISF 760
                                       777.68*****************99735655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1007 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       832  (0.0464053); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.85u 0.35s 00:00:01.20 Elapsed: 00:00:00.54
# Mc/sec: 5654.60
//
Query:       gi|474934395|ref|YP_007687977.1|  [L=172]
Description: TATA-box binding protein (TBP), component of TFIID and TFIIIB [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-34  117.4   0.0    3.9e-18   65.2   0.0    2.0  2  TBP       Transcription factor TFIID (or TATA-binding protein
     0.0066   16.5   0.0        5.2    7.3   0.0    2.3  2  DUF3378   Domain of unknown function (DUF3378)


Domain annotation for each model (and alignments):
>> TBP  Transcription factor TFIID (or TATA-binding protein, TBP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.7   0.0   1.5e-17   1.3e-13       3      83 ..       2      78 ..       1      80 [. 0.94
   2 !   65.2   0.0   4.4e-22   3.9e-18       3      83 ..      90     170 ..      88     172 .] 0.92

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 1.5e-17
                                      EEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHHH CS
                               TBP  3 kiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiapi 81
                                      k +N+v+s ++++eldL+ l++++    ++Y+++r+pg  ++++  +v  +i+++Gk ++ G +s e++r+ ++k+ +i
  gi|474934395|ref|YP_007687977.1|  2 KMENIVCSGSFNQELDLNLLSSRC--PYVQYKKNRYPGAYLKFDGHSV--TIYRTGKYIMPGMRSFEDIRQSFDKVKEI 76
                                      789*****************9998..*****************87666..9**************************99 PP

                                      HH CS
                               TBP 82 lk 83
                                      l+
  gi|474934395|ref|YP_007687977.1| 77 LS 78
                                      97 PP

  == domain 2  score: 65.2 bits;  conditional E-value: 4.4e-22
                                       EEEEEEEEEE-SSCE-HHHHHHHCC..TTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHH CS
                               TBP   3 kiqNvvasanlgleldLeklalkae..krnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakk 77 
                                        ++N+v+s n+++el+L+++ +++   + ++ Yepe fpg+++++++  +t  +FssGk+ i+G++se e+++a + 
  gi|474934395|ref|YP_007687977.1|  90 VVRNIVCSSNIEHELNLSTIYFELVsrDLDVVYEPEAFPGMILKIQD--CTYNVFSSGKFLILGCTSELEAKNADDY 164
                                       69******************98865457899**************88..*************************999 PP

                                       HHHHHH CS
                               TBP  78 iapilk 83 
                                       +++++ 
  gi|474934395|ref|YP_007687977.1| 165 FLNLID 170
                                       999885 PP

>> DUF3378  Domain of unknown function (DUF3378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0   0.00058       5.2      22      52 ..      28      58 ..      15      83 .. 0.86
   2 !    7.2   0.0   0.00062       5.6      33      61 ..     131     159 ..     121     161 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00058
                           DUF3378 22 lrskkppyavfaakkndttItaYtSgKVlFQ 52
                                       + kk+ y     k ++ ++t+Y+ gK ++ 
  gi|474934395|ref|YP_007687977.1| 28 VQYKKNRYPGAYLKFDGHSVTIYRTGKYIMP 58
                                      4557777888889999***********7765 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00062
                           DUF3378  33 aakkndttItaYtSgKVlFQGknaeaeAs 61 
                                         k +d+t +++ SgK l+ G + e eA+
  gi|474934395|ref|YP_007687977.1| 131 ILKIQDCTYNVFSSGKFLILGCTSELEAK 159
                                       46889*******************99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 1018.00
//
Query:       gi|474934396|ref|YP_007687978.1|  [L=617]
Description: hypothetical protein TALC_00823 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-31  110.4   4.2    1.4e-31  110.4   4.2    3.1  2  DUF262    Protein of unknown function DUF262
    4.5e-10   39.5   1.5    5.4e-09   36.0   0.1    2.9  2  DUF1524   Protein of unknown function (DUF1524)
  ------ inclusion threshold ------
      0.014   14.7   0.0      0.028   13.6   0.0    1.5  1  DndB      DNA-sulfur modification-associated
      0.092   13.3   0.1       0.47   11.1   0.0    2.3  2  ATP-cone  ATP cone domain
       0.29   10.9   5.3        2.1    8.1   0.0    3.9  4  DnaA_N    DnaA N-terminal domain


Domain annotation for each model (and alignments):
>> DUF262  Protein of unknown function DUF262
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.4   4.2   3.9e-35   1.4e-31       3     220 ..      13     227 ..      11     228 .. 0.76
   2 ?   -3.4   5.6       2.4   8.7e+03     118     153 ..     229     264 ..     226     453 .. 0.71

  Alignments for each domain:
  == domain 1  score: 110.4 bits;  conditional E-value: 3.9e-35
                            DUF262   3 dllskskrglriPdfQRpyvWeeeqveeLiedlla.................lkgyplGsivlwskaadsagelevi 62 
                                       +ll ++k  ++i  +QR+y+W ++q++eL+ed+ +                 + +y++Gs+++       ++e  +i
  gi|474934396|ref|YP_007687978.1|  13 QLLFNKK--YVIHYYQREYRWGKKQIKELLEDITDeffdnykpddvrkqvaqYGNYYMGSVIV-----TRDSERAII 82 
                                       5655555..9***********************99****************************.....569****** PP

                            DUF262  63 DGQQRltTltlllaatkeesekriknleaeiek.....ekeeededrlkrreresdkellqkllrseklsleekeel 134
                                       DGQQRlt+ltlll +    ++   k+ + ++++     ++     +++  ++++ + e  +++++            
  gi|474934396|ref|YP_007687978.1|  83 DGQQRLTSLTLLLIY----LNHLRKSECPDYTDlspliYS-----EQYGEKTFNINDEARNECMN------------ 138
                                       ***************....222222222222222222211.....11222222222222222222............ PP

                            DUF262 135 aelnsltkkdlakeekrneeknlikayevieeilksa.........llsalktklslieieleseddedqayeiFer 202
                                            +t +d+++  ++n+  n+i+ y  ie+ l+           +l+++ ++l +iei++ se+d   a+++F +
  gi|474934396|ref|YP_007687978.1| 139 ---ALYTGEDYTDPGNNNSVTNIIERYHDIESLLDLRiqtkeilpfFLDWIQNHLIFIEITVTSEQD---AHKVFVT 209
                                       ...233445556666799999999999999996666699999999999999999******9999888...******* PP

                            DUF262 203 lNsrGvpLtasellkall 220
                                       +N+rG++Lt+ e+lk++l
  gi|474934396|ref|YP_007687978.1| 210 MNDRGLSLTPTEMLKGYL 227
                                       ***************987 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.4
                            DUF262 118 qkllrseklsleekeelaelnsltkkdlakeekrne 153
                                       ++++++++ +++++ ++++ nsl k++l++++ ++e
  gi|474934396|ref|YP_007687978.1| 229 SEIIEDSDRAKADELWKQQVNSLLKRNLEEKDADDE 264
                                       567777777777777777777777777743332222 PP

>> DUF1524  Protein of unknown function (DUF1524)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.2     0.083     3e+02      74     109 ..     379     420 ..     364     451 .. 0.78
   2 !   36.0   0.1   1.5e-12   5.4e-09      18     116 ..     457     555 ..     441     611 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.083
                           DUF1524  74 reelvndlgNLtlltkslN......sslsnkpfleKrdlykk 109
                                       + + v  + NL  + + +N      ss++n+ f   ++  +k
  gi|474934396|ref|YP_007687978.1| 379 KIRMVSCFINLYVIRRGVNykdfsySSIKNAIFNITKEIRNK 420
                                       556677789*************9999****999888875544 PP

  == domain 2  score: 36.0 bits;  conditional E-value: 1.5e-12
                           DUF1524  18 sssrkklryilakelesalree.deeege.akklt..iEHilPqslaekwegagqedeekreelvndlgNLtlltks 90 
                                       ++   ++ y+l+    ++++ +   +    +kk+t  iEH+l+   +++   +g+ de +++ ++  +gNL+ll  +
  gi|474934396|ref|YP_007687978.1| 457 PYMLAHITYYLE-CSCDDPNANiV-KYLVpSKKNTfdIEHVLADDFDSNR--DGFTDENDFQTYRSWFGNLILLPAD 529
                                       444456677777.55556665532.222223333368***********88..9999********************* PP

                           DUF1524  91 lNsslsnkpfleKrdlykksslrlnr 116
                                       +N+s++++p+  K   y+  ++  ++
  gi|474934396|ref|YP_007687978.1| 530 KNRSIQDQPYGTKLITYAGENILAKT 555
                                       *************9999987775444 PP

>> DndB  DNA-sulfur modification-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   7.8e-06     0.028      88     122 ..      65     107 ..      37     128 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.8e-06
                              DndB  88 kekvGvlkipmdaeilivDGQHRraAieealk........eep 122
                                       +  +G +++++d+e  i+DGQ+R+ ++  +l         e p
  gi|474934396|ref|YP_007687978.1|  65 NYYMGSVIVTRDSERAIIDGQQRLTSLTLLLIylnhlrksECP 107
                                       4789*********999***********9555443333344444 PP

>> ATP-cone  ATP cone domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.5     9e+03      36      63 ..      35      62 ..      33      63 .. 0.74
   2 ?   11.1   0.0   0.00013      0.47       2      44 ..     390     433 ..     389     447 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.5
                                      HHHHHHHHHHHHHIIT-BHHHHHHHHHH CS
                          ATP-cone 36 iaeeveaevrkrlrdgisteeIqdlvek 63
                                      +++e+ +++ +++ d+ + +++++ v++
  gi|474934396|ref|YP_007687978.1| 35 QIKELLEDITDEFFDNYKPDDVRKQVAQ 62
                                      4567778888888888888888888876 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00013
                                       EEE-TTS-EEE--HHHHHHHHHHHHHH.-HHHHHHHHHHHHHHH CS
                          ATP-cone   2 kViKRdGtvepfdvekIkraiekAceg.seeeideiaeeveaev 44 
                                       +Vi+R   +++f+ + Ik+ai +  ++  +++++e+a+ + + +
  gi|474934396|ref|YP_007687978.1| 390 YVIRRGVNYKDFSYSSIKNAIFNITKEiRNKNVEELAWFLTDSL 433
                                       89**********************99999999999998887666 PP

>> DnaA_N  DnaA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.13   4.8e+02      45      53 ..     181     189 ..     180     196 .. 0.87
   2 ?   -3.0   0.3       1.8   6.5e+03       2      17 ..     242     258 ..     241     259 .. 0.65
   3 ?    8.1   0.0    0.0006       2.1      41      60 ..     261     280 ..     260     282 .. 0.90
   4 ?    1.6   0.0     0.066   2.4e+02      18      35 ..     514     531 ..     505     535 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.13
                            DnaA_N  45 Fardwiesn 53 
                                       F+ dwi+++
  gi|474934396|ref|YP_007687978.1| 181 FFLDWIQNH 189
                                       99*****99 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.8
                            DnaA_N   2 elWs.avlerLkkelge 17 
                                       elW+ +v ++Lk++l+e
  gi|474934396|ref|YP_007687978.1| 242 ELWKqQVNSLLKRNLEE 258
                                       67751577778887776 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0006
                            DnaA_N  41 vpneFardwiesnYldriae 60 
                                       ++ eF++ w++s+Y+  i+e
  gi|474934396|ref|YP_007687978.1| 261 ADDEFIKTWLRSQYAVTIRE 280
                                       5779***********99986 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.066
                            DnaA_N  18 qsfdtWikplklfalknn 35 
                                       q++++W+ +l l  +++n
  gi|474934396|ref|YP_007687978.1| 514 QTYRSWFGNLILLPADKN 531
                                       78*******988777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (617 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       769  (0.0428914); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 4387.33
//
Query:       gi|474934397|ref|YP_007687979.1|  [L=136]
Description: hypothetical protein TALC_00824 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.08   12.7   0.0       0.08   12.7   0.0    1.1  1  Med6      MED6 mediator sub complex component


Domain annotation for each model (and alignments):
>> Med6  MED6 mediator sub complex component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.4e-06      0.08      48     112 ..      47     114 ..       4     135 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.4e-06
                              Med6  48 aeealLkkmkGleyvlahvqepdlfvirkqerksa.tevtvlaaYyiiggniYqapsl..ysvvqsrl 112
                                        ++++L + +G ++ l  +++pdl v r  +  ++  + t   +Y ++g  + qa  l   +++q  l
  gi|474934397|ref|YP_007687979.1|  47 LKMDMLIEKTGSKFYLLLSENPDLIVARTLTEAKDiASQTEKGDYIVVGSFVNQAKALryKRIIQDEL 114
                                       334459999*******************999777735777789**********998652145666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 865.99
//
Query:       gi|474934398|ref|YP_007687980.1|  [L=270]
Description: hypothetical protein TALC_00825 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1690.36
//
Query:       gi|474934399|ref|YP_007687981.1|  [L=70]
Description: hypothetical protein TALC_00826 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 436.43
//
Query:       gi|474934400|ref|YP_007687982.1|  [L=111]
Description: hypothetical protein TALC_00827 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       232  (0.0129399); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 696.84
//
Query:       gi|474934401|ref|YP_007687983.1|  [L=357]
Description: ABC-type Fe3+-hydroxamate transport system, periplasmic component [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.7e-10   39.4   0.0    6.5e-10   39.0   0.0    1.3  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.0   3.6e-14   6.5e-10     109     235 ..     165     288 ..      81     289 .. 0.84

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 3.6e-14
                                       T-HHHHHHHHHHHHHHHHHHHHTS-TT..-EEEEEEEETTE...EEEE-TTSTTTHHHHT.S--EESTTT--STT-E CS
                      Peripla_BP_2 109 gledeaeklvaeidsklaaaksaidse.kpkpvlvfggade.ggyvvagsnsyigdllda.lgieniaaeskkseye 182
                                       g  ++a+++ +++ ++l+ + s i+++   +++l+++ +++ +  +++  ++ + d++ + lg++++ + +   ey 
  gi|474934401|ref|YP_007687983.1| 165 GVAEKADAWKKDLSDTLDLISSTIKEKgLTSKTLYYARGEKnRLLSYTDIGGSFVDFAFTtLGVNYLSSKY---EYN 238
                                       56799**********************74455555555554466777776666666655549999996665...*** PP

                                       EE-HHHHHHH--SEEEEEEHHHHT-S--HHHHT-SHHHHTSHHHHTT-EEEE- CS
                      Peripla_BP_2 183 eisaEqilasdpdvifvsgraeadnktgleflkenpllaelpAvkngrVyald 235
                                       + s Eq+la+dp vi+  +    ++ +  ++l +n ++++++Avkn  +y+++
  gi|474934401|ref|YP_007687983.1| 239 KPSTEQLLADDPKVIVLGSY---QQHALEKELRTNSIWENVTAVKNDEIYRIP 288
                                       ********************...9**************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2257.70
//
Query:       gi|474934402|ref|YP_007687984.1|  [L=336]
Description: ABC-type Fe3+-siderophore transport system, permease component [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-74  249.8  36.1    3.6e-74  249.6  36.1    1.0  1  FecCD          FecCD transport family
      3e-06   26.9  23.2      3e-06   26.9  23.2    2.0  2  ABC-3          ABC 3 transport family
  ------ inclusion threshold ------
       0.13   11.9   9.8      0.053   13.2   1.2    2.6  2  Keratin_assoc  Keratinocyte-associated protein 2


Domain annotation for each model (and alignments):
>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  249.6  36.1     6e-78   3.6e-74       2     311 ..      18     326 ..      17     327 .. 0.98

  Alignments for each domain:
  == domain 1  score: 249.6 bits;  conditional E-value: 6e-78
                             FecCD   2 lllllllslllgavkispsevfeallgka..dsleaeivlelrlprvlaallvGaaLavaGallQtvtrNpLadPsi 76 
                                       +++++++++++g +++s+  ++ +l+g+    ++e++++++lr+pr++aal+vG++L+v+G+l Q +++N+L++P++
  gi|474934402|ref|YP_007687984.1|  18 MAAVFAIAICVGRYQVSLDALMGILSGNRaaYPTEWNVLVKLRIPRTIAALAVGIGLSVSGLLYQELFQNKLVSPDL 94 
                                       678999*******************998889999999**************************************** PP

                             FecCD  77 lGissgaalgavlalllllgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsaltsllll 153
                                       lG+s ga++ga++a+ll+   ls++a++ ++f+ ++la+l  ++++r+ ++ s+++l+L+Gi+v+ +++++  ++++
  gi|474934402|ref|YP_007687984.1|  95 LGVSDGAGVGAAVAILLG---LSSWAITGLSFITGILAVLAAIAISRSVRSRSSATLLLSGIIVGGFAASVLGFVKY 168
                                       ****************96...9******************************************************* PP

                             FecCD 154 ll.neealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrllllllva 229
                                       l+  +++l+si fwl+Gs ++++++k+lll+ ++++++++++ +  ++ l++lg e+ +s G+n++ +++l++ l++
  gi|474934402|ref|YP_007687984.1| 169 LAgPDTTLASIEFWLMGSCEYVNMDKALLLAGAITVCMAIIIPIKWRIYLISLGSEECRSRGINYNAYKWLIIGLAT 245
                                       **9999*********************************************************************** PP

                             FecCD 230 lltavavalvGpigFvGLivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivtaliGapff 306
                                       l+ta++v++vG ++++GL++Phiar++vg++++  +pl+a++G++l+++ad+++r+++  +e+p+ +v+ +iG ++f
  gi|474934402|ref|YP_007687984.1| 246 LMTAATVSVVGCVAWIGLVIPHIARMVVGRNTKFSIPLAAIFGGILMMVADIVSRCFT-TSEIPLLVVMGMIGSVMF 321
                                       *******************************************************997.79**************** PP

                             FecCD 307 iylll 311
                                       +++l+
  gi|474934402|ref|YP_007687984.1| 322 VIILR 326
                                       *9986 PP

>> ABC-3  ABC 3 transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1     0.059   3.5e+02      60      90 ..      12      43 ..       5      48 .. 0.66
   2 !   26.9  23.2     5e-10     3e-06      41     249 ..     100     316 ..      93     327 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.059
                             ABC-3 60 ailvgliaav.alellkrktklkedtaigivl 90
                                      ai v l+aav a+++   +++++ d+++gi+ 
  gi|474934402|ref|YP_007687984.1| 12 AIGVPLMAAVfAIAICVGRYQVSLDALMGILS 43
                                      44444555541455666789999999999975 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 5e-10
                             ABC-3  41 aalpGvalayllgvn...lllgailvgliaavalellkrktklkedtai...givlsvflalglvlvslikk...sk 108
                                        a  G a+a+llg++   ++  ++++g++a +a  +++r  + ++ + +   gi++  f a  l +v++  +   + 
  gi|474934402|ref|YP_007687984.1| 100 GAGVGAAVAILLGLSswaITGLSFITGILAVLAAIAISRSVRSRSSATLllsGIIVGGFAASVLGFVKYLAGpdtTL 176
                                       55678899999999987555557888899989999999999988876533449**9999998888999988877788 PP

                             ABC-3 109 vdldsyLfGniltisqedliliaiieavvllllllfwkelllitfdeelAkveglsvkllkllllalialavvvalq 185
                                       ++++ +L+G+   ++ +  +l+a +  v++++++ +   ++li++  e  +++g++ +++k l++ l  l  ++++ 
  gi|474934402|ref|YP_007687984.1| 177 ASIEFWLMGSCEYVNMDKALLLAGAITVCMAIIIPIKWRIYLISLGSEECRSRGINYNAYKWLIIGLATLMTAATVS 253
                                       899999************999999999999999998889************************************** PP

                             ABC-3 186 avGviLvialliiPaatArrltrslesllivAillglvsvvaGlllSyyldlatGavivlvatl 249
                                       +vG +  i l +iP ++ + ++r+ +  + +A+++g + +++  ++S  + ++  +++v++ ++
  gi|474934402|ref|YP_007687984.1| 254 VVGCVAWIGL-VIPHIARMVVGRNTKFSIPLAAIFGGILMMVADIVSRCFTTSEIPLLVVMGMI 316
                                       ****999986.78*9999999999999999**************************99986543 PP

>> Keratin_assoc  Keratinocyte-associated protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   1.9     0.015        87       3      47 ..     119     166 ..     117     210 .. 0.78
   2 ?   13.2   1.2   8.9e-06     0.053       2      51 ..     276     326 ..     275     331 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.015
                     Keratin_assoc   3 tgtslllssllavlvfalmqlyksklassell..tilgGflgsll.Fv 47 
                                       tg s++   l ++  +a+ + ++s+ +++ ll  +i+gGf +s+l Fv
  gi|474934402|ref|YP_007687984.1| 119 TGLSFITGILAVLAAIAISRSVRSRSSATLLLsgIIVGGFAASVLgFV 166
                                       5778888888788888888888887776665433899****9999454 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 8.9e-06
                     Keratin_assoc   2 stgtslllssllavlvfalmqlyksklassel.ltilgGflgsllFvllLT 51 
                                       +t+ s+ l+++   +++ +  ++++ +++se+ l ++ G++gs++Fv++L 
  gi|474934402|ref|YP_007687984.1| 276 NTKFSIPLAAIFGGILMMVADIVSRCFTTSEIpLLVVMGMIGSVMFVIILR 326
                                       577889999999999****************8456789**********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1006  (0.0561102); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 2123.30
//
Query:       gi|474934403|ref|YP_007687985.1|  [L=266]
Description: ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase component [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-30  106.9   0.0    1.8e-30  106.2   0.0    1.3  1  ABC_tran  ABC transporter
    6.4e-14   52.5   0.1    2.6e-08   34.0   0.0    2.1  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    1.9e-06   27.5   0.2    8.1e-05   22.2   0.2    2.1  1  SMC_N     RecF/RecN/SMC N terminal domain
    0.00045   20.0   0.8       0.63    9.7   0.0    2.1  2  AAA_15    AAA ATPase domain
     0.0014   17.4   0.3       0.79    8.3   0.1    2.0  2  AAA_13    AAA domain
     0.0047   16.7   0.2      0.092   12.5   0.1    2.1  2  AAA_30    AAA domain
     0.0048   17.1   0.0      0.043   14.1   0.0    2.1  1  SbcCD_C   Putative exonuclease SbcCD, C subunit
     0.0057   16.3   0.1     0.0096   15.6   0.1    1.4  1  SRP54     SRP54-type protein, GTPase domain
  ------ inclusion threshold ------
       0.02   15.3   1.0       0.29   11.6   1.0    2.2  1  AAA       ATPase family associated with various cellular acti
      0.026   14.6   0.0       0.18   11.8   0.0    2.1  2  AAA_14    AAA domain
      0.048   12.8   0.0       0.05   12.8   0.0    1.2  1  G-alpha   G-protein alpha subunit
      0.063   13.7   0.0      0.094   13.1   0.0    1.4  1  AAA_16    AAA ATPase domain
      0.072   13.4   2.0        1.4    9.2   2.0    2.2  1  AAA_22    AAA domain
      0.088   13.3   0.1       0.13   12.8   0.1    1.3  1  AAA_23    AAA domain
      0.099   12.4   1.4       0.21   11.4   0.3    2.1  3  AAA_29    P-loop containing region of AAA domain
       0.13   12.1   0.1       0.24   11.3   0.0    1.5  2  ATPase_2  ATPase domain predominantly from Archaea
       0.13   12.8   0.2        2.3    8.8   0.2    2.4  1  AAA_18    AAA domain
       0.33   10.5   1.2        4.3    6.9   0.3    2.1  2  AAA_25    AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.2   0.0   1.8e-33   1.8e-30       1     137 []      20     169 ..      20     169 .. 0.95

  Alignments for each domain:
  == domain 1  score: 106.2 bits;  conditional E-value: 1.8e-33
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l+ ++lk+++g++  ++G nG+GK+tL+k++agl+kp+ G++++dgkd++  + ++ ++ i+++ q+ ++ +++ v+
  gi|474934403|ref|YP_007687985.1|  20 LNGITLKCEKGTVNTLLGLNGCGKTTLIKTMAGLYKPDGGKVTYDGKDIHALSDRERSAYIAYVNQHGNHVSDYPVQ 96 
                                       6899***********************************************9999999*********9999999999 PP

                                       HH.................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xx.................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       +                  ++ e +++ l+ lg++++k +++     +LSgGq+q v +++al+++++++llDEpt+
  gi|474934403|ref|YP_007687985.1|  97 DYllmstinslqpfeepgrKQMEIVDRCLDLLGISGMKSKNI----GQLSGGQRQLVYICAALVQDSEVILLDEPTS 169
                                       99*********9999888555555******************....*****************************96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   5.1e-06    0.0051       1      26 [.      32      55 ..      32      92 .. 0.78
   2 !   34.0   0.0   2.6e-11   2.6e-08     233     299 ..     137     201 ..     117     203 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.1e-06
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarld 26
                                      +n l G Ng+GK++L++++ +l    
  gi|474934403|ref|YP_007687985.1| 32 VNTLLGLNGCGKTTLIKTMAGLY--K 55
                                      699****************9996..3 PP

  == domain 2  score: 34.0 bits;  conditional E-value: 2.6e-11
                            AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHSp 299
                                       ++ +lS G+++l ++ +al ++     ++l+DEp + L+ +  +++l  l ++++++g  +il+TH+p
  gi|474934403|ref|YP_007687985.1| 137 NIGQLSGGQRQLVYICAALVQDS---EVILLDEPTSALDLRNEHTVLSTLkRIAEDTGKTIILSTHDP 201
                                       5789****************999...9********************99945555599*********9 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.2   8.1e-08   8.1e-05      25     197 ..      31     198 ..      21     214 .. 0.65

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 8.1e-08
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--.BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk.skekasvkkaeveitfdnedkklkiekeevsis 100
                                        ++ ++G NG+GK+ l+  +    G  +    + +   + ih+ s++++s+  a+v+ +    ++ +    +++ ++
  gi|474934403|ref|YP_007687985.1|  31 TVNTLLGLNGCGKTTLIKTMA---GLYKPDGGKVTYDGKDIHAlSDRERSAYIAYVNQH---GNHVSDYPVQDYLLM 101
                                       579999***********9994...44444445666666668875566666666666665...455444555666666 PP

                                       EEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT...CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 101 rrvkrkgeseykingkevtkkevsellesagiske...lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDek 174
                                        ++ + +  e    ++        +ll  +g++++   +LSgG+++Lv +        v+ + + llDe  +aLD +
  gi|474934403|ref|YP_007687985.1| 102 STINSLQPFEEPGRKQMEIVDRCLDLLGISGMKSKnigQLSGGQRQLVYICAA----LVQDSEVILLDEPTSALDLR 174
                                       666555554433333333334455555555554444448********976433....46888899************ PP

                                       HHHHHHHHHHHHCTT.SEEEEE-S CS
                                       xxxxxxxxxxxxxxx.xxxxxxxx RF
                             SMC_N 175 nvkkvaellkekskn.aQfivisl 197
                                       n + v + lk+  ++    i+ s 
  gi|474934403|ref|YP_007687985.1| 175 NEHTVLSTLKRIAEDtGKTIILST 198
                                       **********87766344444443 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.2   0.00099      0.98      25      48 ..      32      55 ..      21      81 .. 0.74
   2 !    9.7   0.0   0.00064      0.63     298     367 ..     142     202 ..      95     204 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00099
                            AAA_15 25 ltvliGkNnsGKSsilealdlFln 48
                                      +++l G N++GK+++++ +  + +
  gi|474934403|ref|YP_007687985.1| 32 VNTLLGLNGCGKTTLIKTMAGLYK 55
                                      899*************98865555 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00064
                            AAA_15 298 GsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSph 367
                                       + G+++l+++   ++          ++ ++l++EP   L   +   +  +lk++a+d+ + +i++TH p 
  gi|474934403|ref|YP_007687985.1| 142 SGGQRQLVYICAALVQ---------DSEVILLDEPTSALDLRNEHTVLSTLKRIAEDTGKTIILSTHDPN 202
                                       5555555555544432.........34679*************************************995 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.1   0.00079      0.79      17      39 ..      31      53 ..      24      77 .. 0.87
   2 !    7.3   0.0    0.0015       1.5     526     570 ..     158     200 ..     140     210 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00079
                            AAA_13 17 riNliYGwNGaGKTtLSrllrsl 39
                                       +N + G NG GKTtL + ++ l
  gi|474934403|ref|YP_007687985.1| 31 TVNTLLGLNGCGKTTLIKTMAGL 53
                                      689*************9998877 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0015
                            AAA_13 526 kdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHn 570
                                         +++ +D P S LD      v s +k  +  ++  k ++++TH 
  gi|474934403|ref|YP_007687985.1| 158 DSEVILLDEPTSALDLRNEHTVLSTLKRIA--EDTGKTIILSTHD 200
                                       5689************************99..8999********6 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.1   9.3e-05     0.092      17      50 ..      29      62 ..      23      81 .. 0.86
   2 ?    2.2   0.0      0.13   1.3e+02      67     121 ..     132     196 ..     116     201 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.3e-05
                            AAA_30 17 gdrvavltGpAGtGKttalkalreaweaaggrvi 50
                                      +  v +l G  G GKtt++k+++ +++ +gg+v 
  gi|474934403|ref|YP_007687985.1| 29 KGTVNTLLGLNGCGKTTLIKTMAGLYKPDGGKVT 62
                                      446999*********************9998875 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.13
                            AAA_30  67 gieastiakllkrlk......grarlepgtllivDEagmv.....dtkqlaallkaaekagakvil 121
                                       g+++++i +l   ++      + a ++++++++ DE   +       + l +l ++ae++g ++il
  gi|474934403|ref|YP_007687985.1| 132 GMKSKNIGQLSGGQRqlvyicA-ALVQDSEVILLDEPTSAldlrnEHTVLSTLKRIAEDTGKTIIL 196
                                       6778888888877778888742.5667779999999665554444444455555666666666665 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   4.3e-05     0.043      27      89 ..     135     184 ..     129     185 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.3e-05
                           SbcCD_C  27 srssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                       s+++g+lSGG++  l+y++ a     l++++       ++++LDE  s lD ++ +t+l++l+
  gi|474934403|ref|YP_007687985.1| 135 SKNIGQLSGGQR-QLVYICAA-----LVQDS-------EVILLDEPTSALDLRNEHTVLSTLK 184
                                       7899********.88888766.....45553.......58**************999999987 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   9.7e-06    0.0096       3      36 ..      32      65 ..      30      91 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 9.7e-06
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllva 36
                                      v  l+Gl+G GKTt +  +a l+k +g kv    
  gi|474934403|ref|YP_007687985.1| 32 VNTLLGLNGCGKTTLIKTMAGLYKPDGGKVTYDG 65
                                      56799*******************9998887555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.0   0.00029      0.29       3      24 ..      35      56 ..      34     206 .. 0.48

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00029
                                      EESSTTSSHHHHHHHHHHHHTH CS
                               AAA  3 lyGppGtGKTllakavakelgv 24
                                      l G  G+GKT+l+k +a   + 
  gi|474934403|ref|YP_007687985.1| 35 LLGLNGCGKTTLIKTMAGLYKP 56
                                      7899************998742 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00018      0.18       3      43 ..      31      70 ..      29     112 .. 0.68
   2 ?    0.3   0.0      0.66   6.6e+02      64      90 ..     158     190 ..     133     206 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                            AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderd 43
                                       + ++ G+  +GKTtl+k+++  +  ++   + ++ +d + 
  gi|474934403|ref|YP_007687985.1| 31 TVNTLLGLNGCGKTTLIKTMAGLYK-PDGGKVTYDGKDIHA 70
                                      577899************9985554.444444444444444 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.66
                            AAA_14  64 kktylflDEiqev......pewekalkslvdeg 90 
                                       + ++++lDE   +       ++ ++lk++ +++
  gi|474934403|ref|YP_007687985.1| 158 DSEVILLDEPTSAldlrneHTVLSTLKRIAEDT 190
                                       567888888877755555555556666666655 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     5e-05      0.05      28      61 ..      35      81 ..      24     237 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5e-05
                                      EEESTTSSHHHHHHHHHHHCS--.............--HHHHHCCHH CS
                           G-alpha 28 llGqseSGKsTilkqlkllykkg.............fseeelatwra 61
                                      llG +++GK+T++k +  lyk+               s++e+ ++ a
  gi|474934403|ref|YP_007687985.1| 35 LLGLNGCGKTTLIKTMAGLYKPDggkvtydgkdihaLSDRERSAYIA 81
                                      89******************998777776666666555555544544 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   9.4e-05     0.094      29      76 ..      35      86 ..      26     208 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.4e-05
                            AAA_16 29 lsGesGvGKsslvrellralekdggiflrgkcdql....esaipysalaqal 76
                                      l G  G+GK++l+++ +  ++ dgg +++   d +    ++  +y+a++++ 
  gi|474934403|ref|YP_007687985.1| 35 LLGLNGCGKTTLIKTMAGLYKPDGGKVTYDGKDIHalsdRERSAYIAYVNQH 86
                                      789**************99999999998877777743322223333344443 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   2.0    0.0014       1.4       9     126 ..      34     195 ..      27     205 .. 0.52

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0014
                            AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaee................erpevvfvtlpsstsskdl.lrellralglel 68 
                                       ++ G  G+GKTtl+++++  ++     +                 er+ ++ +  ++++  +d   ++ l   + + 
  gi|474934403|ref|YP_007687985.1|  34 TLLGLNGCGKTTLIKTMAGLYKP----DGgkvtydgkdihalsdrERSAYIAYVNQHGNHVSDYpVQDYLLMSTINS 106
                                       688999**********9998842....22445567777777776533333333333333333333333333333222 PP

                            AAA_22  69 ka.........................erlsseellealeqalrarav....ielliiDEaqh.lr...seealeeL 112
                                                                  + ++  +l    +q +  +a+     e++++DE    l+   ++++l++L
  gi|474934403|ref|YP_007687985.1| 107 LQpfeepgrkqmeivdrcldllgisgmKSKNIGQLSGGQRQLVYICAAlvqdSEVILLDEPTSaLDlrnEHTVLSTL 183
                                       22455544444555554544444444422222222222222222222244455667777766666564337777777 PP

                            AAA_22 113 rsllnlsrkgvqli 126
                                       +++++  ++g ++i
  gi|474934403|ref|YP_007687985.1| 184 KRIAE--DTGKTII 195
                                       77776..5555555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   0.00013      0.13      20      38 ..      31      49 ..      15     106 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                            AAA_23 20 gltlItGpNGaGKTTildA 38
                                       ++ + G NG+GKTT++  
  gi|474934403|ref|YP_007687985.1| 31 TVNTLLGLNGCGKTTLIKT 49
                                      588999**********975 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       5.7   5.7e+03      32      39 ..      12      19 ..      11      25 .. 0.85
   2 ?   11.4   0.3   0.00021      0.21      17      50 ..      25      58 ..      19      65 .. 0.76
   3 ?   -2.7   0.0       5.1   5.1e+03      38      52 ..     206     219 ..     204     226 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 5.7
                            AAA_29 32 GsGKSTll 39
                                      G GK Tl+
  gi|474934403|ref|YP_007687985.1| 12 GYGKGTLI 19
                                      77999997 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00021
                            AAA_29 17 ieidlkg.atlltGpsGsGKSTllDAiqalLvpak 50
                                      ++ + kg +  l G +G GK+Tl+  ++ l  p+ 
  gi|474934403|ref|YP_007687985.1| 25 LKCE-KGtVNTLLGLNGCGKTTLIKTMAGLYKPDG 58
                                      5555.45588899***********98888777765 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 5.1
                            AAA_29  38 llDAiqalLvpakkv 52 
                                       +lDA  +l+ + k +
  gi|474934403|ref|YP_007687985.1| 206 FLDANVFLMDGGK-I 219
                                       5899999998877.4 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00024      0.24      18      52 ..      28      62 ..      19     117 .. 0.84
   2 ?   -2.9   0.0       5.4   5.4e+03     121     150 ..     161     188 ..     147     195 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00024
                          ATPase_2 18 epneiyfiYGpegsGKtaLlkeiienledkdkyvi 52
                                      e+ ++  + G  g+GKt+L+k ++   +  + +v 
  gi|474934403|ref|YP_007687985.1| 28 EKGTVNTLLGLNGCGKTTLIKTMAGLYKPDGGKVT 62
                                      456788889************99877665555555 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.4
                          ATPase_2 121 iiiiDelqklidlglngaellvkeLlnlie 150
                                       +i++De   +    l+++  +++ L ++ e
  gi|474934403|ref|YP_007687985.1| 161 VILLDEPTSAL--DLRNEHTVLSTLKRIAE 188
                                       67777777777..44555666666655554 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.2    0.0023       2.3       3      64 ..      35     125 ..      34     214 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0023
                            AAA_18   3 ltGtpGvGKttlakeLskrlgf................................gvnlrdvakenglllevdpeald 47 
                                       l G  G+GKttl k  + +  +                                g +++d+  +++ll +  +  l+
  gi|474934403|ref|YP_007687985.1|  35 LLGLNGCGKTTLIKTMAGL--YkpdggkvtydgkdihalsdrersayiayvnqhGNHVSDYPVQDYLLMSTINS-LQ 108
                                       78999********999544..23344444445544444455555555666777666666666666666666666.56 PP

                            AAA_18  48 eskrldedkldklldal 64 
                                       ++++  +++++ + ++l
  gi|474934403|ref|YP_007687985.1| 109 PFEEPGRKQMEIVDRCL 125
                                       66666666655555555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.3    0.0043       4.3      32      51 ..      29      48 ..      24      54 .. 0.87
   2 ?    2.1   0.0      0.12   1.2e+02     166     188 ..     177     199 ..     146     203 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0043
                            AAA_25 32 agelallaGapgtGKttlal 51
                                      +g+++ l G  g+GKttl  
  gi|474934403|ref|YP_007687985.1| 29 KGTVNTLLGLNGCGKTTLIK 48
                                      799**************975 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.12
                            AAA_25 166 galvealeriarrtgaavllvhH 188
                                         +++ l+ria+ tg +++l  H
  gi|474934403|ref|YP_007687985.1| 177 HTVLSTLKRIAEDTGKTIILSTH 199
                                       5688999**********999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 1727.08
//
Query:       gi|474934404|ref|YP_007687986.1|  [L=652]
Description: hypothetical protein TALC_00831 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (652 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.49
# Mc/sec: 3994.69
//
Query:       gi|474934405|ref|YP_007687987.1|  [L=55]
Description: hypothetical protein TALC_00832 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 399.70
//
Query:       gi|474934406|ref|YP_007687988.1|  [L=112]
Description: hypothetical protein TALC_00833 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.034   14.6   0.0      0.043   14.2   0.0    1.1  1  PemK_toxin  PemK-like, MazF-like toxin of type II toxin-antit


Domain annotation for each model (and alignments):
>> PemK_toxin  PemK-like, MazF-like toxin of type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.4e-06     0.043       3      99 ..      19     105 ..      17     108 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.4e-06
                                       TEEEEEEE-S--TTS--SEEEEEE-S-HHHHCHSEEEEEEEESSSTSSGCSTTEEEE-HHHCSSSSSSSSEEEECCC CS
                        PemK_toxin   3 GeIvlvdldpsrgseqgkrRpvvVvsndafnekntvivvpltskdkdkkklpfhveleseildlngldkdswvkldq 79 
                                       GeI+l++  p       k Rpvv+  ++ +    + ++   ts++++ +++   + le+      gl k s++  d 
  gi|474934406|ref|YP_007687988.1|  19 GEIWLAEALPFEDGIHSKSRPVVIKRRE-GD---MFLCYKCTSQESTFRERYRVIDLEE-----AGLTKYSYIDYDP 86 
                                       9******97744445589***9998665.44...899999*****99988555555654.....444456******6 PP

                                       EEEEEGGGEEEEEEE--HHH CS
                        PemK_toxin  80 irtvdkarlrkkigklsred 99 
                                       i+ ++++ l  k+g++s+ed
  gi|474934406|ref|YP_007687988.1|  87 IF-IPREQLSYKLGSISEED 105
                                       65.99999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 813.67
//
Query:       gi|474934407|ref|YP_007687989.1|  [L=58]
Description: hypothetical protein TALC_00834 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0014   17.9   0.3      0.028   13.8   0.1    2.2  2  zf-ribbon_3    zinc-ribbon domain
     0.0053   16.7   0.0     0.0093   16.0   0.0    1.4  1  DZR            Double zinc ribbon
     0.0072   16.0   2.3       0.27   11.0   0.4    2.3  2  zinc_ribbon_2  zinc-ribbon domain
  ------ inclusion threshold ------
      0.021   15.3   1.4      0.028   14.9   1.4    1.1  1  DUF2367        Uncharacterized conserved protein (DUF2367)
       0.05   13.3   4.3        1.1    9.0   1.5    2.2  2  zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
       0.06   13.0   1.4        2.8    7.6   0.2    2.1  2  zf_UBZ         Ubiquitin-Binding Zinc Finger
      0.072   13.4   7.3       0.65   10.3   7.3    2.1  1  zf-LITAF-like  LITAF-like zinc ribbon domain
        2.6    7.8   8.9        5.6    6.7   2.6    2.5  2  zf-RRN7        Zinc-finger of RNA-polymerase I-specific TFIIB


Domain annotation for each model (and alignments):
>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   1.3e-05     0.028       4      14 ..       2      12 ..       1      15 [. 0.84
   2 ?    2.4   0.0     0.049   1.1e+02      16      24 ..      41      49 ..      39      51 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.3e-05
                       zf-ribbon_3  4 rCPnCGaplss 14
                                      +CP+CG+++++
  gi|474934407|ref|YP_007687989.1|  2 YCPYCGKIVKA 12
                                      7******8786 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.049
                       zf-ribbon_3 16 dnvCpyCGt 24
                                       +vC+ C +
  gi|474934407|ref|YP_007687989.1| 41 SRVCTECHH 49
                                      689****66 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   4.2e-06    0.0093      14      38 ..       2      51 ..       1      56 [. 0.90

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.2e-06
                               DZR 14 fCseCgtklkavaa.........................edrCpsCgekv 38
                                      +C++Cg+ +ka +                          +++C +C++ +
  gi|474934407|ref|YP_007687989.1|  2 YCPYCGKIVKASKVrwlwvfvflligylpiyliycalvrSRVCTECHHRI 51
                                      9********95554********************************9975 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.4   0.00012      0.27      15      21 ..       2       8 ..       1      11 [. 0.78
   2 ?    4.8   0.1     0.011        25       2       9 ..      44      51 ..      41      55 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00012
                     zinc_ribbon_2 15 FCpyCGt 21
                                      +CpyCG 
  gi|474934407|ref|YP_007687989.1|  2 YCPYCGK 8 
                                      7888885 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.011
                     zinc_ribbon_2  2 CpnCGael 9 
                                      C++C++ +
  gi|474934407|ref|YP_007687989.1| 44 CTECHHRI 51
                                      88888776 PP

>> DUF2367  Uncharacterized conserved protein (DUF2367)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   1.4   1.2e-05     0.028      58     100 ..       3      47 ..       2      50 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.2e-05
                           DUF2367  58 CpaCrvgvLedd..ftclGilcaifffPlGilcClalrerrCsnC 100
                                       Cp C+  v  ++  +  + +++ i + P+ +++C  +r r C++C
  gi|474934407|ref|YP_007687989.1|   3 CPYCGKIVKASKvrWLWVFVFLLIGYLPIYLIYCALVRSRVCTEC 47 
                                       77777555554401444557788999******************* PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1    0.0073        16       5      10 ..       2       7 ..       1      13 [. 0.82
   2 ?    9.0   1.5   0.00049       1.1      20      32 .]      40      52 ..      40      52 .. 0.94

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0073
                     zf-NADH-PPase  5 FCgrCG 10
                                      +C+ CG
  gi|474934407|ref|YP_007687989.1|  2 YCPYCG 7 
                                      799998 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00049
                     zf-NADH-PPase 20 warvCpaCglehY 32
                                      ++rvC  C ++ Y
  gi|474934407|ref|YP_007687989.1| 40 RSRVCTECHHRIY 52
                                      79*********98 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0    0.0096        21       5      16 ..       3      14 ..       1      16 [. 0.83
   2 ?    7.6   0.2    0.0013       2.8       3      14 ..      42      53 ..      40      55 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0096
                            zf_UBZ  5 CerCgkeipese 16
                                      C+ Cgk +  s+
  gi|474934407|ref|YP_007687989.1|  3 CPYCGKIVKASK 14
                                      ******998765 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0013
                            zf_UBZ  3 ylCerCgkeipe 14
                                       +C +C+++i  
  gi|474934407|ref|YP_007687989.1| 42 RVCTECHHRIYK 53
                                      58*******975 PP

>> zf-LITAF-like  LITAF-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   7.3   0.00029      0.65       6      67 ..       1      52 [.       1      55 [. 0.73

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00029
                     zf-LITAF-like  6 vdCpaCqqrvvTsveyksgkltwllalllclfgcllccliP.fcvdslkdvehyCpnCgallg 67
                                      ++Cp+C++ v      k++k+ wl++++++l+g      +P +++ +       C++C++++ 
  gi|474934407|ref|YP_007687989.1|  1 MYCPYCGKIV------KASKVRWLWVFVFLLIGY-----LPiYLIYCALVRSRVCTECHHRIY 52
                                      79****9998......678999999999999996.....341344444555667999998876 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.3    0.0094        21      23      28 ..       2       7 ..       1      10 [. 0.82
   2 ?    6.7   2.6    0.0025       5.6      22      31 ..      42      51 ..      41      52 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0094
                           zf-RRN7 23 yCrrCh 28
                                      yC +C+
  gi|474934407|ref|YP_007687989.1|  2 YCPYCG 7 
                                      9****9 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0025
                           zf-RRN7 22 yyCrrChtqe 31
                                      ++C++Ch+ +
  gi|474934407|ref|YP_007687989.1| 42 RVCTECHHRI 51
                                      69*****976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1039  (0.0579508); expected 358.6 (0.02)
Passed bias filter:                      617  (0.0344135); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 398.46
//
Query:       gi|474934408|ref|YP_007687990.1|  [L=712]
Description: hypothetical protein TALC_00835 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0045   17.5   0.1        2.3    8.7   0.0    3.0  2  PH        PH domain
  ------ inclusion threshold ------
      0.082   12.8   1.2       0.16   11.8   0.1    2.1  2  Myosin_N  Myosin N-terminal SH3-like domain


Domain annotation for each model (and alignments):
>> PH  PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0   0.00026       2.3      20      85 ..     308     364 ..     282     370 .. 0.82
   2 !    5.3   0.0    0.0031        27       3      72 ..     510     584 ..     508     613 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00026
                                       EEEEEEETTEEEEESSTTCTTESSEEEEEESTTEEEEEEECTTSSSSTSEEEEEESTSSSTEEEEE CS
                                PH  20 krwfvLkdsellyykndksekdkepkgsislsncevvevvatedpkrkfcfelriverngsrtyll 85 
                                        +++v+++++l yyk+     +++ +g+is ++ + +        +++++f+++ +e++++++++l
  gi|474934408|ref|YP_007687990.1| 308 THYCVISSEDLTYYKYV---GKEQETGFISEHGDRFE------PIDEEYSFKVTRPEKGEQSRFFL 364
                                       58***************...99999999998888887......67999999998888888777766 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0031
                                       EEEEEEEETSSSSC..SEEEEEEEEETTEEEEESST..TCTTESSEEEEEESTTEEEEEEEC.TTSSSSTSEEEE CS
                                PH   3 keGwLlkkgsgkkk..swkkrwfvLkdsellyyknd..ksekdkepkgsislsncevvevva.tedpkrkfcfel 72 
                                       k+G++ + +  k    ++  r + L+++++++ + d  +++++++p+ +i + +c    +++  + +k++++ ++
  gi|474934408|ref|YP_007687990.1| 510 KSGNMRHSSTIKCDesKFNARMCELSGERIAVVSLDdlDKNPSEDPRITIRIVDCNHNGDPEtCDISKTDNKSRH 584
                                       56666655555444668999*********99999999*****************998877767555555555555 PP

>> Myosin_N  Myosin N-terminal SH3-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1      0.48   4.3e+03      21      28 ..     113     120 ..     112     120 .. 0.79
   2 ?   11.8   0.1   1.8e-05      0.16       9      29 ..     629     649 ..     629     654 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.48
                                       EESSEEEE CS
                          Myosin_N  21 eeGdkvtV 28 
                                       ++Gd+vtV
  gi|474934408|ref|YP_007687990.1| 113 INGDQVTV 120
                                       57899988 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 1.8e-05
                                       STTS-EEEEEEEEESSEEEEE CS
                          Myosin_N   9 pkegyvkGeIkeeeGdkvtVe 29 
                                       +k+gyv G++++ +G++++V+
  gi|474934408|ref|YP_007687990.1| 629 EKNGYVHGTVVSHDGETCIVK 649
                                       79******************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (712 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.70u 0.35s 00:00:01.04 Elapsed: 00:00:00.52
# Mc/sec: 4111.06
//
Query:       gi|474934409|ref|YP_007687991.1|  [L=27]
Description: hypothetical protein TALC_00836 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (27 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       112  (0.00624686); expected 358.6 (0.02)
Passed bias filter:                      107  (0.00596798); expected 358.6 (0.02)
Passed Vit filter:                         3  (0.000167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.47
# Mc/sec: 174.12
//
Query:       gi|474934410|ref|YP_007687992.1|  [L=259]
Description: hypothetical protein TALC_00837 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00031   20.6   0.0    0.00053   19.8   0.0    1.3  1  Peptidase_C93   Bacterial transglutaminase-like cysteine prot
     0.0048   17.3   0.0     0.0074   16.7   0.0    1.3  1  Transglut_core  Transglutaminase-like superfamily


Domain annotation for each model (and alignments):
>> Peptidase_C93  Bacterial transglutaminase-like cysteine proteinase BTLCP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   5.9e-08   0.00053      48      94 ..     130     180 ..     104     185 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5.9e-08
                     Peptidase_C93  48 svNeeikpvtdkelygveerWeypkdg....aGdCedyallKrkeLieaGl 94 
                                        v ++i+ ++d+elyg +e W+ p ++    +GdCed  +l    L ++G+
  gi|474934410|ref|YP_007687992.1| 130 FVQSSIRYTSDQELYGYHEFWAAPCETlrlhKGDCEDTSVLLMSILGAMGY 180
                                       58899*******************87544448*****99998888877776 PP

>> Transglut_core  Transglutaminase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   8.2e-07    0.0074      13      71 ..     119     181 ..     105     190 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 8.2e-07
                    Transglut_core  13 dplekakaiyewvrknveysaprrtpgsrd....aeavletgkGncedfaslfvallRalGip 71 
                                       +++ k++a  ++v+++++y++++   g+++    + ++l+  kG+ced++ l+ ++l a+G  
  gi|474934410|ref|YP_007687992.1| 119 SDYLKIAAALYFVQSSIRYTSDQELYGYHEfwaaPCETLRLHKGDCEDTSVLLMSILGAMGYD 181
                                       456788889999********88888888888888999*******************9999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 1499.14
//
Query:       gi|474934411|ref|YP_007687993.1|  [L=441]
Description: putative Ig domain protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-09   35.7   5.4    7.1e-09   35.7   5.4    8.4 10  He_PIG    Putative Ig domain
  ------ inclusion threshold ------
       0.41   10.8   3.0        3.6    7.8   0.3    3.4  3  bMG10     Bacterial Alpha-2-macroglobulin MG10 domain
       0.92    9.8   8.9        2.1    8.6   0.0    3.3  3  DUF5013   Domain of unknown function (DUF5013)


Domain annotation for each model (and alignments):
>> He_PIG  Putative Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   1.2      0.21   1.2e+03      24      48 ..      50      74 ..      50      75 .. 0.71
   2 ?    2.6   2.7     0.027   1.6e+02      18      39 ..      59      80 ..      56      90 .. 0.89
   3 ?   -3.4   5.2         2   1.2e+04      19      49 .]      93     121 ..      87     134 .. 0.71
   4 !   35.7   5.4   1.2e-12   7.1e-09       1      47 [.     169     210 ..     151     212 .. 0.92
   5 ?    3.6   0.7     0.013        78      22      42 ..     206     225 ..     205     230 .. 0.82
   6 ?   -1.2   0.1       0.4   2.4e+03      23      35 ..     215     227 ..     212     246 .. 0.63
   7 !    7.6   4.8   0.00073       4.3      15      47 ..     269     302 ..     268     304 .. 0.88
   8 ?   -2.3   2.3       0.9   5.4e+03      48      48 ..     318     318 ..     301     360 .. 0.65
   9 !   11.9   6.7   3.4e-05       0.2      15      48 ..     365     406 ..     351     407 .. 0.90
  10 ?   -2.8   0.2       1.3   7.5e+03      33      47 ..     419     432 ..     410     436 .. 0.46

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.21
                            He_PIG 24 titGtpdqtvapGsytftVtatdgs 48
                                      t+t+tp+ +    + + tV a++++
  gi|474934411|ref|YP_007687993.1| 50 TYTWTPTFNIDSSRVSLTVNASTST 74
                                      6899988777766777777777665 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.027
                            He_PIG 18 LdsstGtitGtpdqtvapGsyt 39
                                      +dss  ++t++ +++++pG+++
  gi|474934411|ref|YP_007687993.1| 59 IDSSRVSLTVNASTSTTPGTFS 80
                                      699****************997 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 2
                            He_PIG  19 dsstGtitGtpdqtvapGsytftVtatdgsg 49 
                                       ++ t +i++  d t+a  +  + V at++sg
  gi|474934411|ref|YP_007687993.1|  93 SNKTVSISVA-DGTSAS-TVYVKVKATTTSG 121
                                       6777777777.666554.6667777776665 PP

  == domain 4  score: 35.7 bits;  conditional E-value: 1.2e-12
                            He_PIG   1 tytlttpgsngLPsGLtLdsstGtitGtpdqtvapGsytftVtatdg 47 
                                       tyt+     +gLPsGL+ ++s+G +tGt+ ++ ++ +y++ Vt t +
  gi|474934411|ref|YP_007687993.1| 169 TYTA-----TGLPSGLSVNASNGKVTGTVASNAQAKTYSVKVTGTIA 210
                                       7888.....5**********************9999*******9865 PP

  == domain 5  score: 3.6 bits;  conditional E-value: 0.013
                            He_PIG  22 tGtitGtpdqtvapGsytftV 42 
                                       tGti  +p+qt   G++++ V
  gi|474934411|ref|YP_007687993.1| 206 TGTIATDPTQT-FSGTFNIIV 225
                                       89*********.558888755 PP

  == domain 6  score: -1.2 bits;  conditional E-value: 0.4
                            He_PIG  23 GtitGtpdqtvap 35 
                                        t++Gt +  va 
  gi|474934411|ref|YP_007687993.1| 215 QTFSGTFNIIVAS 227
                                       5778886655543 PP

  == domain 7  score: 7.6 bits;  conditional E-value: 0.00073
                            He_PIG  15 GLtLdsstGtitGt..pdqtvapGsytftVtatdg 47 
                                       G+++++stGt +G   + +tva+G+yt++  at+ 
  gi|474934411|ref|YP_007687993.1| 269 GISMSTSTGT-SGKitVASTVAAGTYTIDYKATNP 302
                                       8999999999.9988899***********999986 PP

  == domain 8  score: -2.3 bits;  conditional E-value: 0.9
                            He_PIG  48 s 48 
                                       s
  gi|474934411|ref|YP_007687993.1| 318 S 318
                                       2 PP

  == domain 9  score: 11.9 bits;  conditional E-value: 3.4e-05
                            He_PIG  15 GLtL.....dsstGtitGt...pdqtvapGsytftVtatdgs 48 
                                       GLtL     ++   t++G+     ++ a+G+ytft+t t++s
  gi|474934411|ref|YP_007687993.1| 365 GLTLsksgtNADKVTLSGQkisTATSLAAGTYTFTLTETQAS 406
                                       9******************9887777888********99987 PP

  == domain 10  score: -2.8 bits;  conditional E-value: 1.3
                            He_PIG  33 vapGsytftVtatdg 47 
                                       v p +++f  ++t+g
  gi|474934411|ref|YP_007687993.1| 419 VDP-VFDFSNSVTSG 432
                                       444.44444444443 PP

>> bMG10  Bacterial Alpha-2-macroglobulin MG10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.49   2.9e+03      23      43 ..      45      65 ..      30      86 .. 0.59
   2 ?    7.8   0.3    0.0006       3.6      91     123 ..     282     314 ..     249     316 .. 0.74
   3 ?    0.8   0.0      0.09   5.4e+02      93     115 ..     387     409 ..     368     417 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.49
                             bMG10 23 lkvGdkvrvrltvttprdley 43
                                      l+ Gd+++++ t + ++ +  
  gi|474934411|ref|YP_007687993.1| 45 LRPGDTYTWTPTFNIDSSRVS 65
                                      566666666655555554433 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0006
                             bMG10  91 vffadylpkgtytfeylvravtpGtfsvppaka 123
                                        + a+++++gtyt++y+++  t+G+ ++  +++
  gi|474934411|ref|YP_007687993.1| 282 ITVASTVAAGTYTIDYKATNPTSGQVATQSVTV 314
                                       456889******************998877765 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.09
                             bMG10  93 fadylpkgtytfeylvravtpGt 115
                                        a++l++gtytf+ + + +++G 
  gi|474934411|ref|YP_007687993.1| 387 TATSLAAGTYTFTLTETQASTGA 409
                                       578899******99877777775 PP

>> DUF5013  Domain of unknown function (DUF5013)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.8      0.12   7.1e+02      59     142 ..     182     265 ..     140     271 .. 0.67
   2 ?    3.6   1.7     0.012        73      39     140 ..     259     354 ..     243     360 .. 0.63
   3 ?    8.6   0.0   0.00035       2.1      54      91 ..     374     411 ..     358     421 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.12
                           DUF5013  59 aieNgkiYQtvt..LpaGkYelsvtvaeengqnsn..gtaylvvakgstLPdlenletalaylsylkvakleaesek 131
                                       +  Ngk+  tv    +a +Y+++vt   ++   +   gt  ++va + tL    +  ta+++++ + ++     s++
  gi|474934411|ref|YP_007687993.1| 182 NASNGKVTGTVAsnAQAKTYSVKVTGTIATDPTQTfsGTFNIIVASSMTLTAPGAQYTAQGTAKDITLS----GSNT 254
                                       456777777776667778888887766655555555577778888888887777777777776655544....4677 PP

                           DUF5013 132 tkaltFtLtee 142
                                       t+a+t ++t++
  gi|474934411|ref|YP_007687993.1| 255 TSATTWQITSQ 265
                                       77778887775 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.012
                           DUF5013  39 Glee.enkegaisletgwdnaaieNgkiYQtvtLpaGkYelsvtvaeengqnsngtaylvvakgstLPdlenletal 114
                                       +++  ++  + is++t       + gki    t+ aG+Y+++ +  + +  +  +++  v+ ++  + ++++   + 
  gi|474934411|ref|YP_007687993.1| 259 TWQItSQAVTGISMSTS----TGTSGKITVASTVAAGTYTIDYKATNPTSGQVATQSVTVTVGSVAINSVSATGGTG 331
                                       45655555555666662....33579**99*********99887776665555566777777776688888775555 PP

                           DUF5013 115 aylsylkvakleaesektkaltFtLt 140
                                       +++s  +++     s +  a++Ft++
  gi|474934411|ref|YP_007687993.1| 332 GNVSAGAIT---LYSVTGTAAEFTVS 354
                                       555444443...23334444566665 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.00035
                           DUF5013  54 gwdnaaieNgkiYQtvtLpaGkYelsvtvaeengqnsn 91 
                                       + d+  +  +ki   ++L aG+Y+++ t  ++++ +  
  gi|474934411|ref|YP_007687993.1| 374 NADKVTLSGQKISTATSLAAGTYTFTLTETQASTGATA 411
                                       3344488999*****************99888776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       957  (0.0533772); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.71u 0.40s 00:00:01.10 Elapsed: 00:00:00.57
# Mc/sec: 2334.52
//
Query:       gi|474934412|ref|YP_007687994.1|  [L=412]
Description: Listeria/Bacterioides repeat protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-21   75.5  14.4    1.1e-07   31.9   0.1    3.9  4  Flg_new   Listeria-Bacteroides repeat domain (List_Bact_rpt)
    0.00048   20.1   4.1       0.05   13.7   0.6    4.0  4  Fer2_4    2Fe-2S iron-sulfur cluster binding domain
  ------ inclusion threshold ------
        4.8    7.5   4.9       0.56   10.5   0.2    1.9  2  DUF3040   Protein of unknown function (DUF3040)


Domain annotation for each model (and alignments):
>> Flg_new  Listeria-Bacteroides repeat domain (List_Bact_rpt)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1      0.78   4.7e+03      15      35 ..     101     121 ..      90     123 .. 0.69
   2 !   27.4   0.4   4.6e-10   2.7e-06      17      62 ..     162     202 ..     145     205 .. 0.79
   3 !   24.6   0.8   3.5e-09   2.1e-05      15      58 ..     226     267 ..     206     274 .. 0.80
   4 !   31.9   0.1   1.9e-11   1.1e-07      13      65 .]     294     344 ..     285     344 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.78
                                       EEETTSB----B--EETTEEE CS
                           Flg_new  15 tvtygetitlpanptkeGYtF 35 
                                       t+ ++ ++  + +p+k+G+t 
  gi|474934412|ref|YP_007687994.1| 101 TYADTGSYHITCTPQKSGFTY 121
                                       555566666666899999986 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 4.6e-10
                                       ETTSB----B--EETTEEEEEEESSTTCCSB--TTT-B--SS-EEE CS
                           Flg_new  17 tygetitlpanptkeGYtFaGWytdsdgttaydfgtkvtptgdvtL 62 
                                       +y ++i+ pa+ptkeG tFaGW+ +   ++++df+t +t    + L
  gi|474934412|ref|YP_007687994.1| 162 NYFSKISAPADPTKEGKTFAGWFYN---GSEFDFDTVIT--TPTVL 202
                                       6889********************8...78999998765..55555 PP

  == domain 3  score: 24.6 bits;  conditional E-value: 3.5e-09
                                       EEETTSB----B--EETTEEEEEEESSTTCCSB--TTT-B--SS CS
                           Flg_new  15 tvtygetitlpanptkeGYtFaGWytdsdgttaydfgtkvtptg 58 
                                       t+++g+ ++++++pt eGYtFaGW  d+ g t + +gt+v  t 
  gi|474934412|ref|YP_007687994.1| 226 TFQQGTVLSSLTAPTYEGYTFAGWCSDE-GRTTILAGTTVL-TD 267
                                       688999999*****************96.666666777654.44 PP

  == domain 4  score: 31.9 bits;  conditional E-value: 1.9e-11
                                       EEEEETTSB----B--EETTEEEEEEESSTTCCSB--TTT-B--SS-EEEEEE CS
                           Flg_new  13 sqtvtygetitlpanptkeGYtFaGWytdsdgttaydfgtkvtptgdvtLyAk 65 
                                       + tv++g+t+  ++ pt eG tF+GWy d+ +t a d gt    t+ +  yAk
  gi|474934412|ref|YP_007687994.1| 294 NVTVDEGKTVADLTVPTQEGKTFQGWYADEACTVALDGGTVL--TAGMHAYAK 344
                                       35899******************************9977744..577777776 PP

>> Fer2_4  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.95   5.7e+03      14      30 ..       4      20 ..       2      29 .. 0.79
   2 ?    3.2   0.0     0.015        88       2      22 ..     214     234 ..     213     241 .. 0.81
   3 ?    1.2   0.0     0.066   3.9e+02      59      79 ..     253     273 ..     244     275 .. 0.83
   4 !   13.7   0.6   8.4e-06      0.05       2      23 ..     284     305 ..     283     340 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.95
                            Fer2_4 14 tvpeGdtvasAllangv 30
                                      tv +G +++ A++ + +
  gi|474934412|ref|YP_007687994.1|  4 TVSKGVSIMLAVIMAAA 20
                                      89999999999887765 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.015
                            Fer2_4   2 rpvtltfDGkevtvpeGdtva 22 
                                       + +t+++DG++ t ++G+ + 
  gi|474934412|ref|YP_007687994.1| 214 TDITVYIDGHASTFQQGTVLS 234
                                       579**********99996554 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.066
                            Fer2_4  59 egepnvracstpvedGlkvet 79 
                                       eg++ + a +t ++dG+ + t
  gi|474934412|ref|YP_007687994.1| 253 EGRTTILAGTTVLTDGMHIYT 273
                                       5777789999*******9977 PP

  == domain 4  score: 13.7 bits;  conditional E-value: 8.4e-06
                            Fer2_4   2 rpvtltfDGkevtvpeGdtvas 23 
                                       +++t+ +DG+ vtv eG+tva+
  gi|474934412|ref|YP_007687994.1| 284 EQITVIVDGQNVTVDEGKTVAD 305
                                       789*****************97 PP

>> DUF3040  Protein of unknown function (DUF3040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   0.5         3   1.8e+04      74      80 ..      13      19 ..       5      22 .. 0.44
   2 ?   10.5   0.2   9.3e-05      0.56      24      82 ..     344     402 ..     339     403 .. 0.80

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 3
                           DUF3040 74 Gfvvmla 80
                                       +v+m+a
  gi|474934412|ref|YP_007687994.1| 13 LAVIMAA 19
                                      2333333 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 9.3e-05
                           DUF3040  24 klaaalrggaar.arrrslrrlavlavllfvaGllllvlGvaaaavvlgvvGfvvmlagv 82 
                                       k+a+a  +++ + + ++  ++l v+a+ + ++G+++ v+G+  + +v+ ++G++++++g+
  gi|474934412|ref|YP_007687994.1| 344 KFADAAATEDGEdSEKQFWEDLPVVAISICAIGAIVAVAGLRYH-PVILAIGVAIIVIGG 402
                                       67777766555556677789999*****************7777.589999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 2670.17
//
Query:       gi|474934413|ref|YP_007687995.1|  [L=417]
Description: Listeria-Bacteroides repeat domain (List_Bact_rpt) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-07   30.5   4.9    3.1e-07   30.5   4.9    3.0  2  Flg_new   Listeria-Bacteroides repeat domain (List_Bact_rpt)
  ------ inclusion threshold ------
      0.016   15.0   0.9      0.016   15.0   0.9    2.3  2  DUF2436   Domain of unknown function (DUF2436)
      0.068   13.6   0.6       0.57   10.7   0.1    2.7  3  MG2       MG2 domain


Domain annotation for each model (and alignments):
>> Flg_new  Listeria-Bacteroides repeat domain (List_Bact_rpt)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   4.9   5.2e-11   3.1e-07       1      64 [.     232     300 ..     232     303 .. 0.73
   2 ?   -1.3   0.2      0.42   2.5e+03      16      20 ..     358     362 ..     333     383 .. 0.56

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 5.2e-11
                                       EEEEEEETTEE..EEEE.....EETTSB----B-.-EETTEEEEEEESSTTCCSB--TTT-B--SS-EEEEE CS
                           Flg_new   1 YtvtFdanGgt..vsqt.....vtygetitlpan.ptkeGYtFaGWytdsdgttaydfgtkvtptgdvtLyA 64 
                                       +t+ +danGg+  vs+t      + ++++tl an ++k+GY F+GW     g+t y++g++v++ ++  ++A
  gi|474934413|ref|YP_007687995.1| 232 HTIVYDANGGNgtVSNTvvtdqNNGNTNVTLAANgFSKAGYAFVGWKI---GNTVYQPGQTVSVGANASVTA 300
                                       69*******654465543212244578999995538***********9...6899****9988776665555 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.42
                                       EETTS CS
                           Flg_new  16 vtyge 20 
                                       vty++
  gi|474934413|ref|YP_007687995.1| 358 VTYNA 362
                                       33322 PP

>> DUF2436  Domain of unknown function (DUF2436)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.9   2.6e-06     0.016      28     102 ..      25     108 ..      16     155 .. 0.68
   2 ?   -0.9   0.1       0.2   1.2e+03      78     101 ..     229     253 ..     195     273 .. 0.47

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.6e-06
                           DUF2436  28 kvvleaadvwgdgsGyqllldadhnty....gqvi.Padtgtletgtas..padyean..feytlPanadpsvsten 95 
                                       +vv + +d w+ ++G  + +d+d+  +     ++     tgt++ ++as  p d+  +   ey lP+ a ++vs + 
  gi|474934413|ref|YP_007687995.1|  25 NVVSDDSDAWNANAGTYIYMDSDYYDFegedCDISeRCTTGTIWGSSASlnPTDHPGPpsTEYYLPQWASGTVSYNL 101
                                       6888899********************9887333313457777777665224444332337*************988 PP

                           DUF2436  96 iivdgta 102
                                       i++dg +
  gi|474934413|ref|YP_007687995.1| 102 IVMDGGG 108
                                       8888743 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.2
                           DUF2436  78 nfeytlPanadp.svsteniivdgt 101
                                       ++ +t+  +a++ + +  n +v+++
  gi|474934413|ref|YP_007687995.1| 229 SYTHTIVYDANGgNGTVSNTVVTDQ 253
                                       2223344444331223344444443 PP

>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.1   1.2e+04      59      76 ..     125     142 ..     110     142 .. 0.58
   2 ?   -0.5   0.0       0.3   1.8e+03      38      73 ..     234     270 ..     212     274 .. 0.59
   3 ?   10.7   0.1   9.5e-05      0.57       9      66 ..     282     341 ..     279     373 .. 0.66

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.1
                                       TEEEEEEE--TT--SEEE CS
                               MG2  59 ggaesefalpeaaklGey 76 
                                        g +s+ ++ ++  +G +
  gi|474934413|ref|YP_007687995.1| 125 YGLSSDRPITDTVDTGVW 142
                                       335666666666666666 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.3
                                       EEEE-TTSS.EEEEEEEEE-CTTEEEEEEE--TT--S CS
                               MG2  38 ltirdpdgk.evkelplatdetggaesefalpeaakl 73 
                                       ++    +g+ +v+++ ++++++g  ++++a +  +k 
  gi|474934413|ref|YP_007687995.1| 234 IVYDANGGNgTVSNTVVTDQNNGNTNVTLAANGFSKA 270
                                       3333444442444444466666666766666655555 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 9.5e-05
                                       SEE-TT-EEEEEEEEESTTCSB---EEEEEEEE-TTSSEEEEEEE..EE-CTTEEEEEEE CS
                               MG2   9 glYrPgetVslkallrdetlqglaklplkltirdpdgkevkelpl..atdetggaesefa 66 
                                       ++Y+Pg+tVs+ a + + +  +  +  +++t ++ +g    + +    +++++g + ++a
  gi|474934413|ref|YP_007687995.1| 282 TVYQPGQTVSVGANASVTATAQWSENTVTATANNISGVSGMSYTNqvGASASNGGSLSYA 341
                                       79*************887777777778888888877776655555223333333344444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       832  (0.0464053); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 3008.32
//
Query:       gi|474934414|ref|YP_007687996.1|  [L=408]
Description: Listeria-Bacteroides repeat domain (List_Bact_rpt) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-06   27.3   3.5      3e-06   27.3   3.5    3.7  3  Flg_new   Listeria-Bacteroides repeat domain (List_Bact_rpt)


Domain annotation for each model (and alignments):
>> Flg_new  Listeria-Bacteroides repeat domain (List_Bact_rpt)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.5     0.024   4.2e+02      45      63 ..     136     154 ..     131     155 .. 0.73
   2 !   27.3   3.5   1.7e-10     3e-06       1      65 []     222     292 ..     222     292 .. 0.76
   3 ?   -1.3   0.9      0.15   2.6e+03       9      12 ..     338     341 ..     323     372 .. 0.50

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.024
                                       CSB--TTT-B--SS-EEEE CS
                           Flg_new  45 ttaydfgtkvtptgdvtLy 63 
                                       +t+++f++++  t d+t y
  gi|474934414|ref|YP_007687996.1| 136 GTQVSFTATYDDTDDMTYY 154
                                       5777888888888888876 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 1.7e-10
                                       EEEEEEETT...EE.EEEEEET....TSB----B-.-EETTEEEEEEESSTTCCSB--TTT-B--SS-EEEEEE CS
                           Flg_new   1 YtvtFdanG...gt.vsqtvty....getitlpan.ptkeGYtFaGWytdsdgttaydfgtkvtptgdvtLyAk 65 
                                       +tv +d nG   g+ v++ vt+    + ++tl +n ++k+G+ FaGW  +   +t y++g++v++ +d t++A+
  gi|474934414|ref|YP_007687996.1| 222 HTVHYDGNGntgGStVDTVVTAqgtgNVSVTLATNgFVKTGHSFAGWLVN---GTVYQPGQTVSVGADQTVTAV 292
                                       69******94444433444554333245778876538************8...89****************996 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.15
                                       TEEE CS
                           Flg_new   9 Ggtv 12 
                                       Ggt+
  gi|474934414|ref|YP_007687996.1| 338 GGTA 341
                                       3332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       864  (0.0481901); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2644.15
//
Query:       gi|474934415|ref|YP_007687997.1|  [L=570]
Description: hypothetical protein TALC_00842 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.6e-87  287.6   9.3    7.8e-35  119.6   1.5    3.2  3  LRR_5           BspA type Leucine rich repeat region (6 copie
    7.1e-16   57.7   0.0      0.022   14.5   0.0    6.4  7  LRR_8           Leucine rich repeat
    1.1e-05   25.5   2.0    3.5e-05   23.9   0.3    2.7  3  Flg_new         Listeria-Bacteroides repeat domain (List_Bact
     0.0034   17.7   0.1        2.7    8.5   0.1    4.0  4  LRR_4           Leucine Rich repeats (2 copies)


Domain annotation for each model (and alignments):
>> LRR_5  BspA type Leucine rich repeat region (6 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.0   0.0   9.8e-33   4.4e-29      11     127 ..      62     179 ..      59     180 .. 0.97
   2 !  119.6   1.5   1.7e-38   7.8e-35       2     128 .]     167     294 ..     166     294 .. 0.98
   3 !   86.7   0.7   2.8e-28   1.2e-24       1      91 [.     280     371 ..     280     378 .. 0.93

  Alignments for each domain:
  == domain 1  score: 101.0 bits;  conditional E-value: 9.8e-33
                             LRR_5  11 cnltsitipssvtsIgeyaFsnctslksitlpsslteigsyaFsncssltsitipssltsigeyaFsncsslkeitl 87 
                                         +t i++ + vt++g +aF+++ +++s++lp slt i++++F++cs l+sitip+ +ts g ++F+nc+sl++  +
  gi|474934415|ref|YP_007687997.1|  62 ETITGIVVGEGVTKLGVSAFAGMDHVTSVSLPGSLTLIDNNCFEDCSALESITIPDGVTSPGRNTFRNCTSLQTAVI 138
                                       478999999******************************************************************** PP

                             LRR_5  88 psnlttigssaFsnc.slesitipssvtkigsnaFsncssl 127
                                           t++g++ Fs+c sles+++ +sv ++g+++F+nc+sl
  gi|474934415|ref|YP_007687997.1| 139 GDGATYVGQYTFSGCsSLESVILGESVASVGDYCFQNCTSL 179
                                       **************************************988 PP

  == domain 2  score: 119.6 bits;  conditional E-value: 1.7e-38
                             LRR_5   2 eIgsyaFync.nltsitipssvtsIgeyaFsnctslksitlpsslteigsyaFsncssltsitipssltsigeyaFs 77 
                                       ++g+y+F+nc +l+++++ + +tsIg+y+F+nctsl++++lps+l e++ y+Fs++  +t+i ip+s+t++  y+F 
  gi|474934415|ref|YP_007687997.1| 167 SVGDYCFQNCtSLSDVDFDEALTSIGQYCFQNCTSLETLDLPSGLLEMKGYCFSGS-GITEIAIPDSCTEVWRYSFL 242
                                       689*****************************************************.******************** PP

                             LRR_5  78 ncsslkeitlpsnlttigssaFsnc.slesitipssvtkigsnaFsncsslk 128
                                       nc+sl ++  p ++t++g s+F++c  le++ +  s t+i++naF++cssl+
  gi|474934415|ref|YP_007687997.1| 243 NCTSLVSVIYPAHITYVGVSCFQGCtALETFVFGGSETEIRDNAFNGCSSLT 294
                                       *************************9**********************9986 PP

  == domain 3  score: 86.7 bits;  conditional E-value: 2.8e-28
                             LRR_5   1 teIgsyaFync.nltsitipssvtsIgeyaFsnctslksitlpsslteigsyaFsncssltsitipssltsigeyaF 76 
                                       teI+++aF++c +lt+  +p+s++++g++aF+nc+sl+++ l + +t++g+yaF+ncss+t++t+ ss+++i++ aF
  gi|474934415|ref|YP_007687997.1| 280 TEIRDNAFNGCsSLTDAWLPESLQTVGKNAFKNCSSLTEVILYEDVTSVGTYAFQNCSSMTELTLGSSMETIDTGAF 356
                                       789************************************************************************** PP

                             LRR_5  77 sncsslkeitlpsnl 91 
                                       ++cs+l +i   s++
  gi|474934415|ref|YP_007687997.1| 357 RDCSQLATIYNASSM 371
                                       ******999876665 PP

>> LRR_8  Leucine rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0     4e-05      0.18      13      56 ..      73     115 ..      68     117 .. 0.93
   2 !    4.3   0.0    0.0075        33      16      52 ..     145     180 ..     141     183 .. 0.82
   3 !   12.6   0.0   1.9e-05     0.087      14      57 ..     166     208 ..     154     212 .. 0.82
   4 !   10.0   0.0   0.00013      0.57      13      32 ..     188     207 ..     181     221 .. 0.80
   5 !    4.4   0.0    0.0072        32      13      52 ..     256     294 ..     254     295 .. 0.81
   6 ?    3.0   0.0      0.02        89      13      29 ..     302     318 ..     299     323 .. 0.66
   7 !   14.5   0.0   4.9e-06     0.022      13      54 ..     325     365 ..     319     366 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4e-05
                                       -SEE-TTSSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE- CS
                             LRR_8  13 ltslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdL 56 
                                        t+l+ +aF g+ ++++ +L    lt +++++f+++++L+s+++
  gi|474934415|ref|YP_007687997.1|  73 VTKLGVSAFAGMDHVTSVSLPGS-LTLIDNNCFEDCSALESITI 115
                                       68999*****************9.****************9875 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0075
                                       E-TTSSTT-TT--EEE--SS---GGGGGGGTT--S-. CS
                             LRR_8  16 lddeaFkglsnLkvLdLsnNllttlspgafsgLpsLr 52 
                                       +++ +F+g+s+L++  L++    ++   +f++++sL 
  gi|474934415|ref|YP_007687997.1| 145 VGQYTFSGCSSLESVILGES-VASVGDYCFQNCTSLS 180
                                       7899*************999.5555579999999886 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 1.9e-05
                                       SEE-TTSSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE-- CS
                             LRR_8  14 tslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLs 57 
                                        s++d +F+++++L   d  +  lt++ + +f++++sL+ LdL 
  gi|474934415|ref|YP_007687997.1| 166 ASVGDYCFQNCTSLSDVDFDEA-LTSIGQYCFQNCTSLETLDLP 208
                                       5788888999999999999876.999999999999999999985 PP

  == domain 4  score: 10.0 bits;  conditional E-value: 0.00013
                                       -SEE-TTSSTT-TT--EEE- CS
                             LRR_8  13 ltslddeaFkglsnLkvLdL 32 
                                       lts+++ +F+++++L++LdL
  gi|474934415|ref|YP_007687997.1| 188 LTSIGQYCFQNCTSLETLDL 207
                                       88999999999999999998 PP

  == domain 5  score: 4.4 bits;  conditional E-value: 0.0072
                                       -SEE-TTSSTT-TT--EEE--SS---GGGGGGGTT--S-. CS
                             LRR_8  13 ltslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLr 52 
                                       +t ++ ++F+g+++L+++  +  + t ++ +af g++sL+
  gi|474934415|ref|YP_007687997.1| 256 ITYVGVSCFQGCTALETFVFGGSE-TEIRDNAFNGCSSLT 294
                                       677888999999999999999994.667789999999986 PP

  == domain 6  score: 3.0 bits;  conditional E-value: 0.02
                                       -SEE-TTSSTT-TT--E CS
                             LRR_8  13 ltslddeaFkglsnLkv 29 
                                       l+ +++ aFk++s+L++
  gi|474934415|ref|YP_007687997.1| 302 LQTVGKNAFKNCSSLTE 318
                                       66677777777777765 PP

  == domain 7  score: 14.5 bits;  conditional E-value: 4.9e-06
                                       -SEE-TTSSTT-TT--EEE--SS---GGGGGGGTT--S-.EE CS
                             LRR_8  13 ltslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsL 54 
                                        ts++  aF+++s++++L L++  ++t++ gaf+++++L  +
  gi|474934415|ref|YP_007687997.1| 325 VTSVGTYAFQNCSSMTELTLGSS-METIDTGAFRDCSQLATI 365
                                       589999****************9.**************9876 PP

>> Flg_new  Listeria-Bacteroides repeat domain (List_Bact_rpt)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.1   4.8e+03      14      37 ..     197     221 ..     182     221 .. 0.74
   2 !   23.9   0.3   7.8e-09   3.5e-05       1      48 [.     396     448 ..     396     463 .. 0.66
   3 ?   -1.1   0.1       0.5   2.2e+03       2      19 ..     514     537 ..     514     549 .. 0.59

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.1
                                       EEEETTSB----.B--EETTEEEEE CS
                           Flg_new  14 qtvtygetitlp.anptkeGYtFaG 37 
                                       q++t+ et++lp    + +GY F G
  gi|474934415|ref|YP_007687997.1| 197 QNCTSLETLDLPsGLLEMKGYCFSG 221
                                       6778888899994457999999987 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 7.8e-09
                                       EEEEEEETTEE.EEEEEET.TSB--...--B--EETTEEEEEEESSTTCCSB- CS
                           Flg_new   1 YtvtFdanGgt.vsqtvty.getit...lpanptkeGYtFaGWytdsdgttay 48 
                                       Y+ ++ a +g  +sqtv++ +e+++   +pa+pt+eGY F+GW     + + y
  gi|474934415|ref|YP_007687997.1| 396 YSASYTASDGLfASQTVYAsDEDVSfrvRPADPTREGYAFDGWTHGTGLYEHY 448
                                       788999988885688855427777633358*************9864434444 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.5
                                       EEEEEETTEE..EEE....EEETT CS
                           Flg_new   2 tvtFdanGgt..vsq....tvtyg 19 
                                       tv+F  +G    v+     tvt+g
  gi|474934415|ref|YP_007687997.1| 514 TVSFVPDGTDttVNAtiilTVTNG 537
                                       899999995422454233336655 PP

>> LRR_4  Leucine Rich repeats (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.71   3.2e+03      28      42 ..      96     110 ..      75     115 .. 0.65
   2 ?   -1.9   0.0       1.2   5.2e+03       3      29 ..     156     183 ..     154     186 .. 0.68
   3 !    8.5   0.1   0.00061       2.7      13      31 ..     188     209 ..     171     213 .. 0.79
   4 ?    3.7   0.0      0.02        91       2      32 ..     315     347 ..     314     354 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.71
                                       EE-.-S-----GGGG CS
                             LRR_4  28 LdLsgNnlitdldeL 42 
                                       L+L +Nn  +d + L
  gi|474934415|ref|YP_007687997.1|  96 LTLIDNNCFEDCSAL 110
                                       444556666665555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.2
                                       --EEE--SS---E-S-..HHH-TT--EEE CS
                             LRR_4   3 LevLdLsnNqltdipl..leklpnLkeLd 29 
                                       Le++ L+   + +++   ++++++L  +d
  gi|474934415|ref|YP_007687997.1| 156 LESVILGE-SVASVGDycFQNCTSLSDVD 183
                                       66666765.57776666777888887766 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.00061
                                       --E-S-..HHH-TT--EEE-.. CS
                             LRR_4  13 ltdipl..leklpnLkeLdL.s 31 
                                       lt+i+   ++++++L++LdL s
  gi|474934415|ref|YP_007687997.1| 188 LTSIGQycFQNCTSLETLDLpS 209
                                       88888888889********955 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.02
                                       S--EEE--SS---E-S-..HHH-TT--EEE-..- CS
                             LRR_4   2 nLevLdLsnNqltdipl..leklpnLkeLdL.sg 32 
                                       +L+++ L    +t+++   ++++ +++eL+L s+
  gi|474934415|ref|YP_007687997.1| 315 SLTEVILYE-DVTSVGTyaFQNCSSMTELTLgSS 347
                                       689999995.599999988889*********433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (570 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 3510.04
//
Query:       gi|474934416|ref|YP_007687998.1|  [L=859]
Description: Listeria-Bacteroides repeat domain (List_Bact_rpt) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-34  117.9  44.0    7.5e-08   32.4   0.0    8.6  8  Flg_new   Listeria-Bacteroides repeat domain (List_Bact_rpt)
  ------ inclusion threshold ------
       0.38   10.9   6.8         17    5.6   1.8    4.0  3  SH3_5     Bacterial SH3 domain
        3.8    7.4   6.8        6.2    6.7   0.1    3.1  3  DUF4307   Domain of unknown function (DUF4307)


Domain annotation for each model (and alignments):
>> Flg_new  Listeria-Bacteroides repeat domain (List_Bact_rpt)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   7.4   1.1e-10   6.7e-07       3      65 .]      58     124 ..      45     124 .. 0.86
   2 ?    1.7   0.3     0.051     3e+02       1      23 [.     183     206 ..     183     224 .. 0.65
   3 ?   -2.4   0.5      0.96   5.7e+03      36      36 ..     300     300 ..     272     336 .. 0.55
   4 !   18.0   0.8   3.9e-07    0.0023       3      43 ..     347     393 ..     346     409 .. 0.74
   5 !   16.1   0.4   1.6e-06    0.0097       2      65 .]     426     495 ..     426     495 .. 0.75
   6 !   24.0   0.1   5.5e-09   3.3e-05       2      65 .]     504     577 ..     504     577 .. 0.73
   7 !   18.7   0.1   2.5e-07    0.0015       2      56 ..     590     653 ..     589     669 .. 0.71
   8 !   32.4   0.0   1.3e-11   7.5e-08       2      65 .]     683     742 ..     683     742 .. 0.93

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1.1e-10
                                       EEEEETTEEE..EEEEET.TSB----B--EETTEEEEEEESSTTCC.SB--TTT-B--SS-EEEEEE CS
                           Flg_new   3 vtFdanGgtv..sqtvty.getitlpanptkeGYtFaGWytdsdgt.taydfgtkvtptgdvtLyAk 65 
                                       v++ +nG +v  ++++++ g++ t+ ++ +k+GY+  GW+++s ++  +y++g+++t+t d t+yA+
  gi|474934416|ref|YP_007687998.1|  58 VQYVLNGNSVyfPTEYKApGTSNTTYSQISKSGYVLMGWSENSGASaPSYYPGQSYTVTTDRTFYAV 124
                                       7788888875558888876888888899***************99757******************6 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.051
                                       EEEEEEETTEEEEEEEET.TSB-- CS
                           Flg_new   1 YtvtFdanGgtvsqtvty.getit 23 
                                       Yt+t + nG t s t+++ +++i+
  gi|474934416|ref|YP_007687998.1| 183 YTLTVNGNGNTLSSTTENtNTSIS 206
                                       999*******97655443155554 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.96
                                       E CS
                           Flg_new  36 a 36 
                                       +
  gi|474934416|ref|YP_007687998.1| 300 K 300
                                       2 PP

  == domain 4  score: 18.0 bits;  conditional E-value: 3.9e-07
                                       EEEEETTEEEEEE....E.ETTSB----.B--EETTEEEEEEESSTT CS
                           Flg_new   3 vtFdanGgtvsqt....v.tygetitlp.anptkeGYtFaGWytdsd 43 
                                       + ++anGg ++ +    v tyg+t  +  +  tk+G+tF GW+    
  gi|474934416|ref|YP_007687998.1| 347 IAYNANGGFYNGSfaelVpTYGYTGLKNgSIVTKDGFTFLGWNATGL 393
                                       78*****8876653344436787776664678***********8754 PP

  == domain 5  score: 16.1 bits;  conditional E-value: 1.6e-06
                                       EEEEEETT.EEEEEE..EETTSB----.B--EETTEEEEEEESST.TCC.SB--TTT-B--SS-EEEEEE CS
                           Flg_new   2 tvtFdanG.gtvsqt..vtygetitlp.anptkeGYtFaGWytds.dgt.taydfgtkvtptgdvtLyAk 65 
                                       t+ F++ G g+ + +  + +g+ + lp +    +GY+F GW++   d +    d+g +v +++  t+yA+
  gi|474934416|ref|YP_007687998.1| 426 TIYFENPGdGSQNFSviTFSGYRYALPvNGIALSGYDFMGWSETRyDVGmGTADAGNSVLVSSTKTFYAV 495
                                       788888765664433114469******445689*********9663445578899999999*******96 PP

  == domain 6  score: 24.0 bits;  conditional E-value: 5.5e-09
                                       EEEEEETT..EEE...EEEEET.TSB----.B--EETTEEEEEEESSTTCC.SB--TTT-..B--SS-EEEEEE CS
                           Flg_new   2 tvtFdanG..gtv...sqtvty.getitlp.anptkeGYtFaGWytdsdgt.taydfgtk..vtptgdvtLyAk 65 
                                       t+ +d nG  gt+   s+tv +    +t    ++  +GY FaGW++   ++  +y +g++  +  +gdvtLyA+
  gi|474934416|ref|YP_007687998.1| 504 TLRYDGNGgiGTMgvqSETVSSvPHYMTVAgCSFAYAGYSFAGWSETRYADsPSYLPGSSycFADSGDVTLYAV 577
                                       689*****444544445577662333444433799***********99885379999999777788*******6 PP

  == domain 7  score: 18.7 bits;  conditional E-value: 2.5e-07
                                       EEEEEETTEEE....EE..EEETTSB-..---.B--EETTEEEEEEESSTTCCSB--TTT-B-- CS
                           Flg_new   2 tvtFdanGgtv....sq..tvtygeti..tlp.anptkeGYtFaGWytdsdgttaydfgtkvtp 56 
                                        + F+ nG +v    +q   +t+++++    p + p+k+   F+GW++ + g++ y++g+ +t 
  gi|474934416|ref|YP_007687998.1| 590 HLIFNGNGQNVtnvpPQayRITSEASAvfYVPsSVPQKDDCRFTGWSETAYGSAVYQPGQRITM 653
                                       578*****884334445344666554411445578***************999****9998653 PP

  == domain 8  score: 32.4 bits;  conditional E-value: 1.3e-11
                                       EEEEEETTEEE.EEEEETTSB----B--EETTEEEEEEESSTTCCSB--TTT-B--SS-EEEEEE CS
                           Flg_new   2 tvtFdanGgtv.sqtvtygetitlpanptkeGYtFaGWytdsdgttaydfgtkvtptgdvtLyAk 65 
                                       tvtF a+ gt  s  v +g+ +t  ++p  eG  F GWy      +++df+t+vt  +d+tL Ak
  gi|474934416|ref|YP_007687998.1| 683 TVTFVADSGTLrSVPVPSGNVVTMISAPAVEGRAFLGWYNL---AEKWDFSTPVT--EDLTLNAK 742
                                       8*********73668************************96...58*******97..9*****98 PP

>> SH3_5  Bacterial SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   1.8    0.0028        17      17      59 ..      61     102 ..      55     105 .. 0.89
   2 ?    5.0   0.0    0.0042        25      41      56 ..     376     391 ..     373     394 .. 0.89
   3 ?   -2.9   0.1       1.3   7.8e+03      46      65 .]     434     453 ..     433     453 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0028
                             SH3_5  17 ikgepslsapvafvlekGdkvfYDqvltaDGyvWisYtsesGv 59 
                                       + ++ s++ p+ +  +    ++Y q+ +  Gyv ++++ +sG+
  gi|474934416|ref|YP_007687998.1|  61 VLNGNSVYFPTEYKAPGTSNTTYSQISK-SGYVLMGWSENSGA 102
                                       678889999*****99999******975.6***********97 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0042
                             SH3_5  41 qvltaDGyvWisYtse 56 
                                       +++t+DG+++++++++
  gi|474934416|ref|YP_007687998.1| 376 SIVTKDGFTFLGWNAT 391
                                       589**********987 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.3
                             SH3_5  46 DGyvWisYtsesGvrrYlpi 65 
                                       DG +  s  ++sG r+ lp+
  gi|474934416|ref|YP_007687998.1| 434 DGSQNFSVITFSGYRYALPV 453
                                       77788888899***999987 PP

>> DUF4307  Domain of unknown function (DUF4307)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1    0.0098        59       4      47 ..       3      46 ..       1      50 [. 0.84
   2 ?    6.7   0.1     0.001       6.2      34      71 ..     782     820 ..     767     826 .. 0.85
   3 ?   -3.5   0.6       1.6   9.4e+03       4      22 ..     838     856 ..     836     858 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0098
                           DUF4307  4 llvillvvlvvvalalvawigysqgsadvsaevvgfevvddstv 47
                                      +++ l++++++v ++++a+ ++s  s+  +a+++g + v ++++
  gi|474934416|ref|YP_007687998.1|  3 RILTLAAAILAVSVVFLAFGMLSDDSDASTASTFGSDSVGAERI 46
                                      56778999999999999999999999999999999998888776 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.001
                           DUF4307  34 aevvgfevvddstvevtfeVtrddgs.pavCiVrAlded 71 
                                       ++  g++v ++++ +vt++Vt ++g  +avC  ++ d +
  gi|474934416|ref|YP_007687998.1| 782 SSIPGHTVANNTSGSVTVTVTTENGPfTAVCHYTVADGQ 820
                                       566799999**********************87776655 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 1.6
                           DUF4307   4 llvillvvlvvvalalvaw 22 
                                       + +i++++++++al +v+ 
  gi|474934416|ref|YP_007687998.1| 838 VYWIAGGIVGILALFVVGR 856
                                       5688889999998888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (859 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.77u 0.32s 00:00:01.09 Elapsed: 00:00:00.51
# Mc/sec: 5056.69
//
Query:       gi|474934417|ref|YP_007687999.1|  [L=626]
Description: hypothetical protein TALC_00844 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.1   13.0   0.4       0.17   12.2   0.4    1.3  1  DUF2390   Protein of unknown function (DUF2390)
       0.39   11.0   3.9       0.17   12.2   0.5    2.1  2  DUF3040   Protein of unknown function (DUF3040)


Domain annotation for each model (and alignments):
>> DUF2390  Protein of unknown function (DUF2390)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.4   1.9e-05      0.17       1      65 [.      98     162 ..      98     164 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.9e-05
                           DUF2390   1 dlWqfalalYarpgveeacLelQdeygldVnllLlalwlaeqgraldaeelaaleaavaewreev 65 
                                       +lW ++ +++ r+   ea+ e+Q   ++d n++Ll + + e++ +++a+++a++++ ++e++e++
  gi|474934417|ref|YP_007687999.1|  98 QLWGMTKEHWVRQAELEAYSEWQSGKEYDGNTVLLGARAYENNATMTANAVAQIDSFLDEVSEKI 162
                                       69******************************************************999998875 PP

>> DUF3040  Protein of unknown function (DUF3040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.2      0.34     3e+03      67      74 ..      27      45 ..       2      57 .. 0.44
   2 ?   12.2   0.5   1.9e-05      0.17      43      83 ..     572     611 ..     557     612 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.34
                           DUF3040 67 a...........vvlgvvG 74
                                      +           ++++v+G
  gi|474934417|ref|YP_007687999.1| 27 TeeepdgfpplvIAVIVAG 45
                                      2334444433333333333 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 1.9e-05
                           DUF3040  43 rlavlavllfvaGllllvlGvaaaavvlgvvGfvvmlagvv 83 
                                       +  +l ++++v+G++l v+G++ +++v++++G+++++ gv+
  gi|474934417|ref|YP_007687999.1| 572 K-NILKIVCIVSGAILAVMGFVRRSPVIAIAGIGLIVFGVF 611
                                       3.67889999**********888889********9999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (626 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       699  (0.0389871); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.48
# Mc/sec: 3881.39
//
Query:       gi|474934418|ref|YP_007688000.1|  [L=91]
Description: hypothetical protein TALC_00845 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.35s 00:00:00.90 Elapsed: 00:00:00.56
# Mc/sec: 490.68
//
Query:       gi|474934419|ref|YP_007688001.1|  [L=91]
Description: hypothetical protein TALC_00846 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
        0.2   11.9   0.9       0.59   10.4   0.2    2.1  2  Tash_PEST  Tash protein PEST motif


Domain annotation for each model (and alignments):
>> Tash_PEST  Tash protein PEST motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   3.3e-05      0.59       7      15 ..      19      27 ..      17      27 .. 0.96
   2 ?   -1.1   0.0      0.13   2.3e+03       3       6 ..      57      60 ..      57      61 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 3.3e-05
                         Tash_PEST  7 TIpVEigSD 15
                                      TI++E++SD
  gi|474934419|ref|YP_007688001.1| 19 TIRMEVSSD 27
                                      9*******9 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.13
                         Tash_PEST  3 LePE 6 
                                      L+PE
  gi|474934419|ref|YP_007688001.1| 57 LDPE 60
                                      8**9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.52
# Mc/sec: 524.12
//
Query:       gi|474934420|ref|YP_007688002.1|  [L=77]
Description: hypothetical protein TALC_00847 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 554.99
//
Query:       gi|474934421|ref|YP_007688003.1|  [L=84]
Description: hypothetical protein TALC_00848 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 573.72
//
Query:       gi|474934422|ref|YP_007688004.1|  [L=113]
Description: hypothetical protein TALC_00849 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 843.25
//
Query:       gi|474934423|ref|YP_007688005.1|  [L=129]
Description: hypothetical protein TALC_00850 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.096   12.6   0.0       0.13   12.2   0.0    1.2  1  DUF5589   Family of unknown function (DUF5589)


Domain annotation for each model (and alignments):
>> DUF5589  Family of unknown function (DUF5589)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     7e-06      0.13      37      86 ..      22      71 ..       8      81 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7e-06
                           DUF5589 37 fawvlaprrksakalarGaesllfidrpdffdypdsdqarllavaqfiGe 86
                                      f  +l+ ++++ +  + G+ s l+ dr  f +y d d +++l     +G+
  gi|474934423|ref|YP_007688005.1| 22 FLKTLTQKPDRVTQDTDGTVSALWEDRNHFDEYSDCDYSKILDFLDNLGD 71
                                      6667889999999****************************987776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 893.32
//
Query:       gi|474934424|ref|YP_007688006.1|  [L=61]
Description: hypothetical protein TALC_00851 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 400.00
//
Query:       gi|474934425|ref|YP_007688007.1|  [L=92]
Description: hypothetical protein TALC_00852 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00025   21.4   0.3     0.0003   21.1   0.3    1.2  1  Lar_restr_allev  Restriction alleviation protein Lar
     0.0092   15.9   1.0      0.018   15.0   0.9    1.5  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
  ------ inclusion threshold ------
      0.026   15.1   1.3       0.56   10.8   0.2    2.2  2  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
      0.026   14.8   0.9      0.031   14.6   0.9    1.2  1  DUF3268          zinc-finger-containing domain
      0.029   13.9   2.6       0.16   11.5   0.0    2.4  2  TF_Zn_Ribbon     TFIIB zinc-binding
      0.046   14.1   1.7       0.87   10.0   0.1    2.2  2  zf-IS66          zinc-finger binding domain of transposase IS
      0.058   13.1   0.2      0.079   12.6   0.2    1.2  1  TackOD1          Thaumarchaeal output domain 1
      0.065   12.7   3.0       0.26   10.7   0.1    2.2  2  zf-ribbon_3      zinc-ribbon domain
       0.11   12.5   0.3       0.19   11.8   0.3    1.4  1  Elf1             Transcription elongation factor Elf1 like
       0.13   12.4   0.3       0.15   12.2   0.3    1.1  1  MqsA_antitoxin   Antitoxin component of bacterial toxin-antit
       0.22   11.4   2.0        6.3    6.8   0.1    2.3  2  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
       0.29   10.9   5.1        2.1    8.2   0.4    2.4  2  zinc_ribbon_2    zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.3     2e-07    0.0003       5      37 ..       2      41 ..       1      58 [. 0.84

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2e-07
                   Lar_restr_allev  5 pCPfCggravlersqrvvaeigq......cvyCadCga.s 37
                                       CP Cg+r++ e+ +  +++  q        +C +Cga  
  gi|474934425|ref|YP_007688007.1|  2 ACPYCGSRKIAEEYTVQTYDLRQefvainHLQCGKCGAyY 41
                                      5*****************99999***************42 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.9   1.2e-05     0.018      20      44 ..       2      38 ..       1      40 [. 0.91

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.2e-05
                     Zn_Tnp_IS1595 20 vCPhCgsr...kayrikt.........rglfqCkeCr 44
                                       CP+Cgsr   + y+++t            +qC +C+
  gi|474934425|ref|YP_007688007.1|  2 ACPYCGSRkiaEEYTVQTydlrqefvaINHLQCGKCG 38
                                      5*******9999999999***9999999999*****8 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.064        95       7      14 ..       2       9 ..       1      24 [. 0.75
   2 ?   10.8   0.2   0.00038      0.56       5      24 ..      31      54 ..      29      76 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.064
                   Zn_ribbon_recom  7 rCgeCGsp 14
                                       C +CGs+
  gi|474934425|ref|YP_007688007.1|  2 ACPYCGSR 9 
                                      5*****98 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00038
                   Zn_ribbon_recom  5 llrCgeCGspmtr...rkrk.gkr 24
                                       l Cg+CG+ ++     + + gkr
  gi|474934425|ref|YP_007688007.1| 31 HLQCGKCGAYYSKtirENPNtGKR 54
                                      588*******97754323334444 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.9   2.1e-05     0.031       4      41 ..       2      42 ..       1      62 [. 0.71

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.1e-05
                           DUF3268  4 rCpyCGekvilvs.aseiYkerskgklly..lCpkCdayvg 41
                                       CpyCG++ i  +   + Y+ r++   +    C kC+ay  
  gi|474934425|ref|YP_007688007.1|  2 ACPYCGSRKIAEEyTVQTYDLRQEFVAINhlQCGKCGAYYS 42
                                      7*****98887762557898887444332247******965 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00011      0.16       1      15 [.       1      15 [.       1      24 [. 0.82
   2 ?    1.7   0.5      0.13   1.9e+02      22      27 ..      34      39 ..      30      45 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                                      EEETTTTCEECHEET CS
                      TF_Zn_Ribbon  1 ykCPnCgstnlveDp 15
                                      + CP+Cgs+++ e++
  gi|474934425|ref|YP_007688007.1|  1 MACPYCGSRKIAEEY 15
                                      67*******996665 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.13
                                      ESSSSB CS
                      TF_Zn_Ribbon 22 CtdCGl 27
                                      C++CG+
  gi|474934425|ref|YP_007688007.1| 34 CGKCGA 39
                                      999985 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00059      0.87       3      25 ..       2      22 ..       2      32 .. 0.82
   2 ?    3.4   0.3      0.07     1e+02       3      12 ..      33      43 ..      31      48 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00059
                           zf-IS66  3 tCpcCGgllkpigedrvreeldi 25
                                      +Cp CG+  ++i+e+ + ++ d+
  gi|474934425|ref|YP_007688007.1|  2 ACPYCGS--RKIAEEYTVQTYDL 22
                                      5*****9..58999988787775 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.07
                           zf-IS66  3 tCpcCGg.llk 12
                                      +C +CG+   k
  gi|474934425|ref|YP_007688007.1| 33 QCGKCGAyYSK 43
                                      8****984444 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   5.3e-05     0.079      89     130 ..       2      38 ..       1      46 [. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.3e-05
                           TackOD1  89 vCpkCkSidieeqelihhftCgnvgpeeeflkegkleCpkCk 130
                                       +Cp C+S +i e+ +++ +     +  +ef+  ++l+C kC 
  gi|474934425|ref|YP_007688007.1|   2 ACPYCGSRKIAEEYTVQTY-----DLRQEFVAINHLQCGKCG 38 
                                       6***********9999876.....6899*************6 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00018      0.26      18      24 ..       2       8 ..       1      15 [. 0.63
   2 ?    2.1   0.6      0.09   1.3e+02      19      23 ..      34      38 ..      30      41 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00018
                       zf-ribbon_3 18 vCpyCGt 24
                                      +CpyCG+
  gi|474934425|ref|YP_007688007.1|  2 ACPYCGS 8 
                                      4666664 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.09
                       zf-ribbon_3 19 CpyCG 23
                                      C +CG
  gi|474934425|ref|YP_007688007.1| 34 CGKCG 38
                                      55555 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.3   0.00013      0.19      23      60 ..       2      46 ..       1      51 [. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00013
                              Elf1 23 dCpfCnheksvevkldkkek.......iaevsCkvCgesfetkvn 60
                                       Cp+C++ k  e    ++ +       i +++C++Cg++++ +++
  gi|474934425|ref|YP_007688007.1|  2 ACPYCGSRKIAEEYTVQTYDlrqefvaINHLQCGKCGAYYSKTIR 46
                                      59999999654333222222466799999**********998776 PP

>> MqsA_antitoxin  Antitoxin component of bacterial toxin-antitoxin system, MqsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3   9.9e-05      0.15       1      47 [.       1      44 [.       1      61 [. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.9e-05
                    MqsA_antitoxin  1 mkCpvCgkaelvrdtrdvpytykgektvikavtgdfCarCGegvlde 47
                                      m Cp Cg+ ++ ++    +y  + e + i++++   C +CG  + ++
  gi|474934425|ref|YP_007688007.1|  1 MACPYCGSRKIAEEYTVQTYDLRQEFVAINHLQ---CGKCGAYYSKT 44
                                      89************9999888888888887776...99999877654 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0042       6.3      27      35 ..       2      10 ..       1      12 [. 0.85
   2 ?    4.1   0.2     0.029        43      13      21 ..      33      41 ..      32      41 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0042
                           DUF35_N 27 vCphCgsdd 35
                                      +Cp+Cgs+ 
  gi|474934425|ref|YP_007688007.1|  2 ACPYCGSRK 10
                                      6******86 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.029
                           DUF35_N 13 rCpdCGtvq 21
                                      +C +CG+++
  gi|474934425|ref|YP_007688007.1| 33 QCGKCGAYY 41
                                      7*****986 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.4    0.0014       2.1      16      21 ..       3       8 ..       1      10 [. 0.84
   2 ?    4.8   0.5     0.016        24      16      21 ..      34      39 ..      30      43 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0014
                     zinc_ribbon_2 16 CpyCGt 21
                                      CpyCG+
  gi|474934425|ref|YP_007688007.1|  3 CPYCGS 8 
                                      ****97 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.016
                     zinc_ribbon_2 16 CpyCGt 21
                                      C +CG+
  gi|474934425|ref|YP_007688007.1| 34 CGKCGA 39
                                      777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 597.39
//
Query:       gi|474934426|ref|YP_007688008.1|  [L=319]
Description: hypothetical protein TALC_00853 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.012   16.0   0.2      0.035   14.5   0.1    1.8  2  SPOR        Sporulation related domain
       0.16   11.2   0.0       0.23   10.7   0.0    1.2  1  Zeta_toxin  Zeta toxin
        3.7    6.9  20.5        5.8    6.3  20.5    1.3  1  FAP         Fibronectin-attachment protein (FAP)


Domain annotation for each model (and alignments):
>> SPOR  Sporulation related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.5   8.8e+03      35      48 ..     271     284 ..     262     286 .. 0.75
   2 ?   14.5   0.1   5.9e-06     0.035      10      34 ..     290     314 ..     290     318 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.5
                                       EEECCSSSCEEEEE CS
                              SPOR  35 avvsgggglyrVrv 48 
                                       +  ++g  +y Vrv
  gi|474934426|ref|YP_007688008.1| 271 VERKKGSLVYEVRV 284
                                       67788999999998 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 5.9e-06
                                       -EES-HHHHHHHHHHCCHHT--... CS
                              SPOR  10 gafsseanAerlaakLrakgfaaav 34 
                                       g+fss++ Ae+l++ L+++gf+a+v
  gi|474934426|ref|YP_007688008.1| 290 GSFSSQSKAEALKRDLKKRGFKARV 314
                                       8*********************875 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   3.9e-05      0.23      95     131 ..     283     319 .]     273     319 .] 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 3.9e-05
                        Zeta_toxin  95 gyniivegtlrspdvvkklaealkkaGYevevvvvav 131
                                       +++  +eg ++s ++++ l+++lkk+G++ +v+ v +
  gi|474934426|ref|YP_007688008.1| 283 RVDGKLEGSFSSQSKAEALKRDLKKRGFKARVYGVRC 319
                                       555568***************************9965 PP

>> FAP  Fibronectin-attachment protein (FAP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3  20.5   0.00097       5.8      42     115 ..     203     270 ..     186     296 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.00097
                               FAP  42 ePaPppPstae..aapaeaaaapaPaapapaPapadpnapeaaPapadPnapapppadPnapappavdPnapepgr 115
                                       +P P   +t +   +  +++++p+ +ap p P pa  ++p++aP+p+ P +  p   +P  pap + +P      +
  gi|474934426|ref|YP_007688008.1| 203 KPVPKRQPTIDdfGPVEPPKPKPKKEAPKPVPKPAPKAEPKPAPKPTIPKSQ-PKKPEPKKPAPAP-AP------K 270
                                       3444443333300344455566666666677777777788888888888874.5556666666633.23......2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2018.23
//
Query:       gi|474934427|ref|YP_007688009.1|  [L=116]
Description: hypothetical protein TALC_00854 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 706.81
//
Query:       gi|474934428|ref|YP_007688010.1|  [L=120]
Description: hypothetical protein TALC_00855 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-09   36.9   0.0    6.3e-09   36.1   0.0    1.4  1  DUF2958   Protein of unknown function (DUF2958)
  ------ inclusion threshold ------
        2.6    8.4   5.1       0.76   10.1   1.0    2.0  2  DUF2949   Protein of unknown function (DUF2949)


Domain annotation for each model (and alignments):
>> DUF2958  Protein of unknown function (DUF2958)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.0     7e-13   6.3e-09       3      93 ..       2     102 ..       1     107 [. 0.80

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 7e-13
                           DUF2958   3 tkelraqLlangraraeeeeiDpvPvvklftplgaatWLlteldPedgdt..lfgLaDlgl....glp.....elgs 68 
                                       t+e +++L +    +++++  D   vvk+f   +aatWL+te +P+d+    l+g++ lgl      p     e g+
  gi|474934428|ref|YP_007688010.1|   2 TAEIEKALKKYPLYSQDGKGGDAKIVVKYFGG-SAATWLITEGEPRDNGDwlLYGFVTLGLpddfA-PgkllwEWGY 76 
                                       67777888888888999999*********986.569*********997533499*99998733220.23334499** PP

                           DUF2958  69 vsLselesir.gplglpverDllFea 93 
                                       ++L++l+++r  p+gl+verD+l e+
  gi|474934428|ref|YP_007688010.1|  77 ITLRQLQEVRfPPFGLGVERDILVEP 102
                                       **********668********98775 PP

>> DUF2949  Protein of unknown function (DUF2949)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.2      0.22   1.9e+03      40      45 ..      54      59 ..      52      60 .. 0.88
   2 ?   10.1   1.0   8.5e-05      0.76      36      51 ..      70      85 ..      69      86 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.22
                           DUF2949 40 YGLvtl 45
                                      YG+vtl
  gi|474934428|ref|YP_007688010.1| 54 YGFVTL 59
                                      *****9 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 8.5e-05
                           DUF2949 36 vLWqYGLvtleqLdki 51
                                      +LW +G +tl qL+++
  gi|474934428|ref|YP_007688010.1| 70 LLWEWGYITLRQLQEV 85
                                      6************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.33s 00:00:00.83 Elapsed: 00:00:00.52
# Mc/sec: 689.67
//
Query:       gi|474934429|ref|YP_007688011.1|  [L=77]
Description: hypothetical protein TALC_00856 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 523.80
//
Query:       gi|474934430|ref|YP_007688012.1|  [L=69]
Description: hypothetical protein TALC_00857 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 472.93
//
Query:       gi|474934431|ref|YP_007688013.1|  [L=203]
Description: hypothetical protein TALC_00858 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1255.94
//
Query:       gi|474934432|ref|YP_007688014.1|  [L=31]
Description: hypothetical protein TALC_00859 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (31 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 229.46
//
Query:       gi|474934433|ref|YP_007688015.1|  [L=26]
Description: hypothetical protein TALC_00860 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (26 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      175  (0.00976072); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 179.98
//
Query:       gi|474934434|ref|YP_007688016.1|  [L=42]
Description: hypothetical protein TALC_00861 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 283.88
//
Query:       gi|474934435|ref|YP_007688017.1|  [L=64]
Description: hypothetical protein TALC_00862 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       769  (0.0428914); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.31s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 421.98
//
Query:       gi|474934436|ref|YP_007688018.1|  [L=46]
Description: hypothetical protein TALC_00863 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.013   15.8   1.1      0.014   15.7   1.1    1.1  1  Wbp11     WW domain binding protein 11


Domain annotation for each model (and alignments):
>> Wbp11  WW domain binding protein 11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   1.1     8e-07     0.014      22      50 ..       2      30 ..       2      44 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 8e-07
                             Wbp11 22 nKkerqkareaklakkdpdeleeeiekLe 50
                                      n ++r+++r   +++k+++e+e+ei++ +
  gi|474934436|ref|YP_007688018.1|  2 NEQDRKQNRRTNMKQKSTNEVENEIDNFD 30
                                      5689**********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1408  (0.078532); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.32s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 289.39
//
Query:       gi|474934437|ref|YP_007688019.1|  [L=162]
Description: hypothetical protein TALC_00864 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-24   86.2   0.0    1.9e-24   85.6   0.0    1.3  1  DUF4313   Domain of unknown function (DUF4313)
  ------ inclusion threshold ------
        0.1   12.0   0.0       0.46    9.9   0.0    2.0  2  DUF4926   Domain of unknown function (DUF4926)


Domain annotation for each model (and alignments):
>> DUF4313  Domain of unknown function (DUF4313)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.6   0.0   2.1e-28   1.9e-24       2      92 ..      15     102 ..      14     111 .. 0.91

  Alignments for each domain:
  == domain 1  score: 85.6 bits;  conditional E-value: 2.1e-28
                           DUF4313   2 levssYasngnlyigLvtkedgleefgdltVnlpgvslepneayidtnnlskdvleflkenklgevlgetakSGyce 78 
                                       l v +Y++n++l+i L+++e +  +f+dltVnl ++ +++ +a++dtnnl+  +++f+++n lge++g++ +SGyc 
  gi|474934437|ref|YP_007688019.1|  15 LFVGEYRNNDRLAIILIDEEGY--DFADLTVNLSQERCPEGCAFLDTNNLP-SAEDFVERNGLGEFTGYYGHSGYCS 88 
                                       6689**************5544..8**************************.9************************ PP

                           DUF4313  79 YpevaFdlerlkel 92 
                                       Yp+++Fd+ ++ ++
  gi|474934437|ref|YP_007688019.1|  89 YPMYRFDMGKIGKV 102
                                       *******9987655 PP

>> DUF4926  Domain of unknown function (DUF4926)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.27   2.5e+03       2      16 ..      36      50 ..      35      54 .. 0.74
   2 ?    9.9   0.0   5.1e-05      0.46      11      40 ..      89     118 ..      87     119 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.27
                           DUF4926  2 ldvVaLledlpekgL 16
                                      +d   L+++l++++ 
  gi|474934437|ref|YP_007688019.1| 36 YDFADLTVNLSQERC 50
                                      677889999988765 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 5.1e-05
                           DUF4926  11 lpekgLrrGqvGTvVevyeegeaYeVEFsd 40 
                                       +p +++ +G++G vV + ++g+++ VE+++
  gi|474934437|ref|YP_007688019.1|  89 YPMYRFDMGKIGKVVSESKKGTVFRVEYFT 118
                                       5788999********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1133.96
//
Query:       gi|474934438|ref|YP_007688020.1|  [L=197]
Description: hypothetical protein TALC_00865 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.014   15.8   0.0      0.026   14.9   0.0    1.4  1  SPOR            Sporulation related domain
       0.32   10.7   2.7       0.39   10.4   2.7    1.1  1  NSP2-B_epitope  Immunogenic region of nsp2 protein of arteriv


Domain annotation for each model (and alignments):
>> SPOR  Sporulation related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   2.9e-06     0.026       9      35 ..      17      45 ..      16      61 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.9e-06
                                      S-EES-HHHHHHHHHHCCHHT--.....E CS
                              SPOR  9 vgafsseanAerlaakLrakgfaaav..a 35
                                      +++fs+e+ A+r  +kLr +g+ a+v  +
  gi|474934438|ref|YP_007688020.1| 17 LASFSDEDKAKREMKKLRREGQQARVytK 45
                                      79********************9987651 PP

>> NSP2-B_epitope  Immunogenic region of nsp2 protein of arterivirus polyprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   2.7   4.4e-05      0.39       3      44 ..      42      83 ..      40     114 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 4.4e-05
                    NSP2-B_epitope  3 nyPrWtPpppPprvqprktksvkslpedkPvPaPrrkvrsdc 44
                                       y +W+P +  p+ +  +tk+  + p++kP P  r kv+ + 
  gi|474934438|ref|YP_007688020.1| 42 VYTKWIPVAERPQENKTQTKKKETKPKKKPQPIIRPKVQPKP 83
                                      699**********************************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1100  (0.0613531); expected 358.6 (0.02)
Passed bias filter:                      639  (0.0356406); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 1159.28
//
Query:       gi|474934439|ref|YP_007688021.1|  [L=93]
Description: hypothetical protein TALC_00866 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.17   11.8   0.0       0.19   11.6   0.0    1.0  1  AAA_31    AAA domain


Domain annotation for each model (and alignments):
>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   1.1e-05      0.19      31      98 ..      11      87 ..       5      91 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.1e-05
                            AAA_31 31 kkvLlvDlDpQanattglgiekne...iektlyevl......ieeknikeaiiktkvenldlipssidLaeaeielv 98
                                       ++L vD Dp +n t  + i ++    +++ ++e+        ++++ +++i + +    +++ +   +ae+  +l 
  gi|474934439|ref|YP_007688021.1| 11 LRMLAVDSDPYKNGTDCCCIVHTAagrYKQAMNEARaisngwYSDSDPSDIIEELEECCKNILTAGYRMAEITAKLY 87
                                      589*************777754443444444444422233337999999*9997777777**********9999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 582.13
//
Query:       gi|474934440|ref|YP_007688022.1|  [L=223]
Description: hypothetical protein TALC_00867 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.31    9.3   4.4       0.39    8.9   4.4    1.1  1  CDC45     CDC45-like protein


Domain annotation for each model (and alignments):
>> CDC45  CDC45-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   4.4   2.2e-05      0.39     101     193 ..     123     217 ..      86     219 .. 0.54

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 2.2e-05
                             CDC45 101 kerivvfDDgdieeeleeereayealeeeeesdeede.eeeeeddddeeeeeeeeedeedeeedeeeskkkrksksd 176
                                       +  + v D++ iee +eee+ + e+   ee + e ++  ee e++ +e ++ee+ + +  e  +e+  + +   ++d
  gi|474934440|ref|YP_007688022.1| 123 NPFVYVSDEEPIEEPVEEEEPEAEETVIEEPVPEGETpAEE-EENGEEPDSEEQGSGDPGEVPEESV-ETEMTGSTD 197
                                       45589999999******977766555555555433332222.2222222222222222222222222.222223444 PP

                             CDC45 177 eeee...sddddersrkrrr 193
                                       +eee   +  + e++ k++r
  gi|474934440|ref|YP_007688022.1| 198 TEEEppaEVPEPEPEPKKKR 217
                                       44445653333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1479.12
//
Query:       gi|474934441|ref|YP_007688023.1|  [L=302]
Description: hypothetical protein TALC_00868 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2205.33
//
Query:       gi|474934442|ref|YP_007688024.1|  [L=269]
Description: hypothetical protein TALC_00869 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1705.12
//
Query:       gi|474934443|ref|YP_007688025.1|  [L=115]
Description: hypothetical protein TALC_00870 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 819.15
//
Query:       gi|474934444|ref|YP_007688026.1|  [L=344]
Description: hypothetical protein TALC_00871 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0003   20.5   0.0    0.00059   19.6   0.0    1.4  1  HTH_23    Homeodomain-like domain
     0.0013   18.4   0.0       0.08   12.5   0.0    2.2  1  AAA_25    AAA domain
      0.004   17.3   0.0     0.0075   16.4   0.0    1.4  1  HTH_28    Helix-turn-helix domain
  ------ inclusion threshold ------
      0.015   15.6   0.0      0.074   13.3   0.1    2.1  2  AAA_22    AAA domain
      0.041   14.3   0.0      0.062   13.7   0.0    1.3  1  AAA       ATPase family associated with various cellular acti


Domain annotation for each model (and alignments):
>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.6e-07   0.00059       6      42 ..     295     332 ..     291     342 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.6e-07
                            HTH_23   6 eRlrillllae.GlsvreIAreLgvsrrTvyrwlkryr 42 
                                        +++i++ +++ G  ++ IA+++gv+++Tv  w k + 
  gi|474934444|ref|YP_007688026.1| 295 LKMEIAKSFRRaGVHIPVIAKAFGVHENTVKAWTKGWD 332
                                       688999999999*********************99993 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   2.2e-05      0.08      20     186 ..       8     150 ..       4     151 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.2e-05
                            AAA_25  20 pprrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgea 96 
                                       p+    +k     g++++ +G +g GKt  a++ +  +++G        p     +++++      +++ ++ + ++
  gi|474934444|ref|YP_007688026.1|   8 PKTAEFIKSTFKPGAVIVSYGMRGGGKTHSAISFCQRMMEGY-Y-----PDMPSHIILVTNVIF--VKKTASDMEQE 76 
                                       555566777778899999999999999999999999999987.2.....344566666666666..78888888888 PP

                            AAA_25  97 lrddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralggdensnsdvgalveale 173
                                       +  + +++ ++ +++             l + ++dale+  ++    + + +D  + +l gd ns+ d++++++ + 
  gi|474934444|ref|YP_007688026.1|  77 A--PPGVHMIHEMKE-------------LFPIVTDALERYGRK-DTMVILLLDEAQNFLLGDMNSQGDMARAMKVFC 137
                                       6..334444433222.............234455668888888.66999999*****************99999999 PP

                            AAA_25 174 riarrtgaavllv 186
                                        i r+++  ++l+
  gi|474934444|ref|YP_007688026.1| 138 GIIRKFNLCLWLI 150
                                       9999999888876 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   2.1e-06    0.0075       3      38 ..     297     333 ..     295     334 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.1e-06
                            HTH_28   3 leiiklla.aGhsvreaArelgisrrtvyrWikryee 38 
                                        ei k    aG+ ++ +A+++g+++ tv+ W k +++
  gi|474934444|ref|YP_007688026.1| 297 MEIAKSFRrAGVHIPVIAKAFGVHENTVKAWTKGWDS 333
                                       566666554799*********************9986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   2.1e-05     0.074       7     105 ..      23     125 ..      17     152 .. 0.69
   2 ?   -2.5   0.0       1.6   5.8e+03      54      91 ..     271     308 ..     256     314 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.1e-05
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee.erpevvfvtlpsstsskdllrellralglelkaerlsseelleal 82 
                                       ++v +G  G GKT+++  + ++  e +++++  +  +v+  + ++++ +d+ +e    ++  ++      +el+  +
  gi|474934444|ref|YP_007688026.1|  23 VIVSYGMRGGGKTHSAISFCQRMMEGYYPDMpSHIILVTNVIFVKKTASDMEQEAPPGVHMIHEM-----KELFPIV 94 
                                       56678999999999999999998888888775444444555666667888888888888876666.....6777777 PP

                            AAA_22  83 eqalrarav...ielliiDEaqhlr.....s 105
                                       ++al+++++    ++l++DEaq++      s
  gi|474934444|ref|YP_007688026.1|  95 TDALERYGRkdtMVILLLDEAQNFLlgdmnS 125
                                       7777777777766**********64454432 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.6
                            AAA_22  54 kdllrellralglelkaerlsseell.ealeqalrarav 91 
                                       ++++  l ++ g++  + r +se+ll   +++ +r+++v
  gi|474934444|ref|YP_007688026.1| 271 REFYDTLPEDDGVPVPD-REKSEHLLkMEIAKSFRRAGV 308
                                       55555565665666666.666666665677777777666 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.7e-05     0.062       3      96 ..      26     143 ..      24     166 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.7e-05
                                       EESSTTSSHHHHHHHHHHHH................THEEEEEETTTCSSS......STTHHHHHHHHHHHHHHHTS CS
                               AAA   3 lyGppGtGKTllakavakel................gvefleisgsellsk......yvgesekkirelfkeakeka 57 
                                        yG  G GKT  a + ++ +                +v f++  +s++ ++      ++ e+++ +  + +++++  
  gi|474934444|ref|YP_007688026.1|  26 SYGMRGGGKTHSAISFCQRMmegyypdmpshiilvtNVIFVKKTASDMEQEappgvhMIHEMKELFPIVTDALERYG 102
                                       59*****************766555544444444434558999999999779***9777777776666666665555 PP

                                       ...TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHT CS
                               AAA  58 ...kpsilfiDEidalaksrsgseseeeervvnqLlteldgv 96 
                                          + +il++DE+ ++   +  +++++  r+++++   + ++
  gi|474934444|ref|YP_007688026.1| 103 rkdTMVILLLDEAQNFLLGD-MNSQGDMARAMKVFCGIIRKF 143
                                       66567*********998888.677778888887777666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 2019.35
//
Query:       gi|474934445|ref|YP_007688027.1|  [L=242]
Description: hypothetical protein TALC_00872 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.062   13.4   0.1          1    9.5   0.0    2.4  2  HTH_21    HTH-like domain


Domain annotation for each model (and alignments):
>> HTH_21  HTH-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   5.8e-05         1      10      31 ..      28      49 ..      24      60 .. 0.84
   2 ?    0.9   0.0     0.028   5.1e+02      17      28 ..     212     223 ..     210     225 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 5.8e-05
                            HTH_21 10 ireifeeskgrYGyrriwaeLr 31
                                      + eif+e  +rYGy  ++ae  
  gi|474934445|ref|YP_007688027.1| 28 LTEIFAEVGRRYGYEDVKAEFT 49
                                      579***************9986 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.028
                            HTH_21  17 skgrYGyrriwa 28 
                                       s+   Gyrr++ 
  gi|474934445|ref|YP_007688027.1| 212 SHDEIGYRRLCS 223
                                       55899****985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1649.02
//
Query:       gi|474934446|ref|YP_007688028.1|  [L=287]
Description: hypothetical protein TALC_00873 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1763.29
//
Query:       gi|474934447|ref|YP_007688029.1|  [L=94]
Description: hypothetical protein TALC_00874 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.55
# Mc/sec: 518.36
//
Query:       gi|474934448|ref|YP_007688030.1|  [L=192]
Description: hypothetical protein TALC_00875 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   12.7   0.1       0.18   12.0   0.1    1.3  1  MG4       Macroglobulin domain MG4


Domain annotation for each model (and alignments):
>> MG4  Macroglobulin domain MG4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   9.8e-06      0.18      14      81 ..      71     142 ..      64     155 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.8e-06
                               MG4  14 lPfsikVlvkdpdgspaknvpVkiealk.....seteekeslttdedGtakfsintpedaksltitvktkdps 81 
                                       + ++++V v ++ g+ ++  +V +e  +       + +  ++t+ ++  +++ in  + +  ++i    k++ 
  gi|474934448|ref|YP_007688030.1|  71 IGYTGTVIVLNERGEQVQYGLVPLEN-RkmvaeAPKRKSPAKTQTKKSWVAMEINSRTGNDRQAIVCSSKEQA 142
                                       67************************.3366553455556677889**********99777777766666543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1118  (0.0623571); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1212.55
//
Query:       gi|474934449|ref|YP_007688031.1|  [L=409]
Description: hypothetical protein TALC_00876 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.068   13.2   0.1        1.6    8.8   0.0    2.5  2  PepSY_2          Peptidase propeptide and YPEB domain
       0.14   12.3   0.3       0.34   11.1   0.3    1.7  1  Alveol-reg_P311  Neuronal protein 3.1 (p311)


Domain annotation for each model (and alignments):
>> PepSY_2  Peptidase propeptide and YPEB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00017       1.6      61      80 ..      42      61 ..      39      64 .. 0.89
   2 ?    1.4   0.0     0.035   3.1e+02      26      45 ..     132     151 ..     126     186 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00017
                           PepSY_2 61 gldkdGkkveikldpatgev 80
                                      ++ k+G+k ei +dp+tg v
  gi|474934449|ref|YP_007688031.1| 42 VTAKNGQKWEIPVDPKTGRV 61
                                      6789**************98 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.035
                           PepSY_2  26 kadwlpreklvakleaqGyk 45 
                                       +a+    e++ ++++aqG+k
  gi|474934449|ref|YP_007688031.1| 132 RAFARELEDAAKSAQAQGMK 151
                                       44555566666666666663 PP

>> Alveol-reg_P311  Neuronal protein 3.1 (p311)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.3   3.8e-05      0.34      18      59 ..     357     400 ..     352     405 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.8e-05
                   Alveol-reg_P311  18 kelegrlpkgrLPvp.kEVNr.KKedeveaaslippgsdglhst 59 
                                       +  ++r  kg LPvp k V + KK d ++++   p+g    +s+
  gi|474934449|ref|YP_007688031.1| 357 NYYKERKAKGTLPVPvKPVRKtKKTDATKGTVAGPVGATAAKSP 400
                                       55678999*******6777655899999999999*999888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.51
# Mc/sec: 2436.31
//
Query:       gi|474934450|ref|YP_007688032.1|  [L=182]
Description: MarR family [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-11   43.3   0.3    0.00019   21.2   0.0    2.2  2  HxlR          HxlR-like helix-turn-helix
    1.4e-06   28.7   3.8    8.7e-05   22.9   0.5    2.7  2  HTH_27        Winged helix DNA-binding domain
    1.9e-05   24.5   0.6      0.046   13.5   0.0    2.2  2  DUF4364       Domain of unknown function (DUF4364)
    3.3e-05   23.8   0.2      0.021   14.8   0.0    2.6  3  HTH_45        Winged helix-turn-helix
    0.00014   21.7   0.4     0.0031   17.4   0.1    2.4  2  MarR          MarR family
    0.00083   19.2   0.2       0.31   11.0   0.1    2.4  2  MarR_2        MarR family
     0.0011   18.9   0.5      0.095   12.7   0.1    2.8  2  PadR          Transcriptional regulator PadR-like family
     0.0021   16.5   0.6      0.037   12.4   0.1    2.0  2  DUF505        Protein of unknown function (DUF505)
  ------ inclusion threshold ------
      0.022   14.3   0.3        1.1    8.8   0.0    2.9  3  HTH_24        Winged helix-turn-helix DNA-binding
      0.028   14.5   0.0       0.16   12.0   0.0    1.9  2  Replic_Relax  Replication-relaxation
      0.053   13.4   0.3       0.59   10.0   0.0    2.4  2  DUF1495       Winged helix DNA-binding domain (DUF1495)


Domain annotation for each model (and alignments):
>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   1.2e-07   0.00019      33      77 ..      41      85 ..      13      94 .. 0.84
   2 !   20.4   0.1   2.1e-07   0.00034      37      79 ..     134     176 ..     110     181 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.2e-07
                                      HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHHH CS
                              HxlR 33 qkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvlq 77
                                      +++L qr+  +e+dg+++ e++++v ++v  sltekG++++ +++
  gi|474934450|ref|YP_007688032.1| 41 TQTLRQRIDSMEKDGIVDVEIVSSVHKQVRISLTEKGTEIALLVS 85
                                      46899**********************************976554 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 2.1e-07
                                       HHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHHHHH CS
                              HxlR  37 aqrLreLeqdglierevypevPpkveYsltekGrslepvlqel 79 
                                       ++ L ++e++gl+ r+v +e    + Yslt++G++++++++++
  gi|474934450|ref|YP_007688032.1| 134 TKVLAKMEKEGLVTRTVSSESYREIRYSLTPMGKQVADAFETI 176
                                       567889******************************9998876 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.2    0.0085        14       7      68 .]      17      77 ..      12      77 .. 0.71
   2 !   22.9   0.5   5.4e-08   8.7e-05       8      68 .]     108     166 ..     105     166 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0085
                            HTH_27  7 lvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLv..ertgdeadrrekrvrlTdkG 68
                                      +++  +++ +r+ + +dl + +n++++     ++ +++ G v  e   +    +++r++lT+kG
  gi|474934450|ref|YP_007688032.1| 17 ALILALYEADRPLIMKDLQDITNHTQT-LRQRIDSMEKDGIVdvEIVSS--VHKQVRISLTEKG 77
                                      555556667777777888888888754.458999999999997533333..3778********9 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 5.4e-08
                            HTH_27   8 vLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68 
                                       +L+l+r   + + ++d+ +++ +++ ++ ++l k+++ GLv+rt + ++ re r++lT+ G
  gi|474934450|ref|YP_007688032.1| 108 ILRLLR-GKEYVVQKDIKDVV-RSYDSTTKVLAKMEKEGLVTRTVSSESYREIRYSLTPMG 166
                                       566666.55555556666654.6788899******************************87 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.1   0.00038      0.61      35      86 ..      43     100 ..      18     119 .. 0.77
   2 !   13.5   0.0   2.8e-05     0.046      32      75 ..     129     175 ..     115     182 .] 0.82

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00038
                           DUF4364  35 dlqqalseLvesglieee...ekenktlykiTekGketl...elfenripksirekid 86 
                                       +l q ++ ++++g +++e   + +++ ++++TekG e++   ++ ++ ip +i ek  
  gi|474934450|ref|YP_007688032.1|  43 TLRQRIDSMEKDGIVDVEivsSVHKQVRISLTEKGTEIAllvSMANTIIPGDISEKSI 100
                                       68899*********99886434499999*********862226677889999988865 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 2.8e-05
                           DUF4364  32 nYfdlqqalseLvesglieee.ek..enktlykiTekGketlelfen 75 
                                       +Y + +++l++++++gl++ + ++    + +y++T+ Gk++++ fe+
  gi|474934450|ref|YP_007688032.1| 129 SYDSTTKVLAKMEKEGLVTRTvSSesYREIRYSLTPMGKQVADAFET 175
                                       6888999***********9885332366779*************996 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.0    0.0057       9.2      35      66 ..      43      81 ..      34      90 .. 0.84
   2 ?   -1.3   0.0       1.4   2.2e+03      32      53 ..     101     122 ..      97     127 .. 0.75
   3 !   14.8   0.0   1.3e-05     0.021      32      75 ..     129     179 ..     107     181 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0057
                            HTH_45 35 llnkYLdmLvekgli.......kkskekYvlTekGlell 66
                                      +l++ +d + + g++        +++   +lTekG e+ 
  gi|474934450|ref|YP_007688032.1| 43 TLRQRIDSMEKDGIVdveivssVHKQVRISLTEKGTEIA 81
                                      67788999999999888888887899999******9985 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.4
                            HTH_45  32 sykllnkYLdmLvekglikksk 53 
                                       + + ++  L  L  k+++ +++
  gi|474934450|ref|YP_007688032.1| 101 NMRYADPILRLLRGKEYVVQKD 122
                                       5666778899999999997765 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 1.3e-05
                            HTH_45  32 sykllnkYLdmLvekgli.......kkskekYvlTekGlelleklkeleel 75 
                                       sy+ + k L ++ ++gl+       + ++  Y+lT  G+++ + ++++ ++
  gi|474934450|ref|YP_007688032.1| 129 SYDSTTKVLAKMEKEGLVtrtvsseSYREIRYSLTPMGKQVADAFETIFRK 179
                                       8*****************999999778999*************99998775 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.096   1.6e+02      32      48 ..      42      58 ..      15      62 .. 0.79
   2 !   17.4   0.1   1.9e-06    0.0031      33      58 ..     132     157 ..     108     158 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.096
                                      HHHHHHHHHHHHTTSEE CS
                              MarR 32 stvtrvldrLekkGlie 48
                                       t+   +d +ek+G ++
  gi|474934450|ref|YP_007688032.1| 42 QTLRQRIDSMEKDGIVD 58
                                      5677789*******986 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 1.9e-06
                                       HHHHHHHHHHHTTSEEEEEETTSTTS CS
                              MarR  33 tvtrvldrLekkGlieRskspeDrRe 58 
                                       ++t+vl ++ek+Gl++R+ s e  Re
  gi|474934450|ref|YP_007688032.1| 132 STTKVLAKMEKEGLVTRTVSSESYRE 157
                                       78****************99998887 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.0    0.0068        11       7      54 ..      15      60 ..       9      68 .. 0.84
   2 !   11.0   0.1   0.00019      0.31      37      58 ..     132     153 ..     128     157 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0068
                                      HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                       a +++aL+ ++++ l +++l + ++++ +++ ++++ +++ G v  +
  gi|474934450|ref|YP_007688032.1| 15 TAALILALYEADRP-LIMKDLQDITNHT-QTLRQRIDSMEKDGIVDVE 60
                                      67889999999987.9999999999998.7999**********99765 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00019
                                       HHHHHHHHHHHTTSEEEEESSS CS
                            MarR_2  37 avsrilkrLvaaGLverrpgpe 58 
                                       +++++l+++++ GLv+r+ ++e
  gi|474934450|ref|YP_007688032.1| 132 STTKVLAKMEKEGLVTRTVSSE 153
                                       789**************97776 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.043        69      34      69 ..      44      77 ..      29      81 .. 0.70
   2 !   12.7   0.1   5.8e-05     0.095      37      72 ..     136     169 ..     108     172 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.043
                                      HHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCC CS
                              PadR 34 lYpaLkrLekeglveseweesgegpprkyYrlTdaG 69
                                      l +  +++ek+g+v+ e + s+ ++ r +  lT++G
  gi|474934450|ref|YP_007688032.1| 44 LRQRIDSMEKDGIVDVEIVSSVHKQVR-I-SLTEKG 77
                                      5567899********999987444433.3.566666 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 5.8e-05
                                       HHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHH CS
                              PadR  37 aLkrLekeglveseweesgegpprkyYrlTdaGrre 72 
                                       +L+++ekeglv+++ + +  + +   Y lT+ G++ 
  gi|474934450|ref|YP_007688032.1| 136 VLAKMEKEGLVTRTVSSE--SYREIRYSLTPMGKQV 169
                                       79************8875..555566*******987 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1     0.018        30      11      70 ..      31      87 ..      25     107 .. 0.68
   2 !   12.4   0.1   2.3e-05     0.037     352     411 ..     122     180 ..     110     182 .] 0.75

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.018
                            DUF505 11 LeklkeeeekkeeeeieveeleeeeilleLelagLvrleepekielTyaGkklaelldel 70
                                      ++ l++ ++++++  + +  + e++ +++ e+   v+  ++++i+lT+ G ++a l+  +
  gi|474934450|ref|YP_007688032.1| 31 MKDLQDITNHTQTLRQRIDSM-EKDGIVDVEIVSSVH--KQVRISLTEKGTEIALLVSMA 87
                                      555555444445555555544.666778888877777..9999*******9999988776 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 2.3e-05
                            DUF505 352 eakdlekWyednfdlreaLysLesfeLieseveekg..kevyvlTeyGekvledqekklrev 411
                                       ++kd+    +++ + ++ L ++e  +L++++v+++   +  y+lT+ G++v +  e+ +r++
  gi|474934450|ref|YP_007688032.1| 122 DIKDVV---RSYDSTTKVLAKMEKEGLVTRTVSSESyrEIRYSLTPMGKQVADAFETIFRKI 180
                                       445554...333344899**************555543678**********99988778877 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0007       1.1      25      47 ..      36      57 ..      15      58 .. 0.73
   2 ?   -2.4   0.0       2.3   3.7e+03       8      23 ..     108     123 ..     108     123 .. 0.78
   3 ?    2.2   0.0      0.08   1.3e+02      37      48 .]     136     147 ..     131     147 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0007
                            HTH_24 25 erlglSpstvnrrlkrLeeeGlI 47
                                      + ++ + +t+++r++ +e++G++
  gi|474934450|ref|YP_007688032.1| 36 DITNHT-QTLRQRIDSMEKDGIV 57
                                      555554.799************8 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.3
                            HTH_24   8 ILelLqknprisqreL 23 
                                       IL+lL+ +    q+++
  gi|474934450|ref|YP_007688032.1| 108 ILRLLRGKEYVVQKDI 123
                                       8999998887777776 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.08
                            HTH_24  37 rlkrLeeeGlIk 48 
                                        l ++e+eGl++
  gi|474934450|ref|YP_007688032.1| 136 VLAKMEKEGLVT 147
                                       6889******96 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.34   5.6e+02      22      68 ..      39      80 ..      22     104 .. 0.74
   2 ?   12.0   0.0    0.0001      0.16      25      69 ..     129     170 ..     109     181 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.34
                      Replic_Relax 22 shratarrrLarLrelgllsr.lrkrvggarggsepyvYaLtpkGarl 68
                                      +h++t+r+r+  +++ g+++  +  +   +++   + +  Lt+kG ++
  gi|474934450|ref|YP_007688032.1| 39 NHTQTLRQRIDSMEKDGIVDVeIVSS---VHK---QVRISLTEKGTEI 80
                                      33347899999999999999855555...333...5667888888765 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.0001
                      Replic_Relax  25 a..tarrrLarLrelgllsr.lrkrvggarggsepyvYaLtpkGarll 69 
                                       +  ++ ++La+++++gl++r +  +       +++++Y Ltp G+++ 
  gi|474934450|ref|YP_007688032.1| 129 SydSTTKVLAKMEKEGLVTRtVSSE------SYREIRYSLTPMGKQVA 170
                                       2456899*************44444......46789********9997 PP

>> DUF1495  Winged helix DNA-binding domain (DUF1495)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1      0.21   3.3e+02      62      87 ..      54      81 ..      25      84 .. 0.69
   2 ?   10.0   0.0   0.00036      0.59      61      88 ..     142     171 ..     113     173 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.21
                           DUF1495 62 lGLveeeeeseglk..lYklteeGieiv 87
                                       G+v  e  s+  k    +lte+G ei+
  gi|474934450|ref|YP_007688032.1| 54 DGIVDVEIVSSVHKqvRISLTEKGTEIA 81
                                      5565554444444422446899998887 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00036
                           DUF1495  61 elGLveeeeeseglk..lYklteeGieive 88 
                                       + GLv+++ +se ++   Y+lt+ G+++++
  gi|474934450|ref|YP_007688032.1| 142 KEGLVTRTVSSESYReiRYSLTPMGKQVAD 171
                                       47********99999999*********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       983  (0.0548274); expected 358.6 (0.02)
Passed bias filter:                      641  (0.0357521); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1108.18
//
Query:       gi|474934451|ref|YP_007688033.1|  [L=79]
Description: hypothetical protein TALC_00878 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0087   16.0   0.0      0.014   15.3   0.0    1.4  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an


Domain annotation for each model (and alignments):
>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   7.8e-07     0.014       8      31 ..      21      44 ..      17      45 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 7.8e-07
                                      EEEE-CCCHHHCCEECTCEEEEEE CS
                    MazE_antitoxin  8 avriPkevrfelgireGdevelev 31
                                       v+ P +v++ +gir Gd + ++v
  gi|474934451|ref|YP_007688033.1| 21 YVTVPVAVAERMGIRDGDYLDVTV 44
                                      59****************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 508.91
//
Query:       gi|474934452|ref|YP_007688034.1|  [L=494]
Description: Site-specific recombinase XerD [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.5e-14   51.6   0.0    2.3e-13   50.3   0.0    1.6  1  Phage_integrase  Phage integrase family


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.3   0.0   1.3e-17   2.3e-13      18     168 ..     320     475 ..     308     478 .. 0.79

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 1.3e-17
                                       HHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSE...EEEECTHHHHHHHHHHHHHH.... CS
                   Phage_integrase  18 slkirdklllellyetGlRisEllsLrvkdldlengvilvheregKgske...ravplseealellkellska.... 87 
                                       s+ + +k +l l+ + GlR +E+++L+++d+     ++l+   +gKg  +   ++  ++++++ +++ +l ++    
  gi|474934452|ref|YP_007688034.1| 320 SATMAEKVALVLCAGMGLRRNEVATLKLSDI--VGDRMLI---RGKGHGAgkiVEKEIPKSVMAVIQAYLPERdlli 391
                                       456789999*********************9..8889999...7777666555999999**************7776 PP

                                       CHCCTTTSBSSBETTSSB--HHHHHHHHHHHHHHCT-S..SC--TTHHHHHHHHHHHHHCTSHHHHHHHHT-SSCCH CS
                   Phage_integrase  88 leeaeksellfaskrgkplsrqtvrkafkraveeagie..kpltpHtlRhsfataLleagvdlrvvqkllGHssist 162
                                        +  ++ +  ++  + +   ++t++ ++ ++  ea +    ++t Ht+R+ ++++Ll +g+ l++v +++ Hss+++
  gi|474934452|ref|YP_007688034.1| 392 RKFGDRYNGSLLIPPYYSNGQRTLNLYVGNLISEASARvgVKATCHTFRRFYCMNLLDNGFELDTVRRMMRHSSVEI 468
                                       333333333333345566666666666666666666666667*********************************** PP

                                       H.HHHHC CS
                   Phage_integrase 163 t.qiYth 168
                                       t + Y+ 
  gi|474934452|ref|YP_007688034.1| 469 TlESYVY 475
                                       *999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (494 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 3678.71
//
Query:       gi|474934453|ref|YP_007688035.1|  [L=233]
Description: sugar fermentation stimulation protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.4e-43  145.6   0.0    1.1e-42  145.3   0.0    1.1  1  SfsA      Sugar fermentation stimulation protein RE domain
    2.3e-24   85.3   0.1    4.1e-24   84.5   0.1    1.4  1  SfsA_N    SfsA N-terminal OB domain


Domain annotation for each model (and alignments):
>> SfsA  Sugar fermentation stimulation protein RE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.3   0.0   1.2e-46   1.1e-42       1     136 [.      88     219 ..      88     221 .. 0.97

  Alignments for each domain:
  == domain 1  score: 145.3 bits;  conditional E-value: 1.2e-46
                                       HHHHHHHHHHHEE..........EEES-EETTEE-SEEEE-S.SSEEEEEEEE--EE..EEEEE-SS--HHHHHHHH CS
                              SfsA   1 qlpnklveealesglielagyeeikrevkygnsriDfllekeeeekcyvEVKsvtleeggialfPdapteRgqkhle 77 
                                       q+pn++v+e + +    l +++++ +e ++g+sr+Df+ e+  ++++ +EVK+vtle++g++lfPdapteRg kh++
  gi|474934453|ref|YP_007688035.1|  88 QAPNAVVKESIGK---ILGKCDRVVPEHTFGDSRFDFYAEQG-GKRIILEVKGVTLEDDGVVLFPDAPTERGLKHVR 160
                                       79*********87...468999****************9998.***************99***************** PP

                                       HHHHHHHTT-EEEEEEEE-SSS--EEEE-TTT-HHHHHHHHHHHHHT-EEEEEEEEE-T CS
                              SfsA  78 eLaelvkegyravvlfvvqredarefkpnkeidpefaealreaaeaGVevlaydckvtp 136
                                       eL++lv+eg  + ++f+vq+ d+++++pn  ++ ef++al+ a++aGV+v+ay+c+v++
  gi|474934453|ref|YP_007688035.1| 161 ELTSLVSEGFDCWICFLVQMGDVKYMSPNYATHMEFGKALEGAEAAGVHVVAYACDVEE 219
                                       ********************************************************987 PP

>> SfsA_N  SfsA N-terminal OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.5   0.1   4.6e-28   4.1e-24       1      63 []      12      85 ..      12      85 .. 0.91

  Alignments for each domain:
  == domain 1  score: 84.5 bits;  conditional E-value: 4.6e-28
                                      EEEEETTEEEEEEE.............EE----S--TTT--TT-EEEEE....ESSS-SEEEEEEEETTEEEE- CS
                            SfsA_N  1 lrRpnRFladveldg...t........vHvpntGrlkelllpGarvllsksdnpkrKtkytleavekegtwvgi 63
                                      + RpnRF+a+v+++g   +        +Hv+ntGr++ell+pG+rv+ls + np r t+y+l+av+k+++++++
  gi|474934453|ref|YP_007688035.1| 12 IDRPNRFIANVRIQGennEpdsypvvrCHVKNTGRCRELLVPGCRVVLSVAGNPDRETPYDLVAVWKGRRLINM 85
                                      78************7655155677778*********************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1728.49
//
Query:       gi|474934454|ref|YP_007688036.1|  [L=321]
Description: hypothetical protein TALC_00881 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.5   10.1   1.9       0.89    9.3   0.6    1.8  2  Connexin  Connexin


Domain annotation for each model (and alignments):
>> Connexin  Connexin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.6     5e-05      0.89      97     163 ..       7      73 ..       1      85 [. 0.51
   2 ?   -0.5   0.0     0.049   8.8e+02     146     167 ..     267     294 ..     236     303 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 5e-05
                          Connexin  97 kiakeekekekeeeekeeeekeeekkkkkekkkkkkkeeekekkkeegkrrirggllrt.Yvlqlllr 163
                                       ++++e++ k+  ++++ +ee++ + k ++ ++k++++++++ +k+++++r+ir++++ + Y   ++l 
  gi|474934454|ref|YP_007688036.1|   7 RSRREKELKR-AQKSRVKEESKLQAKIRRANQKEDSEKRRTIRKNSSASREIRHSVITMvYSSLIILV 73 
                                       4455555444.444444444444444445555555555555556666666777777666254444443 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.049
                          Connexin 146 r......rirggllrtYvlqlllrillE 167
                                       +      ++r +l+++Y++  ++r   E
  gi|474934454|ref|YP_007688036.1| 267 SmmgdisKTRPELMSVYIIMQMIRDQEE 294
                                       0222222458999999999988886555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1922  (0.107201); expected 358.6 (0.02)
Passed bias filter:                      916  (0.0510904); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.51
# Mc/sec: 1889.73
//
Query:       gi|474934455|ref|YP_007688037.1|  [L=313]
Description: hypothetical protein TALC_00882 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-06   26.4   0.0      0.022   14.3   0.0    2.2  2  Hpr_kinase_C  HPr Serine kinase C-terminal domain


Domain annotation for each model (and alignments):
>> Hpr_kinase_C  HPr Serine kinase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   1.2e-06     0.022       8      53 ..     119     165 ..     114     183 .. 0.86
   2 !    9.9   0.0   2.8e-05      0.49      73     113 ..     203     243 ..     192     259 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.2e-06
                                       EEESEEEEETTEEEEEEESTCHHHHHHHHHHHT.TT-EEEEESSEEE CS
                      Hpr_kinase_C   8 svhGvlvdvygvGvLitGesgvGKselaleLik.rghrLvaDDavei 53 
                                       svhG+ v+  +vGv i+  s  GK+  +  L++ r+  L++DD   +
  gi|474934455|ref|YP_007688037.1| 119 SVHGSAVSFDDVGVAIIAPSKAGKTTQSWGLLRdRNSCLISDDWFFV 165
                                       79****************************9965999******8655 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 2.8e-05
                                       EEETTTEEEEHHHHH-GGGB-SEEEEEEEEEEESTT---TT CS
                      Hpr_kinase_C  73 levrglGiidvkklfGaeavrekkeielvveLeewekkkey 113
                                       l+ +g Gi +++ + G+++vr++ +++ v+ Le+ + +k++
  gi|474934455|ref|YP_007688037.1| 203 LDNKGRGIANIRWITGEASVRSTCSLRYVILLEREKGDKNI 243
                                       566899***************************99988664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1866.17
//
Query:       gi|474934456|ref|YP_007688038.1|  [L=173]
Description: Sel1 repeat protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-30  104.1  15.1    1.6e-11   44.5   3.4    4.1  4  Sel1      Sel1 repeat
  ------ inclusion threshold ------
      0.013   16.1   5.3        4.5    8.1   0.1    4.1  3  TPR_6     Tetratricopeptide repeat
        0.8   10.0  10.1         22    5.5   0.0    5.0  5  TPR_2     Tetratricopeptide repeat
        1.3    9.1   5.2        4.9    7.3   0.1    3.6  5  MIT       MIT (microtubule interacting and transport) domain
        8.9    6.3  12.5         12    5.9   0.1    4.6  6  TPR_1     Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> Sel1  Sel1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   3.4   4.5e-15   1.6e-11       1      38 []      17      52 ..      17      52 .. 0.98
   2 !   19.6   0.1   2.9e-07     0.001       1      38 []      53      88 ..      53      88 .. 0.95
   3 !   19.8   0.0   2.5e-07   0.00091       2      37 ..      90     123 ..      89     124 .. 0.90
   4 !   27.0   0.2   1.4e-09   5.1e-06       3      38 .]     127     160 ..     127     160 .. 0.97

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 4.5e-15
                              Sel1  1 aeAmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38
                                      ae++yr G  y+y  G g++kD++kA++wy kAAeqG+
  gi|474934456|ref|YP_007688038.1| 17 AESQYRAG--YAYAVGEGTDKDYSKAMHWYSKAAEQGH 52
                                      79******..***************************9 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 2.9e-07
                              Sel1  1 aeAmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38
                                      aeA +++G  +ly+ G gv++D +kA+e+y ++ e+G+
  gi|474934456|ref|YP_007688038.1| 53 AEAENAVG--ELYHSGCGVEADFSKAMEHYLRSSELGS 88
                                      79******..999***99******************96 PP

  == domain 3  score: 19.8 bits;  conditional E-value: 2.5e-07
                              Sel1   2 eAmyrLGmfylylnGlgvpkDpekAiewyekAAeqG 37 
                                       +Am + G   ly++G gv++ + kA ew+e++  +G
  gi|474934456|ref|YP_007688038.1|  90 DAMLNIG--ILYEFGMGVEQSYGKASEWFERSSGLG 123
                                       69*****..777*******************97666 PP

  == domain 4  score: 27.0 bits;  conditional E-value: 1.4e-09
                              Sel1   3 AmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                       Am rLG   l+++G+g++k  ekA+ +yekA ++G+
  gi|474934456|ref|YP_007688038.1| 127 AMLRLG--KLFEDGRGTEKSAEKALALYEKAESMGN 160
                                       9*****..***********************99997 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.7     0.023        81       1      20 [.      18      41 ..      18      82 .. 0.89
   2 ?    3.7   0.0     0.032   1.1e+02       1      13 [.      90     103 ..      90     114 .. 0.81
   3 ?    8.1   0.1    0.0013       4.5       2      25 ..     127     154 ..     126     166 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.023
                                      HHHHHHHHHHHHH....HHHHHHH CS
                             TPR_6  1 dAlyklalsyrkl....gdtdkAl 20
                                      +++y+++++y  +    +d++kA+
  gi|474934456|ref|YP_007688038.1| 18 ESQYRAGYAYAVGegtdKDYSKAM 41
                                      679*******98767777777775 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.032
                                       HHHHHHHHHHHH.H CS
                             TPR_6   1 dAlyklalsyrk.l 13 
                                       dA+++++ +y+  +
  gi|474934456|ref|YP_007688038.1|  90 DAMLNIGILYEFgM 103
                                       8*********9755 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0013
                                       HHHHHHHHHHHH....HHHHHHHHHHHH CS
                             TPR_6   2 Alyklalsyrkl....gdtdkAlealer 25 
                                       A+++l+++++ +    + ++kAl+++e+
  gi|474934456|ref|YP_007688038.1| 127 AMLRLGKLFEDGrgteKSAEKALALYEK 154
                                       9**********86777777799999987 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.3      0.43   1.5e+03       1      12 [.      17      28 ..      17      29 .. 0.85
   2 ?    5.5   0.0    0.0062        22      15      29 ..      35      49 ..      33      50 .. 0.91
   3 ?    2.8   0.0     0.045   1.6e+02      16      30 ..      72      86 ..      70      90 .. 0.83
   4 ?   -0.7   0.0      0.58   2.1e+03      17      26 ..     109     118 ..     106     119 .. 0.84
   5 ?    3.3   0.4      0.03   1.1e+02      18      27 ..     146     155 ..     142     158 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.43
                             TPR_2  1 aealynlGlayy 12
                                      ae  y+ G+ay+
  gi|474934456|ref|YP_007688038.1| 17 AESQYRAGYAYA 28
                                      68899****996 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0062
                             TPR_2 15 gdyeeAleafekAle 29
                                      +dy +A +++ kA e
  gi|474934456|ref|YP_007688038.1| 35 KDYSKAMHWYSKAAE 49
                                      79***********87 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.045
                             TPR_2 16 dyeeAleafekAlel 30
                                      d+ +A e++ ++ el
  gi|474934456|ref|YP_007688038.1| 72 DFSKAMEHYLRSSEL 86
                                      799******998777 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 0.58
                             TPR_2  17 yeeAleafek 26 
                                       y +A e+fe+
  gi|474934456|ref|YP_007688038.1| 109 YGKASEWFER 118
                                       8899999998 PP

  == domain 5  score: 3.3 bits;  conditional E-value: 0.03
                             TPR_2  18 eeAleafekA 27 
                                       e+Al+++ekA
  gi|474934456|ref|YP_007688038.1| 146 EKALALYEKA 155
                                       7888888888 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.67   2.4e+03       6      22 ..       7      23 ..       6      27 .. 0.80
   2 ?    7.3   0.1    0.0014       4.9      11      32 ..      28      49 ..      26      50 .. 0.86
   3 ?   -1.7   0.0      0.87   3.1e+03      19      32 ..      72      85 ..      69      86 .. 0.76
   4 ?   -2.6   0.0       1.6   5.8e+03      52      59 ..     111     118 ..     106     122 .. 0.54
   5 ?    1.5   0.1     0.088   3.1e+02      18      30 ..     143     155 ..     141     171 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.67
                               MIT  6 elvkkAveeDnagnyee 22
                                      e+++kA   D + +y +
  gi|474934456|ref|YP_007688038.1|  7 EILRKAESGDAESQYRA 23
                                      67889999999999875 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0014
                               MIT 11 AveeDnagnyeeAlelYkeale 32
                                      Av e   ++y++A+++Y++a e
  gi|474934456|ref|YP_007688038.1| 28 AVGEGTDKDYSKAMHWYSKAAE 49
                                      66677889************87 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.87
                               MIT 19 nyeeAlelYkeale 32
                                      ++++A+e Y  + e
  gi|474934456|ref|YP_007688038.1| 72 DFSKAMEHYLRSSE 85
                                      78899999987766 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 1.6
                               MIT  52 kieeYleR 59 
                                       k++e+ eR
  gi|474934456|ref|YP_007688038.1| 111 KASEWFER 118
                                       45555555 PP

  == domain 5  score: 1.5 bits;  conditional E-value: 0.088
                               MIT  18 gnyeeAlelYkea 30 
                                       +  e+Al lY++a
  gi|474934456|ref|YP_007688038.1| 143 KSAEKALALYEKA 155
                                       6678999999987 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.3       2.1   7.7e+03       1      11 [.      17      27 ..      17      28 .. 0.79
   2 ?    5.9   0.1    0.0033        12      15      29 ..      35      49 ..      34      50 .. 0.90
   3 ?    2.8   0.0     0.033   1.2e+02      16      30 ..      72      86 ..      71      90 .. 0.81
   4 ?   -1.4   0.0      0.66   2.4e+03       3      11 ..      91      99 ..      89     100 .. 0.83
   5 ?   -2.8   0.0       1.8   6.5e+03      17      26 ..     109     118 ..     108     119 .. 0.79
   6 ?    2.6   0.7     0.036   1.3e+02      18      27 ..     146     155 ..     145     157 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.1
                                      HHHHHHHHHHH CS
                             TPR_1  1 akalynlGnay 11
                                      a++ y+ G+ay
  gi|474934456|ref|YP_007688038.1| 17 AESQYRAGYAY 27
                                      67789999999 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0033
                                      T-HHHHHHHHHHHHH CS
                             TPR_1 15 gkydeAleyyekALe 29
                                      ++y +A   y+kA e
  gi|474934456|ref|YP_007688038.1| 35 KDYSKAMHWYSKAAE 49
                                      79***********66 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.033
                                      -HHHHHHHHHHHHHH CS
                             TPR_1 16 kydeAleyyekALel 30
                                      ++ +A e+y +  el
  gi|474934456|ref|YP_007688038.1| 72 DFSKAMEHYLRSSEL 86
                                      799******887665 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 0.66
                                      HHHHHHHHH CS
                             TPR_1  3 alynlGnay 11
                                      a  n+G +y
  gi|474934456|ref|YP_007688038.1| 91 AMLNIGILY 99
                                      778****99 PP

  == domain 5  score: -2.8 bits;  conditional E-value: 1.8
                                       HHHHHHHHHH CS
                             TPR_1  17 ydeAleyyek 26 
                                       y +A e +e+
  gi|474934456|ref|YP_007688038.1| 109 YGKASEWFER 118
                                       6789999987 PP

  == domain 6  score: 2.6 bits;  conditional E-value: 0.036
                                       HHHHHHHHHH CS
                             TPR_1  18 deAleyyekA 27 
                                       ++Al+ yekA
  gi|474934456|ref|YP_007688038.1| 146 EKALALYEKA 155
                                       79******99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1220.45
//
Query:       gi|474934457|ref|YP_007688039.1|  [L=140]
Description: hypothetical protein TALC_00884 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-15   56.9   0.0    3.2e-15   56.6   0.0    1.1  1  Flavodoxin_5  Flavodoxin domain
    0.00025   20.8   0.0    0.00031   20.5   0.0    1.1  1  Flavodoxin_3  Flavodoxin domain
  ------ inclusion threshold ------
       0.33   11.1   1.9       0.64   10.2   1.9    1.4  1  zf-CCCH_8     Zinc-finger antiviral protein (ZAP) zinc finger


Domain annotation for each model (and alignments):
>> Flavodoxin_5  Flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.6   0.0   5.4e-19   3.2e-15       2      92 ..      12      98 ..      10     118 .. 0.88

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 5.4e-19
                      Flavodoxin_5  2 ilYsSrdGqTkkiaeriaeelreegelvdvedvekesedlesydavvigasvyygkllpelakFvekhreaLstkpval 80
                                      i+ sS  G+ +k a++iae+l+  ++++d++     + d++ yd+v++g++++ g+  +++ +++  hr++Ls+k++al
  gi|474934457|ref|YP_007688039.1| 12 IFASSLGGHVRKTAKYIAEKLG--CDIFDLKLQ--TNIDVTAYDRVIFGTGIHAGRPYSKVSNYIADHRADLSSKKTAL 86
                                      55677899**************..888888875..689***************************************** PP

                      Flavodoxin_5 81 fsvsltarkpek 92
                                      f+++l + ++ +
  gi|474934457|ref|YP_007688039.1| 87 FICCLYKGERGE 98
                                      *****9655444 PP

>> Flavodoxin_3  Flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   5.1e-08   0.00031       2      77 ..      12      90 ..      10     105 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 5.1e-08
                      Flavodoxin_3  2 ilysSltGNTkkvAeaikealeeekeivsikeakek.veeadvvfvGfwvdkgtadeealkfle....tlknkkillfg 75
                                      i+ sSl G  +k A+ i+e+l +  +i+++k +++  v+++d v+ G+ ++ g + ++++++++    +l+ kk +lf 
  gi|474934457|ref|YP_007688039.1| 12 IFASSLGGHVRKTAKYIAEKLGC--DIFDLKLQTNIdVTAYDRVIFGTGIHAGRPYSKVSNYIAdhraDLSSKKTALFI 88
                                      5668999****************..******9999899***********************996333369999999998 PP

                      Flavodoxin_3 76 Tl 77
                                       +
  gi|474934457|ref|YP_007688039.1| 89 CC 90
                                      66 PP

>> zf-CCCH_8  Zinc-finger antiviral protein (ZAP) zinc finger domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.9   0.00011      0.64       7      21 ..      88     102 ..      87     104 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00011
                         zf-CCCH_8   7 ICKnYKGEgRkqiCs 21 
                                       IC  YKGE + q C+
  gi|474934457|ref|YP_007688039.1|  88 ICCLYKGERGEQQCQ 102
                                       9*************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 872.03
//
Query:       gi|474934458|ref|YP_007688040.1|  [L=88]
Description: putative membrane protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-22   78.3   1.7    5.4e-22   77.8   1.7    1.3  1  DUF1294   Protein of unknown function (DUF1294)
     0.0093   16.2   1.2      0.015   15.5   1.2    1.3  1  DUF4293   Domain of unknown function (DUF4293)
     0.0097   15.6   0.5      0.011   15.4   0.5    1.1  1  DUF1345   Protein of unknown function (DUF1345)
  ------ inclusion threshold ------
      0.086   12.9   2.6       0.21   11.6   1.6    1.8  2  DUF2700   Protein of unknown function (DUF2700)


Domain annotation for each model (and alignments):
>> DUF1294  Protein of unknown function (DUF1294)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.8   1.7   1.2e-25   5.4e-22       1      55 []      14      67 ..      14      67 .. 0.98

  Alignments for each domain:
  == domain 1  score: 77.8 bits;  conditional E-value: 1.2e-25
                           DUF1294  1 nlitfllygiDKrkAkkkkwRipEktLlllallgGslGallgmrlfrHKtkkksF 55
                                      n+ +fl+yg+DK+kAk++kwR++E+tLl+lall G++G+l gm+ f+HKt+k +F
  gi|474934458|ref|YP_007688040.1| 14 NVTAFLAYGWDKHKAKNDKWRTKESTLLALALL-GAFGGLSGMYAFHHKTRKGKF 67
                                      899******************************.9*****************999 PP

>> DUF4293  Domain of unknown function (DUF4293)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   1.2   3.4e-06     0.015       6     101 ..       4      86 ..       3      88 .] 0.74

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.4e-06
                           DUF4293   6 slyLllaailmaaflflplasivtedellsfyalgvstaeaetsvnvsvwvlvilllliailaliaIflyknRklQl 82 
                                       +++L + ++l ++ ++   +            + +   ++++  ++ s++  ++ll     l+ +  f +k Rk  +
  gi|474934458|ref|YP_007688040.1|   4 TIFLAVYVLLNVTAFLAYGWD-----------KHK--AKNDKWRTKESTLLALALLGAFGGLSGMYAFHHKTRKGKF 67 
                                       556666555555555332222...........333..3355566789999999999999****************** PP

                           DUF4293  83 rlclinllllvllyvllal 101
                                       +l+++ ++l ++l+++++ 
  gi|474934458|ref|YP_007688040.1|  68 KLVWLFVVLHIILIAAIVC 86 
                                       ***9999999999888876 PP

>> DUF1345  Protein of unknown function (DUF1345)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.5   2.5e-06     0.011       8      87 ..       2      81 ..       1      86 [. 0.77

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.5e-06
                           DUF1345  8 gwdlaalvylvlvllvllradaeelrkraeredesrvlilllvllaalaslvaivlllasakaekpaekllhlalavat 86
                                       w ++++vy++l ++++l    ++ +++ ++ + ++ ++l+l+ll a+  l ++ +  +++++ k +  +l ++l ++ 
  gi|474934458|ref|YP_007688040.1|  2 NWTIFLAVYVLLNVTAFLAYGWDKHKAKNDKWRTKESTLLALALLGAFGGLSGMYAFHHKTRKGKFKLVWLFVVLHIIL 80
                                      69****************9977777777777777777778888888888888888777777777777767777777666 PP

                           DUF1345 87 v 87
                                      +
  gi|474934458|ref|YP_007688040.1| 81 I 81
                                      5 PP

>> DUF2700  Protein of unknown function (DUF2700)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.12   5.4e+02      79      94 ..      13      27 ..       3      40 .. 0.53
   2 ?   11.6   1.6   4.7e-05      0.21       5      51 ..      39      87 ..      36      88 .] 0.91

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.12
                           DUF2700 79 vvvasfvAsglvekle 94
                                        v++f+A+g  +k +
  gi|474934458|ref|YP_007688040.1| 13 LNVTAFLAYGW-DKHK 27
                                      44678888884.3333 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 4.7e-05
                           DUF2700  5 lvivlailgiirsivlllissdtlttalasii..slllnlllLfGalkn 51
                                      ++++la+lg ++  + ++  ++++ +  ++++  +++l+++l+++++++
  gi|474934458|ref|YP_007688040.1| 39 TLLALALLGAFGGLSGMYAFHHKTRKGKFKLVwlFVVLHIILIAAIVCY 87
                                      6899*************99999999999999988899*******99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       916  (0.0510904); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 644.08
//
Query:       gi|474934459|ref|YP_007688041.1|  [L=327]
Description: Fe-S oxidoreductase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-18   67.3   0.6    3.2e-18   66.7   0.6    1.3  1  Radical_SAM   Radical SAM superfamily
    4.8e-15   55.7   0.0      9e-15   54.8   0.0    1.5  1  Wyosine_form  Wyosine base formation
     0.0014   18.9   1.2      0.009   16.3   0.3    2.4  2  Fer4_12       4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.033   14.3   0.1       0.28   11.3   0.0    2.5  4  Fer4_14       4Fe-4S single cluster domain
       0.35    8.7   0.0       0.47    8.3   0.0    1.1  1  TssR          Type VI secretion system, TssR


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.7   0.6   8.9e-22   3.2e-18       4     161 ..      59     230 ..      56     235 .. 0.84

  Alignments for each domain:
  == domain 1  score: 66.7 bits;  conditional E-value: 8.9e-22
                                       ESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEE.........................SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........................xx RF
                       Radical_SAM   4 trgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilg.........................gg 55 
                                       ++ C++ C+fC+r e    +++ +++ + e +e +++l   +  + +i+g                          g
  gi|474934459|ref|YP_007688041.1|  59 LNECTHTCPFCWRIE----GKDFEVKEWTEPKEMLDAL-IAR-QRKLISGfkgdercdigmfneamepnqvacslAG 129
                                       678***********8....6777777777777777777.444.555555557788888889**************** PP

                                       TGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHH....HHHHHHTCTSHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxx RF
                       Radical_SAM  56 epllypdfvellerlaklavpgiritvetngtlpdeeklerllelgvdrvslgleaadde....kvlklmnrghtfe 128
                                       ep+lyp + e+ ++++ +   g++++++tngt+  +e +e l  l+   +++++ a+d e    +++ ++  ++++e
  gi|474934459|ref|YP_007688041.1| 130 EPTLYPYLGEFFRECHSR---GMTTFLVTNGTM--PERIENLSTLP-RMLYVTVAAPDREtyirTCRPKI--RDGWE 198
                                       *****************8...************..69999999999.*************5554444444..59*** PP

                                       HHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 129 evlealeklreagikrvvdrivglpGendeele 161
                                       +++++le+l +++ + +++r++++ G+n+   e
  gi|474934459|ref|YP_007688041.1| 199 RLMRTLEILPDLRTR-TCIRHTLVDGYNFFRPE 230
                                       ************999.***********985555 PP

>> Wyosine_form  Wyosine base formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.8   0.0   2.5e-18     9e-15       2      61 ..     239     297 ..     238     299 .. 0.97

  Alignments for each domain:
  == domain 1  score: 54.8 bits;  conditional E-value: 2.5e-18
                                       HT-SEEEEEE------------------HHHHHHHHHHHHTSSS.EEEEEEETTTTEEEE CS
                      Wyosine_form   2 aepdFvEvKaytyvGssrsrLtmknvPwheevadfakrlegsaedYellaehrhSrvvll 61 
                                       aepd +E K+y +vG sr+rL+ +n+P+ e++++fa +l +  +  +ll e  +Srvvll
  gi|474934459|ref|YP_007688041.1| 239 AEPDLIEPKGYVFVGGSRQRLSLSNMPTFEGIREFALKLGEEMG-MTLLKEKMDSRVVLL 297
                                       89******************************************.**************8 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.3   2.5e-06     0.009      12     105 ..      59     167 ..      48     185 .. 0.81
   2 ?   -2.9   0.0       2.2   7.8e+03      39      64 ..     276     302 ..     266     307 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.5e-06
                           Fer4_12  12 vsgCnlsCkgCfnketwsfk......................sgkeftkelleeiiedlkkesiegltllGGEPllp 66 
                                       ++ C++ C++C   e ++f+                      sg + ++     ++++++++++   +l  GEP l 
  gi|474934459|ref|YP_007688041.1|  59 LNECTHTCPFCWRIEGKDFEvkewtepkemldaliarqrkliSGFKGDERCDIGMFNEAMEPNQVACSLA-GEPTL- 133
                                       679****************988888888888888888877777777788888888888877777777666.7****. PP

                           Fer4_12  67 enaeallelvkevkeekpekdiwlytgytleelskkeke 105
                                         ++ l e+++e+ ++++  + ++++g++ e +++   +
  gi|474934459|ref|YP_007688041.1| 134 --YPYLGEFFRECHSRGM-TTFLVTNGTMPERIENL--S 167
                                       ..9***************.59999***999999854..3 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.2
                           Fer4_12  39 elleei.iedlkkesiegltllGGEPl 64 
                                       +l ee+ ++ lk++ ++ ++llG E +
  gi|474934459|ref|YP_007688041.1| 276 KLGEEMgMTLLKEKMDSRVVLLGHEGM 302
                                       555544145566677789999997766 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.4     5e+03      62      78 ..      17      33 ..      16      40 .. 0.81
   2 ?   11.3   0.0   7.8e-05      0.28       5      38 ..      59      93 ..      57     103 .. 0.75
   3 ?   -2.0   0.0         1   3.7e+03      56      94 ..     129     162 ..     115     173 .. 0.72
   4 ?   -3.4   0.0       2.8     1e+04      41      56 ..     239     254 ..     229     255 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.4
                           Fer4_14 62 enkkellklvkrlkeey 78
                                      +n+++ +kl+ +lk+++
  gi|474934459|ref|YP_007688041.1| 17 YNDHAAVKLCGWLKQSM 33
                                      4899999***9999987 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 7.8e-05
                           Fer4_14  5 lsgCnlsCkgCdnketwkselgkpqt.eelleqil 38
                                      l+ C++ C++C + e +++e+++  + +e+l++ +
  gi|474934459|ref|YP_007688041.1| 59 LNECTHTCPFCWRIEGKDFEVKEWTEpKEMLDALI 93
                                      689*********99999998888655155555555 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1
                           Fer4_14  56 GePLhyenkkellklvkrlkeeypekkiwletngtleie 94 
                                       GeP +y   + l ++ ++ + ++  +   l tngt+   
  gi|474934459|ref|YP_007688041.1| 129 GEPTLY---PYLGEFFRECHSRG--MTTFLVTNGTMPER 162
                                       788777...67777777777777..77788888887644 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 2.8
                           Fer4_14  41 lkkseikiqglvltGG 56 
                                       ++ + i+++g v++GG
  gi|474934459|ref|YP_007688041.1| 239 AEPDLIEPKGYVFVGG 254
                                       5788899999999999 PP

>> TssR  Type VI secretion system, TssR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0   0.00013      0.47     167     201 ..       2      36 ..       1      40 [. 0.93

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00013
                              TssR 167 sedrkkvLigkkpqlvadsaktsiyGWvssdllqs 201
                                       +e+ +++L+ +++++  d a  +++GW  +++l++
  gi|474934459|ref|YP_007688041.1|   2 DEEYRSTLVKQQYRIYNDHAAVKLCGWLKQSMLHE 36 
                                       68999****************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2061.72
//
Query:       gi|474934460|ref|YP_007688042.1|  [L=484]
Description: DNA polymerase III, delta subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-09   37.6   0.0      1e-08   35.7   0.0    2.1  2  AAA             ATPase family associated with various cellula
    1.8e-05   25.1   0.0    0.00036   20.8   0.0    2.7  2  AAA_22          AAA domain
    8.5e-05   23.0   0.5     0.0025   18.2   0.0    2.8  2  AAA_16          AAA ATPase domain
    0.00029   20.6   0.0    0.00042   20.1   0.0    1.2  1  DNA_pol3_delta  DNA polymerase III, delta subunit
    0.00059   19.9   0.0     0.0015   18.6   0.0    1.7  1  AAA_5           AAA domain (dynein-related subfamily)
     0.0031   17.7   0.1     0.0051   17.0   0.1    1.4  1  RFC1            Replication factor RFC1 C terminal domain
     0.0037   17.5   0.1      0.014   15.6   0.0    2.0  2  AAA_28          AAA domain
  ------ inclusion threshold ------
       0.01   15.8   0.0       0.05   13.6   0.0    2.0  2  AAA_14          AAA domain
      0.025   14.9   0.1      0.058   13.7   0.1    1.6  1  AAA_assoc_2     AAA C-terminal domain
      0.027   14.2   0.0      0.074   12.8   0.0    1.7  2  RuvB_N          Holliday junction DNA helicase RuvB P-loop do
      0.047   13.4   0.0      0.093   12.4   0.0    1.5  1  AAA_24          AAA domain
       0.07   12.8   0.2       0.22   11.2   0.1    1.9  2  AAA_30          AAA domain
        0.1   13.0   0.1        1.1    9.6   0.0    2.7  4  AAA_17          AAA domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.0   7.3e-12     1e-08       1      77 [.      18     102 ..      18     159 .. 0.71
   2 ?   -2.5   0.0       4.5   6.3e+03      34      58 ..     171     197 ..     151     247 .. 0.65

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 7.3e-12
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS..............TSEEEE CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakeka..............kpsilf 63 
                                       ++l+G pG+GKT+ a+a+a+++g  ++e+++s+ +      + + ir +  +a+  +              + + ++
  gi|474934460|ref|YP_007688042.1|  18 MVLIGSPGIGKTSSAEALARDMGWGIVEMNASDQR------TGDAIRSIALRASYYNtfdsegnfmnasrgGRKLVV 88 
                                       789********************************......333333333333111122223345556665579*** PP

                                       EETGGGHHHHH.TTC CS
                               AAA  64 iDEidalaksr.sgs 77 
                                       +DE+d+l+++  + +
  gi|474934460|ref|YP_007688042.1|  89 LDEADSLFGNAdR-G 102
                                       *********9931.2 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.5
                                       CSSSSTTHHHHHHHHHHHHHHHTS..T CS
                               AAA  34 llskyvgesekkirelfkeakeka..k 58 
                                        +sk+ ++++ ++r+ ++++++ a  +
  gi|474934460|ref|YP_007688042.1| 171 AVSKIAENAAGDLRAAVRDLQSLAtgN 197
                                       445555555556665555555555422 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   2.6e-07   0.00036       6     128 ..      16     121 ..      13     129 .. 0.81
   2 ?   -2.1   0.0       3.1   4.3e+03      40      70 ..     318     348 ..     305     376 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.6e-07
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseelleal 82 
                                       + +v++G +G+GKT +++ l++           + ++v+++++ + + + +++  lra          ++ +    +
  gi|474934460|ref|YP_007688042.1|  16 RAMVLIGSPGIGKTSSAEALARDM---------GWGIVEMNASDQRTGDAIRSIALRASY-------YNTFDSEGNF 76 
                                       679*******************98.........9************99999776666666.......4667777889 PP

                            AAA_22  83 eqalraravielliiDEaqhlr...seealeeLrsllnlsrkgvqliLv 128
                                        +a+r  ++  l+++DEa+ l+      a+  + +l++  + + ++iL+
  gi|474934460|ref|YP_007688042.1|  77 MNASRGGRK--LVVLDEADSLFgnaDRGAMPAINDLVK--TALQPVILI 121
                                       999999999..*********998753555555555577..777777776 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.1
                            AAA_22  40 pevvfvtlpsstsskdllrellralglelka 70 
                                        ++++ +++ s+ss+ l++ ++ ++g  +++
  gi|474934460|ref|YP_007688042.1| 318 FPTYLTKMSRSKSSRALRNSIAMKIGGITHT 348
                                       4556666777779999999999999876665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.8e-06    0.0025      18     100 ..       7      85 ..       2     125 .. 0.69
   2 ?    1.6   0.2      0.23   3.2e+02      53     127 ..     137     225 ..     120     253 .. 0.60

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.8e-06
                            AAA_16  18 rvrsgrp..elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesa 92 
                                       ++r g p  ++++l+G +G+GK+s +++l+r   + g+  ++ ++ + +++   +a+ +++ r ++++  ++e +  
  gi|474934460|ref|YP_007688042.1|   7 KWRNGMPaeRAMVLIGSPGIGKTSSAEALAR---DMGWGIVEMNASDQRTG---DAIRSIALRASYYNTFDSEGNFM 77 
                                       667788888******************9997...44577777777777333...55677777777777777776666 PP

                            AAA_16  93 eleawrek 100
                                       ++++  +k
  gi|474934460|ref|YP_007688042.1|  78 NASRGGRK 85 
                                       66665554 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.23
                            AAA_16  53 giflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleeala....................... 106
                                        ++++ k+++          a a   e++lr +++e+  +  +++  k+ e++a                       
  gi|474934460|ref|YP_007688042.1| 137 TYTVQIKFRKP--------TAAAV--EKVLRRICEEEGVSIEPEAVSKIAENAAgdlraavrdlqslatgnprvtlt 203
                                       45566666666........34444..467777777744444444444444444446666555666666666666666 PP

                            AAA_16 107 avpelagaea.srllellkrll 127
                                       ++++l+g e+ s++++l+ +++
  gi|474934460|ref|YP_007688042.1| 204 QASALSGREErSDMYQLMDAIF 225
                                       5555555555666666666665 PP

>> DNA_pol3_delta  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   3.1e-07   0.00042      58     173 ..      84     194 ..      81     195 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3.1e-07
                                       EEEEEEE--.....TT-S-TTHHHHHHHHTTT--SSEEEEEEES.S--HHHHHHHHHTTTEEEEEE----TTTHHHH CS
                    DNA_pol3_delta  58 krivvlknpklltkesklnekllkeLeeylsnlpedtlLiliapkklderkklvklLkkkatvveaktlkeeelkkw 134
                                       +++vvl+ +  l    + +   + +++ ++++  + ++Li+    +l+++ + vk+     + +++ +++ + + k 
  gi|474934460|ref|YP_007688042.1|  84 RKLVVLDEADSL--FGNADRGAMPAINDLVKTALQPVILIVNDWYELSRKSSAVKTYT---VQIKFRKPTAAAVEKV 155
                                       677777777555..33445566666666666666666666554468998888998887...789************* PP

                                       HHHHHHHTT-EE-HHHHHHHHHHHTT-HHHHHHHHHHHH CS
                    DNA_pol3_delta 135 iqkraqelglkiekealelLlelvennlsaikqelekLa 173
                                       + ++++e+g+ ie+ea++ ++e+  ++l+a+ + l+ La
  gi|474934460|ref|YP_007688042.1| 156 LRRICEEEGVSIEPEAVSKIAENAAGDLRAAVRDLQSLA 194
                                       ***********************************9997 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.1e-06    0.0015       2      75 ..      18      93 ..      17     100 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.1e-06
                                      EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--..........--------.G-SEEEEESGG CS
                             AAA_5  2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik.ngttslvdsplvraar.egeilvlDEve 75
                                      ++L+G pG+gK++ ae la+ +++ +++++ +++ t + ++     +   +t  +++ +++a r   +++vlDE +
  gi|474934460|ref|YP_007688042.1| 18 MVLIGSPGIGKTSSAEALARDMGWGIVEMNASDQRTGDAIRSIALRAsYYNTFDSEGNFMNASRgGRKLVVLDEAD 93
                                      68*******************************9999999876554467888889999999999444688899976 PP

>> RFC1  Replication factor RFC1 C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   3.7e-06    0.0051      31      98 ..     308     371 ..     272     425 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.7e-06
                                       HHHTT-EE-SS-----SHHHHHHHHHHHHHHHHHHHTTTTT------HHHHHTTTHHHHHHHHS---- CS
                              RFC1  31 PaslvrgslegrisFpswLGknSktnKnkRllqelqshlrlktsaskselrldylpllkkklvkpLke 98 
                                        +++    ++ ri+Fp++L k+S+ + ++ l + +++++   t++s+ ++  d++p ++    + L +
  gi|474934460|ref|YP_007688042.1| 308 SNQV----TRDRIRFPTYLTKMSRSKSSRALRNSIAMKIGGITHTSRANVLSDTFPRMRIMAQNDLDM 371
                                       2333....334*************999999999*************************9999999887 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0     1e-05     0.014       2      27 ..      18      44 ..      17      54 .. 0.87
   2 ?   -3.2   0.0       6.5     9e+03      23      63 ..     164     186 ..     148     202 .. 0.47

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1e-05
                            AAA_28  2 ivitGgestGKTtlleaLaar.gypvv 27
                                       v++G ++ GKT+ +eaLa++ g+ +v
  gi|474934460|ref|YP_007688042.1| 18 MVLIGSPGIGKTSSAEALARDmGWGIV 44
                                      69*****************87788776 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6.5
                            AAA_28  23 gypvvpEaareileeklakgedalpwvedllafaervleeq 63 
                                       g+++ pEa+ +i e+                   ++ l+++
  gi|474934460|ref|YP_007688042.1| 164 GVSIEPEAVSKIAENA------------------AGDLRAA 186
                                       3333344444444433..................3333333 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.6e-05      0.05       3      89 ..      16     113 ..      14     163 .. 0.77
   2 ?   -0.6   0.0      0.94   1.3e+03      91     125 ..     188     220 ..     170     223 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.6e-05
                            AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderd...........kkladpekllelileklkeekktyl 68 
                                       +++v+ G   +GKT  ++ l+++       i+++n  d+r+           + ++++ + +  +++  +  +++++
  gi|474934460|ref|YP_007688042.1|  16 RAMVLIGSPGIGKTSSAEALARDMG---WGIVEMNASDQRTgdairsialraSYYNTF-DSEGNFMNASR-GGRKLV 87 
                                       7899*****************9999...99********99976654433222111122.34455555433.699*** PP

                            AAA_14  69 flDEiqev.....pewekalkslvde 89 
                                       +lDE+  +     +++  a+++lv++
  gi|474934460|ref|YP_007688042.1|  88 VLDEADSLfgnadRGAMPAINDLVKT 113
                                       ****9988777776666666666665 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.94
                            AAA_14  91 knldvivtGSnskllskeiatslagrvaeielypl 125
                                       ++l+ ++tG     l +  a+ l+gr++  ++y l
  gi|474934460|ref|YP_007688042.1| 188 RDLQSLATGNPRVTLTQ--ASALSGREERSDMYQL 220
                                       56677778877777755..899******9999987 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   4.2e-05     0.058       3      38 ..     163     198 ..     161     237 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.2e-05
                                       X.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       AAA_assoc_2   3 kklkleddalealaeladGDaRkaLnlLElaaeaae 38 
                                       + +++e++a++ +ae a GD R+a   L+ +a+ + 
  gi|474934460|ref|YP_007688042.1| 163 EGVSIEPEAVSKIAENAAGDLRAAVRDLQSLATGNP 198
                                       5799**********************9997776554 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   5.3e-05     0.074      36      62 ..      18      44 ..       5      61 .. 0.84
   2 ?   -3.9   0.0       7.2     1e+04      35      62 ..     372     399 ..     365     406 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.3e-05
                            RuvB_N 36 vllyGpPGlGkttlakiiakelgvklk 62
                                      ++l+G+PG+Gkt+ a+ +a+++g  + 
  gi|474934460|ref|YP_007688042.1| 18 MVLIGSPGIGKTSSAEALARDMGWGIV 44
                                      789*******************98764 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 7.2
                            RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklk 62 
                                        v+l+   Gl    la ++  ++++k+ 
  gi|474934460|ref|YP_007688042.1| 372 RVMLIREAGLEPEELAFLLGVKMDAKII 399
                                       4778888888888899888888888875 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.8e-05     0.093       4      76 ..      17      94 ..      14     101 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.8e-05
                            AAA_24  4 kiliyGpsgiGKTtlakel..gpkplfidtekGlksldadkfpdie.......swedfldevvelaaeladyktlviDt 73
                                       ++++G++giGKT++a  l       ++ +++     d + ++ i+        +++f +e ++ +a   + k +v+D 
  gi|474934460|ref|YP_007688042.1| 17 AMVLIGSPGIGKTSSAEALarDMGWGIVEMNA----SDQRTGDAIRsialrasYYNTFDSEGNFMNASRGGRKLVVLDE 91
                                      689*************9993322222333333....3333333333111333333333333333366666666666666 PP

                            AAA_24 74 ide 76
                                      +d 
  gi|474934460|ref|YP_007688042.1| 92 ADS 94
                                      665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00016      0.22      19     100 ..      16      95 ..      11     190 .. 0.80
   2 ?   -1.0   0.0      0.92   1.3e+03      81      98 ..     210     255 ..     146     279 .. 0.47

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00016
                            AAA_30  19 rvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlk..grarlepgtlli 93 
                                       r +vl G +G GKt + +al++ +    g v + A+ ++  ++++ ++ ++as  + + ++ +  + a+   ++l++
  gi|474934460|ref|YP_007688042.1|  16 RAMVLIGSPGIGKTSSAEALARDMG--WGIVEMNASDQRTGDAIR-SIALRASYYNTFDSEGNfmN-ASRGGRKLVV 88 
                                       6899**********99888765444..3578899********999.99*****9999997777742.455666**** PP

                            AAA_30  94 vDEagmv 100
                                        DEa  +
  gi|474934460|ref|YP_007688042.1|  89 LDEADSL 95 
                                       ***9654 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.92
                            AAA_30  81 k...........................grarlepg.tllivDEag 98 
                                       +                           ++a+ +p+   l++DE  
  gi|474934460|ref|YP_007688042.1| 210 GreersdmyqlmdaifrkhdpvlakkvlREADTDPQtVSLWIDENM 255
                                       0333444444444444444444444444334455553335555555 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00083       1.1       1      38 [.      21      65 ..      21      95 .. 0.76
   2 ?   -2.6   0.0       5.1   7.1e+03      31      57 ..     157     183 ..     154     239 .. 0.62
   3 ?   -3.5   0.0       9.4   1.3e+04      16      31 ..     252     267 ..     246     275 .. 0.78
   4 ?   -0.6   0.0       1.2   1.6e+03      58      87 ..     335     366 ..     304     391 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00083
                                      EE-TTSSHHHHHHHHHHHHTEEEEEH.......HHHHHHHHHTTT CS
                            AAA_17  1 lGgPGsGKgtqceklvekygfthlsa.......Gdllreeakrgg 38
                                      +G PG GK+  +e l++++g  ++++       Gd +r+ a r +
  gi|474934460|ref|YP_007688042.1| 21 IGSPGIGKTSSAEALARDMGWGIVEMnasdqrtGDAIRSIALRAS 65
                                      599**************9966666544444444888887776654 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.1
                                       HHHHHTTTSHSSHHHHCTSHHHHHHHH CS
                            AAA_17  31 reeakrgglakardemrklpleekkel 57 
                                       r  ++++g + + ++++k  ++   +l
  gi|474934460|ref|YP_007688042.1| 157 RRICEEEGVSIEPEAVSKIAENAAGDL 183
                                       555555555444444444444333333 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 9.4
                                       HHHHTEEEEEHHHHHH CS
                            AAA_17  16 vekygfthlsaGdllr 31 
                                        e++ ++  + Gdl+r
  gi|474934460|ref|YP_007688042.1| 252 DENMPYECHTVGDLVR 267
                                       57888999999**999 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHH..HSSEEEEEE-SEEEETTE CS
                            AAA_17  58 qkeaaekiaeea..kkkgvlvdghprikeqag 87 
                                       +  +a ki      ++ +vl d++pr++ +a+
  gi|474934460|ref|YP_007688042.1| 335 RNSIAMKIGGIThtSRANVLSDTFPRMRIMAQ 366
                                       44444444332222678899999999876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (484 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.47
# Mc/sec: 3127.30
//
Query:       gi|474934461|ref|YP_007688043.1|  [L=185]
Description: hypothetical protein TALC_00888 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.3e-16   57.9  16.8    1.5e-11   44.2   6.7    1.8  2  DZR             Double zinc ribbon
    1.9e-13   49.7  15.3    2.6e-07   30.1   4.2    2.4  2  zinc_ribbon_2   zinc-ribbon domain
    9.8e-08   31.2  12.0    0.00085   18.6   3.7    2.4  2  zf-ribbon_3     zinc-ribbon domain
    2.6e-05   24.9  10.8      0.011   16.5   1.0    2.6  2  zinc_ribbon_15  zinc-ribbon family
     0.0027   17.6   9.6        0.2   11.6   0.1    4.2  4  Nudix_N_2       Nudix N-terminal
  ------ inclusion threshold ------
      0.015   14.9   8.6        2.1    8.0   0.1    3.9  4  zf_UBZ          Ubiquitin-Binding Zinc Finger
      0.016   15.1   6.6       0.76    9.8   6.7    2.4  1  zinc-ribbons_6  zinc-ribbons
      0.018   15.1   8.5       0.89    9.7   4.5    3.3  2  Zn-ribbon_8     Zinc ribbon domain
      0.026   13.8   1.5      0.061   12.6   1.5    1.6  1  zf-RanBP        Zn-finger in Ran binding protein and others
      0.087   12.7   5.1        0.6   10.0   0.2    2.4  2  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
       0.14   12.0   2.4        8.8    6.2   0.1    2.1  2  Armet           Degradation arginine-rich protein for mis-fol
       0.29   10.9  14.3        1.3    8.7   0.2    3.8  4  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
       0.29   11.1   8.3        7.8    6.5   2.1    3.0  3  Prok-RING_1     Prokaryotic RING finger family 1
       0.32    9.7   1.8       0.34    9.6   1.2    1.4  1  tRNA-synt_1g    tRNA synthetases class I (M)
       0.32   10.6   6.8        1.2    8.8   2.2    2.1  2  DUF2321         Uncharacterized protein conserved in bacteria
       0.33   11.0   4.2       0.41   10.7   3.4    1.6  1  TerY_C          TerY-C metal binding domain
       0.36   11.0   6.7        1.8    8.8   1.5    3.4  2  Ribosomal_S27   Ribosomal protein S27a
       0.43   11.1   6.4        2.4    8.7   3.9    2.2  2  zf-CHY          CHY zinc finger
       0.61    9.5   5.6       0.98    8.8   0.9    2.0  2  NMD3            NMD3 family
       0.69    9.9   5.9         46    4.1   0.0    3.4  3  Ogr_Delta       Ogr/Delta-like zinc finger
       0.75   10.5   5.7        6.9    7.4   1.1    2.2  2  zinc-ribbon_6   zinc-ribbon domain
       0.79    9.8   8.5       0.95    9.5   1.3    2.2  2  HypA            Hydrogenase/urease nickel incorporation, meta
        1.1    8.9  10.6        2.2    7.9   0.3    3.2  3  TF_Zn_Ribbon    TFIIB zinc-binding
        1.2    9.2  13.2        4.1    7.5   3.4    3.6  2  ADK_lid         Adenylate kinase, active site lid
        1.3    9.3  10.6         17    5.7   0.4    3.5  3  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
        1.7    9.0   6.9        5.7    7.3   0.4    2.7  2  C1_2            C1 domain
        3.7    7.2   8.7        7.5    6.2   1.4    3.3  4  zf_C2H2_13      Zinc finger domain
        4.3    7.3   7.9       0.46   10.4   1.1    2.3  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
        6.1    7.3   7.4         25    5.4   0.1    3.3  3  zf-IS66         zinc-finger binding domain of transposase IS6
        8.6    6.4  16.0        8.6    6.4   0.3    3.6  4  YhfH            YhfH-like protein


Domain annotation for each model (and alignments):
>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   6.7   2.4e-14   1.5e-11       1      49 []       5      68 ..       5      68 .. 0.97
   2 !   26.1   2.4     1e-08   6.2e-06       1      23 [.      50      72 ..      50     124 .. 0.80

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 2.4e-14
                               DZR  1 CpqCgeelppdarfCseCgtklkavaa...............edrCpsCgekvdpearfCpeCG 49
                                      C +Cg+e++++a fC+ Cg+++k++ +               ++ Cp+Cg+++ +e +fC++CG
  gi|474934461|ref|YP_007688043.1|  5 CGECGNEIEDGADFCYFCGATIKSAYSvddsgaihnlsenpdSNLCPRCGAENAKENKFCDQCG 68
                                      99********************98777************************************9 PP

  == domain 2  score: 26.1 bits;  conditional E-value: 1e-08
                               DZR  1 CpqCgeelppdarfCseCgtklk 23
                                      Cp+Cg+e+ ++++fC++Cg++++
  gi|474934461|ref|YP_007688043.1| 50 CPRCGAENAKENKFCDQCGAPMD 72
                                      *********************86 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   3.3   1.6e-08   9.5e-06       2      21 ..       5      24 ..       4      26 .. 0.94
   2 !   30.1   4.2   4.4e-10   2.6e-07       2      22 ..      50      70 ..      49      71 .. 0.97

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.6e-08
                     zinc_ribbon_2  2 CpnCGaelqdnakFCpyCGt 21
                                      C +CG+e++d+a FC  CG+
  gi|474934461|ref|YP_007688043.1|  5 CGECGNEIEDGADFCYFCGA 24
                                      99*****************8 PP

  == domain 2  score: 30.1 bits;  conditional E-value: 4.4e-10
                     zinc_ribbon_2  2 CpnCGaelqdnakFCpyCGtp 22
                                      Cp+CGae+ +++kFC +CG+p
  gi|474934461|ref|YP_007688043.1| 50 CPRCGAENAKENKFCDQCGAP 70
                                      ********************9 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   1.2   3.7e-06    0.0022       4      24 ..       4      24 ..       2      26 .. 0.89
   2 !   18.6   3.7   1.4e-06   0.00085       5      25 ..      50      70 ..      48      71 .. 0.96

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.7e-06
                       zf-ribbon_3  4 rCPnCGa.plssddnvCpyCGt 24
                                       C +CG+ + ++++ +C+ CG+
  gi|474934461|ref|YP_007688043.1|  4 ICGECGNeI-EDGADFCYFCGA 24
                                      6999***77.***********7 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 1.4e-06
                       zf-ribbon_3  5 CPnCGa.plssddnvCpyCGtk 25
                                      CP+CGa + +++ ++C  CG++
  gi|474934461|ref|YP_007688043.1| 50 CPRCGAeN-AKENKFCDQCGAP 70
                                      ********.***********98 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   2.4    0.0002      0.12      66      86 .]       3      23 ..       2      23 .. 0.95
   2 !   16.5   1.0   1.8e-05     0.011      59      86 .]      41      68 ..      26      68 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.0002
                    zinc_ribbon_15 66 keCknCgkeveeefkyCpkCg 86
                                      ++C +Cg+e+e+  ++C +Cg
  gi|474934461|ref|YP_007688043.1|  3 RICGECGNEIEDGADFCYFCG 23
                                      68******************9 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.8e-05
                    zinc_ribbon_15 59 kkessekkeCknCgkeveeefkyCpkCg 86
                                       +e+ +++ C++Cg+e  +e+k+C +Cg
  gi|474934461|ref|YP_007688043.1| 41 LSENPDSNLCPRCGAENAKENKFCDQCG 68
                                      34556699*******************9 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.2      0.15        87      22      29 ..       2       9 ..       1      13 [. 0.76
   2 ?    3.8   0.1     0.093        56       2      16 ..      18      32 ..      17      36 .. 0.78
   3 ?    2.8   0.2      0.19   1.2e+02       3       9 ..      50      56 ..      48      60 .. 0.73
   4 !   11.6   0.1   0.00034       0.2       1      11 [.      62      72 ..      62      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.15
                                      EEEETTTT CS
                         Nudix_N_2 22 RlvCpaCg 29
                                      R +C  Cg
  gi|474934461|ref|YP_007688043.1|  2 RRICGECG 9 
                                      77888887 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.093
                                      B-TTT--B-EEE--T CS
                         Nudix_N_2  2 FCsqCGtpvelripd 16
                                      FC  CG++++ +   
  gi|474934461|ref|YP_007688043.1| 18 FCYFCGATIKSAYSV 32
                                      9******99866555 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.19
                                      -TTT--B CS
                         Nudix_N_2  3 CsqCGtp 9 
                                      C+ CG++
  gi|474934461|ref|YP_007688043.1| 50 CPRCGAE 56
                                      7888865 PP

  == domain 4  score: 11.6 bits;  conditional E-value: 0.00034
                                      -B-TTT--B-E CS
                         Nudix_N_2  1 kFCsqCGtpve 11
                                      kFC qCG+p+ 
  gi|474934461|ref|YP_007688043.1| 62 KFCDQCGAPMD 72
                                      9*******985 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.2     0.063        38       4      14 ..       4      14 ..       2      18 .. 0.86
   2 ?   -0.6   0.0       1.7     1e+03       4      14 ..      18      28 ..      15      32 .. 0.81
   3 ?    6.0   0.1     0.015       8.7       1      10 [.      46      55 ..      46      58 .. 0.83
   4 ?    8.0   0.1    0.0036       2.1       2      15 ..      61      74 ..      60      76 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.063
                            zf_UBZ  4 lCerCgkeipe 14
                                      +C +Cg ei++
  gi|474934461|ref|YP_007688043.1|  4 ICGECGNEIED 14
                                      7*******986 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.7
                            zf_UBZ  4 lCerCgkeipe 14
                                      +C  Cg++i +
  gi|474934461|ref|YP_007688043.1| 18 FCYFCGATIKS 28
                                      68889999976 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.015
                            zf_UBZ  1 dtylCerCgk 10
                                      d+ lC+rCg+
  gi|474934461|ref|YP_007688043.1| 46 DSNLCPRCGA 55
                                      5679****97 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.0036
                            zf_UBZ  2 tylCerCgkeipes 15
                                      + +C++Cg+++ ++
  gi|474934461|ref|YP_007688043.1| 61 NKFCDQCGAPMDVT 74
                                      689******99875 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   6.7    0.0013      0.76       3      43 ..       5      75 ..       3      78 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0013
                                      -SSS-S--EE-S.............................SEEE-TTT--.EEEEEEE-SSS-S---EEE CS
                    zinc-ribbons_6  3 CpeCqqelekrg.............................eqyhCeaCqe.dlkkealCpeCeqelevlk 43
                                      C eC +e+e                                ++  C  C + + k++++C++C+ +++v +
  gi|474934461|ref|YP_007688043.1|  5 CGECGNEIEDGAdfcyfcgatiksaysvddsgaihnlsenpDSNLCPRCGAeNAKENKFCDQCGAPMDVTR 75
                                      666666666444456666666666666777777777777778999****985788899********99875 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   4.5    0.0015      0.89      16      37 ..      19      59 ..       3      60 .. 0.71
   2 ?    4.3   0.2     0.071        43      26      37 ..      60      74 ..      55      77 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0015
                       Zn-ribbon_8 16 e.................vlqsisdaplta.CPeCgs.evr 37
                                                        +++  s++p+   CP+Cg+ +++
  gi|474934461|ref|YP_007688043.1| 19 CyfcgatiksaysvddsgAIHNLSENPDSNlCPRCGAeNAK 59
                                      0444444448888888889999999999999*****97765 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.071
                       Zn-ribbon_8 26 lta.CPeCgs..evr 37
                                      + + C +Cg+  +v+
  gi|474934461|ref|YP_007688043.1| 60 ENKfCDQCGApmDVT 74
                                      556688888855555 PP

>> zf-RanBP  Zn-finger in Ran binding protein and others
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.5    0.0001     0.061       7      27 ..      50      70 ..      49      71 .. 0.97

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0001
                                      -SSS--EEESSSSB-TTT--B CS
                          zf-RanBP  7 CskClvqNfawstkCvaCqap 27
                                      C+ C++ N  ++  C +C+ap
  gi|474934461|ref|YP_007688043.1| 50 CPRCGAENAKENKFCDQCGAP 70
                                      ********************8 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.2     0.001       0.6      25      49 ..       4      28 ..       2      29 .. 0.93
   2 ?    4.5   0.8     0.054        32      25      47 ..      49      71 ..      46      74 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.001
                                      E-HHHHHHHHHTT-B-TTT--B--E CS
                        zf-C3HC4_3 25 lCeeCaekllkrkkkCpiCrrpiek 49
                                      +C eC +++++  + C +C + i++
  gi|474934461|ref|YP_007688043.1|  4 ICGECGNEIEDGADFCYFCGATIKS 28
                                      7********99**********9986 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.054
                                      E-HHHHHHHHHTT-B-TTT--B- CS
                        zf-C3HC4_3 25 lCeeCaekllkrkkkCpiCrrpi 47
                                      lC +C  +  k++k C  C +p+
  gi|474934461|ref|YP_007688043.1| 49 LCPRCGAENAKENKFCDQCGAPM 71
                                      79999999999999999999887 PP

>> Armet  Degradation arginine-rich protein for mis-folding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.5     0.017        10      33      59 ..       6      32 ..       1      50 [. 0.79
   2 ?    6.2   0.1     0.015       8.8      28      57 ..      46      75 ..      36      87 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.017
                             Armet 33 kvCkeakgkenrlCyylgaledaatki 59
                                        C +  ++ + +Cy+ ga+ ++a ++
  gi|474934461|ref|YP_007688043.1|  6 GECGNEIEDGADFCYFCGATIKSAYSV 32
                                      567778888999*********999877 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.015
                             Armet 28 ekelkkvCkeakgkenrlCyylgaledaat 57
                                      +++l   C + + ken++C   ga  d + 
  gi|474934461|ref|YP_007688043.1| 46 DSNLCPRCGAENAKENKFCDQCGAPMDVTR 75
                                      6788899************99999888765 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.2      0.13        78      22      29 ..       3      10 ..       2      13 .. 0.56
   2 ?   -2.3   0.6       6.2   3.7e+03       8      11 ..      21      24 ..      18      28 .. 0.63
   3 ?    8.7   0.2    0.0022       1.3       5      14 ..      49      58 ..      46      60 .. 0.80
   4 ?    8.3   0.1    0.0029       1.8       3      15 ..      61      73 ..      59      75 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.13
                     zf-NADH-PPase 22 rvCpaCgl 29
                                      r C  Cg+
  gi|474934461|ref|YP_007688043.1|  3 RICGECGN 10
                                      44555555 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6.2
                     zf-NADH-PPase  8 rCGa 11
                                       CGa
  gi|474934461|ref|YP_007688043.1| 21 FCGA 24
                                      5665 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0022
                     zf-NADH-PPase  5 FCgrCGapte 14
                                       C+rCGa+++
  gi|474934461|ref|YP_007688043.1| 49 LCPRCGAENA 58
                                      6******976 PP

  == domain 4  score: 8.3 bits;  conditional E-value: 0.0029
                     zf-NADH-PPase  3 hrFCgrCGaptep 15
                                      ++FC +CGap+ +
  gi|474934461|ref|YP_007688043.1| 61 NKFCDQCGAPMDV 73
                                      78********976 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.6     0.014       8.3       5      28 ..       3      24 ..       1      31 [. 0.87
   2 ?    4.7   0.1     0.047        28      14      29 ..      41      56 ..      38      61 .. 0.78
   3 ?    6.5   2.1     0.013       7.8       5      29 ..      48      70 ..      44      76 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.014
                       Prok-RING_1  5 kkCpvCgkelkeedDiVvCpeCgt 28
                                       +C  Cg+e++++ D   C  Cg+
  gi|474934461|ref|YP_007688043.1|  3 RICGECGNEIEDGAD--FCYFCGA 24
                                      5799*********99..6999997 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.047
                       Prok-RING_1 14 lkeedDiVvCpeCgtp 29
                                      l+e+ D   Cp Cg+ 
  gi|474934461|ref|YP_007688043.1| 41 LSENPDSNLCPRCGAE 56
                                      667778889****985 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.013
                       Prok-RING_1  5 kkCpvCgkelkeedDiVvCpeCgtp 29
                                      + Cp Cg e ++e+    C++Cg+p
  gi|474934461|ref|YP_007688043.1| 48 NLCPRCGAENAKEN--KFCDQCGAP 70
                                      67999*99999885..58*****99 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.2   0.00057      0.34     129     162 ..      40      74 ..      16      91 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00057
                                       EE-GGG-EE........-TTS-E.E-TTSSB-E.. CS
                      tRNA-synt_1g 129 flpdryvegtCPkckseeargdq.ceecgkklept 162
                                        l++   +  CP c++e+a++++ c++cg+ ++ t
  gi|474934461|ref|YP_007688043.1|  40 NLSENPDSNLCPRCGAENAKENKfCDQCGAPMDVT 74 
                                       4555555678*********998846*****98855 PP

>> DUF2321  Uncharacterized protein conserved in bacteria (DUF2321)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   2.2     0.002       1.2      26      74 ..       2      55 ..       1      57 [. 0.79
   2 ?    4.7   0.2     0.036        21      24      35 ..      59      70 ..      54      81 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.002
                           DUF2321 26 eeyCekcGekt...itkcpkCsteirGkyyvegvislgk..eyevpsyCkkCgk 74
                                      +  C +cG+++    + c  C++ i+ +y v+++  + +  e +  + C +Cg 
  gi|474934461|ref|YP_007688043.1|  2 RRICGECGNEIedgADFCYFCGATIKSAYSVDDSGAIHNlsENPDSNLCPRCGA 55
                                      567*****987333567999*************999987435556679****96 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.036
                           DUF2321 24 lveeyCekcGek 35
                                      + +++C++cG+ 
  gi|474934461|ref|YP_007688043.1| 59 KENKFCDQCGAP 70
                                      345677777765 PP

>> TerY_C  TerY-C metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   3.4   0.00069      0.41      73     116 ..      15      61 ..       8      77 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00069
                            TerY_C  73 GapgCPhCgnal..afavCeCgkllCidg.eeeatCpwCgkevkfge 116
                                       Ga  C +Cg+++  a +v + g ++ +++ ++++ Cp+Cg e + ++
  gi|474934461|ref|YP_007688043.1|  15 GADFCYFCGATIksAYSVDDSGAIHNLSEnPDSNLCPRCGAENAKEN 61 
                                       8899*****9753388899*******98858999*****98865544 PP

>> Ribosomal_S27  Ribosomal protein S27a
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.3      0.34     2e+02      36      43 ..       2       9 ..       1      11 [. 0.83
   2 ?    8.8   1.5     0.003       1.8       5      43 ..      30      68 ..      26      70 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.34
                                      EEEESSTT CS
                     Ribosomal_S27 36 RkyCGkCg 43
                                      R+ CG Cg
  gi|474934461|ref|YP_007688043.1|  2 RRICGECG 9 
                                      88999998 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.003
                                      CCESSSSSEEESS-B.....-SS-S-TTSBEEECTTEEEESSTT CS
                     Ribosomal_S27  5 Ykvddsgkverlrke.....CpreCGaGvfMAehkdRkyCGkCg 43
                                      Y+vddsg ++ l ++     Cpr CGa+    + k+ k C +Cg
  gi|474934461|ref|YP_007688043.1| 30 YSVDDSGAIHNLSENpdsnlCPR-CGAE----NAKENKFCDQCG 68
                                      9**********987655555888.8886....556666666665 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.9      0.16        93      56      73 ..       4      23 ..       1      32 [. 0.66
   2 ?    8.7   3.9     0.004       2.4      22      65 ..      19      74 ..      18      82 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.16
                            zf-CHY 56 lCkkCkkefaey..fCpiCk 73
                                      +C++C++e+++   fC  C 
  gi|474934461|ref|YP_007688043.1|  4 ICGECGNEIEDGadFCYFCG 23
                                      68888885554433577775 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.004
                            zf-CHY 22 CreCH..........eeledhelerlevkevlcllCeteq.ekavlCkkCkk..efa 65
                                      C+ C           ++ + h+l++   ++ lc +C +e+ ++++ C +C+   +++
  gi|474934461|ref|YP_007688043.1| 19 CYFCGatiksaysvdDSGAIHNLSENPDSN-LCPRCGAENaKENKFCDQCGApmDVT 74
                                      666666666666665455678887777775.59999988856677899998844444 PP

>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.3      0.11        66       1      21 [.       5      24 ..       5      40 .. 0.79
   2 ?    8.8   0.9    0.0016      0.98       1      19 [.      50      67 ..      50      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.11
                              NMD3  1 CcrCGkeieelinglCedCll 21
                                      C +CG+eie+   ++C  C +
  gi|474934461|ref|YP_007688043.1|  5 CGECGNEIEDG-ADFCYFCGA 24
                                      899*****866.779999965 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0016
                              NMD3  1 CcrCGkeieelinglCedC 19
                                      C+rCG+e    +n++C++C
  gi|474934461|ref|YP_007688043.1| 50 CPRCGAENA-KENKFCDQC 67
                                      ********7.55******* PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.4       0.1        63      27      44 ..       7      33 ..       1      35 [. 0.78
   2 ?    3.4   0.2      0.13        78       2      10 ..      50      58 ..      49      62 .. 0.81
   3 ?    4.1   0.0     0.077        46       2      12 ..      64      74 ..      63      79 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.1
                         Ogr_Delta 27 qCsnf.e........Cgatfvaaeeie 44
                                      +C n  e        Cgat+++a ++ 
  gi|474934461|ref|YP_007688043.1|  7 ECGNEiEdgadfcyfCGATIKSAYSVD 33
                                      688877788888888*****9998876 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.13
                         Ogr_Delta  2 CPhCgapaa 10
                                      CP Cga+ a
  gi|474934461|ref|YP_007688043.1| 50 CPRCGAENA 58
                                      *****9755 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.077
                         Ogr_Delta  2 CPhCgapaaar 12
                                      C +Cgap+ ++
  gi|474934461|ref|YP_007688043.1| 64 CDQCGAPMDVT 74
                                      99******875 PP

>> zinc-ribbon_6  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.2     0.048        28       4      30 ..       5      33 ..       3      49 .. 0.76
   2 ?    7.4   1.1     0.012       6.9       4      25 ..      50      71 ..      47      78 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.048
                     zinc-ribbon_6  4 CeqCgqllffenssClkCgaal..gfape 30
                                      C +Cg+++      C  Cga++  +++ +
  gi|474934461|ref|YP_007688043.1|  5 CGECGNEIEDGADFCYFCGATIksAYSVD 33
                                      9******************9874456554 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.012
                     zinc-ribbon_6  4 CeqCgqllffenssClkCgaal 25
                                      C +Cg +   en+ C +Cga +
  gi|474934461|ref|YP_007688043.1| 50 CPRCGAENAKENKFCDQCGAPM 71
                                      ******************9865 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.9     0.057        34      72      95 ..       4      25 ..       1      34 [. 0.79
   2 ?    9.5   1.3    0.0016      0.95      64      95 ..      41      70 ..      31      79 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.057
                                      EETTTS-EEECHHHHHS-TTTSSS CS
                              HypA 72 rCreCgkefeleekalrCpkCgsa 95
                                       C eCg+e+e  ++   C  Cg++
  gi|474934461|ref|YP_007688043.1|  4 ICGECGNEIEDGAD--FCYFCGAT 25
                                      7********96645..59999985 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0016
                                      EEEE--EEEETTTS-EEECHHHHHS-TTTSSS CS
                              HypA 64 ieevpvkvrCreCgkefeleekalrCpkCgsa 95
                                      ++e p +  C +Cg+e  +e+k   C +Cg+ 
  gi|474934461|ref|YP_007688043.1| 41 LSENPDSNLCPRCGAENAKENK--FCDQCGAP 70
                                      567788899*****99987755..6****986 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.3    0.0036       2.2      21      31 ..       4      14 ..       2      16 .. 0.91
   2 ?   -0.9   0.0         2   1.2e+03      22      29 ..      19      26 ..      18      34 .. 0.76
   3 ?    4.7   2.5     0.035        21       3      27 ..      50      69 ..      48      77 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0036
                                      EESSSSBEEEE CS
                      TF_Zn_Ribbon 21 vCtdCGlVled 31
                                      +C++CG+ +ed
  gi|474934461|ref|YP_007688043.1|  4 ICGECGNEIED 14
                                      8*********9 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2
                                      ESSSSBEE CS
                      TF_Zn_Ribbon 22 CtdCGlVl 29
                                      C +CG+ +
  gi|474934461|ref|YP_007688043.1| 19 CYFCGATI 26
                                      88888755 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.035
                                      ETTTTCEECHEETSTTCEEESSSSB CS
                      TF_Zn_Ribbon  3 CPnCgstnlveDpergelvCtdCGl 27
                                      CP Cg +n     +  + +C  CG+
  gi|474934461|ref|YP_007688043.1| 50 CPRCGAEN-----AKENKFCDQCGA 69
                                      9****864.....556668999996 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.6     0.084        50       1       8 [.       2       9 ..       2      11 .. 0.91
   2 ?    7.5   3.4    0.0068       4.1      17      30 ..      57      70 ..      32      74 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.084
                                     EEE-TTT- CS
                           ADK_lid 1 RrvCpkCG 8
                                     Rr+C  CG
  gi|474934461|ref|YP_007688043.1| 2 RRICGECG 9
                                     9******9 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0068
                                      --SSTTB-TTT--. CS
                           ADK_lid 17 pPkveglCDkCGep 30
                                        k++ +CD CG p
  gi|474934461|ref|YP_007688043.1| 57 NAKENKFCDQCGAP 70
                                      3479********98 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.4     0.028        17      11      48 ..       5      39 ..       1      49 [. 0.73
   2 ?    3.1   0.1      0.18   1.1e+02      20      32 ..      44      56 ..      37      59 .. 0.77
   3 ?    4.7   3.6     0.058        35      19      32 ..      57      70 ..      49      88 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.028
                      NOB1_Zn_bind 11 ChaCfkvtkdmtkkFCpkCGnktLkrvavsvdengelk 48
                                      C  C + ++d    FC  CG     + a+svd++g ++
  gi|474934461|ref|YP_007688043.1|  5 CGECGNEIEDG-ADFCYFCGAT--IKSAYSVDDSGAIH 39
                                      77777766664.58*****975..58899999998876 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.18
                      NOB1_Zn_bind 20 dmtkkFCpkCGnk 32
                                      + + + Cp+CG +
  gi|474934461|ref|YP_007688043.1| 44 NPDSNLCPRCGAE 56
                                      567788*****86 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.058
                      NOB1_Zn_bind 19 kdmtkkFCpkCGnk 32
                                      + ++ kFC++CG +
  gi|474934461|ref|YP_007688043.1| 57 NAKENKFCDQCGAP 70
                                      446789******84 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   1.4       0.1        60      21      35 ..       5      22 ..       1      34 [. 0.69
   2 ?    7.3   0.4    0.0095       5.7      11      33 ..      54      76 ..      38      77 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.1
                              C1_2 21 CsaCgrk...idgffYsC 35
                                      C  Cg++   + +f+Y C
  gi|474934461|ref|YP_007688043.1|  5 CGECGNEiedGADFCYFC 22
                                      777888865555666888 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0095
                              C1_2 11 kgedssesfnCsaCgrkidgffY 33
                                        e+ +e++ C+ Cg ++d ++Y
  gi|474934461|ref|YP_007688043.1| 54 GAENAKENKFCDQCGAPMDVTRY 76
                                      56789999*******99887777 PP

>> zf_C2H2_13  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.5     0.087        52      18      25 ..       3      10 ..       2      14 .. 0.87
   2 ?   -1.9   0.0       4.2   2.5e+03      20      29 ..      19      28 ..      18      33 .. 0.76
   3 ?   -1.4   0.2         3   1.8e+03      19      24 ..      49      54 ..      40      58 .. 0.82
   4 ?    6.2   1.4     0.013       7.5      18      29 ..      62      73 ..      44      77 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.087
                        zf_C2H2_13 18 RvCnkCGk 25
                                      R+C +CG 
  gi|474934461|ref|YP_007688043.1|  3 RICGECGN 10
                                      9******7 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.2
                        zf_C2H2_13 20 CnkCGkPisl 29
                                      C  CG  i++
  gi|474934461|ref|YP_007688043.1| 19 CYFCGATIKS 28
                                      888**98876 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 3
                        zf_C2H2_13 19 vCnkCG 24
                                      +C  CG
  gi|474934461|ref|YP_007688043.1| 49 LCPRCG 54
                                      7999*9 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.013
                        zf_C2H2_13 18 RvCnkCGkPisl 29
                                        C++CG P+ +
  gi|474934461|ref|YP_007688043.1| 62 KFCDQCGAPMDV 73
                                      67*******976 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.9       1.1   6.6e+02      30      40 ..       4      14 ..       3      35 .. 0.66
   2 ?   10.4   1.1   0.00077      0.46      27      56 ..      46      71 ..      36      73 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.1
                    OrfB_Zn_ribbon 30 tCseCgsknke 40
                                       C eCg + ++
  gi|474934461|ref|YP_007688043.1|  4 ICGECGNEIED 14
                                      58888887776 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00077
                    OrfB_Zn_ribbon 27 TSktCseCgsknkealsgrtfkCpnCgfea 56
                                       S  C++Cg++n +    ++  C++Cg+ +
  gi|474934461|ref|YP_007688043.1| 46 DSNLCPRCGAENAK----ENKFCDQCGAPM 71
                                      6999*******999....7788****9866 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.2      0.41   2.4e+02       2      10 ..       3      11 ..       2      17 .. 0.81
   2 ?    3.0   0.3      0.23   1.4e+02       4      10 ..      50      56 ..      47      63 .. 0.77
   3 ?    5.4   0.1     0.041        25       2      20 ..      62      80 ..      61      95 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.41
                           zf-IS66  2 rtCpcCGgl 10
                                      r+C +CG +
  gi|474934461|ref|YP_007688043.1|  3 RICGECGNE 11
                                      68****985 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.23
                           zf-IS66  4 CpcCGgl 10
                                      Cp CG++
  gi|474934461|ref|YP_007688043.1| 50 CPRCGAE 56
                                      9***985 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.041
                           zf-IS66  2 rtCpcCGgllkpigedrvr 20
                                      + C++CG++++    + vr
  gi|474934461|ref|YP_007688043.1| 62 KFCDQCGAPMDVTRYVTVR 80
                                      57******98777666665 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   4.8     0.046        28      16      31 ..       5      21 ..       2      23 .. 0.86
   2 ?   -1.1   0.1       3.4     2e+03      16      23 ..      19      26 ..      18      28 .. 0.82
   3 ?    1.3   0.3       0.6   3.6e+02      16      22 ..      50      56 ..      40      60 .. 0.84
   4 ?    6.4   0.3     0.014       8.6      13      24 ..      61      72 ..      58      74 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.046
                              YhfH 16 CteCGkeieEqae.cYg 31
                                      C eCG+eie+ a+ cY+
  gi|474934461|ref|YP_007688043.1|  5 CGECGNEIEDGADfCYF 21
                                      *********99887775 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 3.4
                              YhfH 16 CteCGkei 23
                                      C  CG  i
  gi|474934461|ref|YP_007688043.1| 19 CYFCGATI 26
                                      889**988 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.6
                              YhfH 16 CteCGke 22
                                      C+ CG e
  gi|474934461|ref|YP_007688043.1| 50 CPRCGAE 56
                                      99**975 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.014
                              YhfH 13 kKkCteCGkeie 24
                                      +K C +CG  ++
  gi|474934461|ref|YP_007688043.1| 61 NKFCDQCGAPMD 72
                                      799*****9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       780  (0.0435049); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                        42  (0.00234257); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.51
# Mc/sec: 1098.63
//
Query:       gi|474934462|ref|YP_007688044.1|  [L=265]
Description: ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-24   85.1   0.0    7.9e-24   84.7   0.0    1.2  1  ABC_tran  ABC transporter
      1e-10   41.9   0.1    0.00041   20.3   0.1    2.1  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
     0.0031   17.8   0.0     0.0098   16.2   0.0    1.8  1  AAA_22    AAA domain
     0.0063   16.2   0.1      0.013   15.2   0.1    1.5  1  AAA_29    P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.011   16.2   0.1      0.017   15.6   0.1    1.2  1  AAA_23    AAA domain
      0.015   12.9   0.3      0.018   12.6   0.3    1.0  1  DUF3584   Protein of unknown function (DUF3584)
      0.018   14.8   0.0      0.028   14.1   0.0    1.3  1  AAA_30    AAA domain
      0.019   15.1   0.0       0.28   11.3   0.0    2.1  2  AAA_33    AAA domain
      0.073   12.8   0.5       0.13   12.0   0.5    1.3  1  AAA_15    AAA ATPase domain
      0.085   13.2   0.0       0.15   12.4   0.0    1.3  1  AAA_16    AAA ATPase domain
       0.09   13.3   0.0       0.17   12.5   0.0    1.5  1  AAA_18    AAA domain
       0.12   11.8   0.3       0.51    9.7   0.1    1.9  2  SMC_N     RecF/RecN/SMC N terminal domain
       0.15   12.3   0.0       0.24   11.6   0.0    1.3  1  AAA_28    AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.7   0.0   5.7e-27   7.9e-24       1     136 [.      20     174 ..      20     175 .. 0.92

  Alignments for each domain:
  == domain 1  score: 84.7 bits;  conditional E-value: 5.7e-27
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG..B-HHHCCHCEEEE-SS.--S-TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx.xxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke..qeleslrkeigvlpqe.pqlfpel 74 
                                       l+ ++l++  ge vai+G nG+GK+tLlkll g   p  ++  + ++ + e   ++  lr+++gv++ + ++lf+e+
  gi|474934462|ref|YP_007688044.1|  20 LDGIDLDIGVGENVAIIGLNGSGKTTLLKLLRGDIYPYDDDAGYSMRVFGEkrWSIWDLRSKMGVVSMDlQSLFNEH 96 
                                       6899**************************************99999988877889999**********98888888 PP

                                       B.HHHH...................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEE CS
                                       x.xxxx...................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  75 t.vren...................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpklll 131
                                       t vre                    +++e i   +s++g+++l ++ +      LS G+ +r  +aral+++p++l+
  gi|474934462|ref|YP_007688044.1|  97 TtVREVigsgffgsldifrnvtvteKMEELILCRASEMGIEDLMHREI----GGLSLGEMRRTLIARALITNPRMLI 169
                                       879999**************9887555555777889999999999999....************************* PP

                                       EESTT CS
                                       xxxxx RF
                          ABC_tran 132 lDEpt 136
                                       lDEp+
  gi|474934462|ref|YP_007688044.1| 170 LDEPM 174
                                       ****7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   3.3e-07   0.00046       3      21 ..      34      52 ..      33     105 .. 0.72
   2 !   20.3   0.1     3e-07   0.00041     234     299 ..     144     206 ..     110     209 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3.3e-07
                            AAA_21  3 vliGpNgsGKSnLLdaldl 21
                                      ++iG NgsGK++LL++l++
  gi|474934462|ref|YP_007688044.1| 34 AIIGLNGSGKTTLLKLLRG 52
                                      79***************65 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 3e-07
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSp 299
                                       +  lS G  r   l++  l +++  + l++DEp +gL+  + +++ +++++l+ +g+ +++ TH+ 
  gi|474934462|ref|YP_007688044.1| 144 IGGLSLGEMRR-TLIARALITNP--RMLILDEPMTGLDIVMKSKFRQMFDILTGTGVSIVMITHDL 206
                                       66789999999.99999999998..9**************************************96 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   7.1e-06    0.0098       8     128 ..      33     202 ..      29     209 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.1e-06
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee...................erpevvfvtlpsst.sskdllrellral 64 
                                       ++++G  G+GKTtll+ l+     +++ ++                    + +vv+++l+s+  + +++++ + + +
  gi|474934462|ref|YP_007688044.1|  33 VAIIGLNGSGKTTLLKLLRGDI--YPYDDDagysmrvfgekrwsiwdlrSKMGVVSMDLQSLFnEHTTVREVIGSGF 107
                                       689***************9875..5555556699999*999999999999999999999999988888899999999 PP

                            AAA_22  65 glelka...............................erlsseellealeqalraravielliiDEaqh.lrseeal 109
                                         +l+                                 +ls+ e++++l   +  +   ++li+DE    l    + 
  gi|474934462|ref|YP_007688044.1| 108 FGSLDIfrnvtvtekmeelilcrasemgiedlmhreiGGLSLGEMRRTLIARALITNP-RMLILDEPMTgL-DIVMK 182
                                       9888888889999999999999998888888888888888888888444444444444.599999966667.66666 PP

                            AAA_22 110 eeLrsllnl.srkgvqliLv 128
                                       +++r+++++   +gv+++++
  gi|474934462|ref|YP_007688044.1| 183 SKFRQMFDIlTGTGVSIVMI 202
                                       66666666666666666554 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   9.5e-06     0.013      15      39 ..      23      47 ..      18      51 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 9.5e-06
                            AAA_29 15 htieidlkgatlltGpsGsGKSTll 39
                                       +++i + +++ ++G +GsGK+Tll
  gi|474934462|ref|YP_007688044.1| 23 IDLDIGVGENVAIIGLNGSGKTTLL 47
                                      5677777779**************8 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.1   1.2e-05     0.017      22      39 ..      33      50 ..      15      58 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.2e-05
                            AAA_23 22 tlItGpNGaGKTTildAi 39
                                      ++I+G NG+GKTT+l  +
  gi|474934462|ref|YP_007688044.1| 33 VAIIGLNGSGKTTLLKLL 50
                                      48************9876 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.3   1.3e-05     0.018      15      37 ..      28      50 ..      20      51 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.3e-05
                           DUF3584 15 dldghtnieGtNaaGKTtLlrLi 37
                                       + + + i G N++GKTtLl+L+
  gi|474934462|ref|YP_007688044.1| 28 GVGENVAIIGLNGSGKTTLLKLL 50
                                      5678999**************97 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0     2e-05     0.028      21      96 ..      33     172 ..      28     205 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2e-05
                            AAA_30  21 avltGpAGtGKttalkalreaw....eaaggrviglAptgkaAkvLaeelgieastiakllkrlk............ 81 
                                       +++ G  G+GKtt+lk lr  +    ++ag+++ ++  +     +L+ ++g+ ++ +++l ++++            
  gi|474934462|ref|YP_007688044.1|  33 VAIIGLNGSGKTTLLKLLRGDIypydDDAGYSMRVFGEKRWSIWDLRSKMGVVSMDLQSLFNEHTtvrevigsgffg 109
                                       5789**************753312214448*******************************9999888888888888 PP

                            AAA_30  82 ................................................grarlepgtllivDE 96 
                                                                                       +ra +++ ++li DE
  gi|474934462|ref|YP_007688044.1| 110 sldifrnvtvtekmeelilcrasemgiedlmhreigglslgemrrtliARALITNPRMLILDE 172
                                       887777777777777666666666666666666666666666666666555556666666666 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0002      0.28       3      18 ..      34      49 ..      33      97 .. 0.86
   2 ?    1.7   0.0       0.2   2.7e+02      62     103 ..     157     203 ..     146     213 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0002
                            AAA_33  3 llvGlpGsGKstlaer 18
                                       ++Gl+GsGK+tl++ 
  gi|474934462|ref|YP_007688044.1| 34 AIIGLNGSGKTTLLKL 49
                                      689**********985 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.2
                            AAA_33  62 larkalsagrnvildat.....nlsrrerarflklarrlgvpvrivv 103
                                       +ar   +  r +ild +      ++++++++++ ++   gv + +++
  gi|474934462|ref|YP_007688044.1| 157 IARALITNPRMLILDEPmtgldIVMKSKFRQMFDILTGTGVSIVMIT 203
                                       45566688889999999777777779**********97776655544 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.5   9.3e-05      0.13      25      43 ..      32      50 ..      21      52 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.3e-05
                            AAA_15 25 ltvliGkNnsGKSsileal 43
                                         +iG N+sGK+++l++l
  gi|474934462|ref|YP_007688044.1| 32 NVAIIGLNGSGKTTLLKLL 50
                                      578**************98 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00011      0.15      23      45 ..      29      51 ..      19      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                            AAA_16 23 rpelvllsGesGvGKsslvrell 45
                                       +e+v ++G  G+GK++l++ l+
  gi|474934462|ref|YP_007688044.1| 29 VGENVAIIGLNGSGKTTLLKLLR 51
                                      5689***************9987 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00012      0.17       1      20 [.      33      52 ..      33     102 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                            AAA_18  1 IlltGtpGvGKttlakeLsk 20
                                      +++ G  G+GKttl k L+ 
  gi|474934462|ref|YP_007688044.1| 33 VAIIGLNGSGKTTLLKLLRG 52
                                      689***************64 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   0.00037      0.51      27      42 ..      33      48 ..      23      51 .. 0.86
   2 ?    0.0   0.0      0.35   4.8e+02     143     197 ..     155     204 ..      84     223 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00037
                                      EEEEESTTSSHHHHHH CS
                                      xxxxxxxxxxxxxxxx RF
                             SMC_N 27 taivGpNGSGKsnlld 42
                                       ai+G NGSGK+ ll 
  gi|474934462|ref|YP_007688044.1| 33 VAIIGLNGSGKTTLLK 48
                                      58**********9875 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.35
                                       HHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                             SMC_N 143 tLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivisl 197
                                       tL+a aL+      +p  + +lDe    LD    +k+ ++++  + + + +++i++
  gi|474934462|ref|YP_007688044.1| 155 TLIARALI-----TNP-RMLILDEPMTGLDIVMKSKFRQMFDILTGTgVSIVMITH 204
                                       55555555.....333.367899999999999999998888865533244444444 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00018      0.24       1      23 [.      32      54 ..      32      76 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00018
                            AAA_28  1 kivitGgestGKTtlleaLaarg 23
                                      +++i+G  ++GKTtll+ L  + 
  gi|474934462|ref|YP_007688044.1| 32 NVAIIGLNGSGKTTLLKLLRGDI 54
                                      599**************998554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1726.45
//
Query:       gi|474934463|ref|YP_007688045.1|  [L=545]
Description: Na+/proline symporter [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-41  140.6  37.7    9.6e-41  140.0  37.7    1.3  1  SSF       Sodium:solute symporter family
  ------ inclusion threshold ------
        4.5    6.8   7.7        5.5    6.5   3.0    2.3  2  DUF4225   Protein of unknown function (DUF4225)


Domain annotation for each model (and alignments):
>> SSF  Sodium:solute symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.0  37.7   1.1e-44   9.6e-41       1     406 []      38     470 ..      38     470 .. 0.83

  Alignments for each domain:
  == domain 1  score: 140.0 bits;  conditional E-value: 1.1e-44
                               SSF   1 yflagrsltgfvlglslaasnisaasfvGlaGavaasGlavvlle.lgalllvlllllllaerlr....nagalTlp 72 
                                       y l+  +  ++ +gls +a+ +sa+  +G  G +a+ Gl+ ++l  +++ +++l++++++a+r r    +++a T+ 
  gi|474934463|ref|YP_007688045.1|  38 YLLGRSKTNPVIIGLSYGATFLSASAVIGFGGQAATHGLSLMWLCfMNLFIGLLVAFIFFAPRTRrmgrKLNAATFS 114
                                       4455555667999*****************************98736778899999999*****999999******* PP

                               SSF  73 dylskRfkgkrilvylsalslllvitlklsvdlvggaklielalGln..yetavlllaaltalYtviGGllAvvytd 147
                                       d+l k f++k+i+ +++ + +++++ +++++ l gg   +  + Gln  y   ++++a+++ lY+v+GG++Av+y+d
  gi|474934463|ref|YP_007688045.1| 115 DLLGKMFDSKSIRAFVA-ILIIVMMPIYCAAVLKGGVNSVAVLTGLNdlYDWILIAMAVVVGLYVVFGGIIAVMYND 190
                                       ***********655555.5578999*********************9888899999********************* PP

                               SSF 148 tiqavlmlvgalilliivllevGgleslveklkeaapkv.vdl.........ltpdslkllrdpltalslwlglvlG 214
                                        +qa +m vg  ++l+++++ +Gg+ ++++ l +++++  + +         +    +      l ++ + +g++lG
  gi|474934463|ref|YP_007688045.1| 191 ALQAAIMFVGMGVILVVTFVTLGGVGEAFTDLSNIDTSSaAGVldgfngwtsV--ADFGSSEWMLVVTTFLMGVGLG 265
                                       *************************************8863334565554321..22233344566667779***** PP

                               SSF 215 vaglphilvRflaakdakailkgvlkltivlilvl.....igmisiilfaiklagavpkavgtevgvsniaypeLvv 286
                                       v  +p  +vRf++akd + + ++++++ i+++l++      g++s ++f ++      ++v      ++ ++p+ + 
  gi|474934463|ref|YP_007688045.1| 266 VLTQPQLIVRFMSAKDDRMLDRSLIIGSIFMLLIVgtaytTGALSNVFFMEEHSLTANAYVSGLGLGTDFIVPQYIL 342
                                       ***************99999999999999998886333336778888888877777677777777788999999999 PP

                               SSF 287 kllpnllaG.....lllavmlAaimstltslllsassaftkDlYkkirrk..asakekelvgvsriivlvvislail 356
                                       +++ ++  G     l+l   + a +st+++l+     a   DlY+  ++k  ++  +   ++v ri++ ++ +l+++
  gi|474934463|ref|YP_007688045.1| 343 EVFEDITGGdffvcLFLLSLVCASISTISALMHTIGVAGGYDLYTLWKQKtdGMRMDSSNIRVNRIVTAIMLVLVVV 419
                                       9986654333322265555555667********************88876225678888999999999999999999 PP

                               SSF 357 lavqeeqkgvlklvelafaglasavlavillalfwk.rvneqGAlagliiG 406
                                            +++ ++k  +l +++ a+a l+ +  +l+ k +v +q A+ ++ +G
  gi|474934463|ref|YP_007688045.1| 420 YCYLMPKEIIAKATSLFMGMTAAALLPAFTYGLYTKmKVDKQAAMFSIAAG 470
                                       9998888879999999999***************9879999*9*9988766 PP

>> DUF4225  Protein of unknown function (DUF4225)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.2     0.012   1.1e+02      56      98 ..       4      46 ..       1      72 [. 0.82
   2 ?    6.5   3.0   0.00062       5.5      34      78 ..     160     207 ..     150     247 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.012
                           DUF4225 56 GvalvskasetvvgavaGalLilhGannvvenisyllgreekt 98
                                      Gv + + a++ v++a + ++L + G+ n+ +n +yllgr +++
  gi|474934463|ref|YP_007688045.1|  4 GVSVPIFAVMLVIFAAITIMLGVWGYRNTKNNSEYLLGRSKTN 46
                                      677777889999999999*******************987654 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.00062
                           DUF4225  34 nkvikyvikgigvVagglqivaGvalv...skasetvvgavaGalLil 78 
                                       n+ + +++++++vV+g   +++G+  v    + +  ++++++G+ L++
  gi|474934463|ref|YP_007688045.1| 160 NDLYDWILIAMAVVVGLYVVFGGIIAVmynDALQAAIMFVGMGVILVV 207
                                       678899*****************9887665566777888999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (545 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1044  (0.0582297); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.70u 0.38s 00:00:01.08 Elapsed: 00:00:00.49
# Mc/sec: 3324.62
//
Query:       gi|474934464|ref|YP_007688046.1|  [L=43]
Description: hypothetical protein TALC_00891 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 316.97
//
Query:       gi|474934465|ref|YP_007688047.1|  [L=216]
Description: putative flavoprotein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.051   13.6   0.0      0.063   13.3   0.0    1.4  1  Lactamase_B  Metallo-beta-lactamase superfamily


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.5e-06     0.063      39      80 ..      54      95 ..      38     206 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.5e-06
                                      TSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHH CS
                       Lactamase_B 39 glkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeap 80
                                       l+++++++++l+H+ +D +Ggl+ + ++++  v +++  ++
  gi|474934465|ref|YP_007688047.1| 54 ILGDRPLKYLFLSHFESDECGGLELFLKKYPKLVTVCSSFTA 95
                                      5789************************99876666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       191  (0.0106531); expected 358.6 (0.02)
Passed bias filter:                      191  (0.0106531); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 1258.90
//
Query:       gi|474934466|ref|YP_007688048.1|  [L=407]
Description: hypothetical protein TALC_00893 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.4e-05   22.6   0.0    9.3e-05   22.1   0.0    1.3  1  Peripla_BP_2  Periplasmic binding protein
     0.0027   17.9   7.6     0.0082   16.3   7.6    1.9  1  Dockerin_1    Dockerin type I domain
  ------ inclusion threshold ------
      0.079   12.8   0.3       0.15   11.8   0.3    1.4  1  zf_C2HC_14    C2HC Zing finger domain


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   1.6e-08   9.3e-05     162     235 ..     266     343 ..     195     346 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.6e-08
                                       HHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEH....HHHT-S--HHHHT-S.HHHHTSHHHHTT-EEE CS
                      Peripla_BP_2 162 dlldalgieniaaeskkseyeeisaEqilasdpdvifvsgr....aeadnktgleflken.pllaelpAvkngrVya 233
                                       +++  lg++++a es k+++ +++ ++i  +dpdvifv  +    a+    ++++++ke    l+++ A+k+g+V++
  gi|474934466|ref|YP_007688048.1| 266 YMIKSLGFKSAAGES-KNGGVNCGIDEIIHYDPDVIFVINTgwvyADLTDEQFKSKVKEMfGYLEQTRAYKQGNVFY 341
                                       78899**********.***********************9999**8888889999999997778999*********9 PP

                                       E- CS
                      Peripla_BP_2 234 ld 235
                                       ++
  gi|474934466|ref|YP_007688048.1| 342 IG 343
                                       86 PP

>> Dockerin_1  Dockerin type I domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   7.6   1.4e-06    0.0082       5      56 ..      10      59 ..       6      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.4e-06
                                      TSSSC-SHHHHHHHHHHCTSSEBTTSCCCHGGGSTT-SSCESHHHHHHHHHH CS
                        Dockerin_1  5 NgDgkVnalDalliinylnqregqssssngkaaDvNgDGrvnalDallviny 56
                                      N+D+  n  D+ li+      +g+ +++ + +aD N+DG+v++ D+  v+  
  gi|474934466|ref|YP_007688048.1| 10 NNDNYLNDKDVDLIKSIAK--DGNWDKETNPFADANNDGKVDSSDVDAVNGF 59
                                      9999999999999998888..9************************999765 PP

>> zf_C2HC_14  C2HC Zing finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.3   2.6e-05      0.15      16      32 ..     201     217 ..     197     218 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.6e-05
                        zf_C2HC_14  16 LSkMRaHiatCeKYqey 32 
                                        S M  H a C+KY+ey
  gi|474934466|ref|YP_007688048.1| 201 VSVMTMHQADCKKYIEY 217
                                       688999**********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 2423.11
//
Query:       gi|474934467|ref|YP_007688049.1|  [L=487]
Description: Methylase involved in ubiquinone/menaquinone biosynthesis [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-51  173.0   0.0    1.7e-25   89.5   0.1    2.4  2  Methyltransf_11  Methyltransferase domain
    1.6e-48  163.4   0.0      2e-24   86.1   0.0    2.3  2  Methyltransf_25  Methyltransferase domain
    1.2e-42  145.3   0.0    2.7e-21   76.0   0.0    2.1  2  Methyltransf_31  Methyltransferase domain
    3.8e-31  108.2   0.0    1.1e-15   57.9   0.0    2.1  2  Methyltransf_23  Methyltransferase domain
    1.4e-30  106.4   0.0      2e-16   60.0   0.0    2.1  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    1.1e-26   93.4   0.0      5e-13   49.6   0.0    2.3  2  Methyltransf_12  Methyltransferase domain
    2.2e-16   59.9   0.0      2e-08   34.0   0.0    2.4  2  MTS              Methyltransferase small domain
    5.1e-15   55.6   0.0    4.3e-07   29.6   0.0    2.1  2  PrmA             Ribosomal protein L11 methyltransferase (Prm
    7.8e-14   51.7   0.0    1.5e-07   31.2   0.0    2.1  2  MetW             Methionine biosynthesis protein MetW
    1.3e-12   47.6   0.0    4.9e-06   26.1   0.0    2.2  2  TehB             Tellurite resistance protein TehB
    1.2e-10   41.5   0.0    0.00013   22.0   0.0    2.2  2  Methyltransf_32  Methyltransferase domain
    1.4e-10   41.1   0.0    0.00014   21.6   0.0    2.1  2  NodS             Nodulation protein S (NodS)
    7.2e-10   38.0   0.0    1.3e-07   30.6   0.0    2.1  2  Methyltransf_29  Putative S-adenosyl-L-methionine-dependent m
    2.1e-08   34.2   0.0    0.00044   20.1   0.0    2.3  2  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    4.7e-08   32.7   0.1    2.1e-06   27.4   0.0    3.1  4  CheR             CheR methyltransferase, SAM binding domain
    1.4e-06   28.3   0.1      0.007   16.2   0.0    2.6  2  Methyltransf_8   Hypothetical methyltransferase
    1.4e-05   25.0   0.0       0.13   12.2   0.0    2.4  2  Methyltransf_18  Methyltransferase domain
    2.4e-05   23.6   0.0       0.12   11.4   0.0    2.2  2  DREV             DREV methyltransferase
    2.8e-05   23.3   0.0     0.0092   15.1   0.0    2.2  2  RrnaAD           Ribosomal RNA adenine dimethylase
    3.9e-05   23.1   0.0      0.018   14.3   0.0    2.2  2  CMAS             Mycolic acid cyclopropane synthetase
    3.9e-05   22.7   0.0     0.0062   15.5   0.0    2.1  2  Methyltransf_9   Protein of unknown function (DUF1698)
    7.4e-05   22.9   0.0     0.0035   17.5   0.0    2.2  2  FtsJ             FtsJ-like methyltransferase
    0.00053   19.7   0.0      0.027   14.1   0.1    2.3  2  TPMT             Thiopurine S-methyltransferase (TPMT)
    0.00079   19.2   0.3       0.17   11.6   0.2    2.3  2  Methyltransf_16  Lysine methyltransferase
    0.00081   19.7   0.1       0.12   12.7   0.1    2.4  2  AdoMet_MTase     Predicted AdoMet-dependent methyltransferase
     0.0011   18.6   0.1       0.98    9.0   0.0    2.2  2  Methyltransf_15  RNA cap guanine-N2 methyltransferase
      0.003   17.2   0.0        3.3    7.3   0.0    3.0  3  UPF0020          Putative RNA methylase family UPF0020
     0.0035   16.7   0.0       0.51    9.6   0.0    2.4  2  GidB             rRNA small subunit methyltransferase G
     0.0052   16.0   0.0      0.062   12.5   0.0    2.2  2  N2227            N2227-like protein
     0.0087   15.5   0.0        2.2    7.7   0.0    3.0  2  Methyltransf_4   Putative methyltransferase
  ------ inclusion threshold ------
      0.026   14.3   0.0       0.44   10.3   0.0    2.1  2  Met_10           Met-10+ like-protein
      0.066   12.9   0.0         15    5.2   0.0    2.6  2  N6_N4_Mtase      DNA methylase
       0.18   11.4   0.1         19    4.7   0.0    2.3  2  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
       0.24   10.3   0.0        4.9    6.0   0.0    2.0  2  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.3   0.0   1.2e-25   6.3e-23       1      95 [.      52     144 ..      52     145 .. 0.98
   2 !   89.5   0.1   3.2e-28   1.7e-25       1      96 []     295     390 ..     295     390 .. 0.99

  Alignments for each domain:
  == domain 1  score: 81.3 bits;  conditional E-value: 1.2e-25
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCH CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedp 77 
                                       LdvG+G G+++  l k g++v+g+D+++ m+ +ak+++++ +  ++f+v++a +l fedn+fDl+vs+ v  +++++
  gi|474934467|ref|YP_007688049.1|  52 LDVGTGPGYFTILLSKLGHDVTGIDVTPDMISVAKKNSEGLN--LDFRVMNADELSFEDNTFDLIVSRVVTWTIPNM 126
                                       8*************************************9998..9******************************** PP

                                       HHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  78 ekalkeiaRvLkpgGllv 95 
                                        ++ +e++RvL pgG+++
  gi|474934467|ref|YP_007688049.1| 127 IDCYREWRRVLAPGGRIL 144
                                       ***************997 PP

  == domain 2  score: 89.5 bits;  conditional E-value: 3.2e-28
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCH CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedp 77 
                                       LdvGcG G+++ alakrg+rv+gvD s  ml+ a ++ase+g +v f +a+a  lpf+d+sfD vv+++++ ++ dp
  gi|474934467|ref|YP_007688049.1| 295 LDVGCGCGLVSVALAKRGYRVTGVDCSSVMLEEADRCASENGCEVAFTKANAYLLPFPDSSFDTVVCRNSFWFFRDP 371
                                       8*****************************************99********************************* PP

                                       HHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  78 ekalkeiaRvLkpgGllvi 96 
                                        k+lke++RvL+ gG lvi
  gi|474934467|ref|YP_007688049.1| 372 GKVLKEMHRVLRTGGSLVI 390
                                       ****************996 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.2   0.0   9.6e-24     5e-21       1      97 []      51     141 ..      51     141 .. 0.94
   2 !   86.1   0.0   3.8e-27     2e-24       1      97 []     294     386 ..     294     386 .. 0.96

  Alignments for each domain:
  == domain 1  score: 75.2 bits;  conditional E-value: 9.6e-24
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGS CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhl 77 
                                       vLd+G+G+G +t+ l+k +  ++vtg+D++++m+  a+++   egln++f++++a++l+fed++fDl+vs+ ++  +
  gi|474934467|ref|YP_007688049.1|  51 VLDVGTGPGYFTILLSKLG--HDVTGIDVTPDMISVAKKNS--EGLNLDFRVMNADELSFEDNTFDLIVSR-VV-TW 121
                                       9***************995..*******************9..79*************************6.43.45 PP

                                       SHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  78 sdedlekalkeiarvLkpgG 97 
                                       + +++ ++++e++rvL pgG
  gi|474934467|ref|YP_007688049.1| 122 TIPNMIDCYREWRRVLAPGG 141
                                       6679999************9 PP

  == domain 2  score: 86.1 bits;  conditional E-value: 3.8e-27
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGS CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhl 77 
                                       +Ld+GcG G ++ alakr+  ++vtgvD+s+ mle+a + a+e+g++v f +++a  lpf+d+sfD vv+++++ ++
  gi|474934467|ref|YP_007688049.1| 294 ILDVGCGCGLVSVALAKRG--YRVTGVDCSSVMLEEADRCASENGCEVAFTKANAYLLPFPDSSFDTVVCRNSFWFF 368
                                       8*****************5..*************************************************9999999 PP

                                       SHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  78 sdedlekalkeiarvLkpgG 97 
                                        d+   k+lke++rvL+ gG
  gi|474934467|ref|YP_007688049.1| 369 RDP--GKVLKEMHRVLRTGG 386
                                       855..59************9 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.0   0.0   5.1e-24   2.7e-21       4     121 ..      48     157 ..      45     192 .. 0.86
   2 !   67.2   0.0   2.5e-21   1.3e-18       4     120 ..     291     402 ..     289     432 .. 0.91

  Alignments for each domain:
  == domain 1  score: 76.0 bits;  conditional E-value: 5.1e-24
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlils 80 
                                        lrvlD+G+G G++t+ l  +lg   +v+GiD ++++i++A++n++ l+   + F++ ++ el+  +ed++fDli+s
  gi|474934467|ref|YP_007688049.1|  48 VLRVLDVGTGPGYFTILLS-KLGH--DVTGIDVTPDMISVAKKNSEGLN---LDFRVMNADELS--FEDNTFDLIVS 116
                                       579****************.7765..799***************88555...56**********..*********** PP

                   Methyltransf_31  81 nevlnaladpdkileeiervlkpggilliedprllaelpak 121
                                       + v  +++++ ++++e  rvl pgg++l+ d +  +++ + 
  gi|474934467|ref|YP_007688049.1| 117 RVVTWTIPNMIDCYREWRRVLAPGGRILVFDSNFRSRFFDP 157
                                       *999***************************9954444433 PP

  == domain 2  score: 67.2 bits;  conditional E-value: 2.5e-21
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlils 80 
                                       g+ +lD+GCG G  + +la++   + +v+G+D s  ++e A   a+++g + v F ++++  l+  + d++fD +++
  gi|474934467|ref|YP_007688049.1| 291 GTDILDVGCGCGLVSVALAKR---GYRVTGVDCSSVMLEEADRCASENGCE-VAFTKANAYLLP--FPDSSFDTVVC 361
                                       6789***************76...457***********************7.************..*********** PP

                   Methyltransf_31  81 nevlnaladpdkileeiervlkpggilliedprllaelp.a 120
                                       ++ +  + dp k+l+e++rvl++gg l+i+d  ++ +l+ a
  gi|474934467|ref|YP_007688049.1| 362 RNSFWFFRDPGKVLKEMHRVLRTGGSLVITDNEWMNDLDaA 402
                                       *********************************99999852 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.9   0.0   2.1e-18   1.1e-15       7     123 ..      33     151 ..      26     178 .. 0.88
   2 !   48.1   0.0   2.1e-15   1.1e-12      22     120 ..     290     393 ..     269     422 .. 0.81

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 2.1e-18
                   Methyltransf_23   7 eelsdklerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae...kakkaqkdqfdeqeaaepq 80 
                                       ++++ +++r +p ++   rvLd+G+G G+++ +l++ g++vtg+D  p +++ a+   +  +  +  ++++e ++++
  gi|474934467|ref|YP_007688049.1|  33 QFWAGEILRRAP-EKDVLRVLDVGTGPGYFTILLSKLGHDVTGIDVTPDMISVAKknsEGLNLDFRVMNADELSFED 108
                                       567777777777.89999************************************999988889999999999999** PP

                   Methyltransf_23  81 gkfdlIvlrevlehvpdppellrqiatllkpgGylllseplas 123
                                       ++fdlIv+r v+ ++p++    r  ++ l+pgG++l+ +++ +
  gi|474934467|ref|YP_007688049.1| 109 NTFDLIVSRVVTWTIPNMIDCYREWRRVLAPGGRILVFDSNFR 151
                                       ***********************************99887644 PP

  == domain 2  score: 48.1 bits;  conditional E-value: 2.1e-15
                   Methyltransf_23  22 aggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae.....kakkaqkdqfdeqeaaepqgkfdlIvlrevle 93 
                                       ag  +Ld+GcG G ++  l+++g+ vtgvD s+++ e+a      +     ++++++   ++p+ +fd++v+r+++ 
  gi|474934467|ref|YP_007688049.1| 290 AGTDILDVGCGCGLVSVALAKRGYRVTGVDCSSVMLEEADrcaseNGCEVAFTKANAYLLPFPDSSFDTVVCRNSFW 366
                                       56689********************************9967777644444444444446666999************ PP

                   Methyltransf_23  94 hvpdppellrqiatllkpgGylllsep 120
                                        ++dp ++l+ +++ l+ gG l++++ 
  gi|474934467|ref|YP_007688049.1| 367 FFRDPGKVLKEMHRVLRTGGSLVITDN 393
                                       ************************983 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.0   2.5e-14   1.3e-11      32     153 ..      32     147 ..      12     157 .. 0.84
   2 !   60.0   0.0   3.8e-19     2e-16      38     194 ..     281     432 ..     273     464 .. 0.81

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 2.5e-14
                                       HHHHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TT CS
                   Ubie_methyltran  32 hrlWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanae 108
                                        + W   + ++  +k   +vlDv +G g +++ ls+      +v+++D+ ++m++v++k  +     n++f + na 
  gi|474934467|ref|YP_007688049.1|  32 DQFWAGEILRRAPEKDVLRVLDVGTGPGYFTILLSKLG---HDVTGIDVTPDMISVAKKNSE---GLNLDFRVMNAD 102
                                       57899999999999******************999864...4799***********997543...469********* PP

                                       T-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEE CS
                   Ubie_methyltran 109 eLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvle 153
                                       eL fed++fD++        ++++    +e +rvl pGGr++v++
  gi|474934467|ref|YP_007688049.1| 103 ELSFEDNTFDLIVSRVVTWTIPNMIDCYREWRRVLAPGGRILVFD 147
                                       **********9965444555555556789************9986 PP

  == domain 2  score: 60.0 bits;  conditional E-value: 3.8e-19
                                       HHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS- CS
                   Ubie_methyltran  38 fveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfed 114
                                       +ve + ++  g+++lDv +G g ++++l++   + ++v+++D ++ mL+++ + + e+g  ++ f +ana  Lpf d
  gi|474934467|ref|YP_007688049.1| 281 YVESIGSHIAGTDILDVGCGCGLVSVALAK---RGYRVTGVDCSSVMLEEADRCASENGC-EVAFTKANAYLLPFPD 353
                                       56777788899**************99976...5679**************999888885.8*************** PP

                                       T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE----SHHHHHHHHHHHH.HHHHHHHHHHS.-HHHHHH CS
                   Ubie_methyltran 115 dsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvlefskvelpllsqayelyskevlPvlGkllak.dldsyry 190
                                        sfD+v     +  + D  k+Lke++rvl+ GG lv+ +  +  ++ l+ a   y+++    lG++  +  +  y+ 
  gi|474934467|ref|YP_007688049.1| 354 SSFDTVVCRNSFWFFRDPGKVLKEMHRVLRTGGSLVITD--NEWMNDLDAAGARYVHHNTGELGSIRVNlGYAGYEI 428
                                       ***********************************9855..456667777777777777777777644424555555 PP

                                       HHHH CS
                   Ubie_methyltran 191 Lves 194
                                       + + 
  gi|474934467|ref|YP_007688049.1| 429 IDDV 432
                                       5555 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   0.0   2.9e-13   1.5e-10       1      99 []      52     143 ..      52     143 .. 0.92
   2 !   49.6   0.0   9.6e-16     5e-13       1      99 []     295     388 ..     295     388 .. 0.88

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 2.9e-13
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       L++G+G G ++  l +   + ++tg+D+ p++i   ++k ++  n+++ +++ ++l+ +d     +fDl+v+  v  
  gi|474934467|ref|YP_007688049.1|  52 LDVGTGPGYFTILLSKL--GHDVTGIDVTPDMI-SVAKKNSEGLNLDFRVMNADELSFEDN----TFDLIVSRVVTW 121
                                       8****************..**************.777888888888999999998887765....*******99999 PP

                   Methyltransf_12  78 hlkdirevldnirklLkpgGrl 99 
                                        ++++ +  ++ r++L+pgGr+
  gi|474934467|ref|YP_007688049.1| 122 TIPNMIDCYREWRRVLAPGGRI 143
                                       99******************96 PP

  == domain 2  score: 49.6 bits;  conditional E-value: 9.6e-16
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       L++GcG G ++ al+++  + ++tgvD s+ ++   + + a++++  +++ + +a  l   d  ssfD+vv+ n + 
  gi|474934467|ref|YP_007688049.1| 295 LDVGCGCGLVSVALAKR--GYRVTGVDCSSVML-EEADRCASENGCEVAFTKANAYLLPFPD--SSFDTVVCRNSFW 366
                                       8****************..**************.7777777777777777777777766555..6************ PP

                   Methyltransf_12  78 hlkdirevldnirklLkpgGrl 99 
                                        ++d+ +vl++++++L+ gG l
  gi|474934467|ref|YP_007688049.1| 367 FFRDPGKVLKEMHRVLRTGGSL 388
                                       ********************76 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   7.8e-08   4.1e-05      32     103 ..      48     116 ..      37     117 .. 0.89
   2 !   34.0   0.0   3.8e-11     2e-08      31     141 ..     290     394 ..     265     408 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 7.8e-08
                                       CSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE CS
                               MTS  32 sgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdlivs 103
                                         +vlD+G+G G+ ++ l k   +  vt +dv    + +ak+n e  +l+ +v++ d l+  + + fdlivs
  gi|474934467|ref|YP_007688049.1|  48 VLRVLDVGTGPGYFTILLSKLGHD--VTGIDVTPDMISVAKKNSEGLNLDFRVMNADELSFED-NTFDLIVS 116
                                       4479****************9988..9******************************998655.******97 PP

  == domain 2  score: 34.0 bits;  conditional E-value: 3.8e-11
                                       TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STT.TTSTTS-EEEEEE--- CS
                               MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvl.eeveekkfdlivsNPP 106
                                       +  ++lD+GcG G++++alak+  +  vt vd +   le a + +++n++ev +++ +++   +++ +fd++v+   
  gi|474934467|ref|YP_007688049.1| 290 AGTDILDVGCGCGLVSVALAKRGYR--VTGVDCSSVMLEEADRCASENGCEVAFTKANAYlLPFPDSSFDTVVCRNS 364
                                       4567*****************9888..9***********************999988877257889********888 PP

                                       STTTCHCHHHHHHHHHHHHHHHEEEEEEEEEEEET CS
                               MTS 107 fhagkatelavaeeliaeAkeaLkegGeLliVanr 141
                                       f   ++       ++++e +++L++gG+L+i  n+
  gi|474934467|ref|YP_007688049.1| 365 FWFFRD-----PGKVLKEMHRVLRTGGSLVITDNE 394
                                       877777.....556777778899999999887776 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   8.2e-10   4.3e-07     164     256 ..      50     143 ..      36     146 .. 0.79
   2 !   23.8   0.0   4.8e-08   2.6e-05     162     232 ..     291     361 ..     280     364 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 8.2e-10
                              PrmA 164 evlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseell.keekadvivaNILaevl 239
                                       +vlDvGtG G  +i  +kLg+ +v+++D+ +  ++vak+N e  +++ ++  ++++el  +++++d+iv+ ++   +
  gi|474934467|ref|YP_007688049.1|  50 RVLDVGTGPGYFTILLSKLGH-DVTGIDVTPDMISVAKKNSEGLNLDFRV--MNADELSfEDNTFDLIVSRVVTWTI 123
                                       89******************7.69****************9977776666..445555446899***********99 PP

                              PrmA 240 ielae...dikklvkeggll 256
                                        ++++   +  +++++gg++
  gi|474934467|ref|YP_007688049.1| 124 PNMIDcyrEWRRVLAPGGRI 143
                                       99987222445667777765 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 4.8e-08
                              PrmA 162 geevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellk..eekadviva 232
                                       g+ +lDvG+G G+ ++a ak g  +v++vD  +v ++ a + a+ N++e  ++  +++ ll   ++++d +v+
  gi|474934467|ref|YP_007688049.1| 291 GTDILDVGCGCGLVSVALAKRGY-RVTGVDCSSVMLEEADRCASENGCEVAFTK-ANAYLLPfpDSSFDTVVC 361
                                       6789****************996.79***********************98854.333333123588999998 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   2.5e-06    0.0013      15      85 ..      49     120 ..      39     151 .. 0.77
   2 !   31.2   0.0   2.9e-10   1.5e-07      14     103 ..     291     383 ..     281     391 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.5e-06
                              MetW  15 srvldlGcGdGellellke.ekqvdgrGleldeegvaecvakGlsviqgdldkdlenfedksfdyvvlsqtl 85 
                                        rvld+G+G G +  ll +  ++v+g  +  d  +va+  + Gl++    ++ d   fed++fd++v     
  gi|474934467|ref|YP_007688049.1|  49 LRVLDVGTGPGYFTILLSKlGHDVTGIDVTPDMISVAKKNSEGLNLDFRVMNADELSFEDNTFDLIVSRVVT 120
                                       69*********988888552457777777778888999999***********************99855444 PP

  == domain 2  score: 31.2 bits;  conditional E-value: 2.9e-10
                              MetW  14 gsrvldlGcGdGellellkeekqvdgrGleldeegvae...c.vakGlsviqgdldkdlenfedksfdyvvlsqtlq 86 
                                       g+ +ld+GcG G +   l  +++ +  G++ ++  + e   c  + G +v    ++  l  f+d+sfd vv   ++ 
  gi|474934467|ref|YP_007688049.1| 291 GTDILDVGCGCGLVSVAL-AKRGYRVTGVDCSSVMLEEadrCaSENGCEVAFTKANAYLLPFPDSSFDTVVCRNSFW 366
                                       6789********887777.55999999**99987776522242468******************************* PP

                              MetW  87 atrnpkevldellrigr 103
                                         r+p +vl+e+ r+ r
  gi|474934467|ref|YP_007688049.1| 367 FFRDPGKVLKEMHRVLR 383
                                       ************99865 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   9.2e-09   4.9e-06      33     106 ..      50     121 ..      16     148 .. 0.80
   2 !   19.4   0.0     1e-06   0.00055      25     132 ..     285     390 ..     267     414 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 9.2e-09
                                       EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG----S-.EEEEEEESSGG CS
                              TehB  33 kvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydineaklder.ydfilstvvlm 106
                                       +vld+g g g  ++ ls lg+dvt +d   + i+  ++    e l+ ++ ++++ +e++++++ +d+i+s vv  
  gi|474934467|ref|YP_007688049.1|  50 RVLDVGTGPGYFTILLSKLGHDVTGIDVTPDMISVAKKN--SEGLN-LDFRVMNADELSFEDNtFDLIVSRVVTW 121
                                       79*******************************998765..56666.669*********976449*******964 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 1e-06
                                       HCCCS-S-EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG---.-S-EEEEE CS
                              TehB  25 avkivkpgkvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydineakl.derydfil 100
                                           +  + +ld+gcg g  s+ l+  gy vt +d  +  ++  ++ ++ +  + +  +  +   + + d  +d ++
  gi|474934467|ref|YP_007688049.1| 285 IGSHIAGTDILDVGCGCGLVSVALAKRGYRVTGVDCSSVMLEEADRCASENGCE-VAFTKANAYLLPFpDSSFDTVV 360
                                       4456788899*************************9999888888888766666.4333333333333477889998 PP

                                       EESSGGGS-GGGHHHHHHHHHHTEEEEEEEEE CS
                              TehB 101 stvvlmfleaeripsiienmqectkvggynli 132
                                           + f++     +++++m++  ++gg  +i
  gi|474934467|ref|YP_007688049.1| 361 CRNSFWFFRDP--GKVLKEMHRVLRTGGSLVI 390
                                       88888887654..5788888888888886555 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   2.5e-07   0.00013      22      93 ..      44     110 ..      27     170 .. 0.87
   2 !   17.4   0.1   6.6e-06    0.0035      18      75 ..     283     336 ..     277     348 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.5e-07
                   Methyltransf_32  22 kesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfaelsieeat 93 
                                        e++ l+v+DvG G gY +  l+     +++ v+gid+  ++++ a+k  e l+ +f + ++  els e++t
  gi|474934467|ref|YP_007688049.1|  44 PEKDVLRVLDVGTGPGYFTILLSK----LGHDVTGIDVTPDMISVAKKNSEGLNLDF-RVMNADELSFEDNT 110
                                       4677899*************9999....7***********************99888.77888887776655 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 6.6e-06
                   Methyltransf_32  18 kelakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklg 75 
                                       +++ ++ + ++++DvG+G g  s +la      +++v+g+d+++ + e+a + a++ g
  gi|474934467|ref|YP_007688049.1| 283 ESIGSHIAGTDILDVGCGCGLVSVALAK----RGYRVTGVDCSSVMLEEADRCASENG 336
                                       55566667789*****************....59******************999877 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   2.6e-07   0.00014      41     146 ..      45     148 ..      29     153 .. 0.81
   2 !   17.5   0.0   4.8e-06    0.0025      40     144 ..     287     390 ..     267     411 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.6e-07
                              NodS  41 qgsiadalevGcaaGalterlapyckrltvvdvveeaiararervkesshiswivsdvqqfst.dekfdlivvaevl 116
                                       ++++  +l+vG   G +t  l+ + + +t +dv ++ i+ a++  +   ++ + v +  ++s  d+ fdliv   v 
  gi|474934467|ref|YP_007688049.1|  45 EKDVLRVLDVGTGPGYFTILLSKLGHDVTGIDVTPDMISVAKKNSEG-LNLDFRVMNADELSFeDNTFDLIVSRVVT 120
                                       567889***********************************998887.7888888888888852678*****99999 PP

                              NodS 117 yyiedvaelraavrnlvsllapdgq.lvfGs 146
                                       + i ++ +     r+  ++lap+g+ lvf s
  gi|474934467|ref|YP_007688049.1| 121 WTIPNMID---CYREWRRVLAPGGRiLVFDS 148
                                       88876554...55666777888776356666 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 4.8e-06
                              NodS  40 aqgsiadalevGcaaGalterlapyckrltvvdvveeaiararerv.kesshiswivsdvqqfs.tdekfdlivvae 114
                                       ++   +d+l+vGc  G +++ la    r+t vd  +  ++ a +   ++  ++++++++   +   d  fd++v+ +
  gi|474934467|ref|YP_007688049.1| 287 SHIAGTDILDVGCGCGLVSVALAKRGYRVTGVDCSSVMLEEADRCAsENGCEVAFTKANAYLLPfPDSSFDTVVCRN 363
                                       4555689***************************9999999876651567899**99999888636899******** PP

                              NodS 115 vlyyiedvaelraavrnlvsllapdgqlvf 144
                                        +++ +d  ++   ++++ ++l+++g lv 
  gi|474934467|ref|YP_007688049.1| 364 SFWFFRDPGKV---LKEMHRVLRTGGSLVI 390
                                       ******98876...5666677777777775 PP

>> Methyltransf_29  Putative S-adenosyl-L-methionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.011         6     114     215 ..      44     143 ..      33     169 .. 0.76
   2 !   30.6   0.0   2.4e-10   1.3e-07     103     222 ..     283     395 ..     272     416 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.011
                   Methyltransf_29 114 aggkvrtvlDvGCgvasfgayl..lsrdvltlslapkDeheaqvqfaLeRgvpailavlgtkrlpyPsrsfdlihCs 188
                                        ++ v  vlDvG g   f+  l  l +dv+ + ++p     a+       g+     v+ +  l++  ++fdli  s
  gi|474934467|ref|YP_007688049.1|  44 PEKDVLRVLDVGTGPGYFTILLskLGHDVTGIDVTPDMISVAKK---NSEGLNLDFRVMNADELSFEDNTFDLIV-S 116
                                       567888899**999999987764445688888777754443332...3569999999****************95.6 PP

                   Methyltransf_29 189 rCridwteedgi.lllevdRvlRpgGyf 215
                                       r  + wt  + i    e  Rvl pgG  
  gi|474934467|ref|YP_007688049.1| 117 R-VVTWTIPNMIdCYREWRRVLAPGGRI 143
                                       6.589999888735689********964 PP

  == domain 2  score: 30.6 bits;  conditional E-value: 2.4e-10
                   Methyltransf_29 103 dklaelipliaaggkvrtvlDvGCgvasfgayllsrdvltlslapkDe.heaqvqfaLeRgvpailavlgtkrlpyP 178
                                       +++ + i           +lDvGCg    + +l +r+     +    +  e+    a e g     +   +  lp+P
  gi|474934467|ref|YP_007688049.1| 283 ESIGSHIAG-------TDILDVGCGCGLVSVALAKRGYRVTGVDCSSVmLEEADRCASENGCEVAFTKANAYLLPFP 352
                                       444444443.......469****************998888877666515667789********************* PP

                   Methyltransf_29 179 srsfdlihCsrCridwteedgilllevdRvlRpgGyfvlsappv 222
                                        +sfd++ C r    + ++ g++l e++RvlR+gG +v++ ++ 
  gi|474934467|ref|YP_007688049.1| 353 DSSFDTVVC-RNSFWFFRDPGKVLKEMHRVLRTGGSLVITDNEW 395
                                       *********.5567788999*****************9987765 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   8.4e-07   0.00044      73     170 ..      47     144 ..      27     154 .. 0.76
   2 !   11.7   0.0   0.00029      0.16      54     121 ..     267     335 ..     259     362 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 8.4e-07
                                       TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGGG-SEEEEEES CS
                              PCMT  73 kgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyeekaPYdaihvg 149
                                       ++ rvL+vG+G Gy t +l++l ++++   +i+ ++++++ ak+n + l+l+   v+ +D +  +e++  +d i+  
  gi|474934467|ref|YP_007688049.1|  47 DVLRVLDVGTGPGYFTILLSKLGHDVT---GIDVTPDMISVAKKNSEGLNLD-FRVMNAD-ELSFEDN-TFDLIVSR 117
                                       6789***************99866665...**************99988776.4455566.3455554.58888877 PP

                                       SBBSS--......HHHHHTEEEEEEEE CS
                              PCMT 150 aaapeiP......ealidQLkeGGrlv 170
                                       + +  iP      +++ + L++GGr++
  gi|474934467|ref|YP_007688049.1| 118 VVTWTIPnmidcyREWRRVLAPGGRIL 144
                                       777777732223335667777777766 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00029
                                       EEE--HHHHHHHHHHTT....--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHC CS
                              PCMT  54 atiSaphmvalalelle....lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkl 121
                                       a+ Sa    ++  e++e      +g+ +L+vG+G+G  ++ la   ++  rv +++ +  + eea r   ++
  gi|474934467|ref|YP_007688049.1| 267 AYASAAIETGRSDEYVEsigsHIAGTDILDVGCGCGLVSVALA---KRGYRVTGVDCSSVMLEEADRCASEN 335
                                       556666666666777777444457899*********9988777...56778889999999998888766555 PP

>> CheR  CheR methyltransferase, SAM binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       7.8   4.1e+03      65      82 ..      70      87 ..      65     105 .. 0.87
   2 ?   -1.3   0.0       2.5   1.3e+03     121     172 ..      95     144 ..      87     149 .. 0.65
   3 ?    1.0   0.0      0.47   2.5e+02      62      82 ..     311     330 ..     290     336 .. 0.79
   4 !   27.4   0.0     4e-09   2.1e-06     118     182 ..     337     399 ..     330     405 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 7.8
                                      EEEEEEESSCHHHHHHHH CS
                              CheR 65 vkilAtDidlkvlekAka 82
                                       +++++D+   +++ Ak+
  gi|474934467|ref|YP_007688049.1| 70 HDVTGIDVTPDMISVAKK 87
                                      579999999999999986 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.5
                                       EEEE--TTT-SGGG--EEEEEE-SSGGGC-CHHHHHHHHHHHCCEEEEEEEE CS
                              CheR 121 kFeklnllekksvlgklDvifcrnvliYfdeetqekvlerfaeklkpgglLl 172
                                       +F+ +n+ e +   + +D+i++r v    + ++  + +++ ++ l+pgg++l
  gi|474934467|ref|YP_007688049.1|  95 DFRVMNADELSFEDNTFDLIVSRVVT--WTIPNMIDCYREWRRVLAPGGRIL 144
                                       56666666644556789999999664..234455566666666666666665 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.47
                                       SS-EEEEEEESSCHHHHHHHH CS
                              CheR  62 klkvkilAtDidlkvlekAka 82 
                                       +  ++++++D ++ +le+A +
  gi|474934467|ref|YP_007688049.1| 311 R-GYRVTGVDCSSVMLEEADR 330
                                       3.6899***********9976 PP

  == domain 4  score: 27.4 bits;  conditional E-value: 4e-09
                                       TTEEEEE--TTT-SGGG--EEEEEE-SSGGGC-CHHHHHHHHHHHCCEEEEEEEEE-TTB--SSS CS
                              CheR 118 elvkFeklnllekksvlgklDvifcrnvliYfdeetqekvlerfaeklkpgglLllGhsEslkkl 182
                                       + v F k n+     + +++D ++crn + +f+ +   kvl+++++ l++gg L++ ++E +++l
  gi|474934467|ref|YP_007688049.1| 337 CEVAFTKANAYLLPFPDSSFDTVVCRNSFWFFRDPG--KVLKEMHRVLRTGGSLVITDNEWMNDL 399
                                       579999999999777899**************9986..69********************99864 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0017      0.92     113     165 ..     101     156 ..      49     169 .. 0.83
   2 !   16.2   0.0   1.3e-05     0.007      62     157 ..     280     391 ..     276     395 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0017
                                       TTS-S--TT-EEEEEE.ES---SS-HHHHHHHHHHHEEEEEEEEE..EEEGGG-S- CS
                    Methyltransf_8 113 lakvPledesvdvavf.clslmgtnladflkeanrvlkvGGllkv..aevksrfes 165
                                         ++  ed++ d++v   ++    n+ d  +e +rvl +GG + v  ++ +srf +
  gi|474934467|ref|YP_007688049.1| 101 ADELSFEDNTFDLIVSrVVTWTIPNMIDCYREWRRVLAPGGRILVfdSNFRSRFFD 156
                                       457889******999724567789*****************998833467888864 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.3e-05
                                       HHHHHHCTS-TTS-EEEES-TT-HHH..HH--S-..EEEEESS-S....STTEEE...S-TT..S.....-S--TT- CS
                    Methyltransf_8  62 viirklkkkkdnlvvadlGcGeakia..eavrekekvrsfdlvav....nervva...cdla..k.....vPledes 122
                                       + ++++ ++ + + + d+GcG   ++   a+ +  +v  +d  +v     +r  +   c++a  k     +P  d+s
  gi|474934467|ref|YP_007688049.1| 280 EYVESIGSHIAGTDILDVGCGCGLVSvaLAK-RGYRVTGVDCSSVmleeADRCASengCEVAftKanaylLPFPDSS 355
                                       5566666777777888988876554420333.344777777666522212222212237663222334448****** PP

                                       EEEEEEES--.-SS-HHHHHHHHHHHEEEEEEEEEE CS
                    Methyltransf_8 123 vdvavfclsl.mgtnladflkeanrvlkvGGllkva 157
                                        d +v+  s+    +  + lke++rvl++GG l ++
  gi|474934467|ref|YP_007688049.1| 356 FDTVVCRNSFwFFRDPGKVLKEMHRVLRTGGSLVIT 391
                                       *******9983578999****************997 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00094      0.49      17      65 ..      50      96 ..      38     115 .. 0.83
   2 !   12.2   0.0   0.00024      0.13       8      65 ..     285     339 ..     279     361 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00094
                   Methyltransf_18 17 rvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagled 65
                                      rv+D+Gt  gy +i l k g  + v+ +D+ +  ++ ak+n e  +l+ 
  gi|474934467|ref|YP_007688049.1| 50 RVLDVGTGPGYFTILLSKLG--HDVTGIDVTPDMISVAKKNSEGLNLDF 96
                                      89*************99766..67*****************99888754 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00024
                   Methyltransf_18   8 iaslvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagled 65 
                                       i s++  g+ ++D+G+  g+++++l+k+g   +v+ +D ++  le+a++ ++++g+e 
  gi|474934467|ref|YP_007688049.1| 285 IGSHIA-GTDILDVGCGCGLVSVALAKRGY--RVTGVDCSSVMLEEADRCASENGCEV 339
                                       556666.8899***************9886..69**************9999998864 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00024      0.12      76     185 ..      32     144 ..      27     147 .. 0.78
   2 !    9.9   0.0   0.00069      0.36      91     187 ..     287     391 ..     281     437 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00024
                              DREV  76 eqfrkllaiekespasdqedkklldlGaGdGeitkrvaptfeevyatelsetmrdrlkk......kkynvlsalelq 146
                                       +qf    a e  + a++++  ++ld+G+G G  t  +++  ++v   +++  m+   kk      ++++v+ a el 
  gi|474934467|ref|YP_007688049.1|  32 DQFW---AGEILRRAPEKDVLRVLDVGTGPGYFTILLSKLGHDVTGIDVTPDMISVAKKnseglnLDFRVMNADELS 105
                                       5543...34445678889999****************************999998887733333357********** PP

                              DREV 147 etdvkldlilclnlldrcfdplklledirsalepngrvi 185
                                         d  +dli++  +     + +   ++ r +l+p gr++
  gi|474934467|ref|YP_007688049.1| 106 FEDNTFDLIVSRVVTWTIPNMIDCYREWRRVLAPGGRIL 144
                                       99*******987777666666677777777777777665 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00069
                              DREV  91 sdqedkklldlGaGdGeitkrvaptfeevyatelsetmrdrlkkk....kynv.lsale...lqetdvkldlilcln 159
                                       s    + +ld+G G G ++  +a+   +v   + s+ m +  ++     + +v +++ +   l   d  +d ++c n
  gi|474934467|ref|YP_007688049.1| 287 SHIAGTDILDVGCGCGLVSVALAKRGYRVTGVDCSSVMLEEADRCasenGCEVaFTKANaylLPFPDSSFDTVVCRN 363
                                       55566789*****************99999999999998776554111133442222222324456899******** PP

                              DREV 160 lldrcfdplklledirsalepngrviva 187
                                        +    dp+k+l++++ +l++ g  +++
  gi|474934467|ref|YP_007688049.1| 364 SFWFFRDPGKVLKEMHRVLRTGGSLVIT 391
                                       *********************9998875 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.7e-05    0.0092      15      89 ..      32     107 ..      30     117 .. 0.89
   2 ?    5.9   0.0     0.011       5.8      32      70 ..     292     330 ..     285     379 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.7e-05
                                       -HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT.TCCCEEEE-S-CCGHH CS
                            RrnaAD  15 nkkvineIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls.kdeklkvvhqDflkfe 89 
                                       ++  + eIl+ +  ++ l vl++g+G+G +T  L k    v+ +   ++++ + +k+ + ++    v+++D l fe
  gi|474934467|ref|YP_007688049.1|  32 DQFWAGEILRRAPEKDVLRVLDVGTGPGYFTILLSKLGHDVTGIDVTPDMISVAKKNSEgLNLDFRVMNADELSFE 107
                                       666777899999889999**************************************88888888899999999987 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.011
                                       SEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHC CS
                            RrnaAD  32 ltvleigpGkGilTeeLakrakqvvvlElderLakllqk 70 
                                       + +l++g G G+ ++ Lakr   v+ +   ++++++   
  gi|474934467|ref|YP_007688049.1| 292 TDILDVGCGCGLVSVALAKRGYRVTGVDCSSVMLEEADR 330
                                       579*****************9999998888888877655 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.0    0.0083       4.4      65     134 ..      50     117 ..      37     152 .. 0.74
   2 !   14.3   0.0   3.5e-05     0.018      62     162 ..     290     388 ..     281     404 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0083
                                       EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---.--SEEEEE CS
                              CMAS  65 tlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedlde.kvdrvvsv 134
                                       ++Ld+G+G G+ ++   ++ + +v g+ +  +   +akk+ + l  + + +v  +d   +++  +d +vs 
  gi|474934467|ref|YP_007688049.1|  50 RVLDVGTGPGYFTILL-SKLGHDVTGIDVTPDMISVAKKNSEGL--NLDFRVMNADELSFEDnTFDLIVSR 117
                                       89********998865.556*****************9986655..5566777777777776689999985 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 3.5e-05
                                       TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---.--SEEEEES-G CS
                              CMAS  62 pGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedlde.kvdrvvsvgaf 137
                                       +G  +Ld+GcG G + +  ++r + +v g+  S+   + a +   e + e   +   +    +++  +d vv  + f
  gi|474934467|ref|YP_007688049.1| 290 AGTDILDVGCGCGLVSVALAKR-GYRVTGVDCSSVMLEEADRCASENGCEVAFTKANAYLLPFPDsSFDTVVCRNSF 365
                                       5999*********999999999.**********99998888877777766544444444445555577887776666 PP

                                       GGTSGGGHHHHHHHHHHHS-TT-EE CS
                              CMAS 138 ehvgkenydtffkklkkllkedGll 162
                                         +      +  k+++++l+++G l
  gi|474934467|ref|YP_007688049.1| 366 WFFR--DPGKVLKEMHRVLRTGGSL 388
                                       5553..3345566666666666665 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.018       9.2     118     215 ..      50     143 ..      27     149 .. 0.69
   2 !   15.5   0.0   1.2e-05    0.0062      99     218 ..     277     391 ..     268     401 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.018
                                       EEEEET-TTSHHHHHHHHCT-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---GGGS-T.---EEEEEEES-GG CS
                    Methyltransf_9 118 tildvGcgnGyhlwrmvgegaklvvGidPselfliqfeavrkllgedqrahllplgieqlpe.leafdtvfsmGvly 193
                                       ++ldvG g Gy+   ++++  + v Gid +   +   +   + l+ d r+++     ++l    ++fd + s  v +
  gi|474934467|ref|YP_007688049.1|  50 RVLDVGTGPGYFTI-LLSKLGHDVTGIDVTPDMISVAKKNSEGLNLDFRVMN----ADELSFeDNTFDLIVSRVVTW 121
                                       79*********987.6677778899999988777665555555544444433....355544356777777777777 PP

                                       G-S-HHHHHHHHHCTEEEEEEE CS
                    Methyltransf_9 194 hrrsPldhllqlkdqlvkgGel 215
                                            +d  ++ +  l  gG +
  gi|474934467|ref|YP_007688049.1| 122 TIPNMIDCYREWRRVLAPGGRI 143
                                       7777777777777777776665 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.2e-05
                                       EHHHHHHHHGGGS.--TT-EEEEET-TTSHHHHHHHHCT-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---GG CS
                    Methyltransf_9  99 rsdwkWdrvlphlsdlkgrtildvGcgnGyhlwrmvgegaklvvGidPselfliqfeavrkllgedqrahllplgie 175
                                       rsd   + +  h+    g  ildvGcg G     + ++    v G+d s++ l   +      g   ++        
  gi|474934467|ref|YP_007688049.1| 277 RSDEYVESIGSHI---AGTDILDVGCGCGLVSVAL-AKRGYRVTGVDCSSVMLEEADRCASENG--CEVAFTKANAY 347
                                       6666666666666...7899*********988765.56667899*****998865444433333..33333334445 PP

                                       GS-T.---EEEEEEES-GGG-S-HHHHHHHHHCTEEEEEEEEEE CS
                    Methyltransf_9 176 qlpe.leafdtvfsmGvlyhrrsPldhllqlkdqlvkgGelvle 218
                                        lp   ++fdtv     ++  r P   l +++  l++gG lv+ 
  gi|474934467|ref|YP_007688049.1| 348 LLPFpDSSFDTVVCRNSFWFFRDPGKVLKEMHRVLRTGGSLVIT 391
                                       55655689*********************************985 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   6.7e-06    0.0035      22     111 ..      48     133 ..      19     170 .. 0.76
   2 ?    3.1   0.0      0.17        88      21      58 ..     290     324 ..     274     365 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6.7e-06
                                       T-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS..HHH..TTEEEECS-CCCSSHHHHHCHCHHHSSEEEEEE- CS
                              FtsJ  22 gktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm..apl..pgvttiqgditdpetiekikealserkvdlvvsD 94 
                                       + +v+D+g +PG ++  l++  g  + v ++D+ p   + +  ++ + ++ d++ +++ e+    ++++ +dl+vs 
  gi|474934467|ref|YP_007688049.1|  48 VLRVLDVGTGPGYFTILLSKL-G--HDVTGIDVTPDmiS-VakKNSEGLNLDFRVMNADELS---FEDNTFDLIVSR 117
                                       467************988887.6..79******887542.346999999****999777744...56899*****99 PP

                                       -S-SS-CHHHHHHHHHC CS
                              FtsJ  95 gapdvsgvhdldeylqs 111
                                       ++   +  + +d y++ 
  gi|474934467|ref|YP_007688049.1| 118 VV-TWTIPNMIDCYREW 133
                                       98.88888888888774 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.17
                                       TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSSH CS
                              FtsJ  21 pgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpma 58 
                                        g+ ++D+g++ G  s  l++r g   +v +vD  ++ 
  gi|474934467|ref|YP_007688049.1| 290 AGTDILDVGCGCGLVSVALAKR-G--YRVTGVDCSSVM 324
                                       56789***********999999.5..79*****97763 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.12        63      35      78 ..      45      88 ..      36     138 .. 0.66
   2 !   14.1   0.1   5.1e-05     0.027      40      83 ..     293     334 ..     279     349 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.12
                                      -S--EEEEEET-TT-HHHHHH-BTTEEEEEE-S-HHHHHHHHHH CS
                              TPMT 35 akaglrvlvPlCGkaldlvwlAeqgrevvGvelselAvekffee 78
                                      +k  lrvl  + G ++  + l++ g++v G+++ +  ++ + ++
  gi|474934467|ref|YP_007688049.1| 45 EKDVLRVLDVGTGPGYFTILLSKLGHDVTGIDVTPDMISVAKKN 88
                                      55667888888899999999**************9988775333 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 5.1e-05
                                       EEEEET-TT-HHHHHH-BTTEEEEEE-S-HHHHHHHHHHHTTSG CS
                              TPMT  40 rvlvPlCGkaldlvwlAeqgrevvGvelselAvekffeeanlep 83 
                                        +l  +CG +l  v+lA++g++v Gv+ s   +e++  ++  ++
  gi|474934467|ref|YP_007688049.1| 293 DILDVGCGCGLVSVALAKRGYRVTGVDCSSVMLEEA--DRCASE 334
                                       556669*************************99995..444444 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.027        14      44      91 ..      45      91 ..      17     130 .. 0.74
   2 !   11.6   0.2   0.00033      0.17      42      77 ..     286     319 ..     248     337 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.027
                   Methyltransf_16 44 elsklsvlELGsGtGlvGlavaellpeakviltDl.eellellkkniel 91
                                      e   l+vl++G G G + + + +l  + +v+  D+ ++++ + kkn e 
  gi|474934467|ref|YP_007688049.1| 45 EKDVLRVLDVGTGPGYFTILLSKL--GHDVTGIDVtPDMISVAKKNSEG 91
                                      567789******************..88888777515699999999886 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00033
                   Methyltransf_16  42 anelsklsvlELGsGtGlvGlavaellpeakviltD 77 
                                        ++ +++ +l++G G+Glv +a+a+   + +v+  D
  gi|474934467|ref|YP_007688049.1| 286 GSHIAGTDILDVGCGCGLVSVALAKR--GYRVTGVD 319
                                       56778999****************98..44554444 PP

>> AdoMet_MTase  Predicted AdoMet-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.096        51      59      88 ..      48      77 ..      35      83 .. 0.86
   2 !   12.7   0.1   0.00023      0.12      61      88 ..     293     320 ..     282     328 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.096
                      AdoMet_MTase 59 etsfvdvgcgngllvyvlaaegykgygidl 88
                                           dvg g g +  +l+  g+   gid+
  gi|474934467|ref|YP_007688049.1| 48 VLRVLDVGTGPGYFTILLSKLGHDVTGIDV 77
                                      45678***********************98 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00023
                      AdoMet_MTase  61 sfvdvgcgngllvyvlaaegykgygidl 88 
                                        + dvgcg gl+   la  gy+  g+d 
  gi|474934467|ref|YP_007688049.1| 293 DILDVGCGCGLVSVALAKRGYRVTGVDC 320
                                       678**********************996 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0019      0.98       3      49 ..      50      96 ..      48     117 .. 0.91
   2 !    7.5   0.1    0.0052       2.8       4      39 ..     294     329 ..     291     341 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0019
                   Methyltransf_15  3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsd 49
                                       +lD+ +G G  +i + + ++ v +i++ ++ + +a++N e  + + 
  gi|474934467|ref|YP_007688049.1| 50 RVLDVGTGPGYFTILLSKLGHDVTGIDVTPDMISVAKKNSEGLNLDF 96
                                      589************************************99766655 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0052
                   Methyltransf_15   4 ilDlfsGaGGnviqfalvfekviaieinleklacaq 39 
                                       ilD+ +G+G  ++++a+ + +v +++ +   l+ a 
  gi|474934467|ref|YP_007688049.1| 294 ILDVGCGCGLVSVALAKRGYRVTGVDCSSVMLEEAD 329
                                       8*****************99******9988776655 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.027        14      79     127 ..      72     116 ..      65     118 .. 0.84
   2 !    7.3   0.0    0.0062       3.3      74     127 ..     310     361 ..     296     365 .. 0.88
   3 ?    0.4   0.0      0.85   4.5e+02     148     168 ..     374     394 ..     372     420 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.027
                                       EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE CS
                           UPF0020  79 lygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivt 127
                                       + g+D  + ++  a++N e        +f++++a +L  +++ +d+iv+
  gi|474934467|ref|YP_007688049.1|  72 VTGIDVTPDMISVAKKNSEGL----NLDFRVMNADELSFEDNTFDLIVS 116
                                       78***************9855....567888999999966669****98 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0062
                                       HHH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE CS
                           UPF0020  74 raelklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivt 127
                                       ++ +++ g+D  + +++ a + a++ g +  ++f +a+a  L+ +++++d++v+
  gi|474934467|ref|YP_007688049.1| 310 KRGYRVTGVDCSSVMLEEADRCASENGCE--VAFTKANAYLLPFPDSSFDTVVC 361
                                       4567899****************999875..7899999999999999******9 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.85
                                       HHHHHHHH-TT..-EEEEEES CS
                           UPF0020 148 flrelkrvlrgggrlvlltse 168
                                       +l+e++rvlr+gg lv+  +e
  gi|474934467|ref|YP_007688049.1| 374 VLKEMHRVLRTGGSLVITDNE 394
                                       789********7766654444 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0   0.00097      0.51      49     146 ..      47     145 ..      37     155 .. 0.77
   2 ?    4.7   0.0     0.032        17      47      67 ..     291     309 ..     280     397 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00097
                                       C-..EEEETSTTTTTHHHHHHH-TTSEEEEEES-HHHHHHHHHHHHHCT-SSEEEEES-CCCTTTTT-EEEEEEC-S CS
                              GidB  49 rd.kviDvGsGaGlPGipLaiarpelkltLleslekkiaFLeevkeelklenveivearaeekqeeekydvvtsRAl 124
                                       +  +v+DvG+G+G   i L+ +  ++  t ++ +   i+  ++ +e l+l+  ++++a+  +  e +++d+++sR +
  gi|474934467|ref|YP_007688049.1|  47 DVlRVLDVGTGPGYFTILLSKLGHDV--TGIDVTPDMISVAKKNSEGLNLD-FRVMNADELS-FEDNTFDLIVSRVV 119
                                       3337**************99888775..58999999999999999999999.8888877544.68899999999987 PP

                                       S....SHHHHHHHHCCCEEEEEEEEE CS
                              GidB 125 a....slnelteillkllkegglila 146
                                            ++ ++    +++l +gg+il+
  gi|474934467|ref|YP_007688049.1| 120 TwtipNMIDCYREWRRVLAPGGRILV 145
                                       53333566666666667778887776 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.032
                                       CCC-.EEEETSTTTTTHHHHH CS
                              GidB  47 ekrdkviDvGsGaGlPGipLa 67 
                                         +  ++DvG G Gl ++ La
  gi|474934467|ref|YP_007688049.1| 291 GTD--ILDVGCGCGLVSVALA 309
                                       333..9*********777665 PP

>> N2227  N2227-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.44   2.3e+02     142     197 ..      89     141 ..      42     146 .. 0.72
   2 !   12.5   0.0   0.00012     0.062      58      92 ..     291     325 ..     277     328 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.44
                                       TTS--EEEEES-HHHHH--SSHTT-EEEEEEES-TTSSS-HHHHHHHHHHHEEEEE CS
                             N2227 142 krkknlsmaagdflevykeeeaaesydvvvtcfFiDtaeNvleYletiekvlkpgg 197
                                       ++  nl+  + +  e++    +++++d +v      t  N+++  +   +vl pgg
  gi|474934467|ref|YP_007688049.1|  89 SEGLNLDFRVMNADELSF---EDNTFDLIVSRVVTWTIPNMIDCYREWRRVLAPGG 141
                                       333333333333334444...45899999999999999999999999999999998 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00012
                                       T-EEEEET-TT-HHHHHHHHTT-EEEEEE--HHHH CS
                             N2227  58 kvkilvPGaGlGrlavelatkgyqvegnEfsyfml 92 
                                        ++il  G+G+G ++v la+ gy+v g++ s  ml
  gi|474934467|ref|YP_007688049.1| 291 GTDILDVGCGCGLVSVALAKRGYRVTGVDCSSVML 325
                                       5789999************************9997 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.078        41       5      48 ..      51      92 ..      47     115 .. 0.73
   2 !    7.7   0.0    0.0041       2.2       5      93 ..     294     380 ..     290     402 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.078
                                      EEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHC CS
                    Methyltransf_4  5 vleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkieal 48
                                      vl++G+G G f++ l+k   d+   Gi++  +++  + k+ e l
  gi|474934467|ref|YP_007688049.1| 51 VLDVGTGPGYFTILLSKLGHDV--TGIDVTPDMISVAKKNSEGL 92
                                      89**************997665..58888888887766655544 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0041
                                       EEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-C..CCHHHHCS-TTSEEEEEEE CS
                    Methyltransf_4   5 vleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgda..lkvllelledgslekifil 79 
                                       +l++GcG G + valAk+     + G++ ++ +++++  + + ++   ++ ++ +a  l +  +++ +  +++ f +
  gi|474934467|ref|YP_007688049.1| 294 ILDVGCGCGLVSVALAKRG--YRVTGVDCSSVMLEEAD-RCASENGCEVAFTKANAylLPFPDSSFDTVVCRNSFWF 367
                                       79*******9999999986..66779999888877775.55555556689999998433333456666666666777 PP

                                       S-----SGGGGGGS CS
                    Methyltransf_4  80 FPDPwfKkrhhKrR 93 
                                       F DP  K  ++ +R
  gi|474934467|ref|YP_007688049.1| 368 FRDP-GKVLKEMHR 380
                                       7777.344444444 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00083      0.44     103     177 ..      50     119 ..      39     136 .. 0.77
   2 ?    1.4   0.0      0.42   2.2e+02     101     132 ..     291     320 ..     278     327 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00083
                                       EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---TT-EEEEEE--T CS
                            Met_10 103 vVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevireqladrvvmnlp 177
                                       +V+dv  G G+f+i ++k++  + v +id+ P+ +   k+n +  +++ +v  +++D   +  ++++d +v  ++
  gi|474934467|ref|YP_007688049.1|  50 RVLDVGTGPGYFTILLSKLG--HDVTGIDVTPDMISVAKKNSEGLNLDFRV--MNADELSFE-DNTFDLIVSRVV 119
                                       699***************55..567***********999998765566555..777877775.666666665555 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.42
                                       T-EEEETT-TTTCCHHHCCHHTTSSEEEEEES CS
                            Met_10 101 gevVvdvfAGiGpfaipiakyskakrvlaidl 132
                                       g  ++dv  G G  ++++ak  ++ rv ++d 
  gi|474934467|ref|YP_007688049.1| 291 GTDILDVGCGCGLVSVALAK--RGYRVTGVDC 320
                                       566899**************..9999999985 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.034        18      38      68 ..     129     157 ..     118     223 .. 0.84
   2 ?    5.2   0.0     0.028        15      36      55 ..     372     391 ..     366     435 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.034
                                       HHHHHHHHEEEEEEEEEEE-CCCHHTHHHHH CS
                       N6_N4_Mtase  38 vlkevrrvLkddgsifiniddseikkelkal 68 
                                         +e+rrvL+++g i+++  ds++ ++++  
  gi|474934467|ref|YP_007688049.1| 129 CYREWRRVLAPGGRILVF--DSNFRSRFFDP 157
                                       569**************9..66665534444 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.028
                                       HHHHHHHHHHEEEEEEEEEE CS
                       N6_N4_Mtase  36 ekvlkevrrvLkddgsifin 55 
                                        kvlke++rvL ++gs++i 
  gi|474934467|ref|YP_007688049.1| 372 GKVLKEMHRVLRTGGSLVIT 391
                                       589***************97 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.037        19      16      41 ..      62      87 ..      53      95 .. 0.82
   2 ?    4.2   0.1     0.056        29      12      37 ..     302     326 ..     294     334 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.037
                                      HHHHHHCTSEEEEE-S-HHHHHHHCT CS
                    UDPG_MGDP_dh_N 16 aavlaeighevigvDideekvdklns 41
                                       ++l+++gh+v+g+D+    ++  ++
  gi|474934467|ref|YP_007688049.1| 62 TILLSKLGHDVTGIDVTPDMISVAKK 87
                                      5789************9988876554 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.056
                                       HHHHHHHHHHCTSEEEEE-S-HHHHH CS
                    UDPG_MGDP_dh_N  12 GlvtaavlaeighevigvDideekvd 37 
                                       Glv +++la++g  v+gvD ++   +
  gi|474934467|ref|YP_007688049.1| 302 GLV-SVALAKRGYRVTGVDCSSVMLE 326
                                       444.688************9987665 PP

>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.16        85     193     261 ..      35     104 ..      29     110 .. 0.75
   2 ?    6.0   0.0    0.0094       4.9     202     246 ..     291     335 ..     279     343 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.16
                   tRNA_U5-meth_tr 193 Walevtqeskg.dl...lelycGnGnfslalarnfekvlateiakssveaaqyniaankidnvqiirlsaeel 261
                                       Wa e+++ + + d+   l++  G G f++ l++  + v   +++   +++a++n +     n+++  + a+el
  gi|474934467|ref|YP_007688049.1|  35 WAGEILRRAPEkDVlrvLDVGTGPGYFTILLSKLGHDVTGIDVTPDMISVAKKNSEGL---NLDFRVMNADEL 104
                                       7777766553336511156678999****************************98764...455555666665 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0094
                   tRNA_U5-meth_tr 202 kgdllelycGnGnfslalarnfekvlateiakssveaaqyniaan 246
                                         d+l++ cG G  s+ala++  +v   + +   +e a     +n
  gi|474934467|ref|YP_007688049.1| 291 GTDILDVGCGCGLVSVALAKRGYRVTGVDCSSVMLEEADRCASEN 335
                                       45**********************998888877777776655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (487 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        34  (0.00189637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              34  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 3182.68
//
Query:       gi|474934468|ref|YP_007688050.1|  [L=452]
Description: Na+-driven multidrug efflux pump [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-30  104.4  30.0    1.1e-22   80.5   7.1    2.8  3  MatE             MatE
      3e-06   27.3  22.1    1.3e-05   25.3  10.4    4.9  4  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai


Domain annotation for each model (and alignments):
>> MatE  MatE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.5   7.1   1.2e-26   1.1e-22       1     161 []      26     185 ..      26     185 .. 0.99
   2 ?   -2.8   0.6      0.49   4.4e+03     124     131 ..     196     203 ..     186     216 .. 0.44
   3 !   37.2   6.6   2.4e-13   2.1e-09      16     154 ..     261     403 ..     246     410 .. 0.86

  Alignments for each domain:
  == domain 1  score: 80.5 bits;  conditional E-value: 1.2e-26
                              MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgli 77 
                                       P+++++l++++   +dt+++++lgs a +a+s  +++ s+++++++++++++t+ ++ +lG+++f+ra++ +  +li
  gi|474934468|ref|YP_007688050.1|  26 PMLFSYLVVQVNLYVDTFWTSGLGSAASSAISTITPLYSIITAIGTSIGVGVTSTIAFRLGKGDFERASKLAGNSLI 102
                                       99*************************************************************************** PP

                              MatE  78 lllllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislll 154
                                       l+++ +++++ +++++ ++++ ++++d+ v el+ +y++ +++   al+ + +  + lr+ g  k +++++++s+++
  gi|474934468|ref|YP_007688050.1| 103 LGVAAGIAVSSVMYVLYDPLVDYMGADD-VRELSWDYVLPYFMMSWALITNSIVVALLRSEGAGKKSMVVLVSSAVV 178
                                       ************************9998.9*********************************************** PP

                              MatE 155 niplnyl 161
                                       n+ l++l
  gi|474934468|ref|YP_007688050.1| 179 NMTLDPL 185
                                       **99875 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.49
                              MatE 124 alalqlvl 131
                                       + a+ ++l
  gi|474934468|ref|YP_007688050.1| 196 GAAMATTL 203
                                       22222222 PP

  == domain 3  score: 37.2 bits;  conditional E-value: 2.4e-13
                              MatE  16 dtllvgrl.gskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqglilllllsliiallvl 91 
                                         +++  + g+  +   +  ++ +sl  v++ +l +a+ ++++   G+++  +++ ++ +  +l+l++++i++++++
  gi|474934468|ref|YP_007688050.1| 261 QRVFIIAVaGTLGVMWFNMPWRYVSLSSVPSEALTAAMIPVAAAGMGQGDASKMSLSMDYVAKLNLVIGVILTVVIF 337
                                       5555555666666666777799999**************************************************** PP

                              MatE  92 lfseqilslftqdee...vlelakrylrililgipalalqlvlsgilrgagktkvplyislislll 154
                                       +++++++ +f  d++     e+    lr+l+++i++ +++  +s++l++++ +  ++ ++++ + +
  gi|474934468|ref|YP_007688050.1| 338 VLADPLMGVFIRDPTmeeNREMLVWTLRALAFCIVPSSFTRYFSSTLQAMKSSLKSTKVMIFWAFI 403
                                       **************9666677777889******************************999997655 PP

>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   6.1      0.12     1e+03      55      86 ..      47      84 ..      11     126 .. 0.41
   2 !   25.3  10.4   1.4e-09   1.3e-05      14      85 ..     151     225 ..     139     277 .. 0.76
   3 ?   -0.7   5.3      0.15   1.4e+03      60     136 ..     266     339 ..     264     346 .. 0.60
   4 !   15.9   3.8   1.2e-06     0.011       1      78 [.     363     439 ..     363     449 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.12
                   Polysacc_synt_C 55 ivGaaiatvlallvvavlnlyalrrllgikl......e 86
                                       +G a++++++ ++ ++ ++ a+   +g+ +       
  gi|474934468|ref|YP_007688050.1| 47 GLGSAASSAISTITPLYSIITAIGTSIGVGVtstiafR 84
                                      34444444444444444444444444444333322220 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 1.4e-09
                   Polysacc_synt_C  14 lstvlssiLqglgrqkialkalvigalvklilnllliplf..givGaaiatvlallvvavln.lyalrrllgikl 85 
                                        ++++ ++L + g  k+ +++lv +a+v++ l  lli+ +  g+ Gaa+at+l+ l++avl   ++l  ++ i+l
  gi|474934468|ref|YP_007688050.1| 151 TNSIVVALLRSEGAGKKSMVVLVSSAVVNMTLDPLLIYVLgmGLFGAAMATTLSALFTAVLGlCWYLTGRMTIHL 225
                                       346677788888999**********************8872256**********999999986788888877777 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.15
                   Polysacc_synt_C  60 iatvlallvvavlnlyalrrllgiklellrrllkpllaalvmgiv.vylllllllgllllaalalllavlvgalvYl 135
                                       ia + +l v+ + + ++   l  ++ e   +   + +aa++mg   +    ++ l++   a l+l+++v++ +++++
  gi|474934468|ref|YP_007688050.1| 266 IAVAGTLGVMWFNMPWRYVSLSSVPSE-ALTAAMIPVAAAGMGQGdAS---KMSLSMDYVAKLNLVIGVILTVVIFV 338
                                       555666666666666666666666664.34444677888888888322...22222222224699999999999988 PP

                   Polysacc_synt_C 136 l 136
                                       l
  gi|474934468|ref|YP_007688050.1| 339 L 339
                                       7 PP

  == domain 4  score: 15.9 bits;  conditional E-value: 1.2e-06
                   Polysacc_synt_C   1 vLailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyal 77 
                                       +L+ la+ i+++s+++ +ss Lq+++   + +k++++ a++kl++      lf+   ++ia v++ ++++ ++ y+ 
  gi|474934468|ref|YP_007688050.1| 363 TLRALAFCIVPSSFTRYFSSTLQAMKSSLKSTKVMIFWAFIKLGMIAAGS-LFSFEWVIIALVASHFISSSCMGYMS 438
                                       5899****************************************998877.56656677777777777777776655 PP

                   Polysacc_synt_C  78 r 78 
                                       +
  gi|474934468|ref|YP_007688050.1| 439 Y 439
                                       4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       766  (0.0427241); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.34s 00:00:01.01 Elapsed: 00:00:00.53
# Mc/sec: 2553.10
//
Query:       gi|474934469|ref|YP_007688051.1|  [L=225]
Description: ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase component [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-31  109.5   0.0    2.2e-31  109.2   0.0    1.1  1  ABC_tran      ABC transporter
    1.3e-07   31.8   0.5      0.011   15.5   0.1    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    1.2e-06   29.2   0.1    2.4e-06   28.2   0.1    1.4  1  AAA_23        AAA domain
    8.9e-06   25.3   0.6    3.6e-05   23.3   0.6    1.8  1  SMC_N         RecF/RecN/SMC N terminal domain
    5.6e-05   22.8   0.0    0.00021   21.0   0.0    2.0  2  AAA_29        P-loop containing region of AAA domain
    0.00031   20.6   0.2     0.0018   18.0   0.0    1.9  2  AAA_15        AAA ATPase domain
    0.00041   20.8   0.0    0.00053   20.4   0.0    1.4  1  AAA_16        AAA ATPase domain
    0.00045   20.6   0.1     0.0016   18.9   0.1    2.0  1  AAA           ATPase family associated with various cellular 
    0.00066   19.6   0.1     0.0011   18.9   0.1    1.4  1  Rad17         Rad17 P-loop domain
     0.0011   18.4   0.0     0.0016   17.8   0.0    1.2  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
     0.0027   17.6   0.0     0.0065   16.4   0.0    1.7  1  RsgA_GTPase   RsgA GTPase
     0.0092   16.1   0.8      0.086   12.9   0.1    2.6  2  MMR_HSR1      50S ribosome-binding GTPase
  ------ inclusion threshold ------
       0.01   16.2   0.1       0.03   14.7   0.0    1.9  1  RNA_helicase  RNA helicase
      0.018   15.3   0.3      0.055   13.7   0.3    1.9  1  AAA_22        AAA domain
      0.022   14.7   0.1      0.043   13.7   0.0    1.6  2  NTPase_1      NTPase
      0.026   14.1   0.0      0.042   13.4   0.0    1.2  1  AAA_27        AAA domain
      0.034   14.1   0.0       0.14   12.2   0.0    1.9  2  AAA_5         AAA domain (dynein-related subfamily)
      0.035   14.0   0.3      0.076   12.9   0.3    1.7  1  ATPase_2      ATPase domain predominantly from Archaea
      0.057   12.3   0.2       0.74    8.7   0.1    2.3  2  AAA_PrkA      PrkA AAA domain
      0.061   13.4   0.2        0.1   12.6   0.2    1.5  1  DUF87         Helicase HerA, central domain
      0.064   13.2   0.1       0.15   12.0   0.1    1.7  1  NACHT         NACHT domain
      0.066   13.2   0.1       0.46   10.5   0.0    2.2  2  AAA_14        AAA domain
       0.15   11.3   0.0       0.22   10.8   0.0    1.3  1  Zeta_toxin    Zeta toxin
       0.18   11.9   0.0       0.96    9.6   0.0    2.0  2  AAA_33        AAA domain
        0.2   12.2   0.2       0.43   11.1   0.2    1.9  1  AAA_18        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.2   0.0   3.1e-34   2.2e-31       1     137 []      20     167 ..      20     167 .. 0.88

  Alignments for each domain:
  == domain 1  score: 109.2 bits;  conditional E-value: 3.1e-34
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l+++slk+ +  ++ i+G+nG GKStL+k++++ l+pt+G+il+dg+d+++ ++++l+  ++++p  +q    ++v 
  gi|474934469|ref|YP_007688051.1|  20 LNDISLKIDKPGLYCILGPNGVGKSTLVKCICKILEPTSGQILIDGTDVSKMSRKELSDYVSYVPAFSQDVFSMSVV 96 
                                       799****************************************************************7777777788 PP

                                       HH...............HHHTC...HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx...............xxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en...............esdee...iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       ++               +   +   ++ka++ l ++ l++++     ++LS Gq q+v+lar l+++pk+l+lDEpt
  gi|474934469|ref|YP_007688051.1|  97 DTvmvgrynkktwgsfeH---DlkiVQKAMKLLHIESLATQNY----NELSAGQHQKVSLARGLVQEPKILILDEPT 166
                                       888***987666664432...2445788888888877777777....*****************************9 PP

                                       T CS
                                       x RF
                          ABC_tran 137 a 137
                                       a
  gi|474934469|ref|YP_007688051.1| 167 A 167
                                       7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1     2e-05     0.014       2      19 ..      33      50 ..      32      81 .. 0.72
   2 !   15.5   0.1   1.6e-05     0.011     219     301 ..     115     201 ..      60     203 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2e-05
                            AAA_21  2 nvliGpNgsGKSnLLdal 19
                                       ++ GpNg+GKS+L +++
  gi|474934469|ref|YP_007688051.1| 33 YCILGPNGVGKSTLVKCI 50
                                      589*************99 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.6e-05
                            AAA_21 219 r......gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.n 288
                                               + +l+ ++    +++elS G+ +   l+  l + +   ++l++DEp ++L+ k +  + el+k+ +   
  gi|474934469|ref|YP_007688051.1| 115 DlkivqkAMKLLHIESLATQNYNELSAGQHQKVSLARGLVQEP---KILILDEPTANLDVKYQIYVTELVKSIALaQ 188
                                       0444444778888888889999999999999966666666666...9****************77666664433335 PP

                            AAA_21 289 gaQviltTHSpll 301
                                       g+ v++ +H+  +
  gi|474934469|ref|YP_007688051.1| 189 GIIVLMISHDINI 201
                                       699******9766 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.1   3.3e-09   2.4e-06      15      43 ..      23      54 ..       9      61 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 3.3e-09
                            AAA_23 15 idF...skgltlItGpNGaGKTTildAiklaL 43
                                      i +   ++gl++I GpNG GK+T++ +i+ +L
  gi|474934469|ref|YP_007688051.1| 23 ISLkidKPGLYCILGPNGVGKSTLVKCICKIL 54
                                      45566678********************9665 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.6     5e-08   3.6e-05      23     199 ..      29     197 ..      11     215 .. 0.64

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 5e-08
                                       TSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--...BTTCSSTTEEEEEEEEEETTEESSSSS.S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                             SMC_N  23 sksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk...skekasvkkaeveitfdnedkklkiek.e 95 
                                       ++++ +i+GpNG GKs l+  i+ +L  +s         + li     sk +++  + +v+ +   +++ ++++  +
  gi|474934469|ref|YP_007688051.1|  29 KPGLYCILGPNGVGKSTLVKCICKILEPTSG--------QILIDGtdvSKMSRKELSDYVSYVPAFSQDVFSMSVvD 97 
                                       468899****************888876555........44444433334444455555555544455544444304 PP

                                       CEEEEEEEETTSEEEEEETTEEE-H.HHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  96 evsisrrvkrkgeseykingkevtk.kevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaL 171
                                        v + r  k++   +++ + k v+k  ++ ++ + a  + ++LS G+ + v+la       v+   + +lDe  a+L
  gi|474934469|ref|YP_007688051.1|  98 TVMVGRYNKKTW-GSFEHDLKIVQKaMKLLHIESLATQNYNELSAGQHQKVSLARG----LVQEPKILILDEPTANL 169
                                       455555444443.35555555555534444444445556789******99988754....56677799********* PP

                                       -HHHHHHHHHHHHHHCTTSEEEEE-SSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 172 DeknvkkvaellkeksknaQfivislre 199
                                       D k+   v el+k+      +iv  +++
  gi|474934469|ref|YP_007688051.1| 170 DVKYQIYVTELVKSIALAQGIIVLMISH 197
                                       *************877444444433333 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   2.9e-07   0.00021      16      50 ..      24      58 ..      18      62 .. 0.86
   2 ?   -2.6   0.0       6.8   4.9e+03       9      15 ..     109     116 ..     107     126 .. 0.66

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.9e-07
                            AAA_29 16 tieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      +++id  g + + Gp+G+GKSTl+  i  +L p++
  gi|474934469|ref|YP_007688051.1| 24 SLKIDKPGLYCILGPNGVGKSTLVKCICKILEPTS 58
                                      678898899***************99999998876 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6.8
                            AAA_29   9 Wgtfdg.h 15 
                                       Wg+f++  
  gi|474934469|ref|YP_007688051.1| 109 WGSFEHdL 116
                                       99998732 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.6e-06    0.0018      15      72 ..      21      75 ..      19     148 .. 0.84
   2 ?    0.4   0.0      0.56   4.1e+02     323     354 ..     156     187 ..     150     202 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.6e-06
                            AAA_15 15 kdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifenis 72
                                       d+++++++  l ++ G+N++GKS++++ + ++l+ +    +  i i+  d++++  ++
  gi|474934469|ref|YP_007688051.1| 21 NDISLKIDKPgLYCILGPNGVGKSTLVKCICKILEPT----SGQILIDGTDVSKMSRKE 75
                                      67888888889*******************9999988....566677777766665554 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.56
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkeland 354
                                       +++il+++EP a+L  + q  + +l k++a  
  gi|474934469|ref|YP_007688051.1| 156 EPKILILDEPTANLDVKYQIYVTELVKSIALA 187
                                       6899**********999999999999999865 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   7.4e-07   0.00053      22      67 ..      28      77 ..      17     164 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 7.4e-07
                            AAA_16 22 grpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesa....i 67
                                      + p+l  + G+ GvGKs+lv+++ + le + g  l   +d ++++     
  gi|474934469|ref|YP_007688051.1| 28 DKPGLYCILGPNGVGKSTLVKCICKILEPTSGQILIDGTDVSKMSrkelS 77
                                      5678889*****************99999976665555555544433442 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   2.2e-06    0.0016       2      41 ..      34      82 ..      33     200 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.2e-06
                                      EEESSTTSSHHHHHHHHHHHH..........THEEEEEETTTCSSSSTTH CS
                               AAA  2 llyGppGtGKTllakavakel..........gvefleisgsellskyvge 41
                                      ++ Gp G+GK++l+k ++k l          g+++ ++s +el  +yv+ 
  gi|474934469|ref|YP_007688051.1| 34 CILGPNGVGKSTLVKCICKILeptsgqilidGTDVSKMSRKELS-DYVSY 82
                                      789*****************944433333333444444444444.33333 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   1.6e-06    0.0011      35     148 ..      20     138 ..      13     168 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.6e-06
                             Rad17  35 lkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklre.wlnpvslkepdn.qksdfkgltekesrflsqiesf 109
                                       l+  +L+  k  +  i GP G gkst vk + k+l +   +  ++++ + + +  + sd+ + +  +s+ +  + + 
  gi|474934469|ref|YP_007688051.1|  20 LNDISLKIDKPGLYCILGPNGVGKSTLVKCICKILEPTSGQiLIDGTDVSKMSRkELSDYVSYVPAFSQDVFSMSVV 96 
                                       555667777677999********************987766257899987777735589999988888664444444 PP

                             Rad17 110 keleLkdakylk.....lqklGddlrtdkklilvedlPnkfyrd 148
                                         +  +  +y+k     +++  + ++   kl+ +e l  + y +
  gi|474934469|ref|YP_007688051.1|  97 DTV--MVGRYNKktwgsFEHDLKIVQKAMKLLHIESLATQNYNE 138
                                       444..333333311111333444456666777777777655555 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.3e-06    0.0016      27      92 ..      35     102 ..      16     114 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.3e-06
                      Mg_chelatase  27 lvGppGsGKtmlakrlpsllpplseeealevakiasvagkkeeekllkrrpfraphhsaska..alvG 92 
                                       ++Gp G GK+ l k++ ++l p s +  ++ + ++ +++k+ ++ +   + f +   s+s +   +vG
  gi|474934469|ref|YP_007688051.1|  35 ILGPNGVGKSTLVKCICKILEPTSGQILIDGTDVSKMSRKELSDYVSYVPAFSQDVFSMSVVdtVMVG 102
                                       68*************************************99999999999999988887765114555 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0     9e-06    0.0065      87     122 ..      17      53 ..       3      74 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 9e-06
                                       HTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  87 kegleelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                       ++ l++++ ++++  + +++G+ GvGKStL++ +   
  gi|474934469|ref|YP_007688051.1|  17 SQVLNDISLKIDKpGLYCILGPNGVGKSTLVKCICKI 53 
                                       56677888888888999**************998765 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.1   0.00012     0.086       3      84 ..      34     130 ..      32     164 .. 0.52
   2 ?    1.2   0.0      0.53   3.8e+02      45      57 ..     206     218 ..     146     224 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                                       EEEESTTSSHHHHHHHHHT.......S.TEEESSSTTSSSSEEEEEEE......ETTEEEEEEECGGCSS.HHHHHH CS
                          MMR_HSR1   3 aivGrpNvGKStLinaltg.......e.kaivsdkpgtTrdinegrvk......lkgkeielvDtpGlie.gaseek 64 
                                       +i+G   vGKStL++ +++       +     +d     r+     v+       +  ++ +vDt+  +   +++ +
  gi|474934469|ref|YP_007688051.1|  34 CILGPNGVGKSTLVKCICKileptsgQiLIDGTDVSKMSRKELSDYVSyvpafsQDVFSMSVVDTVM-VGrYNKKTW 109
                                       799***************8443333211112223333333332222223333322224577777765.332345555 PP

                                       .HHHHHHHHHHCTSEEEEEEE CS
                          MMR_HSR1  65 .glgkaflaleeadlillvvd 84 
                                        +++++++ +++a  +l++ +
  gi|474934469|ref|YP_007688051.1| 110 gSFEHDLKIVQKAMKLLHIES 130
                                       344444444444555555554 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.53
                                       TEEEEEEECGGCS CS
                          MMR_HSR1  45 gkeielvDtpGli 57 
                                        ++i+l+ tpG+i
  gi|474934469|ref|YP_007688051.1| 206 ADQIILMNTPGVI 218
                                       2579999999965 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   4.2e-05      0.03       2      26 ..      34      58 ..      33     102 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.2e-05
                      RNA_helicase  2 wlyGpsgeGKStlakeLakallkkl 26
                                      ++ Gp+g+GKStl+k ++k l+ ++
  gi|474934469|ref|YP_007688051.1| 34 CILGPNGVGKSTLVKCICKILEPTS 58
                                      789*************999998555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.3   7.7e-05     0.055       4      31 ..      29      56 ..      26     215 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.7e-05
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleqlde 31
                                      + g+ ++ G+ G+GK+tl++ + + l+ 
  gi|474934469|ref|YP_007688051.1| 29 KPGLYCILGPNGVGKSTLVKCICKILEP 56
                                      578999*************998887753 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0     6e-05     0.043       4      38 ..      35      71 ..      33     125 .. 0.82
   2 ?   -2.9   0.0       7.7   5.5e+03      94     103 ..     155     164 ..     138     202 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6e-05
                                      EE--TTSSHHHHHHHHHHHH.....GGGEEEEEEEEE CS
                          NTPase_1  4 iTGppGvGKtTlvkkvlellkss..gvkvgGfyteev 38
                                      i Gp GvGK+Tlvk +++ l+    ++ ++G  ++++
  gi|474934469|ref|YP_007688051.1| 35 ILGPNGVGKSTLVKCICKILEPTsgQILIDGTDVSKM 71
                                      77****************9975422566666665555 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 7.7
                                       HHH-EEEE-- CS
                          NTPase_1  94 seadviviDE 103
                                       +e+ ++++DE
  gi|474934469|ref|YP_007688051.1| 155 QEPKILILDE 164
                                       5556666666 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   5.8e-05     0.042      16      49 ..      22      53 ..       6      54 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.8e-05
                            AAA_27 16 drsldfsaeeadlhliyGpNEAGKstalrAisdl 49
                                      d s  ++ ++++l  i+GpN  GKst+++ i ++
  gi|474934469|ref|YP_007688051.1| 22 DIS--LKIDKPGLYCILGPNGVGKSTLVKCICKI 53
                                      444..45569*****************9998766 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00019      0.14       3      24 ..      34      56 ..      33      81 .. 0.86
   2 ?   -1.2   0.0       2.6   1.8e+03      63      73 ..     154     164 ..     112     172 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00019
                                      EEE--SSSSHHHHHHHGGGGB.S CS
                             AAA_5  3 lLvGppGtgKselaerlaaal.n 24
                                      +++Gp G+gKs+l++ +++ l  
  gi|474934469|ref|YP_007688051.1| 34 CILGPNGVGKSTLVKCICKILeP 56
                                      89***************999853 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.6
                                       --G-SEEEEES CS
                             AAA_5  63 aregeilvlDE 73 
                                       ++e++il+lDE
  gi|474934469|ref|YP_007688051.1| 154 VQEPKILILDE 164
                                       34888888888 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   0.00011     0.076      21      68 ..      31      79 ..      18     189 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                          ATPase_2 21 eiyfiYGpegsGKtaLlkeiienledk.dkyviyyialreesiskldef 68
                                        y i Gp g+GK++L+k i + le   ++  i  +++++ s ++l+++
  gi|474934469|ref|YP_007688051.1| 31 GLYCILGPNGVGKSTLVKCICKILEPTsGQILIDGTDVSKMSRKELSDY 79
                                      5799***************999985430334444444444444444444 PP

>> AAA_PrkA  PrkA AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1     0.001      0.74      92     115 ..      34      57 ..      22      76 .. 0.80
   2 ?    2.5   0.0     0.074        53      32      75 ..      59     102 ..      55     186 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.001
                          AAA_PrkA  92 yllGPvggGksslverlkklleaa 115
                                        +lGP g Gks+lv+ + k+le +
  gi|474934469|ref|YP_007688051.1|  34 CILGPNGVGKSTLVKCICKILEPT 57 
                                       379*****************9976 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.074
                          AAA_PrkA  32 glelvdtaederlsrifsnetikkypafeedffGleetiekive 75 
                                       g +l+d ++ +++sr    + +   paf++d+f +  +   +v+
  gi|474934469|ref|YP_007688051.1|  59 GQILIDGTDVSKMSRKELSDYVSYVPAFSQDVFSMSVVDTVMVG 102
                                       55677888888888888888888888888888888654444444 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   0.00015       0.1      26      59 ..      33      64 ..      15     185 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00015
                             DUF87 26 lAilgsTGsGKSntvavLleellekkgatililD 59
                                       +ilg  G+GKS++v+ +++ l  ++ +  +++D
  gi|474934469|ref|YP_007688051.1| 33 YCILGPNGVGKSTLVKCICKIL--EPTSGQILID 64
                                      589**************99754..4666555555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00021      0.15       3      24 ..      33      54 ..      31      72 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00021
                                      EEEEC-TTTCHHHHHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqklalaw 24
                                       ++ G++G+GK+tL++ ++  +
  gi|474934469|ref|YP_007688051.1| 33 YCILGPNGVGKSTLVKCICKIL 54
                                      689*************998765 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00064      0.46       4      43 ..      32      70 ..      29      96 .. 0.72
   2 ?   -0.2   0.0       1.3   9.3e+02      53      72 ..     145     164 ..     108     172 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00064
                            AAA_14  4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderd 43
                                      +++i G+  vGK+tl+k + k l  + +  + i+  d ++
  gi|474934469|ref|YP_007688051.1| 32 LYCILGPNGVGKSTLVKCICKILE-PTSGQILIDGTDVSK 70
                                      5789************98886655.555555565555555 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.3
                            AAA_14  53 lelilek.lkeekktylflDE 72 
                                        ++ l++ l  ++ ++l+lDE
  gi|474934469|ref|YP_007688051.1| 145 QKVSLARgLV-QEPKILILDE 164
                                       2222222222.4788999999 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00031      0.22      12      79 ..      26      86 ..      16     106 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00031
                        Zeta_toxin 12 sqerPklillgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPeyeeilkadpkkaseltqkd 79
                                      + ++P l+ + G  G GKs+l + + + le++++ + +d++d+ ++ ++         +++++++ ++
  gi|474934469|ref|YP_007688051.1| 26 KIDKPGLYCILGPNGVGKSTLVKCICKILEPTSGQILIDGTDVSKMSRKEL-------SDYVSYVPAF 86
                                      4589************************************99988775522.......2444444444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0    0.0013      0.96       4      24 ..      35      55 ..      32     111 .. 0.83
   2 ?    0.2   0.0         1   7.4e+02      14      37 ..     148     171 ..     130     209 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0013
                            AAA_33  4 lvGlpGsGKstlaerllkklg 24
                                      + G++G+GKstl++ ++k l 
  gi|474934469|ref|YP_007688051.1| 35 ILGPNGVGKSTLVKCICKILE 55
                                      67***********98887655 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1
                            AAA_33  14 tlaerllkklgavllssdtlrrrl 37 
                                        la++l+++ +  +l+++t+   +
  gi|474934469|ref|YP_007688051.1| 148 SLARGLVQEPKILILDEPTANLDV 171
                                       688999999889999999865444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2    0.0006      0.43       2      22 ..      34      54 ..      34     206 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0006
                            AAA_18  2 lltGtpGvGKttlakeLskrl 22
                                      ++ G+ GvGK+tl k + k l
  gi|474934469|ref|YP_007688051.1| 34 CILGPNGVGKSTLVKCICKIL 54
                                      799*********998775554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.72u 0.34s 00:00:01.06 Elapsed: 00:00:00.55
# Mc/sec: 1225.60
//
Query:       gi|474934470|ref|YP_007688052.1|  [L=356]
Description: ABC-type Fe3+-siderophore transport system, permease component [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-85  286.1  33.3    3.4e-85  285.8  33.3    1.1  1  FecCD     FecCD transport family


Domain annotation for each model (and alignments):
>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  285.8  33.3   1.9e-89   3.4e-85       3     312 .]      36     350 ..      30     350 .. 0.97

  Alignments for each domain:
  == domain 1  score: 285.8 bits;  conditional E-value: 1.9e-89
                             FecCD   3 llllllslllgavkispsevfeallgka.....dsleaeivlelrlprvlaallvGaaLavaGallQtvtrNpLadP 74 
                                       +l+  +sl++g++++ + e+++ ++++      d++ + +v+++rlprvl ++++G +Lav+G+++Q+v++NpLadP
  gi|474934470|ref|YP_007688052.1|  36 VLIAGYSLSAGKTQVGFVETYSTIFHHImgdiqDKFIDYMVVDIRLPRVLGGIIAGSGLAVCGVVMQSVLKNPLADP 112
                                       55667899********99999999999899889999999************************************** PP

                             FecCD  75 silGissgaalgavlallll.lgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsaltsl 150
                                        + G+ssga++ga++a+ ++ ++ ++ ++l+++af+++++ ++++++l+ k+++asp+++i+aGi v ++++a+t++
  gi|474934470|ref|YP_007688052.1| 113 FTTGVSSGASFGATIAISTGmVLYFGYVSLITLAFVCSMVPIFMIIVLS-KTSKASPTTMIMAGIGVMYIFNAFTTV 188
                                       *******************999999************************.*************************** PP

                             FecCD 151 lllllneealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrllllll 227
                                       l+l++n+++l+si++w +Gsls ++++++ ++  +++++l+++ +l+ kl++la+gd++Ak++G++ e++r++llll
  gi|474934470|ref|YP_007688052.1| 189 LKLWANPDDLSSIYTWEVGSLSMVTLDQLPIMGGICIVGLIVVQILSGKLNILATGDDNAKAMGIDAETLRIILLLL 265
                                       ***************************************************************************** PP

                             FecCD 228 valltavavalvGpigFvGLivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivtaliGap 304
                                       + l++a++v+++G igF+GL+ Phi+r++vgad+r+l+p+sa++G+++l+ladl++r +l p+ l+vg+v++++G+p
  gi|474934470|ref|YP_007688052.1| 266 TGLISASIVSFTGLIGFIGLVSPHICRMFVGADNRYLIPASAMFGSMFLILADLIGRAFLGPIMLQVGVVMSFVGGP 342
                                       ***************************************************************************** PP

                             FecCD 305 ffiylllr 312
                                       +fi+l+l+
  gi|474934470|ref|YP_007688052.1| 343 LFIMLILK 350
                                       *****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       769  (0.0428914); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2126.59
//
Query:       gi|474934471|ref|YP_007688053.1|  [L=32]
Description: hypothetical protein TALC_00898 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
          1    8.9   2.4          1    8.9   2.4    1.0  1  DUF3153   Protein of unknown function (DUF3153)


Domain annotation for each model (and alignments):
>> DUF3153  Protein of unknown function (DUF3153)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   2.4   5.8e-05         1     167     184 ..       4      21 ..       2      26 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 5.8e-05
                           DUF3153 167 LgiGlllillllliglll 184
                                       LgiG+++i ++++i+l++
  gi|474934471|ref|YP_007688053.1|   4 LGIGVIVITAIVAIALFI 21 
                                       9**************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (32 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       787  (0.0438954); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.31s 00:00:00.73 Elapsed: 00:00:00.48
# Mc/sec: 198.85
//
Query:       gi|474934472|ref|YP_007688054.1|  [L=336]
Description: putative methanogenesis marker protein 2 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-16   61.0   1.3    2.4e-16   60.1   1.3    1.4  1  AIRS      AIR synthase related protein, N-terminal domain
    2.6e-14   53.7   0.0    1.3e-13   51.3   0.0    2.2  2  AIRS_C    AIR synthase related protein, C-terminal domain
  ------ inclusion threshold ------
      0.039   14.0   0.9        1.9    8.6   0.0    2.2  2  GvpH      GvpH


Domain annotation for each model (and alignments):
>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   1.3   4.1e-20   2.4e-16       1      94 []      43     149 ..      43     149 .. 0.85

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 4.1e-20
                                       SSSEE.........EEEEEEEE.EECC.TCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC...HHHHHHHHHHH CS
                              AIRS   1 dDaav.........vvttdshnrpvlv.epvhfiGakavavnlsDlaamGArPlalllslalp...wleevvrglae 64 
                                       +Daav         ++++d+  ++++  +p+   G+ av vn++D+aamG+r +a++++++++   ++ +++rg++e
  gi|474934472|ref|YP_007688054.1|  43 EDAAVietqegictLFAADGIMESLVNsDPYMA-GYFAVLVNVNDIAAMGGRATAMVDVMSMEdeiICGRMLRGMEE 118
                                       688855555555668888877777776577777.******************************************* PP

                                       HHHHTT-EEEEEEEEEESS.EEEEEEEEEEE CS
                              AIRS  65 aaeelgvplvgGdtsfsne.ptisvtavGlv 94 
                                       ++++++vp+vgG+t+ + +   + ++++G+v
  gi|474934472|ref|YP_007688054.1| 119 GVHRFNVPIVGGHTHPDCSyHALDISVIGTV 149
                                       ***************9966677888888865 PP

>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.36   2.1e+03      97     121 ..      34      60 ..      11      62 .. 0.65
   2 !   51.3   0.0   2.2e-17   1.3e-13      38     153 ..     189     305 ..     152     308 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.36
                                       HHHHH..HHHHHHHCSTTTEEEEEEEH CS
                            AIRS_C  97 fdele..splemllsensGrllvavpp 121
                                       f ++   ++++++++e++++ + ++++
  gi|474934472|ref|YP_007688054.1|  34 FPNVIasEGEDAAVIETQEGICTLFAA 60 
                                       333334478999999999988776665 PP

  == domain 2  score: 51.3 bits;  conditional E-value: 2.2e-17
                                       HHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHHHHHHTTTEEEEEECG..THHHHHHHHHHHHHHHCSTT CS
                            AIRS_C  38 lgdvlleptliyvkralaalkglvkaahDvTgGGLlgalaemapasgvgaeidld..kvpifdelesplemllsens 112
                                         d+  ++++++++++ a++ +lv+a +D+++ G +g+l ++++ s+ ga++dld    p  ++  +++  ++  ++
  gi|474934472|ref|YP_007688054.1| 189 AKDPKTVQRQMDAAARVAEE-HLVHAGKDMSNPGCVGTLGMLLESSEMGAVVDLDaiPAPKGCKDLEDFIHWILSYQ 264
                                       67888888888888888887.**********************************554444444449********** PP

                                       TEEEEEEEHGGH.HHHHHHHHHTTCCCEEEEEEEEESSSEEE CS
                            AIRS_C 113 Grllvavppeea.davlaileeeglpeaavIGevtakeelsv 153
                                       G ++v    ++  ++v++i+++ g+ + av+G++  +++ ++
  gi|474934472|ref|YP_007688054.1| 265 GCGFVYTCDPSCsQKVIDIFSKVGC-TGAVVGKINSSKRYEL 305
                                       *999988877777************.6********9998776 PP

>> GvpH  GvpH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0   0.00031       1.9     101     148 ..      26      75 ..      14      91 .. 0.84
   2 ?    3.9   0.2    0.0082        49      94     123 ..     157     186 ..     144     211 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00031
                              GvpH 101 delvvvadlpGvtded.vdval.etdeqaltlrvdddvverlvlddpdva 148
                                        +l+ v+ +p v   +  d+a+ et+e+  tl   d ++e lv  dp +a
  gi|474934472|ref|YP_007688054.1|  26 VDLLPVSKFPNVIASEgEDAAViETQEGICTLFAADGIMESLVNSDPYMA 75 
                                       578889999999877768887549***********************997 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0082
                              GvpH  94 trasddsdelvvvadlpGvtdedvdvalet 123
                                       + ++ d+d++v+v dl G   +++  a et
  gi|474934472|ref|YP_007688054.1| 157 SSTARDGDDVVMVMDLDGHYPKSIPYAWET 186
                                       567889***********9887777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 1977.64
//
Query:       gi|474934473|ref|YP_007688055.1|  [L=188]
Description: hypothetical protein TALC_00900 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1198.02
//
Query:       gi|474934474|ref|YP_007688056.1|  [L=514]
Description: putative secreted protein containing a PDZ domain [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.5e-20   71.7   0.0    1.4e-19   70.4   0.0    1.7  1  Peptidase_M50  Peptidase family M50
    2.4e-15   56.6   0.5    2.2e-11   43.9   0.1    2.4  2  PDZ_2          PDZ domain
    1.6e-14   53.5   0.0    3.8e-07   29.9   0.0    2.4  2  PDZ_6          PDZ domain
    1.1e-08   35.3   0.0    0.00024   21.4   0.0    2.5  2  PDZ            PDZ domain
  ------ inclusion threshold ------
      0.044   13.1   0.0      0.066   12.5   0.0    1.2  1  DUF4498        Domain of unknown function (DUF4498)
      0.076   13.4   0.5      0.076   13.4   0.5    2.7  2  CstA_5TM       5TM C-terminal transporter carbon starvation C
      0.077   13.0   0.1        1.4    9.0   0.0    2.3  2  Tricorn_PDZ    Tricorn protease PDZ domain


Domain annotation for each model (and alignments):
>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.4   0.0   5.3e-23   1.4e-19       2     231 ..     120     479 ..     119     504 .. 0.84

  Alignments for each domain:
  == domain 1  score: 70.4 bits;  conditional E-value: 5.3e-23
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50   2 filllgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallpLGGyVkmageepeeelseeeaka 78 
                                       ++l+l+i vv+HE++H++  +++g+kve+ + +              Y   ++p+G++V+ ++++            
  gi|474934474|ref|YP_007688056.1| 120 TLLALIIAVVLHEFAHGVQTRANGMKVENTGGL--------------Y--CVVPVGAFVEPDQTD------------ 168
                                       789************************994433..............4..679************............ PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX............................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................................... RF
                     Peptidase_M50  79 flkkspwqrllivlAGplanfilailvfvv............................................... 108
                                        +  s  ++l  + AG+ anfi+a ++f++                                               
  gi|474934474|ref|YP_007688056.1| 169 VDRCSRTAKLDLFSAGISANFIIAGVAFLLfsvvmlggmtnqyednaaiygevegspadiagipsgaiilsmngqav 245
                                       5667999********************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Peptidase_M50 109 ............................................................................. 108
                                                                                                                    
  gi|474934474|ref|YP_007688056.1| 246 lyedfddpvkmsavrgpfylvtityvqdgsgvattsaaipwgmyiskladdspagkaglskgdtivkmndtevftss 322
                                       ***************************************************************************** PP

                                       .............................-EEECECTTTSCEE-SEEEC-........XXXXXXXXXXXXXXXXXXX CS
                                       .............................xxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 109 .............................pkkskeseeekrgviGvspkp........vkkegllealkegvektlk 148
                                                                     +  +e+ +++ g++Gv+ ++         +  + ++   +gv+++ +
  gi|474934474|ref|YP_007688056.1| 323 qftdymkttskgetvtityvdannavqttTAVLEENGNKGYGYLGVYTSTsglnlltpSQVLDKARNPLYGVDSLTD 399
                                       *****999999999999999998887655333344889999999999999776654332222222222334444444 PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 149 vvvltvkalgklitgklslktlggpisiaqlaseaaeaglssflqllalisvnLgilNLlPipvLDGghllfallea 225
                                       + ++++ +l + +     ++ l  +i       +a+ +++ ++l++l+++++ Lgi+N+lP  ++DGg +++  +++
  gi|474934474|ref|YP_007688056.1| 400 LPQALMGYLTMPY---SGFDPLPSSIQWWYGDYNAFFWSFLELLYWLFWLNILLGITNALPAVPFDGGYIFQGWVDR 473
                                       4444444444444...4467776666666666778889999*****************************9988877 PP

                                       XXXXXX CS
                                       xxxxxx RF
                     Peptidase_M50 226 irrkpl 231
                                       + ++  
  gi|474934474|ref|YP_007688056.1| 474 LLERIG 479
                                       765544 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   0.00022      0.57      15      46 ..     214     245 ..     202     275 .. 0.76
   2 !   43.9   0.1   8.5e-15   2.2e-11      15      76 ..     287     348 ..     274     354 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00022
                                       -EEEEEE-TTSGGGGT.--TT-EEEEETTB-- CS
                             PDZ_2  15 gvlvvsVkeggPaakaglkagDvilkvdgkkv 46 
                                        + ++   eg+Pa+ ag+ +g +il+ +g++v
  gi|474934474|ref|YP_007688056.1| 214 NAAIYGEVEGSPADIAGIPSGAIILSMNGQAV 245
                                       5666666799*******************998 PP

  == domain 2  score: 43.9 bits;  conditional E-value: 8.5e-15
                                       -EEEEEE-TTSGGGGT.--TT-EEEEETTB--SSHHHHHHHHHTS-TT-EEEEEEEETTEEE CS
                             PDZ_2  15 gvlvvsVkeggPaakaglkagDvilkvdgkkvksledlislllkkkpGdtVkltvlRdgkkk 76 
                                       g+++ +  +++Pa kagl +gD+i+k ++++v +++++  ++ ++++G+tV++t+   ++  
  gi|474934474|ref|YP_007688056.1| 287 GMYISKLADDSPAGKAGLSKGDTIVKMNDTEVFTSSQFTDYMKTTSKGETVTITYVDANNAV 348
                                       78999**************************************************9866654 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0     8e-08   0.00021       5      30 ..     220     245 ..     217     258 .. 0.86
   2 !   29.9   0.0   1.5e-10   3.8e-07       4      53 ..     292     340 ..     289     342 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 8e-08
                             PDZ_6   5 VdpgsPAdrAGlrvGDiilsvNGqpv 30 
                                        ++gsPAd AG+  G iils NGq v
  gi|474934474|ref|YP_007688056.1| 220 EVEGSPADIAGIPSGAIILSMNGQAV 245
                                       689**********************9 PP

  == domain 2  score: 29.9 bits;  conditional E-value: 1.5e-10
                             PDZ_6   4 aVdpgsPAdrAGlrvGDiilsvNGqpveglsladvaallr.gsagesvvlv 53 
                                           +sPA +AGl  GD+i++ N+++v   +  ++ ++++ +s ge v+++
  gi|474934474|ref|YP_007688056.1| 292 KLADDSPAGKAGLSKGDTIVKMNDTEV--FTSSQFTDYMKtTSKGETVTIT 340
                                       56679**********************..***********99999999987 PP

>> PDZ  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.1   0.00013      0.32      30      58 ..     217     245 ..     202     256 .. 0.82
   2 !   21.4   0.0   9.2e-08   0.00024      27      80 ..     287     340 ..     267     342 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
                                       EEEECTTSHHHHHTSSTTEEEEEETTEET CS
                               PDZ  30 vsevlpggaaeadglkvGDkIlsvNgvdv 58 
                                       +   ++g++a+ +g+  G +Ils+Ng+ v
  gi|474934474|ref|YP_007688056.1| 217 IYGEVEGSPADIAGIPSGAIILSMNGQAV 245
                                       55557899999999************976 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 9.2e-08
                                       SEEEEEECTTSHHHHHTSSTTEEEEEETTEETTTSHHHHHHHHHHTTTSEEEEE CS
                               PDZ  27 gifvsevlpggaaeadglkvGDkIlsvNgvdvenvsheeavqaikgskgkvtLt 80 
                                       g ++s++  +++a ++gl++GD I+++N++ v + s+ +   ++++++++vt+t
  gi|474934474|ref|YP_007688056.1| 287 GMYISKLADDSPAGKAGLSKGDTIVKMNDTEVFTSSQFTDYMKTTSKGETVTIT 340
                                       78********8888888************9998888777777777777787766 PP

>> DUF4498  Domain of unknown function (DUF4498)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.6e-05     0.066     154     179 ..     196     221 ..     175     224 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.6e-05
                           DUF4498 154 frlfkhlvlGGelcQyedelqpYlet 179
                                       f lf++++lGG  +Qyed+   Y e+
  gi|474934474|ref|YP_007688056.1| 196 FLLFSVVMLGGMTNQYEDNAAIYGEV 221
                                       99*****************9999765 PP

>> CstA_5TM  5TM C-terminal transporter carbon starvation CstA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.5     3e-05     0.076      64      93 ..      49      84 ..       2      94 .. 0.73
   2 ?    0.2   0.5      0.36   9.2e+02      74      93 ..     185     204 ..     116     217 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3e-05
                          CstA_5TM 64 g......gintlWplFGaaNQlLAalaLlvvtvwll 93
                                      +      ++  +W+ FG+a Q+ A + ++ ++++++
  gi|474934474|ref|YP_007688056.1| 49 KlmdrlgKYRRFWRFFGIASQVFAFVEMVFMVFMIV 84
                                      03334449*******************999998876 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.36
                          CstA_5TM  74 GaaNQlLAalaLlvvtvwll 93 
                                        +aN ++A++a+l+++v++l
  gi|474934474|ref|YP_007688056.1| 185 ISANFIIAGVAFLLFSVVML 204
                                       46788888888888887776 PP

>> Tricorn_PDZ  Tricorn protease PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.12     3e+02      28      54 ..     221     245 ..     214     254 .. 0.84
   2 ?    9.0   0.0   0.00053       1.4      29      83 ..     295     348 ..     284     354 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.12
                                       S-B-GGGGGS---.TT-EEEEETTEE- CS
                       Tricorn_PDZ  28 earSPLaepGvnvreGdlilavdgepv 54 
                                        + SP    G+    G++il+ +g+ v
  gi|474934474|ref|YP_007688056.1| 221 VEGSPADIAGIP--SGAIILSMNGQAV 245
                                       567888889999..9**********98 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00053
                                       -B-GGGGGS---.TT-EEEEETTEE-BTTB-HHHHHHTT.TTSEEEEEEE-STT-E CS
                       Tricorn_PDZ  29 arSPLaepGvnvreGdlilavdgepvskekgiaelLvgk.agkeveLtvkrkdgka 83 
                                         SP  + G+   +Gd+i++ ++ +v +++++  ++  + +g++v++t+ ++++ +
  gi|474934474|ref|YP_007688056.1| 295 DDSPAGKAGLS--KGDTIVKMNDTEVFTSSQFTDYMKTTsKGETVTITYVDANNAV 348
                                       56899999999..9***************999999876615699999998877644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (514 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1030  (0.0574488); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.48
# Mc/sec: 3213.33
//
Query:       gi|474934475|ref|YP_007688057.1|  [L=221]
Description: putative Rossmann fold enzyme [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.5e-23   82.6   0.0    3.1e-23   82.3   0.0    1.1  1  MAF_flag10  Protein of unknown function DUF115


Domain annotation for each model (and alignments):
>> MAF_flag10  Protein of unknown function DUF115
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.3   0.0   1.7e-27   3.1e-23      25     169 ..      51     186 ..      30     188 .. 0.86

  Alignments for each domain:
  == domain 1  score: 82.3 bits;  conditional E-value: 1.7e-27
                        MAF_flag10  25 nkpaiivgaGPSLeknlellkelrdkaviiaadtalkaLlkegIkPDivvs.lDpqeasyevfkeaekkgdiplvfa 100
                                        +++ ++g  P Le++l  l     + +ii+a++a++  + +gI+PDivv+ lD+    +e   +++++g ++l+ a
  gi|474934475|ref|YP_007688057.1|  51 GDTVTVIGDSPQLESDLRELP---PEGCIISAGSATERVVAAGIRPDIVVTdLDG---PIEAQIGCSRDGAVTLILA 121
                                       37999**********999996...99*****************************...777779999999******* PP

                        MAF_flag10 101 sgvnpellkkykgpkiflvtgstqalelleeekneilfgGgsvantaldlAvklgfkeIiliGqDlayt 169
                                       +g+n +l+++y ++      ++++ + + + + n+ +fgG++++++++ lA+++g+++Iil+G+D++ +
  gi|474934475|ref|YP_007688057.1| 122 HGDNQDLVRAYAPQFR---GKVVL-TTQGKPSGNVLNFGGFTDGDRSVCLARHFGASRIILLGFDFSNP 186
                                       ************9944...33333.223333444499*****************************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       213  (0.0118802); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.20s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1733.67
//
Query:       gi|474934476|ref|YP_007688058.1|  [L=384]
Description: putative membrane protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-89  300.3  13.5    2.4e-89  300.1  13.5    1.0  1  DUF373           Domain of unknown function (DUF373)
  ------ inclusion threshold ------
      0.029   14.2   0.0      0.051   13.5   0.0    1.4  1  Cas_APE2256      CRISPR-associated protein (Cas_APE2256)
       0.07   12.9   0.1       0.13   12.1   0.1    1.4  1  Glycos_transf_2  Glycosyl transferase family 2
       0.14   11.7   0.9       0.46   10.1   0.9    1.8  1  PIRT             Phosphoinositide-interacting protein family
        4.7    7.3  16.4        5.3    7.2   5.6    2.5  2  Fumarate_red_D   Fumarate reductase subunit D


Domain annotation for each model (and alignments):
>> DUF373  Domain of unknown function (DUF373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  300.1  13.5   6.8e-93   2.4e-89       1     335 []       6     356 ..       6     356 .. 0.95

  Alignments for each domain:
  == domain 1  score: 300.1 bits;  conditional E-value: 6.8e-93
                            DUF373   1 ktLvlcvDrDdDlgrkagvktPvvGreavleaavklaladPeDSDvNalfgaikvydeLka..egedvevavvtGde 75 
                                       ++Lvl+vDrDdD+grk gv+tP+vG +a+leaa+k+++++PeDSD+Nal++ai+ y+++ a  + e+v+va+++Gde
  gi|474934476|ref|YP_007688058.1|   6 RVLVLAVDRDDDFGRKGGVQTPCVGVDACLEAAQKFGVKEPEDSDLNALYNAIHEYNDILAshDAEEVQVALICGDE 82 
                                       68********************************************************99877899*********** PP

                            DUF373  76 kvgveadrkiaeqldevlskleadsaivVsDGaeDesvlpiiqsrvkvdsvkrVvVkqsrniEstyyllkkalkdpe 152
                                       +vg ++dr+++eql+evls++ead+++vV+DG+eD+ v+++i+  v+++ vk  vVkq+rn E++ +++  ++k+pe
  gi|474934476|ref|YP_007688058.1|  83 SVGRRSDRRVREQLEEVLSQFEADEIVVVTDGSEDKGVIEYIMGLVHIIDVKATVVKQTRNAETIIAIIAGYMKEPE 159
                                       ***************************************************************************** PP

                            DUF373 153 lrktiLvplGlllliyallll...........lglpelalaiillllGlylllrGfgldelleelleklkesleegr 218
                                        rk +L pl++l++++++++l             + ++++ +i+l++G++++l++++lde+++  l+++ + +++g+
  gi|474934476|ref|YP_007688058.1| 160 KRKRFLAPLSWLIIFISMIYLaanlftsdsvdKFFLGSTTLFIFLAMGVLIMLYAYSLDEKIRGGLHHFMDRVRAGS 236
                                       ******************************99447799*************************************** PP

                            DUF373 219 itfvtyvvallllligiisgyislesvssasvssglltlilafiygavewlalailtaslgkiideylkreekdiar 295
                                       i++v++++a+ll+l+gii g++s++++++    +++++++l+fi++ ++  +++i+++++g ++d y++r+ + ++ 
  gi|474934476|ref|YP_007688058.1| 237 IIIVFVIAAVLLFLFGIILGVYSMDDIYT----TRTTERVLVFIANGMWPALFGIMMYLFGVLVDGYMSRR-SIRYL 308
                                       ****************************9....78999******************************655.55555 PP

                            DUF373 296 llllpflvlaiglvlygasaylls........lsilalslvvgivval 335
                                        ++ ++ vlaigl+++ga +yl+         + i+++ +++gi+va+
  gi|474934476|ref|YP_007688058.1| 309 SIIGCLNVLAIGLIMTGALDYLIGytglfttsYIIIMAEIFSGIIVAV 356
                                       568899****************87999999877778888899998875 PP

>> Cas_APE2256  CRISPR-associated protein (Cas_APE2256)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.4e-05     0.051      17     103 ..      65     155 ..      49     179 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.4e-05
                       Cas_APE2256  17 kkkeqke..elvllssdTaaGklvaeilkeyleeegaevevveieklsdlgree....FreglrnLveklarevknk 87 
                                         ++ +e  ++ l++ d   G+++ + ++e lee   + e  ei+ ++d ++++    +  gl+ +++  a++vk  
  gi|474934476|ref|YP_007688058.1|  65 LASHDAEevQVALICGDESVGRRSDRRVREQLEEVLSQFEADEIVVVTDGSEDKgvieYIMGLVHIIDVKATVVK-- 139
                                       2222222569************************555555555555655554444443888*******9999999.. PP

                       Cas_APE2256  88 kregekvlinaTgGfK 103
                                       +++  + +i++ +G+ 
  gi|474934476|ref|YP_007688058.1| 140 QTRNAETIIAIIAGYM 155
                                       4555557888888874 PP

>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   3.5e-05      0.13      13      73 ..      92     152 ..      87     156 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.5e-05
                                       HHHHHHHHHHHGGCCEEEEEEEEES-.SSCHHHHHGGGCH.C-TTEEEEEESSS-HHHHHHHH CS
                   Glycos_transf_2  13 lletlesllaqdpypdfeiivvDDgS.tDetveileelak.edprvrvirreenvGkagalna 73 
                                       ++e le +l+q   + +ei+vv DgS   +  e +  l++  d + +v+++++n   + a+ a
  gi|474934476|ref|YP_007688058.1|  92 VREQLEEVLSQ--FEADEIVVVTDGSeDKGVIEYIMGLVHiIDVKATVVKQTRNAETIIAIIA 152
                                       7888999****..*************5555666666666699999999999999766666655 PP

>> PIRT  Phosphoinositide-interacting protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.9   0.00013      0.46      50     102 ..     237     294 ..     230     306 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00013
                              PIRT  50 iivlsvGgav..fllGvvittlsrnstlknkdkevf...klsGpaflslGlmllvcGl 102
                                       ii++ v +av  fl+G+++   s++++ +++++e        G     +G+m+ ++G+
  gi|474934476|ref|YP_007688058.1| 237 IIIVFVIAAVllFLFGIILGVYSMDDIYTTRTTERVlvfIANGMWPALFGIMMYLFGV 294
                                       67777777754589*********99998887776441113334333446888888886 PP

>> Fumarate_red_D  Fumarate reductase subunit D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   5.6    0.0015       5.3      27     110 ..     171     252 ..     164     256 .. 0.78
   2 ?    6.1   2.1    0.0032        11      12      65 ..     273     324 ..     266     336 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0015
                    Fumarate_red_D  27 vlililglllplGlldsdalsyekvlafaqswigklvllvviilplwhalhrihhglhdlkihvkkaaklifYglAa 103
                                        +i+i  + l++ l++sd  s++k     ++ +  l++ v+i+l ++   ++i+ glh++  +v + + +i++ +Aa
  gi|474934476|ref|YP_007688058.1| 171 LIIFISMIYLAANLFTSD--SVDKFFLGSTTLFIFLAMGVLIMLYAYSLDEKIRGGLHHFMDRVRAGSIIIVFVIAA 245
                                       467777888888888877..666677777888888888899999999999*********998888778888888888 PP

                    Fumarate_red_D 104 llsvval 110
                                       +l ++  
  gi|474934476|ref|YP_007688058.1| 246 VLLFLFG 252
                                       8766554 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0032
                    Fumarate_red_D  12 lLFgaGGmvaAlvlpvlililglllplGlldsdalsyekvlafaqswigklvll 65 
                                       l+F a Gm+ Al++ +++ ++g+l+  G+++++++ y +++  ++     l++ 
  gi|474934476|ref|YP_007688058.1| 273 LVFIANGMWPALFG-IMMYLFGVLVD-GYMSRRSIRYLSIIGCLNVLAIGLIMT 324
                                       6799********97.677788*9996.888999999999998888777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1305  (0.0727871); expected 358.6 (0.02)
Passed bias filter:                      630  (0.0351386); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.45
# Mc/sec: 2566.38
//
Query:       gi|474934477|ref|YP_007688059.1|  [L=212]
Description: hypothetical protein TALC_00904 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.1e-21   75.6   0.0    4.9e-21   75.3   0.0    1.1  1  Lactamase_B_3  Beta-lactamase superfamily domain
    0.00075   19.1   0.0      0.001   18.7   0.0    1.2  1  Lactamase_B_2  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.3   0.0   5.5e-25   4.9e-21       1     162 [.       2     162 ..       2     163 .. 0.97

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 5.5e-25
                     Lactamase_B_3   1 eltwlghnsflletagarilvDPfka.nlgyeppaeeaDlvlisqaledHahletlkqlaenvkvleegeslevggl 76 
                                       +++w+g ++f + ++ +r+++DP ++ ++g++ p++ aD+vl +++    +  + +k+  +  ++le  ++  vg++
  gi|474934477|ref|YP_007688059.1|   2 YIRWHGLSCFEFYDGRTRVVTDPHDGkSIGLYTPNVYADVVLSTHNSFARNCFRIVKG--THRDFLEYAGDGSVGDF 76 
                                       599*********************999*******************************..7889************* PP

                     Lactamase_B_3  77 eiravatshdavggsergenngflleqdgltiyhlGhlahelsseelkelgrvDvvltPvggpltlgqeealelakr 153
                                       ++ + ++    + + ++g n+++ +++dg+++++ G l+  +++   + l + D++++Pvg   t++ + + e + +
  gi|474934477|ref|YP_007688059.1|  77 SFLGLQSGSLHGSDGNQGANSIYSFSMDGIRVAFTGSLGGIPDDFAVECLRDSDILFVPVGAYSTISIDGVNEFIDM 153
                                       *****9999989899************************************************************** PP

                     Lactamase_B_3 154 LkpklvlPm 162
                                       ++pk+v+P+
  gi|474934477|ref|YP_007688059.1| 154 VRPKVVVPT 162
                                       ********8 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.1e-07     0.001      97     182 ..      72     145 ..      29     163 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.1e-07
                                       EECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HHHH.HHHCT-SEEEEE-S-SSTTHH CS
                     Lactamase_B_2  97 elgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipeeig.erlggadllllditayeddem 172
                                       ++g    ++ +  ++++s  + d n+g +  + +  +g rv+++g +g ip++ + e l++ d+l+++++ay+    
  gi|474934477|ref|YP_007688059.1|  72 SVG----DFSFLGLQSGSLHGSDGNQGANSIYSFSMDGIRVAFTGSLGGIPDDFAvECLRDSDILFVPVGAYST--- 141
                                       444....36666677777778899999999999999***************885449*************9976... PP

                                       HHHHT---ST CS
                     Lactamase_B_2 173 irhmgHltpe 182
                                             ++++
  gi|474934477|ref|YP_007688059.1| 142 ------ISID 145
                                       ......4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1350.81
//
Query:       gi|474934478|ref|YP_007688060.1|  [L=218]
Description: putative translation initiation factor eIF-6 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-61  205.5   5.2    6.4e-61  205.2   5.2    1.0  1  eIF-6     eIF-6 family
  ------ inclusion threshold ------
      0.068   13.4   0.0        1.6    9.0   0.0    2.4  2  DUF1598   Protein of unknown function (DUF1598)


Domain annotation for each model (and alignments):
>> eIF-6  eIF-6 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.2   5.2   7.2e-65   6.4e-61       4     197 .]       6     197 ..       4     197 .. 0.99

  Alignments for each domain:
  == domain 1  score: 205.2 bits;  conditional E-value: 7.2e-65
                                       BTTB--HHHH-EE-SSEEEE-TTS-HHHHHHHHHHHT-EEEE--BTTBS-HHHH-EE-SSEEEEETT--HHHHHHHH CS
                             eIF-6   4 iegsseiGvfarltnkyalvpegveeefvkaieeeLkvevvettiagsrlvGslvvgNsngllvpstvtdeeleklk 80 
                                       ++g+ +iGv a++++++a+v+++++ +f + ++e+L+ve+v++t++g ++vGsl+++Nsng+ v+ +v+ +ele ++
  gi|474934478|ref|YP_007688060.1|   6 VSGTFNIGVNAVANESLAFVTPDADGQFLRDLQEALGVETVTVTVGGAHVVGSLLAMNSNGIAVSGQVEGDELELIR 82 
                                       78999************************************************************************ PP

                                       HHHH---EEE--SS--HHHHEEE-SSEEEE-GGGGG.GHHHHHHHHTSEEEE--BTTBS-TTTSEEE-SSEEEE-TT CS
                             eIF-6  81 eslkleverleekltAlGNvilaNDkvAlvhpdlsketveiiadvLgvevvrgtiagiktvGsaavvtnkgllvhpk 157
                                       ++  l+v rl+++l+A+GN il+ND++A+v+pd s++t ++i++v+gve vrgt+agi+tvGs+++++nkg+++ ++
  gi|474934478|ref|YP_007688060.1|  83 KH--LPVIRLPDELNAAGNNILVNDSGAIVNPDTSDRTLKQISKVFGVEAVRGTVAGINTVGSLCACNNKGCVCPTD 157
                                       *9..89*********************************************************************** PP

                                       --HHHHHHHHHHHT-SEEE--BTTTBS-GGGTEEE-SS-E CS
                             eIF-6 158 ateeeleeleellkveveagTvNrGsklvgsglvaNdkga 197
                                       at ee+++++++l+v+v++++vN+Gsk++g+g+vaN+kga
  gi|474934478|ref|YP_007688060.1| 158 ATPEEIQMIKDVLRVDVQTSSVNHGSKYLGAGIVANTKGA 197
                                       *************************************996 PP

>> DUF1598  Protein of unknown function (DUF1598)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00018       1.6      22      48 ..      23      49 ..      11      58 .. 0.82
   2 ?    1.6   0.0     0.038   3.4e+02      20      52 ..     106     140 ..      95     145 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00018
                           DUF1598 22 qrlspgeveklveglkkaLGrQdvtvt 48
                                      + ++p++  +++++l++aLG  +vtvt
  gi|474934478|ref|YP_007688060.1| 23 AFVTPDADGQFLRDLQEALGVETVTVT 49
                                      3489999***************99985 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.038
                           DUF1598  20 vkqr.lspgeveklveglkkaLGrQdv..tvtGipa 52 
                                       + +  ++p+  ++ ++++ k +G   v  tv Gi++
  gi|474934478|ref|YP_007688060.1| 106 S-GAiVNPDTSDRTLKQISKVFGVEAVrgTVAGINT 140
                                       3.3348999999999*******99998666888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1383.16
//
Query:       gi|474934479|ref|YP_007688061.1|  [L=87]
Description: LSU ribosomal protein L31E [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.6e-11   42.3   0.7    7.8e-11   42.1   0.7    1.1  1  Ribosomal_L31e  Ribosomal protein L31e


Domain annotation for each model (and alignments):
>> Ribosomal_L31e  Ribosomal protein L31e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.7   4.4e-15   7.8e-11      15      70 ..      16      73 ..       5      78 .. 0.88

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 4.4e-15
                    Ribosomal_L31e 15 ihgvgfkkraprAlkeikkfamkemg..tpdvridtrLnkavwakgirnvpyrirvrl 70
                                       +++ + +r  rA+k++++ +m++m+   + v id+++n+ +w++girn+p +i v++
  gi|474934479|ref|YP_007688061.1| 16 AKQAPRSRRTERAVKDVRAAIMRHMKvdAEHVWIDKSVNEKLWENGIRNPPSKIAVKC 73
                                      56778899******************6667889*********************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 645.65
//
Query:       gi|474934480|ref|YP_007688062.1|  [L=53]
Description: LSU ribosomal protein L39E [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-18   65.5  13.4    2.8e-18   65.3  13.4    1.1  1  Ribosomal_L39  Ribosomal L39 protein
  ------ inclusion threshold ------
      0.079   13.2   0.2      0.082   13.1   0.2    1.1  1  Ivy            Inhibitor of vertebrate lysozyme (Ivy)


Domain annotation for each model (and alignments):
>> Ribosomal_L39  Ribosomal L39 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.3  13.4   3.1e-22   2.8e-18       1      42 []      11      52 ..      11      52 .. 0.98

  Alignments for each domain:
  == domain 1  score: 65.3 bits;  conditional E-value: 3.1e-22
                     Ribosomal_L39  1 kKlrLaKalkqNrpvPaWvrlktdrkvrynpkrRhWRrtkLk 42
                                      +K rL K++kqNr+vPaWv+++t+r++ ++pkrR+WR +kLk
  gi|474934480|ref|YP_007688062.1| 11 MKERLNKKVKQNRRVPAWVMIRTNRQFLRHPKRRSWRMSKLK 52
                                      69***************************************8 PP

>> Ivy  Inhibitor of vertebrate lysozyme (Ivy)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   9.2e-06     0.082       3      27 ..       8      32 ..       6      47 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.2e-06
                                      SCCCHHHHHHHCTTS-S--CHHHCT CS
                               Ivy  3 qpeyraawaklvkgekrlPeWvrsg 27
                                       p+++++ +k vk+++r+P+Wv+  
  gi|474934480|ref|YP_007688062.1|  8 PPAMKERLNKKVKQNRRVPAWVMIR 32
                                      6899******************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.52
# Mc/sec: 305.83
//
Query:       gi|474934481|ref|YP_007688063.1|  [L=102]
Description: DNA-binding TFAR19-related protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.7e-29  100.4  21.8    7.4e-29  100.3  21.8    1.0  1  dsDNA_bind      Double-stranded DNA-binding domain
  ------ inclusion threshold ------
       0.11   12.8   2.6       0.16   12.3   2.6    1.3  1  DNA_ligase_A_N  DNA ligase N terminus
       0.17   11.2   7.1       0.22   10.8   7.1    1.1  1  CcmH            Cytochrome C biogenesis protein
       0.73    9.2   7.3        0.8    9.1   7.3    1.1  1  KTI12           Chromatin associated protein KTI12
          2    8.0   8.4        2.4    7.8   8.4    1.2  1  Peptidase_C58   Yersinia/Haemophilus virulence surface antige
        2.7    8.2  13.9       0.93    9.7   9.3    2.0  2  DUF4355         Domain of unknown function (DUF4355)


Domain annotation for each model (and alignments):
>> dsDNA_bind  Double-stranded DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.3  21.8   2.5e-32   7.4e-29       6     111 .]       1     101 [.       1     101 [. 0.92

  Alignments for each domain:
  == domain 1  score: 100.3 bits;  conditional E-value: 2.5e-32
                                       XXXXXXXXXXXXXXX...XXXX--SS..S--SSHHHHTTS--HHHHHHHHHHTTT-HHHHHHHHHHHHHHHH--SS- CS
                        dsDNA_bind   6 laelqaqagsssgsggaseqqeqqqeaseeeakqaiLsqiLepeAreRLsrirlvkperaeavenrLiqlaqsGqlr 82 
                                       +aelq+qa+s+++     + q++qq+++ e++kq+iL+qi++peAr+RL++++l++ + a++ven+Li+laqsG+l+
  gi|474934481|ref|YP_007688063.1|   1 MAELQQQAQSQQA-----QAQQEQQAKQLEAQKQSILRQIMTPEARDRLANVKLANANLAASVENQLIRLAQSGRLQ 72 
                                       89****9998765.....34444445579************************************************ PP

                                       ----HHHHHHHHHHHS---XXXXX..XXX CS
                        dsDNA_bind  83 skvteeqLkeLLeqvaekkketkivisrr 111
                                       s+vt++ Lke+L+q+a +++e +i+++rr
  gi|474934481|ref|YP_007688063.1|  73 SQVTDAMLKEILQQMAPQEREISITYQRR 101
                                       ***************************97 PP

>> DNA_ligase_A_N  DNA ligase N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   2.6   5.4e-05      0.16     111     149 ..      26      93 ..       1      98 [. 0.70

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.4e-05
                                       H.............................HHHHHHHHHHHH-STTHHHHHHHHHHHHHHHS-HHHHH CS
                    DNA_ligase_A_N 111 i.............................eevnelLdklaaagkgsedekkkilkkllkraspeEak 149
                                                                     + v+++L +la++g+ + +   ++lk++l+++ p+E  
  gi|474934481|ref|YP_007688063.1|  26 AqkqsilrqimtpeardrlanvklananlaASVENQLIRLAQSGRLQSQVTDAMLKEILQQMAPQERE 93 
                                       23333344556666666666677777777789************9999999**************986 PP

>> CcmH  Cytochrome C biogenesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   7.1   7.2e-05      0.22       8      80 ..       7      81 ..       1      83 [. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 7.2e-05
                                      XXXXXXGGGGS--SSHHHHHHHHHHHHHEE-TTSSS-..BTTT--SHHHHHHHHHHHHHHHHT--HHHHHHHHHH CS
                              CcmH  8 alaaaaaeedeelkdpaqeararalseeLRClvCqnq..siadSnaelAkdlrrevremlkaGksdeeivdylva 80
                                      ++++++a++++e + +++ea+ +++ ++++ +  +    +++ +na+lA+ + +++ ++ ++G+ ++++ d + +
  gi|474934481|ref|YP_007688063.1|  7 QAQSQQAQAQQEQQAKQLEAQKQSILRQIMTPEARDRlaNVKLANANLAASVENQLIRLAQSGRLQSQVTDAMLK 81
                                      445567788888889999***************9985449999*****************************986 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   7.3   0.00027       0.8     174     247 ..       3      75 ..       1      97 [. 0.87

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00027
                                       TS--SSSTT-------HHHHHHHHHHHHHHHHHHH....HTT--HHH................HHHHHHHHHHH CS
                             KTI12 174 klkpnqatlskplaeanflqeLdketseivkeileaqksavaidkltlpgsseslelpakkltlaeLsrlrrqF 247
                                       +l+++ +++++++++++  ++L+++ ++i+++i+   ++  +  +++l ++++  ++ ++ + la+  rl+ q 
  gi|474934481|ref|YP_007688063.1|   3 ELQQQAQSQQAQAQQEQQAKQLEAQKQSILRQIMT-PEARDRLANVKLANANLAASVENQLIRLAQSGRLQSQV 75 
                                       577888889999999999*****************.8899999***********************99998875 PP

>> Peptidase_C58  Yersinia/Haemophilus virulence surface antigen
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   8.4   0.00079       2.4      49     126 ..       9      86 ..       1      98 [. 0.73

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00079
                                       TS.HHHHHHHHHHHHHHHHHHHHHHTT-SSHHHHHHH..HHHHHTT-EE-S--EEEE...--S-HHHHHHHHHHHH- CS
                     Peptidase_C58  49 ggskgqsraaeiqslysikklqllsqrakaqdqqfqatdtwlkeaglepseeelklg.evagavsaenvsrllkail 124
                                       ++++ q++  ++ ++ +++k ++l+q +   ++++ + + +l +a l +s+e   ++   +g  +++ ++++lk+il
  gi|474934481|ref|YP_007688063.1|   9 QSQQAQAQQEQQAKQLEAQKQSILRQIMTP-EARDRLANVKLANANLAASVENQLIRlAQSGRLQSQVTDAMLKEIL 84 
                                       233556666666677788888888555544.4467777999999999999988877766788899999999999999 PP

                                       ST CS
                     Peptidase_C58 125 dt 126
                                       ++
  gi|474934481|ref|YP_007688063.1|  85 QQ 86 
                                       86 PP

>> DUF4355  Domain of unknown function (DUF4355)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   9.3   0.00031      0.93      44      86 ..       9      51 ..       1      64 [. 0.81
   2 ?    1.5   0.2      0.11   3.4e+02      23      49 ..      70      94 ..      56     102 .] 0.69

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00031
                           DUF4355 44 aeekaeyeleklqkeleelkaelarkelkaearkvlaekkipi 86
                                      +++ a+++ e++ k+le++k+   r+ ++ ear  la  k+  
  gi|474934481|ref|YP_007688063.1|  9 QSQQAQAQQEQQAKQLEAQKQSILRQIMTPEARDRLANVKLAN 51
                                      5788899***************************999877654 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.11
                           DUF4355 23 klekeledeikkeakklakmnaeekae 49
                                       l+ ++ d++   ++ l++m  +e++ 
  gi|474934481|ref|YP_007688063.1| 70 RLQSQVTDAM--LKEILQQMAPQEREI 94
                                      5677777777..667777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3732  (0.208154); expected 358.6 (0.02)
Passed bias filter:                     1056  (0.058899); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 809.59
//
Query:       gi|474934482|ref|YP_007688064.1|  [L=143]
Description: SSU ribosomal protein S19E [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.2e-52  175.2   0.1    5.8e-52  175.0   0.1    1.0  1  Ribosomal_S19e  Ribosomal protein S19e
     0.0048   15.6   0.0     0.0057   15.3   0.0    1.1  1  PhoPQ_related   PhoPQ-activated pathogenicity-related protein
  ------ inclusion threshold ------
      0.095   12.4   0.0        0.3   10.8   0.0    1.8  2  GntR            Bacterial regulatory proteins, gntR family


Domain annotation for each model (and alignments):
>> Ribosomal_S19e  Ribosomal protein S19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.0   0.1   9.8e-56   5.8e-52       1     135 [.       3     138 ..       3     140 .. 0.98

  Alignments for each domain:
  == domain 1  score: 175.0 bits;  conditional E-value: 9.8e-56
                                       TSSSHHHHHHHHHS--S---S-SSS-SSSS-SS-S-SS-SSTTTHHHHHHHHHHHTS--TTSGGGGS----SS-SSS CS
                    Ribosomal_S19e   1 tvkdVpaeelikalaeeLkksgklevPewadlvKtgsakelapededWfyvRaAsilRkvylrgpvGverlrkvYGg 77 
                                       tv+dVpae li ++ae+Lk+++k+ +Pewa+++Ktg + e+ap + dW+y+RaAsi+Rk+y++gp+G ++l+ +YGg
  gi|474934482|ref|YP_007688064.1|   3 TVYDVPAEPLILKVAEKLKQNDKIVAPEWAEFAKTGIHTERAPAQADWWYTRAASIMRKLYVKGPMGTSKLAAEYGG 79 
                                       79*************************************************************************** PP

                                       -------THHHHHHHHHTTSSS--SSS---SS.-HHHHHTHHHHH--SS--S--XXXXX CS
                    Ribosomal_S19e  78 kkrrgvrpshfvkasgsvirkilqqLeklglv.kkekkkgrrltkkGqrlldriaeeva 135
                                         +rg +p++ vk+s+++irk+l qL+++gl+  +++k+gr+++++Gq++ld+ a+ev+
  gi|474934482|ref|YP_007688064.1|  80 YVDRGAKPNRAVKGSRNIIRKCLIQLQDAGLLeATNDKQGRKVSAAGQSMLDNAAKEVF 138
                                       ********************************889999*******************97 PP

>> PhoPQ_related  PhoPQ-activated pathogenicity-related protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   9.6e-07    0.0057     102     137 ..       2      38 ..       1      63 [. 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 9.6e-07
                     PhoPQ_related 102 aelsdvPnqpltfeddgkarkEDdlvAytwrkfle.e 137
                                       ++++dvP +pl+ +  +k ++ D++vA  w++f +  
  gi|474934482|ref|YP_007688064.1|   2 VTVYDVPAEPLILKVAEKLKQNDKIVAPEWAEFAKtG 38 
                                       799******************************9953 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.1   6.3e+03      28      35 ..      71      78 ..      68      79 .. 0.82
   2 ?   10.8   0.0     5e-05       0.3      35      57 ..      92     114 ..      89     121 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.1
                                      HHHHHHHT CS
                              GntR 28 reLaaefg 35
                                      ++Laae+g
  gi|474934482|ref|YP_007688064.1| 71 SKLAAEYG 78
                                      58999998 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 5e-05
                                       TS-HHHHHHHHHHHHHTTSEEEE CS
                              GntR  35 gVsrttvReALrrLeaeglverr 57 
                                       + sr+ +R+ L++L+ +gl+e+ 
  gi|474934482|ref|YP_007688064.1|  92 KGSRNIIRKCLIQLQDAGLLEAT 114
                                       679*****************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 977.91
//
Query:       gi|474934483|ref|YP_007688065.1|  [L=391]
Description: 3-hydroxy-3-methylglutaryl-coenzyme A reductase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     9e-132  439.5  10.8     1e-131  439.3  10.8    1.0  1  HMG-CoA_red  Hydroxymethylglutaryl-coenzyme A reductase
  ------ inclusion threshold ------
        3.2    7.8   6.8         20    5.2   0.3    3.2  3  Titin_Z      Titin Z


Domain annotation for each model (and alignments):
>> HMG-CoA_red  Hydroxymethylglutaryl-coenzyme A reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  439.3  10.8  1.1e-135    1e-131       2     367 .]      21     388 ..      20     388 .. 0.99

  Alignments for each domain:
  == domain 1  score: 439.3 bits;  conditional E-value: 1.1e-135
                                       HHHHHHHHHHS-HHHHHHHTT----HHHHHHHSSS---------EEEEEEEETTE....EEEEEE---STTHHHHHH CS
                       HMG-CoA_red   2 veeRrklleelteeeleelkeesldeevadkmiEnviGyvqlPlGvagpllingk....eylvPmAteEgslvAsas 74 
                                       v+eRr++ e+ t+++le+++++ +++e a +++En+iG+vq+PlG agp++ing+    e+lvPmAt+Eg+l+As+s
  gi|474934483|ref|YP_007688065.1|  21 VDERRAAAEQFTGATLERVGKYCFSSEDAAHNCENMIGAVQIPLGYAGPVKINGEyaqgEFLVPMATTEGALIASVS 97 
                                       79*************************************************************************** PP

                                       HHHHHHHHTT-B.EEEE----EEEEEEEE.--S-HHHHHHHHHTHHHHHHHHHHCSHHCCT-EEEEEEEEE-SSEEE CS
                       HMG-CoA_red  75 rgakainesgGvkttvlkdgmtraqvvllesvedaaelkkwiekkeeleelanaaestsrggglkdievvlagrlvv 151
                                       rg++++n++gGv+++++ d mtra+v++++++e+  ++ +wi  + + +e+++a+  t+++g+l +ie + +gr+++
  gi|474934483|ref|YP_007688065.1|  98 RGMSVMNDAGGVRAKTFGDYMTRAPVLRVRDLEHSCQVIQWI--DAHGDEMRQAVAGTTSHGKLVKIEKFPTGRNLY 172
                                       ******************************************..9******************************** PP

                                       EEEEEE-TTC--HHHHHHHHHHHHHHHHHHHTSEEEEEEE-S--GGGEEEEEEEEEHHHH..-SSTTHHHHHHHHHH CS
                       HMG-CoA_red 152 lrlkvdtgDAmGaNmvnkateaaaelieeefgeeellsilsNlctdkkasainaiegrgksvvaeatigeevvekil 228
                                       lr++++tgDAmG+Nm ++a ea+++lie+e+g ++++s+++N+c+dkk++ain+iegrgk+vvaea i++++vek l
  gi|474934483|ref|YP_007688065.1| 173 LRFSFETGDAMGMNMATIASEAVCRLIEQETG-AVMVSVSGNMCSDKKPAAINMIEGRGKTVVAEALIPADIVEKRL 248
                                       *******************************9.******************************************** PP

                                       HHHHHHHH-HHHH....HHHHHHH.......HHHHHHHHHHTT--HHHHHHHHHHHTTSEEETTTEEEEEEEEE.-- CS
                       HMG-CoA_red 229 kasaealvdlnra.n.igtankGiggfnahaaNgiaAvflAtGqDlaaveesshaiaaleevedgdlygsvtlPsle 303
                                       +asa a+v+ n++ n ig+ ++G++g nahaaN++aAvflAtGqD+a+v e++ +++ +e+v dg+ly+sv +Ps+e
  gi|474934483|ref|YP_007688065.1| 249 HASASAIVETNIRkNlIGSSMAGMLGANAHAANMVAAVFLATGQDPAQVTEGALTLTDCEDV-DGSLYISVRMPSIE 324
                                       **************************************************************.777*********** PP

                                       --SBSHHHHH-HHHHHHHHTT---HH...HHHHHHHHHHHHHHHHHHHHHT-----HHHHHHHH CS
                       HMG-CoA_red 304 VGtvGGgtklppqaellkllgvkgaknakeLaeiiaavgLAqelsalrALaaeglqkgHmklhr 367
                                       VGtvGGgt+lp+qae+l+++g+kga++a++Laeiiaa++LA+els+l+A aa++l k+H +l+r
  gi|474934483|ref|YP_007688065.1| 325 VGTVGGGTSLPTQAEALNMIGCKGAGKARKLAEIIAATVLAGELSTLAAQAAGQLGKAHAELGR 388
                                       *************************************************************987 PP

>> Titin_Z  Titin Z
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1     0.073   6.6e+02       4      30 ..     225     251 ..     208     254 .. 0.89
   2 ?    3.9   0.2    0.0057        51      13      34 ..     279     299 ..     274     305 .. 0.80
   3 ?    5.2   0.3    0.0023        20       6      31 ..     347     373 ..     339     376 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.073
                           Titin_Z   4 VreegkKaAVAtVVaAvDkarvrepla 30 
                                       + e+  K++VA   + +D + +r+ ++
  gi|474934483|ref|YP_007688065.1| 225 MIEGRGKTVVAEALIPADIVEKRLHAS 251
                                       5688889****9999999999999876 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0057
                           Titin_Z  13 VAtVVaAvDkarvrepladtrE 34 
                                       +A +VaAv +a+ + p a + E
  gi|474934483|ref|YP_007688065.1| 279 AANMVAAVFLATGQDP-AQVTE 299
                                       6899**********99.44455 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.0023
                           Titin_Z   6 eegkKa.AVAtVVaAvDkarvreplad 31 
                                       +++ Ka   A ++aA+ +a ++ +la 
  gi|474934483|ref|YP_007688065.1| 347 KGAGKArKLAEIIAATVLAGELSTLAA 373
                                       79999*9*************9999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 2446.36
//
Query:       gi|474934484|ref|YP_007688066.1|  [L=552]
Description: phenylalanyl-tRNA synthetase, beta subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-39  135.0   0.0    3.8e-39  134.4   0.0    1.3  1  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
    1.3e-16   60.6   0.0    9.3e-15   54.7   0.0    2.5  2  B5               tRNA synthetase B5 domain
    1.2e-15   57.6   0.0    2.1e-15   56.9   0.0    1.3  1  B3_4             B3/4 domain
     0.0033   17.6   0.0      0.024   14.9   0.0    2.5  2  PhetRS_B1        Phe-tRNA synthetase beta subunit B1 domain


Domain annotation for each model (and alignments):
>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.4   0.0   8.4e-43   3.8e-39       8     214 .]     354     540 ..     347     540 .. 0.96

  Alignments for each domain:
  == domain 1  score: 134.4 bits;  conditional E-value: 8.4e-43
                   tRNA_synthFbeta   8 apttegelnkeqklrrklrdllagaGlnEvitysfvsekeldklleddderkavelanPlsedqsvlRtsLlpglLe 84 
                                       ++ t g+l +e +++ +++d+++g+G++E+ t ++ ++ +  +l +  +e + v++ nP++e++++lR+ L+p+l+ 
  gi|474934484|ref|YP_007688066.1| 354 VTQTFGKLLPETEFTMNAQDIMVGLGYTEITTLTLSNRRDEFEL-SGFPEVDSVTVTNPITEEHTCLRSYLMPSLMR 429
                                       556677788999*****************************999.677***************************** PP

                   tRNA_synthFbeta  85 vlarNlargnedvrlFEigkvflkdseeelpeeerhlaivltgkreeeswsekaravdfydlkgivealleslgiek 161
                                        l +N +r ++  ++FE+g v++++      ++  hl+++ + +r            +f ++k ++e++l+++++ +
  gi|474934484|ref|YP_007688066.1| 430 ILCNNKHRDLP-QKIFEVGYVIRNN------KNVPHLCALQAASR-----------SSFTEVKSLAESILREFNV-E 487
                                       ***********.*************......9*************...........*******************.* PP

                   tRNA_synthFbeta 162 vefepaehpalhpgrsAeikvdgkevGvlGelhpevleafdlkqrvyvfEldl 214
                                       +++++ ++p++ pgr A i+vdgk++G +Ge++p++   +++ ++v+++E+dl
  gi|474934484|ref|YP_007688066.1| 488 YTLSACDYPTFVPGRGAFIEVDGKKIGLFGEMSPRTITGYEMTHPVMLVEMDL 540
                                       ***************************************************98 PP

>> B5  tRNA synthetase B5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.021        95       2      51 ..       5      56 ..       4      66 .. 0.80
   2 !   54.7   0.0   2.1e-18   9.3e-15       1      67 []     279     344 ..     279     344 .. 0.97

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.021
                                      EEEHHHHHHHHTS---HHHHHHHHHHTT-E...EESSTTCEEEE--TT-TT- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxx RF
                                B5  2 slrvekinkllGidlseeeiikiLkrlgce..riekdkdlllVtvPswRsDl 51
                                      +++++ ++ llG d+s+++i +    lg +  ++  ++d+++++  + R+Dl
  gi|474934484|ref|YP_007688066.1|  5 NISYKDLKGLLGADVSQQTILERIPLLGSDigDNVPGTDEMTIEFFPNRPDL 56
                                      67889999************99988888765566777888888877778887 PP

  == domain 2  score: 54.7 bits;  conditional E-value: 2.1e-18
                                       EEEEHHHHHHHHTS---HHHHHHHHHHTT-E.EESSTTCEEEE--TT-TT--SHHHHHHHHHHHH-G CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                B5   1 vslrvekinkllGidlseeeiikiLkrlgceriekdkdlllVtvPswRsDlereeDliEEvaRlyGY 67 
                                       +++++++++++lG+ ls+e++i+ L r+g+++  + +d+l+  +P++R D+ +++D+ E++a+ yG+
  gi|474934484|ref|YP_007688066.1| 279 ITVSIKECSRYLGTALSSEQCIRALGRMGMNA-RTAGDKLTACIPAYRLDMMHPVDIYEDIAIGYGF 344
                                       68999*************************96.*********************************7 PP

>> B3_4  B3/4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.9   0.0   4.6e-19   2.1e-15      37     134 ..     118     242 ..      98     259 .. 0.90

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 4.6e-19
                                       HHHHHHHHHHHHHT-.....-EEEEEGGGTBTEEE.EEE--TTEEEEBTTS-EEEE-T................... CS
                              B3_4  37 nvVDitNyvmlelgq.....PlhafDldkiqgdiv.vrlakegeklvtldgkerelde................... 88 
                                       ++ ++++++++ +g+     +++++Dldk++++++ +   ++g ++v+l ++e                        
  gi|474934484|ref|YP_007688066.1| 118 SMMELQEKLHITVGRkraklAIGIHDLDKVTPPFTfKTVDPDGISFVPLAKTEPMTPReilekhekgrayahllegk 194
                                       67789******************************88889999*******887776336****************** PP

                                       .TSEEEETEEEEE.EETTTEEBTTTB--TT--EEEEEEEE--HHHHHH CS
                              B3_4  89 .edlviadsekpv.slagvmggeeskvsedTknvfleaaafdpvsirk 134
                                        ++++i+d+e++v s +++++g+ + v+ +T+n ++ +++fd +++ +
  gi|474934484|ref|YP_007688066.1| 195 eKYPIIVDAEGKVlSFPPIINGALTTVTTETRNLLIDVTGFDATAVEG 242
                                       *******************************************88865 PP

>> PhetRS_B1  Phe-tRNA synthetase beta subunit B1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   5.3e-06     0.024      55      82 ..      44      71 ..       1      72 [. 0.77
   2 ?   -1.8   0.0      0.82   3.7e+03      28      42 ..     104     118 ..     102     132 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.3e-06
                         PhetRS_B1 55 iykidipAnryDLLcleglaralkvFlg 82
                                       + i+   nr+DL ++eg+ara++ Fl+
  gi|474934484|ref|YP_007688066.1| 44 EMTIEFFPNRPDLYSVEGIARAMRQFLD 71
                                      57899999****************9986 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.82
                         PhetRS_B1  28 lfefGlElDeiveee 42 
                                       ++ +G+E+ + v  +
  gi|474934484|ref|YP_007688066.1| 104 CAVYGVEVTDTVLRS 118
                                       788999998887554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (552 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.52
# Mc/sec: 3210.89
//
Query:       gi|474934485|ref|YP_007688067.1|  [L=164]
Description: Peroxiredoxin [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.1e-30  103.9   0.0      6e-30  103.7   0.0    1.1  1  AhpC-TSA       AhpC/TSA family
    7.4e-17   61.4   0.0    8.6e-17   61.2   0.0    1.1  1  Redoxin        Redoxin
  ------ inclusion threshold ------
      0.033   14.7   0.0      0.051   14.1   0.0    1.3  1  DUF4174        Domain of unknown function (DUF4174)
      0.034   14.5   0.0      0.064   13.6   0.0    1.5  1  Thioredoxin_8  Thioredoxin-like
      0.065   13.4   0.0       0.11   12.6   0.0    1.4  1  AhpC-TSA_2     AhpC/TSA antioxidant enzyme


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.7   0.0   1.7e-33     6e-30       2     123 ..       5     132 ..       4     133 .. 0.98

  Alignments for each domain:
  == domain 1  score: 103.7 bits;  conditional E-value: 1.7e-33
                                       TSB----EEESTTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHH CS
                          AhpC-TSA   2 gdkapdfelknadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfie 78 
                                       g+++p f + +++getv+ +d+ g   vlffy+kd++p+Ctte  ++ +ly++f+ r++ ++gvs ds esh+kf e
  gi|474934485|ref|YP_007688067.1|   5 GEEFPRFVMADENGETVDSKDLLGLRYVLFFYAKDNTPGCTTECVDFTALYPKFAVRNILLFGVSGDSSESHRKFRE 81 
                                       789************************************************************************** PP

                                       H-H.SSEEEE-TTSHHHHHTT-EETT......TTECSCEEEEE-TTSBEEE CS
                          AhpC-TSA  79 keslnfpllsDeegkvakaygvlkee......kglalratfvidkegkiry 123
                                       k++++ +ll D+++++ak+ g++ e+       ++++r+tf+i k+gk+++
  gi|474934485|ref|YP_007688067.1|  82 KHGIKEKLLVDKDHALAKQVGAFGEKknygkiVQGTIRSTFLIGKDGKVEE 132
                                       *************************9******9****************86 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.2   0.0   2.4e-20   8.6e-17       2     129 ..       4     132 ..       3     149 .. 0.92

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 2.4e-20
                                       TTSBB---ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHHHHH CS
                           Redoxin   2 agdkaPdftlplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndafvke 78 
                                       +g+++P f+ +  +++g++v+ +++ g + v++f++   +P C++e ++++ l+++++ +++  ++v+ d+++  ++
  gi|474934485|ref|YP_007688067.1|   4 KGEEFPRFVMA--DENGETVDSKDLLGLRYVLFFYAKDNTPGCTTECVDFTALYPKFAVRNILLFGVSGDSSESHRK 78 
                                       799******85..5*************************************************************** PP

                                       HHHHTT-TSEEEE-TTSHHHHHTT-TTEEE.GGG....EEE-EEEEEEETTEEEE CS
                           Redoxin  79 fwgkeglkfpvlsDgsaaftkalGlrleedaseg....lrtpryavidedgkvvy 129
                                       f +k+g+k ++l+D ++a++k+ G ++ e++  g      ++++++i +dgkv +
  gi|474934485|ref|YP_007688067.1|  79 FREKHGIKEKLLVDKDHALAKQVG-AFGEKKNYGkivqGTIRSTFLIGKDGKVEE 132
                                       ************************.556666666899989************976 PP

>> DUF4174  Domain of unknown function (DUF4174)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.4e-05     0.051      31      99 ..      51     135 ..      29     149 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.4e-05
                           DUF4174  31 leeqecelaeRklvvltivgsgaketgki......eeeql............saeliselrkelklsekd.fsmvLi 88 
                                       +++   ++a R+++++ + g+++++ +k       +                +     e +++ k+ + +  s +Li
  gi|474934485|ref|YP_007688067.1|  51 FTALYPKFAVRNILLFGVSGDSSESHRKFrekhgiK---EkllvdkdhalakQVGAFGEKKNYGKIVQGTiRSTFLI 124
                                       5667778999********999999999886555542...0444666444444555555566666779999999**** PP

                           DUF4174  89 gkdggvkerye 99 
                                       gkdg+v+e++ 
  gi|474934485|ref|YP_007688067.1| 125 GKDGKVEEKWM 135
                                       ******99876 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.8e-05     0.064       2      95 .]      30     130 ..      28     130 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.8e-05
                                       SEEEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SS-HHHHHHHGGGS.-TTSEE.EE-TT-HHHH... CS
                     Thioredoxin_8   2 kvvlLyfgaswcppckaftpklkelyeklkkkkkveivyvsldkkeeefekylkkn.kkpwlsvpfddkkrnkl... 74 
                                       ++vl+++++++ p c++     ++ly k+   +++ +  vs d++ e+ +k+++k+  k+ l v+ d    +++   
  gi|474934485|ref|YP_007688067.1|  30 RYVLFFYAKDNTPGCTTECVDFTALYPKFA-VRNILLFGVSGDSS-ESHRKFREKHgIKEKLLVDKDHALAKQVgaf 104
                                       799**************************8.66666666666665.5555555555222344433333333333444 PP

                                       ..TT-S--TT.....-SEEEEE-TT-BE CS
                     Thioredoxin_8  75 ..kkkynvka.....iPtlvvldkngev 95 
                                         kk+y+  +     i ++++++k+g+v
  gi|474934485|ref|YP_007688067.1| 105 geKKNYG--KivqgtIRSTFLIGKDGKV 130
                                       4444444..0445678888888888886 PP

>> AhpC-TSA_2  AhpC/TSA antioxidant enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.1e-05      0.11       4      53 ..      53     103 ..      50     150 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.1e-05
                        AhpC-TSA_2   4 rdkpeldaagvklvaigigdp.sakkFvkltgfpfelyvDpsaklyqalgl 53 
                                       ++ p+++ +++ l++++ ++  s +kF++  g++ +l+vD++ +l +++g 
  gi|474934485|ref|YP_007688067.1|  53 ALYPKFAVRNILLFGVSGDSSeSHRKFREKHGIKEKLLVDKDHALAKQVGA 103
                                       5678899999*******999967********************99999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1073.31
//
Query:       gi|474934486|ref|YP_007688068.1|  [L=78]
Description: hypothetical protein TALC_00913 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.30s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 538.60
//
Query:       gi|474934487|ref|YP_007688069.1|  [L=212]
Description: Electron transfer flavoprotein, alpha subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.3e-18   65.1   0.0    8.2e-18   64.9   0.0    1.1  1  ETF       Electron transfer flavoprotein domain


Domain annotation for each model (and alignments):
>> ETF  Electron transfer flavoprotein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.9   0.0   4.6e-22   8.2e-18       9     177 ..      47     206 ..      39     211 .. 0.84

  Alignments for each domain:
  == domain 1  score: 64.9 bits;  conditional E-value: 4.6e-22
                                       .CCCE-HHHHHHHHHHHHHHHHHT--EEEEEEES....S-CHHHHHHCT-SEEEEEE-GGGSS--CCHHHHHHHHHH CS
                               ETF   9 vdgklnpvdlealeaArrlkekaggevtavvvGppeaeealrealaamGadkvilvddpalagydaeatakalaali 85 
                                        + +++++++e l+   ++ +    +v +vv+G+  + +al +++  +G+++++ v   ++ gyd++ ++ a++++i
  gi|474934487|ref|YP_007688069.1|  47 GPPRVSDSTKEVLSRIMEVND--CSRVWGVVFGH-TELKALYHEIYSYGVETLYAVHGTQYIGYDPDVYSLAISQII 120
                                       467778888888888888855..489********.455667888888****************************** PP

                                       HHC--SEEEEESSCCHHHHHHHHHHHCT-EEEEEESEEEEETCCEEEEEECCCCTEEEEEE-TSSSEEEEE-TTSS- CS
                               ETF  86 kkedpdlvlagataigkqvaprlAalLgvplitdvteleveggkltvtRpieggnglaevveadlpavltvrpgafe 162
                                          +p +vl+g t  g ++a r++  L++  +td+t++ev+ ++   +R++ g     e    + p++++v+pg ++
  gi|474934487|ref|YP_007688069.1| 121 VRTEPAMVLFGGTEKGSELACRVSCILNAESATDCTSVEVN-DRNMTVRDAVG-----EYSFGSFPQIASVKPGTYR 191
                                       ****************************************9.54444555555.....77899**********9999 PP

                                       ---S-TT---EEEE- CS
                               ETF 163 paaimaakkkeveev 177
                                         ++++  +++v  +
  gi|474934487|ref|YP_007688069.1| 192 IGEPKKDDRGTVIYW 206
                                       977788888888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1566.15
//
Query:       gi|474934488|ref|YP_007688070.1|  [L=318]
Description: conserved hypothetical protein TIGR00258 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-50  171.1   0.1    2.1e-50  170.7   0.1    1.2  1  NTPase_I-T       Protein of unknown function DUF84
    1.8e-09   38.0   0.0    2.6e-09   37.4   0.0    1.3  1  CTP_transf_like  Cytidylyltransferase-like
       0.01   15.4   0.0      0.015   14.8   0.0    1.4  1  ATP-sulfurylase  ATP-sulfurylase
  ------ inclusion threshold ------
      0.066   12.4   0.1       0.15   11.2   0.0    1.6  2  Pantoate_ligase  Pantoate-beta-alanine ligase
       0.19   12.2   0.0       0.31   11.5   0.0    1.3  1  RAMA             Restriction Enzyme Adenine Methylase Associa


Domain annotation for each model (and alignments):
>> NTPase_I-T  Protein of unknown function DUF84
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.7   0.1   5.8e-54   2.1e-50       1     162 [.     154     311 ..     154     312 .. 0.99

  Alignments for each domain:
  == domain 1  score: 170.7 bits;  conditional E-value: 5.8e-54
                                       S---HHHHHHHHHHHHHHCTTEEEEEEE---SS-SS-BSHHHHHHHHHHHHHHHHHHSTTSSEEEEEEEEEET.... CS
                        NTPase_I-T   1 gSkNpvKveAvkeafeklfkdvevegvsvpsgvsdqPmgdeetlkGAinRaknaleaaeeadygvGlEgGveeleek 77 
                                       gS N vKveAv++++e+++ dv++++ +v+sgv++qP++  +t++GAinRak +l +    d++vG+E+Gv+e +e+
  gi|474934488|ref|YP_007688070.1| 154 GSLNHVKVEAVRSVMERIYGDVRISAAEVESGVPPQPFE-GQTRQGAINRAKLVLGE---HDMAVGIEAGVFERQEG 226
                                       89*************************************.****************9...79*************** PP

                                       TEEEEEE.EEEESS-EEEEE---EE--HHHHHHHCTT--HHHHHHHHHTHCCHHHTTHHHHHHTTTSS-HHHHHHHH CS
                        NTPase_I-T  78 lldvawaavvdkegrvsvgrsasfelPeevveevkegeelgevmdelfgtenikqkeGaigllTkglvtRedlyeqa 154
                                       l+d++++av+dk+gr++vg++++f++P+ v+e+v+ g+ +g++m+e+fg ++i++++Gaig+l+ gl++R++l+eq+
  gi|474934488|ref|YP_007688070.1| 227 LYDIQYCAVYDKDGRITVGCGSGFMYPSAVAEKVRGGMTVGDAMKEVFGITEIGKQQGAIGFLSGGLLDRKSLTEQS 303
                                       ***************************************************************************** PP

                                       HHHHTHHH CS
                        NTPase_I-T 155 vilAlipf 162
                                       v+ A++p+
  gi|474934488|ref|YP_007688070.1| 304 VTAAMVPR 311
                                       ******97 PP

>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.0   7.2e-13   2.6e-09       3     141 ..       6     136 ..       4     138 .. 0.82

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 7.2e-13
                                       EE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHH..TTCTT..EEEEEEESEHHH CS
                   CTP_transf_like   3 gGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRlemlela..kevde..visvdpweltre 75 
                                        GtF+ +H GH +l+++a++  +  ++vg++sd  + ++  ++++ + R   le++  +++++  v+++d+ +  r+
  gi|474934488|ref|YP_007688070.1|   6 AGTFNVLHRGHVALINRAFAVADI-IYVGITSDAMASSTRSDVVPMYLRRTALEKFldTQDKPyrVFEIDDMYGPRD 81 
                                       6***********************.*******************************553333311444444444444 PP

                                       HHHHTTTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHH CS
                   CTP_transf_like  76 vlkklkpdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkir 141
                                        +++  +d  +lv+++++  ++++ +e +   g  +l ++++p       l  + + ++iSst i 
  gi|474934488|ref|YP_007688070.1|  82 MMDS--AD--ILVVSEETAGNADKVNEERVSRGISPLRIEVVP-------LVMSCDGSKISSTNIM 136
                                       4444..48..9**********9999988888888999999888.......999999999****985 PP

>> ATP-sulfurylase  ATP-sulfurylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   4.1e-06     0.015      27      79 ..       8      63 ..       2     134 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.1e-06
                                      ESS---HHHHHHHHHHHHHTSEE....EEEEEB-SB-STTSTTHHHHHHHHHHHHHH CS
                   ATP-sulfurylase 27 trnplHraHeellkraleeeadg....lllhplvgptkpgdvpaevrvrayealiee 79
                                      t n+lHr+H +l++ra    ad     +   ++   t+++ vp ++r  a e+++++
  gi|474934488|ref|YP_007688070.1|  8 TFNVLHRGHVALINRAFA-VADIiyvgITSDAMASSTRSDVVPMYLRRTALEKFLDT 63
                                      78****************.78854444777899999******************998 PP

>> Pantoate_ligase  Pantoate-beta-alanine ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   4.2e-05      0.15      27      54 ..       7      34 ..       2      56 .. 0.85
   2 ?   -2.6   0.0      0.71   2.6e+03     162     191 ..     113     142 ..     107     177 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.2e-05
                                      EE-SS-GHHHHHHHHHHHHHSSEEEEEE CS
                   Pantoate_ligase 27 pTmGaLHeGHlsLvkaakeendvvvvSi 54
                                       T   LH+GH++L+++a + +d++ v i
  gi|474934488|ref|YP_007688070.1|  7 GTFNVLHRGHVALINRAFAVADIIYVGI 34
                                      57779******************99998 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.71
                                       SSEEEEEEEEBETTSEBTTGGGGGS-HHHH CS
                   Pantoate_ligase 162 pveivavpivReedgLAlSSRNkyLseeer 191
                                       p++i +vp v + dg  +SS N    e +r
  gi|474934488|ref|YP_007688070.1| 113 PLRIEVVPLVMSCDGSKISSTNIMRGEYSR 142
                                       678888899999999999998866554444 PP

>> RAMA  Restriction Enzyme Adenine Methylase Associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   8.6e-05      0.31      31      79 ..     216     263 ..     180     274 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.6e-05
                              RAMA  31 leagllepGekllieykgrthkAdlladGkIk...gqefgspsaaakalvGn 79 
                                       +eag+ e  e+l+ +   + + A+  +dG+I    g  f  psa+a +++G+
  gi|474934488|ref|YP_007688070.1| 216 IEAGVFERQEGLY-DI--Q-YCAVYDKDGRITvgcGSGFMYPSAVAEKVRGG 263
                                       7899999999999.33..3.8899*********99999********999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 2032.83
//
Query:       gi|474934489|ref|YP_007688071.1|  [L=71]
Description: Uncharacterized protein containing a Zn-ribbon (DUF2116) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-11   42.4   0.2    6.1e-11   42.1   0.2    1.1  1  DUF2116   Uncharacterized protein containing a Zn-ribbon (DUF
    0.00043   20.1   1.3     0.0007   19.4   1.3    1.3  1  VATC      Vms1-associating treble clef domain
     0.0042   17.0   0.5     0.0048   16.9   0.5    1.1  1  NinG      Bacteriophage Lambda NinG protein
  ------ inclusion threshold ------
        0.1   12.6   4.8       0.34   10.9   0.8    2.2  2  zf-FCS    MYM-type Zinc finger with FCS sequence motif


Domain annotation for each model (and alignments):
>> DUF2116  Uncharacterized protein containing a Zn-ribbon (DUF2116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.2   1.4e-14   6.1e-11       2      57 ..      11      69 ..      10      71 .] 0.88

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 1.4e-14
                           DUF2116  2 pHkHCivCGkaI...pldesfCsekCqeeyekkrkkvarsqqilfgililllavvlvlk 57
                                      +H+HC  CGka    + +e+fCs++C  +  ++ k+  +   +++++l +++av +++ 
  gi|474934489|ref|YP_007688071.1| 11 QHRHCLHCGKAFtgaGFNERFCSQECLDAEGSEAKRKLKKYAVFMVALWAIVAVAVLVV 69
                                      7*********9733368**********999999999999999******99999998875 PP

>> VATC  Vms1-associating treble clef domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   1.3   1.6e-07    0.0007       3      33 ..      12      38 ..      10      41 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.6e-07
                              VATC  3 vlrCsiCgeslegkvyFekfdfrYCstkClr 33
                                      +++C +Cg+++ g      f+ r+Cs +Cl 
  gi|474934489|ref|YP_007688071.1| 12 HRHCLHCGKAFTG----AGFNERFCSQECLD 38
                                      89***********....99**********97 PP

>> NinG  Bacteriophage Lambda NinG protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.5   1.1e-06    0.0048       2      41 ..       8      47 ..       7      55 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.1e-06
                              NinG  2 kkpkrrkCkeCkeafkpakatqavCseecalalkkaekka 41
                                      k p++r+C  C++af+ a  ++++Cs+ec  a  +  k++
  gi|474934489|ref|YP_007688071.1|  8 KIPQHRHCLHCGKAFTGAGFNERFCSQECLDAEGSEAKRK 47
                                      67999************************95554422222 PP

>> zf-FCS  MYM-type Zinc finger with FCS sequence motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.012        54       5      16 ..      14      25 ..      11      30 .. 0.82
   2 ?   10.9   0.8   7.5e-05      0.34      31      39 ..      30      38 ..      28      39 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.012
                            zf-FCS  5 rCwfCkkyikgk 16
                                       C +C+k ++g 
  gi|474934489|ref|YP_007688071.1| 14 HCLHCGKAFTGA 25
                                      599*****9975 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 7.5e-05
                            zf-FCS 31 qFCStsCld 39
                                      +FCS++Cld
  gi|474934489|ref|YP_007688071.1| 30 RFCSQECLD 38
                                      8******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1090  (0.0607954); expected 358.6 (0.02)
Passed bias filter:                      667  (0.0372023); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 474.27
//
Query:       gi|474934490|ref|YP_007688072.1|  [L=198]
Description: hypothetical protein TALC_00917 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-63  212.4   0.0    5.4e-63  212.3   0.0    1.0  1  Methyltrn_RNA_2  Putative SAM-dependent RNA methyltransferase


Domain annotation for each model (and alignments):
>> Methyltrn_RNA_2  Putative SAM-dependent RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.3   0.0     3e-67   5.4e-63       1     196 [.       1     195 [.       1     197 [. 0.98

  Alignments for each domain:
  == domain 1  score: 212.3 bits;  conditional E-value: 3e-67
                                       -EEEEEEESSEESSSHHHCCCTTTTTTSHHHHHHHHHHHHBESSSB-TTEEEEEEEEESSSS-EEEEEETTT--S-- CS
                   Methyltrn_RNA_2   1 mrefvvlankapTdsdiplddlpGaagrldvlarcvsaalfvshgiRedvvvylvLegtpdpprtikieasevkkvs 77 
                                       mr fv+ ++ka+ d+  +lddl+G agr+d+l+rc++ a+ +sh+ Red ++ylvLeg+ d p+t+++e+  v++ +
  gi|474934490|ref|YP_007688072.1|   1 MRYFVITGHKAVADGSWKLDDLGGGAGRMDILCRCINSAFVLSHNLREDCEIYLVLEGGEDAPKTVRVEGRTVRYLN 77 
                                       9**************************************************************************** PP

                                       SSHHHHHHHHHHHHCHCCTGCCSEEEEETTEEEE---HHHHHHHHHCTSEEEEESTTSEEGGGS---SSEEEEEE-T CS
                   Methyltrn_RNA_2  78 pderniailikkalkaveeikkqekkvrpgltVrkegfealleelsekksiillkekGedisnakielnPvFilgdH 154
                                       pder+ a li++a  ++  ik qe + +pg+ ++++gf+++++ lsek + ++lke+G d+++ + + nP+F+lgd 
  gi|474934490|ref|YP_007688072.1|  78 PDERSTASLIRNACLKK-VIKGQEVSPSPGIFISRRGFDEVIDCLSEKGEFVYLKEDGTDVREFQFPENPIFVLGDN 153
                                       ***********998666.7********************************************************** PP

                                       T-SHHHHHHHHHCTTSEEEES-SS---HHHHHHHHHHHHHHH CS
                   Methyltrn_RNA_2 155 idlpeeeekllerlkakrvslgPlsLhadhcvtlihneldkk 196
                                        dl+eeeek l   +  ++s+gP sLhadhc++l++ne+d+ 
  gi|474934490|ref|YP_007688072.1| 154 SDLTEEEEKALLAHSPAKISVGPVSLHADHCIILVQNEMDRR 195
                                       ***************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1323.40
//
Query:       gi|474934491|ref|YP_007688073.1|  [L=454]
Description: signal recognition particle subunit FFH/SRP54 (srp54) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-65  220.2   0.8    4.1e-65  219.1   0.8    1.6  1  SRP54            SRP54-type protein, GTPase domain
    1.1e-30  106.2   2.6    1.1e-30  106.2   2.6    2.4  3  SRP_SPB          Signal peptide binding domain
      1e-19   70.5   0.9    1.2e-18   67.1   0.3    3.0  2  SRP54_N          SRP54-type protein, helical bundle domain
    4.4e-05   23.5   0.0    0.00033   20.7   0.0    2.7  2  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
     0.0018   18.7   0.1     0.0057   17.1   0.0    1.8  2  AAA_16           AAA ATPase domain
  ------ inclusion threshold ------
      0.012   15.0   0.1      0.024   14.1   0.1    1.4  1  ParA             NUBPL iron-transfer P-loop NTPase
      0.027   13.8   0.1      0.064   12.5   0.1    1.6  1  Zeta_toxin       Zeta toxin
      0.069   13.6   2.2       0.67   10.4   0.2    3.1  3  AAA              ATPase family associated with various cellul
       0.13   12.0   0.7         14    5.5   0.1    2.5  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
       0.15   11.8   0.1        1.9    8.3   0.0    2.4  2  CLP1_P           mRNA cleavage and polyadenylation factor CLP
        0.2   11.7   1.7        7.1    6.7   0.1    2.5  2  Peptidase_S49_N  Peptidase family S49 N-terminal


Domain annotation for each model (and alignments):
>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.1   0.8   2.5e-68   4.1e-65       2     196 .]      98     290 ..      97     290 .. 0.98

  Alignments for each domain:
  == domain 1  score: 219.1 bits;  conditional E-value: 2.5e-68
                                       EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHH CS
                             SRP54   2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeavek 78 
                                       + i+lvGl G GKTt+++KLa+++ k+g +v l+ aD++R+aA++QLk+l++k+g++v+++  ++d+++++++++ k
  gi|474934491|ref|YP_007688073.1|  98 QTIMLVGLYGQGKTTSAGKLANYFIKKGFTVGLIGADVYRPAAYDQLKQLGDKVGAEVYGEPGQKDAVKIVRDGLAK 174
                                       789************************************************************************** PP

                                       HHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSSS CS
                             SRP54  79 akeekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgdak 155
                                         ++k  + ++DT+Gr++ +++l+ee+ +i+kv+kpde +lvld+ +gq+a  qa aF++av+++gvi+tk+Dg+ak
  gi|474934491|ref|YP_007688073.1| 175 LADRK--IKIIDTSGRHALEDDLIEEIIAIAKVAKPDERVLVLDSQVGQQAGPQADAFNKAVDVSGVIMTKMDGTAK 249
                                       *9988..5689****************************************************************** PP

                                       TTHHHHHHHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHHT CS
                             SRP54 156 gGaalsiaaelklPikfigvGekiedleefdperlvsrllg 196
                                       gG+als++a ++  i+fig+Ge+i dle+fd++r++srllg
  gi|474934491|ref|YP_007688073.1| 250 GGGALSAVATTDARIVFIGTGEHIRDLEPFDADRFISRLLG 290
                                       ***************************************95 PP

>> SRP_SPB  Signal peptide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       9.1   1.5e+04      68      82 ..     176     190 ..     169     201 .. 0.76
   2 ?   -1.3   0.1       2.1   3.4e+03      12      31 ..     286     305 ..     280     320 .. 0.55
   3 !  106.2   2.6   6.7e-34   1.1e-30       2      99 .]     323     421 ..     322     421 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 9.1
                                       HHHHHHHHHHTTS-H CS
                           SRP_SPB  68 esRkrRiArGsGtsv 82 
                                       + Rk++i   sG++ 
  gi|474934491|ref|YP_007688073.1| 176 ADRKIKIIDTSGRHA 190
                                       479999999999865 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.1
                                       HHHHCCCCCCHHHHCCC... CS
                           SRP_SPB  12 qqikkmGplskllsmiPgms 31 
                                       +++  mG+l+ l++      
  gi|474934491|ref|YP_007688073.1| 286 SRLLGMGDLQGLVEIAKQEI 305
                                       56677888888887655422 PP

  == domain 3  score: 106.2 bits;  conditional E-value: 6.7e-34
                                       SCTHHHHHHHHHHHCCCCCCHHHHCCC.......H.....CCCCCHHHHHHHHHTTSBHHHHHSGCG-..HHHHHHH CS
                           SRP_SPB   2 ftlrdlleqlqqikkmGplskllsmiPgmsae..akae..eeaekklkrieaiidSMTkeErdspekllkesRkrRi 74 
                                       ftl d+++q++ +kkmG l+k+++m+Pg+s+   +     +++e +l+r+++i+dSMT++E+d+p+ l+k +R+ Ri
  gi|474934491|ref|YP_007688073.1| 323 FTLTDMYNQMKAVKKMGTLQKIVGMLPGLSKVedK--IdfDSTEARLDRFKVIMDSMTQQEKDEPS-LIKGKRIDRI 396
                                       9***************************8876542..2468899**********************.8889****** PP

                                       HHHTTS-HHHHHHHHHHHHHHHHHT CS
                           SRP_SPB  75 ArGsGtsvqevnellkqfeqmkkmm 99 
                                       A+G+G+++++v+ellkq+++ kkmm
  gi|474934491|ref|YP_007688073.1| 397 AHGAGVTTTDVRELLKQYNNSKKMM 421
                                       ************************9 PP

>> SRP54_N  SRP54-type protein, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.1   0.3   7.1e-22   1.2e-18       1      75 []       6      83 ..       6      83 .. 0.97
   2 ?   -0.2   0.0      0.74   1.2e+03      34      73 ..     130     170 ..     115     172 .. 0.78

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 7.1e-22
                                      HHHHHHHHHHHHCCSSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTS...S-HHHHHHHHHHHHH CS
                           SRP54_N  1 LgkklnsalkklsgkskideedleealkeleeaLleaDVgvkvvkklienvkkkavgekk...lkpkqqvkkivkdeL 75
                                      Lgk+l+++l ++ +++++de +++++++el++aLl+aDV+v++v kl++nv+++ ++ek     + k++v+k++++eL
  gi|474934491|ref|YP_007688073.1|  6 LGKSLRGVLDRIGSSTTVDENLIKDVCRELQRALLQADVNVQLVLKLTNNVRERSLNEKPpagRSAKDHVRKVIYEEL 83
                                      89***************************************************99**66699999************8 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.74
                                       HHHTT--HHHHHHHHHHHHHHHHCTTS...S-HHHHHHHHHHH CS
                           SRP54_N  34 LleaDVgvkvvkklienvkkkavgekk...lkpkqqvkkivkd 73 
                                       L+ aDV  +++ + ++++ + +vg  +      +++ +kiv+d
  gi|474934491|ref|YP_007688073.1| 130 LIGADVYRPAAYDQLKQLGD-KVG-AEvygEPGQKDAVKIVRD 170
                                       89999999999888888877.888.552433377888888888 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.4   3.9e+03      91     125 ..      25      63 ..      11      66 .. 0.61
   2 !   20.7   0.0     2e-07   0.00033       9      88 ..     107     248 ..     106     436 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.4
                                       TTCHHHHHHHHHHC....TS-EEEEEE--CCHCCCCHHT CS
                                       xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  91 tllkealeelkqry....gvpvlgviprdeavaeaparg 125
                                       ++l++++++++qr      v+v  v++ + +v e   ++
  gi|474934491|ref|YP_007688073.1|  25 ENLIKDVCRELQRAllqaDVNVQLVLKLTNNVRERSLNE 63 
                                       456666666665555655444444777777777766665 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 2e-07
                                       TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH............................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................... RF
                              CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep............................... 54 
                                       G GKTt a +La ++ ++g+ V l+ aD+ ++++    +l++  ++                               
  gi|474934491|ref|YP_007688073.1| 107 GQGKTTSAGKLANYFIKKGFTVGLIGADVYRPAAYD--QLKQLGDKvgaevygepgqkdavkivrdglakladrkik 181
                                       89*******************************873..333333334577788889999999999999999999999 PP

                                       ...................................................CCHCCCHHHHHHCHCHHHH..EEEEE CS
                                       ...................................................xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ...................................................dlkrllellealgkkkalllkiagvv 80 
                                                                                                             +++ gv+
  gi|474934491|ref|YP_007688073.1| 182 iidtsgrhaleddlieeiiaiakvakpdervlvldsqvgqqagpqadafnkA------------------VDVSGVI 240
                                       9999999999998888888888888888887777666544444444444440..................4555555 PP

                                       EEEESS.. CS
                                       xxxxxxxx RF
                              CbiA  81 lnrvdgen 88 
                                        ++ dg +
  gi|474934491|ref|YP_007688073.1| 241 MTKMDGTA 248
                                       55555443 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.1   1.8e+03      80     127 ..      26      83 ..       9      95 .. 0.46
   2 !   17.1   0.0   3.5e-06    0.0057       9     142 ..      80     216 ..      74     227 .. 0.63

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.1
                            AAA_16  80 ellrqlldeaesaeleawrekleeala...........avpelagaea...srllellkrll 127
                                        l++++++e++ a+l+a+    + +l+           +    ++a++    +++ ++ + l
  gi|474934491|ref|YP_007688073.1|  26 NLIKDVCRELQRALLQAD-VNVQLVLKltnnvrerslnE---KPPAGRsakDHVRKVIYEEL 83 
                                       566666666444333322.22333333445555553332...33333233344444444444 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 3.5e-06
                            AAA_16   9 leqLlsale..rvrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysa.laqalareell 82 
                                        e+L ++l+  +  +  p+ ++l+G  G GK++ + +l++++ k+g+ +    +d +       +   ++l + +l 
  gi|474934491|ref|YP_007688073.1|  80 YEELVALLKngDPIALKPQTIMLVGLYGQGKTTSAGKLANYFIKKGFTVGLIGADVY------RPaAYDQL-K-QLG 148
                                       56666666644455556699*************************999988888888......22244444.3.444 PP

                            AAA_16  83 rqllde.....aesaeleawrekleeala..........avpelagaeasrllellkrllallsrderplvlvlD 142
                                        ++++e      +++++   r+                 +  + + a++ +l e++ ++++ +++der  vlvlD
  gi|474934491|ref|YP_007688073.1| 149 DKVGAEvygepGQKDAVKIVRDG-----LakladrkikiIDTSGRHALEDDLIEEIIAIAKVAKPDER--VLVLD 216
                                       44444444444222222222222.....1333346443322223333348888888888888888665..99999 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   1.4e-05     0.024      14      56 ..     107     149 ..      96     183 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.4e-05
                              ParA  14 GVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveee 56 
                                       G GK+t a +lA  + kkg++vgl+ aD+y p   + l+  ++
  gi|474934491|ref|YP_007688073.1| 107 GQGKTTSAGKLANYFIKKGFTVGLIGADVYRPAAYDQLKQLGD 149
                                       88****************************9987666665554 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   3.9e-05     0.064      14      99 ..      95     183 ..      85     190 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.9e-05
                        Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvv.rldpDdlRelhPeyeeilk...a.dpkkaseltqkdaselve 85 
                                        +P  i+l+G  G GK++ a +l++++ ++g  v  + +D +R+    y+++ +   +   + + e  qkda ++v+
  gi|474934491|ref|YP_007688073.1|  95 LKPQTIMLVGLYGQGKTTSAGKLANYFIKKGFTVgLIGADVYRPAA--YDQLKQlgdKvGAEVYGEPGQKDAVKIVR 169
                                       68*************************988877725678****987..88877743333555677778999999999 PP

                        Zeta_toxin  86 kllqeaiengynii 99 
                                         l++++++++ ii
  gi|474934491|ref|YP_007688073.1| 170 DGLAKLADRKIKII 183
                                       99999999999987 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   0.00041      0.67       1     124 [.     100     284 ..     100     289 .. 0.62
   2 ?   -1.2   0.1       1.6   2.5e+03      85     113 ..     324     380 ..     310     399 .. 0.52
   3 ?   -2.2   0.0       3.2   5.1e+03     122     126 ..     391     395 ..     358     421 .. 0.50

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00041
                                       EEEESSTTSSHHHHHHHHHHHH..........THE..........EEEEETTTCSSS.................... CS
                               AAA   1 vllyGppGtGKTllakavakel..........gve..........fleisgsellsk.................... 37 
                                       ++l+G  G GKT+ a  +a+ +          g++                     +                    
  gi|474934491|ref|YP_007688073.1| 100 IMLVGLYGQGKTTSAGKLANYFikkgftvgliGADvyrpaaydqlK----------Qlgdkvgaevygepgqkdavk 166
                                       5899*****************5444333333333333333333330..........234444444444444444444 PP

                                       .....................STTHHHHHHHHHHHHHHHTS.TSEEEEEET.GGGHHHHH..TTCCCHHHHHHHHHH CS
                               AAA  38 .....................yvgesekkirelfkeakeka.kpsilfiDE.idalaksr..sgseseeeervvnqL 89 
                                                                  + i+e+++ ak  + +  +l++D  + +       + ++ +++ +v  ++
  gi|474934491|ref|YP_007688073.1| 167 ivrdglakladrkikiidtsgRHALEDDLIEEIIAIAKVAKpDERVLVLDSqVGQQ---AgpQADAFNKAVDVSGVI 240
                                       44444444444455544444333336777888888887777555899988413333...244467777888899999 PP

                                       HHHHHHTTTS..........SSTEEEEEEESSGGGSTHHHHSTTS CS
                               AAA  90 lteldgvkkk..........eskvivigatnrpdkldpallrgRf 124
                                       +t++dg  k           ++++++ig++ ++++l+p    +Rf
  gi|474934491|ref|YP_007688073.1| 241 MTKMDGTAKGggalsavattDARIVFIGTGEHIRDLEPFDA-DRF 284
                                       99999999989999999999888999999999999988777.776 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.6
                                       HHHHHHHHHHHTTTS............................SSTEEEEEEESSGG CS
                               AAA  85 vvnqLlteldgvkkk............................eskvivigatnrpd 113
                                       ++  ++++++ vkk                              +++ vi+ + + +
  gi|474934491|ref|YP_007688073.1| 324 TLTDMYNQMKAVKKMgtlqkivgmlpglskvedkidfdstearLDRFKVIMDSMTQQ 380
                                       555666666666665555444444444444444444444444444566666555544 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 3.2
                                       TTSSE CS
                               AAA 122 gRfdr 126
                                       +R+dr
  gi|474934491|ref|YP_007688073.1| 391 KRIDR 395
                                       33332 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1    0.0084        14       3      24 ..      99     120 ..      97     131 .. 0.86
   2 ?    4.3   0.0     0.019        31      39     102 ..     181     247 ..     174     260 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0084
                         PduV-EutP   3 killiGkvgsGKttLtqalkge 24 
                                        i+l+G  g GKtt + +l + 
  gi|474934491|ref|YP_007688073.1|  99 TIMLVGLYGQGKTTSAGKLANY 120
                                       79************99988775 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.019
                         PduV-EutP  39 eviDtPGeylenrklysalivts..aeadvialvqdateeesvfppgfasvfnkeviGii.tkidla 102
                                       ++iDt G ++ +  l + +i+++  a+ d  +lv+d++  ++  p++ a   + +v G+i tk+d +
  gi|474934491|ref|YP_007688073.1| 181 KIIDTSGRHALEDDLIEEIIAIAkvAKPDERVLVLDSQVGQQAGPQADAFNKAVDVSGVImTKMDGT 247
                                       79**************999988722455888899998888888887666666667889765999965 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0012       1.9       5      33 ..     108     136 ..     104     140 .. 0.91
   2 ?    0.6   0.0      0.26   4.3e+02     103     139 ..     178     217 ..     162     245 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0012
                            CLP1_P   5 sGKSTlarlLlNyalrkgrkpvyvDlDvG 33 
                                        GK+T a  L+Ny ++kg ++ ++ +Dv 
  gi|474934491|ref|YP_007688073.1| 108 QGKTTSAGKLANYFIKKGFTVGLIGADVY 136
                                       6**************************96 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.26
                            CLP1_P 103 asgliIntpGwvk..glgaellleliealep.dvvvvldq 139
                                       +++ iI+t+G     +  +e + +++++ +p + v+vld+
  gi|474934491|ref|YP_007688073.1| 178 RKIKIIDTSGRHAleDDLIEEIIAIAKVAKPdERVLVLDS 217
                                       5667888888543113334444445555555555666665 PP

>> Peptidase_S49_N  Peptidase family S49 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1    0.0043       7.1     113     139 ..     193     218 ..     163     223 .. 0.85
   2 ?    3.7   0.1     0.036        59      42      74 ..     406     438 ..     394     451 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0043
                   Peptidase_S49_N 113 esLreeitavLsvakpeDevllrLesg 139
                                       ++L eei a+ +vakp+ +vl+ L+s+
  gi|474934491|ref|YP_007688073.1| 193 DDLIEEIIAIAKVAKPDERVLV-LDSQ 218
                                       689*************888887.6665 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.036
                   Peptidase_S49_N  42 evtkLneeykelkeeleealldeeelkaaekke 74 
                                       +v++L ++y++ k+ + +   d++ +k+ +k+ 
  gi|474934491|ref|YP_007688073.1| 406 DVRELLKQYNNSKKMMGSMSKDRKMRKRLQKQF 438
                                       79999**************99999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       866  (0.0483016); expected 358.6 (0.02)
Passed bias filter:                      593  (0.0330749); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.72u 0.35s 00:00:01.06 Elapsed: 00:00:00.55
# Mc/sec: 2486.33
//
Query:       gi|474934492|ref|YP_007688074.1|  [L=336]
Description: putative archaeal coiled-coil protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.14   12.2  34.4      0.035   14.1   5.6    3.8  4  Laminin_II      Laminin Domain II
        8.1    6.3  20.8       0.56   10.1   0.7    4.3  4  Sec34           Sec34-like family


Domain annotation for each model (and alignments):
>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   4.8     0.037   3.4e+02      12      72 ..      36      96 ..      18      97 .. 0.65
   2 ?    9.9  10.7     8e-05      0.71       8      87 ..      60     146 ..      57     165 .. 0.79
   3 ?   14.1   5.6   3.8e-06     0.035       2      73 ..     176     249 ..     175     286 .. 0.83
   4 ?    1.8   1.0     0.024   2.2e+02       5      82 ..     244     323 ..     243     329 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.037
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTG CS
                        Laminin_II 12 akevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLl 72
                                      ++e++e +++ +++le+++++   +n+++e+ +   +++n +++d + +   L++++ +L+
  gi|474934492|ref|YP_007688074.1| 36 TEEIEEPTEEEKARLEQLEADRTVANDEAEKHKVRRDELNAQTKDWKAKRDALNNQVRELV 96
                                      4556666666666666666666666666555555555778888888888888888877776 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 8e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.......XXXXXXXXXXXXXXXX--TTTTTGGGHHH CS
                        Laminin_II   8 anetakevleqlaplsqnlentkeklseinrsveetnekvk.......dankairdArrsvkkLeklapqLldklke 77 
                                       an+ a++ +    +l+++++ +k+k   +n++v+e  +++        ++n+ +rdA+   ++L+ ++ +L +k++e
  gi|474934492|ref|YP_007688074.1|  60 ANDEAEKHKVRRDELNAQTKDWKAKRDALNNQVRELVDEAGkqrqlrdEMNQKVRDAKVVRSDLNTKVSELRAKIQE 136
                                       677777777888999****************999987766444556668999************************* PP

                                       HHHHHHH... CS
                        Laminin_II  78 lkqleeasss 87 
                                       lk  +e ++ 
  gi|474934492|ref|YP_007688074.1| 137 LKPEKEDKEK 146
                                       *987766544 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 3.8e-06
                                       XXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGG CS
                        Laminin_II   2 kelaaeanetakevleq..laplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLld 73 
                                       k+l++++++ ake++e    ++ +++l  + ++ +e+++++e  +++v+++ ++ ++A +++ +L ++a+ + +
  gi|474934492|ref|YP_007688074.1| 176 KKLVKAISQLAKEIEEMekSNEDDEQLGGLYQQFHEVKAQAEVAHKQVSEYAEQAQSAHDKMLTLYQQADSIRK 249
                                       7889999999999987511567789*********************************************9865 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.024
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXX--TTTTTGGGHHHHH CS
                        Laminin_II   5 aaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrs..vkkLeklapqLldklkelk 79 
                                       a+++ + a + +++  + ++  +++ + + e+ ++++   + ++  +k    A+++    + +k+a ++++k+k  +
  gi|474934492|ref|YP_007688074.1| 244 ADSIRKEADAAQAKFVECKNAADEEHKAYLELVGKARDASKSADGIKKKKSAASKKraDGEAKKEAKEIFEKFKAGE 320
                                       67777888888888888888888888888888888888888888555555555544004556789999999999877 PP

                                       HHH CS
                        Laminin_II  80 qle 82 
                                       +l+
  gi|474934492|ref|YP_007688074.1| 321 KLS 323
                                       766 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.8    0.0016        15      19      68 ..      64     113 ..      47     115 .. 0.85
   2 ?    1.9   0.8     0.021   1.9e+02      21      74 ..     108     161 ..     107     168 .. 0.77
   3 ?    4.6   0.8    0.0031        27      17      57 ..     193     233 ..     175     237 .. 0.75
   4 ?   10.1   0.7   6.3e-05      0.56       1      67 [.     226     292 ..     226     295 .. 0.96

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0016
                             Sec34  19 tdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekL 68 
                                       +++ +   +el+ + k+ ++k  +l+++  +l++e  + ++l +e+++k+
  gi|474934492|ref|YP_007688074.1|  64 AEKHKVRRDELNAQTKDWKAKRDALNNQVRELVDEAGKQRQLRDEMNQKV 113
                                       55555566799999*******************************99986 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.021
                             Sec34  21 ealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFeel 74 
                                       e+++++++ +   ++ ++k s+l+++ ++l  e+++ e+  e++ +k + F+++
  gi|474934492|ref|YP_007688074.1| 108 EMNQKVRDAKVVRSDLNTKVSELRAKIQELKPEKEDKEKPEESLAQKKRRFDQM 161
                                       566777777777778888888888888888888888888888888888888776 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.0031
                             Sec34  17 eqtdealeqLeeleekfksvsektsslheaceqlleeqkrl 57 
                                       e+ +e  eqL  l ++f++v+++ +  h++  +  e+ ++ 
  gi|474934492|ref|YP_007688074.1| 193 EKSNEDDEQLGGLYQQFHEVKAQAEVAHKQVSEYAEQAQSA 233
                                       56677788999999999999999999999998887776655 PP

  == domain 4  score: 10.1 bits;  conditional E-value: 6.3e-05
                             Sec34   1 yldqLeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieek 67 
                                       y +q +s ++++ +l +q+d++ ++ +  + kf + ++   + h+a  +l+ + ++ ++ a+ i++k
  gi|474934492|ref|YP_007688074.1| 226 YAEQAQSAHDKMLTLYQQADSIRKEADAAQAKFVECKNAADEEHKAYLELVGKARDASKSADGIKKK 292
                                       678999999*******************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3799  (0.211891); expected 358.6 (0.02)
Passed bias filter:                      641  (0.0357521); expected 358.6 (0.02)
Passed Vit filter:                       132  (0.00736237); expected 17.9 (0.001)
Passed Fwd filter:                        53  (0.0029561); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 1.45u 0.43s 00:00:01.88 Elapsed: 00:00:00.59
# Mc/sec: 1707.73
//
Query:       gi|474934493|ref|YP_007688075.1|  [L=41]
Description: hypothetical protein TALC_00920 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      128  (0.00713927); expected 358.6 (0.02)
Passed Vit filter:                         2  (0.000111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.49
# Mc/sec: 251.26
//
Query:       gi|474934494|ref|YP_007688076.1|  [L=440]
Description: adenylosuccinate lyase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.3e-51  173.6   1.2    8.2e-51  173.2   1.2    1.2  1  Lyase_1        Lyase
      1e-24   86.9   1.7    4.2e-24   84.9   0.1    2.7  3  ADSL_C         Adenylosuccinate lyase C-terminus
      4e-06   26.9   0.2    1.3e-05   25.3   0.0    1.9  2  ASL_C          Adenylosuccinate lyase C-terminal
      0.005   17.6   3.3      0.036   14.8   0.0    3.5  3  ASL_C2         Argininosuccinate lyase C-terminal
  ------ inclusion threshold ------
      0.055   13.6   0.0       0.32   11.2   0.0    2.1  2  DUF4253        Domain of unknown function (DUF4253)
      0.097   13.1   4.2        2.5    8.5   0.1    3.1  3  Ribosomal_S13  Ribosomal protein S13/S18
       0.17   12.6   7.0       0.47   11.1   0.4    3.6  4  HHH_5          Helix-hairpin-helix domain


Domain annotation for each model (and alignments):
>> Lyase_1  Lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.2   1.2   3.2e-54   8.2e-51      12     310 ..       3     283 ..       1     285 [. 0.90

  Alignments for each domain:
  == domain 1  score: 173.2 bits;  conditional E-value: 3.2e-54
                                       HHHHHHHHHHGGGHHHHHCHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHCHCHHCGGHHHBSSSSSHHHHHHHHHH CS
                           Lyase_1  12 giftersrenfrlseedikalaalkkaaakanvdlkeeaaaiikaldevleegklddqfvlkviqegsgtavnmnln 88 
                                        if+e+sr +++++     ++aal++a a+++++ +  a++i +++    +e+  ++  ++++ ++++  a+  +++
  gi|474934494|ref|YP_007688076.1|   3 SIFSESSRIRYQMQ-----VEAALAQAHAQLGEISQADADEISRVAG--SDEVTVERIKEIEKLTNHDLMAMVKAMT 72 
                                       68999999999999.....99**************999999987764..3455667788999999999999999999 PP

                                       HHHHHHTTHSSGIIIIITTT--HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHTTT-EEEEEETTEEEEE CS
                           Lyase_1  89 evigellgekvepndkvhtgqSsnDqvpTalrlalkkalsekLlpaleqLidalkekakefkdvvkiGrThlqdAtP 165
                                       e  +       ++ ++vh g++snD+v+Ta +l++++al + + +++++L  +l + ak ++d++ iGrTh q A P
  gi|474934494|ref|YP_007688076.1|  73 EKCK------GDAGKYVHLGATSNDIVDTATALQIRDAL-DIVAADVDELLFTLAKLAKRERDTLEIGRTHAQFAIP 142
                                       9999......59***************************.66*********************************** PP

                                       EEHHHHHHHHHHHHHHHHHHHHHHHHHHTCEETTTTTTTSSTTTSCCTHHHHHHHHHHHHHCSTEESSSHHHHHHC- CS
                           Lyase_1 166 vtlgqelsayaealerdrerlkellkrllvellgggtavgtglnadpefaelvakelakvtglpvkapnsfeavsdr 242
                                       +t g ++++y ++l r rer+ e+++r +++++ g  avgtg+   ++f++l ++ +++++    + ++  ++v  r
  gi|474934494|ref|YP_007688076.1| 143 ITYGFKIAGYIAELLRFRERIIEITPRAIAGKMAG--AVGTGAALGKNFQKLQIAVMQELDI---TYEPAATQVVGR 214
                                       ***********************************..6666666666777777777776666...7788888***** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHTSTT.TSSEEEEGCCTSSC-TTSTTTEBTHHHHHHHHHHHHH CS
                           Lyase_1 243 DavvellgalkllatsLskfaeDlrllssge.aglvelslaesepGSSiMPgKvNPvqlElltgvagrv 310
                                       D+++el+ +l++l tsL + a ++r l+ +e + + e  +a+ + GSS+M +K+NP+++E++ g a+  
  gi|474934494|ref|YP_007688076.1| 215 DRYTELVCMLATLGTSLERYATEVRNLQRSEiSEVSEYFDAAHQVGSSTMAQKRNPINSENVCGLARVL 283
                                       *******************************9999999************************9998765 PP

>> ADSL_C  Adenylosuccinate lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.76   1.9e+03      25      57 ..      28      60 ..       9      73 .. 0.52
   2 ?   -1.9   0.0         2   5.1e+03      50      66 ..     246     262 ..     209     265 .. 0.71
   3 !   84.9   0.1   1.6e-27   4.2e-24       1      72 [.     349     426 ..     349     427 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.76
                                      HHHHHHHHHHCHHHHHHT-HHHH.CHHCHHHHHT CS
                            ADSL_C 25 VqeaamkaweellelLaadpevk.kseeeldalf 57
                                        e +++ ++e + ++a  +ev+ ++ +e+++l+
  gi|474934494|ref|YP_007688076.1| 28 LGEISQADADE-ISRVAGSDEVTvERIKEIEKLT 60
                                      33333333322.2344444455534333666665 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2
                                       HCHHHHHT-GGGCCTTH CS
                            ADSL_C  50 eeeldalfdpayylgsa 66 
                                        +e+ + fd a+ +gs+
  gi|474934494|ref|YP_007688076.1| 246 ISEVSEYFDAAHQVGSS 262
                                       23788888888888876 PP

  == domain 3  score: 84.9 bits;  conditional E-value: 1.6e-27
                                       TGGGHHHHHHHHH.HTH-HHHHHHHHHHHHHHHHHC...HHHHHHT-HHHHC..HHCHHHHHT-GGGCCTTHHHHHH CS
                            ADSL_C   1 GlifservllaLv.kglgReeAyelVqeaamkawee...llelLaadpevkk..seeeldalfdpayylgsadeivd 71 
                                       Gli++e v++aLv kg+gR++A+e+V+ea+m a ++   lle+L + ++vkk  s+eel++++dpa+y+g + eivd
  gi|474934494|ref|YP_007688076.1| 349 GLIMAEPVMMALVgKGIGRQDAHEIVREASMVAEDRecqLLETLWERDDVKKliSREELEKVMDPANYTGGSKEIVD 425
                                       9************99*******************99***************55*999******************** PP

                                       H CS
                            ADSL_C  72 r 72 
                                       r
  gi|474934494|ref|YP_007688076.1| 426 R 426
                                       9 PP

>> ASL_C  Adenylosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.6   4.2e+03      82     112 ..      32      62 ..      11      65 .. 0.68
   2 !   25.3   0.0   4.9e-09   1.3e-05       4     115 .]     299     417 ..     297     417 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.6
                                       S---HHHHHHHHHCS-S-HHHHHHHHC--CC CS
                             ASL_C  82 kkitkeslkefieslevseeakeeLkaltpa 112
                                       ++ ++++++++  s ev+ e  +e+++lt +
  gi|474934494|ref|YP_007688076.1|  32 SQADADEISRVAGSDEVTVERIKEIEKLTNH 62 
                                       3556777777777777887777888877765 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 4.9e-09
                                       T--TCHHHHHTT.CHHHHHHHHHHHHHHHHHHCCEEE-HHHHHHHHHT-.GGGGHHHHHHHHHHT..T-TTHHHHHH CS
                             ASL_C   4 QRDLtdStvlRn.lgvalahslialksllkglsklevneealaedLden.wevlaEaiqtvlrre..giekpYeklk 76 
                                        RDL++S+  R  l   ++ +   l ++ k +s lev+++++ ++++++   ++aE++ ++l  +  g ++++e ++
  gi|474934494|ref|YP_007688076.1| 299 ERDLSNSSCERFtLPHVFSLIDYMLYKMNKVFSGLEVHRDKMLRNIESAhGLIMAEPVMMALVGKgiGRQDAHEIVR 375
                                       6**********7245667777777889*******************98725789******9975522679******* PP

                                       HHHTTS.---HHHHHHHHHCS-S-HHHH.HHHHC.--CCC-- CS
                             ASL_C  77 eltrgk.kitkeslkefieslevseeak.eeLka.ltpatYi 115
                                       e    + + + + l+++ e  +v++ ++ eeL++ + pa+Y+
  gi|474934494|ref|YP_007688076.1| 376 EASMVAeDRECQLLETLWERDDVKKLISrEELEKvMDPANYT 417
                                       *99888345556667777777899876526786537899996 PP

>> ASL_C2  Argininosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.5      0.32   8.2e+02      21      56 ..      24      62 ..      17     121 .. 0.65
   2 ?   -1.0   0.0       1.2   3.1e+03      30      51 ..     180     201 ..     171     260 .. 0.64
   3 !   14.8   0.0   1.4e-05     0.036      10      66 ..     359     415 ..     353     416 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.32
                                      HHHHHHHHHHHHHHT...T--GGG--HHHHHHH-TT--G CS
                            ASL_C2 21 AHeivgravrlaeek...gkeleeltleelkeispllee 56
                                      AH   g++ ++  ++       +e+t+e +kei++l + 
  gi|474934494|ref|YP_007688076.1| 24 AHAQLGEISQADADEisrVAGSDEVTVERIKEIEKLTNH 62
                                      555555555552222111222456666666666544333 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.2
                                       HHHHHTT--GGG--HHHHHHH- CS
                            ASL_C2  30 rlaeekgkeleeltleelkeis 51 
                                        +  + gk++++l+++ ++e++
  gi|474934494|ref|YP_007688076.1| 180 GTGAALGKNFQKLQIAVMQELD 201
                                       4455567777777777777554 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 1.4e-05
                                       HHHHCTS-HHHHHHHHHHHHHHHHHTT--GGG--HHHHHHH-TT--.GGGGGGSSHHH CS
                            ASL_C2  10 yLvrkGlpFReAHeivgravrlaeekgkeleeltleelkeisplle.edveeaLdpea 66 
                                       +Lv kG+   +AHeiv +a   ae+++++l e   e  + +++l++ e++e+++dp++
  gi|474934494|ref|YP_007688076.1| 359 ALVGKGIGRQDAHEIVREASMVAEDRECQLLETLWER-DDVKKLISrEELEKVMDPAN 415
                                       69999************************77644433.336699999********985 PP

>> DUF4253  Domain of unknown function (DUF4253)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.73   1.9e+03      26      44 ..      58      76 ..      53      83 .. 0.89
   2 ?   11.2   0.0   0.00013      0.32      26      84 ..      86     144 ..      78     163 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.73
                           DUF4253 26 eltnedlvavlrsWeeryg 44
                                      +ltn+dl+a++++  e+++
  gi|474934494|ref|YP_007688076.1| 58 KLTNHDLMAMVKAMTEKCK 76
                                      6899********9999986 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00013
                           DUF4253  26 eltnedlvavlrsWeerygaelvgigfdtlelsvakppkteeealalAaEhyafCpdlv 84 
                                         t++d+v  + + + r + ++v+++ d l ++ ak+ k e+++l++ + h++f+  ++
  gi|474934494|ref|YP_007688076.1|  86 GATSNDIVDTATALQIRDALDIVAADVDELLFTLAKLAKRERDTLEIGRTHAQFAIPIT 144
                                       567899999********************************************997765 PP

>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.4     0.019        50      23      90 ..      31     106 ..       8     115 .. 0.62
   2 ?   -0.8   0.0      0.73   1.9e+03      41      74 ..     236     269 ..     195     277 .. 0.73
   3 ?    8.5   0.1   0.00098       2.5      16      66 ..     359     410 ..     350     440 .] 0.60

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.019
                     Ribosomal_S13  23 iGrrkakiilkkad.....vdedkrigelteeeiekieeivenkaqykipnwi...nrqkdikdGkdshvvendlr 90 
                                       i +  a +i + a+     v++ k i++lt++++  +++ + +k +  + +++      +di d ++  ++   l+
  gi|474934494|ref|YP_007688076.1|  31 ISQADADEISRVAGsdevtVERIKEIEKLTNHDLMAMVKAMTEKCKGDAGKYVhlgATSNDIVDTATALQIRDALD 106
                                       5555555555433311111667777888888888888888888777766666544556778888777777777766 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.73
                     Ribosomal_S13  41 krigelteeeiekieeivenkaqykipnwinrqk 74 
                                       + +++l+  ei+++ e+ +   q  + ++  +++
  gi|474934494|ref|YP_007688076.1| 236 TEVRNLQRSEISEVSEYFDAAHQVGSSTMAQKRN 269
                                       5678899999999999999877777766665554 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.00098
                     Ribosomal_S13  16 altaikGiGrrkakiilkkadvdedkrigeltee..eiekieeivenkaqyki 66 
                                       al   kGiGr+ a++i+++a +  + r  +l e   e + ++++++++  +k+
  gi|474934494|ref|YP_007688076.1| 359 ALVG-KGIGRQDAHEIVREASMVAEDRECQLLETlwERDDVKKLISREELEKV 410
                                       5543.8**************998777776665542233445555555444433 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.4   0.00018      0.47      25      53 ..      27      55 ..      17      59 .. 0.87
   2 ?    1.5   0.2      0.18   4.6e+02      23      37 ..     101     115 ..      92     130 .. 0.77
   3 ?    1.2   0.0      0.23   5.9e+02      20      55 ..     342     377 ..     338     379 .. 0.64
   4 ?   -3.1   0.0       4.9   1.2e+04      34      40 ..     404     410 ..     389     430 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00018
                                      SHHHHHHS-HHHHHTSTTS-HHHHHHHHH CS
                             HHH_5 25 svedlaaadveeLakipGiGkktAeriil 53
                                      ++ ++ +ad++e++++ G  + t+eri++
  gi|474934494|ref|YP_007688076.1| 27 QLGEISQADADEISRVAGSDEVTVERIKE 55
                                      567999*********************76 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.18
                                       --SHHHHHHS-HHHH CS
                             HHH_5  23 iesvedlaaadveeL 37 
                                       i+   d++aadv+eL
  gi|474934494|ref|YP_007688076.1| 101 IRDALDIVAADVDEL 115
                                       555679999999996 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.23
                                       TTT--SHHHHHHS-HHHHHTS.TTS-HHHHHHHHHHH CS
                             HHH_5  20 saGiesvedlaaadveeLaki.pGiGkktAeriilel 55 
                                       ++ ies   l+ a++   a + +GiG   A  i+ e+
  gi|474934494|ref|YP_007688076.1| 342 RN-IESAHGLIMAEPVMMALVgKGIGRQDAHEIVREA 377
                                       55.5555556666655555555788888888887776 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 4.9
                                       HHHHHTS CS
                             HHH_5  34 veeLaki 40 
                                       +eeL k+
  gi|474934494|ref|YP_007688076.1| 404 REELEKV 410
                                       3444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3123.80
//
Query:       gi|474934495|ref|YP_007688077.1|  [L=63]
Description: hypothetical protein TALC_00922 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0038   17.6   0.2     0.0047   17.3   0.2    1.1  1  MgtE      Divalent cation transporter
  ------ inclusion threshold ------
      0.052   13.5   0.7      0.055   13.4   0.7    1.0  1  DUF1275   Protein of unknown function (DUF1275)


Domain annotation for each model (and alignments):
>> MgtE  Divalent cation transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.2   5.2e-07    0.0047      34      98 ..       5      59 ..       1      61 [. 0.79

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.2e-07
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHT-.CTSHHHHHHHHHHHHHHHHHH..HHHHHHHHHHT CS
                              MgtE 34 kvllkelrvvlllgvilgllifllalllgwslllalvvglalvlvllaaallilgvllplllwkl 98
                                       +l++++r ++l+g+i g+l++l  +               +++++ +aal+  g+++p+l++k+
  gi|474934495|ref|YP_007688077.1|  5 PFLRRNMRFGFLVGLITGILLALALYAR--------SEHPIVLVFIPFAALM--GWYTPYLMYKI 59
                                      6799******************985543........3466666777788888..99999998886 PP

>> DUF1275  Protein of unknown function (DUF1275)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.7   6.2e-06     0.055     150     190 ..       7      48 ..       1      50 [. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.2e-06
                           DUF1275 150 larnrrlaiilafllGavvGallvks.aaalwlaaallllva 190
                                       l+rn+r++++++++ G +++ +l+ + ++ ++l+ +  ++++
  gi|474934495|ref|YP_007688077.1|   7 LRRNMRFGFLVGLITGILLALALYARsEHPIVLVFIPFAALM 48 
                                       4599***********************998888888777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 410.94
//
Query:       gi|474934496|ref|YP_007688078.1|  [L=138]
Description: pyridoxamine 5'-phosphate oxidase-like FMN-binding protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-12   47.6   0.0    1.6e-12   47.4   0.0    1.1  1  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
  ------ inclusion threshold ------
      0.016   14.8   0.0      0.019   14.5   0.0    1.1  1  Pyrid_ox_like   Pyridoxamine 5'-phosphate oxidase like
       0.15   11.9   0.0       0.22   11.3   0.0    1.2  1  DUF447          Protein of unknown function (DUF447)


Domain annotation for each model (and alignments):
>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.4   0.0   2.7e-16   1.6e-12      10      83 ..      17      91 ..       4      96 .. 0.88

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 2.7e-16
                                      HHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETT.GSEEEEEEEEEEE CS
                    Putative_PNPOx 10 aeskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallfldde.lgrgvrieGtael 83
                                      ++s++++lAT ++ G Pnv+p+++ +   +d i+++ n+  ++l+n+  np v+++ +  e   + v+++G+a  
  gi|474934496|ref|YP_007688078.1| 17 NQSRIFALATSSKGGIPNVVPIGFLFVANDDEIWVIDNYLNKTLKNILDNPVVSVYAMGGEgGHECVQVKGKAVY 91
                                      577********************888877788***************************99999********975 PP

>> Pyrid_ox_like  Pyridoxamine 5'-phosphate oxidase like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   3.2e-06     0.019       7      83 ..      13      90 ..       7     112 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.2e-06
                     Pyrid_ox_like  7 kelvkdiktamLttteadgklksrPMatqkveedgdlwfltkkdsdkvkeirkdsqvnlafs.deskkkyvsvsGtae 83
                                      +++ ++ ++  L+t++++g  ++ P     v++d+++w + +  ++  k+i  ++ v+++ + +e  ++ v+v+G+a 
  gi|474934496|ref|YP_007688078.1| 13 ADHGNQSRIFALATSSKGGIPNVVPIGFLFVANDDEIWVIDNYLNKTLKNILDNPVVSVYAMgGEGGHECVQVKGKAV 90
                                      5666778888899*999**************************************99997651577889999999985 PP

>> DUF447  Protein of unknown function (DUF447)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   3.6e-05      0.22       7      49 ..      26      71 ..      23      74 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.6e-05
                                      EE-TT.-EEEEEEEEEE..SSSE.EEEEEETTSHHHHHHHHHSEEEE CS
                            DUF447  7 Tksek.rpnaaPiGviv..kgdk.vvlrlfkgsrTleNllengelvi 49
                                      T+s+   pn+ PiG  +  ++d+ +v+  +  ++Tl+N+l n+ +++
  gi|474934496|ref|YP_007688078.1| 26 TSSKGgIPNVVPIGFLFvaNDDEiWVIDNYL-NKTLKNILDNPVVSV 71
                                      4555559*******99987444459999999.6********998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 931.28
//
Query:       gi|474934497|ref|YP_007688079.1|  [L=365]
Description: hypothetical protein TALC_00924 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.2e-12   46.3   0.0    1.4e-11   45.1   0.0    1.6  1  Fic       Fic/DOC family
    0.00023   21.2   0.0    0.00066   19.7   0.0    1.8  1  Fic_N     Fic/DOC family N-terminal
  ------ inclusion threshold ------
      0.013   15.2   0.3      0.058   13.1   0.1    2.1  2  CUE       CUE domain


Domain annotation for each model (and alignments):
>> Fic  Fic/DOC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   0.0   2.3e-15   1.4e-11       3      97 .]     109     214 ..     107     214 .. 0.87

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 2.3e-15
                                       SHHHHHHHHCHS-S------TS--SS-S........T..EEEE---SCCCHHHHHHHHHHHHC...HHT-S-HHHHH CS
                               Fic   3 tledllelhrlllqdigeeagefrdeev........segklesalappeevpaeleelleyln...elekeepleka 68 
                                       + e llel+++l++  g +   f++ ++        ++ +  ++  p+++v++ l++l  +++    + ++++l ++
  gi|474934497|ref|YP_007688079.1| 109 DREGLLELYAILTRYSGYRDEGFKTTDNvivdraadGSVENIHRTVPHDQVEECLAQLYYSFTearCNPEINVLLLI 185
                                       67889999999988888766777666667999999966788899999************9999988888888***** PP

                                       HHHHHHHHHH--SSS-HHHHHHHHHHHHH CS
                               Fic  69 aalhyefekiHPFaDGNgRtarlllnllL 97 
                                        +++  f +iHPF DGNgR++rll+ +lL
  gi|474934497|ref|YP_007688079.1| 186 PCFVMDFLRIHPFLDGNGRMSRLLTTMLL 214
                                       *************************9886 PP

>> Fic_N  Fic/DOC family N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.1e-07   0.00066      22      79 ..      44      98 ..      35     100 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.1e-07
                             Fic_N 22 pnpelLirplvrkEAvlSSeIEgtqttlddlleaeadeeeekskdvkEVlnYvkAley 79
                                       + +++ ++++++   +S +IEg++tt d +++  +++   k+++ kE++ Y++Al++
  gi|474934497|ref|YP_007688079.1| 44 SDMQIFATAMSMR---DSNAIEGIRTTDDRIFSLLSERAVPKNHSEKEIIGYRDALRH 98
                                      5555555555554...799*****************99999889************86 PP

>> CUE  CUE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.48   2.9e+03      15      25 ..     154     164 ..     154     165 .. 0.82
   2 ?   13.1   0.1   9.7e-06     0.058       6      24 ..     305     323 ..     301     324 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.48
                                       S-HHHHHHHHH CS
                               CUE  15 ldeevIravLr 25 
                                       ++ ++++ +L 
  gi|474934497|ref|YP_007688079.1| 154 VPHDQVEECLA 164
                                       5789******5 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 9.7e-06
                                       HHHHHHSTTS-HHHHHHHH CS
                               CUE   6 etLkemFPdldeevIravL 24 
                                       ++L+emFPd+++ +I+  L
  gi|474934497|ref|YP_007688079.1| 305 KDLSEMFPDISVKTIELTL 323
                                       589************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2576.01
//
Query:       gi|474934498|ref|YP_007688080.1|  [L=175]
Description: Inorganic pyrophosphatase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-53  180.4   0.0    2.4e-53  180.2   0.0    1.0  1  Pyrophosphatase  Inorganic pyrophosphatase


Domain annotation for each model (and alignments):
>> Pyrophosphatase  Inorganic pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.2   0.0   1.4e-57   2.4e-53       2     160 .]      21     172 ..      20     172 .. 0.98

  Alignments for each domain:
  == domain 1  score: 180.2 bits;  conditional E-value: 1.4e-57
                                       EEEE-TTCSEEEEEETTTTEEEEEEE-SSSB-BSSEEEEETT--BTCCBEETSSSEEEEEESSS---TTEEEEEEEE CS
                   Pyrophosphatase   2 vvEiprgsnaKyeidkeegklrldrvlftskgypanYGfipqTledtelkGDgDPlDvlvlgeeplspgevvevkvl 78 
                                       ++Ei++gs++Kye+d+e+g + +dr+l ts++yp+nYG ip Tl+      DgDPlDvlv+++ep+ pg + +++++
  gi|474934498|ref|YP_007688080.1|  21 FIEISKGSKMKYELDEETGLIAVDRILSTSTQYPWNYGLIPLTLAL-----DGDPLDVLVISSEPIIPGALAKCRPI 92 
                                       79********************************************.....************************** PP

                                       EEEEEEETTEEEEEEEEEETTSGGGTT-SSGGGSTHHHHHHHHHHHHHTTTTSCCT-SEEEEEEEEHHHHHHHHHHH CS
                   Pyrophosphatase  79 GvlamiDegetDdKiiavpvkdprlkkindiedlpgllleeiehfFetykdlegkkknvkveewkdkeeAekvieea 155
                                       G+++m+D+g +DdK++av  kdp++k+i+di +lp++l eei+hfF+ yk+legk  +++   +++ e+A+k i+++
  gi|474934498|ref|YP_007688080.1|  93 GIMRMVDSGDQDDKVLAVLPKDPMYKEITDIAQLPKHLGEEIQHFFTVYKALEGK--KTEAGIIEGPEAARKTIQAC 167
                                       ***********************99****************************66..689999************** PP

                                       HHHHH CS
                   Pyrophosphatase 156 heryk 160
                                       +++yk
  gi|474934498|ref|YP_007688080.1| 168 MDAYK 172
                                       *9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1200.32
//
Query:       gi|474934499|ref|YP_007688081.1|  [L=290]
Description: ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-34  119.9   0.0    1.5e-34  119.4   0.0    1.2  1  ABC_tran      ABC transporter
    1.4e-07   31.7   0.1     0.0032   17.3   0.0    2.3  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    4.1e-06   27.4   0.0    6.1e-06   26.9   0.0    1.3  1  AAA_23        AAA domain
    4.3e-05   24.0   0.0    8.4e-05   23.0   0.0    1.6  1  AAA_16        AAA ATPase domain
    0.00011   21.9   0.1    0.00021   21.0   0.1    1.4  1  AAA_29        P-loop containing region of AAA domain
    0.00067   19.6   0.0     0.0015   18.5   0.0    1.6  1  RsgA_GTPase   RsgA GTPase
    0.00075   19.5   0.2     0.0015   18.5   0.1    1.5  1  Rad17         Rad17 P-loop domain
    0.00083   19.6   0.0     0.0022   18.3   0.0    1.9  1  AAA_22        AAA domain
    0.00094   19.0   0.1      0.015   15.0   0.0    2.0  2  AAA_15        AAA ATPase domain
     0.0015   18.1   0.0       0.33   10.3   0.0    2.2  2  SMC_N         RecF/RecN/SMC N terminal domain
      0.002   18.2   0.0      0.036   14.1   0.0    2.3  1  MMR_HSR1      50S ribosome-binding GTPase
     0.0082   15.9   1.2       0.06   13.1   0.3    2.6  3  PRK           Phosphoribulokinase / Uridine kinase family
      0.009   16.4   0.4      0.063   13.7   0.4    2.1  1  AAA           ATPase family associated with various cellular 
  ------ inclusion threshold ------
      0.016   15.2   4.1        1.7    8.5   0.6    2.5  2  NTPase_1      NTPase
      0.026   14.5   0.2        0.1   12.6   0.1    1.9  2  AAA_5         AAA domain (dynein-related subfamily)
      0.048   12.8   0.2       0.16   11.1   0.0    1.9  2  NB-ARC        NB-ARC domain
      0.068   13.1   0.1       0.87    9.5   0.0    2.1  2  ATPase_2      ATPase domain predominantly from Archaea
      0.077   12.6   0.0        0.2   11.2   0.0    1.7  1  AAA_25        AAA domain
      0.092   11.5   0.4          3    6.5   0.1    2.1  2  ABC_ATPase    Predicted ATPase of the ABC class
        0.1   12.3   0.1       0.24   11.1   0.1    1.6  1  AAA_30        AAA domain
       0.11   11.9   0.1       0.22   10.9   0.1    1.4  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
       0.15   12.2   0.8       0.76    9.9   0.3    2.1  2  AAA_33        AAA domain
       0.16   11.8   0.1       0.35   10.8   0.1    1.5  1  NACHT         NACHT domain
       0.22   10.3   0.0       0.36    9.6   0.0    1.3  1  Adeno_IVa2    Adenovirus IVa2 protein
       0.24   11.8   0.4       0.54   10.7   0.2    1.7  1  RNA_helicase  RNA helicase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.4   0.0   2.1e-37   1.5e-34       1     136 [.      56     195 ..      56     196 .. 0.97

  Alignments for each domain:
  == domain 1  score: 119.4 bits;  conditional E-value: 2.1e-37
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       ++n++l++k+ge++ ivG++G+GKSt+l+++agll+pt+G+i++ gk+ ++     + +  g+++q+  lfp  +vr
  gi|474934499|ref|YP_007688081.1|  56 VDNLDLDIKKGELISIVGPSGCGKSTILRCIAGLLQPTKGTITMGGKPCTT-----AGSDRGMVFQDFALFPWRSVR 127
                                       589***************************************999999888.....9999***************** PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       +n             e++++ +++l+ +gl++++d ++    ++LSgG+kqrv +ara++ +p ++l+DEp+
  gi|474934499|ref|YP_007688081.1| 128 SNiefglevagvpkeERRRRSDRYLEAMGLQDFADARI----HELSGGMKQRVGIARAMIMHPAVILMDEPF 195
                                       *************9888888******************....*****************************6 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   4.5e-06    0.0032       3      24 ..      70      91 ..      68     117 .. 0.83
   2 !   12.1   0.0   0.00017      0.12     192     298 ..     123     227 ..     115     231 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.5e-06
                            AAA_21  3 vliGpNgsGKSnLLdaldllar 24
                                       ++Gp g+GKS++L+++ +l +
  gi|474934499|ref|YP_007688081.1| 70 SIVGPSGCGKSTILRCIAGLLQ 91
                                      59***************99965 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00017
                            AAA_21 192 lklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEn 268
                                       ++ v++++++ +e+   ++++ +r  +r++  +   d  +  ++elS G+k+  +++ a++  +   +++l DEp  
  gi|474934499|ref|YP_007688081.1| 123 WRSVRSNIEFGLEVAGVPKEERRRRSDRYLEAMGLQDFADARIHELSGGMKQRVGIARAMIMHP---AVILMDEPFG 196
                                       566677777777777777777788788888888889999999***********99999999877...********** PP

                            AAA_21 269 gLHPkllrrll.ell.kelsrngaQviltTHS 298
                                        L+   +r +l e l + l++    ++++THS
  gi|474934499|ref|YP_007688081.1| 197 ALDA-QTRNILqESLvNVLKTSHRTIVFVTHS 227
                                       ****.4444444333344444456*******9 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   8.5e-09   6.1e-06      12      96 ..      58     146 ..      51     189 .. 0.77

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 8.5e-09
                            AAA_23  12 dqeidFsk.gltlItGpNGaGKTTildAiklaLygetprlsrks........grgfeksdveiesegkvkayveltf 79 
                                       + ++d +k  l  I+Gp G+GK+Til++i   L   +++   +         +rg++ +d++++ +++v++ +e+ +
  gi|474934499|ref|YP_007688081.1|  58 NLDLDIKKgELISIVGPSGCGKSTILRCIAGLLQPTKGTITMGGkpcttagsDRGMVFQDFALFPWRSVRSNIEFGL 134
                                       5556665526999*****************99977665544444668888888999999999999999999999988 PP

                            AAA_23  80 enkdgrytrsiererel 96 
                                       e  +       ++er +
  gi|474934499|ref|YP_007688081.1| 135 EVAGV-----PKEERRR 146
                                       87776.....3343333 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   1.2e-07   8.4e-05      19     132 ..      63     216 ..      43     240 .. 0.55

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.2e-07
                            AAA_16  19 vrsgrpelvllsGesGvGKsslvrellralekd..................ggif...lrgkcdqlesaipysa.la 73 
                                       +++g  el+ ++G+sG+GKs+++r+++  l+ +                  g++f   +   +++ +s+i++   +a
  gi|474934499|ref|YP_007688081.1|  63 IKKG--ELISIVGPSGCGKSTILRCIAGLLQPTkgtitmggkpcttagsdrGMVFqdfALFPWRSVRSNIEFGLeVA 137
                                       4444..89*******************87777776666666666666665434444444444444455566644344 PP

                            AAA_16  74 qalareellrqlldeaesaeleawrekleeala........................avpelagaeasrllellkrl 126
                                        +  +ee  r  ++ +e+  l++++++   +l+                        + ++l+     + ++ l++ 
  gi|474934499|ref|YP_007688081.1| 138 GVP-KEERRRRSDRYLEAMGLQDFADARIHELSggmkqrvgiaramimhpavilmdePFGALD----AQTRNILQES 209
                                       444.44555555555555555555554444444455555555555555444443333333333....3333333333 PP

                            AAA_16 127 l.allsr 132
                                       l + l++
  gi|474934499|ref|YP_007688081.1| 210 LvNVLKT 216
                                       3333344 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.1   2.9e-07   0.00021      15      50 ..      59      94 ..      54      98 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.9e-07
                            AAA_29 15 htieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                       +++i+  + + ++GpsG GKST+l  i+ lL p+k
  gi|474934499|ref|YP_007688081.1| 59 LDLDIKKGELISIVGPSGCGKSTILRCIAGLLQPTK 94
                                      567788555999********************9987 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   2.1e-06    0.0015      76     126 ..      41      93 ..      21     108 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.1e-06
                                       TSEEEE--TT.THTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT---- CS
                       RsgA_GTPase  76 gyevllvsak.tkegleelkellkd.ktsvlvGqSGvGKStLinallpelelk 126
                                       g++v++ +++ ++ ++++l   +k+ +++ +vG+SG GKSt++  +++ l+  
  gi|474934499|ref|YP_007688081.1|  41 GLTVIYRNKDkDTLAVDNLDLDIKKgELISIVGPSGCGKSTILRCIAGLLQPT 93 
                                       445555544414467889999999889*****************999876555 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   2.1e-06    0.0015      39      68 ..      60      89 ..      42      96 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.1e-06
                             Rad17 39 vLesrkkriLLisGPsGCgkstvvkvLske 68
                                       L+ +k +++ i GPsGCgkst+++ ++  
  gi|474934499|ref|YP_007688081.1| 60 DLDIKKGELISIVGPSGCGKSTILRCIAGL 89
                                      35556666999*************998765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   3.1e-06    0.0022       4      71 ..      65     161 ..      61     232 .. 0.64

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.1e-06
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee..........erpevvfvtlpsstsskdllrellralglelka 70 
                                       +  ++ ++G+sG+GK+t lr ++  l+  +   +           +++ v ++  ++  ++++++++   l++ +  
  gi|474934499|ref|YP_007688081.1|  65 KGELISIVGPSGCGKSTILRCIAGLLQPTKGTITmggkpcttagSDRGMV-FQDFALFPWRSVRSNIEFGLEVAGVP 140
                                       567899*****************999755444448886666664333333.33344445777777777777776666 PP

                            AAA_22  71 ....................e 71 
                                                           +
  gi|474934499|ref|YP_007688081.1| 141 keerrrrsdryleamglqdfA 161
                                       666444444444444444444 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.1e-05     0.015      16      50 ..      58      93 ..      55     132 .. 0.85
   2 ?    2.0   0.1       0.2   1.4e+02     324     365 ..     186     227 ..     162     229 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.1e-05
                            AAA_15 16 dveidlsee.ltvliGkNnsGKSsilealdlFlnnk 50
                                      + ++d+++  l  ++G+ ++GKS+il+ +  +l+ +
  gi|474934499|ref|YP_007688081.1| 58 NLDLDIKKGeLISIVGPSGCGKSTILRCIAGLLQPT 93
                                      5567777778******************99888865 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.2
                            AAA_15 324 nvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                       ++++l++EP   L  q  ++l ++l +++++++  +++ THS
  gi|474934499|ref|YP_007688081.1| 186 PAVILMDEPFGALDAQTRNILQESLVNVLKTSHRTIVFVTHS 227
                                       67899999999999******************999******9 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00047      0.33      25      45 ..      67      87 ..      49      96 .. 0.82
   2 ?    5.8   0.0     0.011       8.1     136     197 ..     167     227 ..     130     248 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00047
                                      SEEEEEESTTSSHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnlldAil 45
                                      ++ +ivGp G+GKs +l  i 
  gi|474934499|ref|YP_007688081.1| 67 ELISIVGPSGCGKSTILRCIA 87
                                      4679************99885 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.011
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT...SEEEEE-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn...aQfivisl 197
                                       +LSgG k+ v +a      ++   ++ l+De   aLD++ ++++ e l +  k+   + ++v+  
  gi|474934499|ref|YP_007688081.1| 167 ELSGGMKQRVGIARA----MIMHPAVILMDEPFGALDAQTRNILQESLVNVLKTshrTIVFVTHS 227
                                       789998888777654....444556889************9998876654333310033333333 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   5.1e-05     0.036       2      48 ..      69     188 ..      68     286 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.1e-05
                                       EEEEESTTSSHHHHHHHHHT.....S.TEEESSSTTSSSSEEEEEEEETTEE......................... CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltg.....e.kaivsdkpgtTrdinegrvklkgke......................... 47 
                                       + ivG +  GKSt+++ + g     + +  ++ kp tT    +g v  +  +                         
  gi|474934499|ref|YP_007688081.1|  69 ISIVGPSGCGKSTILRCIAGllqptKgTITMGGKPCTTAGSDRGMVF-Q--Dfalfpwrsvrsniefglevagvpke 142
                                       78****************98766643366779999999988888765.2..11223333333444444444444445 PP

                                       .............................................E CS
                          MMR_HSR1  48 .............................................i 48 
                                                                                    +
  gi|474934499|ref|YP_007688081.1| 143 errrrsdryleamglqdfadarihelsggmkqrvgiaramimhpaV 188
                                       5555555555555555555555555555555555555555555551 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.1   7.7e+02     103     126 ..      27      55 ..       9      64 .. 0.70
   2 !   13.1   0.3   8.3e-05      0.06       1      24 [.      68      91 ..      68     106 .. 0.86
   3 ?   -1.2   0.0         2   1.5e+03      67      88 ..     263     284 ..     260     286 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.1
                               PRK 103 keeliegadvlviEGlhalyder.....v 126
                                        ++++eg  ++ iEGl  +y ++      
  gi|474934499|ref|YP_007688081.1|  27 YKDIPEGETLMKIEGLTVIYRNKdkdtlA 55 
                                       467899999999***99999877444542 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 8.3e-05
                               PRK  1 vIgvagsSGaGkttvarklekifg 24
                                      +I++ g+SG+Gk+t+ r +  +++
  gi|474934499|ref|YP_007688081.1| 68 LISIVGPSGCGKSTILRCIAGLLQ 91
                                      69***************9988876 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 2
                               PRK  67 eandfdllyevlkelkegkkvd 88 
                                        a +f +l + ++ + eg++v+
  gi|474934499|ref|YP_007688081.1| 263 AAREFTELRRDILDYLEGQNVM 284
                                       6899**************9987 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.4   8.8e-05     0.063       3      66 ..      71     193 ..      69     245 .. 0.52

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.8e-05
                                       EESSTTSSHHHHHHHHHHHHTHE...................................................... CS
                               AAA   3 lyGppGtGKTllakavakelgve...................................................... 25 
                                       ++Gp G+GK+++ + +a  l+ +                                                      
  gi|474934499|ref|YP_007688081.1|  71 IVGPSGCGKSTILRCIAGLLQPTkgtitmggkpcttagsdrgmvfqdfalfpwrsvrsniefglevagvpkeerrrr 147
                                       79***************998533232333333333334444444444444444444444443333333333333333 PP

                                       ...EEEEETTTCSSS...........STTHHHHHHHHHHHHHHHTS.TSEEEEEET CS
                               AAA  26 ...fleisgsellsk...........yvgesekkirelfkeakeka.kpsilfiDE 66 
                                          +                       + e +  +++ +  a+++  +p ++++DE
  gi|474934499|ref|YP_007688081.1| 148 sdrY----------LeamglqdfadaRIHELSGGMKQRVGIARAMImHPAVILMDE 193
                                       3332..........033333333333555555555555555555555567777777 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.6    0.0023       1.7       2      26 ..      69      93 ..      68     109 .. 0.81
   2 ?    7.5   0.0    0.0048       3.4      90     139 ..     180     233 ..     167     265 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0023
                                      EEEE--TTSSHHHHHHHHHHHH... CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkss 26
                                      + i Gp+G GK+T+++ ++ ll+  
  gi|474934499|ref|YP_007688081.1| 69 ISIVGPSGCGKSTILRCIAGLLQPT 93
                                      6789***************999643 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0048
                                       HHHHHHH-EEEE--.-STTGGG-HHH.HHHHHHHHT.TTSEEEEE--SS-.-SH CS
                          NTPase_1  90 rkalseadviviDE.iGkmElkskkf.keaveevLk.sekpvlavihrrk.dla 139
                                       r ++ ++ vi++DE  G +  +++++ +e++ +vLk s++ +++v h  +  l 
  gi|474934499|ref|YP_007688081.1| 180 RAMIMHPAVILMDEpFGALDAQTRNIlQESLVNVLKtSHRTIVFVTHSVDeALY 233
                                       44557899******88*****998852788******99*******998854333 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00014       0.1       4      31 ..      71      99 ..      69     107 .. 0.78
   2 ?   -1.2   0.0       2.6   1.9e+03      82     102 ..     207     227 ..     166     252 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                                      EE--SSSSHHHHHHHGGGGB.S--EEEEE CS
                             AAA_5  4 LvGppGtgKselaerlaaal.nreveyvq 31
                                      +vGp+G+gKs++ + +a +l  ++ ++ +
  gi|474934499|ref|YP_007688081.1| 71 IVGPSGCGKSTILRCIAGLLqPTKGTITM 99
                                      79******************755555544 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.6
                                       HHHHHHHHHSSEEE..-SSSE CS
                             AAA_5  82 lnsLlslleerrllleeggel 102
                                       ++sL ++l + ++ +   ++ 
  gi|474934499|ref|YP_007688081.1| 207 QESLVNVLKTSHRTIVFVTHS 227
                                       333444444444333333333 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00023      0.16      21      40 ..      67      86 ..      49      96 .. 0.82
   2 ?   -1.4   0.0       1.4     1e+03      88     108 ..     203     223 ..     187     244 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00023
                                      EEEEEEESTTSSHHHHHHHH CS
                            NB-ARC 21 lvvalvGmgGvGKttlakqi 40
                                       ++++vG  G+GK+t+++ i
  gi|474934499|ref|YP_007688081.1| 67 ELISIVGPSGCGKSTILRCI 86
                                      489*************9877 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.4
                                       STTSHHHHHHHHCCCT.TEEEE CS
                            NB-ARC  88 eveslkrklvrlLltk.rfllv 108
                                        +  l++ lv++L+t  r+++ 
  gi|474934499|ref|YP_007688081.1| 203 RNI-LQESLVNVLKTShRTIVF 223
                                       333.899999999988788775 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0    0.0012      0.87      21      43 ..      67      89 ..      59      97 .. 0.82
   2 ?    1.4   0.0      0.36   2.6e+02     121     166 ..     188     227 ..     161     245 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0012
                          ATPase_2 21 eiyfiYGpegsGKtaLlkeiien 43
                                      e + i Gp g+GK+++l+ i+  
  gi|474934499|ref|YP_007688081.1| 67 ELISIVGPSGCGKSTILRCIAGL 89
                                      678899***********988765 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.36
                          ATPase_2 121 iiiiDelqklidlglngaellvkeLlnliesltkekhlcvviclsS 166
                                       +i++De + + d + +      + L++ +++ +k  h ++v+++ S
  gi|474934499|ref|YP_007688081.1| 188 VILMDEPFGALDAQTR------NILQESLVNVLKTSHRTIVFVTHS 227
                                       7888999999866655......455555556666688888888766 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00028       0.2      30      51 ..      63      84 ..      51      92 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00028
                            AAA_25 30 lpagelallaGapgtGKttlal 51
                                      + +gel+ ++G++g+GK+t++ 
  gi|474934499|ref|YP_007688081.1| 63 IKKGELISIVGPSGCGKSTILR 84
                                      689****************985 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1    0.0042         3     241     265 ..      62      87 ..      60      90 .. 0.91
   2 ?    3.0   0.0     0.048        35     321     386 ..     166     231 ..     157     248 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0042
                                       EE-SS.EEEEEE-TTSSHHHHHHHHH CS
                        ABC_ATPase 241 gipkG.vtlIvGggfhGKsTLLeAle 265
                                        i+kG ++ IvG+   GKsT+L+ ++
  gi|474934499|ref|YP_007688081.1|  62 DIKKGeLISIVGPSGCGKSTILRCIA 87 
                                       699**9****************9985 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.048
                                       SS--HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG--B--HHHCHHHHHHH CS
                        ABC_ATPase 321 edASGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskekepitplvdrvrelykk 386
                                       ++ SG + q + i++a+ +   ++L+DE   A     r  + ++lv+  k   +++v   +++ + 
  gi|474934499|ref|YP_007688081.1| 166 HELSGGMKQRVGIARAMIMHPAVILMDEPFGALDAQTRNILQESLVNVLKTSHRTIVFVTHSVDEA 231
                                       56699999********************98888888888887888776666656655555555444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00034      0.24      19      49 ..      67      97 ..      60     108 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00034
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaaggrv 49
                                       +  ++Gp G GK+t+l+ ++ +++  +g++
  gi|474934499|ref|YP_007688081.1| 67 ELISIVGPSGCGKSTILRCIAGLLQPTKGTI 97
                                      47789***************99998876665 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1    0.0003      0.22      25      50 ..      69      94 ..      55     108 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0003
                      Mg_chelatase 25 lllvGppGsGKtmlakrlpsllppls 50
                                      + +vGp+G+GK+ + +++++ll p +
  gi|474934499|ref|YP_007688081.1| 69 ISIVGPSGCGKSTILRCIAGLLQPTK 94
                                      5689******************9876 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.3    0.0011      0.76       1      18 [.      68      85 ..      68     102 .. 0.84
   2 ?    0.1   0.0       1.1     8e+02      61     110 ..     177     232 ..     124     239 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0011
                            AAA_33  1 lvllvGlpGsGKstlaer 18
                                      l+ +vG++G+GKst ++ 
  gi|474934499|ref|YP_007688081.1| 68 LISIVGPSGCGKSTILRC 85
                                      6779**********9875 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.1
                            AAA_33  61 elarkalsagrnvildat..nlsrrer....arflklarrlgvpvrivvvetdeet 110
                                       ++ar +  + + ++ d +   l++++r    + ++++++  +  +  v+ ++de++
  gi|474934499|ref|YP_007688081.1| 177 GIARAMIMHPAVILMDEPfgALDAQTRnilqESLVNVLKTSHRTIVFVTHSVDEAL 232
                                       55555555555555576633355666666667888888877766666777777765 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00049      0.35       2      25 ..      68      91 ..      67      96 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00049
                                      CEEEEC-TTTCHHHHHHHHHHHHC CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalawa 25
                                      l+ + G++G+GK+t l+ +a +++
  gi|474934499|ref|YP_007688081.1| 68 LISIVGPSGCGKSTILRCIAGLLQ 91
                                      6789*************9997775 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00051      0.36      87     120 ..      67      97 ..      44     100 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00051
                        Adeno_IVa2  87 PviGviyGPtGsGksqllrnlissklisPiPetv 120
                                        +i  i GP G+Gks +lr +  + l++P+  t+
  gi|474934499|ref|YP_007688081.1|  67 ELIS-IVGPSGCGKSTILRCI--AGLLQPTKGTI 97 
                                       5555.67************87..45777777665 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   0.00075      0.54       2      21 ..      70      89 ..      69     109 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00075
                      RNA_helicase  2 wlyGpsgeGKStlakeLaka 21
                                       ++Gpsg+GKSt+ + +a  
  gi|474934499|ref|YP_007688081.1| 70 SIVGPSGCGKSTILRCIAGL 89
                                      689**********9985544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 1831.73
//
Query:       gi|474934500|ref|YP_007688082.1|  [L=268]
Description: ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-15   57.4  20.4    1.6e-15   57.3  14.7    2.1  2  BPD_transp_1     Binding-protein-dependent transport system i
  ------ inclusion threshold ------
       0.22   11.4   0.4        4.6    7.1   0.0    2.3  2  Myc_target_1     Myc target protein 1


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.7   0.3    0.0049        44      12      44 ..       7      60 ..       1      90 [. 0.63
   2 !   57.3  14.7   1.8e-19   1.6e-15       2     181 ..      92     258 ..      91     265 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.0049
                      BPD_transp_1 12 rnkkldkllrpliivllslPsfv.laillvlvf....................v 44
                                       n+++ +l+r++  +  sl  fv ++ ++++++                     
  gi|474934500|ref|YP_007688082.1|  7 ENNRVHRLIRTIAVLAVSLVAFVlIWWFVTYMAdmkafptpdkvfdalidlirD 60
                                      578888888888888888777774444444443677666666655555555541 PP

  == domain 2  score: 57.3 bits;  conditional E-value: 1.8e-19
                      BPD_transp_1   2 illGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrs 78 
                                       ++lG+l++  + ++ +++  p i++++ + ++++a++++       ++g l l+ +++++++++++++  +  +++ 
  gi|474934500|ref|YP_007688082.1|  92 VPLGLLLG--YVRPMREITAPWIEIIRPIAPIAWAPIFI------ISFG-LELGPALVVAVGIFFPMLTSIIFGVQR 159
                                       89******..999**************************......7888.6677777778888888888888999** PP

                      BPD_transp_1  79 lpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG.lgtllleailgydyseis 154
                                       ++++++ea+++lGas  qif+k+vlP+++p+i+ g+ + +g  +   v++e+++ + G +g  ll     +++++++
  gi|474934500|ref|YP_007688082.1| 160 IDSNWIEASKTLGASQPQIFVKIVLPATVPYILNGMKVGLGVGWMCIVAAELYAKQLGgIGHYLL-----MMTDNGL 231
                                       ******************************************************66434444433.....3333334 PP

                      BPD_transp_1 155 nggvlalviavlllnlvadilqrlldp 181
                                       ++ ++a++i+++ l l++  l++++++
  gi|474934500|ref|YP_007688082.1| 232 WANAFAAIIVIAFLGLITTGLAEYFSK 258
                                       446667777777777777777777765 PP

>> Myc_target_1  Myc target protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1     0.018   1.6e+02      29      51 ..      21      43 ..       2      46 .. 0.79
   2 ?    7.1   0.0   0.00051       4.6      15      37 ..      79     100 ..      65     104 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.018
                      Myc_target_1 29 mvvGLllgaliyvlltwlsrrra 51
                                      ++v L+   li+ ++t++   +a
  gi|474934500|ref|YP_007688082.1| 21 LAVSLVAFVLIWWFVTYMADMKA 43
                                      6899**************98876 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.00051
                      Myc_target_1  15 sfdledlilaFcvSmvvGLllga 37 
                                       +f l+   +aF+vS+ +GLllg 
  gi|474934500|ref|YP_007688082.1|  79 TF-LKGFAIAFAVSVPLGLLLGY 100
                                       44.78889*************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       946  (0.0527637); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 1595.92
//
Query:       gi|474934501|ref|YP_007688083.1|  [L=417]
Description: hypothetical protein TALC_00928 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-05   24.7   0.0      0.049   13.3   0.0    2.3  2  NMT1_2    NMT1-like family
  ------ inclusion threshold ------
       0.03   13.8   0.3      0.093   12.1   0.1    1.9  2  DUF1593   Protein of unknown function (DUF1593)
      0.034   14.3   0.5       0.29   11.3   0.0    2.3  2  CwsA      Cell wall synthesis protein CwsA


Domain annotation for each model (and alignments):
>> NMT1_2  NMT1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0   0.00015      0.88     195     250 ..      43     100 ..      37     103 .. 0.84
   2 !   13.3   0.0   8.2e-06     0.049       6     107 ..     203     308 ..     198     334 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00015
                            NMT1_2 195 altsqelwkdhPekvlgvredfveknpntaralvkalleAtkwlda..kkenraeaak 250
                                       ++ +++l+++h ++v++ +  ++++n ++++a+++   eA ++++a   ++  a+ ak
  gi|474934501|ref|YP_007688083.1|  43 LALTNDLFDGHTCCVIAGNVTYLDSNADAVKAFLDGYHEAVNRINAalADKSSADYAK 100
                                       5789*****************************************8544444555555 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 8.2e-06
                            NMT1_2   6 eqlklGfial.tdaaplvvakekglfakeGltvelekqaswaelrdkllagelDaahv.ltpapllidlGi..ggak 78 
                                        ++k++ i   ++   l  ak++g+ +++ ++++++ qa+++++ ++l +g+  +++   +pa +   + +  +++ 
  gi|474934501|ref|YP_007688083.1| 203 VTIKVAAIEGdIHQIALWFAKDAGILNNYNVDISVTGQAGGPGVYTALNTGDCNIGFLgAPPATIRCMNNMdiTSSV 279
                                       5566666665134445589***************************************9999998888887888999 PP

                            NMT1_2  79 admkvlaslnlnGqaitlsnklkdkkvsd 107
                                       ++++++ ++n++G +i+l+ + k++  ++
  gi|474934501|ref|YP_007688083.1| 280 EKINIIGRVNSEGSGILLKPGEKASDYIT 308
                                       ******************98755544433 PP

>> DUF1593  Protein of unknown function (DUF1593)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   1.6e-05     0.093       2      69 ..      24      91 ..      23     166 .. 0.84
   2 ?   -1.1   0.0      0.17     1e+03      82     126 ..     298     340 ..     295     358 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.6e-05
                                      EEEEE-TTS-THHHHHHHHHHHTGGGSEEEEEEE-..-BTTB------HHHHHHHHHHHHHHHHHTTTST CS
                           DUF1593  2 vvvltDienepDDaeSlvrlLlyanefdieglvat..ssvwhkkktkpekieeiidaYekvlpnLkkhak 69
                                      +vv+ D +++ DD eS v l l ++ fd +  ++   + ++ +  ++ + ++ ++d Y+++++++++  +
  gi|474934501|ref|YP_007688083.1| 24 LVVMKDRKSDDDDHESYVGLALTNDLFDGHTCCVIagNVTYLD--SNADAVKAFLDGYHEAVNRINAALA 91
                                      69*************************9776555511555554..45679***********999887654 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.17
                                       EE--SS-GGGG-STT--.-HHHHHHHHHHHSS-SS-EEEEESS-S CS
                           DUF1593  82 ksGneelgleavgegkddseGSeliievldkdddrplwvqvWGGa 126
                                       k G+++ +  +v+++    eG+++i++  + +      v  WGG+
  gi|474934501|ref|YP_007688083.1| 298 KPGEKASDYITVQTTAP-AEGAKYIQNPTTGK-YYVFNVANWGGK 340
                                       66777776677777666.99999999998866.367789999996 PP

>> CwsA  Cell wall synthesis protein CwsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   4.9e-05      0.29      87     114 ..       3      30 ..       1      39 [. 0.85
   2 ?    0.8   0.2     0.084     5e+02      56      93 ..     135     172 ..      83     201 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.9e-05
                              CwsA  87 rkrplllagvavavlaGGavafsivrrs 114
                                       +k+++++a+va  ++aG a+a+ +++ +
  gi|474934501|ref|YP_007688083.1|   3 KKQTYVIAAVALLIVAGAAAALVVMKDR 30 
                                       5889******************998765 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.084
                              CwsA  56 aqeaiaqelaaaqevvaglPqaledarkkrrrkrplll 93 
                                        ++++a  l++ +  +a+l ++l++a++ +++  +l +
  gi|474934501|ref|YP_007688083.1| 135 YADTAAGALSTLKTDIATLAETLKNANQIEKSATDLGF 172
                                       56888888999999999999999999887777666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       838  (0.0467399); expected 358.6 (0.02)
Passed bias filter:                      587  (0.0327403); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2863.75
//
Query:       gi|474934502|ref|YP_007688084.1|  [L=580]
Description: ABC-type multidrug transport system, ATPase and permease components [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-32  112.6   0.0    4.9e-32  111.3   0.0    1.7  2  ABC_tran        ABC transporter
    1.9e-23   83.5   5.1    2.5e-23   83.1   4.3    1.5  2  ABC_membrane    ABC transporter transmembrane region
      4e-08   33.0   0.4    1.7e-05   24.3   0.0    2.4  2  SMC_N           RecF/RecN/SMC N terminal domain
    0.00073   19.2   0.1     0.0019   17.9   0.1    1.6  1  AAA_29          P-loop containing region of AAA domain
     0.0062   16.9   0.4      0.016   15.6   0.4    1.7  1  AAA_16          AAA ATPase domain
     0.0075   16.4   0.2      0.014   15.5   0.2    1.3  1  DUF87           Helicase HerA, central domain
  ------ inclusion threshold ------
      0.039   14.4   0.2       0.09   13.3   0.2    1.5  1  AAA_23          AAA domain
      0.069   12.5   2.4       0.16   11.3   2.4    1.7  1  ABC_membrane_2  ABC transporter transmembrane region 2
       0.12   12.6   0.0       0.31   11.3   0.0    1.7  1  AAA_22          AAA domain
       0.14   12.0   0.0       0.34   10.8   0.0    1.7  1  APS_kinase      Adenylylsulphate kinase
       0.16   11.7   0.0       0.31   10.8   0.0    1.4  1  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
          5    7.6   9.0       0.87   10.0   0.3    2.7  3  MFS_MOT1        Molybdate transporter of MFS superfamily


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       5.1   7.7e+03      47      80 ..     215     261 ..     203     287 .. 0.67
   2 !  111.3   0.0   3.3e-35   4.9e-32       2     136 ..     354     503 ..     353     504 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 5.1
                                       CEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.............H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............x RF
                          ABC_tran  47 kdlkeqeleslrkeigvlpqepqlfpeltvren.............e 80 
                                       ++++e++ + l+++++ +   + +fp+++v +n              
  gi|474934502|ref|YP_007688084.1| 215 RKFDETNDRLLDNNVRAIARMSPIFPGMSVIQNlltlsiywigaslI 261
                                       44455777888888888888888899888877766666555544440 PP

  == domain 2  score: 111.3 bits;  conditional E-value: 3.3e-35
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       + vs+++ +ge+vai+Ge+G+GKSt+++l  + ++ t+Ge+l+dg+d++   +e+lr+++g++pq++ +f+++ vre
  gi|474934502|ref|YP_007688084.1| 354 EGVSFSVGKGETVAIIGETGSGKSTIVALAERFYDATSGEVLVDGRDVRLYGHEELRRKLGYVPQQAIIFSGS-VRE 429
                                       689**********************************************************************.*** PP

                                       H............HHHTC.........HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEES CS
                                       x............xxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n............esdee.........iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDE 134
                                       n            +   +         +e+++++l+     d  +++++++LSgGqkqrva+ara+++ p+++llD+
  gi|474934502|ref|YP_007688084.1| 430 NvnygdgseskndD---DvrralriaqAEQFVNSLDEG--LDAQISQHGRNLSGGQKQRVAIARAVCRSPEIYLLDD 501
                                       ******98775531...234555554466666666644..477777999***************************9 PP

                                       TT CS
                                       xx RF
                          ABC_tran 135 pt 136
                                       ++
  gi|474934502|ref|YP_007688084.1| 502 CF 503
                                       86 PP

>> ABC_membrane  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.1   4.3   1.7e-26   2.5e-23       3     253 ..      16     264 ..      14     291 .. 0.93
   2 ?   -0.7   0.1       0.6     9e+02     227     253 ..     271     296 ..     263     300 .. 0.70

  Alignments for each domain:
  == domain 1  score: 83.1 bits;  conditional E-value: 1.7e-26
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHSSTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane   3 liillailagvlsplfplvlgrildtlldkgdpetealnvysllllllglaqfilallqsyllnvtgerlskrlrrk 79 
                                       ++++l+i++  l++ +p +++ +++ l   g +++  ++   + +l+++l+++ +al+   l + ++  +  ++r++
  gi|474934502|ref|YP_007688084.1|  16 AVLVLIIIQVYLDLKIPGYMSDVTNALQREGGSDD--VTSAGVRMLVCALLSLSCALATGALASLVAVDVAYTMRKR 90 
                                       57899************************999999..**************************************** PP

                                       HHHHHHCSTHHHHHHSCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHHH CS
                      ABC_membrane  80 lfkkilrqpmsffdtnsvGellsrltndvsklrdglgeklglffqslltfvgglivmfylgwkltlvllailpliil 156
                                        f+++ r + +  d  ++ +l++r tndv+++  ++++ l +++   ++ v +++ +  ++ + t+++ + +  +++
  gi|474934502|ref|YP_007688084.1|  91 QFDNVQRFSKQDVDAFRAESLITRSTNDVNQILLAVSRGLPMVTKGPILAVWAILKISNTSMQWTIATAVAAGGLMV 167
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane 157 vsaviakilkklkkkeqkavakassvaeEslsgirtVkafgreeyflekfekaleeakkagikkaianglligitql 233
                                       ++a++  ++++l++k q  ++ +++  +E l gir+++a+++ee   +kf++ +++ + ++++++   + +++ + +
  gi|474934502|ref|YP_007688084.1| 168 LTALMIFWVSPLFRKVQWLTDGINRSSRENLDGIRVIRAYNGEEHQSRKFDETNDRLLDNNVRAIARMSPIFPGMSV 244
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHTT CS
                      ABC_membrane 234 lgllsyalalwfGttlvisg 253
                                       +++l+++ ++w+G++l+++ 
  gi|474934502|ref|YP_007688084.1| 245 IQNLLTLSIYWIGASLIMNA 264
                                       *****************985 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.6
                                       HHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                      ABC_membrane 227 ligitqllgllsyalalwfGttlvisg 253
                                       +  +t++++++syal+ +++++l++ g
  gi|474934502|ref|YP_007688084.1| 271 MDLFTDSIVFTSYALM-VMSAFLMMYG 296
                                       5567888888888888.7777777766 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.3    0.0033       4.9      25      41 ..     364     380 ..     350     387 .. 0.82
   2 !   24.3   0.0   1.2e-08   1.7e-05     135     212 ..     443     547 ..     380     552 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0033
                                       SEEEEEESTTSSHHHHH CS
                                       xxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnll 41 
                                       +  ai+G+ GSGKs ++
  gi|474934502|ref|YP_007688084.1| 364 ETVAIIGETGSGKSTIV 380
                                       4578**********997 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 1.2e-08
                                       T...............................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHH CS
                                       x...............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 135 e...............................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkva 180
                                       +                               +LSgG+k+ va+a       ++   +yllD+  +aLD +  +++ 
  gi|474934502|ref|YP_007688084.1| 443 DdvrralriaqaeqfvnsldegldaqisqhgrNLSGGQKQRVAIAR----AVCRSPEIYLLDDCFSALDYRTDRALR 515
                                       055555555555555555555555556666669*******999874....4577778******************** PP

                                       HHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 181 ellkeksknaQfivislreemlekadklvgvt 212
                                       + l++++ +  f++i+ r +++ +ad++v + 
  gi|474934502|ref|YP_007688084.1| 516 DTLRREEGDRSFLIIAQRIGTIMDADRIVVLD 547
                                       **************************998765 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   1.3e-06    0.0019      15      39 ..     356     380 ..     350     390 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.3e-06
                            AAA_29  15 htieidlkgatlltGpsGsGKSTll 39 
                                        ++++   +++ ++G++GsGKST++
  gi|474934502|ref|YP_007688084.1| 356 VSFSVGKGETVAIIGETGSGKSTIV 380
                                       56666644599*************8 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.4     1e-05     0.016      22      88 ..     361     438 ..     356     530 .. 0.42

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1e-05
                            AAA_16  22 grpelvllsGesGvGKsslvrellralekdggif.lrgkcdql......esaipy...sa.laqalareellrqlld 87 
                                       g +e v ++Ge G+GKs++v  + r + ++ g + + g+ ++l      ++++ y   +a + +   re +    ++
  gi|474934502|ref|YP_007688084.1| 361 GKGETVAIIGETGSGKSTIVALAERFYDATSGEVlVDGRDVRLygheelRRKLGYvpqQAiIFSGSVRENVNYGDGS 437
                                       45589***************777776666633332444444443311112333333322223333333333333333 PP

                            AAA_16  88 e 88 
                                       e
  gi|474934502|ref|YP_007688084.1| 438 E 438
                                       3 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   9.5e-06     0.014      26      49 ..     366     388 ..     363     396 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 9.5e-06
                             DUF87  26 lAilgsTGsGKSntvavLleelle 49 
                                       +Ai+g+TGsGKS+ va L e+ + 
  gi|474934502|ref|YP_007688084.1| 366 VAIIGETGSGKSTIVA-LAERFYD 388
                                       7************998.4565555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2     6e-05      0.09      21      36 ..     365     380 ..     349     383 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6e-05
                            AAA_23  21 ltlItGpNGaGKTTil 36 
                                        ++I+G++G+GK+Ti+
  gi|474934502|ref|YP_007688084.1| 365 TVAIIGETGSGKSTIV 380
                                       678************7 PP

>> ABC_membrane_2  ABC transporter transmembrane region 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   2.4   0.00011      0.16      10     185 ..       7     183 ..       1     234 [. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                    ABC_membrane_2  10 kskeallllvlllllvlrtllsvlvaqldgklvkalvaknvraFvlsllkfallavpasfvnsalkYltqkLalafR 86 
                                       + + + l +++l+l++++++l++ +    +++++al++++  + v+s ++ +l++ + s+        t  La  + 
  gi|474934502|ref|YP_007688084.1|   7 SRRDWCLTAAVLVLIIIQVYLDLKIPGYMSDVTNALQREGGSDDVTSAGVRMLVCALLSLS---CALATGALASLVA 80 
                                       55778999999*************************************9999998877765...4567999999999 PP

                    ABC_membrane_2  87 krLtkhllseYlknrtyYkvsnlde.ridnpDqritqDvekFtsslssLlsglvkpildvilftfiLwslsgtlgl. 161
                                       + +  ++ ++ ++n   ++ + +d  r +    r t+Dv++   ++s  l  ++k  +  ++ ++++ ++s + ++ 
  gi|474934502|ref|YP_007688084.1|  81 VDVAYTMRKRQFDNVQRFSKQDVDAfRAESLITRSTNDVNQILLAVSRGLPMVTKGPILAVWAILKISNTSMQWTIa 157
                                       99*************9999999999888999999999******9999999999999999999999999888888887 PP

                    ABC_membrane_2 162 ..lllllyvllatvilriigpplgkl 185
                                         +++   ++l+++++++++p + k+
  gi|474934502|ref|YP_007688084.1| 158 taVAAGGLMVLTALMIFWVSPLFRKV 183
                                       77888899999********9988775 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00021      0.31       8      30 ..     366     388 ..     361     412 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00021
                            AAA_22   8 lvvtGesGtGKTtllrrlleqld 30 
                                       ++++Ge+G+GK+t ++   + +d
  gi|474934502|ref|YP_007688084.1| 366 VAIIGETGSGKSTIVALAERFYD 388
                                       68***********9998887775 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00023      0.34       2      51 ..     363     415 ..     362     421 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00023
                                       -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHT....TTTTTT--S CS
                        APS_kinase   2 gvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvR....hgLnkdLgf 51 
                                       g +v + G +gsGKsti   l+++  +     +l+dG  vR    ++L ++Lg+
  gi|474934502|ref|YP_007688084.1| 363 GETVAIIGETGSGKSTIVA-LAERFYDATSGEVLVDGRDVRlyghEELRRKLGY 415
                                       779999***********75.556677777778899*****94443367777776 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00021      0.31       3      83 ..     367     456 ..     366     483 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00021
                            AAA_21   3 vliGpNgsGKSnLLdaldllarl.........drdvegltdelsggggirkipslldlydpeipfefeieeflsqgv 70 
                                       ++iG  gsGKS++  + + + ++         ++    ++ el+++ g+  +   +++++ ++ +++++    +++ 
  gi|474934502|ref|YP_007688084.1| 367 AIIGETGSGKSTIVALAERFYDAtsgevlvdgRDVRLYGHEELRRKLGYVPQQAIIFSGSVRENVNYGDGSESKNDD 443
                                       79******************999********999999*******************************998888888 PP

                            AAA_21  71 ryryglrlersqv 83 
                                       + r  lr+ +   
  gi|474934502|ref|YP_007688084.1| 444 DVRRALRIAQAEQ 456
                                       8877777766655 PP

>> MFS_MOT1  Molybdate transporter of MFS superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.2         5   7.4e+03      75      93 ..      59      77 ..      41      87 .. 0.52
   2 ?    2.5   0.4      0.12   1.8e+02      41      93 ..     122     181 ..     108     185 .. 0.64
   3 ?   10.0   0.3   0.00058      0.87      68     100 ..     274     306 ..     241     308 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 5
                          MFS_MOT1 75 lGlvllllgltgllerllr 93
                                      l ++ll l++ ++  +l++
  gi|474934502|ref|YP_007688084.1| 59 LVCALLSLSCALATGALAS 77
                                      3333333333333333333 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.12
                          MFS_MOT1  41 lltglfggvPmc....hgAgglaaqyrf..gartgaagillGlvllllgltg.llerllr 93 
                                       +l+++  g+Pm       A  ++ +  +   + t+a ++  G +++l +l+  +++ l r
  gi|474934502|ref|YP_007688084.1| 122 ILLAVSRGLPMVtkgpILAVWAILKISNtsMQWTIATAVAAGGLMVLTALMIfWVSPLFR 181
                                       566666777777777755555555544455555555555666666555555447777766 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00058
                          MFS_MOT1  68 tgaagillGlvllllgltgllerllrliPksvl 100
                                        + ++++++ +l+++++++++  +lr+iP++++
  gi|474934502|ref|YP_007688084.1| 274 FTDSIVFTSYALMVMSAFLMMYGVLRMIPRAMV 306
                                       56799**************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (580 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:00.47
# Mc/sec: 3699.59
//
Query:       gi|474934503|ref|YP_007688085.1|  [L=600]
Description: ABC-type multidrug transport system, ATPase and permease components [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-54  185.0   7.6    3.1e-54  184.5   7.6    1.2  1  ABC_membrane     ABC transporter transmembrane region
    3.7e-30  105.2   0.0    6.5e-30  104.4   0.0    1.4  1  ABC_tran         ABC transporter
    3.6e-05   23.3   0.1     0.0036   16.8   0.1    2.3  2  SMC_N            RecF/RecN/SMC N terminal domain
    0.00033   21.1   0.0    0.00079   19.8   0.0    1.6  1  AAA_16           AAA ATPase domain
    0.00059   20.3   0.0     0.0035   17.8   0.0    2.2  1  AAA              ATPase family associated with various cellul
    0.00069   19.4   0.0     0.0016   18.2   0.0    1.5  1  DEAD             DEAD/DEAH box helicase
    0.00096   19.4   0.2     0.0083   16.4   0.2    2.2  1  AAA_22           AAA domain
     0.0032   17.0   0.0     0.0062   16.1   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
     0.0048   16.0   0.1      0.026   13.6   0.1    2.1  1  T2SSE            Type II/IV secretion system protein
     0.0054   16.5   0.0      0.018   14.8   0.0    1.7  1  AAA_30           AAA domain
     0.0099   15.8   0.0       0.02   14.8   0.0    1.5  1  NTPase_1         NTPase
  ------ inclusion threshold ------
      0.013   15.6   0.0      0.087   12.9   0.1    2.1  2  DUF87            Helicase HerA, central domain
      0.015   15.1   0.1      0.045   13.5   0.0    1.8  2  AAA_24           AAA domain
      0.038   13.9   0.0      0.072   13.0   0.0    1.4  1  RsgA_GTPase      RsgA GTPase
       0.04   13.9   0.0        0.4   10.7   0.0    2.3  2  AAA_5            AAA domain (dynein-related subfamily)
      0.045   14.3   0.0      0.095   13.3   0.0    1.6  1  AAA_18           AAA domain
       0.07   13.4   0.0       0.16   12.2   0.0    1.6  1  AAA_28           AAA domain
       0.08   12.5   0.0       0.22   11.1   0.0    1.7  2  AAA_25           AAA domain
      0.099   12.6   0.0       0.21   11.6   0.0    1.6  1  ResIII           Type III restriction enzyme, res subunit
        0.1   12.4   0.2        5.7    6.7   0.1    2.2  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
       0.14   12.7   0.0       0.24   11.9   0.0    1.3  1  AAA_23           AAA domain
       0.15   12.1   0.0       0.35   11.0   0.0    1.6  1  MMR_HSR1         50S ribosome-binding GTPase
       0.18   11.6   0.0        0.6    9.9   0.0    1.9  1  AAA_29           P-loop containing region of AAA domain
       0.23   11.2   0.1        3.5    7.3   0.0    2.1  2  AAA_11           AAA domain


Domain annotation for each model (and alignments):
>> ABC_membrane  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.5   7.6   4.1e-57   3.1e-54       1     274 []      40     317 ..      40     317 .. 0.97

  Alignments for each domain:
  == domain 1  score: 184.5 bits;  conditional E-value: 4.1e-57
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSTCCHH....HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane   1 liliillailagvlsplfplvlgrildtlldkgdpet....ealnvysllllllglaqfilallqsyllnvtgerls 73 
                                       ++l+++l+il+ vl+++ p vl ri+d+l+++ +  +      ++ ++++ll+l+ ++f+++++  yll  ++e++ 
  gi|474934503|ref|YP_007688085.1|  40 MVLAVVLSILSAVLALIGPQVLRRITDSLSESISEGYdvdmDLIAGLCMMLLVLYGLSFLFGTIEHYLLPAISEKIA 116
                                       57899**************************84444467777899******************************** PP

                                       HHHHHHHHHHHHCSTHHHHHHSCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHH CS
                      ABC_membrane  74 krlrrklfkkilrqpmsffdtnsvGellsrltndvsklrdglgeklglffqslltfvgglivmfylgwkltlvllai 150
                                        r+r++l +k+ r+p+++fd++s+G+++srltnd++++   ++e+l++++++++ + g+ i+mfy++wkl+ v ++ 
  gi|474934503|ref|YP_007688085.1| 117 YRVRKDLNRKMDRLPLGYFDRTSTGDIMSRLTNDADSIGMHFAESLSMLITAITFLAGSSIMMFYTSWKLAAVSMIP 193
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane 151 lpliilvsaviakilkklkkkeqkavakassvaeEslsgirtVkafgreeyflekfekaleeakkagikkaiangll 227
                                       +++ i++++v+  ++++++++++  ++k++ ++eE+ +++  V+a+++ +  +e f+  + + +k+++ + +++g +
  gi|474934503|ref|YP_007688085.1| 194 AVIAIIFMFVLVTRSQRFFRQQMRDLGKMNGHVEETYYAMDIVRAYNGRKGSEETFDGINGSLRKSSFIARVLSGMV 270
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane 228 igitqllgllsyalalwfGttlvisgelsvgdlvvflslfailfgal 274
                                         ++++l +lsy++++++G++++ +ge+++g +v+f+++   ++ ++
  gi|474934503|ref|YP_007688085.1| 271 PRMMEFLDNLSYVIVCVVGSYMIVEGEITYGVIVAFIVYVRHFTRPV 317
                                       ****************************************9998875 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.4   0.0   8.7e-33   6.5e-30       4     137 .]     381     525 ..     378     525 .. 0.90

  Alignments for each domain:
  == domain 1  score: 104.4 bits;  conditional E-value: 8.7e-33
                                       EEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                          ABC_tran   4 vslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                        s ++++ge+vaivG++G+GK+t+++ll++ ++ ++Geil+dg ++++++++s+r+ ++++ q++ + +++ +ren 
  gi|474934503|ref|YP_007688085.1| 381 FSEHVEPGERVAIVGPTGTGKTTVVNLLMRFYDYDSGEILIDGVPVSSISRKSVRSAFAMVLQDSWILSGT-LRENi 456
                                       56789***********************************************************9999999.9**** PP

                                       ......HHHTCHHHHHHHSTTGGTTCBGESTTS.....GGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       ......xxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 ......esdeeiekalsklglkelkdtvvkssp.....ssLSgGqkqrvalarallkkpkllllDEpta 137
                                             +sde+i ka++ +gl ++  t  +  +     s LS Gq+q +++ara+++++++l+lDE+t+
  gi|474934503|ref|YP_007688085.1| 457 aytredASDEDILKAIQDVGLAQFLSTLPEGLDtvivpSALSAGQRQQLSIARAMVRDAPMLILDEATS 525
                                       **999888888999999999999666555433355566*****************************96 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.034        26      27      42 ..     391     406 ..     369     416 .. 0.81
   2 !   16.8   0.1   4.8e-06    0.0036     131     211 ..     491     567 ..     427     573 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.034
                                       EEEEESTTSSHHHHHH CS
                                       xxxxxxxxxxxxxxxx RF
                             SMC_N  27 taivGpNGSGKsnlld 42 
                                        aivGp G GK+ +++
  gi|474934503|ref|YP_007688085.1| 391 VAIVGPTGTGKTTVVN 406
                                       69**********9986 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 4.8e-06
                                       T-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 131 giskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadk 207
                                        i +++LS G+++ ++    +A  +v+ ap+ +lDe  +  D +  + + + +++       +vi++r +++ ++dk
  gi|474934503|ref|YP_007688085.1| 491 VIVPSALSAGQRQQLS----IARAMVRDAPMLILDEATSSVDTRTERHIQDAMDTLMRGRTSFVIAHRLTTILNSDK 563
                                       4555699999998655....56779**********************************************999999 PP

                                       EEEE CS
                                       xxxx RF
                             SMC_N 208 lvgv 211
                                       ++ +
  gi|474934503|ref|YP_007688085.1| 564 ILVM 567
                                       8755 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   1.1e-06   0.00079      25     107 ..     389     501 ..     377     552 .. 0.55

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.1e-06
                            AAA_16  25 elvllsGesGvGKsslvrellralekd............................ggiflrgkcdqlesaipysala 73 
                                       e v ++G+ G+GK+++v+ l+r +  d                            + + l+g+ +++   i+y    
  gi|474934503|ref|YP_007688085.1| 389 ERVAIVGPTGTGKTTVVNLLMRFYDYDsgeilidgvpvssisrksvrsafamvlqDSWILSGTLREN---IAY--TR 460
                                       7899******************999998777777666666666666666666655555566666666...444..33 PP

                            AAA_16  74 qalareellrqlldeaesaeleawrekleeala.......a 107
                                       + ++ e++l+++ d   ++ l+  +e l++++        +
  gi|474934503|ref|YP_007688085.1| 461 EDASDEDILKAIQDVGLAQFLSTLPEGLDTVIVpsalsagQ 501
                                       33333344444444433333333333333333333333330 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   4.7e-06    0.0035       2      99 ..     392     549 ..     391     568 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.7e-06
                                       EEESSTTSSHHHHHHHHHHHH..........THEEEEEETTTCSSS............................... CS
                               AAA   2 llyGppGtGKTllakavakel..........gvefleisgsellsk............................... 37 
                                        ++Gp GtGKT++++ +++            gv++ +is ++++s                                
  gi|474934503|ref|YP_007688085.1| 392 AIVGPTGTGKTTVVNLLMRFYdydsgeilidGVPVSSISRKSVRSAfamvlqdswilsgtlreniaytredasdedi 468
                                       589*****************755555555666999999999999889999999999999999999999999999999 PP

                                       ...........................STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHH CS
                               AAA  38 ...........................yvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvn 87 
                                                                   +++++++   + +++ +      l++DE+ + + +r       e+ +++
  gi|474934503|ref|YP_007688085.1| 469 lkaiqdvglaqflstlpegldtvivpsALSAGQRQQLSIARAMVRD--APMLILDEATSSVDTR------TERHIQD 537
                                       9999999999999999999999996644444444444444433333..499999***9999999......7788888 PP

                                       HHHHHHHHTTTS CS
                               AAA  88 qLlteldgvkkk 99 
                                       ++ t + g ++ 
  gi|474934503|ref|YP_007688085.1| 538 AMDTLMRGRTSF 549
                                       888888877774 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   2.2e-06    0.0016      12     149 ..     386     542 ..     376     552 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.2e-06
                                       HTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST.......SEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxx RF
                              DEAD  12 lgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyid.......lrvlli 81 
                                         g+ v + ++TG+GKT++  + +  ++y+   ++g   +  +P  ++ ++ ++ +  +  + d       lr++  
  gi|474934503|ref|YP_007688085.1| 386 EPGERVAIVGPTGTGKTTVVNLLM--RFYD--YDSGEILIDGVPVSSISRKSVRSAFAMVLQ-DswilsgtLRENIA 457
                                       46899*************966555..5987..677777777899999998888877655553.12344567999977 PP

                                       ET..TSSHHHHHHHHH.TT.CSEEEEEHHHHHHHH........HCTSSH.....CTTEEEEEEETHHHHHHTTTHHH CS
                                       xx..xxxxxxxxxxxx.xx.xxxxxxxxxxxxxxx........xxxxxx.....xxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  82 ig..gvaardqlskld.ng.vdivvgtpgrlddll........stgkln.....lsqvrflVlDEadrlldqgfsdf 141
                                       ++  + + +d l++++  g ++++ + p+ ld ++        ++++l+     +++  +l+lDEa    d   +++
  gi|474934503|ref|YP_007688085.1| 458 YTreDASDEDILKAIQdVGlAQFLSTLPEGLDTVIvpsalsagQRQQLSiaramVRDAPMLILDEATSSVDTRTERH 534
                                       774455568888999534489************777****99866776666666888899************99999 PP

                                       HHHHHHHS CS
                                       xxxxxxxx RF
                              DEAD 142 inrilnql 149
                                       i+  + +l
  gi|474934503|ref|YP_007688085.1| 535 IQDAMDTL 542
                                       99888776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.2   1.1e-05    0.0083       9      32 ..     392     415 ..     387     559 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.1e-05
                            AAA_22   9 vvtGesGtGKTtllrrlleqldee 32 
                                       +++G++GtGKTt+++ l++ +d +
  gi|474934503|ref|YP_007688085.1| 392 AIVGPTGTGKTTVVNLLMRFYDYD 415
                                       79*****************99743 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   8.3e-06    0.0062      26      58 ..     381     413 ..     359     430 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.3e-06
                             AAA_7  26 lelllknkkpvllvGptGtGKtviikdllkkld 58 
                                       ++ +++ +  v +vGptGtGKt++++ l++ +d
  gi|474934503|ref|YP_007688085.1| 381 FSEHVEPGERVAIVGPTGTGKTTVVNLLMRFYD 413
                                       5678899999****************9998766 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.1   3.5e-05     0.026     102     160 ..     361     419 ..     326     426 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.5e-05
                             T2SSE 102 eltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderi 160
                                       e++++d++++    +++ +  ++ v+    + + G+Tg+GKtt+++ l+ + + ++ +i
  gi|474934503|ref|YP_007688085.1| 361 EVDFRDVRFSYVEGKEVIRGFSEHVEPGERVAIVGPTGTGKTTVVNLLMRFYDYDSGEI 419
                                       5566666666666666666667777777788899************9998877665555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   2.4e-05     0.018      21     105 ..     391     532 ..     381     544 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.4e-05
                            AAA_30  21 avltGpAGtGKttalkalreaweaa.g.........grviglAptgkaAkvLaeelgieastiakllkrlk...... 81 
                                       ++++Gp GtGKtt+++ l + ++ + g          ++   +  ++ A vL+++  i + t+ + +  ++      
  gi|474934503|ref|YP_007688085.1| 391 VAIVGPTGTGKTTVVNLLMRFYDYDsGeilidgvpvSSISRKSVRSAFAMVLQDS-WILSGTLRENIAYTRedasde 466
                                       6899**************9999988566666665554444444455555555532.223333333332222344444 PP

                            AAA_30  82 .........................................grarlepgtllivDEa.gmvdtkql 105
                                                                                +ra ++++ +li DEa + vdt++ 
  gi|474934503|ref|YP_007688085.1| 467 dilkaiqdvglaqflstlpegldtvivpsalsagqrqqlsiARAMVRDAPMLILDEAtSSVDTRTE 532
                                       445555555566666666677777777777777777777776666777777777777344566655 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   2.7e-05      0.02       1      50 [.     390     441 ..     390     451 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.7e-05
                                       EEEEE--TTSSHHHHHHHHHHHH.....GGGEEEEEEEEE-------EEEEE CS
                          NTPase_1   1 kvfiTGppGvGKtTlvkkvlellk..ssgvkvgGfyteevreggrrigFkiv 50 
                                       +v+i Gp G+GKtT+v+ +++  +  s ++ ++G+ ++ + ++  r++F +v
  gi|474934503|ref|YP_007688085.1| 390 RVAIVGPTGTGKTTVVNLLMRFYDydSGEILIDGVPVSSISRKSVRSAFAMV 441
                                       5899***************998752155899******************998 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   0.00012     0.087      25      45 ..     390     410 ..     388     423 .. 0.83
   2 ?   -0.2   0.0       1.2   8.9e+02     135     182 ..     457     549 ..     414     569 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                             DUF87  25 HlAilgsTGsGKSntvavLle 45 
                                       ++Ai+g TG+GK++ v +L++
  gi|474934503|ref|YP_007688085.1| 390 RVAIVGPTGTGKTTVVNLLMR 410
                                       79**************99986 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.2
                             DUF87 135 eklssdepveklleelk.............................................kekeelrklknqaia 166
                                         +  d+++e +l+ ++                                             + +e  ++ ++++++
  gi|474934503|ref|YP_007688085.1| 457 AYTREDASDEDILKAIQdvglaqflstlpegldtvivpsalsagqrqqlsiaramvrdapmlILDEATSSVDTRTER 533
                                       44444444444444444555666666666666677777776777777777777777777777777888888999999 PP

                             DUF87 167 rlldkledllrkggsf 182
                                        ++d+ + l+r + sf
  gi|474934503|ref|YP_007688085.1| 534 HIQDAMDTLMRGRTSF 549
                                       9999999999988888 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     6e-05     0.045       4      54 ..     390     443 ..     388     501 .. 0.71
   2 ?   -1.9   0.0         3   2.3e+03     127     171 ..     518     562 ..     508     585 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6e-05
                            AAA_24   4 kiliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie......swedfld 54 
                                       +++i+Gp g+GKTt+++ l     f d + G   +d+  + +i+      +++++l+
  gi|474934503|ref|YP_007688085.1| 390 RVAIVGPTGTGKTTVVNLL---MRFYDYDSGEILIDGVPVSSISrksvrsAFAMVLQ 443
                                       89*****************...88999999999999999998877766663333333 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3
                            AAA_24 127 fiahektrkdedpegeakytrlepklgkktanelkeevDlvlran 171
                                       +i  e t  +++++++   + + + ++ +t+  + + ++++l  +
  gi|474934503|ref|YP_007688085.1| 518 LILDEATSSVDTRTERHIQDAMDTLMRGRTSFVIAHRLTTILNSD 562
                                       666677777788877777788888888888888888888887744 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   9.6e-05     0.072      85     125 ..     373     414 ..     341     423 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.6e-05
                                       TTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT--- CS
                       RsgA_GTPase  85 ktkegleelkellkd.ktsvlvGqSGvGKStLinallpelel 125
                                       + ke ++  +e+++  + +++vG++G GK+t++n l+   + 
  gi|474934503|ref|YP_007688085.1| 373 EGKEVIRGFSEHVEPgERVAIVGPTGTGKTTVVNLLMRFYDY 414
                                       4456677777888777999****************9875555 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00053       0.4       2      24 ..     391     413 ..     390     422 .. 0.82
   2 ?    0.3   0.0      0.85   6.4e+02      81     110 ..     551     581 ..     505     591 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00053
                                       EEEE--SSSSHHHHHHHGGGGBS CS
                             AAA_5   2 vlLvGppGtgKselaerlaaaln 24 
                                       v +vGp+GtgK++++  l +++ 
  gi|474934503|ref|YP_007688085.1| 391 VAIVGPTGTGKTTVVNLLMRFYD 413
                                       568**************998874 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.85
                                       HHHHHHHHHHSSEEE..-SSSEEE---.... CS
                             AAA_5  81 vlnsLlslleerrllleeggelvkakndd.l 110
                                       ++ +L ++l+ +++l++  g+++ +   d l
  gi|474934503|ref|YP_007688085.1| 551 IAHRLTTILNSDKILVMRDGTVIEHGTHDeL 581
                                       6778999999999999999999888776655 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   0.00013     0.095       1      26 [.     391     418 ..     391     472 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00013
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf..gv 26 
                                       +++ G+ G+GKtt+ + L +   +  g+
  gi|474934503|ref|YP_007688085.1| 391 VAIVGPTGTGKTTVVNLLMRFYDYdsGE 418
                                       689***************7743334433 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00021      0.16       1      20 [.     390     409 ..     390     422 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00021
                            AAA_28   1 kivitGgestGKTtlleaLa 20 
                                       +++i+G+ +tGKTt+++ L 
  gi|474934503|ref|YP_007688085.1| 390 RVAIVGPTGTGKTTVVNLLM 409
                                       79**************9986 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0    0.0003      0.22      28      52 ..     383     407 ..     354     423 .. 0.81
   2 ?   -2.8   0.0       5.3   3.9e+03     138     157 ..     510     529 ..     482     558 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0003
                            AAA_25  28 gllpagelallaGapgtGKttlald 52 
                                       +++  ge ++++G++gtGKtt++  
  gi|474934503|ref|YP_007688085.1| 383 EHVEPGERVAIVGPTGTGKTTVVNL 407
                                       48899****************9755 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5.3
                            AAA_25 138 eevegvrlvviDplsralgg 157
                                         v ++ ++++D  ++ ++ 
  gi|474934503|ref|YP_007688085.1| 510 AMVRDAPMLILDEATSSVDT 529
                                       33446777777777665544 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00028      0.21      13      48 ..     379     412 ..     371     543 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00028
                                       HHHT......TTSEEEEEESTTSTHHHHHHHHHHHH CS
                            ResIII  13 enlleklkskrdkrglikmaTGtGKTlvaaklierl 48 
                                       + + e++  +  +r+ i+ +TGtGKT v   l++ +
  gi|474934503|ref|YP_007688085.1| 379 RGFSEHV--EPGERVAIVGPTGTGKTTVVNLLMRFY 412
                                       4444444..4667999************98888765 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1    0.0076       5.7       3      20 ..     392     409 ..     391     439 .. 0.72
   2 ?    3.4   0.0     0.074        55     217     280 ..     465     537 ..     441     552 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0076
                            AAA_21   3 vliGpNgsGKSnLLdald 20 
                                       +++Gp g+GK+++  +l 
  gi|474934503|ref|YP_007688085.1| 392 AIVGPTGTGKTTVVNLLM 409
                                       79***********98883 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.074
                            AAA_21 217 rer............gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrlle 280
                                       +e             ++ +l +g +  + ++ lS G+++ l ++ a+ r++   + l++DE  ++ + +  r++ +
  gi|474934503|ref|YP_007688085.1| 465 DEDilkaiqdvglaqFLSTLPEGLDTVIVPSALSAGQRQQLSIARAMVRDA---PMLILDEATSSVDTRTERHIQD 537
                                       222444455555566899*******************************99...9******888887776666655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00032      0.24      23      38 ..     392     407 ..     379     410 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00032
                            AAA_23  23 lItGpNGaGKTTildA 38 
                                       +I+Gp+G+GKTT+++ 
  gi|474934503|ref|YP_007688085.1| 392 AIVGPTGTGKTTVVNL 407
                                       7***********9986 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00047      0.35       1      21 [.     390     410 ..     390     435 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00047
                                       EEEEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltg 21 
                                       +vaivG + +GK+t++n l++
  gi|474934503|ref|YP_007688085.1| 390 RVAIVGPTGTGKTTVVNLLMR 410
                                       69***************9986 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0    0.0008       0.6      19      39 ..     385     405 ..     378     410 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0008
                            AAA_29  19 idlkgatlltGpsGsGKSTll 39 
                                       +++ + + ++Gp+G+GK+T++
  gi|474934503|ref|YP_007688085.1| 385 VEPGERVAIVGPTGTGKTTVV 405
                                       45555799***********98 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0047       3.5      18      38 ..     389     409 ..     376     441 .. 0.77
   2 ?    1.3   0.0      0.32   2.4e+02     198     234 ..     492     531 ..     487     539 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0047
                            AAA_11  18 eitliqGPPGtgKTktivell 38 
                                       e + i GP GtgKT+++  l+
  gi|474934503|ref|YP_007688085.1| 389 ERVAIVGPTGTGKTTVVNLLM 409
                                       46789*********8775444 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.32
                            AAA_11 198 ivltTlsgagsklleklak...kfdvviIDEAaqavEpst 234
                                       iv + ls  ++++l+ +++   +  ++i DEA+ +v + t
  gi|474934503|ref|YP_007688085.1| 492 IVPSALSAGQRQQLSIARAmvrDAPMLILDEATSSVDTRT 531
                                       6677777777888877766667899********9998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (600 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1028  (0.0573373); expected 358.6 (0.02)
Passed bias filter:                      649  (0.0361983); expected 358.6 (0.02)
Passed Vit filter:                       125  (0.00697194); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.83u 0.33s 00:00:01.15 Elapsed: 00:00:00.65
# Mc/sec: 2779.63
//
Query:       gi|474934504|ref|YP_007688086.1|  [L=178]
Description: hypothetical protein TALC_00931 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-13   50.2  39.8      7e-06   26.3   3.0    3.1  3  DUF308          Short repeat of unknown function (DUF308)
    5.4e-05   23.2   8.8    5.4e-05   23.2   8.8    3.1  3  YtpI            YtpI-like protein
  ------ inclusion threshold ------
      0.029   14.6   4.8      0.029   14.6   4.8    3.3  3  TrbC            TrbC/VIRB2 family
      0.041   12.4   2.1      0.054   12.0   2.1    1.1  1  Pox_E6          Pox virus E6 protein
       0.22   11.8  24.1        3.7    7.9   0.0    4.3  4  PhaG_MnhG_YufB  Na+/H+ antiporter subunit
        0.8    7.9  21.9          1    7.5  21.9    1.1  1  DUF2070         Predicted membrane protein (DUF2070)
        4.6    7.8  33.4        5.8    7.4   1.4    4.6  3  DUF202          Domain of unknown function (DUF202)
        9.2    5.7  20.6          1    8.8   4.6    2.1  2  HupE_UreJ       HupE / UreJ protein


Domain annotation for each model (and alignments):
>> DUF308  Short repeat of unknown function (DUF308)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   9.8   1.1e-05     0.025       1      46 [.      18      63 ..      18      69 .. 0.94
   2 !   26.1  17.0   3.5e-09   7.9e-06       3      70 ..      72     139 ..      71     140 .. 0.95
   3 !   26.3   3.0   3.1e-09     7e-06       1      48 [.     128     175 ..     128     178 .] 0.93

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.1e-05
                            DUF308  1 llGillivlGilalllPvaallalvllfGilllvsGivqiiaafaa 46
                                      ++G++li++Gil+ ++   al ++ +  Gi++l+ G ++i+++++ 
  gi|474934504|ref|YP_007688086.1| 18 IIGLVLIIIGILLAIYQRDALKIILMGAGIVALIVGGAYIYEYLTV 63
                                      68***************************************99865 PP

  == domain 2  score: 26.1 bits;  conditional E-value: 3.5e-09
                            DUF308   3 GillivlGilalllPvaallalvllfGilllvsGivqiiaafaarkknrggrwlglllGilyliaGll 70 
                                       G +li+lGi+++++P++++ +l+ l++++l+v+G++ ++    + +k+    +  +++G l +i+G++
  gi|474934504|ref|YP_007688086.1|  72 GAILIALGIVFIVVPGFVSDVLMALLAVILIVFGALAFVRFAVSDEKTTVPAVINVVIGMLMMILGVY 139
                                       89*************************************88889999999999*************98 PP

  == domain 3  score: 26.3 bits;  conditional E-value: 3.1e-09
                            DUF308   1 llGillivlGilalllPvaallalvllfGilllvsGivqiiaafaark 48 
                                       ++G l+++lG++a+++   ++ ++++++G++++++G++++++a+++ k
  gi|474934504|ref|YP_007688086.1| 128 VIGMLMMILGVYAVFNLEDTADIVMIVIGVFIVIAGAIEVLKAYEQYK 175
                                       68*****************************************96655 PP

>> YtpI  YtpI-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   5.0    0.0059        13      35      73 ..      16      57 ..       2      61 .. 0.77
   2 ?    1.9   0.8      0.11   2.5e+02      50      73 ..      60      83 ..      56      89 .. 0.71
   3 !   23.2   8.8   2.4e-08   5.4e-05       2      81 ..      93     175 ..      92     178 .] 0.78

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0059
                              YtpI 35 sialGlflilfginqllllestvalvv...gavflvlGlanl 73
                                      si++Gl li++gi + +  +++++++    g+v l++G a +
  gi|474934504|ref|YP_007688086.1| 16 SIIIGLVLIIIGILLAIYQRDALKIILmgaGIVALIVGGAYI 57
                                      699999999999999999999999997555789999998765 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.11
                              YtpI 50 llllestvalvvgavflvlGlanl 73
                                      +l    tv+l  ga++++lG++ +
  gi|474934504|ref|YP_007688086.1| 60 YLTVPGTVSLPYGAILIALGIVFI 83
                                      566677788888888888887654 PP

  == domain 3  score: 23.2 bits;  conditional E-value: 2.4e-08
                              YtpI   2 ilivlslvlyvyykvkafrtkdplekkllsakasialGlflilfginqllllestval...vvgavflvlGlanlfa 75 
                                       ++ +l+++l v+  +  +r + + ek  + a  ++++G++++++g+ ++++le+t ++   v+g+ +++ G+++++ 
  gi|474934504|ref|YP_007688086.1|  93 LMALLAVILIVFGALAFVRFAVSDEKTTVPAVINVVIGMLMMILGVYAVFNLEDTADIvmiVIGVFIVIAGAIEVLK 169
                                       56789999999999*********************************999988887651104444444556666776 PP

                              YtpI  76 Girayk 81 
                                       ++ +yk
  gi|474934504|ref|YP_007688086.1| 170 AYEQYK 175
                                       666666 PP

>> TrbC  TrbC/VIRB2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   4.6     0.004       8.9      56      97 ..      17      59 ..       5      61 .. 0.80
   2 ?    0.2   6.6      0.39   8.8e+02      61      97 ..      74     111 ..      65     113 .. 0.74
   3 ?   14.6   4.8   1.3e-05     0.029      53      92 ..     124     163 ..     114     169 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.004
                              TrbC 56 viatiaiivaGimlafgrls.wrtlvmvviGiviifgAssivs 97
                                      +i+ +++i++Gi la  + + ++ ++m +  +++i+g++ i  
  gi|474934504|ref|YP_007688086.1| 17 IIIGLVLIIIGILLAIYQRDaLKIILMGAGIVALIVGGAYIYE 59
                                      7888999999999887777758888888888899999998865 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.39
                              TrbC  61 aiivaGimlafgrls.wrtlvmvviGiviifgAssivs 97 
                                       ++i++Gi+++       + l++++++i i+fgA ++v+
  gi|474934504|ref|YP_007688086.1|  74 ILIALGIVFIVVPGFvSDVLMALLAVILIVFGALAFVR 111
                                       67788888887776635556667777888999988886 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 1.3e-05
                              TrbC  53 lakviatiaiivaGimlafgrlswrtlvmvviGiviifgA 92 
                                       ++ v++ + ++++G+ ++f+ ++  ++vm+viG++i++++
  gi|474934504|ref|YP_007688086.1| 124 VINVVIGMLMMILGVYAVFNLEDTADIVMIVIGVFIVIAG 163
                                       6778888999**************************9876 PP

>> Pox_E6  Pox virus E6 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   2.1   2.4e-05     0.054     467     521 ..      79     133 ..      72     156 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.4e-05
                            Pox_E6 467 anlGlvledykedvilkilshlkcvedvttfvryatkknksilksvvrtilanfn 521
                                       + + +v+  +  dv++++l+ + +v    +fvr+a+  +k+++++v++ ++    
  gi|474934504|ref|YP_007688086.1|  79 GIVFIVVPGFVSDVLMALLAVILIVFGALAFVRFAVSDEKTTVPAVINVVIGMLM 133
                                       455578999***************************************9997654 PP

>> PhaG_MnhG_YufB  Na+/H+ antiporter subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   3.5     0.018        40      35      62 ..      19      46 ..      15      62 .. 0.76
   2 ?    1.8   6.8      0.13   2.9e+02      35      65 ..      71     104 ..      58     114 .. 0.64
   3 ?    6.1   0.1    0.0059        13       2      22 ..     127     147 ..     126     149 .. 0.92
   4 ?    7.9   0.0    0.0016       3.7       1      27 [.     152     178 .]     152     178 .] 0.85

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.018
                    PhaG_MnhG_YufB 35 lGlllillGlllrfslaaslkllliilf 62
                                      +Gl+li++G+ll + +  +lk++l+ + 
  gi|474934504|ref|YP_007688086.1| 19 IGLVLIIIGILLAIYQRDALKIILMGAG 46
                                      79**********6655557777776544 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.13
                    PhaG_MnhG_YufB  35 lGlllillGlllrf.slaa....slkllliilflll 65 
                                        G++li lG+++ +         +l++ll+++++++
  gi|474934504|ref|YP_007688086.1|  71 YGAILIALGIVFIVvP--GfvsdVLMALLAVILIVF 104
                                       5777777777775533..145886666665555543 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0059
                    PhaG_MnhG_YufB   2 lllGalfvllgaigllrlpdv 22 
                                       +++G+l+++lg+++++ l d+
  gi|474934504|ref|YP_007688086.1| 127 VVIGMLMMILGVYAVFNLEDT 147
                                       69***************9996 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.0016
                    PhaG_MnhG_YufB   1 llllGalfvllgaigllrlpdvytRlh 27 
                                       ++++G+++v++gai +l+    y  +h
  gi|474934504|ref|YP_007688086.1| 152 MIVIGVFIVIAGAIEVLKAYEQYKWIH 178
                                       699**************9877776555 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5  21.9   0.00046         1      13     172 ..      12     168 ..       4     174 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00046
                           DUF2070  13 swkvsllliillalligllaflssklfgillfglpalvaflltlpvlrilggrltykrslflalltelivviislla 89 
                                       +w +s+++ ++l+++  lla+  + + +i+l+g  +++ ++    + ++l    t++  +   l+++ iv+i  +++
  gi|474934504|ref|YP_007688086.1|  12 DWLRSIIIGLVLIIIGILLAIYQRDALKIILMGAGIVALIVGGAYIYEYLTVPGTVSLPYGAILIALGIVFI--VVP 86 
                                       577888888888888666666555588888888887777777777888874444444444444455555555..445 PP

                           DUF2070  90 illsallqalvllalvlslalvfalrllvlvavsdesllkavlpaliqpllailllvly....fspesfllllllsl 162
                                        ++s      vl+al+  + +vf+   +v +avsde+++  +++ +++ +l+++l v+      ++++++++++ ++
  gi|474934504|ref|YP_007688086.1|  87 GFVS-----DVLMALLAVILIVFGALAFVRFAVSDEKTTVPAVINVVIGMLMMILGVYAvfnlEDTADIVMIVIGVF 158
                                       5544.....5778999999****************988765555554444444444444666544555555555555 PP

                           DUF2070 163 ifalavylfi 172
                                       i++++++ ++
  gi|474934504|ref|YP_007688086.1| 159 IVIAGAIEVL 168
                                       5555555554 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   1.4    0.0026       5.8      40      58 ..      16      34 ..       3      39 .. 0.79
   2 ?    4.1   6.1     0.028        63      18      57 ..      48      85 ..      35      94 .. 0.77
   3 ?    3.6  10.1     0.042        94      18      64 ..     100     143 ..      96     173 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0026
                            DUF202 40 gkilglilivlgiltllvg 58
                                      + i+gl+li++gil++++ 
  gi|474934504|ref|YP_007688086.1| 16 SIIIGLVLIIIGILLAIYQ 34
                                      3688************996 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.028
                            DUF202 18 lalialglallrffltgepsalgkilglilivlgiltllv 57
                                      +ali+ g+ ++       p +++ + g+ili+lgi++++v
  gi|474934504|ref|YP_007688086.1| 48 VALIVGGAYIYEY--LTVPGTVSLPYGAILIALGIVFIVV 85
                                      4566666666665..6677777899************997 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.042
                            DUF202  18 lalialglallrffltgepsalgkilglilivlgiltllvglvrylr 64 
                                       +++++ +la++rf  + e+++   + ++i +v+g+l++++g++  + 
  gi|474934504|ref|YP_007688086.1| 100 ILIVFGALAFVRFAVSDEKTT---VPAVINVVIGMLMMILGVYAVFN 143
                                       788888889999855444444...66777777777777777776554 PP

>> HupE_UreJ  HupE / UreJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   4.6   0.00046         1      84     146 ..      18      80 ..      14      89 .. 0.83
   2 ?    0.4  11.3      0.17   3.9e+02      43     119 ..      87     163 ..      74     171 .. 0.54

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00046
                         HupE_UreJ  84 gialSvlvlGllvalaarlplaaalalvalfalfHGyAhgaelpaaasalayalGfvlatall 146
                                       +i l ++++G+l+a+ +r  l ++l+ ++++al+ G A+  e  +   +++   G +l  + +
  gi|474934504|ref|YP_007688086.1|  18 IIGLVLIIIGILLAIYQRDALKIILMGAGIVALIVGGAYIYEYLTVPGTVSLPYGAILIALGI 80 
                                       56778899*********************************9988887777666666655555 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.17
                         HupE_UreJ  43 GlwaaqlggrallllplafvaamlvGallglagvelpavEa.gialSvlvlGllvalaarlplaaalalvalfalfH 118
                                       G+++  l  + l ++ ++f a+++v ++++   +++pav + +i + +++lG+  +++ +  + ++++++++f ++ 
  gi|474934504|ref|YP_007688086.1|  87 GFVSDVLM-ALLAVILIVFGALAFVRFAVSDEKTTVPAVINvVIGMLMMILGVYAVFNLEDTADIVMIVIGVFIVIA 162
                                       33333331.22333344555555666666666666666543034445556677666766666666677777666655 PP

                         HupE_UreJ 119 G 119
                                       G
  gi|474934504|ref|YP_007688086.1| 163 G 163
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1385  (0.0772491); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); expected 17.9 (0.001)
Passed Fwd filter:                        64  (0.00356964); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.85u 0.35s 00:00:01.20 Elapsed: 00:00:00.50
# Mc/sec: 1079.04
//
Query:       gi|474934505|ref|YP_007688087.1|  [L=125]
Description: hypothetical protein TALC_00932 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-33  113.7   4.1    3.4e-18   65.2   0.1    2.1  2  DUF1508   Domain of unknown function (DUF1508)
  ------ inclusion threshold ------
      0.029   14.1   0.0      0.029   14.1   0.0    1.2  1  DUF4303   Domain of unknown function (DUF4303)


Domain annotation for each model (and alignments):
>> DUF1508  Domain of unknown function (DUF1508)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   0.7     2e-17   1.8e-13       2      40 ..      10      48 ..       9      55 .. 0.94
   2 !   65.2   0.1   3.8e-22   3.4e-18       1      44 [.      74     118 ..      74     121 .. 0.93

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 2e-17
                                      TTTEEEEEEE-TTS-EEEEEEEBSSHHHHHHHHHHHHHH CS
                           DUF1508  2 knGefrFrLkaaNgevIatsegYsskaaaenGIesVkkn 40
                                      k+G + F L+a+N+e+I+ts+ Y+sk +a+nG+ sV +n
  gi|474934505|ref|YP_007688087.1| 10 KDGGYFFSLYAGNNEIIGTSQVYKSKKSAMNGVGSVGRN 48
                                      9***********************************998 PP

  == domain 2  score: 65.2 bits;  conditional E-value: 3.8e-22
                                       ETTTEEEEEEE-TTS-EEEE.EEEBSSHHHHHHHHHHHHHHTTTC CS
                           DUF1508   1 DknGefrFrLkaaNgevIat.segYsskaaaenGIesVkknapda 44 
                                       D+ ++frFrLka Nge+I++ s+gY++ka a ++IesV+kna ++
  gi|474934505|ref|YP_007688087.1|  74 DSEDQFRFRLKAMNGEIILAaSQGYAAKATAIKCIESVRKNAKSE 118
                                       899***************************************654 PP

>> DUF4303  Domain of unknown function (DUF4303)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.3e-06     0.029      59     123 ..      56     122 ..       7     125 .] 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.3e-06
                           DUF4303  59 e.....lrwsvadWpyadfgdedfedvnkllaardnefeleekefeafrdklleamvkAlkeldkeglfg 123
                                              ++s+ +W+   +++   ++++ +l+a + e  l +++  a + + +++++++ k++++e + +
  gi|474934505|ref|YP_007688087.1|  56 LtvenvPKYSYPEWEIFKDSE---DQFRFRLKAMNGEIILAASQGYAAKATAIKCIESVRKNAKSEIVDK 122
                                       2345667*********99999...79999999999999**************************997765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 797.60
//
Query:       gi|474934506|ref|YP_007688088.1|  [L=99]
Description: hypothetical protein TALC_00933 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.52
# Mc/sec: 573.42
//
Query:       gi|474934507|ref|YP_007688089.1|  [L=330]
Description: hypothetical protein TALC_00934 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.068   13.1  21.0       0.66    9.9   0.6    3.3  3  DUF2721       Protein of unknown function (DUF2721)
       0.29   10.4  19.4        3.4    6.9  19.6    2.0  1  DUF4401       Domain of unknown function (DUF4401)
       0.36    9.8  15.0       0.33    9.9  13.9    1.4  1  7TM_GPCR_Srh  Serpentine type 7TM GPCR chemoreceptor Srh
       0.84   10.1   0.1       0.84   10.1   0.1    3.1  2  DUF202        Domain of unknown function (DUF202)
        1.9    8.8   4.5         16    5.8   0.4    2.8  2  DUF423        Protein of unknown function (DUF423)
        4.2    7.7  10.9       0.61   10.4   6.8    1.7  2  DUF420        Protein of unknown function (DUF420)


Domain annotation for each model (and alignments):
>> DUF2721  Protein of unknown function (DUF2721)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.6   0.00022      0.66      75     125 ..      10      60 ..       7      63 .. 0.84
   2 ?    6.9   6.2    0.0018       5.4      77     121 ..      65     109 ..      61     111 .. 0.83
   3 ?    5.8   0.9    0.0039        12      91     113 ..     149     171 ..     118     200 .. 0.50

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00022
                           DUF2721  75 llvvlvvlllflsallsldlsllaailfvlalllllvslllflrEirlslr 125
                                       +++v+++l+   + +l +d   +  i+ +++ ++++++++l l+E+  sl+
  gi|474934507|ref|YP_007688089.1|  10 IFLVFMMLVTGTAFWLFNDDRDVHNIISICGFAIMVAGSVLILYEMERSLK 60 
                                       56666777777766678899*************************998876 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0018
                           DUF2721  77 vvlvvlllflsallsldlsllaailfvlalllllvslllflrEir 121
                                       ++ +vl ++l +++s +l + ++i f+++++l++++ ++f++ i+
  gi|474934507|ref|YP_007688089.1|  65 MASMVLGIYLFVMFSPNLLSDISISFIISMALMMAGGAVFVFGIN 109
                                       44556667777799************************9998776 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0039
                           DUF2721  91 sldlsllaailfvlalllllvsl 113
                                        l+ s+ + ++f+lal +llv++
  gi|474934507|ref|YP_007688089.1| 149 WLEQSWEMWVIFLLALSFLLVAM 171
                                       44555555555555555555543 PP

>> DUF4401  Domain of unknown function (DUF4401)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9  19.6    0.0011       3.4      35     119 ..       9      98 ..       2     171 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0011
                           DUF4401  35 igalvvGllllaaAvallr.qkkeglfldqlalalslaGqalllfglaesldsssasllllallslalavlfpdall 110
                                       + +lv+ +l++++A++l +  ++ + ++  +++a+++aG +l+l+ + +sl+ s   +++ ++l + l+v+f  +ll
  gi|474934507|ref|YP_007688089.1|   9 AIFLVFMMLVTGTAFWLFNdDRDVHNIISICGFAIMVAGSVLILYEMERSLKDSL--AMASMVLGIYLFVMFSPNLL 83 
                                       67889999*********99677888999************************764..79999999999999999999 PP

                           DUF4401 111 rfLsvlaa......a 119
                                         +s+ ++       
  gi|474934507|ref|YP_007688089.1|  84 SDISISFIismalmM 98 
                                       999999983332220 PP

>> 7TM_GPCR_Srh  Serpentine type 7TM GPCR chemoreceptor Srh
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9  13.9   0.00011      0.33      10     140 ..      33     171 ..      30     195 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00011
                      7TM_GPCR_Srh  10 lhiitvisiPihifgfYcIlfkTPkk......Mksvk..wsLlnlhfwsallDltlslltipylllPalagyplGll 78 
                                       ++ii+++ + i + g  +Il++  ++      M s+   ++L+++   ++l+D+++s+++   l++   a++ +G+ 
  gi|474934507|ref|YP_007688089.1|  33 HNIISICGFAIMVAGSVLILYEMERSlkdslaMASMVlgIYLFVMFSPNLLSDISISFIISMALMMAGGAVFVFGIN 109
                                       5677888888888888888876665511111144554236899999999**************************** PP

                      7TM_GPCR_Srh  79 selgvpteiql..yllvtllalvgvsiillFenRysilvknkkkikwkklrvlylilnyilall 140
                                        + g + +i+   +  ++++a  gv i +++  R+  +     +++w+ + +++l+l ++l+ +
  gi|474934507|ref|YP_007688089.1| 110 LWCGSDYNIVRirVYSLAVMAGSGVQIYFMYVFRHGYVSWL--EQSWEMWVIFLLALSFLLVAM 171
                                       ***99988876225566778889999***********9966..469****99999999998865 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00028      0.84      19      62 ..      15      58 ..      12      62 .. 0.87
   2 ?   -4.1   9.4         6   1.8e+04      17      59 ..      62     108 ..      59     178 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00028
                            DUF202 19 alialglallrffltgepsalgkilglilivlgiltllvglvry 62
                                      +++++g a++ f  + ++ ++ +i+g++++v+g +++l+ + r+
  gi|474934507|ref|YP_007688089.1| 15 MMLVTGTAFWLFNDDRDVHNIISICGFAIMVAGSVLILYEMERS 58
                                      6889999999999999999999****************988776 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 6
                            DUF202  17 slalialglallrffl.....tgepsalgkilglilivlgiltllvgl 59 
                                       sla++++ l+++ f        ++ s +++i++++l+ +g +++++g+
  gi|474934507|ref|YP_007688089.1|  62 SLAMASMVLGIYLFVMfspnlLSDIS-ISFIISMALMMAGGAVFVFGI 108
                                       56666666666665443344322222.245555444444444444333 PP

>> DUF423  Protein of unknown function (DUF423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.3     0.023        68      33      65 ..      41      75 ..      34      83 .. 0.78
   2 ?    5.8   0.4    0.0054        16      50      73 ..      96     119 ..      80     133 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.023
                            DUF423 33 lallavalla..skaaasrllklagllflaGivlF 65
                                      +a+++++ ++   +  +s + +la++ +++Gi lF
  gi|474934507|ref|YP_007688089.1| 41 FAIMVAGSVLilYEMERSLKDSLAMASMVLGIYLF 75
                                      56666666555666678888899*********999 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0054
                            DUF423  50 llklagllflaGivlFSgslylla 73 
                                       l+ + g++f++Gi l +gs y ++
  gi|474934507|ref|YP_007688089.1|  96 LMMAGGAVFVFGINLWCGSDYNIV 119
                                       45555899***********99776 PP

>> DUF420  Protein of unknown function (DUF420)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   6.8   0.00021      0.61       8     131 ..      10     139 ..       3     140 .. 0.68
   2 ?   -2.6   0.1       2.1   6.3e+03      35      48 ..     156     169 ..     151     182 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00021
                            DUF420   8 lnalaavllllglvaikkgkieaHrklmll..afvlsalFlvlYllkhalagetkfggpeeegvirpvYlaiLitHi 82 
                                       +  + ++l++   ++  +++++ H+ + ++  a++++  +l+lY ++  l+++ + ++     ++  +Yl+++++  
  gi|474934507|ref|YP_007688089.1|  10 IFLVFMMLVTGTAFWLFNDDRDVHNIISICgfAIMVAGSVLILYEMERSLKDSLAMAS-----MVLGIYLFVMFSPN 81 
                                       444445555555677899*******98776115566678************9999773.....56666666666666 PP

                            DUF420  83 vLavvvvplvl.vtlvlalkg........kfekHrkiaritvpiwlyvavtGvvvYll 131
                                       +L+ + + +++ ++l++a              +   i+ri v  + + a +Gv +Y++
  gi|474934507|ref|YP_007688089.1|  82 LLSDISISFIIsMALMMAGGAvfvfginlWCGSDYNIVRIRVYSLAVMAGSGVQIYFM 139
                                       665444443331333333333444555449999999********************99 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.1
                            DUF420  35 mllafvlsalFlvl 48 
                                       m+++f+l++ Fl++
  gi|474934507|ref|YP_007688089.1| 156 MWVIFLLALSFLLV 169
                                       66777777777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1053  (0.0587317); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.73u 0.33s 00:00:01.06 Elapsed: 00:00:00.56
# Mc/sec: 1786.65
//
Query:       gi|474934508|ref|YP_007688090.1|  [L=329]
Description: hypothetical protein TALC_00935 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
          1    9.6   4.6       0.42   10.8   1.5    2.0  2  DUF423    Protein of unknown function (DUF423)
        7.9    5.4   8.9         31    3.4   8.9    1.8  1  PalH      PalH/RIM21


Domain annotation for each model (and alignments):
>> DUF423  Protein of unknown function (DUF423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1       1.5   1.4e+04      55      64 ..      22      31 ..      11      40 .. 0.56
   2 ?   10.8   1.5   4.7e-05      0.42      17      71 ..      90     146 ..      67     158 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.5
                            DUF423 55 gllflaGivl 64
                                      +ll++a +++
  gi|474934508|ref|YP_007688090.1| 22 TLLMAASMIV 31
                                      3333333333 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 4.7e-05
                            DUF423  17 alesfetavqYqlyhalallavalla..skaaasrllklagllflaGivlFSgslyl 71 
                                       + ++++ +  Yq+y +l+l+++al +  s     ++ + + + +l+G v+F+ ++ +
  gi|474934508|ref|YP_007688090.1|  90 YYHWVDDGPVYQFYAGLVLCFLALNLmySGYRYMSRNSRTITYILIGSVFFALTITA 146
                                       6678888999***********99988886677778888899999*******999876 PP

>> PalH  PalH/RIM21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   8.9    0.0035        31     137     229 ..      87     182 ..      18     184 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.0035
                              PalH 137 aselekeivsstelkvlelisnlllnlaqvqivirlfsrqkekriiilvGlaliildtilsalllf..skkfldalp 211
                                          + + + ++  ++++  ++ ++l l+ ++  +r +sr+++  ++il+G+++  l  +   +  +  s  +ld l+
  gi|474934508|ref|YP_007688090.1|  87 FMRYYHWVDDGPVYQFYAGLVLCFLALNLMYSGYRYMSRNSRTITYILIGSVFFALTITAELIFYLrmSAGTLDFLE 163
                                       56677778889999************************************887777766666655533346777776 PP

                              PalH 212 al.sylfelalvtlyaalv 229
                                            + +l++++ly+ lv
  gi|474934508|ref|YP_007688090.1| 164 KQgNLIANLVMYILYIGLV 182
                                       5514566888999998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 1911.19
//
Query:       gi|474934509|ref|YP_007688091.1|  [L=376]
Description: hypothetical protein TALC_00936 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-07   30.7   0.0    7.7e-07   29.2   0.0    1.8  1  HNH_2     HNH endonuclease
  ------ inclusion threshold ------
      0.064   13.0   0.0        0.1   12.3   0.0    1.2  1  MiaE_2    tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE)-like


Domain annotation for each model (and alignments):
>> HNH_2  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   8.6e-11   7.7e-07       1      71 [.     264     315 ..     264     316 .. 0.88

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 8.6e-11
                             HNH_2   1 CvitgiddpslleaAHIiPwslssffndlilnrfeigrillekgstidspsNgllLspdiHklFdqflfaf 71 
                                       C+itg++++++l  +H++Pw +ss      +++               +p+NgllL++ ++ lFd++l+++
  gi|474934509|ref|YP_007688091.1| 264 CCITGVSQREVLIGSHVYPWRMSS-----PQEK--------------TNPNNGLLLNKFHDSLFDKYLMTV 315
                                       *********9*********88885.....3333..............59******************9987 PP

>> MiaE_2  tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE)-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.2e-05       0.1      68     131 ..     142     206 ..     134     230 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.2e-05
                                       HHHGGGHHHHHHHHH.TT--SSHHHHHHHHHHHHHHHHHHHHHHCCCS-HHHHHHHHHHS--HHH CS
                            MiaE_2  68 eamePfvaavddfhk.rtaPadwleslvkayvgdsvaadfyrevaeyldadtrelvlavlddtgh 131
                                       e +eP++ a+ + +  +   ad +es+   yv d ++a   r+++  l+  t e+ + + + +g+
  gi|474934509|ref|YP_007688091.1| 142 ELIEPYIEAFPGKNGgQNWSADEIESFCEMYVPDKLSAGDIRAISTSLNKPTEEIREILDALDGK 206
                                       56788888887766425667899***************************998875544443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2271.25
//
Query:       gi|474934510|ref|YP_007688092.1|  [L=145]
Description: Nucleoside 2-deoxyribosyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-23   82.3   0.0    3.3e-23   82.1   0.0    1.1  1  Nuc_deoxyrib_tr  Nucleoside 2-deoxyribosyltransferase
    8.3e-09   35.7   0.0    1.1e-08   35.4   0.0    1.2  1  Nuc_deoxyri_tr2  Nucleoside 2-deoxyribosyltransferase like


Domain annotation for each model (and alignments):
>> Nuc_deoxyrib_tr  Nucleoside 2-deoxyribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.1   0.0   3.7e-27   3.3e-23       1     107 [.       4     113 ..       4     137 .. 0.88

  Alignments for each domain:
  == domain 1  score: 82.1 bits;  conditional E-value: 3.7e-27
                                       EEEESGGGCSCCCHHHHHHHHHHHHTTTTEEE-CC.......TT-TT....--SSHHHHHHHHHHHHHC-SEEEEE- CS
                   Nuc_deoxyrib_tr   1 iYLAgplvFrpdakalaarlkallaengldglaPl.......dneaelelpaeetaraiyeadialirqaDavianl 70 
                                       iYLAgpl F  ++ +++ +l+ +l+e+g+d++ P+         +++++  a+eta  i+  d+al+ ++Da++ n+
  gi|474934510|ref|YP_007688092.1|   4 IYLAGPL-FCTSELEYNLKLRLILKEEGFDLVLPQdnsgsidVGKMSDQSFAKETALDIFSDDLALLGSCDALLLNI 79 
                                       9******.***************************66655532222444489************************* PP

                                       -SSSSSS--HHHHHHHHHHHHCT-EEEEE-S-GCGHH CS
                   Nuc_deoxyrib_tr  71 dpfrgpeaDsGtafEvGyavalgkpvlayttdarelr 107
                                       d+     +D+G ++E+Gya+a g p+++  td r+ +
  gi|474934510|ref|YP_007688092.1|  80 DGRV---PDEGACVELGYAYAKGMPCFGIKTDIRTAE 113
                                       **88...***************************954 PP

>> Nuc_deoxyri_tr2  Nucleoside 2-deoxyribosyltransferase like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.0   1.2e-12   1.1e-08       3     107 ..       3     108 ..       1     109 [. 0.82

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 1.2e-12
                                       EEEEEE---SSSST-HHHHHHHHHHTSSS-EEEEE----SS-----....HHHHH.....HHHHHHHHHHHH-SEEE CS
                   Nuc_deoxyri_tr2   3 svFLaGsteseaetdWredlteaLsaipklgvtvfnPqredwdsel....eedrskkrfreqvewelealekAdvvv 75 
                                       +++LaG+++ ++e +++ +l  +L++   +g++++ Pq +  + ++     ++  k++  +++  +l+ l ++d+++
  gi|474934510|ref|YP_007688092.1|   3 RIYLAGPLFCTSELEYNLKLRLILKE---EGFDLVLPQDNSGSIDVgkmsDQSFAKETALDIFSDDLALLGSCDALL 76 
                                       79******************888866...8********99977666321123334455567889999999******* PP

                                       EEE-TT---HHHHHHHHHHTTSS-EEEEE-TT CS
                   Nuc_deoxyri_tr2  76 fvfdgedsatrslvElglaaakgkkvvlvpkg 107
                                         +dg+  +  + vElg+a+akg ++++++++
  gi|474934510|ref|YP_007688092.1|  77 LNIDGRVPDEGACVELGYAYAKGMPCFGIKTD 108
                                       *****55566689************9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       196  (0.010932); expected 358.6 (0.02)
Passed bias filter:                      190  (0.0105974); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1117.45
//
Query:       gi|474934511|ref|YP_007688093.1|  [L=148]
Description: Membrane protein implicated in regulation of membrane protease activity [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-14   53.6   2.4    2.2e-14   53.6   2.4    1.5  2  NfeD             NfeD-like C-terminal, partner-binding
  ------ inclusion threshold ------
      0.095   12.7   0.1       0.14   12.1   0.1    1.3  1  IPI_T4           Nuclease inhibitor from bacteriophage T4
        0.1   12.2   0.0        0.1   12.2   0.0    1.4  2  DUF1449          Protein of unknown function (DUF1449)


Domain annotation for each model (and alignments):
>> NfeD  NfeD-like C-terminal, partner-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.3       2.1   1.3e+04       4      12 ..      11      19 ..       6      26 .. 0.51
   2 !   53.6   2.4   3.7e-18   2.2e-14       2      84 .]      60     147 ..      57     147 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.1
                                      XXXXXXXXX CS
                              NfeD  4 vvsvlllvl 12
                                      v++++l+++
  gi|474934511|ref|YP_007688093.1| 11 VLGIGLVLV 19
                                      333333333 PP

  == domain 2  score: 53.6 bits;  conditional E-value: 3.7e-18
                                       XXXXXXXXXXXXXXXS---SSS--S...S---GGTTSEEEEEE-B...S.-EEEEETTEEEEEE-.SSB-TT-EEEE CS
                              NfeD   2 favvsvlllvllrplllkklkkkek..ktnaealiGkegvvledi...g.tGrvkvdGeeWsarsegeiekgerVrV 72 
                                       ++v ++ ++v+++ ++ ++l ++e+   t +++l G+eg+v+ ++   + +G+v+++ ++Wsa+++++i++g+ V+V
  gi|474934511|ref|YP_007688093.1|  60 AVVSAIPVTVFTF-WVYRRLGSPEAptTTVSDSLAGREGKVTVEVtpgNmRGKVRIGSDTWSAEADETIPVGTDVVV 135
                                       3444445556666.7777775555563345559*************96368**************999********* PP

                                       EEE-SSSEEEEE CS
                              NfeD  73 veveGltliVep 84 
                                        +  G+++ V++
  gi|474934511|ref|YP_007688093.1| 136 ESAAGVHVHVRR 147
                                       **********96 PP

>> IPI_T4  Nuclease inhibitor from bacteriophage T4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   2.4e-05      0.14       6      45 ..      87     126 ..      83     142 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.4e-05
                                       HHHHH-SSS-SSEEE-TTT--EEES-SSTT.TT-EEEE-SS CS
                            IPI_T4   6 evikankgregkpmislvdgeeikgtvylg.dgwsakkdga 45 
                                        v  +  gregk  + +  g +++g v +g d wsa  d +
  gi|474934511|ref|YP_007688093.1|  87 TVSDSLAGREGKVTVEVTPG-NMRGKVRIGsDTWSAEADET 126
                                       5666678*******998888.69*****99799***99964 PP

>> DUF1449  Protein of unknown function (DUF1449)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.3       1.5   8.9e+03     109     116 ..      12      19 ..       5      31 .. 0.46
   2 ?   12.2   0.0   1.7e-05       0.1      99     149 ..      51     101 ..      37     120 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 1.5
                           DUF1449 109 lllalplv 116
                                       l ++l+lv
  gi|474934511|ref|YP_007688093.1|  12 LGIGLVLV 19 
                                       22222222 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 1.7e-05
                           DUF1449  99 lpallaaaialllalplvrvlaallakilpkdetsavseeslvGrvavivl 149
                                       l+ +++aa+a++ a+p++ ++  +  ++   +  +   ++sl Gr++++++
  gi|474934511|ref|YP_007688093.1|  51 LYSWVTAAVAVVSAIPVTVFTFWVYRRLGSPEAPTTTVSDSLAGREGKVTV 101
                                       678*************9977766666664444444455689*******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1126.54
//
Query:       gi|474934512|ref|YP_007688094.1|  [L=362]
Description: SPFH domain, Band 7 family protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.7e-39  133.7   2.5      1e-38  133.1   2.5    1.2  1  Band_7    SPFH domain / Band 7 family
  ------ inclusion threshold ------
      0.057   13.1   0.3       0.12   12.0   0.3    1.6  1  Band_7_1  SPFH domain-Band 7 family


Domain annotation for each model (and alignments):
>> Band_7  SPFH domain / Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.1   2.5   1.1e-42     1e-38       2     177 ..      27     196 ..      26     197 .. 0.98

  Alignments for each domain:
  == domain 1  score: 133.1 bits;  conditional E-value: 1.1e-42
                            Band_7   2 iieegevgvvvrfGklsrvlepGlhfilPfgrsvtvvsvrvqtldvsvsltvptkDglpvtidvtviyrvpddapkl 78 
                                       i+++ e g+++r Gk  rvl+pGl f+ P++++v++ ++r+ ++dv++ ++v+tkD+ pv++d++++++v +d++ +
  gi|474934512|ref|YP_007688094.1|  27 IVNPYEQGIYTRLGKFIRVLNPGLNFVCPLINEVVKLDLRTEVMDVPK-QEVITKDNSPVNVDAIIYIKV-TDPKNA 101
                                       799*********************************************.*********************.****** PP

                            Band_7  79 vaaveresanldnlirrvlesalrevisemtleellsnreelaeelknelneqlrkyGvevldvritdidpppevaq 155
                                       +++v     n++    ++++ +lr+vi++m+l+++ls+re ++ +l++ l e+ +k+Gv v++v i+++dp+++v+ 
  gi|474934512|ref|YP_007688094.1| 102 FFEV----TNYRLATVNLAQTTLRSVIGQMELDQILSSRENINVQLRDTLDEATDKWGVRVENVEIKEVDPAAKVKG 174
                                       ****....********************************************************************* PP

                            Band_7 156 alaakqaaeaeaqaeiaraeae 177
                                       ++++   ae++++a+i +a ++
  gi|474934512|ref|YP_007688094.1| 175 SMEEQTSAERKRRAAILEADGQ 196
                                       ****************999876 PP

>> Band_7_1  SPFH domain-Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3   1.4e-05      0.12     145     209 ..     120     182 ..      74     184 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.4e-05
                          Band_7_1 145 lsdvlaeskipvldlaakseelaeklkealkeelaeyGlelekleienislpeevekaldkrasm 209
                                       l +v+++ +  + ++ +  e++  +l+++l+e+ ++ G+ +e++ei++++   +v+  +++++s+
  gi|474934512|ref|YP_007688094.1| 120 LRSVIGQME--LDQILSSRENINVQLRDTLDEATDKWGVRVENVEIKEVDPAAKVKGSMEEQTSA 182
                                       444444333..334557789999*************************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       812  (0.0452898); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2340.94
//
Query:       gi|474934513|ref|YP_007688095.1|  [L=58]
Description: hypothetical protein TALC_00941 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.32s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 352.78
//
Query:       gi|474934514|ref|YP_007688096.1|  [L=181]
Description: hypothetical protein TALC_00942 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.023   14.6   0.0       0.32   10.9   0.0    2.0  2  Acetyltransf_10  Acetyltransferase (GNAT) domain
      0.052   13.8   0.0      0.076   13.2   0.0    1.2  1  Cu2_monooxygen   Copper type II ascorbate-dependent monooxyge


Domain annotation for each model (and alignments):
>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.03   2.6e+02      15      54 ..      41      81 ..      24      83 .. 0.78
   2 ?   10.9   0.0   3.6e-05      0.32      64     116 ..     118     173 ..     114     175 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.03
                   Acetyltransf_10 15 efispealrerieegealllvaeeggkivGviel.rdgshi 54
                                      ++++++a++ + ++ + ++l++  +g+i+G+ ++ ++  h+
  gi|474934514|ref|YP_007688096.1| 41 DYLHNKAITMEKRQMSRTYLALGSDGNILGYFTIgMKCMHV 81
                                      56666777766667788889999999****99997777675 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 3.6e-05
                   Acetyltransf_10  64 rgqGigkaLleaveee.aekdgikl..eltvnaspyavpfYeklGFkavgeeqeen 116
                                         +G g+aLl++++   ++ ++      + ++ +++ v++Y + GF  vg+++ en
  gi|474934514|ref|YP_007688096.1| 118 SEKGFGRALLQEALGIlCRANKMVGcrLVRLDCADELVNYYGQTGFFFVGKNESEN 173
                                       579************97766655558899*****************9998877665 PP

>> Cu2_monooxygen  Copper type II ascorbate-dependent monooxygenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   8.5e-06     0.076      29     105 ..       5      85 ..       2      96 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.5e-06
                    Cu2_monooxygen  29 kkhhiikfepii.qkgneelvhhmllyeCeeeeeeeeveesggeCyssekkpeele...sCse..viaawavgaeaf 99 
                                       +++hi  + +++ + g++++ +h+  y+C+ ++e+e+  +++    +++++ +++    s  +  ++  +++g++ +
  gi|474934514|ref|YP_007688096.1|   5 TDYHISSLSSLVdTVGESAISKHLSTYRCARDSEREDYLHNKAITMEKRQMSRTYLalgS--DgnILGYFTIGMKCM 79 
                                       5799******997889999**********8766767666666666566555554444323..245999999999999 PP

                    Cu2_monooxygen 100 tlPeev 105
                                       ++P+e+
  gi|474934514|ref|YP_007688096.1|  80 HVPDET 85 
                                       999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1275.21
//
Query:       gi|474934515|ref|YP_007688097.1|  [L=108]
Description: Phosphoglycerate mutase 1 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.5e-27   96.5   0.1    1.7e-27   96.4   0.1    1.0  1  His_Phos_1  Histidine phosphatase superfamily (branch 1)


Domain annotation for each model (and alignments):
>> His_Phos_1  Histidine phosphatase superfamily (branch 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.4   0.1   9.3e-32   1.7e-27       1      99 [.       4     107 ..       4     108 .] 0.94

  Alignments for each domain:
  == domain 1  score: 96.4 bits;  conditional E-value: 9.3e-32
                                       EEEEE---BTTB--....TT----B-HHHHHHHHHHHHHHTTS---EE..EE-SSHHHHHHHHHHHHCTT...--EE CS
                        His_Phos_1   1 lyLvRHGetewnaegrlqgrtdvpLteeGreqAealaerlagepidai..ysSplkRarqTaeliaealg...lpve 72 
                                       l+LvRHGe+ewn+ + + g+tdv+L+e+G e+A+a++e +++e+++++  y+S lkRa++Ta+ +++a++   ++  
  gi|474934515|ref|YP_007688097.1|   4 LVLVRHGESEWNKLNLFTGWTDVDLSEKGWEEAKAAGEMMKAEGFAFDkcYTSFLKRAIHTAHTALAAMDldwIEEV 80 
                                       79****************************************88887777********************7777777 PP

                                       E-GGGS----GGGTT-B.HHHHHH..H CS
                        His_Phos_1  73 ldegLrEidfGdweglttaeiaeeype 99 
                                       ++ +L+E+++G+++gl+++e ae+y e
  gi|474934515|ref|YP_007688097.1|  81 KTWRLNERHYGALQGLNKSETAEKYGE 107
                                       889********************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.57
# Mc/sec: 569.82
//
Query:       gi|474934516|ref|YP_007688098.1|  [L=73]
Description: hypothetical protein TALC_00944 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.062   13.0   0.0      0.072   12.8   0.0    1.1  1  His_Phos_1  Histidine phosphatase superfamily (branch 1)


Domain annotation for each model (and alignments):
>> His_Phos_1  Histidine phosphatase superfamily (branch 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     4e-06     0.072     143     185 ..       2      44 ..       1      52 [. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4e-06
                                       EEEE-HHHHHHHHHHHHT--GGGGGGB---TT-EEEEEE-SS- CS
                        His_Phos_1 143 lvVsHggvirallarllglpleelrrleldnaslsvlefdegg 185
                                       +v++Hg  +ral+++l g+  ee+ ++++++    v +fd++ 
  gi|474934516|ref|YP_007688098.1|   2 VVFAHGNSLRALVKYLDGMTGEEIAKVNIPTGVPLVYQFDDSM 44 
                                       89************************99998877777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.38
# Mc/sec: 571.00
//
Query:       gi|474934517|ref|YP_007688099.1|  [L=108]
Description: hypothetical protein TALC_00945 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      189  (0.0105416); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 712.88
//
Query:       gi|474934518|ref|YP_007688100.1|  [L=84]
Description: putative acetyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.5e-22   77.1   0.1    9.7e-22   76.9   0.1    1.0  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
    1.5e-07   31.6   0.0    1.7e-07   31.5   0.0    1.0  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    3.5e-07   30.2   0.0    3.9e-07   30.0   0.0    1.0  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    6.5e-07   29.7   0.0    7.8e-07   29.4   0.0    1.1  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.017   15.1   0.0      0.023   14.6   0.0    1.3  1  Acetyltransf_13  ESCO1/2 acetyl-transferase
      0.025   14.7   0.0      0.029   14.4   0.0    1.2  1  Acetyltransf_9   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.9   0.1   3.3e-25   9.7e-22       1      73 [.      13      83 ..      13      84 .] 0.95

  Alignments for each domain:
  == domain 1  score: 76.9 bits;  conditional E-value: 3.3e-25
                   Acetyltransf_CG  1 rfeltldegeevafleYevrkegvldfthTeVpeelrGkGiAkkLvkaalddareeglkvvptCsyvaaylek 73
                                      rf ++ d g+ev++l+Y   ++g+++++hT+V++  rG+GiA k+++aa  +ar+eglkv++tCsy+aa++ +
  gi|474934518|ref|YP_007688100.1| 13 RFTAEKD-GAEVGELTYV-IDDGTMNINHTFVNPDQRGQGIATKMTDAAEAFARAEGLKVIATCSYAAAKIAE 83
                                      7899998.99*******8.9999*********************************************99865 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.0   5.7e-11   1.7e-07      31      99 ..       8      74 ..       2      83 .. 0.86

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 5.7e-11
                                      TTC.EEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEE.EE CS
                    Acetyltransf_1 31 eae.gllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikki.vl 99
                                      + +   + ae+dg  +G +++ +++     ++ i+  +V+p+ rg+G+++++ +a+e +ar eg+k i  +
  gi|474934518|ref|YP_007688100.1|  8 DRCaARFTAEKDGAEVGELTYVIDDG----TMNINHTFVNPDQRGQGIATKMTDAAEAFARAEGLKVIaTC 74
                                      445567789999999****9999999....9**********************************998554 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   1.3e-10   3.9e-07      34      87 ..      14      70 ..       2      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 1.3e-10
                   Acetyltransf_10 34 lvaeeggkivGviel.rdgs..hisllfVdpeyrgqGigkaLleaveeeaekdgikl 87
                                      + ae++g  vG +++  d++   i + fV+p++rgqGi++++ +a+e+ a+ +g+k+
  gi|474934518|ref|YP_007688100.1| 14 FTAEKDGAEVGELTYvIDDGtmNINHTFVNPDQRGQGIATKMTDAAEAFARAEGLKV 70
                                      6788899999999777777779****************************9988774 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   2.6e-10   7.8e-07       6      53 ..      14      68 ..      10      82 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 2.6e-10
                                      EEEEETTEEEEEEEEEEES..TCTEEEEE-GGGTTSSHHHHHHHHTT.....SEE CS
                    Acetyltransf_7  6 fVaeddgkivGfialslld..aeitrlaVdpeyrgkGiGraLleaae.....kgi 53
                                      f ae+dg +vG++ ++++d   +i++ +V+p+ rg+Gi++++ +aae     +g+
  gi|474934518|ref|YP_007688100.1| 14 FTAEKDGAEVGELTYVIDDgtMNINHTFVNPDQRGQGIATKMTDAAEafaraEGL 68
                                      559**********9999999888888*****************972233334553 PP

>> Acetyltransf_13  ESCO1/2 acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   7.9e-06     0.023       5      30 ..      35      60 ..      32      81 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 7.9e-06
                   Acetyltransf_13  5 cGisriWvssshRrkgiAtkLldaar 30
                                      + i+  +v ++ R +giAtk+ daa 
  gi|474934518|ref|YP_007688100.1| 35 MNINHTFVNPDQRGQGIATKMTDAAE 60
                                      679999*****************985 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   9.8e-06     0.029      80     115 ..      41      76 ..      34      84 .] 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 9.8e-06
                                       EE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--S CS
                    Acetyltransf_9  80 avapehrgrgvlskLlaraleemreegqplsllfPs 115
                                        v+p++rg+g+++k++++a + +r+eg +++    +
  gi|474934518|ref|YP_007688100.1|  41 FVNPDQRGQGIATKMTDAAEAFARAEGLKVIATCSY 76 
                                       699***********************9999887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 572.11
//
Query:       gi|474934519|ref|YP_007688101.1|  [L=321]
Description: methionine-R-sulfoxide reductase/methionine-S-sulfoxide reductase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-51  173.7   0.0      4e-51  173.2   0.0    1.2  1  PMSR      Peptide methionine sulfoxide reductase
    6.6e-40  136.0   0.0      1e-39  135.4   0.0    1.3  1  SelR      SelR domain


Domain annotation for each model (and alignments):
>> PMSR  Peptide methionine sulfoxide reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.2   0.0   4.5e-55     4e-51       2     153 .]       8     157 ..       7     157 .. 0.96

  Alignments for each domain:
  == domain 1  score: 173.2 bits;  conditional E-value: 4.5e-55
                                       EEEE-S-HHHHHHHHCTSTTEEEEEEEEESSS-S.S--HHHHHTTTT--EEEEEEEEETTTS-HHHHHHHHHHTS-T CS
                              PMSR   2 avlagGCFWgveklfeklkGvlstevGYagGkte.nptYeevcsgktghaEavevvydpekvsleellelffeihDp 77 
                                       + lagGCFWg+e+l++ ++Gv+stevGYa+G+ +  ptYe+vc+ +tg+ E+v+v+yd+++vsl+ +l +ff ++Dp
  gi|474934519|ref|YP_007688101.1|   8 IWLAGGCFWGTERLISAIDGVVSTEVGYANGDPSvVPTYEDVCRRRTGYRETVHVTYDESRVSLDFILYAFFASIDP 84 
                                       89*****************************65527***************************************** PP

                                       T-SSEETTEESGGG--EEEESSCCHHHHHHHHHHHHHTTHTTSSS---EEEEG-SEEE--CCCTTHHHH-TTS--T CS
                              PMSR  78 tqlnrqgnDvGtqYrsaiyytneeqkevaeevleelqkkkalkkkivteieplkefykaeeyHqqYleknpegych 153
                                       t ++rqgnD G qY++ i++++ e +++++++  + + +    +++ + ++pl++f++aeeyHq+Yleknp+gych
  gi|474934519|ref|YP_007688101.1|  85 TLKDRQGNDAGPQYQACIFWNDGESEKTVRRIAGTEAGR---YDPFNVVLAPLENFFPAEEYHQRYLEKNPHGYCH 157
                                       ******************************999888777...99*******************************8 PP

>> SelR  SelR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.4   0.0   1.1e-43     1e-39       2     121 .]     184     303 ..     183     303 .. 0.96

  Alignments for each domain:
  == domain 1  score: 135.4 bits;  conditional E-value: 1.1e-43
                                       HHCTSHCCHHHHHHHTT-SSTTSSSTSS--SSCEEEETTTS-EEEECCCCE-STTSSSEESS-STTTTEEEEEEECT CS
                              SelR   2 lkkkLtpeqyevlrekgterpftgeyekekekGvyecavcgepLfssetkfdsgcGwpsFaeaikeeavkekkdtsl 78 
                                       l+++Ltp qy+v++e++terpf++ey++e++ G+y+++++gepLf s++k+ds+cGwp+F+++++ ++v + +d++l
  gi|474934519|ref|YP_007688101.1| 184 LESRLTPLQYSVTQEADTERPFENEYDNEFSPGIYVDRITGEPLFLSQDKYDSHCGWPAFSKPLDPNSVVYLEDHKL 260
                                       7899************************************************************************* PP

                                       TSEEEEEEETTCECEEEEEEC.TSSSSS.SEEEEE-CCCEEEEE CS
                              SelR  79 gmertevvcakcdahlGhvFe.dgpkpttgkrycinsvslkfkp 121
                                        ++rtev+++  ++hlGh+F  d ++p t++ryc+ns+sl f p
  gi|474934519|ref|YP_007688101.1| 261 PITRTEVRSRVGNTHLGHLFYgDRFSP-TRARYCMNSASLLFIP 303
                                       *********************777776.6***********9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 2168.44
//
Query:       gi|474934520|ref|YP_007688102.1|  [L=120]
Description: hypothetical protein TALC_00948 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.19   11.6   0.0       0.89    9.5   0.0    1.9  2  DUF2642   Protein of unknown function (DUF2642)


Domain annotation for each model (and alignments):
>> DUF2642  Protein of unknown function (DUF2642)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0     5e-05      0.89      26      51 ..      37      62 ..      26      71 .. 0.85
   2 ?   -0.4   0.0      0.06   1.1e+03      39      53 ..      97     111 ..      93     112 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 5e-05
                           DUF2642 26 ttrgsvrGiLkdvkPDHivveigntv 51
                                       + ++++G+L+++ PD+ ++++g+  
  gi|474934520|ref|YP_007688102.1| 37 EVLDTLSGMLAEAFPDYRQLKVGEGC 62
                                      567899*************9998765 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.06
                           DUF2642  39 kPDHivveigntvfy 53 
                                       +PD +vv  ++++++
  gi|474934520|ref|YP_007688102.1|  97 LPDDVVVICTQELCH 111
                                       699999988887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 772.56
//
Query:       gi|474934521|ref|YP_007688103.1|  [L=475]
Description: amino acid carrier protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   3.7e-128  428.2  36.2   4.8e-128  427.8  36.2    1.1  1  Na_Ala_symp  Sodium:alanine symporter family
  ------ inclusion threshold ------
       0.27   10.6  16.1      0.015   14.7   5.6    2.5  2  TssN         Type VI secretion system, TssN


Domain annotation for each model (and alignments):
>> Na_Ala_symp  Sodium:alanine symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  427.8  36.2  5.4e-132  4.8e-128       8     393 .]      60     460 ..      55     460 .. 0.96

  Alignments for each domain:
  == domain 1  score: 427.8 bits;  conditional E-value: 5.4e-132
                       Na_Ala_symp   8 ksegeissfqAlatalaarvGtGniaGvatAialGGpGAvfWmwvvallGmatkfvEstLaqlYkekdekgevrGGp 84 
                                       ++++ issf+A+++ + ar+G+GniaGvatAi++GGpGAvfWmw++a++G+a++f+EstLaq+Ykek+e+g++ GGp
  gi|474934521|ref|YP_007688103.1|  60 RGTHRISSFEAFCIGMGARIGVGNIAGVATAIVTGGPGAVFWMWIFAIIGSASSFMESTLAQIYKEKKEDGHFYGGP 136
                                       56889************************************************************************ PP

                       Na_Ala_symp  85 ayyiekglkkkwlavlfavlliialglginavqansiasaleeaf..eveklvvgivlavllalvilggikriakva 159
                                       ayy +kgl+++ l+++ avll+i++g+g+ +vq+ + ++al  af  + +++v+++++a ++a++i+ g+k  ak++
  gi|474934521|ref|YP_007688103.1| 137 AYYASKGLGSRRLGIVAAVLLVITFGIGFITVQSCNASQALCGAFefDHNNYVFAAIIAGIAAVIIFKGLKAAAKFS 213
                                       ******************************************986226778************************** PP

                       Na_Ala_symp 160 evvvPvmailYillalvvillniekvpevlalifksAFgleavagGilgaaialGvkRglfSneAGlGsapiaaAaa 236
                                         +vP ma+++i++a++ illni  v +++ +if+ AF+++a+agG++g++i +G+kRg+fSneAGlGs ++ aA+a
  gi|474934521|ref|YP_007688103.1| 214 ANIVPYMALAWIVFAVAAILLNIGGVVNAVYMIFEYAFDASALAGGAIGTIIVTGLKRGVFSNEAGLGSVANIAATA 290
                                       ***************************************************************************** PP

                       Na_Ala_symp 237 evshpvkqGlvqalgvfidtlvvCtatalvill...........segvaltqaalesvl.gsvgalfvaialllFaf 301
                                       +v+hpvkqGl+q++gv +dtl+vCt+talv+l+            eg++l+qa +++++ g+++++++a+ +++Faf
  gi|474934521|ref|YP_007688103.1| 291 DVKHPVKQGLIQSFGVLVDTLIVCTITALVVLSyghfdeimaldLEGAKLVQAVVADAFsGTWTNYIIAMFMFVFAF 367
                                       *********************************887777777766***********999899*************** PP

                       Na_Ala_symp 302 stilgnyyygeknleyllgkkkklliyrvlvlllvf.vgavaslelvwnlaDialglmalvnliaillLskvvvkal 377
                                       ++++g+y ++e n +++  +k+++l++r++v++++f +g+++s++l+ +++D++++lma vn+i ++lLs++v++a+
  gi|474934521|ref|YP_007688103.1| 368 TSLIGYYTMSEANARFVRDDKRSVLVIRIMVVIVAFlAGTCTSVNLADTISDTFMALMAAVNMIIVALLSRKVFEAY 444
                                       ******************989999999998877665168899*********************************** PP

                       Na_Ala_symp 378 kdYekqkkkgkkepvf 393
                                        dY+kq+++g +ep+f
  gi|474934521|ref|YP_007688103.1| 445 VDYKKQRRAGIEEPEF 460
                                       **********988876 PP

>> TssN  Type VI secretion system, TssN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   2.8     0.027   2.4e+02       4      52 ..     188     235 ..     150     277 .. 0.66
   2 ?   14.7   5.6   1.7e-06     0.015      55     148 ..     354     445 ..     338     448 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.027
                              TssN   4 ylllpllavilllilsliakknkllkkkkliiyiLlaglvlalpgllgf 52 
                                       y+++ ++a i + +++++  k +++ + +++ y+ la +v+a+ ++l  
  gi|474934521|ref|YP_007688103.1| 188 YVFAAIIAGIAA-VIIFKGLKAAAKFSANIVPYMALAWIVFAVAAILLN 235
                                       444444444444.555555556666667777777777777777776644 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.7e-06
                              TssN  55 nefvpygyillqilylllGilhlylllkkffkelkekkilfeilltlivillglvlfvlvfnllselqygvwaatsl 131
                                       ++++   ++++  ++ l+G++ +  ++ +f ++ k + +++ i++++++ l g +  v + + +s++ ++++aa ++
  gi|474934521|ref|YP_007688103.1| 354 TNYIIAMFMFVFAFTSLIGYYTMSEANARFVRDDKRSVLVIRIMVVIVAFLAGTCTSVNLADTISDTFMALMAAVNM 430
                                       4667788999999999*****************99999*******************************99777776 PP

                              TssN 132 lvfiipllflktykall 148
                                       +  i+ ll  k+++a++
  gi|474934521|ref|YP_007688103.1| 431 I--IVALLSRKVFEAYV 445
                                       6..56677777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1150  (0.0641419); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.68u 0.34s 00:00:01.02 Elapsed: 00:00:00.48
# Mc/sec: 2970.84
//
Query:       gi|474934522|ref|YP_007688104.1|  [L=70]
Description: hypothetical protein TALC_00950 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 461.68
//
Query:       gi|474934523|ref|YP_007688105.1|  [L=57]
Description: hypothetical protein TALC_00951 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 389.02
//
Query:       gi|474934524|ref|YP_007688106.1|  [L=168]
Description: hypothetical protein TALC_00952 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1082.73
//
Query:       gi|474934525|ref|YP_007688107.1|  [L=137]
Description: hypothetical protein TALC_00953 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 873.61
//
Query:       gi|474934526|ref|YP_007688108.1|  [L=235]
Description: putative dithiol-disulfide isomerase involved in polyketide biosynthesis [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-33  116.4   0.0    1.5e-33  116.2   0.0    1.0  1  DSBA           DSBA-like thioredoxin domain
    4.8e-05   23.6   0.0     0.0035   17.5   0.0    2.2  1  Thioredoxin_4  Thioredoxin
  ------ inclusion threshold ------
      0.011   15.5   0.0      0.021   14.5   0.0    1.4  1  Thioredoxin_5  Thioredoxin


Domain annotation for each model (and alignments):
>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.2   0.0   2.5e-37   1.5e-33       2     191 ..       3     204 ..       2     206 .. 0.94

  Alignments for each domain:
  == domain 1  score: 116.2 bits;  conditional E-value: 2.5e-37
                                       EEEEEBTTBHHHHHHHHHHHHHHHHC..CT.EEEEEEE-SSSCHHHHCT.S.GGG...........SHHHHHHHHHH CS
                              DSBA   2 vdeffDvlCPyCylgkerleklaars..pd.vkvvlrpfelagakkasgnvgpse...........lpeklkylled 64 
                                       +  + D+ CP+Cy+g+ rl+ +++    +d v++ l++f+l+++   +g++++++           +  + k+ ++ 
  gi|474934526|ref|YP_007688108.1|   3 ITYWTDFSCPFCYIGDTRLKNAIRSIgaEDlVEMELKSFQLTPQ---AGPKPRNDmvtgmakhygmSLSEAKERVDA 76 
                                       889********************98899777*************...77777777999*******99999******* PP

                                       HHHHHHHHT....GGSSHHHHHHHHHHHHHHHHHHH..GHHHHHHHHHHHHHTSSS-TSSHHHHHHHHHHTTS.HHH CS
                              DSBA  65 lkrlaeaegiplrfpkdklknstraarlllaagaeg..laekvvrelfealwsegqaitddqellevaekaGldaee 139
                                       ++ ++++eg+++r   ++  n+++a+rl+ +a  +g    e+++ +lf+a++++   i d+++l+ +ae+ G+d ee
  gi|474934526|ref|YP_007688108.1|  77 ISAMGAKEGLEFRYADVQSCNTFDAHRLMKMAFSHGkeEGERMALRLFQAFFGDCVLIADHDVLQGLAEECGFDGEE 153
                                       *****************966*********998888877899************************************ PP

                                       HHHHHTSHHHHHHHHHHHHHHHHTT-SSSSEEEETTCEEEESSSSHHHHHHH CS
                              DSBA 140 ldealeseavkeavrentaaaqslgvtGvPtvvvdgkrmvfGadrldtlada 191
                                       ++e+l+s++++++v  ++++a+ +g++ vP+++v+    v+Ga++ + +a  
  gi|474934526|ref|YP_007688108.1| 154 VREVLSSDRFADQVLADEREARGYGLNAVPFYIVGRY-GVPGAPSTEEFAGL 204
                                       **********************************997.9********99865 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   5.9e-07    0.0035     105     165 ..     102     206 ..       1     207 [. 0.60

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5.9e-07
                                       ................................................HHHHHTS-------HHHHHHHHHHHHHHT CS
                     Thioredoxin_4 105 e............................................aldkdekfeacleeekldalveaeskeakkag 137
                                                                                     + + e++ + l+++++ ++v a+ +ea+  g
  gi|474934526|ref|YP_007688108.1| 102 HrlmkmafshgkeegermalrlfqaffgdcvliadhdvlqglaeeCGFDGEEVREVLSSDRFADQVLADEREARGYG 178
                                       13344444444444444444555555555555555555555555467778899999********************* PP

                                       --SS-EEEETTEEE-TT--HHHHHHHHT CS
                     Thioredoxin_4 138 iestPtfiingekveepqtyeelkalid 165
                                       ++++P  i++   v ++++ ee+  l++
  gi|474934526|ref|YP_007688108.1| 179 LNAVPFYIVGRYGVPGAPSTEEFAGLVK 206
                                       ***********99**********99886 PP

>> Thioredoxin_5  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   3.5e-06     0.021      81     161 ..     105     185 ..      68     189 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.5e-06
                     Thioredoxin_5  81 iKAAelQgkkkgrkFLrklqealflekkniskeellleiaekaglDveefkeDlesklakkafqcDlklakemgvte 157
                                       +K A   gk++g +  ++l +a+f +   i+++++l+ +ae++g D ee +e l+s+  +++  +D + a+ +g + 
  gi|474934526|ref|YP_007688108.1| 105 MKMAFSHGKEEGERMALRLFQAFFGDCVLIADHDVLQGLAEECGFDGEEVREVLSSDRFADQVLADEREARGYGLNA 181
                                       6778888**************************************************99999999999999999999 PP

                     Thioredoxin_5 158 vPtl 161
                                       vP  
  gi|474934526|ref|YP_007688108.1| 182 VPFY 185
                                       9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1651.27
//
Query:       gi|474934527|ref|YP_007688109.1|  [L=195]
Description: putative GTPases (G3E family) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.1e-38  131.1   0.1    3.5e-38  130.9   0.1    1.0  1  cobW          CobW/HypB/UreG, nucleotide-binding domain
     0.0012   18.8   0.1     0.0022   18.0   0.1    1.4  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
     0.0029   17.3   0.1     0.0057   16.3   0.1    1.5  1  SRP54         SRP54-type protein, GTPase domain
     0.0076   16.1   0.0      0.014   15.3   0.0    1.6  1  MobB          Molybdopterin guanine dinucleotide synthesis pr
  ------ inclusion threshold ------
      0.031   14.0   0.6       0.49   10.1   0.0    2.6  3  ATP_bind_1    Conserved hypothetical ATP binding protein
      0.043   13.7   0.5        2.3    8.1   0.0    2.2  2  RsgA_GTPase   RsgA GTPase
      0.078   13.0   0.3       0.27   11.3   0.3    1.9  1  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain
      0.085   11.8   1.1       0.57    9.1   1.1    2.3  1  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
       0.11   12.2   0.0        0.2   11.4   0.0    1.5  1  AAA_30        AAA domain
       0.12   11.8   0.0       0.16   11.4   0.0    1.2  1  KTI12         Chromatin associated protein KTI12
       0.13   12.2   0.0        0.2   11.6   0.0    1.3  1  NACHT         NACHT domain
       0.14   12.1   0.3       0.46   10.5   0.1    1.8  2  AAA_5         AAA domain (dynein-related subfamily)


Domain annotation for each model (and alignments):
>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.9   0.1   2.3e-41   3.5e-38       2     174 ..       3     175 ..       2     178 .. 0.90

  Alignments for each domain:
  == domain 1  score: 130.9 bits;  conditional E-value: 2.3e-41
                                       EEEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCCHCCCT.EEEETTTTECCHCTT-HHHHHHHH CS
                              cobW   2 vtvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaellretgveivelenGciCctlredllkeleal 76 
                                       v++l+GflGsGKT+Ll +l     ++++k+a++vNe ge+++D++ l+++g  +vel  Gc+Cctl+  l+ +l ++
  gi|474934527|ref|YP_007688109.1|   3 VYILGGFLGSGKTSLLMRLAsmFSEKKQKVAILVNESGEIGVDGATLKAQGYDAVELPSGCVCCTLAGTLQTALVNI 79 
                                       789****************988778999************************************************* PP

                                       HHHHTT-SEEEEEECTTTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHH CS
                              cobW  77 eereerldviliEttGlaePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDll 153
                                       +++  ++dv++iE tGla P  v    ++   d   d+++ + D +++++  +k+ee + +q++ +d++++nK+Dl+
  gi|474934527|ref|YP_007688109.1|  80 VNDI-DPDVVIIEPTGLALPHKVKDLVSSADVDEDRDIIIGIADIQRFNDLIKKKEEFFTRQMQGSDFILINKCDLA 155
                                       ****.9*****************33356666688899***********9999************************* PP

                                       CHC..HHHHHHHHHHHHTTS- CS
                              cobW 154 deeallekleerlrqlnpeak 174
                                       ++ +  e+ +++l++  p+++
  gi|474934527|ref|YP_007688109.1| 156 KDGEI-EEATKWLNERFPDKE 175
                                       *9966.666666665555555 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   1.5e-06    0.0022      40      97 ..     121     191 ..      98     194 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.5e-06
                      MMR_HSR1_Xtn  40 vtvDdlidviegnrvYi.pc.....lyvlNKiDlisleeldelare.......pnsvviSaekelnldeLk 97 
                                       ++++++ d i+++ ++  +      ++++NK+Dl+++ e++e ++        ++++++S+++++nld++ 
  gi|474934527|ref|YP_007688109.1| 121 ADIQRFNDLIKKKEEFFtRQmqgsdFILINKCDLAKDGEIEEATKWlnerfpdKEIIPVSVKEGTNLDKVY 191
                                       5567777777665544312212222689******999999999884466887779*************986 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   3.8e-06    0.0057       3      35 ..       3      35 ..       1      39 [. 0.92

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.8e-06
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEE CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllv 35
                                      v++l G+ G+GKT+ l +La +++++++kv++ 
  gi|474934527|ref|YP_007688109.1|  3 VYILGGFLGSGKTSLLMRLASMFSEKKQKVAIL 35
                                      78999*************************985 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   9.4e-06     0.014       5      43 ..       7      45 ..       3     102 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 9.4e-06
                              MobB  5 vgksgsGKTtLleklipelkarglrvgtiKhahhgfdvd 43
                                       g+ gsGKT+Ll +l +++++++ +v+++  ++ ++ vd
  gi|474934527|ref|YP_007688109.1|  7 GGFLGSGKTSLLMRLASMFSEKKQKVAILVNESGEIGVD 45
                                      47889**********************998877666544 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00033      0.49       3      29 ..       8      34 ..       5      37 .. 0.88
   2 ?   -0.1   0.1      0.44   6.6e+02      39      61 ..      97     115 ..      69     148 .. 0.66
   3 ?    0.4   0.0       0.3   4.5e+02     156     182 ..     142     169 ..     110     187 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00033
                        ATP_bind_1  3 GpaGsGKttfvgalseilelrgrsvav 29
                                      G  GsGKt++  +l++++++++++va+
  gi|474934527|ref|YP_007688109.1|  8 GFLGSGKTSLLMRLASMFSEKKQKVAI 34
                                      677*******************99986 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.44
                        ATP_bind_1  39 lpYeaavdirelitledvmedlg 61 
                                       lp +    +++l++ +dv+ed +
  gi|474934527|ref|YP_007688109.1|  97 LPHK----VKDLVSSADVDEDRD 115
                                       4443....678888888888755 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.3
                        ATP_bind_1 156 elPhvvvlnkfDllkek.lekeleffed 182
                                       +    + +nk+Dl+k+   e++ +++++
  gi|474934527|ref|YP_007688109.1| 142 QGSDFILINKCDLAKDGeIEEATKWLNE 169
                                       4445567899999886677777777764 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.027        40     102     129 ..       4      31 ..       2      44 .. 0.76
   2 ?    8.1   0.0    0.0016       2.3      45      93 ..     141     190 ..     103     195 .] 0.74

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.027
                                       EEEECSTTSSHHHHHHHHCTT-----S- CS
                       RsgA_GTPase 102 svlvGqSGvGKStLinallpelelktge 129
                                        +l G  G GK++L+ +l++  + k ++
  gi|474934527|ref|YP_007688109.1|   4 YILGGFLGSGKTSLLMRLASMFSEKKQK 31 
                                       5778889**********99865444444 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0016
                                       TT-EEEEEEE-GGG--HHHHHHHHHHHHHH..TTSEEEE--TTTHTTHHHH CS
                       RsgA_GTPase  45 kgiepvivlnKiDlleeeeeleelkeelea..lgyevllvsaktkegleel 93 
                                        + +  i++nK+Dl+++ e +ee  + l++   + e++ vs+k++++l+++
  gi|474934527|ref|YP_007688109.1| 141 MQGSDFILINKCDLAKDGE-IEEATKWLNErfPDKEIIPVSVKEGTNLDKV 190
                                       5556789************.6666555544114678899999999888876 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3   0.00018      0.27       9      33 ..      11      35 ..       3     189 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00018
                                      TSSHHHHHHHHHHHHHHTT--EEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  9 GvGKTtlaanLaralarrglrVllv 33
                                      G+GKT+l+  La  +++++ +V+ +
  gi|474934527|ref|YP_007688109.1| 11 GSGKTSLLMRLASMFSEKKQKVAIL 35
                                      9****************99999864 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   1.1   0.00038      0.57      34      65 ..       6      37 ..       2     175 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00038
                                      EEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE CS
                              MeaB 34 ltGvPGaGkstlvealglelrrrGkrvavlav 65
                                      l G+ G+Gk  l+ +l+  + ++ ++va+l  
  gi|474934527|ref|YP_007688109.1|  6 LGGFLGSGKTSLLMRLASMFSEKKQKVAILVN 37
                                      56999************************964 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00013       0.2      20     115 ..       3     111 ..       1     122 [. 0.64

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
                            AAA_30  20 vavltGpAGtGKttalkalreaweaag............grviglAptgkaAkvLaeelgieastiakllkrlk... 81 
                                       v +l G  G+GKt +l  l+ ++ +++              v g++ +++  ++++  +g  + t+a  l++     
  gi|474934527|ref|YP_007688109.1|   3 VYILGGFLGSGKTSLLMRLASMFSEKKqkvailvnesgeIGVDGATLKAQGYDAVELPSGCVCCTLAGTLQTALvni 79 
                                       56788999****************99835555555554444455555555555555566667777777664444533 PP

                            AAA_30  82 .grarlepgtllivDEagmvdtkqlaallkaaeka 115
                                        +     + +++i+  +g++  +++++l+++a+ +
  gi|474934527|ref|YP_007688109.1|  80 vN---DIDPDVVIIEPTGLALPHKVKDLVSSADVD 111
                                       21...233377777777777777777777777655 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00011      0.16       5      41 ..       5      41 ..       1      54 [. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                                      EEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH CS
                             KTI12  5 vltGlPssGKstrakeLakaleeekrsvvviddeslg 41
                                      +l G+  sGK+++  +La+ ++e+k++v ++ +es +
  gi|474934527|ref|YP_007688109.1|  5 ILGGFLGSGKTSLLMRLASMFSEKKQKVAILVNESGE 41
                                      7889999***********************9998865 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00013       0.2       3      30 ..       4      31 ..       2      37 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                                      EEEEC-TTTCHHHHHHHHHHHHCTS-SC CS
                             NACHT  3 vilqGeaGsGKTtLlqklalawaegklp 30
                                       il G  GsGKT Ll +la+   e+k++
  gi|474934527|ref|YP_007688109.1|  4 YILGGFLGSGKTSLLMRLASMFSEKKQK 31
                                      5788899*************99998865 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00031      0.46       3      28 ..       5      33 ..       4      40 .. 0.75
   2 ?   -1.3   0.0       1.3   1.9e+03      48      78 ..     124     156 ..     111     171 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00031
                                      EEE--SSSSHHHHHHHGGGGB...S--EE CS
                             AAA_5  3 lLvGppGtgKselaerlaaal...nreve 28
                                      +L G  G+gK++l +rla+++   +++v 
  gi|474934527|ref|YP_007688109.1|  5 ILGGFLGSGKTSLLMRLASMFsekKQKVA 33
                                      678889***************76333333 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.3
                                       ...........--------G-SEEEEESGGG-- CS
                             AAA_5  48 k..ngttslvdsplvraaregeilvlDEverae 78 
                                       +  n+  + ++  ++r+++ ++ ++++  + a+
  gi|474934527|ref|YP_007688109.1| 124 QrfNDLIKKKEEFFTRQMQGSDFILINKCDLAK 156
                                       444555555566666777755555555444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1292.23
//
Query:       gi|474934528|ref|YP_007688110.1|  [L=209]
Description: hypothetical protein TALC_00956 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       878  (0.0489709); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1439.93
//
Query:       gi|474934529|ref|YP_007688111.1|  [L=269]
Description: YqaJ viral recombinase family [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-06   27.3   0.0    6.4e-06   26.4   0.0    1.4  1  YqaJ      YqaJ-like viral recombinase domain
  ------ inclusion threshold ------
      0.087   12.7   0.0        3.8    7.5   0.0    2.5  2  DUF1748   Fungal protein of unknown function (DUF1748)


Domain annotation for each model (and alignments):
>> YqaJ  YqaJ-like viral recombinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   7.1e-10   6.4e-06       5     140 ..      24     170 ..      21     176 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 7.1e-10
                              YqaJ   5 aRrkgisaSdfaaalgtsrvsdsvrllldkvgtaiaeehefkenaftawGtelEplaraeyelatgdkvrd...... 75 
                                        R+k i++++++a+lg+s  s+++++ l+++         +  n+f   G+ lEp++r  y +++  kv+       
  gi|474934529|ref|YP_007688111.1|  24 YRKKKITGTKLGAILGVSDFSTPFKVALELARI----YPGDPPNKFIDAGNILEPKIRS-YVRKNASKVAAmmglpd 95 
                                       599***************************999....4456789*************97.66666669998566666 PP

                              YqaJ  76 .sgglfespsdkflgaspDgiishasid..........alkrrllEikspfealyvstklgrqe....eipeeYmcQ 137
                                        ++ ++e+   +   + +D   ++   +           +++ +lEik+       + k+++++    ++pe+Y++Q
  gi|474934529|ref|YP_007688111.1|  96 gTQVIIEE-PVDKETCGYDHFHDNSTFGglvdgyvaygEKRKAILEIKTSHD----REKWLDEDgnytKVPESYILQ 167
                                       54444444.33334455555555544448888888888889*******9987....66676666667799******* PP

                              YqaJ 138 iqg 140
                                          
  gi|474934529|ref|YP_007688111.1| 168 AGL 170
                                       865 PP

>> DUF1748  Fungal protein of unknown function (DUF1748)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.012   1.1e+02      31      51 ..     112     133 ..      43     137 .. 0.90
   2 ?    7.5   0.0   0.00043       3.8      35      52 ..     216     235 ..     200     251 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.012
                           DUF1748  31 sdkitd.kdikkwvdkYLgvGE 51 
                                       +d+++d +++  +vd Y  +GE
  gi|474934529|ref|YP_007688111.1| 112 YDHFHDnSTFGGLVDGYVAYGE 133
                                       788889899************9 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00043
                           DUF1748  35 td..kdikkwvdkYLgvGEw 52 
                                       ++  kd+++w ++Y++vGE+
  gi|474934529|ref|YP_007688111.1| 216 SEpmKDAEEWYHEYIDVGET 235
                                       44469*************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1836.91
//
Query:       gi|474934530|ref|YP_007688112.1|  [L=265]
Description: Short-chain dehydrogenase of various substrate specificities [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-49  167.6   0.0    2.7e-49  167.3   0.0    1.1  1  adh_short       short chain dehydrogenase
    1.3e-33  116.5   0.0    1.7e-33  116.2   0.0    1.1  1  adh_short_C2    Enoyl-(Acyl carrier protein) reductase
    5.2e-11   42.8   0.0    7.3e-11   42.3   0.0    1.2  1  KR              KR domain
    0.00033   20.2   0.1     0.0014   18.2   0.0    1.9  2  Epimerase       NAD dependent epimerase/dehydratase family
  ------ inclusion threshold ------
      0.015   15.2   0.0      0.023   14.6   0.0    1.5  1  NAD_binding_10  NAD(P)H-binding
      0.017   15.4   0.1       0.13   12.5   0.1    2.1  2  TrkA_N          TrkA-N domain
      0.034   13.3   0.0      0.051   12.7   0.0    1.2  1  RmlD_sub_bind   RmlD substrate binding domain
      0.084   12.4   0.1       0.15   11.6   0.1    1.4  1  NmrA            NmrA-like family
      0.089   12.2   0.0       0.14   11.6   0.0    1.2  1  GDP_Man_Dehyd   GDP-mannose 4,6 dehydratase


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.3   0.0   1.3e-52   2.7e-49       3     192 ..       5     195 ..       3     198 .. 0.98

  Alignments for each domain:
  == domain 1  score: 167.3 bits;  conditional E-value: 1.3e-52
                                       EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT.TSEEEEEE-TTTSHHHHHHHHHHHHHHHSSE CS
                         adh_short   3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee.gakalaiqvDvtdreevealvekavkklgkl 78 
                                       +l+tGassGIG+ ia+ lakeG+++v+v+r+ + l ++ +e++ + + k+ +i +D+++  ++e+++++a++   ++
  gi|474934530|ref|YP_007688112.1|   5 ALITGASSGIGKSIARLLAKEGWNLVLVGRNHQVLDALRSEFNVLnEVKIKIIDADLAEDGAAEQVFREAEEFGISI 81 
                                       89*****************************************999************************88889** PP

                                       SEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHH CS
                         adh_short  79 dvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaa 155
                                       d+Lvn+AG    g f+e + ++  ++i+vN  ++ lltr +lp m++++sG+I nv+Sva+++p + +++Y AsKa+
  gi|474934530|ref|YP_007688112.1|  82 DLLVNCAGFGDLGLFAECDPKKQAEMIHVNDISLTLLTRYFLPGMIERRSGKILNVASVASFQPGPLMSVYYASKAF 158
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHCT CS
                         adh_short 156 vagltrslakelaptgirvnavaPGlvdTdmakelre 192
                                       v ++t++l  el+ tg++v+a++PG+++T +a+++++
  gi|474934530|ref|YP_007688112.1| 159 VLSFTEALDVELRGTGVTVSALCPGPTNTRFAETANA 195
                                       ******************************9998876 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.2   0.0   8.3e-37   1.7e-33       1     186 [.       9     197 ..       9     211 .. 0.89

  Alignments for each domain:
  == domain 1  score: 116.2 bits;  conditional E-value: 8.3e-37
                                       TTTTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSE.E..EE--TTSHHHHHHHHHHHHHHHSSEEEEE CS
                      adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneeakkrveelaeelgae.v..lecDVtdeeqvealveevvekfgklDilv 74 
                                       Ga sgIG+ iA++la+eG+++vl+ +n +  +++++  + l++  +  + +D +++ + e++++e++e   ++D lv
  gi|474934530|ref|YP_007688112.1|   9 GASSGIGKSIARLLAKEGWNLVLVGRNHQVLDALRSEFNVLNEVkIkiIDADLAEDGAAEQVFREAEEFGISIDLLV 85 
                                       899**************************9555554443333223345*******************999******* PP

                                       E-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC.CEEEEEEEGGGTSBSTTTTHHHHHHHHHH CS
                      adh_short_C2  75 nnagiapklkgpfletsreefdraldvnlyslfllakaalp.lmkeg.gsivnlssvgaervvpnynaygaaKaale 149
                                       n+ag+ +   g f+e++ ++ +++++vn  sl+ll++++lp +++++ g+i+n++sv++ +  p  ++y a+Ka + 
  gi|474934530|ref|YP_007688112.1|  86 NCAGFGDL--GLFAECDPKKQAEMIHVNDISLTLLTRYFLPgMIERRsGKILNVASVASFQPGPLMSVYYASKAFVL 160
                                       ********..*******************************8776667***************************** PP

                                       HHHHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTTHH CS
                      adh_short_C2 150 altrylAvelgpkgiRvNavspgpikTlaasgikgfd 186
                                       ++t +l vel   g++v a +pgp++T+ a+ ++ + 
  gi|474934530|ref|YP_007688112.1| 161 SFTEALDVELRGTGVTVSALCPGPTNTRFAETANATG 197
                                       ****************************999887644 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.0   3.7e-14   7.3e-11       4     160 ..       6     163 ..       4     179 .. 0.87

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 3.7e-14
                                       EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS CS
                                KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeep 80 
                                       litG+  g+G+++ar la++g  +lvl++R++++ ++ +++++ l++  +++++++aD+++  a e++++e+++ + 
  gi|474934530|ref|YP_007688112.1|   6 LITGASSGIGKSIARLLAKEGW-NLVLVGRNHQVLDALRSEFNVLNE--VKIKIIDADLAEDGAAEQVFREAEEFGI 79 
                                       9*******************96.8*******9999998888888876..9***********************999* PP

                                       ---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEEEHHHHH--TT-HHHHHHH CS
                                KR  81 pikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled....esldffvlfSSiagllgsagqanYaaaN 153
                                       +i   +++Ag+ + +l++e++ ++ +++++     +  L +++ +    ++   ++ ++S+a++   +  + Y a  
  gi|474934530|ref|YP_007688112.1|  80 SIDLLVNCAGFGDLGLFAECDPKKQAEMIHVNDISLTLLTRYFLPgmieRRSGKILNVASVASFQPGPLMSVYYASK 156
                                       *************************9999998888888888887766656666778888888888888888888877 PP

                                       HHHHHHH CS
                                KR 154 aflDala 160
                                       af+ ++ 
  gi|474934530|ref|YP_007688112.1| 157 AFVLSFT 163
                                       7776665 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0     7e-07    0.0014       1      63 [.       5      74 ..       5     100 .. 0.71
   2 ?   -0.6   0.0      0.38   7.5e+02     163     202 ..     186     228 ..     138     233 .. 0.50

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 7e-07
                                      EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC............EEEE--TT-HHHHHHHHHHH CS
                         Epimerase  1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl............elveldltdrsalerlfkee 63
                                      +l+tGa+  iG+ +++ l+++g++++ + r+ +       + l            +++++dl ++ a e++f+e 
  gi|474934530|ref|YP_007688112.1|  5 ALITGASSGIGKSIARLLAKEGWNLVLVGRNHQVL-----DALrsefnvlnevkiKIIDADLAEDGAAEQVFREA 74
                                      59********************8866555552221.....112222344666667**************999975 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.38
                                       EEEEEEESEEESTT...S-TTS.TTSHHHHHHHHHHTTSSSEEE CS
                         Epimerase 163 naiilrlfnlyGpr...ngege.vsrvipalirkilegkqevtl 202
                                       n+      n  G++   +  +  ++ + ++ irk+ +gk  +++
  gi|474934530|ref|YP_007688112.1| 186 NTRFAETANATGKNvfkQSSSAdPDAIAAYGIRKAMRGK-VIIV 228
                                       344444445555555542222235555555666666666.5555 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.2e-05     0.023       1      61 [.       9      74 ..       9     217 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.2e-05
                                      TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHH......CTTTCEEEE--TT-CCHHHHHHTT- CS
                    NAD_binding_10  1 GAtGkvGrllvkellargghevtalvRnpeklaele......aeeglevvegdvtdvedlaealkga 61
                                      GA+ ++G+ +++ l+++ g++++++ Rn + l++l+      +e +++++++d+ +  + +++++ a
  gi|474934530|ref|YP_007688112.1|  9 GASSGIGKSIARLLAKE-GWNLVLVGRNHQVLDALRsefnvlNEVKIKIIDADLAEDGAAEQVFREA 74
                                      9***********99999.5*********998886653333445679999999999998888888843 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   6.4e-05      0.13       8      42 ..      13      49 ..       5      70 .. 0.80
   2 ?    0.3   0.0       0.4     8e+02      31      65 ..     187     224 ..     185     239 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.4e-05
                                      HHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTT..S CS
                            TrkA_N  8 rvGrslaeeLseggkdvvvidkdeerveelreeg..l 42
                                       +G+s+a+ L ++g++ v++ +++++++ lr e+  l
  gi|474934530|ref|YP_007688112.1| 13 GIGKSIARLLAKEGWNLVLVGRNHQVLDALRSEFnvL 49
                                      59**********8889**************9988643 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.4
                                       HHHHHHHHHTTSEEEE.S-TTSHHHHHHTTGGGES..E CS
                            TrkA_N  31 eerveelreeglevvv.gdatdeevLeeagiekad..a 65 
                                        + +e++ + g +v++  + +d++++++ gi ka    
  gi|474934530|ref|YP_007688112.1| 187 TRFAETANATGKNVFKqSSSADPDAIAAYGIRKAMrgK 224
                                       56677888888775553788999999999999996543 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.5e-05     0.051       3      64 ..       5      93 ..       3     118 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.5e-05
                                      EEEESTTSHHHHHHHHHCTTTSEEEEEE-TT......................T--TTSHHHHHHHHHHH-.....-SE CS
                     RmlD_sub_bind  3 ilvtGanGqlGseLakqlaeeglevlaltre......................eldltdaeavaellkeak.....pdv 54
                                       l+tGa+  +G+ +a++la+eg++++ ++r+                      ++dl++  a++++++ea+      d+
  gi|474934530|ref|YP_007688112.1|  5 ALITGASSGIGKSIARLLAKEGWNLVLVGRNhqvldalrsefnvlnevkikiiDADLAEDGAAEQVFREAEefgisIDL 83
                                      69**************************999999999999999999999999999999999999999876422222689 PP

                                      EEE------H CS
                     RmlD_sub_bind 55 vvnaAAytav 64
                                      +vn+A + + 
  gi|474934530|ref|YP_007688112.1| 84 LVNCAGFGDL 93
                                      9999988765 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   7.5e-05      0.15       2      66 ..       6      75 ..       5      83 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.5e-05
                                      EESSTTSHHHHHHHHHHHHHT-EEEEEES-S.....-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-S CS
                              NmrA  2 lviGaTGrqGksvvrallkaghkvralvRdt.....kselakslkeaGvelvkgdlddkeslvealkgvd 66
                                      l++Ga+  +Gks++r l+k+g++   + R+       + + + l+e   +++ +dl ++   ++++++++
  gi|474934530|ref|YP_007688112.1|  6 LITGASSGIGKSIARLLAKEGWNLVLVGRNHqvldaLRSEFNVLNEVKIKIIDADLAEDGAAEQVFREAE 75
                                      799***************************9998887888899999999999****99999999999987 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   6.8e-05      0.14       1      74 [.       6      74 ..       6      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.8e-05
                                      EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHH CS
                     GDP_Man_Dehyd  1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaev 74
                                      LiTG +  iG  +a+lL ++g + + + r+++ +++ r e      ++ +e ++k++ +Dl +  + e++++e+
  gi|474934530|ref|YP_007688112.1|  6 LITGASSGIGKSIARLLAKEGWNLVLVGRNHQVLDALRSE-----FNVLNEVKIKIIDADLAEDGAAEQVFREA 74
                                      9***********************9998887776655554.....333345689*****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1672.02
//
Query:       gi|474934531|ref|YP_007688113.1|  [L=606]
Description: indolepyruvate ferredoxin oxidoreductase, alpha subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-28   98.8   0.4    5.1e-28   97.8   0.4    1.5  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    8.5e-12   45.3   0.0    1.4e-11   44.6   0.0    1.3  1  POR_N         Pyruvate flavodoxin/ferredoxin oxidoreductase, 
      2e-07   30.8  18.3    3.9e-05   23.5   3.3    3.1  3  Fer4_6        4Fe-4S binding domain
    5.2e-07   29.2  18.4    5.6e-07   29.1   4.0    3.2  3  Fer4          4Fe-4S binding domain
    2.6e-06   27.4  12.0    2.6e-06   27.4  12.0    2.2  3  Fer4_10       4Fe-4S dicluster domain
    5.4e-06   26.4  12.5    1.6e-05   24.9  12.5    1.9  1  Fer4_21       4Fe-4S dicluster domain
    8.8e-06   25.8  12.8    8.8e-06   25.8  12.8    1.9  1  Fer4_9        4Fe-4S dicluster domain
      3e-05   24.5  14.7      0.001   19.6   3.6    2.9  3  Fer4_7        4Fe-4S dicluster domain
      3e-05   23.7   0.5      0.001   18.7   0.1    2.2  2  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
     0.0044   17.0  20.0     0.0048   16.9   3.7    3.0  3  Fer4_2        4Fe-4S binding domain
  ------ inclusion threshold ------
      0.011   15.9   7.7      0.037   14.2   7.7    1.9  1  Fer4_18       4Fe-4S dicluster domain
      0.018   14.8   0.6       0.18   11.5   0.1    2.2  2  Transket_pyr  Transketolase, pyrimidine binding domain
      0.019   15.9   3.2      0.019   15.9   3.2    2.6  2  Fer4_16       4Fe-4S double cluster binding domain
       0.07   13.6  14.0         26    5.4  14.0    2.8  1  Fer4_8        4Fe-4S dicluster domain
       0.42   11.2  14.3      0.049   14.2   2.6    2.8  3  Fer4_17       4Fe-4S dicluster domain
       0.66   10.6  11.7        0.4   11.3   3.5    2.6  2  Fer4_13       4Fe-4S single cluster domain of Ferredoxin I
          3    8.7  11.6       0.27   12.1   3.8    2.4  2  Fer4_22       4Fe-4S dicluster domain
        8.6    7.2  14.1       0.21   12.4   1.9    3.1  3  Fer4_15       4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.8   0.4   5.2e-31   5.1e-28       1     151 [.     389     529 ..     389     531 .. 0.96

  Alignments for each domain:
  == domain 1  score: 97.8 bits;  conditional E-value: 5.2e-31
                                       ESSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEE CS
                      TPP_enzyme_C   1 diGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpit 76 
                                       diGc+tl      +v++p ++ +  +  +mG g +aA G + a  d++ +a++GD++f+++ ++ l  a  ++++i+
  gi|474934531|ref|YP_007688113.1| 389 DIGCYTL------GVQPPFRTAD--FIICMGGGAGAAGGFAQA-TDQKPIAFIGDSTFFHSgVPPLTSALFNHHNIV 456
                                       89*****......99***99888..****************98.588****************************** PP

                                       EEEEE-SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEEEE CS
                      TPP_enzyme_C  77 vvvlnNegygmtggqqepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpali 151
                                       +v+l+N++++mtg+q++p +g+++ g +   ++ vd++ l++++G+k + +v++++v+e  +++k+a++ +g+a++
  gi|474934531|ref|YP_007688113.1| 457 MVILDNRTTAMTGHQPNPGTGRHFGGID---TDAVDIESLVKGIGIKfVETVDPYKVKECVDVMKRAIAFDGVAVV 529
                                       *********************9999888...9***************888************************99 PP

>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   0.0   1.4e-14   1.4e-11       2     172 ..      22     187 ..      21     223 .. 0.85

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 1.4e-14
                                       HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCC CS
                             POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmien 78 
                                       + ++agv++++ YP TPsse+++ l+el ++ ++   ++    +E  a+++ + Aa +G+r++++    Gl  + + 
  gi|474934531|ref|YP_007688113.1|  22 GLFEAGVKFASTYPGTPSSEVGNLLEELSERAGM---YFEFSSNEKTAMEVSAAAASSGVRSFVFMKHVGLNAAADP 95 
                                       67899************************99996...8888899*****************************9999 PP

                                       HHHHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHHS---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEEEEEEH CS
                             POR_N  79 lglaageelPvvivvvaRalpstglsirtdqsDlmaardtglivlasenvqeafdlalvAfnlAekvrvPvivlfDg 155
                                       l+    + +   + ++    ps   s +++q   ++a    + ++ ++n qea d+++ A+ ++e++ +Pv+  +  
  gi|474934531|ref|YP_007688113.1|  96 LMTLTYAGVRGGMLIMSADDPSA-HSSQNEQDNRYYATLALMPMVEPSNPQEAKDFIAPAYEISENLGLPVLFRTTT 171
                                       98776666665555555555555.899*******************************************9877765 PP

                                       HHH.HEEEEEEC-SGG. CS
                             POR_N 156 fllshevekvelpdeed 172
                                        +  h++  v+l +  +
  gi|474934531|ref|YP_007688113.1| 172 RVN-HARGVVTLGKIRN 187
                                       555.9888888766654 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.4       4.2   4.1e+03       6      12 ..     360     366 ..     360     366 .. 0.90
   2 !   17.0   1.5   4.7e-06    0.0047       2      21 ..     550     571 ..     549     575 .. 0.93
   3 !   23.5   3.3   3.9e-08   3.9e-05       2      24 .]     580     602 ..     579     602 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 4.2
                            Fer4_6   6 pdkCigC 12 
                                       p++C gC
  gi|474934531|ref|YP_007688113.1| 360 PSLCAGC 366
                                       799**** PP

  == domain 2  score: 17.0 bits;  conditional E-value: 4.7e-06
                            Fer4_6   2 veidpdkCigCgdC..vrvCPe 21 
                                       +++d +kC+ C+ C  +++CP+
  gi|474934531|ref|YP_007688113.1| 550 ATVDVSKCVKCYTClkMIACPA 571
                                       79*******************7 PP

  == domain 3  score: 23.5 bits;  conditional E-value: 3.9e-08
                            Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                       v+ dp+ CigCg C++vCP ++i
  gi|474934531|ref|YP_007688113.1| 580 VQTDPSQCIGCGMCADVCPKKVI 602
                                       6679***************8876 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.2       6.6   6.6e+03       5      11 ..     360     366 ..     360     366 .. 0.86
   2 !    8.9   2.0    0.0013       1.3       2      15 ..     551     564 ..     550     571 .. 0.89
   3 !   29.1   4.0   5.6e-10   5.6e-07       2      24 .]     581     603 ..     580     603 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 6.6
                                       TTTSSS- CS
                              Fer4   5 eekCigC 11 
                                       +++C gC
  gi|474934531|ref|YP_007688113.1| 360 PSLCAGC 366
                                       689*999 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0013
                                       EEETTTSSS-THHH CS
                              Fer4   2 videekCigCGaCv 15 
                                       ++d +kC++C +C 
  gi|474934531|ref|YP_007688113.1| 551 TVDVSKCVKCYTCL 564
                                       79***********6 PP

  == domain 3  score: 29.1 bits;  conditional E-value: 5.6e-10
                                       EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                       + d++ CigCG C++vCP  +I+
  gi|474934531|ref|YP_007688113.1| 581 QTDPSQCIGCGMCADVCPKKVIE 603
                                       679***************99986 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.5       9.7   9.7e+03      19      46 ..     366     388 ..     361     392 .. 0.61
   2 ?   -2.6   0.0       6.5   6.4e+03      29      48 ..     497     516 ..     492     534 .. 0.66
   3 !   27.4  12.0   2.6e-09   2.6e-06       3      56 .]     551     598 ..     549     598 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 9.7
                           Fer4_10  19 CPadltsvgakgeaseeeavrkkvekCt 46 
                                       CP      ++ ++a+++++ ++ v  C 
  gi|474934531|ref|YP_007688113.1| 366 CPH-----RGMYAATKKAVGNTPVVYCS 388
                                       777.....66666666666666666665 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6.5
                           Fer4_10  29 kgeaseeeavrkkvekCtgc 48 
                                       +g++  e ++  kv++C ++
  gi|474934531|ref|YP_007688113.1| 497 IGIKFVETVDPYKVKECVDV 516
                                       55666667777788888764 PP

  == domain 3  score: 27.4 bits;  conditional E-value: 2.6e-09
                           Fer4_10   3 vidddtCirCgkCvk..aCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                        +d ++C++C +C k  aCPa          + e+++v++++++C+gcg+C+++CP
  gi|474934531|ref|YP_007688113.1| 551 TVDVSKCVKCYTCLKmiACPA--------LVKQEDGTVQTDPSQCIGCGMCADVCP 598
                                       57899********99667***........9999**********************9 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9  12.5   1.6e-08   1.6e-05       1      58 [.     550     603 ..     550     604 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.6e-08
                           Fer4_21   1 AridedkCigCgkC..liaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58 
                                       A++d +kC++C  C  +iaC+     a+ ++++ ++++  ++C+GC +C++vCP +++ie
  gi|474934531|ref|YP_007688113.1| 550 ATVDVSKCVKCYTClkMIACP-----ALVKQEDGTVQTDPSQCIGCGMCADVCP-KKVIE 603
                                       78999*********4447888.....8999999999******************.67776 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8  12.8   8.8e-09   8.8e-06       1      51 []     556     602 ..     556     602 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 8.8e-09
                            Fer4_9   1 kCtgCgaC..veaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       kC++C +C  + aCpa v +ed   +++        +CigCg C+++Cpk++i
  gi|474934531|ref|YP_007688113.1| 556 KCVKCYTClkMIACPALVKQEDGTVQTDPS------QCIGCGMCADVCPKKVI 602
                                       7*******55456**************997......7*************976 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   4.3     0.012        12      27      50 ..     546     571 ..     511     573 .. 0.78
   2 !   19.6   3.6     1e-06     0.001      26      51 ..     575     600 ..     570     601 .. 0.82
   3 !   19.0   3.4   1.6e-06    0.0015       1      19 [.     586     604 ..     586     606 .] 0.90

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.012
                            Fer4_7  27 gtekveidpekClgCgaCva..vCPt 50 
                                        ++++++d +kC+ C+ C +  +CP+
  gi|474934531|ref|YP_007688113.1| 546 AKRSATVDVSKCVKCYTCLKmiACPA 571
                                       346889************88778985 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 1e-06
                            Fer4_7  26 kgtekveidpekClgCgaCvavCPtg 51 
                                       ++  +v+ dp++C+gCg+C++vCP++
  gi|474934531|ref|YP_007688113.1| 575 QEDGTVQTDPSQCIGCGMCADVCPKK 600
                                       445689999***************87 PP

  == domain 3  score: 19.0 bits;  conditional E-value: 1.6e-06
                            Fer4_7   1 rCigCgaCvaaCpvkaiel 19 
                                       +CigCg C+++Cp k+ie+
  gi|474934531|ref|YP_007688113.1| 586 QCIGCGMCADVCPKKVIEV 604
                                       6***************987 PP

>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1     1e-06     0.001       3     146 ..      15     157 ..      13     182 .. 0.75
   2 ?    3.1   0.0     0.063        62      50     105 ..     412     467 ..     410     523 .. 0.63

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1e-06
                                       HHHHHHHHHHHCT--EEEE---CCCHH...HHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHH.H CS
                      TPP_enzyme_N   3 vaealvraLkalgvehvfgvpGsrilp...lldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgp.G 75 
                                       + ea+ r L ++gv+ + ++pG+ + +   ll++lse+ g+ +  +++E +a+    + a +  +  v++ ++g  +
  gi|474934531|ref|YP_007688113.1|  15 GNEAITRGLFEAGVKFASTYPGTPSSEvgnLLEELSERAGMYFEFSSNEKTAMEVSAAAASSGVRSFVFMKHVGLnA 91 
                                       5789999***************98887334777778887********************999999999999999878 PP

                                       HHHCHHHHHHHHHHT--EEEEEEE--CCCHHS..TC--T.-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHH CS
                      TPP_enzyme_N  76 atnaltalaeAkvdriPllvlsgdrptslrgqgvlqqel.dqlalfrpvtkyaervtspeelpealrrAirt 146
                                       a+  l+ l  A v +  +l++s+d p+++ +q+ + +     lal  p++    ++++p+e++  ++ A+++
  gi|474934531|ref|YP_007688113.1|  92 AADPLMTLTYAGVRG-GMLIMSADDPSAHSSQNEQDNRYyATLAL-MPMV----EPSNPQEAKDFIAPAYEI 157
                                       889999998888766.67788888888888855555333333333.3443....555555555555555554 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.063
                                       HHHHHHHHHHHHH.TS-EEEEE-CHHHHHHCHHHHHHHHHHT--EEEEEEE--CCCH CS
                      TPP_enzyme_N  50 gaafaAdgyarat.gkpgvvlvtsgpGatnaltalaeAkvdriPllvlsgdrptslr 105
                                       g a+aA g+a+at +kp +++  s+  + ++++ l +A  ++  ++++  d+ t+  
  gi|474934531|ref|YP_007688113.1| 412 GGAGAAGGFAQATdQKPIAFIGDST-FFHSGVPPLTSALFNHHNIVMVILDNRTTAM 467
                                       6799*********899999888874.4666666666666666666555555555444 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.4       8.4   8.4e+03       9      13 ..     362     366 ..     359     368 .. 0.64
   2 !   10.5   2.4   0.00051      0.51       3      22 .]     550     571 ..     548     571 .. 0.84
   3 !   16.9   3.7   4.9e-06    0.0048       4      21 ..     581     598 ..     579     599 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 8.4
                            Fer4_2   9 rCigC 13 
                                        C gC
  gi|474934531|ref|YP_007688113.1| 362 LCAGC 366
                                       56666 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00051
                            Fer4_2   3 vvvdtdrCigCgaCv..saCPa 22 
                                       + vd  +C+ C +C+   aCPa
  gi|474934531|ref|YP_007688113.1| 550 ATVDVSKCVKCYTCLkmIACPA 571
                                       57999*********75588**8 PP

  == domain 3  score: 16.9 bits;  conditional E-value: 4.9e-06
                            Fer4_2   4 vvdtdrCigCgaCvsaCP 21 
                                       + d+  CigCg C ++CP
  gi|474934531|ref|YP_007688113.1| 581 QTDPSQCIGCGMCADVCP 598
                                       679999***********9 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   7.7   3.7e-05     0.037      53      97 ..     549     599 ..     538     606 .] 0.75

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.7e-05
                           Fer4_18  53 rkekgagdcidcescvkv..cPtgidirkGl.ql...eciscllcidacdk 97 
                                        ++ ++++c++c +c+k+  cP  +   +G  q    +ci c+ c d c k
  gi|474934531|ref|YP_007688113.1| 549 SATVDVSKCVKCYTCLKMiaCPALVKQEDGTvQTdpsQCIGCGMCADVCPK 599
                                       44567899*******98555*********963543337***********65 PP

>> Transket_pyr  Transketolase, pyrimidine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00018      0.18      16     161 ..       5     158 ..       1     174 [. 0.82
   2 ?    1.3   0.1      0.23   2.3e+02      47     168 ..     400     529 ..     368     533 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00018
                                       HHCTTTTEEEEESSTHHHHTTCHCCHHEGGT.................TEGEEE--S-HHHHHHHHHHHHHHCTTEE CS
                      Transket_pyr  16 llkedpevvligaDvaggtfsvrkgllhdqg.................egrvidsgisEqavlgfavGaalagpllv 75 
                                       l++ +++++l+ +++++g f +  +     +                 +g +++++  E+ ++ + ++aa +g    
  gi|474934531|ref|YP_007688113.1|   5 LAESGKQLLLGNEAITRGLFEAGVKFASTYPgtpssevgnlleelserAGMYFEFSSNEKTAMEVSAAAASSG---- 77 
                                       6788889999999999888876666655555668889999999999999999**********99999999999.... PP

                                       EEEEEEHHHHGGGHHGGHHHHHCHHHHHT--EEEEESBSGGGSTTGTTTSBSSHHHHHHTSTTEEEE--SSHHHHHH CS
                      Transket_pyr  76 iveaqFgdFangAqiyadqairsgeakgklkvgvvtrlpigvgedGpehqsaeleaflrlipglkvvrPsdpaetkh 152
                                       +  + F+  +      + +a   ++++  + v   ++ +   + ++ + q  ++ +++++++ + +v Ps+p+e+k 
  gi|474934531|ref|YP_007688113.1|  78 VRSFVFMKHVG----LNAAADP-LMTLTYAGVRGGMLIMSADDPSAHSSQNEQDNRYYATLALMPMVEPSNPQEAKD 149
                                       67778888888....6666666.99********99999998888888888899***********************9 PP

                                       HHHHHHHSS CS
                      Transket_pyr 153 llrrairre 161
                                        +  a++ +
  gi|474934531|ref|YP_007688113.1| 150 FIAPAYEIS 158
                                       999888864 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.23
                                       TEGEEE--S-HHHHHHHHHHHHHHCTTEEEEEEEEHHHHGGG......HHGGHHHHHCHHHHHT--EEEEESBSG.. CS
                      Transket_pyr  47 egrvidsgisEqavlgfavGaalagpllviveaqFgdFangA......qiyadqairsgeakgklkvgvvtrlpi.. 115
                                       ++r  d+ i+  + +g+a G+a a  +++i+ +  ++F+  +       ++++  i+ ++ + ++++ ++ + p   
  gi|474934531|ref|YP_007688113.1| 400 PFRTADFIICMGGGAGAAGGFAQATDQKPIAFIGDSTFFHSGvppltsALFNHHNIV-MVILDNRTTAMTGHQPNpg 475
                                       447777777777777777777766666677777777777755666666666666666.7777777777777766422 PP

                                       .GGSTTGTTTSBSSHHHHHHTSTT...EEEE--SSHHHHHHHHHHHHHSSS.SEEEE CS
                      Transket_pyr 116 .gvgedGpehqsaeleaflrlipg...lkvvrPsdpaetkhllrrairredrkPvvl 168
                                        g ++ G    ++ +e++ + i g   + +v P+   e+  +++rai+  +++  v+
  gi|474934531|ref|YP_007688113.1| 476 tGRHFGGIDTDAVDIESLVKGI-GikfVETVDPYKVKECVDVMKRAIA--FDGVAVV 529
                                       2334445556666666666655.3244556666666666677888888..6444444 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   3.1       1.8   1.8e+03       1      14 [.     556     571 ..     556     586 .. 0.74
   2 ?   15.9   3.2   1.9e-05     0.019       1      19 [.     586     604 ..     586     606 .] 0.89

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.8
                           Fer4_16   1 rCgtCgkCae..vCPt 14 
                                       +C++C  C++  +CP+
  gi|474934531|ref|YP_007688113.1| 556 KCVKCYTCLKmiACPA 571
                                       5*******98557986 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.9e-05
                           Fer4_16   1 rCgtCgkCaevCPtnaike 19 
                                       +C++Cg Ca+vCP ++i+ 
  gi|474934531|ref|YP_007688113.1| 586 QCIGCGMCADVCPKKVIEV 604
                                       5**************9985 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4  14.0     0.026        26       2      65 .]     554     601 ..     553     601 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.026
                            Fer4_8   2 lekCieCgaCqsa..CpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvgi 65 
                                       ++kC++C  C ++  Cp+l ++         e    vq++          +C +cg+C++vCp+++
  gi|474934531|ref|YP_007688113.1| 554 VSKCVKCYTCLKMiaCPALVKQ---------EDGT-VQTDP--------SQCIGCGMCADVCPKKV 601
                                       6788888888866668755444.........2222.44444........59************986 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   2.5      0.16   1.6e+02      42      58 ..     553     571 ..     536     574 .. 0.68
   2 ?    2.2   2.5      0.27   2.7e+02       1      17 [.     556     574 ..     556     584 .. 0.77
   3 ?   14.2   2.6   4.9e-05     0.049      43      59 ..     584     600 ..     571     602 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.16
                           Fer4_17  42 kaslCieCgeCe..rkCPq 58 
                                        +s+C++C  C    +CP+
  gi|474934531|ref|YP_007688113.1| 553 DVSKCVKCYTCLkmIACPA 571
                                       5677777777775556764 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.27
                           Fer4_17   1 rCiqCgyClp..eCpsyea 17 
                                       +C +C  Cl+  +Cp + +
  gi|474934531|ref|YP_007688113.1| 556 KCVKCYTCLKmiACPALVK 574
                                       5999999999777887665 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 4.9e-05
                           Fer4_17  43 aslCieCgeCerkCPqg 59 
                                        s+Ci+Cg+C+ +CP++
  gi|474934531|ref|YP_007688113.1| 584 PSQCIGCGMCADVCPKK 600
                                       57899999999999986 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   1.2      0.11   1.1e+02       1      15 [.     552     566 ..     552     579 .. 0.80
   2 ?   11.3   3.5    0.0004       0.4       2      18 ..     583     599 ..     582     600 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.11
                           Fer4_13   1 VDrdtCiacgaCvel 15 
                                       VD ++C+ c +C ++
  gi|474934531|ref|YP_007688113.1| 552 VDVSKCVKCYTCLKM 566
                                       8999********875 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0004
                           Fer4_13   2 DrdtCiacgaCvelaPd 18 
                                       D ++Ci+cg C++++P+
  gi|474934531|ref|YP_007688113.1| 583 DPSQCIGCGMCADVCPK 599
                                       779*************6 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   2.1       2.1   2.1e+03      77      91 ..     552     566 ..     538     573 .. 0.61
   2 ?   12.1   3.8   0.00027      0.27      69      95 ..     574     600 ..     568     601 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 2.1
                           Fer4_22  77 fgesgCvGCgRCiea 91 
                                       ++ s+Cv C  C ++
  gi|474934531|ref|YP_007688113.1| 552 VDVSKCVKCYTCLKM 566
                                       466677777777553 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00027
                           Fer4_22  69 klsefkekfgesgCvGCgRCieacpvk 95 
                                       k ++ + +++ s+C+GCg C ++cp+k
  gi|474934531|ref|YP_007688113.1| 574 KQEDGTVQTDPSQCIGCGMCADVCPKK 600
                                       556667788999*************97 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       5.5   5.5e+03      13      33 ..     512     530 ..     510     542 .. 0.81
   2 ?    2.2   1.3      0.31     3e+02       2      27 ..     551     577 ..     550     583 .. 0.76
   3 ?   12.4   1.9   0.00021      0.21       2      20 ..     581     599 ..     580     605 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 5.5
                           Fer4_15  13 lCvaeapevfeldedglasvl 33 
                                        Cv++ ++ + +d  g+a+v+
  gi|474934531|ref|YP_007688113.1| 512 ECVDVMKRAIAFD--GVAVVI 530
                                       6999999999998..888655 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.31
                           Fer4_15   2 vvDrdaCigcglCvaea..pevfelded 27 
                                       +vD ++C  c  C++    p +++++ d
  gi|474934531|ref|YP_007688113.1| 551 TVDVSKCVKCYTCLKMIacPALVKQE-D 577
                                       699**********9864448777766.4 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.00021
                           Fer4_15   2 vvDrdaCigcglCvaeape 20 
                                         D ++Cigcg+C++++p+
  gi|474934531|ref|YP_007688113.1| 581 QTDPSQCIGCGMCADVCPK 599
                                       56999************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (606 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 3628.34
//
Query:       gi|474934532|ref|YP_007688114.1|  [L=198]
Description: Pyruvate:ferredoxin oxidoreductase-related 2-oxoacid:ferredoxin oxidoreductase, gamma subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-35  122.4   1.0    2.4e-35  122.2   1.0    1.0  1  POR       Pyruvate ferredoxin/flavodoxin oxidoreductase
  ------ inclusion threshold ------
      0.047   13.3   0.1      0.092   12.3   0.1    1.5  1  IlvN      Acetohydroxy acid isomeroreductase, NADPH-binding d


Domain annotation for each model (and alignments):
>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.2   1.0   2.7e-39   2.4e-35       1     177 []      11     192 ..      11     192 .. 0.96

  Alignments for each domain:
  == domain 1  score: 122.2 bits;  conditional E-value: 2.7e-39
                                       CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEE CS
                               POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglk 77 
                                       GGqGv++a+ +l++aa+++Gy+v++++++g+++rGg++ s++r++de+ +p  + g+adl++a+++ ++ + +   +
  gi|474934532|ref|YP_007688114.1|  11 GGQGVLLASMVLGNAAMESGYNVMMSEVHGMAQRGGSVLSTLRFGDEVYSPLEASGGADLIMAFEPVEAVRSMGLGN 87 
                                       9**********************************************99999999***********8888999999* PP

                                       EEEEEEEECTCGTT-CCHHHCTS-HHHHHHH......T-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHTS-H. CS
                               POR  78 pggiiiynseelkpdelkkakeeerelkerl......gvrvygvdatkiakeiggneraaNtvmlGalaallglpl. 147
                                        ++ i++n + + p +++  +ee+++ ++ l      + +v +++at+ia ++g  ++aaN+vm+Ga+aa+ g+pl 
  gi|474934532|ref|YP_007688114.1|  88 RETRILMNLDPVYPGNVAAGFEEYPKIEDLLesitsqNSHVATISATEIAIKAGK-AVAANAVMIGAVAAMQGFPLk 163
                                       *************************999888*********************888.*****************9998 PP

                                       .HHHHHHHHCCS-CH.HHHHHHHHHHHHHHH CS
                               POR 148 .ealeeaikkrfpkkkeviekNlkafragye 177
                                        + l++ + +++p+k  + ++N kaf+ g+e
  gi|474934532|ref|YP_007688114.1| 164 kDVLKRILLDTVPEK--FRDLNEKAFEMGFE 192
                                       89***********95..9**********986 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1     1e-05     0.092       6      72 ..       4      79 ..       1      93 [. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1e-05
                                      -EEEES-SHHHHHHHHHH.....HHTT--EEEEE-TT-....HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHH CS
                              IlvN  6 kiaviGyGsqGhaqalnl.....rdsgldvvvglregs....ksvkkAkeegfevltvaeavkkadvvmiliPDel 72
                                       + ++G G qG   a  +      +sg +v+++  +g      sv +  + g ev++  ea+  ad++m   P e+
  gi|474934532|ref|YP_007688114.1|  4 SVQIVGVGGQGVLLASMVlgnaaMESGYNVMMSEVHGMaqrgGSVLSTLRFGDEVYSPLEASGGADLIMAFEPVEA 79
                                      689********87765432222279*****98655544222269999999*******************9999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 1111.92
//
Query:       gi|474934533|ref|YP_007688115.1|  [L=203]
Description: Phosphoribosylanthranilate isomerase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-32  112.8   0.0    1.8e-32  112.7   0.0    1.0  1  PRAI      N-(5'phosphoribosyl)anthranilate (PRA) isomerase


Domain annotation for each model (and alignments):
>> PRAI  N-(5'phosphoribosyl)anthranilate (PRA) isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.7   0.0     1e-36   1.8e-32       1     193 [.       4     195 ..       4     196 .. 0.92

  Alignments for each domain:
  == domain 1  score: 112.7 bits;  conditional E-value: 1e-36
                                       TCE----SHHHHHHHHHHTSSEEEEE--TTBTTB--HHHHHHHCCCS--E..EEEEESSS-HHHHHHHHHHCTECEE CS
                              PRAI   1 akicgltrasdvkaavkagadelglifaesskrevseeqaqellekvpak..lVGVfvNqpieevlriaqelgldvv 75 
                                       +k cg++ ++d+ ++     d+ g++f +  +r vs+e+a++l+    +    +GVf  ++  ++ + ++ +g+ +v
  gi|474934533|ref|YP_007688115.1|   4 VKFCGMRYPADIEKVNLLRPDYAGFVFHPGDPRYVSPEDARKLVDMLDPSivPIGVFYRADEPYIADCVERSGVRMV 80 
                                       589*********************************************995556*********************** PP

                                       EE-CGG..-HHHHHHHHHHS-TTSEEEEEEE-SSS--S-SSTT-SEEEEESSS-SSSXXXXGGGGTTSXX.TTEEEE CS
                              PRAI  76 QLHGde.deqeyeellktelpvikalkvaesvdevkearradhvdllllDsgaGGtGelldwsliskllkslkviLA 151
                                       Q+ G   d+   +    te pv++ ++ +   ++v++a+   + d ++lD g+ GtGe +dwsl++++   + ++L 
  gi|474934533|ref|YP_007688115.1|  81 QVSGCTdDTLVTQVRTLTEYPVMRVFRISI-QEDVSDAESSIA-DTVMLDVGHRGTGEYFDWSLLKNFG--RSFFLT 153
                                       ****994455555556689*****999999.345777777777.9************************..5***** PP

                                       SSXXTTTHHHHHT.TXXSEEEEXGGGEEETEEXHHHHHHHHH CS
                              PRAI 152 GGLtpeNvaeaiklegvlgvDvssGVEtnGvkDlekirkfvq 193
                                       G  tpeNv  ai + ++++v v+sGVEt+G+kD++ +r+f++
  gi|474934533|ref|YP_007688115.1| 154 GEFTPENVGSAIVSVRPYAVNVNSGVETDGKKDADRMRRFLD 195
                                       ***************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1193.02
//
Query:       gi|474934534|ref|YP_007688116.1|  [L=140]
Description: hypothetical protein TALC_00963 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.5e-07   28.5   1.5      0.012   15.3   0.1    2.2  2  zinc_ribbon_2   zinc-ribbon domain
    6.6e-05   22.8   6.9     0.0053   16.7   1.5    2.5  2  DUF1610         Domain of unknown function (DUF1610)
    0.00014   21.8   0.6     0.0006   19.8   0.7    1.4  1  DZR             Double zinc ribbon
    0.00034   20.1   2.2    0.00056   19.4   2.2    1.3  1  TF_Zn_Ribbon    TFIIB zinc-binding
    0.00038   19.7   3.7     0.0022   17.3   3.7    2.0  1  zf-ribbon_3     zinc-ribbon domain
    0.00092   19.1   1.7        1.1    9.3   0.1    2.4  2  Nudix_N_2       Nudix N-terminal
     0.0061   16.5   0.7     0.0098   15.8   0.7    1.3  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
  ------ inclusion threshold ------
      0.012   15.3   1.0        1.2    8.8   0.1    2.3  2  zf-RRN7         Zinc-finger of RNA-polymerase I-specific TFII
      0.018   14.7   2.5        2.3    7.9   0.0    2.2  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
      0.042   13.5   0.8       0.21   11.2   0.1    2.1  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
      0.097   12.7   0.2       0.14   12.1   0.2    1.3  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.11   11.4   0.1       0.12   11.3   0.1    1.1  1  CitF            Citrate lyase, alpha subunit (CitF)
       0.12   11.8   0.3       0.22   11.0   0.3    1.4  1  zf_Rg           Reverse gyrase zinc finger
       0.15   12.3   1.7        3.7    7.8   0.2    2.4  2  zf-RING_7       C4-type zinc ribbon domain
       0.18   11.6   1.8        1.7    8.4   2.0    2.1  2  zinc_ribbon_5   zinc-ribbon domain
       0.19   11.8   0.4       0.24   11.4   0.4    1.1  1  DUF1451         Zinc-ribbon containing domain
       0.29   11.1   2.1        1.9    8.5   0.1    2.3  2  zinc_ribbon_4   zinc-ribbon domain


Domain annotation for each model (and alignments):
>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   1.2e-05     0.012       1      11 [.       7      18 ..       7      22 .. 0.78
   2 !   12.3   0.2   9.8e-05       0.1       1      11 [.      25      35 ..      25      38 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.2e-05
                     zinc_ribbon_2  1 fCpnCGaelq.d 11
                                      +CpnCG++++ d
  gi|474934534|ref|YP_007688116.1|  7 YCPNCGTKISmD 18
                                      899999999734 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 9.8e-05
                     zinc_ribbon_2  1 fCpnCGaelqd 11
                                      fC++CG++l +
  gi|474934534|ref|YP_007688116.1| 25 FCTSCGTKLRP 35
                                      89999999964 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   1.5     5e-06    0.0053      15      23 ..       4      12 ..       2      13 .. 0.91
   2 !    8.7   0.3    0.0015       1.6       1      12 [.      26      37 ..      26      40 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5e-06
                           DUF1610 15 vvFpCPNCG 23
                                      v+F+CPNCG
  gi|474934534|ref|YP_007688116.1|  4 VSFYCPNCG 12
                                      99******9 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0015
                           DUF1610  1 CtSCGaelaprE 12
                                      CtSCG  l p +
  gi|474934534|ref|YP_007688116.1| 26 CTSCGTKLRPDG 37
                                      *****9998876 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.7   5.7e-07    0.0006       1      24 [.       8      35 ..       8      43 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5.7e-07
                               DZR  1 CpqCgeelppdar....fCseCgtklka 24
                                      Cp+Cg++++ d+     fC  Cgtkl++
  gi|474934534|ref|YP_007688116.1|  8 CPNCGTKISMDDSrefgFCTSCGTKLRP 35
                                      9999999766555567799999999985 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   2.2   5.3e-07   0.00056       1      29 [.       6      33 ..       6      38 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 5.3e-07
                                      EEETTTTCEECHEETSTTCEEESSSSBEE CS
                      TF_Zn_Ribbon  1 ykCPnCgstnlveDpergelvCtdCGlVl 29
                                      + CPnCg++ +  D +r   +Ct+CG+ l
  gi|474934534|ref|YP_007688116.1|  6 FYCPNCGTK-ISMDDSREFGFCTSCGTKL 33
                                      68*****86.8999887777******987 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   3.7   2.1e-06    0.0022       4      26 .]       7      33 ..       5      33 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.1e-06
                       zf-ribbon_3  4 rCPnCGaplssddn....vCpyCGtkl 26
                                      +CPnCG+++s dd+    +C++CGtkl
  gi|474934534|ref|YP_007688116.1|  7 YCPNCGTKISMDDSrefgFCTSCGTKL 33
                                      8******88999998899*******97 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.1     0.001       1.1       2      11 ..       7      16 ..       7      23 .. 0.87
   2 !    8.6   0.3    0.0016       1.7       2      11 ..      25      34 ..      24      37 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.001
                                      B-TTT--B-E CS
                         Nudix_N_2  2 FCsqCGtpve 11
                                      +C++CGt+++
  gi|474934534|ref|YP_007688116.1|  7 YCPNCGTKIS 16
                                      9******976 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0016
                                      B-TTT--B-E CS
                         Nudix_N_2  2 FCsqCGtpve 11
                                      FC++CGt+++
  gi|474934534|ref|YP_007688116.1| 25 FCTSCGTKLR 34
                                      9******986 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.7   9.3e-06    0.0098      28      59 ..       5      36 ..       3      38 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 9.3e-06
                    OrfB_Zn_ribbon 28 SktCseCgsknkealsgrtfkCpnCgfeadrD 59
                                      S  C++Cg k + ++s++   C++Cg+++  D
  gi|474934534|ref|YP_007688116.1|  5 SFYCPNCGTKISMDDSREFGFCTSCGTKLRPD 36
                                      668**********88888889*****997655 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1    0.0012       1.2      22      31 ..       6      15 ..       5      16 .. 0.90
   2 ?    5.3   0.1     0.015        16      23      30 ..      25      32 ..      23      33 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0012
                           zf-RRN7 22 yyCrrChtqe 31
                                      +yC +C+t++
  gi|474934534|ref|YP_007688116.1|  6 FYCPNCGTKI 15
                                      9*******97 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.015
                           zf-RRN7 23 yCrrChtq 30
                                      +C++C+t+
  gi|474934534|ref|YP_007688116.1| 25 FCTSCGTK 32
                                      8******7 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0022       2.3       5      14 ..       7      16 ..       6      20 .. 0.81
   2 ?    6.4   0.6    0.0067       7.1       3      15 ..      23      35 ..      21      36 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0022
                     zf-NADH-PPase  5 FCgrCGapte 14
                                      +C+ CG++  
  gi|474934534|ref|YP_007688116.1|  7 YCPNCGTKIS 16
                                      8999999866 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0067
                     zf-NADH-PPase  3 hrFCgrCGaptep 15
                                        FC  CG++ +p
  gi|474934534|ref|YP_007688116.1| 23 FGFCTSCGTKLRP 35
                                      68*******9886 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1    0.0002      0.21       2      18 ..       5      21 ..       4      22 .. 0.86
   2 ?    0.5   0.1      0.45   4.7e+02       4      12 ..      25      33 ..      23      36 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0002
                            zf_UBZ  2 tylCerCgkeipeselq 18
                                      ++ C+ Cg++i++++  
  gi|474934534|ref|YP_007688116.1|  5 SFYCPNCGTKISMDDSR 21
                                      689**********9865 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.45
                            zf_UBZ  4 lCerCgkei 12
                                      +C  Cg+++
  gi|474934534|ref|YP_007688116.1| 25 FCTSCGTKL 33
                                      7*****976 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   0.00014      0.14      68      95 ..       3      32 ..       1      43 [. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                                      --EEEETTTS-EEECHH.H.HHS-TTTSSS CS
                              HypA 68 pvkvrCreCgkefelee.k.alrCpkCgsa 95
                                      +v+++C +Cg+++++++ +    C +Cg++
  gi|474934534|ref|YP_007688116.1|  3 EVSFYCPNCGTKISMDDsReFGFCTSCGTK 32
                                      6899**********887433337****975 PP

>> CitF  Citrate lyase, alpha subunit (CitF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00011      0.12     361     403 ..      54      97 ..      36     124 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                              CitF 361 aaklsiivaplvrGriptvve.evttvitpGesvdvlvtdvGia 403
                                          + i+++p v+G ++  v+ ++   + pG+s+dv+    Gi 
  gi|474934534|ref|YP_007688116.1|  54 NGSVRIVISPKVKGPLTIAVNrNLPVTMEPGSSMDVIFPGYGIP 97 
                                       56789***********9988725556689********9999985 PP

>> zf_Rg  Reverse gyrase zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.3   0.00021      0.22       9      31 ..       7      29 ..       4      32 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00021
                             zf_Rg  9 lCPNCgGdisdeRlekGLpCkrC 31
                                       CPNCg +is +       C++C
  gi|474934534|ref|YP_007688116.1|  7 YCPNCGTKISMDDSREFGFCTSC 29
                                      6********98866655567776 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.2    0.0035       3.7      23      30 ..       5      12 ..       1      13 [. 0.77
   2 ?    3.5   0.1     0.077        81       2      11 ..      26      35 ..      25      36 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0035
                                      -EE-TTT- CS
                         zf-RING_7 23 vvtCpeCG 30
                                       ++Cp+CG
  gi|474934534|ref|YP_007688116.1|  5 SFYCPNCG 12
                                      389****9 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.077
                                      ETTT--B--C CS
                         zf-RING_7  2 CgGChmelpp 11
                                      C+ C+++l+p
  gi|474934534|ref|YP_007688116.1| 26 CTSCGTKLRP 35
                                      9999999988 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   2.0    0.0016       1.7       5      23 ..       8      24 ..       6      31 .. 0.81
   2 ?    1.3   0.2      0.29     3e+02       5      13 ..      26      34 ..      24      37 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0016
                     zinc_ribbon_5  5 CpdCdtkFklvdsklKksg 23
                                      Cp+C+tk  ++ds+  + g
  gi|474934534|ref|YP_007688116.1|  8 CPNCGTKISMDDSR--EFG 24
                                      ************98..666 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.29
                     zinc_ribbon_5  5 CpdCdtkFk 13
                                      C  C+tk +
  gi|474934534|ref|YP_007688116.1| 26 CTSCGTKLR 34
                                      999***976 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.4   0.00023      0.24     111     140 ..       2      31 ..       1      33 [. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00023
                           DUF1451 111 glGtlvCekCgkelalkkteeippCpkCga 140
                                       g   + C +Cg++++++ ++e   C +Cg 
  gi|474934534|ref|YP_007688116.1|   2 GEVSFYCPNCGTKISMDDSREFGFCTSCGT 31 
                                       566799**********************97 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1    0.0018       1.9       4      17 ..       7      20 ..       5      21 .. 0.82
   2 ?    1.8   0.3      0.21   2.3e+02      28      34 ..      26      32 ..      25      34 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0018
                     zinc_ribbon_4  4 tCpsCkakyeidde 17
                                       Cp+C++k + dd+
  gi|474934534|ref|YP_007688116.1|  7 YCPNCGTKISMDDS 20
                                      699**999888886 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.21
                     zinc_ribbon_4 28 CskCghv 34
                                      C+ Cg++
  gi|474934534|ref|YP_007688116.1| 26 CTSCGTK 32
                                      5555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                       119  (0.00663729); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 907.79
//
Query:       gi|474934535|ref|YP_007688117.1|  [L=227]
Description: Cell division GTPase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.7e-26   92.5   0.4    1.8e-25   90.3   0.4    1.9  1  Tubulin    Tubulin/FtsZ family, GTPase domain
    0.00026   20.3   0.7       0.17   11.0   0.1    2.3  2  Tubulin_2  Tubulin like
  ------ inclusion threshold ------
       0.23   11.3   0.0       0.43   10.4   0.0    1.3  1  RD3        RD3 protein


Domain annotation for each model (and alignments):
>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.3   0.4     3e-29   1.8e-25       1     192 [.      14     168 ..      14     173 .. 0.95

  Alignments for each domain:
  == domain 1  score: 90.3 bits;  conditional E-value: 3e-29
                                       EEEEEEEHHHHHHHHHHHHH...HHHCH....HHHT.....TTEEEEE....EEESBHHHHHTS-GS......EEEE CS
                           Tubulin   1 eiivigvGqcGnqignelwellakehgiqsdgdslesfFsesgkveyiprsvaidtdpqvlneikagselfnpnkll 77 
                                       +i vigvG++G++i+++l+       ++              ++v  i    a++td+++l+ + a+       ++ 
  gi|474934535|ref|YP_007688117.1|  14 RIAVIGVGGAGCRIVSMLYG------KM--------------SRVGVI----AVNTDRKALEDTSAD------YRMY 60 
                                       589*****************......45..............447777....***************......**** PP

                                       --CCCCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE.SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEEE CS
                           Tubulin  78 lgkegagnngaggypevgkeaaeeileeirkevekcdslqgffitaslgGGTGSGlgpvilevlkeeypkalvvtvv 154
                                       ++ke ++++g +g+  +gk++a+  ++e+r+ +++ d+    fi+a++gGGTGSG++pvi++++  e  +    +v 
  gi|474934535|ref|YP_007688117.1|  61 ICKEVTKGLGTRGDARLGKKCAQIHADELREVISQYDY---AFIVAGMGGGTGSGASPVIADICASE--GLHYGAVA 132
                                       **************************************...**************************..9999**** PP

                                       EE--GG.G-HHHHHHHHHHHHHHHHT-SEEEEEEHHHH CS
                           Tubulin 155 vlPsefsevvvepynailalkelieesdavividNdaL 192
                                       ++P++f  +  +   a+++ ++l   +  v+ ++Nd+ 
  gi|474934535|ref|YP_007688117.1| 133 IMPFSF--ESDRATRAAEGFRALHVVCKDVVRFENDRA 168
                                       ****99..6789999********************975 PP

>> Tubulin_2  Tubulin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.1   0.00025       1.5       2      21 ..      17      36 ..      16      59 .. 0.88
   2 !   11.0   0.1   2.9e-05      0.17     157     174 ..      98     115 ..      71     152 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00025
                         Tubulin_2  2 viGLGGtGgkvlaelrrrlr 21
                                      viG+GG G+++++ l +++ 
  gi|474934535|ref|YP_007688117.1| 17 VIGVGGAGCRIVSMLYGKMS 36
                                      7************9998875 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 2.9e-05
                         Tubulin_2 157 nvfVvgSLaGGTGSGifl 174
                                         f+v ++ GGTGSG   
  gi|474934535|ref|YP_007688117.1|  98 YAFIVAGMGGGTGSGASP 115
                                       569************765 PP

>> RD3  RD3 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   7.1e-05      0.43      52      98 ..      51      96 ..      43     100 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 7.1e-05
                               RD3 52 aetgvDYswlastprkrkqisaserleLEelCakikPsecgkvisrf 98
                                      + t++DY+  ++++  +k + +    +L + Ca+i+++e  +vis++
  gi|474934535|ref|YP_007688117.1| 51 EDTSADYRMYICKE-VTKGLGTRGDARLGKKCAQIHADELREVISQY 96
                                      57889******988.7899**************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1707.35
//
Query:       gi|474934536|ref|YP_007688118.1|  [L=118]
Description: hypothetical protein TALC_00965 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00085   19.2   0.1      0.003   17.4   0.1    1.9  1  RHH_1     Ribbon-helix-helix protein, copG family
  ------ inclusion threshold ------
      0.015   15.5   0.1      0.032   14.4   0.1    1.5  1  RHH_8     Ribbon-Helix-Helix transcriptional regulator family


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   3.3e-07     0.003       2      36 ..       8      43 ..       8      44 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.3e-07
                                      EEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHHHH CS
                             RHH_1  2 vsirldeellerLdelarrrg.rSrSelIReAlrey 36
                                      v++++ +e++e+L +   + +  +rS++IReA+r y
  gi|474934536|ref|YP_007688118.1|  8 VTLKMTAEEAEALTQYLMDHDiDNRSDFIREAIRTY 43
                                      68889999999999988888999***********98 PP

>> RHH_8  Ribbon-Helix-Helix transcriptional regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   3.6e-06     0.032      29      93 ..      31      93 ..      24     106 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.6e-06
                             RHH_8 29 nRtDlirtairaqLakhddalkqavkrkslvlGvtklsraeleevqaenkqlelkvvGllsiddd 93
                                      nR+D+ir+air+ +   +++  + + ++ + + ++ ++ + +e++++++   + +      +++d
  gi|474934536|ref|YP_007688118.1| 31 NRSDFIREAIRTYMVGASET--NETGEDGIYVRLNGIQLQTIENMRRDGTIFDAESYIRKLVEND 93
                                      9************9998875..4456677777888888888888888777666655544555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 907.10
//
Query:       gi|474934537|ref|YP_007688119.1|  [L=969]
Description: leucyl-tRNA synthetase, archaeal and cytosolic family [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.1e-42  143.7   0.0    2.6e-32  111.9   0.0    2.9  2  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    2.1e-18   66.7   0.0    4.7e-18   65.6   0.0    1.6  1  Anticodon_1    Anticodon-binding domain of tRNA
    5.2e-10   38.6   0.2    5.5e-05   22.1   0.1    2.6  3  tRNA-synt_1g   tRNA synthetases class I (M)
    6.5e-05   22.5   0.0    0.00021   20.9   0.0    1.8  2  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
  ------ inclusion threshold ------
      0.034   13.5   0.0       0.53    9.6   0.0    2.3  2  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.9   0.0   7.2e-36   2.6e-32       2     304 ..      12     326 ..      11     353 .. 0.83
   2 !   27.1   0.3   3.3e-10   1.2e-06     320     602 .]     403     682 ..     399     682 .. 0.77

  Alignments for each domain:
  == domain 1  score: 111.9 bits;  conditional E-value: 7.2e-36
                       tRNA-synt_1   2 lyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaiea 78 
                                       +++ W ++++ ++e    + k++f+l+   P  tG lH+Gh    t  d + rykrm+G++vl+ +G+   G     
  gi|474934537|ref|YP_007688119.1|  12 WQKAWADAKLNESE--RIDGKPKFMLIFAYPGLTGYLHVGHLRGYTYTDALGRYKRMTGYNVLFPVGTHATGNG-AI 85 
                                       78899999988777..7778************************************************999965.45 PP

                       tRNA-synt_1  79 kvekklgakekkerkklgr....eefrekvre...wkaeyae.eirkqvkrlGvsvDfdreylTldkeleeavkevf 147
                                        + +k+++k++k++  l r    e+++++ +e    ++ +    +++ ++r+G   D+ r   Tl++++ + +++ f
  gi|474934537|ref|YP_007688119.1|  86 SLANKIARKDEKTVDYLIRngcpEDMIDRLKEpmdVVNFFNGvYQNDYWRRFGFLSDWRRFTCTLYPDYAQFIRWQF 162
                                       6777888888888877655222256777777622233334441466779**************************** PP

                       tRNA-synt_1 148 vrladkgliyrgkklvnwstkl.ktalselEv....eykdkkdalihvafpladkeevklviaTTtPeTllgdtava 219
                                        +l +k l+ +  +  ++++     a+   E+        +++  + ++f  ++ +   lv+aT +PeT++g++   
  gi|474934537|ref|YP_007688119.1| 163 SKLKEKNLLIQKPYYAPFCPVHgPVAVDPSETdiskGGLAETQEYTLLKFWCEERKF-FLVAATLRPETVFGQVCFW 238
                                       *******************85413455444442121112234666778888888877.9****************** PP

                       tRNA-synt_1 220 vnpeldyv...itkeklilaeallkslvkkesekkiledergkeLegkevelplvnrkipiiaddyvdkeaGtGvVk 293
                                         p+l+y    +++e++++ e+  +++  + +  +    + gk+L+g+ ++lp++ ++ip+   ++vd + GtG+V 
  gi|474934537|ref|YP_007688119.1| 239 ARPDLEYRiveKNGERWVISEQCAEKMRLQFDGVTDAGSIAGKDLIGLMCTLPMMHKQIPVFPAEFVDPDVGTGLVT 315
                                       *******98888999******9999998888888999**************************************** PP

                       tRNA-synt_1 294 iaPahdedDye 304
                                         P   + D+ 
  gi|474934537|ref|YP_007688119.1| 316 SCPSDAPADWD 326
                                       ***98888875 PP

  == domain 2  score: 27.1 bits;  conditional E-value: 3.3e-10
                       tRNA-synt_1 320 dgtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvrvke..ladaalka 394
                                        g+++e ++ef+g++v++a++   +++ + g      + +++v +c  ++ + i r+ +qWf++  +  l+++a ++
  gi|474934537|ref|YP_007688119.1| 403 MGVMKEVCGEFAGIRVEEAKDRTQQAMLKSGEAEIFRDLTMEV-VCRCGERVHIRRIDDQWFINYADrdLTESAKAS 478
                                       5999***********************************9998.677788888999********98777******** PP

                       tRNA-synt_1 395 vekvqfvpkskekryaswleniqdW.ciSRqrwWGhriplfvsketeevvvreelk..elvagreeeeaek..kale 466
                                       +e +++ p   +++ +  l   ++  c+    w G++ p + +k t e + ++ l   +++ ++ ++++++  ++++
  gi|474934537|ref|YP_007688119.1| 479 TEGMTLLPPEWNNNVKGVLDWYRERaCVRLGNWLGTKFP-WDEKWTIEAISDSTLYpiYYTISLYANDGRIkpEQMT 554
                                       **99999877666666666655554155556677****9.6666666666655443112233334444443013444 PP

                       tRNA-synt_1 467 keakdklkkekgelekdedvlDvWFsSgswpfstlgypeedteelkkffpadmlleGlDiirgWvarlillslaltg 543
                                        ++ d +  ekgel+ +         S+s+ +s     e+ +++++  +p d+ l G   +   +   +l   a+  
  gi|474934537|ref|YP_007688119.1| 555 WDFFDYVILEKGELKSV---------SASTGISEELL-ETIRKDVHYWYPLDLNLGGKEHMTVHFPVFLLNHRAILP 621
                                       45566666777777766.........56666665443.35599******************9999999998887764 PP

                       tRNA-synt_1 544 se.PfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltli.lsdvgrdinls 602
                                       +    + +lv+  v+ ++  K+SKs+g        +k ygada+Rl+ +  +++  d++++
  gi|474934537|ref|YP_007688119.1| 622 DDmQPRGILVNWYVTGKNKDKISKSKGGAQPIPGAVKDYGADAMRLYYAhVASMFVDVEWD 682
                                       4334599********************998888999***********99889998888875 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.6   0.0   1.3e-21   4.7e-18       1     137 [.     716     835 ..     716     846 .. 0.80

  Alignments for each domain:
  == domain 1  score: 65.6 bits;  conditional E-value: 1.3e-21
                       Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrll 77 
                                       d w+ls+ln  vke++ea+++y+++++++  y  ++nd+ +wy +   +        ++    +++  +l+ ++  +
  gi|474934537|ref|YP_007688119.1| 716 DAWLLSRLNTHVKEIREAMDRYDLRQMCTVTYFDIVNDM-KWYERRGGK--------NR----ATVMRALRIWINAM 779
                                       89*************************************.999555322........23....89************ PP

                       Anticodon_1  78 aPfmPfitEelwqreeeelgkkesimlaewpe.kaeelekele..eeevellkeivkairklr 137
                                        P++P+++Eelw    +e g +  +  a++pe +++ +++ +e  e    l++e++   +++r
  gi|474934537|ref|YP_007688119.1| 780 MPVTPHMAEELW----HEAGFEGLVAAAQFPEyDPAVADASAEygE---GLIQEVIDDTNEIR 835
                                       ************....88899999*******988876655552233...33344544444444 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.1   1.5e-08   5.5e-05       7      58 ..      39      90 ..      34     106 .. 0.81
   2 ?   -3.6   0.0      0.98   3.5e+03      85     125 ..     143     183 ..     117     185 .. 0.74
   3 !   13.6   0.0   5.6e-06      0.02     295     369 ..     604     684 ..     598     699 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.5e-08
                                      -B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHH CS
                      tRNA-synt_1g  7 lpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAek 58
                                       p  +g lH+Ghl+ +  +D++ Rykr++g++vlf  gt + G      A+k
  gi|474934537|ref|YP_007688119.1| 39 YPGLTGYLHVGHLRGYTYTDALGRYKRMTGYNVLFPVGTHATGNGAISLANK 90
                                      5556899********************************9999876655555 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 0.98
                                       -SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETT CS
                      tRNA-synt_1g  85 fdkygrttseehkelvqeifkklkekgliyekeieqlycpk 125
                                       +  ++ t   +  ++ +  f+klkek+l+ +k +   +cp 
  gi|474934537|ref|YP_007688119.1| 143 WRRFTCTLYPDYAQFIRWQFSKLKEKNLLIQKPYYAPFCPV 183
                                       44688888888888899999999999999999999999985 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 5.6e-06
                                       HHHTHHHHHHHHTT--.....--S-EEEE--EEE--.------------HHHHHHHH-HHHHHHHHHHHS-TTS-EE CS
                      tRNA-synt_1g 295 FHtifwPaillgaelk.....lpkkvvaheyltveg.kKlSkSrgvvvkakealerldadllRYylaaeapekkDld 365
                                       + t+ +P +ll ++       +p+ + ++ y+t ++ +K+SkS+g +  +  a++ + ad++R y+a  a+   D++
  gi|474934537|ref|YP_007688119.1| 604 HMTVHFPVFLLNHRAIlpddmQPRGILVNWYVTGKNkDKISKSKGGAQPIPGAVKDYGADAMRLYYAHVASMFVDVE 680
                                       55889999999955542233378889999999976626******************************999999988 PP

                                       E-HH CS
                      tRNA-synt_1g 366 fswe 369
                                       + ++
  gi|474934537|ref|YP_007688119.1| 681 WDED 684
                                       7665 PP

>> tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   5.9e-08   0.00021      81     127 ..     279     326 ..     210     344 .. 0.74
   2 ?   -3.6   0.0       1.9   6.9e+03     139     179 ..     379     424 ..     373     428 .. 0.48

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 5.9e-08
                     tRNA-synt_1_2  81 eGv.ftglkaihPitgekipiwvanyvlmeygtgavmavPahdqrDfe 127
                                        G    gl+++ P+ +++ip++ a++v  + gtg v ++P+    D++
  gi|474934537|ref|YP_007688119.1| 279 AGKdLIGLMCTLPMMHKQIPVFPAEFVDPDVGTGLVTSCPSDAPADWD 326
                                       454457999********************************9999986 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.9
                     tRNA-synt_1_2 139 vikpedeekkle.eseeayte...egilvn.sgefdglkskeakek 179
                                       v  p+ + + le  ++++y++    g++ +  gef g++++eak++
  gi|474934537|ref|YP_007688119.1| 379 VTDPARKAELLEeAKKQVYKDgyhMGVMKEvCGEFAGIRVEEAKDR 424
                                       5555544433331233444332224555552357777777777765 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00015      0.53      21      50 ..      44      73 ..      33     125 .. 0.83
   2 ?    1.2   0.0     0.054   1.9e+02     250     283 ..     639     672 ..     593     691 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00015
                                      S--BHHHHHHHHHHHHHHHHHHHTT-EEEE CS
                      tRNA-synt_1e 21 dashlGhaRslvafDilrrilqalgYdvqf 50
                                       + h+Gh R +  +D l r+ +++gY+v f
  gi|474934537|ref|YP_007688119.1| 44 GYLHVGHLRGYTYTDALGRYKRMTGYNVLF 73
                                      679*************************98 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.054
                                       TTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS CS
                      tRNA-synt_1e 250 egekmsksLknfitikdvlkkfdprqlRllllsa 283
                                       +++k+sks +    i  ++k + + ++Rl+ +++
  gi|474934537|ref|YP_007688119.1| 639 NKDKISKSKGGAQPIPGAVKDYGADAMRLYYAHV 672
                                       679*************************987654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (969 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.77u 0.29s 00:00:01.06 Elapsed: 00:00:00.48
# Mc/sec: 6046.87
//
Query:       gi|474934538|ref|YP_007688120.1|  [L=226]
Description: conserved hypothetical protein TIGR00266 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-55  188.2   2.2    1.6e-55  188.0   2.2    1.0  1  AIM24     Mitochondrial biogenesis AIM24
  ------ inclusion threshold ------
      0.024   14.8   0.4         11    6.1   0.1    3.0  3  HepII_C   Heparinase II C-terminal domain


Domain annotation for each model (and alignments):
>> AIM24  Mitochondrial biogenesis AIM24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.0   2.2   1.8e-59   1.6e-55       1     201 []       3     208 ..       3     208 .. 0.98

  Alignments for each domain:
  == domain 1  score: 188.0 bits;  conditional E-value: 1.8e-59
                                       EEEESSSS-EEEEEE-TT-EEEE-CCGEEEEETTEEEEE....--------------EEEEEEES.SS-EEEEE--S CS
                             AIM24   1 fevlgepssllsvtLspgeelyaerGalvamsgkvemet....gllkalkrlltgeslfllkftakissgtvllapk 73 
                                       +++ g++ +++ v+L+pge+ +   G++ +m+g+++me+    g++ +lkr l+ge++f l+++++ ++g + l+ +
  gi|474934538|ref|YP_007688120.1|   3 YTITGDNLQFVNVELQPGETFFSSGGSMRYMTGNMRMESkatgGMFAGLKRKLAGETFFQLQYHTEGGPGVLGLGGD 79 
                                       6899*************************************************************9999******** PP

                                       SSEEEEEEEGGTT.EEEEEGGGEEEEETT-EEEEEEEE--.SSGGGTS-EEEEEEESSSEEEEEEECSEEEEEEE.E CS
                             AIM24  74 lpgtivtlelgggdwlivqkdafLAatgnveldikfqkgl.kglfggeglflqkltGrGlvalsgyGaiyeielkag 149
                                        pg+iv l++ ++ +++vqk+ +L ++ +v++d++fqk+l + lfggegl+l+kl+G+G++++ ++G+++ ++lk+g
  gi|474934538|ref|YP_007688120.1|  80 CPGKIVALDM-NEGNWLVQKQGYLGSEAGVTIDMAFQKKLgAILFGGEGLVLEKLSGSGTAFIGACGDFVIVDLKPG 155
                                       *********9.5558***********************999999********************************* PP

                                       EEEEEEGGGEEEEETTEEEEEEEETT---STTTTS-E.EEEEEEEEEEEEESS CS
                             AIM24 150 eelvvdpghlvafsgslkfdiervgglkrrligGegl.flkltGpgtvllqsr 201
                                       e ++v +g+ va+++s+k+di ++gg+k++l+gGegl +++ltGpg+++lqs+
  gi|474934538|ref|YP_007688120.1| 156 EIYKVSSGNAVAWQESVKYDIAAAGGIKTALFGGEGLfVTTLTGPGRIILQSM 208
                                       ****************************************************7 PP

>> HepII_C  Heparinase II C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.13   1.2e+03      37      51 ..       7      21 ..       2      44 .. 0.78
   2 ?    6.1   0.1    0.0013        11      40      61 ..      82     103 ..      66     134 .. 0.76
   3 ?    4.7   0.0    0.0035        32      41      68 ..     146     173 ..     143     182 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.13
                                      SS-EEEEE-SB-SEE CS
                           HepII_C 37 sqtlkfvvtDlapGt 51
                                       ++l+fv  +l+pG 
  gi|474934538|ref|YP_007688120.1|  7 GDNLQFVNVELQPGE 21
                                      467999999999996 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0013
                                       EEEEE-SB-SEEEEEEETTEEE CS
                           HepII_C  40 lkfvvtDlapGtwqVlkdGkkl 61 
                                        k v  D++ G w V+k+G   
  gi|474934538|ref|YP_007688120.1|  82 GKIVALDMNEGNWLVQKQGYLG 103
                                       578889************9765 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.0035
                                       EEEE-SB-SEEEEEEETTEEEEEEEEE- CS
                           HepII_C  41 kfvvtDlapGtwqVlkdGkkldsaklvs 68 
                                       +fv+ Dl+pG    +  G+ +  +++v+
  gi|474934538|ref|YP_007688120.1| 146 DFVIVDLKPGEIYKVSSGNAVAWQESVK 173
                                       59*******9866667898888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       249  (0.0138881); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1809.60
//
Query:       gi|474934539|ref|YP_007688121.1|  [L=113]
Description: hypothetical protein TALC_00968 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0078   16.5   0.4     0.0078   16.5   0.4    1.0  1  EI24      Etoposide-induced protein 2.4 (EI24)
  ------ inclusion threshold ------
      0.013   14.5   5.8      0.016   14.2   5.8    1.0  1  AbrB      Transition state regulatory protein AbrB
      0.014   15.1   0.3      0.016   15.0   0.3    1.1  1  DUF5381   Family of unknown function (DUF5381)
      0.026   14.2   0.5      0.031   13.9   0.5    1.2  1  Wzy_C     O-Antigen ligase
       0.13   12.2   0.1       0.13   12.2   0.1    2.2  2  DUF4492   Domain of unknown function (DUF4492)
       0.78    8.4   6.6       0.97    8.1   6.6    1.1  1  DUF2207   Predicted membrane protein (DUF2207)
       0.84   10.0   8.9        1.1    9.7   8.9    1.1  1  MgtE      Divalent cation transporter
        1.6    8.7   6.1       0.61   10.0   0.5    2.0  2  DUF4714   Domain of unknown function (DUF4714)
        8.6    7.4   9.6        3.4    8.7   0.6    2.3  2  Pilin_N   Archaeal Type IV pilin, N-terminal
        9.1    6.8   7.2         15    6.2   7.2    1.4  1  DUF202    Domain of unknown function (DUF202)
        9.5    5.7   8.2         12    5.3   8.2    1.2  1  DUF1129   Protein of unknown function (DUF1129)


Domain annotation for each model (and alignments):
>> EI24  Etoposide-induced protein 2.4 (EI24)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.4   4.8e-06    0.0078      19      70 ..      13      70 ..       3     103 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.8e-06
                                      HHHHHHHHHHHHHHHHHHHH-......TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              EI24 19 lllplllnlllfllllvlllw......vllasllvllllllplwlfplvalllaapfy 70
                                      +++ +ll+l+++++++vl++       +++a+++v+l++++++ ++ +  ++la p+y
  gi|474934539|ref|YP_007688121.1| 13 AWVLVLLALVIIGAAVVLYMYpeiledIVMAAVFVVLIIIALIVITYVAMFILAIPMY 70
                                      6788899999999776666635557875566666666666666666677777777776 PP

>> AbrB  Transition state regulatory protein AbrB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   5.8   9.5e-06     0.016     205     255 ..      16      66 ..       6      73 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.5e-06
                              AbrB 205 llalaqlliGasiGlrftreslrellralpaallstlllialcallallla 255
                                       l+ la+++iGa++ l + +e+l++++ a++ ++l++++li++++++ ++la
  gi|474934539|ref|YP_007688121.1|  16 LVLLALVIIGAAVVLYMYPEILEDIVMAAVFVVLIIIALIVITYVAMFILA 66 
                                       455566666666666666666666666666666666666666666655555 PP

>> DUF5381  Family of unknown function (DUF5381)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.3   9.6e-06     0.016      13      89 ..      15     100 ..       3     106 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 9.6e-06
                           DUF5381  13 vllflatvglglag.lfllfeglkfeskyslly.iiigiigtifgliillmvlpallkkGkvl.....fti..keGe 80 
                                       vl++la v++g a  l++  e+l+     ++++ +ii  + +i ++ +++  +p +++kG+ +     ++i  +eG 
  gi|474934539|ref|YP_007688121.1|  15 VLVLLALVIIGAAVvLYMYPEILEDIVMAAVFVvLIIIALIVITYVAMFILAIPMYIHKGEQVqvgasYSIddVEGT 91 
                                       66778888887765145555566555544444313444445555667789999*******87644555677333677 PP

                           DUF5381  81 nGkvisrkk 89 
                                        G+v s++k
  gi|474934539|ref|YP_007688121.1|  92 GGEVRSDEK 100
                                       777777766 PP

>> Wzy_C  O-Antigen ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.5   1.9e-05     0.031      17      70 ..      12      76 ..      10     109 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.9e-05
                             Wzy_C 17 sgiigl...lvalivlliifykrri........pfllllgilvgvilliilfvlstnletlknit 70
                                      ++++ +   lv++++++++++ + i        +f++l++i+++vi+ ++ f+l   ++  k ++
  gi|474934539|ref|YP_007688121.1| 12 GAWVLVllaLVIIGAAVVLYMYPEIledivmaaVFVVLIIIALIVITYVAMFILAIPMYIHKGEQ 76
                                      56666622344444444555555557999999888888888888888888888776666655554 PP

>> DUF4492  Domain of unknown function (DUF4492)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   7.9e-05      0.13      16      46 ..       9      39 ..       5      44 .. 0.91
   2 ?   -3.0   6.7       4.3     7e+03      21      36 ..      47      62 ..      40      78 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.9e-05
                           DUF4492 16 lGktLwliiliKLfiifvvLklfffpdvLke 46
                                      +Gk  w+++l+ L+ii + + l+++p++L++
  gi|474934539|ref|YP_007688121.1|  9 VGKGAWVLVLLALVIIGAAVVLYMYPEILED 39
                                      89**************************986 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.3
                           DUF4492 21 wliiliKLfiifvvLk 36
                                       ++i+i L++i  v  
  gi|474934539|ref|YP_007688121.1| 47 VVLIIIALIVITYVAM 62
                                      5778888888876644 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   6.6   0.00059      0.97     388     442 ..      13      75 ..       3      80 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00059
                           DUF2207 388 lgliilglilillallllvll........lvfllilllillliaiivlllfsrllgrrteeGa 442
                                        ++++l+ ++i++a+++l++         +   +++l+i++li+i ++++f   ++ +  +G 
  gi|474934539|ref|YP_007688121.1|  13 AWVLVLLALVIIGAAVVLYMYpeiledivMAAVFVVLIIIALIVITYVAMFILAIPMYIHKGE 75 
                                       344444444444554444444788998885555555555555555666666555665555555 PP

>> MgtE  Divalent cation transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   8.9   0.00065       1.1      39      89 ..      13      65 ..       2      74 .. 0.51

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00065
                                      HHHHHHHHHHHHHHHHHHHHH..HHT-.CTSHHHHHHHHHHHHHHHHHH........HH CS
                              MgtE 39 elrvvlllgvilgllifllal..llgwslllalvvglalvlvllaaall......ilgv 89
                                       +++vll +vi+g++++l+++  +l        +v++a+++vl++ al+      ++  
  gi|474934539|ref|YP_007688121.1| 13 AWVLVLLALVIIGAAVVLYMYpeILED------IVMAAVFVVLIIIALIvityvaMFIL 65
                                      466788888888888888866333333......33333333333333332221112223 PP

>> DUF4714  Domain of unknown function (DUF4714)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.8      0.15   2.5e+02      81     106 ..      10      34 ..       3      44 .. 0.60
   2 ?   10.0   0.5   0.00037      0.61      85     116 ..      48      79 ..      41      91 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.15
                           DUF4714  81 grgafll.llallvltclalailavyl 106
                                       g+ga++l llal+++   a  +l +y 
  gi|474934539|ref|YP_007688121.1|  10 GKGAWVLvLLALVIIG--AAVVLYMYP 34 
                                       5677655156666554..334555565 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00037
                           DUF4714  85 fllllallvltclalailavylsvlqseslrv 116
                                        l+++al+v+t +a+ ila+ + + + e ++v
  gi|474934539|ref|YP_007688121.1|  48 VLIIIALIVITYVAMFILAIPMYIHKGEQVQV 79 
                                       58899***************999999998877 PP

>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   2.6      0.12     2e+02       9      23 ..      15      29 ..      13      37 .. 0.89
   2 ?    8.7   0.6    0.0021       3.4      10      48 ..      47      87 ..      40     107 .. 0.61

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.12
                           Pilin_N  9 viLmvaitvIlaAvi 23
                                      v+ ++a+++I aAv+
  gi|474934539|ref|YP_007688121.1| 15 VLVLLALVIIGAAVV 29
                                      6789**********9 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0021
                           Pilin_N 10 iLmvaitvIlaAviaafvlgl..asneekapqasievkids 48
                                      + ++ i +I++  +a f+l +     + ++ q+  + +id+
  gi|474934539|ref|YP_007688121.1| 47 VVLIIIALIVITYVAMFILAIpmYIHKGEQVQVGASYSIDD 87
                                      44566777888999999999854333333333333333333 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   7.2     0.009        15      12      59 ..      13      58 ..      12      71 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.009
                            DUF202 12 aWlRtslalialglallrffltgepsalg.kilglilivlgiltllvgl 59
                                      aW+ ++lal+++g+a++       p+ l   +++++++vl i++l+v +
  gi|474934539|ref|YP_007688121.1| 13 AWVLVLLALVIIGAAVVLY---MYPEILEdIVMAAVFVVLIIIALIVIT 58
                                      8****************84...444444325667676666666666543 PP

>> DUF1129  Protein of unknown function (DUF1129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   8.2    0.0073        12     140     197 ..       3      60 ..       1      73 [. 0.84

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0073
                           DUF1129 140 kkkrpplwkrllilllllvvwlvlftlvallpaviNpvLpplvliiigviafvvryyl 197
                                       + +++p+ k +++l+ll +v++ + +++ + p+ +   +++ v +++ +ia++v  y+
  gi|474934539|ref|YP_007688121.1|   3 TVEKRPVGKGAWVLVLLALVIIGAAVVLYMYPEILEDIVMAAVFVVLIIIALIVITYV 60 
                                       56899999**********************9999999988887777777777666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1614  (0.0900218); expected 358.6 (0.02)
Passed bias filter:                      773  (0.0431145); expected 358.6 (0.02)
Passed Vit filter:                       146  (0.00814323); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 685.52
//
Query:       gi|474934540|ref|YP_007688122.1|  [L=189]
Description: polyprenyl P-hydroxybenzoate and phenylacrylic acid decarboxylase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-16   59.8   0.0    3.4e-16   59.4   0.0    1.1  1  Flavoprotein  Flavoprotein


Domain annotation for each model (and alignments):
>> Flavoprotein  Flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.4   0.0   1.9e-20   3.4e-16       1     125 [.       1     160 [.       1     176 [. 0.82

  Alignments for each domain:
  == domain 1  score: 59.4 bits;  conditional E-value: 1.9e-20
                                       EEEEEEE-SSCGGGCHHHHHHHHHHTTEEEEEEESCHHHHCCHHG.GS....TCSSHHHHHHCT............. CS
                      Flavoprotein   1 kkillgiTGsvaaikalellekLkkegievqvvltkaAkkfiske.klklaaredpilhielrr............. 63 
                                       ++ ++ +TG+++a ++++ll++L     e  +v++++Ak ++ +e  ++++            +             
  gi|474934540|ref|YP_007688122.1|   1 MRFVVTMTGASGAAYGVRLLRELPG---EKILVMSRTAKAILPEEtHCTVD------------Qvyamadavyeddd 62 
                                       6899********************8...6779***********88333332............22233334455577 PP

                                       ..........TESEEEEEEEEHHHHHHHHTT--SSHH..............................HHHHHTHCCT CS
                      Flavoprotein  64 ..........wadllviaPasantlakianGiadnll..............................tlilratakk 100
                                                  +d+l ++P+s  + ak+a+Giad+l+                               l+    a+ 
  gi|474934540|ref|YP_007688122.1|  63 lfapvasgtfDYDALFVCPCSESSAAKFACGIADTLIsravacaikegrktvlvtrespksaimlenELK---LARN 136
                                       7778999999*************************************************97665544223...3556 PP

                                       TEEEEE.--HHCCTCSTCHHHHHHH CS
                      Flavoprotein 101 piliaPamnpamyenpqtlknlekl 125
                                       + +++  +np +y +pqt+++++ +
  gi|474934540|ref|YP_007688122.1| 137 GCVMMD-ANPGFYPKPQTVDDIVGF 160
                                       666666.**************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1238.73
//
Query:       gi|474934541|ref|YP_007688123.1|  [L=634]
Description: universal archaeal KH-domain/beta-lactamase-domain protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-23   83.3   0.0    2.8e-23   82.3   0.0    1.6  1  Beta-Casp      Beta-Casp domain
    1.9e-21   75.8   5.4    1.6e-18   66.4   0.0    3.1  4  KH_7           KH domain
    1.2e-17   63.6   0.0      3e-17   62.3   0.0    1.8  1  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    6.1e-15   55.2   0.0    1.2e-14   54.2   0.0    1.4  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
      2e-14   53.6   0.0    4.1e-14   52.6   0.0    1.6  1  Lactamase_B_2  Beta-lactamase superfamily domain
    3.1e-14   53.5   0.6    2.5e-13   50.5   0.6    2.2  1  Lactamase_B    Metallo-beta-lactamase superfamily
    0.00044   20.2   0.0    0.00099   19.0   0.0    1.5  1  Lactamase_B_3  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
        0.1   12.7   0.1       0.99    9.5   0.0    2.4  2  Resolvase      Resolvase, N terminal domain
       0.13   11.6   0.0       0.48    9.7   0.0    1.8  2  HEM4           Uroporphyrinogen-III synthase HemD


Domain annotation for each model (and alignments):
>> Beta-Casp  Beta-Casp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.3   0.0   1.4e-26   2.8e-23       2     110 .]     420     544 ..     419     544 .. 0.88

  Alignments for each domain:
  == domain 1  score: 82.3 bits;  conditional E-value: 1.4e-26
                                       HHHHHHH..HCTT..TTS-S-EEEEE-HHHHHHHHHGGGGGG.........................E-SHH....H CS
                         Beta-Casp   2 qellylLeelwkekkledlklpiyldsplaskatevYkeyae.........................veakslewme 53 
                                       qe+++++eel + ++     +p+yld+ ++ +at+++++y+e                         ve+       
  gi|474934541|ref|YP_007688123.1| 420 QEVMLVIEELERTGAI--DPIPVYLDG-MIWEATAIHTAYPEylnnnlrtdifqnnhnpflseifhkVET------A 487
                                       9**********99762..239******.*************9***********99999998877633222......3 PP

                                       HHH..HHHS-SSEEEEES-TTSSSSHHHHHHHHHTTSTTSEEEESS---TTSHHHHH CS
                         Beta-Casp  54 skkeelnsskgpkvilassgmlegGrsrellkklledprntvilvgyqaegTlgrkl 110
                                       +++ee+ +s++p+++la+sgm++gG++ e+++++++d rn +++vgyq+e +lgr++
  gi|474934541|ref|YP_007688123.1| 488 DMREEICHSPDPCIVLATSGMMSGGPVMEYFREWCDDDRNWLLFVGYQSETSLGRTI 544
                                       3444677899*********************************************86 PP

>> KH_7  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.4   0.0     8e-22   1.6e-18       3      66 ..       6      69 ..       4      71 .. 0.96
   2 !   11.1   0.1   0.00015       0.3       5      26 ..      75      96 ..      72     112 .. 0.92
   3 ?   -3.9   0.1         7   1.4e+04      44      55 ..     159     170 ..     157     172 .. 0.75
   4 ?   -3.8   0.1       6.6   1.3e+04       5      24 ..     581     600 ..     579     601 .. 0.78

  Alignments for each domain:
  == domain 1  score: 66.4 bits;  conditional E-value: 8e-22
                              KH_7  3 vleelkekieeklPkevkitdveFEGPelViYtknpklfaengdlirklAkelrkRiviRpDps 66
                                       ++ l+e++   +Pk++k++++eFEG+ +V+Y kn ++f++n+ l r++A+++r+R+  RpDp+
  gi|474934541|ref|YP_007688123.1|  6 LFDSLREQVSGMIPKDMKVSSIEFEGSLIVVYLKNYDEFSSNTALPRQIAQTVRRRVEFRPDPQ 69
                                      57899*********************************************************97 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00015
                              KH_7  5 eelkekieeklPkevkitdveF 26
                                      +e+++ki + +Pk+++itd++F
  gi|474934541|ref|YP_007688123.1| 75 DEVEKKIRSLIPKKAEITDINF 96
                                      799*****************99 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 7
                              KH_7  44 ngdlirklAkel 55 
                                       ++++++k+A++l
  gi|474934541|ref|YP_007688123.1| 159 RQKILKKVARNL 170
                                       678888888877 PP

  == domain 4  score: -3.8 bits;  conditional E-value: 6.6
                              KH_7   5 eelkekieeklPkevkitdv 24 
                                       ++l++ ie+  Pk  ki  v
  gi|474934541|ref|YP_007688123.1| 581 KQLMQFIETMSPKPSKIIVV 600
                                       67888899999998888755 PP

>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.3   0.0   1.5e-20     3e-17       3      62 .]     563     625 ..     561     625 .. 0.95

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 1.5e-20
                             RMMBL   3 pvkarieeid.fSgHadknellelirklkprn..vilvHGeeeatsalarllkeeegidvfiP 62 
                                        +++  e++d fSgH+d+ +l+++i++++p++  +i+vHGe +++s+la+ + ++ +i +++P
  gi|474934541|ref|YP_007688123.1| 563 QIRMNRETVDgFSGHSDRKQLMQFIETMSPKPskIIVVHGEDRKCSDLASSIFQKCKIQTVAP 625
                                       79**************************************************99999988776 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.2   0.0   5.8e-18   1.2e-14       1     157 [.     198     346 ..     198     367 .. 0.84

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 5.8e-18
                     Lactamase_B_6   1 lLeldnvkiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallyakfksklllnipvyatlpvvk 77 
                                       lL+  n kiL+D+G d  ++ +     +  + ++++d+++++ha l+h G ++ l++     ++ + pvy+t p+  
  gi|474934541|ref|YP_007688123.1| 198 LLTTKNSKILIDCGLDPGSDATPYFNIPEANPLSDIDAVVITHAHLDHCGTLPALFK-----YGYDGPVYCTAPTRD 269
                                       688899**********98665544444556679*****************9887774.....67899********** PP

                     Lactamase_B_6  78 LGrvslldlyaskgllgpedseeleledideafdkiktlkYsQklelkskldgltitaynaGhtlGGti..Wkiske 152
                                       L  ++ ld ++ +   g+ +++  + +d+++   + ++lkY  ++++     ++ +t  naGh lG +i  ++i ++
  gi|474934541|ref|YP_007688123.1| 270 LMALLQLDNIKLA--WGEAKKALYDAKDVRNEILHTIPLKYGETTDIAP---DVRLTLQNAGHILGSAIahFHIGDG 341
                                       *999999998755..778888999*********************9995...7999999********9855667666 PP

                     Lactamase_B_6 153 sekiv 157
                                       ++++ 
  gi|474934541|ref|YP_007688123.1| 342 LHNVA 346
                                       66665 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   0.0     2e-17   4.1e-14       2     166 ..     205     378 ..     204     413 .. 0.76

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 2e-17
                                       EEEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC.C--EEEEEEEEHHHHH......... CS
                     Lactamase_B_2   2 riLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlre.lrpkklplyapkgvla......... 68 
                                        iLiD+g+d    a+++  + +  + l++idaV++thaH DH+  l+ l + ++  + p+y+++ +++         
  gi|474934541|ref|YP_007688123.1| 205 KILIDCGLDPGSDATPYF-NIPEANPLSDIDAVVITHAHLDHCGTLPALFKyGY--DGPVYCTAPTRDlmallqldn 278
                                       59*******766688888.4445667779**********************443..479****98888666555555 PP

                                       .....HCCTTCGHHHCHTT............TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEE CS
                     Lactamase_B_2  69 .....vleanfvylaleee............pavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGl 128
                                                        e+             ++++ +l+ ge+++++ +++++t+  a h  g         ++ +
  gi|474934541|ref|YP_007688123.1| 279 iklawG-----------EAkkalydakdvrnEILHTIPLKYGETTDIA-PDVRLTLQNAGHILGS-------AIAHF 336
                                       544442...........33455555555558899999999*******9.5888898888888888.......99*** PP

                                       EEECTTEEEEEESS-S---....HHHHHHHCT-SEEEEE-S- CS
                     Lactamase_B_2 129 riegggkrvyyigDtgyip....eeigerlggadlllldita 166
                                        i++g ++v+++gDt++ +     ++ +++  ++ l+++ t+
  gi|474934541|ref|YP_007688123.1| 337 HIGDGLHNVAFSGDTKFEKtwlfNQANNKFPRLETLVVESTY 378
                                       ****************65544444555677777777777765 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5   0.6   1.3e-16   2.5e-13       5     160 ..     193     360 ..     190     401 .. 0.73

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 1.3e-16
                                       SSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHC CS
                       Lactamase_B   5 pvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapa 81 
                                       + ++ l++++++ iLiD+G+++  +   +    +  ++ d+dav++TH+HlDH+G l+ l +     ++++ + ++ 
  gi|474934541|ref|YP_007688123.1| 193 GRSASLLTTKNSKILIDCGLDPGSDATPYFNIPEANPLSDIDAVVITHAHLDHCGTLPALFKYGYDGPVYCTAPTRD 269
                                       568999*********************99777788999********************9988887777777777777 PP

                                       CHCHHHHH.HHHHCCHH..............TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTC CS
                       Lactamase_B  82 lfmeeadd.aasrkgll..............lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveyggg 143
                                       l      d    +   +               ++ + ++    e  +   +    ++ + ++ g+   h+++++g  
  gi|474934541|ref|YP_007688123.1| 270 LMALLQLDnIKLA---WgeakkalydakdvrNEILHTIPLKYGETTDIAPDVRLTLQNAGHILGSAIAHFHIGDGLH 343
                                       7666664403344...2456*******97653334444444444444444444445556788888999********* PP

                                       CEEEECTTTSSHHCCCC CS
                       Lactamase_B 144 kvlftGDallagetgri 160
                                       +v+f+GD+ ++  ++  
  gi|474934541|ref|YP_007688123.1| 344 NVAFSGDTKFEKTWLFN 360
                                       ********997766555 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   4.9e-07   0.00099       6      51 ..     193     247 ..     190     290 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 4.9e-07
                     Lactamase_B_3   6 ghnsflletagarilvDPf........ka.nlgyeppaeeaDlvlisqaledHah 51 
                                       g ++ ll+t++ +il+D +         + n+  ++p  ++D+v+i++a+ dH+ 
  gi|474934541|ref|YP_007688123.1| 193 GRSASLLTTKNSKILIDCGldpgsdatPYfNIPEANPLSDIDAVVITHAHLDHCG 247
                                       789999**********9886666655422455555555***************95 PP

>> Resolvase  Resolvase, N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.47   9.4e+02       2      13 ..     149     161 ..     148     195 .. 0.78
   2 ?    9.5   0.0    0.0005      0.99      35      75 ..     567     605 ..     545     614 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.47
                                       EEEEEES---.-- CS
                         Resolvase   2 igYaRvStee.qd 13 
                                        gY+R S +e q+
  gi|474934541|ref|YP_007688123.1| 149 RGYIRYSHDErQK 161
                                       59******99655 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0005
                                       ...EEEE.S-TT-TT-HHHHHHHHHHTT-EE.EEEESSCCC CS
                         Resolvase  35 vkefeDkgvSGakleRpglkrllaalregkgdvlvvekldR 75 
                                        +e +D  +SG + +R++l+++++ ++++  +++vv+  dR
  gi|474934541|ref|YP_007688123.1| 567 NRETVDG-FSGHS-DRKQLMQFIETMSPKPSKIIVVHGEDR 605
                                       4466777.99999.9*************999*****98887 PP

>> HEM4  Uroporphyrinogen-III synthase HemD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00024      0.48      89     129 ..     377     418 ..     371     442 .. 0.71
   2 ?   -1.7   0.0      0.76   1.5e+03     101     129 ..     577     606 ..     524     614 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00024
                                       HTT---SEE-..SSSHHHHGGGS-.---E.EEEEE-SS.S-- CS
                              HEM4  89 elglrvdlvpseegtaegLaeelaeslag.krvlllrgeiar 129
                                        +g ++d+ ps+++ +e+L e+++e+ +  +++l+++   +r
  gi|474934541|ref|YP_007688123.1| 377 TYGGKKDFQPSRKEASEQLGEFIKEAASHgGKILIPVFAVGR 418
                                       5899*********************66666999996544443 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.76
                                       SSSHHHHGGGS-.---E.EEEEE-SS.S-- CS
                              HEM4 101 egtaegLaeelaeslag.krvlllrgeiar 129
                                         + ++L+++++   ++ +++++++ge+++
  gi|474934541|ref|YP_007688123.1| 577 HSDRKQLMQFIETMSPKpSKIIVVHGEDRK 606
                                       556689999999988888999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (634 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.48
# Mc/sec: 3995.65
//
Query:       gi|474934542|ref|YP_007688124.1|  [L=216]
Description: 20S proteasome, alpha and beta subunits [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.5e-49  168.1   2.8    1.7e-49  167.9   2.8    1.0  1  Proteasome  Proteasome subunit


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.9   2.8   9.4e-54   1.7e-49       1     190 []      12     190 ..      12     190 .. 0.96

  Alignments for each domain:
  == domain 1  score: 167.9 bits;  conditional E-value: 9.4e-54
                                       HHHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSS CS
                        Proteasome   1 vkkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygr 77 
                                       vk+Gtt++G+k kdgvvla+d+rat+g+ +++++ v+K++ i d++g++++Gl++Da+ +vr+++++++ y+++ g 
  gi|474934542|ref|YP_007688124.1|  12 VKTGTTTIGMKIKDGVVLATDQRATMGNLIANSH-VQKVYPIADNLGMTISGLVGDAQLMVRYMQSQVSIYEMQKGA 87 
                                       79****************************7777.9***************************************** PP

                                       GTCHHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHH CS
                        Proteasome  78 pipverlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekey 154
                                       +++v      +aa+l++   r+    f+++ ++ag+d++g  +++++d +G +ie++ +++ Gsgs  a++ale++y
  gi|474934542|ref|YP_007688124.1|  88 QMSVA-----TAATLLGSVIRQ---GFYLGPILAGYDRTG-GHVFSVDGAGGVIEDD-YTSSGSGSVTAYGALESLY 154
                                       *****.....888888888888...68**********999.6**************6.******************* PP

                                       STTBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEEEE CS
                        Proteasome 155 kedltleeavelavkalkealerdklsgknievavi 190
                                       k+++t+e+a+++a+  l++a +rd+++g+++ + +i
  gi|474934542|ref|YP_007688124.1| 155 KPNMTKEQAIDVAIAGLNAARRRDNYTGDGMLILII 190
                                       *****************************9877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1493.87
//
Query:       gi|474934543|ref|YP_007688125.1|  [L=749]
Description: ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   3.1e-112  375.8   0.0   5.1e-112  375.1   0.0    1.4  1  Ribonuc_red_lgC  Ribonucleotide reductase, barrel domain


Domain annotation for each model (and alignments):
>> Ribonuc_red_lgC  Ribonucleotide reductase, barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  375.1   0.0  2.8e-116  5.1e-112       1     524 []      68     541 ..      68     541 .. 0.93

  Alignments for each domain:
  == domain 1  score: 375.1 bits;  conditional E-value: 2.8e-116
                                       EEE......BSS-EEEE-X..............XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC   1 ssCfvlsv.edslesIletvkeaallskaggGvGlnlsklRakgslvkgtegaasGpvsfmklidavadvvkqgGkR 76 
                                       s+C+v+++ eds+esI++ +++aa+++++ggGvG++lskl ++g+ +++t++a+sG vsf +l+  v+  + q G R
  gi|474934543|ref|YP_007688125.1|  68 SNCYVIEPpEDSIESIFQCASKAARTFSYGGGVGIDLSKLAPRGAKINNTASATSGAVSFTDLFSMVTGLIGQHG-R 143
                                       79****999******************************************************************.* PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXX......... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC  77 rGAamvylevwHpDiekfidaKekntgeeenrlsnlnisvgvpdlFmeavkedkdwtLfs..Prtvvkleklygeef 151
                                       rGA m+++++ HpD e+f+ +K     ++  r++++n+s++v+d+Fme v++++++  +   P+t            
  gi|474934543|ref|YP_007688125.1| 144 RGALMLTMSCEHPDLEEFMAVK-----TDLDRVTKANMSIRVTDKFMECVRDKETFVQTFvrPET------------ 203
                                       **********************.....3588*********************9999766622552............ PP

                                       ................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 152 eeeyeeleekakikkkevkakeLfeeiaesawetgePgvlfkDtiNrrnvlekakggkIratNlCgEiplleyesva 228
                                                 ++ + k+ +a   f+++ ++ w++gePg l++D+i ++n l+     +   tN+C+E+pl+   s  
  gi|474934543|ref|YP_007688125.1| 204 ----------NDTTVKNLDAYGFFKKLCYANWDYGEPGCLYWDRISKWNLLSEFPDYEYAGTNPCAEEPLPAGGS-- 268
                                       ..........2345569**********************************88889*******************.. PP

                                       .XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 229 vCnLasinLakfvkkdeegkkefdwdelkkviqlvvraLdnvidv..nkyplpeiekntkktRriGlGvmgladala 303
                                        C L+s+nL++fv     ++ +fd +e+++ + + vraL++v++      pl+e++++    R+iGlG+mglad+l+
  gi|474934543|ref|YP_007688125.1| 269 -CLLGSMNLSEFV-----KDGKFDEEEFREGVAICVRALNDVLEEglPLHPLQEQKDSVAGWRQIGLGIMGLADMLI 339
                                       .************.....358**********************974467899************************* PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX......XXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 304 klgipydseealkfarkitelltyyaykaSvelAkergpfplfekskyskgilpvdefeekekedweeLreeikkyG 380
                                       kl++ y+++ea++f +k+ + ++ +a+ aS++lAkerg fp  +  ++       ++         ee++e +k+yG
  gi|474934543|ref|YP_007688125.1| 340 KLEMTYGTKEAMDFCHKLGRIMADAALIASANLAKERGRFPRCNIDQILASPYFQEN-------ASEEAVELVKQYG 409
                                       *******************************************99999999633333.......489********** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 381 lrnamvtalaPTgsiSliagtssgiePifalvykksvtv....geflevnpvfee.eLkklglwseellkkilesvq 452
                                       lrn++++++aPTg+ S + g s giePifa ++++++t+    +ef++v p +++  + + gl+     ++      
  gi|474934543|ref|YP_007688125.1| 410 LRNSQILTIAPTGTLSTMLGISGGIEPIFATHFERRTTSlsdhDEFYKVYPPVVKdYMDAHGLK-----DD------ 475
                                       ***************************************9999999999776643034444444.....33...... PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 453 gleeipeeikrvfktaldidqedhikaqaaiqkwidqsiSktinlpneatvedvkelyllAwklGlKgvtyY 524
                                             +e+ ++f+ta ++d ++ +++q ++q++id siS t+nlp++ + e+v +ly++Aw+ G+Kgvt++
  gi|474934543|ref|YP_007688125.1| 476 ------SELPPFFVTAQNLDYKQRLNLQGTWQMHIDASISSTVNLPEDFPEENVYDLYIYAWQIGCKGVTVF 541
                                       ......7899************************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (749 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1016  (0.056668); expected 358.6 (0.02)
Passed bias filter:                      704  (0.039266); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.69u 0.33s 00:00:01.02 Elapsed: 00:00:00.47
# Mc/sec: 4800.76
//
Query:       gi|474934544|ref|YP_007688126.1|  [L=470]
Description: hypothetical protein TALC_00973 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0001   22.2   0.3     0.0001   22.2   0.3    3.4  3  T2SSF     Type II secretion system (T2SS), protein F
  ------ inclusion threshold ------
      0.079   12.5   0.0       0.12   11.9   0.0    1.2  1  Myb_Cef   pre-mRNA splicing factor component


Domain annotation for each model (and alignments):
>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.3   1.2e-08    0.0001       4     123 ..      25     153 ..      22     156 .. 0.78
   2 ?   -5.9   2.8         2   1.8e+04     109     122 ..     176     189 ..     174     191 .. 0.53
   3 ?    1.0   0.2     0.044     4e+02      44      44 ..     319     319 ..     254     400 .. 0.51

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.2e-08
                                       HHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTS..SHHHHHC.........T-TT.TS-HHHHHHHH CS
                             T2SSF   4 qlatllsaGvplveaLellaeeaengplaeelkriarrlraGg..slseale.........rtpssefpelvvqlir 69 
                                        +   l++G +l++a++ +a+   ++  ++ ++++ ++ +     +++++l+         +   s + + + ++i+
  gi|474934544|ref|YP_007688126.1|  25 MMTAVLGNGGSLDAAIREVASDG-PPLSRRMFRSVTDDADTRVesDMRTSLRerlsalpegS---SSYGMAMHMVIS 97 
                                       578899*****************.***************99998866777776665554321...344444444444 PP

                                       HH..HHHT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXX CS
                             T2SSF  70 ag..eeggnLaevLerlaeyleeerelrrkllaallepllllvvallvllillail 123
                                       a   + +g  + +L+++++   + ++ + k+ +++l +  + v+++ ++++++++ 
  gi|474934544|ref|YP_007688126.1|  98 ASdtRDTGERERMLKDASDIALQGLREAGKSYSSSLNVPCMTVFGVGIMIPMVLMS 153
                                       4322678999**************************98777777777777777764 PP

  == domain 2  score: -5.9 bits;  conditional E-value: 2
                                       XXXXXXXXXXXXXX CS
                             T2SSF 109 lvvallvllillai 122
                                       +v++++++++++ +
  gi|474934544|ref|YP_007688126.1| 176 AVTVVIIPMFVMCV 189
                                       45555555555554 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.044
                                       T CS
                             T2SSF  44 a 44 
                                        
  gi|474934544|ref|YP_007688126.1| 319 T 319
                                       2 PP

>> Myb_Cef  pre-mRNA splicing factor component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.3e-05      0.12      52     113 ..      62     123 ..      51     134 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.3e-05
                           Myb_Cef  52 eekqrqkeakeqLrsgLasLPkPkndyeivvpeeeeeee.eeeee.eeekveeDaadidarkka 113
                                       +  + +++++ +Lr++L++LP+ +  y + +      ++ ++  + e+e + +Da+di  +  +
  gi|474934544|ref|YP_007688126.1|  62 ADTRVESDMRTSLRERLSALPEGSSSYGMAMHMVISASDtRD--TgERERMLKDASDIALQGLR 123
                                       44567899*********************9977664322233..34699********9876555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (470 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 3297.08
//
Query:       gi|474934545|ref|YP_007688127.1|  [L=590]
Description: Type IV secretory pathway, VirB11 components,-related ATPase involved in archaeal flagella biosynthesis [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.3e-32  110.5   0.1    1.5e-31  109.5   0.0    1.5  2  T2SSE         Type II/IV secretion system protein
  ------ inclusion threshold ------
       0.02   14.6   0.0      0.048   13.4   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
      0.043   13.0   0.0        0.1   11.7   0.0    1.6  1  DUF815        Protein of unknown function (DUF815)
      0.073   12.4   0.0       0.14   11.5   0.0    1.4  1  FtsK_SpoIIIE  FtsK/SpoIIIE family
      0.087   12.3   0.0       0.17   11.4   0.0    1.4  1  AAA_7         P-loop containing dynein motor region
        0.1   13.0   0.0       0.23   11.8   0.0    1.7  1  AAA_16        AAA ATPase domain
       0.15   12.6   0.0       0.57   10.7   0.0    1.7  1  ABC_tran      ABC transporter


Domain annotation for each model (and alignments):
>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.5   3.8e+03       9      48 ..     109     150 ..     102     176 .. 0.67
   2 !  109.5   0.0     6e-35   1.5e-31       4     251 ..     187     455 ..     184     472 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.5
                             T2SSE   9 lddekvsdihvekpervkvrervdg..ielreveelekaale 48 
                                       ++ + v+ i++e  ++v+ ++r++g   +  +v +++k+ + 
  gi|474934545|ref|YP_007688127.1| 109 VASDAVNGIIIEAIDAVRKEFRKNGgrADRYAVDSVSKEVIG 150
                                       467788889999999988888887733444445555555555 PP

  == domain 2  score: 109.5 bits;  conditional E-value: 6e-35
                             T2SSE   4 lleallddekvsdihvekper.vkvrervdg.......ielreveelekaalerlisriaalakldiseerplqdar 72 
                                       +++ ll+d+k  di v  p +  +++ ++ g       ++ r+   +++++++ li+ ++  ++l   e++p+++  
  gi|474934545|ref|YP_007688127.1| 187 VFDILLADPKLEDIYVDAPCDkNRIHVTMSGvdgtnshLRCRTNLVVDRREVMNLINVLKRDSGLPYCESSPVLETD 263
                                       56788999999999999875548887766554446656778889999****************************** PP

                             T2SSE  73 lpekgvrlrvvllPvvag.ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllya 148
                                       + +  +r  vv  P++    a++iRk+sa+  t+  l+a+++ ++  a ++++ v++r ++lv G+ g GK+ ll a
  gi|474934545|ref|YP_007688127.1| 264 MRQYDARATVVGFPMSPLgDAVAIRKHSANPWTMTRLIANGTISHLDAGLISYLVQNRATFLVCGARGAGKSSLLSA 340
                                       ***************99889********************************************************* PP

                             T2SSE 149 llkeinksderivtvEDpvEiqleganqvqlnak..........kakvtfadllraaLRlrPDrimvGEiRdketle 215
                                       ++ e++ s +ri+t+ED+ E+  e   ++  + +          +     +++lr +LRl    i++GE+R++e+ +
  gi|474934545|ref|YP_007688127.1| 341 MMFEFPVS-QRILTIEDTLELPGERLRCMGYKVQsllvddrmdgDSLSRSNEALRVSLRLGESAIILGEVRGEEART 416
                                       ********.************9999988888888888888888766777899************************* PP

                             T2SSE 216 ilkAvnTGHlgs..lsTlHansaagalerL.eqlgaeve 251
                                       + +++ TG  gs  ++T+H +sa+ ++er+ +++g   e
  gi|474934545|ref|YP_007688127.1| 417 LYQSMRTGRAGSsiMGTIHGDSAKTVFERVvHDMGISPE 455
                                       ***********9889**************6367984433 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.9e-05     0.048      23      43 ..     322     342 ..     312     349 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.9e-05
                            AAA_29  23 gatlltGpsGsGKSTllDAiq 43 
                                        ++l+ G+ G+GKS+ll A++
  gi|474934545|ref|YP_007688127.1| 322 ATFLVCGARGAGKSSLLSAMM 342
                                       3699*************9997 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0     4e-05       0.1      55      78 ..     323     346 ..     302     368 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4e-05
                            DUF815  55 nvLLwGarGtGKSslvkallneya 78 
                                         L+ GarG+GKSsl+ a++ e+ 
  gi|474934545|ref|YP_007688127.1| 323 TFLVCGARGAGKSSLLSAMMFEFP 346
                                       46999*************998764 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   5.5e-05      0.14      38      61 ..     320     343 ..     297     345 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.5e-05
                                       S-.SEEEE--TTSSHHHHHHHHHH CS
                      FtsK_SpoIIIE  38 mashllvaGatgsGKStalntLil 61 
                                       + +  lv+Ga g GKS  l +++ 
  gi|474934545|ref|YP_007688127.1| 320 NRATFLVCGARGAGKSSLLSAMMF 343
                                       44568*****************95 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   6.7e-05      0.17      25      58 ..     313     346 ..     307     356 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.7e-05
                             AAA_7  25 llelllknkkpvllvGptGtGKtviikdllkkld 58 
                                       l++ l++n+  +l++G  G GK+++++ ++ +++
  gi|474934545|ref|YP_007688127.1| 313 LISYLVQNRATFLVCGARGAGKSSLLSAMMFEFP 346
                                       68899*********************99887776 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   8.9e-05      0.23      26     123 ..     323     421 ..     305     433 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.9e-05
                            AAA_16  26 lvllsGesGvGKsslvrellralekd.ggiflrgkcdqlesaipysa.laqalareellrqlldeaesaeleawrek 100
                                         l+ G++G GKssl+ + + ++  + ++++++ + +  ++ ++     +q l   +   + ++ ++s+e+ + + +
  gi|474934545|ref|YP_007688127.1| 323 TFLVCGARGAGKSSLLSAMMFEFPVSqRILTIEDTLELPGERLRCMGyKVQSL-LVDDRMDGDSLSRSNEALRVSLR 398
                                       679*************6655444333146666666666655544444344444.22444444444667777777777 PP

                            AAA_16 101 leealaavpelagaeasrllell 123
                                       l e++ + +e++g+ea+ l++ +
  gi|474934545|ref|YP_007688127.1| 399 LGESAIILGEVRGEEARTLYQSM 421
                                       77777777777777776666655 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00022      0.57       8      37 ..     318     347 ..     313     392 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00022
                                       EETTSEEEEEESTTSSHHHHHHHHTTSS-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkp 37 
                                       +++  +  + G  GaGKS+Ll++++ +   
  gi|474934545|ref|YP_007688127.1| 318 VQNRATFLVCGARGAGKSSLLSAMMFEFPV 347
                                       5666778899*************9877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (590 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 3768.58
//
Query:       gi|474934546|ref|YP_007688128.1|  [L=170]
Description: hypothetical protein TALC_00975 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.89    9.6  10.1        4.9    7.3   1.9    2.4  3  DZR       Double zinc ribbon


Domain annotation for each model (and alignments):
>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   1.0   0.00049       8.8      29      48 ..      26      45 ..      11      46 .. 0.84
   2 ?    6.7   6.0   0.00039       7.1       1      37 [.      28     102 ..      28     112 .. 0.92
   3 ?    7.3   1.9   0.00027       4.9      10      36 ..      91     141 ..      86     147 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.00049
                               DZR 29 drCpsCgekvdpearfCpeC 48
                                        C  C++  d+++ +C  C
  gi|474934546|ref|YP_007688128.1| 26 VDCRGCQQVPDAGSPVCIRC 45
                                      67999999999999999999 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.00039
                               DZR   1 CpqCgeelppdarfCseCgtklkavaa......................................edrCpsCgek 37 
                                       C  C++  ++++ +C +C t+  a +                                        +rC +C+++
  gi|474934546|ref|YP_007688128.1|  28 CRGCQQVPDAGSPVCIRCITSAIASEGnsdrirltagkdteisgdaadilcdlatmdrspvpvsgDRRCRQCQRS 102
                                       999******************885555899**********************************99******986 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.00027
                               DZR  10 pdarfCseCgtklkavaa........................edrCpsCge 36 
                                       +++r C +C+ ++ av +                        +  C sC +
  gi|474934546|ref|YP_007688128.1|  91 SGDRRCRQCQRSPWAVMDaawadfpepnfayakgrlhsesgdMAECASCMQ 141
                                       57899*******9988889999********************99*****76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1036.65
//
Query:       gi|474934547|ref|YP_007688129.1|  [L=475]
Description: Carbon starvation protein, predicted membrane protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-45  154.6  21.6    4.9e-32  111.3   9.3    3.2  3  CstA            Carbon starvation protein CstA
    1.3e-17   64.2   8.6    1.3e-17   64.2   8.6    3.8  3  CstA_5TM        5TM C-terminal transporter carbon starvation 
  ------ inclusion threshold ------
       0.01   14.6   5.1       0.01   14.6   5.1    3.8  3  Na_H_Exchanger  Sodium/hydrogen exchanger family
        9.3    6.0   7.6        4.3    7.1   0.2    3.5  3  Neurensin       Neurensin


Domain annotation for each model (and alignments):
>> CstA  Carbon starvation protein CstA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.3   9.3   1.1e-35   4.9e-32       4     203 ..       1     198 [.       1     198 [. 0.94
   2 !   57.3   4.4   2.7e-19   1.2e-15     221     343 ..     159     275 ..     151     287 .. 0.85
   3 ?   -1.5   6.0       0.2   9.1e+02     144     207 ..     361     429 ..     316     466 .. 0.49

  Alignments for each domain:
  == domain 1  score: 111.3 bits;  conditional E-value: 1.1e-35
                              CstA   4 vllvvvavvvfviayrfYgkfiakkvlklddkraTPaerledgkdyvptnklvlfghhFasiagagPlvGpvlAaqf 80 
                                       +++++++++ ++++y fY+k i++++     +++TPa   +dg+dy+p+ ++  +  +   iag+gP+ G+ + a++
  gi|474934547|ref|YP_007688129.1|   1 MMILILGAIALLLGYLFYSKLIERTIRPF--REPTPAVSRDDGRDYTPMPRWKNHLIQLLNIAGTGPIFGALMGAKW 75 
                                       578999999****************6554..579******************************************* PP

                              CstA  81 GylPgllWilvGavfagavhDfvvlvasvrrkgkslgelakkelgkvakllallaillililvlavlalvvvkalae 157
                                       G + ++lWi++G+++ gavhD+++ ++svr++g s++ +a+k+lgk a+  +l+  +++li+  a++a   ++ l++
  gi|474934547|ref|YP_007688129.1|  76 GSI-VFLWIVFGTILGGAVHDYMSGMMSVRNDGSSFTAIAHKYLGKWARYPLLVLLVFLLIMWSATFARCAADLLVD 151
                                       *99.99*********************************************************************** PP

                              CstA 158 spaavfsviltipialllGvllrklrkg.vleasvigvvllllavvv 203
                                            +   + +++a ++  +l  ++k    +  v gv+l+++avvv
  gi|474934547|ref|YP_007688129.1| 152 ITGLPLMFWMALILAYFIASALIPINKLiGRIYPVFGVLLIVMAVVV 198
                                       9999999999********99999999985677889999999999875 PP

  == domain 2  score: 57.3 bits;  conditional E-value: 2.7e-19
                              CstA 221 tlaivlivYvfvAsvlPvwlllaPrdYlstflligtivllalgilv...vapelklpavtefvdgegpvfagslfPl 294
                                        +++++++Y ++ + +P+ +l+     +   lli++ v++++g+++     p+++l+    + + +g+    + fP 
  gi|474934547|ref|YP_007688129.1| 159 FWMALILAYFIASALIPINKLIGRIYPVFGVLLIVMAVVVIAGLVIggyGFPSMTLEN---L-HPNGD----TYFPD 227
                                       69999****************987777999999999999999*999544456666666...3.34444....59*** PP

                              CstA 295 lfitiACGaiSGFHslvssgttskllekesdarlvgygamllEslvail 343
                                       + it+ACGaiSGFH+   s   ++ l+ e+d r v ygam++Es++a++
  gi|474934547|ref|YP_007688129.1| 228 MLITVACGAISGFHAT-QSPMIARCLKDERDGRRVFYGAMVIESVIALV 275
                                       ***************6.677899**********************9986 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.2
                              CstA 144 lavlalvvvkal..aespaavfsviltipialllGvllrklrkg...vleasvigvvllllavvvgsev 207
                                       la+ a++v   +   +  +  +s++ +++ a++l +++ +l ++    + + v ++  +++++vv+s +
  gi|474934547|ref|YP_007688129.1| 361 LAIAAIIVLLCFidFTVLWNYTSWLNQTLAAIVLWTATVFLLRTvsnRAYSLVTALPAMFMTMVVSSFI 429
                                       333333333333112223444444444444444433332222221111122222222333333333333 PP

>> CstA_5TM  5TM C-terminal transporter carbon starvation CstA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.2     0.038   1.7e+02      57      75 ..      69      87 ..      43      88 .. 0.75
   2 ?   -0.5   3.6      0.35   1.6e+03      47      84 ..     160     198 ..     120     206 .. 0.71
   3 !   64.2   8.6     3e-21   1.3e-17       3     114 ..     314     426 ..     312     428 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.038
                          CstA_5TM 57 avllllwggintlWplFGa 75
                                      a++ ++wg+i  lW +FG+
  gi|474934547|ref|YP_007688129.1| 69 ALMGAKWGSIVFLWIVFGT 87
                                      33336899**********7 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.35
                          CstA_5TM  47 yvatliavalavllllwg.gintlWplFGaaNQlLAala 84 
                                       ++a ++a ++a +l+ ++  i  ++p+FG+   ++A ++
  gi|474934547|ref|YP_007688129.1| 160 WMALILAYFIASALIPINkLIGRIYPVFGVLLIVMAVVV 198
                                       566666777666663333467799****99666666555 PP

  == domain 3  score: 64.2 bits;  conditional E-value: 3e-21
                          CstA_5TM   3 vaytfailfvalfalTtlDtatRlaRyilqellgelkkkaltnkyvatliavalavllllwggintlWplFGaaNQl 79 
                                       ++ ++a+l v+++ +T+ Dta R aR+++q+  +   +++ + +++ tl+++a++vll+++  +++lW + ++ NQ+
  gi|474934547|ref|YP_007688129.1| 314 IGGVLAVLGVIVCPITSGDTALRSARLMVQDDREVDPSDT-KFTLMITLAIAAIIVLLCFID-FTVLWNYTSWLNQT 388
                                       57789**************************998544444.445566666666666665555.************** PP

                          CstA_5TM  80 LAalaLlvvtvwllktgr...kalvtliPmvfmlvvtl 114
                                       LAa++L+++tv+ll+t     + lvt++P++fm++v+ 
  gi|474934547|ref|YP_007688129.1| 389 LAAIVLWTATVFLLRTVSnraYSLVTALPAMFMTMVVS 426
                                       **************554446899***********9975 PP

>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   3.2     0.076   3.4e+02     173     217 ..      70     112 ..      54     144 .. 0.82
   2 ?   -2.6  19.8      0.39   1.8e+03      18     215 ..     122     349 ..     107     371 .. 0.71
   3 ?   14.6   5.1   2.3e-06      0.01      75     130 ..     407     462 ..     401     469 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.076
                                       SSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTHHHHHHH CS
                    Na_H_Exchanger 173 etslllllliflvvavgglllglvigwllrlitrftdddrelevl 217
                                         ++ +++++fl++++g +l+g+v  +++  ++ +  +d +++++
  gi|474934547|ref|YP_007688129.1|  70 LMGAKWGSIVFLWIVFGTILGGAVHDYMSGMMSVR--NDGSSFTA 112
                                       455669999***************99999999888..66666655 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.39
                                       TTSXHHHHHHHHHHHHTTTTTS........HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHHHHHHHHHHHHHHHH CS
                    Na_H_Exchanger  18 lklpeivgliiaGlllGpsglglieps...eedlevlselglilllFlaGleldlrelrknlksilllallgvlitv 91 
                                        + p +v+l+++ ++    +   +++     + l +++   lil  F a+  +++++l   + +++ ++l+++++ v
  gi|474934547|ref|YP_007688129.1| 122 ARYPLLVLLVFLLIMWSATFARCAADLlvdITGLPLMFWMALILAYFIASALIPINKLIGRIYPVFGVLLIVMAVVV 198
                                       5555555555554444444444333334433677888888999999******************************* PP

                                       HHHHHHHH.H................HTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHHH CS
                    Na_H_Exchanger  92 vliGlllyll................lilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvlnD 152
                                       ++ Gl+++ +                +++++ ++ a  + + + at  +++++ lk+e+  ++ ++  ++ esv+  
  gi|474934547|ref|YP_007688129.1| 199 IA-GLVIGGYgfpsmtlenlhpngdtYFPDMLITVACGAISGFHATQSPMIARCLKDERDGRRVFYGAMVIESVIAL 274
                                       **.99999559999*******9999988899999999889999********************************99 PP

                                       HHCCCCCHHHHHHTX.....XXXXTSSSTS........XHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS..CTHHHH CS
                    Na_H_Exchanger 153 avavvllavllalak.....eeaggetsll........lllliflvvavgglllglvigwllrlitrft..dddrel 214
                                       + a   la++ + a+     +++g+    +         ++ i  v+av+g+++  +++  ++l ++++  +ddre+
  gi|474934547|ref|YP_007688129.1| 275 VWATAGLAFYSGTAGlatelSRIGAS---GvvydistgVAGSIGGVLAVLGVIVCPITSGDTALRSARLmvQDDREV 348
                                       99999999999998666554222222...134455554444444555555555555555555555555566555544 PP

                                       H CS
                    Na_H_Exchanger 215 e 215
                                        
  gi|474934547|ref|YP_007688129.1| 349 D 349
                                       3 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 2.3e-06
                                       THHHHHHHHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC CS
                    Na_H_Exchanger  75 nlksilllallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlail 130
                                       n+  +l+ al+ ++ t+v+++++++ + ++g+++  a+++ga+++a+++v+ ++++
  gi|474934547|ref|YP_007688129.1| 407 NRAYSLVTALPAMFMTMVVSSFIMHSGQGFGLDYNTAIIIGAVVTAVSVVAYARTV 462
                                       56668999*****************76789*********************98876 PP

>> Neurensin  Neurensin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.2   0.00095       4.3      50      69 ..       2      21 ..       1      31 [. 0.89
   2 ?   -0.2   0.4      0.17   7.7e+02      96     118 ..     178     200 ..     171     211 .. 0.69
   3 ?    0.2   0.1      0.12   5.6e+02     101     123 ..     310     332 ..     303     340 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00095
                         Neurensin 50 lvlllGvtallvGylvprrl 69
                                      ++l+lG++all+Gyl  ++l
  gi|474934547|ref|YP_007688129.1|  2 MILILGAIALLLGYLFYSKL 21
                                      89*************98775 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.17
                         Neurensin  96 klaGavllclGglllalsllvpa 118
                                       kl+G +   +G ll++++++v a
  gi|474934547|ref|YP_007688129.1| 178 KLIGRIYPVFGVLLIVMAVVVIA 200
                                       66666666677776666666544 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.12
                         Neurensin 101 vllclGglllalsllvpalsksd 123
                                       v+ ++Gg+l +l+++v ++ + d
  gi|474934547|ref|YP_007688129.1| 310 VAGSIGGVLAVLGVIVCPITSGD 332
                                       67799*******99998877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1163  (0.064867); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.72u 0.29s 00:00:01.01 Elapsed: 00:00:00.48
# Mc/sec: 2979.74
//
Query:       gi|474934548|ref|YP_007688130.1|  [L=639]
Description: Collagenase-related protease [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.3e-72  242.0   0.1      5e-61  205.8   0.0    3.2  3  Peptidase_U32  Peptidase family U32


Domain annotation for each model (and alignments):
>> Peptidase_U32  Peptidase family U32
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.8   0.0   2.8e-65     5e-61       1     229 [.      76     284 ..      76     287 .. 0.94
   2 !   16.1   0.1   2.7e-07    0.0049      62     106 ..     502     545 ..     484     554 .. 0.87
   3 !   16.4   0.0   2.1e-07    0.0037     138     194 ..     556     613 ..     545     622 .. 0.87

  Alignments for each domain:
  == domain 1  score: 205.8 bits;  conditional E-value: 2.8e-65
                     Peptidase_U32   1 leklrkyleklaelgvdavivqDpgvlelareeapelelhlStqanitnseavrflkelGasrvvlaRElsleeika 77 
                                       +e++  ++++l+++g+dav vqD+g+l+ ++    +++ h+Stq+ i++++++++++e+G+sr+vl REl++eei+ 
  gi|474934548|ref|YP_007688130.1|  76 MEDAVSFVRFLKDIGADAVLVQDIGLLKSLHSV--DIAKHASTQMGIHSARGLEWCSENGISRAVLNRELTMEEIES 150
                                       57788999*********************9999..****************************************** PP

                     Peptidase_U32  78 ikekvpdvelEvfvhGalcvaysGrcllssylsgrsanrgecaqpcrldyrlieekekgeeepieedekgtyllspk 154
                                       ++++   ve+Evfv+Galc++ sG cl+ss+++grs+nrg+caqpcr++y++ +e+               y ls+ 
  gi|474934548|ref|YP_007688130.1| 151 LARDS-PVETEVFVQGALCYCLSGGCLFSSLVGGRSGNRGACAQPCRKKYTFDDETS--------------YRLSNA 212
                                       *****.8********************************************666554..............88**** PP

                     Peptidase_U32 155 dlclieelpelleaGvdslKIeGRmkspeyvatvvrvYreaidallagreevkeelkeeleklanrgltsgfllg 229
                                       dl +i++l++l +aGv+s KIeGRm+s+ y++  +rvY  a   l  ++    +e  e l++++nrg+++g+l g
  gi|474934548|ref|YP_007688130.1| 213 DLYGIDYLKRLEKAGVTSAKIEGRMRSQAYAYLATRVYASANRGLPPEE---YAEETELLRTVFNRGFSDGYLGG 284
                                       *****************************************99998776...66666779999*********976 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 2.7e-07
                     Peptidase_U32  62 srvvlaRElsleeikaikekvpdvelEvfvhGalcvaysGrclls 106
                                        ++ l+ Els+eei++i+++     lEv v+G + ++  +   ++
  gi|474934548|ref|YP_007688130.1| 502 YQATLSVELSAEEIQEIARHY-PGRLEVMVFGRTELMCTRDPGMH 545
                                       5789*****************.89*********999988776665 PP

  == domain 3  score: 16.4 bits;  conditional E-value: 2.1e-07
                     Peptidase_U32 138 eepieedekgt.yllspkdlclieelpelleaGvdslKIeGRmkspeyvatvvrvYre 194
                                         p+++d++g  ++l++ dl+l+ +l++l + G++s  I+ R + ++ +  v+r++ +
  gi|474934548|ref|YP_007688130.1| 556 RFPVYRDQRGLsHILNSSDLMLLPYLQQLGKFGIESAGIDLRKRPEKIARIVARAFAQ 613
                                       456777888777**********************************999999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (639 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 3872.50
//
Query:       gi|474934549|ref|YP_007688131.1|  [L=134]
Description: hypothetical protein TALC_00978 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0032   17.8   0.0     0.0064   16.8   0.0    1.5  1  CYSTM     Cysteine-rich TM module stress tolerance


Domain annotation for each model (and alignments):
>> CYSTM  Cysteine-rich TM module stress tolerance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   3.6e-07    0.0064      17      38 ..       4      25 ..       3      29 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.6e-07
                             CYSTM 17 pqkgdgGclagClaALcCCclc 38
                                      +++gd G+l+++ +A+++C ++
  gi|474934549|ref|YP_007688131.1|  4 NRRGDIGFLEAMVSAMAVCLVL 25
                                      789999*************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 908.11
//
Query:       gi|474934550|ref|YP_007688132.1|  [L=149]
Description: hypothetical protein TALC_00979 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 978.32
//
Query:       gi|474934551|ref|YP_007688133.1|  [L=174]
Description: Uncharacterized protein family (UPF0153) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-13   50.1   1.1    4.9e-13   49.6   1.1    1.3  1  CxxCxxCC  Putative zinc- or iron-chelating domain


Domain annotation for each model (and alignments):
>> CxxCxxCC  Putative zinc- or iron-chelating domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   1.1   2.7e-17   4.9e-13       1      72 [.      39     121 ..      39     147 .. 0.88

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 2.7e-17
                          CxxCxxCC   1 eCkeCgaCCkelkvklteedlerlkaaevaeeeeeskkiak............adgrCvfldeetklCkiYeeRpki 65 
                                       +C++Cg+CC++ ++ ++++++er+ aa   +  ++ ++++             a+++C+fl +++ +C+i+++Rp+i
  gi|474934551|ref|YP_007688133.1|  39 PCEMCGKCCHQPNIIIRPDEVERVCAAAGTDLYTFMTQYVYqtgdgrilfnkrAGEPCRFLGKDN-RCTIWKDRPQI 114
                                       5***********************888887777777777667**********************6.*********** PP

                          CxxCxxCC  66 crlfpas 72 
                                       c  fp  
  gi|474934551|ref|YP_007688133.1| 115 CDDFPYL 121
                                       ***9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1259.17
//
Query:       gi|474934552|ref|YP_007688134.1|  [L=100]
Description: hypothetical protein TALC_00981 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.11   12.1   5.2       0.13   11.8   5.2    1.1  1  DUF1700      Protein of unknown function (DUF1700)
       0.22   11.5   5.9       0.28   11.1   4.3    2.1  2  Herpes_pp38  Herpesvirus pp38 phosphoprotein
        1.8    8.2   8.0        2.5    7.8   8.0    1.2  1  Tetraspanin  Tetraspanin family


Domain annotation for each model (and alignments):
>> DUF1700  Protein of unknown function (DUF1700)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   5.2   2.2e-05      0.13      98     160 ..      31      94 ..      19      97 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.2e-05
                           DUF1700  98 ipliviislvlsllvvalallvsplvllvksllkgfeelsln.vfvsigllglGllllivayyl 160
                                       + +i+++ +++ ++ +al++ + +l+  ++s+ +g+  +  +  +    + g+Glll+++a++ 
  gi|474934552|ref|YP_007688134.1|  31 TGIIGMVCFLIGVYAGALVFGACGLFFGGNSFGHGVKVMHESdDYKPAVISGVGLLLSVIAFMF 94 
                                       45788899999999***********************9998889****************9975 PP

>> Herpes_pp38  Herpesvirus pp38 phosphoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.61   3.6e+03      51      58 ..      26      33 ..      15      38 .. 0.53
   2 ?   11.1   4.3   4.6e-05      0.28      15      41 ..      43      69 ..      35      99 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.61
                       Herpes_pp38 51 llAFlAGi 58
                                       lA   Gi
  gi|474934552|ref|YP_007688134.1| 26 FLALATGI 33
                                      23333444 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 4.6e-05
                       Herpes_pp38 15 vsakiLllGsCisFaaGtLvGktadvk 41
                                      v a  L++G+C  F+ G   G++ +v 
  gi|474934552|ref|YP_007688134.1| 43 VYAGALVFGACGLFFGGNSFGHGVKVM 69
                                      67889******************9984 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   8.0   0.00041       2.5       7      69 ..      26     100 .]      22     100 .] 0.82

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00041
                                       XXXXXXXXXXXXXXXXXXXXXX...............XXX.....................XXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Tetraspanin   7 ffnllfwligivllavGvwlrl...............khaeaalacllsesaedpailaillivvGvllfllgflGc 68 
                                       f++l + +ig+v++ +Gv++                        +  +++ + +pa+++ + ++++v+ f++gf+G+
  gi|474934552|ref|YP_007688134.1|  26 FLALATGIIGMVCFLIGVYAGAlvfgacglffggnsfG---HGVKVMHESDDYKPAVISGVGLLLSVIAFMFGFVGV 99 
                                       6677788999999999999988899999999**95553...44556677788999999999**************98 PP

                                       X CS
                                       x RF
                       Tetraspanin  69 i 69 
                                       i
  gi|474934552|ref|YP_007688134.1| 100 I 100
                                       6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 655.51
//
Query:       gi|474934553|ref|YP_007688135.1|  [L=198]
Description: Methylase involved in ubiquinone/menaquinone biosynthesis [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-25   90.0   0.0    1.9e-25   89.3   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    7.8e-25   87.4   0.1    1.3e-24   86.7   0.1    1.4  1  Methyltransf_25  Methyltransferase domain
    2.2e-16   60.1   0.0    2.7e-16   59.9   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    4.1e-16   59.5   0.0    5.5e-16   59.1   0.0    1.2  1  Methyltransf_12  Methyltransferase domain
    9.4e-16   58.0   0.0    1.1e-15   57.7   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
      2e-10   40.4   0.0    2.8e-10   39.9   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    2.4e-10   40.2   0.0    2.6e-10   40.1   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
    2.6e-06   27.2   0.0    3.7e-06   26.7   0.0    1.2  1  MetW             Methionine biosynthesis protein MetW
    0.00015   21.2   0.0    0.00019   20.9   0.0    1.2  1  TehB             Tellurite resistance protein TehB
    0.00016   21.6   0.1    0.00041   20.3   0.1    1.6  1  Methyltransf_8   Hypothetical methyltransferase
    0.00044   19.9   0.0    0.00065   19.4   0.0    1.2  1  NodS             Nodulation protein S (NodS)
    0.00095   18.7   0.0     0.0013   18.4   0.0    1.2  1  MTS              Methyltransferase small domain
     0.0045   16.7   0.0     0.0086   15.8   0.0    1.7  1  TPMT             Thiopurine S-methyltransferase (TPMT)
     0.0059   16.4   0.0      0.019   14.7   0.0    1.8  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
  ------ inclusion threshold ------
      0.015   14.2   0.0       0.02   13.8   0.0    1.1  1  Methyltransf_9   Protein of unknown function (DUF1698)
      0.085   12.8   0.0       0.13   12.2   0.0    1.3  1  Methyltransf_32  Methyltransferase domain
       0.19   11.4   0.0       0.31   10.7   0.0    1.4  1  GCD14            tRNA methyltransferase complex GCD14 subunit


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.3   0.0   1.8e-28   1.9e-25       1      95 [.      37     130 ..      37     131 .. 0.98

  Alignments for each domain:
  == domain 1  score: 89.3 bits;  conditional E-value: 1.8e-28
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-..C CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhv..e 75 
                                       Ld+GcG+G+ ++ l + g+rv+g+D+s++++++++e   ++g   efv ad+++lpf d+sfD+vv+ + l+hv  e
  gi|474934553|ref|YP_007688135.1|  37 LDAGCGNGKTSASLIQDGCRVTGFDFSPRAVAACRELFGDRG---EFVTADVRDLPFGDSSFDCVVAVHILEHVpaE 110
                                       8****************************************9...79***************************999 PP

                                       CHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  76 dpekalkeiaRvLkpgGllv 95 
                                       d  ka++e+ RvL pgG+++
  gi|474934553|ref|YP_007688135.1| 111 DIPKAVSELLRVLVPGGRIY 130
                                       *****************997 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.7   0.1   1.3e-27   1.3e-24       1      97 []      36     127 ..      36     127 .. 0.96

  Alignments for each domain:
  == domain 1  score: 86.7 bits;  conditional E-value: 1.3e-27
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGS CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhl 77 
                                       vLd+GcG+G++++ l + +  ++vtg+D+s+++++a+re + +   + efv++d++dlpf d+sfD+vv+++ l+h+
  gi|474934553|ref|YP_007688135.1|  36 VLDAGCGNGKTSASLIQDG--CRVTGFDFSPRAVAACRELFGD---RGEFVTADVRDLPFGDSSFDCVVAVHILEHV 107
                                       9*****************5..********************55...67**********************877**** PP

                                       SHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  78 sdedlekalkeiarvLkpgG 97 
                                       + ed++ka++e+ rvL pgG
  gi|474934553|ref|YP_007688135.1| 108 PAEDIPKAVSELLRVLVPGG 127
                                       *******************9 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.9   0.0   2.5e-19   2.7e-16      22     124 ..      32     138 ..      21     180 .. 0.84

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 2.5e-19
                   Methyltransf_23  22 aggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae..kakkaqkdqfdeqeaaepqgkfdlIvlrevlehvp 96 
                                       +g+rvLd GcG G ++ +l + g+ vtg+D sp+av+  +    +  +++ +d  + ++ + +fd++v+ + lehvp
  gi|474934553|ref|YP_007688135.1|  32 PGSRVLDAGCGNGKTSASLIQDGCRVTGFDFSPRAVAACRelFGDRGEFVTADVRDLPFGDSSFDCVVAVHILEHVP 108
                                       689*********************************99998855555666677778888999*************** PP

                   Methyltransf_23  97 ..dppellrqiatllkpgGylllseplasl 124
                                         d p++++ + + l pgG+++l+ +++ +
  gi|474934553|ref|YP_007688135.1| 109 aeDIPKAVSELLRVLVPGGRIYLQAFAVGD 138
                                       999*********************987655 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.1   0.0   5.2e-19   5.5e-16       1      99 []      37     129 ..      37     129 .. 0.92

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 5.2e-19
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       L+ GcG+G +++ l ++  ++++tg D+sp+a+++ +e + +r++    +v+ +++dl   d+  sfD vva + l+
  gi|474934553|ref|YP_007688135.1|  37 LDAGCGNGKTSASLIQD--GCRVTGFDFSPRAVAACRELFGDRGE----FVTADVRDLPFGDS--SFDCVVAVHILE 105
                                       89***************..**************888888888886....88888888776655..************ PP

                   Methyltransf_12  78 hl..kdirevldnirklLkpgGrl 99 
                                       h+  +di ++++++ ++L+pgGr+
  gi|474934553|ref|YP_007688135.1| 106 HVpaEDIPKAVSELLRVLVPGGRI 129
                                       **********************96 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.7   0.0     1e-18   1.1e-15       4     119 ..      33     140 ..      30     179 .. 0.84

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 1e-18
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlils 80 
                                       g rvlD+GCG+G+ +  l +   ++++v+G+D+s++a+  +re    l+ d+ eF  +d+ +l+  + d++fD +++
  gi|474934553|ref|YP_007688135.1|  33 GSRVLDAGCGNGKTSASLIQ---DGCRVTGFDFSPRAVAACRE----LFGDRGEFVTADVRDLP--FGDSSFDCVVA 100
                                       679****************4...4789****************....577899***********..*********** PP

                   Methyltransf_31  81 nevlnala..dpdkileeiervlkpggilliedprllaelp 119
                                         +l +++  d +k+  e+ rvl pgg++ ++ +    +++
  gi|474934553|ref|YP_007688135.1| 101 VHILEHVPaeDIPKAVSELLRVLVPGGRIYLQAFA-VGDFR 140
                                       ****6666126679999*************99888.55554 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.0   2.7e-13   2.8e-10      30     152 ..      14     132 ..       4     139 .. 0.90

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 2.7e-13
                                       TTHHHHHH.HHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE- CS
                   Ubie_methyltran  30 gihrlWkk.fveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqa 105
                                       g+ r W+       ++  +g++vlD  +G g  +++l   +++  +v++ D+++  +   ++   ++g    ef++a
  gi|474934553|ref|YP_007688135.1|  14 GQPRSWRGtSSVSWMGIPPGSRVLDAGCGNGKTSASL---IQDGCRVTGFDFSPRAVAACRELFGDRG----EFVTA 83 
                                       67899999788999*****************999877...677889*************999999988....8**** PP

                                       -TTT-TTS-T-EEEEEEES-GGG-S..-HHHHHHHHHHHEEEEEEEEEE CS
                   Ubie_methyltran 106 naeeLpfeddsfDvvtvsfGlrnvt..DklkaLkeayrvlkpGGrlvvl 152
                                       +  +Lpf d sfD+v   + l  v+  D++ka+ e+ rvl pGGr++  
  gi|474934553|ref|YP_007688135.1|  84 DVRDLPFGDSSFDCVVAVHILEHVPaeDIPKAVSELLRVLVPGGRIYLQ 132
                                       *******************9*99876699****************9975 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.0   2.4e-13   2.6e-10      56     171 ..      26     138 ..       4     178 .. 0.86

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 2.4e-13
                                       TTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-----SEEE CS
                              CMAS  56 eklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedldekvdrvv 132
                                         +++ pG+++Ld GcG G++    ++  + +v g  +S    + +++ + +++   +++v+ l + d    +d vv
  gi|474934553|ref|YP_007688135.1|  26 SWMGIPPGSRVLDAGCGNGKTSASLIQD-GCRVTGFDFSPRAVAACRELFGDRGEFVTADVRDLPFGD--SSFDCVV 99 
                                       557889**********************.**********************99977777777666665..69***** PP

                                       EES-GGGTSGGGHHHHHHHHHHHS-TT-EEEEEEEEE-- CS
                              CMAS 133 svgafehvgkenydtffkklkkllkedGllllhtitslh 171
                                       +v ++ehv  e  ++ +++l ++l ++G++ l++    +
  gi|474934553|ref|YP_007688135.1| 100 AVHILEHVPAEDIPKAVSELLRVLVPGGRIYLQAFAVGD 138
                                       ********************************9976654 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   3.5e-09   3.7e-06      11     101 ..      30     122 ..      23     133 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 3.5e-09
                              MetW  11 ikpgsrvldlGcGdGellellkeekqvdgrGleldeegvaecva....kGlsviqgdldkdlenfedksfdyvvlsq 83 
                                       i+pgsrvld GcG+G+    l +  + +  G + + ++va+c +    +G  v     d     f d+sfd vv   
  gi|474934553|ref|YP_007688135.1|  30 IPPGSRVLDAGCGNGKTSASLIQ-DGCRVTGFDFSPRAVAACRElfgdRGEFVTA---DVRDLPFGDSSFDCVVAVH 102
                                       89*************99876644.589999************6432225554443...33334699********999 PP

                              MetW  84 tlqatrnpk..evldellri 101
                                        l  +   +  + ++ellr+
  gi|474934553|ref|YP_007688135.1| 103 ILEHVPAEDipKAVSELLRV 122
                                       99887543322566778876 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.8e-07   0.00019      32     129 ..      34     128 ..      23     174 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.8e-07
                                       -EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG---.-S-EEEEEEESSGGG CS
                              TehB  32 gkvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydineakl.derydfilstvvlmf 107
                                       ++vld gcg+g+ s  l   g  vt +d    ++a  +e+        +++ + d+    + d  +d +++  +l  
  gi|474934553|ref|YP_007688135.1|  34 SRVLDAGCGNGKTSASLIQDGCRVTGFDFSPRAVAACRELFGDRGEF-VTADVRDLP---FgDSSFDCVVAVHILEH 106
                                       589*********************************99987654433.566666654...42789************ PP

                                       S-GGGHHHHHHHHHHTEEEEEE CS
                              TehB 108 leaeripsiienmqectkvggy 129
                                       + ae ip+ ++++ +   +gg 
  gi|474934553|ref|YP_007688135.1| 107 VPAEDIPKAVSELLRVLVPGGR 128
                                       *************999999995 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   3.8e-07   0.00041      76     156 ..      36     131 ..      30     148 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.8e-07
                                       EEEES-TT-HHH.HH--S-..EEEEESS-S...........STTEEES-TTS-S--TT-EE..EEEEES-.--SS-H CS
                    Methyltransf_8  76 vadlGcGeakia.eavrekekvrsfdlvav...........nervvacdlakvPledesvd..vavfcls.lmgtnl 137
                                       v d GcG+ k + + +++  +v  fd+ +              + v+ d++ +P  d+s d  vav+ l  + ++++
  gi|474934553|ref|YP_007688135.1|  36 VLDAGCGNGKTSaSLIQDGCRVTGFDFSPRavaacrelfgdRGEFVTADVRDLPFGDSSFDcvVAVHILEhVPAEDI 112
                                       889******986477889999*99998653111122222112357899*************44455666524589** PP

                                       HHHHHHHHHHEEEEEEEEE CS
                    Methyltransf_8 138 adflkeanrvlkvGGllkv 156
                                        + + e  rvl +GG +++
  gi|474934553|ref|YP_007688135.1| 113 PKAVSELLRVLVPGGRIYL 131
                                       ***************9886 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   6.2e-07   0.00065      46     142 ..      35     129 ..      29     141 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 6.2e-07
                              NodS  46 dalevGcaaGalterlapyckrltvvdvveeaiararervkesshiswivsdvqqfst.dekfdlivvaevlyyied 121
                                        +l+ Gc  G  +  l     r+t  d  ++a+a +re   +     ++++dv+ +   d  fd +v   +l ++  
  gi|474934553|ref|YP_007688135.1|  35 RVLDAGCGNGKTSASLIQDGCRVTGFDFSPRAVAACRELFGD--RGEFVTADVRDLPFgDSSFDCVVAVHILEHVP- 108
                                       689*************************************99..56789******9853789***********996. PP

                              NodS 122 vaelraavrnlvsllapdgql 142
                                        +++  av +l+++l p+g++
  gi|474934553|ref|YP_007688135.1| 109 AEDIPKAVSELLRVLVPGGRI 129
                                       6899*************9986 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.2e-06    0.0013      33     102 ..      34      99 ..      25     133 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.2e-06
                                       SEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTST.TS-EEEEE CS
                               MTS  33 gkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeve.ekkfdliv 102
                                        +vlD GcG+G  +a+l +   +  vt +d + rA+++++e + + +   e+v+ dv +    + +fd++v
  gi|474934553|ref|YP_007688135.1|  34 SRVLDAGCGNGKTSASLIQDGCR--VTGFDFSPRAVAACRELFGDRG---EFVTADVRDLPFgDSSFDCVV 99 
                                       68***************996665..**************99887765...677777766433377777777 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   8.2e-06    0.0086      36      75 ..      31      70 ..      24     187 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8.2e-06
                                      S--EEEEEET-TT-HHHHHH-BTTEEEEEE-S-HHHHHHH CS
                              TPMT 36 kaglrvlvPlCGkaldlvwlAeqgrevvGvelselAvekf 75
                                      ++g rvl  +CG++   + l + g +v G ++s+ Av++ 
  gi|474934553|ref|YP_007688135.1| 31 PPGSRVLDAGCGNGKTSASLIQDGCRVTGFDFSPRAVAAC 70
                                      7899*********************************974 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.8e-05     0.019      66     169 ..      25     129 ..      20     133 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.8e-05
                                       HHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGGG-S CS
                              PCMT  66 lellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyeekaP 142
                                       + ++ + +g+rvL+ G+G G  +a    l+++ +rv + + +++ v++  r+l  +  e v+  v D   G   +  
  gi|474934553|ref|YP_007688135.1|  25 VSWMGIPPGSRVLDAGCGNGKTSA---SLIQDGCRVTGFDFSPRAVAAC-RELFGDRGEFVTADVRDLPFGDSSFDC 97 
                                       67999***************9876...6799999999999999977655.455555556666677776666666666 PP

                                       EEEEEE..SSBBSS--HH...HHHTEEEEEEE CS
                              PCMT 143 Ydaihv..gaaapeiPea...lidQLkeGGrl 169
                                         a+h+   + a++iP+a   l++ L +GGr+
  gi|474934553|ref|YP_007688135.1|  98 VVAVHIleHVPAEDIPKAvseLLRVLVPGGRI 129
                                       66655533466677776533356666677775 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.9e-05      0.02     117     222 ..      34     136 ..      24     146 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.9e-05
                                       -EEEEET-TTSHHHHHHHHCT-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---GGGS-T.---EEEEEEES-G CS
                    Methyltransf_9 117 rtildvGcgnGyhlwrmvgegaklvvGidPselfliqfeavrkllgedqrahllplgieqlpe.leafdtvfsmGvl 192
                                        ++ld GcgnG     ++ +g + v G d s        a r+l g+  +   +   + +lp   ++fd v ++ +l
  gi|474934553|ref|YP_007688135.1|  34 SRVLDAGCGNGKTSASLIQDGCR-VTGFDFSPRA---VAACRELFGDRGE--FVTADVRDLPFgDSSFDCVVAVHIL 104
                                       689*********99999988775.7899988865...5799****87544..45579*****97889********** PP

                                       GG-S-H.H.HHHHHHHCTEEEEEEEEEEEE-B CS
                    Methyltransf_9 193 yhrrsP.l.dhllqlkdqlvkgGelvletlvi 222
                                        h  +  +   +++l   lv gG + l++  +
  gi|474934553|ref|YP_007688135.1| 105 EHVPAEdIpKAVSELLRVLVPGGRIYLQAFAV 136
                                       **755323256788999999999999988765 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00012      0.13      28      71 ..      35      74 ..      30     103 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                   Methyltransf_32 28 tvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekra 71
                                      +v+D+G+G+g  s  l +     +++v+g+d + + v++++++ 
  gi|474934553|ref|YP_007688135.1| 35 RVLDAGCGNGKTSASLIQ----DGCRVTGFDFSPRAVAACRELF 74
                                      79**********999999....59**************999875 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0    0.0003      0.31      37     130 ..      29     114 ..      23     130 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0003
                             GCD14  37 elkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvthrDvc..keGfdeevs 111
                                        + pGs+v+++G G g  s ++++      ++  f+f  + +   re f +++  ++vt  +rD+    + fd    
  gi|474934553|ref|YP_007688135.1|  29 GIPPGSRVLDAGCGNGKTSASLIQ---DGCRVTGFDFSPRAVAACRELFGDRG--EFVTADVRDLPfgDSSFD---- 96 
                                       5789****************9965...57799999999888888888888775..788888888753233442.... PP

                             GCD14 112 gkvDavfLDlPaPweaiph 130
                                         v av +    P e ip+
  gi|474934553|ref|YP_007688135.1|  97 -CVVAVHILEHVPAEDIPK 114
                                       .233444444444444554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1201.66
//
Query:       gi|474934554|ref|YP_007688136.1|  [L=432]
Description: phenylacetate-CoA ligase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-28   98.3   0.1    4.4e-28   97.4   0.1    1.5  1  AMP-binding_C_2  AMP-binding enzyme C-terminal domain
    4.9e-18   64.9   0.8      1e-17   63.9   0.8    1.5  1  AMP-binding      AMP-binding enzyme
    4.3e-08   32.6   0.0     0.0064   15.6   0.0    2.1  2  LuxE             Acyl-protein synthetase, LuxE


Domain annotation for each model (and alignments):
>> AMP-binding_C_2  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.4   0.1   7.4e-32   4.4e-28       1      96 []     334     430 ..     334     430 .. 0.99

  Alignments for each domain:
  == domain 1  score: 97.4 bits;  conditional E-value: 7.4e-32
                                       TEEE-HHHHHHHHHT-TTEEEEEEEEEEEETTEEEEEEEEEE-T.T----HHHHHHHHHHHHHHHHHHHSS--EEEE CS
                   AMP-binding_C_2   1 GvnvfPsqieevlkeieevepeYqivvtregelDelevkvEvke.gfsdelkelealekkiakklksklgvsvkvel 76 
                                       G+nvfPsqie  l++i++v+++Y+i v+reg+lD++ ++vE+++ +fsd+l+++++l++ i+++lk+ l++ v+vel
  gi|474934554|ref|YP_007688136.1| 334 GINVFPSQIEYTLMRIPQVGDQYMINVSREGDLDRMVIQVEIRPeAFSDKLEDMQNLRSYIEAQLKKYLNIAVTVEL 410
                                       99******************************************889****************************** PP

                                       E-TT-S---------EEE-S CS
                   AMP-binding_C_2  77 vepgtlprsegKakrviDkR 96 
                                        +pg+lpr +gKakrv D+R
  gi|474934554|ref|YP_007688136.1| 411 KAPGELPRFDGKAKRVNDTR 430
                                       ******************98 PP

>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.9   0.8   1.7e-21     1e-17     155     369 ..      78     284 ..      38     333 .. 0.79

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 1.7e-21
                                       S-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHH.HHHC.SCCTTT-EE.EESS-TTSCHHHHHHHHHHHHTT CS
                       AMP-binding 155 elkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslk.letr.fklkeddvv.lsilplahifglilelllallsG 228
                                       ++++++++    +SGT GkP  V ++ + l + + +l+    +  +l++dd++ +++    +  gl    ++a   G
  gi|474934554|ref|YP_007688136.1|  78 TVEKSEIVRYHMSSGTSGKPTCVAYTRNDLGYWTEALArS-LTaAGLTADDTIqIAYGYGLFTGGL-GLHYGAERIG 152
                                       5667777777789*****************8887887642.3336688999995666666666666.99******** PP

                                       -EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHH.CHHHHCCGTT-SEEEEESS-EBHHHHHH CS
                       AMP-binding 229 atvvllpkdaa.ldpklllelieklkvtviagvPrvlealle.sgalk.aakkakdlsslrlvllggeplspellrf 302
                                       atv  +++ ++ +     le++++l++t ia++P+ l +l+  +++    +k+  d  slr ++lg+ep s+++  +
  gi|474934554|ref|YP_007688136.1| 153 ATVLPASTGNTqR----QLEMMQDLQCTAIACTPSYLTHLITtARQMGiDWKR--D-MSLRRCILGAEPWSETMRGK 222
                                       *999988887733....38*******************998756555522333..4.46****************** PP

                                       HHHHHTCEEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEE CS
                       AMP-binding 303 fralfgeevlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellv 369
                                       f++ +g + +++YG +E +g ++ +++e++    +++ + +  + ++i+D+etge +++g++Gel+ 
  gi|474934554|ref|YP_007688136.1| 223 FEEATGAKCIDIYGTSEQAGPMF-CECEHQ--HGPHISPDI--MYCEILDPETGESLEPGNKGELVC 284
                                       **********************8.665555..345566665..56789****************984 PP

>> LuxE  Acyl-protein synthetase, LuxE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.1e-06    0.0064      21     136 ..      12     130 ..       5     133 .. 0.86
   2 !   14.9   0.0   1.7e-06      0.01     266     358 ..     231     326 ..     223     337 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-06
                              LuxE  21 eeekeklrkkflldelvnhykhneeyrkycqknkvddlvtegevddiPviPvsvfkai....gtkllsvsedeikak 93 
                                       ++e  kl  k l   + n y  n+ y    +   v ++ +e  ++di  +P  v + +      k+ +v++ ei  +
  gi|474934554|ref|YP_007688136.1|  12 QDEMRKLQYKELKTLVNNLYSFNRFYHDRMRAAGVTPMDIE-SLADITKLPFMVKQDLrdnyPDKMFTVEKSEIVRY 87 
                                       6888899999998889999******************9999.8********99987652222689************ PP

                              LuxE  94 lqssatsGlkstvlldklsierllravarvmkevlspkdrqie 136
                                         ss+tsG ++ v+  +  +   + a+ar++   +   d  i+
  gi|474934554|ref|YP_007688136.1|  88 HMSSGTSGKPTCVAYTRNDLGYWTEALARSLTAAGLTADDTIQ 130
                                       *****************99999999999999887776666665 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.7e-06
                              LuxE 266 vvdiygfteqvelntpdfkdelkrkrvysdviir...deetlkvvgdGkvGlleyvdalstsyPafvvltddlGvie 339
                                         diyg +eq +  +++++ +    ++ +d++     d+et +   +G  G l       ++ P       d+  ++
  gi|474934554|ref|YP_007688136.1| 231 CIDIYGTSEQAGPMFCECEHQHGP-HISPDIMYCeilDPETGESLEPGNKGELVCTMLKKEAMPMIRYKMRDITSLN 306
                                       68**********999999877654.666666543378**************9999999999***999999******* PP

                              LuxE 340 eslcegqkaGklv.kvlrrv 358
                                       e  ce++++  ++ ++ +r 
  gi|474934554|ref|YP_007688136.1| 307 EETCECGRTTPRLsRITGRS 326
                                       *9*****9876652566665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 2477.97
//
Query:       gi|474934555|ref|YP_007688137.1|  [L=141]
Description: ACT domain-containing protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.2e-08   31.7   0.0    0.00035   20.3   0.0    2.4  2  ACT       ACT domain
    1.7e-05   25.3   0.1     0.0029   18.2   0.1    2.3  2  ACT_4     ACT domain
  ------ inclusion threshold ------
      0.027   14.3   0.9        3.4    7.5   0.2    2.7  2  ACT_7     ACT domain


Domain annotation for each model (and alignments):
>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0   0.00017         1       2      30 ..       8      36 ..       7      65 .. 0.73
   2 !   20.3   0.0   5.9e-08   0.00035       3      60 ..      75     130 ..      74     131 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00017
                                      EEEEEEESSTTHHHHHHHHHHHTTSEEEE CS
                               ACT  2 vlrvgvpDrPGlLarvfgaladrgiNids 30
                                       l+++v + PG La v+ +l +  iN   
  gi|474934555|ref|YP_007688137.1|  8 QLSIFVNNSPGSLANVAKTLQECSINMKA 36
                                      799*****************987777655 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 5.9e-08
                                       EEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHH CS
                               ACT   3 lrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevle 60 
                                       + v  +++PG L + +++l+ +giNi+    ++s+    +  f+ +   e+ ++++++
  gi|474934555|ref|YP_007688137.1|  75 IGVKIKNVPGSLYEASNVLGTAGINIEYGYAFTSKT--LEGLFMRVDSPEKAIAALEK 130
                                       778899****************************99..99999999999998888877 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   4.8e-07    0.0029       4      42 ..       4      42 ..       1      66 [. 0.88
   2 !    5.3   0.0    0.0052        31       9      38 ..      75     104 ..      72     117 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4.8e-07
                             ACT_4  4 sytvrleveaedrkglLaditqviseekanivsvnaktr 42
                                      +  ++l++ +++++g La+++++++e+ +n++++n+ + 
  gi|474934555|ref|YP_007688137.1|  4 NIITQLSIFVNNSPGSLANVAKTLQECSINMKACNLAES 42
                                      66789******************************9884 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0052
                             ACT_4   9 leveaedrkglLaditqviseekanivsvn 38 
                                       + v+ ++ +g L + ++v+  +++ni+   
  gi|474934555|ref|YP_007688137.1|  75 IGVKIKNVPGSLYEASNVLGTAGINIEYGY 104
                                       568999********************8655 PP

>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0    0.0049        29      18      40 ..      14      36 ..       4      45 .. 0.84
   2 ?    7.5   0.2   0.00056       3.4       8      40 ..      71     102 ..      66     130 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0049
                                      -SS--HHHHHHHHHHTTT---EE CS
                             ACT_7 18 fdvtGivaklaspLaeagIsifq 40
                                       +++G +a +a+ L e  I++ +
  gi|474934555|ref|YP_007688137.1| 14 NNSPGSLANVAKTLQECSINMKA 36
                                      479****************9865 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00056
                                       EEEE-S-.---SS--HHHHHHHHHHTTT---EE CS
                             ACT_7   8 klsvvgsglpfdvtGivaklaspLaeagIsifq 40 
                                       k  ++g +++  v+G + + +++L  agI+i +
  gi|474934555|ref|YP_007688137.1|  71 KTEIIGVKIKN-VPGSLYEASNVLGTAGINIEY 102
                                       56789998988.*******************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 918.33
//
Query:       gi|474934556|ref|YP_007688138.1|  [L=316]
Description: Selenocysteine-specific translation elongation factor [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-07   31.2   0.4    7.4e-07   29.5   0.1    2.1  3  GTP_EFTU_D2  Elongation factor Tu domain 2
  ------ inclusion threshold ------
       0.13   12.6   0.0       0.28   11.6   0.0    1.5  1  IncF         Inclusion membrane protein F
       0.27   11.2   1.4        0.5   10.3   1.4    1.5  1  FhuF_C       FhuF 2Fe-2S C-terminal domain


Domain annotation for each model (and alignments):
>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.3     8e+03      16      30 ..      76      88 ..      75     111 .. 0.63
   2 ?   -3.5   0.0       2.5   1.5e+04      30      48 ..     122     140 ..     114     143 .. 0.62
   3 !   29.5   0.1   1.2e-10   7.4e-07       1      72 [.     160     225 ..     160     227 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.3
                                      TEEEEEECTCTTSEE CS
                       GTP_EFTU_D2 16 Gdevrilgndtskke 30
                                      G+++++  +d+++k 
  gi|474934556|ref|YP_007688138.1| 76 GETIVM--LDSQRKD 88
                                      889999..7776654 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.5
                                       EEEEEEEEEEEETEEESEE CS
                       GTP_EFTU_D2  30 eivtrissletfhededea 48 
                                       +i  ri  +e+ +++++ a
  gi|474934556|ref|YP_007688138.1| 122 PIAMRIALIEMAKAEKRVA 140
                                       4556666667776666655 PP

  == domain 3  score: 29.5 bits;  conditional E-value: 1.2e-10
                                       EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCE CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdt 72 
                                       Gtv+lg+v +G ++  d++ +   +++k+   +  +s++++  d +  v+g+++G+ +++++ ++ + +G +
  gi|474934556|ref|YP_007688138.1| 160 GTVVLGSVADGWFRIHDKMTV--WPVKKE---VVLRSIQKHDIDAQDGVKGDHVGLALKGIDSDE-LDRGFV 225
                                       9********************..888888...*********************************.999988 PP

>> IncF  Inclusion membrane protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   4.6e-05      0.28      68     102 ..      61      96 ..      52      98 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.6e-05
                              IncF  68 gplavlvattlasflcaacvlfi.aakdrgwiastn 102
                                         +avlv   + sfl  + v++    kdrgwi   n
  gi|474934556|ref|YP_007688138.1|  61 AEFAVLVVDKIDSFLGETIVMLDsQRKDRGWIVLRN 96 
                                       678*************99998751579*****8665 PP

>> FhuF_C  FhuF 2Fe-2S C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.4   8.4e-05       0.5       9      20 ..     138     149 ..     138     149 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 8.4e-05
                            FhuF_C   9 rlpggeyCgsCP 20 
                                       r++g ++CgsCP
  gi|474934556|ref|YP_007688138.1| 138 RVAGDGTCGSCP 149
                                       789********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2219.66
//
Query:       gi|474934557|ref|YP_007688139.1|  [L=433]
Description: Coenzyme F390 synthetase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-21   76.1   0.0    3.9e-21   75.1   0.0    1.5  1  AMP-binding_C_2  AMP-binding enzyme C-terminal domain
    1.2e-15   57.1   0.1    3.1e-15   55.7   0.0    1.6  2  AMP-binding      AMP-binding enzyme
  ------ inclusion threshold ------
      0.047   12.5   0.1       0.55    9.0   0.0    2.4  3  VGCC_alpha2      Neuronal voltage-dependent calcium channel a
      0.052   12.4   0.0       0.92    8.3   0.0    2.1  2  GH3              GH3 auxin-responsive promoter
      0.067   13.3   0.0       0.15   12.2   0.0    1.5  1  DUF2505          Protein of unknown function (DUF2505)


Domain annotation for each model (and alignments):
>> AMP-binding_C_2  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.1   0.0   1.1e-24   3.9e-21       1      96 []     334     430 ..     334     430 .. 0.99

  Alignments for each domain:
  == domain 1  score: 75.1 bits;  conditional E-value: 1.1e-24
                                       TEEE-HHHHHHHHHT-TTEEEEEEEEEEEETTEEEEEEEEEE-T.T----HHHHHHHHHHHHHHHHHHHSS--EEEE CS
                   AMP-binding_C_2   1 GvnvfPsqieevlkeieevepeYqivvtregelDelevkvEvke.gfsdelkelealekkiakklksklgvsvkvel 76 
                                       G+nvfPsqie+v+ e++ ++p Y+i++t+e+ +D++ v vE+++ +++++++e  a++ +++ +lk+ l++++ v++
  gi|474934557|ref|YP_007688139.1| 334 GINVFPSQIESVIGEMDFLAPFYHITLTNENYMDKMVVDVEIDPaHLTEDTTEIGAMSTQVQLRLKEILNLKAIVRM 410
                                       99******************************************8899999************************** PP

                                       E-TT-S---------EEE-S CS
                   AMP-binding_C_2  77 vepgtlprsegKakrviDkR 96 
                                         pgtl+r egKak v+D+R
  gi|474934557|ref|YP_007688139.1| 411 NLPGTLERFEGKAKHVTDNR 430
                                       *******************9 PP

>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   0.0   8.6e-19   3.1e-15     156     369 ..      80     284 ..      17     288 .. 0.79
   2 ?   -1.4   0.0      0.19   6.8e+02     411     423 .]     321     333 ..     313     333 .. 0.88

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 8.6e-19
                                       -BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHC..SCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-E CS
                       AMP-binding 156 lkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletr..fklkeddvvlsilplahifglilelllallsGat 230
                                          +dl+ +  +SGTTG+P  V ++++ l + + sl  +    f+++++dv+  +  +   +g   + ++a   G+t
  gi|474934557|ref|YP_007688139.1|  80 RPYEDLVRVHVSSGTTGRPTVVGYTQKDLDNWTDSLC-RGMmsFGVTRKDVFQNMHGYGLFTGGLGAHYAAERIGCT 155
                                       33499999999*****************988878874.3334488999*******99999999889*********** PP

                                       EEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHH CS
                       AMP-binding 231 vvllpkdaa.ldpklllelieklkvtviagvPrvlealle.sgalkaakkakdlsslrlvllggeplspellrffra 305
                                       vv  ++ ++ ++    ++l+++l v+++ag+P+ + ++++  +++  ++  +++ +++ +l+ggep s ++ +++++
  gi|474934557|ref|YP_007688139.1| 156 VVPTSTGNTdRQ----IQLMQDLPVSCLAGTPSYYFHIADvCDQRGIDM--RKCMKVKRALAGGEPWSDAMRKKLYE 226
                                       *99888777333....89********************77443333333..367789999***************** PP

                                       HHTCEEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEE CS
                       AMP-binding 306 lfgeevlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellv 369
                                       ++g + +++YG +E  g ++  +  e+    g +      + +++vD + g  ++d+e+Gel+v
  gi|474934557|ref|YP_007688139.1| 227 RTGIRAYNCYGASEFYGPMF-TE-CEK--ADG-AHVWADLCLMEVVDKN-GDHCADEEKGELVV 284
                                       ******************98.44.333..233.445557899******9.999*********98 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.19
                                       EEEEECCCEEEET CS
                       AMP-binding 411 eivgRkkdliklr 423
                                       +i gR++d+i++r
  gi|474934557|ref|YP_007688139.1| 321 RISGRADDMIVVR 333
                                       799*******986 PP

>> VGCC_alpha2  Neuronal voltage-dependent calcium channel alpha 2acd
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       0.1   3.7e+02     165     188 ..      93     117 ..      58     132 .. 0.81
   2 ?   -1.2   0.0      0.19   6.9e+02     333     363 ..     176     206 ..     161     210 .. 0.85
   3 ?    9.0   0.0   0.00015      0.55     115     176 ..     350     411 ..     331     430 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.1
                       VGCC_alpha2 165 ekllkPavvGv.kldleaWvekfsn 188
                                       +++ +P+vvG  + dl++W++++ +
  gi|474934557|ref|YP_007688139.1|  93 GTTGRPTVVGYtQKDLDNWTDSLCR 117
                                       56779*****6378******99854 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.19
                       VGCC_alpha2 333 esCiteqtqyyfeneeksfsgvldcgncsrl 363
                                        sC+     yyf+  +   +  +d  +c ++
  gi|474934557|ref|YP_007688139.1| 176 VSCLAGTPSYYFHIADVCDQRGIDMRKCMKV 206
                                       58999999*****************999876 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00015
                       VGCC_alpha2 115 tyessfykrsldndlyiftptlfsaeaepseaeeetvgi.lvskavelkidekllkPavvGvk 176
                                       ++ + fy+ +l n++y+ +  + + e +p++ +e+t++i  +s+ v+l+++e+l   a+v ++
  gi|474934557|ref|YP_007688139.1| 350 DFLAPFYHITLTNENYMDKM-VVDVEIDPAHLTEDTTEIgAMSTQVQLRLKEILNLKAIVRMN 411
                                       68899***********8776.5899999**********9668**********98777776544 PP

>> GH3  GH3 auxin-responsive promoter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0   0.00026      0.92      76     115 ..      85     123 ..      79     176 .. 0.80
   2 ?    1.9   0.0     0.021        77     370     418 ..     294     347 ..     281     400 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00026
                                       -SEEEEECCEETTEEEEEEESHHHHHHHHHH.HHHHHHHH CS
                               GH3  76 iklfalsSGTtsgksKliPvteeslkelallvlallaall 115
                                       +++   sSGTt g++ ++ +t++ l++++  +++ ++++ 
  gi|474934557|ref|YP_007688139.1|  85 LVRVHVSSGTT-GRPTVVGYTQKDLDNWTDSLCRGMMSFG 123
                                       567789*****.***************8887666655554 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.021
                                       -SSEEECEEEEEE....EEETTEEEE.EEEECCTEEE-SSSS-CCHHHHHHHHH CS
                               GH3 370 LyRYrigDvvrvt....gfynkaPrl.eFvgRknvvlsidgeklteeelqkave 418
                                       L RY+igD+  vt    +   + Prl +++gR + ++ ++g  +  +++++++ 
  gi|474934557|ref|YP_007688139.1| 294 LIRYKIGDISSVTwekcECGRTHPRLaRISGRADDMIVVRGINVFPSQIESVIG 347
                                       89********99943333445678543688888888888888888888887776 PP

>> DUF2505  Protein of unknown function (DUF2505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.1e-05      0.15      14      80 ..     357     432 ..     353     433 .] 0.94

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.1e-05
                           DUF2505  14 yaaltdeeywearleevgaeesevtseeveedgvtvtvtqtlpa.........dalPeavrkvvsgdlkitrtesw 80 
                                       +  lt+e y ++ + +v+ + +++t+++ e ++++++v+  l +          +lP+++ ++ ++  ++t+++sw
  gi|474934557|ref|YP_007688139.1| 357 HITLTNENYMDKMVVDVEIDPAHLTEDTTEIGAMSTQVQLRLKEilnlkaivrMNLPGTLERFEGKAKHVTDNRSW 432
                                       5579**************************999999999999999999**************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2739.92
//
Query:       gi|474934558|ref|YP_007688140.1|  [L=138]
Description: S-adenosylmethionine decarboxylase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.6e-19   70.1   0.0      2e-19   69.8   0.0    1.1  1  AdoMet_dc  S-adenosylmethionine decarboxylase


Domain annotation for each model (and alignments):
>> AdoMet_dc  S-adenosylmethionine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.8   0.0   1.1e-23     2e-19       3     105 ..      29     136 ..      27     137 .. 0.93

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 1.1e-23
                                       EEEEES--HHHCTSHHHHHHHHHHHHHHCT-E.EEEEEEEE-....SSS-EEEEEEETTEEEEEEEEGGGTEEEEEE CS
                         AdoMet_dc   3 lvdlygcdpelledaelleqilteaaeaigat.vlsvafhkf....epeGvsvvvliaeShlsiHtwpetgyaaiDv 74 
                                        +dl +cd ++++d + + q+  +++++i+++   + ++  f    + +G+s+  li++S +s H+  +t  a +Dv
  gi|474934558|ref|YP_007688140.1|  29 SIDLGECDHQKISDGKYIAQFAIDVCKEIKMKrYGEPYVVFFgdepKVQGYSLCQLIETSMISGHFAEDTDRAFVDV 105
                                       589****************************967777777779866669**************************** PP

                                       EEESTHHHHHHHHHHHHHHT-SEEEEEEEEE CS
                         AdoMet_dc  75 ftcgeispekaleylieafkadrvtvdelkR 105
                                       f+c+e+ pek ++y++e+f+a+++++++  R
  gi|474934558|ref|YP_007688140.1| 106 FSCKEFPPEKTAKYVAEYFGAKKMEYSVSFR 136
                                       ************************9988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 896.99
//
Query:       gi|474934559|ref|YP_007688141.1|  [L=62]
Description: hypothetical protein TALC_00988 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.53
# Mc/sec: 350.33
//
Query:       gi|474934560|ref|YP_007688142.1|  [L=94]
Description: hypothetical protein TALC_00989 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 602.81
//
Query:       gi|474934561|ref|YP_007688143.1|  [L=166]
Description: conserved hypothetical protein TIGR00481 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-26   93.0   0.0      2e-26   92.8   0.0    1.0  1  PBP       Phosphatidylethanolamine-binding protein


Domain annotation for each model (and alignments):
>> PBP  Phosphatidylethanolamine-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.8   0.0   1.1e-30     2e-26       6     132 .]      24     162 ..      12     162 .. 0.86

  Alignments for each domain:
  == domain 1  score: 92.8 bits;  conditional E-value: 1.1e-30
                                       G...CSBGGS-EEEEES--TTSSEEEEEEEETTSCCTCT.TEEEEEEEEEETTSSEE-TTC.......EE-B-TTSS CS
                               PBP   6 y...egentsPplswsdvpegtksyalvviDpDapkvse.tflHwvvtnipasvtslpega.......vqgknslge 71 
                                       +   +++ +s+pl+++++p+gt s+a+++ DpD  +v++ +++Hw+v++++  ++ l+e+a       vqg +s+  
  gi|474934561|ref|YP_007688143.1|  24 FnaaNMPSLSFPLKIEGAPAGTASFAIIFDDPDSVPVCGfKWVHWLVAGLQ--KNGLEEDAsrkasgiVQGVTSWYG 98 
                                       1444566888************************999*999*********9..999**9999999999888888888 PP

                                       ......CCCCS---B--STTS..EEEEEEEEEESSSG--BGSS-SHHHHHHHHCTTEEEEEEEEEEE CS
                               PBP  72 ......esesgYlgpcPpkgdgkHrYvfllyaldvealdlkagftraelgaaiaghvlakatlagnY 132
                                             +  s Y+gp+Pp++   H+Yv+++ ald+    l++gf+++ l++  + h+lakatl+g Y
  gi|474934561|ref|YP_007688143.1|  99 hgsddrDLVSCYGGPYPPDRP--HEYVLTVLALDFVP-VLRNGFDYDTLMKVAKTHILAKATLKGVY 162
                                       6655445555***********..************95.6999999999999999**********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1129.06
//
Query:       gi|474934562|ref|YP_007688144.1|  [L=594]
Description: TPR repeat protein, SEL1 subfamily [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.2e-46  154.3  50.0      2e-09   37.8   1.1   13.7 16  Sel1         Sel1 repeat
  ------ inclusion threshold ------
      0.044   13.4   0.1         13    5.4   0.1    3.0  3  HTH_Bact     Helix-turn-helix bacterial domain
       0.14   12.6   0.0         20    5.6   0.0    2.2  2  Metallophos  Calcineurin-like phosphoesterase
       0.27   11.9  20.0         14    6.4   0.6    7.2  9  TPR_16       Tetratricopeptide repeat
        1.8    8.7   4.7        4.9    7.3   0.1    3.5  3  MIT          MIT (microtubule interacting and transport) doma


Domain annotation for each model (and alignments):
>> Sel1  Sel1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.1   0.00024      0.85      23      38 .]      25      40 ..      18      40 .. 0.90
   2 ?    0.5   0.0      0.31   1.1e+03       7      29 ..      47      68 ..      42      70 .. 0.77
   3 ?   -3.6   0.2         5   1.8e+04      32      38 .]     105     111 ..     103     111 .. 0.83
   4 !    7.7   0.1    0.0016       5.8       6      38 .]     117     147 ..     112     147 .. 0.88
   5 ?    5.2   0.0      0.01        37       3      38 .]     152     183 ..     150     183 .. 0.80
   6 !   16.0   0.2   3.9e-06     0.014       2      31 ..     185     212 ..     184     217 .. 0.92
   7 ?   -1.9   0.1       1.7   6.1e+03       5      37 ..     224     254 ..     222     255 .. 0.67
   8 ?   -1.1   0.0      0.97   3.5e+03       1      37 [.     256     289 ..     256     289 .. 0.82
   9 !   21.5   0.6   7.5e-08   0.00027       1      37 [.     291     326 ..     291     326 .. 0.82
  10 !    7.9   0.0    0.0014       5.1       3      38 .]     330     363 ..     328     363 .. 0.87
  11 !   10.9   0.0   0.00017      0.61       2      37 ..     365     398 ..     364     399 .. 0.87
  12 !   12.0   0.2   7.2e-05      0.26       3      37 ..     402     434 ..     401     435 .. 0.84
  13 !   25.0   0.0   5.9e-09   2.1e-05       2      38 .]     437     471 ..     436     471 .. 0.93
  14 !   37.8   1.1   5.4e-13     2e-09       3      38 .]     474     507 ..     472     507 .. 0.95
  15 ?   -2.3   0.0       2.4   8.7e+03      27      38 .]     534     545 ..     534     545 .. 0.85
  16 !   25.0   1.4   6.2e-09   2.2e-05       1      38 []     546     581 ..     546     581 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00024
                              Sel1 23 pekAiewyekAAeqGd 38
                                      +e+A+ +y kAAe+G+
  gi|474934562|ref|YP_007688144.1| 25 VEEAFSLYLKAAEMGH 40
                                      689************9 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.31
                              Sel1  7 LGmfylylnGl.gvpkDpekAiew 29
                                      +   ++y++G  g+p D+ + + w
  gi|474934562|ref|YP_007688144.1| 47 VS--QYYYAGVaGIPEDRGLSMVW 68
                                      66..777****99**999887766 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 5
                              Sel1  32 kAAeqGd 38 
                                       kAAe G+
  gi|474934562|ref|YP_007688144.1| 105 KAAESGS 111
                                       9***996 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0016
                              Sel1   6 rLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                         G  ++y+ G g+ +D   A+  +e + e+G+
  gi|474934562|ref|YP_007688144.1| 117 LAG--MCYELGIGTFPDGYAAYAMFESSSEAGN 147
                                       568..666*********************9997 PP

  == domain 5  score: 5.2 bits;  conditional E-value: 0.01
                              Sel1   3 AmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                       A+ +L+       G+g  +D+e++i ++++ Ae G+
  gi|474934562|ref|YP_007688144.1| 152 AQLALC----MIRGTGCVRDRERGIDLLRQVAEGGS 183
                                       455555....47888999***********9999885 PP

  == domain 6  score: 16.0 bits;  conditional E-value: 3.9e-06
                              Sel1   2 eAmyrLGmfylylnGlgvpkDpekAiewye 31 
                                        A+ +++   ++++G gv+k++++A+e+y+
  gi|474934562|ref|YP_007688144.1| 185 RACLKYA--WCLEHGWGVKKNRKEAYEFYK 212
                                       599****..********************8 PP

  == domain 7  score: -1.9 bits;  conditional E-value: 1.7
                              Sel1   5 yrLGmfylylnGlgvpkDpekAiewyekAAeqG 37 
                                       y +G   +  +G g    ++ A  w+  A + G
  gi|474934562|ref|YP_007688144.1| 224 YEVG--RCCIDGIGAAESIDDAAAWFLIARKEG 254
                                       5566..555666665557778999998887665 PP

  == domain 8  score: -1.1 bits;  conditional E-value: 0.97
                              Sel1   1 aeAmyrLGmfylylnGlgvpkDpekAiewyekAAeqG 37 
                                       +eA +  +   + l+G++ ++ p ++++++ k Ae G
  gi|474934562|ref|YP_007688144.1| 256 PEAEFGIA--RCTLAGKMPER-PPEGLKLLIKCAEEG 289
                                       68999999..88899998888.888888888877765 PP

  == domain 9  score: 21.5 bits;  conditional E-value: 7.5e-08
                              Sel1   1 aeAmyrLGmfylylnGl.gvpkDpekAiewyekAAeqG 37 
                                       ++Am++L+  +ly +    v kDpe   ewy++AA  G
  gi|474934562|ref|YP_007688144.1| 291 PDAMMMLA--QLYAKDGkLVRKDPEASAEWYRRAALSG 326
                                       68******..655555437****************765 PP

  == domain 10  score: 7.9 bits;  conditional E-value: 0.0014
                              Sel1   3 AmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                       Am   G   +y +G+ + k+   A+++y +AA++G+
  gi|474934562|ref|YP_007688144.1| 330 AMVITG--DAYATGTVLQKNTADAFRFYMMAANMGN 363
                                       777788..777****8888***************97 PP

  == domain 11  score: 10.9 bits;  conditional E-value: 0.00017
                              Sel1   2 eAmyrLGmfylylnGlgvpkDpekAiewyekAAeqG 37 
                                       e m++ G   ++  G+g+++D+ +++++  +AAe G
  gi|474934562|ref|YP_007688144.1| 365 EGMHMAG--SALISGTGTKRDETEGFRLCSMAAEDG 398
                                       6788888..66688999****************987 PP

  == domain 12  score: 12.0 bits;  conditional E-value: 7.2e-05
                              Sel1   3 AmyrLGmfylylnGlgvpkDpekAiewyekAAeqG 37 
                                       + y+++  ++y +G+g++kD  kAi      Ae+G
  gi|474934562|ref|YP_007688144.1| 402 SEYAVA--CCYADGRGTEKDTGKAISMHLALAEKG 434
                                       7899**..999*************97766666666 PP

  == domain 13  score: 25.0 bits;  conditional E-value: 5.9e-09
                              Sel1   2 eAmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                        +m  LG  + y++G gv+ +  +A++w+e+ A++++
  gi|474934562|ref|YP_007688144.1| 437 KSMLFLG--ETYYKGEGVEENLPEAVRWFEMGAAKDN 471
                                       589****..8889********************9986 PP

  == domain 14  score: 37.8 bits;  conditional E-value: 5.4e-13
                              Sel1   3 AmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                       +my LG   +y++G+gv++D+ekA ewy kAA++G+
  gi|474934562|ref|YP_007688144.1| 474 CMYFLG--DAYDHGKGVEADEEKAKEWYGKAAKKGH 507
                                       6*****..888************************8 PP

  == domain 15  score: -2.3 bits;  conditional E-value: 2.4
                              Sel1  27 iewyekAAeqGd 38 
                                       ++ + ++Ae+Gd
  gi|474934562|ref|YP_007688144.1| 534 FQMFLRSAEAGD 545
                                       57799****997 PP

  == domain 16  score: 25.0 bits;  conditional E-value: 6.2e-09
                              Sel1   1 aeAmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                       a +my +G +y  + G g  +D e+A+ wyekAA +G+
  gi|474934562|ref|YP_007688144.1| 546 AQSMYIVGRYY--ESGIGMNADLESARAWYEKAAGKGN 581
                                       579*****555..*********************8876 PP

>> HTH_Bact  Helix-turn-helix bacterial domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0    0.0095        34      21      42 ..     293     314 ..     287     318 .. 0.86
   2 ?    5.4   0.1    0.0036        13      19      37 ..     436     453 ..     427     456 .. 0.85
   3 ?   -3.2   0.0       1.8   6.5e+03      19      29 ..     472     482 ..     471     489 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0095
                                       B-TTHHHHHHHHHHHHHHTT-- CS
                          HTH_Bact  21 sMsLlGQLyYqkgecleklgfs 42 
                                        M++l QLy   g++++k+  +
  gi|474934562|ref|YP_007688144.1| 293 AMMMLAQLYAKDGKLVRKDPEA 314
                                       6************999998655 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0036
                                       TTB-TTHHHHHHHHHHHHH CS
                          HTH_Bact  19 insMsLlGQLyYqkgecle 37 
                                       i+sM +lG  yY kge +e
  gi|474934562|ref|YP_007688144.1| 436 IKSMLFLGETYY-KGEGVE 453
                                       79*******987.788766 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 1.8
                                       TTB-TTHHHHH CS
                          HTH_Bact  19 insMsLlGQLy 29 
                                       in M +lG  y
  gi|474934562|ref|YP_007688144.1| 472 INCMYFLGDAY 482
                                       789****9755 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0      0.01        37      23      76 ..     317     371 ..     308     412 .. 0.75
   2 ?    5.6   0.0    0.0055        20      13      51 ..     451     494 ..     426     519 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.01
                                       HHHHHHHHHTTESEEEEEST.SSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTS.....C CS
                       Metallophos  23 kllddllreekpdlvllaGD.lvdrgdlekellellaalvkypipvylllGNHe.....g 76 
                                       +++++++ + ++ +++++GD +  +++l+k +++ +++  +     ++ +GN e     g
  gi|474934562|ref|YP_007688144.1| 317 EWYRRAALSGRATAMVITGDaYATGTVLQKNTADAFRFYMM-----AANMGNTEgmhmaG 371
                                       56666655568889999***777777*********888888.....******99444440 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0055
                                       TCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS.....HHHH CS
                       Metallophos  13 lgggqlddllkllddllreekpdlvllaGDlvdrg.....dlek 51 
                                         +++l++++++++  +++ +++ + ++GD +d+g     d ek
  gi|474934562|ref|YP_007688144.1| 451 GVEENLPEAVRWFEMGAAKDNINCMYFLGDAYDHGkgveaDEEK 494
                                       5568899999999888777677777777*****99888763333 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.4       0.5   1.8e+03      45      63 ..      20      38 ..      14      53 .. 0.63
   2 ?    5.0   0.0     0.011        40       5      45 ..      85     123 ..      82     139 .. 0.81
   3 ?   -2.8   0.0       3.1   1.1e+04      14      46 ..     169     196 ..     166     212 .. 0.73
   4 ?    0.5   0.0      0.28     1e+03      13      40 ..     240     262 ..     223     270 .. 0.65
   5 ?    6.4   0.6     0.004        14      34      61 ..     291     323 ..     286     330 .. 0.87
   6 ?    3.9   1.0     0.023        84       9      45 ..     308     339 ..     296     355 .. 0.77
   7 ?   -0.8   0.0       0.7   2.5e+03      37      64 ..     439     468 ..     437     472 .. 0.78
   8 ?    0.6   0.0      0.25     9e+02      37      64 ..     475     502 ..     473     505 .. 0.82
   9 ?    4.9   0.6     0.012        41      31      65 ..     543     581 ..     534     584 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.5
                            TPR_16 45 lrqgrlaeAaalyraalra 63
                                      +++ r++eA  ly++a++ 
  gi|474934562|ref|YP_007688144.1| 20 AKNERVEEAFSLYLKAAEM 38
                                      4556666666666665533 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.011
                            TPR_16   5 raalragdyddAaaaleaalkrdpssPdaaeAllllgdaal 45 
                                       + ++ +g++++ ++++e alk++   +  ++  +l g ++ 
  gi|474934562|ref|YP_007688144.1|  85 DTLVGRGRFPEPEELFENALKAAE--SGSPAGKFLAGMCYE 123
                                       678999*****************5..557788888777775 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 3.1
                            TPR_16  14 ddAaaaleaalkrdpssPdaaeAllllgdaalr 46 
                                       ++ + +l+++ + +      ++A l +++++ +
  gi|474934562|ref|YP_007688144.1| 169 ERGIDLLRQVAEGG-----SVRACLKYAWCLEH 196
                                       66667777777777.....77888888888877 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.28
                            TPR_16  13 yddAaaaleaalkrdpssPdaaeAllll 40 
                                        ddAaa + +a+k +     ++eA ++ 
  gi|474934562|ref|YP_007688144.1| 240 IDDAAAWFLIARKEG-----CPEAEFGI 262
                                       455555555555555.....55555555 PP

  == domain 5  score: 6.4 bits;  conditional E-value: 0.004
                            TPR_16  34 aeAllllgdaalrq.....grlaeAaalyraal 61 
                                       ++A++ l++++++      ++ ++ a++yr+a+
  gi|474934562|ref|YP_007688144.1| 291 PDAMMMLAQLYAKDgklvrKDPEASAEWYRRAA 323
                                       689999*****999999999***********86 PP

  == domain 6  score: 3.9 bits;  conditional E-value: 0.023
                            TPR_16   9 ragdyddAaaaleaalkrdpssPdaaeAllllgdaal 45 
                                        ++d+++ a+ +++a  ++     +a A+   gda++
  gi|474934562|ref|YP_007688144.1| 308 VRKDPEASAEWYRRAALSG-----RATAMVITGDAYA 339
                                       4667777777777777777.....8888888888876 PP

  == domain 7  score: -0.8 bits;  conditional E-value: 0.7
                            TPR_16  37 llllgdaalrq....grlaeAaalyraalraa 64 
                                       +l+lg+ +++      +l+eA+ +++   +aa
  gi|474934562|ref|YP_007688144.1| 439 MLFLGETYYKGegveENLPEAVRWFEM--GAA 468
                                       678888888888888999999999998..555 PP

  == domain 8  score: 0.6 bits;  conditional E-value: 0.25
                            TPR_16  37 llllgdaalrqgrlaeAaalyraalraa 64 
                                       +++lgda+ + + +++ ++  +++++ a
  gi|474934562|ref|YP_007688144.1| 475 MYFLGDAYDHGKGVEADEEKAKEWYGKA 502
                                       79*******9998888888888888665 PP

  == domain 9  score: 4.9 bits;  conditional E-value: 0.012
                            TPR_16  31 PdaaeAllllgdaalrq....grlaeAaalyraalraap 65 
                                         +a++++  g+ +        +l+ A+a+y++a++ + 
  gi|474934562|ref|YP_007688144.1| 543 AGDAQSMYIVGRYYESGigmnADLESARAWYEKAAGKGN 581
                                       4488999999999999899989999********997665 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1    0.0014       4.9       8      32 ..      13      37 ..       7      40 .. 0.88
   2 ?    1.0   0.2      0.13   4.7e+02      17      29 ..     201     213 ..     200     213 .. 0.88
   3 ?   -2.6   0.0       1.7   6.2e+03      18      30 ..     346     358 ..     345     360 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0014
                               MIT  8 vkkAveeDnagnyeeAlelYkeale 32
                                      ++ A e+ +++  eeA++lY +a e
  gi|474934562|ref|YP_007688144.1| 13 FRDAQELAKNERVEEAFSLYLKAAE 37
                                      6789*****************9987 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.13
                               MIT  17 agnyeeAlelYke 29 
                                       ++n +eA+e Yk+
  gi|474934562|ref|YP_007688144.1| 201 KKNRKEAYEFYKS 213
                                       6899*******95 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.7
                               MIT  18 gnyeeAlelYkea 30 
                                       +n ++A++ Y  a
  gi|474934562|ref|YP_007688144.1| 346 KNTADAFRFYMMA 358
                                       79999*****877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (594 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.73u 0.35s 00:00:01.08 Elapsed: 00:00:00.56
# Mc/sec: 3217.16
//
Query:       gi|474934563|ref|YP_007688145.1|  [L=36]
Description: hypothetical protein TALC_00992 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (36 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.33s 00:00:00.82 Elapsed: 00:00:00.53
# Mc/sec: 205.99
//
Query:       gi|474934564|ref|YP_007688146.1|  [L=178]
Description: 2'-5' RNA ligase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.5e-24   83.7   0.0    7.1e-16   58.2   0.0    2.1  2  LigT_PEase       LigT like Phosphoesterase
    3.8e-15   56.1   0.0    4.6e-15   55.8   0.0    1.0  1  2_5_RNA_ligase2  2'-5' RNA ligase superfamily
    8.6e-06   25.8   0.0    1.3e-05   25.2   0.0    1.2  1  AKAP7_NLS        AKAP7 2'5' RNA ligase-like domain


Domain annotation for each model (and alignments):
>> LigT_PEase  LigT like Phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.2   0.0   1.2e-19   7.1e-16      13      87 .]      15      89 ..       6      89 .. 0.87
   2 !   23.9   0.0   5.9e-09   3.5e-05      11      87 .]      98     170 ..      92     170 .. 0.86

  Alignments for each domain:
  == domain 1  score: 58.2 bits;  conditional E-value: 1.2e-19
                                      HHHHHHHHHHCCTTEEETSGGGSEEEEEEEEEESHHHHHHHHHHHHHHHHTSBEEEEEEEEEEEEEECCSCCEEE CS
                        LigT_PEase 13 rlaaeleralaklglkpvrpfnpHiTLaflgevdeekvpellealaeiasgaepfelkvdgvglfpsrlrprviy 87
                                       la  l++  a +g++pv + ++HiTLaf+gevdee+++++ e ++   +++ + +++++g+g+fps++rprvi+
  gi|474934564|ref|YP_007688146.1| 15 DLAPFLKDIGAVRGVRPVSAVQLHITLAFVGEVDEERIDDIAECVEAEVREKGSARITLKGAGAFPSEKRPRVIW 89
                                      4444444444789*************************************************************9 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 5.9e-09
                                       HHHHHHHHHHHHCCTTEEET.SGGGSEEEEEEEEEESHHHHHHHHHHHHHHHHTSBEEEEEEEEEEEEEECC.SCCE CS
                        LigT_PEase  11 larlaaeleralaklglkpv.rpfnpHiTLaflgevdeekvpellealaeiasgaepfelkvdgvglfpsrl.rprv 85 
                                       l+ +aa+++r++a++g++++ +pf+ HiT++++    + +v+ l+  +++     e f++  + v +++s l ++++
  gi|474934564|ref|YP_007688146.1|  98 LEGIAAGIRRRFAAKGIPFDeKPFKAHITVGRVDR--PTDVSGLIGVYRRT----EFFSFICRSVMVVRSDLsPSGP 168
                                       78899****************************87..77899888888766....4588999999999999988888 PP

                                       EE CS
                        LigT_PEase  86 iy 87 
                                        y
  gi|474934564|ref|YP_007688146.1| 169 TY 170
                                       76 PP

>> 2_5_RNA_ligase2  2'-5' RNA ligase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8   0.0   7.6e-19   4.6e-15       6     149 ..      17     162 ..      13     165 .. 0.89

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 7.6e-19
                   2_5_RNA_ligase2   6 aapiealrrslydkayprwppHitLlypfvededl.adlaellsrlaketepfevrldgfgvFeh.kks.vvylsvs 79 
                                       a++++++ ++ +  +++++++HitL++ ++ de   +d+ae++++ ++e    +++l+g+g F++ k   v+++ v+
  gi|474934564|ref|YP_007688146.1|  17 APFLKDIGAVRGVRPVSAVQLHITLAFVGEVDEERiDDIAECVEAEVREKGSARITLKGAGAFPSeKRPrVIWAGVE 93 
                                       55555566566888899************9999878*****************************86667******* PP

                   2_5_RNA_ligase2  80 dsealqalraallealpeagdkedsgeftPHlTiaqsadstsaaelleklaqalpplefevdevallrrd 149
                                       +  +l+ + a +++ ++++g   d+++f+ H+T+++ +++t+ + l+    +  + ++f +++v ++r d
  gi|474934564|ref|YP_007688146.1|  94 TGLPLEGIAAGIRRRFAAKGIPFDEKPFKAHITVGRVDRPTDVSGLIGVY-RRTEFFSFICRSVMVVRSD 162
                                       *******************888888*****************99998888.8888888888888888876 PP

>> AKAP7_NLS  AKAP7 2'5' RNA ligase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   2.2e-09   1.3e-05      41     146 ..      35     128 ..      30     138 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2.2e-09
                                       T--EEEEEEE---SHHHHHHHHHHHHHHHHHHHHHHTTS--EEEEEEEEEE.....TTTEEEEEE--SHHHHHHHHH CS
                         AKAP7_NLS  41 eklHlTllvlkLknkeeiaaakevLkevkeeikdaldnkplslrlkGletfnddpakarVlYakveeesneekLqel 117
                                        +lH+Tl  +   ++e+i++ +e+   v++e+++     + +++lkG + f  ++++ rV++a+ve+      L+ +
  gi|474934564|ref|YP_007688146.1|  35 VQLHITLAFVGEVDEERIDDIAEC---VEAEVREK---GSARITLKGAGAF-PSEKRPRVIWAGVET---GLPLEGI 101
                                       579999999888899999888765...45567777...9************.79999*********4...679**** PP

                                       HHHHHHHHHTTT--B--SS-.---EEEEE CS
                         AKAP7_NLS 118 adriikafeeaglvlekdkkkvklHaTlm 146
                                       a  i+++f ++g+  +++   +k H+T+ 
  gi|474934564|ref|YP_007688146.1| 102 AAGIRRRFAAKGIPFDEKP--FKAHITVG 128
                                       *************998875..59999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       228  (0.0127168); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 1272.78
//
Query:       gi|474934565|ref|YP_007688147.1|  [L=248]
Description: hypothetical protein TALC_00994 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1751.14
//
Query:       gi|474934566|ref|YP_007688148.1|  [L=265]
Description: methylthioadenosine nucleosidase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.5e-53  180.8   1.1    2.9e-53  180.5   1.1    1.0  1  PNP_UDP_1  Phosphorylase superfamily


Domain annotation for each model (and alignments):
>> PNP_UDP_1  Phosphorylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.5   1.1   1.6e-57   2.9e-53       1     232 [.      35     260 ..      35     262 .. 0.93

  Alignments for each domain:
  == domain 1  score: 180.5 bits;  conditional E-value: 1.6e-57
                                       CEEEEESSHHHHHHHHHHEEEEEEEEEE.TTEEEEEEEETTEEEEEEE--SSHHHHHHHHHHHHHHHC--SEEEEEE CS
                         PNP_UDP_1   1 kiaiivgspgevellaespleetpfgregrgfkfvtGtlkgkpvvivstGiGkpnaavvaeirllkefgvkaiiriG 77 
                                       +++ii+++ +ev+ l++s+  + ++     g +f +Gtl+gk vv+v++G+Gk+na  +++  l+ +fgv++ii++G
  gi|474934566|ref|YP_007688148.1|  35 RLGIIGAMDDEVDSLKASMHIDRKETVA--GMEFCIGTLEGKDVVVVRCGMGKVNAG-ICANTLINQFGVDRIINTG 108
                                       689***************6666666666..***************************.******************* PP

                                       EEEESSTTT-TT-EEEEEEEEESSSCCGCCTHHCCTCCCCTTSSEE--HHHHHHHHHCHHTTT..TTEEEEEEEEES CS
                         PNP_UDP_1  78 taGglnpdlkvGDvvipddainfdgrsplygpkeegqyfpdsydapadpelrallkeaaealg..ikvhrGvvatad 152
                                       +aG+l+++l +GD+vi+++a+++d++  + g+  ++ ++ +  ++pad++l++ + +aa++    ik + G v+++d
  gi|474934566|ref|YP_007688148.1| 109 VAGSLDNGLDIGDLVISSEAVQHDFDVSPIGFAKGEIPYTGLVAFPADASLIDSALRAASECApeIKAVKGRVCSGD 185
                                       ********************************9999*********************6666666788888******* PP

                                       ESS-CHHHHHHHHHHTC-CEEESSHHHHHHHHHHTT--EEEEEEEEETTTBETTCTCH.HCCCHHHHHHHHHHHHHH CS
                         PNP_UDP_1 153 gfyaeteaelrllrrlgadaveMEtaavaqlArelgipfaairvvsdlaaggadaeatheeveefaqeaaknaaall 229
                                       +f + +e+++r+ +++g  + eME+ a+a+++ +++ip+++ir++sd      d++++ ++  ef +eaa+++a ++
  gi|474934566|ref|YP_007688148.1| 186 QFINTNEQKDRITADFGGLCCEMEGGAIAHACCLNEIPYVIIRAISD----KPDGSSS-MDYSEFEKEAAQRCASIV 257
                                       ***********************************************....5555665.***************998 PP

                                       HHH CS
                         PNP_UDP_1 230 lal 232
                                         +
  gi|474934566|ref|YP_007688148.1| 258 HYM 260
                                       765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1711.27
//
Query:       gi|474934567|ref|YP_007688149.1|  [L=94]
Description: hypothetical protein TALC_00996 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 616.87
//
Query:       gi|474934568|ref|YP_007688150.1|  [L=104]
Description: nitrogen regulatory protein P-II [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.7e-31  106.4   1.0    1.1e-30  106.3   1.0    1.0  1  P-II      Nitrogen regulatory protein P-II


Domain annotation for each model (and alignments):
>> P-II  Nitrogen regulatory protein P-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.3   1.0     6e-35   1.1e-30       1     100 [.       4     103 ..       4     104 .] 0.98

  Alignments for each domain:
  == domain 1  score: 106.3 bits;  conditional E-value: 6e-35
                                       EEEEEEGGGHHHHHHHHHHTTGGCEEEEEEEEEESTCCEEEECTTEEEEEEEEEEEEEEEEEEGGGHHHHHHHHHHH CS
                              P-II   1 ieaiirpekleevkeaLekagvkgltvtevkGrGkqkghtelyrgaeyevellpkvkleivvsdedvekvveaiika 77 
                                       i+ai rpekl+ vk+aL++ag+++lt+tev+GrG+q g +   r  +  v+ ++k++++ivv+d + ++++eai +a
  gi|474934568|ref|YP_007688150.1|   4 ITAIFRPEKLQPVKDALKEAGINALTITEVRGRGQQSGIVFSNRVGSLVVDEIEKTRIDIVVEDCEEDATIEAIRNA 80 
                                       89*************************************9999999999999************************* PP

                                       H-SSSTTSEEEEEEEESEEEETT CS
                              P-II  78 aktgeiGDGkiFvlpveevirir 100
                                       a tg++GDG+iFv+pve+ irir
  gi|474934568|ref|YP_007688150.1|  81 ASTGHMGDGRIFVMPVERSIRIR 103
                                       **********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 694.56
//
Query:       gi|474934569|ref|YP_007688151.1|  [L=424]
Description: ammonium transporter [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.5e-114  382.8  38.0   1.7e-114  382.6  38.0    1.0  1  Ammonium_transp  Ammonium Transporter Family


Domain annotation for each model (and alignments):
>> Ammonium_transp  Ammonium Transporter Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  382.6  38.0  9.6e-119  1.7e-114       2     399 .]      27     421 ..      26     421 .. 0.97

  Alignments for each domain:
  == domain 1  score: 382.6 bits;  conditional E-value: 9.6e-119
                                       HHHHHHHHHHHHHHHHHHHHHHHSSGGGHHHHHHHHHHHHHHHHHHHHHTHHHHHHSSCBSSSSSCE-.TTTTSCCG CS
                   Ammonium_transp   2 flllsaalvifmqagfalleaglvrsknvlnilvknlldlavvvllyvlfGyslafgkskgvsgfign.lglsaagv 77 
                                       ++l+++alv++m++g+al+++g+ r++++++i+ +  + ++++ l + ++Gy+laf+ +  ++g+ign  ++ + ++
  gi|474934569|ref|YP_007688151.1|  27 WILVCSALVFIMTPGVALFYGGMLRKQSMTSIMAQTAIIMGIMALSWAIVGYTLAFSGD--IGGLIGNlDDVLLENI 101
                                       9*********************************************************9..*******856777777 PP

                                       CCTTCCHHH......HHHHHHHHHHHHHHHHHHHCTTTB-HHHHHHHHHHHHHHTHHHHHHHHHS.SSHHHHTT--. CS
                   Ammonium_transp  78 qdetlldgl......fflfqlafaataitivsgavaerikfsayllfsallgtlvyppvahwvwgeggwlaklgvli 148
                                       + +t+++g+      f+lfq++fa+++++iv ga +er++f+a  +f+a+++ lvy+p+ahwvwg gg+++++ ++ 
  gi|474934569|ref|YP_007688151.1| 102 DYGTIPEGStipemeFMLFQMMFAMITAGIVLGACMERVRFNAIAVFIAFWSVLVYAPMAHWVWG-GGLFDQHLTVL 177
                                       777777777777778**************************************************.******99999 PP

                                       -SSSTTTTHHHHHHHHHHHHHHHS-STTTTGTTTSS--GSBHHHHHHHHHHHHHHHHHHHHGGGSSSSHHHHH.HHH CS
                   Ammonium_transp 149 DfAgstvVHlvggvagLaaalvlgkregrfegkeeaikghnlpfavlGtllLwfgWfgFNaGsaltankrararaav 225
                                       DfAg+tvVH++++  gLa+a+++g+r +r+       +gh++p++++G+++LwfgW+gFN+Gs l+a+++a + a+v
  gi|474934569|ref|YP_007688151.1| 178 DFAGGTVVHMCAATTGLALAVFVGRRSERV-----LRRGHSMPMVFIGFAMLWFGWLGFNGGSGLAADGTAVN-AVV 248
                                       ***************************998.....99************************************.*** PP

                                       HHHHHHHHHHHHHHHHHHHHCSS-BHHHHHHHHHHHHHHHTTTTTTS-HHHHHHHHHHHHHHHHHHHHHHHHHHTC- CS
                   Ammonium_transp 226 tTllAaaagaltallisrlkegkinvlglanGilAGlVAiTaacavvepwgAliiGlvAgvlsvlgvkklkeklkid 302
                                       +T++A aag++ + ++++ + g+   lgl++G+lAGlVAiT+a+++v+p  A+iiGlvAgv++++gv +++++ + d
  gi|474934569|ref|YP_007688151.1| 249 VTMIAPAAGMISWAAVQYRQMGHTGALGLISGALAGLVAITPAAGYVKPGPAIIIGLVAGVVCYYGVLFMRSRSGAD 325
                                       ********************************************************************9******** PP

                                       CTTHHHHHHHHHHHHHHHHHHHHTSHHHCSSHSSTTGGGT-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSB CS
                   Ammonium_transp 303 DsldvvavHgvgGiwGllavgifaaekvvaskisggllsgegkqlvvqligilvilayafvvtlilllllklllgLr 379
                                       D+ldv++vHgvg+iwG++a+g+fa+++ v ++ ++gl++g+ +++  q+++++v++a+ f+ +++l+++++ ++  r
  gi|474934569|ref|YP_007688151.1| 326 DALDVFGVHGVGAIWGAVATGLFANPSMV-ADGYEGLFYGGISLFLGQIAAVIVTVAFCFAASYLLIWVISRFVRVR 401
                                       **************************965.*********************************************** PP

                                       --HHHHHHSHHHHHHSSSSB CS
                   Ammonium_transp 380 vseeeeevglDvaehgetay 399
                                       ++eeee vg+D++e +e  y
  gi|474934569|ref|YP_007688151.1| 402 LTEEEEAVGADISELAEPSY 421
                                       **************998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1000  (0.0557756); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 3140.42
//
Query:       gi|474934570|ref|YP_007688152.1|  [L=163]
Description: hypothetical protein TALC_00999 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-06   27.3   2.7    4.7e-06   26.5   2.7    1.4  1  Big_1            Bacterial Ig-like domain (group 1)
    0.00027   21.2   0.2    0.00052   20.2   0.2    1.6  1  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
     0.0022   17.8   0.1     0.0063   16.3   0.1    1.7  1  DUF824           Salmonella repeat of unknown function (DUF82
     0.0027   17.8   0.1     0.0045   17.1   0.1    1.3  1  MG4              Macroglobulin domain MG4
  ------ inclusion threshold ------
      0.034   14.4   0.4      0.055   13.8   0.4    1.5  1  Invasin_D3       Invasin, domain 3


Domain annotation for each model (and alignments):
>> Big_1  Bacterial Ig-like domain (group 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   2.7   1.3e-09   4.7e-06       8      52 ..      82     127 ..      74     138 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.3e-09
                             Big_1   8 tltatvkDangnpvagatVtfsvsg.galsassgtTdanGkatvtl 52 
                                       + t++v D++gn+v+ga Vt+s  g +++ ++  +Td nG a++  
  gi|474934570|ref|YP_007688152.1|  82 MMTVHVADSSGNAVKGAVVTLSGLGvDNNGNNHIQTDGNGDAEFDY 127
                                       68***********************77777************9865 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.2   1.5e-07   0.00052       4      45 ..      85     128 ..      83     156 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.5e-07
                   CarboxypepD_reg   4 GrVtdasgapiagatVtvtn..adtgtvastttdadGafrlrgl 45 
                                        +V d+sg++++ga Vt++    d++ +   +td +G+  ++ +
  gi|474934570|ref|YP_007688152.1|  85 VHVADSSGNAVKGAVVTLSGlgVDNNGNNHIQTDGNGDAEFDYI 128
                                       5899**************985458999***********999855 PP

>> DUF824  Salmonella repeat of unknown function (DUF824)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   1.7e-06    0.0063      16      37 ..      82     103 ..      81     105 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.7e-06
                            DUF824  16 pltitvkDasGnPvpnapftlt 37 
                                       ++t++v D+sGn+v+ a +tl+
  gi|474934570|ref|YP_007688152.1|  82 MMTVHVADSSGNAVKGAVVTLS 103
                                       7******************996 PP

>> MG4  Macroglobulin domain MG4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   1.3e-06    0.0045      16      63 ..      81     128 ..      77     140 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.3e-06
                               MG4  16 fsikVlvkdpdgspaknvpVkiealkseteekeslttdedGtakfsin 63 
                                       f ++V v d+ g+ +k+  V+++ l+ + + ++ ++td +G a+f + 
  gi|474934570|ref|YP_007688152.1|  81 FMMTVHVADSSGNAVKGAVVTLSGLGVDNNGNNHIQTDGNGDAEFDYI 128
                                       899*********************776788899999*******99765 PP

>> Invasin_D3  Invasin, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.4   1.5e-05     0.055      23      63 ..      82     124 ..      63     157 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.5e-05
                        Invasin_D3  23 tltvtlkDangnpvsgltvtfstt...sagtlsavtdngdGtyt 63 
                                       + tv + D +gn+v+g+ vt+s     ++g  + ++++g+G  +
  gi|474934570|ref|YP_007688152.1|  82 MMTVHVADSSGNAVKGAVVTLSGLgvdNNG-NNHIQTDGNGDAE 124
                                       479*******************44332555.4778899999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 947.78
//
Query:       gi|474934571|ref|YP_007688153.1|  [L=142]
Description: hypothetical protein TALC_01000 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 968.38
//
Query:       gi|474934572|ref|YP_007688154.1|  [L=130]
Description: hypothetical protein TALC_01001 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 983.00
//
Query:       gi|474934573|ref|YP_007688155.1|  [L=401]
Description: Selenocysteine lyase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.8e-106  356.3   0.0     2e-106  356.1   0.0    1.0  1  Aminotran_5      Aminotransferase class-V
    4.4e-06   26.1   0.0    5.9e-06   25.7   0.0    1.2  1  Aminotran_1_2    Aminotransferase class I and II
    0.00034   19.3   0.0    0.00051   18.7   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
  ------ inclusion threshold ------
      0.017   14.4   0.1      0.034   13.5   0.1    1.4  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
       0.03   13.6   0.0      0.038   13.3   0.0    1.3  1  Beta_elim_lyase  Beta-eliminating lyase


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  356.1   0.0  5.6e-110    2e-106       1     371 []      19     388 ..      19     388 .. 0.99

  Alignments for each domain:
  == domain 1  score: 356.1 bits;  conditional E-value: 5.6e-110
                                       EEEBTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHH CS
                       Aminotran_5   1 iyldsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlv 77 
                                       +yldsa  +  p++V+da++eyy++  a + rsvhhl++e++  v+e+re++  ++n e+ +  +ft++tt++in+v
  gi|474934573|ref|YP_007688155.1|  19 VYLDSACQSLRPDSVIDAIREYYERCPACGGRSVHHLSNEVSVRVDETRETLCSFFNGEDPDHFVFTRNTTDGINTV 95 
                                       7**************************************************************************** PP

                                       HHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTE CS
                       Aminotran_5  78 alslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGt 154
                                       a +++  lk+gd +v+t++eh++n vpw +l++  g+ ++      eg  d++ +++++ +++klv+++hvsnvtG+
  gi|474934573|ref|YP_007688155.1|  96 AGGFG--LKKGDVVVTTDSEHNSNYVPWLNLRDSVGIVIRRSVSGTEGIFDIESFKEQMGKDVKLVSVCHVSNVTGV 170
                                       ****5..9********************************************************************* PP

                                       B--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTTTTSSTT-EEEEEEHHHHHTS..SS.STTSE CS
                       Aminotran_5 155 iqpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghKllgPtGiGvlyvrkellekleplllggemv 231
                                         pv++++++a+++ga vlvD+++a++hi++d+++ g+Df+afs hKllgP+G Gvly+r+ +le+l    +gg++v
  gi|474934573|ref|YP_007688155.1| 171 EVPVKDVADIAHEYGAKVLVDGCAAAPHIKVDIRDSGADFYAFSMHKLLGPSGFGVLYGRPGILEELGMRSFGGGTV 247
                                       ***************************************************************************** PP

                                       EEEETTEEEEHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTC CS
                       Aminotran_5 232 eevsleettfaeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlkslpgvrlygpdkaerr 308
                                         v+++++tfa  p +feaG    ag+ g +aa++y+++ig++++e+h+ el +y+++ ++++ g+ ++gp++  +r
  gi|474934573|ref|YP_007688155.1| 248 GMVTYDSATFAPVPDRFEAGLQDYAGVFGTKAAIDYISKIGMDEVERHDSELVKYMMDSVEDVRGLSVVGPSDPSKR 324
                                       ***************************************************************************** PP

                                       BSEEEEEETTCSHHHHHHHHHHT.TEEEEEE-TTTHHHHHHTT.S-EEEEE--TTS-HHHHHHH CS
                       Aminotran_5 309 asivsfnfkgvhaedvatlLdee.gIavrsGhhcaqplmkrlalegtvRaSlyiynteeevdrl 371
                                       +si+sfn++g+ ++d+a++Ld+  gI++rsG hca+ +++ ++++g+ RaS y+yn++ ++dr+
  gi|474934573|ref|YP_007688155.1| 325 RSIFSFNIAGLLSHDIAMMLDSIdGIMIRSGMHCAHSFFDGRGIDGSARASVYLYNDKSDIDRF 388
                                       **********************99**************************************97 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   1.7e-09   5.9e-06      44     187 ..      62     191 ..      16     228 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.7e-09
                                       THHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-.THHHHHHHHTTSEEEE CS
                     Aminotran_1_2  44 dglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdpty.asyknilrlsggevvr 119
                                       +  +e +e+l++f++      ++++  v + + ++ ++ ++  +  l +gd+++  d  + ++y + l+l+++  + 
  gi|474934573|ref|YP_007688155.1|  62 R-VDETRETLCSFFN-----GEDPDHFVFTRNTTDGINTVAGGFG-LKKGDVVVTTDSEHnSNYVPWLNLRDSVGIV 131
                                       4.5799*********.....899**78888788887777777777.*********99999568***********666 PP

                                       EEBEET.TTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEE CS
                     Aminotran_1_2 120 yplyse.edfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvD 187
                                       ++ + +  +   d+e+++e+  +       +k++ v+ ++N tG+  + +++ ++   a++y++ ++vD
  gi|474934573|ref|YP_007688155.1| 132 IRRSVSgTEGIFDIESFKEQMGK------DVKLVSVCHVSNVTGVEVPVKDVADI---AHEYGAKVLVD 191
                                       665555488889***********......88************************...**********9 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.4e-07   0.00051      89     200 ..     102     219 ..      94     226 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.4e-07
                                       -TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEE.EST....TSHHHHHHHCCTTEEEEEEESS-TTTT----HHHHH CS
                   Cys_Met_Meta_PP  89 kaGdeivvsddlYggtqrllkkvlkklgievkf.vdt....sdleelekaikentklvylEtptnpllkvvDiekia 160
                                       k+Gd +v++d+ +++ +    ++   +gi ++  v       d+e++++++ + +klv +  ++n +   v ++++a
  gi|474934573|ref|YP_007688155.1| 102 KKGDVVVTTDSEHNSNYVPWLNLRDSVGIVIRRsVSGtegiFDIESFKEQMGKDVKLVSVCHVSNVTGVEVPVKDVA 178
                                       667777777777777666666666666666543132223335899******************************** PP

                                       HHHHHTT-EEEEEGTTTHTTTS-GG.GGT-SEEEEETTTTT CS
                   Cys_Met_Meta_PP 161 klakkagvlvvvDntfaspllqrpl.klgaDivvhSaTKyl 200
                                       ++a++ g+ v+vD + a+p +   + + gaD    S+ K l
  gi|474934573|ref|YP_007688155.1| 179 DIAHEYGAKVLVDGCAAAPHIKVDIrDSGADFYAFSMHKLL 219
                                       *******************6655552688998888887766 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   9.5e-06     0.034      39     170 ..      80     216 ..      62     218 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.5e-06
                                       SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE...-B-TTTSSB-GGGCGGG--TTE CS
                   DegT_DnrJ_EryC1  39 khaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfv...Dvdpdtynidpaaieaaitert 112
                                       +h + + + t+++  +   +g+++gd V+++     +   + l+l   +  v    v  +    d ++ ++   +  
  gi|474934573|ref|YP_007688155.1|  80 DHFVFTRNTTDGINTVAGGFGLKKGDVVVTTDSEHNSNYVPWLNLRDSVGIVirrSVSGTEGIFDIESFKEQMGKDV 156
                                       688999999*****99999************999988887777777666555444899999**************** PP

                                       EEEEEB-G...GGB---HHHHHHHHHHCT-EEEEE-TT-TT.-EETTEECCCSSSEEEEE-B CS
                   DegT_DnrJ_EryC1 113 kaIlpVhl...yGqvadmdalkaiaakhglkvieDaAhAlG.atykgkkvGalgdaavfSFy 170
                                       k + + h+    G  + ++ + +ia+++g kv+ D + A    +++ +  G  +d+ +fS++
  gi|474934573|ref|YP_007688155.1| 157 KLVSVCHVsnvTGVEVPVKDVADIAHEYGAKVLVDGCAAAPhIKVDIRDSG--ADFYAFSMH 216
                                       9999988633379999*******************8877662444445555..467777776 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.1e-05     0.038     101     211 ..     136     230 ..      78     309 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.1e-05
                                       E-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHH CS
                   Beta_elim_lyase 101 lknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaaks 177
                                       + + e G +d+e++++ + +      ++kl+s+    n+  G  v++   + va+ia++yg ++++Dg+    aa +
  gi|474934573|ref|YP_007688155.1| 136 VSGTE-GIFDIESFKEQMGK------DVKLVSVCHVSNV-TGVEVPV---KDVADIAHEYGAKVLVDGC---AAAPH 198
                                       44445.77777777776666......5889998888886.6777775...67899*************8...57778 PP

                                       HTS-CHHHHTTSSEEEEESSSTT--SS-.EEEEE- CS
                   Beta_elim_lyase 178 lgeivkemfsyvDsvtmslkKdllanvG.gvlafr 211
                                       +++++++  s++D   +s+ K  l + G gvl +r
  gi|474934573|ref|YP_007688155.1| 199 IKVDIRD--SGADFYAFSMHKL-LGPSGfGVLYGR 230
                                       8888887..7788888888885.445666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2476.01
//
Query:       gi|474934574|ref|YP_007688156.1|  [L=326]
Description: GMP synthase (glutamine-hydrolyzing), C-terminal domain or B subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-35  120.8   0.0    3.2e-35  120.1   0.0    1.4  1  GMP_synt_C       GMP synthase C terminal domain
    2.5e-08   33.4   0.3    3.2e-06   26.4   0.1    2.1  2  NAD_synthase     NAD synthase
    1.3e-05   25.0   0.0      2e-05   24.5   0.0    1.3  1  ATP_bind_3       PP-loop family
    0.00017   20.5   0.1    0.00026   19.9   0.1    1.3  1  tRNA_Me_trans    tRNA methyl transferase
    0.00018   21.2   0.0    0.00025   20.7   0.0    1.3  1  ThiI             Thiamine biosynthesis protein (ThiI)
    0.00022   20.8   0.0     0.0073   15.8   0.0    2.2  2  QueC             Queuosine biosynthesis protein QueC
    0.00081   19.2   0.0     0.0012   18.6   0.0    1.3  1  Asn_synthase     Asparagine synthase
  ------ inclusion threshold ------
      0.011   15.8   0.0      0.016   15.3   0.0    1.3  1  PAPS_reduct      Phosphoadenosine phosphosulfate reductase fa
       0.02   14.2   0.1      0.029   13.7   0.1    1.2  1  Arginosuc_synth  Arginosuccinate synthase


Domain annotation for each model (and alignments):
>> GMP_synt_C  GMP synthase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.1   0.0   1.6e-38   3.2e-35       1      92 []     234     325 ..     234     325 .. 0.99

  Alignments for each domain:
  == domain 1  score: 120.1 bits;  conditional E-value: 1.6e-38
                                       CCCCTTT-GGGSSEEEEEEEEEEE----------EEEEEEEEE---------B----HHHHHHHHHHHHHHSTT--- CS
                        GMP_synt_C   1 eelkkaglykkiwQafavllpvksvGvmgdkRtyeyvvalRaveseDamtadvaelpyevLekissrivnevkgvnr 77 
                                       ee+++agl+ k+wQ+f+++++++s+Gv++ +R +++ v++Rav+++Damta+v e+p+ +L+ki+sri+ evkgvnr
  gi|474934574|ref|YP_007688156.1| 234 EEFANAGLQGKVWQYFTIVPDYRSTGVRDGQRLWDWPVVIRAVNTKDAMTATVEEVPWPLLNKITSRILAEVKGVNR 310
                                       7899************************************************************************* PP

                                       EEEE---TTTS-S-- CS
                        GMP_synt_C  78 vvyditskPpatiEw 92 
                                       v+yd++ kP+atiEw
  gi|474934574|ref|YP_007688156.1| 311 VLYDLSPKPCATIEW 325
                                       *************** PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.1   1.6e-09   3.2e-06      10      88 ..      28     104 ..      18     120 .. 0.77
   2 !    4.9   0.0    0.0062        12     148     177 ..     174     203 ..     168     207 .. 0.93

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 1.6e-09
                                       HHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE---HHHHH CS
                      NAD_synthase  10 keyvkkagakgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidikpivr 86 
                                       +   k+ g  +v+l lSGGvDSs+vaal  ka+g  n + + + +    + ++e+ + +  n +++ + + ++ + r
  gi|474934574|ref|YP_007688156.1|  28 EALQKQIGNGKVLLALSGGVDSSVVAALLIKAIG-SNLTCVHVNHGLLRKGEAEQVIDVFRN-QMKANLVYVDATDR 102
                                       33445667789**********************6.578888888888888888888888888.77777777776666 PP

                                       HH CS
                      NAD_synthase  87 af 88 
                                        +
  gi|474934574|ref|YP_007688156.1| 103 FL 104
                                       55 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0062
                                       BETTTTS-HHHHHHHHHHTT--HHHHCS-- CS
                      NAD_synthase 148 lapiaellKtevkeLakelnvPervlkkpP 177
                                       ++p++ l+K ev+   k+l+ P++++ ++P
  gi|474934574|ref|YP_007688156.1| 174 VEPVKLLFKDEVRVVGKQLGLPDSMVYRQP 203
                                       579*********************999998 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   9.8e-09     2e-05       1      63 [.      38      96 ..      38     121 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 9.8e-09
                                      EEEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEE CS
                        ATP_bind_3  1 kvlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklniklei 63
                                      kvl+A+SgG+DS +   ll k     g++l+++hv+hgl  + ++e +++  + ++++ +l++
  gi|474934574|ref|YP_007688156.1| 38 KVLLALSGGVDSSVVAALLIKA---IGSNLTCVHVNHGLLRKGEAE-QVIDVFRNQMKANLVY 96
                                      589***************9999...568**********98776554.5666666666665554 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   1.3e-07   0.00026       2      33 ..      38      70 ..      37      99 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.3e-07
                     tRNA_Me_trans  2 kvvvalSgGVDSsvaaallkeq.gyevigvflk 33
                                      kv+ alSgGVDSsv+aall ++ g +++ v+++
  gi|474934574|ref|YP_007688156.1| 38 KVLLALSGGVDSSVVAALLIKAiGSNLTCVHVN 70
                                      799**********98877755426777777765 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   1.3e-07   0.00025       3      57 ..      36      91 ..      34     136 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.3e-07
                              ThiI  3 qgkvlaLlSgGiDSpVaaylllkR.Gcrvvlvhlknepgtseeaiekveklaella 57
                                      +gkvl+ lSgG+DS V a ll+k  G +  +vh++  +  + ea++++ +  + + 
  gi|474934574|ref|YP_007688156.1| 36 NGKVLLALSGGVDSSVVAALLIKAiGSNLTCVHVNHGLLRKGEAEQVIDVFRNQMK 91
                                      69************99888888755*********9888888888888877666554 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   3.7e-06    0.0073       2      59 ..      39      97 ..      38     128 .. 0.76
   2 ?    2.9   0.0     0.034        68     126     176 ..     144     195 ..     127     202 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.7e-06
                                      EEEE--SSHHHHHHHHHHHHH.-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEE CS
                              QueC  2 avvllSGGlDSttvlalakke.gkevealtfdYgqrhkkeleaakkiakelgveehkil 59
                                      +++ lSGG+DS++v+al  k+ g ++++++++ g  +k e e + ++++++  ++   +
  gi|474934574|ref|YP_007688156.1| 39 VLLALSGGVDSSVVAALLIKAiGSNLTCVHVNHGLLRKGEAEQVIDVFRNQMKANLVYV 97
                                      6789*********99877655279**********9999999988888776543344444 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.034
                                       TT--GGGSHHH.HHHHHHHHHHHHTS--EEE-TTTT--HHHHHHHHHHTTHH CS
                              QueC 126 fsgYPDcrdef.vkalnkalnlgedkkieieaPlidlsKaeivklgkelgvp 176
                                        + YPD  +   vka +++  l e+  +e++ P+  l K e+  +gk+lg+p
  gi|474934574|ref|YP_007688156.1| 144 GTIYPDILESHgVKAHHNVGGLPEKFGFELVEPVKLLFKDEVRVVGKQLGLP 195
                                       5789998665438888889999999************************976 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   5.8e-07    0.0012      17      50 ..      36      69 ..      27     105 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 5.8e-07
                      Asn_synthase 17 dvpvGalLSGGlDSSliaalaarqsksplktFsi 50
                                        +v + LSGG+DSS++aal+ +   s+l+++++
  gi|474934574|ref|YP_007688156.1| 36 NGKVLLALSGGVDSSVVAALLIKAIGSNLTCVHV 69
                                      5678899*************98887777777766 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0     8e-06     0.016       2      76 ..      39     115 ..      38     140 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 8e-06
                                       EEEE--SSCTCHHHHHHHHHHCTT.HEEEEEE-STB-H.HHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-T CS
                       PAPS_reduct   2 lvvsvsgGkdslVllhLalkafkp.vpvvfvdtghefp.etiefvdeleeryglrlkvyepeeevaekinaekhgss 76 
                                       + ++ sgG ds+V+  L++ka     + v+v+ g   + e  + +d ++++++ +l +++  +++ +k++  + +++
  gi|474934574|ref|YP_007688156.1|  39 VLLALSGGVDSSVVAALLIKAIGSnLTCVHVNHGLLRKgEAEQVIDVFRNQMKANLVYVDATDRFLDKLAGVSDPEQ 115
                                       56899***************9988469*******8765499999999999999999999999888888777666655 PP

>> Arginosuc_synth  Arginosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   1.4e-05     0.029       2      65 ..      41     105 ..      40     110 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.4e-05
                   Arginosuc_synth   2 LaysGGlDtsviikllkeklgeeviavavdvGq.eeedldevkekalklgavksvvvDakeefve 65 
                                       La sGG+D sv+ +ll + +g++   v v+ G   + + ++v +  ++  +++ v vDa + f +
  gi|474934574|ref|YP_007688156.1|  41 LALSGGVDSSVVAALLIKAIGSNLTCVHVNHGLlRKGEAEQVIDVFRNQMKANLVYVDATDRFLD 105
                                       9*****************************99623357777777777777789999999999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 2679.10
//
Query:       gi|474934575|ref|YP_007688157.1|  [L=449]
Description: putative ATPase (AAA+ superfamily) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.6e-23   81.2   0.2    1.2e-22   80.3   0.2    1.4  1  AAA_14        AAA domain
    2.2e-19   69.8   0.0    3.7e-19   69.1   0.0    1.4  1  DUF4143       Domain of unknown function (DUF4143)
     0.0018   18.7   0.1      0.012   16.0   0.0    2.2  3  AAA_16        AAA ATPase domain
     0.0023   18.4   0.0     0.0041   17.6   0.0    1.4  1  AAA           ATPase family associated with various cellular 
  ------ inclusion threshold ------
      0.011   16.0   0.0      0.045   14.0   0.0    1.9  1  AAA_22        AAA domain
      0.022   15.2   0.0      0.049   14.1   0.0    1.6  1  NERD          Nuclease-related domain
      0.024   15.2   0.0      0.066   13.8   0.0    1.8  1  AAA_18        AAA domain
       0.04   13.3   0.0      0.064   12.7   0.0    1.3  1  TniB          Bacterial TniB protein
        0.2   12.1   0.0       0.51   10.7   0.0    1.8  1  RNA_helicase  RNA helicase


Domain annotation for each model (and alignments):
>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.3   0.2     6e-26   1.2e-22       5     131 .]      24     156 ..      21     156 .. 0.87

  Alignments for each domain:
  == domain 1  score: 80.3 bits;  conditional E-value: 6e-26
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe....kllelilek.lke.....ekktylflD 71 
                                       l+++GaRrvGK+t++++++ke++   +s++ i++ + +d++++ ++    +l+ l+ ++ lk+     e+++ +++D
  gi|474934575|ref|YP_007688157.1|  24 LMLQGARRVGKSTIAEKFAKEQY---KSYMLIDFVEADDETRRIFNeyraDLDMLFNRLqLKTrvklyERQSAIIFD 97 
                                       789********************...**********9998888665556544444444443336788889999**** PP

                            AAA_14  72 EiqevpewekalkslvdegknldvivtGSnskllskeiatslagrvaeielyplsfaEfl 131
                                       E+q  p +++++k lv++g ++d+i tGS+  ++sk    ++  ++ +i+++p++f+E+l
  gi|474934575|ref|YP_007688157.1|  98 EVQAFPLAREMIKALVRDG-RYDYIETGSLITVKSKVSGIRVPSEEHKIDMHPMDFEEWL 156
                                       *******************.99************************************86 PP

>> DUF4143  Domain of unknown function (DUF4143)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.1   0.0   1.8e-22   3.7e-19      18     122 .]     240     399 ..     178     399 .. 0.86

  Alignments for each domain:
  == domain 1  score: 69.1 bits;  conditional E-value: 1.8e-22
                                       x...........................................xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxx RF
                           DUF4143  18 k...........................................glverlppwse..spnskkrlrkspKlyfvDtG 49 
                                       +                                           ++++r++  s+   +   ++++ + K+y++DtG
  gi|474934575|ref|YP_007688157.1| 240 RalalfnsipailssphkvlspvkvrkgsrkreydsavkwlcdaMIFNRCRCSSNpgIAIGLSEDVGRVKCYLLDTG 316
                                       266667777777777777777777777888888999999999999******99999999****************** PP

                                       xxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....x.xxxxxxxxxxxx RF
                           DUF4143  50 Llvallgldkeelleds..........enkGallEnlVaqeLlkysekegaklyyyrdk....n.gaEvDfvielkg 111
                                       Ll++l++ +++e l d           +n+G+l+En+VaqeL+     +g++l++ +++    n ++EvDf++  + 
  gi|474934575|ref|YP_007688157.1| 317 LLISLAFQNDREGLADTygllldgklsINRGMLFENMVAQELVC----RGYDLWFTEFEkkgsNrKYEVDFILP-GR 388
                                       ************99999***************************....8********9999*966********8.68 PP

                                       xxxxxxxxxxx RF
                           DUF4143 112 gkivpiEvKss 122
                                         ivp+EvKs+
  gi|474934575|ref|YP_007688157.1| 389 AGIVPLEVKSG 399
                                       89*******96 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0     6e-06     0.012      18      55 ..      16      52 ..       4      94 .. 0.73
   2 ?   -0.6   0.0      0.77   1.5e+03     126     161 ..      84     115 ..      52     127 .. 0.69
   3 ?   -2.1   0.0       2.3   4.5e+03      90     125 ..     211     247 ..     165     259 .. 0.54

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6e-06
                            AAA_16 18 rvrsgrpelvllsGesGvGKsslvrellralekdggif 55
                                      +++ gr ++++l G++ vGKs+++++++++  k++++ 
  gi|474934575|ref|YP_007688157.1| 16 NASNGR-SSLMLQGARRVGKSTIAEKFAKEQYKSYMLI 52
                                      566666.89*******************9888875444 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.77
                            AAA_16 126 llallsrderplvlvlDdlqwadeaslqllaaLlrl 161
                                        ++l++r +    +++D++q   +  +++++aL+r+
  gi|474934575|ref|YP_007688157.1|  84 RVKLYER-Q--SAIIFDEVQA-FPLAREMIKALVRD 115
                                       3444444.3..4899999994.44466666777765 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 2.3
                            AAA_16  90 esaeleawrekleeala.avpelagaeasrllellkr 125
                                       +  e+e+ ++ ++e ++ ++ +++ga+ +r l+l+++
  gi|474934575|ref|YP_007688157.1| 211 DIMEAEYVKKDILELYReDIHKIPGAAMERALALFNS 247
                                       3334555555555555553333334433444444433 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0     2e-06    0.0041       2      74 ..      25     106 ..      24     117 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2e-06
                                       EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS...STTHHHHHHHHHHHHHHHTS......TSEEEEEETGGG CS
                               AAA   2 llyGppGtGKTllakavakelgvefleisgsellsk...yvgesekkirelfkeakeka......kpsilfiDEida 69 
                                       +l G   +GK+++a+  ake   +++ i+  e  ++   ++ e  +++ +lf++++ k       ++s +++DE+ a
  gi|474934575|ref|YP_007688157.1|  25 MLQGARRVGKSTIAEKFAKEQYKSYMLIDFVEADDEtrrIFNEYRADLDMLFNRLQLKTrvklyeRQSAIIFDEVQA 101
                                       7889999*************87666666655555444559**************9777778999767********99 PP

                                       HHHHH CS
                               AAA  70 laksr 74 
                                       +  +r
  gi|474934575|ref|YP_007688157.1| 102 FPLAR 106
                                       86666 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.3e-05     0.045       4     112 ..      20     112 ..      17     126 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.3e-05
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevv...fvtlpsstsskdllrellralglelkaerlssee 77 
                                       ++++l++ G   +GK+t +++++++           ++++   fv++  +t  + +++e   +l+           +
  gi|474934575|ref|YP_007688157.1|  20 GRSSLMLQGARRVGKSTIAEKFAKEQ---------YKSYMlidFVEADDET--RRIFNEYRADLDM-------LFNR 78 
                                       68999*******************98.........7777734555555555..6666666666663.......2223 PP

                            AAA_22  78 llealeqalraravielliiDEaqhlrs..eealeeL 112
                                       l  + +  l +r+   ++i DE+q + +   e+++ L
  gi|474934575|ref|YP_007688157.1|  79 LQLKTRVKLYERQS--AIIFDEVQAF-PlaREMIKAL 112
                                       33344444555555..8999999998.5558887777 PP

>> NERD  Nuclease-related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.5e-05     0.049       1      56 [.     346     401 ..     346     427 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.5e-05
                              NERD   1 kgaegEravakeLkelkedeylvlhdvrlrpgtg..eiDhlvispkgifviEvKnwsG 56 
                                       +g+  E++va+eL    +++ l ++ ++ ++ ++  e+D+++ ++ gi+ +EvK+ + 
  gi|474934575|ref|YP_007688157.1| 346 RGMLFENMVAQELV--CRGYDLWFTEFEKKGSNRkyEVDFILPGRAGIVPLEVKSGRS 401
                                       58899*********..99999999999997774468******************9443 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.3e-05     0.066       3      92 ..      26     109 ..      24     129 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.3e-05
                            AAA_18   3 ltGtpGvGKttlakeLskrlgf.gvnlrdvakenglllevdpealdeskrldedkldklldaleenss.....alee 73 
                                       l G+ +vGK+t+a+  +k+  + ++ l+d +  ++     ++e           +++ l  ++++         +e 
  gi|474934575|ref|YP_007688157.1|  26 LQGARRVGKSTIAEKFAKEQ-YkSYMLIDFVEADDETRRIFNE-----------YRADLDMLFNRLQLktrvkLYER 90 
                                       78999*************95.5555555555555544444444...........44444444444433444555777 PP

                            AAA_18  74 gknlvidghlaeleseaak 92 
                                       ++ +++d + a ++  +++
  gi|474934575|ref|YP_007688157.1|  91 QSAIIFDEVQAFPLAREMI 109
                                       8888888888888777665 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.2e-05     0.064      32      61 ..      19      47 ..       6     100 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.2e-05
                              TniB 32 rkrmpnlllvGdsnnGKtmivekFarlhpp 61
                                      + r ++l+l G   +GK++i+ekFa+++ +
  gi|474934575|ref|YP_007688157.1| 19 NGR-SSLMLQGARRVGKSTIAEKFAKEQYK 47
                                      334.899******************98755 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00026      0.51       2      59 ..      25     100 ..      24     114 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00026
                      RNA_helicase   2 wlyGpsgeGKStlakeLakallkkl..................klkkkdsvysrnpeddfwdgYtgqevvvidDfg 59 
                                       +l+G++++GKSt+a+++ak+  k++                       d ++ r   ++ ++ Y++q ++++d++ 
  gi|474934575|ref|YP_007688157.1|  25 MLQGARRVGKSTIAEKFAKEQYKSYmlidfveaddetrrifneYRADLDMLFNRLQLKTRVKLYERQSAIIFDEVQ 100
                                       799****************999888777777777777666664222234444466666666667777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 3072.29
//
Query:       gi|474934576|ref|YP_007688158.1|  [L=595]
Description: Amino acid transporter [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-51  174.5  40.6    4.9e-51  173.9  40.2    1.4  2  AA_permease_2  Amino acid permease
    1.8e-23   82.9  31.4      3e-23   82.2  31.4    1.3  1  AA_permease    Amino acid permease
  ------ inclusion threshold ------
       0.13   11.9   0.8        9.9    5.9   0.0    2.9  2  DUF3918        Protein of unknown function (DUF3918)


Domain annotation for each model (and alignments):
>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.9  40.2   8.2e-55   4.9e-51       1     404 [.      31     457 ..      31     489 .. 0.80
   2 ?   -1.5   0.1      0.15   8.7e+02     144     170 ..     472     497 ..     466     521 .. 0.69

  Alignments for each domain:
  == domain 1  score: 173.9 bits;  conditional E-value: 8.2e-55
                     AA_permease_2   1 lsllsafalvigsvig.sgifvknlaasggpalilwvwiavligslavllvyaElssa..lprsgG..iyvyt.... 68 
                                       +++ +  ++++g++i  ++++    a+++  ++i+++ ++vl g +a+ l++ E+++a   p  gG  ++v+t    
  gi|474934576|ref|YP_007688158.1|  31 IDWKQGMIIAMGVPILiLPGIYD-IAGTAWGLSIMIWTVSVLQG-FAQNLAIGEMAAAleTPGIGGcaQKVFTkpne 105
                                       67888889999998664666655.67776666777788889999.8*********7642555555544556665555 PP

                     AA_permease_2  69 .kaafgkkvaflsawfnwfayvpvlasilsvaasyllnalgp........dlqgntwltyliaiaililvalinirg 136
                                        +++fg++++ ++aw++wf + pv+++ +   + y+  ++          d +g+  l+++++i+++  ++ + ++g
  gi|474934576|ref|YP_007688158.1| 106 gRYGFGRFIGAFTAWSYWFTWTPVIPIFTCTSVDYISKFMEHymemepldD-TGTLLLSLGFGILVFSMIVYVGSKG 181
                                       55557*********************************9976666775532.2445588999*************** PP

                     AA_permease_2 137 ikesakiqnilgilkillpliiliilglitvdgggfssl....stetdtffpngwpg....v...llgllivlwsfd 202
                                        +++a++  il+++ i +pl+++i++++i + +g  +        + ++ +p+gw++    +   +++++ ++w+ +
  gi|474934576|ref|YP_007688158.1| 182 LSGGARAGLILALIAI-VPLLVVILFPIIGITAGEGDLTgftiDRISENLTPDGWDWdagdFmmvFGMFAYAQWCAC 257
                                       ****************.6***********998876665566666666789******854441444666777****** PP

                     AA_permease_2 203 Gfesaanvseevkk..kdvpkaifigllivlvlyllvniaflgvvpddeianlsnlgsvaalffeavggkvvaiivv 277
                                       ++esaa +  e k+  kdvpka+++++l++l ly+lv+++++g + +++i+  +  +s++ + ++  +g ++ ii+ 
  gi|474934576|ref|YP_007688158.1| 258 AWESAATYGAEYKNpgKDVPKALISAGLVCLALYFLVPFVVYGMMDPETIEAWG--VSTLYPIAQYDFGNIGLIIAL 332
                                       ***********999889*********************************9754..3456666666667999***** PP

                     AA_permease_2 278 ilialsllgaintavigssrvlealardgvlPrffakvnkfgspiraiiltaivslillllfllassaaynfllsvs 354
                                       il++ +++  i ta++gssr+l+ ++ +g +P+ f  +nk+g+p++a+++++   +i+++++ ++   ++ ++l++s
  gi|474934576|ref|YP_007688158.1| 333 ILLIAGMVMLIQTAFLGSSRTLYFMGHEGNMPKIFTYTNKNGAPLVAMMYQFAMGIIFIIIIHFG---SVGMILAAS 406
                                       *******************************************************9999988886...69******* PP

                     AA_permease_2 355 slgliisyllliigalilrkkrphl..krpgkilvaiigalfllfllvalff 404
                                       s+g+ +  ++ +++ +  r++++ +  +rp++++++++ + ++l   + +f+
  gi|474934576|ref|YP_007688158.1| 407 SFGFSFALGMGMLAFITARRNPRFRdlPRPYRAPPGWFYVACFLMC-YQFFV 457
                                       **999999988877777777766446699***99999876666543.33332 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.15
                     AA_permease_2 144 qnilgilkillpliiliilglitvdgg 170
                                        n ++ + i + +i+li ++++++ ++
  gi|474934576|ref|YP_007688158.1| 472 ENGTFSVII-GAVILLIYVPVWVAIQH 497
                                       555666666.56666666666666554 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.2  31.4   5.1e-27     3e-23      69     471 ..     109     496 ..      35     505 .. 0.73

  Alignments for each domain:
  == domain 1  score: 82.2 bits;  conditional E-value: 5.1e-27
                       AA_permease  69 flgpelGfviGlnylfswitvla.leltaasiliqfwelvtdlpkawvt.........gavflvvlliinlvgvkvy 135
                                         g+  G +++++y+f+w  v++ + +t + ++ +f+e + ++  ++ t         g++++ +++ +   g+ + 
  gi|474934576|ref|YP_007688158.1| 109 GFGRFIGAFTAWSYWFTWTPVIPiFTCTSVDYISKFMEHYMEMEPLDDTgtlllslgfGILVFSMIVYVGSKGLSGG 185
                                       46788999***********9998256777777778888877777677779999988875444455556666777789 PP

                       AA_permease 136 geaefilalikiiaiiafiivgiillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaf 212
                                       ++a +ilali+i+ ++ +i++ ii+++ g++       f+ d  s   +nl+p+  + + g f+ ++++f+ +   +
  gi|474934576|ref|YP_007688158.1| 186 ARAGLILALIAIVPLLVVILFPIIGITAGEGDLT---GFTIDRIS---ENLTPDGWDWDAGDFMMVFGMFAYAQWCA 256
                                       9999***********9999999777766665544...36666666...88888855777888*************** PP

                       AA_permease 213 tGielvaiiagEvkdPeksiPkailqvviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvla 289
                                          e+ a+ ++E k+P k++Pka +++ +  + +Y l+ +++  +++          +s+  ++ i++   g+++l 
  gi|474934576|ref|YP_007688158.1| 257 CAWESAATYGAEYKNPGKDVPKALISAGLVCLALYFLVPFVVYGMMDPETIEAWG--VST--LYPIAQYDFGNIGLI 329
                                       **************************************99999999888877776..555..999********9998 PP

                       AA_permease 290 plinaviltaalssansslysasRvlyslakdglaPkvlkkvskrgvPlraillsmiisllalllaslnlaapivfn 366
                                         ++++i + ++ +   +   +sR+ly++ ++g +Pk++++ +k+g Pl+a+++ ++++ +++++  + +       
  gi|474934576|ref|YP_007688158.1| 330 IALILLIAGMVMLI-QTAFLGSSRTLYFMGHEGNMPKIFTYTNKNGAPLVAMMYQFAMGIIFIIIIHFGSV-----G 400
                                       88777776665554.5556689*****************************************99999999.....9 PP

                       AA_permease 367 fllaisaliglivwlliilsylrfRkalkyqgrsieelgfkaallplgvilvlaali..iillilalyayltvkkgp 441
                                       ++la+s + + + +++ +l+++  R+       + ++l+   +  p +++++ ++++  +++li  l++  +     
  gi|474934576|ref|YP_007688158.1| 401 MILAASSFGFSFALGMGMLAFITARRN-----PRFRDLPRPYRAPPGWFYVACFLMCyqFFVLIPCLAYWCI----- 467
                                       99********************88877.....3455555555555555555555544114444444444444..... PP

                       AA_permease 442 kdwgaasfaaaylivllfliilvgvklhvk 471
                                        + g ++  ++ +i  ++l+i+v v+++++
  gi|474934576|ref|YP_007688158.1| 468 -NGGIENGTFSVIIGAVILLIYVPVWVAIQ 496
                                       .44566666666666677777766666554 PP

>> DUF3918  Protein of unknown function (DUF3918)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.2     0.011        66       8      21 ..     161     174 ..     157     177 .. 0.90
   2 ?    5.9   0.0    0.0017       9.9      10      24 ..     413     427 ..     411     431 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.011
                           DUF3918   8 llalGaGaaayqma 21 
                                       ll+lG G++++ m+
  gi|474934576|ref|YP_007688158.1| 161 LLSLGFGILVFSMI 174
                                       89**********97 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0017
                           DUF3918  10 alGaGaaayqmaqkn 24 
                                       alG G++a+  a++n
  gi|474934576|ref|YP_007688158.1| 413 ALGMGMLAFITARRN 427
                                       9********999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (595 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       869  (0.048469); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.79u 0.34s 00:00:01.13 Elapsed: 00:00:00.53
# Mc/sec: 3360.98
//
Query:       gi|474934577|ref|YP_007688159.1|  [L=139]
Description: hypothetical protein TALC_01006 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00076   19.8   0.0    0.00092   19.5   0.0    1.2  1  AlbA_2    Putative DNA-binding domain


Domain annotation for each model (and alignments):
>> AlbA_2  Putative DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   5.1e-08   0.00092      22     114 ..      25     112 ..       9     125 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 5.1e-08
                            AlbA_2  22 iakticAfaNseg.GtlliGVeDdgkvvGvecsdqeedqlrlelksiikrfkpkvlpdiervelkgkkvlvvkveks 97 
                                        +k + A++N ++   +liG+  dg+ +G    d +ed+  +    ++ +++  +++++   +l+g+ ++ +   ++
  gi|474934577|ref|YP_007688159.1|  25 SLKAMTAMLNRSNrAEILIGIGPDGEPSGE---DLSEDDIPEVVRRMSAKIDHLPEYSVNLDSLEGRPFIRIS-ARG 97 
                                       5899******7666****************...8888888888888************************999.556 PP

                            AlbA_2  98 kkkplyeneegvvyiRr 114
                                        + p  ++ +g +yiR+
  gi|474934577|ref|YP_007688159.1|  98 YETP--YTFDGWFYIRK 112
                                       6677..79999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 829.23
//
Query:       gi|474934578|ref|YP_007688160.1|  [L=266]
Description: dihydrodipicolinate reductase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-43  148.0   0.1    1.9e-43  147.4   0.1    1.3  1  DapB_C          Dihydrodipicolinate reductase, C-terminus
    2.5e-29  101.9   2.0    4.3e-29  101.2   2.0    1.4  1  DapB_N          Dihydrodipicolinate reductase, N-terminus
    0.00084   19.8   0.3     0.0018   18.7   0.3    1.6  1  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai
      0.007   16.3   2.4      0.013   15.4   2.4    1.5  1  NAD_binding_10  NAD(P)H-binding
  ------ inclusion threshold ------
      0.054   14.1   0.7       0.14   12.8   0.7    1.7  1  NAD_binding_3   Homoserine dehydrogenase, NAD binding domain


Domain annotation for each model (and alignments):
>> DapB_C  Dihydrodipicolinate reductase, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.4   0.1   5.2e-47   1.9e-43       1     121 []     133     265 ..     133     265 .. 0.91

  Alignments for each domain:
  == domain 1  score: 147.4 bits;  conditional E-value: 5.2e-47
                                       HHHHHHHHHHHHCCCSTTT-EEEEEEEESTT--SSS-HHHHHHHHHHH.................-S-ETTCCCEEE CS
                            DapB_C   1 GvnlllklveeaakllkeaydveiiEkHhnkKaDaPSGTAlalaeaia..egke...........arkkkeigihsv 64 
                                       Gv +++kl++ aak l +ay+veiiE+Hhn+K+DaPSGTAl+ a+ i+                   +  eigihs+
  gi|474934578|ref|YP_007688160.1| 133 GVGVFFKLCKAAAKDLGNAYEVEIIEAHHNQKKDAPSGTALTAADIISkeL--GgkeyvygrqgvCPRGTEIGIHSI 207
                                       899*********************************************550..24456666656644557******* PP

                                       ETTT--CCCCEEEECTTEEEEEEEEEESCHHHHHHHHHHHHHH.HCTSS.EESHHHHH CS
                            DapB_C  65 RgggvvgehevlfagegevieikhealsreiFaeGallaaewlakkkkg.lysmedvL 121
                                       Rgg++vg+h+v+f g++e+iei+h+a+sre+F+ Ga+ aa+w++++kkg +y+m dvL
  gi|474934578|ref|YP_007688160.1| 208 RGGDIVGDHTVMFIGNSERIEIRHQAHSREVFVGGAVMAAQWVVRQKKGaVYEMADVL 265
                                       ******************************************99999999*******8 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.2   2.0   1.2e-32   4.3e-29       2     124 .]       5     130 ..       4     130 .. 0.96

  Alignments for each domain:
  == domain 1  score: 101.2 bits;  conditional E-value: 1.2e-32
                                       EEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEB..SSHHHHHHH..-SEEEE- CS
                            DapB_N   2 kvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavt..ddleevlek..advliDF 74 
                                       + a+vGa GrmG+ +v+ + ++e+++++aa+d  +   +gkd+ge++glgk++v+v+  +dle+vl++  +dvl+DF
  gi|474934578|ref|YP_007688160.1|   5 RAALVGACGRMGQMIVRRIMATEGITVSAAFDLVN---VGKDIGEIAGLGKIDVPVSdpKDLEKVLKEskTDVLLDF 78 
                                       6799*****************************99...9******************999*******999******* PP

                                       S-HHHHHHHHHHHHHTT-EEEE--SS--HHHHHHHHHHTTT..SEEEE-S-- CS
                            DapB_N  75 TtpeavlenlklalekgvklViGTTGlseeelaeleelakk..igvviapNf 124
                                       T+  a+  n+ +a+++gv+l+iGTTGls++++++++++  +  +++vi++N+
  gi|474934578|ref|YP_007688160.1|  79 TVAPATAVNAPVAAKAGVNLIIGTTGLSADQKKNITDAIVQnnVAAVISSNY 130
                                       *************************************775557********7 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.3     5e-07    0.0018       1      94 [.       5      99 ..       5     128 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 5e-07
                                      EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEE.GGGGGC...TT-SEEEE-SC CS
                    Semialdhyde_dh  1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavkaleegkdlkved.vdeeel...kevdivflalp 75
                                      ++a+vGa G +Gq ++r++     +++++++   +  Gk + e ++   ++ d++v+d  d e++   ++ d+++  + 
  gi|474934578|ref|YP_007688160.1|  5 RAALVGACGRMGQMIVRRIMATEGITVSAAFDLVN-VGKDIGEIAG--LGKIDVPVSDpKDLEKVlkeSKTDVLLDFTV 80
                                      579*******************************9.********88..89999999998888888888999******** PP

                                      HHHHHHHHHHHHHTTSEEE CS
                    Semialdhyde_dh 76 agvskelapklaeagvkvi 94
                                      a +++  ap +a+agv +i
  gi|474934578|ref|YP_007688160.1| 81 APATAVNAPVAAKAGVNLI 99
                                      ***************9766 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   2.4   3.6e-06     0.013       1     102 [.      10     135 ..      10     172 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.6e-06
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SE.EEES-........ CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgada.Vvsal........ 68 
                                       GA G+ G+ +v+++ a +g++v a     +  +++ + +gl  +++ v+d++dl+++lk   + V+  +        
  gi|474934578|ref|YP_007688160.1|  10 GACGRMGQMIVRRIMATEGITVSAAFDLVNVGKDIGEIAGLGKIDVPVSDPKDLEKVLKESKTdVLLDFtvapatav 86 
                                       9***********************99999999999999********************9765445444434455444 PP

                                       .......--TCCHHHH..............HHHHHHHHHHCT--EEEEEEE.TTTT CS
                    NAD_binding_10  69 .......ggggkdeeg..............aknivdaakeagvkRfvlvsa.igvg 102
                                              +       g               kni da  +++v  ++   + igvg
  gi|474934578|ref|YP_007688160.1|  87 napvaakA-------GvnliigttglsadqKKNITDAIVQNNVAAVISSNYsIGVG 135
                                       44443330.......13333333344444499999999999998777654325554 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.7   3.9e-05      0.14      44      99 ..      56     111 ..      12     126 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.9e-05
                                       --CB---HHHHHHHHS-EEEEE-S--HHHHTTHHHHHHTTEEEE-S--CGGG-HHH CS
                     NAD_binding_3  44 sealtldlddliahldpdvvVEcasseavaelvlkaLkagkdvvtankgaladeal 99 
                                       +   ++dl++++++ + dv+++ +   a+a  ++ a kag+++++   g+ ad+++
  gi|474934578|ref|YP_007688160.1|  56 PVSDPKDLEKVLKESKTDVLLDFTVAPATAVNAPVAAKAGVNLIIGTTGLSADQKK 111
                                       4556899******99*************************************6554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1700.30
//
Query:       gi|474934579|ref|YP_007688161.1|  [L=546]
Description: hypothetical protein TALC_01008 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-05   23.9   1.4    2.8e-05   23.9   1.4    2.2  3  Big_2           Bacterial Ig-like domain (group 2)
  ------ inclusion threshold ------
      0.024   15.1   0.7      0.069   13.6   0.0    2.1  3  Transglut_core  Transglutaminase-like superfamily
       0.15   11.9   0.0       0.27   11.0   0.0    1.3  1  Peptidase_C93   Bacterial transglutaminase-like cysteine prot


Domain annotation for each model (and alignments):
>> Big_2  Bacterial Ig-like domain (group 2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   1.4   4.7e-09   2.8e-05      24      70 ..      60     110 ..      38     116 .. 0.87
   2 ?   -3.5   0.0       1.7     1e+04      37      47 ..     145     155 ..     124     159 .. 0.63
   3 ?   -3.9   0.0       2.2   1.3e+04      54      67 ..     209     222 ..     209     223 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 4.7e-09
                                       EEEESTT-S-.--EEEEECC-SSEEEE...TCCEECCCSSEEEEEEEEETT CS
                             Big_2  24 vevtpssasd.kkvtwtssngsvAtVs...atGlVtavaaGkatitatskd 70 
                                       v++ p+   d + vtwtss++s+AtV+    t +++a a  ++titat  +
  gi|474934579|ref|YP_007688161.1|  60 VIILPQYGVDpSVVTWTSSDTSLATVDkgvVTFTGSATAGSTVTITATLEE 110
                                       6677777777788**************988888889999999999999876 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.7
                                       EEEECC-SSEE CS
                             Big_2  37 twtssngsvAt 47 
                                         +s+n+++A+
  gi|474934579|ref|YP_007688161.1| 145 NLSSENKDYAV 155
                                       34677777776 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 2.2
                                       ECCCSSEEEEEEEE CS
                             Big_2  54 VtavaaGkatitat 67 
                                       V av+ G++t t+t
  gi|474934579|ref|YP_007688161.1| 209 VMAVSHGDTTYTFT 222
                                       66899999997766 PP

>> Transglut_core  Transglutaminase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0         2   1.2e+04      14      43 ..     202     233 ..     193     256 .. 0.62
   2 ?   -3.6   0.1       2.5   1.5e+04      11      33 ..     283     306 ..     279     317 .. 0.66
   3 ?   13.6   0.0   1.2e-05     0.069      12      73 ..     373     446 ..     367     453 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2
                    Transglut_core  14 plekakaiyewvrknveys..aprrtpgsrda 43 
                                       +++ ak ++   ++  +y+   p++ pgs +a
  gi|474934579|ref|YP_007688161.1| 202 SYDWAKIVMAVSHGDTTYTftYPENVPGSTNA 233
                                       45555555555565555554455555555554 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.5
                    Transglut_core  11 akdplekakaiyewvrknveys.a 33 
                                         d++  +++ y+w   +++y+ +
  gi|474934579|ref|YP_007688161.1| 283 SMDSTGTVVRQYSWGDYSMTYEfQ 306
                                       566778888888888877777732 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 1.2e-05
                    Transglut_core  12 kdplekakaiyewvrknveys..........aprrtpgsrd..........aeavletgkGncedfaslfvallRal 68 
                                       +d+++ a+ ++++v+  ++y+          +        d          + +++ tg G+ced++ l++al  a+
  gi|474934579|ref|YP_007688161.1| 373 SDRYAYANYLAQFVQVCFQYDydayiygvysK--------DyvdstdywayPAETIYTGMGDCEDTSILLAALHNAA 441
                                       56677777888888866666654555444421........02223344567899999******************** PP

                    Transglut_core  69 GipaR 73 
                                       G  a 
  gi|474934579|ref|YP_007688161.1| 442 GYSAG 446
                                       98875 PP

>> Peptidase_C93  Bacterial transglutaminase-like cysteine proteinase BTLCP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   4.5e-05      0.27      53      95 ..     398     444 ..     379     450 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.5e-05
                     Peptidase_C93  53 ikpvtdkelygveerWeypkd....gaGdCedyallKrkeLieaGlp 95 
                                       i  v  k+  +++++W+yp++    g+GdCed  +l      +aG++
  gi|474934579|ref|YP_007688161.1| 398 IYGVYSKDYVDSTDYWAYPAEtiytGMGDCEDTSILLAALHNAAGYS 444
                                       6666778888999******8544449******998876666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (546 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.26s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 3272.65
//
Query:       gi|474934580|ref|YP_007688162.1|  [L=230]
Description: Sel1 repeat protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-19   68.9   9.5    1.1e-07   32.3   0.2    4.7  5  Sel1      Sel1 repeat


Domain annotation for each model (and alignments):
>> Sel1  Sel1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1      0.45   8.1e+03       7      18 ..      19      29 ..      18      32 .. 0.70
   2 !   20.5   0.1   3.1e-08   0.00055       6      30 ..      69      91 ..      67      99 .. 0.84
   3 !    4.0   0.0    0.0048        86       1      37 [.     100     135 ..     100     136 .. 0.81
   4 !   32.3   0.2   5.9e-12   1.1e-07       3      38 .]     139     172 ..     137     172 .. 0.92
   5 !   15.4   0.0   1.3e-06     0.023       7      38 .]     179     208 ..     177     208 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.45
                              Sel1  7 LGmfylylnGl.g 18
                                      L+  + yl Gl g
  gi|474934580|ref|YP_007688162.1| 19 LC--QSYLRGLvG 29
                                      67..777999964 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 3.1e-08
                              Sel1  6 rLGmfylylnGlgvpkDpekAiewy 30
                                       +G  ++y++G g+++Dp+ Aiewy
  gi|474934580|ref|YP_007688162.1| 69 WMG--LMYEKGIGTEQDPHVAIEWY 91
                                      699..677****************9 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.0048
                              Sel1   1 aeAmyrLGmfylylnGl.gvpkD...pekAiewyekAAeqG 37 
                                       +e++y  G  y   +G  g+ ++   ++++i+ +  +A++G
  gi|474934580|ref|YP_007688162.1| 100 PECQYEIG--Y---AGIsGLFPNsisQSEGIRMMAASADRG 135
                                       689*****..9...888778886666888999998888888 PP

  == domain 4  score: 32.3 bits;  conditional E-value: 5.9e-12
                              Sel1   3 AmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                       A+  +Gm+y    Glgv++Dp+kA+ +y kA e+G+
  gi|474934580|ref|YP_007688162.1| 139 ALSFMGMMY--AVGLGVERDPQKAFSYYCKASEAGS 172
                                       7889**888..**********************996 PP

  == domain 5  score: 15.4 bits;  conditional E-value: 1.3e-06
                              Sel1   7 LGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                       ++   +y++G gv +D++kA++ y+  A++Gd
  gi|474934580|ref|YP_007688162.1| 179 VA--FCYQHGFGVTQDIRKAMKMYQGLADKGD 208
                                       57..899*****************97777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1475.42
//
Query:       gi|474934581|ref|YP_007688163.1|  [L=105]
Description: hypothetical protein TALC_01010 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       230  (0.0128284); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 779.56
//
Query:       gi|474934582|ref|YP_007688164.1|  [L=431]
Description: hypothetical protein TALC_01011 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-05   23.7   0.6    0.00019   21.3   0.2    2.3  2  CarbopepD_reg_2  CarboxypepD_reg-like domain
    0.00017   21.7   2.8    0.00065   19.9   1.5    2.5  2  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
  ------ inclusion threshold ------
       0.18   11.7   0.5       0.77    9.7   0.1    2.1  2  DUF1416          Protein of unknown function (DUF1416)
        2.4    8.8   6.1         20    5.9   0.7    3.1  2  Cadherin_4       Bacterial cadherin-like domain


Domain annotation for each model (and alignments):
>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.2   4.3e-08   0.00019       3      60 ..     195     248 ..     193     259 .. 0.84
   2 ?   -0.5   0.0      0.29   1.3e+03      49      64 ..     323     338 ..     316     354 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 4.3e-08
                   CarbopepD_reg_2   3 GtVvdketkeplpgatVyvkgtkkgtvTdenGnFelknlpagkytLvvsyvGyktqek 60 
                                       G V++  ++ p++ga+V++ g++   vTd+nG+F+l+ l   + tL v + G+ t+++
  gi|474934582|ref|YP_007688164.1| 195 GFVTS--GGAPVAGASVHLAGSE--DVTDANGEFSLTVLYGTEGTLAVGATGFFTASV 248
                                       55554..578*********9886..69*********98888889********988765 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.29
                   CarbopepD_reg_2  49 vvsyvGyktqekkvtv 64 
                                        +s++G+ +++ +vt 
  gi|474934582|ref|YP_007688164.1| 323 AFSFLGFGSESDQVTS 338
                                       69*******9999985 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.51   2.3e+03      47      64 ..     169     186 ..     163     190 .. 0.75
   2 !   19.9   1.5   1.5e-07   0.00065       3      64 ..     194     248 ..     193     262 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.51
                   CarboxypepD_reg  47 pgtysvtvsapGyatatr 64 
                                        g y+ tvs + + +a+ 
  gi|474934582|ref|YP_007688164.1| 169 NGAYRFTVSGDAFVSAAL 186
                                       488899998888877765 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 1.5e-07
                   CarboxypepD_reg   3 sGrVtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatr 64 
                                       +G Vt + gap+aga+V ++       ++ +tda+G+f+l+ l  ++ ++ v a+G+ ta++
  gi|474934582|ref|YP_007688164.1| 194 NGFVT-SGGAPVAGASVHLA------GSEDVTDANGEFSLTVLYGTEGTLAVGATGFFTASV 248
                                       68888.69************......67789**********9999999*********99876 PP

>> DUF1416  Protein of unknown function (DUF1416)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.32   1.4e+03      41      62 ..     155     175 ..     151     188 .. 0.77
   2 ?    9.7   0.1   0.00017      0.77      18      59 ..     189     236 ..     175     248 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.32
                           DUF1416  41 LdssgeFtaevvtsaeGefrFf 62 
                                       Lds g  taev    +G++rF 
  gi|474934582|ref|YP_007688164.1| 155 LDSVGCDTAEVSF-VNGAYRFT 175
                                       7888888999865.67999995 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00017
                           DUF1416  18 keaviqGkvtrdgepvggayvRL......LdssgeFtaevvtsaeGef 59 
                                        e +++G vt++g+pv+ga v L       d++geF+  v  ++eG+ 
  gi|474934582|ref|YP_007688164.1| 189 IECLLNGFVTSGGAPVAGASVHLagsedvTDANGEFSLTVLYGTEGTL 236
                                       57899****************993333334778888888888888865 PP

>> Cadherin_4  Bacterial cadherin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.5     0.017        78      28      71 ..     203     245 ..     175     245 .. 0.68
   2 ?    5.9   0.7    0.0044        20       4      25 ..     282     303 ..     267     319 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.017
                        Cadherin_4  28 pltitagnvlandtDvd..gddltvtavtvagtyGtltlnadGsft 71 
                                       p+ +++   la   Dv   +++++ t +   gt Gtl + a+G ft
  gi|474934582|ref|YP_007688164.1| 203 PVAGASV-HLAGSEDVTdaNGEFSLTVL--YGTEGTLAVGATGFFT 245
                                       5555322.23344444311334666655..5899*********997 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0044
                        Cadherin_4   4 titvtgvndaPvavddsatvte 25 
                                       ++t+  vnd P  ++ s++ +e
  gi|474934582|ref|YP_007688164.1| 282 SVTIGTVNDVPYGTPVSISGPE 303
                                       5677777777777777777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       205  (0.011434); expected 358.6 (0.02)
Passed bias filter:                      181  (0.0100954); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2986.33
//
Query:       gi|474934583|ref|YP_007688165.1|  [L=213]
Description: hypothetical protein TALC_01012 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-08   35.4   0.0    1.3e-08   35.0   0.0    1.1  1  SUFU      Suppressor of fused protein (SUFU)


Domain annotation for each model (and alignments):
>> SUFU  Suppressor of fused protein (SUFU)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.0   7.5e-13   1.3e-08       4     152 ..      34     185 ..      31     196 .. 0.77

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 7.5e-13
                              SUFU   4 pldvlsvpd.eepghwhyvTlGlsdlpmd.......epeeaeadpesgpraELvlrlrkd...eesvareeptwpar 69 
                                       p++++++p+ +   +w ++T+G  +  ++       +    e  +    r E+++ l+++   ee+  re++   + 
  gi|474934583|ref|YP_007688165.1|  34 PVQIAIYPPtPSFWFWKIATVGACESENPpfriggrT----E-RKMVRRRNEFIIFLPAEwgpEED--REKWDFHIA 103
                                       788999988677999*********9999976644322....2.2344689********88876443..5889999** PP

                              SUFU  70 lLqvlArypfeeggtwlgpghtipnndplplaentkleglllvep....ddeel.taietpggkeVrflqlvpitee 141
                                       lL+  A++ +e+ggt ++ g+++      pl+++ k+++  ++ p     + ++ +++      +V  lq++pi++e
  gi|474934583|ref|YP_007688165.1| 104 LLKKAAAFHHETGGT-VMLGSIL------PLEHDGKVQYAFMAYPhvfgPGTRFfFSCGPLRSWKVACLQVIPISSE 173
                                       ***********8777.******9......344699999999999999774444424443334444************ PP

                              SUFU 142 Elefarek.gad 152
                                        +++a ++ +++
  gi|474934583|ref|YP_007688165.1| 174 DAAAAIDEtSSN 185
                                       **9998874444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       181  (0.0100954); expected 358.6 (0.02)
Passed bias filter:                      174  (0.00970495); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1384.68
//
Query:       gi|474934584|ref|YP_007688166.1|  [L=179]
Description: TATA binding protein of transcription factor TFIID [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.4e-61  201.8   0.0    2.2e-29  101.3   0.0    2.0  2  TBP       Transcription factor TFIID (or TATA-binding protein
      1e-05   25.5   0.0      0.088   12.9   0.0    2.3  2  DUF3378   Domain of unknown function (DUF3378)
  ------ inclusion threshold ------
      0.014   15.6   0.0       0.29   11.4   0.0    2.1  2  PucR      Purine catabolism regulatory protein-like family
       0.12   12.8   0.1        8.7    6.7   0.0    2.3  2  EccE      Putative type VII ESX secretion system translocon, 


Domain annotation for each model (and alignments):
>> TBP  Transcription factor TFIID (or TATA-binding protein, TBP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.9   0.0   2.6e-32   1.2e-28       3      84 ..       2      81 ..       1      82 [. 0.96
   2 !  101.3   0.0   4.8e-33   2.2e-29       2      84 ..      92     174 ..      91     175 .. 0.97

  Alignments for each domain:
  == domain 1  score: 98.9 bits;  conditional E-value: 2.6e-32
                                      EEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHHH CS
                               TBP  3 kiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiapi 81
                                      ki+Nvvas++lg+eldL+k++ ++  ++aeY+p++fpglvyrl+epk++ l+F+sGk+v+tG ks +e+++a+ k+a+ 
  gi|474934584|ref|YP_007688166.1|  2 KIENVVASTSLGQELDLNKIEDSL--EGAEYNPQQFPGLVYRLKEPKTATLLFRSGKIVCTGGKSYDEVKAAITKVAKD 78
                                      9*******************9887..***************************************************99 PP

                                      HHH CS
                               TBP 82 lkk 84
                                      l++
  gi|474934584|ref|YP_007688166.1| 79 LEQ 81
                                      976 PP

  == domain 2  score: 101.3 bits;  conditional E-value: 4.8e-33
                                       EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHH CS
                               TBP   2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakki 78 
                                       +++qN+vas +lg+e++L+++a ++  +++eYepe+fpglvyrl++pkv++l+F sGk+v+tGak +e++ +a++ki
  gi|474934584|ref|YP_007688166.1|  92 IEVQNIVASSDLGQEINLNTVAITLGLEKVEYEPEQFPGLVYRLDDPKVVVLLFGSGKMVCTGAKVPEDVVRAVDKI 168
                                       89********************9988*************************************************** PP

                                       HHHHHH CS
                               TBP  79 apilkk 84 
                                       a  l++
  gi|474934584|ref|YP_007688166.1| 169 AAELRD 174
                                       *99986 PP

>> DUF3378  Domain of unknown function (DUF3378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0     2e-05     0.088      14      58 ..      21      66 ..      13      83 .. 0.79
   2 !   10.5   0.0   0.00011       0.5      24      55 ..     125     156 ..     119     163 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2e-05
                           DUF3378 14 mkeyyksk.lrskkppyavfaakkndttItaYtSgKVlFQGknaea 58
                                      ++  ++    + ++ p+ v++ k+++t   +++SgK++  G +   
  gi|474934584|ref|YP_007688166.1| 21 IEDSLEGAeYNPQQFPGLVYRLKEPKTATLLFRSGKIVCTGGKSYD 66
                                      555555442567889***********************99877655 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00011
                           DUF3378  24 skkppyavfaakkndttItaYtSgKVlFQGkn 55 
                                        ++ p+ v++ +++++++ ++ SgK +  G++
  gi|474934584|ref|YP_007688166.1| 125 PEQFPGLVYRLDDPKVVVLLFGSGKMVCTGAK 156
                                       6789**********************988876 PP

>> PucR  Purine catabolism regulatory protein-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.052   2.3e+02      36      67 ..      49      80 ..      24      86 .. 0.50
   2 ?   11.4   0.0   6.5e-05      0.29      29      92 ..      97     167 ..      87     170 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.052
                              PucR 36 aellrggeLllttglalkddpealaelvrela 67
                                      + l+r g ++ t g + ++ ++a+ ++ ++l 
  gi|474934584|ref|YP_007688166.1| 49 TLLFRSGKIVCTGGKSYDEVKAAITKVAKDLE 80
                                      23344555555555555444444555444444 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 6.5e-05
                              PucR  29 vlevpdiaellrggeLllttglal.kddpealaelvrelaeagvaaLviklgr......eipeelieaade 92 
                                       ++   d  + ++ + + +t gl   + +pe++  lv +l + +v+ L ++ g+      ++pe++++a d+
  gi|474934584|ref|YP_007688166.1|  97 IVASSDLGQEINLNTVAITLGLEKvEYEPEQFPGLVYRLDDPKVVVLLFGSGKmvctgaKVPEDVVRAVDK 167
                                       455556667788888999999999899************************94445677********9987 PP

>> EccE  Putative type VII ESX secretion system translocon, EccE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0     0.002       8.7      36      72 ..      68     104 ..      38     116 .. 0.88
   2 ?    4.0   0.0     0.014        63      36      53 ..     161     178 ..     153     179 .] 0.85

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.002
                              EccE  36 aaaaarRlakaLreqGirarvleaeeldaalaalavg 72 
                                       + aa +++ak L++++i+ ++  + e++  +a +  g
  gi|474934584|ref|YP_007688166.1|  68 VKAAITKVAKDLEQADIKITIEPKIEVQNIVASSDLG 104
                                       568899***************9999999998887655 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.014
                              EccE  36 aaaaarRlakaLreqGir 53 
                                       +++a +++a++Lr++G+ 
  gi|474934584|ref|YP_007688166.1| 161 VVRAVDKIAAELRDAGLM 178
                                       7899***********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1104.41
//
Query:       gi|474934585|ref|YP_007688167.1|  [L=121]
Description: hypothetical protein TALC_01015 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-07   30.2   0.1    7.9e-07   29.5   0.1    1.4  1  TPR_19    Tetratricopeptide repeat
    8.6e-07   29.5   0.1    1.7e-06   28.5   0.0    1.6  2  TPR_16    Tetratricopeptide repeat
    1.1e-05   25.8   0.8    0.00011   22.7   0.0    2.5  3  TPR_14    Tetratricopeptide repeat
    2.5e-05   23.8   0.0    6.9e-05   22.5   0.0    1.8  2  TPR_11    TPR repeat
    0.00019   21.6   0.0    0.00066   19.9   0.0    1.9  2  TPR_17    Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.013   15.6   0.1      0.038   14.1   0.0    1.7  2  TPR_9     Tetratricopeptide repeat
      0.013   15.5   1.5       0.45   10.8   0.2    2.9  4  TPR_2     Tetratricopeptide repeat
      0.036   14.4   0.1      0.074   13.4   0.0    1.5  2  TPR_20    Tetratricopeptide repeat
       0.22   12.2   1.8         35    5.3   0.1    3.4  4  TPR_6     Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.1     4e-10   7.9e-07       1      51 [.      67     117 ..      67     121 .] 0.90

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 4e-10
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdal 51 
                                       l+  gd++ A+++l+  l++dp++++a++ L ++l + g+ de  ++ +++
  gi|474934585|ref|YP_007688167.1|  67 LISKGDLQGAISRLRTYLEDDPEDPDAWMELGKLLCEIGEADEGYKAFAEA 117
                                       5778**************************************977776665 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       6.8   1.4e+04      14      25 ..      44      55 ..      43      58 .. 0.62
   2 !   28.5   0.0   8.6e-10   1.7e-06       5      63 ..      65     120 ..      61     121 .] 0.90

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 6.8
                            TPR_16 14 ddAaaaleaalk 25
                                      + A+  + ++l+
  gi|474934585|ref|YP_007688167.1| 44 RNARTEYLRVLD 55
                                      556666767666 PP

  == domain 2  score: 28.5 bits;  conditional E-value: 8.6e-10
                            TPR_16   5 raalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalra 63 
                                       r ++  gd + A+ +l+++l++d   P++++A+++lg ++ + g+ +e   ++++a ++
  gi|474934585|ref|YP_007688167.1|  65 RRLISKGDLQGAISRLRTYLEDD---PEDPDAWMELGKLLCEIGEADEGYKAFAEARKH 120
                                       778899*****************...88888*****************99999998776 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       6.6   1.3e+04      20      27 ..      46      53 ..      39      59 .. 0.57
   2 !   22.7   0.0   5.6e-08   0.00011       8      44 .]      64     100 ..      60     101 .. 0.91
   3 !    7.5   0.2    0.0044       8.7       3      29 ..      93     119 ..      93     121 .] 0.92

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 6.6
                            TPR_14 20 Aiallrra 27
                                      A++ + r+
  gi|474934585|ref|YP_007688167.1| 46 ARTEYLRV 53
                                      44444444 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 5.6e-08
                            TPR_14   8 aeallalGdpdeAiallrralalaPddaeawlllaql 44 
                                       ++ l   Gd+++Ai  lr +l+++P+d++aw++l++l
  gi|474934585|ref|YP_007688167.1|  64 VRRLISKGDLQGAISRLRTYLEDDPEDPDAWMELGKL 100
                                       5668889***************************986 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0044
                            TPR_14   3 allalaeallalGdpdeAiallrrala 29 
                                       a+++l+++l + G+ de  +++ +a +
  gi|474934585|ref|YP_007688167.1|  93 AWMELGKLLCEIGEADEGYKAFAEARK 119
                                       89*********************9976 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       2.3   4.5e+03      13      21 ..      46      54 ..      44      55 .. 0.80
   2 !   22.5   0.0   3.5e-08   6.9e-05       4      40 ..      67     103 ..      65     105 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.3
                            TPR_11 13 AieaYkkAl 21
                                      A ++Y + l
  gi|474934585|ref|YP_007688167.1| 46 ARTEYLRVL 54
                                      889999987 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 3.5e-08
                            TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlayyk 40 
                                       + ++G++ +Ai ++++ l+ dP++++a+ +LG+++ +
  gi|474934585|ref|YP_007688167.1|  67 LISKGDLQGAISRLRTYLEDDPEDPDAWMELGKLLCE 103
                                       789*****************************99755 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.7   3.5e+03      25      32 ..      69      76 ..      40      78 .. 0.62
   2 !   19.9   0.0   3.3e-07   0.00066       5      31 ..      83     109 ..      80     118 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.7
                            TPR_17 25 knGdlmtA 32
                                      ++Gdl+ A
  gi|474934585|ref|YP_007688167.1| 69 SKGDLQGA 76
                                      56677666 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 3.3e-07
                            TPR_17   5 aleldPnnadaynnLAelllknGdlmt 31 
                                        le dP ++da+ +L++ll+++G+ ++
  gi|474934585|ref|YP_007688167.1|  83 YLEDDPEDPDAWMELGKLLCEIGEADE 109
                                       6899*******************9875 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.9e-05     0.038      42      65 ..      70      93 ..      66      95 .. 0.92
   2 ?    6.8   0.0    0.0037       7.3      25      51 ..      87     113 ..      87     117 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.9e-05
                             TPR_9 42 lGclsaAladLeaylalapdapda 65
                                       G+l++A+  L +yl+ +p++pda
  gi|474934585|ref|YP_007688167.1| 70 KGDLQGAISRLRTYLEDDPEDPDA 93
                                      59*********************8 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0037
                             TPR_9  25 aPddpeerrdRGlllaqlGclsaAlad 51 
                                       +P+dp+ +++ G ll + G   ++ ++
  gi|474934585|ref|YP_007688167.1|  87 DPEDPDAWMELGKLLCEIGEADEGYKA 113
                                       69***************9998777665 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       7.2   1.4e+04      19      28 ..      18      27 ..      17      27 .. 0.76
   2 ?   -1.9   0.0       2.6   5.2e+03      19      29 ..      45      55 ..      43      57 .. 0.77
   3 ?    2.7   0.0     0.085   1.7e+02      12      34 .]      68      90 ..      65      90 .. 0.88
   4 ?   10.8   0.2   0.00023      0.45       1      30 [.      91     120 ..      91     121 .] 0.93

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 7.2
                             TPR_2 19 eAleafekAl 28
                                      +A++ f k+l
  gi|474934585|ref|YP_007688167.1| 18 KAADEFGKVL 27
                                      7888888876 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.6
                             TPR_2 19 eAleafekAle 29
                                       A+  + ++l 
  gi|474934585|ref|YP_007688167.1| 45 NARTEYLRVLD 55
                                      68999999886 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.085
                             TPR_2 12 yklgdyeeAleafekAleldPnn 34
                                      + +gd++ A+  ++  le dP++
  gi|474934585|ref|YP_007688167.1| 68 ISKGDLQGAISRLRTYLEDDPED 90
                                      678**********9999999986 PP

  == domain 4  score: 10.8 bits;  conditional E-value: 0.00023
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAlel 30 
                                       ++a+++lG+++ + g+ +e  +af +A ++
  gi|474934585|ref|YP_007688167.1|  91 PDAWMELGKLLCEIGEADEGYKAFAEARKH 120
                                       689************************886 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       4.4   8.8e+03      65      83 ..      48      66 ..      42      70 .. 0.61
   2 ?   13.4   0.0   3.7e-05     0.074       7      46 ..      76     115 ..      72     120 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.4
                            TPR_20 65 lkifealgsqdplvakyRr 83
                                       +++ +l+++   +a+ Rr
  gi|474934585|ref|YP_007688167.1| 48 TEYLRVLDEESGGMATVRR 66
                                      5666667766666666666 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 3.7e-05
                            TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeAleqLl 46 
                                        ++ l++ l+++p+d da ++l ++l + g+ +e  +++ 
  gi|474934585|ref|YP_007688167.1|  76 AISRLRTYLEDDPEDPDAWMELGKLLCEIGEADEGYKAFA 115
                                       6899***************************999887765 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.59   1.2e+03      18      31 ..      18      32 ..      11      32 .. 0.56
   2 ?   -1.5   0.0       2.5   5.1e+03      17      29 ..      44      56 ..      42      59 .. 0.72
   3 ?    3.3   0.0     0.079   1.6e+02      13      32 ..      70      89 ..      60      90 .. 0.81
   4 ?    5.3   0.1     0.017        35       1      30 [.      92     121 .]      92     121 .] 0.91

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.59
                                      HHHHHHHHHHHH.-T CS
                             TPR_6 18 kAlealerlike.YP 31
                                      kA + + +++++ YP
  gi|474934585|ref|YP_007688167.1| 18 KAADEFGKVLTDrYP 32
                                      555555555544387 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.5
                                      HHHHHHHHHHHHH CS
                             TPR_6 17 dkAlealerlike 29
                                      ++A++ + r+++e
  gi|474934585|ref|YP_007688167.1| 44 RNARTEYLRVLDE 56
                                      5688877777765 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.079
                                      HHHHHHHHHHHHHHHHH-TT CS
                             TPR_6 13 lgdtdkAlealerlikeYPd 32
                                       gd + A+  l+  +++ P+
  gi|474934585|ref|YP_007688167.1| 70 KGDLQGAISRLRTYLEDDPE 89
                                      379************99996 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.017
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH- CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerlikeY 30 
                                       dA + l++++ + g++d+  +a+ + +k Y
  gi|474934585|ref|YP_007688167.1|  92 DAWMELGKLLCEIGEADEGYKAFAEARKHY 121
                                       79999*******88*********9998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 730.82
//
Query:       gi|474934586|ref|YP_007688168.1|  [L=254]
Description: 2-polyprenylphenol hydroxylase-related flavodoxin oxidoreductase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.5e-11   42.1   6.9    1.3e-10   40.9   6.9    1.7  1  DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydr
    1.2e-05   25.6   0.0    2.9e-05   24.3   0.0    1.6  1  FAD_binding_6    Oxidoreductase FAD-binding domain
  ------ inclusion threshold ------
       0.13   12.1   0.1        1.2    8.9   0.0    2.4  2  DMRL_synthase    6,7-dimethyl-8-ribityllumazine synthase
       0.16   12.1   0.9         16    5.6   0.1    2.2  2  NAD_binding_6    Ferric reductase NAD binding domain


Domain annotation for each model (and alignments):
>> DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   6.9   2.8e-14   1.3e-10       1      41 [.     201     233 ..     201     234 .. 0.95

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 2.8e-14
                                       ----SSSSSSS-TTEEEETTCTT.CEEETTTT-CEEECCCB CS
                   DHODB_Fe-S_bind   1 eerMaCGvGaClgCvvktkggdggeykrvCkdGPvFdadev 41 
                                       e++M+CG G+C++Cv++         +rvCkdGPvF+ +++
  gi|474934586|ref|YP_007688168.1| 201 ERHMKCGAGVCGCCVIDG--------QRVCKDGPVFTREQI 233
                                       89***************9........69*********9997 PP

>> FAD_binding_6  Oxidoreductase FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   6.5e-09   2.9e-05       4      96 ..       7      86 ..       5      88 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 6.5e-09
                                      EEEEEECCTTEEEEEEEESTTTS-----TT-EEEEEECETTCCEEEEEE.BSSTTECCEE.EEEEE--TT-HHHHHHHC CS
                     FAD_binding_6  4 ltekeevsedtrifrfklpsekqklglpvGqhvflrlkikgeaviRsYtpissenekGel.ellvkvypgGkmsqaLde 81
                                      +  ++e s dt++++f+l+++++     +Gq+v++ ++  +e       p+s + ++G++  + vk +  G  s+ L+e
  gi|474934586|ref|YP_007688168.1|  7 VLGVTEESYDTKTIEFQLDDKAS-----PGQFVMVWVPGAEE------VPMSLS-KTGRIkSITVKAV--GPSSKKLHE 71
                                      5667899************8888.....9*********6666......355554.5666614666665..********* PP

                                      S-TT-EEEEEEEE-S CS
                     FAD_binding_6 82 lkigdtleikGPlGk 96
                                      l +gd+++++GP+G+
  gi|474934586|ref|YP_007688168.1| 72 LTVGDSIRVRGPYGH 86
                                      **************8 PP

>> DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00027       1.2      32      56 ..      28      52 ..      11      78 .. 0.82
   2 ?    0.3   0.1      0.13   5.7e+02      63      69 ..     171     177 ..     153     222 .. 0.53

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00027
                                      TSSCCEEEEEESSCCCHHHHHHHHC CS
                     DMRL_synthase 32 vaeenidvvtVPGafElplaakkla 56
                                      ++  ++++v+VPGa E+p+ ++k+ 
  gi|474934586|ref|YP_007688168.1| 28 ASPGQFVMVWVPGAEEVPMSLSKTG 52
                                      4457899************998865 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.13
                                       SEEEEEE CS
                     DMRL_synthase  63 davialG 69 
                                       d via+G
  gi|474934586|ref|YP_007688168.1| 171 DCVIACG 177
                                       4444444 PP

>> NAD_binding_6  Ferric reductase NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1    0.0035        16       3      24 ..      95     116 ..      93     131 .. 0.87
   2 ?    5.1   0.1    0.0051        23     133     155 ..     167     189 ..     155     190 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0035
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                     NAD_binding_6   3 nvllvagGiGitpfisilkdll 24 
                                       n l+v+gG+G++ +++ +k+ +
  gi|474934586|ref|YP_007688168.1|  95 NYLIVGGGVGVASIMPAVKESG 116
                                       6689************999866 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0051
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                     NAD_binding_6 133 knssvgvfvCGppklvkevkklv 155
                                       +n    v+ CGpp++++ ++k++
  gi|474934586|ref|YP_007688168.1| 167 ENHYDCVIACGPPVMLYFLYKAC 189
                                       45555799*********999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1752.10
//
Query:       gi|474934587|ref|YP_007688169.1|  [L=298]
Description: dihydroorotate dehydrogenase (subfamily 1) family protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.6e-57  193.5   0.1    5.2e-57  193.3   0.1    1.0  1  DHO_dh        Dihydroorotate dehydrogenase
      1e-11   44.5   0.5      7e-08   31.9   0.2    2.2  2  Dus           Dihydrouridine synthase (Dus)
    2.5e-05   23.9   1.9    7.9e-05   22.2   0.7    2.1  2  NMO           Nitronate monooxygenase
     0.0028   17.1   0.1      0.078   12.4   0.0    2.4  3  His_biosynth  Histidine biosynthesis protein


Domain annotation for each model (and alignments):
>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.3   0.1   1.1e-60   5.2e-57       4     295 .]       3     281 ..       1     281 [. 0.90

  Alignments for each domain:
  == domain 1  score: 193.3 bits;  conditional E-value: 1.1e-60
                                       EEETTEEESSSEEE-TTSSTT.SSSHHHHHCTTSSEEEEEEE-SS-B--S-S--EEEETTCTEEEE---S-BS-HHH CS
                            DHO_dh   4 tkvlglkfknpiglAaGfdke.geeilkllklgfgaieigsvtpkpqeGnpkPrvfrlkedrsvlNslGlnneGlda 79 
                                       t v +l ++ p ++A+G++ e g ++ +++++g+ga+ ++s+++++++G+++P   ++k +  ++N++Gl+n+G+d 
  gi|474934587|ref|YP_007688169.1|   3 TAVGKLALERPGMVASGIMDEtGASMVRMIEAGAGAVVTKSIGLEARPGHANPCFTEVKGG--FVNAMGLPNPGIDL 77 
                                       6777889999*******976516778899********************************..************** PP

                                       HHHHHHHHHHHHHCC.CEEEEEEE-TTSS.HHHHHHHHHHHHGGG.ESEEEEES-SCTCC.TSCCCGCHHHHHHHHH CS
                            DHO_dh  80 vlekllkrrkeqeekkelginlskakktenavddyvevvrkigpf.adilelNvSsPntp.glrdlqekeelkaill 154
                                         e+++  + +        i+ s+ +++   + +++e++ k++ + a ++elN+S+P+++ ++ ++++++el ++++
  gi|474934587|ref|YP_007688169.1|  78 FREEMEVAVPH------GNIVGSIFGSN---AKEFAELAGKMEDYgACAIELNLSCPHAKgYGMEVGTDPELVRAIV 145
                                       ****9999977......34677777776...778*********774779***********889************** PP

                                       HHHHHHHSSEEEEEE-SSSSHHHHHHHHHHHHHHTECEEEE...BSEE--CTTCCGCCCCTTSSEEEEEGGGHHHHH CS
                            DHO_dh 155 kvvkevskvpvlvKlaPdltdeekkdiadvllelkldgiivtNttvqrlaidlkseknvkanktGGlsGkalkdial 231
                                       + vk++ ++pv++Kl+P+      ++ia  ++  + d+i+++Nt    + i  +  k+   n++GGlsG+a++ +++
  gi|474934587|ref|YP_007688169.1| 146 SDVKAAVSIPVWAKLTPN--THILNEIALAAQDGGCDAIVAINTLK-AMVISPEFGKPFLSNRFGGLSGPAVRAVGV 219
                                       *****************5..55566666666777788888888755.555*************************** PP

                                       HHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHHHHHHHHHH CS
                            DHO_dh 232 kvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakkikkeleelL 295
                                       ++i +ly+ ++  ip++gvGGi+  +Da  +i+aGA + q+++a+ ++gp +++k+ ++l e++
  gi|474934587|ref|YP_007688169.1| 220 RNIFDLYDAVS--IPLVGVGGISDWRDAAQYIMAGAVAFQIGSAVAKDGPEVFSKVNRGLSEFM 281
                                       ***********..***********************************************9987 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.2   1.6e-11     7e-08      60     156 ..      95     183 ..      85     184 .. 0.88
   2 !   10.6   0.0   4.8e-05      0.21     173     224 ..     220     271 ..     215     284 .. 0.83

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 1.6e-11
                                       EE-S-HHHHHHHHHHHHHTT-SCEEEEESSTTEEETTEEEGGGGGGSHHHHHHHHHHHHCCSSS-EEEEEESESSTT CS
                               Dus  60 lggsdpallaeaAklvadlgadeIdlNvGCPskkvtrggaGaaLlrkpdlvaqivkavvkaveiPvtvkirigidde 136
                                       ++gs++++ ae A + +d+ga +I+lN+ CP  k  + ++G     +p+lv  iv+ v+ av+iPv +k     +  
  gi|474934587|ref|YP_007688169.1|  95 IFGSNAKEFAELAGKMEDYGACAIELNLSCPHAKGYGMEVG----TDPELVRAIVSDVKAAVSIPVWAKLTPNTH-- 165
                                       789****************************9876666666....79********************99865544.. PP

                                       TC.HHHHHHHHHHCT-SEEE CS
                               Dus 137 eenalelakiveaaGaqalt 156
                                          + e+a ++++ G++a++
  gi|474934587|ref|YP_007688169.1| 166 --ILNEIALAAQDGGCDAIV 183
                                       ..578899999999999886 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 4.8e-05
                                       HHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCH.HCCSTTHHH CS
                               Dus 173 eaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrg.algnPwlfa 224
                                       ++I ++ +avsip+++ G+I d++da + +   Ga +  ig + a   P +f 
  gi|474934587|ref|YP_007688169.1| 220 RNIFDLYDAVSIPLVGVGGISDWRDAAQYIMA-GAVAFQIGSAvAKDGPEVFS 271
                                       5788999*******************999988.99999999873455688886 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       0.1   4.6e+02     174     198 ..     132     158 ..     123     159 .. 0.76
   2 !   22.2   0.7   1.8e-08   7.9e-05     168     224 ..     207     261 ..     167     265 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.1
                               NMO 174 pevgd..kglfaLvpqvldavdiPviA 198
                                       +evg+  +   a+v  v+ av+iPv A
  gi|474934587|ref|YP_007688169.1| 132 MEVGTdpELVRAIVSDVKAAVSIPVWA 158
                                       5566553445578999********987 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 1.8e-08
                               NMO 168 GGhqGtpevgdkglfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtr 224
                                       GG  G p+v  +g  ++ +   dav+iP++  GGi d r+ a  + +GA + qig++
  gi|474934587|ref|YP_007688169.1| 207 GGLSG-PAVRAVGVRNIFD-LYDAVSIPLVGVGGISDWRDAAQYIMAGAVAFQIGSA 261
                                       77777.5555555555554.689********************************98 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.61   2.8e+03      77     104 ..      15      44 ..       4      61 .. 0.68
   2 ?    1.8   0.0     0.031   1.4e+02     147     194 ..     101     152 ..      69     158 .. 0.70
   3 !   12.4   0.0   1.8e-05     0.078      68     114 ..     225     272 ..     213     280 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.61
                                       EEESSSSSHH..HHHHHHHCT-SEEEESHH CS
                      His_biosynth  77 qvGGGIrsle..dveelleagadkviigta 104
                                       +v +GI +    ++ +++eaga  v+  + 
  gi|474934587|ref|YP_007688169.1|  15 MVASGIMDETgaSMVRMIEAGAGAVVTKSI 44 
                                       566666665411345677777777766655 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.031
                                       EEHHHHHHHHHHTT-SEEEEE....ETTTTTTSS---HHHHHHHHHHHSSEE CS
                      His_biosynth 147 ldavelakkleelgageillt....didrdGtlsGpdleltkelaeavkipv 194
                                        ++ ela k+e++ga++i l+      +  G++ G d el++++ + vk  v
  gi|474934587|ref|YP_007688169.1| 101 KEFAELAGKMEDYGACAIELNlscpHAKGYGMEVGTDPELVRAIVSDVKAAV 152
                                       4677888888888888875442222677789999999999999888776655 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 1.8e-05
                                       HHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-.THHHHH CS
                      His_biosynth  68 iaeevfipvqvGGGIrsledveelleagadkviigtaavkn.pelike 114
                                       + ++v+ip+   GGI++  d+++++ aga    ig+a++k+ pe++++
  gi|474934587|ref|YP_007688169.1| 225 LYDAVSIPLVGVGGISDWRDAAQYIMAGAVAFQIGSAVAKDgPEVFSK 272
                                       567899999999*************************88774676665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1802.32
//
Query:       gi|474934588|ref|YP_007688170.1|  [L=112]
Description: hypothetical protein TALC_01018 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.012   14.8   4.4      0.014   14.6   4.4    1.0  1  FAT       FAT domain


Domain annotation for each model (and alignments):
>> FAT  FAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   4.4   7.9e-07     0.014     223     310 ..      18     103 ..       5     111 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 7.9e-07
                                       SS-SS---............HHHHCCCTCCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCCCCHHHHHC CS
                               FAT 223 elqsgleaqkeptnleeftkllarcylkkGewqealqkldwseekieeilqsysaateidpswykawhtwalfnfev 299
                                       + q++ ea+  +++++++++++a++  + Ge + al+  d ++e ++ei + y +a e+d++++k   + a + + +
  gi|474934588|ref|YP_007688170.1|  18 TEQKADEAR-YNSKISDKKNEKAKAIKEAGEKMFALYL-DGKSEINDEIKALYEKAIECDKEIEKLEKEKAEMVDAA 92 
                                       334455555.9999***********************9.788889*******************9999988888888 PP

                                       CHHHHHHSSSS CS
                               FAT 300 vskeeeqkeee 310
                                        ++ +++++e 
  gi|474934588|ref|YP_007688170.1|  93 KKERQDRRDEV 103
                                       88887775554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2377  (0.132579); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 787.14
//
Query:       gi|474934589|ref|YP_007688171.1|  [L=448]
Description: K+ transport systems, NAD-binding component [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-35  120.6   2.5      2e-17   63.5   0.1    2.3  2  TrkA_N         TrkA-N domain
    1.5e-15   56.8   0.4    6.7e-08   32.3   0.0    2.7  2  TrkA_C         TrkA-C domain
  ------ inclusion threshold ------
      0.016   15.6   1.0      0.087   13.3   0.1    2.2  2  NAD_binding_7  Putative NAD(P)-binding
      0.075   11.7   0.6       0.26    9.9   0.6    1.9  1  HI0933_like    HI0933-like protein
        0.3   10.3   4.0       0.18   11.1   0.4    2.0  2  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain


Domain annotation for each model (and alignments):
>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.5   0.1   5.5e-21     2e-17       1     114 [.       3     117 ..       3     119 .. 0.92
   2 !   57.0   0.2   5.8e-19   2.1e-15       1     114 [.     225     341 ..     225     343 .. 0.93

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 5.5e-21
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTT.SEEEES-TTSHHHHHHT.TGGGESEEEE-SSSHHH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeg.levvvgdatdeevLeea.giekadaviaatgddea 75 
                                       +i++G+G+vG++ a+  s++++ v+v +kd e+++ +++   + v++gda+++++L+ a +  + d+++ a++dd  
  gi|474934589|ref|YP_007688171.1|   3 VIVAGAGNVGMASAKAASAYNE-VLVLEKDAEKADIAKNVLpVSVMKGDASNPKTLKGAiDKFHPDVILSAVKDDSM 78 
                                       79*****************995.**************9999888*************987888999*********** PP

                                       HHHHHHHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEE CS
                            TrkA_N  76 nilavllakelnpkkkiiaraqdpehaellkklgadvvi 114
                                       n++++++ak l+p++++ia ++d e++      g+d +i
  gi|474934589|ref|YP_007688171.1|  79 NLFICMMAKRLMPDIRTIATIRDNEFVIEGGYPGVDSII 117
                                       ************************997666666777766 PP

  == domain 2  score: 57.0 bits;  conditional E-value: 5.8e-19
                                       EEEES-SHHHHHHHHHHHH.TT.EEEEEEESSHHHHHHHHHTT..SEEEES-TTSHHHHHHTTGGGESEEEE-SSSH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLse.gg.kdvvvidkdeerveelreeg..levvvgdatdeevLeeagiekadaviaatgdd 73 
                                       ++i+G+ ++G ++a  + +  g k v +id d  +++ ++++   + vv+g+++d+ +L++  +++ d++i +t+  
  gi|474934589|ref|YP_007688171.1| 225 FVILGATEMGIAVASAIADsPGkKFVKIIDEDIVKCKDAARRLggVIVVNGSVADPVFLRSESVDRSDVLISVTDYE 301
                                       79****************964467799************98887888****************************** PP

                                       HHHHHHHHHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEE CS
                            TrkA_N  74 eanilavllakelnpkkkiiaraqdpehaellkklgadvvi 114
                                       e+n+la+++    ++  kii+r  +++++ ++k +g++ +i
  gi|474934589|ref|YP_007688171.1| 302 EKNLLACMTSI-RFGINKIISRYTTDDYEGIFKYAGIESII 341
                                       *********95.58889********************9998 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.0   1.9e-11   6.7e-08       4      69 ..     152     216 ..     149     217 .. 0.92
   2 !   22.0   0.1   2.9e-08    0.0001      11      61 ..     384     433 ..     375     442 .. 0.87

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 1.9e-11
                                       EEEE--GGGTTSBHHHHTHHHHS-EEEEEE-T-EEES--TT-B--TT-EEEEEEEHHHHHHHHHHH CS
                            TrkA_C   4 vtvpagsplvGktlkelnlrargvlvvairRggeliipsgdtvLeeGDvllvvgspsdlaelrell 69 
                                       ++v  g+ ++Gk+  +l++++   +v+a+ Rg+e i    + + +e+D+llv+gs ++l e+  l 
  gi|474934589|ref|YP_007688171.1| 152 FRVVRGADIIGKPFMDLRIPE-FSNVIAVYRGKETITDLLSAEVHENDRLLVLGSYESLLEFNQLV 216
                                       788899***************.**********88888888*******************9998875 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 2.9e-08
                                       GGTTSBHHHHTHHHHS-EEEEEE-T-EEES--TT-B--TT-EEEEEEEHHH CS
                            TrkA_C  11 plvGktlkelnlrargvlvvairRggeliipsgdtvLeeGDvllvvgspsd 61 
                                       p+ +k+l+++ l++ gv ++ai Rg+++i ps ++++ +GD+  ++ ++ d
  gi|474934589|ref|YP_007688171.1| 384 PFRNKPLGDVYLPR-GVKIAAIIRGDDIIYPSLTDRISKGDEFMLYLHDVD 433
                                       7889**********.***************************999877665 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   2.4e-05     0.087       9      84 ..       2      88 ..       1     102 [. 0.78
   2 ?    0.4   0.1      0.25     9e+02      11      75 ..     226     304 ..     218     311 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.4e-05
                     NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtvvapevkeele..........elvk...laeeelekdlegad..lviaatddr 72
                                      kv+v+G+G+v++  ++   ++  +v v+ ++  e+++             k    ++++l++ +++++  +++ a++d+
  gi|474934589|ref|YP_007688171.1|  2 KVIVAGAGNVGMASAKAASAY-NEVLVLEKDA-EKADiaknvlpvsvM--KgdaSNPKTLKGAIDKFHpdVILSAVKDD 76
                                      799************999999.9999999994.222244555444330..13324677788999998888********* PP

                     NAD_binding_7 73 elneriaeaaka 84
                                      ++n  i+ +ak+
  gi|474934589|ref|YP_007688171.1| 77 SMNLFICMMAKR 88
                                      ******999984 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.25
                     NAD_binding_7  11 lvvGgGevAarkvrklleag..akvtvvapevkeele.......elvklaeee...........l..ekdlegadlv 65 
                                       ++ G+ e++   ++ ++++   + v+++++++ + ++       +                   +  ++++++ d++
  gi|474934589|ref|YP_007688171.1| 226 VILGATEMGIAVASAIADSPgkKFVKIIDEDIVK-CKdaarrlgG-------VivvngsvadpvFlrSESVDRSDVL 294
                                       5666666666666666664422336667777422.2222233321.......0222222223332445779999999 PP

                     NAD_binding_7  66 iaatddreln 75 
                                       i +td +e n
  gi|474934589|ref|YP_007688171.1| 295 ISVTDYEEKN 304
                                       9999877765 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.6   7.2e-05      0.26       2      34 ..       2      33 ..       1      99 [. 0.73

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 7.2e-05
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSS CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakk 34
                                      +viv G+G  G+ a+++aa++ ++Vl+lek  +
  gi|474934589|ref|YP_007688171.1|  2 KVIVAGAGNVGM-ASAKAASAYNEVLVLEKDAE 33
                                      79*********6.6667779999******9843 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.4     5e-05      0.18      30      99 ..       2      73 ..       1      76 [. 0.83
   2 ?   -0.0   0.2      0.12   4.5e+02      24      96 ..     219     295 ..     213     300 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5e-05
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTTCECEEHCHHHHHHHHHHHH-..SEEEE-- CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqles.lgakfvevlksqeellaeavkea..dvvigtv 99
                                      kv+v G+G +G++++++a++   +V vl+++++++   ++ l  ++++  +s+ ++l+ a+ +   dv+ ++v
  gi|474934589|ref|YP_007688171.1|  2 KVIVAGAGNVGMASAKAASAY-NEVLVLEKDAEKADIAKNvLPVSVMKGDASNPKTLKGAIDKFhpDVILSAV 73
                                      89*************988876.68999**99999999988888888888999999999988764337777776 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.12
                                       TCB---EE.EEEST...SHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTTCECEE...HCHHHHHHHHHHHH- CS
                       AlaDh_PNT_C  24 pgvepakv.lviGg...GvaGlqAiatakglgakVtvlDvrparleqles.lgakfvev...lksqeellaeavkea 92 
                                       +  +pa+  +++G+   G+a  +Aia + g    V+++D ++ + +     lg+  + v   ++    l +e+v ++
  gi|474934589|ref|YP_007688171.1| 219 K--KPARSfVILGAtemGIAVASAIADSPGK-KFVKIIDEDIVKCKDAARrLGGV-IVVngsVADPVFLRSESVDRS 291
                                       4..5666414567755566666666655553.34788888877777666656655.444232222233345566666 PP

                                       SEEE CS
                       AlaDh_PNT_C  93 dvvi 96 
                                       dv+i
  gi|474934589|ref|YP_007688171.1| 292 DVLI 295
                                       6666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 2650.36
//
Query:       gi|474934590|ref|YP_007688172.1|  [L=522]
Description: Trk-type K+ transport systems, membrane component [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-40  137.7  24.5    1.6e-38  132.4  24.5    2.1  1  TrkH      Cation transport protein
  ------ inclusion threshold ------
       0.86    8.9   5.0        3.1    7.1   1.6    2.6  2  DUF3810   Protein of unknown function (DUF3810)
        7.8    6.7   6.9        6.7    6.9   0.1    3.4  3  DUF872    Eukaryotic protein of unknown function (DUF872)


Domain annotation for each model (and alignments):
>> TrkH  Cation transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.4  24.5   2.6e-42   1.6e-38      64     491 ..     109     494 ..      97     500 .. 0.85

  Alignments for each domain:
  == domain 1  score: 132.4 bits;  conditional E-value: 2.6e-42
                              TrkH  64 ldalfeavsgltttglsvivveeslprsgltlraqlqqiGglgvvvlaylslptlgrgsaflylseaqkeelggkel 140
                                        da++e vsg tttg + +++ e +   +l +ra +q+ Gg++vv +  l lp +g g+  l+++e  ++  g+   
  gi|474934590|ref|YP_007688172.1| 109 VDAVYEGVSGYTTTGSTIMTDIEGAESCILLWRALIQWAGGITVVIIFTLLLPMIGMGGKNLGSNEFGGSDNGEY-S 184
                                       79***************************************99999999999***************66665554.4 PP

                              TrkH 141 rslselikilvvyyvgleilafvllvvliytakaysevvdstgvsplwwaffhsmSafnnlGfsltpnSlasfnkni 217
                                        sls+++     +yv+l+++ fv+l            ++        ++ +++smS + ++G+    nS+a f    
  gi|474934590|ref|YP_007688172.1| 185 TSLSSVALNFFRIYVLLTAAEFVIL---------IALGM------TPFESICTSMSCVPTGGLLPFNNSMADFGF-- 244
                                       5889999889999999999999999.........44456......668999**********************98.. PP

                              TrkH 218 villvaiifiilGnigFpillrviiaikkkilrdlkqikeslsflldlprrcftLllasgfvwllllelavlnvtdn 294
                                        i++ +++f+ilG+ +F  l+r++  ++                l+  + r+++L +   ++ ++++  +       
  gi|474934590|ref|YP_007688172.1| 245 AIQATTLVFMILGASNFLFLFRLLFHRDRTL-------------LKSREWRVMLLWFLGVALFMTAVV-W------- 300
                                       89*********************99877555.............567888888555544444444443.3....... PP

                              TrkH 295 ilfilldegslvvksipkgsrvlkalFqsvstrta.GFsvvdlsnlhpaikvllvlmmyigglpgStaggIrrtnvy 370
                                              ++  +  ++  g+ + ++l+ ++++ t  GF+v d+  ++    ++l+++ ++gg +gStaggI++ +++
  gi|474934590|ref|YP_007688172.1| 301 -------FDGNYRTDYI-GETFWDSLYAVTCAGTSsGFAVSDYTIWPILAVLMLMVVEFVGGTSGSTAGGIKIYRLM 369
                                       .......3444555555.8********************************************************** PP

                              TrkH 371 eefslgkyeieqekepkavskksidgkhlerq....llvdlwslflvlliilileglklsdvqepdfsffdiLfevv 443
                                       ++ + + + +e+  +p+av + s+dg h++ +    +l  ++ +++++l+ + l  l  +++ +   +f+d+++ v+
  gi|474934590|ref|YP_007688172.1| 370 TMKAYIAAGMEKIMHPNAVTTMSVDGSHVDTDnaasVLSTVFLFVVGCLVGIGLI-LFFQNESGHPIEFLDSIGLVI 445
                                       *****************************98611114455555666666554443.4467777778*********** PP

                              TrkH 444 SaygtvGLSlGa.knaslsaqlttisklvlialmirGrlrglpvlldra 491
                                       S + ++G S+G+   +s+ a l+++ k+v+  lm++Gr++++ vl+ + 
  gi|474934590|ref|YP_007688172.1| 446 SSICNAGASIGNfGPMSSMAPLQPATKIVMTSLMFLGRMEMVFVLMVFT 494
                                       ***********889***************************98887765 PP

>> DUF3810  Protein of unknown function (DUF3810)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1     0.018   1.1e+02      40      83 ..       7      52 ..       1      58 [. 0.69
   2 ?    7.1   1.6   0.00051       3.1      20      85 ..     242     307 ..     234     320 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.018
                           DUF3810 40 lvlai..klkkrkkkkkrllkvllrvllvllvvyflftllwglnYy 83
                                      +++ +  +l++ ++ + + l v+ ++l v+l++ + + l++g nY 
  gi|474934590|ref|YP_007688172.1|  7 VMKERirRLQRFQSGTVKTLGVVETLLGVMLLLTAAYALFCGENYE 52
                                      333333444555556666777888999999999999999*****96 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.00051
                           DUF3810  20 fpFSvgellivllillvilylvlaiklkkrkkkkkrllkvllrvllvllvvyflftllwglnYyre 85 
                                       f F++   ++v++il +  +l+l++ l +r +   + +++ + +l++l v++f+  ++w+   yr+
  gi|474934590|ref|YP_007688172.1| 242 FGFAIQATTLVFMILGASNFLFLFRLLFHRDRTLLKSREWRVMLLWFLGVALFMTAVVWFDGNYRT 307
                                       7899999999*****999999999977778888888899999999999999999999998666655 PP

>> DUF872  Eukaryotic protein of unknown function (DUF872)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   1.5      0.12     7e+02      51      96 ..      29      71 ..      18      77 .. 0.69
   2 ?   -2.1   0.0      0.68   4.1e+03      50      65 ..     284     299 ..     278     306 .. 0.78
   3 ?    6.9   0.1    0.0011       6.7      41      75 ..     401     434 ..     375     446 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.12
                            DUF872 51 lLlllGlvLlllgvvilvepseGvssavflvlGlllfiPGvYhvvy 96
                                      + +llG++Lll++++ l     G++   fl++  + +i G+ + ++
  gi|474934590|ref|YP_007688172.1| 29 VETLLGVMLLLTAAYALF---CGENYEPFLFPAPVFLIMGMIQYMF 71
                                      556789999888877665...4677777777777777766665555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.68
                            DUF872  50 llLlllGlvLlllgvv 65 
                                       +lL +lG++L +++vv
  gi|474934590|ref|YP_007688172.1| 284 MLLWFLGVALFMTAVV 299
                                       5788899999888776 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0011
                            DUF872  41 knrkvvlaallLlllGlvLlllgvvilvepseGvs 75 
                                       +n  +vl +++L ++G+ L+ +g++++ +  +G+ 
  gi|474934590|ref|YP_007688172.1| 401 DNAASVLSTVFLFVVGC-LVGIGLILFFQNESGHP 434
                                       6999************9.79999999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (522 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       869  (0.048469); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 3399.91
//
Query:       gi|474934591|ref|YP_007688173.1|  [L=169]
Description: hypothetical protein TALC_01021 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       172  (0.0095934); expected 358.6 (0.02)
Passed bias filter:                      146  (0.00814323); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1196.98
//
Query:       gi|474934592|ref|YP_007688174.1|  [L=696]
Description: putative low-complexity protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-33  114.5  28.5    2.2e-08   33.6   0.0    8.0  8  Pentapeptide    Pentapeptide repeats (8 copies)
    4.3e-31  106.9  21.7    4.7e-09   36.3   1.3    5.5  5  Pentapeptide_4  Pentapeptide repeats (9 copies)
    9.3e-20   70.5  48.6      0.001   19.1   0.9    8.3  7  Pentapeptide_3  Pentapeptide repeats (9 copies)
  ------ inclusion threshold ------
      0.033   14.8   2.8       0.11   13.0   2.8    1.9  1  DUF2627         Protein of unknown function (DUF2627)
       0.24   11.4  14.7        1.6    8.7   2.2    3.5  3  CfAFP           Choristoneura fumiferana antifreeze protein (
        2.5    7.3   8.3        4.7    6.3   8.3    1.4  1  MIG-14_Wnt-bd   Wnt-binding factor required for Wnt secretion


Domain annotation for each model (and alignments):
>> Pentapeptide  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   3.8e-06     0.011       7      28 ..     373     394 ..     368     396 .. 0.57
   2 !    8.1   0.2   0.00067         2      16      39 ..     402     425 ..     400     425 .. 0.72
   3 !   33.6   0.0   7.3e-12   2.2e-08       2      40 .]     438     476 ..     437     476 .. 0.94
   4 !   10.0   1.1   0.00018      0.54       5      38 ..     486     519 ..     482     521 .. 0.73
   5 !    9.7   1.8   0.00022      0.65       1      38 [.     497     534 ..     497     535 .. 0.96
   6 !    7.4   0.4    0.0011       3.4       1      38 [.     527     564 ..     525     566 .. 0.85
   7 !   27.0   0.8   8.3e-10   2.5e-06       1      39 [.     562     600 ..     562     600 .. 0.97
   8 !   29.2   0.2   1.7e-10     5e-07       1      38 [.     636     673 ..     632     677 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.8e-06
                                       B-CCSCCEECCCESEEECT-B- CS
                      Pentapeptide   7 nLsganLsganlsgAnLtgAnl 28 
                                       +Lsg nL+g ++sgA+++++ l
  gi|474934592|ref|YP_007688174.1| 373 DLSGVNLRGYDFSGAVMRNTIL 394
                                       5666666666666666666554 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00067
                                       CCCESEEECT-B-TT-EECCEEEC CS
                      Pentapeptide  16 anlsgAnLtgAnlsgAdLsganLs 39 
                                       +++s +++++A+ s++dLs a+++
  gi|474934592|ref|YP_007688174.1| 402 VSFSKSVMDCADASRCDLSMADFR 425
                                       567788888888888888877775 PP

  == domain 3  score: 33.6 bits;  conditional E-value: 7.3e-12
                                       B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
                      Pentapeptide   2 nLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                                        + ++nLs+a+++g+++ +A++++A++s ++L+g+ +++
  gi|474934592|ref|YP_007688174.1| 438 KMVRVNLSHASMEGSSFANATFRHATMSETRLEGCVMKN 476
                                       5789*******************************9986 PP

  == domain 4  score: 10.0 bits;  conditional E-value: 0.00018
                                       T-B-CCSCCEECCCESEEECT-B-TT-EECCEEE CS
                      Pentapeptide   5 gAnLsganLsganlsgAnLtgAnlsgAdLsganL 38 
                                       + ++sga+++ +n+s+ + t++ + ++ +  ++L
  gi|474934592|ref|YP_007688174.1| 486 DSDFSGADFRVSNCSDVTATNVRFANSIFDHSRL 519
                                       6677888888888888888888777777776655 PP

  == domain 5  score: 9.7 bits;  conditional E-value: 0.00022
                                       -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEE CS
                      Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganL 38 
                                       +n+s++  ++  + ++ + ++ L + + +g+d++g+n+
  gi|474934592|ref|YP_007688174.1| 497 SNCSDVTATNVRFANSIFDHSRLADGTYRGCDFTGTNF 534
                                       79***********************************9 PP

  == domain 6  score: 7.4 bits;  conditional E-value: 0.0011
                                       -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEE CS
                      Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganL 38 
                                       ++++g+n+  +  ++   +++ L+ + + +A  +++++
  gi|474934592|ref|YP_007688174.1| 527 CDFTGTNFGSSAVNNMYIEDTILNASRFDNAEIMECIF 564
                                       88999999999999999999999999999999888887 PP

  == domain 7  score: 27.0 bits;  conditional E-value: 8.3e-10
                                       -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEEC CS
                      Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLs 39 
                                       +++ ++ +  ++ s  n++g++L g+++s A+Ls+++++
  gi|474934592|ref|YP_007688174.1| 562 CIFVNCSFYDSYCSSINFTGSVLMGTDFSEARLSDCDFN 600
                                       89***********************************96 PP

  == domain 8  score: 29.2 bits;  conditional E-value: 1.7e-10
                                       -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEE CS
                      Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganL 38 
                                       A+++ A L g+ +s++ l ++++t+++l+g+ + ++ +
  gi|474934592|ref|YP_007688174.1| 636 AEFTYATLAGSRFSNTRLVNCDFTDCDLTGTSFPDCVF 673
                                       67888888888888888888888888888888877766 PP

>> Pentapeptide_4  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   4.8e-06     0.014      15      76 ..     371     443 ..     367     444 .. 0.75
   2 !   36.3   1.3   1.6e-12   4.7e-09       4      72 ..     445     514 ..     442     518 .. 0.92
   3 !   24.2   1.4   9.6e-09   2.9e-05       5      68 ..     501     564 ..     497     566 .. 0.95
   4 !   21.9   1.7     5e-08   0.00015      11      50 ..     562     601 ..     557     606 .. 0.55
   5 !   29.1   0.9   2.8e-10   8.5e-07       8      63 ..     618     673 ..     614     677 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.8e-06
                    Pentapeptide_4  15 nvnFsearlrdcnFtecrl..........snvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsd.klkdid 76 
                                       + ++s ++lr+ +F+++ +           +v+F++++ + +d + +dl  a F  +  k+++f++ k+++++
  gi|474934592|ref|YP_007688174.1| 371 GKDLSGVNLRGYDFSGAVMrntiladgayIDVSFSKSVMDCADASRCDLSMADFRYSSSKSAVFDGsKMVRVN 443
                                       445555555555555555544444766668888*******************************998998875 PP

  == domain 2  score: 36.3 bits;  conditional E-value: 1.6e-12
                    Pentapeptide_4   4 trcsfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsd.kl 72 
                                       + +s++++ ++n++F++a++ ++++++c ++n++  +++++d+df+++d++ ++ s ++ +nv+f +  +
  gi|474934592|ref|YP_007688174.1| 445 SHASMEGSSFANATFRHATMSETRLEGCVMKNAEVLSSVIEDSDFSGADFRVSNCSDVTATNVRFANsIF 514
                                       56899************************************************************65355 PP

  == domain 3  score: 24.2 bits;  conditional E-value: 9.6e-09
                    Pentapeptide_4   5 rcsfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnf 68 
                                       +++  n+ ++n  F ++rl d + ++c+++ +nF ++ +++  ++++ l+ ++F + ++ ++ f
  gi|474934592|ref|YP_007688174.1| 501 DVTATNVRFANSIFDHSRLADGTYRGCDFTGTNFGSSAVNNMYIEDTILNASRFDNAEIMECIF 564
                                       78999*****************************************************999988 PP

  == domain 4  score: 21.9 bits;  conditional E-value: 5e-08
                    Pentapeptide_4  11 cklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfae 50 
                                       c++ n++F+ ++  + nFt++ l+ + F+e+ lsd+df++
  gi|474934592|ref|YP_007688174.1| 562 CIFVNCSFYDSYCSSINFTGSVLMGTDFSEARLSDCDFNK 601
                                       5555555555555555555555555555555555555543 PP

  == domain 5  score: 29.1 bits;  conditional E-value: 2.8e-10
                    Pentapeptide_4   8 fnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnl 63 
                                       f+ ++ +n +++ ++++d+ Ft++ l   +F+++ l ++df+++dl+ +sF  c +
  gi|474934592|ref|YP_007688174.1| 618 FRHATMTNNTYTDSKIEDAEFTYATLAGSRFSNTRLVNCDFTDCDLTGTSFPDCVF 673
                                       77777788888888888888888888888888888888888888888888888865 PP

>> Pentapeptide_3  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.2   0.00013      0.38       2      47 ..     375     427 ..     369     428 .. 0.81
   2 !   19.1   0.9   3.5e-07     0.001       5      47 ..     433     472 ..     415     478 .. 0.57
   3 !   17.5   3.0   1.1e-06    0.0033       2      47 ..     465     512 ..     459     513 .. 0.75
   4 !   11.8   6.2   6.8e-05       0.2       4      47 ..     497     537 ..     496     538 .. 0.91
   5 !   10.1   6.0   0.00023      0.68       8      47 ..     526     567 ..     514     575 .. 0.52
   6 !   19.0   4.6     4e-07    0.0012       1      47 [.     554     602 ..     554     604 .. 0.92
   7 !   17.7   7.0   9.8e-07    0.0029       3      44 ..     635     673 ..     613     677 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00013
                    Pentapeptide_3   2 sganFsgaadFrgatFsgaa.........sFsnadFgsadFsgarFtgdvdFsga 47 
                                       sg+n++g  dF+ga+ ++++         sFs ++++ ad s++  +  +dF+ +
  gi|474934592|ref|YP_007688174.1| 375 SGVNLRGY-DFSGAVMRNTIladgayidvSFSKSVMDCADASRCDLS-MADFRYS 427
                                       67888888.888888888877755455555****************9.9999977 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 3.5e-07
                    Pentapeptide_3   5 nFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsga 47 
                                       +F+g+  + +++ s a s++++ F +a+F++a+++ +++++g+
  gi|474934592|ref|YP_007688174.1| 433 VFDGS-KMVRVNLSHA-SMEGSSFANATFRHATMS-ETRLEGC 472
                                       44444.4444444444.455555555555555554.5554444 PP

  == domain 3  score: 17.5 bits;  conditional E-value: 1.1e-06
                    Pentapeptide_3   2 sganFsgaadFrgatFsgaa....sFsnadFgsadFsgarFtgdvdFsga 47 
                                       s+++++g+  + +a   +++    +Fs+adF+ ++ s+++ t +v+F ++
  gi|474934592|ref|YP_007688174.1| 465 SETRLEGC-VMKNAEVLSSViedsDFSGADFRVSNCSDVTAT-NVRFANS 512
                                       46777777.777777777777766699999999999999999.9999887 PP

  == domain 4  score: 11.8 bits;  conditional E-value: 6.8e-05
                    Pentapeptide_3   4 anFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsga 47 
                                       +n+s+  + ++++F ++  F+++++ + + +g+ Ft +++F+ +
  gi|474934592|ref|YP_007688174.1| 497 SNCSDV-TATNVRFANS-IFDHSRLADGTYRGCDFT-GTNFGSS 537
                                       578888.99********.5*****************.****865 PP

  == domain 5  score: 10.1 bits;  conditional E-value: 0.00023
                    Pentapeptide_3   8 gaadFrgatFsgaa.s...FsnadFgsadFsgarFtgdvdFsga 47 
                                       g+ dF+g++F ++a +    +++ ++ ++F++a +  ++ F ++
  gi|474934592|ref|YP_007688174.1| 526 GC-DFTGTNFGSSAvNnmyIEDTILNASRFDNAEIM-ECIFVNC 567
                                       34.555555555554134444444444444444444.4444444 PP

  == domain 6  score: 19.0 bits;  conditional E-value: 4e-07
                    Pentapeptide_3   1 FsganFsgaadFrgatFsgaa....sFsnadFgsadFsgarFtgdvdFsga 47 
                                       F++a+   +  F ++ F+++     +F+++++ + dFs+ar + d+dF+ +
  gi|474934592|ref|YP_007688174.1| 554 FDNAEIMEC-IFVNCSFYDSYcssiNFTGSVLMGTDFSEARLS-DCDFNKT 602
                                       899999999.**********997777****************9.****976 PP

  == domain 7  score: 17.7 bits;  conditional E-value: 9.8e-07
                    Pentapeptide_3   3 ganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdF 44 
                                       +a+F+ a ++ g++Fs++ +  n+dF+++d+ g+ F  d+ F
  gi|474934592|ref|YP_007688174.1| 635 DAEFTYA-TLAGSRFSNT-RLVNCDFTDCDLTGTSFP-DCVF 673
                                       4556666.6666666666.666666666666666664.6655 PP

>> DUF2627  Protein of unknown function (DUF2627)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   2.8   3.8e-05      0.11       5      65 ..       8      72 ..       5      80 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.8e-05
                           DUF2627  5 a.lliLvipgllaayGiklmrdalfgilss.pfssl..wlqflaGlllfaiglgfiaGfilhrdr 65
                                      a ++iL i +lla+ Gi  + d  ++  ++ + +++   + +++G  ++a+g   i Gfi++ + 
  gi|474934592|ref|YP_007688174.1|  8 AyWFILAIIILLAVTGINELTDGRITDWENsTLDDImgNIMVFLGSTIIAVGGVTITGFIFFIES 72
                                      4379******************8777765515566655455677888888888899*****9775 PP

>> CfAFP  Choristoneura fumiferana antifreeze protein (CfAFP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   2.2   0.00053       1.6      26     115 ..     409     500 ..     387     507 .. 0.83
   2 ?    7.5   3.3    0.0013       3.8      32     134 ..     497     599 ..     493     602 .. 0.84
   3 ?    4.2   0.2     0.013        40      35      80 ..     624     664 ..     611     677 .. 0.48

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00053
                             CfAFP  26 sqisanskcvkstltncyi.dnsel.essictrsqysdayvkksvttdcnidksqlygttctgsrydGvyitssttt 100
                                          ++ s+c  s++ + y   +s + + s  +r + s+a +  s  +++  +++ +  t   g   +   + ss   
  gi|474934592|ref|YP_007688174.1| 409 MDCADASRCDLSMADFRYSsSKSAVfDGSKMVRVNLSHASMEGSSFANATFRHATMSETRLEGCVMKNAEVLSSVIE 485
                                       4567889*******9999625788889************************************************** PP

                             CfAFP 101 gtrisGpgcsissct 115
                                       ++  sG   ++s+c 
  gi|474934592|ref|YP_007688174.1| 486 DSDFSGADFRVSNCS 500
                                       *************96 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0013
                             CfAFP  32 skcvkstltncyidnselessictrsqysdayvkksvttdcnidksqlygttctgsrydGvyitsstttgtrisGpg 108
                                       s+c   t+tn    ns  + s  +   y ++  + +   +  +++  +  t   +sr+d   i      +++     
  gi|474934592|ref|YP_007688174.1| 497 SNCSDVTATNVRFANSIFDHSRLADGTYRGCDFTGTNFGSSAVNNMYIEDTILNASRFDNAEIMECIFVNCSFYDSY 573
                                       89*************************************************************99999999999988 PP

                             CfAFP 109 csissctitrGvaapsaackisGctl 134
                                       cs  + t +  + +  +  ++s c +
  gi|474934592|ref|YP_007688174.1| 574 CSSINFTGSVLMGTDFSEARLSDCDF 599
                                       86544443333445556667777765 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.013
                             CfAFP  35 vkstltncyidnselessictrsqysdayvkksvttdcnidksqly 80 
                                        + t t   i+++e   ++ + s++s++ ++++  tdc++      
  gi|474934592|ref|YP_007688174.1| 624 TNNTYTDSKIEDAEFTYATLAGSRFSNTRLVNCDFTDCDL-----T 664
                                       2333333334444443333344444444444444444433.....2 PP

>> MIG-14_Wnt-bd  Wnt-binding factor required for Wnt secretion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   8.3    0.0016       4.7     152     254 ..      47     150 ..       4     169 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0016
                     MIG-14_Wnt-bd 152 tlsfylpklllvlllwlvllvlalyerleqlkdpfysiwss.......alilkilaiilavlyflyLlylifrsfse 221
                                        + f    +++v+ ++++ ++++ +e +++l d    + ++       +l+  i+ +++ ++y+++   +++++f +
  gi|474934592|ref|YP_007688174.1|  47 IMVFLGSTIIAVGGVTITGFIFF-IESIRRLVDTNPVYADTvddmrrrLLYAVIVSFAICIIYAIVCGLCMVTVFDD 122
                                       45556666777777777777776.44445554444444444334433322555555555566666666666666666 PP

                     MIG-14_Wnt-bd 222 irskrvkegdiRfkflilltllvlavlvifiil 254
                                       +  + +     R    + l+++++++l+ +iil
  gi|474934592|ref|YP_007688174.1| 123 VGGNHA-----RSVTAAALISVYIILLIENIIL 150
                                       666444.....6666677777777777766666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (696 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.74u 0.31s 00:00:01.05 Elapsed: 00:00:00.47
# Mc/sec: 4423.48
//
Query:       gi|474934593|ref|YP_007688175.1|  [L=626]
Description: hypothetical protein TALC_01023 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (626 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.48
# Mc/sec: 3954.15
//
Query:       gi|474934594|ref|YP_007688176.1|  [L=115]
Description: Membrane transporter of cations and cationic drugs [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-09   38.1   4.2    2.5e-09   37.7   4.2    1.2  1  Multi_Drug_Res  Small Multidrug Resistance protein
     0.0026   17.9   5.3     0.0032   17.7   5.3    1.1  1  UPF0060         Uncharacterised BCR, YnfA/UPF0060 family
     0.0065   15.7   0.0     0.0071   15.5   0.0    1.2  1  Nuc_sug_transp  Nucleotide-sugar transporter
  ------ inclusion threshold ------
       0.01   16.0   3.4       0.01   16.0   3.4    2.0  2  EamA            EamA-like transporter family
      0.015   14.3   3.1       0.03   13.3   3.1    1.7  1  CRT-like        CRT-like, chloroquine-resistance transporter-
      0.016   14.4   0.3      0.017   14.3   0.3    1.2  1  UAA             UAA transporter family
       0.21   11.6   5.6       0.37   10.8   5.6    1.4  1  TspO_MBR        TspO/MBR family


Domain annotation for each model (and alignments):
>> Multi_Drug_Res  Small Multidrug Resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   4.2   9.6e-13   2.5e-09       2      91 ..       3      93 ..       2     104 .. 0.93

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 9.6e-13
                                      X-HHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHHH--.-----HHHHHHHHHHHHHHHHHHHHH- CS
                    Multi_Drug_Res  2 nwvllvlAillevvgailLklsegftkltpsllvivgygisfllLskalks.lpvsvAYavwsGiGtvlivlvgillfg 79
                                       w+++++A+l ++ ga    ls+ ++k  + + + ++  is++++ k +   +p + AYavw Gi  v+++++ i+++g
  gi|474934594|ref|YP_007688176.1|  3 PWFYITVAGLIDILGAYTTALSDSLNKPLWLIPMWCFAFISIAVMNKGIAMkVPPGPAYAVWVGIADVGTLVFDIIVLG 81
                                      59*************************99999999999999999999987559************************** PP

                                      -------HHHHH CS
                    Multi_Drug_Res 80 eslslkkligla 91
                                      +++ + +++   
  gi|474934594|ref|YP_007688176.1| 82 DRFTAYQILAAL 93
                                      ******998654 PP

>> UPF0060  Uncharacterised BCR, YnfA/UPF0060 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   5.3   1.2e-06    0.0032       7     101 ..       6     102 ..       1     107 [. 0.82

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.2e-06
                           UPF0060   7 lfllaalaeigGaylvwlwlreaksvllalvaa...illavygflatlqpaafGrvyaayGGvfvvlallwglvvdg 80 
                                       +  +a+l +i Gay + l    +k+++l  + +   i++av     +++    G +ya + G+  v++l++ ++v g
  gi|474934594|ref|YP_007688176.1|   6 YITVAGLIDILGAYTTALSDSLNKPLWLIPMWCfafISIAVMNKGIAMK-VPPGPAYAVWVGIADVGTLVFDIIVLG 81 
                                       67899**********************9866550014445544444444.4579*********************** PP

                           UPF0060  81 vkldlydwiGalialvGvlvi 101
                                        + + y ++ al+ +vGv+ +
  gi|474934594|ref|YP_007688176.1|  82 DRFTAYQILAALVIIVGVIGV 102
                                       *****************9865 PP

>> Nuc_sug_transp  Nucleotide-sugar transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.8e-06    0.0071     111     160 ..      60     109 ..      34     115 .] 0.86

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.8e-06
                    Nuc_sug_transp 111 tyqvtyqlkilttalfsvllLkrklskkqWlslllLvaGvalvqlkqkes 160
                                       +y v   +  + t +f +++L+ +++ +q l+ l++++Gv+ vq++ ++ 
  gi|474934594|ref|YP_007688176.1|  60 AYAVWVGIADVGTLVFDIIVLGDRFTAYQILAALVIIVGVIGVQYEGSKD 109
                                       56666666778899*******************************97765 PP

>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.65   1.7e+03      62      80 ..       2      20 ..       1      29 [. 0.76
   2 ?   16.0   3.4     4e-06      0.01     103     135 ..      70     102 ..      25     104 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.65
                              EamA 62 kdwllllllgllgtvlafl 80
                                      ++w+++ + gl+ ++ a+ 
  gi|474934594|ref|YP_007688176.1|  2 NPWFYITVAGLIDILGAYT 20
                                      6788888888888888875 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 4e-06
                              EamA 103 vftlilsvlllgekltlkqllgivlillGvlli 135
                                       v tl++ +++lg ++t +q+l++++i++Gv+ +
  gi|474934594|ref|YP_007688176.1|  70 VGTLVFDIIVLGDRFTAYQILAALVIIVGVIGV 102
                                       779***************************976 PP

>> CRT-like  CRT-like, chloroquine-resistance transporter-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   3.1   1.2e-05      0.03     108     137 ..      72     101 ..       6     113 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.2e-05
                          CRT-like 108 tllasllllkerysliqylGAlviilgvvv 137
                                       tl++ +++l +r+  +q+l Alvii+gv+ 
  gi|474934594|ref|YP_007688176.1|  72 TLVFDIIVLGDRFTAYQILAALVIIVGVIG 101
                                       89999***********************94 PP

>> UAA  UAA transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.3   6.7e-06     0.017      68     140 ..      37     109 ..       3     115 .] 0.69

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.7e-06
                               UAA  68 lvalffitsvlnne.alkydisvPvhiifrssklipvmilGililgkrYsllqylsvllltlGviiftllsakd 140
                                         + f+ + v+n+  a+k   + P+  +      + +++  i++lg r++  q+l++l++ +Gvi + +  +kd
  gi|474934594|ref|YP_007688176.1|  37 WCFAFISIAVMNKGiAMKV-PPGPAYAVWVGIADVGTLVFDIIVLGDRFTAYQILAALVIIVGVIGVQYEGSKD 109
                                       4444555555554324444.45677777777778899****************************998866665 PP

>> TspO_MBR  TspO/MBR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   5.6   0.00015      0.37       5      97 ..       9     102 ..       5     105 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00015
                                       HHHHHHHHHHHHHHCCHHHHHHS---TTS--HHHHTTHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHHHHTS CS
                          TspO_MBR   5 lpllvgllgglftkseeewykslrkPpwaPpdwvfppvWtvlyilmgvaa.......ylvwkalalyavqlvlnllw 74 
                                       ++ l+ +lg++ t+      +sl+kP w  p w f+++ ++++   g+a+       y vw  + + +  lv+ ++ 
  gi|474934594|ref|YP_007688176.1|   9 VAGLIDILGAYTTA----LSDSLNKPLWLIPMWCFAFISIAVMN-KGIAMkvppgpaYAVWVGI-ADVGTLVFDIIV 79 
                                       34445566666555....3689**************87766654.5666555667777788886.667778888888 PP

                                       GGCTTTTTSGGGHHHHHHHHHHH CS
                          TspO_MBR  75 splffglkspvlalvdivallgl 97 
                                           f++ ++++alv+iv ++g+
  gi|474934594|ref|YP_007688176.1|  80 LGDRFTAYQILAALVIIVGVIGV 102
                                       88889999999999999888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 760.48
//
Query:       gi|474934595|ref|YP_007688177.1|  [L=111]
Description: Membrane transporter of cations and cationic drugs [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-17   63.4   7.8      3e-17   63.1   7.8    1.2  1  Multi_Drug_Res  Small Multidrug Resistance protein
      3e-06   27.5   7.1    3.6e-06   27.2   7.1    1.1  1  EamA            EamA-like transporter family
     0.0036   16.7   5.6      0.004   16.5   5.6    1.0  1  TPT             Triose-phosphate Transporter family
  ------ inclusion threshold ------
      0.021   14.9   0.6      0.021   14.9   0.6    1.4  1  TMEM234         Putative transmembrane family 234
      0.083   12.9   0.3       0.22   11.5   0.1    1.8  1  DUF543          Domain of unknown function (DUF543)


Domain annotation for each model (and alignments):
>> Multi_Drug_Res  Small Multidrug Resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.1   7.8   8.4e-21     3e-17       4      93 .]       8      97 ..       5     106 .. 0.95

  Alignments for each domain:
  == domain 1  score: 63.1 bits;  conditional E-value: 8.4e-21
                                      HHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHH---- CS
                    Multi_Drug_Res  4 vllvlAillevvgailLklsegftkltpsllvivgygisfllLskalkslpvsvAYavwsGiGtvlivlvgillfgesl 82
                                       +l++A++ e +++i+L  s+ f+ + +  ++ vg+++s +++s++l+ +pv+vAYa+w+G+G +++v ++ +lf++++
  gi|474934595|ref|YP_007688177.1|  8 CWLIAAGIIEPIWVIALTKSDSFRVKSWATVAAVGIMLSPVVMSMSLRDIPVGVAYAMWTGMGSIFTVCASAILFKDRI 86
                                      59***************************************************************************** PP

                                      ----HHHHHHH CS
                    Multi_Drug_Res 83 slkkliglali 93
                                           + + li
  gi|474934595|ref|YP_007688177.1| 87 TPRMAFYISLI 97
                                      98888888776 PP

>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   7.1     1e-09   3.6e-06      38     136 ..       9     105 ..       2     106 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 1e-09
                              EamA  38 fliagillliiallkegklaklslkdwllllllgllgtvlafllffyalkktsasnasli.tslePvftlilsvlll 113
                                       +lia+ +  +i ++   k +++++k+w+ ++ +   g++l ++++ ++l+++++++a  + t +  +ft++ s++l+
  gi|474934595|ref|YP_007688177.1|   9 WLIAAGIIEPIWVIALTKSDSFRVKSWATVAAV---GIMLSPVVMSMSLRDIPVGVAYAMwTGMGSIFTVCASAILF 82 
                                       344444444444444444458999999886555...57999**************998888**************** PP

                              EamA 114 gekltlkqllgivlillGvllil 136
                                       + ++t +  + i li++G++ i+
  gi|474934595|ref|YP_007688177.1|  83 KDRITPRMAFYISLIIVGAIAIS 105
                                       *******************9886 PP

>> TPT  Triose-phosphate Transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   5.6   1.1e-06     0.004      45     135 ..      15     104 ..       4     108 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.1e-06
                               TPT  45 lilvlwalglkkrpkisseflkailplalvktlghvlavvslskvaVSfthtvK.asePiFtvilsrlllgeklsll 120
                                       +i ++w++ l+k   + ++ ++++    +  +l+ v+  +sl  ++V  +  +   +  iFtv  s++l++++++  
  gi|474934595|ref|YP_007688177.1|  15 IIEPIWVIALTKSDSFRVKSWATVAA--VGIMLSPVVMSMSLRDIPVGVAYAMWtGMGSIFTVCASAILFKDRITPR 89 
                                       45789999999999999999998865..55578999999****9999888776515779*************99887 PP

                               TPT 121 vylsLlpivgGvala 135
                                       +   +  i++G +  
  gi|474934595|ref|YP_007688177.1|  90 MAFYISLIIVGAIAI 104
                                       766666666665544 PP

>> TMEM234  Putative transmembrane family 234
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.6   5.8e-06     0.021      57     113 ..      46     102 ..      19     105 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.8e-06
                           TMEM234  57 gSvlfflllgkadlslavpiaNslafvfTvltelllgekvlkkktvlgmllvvvgia 113
                                       + v+  ++l+ +++ +a ++   + ++fTv  + +l ++ ++ ++   + l++vg +
  gi|474934595|ref|YP_007688177.1|  46 SPVVMSMSLRDIPVGVAYAMWTGMGSIFTVCASAILFKDRITPRMAFYISLIIVGAI 102
                                       4588899**********************************************9975 PP

>> DUF543  Domain of unknown function (DUF543)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   6.2e-05      0.22      31      53 ..      66      88 ..      60      94 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.2e-05
                            DUF543 31 kvglgllvGvvasvllfrrRaap 53
                                       +g+g+++ v as +lf+ R  p
  gi|474934595|ref|YP_007688177.1| 66 WTGMGSIFTVCASAILFKDRITP 88
                                      589***************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 834.74
//
Query:       gi|474934596|ref|YP_007688178.1|  [L=278]
Description: hypothetical protein TALC_01026 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00039   20.9   5.3        4.9    7.7   0.0    4.4  4  TPR_19        Tetratricopeptide repeat
     0.0048   16.9   0.0       0.11   12.6   0.0    2.3  2  SRP_TPR_like  Putative TPR-like repeat
  ------ inclusion threshold ------
      0.013   15.6   0.5       0.62   10.3   0.0    2.5  2  TPR_9         Tetratricopeptide repeat
      0.052   13.9   0.1       0.78   10.2   0.0    2.6  2  HEAT_2        HEAT repeats


Domain annotation for each model (and alignments):
>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0011       4.9      17      61 ..      63     106 ..      15     111 .. 0.91
   2 ?    2.8   0.0     0.038   1.7e+02      24      57 ..     130     164 ..     115     176 .. 0.75
   3 !    7.7   0.9    0.0011       5.1       2      57 ..     176     229 ..     175     236 .. 0.87
   4 ?    1.8   0.0     0.077   3.5e+02      18      34 ..     258     274 ..     242     275 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0011
                            TPR_19  17 alqedpknaearllLAeallalgqldeAealLdalpeedpddary 61 
                                       ++++ p +++ r+   + l++lg l+eA ++L++l ++d+   r+
  gi|474934596|ref|YP_007688178.1|  63 IMSHLPSDPAMRYEVGQGLISLGCLKEAGQALADLEPSDKV-RRA 106
                                       6788899****************************999987.444 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.038
                            TPR_19  24 naearllL.AeallalgqldeAealLdalpeedpd 57 
                                       ++e+   L +++l ++g  d+A+a  d++++ +  
  gi|474934596|ref|YP_007688178.1| 130 MLEIDRVLkVQVLGSMGKHDKAIAEADEIQKLFGT 164
                                       5555555558888899*********9999987765 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0011
                            TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                       + +g+  +A+++ ++  + ++k+a+  +l+A  ++ +g+ ++A a  ++++++d +
  gi|474934596|ref|YP_007688178.1| 176 VLAGRSKDAAKFAKE--KMKAKDADGYALMAYFQWLNGNSTAAGAFSSKALAQDNN 229
                                       5689999********..5589999999999************99998888888877 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.077
                            TPR_19  18 lqedpknaearllLAea 34 
                                        +++p+n++a   LA +
  gi|474934596|ref|YP_007688178.1| 258 NEKEPGNPAAFRVLAMC 274
                                       47799999999999987 PP

>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   2.3e-05      0.11      23      95 ..      80     152 ..      64     160 .. 0.86
   2 ?    2.0   0.1     0.045     2e+02       7      43 ..     157     194 ..     152     226 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.3e-05
                      SRP_TPR_like  23 aliklekyeeaLkllkkgsalsedvrfEkaYvlYklkkykkalkilkkveaee.kvkvlksqvlYrlgsyekAY 95 
                                        li+l+  +ea ++l++ +  s++vr  +a v+Y + + ++al+ l  +e+     +vlk qvl  +g+++kA 
  gi|474934596|ref|YP_007688178.1|  80 GLISLGCLKEAGQALADLE-PSDKVRRARAAVFYGTGRDNDALSELGAMEKMLeIDRVLKVQVLGSMGKHDKAI 152
                                       5899999999999999998.8999999********************9999863668999****9999999985 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.045
                      SRP_TPR_like   7 kilrlegk.elkkfkvvaliklekyeeaLkllkkgsal 43 
                                       +i +l g+   ++  v al+ +++ ++a k++k++ + 
  gi|474934596|ref|YP_007688178.1| 157 EIQKLFGTyRSNRAYVSALVLAGRSKDAAKFAKEKMKA 194
                                       555554431456778999*************9976633 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00014      0.62      18      53 ..      60      95 ..      58      99 .. 0.87
   2 ?    2.9   0.3     0.028   1.2e+02      32      55 ..     104     127 ..      94     138 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00014
                             TPR_9 18 verllllaPddpeerrdRGlllaqlGclsaAladLe 53
                                      ++ ++   P dp  r++ G+ l  lGcl++A ++L 
  gi|474934596|ref|YP_007688178.1| 60 LDVIMSHLPSDPAMRYEVGQGLISLGCLKEAGQALA 95
                                      57778889*********************9987774 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.028
                             TPR_9  32 rrdRGlllaqlGclsaAladLeay 55 
                                       rr R+ + +  G+ + Al +L a+
  gi|474934596|ref|YP_007688178.1| 104 RRARAAVFYGTGRDNDALSELGAM 127
                                       8*****************999776 PP

>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.15   6.9e+02      28      52 ..       2      26 ..       1      37 [. 0.80
   2 ?   10.2   0.0   0.00017      0.78      11      84 ..      34     109 ..      24     110 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.15
                            HEAT_2 28 gnpealpaLvellededpavRraaa 52
                                      +n+eal+a++e ++ e+ +v    +
  gi|474934596|ref|YP_007688178.1|  2 DNKEALNAIRENIKEEKFDVAGPQI 26
                                      7899*********999999865555 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00017
                            HEAT_2  11 dpdpevrraairaLgrignpealpaLvell.ed..edpavRraaaeaLgaig.dpealpaLkellddddddvvReaA 83 
                                         dp +  + +  L +ign+  +p +++++ ++  +dpa R+++ + L  +g ++ea +aL++  ++++d v+R++A
  gi|474934596|ref|YP_007688178.1|  34 QGDPMTLLTCASMLRTIGNDADFPGILDVImSHlpSDPAMRYEVGQGLISLGcLKEAGQALAD--LEPSDKVRRARA 108
                                       5566666777788888888877888888666667689***************88*********..478999999888 PP

                            HEAT_2  84 a 84 
                                       a
  gi|474934596|ref|YP_007688178.1| 109 A 109
                                       6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1675.00
//
Query:       gi|474934597|ref|YP_007688179.1|  [L=449]
Description: hypothetical protein TALC_01027 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.014   15.5   0.9      0.032   14.3   0.9    1.5  1  Elf1             Transcription elongation factor Elf1 like
      0.032   15.0   0.7        1.3   10.0   0.1    3.7  4  TPR_14           Tetratricopeptide repeat
        0.2   11.7   2.2       0.51   10.4   2.2    1.6  1  Molybdop_Fe4S4   Molybdopterin oxidoreductase Fe4S4 domain
       0.34   11.3   4.3       0.17   12.3   1.5    2.0  2  Lar_restr_allev  Restriction alleviation protein Lar


Domain annotation for each model (and alignments):
>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.9   7.2e-06     0.032      24      54 ..      26      56 ..      23      64 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.2e-06
                              Elf1 24 CpfCnheksvevkldkkekiaevsCkvCges 54
                                      Cp+C+ + sve ++ ++e i ++ C+ Cg++
  gi|474934597|ref|YP_007688179.1| 26 CPVCGRKCSVEASVRNEELIVSALCGECGKT 56
                                      ****************************986 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.46   2.1e+03       9      30 ..     151     172 ..     139     182 .. 0.79
   2 ?   -2.1   0.0       2.3     1e+04       7      25 ..     188     206 ..     185     215 .. 0.76
   3 ?   10.0   0.1   0.00029       1.3       7      39 ..     236     272 ..     233     274 .. 0.79
   4 ?   -2.7   0.0       3.6   1.6e+04       4      11 ..     319     326 ..     314     348 .. 0.63

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.46
                            TPR_14   9 eallalGdpdeAiallrralal 30 
                                         + ++G   + ial++++l  
  gi|474934597|ref|YP_007688179.1| 151 FTMIEAGSVSDGIALFEKYLPV 172
                                       5567899999*******99865 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.3
                            TPR_14   7 laeallalGdpdeAiallr 25 
                                       la a+l  G+ +++++  r
  gi|474934597|ref|YP_007688179.1| 188 LALAHLSDGNIADSVKDIR 206
                                       7888999999988877555 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00029
                            TPR_14   7 laeallalGdpdeAiallrralala....Pddaeawl 39 
                                       l+ +l a +d+++A++++r+a++ +    P+d+++++
  gi|474934597|ref|YP_007688179.1| 236 LGTLLTAKRDWKGAMRAYRAAVDEClsmePADDVLRF 272
                                       78889999*************9865333377777766 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 3.6
                            TPR_14   4 llalaeal 11 
                                       ll++a++l
  gi|474934597|ref|YP_007688179.1| 319 LLQRARYL 326
                                       44444444 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   2.2   0.00011      0.51       7      26 ..      25      44 ..      21      59 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00011
                                      E-SSBTT--EEEEEEETTEE CS
                    Molybdop_Fe4S4  7 aCpyCgvgCglevhvkdgki 26
                                       Cp Cg +C++e++v++++ 
  gi|474934597|ref|YP_007688179.1| 25 PCPVCGRKCSVEASVRNEEL 44
                                      6**************99875 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.5   3.8e-05      0.17       4      36 ..      24      55 ..      22      70 .. 0.82
   2 ?   -2.8   0.1       1.9   8.5e+03      34      53 ..     274     292 ..     266     296 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.8e-05
                   Lar_restr_allev  4 kpCPfCggravlersqrvvaeigqcvyCadCga 36
                                       pCP Cg +  +e s r+ + i     C +Cg 
  gi|474934597|ref|YP_007688179.1| 24 APCPVCGRKCSVEASVRNEELIV-SALCGECGK 55
                                      5*****************99766.888999998 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.9
                   Lar_restr_allev  34 Cgastpwfkiaedeaeaeke 53 
                                       C + + +f  a+ + +aek+
  gi|474934597|ref|YP_007688179.1| 274 CRV-SEEFASAASQGQAEKK 292
                                       777.6778888888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2988.08
//
Query:       gi|474934598|ref|YP_007688180.1|  [L=347]
Description: putative ATP-binding protein involved in virulence [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.9e-18   65.1   0.6    2.4e-16   60.4   0.6    2.2  1  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    2.2e-15   57.2   0.2    3.2e-12   46.9   0.0    2.1  2  AAA_15    AAA ATPase domain
    6.9e-06   25.7   0.0    2.1e-05   24.1   0.0    1.8  1  SMC_N     RecF/RecN/SMC N terminal domain
    1.7e-05   25.4   1.3    2.4e-05   24.9   1.2    1.3  1  AAA_23    AAA domain
    0.00012   22.6   0.0     0.0095   16.5   0.0    2.4  1  ABC_tran  ABC transporter
  ------ inclusion threshold ------
      0.059   13.6   0.1        0.6   10.3   0.0    2.3  2  DUF5069   Domain of unknown function (DUF5069)
      0.093   13.2   0.1          2    8.8   0.0    2.3  2  AAA       ATPase family associated with various cellular acti


Domain annotation for each model (and alignments):
>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.4   0.6   9.3e-20   2.4e-16     219     302 ..     223     332 ..      32     333 .. 0.62

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 9.3e-20
                            AAA_21 219 r........................gvvflen.gdgqelparelSdGtkrll.alltallralkkgsllliDEpEng 269
                                       +                        g++  ++  +g  +p++ +S+G k++l  ++ +l+r+  +gsl++iDEpE +
  gi|474934598|ref|YP_007688180.1| 223 AenivvfkdiintvyinktvtlndaGFFEAKMdRSGTVVPLSVFSSGEKQMLiIFYILLFRTE-PGSLVVIDEPEVS 298
                                       03333333333333333344444454444444056667777777*******835555555555.55*********** PP

                            AAA_21 270 LHPkllrrllellkelsr.ngaQviltTHSplll 302
                                       LH +++    ++l++ sr ++   ++tTHSp+++
  gi|474934598|ref|YP_007688180.1| 299 LHVSWQQQMGKFLSDVSRlRDLRMLVTTHSPSVI 332
                                       *******************************997 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   1.0   0.00066       1.7       1      79 [.       1      86 [.       1     178 [. 0.56
   2 !   46.9   0.0   1.2e-15   3.2e-12     234     369 .]     181     332 ..     130     332 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00066
                            AAA_15  1 MkIkkikikNFRslkd..veidlsee.ltvliGkNnsGKSsilealdlFlnnkekkn................kkviki 60
                                      M+++ki++  F+ + +   ei+l ++ +t +   N+ GKS++l++    l+ + ++                 +     
  gi|474934598|ref|YP_007688180.1|  1 MRLSKIEV--FGLFNEydYEIQLCDSyVTYIHSQNGMGKSTVLKLVCSVLKGNLEFVrttnfermdltfddgsF----- 72
                                      66666666..555544336888877779999999************9999999666678888886666666442..... PP

                            AAA_15 61 ekedleifeniseskdikI 79
                                          l ++ n++ + +++I
  gi|474934598|ref|YP_007688180.1| 73 ----LFVE-NRNQELNVQI 86
                                      ....3222.2222222222 PP

  == domain 2  score: 46.9 bits;  conditional E-value: 1.2e-15
                            AAA_15 234 l....................eeelteklkeiqeklkeidkklaeelk..kilkkkidkik.kfnykgkkneeieik 287
                                       +                    +e+ ++ + ++q+  +e +       +   ++k++i+++  +  +  ++  + e k
  gi|474934598|ref|YP_007688180.1| 181 FypeipsgyrfppsryeisqyREDYRRLALQLQKYCDEYYRFA----EniVVFKDIINTVYiNKTVTLNDAGFFEAK 253
                                       3555555555555555544444455555555555555555554....133556666666543333333334444444 PP

                            AAA_15 288 ...ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQvii 361
                                          +++ +pl+  +sG +++l  i+ il ++       +  +++i+EPE++LH + q+++ k l ++++  +   ++
  gi|474934598|ref|YP_007688180.1| 254 mdrSGTVVPLSVFSSGEKQMLI-IFYILLFRTE-----PGSLVVIDEPEVSLHVSWQQQMGKFLSDVSRLRDLRMLV 324
                                       889**************99764.4445544444.....57************************************* PP

                            AAA_15 362 tTHSphii 369
                                       tTHSp +i
  gi|474934598|ref|YP_007688180.1| 325 TTHSPSVI 332
                                       *****987 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   8.2e-09   2.1e-05       5     203 ..       6     333 ..       2     344 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 8.2e-09
                                       EEEES.ETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCC..C--....BTTCSST CS
                                       xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxx....xxxxxxx RF
                             SMC_N   5 leien.FksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdl..ihk....skekasv 74 
                                       +e+ + F  y  +  i   ++ +t i  +NG GKs +l  ++ vL   + + +r ++++++   +        +++ 
  gi|474934598|ref|YP_007688180.1|   6 IEVFGlFNEY--DYEIQLCDSYVTYIHSQNGMGKSTVLKLVCSVLKG-NLEFVRTTNFERMdlTFDdgsfLFVENRN 79 
                                       5554435555..45566678889**********************85.66699999987651155555442334555 PP

                                       TEEEEEEEEEETTEESSSSSSC.EEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT............... CS
                                       xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............... RF
                             SMC_N  75 kkaeveitfdnedkklkiekee.vsisrrvkrkgeseykingkevtkkevsellesagiske............... 135
                                       ++ +v+i  +n +++  i  +e  s+ r v+ + e  y  + ++     ++  +++   ++                
  gi|474934598|ref|YP_007688180.1|  80 QELNVQISRNNVEEE--IGINElQSLLRCVYIGPERAYIYDSENHLVPSLMIYMNELSQNIRkakadtvlhdveddg 154
                                       666677765555555..443332577888888889999999999888888888886555555669************ PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|474934598|ref|YP_007688180.1| 155 kertdaeldqwfrdleaklsyidqagfypeipsgyrfppsryeisqyredyrrlalqlqkycdeyyrfaenivvfkd 231
                                       ***************************************************************************** PP

                                       .................................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHH CS
                                       .................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 .................................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkv 179
                                                                        ++S Gek+++ +  ++ + + +p +l+++De +  L  +  +++
  gi|474934598|ref|YP_007688180.1| 232 iintvyinktvtlndagffeakmdrsgtvvplsVFSSGEKQMLIIFYIL-LFRTEPGSLVVIDEPEVSLHVSWQQQM 307
                                       *****************************************99887665.8899*********************** PP

                                       HHHHH..HHCTTSEEEEE-SSHHHCC CS
                                       xxxxx..xxxxxxxxxxxxxxxxxxx RF
                             SMC_N 180 aellk..eksknaQfivislreemle 203
                                        ++l   ++  +  ++v++++  +++
  gi|474934598|ref|YP_007688180.1| 308 GKFLSdvSRLRDLRMLVTTHSPSVIH 333
                                       ****94445567999****9988776 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   1.2   9.4e-09   2.4e-05       4     115 ..       6     153 ..       5     219 .. 0.71

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 9.4e-09
                            AAA_23   4 ienfrsf..rdqeidF.skgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiese.....gkvk 72 
                                       ie f+ f   d ei++ ++ +t I+ +NG GK+T+l  ++ +L g  +     + ++fe+ d ++ ++     ++ +
  gi|474934598|ref|YP_007688180.1|   6 IEVFGLFneYDYEIQLcDSYVTYIHSQNGMGKSTVLKLVCSVLKGNLE---FVRTTNFERMDLTFDDGsflfvENRN 79 
                                       7778899766788999999**************************654...44467788888888777888765555 PP

                            AAA_23  73 ayveltfenkdgry...............................trsiererelskkkgkttkkaklelleid 115
                                       + + +++++++ ++                                  + ++ els++  k + ++ l  +e+d
  gi|474934598|ref|YP_007688180.1|  80 QELNVQISRNNVEEeiginelqsllrcvyigperayiydsenhlvPSLMIYMNELSQNIRKAKADTVLHDVEDD 153
                                       66777776666666668888888888888888887777777777755555555555555555555555555553 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   3.7e-06    0.0095      12      80 ..      25     198 ..      16     297 .. 0.55

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.7e-06
                                       SEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET.TCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH....... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx....... RF
                          ABC_tran  12 ekvaivGenGaGKStLlkllagllkpteGeilld.gkdlkeqeleslrkeigvlpqe.pqlfpeltvren....... 79 
                                        ++ i  +nG GKSt+lkl++  lk    ++++   +++++ +l++ + ++ +++   ++l+ ++  r+n       
  gi|474934598|ref|YP_007688180.1|  25 YVTYIHSQNGMGKSTVLKLVCSVLKG---NLEFVrTTNFERMDLTFDDGSFLFVENRnQELNVQI-SRNNveeeigi 97 
                                       56778889***************985...554443677777778888887777777633333333.34446667888 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                          ABC_tran  80 ............................................................................. 79 
                                                                                                                    
  gi|474934598|ref|YP_007688180.1|  98 nelqsllrcvyigperayiydsenhlvpslmiymnelsqnirkakadtvlhdveddgkertdaeldqwfrdleakls 174
                                       88888888888888888888888888888888888888885555555555555555555555544444444444444 PP

                                       .......................H CS
                                       .......................x RF
                          ABC_tran  80 .......................e 80 
                                                               
  gi|474934598|ref|YP_007688180.1| 175 yidqagfypeipsgyrfppsryeI 198
                                       444444444444444444444440 PP

>> DUF5069  Domain of unknown function (DUF5069)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.29   7.3e+02      38      69 ..      63      95 ..      49     102 .. 0.84
   2 ?   10.3   0.0   0.00023       0.6      51      94 ..     129     171 ..     105     180 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.29
                           DUF5069 38 n.ctlDarllsFlgidpealreavlsgksDeei 69
                                         t+D+  + F++  +++l+ ++++ + +eei
  gi|474934598|ref|YP_007688180.1| 63 MdLTFDDGSFLFVENRNQELNVQISRNNVEEEI 95
                                      36799**9****************999999887 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00023
                           DUF5069  51 idpealreavlsgksDeeilawvkenakprsaeeieeWnkslek 94 
                                       i  ++l++ + + k D  +l +v++++k r+++e+++W + le 
  gi|474934598|ref|YP_007688180.1| 129 IYMNELSQNIRKAKAD-TVLHDVEDDGKERTDAELDQWFRDLEA 171
                                       5667888888887776.69*******************998876 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00079         2       2      33 ..      28      61 ..      27     143 .. 0.64
   2 ?    1.9   0.0      0.11   2.7e+02      58     116 ..     285     333 ..     229     339 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00079
                                      EEESSTTSSHHHHHHHHHHHHT..HEEEEEETTT CS
                               AAA  2 llyGppGtGKTllakavakelg..vefleisgse 33
                                      +++   G+GK+++ k v++ l+   ef+++   e
  gi|474934598|ref|YP_007688180.1| 28 YIHSQNGMGKSTVLKLVCSVLKgnLEFVRTTNFE 61
                                      577889**************97444444443333 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.11
                                       TS.EEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGST CS
                               AAA  58 kp.silfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkld 116
                                       +p s ++iDE +     +           ++q+ ++l++v++  +++ ++++t++p+ + 
  gi|474934598|ref|YP_007688180.1| 285 EPgSLVVIDEPEVSLHVS----------WQQQMGKFLSDVSRL-RDLRMLVTTHSPSVIH 333
                                       355788888877665555..........789999999999996.5599999999988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 2369.79
//
Query:       gi|474934599|ref|YP_007688181.1|  [L=286]
Description: hypothetical protein TALC_01029 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.4e-16   58.4   0.0    1.2e-15   58.0   0.0    1.1  1  DUF4435   Protein of unknown function (DUF4435)


Domain annotation for each model (and alignments):
>> DUF4435  Protein of unknown function (DUF4435)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.0   0.0   6.8e-20   1.2e-15       3     230 ..      24     237 ..      22     243 .. 0.77

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 6.8e-20
                           DUF4435   3 ivlyvEgyDdekfyrtlldelendkeyfellggkkkvlkivkllekeelgrdvlaiVDrDfdylkqnkilnnprifv 79 
                                        +l+vEg  d ++y+++++   +  ++++ + +k++v + v +  +++++r++++iVD+D d + ++  +++p +f+
  gi|474934599|ref|YP_007688181.1|  24 TFLIVEGVTDCRLYQKFVE---DGVNIII-AHSKDNVRRSVAEC-QKRGDRRIVGIVDKDIDGMLGK--KRQPPVFE 93 
                                       69******88769999888...7799***.**************.9*******************99..******** PP

                           DUF4435  80 tyaYaIENflcyaesLhkvlvevltlndrdyktifdlfeqfleelseiiiplflwnvlfyrkklekdiklslslqev 156
                                       t+ ++ E + +++++L+ vl e+    d   +   +++ +++ +  +++ ++ +   ++yr+       + ls+++ 
  gi|474934599|ref|YP_007688181.1|  94 TDLHDMESMIMCSRALDDVLAEYGNRED--VEAFEKAHGSIRDAVARAASAVGALMYISYRRG------MNLSFKDL 162
                                       ***********************74444..334444666666666666655555555888886......35788888 PP

                           DUF4435 157 dlssiekitleeikvenkieelkeefpdkieeekeeikkelrkl.nq.qdlklyiqGhflfefvvslileivkeel 230
                                       d + +++    e ++ + +  +  ++  ++   k +i +++r++ ++ +  + +++Gh+ +++++  +++++ + +
  gi|474934599|ref|YP_007688181.1| 163 DHEYFVNRRTLEADIPKMVTLVYSQSMGQMYP-KAAIVDQIRSMlKDlDSPWDAVRGHDAVDILAIGLRNSFGSYN 237
                                       88888777666666655555555555555544.5667777776654436789************999888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.36s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 1603.83
//
Query:       gi|474934600|ref|YP_007688182.1|  [L=83]
Description: exodeoxyribonuclease VII, small subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-16   60.7   2.2    1.3e-16   60.4   2.2    1.1  1  Exonuc_VII_S  Exonuclease VII small subunit
  ------ inclusion threshold ------
      0.031   14.4   0.3       0.36   11.0   0.1    2.1  2  ArnB_C        Archaellum regulatory network B, C-terminal dom
      0.071   13.4   0.7       0.22   11.9   0.7    1.8  1  GAT           GAT domain


Domain annotation for each model (and alignments):
>> Exonuc_VII_S  Exonuclease VII small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.4   2.2   2.1e-20   1.3e-16       1      52 []      14      65 ..      14      65 .. 0.99

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 2.1e-20
                      Exonuc_VII_S  1 FEealaeLeeIvekLEsgelsLeeslklyeeGvkLlkeCekkLdeaeqkvek 52
                                      FEe+++ L e+ve+LEsg l+L++sl+ ye++v++ ++C++ Ldea++kv+k
  gi|474934600|ref|YP_007688182.1| 14 FEESMKVLSELVEQLESGTLDLDKSLEVYERAVAIREHCRAILDEADRKVQK 65
                                      9*************************************************97 PP

>> ArnB_C  Archaellum regulatory network B, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.056   3.4e+02      18      37 ..       7      26 ..       3      32 .. 0.73
   2 ?   11.0   0.1     6e-05      0.36      23      49 ..      55      80 ..      34      81 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.056
                                      HHHHTT-HHHHHHHHHHHHH CS
                            ArnB_C 18 ealeagnlkeATrilqelee 37
                                      +++++ +++e  ++l+el e
  gi|474934600|ref|YP_007688182.1|  7 SDVQNMSFEESMKVLSELVE 26
                                      67778888888888888765 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 6e-05
                                      T-HHHHHHHHHHHHHHHHHHT-HHHHH CS
                            ArnB_C 23 gnlkeATrilqeleeiAeqTrrieliE 49
                                        l+eA r++q++  +A+  rr+++ E
  gi|474934600|ref|YP_007688182.1| 55 I-LDEADRKVQKIISTANGDRREDFRE 80
                                      3.89********************987 PP

>> GAT  GAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.7   3.7e-05      0.22       2      46 ..      16      69 ..      15      81 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.7e-05
                               GAT  2 nnaklLsemLsstepd.....eellenellkeLyetcka....mqpriqkliee 46
                                      +++k+Lse+++++e++     ++l+  e      e+c+a    + +++qk+i++
  gi|474934600|ref|YP_007688182.1| 16 ESMKVLSELVEQLESGtldldKSLEVYERAVAIREHCRAildeADRKVQKIIST 69
                                      79***********96633233344444444445555553222245555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       870  (0.0485247); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 471.95
//
Query:       gi|474934601|ref|YP_007688183.1|  [L=443]
Description: exodeoxyribonuclease VII, large subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-88  296.8   0.1    2.6e-88  296.5   0.1    1.1  1  Exonuc_VII_L     Exonuclease VII, large subunit
    3.9e-26   91.1   0.1    3.3e-25   88.1   0.0    2.5  3  tRNA_anti_2      OB-fold nucleic acid binding domain
     0.0004   20.3   0.0     0.0011   18.9   0.0    1.8  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
  ------ inclusion threshold ------
      0.099   11.2   0.1       0.16   10.5   0.1    1.2  1  DUF1846          Domain of unknown function (DUF1846)
       0.59   10.0   4.2        2.2    8.1   2.8    2.3  2  Apolipoprotein   Apolipoprotein A1/A4/E domain


Domain annotation for each model (and alignments):
>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  296.5   0.1   7.3e-92   2.6e-88       1     303 [.     123     434 ..     123     435 .. 0.94

  Alignments for each domain:
  == domain 1  score: 296.5 bits;  conditional E-value: 7.3e-92
                      Exonuc_VII_L   1 lfdeerkkplpklpkrigvvtsptgaairDilrtlkrrgplveillfpalvQGeeaaaeiikalekanalkeaDvli 77 
                                       lfd ++k+++pk+pk+igvvtsptga+i+Dil+t+kr +p v ill+p++vQGe aa+ei++ +e +n+++  Dv+i
  gi|474934601|ref|YP_007688183.1| 123 LFDSSKKRKIPKYPKTIGVVTSPTGAVIHDILTTTKRLYP-VDILLAPSAVQGEAAAKEIVAGIELLNRQNV-DVII 197
                                       7***************************************.***********************99996655.**** PP

                      Exonuc_VII_L  78 iaRGGGSleDLwaFndeelaraiaaskiPvisavGHEtDttiaDfvAdlrapTPtaaAelvvpdkaeleeqleeler 154
                                       ++RGGGSleDLw+Fn+e ++rai +sk+Pvis vGHEtD+t++Df+Adlra+TPtaaAe +v+d++e++++l +++ 
  gi|474934601|ref|YP_007688183.1| 198 VGRGGGSLEDLWPFNEEIVVRAIRNSKVPVISSVGHETDFTLSDFAADLRAATPTAAAEQAVRDSKEIKDELTQYTV 274
                                       ***************************************************************************** PP

                      Exonuc_VII_L 155 rlekaikrlleekkqrleklasrl..kspeellerkrqrldeleerleralkkqlkkkrerleelkerlk....ekl 225
                                       r++ka+++  e+ + r+  l+ +l  ++++e++er   +ld++e r ++a++ ++++ ++r+  ++++ +    + +
  gi|474934601|ref|YP_007688183.1| 275 RMNKALTTVTERMRGRFVFLDGKLdpRRAREMVERLGMELDNCEMRSKAAVEGSVSEMHRRFVLIQNSPEpalrQIV 351
                                       *********************9997559999********************************99977655775566 PP

                      Exonuc_VII_L 226 eekkerlkklkerle.....lleekkerleeleeklealsplkvLkrGyaivrkedgkvvtsakdlkkgdeleirla 297
                                       ++k+++   l +r++     ++++k+++ e++++k++alsp +vL rGy++v   dg+++ts+k+++ g++++ir++
  gi|474934601|ref|YP_007688183.1| 352 ASKRSDAGYLFQRMDpavtgIIRRKQSQEETVSAKVDALSPYSVLDRGYSFVAGPDGRALTSVKSIEVGSKVTIRMR 428
                                       666666666667777777788*********************************99********************* PP

                      Exonuc_VII_L 298 dgevka 303
                                       dg+++a
  gi|474934601|ref|YP_007688183.1| 429 DGKAEA 434
                                       **9986 PP

>> tRNA_anti_2  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.1   0.0   9.3e-29   3.3e-25       1      94 [.       5      99 ..       5     100 .. 0.95
   2 ?   -3.2   0.0       2.9     1e+04      41      60 ..     237     256 ..     230     278 .. 0.68
   3 ?   -0.7   0.0      0.47   1.7e+03      15      33 ..     316     334 ..     304     342 .. 0.74

  Alignments for each domain:
  == domain 1  score: 88.1 bits;  conditional E-value: 9.3e-29
                       tRNA_anti_2  1 lsVseltraikell.eaelkkavwvrGeisnlkrkasghvYftLkDekakisavifrsraaklkftledGmkVlvkgrl 78
                                      ++V+el+++ k+ll  a + k++wv Geisn+k+ +sgh Yft+kD+  +is v+fr ++++l+f++ d mk+ + g++
  gi|474934601|ref|YP_007688183.1|  5 ITVTELNARAKDLLtGAPFLKDIWVVGEISNFKTYTSGHSYFTIKDSGGAISSVMFRYARSRLDFQPADAMKIEAYGHV 83
                                      59************96667788**********8778******************************************* PP

                       tRNA_anti_2 79 svYeprGsyqlivedi 94
                                      ++Ye++Gsyq+ive++
  gi|474934601|ref|YP_007688183.1| 84 DLYEKTGSYQFIVESM 99
                                      **************98 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.9
                       tRNA_anti_2  41 ftLkDekakisavifrsraa 60 
                                       ftL+D  a ++a+    +a+
  gi|474934601|ref|YP_007688183.1| 237 FTLSDFAADLRAATPTAAAE 256
                                       77888777777766554443 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.47
                       tRNA_anti_2  15 eaelkkavwvrGeisnlkr 33 
                                       + e++++  v+G +s+++r
  gi|474934601|ref|YP_007688183.1| 316 NCEMRSKAAVEGSVSEMHR 334
                                       556778899******9954 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   3.1e-07    0.0011       2      75 ..      28     101 ..      27     102 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3.1e-07
                                       EEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEEC.TTSSEEEEEEEEEE CS
                   tRNA_anti-codon   2 tvaGrvtsisdrsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrr.pggelelkveeiel 75 
                                       +v+G++++ + + ++++++++++D  g i  v+fr + ++l  +    + ++++G v  + ++g ++ +ve++++
  gi|474934601|ref|YP_007688183.1|  28 WVVGEISNFK-TYTSGHSYFTIKDSGGAISSVMFRYARSRLDFQPADAMKIEAYGHVDLYeKTGSYQFIVESMKV 101
                                       89*******8.999*********************5666666666666777777******88889*****99985 PP

>> DUF1846  Domain of unknown function (DUF1846)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   4.4e-05      0.16      97     179 ..      87     174 ..      79     179 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 4.4e-05
                                       HHHHHTT-EEEEEEEECE-TT-.HHHHHHHHHHTTT-.EEEEEE--TTTTT-HHHHSSTTTGGGS-----SSSEE.. CS
                           DUF1846  97 dafrelgllvgsvvitkyeeqk.aaeafkkkleklgi.kvykhyaiegYPsdvelivsdeGyGkndyiettrplv.. 169
                                       ++  +++++v+s+ ++   +   + e++kkkle+ g+ ++ k+++i+ YP+ +  + s  G    d + tt+ l   
  gi|474934601|ref|YP_007688183.1|  87 EKTGSYQFIVESMKVSGIGDLYlKYEELKKKLEAEGLfDSSKKRKIPKYPKTIGVVTSPTGAVIHDILTTTKRLYpv 163
                                       5566677777777777776655478899*******974788999***************************987522 PP

                                       .EEE-SSTTS- CS
                           DUF1846 170 .vvtaPGpgsG 179
                                        ++ aP +  G
  gi|474934601|ref|YP_007688183.1| 164 dILLAPSAVQG 174
                                       25556666555 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       2.2   7.8e+03      90      99 ..     111     120 ..     107     124 .. 0.57
   2 ?    8.1   2.8    0.0006       2.2      62     183 ..     263     385 ..     238     392 .. 0.49

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.2
                                       HHCCHHCHCC CS
                    Apolipoprotein  90 aeelqeqlav 99 
                                       +eel+++l++
  gi|474934601|ref|YP_007688183.1| 111 YEELKKKLEA 120
                                       4555555544 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0006
                                       HCCCHHHHHHHHHCCHHHHHHHHHHHHCHHCCHHCHCCH.CHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHH CS
                    Apolipoprotein  62 eqlgqnleelrqrlapyteelrerlaadaeelqeqlavy.aeelrerlerhvealkarlapyveelrqklaerleel 137
                                       ++++++l ++  r++ ++  ++er++ +   l  +l++  a+e+ erl  ++++   r ++ ve  ++++++r   +
  gi|474934601|ref|YP_007688183.1| 263 KEIKDELTQYTVRMNKALTTVTERMRGRFVFLDGKLDPRrAREMVERLGMELDNCEMRSKAAVEGSVSEMHRRFVLI 339
                                       12222222222222222222222333344444444444312346666666666666666666666666666666666 PP

                                       HH-----..-----SSSHHHHHHHTS-TTSHHHHHS--XXXXXXXX CS
                    Apolipoprotein 138 keslaphaeeveerlssrveelrekleeqaeelrerleanleelka 183
                                       ++s +p+++++ +  +s +  l +++++++  + +r + + e++ a
  gi|474934601|ref|YP_007688183.1| 340 QNSPEPALRQIVASKRSDAGYLFQRMDPAVTGIIRRKQSQEETVSA 385
                                       6666666666666666666666666666555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.64u 0.34s 00:00:00.98 Elapsed: 00:00:00.51
# Mc/sec: 2593.14
//
Query:       gi|474934602|ref|YP_007688184.1|  [L=121]
Description: Uncharacterized protein, possibly involved in aromatic compounds catabolism [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-07   30.6   0.3    4.6e-07   30.1   0.3    1.2  1  4HBT      Thioesterase superfamily
     0.0026   17.9   0.0      0.004   17.3   0.0    1.2  1  DUF4442   Domain of unknown function (DUF4442)


Domain annotation for each model (and alignments):
>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.3   5.1e-11   4.6e-07       1      65 [.      59     118 ..      59     120 .. 0.94

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 5.1e-11
                                       TSSB-HHHHHHHHHHHHHHHHHHTTSTTEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEE CS
                              4HBT   1 gGvvhgGvylallDeaagaalrslggrgilvvvvelsidflrpvrlgdeltvearvlrlgrtsav 65 
                                       +G+ hgG+++  lD+a +++ + +g     +v+ + +++f rp+r + ++++ a+v++ +++ a+
  gi|474934602|ref|YP_007688184.1|  59 NGFWHGGTTYGVLDHAFAILTNIRGH----AVGQNSNLNFYRPGRGD-TVRAVATVVNESGSLAY 118
                                       699**********************9....6****************.*********98888775 PP

>> DUF4442  Domain of unknown function (DUF4442)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   4.5e-07     0.004      10      99 ..      24     110 ..      20     115 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.5e-07
                                       HHHSGGGGGG--EEEEEETTEEEEEE---GGGB-TTSSB-HHHHHHHHHHHHHHHHHHHS-TTEEEEEEEEEEEE-S CS
                           DUF4442  10 slkaPYfgtvgprieelepgraevrlkkrrrvrNhigtvHAiAicnlaElamGllaeatlpdthrwipkgmevdYla 86 
                                       +l aP+f+  g++  +++ +r+e+++  ++r rN  g  H++  + +++ a+ +l++  ++ +   + ++++ ++++
  gi|474934602|ref|YP_007688184.1|  24 MLNAPFFALNGMKPVSISLDRVEISMDVKPRDRNSNGFWHGGTTYGVLDHAFAILTN--IRGH--AVGQNSNLNFYR 96 
                                       5689************************************************99874..4444..457899999999 PP

                                       ---S-.EEEEEE-T CS
                           DUF4442  87 katgd.ltavaele 99 
                                       +++gd ++ava++ 
  gi|474934602|ref|YP_007688184.1|  97 PGRGDtVRAVATVV 110
                                       99997589999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 705.75
//
Query:       gi|474934603|ref|YP_007688185.1|  [L=154]
Description: hypothetical protein TALC_01033 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00014   21.1   2.8     0.0002   20.7   2.8    1.2  1  zf-ribbon_3     zinc-ribbon domain
    0.00079   19.4   0.8     0.0012   18.9   0.8    1.2  1  DZR             Double zinc ribbon
     0.0013   18.3   3.5     0.0021   17.7   3.5    1.3  1  zinc_ribbon_2   zinc-ribbon domain
     0.0067   16.5   4.4       0.02   14.9   4.4    1.9  1  UPF0547         Uncharacterised protein family UPF0547
  ------ inclusion threshold ------
      0.056   13.0   2.0       0.17   11.4   0.2    2.3  2  TF_Zn_Ribbon    TFIIB zinc-binding
      0.075   12.7   0.1      0.097   12.3   0.1    1.1  1  DUF2321         Uncharacterized protein conserved in bacteria
      0.079   13.3  12.3        0.3   11.4  12.3    2.0  1  TM2             TM2 domain
       0.23   11.4   0.9        0.4   10.6   0.9    1.5  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
        0.4    8.9   2.8       0.47    8.7   2.8    1.0  1  DUF2070         Predicted membrane protein (DUF2070)
       0.46   10.2   2.5        0.7    9.6   0.1    2.1  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
       0.66   10.3   7.4         12    6.2   0.3    3.6  3  zf-LITAF-like   LITAF-like zinc ribbon domain
        3.2    8.6   7.8       0.16   12.7   2.5    1.6  1  zinc_ribbon_15  zinc-ribbon family


Domain annotation for each model (and alignments):
>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   2.8   1.3e-07    0.0002       3      22 ..       3      22 ..       1      26 [. 0.91

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.3e-07
                       zf-ribbon_3  3 vrCPnCGaplssddnvCpyC 22
                                      ++CPnCGa++ +   +Cp C
  gi|474934603|ref|YP_007688185.1|  3 RYCPNCGAVVPENSLNCPQC 22
                                      69******99********** PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.8   7.8e-07    0.0012       1      22 [.       5      26 ..       2      36 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 7.8e-07
                               DZR  1 CpqCgeelppdarfCseCgtkl 22
                                      Cp+Cg+ +p+++  C++C t++
  gi|474934603|ref|YP_007688185.1|  5 CPNCGAVVPENSLNCPQCYTDI 26
                                      6666666666666666666665 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   3.5   1.4e-06    0.0021       1      19 [.       4      22 ..       4      26 .. 0.98

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.4e-06
                     zinc_ribbon_2  1 fCpnCGaelqdnakFCpyC 19
                                      +CpnCGa +++n+  Cp+C
  gi|474934603|ref|YP_007688185.1|  4 YCPNCGAVVPENSLNCPQC 22
                                      8****************** PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   4.4   1.4e-05      0.02       3      20 ..       5      22 ..       3      27 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.4e-05
                           UPF0547  3 CPeCeakvPvaaqfCphC 20
                                      CP C a vP++   Cp C
  gi|474934603|ref|YP_007688185.1|  5 CPNCGAVVPENSLNCPQC 22
                                      ****************** PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   0.00012      0.17      21      33 ..       4      16 ..       2      18 .. 0.89
   2 ?    0.6   0.1      0.28   4.2e+02       3      16 ..      19      38 ..      17      41 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                                      EESSSSBEEEECC CS
                      TF_Zn_Ribbon 21 vCtdCGlVledns 33
                                      +C++CG+V+ +ns
  gi|474934603|ref|YP_007688185.1|  4 YCPNCGAVVPENS 16
                                      6********9998 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.28
                                      ETTTTCEEC.......HEETS CS
                      TF_Zn_Ribbon  3 CPnCgstnl.......veDpe 16
                                      CP C ++ +       ++D++
  gi|474934603|ref|YP_007688185.1| 19 CPQCYTD-IprggyvnERDHM 38
                                      9999753.4556655566666 PP

>> DUF2321  Uncharacterized protein conserved in bacteria (DUF2321)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   6.5e-05     0.097      26      70 ..       2      49 ..       1      62 [. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.5e-05
                           DUF2321 26 eeyCekcGekt...itkcpkCsteirGkyyvegvislgkeyevpsyCk 70
                                      + yC +cG+ +     +cp+C t+i    yv++   ++++ + + + +
  gi|474934603|ref|YP_007688185.1|  2 SRYCPNCGAVVpenSLNCPQCYTDIPRGGYVNERDHMREHRTKEDFVS 49
                                      68******976222568********76668887777887776666665 PP

>> TM2  TM2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4  12.3    0.0002       0.3       2      46 ..      55     105 ..      54     149 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0002
                               TM2   2 kksklvaylLwf...fLGglGvHRFYlG.ktgsGvlqlltfv..Gglgiww 46 
                                        k++ +a+lL++   f+G+lG+  +Yl  ++  G  +l t++  ++  ++ 
  gi|474934603|ref|YP_007688185.1|  55 HKKRSLALLLAIipaFFGILGLGQIYLDrRYARGYMYLATGLlfFLSAVGL 105
                                       689999******9999************77888999999996542222233 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.9   0.00027       0.4      28      55 ..       2      25 ..       1      38 [. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00027
                    OrfB_Zn_ribbon 28 SktCseCgsknkealsgrtfkCpnCgfe 55
                                      S  C++Cg+++ e    + ++Cp+C + 
  gi|474934603|ref|YP_007688185.1|  2 SRYCPNCGAVVPE----NSLNCPQCYTD 25
                                      899**********....88999999765 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   2.8   0.00031      0.47      70     147 ..      56     133 ..      44     152 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00031
                           DUF2070  70 rslflalltelivviisllaillsallqalvllalvlslalvfalrllvlvavsdesllkavlpaliqpllailllv 146
                                       ++  lall ++i +++ +l++   +l  ++   ++ l+  l f+l+ + l+++++ +++  v++ + + ++++l+++
  gi|474934603|ref|YP_007688185.1|  56 KKRSLALLLAIIPAFFGILGLGQIYLDRRYARGYMYLATGLLFFLSAVGLFVLGSGHEWATVILFIPIFISMFLYFL 132
                                       33667788888887777777776665578888888888889999999999999999999888664433333333333 PP

                           DUF2070 147 l 147
                                        
  gi|474934603|ref|YP_007688185.1| 133 T 133
                                       2 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00047       0.7       4      11 ..       3      10 ..       1      12 [. 0.60
   2 ?    0.0   0.3      0.47     7e+02      24      27 ..      19      22 ..      16      24 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00047
                     zf-NADH-PPase  4 rFCgrCGa 11
                                      r+C+ CGa
  gi|474934603|ref|YP_007688185.1|  3 RYCPNCGA 10
                                      66666665 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.47
                     zf-NADH-PPase 24 CpaC 27
                                      Cp+C
  gi|474934603|ref|YP_007688185.1| 19 CPQC 22
                                      8888 PP

>> zf-LITAF-like  LITAF-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.3    0.0083        12      57      66 ..       3      12 ..       1      16 [. 0.82
   2 ?    4.3   0.1     0.033        50       6      39 ..      17      73 ..      14      82 .. 0.64
   3 ?    2.3   0.4      0.14     2e+02      23      52 ..      94     128 ..      86     134 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0083
                     zf-LITAF-like 57 hyCpnCgall 66
                                       yCpnCga++
  gi|474934603|ref|YP_007688185.1|  3 RYCPNCGAVV 12
                                      69****9986 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.033
                     zf-LITAF-like  6 vdCpaCqqrv.....................vTsveyksgkltw..llalllclfgc 39
                                      ++Cp+C + +                     v+++e++++k     lla++  +fg+
  gi|474934603|ref|YP_007688185.1| 17 LNCPQCYTDIprggyvnerdhmrehrtkedfVSQIEKRHKKRSLalLLAIIPAFFGI 73
                                      678888777777777777777777777777777777665554441155677777775 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.14
                     zf-LITAF-like  23 sgkltwllalllclfgc.....llccliPfcvdsl 52 
                                       +g l +l a+ l+++g       ++++iP++++++
  gi|474934603|ref|YP_007688185.1|  94 TGLLFFLSAVGLFVLGSghewaTVILFIPIFISMF 128
                                       46667777777777777788665668888888765 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   2.5   0.00011      0.16      66      85 ..       3      22 ..       1      23 [. 0.95

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                    zinc_ribbon_15 66 keCknCgkeveeefkyCpkC 85
                                      ++C+nCg++v e++  Cp+C
  gi|474934603|ref|YP_007688185.1|  3 RYCPNCGAVVPENSLNCPQC 22
                                      79****************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1178  (0.0657036); expected 358.6 (0.02)
Passed bias filter:                      735  (0.040995); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 950.74
//
Query:       gi|474934604|ref|YP_007688186.1|  [L=185]
Description: hypothetical protein TALC_01034 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.021   14.9   0.0      0.031   14.4   0.0    1.3  1  GAGBD     GAG-binding domain on surface antigen


Domain annotation for each model (and alignments):
>> GAGBD  GAG-binding domain on surface antigen
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.7e-06     0.031      81     121 ..     117     159 ..      80     174 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.7e-06
                             GAGBD  81 vhakiElltRqvaqYrkkYpdnt..eiekliksnlkqtkngnY 121
                                        h+   ++tRq   Y+ kYp+++   i k +++++++ +  n 
  gi|474934604|ref|YP_007688186.1| 117 AHILPSIMTRQPISYKCKYPEDEpdTIVKAYRKTFRRQDPANV 159
                                       5666679*************986448*********98876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 1165.40
//
Query:       gi|474934605|ref|YP_007688187.1|  [L=332]
Description: Fe-S oxidoreductase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-08   35.1  26.2    7.9e-07   29.1  14.9    2.9  3  Fer4_10       4Fe-4S dicluster domain
    5.1e-08   32.4  22.1    0.00018   21.1   2.1    3.3  3  Fer4          4Fe-4S binding domain
    1.2e-06   29.0  13.1    1.2e-06   29.0  13.1    2.9  2  Fer4_7        4Fe-4S dicluster domain
    2.4e-06   27.3  13.4    0.00024   21.0   3.6    3.7  3  Fer4_2        4Fe-4S binding domain
    7.2e-06   26.1  13.6    7.2e-06   26.1  13.6    3.0  2  Fer4_9        4Fe-4S dicluster domain
    1.1e-05   25.7  24.2    0.00028   21.3  14.0    3.3  3  Fer4_8        4Fe-4S dicluster domain
    3.2e-05   23.9  13.8    3.2e-05   23.9  13.8    3.5  3  Fer4_21       4Fe-4S dicluster domain
    0.00011   22.1  12.1    0.00079   19.4   3.5    3.5  3  Fer4_6        4Fe-4S binding domain
    0.00031   21.0  14.5     0.0018   18.6   2.1    3.6  2  Fer4_4        4Fe-4S binding domain
    0.00075   20.0  10.6       0.17   12.5   2.4    2.8  2  Fer4_13       4Fe-4S single cluster domain of Ferredoxin I
      0.002   18.6  13.8      0.002   18.6  13.8    3.8  3  Fer4_17       4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.02   15.8   1.7       0.02   15.8   1.7    3.8  4  Fer4_16       4Fe-4S double cluster binding domain
      0.024   15.6  16.6      0.028   15.3   5.2    4.1  3  Fer4_3        4Fe-4S binding domain
      0.027   15.3   1.8      0.027   15.3   1.8    3.4  4  Fer4_22       4Fe-4S dicluster domain
        0.1   12.4   0.0       0.17   11.7   0.0    1.3  1  Asp_Glu_race  Asp/Glu/Hydantoin racemase
        1.3    9.8  14.1        4.7    8.0   2.6    3.2  3  Fer4_15       4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1  14.9     7e-10   7.9e-07       6      56 .]      13      61 ..       8      61 .. 0.85
   2 !   19.4   3.4   7.5e-07   0.00084       7      23 ..      48      64 ..      42      88 .. 0.75
   3 ?   -2.5   0.1       5.1   5.8e+03      41      48 ..     179     186 ..     169     188 .. 0.57

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 7e-10
                           Fer4_10  6 ddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      ++ Ci+C++C+kaCP+   ++g+ +  s  +  ++kve C+gcg+C+e+CP
  gi|474934605|ref|YP_007688187.1| 13 RELCIGCKACRKACPS--FANGGCDPFSVMQGLEGKVEMCIGCGKCTEVCP 61
                                      689*************..666666666777788899**************9 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 7.5e-07
                           Fer4_10  7 dtCirCgkCvkaCPadl 23
                                      + Ci+CgkC+++CP+++
  gi|474934605|ref|YP_007688187.1| 48 EMCIGCGKCTEVCPVTN 64
                                      67999999999999955 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 5.1
                           Fer4_10  41 kvekCtgc 48 
                                        v  C gc
  gi|474934605|ref|YP_007688187.1| 179 TVTLCSGC 186
                                       44444444 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   2.1   1.6e-07   0.00018       6      20 ..      14      28 ..      12      30 .. 0.90
   2 !   21.0   6.3   1.8e-07    0.0002       6      20 ..      48      62 ..      46      63 .. 0.94
   3 ?   -2.1   0.3       3.6     4e+03       7      11 ..     182     186 ..     181     187 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.6e-07
                                      TTSSS-THHHHHSTT CS
                              Fer4  6 ekCigCGaCvevCPv 20
                                      e+CigC+aC ++CP 
  gi|474934605|ref|YP_007688187.1| 14 ELCIGCKACRKACPS 28
                                      89************6 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 1.8e-07
                                      TTSSS-THHHHHSTT CS
                              Fer4  6 ekCigCGaCvevCPv 20
                                      e+CigCG+C evCPv
  gi|474934605|ref|YP_007688187.1| 48 EMCIGCGKCTEVCPV 62
                                      89************8 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 3.6
                                       TSSS- CS
                              Fer4   7 kCigC 11 
                                       +C gC
  gi|474934605|ref|YP_007688187.1| 182 LCSGC 186
                                       79999 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0  13.1   1.1e-09   1.2e-06       2      50 ..      16      62 ..      15      64 .. 0.82
   2 ?   -1.8   0.2       4.4   4.9e+03      29      41 ..     174     186 ..     147     188 .. 0.62

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 1.1e-09
                            Fer4_7  2 CigCgaCvaaCpvkaiel.deeenekgtekveidpekClgCgaCvavCPt 50
                                      CigC+aC +aCp+ a    d++++   ++ +e++ e+C+gCg+C +vCP+
  gi|474934605|ref|YP_007688187.1| 16 CIGCKACRKACPSFANGGcDPFSV---MQGLEGKVEMCIGCGKCTEVCPV 62
                                      ************776665145544...5569******************8 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.4
                            Fer4_7  29 ekveidpekClgC 41 
                                       +k +   + C+gC
  gi|474934605|ref|YP_007688187.1| 174 AKGRDTVTLCSGC 186
                                       4444445567777 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   2.2   7.5e-07   0.00084       7      21 ..      13      27 ..       8      28 .. 0.92
   2 !   21.0   3.6   2.1e-07   0.00024       8      21 ..      48      61 ..      46      62 .. 0.91
   3 ?   -1.5   0.3       3.1   3.5e+03      10      14 ..     183     187 ..     180     188 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 7.5e-07
                            Fer4_2  7 tdrCigCgaCvsaCP 21
                                      ++ CigC+aC++aCP
  gi|474934605|ref|YP_007688187.1| 13 RELCIGCKACRKACP 27
                                      689************ PP

  == domain 2  score: 21.0 bits;  conditional E-value: 2.1e-07
                            Fer4_2  8 drCigCgaCvsaCP 21
                                      ++CigCg+C+ +CP
  gi|474934605|ref|YP_007688187.1| 48 EMCIGCGKCTEVCP 61
                                      89************ PP

  == domain 3  score: -1.5 bits;  conditional E-value: 3.1
                            Fer4_2  10 CigCg 14 
                                       C gC+
  gi|474934605|ref|YP_007688187.1| 183 CSGCS 187
                                       99995 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1  13.6   6.4e-09   7.2e-06       2      48 ..      16      62 ..      15      65 .. 0.82
   2 ?   -0.7   0.0       1.5   1.7e+03      30      40 ..     174     187 ..     156     188 .. 0.59

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 6.4e-09
                            Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpk 48
                                      C+gC+aC +aCp+ ++ + +    ++  + + e CigCg+C+e+Cp 
  gi|474934605|ref|YP_007688187.1| 16 CIGCKACRKACPSFANGGCDPFSVMQGLEGKVEMCIGCGKCTEVCPV 62
                                      ***********99888776666666665555589************6 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.5
                            Fer4_9  30 aase...eaCigCg 40 
                                       a++    + C gC 
  gi|474934605|ref|YP_007688187.1| 174 AKGRdtvTLCSGCS 187
                                       33335566788885 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3  14.0   2.5e-07   0.00028       5      64 ..      16      63 ..      13      64 .. 0.90
   2 !   17.7   2.4   3.3e-06    0.0037       2      26 ..      47      72 ..      45      78 .. 0.74
   3 ?   -0.4   0.1       1.4   1.6e+03      33      54 ..     173     186 ..     145     188 .. 0.49

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.5e-07
                            Fer4_8  5 CieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                      Ci+C aC++aCp++ + + ++++  ++ ++      +      ++ C +cg+CtevCpv 
  gi|474934605|ref|YP_007688187.1| 16 CIGCKACRKACPSFANGGCDPFSVMQGLEG------K------VEMCIGCGKCTEVCPVT 63
                                      ******************999999888777......3......689************96 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 3.3e-06
                            Fer4_8  2 lekCieCgaCqsaCpvlrrtk.khll 26
                                      +e Ci+Cg C++ Cpv + ++ ++ +
  gi|474934605|ref|YP_007688187.1| 47 VEMCIGCGKCTEVCPVTNPKDvMMQM 72
                                      56788888888888888877766555 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.4
                            Fer4_8  33 aedvqeeqvleeeealwsCttc 54 
                                       ++        ++++++  C++c
  gi|474934605|ref|YP_007688187.1| 173 KA--------KGRDTVTLCSGC 186
                                       22........225557888888 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9  13.8   2.9e-08   3.2e-05       6      55 ..      14      64 ..      10      70 .. 0.85
   2 ?   -2.8   0.0       6.4   7.2e+03      40      44 ..     182     186 ..     162     188 .. 0.70
   3 ?    2.1   3.0       0.2   2.2e+02      28      56 ..     261     287 ..     249     290 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 2.9e-08
                           Fer4_21  6 dkCigCgkCliaCedtshqaie.idaktvlkvvedeCvGCnlCssvCPved 55
                                      + CigC+ C +aC+  +    + ++  + l+   + C+GC  C++vCPv++
  gi|474934605|ref|YP_007688187.1| 14 ELCIGCKACRKACPSFANGGCDpFSVMQGLEGKVEMCIGCGKCTEVCPVTN 64
                                      78************88877664377778888899***************75 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6.4
                           Fer4_21  40 eCvGC 44 
                                        C GC
  gi|474934605|ref|YP_007688187.1| 182 LCSGC 186
                                       57777 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.2
                           Fer4_21  28 idaktvlkvvedeCvGCnlCssvCPvedc 56 
                                       + +++ ++ +e+eC G +  +  CP  +c
  gi|474934605|ref|YP_007688187.1| 261 GVNEALMREREEECRGADAIILCCP--NC 287
                                       5567778889***************..56 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   1.4   1.4e-05     0.015       6      21 ..      13      28 ..       8      31 .. 0.88
   2 !   19.4   3.5   7.1e-07   0.00079       7      21 ..      48      62 ..      46      69 .. 0.90
   3 ?   -1.9   0.4       3.8   4.3e+03       8      13 ..     182     187 ..     181     188 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.4e-05
                            Fer4_6  6 pdkCigCgdCvrvCPe 21
                                      +++CigC +C ++CP 
  gi|474934605|ref|YP_007688187.1| 13 RELCIGCKACRKACPS 28
                                      79*************5 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 7.1e-07
                            Fer4_6  7 dkCigCgdCvrvCPe 21
                                      + CigCg+C+ vCP 
  gi|474934605|ref|YP_007688187.1| 48 EMCIGCGKCTEVCPV 62
                                      68************4 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 3.8
                            Fer4_6   8 kCigCg 13 
                                       +C gC 
  gi|474934605|ref|YP_007688187.1| 182 LCSGCS 187
                                       799996 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   4.8   1.6e-05     0.018       2      15 ..      14      27 ..      13      38 .. 0.92
   2 !   18.6   2.1   1.6e-06    0.0018       2      16 ..      48      62 ..      48      71 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.6e-05
                            Fer4_4  2 erCigCgsCvaaCP 15
                                      e CigC++C+ aCP
  gi|474934605|ref|YP_007688187.1| 14 ELCIGCKACRKACP 27
                                      67************ PP

  == domain 2  score: 18.6 bits;  conditional E-value: 1.6e-06
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      e CigCg+C+ +CP+
  gi|474934605|ref|YP_007688187.1| 48 EMCIGCGKCTEVCPV 62
                                      68************5 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   2.4   0.00015      0.17       3      18 ..      13      28 ..      13      30 .. 0.90
   2 !   11.3   1.3   0.00034      0.38       5      17 ..      49      61 ..      47      76 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00015
                           Fer4_13  3 rdtCiacgaCvelaPd 18
                                      r+ Ci+c+aC++++P 
  gi|474934605|ref|YP_007688187.1| 13 RELCIGCKACRKACPS 28
                                      578************7 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00034
                           Fer4_13  5 tCiacgaCvelaP 17
                                       Ci+cg+C e++P
  gi|474934605|ref|YP_007688187.1| 49 MCIGCGKCTEVCP 61
                                      7************ PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6  13.8   1.8e-06     0.002       2      57 ..      16      61 ..      15      65 .. 0.91
   2 ?    0.5   0.1      0.82   9.2e+02      28      50 ..     165     187 ..     147     188 .. 0.70
   3 ?   -1.6   0.8       3.6     4e+03       7      16 ..     282     291 ..     273     299 .. 0.64

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.8e-06
                           Fer4_17  2 CiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCP 57
                                      Ci+C++C+++Cps+++ + +p ++++      le+     k++ Ci+Cg+C+++CP
  gi|474934605|ref|YP_007688187.1| 16 CIGCKACRKACPSFANGGCDPFSVMQG-----LEG-----KVEMCIGCGKCTEVCP 61
                                      ************************998.....333.....6899***********9 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.82
                           Fer4_17  28 aaklglleeaekeekaslCieCg 50 
                                       a+k+ + ++a+ ++++ lC++C 
  gi|474934605|ref|YP_007688187.1| 165 AFKFRMRGKAKGRDTVTLCSGCS 187
                                       45555556666668999999996 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 3.6
                           Fer4_17   7 yClpeCpsye 16 
                                        C p+C  ++
  gi|474934605|ref|YP_007688187.1| 282 LCCPNCMLFY 291
                                       3888888765 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   3.0   0.00061      0.69       2      14 ..      16      28 ..      15      33 .. 0.89
   2 ?   15.8   1.7   1.8e-05      0.02       2      14 ..      50      62 ..      44      74 .. 0.80
   3 ?   -0.5   0.2       2.2   2.4e+03      32      62 ..     157     188 ..     146     189 .. 0.71
   4 ?   -0.7   0.9       2.5   2.8e+03      41      61 ..     267     288 ..     238     290 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00061
                           Fer4_16  2 CgtCgkCaevCPt 14
                                      C++C++C ++CP+
  gi|474934605|ref|YP_007688187.1| 16 CIGCKACRKACPS 28
                                      ************7 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.8e-05
                           Fer4_16  2 CgtCgkCaevCPt 14
                                      C++CgkC+evCP+
  gi|474934605|ref|YP_007688187.1| 50 CIGCGKCTEVCPV 62
                                      7777777777776 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 2.2
                           Fer4_16  32 syntaekkdlaedeekckkqeai.tgCdiCqd 62 
                                       sy++a+++ ++ + + + k+ ++ t C  C d
  gi|474934605|ref|YP_007688187.1| 157 SYTDADRDAFKFRMRGKAKGRDTvTLCSGCSD 188
                                       55666777777777777766555599999975 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 2.5
                           Fer4_16  41 laedeekckkqeai.tgCdiCq 61 
                                       ++e+ee+c  + ai   C +C+
  gi|474934605|ref|YP_007688187.1| 267 MREREEECRGADAIiLCCPNCM 288
                                       5677788886666657777887 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   3.5     9e-05       0.1       1      13 [.      16      28 ..      16      30 .. 0.94
   2 ?   15.3   5.2   2.5e-05     0.028       1      13 [.      50      62 ..      50      64 .. 0.94
   3 ?   -2.2   0.4       9.9   1.1e+04       1       5 [.     183     187 ..     182     188 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9e-05
                            Fer4_3  1 CtgCgaCvevCPv 13
                                      C+gC aC ++CP+
  gi|474934605|ref|YP_007688187.1| 16 CIGCKACRKACPS 28
                                      ************7 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2.5e-05
                            Fer4_3  1 CtgCgaCvevCPv 13
                                      C+gCg C evCPv
  gi|474934605|ref|YP_007688187.1| 50 CIGCGKCTEVCPV 62
                                      ************7 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 9.9
                            Fer4_3   1 CtgCg 5  
                                       C gC+
  gi|474934605|ref|YP_007688187.1| 183 CSGCS 187
                                       77885 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   1.0    0.0042       4.7      79      94 ..      13      28 ..       5      30 .. 0.80
   2 ?   15.3   1.8   2.4e-05     0.027      78      94 ..      46      62 ..      37      64 .. 0.85
   3 ?   -2.5   0.0       8.5   9.5e+03      78      85 ..     179     186 ..     160     188 .. 0.64
   4 ?   -1.9   0.8       5.8   6.5e+03       2      16 ..     274     288 ..     229     291 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0042
                           Fer4_22 79 esgCvGCgRCieacpv 94
                                      ++ C+GC  C +acp+
  gi|474934605|ref|YP_007688187.1| 13 RELCIGCKACRKACPS 28
                                      5689999999999985 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2.4e-05
                           Fer4_22 78 gesgCvGCgRCieacpv 94
                                      + ++C+GCg+C+e+cpv
  gi|474934605|ref|YP_007688187.1| 46 KVEMCIGCGKCTEVCPV 62
                                      5689***********97 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 8.5
                           Fer4_22  78 gesgCvGC 85 
                                         + C GC
  gi|474934605|ref|YP_007688187.1| 179 TVTLCSGC 186
                                       45677777 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 5.8
                           Fer4_22   2 ClsCgaCtlvCptCs 16 
                                       C +  a  l+Cp C+
  gi|474934605|ref|YP_007688187.1| 274 CRGADAIILCCPNCM 288
                                       444444556677776 PP

>> Asp_Glu_race  Asp/Glu/Hydantoin racemase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00015      0.17      58     116 ..     266     324 ..     221     326 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00015
                                       HHHHHHHHHCTTESEEEE--CHHHHHHHHHHHH-SSEEEECHHHHHHHHHH...HSS-EEEE CS
                      Asp_Glu_race  58 lleaakkLekagadaiviaCnTahavadelqkkikiPvlgiveataealka...tgvkkvgl 116
                                       l+++ ++ e  gadai+++C     ++d+  +   iPvl+i e ++ a+     ++ +k+gl
  gi|474934605|ref|YP_007688187.1| 266 LMREREE-ECRGADAIILCCPNCMLFYDGYPD--GIPVLHISELVCLAAGDsstQRFHKIGL 324
                                       4555555.6789********77779***9995..5*************99966666666665 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   2.6    0.0042       4.7       5      22 ..      13      30 ..      12      48 .. 0.81
   2 ?    7.6   1.9    0.0056       6.3       7      27 ..      49      67 ..      46      88 .. 0.74
   3 ?   -1.6   0.0       4.2   4.7e+03      18      31 ..     162     175 ..     159     196 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0042
                           Fer4_15  5 rdaCigcglCvaeapevf 22
                                      r++Cigc +C +++p + 
  gi|474934605|ref|YP_007688187.1| 13 RELCIGCKACRKACPSFA 30
                                      799************765 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0056
                           Fer4_15  7 aCigcglCvaeapevfelded 27
                                       Cigcg C +++p  +++ +d
  gi|474934605|ref|YP_007688187.1| 49 MCIGCGKCTEVCP--VTNPKD 67
                                      6***********9..444444 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 4.2
                           Fer4_15  18 apevfeldedglas 31 
                                       + + f++  +g+a+
  gi|474934605|ref|YP_007688187.1| 162 DRDAFKFRMRGKAK 175
                                       56777777778774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2027.00
//
Query:       gi|474934606|ref|YP_007688188.1|  [L=367]
Description: hypothetical protein TALC_01036 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00018   20.9   3.3    0.00018   20.9   3.3    3.1  2  DUF4763          Domain of unknown function (DUF4763)
    0.00045   20.6   9.3    0.00045   20.6   9.3    4.6  3  HrpB7            Bacterial type III secretion protein (HrpB7)
    0.00048   18.4   8.0    0.00048   18.4   8.0    3.3  2  HOOK             HOOK protein
     0.0026   18.0   2.5     0.0026   18.0   2.5    4.7  3  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
  ------ inclusion threshold ------
      0.068   13.1   5.8        1.7    8.6   0.4    3.1  2  DUF2536          Protein of unknown function (DUF2536)
      0.081   13.0   0.5      0.081   13.0   0.5    4.0  3  bZIP_1           bZIP transcription factor
        0.1   12.5   4.1         11    6.0   0.1    3.8  3  GIT_CC           GIT coiled-coil Rho guanine nucleotide excha
       0.13   12.4  32.9       0.47   10.6   3.1    6.6  6  Cnn_1N           Centrosomin N-terminal motif 1
       0.15   12.2  41.0      0.075   13.3   4.5    4.2  4  ATG16            Autophagy protein 16 (ATG16)
       0.16   12.6  26.7        2.1    9.0   1.8    5.5  5  HIP1_clath_bdg   Clathrin-binding domain of Huntingtin-intera
       0.17   12.0   3.4       0.24   11.5   0.8    2.6  2  Suppressor_APC   Adenomatous polyposis coli tumour suppressor
       0.31   11.5  22.5       0.22   12.0   1.4    6.2  7  FlaC_arch        Flagella accessory protein C (FlaC)
       0.36   11.0  21.3       0.93    9.6   1.3    4.6  4  DUF2730          Protein of unknown function (DUF2730)
       0.49   11.3   8.2        3.5    8.7   0.2    4.0  4  TPR_14           Tetratricopeptide repeat
       0.57   10.5  11.7        9.7    6.6   0.5    4.5  4  BLOC1_2          Biogenesis of lysosome-related organelles co
        1.1    9.8  22.2        4.3    7.9   2.1    4.5  4  DUF16            Protein of unknown function DUF16
        1.8    7.1  26.0       0.17   10.5   1.2    2.7  3  AAA_13           AAA domain
        1.9    8.6  13.9        7.6    6.6   0.3    4.4  4  Bcr-Abl_Oligo    Bcr-Abl oncoprotein oligomerisation domain
        2.1    8.5  17.6        5.4    7.1   0.5    4.3  4  Mod_r            Modifier of rudimentary (Mod(r)) protein
        2.2    8.4   5.9        9.1    6.4   0.1    3.4  2  Prp19            Prp19/Pso4-like
        2.3    7.4  18.2        2.2    7.5   5.8    3.6  4  TMPIT            TMPIT-like protein
          3    8.1  30.7       0.49   10.7   2.5    5.5  6  ABC_tran_CTD     ABC transporter C-terminal domain
        3.4    8.3  27.6          3    8.5   0.5    6.4  5  SlyX             SlyX
        3.9    6.3  36.9        0.2   10.5   7.1    4.0  4  Spc7             Spc7 kinetochore protein
          4    7.7   8.5        6.3    7.0   0.1    3.9  4  DUF2508          Protein of unknown function (DUF2508)
        4.5    6.9   8.1        1.9    8.1   0.4    3.3  2  Nup54_57_C       NUP57/Nup54 C-terminal domain
        5.7    7.6  20.8         19    5.9   1.4    4.7  4  YabA             Initiation control protein YabA
        6.8    6.5  20.0    3.3e+02    0.9  20.0    3.3  1  Yuri_gagarin     Yuri gagarin
        7.4    6.7  41.8        1.6    8.8   3.0    6.2  6  DHR10            Designed helical repeat protein 10 domain
        8.4    6.1  31.6       0.93    9.2   1.8    5.3  4  DUF4201          Domain of unknown function (DUF4201)


Domain annotation for each model (and alignments):
>> DUF4763  Domain of unknown function (DUF4763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   6.5         5     3e+03      11      82 ..      14      77 ..       8     143 .. 0.45
   2 !   20.9   3.3     3e-07   0.00018      50     162 ..     224     341 ..     183     346 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 5
                           DUF4763 11 leveqklsqvsqseqldveeeisseselpaeqeeeeeeldLdeiydelekiKqrvlelrskLalnvpecPei 82
                                       eve+k+++v+++e     + i ++ ++ +    +   + L    + l   ++ ++e r++   +vpe P++
  gi|474934606|ref|YP_007688188.1| 14 REVEEKKQRVKSVE-----KAIAEKRGTNQ---ATMLAVSLRNLKADLANAEAALEEARKNPPEDVPETPSA 77
                                      44555444554444.....44444443332...333344444444444444445555555444444444443 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 3e-07
                           DUF4763  50 dLdeiydelekiKqrvlelrskLalnvp..ecPei...decvdedlelelltseqpeileLqrnnhkLrqqlaelqq 121
                                       d+d     +e +++ ++ +r++La+  +   +Pe     +++   +e+ +l+++   i++L  +n  Lr ql+el++
  gi|474934606|ref|YP_007688188.1| 224 DIDGRIRMIEHLREELDAVRKELAIANArlGKPEDkvmCDTTRVTVEAGRLKEMDNSIRTLGAENYELRRQLDELKK 300
                                       44444455556666666666666655554445555322455667788999999************************ PP

                           DUF4763 122 hlkasrkslkelreslcqekkrlrklqkrlneldsfkrkle 162
                                        +  ++ +++el+    ++ +++ +lq+r+  l+   +k++
  gi|474934606|ref|YP_007688188.1| 301 ERDVMKRNIRELTVHCDNSDRQIIELQSRIRTLNAAAEKAA 341
                                       ******************************99987666665 PP

>> HrpB7  Bacterial type III secretion protein (HrpB7)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   7.2       1.2   7.1e+02      92     148 ..       6      62 ..       2      67 .. 0.67
   2 ?    1.0   0.9      0.83     5e+02      19      61 ..     125     167 ..     120     170 .. 0.78
   3 !   20.6   9.3   7.5e-07   0.00045      11     128 ..     226     342 ..     217     353 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1.2
                             HrpB7  92 eaelaaarqaldaaedavaatarkiaRndaqidacrerierlrraaeraredaadEE 148
                                       +a +++++ ++++++++v+ ++++ia  ++  +a+   +   + +a+ a+ +aa EE
  gi|474934606|ref|YP_007688188.1|   6 NATIERLEREVEEKKQRVKSVEKAIAEKRGTNQATMLAVSLRNLKADLANAEAALEE 62 
                                       566788888888888888888888888887777776665555555554444444444 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.83
                             HrpB7  19 rlraeleaaraalaaaeaalaaaqaqveaardavraheerldd 61 
                                       ++r +l++ ra l+   aa a+    ++  r++ ++++ rl++
  gi|474934606|ref|YP_007688188.1| 125 NARGDLANMRAMLEDMLAAEAEEDPDTSSVRKDIADRKVRLKE 167
                                       5677888888888888888888888888888888888888776 PP

  == domain 3  score: 20.6 bits;  conditional E-value: 7.5e-07
                             HrpB7  11 errarreerlraeleaaraalaaaeaalaaaqaqveaardavraheerlddlttgsspfsiadylacrayrdvlegr 87 
                                         r r  e lr+el a r++la a+a l + +++v  ++++v   + rl+++      +++++y  +r+ +d+l+ +
  gi|474934606|ref|YP_007688188.1| 226 DGRIRMIEHLREELDAVRKELAIANARLGKPEDKVMCDTTRVTVEAGRLKEMDNSIRTLGAENY-ELRRQLDELKKE 301
                                       56889999*****************************************************999.68999******* PP

                             HrpB7  88 vraaeaelaaarqaldaaedavaatarkiaRndaqidacre 128
                                         +++++++ ++   d+  +++ + + +i+ ++a++++ ++
  gi|474934606|ref|YP_007688188.1| 302 RDVMKRNIRELTVHCDNSDRQIIELQSRIRTLNAAAEKAAR 342
                                       **********************************9998754 PP

>> HOOK  HOOK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   1.4     0.062        37     479     560 ..     164     246 ..     158     261 .. 0.68
   2 !   18.4   8.0     8e-07   0.00048     197     292 ..     234     345 ..     214     349 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.062
                              HOOK 479 kltelqelledanr..rkneLetenrlanqrileLeaqveelqkalqeqgskaedssllkkkleehleklkevqeel 553
                                       +l+el +  ed     ++n++e  +r  +  i +L  ++ e ++  ++   ++e    lk++++ ++  ++++ eel
  gi|474934606|ref|YP_007688188.1| 164 RLKELDRDYEDETDpvKRNNIEVSRRFLQMEINSLLIRLSEAERGIEAGSPESE-IEDLKRDIDGRIRMIEHLREEL 239
                                       555555555555432267888888888888888888888888887766443333.4668888888888888888887 PP

                              HOOK 554 qkkkeql 560
                                          ++ l
  gi|474934606|ref|YP_007688188.1| 240 DAVRKEL 246
                                       7655544 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 8e-07
                              HOOK 197 llqeEknaLlaenkklqerlsele................ngeesgtiqltskkylelqkqleqlqeelfrlEtard 257
                                        l eE  a+++e   +++rl + e                  e +++i + +  + el++ql++l+ e   +     
  gi|474934606|ref|YP_007688188.1| 234 HLREELDAVRKELAIANARLGKPEdkvmcdttrvtveagrLKEMDNSIRTLGAENYELRRQLDELKKERDVMKRNIR 310
                                       45566666666666666666666666666666666665543345667778999999*************99999999 PP

                              HOOK 258 dyrlkceelekevlelqqrneeltslaeEaqaLkD 292
                                       ++ ++c++ +++++elq+r+  l+++ae a+  +D
  gi|474934606|ref|YP_007688188.1| 311 ELTVHCDNSDRQIIELQSRIRTLNAAAEKAARDRD 345
                                       ***************************99987665 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   4.3      0.46   2.8e+02      19      47 ..       7      35 ..       4      69 .. 0.57
   2 ?   -0.2   1.1       1.9   1.2e+03      40      90 ..     186     235 ..     163     247 .. 0.54
   3 !   18.0   2.5   4.3e-06    0.0026      13      77 ..     273     334 ..     263     362 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.46
                       TMF_TATA_bd 19 seirrlEgElaslkeelerleaerdeare 47
                                      ++i rlE E+++ k++++++e+   e r 
  gi|474934606|ref|YP_007688188.1|  7 ATIERLEREVEEKKQRVKSVEKAIAEKRG 35
                                      56777777777777777777655444333 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.9
                       TMF_TATA_bd  40 aerdeareeivklmkeneelkelkkeleelekeleelqeryetlLellGek 90 
                                        +r+ ++ ei +l+ +  e ++   e  + e+e+e+l++  +    ++   
  gi|474934606|ref|YP_007688188.1| 186 VSRRFLQMEINSLLIRLSEAERGI-EAGSPESEIEDLKRDIDGRIRMIEHL 235
                                       555555556655554444443332.23344455555555444444444444 PP

  == domain 3  score: 18.0 bits;  conditional E-value: 4.3e-06
                       TMF_TATA_bd  13 lverlsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelq 77 
                                        ++++  +ir l +E  +l+++l +l++erd +++ i +l+  +++ +++  e   l+++++ l+
  gi|474934606|ref|YP_007688188.1| 273 RLKEMDNSIRTLGAENYELRRQLDELKKERDVMKRNIRELTVHCDNSDRQIIE---LQSRIRTLN 334
                                       5789*************************************999987765443...334333333 PP

>> DUF2536  Protein of unknown function (DUF2536)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.4    0.0029       1.7      18      42 ..      21      45 ..       6      55 .. 0.83
   2 ?    5.7   0.5     0.023        14       4      41 ..      85     121 ..      82     125 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0029
                           DUF2536 18 edlkeLEkkineqienNkallLeVh 42
                                      +++k+ Ek+i+e+  +N+a +L V 
  gi|474934606|ref|YP_007688188.1| 21 QRVKSVEKAIAEKRGTNQATMLAVS 45
                                      67899*****************995 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.023
                           DUF2536   4 qldliedKvEfFEAedlkeLEkkineqienNkallLeV 41 
                                       ++  +e  +E  EA+ ++++E  i+ +  +N+a +L V
  gi|474934606|ref|YP_007688188.1|  85 TISDLEKQIEKQEAT-VRKIEATISAKKGSNQANMLAV 121
                                       566788999999996.799*****************98 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.4      0.82   4.9e+02      28      62 ..       9      22 ..       6      38 .. 0.53
   2 ?   -1.2   0.0       3.7   2.2e+03      43      55 ..     233     245 ..     215     248 .. 0.61
   3 ?   13.0   0.5   0.00013     0.081      29      63 ..     275     309 ..     272     310 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.82
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1 28 ieeLerrvkaLekeNksLkseleelkkevekLksk 62
                                      ie+Ler+v+                     ++k+ 
  gi|474934606|ref|YP_007688188.1|  9 IERLEREVE---------------------EKKQR 22
                                      444444444.....................33333 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.7
                                       HHHHHHHHHHHHH CS
                            bZIP_1  43 ksLkseleelkke 55 
                                       + L++el+  +ke
  gi|474934606|ref|YP_007688188.1| 233 EHLREELDAVRKE 245
                                       4466666666655 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 0.00013
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  29 eeLerrvkaLekeNksLkseleelkkevekLkskv 63 
                                       +e  +   +L +eN +L+ +l+elkke++ +k ++
  gi|474934606|ref|YP_007688188.1| 275 KEMDNSIRTLGAENYELRRQLDELKKERDVMKRNI 309
                                       666777889**********************9875 PP

>> GIT_CC  GIT coiled-coil Rho guanine nucleotide exchange factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       3.4     2e+03      21      34 ..      49      62 ..      46      65 .. 0.85
   2 ?    6.0   0.1     0.018        11      45      66 .]     273     294 ..     225     294 .. 0.90
   3 ?    5.5   0.1     0.026        16      20      58 ..     297     335 ..     296     343 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 3.4
                            GIT_CC 21 lKkalaaseakiqq 34
                                      lK  la++ea +++
  gi|474934606|ref|YP_007688188.1| 49 LKADLANAEAALEE 62
                                      899******98875 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.018
                            GIT_CC  45 elrlLQskvqkLqaeNaqlrdq 66 
                                        l+++ +++ +L aeN +lr+q
  gi|474934606|ref|YP_007688188.1| 273 RLKEMDNSIRTLGAENYELRRQ 294
                                       5899****************97 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.026
                            GIT_CC  20 elKkalaaseakiqqLlkvNtslsdelrlLQskvqkLqa 58 
                                       elKk+     + i +L     +  +++ +LQs + +L+a
  gi|474934606|ref|YP_007688188.1| 297 ELKKERDVMKRNIRELTVHCDNSDRQIIELQSRIRTLNA 335
                                       778888888888899988889999*************97 PP

>> Cnn_1N  Centrosomin N-terminal motif 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   1.1     0.027        16      51      73 .]       8      30 ..       4      30 .. 0.91
   2 ?    2.3   0.2      0.31   1.9e+02      43      71 ..      37      65 ..      31      67 .. 0.80
   3 ?    0.6   2.2       1.1   6.5e+02      29      71 ..      59     105 ..      48     107 .. 0.62
   4 ?   -0.3   3.9       2.1   1.2e+03      48      68 ..     119     139 ..      81     188 .. 0.54
   5 ?    8.1   0.2    0.0048       2.9      12      70 ..     191     250 ..     183     253 .. 0.88
   6 ?   10.6   3.1   0.00079      0.47       2      56 ..     274     334 ..     273     347 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.027
                            Cnn_1N 51 eveslqkelkekkkllreaekai 73
                                      ++e l++e++ekk+++++ ekai
  gi|474934606|ref|YP_007688188.1|  8 TIERLEREVEEKKQRVKSVEKAI 30
                                      6899****************986 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.31
                            Cnn_1N 43 kenielkveveslqkelkekkkllreaek 71
                                      ++ + l v + +l+ +l + +  l+ea k
  gi|474934606|ref|YP_007688188.1| 37 NQATMLAVSLRNLKADLANAEAALEEARK 65
                                      56677889999999999999999998876 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 1.1
                            Cnn_1N  29 rleklse....eqkeellkenielkveveslqkelkekkkllreaek 71 
                                       +le+ ++    +  e   + + e k ++ +l+k++++ +  +r+ e 
  gi|474934606|ref|YP_007688188.1|  59 ALEEARKnppeDVPETPSAPRQEEKLTISDLEKQIEKQEATVRKIEA 105
                                       44443333333666666666778888888899999998888888775 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 2.1
                            Cnn_1N  48 lkveveslqkelkekkkllre 68 
                                       l v +++ + +l +++ +l++
  gi|474934606|ref|YP_007688188.1| 119 LAVSLKNARGDLANMRAMLED 139
                                       444444444444444444443 PP

  == domain 5  score: 8.1 bits;  conditional E-value: 0.0048
                            Cnn_1N  12 LkKENFdLKLriyfLeerleklseeqkeellkenielkvev.eslqkelkekkkllreae 70 
                                       L+ E  +L +r+ + e  +e++s+e+  e lk  i+ ++++ e+l+ el++ +k+l  a+
  gi|474934606|ref|YP_007688188.1| 191 LQMEINSLLIRLSEAERGIEAGSPESEIEDLKRDIDGRIRMiEHLREELDAVRKELAIAN 250
                                       7888889999**************9999999999**99985489**********998665 PP

  == domain 6  score: 10.6 bits;  conditional E-value: 0.00079
                            Cnn_1N   2 lrEqeeqidkLkKENFdLKLriyfLeerleklse......eqkeellkenielkveveslq 56 
                                       l+E++++i +L  EN+ L+ ++ +L+++ + ++        + ++  ++ iel+ ++ +l 
  gi|474934606|ref|YP_007688188.1| 274 LKEMDNSIRTLGAENYELRRQLDELKKERDVMKRnireltVHCDNSDRQIIELQSRIRTLN 334
                                       7999999999999999888888777776665555444444444444444444554444444 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   7.0     0.098        58     122     176 ..       6      62 ..       2      66 .. 0.75
   2 ?    1.6  12.7      0.46   2.8e+02      26     171 ..      52     206 ..      40     212 .. 0.53
   3 ?    7.9   0.7    0.0056       3.4     135     176 ..     214     255 ..     189     259 .. 0.84
   4 ?   13.3   4.5   0.00013     0.075     101     170 ..     271     340 ..     264     360 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.098
                             ATG16 122 eerlaeleaeraaletklkdreeelrekeklvq..dlqDElsaLqlqlnqaEeklrk 176
                                       ++++++le+e+++ ++++k+ e++++ek+ ++q  +l   l  L+  l  aE++l++
  gi|474934606|ref|YP_007688188.1|   6 NATIERLEREVEEKKQRVKSVEKAIAEKRGTNQatMLAVSLRNLKADLANAEAALEE 62 
                                       5689999*********************99999444444555555566666666655 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.46
                             ATG16  26 rLldrtsaleaenaklekaaasaks...sksskksakekeasasqsnskqsakiqsleqklaqlreelaelyksrge 99 
                                       +L++  +ale+ +++ ++   +++s   +       +ek+     + s+ +++i+++e+++ ++ +  ++   s++ 
  gi|474934606|ref|YP_007688188.1|  52 DLANAEAALEEARKNPPEDVPETPSaprQ-------EEKL-----TISDLEKQIEKQEATVRKIEATISAKKGSNQA 116
                                       45555555555555553333333332110.......1111.....23345666666666666666555555544443 PP

                             ATG16 100 ..laqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvq................dlqD 158
                                         la +l+++   l+  ++ l+ + ++ ae   + +++++ ++dr+ +l+e+++  +                 lq 
  gi|474934606|ref|YP_007688188.1| 117 nmLAVSLKNARGDLANMRAMLEDMLAAEAEEDPDTSSVRKDIADRKVRLKELDRDYEdetdpvkrnnievsrrFLQM 193
                                       11355666666666666666666666666666677777777777777777777777733333333333333445666 PP

                             ATG16 159 ElsaLqlqlnqaE 171
                                       E+++L ++l+ aE
  gi|474934606|ref|YP_007688188.1| 194 EINSLLIRLSEAE 206
                                       6666666666655 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0056
                             ATG16 135 letklkdreeelrekeklvqdlqDElsaLqlqlnqaEeklrk 176
                                        e +++d++  + ++ ++++ l++El+a + +l  a ++l k
  gi|474934606|ref|YP_007688188.1| 214 PESEIEDLKRDIDGRIRMIEHLREELDAVRKELAIANARLGK 255
                                       57899****************************999999876 PP

  == domain 4  score: 13.3 bits;  conditional E-value: 0.00013
                             ATG16 101 aqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqa 170
                                       a rl+e+ +++++l ++  e +++l+el++er ++++++++++ +    ++ + +lq  + +L+ ++++a
  gi|474934606|ref|YP_007688188.1| 271 AGRLKEMDNSIRTLGAENYELRRQLDELKKERDVMKRNIRELTVHCDNSDRQIIELQSRIRTLNAAAEKA 340
                                       5588888888888888888888888888888888888888888888888888888888888888877665 PP

>> HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interacting protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   1.8    0.0035       2.1      51      93 ..       6      50 ..       1      55 [. 0.76
   2 ?    3.6   2.5      0.17        99      45      84 ..      77     116 ..      47     130 .. 0.78
   3 ?    2.1   0.8      0.49   2.9e+02      14      70 ..     118     181 ..     110     208 .. 0.64
   4 ?    6.5   0.1     0.021        13      44      79 ..     222     257 ..     201     271 .. 0.81
   5 ?    6.1   0.2     0.028        17      65      98 ..     271     304 ..     265     305 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0035
                    HIP1_clath_bdg 51 keelekLkreleakraelarlkssLesseqsge..qlssqlaaLq 93
                                      + ++e+L+re+e+k++++++++++++++  +++   l+ +l +L+
  gi|474934606|ref|YP_007688188.1|  6 NATIERLEREVEEKKQRVKSVEKAIAEKRGTNQatMLAVSLRNLK 50
                                      5689*********************99876654114556666665 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.17
                    HIP1_clath_bdg  45 rkleeqkeelekLkreleakraelarlkssLesseqsgeq 84 
                                          +e k ++  L++++e+++a + +++++++ ++ s++ 
  gi|474934606|ref|YP_007688188.1|  77 APRQEEKLTISDLEKQIEKQEATVRKIEATISAKKGSNQA 116
                                       55678999999********************988877643 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.49
                    HIP1_clath_bdg  14 qlsva.rqaqeeverekkeleeelerlkeeaerkle......eqkeelekLkreleakraelar 70 
                                       +l v+ ++a+ ++++ +  le+ l +  ee     +      ++k  l++L r+ e++ + ++r
  gi|474934606|ref|YP_007688188.1| 118 MLAVSlKNARGDLANMRAMLEDMLAAEAEEDPDTSSvrkdiaDRKVRLKELDRDYEDETDPVKR 181
                                       5444326778888888888888877655554333333444557778888888887777666655 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.021
                    HIP1_clath_bdg  44 erkleeqkeelekLkreleakraelarlkssLesse 79 
                                       +r ++ +   +e+L++el a r+ela +++ L + e
  gi|474934606|ref|YP_007688188.1| 222 KRDIDGRIRMIEHLREELDAVRKELAIANARLGKPE 257
                                       455666777899999999999999999998887665 PP

  == domain 5  score: 6.1 bits;  conditional E-value: 0.028
                    HIP1_clath_bdg  65 raelarlkssLesseqsgeqlssqlaaLqaEkes 98 
                                         +l+++ +s+++   ++ +l  ql++L++E+++
  gi|474934606|ref|YP_007688188.1| 271 AGRLKEMDNSIRTLGAENYELRRQLDELKKERDV 304
                                       56789999************************97 PP

>> Suppressor_APC  Adenomatous polyposis coli tumour suppressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       5.1   3.1e+03      57      76 ..       9      28 ..       2      32 .. 0.66
   2 ?   11.5   0.8   0.00041      0.24       2      59 ..     289     346 ..     288     361 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 5.1
                    Suppressor_APC 57 tdliqerlefelariqevnr 76
                                       +  ++++e + +r+++v +
  gi|474934606|ref|YP_007688188.1|  9 IERLEREVEEKKQRVKSVEK 28
                                      45556667777788888765 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00041
                    Suppressor_APC   2 ynmlkrlkeLeqekdlLlqgLeaveraRdWylqqlrevqerqkslgkvetqfdlqtdl 59 
                                       y++ ++l+eL++e+d++ + +  +    d   +q+ e+q r++ l++ ++++    d+
  gi|474934606|ref|YP_007688188.1| 289 YELRRQLDELKKERDVMKRNIRELTVHCDNSDRQIIELQSRIRTLNAAAEKAARDRDA 346
                                       67889*****************************************999976666665 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.3      0.13        75       2      23 ..       9      30 ..       5      39 .. 0.62
   2 ?   -0.0   0.0         2   1.2e+03       9      28 ..      46      65 ..      40      67 .. 0.80
   3 ?    4.0   0.6      0.11        66      16      37 ..      86     107 ..      80     121 .. 0.69
   4 ?   -1.9   0.0       7.5   4.5e+03      10      33 ..     117     140 ..     110     141 .. 0.73
   5 ?    0.1   0.2       1.8   1.1e+03      10      37 ..     196     225 ..     191     239 .. 0.52
   6 ?    1.7   0.1      0.58   3.5e+02       6      34 ..     215     243 ..     211     252 .. 0.59
   7 ?   12.0   1.4   0.00036      0.22       1      40 [.     273     312 ..     273     314 .. 0.95

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.13
                         FlaC_arch  2 idelEnklsklsteletvkken 23
                                      i+ lE ++++ + ++++v+k +
  gi|474934606|ref|YP_007688188.1|  9 IERLEREVEEKKQRVKSVEKAI 30
                                      4555555655555555555554 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 2
                         FlaC_arch  9 lsklsteletvkkeneelsk 28
                                      l +l+  l+++++ +ee +k
  gi|474934606|ref|YP_007688188.1| 46 LRNLKADLANAEAALEEARK 65
                                      67888889999999988776 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.11
                         FlaC_arch  16 letvkkeneelsksveelkenV 37 
                                       ++ ++k++e+ + +v +++ ++
  gi|474934606|ref|YP_007688188.1|  86 ISDLEKQIEKQEATVRKIEATI 107
                                       5566666666666666666655 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 7.5
                         FlaC_arch  10 sklsteletvkkeneelsksveel 33 
                                       + l ++l++++ ++ +++  +e++
  gi|474934606|ref|YP_007688188.1| 117 NMLAVSLKNARGDLANMRAMLEDM 140
                                       567778888888888877777765 PP

  == domain 5  score: 0.1 bits;  conditional E-value: 1.8
                         FlaC_arch  10 sklsteletvkkeneels..ksveelkenV 37 
                                       ++l ++l+ +++ +e  s  +++e+lk+++
  gi|474934606|ref|YP_007688188.1| 196 NSLLIRLSEAERGIEAGSpeSEIEDLKRDI 225
                                       555555555555554332114455555544 PP

  == domain 6  score: 1.7 bits;  conditional E-value: 0.58
                         FlaC_arch   6 Enklsklsteletvkkeneelsksveelk 34 
                                       E+++++l+  ++   + +e+l+++++ + 
  gi|474934606|ref|YP_007688188.1| 215 ESEIEDLKRDIDGRIRMIEHLREELDAVR 243
                                       56666666655555555555555555443 PP

  == domain 7  score: 12.0 bits;  conditional E-value: 0.00036
                         FlaC_arch   1 ridelEnklsklsteletvkkeneelsksveelkenVkdl 40 
                                       r++e++n +  l  e   ++++++el+k+ + +k+n+++l
  gi|474934606|ref|YP_007688188.1| 273 RLKEMDNSIRTLGAENYELRRQLDELKKERDVMKRNIREL 312
                                       899**********************************997 PP

>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.3    0.0015      0.93      35      88 ..       9      62 ..       6      66 .. 0.92
   2 ?    8.3   1.0    0.0041       2.4      35      89 ..      86     140 ..      78     144 .. 0.91
   3 ?    1.3   0.1       0.6   3.6e+02      41      92 ..     194     245 ..     179     253 .. 0.77
   4 ?    3.6   0.6      0.11        68      32      95 ..     236     304 ..     234     310 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0015
                           DUF2730 35 leklaekveendkrlteletkvenLPtakdlekLkllladlrgelkaleaevrq 88
                                      +e+l+ +vee+++r++++e  +++   +++   L + l++l+++l ++ea +++
  gi|474934606|ref|YP_007688188.1|  9 IERLEREVEEKKQRVKSVEKAIAEKRGTNQATMLAVSLRNLKADLANAEAALEE 62
                                      6789999***************************************99998876 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0041
                           DUF2730  35 leklaekveendkrlteletkvenLPtakdlekLkllladlrgelkaleaevrql 89 
                                       ++ l++++e+++  + ++e++++     ++ + L + l++ rg+l +++a ++ +
  gi|474934606|ref|YP_007688188.1|  86 ISDLEKQIEKQEATVRKIEATISAKKGSNQANMLAVSLKNARGDLANMRAMLEDM 140
                                       6788999*****************************************9988765 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.6
                           DUF2730  41 kveendkrlteletkvenLPtakdlekLkllladlrgelkaleaevrqlshq 92 
                                       ++++   rl+e+e  +e    ++++e+Lk ++ +    +++l++e++++++ 
  gi|474934606|ref|YP_007688188.1| 194 EINSLLIRLSEAERGIEAGSPESEIEDLKRDIDGRIRMIEHLREELDAVRKE 245
                                       5666667999999999998889999999988877777777777777777765 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.11
                           DUF2730  32 redleklaekveendkrlteletkvenLPtak.....dlekLkllladlrgelkaleaevrqlshqvdL 95 
                                       re+l  + ++++  + rl + e kv    t++      l++++  ++ l +e  +l++++++l++  d+
  gi|474934606|ref|YP_007688188.1| 236 REELDAVRKELAIANARLGKPEDKVMCDTTRVtveagRLKEMDNSIRTLGAENYELRRQLDELKKERDV 304
                                       566666666666777777777777655444431111146788899999999999999999999988775 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1       0.2   1.2e+02       7      34 ..      42      70 ..      37      74 .. 0.70
   2 ?    8.7   0.2    0.0059       3.5       6      33 ..     119     146 ..     115     159 .. 0.76
   3 ?    0.4   0.0       2.7   1.6e+03       3      19 ..     242     258 ..     240     260 .. 0.86
   4 ?   -1.2   0.2         9   5.4e+03      21      37 ..     330     346 ..     325     351 .. 0.64

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.2
                            TPR_14  7 laeallal.GdpdeAiallrralalaPdd 34
                                      la  l++l  d++ A+a+l++a +  P+d
  gi|474934606|ref|YP_007688188.1| 42 LAVSLRNLkADLANAEAALEEARKNPPED 70
                                      5555555526999*********6655555 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0059
                            TPR_14   6 alaeallalGdpdeAiallrralalaPd 33 
                                       +++++  a+Gd++ ++a+l+++la+  +
  gi|474934606|ref|YP_007688188.1| 119 LAVSLKNARGDLANMRAMLEDMLAAEAE 146
                                       556777899**************96432 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 2.7
                            TPR_14   3 allalaeallalGdpde 19 
                                       ++++la a ++lG+p++
  gi|474934606|ref|YP_007688188.1| 242 VRKELAIANARLGKPED 258
                                       5789*********9985 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 9
                            TPR_14  21 iallrralalaPddaea 37 
                                       i+ l++a ++a  d++a
  gi|474934606|ref|YP_007688188.1| 330 IRTLNAAAEKAARDRDA 346
                                       56677777766665544 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.97   5.8e+02      56      75 ..      12      31 ..       4      59 .. 0.69
   2 ?    6.0   0.3     0.025        15      63      88 ..      82     107 ..      76     111 .. 0.80
   3 ?    1.0   0.0       0.9   5.4e+02      69      91 ..     224     246 ..     212     249 .. 0.86
   4 ?    6.6   0.5     0.016       9.7      16      82 ..     275     338 ..     261     340 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.97
                           BLOC1_2 56 kyeelqpylqqidqiekqvt 75
                                      ++ e+++++q+++ +ek ++
  gi|474934606|ref|YP_007688188.1| 12 LEREVEEKKQRVKSVEKAIA 31
                                      33355555555555555544 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.025
                           BLOC1_2  63 ylqqidqiekqvteLeeavseLDeys 88 
                                        +  i ++ekq+++ e++v ++++ +
  gi|474934606|ref|YP_007688188.1|  82 EKLTISDLEKQIEKQEATVRKIEATI 107
                                       55678999999999999999998765 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.9
                           BLOC1_2  69 qiekqvteLeeavseLDeyskeL 91 
                                       +i+ +++ +e++ +eLD+  keL
  gi|474934606|ref|YP_007688188.1| 224 DIDGRIRMIEHLREELDAVRKEL 246
                                       78999999999999999999988 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.016
                           BLOC1_2  16 eatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavs 82 
                                       +   + +++L + N +  ++ ++lk++ + +++++ +l     + ++  +qi +++ ++++L +a++
  gi|474934606|ref|YP_007688188.1| 275 KEMDNSIRTLGAENYELRRQLDELKKERDVMKRNIRELTV---HCDNSDRQIIELQSRIRTLNAAAE 338
                                       4455667777777777777777777777777777777777...666667788888888888888776 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   2.3      0.72   4.3e+02      57      80 ..       9      32 ..       3      66 .. 0.52
   2 ?    7.9   2.1    0.0071       4.3      44      76 ..      61     112 ..      44     140 .. 0.64
   3 ?    4.9   0.2     0.062        37      42      99 ..     194     253 ..     150     261 .. 0.51
   4 ?    7.6   0.7    0.0089       5.3      16      61 ..     286     334 ..     249     363 .. 0.55

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.72
                                      HHHHHHHHHHHHHHHHHHHH.... CS
                             DUF16 57 vekqgekikelkveqkaqgeelnk 80
                                      +e+++ +++e k+++k  ++++ +
  gi|474934606|ref|YP_007688188.1|  9 IERLEREVEEKKQRVKSVEKAIAE 32
                                      333344444444444443333332 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0071
                                       H......................HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             DUF16  44 d...................klgeqinkleqkvekqgekikelkveqkaqge 76 
                                       +                     +  i+ le+++ekq++ ++++++++ a++ 
  gi|474934606|ref|YP_007688188.1|  61 EearknppedvpetpsaprqEEKLTISDLEKQIEKQEATVRKIEATISAKKG 112
                                       5555555555555555553334446889999999999999999999888765 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.062
                                       HHH...HHHHHHHHHHHH..HHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHH CS
                             DUF16  42 kvdklgeqinkleqkvek..qgekikelkveqkaqgeelnkvdetleliletLqkinkRl 99 
                                       ++++l  ++++ e  +e+   + +i++lk +++ + + ++++ e l+ + + L+  n Rl
  gi|474934606|ref|YP_007688188.1| 194 EINSLLIRLSEAERGIEAgsPESEIEDLKRDIDGRIRMIEHLREELDAVRKELAIANARL 253
                                       334444444444444443112445555555555555555555555555555555555555 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.0089
                                       XTTB-BHHHHHHB-.....BHHHHHHHHHHHH...HHHHHHHHHHHHHH CS
                             DUF16  16 kteYVTrkqlnefkds...nkqrLkkieakvdklgeqinkleqkvekqg 61 
                                        ++Y  r+ql+e k++    k +++++  + d  + qi +l+  +++++
  gi|474934606|ref|YP_007688188.1| 286 AENYELRRQLDELKKErdvMKRNIRELTVHCDNSDRQIIELQSRIRTLN 334
                                       3445555555555544333333333333333333333333333333333 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0  14.6     0.053        32     291     467 ..       8     186 ..       4     198 .. 0.68
   2 ?   -0.9   0.1       0.8   4.8e+02     409     442 ..     216     249 ..     200     277 .. 0.57
   3 ?   10.5   1.2   0.00028      0.17      83     150 ..     280     349 ..     266     364 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.053
                            AAA_13 291 liekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfksvelesvkakiesi 367
                                       +ie++e++ +e ++++k+v + a ++++  ++   l   +++l++ L +++ ale+ rk+p ++v  + ++++ e  
  gi|474934606|ref|YP_007688188.1|   8 TIERLEREVEEKKQRVKSVEK-AIAEKRGTNQATMLAVSLRNLKADLANAEAALEEARKNPPEDVPETPSAPRQE-E 82 
                                       344555555444455544444.33334456666667778899999999999999999999999887776666665.4 PP

                            AAA_13 368 kklvaeineliakhNekvanleeekeeakkklelhlv....eeleseldeykkkykklekaieklekelkeeeaelk 440
                                       k  +++++++i+k  ++v ++e+  ++ k + ++ ++    ++++ +l ++   ++++ +a  + + + +   ++++
  gi|474934606|ref|YP_007688188.1|  83 KLTISDLEKQIEKQEATVRKIEATISAKKGSNQANMLavslKNARGDLANMRAMLEDMLAAEAEEDPDTSSVRKDIA 159
                                       66788888888888888888887666555444444433333777778877777777777777777777777788888 PP

                            AAA_13 441 kleeeikeLekqlrdekpaaeeinkeL 467
                                        ++ + keL +  +de+ +++  n e+
  gi|474934606|ref|YP_007688188.1| 160 DRKVRLKELDRDYEDETDPVKRNNIEV 186
                                       888889999999999998888777665 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.8
                            AAA_13 409 seldeykkkykklekaieklekelkeeeaelkkl 442
                                       se++ +k+++++  + ie+l +el++  +el+ +
  gi|474934606|ref|YP_007688188.1| 216 SEIEDLKRDIDGRIRMIEHLREELDAVRKELAIA 249
                                       3333333333333333333333333333333333 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00028
                            AAA_13  83 pvftLGeesiekqekieklkkeikkleekleaaeaqlqkaekekkklekele..deawkkivkkknsals 150
                                       ++ tLG+e+ e ++++++lkke++ +++++++ +   ++++++  +l++ ++  + a++k+++  ++al 
  gi|474934606|ref|YP_007688188.1| 280 SIRTLGAENYELRRQLDELKKERDVMKRNIRELTVHCDNSDRQIIELQSRIRtlNAAAEKAARDRDAALI 349
                                       6889*****************************9999999998777777665445666666666666555 PP

>> Bcr-Abl_Oligo  Bcr-Abl oncoprotein oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.3     0.013       7.6      25      51 ..       8      34 ..       4      42 .. 0.75
   2 ?    5.7   0.1     0.025        15      21      50 ..      81     110 ..      59     114 .. 0.78
   3 ?   -0.3   0.1       1.8   1.1e+03      24      42 ..     230     248 ..     214     267 .. 0.70
   4 ?    2.4   0.7      0.26   1.5e+02      25      61 ..     294     330 ..     286     345 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.013
                     Bcr-Abl_Oligo 25 svedieqeLerCkaslrrLekelneek 51
                                      ++e +e+e+e+ k+ ++ +ek ++e +
  gi|474934606|ref|YP_007688188.1|  8 TIERLEREVEEKKQRVKSVEKAIAEKR 34
                                      567777788877888887777777765 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.025
                     Bcr-Abl_Oligo  21 meLdsvedieqeLerCkaslrrLekelnee 50 
                                        e  +++d+e+++e+  a +r++e  ++  
  gi|474934606|ref|YP_007688188.1|  81 EEKLTISDLEKQIEKQEATVRKIEATISAK 110
                                       344589******************998866 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.8
                     Bcr-Abl_Oligo  24 dsvedieqeLerCkaslrr 42 
                                       + +e + +eL+  +++l  
  gi|474934606|ref|YP_007688188.1| 230 RMIEHLREELDAVRKELAI 248
                                       4566777777777776655 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.26
                     Bcr-Abl_Oligo  25 svedieqeLerCkaslrrLekelneekfkviyLqtll 61 
                                        ++++++e +  k ++r+L  +  +   ++i Lq+ +
  gi|474934606|ref|YP_007688188.1| 294 QLDELKKERDVMKRNIRELTVHCDNSDRQIIELQSRI 330
                                       5678999*************99999999999999866 PP

>> Mod_r  Modifier of rudimentary (Mod(r)) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.5     0.009       5.4      55     109 ..       8      62 ..       3      71 .. 0.89
   2 ?    0.4   2.2         1   6.1e+02      27      81 ..     122     176 ..      82     205 .. 0.62
   3 ?    3.3   0.0      0.14        82      53      85 ..     215     247 ..     183     269 .. 0.84
   4 ?    6.3   0.8     0.016       9.6      25      87 ..     271     333 ..     258     345 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.009
                             Mod_r  55 eleelrselqekleelkelekefeekeqeldellqkfspdallarLqtavaeaee 109
                                       ++e l  e++ek + +k++ek+  ek    ++ +  +s+ +l+a L +a a+ ee
  gi|474934606|ref|YP_007688188.1|   8 TIERLEREVEEKKQRVKSVEKAIAEKRGTNQATMLAVSLRNLKADLANAEAALEE 62 
                                       68899999*******************99999999********999999888877 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1
                             Mod_r  27 evkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeeke 81 
                                       ++k+ + ++ +++a  e+++ +  ++ p+   +r++++++   lkel + +e+ +
  gi|474934606|ref|YP_007688188.1| 122 SLKNARGDLANMRAMLEDMLAAEAEEDPDTSSVRKDIADRKVRLKELDRDYEDET 176
                                       3455555666666666666666777777888888888888888888888887765 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.14
                             Mod_r  53 epeleelrselqekleelkelekefeekeqeld 85 
                                       e e+e+l+ ++  ++  +++l++e+++  +el 
  gi|474934606|ref|YP_007688188.1| 215 ESEIEDLKRDIDGRIRMIEHLREELDAVRKELA 247
                                       569999999999999999999999999999885 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.016
                             Mod_r  25 lpevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldel 87 
                                       + ++k+++++   l aen +l ++  +l++e +  + ++ e   ++++  ++  e++++  +l
  gi|474934606|ref|YP_007688188.1| 271 AGRLKEMDNSIRTLGAENYELRRQLDELKKERDVMKRNIRELTVHCDNSDRQIIELQSRIRTL 333
                                       456778888888888888888777777788888888888888888888888888877776655 PP

>> Prp19  Prp19/Pso4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0      0.11        68      25      40 ..     234     249 ..     218     250 .. 0.79
   2 ?    6.4   0.1     0.015       9.1      19      36 ..     284     301 ..     272     303 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHHHHHHH CS
                             Prp19  25 elrkqleqtrqeLsqa 40 
                                       +lr++l+++r+eL+ a
  gi|474934606|ref|YP_007688188.1| 234 HLREELDAVRKELAIA 249
                                       6999999999999865 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.015
                                       HHHHHHHHHHHHHHHHHH CS
                             Prp19  19 lmletfelrkqleqtrqe 36 
                                       l  e++elr+ql+++++e
  gi|474934606|ref|YP_007688188.1| 284 LGAENYELRRQLDELKKE 301
                                       5679************98 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   5.8    0.0037       2.2       5      94 ..      10     112 ..       4     125 .. 0.67
   2 ?    3.7   1.3     0.049        30       7      85 ..      89     168 ..      87     179 .. 0.69
   3 ?    1.4   0.2      0.25   1.5e+02      75      86 ..     158     169 ..     113     269 .. 0.56
   4 ?    5.4   1.1     0.016       9.6       8      69 ..     278     345 ..     271     364 .. 0.45

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0037
                             TMPIT   5 eelekefkeleetakeykqkleel..sklqskcskeikkqkkrlkelksslkklkksvk...........eeeeeev 68 
                                       e+le+e++e +++ k++++ ++e   +++ + ++ ++++ k +l + +++l++ +k+             +ee+ ++
  gi|474934606|ref|YP_007688188.1|  10 ERLEREVEEKKQRVKSVEKAIAEKrgTNQATMLAVSLRNLKADLANAEAALEEARKNPPedvpetpsaprQEEKLTI 86 
                                       4444555544444444444444331123334444555566666666666666666553377888899988889999* PP

                             TMPIT  69 eelkeelkerkkvlkevesllpkkng 94 
                                       ++l++++++++++++++e+++ +k+g
  gi|474934606|ref|YP_007688188.1|  87 SDLEKQIEKQEATVRKIEATISAKKG 112
                                       ********************999977 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.049
                             TMPIT   7 lekefkeleetakeykqkl..eelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkv 81 
                                       lek++++ e+t +++++++  ++ s++ + ++ ++k+ + +l +++++l+++ ++ ++ee+  ++++++++++rk  
  gi|474934606|ref|YP_007688188.1|  89 LEKQIEKQEATVRKIEATIsaKKGSNQANMLAVSLKNARGDLANMRAMLEDMLAA-EAEEDPDTSSVRKDIADRKVR 164
                                       5566666666666655544114556666777788888888888888888888877.467777788888888888888 PP

                             TMPIT  82 lkev 85 
                                       lke+
  gi|474934606|ref|YP_007688188.1| 165 LKEL 168
                                       8876 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.25
                             TMPIT  75 lkerkkvlkeve 86 
                                       +++rk  lke++
  gi|474934606|ref|YP_007688188.1| 158 IADRKVRLKELD 169
                                       333333333322 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.016
                             TMPIT   8 ekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk......eeeeeeve 69 
                                        +++++l +++ e++++l+el+k  + ++++i++ + ++ + ++++ +l+++++      e+ ++  +
  gi|474934606|ref|YP_007688188.1| 278 DNSIRTLGAENYELRRQLDELKKERDVMKRNIRELTVHCDNSDRQIIELQSRIRtlnaaaEKAARDRD 345
                                       55555555555555555555555555555555554444444444444444443212111123333333 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   3.4    0.0035       2.1       9      60 ..       8      63 ..       1      65 [. 0.81
   2 ?   10.7   2.5   0.00081      0.49       6      46 ..      82     121 ..      79     143 .. 0.73
   3 ?   -1.5   0.0       5.3   3.2e+03      33      58 ..     148     173 ..     128     177 .. 0.57
   4 ?    3.4   0.4      0.16        94       9      35 ..     231     257 ..     217     284 .. 0.79
   5 ?    0.3   0.2       1.5   8.8e+02      11      32 ..     275     296 ..     266     323 .. 0.68
   6 ?   -0.0   1.7       1.8   1.1e+03      14      34 ..     320     340 ..     286     353 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0035
                      ABC_tran_CTD  9 eleeleaeIeaLEeeiaeleaeladpelysdpek....laelsaeleeleaeLeel 60
                                       +e+le+e e+  ++ +++e+++a+   +++ +     l  l a l+++ea+Lee+
  gi|474934606|ref|YP_007688188.1|  8 TIERLEREVEEKKQRVKSVEKAIAEKRGTNQATMlavsLRNLKADLANAEAALEEA 63
                                      5899********************99987555334444788888899999999986 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00081
                      ABC_tran_CTD   6 eqreleeleaeIeaLEeeiaeleaeladpelysdpeklael 46 
                                       e+  +  le++Ie+ E+   ++ea +++    s+++ + ++
  gi|474934606|ref|YP_007688188.1|  82 EKLTISDLEKQIEKQEATVRKIEATISAKKG-SNQANMLAV 121
                                       7777899********************9886.444444433 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 5.3
                      ABC_tran_CTD  33 dpelysdpeklaelsaeleeleaeLe 58 
                                       dp+  s  + +a+   +l+el+ + e
  gi|474934606|ref|YP_007688188.1| 148 DPDTSSVRKDIADRKVRLKELDRDYE 173
                                       44433333446666666666665554 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.16
                      ABC_tran_CTD   9 eleeleaeIeaLEeeiaeleaeladpe 35 
                                        +e+l +e++a  +e+a  +a+l +pe
  gi|474934606|ref|YP_007688188.1| 231 MIEHLREELDAVRKELAIANARLGKPE 257
                                       567888888888888888888888887 PP

  == domain 5  score: 0.3 bits;  conditional E-value: 1.5
                      ABC_tran_CTD  11 eeleaeIeaLEeeiaeleaela 32 
                                       +e+++ I  L +e  el  +l 
  gi|474934606|ref|YP_007688188.1| 275 KEMDNSIRTLGAENYELRRQLD 296
                                       5555555555555555555544 PP

  == domain 6  score: -0.0 bits;  conditional E-value: 1.8
                      ABC_tran_CTD  14 eaeIeaLEeeiaeleaeladp 34 
                                       +++I +L+ +i +l+a+ +++
  gi|474934606|ref|YP_007688188.1| 320 DRQIIELQSRIRTLNAAAEKA 340
                                       345555555666555555554 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.5     0.032        19      31      56 ..       7      32 ..       4      39 .. 0.83
   2 ?    4.0   1.0      0.13        77       5      30 ..      86     111 ..      82     157 .. 0.65
   3 ?    3.8   0.3      0.15        89      18      52 ..     217     251 ..     191     260 .. 0.80
   4 ?    8.5   0.5     0.005         3      12      51 ..     274     313 ..     272     321 .. 0.89
   5 ?    0.9   0.1       1.2   7.4e+02      31      55 ..     321     338 ..     315     348 .. 0.52

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.032
                                      HHHHHHHHHHHHHHHT-XXXXXXXXX CS
                              SlyX 31 qqidrlqrqlrllaerlkeleessga 56
                                       +i+rl+r++++ ++r+k++e++ ++
  gi|474934606|ref|YP_007688188.1|  7 ATIERLEREVEEKKQRVKSVEKAIAE 32
                                      689***************99988664 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.13
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SlyX   5 leeLEiklafqedtieeLndvvaeqq 30 
                                       + +LE ++  qe t+ +  +++ +  
  gi|474934606|ref|YP_007688188.1|  86 ISDLEKQIEKQEATVRKIEATISAKK 111
                                       67788888888888888877776654 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.15
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXX CS
                              SlyX  18 tieeLndvvaeqqqqidrlqrqlrllaerlkelee 52 
                                        ie+L + +    + i++l+++l++++++l+ +++
  gi|474934606|ref|YP_007688188.1| 217 EIEDLKRDIDGRIRMIEHLREELDAVRKELAIANA 251
                                       57777777777788999999999999998855544 PP

  == domain 4  score: 8.5 bits;  conditional E-value: 0.005
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXX CS
                              SlyX  12 lafqedtieeLndvvaeqqqqidrlqrqlrllaerlkele 51 
                                       l  +++ i +L ++ +e ++q+d+l+++ + ++++++el 
  gi|474934606|ref|YP_007688188.1| 274 LKEMDNSIRTLGAENYELRRQLDELKKERDVMKRNIRELT 313
                                       55678999****************************9986 PP

  == domain 5  score: 0.9 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHHHHT-XXXXXXXX CS
                              SlyX  31 qqidrlqrqlrllaerlkeleessg 55 
                                       +qi +lq ++r l+          +
  gi|474934606|ref|YP_007688188.1| 321 RQIIELQSRIRTLNAAA-------E 338
                                       44445555554444433.......3 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   4.6     0.013       7.8     207     268 ..       8      71 ..       4      77 .. 0.81
   2 ?   -0.7  10.4      0.85   5.1e+02     158     276 ..      86     203 ..      79     226 .. 0.45
   3 ?    4.1   0.3     0.031        18     184     237 ..     200     254 ..     191     264 .. 0.71
   4 ?   10.5   7.1   0.00033       0.2     155     258 ..     243     345 ..     218     348 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.013
                              Spc7 207 elaelkaeieekkkelaelqeqleeleekiee..lkeqkseleeeiaeaervleeckgwsesev 268
                                       ++++l+ e+eekk++++++++ ++e++ + ++  l+ + ++l++++a+ae  lee ++   ++v
  gi|474934606|ref|YP_007688188.1|   8 TIERLEREVEEKKQRVKSVEKAIAEKRGTNQAtmLAVSLRNLKADLANAEAALEEARKNPPEDV 71 
                                       6788899999999999999999999876554411678899999999999999999998877777 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.85
                              Spc7 158 Lekqeeeldellpeleeekaeleeeleklqeaaeelesid.keeLeelreelaelkaeieekkkelaelqeqleele 233
                                       +++ e+++++    +++ +a+++++  + q+    ++  + + +L+++r  l++  a  +e   +++++++++++ +
  gi|474934606|ref|YP_007688188.1|  86 ISDLEKQIEKQEATVRKIEATISAKKGSNQANMLAVSLKNaRGDLANMRAMLEDMLAAEAEEDPDTSSVRKDIADRK 162
                                       44444444444444444444444444444442222222222444444444444444444444444444444444444 PP

                              Spc7 234 ekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevk 276
                                        +++el+  +++  + ++  ++ +e  +++ + e+++l  +++
  gi|474934606|ref|YP_007688188.1| 163 VRLKELDRDYEDETDPVK--RNNIEVSRRFLQMEINSLLIRLS 203
                                       444444444444444443..23344445555555555544444 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.031
                              Spc7 184 eklqeaaeeles.idkeeLeelreelaelkaeieekkkelaelqeqleeleekie 237
                                        +l ea++ +e+ + + e+e l+++++     ie++++el+ ++++l+  ++++ 
  gi|474934606|ref|YP_007688188.1| 200 IRLSEAERGIEAgSPESEIEDLKRDIDGRIRMIEHLREELDAVRKELAIANARLG 254
                                       5566666666664557888888888888888888888888888888887777765 PP

  == domain 4  score: 10.5 bits;  conditional E-value: 0.00033
                              Spc7 155 kelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqlee 231
                                       +++L+  ++ l +  +++    ++++ e+ +l+e+ +++ ++  e+  elr++l+elk+e +  k+++ el+   ++
  gi|474934606|ref|YP_007688188.1| 243 RKELAIANARLGKPEDKVMCDTTRVTVEAGRLKEMDNSIRTLGAEN-YELRRQLDELKKERDVMKRNIRELTVHCDN 318
                                       2333333333333344444455577777778888777777776666.579999999999999999999999999999 PP

                              Spc7 232 leekieelkeqkseleeeiaeaervle 258
                                       ++ +i el++++++l+++ ++a r ++
  gi|474934606|ref|YP_007688188.1| 319 SDRQIIELQSRIRTLNAAAEKAARDRD 345
                                       999999999999999999999998776 PP

>> DUF2508  Protein of unknown function (DUF2508)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1         6   3.6e+03      21      38 ..       8      25 ..       7      42 .. 0.72
   2 ?   -1.2   0.1       3.9   2.3e+03      18      38 ..      42      62 ..      22      67 .. 0.72
   3 ?    7.0   0.1     0.011       6.3      21      56 ..     217     252 ..     216     253 .. 0.95
   4 ?    3.2   0.2      0.16        97      14      39 ..     287     312 ..     277     330 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 6
                           DUF2508 21 eIektkeelesakslfen 38
                                      +Ie++ +e e++k+ +  
  gi|474934606|ref|YP_007688188.1|  8 TIERLEREVEEKKQRVKS 25
                                      577777777777776654 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.9
                           DUF2508 18 LleeIektkeelesakslfen 38
                                      L  ++ ++k +l++a++++e 
  gi|474934606|ref|YP_007688188.1| 42 LAVSLRNLKADLANAEAALEE 62
                                      555677778888877777665 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.011
                           DUF2508  21 eIektkeelesakslfensvDlsdeliyqlklaeak 56 
                                       eIe++k++++   +++e+  +  d +  +l++a+a+
  gi|474934606|ref|YP_007688188.1| 217 EIEDLKRDIDGRIRMIEHLREELDAVRKELAIANAR 252
                                       8********************99**********998 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.16
                           DUF2508  14 edeeLleeIektkeelesakslfens 39 
                                       e+ eL ++++++k+e ++ k++++  
  gi|474934606|ref|YP_007688188.1| 287 ENYELRRQLDELKKERDVMKRNIREL 312
                                       6779*************999988754 PP

>> Nup54_57_C  NUP57/Nup54 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.4    0.0032       1.9      15      28 ..     232     245 ..     232     246 .. 0.92
   2 ?    1.9   0.4      0.28   1.7e+02      19      28 ..     292     301 ..     290     306 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0032
                        Nup54_57_C  15 LqHLkKElEsikkD 28 
                                       + HL+ El++++k+
  gi|474934606|ref|YP_007688188.1| 232 IEHLREELDAVRKE 245
                                       68***********9 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.28
                        Nup54_57_C  19 kKElEsikkD 28 
                                       +++l+++kk+
  gi|474934606|ref|YP_007688188.1| 292 RRQLDELKKE 301
                                       5666666665 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.7       0.1        60       9      62 ..       8      63 ..       4      75 .. 0.76
   2 ?    2.6   1.6      0.36   2.2e+02       9      53 ..      85     145 ..      78     180 .. 0.63
   3 ?    5.8   0.1     0.037        22       1      57 [.     193     251 ..     193     271 .. 0.73
   4 ?    5.9   1.4     0.032        19      10      52 ..     274     316 ..     267     353 .. 0.63

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.1
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHXXXXXXXXXX CS
                              YabA  9 kleeleeqleelleeleelkeelaelleenae..Leleneklrerleeeekkekek 62
                                      ++e+le+++ee +++++++++++ae    n++  L +  ++l+  l+++e++ +e 
  gi|474934606|ref|YP_007688188.1|  8 TIERLEREVEEKKQRVKSVEKAIAEKRGTNQAtmLAVSLRNLKADLANAEAALEEA 63
                                      6899*******************998877764238888899999995555444433 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.36
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHH..............X CS
                              YabA   9 kleeleeqleelleeleelkeelaelleenae..Leleneklrerl..............e 53 
                                       ++++le+q+e+  ++++++++++++    n++  L +  ++ r  l              +
  gi|474934606|ref|YP_007688188.1|  85 TISDLEKQIEKQEATVRKIEATISAKKGSNQAnmLAVSLKNARGDLanmramledmlaaeA 145
                                       5788999999999999999999887766665322666555555444444444444443322 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.037
                                       X-HHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXX CS
                              YabA   1 mdkkelfdkleeleeqlee..lleeleelkeelaelleenaeLeleneklrerleeeek 57 
                                       m+ ++l+ +l+e e+ +e+    +e+e+lk+++   +   ++L+ e + +r++l+ +++
  gi|474934606|ref|YP_007688188.1| 193 MEINSLLIRLSEAERGIEAgsPESEIEDLKRDIDGRIRMIEHLREELDAVRKELAIANA 251
                                       55666777777777766541156899**************************9944333 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.032
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YabA  10 leeleeqleelleeleelkeelaelleenaeLeleneklrerl 52 
                                       l+e+++++++l +e  el+++l el +e + ++ + ++l  + 
  gi|474934606|ref|YP_007688188.1| 274 LKEMDNSIRTLGAENYELRRQLDELKKERDVMKRNIRELTVHC 316
                                       5566666666666666666666666666666665555554444 PP

>> Yuri_gagarin  Yuri gagarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9  20.0      0.56   3.3e+02      55     162 ..     248     356 ..       7     363 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.56
                      Yuri_gagarin  55 vanerlaceidalketlkdrdeqikqlqsmitsysdl.sennrlkeeiydlkqknceqarkvrelaeelkgeeeqrv 130
                                       +an rl    d++            +l++m +s   l  en  l+ ++ +lk+   +  r++rel+ + ++ + q +
  gi|474934606|ref|YP_007688188.1| 248 IANARLGKPEDKVMCDTTRVTVEAGRLKEMDNSIRTLgAENYELRRQLDELKKERDVMKRNIRELTVHCDNSDRQII 324
                                       555555554444444444444555678888888888846999*********************************** PP

                      Yuri_gagarin 131 elvdkyekllasfeeqckelkranrrvqslqe 162
                                       el ++   l a+ e+  ++   a  +++sl+ 
  gi|474934606|ref|YP_007688188.1| 325 ELQSRIRTLNAAAEKAARDRDAALIKIESLNL 356
                                       *******************9999999999975 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   3.0    0.0026       1.6      78     113 ..       7      42 ..       4      46 .. 0.93
   2 ?    5.8   2.0     0.022        13      74     112 ..      80     118 ..      73     122 .. 0.73
   3 ?    4.1   0.4      0.08        48      45      79 ..     137     171 ..     120     175 .. 0.85
   4 ?    1.0   0.2      0.71   4.2e+02      30      55 ..     220     245 ..     201     255 .. 0.51
   5 ?    8.1   5.5    0.0045       2.7      54     112 ..     290     348 ..     274     356 .. 0.88
   6 ?   -1.3   0.0       3.6   2.1e+03      23      37 ..     349     363 ..     345     364 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0026
                             DHR10  78 rkeerlqrqlenaeeklerlreqaeekreaakarle 113
                                       +++erl+r +e ++++   +++  +ekr  ++a++ 
  gi|474934606|ref|YP_007688188.1|   7 ATIERLEREVEEKKQRVKSVEKAIAEKRGTNQATML 42 
                                       689*******************************96 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.022
                             DHR10  74 relerkeerlqrqlenaeeklerlreqaeekreaakarl 112
                                       +e + +++ l++q+e+ e    + + + ++k+ +++a +
  gi|474934606|ref|YP_007688188.1|  80 QEEKLTISDLEKQIEKQEATVRKIEATISAKKGSNQANM 118
                                       455566777888888888888888888888887777776 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.08
                             DHR10  45 ieaelakleeakkklkelrdaleekeielrelerk 79 
                                       +e+ la++ e++ + ++ r+ +++++ +l+el+r 
  gi|474934606|ref|YP_007688188.1| 137 LEDMLAAEAEEDPDTSSVRKDIADRKVRLKELDRD 171
                                       577899**************************985 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.71
                             DHR10  30 vvekdlrsciklleeieaelakleea 55 
                                       ++++d+   i+++e + +el +++++
  gi|474934606|ref|YP_007688188.1| 220 DLKRDIDGRIRMIEHLREELDAVRKE 245
                                       23333333333333333333333333 PP

  == domain 5  score: 8.1 bits;  conditional E-value: 0.0045
                             DHR10  54 eakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqaeekreaakarl 112
                                       e +++l+el+++ + ++++ rel+ + +   rq+   + ++  l   ae+ +++ +a+l
  gi|474934606|ref|YP_007688188.1| 290 ELRRQLDELKKERDVMKRNIRELTVHCDNSDRQIIELQSRIRTLNAAAEKAARDRDAAL 348
                                       66899**************************************9999998877766665 PP

  == domain 6  score: -1.3 bits;  conditional E-value: 3.6
                             DHR10  23 akidalqvvekdlrs 37 
                                       +ki++l+ + kd+r+
  gi|474934606|ref|YP_007688188.1| 349 IKIESLNLYIKDMRR 363
                                       79***********96 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   2.5     0.062        37      58     112 ..       9      65 ..       4      67 .. 0.66
   2 ?   -0.6   4.9       1.6   9.4e+02      37     127 ..      82     171 ..      79     198 .. 0.63
   3 ?    9.2   1.8    0.0016      0.93      92     133 ..     273     314 ..     264     324 .. 0.90
   4 ?    0.1   0.3      0.99   5.9e+02      89     132 ..     312     355 ..     306     363 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.062
                           DUF4201  58 IeernkeLkrlkkkttktvh..althlkeklhmleselselkkelkekeerlaklrk 112
                                       Ie+ + e+++ k+++++  +  a +   + ++ml+  l++lk +l + e+ l++ rk
  gi|474934606|ref|YP_007688188.1|   9 IERLEREVEEKKQRVKSVEKaiAEKRGTNQATMLAVSLRNLKADLANAEAALEEARK 65 
                                       5544444444444444444400444555677799999999**999999999999998 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.6
                           DUF4201  37 egLtlidFeqlqienqalnkkIeernkeLkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrke 113
                                       e+Lt++d e+   + +a + kIe  +   k+ +++++     l++ +  l  ++++l+++     e + +  ++rk 
  gi|474934606|ref|YP_007688188.1|  82 EKLTISDLEKQIEKQEATVRKIEA-TISAKKGSNQANMLAVSLKNARGDLANMRAMLEDMLAAEAEEDPDTSSVRKD 157
                                       556666666555555555555554.4455555555555555566666666666666666666666666666666666 PP

                           DUF4201 114 lykvklerdklrkq 127
                                       +   k + + l+++
  gi|474934606|ref|YP_007688188.1| 158 IADRKVRLKELDRD 171
                                       66555555555554 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0016
                           DUF4201  92 elselkkelkekeerlaklrkelykvklerdklrkqneklkq 133
                                        l+e+ ++++++ ++  +lr++l ++k+erd +++  ++l  
  gi|474934606|ref|YP_007688188.1| 273 RLKEMDNSIRTLGAENYELRRQLDELKKERDVMKRNIRELTV 314
                                       57899******************************9999976 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.99
                           DUF4201  89 leselselkkelkekeerlaklrkelykvklerdklrkqneklk 132
                                       l+  + +   ++ e++ r++ l +  +k+  +rd +  + e l+
  gi|474934606|ref|YP_007688188.1| 312 LTVHCDNSDRQIIELQSRIRTLNAAAEKAARDRDAALIKIESLN 355
                                       55566677777888888888888888888888888877777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1817  (0.101344); expected 358.6 (0.02)
Passed bias filter:                      677  (0.0377601); expected 358.6 (0.02)
Passed Vit filter:                       123  (0.00686039); expected 17.9 (0.001)
Passed Fwd filter:                        78  (0.00435049); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 1.38u 0.31s 00:00:01.69 Elapsed: 00:00:00.58
# Mc/sec: 1906.28
//
Query:       gi|474934607|ref|YP_007688189.1|  [L=163]
Description: hypothetical protein TALC_01037 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.4   11.2   2.7        1.1    9.8   0.8    2.2  2  UK        Virulence determinant


Domain annotation for each model (and alignments):
>> UK  Virulence determinant
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.8   6.3e-05       1.1      59      75 ..      84     100 ..      77     115 .. 0.87
   2 ?    1.0   0.0     0.035   6.3e+02      64      87 ..     115     138 ..     103     144 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 6.3e-05
                                UK  59 ikrgndvpcccprkmts 75 
                                       + rgnd+  cc r m+s
  gi|474934607|ref|YP_007688189.1|  84 VCRGNDIVICCCRDMAS 100
                                       679************98 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.035
                                UK  64 dvpcccprkmtsadkkfsvfgkgs 87 
                                        vp c p      +  + + gkg 
  gi|474934607|ref|YP_007688189.1| 115 YVPGCTPEVCRDGEDTYVITGKGG 138
                                       5999****9999999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       975  (0.0543812); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 934.84
//
Query:       gi|474934608|ref|YP_007688190.1|  [L=914]
Description: hypothetical protein TALC_01038 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-11   42.7   1.7    1.1e-09   38.6   1.7    2.8  1  PDDEXK_1  PD-(D/E)XK nuclease superfamily
  ------ inclusion threshold ------
      0.026   14.3   0.1      0.095   12.5   0.1    1.9  2  YfkB      YfkB-like domain
       0.12   12.4   0.6        0.8    9.8   0.2    2.4  2  Cas_Cas4  Domain of unknown function DUF83


Domain annotation for each model (and alignments):
>> PDDEXK_1  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   1.7   1.8e-13   1.1e-09       2     254 ..     523     899 ..     522     900 .. 0.66

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 1.8e-13
                          PDDEXK_1   2 lSvsrletfleCplrfflryllglreeeeleapdlGtlvHaaleefye..wkkldke..dleelleeaveelwpell 74 
                                       +S s+++ +++Cp +f +r  l +  +e+ +++ +G+++H   e  y   + ++ k+  d + +++++++ + p  +
  gi|474934608|ref|YP_007688190.1| 523 FSKSTYNLWATCPVSFLFREALPFGSTEDNQRSLYGSVFHWFTEFAYCypE-EVLKHkdDPDYYVAKLMALYEPMIE 598
                                       799********************9777777777**********87776852.3333334555555444443333322 PP

                          PDDEXK_1  75 leeei.....lessarlrylaeklkevleklve.rlaeeleakrg..frpvalelefg.........gekvrLkGri 134
                                         + +      + s+ l+ ++  ++e+l    + +++  ++ +r+  f  ++++ +f+         +      +++
  gi|474934608|ref|YP_007688190.1| 599 SGN-VevertRLRSNILQMMQFLEEEILPIDTKgAVKPVEKNERNplFAWEGHDEKFDnvekteyccD--KHASAQY 672
                                       222.2111121222222333333333333334434444444444456666666656667888887663..34789** PP

                          PDDEXK_1 135 DrvddkegelriiDyKtgsappkskelaelkegl........QlllYllalaegeelkeegepagalylrleepkvk 203
                                       D+  + ++  r+iDyKtg+   k+ + + ++++l        Q l+Yl++  + +   +   p + +++++  +   
  gi|474934608|ref|YP_007688190.1| 673 DL--SFGN--RVIDYKTGK---KKGS-QSVYNHLslikdfesQPLFYLYVRSRLHGDMNT--PTEFTLFFVTSQ--P 737
                                       **..4455..9********...3333.36999999******************9444433..888888888552..2 PP

                          PDDEXK_1 204 ............................................................................. 203
                                                                                                                    
  gi|474934608|ref|YP_007688190.1| 738 sdikayltsesyplenllvkviynpgmkaanldairrgitsprainkkkfapkvdqvmellsslfndpdkcsyenvs 814
                                       33579999999999999999999999999999999999998888888888777777777777777777777777777 PP

                          PDDEXK_1 204 .............................deevvkkmalteeeleallqeleelaeeilagefparpskk.....Ce 246
                                                                     +++ + ++ ++e le+++++++  ++ + +  f +   +      C+
  gi|474934608|ref|YP_007688190.1| 815 rllavaeleddetarkhaydiigelrpikYSKKERTVEVSREYLESFADQVSMDWNDASSAMFGPIYRRPniireCK 891
                                       777666666655555555555555555554444444478888888888888888555554433333333335566** PP

                          PDDEXK_1 247 yCpyksvC 254
                                        C+yk++C
  gi|474934608|ref|YP_007688190.1| 892 KCDYKKYC 899
                                       ******** PP

>> YfkB  YfkB-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   1.6e-05     0.095       6      71 ..      92     157 ..      88     165 .. 0.92
   2 ?   -2.6   0.0      0.71   4.3e+03       8      40 ..     289     321 ..     287     333 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.6e-05
                              YfkB   6 faselevlsldelreaieklldvrdedvwmlfGtlPfyacseeeedrellkrlaeeknvtvrndpd 71 
                                       + + l++ +++ ++++++k l+ r+++v+ ++ tl   +  +++ + e++ r+++ k v+v nd d
  gi|474934608|ref|YP_007688190.1|  92 YNEILNIREIRRYKSEVDKYLHGREKRVYEVYQTLRTREALQNNCNDEIMGRFYAGKKVAVVNDED 157
                                       556688888899999*************************************************98 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.71
                              YfkB   8 selevlsldelreaieklldvrdedvwmlfGtl 40 
                                       ++++ lsl+++ ++i+++l   d+++  l+G +
  gi|474934608|ref|YP_007688190.1| 289 NKIDNLSLSKVYSSIDSILANPDDRTLELLGIM 321
                                       57889999999********99999998888876 PP

>> Cas_Cas4  Domain of unknown function DUF83
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.21   1.3e+03     118     149 ..     359     390 ..     357     401 .. 0.88
   2 ?    9.8   0.2   0.00013       0.8     107     161 ..     844     900 ..     828     901 .. 0.64

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.21
                          Cas_Cas4 118 lteelreelekaikeieeiissekppkvkkkk 149
                                       +++++  el  ai++++++ ++e++p+ +kk 
  gi|474934608|ref|YP_007688190.1| 359 INDKDVTELAYAISNVQDLRHNEQIPEFEKKG 390
                                       78899999******************999875 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00013
                          Cas_Cas4 107 ypkekkreevelteelr....eelekaikeieeiissekppkvkkkkiCkkCayaelCl 161
                                       y k  k+++ve+++e      +++    +++++ +    +++++  + CkkC y+++Cl
  gi|474934608|ref|YP_007688190.1| 844 YSK--KERTVEVSREYLesfaDQVSMDWNDASSAMFGPIYRRPNIIRECKKCDYKKYCL 900
                                       333..33345555544400004455556677788888889999999************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (914 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.21s 00:00:00.77 Elapsed: 00:00:00.38
# Mc/sec: 7214.49
//
Query:       gi|474934609|ref|YP_007688191.1|  [L=1057]
Description: ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.6e-46  156.7   0.4      2e-45  155.7   0.4    1.6  1  UvrD-helicase    UvrD/REP helicase N-terminal domain
    9.1e-28   97.6   0.0    1.4e-14   54.2   0.0    3.3  3  UvrD_C           UvrD-like helicase C-terminal domain
    1.3e-19   71.0   0.3    1.2e-18   67.8   0.3    2.3  1  AAA_19           AAA domain
    5.6e-09   35.7   0.1     0.0016   18.2   0.0    2.5  2  UvrD_C_2         UvrD-like helicase C-terminal domain
    2.7e-06   27.5   0.0    7.6e-06   26.0   0.0    1.7  1  PDDEXK_1         PD-(D/E)XK nuclease superfamily
    6.2e-06   26.1   0.0    1.7e-05   24.6   0.0    1.7  2  AAA_30           AAA domain
      0.003   17.4   0.1     0.0061   16.4   0.1    1.5  1  AAA_11           AAA domain
  ------ inclusion threshold ------
      0.038   13.2   0.0      0.059   12.6   0.0    1.3  1  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.043   13.6   0.4         20    4.8   0.0    4.1  4  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.052   13.6   0.1       0.16   12.0   0.1    1.8  1  ResIII           Type III restriction enzyme, res subunit
      0.072   13.4   0.0       0.24   11.7   0.0    1.9  1  AAA_22           AAA domain
      0.093   13.0   0.0        0.3   11.4   0.0    1.8  1  BLM10_N          Proteasome-substrate-size regulator, N-termi
      0.097   12.5   0.1       0.24   11.2   0.1    1.7  2  Helicase_RecD    Helicase
        0.1   12.9   0.0       0.38   11.1   0.0    2.0  2  AAA_16           AAA ATPase domain
       0.11   12.0   3.9       0.22   11.1   0.0    3.0  4  AAA_12           AAA domain
       0.17   11.4   0.5       0.35   10.4   0.5    1.5  1  PRTase_2         Phosphoribosyl transferase


Domain annotation for each model (and alignments):
>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.7   0.4   1.8e-48     2e-45       1     314 [.       4     395 ..       4     396 .. 0.70

  Alignments for each domain:
  == domain 1  score: 155.7 bits;  conditional E-value: 1.8e-48
                                       SSHHHHHHHHS-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHH..HHHHCCHH CS
                     UvrD-helicase   1 lnpeqreaiaslggpilveAsAGsGKTfvlaerilrlikeeeiepdrilvvTFTnkAaeElkeRiee..alkkaeqe 75 
                                       ln++q++++ +++g ++v A++G+GKT++++er +r ++++ ie ++++++TFTn AaeE+++Ri++  a kkaeqe
  gi|474934609|ref|YP_007688191.1|   4 LNDSQQRIVDTTEGIVVVDAGPGTGKTATVTERCIRILQKN-IEGKDVIMMTFTNNAAEEMRQRIAKkiAEKKAEQE 79 
                                       699*********************************99999.*************************6555667777 PP

                                       CTT-H.......HHHHHHHHCTTSEEEEHHHHHHHHHHHHHGGTT................................ CS
                     UvrD-helicase  76 ssdde.......rlrlalqnlseanisTlHsfcqkilkkeanrig................................ 113
                                       ++ d+        + l l++ +e++++T++sfc  +l ++   +                                 
  gi|474934609|ref|YP_007688191.1|  80 RIIDTldkkdivDYDLILRKSREMMVCTFDSFCMTVLSQYPAPASkelglssvlshhasvstndalnhlyfckflne 156
                                       7777789999999999************************9998888998888666666666665555555555555 PP

                                       .........................................SHTTTEEECHHHHHHCCHHHHHHHHHSCHSHTTTTH CS
                     UvrD-helicase 114 .........................................ldpnfrildeedeedlkqqellkelleksaddslnl 149
                                                                                ++ ++ + d+  +  ++ ++   ell    d+ l+ 
  gi|474934609|ref|YP_007688191.1| 157 ylaendlgefapifssdpkslqaiierllsicviptkniwfWRDGILVDDDGGKTEIDHLSGCRELLR---DELLKK 230
                                       55555555555555555555555555555555555555555555555555555445555555555554...333333 PP

                                       HHHHHHHHHHHHHCCCCCHHHHCCCHHHHHCHHHHHHHHHHHTTCCTTHHCHSSTSCSHHHHHHHHHHHHHHHHHHH CS
                     UvrD-helicase 150 dkkkleklikelsksrnikkeelslskskaeelrelvskakekqlspkelkkafekasdlqkkiaeflkeyqeqkke 226
                                       d + l+k++   +++        +  ks  ++  +  +++ ++ l ++ l++   ++++l ++i +++  y +++ +
  gi|474934609|ref|YP_007688191.1| 231 DLSYLRKNVD--TLPP-------EYRKSDDKDAPAEDETYVKSSLVENALTD--SQQKKLIDAIHDLMFAYIDRCVK 296
                                       3333333322..1111.......11222222222222333333333333333..44556889999999999999999 PP

                                       HTCEEHHHHHHHHHHHHHH.....CHHHHHHHHH...HSSEEEESSGGG-BHHHHHHHHH...HHTTTTTEEEEE-G CS
                     UvrD-helicase 227 enalDfsdllhallellee.....neelaealre...rykeiliDEyQDTnkiQyrilkl...lasgheelfmvGDp 292
                                        n l fs + + +l  l +      +++ +++++   ++k++ +DE+QDTn++ ++i  +   l+++  +l++vGD 
  gi|474934609|ref|YP_007688191.1| 297 DNHLTFSLIKCLALVTLYKlrtpdSDSIYDEIQSesfKFKYVTVDEFQDTNPADMSITLMildLYKDSYNLCVVGDW 373
                                       999***99988887777777999966666666542228****************9987772225666667******* PP

                                       GG--GGGGTB-THHHHHHHHHS CS
                     UvrD-helicase 293 kQsIYgFRgAdielflkkkkdf 314
                                       kQ IY+FR+ di++++ +++++
  gi|474934609|ref|YP_007688191.1| 374 KQGIYEFRNTDIRNLMFFDHNV 395
                                       ***************9988875 PP

>> UvrD_C  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.11   1.2e+02      35     124 ..      10      97 ..       2     285 .. 0.85
   2 !   37.8   0.0   1.3e-12   1.4e-09       3     129 ..     421     576 ..     419     590 .. 0.86
   3 !   54.2   0.0   1.3e-17   1.4e-14     264     347 ..     664     790 ..     579     792 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.11
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C  35 ktvekgekivvleaeteeeEaekiaatikallekneklediavLvRsnkdadkiskaLkkegipfnvvdeekfFkre 111
                                       + v  +e ivv +a      +  + +   ++l+kn++ +d+  ++ +n+ a+++ + + k+ i  ++ ++e++ ++ 
  gi|474934609|ref|YP_007688191.1|  10 RIVDTTEGIVVVDAGPGTGKTATVTERCIRILQKNIEGKDVIMMTFTNNAAEEMRQRIAKK-IAEKKAEQERIIDTL 85 
                                       5555666677777776666777777777777779999999999999999999998888765.555558888888888 PP

                                       xxxxxxxxxxxxx RF
                            UvrD_C 112 eikdilaylklla 124
                                         kdi  y +l++
  gi|474934609|ref|YP_007688191.1|  86 DKKDIVDY-DLIL 97 
                                       88887766.4444 PP

  == domain 2  score: 37.8 bits;  conditional E-value: 1.3e-12
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                            UvrD_C   3 LekNyRStksLlkaankflenilnrralekek............ktvekgekivvleaeteeeEaekiaatikall. 66 
                                       L +NyRS++ +++++ + l   ++++ +++e+            +  e++ + + +++++++e  + + + ++  + 
  gi|474934609|ref|YP_007688191.1| 421 LDINYRSSSLIIRCSFHSLIIDCGENKHTYEEadihkivasdanTVLEENTSFERIQCNNKDEQIRAVLSSVMGYVr 497
                                       89**************9996666663333222347677777765444555588889999999999999999999999 PP

                                       ................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C  67 ................ekneklediavLvRsnkdadkiskaLkkegipfnvvdeekfFkreeikdilaylkllankq 127
                                                        ++++++diavL+R+n + + +++a  + gip  + ++++  +++e k +la l+ + n+ 
  gi|474934609|ref|YP_007688191.1| 498 ggkyqvwgadkdgnmvLRKPEYSDIAVLCRTNPECRAVKTACDEFGIPSYINGDQEVMNTPEAKMLLAWLRFVENQA 574
                                       *************99999*********************************************************99 PP

                                       xx RF
                            UvrD_C 128 dk 129
                                       d 
  gi|474934609|ref|YP_007688191.1| 575 DP 576
                                       85 PP

  == domain 3  score: 54.2 bits;  conditional E-value: 1.3e-17
                                       xxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxx..................... RF
                            UvrD_C 264 lneileiatLseseleeskkk...ekipiiTiHqAKGlEFdvVflagleeg..tfP..................... 314
                                       + +i+e+  + e+++ ++++    + i+i T+H++KGlE+++V++  ++++  +fP                     
  gi|474934609|ref|YP_007688191.1| 664 IIKIIEYD-IDEESDYNVDSIpedNVITIQTLHKSKGLEYPIVIIPYVNKKgsKFPlnqgdrinyvlndlaglrckk 739
                                       34444443.666666666665667899******************999875449*********************** PP

                                       ................xxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C 315 ................syrskk..ekrleEEkRlfYVaiTRAkkrLfisys 347
                                                       +y ++k   +  +EE+Rl++V+i+RAk+ ++++++
  gi|474934609|ref|YP_007688191.1| 740 ivegdgnnfwnlenwrTYVANKykPDSYNEERRLLFVGISRAKQYVTMIAH 790
                                       *******99988888866666688889*********************987 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.8   0.3   1.1e-21   1.2e-18       1     146 []       8     381 ..       8     381 .. 0.87

  Alignments for each domain:
  == domain 1  score: 67.8 bits;  conditional E-value: 1.1e-21
                            AAA_19   1 qreavealkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae......... 68 
                                       q+++v +++e++++v aGpGtGKT ++++++  +++ + ++ +++++++ft+ Aa+e+r+r+a+  ae         
  gi|474934609|ref|YP_007688191.1|   8 QQRIV-DTTEGIVVVDAGPGTGKTATVTERCIRILQKN-IEGKDVIMMTFTNNAAEEMRQRIAKKIAEkkaeqerii 82 
                                       88999.999******************99988877777.5579*******************6666658999****8 PP

                            AAA_19  69 ......................atTiHrlal.............................................. 77 
                                                              +T+ ++ +                                              
  gi|474934609|ref|YP_007688191.1|  83 dtldkkdivdydlilrksremmVCTFDSFCMtvlsqypapaskelglssvlshhasvstndalnhlyfckflneyla 159
                                       8888888888888888888888788888777********************************************** PP

                            AAA_19  78 ............................................................................. 77 
                                                                                                                    
  gi|474934609|ref|YP_007688191.1| 160 endlgefapifssdpkslqaiierllsicviptkniwfwrdgilvdddggkteidhlsgcrellrdellkkdlsylr 236
                                       ***************************************************************************** PP

                            AAA_19  78 ..........................................................................ldf 80 
                                                                                                                 +  
  gi|474934609|ref|YP_007688191.1| 237 knvdtlppeyrksddkdapaedetyvksslvenaltdsqqkklidaihdlmfayidrcvkdnhltfslikclalV-- 311
                                       ****************************************************99999988877555555554442.. PP

                            AAA_19  81 ddlltealelle.............eaeeekklqeeellivDEfqdvdelqyr...LlkallgekkklllvGDpdQl 141
                                                                ++ +++ + + +++ vDEfqd+++  ++   ++  l++++ +l++vGD +Q 
  gi|474934609|ref|YP_007688191.1| 312 -----------TlyklrtpdsdsiyDEIQSESF-KFKYVTVDEFQDTNPADMSitlMILDLYKDSYNLCVVGDWKQG 376
                                       ...........0334555555555333344444.566**********94433311145566667766********** PP

                            AAA_19 142 iyvfr 146
                                       iy+fr
  gi|474934609|ref|YP_007688191.1| 377 IYEFR 381
                                       ***97 PP

>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.8e-05      0.02       4      24 ..     691     709 ..     689     717 .. 0.85
   2 !   18.2   0.0   1.4e-06    0.0016      19      51 ..     757     787 ..     752     788 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.8e-05
                          UvrD_C_2   4 altihkaQGsefpaVivfdpd 24 
                                       + t hk++G+e+p+Vi+  p+
  gi|474934609|ref|YP_007688191.1| 691 IQTLHKSKGLEYPIVII--PY 709
                                       6699************9..55 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 1.4e-06
                          UvrD_C_2  19 ivfdpdlaaarmgelrrrlLYtavTRAreklil 51 
                                       +v++ +  +++++   rrlL+++++RA++ +++
  gi|474934609|ref|YP_007688191.1| 757 YVANKYKPDSYNE--ERRLLFVGISRAKQYVTM 787
                                       6767777777866..5*************9987 PP

>> PDDEXK_1  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   6.8e-09   7.6e-06      94     178 ..     910     989 ..     825    1037 .. 0.62

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 6.8e-09
                          PDDEXK_1  94 kevleklverlaeeleakrg...frpvalelefggekvrLkGriDrvd.dkegelriiDyKtgsappkskelaelke 166
                                       ++vl++l ++    +++  +   f p+a e + +++kv+L+G+iD++  d++  ++i D+Kt      ++   + ++
  gi|474934609|ref|YP_007688191.1| 910 EAVLANLPDTDPGLRKS--EipcFLPIATE-KHSNRKVTLRGIIDMLYvDRDV-IEIHDWKTDV-S-DRF---REEY 977
                                       34444443333332233..13589999999.444589***********66666.*******765.2.333...4578 PP

                          PDDEXK_1 167 glQlllYllala 178
                                        +Ql +Y++a++
  gi|474934609|ref|YP_007688191.1| 978 MVQLSIYAYAAK 989
                                       88********97 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   1.6e-08   1.7e-05       2      67 ..       4      68 ..       3      97 .. 0.80
   2 ?   -2.3   0.0       2.7     3e+03      91     127 ..     337     375 ..     322     376 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.6e-08
                            AAA_30  2 lnaeQaaavealltsgdrvavltGpAGtGKttalkal.reaweaa..ggrviglAptgkaAkvLaeelg 67
                                      ln++Q+++v+  +t+g  ++v+ +++GtGKt ++++   ++++++  g++vi+++ t++aA+++++ + 
  gi|474934609|ref|YP_007688191.1|  4 LNDSQQRIVD--TTEG--IVVVDAGPGTGKTATVTERcIRILQKNieGKDVIMMTFTNNAAEEMRQRIA 68
                                      6777777776..3344..9************99987657777776679*****************8764 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.7
                            AAA_30  91 llivDEagmvdtkqlaallkaaek..agakvilvGDerQ 127
                                        + vDE   ++ +++   l +++   ++  + +vGD +Q
  gi|474934609|ref|YP_007688191.1| 337 YVTVDEFQDTNPADMSITLMILDLykDSYNLCVVGDWKQ 375
                                       6778888877666665554444442137999*****999 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   5.5e-06    0.0061       2      85 ..       4      78 ..       3      88 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.5e-06
                            AAA_11  2 lndsqreaiksalseseitliqGPPGtgKTktivellsqllsrrkseeeksakpriLvCapSNaAvDellerllrglld 80
                                      lndsq++ + +   +++i+++   PGtgKT t++e + ++l      +++ +++ + + + +N+A  e+ +r+++++ +
  gi|474934609|ref|YP_007688191.1|  4 LNDSQQRIVDT---TEGIVVVDAGPGTGKTATVTERCIRIL------QKNIEGKDVIMMTFTNNAAEEMRQRIAKKIAE 73
                                      67777766654...456899***************999993......4689999999999**************96666 PP

                            AAA_11 81 segek 85
                                      ++ e+
  gi|474934609|ref|YP_007688191.1| 74 KKAEQ 78
                                      55544 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.2e-05     0.059       3      68 ..      18      79 ..      16     109 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.2e-05
                           DUF2075  3 vvlVtGvaGtGKtvvllnllael.eddeeertavylsvNhplvlvlrealakkeekkkkkeafekls 68
                                      +v+V  ++GtGKt    +   ++ +++ e++ +++++  ++  + +r+++akk       e+ ++ +
  gi|474934609|ref|YP_007688191.1| 18 IVVVDAGPGTGKTATVTERCIRIlQKNIEGKDVIMMTFTNNAAEEMRQRIAKKI-----AEKKAEQE 79
                                      789999****************999999**********************9999.....22222333 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.018        20       2      59 ..      20      77 ..      19     152 .. 0.76
   2 ?    1.4   0.0      0.19   2.1e+02      50     115 ..     325     391 ..     290     411 .. 0.68
   3 ?   -0.3   0.0      0.64   7.2e+02     184     205 ..     690     711 ..     641     717 .. 0.79
   4 ?    0.8   0.0      0.31   3.4e+02     205     231 ..     761     786 ..     755     789 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.018
                   Viral_helicase1  2 vvhGvpGcGKStlirkllrtsliltvn..rptaelltegkpklpnlsvrtvdsflmalvk 59
                                      vv++ pG GK+  + + +     l++n   + +++ t   + ++  + r ++++ +++ +
  gi|474934609|ref|YP_007688191.1| 20 VVDAGPGTGKTATVTERCIRI--LQKNieGKDVIMMTFTNNAAEEMRQRIAKKIAEKKAE 77
                                      9**********9999888773..3333003335555555566666666666666555443 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.19
                   Viral_helicase1  50 vdsflmalvkstkgkililDEylllhaG...yilllaalsk.aklvilfGDplQipfhsrnasfllahlp 115
                                        d++++      k+k++ +DE++  +++   + l+++ l+k + +++++GD +Q+ ++ rn ++ +  ++
  gi|474934609|ref|YP_007688191.1| 325 YDEIQSESF---KFKYVTVDEFQDTNPAdmsITLMILDLYKdSYNLCVVGDWKQGIYEFRNTDIRNLMFF 391
                                       455555554...4899999999998876332233344433313467889******999999987776655 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.64
                   Viral_helicase1 184 evttvhevqGltfdkVtlvllk 205
                                        + t h   Gl+++ V++ + +
  gi|474934609|ref|YP_007688191.1| 690 TIQTLHKSKGLEYPIVIIPYVN 711
                                       589**************98765 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.31
                   Viral_helicase1 205 ketdlelisesrenllvAlTRhrkslv 231
                                       k ++++ ++e+r  l+v+++R+++ ++
  gi|474934609|ref|YP_007688191.1| 761 KYKPDS-YNEERRLLFVGISRAKQYVT 786
                                       454544.7778***********98765 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00014      0.16      27      96 ..      19      89 ..       4     119 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                                      EEEEESTTSTHHHHHHHHHHHH-S......-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B-- CS
                            ResIII 27 glikmaTGtGKTlvaaklierllkkgkee.kflflvprkslleqtleefkkflseaykeigkkvsgdkkka 96
                                      +++ +  GtGKT + ++ + r+l+k+ e   ++++  +++  e ++++++k + e+++e++ +++   kk 
  gi|474934609|ref|YP_007688191.1| 19 VVVDAGPGTGKTATVTERCIRILQKNIEGkDVIMMTFTNNAAEEMRQRIAKKIAEKKAEQERIIDTLDKKD 89
                                      4566778********7777776666554449******************9999999888777776655554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00021      0.24       4      75 ..      15      87 ..      11     136 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00021
                            AAA_22  4 tagilvvtGesGtGKTtll.rrlleqldeeakaee.erpevvfvtlpsstsskdllrellralglelka.....erlss 75
                                      t+gi+vv + +GtGKT ++ +r  + l     +++ e+++v+ +t ++    +++++++++++ +++ +      +l++
  gi|474934609|ref|YP_007688191.1| 15 TEGIVVVDAGPGTGKTATVtERCIRIL-----QKNiEGKDVIMMTFTNNA-AEEMRQRIAKKIAEKKAEqeriiDTLDK 87
                                      799*************76515555555.....445579****99999999.9999999999999887775555544444 PP

>> BLM10_N  Proteasome-substrate-size regulator, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00027       0.3      40      71 ..     924     955 ..     921     957 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00027
                           BLM10_N  40 rtfpyeklLPYkvEsekerakyLshilknLYi 71 
                                       r+ +++  LP ++E++++r+  L+ i+  LY+
  gi|474934609|ref|YP_007688191.1| 924 RKSEIPCFLPIATEKHSNRKVTLRGIIDMLYV 955
                                       56677889***********************8 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00022      0.24       1      58 [.      20      79 ..      20     104 .. 0.82
   2 ?   -3.8   0.0       9.1     1e+04      62      88 ..     321     347 ..     304     354 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00022
                     Helicase_RecD  1 vltAdRGRGKSaalGlalaaliaegk..snilvtapskenvktlfeflakglealglkee 58
                                      v+ A++G+GK+a++   + ++++++   +++++   ++++++++ +++ak++ + + ++e
  gi|474934609|ref|YP_007688191.1| 20 VVDAGPGTGKTATVTERCIRILQKNIegKDVIMMTFTNNAAEEMRQRIAKKIAEKKAEQE 79
                                      688*********************989999999999999999999999999987665552 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 9.1
                     Helicase_RecD  62 kkaekaelrvrkqrieyiapdellklk 88 
                                       ++++  e+++++ +++y++ de+++++
  gi|474934609|ref|YP_007688191.1| 321 SDSIYDEIQSESFKFKYVTVDEFQDTN 347
                                       555566788889999999999998876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00033      0.38      12     101 ..       4      81 ..       1     159 [. 0.68
   2 ?   -1.7   0.0       2.9   3.2e+03     138     161 ..     337     360 ..     220     370 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00033
                            AAA_16  12 LlsalervrsgrpelvllsGesGvGKsslv.rellralekdggiflrgkcdqlesaipysalaqalareellrqlld 87 
                                       L++  +r+ + ++++v++   +G+GK++ v +++ r l+k+    ++gk +     ++   +++ + +ee  + ++ 
  gi|474934609|ref|YP_007688191.1|   4 LNDSQQRIVDTTEGIVVVDAGPGTGKTATVtERCIRILQKN----IEGKDVIM---MT---FTNNA-AEEMRQRIAK 69 
                                       66666788888899****************86677788888....88888888...22...44444.3222222222 PP

                            AAA_16  88 eaesaeleawrekl 101
                                       +  + e  a +e++
  gi|474934609|ref|YP_007688191.1|  70 K-IA-EKKAEQERI 81 
                                       2.22.333333333 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.9
                            AAA_16 138 vlvlDdlqwadeaslqllaaLlrl 161
                                       ++++D++q+  +a++++   +l+l
  gi|474934609|ref|YP_007688191.1| 337 YVTVDEFQDTNPADMSITLMILDL 360
                                       566677776666666665555555 PP

>> AAA_12  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.2       0.5   5.6e+02      95     143 ..      33      95 ..      28     111 .. 0.64
   2 ?   -2.8   0.0       3.6     4e+03     112     152 ..     306     344 ..     260     347 .. 0.60
   3 ?   -2.0   0.0         2   2.2e+03      19      34 ..     420     435 ..     410     540 .. 0.70
   4 ?   11.1   0.0   0.00019      0.22     102     197 ..     618     790 ..     596     792 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.5
                            AAA_12  95 vvklvekllkkgseeerkkigvitpYraqvellkkklkekeeekseke................i 143
                                       v++ + ++l+k  e   k++  +t+ ++ +e +++++++k  ek++++                +
  gi|474934609|ref|YP_007688191.1|  33 VTERCIRILQKNIEG--KDVIMMTFTNNAAEEMRQRIAKKIAEKKAEQeriidtldkkdivdydL 95 
                                       444444555555555..79999999999999***9999998888776665544444444444440 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.6
                            AAA_12 112 kkigvitpYraqvellkkklkekeeeksekeievntvdgfQ 152
                                       k ++ +t Y+       +  +e ++  ++ +++  tvd+fQ
  gi|474934609|ref|YP_007688191.1| 306 KCLALVTLYKLRTPDSDSIYDEIQS--ESFKFKYVTVDEFQ 344
                                       4455566665544333333332222..23348888999998 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 2
                            AAA_12  19 lLdtqYRmhpeIsrfp 34 
                                        Ld++YR+ + I r +
  gi|474934609|ref|YP_007688191.1| 420 PLDINYRSSSLIIRCS 435
                                       5888888888887754 PP

  == domain 4  score: 11.1 bits;  conditional E-value: 0.00019
                            AAA_12 102 llkkgsee..erkkigvitpYraqv.ellkkklkekeeekseke...........................ievntv 148
                                       l+kk s+     ++i  ++ Y +++ +++ +++++ ++++  +                            i+++t 
  gi|474934609|ref|YP_007688191.1| 618 LVKKKSRIinLVSSIFAVCGYDNDItQTILSEIASMHRNNLLTIsdiikiieydideesdynvdsipednvITIQTL 694
                                       55555444444455666666655532334444443222222211344445555555555566777788888****** PP

                            AAA_12 149 dgfQGrekdviilslVRsnekk...............................................eigflkde 178
                                        +  G e  ++i+  V ++ +k                                                 +  +++
  gi|474934609|ref|YP_007688191.1| 695 HKSKGLEYPIVIIPYVNKKGSKfplnqgdrinyvlndlaglrckkivegdgnnfwnlenwrtyvankykPDSYNEER 771
                                       ******************96667777889999999999***************************999534467777 PP

                            AAA_12 179 rrlNValTRAkskliivGn 197
                                       r l V ++RAk+ + ++ +
  gi|474934609|ref|YP_007688191.1| 772 RLLFVGISRAKQYVTMIAH 790
                                       8889********9999876 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.5   0.00031      0.35     113     176 ..       7      73 ..       2      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00031
                          PRTase_2 113 edeellaaakelvLvDDEistGktal...nliralqeklprkryvvvslvdwrseedeaafaaleee 176
                                       ++++++++++ +v+vD    tGkta+   + ir lq+++  k +++++ ++   ee ++++a+  +e
  gi|474934609|ref|YP_007688191.1|   7 SQQRIVDTTEGIVVVDAGPGTGKTATvteRCIRILQKNIEGKDVIMMTFTNNAAEEMRQRIAKKIAE 73 
                                       678899999***************97222468888899999***********999988887765544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1057 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1041  (0.0580624); expected 358.6 (0.02)
Passed bias filter:                      743  (0.0414412); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.92u 0.30s 00:00:01.22 Elapsed: 00:00:00.50
# Mc/sec: 6378.65
//
Query:       gi|474934610|ref|YP_007688192.1|  [L=441]
Description: hypothetical protein TALC_01040 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.2   11.6   0.0       0.44   10.5   0.0    1.5  1  DUF4898   Domain of unknown function (DUF4898)


Domain annotation for each model (and alignments):
>> DUF4898  Domain of unknown function (DUF4898)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   2.5e-05      0.44      25      52 ..     321     348 ..     312     355 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 2.5e-05
                           DUF4898  25 sdyekffnfilPkdkkivvvvpsdlede 52 
                                        +y + f+f++P ++++ v v +d+   
  gi|474934610|ref|YP_007688192.1| 321 DNYDRSFRFFVPANSSFSVCVEYDMSAY 348
                                       6999********************9864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 2591.99
//
Query:       gi|474934611|ref|YP_007688193.1|  [L=320]
Description: hypothetical protein TALC_01041 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00015   21.8  15.2    0.00015   21.8  15.2    2.1  2  ABC2_membrane_4  ABC-2 family transporter protein
  ------ inclusion threshold ------
        7.9    6.0  37.0        3.3    7.2  30.2    2.8  2  ABC2_membrane_5  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8  15.2   1.7e-08   0.00015       9     175 ..      57     222 ..      52     226 .. 0.75
   2 ?   -5.8  13.1         2   1.8e+04      17     142 ..     186     303 ..     183     311 .. 0.62

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.7e-08
                   ABC2_membrane_4   9 lkrskivwllvlaallvpllallyfnllgktgldpaefyslsvfgftll..lllplilgiiasylifrEeqndtlkn 83 
                                       + r++ +w++++ +ll+p++  +  + l+++++ ++ +  +++ g+ +l  l+ +li  i ++ ++ +E+ + t+  
  gi|474934611|ref|YP_007688193.1|  57 FTRQRAMWVMLVFLLLIPVVY-FSLTSLSADAFGTTHVLNMYMAGILCLlpLMSMLIASISCGAMLPQEFNERTVYL 132
                                       56999**********999864.444566666766666666666666666334445555566777889********** PP

                   ABC2_membrane_4  84 LltiPvsrtklllaKlivllllsvllmlvtflitvlfallsgfvgfsvklvlellkkclelgllvffavlpiialvl 160
                                        l +P  r+ ++++K+++ l l+v ++ +++ i    a+++g+ +++v+ ++ l++ +++ ++ vf   +   +l++
  gi|474934611|ref|YP_007688193.1| 133 SLPLPLDRKIFFIGKFMAGLTLTVGVISAAYGI----AVFLGMQRTDVAYTADLFVSYIVSIAAVFNYCAFTYFLSS 205
                                       ******************999988887665544....4567888888888899999999888877777777778854 PP

                   ABC2_membrane_4 161 .lkk.syvlpliltlvy 175
                                          + s++lpli+ lv+
  gi|474934611|ref|YP_007688193.1| 206 rSARgSSMLPLIMMLVI 222
                                       3555378******9997 PP

  == domain 2  score: -5.8 bits;  conditional E-value: 2
                   ABC2_membrane_4  17 llvlaallvpllallyfnllgktgldpaefyslsvfgftlllllplilgiiasylifrEeqndtlknLltiPvsrtk 93 
                                        +v++a+++ + a++yf   ++++++ +++     +++ ++l++  +++ + +y +++   + + + L  +Pv  t 
  gi|474934611|ref|YP_007688193.1| 186 YIVSIAAVFNYCAFTYFL--SSRSARGSSM-----LPLIMMLVIIPVICTVLAYGMNKVGFEAGANALGYVPVFATD 255
                                       455555666666666653..3444443344.....343344444445555666777777777888999999999999 PP

                   ABC2_membrane_4  94 lllaKlivllllsvllmlvtflitvlfallsgfvgfsvklvlellkkcl 142
                                       + +  l + ++  + ++++  + +++  l+ gf++ +   ++ ++ + l
  gi|474934611|ref|YP_007688193.1| 256 MSMNMLGIPFI-GITFSFMGIMGSAISMLIPGFAVGTNYVIMVAVSIAL 303
                                       99987777766.7899999999999988888887665444444443333 PP

>> ABC2_membrane_5  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2  30.2   0.00037       3.3      32     194 ..      82     273 ..      54     285 .. 0.66
   2 ?   -3.5   7.4      0.68   6.1e+03     152     189 ..     263     303 ..     245     314 .. 0.45

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00037
                   ABC2_membrane_5  32 l...............ndsvllifsilslvisiililttlsyDekskwnkylltLPvtrkeiVksKYlfvlililia 93 
                                       +                 ++l ++ ++s++i++i +  +l ++ ++++ ++ l LP++rk   + K++ +l l++ +
  gi|474934611|ref|YP_007688193.1|  82 SlsadafgtthvlnmyMAGILCLLPLMSMLIASISCGAMLPQEFNERTVYLSLPLPLDRKIFFIGKFMAGLTLTVGV 158
                                       35555555333222222334445566667777776778888899999999************************999 PP

                   ABC2_membrane_5  94 ilitlllliiavlikgn.vtisevllsiliglvialiflaivlPlyfkfgvekgri..vliiiifgiifllvaifsl 167
                                       i   + +++  ++ +     + +++ s++++++ ++ ++a+++ l  +     + +  +++++i+ +i+ + a + +
  gi|474934611|ref|YP_007688193.1| 159 ISAAYGIAVFLGMQRTDvAYTADLFVSYIVSIAAVFNYCAFTYFLSSRSARGSSMLplIMMLVIIPVICTVLA-YGM 234
                                       99999999888888877655689999*****************999999965555454444444444332222.333 PP

                   ABC2_membrane_5 168 .........skl...elslidlsnyilliillviillli 194
                                                + l    ++ +d+s  +l i +++i++ ++
  gi|474934611|ref|YP_007688193.1| 235 nkvgfeagaNALgyvPVFATDMSMNMLGIPFIGITFSFM 273
                                       244555555222555777777777777777777765433 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 0.68
                   ABC2_membrane_5 152 iiifgiifllvaifsl...sklelslidlsnyilliillvi 189
                                       i ++gi f ++ i+ +   + +  + ++++++i++ +++++
  gi|474934611|ref|YP_007688193.1| 263 IPFIGITFSFMGIMGSaisMLIPGFAVGTNYVIMVAVSIAL 303
                                       33333333333333321212222223333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1226  (0.0683808); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.51
# Mc/sec: 1872.36
//
Query:       gi|474934612|ref|YP_007688194.1|  [L=340]
Description: ABC-type multidrug transport system, ATPase component [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.6e-31  108.2   0.0    7.3e-31  107.5   0.0    1.3  1  ABC_tran      ABC transporter
    3.3e-16   60.0   0.1    3.6e-09   36.9   0.0    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    2.6e-07   30.4   0.0    4.3e-07   29.7   0.0    1.2  1  AAA_27        AAA domain
    1.6e-06   27.7   0.1    3.6e-06   26.6   0.1    1.5  1  AAA_29        P-loop containing region of AAA domain
    2.3e-05   25.0   0.1    4.3e-05   24.1   0.1    1.4  1  AAA_23        AAA domain
     0.0012   18.3   0.1     0.0087   15.5   0.1    2.2  1  SMC_N         RecF/RecN/SMC N terminal domain
     0.0053   16.5   0.0      0.011   15.5   0.0    1.4  1  AAA_15        AAA ATPase domain
  ------ inclusion threshold ------
      0.019   14.7   0.1      0.033   13.9   0.1    1.5  1  AAA_30        AAA domain
      0.064   13.3   1.4        1.7    8.7   0.3    2.4  2  DUF87         Helicase HerA, central domain
      0.076   12.9   0.0       0.14   12.0   0.0    1.4  1  Rad17         Rad17 P-loop domain
      0.082   13.2   0.0       0.21   11.8   0.0    1.8  1  AAA_22        AAA domain
       0.19   11.1   0.7       0.56    9.6   0.2    2.0  2  Mg_chelatase  Magnesium chelatase, subunit ChlI


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.5   0.0   4.9e-34   7.3e-31       1     137 []      42     185 ..      42     185 .. 0.96

  Alignments for each domain:
  == domain 1  score: 107.5 bits;  conditional E-value: 4.9e-34
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       ++n+sl++k+ge ++i+G+nGaGKSt lk+++gll+pt+Gei ++g d ++  ++++  ++g++ ++pq  p+ + +
  gi|474934612|ref|YP_007688194.1|  42 VDNLSLSVKKGEFMGILGPNGAGKSTTLKAITGLLTPTSGEIFVNGIDARK--HREAMCHVGCVIETPQCYPKFSPA 116
                                       589******************************************999999..999999***************999 PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       e              e + +  ++l++l++  ++ +++      +S+G+kqrvala+all +p+++llDEpt+
  gi|474934612|ref|YP_007688194.1| 117 EMleyvgqihglsksEIQIRSRDVLEELRMWPWRGKNI----GGFSKGMKQRVALAAALLPNPDVILLDEPTS 185
                                       999********99777777799****************....*****************************96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.1   1.6e-07   0.00025       1      24 [.      54      77 ..      54      95 .. 0.78
   2 !   36.9   0.0   2.4e-12   3.6e-09     234     297 ..     154     214 ..     152     219 .. 0.95

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.6e-07
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllar 24
                                      ++++ GpNg+GKS+ L+a+ +l  
  gi|474934612|ref|YP_007688194.1| 54 FMGILGPNGAGKSTTLKAITGLLT 77
                                      689****************99963 PP

  == domain 2  score: 36.9 bits;  conditional E-value: 2.4e-12
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                       +  +S G+k+  al++all  +   +++l+DEp +gL+P+ + ++ ++l+ l+++g  ++++TH
  gi|474934612|ref|YP_007688194.1| 154 IGGFSKGMKQRVALAAALLPNP---DVILLDEPTSGLDPRGMIEIRQILNGLKQRGLTLMISTH 214
                                       6779***************999...9***********************999999********* PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   2.9e-10   4.3e-07       8      50 ..      33      76 ..      29      82 .. 0.92

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 2.9e-10
                            AAA_27  8 LeryGkftdr.sldfsaeeadlhliyGpNEAGKstalrAisdll 50
                                      ++ryG+ft   +l++s ++ ++  i+GpN AGKst+l+Ai+ ll
  gi|474934612|ref|YP_007688194.1| 33 VKRYGNFTAVdNLSLSVKKGEFMGILGPNGAGKSTTLKAITGLL 76
                                      589*****8548*****************************997 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.1   2.4e-09   3.6e-06      12      55 ..      42      86 ..      35      91 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 2.4e-09
                            AAA_29 12 fdghtieidlkgatlltGpsGsGKSTllDAiqalLvpak.kvrfN 55
                                       d+ +++++  +++ + Gp+G+GKST l Ai+ lL+p++ ++  N
  gi|474934612|ref|YP_007688194.1| 42 VDNLSLSVKKGEFMGILGPNGAGKSTTLKAITGLLTPTSgEIFVN 86
                                      455566777445999**********************99666666 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.1   2.9e-08   4.3e-05      11      50 ..      43      83 ..      33     110 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 2.9e-08
                            AAA_23 11 rdqeidFsk.gltlItGpNGaGKTTildAiklaLygetprl 50
                                      ++ ++  +k  +  I GpNGaGK+T l Ai+  L+  +++ 
  gi|474934612|ref|YP_007688194.1| 43 DNLSLSVKKgEFMGILGPNGAGKSTTLKAITGLLTPTSGEI 83
                                      55555555514668******************999766554 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   5.8e-06    0.0087      24      49 ..      52      77 ..      32     238 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.8e-06
                                      SSEEEEEESTTSSHHHHHHHHHHHCT CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 24 ksftaivGpNGSGKsnlldAilFvLG 49
                                       +f  i+GpNG+GKs  l Ai  +L 
  gi|474934612|ref|YP_007688194.1| 52 GEFMGILGPNGAGKSTTLKAITGLLT 77
                                      46999****************86666 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   7.3e-06     0.011      10      60 ..      38      85 ..      37      99 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.3e-06
                            AAA_15 10 NFRslkdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkviki 60
                                      NF + ++ ++++++  ++ + G+N++GKS+ l+a+  +l+ +    + +i++
  gi|474934612|ref|YP_007688194.1| 38 NFTAVDNLSLSVKKGeFMGILGPNGAGKSTTLKAITGLLTPT----SGEIFV 85
                                      8888999999999888*******************9999876....444444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   2.2e-05     0.033      18      51 ..      52      85 ..      44     183 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.2e-05
                            AAA_30 18 drvavltGpAGtGKttalkalreaweaaggrvig 51
                                        ++ + Gp G+GK+t+lka++ +++   g++++
  gi|474934612|ref|YP_007688194.1| 52 GEFMGILGPNGAGKSTTLKAITGLLTPTSGEIFV 85
                                      3488999***************999887666655 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.3    0.0011       1.7      26      44 ..      55      73 ..      34      85 .. 0.77
   2 ?    3.3   0.0     0.051        77     175     220 ..     228     270 ..     194     272 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0011
                             DUF87 26 lAilgsTGsGKSntvavLl 44
                                      ++ilg  G+GKS+t + + 
  gi|474934612|ref|YP_007688194.1| 55 MGILGPNGAGKSTTLKAIT 73
                                      89*************9986 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.051
                             DUF87 175 llrkggsfsnsstdliallleklekegkitiidlsgvdelaqqlvv 220
                                       ++++g++    s d+++l+  ++ +e+++ti dl  + +l+++ ++
  gi|474934612|ref|YP_007688194.1| 228 MINHGKQV--ISGDVNSLIHSVARDEKSVTI-DLRTIGSLTSDFYT 270
                                       67777777..899999999888999999999.***99999988766 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   9.6e-05      0.14      35      81 ..      42      89 ..      38     113 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.6e-05
                             Rad17 35 lkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklre.wlnpvs 81
                                      ++  +L  +k + + i GP G gkst++k ++  l++   e ++n++ 
  gi|474934612|ref|YP_007688194.1| 42 VDNLSLSVKKGEFMGILGPNGAGKSTTLKAITGLLTPTSGEiFVNGID 89
                                      566678888888999***************999888776553566666 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00014      0.21       6     117 ..      53     200 ..      48     219 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00014
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee..................erpevv.fvtlpsstsskdllrellra 63 
                                        ++ + G+ G+GK+t+l+ ++  l+                         +   v+ + ++  + s++++l+ + ++
  gi|474934612|ref|YP_007688194.1|  53 EFMGILGPNGAGKSTTLKAITGLLTPT----SgeifvngidarkhreamcHVGCVIeTPQCYPKFSPAEMLEYVGQI 125
                                       567799**************9998532....1335677888875544332222222444444444788888888777 PP

                            AAA_22  64 lglelka.................erlsseell.ealeqalrarav...ielliiDEaqh.lrseealeeLrslln 117
                                        gl++++                 ++++   +   + ++ + a+a    + ++++DE    l  ++ + e+r++ln
  gi|474934612|ref|YP_007688194.1| 126 HGLSKSEiqirsrdvleelrmwpwRGKNIGGFSkGMKQRVALAAALlpnPDVILLDEPTSgL-DPRGMIEIRQILN 200
                                       77777777777777777666666655555555533333333333336666777777766666.4555555555555 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.2   0.00037      0.56      11      52 ..      41      82 ..      32     141 .. 0.83
   2 ?   -1.1   0.0       0.7   1.1e+03      52     103 ..     190     241 ..     184     247 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00037
                      Mg_chelatase 11 akraleiaaaGgHnlllvGppGsGKtmlakrlpsllpplsee 52
                                      a   l +++  g  + ++Gp G+GK+   k++++ll+p s e
  gi|474934612|ref|YP_007688194.1| 41 AVDNLSLSVKKGEFMGILGPNGAGKSTTLKAITGLLTPTSGE 82
                                      555666666666677799******************998765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.7
                      Mg_chelatase  52 eealevakiasvagkkeeekllkrrpfraphhsaskaalvGggskpkpGeis 103
                                       + ++e+++i    +++  + ++++  +++  + +++++++  g+++  G++ 
  gi|474934612|ref|YP_007688194.1| 190 RGMIEIRQILNGLKQRGLTLMISTHILKEVSEMCTSVTMINHGKQVISGDVN 241
                                       5678888887777777778888889999999999999999999999999984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.59u 0.36s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 1936.03
//
Query:       gi|474934613|ref|YP_007688195.1|  [L=45]
Description: hypothetical protein TALC_01043 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 318.17
//
Query:       gi|474934614|ref|YP_007688196.1|  [L=88]
Description: hypothetical protein TALC_01044 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      0.006   16.4   0.0     0.0081   16.0   0.0    1.2  1  DUF2185   Protein of unknown function (DUF2185)
  ------ inclusion threshold ------
        1.6    8.9   7.7        1.7    8.8   2.5    2.1  2  DUF1206   Domain of Unknown Function (DUF1206)


Domain annotation for each model (and alignments):
>> DUF2185  Protein of unknown function (DUF2185)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   9.1e-07    0.0081      22      45 ..      34      57 ..      29      71 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 9.1e-07
                           DUF2185 22 peeenDSGWrffagdesdeyindk 45
                                       + +nDSGW f+++d +++y  + 
  gi|474934614|ref|YP_007688196.1| 34 IAADNDSGWEFYNDDVDHDYEINY 57
                                      4567***************96555 PP

>> DUF1206  Domain of Unknown Function (DUF1206)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.2    0.0096        86      47      64 ..       5      22 ..       3      31 .. 0.76
   2 ?    8.8   2.5   0.00019       1.7      47      69 ..      59      81 ..      58      82 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.0096
                           DUF1206 47 vllglvglgllgyglwql 64
                                      +++++++++++++g  +l
  gi|474934614|ref|YP_007688196.1|  5 IMIAALAVVFIAAGSASL 22
                                      567788888888876655 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00019
                           DUF1206 47 vllglvglgllgyglwqlveAvt 69
                                      +l +l+ +g+l++++++++ A++
  gi|474934614|ref|YP_007688196.1| 59 ILHILLTIGILAFAAYCVYLAIY 81
                                      6778999**************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 618.22
//
Query:       gi|474934615|ref|YP_007688197.1|  [L=871]
Description: ATPase, P-type (transporting), HAD superfamily, subfamily IC [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-40  138.7   1.0    1.5e-40  138.7   1.0    3.3  4  E1-E2_ATPase     E1-E2 ATPase
    1.3e-25   91.0   0.1      2e-25   90.3   0.1    1.3  1  Hydrolase        haloacid dehalogenase-like hydrolase
    0.00033   20.5   0.3     0.0015   18.4   0.4    2.0  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
    0.00053   19.6   0.1    0.00053   19.6   0.1    2.7  3  Cation_ATPase_N  Cation transporter/ATPase, N-terminus
     0.0015   18.6   0.1      0.014   15.5   0.1    2.3  2  HAD_2            Haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       1.2   4.2e+03     106     137 ..      27      58 ..      20      77 .. 0.61
   2 !  138.7   1.0   4.1e-44   1.5e-40       4     180 ..      96     273 ..      94     274 .. 0.98
   3 ?    1.6   0.4     0.048   1.7e+02      76     158 ..     559     641 ..     540     649 .. 0.77
   4 ?   -6.0   4.4         5   1.8e+04     120     139 ..     770     789 ..     737     824 .. 0.52

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.2
                                       ----HHHHHHHHHHHHHHHHHHHHHHHHHHS- CS
                      E1-E2_ATPase 106 skktplqkkldklgkvlvpvvlliallvflia 137
                                       ++++ l  +l++l   + ++ ++i++++++++
  gi|474934615|ref|YP_007688197.1|  27 ASQSYLSIFLRNLLTPFNIILFVIGAALLAFH 58 
                                       55666667777777777666666666666554 PP

  == domain 2  score: 138.7 bits;  conditional E-value: 4.1e-44
                                       --EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-S.EEE-TTTS---S-EE-G-TTEE-TT-EEEE- CS
                      E1-E2_ATPase   4 pptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsa.evdesaLTGEslpvekekgdmvfsGtvvvsg 79 
                                        p+a+v+rdg+ + id +++v+GDiv l agd+ ++Dg+i+e+ + e+des+LTGEs  v+k+ g+ ++sG+v v g
  gi|474934615|ref|YP_007688197.1|  96 RPKATVVRDGKDTVIDRADIVMGDIVHLCAGDQAQVDGEIIEERSiEMDESLLTGESNTVRKHPGEVIYSGSVCVTG 172
                                       689************************************************************************** PP

                                       EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHH CS
                      E1-E2_ATPase  80 eakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralallv 156
                                       e+ + V ++g++t+ + +++++++ ++k+tplqk+ + ++++l++v+++++++++++  ++g++ ++ ++r  ++++
  gi|474934615|ref|YP_007688197.1| 173 ECWFQVNKVGNETFSSNMTAAAKKVERKTTPLQKETNAVTEFLIIVAFFFMFVLAILDAVRGDFEIDGFIRQAVIVL 249
                                       ***********************************************************************999999 PP

                                       HHS-TTHHHHHHHHHHHHHHHHHH CS
                      E1-E2_ATPase 157 aaiPcaLplavplalalgarrlak 180
                                        ++P+aL l+++l+++++a  +a+
  gi|474934615|ref|YP_007688197.1| 250 DIVPIALFLLITLTYMIAAVHMAD 273
                                       *******************99986 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.048
                                       EEE-EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHH CS
                      E1-E2_ATPase  76 vvsgeakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallral 152
                                         sg a++v+  + ++  +  + +++ e k++ +++  +l+ + +  +++++++++l++ +  +   +++++l+ ++
  gi|474934615|ref|YP_007688197.1| 559 TASGAARGVADMILMKDDFTALPKAIVEGKRTVSSMRDILRLYLARNFVLMFIVLVLLIGLDKVPLLPIQNTLYAFI 635
                                       56788888888888888888888888888888888888888888887777777777777776666666668888888 PP

                                       HHHHHH CS
                      E1-E2_ATPase 153 allvaa 158
                                       ++ +aa
  gi|474934615|ref|YP_007688197.1| 636 TVSIAA 641
                                       888887 PP

  == domain 4  score: -6.0 bits;  conditional E-value: 5
                                       HHHHHHHHHHHHHHHHS-ST CS
                      E1-E2_ATPase 120 kvlvpvvlliallvfliall 139
                                       + + p++l++++++ l+a++
  gi|474934615|ref|YP_007688197.1| 770 RRYLPTMLALLMFASLVAVY 789
                                       33444444444443333333 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.3   0.1   5.5e-29     2e-25       1     209 [.     290     551 ..     290     552 .. 0.82

  Alignments for each domain:
  == domain 1  score: 90.3 bits;  conditional E-value: 5.5e-29
                                       SSEEEEESBTTTBCHHHHHHHHHHHH.......CHHHHHHHHHHHHCHHHHHHHHHHHHH.HHHHHHHHHETTTE.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx.. RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsa.......alalaaaletgsehpigkalvaaakar.sgaltgfatfigrg.. 67 
                                       ++tv++Dk+GT+tt + + edv+ +         l +  a  tgs+     a+++ + +   + l++++ + +r   
  gi|474934615|ref|YP_007688197.1| 290 VDTVCMDKTGTITTNNLVFEDVFYYTddrersdRLIREFASTTGSRNKTVIAIQEHFGEAeCELLDEIQFSSERKfs 366
                                       68********************9999999666655555566666777777777444444434444555555555566 PP

                                       ...........HHHHTHHHHHHHH.HCHHHHHHHHHHHHHHCHHHHHH.................TTHHHHHHHHHH CS
                                       ...........xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx.................xxxxxxxxxxxx RF
                         Hydrolase  68 ...........ayaigkpewltal.dippdlgaaigsaqsqgrtvall.................qaralavftiad 115
                                                  ++ +g    l+++ + +  ++++i+++ ++g  +++l                 +  + av++i d
  gi|474934615|ref|YP_007688197.1| 367 avrvksedhedTIVMGAWSVLKKHtKNTGGVEEKIDELSAAGLRSVVLfdggrsvlhmndeiylpELTVFAVIAIRD 443
                                       6667778888899999999999999**********************************99999999********** PP

                                       THHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT..........GGGESEEEEHHCES...........S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxx...........x RF
                         Hydrolase 116 plkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG..........ddyfdaviasdiet...........v 171
                                       +  v+p+ +e ++++ ++g +v +++gdnp t+e++ + +           d     ++++  e+           +
  gi|474934615|ref|YP_007688197.1| 444 E--VRPDCKEIIHQFTSNGMDVKVISGDNPDTVEALFSLAEipgerkrisgD-----ELSQMSEEmfdktvletniF 513
                                       *..********************************99999999998555532.....33333333444446667888 PP

                                       TTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 172 akpspegkvaaireLqgkpeevamVGDgvnDaaalaaA 209
                                       +  +pe+k+++i+ L+ +++ vamVGDgvnD+  +++A
  gi|474934615|ref|YP_007688197.1| 514 GRMKPEQKERVIDSLKRNGRYVAMVGDGVNDVRSIKKA 551
                                       888*************99999************99988 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.58   2.1e+03      16      49 ..     445     478 ..     442     486 .. 0.83
   2 !   18.4   0.4   4.1e-07    0.0015     193     254 ..     522     583 ..     487     584 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.58
                                       --HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHH CS
                       Hydrolase_3  16 isektkeaikklkekgikvviATGRslravlpvl 49 
                                       + +  ke+i+++ ++g+ v + +G ++ +v+ ++
  gi|474934615|ref|YP_007688197.1| 445 VRPDCKEIIHQFTSNGMDVKVISGDNPDTVEALF 478
                                       6778899************999999888887766 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 4.1e-07
                                       HHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GGGTHHHHH CS
                       Hydrolase_3 193 kklakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnnedGVaka 254
                                       ++++  l+ +   v+ +GDg ND+  +++a +gv m+ as  +  +Ad++  + +  ++ ka
  gi|474934615|ref|YP_007688197.1| 522 ERVIDSLKRNGRYVAMVGDGVNDVRSIKKAQVGVSMETASGAARGVADMILMKDDFTALPKA 583
                                       6788889999999************************************9988777666665 PP

>> Cation_ATPase_N  Cation transporter/ATPase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   1.5e-07   0.00053      19      67 ..       4      52 ..       2      54 .. 0.96
   2 ?   -4.0   0.3       3.6   1.3e+04      56      67 ..     738     749 ..     737     749 .. 0.86
   3 ?   -0.3   0.1      0.25   8.9e+02      48      69 .]     766     787 ..     763     787 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.5e-07
                   Cation_ATPase_N 19 nGLtqaeaaerlkkyGpNelkekkkkslwvkllkqftnplvilLlvaal 67
                                      +GLt++e++er k   +N  + +  +s++ ++l+++  p+ i+L+v ++
  gi|474934615|ref|YP_007688197.1|  4 TGLTEQEVQERSKAGMRNGEEGRASQSYLSIFLRNLLTPFNIILFVIGA 52
                                      7********************************************9876 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 3.6
                   Cation_ATPase_N  56 nplvilLlvaal 67 
                                       n ++++L++a++
  gi|474934615|ref|YP_007688197.1| 738 NAMLLFLMMAGI 749
                                       88999***9986 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.25
                   Cation_ATPase_N  48 vkllkqftnplvilLlvaalvs 69 
                                       +++++ +   ++ lL++a+lv+
  gi|474934615|ref|YP_007688197.1| 766 KQFVRRYLPTMLALLMFASLVA 787
                                       5889999999*********995 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.17   6.2e+02      73     130 ..     386     444 ..     324     476 .. 0.65
   2 !   15.5   0.1     4e-06     0.014     111     174 ..     493     554 ..     444     557 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.17
                             HAD_2  73 kkkkevkpydgvkelLeeLkeagyklgivTsksreaveekle.qlgiesyFdvivtsed 130
                                         kk++k   gv+e ++eL++ag++  +  ++ r+++ ++ e  l   ++F vi + ++
  gi|474934615|ref|YP_007688197.1| 386 VLKKHTKNTGGVEEKIDELSAAGLRSVVLFDGGRSVLHMNDEiYLPELTVFAVIAIRDE 444
                                       33346888889999999998888877776666555554433312333355555555555 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 4e-06
                             HAD_2 111 ekleqlgiesyFdvivtsedvekk.KPdpeviekaleklklkkeeviyvGDsptDieaakkagik 174
                                       ++l+q+  e++Fd+ v +++++++ K  pe  e+++++lk +   v +vGD  +D+ + kka + 
  gi|474934615|ref|YP_007688197.1| 493 DELSQMS-EEMFDKTVLETNIFGRmK--PEQKERVIDSLKRNGRYVAMVGDGVNDVRSIKKAQVG 554
                                       5666666.89****999999876658..56669****************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (871 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       902  (0.0503096); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.69u 0.28s 00:00:00.97 Elapsed: 00:00:00.68
# Mc/sec: 3870.40
//
Query:       gi|474934616|ref|YP_007688198.1|  [L=252]
Description: hypothetical protein TALC_01046 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00011   22.8   0.0     0.0013   19.3   0.0    2.1  1  RNase_T   Exonuclease


Domain annotation for each model (and alignments):
>> RNase_T  Exonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   7.2e-08    0.0013       2     164 ..      20     229 ..      19     230 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 7.2e-08
                                       EEEEEESSSTT................................CTTS-EEEEEEEEEETTCC......EEEEEEEEE CS
                           RNase_T   2 viDlEttglda................................kekdeiieiaaisidggen......eigetfhfy 40 
                                       v+D+Ettgl+                                    d ++ i+  +++ ++       + +  +++ 
  gi|474934616|ref|YP_007688198.1|  20 VLDTETTGLKGglydrdpnadpffrrsrlddrggsgydsldwtRYGDLVVDIGICEVCLSTGevkevySSIVGYDTE 96 
                                       78899999988888899999999999999999999998888884466666666666666655334335444445555 PP

                                       EEHSSHCSSSHHHHHHHHHCHHHHHTCEBHHHHHHHHHHHHHHHTCCCETTTCEEEESSHHHHHHHHHHHHHHHHHC CS
                           RNase_T  41 vkptelakltdecteftgitqemldeapsfkevleefkellrklallvahnaafdvgflraadkrilkkevpkrnqf 117
                                         p+e+  l  ++ + +  t  ++  ap f +v ++++++++ ++ l  +n+ fd+    + +  +lk  +++  ++
  gi|474934616|ref|YP_007688198.1|  97 NWPEEM--LHSWIFDNSDLTVGQVSSAPRFSKVKKDIASIVK-GRWLTTYNVQFDLDLFIYRFPWNLKDSFMECRDI 170
                                       668888..999*******************************.999999**************99999999955555 PP

                                       SEHCECHHHHHHHHHC......HHHHHHHHHTTCHSSSS......TSSHHHHHHHHHHH CS
                           RNase_T 118 ldtlildkatlkelar......tsldklaeklgleedgr......aHrAldDaeatakl 164
                                         +++ +++  + l++       +ld++ e++++ ed         HrAl+Da+ + ++
  gi|474934616|ref|YP_007688198.1| 171 MFSARDVCKLESPLYGvkeyryPKLDYAYETILKGEDPAgidgvqDHRALSDAKVASYV 229
                                       5555555554444444456666788888887777776666666678*******998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1496.22
//
Query:       gi|474934617|ref|YP_007688199.1|  [L=63]
Description: hypothetical protein TALC_01047 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0013   18.7   0.0     0.0016   18.4   0.0    1.1  1  ThiS-like  ThiS-like ubiquitin
     0.0042   17.7   0.0     0.0048   17.5   0.0    1.0  1  ThiS       ThiS family
  ------ inclusion threshold ------
      0.063   13.3   0.1       0.14   12.2   0.1    1.7  2  Fer2_4     2Fe-2S iron-sulfur cluster binding domain


Domain annotation for each model (and alignments):
>> ThiS-like  ThiS-like ubiquitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   2.7e-07    0.0016       3      55 ..       4      58 ..       3      59 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.7e-07
                         ThiS-like  3 IklNekeveveegttlealkekikpdaD..vvIlNGFpikeDteLkegDevflIk 55
                                      +++N+k++e   g t+e+  +++  + D  +++l+G p+  D ++++g +v  Ik
  gi|474934617|ref|YP_007688199.1|  4 VTVNGKTIEAAVGETIEDTIRNSGFNPDafLFVLDGKPVPMDSPIEDGWNVRAIK 58
                                      79*************998766655555555******************9998887 PP

>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0     8e-07    0.0048       1      77 []       4      63 .]       4      63 .] 0.97

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 8e-07
                                      EEETTCCHHHHTCEEEEESSTSBHHHHHHHHHHHTCHHGTTTTEEEEETTEEEGCCTTTSB--TTCEEEEEESTTC- CS
                              ThiS  1 vllfaelrelageeelelaegstvaelleaLgerypelalerrvavavNgeivprlwldtelkdgDevailppVaGG 77
                                      v+++++  e+a         g+t+++ +++ g++       + + + ++g+ vp    d ++ dg  v  + + +GG
  gi|474934617|ref|YP_007688199.1|  4 VTVNGKTIEAAV--------GETIEDTIRNSGFNP------DAFLFVLDGKPVPM---DSPIEDGWNVRAIKVASGG 63
                                      789999999999........***************......**************...*****************99 PP

>> Fer2_4  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   2.3e-05      0.14       5      29 ..       3      27 ..       1      47 [. 0.88
   2 ?   -1.5   0.0      0.46   2.7e+03      70      78 ..      47      55 ..      36      58 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.3e-05
                            Fer2_4  5 tltfDGkevtvpeGdtvasAllang 29
                                      t+t++Gk++++  G+t+ + + + g
  gi|474934617|ref|YP_007688199.1|  3 TVTVNGKTIEAAVGETIEDTIRNSG 27
                                      89***************99887776 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.46
                            Fer2_4 70 pvedGlkve 78
                                      p+edG +v+
  gi|474934617|ref|YP_007688199.1| 47 PIEDGWNVR 55
                                      566666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 390.81
//
Query:       gi|474934618|ref|YP_007688200.1|  [L=277]
Description: Cobyric acid synthase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-13   49.3   0.0    6.7e-13   48.8   0.0    1.1  1  CbiA      CobQ/CobB/MinD/ParA nucleotide binding domain
    1.8e-09   37.7   0.0    2.7e-07   30.6   0.0    2.0  2  AAA_26    AAA domain
  ------ inclusion threshold ------
       0.02   14.2   0.1      0.036   13.4   0.1    1.4  2  VirC1     VirC1 protein
       0.11   12.4   0.1       0.51   10.2   0.0    1.9  2  MobB      Molybdopterin guanine dinucleotide synthesis protei


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.0   1.5e-16   6.7e-13       1     115 [.       4     225 ..       4     234 .. 0.94

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 1.5e-16
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH.HTTEB-HHHH...................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx...................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai.leglendiep...................... 54 
                                       i++ +t++G+GKTtl a  +r l ++g++V++++a + + n+ +  +g+e+   +                      
  gi|474934618|ref|YP_007688200.1|   4 ILFLGTSSGAGKTTLDAVYCRHLVKKGKKVAPFKASNLSLNSYVtEDGKEIGMGQafqawasgieptgdmnpvllkp 80 
                                       6789******************************9999999986766666666669999****************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|474934618|ref|YP_007688200.1|  81 sgngrmqvvlrgelfmdigqgkdfdrdaimekaaesydrllseydvvvcegsgspaelnlqardlanvgmmrarnip 157
                                       ***************************************************************************** PP

                                       .....CCHCCCHHHHHHCHCHHHH........EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE-- CS
                                       .....xxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 .....dlkrllellealgkkkall......lkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprd 115
                                            d++r +++++a++++   l       +++ +++nr++g+     lk++++++++ +g+++ gv+p+ 
  gi|474934618|ref|YP_007688200.1| 158 cvlvaDIER-GGVFAAIYGTWL-LipedvrHLMKAFIINRFRGD--ASILKSGIDRIEELTGMKCAGVVPYE 225
                                       *********.********9943.36999999999**********..9999******99888*********96 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   0.0    0.0033        15       3      37 ..       4      38 ..       2      83 .. 0.84
   2 !   30.6   0.0   6.1e-11   2.7e-07      88     192 ..     110     226 ..      86     228 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0033
                            AAA_26  3 ifvtgtdtgvGKTvvslgLvralkrkgvkvgyfKP 37
                                      i+  gt+ g+GKT++ +  +r l +kg kv+ fK 
  gi|474934618|ref|YP_007688200.1|  4 ILFLGTSSGAGKTTLDAVYCRHLVKKGKKVAPFKA 38
                                      77789*************************99985 PP

  == domain 2  score: 30.6 bits;  conditional E-value: 6.1e-11
                            AAA_26  88 lekiv...kelekdadivvVEGagglg..vpiteellnadiaknlgapvilVargglg.tinqllltiealrqknvr 158
                                       +ek     ++l  ++d+vv+EG+g+    + ++++l n+ ++++ ++p +lVa +++g  +++++ t+ +  + +vr
  gi|474934618|ref|YP_007688200.1| 110 MEKAAesyDRLLSEYDVVVCEGSGSPAelNLQARDLANVGMMRARNIPCVLVADIERGgVFAAIYGTWLLIPE-DVR 185
                                       4444455599**************99843458899********************996267777777777765.454 PP

                            AAA_26 159 ..vlGvilNkvrnpe.....nvetlekksgipvlGvvPylp 192
                                          ++ i+N++r ++      ++ +e+ +g++  GvvPy++
  gi|474934618|ref|YP_007688200.1| 186 hlMKAFIINRFRGDAsilksGIDRIEELTGMKCAGVVPYET 226
                                       457889********556666******************975 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   7.9e-06     0.036       4      40 ..       4      40 ..       1      56 [. 0.85
   2 ?   -3.9   0.0       1.5   6.7e+03      72      99 ..     110     139 ..     108     141 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.9e-06
                             VirC1  4 itfcslkGGaGkttalmglcsalasdgkrvalfeade 40
                                      i f     GaGktt     c  l+ +gk+va f+a +
  gi|474934618|ref|YP_007688200.1|  4 ILFLGTSSGAGKTTLDAVYCRHLVKKGKKVAPFKASN 40
                                      56666778*************************9964 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 1.5
                             VirC1  72 leaayeeae..geGfdyaladtrgGsseln 99 
                                       +e+a e  +  ++ +d+++ +  g  +eln
  gi|474934618|ref|YP_007688200.1| 110 MEKAAESYDrlLSEYDVVVCEGSGSPAELN 139
                                       566655554224678888888888888887 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00011      0.51       2      38 ..       5      41 ..       4      53 .. 0.82
   2 ?   -0.9   0.0      0.31   1.4e+03      82      98 ..     114     131 ..      99     135 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00011
                              MobB  2 lgivgksgsGKTtLleklipelkarglrvgtiKhahh 38
                                      l +   sg+GKTtL     ++l ++g +v+  K ++ 
  gi|474934618|ref|YP_007688200.1|  5 LFLGTSSGAGKTTLDAVYCRHLVKKGKKVAPFKASNL 41
                                      4555679***********************9998765 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.31
                              MobB  82 eellarl.sevDlvlvEG 98 
                                       +e  +rl se+D+v+ EG
  gi|474934618|ref|YP_007688200.1| 114 AESYDRLlSEYDVVVCEG 131
                                       33344444778****999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 2163.54
//
Query:       gi|474934619|ref|YP_007688201.1|  [L=607]
Description: cobyric acid synthase CobQ [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-45  155.8   0.1    1.6e-45  155.1   0.1    1.4  1  GATase_3  CobB/CobQ-like glutamine amidotransferase domain
    4.6e-21   74.5  13.5    9.2e-21   73.6  13.5    1.4  1  zf-like   Cysteine-rich small domain
    4.7e-13   49.4   0.1      5e-12   46.1   0.1    2.1  1  AAA_26    AAA domain
    1.2e-11   44.8   0.0    2.5e-11   43.7   0.0    1.5  1  CbiA      CobQ/CobB/MinD/ParA nucleotide binding domain
    8.6e-05   22.4   0.0    0.00021   21.1   0.0    1.6  1  GATase    Glutamine amidotransferase class-I
  ------ inclusion threshold ------
       0.04   13.2   0.0       0.33   10.2   0.0    2.2  2  DUF1611   Domain of unknown function (DUF1611_C) P-loop domai
       0.17   11.7   0.0       0.32   10.8   0.0    1.3  1  SNO       SNO glutamine amidotransferase family


Domain annotation for each model (and alignments):
>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.1   0.1   6.4e-49   1.6e-45       1     195 [.     365     551 ..     365     552 .. 0.89

  Alignments for each domain:
  == domain 1  score: 155.1 bits;  conditional E-value: 6.4e-49
                          GATase_3   1 kiavirlpaisnytdldpLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggp 77 
                                       +i v++lp+i+n+tdldpL ++++  v++++ +  ++++ ad++++pG+k+ti+dl +++e+g+ +aik++   ++p
  gi|474934619|ref|YP_007688201.1| 365 RISVVKLPRIANFTDLDPL-YTEDTTVIYAE-TPAEIES-ADAIVIPGTKNTIDDLGWMKETGIFDAIKRMK-GKVP 437
                                       699****************.66889999999.8999966.******************************65.69** PP

                          GATase_3  78 vlgiCGGlqmLGeeiedpegvegeag.eveglglLdietefek.ekltgqvegevelaaegeevkGyEiHsGrtilk 152
                                       +lgiCGG+qm+G+ ++dp+g+eg++    eglg++d e   ++ +k++  ++ ++e+ + g +++GyEiH+G +   
  gi|474934619|ref|YP_007688201.1| 438 ILGICGGYQMMGKVLHDPNGIEGRVAgDTEGLGFFDNESYWGEyKKRV--IRDHAEMIEGGGQIEGYEIHMGMSEI- 511
                                       ***********************6655***************987777..44554467778***********6665. PP

                          GATase_3 153 ekakpllkvkvggnngekdGavkksedgnvlGtYlHglfdnrn 195
                                        ++kpl+++++ g++g+++G v  +ed+ ++GtY+Hg++d+ +
  gi|474934619|ref|YP_007688201.1| 512 -REKPLFRITNVGRKGDTEGSV--REDEMLYGTYIHGVLDKPA 551
                                       .569*****87666669*****..78************99865 PP

>> zf-like  Cysteine-rich small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.6  13.5   3.6e-24   9.2e-21       5      73 ..      18      87 ..      15      92 .. 0.92

  Alignments for each domain:
  == domain 1  score: 73.6 bits;  conditional E-value: 3.6e-24
                           zf-like  5 fsnkeCeyyPCHktedenClfCyCPlYaledeelGefveteng..kvkdCskCllvHkkevadellkklke 73
                                       +n+eC+y+PCH+ +++nC+fCyCP+Y++ede lG f+e+++g   v++C +Cl+ H++ev++   +k++e
  gi|474934619|ref|YP_007688201.1| 18 HCNRECDYHPCHF-KGQNCSFCYCPFYPCEDEDLGYFMESRHGgnPVWACDDCLFCHRNEVVEFTFEKIRE 87
                                      689**********.9*************************998888***************9988888776 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   0.1   1.9e-15     5e-12       1     191 [.     114     341 ..     114     344 .. 0.80

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 1.9e-15
                            AAA_26   1 rtifvtgtdtgvGKTvvslgLvralkrkgvkvgyfKPiqtgie.....ededselike....llgldqtyelpepla 68 
                                       r+++v+g + ++GK+++ ++L r+l+r+g+ ++ fK  +  ++     ++++ + i+     ++gl+ +  +++p++
  gi|474934619|ref|YP_007688201.1| 114 RAVMVVGATSDAGKSLTVAALGRILHRRGYLAAPFKSQNMSLNskvsvRGGEMAMIQMlqaqAMGLTVPDMHMNPIL 190
                                       689*********************************987777766666455444444444459999999999***** PP

                            AAA_26  69 lsaplspelaarqeg....edidlekiv................kelekdadivvVEGagglgvp.itee.llnadi 123
                                       l+    +++++   +     d d++++                 + l+  +d+vv EGag+  +  i ++   n   
  gi|474934619|ref|YP_007688201.1| 191 LKPK-GNTVSQVMVEgkpfGDYDVADYYgkfvpnegveivrrnvEFLKRHYDLVVMEGAGSPAEInIYDKdIANMGA 266
                                       *854.333333332223447888888878888*********9977789999**********9976255554567777 PP

                            AAA_26 124 aknlgapvilVarggl.gtinqllltiealr.qknvrvlGvilNkvrnp.....envetlekksgipvlGvvPyl 191
                                       a+  +a  ilV++++  g+++ +l t+ ++  +  +r++G+ilN+vr +        ++le   gipv+G++P+ 
  gi|474934619|ref|YP_007688201.1| 267 ARIADANCILVVNVEWgGSFAYALGTARLMPeEDRKRIKGIILNNVRGDvskmrSGADELERIAGIPVIGIIPHM 341
                                       8888**********99569*********996255779************7766559*****************85 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   0.0   9.8e-15   2.5e-11       1     115 [.     116     341 ..     116     349 .. 0.89

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 9.8e-15
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH.HTTEB-HHHH...................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx...................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai.leglendiep...................... 54 
                                       +++++ ++++GK+ ++a+L+r+l rrg+  ++++ ++++ n+++ + g e+   +                      
  gi|474934619|ref|YP_007688201.1| 116 VMVVGATSDAGKSLTVAALGRILHRRGYLAAPFKSQNMSLNSKVsVRGGEMAMIQmlqaqamgltvpdmhmnpillk 192
                                       689****************************************99677776666679999***************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|474934619|ref|YP_007688201.1| 193 pkgntvsqvmvegkpfgdydvadyygkfvpnegveivrrnveflkrhydlvvmegagspaeiniydkdianmgaari 269
                                       ***************************************************************************** PP

                                       .........CCHCCCHHHHHHCHCHHHH........EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE-- CS
                                       .........xxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 .........dlkrllellealgkkkall......lkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprd 115
                                                +++ ++ ++ alg+  + l       +i+g++ln v+g+    +++++ +el++  g+pv+g+ip  
  gi|474934619|ref|YP_007688201.1| 270 adancilvvNVEWGGSFAYALGTA-R-LmpeedrKRIKGIILNNVRGD--VSKMRSGADELERIAGIPVIGIIPHM 341
                                       *99999888554444444444433.2.13566668*************..999999999998655********975 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   8.1e-08   0.00021      27      88 ..     391     452 ..     380     515 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 8.1e-08
                                       EETTSHHHHHHHTHHSTSEEEEEEESSCTT......TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHT CS
                            GATase  27 vpidasaeeilellknpdgilvsgGpgspg......vegkieaikearenkiPiLGICLGmQllaief 88 
                                       +  +++ae+     +++d+i+++g  ++         +g  +aik++ + k+PiLGIC G Q++++ +
  gi|474934619|ref|YP_007688201.1| 391 IYAETPAEI-----ESADAIVIPGTKNTIDdlgwmkETGIFDAIKRMKG-KVPILGICGGYQMMGKVL 452
                                       444444444.....479999999998888888888888999*****999.**************9876 PP

>> DUF1611  Domain of unknown function (DUF1611_C) P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00013      0.33      11      52 ..     112     153 ..     104     178 .. 0.84
   2 ?   -0.2   0.0       0.2     5e+02     155     192 ..     301     338 ..     291     342 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00013
                           DUF1611  11 kakrvlvvGTdcavGKrttaleleealeerGlkaafvaTgqt 52 
                                       +++ v+vvG  +++GK  t  +l + l +rG+ aa +    +
  gi|474934619|ref|YP_007688201.1| 112 PGRAVMVVGATSDAGKSLTVAALGRILHRRGYLAAPFKSQNM 153
                                       6789***************************98887666555 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.2
                           DUF1611 155 kkkvvgislNtknlseeeakealeeleeelglpvvdpv 192
                                       +k++ gi lN    +  ++++ ++ele+  g+pv  ++
  gi|474934619|ref|YP_007688201.1| 301 RKRIKGIILNNVRGDVSKMRSGADELERIAGIPVIGII 338
                                       34799****************************98765 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00012      0.32      26      85 ..     394     452 ..     376     458 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00012
                                       -SGGGGCC-SEEEE-SS-HHHHHH.HHHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCEE CS
                               SNO  26 krkedlaevdaliiPGGestamsk.liertglyedllefvknsekvvlGtCaGlillskel 85 
                                        ++ +++  da++iPG   t   +  +++tg++++++ +  +++ ++lG C G  ++ k l
  gi|474934619|ref|YP_007688201.1| 394 ETPAEIESADAIVIPGTKNTIDDLgWMKETGIFDAIKRM--KGKVPILGICGGYQMMGKVL 452
                                       56788999********9998665436999**99999765..5668********98887755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (607 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.47
# Mc/sec: 3854.50
//
Query:       gi|474934620|ref|YP_007688202.1|  [L=214]
Description: hypothetical protein TALC_01050 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00046   20.0   0.4     0.0018   18.2   0.1    2.2  2  zinc_ribbon_4    zinc-ribbon domain
     0.0049   16.9   0.2      0.008   16.2   0.2    1.3  1  UPF0547          Uncharacterised protein family UPF0547
     0.0096   15.7   0.1      0.026   14.3   0.1    1.7  1  zinc_ribbon_5    zinc-ribbon domain
  ------ inclusion threshold ------
      0.034   13.5   0.1      0.062   12.7   0.1    1.4  1  zf-ribbon_3      zinc-ribbon domain
      0.097   13.4   0.0       0.36   11.5   0.0    2.0  1  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
       0.12   11.8   0.0       0.29   10.6   0.0    1.6  1  Mu-like_Com      Mu-like prophage protein Com
       0.13   12.1  21.5       0.53   10.2   0.2    5.2  5  PKcGMP_CC        Coiled-coil N-terminus of cGMP-dependent pro
       0.21   11.8   6.3       0.56   10.4   6.2    1.7  1  Binary_toxB_3    Clostridial binary toxin B/anthrax toxin PA 
       0.55   10.6   6.8        1.6    9.2   1.0    2.2  2  RNA_pol_A_bac    RNA polymerase Rpb3/RpoA insert domain
        0.9   10.0  12.0       0.37   11.3   4.4    2.5  2  PhoU             PhoU domain
        1.2    8.8  16.9        1.5    8.5  16.9    1.1  1  AAA_15           AAA ATPase domain
        1.7    8.9  20.6       0.81   10.0   4.6    3.1  3  DUF641           Plant protein of unknown function (DUF641)
        2.1    7.6  13.2          3    7.1  13.2    1.3  1  DUF4407          Domain of unknown function (DUF4407)
        4.7    6.5  20.0        1.6    8.0  16.4    2.1  2  FAM76            FAM76 protein
        8.3    6.6   6.4         16    5.7   6.4    1.6  1  MetallophosC     C terminal of Calcineurin-like phosphoestera


Domain annotation for each model (and alignments):
>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   1.5e-06    0.0018       3      18 ..       4      19 ..       3      28 .. 0.83
   2 ?   -2.6   0.0       4.5   5.3e+03      14      28 ..      61      75 ..      60      76 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.5e-06
                     zinc_ribbon_4  3 itCpsCkakyeiddek 18
                                      i Cp+C+++++id++ 
  gi|474934620|ref|YP_007688202.1|  4 IKCPHCGTVFQIDEND 19
                                      99***********985 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.5
                     zinc_ribbon_4 14 iddeklpakgvkvrC 28
                                      i +e l +++  ++C
  gi|474934620|ref|YP_007688202.1| 61 IHAELLNKTREQLTC 75
                                      777888888888888 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.2   6.7e-06     0.008      16      25 ..       5      14 ..       2      15 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6.7e-06
                           UPF0547 16 fCphCGyvFq 25
                                      +CphCG+vFq
  gi|474934620|ref|YP_007688202.1|  5 KCPHCGTVFQ 14
                                      8********8 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   2.2e-05     0.026       3      18 ..       4      19 ..       3      30 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.2e-05
                     zinc_ribbon_5  3 irCpdCdtkFklvdsk 18
                                      i+Cp C+t F++++  
  gi|474934620|ref|YP_007688202.1|  4 IKCPHCGTVFQIDEND 19
                                      89*********99876 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   5.2e-05     0.062       2      25 ..       3      12 ..       2      18 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.2e-05
                       zf-ribbon_3  2 tvrCPnCGaplssddnvCpyCGtk 25
                                      +++CP+CG+              +
  gi|474934620|ref|YP_007688202.1|  3 EIKCPHCGT--------------V 12
                                      455555555..............4 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0    0.0003      0.36       3      28 ..       4      32 ..       2      41 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0003
                           zf-ISL3  3 hrCPnCgsk...tvvkhgkkerrvrhlpi 28
                                      ++CP+Cg +      + +k  ++vr+  +
  gi|474934620|ref|YP_007688202.1|  4 IKCPHCGTVfqiDENDYSKIVSQVRDAEF 32
                                      78*******85555888889999999887 PP

>> Mu-like_Com  Mu-like prophage protein Com
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00024      0.29      24      33 ..       3      12 ..       2      18 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00024
                       Mu-like_Com 24 tiKCPRCGtL 33
                                      +iKCP CGt+
  gi|474934620|ref|YP_007688202.1|  3 EIKCPHCGTV 12
                                      59*******7 PP

>> PKcGMP_CC  Coiled-coil N-terminus of cGMP-dependent protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.3         3   3.6e+03      11      21 ..      34      44 ..      34      51 .. 0.58
   2 ?   10.2   0.2   0.00045      0.53      13      34 ..      73      94 ..      67      94 .. 0.90
   3 ?    0.7   0.2      0.41   4.9e+02      19      27 ..     108     116 ..      95     119 .. 0.74
   4 ?    9.5   1.1   0.00071      0.84      15      32 ..     140     157 ..     135     158 .. 0.91
   5 ?    4.1   0.2     0.036        43      14      25 ..     175     186 ..     168     186 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3
                         PKcGMP_CC 11 RELEkrlaekd 21
                                      +E+E r++  +
  gi|474934620|ref|YP_007688202.1| 34 KEMEFRVQHYE 44
                                      67887776433 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00045
                         PKcGMP_CC 13 LEkrlaekdeEIqELrskLDKf 34
                                      L + ++ +d  I++L++k D f
  gi|474934620|ref|YP_007688202.1| 73 LTCEINSRDRQIADLKAKIDQF 94
                                      7899***************977 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.41
                         PKcGMP_CC  19 ekdeEIqEL 27 
                                        kd EI++L
  gi|474934620|ref|YP_007688202.1| 108 AKDREIADL 116
                                       488888887 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.00071
                         PKcGMP_CC  15 krlaekdeEIqELrskLD 32 
                                       ++++ kd EI +Lr + D
  gi|474934620|ref|YP_007688202.1| 140 EQINSKDREIDDLRHQMD 157
                                       589************998 PP

  == domain 5  score: 4.1 bits;  conditional E-value: 0.036
                         PKcGMP_CC  14 EkrlaekdeEIq 25 
                                       E++l+ kd+E++
  gi|474934620|ref|YP_007688202.1| 175 EAQLKAKDDEVE 186
                                       89********95 PP

>> Binary_toxB_3  Clostridial binary toxin B/anthrax toxin PA domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   6.2   0.00047      0.56      18     101 ..      92     179 ..      83     180 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00047
                                       SSS-EEEEEE-B-SSSTGGGGS--EBHHHH.....HHHTT-..-B-SSSS-EETTEEGGGEEEEE-HHHHHHHHHHH CS
                     Binary_toxB_3  18 dgsllerriaavdPddpneltkPdltlgea.....lekavG..aeeekeklsykdesidevdfifdrrtekkikkel 87 
                                       d+ +le+ +a +  +d ++    dl  +++      ++a+    +e+ e+++ kd +id+++   d+   +ki k++
  gi|474934620|ref|YP_007688202.1|  92 DQFELEKSMAVKKVEDAKDREIADLVAKQSnweneKRLALSeaEKEKIEQINSKDREIDDLRHQMDQ---EKITKKI 165
                                       5567788888888888888888888777653222223444410345557888899999999988886...69***** PP

                                       HTTT-SSTTTGGGG CS
                     Binary_toxB_3  88 eelkakniydvtir 101
                                       e+ + kn+y+ +++
  gi|474934620|ref|YP_007688202.1| 166 EQENMKNLYEAQLK 179
                                       **********9987 PP

>> RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.5     0.031        37      30      91 ..      28      90 ..      11     105 .. 0.74
   2 ?    9.2   1.0    0.0013       1.6      17      82 ..     127     191 ..     124     197 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.031
                                      HHHHHHHCTT-ETSSSSTTCSEEEEEEEEESSECEEGGGCBES..SSSCEESSTTSEEEEEETT CS
                     RNA_pol_A_bac 30 leillnlkelveeeeegeeeksvelkLnvkgpgevtagdlkle..dadveivnpdilIakLrkg 91
                                      ++  +++ke+++  +++e ek+  ++L++   +++ a+ l+    + ++ei ++d  Ia L+ +
  gi|474934620|ref|YP_007688202.1| 28 RD-AEFSKEMEFRVQHYEREKEDAISLTKAEGERIHAELLNKTreQLTCEINSRDRQIADLKAK 90
                                      33.467777763456777777779*****99999******987556678899999999999865 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0013
                                       CHHHCSTCBSSCHHHHHHHHCTT-.ETSSSSTTCSEEEEEEEEESSECEEGGGCBESSSSCEESSTT CS
                     RNA_pol_A_bac  17 Hrlgliplvsedvleillnlkelv.eeeeegeeeksvelkLnvkgpgevtagdlkledadveivnpd 82 
                                        rl+l +  +e++ +   n+k+ +  +  ++ ++++++ k++ ++ ++ + ++lk +d++ve   + 
  gi|474934620|ref|YP_007688202.1| 127 KRLALSEAEKEKIEQ--INSKDREiDDLRHQMDQEKITKKIEQENMKNLYEAQLKAKDDEVEFYTDR 191
                                       588999999999999..6777765447889999999*************************998665 PP

>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   1.0       0.1   1.2e+02      24      58 ..      71     105 ..      59     132 .. 0.64
   2 ?   11.3   4.4   0.00031      0.37      18      58 ..     130     170 ..     125     184 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.1
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG- CS
                              PhoU  24 telarevierddeidrlekeiersllealakrqpl 58 
                                       + l  e+ +rd++i +l  +i+   le+ +  +++
  gi|474934620|ref|YP_007688202.1|  71 EQLTCEINSRDRQIADLKAKIDQFELEKSMAVKKV 105
                                       35557899999999999988855555554443333 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00031
                                       HHHCT-HHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHGG- CS
                              PhoU  18 aleekdtelarevierddeidrlekei.ersllealakrqpl 58 
                                       al+e ++e ++++ ++d+eid+l++++ ++++ +++ +++ +
  gi|474934620|ref|YP_007688202.1| 130 ALSEAEKEKIEQINSKDREIDDLRHQMdQEKITKKIEQEN-M 170
                                       799999*****************99996677676665433.3 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5  16.9    0.0012       1.5     126     278 ..      15     175 ..      10     203 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0012
                            AAA_15 126 lkknelsdekisvekkkskkelpkekeeklekekeelkidkedlkklikkleeslkkee........elknvlksai 194
                                       +++n++s+   +v + + +ke +   ++++ ++++ ++++k + +++  +l +++ ++         +    lk++i
  gi|474934620|ref|YP_007688202.1|  15 IDENDYSKIVSQVRDAEFSKEMEFRVQHYEREKEDAISLTKAEGERIHAELLNKTREQLtceinsrdRQIADLKAKI 91 
                                       45555666666666666666666677788888888999998888888887777777777888888888899999999 PP

                            AAA_15 195 ikllli..sakRnvsdedsekkssllgklkekileealqekleeelteklkeiqeklkeidkklaeelkkilkkkid 269
                                       ++++l   +a+++v+d ++ ++ +l  k+ ++ +e+ l   l+e  +ek+++i++k +eid+   +  +++++kki+
  gi|474934620|ref|YP_007688202.1|  92 DQFELEksMAVKKVEDAKDREIADLVAKQSNWENEKRL--ALSEAEKEKIEQINSKDREIDDLRHQMDQEKITKKIE 166
                                       99999722578999999999999999999999988644..3466666666666666666666665556666666666 PP

                            AAA_15 270 kikkfnykg 278
                                       + ++ n  +
  gi|474934620|ref|YP_007688202.1| 167 QENMKNLYE 175
                                       654322222 PP

>> DUF641  Plant protein of unknown function (DUF641)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   4.6   0.00068      0.81      46     123 ..      23      99 ..      14     104 .. 0.78
   2 ?    4.8   5.5     0.029        35      82     122 ..     124     163 ..     103     169 .. 0.72
   3 ?    1.3   0.5      0.33     4e+02      90     110 ..     167     187 ..     158     191 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00068
                            DUF641  46 vvseLkklselkrlyrkkqkkkaseaeeseleaeiqeqrsllktyeitvkkleaelkakdseieeLkekLeeaeksn 122
                                       +vs+ +     k++ ++ q+ +++ +e++   ++++ +r   + +++t ++l  e++++d +i  Lk+k+++ e ++
  gi|474934620|ref|YP_007688202.1|  23 IVSQVRDAEFSKEMEFRVQHYERE-KEDAISLTKAEGERIHAELLNKTREQLTCEINSRDRQIADLKAKIDQFELEK 98 
                                       677777777777765554444444.67777778888899999*****************************988776 PP

                            DUF641 123 k 123
                                       +
  gi|474934620|ref|YP_007688202.1|  99 S 99 
                                       5 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.029
                            DUF641  82 eqrsllktyeitvkkleaelkakdseieeLkekLeeaeksn 122
                                       e+ + l+  e+  +k+e ++++kd ei+ L++++++++  +
  gi|474934620|ref|YP_007688202.1| 124 ENEKRLALSEAEKEKIE-QINSKDREIDDLRHQMDQEKITK 163
                                       35566667777777775.89**************9987654 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.33
                            DUF641  90 yeitvkkleaelkakdseiee 110
                                       +e + +  ea+lkakd e+e 
  gi|474934620|ref|YP_007688202.1| 167 QENMKNLYEAQLKAKDDEVEF 187
                                       45666777999*****99986 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1  13.2    0.0025         3     130     221 ..      58     171 ..      23     193 .. 0.57

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0025
                           DUF4407 130 a..............ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk..........gtgttgvaGkg 182
                                                      lt e++  ++qia+l+a+id+ e + + + +++++  d +               +++    
  gi|474934620|ref|YP_007688202.1|  58 GerihaellnktreqLTCEINSRDRQIADLKAKIDQFELEKSMAVKKVEDAKDREIadlvakqsnwE--NEKRLALS 132
                                       2444444533333337777777777777777777776666666666666666655455555554321..22345555 PP

                           DUF4407 183 paakekkaqldaaqaelaelkakldatarlaalraelae 221
                                       +a kek +q++ +++e+++l+ ++d+++ +++ ++e  +
  gi|474934620|ref|YP_007688202.1| 133 EAEKEKIEQINSKDREIDDLRHQMDQEKITKKIEQENMK 171
                                       555667788888888888888886633333333333332 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.94   1.1e+03      32      52 ..       3      23 ..       1      32 [. 0.77
   2 ?    8.0  16.4    0.0013       1.6     176     294 ..      39     158 ..      11     166 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.94
                             FAM76 32 vvkCtyCrsefqqesketsti 52
                                       +kC +C + fq ++++ s+i
  gi|474934620|ref|YP_007688202.1|  3 EIKCPHCGTVFQIDENDYSKI 23
                                      589999999999888775555 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0013
                             FAM76 176 skkh..kkrssrlevskleeeklaeekesnetskk.sldsnssdhlvavtqLkeeias..lkkqleqkdqellekdk 247
                                       + +h  ++++  ++ +k+e e+  +++  n+t+++ +++ ns d+  ++++Lk +i +  l+k ++ k +e  +kd+
  gi|474934620|ref|YP_007688202.1|  39 RVQHyeREKEDAISLTKAEGER-IHAELLNKTREQlTCEINSRDR--QIADLKAKIDQfeLEKSMAVKKVE-DAKDR 111
                                       2222112333345555555333.3443444443333666666665..778999999753389999999877.79*** PP

                             FAM76 248 kitelkaellekekelreklkelekeakekieklekkirellkevae 294
                                       +i++l a++ + e+e r  l+e eke  e+i++ +++i +l++++ +
  gi|474934620|ref|YP_007688202.1| 112 EIADLVAKQSNWENEKRLALSEAEKEKIEQINSKDREIDDLRHQMDQ 158
                                       *****************************************998765 PP

>> MetallophosC  C terminal of Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   6.4     0.013        16      51     151 ..      99     186 ..      10     192 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.013
                      MetallophosC  51 qmrlyapgevkkgakk......akknsvvvnvwngdpgwkVevyedgkalemervseeDpvvletydelsakkarke 121
                                       +m +           k      ++  ++v++  n++++ ++ ++e  k++ +e+++++D ++       ++ +++++
  gi|474934620|ref|YP_007688202.1|  99 SMAVK----------KvedakdREIADLVAKQSNWENEKRLALSEAEKEK-IEQINSKDREI-------DDLRHQMD 157
                                       33333..........033333356789999999**********9998888.99999999833.......33334443 PP

                      MetallophosC 122 alrkkarlaepkkssHlfeaklssgtktve 151
                                        ++k ++ +e+++++ l+ea+l++++ +ve
  gi|474934620|ref|YP_007688202.1| 158 -QEKITKKIEQENMKNLYEAQLKAKDDEVE 186
                                       .344444456678899*******9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2520  (0.140554); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 1360.23
//
Query:       gi|474934621|ref|YP_007688203.1|  [L=242]
Description: Iron-regulated ABC transporter ATPase subunit SufC [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      8e-20   71.8   0.0    1.2e-19   71.2   0.0    1.3  1  ABC_tran     ABC transporter
    4.2e-07   30.1   0.2     0.0035   17.2   0.2    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    4.9e-05   23.0   0.0    0.00012   21.8   0.0    1.6  1  AAA_29       P-loop containing region of AAA domain
    0.00015   22.4   1.0    0.00027   21.5   1.0    1.7  1  AAA_23       AAA domain
    0.00031   20.2   0.3     0.0053   16.2   0.1    2.2  2  SMC_N        RecF/RecN/SMC N terminal domain
     0.0025   17.8   0.1     0.0038   17.2   0.1    1.2  1  RsgA_GTPase  RsgA GTPase
     0.0035   16.9   0.1     0.0094   15.5   0.1    1.7  2  AAA_25       AAA domain
  ------ inclusion threshold ------
      0.013   14.7   0.1      0.018   14.2   0.1    1.2  1  DAP3         Mitochondrial ribosomal death-associated protein
      0.014   15.0   0.0      0.026   14.1   0.0    1.4  1  AAA_27       AAA domain
      0.022   14.7   0.1      0.035   14.0   0.1    1.3  1  NACHT        NACHT domain
      0.022   14.5   0.2      0.066   12.9   0.1    1.7  2  AAA_15       AAA ATPase domain
      0.038   14.1   0.0      0.047   13.7   0.0    1.2  1  Dynamin_N    Dynamin family
      0.039   14.3   0.1      0.064   13.6   0.1    1.3  1  AAA_16       AAA ATPase domain
      0.075   12.9   0.0       0.12   12.3   0.0    1.3  1  ATPase_2     ATPase domain predominantly from Archaea
      0.088   12.9   0.2       0.11   12.6   0.2    1.5  1  MMR_HSR1     50S ribosome-binding GTPase
       0.15   12.4   0.4       0.23   11.9   0.4    1.6  1  AAA          ATPase family associated with various cellular a
       0.16   11.7   0.1       0.25   11.1   0.1    1.3  1  IstB_IS21    IstB-like ATP binding protein
       0.18   11.8   0.3       0.38   10.8   0.3    1.5  1  TsaE         Threonylcarbamoyl adenosine biosynthesis protein
       0.22   10.3   0.0       0.32    9.7   0.0    1.2  1  Adeno_IVa2   Adenovirus IVa2 protein


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.2   0.0   1.2e-22   1.2e-19       1     136 [.      19     159 ..      19     160 .. 0.87

  Alignments for each domain:
  == domain 1  score: 71.2 bits;  conditional E-value: 1.2e-22
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHT..TSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlklla..gllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpel 74 
                                       lk v+++l+ege+ +++G+nG+GKStLl+ ++  g++k t+G+i+++g+d+++    ++++  ig++ q p    ++
  gi|474934621|ref|YP_007688203.1|  19 LKGVTMNLEEGETCVLFGPNGSGKSTLLASIMgyGMTKVTSGTITFKGTDITHmPVDQRAKLGIGMMMQRPPNVIGV 95 
                                       789****************************72257888**************7677788889*******8888888 PP

                                       BHHHH.....HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  75 tvren.....esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       t+++      +  +  +   ++++++++ ++ v      +SgG+ +r +l ++ ++ p++++lDEp 
  gi|474934621|ref|YP_007688203.1|  96 TLGSLvaataKNGKGKAGKENEFKMQDFMNRDV---NVGFSGGEIKRSELLQLSAQSPDFVMLDEPE 159
                                       888888776544444777788999999999998...679**************************95 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.2   3.7e-06    0.0035       3      19 ..      33      49 ..      32      71 .. 0.80
   2 !   11.1   0.0   0.00027      0.25     252     297 ..     145     198 ..     142     204 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.7e-06
                            AAA_21  3 vliGpNgsGKSnLLdal 19
                                      vl GpNgsGKS+LL  +
  gi|474934621|ref|YP_007688203.1| 33 VLFGPNGSGKSTLLASI 49
                                      89************877 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00027
                            AAA_21 252 lralkkgsllliDEpEngLHPkllrrll....ell.....kelsr..ngaQviltTH 297
                                       l+a  +++++ +DEpE+g + + +  +     el+         +  +g+  ++ TH
  gi|474934621|ref|YP_007688203.1| 145 LSAQ-SPDFVMLDEPESGVDLENIGLIGrkvhELIygnedAV--EreKGVSAFVITH 198
                                       4444.44**************999666655558887775333..1468899999999 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   1.2e-07   0.00012      13      41 ..      20      48 ..      17      52 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.2e-07
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDA 41
                                      +g t+++++ ++++l Gp+GsGKSTll +
  gi|474934621|ref|YP_007688203.1| 20 KGVTMNLEEGETCVLFGPNGSGKSTLLAS 48
                                      567888886669**************955 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   1.0   2.9e-07   0.00027      12      59 ..      21      70 ..      16     188 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.9e-07
                            AAA_23 12 dqeidFskglt.lItGpNGaGKTTildAik.laLygetprlsrksgrgfe 59
                                      +++ +++ g t +++GpNG+GK+T+l  i  ++++  t+++ + +g+++ 
  gi|474934621|ref|YP_007688203.1| 21 GVTMNLEEGETcVLFGPNGSGKSTLLASIMgYGMTKVTSGTITFKGTDIT 70
                                      55666655433289************999767888888777666665555 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   5.6e-06    0.0053      20      48 ..      24      50 ..      14      64 .. 0.76
   2 ?    2.0   0.0      0.13   1.2e+02     160     185 ..     151     176 ..     118     213 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.6e-06
                                      EETTSSEE.EEEESTTSSHHHHHHHHHHHC CS
                                      xxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 20 lpfsksft.aivGpNGSGKsnlldAilFvL 48
                                      ++++++ t ++ GpNGSGKs ll +i   +
  gi|474934621|ref|YP_007688203.1| 24 MNLEEGETcVLFGPNGSGKSTLLASI---M 50
                                      555555441678*************9...3 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.13
                                       SEEEECTTTTTS-HHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 160 plyllDeidaaLDeknvkkvaellke 185
                                        +++lDe ++  D +n+  + + ++e
  gi|474934621|ref|YP_007688203.1| 151 DFVMLDEPESGVDLENIGLIGRKVHE 176
                                       4999************9999887765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1     4e-06    0.0038      83     122 ..      12      52 ..       3      71 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4e-06
                                       -TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  83 saktkegleelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                       +a  +e l+ ++ +l++ +t+vl G+ G GKStL+ ++++ 
  gi|474934621|ref|YP_007688203.1|  12 EAGGREILKGVTMNLEEgETCVLFGPNGSGKSTLLASIMGY 52 
                                       555566777788889888******************99985 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   9.9e-06    0.0094      30      54 ..      26      50 ..       9      77 .. 0.85
   2 ?   -3.0   0.0       4.7   4.4e+03     174     190 ..     184     200 ..     177     201 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 9.9e-06
                            AAA_25 30 lpagelallaGapgtGKttlaldla 54
                                      l +ge+++l+G+ g+GK+tl+ +++
  gi|474934621|ref|YP_007688203.1| 26 LEEGETCVLFGPNGSGKSTLLASIM 50
                                      589*****************99875 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.7
                            AAA_25 174 riarrtgaavllvhHvg 190
                                        ++r++g+  +++ H+g
  gi|474934621|ref|YP_007688203.1| 184 AVEREKGVSAFVITHTG 200
                                       56789999999999997 PP

>> DAP3  Mitochondrial ribosomal death-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   1.9e-05     0.018      24      50 ..      30      56 ..      17      65 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.9e-05
                                      -EEEEE-SSSSSTTTTHHHHHHHGGGS CS
                              DAP3 24 krlvltGekgsGKSvlLlqalayAlek 50
                                      +  vl G +gsGKS+lL+ ++ y+++k
  gi|474934621|ref|YP_007688203.1| 30 ETCVLFGPNGSGKSTLLASIMGYGMTK 56
                                      5689********************997 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.7e-05     0.026       6      59 ..       9      60 ..       4      71 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.7e-05
                            AAA_27  6 LdLeryGkftdrsldfsaeeadlhliyGpNEAGKstalrAisdllfGipertkd 59
                                      L++e+ G+   + ++++ ee +  +++GpN +GKst+l++i    +G+ + t+ 
  gi|474934621|ref|YP_007688203.1|  9 LHVEAGGREILKGVTMNLEEGETCVLFGPNGSGKSTLLASIM--GYGMTKVTSG 60
                                      555555554444455555678889***************995..4777776665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   3.7e-05     0.035       2      21 ..      31      50 ..      30      55 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.7e-05
                                      CEEEEC-TTTCHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqkla 21
                                      +++l G++GsGK+tLl++++
  gi|474934621|ref|YP_007688203.1| 31 TCVLFGPNGSGKSTLLASIM 50
                                      7999**************98 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1     7e-05     0.066      14      43 ..      19      49 ..      17      55 .. 0.87
   2 ?   -1.9   0.0       2.2     2e+03     320     333 ..     146     159 ..     136     161 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7e-05
                            AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsileal 43
                                      lk v+++l+e  + vl G+N+sGKS++l  +
  gi|474934621|ref|YP_007688203.1| 19 LKGVTMNLEEGeTCVLFGPNGSGKSTLLASI 49
                                      566889999986779************9877 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.2
                            AAA_15 320 keeknvilliEEPE 333
                                       + +++++++++EPE
  gi|474934621|ref|YP_007688203.1| 146 SAQSPDFVMLDEPE 159
                                       567899*******9 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0     5e-05     0.047       2      41 ..      33      83 ..      32     156 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5e-05
                                      EEEEBTTTTHHHHHHHHHTS--S---SSS---S-EEEEE...........C CS
                         Dynamin_N  2 avvGsqSsGKSSvlnaLlgedilprgpnptTrrplelql...........g 41
                                      +++G   sGKS++l +++g  +  + ++ +T + + +++           g
  gi|474934621|ref|YP_007688203.1| 33 VLFGPNGSGKSTLLASIMGYGMTKVTSGTITFKGTDITHmpvdqraklgiG 83
                                      789***************************999999988555555555550 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   6.8e-05     0.064      23      45 ..      28      50 ..       9      74 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.8e-05
                            AAA_16 23 rpelvllsGesGvGKsslvrell 45
                                      ++e ++l G+ G+GKs+l+ +++
  gi|474934621|ref|YP_007688203.1| 28 EGETCVLFGPNGSGKSTLLASIM 50
                                      348999*************9876 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00013      0.12      16      40 ..      25      49 ..      16      54 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                          ATPase_2 16 erepneiyfiYGpegsGKtaLlkei 40
                                      + e+ e  +++Gp gsGK++Ll  i
  gi|474934621|ref|YP_007688203.1| 25 NLEEGETCVLFGPNGSGKSTLLASI 49
                                      45667889*************9877 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   0.00011      0.11       2      42 ..      32      75 ..      31     198 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                                      EEEEESTTSSHHHHHHHHHTS...TEEESSSTTSSSSEEEEEEE CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltge...kaivsdkpgtTrdinegrvk 42
                                      ++++G   +GKStL+ +++g    k+  + + ++ +di++  v+
  gi|474934621|ref|YP_007688203.1| 32 CVLFGPNGSGKSTLLASIMGYgmtKVTSGTITFKGTDITHMPVD 75
                                      6899***************9544477778888888888877776 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.4   0.00024      0.23       2      44 ..      33      79 ..      32     199 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00024
                                      EEESSTTSSHHHHHHHHHHH....HTHEEEEEETTTCSSSSTTHHHH CS
                               AAA  2 llyGppGtGKTllakavake....lgvefleisgsellskyvgesek 44
                                      +l+Gp G GK++l  +++      + +  ++++g++++ + v +++k
  gi|474934621|ref|YP_007688203.1| 33 VLFGPNGSGKSTLLASIMGYgmtkVTSGTITFKGTDITHMPVDQRAK 79
                                      79***************998543334567888888888765555544 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00026      0.25      44      69 ..      26      52 ..      17      71 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00026
                         IstB_IS21 44 iekkenivllGpsGvGKshlaia.lgv 69
                                      +e+ e +vl+Gp G GKs l ++ +g+
  gi|474934621|ref|YP_007688203.1| 26 LEEGETCVLFGPNGSGKSTLLASiMGY 52
                                      57889************9765541444 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.3    0.0004      0.38      18      54 ..      26      63 ..      10      70 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0004
                                      H..TEEEEEEESTTSSHHHHHHHHHHHTT------TTTT CS
                              TsaE 18 l..gdvilLeGdLGaGKTtlvrglakalgveevkSPTFt 54
                                      l  g++ +L G+ G+GK+tl  +++ ++g+++v+S T t
  gi|474934621|ref|YP_007688203.1| 26 LeeGETCVLFGPNGSGKSTLLASIM-GYGMTKVTSGTIT 63
                                      2447789**************9986.568999***9865 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00034      0.32      90     125 ..      32      67 ..      20      81 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00034
                        Adeno_IVa2  90 GviyGPtGsGksqllrnlissklisPiPetvifitP 125
                                        v++GP GsGks ll +++   + + +  t+ f   
  gi|474934621|ref|YP_007688203.1|  32 CVLFGPNGSGKSTLLASIMGYGMTKVTSGTITFKGT 67 
                                       589*****************9999999999988655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 1596.09
//
Query:       gi|474934622|ref|YP_007688204.1|  [L=405]
Description: ABC-type transport system involved in Fe-S cluster assembly, permease component [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-53  180.0   0.6    6.4e-53  179.6   0.6    1.2  1  UPF0051   Uncharacterized protein family (UPF0051)


Domain annotation for each model (and alignments):
>> UPF0051  Uncharacterized protein family (UPF0051)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.6   0.6   3.6e-57   6.4e-53       2     218 .]     155     378 ..     154     378 .. 0.95

  Alignments for each domain:
  == domain 1  score: 179.6 bits;  conditional E-value: 3.6e-57
                           UPF0051   2 qfertlivveegaevtiieeyagc............gvveifvgenAklkyvkvqnwsedavnlstkraeegrdakl 66 
                                       q+ +++i+v+++a++ ++   +gc            gv+e+++g+nA+l++++v++ws+++ + +++++  g+++++
  gi|474934622|ref|YP_007688204.1| 155 QNLHNIIIVGDDASCDMV---TGCttvhhandslhvGVSEMYIGNNASLSFTMVHSWSNQTAVRPRTNVIMGKNSNY 228
                                       788***************...888888888899999***********************9999999999899***** PP

                           UPF0051  67 elttvslggk.ltrkepsvelkgegaeaelnglylakgkqhldtrtkvdhngpntssrilskgvlkdearavfrgki 142
                                         ++v l     + + p++ l+ge++++++n++++a++++++dt+  +++n+pnt ++i+s++++  +++ + rgk+
  gi|474934622|ref|YP_007688204.1| 229 VNNYVVLDPVgTIQSFPNAFLNGENSRCSFNTMCIAHENSNIDTGGCAILNAPNTGAEIVSRNISY-GGKMIARGKL 304
                                       *******9883445589*************************************************.599******* PP

                           UPF0051 143 kvrkgaqktdahqenrnLllsdkaradtiPeleidaddvkasHgAtvGkideeqlfYLmsRGlseeeArrlivrgf 218
                                        v  +a +++ah e+++++l+d++  ++iPele++  dv ++H+A+vGki+++q+ YLm+RGls++eA ++ivrgf
  gi|474934622|ref|YP_007688204.1| 305 -V-GNAPGAKAHLECKSIILKDGGITHAIPELEATCADVDMTHEAAVGKIAQDQIDYLMTRGLSQDEAVSMIVRGF 378
                                       .5.55**********************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2512.86
//
Query:       gi|474934623|ref|YP_007688205.1|  [L=488]
Description: hypothetical protein TALC_01053 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (488 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       939  (0.0523733); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.48
# Mc/sec: 3081.40
//
Query:       gi|474934624|ref|YP_007688206.1|  [L=156]
Description: hypothetical protein TALC_01055 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1039.14
//
Query:       gi|474934625|ref|YP_007688207.1|  [L=152]
Description: putative exosome subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.6e-25   88.5   0.1    4.4e-25   88.3   0.1    1.1  1  RNA_binding  RNA binding


Domain annotation for each model (and alignments):
>> RNA_binding  RNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.3   0.1   2.5e-29   4.4e-25       2     118 ..       8     119 ..       7     120 .. 0.96

  Alignments for each domain:
  == domain 1  score: 88.3 bits;  conditional E-value: 2.5e-29
                                       EEEEEEE-TTC-HHHHHHHHHTTSTTSE---EEEEEE-CCC-EEEEEEEEESSHHH.HHHHHHHHHHHCCCCHHHHH CS
                       RNA_binding   2 ievrafvhaTEdeekVlealsnllpeeeveieeeeaeGhygnpitileaelekkka.kkvlkkllellreeeikeLl 77 
                                       ++v++f++aTE+e+ V+e+++++  ++  e+++  +e+ +gn+++il+a ++k+++ ++v+ +l ++l+ e    ++
  gi|474934625|ref|YP_007688207.1|   8 LRVETFCYATEKEDLVAETFASVSGTD--EFRTDISESEHGNQMLILQAMMTKQREqDAVFVNLGQKLTGE----IS 78 
                                       689**********************88..59999**********************************988....9* PP

                                       HCCHCCB-TTSEEEEEEEHHHHHTT---BESSSSEEEEEEE CS
                       RNA_binding  78 keleervdekgklylrldKQaaylgklslvegddvIkvkik 118
                                       ++ e++vd+++++ylrldKQ+a+ g++++++++dvI+v+ k
  gi|474934625|ref|YP_007688207.1|  79 EKAEDMVDDDCVFYLRLDKQKAVCGEYAIAHHGDVISVTGK 119
                                       **************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1065.62
//
Query:       gi|474934626|ref|YP_007688208.1|  [L=427]
Description: Hemolysins-related protein containing CBS domains [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.7e-49  166.2   1.0    9.6e-49  165.5   1.0    1.3  1  DUF21      Cyclin M transmembrane N-terminal domain
    1.8e-15   56.7   1.6    5.4e-15   55.2   0.4    2.3  2  CorC_HlyC  Transporter associated domain
    1.2e-09   38.5   6.3    1.2e-05   25.7   0.4    3.7  4  CBS        CBS domain
      0.007   16.4   0.1      0.019   15.0   0.1    1.7  1  AgrD       Staphylococcal AgrD protein
     0.0091   16.1   0.9      0.073   13.2   0.3    2.4  2  CtsR_C     CtsR C-terminal dimerization domain


Domain annotation for each model (and alignments):
>> DUF21  Cyclin M transmembrane N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.5   1.0   2.7e-52   9.6e-49       2     176 .]      11     190 ..      10     190 .. 0.96

  Alignments for each domain:
  == domain 1  score: 165.5 bits;  conditional E-value: 2.7e-52
                             DUF21   2 iivlllllsaffsgaEtAlvslsrlrleelaekgk.kkakrllkllknperlLstlligntlvnillsalatalfve 77 
                                       ++v+ll+lsaffs+ EtA++s+sr+rl++++ +g+ +k +r+l   ++ +r+L+t+l+gn++vni++s++ ta+++e
  gi|474934626|ref|YP_007688208.1|  11 LMVVLLALSAFFSATETAYSSMSRTRLKSMDPDGEnRKVQRALANSEDFDRFLTTILVGNNIVNIASSTICTAILSE 87 
                                       789******************************9867788888888899**************************** PP

                             DUF21  78 llaegalavviatvivtllilvfgEilPkslalkyaekialalapplrvlmvllyPlvwllskllnlil.....ese 149
                                       +++  +++v+ atv++ +++lv+gEi+Pk++a+k+ae+++ ++++ ++++mv+l+P++w++ kl+ ++       + 
  gi|474934626|ref|YP_007688208.1|  88 VFG-PEWGVIYATVLMITVLLVVGEITPKTFAKKNAERFSIRVSGTVHWVMVILSPITWVFLKLTHGVSrvagaDGV 163
                                       ***.58********************************************************************99* PP

                             DUF21 150 sepavseeelkklveeseeegvieeee 176
                                       +ep+++e+el  +++e ++eg++e++e
  gi|474934626|ref|YP_007688208.1| 164 EEPTITEDELAVMIDEIQQEGTLEKSE 190
                                       ************************987 PP

>> CorC_HlyC  Transporter associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.27   9.8e+02      32      56 ..     313     337 ..     292     341 .. 0.75
   2 !   55.2   0.4   1.5e-18   5.4e-15       2      78 ..     340     416 ..     339     419 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.27
                                       -SBHHHHHHHHH-S---TT-EEEEE CS
                         CorC_HlyC  32 yeTlgGlllellgriPkegesvevd 56 
                                       + T+ + l el g+i +eg++v++ 
  gi|474934626|ref|YP_007688208.1| 313 MVTMEDVLEELVGEIYDEGDVVRYP 337
                                       4577778888999999999977775 PP

  == domain 2  score: 55.2 bits;  conditional E-value: 1.5e-18
                                       EECTTEEEEETT-BHHHHHHHHTSTTHHCT-S..BHHHHHHHHH-S---TT-EEEEEETTEEEEEEEEETTCEEEEE CS
                         CorC_HlyC   2 eldegsylvdGslpldeleeelglelpeedye..TlgGlllellgriPkegesvevdleglrftVlemdgrrIkkvr 76 
                                       ++++g+y+v G++++ e+ e lg +++e++y+  ++gG++  + +riP++g+  evd +++r++V+++ +rrI++v 
  gi|474934626|ref|YP_007688208.1| 340 KEPDGTYTVLGDANIFEVMEKLGQRFDEDEYDsvSVGGYIYYKEQRIPQVGD--EVDAGNVRMIVKSIRNRRIREVT 414
                                       678**************************9998899****************..99988*****************8 PP

                                       EE CS
                         CorC_HlyC  77 ve 78 
                                       + 
  gi|474934626|ref|YP_007688208.1| 415 FV 416
                                       75 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   2.1e-05     0.076       1      54 [.     205     261 ..     205     264 .. 0.81
   2 !   25.7   0.4   3.3e-09   1.2e-05       1      56 [.     270     324 ..     270     325 .. 0.83
   3 ?   -0.2   0.0      0.39   1.4e+03      11      25 ..     347     361 ..     331     374 .. 0.79
   4 ?   -2.1   0.1       1.5   5.4e+03      20      39 ..     400     420 ..     396     420 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.1e-05
                                       HHHHSBS..SCEEEETTSBHHHHHHHHHHHTSSEEEEEETTT..BEEEEEEHHHHHHH CS
                               CBS   1 Vgdimtr..dvvtvppdttleealelmrekgvsrlPVVdedg..klvGivtlrDllra 54 
                                       V++i+t+  d+  vp + ++e   e ++e+ +sr+PV  e    +++G v l+D +++
  gi|474934626|ref|YP_007688208.1| 205 VEEICTPrvDMTAVPVTIDMESMKEVFAETQYSRIPVY-EGTidRVIGAVFLKDFFSK 261
                                       7889888445589999999999999998888*******.333668*****99998875 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 3.3e-09
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEE.ETTTBEEEEEEHHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVV.dedgklvGivtlrDllrall 56 
                                       V+di  r+v +vp +t l+ +l+ + ++++ +l +V d++g  vG+vt++D+l+ l+
  gi|474934626|ref|YP_007688208.1| 270 VTDI-IRPVKFVPASTMLSTVLNDLQKAKL-HLAIVlDDYGGTVGMVTMEDVLEELV 324
                                       5666.5888999*************66668.665544****************9986 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.39
                                       EEETTSBHHHHHHHH CS
                               CBS  11 tvppdttleealelm 25 
                                       tv  d+++ e++e++
  gi|474934626|ref|YP_007688208.1| 347 TVLGDANIFEVMEKL 361
                                       8888999*****998 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 1.5
                                       HHHHHHHHHTSSEE.EEEETT CS
                               CBS  20 ealelmrekgvsrl.PVVded 39 
                                        +++ +r+++++ + +V+ded
  gi|474934626|ref|YP_007688208.1| 400 MIVKSIRNRRIREVtFVIDED 420
                                       566778777799888999876 PP

>> AgrD  Staphylococcal AgrD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   5.3e-06     0.019       9      38 ..      61      92 ..      58      93 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.3e-06
                              AgrD  9 dFiTtIL..kfIGtvAadSvCdsifDEvEVPk 38
                                       F+TtIL  ++I ++A+  +C  i+ Ev  P+
  gi|474934626|ref|YP_007688208.1| 61 RFLTTILvgNNIVNIASSTICTAILSEVFGPE 92
                                      7******778*****************97665 PP

>> CtsR_C  CtsR C-terminal dimerization domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.3     2e-05     0.073      16      48 ..     167     199 ..     163     209 .. 0.91
   2 ?    0.2   0.0      0.24   8.6e+02      11      32 ..     387     408 ..     381     410 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2e-05
                            CtsR_C  16 siseqdaeaiiqrLleegliterEakLmkaals 48 
                                        i+e +   +i+  ++eg + + E +L+k+a+ 
  gi|474934626|ref|YP_007688208.1| 167 TITEDELAVMIDEIQQEGTLEKSESELIKSAME 199
                                       799****************************96 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.24
                            CtsR_C  11 nsigdsiseqdaeaiiqrLlee 32 
                                         +gd+++  +++ i++   ++
  gi|474934626|ref|YP_007688208.1| 387 PQVGDEVDAGNVRMIVKSIRNR 408
                                       579*************987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1159  (0.0646439); expected 358.6 (0.02)
Passed bias filter:                      850  (0.0474092); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.73u 0.34s 00:00:01.07 Elapsed: 00:00:00.53
# Mc/sec: 2418.25
//
Query:       gi|474934627|ref|YP_007688209.1|  [L=75]
Description: Uncharacterized protein conserved in bacteria [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-13   49.3   0.1    3.5e-13   49.0   0.1    1.1  1  PC4       Transcriptional Coactivator p15 (PC4)


Domain annotation for each model (and alignments):
>> PC4  Transcriptional Coactivator p15 (PC4)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.1     2e-17   3.5e-13       2      52 .]      20      68 ..      19      68 .. 0.93

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 2e-17
                                      CTTCCEEEEEEEETTE.EEEEEEEEEECTTEEEEEEEEEEEEHHHHHHHHHH CS
                               PC4  2 elskkrrvtvrefkGk.tlvdIReyyekdgelkPgkKGIsLtleqweaLkka 52
                                      ++++k+++++ +++G+ +++dIRe+ +  +  k ++KGI+L++e+ + Lkka
  gi|474934627|ref|YP_007688209.1| 20 SKGWKKELNLVSWNGRePKYDIREWSP--DGSK-MGKGITLSAEEAAVLKKA 68
                                      589************************..6677.78**************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 511.60
//
Query:       gi|474934628|ref|YP_007688210.1|  [L=179]
Description: Rubrerythrin [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.9e-27   94.3  11.5    1.8e-25   90.0  11.5    2.0  1  Rubrerythrin   Rubrerythrin
    1.9e-07   31.1   8.2    1.8e-05   24.7   8.2    2.1  1  Ferritin       Ferritin-like domain
     0.0022   18.2   2.7     0.0037   17.4   2.7    1.4  1  Ferritin_2     Ferritin-like domain
     0.0098   15.9   0.6      0.016   15.2   0.6    1.3  1  zf-C2HC5       Putative zinc finger motif, C2HC5-type
  ------ inclusion threshold ------
      0.011   15.8   0.2      0.022   14.8   0.2    1.6  1  HypA           Hydrogenase/urease nickel incorporation, metal
       0.02   14.6   0.1          9    6.1   0.0    2.6  3  Yae1_N         Essential protein Yae1, N terminal
      0.049   13.2   0.3        0.1   12.2   0.3    1.5  1  RecR           RecR protein
      0.058   13.3   1.0      0.058   13.3   1.0    2.0  2  HalOD2         Halobacterial output domain 2
      0.097   12.5   0.3       0.15   11.9   0.3    1.3  1  MCM_OB         MCM OB domain
       0.23   11.8   4.9       0.74   10.2   4.9    1.9  1  DUF4379        Probable Zinc-ribbon domain
          1    9.5   4.2        2.8    8.1   4.2    1.7  1  Zn-ribbon_8    Zinc ribbon domain
        2.1    8.2   5.3         17    5.3   0.3    2.6  3  TFIIS_C        Transcription factor S-II (TFIIS)
        4.3    7.2   5.9        4.4    7.2   4.4    1.8  2  zinc_ribbon_2  zinc-ribbon domain
        4.8    6.7   6.6         22    4.6   1.2    2.2  1  zf-ribbon_3    zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.0  11.5   1.4e-28   1.8e-25       2     136 ..      11     126 ..      10     127 .. 0.95

  Alignments for each domain:
  == domain 1  score: 90.0 bits;  conditional E-value: 1.4e-28
                                       HHHHHHHHHHHHHHHHHHHHHCHH.TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------T CS
                      Rubrerythrin   2 iLekAiagEssarrlYkelaekak.egypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakpk 77 
                                       +L++A+agEs+ar+ Y+++a++ak egy+qia lF+e+Ae+E+eHaki +k+l +                      
  gi|474934628|ref|YP_007688210.1|  11 NLQAAFAGESQARNKYTYFASQAKkEGYEQIADLFLETAENEKEHAKIWFKALHDGSV-P----------------- 69 
                                       89*****************************************************333.3................. PP

                                       TGGHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  78 flttaknLeeaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerlrkl 136
                                          t +nL++a+ g+ +e+++my++++e a+keg++++++lf+++ + E +Heer+ +l
  gi|474934628|ref|YP_007688210.1|  70 --DTITNLKDAASGENYEHTTMYKEFAETARKEGFDQIANLFEAVGKIEAHHEERYLQL 126
                                       ..4689**************************************************988 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   8.2   1.4e-08   1.8e-05       2     140 ..      10     131 ..       9     132 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.4e-08
                                       HHHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHHC-SSSSC CS
                          Ferritin   2 kaLneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltraeleeieapkef 78 
                                       + L++++a e +a ++y ++a+ +k +g+e++a +f e ae e eha+  ++ + +        +            
  gi|474934628|ref|YP_007688210.1|  10 ANLQAAFAGESQARNKYTYFASQAKKEGYEQIADLFLETAENEKEHAKIWFKALHDGSV-----P------------ 69 
                                       689*********************************************99999987665.....3............ PP

                                       SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Ferritin  79 gsveevleaalehekkvteslrelielaeeegDpatadfledfleeqeeheweleallekle 140
                                       +++ +   aa    ++ t++++e +e a++eg ++ a+++e + + + +he+   +ll+++e
  gi|474934628|ref|YP_007688210.1|  70 DTITNLKDAASGENYEHTTMYKEFAETARKEGFDQIANLFEAVGKIEAHHEERYLQLLKNIE 131
                                       3677778899999999**************************99999999999999999886 PP

>> Ferritin_2  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   2.7   2.9e-06    0.0037       6      96 ..      12     113 ..       8     132 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.9e-06
                        Ferritin_2   6 LnfAlnlEyleaafYtaalegaslddkalldaevrevaeeiakheeaHveflkaaleGaaavakptfdf........ 74 
                                       L+ A + E ++ + Yt+ +++a    k+   +++ +++ e a++e++H++++ +al+ +  v++   ++        
  gi|474934628|ref|YP_007688210.1|  12 LQAAFAGESQARNKYTYFASQA----KKEGYEQIADLFLETAENEKEHAKIWFKALH-DGSVPDTITNLkdaasgen 83 
                                       8999999************966....77788899**********************6.6666677667777788887 PP

                        Ferritin_2  75 ........afdpfadeksflalaavlEdvg 96 
                                               +f ++a+++ f + a  +E vg
  gi|474934628|ref|YP_007688210.1|  84 yehttmykEFAETARKEGFDQIANLFEAVG 113
                                       788888888999999999999999999988 PP

>> zf-C2HC5  Putative zinc finger motif, C2HC5-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.6   1.2e-05     0.016      19      43 ..     145     168 ..     140     174 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.2e-05
                          zf-C2HC5  19 nClnCGkiiCakeglskpCsfCgsp 43 
                                        C nCG i   ke++ k C+ C++p
  gi|474934628|ref|YP_007688210.1| 145 KCRNCGHIHVGKEAP-KVCPVCKHP 168
                                       7**************.******987 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.2   1.7e-05     0.022      20      96 ..      99     169 ..      86     178 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.7e-05
                                       CTT..EEEEEEEEEETTCT--HHHHHHHHHHHHCC.TTTT-EEEEEEE--EEEETTTS-EEECHHHHHS-TTTSSS- CS
                              HypA  20 eaaarkvtkvkvevGelsgvepeaLefafellaegtvlegaeLeieevpvkvrCreCgkefeleekalrCpkCgsad 96 
                                       +++++++ ++   vG+++  ++e   + ++ +++g v++      +++ v+ +Cr+Cg+    +e+   Cp C++ +
  gi|474934628|ref|YP_007688210.1|  99 KEGFDQIANLFEAVGKIEAHHEERYLQLLKNIEDGVVFK------KDEVVVWKCRNCGHIHVGKEAPKVCPVCKHPQ 169
                                       555555555555566655555555555555555554444......56668899*****88876654457****9876 PP

>> Yae1_N  Essential protein Yae1, N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       4.1   5.2e+03      11      18 ..       9      16 ..       8      16 .. 0.86
   2 ?    6.1   0.0     0.007         9      17      33 ..      33      49 ..      30      52 .. 0.85
   3 ?    5.8   0.0    0.0086        11      17      36 ..      97     116 ..      94     117 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 4.1
                            Yae1_N 11 eqglqeGf 18
                                      e++lq+ f
  gi|474934628|ref|YP_007688210.1|  9 EANLQAAF 16
                                      899**988 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.007
                            Yae1_N 17 GfdeGyqeGaqlGlelG 33
                                       + eGy++ a+l+le  
  gi|474934628|ref|YP_007688210.1| 33 AKKEGYEQIADLFLETA 49
                                      688***********976 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0086
                            Yae1_N  17 GfdeGyqeGaqlGlelGqil 36 
                                        + eG+ + a l+ ++G+i+
  gi|474934628|ref|YP_007688210.1|  97 ARKEGFDQIANLFEAVGKIE 116
                                       6889**************96 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3   7.9e-05       0.1      18      37 ..     145     168 ..     142     169 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.9e-05
                                       E-TTT--EESSS....S-CCCCST CS
                              RecR  18 hCsrCgnlteed....lCaICsdp 37 
                                        C++Cg++        +C++C+ p
  gi|474934628|ref|YP_007688210.1| 145 KCRNCGHIHVGKeapkVCPVCKHP 168
                                       7*******555445568****988 PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.0   4.5e-05     0.058      30      44 ..     142     156 ..     132     162 .. 0.83
   2 ?   -2.0   0.1       2.7   3.5e+03       2       9 ..     159     166 ..     158     168 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.5e-05
                            HalOD2  30 yvWkCtrCGevqaaA 44 
                                        vWkC +CG++  + 
  gi|474934628|ref|YP_007688210.1| 142 VVWKCRNCGHIHVGK 156
                                       69********98875 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.7
                            HalOD2   2 PekCseCs 9  
                                       P+ C+ C+
  gi|474934628|ref|YP_007688210.1| 159 PKVCPVCK 166
                                       899**996 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3   0.00012      0.15      26      64 ..     135     170 ..     130     178 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                                       -EEEEEEEEEEETTT-.-EEES----SB-..TTT-HHH- CS
                            MCM_OB  26 vkpklkkavfeckkcgktveveleePrkCeekeCeskdp 64 
                                       v++k + +v +c++cg+ ++v  e P+ C  + C++ ++
  gi|474934628|ref|YP_007688210.1| 135 VFKKDEVVVWKCRNCGH-IHVGKEAPKVC--PVCKHPQS 170
                                       6677788999******8.7777888****..99*96543 PP

>> DUF4379  Probable Zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   4.9   0.00058      0.74      20      39 ..     134     153 ..     118     167 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00058
                           DUF4379  20 vtpgskkkvwWkCakCgheW 39 
                                       v  ++ + v WkC++Cgh +
  gi|474934628|ref|YP_007688210.1| 134 VVFKKDEVVVWKCRNCGHIH 153
                                       67778899*********965 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   4.2    0.0022       2.8       7      34 ..     145     167 ..     143     170 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0022
                       Zn-ribbon_8   7 rCeeCghefevlqsisdapltaCPeCgs 34 
                                       +C++Cgh +       ++++++CP C++
  gi|474934628|ref|YP_007688210.1| 145 KCRNCGHIHV-----GKEAPKVCPVCKH 167
                                       8*****6665.....3344577****86 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       5.4   6.9e+03       9      18 ..      24      33 ..      23      35 .. 0.70
   2 ?    4.8   0.1      0.02        26      27      36 ..     142     151 ..     139     153 .. 0.79
   3 ?    5.3   0.3     0.014        17       2      13 ..     161     172 ..     160     175 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 5.4
                           TFIIS_C  9 reayffqlQt 18
                                      ++ ++f  Q 
  gi|474934628|ref|YP_007688210.1| 24 NKYTYFASQA 33
                                      5677888886 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.02
                           TFIIS_C  27 vfykCtkCgh 36 
                                       v  kC +Cgh
  gi|474934628|ref|YP_007688210.1| 142 VVWKCRNCGH 151
                                       6679999998 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.014
                           TFIIS_C   2 kCpkCgsreayf 13 
                                        Cp C++ + yf
  gi|474934628|ref|YP_007688210.1| 161 VCPVCKHPQSYF 172
                                       6******99986 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.9     5e+03       8      15 ..     129     136 ..     128     136 .. 0.82
   2 ?    7.2   4.4    0.0034       4.4       1      22 [.     145     168 ..     145     169 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.9
                     zinc_ribbon_2   8 elqdnakF 15 
                                        ++d+++F
  gi|474934628|ref|YP_007688210.1| 129 NIEDGVVF 136
                                       589**998 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0034
                     zinc_ribbon_2   1 fCpnCGaelq.dnakF.CpyCGtp 22 
                                       +C nCG+ +  ++a+  Cp C +p
  gi|474934628|ref|YP_007688210.1| 145 KCRNCGHIHVgKEAPKvCPVCKHP 168
                                       8********8355555*****887 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   1.2     0.018        22       4      11 ..     161     168 ..     158     170 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.018
                       zf-ribbon_3   4 rCPnCGap 11 
                                        CP C++p
  gi|474934628|ref|YP_007688210.1| 161 VCPVCKHP 168
                                       69***997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1008  (0.0562218); expected 358.6 (0.02)
Passed bias filter:                      644  (0.0359195); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1101.75
//
Query:       gi|474934629|ref|YP_007688211.1|  [L=288]
Description: hypothetical protein TALC_01060 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00046   20.1   0.0     0.0051   16.7   0.0    2.0  1  Abhydrolase_3   alpha/beta hydrolase fold
  ------ inclusion threshold ------
      0.018   14.6   0.0        2.2    7.7   0.0    2.1  2  DLH             Dienelactone hydrolase family
      0.034   14.1   0.0      0.095   12.6   0.0    1.8  1  Pertussis_S2S3  Pertussis toxin, subunit 2 and 3, C-terminal 


Domain annotation for each model (and alignments):
>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   8.5e-07    0.0051      20     204 ..      79     256 ..      60     259 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 8.5e-07
                                       HHHHHHHHHTSEEEEEE---T.TTS-TTHHHHHHHHHHHHHHHTHHHHTETTCEEEEEEETHHHHHHHHHHHHHHHT CS
                     Abhydrolase_3  20 lcrelakelgavvvsvdYrlA.PehpfPaavedalaalrwlaeqawelgadpsrivlaGdSaGGnlaaavalrarde 95 
                                       +c+ +ak  g++v++ d r    +++f   ++d+ + l+w+ + a+e+g+d +r++ aG+  G   a+ +al +  +
  gi|474934629|ref|YP_007688211.1|  79 MCQMFAK-RGYAVINADVRAIdSKTRFEDILDDINRLLCWIPTVAEEYGLDMNRVYAAGTFRGSPPALWAALICNGN 154
                                       5554444.46667777776543789999****************99*****************99888888777776 PP

                                       T---............EEEEEEESE-SSTSSTTSHHHHHCHHTTTSSSSCHHHHHHHHHHHSSGGGGGSTTTSGGGC CS
                     Abhydrolase_3  96 gepk............vagqvliyPvtdlertesesikkaeeladgplltraaldlfwrlylpeadrddplasplla 160
                                         ++            ++g+ l++Pv +   t   +            l  + ++++ +ly ++ ++ +  a p ++
  gi|474934629|ref|YP_007688211.1| 155 R-IRelmdvkafpdyeIRGLGLFSPVYMG--T---E------------LDHKLVKALKTLYRQNPELLQA-AIPARN 212
                                       3.333567778888888888888888733..3...1............2222345556677765555544.455666 PP

                                       S-SST---EEEEEETT-TTHHHHHHHHHHHHHTT--EEEEEETT CS
                     Abhydrolase_3 161 edlsglpptlvvvaefDplrdegeayaerlraagvevelieyeg 204
                                       ++l+ lpp+++   ++++  + +e++ + l ++ v++el+ +e+
  gi|474934629|ref|YP_007688211.1| 213 HNLEVLPPVFISASDRELTASPAERLRRLLSKNRVDCELMMFEN 256
                                       69*************************************99987 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.003        18      12      48 ..      56      95 ..      46     115 .. 0.70
   2 ?    7.7   0.0   0.00038       2.2     151     195 ..     223     269 ..     206     284 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.003
                               DLH 12 kkpvvvviqeifGvn...dnikdiserlaeeGYvalaPdl 48
                                      + pvvv ++     +       d+++ +a+ GY+++ +d+
  gi|474934629|ref|YP_007688211.1| 56 PLPVVVYFNRGTMARharAAAVDMCQMFAKRGYAVINADV 95
                                      55666666543222234455569*************9998 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00038
                               DLH 151 fgeeDefipadevekleealkaanvdlelkvYpgag..HaFandsre 195
                                       +   D   +a+ +e+l+  l+++ vd+el ++++a+   +Fa++ + 
  gi|474934629|ref|YP_007688211.1| 223 ISASDRELTASPAERLRRLLSKNRVDCELMMFENAYlsRGFAEKAPM 269
                                       445799999999**********************9833467776655 PP

>> Pertussis_S2S3  Pertussis toxin, subunit 2 and 3, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.6e-05     0.095      13      67 ..      62     118 ..      51     135 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.6e-05
                                       EEEEEEEEEEEEETTS-EEEEEEETTEEEEEEEE-SSSST..TCCCHHHHHHHHHHH CS
                    Pertussis_S2S3  13 yysnvtatrlldstnsrlcavfvrdGqpvigacisPyeGr..yresyaalrrllell 67 
                                       y+ + t++r   ++  ++c +f + G +vi+a +   + +  + ++ + + rll  +
  gi|474934629|ref|YP_007688211.1|  62 YFNRGTMARHARAAAVDMCQMFAKRGYAVINADVRAIDSKtrFEDILDDINRLLCWI 118
                                       8888999*************************9998887655889999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1913.86
//
Query:       gi|474934630|ref|YP_007688212.1|  [L=218]
Description: hypothetical protein TALC_01061 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.8e-09   37.6   3.3     0.0009   19.9   0.1    4.3  4  TPR_14      Tetratricopeptide repeat
    2.4e-09   37.5   5.8    1.8e-05   25.1   0.1    3.6  4  TPR_19      Tetratricopeptide repeat
      3e-07   30.0   7.5       0.29   11.4   0.1    4.3  4  TPR_2       Tetratricopeptide repeat
    1.5e-06   28.2   4.1     0.0057   16.8   0.5    3.3  3  TPR_9       Tetratricopeptide repeat
    5.4e-06   26.4   7.1       0.28   11.7   0.4    5.0  5  TPR_17      Tetratricopeptide repeat
    7.6e-06   25.7   5.6       0.03   14.5   0.1    3.8  4  TPR_8       Tetratricopeptide repeat
    0.00047   20.0   3.7       0.27   11.4   0.1    3.7  4  TPR_7       Tetratricopeptide repeat
    0.00057   19.6   3.9        2.5    8.1   0.1    3.7  3  TPR_1       Tetratricopeptide repeat
     0.0024   18.5   6.7       0.45   11.2   0.6    3.5  4  TPR_16      Tetratricopeptide repeat
     0.0086   16.7   6.3        1.7    9.4   0.1    4.1  5  TPR_6       Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.012   15.5   0.0        4.2    7.4   0.0    2.4  2  DUF4312     Domain of unknown function (DUF4312)
      0.055   13.6   3.2        1.3    9.1   0.1    3.1  4  Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
          1    9.9   6.0         30    5.2   0.1    2.9  2  COX16       Cytochrome c oxidase assembly protein COX16
        1.7    9.0   6.3        3.1    8.2   0.1    3.1  3  TPR_12      Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   7.1e-07    0.0009       5      43 ..       8      48 ..       5      49 .. 0.83
   2 ?    0.8   0.0      0.93   1.2e+03      23      42 ..      63      82 ..      50      84 .. 0.81
   3 !   11.4   0.3   0.00037      0.48       5      43 ..     120     159 ..     114     160 .. 0.79
   4 ?    4.9   0.0     0.045        58       5      38 ..     155     189 ..     152     196 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 7.1e-07
                            TPR_14  5 lalaea..llalGdpdeAiallrralalaPddaeawlllaq 43
                                       a+a+a   +++G+p++A++ l+++l+ +P + + +++la+
  gi|474934630|ref|YP_007688212.1|  8 DAIAKArrQEESGNPQGAADTLEKYLQEDPHNVAPRIELAR 48
                                      555555115789****************************8 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.93
                            TPR_14 23 llrralalaPddaeawllla 42
                                       l+ +l+l P++ +a+ ++ 
  gi|474934630|ref|YP_007688212.1| 63 QLDIVLDLEPENVDALKAMT 82
                                      6888999******9998875 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00037
                            TPR_14   5 lalaeallalG.dpdeAiallrralalaPddaeawlllaq 43 
                                       +++a +l+ +  d++++++++++a +++Pd  e++  +a 
  gi|474934630|ref|YP_007688212.1| 120 AQYAVFLRKQMtDFKKSAEYYEKATRADPDRYEYHQDYAV 159
                                       4555555544348*********************999986 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.045
                            TPR_14   5 lalaea.llalGdpdeAiallrralalaPddaeaw 38 
                                       +++a + l  l+d+ +A   l+++l+l P+++ ++
  gi|474934630|ref|YP_007688212.1| 155 QDYAVLlLNDLRDYVKAKHELEEVLRLKPNNLSVR 189
                                       56665515679*******************99887 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.1   1.4e-08   1.8e-05       3      66 ..      18      80 ..      17      82 .. 0.88
   2 ?    1.0   0.0      0.49   6.3e+02      17      42 ..      67      92 ..      57      93 .. 0.84
   3 ?    3.0   0.9      0.11   1.5e+02      20      62 ..     110     154 ..      97     158 .. 0.71
   4 !   12.8   0.4   9.9e-05      0.13       6      58 ..     132     185 ..     128     198 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.4e-08
                            TPR_19  3 aegdyaeAlalleqalqedpknaearllLAeall.algqldeAealLdalpeedpddaryasLlA 66
                                      ++g+++ A++ le+ lqedp+n + r+ LA+++  +l++ ++    Ld +++ +p   ++ +L+A
  gi|474934630|ref|YP_007688212.1| 18 ESGNPQGAADTLEKYLQEDPHNVAPRIELARVYCySLNDKNQGLFQLDIVLDLEPE--NVDALKA 80
                                      689*****************************962669999999999999999998..7777776 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.49
                            TPR_19 17 alqedpknaearllLAeallalgqld 42
                                      +l+ +p+n +a+ ++  + +++++++
  gi|474934630|ref|YP_007688212.1| 67 VLDLEPENVDALKAMTTIKMQNKRFN 92
                                      689999**999999988888888875 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.11
                            TPR_19  20 edpk.naearllLAeallal.gqldeAealLdalpeedpddarya 62 
                                       +dpk +a++++++A  l ++  ++++  +  +++ ++dpd  +y+
  gi|474934630|ref|YP_007688212.1| 110 KDPKeYAAVAAQYAVFLRKQmTDFKKSAEYYEKATRADPDRYEYH 154
                                       466667788888888777777888888888888888888855554 PP

  == domain 4  score: 12.8 bits;  conditional E-value: 9.9e-05
                            TPR_19   6 dyaeAlalleqalqedpknaearllLAeallal.gqldeAealLdalpeedpdd 58 
                                       d+   ++++e+a  +dp+  e   ++A +ll+   ++ +A+  L+++++ +p++
  gi|474934630|ref|YP_007688212.1| 132 DFKKSAEYYEKATRADPDRYEYHQDYAVLLLNDlRDYVKAKHELEEVLRLKPNN 185
                                       7788899************************987****************9994 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.3    0.0016       2.1       8      34 .]      13      39 ..       6      39 .. 0.88
   2 ?   -0.8   0.0       1.7   2.2e+03      11      34 .]      51      74 ..      49      74 .. 0.83
   3 !   11.4   0.1   0.00022      0.29      14      33 ..     130     149 ..     126     150 .. 0.90
   4 !   11.4   0.1   0.00022      0.29      14      34 .]     165     185 ..     164     185 .. 0.95

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0016
                             TPR_2  8 GlayyklgdyeeAleafekAleldPnn 34
                                      ++  +++g+++ A++ +ek l+ dP+n
  gi|474934630|ref|YP_007688212.1| 13 ARRQEESGNPQGAADTLEKYLQEDPHN 39
                                      6667899******************97 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.7
                             TPR_2 11 yyklgdyeeAleafekAleldPnn 34
                                      +y l+d ++ l  ++ +l l+P+n
  gi|474934630|ref|YP_007688212.1| 51 CYSLNDKNQGLFQLDIVLDLEPEN 74
                                      788889888888999999999987 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00022
                             TPR_2  14 lgdyeeAleafekAleldPn 33 
                                       + d+++ +e++ekA + dP+
  gi|474934630|ref|YP_007688212.1| 130 MTDFKKSAEYYEKATRADPD 149
                                       669****************8 PP

  == domain 4  score: 11.4 bits;  conditional E-value: 0.00022
                             TPR_2  14 lgdyeeAleafekAleldPnn 34 
                                       l dy +A++ +e++l+l Pnn
  gi|474934630|ref|YP_007688212.1| 165 LRDYVKAKHELEEVLRLKPNN 185
                                       789****************98 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.5   4.4e-06    0.0057      26      68 ..       3      47 ..       1      50 [. 0.84
   2 !    7.8   0.0    0.0029       3.7      25      70 ..      36      82 ..      36      85 .. 0.91
   3 !    7.5   0.2    0.0036       4.6      10      62 ..     132     185 ..     126     197 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.4e-06
                             TPR_9 26 PddpeerrdRGlllaqlGclsaAladLeaylalap..dapdaeai 68
                                       d++++    ++ ++++G++++A++ Le yl+ +p   ap +e++
  gi|474934630|ref|YP_007688212.1|  3 KDPAYDAIAKARRQEESGNPQGAADTLEKYLQEDPhnVAPRIELA 47
                                      57888899999999*********************6656666655 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0029
                             TPR_9 25 aPddpeerrdRGlll.aqlGclsaAladLeaylalapdapdaeaira 70
                                      +P+ +  r + ++++ + l++ +++l+ L+  l+l+p++ da  ++ 
  gi|474934630|ref|YP_007688212.1| 36 DPHNVAPRIELARVYcYSLNDKNQGLFQLDIVLDLEPENVDALKAMT 82
                                      69999999******9889***********************998875 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0036
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaq.lGclsaAladLeaylalapda 62 
                                       d+ +  +++e     +Pd+ e + d ++ll   l ++ +A  +Le  l+l p++
  gi|474934630|ref|YP_007688212.1| 132 DFKKSAEYYEKATRADPDRYEYHQDYAVLLLNdLRDYVKAKHELEEVLRLKPNN 185
                                       777888999999999************8876549**************999965 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.1    0.0017       2.1       2      29 ..      29      57 ..      28      63 .. 0.82
   2 ?    0.1   0.0       1.1   1.3e+03       6      16 ..      68      78 ..      67      88 .. 0.89
   3 ?    0.7   0.0      0.67   8.6e+02       8      26 ..     110     129 ..     109     136 .. 0.82
   4 !   11.7   0.4   0.00022      0.28       1      32 [.     139     171 ..     139     173 .. 0.86
   5 ?    3.7   0.1     0.076        97       2      19 ..     175     192 ..     174     192 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0017
                            TPR_17  2 ylkaleldPnnadaynnLAelll.knGdl 29
                                      ++k l+ dP n+ +  +LA++++ +++d+
  gi|474934630|ref|YP_007688212.1| 29 LEKYLQEDPHNVAPRIELARVYCySLNDK 57
                                      6899******************8744443 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.1
                            TPR_17  6 leldPnnaday 16
                                      l+l+P n+da+
  gi|474934630|ref|YP_007688212.1| 68 LDLEPENVDAL 78
                                      7899****997 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.67
                            TPR_17   8 ldPn.nadaynnLAelllkn 26 
                                       +dP+ +a +  ++A++l+k+
  gi|474934630|ref|YP_007688212.1| 110 KDPKeYAAVAAQYAVFLRKQ 129
                                       5777689999*****99875 PP

  == domain 4  score: 11.7 bits;  conditional E-value: 0.00022
                            TPR_17   1 lylkaleldPnnadaynnLAelll.knGdlmtA 32 
                                       +y+ka + dP+  + ++ +A+lll  + d+ +A
  gi|474934630|ref|YP_007688212.1| 139 YYEKATRADPDRYEYHQDYAVLLLnDLRDYVKA 171
                                       6*********************99455777777 PP

  == domain 5  score: 3.7 bits;  conditional E-value: 0.076
                            TPR_17   2 ylkaleldPnnadaynnL 19 
                                       ++++l+l Pnn  + nn+
  gi|474934630|ref|YP_007688212.1| 175 LEEVLRLKPNNLSVRNNY 192
                                       5899***********997 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.27   3.5e+02      13      33 ..      18      38 ..       9      39 .. 0.86
   2 ?   -1.6   0.0       3.4   4.3e+03       7      20 ..      46      60 ..      44      74 .. 0.65
   3 !   14.5   0.1   2.4e-05      0.03      12      33 ..     128     149 ..     118     150 .. 0.90
   4 !    9.9   0.1   0.00072      0.92       9      34 .]     160     185 ..     151     185 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.27
                                      HTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8 13 klgdyeeAkeyyekaleldpd 33
                                      + g+ + A  ++ek+l+ dp 
  gi|474934630|ref|YP_007688212.1| 18 ESGNPQGAADTLEKYLQEDPH 38
                                      6789999999*******9997 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.4
                                      HHHHH.HHTT-HHHH CS
                             TPR_8  7 lgsiy.lklgdyeeA 20
                                      l+++y  +l+d+++ 
  gi|474934630|ref|YP_007688212.1| 46 LARVYcYSLNDKNQG 60
                                      677777888887765 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 2.4e-05
                                       HHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8  12 lklgdyeeAkeyyekaleldpd 33 
                                       +++ d++++ eyyeka+++dpd
  gi|474934630|ref|YP_007688212.1| 128 KQMTDFKKSAEYYEKATRADPD 149
                                       7899*****************8 PP

  == domain 4  score: 9.9 bits;  conditional E-value: 0.00072
                                       HHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   9 siylklgdyeeAkeyyekaleldpdn 34 
                                       +++ +l dy +Ak  +e++l+l+p+n
  gi|474934630|ref|YP_007688212.1| 160 LLLNDLRDYVKAKHELEEVLRLKPNN 185
                                       5679********************97 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.1    0.0063       8.1       1      34 [.       6      39 ..       6      41 .. 0.90
   2 ?   -2.8   0.0       6.8   8.7e+03       5      11 ..      46      52 ..      45      56 .. 0.74
   3 !   11.4   0.1   0.00021      0.27      11      33 ..     129     149 ..     123     152 .. 0.84
   4 ?    0.3   0.0      0.74   9.4e+02      11      32 ..     164     183 ..     158     189 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0063
                             TPR_7  1 aLlnLarlysr..lGdyeeAielyeqsLaltkdped 34
                                      a++++a ++++   G+ + A++ +e+   l +dp++
  gi|474934630|ref|YP_007688212.1|  6 AYDAIAKARRQeeSGNPQGAADTLEK--YLQEDPHN 39
                                      799999**99999*************..99999876 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6.8
                             TPR_7  5 Larlysr 11
                                      Lar+y+ 
  gi|474934630|ref|YP_007688212.1| 46 LARVYCY 52
                                      8999986 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00021
                             TPR_7  11 rlGdyeeAielyeqsLaltkdpe 33 
                                       ++ d+++ +e+ye+  a++ dp+
  gi|474934630|ref|YP_007688212.1| 129 QMTDFKKSAEYYEK--ATRADPD 149
                                       588***********..**99986 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 0.74
                             TPR_7  11 rlGdyeeAielyeqsLaltkdp 32 
                                       +l+dy +A   +e+  +l+  p
  gi|474934630|ref|YP_007688212.1| 164 DLRDYVKAKHELEE--VLRLKP 183
                                       5999*999999999..555444 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1     0.063        81      14      34 .]      19      39 ..      16      39 .. 0.91
   2 !    8.1   0.1    0.0019       2.5      16      33 ..     132     149 ..     128     150 .. 0.91
   3 !    7.5   0.1    0.0029       3.7      10      34 .]     161     185 ..     160     185 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.063
                                      TT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1 14 lgkydeAleyyekALelnPnn 34
                                       g+++ A +  ek L+ +P+n
  gi|474934630|ref|YP_007688212.1| 19 SGNPQGAADTLEKYLQEDPHN 39
                                      6999***************98 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0019
                                       -HHHHHHHHHHHHHHSTT CS
                             TPR_1  16 kydeAleyyekALelnPn 33 
                                       ++++  eyyekA + +P+
  gi|474934630|ref|YP_007688212.1| 132 DFKKSAEYYEKATRADPD 149
                                       7999*********99997 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0029
                                       HHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  10 ayfklgkydeAleyyekALelnPnn 34 
                                       ++  l +y +A    e++L+l Pnn
  gi|474934630|ref|YP_007688212.1| 161 LLNDLRDYVKAKHELEEVLRLKPNN 185
                                       567899******************8 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0021       2.7       2      43 ..      11      49 ..      10      51 .. 0.85
   2 ?   -1.5   0.0       3.3   4.2e+03      20      37 ..      64      78 ..      52      80 .. 0.83
   3 ?   -2.4   0.1       6.5   8.3e+03      26      38 ..     110     122 ..     107     124 .. 0.62
   4 !   11.2   0.6   0.00035      0.45      11      54 ..     131     172 ..     126     185 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0021
                            TPR_16  2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgda 43
                                      a+ar   ++g+++ Aa  le +l  d   P +++ + +l+++
  gi|474934630|ref|YP_007688212.1| 11 AKARRQEESGNPQGAADTLEKYLQED---PHNVAPRIELARV 49
                                      7899999*****************99...9888777666665 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.3
                            TPR_16 20 leaalkrdpssPdaaeAl 37
                                      l+++l++    P++++Al
  gi|474934630|ref|YP_007688212.1| 64 LDIVLDLE---PENVDAL 78
                                      78899999...9999996 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 6.5
                            TPR_16  26 rdpssPdaaeAll 38 
                                       +dp++ +a++A++
  gi|474934630|ref|YP_007688212.1| 110 KDPKEYAAVAAQY 122
                                       5566666666666 PP

  == domain 4  score: 11.2 bits;  conditional E-value: 0.00035
                            TPR_16  11 gdyddAaaaleaalkrdpssPdaaeAllllgdaal.rqgrlaeAa 54 
                                        d+ + a+++e a+++d   Pd++e +  +++++l  + ++ +A 
  gi|474934630|ref|YP_007688212.1| 131 TDFKKSAEYYEKATRAD---PDRYEYHQDYAVLLLnDLRDYVKAK 172
                                       588999***********...**************97779998886 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.1    0.0013       1.7       6      32 ..      10      38 ..       5      39 .. 0.82
   2 ?   -2.3   0.0       7.6   9.7e+03       6      31 ..      46      72 ..      45      74 .. 0.62
   3 ?   -1.9   0.0       5.6   7.1e+03      18      27 ..      94     103 ..      92     103 .. 0.79
   4 ?    6.1   0.4     0.015        20       9      32 ..     125     149 ..     119     149 .. 0.83
   5 ?    1.1   0.0       0.6   7.7e+02       7      32 ..     158     184 ..     156     185 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0013
                                      HHHHHHHH..HHHHHHHHHHHHHHHH-TT CS
                             TPR_6  6 lalsyrkl..gdtdkAlealerlikeYPd 32
                                      +a+++r+   g+++ A ++le+ ++e P 
  gi|474934630|ref|YP_007688212.1| 10 IAKARRQEesGNPQGAADTLEKYLQEDPH 38
                                      67777764579***************996 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 7.6
                                      HHHHHHH.HHHHHHHHHHHHHHHHH-T CS
                             TPR_6  6 lalsyrk.lgdtdkAlealerlikeYP 31
                                      la+ y   l+d+ + l  l+ +++  P
  gi|474934630|ref|YP_007688212.1| 46 LARVYCYsLNDKNQGLFQLDIVLDLEP 72
                                      566666557788777666666666555 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 5.6
                                       HHHHHHHHHH CS
                             TPR_6  18 kAlealerli 27 
                                       +  e+++rl+
  gi|474934630|ref|YP_007688212.1|  94 ETDEIFQRLL 103
                                       56799***96 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.015
                                       HHHH.HHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   9 syrk.lgdtdkAlealerlikeYPd 32 
                                        +rk ++d  k+ e++e+  +  Pd
  gi|474934630|ref|YP_007688212.1| 125 FLRKqMTDFKKSAEYYEKATRADPD 149
                                       5566589************999987 PP

  == domain 5  score: 1.1 bits;  conditional E-value: 0.6
                                       HHHHHH.HHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   7 alsyrk.lgdtdkAlealerlikeYPd 32 
                                       a ++++ l d+ kA+  le++++  P+
  gi|474934630|ref|YP_007688212.1| 158 AVLLLNdLRDYVKAKHELEEVLRLKPN 184
                                       56666668899********99986665 PP

>> DUF4312  Domain of unknown function (DUF4312)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.012        15      35      55 ..      65      85 ..      52      91 .. 0.86
   2 ?    7.4   0.0    0.0033       4.2      23      59 ..     163     200 ..     157     201 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.012
                           DUF4312 35 evllriePvdvkvvkaeeeey 55
                                      +++l +eP++v+ +ka ++ +
  gi|474934630|ref|YP_007688212.1| 65 DIVLDLEPENVDALKAMTTIK 85
                                      79*************987654 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0033
                           DUF4312  23 skvqkkvlket.eevllriePvdvkvvkaeeeeytEkF 59 
                                       ++++  v  +   e +lr++P++ +v +  e+  +EkF
  gi|474934630|ref|YP_007688212.1| 163 NDLRDYVKAKHeLEEVLRLKPNNLSVRNNYERLMREKF 200
                                       5566666444314779*********************9 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       6.1   7.8e+03      22      34 ..      27      39 ..      23      39 .. 0.72
   2 ?    3.8   0.0     0.048        62      23      39 ..      63      79 ..      51      90 .. 0.70
   3 ?   -2.5   0.0       4.4   5.6e+03      15      32 ..     131     148 ..     129     150 .. 0.68
   4 ?    9.1   0.1    0.0011       1.3      14      38 ..     165     189 ..     164     204 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 6.1
                                      HHHHHHHHHTTS- CS
                        Fis1_TPR_C 22 ryvdalLeiEPen 34
                                        ++  L+ +P n
  gi|474934630|ref|YP_007688212.1| 27 DTLEKYLQEDPHN 39
                                      5667778888887 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.048
                                      HHHHHHHHTTS-HHHHH CS
                        Fis1_TPR_C 23 yvdalLeiEPenrQaqs 39
                                       +d +L +EPen  a++
  gi|474934630|ref|YP_007688212.1| 63 QLDIVLDLEPENVDALK 79
                                      57999*******87765 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 4.4
                                       T-HHHHHHHHHHHHHHTT CS
                        Fis1_TPR_C  15 geYseArryvdalLeiEP 32 
                                        +++++ +y +   + +P
  gi|474934630|ref|YP_007688212.1| 131 TDFKKSAEYYEKATRADP 148
                                       577777777777666666 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.0011
                                       HT-HHHHHHHHHHHHHHTTS-HHHH CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPenrQaq 38 
                                       l++Y +A+  ++ +L++ P+n  ++
  gi|474934630|ref|YP_007688212.1| 165 LRDYVKAKHELEEVLRLKPNNLSVR 189
                                       79*******************9886 PP

>> COX16  Cytochrome c oxidase assembly protein COX16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   2.4     0.036        46      29      71 ..     110     153 ..      64     155 .. 0.84
   2 ?    5.2   0.1     0.024        30      37      65 ..     174     199 ..     158     205 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.036
                             COX16  29 rdrk.vkelskeealelkkkrrkvdleeeyerlqakldlddWen 71 
                                       +d k + ++ ++ a+ l+k+  +++  +ey++ +   d d +e+
  gi|474934630|ref|YP_007688212.1| 110 KDPKeYAAVAAQYAVFLRKQMTDFKKSAEYYEKATRADPDRYEY 153
                                       333357788999999999***********9999999999*9998 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.024
                             COX16  37 skeealelkkkrrkvdleeeyerlqakld 65 
                                       + ee l+   k++++++++ yerl+ + +
  gi|474934630|ref|YP_007688212.1| 174 ELEEVLR--LKPNNLSVRNNYERLMRE-K 199
                                       4445555..478899**********96.4 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.2      0.42   5.3e+02      52      72 ..      13      33 ..       6      34 .. 0.78
   2 ?    8.2   0.1    0.0024       3.1      24      75 ..      97     147 ..      84     149 .. 0.77
   3 ?    6.5   2.1    0.0079        10       4      74 ..     118     181 ..     115     184 .. 0.62

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.42
                            TPR_12 52 grlyralgryeeAlelleeal 72
                                      +r ++++g+++ A + le+ l
  gi|474934630|ref|YP_007688212.1| 13 ARRQEESGNPQGAADTLEKYL 33
                                      4446689**********9988 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0024
                            TPR_12  24 ellekaleiarrllGpdhpltattlrnLgrlyr.algryeeAlelleealaia 75 
                                       e++++ l ++ +  +p+   +a++   ++  +r ++ ++++  e++e+a++++
  gi|474934630|ref|YP_007688212.1|  97 EIFQRLLPLVAKRKDPKE--YAAVAAQYAVFLRkQMTDFKKSAEYYEKATRAD 147
                                       778888888877766654..677777777777647799999999*99999876 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0079
                            TPR_12   4 talnnlaavlrr.lgrydeAlellekaleiarrllGpdhpltattlrnLgrlyr.algryeeAlelleealai 74 
                                        a+ ++a++lr+ + ++ ++ e++eka ++      pd+++   + ++++ l++  l +y +A   lee+l++
  gi|474934630|ref|YP_007688212.1| 118 VAA-QYAVFLRKqMTDFKKSAEYYEKATRAD-----PDRYE---YHQDYAVLLLnDLRDYVKAKHELEEVLRL 181
                                       455.788888665889999999999996666.....44422...45555555433556666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1497.40
//
Query:       gi|474934631|ref|YP_007688213.1|  [L=344]
Description: hypothetical protein TALC_01062 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       802  (0.044732); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2136.20
//
Query:       gi|474934632|ref|YP_007688214.1|  [L=58]
Description: hypothetical protein TALC_01063 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.012   15.6   1.3      0.013   15.4   1.3    1.2  1  Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
      0.063   13.2   3.1       0.07   13.1   3.1    1.2  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.12   12.4   3.2        4.8    7.3   4.1    2.0  2  zinc_ribbon_6   Zinc-ribbon


Domain annotation for each model (and alignments):
>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   1.3   2.2e-06     0.013       3      30 ..      14      41 ..      12      55 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.2e-06
                                      EEEEE-SSBTT--EEEEEEETTEEEEEE CS
                    Molybdop_Fe4S4  3 vvktaCpyCgvgCglevhvkdgkivkve 30
                                      + kt+C+ Cg  C +  ++  g+ v+ +
  gi|474934632|ref|YP_007688214.1| 14 TFKTTCSECGKECEVPFKPTEGRPVYCR 41
                                      78*****************999998776 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   3.1   1.2e-05      0.07      29      57 ..      17      48 ..       6      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.2e-05
                    OrfB_Zn_ribbon 29 ktCseCgsknke...alsgrtfkCpnCgfead 57
                                      +tCseCg++ +    + +gr ++C++C  ++ 
  gi|474934632|ref|YP_007688214.1| 17 TTCSECGKECEVpfkPTEGRPVYCRDCFPKHR 48
                                      58*********99*999**********76655 PP

>> zinc_ribbon_6  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   4.1    0.0008       4.8      25      47 ..      12      34 ..       6      43 .. 0.75
   2 ?    3.9   0.2    0.0094        56      30      36 ..      38      44 ..      32      50 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0008
                     zinc_ribbon_6 25 nkkvkilCnDCekksevkfhvlg 47
                                      +++ k +C  C+k++ev+f+   
  gi|474934632|ref|YP_007688214.1| 12 RETFKTTCSECGKECEVPFKPTE 34
                                      4567889************9765 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0094
                     zinc_ribbon_6 30 ilCnDCe 36
                                      ++C+DC 
  gi|474934632|ref|YP_007688214.1| 38 VYCRDCF 44
                                      89****6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.30s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 381.65
//
Query:       gi|474934633|ref|YP_007688215.1|  [L=82]
Description: hypothetical protein TALC_01064 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 543.00
//
Query:       gi|474934634|ref|YP_007688216.1|  [L=132]
Description: Pyridoxamine 5'-phosphate oxidase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.2e-06   26.8   0.0    5.4e-06   26.5   0.0    1.2  1  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase


Domain annotation for each model (and alignments):
>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0     3e-10   5.4e-06       3      82 ..       6      84 ..       4      92 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 3e-10
                                      HHHHHHHHHS.SEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETTGSEEEEEEEE CS
                    Putative_PNPOx  3 eelreflaes.kavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallflddelgrgvrieGt 80
                                      ++++++l+++  + vl T+++ GrP++ + + +a +  +++v+    + r  +nl++np++a+l+      ++++i+ +
  gi|474934634|ref|YP_007688216.1|  6 QKVLDLLNDPaTVKVLVTASKGGRPHAIVAGTIAAPSPETMVIGEVLMKRASANLQANPKAAFLISKGT--ESYEINVR 82
                                      567777777635569****************999999999************************98888..55555555 PP

                                      EE CS
                    Putative_PNPOx 81 ae 82
                                      a+
  gi|474934634|ref|YP_007688216.1| 83 AK 84
                                      44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 836.21
//
Query:       gi|474934635|ref|YP_007688217.1|  [L=2782]
Description: Listeria/Bacterioides repeat protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-16   60.3  50.5    8.1e-12   45.1   2.2   10.4 10  Flg_new   Listeria-Bacteroides repeat domain (List_Bact_rpt)


Domain annotation for each model (and alignments):
>> Flg_new  Listeria-Bacteroides repeat domain (List_Bact_rpt)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.2   3.7e-06     0.066       3      64 ..    1042    1109 ..    1041    1110 .. 0.80
   2 !   45.1   2.2   4.5e-16   8.1e-12       1      65 []    1113    1180 ..    1113    1180 .. 0.90
   3 ?    0.6   0.3     0.036   6.4e+02       1      65 []    1211    1287 ..    1211    1287 .. 0.61
   4 !    5.1   0.0    0.0014        26      28      55 ..    1340    1367 ..    1294    1372 .. 0.85
   5 !    4.6   0.2    0.0021        38       9      55 ..    1467    1515 ..    1463    1522 .. 0.70
   6 ?   -3.9   0.1      0.91   1.6e+04      34      42 ..    1563    1571 ..    1562    1575 .. 0.84
   7 ?   -0.2   0.1     0.063   1.1e+03      19      59 ..    1717    1756 ..    1698    1758 .. 0.58
   8 !   15.4   1.0   8.6e-07     0.015       9      51 ..    1800    1842 ..    1795    1854 .. 0.77
   9 !    5.1   0.2    0.0015        26       3      52 ..    2026    2075 ..    2024    2093 .. 0.76
  10 ?   -0.8   1.0       0.1   1.8e+03      26      52 ..    2130    2157 ..    2101    2163 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.7e-06
                                        EEEEETT.EEEEE.EEETTSB----B--EETTEEEEEEES.......STTCCSB--TTT-B--SS-EEEEE CS
                           Flg_new    3 vtFdanG.gtvsq.tvtygetitlpanptkeGYtFaGWyt.......dsdgttaydfgtkvtptgdvtLyA 64  
                                        vtF  +  gt s  ++t g+ ++l ++p+ +  +F GWy        d+++t+aydf+t+ t  +++ L A
  gi|474934635|ref|YP_007688217.1| 1042 VTFIDDKkGTSSVrSFTFGSYMELVDTPS-TEANFIGWYIiesaseeDKKFTKAYDFSTQLT--QNIILLA 1109
                                        889886447765439**********9995.678******76666655888899***999875..9*99988 PP

  == domain 2  score: 45.1 bits;  conditional E-value: 4.5e-16
                                        EEEEEEETTEEEEE....EEETTSB----B--EETTEEEEEEESSTTCCSB--TTT-B--SS-EEEEEE CS
                           Flg_new    1 YtvtFdanGgtvsq....tvtygetitlpanptkeGYtFaGWytdsdgttaydfgtkvtptgdvtLyAk 65  
                                        Y vtFd  +gt+s+    +v+ g +i++ ++ t+eGY+  GW++d+ +t+++  +t+ + tgd+tLyAk
  gi|474934635|ref|YP_007688217.1| 1113 YVVTFDRMDGTTSTmyvnQVEGGVKISTIDQGTREGYDAGGWFKDQLCTNQWVDNTDKV-TGDITLYAK 1180
                                        99*****999876633336888**********************************975.8*******9 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.036
                                        EEEEEEETTEEEEE..EEETTSB----..B-..-EETTEEEEEEESSTTC.CSB--TTT-.....B--SS-EEEE CS
                           Flg_new    1 YtvtFdanGgtvsq..tvtygetitlp..an..ptkeGYtFaGWytdsdg.ttaydfgtk.....vtptgdvtLy 63  
                                        Y+vt+    g v+   +v +g ++ l   ++  p+    +F  W+   +g +t+++ +t      +  ++++ Ly
  gi|474934635|ref|YP_007688217.1| 1211 YNVTYGGTFGVVDAdwSVSHGLSTYLDhaKDilPSAVKVDFIRWSATVNGaDTEVYDDTAvnflrTDGSSSIVLY 1285
                                        56666555555443234555422222212222377788899****999996588888887677666667899999 PP

                                        EE CS
                           Flg_new   64 Ak 65  
                                        A+
  gi|474934635|ref|YP_007688217.1| 1286 AV 1287
                                        95 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.0014
                                        -EETTEEEEEEESSTTCCSB--TTT-B- CS
                           Flg_new   28 ptkeGYtFaGWytdsdgttaydfgtkvt 55  
                                         ++ G+t +GW   sdg+++y +gt+++
  gi|474934635|ref|YP_007688217.1| 1340 ASRVGWTLDGWAMVSDGDARYGSGTSIK 1367
                                        6899*****************9999875 PP

  == domain 5  score: 4.6 bits;  conditional E-value: 0.0021
                                        TEEEEE..EEETTSB----B--EETTEEEEEEESSTTCC.SB--TTT-B- CS
                           Flg_new    9 Ggtvsq..tvtygetitlpanptkeGYtFaGWytdsdgt.taydfgtkvt 55  
                                        Gg ++   +++yget+t   +p  eGY+F  W  + ++t +  + +t++ 
  gi|474934635|ref|YP_007688217.1| 1467 GGMAPSsfNAYYGETVTVRFTP-DEGYQFIRWIVSGEATlNGNTQSTTFI 1515
                                        5555552357899999988766.8********998877655545555555 PP

  == domain 6  score: -3.9 bits;  conditional E-value: 0.91
                                        EEEEEESST CS
                           Flg_new   34 tFaGWytds 42  
                                        tF GW +d+
  gi|474934635|ref|YP_007688217.1| 1563 TFRGWDEDN 1571
                                        8****9885 PP

  == domain 7  score: -0.2 bits;  conditional E-value: 0.063
                                        TSB----..B--EETTEEEEEEESSTTCCSB--TTT-B--SS- CS
                           Flg_new   19 getitlp..anptkeGYtFaGWytdsdgttaydfgtkvtptgd 59  
                                         ++++     + + +GY+F+G + d   t +y++g + t++g+
  gi|474934635|ref|YP_007688217.1| 1717 VNSVQGAgsIDLSAAGYVFTGFNRD---TISYSAGMSGTVEGN 1756
                                        344443322468999******9988...667777766666665 PP

  == domain 8  score: 15.4 bits;  conditional E-value: 8.6e-07
                                        TEEEEEEEETTSB----B--EETTEEEEEEESSTTC.CSB--TT CS
                           Flg_new    9 GgtvsqtvtygetitlpanptkeGYtFaGWytdsdg.ttaydfg 51  
                                        +g +++tv yge+i lp+  +k+GYtF  W   ++  t+ y+ +
  gi|474934635|ref|YP_007688217.1| 1800 DGIYTKTVWYGESIALPT-VSKDGYTFLRWTIGETTiTSPYTYE 1842
                                        6778899********998.************9887756777654 PP

  == domain 9  score: 5.1 bits;  conditional E-value: 0.0015
                                        EEEEETTEEEEEEEETTSB----B--EETTEEEEEEESSTTCCSB--TTT CS
                           Flg_new    3 vtFdanGgtvsqtvtygetitlpanptkeGYtFaGWytdsdgttaydfgt 52  
                                        ++  +n++  +    +g++++++  +  +GY    Wytd  +t ++d + 
  gi|474934635|ref|YP_007688217.1| 2026 ISLYLNDEIFNVINVNGNSYDELGWFIMDGYSSSPWYTDRACTVQVDDSV 2075
                                        5555666666666667889999999999***************9998764 PP

  == domain 10  score: -0.8 bits;  conditional E-value: 0.1
                                        B--EETT..EEEEEEESSTTCCSB--TTT CS
                           Flg_new   26 anptkeG..YtFaGWytdsdgttaydfgt 52  
                                        anp   G   +FaGW  + ++++ y+f++
  gi|474934635|ref|YP_007688217.1| 2130 ANPFSGGgnRVFAGWAVS-QYGNIYYFDE 2157
                                        45543332368*****96.6889999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (2782 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 1.17u 0.37s 00:00:01.54 Elapsed: 00:00:00.55
# Mc/sec: 15284.62
//
Query:       gi|474934636|ref|YP_007688218.1|  [L=732]
Description: hypothetical protein TALC_01067 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (732 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.68u 0.29s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 4437.67
//
Query:       gi|474934637|ref|YP_007688219.1|  [L=32]
Description: hypothetical protein TALC_01068 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (32 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 226.91
//
Query:       gi|474934638|ref|YP_007688220.1|  [L=311]
Description: Thioredoxin reductase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-37  128.9   0.6    2.6e-37  128.7   0.6    1.0  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    1.8e-26   93.1   0.4    1.2e-23   83.8   0.4    2.1  1  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    4.5e-09   35.5   2.7    0.00016   20.5   0.4    3.1  4  HI0933_like    HI0933-like protein
    6.9e-09   35.7   0.7    0.00013   21.6   0.0    2.2  2  DAO            FAD dependent oxidoreductase
    1.7e-07   31.7   5.1    1.4e-06   28.8   0.3    3.3  4  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    5.1e-06   26.1   0.1    0.00018   21.0   0.0    2.1  2  FAD_oxidored   FAD dependent oxidoreductase
    2.3e-05   23.7   0.5    8.1e-05   21.9   0.7    1.8  2  FAD_binding_2  FAD binding domain
    0.00018   20.8   1.1    0.00045   19.5   0.2    2.0  2  Thi4           Thi4 family
    0.00062   19.0   0.1       0.19   10.9   0.0    2.1  2  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
     0.0011   19.2   0.1     0.0029   17.8   0.1    1.8  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
  ------ inclusion threshold ------
      0.019   14.3   0.0      0.036   13.4   0.0    1.5  1  Amino_oxidase  Flavin containing amine oxidoreductase
      0.025   13.8   0.8      0.049   12.9   0.7    1.5  1  FAD_binding_3  FAD binding domain
      0.035   13.2   2.5      0.097   11.7   0.4    2.3  2  GIDA           Glucose inhibited division protein A
       0.19   10.7   0.6       0.75    8.8   0.1    2.0  2  Lycopene_cycl  Lycopene cyclase protein


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.7   0.6     2e-40   2.6e-37       1     293 [.       3     293 ..       3     294 .. 0.85

  Alignments for each domain:
  == domain 1  score: 128.7 bits;  conditional E-value: 2e-40
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHH...HCHHHHHHHHHHHHH........HHHHCHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxx........xxxxxxxxx RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcll...skallgvaedaeias........evvkklnqg 66 
                                       +dv++iG+GpAGl+a ++++ + +k++++++++  ++g+ +     k ++++++++ i +         + ++l+  
  gi|474934638|ref|YP_007688220.1|   3 YDVIIIGAGPAGLTAGIYARSKMMKTLILDSGR--VGGQLVAlypEKGIHNYPGFETIQArklsdklyAQAESLE-- 75 
                                       69***********************99996333..444443334499*********9888999998774445555.. PP

                                       CCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---E...EE-BCTCTTC.TTBEECCSECHHHHHHCCSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  67 ielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGs...sprdlgipGvaenvgklvrtldsaealklkl 140
                                        + + +e+v +i++g +k+ +++ +     +++  ++++A+G    +p+++g +G+    gk+   +    ++k++l
  gi|474934638|ref|YP_007688220.1|  76 CDIRENEPVDTIENGDQKLLVTTPN----GTYEGMSVIVAIGMgrfTPKRMGAEGEDRLEGKG---VSYILPVKEEL 145
                                       55567778*************7665....39***********745567777888887777666...778899***** PP

                                       -TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 141 lpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgngekle 217
                                       + k++v  GgG+ +++++  + ++  ++t+v++r ++       + ++  + l +++v+  +++svk ++g+++ le
  gi|474934638|ref|YP_007688220.1| 146 VGKKVVLFGGGNSAIDMSLIADSV-TDTTIVHRRAEFR------ADEISVKNLDESNVRKIMNASVKSFNGEEK-LE 214
                                       ********************8777.88**********7......899999***********************9.55 PP

                                       ..EEETTSCE..EEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTECCSS--HHHH CS
                                       ..xxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 218 ..vvledgee..idadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDvaggkggpelaqaA 290
                                         + +++g+e  i+adl vv +G++++   l +k +l l+e+g+i++   + t+ pgi+a+GD ++  g+++++ +A
  gi|474934638|ref|YP_007688220.1| 215 siTLEQEGKElvIPADLAVVNIGITADLGVL-KKWNLDLTENGYIKTGLDMSTSRPGIFACGDAVDYPGKYKQIITA 290
                                       556666666689***************9999.********************************9888888888888 PP

                                       HHH CS
                                       xxx RF
                       Pyr_redox_2 291 vqq 293
                                         +
  gi|474934638|ref|YP_007688220.1| 291 CGE 293
                                       766 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.8   0.4   9.7e-27   1.2e-23       1     305 []       6     275 ..       6     275 .. 0.77

  Alignments for each domain:
  == domain 1  score: 83.8 bits;  conditional E-value: 9.7e-27
                       Pyr_redox_3   1 iIiGaGPaGlaaaielkkagledylilEkgnig.nsiyrypkemtfispsftsekleipdlnaiseetspafslkee 76 
                                       iIiGaGPaGl+a+i ++ + + + lil+ g++g + +  yp++           ++e+     i             
  gi|474934638|ref|YP_007688220.1|   6 IIIGAGPAGLTAGIYARSKMM-KTLILDSGRVGgQLVALYPEKGIHN-----YPGFET-----I------------- 58 
                                       8********************.689*****88715556677654321.....122222.....2............. PP

                       Pyr_redox_3  77 klsrkealeYlrevaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGefd.kPnklnipGeek.lvk 151
                                         +++++ + l + a+s e +i+++e V ++++ d++  v+t ++tye  +vi+A+G     P++++ +Ge++   k
  gi|474934638|ref|YP_007688220.1|  59 --QARKLSDKLYAQAESLECDIRENEPVDTIENGDQKLLVTTPNGTYEGMSVIVAIGMGRfTPKRMGAEGEDRlEGK 133
                                       ..2333444455668999*************************************9875425**********74455 PP

                       Pyr_redox_3 152 .hyskvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeeki 227
                                        +++  +  +++ g+kvv  Gg+nSa+D+ l +++   + t+v+r++e +++e    +s+k   e++++++++ +  
  gi|474934638|ref|YP_007688220.1| 134 gVSYILPVKEELVGKKVVLFGGGNSAIDMSL-IADSVTDTTIVHRRAEFRADE----ISVKNLDESNVRKIMNASVK 205
                                       2555557778999****************99.66777999******9988884....77888888888777664422 PP

                       Pyr_redox_3 228 kvlfnaevkeikekeeeykvktedgkkvevkddvvlatGykpdlsflkkslfeldedgrpvlteeteetnvpglfla 304
                                        +  ++++++i+       +++e ++ v   d  v+ +G + dl +lkk  ++l+e+g+++ t  +++t  pg+f +
  gi|474934638|ref|YP_007688220.1| 206 SFNGEEKLESIT-------LEQEGKELVIPADLAVVNIGITADLGVLKKWNLDLTENGYIK-TGLDMSTSRPGIFAC 274
                                       333344444444.......444444445556667777************999999999987.789**********99 PP

                       Pyr_redox_3 305 G 305
                                       G
  gi|474934638|ref|YP_007688220.1| 275 G 275
                                       9 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.4   1.3e-07   0.00016       1      34 [.       3      36 ..       3      43 .. 0.90
   2 !   13.6   0.0   1.5e-05      0.02     106     174 ..      58     126 ..      52     147 .. 0.86
   3 ?   -2.6   0.0       1.3   1.7e+03     116     147 ..     188     218 ..     185     237 .. 0.64
   4 ?   -2.6   0.0       1.3   1.6e+03     370     389 ..     264     282 ..     262     283 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.3e-07
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSS CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakk 34
                                      +dvi+iG+G+AGl a i a+++  ++l+l++++ 
  gi|474934638|ref|YP_007688220.1|  3 YDVIIIGAGPAGLTAGIYARSKMMKTLILDSGRV 36
                                      59****************************9865 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 1.5e-05
                                       .-CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE---.-SS-GG.GT--S CS
                       HI0933_like 106 dkaedivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtG.GlSiPk.lGstg 174
                                        +a+++ d l +++++ ++++r ++ v ++e+  d+k+ v+t  ++++e  ++++A+G G   Pk +G++g
  gi|474934638|ref|YP_007688220.1|  58 IQARKLSDKLYAQAESLECDIRENEPVDTIEN-GDQKLLVTT-PNGTYEGMSVIVAIGmGRFTPKrMGAEG 126
                                       4899999***********************77.555599999.9*************96666664367765 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.3
                                       HHHHHHHT-EEE-S--EEEEECETTE.EEEEE CS
                       HI0933_like 116 lkelkeagvklrletevksvekeedgkfrvkt 147
                                       +k+l+e++v+  ++ +vks++ ee+   ++++
  gi|474934638|ref|YP_007688220.1| 188 VKNLDESNVRKIMNASVKSFNGEEKL-ESITL 218
                                       57889999999999999999554433.44444 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 1.3
                                       -BBTTSTTEEE-GGGBSEEE CS
                       HI0933_like 370 meskkvpgLffaGEvlDveg 389
                                       m s + pg+f +G  +D  g
  gi|474934638|ref|YP_007688220.1| 264 M-STSRPGIFACGDAVDYPG 282
                                       4.7789*********99766 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.8   6.5e-05     0.083       1      35 [.       4      38 ..       4      42 .. 0.86
   2 !   21.6   0.0     1e-07   0.00013     126     236 ..      45     147 ..      38     217 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.5e-05
                                      EEEEECTSHHHHHHHHHHHHTT...EEEEESSSSTTSS CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg...Vtllekgdiagsg 35
                                      dv+iiG+G +Gl++  ++ r +   +++l++g ++g g
  gi|474934638|ref|YP_007688220.1|  4 DVIIIGAGPAGLTAGIYA-RSKmmkTLILDSG-RVG-G 38
                                      9*****************.655688******9.555.4 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 1e-07
                                       TTSTTTSEEEE.ETTEEEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE-- CS
                               DAO 126 palpgllgalf.ypdtgqvdpakltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaa 200
                                       p      ++++ yp+  +++++kl   l+++ae+l ++i+e+++v  +e+ d k     +ttp g+ +    v++a 
  gi|474934638|ref|YP_007688220.1|  45 P-----EKGIHnYPGFETIQARKLSDKLYAQAESLECDIRENEPVDTIENGDQK-LL--VTTPnGTYE-GMSVIVAI 112
                                       4.....46788899999*******************************875433.33..599989853.366***** PP

                                       GGGHHHH.HTT..CTTTSEEEEEEEEEEEEEECCTHSTG CS
                               DAO 201 Gawsdll.gll..keldlpispvrgqvlvlkplseklvs 236
                                       G + +++ +++  +  + +    +g ++ l p++e+lv 
  gi|474934638|ref|YP_007688220.1| 113 GMG-RFTpKRMgaE-GEDR-LEGKGVSYIL-PVKEELVG 147
                                       987.4556444442.2224.4458888888.77776554 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1      0.14   1.8e+02       2      20 ..       5      23 ..       4      39 .. 0.79
   2 ?   -1.8   0.0       3.9   4.9e+03      45      72 ..      66      93 ..      56      98 .. 0.71
   3 ?   -0.8   0.0       1.8   2.3e+03      36      59 ..     116     139 ..     106     144 .. 0.81
   4 !   28.8   0.3   1.1e-09   1.4e-06       1      79 [.     149     219 ..     149     223 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.14
                                      EEEECSSHHHHHHHHHHHH CS
                         Pyr_redox  2 vvvvGgGyiglElAgalae 20
                                      v+++G+G  gl ++ +++ 
  gi|474934638|ref|YP_007688220.1|  5 VIIIGAGPAGLTAGIYARS 23
                                      89*********98887765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.9
                                      HHHHHHHHTTEEEECSEEEEEEEEETTS CS
                         Pyr_redox 45 ilqeklekngievllntkveeiegsedg 72
                                       l  + e +  +++ n+ v  ie  +++
  gi|474934638|ref|YP_007688220.1| 66 KLYAQAESLECDIRENEPVDTIENGDQK 93
                                      4555667778889999999999955554 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.8
                                       TTSSHHHHHHHHHHHHHTTEEEEC CS
                         Pyr_redox  36 rllDeeaskilqeklekngievll 59 
                                       r  ++ ++++ +++le +g+  +l
  gi|474934638|ref|YP_007688220.1| 116 RFTPKRMGAEGEDRLEGKGVSYIL 139
                                       667889999999*******98876 PP

  == domain 4  score: 28.8 bits;  conditional E-value: 1.1e-09
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEE CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedgvesvk 77 
                                       kvv  GgG++++++  ++     ++t+v+r+ +++      a +i  ++l + +++ ++n++v++++g+e+ +es++
  gi|474934638|ref|YP_007688220.1| 149 KVVLFGGGNSAIDMSLIADSVT-DTTIVHRRAEFR------ADEISVKNLDESNVRKIMNASVKSFNGEEK-LESIT 217
                                       68999*********98877666.************......*****************************9.9***9 PP

                                       EE CS
                         Pyr_redox  78 lk 79 
                                       l+
  gi|474934638|ref|YP_007688220.1| 218 LE 219
                                       97 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.4e-07   0.00018       1      50 [.       4      52 ..       4     104 .. 0.78
   2 ?    3.1   0.1     0.037        47      92     138 ..     186     231 ..     166     233 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.4e-07
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignk 50
                                      Dv+++G+gpaG++A i A  +  k+l+++  g++GG+l +      i+n+
  gi|474934638|ref|YP_007688220.1|  4 DVIIIGAGPAGLTAGIYARSKMMKTLILDS-GRVGGQLVALYPEKGIHNY 52
                                      9***********************999875.779***9988777777777 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.037
                      FAD_oxidored  92 vleemlaeagvtvllntrlvevekegkriesvtveskegrktirAkv 138
                                       +  + l+e++v+ ++n+ +++ + e+ ++es+t+e++ ++ +i A++
  gi|474934638|ref|YP_007688220.1| 186 ISVKNLDESNVRKIMNASVKSFNGEE-KLESITLEQEGKELVIPADL 231
                                       44556799***************997.9******8655799998876 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.7   6.3e-08   8.1e-05       1      39 [.       4      41 ..       4      43 .. 0.92
   2 ?   -2.5   0.0       1.6     2e+03     140     170 ..      60      90 ..      52     100 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 6.3e-08
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGG CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggata 39
                                      Dvi+iG+G AGL+A++ a+ +  k+++++ + + gg+++
  gi|474934638|ref|YP_007688220.1|  4 DVIIIGAGPAGLTAGIYARSKMMKTLILDSGRV-GGQLV 41
                                      9****************************9987.77765 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.6
                                       HHHHHHHHHHHHHTCTEEEEESEEEEEEEEC CS
                     FAD_binding_2 140 ghallarlvesarkagvdfqerteadeLive 170
                                        ++l   l+++a+++++d++e+ ++d++   
  gi|474934638|ref|YP_007688220.1|  60 ARKLSDKLYAQAESLECDIRENEPVDTIENG 90 
                                       56777789999999999*9999999998554 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.2   3.5e-07   0.00045      17      49 ..       2      33 ..       1      40 [. 0.85
   2 ?   -1.1   0.0      0.71   9.1e+02      88     118 ..     170     202 ..     146     208 .. 0.62

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 3.5e-07
                                      EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                              Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailer 49
                                      + Dv+i+GaG++GLta+ y   k  +k++il++
  gi|474934638|ref|YP_007688220.1|  2 VYDVIIIGAGPAGLTAGIYARSK-MMKTLILDS 33
                                      67***************997777.999999976 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.71
                                       SSEEEESEHHHHHH.HHHHHHHTSTTE.EEEES CS
                              Thi4  88 gdyvvvkdaalfts.tllskvlqlanv.kllna 118
                                        d  +v   a+f + ++ +k l+ +nv k++na
  gi|474934638|ref|YP_007688220.1| 170 TDTTIVHRRAEFRAdEISVKNLDESNVrKIMNA 202
                                       445556666666552456666666666344444 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0    0.0034       4.4       2      33 ..       2      31 ..       1      35 [. 0.78
   2 !   10.9   0.0   0.00015      0.19     133     230 ..      94     183 ..      58     223 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0034
                       K_oxygenase  2 ilDligiGiGpsnLsLailleevkkelkalfl 33
                                      ++D+i+iG+Gp+ L+  i ++++   +k+l l
  gi|474934638|ref|YP_007688220.1|  2 VYDVIIIGAGPAGLTAGIYARSKM--MKTLIL 31
                                      79***********99877777665..566555 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00015
                       K_oxygenase 133 ltveskdaegeeeelearnlvlgvGtepkiPevleklegkervv.HsseylerkeellakkriaVvGsGqSaaeife 208
                                       l v++      + ++e  ++++++G  +  P+ + +  + +r+     +y    +e+l +k+++  G+G Sa ++  
  gi|474934638|ref|YP_007688220.1|  94 LLVTT-----PNGTYEGMSVIVAIGMGRFTPKRMGAEGE-DRLEgKGVSYILPVKEELVGKKVVLFGGGNSAIDMS- 163
                                       44443.....46789999****************98664.5554145599999999****************7753. PP

                       K_oxygenase 209 dllrrqkkvelklvtrsealep 230
                                        l++++  ++ ++v r++++++
  gi|474934638|ref|YP_007688220.1| 164 -LIADSV-TDTTIVHRRAEFRA 183
                                       .444332.45556666655554 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   2.3e-06    0.0029       1      35 [.       7      40 ..       7      54 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.3e-06
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGra 35
                                      I+GaG +Gl+a  +++ +  + l+l+++ r+GG++
  gi|474934638|ref|YP_007688220.1|  7 IIGAGPAGLTAGIYARSKMMKTLILDSG-RVGGQL 40
                                      9**************************8.889875 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.8e-05     0.036     213     263 ..      64     115 ..      21     124 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.8e-05
                                       HHHHHH..TTTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S-HH CS
                     Amino_oxidase 213 pealae..elrgldirlntrVkeikregdgvtvtledgevveaDaVvvTvplg 263
                                        + l +  e+++ dir n++V  i+ ++ +  vt+ +g+  e+ +V+v++ +g
  gi|474934638|ref|YP_007688220.1|  64 SDKLYAqaESLECDIRENEPVDTIENGDQKLLVTTPNGTY-EGMSVIVAIGMG 115
                                       455555667999**************************97.*********987 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.7   3.9e-05     0.049       2      23 ..       3      24 ..       2      82 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.9e-05
                                      EEEEEE--SHHHHHHHHHHHHT CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLsea 23
                                      +dV+I+GaGpaGl+++   +++
  gi|474934638|ref|YP_007688220.1|  3 YDVIIIGAGPAGLTAGIYARSK 24
                                      69************99765555 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.4   7.6e-05     0.097       1      28 [.       4      31 ..       4      59 .. 0.87
   2 ?    0.5   0.0       0.2   2.5e+02     113     195 ..      78     158 ..      61     205 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.6e-05
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEE CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi 28
                                      dvi+iG+G AG+ A + a  + +k+l++
  gi|474934638|ref|YP_007688220.1|  4 DVIIIGAGPAGLTAGIYARSKMMKTLIL 31
                                      8****************99999999887 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.2
                                       EEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT-BT-EEEETTEEEESSCTTC--B-THHHHHHHTT--EEE CS
                              GIDA 113 iieeeveeliveekkvkgvvtedgetikakavviatGtflkgkihigekelsaGrlgeltseglseslkelgfellr 189
                                       i+e+e  +  +e++  k +vt+ + t++  +v++a G   + ++     e + +  g+  s+ l  + + +g++++ 
  gi|474934638|ref|YP_007688220.1|  78 IRENEPVDT-IENGDQKLLVTTPNGTYEGMSVIVAIGM-GRFTPKRMGAEGEDRLEGKGVSYILPVKEELVGKKVVL 152
                                       555554444.3577778888999999999999999998.22222222222222224444444444444447777776 PP

                                       EEEEE- CS
                              GIDA 190 lktgtp 195
                                       + +g +
  gi|474934638|ref|YP_007688220.1| 153 FGGGNS 158
                                       666653 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1   0.00059      0.75       1      13 [.       4      16 ..       4      36 .. 0.75
   2 ?   -0.6   0.0      0.41   5.3e+02      99     141 ..     194     238 ..     176     247 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00059
                     Lycopene_cycl  1 DvvviGaGpAgls 13
                                      Dv++iGaGpAgl 
  gi|474934638|ref|YP_007688220.1|  4 DVIIIGAGPAGLT 16
                                      9**********97 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.41
                     Lycopene_cycl  99 engvklleakvesveeeeageslvvleggr..kirarlvvdargl 141
                                       +n +k ++a v+s + ee+ es    ++g+   i+a l+v+  g+
  gi|474934638|ref|YP_007688220.1| 194 SNVRKIMNASVKSFNGEEKLESITLEQEGKelVIPADLAVVNIGI 238
                                       456788999999999999966655555566688999999988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.51
# Mc/sec: 1840.05
//
Query:       gi|474934639|ref|YP_007688221.1|  [L=56]
Description: 4Fe-4S binding domain protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-18   65.9  22.0    1.7e-10   40.2   7.1    2.1  2  Fer4             4Fe-4S binding domain
    2.1e-13   49.7  20.5    8.9e-07   28.7   5.8    2.1  2  Fer4_6           4Fe-4S binding domain
    1.2e-11   45.0  14.1    2.1e-11   44.2  14.1    1.4  1  Fer4_7           4Fe-4S dicluster domain
    3.1e-11   42.7  16.0    3.8e-06   26.7   3.8    2.1  2  Fer4_2           4Fe-4S binding domain
    7.5e-11   42.0  28.2      6e-08   32.7  16.2    1.9  2  Fer4_10          4Fe-4S dicluster domain
    1.8e-10   40.8  12.6    2.5e-10   40.3  12.6    1.3  1  Fer4_9           4Fe-4S dicluster domain
    1.8e-10   40.8  14.4    4.2e-06   26.8   3.9    2.0  2  Fer4_21          4Fe-4S dicluster domain
    2.2e-10   41.3  11.9    7.9e-06   26.7   3.8    2.0  2  Fer4_16          4Fe-4S double cluster binding domain
    3.1e-08   33.5  14.2    0.00033   20.9   2.1    2.1  2  Fer4_4           4Fe-4S binding domain
    4.4e-07   30.2   8.5     0.0021   18.5   0.7    2.1  2  Fer4_8           4Fe-4S dicluster domain
    7.7e-07   29.6   8.7     0.0046   17.5   1.7    2.1  2  Fer4_17          4Fe-4S dicluster domain
    8.5e-06   26.4  19.6       0.01   16.7   6.5    2.2  2  Fer4_3           4Fe-4S binding domain
    9.2e-05   23.2   8.3     0.0069   17.2   1.5    2.0  2  Fer4_22          4Fe-4S dicluster domain
    0.00068   20.1  18.1      0.085   13.4   4.5    2.2  2  Fer4_13          4Fe-4S single cluster domain of Ferredoxin I
     0.0044   17.7  16.1       0.27   12.0   2.4    2.9  2  Fer4_15          4Fe-4S single cluster domain
     0.0046   17.1  15.2     0.0087   16.2  15.2    1.5  1  Fer4_18          4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.94    9.6  10.2          2    8.5  10.2    1.7  1  Fer4_19          Divergent 4Fe-4S mono-cluster


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   7.1   1.6e-13   1.7e-10       1      24 []       2      25 ..       2      25 .. 0.95
   2 !   32.1   6.9     6e-11   6.3e-08       2      24 .]      31      53 ..      30      53 .. 0.95

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 1.6e-13
                                      EEEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  1 vvideekCigCGaCvevCPvgAIt 24
                                      ++++e+kC+gCG+C++vCP++AI+
  gi|474934639|ref|YP_007688221.1|  2 PKVIEDKCVGCGNCADVCPNDAIE 25
                                      5899*******************6 PP

  == domain 2  score: 32.1 bits;  conditional E-value: 6e-11
                                      EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  2 videekCigCGaCvevCPvgAIt 24
                                      vide kC+ C aCv+ CP gAI+
  gi|474934639|ref|YP_007688221.1| 31 VIDEAKCVECDACVDECPSGAIE 53
                                      8*********************6 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   5.8   8.4e-10   8.9e-07       2      24 .]       2      24 ..       1      24 [. 0.93
   2 !   27.4   6.8   2.2e-09   2.3e-06       1      24 []      29      52 ..      29      52 .. 0.97

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 8.4e-10
                            Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                      + + +dkC+gCg+C++vCP +ai
  gi|474934639|ref|YP_007688221.1|  2 PKVIEDKCVGCGNCADVCPNDAI 24
                                      7899***************9997 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 2.2e-09
                            Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                      v++id+ kC+ C++Cv+ CP gai
  gi|474934639|ref|YP_007688221.1| 29 VAVIDEAKCVECDACVDECPSGAI 52
                                      699********************8 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2  14.1     2e-14   2.1e-11       1      52 []       8      51 ..       8      51 .. 0.96

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 2e-14
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      +C+gCg+C+++Cp++aie++++        ++id+ kC+ C+aCv++CP+ga
  gi|474934639|ref|YP_007688221.1|  8 KCVGCGNCADVCPNDAIEIKDV--------AVIDEAKCVECDACVDECPSGA 51
                                      7******************998........799*****************98 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   3.8   3.6e-09   3.8e-06       3      22 .]       2      21 ..       1      21 [. 0.92
   2 !   22.3   4.4     9e-08   9.5e-05       3      21 ..      30      48 ..      28      49 .. 0.92

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 3.6e-09
                            Fer4_2  3 vvvdtdrCigCgaCvsaCPa 22
                                      ++v +d+C+gCg C ++CP+
  gi|474934639|ref|YP_007688221.1|  2 PKVIEDKCVGCGNCADVCPN 21
                                      6789***************5 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 9e-08
                            Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                      +v+d+++C++C aCv+ CP
  gi|474934639|ref|YP_007688221.1| 30 AVIDEAKCVECDACVDECP 48
                                      799**************** PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7  16.2   5.7e-11     6e-08       4      56 .]       4      48 ..       1      48 [. 0.93
   2 !   20.3   4.1   4.3e-07   0.00045       2      21 ..      30      49 ..      29      55 .. 0.89

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 5.7e-11
                           Fer4_10  4 idddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      + +d+C++Cg+C ++CP         ++++++++  ++  kC +c aCv++CP
  gi|474934639|ref|YP_007688221.1|  4 VIEDKCVGCGNCADVCPN--------DAIEIKDVAVIDEAKCVECDACVDECP 48
                                      5679**************........9999999999999*************9 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 4.3e-07
                           Fer4_10  2 vvidddtCirCgkCvkaCPa 21
                                      +vid+ +C++C +Cv+ CP+
  gi|474934639|ref|YP_007688221.1| 30 AVIDEAKCVECDACVDECPS 49
                                      589****************9 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3  12.6   2.4e-13   2.5e-10       1      51 []       8      52 ..       7      52 .. 0.96

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 2.4e-13
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                      kC+gCg+C ++Cp+++++ ++++ +++       +C++C aCv+ Cp+gai
  gi|474934639|ref|YP_007688221.1|  8 KCVGCGNCADVCPNDAIEIKDVAVIDEA------KCVECDACVDECPSGAI 52
                                      7************************997......7*************998 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   3.9     4e-09   4.2e-06      35      58 ..       3      25 ..       1      26 [. 0.90
   2 !   20.0   2.8   5.2e-07   0.00055       1      23 [.      30      52 ..      29      54 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 4e-09
                           Fer4_21 35 kvvedeCvGCnlCssvCPvedcie 58
                                      kv+ed+CvGC  C++vCP +d+ie
  gi|474934639|ref|YP_007688221.1|  3 KVIEDKCVGCGNCADVCP-NDAIE 25
                                      799***************.79997 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 5.2e-07
                           Fer4_21  1 AridedkCigCgkCliaCedtsh 23
                                      A+ide+kC++C  C+  C+ +++
  gi|474934639|ref|YP_007688221.1| 30 AVIDEAKCVECDACVDECPSGAI 52
                                      78999999999999999997665 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   3.8   7.4e-09   7.9e-06       1      30 [.       8      37 ..       8      38 .. 0.92
   2 !   20.9   2.8   5.1e-07   0.00054       1      19 [.      36      54 ..      36      56 .] 0.92

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 7.4e-09
                           Fer4_16  1 rCgtCgkCaevCPtnaikekkekeiearec 30
                                      +C++Cg+Ca+vCP +ai+ k  ++i+  +c
  gi|474934639|ref|YP_007688221.1|  8 KCVGCGNCADVCPNDAIEIKDVAVIDEAKC 37
                                      6*****************999999999888 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 5.1e-07
                           Fer4_16  1 rCgtCgkCaevCPtnaike 19
                                      +C++C +C++ CP++ai+ 
  gi|474934639|ref|YP_007688221.1| 36 KCVECDACVDECPSGAIEP 54
                                      6****************86 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   2.1   3.2e-07   0.00033       2      15 ..       7      20 ..       6      29 .. 0.92
   2 !   18.5   4.5   1.9e-06     0.002       3      17 .]      36      50 ..      34      50 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 3.2e-07
                            Fer4_4  2 erCigCgsCvaaCP 15
                                      ++C+gCg C ++CP
  gi|474934639|ref|YP_007688221.1|  7 DKCVGCGNCADVCP 20
                                      89************ PP

  == domain 2  score: 18.5 bits;  conditional E-value: 1.9e-06
                            Fer4_4  3 rCigCgsCvaaCPqg 17
                                      +C++C++Cv+ CP+g
  gi|474934639|ref|YP_007688221.1| 36 KCVECDACVDECPSG 50
                                      8************86 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.7     2e-06    0.0021       4      63 ..       8      21 ..       4      32 .. 0.67
   2 !   16.4   1.7   8.9e-06    0.0094       4      17 ..      36      49 ..      33      54 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2e-06
                            Fer4_8  4 kCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63
                                      k                                              C++cg+C++vCp+
  gi|474934639|ref|YP_007688221.1|  8 K----------------------------------------------CVGCGNCADVCPN 21
                                      4..............................................5555555555554 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 8.9e-06
                            Fer4_8  4 kCieCgaCqsaCpv 17
                                      kC+eC aC ++Cp+
  gi|474934639|ref|YP_007688221.1| 36 KCVECDACVDECPS 49
                                      79999999999986 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   1.7   4.3e-06    0.0046      44      59 ..       7      22 ..       2      24 .. 0.89
   2 !   16.9   0.8   6.4e-06    0.0068      45      59 ..      36      50 ..      25      55 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.3e-06
                           Fer4_17 44 slCieCgeCerkCPqg 59
                                      ++C++Cg+C+ +CP++
  gi|474934639|ref|YP_007688221.1|  7 DKCVGCGNCADVCPND 22
                                      68************97 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 6.4e-06
                           Fer4_17 45 lCieCgeCerkCPqg 59
                                      +C+eC  C+ +CP+g
  gi|474934639|ref|YP_007688221.1| 36 KCVECDACVDECPSG 50
                                      577777777777765 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   6.5   9.9e-06      0.01       1      15 []       9      23 ..       9      23 .. 0.97
   2 !   15.9   5.1   1.8e-05     0.019       1      15 []      37      51 ..      37      51 .. 0.98

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 9.9e-06
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+gCg C +vCP++A
  gi|474934639|ref|YP_007688221.1|  9 CVGCGNCADVCPNDA 23
                                      ************998 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.8e-05
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+ C aCv+ CP+gA
  gi|474934639|ref|YP_007688221.1| 37 CVECDACVDECPSGA 51
                                      **************9 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   1.5   6.5e-06    0.0069      79      94 ..       6      21 ..       1      23 [. 0.84
   2 !   10.6   0.8   0.00075      0.79      77      94 ..      32      49 ..      25      51 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 6.5e-06
                           Fer4_22 79 esgCvGCgRCieacpv 94
                                      e +CvGCg C ++cp+
  gi|474934639|ref|YP_007688221.1|  6 EDKCVGCGNCADVCPN 21
                                      678***********97 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00075
                           Fer4_22 77 fgesgCvGCgRCieacpv 94
                                      ++e +Cv C  C++ cp+
  gi|474934639|ref|YP_007688221.1| 32 IDEAKCVECDACVDECPS 49
                                      577889999999999986 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   4.5     8e-05     0.085       2      18 ..       6      21 ..       5      23 .. 0.92
   2 !   12.7   5.7   0.00014      0.14       1      18 [.      32      49 ..      32      50 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8e-05
                           Fer4_13  2 DrdtCiacgaCvelaPd 18
                                      + d+C++cg+C++++P+
  gi|474934639|ref|YP_007688221.1|  6 E-DKCVGCGNCADVCPN 21
                                      5.9*************6 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00014
                           Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                      +D+ +C++c+aCv+ +P 
  gi|474934639|ref|YP_007688221.1| 32 IDEAKCVECDACVDECPS 49
                                      899**************5 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   6.0    0.0016       1.7       5      20 ..       6      21 ..       3      27 .. 0.87
   2 !   12.0   2.4   0.00025      0.27       2      20 ..      31      49 ..      30      54 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0016
                           Fer4_15  5 rdaCigcglCvaeape 20
                                      +d+C gcg+C++++p+
  gi|474934639|ref|YP_007688221.1|  6 EDKCVGCGNCADVCPN 21
                                      599***********85 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00025
                           Fer4_15  2 vvDrdaCigcglCvaeape 20
                                      v+D+ +C  c +Cv+e+p 
  gi|474934639|ref|YP_007688221.1| 31 VIDEAKCVECDACVDECPS 49
                                      79***************95 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2  15.2   8.3e-06    0.0087      58      96 ..       6      48 ..       2      53 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 8.3e-06
                           Fer4_18 58 agdcidcescvkvcPt.gidirkGlql...eciscllcidacd 96
                                      + +c+ c+ c +vcP   i+i++   +   +c++c  c+d c 
  gi|474934639|ref|YP_007688221.1|  6 EDKCVGCGNCADVCPNdAIEIKDVAVIdeaKCVECDACVDECP 48
                                      568************8359**9987652227**********95 PP

>> Fer4_19  Divergent 4Fe-4S mono-cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5  10.2    0.0019         2      13      60 ..       7      53 ..       4      56 .] 0.75

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0019
                           Fer4_19 13 elCihsgnCvkglpevFdpkrkpwikpdeasteeiievverCPSGALs 60
                                      + C + gnC    p+      k     dea+  e  + v++CPSGA++
  gi|474934639|ref|YP_007688221.1|  7 DKCVGCGNCADVCPNDAIE-IKDVAVIDEAKCVECDACVDECPSGAIE 53
                                      5677778887766653322.234578899999**************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      190  (0.0105974); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 398.05
//
Query:       gi|474934640|ref|YP_007688222.1|  [L=54]
Description: Dissimilatory sulfite reductase (desulfoviridin), alpha and beta subunits [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.9e-15   54.6  21.2    1.2e-08   34.4   7.4    2.1  2  Fer4        4Fe-4S binding domain
      9e-13   47.7  20.6    1.4e-06   28.1   6.1    2.1  2  Fer4_6      4Fe-4S binding domain
      4e-12   46.1  24.9    3.3e-09   36.7  13.3    1.5  2  Fer4_9      4Fe-4S dicluster domain
    7.5e-10   39.3  13.5    1.6e-09   38.2  13.5    1.5  1  Fer4_7      4Fe-4S dicluster domain
    3.1e-09   36.4  16.0    2.8e-05   23.9   4.0    2.1  2  Fer4_2      4Fe-4S binding domain
    6.8e-09   36.5  11.3    9.8e-06   26.4   4.2    2.0  2  Fer4_16     4Fe-4S double cluster binding domain
    1.5e-08   34.6  13.2    1.7e-08   34.4  13.2    1.1  1  Fer4_10     4Fe-4S dicluster domain
    2.5e-08   33.9  16.2    0.00017   21.6   3.6    2.0  2  Fer4_21     4Fe-4S dicluster domain
    1.2e-07   31.7  13.6    0.00018   21.8   1.9    2.1  2  Fer4_4      4Fe-4S binding domain
    1.5e-06   28.5  10.2    0.00094   19.6   1.2    2.1  2  Fer4_8      4Fe-4S dicluster domain
      4e-06   27.3   8.2      0.004   17.7   1.6    2.1  2  Fer4_17     4Fe-4S dicluster domain
    0.00045   20.4  14.3    0.00054   20.1  14.3    1.1  1  Fer4_18     4Fe-4S dicluster domain
     0.0069   17.2  20.4      0.033   15.1   8.0    2.2  2  Fer4_3      4Fe-4S binding domain
     0.0075   16.8  18.8      0.075   13.6   4.6    2.2  2  Fer4_13     4Fe-4S single cluster domain of Ferredoxin I
  ------ inclusion threshold ------
      0.015   16.1  13.3       0.48   11.3   2.3    2.0  3  Fer4_22     4Fe-4S dicluster domain
       0.16   12.7  17.2       0.29   11.9   3.4    2.6  2  Fer4_15     4Fe-4S single cluster domain
        3.5    7.5   8.6        4.6    7.1   1.2    2.2  2  zf-C2H2_11  zinc-finger C2H2-type


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   7.4   1.2e-11   1.2e-08       1      24 []       2      25 ..       2      25 .. 0.95
   2 !   26.7   5.8     3e-09   3.2e-06       2      24 .]      31      53 ..      30      53 .. 0.93

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 1.2e-11
                                      EEEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  1 vvideekCigCGaCvevCPvgAIt 24
                                      ++i+ e C++CGaC++vCP gAIt
  gi|474934640|ref|YP_007688222.1|  2 PKIIAENCVACGACADVCPEGAIT 25
                                      5899*******************7 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 3e-09
                                      EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  2 videekCigCGaCvevCPvgAIt 24
                                      vid +kC+ CGaCv+ C  +AI+
  gi|474934640|ref|YP_007688222.1| 31 VIDDSKCVDCGACVDECNSDAIE 53
                                      8****************999996 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   6.1   1.3e-09   1.4e-06       2      24 .]       2      24 ..       1      24 [. 0.94
   2 !   26.0   6.6   6.2e-09   6.6e-06       1      24 []      29      52 ..      29      52 .. 0.94

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 1.3e-09
                            Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                      + i +++C+ Cg+C++vCPegai
  gi|474934640|ref|YP_007688222.1|  2 PKIIAENCVACGACADVCPEGAI 24
                                      78999*****************8 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 6.2e-09
                            Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                      v++id++kC++Cg+Cv+ C  +ai
  gi|474934640|ref|YP_007688222.1| 29 VAVIDDSKCVDCGACVDECNSDAI 52
                                      699****************99887 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   3.7   4.6e-07   0.00048      34      51 .]       7      24 ..       3      24 .. 0.89
   2 !   36.7  13.3   3.2e-12   3.3e-09       1      51 []       8      52 ..       8      52 .. 0.96

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 4.6e-07
                            Fer4_9 34 eaCigCgaCveaCpkgai 51
                                      e+C+ CgaC+++Cp+gai
  gi|474934640|ref|YP_007688222.1|  7 ENCVACGACADVCPEGAI 24
                                      48*************997 PP

  == domain 2  score: 36.7 bits;  conditional E-value: 3.2e-12
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                      +C+ CgaC ++Cp g+++ d+++ ++        +C++CgaCv+ C+++ai
  gi|474934640|ref|YP_007688222.1|  8 NCVACGACADVCPEGAITIDDVAVIDDS------KCVDCGACVDECNSDAI 52
                                      6************************997......7*************997 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2  13.5   1.5e-12   1.6e-09       2      52 .]       9      51 ..       8      51 .. 0.95

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 1.5e-12
                            Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      C+ CgaC+++Cp +ai++d++        ++id +kC++CgaCv++C ++a
  gi|474934640|ref|YP_007688222.1|  9 CVACGACADVCPEGAITIDDV--------AVIDDSKCVDCGACVDECNSDA 51
                                      ******************998........79****************9986 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   4.0   2.7e-08   2.8e-05       3      22 .]       2      21 ..       1      21 [. 0.90
   2 !   18.7   4.1   1.2e-06    0.0013       3      20 ..      30      47 ..      28      49 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 2.7e-08
                            Fer4_2  3 vvvdtdrCigCgaCvsaCPa 22
                                      +++ +++C++CgaC ++CP+
  gi|474934640|ref|YP_007688222.1|  2 PKIIAENCVACGACADVCPE 21
                                      67889**************5 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 1.2e-06
                            Fer4_2  3 vvvdtdrCigCgaCvsaC 20
                                      +v+d  +C+ CgaCv+ C
  gi|474934640|ref|YP_007688222.1| 30 AVIDDSKCVDCGACVDEC 47
                                      78999************9 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   4.2   9.3e-09   9.8e-06       1      30 [.       8      37 ..       8      38 .. 0.91
   2 !   15.7   2.2     2e-05     0.021       1      18 [.      36      53 ..      36      54 .] 0.93

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 9.3e-09
                           Fer4_16  1 rCgtCgkCaevCPtnaikekkekeiearec 30
                                      +C+ Cg+Ca+vCP++ai+ +  ++i+  +c
  gi|474934640|ref|YP_007688222.1|  8 NCVACGACADVCPEGAITIDDVAVIDDSKC 37
                                      6*****************998899988887 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 2e-05
                           Fer4_16  1 rCgtCgkCaevCPtnaik 18
                                      +C++Cg+C++ C ++ai+
  gi|474934640|ref|YP_007688222.1| 36 KCVDCGACVDECNSDAIE 53
                                      6***************97 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4  13.2   1.6e-11   1.7e-08       3      55 ..       3      47 ..       1      48 [. 0.95

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 1.6e-11
                           Fer4_10  3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55
                                      +i ++ C+ Cg+C ++CP         g+++++++  ++ +kC +cgaCv++C
  gi|474934640|ref|YP_007688222.1|  3 KIIAENCVACGACADVCPE--------GAITIDDVAVIDDSKCVDCGACVDEC 47
                                      678899*************........************************** PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   3.6   1.6e-07   0.00017      35      58 ..       3      25 ..       1      26 [. 0.88
   2 !   18.7   4.7   1.3e-06    0.0014       1      26 [.      30      52 ..      30      54 .] 0.87

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.6e-07
                           Fer4_21 35 kvvedeCvGCnlCssvCPvedcie 58
                                      k+++++Cv+C  C++vCP e++i+
  gi|474934640|ref|YP_007688222.1|  3 KIIAENCVACGACADVCP-EGAIT 25
                                      5789**************.89998 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 1.3e-06
                           Fer4_21  1 AridedkCigCgkCliaCedtshqai 26
                                      A+id++kC++Cg C+  C+  +   i
  gi|474934640|ref|YP_007688222.1| 30 AVIDDSKCVDCGACVDECNSDA---I 52
                                      89*****************644...4 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   1.9   1.7e-07   0.00018       2      16 ..       7      21 ..       6      28 .. 0.92
   2 !   15.8   4.2   1.4e-05     0.014       3      15 ..      36      48 ..      34      50 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.7e-07
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      e+C+ Cg+C ++CP 
  gi|474934640|ref|YP_007688222.1|  7 ENCVACGACADVCPE 21
                                      89************6 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.4e-05
                            Fer4_4  3 rCigCgsCvaaCP 15
                                      +C++Cg+Cv+ C 
  gi|474934640|ref|YP_007688222.1| 36 KCVDCGACVDECN 48
                                      8***********6 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   1.2   8.9e-07   0.00094      48      64 ..       6      22 ..       2      26 .. 0.76
   2 !   14.2   2.1   4.4e-05     0.046       3      16 ..      35      48 ..      33      52 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 8.9e-07
                            Fer4_8 48 lwsCttcgaCtevCpvg 64
                                      +++C++cgaC++vCp+g
  gi|474934640|ref|YP_007688222.1|  6 AENCVACGACADVCPEG 22
                                      56788888888888875 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 4.4e-05
                            Fer4_8  3 ekCieCgaCqsaCp 16
                                      +kC+ CgaC ++C 
  gi|474934640|ref|YP_007688222.1| 35 SKCVDCGACVDECN 48
                                      68999999999996 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   1.6   3.8e-06     0.004      43      59 ..       6      22 ..       1      24 [. 0.86
   2 !   14.2   0.6   4.5e-05     0.048      45      58 ..      36      49 ..      25      53 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.8e-06
                           Fer4_17 43 aslCieCgeCerkCPqg 59
                                      a++C+ Cg C+ +CP+g
  gi|474934640|ref|YP_007688222.1|  6 AENCVACGACADVCPEG 22
                                      789***********986 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 4.5e-05
                           Fer4_17 45 lCieCgeCerkCPq 58
                                      +C+ Cg C+ +C +
  gi|474934640|ref|YP_007688222.1| 36 KCVDCGACVDECNS 49
                                      56666666666654 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1  14.3   5.1e-07   0.00054      59      97 ..       7      49 ..       3      53 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 5.1e-07
                           Fer4_18 59 gdcidcescvkvcPtg.idirkGlql...eciscllcidacdk 97
                                       +c++c++c +vcP g i i +   +   +c+ c+ c+d c++
  gi|474934640|ref|YP_007688222.1|  7 ENCVACGACADVCPEGaITIDDVAVIddsKCVDCGACVDECNS 49
                                      68************8756666665442228***********95 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   8.0   3.2e-05     0.033       1      15 []       9      23 ..       9      23 .. 0.97
   2 !    8.3   4.5    0.0047         5       1      11 [.      37      47 ..      37      51 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.2e-05
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+ CgaC +vCP+gA
  gi|474934640|ref|YP_007688222.1|  9 CVACGACADVCPEGA 23
                                      999***********9 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0047
                            Fer4_3  1 CtgCgaCvevC 11
                                      C+ CgaCv+ C
  gi|474934640|ref|YP_007688222.1| 37 CVDCGACVDEC 47
                                      999******99 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   4.6   7.1e-05     0.075       4      18 ..       7      21 ..       5      22 .. 0.93
   2 !    9.3   6.3    0.0016       1.7       1      16 [.      32      47 ..      32      50 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.1e-05
                           Fer4_13  4 dtCiacgaCvelaPd 18
                                      ++C+acgaC++++P+
  gi|474934640|ref|YP_007688222.1|  7 ENCVACGACADVCPE 21
                                      79************8 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0016
                           Fer4_13  1 VDrdtCiacgaCvela 16
                                      +D ++C++cgaCv+ +
  gi|474934640|ref|YP_007688222.1| 32 IDDSKCVDCGACVDEC 47
                                      799**********998 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   3.4   0.00054      0.57      81      94 ..       8      21 ..       2      24 .. 0.70
   2 ?   11.2   2.8    0.0005      0.53       2      14 ..       9      21 ..       8      34 .. 0.74
   3 ?   11.3   2.3   0.00046      0.48      77      94 ..      32      49 ..      23      51 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00054
                           Fer4_22 81 gCvGCgRCieacpv 94
                                       Cv Cg C ++cp+
  gi|474934640|ref|YP_007688222.1|  8 NCVACGACADVCPE 21
                                      67777777777765 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0005
                           Fer4_22  2 ClsCgaCtlvCpt 14
                                      C++CgaC+ vCp 
  gi|474934640|ref|YP_007688222.1|  9 CVACGACADVCPE 21
                                      7777777777764 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00046
                           Fer4_22 77 fgesgCvGCgRCieacpv 94
                                      ++ s+Cv Cg C++ c++
  gi|474934640|ref|YP_007688222.1| 32 IDDSKCVDCGACVDECNS 49
                                      58899***********86 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   6.0     0.019        20       6      20 ..       7      21 ..       4      28 .. 0.78
   2 ?   11.9   3.4   0.00028      0.29       2      19 ..      31      49 ..      30      54 .] 0.85

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.019
                           Fer4_15  6 daCigcglCvaeape 20
                                      ++C  cg+C++++pe
  gi|474934640|ref|YP_007688222.1|  7 ENCVACGACADVCPE 21
                                      679999999999976 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00028
                           Fer4_15  2 vvDrdaCigcglCvaea.p 19
                                      v+D ++C  cg+Cv+e+ +
  gi|474934640|ref|YP_007688222.1| 31 VIDDSKCVDCGACVDECnS 49
                                      79**************944 PP

>> zf-C2H2_11  zinc-finger C2H2-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   1.1     0.025        27       7      13 ..       9      15 ..       6      15 .. 0.89
   2 ?    7.1   1.2    0.0044       4.6       6      13 ..      36      43 ..      35      44 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.025
                        zf-C2H2_11  7 CleCGlc 13
                                      C+ CG c
  gi|474934640|ref|YP_007688222.1|  9 CVACGAC 15
                                      ******9 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0044
                        zf-C2H2_11  6 qCleCGlc 13
                                      +C++CG c
  gi|474934640|ref|YP_007688222.1| 36 KCVDCGAC 43
                                      8******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      173  (0.00964917); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.49
# Mc/sec: 334.32
//
Query:       gi|474934641|ref|YP_007688223.1|  [L=54]
Description: 4Fe-4S binding domain protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.9e-16   58.5  20.5    1.4e-08   34.2   7.2    2.0  2  Fer4        4Fe-4S binding domain
    1.2e-13   50.4  20.0    5.8e-07   29.3   6.0    2.0  2  Fer4_6      4Fe-4S binding domain
    6.5e-12   45.4  25.9    5.3e-09   36.1  14.0    1.6  2  Fer4_9      4Fe-4S dicluster domain
    4.3e-10   40.0  13.4    1.2e-09   38.6  13.6    1.6  1  Fer4_7      4Fe-4S dicluster domain
    1.2e-09   37.6  15.2    2.6e-05   24.0   4.0    2.1  2  Fer4_2      4Fe-4S binding domain
    2.4e-09   38.0  11.7    1.3e-06   29.2   4.0    2.0  2  Fer4_16     4Fe-4S double cluster binding domain
    8.7e-09   35.4  13.5      1e-08   35.1  13.5    1.1  1  Fer4_10     4Fe-4S dicluster domain
      2e-08   34.3  16.2    0.00023   21.2   3.5    2.0  2  Fer4_21     4Fe-4S dicluster domain
      2e-08   34.1  13.5    0.00011   22.4   2.0    2.1  2  Fer4_4      4Fe-4S binding domain
    3.9e-07   30.4   9.0    0.00073   19.9   0.9    2.1  2  Fer4_8      4Fe-4S dicluster domain
    8.4e-05   23.0  14.4      0.015   15.8   3.7    2.1  2  Fer4_17     4Fe-4S dicluster domain
    0.00042   21.0  18.9      0.061   14.3   8.1    2.2  2  Fer4_3      4Fe-4S binding domain
     0.0008   19.9  18.7        0.1   13.1   5.2    2.3  2  Fer4_13     4Fe-4S single cluster domain of Ferredoxin I
     0.0027   17.9  13.1     0.0039   17.4  13.1    1.2  1  Fer4_18     4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.022   15.5  16.6      0.053   14.3   3.2    2.5  2  Fer4_15     4Fe-4S single cluster domain
      0.026   15.4  12.7       0.65   10.9   3.3    2.0  2  Fer4_22     4Fe-4S dicluster domain
        3.5    7.5   8.1        5.8    6.8   0.9    2.2  2  zf-C2H2_11  zinc-finger C2H2-type


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   7.2   1.3e-11   1.4e-08       1      24 []       2      25 ..       2      25 .. 0.95
   2 !   30.8   5.3   1.6e-10   1.7e-07       2      24 .]      31      53 ..      30      53 .. 0.95

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 1.3e-11
                                      EEEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  1 vvideekCigCGaCvevCPvgAIt 24
                                      ++i+ e C++CGaC+++CP gAIt
  gi|474934641|ref|YP_007688223.1|  2 PKIIAENCVACGACADACPEGAIT 25
                                      5899*******************7 PP

  == domain 2  score: 30.8 bits;  conditional E-value: 1.6e-10
                                      EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  2 videekCigCGaCvevCPvgAIt 24
                                      vid +kCi CGaCv+ C  +AI+
  gi|474934641|ref|YP_007688223.1| 31 VIDDSKCIDCGACVDECSSDAIE 53
                                      8********************96 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   6.1   1.9e-09     2e-06       2      24 .]       2      24 ..       1      24 [. 0.94
   2 !   29.3   6.0   5.5e-10   5.8e-07       1      24 []      29      52 ..      29      52 .. 0.95

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 1.9e-09
                            Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                      + i +++C+ Cg+C+++CPegai
  gi|474934641|ref|YP_007688223.1|  2 PKIIAENCVACGACADACPEGAI 24
                                      78999*****************8 PP

  == domain 2  score: 29.3 bits;  conditional E-value: 5.5e-10
                            Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                      v++id++kCi+Cg+Cv+ C  +ai
  gi|474934641|ref|YP_007688223.1| 29 VAVIDDSKCIDCGACVDECSSDAI 52
                                      699*****************9998 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   4.0   4.6e-07   0.00048      34      51 .]       7      24 ..       3      24 .. 0.89
   2 !   36.1  14.0     5e-12   5.3e-09       1      51 []       8      52 ..       8      52 .. 0.95

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 4.6e-07
                            Fer4_9 34 eaCigCgaCveaCpkgai 51
                                      e+C+ CgaC++aCp+gai
  gi|474934641|ref|YP_007688223.1|  7 ENCVACGACADACPEGAI 24
                                      48*************997 PP

  == domain 2  score: 36.1 bits;  conditional E-value: 5e-12
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                      +C+ CgaC +aCp g++++++++ ++        +Ci+CgaCv+ C ++ai
  gi|474934641|ref|YP_007688223.1|  8 NCVACGACADACPEGAITMEDVAVIDDS------KCIDCGACVDECSSDAI 52
                                      6************************997......7*************987 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6  13.6   1.1e-12   1.2e-09       2      52 .]       9      51 ..       8      51 .. 0.95

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 1.1e-12
                            Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      C+ CgaC++aCp +ai+++++        ++id +kC++CgaCv++C ++a
  gi|474934641|ref|YP_007688223.1|  9 CVACGACADACPEGAITMEDV--------AVIDDSKCIDCGACVDECSSDA 51
                                      ******************887........79****************9986 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   4.0   2.5e-08   2.6e-05       3      22 .]       2      21 ..       1      21 [. 0.90
   2 !   19.9   3.4   5.3e-07   0.00056       3      20 ..      30      47 ..      28      49 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.5e-08
                            Fer4_2  3 vvvdtdrCigCgaCvsaCPa 22
                                      +++ +++C++CgaC +aCP+
  gi|474934641|ref|YP_007688223.1|  2 PKIIAENCVACGACADACPE 21
                                      67889**************5 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 5.3e-07
                            Fer4_2  3 vvvdtdrCigCgaCvsaC 20
                                      +v+d  +Ci CgaCv+ C
  gi|474934641|ref|YP_007688223.1| 30 AVIDDSKCIDCGACVDEC 47
                                      78999************9 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   4.0   1.3e-09   1.3e-06       1      31 [.       8      38 ..       8      39 .. 0.94
   2 !   16.2   2.2   1.4e-05     0.015       1      18 [.      36      53 ..      36      54 .] 0.93

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 1.3e-09
                           Fer4_16  1 rCgtCgkCaevCPtnaikekkekeieareci 31
                                      +C+ Cg+Ca++CP++ai+++  ++i+  +ci
  gi|474934641|ref|YP_007688223.1|  8 NCVACGACADACPEGAITMEDVAVIDDSKCI 38
                                      6*******************99999999997 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.4e-05
                           Fer4_16  1 rCgtCgkCaevCPtnaik 18
                                      +C++Cg+C++ C ++ai+
  gi|474934641|ref|YP_007688223.1| 36 KCIDCGACVDECSSDAIE 53
                                      6***************97 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1  13.5   9.8e-12     1e-08       3      55 ..       3      47 ..       1      48 [. 0.95

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 9.8e-12
                           Fer4_10  3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55
                                      +i ++ C+ Cg+C +aCP         g+++ e++  ++ +kC++cgaCv++C
  gi|474934641|ref|YP_007688223.1|  3 KIIAENCVACGACADACPE--------GAITMEDVAVIDDSKCIDCGACVDEC 47
                                      678899*************........************************** PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   3.5   2.2e-07   0.00023      35      59 .]       3      26 ..       1      26 [. 0.90
   2 !   19.4   4.9     8e-07   0.00084       1      26 [.      30      52 ..      30      54 .] 0.86

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.2e-07
                           Fer4_21 35 kvvedeCvGCnlCssvCPvedciem 59
                                      k+++++Cv+C  C++ CP e++i+m
  gi|474934641|ref|YP_007688223.1|  3 KIIAENCVACGACADACP-EGAITM 26
                                      57899*************.8***99 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 8e-07
                           Fer4_21  1 AridedkCigCgkCliaCedtshqai 26
                                      A+id++kCi+Cg C+  C+  +   i
  gi|474934641|ref|YP_007688223.1| 30 AVIDDSKCIDCGACVDECSSDA---I 52
                                      89****************9644...4 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   2.0   1.1e-07   0.00011       2      16 ..       7      21 ..       6      28 .. 0.91
   2 !   17.6   4.0   3.7e-06    0.0039       3      16 ..      36      49 ..      34      50 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.1e-07
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      e+C+ Cg+C +aCP 
  gi|474934641|ref|YP_007688223.1|  7 ENCVACGACADACPE 21
                                      89************6 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 3.7e-06
                            Fer4_4  3 rCigCgsCvaaCPq 16
                                      +Ci+Cg+Cv+ C++
  gi|474934641|ref|YP_007688223.1| 36 KCIDCGACVDECSS 49
                                      8***********86 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.9   6.9e-07   0.00073       3      63 ..       7      21 ..       3      32 .. 0.68
   2 !   15.4   1.7   1.7e-05     0.018       3      16 ..      35      48 ..      33      53 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 6.9e-07
                            Fer4_8  3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63
                                      e+C+ CgaC +aCp                                              +
  gi|474934641|ref|YP_007688223.1|  7 ENCVACGACADACP----------------------------------------------E 21
                                      56777777777776..............................................3 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.7e-05
                            Fer4_8  3 ekCieCgaCqsaCp 16
                                      +kCi CgaC ++C 
  gi|474934641|ref|YP_007688223.1| 35 SKCIDCGACVDECS 48
                                      69***********5 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   3.7   1.4e-05     0.015      43      59 ..       6      22 ..       1      24 [. 0.87
   2 !   12.9   3.2   0.00012      0.12       1      15 [.      36      50 ..      36      54 .] 0.79

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.4e-05
                           Fer4_17 43 aslCieCgeCerkCPqg 59
                                      a++C+ Cg C+ +CP+g
  gi|474934641|ref|YP_007688223.1|  6 AENCVACGACADACPEG 22
                                      789************86 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00012
                           Fer4_17  1 rCiqCgyClpeCpsy 15
                                      +Ci Cg+C++eC+s 
  gi|474934641|ref|YP_007688223.1| 36 KCIDCGACVDECSSD 50
                                      699999999999875 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   8.1   5.8e-05     0.061       1      15 []       9      23 ..       9      23 .. 0.97
   2 !   12.8   3.0   0.00017      0.18       1      15 []      37      51 ..      37      51 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.8e-05
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+ CgaC ++CP+gA
  gi|474934641|ref|YP_007688223.1|  9 CVACGACADACPEGA 23
                                      999***********9 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00017
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+ CgaCv+ C ++A
  gi|474934641|ref|YP_007688223.1| 37 CIDCGACVDECSSDA 51
                                      9**********9987 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   5.2   9.8e-05       0.1       4      18 ..       7      21 ..       5      22 .. 0.93
   2 !   12.8   5.5   0.00013      0.13       1      16 [.      32      47 ..      32      53 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.8e-05
                           Fer4_13  4 dtCiacgaCvelaPd 18
                                      ++C+acgaC++++P+
  gi|474934641|ref|YP_007688223.1|  7 ENCVACGACADACPE 21
                                      79************8 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00013
                           Fer4_13  1 VDrdtCiacgaCvela 16
                                      +D ++Ci+cgaCv+ +
  gi|474934641|ref|YP_007688223.1| 32 IDDSKCIDCGACVDEC 47
                                      799**********999 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4  13.1   3.7e-06    0.0039      59      96 ..       7      48 ..       3      53 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.7e-06
                           Fer4_18 59 gdcidcescvkvcPtg.idirkGl...qleciscllcidacd 96
                                       +c++c++c + cP g i + +       +ci c+ c+d c+
  gi|474934641|ref|YP_007688223.1|  7 ENCVACGACADACPEGaITMEDVAvidDSKCIDCGACVDECS 48
                                      68************8744444443111568***********7 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   5.6     0.012        13       6      20 ..       7      21 ..       4      28 .. 0.82
   2 ?   14.3   3.2     5e-05     0.053       2      19 ..      31      48 ..      30      54 .] 0.85

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.012
                           Fer4_15  6 daCigcglCvaeape 20
                                      ++C  cg+C++++pe
  gi|474934641|ref|YP_007688223.1|  7 ENCVACGACADACPE 21
                                      689999999999986 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 5e-05
                           Fer4_15  2 vvDrdaCigcglCvaeap 19
                                      v+D ++Ci cg+Cv+e++
  gi|474934641|ref|YP_007688223.1| 31 VIDDSKCIDCGACVDECS 48
                                      79**************94 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   3.3   0.00061      0.65      80      94 ..       7      21 ..       2      24 .. 0.79
   2 ?   10.5   1.9   0.00079      0.83      77      94 ..      32      49 ..      23      51 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00061
                           Fer4_22 80 sgCvGCgRCieacpv 94
                                      + Cv Cg C +acp+
  gi|474934641|ref|YP_007688223.1|  7 ENCVACGACADACPE 21
                                      679999999999986 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00079
                           Fer4_22 77 fgesgCvGCgRCieacpv 94
                                      ++ s+C+ Cg C++ c +
  gi|474934641|ref|YP_007688223.1| 32 IDDSKCIDCGACVDECSS 49
                                      578899999999999976 PP

>> zf-C2H2_11  zinc-finger C2H2-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   1.1     0.025        27       7      13 ..       9      15 ..       6      15 .. 0.89
   2 ?    6.8   0.9    0.0055       5.8       6      13 ..      36      43 ..      35      44 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.025
                        zf-C2H2_11  7 CleCGlc 13
                                      C+ CG c
  gi|474934641|ref|YP_007688223.1|  9 CVACGAC 15
                                      ******9 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0055
                        zf-C2H2_11  6 qCleCGlc 13
                                      +C +CG c
  gi|474934641|ref|YP_007688223.1| 36 KCIDCGAC 43
                                      8******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      166  (0.00925874); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 358.44
//
Query:       gi|474934642|ref|YP_007688224.1|  [L=345]
Description: Cytosine deaminase-related metal-dependent hydrolase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.6e-10   39.7   0.0      5e-09   35.9   0.0    2.0  1  Amidohydro_1  Amidohydrolase family
  ------ inclusion threshold ------
       0.17   11.3   0.9          2    7.8   0.1    2.2  2  Amidohydro_3  Amidohydrolase family


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.0   5.6e-13     5e-09       1     260 [.      42     270 ..      42     300 .. 0.80

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 5.6e-13
                                       EEEE-EEEEEEECETTECSSS....GHHHHH.............STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSST CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrga....tledwl.............vppetaaealesgiktalksGtttvadmgatts 60 
                                       i++P ++D H+H  +   r +     le+++             +p + +   + +  k a+++G+  ++d+++  +
  gi|474934642|ref|YP_007688224.1|  42 IIVPSFVDCHTHCADAGAR-PsqgmSLEELVappdglkhrylreTPRSKLVNDMCQYGKDAFRNGVSAFIDFREGGV 117
                                       79**********9866444.36999999999*******************************************976 PP

                                       HHHHHHHHHHHTSSSEEEEEEESSEGGS.GCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHH CS
                      Amidohydro_1  61 tgiealleaaeelplglrilggkvsldr.gsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelke 136
                                       +g + l+e+  ++           ++ r +saet++++++ +++ a              ++a ++   +++ + ++
  gi|474934642|ref|YP_007688224.1| 118 DGCRMLRESGAQA----------AVYGRpSSAETDPNEIRDILTVA-------------DGIAISSVSDIPRRTAEM 171
                                       5555555533332..........233356999**********9999.............9999************** PP

                                       HHHHHHHHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHHHHHH CS
                      Amidohydro_1 137 alkeakkrdlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkea 213
                                       ++++++k+  p+a Ha+e       ++++++    +  +l+        ++  + ++h++  t+++++  +e+  ++
  gi|474934642|ref|YP_007688224.1| 172 IADVCRKERRPFALHASE------RVREDID----F--ILSL-------EP--AFVVHMTEATAADMRACAEN--DV 225
                                       ****************66......5566666....3..5555.......33..34577777778899999999..** PP

                                       CEEHHHHHHHHSEHHHHHHHHHHHHTSCEEEEEECTTSSCCGGHHHH CS
                      Amidohydro_1 214 gvahcpfsnsilrsgrealrkaldeGvkvglgtDgaasgnslnllee 260
                                        ++ cp+sn   ++ +++l+ ++d+G+ ++lgtD +a+   +++ +e
  gi|474934642|ref|YP_007688224.1| 226 PIVACPRSNAFFGK-TPNLALMMDSGAEISLGTD-NAMLCDPDMRKE 270
                                       ***********997.67*****************.555555554333 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1   0.00023         2      10      35 ..      43      69 ..      41      79 .. 0.79
   2 ?    1.4   0.1     0.019   1.7e+02     357     381 ..     240     265 ..     198     271 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00023
                      Amidohydro_3 10 vlPGFvDsHtHlagggvnl.rllrlpd 35
                                       +P FvD HtH a +g+   ++++l++
  gi|474934642|ref|YP_007688224.1| 43 IVPSFVDCHTHCADAGARPsQGMSLEE 69
                                      68*********9999966666666665 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.019
                      Amidohydro_3 357 stpvkellnagvkvalgsD.apvgpf 381
                                       +++++++++ g  ++lg+D a ++ +
  gi|474934642|ref|YP_007688224.1| 240 TPNLALMMDSGAEISLGTDnAMLCDP 265
                                       3889***************7766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       229  (0.0127726); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 2148.27
//
Query:       gi|474934643|ref|YP_007688225.1|  [L=149]
Description: Universal stress protein UspA-related nucleotide-binding protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-25   88.8   0.1    5.3e-25   88.6   0.1    1.1  1  Usp       Universal stress protein family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.6   0.1   2.9e-29   5.3e-25       2     141 .]       3     140 ..       2     140 .. 0.95

  Alignments for each domain:
  == domain 1  score: 88.6 bits;  conditional E-value: 2.9e-29
                                       -SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
                               Usp   2 ykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeag 78 
                                       + +Il+++Dg  ++ +A+ +++elak +g+++++l+++d + ++  ++ +  +   +  ++e   + d  +++ae++
  gi|474934643|ref|YP_007688225.1|   3 FTKILLPTDGRVYTSAAIGKGIELAKISGGTITALYILDQSVYSNMPMDAAIVNVYQTLEKEGHDAMDYVRKKAEEA 79 
                                       679****************************************999999999888888888888888889******* PP

                                       TCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  79 gvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       gv+ e +++eg pa +i+ +  +  +d++V+G+ gr+g+s++l+GSv+e+v++ a+cpV+vVr
  gi|474934643|ref|YP_007688225.1|  80 GVQFEEKIVEGVPAATINSLSAD--YDIVVMGTLGRTGVSKALMGSVAEKVIEGAKCPVMVVR 140
                                       *******************9876..9************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 1025.01
//
Query:       gi|474934644|ref|YP_007688226.1|  [L=127]
Description: Universal stress protein UspA-related nucleotide-binding protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-26   92.2   1.4    1.3e-24   87.3   1.4    2.0  1  Usp       Universal stress protein family
  ------ inclusion threshold ------
      0.018   15.0   0.2        5.9    6.9   0.0    2.1  2  FR47      FR47-like protein


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.3   1.4   1.5e-28   1.3e-24       2     141 .]       3     124 ..       2     124 .. 0.89

  Alignments for each domain:
  == domain 1  score: 87.3 bits;  conditional E-value: 1.5e-28
                                       -SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
                               Usp   2 ykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeag 78 
                                       +++IlV++Dgs+++++A+e+A+ela+  g+++++l+v d  +s+ ++ ++ +   +  e+                 
  gi|474934644|ref|YP_007688226.1|   3 FQNILVPTDGSDNTRAAIEKAFELARIAGGRITALYVKDKGSSDGTASSAVSKVSQLGEQ----------------Y 63 
                                       799**********************************99887766665555444444433................4 PP

                                       TCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  79 gvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       gv ve  +e+g+pa +i+ +  e   d iV+G+ gr+g++++l+GSv+e v+++a cpV+vVr
  gi|474934644|ref|YP_007688226.1|  64 GVPVEERIESGSPAAVIAGMSSE--FDVIVMGTLGRTGFKKVLVGSVAETVVKNAVCPVIVVR 124
                                       79***************999888..899**********************************8 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0   0.00065       5.9      15      48 ..      25      58 ..      15      67 .. 0.86
   2 ?    6.4   0.1     0.001       8.9      28      63 ..      90     125 ..      81     127 .] 0.86

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00065
                                      EEEE-TTSSEEEEEE-GGG-SSSHHHHHHHHHHH CS
                              FR47 15 wilrkdggelgalqvlpehrrrGlgsrlvkalak 48
                                      ++ r  gg + al+v+++    G +s+ v+++++
  gi|474934644|ref|YP_007688226.1| 25 ELARIAGGRITALYVKDKGSSDGTASSAVSKVSQ 58
                                      6677789**********************99987 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.001
                                       EE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEET CS
                              FR47  28 qvlpehrrrGlgsrlvkalakeiaergktvllvvva 63 
                                        v  +  r G+ ++lv ++a+ ++++   +++vv+ 
  gi|474934644|ref|YP_007688226.1|  90 IVMGTLGRTGFKKVLVGSVAETVVKNAVCPVIVVRK 125
                                       566677899****************99999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.49
# Mc/sec: 776.77
//
Query:       gi|474934645|ref|YP_007688227.1|  [L=281]
Description: putative transcriptional regulator, contains C-terminal CBS domains [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.8e-46  154.2   7.8      7e-15   55.2   0.0    4.1  4  CBS       CBS domain
  ------ inclusion threshold ------
      0.015   15.3   0.3         38    4.5   0.0    4.0  4  PRC       PRC-barrel domain
      0.048   14.3   0.0         40    4.9   0.0    3.3  3  GAF       GAF domain
      0.099   12.9   0.0       0.62   10.4   0.0    2.3  2  IF3_N     Translation initiation factor IF-3, N-terminal doma


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   0.3   3.6e-15   1.6e-11       1      55 [.       4      59 ..       4      61 .. 0.96
   2 !   55.2   0.0   1.6e-18     7e-15       4      56 ..      67     118 ..      62     119 .. 0.91
   3 !   26.6   0.1   1.3e-09   5.9e-06       2      53 ..     127     178 ..     126     181 .. 0.91
   4 !   30.2   0.1     1e-10   4.5e-07       1      55 [.     222     276 ..     222     278 .. 0.93

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 3.6e-15
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEE.ETTTBEEEEEEHHHHHHHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVV.dedgklvGivtlrDllral 55
                                      V+dimt+ +++v    + ++a++lm+++++++lPVV  +dgkl Giv++rD++r+ 
  gi|474934645|ref|YP_007688227.1|  4 VADIMTPAPIVVEVPGNRSDAINLMVRNKLTGLPVVrTSDGKLMGIVSRRDIFRKF 59
                                      89***************************99******99**************976 PP

  == domain 2  score: 55.2 bits;  conditional E-value: 1.6e-18
                                       HSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   4 imtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       im ++ vt+ p++++eea+++++ ++++rlPVV + gklvGi+t +Dll+ ++
  gi|474934645|ref|YP_007688227.1|  67 IMKKNCVTIGPNEPIEEAARRFAINRFHRLPVV-DGGKLVGIITPTDLLKEIK 118
                                       6*********************7566*******.6999************986 PP

  == domain 3  score: 26.6 bits;  conditional E-value: 1.3e-09
                                       HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                       +d+ ++  vt+++ ++l+  +  mr ++vs++PV+d+ g l Gi+t+rDl++
  gi|474934645|ref|YP_007688227.1| 127 EDVISTTCVTAYEGDPLAYMVSAMRISDVSAMPVLDSKGDLSGIITDRDLFS 178
                                       78999999****************8444*********************975 PP

  == domain 4  score: 30.2 bits;  conditional E-value: 1e-10
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       V+d+m r + tv   t+l e++++m + +++++PV    ++lvG++ + D+lra+
  gi|474934645|ref|YP_007688227.1| 222 VSDYMVRSPTTVFRKTPLNEVARIMLKFDFGQVPVHGTKDELVGMIYDVDVLRAM 276
                                       89***********************9999******867778************97 PP

>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.022        97       7      32 ..      31      58 ..      26      77 .. 0.76
   2 ?    0.4   0.0      0.15   6.8e+02       4      26 ..      88     111 ..      85     121 .. 0.79
   3 ?    4.5   0.0    0.0084        38       4      27 ..     150     173 ..     148     178 .. 0.92
   4 ?    1.3   0.1     0.082   3.7e+02      13      29 ..     255     271 ..     249     274 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.022
                                      ---TT-EEEETT.SSEEEEE..EEEEEET CS
                               PRC  7 sdliGkeVyted.GeklGkV..kDvvide 32
                                      ++l G++V+ ++ G+  G V   D+ + +
  gi|474934645|ref|YP_007688227.1| 31 NKLTGLPVVRTSdGKLMGIVsrRDI-FRK 58
                                      7899***999998*****9977777.554 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.15
                                       CCS---TT-EEEETTSSEEEEE..E CS
                               PRC   4 frasdliGkeVytedGeklGkV..k 26 
                                       f+++++  ++V+++ G+ +G +  +
  gi|474934645|ref|YP_007688227.1|  88 FAINRFHRLPVVDG-GKLVGIItpT 111
                                       78889999999999.7999988444 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.0084
                                       CCS---TT-EEEETTSSEEEEEEE CS
                               PRC   4 frasdliGkeVytedGeklGkVkD 27 
                                       +r+sd+  ++V +++G+  G ++D
  gi|474934645|ref|YP_007688227.1| 150 MRISDVSAMPVLDSKGDLSGIITD 173
                                       799**************9999987 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.082
                                       EEEETTSSEEEEEEEEE CS
                               PRC  13 eVytedGeklGkVkDvv 29 
                                       +V  +++e +G ++Dv 
  gi|474934645|ref|YP_007688227.1| 255 PVHGTKDELVGMIYDVD 271
                                       7778899********95 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.035   1.6e+02      86     122 ..      29      67 ..       3      73 .. 0.70
   2 ?    4.9   0.0    0.0088        40      81     106 ..      84     109 ..      67     129 .. 0.84
   3 ?    2.6   0.0     0.044     2e+02      81     106 ..     146     172 ..     123     188 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.035
                                       TESEEEEEEEEE..TTEEEEEEEEEE.SSSCSHHHHHHHH CS
                               GAF  86 girsslvvPlvn..dgelwGllvlhn.psppftreelell 122
                                         + + ++P+v   dg+l+G+++  +  ++ f++e+l l+
  gi|474934645|ref|YP_007688227.1|  29 VRNKLTGLPVVRtsDGKLMGIVSRRDiFRK-FDEEQLSLI 67 
                                       33477899***556*******998886555.888888776 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0088
                                       HHHHTTESEEEEEEEEETTEEEEEEE CS
                               GAF  81 llenmgirsslvvPlvndgelwGllv 106
                                        ++++ i+ +  +P+v++g+l+G+++
  gi|474934645|ref|YP_007688227.1|  84 AARRFAINRFHRLPVVDGGKLVGIIT 109
                                       567888889999***********997 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.044
                                       HHHHTTESEEEEEEEEE.TTEEEEEEE CS
                               GAF  81 llenmgirsslvvPlvn.dgelwGllv 106
                                        +++m i  + ++P+++ +g+l G+++
  gi|474934645|ref|YP_007688227.1| 146 MVSAMRISDVSAMPVLDsKGDLSGIIT 172
                                       56789999********88999999986 PP

>> IF3_N  Translation initiation factor IF-3, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00014      0.62      15      41 ..      42      68 ..      21      74 .. 0.89
   2 ?   -1.4   0.0      0.65   2.9e+03      12      36 ..      98     121 ..      90     124 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00014
                                      SSS-EEEEEEHHHHHHHHHHHTSEEEE CS
                             IF3_N 15 edGeqlGvistreAlrlaeekgldLVe 41
                                      +dG+ +G++s+r++ r  +e++l L++
  gi|474934645|ref|YP_007688227.1| 42 SDGKLMGIVSRRDIFRKFDEEQLSLIM 68
                                      56999********************96 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.65
                                       EE-SSS-EEEEEEHHHHHHHHHHHT CS
                             IF3_N  12 lvdedGeqlGvistreAlrlaeekg 36 
                                       +v + G+ +G+i+  + l+ +++++
  gi|474934645|ref|YP_007688227.1|  98 VV-DGGKLVGIITPTDLLKEIKNMK 121
                                       44.4478889999999999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1756.58
//
Query:       gi|474934646|ref|YP_007688228.1|  [L=570]
Description: glycyl-tRNA synthetase, dimeric type [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.4e-18   65.2   0.0      1e-17   64.1   0.0    1.6  1  HGTP_anticodon  Anticodon binding domain
    3.2e-08   33.8   0.0    6.9e-08   32.7   0.0    1.5  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
  ------ inclusion threshold ------
      0.086   12.9   0.1       0.18   11.8   0.1    1.5  1  DZR             Double zinc ribbon
       0.16   12.2   0.0       0.38   11.0   0.0    1.6  1  Rdx             Rdx family
        0.5    9.8   1.9        5.5    6.5   0.2    2.4  2  zf-ribbon_3     zinc-ribbon domain


Domain annotation for each model (and alignments):
>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.1   0.0   2.8e-21     1e-17       1      93 [.     467     560 ..     467     561 .. 0.90

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 2.8e-21
                                       SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHH...HTEEEEEET CS
                    HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekele...kgtvtvrdr 74 
                                       +v v pl  k+  l ++a+kl+++++ +  ++ +d ++++ig++++++d++g+p++++v++++l    kgtvt+rdr
  gi|474934646|ref|YP_007688228.1| 467 KVGVFPLMAKDG-LDDVARKLCDDIHTHRAEAYYD-EAGNIGRRYARMDEAGTPWCITVDYDTLSgdnKGTVTIRDR 541
                                       688999999655.***************8655554.9***************************65557******** PP

                                       TTCEEEEEETTHHHHHHHH CS
                    HGTP_anticodon  75 dtreqervsldelveklke 93 
                                       dt++q r+ ++++++++++
  gi|474934646|ref|YP_007688228.1| 542 DTKDQKRIRMEDAPNIISD 560
                                       **************99975 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0   1.9e-11   6.9e-08      12      79 ..     160     229 ..     152     236 .. 0.80

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 1.9e-11
                                       EE-SSSHHHHHHHHHHHEE.EBGGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEES.GGGHHHH CS
                                       xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                      tRNA-synt_2b  12 iLkPtneetfvelirdevl.rskrLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfha.easldds 79 
                                       +++P+  +++   + +    + ++LP+ ++q+++ yR+E    +G++R+reF++ + + f+   ++++  
  gi|474934646|ref|YP_007688228.1| 160 YMRPETAQGIFVNFLNLYRyNREKLPMGVMQTGRGYRNEIAPRQGMIRMREFNMMEVELFVDpGDKSWPR 229
                                       788988888877777664347788****************8466*****************944666655 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1     5e-05      0.18      10      40 ..      86     139 ..      81     144 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5e-05
                               DZR  10 pdarfCseCgtklkavaa........................edrCpsCgekvdp 40 
                                       ++  +C +Cg++ + + +                        +++C sCg k+ p
  gi|474934646|ref|YP_007688228.1|  86 DKITYCTQCGAPWR-ADHlvkefyenpdtmteaeldqafvdhNIVCASCGGKLGP 139
                                       55679*******97.3446899999************************987655 PP

>> Rdx  Rdx family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00011      0.38       3      29 ..      87     113 ..      87     194 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
                                       EEEEETTTTTHHHHHHHHHHHHHHCCC CS
                               Rdx   3 tIeYCtqCkwmlraaelaqellstfpe 29 
                                       +I+YCtqC+   ra  l +e  ++  +
  gi|474934646|ref|YP_007688228.1|  87 KITYCTQCGAPWRADHLVKEFYENPDT 113
                                       69**************99998876554 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1     0.033   1.2e+02       4      11 ..      90      97 ..      88     101 .. 0.78
   2 ?    6.5   0.2    0.0015       5.5      16      26 .]     127     137 ..     125     137 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.033
                       zf-ribbon_3  4 rCPnCGap 11
                                      +C +CGap
  gi|474934646|ref|YP_007688228.1| 90 YCTQCGAP 97
                                      78899986 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0015
                       zf-ribbon_3  16 dnvCpyCGtkl 26 
                                        +vC++CG+kl
  gi|474934646|ref|YP_007688228.1| 127 NIVCASCGGKL 137
                                       589*****997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (570 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.52
# Mc/sec: 3273.78
//
Query:       gi|474934647|ref|YP_007688229.1|  [L=391]
Description: CBS-domain-containing membrane protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-33  114.3   9.8    3.2e-08   33.9   0.2    4.4  4  CBS       CBS domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   2.4e-10   4.3e-06       1      54 [.      24      76 ..      24      79 .. 0.93
   2 !   23.3   0.1   3.7e-09   6.7e-05       8      54 ..      91     136 ..      83     139 .. 0.88
   3 !   33.5   0.8   2.4e-12   4.3e-08       3      52 ..     150     199 ..     148     201 .. 0.93
   4 !   33.9   0.2   1.8e-12   3.2e-08       2      55 ..     224     276 ..     223     278 .. 0.89

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 2.4e-10
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54
                                      Vgdi  +d+++++p++t+++ l lmr++g+  +PV  +dg+++G+     +lr+
  gi|474934647|ref|YP_007688229.1| 24 VGDIIVKDFPSLNPEDTVSDSLALMRRTGFQEIPVA-KDGEYIGMMRYGTILRK 76
                                      89***************************99****9.9******9888888875 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 3.7e-09
                                       SCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS   8 dvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                        ++t++++t + +++elm+ +++++l V+   +k+ Giv+++ l++ 
  gi|474934647|ref|YP_007688229.1|  91 SLPTIDEETEITKIAELMVTNNCRQLAVL-TGKKVTGIVSRTALIQI 136
                                       468***************9999******9.4667********99975 PP

  == domain 3  score: 33.5 bits;  conditional E-value: 2.4e-12
                                       HHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHH CS
                               CBS   3 dimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDll 52 
                                       +imt++vv+v+ ++ l+ a+++mr+ +++ lPVVd+ gkl G+v ++ ++
  gi|474934647|ref|YP_007688229.1| 150 EIMTTPVVYVNDNDMLAVAVDKMRDLDIRTLPVVDSAGKLNGVVGMKEVI 199
                                       89*********************9888*****************988876 PP

  == domain 4  score: 33.9 bits;  conditional E-value: 1.8e-12
                                       HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       +++  + v+t++ ++++e a ++m +k++s lPV+ +dg+lvG++t+ D+++++
  gi|474934647|ref|YP_007688229.1| 224 SSVSVTSVLTINWEDSMEAASDIMSSKKISTLPVL-DDGELVGVLTEYDIIELM 276
                                       56666788899999**********9999*******.69*************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2388.53
//
Query:       gi|474934648|ref|YP_007688230.1|  [L=873]
Description: valyl-tRNA synthetase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.5e-122  409.9   0.0     5e-121  404.9   0.0    2.4  2  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    1.7e-33  115.7   0.1    3.1e-33  114.9   0.1    1.4  1  Anticodon_1    Anticodon-binding domain of tRNA
    3.4e-21   75.4   0.6    5.5e-13   48.4   0.0    3.2  3  tRNA-synt_1g   tRNA synthetases class I (M)
    2.4e-06   27.2   0.0     0.0003   20.4   0.0    2.4  2  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
     0.0066   15.8   0.0        1.5    8.1   0.0    2.3  2  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
  ------ inclusion threshold ------
       0.19   11.1   2.4        2.1    7.8   0.1    3.2  3  zf-TFIIB       Transcription factor zinc-finger
       0.56   10.4   2.5        2.9    8.1   0.1    2.7  3  FYVE           FYVE zinc finger
       0.95    9.5   8.5         14    5.8   4.4    3.2  3  DZR            Double zinc ribbon
        2.4    8.5   5.8         31    4.9   0.1    3.8  4  zinc_ribbon_9  zinc-ribbon


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  404.9   0.0  2.5e-124    5e-121       2     601 ..      12     566 ..      11     567 .. 0.95
   2 ?   -2.5   0.0      0.57   1.1e+03      97     123 ..     725     751 ..     720     758 .. 0.87

  Alignments for each domain:
  == domain 1  score: 404.9 bits;  conditional E-value: 2.5e-124
                       tRNA-synt_1   2 lyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaiea 78 
                                       + ++W ee+v++     + +k+ +++  +P y  GslH+Gha   +l d+  ry+rmkG++v +   +D  G +ie 
  gi|474934648|ref|YP_007688230.1|  12 WEDMWREEKVYRFD--PKSDKPIYSIDNPPRYTSGSLHLGHATGYSLIDFAARYHRMKGNNVFFPLCFDVNGTPIEV 86 
                                       6689*******988..77789******************************************************** PP

                       tRNA-synt_1  79 kvekklgakekkerkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgl 155
                                        vekk+g+++     +  ree+r+ + ++++ +++e++++++ lG s+D +  y T  + +   ++  fv+l+++gl
  gi|474934648|ref|YP_007688230.1|  87 RVEKKFGINK----LDTPREEYRKLCSDYANGFIKEMTHDFEILGESMDPSIYYQTDAPYYRSITQLSFVKLFNRGL 159
                                       ******9998....59****************************************99999999999********** PP

                       tRNA-synt_1 156 iyrgkklvnwstklktalselEveykdkkdalihvafpladkeevklviaTTtPeTllgdtavavnpeldyvitkek 232
                                       +y+++ +vnw++++ tal+++Eveykd+ + l +++f++a+++  ++++aTT+Pe l + + vav+p+         
  gi|474934648|ref|YP_007688230.1| 160 VYKANFPVNWCPHCMTALADAEVEYKDNVNKLNYLKFQIAGEDG-YVMVATTRPELLCTCKVVAVHPD--------- 226
                                       ********************************************.***********************......... PP

                       tRNA-synt_1 233 lilaeallkslvkkesekkiledergkeLegkevelplvnrkipiiaddyvdkeaGtGvVkiaPahdedDyevgkky 309
                                                             d++ ++L+gke++ p+ +r+++iiad  v+k+ GtG V i    d+ D e  +ky
  gi|474934648|ref|YP_007688230.1| 227 ----------------------DKEKAHLVGKELITPIYGRHVKIIADPKVEKDYGTGNVMICTIGDKSDLEWIMKY 281
                                       ......................8999*************************************************** PP

                       tRNA-synt_1 310 nlevinildedgtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvrvke 386
                                        le+   +de g++te a++++g+ v +ar + +e+lk+ g+l ++e++  +v +c+r k+pi+y  ++qWf + ++
  gi|474934648|ref|YP_007688230.1| 282 HLELEKGIDETGCMTELAGKYAGMPVAEARAQAIEDLKAMGVLDHQEDNPQQVSVCWRCKAPIEYLQVPQWFLKTTT 358
                                       ***************************************************************************** PP

                       tRNA-synt_1 387 ladaalkavekvqfvpkskekryaswleniq.dWciSRqrwWGhriplfvsketeevvvreelkelvagreeeeaek 462
                                       ++da+lk  +++++ p++ + r ++w +  + dW++SRqr+  ++ip++  k+ +  v+ +e        ++++  +
  gi|474934648|ref|YP_007688230.1| 359 FRDAILKRADEINWFPEFMKIRLQDWTKSLEwDWVLSRQRIFATPIPVWECKKCGHAVCATEA-------QARAYVD 428
                                       ****************************9876***********************99993332.......3344445 PP

                       tRNA-synt_1 463 kalekeakdklkkekgelekdedvlDvWFsSgswpfstlgypeedteelkkffpadmlleGlDiirgWvarlillsl 539
                                        +l+   +dk  +  gele  +dv+D+W +S+ +      +   d+e ++k++p+++  +  Diir W   +il + 
  gi|474934648|ref|YP_007688230.1| 429 PTLDAAPVDKCPECGGELEGCTDVFDTWMDSSGSSLYNCFWER-DEEMFRKMYPMSLRPQSHDIIRSWAFYSILRAE 504
                                       555667888888889**************97665555555655.599****************************** PP

                       tRNA-synt_1 540 altgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltlilsdvgrdinl 601
                                       ++ +s+P+ ++++hg++++ +G  m  s gNvidp+ +++kygadalR++ ++ + g d ++
  gi|474934648|ref|YP_007688230.1| 505 QIADSRPWDNIMIHGFIMAPDGTPMHTSAGNVIDPIPILEKYGADALRYYAASCSLGTDHAF 566
                                       ****************************************************9999998765 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.57
                       tRNA-synt_1  97 reefrekvrewkaeyaeeirkqvkrlG 123
                                       ++e+++ vr+wkae++ +i+ ++++l 
  gi|474934648|ref|YP_007688230.1| 725 AAEIIATVRAWKAEQKLNINADIEKLE 751
                                       578999****************99985 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.9   0.1   1.6e-36   3.1e-33       1     149 [.     609     748 ..     609     752 .. 0.89

  Alignments for each domain:
  == domain 1  score: 114.9 bits;  conditional E-value: 1.6e-36
                       Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrll 77 
                                       drwil +l k+v++vte++e y+f+ka +++ +f+w+ ++d y+e+vk r ++       a++++l++v+ + +++l
  gi|474934648|ref|YP_007688230.1| 609 DRWILGRLWKTVRSVTESIEVYQFDKAMKSVEDFIWHVFADDYVEMVKGRDDD-------AVKYTLYTVFLNAVKIL 678
                                       9************************************************9743.......366************** PP

                       Anticodon_1  78 aPfmPfitEelwqreeeelgkkesimlaewpekaeelekeleeeevellkeivkairklrselkikpsselk 149
                                       aPfmP+itEe++q + +++++ +s++l ewp  + e + ++  ++ + + ei+ ++r+ ++e+k++ +++++
  gi|474934648|ref|YP_007688230.1| 679 APFMPHITEEVYQTHFRQFDGCRSVHLTEWPV-PGEIDCDA-VKAGDAAAEIIATVRAWKAEQKLNINADIE 748
                                       ************9966678888*********5.54554444.46999999************9999887754 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.4   0.0   2.8e-16   5.5e-13       7     136 ..      39     183 ..      33     191 .. 0.82
   2 ?    0.8   0.1     0.079   1.6e+02     167     238 ..     335     405 ..     306     415 .. 0.78
   3 !   22.5   0.0   2.1e-08   4.2e-05     300     375 ..     497     575 ..     452     592 .. 0.74

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 2.8e-16
                                       -B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHT.TS....-H....HHHHHHHH... CS
                      tRNA-synt_1g   7 lpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAeke.gv....tp....eelvekvh... 71 
                                         Y++g+lHlGh++ +   D  aRy+r++g++v+f    D  Gtpie++ ek+ g+    tp    ++l++++    
  gi|474934648|ref|YP_007688230.1|  39 PRYTSGSLHLGHATGYSLIDFAARYHRMKGNNVFFPLCFDVNGTPIEVRVEKKfGInkldTPreeyRKLCSDYAngf 115
                                       57************9999*******************************9886555222334222245777776111 PP

                                       .HHHHHHHHHTT---S..EEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-E CS
                      tRNA-synt_1g  72 .eeikelfkklnisfd..kygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdryve 136
                                        +e++++f+ l+ s d   y++t+    ++++q  f kl ++gl+y+ +  + +cp++ + l+d +ve
  gi|474934648|ref|YP_007688230.1| 116 iKEMTHDFEILGESMDpsIYYQTDAPYYRSITQLSFVKLFNRGLVYKANFPVNWCPHCMTALADAEVE 183
                                       1455666666666776446**********************************************997 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.079
                                       ..........EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EET CS
                      tRNA-synt_1g 167 pksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvP 238
                                       +++  +++  e+ +  ++f+k   f++++ +  +e +   +e +k  +++w k+   d+ +sr+  ++ p+P
  gi|474934648|ref|YP_007688230.1| 335 SVCWRCKAPIEYLQVPQWFLKTTTFRDAILKRADEIN-WFPEFMKIRLQDWTKSLEWDWVLSRQRIFATPIP 405
                                       56777888888889999***********999884333.34555555678898885569*******9*99999 PP

  == domain 3  score: 22.5 bits;  conditional E-value: 2.1e-08
                                       HHHHHHH...TT----S-EEEE--EEE.--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHHH CS
                      tRNA-synt_1g 300 wPaillg...aelklpkkvvaheyltv.egkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswedfv 372
                                       + +il +   a+ +  ++++ h++++  +g  + +S g+v+++  +le++ ad+lRYy a+  +  +D  f++e++v
  gi|474934648|ref|YP_007688230.1| 497 FYSILRAeqiADSRPWDNIMIHGFIMApDGTPMHTSAGNVIDPIPILEKYGADALRYYAAS-CSLGTDHAFREETVV 572
                                       44555564556667889*******98647889*************************9765.678889999999998 PP

                                       HHH CS
                      tRNA-synt_1g 373 erv 375
                                       +  
  gi|474934648|ref|YP_007688230.1| 573 RGK 575
                                       754 PP

>> tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.011        23      12      45 ..     194     227 ..     192     233 .. 0.91
   2 !   20.4   0.0   1.5e-07    0.0003      85     143 ..     234     292 ..     226     319 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.011
                     tRNA-synt_1_2  12 iefkveeseeklevfttrpdtlfGvtfvalapeh 45 
                                       ++f++++++  + v ttrp+ l   + va+ p+ 
  gi|474934648|ref|YP_007688230.1| 194 LKFQIAGEDGYVMVATTRPELLCTCKVVAVHPDD 227
                                       79******99*****************9998876 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 1.5e-07
                     tRNA-synt_1_2  85 tglkaihPitgekipiwvanyvlmeygtgavmavPahdqrDfeFakkynlpikqvikpe 143
                                        g + i Pi g+++ i     v  +ygtg vm +   d+ D+e+  ky+l++++ i ++
  gi|474934648|ref|YP_007688230.1| 234 VGKELITPIYGRHVKIIADPKVEKDYGTGNVMICTIGDKSDLEWIMKYHLELEKGIDET 292
                                       577899*********************************************99988765 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.2   0.0    0.0056        11      22      89 ..      45     125 ..      41     196 .. 0.64
   2 !    8.1   0.0   0.00073       1.5     234     296 ..     508     571 ..     500     576 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0056
                                       --BHHHHHHHHHHHHHHHHHHHTT-EEEE....EEEBB--SHHHHHHHHHTTS-..............HHHHHHHHH CS
                      tRNA-synt_1e  22 ashlGhaRslvafDilrrilqalgYdvqf....vqnvtDidDkiikrareeeks..............vkelaekfi 80 
                                         hlGha  +  +D  +r+ +++g +v f      n t i+ ++ k+                     +++ a+ fi
  gi|474934648|ref|YP_007688230.1|  45 SLHLGHATGYSLIDFAARYHRMKGNNVFFplcfDVNGTPIEVRVEKKF-----GinkldtpreeyrklCSDYANGFI 116
                                       68**********************999762111345555555443332.....122222444443333333333344 PP

                                       HHHHHHHHH CS
                      tRNA-synt_1e  81 eefkkdlea 89 
                                       +e+++d+e 
  gi|474934648|ref|YP_007688230.1| 117 KEMTHDFEI 125
                                       444444444 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00073
                                       S.S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS-TTS-EEE-HHHH CS
                      tRNA-synt_1e 234 d.kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRllllsahyrsqldfkeell 296
                                       d +++ ++ +h  ++  +g  m  s +n+i    +l+k+ + +lR++ +s    +   f+ee++
  gi|474934648|ref|YP_007688230.1| 508 DsRPWDNIMIHGFIMAPDGTPMHTSAGNVIDPIPILEKYGADALRYYAASCSLGTDHAFREETV 571
                                       447888999998888889******************************9999998888888876 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.45     9e+02       2      13 ..     170     181 ..     164     187 .. 0.80
   2 ?    0.6   0.0      0.19   3.7e+02      17      26 ..     404     413 ..     396     413 .. 0.84
   3 ?    7.8   0.1     0.001       2.1      16      27 ..     433     444 ..     416     446 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.45
                          zf-TFIIB   2 CPkCqdeleese 13 
                                       CP C ++l ++e
  gi|474934648|ref|YP_007688230.1| 170 CPHCMTALADAE 181
                                       888888887665 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.19
                          zf-TFIIB  17 veidyCpqCr 26 
                                       ++++ C +C+
  gi|474934648|ref|YP_007688230.1| 404 IPVWECKKCG 413
                                       89*******7 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.001
                          zf-TFIIB  16 gveidyCpqCrG 27 
                                         ++d+Cp+C+G
  gi|474934648|ref|YP_007688230.1| 433 AAPVDKCPECGG 444
                                       5689*******9 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.0         9   1.8e+04      56      64 ..     167     175 ..     162     178 .. 0.58
   2 ?    1.2   0.0      0.21   4.2e+02      48      65 ..     326     343 ..     266     346 .. 0.78
   3 ?    8.1   0.1    0.0015       2.9      27      64 ..     408     444 ..     399     448 .. 0.81

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 9
                                       EEE-HHHHH CS
                              FYVE  56 vrvCkeCla 64 
                                       v  C +C+ 
  gi|474934648|ref|YP_007688230.1| 167 VNWCPHCMT 175
                                       445555554 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.21
                                       GGGTEEEEEEE-HHHHHH CS
                              FYVE  48 ekeaeeksvrvCkeClae 65 
                                       ++e++ ++v vC +C+a 
  gi|474934648|ref|YP_007688230.1| 326 HQEDNPQQVSVCWRCKAP 343
                                       678888999999999875 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0015
                                       E-TTT--EE-STTS-EEE.EEGGGTEEEEEEE-HHHHH CS
                              FYVE  27 hCrlCGkvvCekCssklvallekeaeeksvrvCkeCla 64 
                                        C+ CG++vC++  + ++ +   + + ++v  C eC  
  gi|474934648|ref|YP_007688230.1| 408 ECKKCGHAVCATEAQARAYVD-PTLDAAPVDKCPECGG 444
                                       6*********99888888666.5677788888888865 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.23   4.5e+02      15      22 ..     170     177 ..     163     188 .. 0.69
   2 ?    2.0   0.0      0.11   2.1e+02       6      23 ..     328     345 ..     317     355 .. 0.80
   3 ?    5.8   4.4     0.007        14      15      36 ..     409     444 ..     406     449 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.23
                               DZR  15 CseCgtkl 22 
                                       C++C t+l
  gi|474934648|ref|YP_007688230.1| 170 CPHCMTAL 177
                                       44444444 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.11
                               DZR   6 eelppdarfCseCgtklk 23 
                                       e++p++  +C +C+++++
  gi|474934648|ref|YP_007688230.1| 328 EDNPQQVSVCWRCKAPIE 345
                                       567777778888877764 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.007
                               DZR  15 CseCgtklkavaa..............edrCpsCge 36 
                                       C++Cg+++ a++a               d+Cp+Cg 
  gi|474934648|ref|YP_007688230.1| 409 CKKCGHAVCATEAqarayvdptldaapVDKCPECGG 444
                                       ********9888899*******************96 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.053   1.1e+02      17      35 .]     101     119 ..      97     119 .. 0.79
   2 ?   -0.1   0.2      0.57   1.1e+03      23      27 ..     169     173 ..     163     176 .. 0.81
   3 ?   -2.1   0.2       2.5     5e+03      20      28 ..     332     341 ..     325     344 .. 0.59
   4 ?    4.9   0.1     0.016        31      22      29 ..     436     444 ..     420     446 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.053
                     zinc_ribbon_9  17 dedsdvlCPhCgggFVEei 35 
                                       +e+  +lC ++ +gF+ e+
  gi|474934648|ref|YP_007688230.1| 101 REEYRKLCSDYANGFIKEM 119
                                       4444578*********998 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.57
                     zinc_ribbon_9  23 lCPhC 27 
                                        CPhC
  gi|474934648|ref|YP_007688230.1| 169 WCPHC 173
                                       5**** PP

  == domain 3  score: -2.1 bits;  conditional E-value: 2.5
                     zinc_ribbon_9  20 sdv.lCPhCg 28 
                                       ++v +C +C+
  gi|474934648|ref|YP_007688230.1| 332 QQVsVCWRCK 341
                                       3333688886 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.016
                     zinc_ribbon_9  22 v.lCPhCgg 29 
                                       v  CP+Cgg
  gi|474934648|ref|YP_007688230.1| 436 VdKCPECGG 444
                                       245*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (873 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.78u 0.31s 00:00:01.09 Elapsed: 00:00:00.52
# Mc/sec: 5035.72
//
Query:       gi|474934649|ref|YP_007688231.1|  [L=52]
Description: Rubredoxin [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.1e-21   75.7   8.5    2.3e-21   75.5   8.5    1.0  1  Rubredoxin  Rubredoxin
  ------ inclusion threshold ------
       0.56   10.4   4.9        1.6    8.9   4.9    1.9  1  zf-Mss51    Zinc-finger of mitochondrial splicing suppressor 


Domain annotation for each model (and alignments):
>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.5   8.5   2.6e-25   2.3e-21       1      47 []       3      48 ..       3      48 .. 0.99

  Alignments for each domain:
  == domain 1  score: 75.5 bits;  conditional E-value: 2.6e-25
                                      EEEETTT-BEEETTTBBGGGTB-TT--GGGS-TT-BBTTTB-BGGGE CS
                        Rubredoxin  1 kyeCkvCgyvYdpakGdpdegiapgTkFedlPddWvCPdCgvekeqF 47
                                      kyeC vCgy+Yd++kG p++giapgTk+ed+Pdd++CPdCg++ke+F
  gi|474934649|ref|YP_007688231.1|  3 KYEC-VCGYIYDEEKGCPSQGIAPGTKWEDVPDDFECPDCGLKKEDF 48
                                      79**.****************************************99 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   4.9   0.00018       1.6      11      24 ..      30      43 ..       1      45 [. 0.79

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00018
                          zf-Mss51 11 apkhvdfeCpdCGi 24
                                      +  + dfeCpdCG+
  gi|474934649|ref|YP_007688231.1| 30 EDVPDDFECPDCGL 43
                                      566789*******7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 393.47
//
Query:       gi|474934650|ref|YP_007688232.1|  [L=111]
Description: Rubredoxin [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.9e-35  118.3  12.7      2e-20   72.5   3.8    2.1  2  Rubredoxin       Rubredoxin
    9.5e-05   22.4   0.4      0.061   13.4   0.1    2.1  2  HypA             Hydrogenase/urease nickel incorporation, met
     0.0002   20.8  16.5       0.31   10.6   0.2    3.6  3  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0026   17.6   9.8     0.0081   16.1   1.6    3.0  3  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
     0.0033   17.5   0.5     0.0033   17.5   0.5    3.5  4  zf-piccolo       Piccolo Zn-finger
  ------ inclusion threshold ------
      0.046   13.8  17.8        2.9    8.1   6.3    3.4  4  Zn-ribbon_8      Zinc ribbon domain
      0.049   14.3  12.5        1.3    9.8   0.6    4.0  4  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
       0.05   13.5  14.2        1.3    9.0   0.3    4.0  4  Nudix_N_2        Nudix N-terminal
      0.057   13.5  10.5         24    5.0  10.5    3.0  1  DZR              Double zinc ribbon
      0.064   13.7  19.2       0.77   10.3   0.1    4.2  4  zf-C2H2          Zinc finger, C2H2 type
       0.13   12.4   0.1       0.13   12.4   0.1    3.3  3  zf-Sec23_Sec24   Sec23/Sec24 zinc finger
        0.2   12.3   3.0       0.59   10.8   0.5    2.4  2  RbpA             RNA polymerase-binding protein
       0.22   11.3  11.2       0.14   11.9   1.4    3.0  3  Ribosomal_S27e   Ribosomal protein S27
       0.26   11.4  12.2       0.78    9.8   0.6    2.6  3  Elf1             Transcription elongation factor Elf1 like
       0.26   11.3  14.4       0.99    9.4   0.4    3.2  3  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
       0.27   11.2   0.2       0.27   11.2   0.2    3.2  3  Zn_ribbon_SprT   SprT-like zinc ribbon domain
        0.3   11.2  13.0        1.1    9.4   4.5    2.7  2  PHD_4            PHD-finger
       0.33   10.6  18.9        2.1    8.0   0.1    4.5  4  zf_UBZ           Ubiquitin-Binding Zinc Finger
       0.52   10.1  15.9        5.1    6.9   0.2    4.3  4  zinc_ribbon_2    zinc-ribbon domain
       0.85    9.4  18.0       0.36   10.6   0.5    3.9  3  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
        2.3    8.3   5.8        2.1    8.4   0.6    2.4  2  Mut7-C           Mut7-C RNAse domain
        2.9    8.0  16.3         10    6.2   9.9    3.7  2  ADK_lid          Adenylate kinase, active site lid
          3    8.3  16.2        1.4    9.3   0.7    3.0  2  Lar_restr_allev  Restriction alleviation protein Lar
          3    8.2  12.2        2.8    8.3   0.2    3.2  3  C1_2             C1 domain
        3.3    8.8  17.3         12    7.0   0.1    4.3  4  zf-C2H2_4        C2H2-type zinc finger
        4.7    7.2  19.2         13    5.8   4.9    3.7  3  Prok-RING_1      Prokaryotic RING finger family 1
        6.7    6.6  11.8         18    5.2   0.1    4.0  4  A2L_zn_ribbon    A2L zinc ribbon domain
        7.4    6.8  19.7       0.84    9.8   0.4    3.9  3  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
        7.8    6.6  12.0       0.28   11.2   2.4    2.7  3  Zn_Tnp_IS91      Transposase zinc-binding domain
        7.9    6.3  16.1        4.1    7.2   0.6    3.8  3  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
        8.9    6.4  11.2         13    5.9   0.2    3.8  4  zf-C2H2_6        C2H2-type zinc finger


Domain annotation for each model (and alignments):
>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.5   3.8   3.5e-23     2e-20       1      47 []       3      49 ..       3      49 .. 0.98
   2 !   51.4   1.6   1.3e-16   7.7e-14       2      47 .]      58     103 ..      57     103 .. 0.97

  Alignments for each domain:
  == domain 1  score: 72.5 bits;  conditional E-value: 3.5e-23
                                      EEEETTT-BEEETTTBBGGGTB-TT--GGGS-TT-BBTTTB-BGGGE CS
                        Rubredoxin  1 kyeCkvCgyvYdpakGdpdegiapgTkFedlPddWvCPdCgvekeqF 47
                                      +y C  Cg vY +a+Gd d+g+apgT+++dlPddW+CPdCg++ke+F
  gi|474934650|ref|YP_007688232.1|  3 RYVCGECGRVYSEASGDGDSGVAPGTPWADLPDDWECPDCGAPKESF 49
                                      79*******************************************99 PP

  == domain 2  score: 51.4 bits;  conditional E-value: 1.3e-16
                                       EEETTT-BEEETTTBBGGGTB-TT--GGGS-TT-BBTTTB-BGGGE CS
                        Rubredoxin   2 yeCkvCgyvYdpakGdpdegiapgTkFedlPddWvCPdCgvekeqF 47 
                                       + C++Cg+  ++++G+++ +iapgT ++d+ d+++CP+Cg +k+ F
  gi|474934650|ref|YP_007688232.1|  58 HVCSMCGFRVEEDRGNARANIAPGTVWDDVSDTFTCPVCGCPKTVF 103
                                       68*****************************************988 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.1    0.0001     0.061      71     108 ..       4      58 ..       2      62 .. 0.85
   2 !    8.6   0.6     0.003       1.8      71      97 ..      58     101 ..      51     108 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.0001
                                       EEETTTS-EEECHH.H.HH...............S-TTTSSS-EEEEESSSEEEE CS
                              HypA  71 vrCreCgkefelee.k.al...............rCpkCgsadveivsGeellvk 108
                                       + C eCg+ +++++ + +                +Cp+Cg+ + ++ + e ++v+
  gi|474934650|ref|YP_007688232.1|   4 YVCGECGRVYSEASgDgDSgvapgtpwadlpddwECPDCGAPKESFSKAERCKVH 58 
                                       68*****9999876444337899********************999999999886 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.003
                                       EEETTTS-EEECHH.HHH.................S-TTTSSS-E CS
                              HypA  71 vrCreCgkefelee.kal.................rCpkCgsadv 97 
                                         C+ Cg ++e+++ + +                 +Cp Cg  ++
  gi|474934650|ref|YP_007688232.1|  58 HVCSMCGFRVEEDRgN-AraniapgtvwddvsdtfTCPVCGCPKT 101
                                       469****999988743.2357899****************98765 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.2   0.00054      0.31      20      35 ..       4      19 ..       3      22 .. 0.89
   2 !    8.4   4.5    0.0026       1.5       3      33 ..      39      71 ..      38      75 .. 0.84
   3 !    9.0   0.5    0.0017      0.96       1      15 [.      91     106 ..      81     111 .] 0.73

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00054
                                      EEESSSSBEEEECCCC CS
                      TF_Zn_Ribbon 20 lvCtdCGlVlednsid 35
                                      +vC++CG V  + s d
  gi|474934650|ref|YP_007688232.1|  4 YVCGECGRVYSEASGD 19
                                      8********9998877 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0026
                                      ETTTTCEE.CHEETSTTCE.EESSSSBEEEECC CS
                      TF_Zn_Ribbon  3 CPnCgstn.lveDpergel.vCtdCGlVledns 33
                                      CP+Cg ++     +er  + vC+ CG  +e++ 
  gi|474934650|ref|YP_007688232.1| 39 CPDCGAPKeSFSKAERCKVhVCSMCGFRVEEDR 71
                                      ******87678889999999******8888775 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0017
                                       EEETTTTCEE.CHEET CS
                      TF_Zn_Ribbon   1 ykCPnCgstn.lveDp 15 
                                       ++CP+Cg ++ + +D+
  gi|474934650|ref|YP_007688232.1|  91 FTCPVCGCPKtVFRDY 106
                                       5788888777455555 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.55   3.2e+02      31      40 ..       6      15 ..       2      23 .. 0.66
   2 !   16.1   1.6   1.4e-05    0.0081      30      67 ..      38      79 ..      37      80 .. 0.89
   3 ?    4.6   0.2     0.055        32      45      53 ..      89      97 ..      82     107 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.55
                    OrfB_Zn_ribbon 31 CseCgsknke 40
                                      C eCg++ +e
  gi|474934650|ref|YP_007688232.1|  6 CGECGRVYSE 15
                                      6666666555 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.4e-05
                    OrfB_Zn_ribbon 30 tCseCgsknke...alsgrtfkCpnCgfeadrDv.nAaiNil 67
                                      +C+ Cg+ ++    a   ++++C+ Cgf+   D  nA  Ni+
  gi|474934650|ref|YP_007688232.1| 38 ECPDCGAPKESfskAERCKVHVCSMCGFRVEEDRgNARANIA 79
                                      7***********9888889**********9999548888986 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.055
                    OrfB_Zn_ribbon 45 rtfkCpnCg 53
                                      +tf+Cp Cg
  gi|474934650|ref|YP_007688232.1| 89 DTFTCPVCG 97
                                      566666665 PP

>> zf-piccolo  Piccolo Zn-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.91   5.2e+02      29      35 ..       4      10 ..       2      19 .. 0.79
   2 ?   -0.3   0.3       2.1   1.2e+03      46      53 ..      35      42 ..      23      47 .. 0.70
   3 !   17.5   0.5   5.8e-06    0.0033      20      40 ..      49      69 ..      43      76 .. 0.82
   4 ?    0.5   0.3       1.2     7e+02       2       7 ..      92      97 ..      91     107 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.91
                        zf-piccolo 29 qvCnlCG 35
                                       vC  CG
  gi|474934650|ref|YP_007688232.1|  4 YVCGECG 10
                                      6999999 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 2.1
                        zf-piccolo 46 keWlclnC 53
                                       +W c  C
  gi|474934650|ref|YP_007688232.1| 35 DDWECPDC 42
                                      57777777 PP

  == domain 3  score: 17.5 bits;  conditional E-value: 5.8e-06
                        zf-piccolo 20 yntCteCkkqvCnlCGFnptp 40
                                      +++   Ck +vC++CGF  + 
  gi|474934650|ref|YP_007688232.1| 49 FSKAERCKVHVCSMCGFRVEE 69
                                      778889***********8765 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 1.2
                        zf-piccolo  2 lCplCk 7 
                                      +Cp+C 
  gi|474934650|ref|YP_007688232.1| 92 TCPVCG 97
                                      688885 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1    0.0088       5.1       6      17 ..       4      15 ..       3      26 .. 0.83
   2 ?    7.2   0.3    0.0098       5.6      25      34 ..      34      44 ..      28      49 .. 0.71
   3 ?    8.1   6.3     0.005       2.9       6      37 ..      37      68 ..      36      70 .. 0.85
   4 ?    4.9   5.3      0.05        29       8      34 ..      60      98 ..      56     104 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0088
                       Zn-ribbon_8  6 YrCeeCghefev 17
                                      Y C eCg+++ +
  gi|474934650|ref|YP_007688232.1|  4 YVCGECGRVYSE 15
                                      9******99875 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0098
                       Zn-ribbon_8 25 plta.CPeCgs 34
                                      p+   CP+Cg+
  gi|474934650|ref|YP_007688232.1| 34 PDDWeCPDCGA 44
                                      44555999998 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.005
                       Zn-ribbon_8  6 YrCeeCghefevlqsisdapltaCPeCgsevr 37
                                       +C +Cg   e + ++ + +  +C  Cg +v+
  gi|474934650|ref|YP_007688232.1| 37 WECPDCGAPKESFSKAERCKVHVCSMCGFRVE 68
                                      58***********9988887777****97775 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.05
                       Zn-ribbon_8  8 CeeCghefe..............vlqsisdaplta.CPeCgs 34
                                      C +Cg + e              v+  +s   +t  CP Cg 
  gi|474934650|ref|YP_007688232.1| 60 CSMCGFRVEedrgnaraniapgtVWDDVS---DTFtCPVCGC 98
                                      99999999977777666555555555444...6667****97 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.79   4.5e+02       4      10 ..       5      11 ..       2      18 .. 0.77
   2 ?    5.2   0.4      0.06        35       3      12 ..      37      46 ..      35      55 .. 0.82
   3 ?    4.2   0.1      0.12        69       2      18 ..      57      73 ..      56      79 .. 0.82
   4 ?    9.8   0.6    0.0022       1.3       3      18 ..      91     106 ..      89     110 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.79
                           zf-ISL3  4 rCPnCgs 10
                                      +C +Cg+
  gi|474934650|ref|YP_007688232.1|  5 VCGECGR 11
                                      5888886 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.06
                           zf-ISL3  3 hrCPnCgskt 12
                                      + CP Cg+++
  gi|474934650|ref|YP_007688232.1| 37 WECPDCGAPK 46
                                      78*****986 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.12
                           zf-ISL3  2 phrCPnCgsktvvkhgk 18
                                      +h+C  Cg ++  ++g+
  gi|474934650|ref|YP_007688232.1| 57 VHVCSMCGFRVEEDRGN 73
                                      79*******99888875 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 0.0022
                           zf-ISL3   3 hrCPnCgsktvvkhgk 18 
                                        +CP Cg+++ v +++
  gi|474934650|ref|YP_007688232.1|  91 FTCPVCGCPKTVFRDY 106
                                       69*******9887765 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.3    0.0022       1.3      22      31 ..       3      12 ..       1      13 [. 0.90
   2 ?    5.7   2.9     0.025        14       3      30 ..      39      65 ..      39      65 .. 0.83
   3 ?    4.6   0.2     0.054        31       3      10 ..      60      67 ..      58      72 .. 0.65
   4 ?    3.7   0.3       0.1        59       3       9 ..      93      99 ..      91     109 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0022
                                      EEEETTTTEE CS
                         Nudix_N_2 22 RlvCpaCgti 31
                                      R+vC  Cg +
  gi|474934650|ref|YP_007688232.1|  3 RYVCGECGRV 12
                                      ********98 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.025
                                      -TTT--B-EEE--TT-SS-EEEETTTTE CS
                         Nudix_N_2  3 CsqCGtpvelripdgDnreRlvCpaCgt 30
                                      C+ CG+p +    + +    +vC+ Cg+
  gi|474934650|ref|YP_007688232.1| 39 CPDCGAP-KESFSKAERCKVHVCSMCGF 65
                                      999**99.66777788888899999996 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.054
                                      -TTT--B- CS
                         Nudix_N_2  3 CsqCGtpv 10
                                      Cs+CG +v
  gi|474934650|ref|YP_007688232.1| 60 CSMCGFRV 67
                                      66666665 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.1
                                      -TTT--B CS
                         Nudix_N_2  3 CsqCGtp 9 
                                      C+ CG p
  gi|474934650|ref|YP_007688232.1| 93 CPVCGCP 99
                                      8888887 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0  10.5     0.042        24       1      34 [.      39      96 ..       1     102 [. 0.56

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.042
                               DZR  1 CpqCgee.......lppdarfCseCgtklkavaa.................edrCpsC 34
                                      Cp Cg++        + + ++Cs Cg ++++                      +Cp C
  gi|474934650|ref|YP_007688232.1| 39 CPDCGAPkesfskaERCKVHVCSMCGFRVEEDRGnaraniapgtvwddvsdTFTCPVC 96
                                      5555555444332222222255555555543332555555555555555555555555 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1    0.0013      0.77       1      12 [.       4      15 ..       4      18 .. 0.87
   2 ?    6.4   0.7     0.024        14       2      13 ..      38      52 ..      37      59 .. 0.79
   3 ?    2.7   0.8      0.36   2.1e+02       1       8 [.      58      65 ..      54      68 .. 0.84
   4 ?    5.3   2.5     0.054        31       1      11 [.      91     104 ..      91     108 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0013
                                      EEETTTTEEESS CS
                           zf-C2H2  1 ykCpdCgksFkr 12
                                      y+C++Cg++++ 
  gi|474934650|ref|YP_007688232.1|  4 YVCGECGRVYSE 15
                                      9********985 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.024
                                      EETTTT...EEESSH CS
                           zf-C2H2  2 kCpdCg...ksFkrk 13
                                      +CpdCg   +sF+  
  gi|474934650|ref|YP_007688232.1| 38 ECPDCGapkESFSKA 52
                                      7*****999888876 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.36
                                      EEETTTTE CS
                           zf-C2H2  1 ykCpdCgk 8 
                                      ++C+ Cg 
  gi|474934650|ref|YP_007688232.1| 58 HVCSMCGF 65
                                      68999996 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.054
                                       EEETTTT...EEES CS
                           zf-C2H2   1 ykCpdCg...ksFk 11 
                                       ++Cp+Cg    +F+
  gi|474934650|ref|YP_007688232.1|  91 FTCPVCGcpkTVFR 104
                                       89**8886665555 PP

>> zf-Sec23_Sec24  Sec23/Sec24 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.52     3e+02      24      31 ..      37      44 ..      29      50 .. 0.82
   2 ?    1.6   2.8      0.51   2.9e+02      20      32 ..      54      66 ..      39      69 .. 0.67
   3 ?   12.4   0.1   0.00022      0.13       8      39 .]      75     106 ..      72     106 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.52
                    zf-Sec23_Sec24 24 wiCnfCnh 31
                                      w C+ C+ 
  gi|474934650|ref|YP_007688232.1| 37 WECPDCGA 44
                                      99*99986 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.51
                    zf-Sec23_Sec24 20 ggkrwiCnfCnhk 32
                                      + k  +C +C+++
  gi|474934650|ref|YP_007688232.1| 54 RCKVHVCSMCGFR 66
                                      446789****987 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.00022
                    zf-Sec23_Sec24   8 raylNpfckidfggkrwiCnfCnhknevppeY 39 
                                       ra + p + +d+ + +++C+ C++   v ++Y
  gi|474934650|ref|YP_007688232.1|  75 RANIAPGTVWDDVSDTFTCPVCGCPKTVFRDY 106
                                       6667888999*************998877766 PP

>> RbpA  RNA polymerase-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.5     0.001      0.59      45      62 ..      31      48 ..      13      59 .. 0.82
   2 ?    2.3   0.2      0.44   2.6e+02      46      59 ..      86      99 ..      46     110 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.001
                              RbpA 45 aevPetwecrrcGkeakl 62
                                      a++P+ wec+ cG++ + 
  gi|474934650|ref|YP_007688232.1| 31 ADLPDDWECPDCGAPKES 48
                                      799**********98765 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.44
                              RbpA 46 evPetwecrrcGke 59
                                      +v +t++c+ cG +
  gi|474934650|ref|YP_007688232.1| 86 DVSDTFTCPVCGCP 99
                                      56666777777765 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.22   1.3e+02      29      41 ..       6      18 ..       2      22 .. 0.82
   2 ?   11.9   1.4   0.00024      0.14       9      41 ..      38      72 ..      36      85 .. 0.81
   3 ?    2.1   1.0      0.27   1.6e+02       9      21 ..      92     104 ..      90     109 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.22
                                      ESSSTCEEEEECS CS
                    Ribosomal_S27e 29 CisCgkvLvePtG 41
                                      C  Cg+v  e  G
  gi|474934650|ref|YP_007688232.1|  6 CGECGRVYSEASG 18
                                      99****9887655 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00024
                                      E-TTTS-EEEEESS-SS..-EEESSSTCEEEEECS CS
                    Ribosomal_S27e  9 kCpdCenetvvFshaat..vvkCisCgkvLvePtG 41
                                       CpdC++ +  Fs+a++  v  C  Cg  + e +G
  gi|474934650|ref|YP_007688232.1| 38 ECPDCGAPKESFSKAERckVHVCSMCGFRVEEDRG 72
                                      6**************9732457*****88887777 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.27
                                       E-TTTS-EEEEES CS
                    Ribosomal_S27e   9 kCpdCenetvvFs 21 
                                        Cp C+  ++vF 
  gi|474934650|ref|YP_007688232.1|  92 TCPVCGCPKTVFR 104
                                       5**********96 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       5.6   3.2e+03      48      55 ..       6      13 ..       3      17 .. 0.73
   2 ?    9.1   1.4    0.0023       1.3      18      56 ..      33      68 ..      28      79 .. 0.87
   3 ?    9.8   0.6    0.0014      0.78      18      33 ..      87     102 ..      74     110 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 5.6
                              Elf1 48 CkvCgesf 55
                                      C+ Cg  +
  gi|474934650|ref|YP_007688232.1|  6 CGECGRVY 13
                                      88888655 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0023
                              Elf1 18 lptkFdCpfCnheksvevkldkkekiaevsCkvCgesfe 56
                                      lp  ++Cp C++    + +++k e+  +  C++Cg ++e
  gi|474934650|ref|YP_007688232.1| 33 LPDDWECPDCGAP---KESFSKAERCKVHVCSMCGFRVE 68
                                      78899********...899***************98776 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.0014
                              Elf1  18 lptkFdCpfCnheksv 33 
                                       ++ +F+Cp+C+  k+v
  gi|474934650|ref|YP_007688232.1|  87 VSDTFTCPVCGCPKTV 102
                                       6789********9998 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.37   2.1e+02      37      45 ..       3      11 ..       1      18 [. 0.67
   2 ?    5.5   4.6      0.03        17      18      45 ..      36      65 ..      29      66 .. 0.77
   3 ?    9.4   0.4    0.0017      0.99      18      28 ..      87     100 ..      79     105 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.37
                     Zn_Tnp_IS1595 37 lfqCkeCrk 45
                                      ++ C eC++
  gi|474934650|ref|YP_007688232.1|  3 RYVCGECGR 11
                                      455666654 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.03
                     Zn_Tnp_IS1595 18 gfvCPhCgsr..kayriktrglfqCkeCrk 45
                                         CP Cg    ++ + ++ +++ C+ C+ 
  gi|474934650|ref|YP_007688232.1| 36 DWECPDCGAPkeSFSKAERCKVHVCSMCGF 65
                                      467*****88656666666999****9985 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0017
                     Zn_Tnp_IS1595  18 g...fvCPhCgsrk 28 
                                           f+CP Cg+ k
  gi|474934650|ref|YP_007688232.1|  87 VsdtFTCPVCGCPK 100
                                       4444*******974 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.9      0.03        18       4      12 ..       3      11 ..       2      14 .. 0.79
   2 ?   11.2   0.2   0.00046      0.27       5      33 ..      37      66 ..      34      69 .. 0.85
   3 ?    1.7   1.0      0.44   2.5e+02       5      11 ..      91      97 ..      88     102 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.03
                    Zn_ribbon_SprT  4 vYrCtgCgr 12
                                       Y+C+ Cgr
  gi|474934650|ref|YP_007688232.1|  3 RYVCGECGR 11
                                      599****96 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00046
                    Zn_ribbon_SprT  5 YrCtgCgreythhlsirrhn...YrCrrCkgt 33
                                      + C++Cg   + ++ ++ ++   + C  C+ +
  gi|474934650|ref|YP_007688232.1| 37 WECPDCG--APKESFSKAERckvHVCSMCGFR 66
                                      99*****..6888888*999999999999865 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.44
                    Zn_ribbon_SprT  5 YrCtgCg 11
                                       +C+ Cg
  gi|474934650|ref|YP_007688232.1| 91 FTCPVCG 97
                                      5788888 PP

>> PHD_4  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   4.5    0.0019       1.1      52      67 ..      27      42 ..       4      43 .. 0.85
   2 ?    6.5   1.3     0.015       8.9      29      67 ..      56      96 ..      45      97 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0019
                             PHD_4 52 gvvnedlpnsWeCpkC 67
                                      g+   dlp +WeCp C
  gi|474934650|ref|YP_007688232.1| 27 GTPWADLPDDWECPDC 42
                                      55567*********** PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.015
                             PHD_4 29 slmeCsvCyeivHpe..ClkekegegvvnedlpnsWeCpkC 67
                                      ++  Cs+C   v  +   ++ + ++g+v +d+     Cp C
  gi|474934650|ref|YP_007688232.1| 56 KVHVCSMCGFRVEEDrgNARANIAPGTVWDDVSDTFTCPVC 96
                                      555688887776544114555578999************99 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1    0.0037       2.1       1      14 [.       2      15 ..       2      17 .. 0.84
   2 ?    6.7   0.2    0.0095       5.5       1      13 [.      35      47 ..      35      53 .. 0.74
   3 ?    4.1   0.1     0.059        34       3      15 ..      58      70 ..      56      71 .. 0.87
   4 ?    3.3   1.6      0.11        64       1       9 [.      89      97 ..      89      99 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0037
                            zf_UBZ  1 dtylCerCgkeipe 14
                                      d y+C +Cg+  +e
  gi|474934650|ref|YP_007688232.1|  2 DRYVCGECGRVYSE 15
                                      68*******98876 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0095
                            zf_UBZ  1 dtylCerCgkeip 13
                                      d + C++Cg++ +
  gi|474934650|ref|YP_007688232.1| 35 DDWECPDCGAPKE 47
                                      6799*****8755 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.059
                            zf_UBZ  3 ylCerCgkeipes 15
                                      ++C+ Cg +++e+
  gi|474934650|ref|YP_007688232.1| 58 HVCSMCGFRVEED 70
                                      68******99985 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.11
                            zf_UBZ  1 dtylCerCg 9 
                                      dt++C+ Cg
  gi|474934650|ref|YP_007688232.1| 89 DTFTCPVCG 97
                                      79******8 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.2       0.2   1.2e+02       2       7 ..       6      11 ..       3      15 .. 0.68
   2 ?    6.9   0.2    0.0088       5.1       2       8 ..      39      45 ..      38      52 .. 0.75
   3 ?    3.9   0.3     0.081        47      16      21 ..      60      65 ..      53      70 .. 0.68
   4 ?    5.8   0.8      0.02        12      13      22 ..      89      99 ..      85     100 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.2
                     zinc_ribbon_2  2 CpnCGa 7 
                                      C +CG+
  gi|474934650|ref|YP_007688232.1|  6 CGECGR 11
                                      555654 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0088
                     zinc_ribbon_2  2 CpnCGae 8 
                                      Cp CGa+
  gi|474934650|ref|YP_007688232.1| 39 CPDCGAP 45
                                      6666665 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.081
                     zinc_ribbon_2 16 CpyCGt 21
                                      C+ CG+
  gi|474934650|ref|YP_007688232.1| 60 CSMCGF 65
                                      666665 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.02
                     zinc_ribbon_2 13 akF.CpyCGtp 22
                                      ++F Cp CG p
  gi|474934650|ref|YP_007688232.1| 89 DTFtCPVCGCP 99
                                      67779999965 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.4     0.041        24      22      28 ..       4      10 ..       2      18 .. 0.64
   2 ?    1.5   5.1      0.42   2.4e+02       5      17 ..      37      51 ..      34      68 .. 0.87
   3 ?   10.6   0.5   0.00062      0.36       6      15 ..      92     103 ..      90     108 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.041
                           zf-RRN7 22 yyCrrCh 28
                                      y+C +C+
  gi|474934650|ref|YP_007688232.1|  4 YVCGECG 10
                                      5555554 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.42
                           zf-RRN7  5 ppCgvCgc..rsftl 17
                                      + C+ Cg+   sf  
  gi|474934650|ref|YP_007688232.1| 37 WECPDCGApkESFSK 51
                                      68******9778875 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00062
                           zf-RRN7   6 pCgvCgc..rsf 15 
                                        C+vCgc  + f
  gi|474934650|ref|YP_007688232.1|  92 TCPVCGCpkTVF 103
                                       7******95344 PP

>> Mut7-C  Mut7-C RNAse domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.5      0.31   1.8e+02      93     104 ..       6      17 ..       2      46 .. 0.49
   2 ?    8.4   0.6    0.0037       2.1      88     130 ..      55      97 ..      45     100 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.31
                            Mut7-C  93 CvaCngeleeve 104
                                       C++C  + +e++
  gi|474934650|ref|YP_007688232.1|   6 CGECGRVYSEAS 17 
                                       444444444444 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0037
                            Mut7-C  88 pelsrCvaCngeleevekeevkervpekvyeeadeftrCekCr 130
                                        +++ C +C  ++ee + +  ++ +p  v +  ++ ++C+ C+
  gi|474934650|ref|YP_007688232.1|  55 CKVHVCSMCGFRVEEDRGNARANIAPGTVWDDVSDTFTCPVCG 97 
                                       45789***********99999999999***************7 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   9.9     0.018        10       1      29 [.       3      44 ..       3      64 .. 0.76
   2 ?    1.7   0.4      0.46   2.7e+02       3      29 ..      92      98 ..      90     105 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.018
                                      EEE-TTT--EEETT...............TB--SSTTB-TTT-- CS
                           ADK_lid  1 RrvCpkCGrsYhvv...............fnpPkveglCDkCGe 29
                                      R vC  CGr+Y+ +                  P  +  C +CG 
  gi|474934650|ref|YP_007688232.1|  3 RYVCGECGRVYS-EasgdgdsgvapgtpwADLP-DDWECPDCGA 44
                                      99*********9.54777776665554321333.6777777776 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.46
                                      E-TTT--EEETTTB--SSTTB-TTT-- CS
                           ADK_lid  3 vCpkCGrsYhvvfnpPkveglCDkCGe 29
                                      +                    C +CG 
  gi|474934650|ref|YP_007688232.1| 92 T--------------------CPVCGC 98
                                      4....................555555 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   8.9      0.47   2.7e+02       5      47 ..      38      71 ..       5      86 .. 0.79
   2 ?    9.3   0.7    0.0024       1.4       5      19 ..      92     106 ..      89     110 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.47
                   Lar_restr_allev  5 pCPfCggravlersqrvvaeigqcvyCadCgastpwfkiaede 47
                                       CP Cg +++ +    + +    +  C  Cg      + +ed+
  gi|474934650|ref|YP_007688232.1| 38 ECPDCGAPKESFSKAERCK----VHVCSMCGF-----RVEEDR 71
                                      5999999999998888888....888988998.....223333 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0024
                   Lar_restr_allev   5 pCPfCggravlersq 19 
                                        CP Cg++++++r++
  gi|474934650|ref|YP_007688232.1|  92 TCPVCGCPKTVFRDY 106
                                       5**********9986 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.3      0.83   4.8e+02      32      39 ..       3      10 ..       1      15 [. 0.73
   2 ?    5.0   1.6     0.052        30      17      42 ..      35      67 ..      31      70 .. 0.72
   3 ?    8.3   0.2    0.0048       2.8      14      34 ..      86     107 ..      83     107 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.83
                              C1_2 32 fYsCseCd 39
                                      +Y C eC 
  gi|474934650|ref|YP_007688232.1|  3 RYVCGECG 10
                                      58898884 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.052
                              C1_2 17 esfnCsaCgrkidgff.......YsCseCdfsl 42
                                      ++++C  Cg + ++f          Cs+C f +
  gi|474934650|ref|YP_007688232.1| 35 DDWECPDCGAPKESFSkaerckvHVCSMCGFRV 67
                                      578899999994444444668889999999976 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0048
                              C1_2  14 dssesfnCsaCgrkidgff.Ys 34 
                                       d s++f+C +Cg + + f+ Y+
  gi|474934650|ref|YP_007688232.1|  86 DVSDTFTCPVCGCPKTVFRdYH 107
                                       67899*********87787886 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1     0.021        12       1      12 [.       4      15 ..       4      18 .. 0.85
   2 ?    5.0   0.6     0.097        56       2      12 ..      38      51 ..      37      59 .. 0.56
   3 ?    2.2   0.4      0.73   4.2e+02       1      10 [.      58      65 ..      58      70 .. 0.75
   4 ?    4.9   1.4       0.1        58       1       9 [.      91      99 ..      91     108 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.021
                         zf-C2H2_4  1 fkCpiCgksFss 12
                                      + C  Cg+++s 
  gi|474934650|ref|YP_007688232.1|  4 YVCGECGRVYSE 15
                                      89********75 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.097
                         zf-C2H2_4  2 kCpiC...gksFss 12
                                      +Cp C   ++sFs 
  gi|474934650|ref|YP_007688232.1| 38 ECPDCgapKESFSK 51
                                      8****554444433 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.73
                         zf-C2H2_4  1 fkCpiCgksF 10
                                      + C+ C   F
  gi|474934650|ref|YP_007688232.1| 58 HVCSMC--GF 65
                                      57****..55 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.1
                         zf-C2H2_4  1 fkCpiCgks 9 
                                      f+Cp+Cg +
  gi|474934650|ref|YP_007688232.1| 91 FTCPVCGCP 99
                                      89***9543 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1      0.15        85      21      30 ..       4      13 ..       1      16 [. 0.80
   2 ?    5.8   4.9     0.023        13      23      44 ..      39      58 ..      33      68 .. 0.81
   3 ?    1.4   7.4      0.52     3e+02       7      29 ..      60      99 ..      56     102 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.15
                       Prok-RING_1 21 VvCpeCgtpy 30
                                       vC eCg +y
  gi|474934650|ref|YP_007688232.1|  4 YVCGECGRVY 13
                                      69*****887 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.023
                       Prok-RING_1 23 CpeCgtpyHraCyekagkCvne 44
                                      Cp+Cg+p  ++ ++ka++C  +
  gi|474934650|ref|YP_007688232.1| 39 CPDCGAP--KESFSKAERCKVH 58
                                      *******..7999999999444 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.52
                       Prok-RING_1  7 CpvCgkelkee.................dDiVvCpeCgtp 29
                                      C++Cg +++e+                 +D  +Cp+Cg p
  gi|474934650|ref|YP_007688232.1| 60 CSMCGFRVEEDrgnaraniapgtvwddvSDTFTCPVCGCP 99
                                      55555555555555555555556664457889******98 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.032        18      21      29 ..       3      11 ..       1      14 [. 0.71
   2 ?    4.3   0.1     0.059        34      24      29 ..      39      44 ..      35      48 .. 0.80
   3 ?    0.8   0.3      0.76   4.4e+02       5      10 ..      59      64 ..      56      66 .. 0.66
   4 ?    1.9   0.3      0.35     2e+02       5      29 ..      92      98 ..      88     105 .. 0.63

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.032
                     A2L_zn_ribbon 21 ylvCieCga 29
                                       +vC eCg 
  gi|474934650|ref|YP_007688232.1|  3 RYVCGECGR 11
                                      588888885 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.059
                     A2L_zn_ribbon 24 CieCga 29
                                      C++Cga
  gi|474934650|ref|YP_007688232.1| 39 CPDCGA 44
                                      999997 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.76
                     A2L_zn_ribbon  5 vCsvCg 10
                                      vCs Cg
  gi|474934650|ref|YP_007688232.1| 59 VCSMCG 64
                                      566664 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.35
                     A2L_zn_ribbon  5 vCsvCggngilnseqgylvCieCga 29
                                      +                  C+ Cg+
  gi|474934650|ref|YP_007688232.1| 92 T------------------CPVCGC 98
                                      4..................555554 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1      0.55   3.2e+02      16      26 ..       3      13 ..       2      19 .. 0.82
   2 ?    9.8   0.4    0.0015      0.84      16      26 ..      36      46 ..      28      54 .. 0.85
   3 ?    0.7   8.6         1   5.8e+02      15      26 ..      89     100 ..      50     109 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.55
                          zf-Mss51 16 dfeCpdCGipt 26
                                      ++ C +CG ++
  gi|474934650|ref|YP_007688232.1|  3 RYVCGECGRVY 13
                                      699*****765 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0015
                          zf-Mss51 16 dfeCpdCGipt 26
                                      d eCpdCG p 
  gi|474934650|ref|YP_007688232.1| 36 DWECPDCGAPK 46
                                      78******995 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 1
                          zf-Mss51  15 vdfeCpdCGipt 26 
                                        +f+Cp CG p 
  gi|474934650|ref|YP_007688232.1|  89 DTFTCPVCGCPK 100
                                       579*******96 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.73   4.2e+02      39      66 ..       3      12 ..       1      19 [. 0.61
   2 ?   11.2   2.4   0.00049      0.28      40      74 ..      37      74 ..      34      87 .. 0.78
   3 ?   -0.4   0.5         2   1.2e+03      41      65 ..      92      98 ..      82     107 .. 0.63

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.73
                       Zn_Tnp_IS91 39 ryeCeeCghekivyfsCksrhCpsCqkk 66
                                      ry C eCg                    
  gi|474934650|ref|YP_007688232.1|  3 RYVCGECGR------------------V 12
                                      566666664..................4 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00049
                       Zn_Tnp_IS91 40 yeCeeCg...hekivyfsCksrhCpsCqkkateewlek 74
                                      +eC++Cg   ++   + +Ck   C+ C+ + +e+  ++
  gi|474934650|ref|YP_007688232.1| 37 WECPDCGapkESFSKAERCKVHVCSMCGFRVEEDRGNA 74
                                      89****855344556789**********9988877654 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 2
                       Zn_Tnp_IS91 41 eCeeCghekivyfsCksrhCpsCqk 65
                                                         Cp C+ 
  gi|474934650|ref|YP_007688232.1| 92 T------------------CPVCGC 98
                                      3..................444443 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.6    0.0071       4.1       1       8 [.       4      11 ..       4      19 .. 0.82
   2 ?    3.6   4.3      0.09        52       3      27 ..      39      67 ..      37      67 .. 0.72
   3 ?    1.0   0.1      0.59   3.4e+02      15      25 ..      88      98 ..      82     100 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0071
                                      -B-SSS-- CS
                    DNA_RNApol_7kD  1 YiCgeCga 8 
                                      Y CgeCg 
  gi|474934650|ref|YP_007688232.1|  4 YVCGECGR 11
                                      9*****97 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.09
                                      -SSS--B--.--SSS---...-SSS---- CS
                    DNA_RNApol_7kD  3 CgeCgaevs.lkkgdpiR...CkeCGhRi 27
                                      C +Cga+ +  +k +  +   C  CG+R+
  gi|474934650|ref|YP_007688232.1| 39 CPDCGAPKEsFSKAERCKvhvCSMCGFRV 67
                                      888888877666666555555889***97 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.59
                                      SS----SSS-- CS
                    DNA_RNApol_7kD 15 gdpiRCkeCGh 25
                                      +d   C  CG+
  gi|474934650|ref|YP_007688232.1| 88 SDTFTCPVCGC 98
                                      56667999997 PP

>> zf-C2H2_6  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.2     0.022        13       1      12 [.       3      14 ..       3      15 .. 0.89
   2 ?   -1.4   0.1       4.6   2.6e+03       3       9 ..      38      44 ..      37      44 .. 0.85
   3 ?    3.3   0.3      0.15        87       1       8 [.      57      64 ..      57      65 .. 0.92
   4 ?    2.9   0.2       0.2   1.2e+02       2       8 ..      91      97 ..      90      97 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.022
                         zf-C2H2_6  1 vheCsvCsksFp 12
                                      +++C +C+++++
  gi|474934650|ref|YP_007688232.1|  3 RYVCGECGRVYS 14
                                      59*******996 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.6
                         zf-C2H2_6  3 eCsvCsk 9 
                                      eC+ C++
  gi|474934650|ref|YP_007688232.1| 38 ECPDCGA 44
                                      8*99986 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.15
                         zf-C2H2_6  1 vheCsvCs 8 
                                      vh+Cs C+
  gi|474934650|ref|YP_007688232.1| 57 VHVCSMCG 64
                                      7******7 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.2
                         zf-C2H2_6  2 heCsvCs 8 
                                      + C+vC+
  gi|474934650|ref|YP_007688232.1| 91 FTCPVCG 97
                                      89****7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        43  (0.00239835); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 655.58
//
Query:       gi|474934651|ref|YP_007688233.1|  [L=482]
Description: Superfamily II DNA and RNA helicase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.3e-46  157.8   0.0    5.5e-44  150.0   0.0    2.3  2  DEAD        DEAD/DEAH box helicase
    5.3e-35  120.1   0.0      2e-34  118.3   0.0    2.0  2  Helicase_C  Helicase conserved C-terminal domain
    3.9e-14   52.4   4.0    4.2e-14   52.3   1.1    2.5  3  DbpA        DbpA RNA binding domain
    3.6e-06   27.1   0.0    1.6e-05   25.0   0.0    2.0  2  ResIII      Type III restriction enzyme, res subunit
    0.00085   18.7   0.0     0.0019   17.6   0.0    1.6  1  CMS1        U3-containing 90S pre-ribosomal complex subunit
     0.0033   17.8   0.0      0.014   15.7   0.0    2.0  2  AAA_19      AAA domain
  ------ inclusion threshold ------
      0.051   13.3   0.2       0.13   12.0   0.2    1.7  1  AAA_30      AAA domain
      0.054   13.8   0.2       0.22   11.8   0.1    2.1  2  AAA_22      AAA domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.0   0.0   2.5e-47   5.5e-44       1     175 [.      29     198 ..      29     199 .. 0.94
   2 !    5.5   0.0     0.006        13      46     105 ..     245     304 ..     232     328 .. 0.73

  Alignments for each domain:
  == domain 1  score: 150.0 bits;  conditional E-value: 2.5e-47
                                       -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlr 77 
                                       t+iQ+ea+p  l+g d++++a+TG+GKT+ f   +l++v    ++++p a++++PtreLa q+++++ ++ ky++  
  gi|474934651|ref|YP_007688233.1|  29 TPIQEEAVPRGLNGYDLIAQAQTGTGKTGTFGTIILSKVPA--KQRTPSAIVLTPTRELALQVAEEIGRMSKYTGHV 103
                                       89*************************************75..99*****************************966 PP

                                       EEEEET....TSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSH CS
                                       xxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  78 vlliig....gvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlp 150
                                       +l i+g      + ++q++ l++gvdiv gtpgr+ dl+++++lnls +r++V+DE dr+ld+gf ++++ i+ ++ 
  gi|474934651|ref|YP_007688233.1| 104 CLPIYGgsggAASIERQVDMLEKGVDIVAGTPGRVRDLIEREYLNLSAIRVIVMDESDRMLDMGFMEDVKFIFDAC- 179
                                       668888444337779999**********************************************************. PP

                                       HHCTTSTTTSEEEEEESSBSHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 151 qitcdgklqrqvivlSATlpkdvkk 175
                                             +++rq++++SAT+p+d+k 
  gi|474934651|ref|YP_007688233.1| 180 ------PAERQMMMFSATMPEDIKM 198
                                       ......67889**********9986 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.006
                                       TS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHH...HTT.CSEEEEEH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxx.xxxxxxxx RF
                              DEAD  46 tgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardqlskl...dng.vdivvgtp 105
                                       ++pkali + t +++    ++lk++      +v+++ g+ ++++  +++   + g vdi+++t 
  gi|474934651|ref|YP_007688233.1| 245 DNPKALIFCQTIKMVDMLEDRLKEYHY----KVEALHGDMPQKKRERVMddfRDGkVDILIATD 304
                                       678999999999999988888888888....5556667655555555553333446*****996 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.3   0.0   8.7e-38     2e-34      15     111 .]     245     341 ..     234     341 .. 0.91
   2 ?   -3.2   0.0       4.7     1e+04      97     107 ..     418     428 ..     401     429 .. 0.75

  Alignments for each domain:
  == domain 1  score: 118.3 bits;  conditional E-value: 8.7e-38
                                       TTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEE CS
                        Helicase_C  15 eggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVin 90 
                                       ++ k+lif++ti+++++  + l ++ ++kv +lhg++pq++re+++++f++g++d+Liatdva+rG+d+++vn+V+n
  gi|474934651|ref|YP_007688233.1| 245 DNPKALIFCQTIKMVDMlEDRL-KEYHYKVEALHGDMPQKKRERVMDDFRDGKVDILIATDVAARGLDVDDVNYVVN 320
                                       6889***********8755555.4447************************************************** PP

                                       SSSSSSHHHHHHHHTTSSSTT CS
                        Helicase_C  91 fdlprnvtsyiqriGRtgRag 111
                                       +d+p+ +++yi+riGRtgRag
  gi|474934651|ref|YP_007688233.1| 321 YDMPDMLDTYIHRIGRTGRAG 341
                                       *******************97 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.7
                                       HHHHHHHHTTS CS
                        Helicase_C  97 vtsyiqriGRt 107
                                       +++yi r+GR+
  gi|474934651|ref|YP_007688233.1| 418 LADYIMRAGRI 428
                                       47889999996 PP

>> DbpA  DbpA RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.59   1.3e+03       2      11 ..     225     234 ..     224     235 .. 0.89
   2 ?   -2.9   0.0       3.2   7.2e+03      46      63 ..     280     297 ..     279     298 .. 0.84
   3 !   52.3   1.1   1.9e-17   4.2e-14       1      71 [.     402     472 ..     402     473 .. 0.98

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.59
                                       EEES-SGGGT CS
                              DbpA   2 lfinvGkkdk 11 
                                       ++i+vG+++k
  gi|474934651|ref|YP_007688233.1| 225 YYISVGRRNK 234
                                       89*****987 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.2
                                       E-TT-HHHHHHHHTT--S CS
                              DbpA  46 vpkekaeevlkalkkkki 63 
                                        p++k e+v++ ++++k+
  gi|474934651|ref|YP_007688233.1| 280 MPQKKRERVMDDFRDGKV 297
                                       58899999***9999887 PP

  == domain 3  score: 52.3 bits;  conditional E-value: 1.9e-17
                                       EEEES-SGGGT--HHHHHHHHHTCTTB-GGGEEEEEE-SS-EEEEE-TT-HHHHHHHHTT--SSS----EE CS
                              DbpA   1 rlfinvGkkdklrpgdivgaiakeaglsgkdIGkIdildkfSfvevpkekaeevlkalkkkkikGrkvrve 71 
                                       r+ i++Gk d++ + ++ ++i + + +  + IGkI++ ++ S+vev+k++ +++l  + k++++G+kvr++
  gi|474934651|ref|YP_007688233.1| 402 RFEISLGKDDNIGKVKLADYIMRAGRIMDNAIGKIQLGKTKSMVEVHKDFGNRMLMDVPKMTFRGKKVRIR 472
                                       899******************************************************************98 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   7.1e-09   1.6e-05      27     170 ..      45     193 ..      27     194 .. 0.73
   2 ?   -2.7   0.0       2.3   5.3e+03      55      80 ..     247     272 ..     234     300 .. 0.72

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 7.1e-09
                                       EEEEESTTSTHHHHHHHHHHHH-.S.....-EEEEESSHHHHHHHHHHGGGGTGG.............GEEEESSS- CS
                            ResIII  27 glikmaTGtGKTlvaaklierll.kkgkeekflflvprkslleqtleefkkflseayke.........igkkvsgdk 93 
                                       ++ ++ TGtGKT +   +i +    k++   +++l p+++l  q  ee+ ++++ + +             +++ + 
  gi|474934651|ref|YP_007688233.1|  45 LIAQAQTGTGKTGTFGTIILSKVpAKQRTPSAIVLTPTRELALQVAEEIGRMSKYTGHVclpiyggsgGAASIERQV 121
                                       778999*********777766550555556*******************9988877665777655533112222222 PP

                                       B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHH...HHT---.SEEEEEE CS
                            ResIII  94 kkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswrei...lekfke.avllglT 166
                                       +      ++  +i+  t  ++   +     e+e l  +++ vi++DE+ r+ ++ +++ +    +++++   ++ ++
  gi|474934651|ref|YP_007688233.1| 122 D----MLEKGVDIVAGTPGRVRDLI-----EREYLNLSAIRVIVMDESDRMLDMGFMEDVkfiFDACPAeRQMMMFS 189
                                       2....44779999999999999999.....88888999999************987777733355553347788899 PP

                                       SS-S CS
                            ResIII 167 ATpe 170
                                       AT++
  gi|474934651|ref|YP_007688233.1| 190 ATMP 193
                                       9986 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.3
                                       .-EEEEESSHHHHHHHHHHGGGGTGG CS
                            ResIII  55 ekflflvprkslleqtleefkkflse 80 
                                        k+l++++++++++ +++++k++  +
  gi|474934651|ref|YP_007688233.1| 247 PKALIFCQTIKMVDMLEDRLKEYHYK 272
                                       47888899998888888888877655 PP

>> CMS1  U3-containing 90S pre-ribosomal complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   8.3e-07    0.0019     167     210 ..     118     160 ..      62     169 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 8.3e-07
                              CMS1 167 eesvtylkksrigiavGtpgRildLleeeslsvdeLkrivlDas 210
                                       e +v +l k  + i  GtpgR+ dL+e e l+++ ++ iv+D s
  gi|474934651|ref|YP_007688233.1| 118 ERQVDMLEK-GVDIVAGTPGRVRDLIEREYLNLSAIRVIVMDES 160
                                       556666654.488999**************************88 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   6.2e-06     0.014       1      75 [.      32     104 ..      32     223 .. 0.71
   2 ?   -0.6   0.0      0.67   1.5e+03      43      75 ..     247     279 ..     232     396 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.2e-06
                            AAA_19   1 qreave.alkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgaeatTiHrl 75 
                                       q+eav   l+   l+  a  GtGKT +  +i+   v ++++   + +++++t+  a +++e++    ++ +T H  
  gi|474934651|ref|YP_007688233.1|  32 QEEAVPrGLNGYDLIAQAQTGTGKTGTFGTIILSKVPAKQRT-PSAIVLTPTRELALQVAEEIG--RMSKYTGHVC 104
                                       78999559999999999*****************99999987.567789**********99993..3445566633 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.67
                            AAA_19  43 eeillvaftgrAakelrerlaalgaeatTiHrl 75 
                                        + l+ + t + ++ l++rl+++  + + +H+ 
  gi|474934651|ref|YP_007688233.1| 247 PKALIFCQTIKMVDMLEDRLKEYHYKVEALHGD 279
                                       567788888888888889988888888888865 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   5.8e-05      0.13       6      71 ..      32      98 ..      29     174 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.8e-05
                            AAA_30  6 QaaavealltsgdrvavltGpAGtGKttalkal..reaweaa.ggrviglAptgkaAkvLaeelgieas 71
                                      Q++av + l++ d   ++++  GtGKt + +++   ++ +++   + i+l+pt + A ++aee+g  ++
  gi|474934651|ref|YP_007688233.1| 32 QEEAVPRGLNGYD--LIAQAQTGTGKTGTFGTIilSKVPAKQrTPSAIVLTPTRELALQVAEEIGRMSK 98
                                      7777777777777..7999*********999987666666665799****************9994332 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   9.8e-05      0.22      13     119 ..      50     181 ..      45     197 .. 0.59
   2 ?   -3.4   0.0       4.9   1.1e+04      12      28 ..     434     450 ..     433     456 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.8e-05
                            AAA_22  13 esGtGKTtllrrlleqldeeakaee......erpevvfvtlpsstsskdllrellralglelka............. 70 
                                       ++GtGKT +  ++  +++ +++ +       +               ++l+ ++++++g+  k+             
  gi|474934651|ref|YP_007688233.1|  50 QTGTGKTGTFGTIILSKVPAKQRTPsaivltP--------------TRELALQVAEEIGRMSKYtghvclpiyggsg 112
                                       56666666666666666533222222222220..............2334444444444333334444444444444 PP

                            AAA_22  71 ..................erlsseellealeqalraravielliiDEaqh.lrseealeeLrsllnl..s 119
                                                           ++  ++++++e+   + ++i++++ DE ++ l  +  +e+++ +++   +
  gi|474934651|ref|YP_007688233.1| 113 gaasierqvdmlekgvdiVAGTPGRVRDLIEREYLNLSAIRVIVMDESDRmL-DMGFMEDVKFIFDAcpA 181
                                       4444444444454445555577788888888888888889**********77.89999999999985442 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 4.9
                            AAA_22  12 GesGtGKTtllrrlleq 28 
                                       G    GKT ++ ++++ 
  gi|474934651|ref|YP_007688233.1| 434 GKIQLGKTKSMVEVHKD 450
                                       66678***999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (482 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 3137.06
//
Query:       gi|474934652|ref|YP_007688234.1|  [L=160]
Description: ybaK/ebsC protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.1e-25   90.1   0.0    1.2e-25   89.9   0.0    1.1  1  tRNA_edit  Aminoacyl-tRNA editing domain


Domain annotation for each model (and alignments):
>> tRNA_edit  Aminoacyl-tRNA editing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.9   0.0     7e-30   1.2e-25       5     122 ..      33     149 ..      29     150 .. 0.97

  Alignments for each domain:
  == domain 1  score: 89.9 bits;  conditional E-value: 7e-30
                         tRNA_edit   5 ktieelaaalgvdpsaiaKtlvlkdkkgelvlvllpgdreldlkklakllgakklrlaseeelrellgvepGgvgPl 81 
                                        t  + a+ lg dp+++ Ktlv + k+++++++++p +reldlkk+a+++g+k++ ++  ++l+  +g+++Gg++Pl
  gi|474934652|ref|YP_007688234.1|  33 MTGTDIASLLGEDPDRCFKTLVTQGKSDRFYVFVIPVNRELDLKKAAAAVGEKSICMIRSKDLLSTTGYVHGGCSPL 109
                                       677899*********************************************************************** PP

                         tRNA_edit  82 glkaagvpvllDeslkeyptvvvgagengatlelspedlrk 122
                                       g+  + +++++ e++ + ++++v++g+ g ++el+p+dlrk
  gi|474934652|ref|YP_007688234.1| 110 GM-RKHLTTVFHETADKGERIYVSGGKVGVQVELDPADLRK 149
                                       **.8***********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 968.55
//
Query:       gi|474934653|ref|YP_007688235.1|  [L=496]
Description: Uncharacterized protein conserved in bacteria [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.6e-219  729.5   0.0   1.8e-219  729.3   0.0    1.0  1  DUF1846   Domain of unknown function (DUF1846)


Domain annotation for each model (and alignments):
>> DUF1846  Domain of unknown function (DUF1846)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  729.3   0.0    1e-223  1.8e-219       1     489 []       5     493 ..       5     493 .. 1.00

  Alignments for each domain:
  == domain 1  score: 729.3 bits;  conditional E-value: 1e-223
                                       --B-HHHHHHHHHHHHHHHHHHTTSEEEEEE-S-SS--HHHHHHSTT--TTHHHHHHHGGGGGEEEEEEEECHHHHT CS
                           DUF1846   1 igFdnekYlklqsekikerieqfggkLYlefGGklfdDlhasRvLpGfepdsklkllkklkdeveivivinakdiek 77 
                                       igFd++kY ++qs +i +r+++fggkLYle+GGk+fdDlhasRvLpGf+pdsk+++++ lkd+ve ++++n++diek
  gi|474934653|ref|YP_007688235.1|   5 IGFDSQKYYDEQSGAILKRMQEFGGKLYLEVGGKIFDDLHASRVLPGFTPDSKIRMIAALKDKVEAIVAVNCNDIEK 81 
                                       79*************************************************************************** PP

                                       T-BETTTSSBHHHHHHHHHHHHHHTT-EEEEEEEECE-TT-HHHHHHHHHHTTT-EEEEEE--TTTTT-HHHHSSTT CS
                           DUF1846  78 nkvRadlgitYdedvlrlidafrelgllvgsvvitkyeeqkaaeafkkkleklgikvykhyaiegYPsdvelivsde 154
                                       +k+R+d+gitYd++ lr++d++r++g+  + +v+t+y++q++a+af++ l+++gik++ hy+iegYP+d+++ivsde
  gi|474934653|ref|YP_007688235.1|  82 SKIRGDYGITYDAEALRMLDEYRSYGIEANVIVLTMYAHQPHADAFRRLLDSRGIKSFLHYPIEGYPNDTATIVSDE 158
                                       ***************************************************************************** PP

                                       TGGGS-----SSSEEEEE-SSTTS-HHHHHHHHHHHHHCTT--EEEEEE--SS-TTS-TTSHHHHHHHHT-SSGCGS CS
                           DUF1846 155 GyGkndyiettrplvvvtaPGpgsGklatclsqlYhenkrgvkagYakfetFPiWnlplkhpvnlaYeaatadlnDv 231
                                       GyGkn+++et++p+vvv++PGpgsGk+a+c+sq+Y +nk+g+k+gYak+etFP+Wnlpl+hpvn+aYeaatadl D+
  gi|474934653|ref|YP_007688235.1| 159 GYGKNEFVETDKPVVVVSGPGPGSGKMAVCMSQVYLDNKKGIKSGYAKYETFPVWNLPLNHPVNIAYEAATADLGDI 235
                                       ***************************************************************************** PP

                                       EEE-HHHHHHHS---EEEHHHHHHHHHHHHHHHHHHSS-S-SSHHHHB---GGGGBS-HHHHHHHHHHHHHHHHHHH CS
                           DUF1846 232 nmiDpfhleaygktavnYnRDveifPvlkailekitgespyksPtdmGvnmvgfcivddeavkeaskqeiirRyyka 308
                                       n iDp+h+eaygk+a+nYnRD+e fPvlka+leki+ge+pyksPtdmGvn+vg ci+dd+av+ ask+ei+rR++k+
  gi|474934653|ref|YP_007688235.1| 236 NAIDPWHMEAYGKIAINYNRDIESFPVLKALLEKIYGECPYKSPTDMGVNIVGSCITDDDAVCIASKREIVRRFFKY 312
                                       ***************************************************************************** PP

                                       HHHHHHHT--SHHHHHHHHHHHHHT--GGGSTTHHHHHHHHHHHSS-EEEEE-TTS-EEEEE--SSB-HHHHHHHHH CS
                           DUF1846 309 lvelkkgkvdeeeveklellmkkagiseedrkvvaaakekaeetkeeaaaieledgtivtgktsellgassalllna 385
                                       +v+  +gk+   +ve++e lm+kag s++d +++++ +e++++t  ++a +el+dgt+vtgk++++l+a sa+++n 
  gi|474934653|ref|YP_007688235.1| 313 AVDGLEGKTMPVVVERAEALMRKAGTSPNDFELYRRVHEESANTACRIAGLELPDGTVVTGKATSQLSAVSAVMING 389
                                       ***************************************************************************** PP

                                       HHHHHT--TT---S-HHHHHHHHHHHHHTS--S---B-HHHHHHHHHHHTTT-HHHHHHHGGGGGGTT-EEEESS-- CS
                           DUF1846 386 lkelagiddevkllspeviepiqklktkvlgsknprlhldevlialsisaatneeakkaleqlkklkgcevhstvil 462
                                       lk+lagid +++++++++i+piq l+t+++gs+++rl+lde+l+al++sa+tn++a+kal+q+ kl+gc++h+++ +
  gi|474934653|ref|YP_007688235.1| 390 LKHLAGIDYKQDIIAESIIRPIQMLRTEIFGSDSKRLRLDEMLTALAVSAETNPDAAKALSQIGKLRGCDIHASTTM 466
                                       ***************************************************************************** PP

                                       -HHHHHHHHHTT-EEEE-S---XXXXX CS
                           DUF1846 463 sevdekvlrklginltsepkyeskkly 489
                                        ++ +++lrklgin tsep+ +++ ly
  gi|474934653|ref|YP_007688235.1| 467 YAQGRTALRKLGINATSEPVLQTRLLY 493
                                       *********************999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (496 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.24s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 3367.46
//
Query:       gi|474934654|ref|YP_007688236.1|  [L=28]
Description: hypothetical protein TALC_01086 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (28 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       176  (0.0098165); expected 358.6 (0.02)
Passed bias filter:                      148  (0.00825478); expected 358.6 (0.02)
Passed Vit filter:                         3  (0.000167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 214.81
//
Query:       gi|474934655|ref|YP_007688237.1|  [L=588]
Description: Superfamily II DNA and RNA helicase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-49  167.5   0.0    3.8e-49  166.8   0.0    1.4  1  DEAD           DEAD/DEAH box helicase
    4.5e-31  107.5   0.1    2.9e-29  101.6   0.1    2.7  2  Helicase_C     Helicase conserved C-terminal domain
    5.7e-10   39.1   1.2    1.3e-09   37.9   0.2    2.2  2  DbpA           DbpA RNA binding domain
    3.7e-09   36.8   0.0    7.3e-09   35.9   0.0    1.4  1  ResIII         Type III restriction enzyme, res subunit
      0.001   17.9   0.3        1.3    7.8   0.2    3.5  4  UTP25          Utp25, U3 small nucleolar RNA-associated SSU p
     0.0029   16.8   0.1     0.0052   16.0   0.1    1.4  1  ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
  ------ inclusion threshold ------
      0.027   13.8   0.0      0.027   13.8   0.0    2.0  2  CMS1           U3-containing 90S pre-ribosomal complex subuni
       0.03   14.0   0.0       0.11   12.2   0.0    1.9  2  MukB_hinge     MukB hinge domain
      0.045   14.1   0.3       0.13   12.5   0.0    2.0  2  AAA_19         AAA domain
       0.24   11.7   2.4       0.62   10.3   0.3    2.5  2  AAA_22         AAA domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.8   0.0   2.1e-52   3.8e-49       1     175 [.      13     178 ..      13     179 .. 0.96

  Alignments for each domain:
  == domain 1  score: 166.8 bits;  conditional E-value: 2.1e-52
                                       -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlr 77 
                                       t++Q +aip  l+g+d++++a+TG+GKT+ +   +l++  e  g+ gp  li++PtreLa q++++l ++ ky + +
  gi|474934655|ref|YP_007688237.1|  13 TPVQTAAIPVGLNGEDLFAQAQTGTGKTGTYGSIILSRT-E-AGSAGPTSLILVPTRELATQVAEELDRLSKYSRHT 87 
                                       79**********************************777.3.7******************************9988 PP

                                       EEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  78 vlliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitc 154
                                        l i+ggv+ ++q+++l++g+d++v+tpgrl dl++++++nls+++++VlDEadr+ld+gf + +n iln+l     
  gi|474934655|ref|YP_007688237.1|  88 SLPIYGGVSIENQVKELKKGADVIVATPGRLKDLIERKSVNLSEISIVVLDEADRMLDMGFAPSVNMILNRL----- 159
                                       889*********************************************************************..... PP

                                       TSTTTSEEEEEESSBSHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 155 dgklqrqvivlSATlpkdvkk 175
                                         +++rq++++SAT+p+dv+k
  gi|474934655|ref|YP_007688237.1| 160 --PKKRQTMMFSATMPDDVRK 178
                                       ..67789**********9987 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.084   1.5e+02      14      73 ..      55     114 ..      45     145 .. 0.73
   2 !  101.6   0.1   1.6e-32   2.9e-29       5     111 .]     217     321 ..     213     321 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.084
                                       TTTSEEEEEESSHHHHHH....HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEES CS
                        Helicase_C  14 eeggkilifvntidrlek....vklllekkgikvavlhgelpqnereeileqfnkgesdvLiat 73 
                                       + g ++li v+t++ + +    ++ l + +  ++++++g  + +++ + l++      dv++at
  gi|474934655|ref|YP_007688237.1|  55 SAGPTSLILVPTRELATQvaeeLDRLSKYSRHTSLPIYGGVSIENQVKELKKG----ADVIVAT 114
                                       56778999999999443343345555555589999999999999988888776....4677777 PP

  == domain 2  score: 101.6 bits;  conditional E-value: 1.6e-32
                                       HHHHHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSS CS
                        Helicase_C   5 allellkleeeggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGi 80 
                                        l++++  e    k+++f++t+++++  ++ + ++ +++v  +hg+  q++re+i+++f++g+ +vLia+dva+rG+
  gi|474934655|ref|YP_007688237.1| 217 ELIHII--EDGYPKMMVFCRTKRKVDFlTRKM-KRDKYSVEGIHGDVGQSKRERIIQEFKDGDLKVLIASDVASRGL 290
                                       555565..677789***********7655555.4458**************************************** PP

                                       TSTTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                        Helicase_C  81 dipkvnlVinfdlprnvtsyiqriGRtgRag 111
                                       di++v++V+nfd+p ++++yi+riGRtgRag
  gi|474934655|ref|YP_007688237.1| 291 DIDGVDVVVNFDIPVDPETYIHRIGRTGRAG 321
                                       *****************************97 PP

>> DbpA  DbpA RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       4.1   7.3e+03      12      37 ..     272     297 ..     270     301 .. 0.81
   2 !   37.9   0.2   7.4e-13   1.3e-09       1      67 [.     510     576 ..     510     580 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.1
                                       --HHHHHHHHHTCTTB-GGGEEEEEE CS
                              DbpA  12 lrpgdivgaiakeaglsgkdIGkIdi 37 
                                       ++ gd+  +ia +   +g dI  +d+
  gi|474934655|ref|YP_007688237.1| 272 FKDGDLKVLIASDVASRGLDIDGVDV 297
                                       78899999999999999999988887 PP

  == domain 2  score: 37.9 bits;  conditional E-value: 7.4e-13
                                       EEEES-SGGGT--HHHHHHHHHTCTTB-GGGEEEEEE-SS-EEEEE-TT-HHHHHHHHTT--SSS-- CS
                              DbpA   1 rlfinvGkkdklrpgdivgaiakeaglsgkdIGkIdildkfSfvevpkekaeevlkalkkkkikGrk 67 
                                       rl +++G +d+++  ++ ++i + ag+  kdIG+I+++ + S v+v +  ++ev++ + +++++ ++
  gi|474934655|ref|YP_007688237.1| 510 RLELSIGSNDGVTVDNLAKFIVRVAGIAPKDIGNIHVYADKSRVQVVRWRSQEVVDEVFGQTFNDKR 576
                                       799*******************************************************999999765 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.0     4e-12   7.3e-09      27     170 ..      29     173 ..      22     174 .. 0.83

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 4e-12
                                       EEEEESTTSTHHHHHHHHHHHH-S......-EEEEESSHHHHHHHHHHGGGGTGG.........GEEEESSS-B--. CS
                            ResIII  27 glikmaTGtGKTlvaaklierllkkgkee.kflflvprkslleqtleefkkflseayke.....igkkvsgdkkkak 97 
                                       ++ ++ TGtGKT ++ ++i + +++g+     l+lvp+++l  q  ee+ ++++  ++          vs +++ + 
  gi|474934655|ref|YP_007688237.1|  29 LFAQAQTGTGKTGTYGSIILSRTEAGSAGpTSLILVPTRELATQVAEELDRLSKYSRHTslpiyG--GVSIENQVK- 102
                                       567899******************99887799**************9999998888777677432..333333333. PP

                                       ......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS....TTTHHHHHT-.--SEEEEEESS-S CS
                            ResIII  98 ekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak...kswreilekf.keavllglTATpe 170
                                        + ++ ++++v+t  +l+  +     e+++   +++ +++ DEa r+ ++    s++ il+ + k+   + ++AT++
  gi|474934655|ref|YP_007688237.1| 103 -ELKKGADVIVATPGRLKDLI-----ERKSVNLSEISIVVLDEADRMLDMgfaPSVNMILNRLpKKRQTMMFSATMP 173
                                       .458899**************.....9999999999*************96656999999998455777999***86 PP

>> UTP25  Utp25, U3 small nucleolar RNA-associated SSU processome protein 25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.017        31      75     102 ..      57      84 ..      49     102 .. 0.84
   2 !    7.8   0.2    0.0007       1.3     162     222 ..     108     163 ..      93     172 .. 0.80
   3 ?    1.3   0.0     0.064   1.2e+02     242     272 ..     159     189 ..     152     204 .. 0.82
   4 ?    2.2   0.0     0.035        62     346     417 ..     242     311 ..     218     346 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.017
                             UTP25  75 rpkvLillptreaalevvelllklleae 102
                                        p  Lil+ptre a++v e+l +l++ +
  gi|474934655|ref|YP_007688237.1|  57 GPTSLILVPTRELATQVAEELDRLSKYS 84 
                                       5788**************9998888766 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0007
                             UTP25 162 sdiiiaSPlglrliieeedkkkrdtdfLsSiEvlivdqadvl.emQnwehvetvlkhlnkip 222
                                       +d+i+a P  l+ +ie      r++  Ls i ++++d+ad +  m     v+++l++l k+ 
  gi|474934655|ref|YP_007688237.1| 108 ADVIVATPGRLKDLIE------RKSVNLSEISIVVLDEADRMlDMGFAPSVNMILNRLPKKR 163
                                       8**************9......45567*************7615777778888876665543 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.064
                             UTP25 242 akllRQtlvfssyetpeinslfnskleNlaG 272
                                         + RQt++fs+ +  +++++  +++ N++ 
  gi|474934655|ref|YP_007688237.1| 159 LPKKRQTMMFSATMPDDVRKMAVKYMINYRE 189
                                       5667******************9*9999986 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.035
                             UTP25 346 vrnylkeekvsfaaiseysskkevsraRelFfkgkkkvlLyteRlhffrRykikgvkkvilYklPenpefys 417
                                       +++ +k++k+s   i+    +++ +r  ++F++g+ kvl+ ++ +   r  +i gv  v+ +++P  pe y 
  gi|474934655|ref|YP_007688237.1| 242 LTRKMKRDKYSVEGIHGDVGQSKRERIIQEFKDGDLKVLIASDVAS--RGLDIDGVDVVVNFDIPVDPETYI 311
                                       4567888999999999999999999999**************9885..899***************999885 PP

>> ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   2.9e-06    0.0052      51     132 ..     217     302 ..     178     332 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.9e-06
                     ERCC3_RAD25_C  51 fLikyhekrgDkiivfsDnvfaLkeyakklkkp.y....iyGetseaerlkilqkfkknpkvntiflskvgDtsiDl 122
                                        Li++ e    k++vf+     +  +++k+k+  y    i+G++ +++r +i+q+fk   ++++++ s v+   +D+
  gi|474934655|ref|YP_007688237.1| 217 ELIHIIEDGYPKMMVFCRTKRKVDFLTRKMKRDkYsvegIHGDVGQSKRERIIQEFKDG-DLKVLIASDVASRGLDI 292
                                       5777778888899999988777777777766531233449****************987.689999*********** PP

                     ERCC3_RAD25_C 123 Peanvliqis 132
                                           v++  +
  gi|474934655|ref|YP_007688237.1| 293 DGVDVVVNFD 302
                                       *999998765 PP

>> CMS1  U3-containing 90S pre-ribosomal complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.5e-05     0.027     164     209 ..      95     139 ..      47     145 .. 0.78
   2 ?   -6.5   3.9        10   1.8e+04      19      40 ..     381     402 ..     366     444 .. 0.51

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.5e-05
                              CMS1 164 ikleesvtylkksrigiavGtpgRildLleeeslsvdeLkrivlDa 209
                                       + +e++v+ lkk    + v tpgR+ dL+e +s++++e+  +vlD 
  gi|474934655|ref|YP_007688237.1|  95 VSIENQVKELKKG-ADVIVATPGRLKDLIERKSVNLSEISIVVLDE 139
                                       5678888888876.467799************************96 PP

  == domain 2  score: -6.5 bits;  conditional E-value: 10
                              CMS1  19 kksekkRskkkerkkgklketq 40 
                                       kk   +   k+ +k + l++t 
  gi|474934655|ref|YP_007688237.1| 381 KKVAAETAAKAPEKAARLRKTV 402
                                       3333333333444444443333 PP

>> MukB_hinge  MukB hinge domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   6.1e-05      0.11     114     155 ..      71     112 ..      63     118 .. 0.88
   2 ?   -3.0   0.0       2.9   5.1e+03      92     108 ..     205     221 ..     175     239 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.1e-05
                        MukB_hinge 114 avlvkdsdrqlRysrfPevPlfGraaRekrleaLraerdela 155
                                       + + ++ dr  +ysr+ ++P+ G ++ e+++++L++ +d ++
  gi|474934655|ref|YP_007688237.1|  71 TQVAEELDRLSKYSRHTSLPIYGGVSIENQVKELKKGADVIV 112
                                       56778889****************************999876 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.9
                        MukB_hinge  92 yliegdpdafdesvfea 108
                                       y+i  + d+ +++++++
  gi|474934655|ref|YP_007688237.1| 205 YFIMTNRDSKRDELIHI 221
                                       88888888888877654 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   7.5e-05      0.13       1     112 [.      16     141 ..      16     169 .. 0.58
   2 ?   -2.4   0.1         3   5.4e+03      55      75 ..     371     391 ..     358     442 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.5e-05
                            AAA_19   1 qreave.alkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae......at 70 
                                       q++a+   l+ + l+  a  GtGKT +   i+    e+g+    + l++ +t+  a +++e+l+ l +         
  gi|474934655|ref|YP_007688237.1|  16 QTAAIPvGLNGEDLFAQAQTGTGKTGTYGSIILSRTEAGSAG-PTSLILVPTRELATQVAEELDRLSKYsrhtslP- 90 
                                       5666655778888888999********************887.5667788***********997766543323220. PP

                            AAA_19  71 TiHrlal............ldfddlltealelle.................eaeeekklqeeellivDEfq 112
                                             +            l             +                 e +++ +l e  +++ DE+ 
  gi|474934655|ref|YP_007688237.1|  91 ------IyggvsienqvkeL-------------KkgadvivatpgrlkdliE-RKSVNLSEISIVVLDEAD 141
                                       ......12222323222220.............2222222233333334322.233344333467777764 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3
                            AAA_19  55 akelrerlaalgaeatTiHrl 75 
                                       ake+++r aa +++a+T  + 
  gi|474934655|ref|YP_007688237.1| 371 AKEIKQRNAAKKVAAETAAKA 391
                                       566666665656666665544 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.3   0.00035      0.62      14     112 ..      35     155 ..      29     179 .. 0.50
   2 ?   -0.3   0.1      0.65   1.2e+03      37      71 ..     386     430 ..     369     446 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00035
                            AAA_22  14 sGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka.................... 70 
                                       +GtGKT ++  +  + +e+ +a     ++ ++ +p     ++l+++++++l++  k+                    
  gi|474934655|ref|YP_007688237.1|  35 TGTGKTGTYGSIILSRTEAGSAG----PTSLILVPT----RELATQVAEELDRLSKYsrhtslpiyggvsienqvke 103
                                       66666666666666654332221....111222222....2333333333333222233445666666666666666 PP

                            AAA_22  71 ..........erlsseellealeqalraravielliiDEaqh.lr.s.eealeeL 112
                                                  +    +l +++e+ + + + i+++++DEa++ l+   +  ++ +
  gi|474934655|ref|YP_007688237.1| 104 lkkgadvivaTP---GRLKDLIERKSVNLSEISIVVLDEADRmLDmGfAPSVNMI 155
                                       666666633334...4444444444444444677********6645243333333 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.65
                            AAA_22  37 e......erpevv..fvtlpsstsskdllrellralglelka..e 71 
                                       e      e++  +  +v++++++++k+ +r l  al+++ k+  +
  gi|474934655|ref|YP_007688237.1| 386 EtaakapEKAARLrkTVEAAEEGGRKKTARTLSGALDRPVKGkaK 430
                                       133334422222356899999999999999999999998888552 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (588 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1036  (0.0577835); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.71u 0.30s 00:00:01.01 Elapsed: 00:00:00.47
# Mc/sec: 3752.90
//
Query:       gi|474934656|ref|YP_007688238.1|  [L=544]
Description: putative metal-binding protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.5e-61  207.0   6.0    4.8e-61  206.1   3.7    2.1  2  RACo_C_ter   C-terminal domain of RACo the ASKHA domain
    5.5e-18   65.2   0.1    1.6e-16   60.4   0.1    2.3  2  Raco_middle  RACo middle region
    2.8e-05   24.0  12.3      0.017   15.2   3.0    2.7  2  Fer4_6       4Fe-4S binding domain
    3.5e-05   23.4  12.2      0.004   16.9   2.5    3.0  3  Fer4         4Fe-4S binding domain
    8.4e-05   22.5   0.2    0.00025   20.9   0.2    1.7  2  Pan_kinase   Type III pantothenate kinase
    0.00023   22.1  12.4      0.044   14.7   4.5    2.8  2  Fer4_16      4Fe-4S double cluster binding domain
    0.00044   20.4  16.0    0.00081   19.5  15.2    1.9  1  Fer4_9       4Fe-4S dicluster domain
    0.00048   20.2  11.9     0.0014   18.7  11.9    1.8  1  Fer4_21      4Fe-4S dicluster domain
    0.00068   20.2  16.4     0.0012   19.4  15.5    2.0  2  Fer4_7       4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.015   15.4  17.6       0.14   12.3  18.1    2.4  2  Fer4_10      4Fe-4S dicluster domain
      0.029   14.9  13.3      0.087   13.4   2.8    2.8  2  Fer4_4       4Fe-4S binding domain
        1.4    9.4  16.6        1.2    9.7   3.3    2.6  2  Fer4_8       4Fe-4S dicluster domain
        2.3    8.8  17.8        2.6    8.6   3.4    2.6  2  Fer4_17      4Fe-4S dicluster domain
        6.9    6.8  18.7          3    7.9   6.8    2.4  2  DUF326       Domain of Unknown Function (DUF326)


Domain annotation for each model (and alignments):
>> RACo_C_ter  C-terminal domain of RACo the ASKHA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0       0.2   2.6e+02     141     172 ..      59      90 ..      44      94 .. 0.91
   2 !  206.1   3.7   3.7e-64   4.8e-61       1     259 [.     172     432 ..     172     433 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.2
                                       HHHHHHHHHHHHHHHHTT--GGG--EEEEESS CS
                        RACo_C_ter 141 kakaAiyagiktLleevglevediekvylAGa 172
                                       +a + i+++++ L +++g++++++ ++ ++G 
  gi|474934656|ref|YP_007688238.1|  59 NATGLIRTAANQLFHALGVDLSKVVRIGVCGN 90 
                                       588999********************999996 PP

  == domain 2  score: 206.1 bits;  conditional E-value: 3.7e-64
                                       S-EEEEEESSSEEEEEE-SS.-EEEEEEE--SCCCTTTSTTBE-SSTTEEEEEEEEGGGSSEEEEECTSS-...... CS
                        RACo_C_ter   1 elslliDiGTNaEivlgnkd.ellaasaaaGPAlEGaeikcGmrAapgAIedveidpetlevelkvigdek...... 70 
                                       e +l++D+GTNaE++l  +d +++++saaaGPA+EG+ei+ Gm+AapgAI+d+ i++e   ++++v++d+       
  gi|474934656|ref|YP_007688238.1| 172 EPCLVVDYGTNAEMALICGDgRIITGSAAAGPAMEGQEIERGMLAAPGAISDIDITDEG--WQCTVLDDNMidrtgd 246
                                       679************9986549************************************9..9*****8877788899 PP

                                       ................-SEEEHHHHHHHHHHHHHTTSB-TTS-B-GGG-TTTEEEETTCEEEEEE-GGGSSSS-EEE CS
                        RACo_C_ter  71 ................akGicGsGiidliaelleagiidkkgklnkelkserireeeetleyvlakaeetetkdivi 131
                                                       a Gi+G+G +++++  +++gii+  +++             +t++  l+ ++     +i i
  gi|474934656|ref|YP_007688238.1| 247 lidpmtgktvkkgevdAIGITGTGTVAALYCGIQKGIINP-PEI-------------KTEDGRLHLQN-----GIDI 304
                                       9999999999999999**********************65.677.............56788899987.....9*** PP

                                       EHHHHHHHHHHHHHHHHHHHHHHHHTT--GGG--EEEEESSGGGCEEHHHHHHHTSS-SS-GGGEEEECSHHHHHHH CS
                        RACo_C_ter 132 tekDieelikakaAiyagiktLleevglevediekvylAGafGsyidaekAitiGllPdlelekvvqvGNtslagAr 208
                                       t++D++e++ka++A++ag+ tLl+++g+ + d++++y++Ga+G y+da kA++iG++    + k+ q+GNts+++Ar
  gi|474934656|ref|YP_007688238.1| 305 TSHDVDEAGKAIGAMRAGFLTLLNAAGMWTGDVKTAYMSGASGLYVDAIKAQQIGMVVP-GATKLIQFGNTSIEMAR 380
                                       ********************************************************988.89*************** PP

                                       HHHCBHHHHHHHHHHHHHE..EE--TTSSSHHHHHHHHHSSSS-SSGGG-ST- CS
                        RACo_C_ter 209 eallseealeeleeiarki..tyielateeeFqeeyvaalflphtdlelfpsv 259
                                       ++ +++  l+ l++ a+++  +++++at+e F++ y+ + +++ +++ +++++
  gi|474934656|ref|YP_007688238.1| 381 RIAMNKVDLDFLRSFAESLkaEHCMFATSEVFKNIYSIEYSVWCSSM-PMSMY 432
                                       *****************9999**********************9999.77776 PP

>> Raco_middle  RACo middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.4   0.1   1.2e-19   1.6e-16       1     163 []       6     170 ..       6     170 .. 0.84
   2 ?    2.2   0.0       0.1   1.3e+02      47     105 ..     226     282 ..     217     309 .. 0.83

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 1.2e-19
                       Raco_middle   1 yGlavDiGtTtvvaaLvdletgkelaeasalNpQikyGeDvlsRiayakeeeegleklqkavveeinelieelleea 77 
                                       yG+a+DiGt+ + ++ +dlet++++a+a +  +    G +v+  ++ya++  +g e+ + ++ ++ n+    l +  
  gi|474934656|ref|YP_007688238.1|   6 YGIALDIGTSGLRCQAIDLETEETVATAITQRHP-IPGMNVIDHVNYAMK--SGEENATGLIRTAANQ----LFHAL 75 
                                       9*************************99876555.56*************..6666666666655555....55666 PP

                       Raco_middle  78 giekeeiyevvvagNttMlhlllgldpkslaka........pyvpvvseavelkakelgl.kinpeakvyvlpnvss 145
                                       g++ +++ ++ v+gNt  + l+ g++ + la a          vp  ++ v+l+ak++g+ +++pe++v++ p+v +
  gi|474934656|ref|YP_007688238.1|  76 GVDLSKVVRIGVCGNTFQMSLFQGIEIRDLAFAgqnmldrlGVVPPKRDGVVLPAKDVGItDVSPECVVIIPPAVRH 152
                                       999***********************998875511111111578889999*********9458************** PP

                       Raco_middle 146 yvGgDivagilasglhks 163
                                        +G+D++a +l++++hks
  gi|474934656|ref|YP_007688238.1| 153 EIGADAIAMLLMTNVHKS 170
                                       ***************985 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.1
                       Raco_middle  47 yakeeeegleklqkavveeinelieelleeagiekeeiyevvvagNttMlhlllgldpk 105
                                       +++e   + + l + +++   +li+ ++ ++ ++k e+ ++ + g  t   l +g++  
  gi|474934656|ref|YP_007688238.1| 226 ITDE-GWQCTVLDDNMIDRTGDLIDPMTGKT-VKKGEVDAIGITGTGTVAALYCGIQKG 282
                                       5555.55677899999999999**9999887.9**********************9865 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   1.9   5.2e-05     0.066       9      24 .]     485     500 ..     463     500 .. 0.86
   2 !   15.2   3.0   1.3e-05     0.017       7      24 .]     516     535 ..     514     535 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.2e-05
                            Fer4_6   9 CigCgdCvrvCPegai 24 
                                       C+ C +C++ CPe+a+
  gi|474934656|ref|YP_007688238.1| 485 CVFCKKCMKECPEQAL 500
                                       555***********97 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.3e-05
                            Fer4_6   7 dkCig..CgdCvrvCPegai 24 
                                       d+C g  C++C+r+CP +++
  gi|474934656|ref|YP_007688238.1| 516 DRCAGtaCRRCERACPKNVL 535
                                       8999777*********9875 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       3.9     5e+03       6      20 ..     465     469 ..     463     471 .. 0.59
   2 !   16.9   2.5   3.1e-06     0.004       7      24 .]     484     501 ..     482     501 .. 0.91
   3 !   12.5   0.4     8e-05       0.1       9      23 ..     521     535 ..     521     536 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3.9
                                       TTSSS-THHHHHSTT CS
                              Fer4   6 ekCigCGaCvevCPv 20 
                                       +           CPv
  gi|474934656|ref|YP_007688238.1| 465 D----------KCPV 469
                                       3..........4666 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 3.1e-06
                                       TSSS-THHHHHSTTTEEE CS
                              Fer4   7 kCigCGaCvevCPvgAIt 24 
                                        C++C++C++ CP  A++
  gi|474934656|ref|YP_007688238.1| 484 GCVFCKKCMKECPEQALE 501
                                       5*************9985 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 8e-05
                                       SS-THHHHHSTTTEE CS
                              Fer4   9 igCGaCvevCPvgAI 23 
                                       ++C +C+ +CP +++
  gi|474934656|ref|YP_007688238.1| 521 TACRRCERACPKNVL 535
                                       58*********9986 PP

>> Pan_kinase  Type III pantothenate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.2     2e-07   0.00025     101     159 ..     151     209 ..     131     227 .. 0.87
   2 ?   -2.9   0.0       3.9   4.9e+03       4      16 ..     369     381 ..     368     433 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2e-07
                                       GGGS-HHHHHHHHHHHHHCTTSEEEEEEESSEEEEEEEETTSEEEEEEEEE-HHHHHHH CS
                        Pan_kinase 101 pkelGaDRwvaavaarellpgkpllvvdfGTAttfdavsadgeylGGlIaPGlalmlea 159
                                        +e+GaD ++ ++    +++++p+lvvd+GT   + ++  dg+ + G  a+G a+  + 
  gi|474934656|ref|YP_007688238.1| 151 RHEIGADAIAMLLMTNVHKSKEPCLVVDYGTNAEMALICGDGRIITGSAAAGPAMEGQE 209
                                       689*******999988866899******************************9987665 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.9
                                       EEE-SSEEEEEEE CS
                        Pan_kinase   4 iDiGNtrikwalf 16 
                                       i  GNt+i +a  
  gi|474934656|ref|YP_007688238.1| 369 IQFGNTSIEMARR 381
                                       7789999988754 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   4.5   3.4e-05     0.044       2      33 ..     485     516 ..     484     521 .. 0.87
   2 !   10.3   2.1    0.0008         1       3      20 ..     521     538 ..     517     542 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.4e-05
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearecisy 33 
                                       C+ C+kC++ CP++a++ +ke  +    c+s 
  gi|474934656|ref|YP_007688238.1| 485 CVFCKKCMKECPEQALEIRKEGDVSVAYCMSD 516
                                       999**************999999888888775 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0008
                           Fer4_16   3 gtCgkCaevCPtnaikek 20 
                                       + C++C  +CP n+++++
  gi|474934656|ref|YP_007688238.1| 521 TACRRCERACPKNVLHMD 538
                                       46***********99887 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5  15.2   6.3e-07   0.00081       2      50 ..     485     534 ..     484     535 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 6.3e-07
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaC..igCgaCveaCpkga 50 
                                       C+ C++C++ Cp ++ + ++ +      + s+ +C  + C++C+ aCpk++
  gi|474934656|ref|YP_007688238.1| 485 CVFCKKCMKECPEQALEIRKEGDVSVAYCMSD-RCagTACRRCERACPKNV 534
                                       *****************999999999999998.9*7777*********984 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7  11.9   1.1e-06    0.0014       6      59 .]     483     537 ..     481     537 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.1e-06
                           Fer4_21   6 dkCigCgkCliaCedtshqaieidaktvlkvvedeCvG..CnlCssvCPvedciem 59 
                                       d C+ C+kC++ C++++ +  +  + +v+  ++d+C G  C  C   CP +++++m
  gi|474934656|ref|YP_007688238.1| 483 DGCVFCKKCMKECPEQALEIRKEGDVSVAYCMSDRCAGtaCRRCERACP-KNVLHM 537
                                       57************855543333344555668****6555*********.687776 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   4.1   0.00013      0.16      32      52 .]     479     499 ..     464     499 .. 0.80
   2 !   19.4  15.5   9.3e-07    0.0012       2      52 .]     485     534 ..     484     534 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
                            Fer4_7  32 eidpekClgCgaCvavCPtga 52 
                                       +++ + C++C++C+++CP +a
  gi|474934656|ref|YP_007688238.1| 479 KGEIDGCVFCKKCMKECPEQA 499
                                       567899************886 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 9.3e-07
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClg..CgaCvavCPtga 52 
                                       C+ C++C++ Cp +a+e+++e +      ++  +++C g  C++C+++CP+++
  gi|474934656|ref|YP_007688238.1| 485 CVFCKKCMKECPEQALEIRKEGDV---SVAYCMSDRCAGtaCRRCERACPKNV 534
                                       ******************998543...44778899**6544*********986 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3  18.1   0.00011      0.14       7      56 .]     483     531 ..     478     531 .. 0.68
   2 ?    3.7   7.3     0.051        66       6      21 ..     515     532 ..     511     540 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                           Fer4_10   7 dtCirCgkCvkaCPadltsvgakgeaseeeavrk..kvekCtg..cgaCveaCP 56 
                                       d C+ C+kC+k CP      +a ++++e+++      +++C g  c  C +aCP
  gi|474934656|ref|YP_007688238.1| 483 DGCVFCKKCMKECPE-----QALEIRKEGDVSVAycMSDRCAGtaCRRCERACP 531
                                       78*************.....33333333322222235666655889*******9 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.051
                           Fer4_10   6 ddtC..irCgkCvkaCPa 21 
                                       +d+C  + C++C +aCP 
  gi|474934656|ref|YP_007688238.1| 515 SDRCagTACRRCERACPK 532
                                       68897789*********8 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   3.0     0.017        21       3      16 ..     484     497 ..     482     500 .. 0.87
   2 ?   13.4   2.8   6.8e-05     0.087       1      16 [.     515     532 ..     515     536 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.017
                            Fer4_4   3 rCigCgsCvaaCPq 16 
                                        C+ C++C+  CP 
  gi|474934656|ref|YP_007688238.1| 484 GCVFCKKCMKECPE 497
                                       6999*********6 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 6.8e-05
                            Fer4_4   1 qerC..igCgsCvaaCPq 16 
                                       ++rC  + C++C++aCP 
  gi|474934656|ref|YP_007688238.1| 515 SDRCagTACRRCERACPK 532
                                       599*888**********6 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   3.3    0.0009       1.2      44      63 ..     464     497 ..     423     499 .. 0.70
   2 ?    2.6  16.1      0.15   1.9e+02       2      65 .]     482     534 ..     481     534 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0009
                            Fer4_8  44 e..............eealwsCttcgaCtevCpv 63 
                                       +              +  ++ C+ c++C ++Cp+
  gi|474934656|ref|YP_007688238.1| 464 TdkcpvkvvasgtflKGEIDGCVFCKKCMKECPE 497
                                       0455555555566667789999999999999998 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.15
                            Fer4_8   2 lekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsC..ttcgaCtevCpvgi 65 
                                       ++ C+ C  C+++Cp         l+ r+e     +  ++       ++C  t+c++C+++Cp+++
  gi|474934656|ref|YP_007688238.1| 482 IDGCVFCKKCMKECPE------QALEIRKEGDV-SVAYCM------SDRCagTACRRCERACPKNV 534
                                       567***********92......23333333233.334444......5677779**********986 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   3.4    0.0021       2.6      42      59 ..     481     498 ..     470     499 .. 0.87
   2 ?    5.9   5.5     0.014        18      42      60 ..     514     534 ..     500     535 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0021
                           Fer4_17  42 kaslCieCgeCerkCPqg 59 
                                       +++ C+ C++C ++CP++
  gi|474934656|ref|YP_007688238.1| 481 EIDGCVFCKKCMKECPEQ 498
                                       6889************85 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.014
                           Fer4_17  42 kaslC..ieCgeCerkCPqgl 60 
                                       + ++C  + C++Cer+CP+++
  gi|474934656|ref|YP_007688238.1| 514 MSDRCagTACRRCERACPKNV 534
                                       556773357*********986 PP

>> DUF326  Domain of Unknown Function (DUF326)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   4.0     0.029        38      11      18 ..     488     495 ..     487     497 .. 0.96
   2 ?    7.9   6.8    0.0024         3       6      18 ..     517     530 ..     514     532 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.029
                                       HHHHHHHH CS
                            DUF326  11 CrkCAkaC 18 
                                       C+kC+k+C
  gi|474934656|ref|YP_007688238.1| 488 CKKCMKEC 495
                                       ******** PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0024
                                       HHH.HHHHHHHHHH CS
                            DUF326   6 kCA.kaCrkCAkaC 18 
                                       +CA  aCr+C +aC
  gi|474934656|ref|YP_007688238.1| 517 RCAgTACRRCERAC 530
                                       69*9********** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (544 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 3876.60
//
Query:       gi|474934657|ref|YP_007688239.1|  [L=278]
Description: hypothetical protein TALC_01089 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-05   23.9   0.2    0.00095   18.6   0.0    2.3  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
    6.7e-05   22.3   0.0    0.00053   19.3   0.0    2.2  1  THF_DHG_CYH_C    Tetrahydrofolate dehydrogenase/cyclohydrolas
    0.00092   19.3   2.5     0.0015   18.7   0.5    2.0  2  AdoHcyase_NAD    S-adenosyl-L-homocysteine hydrolase, NAD bin
    0.00099   18.5   0.2     0.0013   18.1   0.2    1.3  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
     0.0017   18.8   0.1      0.005   17.3   0.1    1.7  2  NAD_binding_7    Putative NAD(P)-binding
     0.0029   17.2   0.1      0.036   13.6   0.1    2.1  2  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
      0.003   17.7   0.0     0.0057   16.8   0.0    1.4  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
     0.0039   17.2   0.1      0.006   16.6   0.1    1.4  1  Mrr_cat          Restriction endonuclease
     0.0057   16.9   0.2      0.013   15.8   0.2    1.6  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
  ------ inclusion threshold ------
      0.017   15.1   0.0      0.028   14.5   0.0    1.3  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
      0.022   15.0   0.5      0.057   13.7   0.1    1.9  2  TrkA_N           TrkA-N domain
       0.03   14.3   1.9       0.12   12.4   0.4    2.4  3  ADH_zinc_N       Zinc-binding dehydrogenase
       0.05   13.3   0.4      0.094   12.4   0.4    1.4  1  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd
      0.072   13.0   0.4       0.11   12.3   0.4    1.3  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding


Domain annotation for each model (and alignments):
>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.037        47      43      68 ..      61      89 ..      31      99 .. 0.84
   2 !   18.6   0.0   7.4e-07   0.00095      29      93 ..     140     207 ..     114     216 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.037
                                      S-SHHH...HHHHHHHHHTT-EEEEESSS CS
                      2-Hacid_dh_C 43 GlGrIG...qavakrlkafgmkviaydrs 68
                                      GlG IG   ++va++++ +gm+ ++++r+
  gi|474934657|ref|YP_007688239.1| 61 GLGVIGgfsKSVADIVRDMGMECFVTERT 89
                                      77777755589***********9999886 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 7.4e-07
                                       GSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH...CHHHHTCEECSHHHHHHH-S CS
                      2-Hacid_dh_C  29 llgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkee...eeeelgvelvsleellaesD 93 
                                            l+gk v + G+Gr+G+++  +l+a g++v++ d+ k+k e   +++   +  ++++e+   + 
  gi|474934657|ref|YP_007688239.1| 140 GAADGLEGKDVFVRGAGRVGSNMVALLRAAGARVTVGDVIKEKAEavaKANPGTCVADDIDEATYAAH 207
                                       456689*********************************99988754223332334556666665555 PP

>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   4.2e-07   0.00053      17      73 ..     128     183 ..     117     264 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4.2e-07
                                       -HHHHHHHHHHHHCT---TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCCH CS
                     THF_DHG_CYH_C  17 pctpkgvvellketgielegkkvvvvGrsnivgkplallLleknatVtvchsktkdl 73 
                                        ct++g ve l+ +   legk+v+v G+++ vg+ + +lL +++a Vtv +   ++ 
  gi|474934657|ref|YP_007688239.1| 128 YCTAAGYVEALRGAADGLEGKDVFVRGAGR-VGSNMVALLRAAGARVTVGDVIKEKA 183
                                       5**************************986.9**********999999865544333 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.57   7.3e+02      32      56 ..      66      90 ..      46     116 .. 0.71
   2 !   18.7   0.5   1.1e-06    0.0015       1      54 [.     126     178 ..     126     213 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.57
                                      SHHHHHHHHHHHHCT-EEEEE-S-H CS
                     AdoHcyase_NAD 32 GdvGkGcaaslkglGarvivtevdP 56
                                      G   k  a+ ++ +G    vte   
  gi|474934657|ref|YP_007688239.1| 66 GGFSKSVADIVRDMGMECFVTERTD 90
                                      3334888999999999999998554 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 1.1e-06
                                       HHHHHCCCCCHHHHHHH-S--TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S CS
                     AdoHcyase_NAD   1 nlygcreslvdgikratdvllaGkvavvaGyGdvGkGcaaslkglGarvivtev 54 
                                       n y++    v++++ a+d  l Gk + v G G vG    a l+++Garv+v +v
  gi|474934657|ref|YP_007688239.1| 126 NSYCTAAGYVEALRGAADG-LEGKDVFVRGAGRVGSNMVALLRAAGARVTVGDV 178
                                       6799999999999999997.58*****************************987 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.2     1e-06    0.0013      19      72 ..     138     191 ..     119     259 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1e-06
                                       TTCEETCB---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTT CS
                       AlaDh_PNT_C  19 laGgvpgvepakvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslga 72 
                                       l G   g e   v+v G+G +G + +a  ++ ga+Vtv Dv ++++e + + + 
  gi|474934657|ref|YP_007688239.1| 138 LRGAADGLEGKDVFVRGAGRVGSNMVALLRAAGARVTVGDVIKEKAEAVAKANP 191
                                       567778888999***********************************9988443 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       4.7     6e+03      27      39 ..      98     110 ..      94     131 .. 0.67
   2 !   17.3   0.1   3.9e-06     0.005       5      62 ..     145     202 ..     143     224 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4.7
                     NAD_binding_7  27 leagakvtvvape 39 
                                       ++ ga+++++a +
  gi|474934657|ref|YP_007688239.1|  98 IDRGADIILMADD 110
                                       5667777777776 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 3.9e-06
                     NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtv..vapevkeeleelvklaeeel.ekdlega 62 
                                       l+gk v v G+G+v+ + v  l +aga+vtv  v +e   ++e   k+++ ++  +d+++a
  gi|474934657|ref|YP_007688239.1| 145 LEGKDVFVRGAGRVGSNMVALLRAAGARVTVgdVIKE---KAEAVAKANPGTCvADDIDEA 202
                                       689****************************664444...566666666544435666654 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.19   2.5e+02      15      54 ..      68     107 ..      61     117 .. 0.80
   2 !   13.6   0.1   2.8e-05     0.036       2      70 ..     145     215 ..     144     227 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.19
                                       HHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEH CS
                              IlvN  15 qGhaqalnlrdsgldvvvglregsksvkkAkeegfevltv 54 
                                         ++ a  +rd g++  v+ r++   + +A ++g +++ +
  gi|474934657|ref|YP_007688239.1|  68 FSKSVADIVRDMGMECFVTERTDVWGFGEAIDRGADIILM 107
                                       456789999**********999998888888888877655 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 2.8e-05
                                       HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-..HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-H CS
                              IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregs..ksvkkAkeegfevltvaeavkkadvvmiliPD 70 
                                       l+gk + v G G  G +    lr +g  v+vg   ++  + v+kA+       +++ea+ +a ++++  P 
  gi|474934657|ref|YP_007688239.1| 145 LEGKDVFVRGAGRVGSNMVALLRAAGARVTVGDVIKEkaEAVAKANPGTCVADDIDEATYAAHLLLNASPS 215
                                       789*****************************65444115777777777888899*****99999888775 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   4.4e-06    0.0057       4      55 ..     152     205 ..     149     216 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.4e-06
                                       EE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT..EEE-SSHHHHHHH CS
                     NAD_binding_2   4 fiGlGvMGsnmalnllkagykvavynrtkekveelvaeg..akaaesieelvas 55 
                                       + G G  Gsnm+  l +ag +v+v ++ kek+e++++++    +a++i e++ +
  gi|474934657|ref|YP_007688239.1| 152 VRGAGRVGSNMVALLRAAGARVTVGDVIKEKAEAVAKANpgTCVADDIDEATYA 205
                                       5699********************************997667777777776654 PP

>> Mrr_cat  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   4.7e-06     0.006       9      79 ..      68     148 ..      65     189 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.7e-06
                                       HHHHHHHHHHHHSSS.......EEE---B-TTSSB--EEEETTEEEEEEEEEEE--TS-...B-HHHHHHHHHHCTT CS
                           Mrr_cat   9 FeklvaellealGyk.......eveltgrsgDggiDliakkdplgserilvqaKryknk...vgvkeVqeligalkk 75 
                                       F k va++++ +G++       +v   g++ D g+D+i+++d+ +   + v a +y+n+   + +  V++l+ga+++
  gi|474934657|ref|YP_007688239.1|  68 FSKSVADIVRDMGMEcfvtertDVWGFGEAIDRGADIILMADDEQYMAYSVAAGKYSNNsycTAAGYVEALRGAADG 144
                                       9999*************99999899999999************9999*********86445567777*****99998 PP

                                       S..S CS
                           Mrr_cat  76 rgad 79 
                                        + +
  gi|474934657|ref|YP_007688239.1| 145 LEGK 148
                                       5444 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.2     1e-05     0.013       2      63 ..     151     208 ..     150     212 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1e-05
                                       EEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHH CS
                   Sacchrp_dh_NADP   2 liiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavL 63 
                                        + GaG+vG+ ++ ll + +    ++tv d  kek+ea+a ka+  ++ a  +d + y+a+L
  gi|474934657|ref|YP_007688239.1| 151 FVRGAGRVGSNMVALLRAAGA---RVTVGDVIKEKAEAVA-KANPGTCVADDIDEATYAAHL 208
                                       567**************9986...8**********99997.569999999999999998855 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   2.2e-05     0.028       8      79 ..     143     209 ..     136     219 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.2e-05
                                       S..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEE CS
                      Shikimate_DH   8 eslkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvv 79 
                                       + l++k v + GaG++++ ++  L a+g++ v+v     e+a+++a+   g+    +  ++++e+  +a+++
  gi|474934657|ref|YP_007688239.1| 143 DGLEGKDVFVRGAGRVGSNMVALLRAAGAR-VTVGDVIKEKAEAVAKANPGT----CVADDIDEATYAAHLL 209
                                       57899************************9.***************999777....5555555555555555 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   4.5e-05     0.057       2      54 ..     151     203 ..     150     212 .. 0.86
   2 ?   -3.3   0.0       8.1     1e+04      49      59 ..     236     246 ..     235     249 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.5e-05
                                       EEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHH CS
                            TrkA_N   2 iiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeev 54 
                                        + G+GrvG++++  L+++g +v+v d  +e++e +++ +  + v+d  de++
  gi|474934657|ref|YP_007688239.1| 151 FVRGAGRVGSNMVALLRAAGARVTVGDVIKEKAEAVAKANPGTCVADDIDEAT 203
                                       578***************6657***************9998888888777776 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 8.1
                                       TTSHHHHHHTT CS
                            TrkA_N  49 atdeevLeeag 59 
                                       + dee+L++a+
  gi|474934657|ref|YP_007688239.1| 236 VYDEETLKKAK 246
                                       56899999986 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       4.8   6.1e+03      13      24 ..      34      45 ..      32      55 .. 0.71
   2 ?    0.1   0.0      0.58   7.4e+02      26      50 ..      72      98 ..      58     133 .. 0.66
   3 ?   12.4   0.4     9e-05      0.12       2      33 ..     158     189 ..     158     209 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.8
                                      TT-EEEEEESSH CS
                        ADH_zinc_N 13 lGaeviavdsse 24
                                      lG++ i+vd+++
  gi|474934657|ref|YP_007688239.1| 34 LGFRAIGVDPTK 45
                                      788888888876 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.58
                                      HHHHHHHTTESEEEET.......TTCHHHHHH CS
                        ADH_zinc_N 26 klelakklGadeviny.......keadlveri 50
                                       +++++++G++ ++++             e+i
  gi|474934657|ref|YP_007688239.1| 72 VADIVRDMGMECFVTErtdvwgfG-----EAI 98
                                      468999999999999853333333.....333 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 9e-05
                                       HHHHHHHHHHHTT-EEEEEESSHHHHHHHHHT CS
                        ADH_zinc_N   2 vGlaavqlAkalGaeviavdsseeklelakkl 33 
                                       vG+  v+l++a+Ga+v++ d+ +ek+e ++k 
  gi|474934657|ref|YP_007688239.1| 158 VGSNMVALLRAAGARVTVGDVIKEKAEAVAKA 189
                                       899************************99986 PP

>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.4   7.4e-05     0.094      14      59 ..     134     174 ..     119     179 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.4e-05
                                       HHHHHHHHHHHTTTS-STTEEEEEE--SHHHHHHHHHHHHCT-EEE CS
                     ELFV_dehydrog  14 vvyyveemlkklkldslegkrvaisGsGnvgsyaallltelgakvv 59 
                                        v    e+l+  + d legk v + G G vgs+++ ll  +ga+v+
  gi|474934657|ref|YP_007688239.1| 134 YV----EALRG-AADGLEGKDVFVRGAGRVGSNMVALLRAAGARVT 174
                                       33....34444.333599********************99999874 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.4   8.8e-05      0.11       2      40 ..     150     188 ..     149     202 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.8e-05
                                       EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHH CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekale 40 
                                       v v GaG +G+ + a++ +ag +V++ d+ +e++e++++
  gi|474934657|ref|YP_007688239.1| 150 VFVRGAGRVGSNMVALLRAAGARVTVGDVIKEKAEAVAK 188
                                       7789*************************8888887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1728.73
//
Query:       gi|474934658|ref|YP_007688240.1|  [L=381]
Description: Carbamoylphosphate synthase large subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-13   49.1   0.1      6e-12   45.9   0.1    2.2  2  ATP-grasp_3      ATP-grasp domain
    1.4e-11   44.3   0.0    2.2e-11   43.7   0.0    1.3  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
      9e-08   31.9   0.2    5.2e-07   29.4   0.2    2.0  1  ATP-grasp_4      ATP-grasp domain
    3.9e-05   23.2   0.1    7.9e-05   22.2   0.1    1.5  1  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
     0.0033   17.2   0.0     0.0095   15.7   0.0    1.7  2  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T


Domain annotation for each model (and alignments):
>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.9   0.1   1.7e-15     6e-12      10     158 ..     104     252 ..      96     255 .. 0.85
   2 ?    0.5   0.0      0.15   5.5e+02     134     149 ..     319     334 ..     301     346 .. 0.76

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 1.7e-15
                                       HHTTT.S---....-EESS--SSSEEEEESS-------B--SS--TTE.............EEEE---SEEEEEEEE CS
                       ATP-grasp_3  10 kLkeagvkvPtkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve......lvqefieGkplSvsll 80 
                                        + + gv++P         e   +++vKp+  +g+ +v+ v+++ee e+a+++v+      ++qef+ Gk+lS++++
  gi|474934658|ref|YP_007688240.1| 104 IMADLGVPLP-----RPYPECGFPIIVKPSGQSGSVGVSEVNNEEEMEMALQKVKdlndtpVIQEFVHGKSLSIETI 175
                                       5556666777.....4455557799***************************999********************** PP

                                       E.SSSEEEEEEEEEEEET....TEEEEEEES----HHHHHHHHHHHHHTTSTT--EEEEEEEEESS.SEEEEEEESS CS
                       ATP-grasp_3  81 sdgekvlvlavnrqliekaekefvyaGnvtpietelkeevvelaeevvekleglaGyvGvDlvlkdeepyviEvNPR 157
                                       ++g++++   + + +++ + +      +      e++ ++   +++v e++  l+G++  + +  +++  v+E+ +R
  gi|474934658|ref|YP_007688240.1| 176 GNGKTAQAYITTEVVLDENYDCKQVLCQPGILSDEEDTRFGMCIKQVAEAI-HLNGLMDMEAIGDKNGFRVLEIDAR 251
                                       ************9999986665444444444455669999999********.************************* PP

                                       - CS
                       ATP-grasp_3 158 l 158
                                       +
  gi|474934658|ref|YP_007688240.1| 252 I 252
                                       8 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.15
                                       --EEEEEEEEESS.SE CS
                       ATP-grasp_3 134 laGyvGvDlvlkdeep 149
                                       l+G++G D +++d+ep
  gi|474934658|ref|YP_007688240.1| 319 LRGMFGADEMITDYEP 334
                                       89***********554 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   0.0   6.1e-15   2.2e-11      34     114 ..     118     198 ..     114     260 .. 0.76

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 6.1e-15
                                       HC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT-SCEEEEE--ESEEEEEEEEETSSCEEEEEEEEE-SSSS CS
                   Dala_Dala_lig_C  34 elgypvfVKpareGSSvGvskveseeelkeaieeafkydekvlvEeaiegreievavlgneklevsevgeivvkkgf 110
                                       e g+p++VKp+ +  SvGvs+v++eee++ a+++    + + ++ e+++g+ + +  +gn+k+  + +   vv ++ 
  gi|474934658|ref|YP_007688240.1| 118 ECGFPIIVKPSGQSGSVGVSEVNNEEEMEMALQKVKDLNDTPVIQEFVHGKSLSIETIGNGKTAQAYITTEVVLDEN 194
                                       579**********************************************************9655555555555555 PP

                                       S-HH CS
                   Dala_Dala_lig_C 111 ydye 114
                                       yd +
  gi|474934658|ref|YP_007688240.1| 195 YDCK 198
                                       5544 PP

>> ATP-grasp_4  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.2   1.5e-10   5.2e-07       2     136 ..     120     237 ..     119     255 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1.5e-10
                       ATP-grasp_4   2 slPvviKPsvgffSlGVykinneeewkaavaaieeeleqakeeykeevveeesflvEeyieGeEfavdayfdeeGep 78 
                                        +P+++KPs +++S+GV+ +nneee + a++++++               +++ ++ e+++G+  +++     +G++
  gi|474934658|ref|YP_007688240.1| 120 GFPIIVKPSGQSGSVGVSEVNNEEEMEMALQKVKDL--------------NDTPVIQEFVHGKSLSIETIG--NGKT 180
                                       69****************************999944..............334568888888888888877..8888 PP

                       ATP-grasp_4  79 vilnilkkefaseedvsdrlyvtsakvieetlealeellkevnallglknfpvHiElr 136
                                         + i++   ++e++  +++ + +  ++ e+  ++  ++k+v++++ l+ + + +E  
  gi|474934658|ref|YP_007688240.1| 181 AQAYITTEVVLDENYDCKQVLCQPGILSDEEDTRFGMCIKQVAEAIHLN-GLMDMEAI 237
                                       8888888888888888888888888888888888888888888888874.45555555 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.1   2.2e-08   7.9e-05      36     207 ..     118     280 ..     115     284 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 2.2e-08
                                       HH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHSTS-EEEEE--SSSEEEEEEEEEETTS-EEEEEE CS
                       CPSase_L_D2  36 eigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgnkqvlvekslkgpkeiEvevlrDakgnvitvce 112
                                       e+g+P+i+k++   G  G   ++neee++ +++k  +        ++  ++++++g k + +e +   k    ++++
  gi|474934658|ref|YP_007688240.1| 118 ECGFPIIVKPSGQSGSVGVSEVNNEEEMEMALQKVKDLN------DTPVIQEFVHG-KSLSIETIGNGKTAQAYITT 187
                                       68**************************99999988887......78999***998.89*********999999999 PP

                                       EEECCECTCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT-EEEEEEEEEEETTTTEEEEEEEESS--CCHHHHH. CS
                       CPSase_L_D2 113 renslqlrtqkvievAPsqtLtdeerqalreaavkvvrevgvvgagtveflldpkskeyyviEvNtRlsvesalae. 188
                                          +++    k +   P   L+dee  + +    +v++++++ g   +e + d  ++ + v+E+ +R+  + +    
  gi|474934658|ref|YP_007688240.1| 188 EVVLDENYDCKQVLCQPG-ILSDEEDTRFGMCIKQVAEAIHLNGLMDMEAIGD--KNGFRVLEIDARIPSQTPACIl 261
                                       888888899999999997.699999999**9999***************9888..599**********887776541 PP

                                       HHHS--HHHHHHHHHTT-- CS
                       CPSase_L_D2 189 kaTGldlvkeaakialgek 207
                                       + T ++l+ e  + a+g++
  gi|474934658|ref|YP_007688240.1| 262 AGTSINLLDELYRAASGQE 280
                                       5588999999999888875 PP

>> ATPgrasp_Ter  ATP-grasp in the biosynthetic pathway with Ter operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0         2   7.3e+03      33      58 ..      26      50 ..      13      54 .. 0.55
   2 !   15.7   0.0   2.7e-06    0.0095      52     112 ..     218     280 ..     200     295 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2
                      ATPgrasp_Ter 33 RrKekgglqelekdeelielaerlae 58
                                      Rr +    ++++++++ i+++++  +
  gi|474934658|ref|YP_007688240.1| 26 RRED-APARSISDSSATIDVVAEPEK 50
                                      4444.555566666666666555444 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 2.7e-06
                      ATPgrasp_Ter  52 laerlaeefgldglvnvQvrededgpkLLEiNpRasGGlgysalaG..vnlpylalklllgle 112
                                         +++ae+++l+gl+ +    d++g ++LEi +R+ + +   +laG  +nl +   +++ g+e
  gi|474934658|ref|YP_007688240.1| 218 CIKQVAEAIHLNGLMDMEAIGDKNGFRVLEIDARIPSQTPACILAGtsINLLDELYRAASGQE 280
                                       5689*****************************************855788877777777754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.62u 0.36s 00:00:00.98 Elapsed: 00:00:00.55
# Mc/sec: 2102.31
//
Query:       gi|474934659|ref|YP_007688241.1|  [L=273]
Description: Seryl-tRNA synthetase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-12   45.4   0.0    8.9e-12   44.9   0.0    1.2  1  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
    1.2e-08   34.4   0.0    3.9e-06   26.2   0.0    2.9  2  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    7.9e-08   32.1   0.0    4.3e-07   29.7   0.0    1.8  1  tRNA-synt_2d     tRNA synthetases class II core domain (F)
    9.2e-08   32.3   0.0    4.1e-06   26.9   0.0    2.7  2  tRNA-synt_2b     tRNA synthetase class II core domain (G, H, 


Domain annotation for each model (and alignments):
>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.9   0.0     2e-15   8.9e-12      17     188 ..      60     218 ..      49     234 .. 0.89

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 2e-15
                   tRNA_synthFbeta  17 keqklrrklrdllagaGlnEvitysfvsekeldklleddderkavelanPlsedqsvlRtsLlpglLevlarNlarg 93 
                                          +l   ++ +l++ G+ Ev t  ++ ++ l ++  + +  + +  +    +d  +lR+ L p+l  v+++ +++ 
  gi|474934659|ref|YP_007688241.1|  60 ALTRLMADIAAALTAEGFIEVRTPIMITKDALTRM--TITPGRPLYKQVFWIDDNRALRPMLAPSLYSVMRSLRDHT 134
                                       5667888999*************************..5577777777888899************************ PP

                   tRNA_synthFbeta  94 nedvrlFEigkvflkd.seeelpeeerhlaivltgkreeeswsekaravdfydlkgivealleslgiekvefepaeh 169
                                          v++FE+g +f+ +  ++   ee ++l +v +g++          +   ++lk+ ++ +++ +g+e+++++++e 
  gi|474934659|ref|YP_007688241.1| 135 DGPVKIFEMGPCFRREsHSGMHLEEFTMLNLVDMGPN----------EDAIETLKKYIDVVMKVVGLENYDLVQEES 201
                                       ****************888899***************..........7889*************************9 PP

                   tRNA_synthFbeta 170 palhpgrsAeikvdgkevG 188
                                         +    + +++++g+ev 
  gi|474934659|ref|YP_007688241.1| 202 DVYKE--TIDVEINGQEVC 218
                                       99987..567777777664 PP

>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   8.8e-10   3.9e-06      29     146 ..      65     190 ..      59     210 .. 0.74
   2 !    5.6   0.0    0.0016       7.2     271     306 ..     224     259 ..     168     262 .. 0.71

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 8.8e-10
                                       HHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE......-E-..S-SHHHHHHHHHC....THSE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxx..xxxxxxxxxxxxx....xxxx RF
                       tRNA-synt_2  29 tkavrkyleengfieietPiLsksdteegarlFkvksrekekeff......aLt..qspqlylelliva....gidr 93 
                                       ++ +   l+ +gfie+ tPi++++   +  r   ++ r   k+ f      aL+   +p ly  +        g  +
  gi|474934659|ref|YP_007688241.1|  65 MADIAAALTAEGFIEVRTPIMITK--DALTRMTITPGRPLYKQVFwiddnrALRpmLAPSLYSVMRSLRdhtdGPVK 139
                                       566778899*************99..677778888888887777779999977533578888654432222225779 PP

                                       EEEEEEEE--S--BTTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  94 vfqiaraFRaEdsrtdrhlaEFtqieaemsfieeedimqvleelikslvkevl 146
                                       +f+++++FR E+++   hl+EFt++++ +    +ed +++l++ i  ++k v 
  gi|474934659|ref|YP_007688241.1| 140 IFEMGPCFRRESHS-GMHLEEFTMLNL-VDMGPNEDAIETLKKYIDVVMKVVG 190
                                       ***********887.78999*****98.5677777788888888877777774 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0016
                                       HHHHHHHHCT--SEEEEEEEHHHHHHHHCT-SSGGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 271 swylealeyGapphgGlglGldRlvmlllgsesIrd 306
                                        +yl+a +    p +G g+Gl+Rl++l  + + +r+
  gi|474934659|ref|YP_007688241.1| 224 PHYLDAAHDVHEPWSGAGFGLERLLALREKYSTVRK 259
                                       48999999999999**********998877777776 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   9.5e-11   4.3e-07      16     233 ..      58     259 ..      44     266 .. 0.80

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 9.5e-11
                                       -SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCH.TTSEBTCTSSS-ECESEEE-SSTHHHH CS
                      tRNA-synt_2d  16 lhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdm.qdtFylkkpekaveekllLRthttavq 91 
                                       + +lt+++ +i+  +++ gf ev+ p +       daL     +p R + +++F++       ++++ LR    +  
  gi|474934659|ref|YP_007688241.1|  58 RPALTRLMADIAAALTAEGFIEVRTPIM----ITKDALTRMTITPGRPLyKQVFWI-------DDNRALRPMLAPSL 123
                                       55689999999************99988....888999999999999863678999.......56778998888887 PP

                                       HHHH....TTS-SSEEEEEEEEEEBSST-SSSB-SEEEEEEEEEEET.T--HHHHHHHHHHHHHHHCTSTEEEEEEE CS
                      tRNA-synt_2d  92 irtl....ekkkppikiisigrvfRrdavDathlaeFhqveglvvde.nvsladlkgvleellkklfgaevkvrfrp 163
                                         ++    ++ + p+ki+ +g +fRr++    hl eF+ ++ + ++  +  +++lk+ ++ ++k + g e +  + +
  gi|474934659|ref|YP_007688241.1| 124 YSVMrslrDHTDGPVKIFEMGPCFRRESHSGMHLEEFTMLNLVDMGPnEDAIETLKKYIDVVMKVV-GLE-NYDLVQ 198
                                       777766678888*******************************99862567999999999999888.999.666666 PP

                                       CEETTEEEEEEEEEEECCSSSSEEEEEEEEEE-HHHHHHT.T-.TTSEEEEEEEEHHHHHHHHHT-SSGHH CS
                      tRNA-synt_2d 164 syfpftePsaevdvylvekkkkwlEllgaGmvrpevleav.gideevsgfafGlGveRlamlkygieDiRe 233
                                       + +  ++  ++v++          E++ a  v p+ l+a+ ++  + +  + G+G+eRl  l+ +++ +R+
  gi|474934659|ref|YP_007688241.1| 199 EESDVYKETIDVEING-------QEVCSAA-VGPHYLDAAhDV--HEPWSGAGFGLERLLALREKYSTVRK 259
                                       6666666677777755.......4677664.567777665255..66667778888999999999999986 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.27   1.2e+03     135     159 ..      28      52 ..      20      70 .. 0.68
   2 !   26.9   0.0   9.1e-10   4.1e-06       8     120 ..     110     212 ..     107     253 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.27
                                       EEEETHHHHHTTEEEECTTSSEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b 135 qklgtrlserlgatvldennreksv 159
                                       + +++ +s+ ++a ++d++ + +  
  gi|474934659|ref|YP_007688241.1|  28 SARDKAFSRDMSAATKDNEAKIQAM 52 
                                       5666789999999998888877655 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 9.1e-10
                                       SEEEEE-SSSHHHHHHHHHHHEEEB.GGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b   8 dreyiLkPtneetfvelirdevlrs.krLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeaslddslrdl 83 
                                       d++ +L+P+  + +++++r   lr+  + P+k++++++++R+E    +G + + eF++ + + ++ ++++ + l+++
  gi|474934659|ref|YP_007688241.1| 110 DDNRALRPMLAPSLYSVMR-S-LRDhTDGPVKIFEMGPCFRRESH--SG-MHLEEFTMLNLVDMGPNEDAIETLKKY 181
                                       56789**************.3.788677***************98..89.99**************99566666555 PP

                                       HHHHHHHHHHTT.SCEEEEEEGTTSCBTTSEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  84 ikaisriferlglefraiielmsaksadykdkkefea 120
                                       i   + + + +gle + +++  s+    yk++ ++e+
  gi|474934659|ref|YP_007688241.1| 182 I---DVVMKVVGLENYDLVQEESD---VYKETIDVEI 212
                                       5...55666688888877777664...3777666664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1696.83
//
Query:       gi|474934660|ref|YP_007688242.1|  [L=459]
Description: Monomethylamine methyltransferase MtmB [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   4.1e-244  810.3   0.1   4.6e-244  810.2   0.1    1.0  1  MtmB      Monomethylamine methyltransferase MtmB


Domain annotation for each model (and alignments):
>> MtmB  Monomethylamine methyltransferase MtmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  810.2   0.1  2.6e-248  4.6e-244       1     450 []       7     457 ..       7     457 .. 1.00

  Alignments for each domain:
  == domain 1  score: 810.2 bits;  conditional E-value: 2.6e-248
                              MtmB   1 ldvydaykrakkGekveedewdyveipqkaeelkekydikfenefiPededladrlfqaGlelLvetGvycidterv 77 
                                       +d++day+r+++G+kv+ed+wdyv++p++a ++kekydi+f+++++Pededl+drlfqaGl++Lv+tG+y+++++rv
  gi|474934660|ref|YP_007688242.1|   7 VDIFDAYTRFNNGKKVREDAWDYVTVPTNALAMKEKYDINFTDDIVPEDEDLCDRLFQAGLDMLVTTGFYNTTLGRV 83 
                                       69*************************************************************************** PP

                              MtmB  78 ikvteeeilegikkapkklelGegkdaveleerksndskkPiiqgGPtGapvsedvfleviqsyaqeplvdtivsGv 154
                                       +++te+eilegi++apk+l+lG+gkd+v +e+r++n  k+Pii++GPtGapvsed+f e+i+syaqep+vdtivsGv
  gi|474934660|ref|YP_007688242.1|  84 LYLTEDEILEGIRRAPKRLRLGSGKDMVVCEARQGNVPKAPIIEAGPTGAPVSEDIFSEMIRSYAQEPVVDTIVSGV 160
                                       ***************************************************************************** PP

                              MtmB 155 letvegkeaktksPfeikatlaearlvkeatslagrpglalkGpetplsaagrlaadlae.glresdshevsqLnel 230
                                       l+tv++++++t++P+ei+atlae+r+++ea+sl+grpg++++Gpetpls+agrl+adl+e g+r++d he+sqLnel
  gi|474934660|ref|YP_007688242.1| 161 LDTVCHQASSTNTPWEIRATLAEIRHIREACSLCGRPGMGIOGPETPLSSAGRLSADLTEwGMRKEDLHECSQLNEL 237
                                       ***********************************************************99**************** PP

                              MtmB 231 kidvealnliagykangdvilveqmPifGGyaggieetaivdvattlasfvltdasfhldGpihirwgstttretlq 307
                                       kid++ +n+iag+k+ngd+i+veqmPifGGy+gg+eetai+d+a+tlasf ++d+++hldGpihirwgstttretl+
  gi|474934660|ref|YP_007688242.1| 238 KIDTNLMNMIAGWKTNGDIIMVEQMPIFGGYSGGMEETAICDIACTLASFSMMDCDLHLDGPIHIRWGSTTTRETLK 314
                                       ***************************************************************************** PP

                              MtmB 308 iaahaaaaidantdlllanqyytlaGpctemclletaaqaiadtasGrellsGvaaakGvvkdkttGlearlmgeva 384
                                       iaah+aaa+d ntdlll+nqyytlaGpctemclletaaqa+adt+sGrel+sG+aaakGvvkdkttG+ear+mge+a
  gi|474934660|ref|YP_007688242.1| 315 IAAHVAAAVDLNTDLLLGNQYYTLAGPCTEMCLLETAAQAVADTVSGRELISGPAAAKGVVKDKTTGMEARMMGEAA 391
                                       ***************************************************************************** PP

                              MtmB 385 iaaaglevsevneildklvskyeknyakaPaGkrfqeCydvktvePtdeyldvydkalkkleelGl 450
                                       iaaag++v e+n++ld+++s yek++a++P Gkrfq+Cydv+tv+P++ey+d+ydk++++l+++Gl
  gi|474934660|ref|YP_007688242.1| 392 IAAAGMDVGEANAVLDNIISLYEKDFARPPPGKRFQDCYDVTTVTPSKEYMDIYDKVIETLNKCGL 457
                                       *****************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 2618.97
//
Query:       gi|474934661|ref|YP_007688243.1|  [L=461]
Description: Monomethylamine methyltransferase MtmB [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.3e-240  798.8   1.0   1.4e-240  798.6   1.0    1.0  1  MtmB      Monomethylamine methyltransferase MtmB
  ------ inclusion threshold ------
      0.033   14.5   1.2        0.6   10.4   0.1    2.9  3  DUF2173   Uncharacterized conserved protein (DUF2173)


Domain annotation for each model (and alignments):
>> MtmB  Monomethylamine methyltransferase MtmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  798.6   1.0  1.6e-244  1.4e-240       1     450 []       7     457 ..       7     457 .. 1.00

  Alignments for each domain:
  == domain 1  score: 798.6 bits;  conditional E-value: 1.6e-244
                              MtmB   1 ldvydaykrakkGekveedewdyveipqkaeelkekydikfenefiPededladrlfqaGlelLvetGvycidterv 77 
                                       l+v+d+++r+kkG+kvee+ewdy++ipq+a++lkeky+i+f+nefiPed++ +++lfqaGle+LvetG+yc+d+++v
  gi|474934661|ref|YP_007688243.1|   7 LTVCDTFDRFKKGKKVEESEWDYTIIPQNATALKEKYKIDFGNEFIPEDNESKNALFQAGLEMLVETGFYCTDMKKV 83 
                                       689************************************************************************** PP

                              MtmB  78 ikvteeeilegikkapkklelGegkdaveleerksndskkPiiqgGPtGapvsedvfleviqsyaqeplvdtivsGv 154
                                       ++vteee++egi+k+pkkl lGeg+d++++ +r++n+  kPiiqgGPtG+p+sedvf++v+qsyaqe++vd++v+Gv
  gi|474934661|ref|YP_007688243.1|  84 MHVTEEEVWEGIYKTPKKLILGEGRDIARFYPRHGNSPVKPIIQGGPTGSPISEDVFVQVMQSYAQEAVVDDLVDGV 160
                                       ***************************************************************************** PP

                              MtmB 155 letvegkeaktksPfeikatlaearlvkeatslagrpglalkGpetplsaagrlaadlae.glresdshevsqLnel 230
                                       ++t+eg++ak+++P+ei+at+ae+r+++ea+++agrpgl+++Gpetpl++a+rlaad+++ g+r +d+he+sqLnel
  gi|474934661|ref|YP_007688243.1| 161 MTTLEGHPAKSGTPYEIRATMAELRATQEARERAGRPGLGVOGPETPLTEAARLAADMKHaGHRVTDAHECSQLNEL 237
                                       **********************************************************966**************** PP

                              MtmB 231 kidvealnliagykangdvilveqmPifGGyaggieetaivdvattlasfvltdasfhldGpihirwgstttretlq 307
                                       k+d+++ln++ag+++ngd+i++eqmPifGGy+gg+eetai+dvattlasf+l++++fhldGpihirwg+tt+re+lq
  gi|474934661|ref|YP_007688243.1| 238 KMDMCGLNMLAGWTVNGDTIMIEQMPIFGGYTGGMEETAICDVATTLASFALFNGNFHLDGPIHIRWGTTTNRESLQ 314
                                       ***************************************************************************** PP

                              MtmB 308 iaahaaaaidantdlllanqyytlaGpctemclletaaqaiadtasGrellsGvaaakGvvkdkttGlearlmgeva 384
                                       iaaha+aa+d+ntdlllanqyy++aGpctemcl+eta+qai+dt sGrellsG+aaakGvv+dkttG+ear mg +a
  gi|474934661|ref|YP_007688243.1| 315 IAAHACAAVDNNTDLLLANQYYPMAGPCTEMCLIETAVQAINDTGSGRELLSGSAAAKGVVQDKTTGMEARAMGVAA 391
                                       ***************************************************************************** PP

                              MtmB 385 iaaaglevsevneildklvskyeknyakaPaGkrfqeCydvktvePtdeyldvydkalkkleelGl 450
                                       ++aag++vs++nei+++lvs+ye++y++aPaGkrfqeCydv tv+Pt+eyldvydka+++l+++Gl
  gi|474934661|ref|YP_007688243.1| 392 MTAAGMKVSDLNEIIETLVSEYEQHYNDAPAGKRFQECYDVLTVKPTQEYLDVYDKAMQHLRDAGL 457
                                       ****************************************************************98 PP

>> DUF2173  Uncharacterized conserved protein (DUF2173)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   6.7e-05       0.6      33      80 ..     210     259 ..     202     263 .. 0.83
   2 ?    1.3   0.0     0.046   4.1e+02      15      46 ..     292     324 ..     288     341 .. 0.78
   3 ?   -2.4   0.1      0.64   5.7e+03      30      53 ..     382     399 ..     368     410 .. 0.45

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 6.7e-05
                           DUF2173  33 eeaemlakmcaantrmvk.mqadgleal.tgkkGwepvnGwavrgaelsv 80 
                                       e+a+++a m +a +r+++ +++++l++l ++++G++ + Gw+v+g ++ +
  gi|474934661|ref|YP_007688243.1| 210 EAARLAADMKHAGHRVTDaHECSQLNELkMDMCGLNMLAGWTVNGDTIMI 259
                                       67899999999999988626899998874689*************98765 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.046
                           DUF2173  15 gefsddGelveykG.eldeeeaemlakmcaant 46 
                                       g+f  dG +    G   + e ++++a+ caa+ 
  gi|474934661|ref|YP_007688243.1| 292 GNFHLDGPIHIRWGtTTNRESLQIAAHACAAVD 324
                                       567777777777776677899*********976 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.64
                           DUF2173  30 ldeeeaemlakmcaantrmvkmqa 53 
                                       ++ ++      m +a +  + m++
  gi|474934661|ref|YP_007688243.1| 382 MEARA------MGVAAMTAAGMKV 399
                                       33333......3333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2858.63
//
Query:       gi|474934662|ref|YP_007688244.1|  [L=212]
Description: putative cobalamin binding protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-20   73.0   0.3    4.7e-20   71.8   0.1    1.6  2  B12-binding      B12 binding domain
    1.7e-12   47.6   0.4    2.6e-12   47.0   0.4    1.3  1  B12-binding_2    B12 binding domain
  ------ inclusion threshold ------
       0.06   13.0   0.0       0.12   12.1   0.0    1.4  1  Transposon_TraM  Conjugative transposon, TraM
        0.1   11.1   0.0       0.15   10.6   0.0    1.1  1  AMP-binding      AMP-binding enzyme


Domain annotation for each model (and alignments):
>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.53   2.4e+03      34      46 ..      31      43 ..       6      81 .. 0.58
   2 !   71.8   0.1   1.1e-23   4.7e-20       2     117 ..      94     201 ..      93     204 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.53
                       B12-binding 34 lganvenedivaa 46
                                      ++a++++ di+++
  gi|474934662|ref|YP_007688244.1| 31 IDAKIPVNDIMDK 43
                                      3555555555554 PP

  == domain 2  score: 71.8 bits;  conditional E-value: 1.1e-23
                       B12-binding   2 kvllatvggdlhplGlavlaaalrdagfeVqllganvenedivaairaekpdvvglSalltsqleavkelvellkri 78 
                                       +v+++tv+gd+h++G++v  a+lr ag++V+++g +++ +++++a++++++ ++g Sal+t++lea +elv + k++
  gi|474934662|ref|YP_007688244.1|  94 TVVMGTVEGDIHEIGKNVCCAMLRGAGYNVIDIGPDADSDAFLEAAEDNDATILGGSALMTTTLEAQRELVIANKEA 170
                                       699************************************************************************** PP

                       B12-binding  79 rprvkvvvGGahpsldpeetleaklgiddvvvgegedal 117
                                       + + k ++GGa+     e++ e  +g +d   g+ e+ +
  gi|474934662|ref|YP_007688244.1| 171 GGNYKCIFGGAP--CSKEWCDE--IG-AD---GYSETGA 201
                                       **********99..66666444..99.88...8888765 PP

>> B12-binding_2  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   0.4   5.8e-16   2.6e-12       3      75 .]       9      81 ..       7      81 .. 0.95

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 5.8e-16
                     B12-binding_2  3 erlhwaivhgdkegieelidealaqgsaavdvlndvllpamkeVGdlfgagelflpqvllsaevmkkavahLe 75
                                       +l+++i   + + ++e++++a++++  + d+++++l ++m+ +G +f+a e++lpqv+ ++++m+ a+++Le
  gi|474934662|ref|YP_007688244.1|  9 ADLKKSIETWNVALVKEATQKAIDAKIPVNDIMDKGLGKGMETIGVRFDAAEIYLPQVVAASKTMEVALKMLE 81
                                      578999999999***********99999*****************************************9997 PP

>> Transposon_TraM  Conjugative transposon, TraM
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.6e-05      0.12      61      92 ..      70     101 ..      59     106 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.6e-05
                   Transposon_TraM  61 tdGsrvrLrLleditvggtlipkgtllyGtvk 92 
                                       ++  +v L++le++++g   + kgt+++Gtv+
  gi|474934662|ref|YP_007688244.1|  70 SKTMEVALKMLEPLMAGSGGVTKGTVVMGTVE 101
                                       56678************************985 PP

>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   3.3e-05      0.15     220     302 ..     110     190 ..     102     201 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 3.3e-05
                                       HHHHHHHTT-EEEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT.-SEEEEESS-E CS
                       AMP-binding 220 elllallsGatvvllpkdaaldpklllelieklkvtviagvPrvleallesgalkaakkakdlss.lrlvllggepl 295
                                       ++++a+l+Ga   +++  +++d++++le+ e+  +t++ g   +   l ++++l    ++k+ ++  + +++gg+p+
  gi|474934662|ref|YP_007688244.1| 110 NVCCAMLRGAGYNVIDIGPDADSDAFLEAAEDNDATILGGSALMTTTLEAQRELV--IANKEAGGnYK-CIFGGAPC 183
                                       6899************99999999999*********8888777777775565444..45568899455.689***** PP

                                       BHHHHHH CS
                       AMP-binding 296 spellrf 302
                                       s+e  ++
  gi|474934662|ref|YP_007688244.1| 184 SKEWCDE 190
                                       *998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1466.65
//
Query:       gi|474934663|ref|YP_007688245.1|  [L=128]
Description: Membrane transporter of cations and cationic drugs [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.5e-13   49.7  11.1    5.1e-13   49.5  10.7    1.3  1  Multi_Drug_Res  Small Multidrug Resistance protein
  ------ inclusion threshold ------
      0.065   12.2   0.2      0.074   12.0   0.2    1.1  1  TMEM151         TMEM151 family
        1.7    8.5   8.3        1.7    8.6   0.3    2.1  2  DUF2721         Protein of unknown function (DUF2721)


Domain annotation for each model (and alignments):
>> Multi_Drug_Res  Small Multidrug Resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5  10.7   8.5e-17   5.1e-13       2      90 ..      13     102 ..      12     106 .. 0.92

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 8.5e-17
                                       X-HHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHHH--.-----HHHHHHHHHHHHHHHHHHHH CS
                    Multi_Drug_Res   2 nwvllvlAillevvgailLklsegftkltpsllvivgygisfllLskalks.lpvsvAYavwsGiGtvlivlvgill 77 
                                       +w++lv+ +++ + ++i   +++ ft+  + l++iv+++is++++ + +++ +   +AYavw G+G+vl+v+v++ll
  gi|474934663|ref|YP_007688245.1|  13 AWIVLVMGGVFQIGWSIGVDYTDSFTNIGWDLVTIVFLVISMVCMEWPMRNgIAFTTAYAVWIGVGVVLTVVVSHLL 89 
                                       7************************************************988************************* PP

                                       H--------HHHH CS
                    Multi_Drug_Res  78 fgeslslkkligl 90 
                                         e++ ++  + l
  gi|474934663|ref|YP_007688245.1|  90 GLETITIAMALCL 102
                                       8888877655544 PP

>> TMEM151  TMEM151 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   1.2e-05     0.074     249     280 ..      41      72 ..      32      96 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.2e-05
                           TMEM151 249 PWytsrvvfWlasllllsWPLrvlaeyrtayv 280
                                        W + ++vf ++s++ + WP+r  + + tay 
  gi|474934663|ref|YP_007688245.1|  41 GWDLVTIVFLVISMVCMEWPMRNGIAFTTAYA 72 
                                       688899************************96 PP

>> DUF2721  Protein of unknown function (DUF2721)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.3   0.00028       1.7      61     109 ..       9      57 ..       3      59 .. 0.89
   2 ?    3.4   2.7     0.011        65      72     108 ..      71     107 ..      61     119 .. 0.54

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00028
                           DUF2721  61 rlirrailllvlsallvvlvvlllflsallsldlsllaailfvlallll 109
                                       rl  + i+l++ +++ +  ++ + + ++++++ ++l+  ++ v++++++
  gi|474934663|ref|YP_007688245.1|   9 RLAVAWIVLVMGGVFQIGWSIGVDYTDSFTNIGWDLVTIVFLVISMVCM 57 
                                       666677889999999999999999************************8 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.011
                           DUF2721  72 lsallvvlvvlllflsallsldlsllaailfvlalll 108
                                        ++ + v vvl++++s+ll l++ ++a +l ++  ++
  gi|474934663|ref|YP_007688245.1|  71 YAVWIGVGVVLTVVVSHLLGLETITIAMALCLMVTIA 107
                                       4444555566666666666555555555554443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1106  (0.0616878); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 943.82
//
Query:       gi|474934664|ref|YP_007688246.1|  [L=89]
Description: Membrane transporter of cations and cationic drugs [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-13   50.0   2.2    4.7e-13   49.6   2.2    1.2  1  Multi_Drug_Res   Small Multidrug Resistance protein
    0.00039   20.6   3.4    0.00044   20.4   3.4    1.1  1  EamA             EamA-like transporter family
  ------ inclusion threshold ------
       0.38    9.5   5.0       0.39    9.4   5.0    1.1  1  DUF2207          Predicted membrane protein (DUF2207)
       0.74    8.7   3.3       0.82    8.6   3.3    1.1  1  DUF3488          Domain of unknown function (DUF3488)
          2    8.5   5.6        6.7    6.8   0.2    2.1  2  DUF4337          Domain of unknown function (DUF4337)
        9.7    5.8   8.4         42    3.7   8.4    1.8  1  DUF4131          Domain of unknown function (DUF4131)


Domain annotation for each model (and alignments):
>> Multi_Drug_Res  Small Multidrug Resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   2.2   1.6e-16   4.7e-13      22      93 .]       3      74 ..       1      74 [. 0.96

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 1.6e-16
                                      ------------HHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHH--------HHHHHHH CS
                    Multi_Drug_Res 22 lsegftkltpsllvivgygisfllLskalkslpvsvAYavwsGiGtvlivlvgillfgeslslkkliglali 93
                                       se f+ + + + ++v +++ ++lL+ a+  +  +v+Ya+++GiG+++iv++g +l+ e+l   +++++++i
  gi|474934664|ref|YP_007688246.1|  3 KSENFKYKGWGIAAVVLVLLCLYLLAVAVAVIGPGVSYAILAGIGAIGIVVIGRVLYREKLTPRRMMFVGMI 74
                                      5899999**************************************************************997 PP

>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   3.4   1.5e-07   0.00044      58     135 ..       6      81 ..       1      83 [. 0.73

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.5e-07
                              EamA  58 klslkdwllllllgllgtvlaf.llffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvl 133
                                       ++++k+w +    +++ ++l+  ll +     ++    +++  +  + +++++ +l++eklt + ++ +++i++G++
  gi|474934664|ref|YP_007688246.1|   6 NFKYKGWGIA---AVVLVLLCLyLLAVAVAVIGPGVSYAILAGIGAIGIVVIGRVLYREKLTPRRMMFVGMIVAGII 79 
                                       4566666664...4444455550555555555555577788999999*****************************9 PP

                              EamA 134 li 135
                                        +
  gi|474934664|ref|YP_007688246.1|  80 GV 81 
                                       87 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   5.0   0.00013      0.39     376     435 ..       5      65 ..       1      81 [. 0.55

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00013
                           DUF2207 376 gkkklkklsalglgliilglilillallllvlllvfllillli.llliaiivlllfsrllg 435
                                       ++ k+k +++++++l++l+l+l+ +a+++++++++++ + +++ +++++i+ +l+  +l++
  gi|474934664|ref|YP_007688246.1|   5 ENFKYKGWGIAAVVLVLLCLYLLAVAVAVIGPGVSYAILAGIGaIGIVVIGRVLYREKLTP 65 
                                       4445555666666666666666655555555554444444444044444444444444444 PP

>> DUF3488  Domain of unknown function (DUF3488)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   3.3   0.00028      0.82       3      67 ..      24      86 ..      16      89 .] 0.83

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00028
                           DUF3488  3 lwlllalalallplalrlplwvlllaalllvwrlllarrraplpsrwlllllallavallllsyg 67
                                      l ll+++++++ p +++  l  +++++++++ r+l+  r+   p+r++ +++ +++++++ l +g
  gi|474934664|ref|YP_007688246.1| 24 LYLLAVAVAVIGPGVSYAILAGIGAIGIVVIGRVLY--REKLTPRRMMFVGMIVAGIIGVRLVSG 86
                                      56889999999****************999989755..677788878888888888888877766 PP

>> DUF4337  Domain of unknown function (DUF4337)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   1.3     0.015        44     111     157 ..       6      54 ..       2      58 .. 0.73
   2 ?    6.8   0.2    0.0023       6.7     136     158 ..      63      85 ..      60      88 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.015
                           DUF4337 111 neasdkfdlasalL.qiaIvlaaial.ltkkklllylslvlglvGlvlf 157
                                       n +++ + +a ++L  +++ l a+a+ +++  + +++  ++g++G+v++
  gi|474934664|ref|YP_007688246.1|   6 NFKYKGWGIAAVVLvLLCLYLLAVAVaVIGPGVSYAILAGIGAIGIVVI 54 
                                       5677778887766515799999998536777777778888899998875 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0023
                           DUF4337 136 ltkkklllylslvlglvGlvlfl 158
                                       lt ++++++ ++v+g++G+ l+ 
  gi|474934664|ref|YP_007688246.1|  63 LTPRRMMFVGMIVAGIIGVRLVS 85 
                                       789***************98765 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   8.4     0.014        42       5      51 ..       9      61 ..       5      85 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.014
                           DUF4131  5 lalvllalllllllllllllrr......rprrrvllllllllllallgfalra 51
                                      ++ + +a+++l+ll+l+ll           ++ +l++++++ +++ + +++r 
  gi|474934664|ref|YP_007688246.1|  9 YKGWGIAAVVLVLLCLYLLAVAvavigpGVSYAILAGIGAIGIVVIGRVLYRE 61
                                      77899999999999999987667777775566666666666666655555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       975  (0.0543812); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 556.87
//
Query:       gi|474934665|ref|YP_007688247.1|  [L=47]
Description: hypothetical protein TALC_01098 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.24s 00:00:00.55 Elapsed: 00:00:00.37
# Mc/sec: 380.03
//
Query:       gi|474934666|ref|YP_007688248.1|  [L=107]
Description: hypothetical protein TALC_01099 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.06   13.3   0.1        4.6    7.3   0.0    2.1  2  PadR      Transcriptional regulator PadR-like family
      0.062   12.5   0.0      0.077   12.1   0.0    1.1  1  SmaI      Type II site-specific deoxyribonuclease
       0.11   13.2   0.0        1.2    9.8   0.0    2.0  2  RTP       Replication terminator protein


Domain annotation for each model (and alignments):
>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0   0.00077       4.6       1      23 [.      11      33 ..      11      39 .. 0.91
   2 ?    4.2   0.0    0.0068        41      62      74 ..      82      94 ..      69      95 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00077
                                      HHHHHCCS-EEHHHHHHHHHCCS CS
                              PadR  1 iLalleeqpsyGyeiikeleels 23
                                      iL+l++++p+  yei++ l+  +
  gi|474934666|ref|YP_007688248.1| 11 ILELVDKKPMWNYEIVDILKGEY 33
                                      8****************999775 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0068
                                      EEEESHCCCHHHH CS
                              PadR 62 yYrlTdaGrrela 74
                                       Y++T+ Gr++l+
  gi|474934666|ref|YP_007688248.1| 82 KYEITPYGRDTLN 94
                                      5********9987 PP

>> SmaI  Type II site-specific deoxyribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.3e-05     0.077     153     202 ..      11      61 ..       7      76 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.3e-05
                              SmaI 153 ilralskapdwlyelveipk.slllkaanGelelkkeskqfpkpGycyvle 202
                                       il  ++k p w ye+v+i k +  l +a G+ ++  +  ++   G+c+ +e
  gi|474934666|ref|YP_007688248.1|  11 ILELVDKKPMWNYEIVDILKgEYNLDSAIGRDNINYDCIETVSAGFCKEIE 61 
                                       677789************993455678899999999999999999998665 PP

>> RTP  Replication terminator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0    0.0002       1.2       8      36 ..       5      33 ..       1      42 [. 0.91
   2 ?    1.5   0.0     0.074   4.4e+02      19      37 ..      84     101 ..      70     106 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0002
                                      HHHHHHHHHHHHTT-EBCTCHHHHHHHHH CS
                               RTP  8 AFlklylitlvekkklyglklldelkkeF 36
                                      A lk+ +++lv+kk+++ ++++d lk e+
  gi|474934666|ref|YP_007688248.1|  5 APLKFRILELVDKKPMWNYEIVDILKGEY 33
                                      669***********************987 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.074
                                       HTT-EBCTCHHHHHHHHHT CS
                               RTP  19 ekkklyglklldelkkeFk 37 
                                       e ++ yg   l+elk++ +
  gi|474934666|ref|YP_007688248.1|  84 EITP-YGRDTLNELKAKVR 101
                                       3333.66666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       249  (0.0138881); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 753.00
//
Query:       gi|474934667|ref|YP_007688249.1|  [L=364]
Description: Integral membrane protein DUF6 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.2e-09   38.4  44.8    2.3e-05   24.6  14.4    3.2  2  EamA       EamA-like transporter family
  ------ inclusion threshold ------
        1.1    9.5   0.0        1.1    9.5   0.0    3.1  4  DPM3       Dolichol-phosphate mannosyltransferase subunit 3 (


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3  22.4   9.5e-07    0.0085       2     136 ..      18     179 ..      17     180 .. 0.75
   2 !   24.6  14.4   2.6e-09   2.3e-05       2     115 ..     194     315 ..     193     346 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9.5e-07
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltf...........vrfliagilllii........allkegkl... 56 
                                       +gi+ all a+ w++++v   ++ +  + l +++           v++++a ill+++        ++++ g l   
  gi|474934667|ref|YP_007688249.1|  18 FGIIAALLCAIYWGVWYVPGYAIWEMPDFLPAAMdnmiadgygddVTYTMACILLCLVnaiidtliLFIWNGALgki 94 
                                       68999999999999999988666333333333334455577777777777777776665555665544444444544 PP

                              EamA  57 .....aklslkdwllllllgllgtvlafllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivli 128
                                              +  k+   +++++ ++++ a +  + a + +++++a+++  l  ++ +i+svl+l++k+t++ +++++++
  gi|474934667|ref|YP_007688249.1|  95 gelkrTFIEFKAANVYFVYAGICGAGAVFGTYVAAQFLNPGFAAVAGVLYALVGTIMSVLYLHQKVTKRGYIAVIIM 171
                                       33354445555566669999999999999999********************************************* PP

                              EamA 129 llGvllil 136
                                       ++G+++++
  gi|474934667|ref|YP_007688249.1| 172 IVGAFVLF 179
                                       *****986 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 2.6e-09
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegkl.......aklslkd....wlll 67 
                                       lg+l     a++w++ ++++ ++l +++p     +rf+  +il +i++++ +++        +          +ll 
  gi|474934667|ref|YP_007688249.1| 194 LGVLGGAMCAICWGLEGTFAGKALDYCEPDIGIQLRFFWETILWIIVCVVLAISGvpifstiSTV---VtdpyILLA 267
                                       68899999*******************99976666776555555555555555554335443222...244545555 PP

                              EamA  68 lllgllgtvlafllffyalkktsasnaslitslePvftlilsvlllge 115
                                       ++l  ++++ +++ +++++  +++++   i sl  ++++i+ vl++g 
  gi|474934667|ref|YP_007688249.1| 268 VFLLGFSFAWCYVTWYKSFPFIGVARGQAIGSLYAACSIIFMVLFFGV 315
                                       77777****************************************975 PP

>> DPM3  Dolichol-phosphate mannosyltransferase subunit 3 (DPM3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1      0.99   8.9e+03      11      61 ..      22      32 ..      14      40 .. 0.51
   2 ?   -1.8   0.4       0.4   3.6e+03      54      61 ..     146     153 ..     121     182 .. 0.51
   3 ?   -2.9   2.5      0.89     8e+03      16      57 ..     235     255 ..     226     282 .. 0.46
   4 ?    9.5   0.0   0.00012       1.1       3      56 ..     293     346 ..     291     347 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.99
                              DPM3 11 allllalwlalllrlvslplskvqdevvpvlPlwalvlfGayslatlgygv 61
                                      a+ll a+                                         +gv
  gi|474934667|ref|YP_007688249.1| 22 AALLCAI----------------------------------------YWGV 32
                                      3333333........................................3333 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.4
                              DPM3  54 latlgygv 61 
                                       l+  +++v
  gi|474934667|ref|YP_007688249.1| 146 LVGTIMSV 153
                                       22222222 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 0.89
                              DPM3  16 alwlalllrlvslplskvqdevvpvlPlwalvlfGayslatl 57 
                                       +lw+++++ l                      + G+    t+
  gi|474934667|ref|YP_007688249.1| 235 ILWIIVCVVLA---------------------ISGVPIFSTI 255
                                       34444443333.....................2222222222 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.00012
                              DPM3   3 raqktlalallllalwlalllrlvslplskvqdevvpvlPlwalvlfGayslat 56 
                                       r+q + +l +++++++++l++++ s    +   +v+p++  +++ lfG+y++at
  gi|474934667|ref|YP_007688249.1| 293 RGQAIGSLYAACSIIFMVLFFGVDSAIGGHDMAHVLPTIGGLLICLFGSYLIAT 346
                                       88899999999******99999886666999999****************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       960  (0.0535445); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.40
# Mc/sec: 2728.26
//
Query:       gi|474934668|ref|YP_007688250.1|  [L=216]
Description: trimethylamine corrinoid protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-18   66.2   0.8    4.1e-17   62.3   0.2    2.1  2  B12-binding    B12 binding domain
    2.2e-15   56.8   0.3    4.6e-15   55.8   0.3    1.6  1  B12-binding_2  B12 binding domain


Domain annotation for each model (and alignments):
>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.017   1.5e+02      32      82 ..      13      65 ..       6      71 .. 0.77
   2 !   62.3   0.2   4.6e-21   4.1e-17       2     116 ..      95     203 ..      94     209 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.017
                       B12-binding 32 qllganven.edivaairaekpdvvgl.Sal.ltsqleavkelvellkrirprv 82
                                       +l +n++  +++++ + a ++d+v l +   +t+ +++v +l e++k+  p++
  gi|474934668|ref|YP_007688250.1| 13 AVLKYNINEaKAVANDALAQNADLVNLiT-EgFTKGINQVGDLYEQKKAFLPHI 65
                                      5667777776888889999*****87723.249999999999999988877765 PP

  == domain 2  score: 62.3 bits;  conditional E-value: 4.6e-21
                       B12-binding   2 kvllatvggdlhplGlavlaaalrdagfeVqllganvenedivaairaekpdvvglSalltsqleavkelvel..lk 76 
                                       k+++ t++gd+h++G+++ a +l+ agf+V++lg +++ +di++a++++++ +vg Sal+ts++ + k+  e   ++
  gi|474934668|ref|YP_007688250.1|  95 KFVICTIEGDIHSIGKDICAIMLKVAGFDVVNLGRDIPLKDIAQAAEDNAAIAVGTSALMTSTMVNQKAFEEImkKR 171
                                       67899*************************************************************99999998777 PP

                       B12-binding  77 rirprvkvvvGGahpsldpeetleaklgiddvvvgegeda 116
                                       + + +  + vGGa+++  +++   + +g+d+    + e+a
  gi|474934668|ref|YP_007688250.1| 172 GLKGKCLTNVGGAPVTQQWAD---E-IGADV----YSENA 203
                                       888899********9999999...7.99665....55544 PP

>> B12-binding_2  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8   0.3   5.1e-19   4.6e-15       3      74 ..       8      79 ..       6      80 .. 0.97

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 5.1e-19
                     B12-binding_2  3 erlhwaivhgdkegieelidealaqgsaavdvlndvllpamkeVGdlfgagelflpqvllsaevmkkavahL 74
                                      +r  +a+++ + ++++++++ alaq+ ++v ++ +++ +++++VGdl+++++ flp+ + +a++m+++v++L
  gi|474934668|ref|YP_007688250.1|  8 KRAEQAVLKYNINEAKAVANDALAQNADLVNLITEGFTKGINQVGDLYEQKKAFLPHIMAAANAMNAGVDIL 79
                                      68899*****************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1657.69
//
Query:       gi|474934669|ref|YP_007688251.1|  [L=494]
Description: Trimethylamine:corrinoid methyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-85  286.6   0.1    2.6e-85  286.3   0.1    1.0  1  MTTB      Trimethylamine methyltransferase (MTTB)


Domain annotation for each model (and alignments):
>> MTTB  Trimethylamine methyltransferase (MTTB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  286.3   0.1   1.4e-89   2.6e-85      30     499 ..       8     481 ..       2     484 .. 0.94

  Alignments for each domain:
  == domain 1  score: 286.3 bits;  conditional E-value: 1.4e-89
                              MTTB  30 pyellseeeleaieeaalriLeeiGiefldpealellkaaGakv..egervrfdrglvreliakapreftlharnPe 104
                                       ++el++++e+ +i+ea  +iL++ G+++ d e l+++++ G++v   +++v++++ +++ ++a++p++ftl +r+ +
  gi|474934669|ref|YP_007688251.1|   8 KFELFTDDEIRRIDEATRDILSTYGVQVSDSEGLDIFEKGGCEVdrATQMVKIPNYVIDRALATCPHKFTLYGRDES 84 
                                       6899****************************************88899**************************** PP

                              MTTB 105 rdveig.gknvvfapvagaPfvrDlerg....rregtledfrnlvkLaqmldvlhhsggtvvepvDvpvnkr.hldv 175
                                       r+ +     +v+++  +   ++ D++       r++  +d+++++  ++ l+ +  ++  +v ++D   +   + + 
  gi|474934669|ref|YP_007688251.1|  85 RTFDQAwMGKVHYTCFGTGIQMCDYKAPgkfeTRDSVGQDIADIAHTIDALPGFSYFS-LPVSARDWAGKGSeDTHE 160
                                       **97542678899999999999999863322378999999999999999999999998.7788***99876659*** PP

                              MTTB 176 lyakltlsdkvfmgsvtekeraedsiemlrivfGaeeeefranpvvttiinvnsPlkfdetmlealeayaragqavi 252
                                       l   l+ +  +f+ +    e++e   e++++    +e++ r++p+  +++  +sPl + +++++ + ++ar g+++ 
  gi|474934669|ref|YP_007688251.1| 161 LLLALENTTMHFHHIDPVAENMEFYWEIAKAYYHGDEKAARDKPIFSCLVCPTSPLELSHNAVGCISKAARFGIPCN 237
                                       ******************************9876666667************************************* PP

                              MTTB 253 vtpfilaGAmaPvtvagavaqalAEaLagialtqlvrpgapviyGtftssvdlksGApafGtpeaalatlvagqlAr 329
                                       v++  +aG  ++v +ag+++  +AE+Lagi+l+qlv pga+v yG+ t++ dlk G    G+pe  l+++++++l++
  gi|474934669|ref|YP_007688251.1| 238 VLSMAMAGGSSSVFLAGTLVTHNAEVLAGIVLSQLVAPGAKVWYGSSTTTFDLKRGTAPVGSPELGLISAAVAKLGQ 314
                                       ***************************************************************************** PP

                              MTTB 330 rlglPlrssggltasklpDaQaayesanslwaavlaganlvlhaAGwleggLvasyekfilDadvlgmiarllegie 406
                                       +++lP+ ++g+ t++k+pD+Qa +e++++ + a+lag+n+++ + G+le g ++s+e++i+D+d+++m  r ++gi+
  gi|474934669|ref|YP_007688251.1| 315 YYKLPVFTAGMOTDAKVPDGQASHEKTITSLFAALAGVNMIYGS-GMLELGVTFSIEQMIVDNDIINMERRAMDGIP 390
                                       *****************************************965.******************************** PP

                              MTTB 407 vseealaldairevgpgghflgtahTlaryetafyepelsdnknfeeWeeeGakdaeerAnekvkkiLaeyeepkld 483
                                       v++e+la++ai+e+g g+ f++++ T+++ e a  +p+ +d+   ++W+++G+kd+ ++A++++ +i +++  +++d
  gi|474934669|ref|YP_007688251.1| 391 VTDETLAVEAIKEIGVGNDFIAHPSTMENIELAS-DPACFDRYMLGDWKAAGSKDVIDVAHDIYMDIKKNHVVKPID 466
                                       *******************************995.9***************************************** PP

                              MTTB 484 eaideeLrdfiarrka 499
                                       +++  ++++  a++ +
  gi|474934669|ref|YP_007688251.1| 467 ADVLAKMEAI-AKKAD 481
                                       ******9986.55554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (494 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 3352.79
//
Query:       gi|474934670|ref|YP_007688252.1|  [L=469]
Description: dimethylamine:corrinoid methyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   5.4e-245  813.2  12.6   6.2e-245  813.0  12.6    1.0  1  Dimeth_Pyl       Dimethylamine methyltransferase (Dimeth_PyL)
  ------ inclusion threshold ------
      0.023   14.9   0.1      0.079   13.2   0.1    1.9  2  Antimicrobial_7  Scorpion antimicrobial peptide
      0.091   12.1   0.0        0.2   11.1   0.0    1.5  1  AroM             AroM protein


Domain annotation for each model (and alignments):
>> Dimeth_Pyl  Dimethylamine methyltransferase (Dimeth_PyL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  813.0  12.6    1e-248  6.2e-245       1     462 [.       4     465 ..       4     466 .. 1.00

  Alignments for each domain:
  == domain 1  score: 813.0 bits;  conditional E-value: 1e-248
                        Dimeth_Pyl   1 aeyklrlGdgkrvyltkekiledieaGiadaadlaevpalsedeiekladilvskeklvsveaGkevvltydiGtlk 77 
                                       +ey++rlGdgkrv++tke i++d++aG+adaad++++pal+e ++e+ladi+++k+++v+ve+G+evvltydiG+l+
  gi|474934670|ref|YP_007688252.1|   4 TEYYTRLGDGKRVTMTKEAIMADLQAGTADAADMGGIPALNESQLEQLADIVMDKNRVVGVEPGNEVVLTYDIGQLD 80 
                                       59*************************************************************************** PP

                        Dimeth_Pyl  78 legdqgnsglgieisrlegvliheralgadtlelahidysikpvkpvvaeeaqameviqqnlvvpllyGampnlgly 154
                                       ++gd+gnsg+g++++rle++l+heralg+dt+elah+dys+kpvkpv+a+e+q+me+iq+++++p++yGampn+gly
  gi|474934670|ref|YP_007688252.1|  81 FTGDNGNSGNGVDMGRLEAALLHERALGSDTFELAHSDYSVKPVKPVIAMEMQTMEEIQNEIIIPFFYGAMPNMGLY 157
                                       ***************************************************************************** PP

                        Dimeth_Pyl 155 yapdGpfenpadllrefkieeakesiekaadhlardivyvvskllkagadGvnfdttasaGdadfvatlkavealrk 231
                                       yapdGp++npadl+refki+e+++ +e a +hl+rdi+yv +k+++agadG++fdt+asaGdadfv++l+++e lrk
  gi|474934670|ref|YP_007688252.1| 158 YAPDGPYGNPADLMREFKIDESMQMSELASAHLTRDIEYVGNKIFAAGADGFDFDTIASAGDADFVGSLNGIELLRK 234
                                       ***************************************************************************** PP

                        Dimeth_Pyl 232 kfpniyielGmagelvlGihGeleydGktlaGlyphqqvklvekaGanvfGpvvntntskslawnlaravtlvkeav 308
                                       ++pn+yi++Gmage+v+GihG++ey+Gk++aG++p qq+k++e+aGanvfG+v+ntnts++lawnlar+vt+ k+av
  gi|474934670|ref|YP_007688252.1| 235 ANPNMYINAGMAGENVMGIHGSIEYKGKSVAGMFPAQQIKMCEQAGANVFGTVCNTNTSRTLAWNLARSVTFAKSAV 311
                                       ***************************************************************************** PP

                        Dimeth_Pyl 309 kasdipvhvnlGmGvGGiplletppidavsraskalveiakvdGikvGvGdpvGmaiahvlasGmgGirtaGdlvar 385
                                       +a ++pvhv+lGmGvGGip++etppidav+r+ska+ve+a+ dG+++GvGdp Gm+++h++asGmgGir aGd+var
  gi|474934670|ref|YP_007688252.1| 312 DAKSLPVHVDLGMGVGGIPMFETPPIDAVTRCSKAMVEVAHADGVOIGVGDPCGMDVTHYMASGMGGIRGAGDMVAR 388
                                       ***************************************************************************** PP

                        Dimeth_Pyl 386 melsknmkideakeyvakklgveeldladevvmrdlreelgiGvvtsvaGaakGiaaklnieklldikinscekfrn 462
                                       m + knm id+akeyvakklgv+++dl devvmrdlreel+iGvvt+++Ga++Giaaklniek+l+i+inscekfr 
  gi|474934670|ref|YP_007688252.1| 389 MMYGKNMTIDKAKEYVAKKLGVTTMDLGDEVVMRDLREELKIGVVTGLPGAPRGIAAKLNIEKILGITINSCEKFRG 465
                                       ***************************************************************************95 PP

>> Antimicrobial_7  Scorpion antimicrobial peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.6   9.7e+03      33      39 ..     195     201 ..     177     204 .. 0.72
   2 ?   13.2   0.1   1.3e-05     0.079      24      42 ..     393     411 ..     390     412 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.6
                   Antimicrobial_7  33 NfVAeKi 39 
                                        +V +Ki
  gi|474934670|ref|YP_007688252.1| 195 EYVGNKI 201
                                       6999999 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.3e-05
                   Antimicrobial_7  24 KnkalNAAKNfVAeKiGat 42 
                                       Kn  +  AK +VA K+G+t
  gi|474934670|ref|YP_007688252.1| 393 KNMTIDKAKEYVAKKLGVT 411
                                       8999**************9 PP

>> AroM  AroM protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   3.3e-05       0.2      54      84 ..       6      36 ..       2      42 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.3e-05
                              AroM 54 lvsrlrdGesvvlskekveprlqaaiaklee 84
                                      + +rl dG+ v+++ke+++++lqa +a++ +
  gi|474934670|ref|YP_007688252.1|  6 YYTRLGDGKRVTMTKEAIMADLQAGTADAAD 36
                                      68*********************99888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3492.67
//
Query:       gi|474934671|ref|YP_007688253.1|  [L=213]
Description: dimethylamine corrinoid protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-22   80.4   0.8    1.6e-22   79.8   0.3    1.5  2  B12-binding    B12 binding domain
      2e-17   63.4   0.5    4.2e-17   62.4   0.5    1.5  1  B12-binding_2  B12 binding domain


Domain annotation for each model (and alignments):
>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0      0.88   7.9e+03      64      89 ..      46      71 ..      39      79 .. 0.62
   2 !   79.8   0.3   1.7e-26   1.6e-22       2     118 ..      95     205 ..      94     208 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.88
                       B12-binding 64 qleavkelvellkrirprvkvvvGGa 89
                                       +++v  l e+ k   p+v  ++GG 
  gi|474934671|ref|YP_007688253.1| 46 GMSDVGVLFERGKLFLPHVLSAAGGM 71
                                      55666666666666667777777774 PP

  == domain 2  score: 79.8 bits;  conditional E-value: 1.7e-26
                       B12-binding   2 kvllatvggdlhplGlavlaaalrdagfeVqllganvenedivaairaekpdvvglSalltsqleavkelvel..lk 76 
                                       +v+++tv+gd+h++G+ +   +l+ agf+V++lg +v+++++++++ ++   +vg+Sal+t+++  +k ++++    
  gi|474934671|ref|YP_007688253.1|  95 SVVMGTVEGDVHDIGKSICSTMLQCAGFDVHDLGRDVPTPKFLDEVTKNGCTMVGMSALMTTTMVVMKTVIDQlkDL 171
                                       699**********************************************************************8877 PP

                       B12-binding  77 rirprvkvvvGGahpsldpeetleaklgiddvvvgegedale 118
                                       ++r++++v+vGGa+ + ++++   + +g +d    +ge+a e
  gi|474934671|ref|YP_007688253.1| 172 GVRDKTIVMVGGAPITQAYAD---K-IG-AD---IYGESASE 205
                                       999***********9999999...7.**.55...58888765 PP

>> B12-binding_2  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.4   0.5   4.6e-21   4.2e-17       3      74 ..       8      78 ..       6      79 .. 0.96

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 4.6e-21
                     B12-binding_2  3 erlhwaivhgdkegieelidealaqgsaavdvlndvllpamkeVGdlfgagelflpqvllsaevmkkavahL 74
                                      +++++a+v+ + +gi++++d+ala+g+a+ d++n ++ ++m +VG lf++g+lflp+vl +a  m ka++ L
  gi|474934671|ref|YP_007688253.1|  8 KAIKDAMVAYKVQGIVDAVDKALAAGMAPNDIIN-AMGDGMSDVGVLFERGKLFLPHVLSAAGGMTKAMEKL 78
                                      5799*****************************8.7*********************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1348.00
//
Query:       gi|474934672|ref|YP_007688254.1|  [L=474]
Description: Aspartyl aminopeptidase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-80  270.0   0.0    4.2e-80  269.7   0.0    1.0  1  Peptidase_M18  Aminopeptidase I zinc metalloprotease (M18)
      5e-05   22.5   0.0     0.0018   17.3   0.0    2.2  2  Peptidase_M42  M42 glutamyl aminopeptidase


Domain annotation for each model (and alignments):
>> Peptidase_M18  Aminopeptidase I zinc metalloprotease (M18)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  269.7   0.0   4.6e-84   4.2e-80       6     432 .]      50     466 ..      47     466 .. 0.93

  Alignments for each domain:
  == domain 1  score: 269.7 bits;  conditional E-value: 4.6e-84
                                       -SHHHHHHHHHHHHHCTT-EESTTTS-STSTTCEEEEEEETTTEEEEEEEETTS-GGG--EEEEEE---SEEEEECC CS
                     Peptidase_M18   6 ptpyhvvaevaekllkagfkelsekekwkiepggkyfvtrngssliAFavgkkykaengfsiigaHtDsptlrvKpk 82 
                                       +t++++v++    ++k+g+ke +   k+  + g+k f   +g++li  ++gk+ +  +g+++ +aH Dsp+l+ Kp+
  gi|474934672|ref|YP_007688254.1|  50 KTEREIVDYTLPIAKKKGYKEFKYGTKY--KAGDKVFFNNRGKNLILCTIGKQ-PVSEGVRVSVAHADSPRLDFKPN 123
                                       89**************************..8899****************999.99********************* PP

                                       EEEEETTEEEEEEEEESS.SS.GGGTT--EEEEEEEEECTT--EEEEEECCSTT---BBB----GGG-GG..GSS-- CS
                     Peptidase_M18  83 skkkaegylqvgvetYGggiw.etWldrdLsvaGrvlvkkkkeekleaklvnierPvlriPnlaiHLdrdineefkf 158
                                       +  +++++ + ++++YGg i+ ++W+  +Ls+ G+v++ +  ++++  +  + e+P++ i +l++HL+ +   ++ +
  gi|474934672|ref|YP_007688254.1| 124 PLFETTDMAYFKTHYYGG-IKkYQWMTIPLSLHGVVTLSNG-KSVTVRIGEDAEDPLFCISDLLVHLAGNQ-VKKPM 197
                                       ******************.887******************9.699999********************995.77777 PP

                                       TTTTTSEEEEEEEE------TTCCCT.CCHHHHHHHHHHHHTS-CCCCCCCEEEEEE-S--EEETTTT-EEEESSHH CS
                     Peptidase_M18 159 neetelepilglaeeeeeekedkekknkhkkalleliaeelgvevedivdlelilvdaqkakivGiekeflfaprlD 235
                                        e  + e++ +l    + + +d++ k+k k ++++ + +++g++++d+++ el+  +a + ++ G++  +++a+++D
  gi|474934672|ref|YP_007688254.1| 198 YEAIDAEQMNILVG--SWPVDDEKVKEKIKLNIMQILNKKYGIKEKDFLSAELCACPAYQPRDLGLDRSMVAAYGQD 272
                                       78888888888855..88888888889************************************************** PP

                                       HHHHHHHHHHHHCCCCHT-TTTS-SEEEEEEESSCCGTS-STTSGGCTHHHHHHHHHHHHHCSTT-HCHHHHHC-EE CS
                     Peptidase_M18 236 nkvscfaaleallesaedsleeedkvrivalfDnEEvGStsaqGadsnfleevlerisialkkseafeeavlakSll 312
                                       +kv++fa  +a +++ +     e  + ++++ D+EE GS++ +G +s f + +le++  a +    + ++vl kS++
  gi|474934672|ref|YP_007688254.1| 273 DKVCAFAQFKAEIDTVSP----E-FTTMMVFADKEETGSDGPTGMRSVFWKDFLEDLAEAYG---FNVRHVLRKSIC 341
                                       ************999554....4.88999999*************************99984...34456789**** PP

                                       EEE--EE---TTSGGGS-TTTS--TTSEEEEEEETTSS..STT-HHHHHH...HHHHHHHHC-EEEEEEE-TTS--- CS
                     Peptidase_M18 313 iSaDvahaihPnysskheenhapllnkGvvikvnanqr..yatnsagaal...lkevaqkanvklQelvvrndspcG 384
                                       +S Dv++a++P +++ +e+ +  +l+ G+v++++++ r  y tn+a+a++   l+++ ++a++++Q+ ++  +  +G
  gi|474934672|ref|YP_007688254.1| 342 LSCDVNAAVDPGWPEAFEPTNCSFLGRGPVVSKYTGARgkYSTNDASAEVmgyLRRILEEADIPWQVGELGRVDVGG 418
                                       ***********************************99999******9997222566778999********9999999 PP

                                       -HCHHHHHHHHT-EEEEEE-EEBSTTSSSEEEECCHHHHHHHHHHHCC CS
                     Peptidase_M18 385 stigpilaaktGirtiDlGaaqlsmHSireltgskdveeavklfkaFf 432
                                       +++ ++  +   i t+D+G ++lsmH ++e+t+++d ++ +k+  aFf
  gi|474934672|ref|YP_007688254.1| 419 GGTIASEISVHNIDTVDMGVPVLSMHAPMEVTSKTDDYMLYKAVFAFF 466
                                       99899999999******************************9999998 PP

>> Peptidase_M42  M42 glutamyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.8   0.0    0.0053        48     124     172 ..     262     308 ..     234     315 .. 0.80
   2 !   17.3   0.0     2e-07    0.0018     187     285 ..     343     454 ..     331     460 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.0053
                                       TTECEEETTHHHHHHHHHHHHHHHHHCTSS-SSEEEEEEESTCTTTSHH CS
                     Peptidase_M42 124 angkivskalDdragvavllellkelkeeeleatvylvatvqEEvGlrG 172
                                       + + ++++  Dd+++  +  ++     + e   t+++v+  +EE G  G
  gi|474934672|ref|YP_007688254.1| 262 DRSMVAAYGQDDKVCAFAQFKAEIDTVSPE--FTTMMVFADKEETGSDG 308
                                       4555889999***99988777755555554..**************988 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 2e-07
                                       EEEEEEE-CSTTSTTTTSS....TTS-CEEEEEETT......CCSHHHHHHHHHHHHHHTT--EEEE...E..ESSS CS
                     Peptidase_M42 187 avDvtaagdtpgskekeak....lgkGpvirvkDas......giyhpklrkkllelAkknnipyqle...v..lsgg 248
                                         Dv aa d    +  e +    lg Gpv++ +           ++ ++   l+++ ++++ip q+       + gg
  gi|474934672|ref|YP_007688254.1| 343 SCDVNAAVDPGWPEAFEPTncsfLGRGPVVSKYTGArgkystNDASAEVMGYLRRILEEADIPWQVGelgRvdVGGG 419
                                       5555555444333333322445699999998886556666555677899****************983222113455 PP

                                       SSTHHHHHTSTTTSEEEEEEEEEBSTTSTTEEEEHHH CS
                     Peptidase_M42 249 gtDAgaihltgegvptalisiptryiHspvevahldd 285
                                       gt A++i +  +++ t+ +++p+  +H+p+ev+++ d
  gi|474934672|ref|YP_007688254.1| 420 GTIASEISV--HNIDTVDMGVPVLSMHAPMEVTSKTD 454
                                       666666555..69********************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 3598.11
//
Query:       gi|474934673|ref|YP_007688255.1|  [L=251]
Description: ubiquinone/menaquinone biosynthesis methyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-55  187.1   0.2    3.6e-55  186.8   0.2    1.0  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      2e-23   82.9   0.0    3.7e-23   82.0   0.0    1.5  2  Methyltransf_31  Methyltransferase domain
    6.3e-23   81.3   0.0    1.6e-22   79.9   0.0    1.7  1  Methyltransf_11  Methyltransferase domain
    1.9e-21   76.5   0.0    4.9e-21   75.3   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
    7.4e-15   55.5   0.0    1.2e-14   54.9   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    8.5e-10   38.7   0.0    1.1e-09   38.4   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    4.5e-07   29.4   0.0    6.5e-07   28.9   0.0    1.2  1  Methyltransf_2   O-methyltransferase domain
    2.7e-06   27.4   0.3    2.3e-05   24.4   0.1    2.2  1  Methyltransf_8   Hypothetical methyltransferase
    4.6e-05   22.6   0.0      7e-05   22.0   0.0    1.3  1  DREV             DREV methyltransferase
    0.00062   19.6   0.0     0.0011   18.8   0.0    1.4  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0011   18.6   0.0     0.0016   18.0   0.0    1.3  1  MTS              Methyltransferase small domain
     0.0014   18.1   0.0      0.017   14.6   0.0    2.1  2  Methyltransf_4   Putative methyltransferase
     0.0026   17.7   0.0      0.042   13.8   0.0    2.1  1  ADH_zinc_N       Zinc-binding dehydrogenase
     0.0066   16.6   0.0      0.029   14.5   0.0    1.9  1  FtsJ             FtsJ-like methyltransferase
     0.0069   16.3   0.0       0.01   15.7   0.0    1.3  1  Methyltransf_18  Methyltransferase domain
  ------ inclusion threshold ------
      0.013   15.2   0.0      0.059   13.0   0.0    2.3  2  UPF0020          Putative RNA methylase family UPF0020
      0.017   14.4   0.0        0.7    9.0   0.0    2.1  2  NNMT_PNMT_TEMT   NNMT/PNMT/TEMT family
      0.034   12.7   0.0      0.053   12.1   0.0    1.2  1  Methyltransf_29  Putative S-adenosyl-L-methionine-dependent m
      0.036   13.4   0.0      0.074   12.4   0.0    1.5  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
        0.1   12.3   0.0       0.19   11.5   0.0    1.4  1  Met_10           Met-10+ like-protein
       0.14   12.2   0.0       0.22   11.5   0.0    1.3  1  Methyltransf_32  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.8   0.2   4.2e-58   3.6e-55       4     233 .]      15     250 ..      12     250 .. 0.96

  Alignments for each domain:
  == domain 1  score: 186.8 bits;  conditional E-value: 4.2e-58
                                       XXXXXXXXXXX-HHHHHHHHHHHHHTTTHHHHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES CS
                   Ubie_methyltran   4 lkeekvkevfesvaskyDlmndvlslgihrlWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDi 80 
                                        kee+vk+vf +++s yD mnd++s+++ + W+k +++l ++ +g++  D+ +Gtg +af +++++g +g+v ++D+
  gi|474934673|ref|YP_007688255.1|  15 GKEEYVKDVFTQISSFYDEMNDIMSMNMIKGWHKTMIRLAGDISGKTCADIGTGTGKIAFLVAQHAGPEGTVYGIDL 91 
                                       5899************************************************************************* PP

                                       -HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE--- CS
                   Ubie_methyltran  81 nenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvlefskv 157
                                        + m++ +++++  +  + ++f ++na eL+ ed s D+vt ++ lrnvtD++k L e+yrvl+pGG++vv e++ +
  gi|474934673|ref|YP_007688255.1|  92 TPAMIDYAKEHMPADLPKPVDFRVGNALELELEDCSVDLVTSGYMLRNVTDIQKCLSEMYRVLRPGGKVVVAEMATP 168
                                       ***************************************************************************** PP

                                       -SHHHHHHHHHHHH.HHHHH......HHHHHS-HHHHHHHHHHHHHS--HHHHHHHHHHTTEEEEEEEEEGGGTEEE CS
                   Ubie_methyltran 158 elpllsqayelyskevlPvl......GkllakdldsyryLvesirafPdqetlkeliedaGfksveyesltgGvvai 228
                                        + +++  y+ly+ + + ++      Gk +  +   y +L++si+ fP    +++ +  aGf++v++++  +G+++i
  gi|474934673|ref|YP_007688255.1| 169 DNRVIRYFYNLYMNKRVRRIarkydkGKQIDGHQAAYDWLADSIKGFPHGRVMADKFSAAGFRNVRFHNKMFGAACI 245
                                       ************98877765344455888888999****************************************** PP

                                       EEEEE CS
                   Ubie_methyltran 229 higvk 233
                                       + gvk
  gi|474934673|ref|YP_007688255.1| 246 YEGVK 250
                                       *9998 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.0   0.0   4.4e-26   3.7e-23       3     113 ..      58     166 ..      56     212 .. 0.87
   2 ?   -3.0   0.0       6.7   5.7e+03      50      60 ..     227     237 ..     220     241 .. 0.78

  Alignments for each domain:
  == domain 1  score: 82.0 bits;  conditional E-value: 4.4e-26
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlil 79 
                                       +g++  D+G+GtG+++f  a+ +gp+++v+GiD ++ +i +A+e+      + v F++g++ ele  led ++Dl++
  gi|474934673|ref|YP_007688255.1|  58 SGKTCADIGTGTGKIAFLVAQHAGPEGTVYGIDLTPAMIDYAKEHMPADLPKPVDFRVGNALELE--LEDCSVDLVT 132
                                       577889***********************************************************..9********* PP

                   Methyltransf_31  80 snevlnaladpdkileeiervlkpggilliedpr 113
                                       s   l  ++d +k+l e+ rvl+pgg ++++++ 
  gi|474934673|ref|YP_007688255.1| 133 SGYMLRNVTDIQKCLSEMYRVLRPGGKVVVAEMA 166
                                       ******************************9998 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.7
                   Methyltransf_31  50 klgldnveFeq 60 
                                         g+ nv+F+ 
  gi|474934673|ref|YP_007688255.1| 227 AAGFRNVRFHN 237
                                       57999**9985 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.9   0.0   1.9e-25   1.6e-22       2      96 .]      64     162 ..      63     162 .. 0.96

  Alignments for each domain:
  == domain 1  score: 79.9 bits;  conditional E-value: 1.9e-25
                                       EET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEES-CCC- CS
                   Methyltransf_11   2 dvGcGtGrlaealakrg...arvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvssevlhhv 74 
                                       d+G+GtG++a  +a+++   ++v+g+Dl+++m+++ake+ + + +  v+f+v++a +l +ed s+Dlv+s  +l +v
  gi|474934673|ref|YP_007688255.1|  64 DIGTGTGKIAFLVAQHAgpeGTVYGIDLTPAMIDYAKEHMPADLPkPVDFRVGNALELELEDCSVDLVTSGYMLRNV 140
                                       9*************7777**********************9998899****************************** PP

                                       CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  75 edpekalkeiaRvLkpgGllvi 96 
                                        d +k+l+e++RvL+pgG++v+
  gi|474934673|ref|YP_007688255.1| 141 TDIQKCLSEMYRVLRPGGKVVV 162
                                       ******************9986 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.3   0.0   5.7e-24   4.9e-21       3      97 .]      64     158 ..      63     158 .. 0.94

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 5.7e-24
                                       EET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEESTGGGS CS
                   Methyltransf_25   3 dlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssgalhhl 77 
                                       d+G+GtG++++ +a++ g +++v+g+D++++m+++a+e++ ++ +  v+f++g+a +l++ed s+Dlv+s ++l  +
  gi|474934673|ref|YP_007688255.1|  64 DIGTGTGKIAFLVAQHAGpEGTVYGIDLTPAMIDYAKEHMPADLPkPVDFRVGNALELELEDCSVDLVTSGYMLRNV 140
                                       9***************966*********************887669************************7667776 PP

                                       SHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  78 sdedlekalkeiarvLkpgG 97 
                                       +  d++k+l+e++rvL+pgG
  gi|474934673|ref|YP_007688255.1| 141 T--DIQKCLSEMYRVLRPGG 158
                                       6..99**************9 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   0.0   1.4e-17   1.2e-14       2      98 ..      64     159 ..      63     160 .. 0.89

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 1.4e-17
                   Methyltransf_12   2 eiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.ssfDlvvasnvl 76 
                                       +iG+GtG +++ ++++  p+ +++g+D+ p++i+ ake++ +  ++ +++   +al+l+    +  s+Dlv++   l
  gi|474934673|ref|YP_007688255.1|  64 DIGTGTGKIAFLVAQHAgPEGTVYGIDLTPAMIDYAKEHMPADLPKPVDFRVGNALELEL---EdCSVDLVTSGYML 137
                                       8********************************999999999998665555555555544...445*********** PP

                   Methyltransf_12  77 hhlkdirevldnirklLkpgGr 98 
                                        ++ di++ l++++++L+pgG+
  gi|474934673|ref|YP_007688255.1| 138 RNVTDIQKCLSEMYRVLRPGGK 159
                                       *********************8 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.0   1.3e-12   1.1e-09      15     138 ..      52     183 ..      38     233 .. 0.76

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 1.3e-12
                   Methyltransf_23  15 rllpklraggrvLdiGcGtG.illevlrengf..svtgvDlspeaveiae...kakkaqkdqfdeqeaaepqg.... 81 
                                       rl++ + +g+ + diG+GtG i   v++  g   +v+g+Dl p++++ a+    a+  +++           +    
  gi|474934673|ref|YP_007688255.1|  52 RLAG-DISGKTCADIGTGTGkIAFLVAQHAGPegTVYGIDLTPAMIDYAKehmPADLPKPV-----------Dfrvg 116
                                       5665.78899999*******777777788899999************98444422222333...........23333 PP

                   Methyltransf_23  82 ..........kfdlIvlrevlehvpdppellrqiatllkpgGylllseplaslkedrllldwlylvp 138
                                                 + dl+++ ++l +v d  + l+ +++ l+pgG +++ e + ++ +  ++ ++ly+++
  gi|474934673|ref|YP_007688255.1| 117 naleleledcSVDLVTSGYMLRNVTDIQKCLSEMYRVLRPGGKVVVAEMATPDNRVIRYFYNLYMNK 183
                                       3466666778**************************************8887743333333444433 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   7.6e-10   6.5e-07      64     173 ..      60     171 ..      16     196 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 7.6e-10
                                       SEEEEET-TTSHHHHHHHH.H-TT-EEEEEE-.HHHHHHHHHHS-----TTEEEEES-TTTS---..--SEEEEESS CS
                    Methyltransf_2  64 kslvDvGGGtGalakaivs.ayPtikvivfDl.peVveaAkehlsageeervefvgGdffkdslP..eaDaillkrv 136
                                       k+  D+G GtG +a  +++ a P+ +v   Dl p  +  Akeh+ a++ + v+f  G+  + +l   + D++    +
  gi|474934673|ref|YP_007688255.1|  60 KTCADIGTGTGKIAFLVAQhAGPEGTVYGIDLtPAMIDYAKEHMPADLPKPVDFRVGNALELELEdcSVDLVTSGYM 136
                                       5678*******9998877615699999999997899************************99998556788888888 PP

                                       GGGS-HHHHHHHHHHHHHH--TT-EEEEEE----TTS CS
                    Methyltransf_2 137 lhDwsdekcvklLkrvkkalpagGkvivveavlgadp 173
                                       l   +d  ++k L ++++ l++gGkv+v+e+  + ++
  gi|474934673|ref|YP_007688255.1| 137 LRNVTD--IQKCLSEMYRVLRPGGKVVVAEMATPDNR 171
                                       887766..8899******************9876554 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.1   2.7e-08   2.3e-05      76     160 ..      62     166 ..      48     180 .. 0.66

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 2.7e-08
                                       EEEES-TT-HHHHH--S....-..EEEEESS-S....STTEEES-T.T..........S-S--TT-EEEEEEES--- CS
                    Methyltransf_8  76 vadlGcGeakiaeavre....kekvrsfdlvav....nervvacdl.a..........kvPledesvdvavfclslm 133
                                        ad+G G  kia+ v +    +  v  +dl++      ++ ++ dl +          ++ led svd++     l 
  gi|474934673|ref|YP_007688255.1|  62 CADIGTGTGKIAFLVAQhagpEGTVYGIDLTPAmidyAKEHMPADLpKpvdfrvgnalELELEDCSVDLVTSGYMLR 138
                                       577777777777444431111346777777654111123333444311111112222246799******99988774 PP

                                       .SS-HHHHHHHHHHHEEEEEEEEEEEEG CS
                    Methyltransf_8 134 .gtnladflkeanrvlkvGGllkvaevk 160
                                        +t++++ l e++rvl++GG + vae+ 
  gi|474934673|ref|YP_007688255.1| 139 nVTDIQKCLSEMYRVLRPGGKVVVAEMA 166
                                       38************************86 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   8.2e-08     7e-05      89     187 ..      53     163 ..      31     176 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 8.2e-08
                              DREV  89 pasdqedkklldlGaGdGeitkrvaptfee...vyatelsetmrdrlkk.........kkynvlsalelqetdvkld 153
                                        a d   k+  d+G+G G+i+  va++      vy  +l+  m+d  k           +++v  alel+  d   d
  gi|474934673|ref|YP_007688255.1|  53 LAGDISGKTCADIGTGTGKIAFLVAQHAGPegtVYGIDLTPAMIDYAKEhmpadlpkpVDFRVGNALELELEDCSVD 129
                                       56677889999***************9976678999998888887654311111111368***************** PP

                              DREV 154 lilclnlldrcfdplklledirsalepngrviva 187
                                       l+++  +l    d  k l +++ +l+p g+v+va
  gi|474934673|ref|YP_007688255.1| 130 LVTSGYMLRNVTDIQKCLSEMYRVLRPGGKVVVA 163
                                       *********************************8 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.3e-06    0.0011      31     132 ..      17     117 ..      15     163 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.3e-06
                                       GGGSSCGGGG.GTTSSS-EEEETTEEE--HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEES CS
                              PCMT  31 eefvpesfke.kaYedaplsigynatiSaphmvalalellelkkgarvLevGsGsGyltavlarlvgekgrvvsier 106
                                       ee+v++ f + +++ d   +i   + i     + +++ l     g+   ++G+G+G  + ++a+  g++g+v +i+ 
  gi|474934673|ref|YP_007688255.1|  17 EEYVKDVFTQiSSFYDEMNDIMSMNMIKG--WHKTMIRLAGDISGKTCADIGTGTGKIAFLVAQHAGPEGTVYGIDL 91 
                                       56666666665555555555555555543..345566666656788999**************************** PP

                                       BHHHHHHHHHHHHHCTTCSEEEEES- CS
                              PCMT 107 ikelveeakrnlkkldlenvivvvgD 132
                                       ++ +++ ak+++ ++  + v ++vg 
  gi|474934673|ref|YP_007688255.1|  92 TPAMIDYAKEHMPADLPKPVDFRVGN 117
                                       **********9999988888888875 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.9e-06    0.0016      31     141 ..      58     165 ..      36     191 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.9e-06
                                       TCSEEEEET-TTSHHHHHHHHH.TTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTT.TSTTS-EEEEEE- CS
                               MTS  31 lsgkvlDlGcGaGvlgaalake.speaevtlvdvdarAlesakenleankle.vevvasdvle.eveekkfdlivsN 104
                                         ++ +D+G+G+G ++  +a++  pe +v  +d   + ++ ake + a   + v+++  ++le e+e+ ++dl+ s 
  gi|474934673|ref|YP_007688255.1|  58 SGKTCADIGTGTGKIAFLVAQHaGPEGTVYGIDLTPAMIDYAKEHMPADLPKpVDFRVGNALElELEDCSVDLVTSG 134
                                       456699**********998876268999**********************999******99986789999***9998 PP

                                       --STTTCHCHHHHHHHHHHHHHHHEEEEEEEEEEEET CS
                               MTS 105 PPfhagkatelavaeeliaeAkeaLkegGeLliVanr 141
                                         +++ ++     +++ + e  ++L++gG+  +Va+ 
  gi|474934673|ref|YP_007688255.1| 135 YMLRNVTD-----IQKCLSEMYRVLRPGGKV-VVAEM 165
                                       88888777.....777888888889998886.45554 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0     2e-05     0.017       3      62 ..      60     120 ..      58     132 .. 0.86
   2 ?    1.2   0.0      0.26   2.2e+02      98     116 ..     145     163 ..     138     194 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2e-05
                                       EEEEEET-TTSHHHHHHHHHS.TTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCC CS
                    Methyltransf_4   3 pvvleiGcGkGeflvalAkkn.PdknflGiEirvkvvakvlkkiealelkNlrilrgdalk 62 
                                       +++++iG+G G++    A++  P+ ++ Gi++   +++++ +++ a+  k +    g+al+
  gi|474934673|ref|YP_007688255.1|  60 KTCADIGTGTGKIAFLVAQHAgPEGTVYGIDLTPAMIDYAKEHMPADLPKPVDFRVGNALE 120
                                       689*********9999998644**********************99988877777777755 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.26
                                       HHHHHHHHHEEEEEEEEEE CS
                    Methyltransf_4  98 ellkelarvLkkgGvlela 116
                                       + l+e+ rvL++gG +++a
  gi|474934673|ref|YP_007688255.1| 145 KCLSEMYRVLRPGGKVVVA 163
                                       67999*********99764 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   4.9e-05     0.042       1     113 [.      68     189 ..      68     208 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.9e-05
                                       HHHHHHHHHHHHTT-..EEEEEESSHHHHHHHHH.TTESEEEETTTCHHHHHHHHHTTTSSEEE.....EEESSC.S CS
                        ADH_zinc_N   1 gvGlaavqlAkalGa..eviavdsseeklelakk.lGadevinykeadlverikeltggegvdv.....vfecvG.s 68 
                                       g G +a  +A ++G   +v+++d ++  +++ak+ + ad      + ++  +++   ++  vd+      +  v  +
  gi|474934673|ref|YP_007688255.1|  68 GTGKIAFLVAQHAGPegTVYGIDLTPAMIDYAKEhMPADLPKPV-DFRVGNALELELEDCSVDLvtsgyMLRNVTdI 143
                                       67899999999999999999999999999999996656655554.22555555555555555553333334444448 PP

                                       HHHHHHHHHCEEEEEEEEECSC.TSSEEEEEHHHHHHTT-EEEEE- CS
                        ADH_zinc_N  69 gatleaalkllkpgGrlvvvGg.gkgeeefdlrnlllkeksilGsl 113
                                       +++l++ +++l+pgG++vv  +   ++ +++ ++ l+ +k+++ + 
  gi|474934673|ref|YP_007688255.1| 144 QKCLSEMYRVLRPGGKVVVAEMaTPDNRVIRYFYNLYMNKRVRRIA 189
                                       99*****************999755555588888888888887665 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   3.4e-05     0.029      21      96 ..      58     136 ..      31     195 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.4e-05
                                       TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS...........HHH.TTEEEECS-CCCSSHHHHHCHCHHH CS
                              FtsJ  21 pgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm...........apl.pgvttiqgditdpetiekikealse 85 
                                        gkt+ D+g ++G  +  ++q+ g++g v+++Dl p            + l + v +  g+ ++ e ++        
  gi|474934673|ref|YP_007688255.1|  58 SGKTCADIGTGTGKIAFLVAQHAGPEGTVYGIDLTPAmidyakehmpaD-LpKPVDFRVGNALELELED-------- 125
                                       5799*******************99*********997566655443322.2244555555555444444........ PP

                                       SSEEEEEE--S CS
                              FtsJ  86 rkvdlvvsDga 96 
                                         vdlv+s   
  gi|474934673|ref|YP_007688255.1| 126 CSVDLVTSGYM 136
                                       23444444433 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.2e-05      0.01      15      86 ..      59     131 ..      48     163 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.2e-05
                   Methyltransf_18  15 gsrvaDiGtDHgylpiylvke.gkakkviasDinegplekakeniekagledkievrlsdGleklkeee.vdtv 86 
                                       g+++aDiGt  g +++ ++++ g   +v+ +D+ +  ++ ake++   +l + +++r+++ le   e+  vd v
  gi|474934673|ref|YP_007688255.1|  59 GKTCADIGTGTGKIAFLVAQHaGPEGTVYGIDLTPAMIDYAKEHMPA-DLPKPVDFRVGNALELELEDCsVDLV 131
                                       789************9999762567899*****************86.799***********965444326655 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.9   2.4e+03     141     165 ..      27      50 ..      25      56 .. 0.80
   2 ?   13.0   0.0   6.9e-05     0.059      75     146 ..      82     152 ..      37     203 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.9
                                       HHHHHHHHHHHHHHH-TT..-EEEE CS
                           UPF0020 141 lekLYseflrelkrvlrgggrlvll 165
                                       + ++Y+e+ + ++ ++ + g+   +
  gi|474934673|ref|YP_007688255.1|  27 ISSFYDEMNDIMSMNMIK-GWHKTM 50 
                                       568999999999999988.887665 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 6.9e-05
                                       HH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE----------HHHHHHHHH CS
                           UPF0020  75 aelklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGerlgskkalekLYs 146
                                       +e  +yg+Dl +++++ a+e    a + + ++f++ +a +L+l++ +vd++ + +   + ++ +k l ++Y+
  gi|474934673|ref|YP_007688255.1|  82 PEGTVYGIDLTPAMIDYAKEHM-PADLPKPVDFRVGNALELELEDCSVDLVTSGYMLRNVTDIQKCLSEMYR 152
                                       56679*************9975.79*****************8888***99886543333333444444444 PP

>> NNMT_PNMT_TEMT  NNMT/PNMT/TEMT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.046        40      19      66 ..      17      68 ..       5      79 .. 0.68
   2 ?    9.0   0.0   0.00082       0.7     160     199 ..     125     164 ..     109     184 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.046
                                      HHHHHHHCSTTTT..STCCCCHHHHHHHHHHHHHH..TSSS-ECEEEEET-T CS
                    NNMT_PNMT_TEMT 19 raYLekyykkase..daaeeqvvlfaLknllqtla..tgekkgdtllDiGaG 66
                                      ++Y ++ +++ s   d +++ ++  ++k+ ++t+   +g+ +g+t  DiG+G
  gi|474934673|ref|YP_007688255.1| 17 EEYVKDVFTQISSfyDEMNDIMSMNMIKGWHKTMIrlAGDISGKTCADIGTG 68
                                      467777777766522444444666777777776642247999********99 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00082
                                       EEEEEESSHHHH-SSHHHHHHHHHHHHTTEEEEEEEEEEE CS
                    NNMT_PNMT_TEMT 160 dvvvtifcleaacedleeylralrnlasllkpGGhlvlgg 199
                                       d+ v + +  +  +++   +++l ++ ++l+pGG +v+ +
  gi|474934673|ref|YP_007688255.1| 125 DCSVDLVTSGYMLRNVTDIQKCLSEMYRVLRPGGKVVVAE 164
                                       7888888888999999*******************99876 PP

>> Methyltransf_29  Putative S-adenosyl-L-methionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   6.2e-05     0.053     442     488 ..     139     185 ..     128     199 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.2e-05
                   Methyltransf_29 442 krCeledillemdRilRPeGaviirdkvevlekvkkllkalkWevkl 488
                                       +  ++++ l em R+lRP+G+v++ + ++  ++v ++  +l  ++++
  gi|474934673|ref|YP_007688255.1| 139 NVTDIQKCLSEMYRVLRPGGKVVVAEMATPDNRVIRYFYNLYMNKRV 185
                                       45688999****************99887777776666666655555 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   8.7e-05     0.074     162     258 ..      59     162 ..      38     173 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.7e-05
                              PrmA 162 geevlDvGtGSGiLa.iaaakLgak.kvvavDiDevAvkvakeNaelNkvea.klev..alseellkeekadvivaN 233
                                       g++  D+GtG+G +a ++a+  g + +v+++D+ +  ++ ake +     +   ++v  al+ el ++ ++d++ + 
  gi|474934673|ref|YP_007688255.1|  59 GKTCADIGTGTGKIAfLVAQHAGPEgTVYGIDLTPAMIDYAKEHMPADLPKPvDFRVgnALELEL-EDCSVDLVTSG 134
                                       68999*******8874566666654389***************9999877776777732233344.45889999988 PP

                              PrmA 234 ILaev...lielaedikklvkeggllil 258
                                        + +    + + ++++++++++gg +++
  gi|474934673|ref|YP_007688255.1| 135 YMLRNvtdIQKCLSEMYRVLRPGGKVVV 162
                                       7665512345567788999999998876 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00022      0.19      78     143 ..      34     102 ..      11     108 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00022
                                       TTTS---GGGHHHHHHHHTT--T..T-EEEETT-TTTCCHHHCCHHTTS.SEEEEEES-HHHHHHHHHH CS
                            Met_10  78 vskvyfsskleaErerlaklvee..gevVvdvfAGiGpfaipiakyska.krvlaidlnPesvkylken 143
                                       + +++  +  +  ++++++l+ +  g++  d+  G G+ a  +a+++ +  +v++idl P+ + y ke 
  gi|474934673|ref|YP_007688255.1|  34 MNDIMSMNMIKGWHKTMIRLAGDisGKTCADIGTGTGKIAFLVAQHAGPeGTVYGIDLTPAMIDYAKEH 102
                                       56666666777778999999764449999***************99865269*************9875 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00026      0.22      25      69 ..      58     101 ..      33     107 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00026
                   Methyltransf_32  25 galtvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaek 69 
                                       + +t +D+G G g  +f +a+ ++  +  v+gid+  ++++ a++
  gi|474934673|ref|YP_007688255.1|  58 SGKTCADIGTGTGKIAFLVAQ-HAGPEGTVYGIDLTPAMIDYAKE 101
                                       567999**************9.55689*********999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 1491.38
//
Query:       gi|474934674|ref|YP_007688256.1|  [L=301]
Description: 1,4-dihydroxy-2-naphthoate octaprenyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.7e-34  118.2  15.3    3.7e-34  118.2  15.3    1.3  1  UbiA           UbiA prenyltransferase family
  ------ inclusion threshold ------
       0.12   11.6   2.2        2.1    7.5   0.1    2.1  2  MIG-14_Wnt-bd  Wnt-binding factor required for Wnt secretion


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.2  15.3   4.1e-38   3.7e-34       2     226 ..      24     253 ..      23     271 .. 0.82

  Alignments for each domain:
  == domain 1  score: 118.2 bits;  conditional E-value: 4.1e-38
                              UbiA   2 lipalvg.lalaaggspdlllllllllgtllaaaaanalNdyfDreiDadme..rtpnRPlvsGrispkealifaiv 75 
                                       ++p+++g +++     + ++l++ ++++++l+++aan+lN y D+ ++ d+    t+   lv+G ++pk++l+++++
  gi|474934674|ref|YP_007688256.1|  24 VVPVIIGgAVALKDDGFVWWLFIMIVVCGCLLQSAANILNTYGDFVKGTDTVenETRSPELVTGTLTPKKVLTVGLL 100
                                       78888888666667778888***************************9998766667778***************** PP

                              UbiA  76 llilgllll...alllnpltallgllalllyvvYt.glrlKrrtllgtvvggiafglppllgwaa.vtgslsllall 147
                                       +l + +l++   ++ +++ ++l+gl+++  + +Yt g+ +K+ +l g++ +++++gl+ ++g ++ ++  +s+++++
  gi|474934674|ref|YP_007688256.1| 101 CLGIVALCGlvfIWHTGWEMLLFGLFGIGGASLYTvGMSYKYLGL-GQIGCFLCMGLLMPVGTYYtMADAWSWEPVI 176
                                       *9999999999************************647*******.************999*999777777****** PP

                              UbiA 148 lalavflltwaialandlrdregDrkagiktlpvvl..Grkaarillalllavlllallllllalllllylllalll 222
                                       l+l+++++++a++  n lrd+++Drka++ tl  ++  G ++ ++l+  l+ +++    l+ + +++   ++ +l++
  gi|474934674|ref|YP_007688256.1| 177 LGLPNAFMITAVLCGNELRDYDEDRKANVGTLCGRMsyGSARKLYLIENLMGFAI----LAAIVAVGYAHWACLLAF 249
                                       ************************************4444444444222222222....234444455555555555 PP

                              UbiA 223 aala 226
                                       aal+
  gi|474934674|ref|YP_007688256.1| 250 AALW 253
                                       5544 PP

>> MIG-14_Wnt-bd  Wnt-binding factor required for Wnt secretion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.3    0.0025        22     157     253 ..      43     159 ..      35     190 .. 0.46
   2 ?    7.5   0.1   0.00023       2.1     194     224 ..     222     257 ..     175     300 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0025
                     MIG-14_Wnt-bd 157 lpklllvlllwlvllvlalyerleqlkdpfysiwss.........al.....ilkilaiilavlyflyLlylifrsf 219
                                       +  +++v+ ++l+     +++++ ++   +     +         +        k+l++ l++l ++ L+ l+f  +
  gi|474934674|ref|YP_007688256.1|  43 WLFIMIVVCGCLLQSAANILNTYGDFVKGTD----TvenetrspeLVtgtltPKKVLTVGLLCLGIVALCGLVF--I 113
                                       2223333333333332233333322222222....222224444311444453344444444444444444444..2 PP

                     MIG-14_Wnt-bd 220 seirskrvk.............egdiRfkflilltllvlavlvifii 253
                                       +++ + ++               + + +k+l l  + +++++++ + 
  gi|474934674|ref|YP_007688256.1| 114 WHTGW-EMLlfglfgiggaslyTVGMSYKYLGLGQIGCFLCMGLLMP 159
                                       33333.22224444444444434444666666666666555555555 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00023
                     MIG-14_Wnt-bd 194 l.....ilkilaiilavlyflyLlylifrsfseirs 224
                                       l     +++ila+i+av y+ + + l f ++++ ++
  gi|474934674|ref|YP_007688256.1| 222 LienlmGFAILAAIVAVGYAHWACLLAFAALWDAKR 257
                                       1334459**********************9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2161.48
//
Query:       gi|474934675|ref|YP_007688257.1|  [L=331]
Description: putative Na+-dependent transporter [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-08   33.6  17.9    2.9e-08   33.6  17.9    2.0  2  SBF       Sodium Bile acid symporter family
  ------ inclusion threshold ------
       0.28   11.8  20.4        1.5    9.4   0.3    3.5  3  TcpE      TcpE family


Domain annotation for each model (and alignments):
>> SBF  Sodium Bile acid symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6  17.9   3.2e-12   2.9e-08       2     183 ..      46     211 ..      45     225 .. 0.86
   2 ?   -0.1   0.2     0.068   6.1e+02      20      99 ..     258     292 ..     249     318 .. 0.58

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 3.2e-12
                               SBF   2 ilLilmmfpmglkveveklkellkr...pkalllglvlqwvikPllmfilakillrdlklepelavGlilvglapgg 75 
                                       +lL  mm+  +  + +++l+ +++     ka+llglv   vi Pl ++++       +   +++a Gl+ +++ p +
  gi|474934675|ref|YP_007688257.1|  46 FLLAAMMCLTLSRIPFRNLNPVTNWksvTKAVLLGLVFASVI-PLAAYVILN----QIPSYEKYANGLVFIAATPFA 117
                                       68999**************9987665789*************.****99888....455559*************** PP

                               SBF  76 amsnvwtylakGdlelsvvlvalstllailltPlllyllaksleqttlkvpieeivksvlivviiPliaGillryil 152
                                       a++  ++ +++Gdle ++  +++  +++++ +P+++++ +++l      v++  +v++v+ +++iPl++  ll ++ 
  gi|474934675|ref|YP_007688257.1| 118 ASVGPLSLILRGDLEHALRSTIIVYVVSLVWIPFIIWITLGEL------VDMFDVVLTVIKIIGIPLVVSRLLTKVK 188
                                       *******************************************......******************9876666655 PP

                               SBF 153 lkhkGrewfeskllpavspisligllltivv 183
                                       +         + ++ +v   ++++l+++ v 
  gi|474934675|ref|YP_007688257.1| 189 ID--------KTIMSVVLNCTIAFLVWLSVS 211
                                       55........455555555566655555554 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.068
                               SBF  20 lkellkrpkalllglvlqwvikPllmfilakillrdlklepelavGlilvglapggamsnvwtylakGdlelsvvlv 96 
                                       +  + ++ k ++++l + ++ +P ++ ++                                               +
  gi|474934675|ref|YP_007688257.1| 258 ILMISYKNKGIAIALCVSLMKGPEIGNAMV---------------------------------------------AI 289
                                       555555566666666666655555544443.............................................33 PP

                               SBF  97 als 99 
                                       a+s
  gi|474934675|ref|YP_007688257.1| 290 AAS 292
                                       333 PP

>> TcpE  TcpE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.3   0.00017       1.5      27      58 ..      41      83 ..      36     110 .. 0.75
   2 ?    8.8   7.8   0.00025       2.3      27      78 ..     137     192 ..     130     211 .. 0.67
   3 ?    0.8   0.3     0.078     7e+02      38      80 ..     272     313 ..     255     317 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00017
                              TcpE 27 sqiivfvlvlvlllllaslipv.ikgvl.pfl.........ll 58
                                      s+i+vf l ++++l+l  +++  +++v+ ++          + 
  gi|474934675|ref|YP_007688257.1| 41 SNITVFLLAAMMCLTLSRIPFRnLNPVTnWKSvtkavllglVF 83
                                      689*************999999999999844343422223222 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00025
                              TcpE  27 sqiivfvlvlv.....lllllaslipvikgvlpflllyivipvvltwllselepdgK 78 
                                       s+iiv+v++lv     ++++l++l+ +++ v + ++++i+ip v+++ll+++++d  
  gi|474934675|ref|YP_007688257.1| 137 STIIVYVVSLVwipfiIWITLGELVDMFDVV-LTVIKIIGIPLVVSRLLTKVKIDKT 192
                                       4566666665411111444444444444444.355*******************964 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.078
                              TcpE  38 lllllaslipv..ikgvlpflllyivipvvltwllselepdgKkl 80 
                                       l++ l++      i ++++ ++  ivi v+ + ++ ++ +  K++
  gi|474934675|ref|YP_007688257.1| 272 LCVSLMK---GpeIGNAMVAIAASIVIEVIWVAFMDSVLFSKKRM 313
                                       3333322...22344555445788888888888888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       939  (0.0523733); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1999.75
//
Query:       gi|474934676|ref|YP_007688258.1|  [L=319]
Description: protein of unknown function (DUF1848) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-95  318.6   0.0    4.3e-95  318.4   0.0    1.0  1  DUF1848   Domain of unknown function (DUF1848)


Domain annotation for each model (and alignments):
>> DUF1848  Domain of unknown function (DUF1848)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  318.4   0.0   2.4e-99   4.3e-95       2     265 .]       3     260 ..       2     260 .. 0.98

  Alignments for each domain:
  == domain 1  score: 318.4 bits;  conditional E-value: 2.4e-99
                           DUF1848   2 isaSrrtDipafyseWflnrlkegyvlvrnPfnkkqvsrvslspedvdlivFwtknpkpllkkleelkergiklyfq 78 
                                       i +SrrtDipaf++eWf+nr+++gy+lvrnP+++  v+rv+l++++vd+++F+tk+p+p++++l+el ++g+ ++fq
  gi|474934676|ref|YP_007688258.1|   3 ICVSRRTDIPAFHAEWFMNRVRAGYCLVRNPIYRPVVYRVDLTRKNVDAFIFITKDPRPMMPYLKELGSMGYMYTFQ 79 
                                       889************************************************************************** PP

                           DUF1848  79 fTltdyekelepnvpsleerietfkelseklgkerviwRyDPilltekltvelhlekfeklaeelkgytekvviSfv 155
                                       +T+t+y+k++ep+vp ++++ ++fkels ++gk+r++wRyDPi+l+++++ve+h++kf  l++el+gyt+++++Sfv
  gi|474934676|ref|YP_007688258.1|  80 VTITPYGKDIEPGVPFKADIADAFKELSARIGKDRIAWRYDPIILNDRIDVEYHRRKFGLLCRELEGYTDRCIFSFV 156
                                       ***************************************************************************** PP

                           DUF1848 156 dlykkvkrnlkkklelrelseeekeelaeelaeiakklglelatCaekedlselgieknkCidkellerllgkklka 232
                                       d+y k++ +     +lr++s++e+++la++la ia+++g++l+ C+ ++dls++gie++ Cid++ + +l    ++ 
  gi|474934676|ref|YP_007688258.1| 157 DMYGKLSGRK----DLRSVSHKEMDDLAQALAPIAAEHGIRLTYCCARRDLSAYGIEPAGCIDRRQMISLGI-PFE- 227
                                       ******9998....599**************************************************99874.443. PP

                           DUF1848 233 kkdkgqrkeCgCveskDiGayntClhgCvYCYA 265
                                       + d+  r+ C+Cv+++DiGay+tC hgCvYCYA
  gi|474934676|ref|YP_007688258.1| 228 ELDTPLREGCRCVKNIDIGAYDTCDHGCVYCYA 260
                                       69999***************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.36
# Mc/sec: 2677.54
//
Query:       gi|474934677|ref|YP_007688259.1|  [L=155]
Description: O-6-methylguanine DNA methyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-25   88.7   0.0    3.4e-25   88.0   0.0    1.4  1  DNA_binding_1    6-O-methylguanine DNA methyltransferase, DNA
  ------ inclusion threshold ------
      0.042   14.7   0.0      0.062   14.1   0.0    1.3  1  Methyltransf_1N  6-O-methylguanine DNA methyltransferase, rib


Domain annotation for each model (and alignments):
>> DNA_binding_1  6-O-methylguanine DNA methyltransferase, DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.0   0.0   3.8e-29   3.4e-25       2      80 ..      75     152 ..      74     153 .. 0.96

  Alignments for each domain:
  == domain 1  score: 88.0 bits;  conditional E-value: 3.8e-29
                                       HHHHHHHHHTTS-TT-BEEHHHHHHHTT.TSCHHHHHHHHHTSSBTTTSGGGGEEBTTSBCCTTTTCHHHHHHHHHH CS
                     DNA_binding_1   2 fqqrVwellrqIpyGkvttYgeiAkllgkpkaaraVgqalaanplailvPcHRVvgadgklggyagglerkralLea 78 
                                       f+  V+  +++IpyG+++tY+++A++ g+p+aaraVg+++a+n l+il+PcHRV+++ g +g+y+gg++ k++lL+ 
  gi|474934677|ref|YP_007688259.1|  75 FAVDVLVSMSEIPYGETVTYSQLAEKSGHPGAARAVGTVCANNVLPILIPCHRVLASTG-IGQYSGGVALKQRLLNI 150
                                       77789999***************************************************.***************99 PP

                                       TT CS
                     DNA_binding_1  79 Eg 80 
                                       E+
  gi|474934677|ref|YP_007688259.1| 151 EK 152
                                       95 PP

>> Methyltransf_1N  6-O-methylguanine DNA methyltransferase, ribonuclease-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   6.9e-06     0.062      36      76 ..      28      69 ..       8      70 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.9e-06
                                      CHHHCCCTTTSC..CHCCHHHHHHHHHHHHHHHHS--B-SHCH CS
                   Methyltransf_1N 36 lkelpkllkqde..elpalaelkqaleeYfageekpaltlPld 76
                                      +  ++++l++ e   +p  + ++ +++eY+ag +k  + +P +
  gi|474934677|ref|YP_007688259.1| 28 VYLPSQNLPAMEegTDPVMEQAVREIDEYLAGRRK-VFDVPIS 69
                                      4445666666666777*******************.9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 896.42
//
Query:       gi|474934678|ref|YP_007688260.1|  [L=230]
Description: hypothetical protein TALC_01111 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-06   28.1   0.0      2e-06   27.7   0.0    1.2  1  DNA_alkylation  DNA alkylation repair enzyme


Domain annotation for each model (and alignments):
>> DNA_alkylation  DNA alkylation repair enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0   1.1e-10     2e-06       2     146 ..       7     143 ..       6     178 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.1e-10
                    DNA_alkylation   2 kaeLealadpekaeemqryfkegdeflGvkvpelrklakeffkelkleeelqelaeeLwksperEerllAldlltqa 78 
                                       ++eL++lad++ +   +r   +  + +Gvk+p lr +a+++ +e   +  +   +   + s+  E+ ++  +++  a
  gi|474934678|ref|YP_007688260.1|   7 ESELQSLADEQYRIFNSRISASPKRSIGVKMPLLRGIARRINRE---D--W--RTFVQYPSESLEHCVVKGLVIATA 76 
                                       689*************************************7777...3..3..233346666677776666666555 PP

                    DNA_alkylation  79 kkklaeadlelyeklvetinnWdlvDslaskivgalladkperrdllkeWaksenlWerRaAivatlk 146
                                       k + + ++l+l e+++ +i++W+++D+++s+   +  + +++  +  + + +  +++ +R+++v++l+
  gi|474934678|ref|YP_007688260.1|  77 KCSGD-ERLALTEDFIGEIEEWNTCDTFCSAWKIDSGETSDRLFSRCESLLETGKEFPMRVGAVMMLS 143
                                       55555.56*********************998888878878899999999999999999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1486.61
//
Query:       gi|474934679|ref|YP_007688261.1|  [L=190]
Description: hypothetical protein TALC_01112 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.19   10.0   0.0       0.31    9.3   0.0    1.3  1  Vps62     Vacuolar protein sorting-associated protein 62


Domain annotation for each model (and alignments):
>> Vps62  Vacuolar protein sorting-associated protein 62
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   1.8e-05      0.31      54     172 ..      20     167 ..      16     185 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 1.8e-05
                             Vps62  54 vtfykpseiPegfsvlGhyaqpnnkplrgfvLvakdvskske.............................keaLkk 101
                                        t++  ++i + f ++G  +q+ ++ +    L++k++ ++k                              +e +++
  gi|474934679|ref|YP_007688261.1|  20 STVFLKNGIASAFEMFGGRCQEVKHLVAKLDLAVKESGEKKGeklcevsfgiissrfgfvpadytvmnyppEEVMST 96 
                                       57888899999***********9999999999999998766578999999999999999999999999999999*** PP

                             Vps62 102 PldytlvwsseslkeeeekagyfWlPvppeGykalGlvvttspekPeldevrCvradltdeceaeelilea 172
                                       P dy+ v   ++   +   ++ ++        k +  ++ + +  P+   ++   +dl + ce++++++  
  gi|474934679|ref|YP_007688261.1|  97 PEDYERVQKEKDYLGKILYTCTMFDRIIVCVPKHMMEMIIDADVLPKGRVIAVTSKDLKQVCEERDWMWLE 167
                                       *******99999988888877777777777778888888899999**99999999***********99964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 1095.69
//
Query:       gi|474934680|ref|YP_007688262.1|  [L=362]
Description: hydrogenase expression/formation protein HypD [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   3.1e-129  431.1   1.4   3.7e-129  430.8   1.4    1.0  1  HypD        Hydrogenase formation hypA family
  ------ inclusion threshold ------
      0.086   12.7   0.0       0.15   11.8   0.0    1.3  1  Ligase_CoA  CoA-ligase


Domain annotation for each model (and alignments):
>> HypD  Hydrogenase formation hypA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  430.8   1.4  4.1e-133  3.7e-129       3     350 ..      12     358 ..       8     359 .. 0.95

  Alignments for each domain:
  == domain 1  score: 430.8 bits;  conditional E-value: 4.1e-133
                                       HHHHHHHHHHHHHTSS-EEEEE--HHHHHHHHHTTHHHHS-T.TEEEEE-S--TTTTS-HHHHHHHHHHHHH--EEE CS
                              HypD   3 akkllekikkeakkerelkimevCGghthaivryglrslLpe.nielisGPGCpVCvtpeeeidkaielaekeevil 78 
                                       a k++++ik++   + ++++m++CG+h+ +ivr+gl+slL++  ie+ +GPGCpVCvt+++ei +ai++a++ ++++
  gi|474934680|ref|YP_007688262.1|  12 AAKIVKAIKDL---DVKCRVMHICGTHQDTIVRFGLTSLLEDaGIEVHQGPGCPVCVTTSREIADAITMARN-GLTI 84 
                                       34444555444...689***********************9747**************************99.**** PP

                                       EE-CCHHG---TT--HHHHHHTT-EEEE-SSHHHHHHHHHH-TTSEEEEEEEE-HHHHHHHHHHHHHHHHHT-SSEE CS
                              HypD  79 atfgDmlrvpgskksLleakaegadvrivyspldalkiakenpdkevvflavGFEttapatalalleakkeglknfs 155
                                       ++fgDm+rvp++ +sL++aka+g+dvrivys+ da+++a+++p k++vf++vGFEttap+t + l +   + ++nf+
  gi|474934680|ref|YP_007688262.1|  85 CAFGDMMRVPTTIGSLFDAKADGCDVRIVYSIEDAVRMARAEPAKKFVFVGVGFETTAPSTGVPLVH--GDAPENFT 159
                                       *****************************************************************99..999***** PP

                                       EEEEEE-HHHHHHHHHHTT.---SEEEEEHHHHHHHTTHHHHHHHHHH---EEEE-SSHHHHHHHHHHHHHHHHTT- CS
                              HypD 156 vlsshklvppalealleseelkidgfiapghvstviGlkayeelaeeykvpvvvaGFepldilqailmlvkqleege 232
                                       v+s+h++++p+++ +l   e+kidg+i+pghv++++Gl ++++++e+ ++p+vv+GFepld+l++ + l kq+++g+
  gi|474934680|ref|YP_007688262.1| 160 VYSCHRYTVPCIDKILGMGEVKIDGLIQPGHVCVITGLGPFRKFSEQCGIPQVVCGFEPLDMLMSCYLLAKQIHDGK 236
                                       ***************************************************************************** PP

                                       --EEETTTTT--TT--HHHHHHHHHHEEEEEEEETTTEEEEEEEEEE-GGGGGGBGGGT---....-S---SS-TT- CS
                              HypD 233 aeveneYkrvvkeegnkkaqklieevfevrdaewRglgvipksglklreeyaefdaekkfel....ekeeekekkac 305
                                       a +eneY+r+v+++gn+ka+++++evf ++d ewRg++vi++s ++l++e+a++da+k +e     + + e+++++c
  gi|474934680|ref|YP_007688262.1| 237 AVIENEYSRLVRDNGNEKARQILSEVFYPTDGEWRGFPVIENSIMTLKPEFADHDAKKVYEDilkkTPSVEEDANGC 313
                                       ************************************************************8777655566778899* PP

                                       -HHHHHTTS--GGGSTTBTTTB-SSS-SSHHHHSTT-HHHHHHHT CS
                              HypD 306 kcgevlkGkakPedCklFgkaCtpenpvGacmvSsEGaCaayyky 350
                                       +cgevl+G ++ e+C+lFg+aC+p++p G+cmvS EG C++ y++
  gi|474934680|ref|YP_007688262.1| 314 SCGEVLRGLIDSEQCPLFGTACKPTSPQGPCMVSMEGNCNIAYRF 358
                                       *******************************************98 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.7e-05      0.15      88     140 ..       8      56 ..       6      59 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.7e-05
                                       HHHHHHHHHHHHHHTT...--S-EEEEEECTTHH.....HHHHHHHTTTSSEE CS
                        Ligase_CoA  88 hedpaaellkaikeakaegrelpvvarvaGteadpqelseqakaleeagveia 140
                                        e+ aa+++kaik+++     +  v +++Gt++d+  + +    le+ag+e+ 
  gi|474934680|ref|YP_007688262.1|   8 DEETAAKIVKAIKDLD----VKCRVMHICGTHQDTIVRFGLTSLLEDAGIEVH 56 
                                       6899***********8....778899********99999**********9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2582.84
//
Query:       gi|474934681|ref|YP_007688263.1|  [L=136]
Description: Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-28   98.1   0.0    3.3e-28   97.9   0.0    1.0  1  HypA             Hydrogenase/urease nickel incorporation, met
  ------ inclusion threshold ------
      0.039   13.6   3.1       0.47   10.2   0.1    2.4  2  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
      0.076   12.7   0.0      0.096   12.4   0.0    1.1  1  UL141            Herpes-like virus membrane glycoprotein UL14
      0.094   13.1   4.4       0.21   12.0   1.1    2.4  2  zf-IS66          zinc-finger binding domain of transposase IS
      0.097   13.0   0.1       0.18   12.2   0.1    1.5  1  nos_propeller_2  Nitrous oxide reductase propeller repeat 2
        0.1   12.7   2.3       0.31   11.2   2.3    1.8  1  Zn-ribbon_8      Zinc ribbon domain
       0.14   12.3   0.1       0.23   11.6   0.1    1.4  1  TxDE             Toxoflavin-degrading enzyme
       0.14   12.3   0.1       0.38   10.9   0.1    1.7  1  CUT              CUT domain
        7.4    6.4   6.3        3.6    7.4   0.4    2.3  2  Rubredoxin_2     Rubredoxin metal binding domain


Domain annotation for each model (and alignments):
>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.9   0.0   1.7e-31   3.3e-28       1     111 [.      10     131 ..      10     132 .. 0.95

  Alignments for each domain:
  == domain 1  score: 97.9 bits;  conditional E-value: 1.7e-31
                                       XCHHHHHHHHHHHHHHHHCCTT..EEEEEEEEEETTCT--HHHHHHHHHHHHCC.TTTT-EEEEEEE--EEEETTTS CS
                              HypA   1 MHElsiaesivevveeeakeaaarkvtkvkvevGelsgvepeaLefafellaegtvlegaeLeieevpvkvrCreCg 77 
                                       MHE+s++ +iv++v +e+k+ +++kv++v++ vG+l+++ +e+++fa+e+l++g++l+g++L+i+ +pv++rCr+Cg
  gi|474934681|ref|YP_007688263.1|  10 MHEASVTADIVDAVLQELKNYKVTKVNEVTIVVGDLTQLGTEQMQFAWEVLTDGNILKGSRLTIKPQPVVLRCRSCG 86 
                                       ********************9******************************************************** PP

                                       -EEECHHHHH............S-TTTSSS-EEEEESSSEEEEEEE CS
                              HypA  78 kefeleekal............rCpkCgsadveivsGeellvksie 111
                                        e+  ++ ++            +Cp+Cg+ +v++++G+ ++++s++
  gi|474934681|ref|YP_007688263.1|  87 FEGPAKTVDFgegssdhnipvlSCPDCGG-KVDVIEGSACRIESFD 131
                                       99997763446789999***********9.79***********997 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00023      0.47       9      25 ..      70      87 ..      68      88 .. 0.71
   2 ?    3.6   0.5     0.028        55       3      16 ..     110     123 ..     106     126 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00023
                                      B----SSS--.--SSS-- CS
                    DNA_RNApol_7kD  9 evslkkgdpi.RCkeCGh 25
                                      + ++k++ ++ RC+ CG+
  gi|474934681|ref|YP_007688263.1| 70 RLTIKPQPVVlRCRSCGF 87
                                      66677765434******8 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.028
                                       -SSS--B----SSS CS
                    DNA_RNApol_7kD   3 CgeCgaevslkkgd 16 
                                       C +Cg +v +++g 
  gi|474934681|ref|YP_007688263.1| 110 CPDCGGKVDVIEGS 123
                                       77788887766665 PP

>> UL141  Herpes-like virus membrane glycoprotein UL141
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   4.8e-05     0.096      95     178 ..      27     112 ..      10     119 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.8e-05
                                       EE-SSEEEEEEEEEEESSEEE-------------..-S--SSSB-.B-SSGGGEEEESSS-------EEEEE----- CS
                             UL141  95 lrneshslitertvlladledlrrsdepscdlal..Grrsltdql.wspdpsrlrsidcGlererqrvvfyigrada 168
                                       l+n+  + + e t+++ dl +l   +       l  G+  ++ +l   p+p  lr   cG+e+  + v f  g +d 
  gi|474934681|ref|YP_007688263.1|  27 LKNYKVTKVNEVTIVVGDLTQLGTEQMQFAWEVLtdGNILKGSRLtIKPQPVVLRCRSCGFEGPAKTVDFGEGSSDH 103
                                       679999999999999999999988877555444322677676665268***************99988887666665 PP

                                       ---------- CS
                             UL141 169 edclkpacee 178
                                        ++   +c++
  gi|474934681|ref|YP_007688263.1| 104 -NIPVLSCPD 112
                                       .555667766 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1      0.16   3.2e+02      39      46 .]      79      86 ..      75      88 .. 0.83
   2 ?   12.0   1.1   0.00011      0.21       3      27 ..     109     134 ..     108     136 .] 0.87

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.16
                           zf-IS66 39 kyaCpcCe 46
                                      +++C++C+
  gi|474934681|ref|YP_007688263.1| 79 VLRCRSCG 86
                                      57899996 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00011
                           zf-IS66   3 tCpcCGgllkpigedrvr.eeldipP 27 
                                       +Cp+CGg+++ i++ + r e +di +
  gi|474934681|ref|YP_007688263.1| 109 SCPDCGGKVDVIEGSACRiESFDIEE 134
                                       6******9999999988899999875 PP

>> nos_propeller_2  Nitrous oxide reductase propeller repeat 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   8.9e-05      0.18      48      68 ..      45      65 ..      23      66 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.9e-05
                   nos_propeller_2 48 fsaidaetmevawqviVdGNL 68
                                      ++ + +e+m+ aw+v+ dGN+
  gi|474934681|ref|YP_007688263.1| 45 LTQLGTEQMQFAWEVLTDGNI 65
                                      677889**************6 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   2.3   0.00015      0.31       7      36 ..      81     117 ..      79     119 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00015
                       Zn-ribbon_8   7 rCeeCghefe......vlqsis.dap.lta.CPeCgsev 36 
                                       rC++Cg  fe       + + s d + ++  CP+Cg++v
  gi|474934681|ref|YP_007688263.1|  81 RCRSCG--FEgpaktvDFGEGSsDHNiPVLsCPDCGGKV 117
                                       9*****..99989766333333344444447*****976 PP

>> TxDE  Toxoflavin-degrading enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00012      0.23       3      42 ..      12      51 ..      10      56 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
                              TxDE  3 EiglttedvksvgeqLeeigIplrdneeiepdaLNFlGek 42
                                      E ++t + v +v ++L++++++  ++ +i    L+ lG +
  gi|474934681|ref|YP_007688263.1| 12 EASVTADIVDAVLQELKNYKVTKVNEVTIVVGDLTQLGTE 51
                                      789***********************99988888888765 PP

>> CUT  CUT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00019      0.38       3      25 ..      12      34 ..      10      80 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00019
                               CUT  3 eeldtkdiaqkvkeeLkrasisq 25
                                      e  +t+di++ v +eLk++++++
  gi|474934681|ref|YP_007688263.1| 12 EASVTADIVDAVLQELKNYKVTK 34
                                      5679****************764 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.4    0.0018       3.6       2      11 ..      81      90 ..      81      91 .. 0.86
   2 ?    1.4   1.1      0.13   2.6e+02      17      21 ..     110     114 ..     109     115 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0018
                      Rubredoxin_2  2 vCsqCGfesa 11
                                      +C++CGfe +
  gi|474934681|ref|YP_007688263.1| 81 RCRSCGFEGP 90
                                      8******976 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.13
                      Rubredoxin_2  17 CpsCg 21 
                                       Cp+Cg
  gi|474934681|ref|YP_007688263.1| 110 CPDCG 114
                                       99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 780.88
//
Query:       gi|474934682|ref|YP_007688264.1|  [L=206]
Description: DNA-(apurinic or apyrimidinic site) lyase/endonuclease III [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-21   75.6   0.0    4.5e-21   75.3   0.0    1.1  1  HhH-GPD   HhH-GPD superfamily base excision DNA repair protei
    0.00015   21.5   0.0    0.00031   20.4   0.0    1.6  1  HHH       Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.042   14.4   0.0          5    7.8   0.0    2.3  2  HHH_5     Helix-hairpin-helix domain


Domain annotation for each model (and alignments):
>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.3   0.0   7.6e-25   4.5e-21       1     107 [.      31     165 ..      31     166 .. 0.96

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 7.6e-25
                                       HHHHHHTTS-HHHHHHHHHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH........... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........... RF
                           HhH-GPD   1 vsailsqqtsderanriierlferfgfptpedladadeekLrelirelGfyrrKakyikelArilv........... 66 
                                       v++ilsq+t+d ++ ++   lf +   pt  ++a+ad+++++ l+r++Gf+++Kak i +++ril            
  gi|474934682|ref|YP_007688264.1|  31 VATILSQRTKDDNTRKASDALFTK--YPTIGAIAEADPADVAVLVRPAGFPNQKAKAIVDCCRILRdeyggkvpedt 105
                                       789*********************..59************************************************* PP

                                       ....................S-SSS--TTSHHHHHHHHHHTTSSSSTTHHHHHHHHHHHHH CS
                                       ....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           HhH-GPD  67 ....................gkpdvlivvDvhvrrilkrlrsikekktkkkvekkleelle 107
                                                           +   + ++vD+hv+ri + ++++++ kt++++e +l++l +
  gi|474934682|ref|YP_007688264.1| 106 demcklpmvgrktaacvrsyAMLIPSVCVDTHVHRISNLMGLVHT-KTPEETEYALMDLTP 165
                                       ******************9866679999*****************.6*******9988765 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   5.2e-08   0.00031       1      30 []      96     125 ..      96     125 .. 0.96

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 5.2e-08
                                       SHHHHHTSSHHHHHTSTT-SHHHHHHHHHH CS
                               HHH   1 sleglipasreeLlalPGVGpktAeaIlsy 30 
                                       +++g +p + +e ++lP VG+ktA +++sy
  gi|474934682|ref|YP_007688264.1|  96 EYGGKVPEDTDEMCKLPMVGRKTAACVRSY 125
                                       589*************************98 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0   0.00084         5      17      53 ..      50      88 ..      44      91 .. 0.77
   2 ?    4.4   0.0      0.01        60      32      48 ..     103     119 ..     100     123 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00084
                                      HHHTTT--SHHHHHHS-HHH...HHTSTTS-HHHHHHHHH CS
                             HHH_5 17 allsaGiesvedlaaadvee...LakipGiGkktAeriil 53
                                      al  + + ++ ++a+ad+++   L +  G+ + +A+ i++
  gi|474934682|ref|YP_007688264.1| 50 ALFTK-YPTIGAIAEADPADvavLVRPAGFPNQKAKAIVD 88
                                      55556.8899*****976554449999*********9997 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.01
                                       S-HHHHHTSTTS-HHHH CS
                             HHH_5  32 adveeLakipGiGkktA 48 
                                       +d++e +k+p +G ktA
  gi|474934682|ref|YP_007688264.1| 103 EDTDEMCKLPMVGRKTA 119
                                       5899************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1544.70
//
Query:       gi|474934683|ref|YP_007688265.1|  [L=413]
Description: folylpolyglutamate synthase/dihydrofolate synthase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-15   56.9   0.0    4.4e-15   56.2   0.0    1.3  1  Mur_ligase_M  Mur ligase middle domain


Domain annotation for each model (and alignments):
>> Mur_ligase_M  Mur ligase middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.2   0.0   2.5e-19   4.4e-15       1     189 [.      38     254 ..      38     257 .. 0.84

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 2.5e-19
                                       EESSS-HHHHHHHHHHHHHCTEEEEETTC...........................................SS-TH CS
                      Mur_ligase_M   1 vTGtnGKTTtteliaailekagkvigtvg...........................................ttnne 34 
                                       v+G++GK +t  ++a++l+++g  +g+                                              t  e
  gi|474934683|ref|YP_007688265.1|  38 VAGSDGKGSTCAIMASVLRAKGLRVGLYTsphilefreritvngeaisdadlsrivggarhfvddmresdmsCTFFE 114
                                       89*******************88888877888****************************************77888 PP

                                       HHHHHHHHHHHHTT-SEEEEE--HCHHHCTTTCCHCBESEEEE---TSTTHHHH.SSHHHHHHHHHHHHHTSETTCE CS
                      Mur_ligase_M  35 iglpktlaemekkeaeyavlEvsshglgekrlegllkpdvavitnispdHldfh.gtlenyaeaKaelferlkeegi 110
                                       +++  +++ +++ ++++av+Ev++   g     ++++p v vi nis +H++++ +t+e++a++Ka +++       
  gi|474934683|ref|YP_007688265.1| 115 VTTAVAFQYFRERQVDVAVVEVGMG--GRFDATNVIRPLVSVISNISMEHMEYLgDTIEKIAYEKAGIIKDGV---P 186
                                       9999999999999************..553333449******************89*************8655...3 PP

                                       EEEETTSC...CHHHHHCTCCTCEEEEESSSTSECEEEEEEEEETTEEEEEEEEETTEEEEEEESSCSCHHHHHHHH CS
                      Mur_ligase_M 111 avinaddpyakelikklkkakvkvvtfglekeaedlraknieeksegteiellevkggeleieipllGkhnvyNala 187
                                       av+ +   +++ + ++++++++ +  ++  + a        ++++ g+e+   ++kg+   + ++++G+  ++Na++
  gi|474934683|ref|YP_007688265.1| 187 AVTINSGAALDVVSQAAAERNSPLTVIDAGSIA------VTKNSERGVEF---TYKGE--SYFVSIPGRNEAKNAVL 252
                                       555556666888888888888887777776655......34455567775...35555..4778899********99 PP

                                       HH CS
                      Mur_ligase_M 188 ai 189
                                       a+
  gi|474934683|ref|YP_007688265.1| 253 AL 254
                                       97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 3103.22
//
Query:       gi|474934684|ref|YP_007688266.1|  [L=264]
Description: Asparagine synthase (glutamine-hydrolyzing) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.1e-26   91.3   1.6    4.6e-24   85.7   1.0    2.0  2  Asn_synthase   Asparagine synthase
  ------ inclusion threshold ------
      0.016   14.3   0.1      0.027   13.6   0.1    1.4  1  NAD_synthase   NAD synthase
      0.077   13.4   1.4        3.5    8.1   0.2    2.7  3  FUN14          FUN14 family
        0.1   11.7   0.0       0.14   11.2   0.0    1.2  1  Rad1           Repair protein Rad1/Rec1/Rad17
       0.11   13.1   0.0        9.1    6.9   0.0    2.3  2  Biotin_carb_N  Biotin carboxylase, N-terminal domain
       0.17   12.0   0.0       0.39   10.8   0.0    1.6  1  TetR_C_9       Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.7   1.0   1.5e-27   4.6e-24       2     142 ..       8     142 ..       7     176 .. 0.89
   2 !    5.5   0.0    0.0039        12     210     295 ..     150     237 ..     140     259 .. 0.80

  Alignments for each domain:
  == domain 1  score: 85.7 bits;  conditional E-value: 1.5e-27
                      Asn_synthase   2 lrelLedaVkrrlradvpvGalLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtelv 78 
                                       +++lL+ aV  rl++  +v++ +SGG+DS+lia la r++  +++ +++g+  +gs ++++a+ +ae lg + +++v
  gi|474934684|ref|YP_007688266.1|   8 VADLLDSAVG-RLVSGKKVAIAFSGGIDSGLIAGLAMRHAS-KVTLYTAGT--EGSHDIEAAESAAELLGGDLRTIV 80 
                                       789*******.***************************996.*********..************************ PP

                      Asn_synthase  79 lteeelldalpdviyhlee..pfadrsaiplyllsrlakrkgvkvvLsGeGaDElfgGYpyfykaa 142
                                       l+ + +ld ++  i ++ +  p++ + ++ply + r   ++    vL G+GaDE f+GY+  y   
  gi|474934684|ref|YP_007688266.1|  81 LDDDTILDSIKCQIDITGTdsPLVLAFETPLYNVLRTCTED---TVLGGQGADEQFAGYQ-KYVGM 142
                                       ****************99999*****************666...8**************9.55444 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0039
                      Asn_synthase 210 elyldlktllpgdllrkDrasmahglEaRvPflDhrlvevalrlppelklrg..gieKyiLRealegylPeeileRp 284
                                         + dl +l+ ++  ++ ++s +++    +P+lD++l  ++ + p+++   +  +  K +L  a+  +    ++eRp
  gi|474934684|ref|YP_007688266.1| 150 HIVEDLSRLYSETKPHEKKLSDHFSKAIGYPYLDRELSALVRAAPIDEIRPPdaDVRKKVLCDAAVALGFGFLAERP 226
                                       55667777777777788888888999999**************9998766667899999999999999999999999 PP

                      Asn_synthase 285 Kegfsapvgew 295
                                       K+++++++g+ 
  gi|474934684|ref|YP_007688266.1| 227 KKAAQYGSGTM 237
                                       99999977765 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   8.9e-06     0.027       6      82 ..       9      82 ..       4     100 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.9e-06
                                      HHHHHHHHHHCTT.SEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE---H CS
                      NAD_synthase  6 vdflkeyvkkaga.kgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidik 82
                                       d l + v +  + k+v +  SGG+DS l+a la +       ++l+    ++  +d+e+a   ae lg +  ti ++
  gi|474934684|ref|YP_007688266.1|  9 ADLLDSAVGRLVSgKKVAIAFSGGIDSGLIAGLAMRHA---SKVTLYT-AGTEGSHDIEAAESAAELLGGDLRTIVLD 82
                                      5667777766665599*****************98766...4556666.66777888999988888888777776655 PP

>> FUN14  FUN14 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.2    0.0012       3.5       2      28 ..      30      56 ..      29      59 .. 0.90
   2 ?    3.3   0.1     0.037   1.1e+02      25      71 ..     123     172 ..     122     223 .. 0.70
   3 ?   -0.8   0.0      0.73   2.2e+03      16      32 ..     207     223 ..     203     232 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0012
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             FUN14  2 giGaviGlvtGfalkkvgKlaaiavGg 28
                                      ++G  +Gl++G+a+++++K+ ++++G 
  gi|474934684|ref|YP_007688266.1| 30 SGGIDSGLIAGLAMRHASKVTLYTAGT 56
                                      578889*****************9996 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.037
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...x RF
                             FUN14  25 avGggllllqilasqgyikvnwdkiekdveelldrnkdgklgtede...k 71 
                                       ++Gg+ +  q++ +q y+ +  ++++ ++ e l+r ++++  +e++   +
  gi|474934684|ref|YP_007688266.1| 123 VLGGQGADEQFAGYQKYVGMKGEQLRDHIVEDLSRLYSETKPHEKKlsdH 172
                                       57888888899999999999999999999988888887777766444431 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.73
                                       xxxxxxxxxxxxxxxxx RF
                             FUN14  16 kkvgKlaaiavGgglll 32 
                                       kkv   aa+a+G g+l+
  gi|474934684|ref|YP_007688266.1| 207 KKVLCDAAVALGFGFLA 223
                                       77778899999999985 PP

>> Rad1  Repair protein Rad1/Rec1/Rad17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   4.5e-05      0.14     114     185 ..      85     157 ..      42     163 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.5e-05
                              Rad1 114 ssakatscklsYkgeGsPLvliLee..agvtttcelsTyepeedldleldrqevvlkvilkselLhs.alteLda 185
                                       + + + +c++  +g++sPLvl +e    +v+ tc   T    +  d ++     + +v +k+e L++ ++++L++
  gi|474934684|ref|YP_007688266.1|  85 TILDSIKCQIDITGTDSPLVLAFETplYNVLRTCTEDTVLGGQGADEQF--AGYQKYVGMKGEQLRDhIVEDLSR 157
                                       5566779***************************************999..788899999999998735566665 PP

>> Biotin_carb_N  Biotin carboxylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.026        77       3      69 ..      23      89 ..      21      94 .. 0.87
   2 ?    6.9   0.0    0.0031       9.1      76      93 ..     213     230 ..     203     237 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.026
                                      -EEEE---HHHHHHHHHHHHHTT-EEEEEEEGGGTTSHHHHHSSEEEEEESSTTCCGGG-HHHHHHH CS
                     Biotin_carb_N  3 kkvlianrGeiAvriiravrelgietvavyseedanslhvreadeavelgpasasesYlniekivka 69
                                      kkv+ia  G i   +i  +   + + v++y++  + s  +++a++a el +++ ++  l+ + i++ 
  gi|474934684|ref|YP_007688266.1| 23 KKVAIAFSGGIDSGLIAGLAMRHASKVTLYTAGTEGSHDIEAAESAAELLGGDLRTIVLDDDTILDS 89
                                      789999999999999999999999***********************99988888888888777765 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0031
                                       SEEE--SSTTTT-HHHHH CS
                     Biotin_carb_N  76 davhpGyGflsEnaefae 93 
                                        av  G+Gfl+E+++ a+
  gi|474934684|ref|YP_007688266.1| 213 AAVALGFGFLAERPKKAA 230
                                       36999********98776 PP

>> TetR_C_9  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00013      0.39       5      39 ..     166     196 ..     161     214 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00013
                                       HHHHHHHHHHHHHHHHH-TTHHHHHHHHHHHS-HH CS
                          TetR_C_9   5 eeklrrhlakvidtyydypylyrllaalvrdadee 39 
                                       e+kl  h++k i     ypyl r l alvr a  +
  gi|474934684|ref|YP_007688266.1| 166 EKKLSDHFSKAI----GYPYLDRELSALVRAAPID 196
                                       788999999998....5*************98655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.59u 0.37s 00:00:00.96 Elapsed: 00:00:00.56
# Mc/sec: 1429.29
//
Query:       gi|474934685|ref|YP_007688267.1|  [L=147]
Description: putative transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain and a metal-binding domain [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-27   94.4   2.1    5.3e-27   93.8   2.1    1.3  1  NikR_C    NikR C terminal nickel binding domain
    7.9e-09   35.1   0.5    1.6e-08   34.2   0.5    1.6  1  RHH_1     Ribbon-helix-helix protein, copG family


Domain annotation for each model (and alignments):
>> NikR_C  NikR C terminal nickel binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.8   2.1   5.9e-31   5.3e-27       1      76 [.      56     131 ..      56     132 .. 0.98

  Alignments for each domain:
  == domain 1  score: 93.8 bits;  conditional E-value: 5.9e-31
                                       EEEEEEEEETTSTTHHHHHHHHHHHHSSEEEEEEEEEESSSEEEEEEEEEE-HHHHHHHHHHHHTSTTEEEEEEEE CS
                            NikR_C   1 vGvitivydhhqrelserltdiqheyhdliisslhvhldhdncLevivlkGeaeeikelaeklralkgVkhvkltl 76 
                                       +Gvit++ydh++ +lse++t+iqh +++ + +++h+hldhd+c+e+++++Ge +e+k++ + l +lkgV ++klt+
  gi|474934685|ref|YP_007688267.1|  56 CGVITMIYDHDTIGLSEKITEIQHASSQNVFTTIHMHLDHDRCMEIVAVEGELAELKKINNDLGSLKGVLRCKLTM 131
                                       59*************************************************************************8 PP

>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.5   1.8e-12   1.6e-08       1      37 [.       6      43 ..       6      45 .. 0.94

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 1.8e-12
                                      EEEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHHHHH CS
                             RHH_1  1 rvsirldeellerLdelarrrg.rSrSelIReAlreyl 37
                                      r+ ++l+ ell+++d+++++ g +SrSe+IR+++r+ l
  gi|474934685|ref|YP_007688267.1|  6 RIGVSLEPELLAEFDKIIAKKGyVSRSEAIRDLVRDSL 43
                                      899*******************************9866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1025.63
//
Query:       gi|474934686|ref|YP_007688268.1|  [L=177]
Description: hypothetical protein TALC_01119 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       205  (0.011434); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 1268.03
//
Query:       gi|474934687|ref|YP_007688269.1|  [L=813]
Description: Topoisomerase IA [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   5.2e-117  391.3   0.0   6.8e-117  390.9   0.0    1.1  1  Topoisom_bac     DNA topoisomerase
    8.5e-22   76.7  22.2    5.4e-12   45.3   5.6    4.6  4  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
    8.2e-19   67.7   0.3    4.8e-18   65.3   0.2    2.3  2  Toprim           Toprim domain
  ------ inclusion threshold ------
      0.011   15.9  13.7          1    9.5   0.2    4.6  4  Zn-ribbon_8      Zinc ribbon domain
      0.023   15.1   0.1      0.056   13.9   0.1    1.6  1  Toprim_4         Toprim domain
      0.024   15.2   9.8      0.074   13.6   0.8    3.6  3  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
      0.085   12.3  14.2        1.6    8.3   0.4    4.6  4  zf-ribbon_3      zinc-ribbon domain
       0.22   11.8   8.8         50    4.3   0.0    4.6  4  zinc_ribbon_9    zinc-ribbon
       0.22   11.8   1.1        0.5   10.6   0.0    2.1  2  DUF2283          Protein of unknown function (DUF2283)
       0.28   11.2  18.0        2.4    8.2   1.0    3.5  2  DZR              Double zinc ribbon
       0.45   10.7  13.2        1.1    9.5   0.1    4.1  4  Auto_anti-p27    Sjogren's syndrome/scleroderma autoantigen 1
        1.3    9.7  11.4        5.8    7.7   0.3    4.5  4  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
        1.4    9.0  21.4          1    9.4   2.4    4.7  4  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
        2.2    8.2   5.6         42    4.1   0.0    3.8  4  zf-FPG_IleRS     Zinc finger found in FPG and IleRS
        2.2    8.3  11.7         12    5.9   5.4    3.6  2  HypA             Hydrogenase/urease nickel incorporation, met
        3.6    7.4  15.4        6.6    6.6   0.5    4.4  4  zinc_ribbon_2    zinc-ribbon domain
        7.7    7.0  12.0         40    4.7   0.1    4.4  4  zf-IS66          zinc-finger binding domain of transposase IS


Domain annotation for each model (and alignments):
>> Topoisom_bac  DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  390.9   0.0  6.5e-120  6.8e-117       2     412 ..     153     554 ..     152     555 .. 0.92

  Alignments for each domain:
  == domain 1  score: 390.9 bits;  conditional E-value: 6.5e-120
                      Topoisom_bac   2 inenlvdaaeaRrelDwliGinlsrlltkklkg..kkvlsaGRVqtptLaliveRereienFvpeeyweveatlkke 76 
                                       ++e+l++aaeaR+++D+ +G+ l+rl++++  +  k+++s+GRVq+ptL+l+v+R++eienFvp +yw++++ +   
  gi|474934687|ref|YP_007688269.1| 153 PDEKLAQAAEARQIVDLSWGAVLTRLISLSSGQvgKNFMSVGRVQSPTLKLLVDRNEEIENFVPVPYWTIQGRFGML 229
                                       789**************************4444559************************************97444 PP

                      Topoisom_bac  77 kkekekkkkkkkerikdkeeaeaileklkk.keakvesvekkekkkppplpfdtttLqkeasrklglsakktlsiaq 152
                                       +  +  + +++ + i+d+e+aeai+++ k+ kea+v+s+ek  k++++p pfdtt +q ea+++ g+ ++ ++++a+
  gi|474934687|ref|YP_007688269.1| 230 A--F--RGTHEAGDIFDREKAEAIYNRTKDvKEATVSSCEKGLKEEYRPPPFDTTMMQVEANKI-GIPPSAAMKLAE 301
                                       3..3..4799******************99669*************7777*************8.************ PP

                      Topoisom_bac 153 kLYekaglitYpRTdstrlseeaelkailealakkygkeylefaekllkktkkksvvknkkveaHeAIrPteelpkl 229
                                       +LY+  g+i+YpRT++t ++++  lk +le+l++    e++e a++ l++ + +  +++  +++H++I+Pt+  +++
  gi|474934687|ref|YP_007688269.1| 302 DLYTG-GYISYPRTENTEYPRTLSLKGVLEKLKDS---EFAEEAAEILAQDRISPSRGKRRTTDHPPIYPTAG-ATQ 373
                                       ****7.****************77*********94...688888888887776557778888*********55.567 PP

                      Topoisom_bac 230 kelsddekklYelIvrrflaslmkdakyeettvkleveeeefkasgktilekGfkkvykeekkeeeeeelpelkege 306
                                        +l++d++klYelIvrrf+a+++++a+ e+t++ ++v++e+f a+g + +ekG+kk+y +     e +++pe+++ge
  gi|474934687|ref|YP_007688269.1| 374 AKLKGDKWKLYELIVRRFMATVAPNAVAETTKAVIDVAGEKFVAEGYIQKEKGWKKYYGKYLRAAE-SRVPEMAVGE 449
                                       9*********************************************************65555554.48******** PP

                      Topoisom_bac 307 evkvkeveleekkTkppkryteasLikamekagiGtpaTraeiieklvergYverkkkslvptelGkalvellekf. 382
                                       +++v +++ ee +Tkpp ry+++sLi++m++  +Gt++Tr++ii kl++r+Yv+   ++l+pt  G+al+++le+  
  gi|474934687|ref|YP_007688269.1| 450 KIDVRSITNEESQTKPPYRYNQGSLIQEMDRLQLGTKSTRHDIIGKLFSRNYVQG--NYLIPTASGIALTKALEHHg 524
                                       *****************************************************99..58**************9998 PP

                      Topoisom_bac 383 kdlvspelTaeleekLdeIaegkadakevl 412
                                         +++pe+Ta+le ++  Ia g+++  +v+
  gi|474934687|ref|YP_007688269.1| 525 GGITEPEMTAKLEMDMLSIAGGEKSLGDVV 554
                                       99**********************998887 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   5.6   5.1e-15   5.4e-12       2      38 ..     590     626 ..     589     627 .. 0.93
   2 ?    5.4   0.1     0.015        15       2      11 ..     635     645 ..     634     652 .. 0.69
   3 !   27.7   1.5   1.6e-09   1.7e-06       4      37 ..     675     710 ..     673     712 .. 0.94
   4 !    7.6   0.1    0.0031       3.3       2      13 ..     720     731 ..     719     734 .. 0.85

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 5.1e-15
                                       EE-SSS--EEEEEE-SSSEEEEESST.T----EEB-G CS
                    zf-C4_Topoisom   2 ekCPkCggdLvlkrgkkGkFvGCsnYPeCkftkklkk 38 
                                       + CP+Cg+ + +k++k+G F+GC+ YPeCk + +l+k
  gi|474934687|ref|YP_007688269.1| 590 GVCPECGNSMTVKKSKNGNFIGCNGYPECKKAFPLPK 626
                                       78****************************9988876 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.015
                                       EE-SSS-.-EE CS
                    zf-C4_Topoisom   2 ekCPkCg.gdL 11 
                                        +CP+Cg + +
  gi|474934687|ref|YP_007688269.1| 635 DTCPECGlALI 645
                                       58*****5544 PP

  == domain 3  score: 27.7 bits;  conditional E-value: 1.6e-09
                                       -SSS-.-EEEEEE-SSS.EEEEESST.T----EEB- CS
                    zf-C4_Topoisom   4 CPkCg.gdLvlkrgkkG.kFvGCsnYPeCkftkklk 37 
                                       CP Cg g + +  +k G +F GCs  P C+ t++l 
  gi|474934687|ref|YP_007688269.1| 675 CPTCGkGTIRVMFSKAGrRFAGCSEWPACTQTYPLR 710
                                       *********************************986 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.0031
                                       EE-SSS--EEEE CS
                    zf-C4_Topoisom   2 ekCPkCggdLvl 13 
                                       + CP+Cg++L+ 
  gi|474934687|ref|YP_007688269.1| 720 NACPECGAPLIS 731
                                       67*******986 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.3   0.2   4.6e-21   4.8e-18       2     102 ..       4     137 ..       3     138 .. 0.87
   2 ?   -1.4   0.0       2.6   2.7e+03      22      45 ..     347     373 ..     334     414 .. 0.72

  Alignments for each domain:
  == domain 1  score: 65.3 bits;  conditional E-value: 4.6e-21
                                       EEEESSHHHHHHHHHTHT....................STEEEEEEESSSSEEEHS.....TTEEEEE......... CS
                            Toprim   2 lvivEgpsdaktiakalg....................sgfqavtaslGhildlet.....efkpvye......... 44 
                                       l+i E+ ++a+ ia +l+                    +++++v++++Ghi++l+      ++k+v           
  gi|474934687|ref|YP_007688269.1|   4 LIITEKANAARRIATILSdgkshsasaggvtsltfasnGDEYNVVSLRGHIMELDYpekysDWKAVSPvelvnatqi 80 
                                       89******************************************************777764444444666655556 PP

                                       ECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHHHHHHHHHHHHTHHHTTTEEEEEESS CS
                            Toprim  45 eiedkkkvlkalkelakradeiilatDpDreGeaiawellevlkellenkigrvefse 102
                                       +    k++l+ + el+ +adeii+atD DreGe i++e +++++  +  k++r++fs 
  gi|474934687|ref|YP_007688269.1|  81 KTVRVKSILSKISELSAKADEIIIATDYDREGELIGMETVKAAG-VDMGKVKRAKFSA 137
                                       66677777777*****************************9998.666689****986 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.6
                                       EEEEEEESSSSEEEHSTTEEEEE.....E CS
                            Toprim  22 fqavtaslGhildletefkpvye.....e 45 
                                       + ++ +s+G+ ++ ++  +p+y      +
  gi|474934687|ref|YP_007688269.1| 347 QDRISPSRGKRRTTDH--PPIYPtagatQ 373
                                       6789999999999999..77776333331 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.075        79      28      35 ..     591     599 ..     581     604 .. 0.75
   2 ?    9.5   0.2   0.00098         1      11      40 .]     618     648 ..     616     648 .. 0.72
   3 ?    4.8   0.5      0.03        32      25      39 ..     671     685 ..     661     686 .. 0.70
   4 ?    4.5   0.4     0.036        38      26      35 ..     719     728 ..     701     731 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.075
                       Zn-ribbon_8  28 aCPeCgs.e 35 
                                       +CPeCg   
  gi|474934687|ref|YP_007688269.1| 591 VCPECGNsM 599
                                       499999852 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00098
                       Zn-ribbon_8  11 Cghefe....vlqsisdapltaCPeCgsevrrvi 40 
                                       C++ f     ++++++   + +CPeCg ++ rvi
  gi|474934687|ref|YP_007688269.1| 618 CKKAFPlpkgAMVQMT---EDTCPECGLALIRVI 648
                                       7777776555666677...667*****9999987 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.03
                       Zn-ribbon_8  25 pltaCPeCgsevrrv 39 
                                       +l +CP+Cg+ + rv
  gi|474934687|ref|YP_007688269.1| 671 DLGPCPTCGKGTIRV 685
                                       4556*****966665 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.036
                       Zn-ribbon_8  26 ltaCPeCgse 35 
                                         aCPeCg++
  gi|474934687|ref|YP_007688269.1| 719 GNACPECGAP 728
                                       457*****96 PP

>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   5.3e-05     0.056      36      78 ..      79     123 ..      61     134 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.3e-05
                          Toprim_4  36 girpeklkt.enlve....aekkvkevilaldgDaeGeataerlaell 78 
                                       +i+  + k+             k++e+i+a+d D eGe   ++ +++ 
  gi|474934687|ref|YP_007688269.1|  79 QIKTVRVKSiL---SkiseLSAKADEIIIATDYDREGELIGMETVKAA 123
                                       44433333322...1233577788**************9888888744 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.8     7e-05     0.074       7      26 ..     591     615 ..     589     624 .. 0.73
   2 ?    1.3   0.3      0.47   4.9e+02       8      44 ..     637     683 ..     636     687 .. 0.51
   3 ?    3.9   0.1     0.074        78       8      35 ..     722     749 ..     721     764 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7e-05
                   Zn_ribbon_recom   7 rCgeCGspmtrrkrkgkr.....hy 26 
                                       +C eCG++mt++k+k++       y
  gi|474934687|ref|YP_007688269.1| 591 VCPECGNSMTVKKSKNGNfigcnGY 615
                                       7***********9987654444333 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.47
                   Zn_ribbon_recom   8 CgeCGspmtr.rkrk...gkr.hyYrCstyrrkgk.....kCsnhsi 44 
                                       C eCG +++r  +r+   + + +  +C ++  k       +C +++i
  gi|474934687|ref|YP_007688269.1| 637 CPECGLALIRvIRRGmppSTQcIDPKCVSNTAKNDlgpcpTCGKGTI 683
                                       9*****99994333344322233334443322222344555655555 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.074
                   Zn_ribbon_recom   8 CgeCGspmtrrkrkgkrhyYrCstyrrk 35 
                                       C eCG+p++  ++  + +   C +++++
  gi|474934687|ref|YP_007688269.1| 722 CPECGAPLISVGSLTECINLDCPSRKKH 749
                                       ********99887677788888776555 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.2      0.03        31       5      10 ..     592     597 ..     591     604 .. 0.74
   2 ?    4.2   0.2     0.029        31       4      23 ..     636     641 ..     616     645 .. 0.78
   3 ?    2.6   0.4     0.093        98       5      10 ..     675     680 ..     674     685 .. 0.80
   4 ?    8.3   0.4    0.0015       1.6       4      12 ..     721     730 ..     719     734 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.03
                       zf-ribbon_3   5 CPnCGa 10 
                                       CP+CG+
  gi|474934687|ref|YP_007688269.1| 592 CPECGN 597
                                       777776 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.029
                       zf-ribbon_3   4 rCPnCGaplssddnvCpyCG 23 
                                       +              Cp CG
  gi|474934687|ref|YP_007688269.1| 636 T--------------CPECG 641
                                       4..............55555 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.093
                       zf-ribbon_3   5 CPnCGa 10 
                                       CP CG+
  gi|474934687|ref|YP_007688269.1| 675 CPTCGK 680
                                       999997 PP

  == domain 4  score: 8.3 bits;  conditional E-value: 0.0015
                       zf-ribbon_3   4 rCPnCGa.pl 12 
                                        CP+CGa ++
  gi|474934687|ref|YP_007688269.1| 721 ACPECGApLI 730
                                       5888888445 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.048        50      21      29 ..     580     597 ..     562     599 .. 0.60
   2 ?    3.4   0.0     0.087        92      19      28 ..     633     641 ..     628     646 .. 0.79
   3 ?    1.9   0.2      0.27   2.8e+02      19      30 ..     671     681 ..     662     686 .. 0.70
   4 ?    4.1   0.2     0.054        57       8      29 ..     703     727 ..     702     730 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.048
                     zinc_ribbon_9  21 d........v.lCPhCgg 29 
                                                v +CP+Cg+
  gi|474934687|ref|YP_007688269.1| 580 KaalkkqqyVgVCPECGN 597
                                       044444444556****97 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.087
                     zinc_ribbon_9  19 dsdvlCPhCg 28 
                                       ++d+ CP+Cg
  gi|474934687|ref|YP_007688269.1| 633 TEDT-CPECG 641
                                       5667.****8 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.27
                     zinc_ribbon_9  19 dsdvlCPhCggg 30 
                                       d  + CP Cg g
  gi|474934687|ref|YP_007688269.1| 671 DLGP-CPTCGKG 681
                                       3337.****988 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.054
                     zinc_ribbon_9   8 CdrfVsvspdedsdv...lCPhCgg 29 
                                       C+++  ++p+ + ++   +CP+Cg 
  gi|474934687|ref|YP_007688269.1| 703 CTQTYPLRPRGTIIPtgnACPECGA 727
                                       7777777777777744557****95 PP

>> DUF2283  Protein of unknown function (DUF2283)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00047       0.5      27      45 ..      99     119 ..      81     122 .. 0.77
   2 ?   -1.7   0.2       3.4   3.5e+03      20      42 ..     554     576 ..     539     582 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00047
                           DUF2283  27 dddii..lDfDedGrlvGIEi 45 
                                       +d+ii   D+D++G+l+G+E 
  gi|474934687|ref|YP_007688269.1|  99 ADEIIiaTDYDREGELIGMET 119
                                       55666457***********96 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.4
                           DUF2283  20 veeseevdddiilDfDedGrlvG 42 
                                       vees+++  ++ + ++++ + +G
  gi|474934687|ref|YP_007688269.1| 554 VEESQNMLRNVAITISNEEEAIG 576
                                       78899999999999999998888 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4  10.0      0.15   1.6e+02       7      49 .]     621     679 ..     582     683 .. 0.51
   2 ?    8.2   1.0    0.0023       2.4      11      33 ..     718     740 ..     701     753 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.15
                               DZR   7 e........lppdarfCseCgtklkavaa.....edrC..psCgek.vdpearfCpeCG 49 
                                       +        ++    +C+eCg +l +v +     +++C  p+C +  ++++   Cp CG
  gi|474934687|ref|YP_007688269.1| 621 AfplpkgamVQMTEDTCPECGLALIRVIRrgmppSTQCidPKCVSNtAKNDLGPCPTCG 679
                                       24444444444455566666666665555666665555444555553444444455555 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0023
                               DZR  11 darfCseCgtklkavaaedrCps 33 
                                         + C+eCg++l +v + + C +
  gi|474934687|ref|YP_007688269.1| 718 TGNACPECGAPLISVGSLTECIN 740
                                       4568********99999777765 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.4      0.87   9.2e+02      17      26 ..     591     600 ..     590     612 .. 0.59
   2 ?    9.5   0.1     0.001       1.1      12      27 ..     631     646 ..     626     652 .. 0.90
   3 ?    0.6   0.1      0.62   6.6e+02      17      26 ..     674     685 ..     673     694 .. 0.73
   4 ?    6.1   0.3     0.012        12      15      26 ..     719     730 ..     718     740 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.87
                     Auto_anti-p27  17 tCpvCgvPLm 26 
                                       +Cp+Cg  + 
  gi|474934687|ref|YP_007688269.1| 591 VCPECGNSMT 600
                                       59***54433 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.001
                     Auto_anti-p27  12 tMLaetCpvCgvPLmr 27 
                                        M+++tCp+Cg  L r
  gi|474934687|ref|YP_007688269.1| 631 QMTEDTCPECGLALIR 646
                                       5**********99987 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.62
                     Auto_anti-p27  17 tCpvC..gvPLm 26 
                                        Cp+C  g++ +
  gi|474934687|ref|YP_007688269.1| 674 PCPTCgkGTIRV 685
                                       5****8877765 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.012
                     Auto_anti-p27  15 aetCpvCgvPLm 26 
                                       +  Cp+Cg+PL 
  gi|474934687|ref|YP_007688269.1| 719 GNACPECGAPLI 730
                                       678*******97 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.3    0.0055       5.8       3      18 ..     590     605 ..     589     608 .. 0.84
   2 ?    1.7   0.1      0.41   4.4e+02       4       9 ..     636     641 ..     633     650 .. 0.84
   3 ?    2.8   0.1      0.18   1.9e+02       4      17 ..     674     687 ..     671     692 .. 0.81
   4 ?    1.7   0.3      0.41   4.4e+02       4      11 ..     721     728 ..     719     739 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0055
                           zf-ISL3   3 hrCPnCgsktvvkhgk 18 
                                        +CP+Cg+ + vk++k
  gi|474934687|ref|YP_007688269.1| 590 GVCPECGNSMTVKKSK 605
                                       58*******9888876 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.41
                           zf-ISL3   4 rCPnCg 9  
                                       +CP+Cg
  gi|474934687|ref|YP_007688269.1| 636 TCPECG 641
                                       8****9 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.18
                           zf-ISL3   4 rCPnCgsktvvkhg 17 
                                        CP+Cg+ t +++ 
  gi|474934687|ref|YP_007688269.1| 674 PCPTCGKGTIRVMF 687
                                       6*****98888765 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.41
                           zf-ISL3   4 rCPnCgsk 11 
                                       +CP+Cg++
  gi|474934687|ref|YP_007688269.1| 721 ACPECGAP 728
                                       7*****85 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   1.2      0.23   2.5e+02       2       7 ..     592     597 ..     591     619 .. 0.85
   2 ?    7.4   0.1    0.0043       4.5       1      11 [.     636     646 ..     636     651 .. 0.90
   3 ?    1.1   0.4      0.39   4.1e+02       2      11 ..     675     684 ..     674     686 .. 0.83
   4 ?    9.4   2.4   0.00098         1       2      26 ..     722     744 ..     721     744 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.23
                    DNA_ligase_ZBD   2 CPvCGs 7  
                                       CP+CG 
  gi|474934687|ref|YP_007688269.1| 592 CPECGN 597
                                       ****95 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0043
                    DNA_ligase_ZBD   1 hCPvCGsavvR 11 
                                       +CP+CG a++R
  gi|474934687|ref|YP_007688269.1| 636 TCPECGLALIR 646
                                       7*****99998 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.39
                    DNA_ligase_ZBD   2 CPvCGsavvR 11 
                                       CP CG  ++R
  gi|474934687|ref|YP_007688269.1| 675 CPTCGKGTIR 684
                                       *****87666 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.00098
                    DNA_ligase_ZBD   2 CPvCGsavvReegeaiyRCtnlsCp 26 
                                       CP+CG++++    ++ + C+nl+Cp
  gi|474934687|ref|YP_007688269.1| 722 CPECGAPLI--SVGSLTECINLDCP 744
                                       ********8..55799********9 PP

>> zf-FPG_IleRS  Zinc finger found in FPG and IleRS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.43   4.5e+02       3      10 ..     591     598 ..     591     608 .. 0.77
   2 ?   -1.5   0.1       2.3   2.4e+03       4      10 ..     637     643 ..     635     648 .. 0.74
   3 ?    3.1   0.1     0.085        90       3      10 ..     674     681 ..     673     690 .. 0.82
   4 ?    4.1   0.0      0.04        42       1      15 [.     719     733 ..     719     737 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.43
                                       B-TTT--B CS
                      zf-FPG_IleRS   3 pCpRCwry 10 
                                       +Cp C++ 
  gi|474934687|ref|YP_007688269.1| 591 VCPECGNS 598
                                       6*****95 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.3
                                       -TTT--B CS
                      zf-FPG_IleRS   4 CpRCwry 10 
                                       Cp C+  
  gi|474934687|ref|YP_007688269.1| 637 CPECGLA 643
                                       9***955 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.085
                                       B-TTT--B CS
                      zf-FPG_IleRS   3 pCpRCwry 10 
                                       pCp+C+  
  gi|474934687|ref|YP_007688269.1| 674 PCPTCGKG 681
                                       9****975 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.04
                                       TSB-TTT--BBEEEE CS
                      zf-FPG_IleRS   1 GepCpRCwryiervg 15 
                                       G  Cp C+ ++ +vg
  gi|474934687|ref|YP_007688269.1| 719 GNACPECGAPLISVG 733
                                       667*******99998 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   5.4     0.012        12      53      99 ..     571     647 ..     547     694 .. 0.80
   2 ?    0.8   0.4      0.45   4.8e+02      76      99 ..     703     732 ..     695     740 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.012
                                       CC.T.TTT-EEEEEEE--EEEETTTS-EEECHHHHH.............................S-TTTSSS-EEE CS
                              HypA  53 egtv.legaeLeieevpvkvrCreCgkefeleekal.............................rCpkCgsadvei 99 
                                       e+++  ++ + ++++++ +  C eCg+++++++++                              +Cp+Cg a +++
  gi|474934687|ref|YP_007688269.1| 571 EEEAiGDEIKAALKKQQYVGVCPECGNSMTVKKSKNgnfigcngypeckkafplpkgamvqmtedTCPECGLALIRV 647
                                       33332445566699999*************88742246799************************999999876665 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.45
                                       TS-EEECHHH.HH.....S-TTTSSS-EEE CS
                              HypA  76 Cgkefeleek.al.....rCpkCgsadvei 99 
                                       C +++ l+ + ++      Cp+Cg+  +++
  gi|474934687|ref|YP_007688269.1| 703 CTQTYPLRPRgTIiptgnACPECGAPLISV 732
                                       6666665543222555668*****987766 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1     0.029        31       2       8 ..     592     598 ..     591     601 .. 0.80
   2 ?    3.7   0.0     0.049        52       9      20 ..     630     641 ..     627     644 .. 0.69
   3 ?   -1.3   2.5       1.9     2e+03       2       7 ..     675     680 ..     674     681 .. 0.64
   4 ?    6.6   0.5    0.0062       6.6      16      23 .]     722     729 ..     720     729 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.029
                     zinc_ribbon_2   2 CpnCGae 8  
                                       Cp+CG+ 
  gi|474934687|ref|YP_007688269.1| 592 CPECGNS 598
                                       9999985 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.049
                     zinc_ribbon_2   9 lqdnakFCpyCG 20 
                                       +q ++  Cp+CG
  gi|474934687|ref|YP_007688269.1| 630 VQMTEDTCPECG 641
                                       566677788888 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.9
                     zinc_ribbon_2   2 CpnCGa 7  
                                       Cp CG+
  gi|474934687|ref|YP_007688269.1| 675 CPTCGK 680
                                       666665 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.0062
                     zinc_ribbon_2  16 CpyCGtpl 23 
                                       Cp+CG+pl
  gi|474934687|ref|YP_007688269.1| 722 CPECGAPL 729
                                       88888886 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1      0.12   1.3e+02       3      11 ..     591     599 ..     590     605 .. 0.78
   2 ?    4.7   0.1     0.038        40       1      10 [.     634     644 ..     634     650 .. 0.72
   3 ?   -0.3   0.1       1.4   1.5e+03       4      10 ..     675     682 ..     674     693 .. 0.77
   4 ?    3.6   0.9     0.086        91       3      15 ..     721     733 ..     720     747 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.12
                           zf-IS66   3 tCpcCGgll 11 
                                       +Cp+CG  +
  gi|474934687|ref|YP_007688269.1| 591 VCPECGNSM 599
                                       7*****965 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.038
                           zf-IS66   1 prtCpcCGg.l 10 
                                       ++tCp+CG  l
  gi|474934687|ref|YP_007688269.1| 634 EDTCPECGLaL 644
                                       689*****834 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.4
                           zf-IS66   4 CpcCGg.l 10 
                                       Cp CG+ +
  gi|474934687|ref|YP_007688269.1| 675 CPTCGKgT 682
                                       99999755 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.086
                           zf-IS66   3 tCpcCGgllkpig 15 
                                       +Cp+CG++l  +g
  gi|474934687|ref|YP_007688269.1| 721 ACPECGAPLISVG 733
                                       6*****9666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (813 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       851  (0.047465); expected 358.6 (0.02)
Passed bias filter:                      636  (0.0354733); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        42  (0.00234257); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.74u 0.28s 00:00:01.02 Elapsed: 00:00:00.50
# Mc/sec: 4930.42
//
Query:       gi|474934688|ref|YP_007688270.1|  [L=198]
Description: GTP:adenosylcobinamide-phosphate guanylyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.4e-15   56.4   0.0    4.9e-15   56.2   0.0    1.1  1  NTP_transf_3  MobA-like NTP transferase domain
    7.1e-08   32.5   0.1      1e-07   31.9   0.1    1.3  1  IspD          2-C-methyl-D-erythritol 4-phosphate cytidylyltr
    0.00023   21.2   0.0    0.00034   20.6   0.0    1.3  1  CTP_transf_3  Cytidylyltransferase
     0.0003   20.1   0.1    0.00043   19.5   0.1    1.2  1  CofC          Guanylyl transferase CofC like
  ------ inclusion threshold ------
       0.03   14.1   0.0      0.043   13.6   0.0    1.2  1  DUF2064       Uncharacterized protein conserved in bacteria (


Domain annotation for each model (and alignments):
>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.2   0.0   1.4e-18   4.9e-15       2     125 ..       4     130 ..       3     176 .. 0.87

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 1.4e-18
                                       EEEEESS-TTTTT...THHHHCCCCCCHHHHHHHHHCTT..-CEEEEECSH..CHHHHHHTTCTS-EEE-TTSS-SH CS
                      NTP_transf_3   2 viLAGGrSsRmgg...dKallplggkpllervldalraa.gvdevvvvggd..eevlaalarlgvrvvededpgkgp 72 
                                       +i AGG+++Rmg+   +K++  +ggk ++erv++a++ a +vd+v+v++ +  ++ +a l++ gv++++ +  g   
  gi|474934688|ref|YP_007688270.1|   4 LINAGGKGTRMGEtgiEKPMQIIGGKHVVERVVKAMQFAeTVDRVLVSVSPntPKTEAFLKDMGVETIRTS--GDDF 78 
                                       666*********7779***********************559******8665689999************8..899* PP

                                       HHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSS CS
                      NTP_transf_3  73 laslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvptyeg 125
                                       +  l+   ++  + ++v+ ++ D+Pl++++++++ + a+ ++ ++++v ++++
  gi|474934688|ref|YP_007688270.1|  79 MMDLHQSFESM-SGKYVVTCPSDIPLINAQIIDQAVSAFVPEMQSMIVMVDAE 130
                                       *********98.8**************************99988887776654 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.1   2.9e-11     1e-07       2     126 ..       2     125 ..       1     136 [. 0.87

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 2.9e-11
                                       EEEEECTTSSCTT-.SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGGCCEEEE.E--SS CS
                              IspD   2 vvvipAAGsGkRmk.aglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllldksiqlv.aGGde 76 
                                        ++i A G+G+Rm+ +g +K    + g+ ++e+ v+a++  ++vd+++v vs++  +++e++l d  ++ +   Gd+
  gi|474934688|ref|YP_007688270.1|   2 EALINAGGKGTRMGeTGIEKPMQIIGGKHVVERVVKAMQFAETVDRVLVSVSPNT-PKTEAFLKDMGVETIrTSGDD 77 
                                       689**********73699***********************************99.99*****99888877257999 PP

                                       HHHHHHHHHHTTSSTTSEEEE--TT-TT--HHHHHHHHHHHHTTCSEEEE CS
                              IspD  77 RaesVlnglkalegeakfVLvHDaARpllkaadiaellaaaeqstqgail 126
                                             ++++ ++g+  +V+   +  pl++a+ i++ + a   ++q++i+
  gi|474934688|ref|YP_007688270.1|  78 FMMDLHQSFESMSGK--YVVTCPSDIPLINAQIIDQAVSAFVPEMQSMIV 125
                                       999999999998887..888888888999999999988887777777765 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   9.4e-08   0.00034       8     118 ..      14     119 ..      11     151 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 9.4e-08
                                       SSSSSSTTGGGSEETTEEHHHHHHHHHHHTTTTSE..EEEEES-HHHHHHHHHTTSEEEE--TTCSSHHHHHHHHHH CS
                      CTP_transf_3   8 sgSkRlpgKnlldlggkpliayvleaalkskafek..vivaTDseeiknvakefgasvlvtrsslesdterflevvk 82 
                                       +g +++ +K+++ +ggk  +++v++a   ++++++  v v+    +++ ++k++g++ ++t++     ++ +++  +
  gi|474934688|ref|YP_007688270.1|  14 MGETGI-EKPMQIIGGKHVVERVVKAMQFAETVDRvlVSVSPNTPKTEAFLKDMGVETIRTSG-----DDFMMDLHQ 84 
                                       555554.7***************************66667778999********999999875.....556666666 PP

                                       HHTTT.TTSEEEEE-TT-TT--HHHHHHHHHHHHHS CS
                      CTP_transf_3  83 aflmseneeiivnlqGdnPllqeevikkaietlken 118
                                        f++    +++v   +d Pl++ + i++a+++   +
  gi|474934688|ref|YP_007688270.1|  85 SFESM-SGKYVVTCPSDIPLINAQIIDQAVSAFVPE 119
                                       66555.4559999999*************9987655 PP

>> CofC  Guanylyl transferase CofC like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   1.2e-07   0.00043      41     108 ..      42     111 ..      28     130 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.2e-07
                              CofC  41 lkrld.vlv.vsedeevleyaldelgvevvkekekdlntavekafeeieekeviiipsdiPlikkedvkd 108
                                       ++++d vlv vs +    e  l+ +gve+++    d+   +++ fe++  k v+  psdiPli+ + +++
  gi|474934688|ref|YP_007688270.1|  42 AETVDrVLVsVSPNTPKTEAFLKDMGVETIRTSGDDFMMDLHQSFESMSGKYVVTCPSDIPLINAQIIDQ 111
                                       3457743322555555666667899**************************************9998876 PP

>> DUF2064  Uncharacterized protein conserved in bacteria (DUF2064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.2e-05     0.043      11      85 ..      45     115 ..      34     130 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.2e-05
                                       SEEEEEE----TTHHHHHHHH-TTSEEEE--SSSHHHHHHHHHHHHHHTT-SEEEEE-SS-TT--HHHHHHHHHH CS
                           DUF2064  11 aevvlaldgaldkalaeqlalakglevlpQqggdlgeRlarafdrafeageepvlliGsDcpqltaalleqAfea 85 
                                       +++ + ++ + ++ + e++ +  g+e ++ +g+d+   l++ f++     ++ v+   sD+p ++a++++qA++a
  gi|474934688|ref|YP_007688270.1|  45 VDR-VLVSVSPNTPKTEAFLKDMGVETIRTSGDDFMMDLHQSFESM---SGKYVVTCPSDIPLINAQIIDQAVSA 115
                                       333.33344444444445699999**********************...7789*******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1453.93
//
Query:       gi|474934689|ref|YP_007688271.1|  [L=312]
Description: cobalamin 5'-phosphate synthase/cobalamin synthase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-33  116.8  19.0    1.7e-33  116.5  19.0    1.1  1  CobS             Cobalamin-5-phosphate synthase
  ------ inclusion threshold ------
      0.044   12.5   0.1      0.044   12.5   0.1    2.9  2  DUF2207          Predicted membrane protein (DUF2207)
          3    8.5  11.4       0.51   10.9   1.6    3.2  3  Phage_holin_1    Bacteriophage holin
        6.8    7.5   9.6        5.2    7.9   1.9    3.0  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase


Domain annotation for each model (and alignments):
>> CobS  Cobalamin-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.5  19.0   3.8e-37   1.7e-33       2     204 .]      53     301 ..      52     301 .. 0.75

  Alignments for each domain:
  == domain 1  score: 116.5 bits;  conditional E-value: 3.8e-37
                              CobS   2 lsflTrlPvp.......elaralaffPlvGlllGlll.llallllllll..llaallavaalvlltgglHlDGlaDt 68 
                                       lsf+T++ ++       ++++ ++++P++G+++Gl++ ++++++ ++     + a++a+a++++l+++lH+DGlaD+
  gi|474934689|ref|YP_007688271.1|  53 LSFFTIFKLNvgeresdAMEKNFWLVPIIGFIIGLAAfIVVFIIDYVIGglFIEAVAAIATVLILSKFLHFDGLADF 129
                                       89*****997666655555889**************9877777777666854477777777788************* PP

                              CobS  69 aDglgsgrdrerrleImkDsrvGafGvlalvlvlllkvaalaala.........lllapvlsRlaallaiallpyae 136
                                       +Dg+++++d+e+ ++++kD+++Ga+G+ ++++v ++ +a+ + ++         +l ++++ + a+++a+a++++  
  gi|474934689|ref|YP_007688271.1| 130 GDGMVASGDKEKHVRALKDTTIGAGGLGVAFIVTMVSIACYTGIPwgivgvpfiVLGIEAVVKNAQVVAAAFGEPSD 206
                                       ****8888********************************644445555777876788****************774 PP

                              CobS 137 eglgalfaeaqkk.........lvllal......................avlllllall........laallvall 174
                                          g+++ae+  +         +    +                               +        la +lv + 
  gi|474934689|ref|YP_007688271.1| 207 GMAGKQVAETGMNsmilstilaA----VfmaiavvlgvlysdfdfgdvgkE--------MavmiivpvLASVLVGFG 271
                                       44555555533334443332221....122223344556666666666652........033333333666667779 PP

                              CobS 175 lrrlarrklggvtGDvlGavieltellvll 204
                                       ++++a+r++g v+GD+lGa++e+++++ ll
  gi|474934689|ref|YP_007688271.1| 272 MAKIANRTFGFVNGDILGATNEIARAVSLL 301
                                       9*************************9986 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   9.8e-06     0.044     357     462 ..      24     133 ..       4     146 .. 0.79
   2 ?   -8.9  13.7         4   1.8e+04     382     425 ..     224     266 ..     137     298 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.8e-06
                           DUF2207 357 lkkwksavkkkergyfdkkgkkklkklsalglgliilglilillallllvll..........lvfllilllilllia 423
                                       +++        +++  ++k+kk  + + ++  + ++l+++ i+ ++    ++          + +  i+++i++l+a
  gi|474934689|ref|YP_007688271.1|  24 FQDS-------QEQVSEEKPKKSSNPVPIVDAIKGMLSFFTIFKLN----VGeresdameknFWLVPIIGFIIGLAA 89 
                                       3333.......44455588899988888888888888888775554....444577****999999999******** PP

                           DUF2207 424 iivlllfsrllgrrteeGaellakwkgFkkyLe.....Dfsefk 462
                                       +iv++++ +++g +  e  ++ a ++ + k+L      Df +  
  gi|474934689|ref|YP_007688271.1|  90 FIVVFIIDYVIGGLFIEAVAAIATVLILSKFLHfdglaDFGDGM 133
                                       *************9999999999999999999998888877655 PP

  == domain 2  score: -8.9 bits;  conditional E-value: 4
                           DUF2207 382 klsalglgliilglilillallllvll........lvfllilllillliaii 425
                                       + ++++++ +i++++++         l        +   + +++i++++a++
  gi|474934689|ref|YP_007688271.1| 224 STILAAVFMAIAVVLGV---------LysdfdfgdVGKEMAVMIIVPVLASV 266
                                       11111122222222222.........12233334444444444444444444 PP

>> Phage_holin_1  Bacteriophage holin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   1.2     0.063   2.8e+02       9      55 ..      72     118 ..      70     124 .. 0.74
   2 ?   10.9   1.6   0.00011      0.51       9      60 ..     219     272 ..     217     284 .. 0.81
   3 ?   -1.7   0.0      0.99   4.5e+03      37      56 ..     289     306 ..     272     310 .. 0.61

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.063
                     Phage_holin_1   9 nkafwvalisavlllilavlglfgldltvaklaeqllqivsavlsll 55 
                                       +k fw+  i  +++ + a++ +f +d+ +  l  + ++++ +vl+l 
  gi|474934689|ref|YP_007688271.1|  72 EKNFWLVPIIGFIIGLAAFIVVFIIDYVIGGLFIEAVAAIATVLILS 118
                                       68899888888888888899999999999966666666666666665 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00011
                     Phage_holin_1   9 nkafwvalisavlllilavlglfgldltvaklaeql..lqivsavlsllaalGv 60 
                                       n + + ++++av+++i +vlg+ ++d+++ ++++++  + iv ++ s+l+  G+
  gi|474934689|ref|YP_007688271.1| 219 NSMILSTILAAVFMAIAVVLGVLYSDFDFGDVGKEMavMIIVPVLASVLVGFGM 272
                                       6677899***********************998765114555577788777765 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.99
                     Phage_holin_1  37 vaklaeqllqivsavlslla 56 
                                        a  ++++  +vs++l+l++
  gi|474934689|ref|YP_007688271.1| 289 GA--TNEIARAVSLLLMLFV 306
                                       44..6777777777776654 PP

>> CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   1.9    0.0012       5.2       8      48 ..      80     135 ..      77     146 .. 0.72
   2 ?    3.0   1.1     0.038   1.7e+02      26      41 ..     172     239 ..     151     310 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0012
                                       HHHHHHHHHHHHGGGS-H............HHHHHHHH.......HHHHHTTHHHHHH CS
                   CDP-OH_P_transf   8 llrlllsvlailllltyyp..........lvlaillll.......iasltDalDGklA 48 
                                       +++++++++a+++++++++             ai+ +l       + +l+D+ DG++A
  gi|474934689|ref|YP_007688271.1|  80 IIGFIIGLAAFIVVFIIDYvigglfieavA--AIATVLilskflhFDGLADFGDGMVA 135
                                       578888888888888888777788777442..333332234544688999*******9 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.038
                                       ......................................................HHHHHHHHHHHHHT CS
                   CDP-OH_P_transf  26 p....................................................lvlailllliasltD 41 
                                       +                                                    ++la++++ ia++++
  gi|474934689|ref|YP_007688271.1| 172 GipwgivgvpfivlgieavvknaqvvaaafgepsdgmagkqvaetgmnsmilsTILAAVFMAIAVVLG 239
                                       34455555555555566666666666666666666666666666666666666667777776666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1360  (0.0758548); expected 358.6 (0.02)
Passed bias filter:                      654  (0.0364772); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.68u 0.36s 00:00:01.04 Elapsed: 00:00:00.54
# Mc/sec: 1745.18
//
Query:       gi|474934690|ref|YP_007688272.1|  [L=370]
Description: hypothetical protein TALC_01123 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.1e-43  147.2   0.3    7.7e-43  146.8   0.3    1.1  1  CbiZ      Adenosylcobinamide amidohydrolase


Domain annotation for each model (and alignments):
>> CbiZ  Adenosylcobinamide amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.8   0.3   4.3e-47   7.7e-43       1     192 []      22     218 ..      22     218 .. 0.95

  Alignments for each domain:
  == domain 1  score: 146.8 bits;  conditional E-value: 4.3e-47
                              CbiZ   1 rfeeprrvlssavlngGlrelravlnhqvpegyeredpeeyleeyleelglppektvgllTaadmenaaiaeee.fe 76 
                                       rf+e+++vlssa++ngG   +++v+++qvp++y++ +  + l++  +++gl p+++vg++T+a+++ +  + +e  +
  gi|474934690|ref|YP_007688272.1|  22 RFTERMEVLSSAPMNGGHCVTDTVFIMQVPHDYRSGNYIQDLRDKQAQYGL-PSDSVGFMTSAEVKYVFSTACEeAD 97 
                                       699**********************************88999*********.7*************99777666378 PP

                              CbiZ  77 dlevtavvTaGvesnavragd.............edeeaekpGTINiivlinaaLtdaalvralitatEAKtaalqd 140
                                       + +v +++TaGv +navragd             e +++  +GTINi+ +++++++d   ++a+i ++E+K+ a++d
  gi|474934690|ref|YP_007688272.1|  98 GERVFVAATAGV-TNAVRAGDpltgweeksarsmEIYRKLIAGTINIVAVVPHPMDDMGKINAMIPLVEGKAMAMHD 173
                                       889*********.*********************88899************************************** PP

                              CbiZ 141 lgvrsrysegatGTgTDaiavaadkegeeeltyaGkhtklGeliaraVyeAv 192
                                       +g++       tGT++Da+a++++  +e ++++aG+ t  G  +ar V++Av
  gi|474934690|ref|YP_007688272.1| 174 MGYP------ETGTTSDAMAIVSPVGNE-RISFAGTGTPAGMSLARGVRKAV 218
                                       ***9......8*************6555.7*********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2511.10
//
Query:       gi|474934691|ref|YP_007688273.1|  [L=346]
Description: cobalamin biosynthesis protein CobD [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.5e-71  238.6   0.3    9.8e-71  238.2   0.3    1.1  1  CobD_Cbib       CobD/Cbib protein
  ------ inclusion threshold ------
       0.34   10.8   5.7        1.7    8.6   5.7    2.2  1  Transport_MerF  Membrane transport protein MerF


Domain annotation for each model (and alignments):
>> CobD_Cbib  CobD/Cbib protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  238.2   0.3   1.1e-74   9.8e-71       3     268 ..      13     300 ..      11     323 .. 0.87

  Alignments for each domain:
  == domain 1  score: 238.2 bits;  conditional E-value: 1.1e-74
                         CobD_Cbib   3 lAlllDlllgdprrllhPvvligklisalekrlr.k.akkerlaGvllalllvllallvalllllla...laall.. 72 
                                         ll+D+++gd ++++hP++++g+l++a+++rl+ + ++  ++ G+l  +l+++l+ ++al++l+l+   l   +  
  gi|474934691|ref|YP_007688273.1|  13 STLLIDRYVGDVPNRYHPLRWMGNLLDAIDRRLHnRtSWWATVVGFLSYMLVLVLFSFAALMILMLVrygL---Agv 86 
                                       5689*****************************52344456679988888777777777777777664432...234 PP

                         CobD_Cbib  73 ................glvlealllkltlalrsLleevrkvakal.kgdleaaReavsmiVgRdtseldeeeiarAa 132
                                                        +v+++ll+k+t +l   +++++ ++++l +gdl+aa  +++m+V+R+t+ +de+++++++
  gi|474934691|ref|YP_007688273.1|  87 cgfeifgqgsdlgeiaWIVMTGLLVKVTYSLFLFRKNCSVIMDDLrNGDLDAAADKTQMMVNRKTRGMDEPHLTSSC 163
                                       577889999999988666999************************66****************************** PP

                         CobD_Cbib 133 vEsvaENlsDgvvaPlfyflllglpgalaykavnTlDsmvGYkneryedfGwaaArlDDllnyiPARltalllala. 208
                                       +E+++ENl+D+vv+P fy+ +lg+ ga++++++n +D+m+G +ne+y+ +G+++Ar+DD+l +iP+Rl+ l++ +a 
  gi|474934691|ref|YP_007688273.1| 164 CETISENLVDSVVSPFFYYGILGMFGAVMFRCANLMDAMWGRRNEKYNMLGHFPARWDDVLGFIPSRLSPLFIGFAa 240
                                       *************************************************************************9985 PP

                         CobD_Cbib 209 .........aalriarrdarkhpSpNsgwpeaalAgalgvrLggpnvY.lgkleekptlgdkkrpleaed 268
                                                 a+++a r+++ +pSpNsgwp+ a+A+a+g+++++++vY +g+    p+         ++d
  gi|474934691|ref|YP_007688273.1| 241 wlmrlknrrPAMKAAIREHKLTPSPNSGWPMTATAAAMGISFEKKDVYvMGEG-PLPS---------IDD 300
                                       55555555544*************************************76643.2333.........334 PP

>> Transport_MerF  Membrane transport protein MerF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   5.7   0.00018       1.7      13      42 ..      52      81 ..      51      83 .. 0.96

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00018
                    Transport_MerF 13 LsAlvGYLDYVLlPaLaifigLtvyaywrk 42
                                      ++ +vG+L Y+L+ +L  f +L ++ ++r+
  gi|474934691|ref|YP_007688273.1| 52 WATVVGFLSYMLVLVLFSFAALMILMLVRY 81
                                      789*************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2195.40
//
Query:       gi|474934692|ref|YP_007688274.1|  [L=372]
Description: Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-53  182.2   0.0    1.9e-53  181.9   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
     0.0001   21.4   0.0    0.00041   19.4   0.0    1.8  2  Aminotran_5      Aminotransferase class-V
  ------ inclusion threshold ------
      0.065   11.7   0.0      0.091   11.3   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
       0.14   11.1   0.0       0.21   10.5   0.0    1.2  1  mRNA_stabil      mRNA stabilisation
        0.2   10.9   0.0        0.3   10.3   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.9   0.0   5.4e-57   1.9e-53      24     360 ..      44     359 ..      26     361 .. 0.92

  Alignments for each domain:
  == domain 1  score: 181.9 bits;  conditional E-value: 5.4e-57
                                       HHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEE CS
                     Aminotran_1_2  24 akaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpd 100
                                       a + +    a g++  y++     e +e +ak++       + +e +vv+g G++++i  +++++  ++gd +l+p+
  gi|474934692|ref|YP_007688274.1|  44 AAEVQ---KALGGIGHYPDAL-CTEDREVIAKYFD------IRPE-NVVMGAGSSEIIRNFPAAF-MERGDLVLMPR 108
                                       44443...4888889999988.89999********......8899.*******************.9********** PP

                                       SS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHH CS
                     Aminotran_1_2 101 ptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldla 177
                                       p++a+y++ ++++g++v ++ l++  +fh+d+e+le +l++      + k +++++p+NPtG+v +++ + k+++++
  gi|474934692|ref|YP_007688274.1| 109 PSFAEYTQQIKIAGAQVDYFDLSPDSGFHIDFEDLESQLQST-----QYKALYLCNPNNPTGVVESKDNILKIVKVC 180
                                       ****************************************95.....56899************************* PP

                                       HHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTSSH CS
                     Aminotran_1_2 178 kkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsrpflsss 254
                                       +    l+f+De+  g+  +  d  +  + +++++nll++ s+ K+f+++G R+G+ l+n++++  ++k+s p++  +
  gi|474934692|ref|YP_007688274.1| 181 EDMDTLVFLDETLLGLSKD-ADLRSCASYINDYTNLLVAESFTKSFAIPGMRIGFGLSNPEICAEMQKVSLPWNLGT 256
                                       ************9999887.67777799***********************************************99 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEEEEETHH..CHHHHHHHHHHTCT CS
                     Aminotran_1_2 255 llqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmflltdlsae..takelskkLleevg 329
                                       + qa+v   +++      +++ ++++l k+++ + ++L+++g++v +    +f+++ ++++  t  e++k++l+e g
  gi|474934692|ref|YP_007688274.1| 257 VEQAVVKYLTDNMG----YVDVAAKELRKESEIMQARLEDIGFPVGPVSDSFFYFVSCRPLglTGAEMQKMMLKE-G 328
                                       99888887777766....9********************************************************.* PP

                                       EEEEEGGGGTS..TTEEEEECTTS-HHHHHHHH CS
                     Aminotran_1_2 330 vyvtpgtsftv..pgrlRitvAglteeeleelv 360
                                       + v+ + sf+   +  +R +v   +++ +e+++
  gi|474934692|ref|YP_007688274.1| 329 IMVRDCASFGPqfEDYIRYCV--KDRARNERFI 359
                                       **********999********..9998888876 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.1e-07   0.00041      29     175 ..      46     190 ..      42     205 .. 0.78
   2 ?   -0.8   0.0      0.16   5.6e+02     263     336 ..     260     332 ..     256     340 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.1e-07
                                       SSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHH CS
                       Aminotran_5  29 nvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpw 105
                                        v+++++  g+   +  +e re +a+ + ++  e+++   G++e i  ++ ++   +++gd +++ +    a+    
  gi|474934692|ref|YP_007688274.1|  46 EVQKALGGIGHYPDALCTEDREVIAKYFDIRP-ENVVMGAGSSEIIRNFPAAF---MERGDLVLMPR-PSFAEY--T 115
                                       55566666666667778899999*******97.99999999998887777777...78888777655.566777..8 PP

                                       HHHHHHHTEEEEEEEB..ETTSCBEGGGHHHH--.TTEEEEEEESBETTTTEB--HHHHHHHHHH.T..T-EEEEE CS
                       Aminotran_5 106 qelakrtgakvkvipl..deegeldldeleklln.ektklvaithvsnvtGtiqpveeigklakk.k..galvlvD 175
                                       q+++   ga+v+++ l  d++ ++d ++le++l+  ++k+++++  +n tG+++  ++i k++k  +  + lv++D
  gi|474934692|ref|YP_007688274.1| 116 QQIK-IAGAQVDYFDLspDSGFHIDFEDLESQLQsTQYKALYLCNPNNPTGVVESKDNILKIVKVcEdmDTLVFLD 190
                                       9997.88*****9865116677999********769*****************99888888777532126666666 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.16
                                       HHHHHH.HCHHHHHHHHHHHHHH.HHHHHHHCTSTTEEEES.-B-CTCBSEEEEEETTCSHHHHHHHHHHTTEEEE CS
                       Aminotran_5 263 aaleyl.eeigleaiekhekela.eyllerlkslpgvrlygpdkaerrasivsfnfkgvhaedvatlLdeegIavr 336
                                       a+++yl +++g+  ++++e ++  e +++rl++++     gp + +     vs+   g+  +++++++ +egI+vr
  gi|474934692|ref|YP_007688274.1| 260 AVVKYLtDNMGYVDVAAKELRKEsEIMQARLEDIGFPV--GP-VSDSFFYFVSCRPLGLTGAEMQKMMLKEGIMVR 332
                                       78899988899888888776665155667888887774..43.667777888888888888888888888888887 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.5e-05     0.091      86     177 ..      96     194 ..      77     217 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.5e-05
                                       TTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEEST.......TSHHHHHHHCCT.TEEEEEEESS-TTTT--- CS
                   Cys_Met_Meta_PP  86 allkaGdeivvsddlYggtqrllkkvlkklgievkfvdt.......sdleelekaike.ntklvylEtptnpllkvv 154
                                       a+++ Gd +++ +  +    +++k    +    v+++d         d+e+le+++++ + k++yl  p np+  v 
  gi|474934692|ref|YP_007688274.1|  96 AFMERGDLVLMPRPSFAEYTQQIKIAGAQ----VDYFDLspdsgfhIDFEDLESQLQStQYKALYLCNPNNPTGVVE 168
                                       56667777777776666555555554443....33333322223437899******99899***********97664 PP

                                       ..-.HHHHHHHHHHTT-EEEEEGTTT CS
                   Cys_Met_Meta_PP 155 ..D.iekiaklakkagvlvvvDntfa 177
                                         D i ki+k++ + ++lv++D t++
  gi|474934692|ref|YP_007688274.1| 169 skDnILKIVKVCEDMDTLVFLDETLL 194
                                       2234888899999999*******985 PP

>> mRNA_stabil  mRNA stabilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0     6e-05      0.21      86     163 ..     114     194 ..     105     197 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 6e-05
                       mRNA_stabil  86 npqayslrrffkdylllKkslgeeltkedLvefLkivltnke...ksknysdLvksnkvvvkaLklykdleesiikd 159
                                       + q++++     dy+ l   +g+++  edL + L+ +  +     + +n    v+s++ ++k++k  +d ++ ++ d
  gi|474934692|ref|YP_007688274.1| 114 YTQQIKIAGAQVDYFDLSPDSGFHIDFEDLESQLQSTQYKALylcNPNNPTGVVESKDNILKIVKVCEDMDTLVFLD 190
                                       677888888889***********************998887778799***********************999*999 PP

                       mRNA_stabil 160 eevi 163
                                       e+++
  gi|474934692|ref|YP_007688274.1| 191 ETLL 194
                                       9875 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   8.5e-05       0.3      89     167 ..     117     190 ..      73     192 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 8.5e-05
                                       HHHHC.C--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EE CS
                   Beta_elim_lyase  89 aiael.agvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygipl 164
                                       +i+   a+v   dl  ++   +d+e+le+ ++       + k+++l + nn   G v s +++ ++ +++++ +  +
  gi|474934692|ref|YP_007688274.1| 117 QIKIAgAQVDYFDLSPDSGFHIDFEDLESQLQS-----TQYKALYLCNPNNP-TGVVESKDNILKIVKVCEDMDTLV 187
                                       2333335666667777776799**********9.....578**********5.9*********************99 PP

                                       EEE CS
                   Beta_elim_lyase 165 hlD 167
                                       +lD
  gi|474934692|ref|YP_007688274.1| 188 FLD 190
                                       999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 2159.56
//
Query:       gi|474934693|ref|YP_007688275.1|  [L=41]
Description: hypothetical protein TALC_01126 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       142  (0.00792013); expected 358.6 (0.02)
Passed bias filter:                      115  (0.00641419); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 300.06
//
Query:       gi|474934694|ref|YP_007688276.1|  [L=162]
Description: deoxycytidine triphosphate deaminase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-12   46.6   0.0    4.3e-12   45.8   0.0    1.4  2  dUTPase   dUTPase


Domain annotation for each model (and alignments):
>> dUTPase  dUTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0      0.35   6.3e+03      14      22 ..      31      39 ..      21      48 .. 0.61
   2 !   45.8   0.0   2.4e-16   4.3e-12      25     125 ..      55     155 ..      49     157 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.35
                                      SSEEEE-SS CS
                           dUTPase 14 AgyDlsaak 22
                                       gyD+++a+
  gi|474934694|ref|YP_007688276.1| 31 NGYDVRVAE 39
                                      466666553 PP

  == domain 2  score: 45.8 bits;  conditional E-value: 2.4e-16
                                       EEETTEEEEEEEEEEEE--TTEEEEEEE-HHHHHHHEEEEEEEEETTBTSEEEEEEEE-SSS-EEE-TT-EEEEEEE CS
                           dUTPase  25 tvkpgetvlvptdisiklpdglaalilpRSglaakglivvpgvidsdyrGevkvvlfnltkkdvkikkgdRiAqLif 101
                                        ++p++   v+t   + ++d++ + +  R +  +kg+i   g +d+ ++G + +  +n+++ +v+i+ g+R +qL+f
  gi|474934694|ref|YP_007688276.1|  55 KIPPKTMFYVSTIERVRMADDVCGNLWLRTSWIRKGIIAAFGMVDAGFEGTLTLGSYNSSDHEVEIPIGERYCQLVF 131
                                       68899999********************************************************************* PP

                                       EEBECGEEEEESSTTTESSBTTXT CS
                           dUTPase 102 ariltaeleevetlkatergeggf 125
                                       + +  ++ + +e+ +  ++ + g+
  gi|474934694|ref|YP_007688276.1| 132 QTMSSPSEKSYEKRSGHYQNQTGV 155
                                       *99999999999999999988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 970.54
//
Query:       gi|474934695|ref|YP_007688277.1|  [L=333]
Description: putative methyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-60  204.1   0.0    2.5e-60  203.7   0.0    1.1  1  Met_10           Met-10+ like-protein
    6.2e-18   64.4   0.0    1.3e-17   63.3   0.0    1.6  1  Trm5_N           tRNA methyltransferase 5 N-terminal domain
  ------ inclusion threshold ------
      0.012   15.1   0.0      0.016   14.6   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      0.049   13.6   0.0       0.19   11.6   0.0    2.0  3  Methyltransf_18  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.7   0.0   5.5e-64   2.5e-60       2     198 ..      84     280 ..      83     281 .. 0.97

  Alignments for each domain:
  == domain 1  score: 203.7 bits;  conditional E-value: 5.5e-64
                                       EEEEETTEEEEEB-TTSSHHHHHHHHHHHHHS.S-SCEEEE-S-SBTTTTB--EEEEEES-.SEEEEEETTEEEEEE CS
                            Met_10   2 kfeiiGdvvilnlreelkeykkvigevildkt.kvktvlrkvsevegefRtfelevlaGsdstetihkEngcrfklD 77 
                                        f++iGd++i++l++ lk+y+ +ig++++++t ++++v+++ +  +gefR++el  ++G++s+e+ihkEng+r+  D
  gi|474934695|ref|YP_007688277.1|  84 AFDVIGDIAIMKLEDGLKPYSGEIGRALVQVTpNIRAVFDDAGV-KGEFRVRELVKIYGEGSSEVIHKENGVRMMTD 159
                                       59*************************************99875.******************************** PP

                                       TTTS---GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEE CS
                            Met_10  78 vskvyfsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvk 154
                                        skvyf+++l++Er+r+a++v++ge++ d+fAG+ pf  +i + +++ +v++idlnPe  ++++en++lN++ k ++
  gi|474934695|ref|YP_007688277.1| 160 PSKVYFNPRLATERMRIARMVRPGETITDMFAGVAPFGCVICRNADPGIVYSIDLNPECERFMRENMRLNRITK-IE 235
                                       ************************************************************************86.78 PP

                                       EEES-GGG---.TT-EEEEEE--TTTGGGGHHHHHHHEEEEEEEE CS
                            Met_10 155 pileDgrevir.eqladrvvmnlpksaieFldkvlaalkdggvih 198
                                       pi +Dgrev++   +adrv+mnlp+ a eFl+++l ++k gg++h
  gi|474934695|ref|YP_007688277.1| 236 PIIGDGREVVKtLPKADRVLMNLPQIADEFLQDALGCVKSGGMVH 280
                                       **********97789***************************999 PP

>> Trm5_N  tRNA methyltransferase 5 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.3   0.0     3e-21   1.3e-17       1      46 [.       4      50 ..       4      51 .. 0.94

  Alignments for each domain:
  == domain 1  score: 63.3 bits;  conditional E-value: 3e-21
                                      EEEEEGGGHHHHHHHHHHTT-B-TTS--EEETTEEEEEB-S--.HHH CS
                            Trm5_N  1 cikVpkkegEkvRkkLlekglLdrnyKIksdddylyIPvkeep.egy 46
                                      c++Vpk+egE+vRk+L++ g+Ld++++I +d+d+l+IP+  +  egy
  gi|474934695|ref|YP_007688277.1|  4 CVRVPKSEGEQVRKALMDGGILDHRHRIGADGDFLLIPILADSyEGY 50
                                      ***************************************99875556 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   3.5e-06     0.016     158     265 ..     179     288 ..     171     315 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.5e-06
                              PrmA 158 lvkegeevlDvGtGSGiLaiaaak.LgakkvvavDiDevAvkvakeNaelNkveakleva.lseellk.eekadviv 231
                                       +v++ge++ D+ +G +    +  +  +   v+ +D+++   +  +eN++lN++++   ++   +e++k   kad ++
  gi|474934695|ref|YP_007688277.1| 179 MVRPGETITDMFAGVAPFGCVICRnADPGIVYSIDLNPECERFMRENMRLNRITKIEPIIgDGREVVKtLPKADRVL 255
                                       56666666666666665554443314455689***********************776651345555545689**** PP

                              PrmA 232 aNILaevlielaedikklvkeggllilSGilkek 265
                                        N L ++  e+++d+  +vk+gg++ +  il++ 
  gi|474934695|ref|YP_007688277.1| 256 MN-LPQIADEFLQDALGCVKSGGMVHMHKILERS 288
                                       **.89*********************99999875 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.3     6e+03     114     130 ..       5      21 ..       2      24 .. 0.80
   2 ?   11.6   0.0   4.3e-05      0.19       5      86 ..     174     254 ..     168     257 .. 0.89
   3 ?   -3.5   0.0         2     9e+03      95     120 ..     280     303 ..     276     313 .. 0.62

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.3
                   Methyltransf_18 114 ilqpnseaeelRkylve 130
                                       +  p+se e++Rk l++
  gi|474934695|ref|YP_007688277.1|   5 VRVPKSEGEQVRKALMD 21 
                                       556999999****9987 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 4.3e-05
                   Methyltransf_18   5 LkaiaslvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklkee 81 
                                       + +ia++v++g+++ D  +  +   + ++++     v+ +D+n+++ +  +en++ +++ +kie +++dG e++k+ 
  gi|474934695|ref|YP_007688277.1| 174 M-RIARMVRPGETITDMFAGVAPFGCVICRNADPGIVYSIDLNPECERFMRENMRLNRI-TKIEPIIGDGREVVKTL 248
                                       4.69***************************************************9998.68*********999854 PP

                   Methyltransf_18  82 e.vdtv 86 
                                         +d v
  gi|474934695|ref|YP_007688277.1| 249 PkADRV 254
                                       336655 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 2
                   Methyltransf_18  95 lileILeeakeklkkikklilqpnse 120
                                        + +ILe++  +l+ +k+ i + +s+
  gi|474934695|ref|YP_007688277.1| 280 HMHKILERS--ELEGYKEQITSKMSD 303
                                       567788877..455556666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 2301.34
//
Query:       gi|474934696|ref|YP_007688278.1|  [L=266]
Description: diphthine synthase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-24   86.3   0.0    3.3e-24   86.0   0.0    1.1  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.0   0.0   1.9e-28   3.3e-24       2     207 ..       5     220 ..       4     225 .. 0.80

  Alignments for each domain:
  == domain 1  score: 86.0 bits;  conditional E-value: 1.9e-28
                      TP_methylase   2 lylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealra 78 
                                       l+++G+G+ + + +Tv+Al+alk++d ++g+  ++++ +   +++   le+  gk+ e+  +   e   a+++ +++
  gi|474934696|ref|YP_007688278.1|   5 LIFIGLGLSGVDGMTVAALNALKNCDRIFGEF-YTSSVIGVEVKD---LEEAIGKKIEVVYRSEVEEGHAIIDSAKE 77 
                                       89***************************988.666666544433...33333333333333344444444555555 PP

                      TP_methylase  79 gkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl.lpglakeeerel 154
                                           +++++GD ++++t+  l   ++a+++gi+v++  G+s+++a+++ +g+ ++++g ++++  l++   ++++ +
  gi|474934696|ref|YP_007688278.1|  78 C-STAFITAGDTMLATTHVDLR--IQAQYEGIPVRIFNGISIFTAVPTMFGLQPYKFGRAVTIPfLERN-YQPKSPY 150
                                       4.59*****************6..****************************************96663.4789999 PP

                      TP_methylase 155 eallan....gdtlvllkaprk......laelaelL.......kealyddttpvavveragtedervvrg 207
                                       +++++n     +tl+ll+ + +      ++e++e+L       +e l  d t + v+++ag +d+++v g
  gi|474934696|ref|YP_007688278.1| 151 DHIMENkkrgLHTLILLDIRAEelrymtAKEALEWLisgeekwQEGLITDKTLMCVISHAGAPDQKIVAG 220
                                       99999999999******77774566666777777778888877777677778***************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1721.00
//
Query:       gi|474934697|ref|YP_007688279.1|  [L=697]
Description: Acyl-CoA synthetase (NDP forming) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.1e-70  235.7   0.3    7.1e-70  234.9   0.3    1.4  1  ATP-grasp_5    ATP-grasp domain
    1.2e-48  164.4   0.5    2.5e-48  163.4   0.0    1.8  2  Succ_CoA_lig   Succinyl-CoA ligase like flavodoxin domain
    4.6e-20   72.3   0.0    1.2e-19   70.9   0.0    1.7  1  CoA_binding_2  CoA binding domain
    3.4e-11   43.7   1.9    6.7e-11   42.7   0.8    2.1  2  CoA_binding    CoA binding domain
    0.00024   20.7   1.6     0.0005   19.7   1.6    1.6  1  ATP-grasp_2    ATP-grasp domain


Domain annotation for each model (and alignments):
>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.9   0.3     2e-73   7.1e-70       2     219 ..     475     692 ..     474     695 .. 0.97

  Alignments for each domain:
  == domain 1  score: 234.9 bits;  conditional E-value: 2e-73
                       ATP-grasp_5   2 alaegrtlLteaeakelleaygipvvetrlassaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeevr 78 
                                       a aegr  Lteae k++++ayg+pv+    ++s+++av+a+++i ypvv+Ki spdi hKtdvgGv +++kdae+ +
  gi|474934697|ref|YP_007688279.1| 475 AVAEGRYSLTEAEGKKIFQAYGVPVPGEASVTSEKDAVDACNKICYPVVMKIISPDIQHKTDVGGVVVGVKDAEAAK 551
                                       789************************************************************************** PP

                       ATP-grasp_5  79 aaaeeilervkekspeariegvlVqemakrggrElivgvteDpvFGpvilfGlGGtavevlkdvavalpplnstlar 155
                                       +a+++i+++ k+++pear++gv++q+m+   g+E+i+++ +D +FGpv++fGlGG++ve+l++ + +++p+++++  
  gi|474934697|ref|YP_007688279.1| 552 NAFNSIMANCKKNKPEARLDGVSIQQMVS--GQEVILSMVRDVQFGPVVSFGLGGIYVEILREISQKHVPMTEQQLD 626
                                       *****************************..********************************************** PP

                       ATP-grasp_5 156 eliertkaskllkgvrgekkadlaaleellvrlsqLvvdlpeIreldinPllveeeg..vvalDar 219
                                       ++i +tka+kll+g rg + ad++a+++++ r+  + v+ peI+e++inP+lv ++g  + a+D+ 
  gi|474934697|ref|YP_007688279.1| 627 DMITSTKAYKLLSGARGLPVADIDAIKDVIRRIVLISVENPEIKEIEINPVLVGKKGegCYAVDCL 692
                                       ******************77*********************************995545****986 PP

>> Succ_CoA_lig  Succinyl-CoA ligase like flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.4   0.0   6.8e-52   2.5e-48       1     138 []     150     287 ..     150     287 .. 0.99
   2 ?   -3.3   0.1       2.1   7.4e+03       4      23 ..     298     317 ..     296     322 .. 0.81

  Alignments for each domain:
  == domain 1  score: 163.4 bits;  conditional E-value: 6.8e-52
                      Succ_CoA_lig   1 pGkialisqSGalalalldwaasrglgfskvvslGneadvdvadlleylaedpetkvillylEsirdgrkflsaarr 77 
                                       +G+i+++sqSGa+++++ldw  ++g+g++++v++Gn++d+d+ad+++y++edp+tkvi++y+E+i++g++f++a+++
  gi|474934697|ref|YP_007688279.1| 150 AGNISIMSQSGAVGSSILDWFCTSGMGVANFVTFGNKSDLDEADFIRYFSEDPDTKVIGMYIEGISNGERFIKAIEE 226
                                       59*************************************************************************** PP

                      Succ_CoA_lig  78 aarkkpvvvlksGrseagaraaashtgalagsdavvdaafrqaGvlrvdsleelfdaaell 138
                                       +  kkp+vv+ksG++eag++aa+shtg++agsdav + +f++  + r+ +l+e+fda++++
  gi|474934697|ref|YP_007688279.1| 227 MPIKKPIVVFKSGKTEAGSKAASSHTGSIAGSDAVNNVVFKKLNIHRAFDLDEMFDALMAF 287
                                       *********************************************************9876 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.1
                      Succ_CoA_lig   4 ialisqSGalalalldwaas 23 
                                       i++i+  G+l+++ +d+a s
  gi|474934697|ref|YP_007688279.1| 298 IGIITNAGGLGVMSADAAFS 317
                                       89999999999999888765 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.9   0.0   3.4e-23   1.2e-19       2     112 ..       9     131 ..       8     134 .. 0.95

  Alignments for each domain:
  == domain 1  score: 70.9 bits;  conditional E-value: 3.4e-23
                                       -EEEET--S-TTSHHHHHHHHHHH...HT--EEEESSS-SEETTEES----T....T--EEEE-S-HHHHGGGHHHH CS
                     CoA_binding_2   2 tiaVvGasdnpgkfgykvlrylle...hglpvvpVnpkeeeilgekvyaslaedpepvdlvdvftppeatpeivkea 75 
                                         aV+Gas++++k g ++++++ +   +g + +p+npk++ei g k+ya+++e  epvd+++v+++++ + + +k++
  gi|474934697|ref|YP_007688279.1|   9 ALAVIGASADETKLGGMLVKNMIDagfKG-KLYPINPKGGEIMGYKAYANVKEIGEPVDVAVVAVKRDFVIQAIKDC 84 
                                       67**********************88778.9*********************878********************** PP

                                       HHH--SEEEE-TT..........---HHHHHHHHHTT-EEE.ES-HH CS
                     CoA_binding_2  76 lalgakavwlqpg..........sedeeaaelaeeagirvvgdrCil 112
                                       +++g+k v +  +            +ee+++ a++ g+r++g++C +
  gi|474934697|ref|YP_007688279.1|  85 GEAGIKYVSILTAgfkedspegkKLEEELVATAKACGVRIMGPNCFG 131
                                       ********998888*******************************87 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   0.8   1.9e-14   6.7e-11       5      96 .]       9      98 ..       6      98 .. 0.96
   2 ?   -3.4   0.0       4.5   1.6e+04      44      61 ..     640     656 ..     626     664 .. 0.69

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 1.9e-14
                                      EEEEETTTSHHHHHH.HHHHHHHHECEE.EEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHHH CS
                       CoA_binding  5 kviviGagglgiagl.yhfkeklkygik.avfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeavde 81
                                        +viGa+  +++++   +k++++ g+k +++++np+  g e+ g ++y +v+e+ e   vdvav++v  +++ +a+++
  gi|474934697|ref|YP_007688279.1|  9 ALAVIGASADETKLGgMLVKNMIDAGFKgKLYPINPK--GGEIMGYKAYANVKEIGEP--VDVAVVAVKRDFVIQAIKD 83
                                      579**********************************..*******************..******************* PP

                                      HHHTT-SEEEEESST CS
                       CoA_binding 82 lveagikgiviiteg 96
                                      + eagik + i t+g
  gi|474934697|ref|YP_007688279.1| 84 CGEAGIKYVSILTAG 98
                                      *********999976 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 4.5
                                       EETTEEEESCHHHHHHHC CS
                       CoA_binding  44 evlglpvyksvdeleekt 61 
                                         +glpv  ++d +++ +
  gi|474934697|ref|YP_007688279.1| 640 GARGLPVA-DIDAIKDVI 656
                                       55789999.888888765 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   1.6   1.4e-07    0.0005       2     201 ..     483     678 ..     482     679 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.4e-07
                                       E-HHHHHHHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTCCCT..TCEEEESSHHHHHHHHHCCT CS
                       ATP-grasp_2   2 lhEyqakeilakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGRGKa..gGvklvkskeeakeaakell 76 
                                       l E ++k+i++ ygv+vp  + ++s+++a +a +k+   + v+K  +      K+  gGv +  +  ea++ a + +
  gi|474934697|ref|YP_007688279.1| 483 LTEAEGKKIFQAYGVPVPGEASVTSEKDAVDACNKICYPV-VMKI-ISPDIQHKTdvGGVVVGVKDAEAAKNAFNSI 557
                                       78999*******************************9988.7774.5555555555599887555544444444444 PP

                                       TSEEE-TTS-TT-EEE--EEEEE---ECEEEEEEEEEETTTTEEEEEEESSTTS-HHHHHHH-GGGEEEEEEBTTTB CS
                       ATP-grasp_2  77 gkelvtkqtgkeGkkvekvlveealdikkElYlsivlDraskkvvviaSseGGvdiEevaakkPekiikvaidpakg 153
                                        ++ +    +k   + + v +++++   +E+ ls+v D +     v+    GG+ +E + + + +++  ++ +    
  gi|474934697|ref|YP_007688279.1| 558 MANCK---KNKPEARLDGVSIQQMVS-GQEVILSMVRDVQF--GPVVSFGLGGIYVEILREISQKHVPMTEQQLDDM 628
                                       44555...456667899999988876.68999**9977655..45566679*****988888877777776666666 PP

                                       --HHHHHHHH.HHCT--CHHHHHHHHHHHHHHHHHHHT.TEEEEEEEEEE CS
                       ATP-grasp_2 154 lkeeqareia.kklglekelvkkaakiikklyklfvel.datlvEiNPLv 201
                                       +++++a +++  + gl+   ++ ++++i +++ + ve  + + +EiNP+ 
  gi|474934697|ref|YP_007688279.1| 629 ITSTKAYKLLsGARGLPVADIDAIKDVIRRIVLISVENpEIKEIEINPVL 678
                                       777666665515779*****************9988754899******75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (697 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.48
# Mc/sec: 4323.01
//
Query:       gi|474934698|ref|YP_007688280.1|  [L=225]
Description: hypothetical protein TALC_01131 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0063   16.6   0.9     0.0089   16.1   0.2    1.6  2  DUF45     Protein of unknown function DUF45


Domain annotation for each model (and alignments):
>> DUF45  Protein of unknown function DUF45
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0      0.35   6.2e+03     126     143 ..      20      37 ..       4      40 .. 0.70
   2 !   16.1   0.2     5e-07    0.0089     161     206 ..     170     220 ..     167     221 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.35
                             DUF45 126 klgvkprsvsikdmktrW 143
                                        ++v+++ vs+kd k rW
  gi|474934698|ref|YP_007688280.1|  20 YTDVNAEFVSFKDFKVRW 37 
                                       456688889999999999 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 5e-07
                             DUF45 161 appevidYVvvHElaHlle......knHskrFwalvekllPdwkeakkeLkr 206
                                       +p+ v+dY + HEl+H+l       k Hsk++ +++e+ +P + +a + L++
  gi|474934698|ref|YP_007688280.1| 170 VPEYVLDYCLYHELCHILLgfdpegKMHSKKY-SEIESRYPMMADALQYLRE 220
                                       699*************9843333337899986.5678888888888887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1619.26
//
Query:       gi|474934699|ref|YP_007688281.1|  [L=176]
Description: isochorismatase family protein Amidases nicotinamidase -like protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-22   80.5   0.0    2.7e-22   79.8   0.0    1.3  1  Isochorismatase  Isochorismatase family


Domain annotation for each model (and alignments):
>> Isochorismatase  Isochorismatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.8   0.0   1.5e-26   2.7e-22       2     145 ..      12     142 ..      11     156 .. 0.92

  Alignments for each domain:
  == domain 1  score: 79.8 bits;  conditional E-value: 1.5e-26
                   Isochorismatase   2 alvviDmqndfveegvkeseeisavveninkllkaarkagipviftrdvheleevkgdlderkaaphfkpgttgael 78 
                                       a+vviD q++f+ +  + +e+++a+v+ +n++ + +rkag pvif+++  +               +  +g+ g e+
  gi|474934699|ref|YP_007688281.1|  12 AFVVIDAQRKFFLDRPDWKERCAAAVKDVNEFSAMFRKAGNPVIFVKFKGP-------------TCRPYEGEDGDEF 75 
                                       89*********98999999********************************.............666678******* PP

                   Isochorismatase  79 vpelaplegdvvvdKtrfsafagtdldeiLkelgiktivlaGiatdvCVeatardaldlGyevvvvs 145
                                       ++ ++ +egd+ v+K+++++f +t+l+e++k++g +  v aG  +++CV +t  +a+d+  + ++++
  gi|474934699|ref|YP_007688281.1|  76 FEGIETREGDIYVEKENMNSFLDTNLEEVIKSNGCDIAVMAGTVAQYCVISTYFAAFDHKITSYLAQ 142
                                       ***********************************************************88888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1203.46
//
Query:       gi|474934700|ref|YP_007688282.1|  [L=276]
Description: hypothetical protein TALC_01133 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-13   50.7   3.6    3.2e-13   50.2   3.6    1.2  1  CbiZ      Adenosylcobinamide amidohydrolase
  ------ inclusion threshold ------
      0.012   15.7   0.6       0.02   14.9   0.6    1.3  1  DUF2561   Protein of unknown function (DUF2561)


Domain annotation for each model (and alignments):
>> CbiZ  Adenosylcobinamide amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   3.6   3.5e-17   3.2e-13      77     192 .]      72     185 ..      60     185 .. 0.86

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 3.5e-17
                              CbiZ  77 dlevtavvTaGvesnavragdedeeaekpGTINiivlinaaLtdaalvralitatEAKtaalqdlgvrsrysegatG 153
                                        ++v+av+ a + +  vrag++   + + G I ++++i+a+ +     ra++tatEA ta++++lg+ ++ +++ +G
  gi|474934700|ref|YP_007688282.1|  72 TTRVAAVAVADIGRGHVRAGER--PDTSGGGISLVLMIDADVPVLGTSRAMVTATEAITAVIRELGIGNNGRGTSSG 146
                                       5678888888887778899996..88999**************************************9666655777 PP

                              CbiZ 154 TgTDaiavaadkegeeeltyaGkhtklGeliaraVyeAv 192
                                            ++v+++ +++ +l  +Gkh+klGeli+r++ eAv
  gi|474934700|ref|YP_007688282.1| 147 MVLQDMTVVCRRDSKLRLLGTGKHSKLGELIGRTTIEAV 185
                                       77777788888899999********************98 PP

>> DUF2561  Protein of unknown function (DUF2561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.6   2.2e-06      0.02      37      97 ..      71     127 ..      63     148 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.2e-06
                           DUF2561  37 GvsvaatvaLvdLgrGfaksaedshttwvLyavivvsa.lvivgavPlLLrarrvaeaePaa 97 
                                       G +  a+va++d+grG+ ++ e ++t+       ++s  l+i + vP+L  +r + +a  a+
  gi|474934700|ref|YP_007688282.1|  71 GTTRVAAVAVADIGRGHVRAGERPDTS-----GGGISLvLMIDADVPVLGTSRAMVTATEAI 127
                                       5666799*******************9.....3456640566677****9999988776544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       237  (0.0132188); expected 358.6 (0.02)
Passed bias filter:                      190  (0.0105974); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1966.69
//
Query:       gi|474934701|ref|YP_007688283.1|  [L=346]
Description: hypothetical protein TALC_01134 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-37  128.2   0.1    5.8e-37  127.7   0.1    1.2  1  CbiZ      Adenosylcobinamide amidohydrolase


Domain annotation for each model (and alignments):
>> CbiZ  Adenosylcobinamide amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.7   0.1   3.2e-41   5.8e-37       4     168 ..       5     185 ..       3     194 .. 0.92

  Alignments for each domain:
  == domain 1  score: 127.7 bits;  conditional E-value: 3.2e-41
                              CbiZ   4 eprrvlssavlngGlre.lravlnhqvpegyered........peeyleeyleelglppektvgllTaadmenaaia 71 
                                       ++ rvls+  +ngG+++  +av+n+++  g  + +          ey++e++++lg++p+++v+  Taa+mena++ 
  gi|474934701|ref|YP_007688283.1|   5 DKFRVLSTGYFNGGFTDsPKAVINMSSLGGNLEYQmmvgnrsvVGEYTAECFRKLGFDPADVVAEGTAANMENASVG 81 
                                       6789*********************98887777776778777768999999************************** PP

                              CbiZ  72 eeefedlevtavvTaGvesnavragd......edeeaekpGTINiivlinaaLtdaalvralitatEAKtaalqdlg 142
                                       + +++ + v++++TaG+++n+++agd      ++   ek GTI +i+ ++a+L+d+a+++++ ++++AK+ ++q+ +
  gi|474934701|ref|YP_007688283.1|  82 TLKCGSVPVSVAITAGIRGNGGCAGDpasfdeAKRYMEKNGTIVMIMSVEAELSDSAMLQLMNIMVQAKSCVIQEFQ 158
                                       ******************************995568899************************************** PP

                              CbiZ 143 vrsryseg.atGTgTDaiavaadkege 168
                                       ++s ys++ atG+gTD+ia++++k  +
  gi|474934701|ref|YP_007688283.1| 159 AKSLYSHRiATGSGTDQIAIISRKGAT 185
                                       **********************95444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2533.45
//
Query:       gi|474934702|ref|YP_007688284.1|  [L=464]
Description: hypothetical protein TALC_01135 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.52   10.5   7.2        1.4    9.1   7.2    1.7  1  Dockerin_1  Dockerin type I domain
        1.2    8.7   3.7       0.94    9.1   0.1    2.7  2  EF-hand_5   EF hand


Domain annotation for each model (and alignments):
>> Dockerin_1  Dockerin type I domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   7.2   0.00016       1.4       7      56 ..      54     102 ..      49     104 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00016
                                       SSC-SHHHHHHHHHHCTSSEBTTSCCCHGGGSTT-SSCESHHHHHHHHHH CS
                        Dockerin_1   7 DgkVnalDalliinylnqregqssssngkaaDvNgDGrvnalDallviny 56 
                                       D  +++ D+ +i++ +  +++  +  +   aD N+DG+v+a D +lv n 
  gi|474934702|ref|YP_007688284.1|  54 DADIDSDDLDVIQKIID-QKEGYTLAKYGLADANRDGKVTADDKTLVQNI 102
                                       67789999999999999.6777777777789************9999986 PP

>> EF-hand_5  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1    0.0001      0.94       8      19 ..      83      94 ..      82      95 .. 0.89
   2 ?   -1.7   0.6      0.28   2.5e+03      10      15 ..     439     444 ..     439     444 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0001
                                      H-SS-SSCE-HH CS
                         EF-hand_5  8 iDlNgDGkIske 19
                                      +D+N+DGk++++
  gi|474934702|ref|YP_007688284.1| 83 ADANRDGKVTAD 94
                                      7********986 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.28
                                       SS-SSC CS
                         EF-hand_5  10 lNgDGk 15 
                                       +N+DGk
  gi|474934702|ref|YP_007688284.1| 439 KNKDGK 444
                                       7****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.68u 0.33s 00:00:01.01 Elapsed: 00:00:00.55
# Mc/sec: 2530.42
//
Query:       gi|474934703|ref|YP_007688285.1|  [L=358]
Description: ABC-type Fe3+-siderophore transport system, permease component [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.1e-78  262.2  27.1    6.5e-78  261.9  27.1    1.0  1  FecCD       FecCD transport family
  ------ inclusion threshold ------
        1.8    7.4   2.8        3.2    6.5   2.8    1.4  1  VSP         Giardia variant-specific surface protein


Domain annotation for each model (and alignments):
>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  261.9  27.1   7.3e-82   6.5e-78       2     312 .]      31     350 ..      30     350 .. 0.97

  Alignments for each domain:
  == domain 1  score: 261.9 bits;  conditional E-value: 7.3e-82
                             FecCD   2 lllllllslllgavkispsevfeallgka..........dsleaeivlelrlprvlaallvGaaLavaGallQtvtr 68 
                                       ++ + +ls+++ ++ +s+ e+f ++ ++           + +e+ iv+e  +pr++a + +Ga+L++ Ga++Q+v++
  gi|474934703|ref|YP_007688285.1|  31 CITFAVLSMAINQYGLSLGEIFGIIKDHVhgnintddyrEYIEDLIVFESYIPRAIACITAGAILGAGGAVMQSVIK 107
                                       677889999*************99887778888888877777888******************************** PP

                             FecCD  69 NpLadPsilGissgaalgavlallll.lgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsall 144
                                       NpLad++++G+s+ga lg+ ++++l+    ++ f+l++ afl++l+ +++v++++   +++++ +++ +Gia+s+l+
  gi|474934703|ref|YP_007688285.1| 108 NPLADSYTMGLSAGALLGVSCFVILGiGVVSGNFGLMANAFLFSLIPCGVVIVFS-VFRNTTSNMIVFVGIAISFLF 183
                                       *************************98888999**********************.99******************* PP

                             FecCD 145 saltsllllllneealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervr 221
                                       sa+t+++ +++ +e+le+++ w +Gsl++ + + +l+l++ ++++++ ll+la k+d+ a gd+ +k+lGv+  r+r
  gi|474934703|ref|YP_007688285.1| 184 SAITTFINYTAAPEQLEEVYKWSIGSLGRLDPDCILFLIPSTIIMIVSLLFLADKIDITAAGDKYSKTLGVDAPRIR 260
                                       ***************************************************************************** PP

                             FecCD 222 llllllvalltavavalvGpigFvGLivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivt 298
                                       ++++l+v+l t+++v++vG+igF+GL++P+i+r+++g++ ++l+p+s ++Ga+lll+ad++ar+l+ p   pvg+vt
  gi|474934703|ref|YP_007688285.1| 261 IVAILIVSLFTSITVCFVGTIGFIGLVIPNIVRIYAGSNSKTLIPISSIAGATLLLAADCVARMLI-PGGFPVGFVT 336
                                       *****************************************************************9.8899****** PP

                             FecCD 299 aliGapffiylllr 312
                                       +l+G+p+++++l+r
  gi|474934703|ref|YP_007688285.1| 337 SLVGGPMMLFILMR 350
                                       ************97 PP

>> VSP  Giardia variant-specific surface protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   2.8   0.00036       3.2     334     388 ..      87     145 ..      80     151 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.00036
                               VSP 334 dclscappssdkGsvlcylikds.gstnksGlstGaiaGisvavvv...vvgGlvGflc 388
                                        c++    ++  G+v+  +ik+    +   Gls+Ga+ G+s  v++   vv+G  G++ 
  gi|474934703|ref|YP_007688285.1|  87 ACITAGAILGAGGAVMQSVIKNPlADSYTMGLSAGALLGVSCFVILgigVVSGNFGLMA 145
                                       5777788889999********996688899***********999874456777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       838  (0.0467399); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 2426.37
//
Query:       gi|474934704|ref|YP_007688286.1|  [L=363]
Description: ABC-type Fe3+-siderophore transport system, permease component [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-83  279.7  40.7      3e-83  279.4  40.7    1.0  1  FecCD     FecCD transport family
    2.2e-05   24.1  35.1    8.3e-05   22.2  35.3    2.0  1  ABC-3     ABC 3 transport family


Domain annotation for each model (and alignments):
>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  279.4  40.7   3.4e-87     3e-83       2     312 .]      33     357 ..      30     357 .. 0.97

  Alignments for each domain:
  == domain 1  score: 279.4 bits;  conditional E-value: 3.4e-87
                             FecCD   2 lllllllslllgavkispsevfeallgka.........dsleaeivlelrlprvlaallvGaaLavaGallQtvtrN 69 
                                       +++ll lsl++g+ +is+ e +++l+ k          + l+  iv e+rlp ++ a+++Ga+LavaGa +Q+v++N
  gi|474934704|ref|YP_007688286.1|  33 VIILLGLSLMIGDRDISFFEAYRLLFMKItggepvdthEFLDLYIVAEVRLPMAVFAIIAGASLAVAGAAMQSVMNN 109
                                       589999********************999999887554444455********************************* PP

                             FecCD  70 pLadPsilGissgaalgavlallll.....lgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavs 141
                                       pLad ++ Gissga+lg++++++l+      +s  +f++++ af+++l+ ++++l+++ +r ++sp++liLaGiavs
  gi|474934704|ref|YP_007688286.1| 110 PLADAYTTGISSGASLGVAVSMVLGislvtNTSVAQFGTITNAFIFSLIPMMMILAVS-SRMNTSPASLILAGIAVS 185
                                       ****************************9999999***********************.****************** PP

                             FecCD 142 allsaltsllllllneealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnve 218
                                       ++l+a+tsll+l+++ ++++++++w +Gs+s + w++v +++ ++++++++++l+a+k++++++g++ Ak+lG+++e
  gi|474934704|ref|YP_007688286.1| 186 YFLNAFTSLLMLVADGQTMQAVYNWQIGSISAIGWTEVPFMATVSIAGMIFMILCANKFNIMTMGESSAKALGLDIE 262
                                       ***************************************************************************** PP

                             FecCD 219 rvrllllllvalltavavalvGpigFvGLivPhiarllvgadhrkllplsallGallllladllarllls.ptelpv 294
                                        +rl+ +++++l++a++++++G+igFvGL+ Ph++r ++++d+r+++p+sa+lGa+++l ++l+   +      +pv
  gi|474934704|ref|YP_007688286.1| 263 SFRLISMIIISLMVASVISFTGIIGFVGLVCPHMIRSVIHSDNRYVMPASAMLGAVMMLSCQLVTVAISPdTLSIPV 339
                                       ********************************************************************997788*** PP

                             FecCD 295 givtaliGapffiylllr 312
                                       g++++++Gap+f+yl++r
  gi|474934704|ref|YP_007688286.1| 340 GVILSFVGAPIFLYLIVR 357
                                       ****************97 PP

>> ABC-3  ABC 3 transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2  35.3   9.2e-09   8.3e-05      32     235 ..     113     330 ..      82     357 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 9.2e-09
                             ABC-3  32 sllgdalsHaalpGvalayllgvn...........lllgailvgliaavalellkrktklkedtai..givlsvfl. 94 
                                            ++s  a  Gva+ ++lg++            ++ a++++li  +++ +++++  ++  ++i  gi +s fl 
  gi|474934704|ref|YP_007688286.1| 113 DAYTTGISSGASLGVAVSMVLGISlvtntsvaqfgTITNAFIFSLIPMMMILAVSSRMNTSPASLIlaGIAVSYFLn 189
                                       455667888888999999999999999999999999999***************99998887655444*******95 PP

                             ABC-3  95 alglvlvslikk.skvdldsyLfGniltisqedliliaiieavvllllllfwkelllitfdeelAkveglsvkllkl 170
                                       a+  +l+  +++ + + + ++  G+i +i  +++  +a +++  ++ ++l   ++ ++t+ e+ Ak+ gl ++ ++l
  gi|474934704|ref|YP_007688286.1| 190 AFTSLLMLVADGqTMQAVYNWQIGSISAIGWTEVPFMATVSIAGMIFMILCANKFNIMTMGESSAKALGLDIESFRL 266
                                       55544444444449999************************************************************ PP

                             ABC-3 171 lllalialavvvalqavGviLvialliiPaatArrltrslesllivAillglvsvvaGlllSyyl 235
                                       + +++i+l v+ ++ + G+i  +  l+ P ++   + ++ + ++  +++lg+v +++  l+ + +
  gi|474934704|ref|YP_007688286.1| 267 ISMIIISLMVASVISFTGIIGFVG-LVCPHMIRSVIHSDNRYVMPASAMLGAVMMLSCQLVTVAI 330
                                       *******************98887.579***********************99998876665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       944  (0.0526521); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2503.25
//
Query:       gi|474934705|ref|YP_007688287.1|  [L=579]
Description: ABC-type multidrug transport system, ATPase and permease components [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-29  102.9   0.0    3.5e-29  102.1   0.0    1.4  1  ABC_tran      ABC transporter
    3.5e-23   82.6  10.4    4.7e-23   82.2  10.4    1.2  1  ABC_membrane  ABC transporter transmembrane region
    2.5e-06   27.1   0.0    9.2e-06   25.3   0.0    1.7  1  SMC_N         RecF/RecN/SMC N terminal domain
     0.0015   19.0   0.1     0.0033   17.8   0.1    1.7  1  AAA_16        AAA ATPase domain
     0.0039   16.9   0.1     0.0077   16.0   0.1    1.4  1  AAA_30        AAA domain
  ------ inclusion threshold ------
      0.011   14.9   0.4      0.019   14.1   0.0    1.5  2  T2SSE         Type II/IV secretion system protein
      0.011   16.0   0.0       0.02   15.1   0.0    1.5  1  AAA_22        AAA domain
      0.012   15.5   0.0      0.026   14.4   0.0    1.5  1  RsgA_GTPase   RsgA GTPase
      0.015   15.0   0.1      0.032   14.0   0.1    1.5  1  AAA_29        P-loop containing region of AAA domain
      0.023   14.6   0.2      0.045   13.7   0.2    1.5  1  NTPase_1      NTPase
      0.024   13.9   0.0      0.052   12.8   0.0    1.5  1  Zeta_toxin    Zeta toxin
      0.043   13.7   0.6      0.071   13.0   0.6    1.3  1  RIFIN         Rifin
       0.08   10.4   0.1       0.12    9.9   0.1    1.2  1  DUF3584       Protein of unknown function (DUF3584)
       0.12   12.0   0.0       0.27   10.8   0.0    1.5  1  AAA_25        AAA domain
       0.16   11.5   0.1        0.3   10.6   0.1    1.4  1  AAA_7         P-loop containing dynein motor region
       0.17   12.4   0.0       0.34   11.4   0.0    1.4  1  AAA_23        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.1   0.0   3.1e-32   3.5e-29       1     136 [.     354     501 ..     354     502 .. 0.92

  Alignments for each domain:
  == domain 1  score: 102.1 bits;  conditional E-value: 3.1e-32
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l+ +s+++++ge+va++G++G+GK+tL++l+ +l++ t+G+++++g d+k+ ++  lr+ ig+ +q p lf+++ + 
  gi|474934705|ref|YP_007688287.1| 354 LEGISFQVRRGETVAVTGQTGTGKTTLMNLVPRLYDATSGSVKVNGVDVKDYDIGYLRSMIGYATQRPMLFSGTLAF 430
                                       6789**********************************************************************555 PP

                                       HH............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       +                ++++ + + l+++e  +tvv++++++LSgGqkqrv++ara++kkp+++++D+ +
  gi|474934705|ref|YP_007688287.1| 431 NIgygkencteeemLHASRVACLNEYLEQHEGLETVVQQRGANLSGGQKQRVSIARAVCKKPEIYIFDDTF 501
                                       55999988776665555558999999999999************************************975 PP

>> ABC_membrane  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.2  10.4   4.2e-26   4.7e-23       6     272 ..      20     281 ..      14     292 .. 0.91

  Alignments for each domain:
  == domain 1  score: 82.2 bits;  conditional E-value: 4.2e-26
                                       HHHHHHHHHHHHHHHHHHHHHHHHHSSTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane   6 llailagvlsplfplvlgrildtlldkgdpetealnvysllllllglaqfilallqsyllnvtgerlskrlrrklfk 82 
                                       ++  l+ + ++ +p ++ +i+  l+  +d+++  +    ++++++ ++++i++++   +  +++    k+lrr+ f+
  gi|474934705|ref|YP_007688287.1|  20 VFVSLQVWFDLEIPGYMTKITVLLNNGSDTSS--IMNEGIAMIGCSIGSVICSIAAGGVAAYVAAEFAKALRREQFR 94 
                                       66667788888899999999999999999999..9999*************************************** PP

                                       HHHCSTHHHHHHSCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane  83 kilrqpmsffdtnsvGellsrltndvsklrdglgeklglffqslltfvgglivmfylgwkltlvllailpliilvsa 159
                                       k+ + + +   + +  +l++r tndv +++++++++  l++   +++ ++l+ + + +w  t v+++ l  i++v++
  gi|474934705|ref|YP_007688287.1|  95 KVQSFSPQEMGRFDIYSLITRSTNDVIQIQQAVASTSQLVVKVPVMIYIALGKVATGSWEWTEVTIVGLAAIVVVQI 171
                                       ****9999999999999************************************************************ PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane 160 viakilkklkkkeqkavakassvaeEslsgirtVkafgreeyflekfekaleeakkagikkaianglligitqllgl 236
                                       ++   + +  ++ qk+++ +++ ++E l+g+r+++af++eey ++k++ a++e  ++++ + ++ +++ +++ ++++
  gi|474934705|ref|YP_007688287.1| 172 FMLCYVIPRYRRVQKYTDGMNRTVREGLTGVRVIRAFNAEEYQNSKIDGANTELTENNLYASRLLAFTRPFNGVVQN 248
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHH CS
                      ABC_membrane 237 lsyalalwfGttlvisgelsvgdlvvflslfailfg 272
                                        ++++++++G++ +++ + s++d   ++++++++++
  gi|474934705|ref|YP_007688287.1| 249 MLTVAIYVLGAQIILA-AASPDD--GLTTFSNMVVF 281
                                       **************98.555555..44444443222 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   8.2e-09   9.2e-06     102     212 ..     386     545 ..     183     549 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 8.2e-09
                                       EEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT........................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................................... RF
                             SMC_N 102 rvkrkgeseykingkevtkkevsellesagiske........................................... 135
                                       r++   + ++k+ng +v+  ++  l ++ g   +                                           
  gi|474934705|ref|YP_007688287.1| 386 RLYDATSGSVKVNGVDVKDYDIGYLRSMIGYATQrpmlfsgtlafnigygkencteeemlhasrvaclneyleqheg 462
                                       33334444455555555555555555555554448999999999999999999999999999999999999999999 PP

                                       ..........CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHC CS
                                       ..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 ..........lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreeml 202
                                                 +LSgG+k+ v++a       +k+  +y++D+  +aLD+k  + v + l+++++ +  +++s r +++
  gi|474934705|ref|YP_007688287.1| 463 letvvqqrgaNLSGGQKQRVSIAR----AVCKKPEIYIFDDTFSALDFKTDALVRRNLDRETSGSTTLIVSQRIGTI 535
                                       9999999999********998864....4678888****************************************** PP

                                       CC-SCEEEEE CS
                                       xxxxxxxxxx RF
                             SMC_N 203 ekadklvgvt 212
                                       ++ad++v ++
  gi|474934705|ref|YP_007688287.1| 536 RNADRIVVIS 545
                                       *****99876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   2.9e-06    0.0033      19      53 ..     361     393 ..     352     528 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.9e-06
                            AAA_16  19 vrsgrpelvllsGesGvGKsslvrellralekdgg 53 
                                       vr+g  e v ++G+ G+GK++l++ ++r + ++ g
  gi|474934705|ref|YP_007688287.1| 361 VRRG--ETVAVTGQTGTGKTTLMNLVPRLYDATSG 393
                                       5555..78*******************86666533 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   6.8e-06    0.0077      19      50 ..     365     396 ..     359     422 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6.8e-06
                            AAA_30  19 rvavltGpAGtGKttalkalreaweaaggrvi 50 
                                        ++++tG  GtGKtt+++ + ++++a  g+v 
  gi|474934705|ref|YP_007688287.1| 365 ETVAVTGQTGTGKTTLMNLVPRLYDATSGSVK 396
                                       47899******************999955543 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.7e-05     0.019     119     149 ..     354     384 ..     332     396 .. 0.82
   2 ?   -3.7   0.1       4.2   4.7e+03     140     165 ..     521     546 ..     520     549 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.7e-05
                             T2SSE 119 aevlrkavrerglilvsGgTgsGKttllyal 149
                                        e ++  vr+  ++ v+G Tg+GKttl++ +
  gi|474934705|ref|YP_007688287.1| 354 LEGISFQVRRGETVAVTGQTGTGKTTLMNLV 384
                                       5566778899999**************9975 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 4.2
                             T2SSE 140 sGKttll.yallkeinksderivtvED 165
                                       sG ttl+    + +i +  +riv++ D
  gi|474934705|ref|YP_007688287.1| 521 SGSTTLIvSQRIGTIRNA-DRIVVISD 546
                                       788887756778888888.99999988 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   1.8e-05      0.02       7      31 ..     366     390 ..     361     458 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.8e-05
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqlde 31 
                                        ++vtG++GtGKTtl++ + + +d+
  gi|474934705|ref|YP_007688287.1| 366 TVAVTGQTGTGKTTLMNLVPRLYDA 390
                                       578**************99998864 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.3e-05     0.026      89     120 ..     353     385 ..     341     400 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.3e-05
                                       THHHHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase  89 gleelkellkd.ktsvlvGqSGvGKStLinall 120
                                       +le ++ +++  +t+++ Gq+G GK+tL+n + 
  gi|474934705|ref|YP_007688287.1| 353 TLEGISFQVRRgETVAVTGQTGTGKTTLMNLVP 385
                                       5667777777669*****************764 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   2.8e-05     0.032      15      39 ..     357     381 ..     352     398 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.8e-05
                            AAA_29  15 htieidlkgatlltGpsGsGKSTll 39 
                                        ++++++ +++ +tG++G+GK+Tl+
  gi|474934705|ref|YP_007688287.1| 357 ISFQVRRGETVAVTGQTGTGKTTLM 381
                                       5667775669**************8 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2     4e-05     0.045       2      37 ..     367     404 ..     366     416 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4e-05
                                       EEEE--TTSSHHHHHHHHHHHH.....GGGEEEEEEEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkss..gvkvgGfytee 37 
                                       v++TG+ G+GKtTl++ v +l +     vkv+G+ +++
  gi|474934705|ref|YP_007688287.1| 367 VAVTGQTGTGKTTLMNLVPRLYDATsgSVKVNGVDVKD 404
                                       89************999977765432268888887665 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.6e-05     0.052      16      57 ..     364     405 ..     351     414 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.6e-05
                        Zeta_toxin  16 PklillgGqpGAGKselaellkdelerqgnvvrldpDdlRel 57 
                                          + + Gq+G GK++l++l+ +  +++++ v++++ d++ +
  gi|474934705|ref|YP_007688287.1| 364 GETVAVTGQTGTGKTTLMNLVPRLYDATSGSVKVNGVDVKDY 405
                                       5678899***************************99888876 PP

>> RIFIN  Rifin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.6   6.3e-05     0.071     253     309 ..     132     187 ..      52     193 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.3e-05
                             RIFIN 253 aaaeataeaekaetaaveattaslqtaiiasivaivvIvLimvIIYLiLRYrRKkKm 309
                                       +   +   ++   + +v++ + ++++  i+   aivv+ + m   Y+i RYrR +K 
  gi|474934705|ref|YP_007688287.1| 132 QLVVKVPVMIYIALGKVATGSWEWTEVTIVGLAAIVVVQIFM-LCYVIPRYRRVQKY 187
                                       333444555666778888889999999999999987766555.78********9986 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00011      0.12       6      44 ..     353     391 ..     350     421 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00011
                           DUF3584   6 flkGrvaeldldghtnieGtNaaGKTtLlrLiPlFYGee 44 
                                        l G   +++  + + + G  + GKTtL+ L+P  Y ++
  gi|474934705|ref|YP_007688287.1| 353 TLEGISFQVRRGETVAVTGQTGTGKTTLMNLVPRLYDAT 391
                                       5666666677778899*****************999665 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00024      0.27      30      49 ..     361     380 ..     336     383 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00024
                            AAA_25  30 lpagelallaGapgtGKttl 49 
                                       +++ge+++++G++gtGKttl
  gi|474934705|ref|YP_007688287.1| 361 VRRGETVAVTGQTGTGKTTL 380
                                       579****************9 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00027       0.3      30      53 ..     361     384 ..     356     398 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00027
                             AAA_7  30 lknkkpvllvGptGtGKtviikdl 53 
                                       ++++  v ++G+tGtGKt++++ +
  gi|474934705|ref|YP_007688287.1| 361 VRRGETVAVTGQTGTGKTTLMNLV 384
                                       678899*************99865 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0003      0.34      21      37 ..     366     382 ..     350     404 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0003
                            AAA_23  21 ltlItGpNGaGKTTild 37 
                                        +++tG++G+GKTT+++
  gi|474934705|ref|YP_007688287.1| 366 TVAVTGQTGTGKTTLMN 382
                                       5689***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (579 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       824  (0.0459591); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.68u 0.34s 00:00:01.02 Elapsed: 00:00:00.48
# Mc/sec: 3594.40
//
Query:       gi|474934706|ref|YP_007688288.1|  [L=592]
Description: ABC-type multidrug transport system, ATPase and permease components [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-47  161.1  13.3    5.6e-47  160.7  13.3    1.1  1  ABC_membrane  ABC transporter transmembrane region
    4.1e-33  114.8   0.0    6.5e-33  114.2   0.0    1.3  1  ABC_tran      ABC transporter
    0.00017   21.9   0.0     0.0009   19.5   0.0    2.1  1  AAA_22        AAA domain
    0.00061   19.7   0.0     0.0012   18.8   0.0    1.4  1  RsgA_GTPase   RsgA GTPase
    0.00086   19.9   0.0     0.0017   18.9   0.0    1.4  1  AAA_23        AAA domain
     0.0016   17.9   0.5       0.14   11.6   0.5    2.3  1  SMC_N         RecF/RecN/SMC N terminal domain
     0.0035   16.2   1.8      0.064   12.0   0.5    2.2  2  ABC_ATPase    Predicted ATPase of the ABC class
     0.0036   17.4   0.0      0.012   15.7   0.0    1.9  2  MMR_HSR1      50S ribosome-binding GTPase
     0.0036   17.0   0.3      0.013   15.2   0.0    2.0  2  AAA_29        P-loop containing region of AAA domain
     0.0048   16.6   0.1      0.016   14.9   0.1    2.0  1  AAA_30        AAA domain
     0.0056   17.1   0.0      0.011   16.1   0.0    1.6  1  AAA_16        AAA ATPase domain
  ------ inclusion threshold ------
      0.014   15.9   0.0      0.055   14.0   0.0    2.0  2  AAA_18        AAA domain
      0.022   14.8   0.0      0.057   13.4   0.0    1.6  1  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
      0.022   13.8   0.0      0.045   12.8   0.0    1.5  1  T2SSE         Type II/IV secretion system protein
      0.041   13.5   0.0      0.093   12.3   0.0    1.6  1  cobW          CobW/HypB/UreG, nucleotide-binding domain
      0.058   13.3   0.1       0.17   11.8   0.0    1.8  2  NTPase_1      NTPase
      0.066   13.5   0.0       0.13   12.5   0.0    1.5  1  AAA_28        AAA domain
      0.069   12.4   0.0       0.14   11.4   0.0    1.4  1  Zeta_toxin    Zeta toxin
      0.089   12.5   0.0       0.18   11.5   0.0    1.5  1  AAA_24        AAA domain
      0.094   12.9   0.0        0.2   11.8   0.0    1.6  1  AAA_33        AAA domain
       0.11   11.9   0.0       0.25   10.8   0.0    1.5  1  AAA_7         P-loop containing dynein motor region
       0.14   12.0   0.0       0.37   10.6   0.0    1.7  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
       0.16   12.0   0.1       0.43   10.6   0.0    1.6  1  DUF87         Helicase HerA, central domain


Domain annotation for each model (and alignments):
>> ABC_membrane  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.7  13.3   7.2e-50   5.6e-47       4     274 .]      35     307 ..      32     307 .. 0.97

  Alignments for each domain:
  == domain 1  score: 160.7 bits;  conditional E-value: 7.2e-50
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHSS..TCCHH..HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane   4 iillailagvlsplfplvlgrildtlldk..gdpet..ealnvysllllllglaqfilallqsyllnvtgerlskrl 76 
                                       +  l++++ +ls+l p++l+ ++d + +   ++       +++++++l++++l++++++++ +y++  +++r     
  gi|474934706|ref|YP_007688288.1|  35 AAALSAISSFLSLLGPYFLSDMTDLIQEGltSE--MdyGGVKHLAIILASVYLISGLINFGENYMMATVSQRSAQMF 109
                                       567899********************9975444..24589************************************* PP

                                       HHHHHHHHHCSTHHHHHHSCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHH CS
                      ABC_membrane  77 rrklfkkilrqpmsffdtnsvGellsrltndvsklrdglgeklglffqslltfvgglivmfylgwkltlvllailpl 153
                                       r ++ +ki r p+ +fd+ s G+++sr+tndv+ l +++++ +g +++s++++ g++++m++++  ltl+ lai++ 
  gi|474934706|ref|YP_007688288.1| 110 RYDISRKINRIPLHYFDKSSKGDIMSRVTNDVDVLGTSMNQCIGSLVTSITVLSGTFVLMLIMNIPLTLLSLAIAVT 186
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane 154 iilvsaviakilkklkkkeqkavakassvaeEslsgirtVkafgreeyflekfekaleeakkagikkaianglligi 230
                                        +  ++ +ak+++k+++ +qk+++ ++ ++eE+ +g+ +V +++++++  e+f+  +ee +++++k+ ++ g+++ +
  gi|474934706|ref|YP_007688288.1| 187 GFAAIKTVAKKTQKYFRSQQKNLGAMNGLIEEQYTGHAVVSLYAGQREAMERFTAINEELRHSAFKSSFLGGISFHV 263
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane 231 tqllgllsyalalwfGttlvisgelsvgdlvvflslfailfgal 274
                                       + l++++ y+l+++ G++l ++g +s+g +++f+ +  +++ga+
  gi|474934706|ref|YP_007688288.1| 264 SGLISNAGYVLICVTGAALYLDGRISFGVIIAFMIYVKLFTGAF 307
                                       ***************************************99986 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.2   0.0   8.3e-36   6.5e-33       2     137 .]     369     516 ..     368     516 .. 0.94

  Alignments for each domain:
  == domain 1  score: 114.2 bits;  conditional E-value: 8.3e-36
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       ++ s ++k+g++vaivG++GaGK+tL++ll++ ++ ++G+il+dg+++++ ++e++r+ +g++ q++ +f+++ vre
  gi|474934706|ref|YP_007688288.1| 369 HDFSADIKPGQMVAIVGPTGAGKTTLINLLMRFYEVDSGDILIDGRSVRSMSREQVRRMFGMVLQDSWVFEGT-VRE 444
                                       68899*******************************************************************9.*** PP

                                       H.......HHHTCHHHHHHHSTTGG......TTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       x.......xxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.......esdeeiekalsklglke......lkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       n        sd++++++ + +gl++         +++ +s++s+S Gq+q +a+ara++++p++++lDE+t+
  gi|474934706|ref|YP_007688288.1| 445 NivfnrenVSDSKLDEVCQAVGLNHfisalpEGYDTLMKSDESVSAGQRQQIAIARAMISDPPMMILDEATS 516
                                       *****99999999************8888774555555788*****************************96 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.1e-06    0.0009       4      33 ..     377     406 ..     373     543 .. 0.63

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.1e-06
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeea 33 
                                         ++++++G++G+GKTtl++ l++ ++ ++
  gi|474934706|ref|YP_007688288.1| 377 PGQMVAIVGPTGAGKTTLINLLMRFYEVDS 406
                                       57899*******************996543 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.6e-06    0.0012      90     124 ..     368     403 ..     353     419 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.6e-06
                                       HHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-- CS
                       RsgA_GTPase  90 leelkellkd.ktsvlvGqSGvGKStLinallpele 124
                                       +++ ++ +k  +++++vG++G+GK+tLin l+   e
  gi|474934706|ref|YP_007688288.1| 368 IHDFSADIKPgQMVAIVGPTGAGKTTLINLLMRFYE 403
                                       566677777779******************987555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   2.2e-06    0.0017      20      39 ..     379     398 ..     358     400 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.2e-06
                            AAA_23  20 gltlItGpNGaGKTTildAi 39 
                                        +++I+Gp+GaGKTT+++ +
  gi|474934706|ref|YP_007688288.1| 379 QMVAIVGPTGAGKTTLINLL 398
                                       699**************865 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.5   0.00017      0.14      27     212 ..     381     559 ..     365     564 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00017
                                       EEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  27 taivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrv 103
                                        aivGp G+GK+ l++ +        ++    ++ + li   ++ +s+++ +v  +f    +++ + +  v  +   
  gi|474934706|ref|YP_007688288.1| 381 VAIVGPTGAGKTTLINLL--------MRFYEVDSGDILIDG-RSVRSMSREQVRRMFGMVLQDSWVFEGTVREN--- 445
                                       556666666666665554........122233444444544.55555555555555544433322222222222... PP

                                       ETTSEEEEEETTEEE-HHHHHHHHHCTT-STT................CS-HHHHHHHHHHHHHHHHCCS--SEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 104 krkgeseykingkevtkkevsellesagiske................lLSgGektLvalaLlfAiqkvkpaplyll 164
                                              + +n+++v+ +++ e+ + +g++                  + S G+++ +a+a      +++  p+++l
  gi|474934706|ref|YP_007688288.1| 446 -------IVFNRENVSDSKLDEVCQAVGLNHFisalpegydtlmksdeSVSAGQRQQIAIA----RAMISDPPMMIL 511
                                       .......233333333333333333333333355555555555555669999999988875....5689999***** PP

                                       CTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 165 DeidaaLDeknvkkvaellkeksknaQfivislreemlekadklvgvt 212
                                       De  +  D    k + +  ++       +vi++r  ++ +ad ++ v+
  gi|474934706|ref|YP_007688288.1| 512 DEATSSVDPLTEKMIQNAARNMIAGRTSFVIAHRLSTIVDADVIMVVK 559
                                       ***************9999999999999*********99999988775 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.041        32     242     264 ..     375     398 ..     372     416 .. 0.84
   2 !   12.0   0.5   8.2e-05     0.064     298     365 ..     463     529 ..     440     566 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.041
                                       E-SS.EEEEEE-TTSSHHHHHHHH CS
                        ABC_ATPase 242 ipkG.vtlIvGggfhGKsTLLeAl 264
                                       i+ G +++IvG+   GK+TL++ l
  gi|474934706|ref|YP_007688288.1| 375 IKPGqMVAIVGPTGAGKTTLINLL 398
                                       67777899************9976 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 8.2e-05
                                       EEE--TTTB---CCC--STTEEESS--HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHH CS
                        ABC_ATPase 298 kgvDispFinnLPegkdttkfstedASGStsqAanimealeagakllLiDEDtsAtNlmirDermqel 365
                                       + v +  Fi++LPeg dt   s e  S    q  +i++a+  + +++++DE ts +  +   +++q+ 
  gi|474934706|ref|YP_007688288.1| 463 QAVGLNHFISALPEGYDTLMKSDESVSAGQRQQIAIARAMISDPPMMILDEATSSVDPLT-EKMIQNA 529
                                       678899************************************************987766.4444444 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.5e-05     0.012       2      21 ..     381     400 ..     380     423 .. 0.85
   2 ?   -2.6   0.0       7.3   5.7e+03      68      84 ..     544     560 ..     494     573 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.5e-05
                                       EEEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltg 21 
                                       vaivG + +GK+tLin l++
  gi|474934706|ref|YP_007688288.1| 381 VAIVGPTGAGKTTLINLLMR 400
                                       8****************987 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 7.3
                                       HHHHHHHCTSEEEEEEE CS
                          MMR_HSR1  68 kaflaleeadlillvvd 84 
                                       +++  + +ad+i++v d
  gi|474934706|ref|YP_007688288.1| 544 HRLSTIVDADVIMVVKD 560
                                       33344555677766666 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.7e-05     0.013      15      39 ..     371     395 ..     366     400 .. 0.84
   2 ?   -2.0   0.1       3.9   3.1e+03      36      44 ..     547     555 ..     547     561 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.7e-05
                            AAA_29  15 htieidlkgatlltGpsGsGKSTll 39 
                                        +++i++ +++ ++Gp+G+GK+Tl+
  gi|474934706|ref|YP_007688288.1| 371 FSADIKPGQMVAIVGPTGAGKTTLI 395
                                       567888888***************9 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.9
                            AAA_29  36 STllDAiqa 44 
                                       ST++DA  +
  gi|474934706|ref|YP_007688288.1| 547 STIVDADVI 555
                                       9****9654 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   2.1e-05     0.016      18      49 ..     378     409 ..     372     535 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.1e-05
                            AAA_30  18 drvavltGpAGtGKttalkalreaweaaggrv 49 
                                        ++++++Gp G+GKtt+++ l + +e + g++
  gi|474934706|ref|YP_007688288.1| 378 GQMVAIVGPTGAGKTTLINLLMRFYEVDSGDI 409
                                       56999*****************9999885444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.4e-05     0.011      25      60 ..     379     415 ..     366     536 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.4e-05
                            AAA_16  25 elvllsGesGvGKsslvrellralekd.ggiflrgkc 60 
                                       ++v ++G+ G GK++l++ l+r +e d g i++ g+ 
  gi|474934706|ref|YP_007688288.1| 379 QMVAIVGPTGAGKTTLINLLMRFYEVDsGDILIDGRS 415
                                       79*******************9777663233344444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       7.5   5.9e+03      81     112 ..     214     241 ..     191     248 .. 0.66
   2 ?   14.0   0.0   7.1e-05     0.055       1      44 [.     381     422 ..     381     459 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 7.5
                            AAA_18  81 ghlaeleseaakdikkvvLtaspeelleRlek 112
                                       g+++e +   a+    v L+a   e +eR+ +
  gi|474934706|ref|YP_007688288.1| 214 GLIEEQYTGHAV----VSLYAGQREAMERFTA 241
                                       333333333333....9999999999999865 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 7.1e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpe 44 
                                       +++ G+ G+GKttl + L +     v ++d++ +++++ +   e
  gi|474934706|ref|YP_007688288.1| 381 VAIVGPTGAGKTTLINLLMRFY--EVDSGDILIDGRSVRSMSRE 422
                                       689***************7764..77777777777776666655 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   7.3e-05     0.057      11      45 ..     372     404 ..     363     410 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.3e-05
                                       HHHHHHCH..TEEEEEEESTTSSHHHHHHHHHHHTT- CS
                              TsaE  11 gkklakal..gdvilLeGdLGaGKTtlvrglakalgv 45 
                                        ++    +  g+++++ G+ GaGKTtl+  l++ ++v
  gi|474934706|ref|YP_007688288.1| 372 SAD----IkpGQMVAIVGPTGAGKTTLINLLMRFYEV 404
                                       333....244899****************99998766 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   5.7e-05     0.045     127     156 ..     376     405 ..     324     424 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.7e-05
                             T2SSE 127 rerglilvsGgTgsGKttllyallkeinks 156
                                       +  +++ + G+Tg GKttl++ l+ + + +
  gi|474934706|ref|YP_007688288.1| 376 KPGQMVAIVGPTGAGKTTLINLLMRFYEVD 405
                                       556788999************999877655 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00012     0.093       3      21 ..     381     399 ..     379     413 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00012
                                       EEEEESTTCCHHHHHHHHH CS
                              cobW   3 tvltGflGsGKTtLlnhll 21 
                                       + ++G+ G+GKTtL+n l+
  gi|474934706|ref|YP_007688288.1| 381 VAIVGPTGAGKTTLINLLM 399
                                       689************9887 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       8.4   6.5e+03      43      62 ..     219     238 ..     183     250 .. 0.63
   2 ?   11.8   0.0   0.00021      0.17       2      50 ..     381     431 ..     380     443 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 8.4
                                       ---EEEEEET.T--EEEEEE CS
                          NTPase_1  43 rrigFkivdlasgeegiLar 62 
                                       + +g  +v+l  g+++ + r
  gi|474934706|ref|YP_007688288.1| 219 QYTGHAVVSLYAGQREAMER 238
                                       44566666666666666555 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00021
                                       EEEE--TTSSHHHHHHHHHH..HH...GGGEEEEEEEEE-------EEEEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvle..llkssgvkvgGfyteevreggrrigFkiv 50 
                                       v+i Gp G GKtTl++ +++  +++s ++ ++G  ++ + +++ r  F +v
  gi|474934706|ref|YP_007688288.1| 381 VAIVGPTGAGKTTLINLLMRfyEVDSGDILIDGRSVRSMSREQVRRMFGMV 431
                                       7899*************9983356677999999999999999888888776 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00017      0.13       2      41 ..     381     426 ..     380     445 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00017
                            AAA_28   2 ivitGgestGKTtlleaLaar.....gypvv.pEaareileeklak 41 
                                       ++i+G+ ++GKTtl++ L +      g   +  +++r + +e+ ++
  gi|474934706|ref|YP_007688288.1| 381 VAIVGPTGAGKTTLINLLMRFyevdsGDILIdGRSVRSMSREQVRR 426
                                       89***************98533334433344466666666666655 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00018      0.14      17      59 ..     379     421 ..     366     454 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00018
                        Zeta_toxin  17 klillgGqpGAGKselaellkdelerqgnvvrldpDdlRelhP 59 
                                        ++ ++G +GAGK++l++ll +  e +++ + +d+ ++R++ +
  gi|474934706|ref|YP_007688288.1| 379 QMVAIVGPTGAGKTTLINLLMRFYEVDSGDILIDGRSVRSMSR 421
                                       58899***************99999888888999988888764 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00024      0.18       3      32 ..     379     405 ..     378     480 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00024
                            AAA_24   3 lkiliyGpsgiGKTtlakelgpkplfidte 32 
                                       ++++i+Gp g+GKTtl++ l  ++    ++
  gi|474934706|ref|YP_007688288.1| 379 QMVAIVGPTGAGKTTLINLL-MRFYE--VD 405
                                       689**************999.44444..44 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00025       0.2       1      32 [.     380     409 ..     380     473 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00025
                            AAA_33   1 lvllvGlpGsGKstlaerllkklgavllssdt 32 
                                       +v +vG+ G+GK+tl+  l+  + +++ s d+
  gi|474934706|ref|YP_007688288.1| 380 MVAIVGPTGAGKTTLINLLM--RFYEVDSGDI 409
                                       6889************9998..4455544454 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00032      0.25      31      57 ..     376     402 ..     371     417 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00032
                             AAA_7  31 knkkpvllvGptGtGKtviikdllkkl 57 
                                       k ++ v +vGptG GKt++i+ l++ +
  gi|474934706|ref|YP_007688288.1| 376 KPGQMVAIVGPTGAGKTTLINLLMRFY 402
                                       5678899*************9988755 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00047      0.37       2      19 ..     381     398 ..     380     428 .. 0.77
   2 ?   -2.2   0.0       3.6   2.8e+03     236     272 ..     487     520 ..     437     528 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00047
                            AAA_21   2 nvliGpNgsGKSnLLdal 19 
                                        +++Gp g+GK++L+ +l
  gi|474934706|ref|YP_007688288.1| 381 VAIVGPTGAGKTTLINLL 398
                                       68*************999 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.6
                            AAA_21 236 elSdGtkrllalltallralkkgsllliDEpEngLHP 272
                                       ++S G+++ +a++ a+++++   +  ++DE  ++ +P
  gi|474934706|ref|YP_007688288.1| 487 SVSAGQRQQIAIARAMISDP---PMMILDEATSSVDP 520
                                       34999999988888888888...99999999999988 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00055      0.43      26      45 ..     381     400 ..     378     411 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00055
                             DUF87  26 lAilgsTGsGKSntvavLle 45 
                                       +Ai+g TG+GK++++ +L++
  gi|474934706|ref|YP_007688288.1| 381 VAIVGPTGAGKTTLINLLMR 400
                                       7**************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (592 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       885  (0.0493614); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.84u 0.35s 00:00:01.19 Elapsed: 00:00:00.57
# Mc/sec: 3153.23
//
Query:       gi|474934707|ref|YP_007688289.1|  [L=417]
Description: Nitrogenase molybdenum-iron protein, alpha and beta chains [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-28  100.2   0.0    1.3e-28   99.9   0.0    1.1  1  Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase


Domain annotation for each model (and alignments):
>> Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.9   0.0     7e-33   1.3e-28       3     397 ..       9     416 ..       8     417 .] 0.84

  Alignments for each domain:
  == domain 1  score: 99.9 bits;  conditional E-value: 7e-33
                                       HHHHHHHHTTBTTEEEEEES-HHH....HHCCCCHHHCHHS........S-HS-EEEE--HHHHSSSSHHHHHHHHH CS
                    Oxidored_nitro   3 plGAalvllgikdalplvhGpqGC....atyaralltrhfr........epiplastdltekdavfGgeekLkeaik 67 
                                       + G++l++ ++ d ++++hGp GC    +++a++++ r f+        +   l ++ ++ +d ++G+ +k+  +i 
  gi|474934707|ref|YP_007688289.1|   9 FYGSMLAAESVIDGMTILHGPGGCrglaSSIASRYVPREFKtvegdfffHRSRLPCSYVDADDYIYGSSKKI-GMIL 84 
                                       579*********************88888888999999999887755544447**************99997.5677 PP

                                       HHHHHC-TSEEEEEE-HHHHHTTTTHHHHHHHHHHHHTSSEEEEEE--TT.SSSHHHHHHHHHHHHHHHCTT-TT-- CS
                    Oxidored_nitro  68 eivkrykpkaIgVittClteliGdDieavareaeeelgeipvipvstpgf.ggsqseGydaalealvrklvgkkgek 143
                                        + k  + k  +V+++  + liGd ++  + +        +v ++      ++++  Gyda+l  ++rklv  k ek
  gi|474934707|ref|YP_007688289.1|  85 DLLKSEDTKFAVVLESPGASLIGDKLQDEVIASGMSD---KV-AILGKCLmSETFGRGYDAVLCLMARKLVR-KAEK 156
                                       7777778*******************98666664443...23.3444444599*****************98.99** PP

                                       -SSEEEEEEETTCGH...GHHHHHHHHHHHHTEEEEEEECTSB-HHHHGGGGG-SEEEEESHHCHHHHHHHHHHHH- CS
                    Oxidored_nitro 144 eprkvnilgeynlgp...gdlrelkelleklGlevnavftggtsleelraagraklnlvlcprsanyaaelleekfg 217
                                        p++vn++g + + +   + ++el +ll+ +Glev a +   ++l+++r++++a +n+++cp++  +++ + e + g
  gi|474934707|ref|YP_007688289.1| 157 VPKRVNLVGLPYVFKgcySLVKELHRLLSMMGLEVIADIGTACTLDQFRESSKAVVNVCVCPEYFSETGTYYENELG 233
                                       ********877554478899*******************************************9999********** PP

                                       --EEE..EE-SSSHHHHHHHHHHHHHHHTCHHHHH..HH...HHHHHHHHHHHHHHHHHHTT-EEEEECSSHHHHHH CS
                    Oxidored_nitro 218 vpyik..lvspiGleatdaflrelakllgkevape..ri...aeerarlldaladyheylagkrvaiygdpdrvval 287
                                       +p ++  +++p+G +a  a+++++a+++ ++ +p+   i   ++e +r++ a + + e  + + + + ++p+ ++ l
  gi|474934707|ref|YP_007688289.1| 234 IPTVRgpMGAPVGYDALRAWIQAVAEATSCDPSPAlsFIgedEAEVKRFVSAALGIGEASQYRGFSVLAEPSVALPL 310
                                       *****9999********************4444441133221334588999999999999***************** PP

                                       HHHHH.HHT-EEEEEEESSS-HHHHHHHHHHS.TT.SEEEES..CHHHHHHHHHHHT-SEEEE-CC.HHHHHHH.TT CS
                    Oxidored_nitro 288 arllk.elGmevvaagtetahrddeerlkaeleegepevidd.adleeleelikelkpdlllggsk.eryiaek.lg 360
                                       +rl++ ++ m++va+  ++++  +e +l+         v+d+    + le     +  ++++g      y+a++ l 
  gi|474934707|ref|YP_007688289.1| 311 VRLMAkDMHMTPVAVELTEHDGVYENELRS--------VLDRmGCPKALETEFGSCFSEVVFGPGAmVEYLAQAdLC 379
                                       *****9***********9997776665554........555533457888889999999999977655555554145 PP

                                       --EEE-TS-ECCTTTCSS---SHHHHHHHHHHHHHHH CS
                    Oxidored_nitro 361 iplvrvgfPildrhgyargpyvGYeGalnllddiana 397
                                          + + +P +d ++ a + ++G +G  ++ +++ n+
  gi|474934707|ref|YP_007688289.1| 380 STYFDIFIPSKDYLDIAPKSIIGLDGCRRITEKVLNT 416
                                       6678899999999999999999999999999998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 2419.01
//
Query:       gi|474934708|ref|YP_007688290.1|  [L=698]
Description: Nitrogenase subunit NifH (ATPase) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.4e-84  281.4   1.8    1.1e-83  280.8   1.8    1.2  1  Fer4_NifH       4Fe-4S iron sulfur cluster binding proteins, 
    7.8e-50  169.7   0.0    1.1e-49  169.2   0.0    1.1  1  Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
    4.9e-13   49.2   0.0    1.1e-12   48.1   0.0    1.6  1  CbiA            CobQ/CobB/MinD/ParA nucleotide binding domain
      4e-09   36.3   0.1    6.5e-06   25.8   0.2    2.4  2  ParA            NUBPL iron-transfer P-loop NTPase
    1.3e-08   35.0   0.7    1.7e-07   31.3   0.6    2.2  2  AAA_31          AAA domain
    5.1e-08   32.5   0.2    1.9e-07   30.6   0.2    1.8  2  ArsA_ATPase     Anion-transporting ATPase
    0.00044   20.1   0.1     0.0088   15.9   0.0    2.2  2  AAA_26          AAA domain
     0.0015   17.9   0.1      0.003   16.9   0.1    1.4  1  MipZ            ATPase MipZ
     0.0016   17.5   0.1      0.013   14.5   0.0    2.1  2  MeaB            Methylmalonyl Co-A mutase-associated GTPase M
  ------ inclusion threshold ------
      0.082   13.3   0.0       0.19   12.1   0.0    1.6  1  AAA_16          AAA ATPase domain
      0.099   12.3   0.0        0.4   10.3   0.1    1.9  2  SRP54           SRP54-type protein, GTPase domain
        0.1   11.8   0.5       0.16   11.2   0.5    1.2  1  NB-ARC          NB-ARC domain
       0.13   12.1   0.1       0.24   11.3   0.1    1.4  1  NTPase_1        NTPase
       0.14   11.8   0.2       0.23   11.2   0.2    1.3  1  AAA_24          AAA domain


Domain annotation for each model (and alignments):
>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  280.8   1.8   8.8e-87   1.1e-83       1     261 [.       2     262 ..       2     269 .. 0.90

  Alignments for each domain:
  == domain 1  score: 280.8 bits;  conditional E-value: 8.8e-87
                         Fer4_NifH   1 rkiaiyGkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllggkaqetvldtlrekgavedvkvedvvkkG 77 
                                       ++iaiyGkGGiGkst s+n+s  l+++g kv +vGCDPk+Dstrlll+gk q+tvld +++    ed  ++d v  G
  gi|474934708|ref|YP_007688290.1|   2 KQIAIYGKGGIGKSTVSANISYQLSKKGFKVAQVGCDPKHDSTRLLLNGKSQTTVLDHINSGS--ED--IGDTVSIG 74 
                                       69********************************************************98766..55..689***** PP

                         Fer4_NifH  78 yggvkcvesGGPepGvGCaGrgvitaielleelgayd.dlDfvlyDvLGDvvCGGfalPiredkaqevyivtsgelm 153
                                        +gv c+e+GGPepGvGCaGrg+ ta++++e++++ d d+D++lyDvLGDvvCGGfa+P+r+++a+ v+ivtsge+m
  gi|474934708|ref|YP_007688290.1|  75 KNGVVCIETGGPEPGVGCAGRGILTAFNFIENNNVVDkDTDIILYDVLGDVVCGGFAVPLRRKYADAVFIVTSGEFM 151
                                       ************************************967************************************** PP

                         Fer4_NifH 154 alyaanniakgiekyaksggvrlgGliinsrkvddereliekfaeelgtkvlevvPrdeivrkaelrkktvieyape 230
                                       +lyaann+ kgi+++ + +  r++Gli n r  + e e +++fa+++g+++++ +Pr+ +  +ae +  tv e  p+
  gi|474934708|ref|YP_007688290.1| 152 SLYAANNVLKGIRNFDNDK-SRVAGLILNCRGNEGEYEYVKNFADAVGLPIVARIPRSRKFYEAESEGVTVSEKYPD 227
                                       ***************9865.6****************************************************9999 PP

                         Fer4_NifH 231 se...qakeyrelarkilenkklviPk.plsedeL 261
                                       se      +   + + i +++  + P  pl++d+L
  gi|474934708|ref|YP_007688290.1| 228 SEeysAIGQIVSIIQGINDASGKLYPAvPLNDDDL 262
                                       88222223334445566666666666436666666 PP

>> Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.2   0.0     9e-53   1.1e-49       3     369 ..     297     675 ..     295     682 .. 0.85

  Alignments for each domain:
  == domain 1  score: 169.2 bits;  conditional E-value: 9e-53
                                       HHHHHHHHTTBTTEEEEEES-HHHHHCCCCHHHCHHS........S-H..S-EEEE--HHHHSSSSHHHHHHHHHHH CS
                    Oxidored_nitro   3 plGAalvllgikdalplvhGpqGCatyaralltrhfr........epi..plastdltekdavfGgeekLkeaikei 69 
                                       ++ A+   + i da ++vh+p +C ++++    +           +++   +++tdlt  + +fGg++ L   i+  
  gi|474934708|ref|YP_007688290.1| 297 AALAVGYCMTIYDADVVVHAPKSCHYFFTSGCDSGLVylnkskkiRNVsnRIFCTDLTDYSSIFGGAKELGSIIESR 373
                                       44555556789999**********888876655544444445455444656************************99 PP

                                       HHHC-TSEEEEEE-HHHHHTTTTHHHHHHHHHHHHTSSEEEEEE--TT.SSSHHHHHHHHHHHHHHHCTT-TT---S CS
                    Oxidored_nitro  70 vkrykpkaIgVittClteliGdDieavareaeeelgeipvipvstpgf.ggsqseGydaalealvrklvgkkgekep 145
                                       +++   k+++V+ttC++++iGdD+++++r+++e+++ + ++pv++ g  +g ++++ +++++++++ + +++++ e+
  gi|474934708|ref|YP_007688290.1| 374 IAAG-TKTVFVVTTCVPGIIGDDVGGICRRIQEKHPGTFIVPVEVDGIlSGGYMQAREVTIRSICKVV-DRSVKPEK 448
                                       9996.9***********************************************************888.78****** PP

                                       SEEEEEEETTCGH....GHHHHHHHHHHHHTEEEEEEECTSB-HHHHGGGGG-SEEEEESHH.CHHHHHHHHHHHH- CS
                    Oxidored_nitro 146 rkvnilgeynlgp....gdlrelkelleklGlevnavftggtsleelraagraklnlvlcpr.sanyaaelleekfg 217
                                       + vn++g y+         ++   ++le lGl+vn+ +  + +++e+r++ +  lnl+++ + s++ +++ le++ g
  gi|474934708|ref|YP_007688290.1| 449 GAVNLIGYYES-IdkaiRSADDTDRILEGLGLRVNCKAFDENTFDEIRNLRKGGLNLMAGFSvSNRMTCQQLEKELG 524
                                       ******99953.335789999***************************************99556699********* PP

                                       --EEEEE-SSSHHHHHHHHHHHHHHHT..CHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEECSSHHHHHH.HHHH CS
                    Oxidored_nitro 218 vpyiklvspiGleatdaflrelakllg..kevaperiaeerarlldaladyheylagkrvaiygdpdrvval.arll 291
                                       +p++  ++p+Gl++ +++++  +k +g    v  + ia  ++ ++   ++y  +++g r+++y+   + + +  +++
  gi|474934708|ref|YP_007688290.1| 525 IPWYPDPMPVGLAESKDWIESFGKHMGvpDGVRSDLIASLSEDFEGFREEYGGRFKGLRAVLYVPSATNINWlFEIM 601
                                       ***************************65445444455545555555566778888**********88888625899 PP

                                       HHHT-EEEEEEESSS-HHHH.HHHHHHS.TT.SEEEES.CHHHHHHHHHHHT-SEEEE-CCHHHHHHHTT--EEE-T CS
                    Oxidored_nitro 292 kelGmevvaagtetahrdde.erlkaeleegepeviddadleeleelikelkpdlllggskeryiaeklgiplvrvg 367
                                       + lG+e+  + ++ ++r    +  + ++e++  ++  ++d++ l e++++ +pd++lg+s+   +  +l+ p++ +g
  gi|474934708|ref|YP_007688290.1| 602 EVLGAEITDIFCPINSRWNLsD--EIHFENSGIHIESNVDFDMLLERLERIRPDMVLGSSQ---MLSRLEYPHFNFG 673
                                       99************97766634..44466666689999*********************98...4557888888888 PP

                                       S- CS
                    Oxidored_nitro 368 fP 369
                                        P
  gi|474934708|ref|YP_007688290.1| 674 TP 675
                                       88 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   0.0   8.8e-16   1.1e-12       4     127 ..       6     220 ..       4     221 .. 0.86

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 8.8e-16
                                       EESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH.HTTEB-HHHH......................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx......................... RF
                              CbiA   4 astkGGvGKTtlaanLaralarrglrVllvDaDpqannlai.leglendiep......................... 54 
                                       + +kGG GK+t++an+   l+++g++V+ v +Dp   ++++ l g++    +                         
  gi|474934708|ref|YP_007688290.1|   6 IYGKGGIGKSTVSANISYQLSKKGFKVAQVGCDPKHDSTRLlLNGKS----Qttvldhinsgsedigdtvsigkngv 78 
                                       679********************************999995333333....334569999***************** PP

                                       ............................................................................C CS
                                       ............................................................................x RF
                              CbiA  55 ............................................................................d 55 
                                                                                                                    
  gi|474934708|ref|YP_007688290.1|  79 vcietggpepgvgcagrgiltafnfiennnvvdkdtdiilydvlgdvvcggfavplrrkyadavfivtsgefmslyA 155
                                       *******************************************************************9998884443 PP

                                       CHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  56 lkrllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeapargep 127
                                            ++l+ +++  +++ ++ag++ln  ++e e++  k++ + +    g+p+++ ipr+ +++ea+++g +
  gi|474934708|ref|YP_007688290.1| 156 ---ANNVLKGIRNFDNDKSRVAGLILNCRGNEGEYEYVKNFADAV----GLPIVARIPRSRKFYEAESEGVT 220
                                       ...44444444433333489********88887777777776666....*******************9976 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.2   5.1e-09   6.5e-06      10      43 ..       7      40 ..       2      68 .. 0.81
   2 !    7.8   0.0    0.0015         2     151     243 ..     157     239 ..     132     242 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 5.1e-09
                              ParA 10 SgKGGVGKStvavnlAlaLakkglkvgllDaDiy 43
                                       gKGG+GKStv++n++++L+kkg+kv+ +  D  
  gi|474934708|ref|YP_007688290.1|  7 YGKGGIGKSTVSANISYQLSKKGFKVAQVGCDPK 40
                                      59************************98877755 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0015
                              ParA 151 advkkaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkplvl 227
                                       ++v k+i+ f++ k +v G++ N  g        +      + ++++a+++g+p++++ip + ++ ea  eg ++ +
  gi|474934708|ref|YP_007688290.1| 157 NNVLKGIRNFDNDKSRVAGLILNCRGNE-----GE-----YEYVKNFADAVGLPIVARIPRSRKFYEAESEGVTVSE 223
                                       4555666666666666666666543322.....22.....2467899****************************** PP

                              ParA 228 kepeseaakaleeiae 243
                                       k p+se  +a+ +i++
  gi|474934708|ref|YP_007688290.1| 224 KYPDSEEYSAIGQIVS 239
                                       *******999999986 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.6   1.4e-10   1.7e-07       1      71 [.       1      69 [.       1      79 [. 0.78
   2 ?    1.2   0.0      0.23   2.9e+02     140     170 ..     139     169 ..     108     174 .. 0.89

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 1.4e-10
                            AAA_31  1 gkvIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekneiektlyevli.eeknike 71
                                      +k Iai+  KGG+GK+T s n+++ l+k+g kv  v +Dp   +t  l   + + ++t+++ ++  +++i +
  gi|474934708|ref|YP_007688290.1|  1 MKQIAIY-GKGGIGKSTVSANISYQLSKKGFKVAQVGCDPKHDSTRLLL--NGKSQTTVLDHINsGSEDIGD 69
                                      5777776.5***********************************99654..333445666555446666655 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.23
                            AAA_31 140 sdsviipvqaeayaleGleqllktieevkkk 170
                                       +d v i++  e+++l+ ++++lk i++++++
  gi|474934708|ref|YP_007688290.1| 139 ADAVFIVTSGEFMSLYAANNVLKGIRNFDND 169
                                       89***********************998765 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.2   1.5e-10   1.9e-07       1      42 [.       1      42 [.       1      56 [. 0.94
   2 ?   -1.3   0.0      0.75   9.6e+02     208     234 ..     141     167 ..     134     179 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 1.5e-10
                                      -EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTH CS
                       ArsA_ATPase  1 lkvilvgGKGGVGKttvsaatavklsekgkkvllistDPAhs 42
                                      +k i + GKGG+GK+tvsa ++++ls+kg kv  +  DP h 
  gi|474934708|ref|YP_007688290.1|  1 MKQIAIYGKGGIGKSTVSANISYQLSKKGFKVAQVGCDPKHD 42
                                      788999*********************************995 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.75
                                       EEEEEEESSHHHHHHHHHHHHHHHHTT CS
                       ArsA_ATPase 208 sfrlVvipEklslkEteRaikeLkkyg 234
                                       ++++V+  E++sl+  +  +k + +++
  gi|474934708|ref|YP_007688290.1| 141 AVFIVTSGEFMSLYAANNVLKGIRNFD 167
                                       7899**********9888877766665 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.2      0.17   2.2e+02      11      33 ..      11      33 ..       8      35 .. 0.93
   2 !   15.9   0.0   6.9e-06    0.0088     138     193 ..     152     210 ..     136     214 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.17
                            AAA_26 11 gvGKTvvslgLvralkrkgvkvg 33
                                      g+GK++vs+ + + l++kg+kv+
  gi|474934708|ref|YP_007688290.1| 11 GIGKSTVSANISYQLSKKGFKVA 33
                                      79******************986 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 6.9e-06
                            AAA_26 138 glgtinqllltiealrqknvrvlGvilNkvrnp...envetlekksgipvlGvvPylpd 193
                                        l + n++l  i  + + + rv+G+ilN+  n+   e v+++  + g+p+++++P +++
  gi|474934708|ref|YP_007688290.1| 152 SLYAANNVLKGIRNFDNDKSRVAGLILNCRGNEgeyEYVKNFADAVGLPIVARIPRSRK 210
                                       345699***********************7777444455555566669*******9875 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   2.3e-06     0.003       9      53 ..       9      53 ..       4      65 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.3e-06
                                      STTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHHHHHHH CS
                              MipZ  9 kGGsGksttavhvavaLlkkGarvaaidldlrqrtlarylenraa 53
                                      kGG Gkst++  +   L+kkG++va +  d +  +    l+ +++
  gi|474934708|ref|YP_007688290.1|  9 KGGIGKSTVSANISYQLSKKGFKVAQVGCDPKHDSTRLLLNGKSQ 53
                                      9*****************************998887766666655 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0     1e-05     0.013      31      70 ..       3      42 ..       1      55 [. 0.91
   2 ?    0.4   0.0       0.2   2.5e+02      86     113 ..     404     431 ..     374     438 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1e-05
                                      EEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE----- CS
                              MeaB 31 vvGltGvPGaGkstlvealglelrrrGkrvavlavDPssp 70
                                      ++ + G  G Gkst+  ++  +l ++G +va +  DP   
  gi|474934708|ref|YP_007688290.1|  3 QIAIYGKGGIGKSTVSANISYQLSKKGFKVAQVGCDPKHD 42
                                      678999*******************************755 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.2
                                       CCTSTTEEEEEE-----HHHHHHHHHHH CS
                              MeaB  86 lavdegvfiRslpsrGalGGlaaktrev 113
                                        ++++g fi ++   G+l G  +++rev
  gi|474934708|ref|YP_007688290.1| 404 QEKHPGTFIVPVEVDGILSGGYMQAREV 431
                                       3579**************9999999997 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00015      0.19      27      67 ..       4      44 ..       2      66 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00015
                            AAA_16 27 vllsGesGvGKsslvrellralekdggiflrgkcdqlesai 67
                                      + ++G  G+GKs++   +  +l+k+g+ +++  cd  + ++
  gi|474934708|ref|YP_007688290.1|  4 IAIYGKGGIGKSTVSANISYQLSKKGFKVAQVGCDPKHDST 44
                                      679***********************999999999875554 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00031       0.4       3      38 ..       3      38 ..       1      46 [. 0.93
   2 ?   -1.5   0.0       1.3   1.6e+03      81     142 ..     136     199 ..     132     203 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00031
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                       i++ G  G+GK t  a ++ +l+k+g kv+ v +D
  gi|474934708|ref|YP_007688290.1|  3 QIAIYGKGGIGKSTVSANISYQLSKKGFKVAQVGCD 38
                                      58899**************************99999 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.3
                                       HTTSSEEEEEE--SSTTHHHHHHHHHHHHHHH..SSSEEEEEEETTBHTHHHHHHHHHHHHSSC CS
                             SRP54  81 eekidvvlvDTaGrlqndkelmeelkkikkvv..kpdevllvldattgqeavkqakaFkeavgi 142
                                       ++ +d+v++ T+G   +  +  + lk i+++   k+    l+l+    +  ++ +k+F++avg+
  gi|474934708|ref|YP_007688290.1| 136 RKYADAVFIVTSGEFMSLYAANNVLKGIRNFDndKSRVAGLILNCRGNEGEYEYVKNFADAVGL 199
                                       6778999999999998888888888888888733333445888888888888888888888776 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.5   0.00012      0.16      23      44 ..       4      25 ..       1      36 [. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                                      EEEEESTTSSHHHHHHHHCCSH CS
                            NB-ARC 23 valvGmgGvGKttlakqilnks 44
                                      +a++G+gG+GK+t++++i  ++
  gi|474934708|ref|YP_007688290.1|  4 IAIYGKGGIGKSTVSANISYQL 25
                                      89***************98764 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00018      0.24       2      32 ..       4      34 ..       3      45 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00018
                                      EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32
                                      ++i G+ G+GK+T+  +++ +l+++g+kv+ 
  gi|474934708|ref|YP_007688290.1|  4 IAIYGKGGIGKSTVSANISYQLSKKGFKVAQ 34
                                      7899************************975 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00018      0.23       4      22 ..       3      21 ..       1      38 [. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00018
                            AAA_24  4 kiliyGpsgiGKTtlakel 22
                                      +i+iyG+ giGK+t+ +++
  gi|474934708|ref|YP_007688290.1|  3 QIAIYGKGGIGKSTVSANI 21
                                      79************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (698 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.81u 0.33s 00:00:01.14 Elapsed: 00:00:00.57
# Mc/sec: 3718.04
//
Query:       gi|474934709|ref|YP_007688291.1|  [L=1229]
Description: Cobalamin biosynthesis protein CobN-related Mg-chelatase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
          0 1059.6   0.0          0 1059.4   0.0    1.0  1  CobN-Mg_chel    CobN/Magnesium Chelatase
  ------ inclusion threshold ------
        0.1   12.6   0.1        3.1    7.9   0.0    2.5  2  Dehydratase_SU  Dehydratase small subunit


Domain annotation for each model (and alignments):
>> CobN-Mg_chel  CobN/Magnesium Chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1059.4   0.0         0         0       5    1087 ..     119    1207 ..     115    1209 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1059.4 bits;  conditional E-value: 0
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel    5 keggveNlknllryladkllgkkeeeveppvelpeegiyhpdakelfesleeylewykkakkekaptvgilfyra 79  
                                        + + ++N  ++l+++a++l    ++++++pv+ p   iyh                  + k+ +  t gilf ++
  gi|474934709|ref|YP_007688291.1|  119 AFKCPDNDYRFLWWAAKRLGF-VDSDPPEPVSCPPYEIYH------------------TPKDGDGITAGILFVNS 174 
                                        556678888888888888875.666788999999999999..................23578899********* PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...x..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel   80 hllagntavidaliraleerglnvlpvfvssl...d..seaqealeelftkegeekvdalinttsfalvkgpaee 149 
                                        + + gn+++ida+i++le+ +++vl+v  s +   +    ++e le+ ft+ g++ +d+li++t+ a ++ +++ 
  gi|474934709|ref|YP_007688291.1|  175 QKFYGNMDYIDAIIEHLESMDIRVLAVGGS-FdcmRavGGTREILEKNFTSGGKPLIDVLISLTGYANTNCTDGF 248 
                                        *************************99544.33541568899999*********************888777655 PP

                                        xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  150 eeeeaeeea.lkelnvPvlqailssqsreeWeessqGlspldlamsvalpEldGriepvvisfkeeeeeetevek 223 
                                        + ++  e++  + l+vP++ +++++++++++e+++ Gl + d++ +v+ pEldG ++ v++s ++    ++e +k
  gi|474934709|ref|YP_007688291.1|  249 APNTDGESSyRALLDVPIVFGLSVHGNYHDFEDEKVGLGKKDFQSNVIYPELDGNVIAVPVSYTA----KDEPKK 319 
                                        55444444456779*************************************************54....456799 PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  224 yepipervervadlaarwarLrrkpnaekkvaiilanyppgegrlgnavgLdvpaSlvnlLkalkeeGYdveelp 298 
                                          piper++++++l+++w +Lrrkp++e+kvai+++++ p+ g +g+a+gLd+++S+  lL+++ + GY++e+ p
  gi|474934709|ref|YP_007688291.1|  320 SIPIPERIDHLCRLTKAWGSLRRKPASERKVAIMMWQSRPNSGVIGAAAGLDTIESVSDLLRRMDSLGYRIENVP 394 
                                        9**********************************************************************999* PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  299 esgdeLiellleggtndpeweelkv...gaaallpaeeYeewfeeLpeelreeveerWgeppgemveeeksgekk 370 
                                        e g++Li+++le+ tnd + +++++   ++a+l+++ +Y++ ++++p+  re  e+ Wgeppg    e +s++++
  gi|474934709|ref|YP_007688291.1|  395 ECGKDLIDEVLENITNDLDNQSMATvleRSADLVTVPDYRRRYDNIPAWDREMTEHSWGEPPG----EIMSHKDR 465 
                                        ******************99666545669**********************************....778899** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  371 lvipglqlGnvfvgvQPargyeedpsklyhdpdlpPthqYlAfYlWlreefgadavvHvGkHGtlEwlPGKqvgl 445 
                                        +vipgl  Gnvfv+ QP+rg+ e+ +++ hdp l  +hqY A+Y W++++f+ad++ H+G+HGtlEwlPG +vgl
  gi|474934709|ref|YP_007688291.1|  466 IVIPGLVKGNVFVCYQPMRGWAEQMDQNTHDPLLFTQHQYNAYYWWIKNVFKADMIFHMGTHGTLEWLPGVNVGL 540 
                                        *************************************************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                      CobN-Mg_chel  446 seecyPdillgdlPhlYpYivnnpgEGtqAKRRsyAviidHltPpmtraelygelaeLeelideYeeaesldpe. 519 
                                        s++c Pd +l ++P++YpY+vn+pgEG+qAKRRs++v+i H+ P m+ra++ g+++e+  l+++Y + +   ++ 
  gi|474934709|ref|YP_007688291.1|  541 SQKCNPDYVLDAVPNIYPYTVNDPGEGMQAKRRSESVLIGHMPPTMARADSFGKMQEIGVLLQDYFKYRGDASQs 615 
                                        *******************************************************************99996664 PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  520 rlkalreqilelveelnldkdlgleeakeeeeeefeellekldgyleelkeaqirdglhilGeapegeqlvdlvv 594 
                                         +  + +qi e ++e nl kdlg ee  +  +e fee+l  l++y++ l+ea++r +lhi+G++p++++  d+v+
  gi|474934709|ref|YP_007688291.1|  616 AKGVMVSQIYEAAKENNLFKDLGIEE--DPGAEGFEEYLIPLHEYIMGLEEALVRADLHIIGRPPAEHHFDDMVY 688 
                                        7778888***************8875..6789******************************************* PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  595 ailrleneegesltealaealgldlde...leeksekelrtagdalealeeeaeelveelleeeaeeeeaeaeel 666 
                                        +++rl+n++ +sl++a a+   +d+++   + ++   + + ++da+ ++++e++el++ l +e   +  ++ ++l
  gi|474934709|ref|YP_007688291.1|  689 SLTRLDNGDIRSLRDAYADYRSVDIQNaiaNPTEVGPTGELNSDAVTRIDAEERELISLLRTEFDYDPGKAVKHL 763 
                                        *************************9977644555556678999***********99998877444444444444 PP

                                        xxxxxxxxx..................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  667 eeeeeeeee..................eteeEitallraLdGeyippgpsGdptrgraevLPTGrNfysvDprai 723 
                                        e +  +  +                   ++ E +++++aLdG+++ pgpsG+p+rg+a++LP GrNfys+Dp+ +
  gi|474934709|ref|YP_007688291.1|  764 EGKYGKVPDdlctsieftcnrvvpnirLMTYEAEHMMDALDGRFVIPGPSGSPVRGNADILPMGRNFYSLDPDCV 838 
                                        44444444489***************86669******************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                      CobN-Mg_chel  724 PteaAwevGkklaeellerylqehgeyPekvglslwgtetmrteGediAqiLallGvrPvwdaa.grvvdlelip 797 
                                        Pt++Awe+G+ +a++++ery+++ g+yP+++g+++w+t++m t+G+d A +L+llGvrPvw++  g+vvdle++p
  gi|474934709|ref|YP_007688291.1|  839 PTHTAWEIGRGMADQMIERYVADRGTYPREIGVVIWATDMMTTGGDDAAYVLWLLGVRPVWSKVgGQVVDLEIVP 913 
                                        *************************************************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxx RF
                      CobN-Mg_chel  798 leeLgRPRiDVtvriSGffRDafpnlielldkavelvaeldEpeedNfvrkhvleeeaeleeke....eaeerat 868 
                                         +eLgRPR+DVt++i+G+fRD+fp  i+l+d+a+++va+ldE+ee+N ++++ +++  e  +++    ea+ r +
  gi|474934709|ref|YP_007688291.1|  914 AKELGRPRVDVTLNITGLFRDTFPGTIDLIDDAIKMVANLDESEEENALAANLRRDIVESIAEGltpdEARIRNS 988 
                                        ********************************************************99999844444377799** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  869 yRvFgskpGaYgagvqeliessnWedeedLaeaYlnwssyaYgkgaegeeaeeafearLkrvdvvvqnqdsrehd 943 
                                        +R+Fg++ G+Yg+gv +lies++W++++dLa++Y + ssy Y+kg+ g++ ++ f +r++rv ++++n  sre d
  gi|474934709|ref|YP_007688291.1|  989 VRIFGEALGTYGNGVGNLIESGKWDETKDLADVYADLSSYGYSKGSFGVPMKKEFVKRFSRVTATIKNAPSREFD 1063
                                        *************************************************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  944 lldsddyyqflGGltaavrslsgkkpeayfgdssnpenpkvrtlkeeiarelrsrvlNPkWiegmmrhGykGafe 1018
                                        +ld+dd++q+lGG++a vr++  k+  +y+gd+s+p+++k+r  +ee++  +rs+v NPk+ +g+m+hGy+Ga+e
  gi|474934709|ref|YP_007688291.1| 1064 ILDIDDVWQYLGGMNAFVRAYGQKDFVSYMGDNSDPKKTKIRGTQEELRFLFRSKVTNPKFNNGLMEHGYRGASE 1138
                                        *************************************************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel 1019 laatvdnlfgwdatadvvddwvyeevaetYvlDeevrefleekNpwAlreiaerLlEaarrglWeasee 1087
                                        +a+  +++++w at+++ +dw+y+ +++tY++De+v e++++ Np+A+ +i ++L Ea++rglW+as+e
  gi|474934709|ref|YP_007688291.1| 1139 MAKITEYTMAWGATSGIAEDWMYDTLVDTYLKDEKVLEWMDDVNPYAVMNILNTLHEAIDRGLWNASDE 1207
                                        *******************************************************************98 PP

>> Dehydratase_SU  Dehydratase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0   0.00034       3.1      54      81 ..     407     434 ..     400     438 .. 0.90
   2 ?    1.6   0.0      0.03   2.7e+02      45      70 ..     943     968 ..     927     975 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00034
                    Dehydratase_SU  54 qiAesagrkqlaknlrRaaElvkvpder 81 
                                       +i ++ +++++a+ l+R+a+lv+vpd r
  gi|474934709|ref|YP_007688291.1| 407 NITNDLDNQSMATVLERSADLVTVPDYR 434
                                       789999*******************975 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.03
                    Dehydratase_SU  45 tpetLelqaqiAesagrkqlaknlrR 70 
                                        ++++++ a++ es++ ++la+nlrR
  gi|474934709|ref|YP_007688291.1| 943 IDDAIKMVANLDESEEENALAANLRR 968
                                       57899********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.84u 0.34s 00:00:01.18 Elapsed: 00:00:00.51
# Mc/sec: 7242.46
//
Query:       gi|474934710|ref|YP_007688292.1|  [L=126]
Description: putative gamma-carboxymuconolactone decarboxylase subunit -like protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.4e-15   54.4   0.0    1.2e-14   54.1   0.0    1.2  1  CMD       Carboxymuconolactone decarboxylase family


Domain annotation for each model (and alignments):
>> CMD  Carboxymuconolactone decarboxylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.1   0.0   6.8e-19   1.2e-14       9      74 ..      38     103 ..      30     114 .. 0.88

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 6.8e-19
                                       HHHHHHCCGSSTS-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHSHH CS
                               CMD   9 alreallareggLdpkereLialavsaangceyCvdaHtraAleaGvteeeiaevlaqaaayagwp 74 
                                       ++++++++ +++ dpk r+L+ la++aa+g eyC++a +++A++ G+te+e+ evl +aa ++ + 
  gi|474934710|ref|YP_007688292.1|  38 DFGKSVFEGKSSFDPKMRHLLGLAAAAALGGEYCMKAQMKDAKDLGATEDEVIEVLEIAAYMCMTR 103
                                       678888887889*************************************************99655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 796.79
//
Query:       gi|474934711|ref|YP_007688293.1|  [L=110]
Description: hypothetical protein TALC_01144 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-07   31.8   0.0    1.5e-07   31.6   0.0    1.1  1  Fe-S_biosyn     Iron-sulphur cluster biosynthesis
  ------ inclusion threshold ------
       0.11   11.1   0.0       0.13   10.9   0.0    1.0  1  Glyco_hydro_36  Glycosyl hydrolase 36 superfamily, catalytic 


Domain annotation for each model (and alignments):
>> Fe-S_biosyn  Iron-sulphur cluster biosynthesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   1.6e-11   1.5e-07       3     109 ..       2     103 ..       1     105 [. 0.89

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 1.6e-11
                                       EEE-HHHHHHHHHHHHCTTEC...EEEEEECCTSCCGGS.TT.EEEEEEEEESSTSTTTEEEEE.ETTEEEEEEGGG CS
                       Fe-S_biosyn   3 itlteaAaeklkkllaedkke...lrLdvddgggpyskggCsiggkyslvlvdeedeeydevle.snggkvyvksys 75 
                                       +t+t++A + + +ll++++k+   + +++           Cs g ++ + + +e+ +e ++v e  +++k+++++++
  gi|474934711|ref|YP_007688293.1|   2 VTITADAEKFIDDLLEKNQKQgwgIKIYLSGYA-------CS-GPQFGMSFQKEA-AEGETVDEtAKNFKMFYDDET 69 
                                       79***************99999**999999888.......**.************.66666666699********** PP

                                       HHHS.TTEEEEEEEE.TTEEEEEEETCCEEEEEEE CS
                       Fe-S_biosyn  76 lvfldeglvldfved.lgtlgLksdngilddnvgl 109
                                       +  l e+ v+ fv+d +++ gL+  n+++++  ++
  gi|474934711|ref|YP_007688293.1|  70 AKSL-EDCVIEFVDDpNFGTGLSIRNPNFNGCSSC 103
                                       ****.89*****98857799********9986666 PP

>> Glyco_hydro_36  Glycosyl hydrolase 36 superfamily, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   1.4e-05      0.13     227     314 ..       7      98 ..       3     103 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 1.4e-05
                    Glyco_hydro_36 227 kaekaadklreaiekyaWdGewflRaytkdgekiGskeneeg.kiflesqslavlsGigkderakvaldsvekyLdt 302
                                        aek  d+l e  +k++W  + +l +y   g + G   ++e+ +     ++   +     de ak   d v +++d 
  gi|474934711|ref|YP_007688293.1|   7 DAEKFIDDLLEKNQKQGWGIKIYLSGYACSGPQFGMSFQKEAaEGETVDETAKNFKMFYDDETAKSLEDCVIEFVDD 83 
                                       689999*****************************665555403444444555555566777888888888888887 PP

                    Glyco_hydro_36 303 e...yGlvlqqPafs 314
                                       +    Gl +++P f+
  gi|474934711|ref|YP_007688293.1|  84 PnfgTGLSIRNPNFN 98 
                                       664456778888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 707.28
//
Query:       gi|474934712|ref|YP_007688294.1|  [L=516]
Description: ERCC4-like helicase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-23   83.7   0.0    3.2e-21   75.7   0.1    2.5  2  Helicase_C  Helicase conserved C-terminal domain
      7e-20   71.7   0.0    1.2e-19   71.0   0.0    1.4  1  ResIII      Type III restriction enzyme, res subunit
    2.2e-17   63.4   0.0    5.3e-15   55.6   0.0    2.6  3  DEAD        DEAD/DEAH box helicase
  ------ inclusion threshold ------
      0.026   13.9   0.0      0.052   12.9   0.0    1.4  1  DUF3638     Protein of unknown function (DUF3638)
      0.032   13.5   0.0      0.062   12.5   0.0    1.4  1  DUF2075     Uncharacterized conserved protein (DUF2075)
      0.084   13.5   0.1       0.54   10.9   0.0    2.1  2  DUF4404     Domain of unknown function (DUF4404)
       0.19   11.3   0.9       0.48   10.0   0.3    1.9  2  SRP54       SRP54-type protein, GTPase domain


Domain annotation for each model (and alignments):
>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.6   0.0    0.0078        20      14      61 ..      55     104 ..      45     177 .. 0.88
   2 !   75.7   0.1   1.3e-24   3.2e-21       9     110 ..     351     460 ..     343     461 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0078
                                       TTTSEEEEEESSHHHHHH.HHHHHHHT...TSTEEEESTTSTHHHHHHHHHH CS
                        Helicase_C  14 eeggkilifvntidrlek.vklllekk...gikvavlhgelpqnereeileq 61 
                                        +g+k+li+++t+  +++   ++   +   ++ +  l+g++  ++r +++++
  gi|474934712|ref|YP_007688294.1|  55 TKGRKVLIMAPTKPLVDQhRGYFS--SvlpSFVIGLLNGNMDPKKRADVVSA 104
                                       6899**********9999877773..334799**************998865 PP

  == domain 2  score: 75.7 bits;  conditional E-value: 1.3e-24
                                       HH...HHTTTTSEEEEEESSHHHHHH.HHHHHHHT....TSTEEEESTT....STHHHHHHHHHHHHTTSSSEEEES CS
                        Helicase_C   9 ll...kleeeggkilifvntidrlek.vklllekk....gikvavlhge....lpqnereeileqfnkgesdvLiat 73 
                                       l+    +e eg+ki+if++++++++  ++          g kv++l g+     +q+e++ +l++f++g ++v++at
  gi|474934712|ref|YP_007688294.1| 351 LVsrvLSEGEGSKIIIFTQYRESCDIiAEK----VsavgGAKVCKLIGQanggQKQKEQIGTLDDFRRGVYNVVVAT 423
                                       4344448899**************655444....345569999999877666699********************** PP

                                       GGGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSST CS
                        Helicase_C  74 dvaerGidipkvnlVinfdlprnvtsyiqriGRtgRa 110
                                       +v+e+G+di + n Vi++++  +  + iqr+GRtgR 
  gi|474934712|ref|YP_007688294.1| 424 SVGEEGLDIASTNAVIFYEPVPSEIRTIQRRGRTGRK 460
                                       ************************************7 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.0   0.0   4.5e-23   1.2e-19      24     169 ..      29     166 ..      13     168 .. 0.89

  Alignments for each domain:
  == domain 1  score: 71.0 bits;  conditional E-value: 4.5e-23
                                       TSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--.... CS
                            ResIII  24 dkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgdkkka.kek 99 
                                       +++ l+ ++TG GKT vaa++++++l+kg+  k+l+++p+k l++q +  f+++l++    + + ++g+ + + ++ 
  gi|474934712|ref|YP_007688294.1|  29 RENTLVILPTGLGKTAVAARVAAEVLTKGR--KVLIMAPTKPLVDQHRGYFSSVLPSF---VIGLLNGNMDPKkRAD 100
                                       56889**********************988..************************86...6777777766663344 PP

                                       ....-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHHHHT---.SEEEEEESS- CS
                            ResIII 100 dstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswreilekfke.avllglTATp 169
                                         + ++++++t q + +d+     +s +++ + f ++++DEaH+++++ ++  ++e++++  +++g+TA p
  gi|474934712|ref|YP_007688294.1| 101 VVSASDMIISTPQCIENDL-----DSRRYSLKDFGLVVFDEAHKATGSYAYVGVAEHISPgTYVIGMTASP 166
                                       67899**************.....9**********************889********9989*******98 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.6   0.0   2.1e-18   5.3e-15       3     175 ..      19     172 ..      17     173 .. 0.77
   2 ?   -3.3   0.0       2.5   6.4e+03      99     113 ..     206     222 ..     198     240 .. 0.63
   3 !    5.1   0.0    0.0069        18      37     105 ..     353     424 ..     331     440 .. 0.78

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 2.1e-18
                                       HHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   3 iQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvl 79 
                                       +Qa + + ++  ++ lv  +TG GKT++++  + + +     ++g k+li++Pt+ L+ q+   +++++      + 
  gi|474934712|ref|YP_007688294.1|  19 YQADMAKGCM-RENTLVILPTGLGKTAVAARVAAEVL-----TKGRKVLIMAPTKPLVDQHRGYFSSVLPSF--VIG 87 
                                       5666666666.679****************9999888.....5789***********************963..333 PP

                                       EEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  80 liiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdg 156
                                       l+ g+ + ++  +++ +  d++++tp+ + + l++++ +l+++ ++V+DEa++   +     +  +++++       
  gi|474934712|ref|YP_007688294.1|  88 LLNGNMDPKKRADVV-SASDMIISTPQCIENDLDSRRYSLKDFGLVVFDEAHKATGS---YAYVGVAEHI------S 154
                                       455666666666666.99*************9998999**************99887...2233333344......1 PP

                                       T.TTSEEEEEESSBSHHHHH CS
                                       x.xxxxxxxxxxxxxxxxxx RF
                              DEAD 157 k.lqrqvivlSATlpkdvkk 175
                                       +     vi ++A + +d+kk
  gi|474934712|ref|YP_007688294.1| 155 PgT--YVIGMTASPGSDLKK 172
                                       211..266666666666665 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.5
                                       SEEEEEHHHHHHHH..H CS
                                       xxxxxxxxxxxxxx..x RF
                              DEAD  99 divvgtpgrlddll..s 113
                                       +ivv  p+ l+d+    
  gi|474934712|ref|YP_007688294.1| 206 RIVVNMPQDLVDVSnmF 222
                                       68899999998866332 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.0069
                                       HHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEET....TSSHHHHHHHHH...TT.CSEEEEEH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxx...xx.xxxxxxxx RF
                              DEAD  37 qivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliig....gvaardqlskld...ng.vdivvgtp 105
                                       ++v+   + +g k++i +  re +  ++++++ ++     +v+ +ig    g+++++q+ +ld   +g +++vv+t 
  gi|474934712|ref|YP_007688294.1| 353 SRVL--SEGEGSKIIIFTQYRESCDIIAEKVSAVGG---AKVCKLIGqangGQKQKEQIGTLDdfrRGvYNVVVATS 424
                                       3343..477889**********************99...47776666555589999999999655355889999885 PP

>> DUF3638  Protein of unknown function (DUF3638)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     2e-05     0.052      24      93 ..      17      82 ..      13      90 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2e-05
                           DUF3638 24 ReeQaevAkemispssgensvlQLnmGeGKssvIvPivaaaladgkkLvrvivlkpllkqmaqlLvskLg 93
                                      R+ Qa++Ak  +    +en+++ L  G GK++v   ++a +l++g+k++ +  +kpl++q + + +s L 
  gi|474934712|ref|YP_007688294.1| 17 RRYQADMAKGCM----RENTLVILPTGLGKTAVAARVAAEVLTKGRKVLIMAPTKPLVDQHRGYFSSVLP 82
                                      556666666666....59******************************************9988888775 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.4e-05     0.062      11     101 ..      39     141 ..      33     153 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.4e-05
                           DUF2075  11 GtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakke............ekkkkkeafeklssfinnls 75 
                                       G GKt v+ +++ae+    ++r++ ++   +plv+  r  +++               +kk+ ++++ ++ +i + +
  gi|474934712|ref|YP_007688294.1|  39 GLGKTAVAARVAAEV--LTKGRKVLIMAPTKPLVDQHRGYFSSVLpsfvigllngnmDPKKRADVVSASDMIISTPQ 113
                                       88*************..999999999999999999888888777777788888777677777888888888888777 PP

                           DUF2075  76 ef..kkaeekkeepkedvvivDEAhrll 101
                                           +   ++ + +++ +v++DEAh+++
  gi|474934712|ref|YP_007688294.1| 114 CIenDLDSRRYSLKDFGLVVFDEAHKAT 141
                                       55866677788899************97 PP

>> DUF4404  Domain of unknown function (DUF4404)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00021      0.54      15      79 ..     288     357 ..     283     358 .. 0.83
   2 ?   -0.6   0.1      0.81   2.1e+03      22      34 ..     489     501 ..     471     510 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00021
                           DUF4404  15 nesldeetralLeslaedieellaeedaaaeeee.....laerlneaverFeeeHPklagvlreildsLa 79 
                                        + ++++  ++L+s+ ++i+e  ++ed   +++e       +++ ++v++  +eHPk+++++  +  +L+
  gi|474934712|ref|YP_007688294.1| 288 IDYAETQGMSTLRSFLQKINEGAESEDGSRADRElvsreNYKKIWKIVSTSRVEHPKISRIMSLVSRVLS 357
                                       5555666677899999999999999999999998887777788999****************99999887 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.81
                           DUF4404  22 tralLeslaedie 34 
                                        r++Le+l +d++
  gi|474934712|ref|YP_007688294.1| 489 MRERLETLSRDLS 501
                                       3445555555544 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.3   0.00019      0.48       7      36 ..      35      64 ..      30      67 .. 0.89
   2 ?   -2.3   0.0       1.1   2.9e+03     113     138 ..     461     486 ..     446     489 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00019
                                      EESTTSSHHHHHHHHHHHHHHTTS-EEEEE CS
                             SRP54  7 vGlqGaGKTttlaKLaallkkegkkvllva 36
                                      + ++G GKT  +a++aa + ++g+kvl++a
  gi|474934712|ref|YP_007688294.1| 35 ILPTGLGKTAVAARVAAEVLTKGRKVLIMA 64
                                      5579***********************998 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.1
                                       SSSEEEEEEETTBHTHHHHHHHHHHH CS
                             SRP54 113 kpdevllvldattgqeavkqakaFke 138
                                       ++ ev++ + a t  e+v+qa++ ke
  gi|474934712|ref|YP_007688294.1| 461 NDGEVYMLIAADTMDEVVEQASKKKE 486
                                       55677788888888888888777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (516 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       805  (0.0448993); expected 358.6 (0.02)
Passed bias filter:                      696  (0.0388198); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:00.49
# Mc/sec: 3171.47
//
Query:       gi|474934713|ref|YP_007688295.1|  [L=605]
Description: DNA ligase I, ATP-dependent (dnl1) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.6e-52  177.0   0.0    5.3e-52  176.4   0.0    1.2  1  DNA_ligase_A_M  ATP dependent DNA ligase domain
    3.1e-38  131.8   0.0    5.2e-38  131.1   0.0    1.4  1  DNA_ligase_A_N  DNA ligase N terminus
    5.8e-20   71.7   0.0    1.1e-19   70.9   0.0    1.5  1  DNA_ligase_A_C  ATP dependent DNA ligase C terminal region


Domain annotation for each model (and alignments):
>> DNA_ligase_A_M  ATP dependent DNA ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.4   0.0   8.9e-56   5.3e-52       2     204 .]     227     435 ..     226     435 .. 0.95

  Alignments for each domain:
  == domain 1  score: 176.4 bits;  conditional E-value: 8.9e-56
                                       EEEEEESCHHHHHHHTTTSEEEEEEEESSEEEEEE..E.ETTEEEEEETTS-B-GGGCHHHHHHHHHHBSTTESEEE CS
                    DNA_ligase_A_M   2 mLAeslksiekalkkleekafivEiKyDGeRaqvh..k.egdkvklfSRrlkditaakpelvkalkeafkkdeksvi 75 
                                       mLAe+l+s+ ++++++ +++  +E+KyDG R+q h  k +g+ vkl+SRrl+d+t+++p++ +al++++  +  ++i
  gi|474934713|ref|YP_007688295.1| 227 MLAERLRSLPDIIDRM-GGKCAFEYKYDGIRVQAHirKgDGGFVKLYSRRLEDMTSNFPDIAEALQRQLRGS--EAI 300
                                       9***************.56666*********888854568999**********************9999887..8** PP

                                       EEEEEEEEETTTTCBEHHHHHCHHHHCHCCTHHHHHHSEEEEEEEEEEEETTEEHTTSCHHHHHHHHHHHB.....- CS
                    DNA_ligase_A_M  76 lDGElvavdketgeilpfqklasrkkkkkkveeklkeaelclfvFDiLyldgesltdeplkeRrklLeeil.....k 147
                                       ++GE+va+d+ t++ +pfq +++r +kk+ ++++++ +++++f+FD+Lyldg+++t  p+ +Rr++Le ++      
  gi|474934713|ref|YP_007688295.1| 301 IEGECVAIDPSTDNLMPFQNVTHR-RKKHGMSQAVEDVPVRIFMFDLLYLDGTDYTLSPYPKRREILEGAFdvntdP 376
                                       ************************.99999*****************************************999999 PP

                                       -BTTTEEE--EEEESSHHHHHHHHHHHHHTTECEEEEEE..TT-CC-TTCEEEEEEEEE CS
                    DNA_ligase_A_M 148 esedrvelaeslevkdveeleelleeaiseglEGlvvKn..pdskYepgkrsknwlKvK 204
                                       + +d+v + ++ ++++ ++++++++ ai++++EG+++K+   +s+Y++g+r+  w+K+K
  gi|474934713|ref|YP_007688295.1| 377 STYDHVGYTTRAVIDNDDDAQRFFDTAIASKCEGIIAKSleDESIYRAGSRGFLWIKYK 435
                                       999************************************8789***************9 PP

>> DNA_ligase_A_N  DNA ligase N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.1   0.0   8.7e-42   5.2e-38       2     173 .]       3     176 ..       2     176 .. 0.97

  Alignments for each domain:
  == domain 1  score: 131.1 bits;  conditional E-value: 8.7e-42
                                       CHHHHHHHHHHCC.---HHHHHHHHHHHHHTS-..SHHHHHHHHHH....SS-CCCS------HHHHHHHHHHHHT- CS
                    DNA_ligase_A_N   2 FaelaelfekieestkkrlekrailanffrkvesagpedlypalrL....llPdydgreygigesllakalaealgl 74 
                                       F+++ae+f+++e+ t++rle+++il++ff+ v+   p dl ++++L    l Pd+   e+g+ ++l+ +a++ ++g+
  gi|474934713|ref|YP_007688295.1|   3 FSDIAEVFDRLEH-TSSRLEMTDILSDFFKRVD---PRDLRQIIYLsvgrLHPDFYPQELGMADKLVLRAISAVSGR 75 
                                       9************.99*************8875...99*************************************** PP

                                       -HHHHHHHHHHHS-HHHHHHHHHCCHHHH.------BHHHHHHHHHHHHH-.STTHHHHHHHHHHHHHHHS-HHHHH CS
                    DNA_ligase_A_N  75 skkkikdalakvgDlgevaeevlskrstl.akkspltieevnelLdklaaa.gkgsedekkkilkkllkraspeEak 149
                                       ++ ++++ + ++gD g++ae++++k++++   ++plt e v e L  + +a gk+s+d+k+k l+++l+ ++p Ea+
  gi|474934713|ref|YP_007688295.1|  76 PQSEVDQLSIRIGDPGDIAEQLIQKKKQMtLFSEPLTFEAVIEGLTAIETAsGKDSQDRKMKHLSRMLHDSGPVEAR 152
                                       *9999999999******************99*****************8888************************* PP

                                       HHHHHHCT---SS--HHHHHHHHH CS
                    DNA_ligase_A_N 150 yliriilkdlriglsektvldala 173
                                       y++ri+++++r+g++  tv+dala
  gi|474934713|ref|YP_007688295.1| 153 YICRIVTGRMRVGAGSMTVMDALA 176
                                       **********************97 PP

>> DNA_ligase_A_C  ATP dependent DNA ligase C terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.9   0.0   1.8e-23   1.1e-19       1      99 []     460     570 ..     460     570 .. 0.92

  Alignments for each domain:
  == domain 1  score: 70.9 bits;  conditional E-value: 1.8e-23
                                       GGGSEEEEEEEEEE..TTEEEEEEEE-SS--HHHHHHHHHHHGGGEECTTCESS---HHHHTTEEE-TT-EEEEEES CS
                    DNA_ligase_A_C   1 rgglvgslllgvyd..dgkleyvgkvgtGfsdaeleelrkklkelerkkppfaekvpeeekrdvWvePelvveVkfa 75 
                                       r+g++g+ll+++yd  +gk+ + +k gtGf+da l+ l   l++++ +++p +  v +e  +dvW+ P +v+eV++a
  gi|474934713|ref|YP_007688295.1| 460 RAGVYGALLMAAYDpdTGKFCTTCKLGTGFDDAFLASLPSLLDRYRSESKPTS--VFAEMVPDVWFVPGVVLEVTAA 534
                                       6799***************************************9999988884..444445779************* PP

                                       EEECTSSSTT...........EECT-EEE.EE-TTS CS
                    DNA_ligase_A_C  76 eitasgkyka...........slRfPrfk.rlReDk 99 
                                       +i+ s+ ++a            lRfPrf+ r+R+Dk
  gi|474934713|ref|YP_007688295.1| 535 DISISPIHTAaygsvkedaglGLRFPRFTgRVRDDK 570
                                       ***************************9989****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (605 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.40
# Mc/sec: 4517.73
//
Query:       gi|474934714|ref|YP_007688296.1|  [L=81]
Description: DNA-directed RNA polymerase, subunit L [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-11   43.6   0.0    2.3e-11   43.3   0.0    1.1  1  RNA_pol_L_2  RNA polymerase Rpb3/Rpb11 dimerisation domain


Domain annotation for each model (and alignments):
>> RNA_pol_L_2  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3   0.0   1.3e-15   2.3e-11       2      67 ..      13      77 ..      12      80 .. 0.89

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 1.3e-15
                                      EEEEEES--HHHHHHHHHHHTTSTTEEEEEEECSSTTTSEEEEEEEESTSS-HHHHHHHHHHHHHH CS
                       RNA_pol_L_2  2 ltfeingEDhTLgnlLrhlllknpsVefagYkipHPlepkmnlriqtkssnnpleaLkkalkdlld 67
                                      ++f +++ + T+  ++ + l+k+p+V fa+Y ++HP  +   l ++ k s +p +a+k+a++++ +
  gi|474934714|ref|YP_007688296.1| 13 VRFGLKDANSTIIEPIIEFLNKDPEVVFARYIVDHPDLDDPILEVKVK-SGTPEDAVKRAAESVGK 77
                                      68999*******************************988888888875.589*********98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 543.25
//
Query:       gi|474934715|ref|YP_007688297.1|  [L=437]
Description: conserved hypothetical protein TIGR00094 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.4e-147  491.8   0.0   1.6e-147  491.7   0.0    1.0  1  TruD      tRNA pseudouridine synthase D (TruD)


Domain annotation for each model (and alignments):
>> TruD  tRNA pseudouridine synthase D (TruD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  491.7   0.0  9.1e-152  1.6e-147       2     416 .]      13     429 ..      12     429 .. 0.97

  Alignments for each domain:
  == domain 1  score: 491.7 bits;  conditional E-value: 9.1e-152
                              TruD   2 lgielyvtdtegigGrlrespeDFiVeEieefsge.eeadegeylvlrvekrnwdtldlvrelaralgisrkrvgfa 77 
                                       +g+ +y++ ++g+gGrl++++ DFiV+Ei   s + e +d+g++++++v+ rnw+t+++vr lar++ +sr+r+gfa
  gi|474934715|ref|YP_007688297.1|  13 IGMLYYLSGADGTGGRLKADAGDFIVDEI---SSRpEPSDRGKFTIATVRARNWETNRMVRLLARQMDMSRERIGFA 86 
                                       89***************************...44445799************************************* PP

                              TruD  78 GtKDkrAvTtQlisirkvepeelealeikdvelevvgrarrklrlGdLaGNkFeirvrdv.aeeeeaakraeeilee 153
                                       GtKDkrAvTtQl+s   + p++le++++kd+e+++v +a+r +rlGdL+GN+F+irv++v +++ e ++ ++++ ++
  gi|474934715|ref|YP_007688297.1|  87 GTKDKRAVTTQLMSF-MCPPSQLEKVDLKDIEISDVYTAKRGMRLGDLIGNRFTIRVTGVgKTAGEISSITDAVRAD 162
                                       **************5.58999***************************************99999************ PP

                              TruD 154 leekggvPNyfGvQRFGsrrpvthlvGkaivkgdleeAvelyvgkpfeeesedtrea..reavaetgdleealeelp 228
                                       +++ gg+PNyfGvQRFG +rp+th+vG+++v+gd+e+Av++yv++p++ees+d ++a  r+++ae++d+++ ++++p
  gi|474934715|ref|YP_007688297.1| 163 IKAAGGFPNYFGVQRFGVIRPITHKVGEYLVRGDVEGAVKCYVCDPASEESKDEQAAemRRKLAESDDWSSLIHDIP 239
                                       *************************************************999888766699999************* PP

                              TruD 229 kslryErallkrLaekpkdykkAlealpknLqrlFvhAyqSylFNrvlseRlerglpldepveGDvvifaeer.lpd 304
                                       +s+++Er+++++L+++p+dy ++++ lp+nLq++FvhAyqSylFN +lseR++rglpl++pv GDvv+  + + +pd
  gi|474934715|ref|YP_007688297.1| 240 DSMSFERTMVSYLMDNPGDYVGSIRILPTNLQMMFVHAYQSYLFNLMLSERIARGLPLNRPVLGDVVVPVDIDgIPD 316
                                       ********************************************************************998778*** PP

                              TruD 305 tdrlqlvteknveevkrliergrafvtaplvGtetelaegevgeierevleeegleledFklpklpelsskGtrRai 381
                                       ++++ l tekn++ ++r+++ grafvt  l+G+e+ +aege+geier++++++g+++ dF +p+l+++ss+G+rR+i
  gi|474934715|ref|YP_007688297.1| 317 HEKQILTTEKNIDLAERQVKLGRAFVTHALYGSESVFAEGEPGEIERKIVSDAGVKAGDFYIPELQHCSSEGDRREI 393
                                       ***************************************************************************** PP

                              TruD 382 llrvedlelsaeede.ltleFsLpkGsYATvvlrEi 416
                                       +++v+dl++s+ + + +t++FsLpkG+YAT+++rE+
  gi|474934715|ref|YP_007688297.1| 394 VCPVKDLAVSDVQGSsYTVSFSLPKGNYATCLMREF 429
                                       *****99988765444*******************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2693.78
//
Query:       gi|474934716|ref|YP_007688298.1|  [L=1211]
Description: Tfp pilus assembly protein PilF [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-41  140.4  39.9    3.7e-06   27.3   0.6   14.6 16  TPR_19           Tetratricopeptide repeat
    3.2e-30  102.2  39.3     0.0078   16.9   0.7   19.3 21  TPR_14           Tetratricopeptide repeat
    5.9e-27   91.6  31.0       0.12   12.6   0.2   19.2 21  TPR_2            Tetratricopeptide repeat
    2.1e-19   68.0  17.0       0.11   12.8   0.0   13.9 13  TPR_8            Tetratricopeptide repeat
    4.5e-19   68.8  41.2     0.0026   18.4   3.2   13.7 14  TPR_16           Tetratricopeptide repeat
    2.3e-18   65.6  22.9      0.025   14.3   0.1   11.7 12  TPR_11           TPR repeat
    3.6e-17   62.3  12.5      0.025   14.8   0.0    9.5 10  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    3.1e-15   55.2  19.7      0.013   15.3   0.0   11.1 12  TPR_1            Tetratricopeptide repeat
    2.2e-14   52.7   1.5         11    6.6   0.0   11.8 10  TPR_17           Tetratricopeptide repeat
    2.8e-12   46.6  21.3       0.62   10.3   0.0   11.3 12  TPR_9            Tetratricopeptide repeat
    1.6e-10   40.7  17.6     0.0074   15.5   0.0    7.4  7  TPR_15           Tetratricopeptide repeat
    2.2e-09   37.5  31.9       0.11   12.8   2.5   12.3 13  TPR_12           Tetratricopeptide repeat
    2.5e-09   36.6  18.7      0.082   11.8   0.3    7.9  7  NARP1            NMDA receptor-regulated protein 1
    7.9e-07   28.4   1.2      0.045   12.8   0.0    4.3  4  ChAPs            ChAPs (Chs5p-Arf1p-binding proteins)
    2.5e-06   28.0  10.1        2.5    8.6   0.2    7.5  7  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
    2.7e-05   24.5  28.9         56    4.7   0.0   14.1 14  TPR_6            Tetratricopeptide repeat
    4.8e-05   23.8  15.9       0.46   10.9   0.0    6.6  7  BTAD             Bacterial transcriptional activator domain
    0.00013   22.3  26.7       0.39   11.1   0.3   10.1 13  TPR_20           Tetratricopeptide repeat
    0.00015   21.8   1.5       0.62   10.2   0.0    5.5  5  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
     0.0033   17.3  19.8         13    6.0   0.1   11.2 10  TPR_7            Tetratricopeptide repeat
     0.0055   16.2   7.1      0.051   13.0   0.2    4.5  5  Coatomer_E       Coatomer epsilon subunit
     0.0072   16.5   7.5       0.57   10.6   0.1    5.7  3  PPR              PPR repeat
  ------ inclusion threshold ------
      0.018   14.3   0.2        4.6    6.4   0.1    3.0  2  FAT              FAT domain
      0.032   13.8   7.9        5.9    6.6   0.0    5.0  4  HrpB1_HrpK       Bacterial type III secretion protein (HrpB1_


Domain annotation for each model (and alignments):
>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1       1.2   9.3e+02      19      49 ..      76     106 ..      71     123 .. 0.87
   2 ?   -0.1   0.0       1.8   1.3e+03      31      58 ..     121     148 ..     113     158 .. 0.80
   3 ?    5.4   0.0     0.035        26       2      27 ..     233     258 ..     232     268 .. 0.88
   4 !   21.0   0.0   4.6e-07   0.00034       5      53 ..     270     318 ..     266     330 .. 0.93
   5 !   11.6   0.2   0.00041       0.3       4      60 ..     337     393 ..     334     401 .. 0.89
   6 !   12.5   0.1   0.00022      0.16       2      45 ..     369     412 ..     368     413 .. 0.95
   7 !   20.8   0.0   5.5e-07   0.00041       9      68 .]     410     469 ..     406     469 .. 0.95
   8 !   13.5   0.6   0.00011     0.079       1      62 [.     500     561 ..     500     566 .. 0.91
   9 ?    5.6   0.0      0.03        22       5      64 ..     572     630 ..     569     635 .. 0.87
  10 !   11.9   0.1   0.00033      0.25       3      57 ..     638     692 ..     636     704 .. 0.91
  11 !   18.7   0.3   2.5e-06    0.0019       5      41 ..     707     743 ..     703     745 .. 0.92
  12 ?    5.4   0.1     0.036        27      12      45 ..     748     781 ..     743     799 .. 0.83
  13 !   12.8   0.0   0.00018      0.13       1      60 [.     819     878 ..     819     890 .. 0.91
  14 ?    0.3   0.1       1.4     1e+03       5      45 ..     891     930 ..     887     932 .. 0.83
  15 !   27.3   0.6     5e-09   3.7e-06       7      68 .]     926     986 ..     921     986 .. 0.95
  16 ?   -1.1   0.0       3.7   2.7e+03      38      51 ..    1146    1159 ..    1128    1165 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.2
                            TPR_19  19 qedpknaearllLAeallalgqldeAealLd 49 
                                       ++ p++  a l+ A +l   g ++eA+  L+
  gi|474934716|ref|YP_007688298.1|  76 KQRPQDCKASLAAASCLARKGIVNEARTYLE 106
                                       56789999999****************9887 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.8
                            TPR_19  31 LAeallalgqldeAealLdalpeedpdd 58 
                                        Ae+l+a  +++eA + L   +++dp +
  gi|474934716|ref|YP_007688298.1| 121 KAEVLVADQHTQEAAKSLMGSLRSDPLN 148
                                       5899999999999999999888888874 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.035
                            TPR_19   2 laegdyaeAlalleqalqedpknaea 27 
                                        +egd  +A++++e+a +  p++ ++
  gi|474934716|ref|YP_007688298.1| 233 RDEGDWVNAQRMYEKASKSMPDDINV 258
                                       689*************9999998765 PP

  == domain 4  score: 21.0 bits;  conditional E-value: 4.6e-07
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpe 53 
                                       gd + Ala++++a ++dp n+ +  +L++ +++lg   eA ++L++ ++
  gi|474934716|ref|YP_007688298.1| 270 GDAETALARFRSAEAHDPANPIVVRGLIRGYMSLGKNSEALEILNEFLD 318
                                       89******************************************98666 PP

  == domain 5  score: 11.6 bits;  conditional E-value: 0.00041
                            TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddar 60 
                                       +g  aeA +  +++l  +p++a a + + + ++a g+l eAea  +a+   +++d++
  gi|474934716|ref|YP_007688298.1| 337 MGYSAEASEVASAILNTYPGDATACIVMSKSMVAEGNLREAEAYAKAAVSNNRKDPE 393
                                       66678899999999999********************************99999975 PP

  == domain 6  score: 12.5 bits;  conditional E-value: 0.00022
                            TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAe 45 
                                       +aeg++ eA a+ ++a + + k++e ++++ +++l l ++ +A 
  gi|474934716|ref|YP_007688298.1| 369 VAEGNLREAEAYAKAAVSNNRKDPESLAQMSRVYLVLRHTSKAV 412
                                       69***********************************9999995 PP

  == domain 7  score: 20.8 bits;  conditional E-value: 5.5e-07
                            TPR_19   9 eAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasLlAkl 68 
                                        A+++ ++a ++d+k+  a+  L+e++ ++g+ d A++++ +++e dp + ++a++l kl
  gi|474934716|ref|YP_007688298.1| 410 KAVRYAKRAVSADAKSVTALTTLMEVYREAGENDMAMETCRKILEIDPHNDEAANVLSKL 469
                                       6999*********************************************99999999886 PP

  == domain 8  score: 13.5 bits;  conditional E-value: 0.00011
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62 
                                       l+ae +yaeA +l +   +++ + a++r l  +a +alg++ +A a  + + + +p +a+++
  gi|474934716|ref|YP_007688298.1| 500 LIAERKYAEAEKLCRDNDDKYGNVAAVRRLRGNAEYALGEFLKASASFASAAALEPECAEIW 561
                                       799*************988899999999999*********************9999987765 PP

  == domain 9  score: 5.6 bits;  conditional E-value: 0.03
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasL 64 
                                       gd+++A a++ qa   d kn+  ++    ++   g+  +A +  +++ e d+  + ya +
  gi|474934716|ref|YP_007688298.1| 572 GDLDSAEAAYNQAVLLDMKNPHYWISKGCVQEMKGNKVAAVDSFNRAIELDQS-STYALV 630
                                       99999*******99999999999998899999999999999999999999999.888755 PP

  == domain 10  score: 11.9 bits;  conditional E-value: 0.00033
                            TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                       + g++ +A++++  a + dpkn +++   ++++la+ ++++A  + ++l ++dpd
  gi|474934716|ref|YP_007688298.1| 638 EYGRFSDAINFMDLAEATDPKNNDIQKIKMQIYLAATRFTDAAYIGKKLVKKDPD 692
                                       6799**************************************9999999999999 PP

  == domain 11  score: 18.7 bits;  conditional E-value: 2.5e-06
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgql 41 
                                        d a+A +ll +al++dp+n +++  + e++ ++g+ 
  gi|474934716|ref|YP_007688298.1| 707 DDTAAARKLLDKALADDPDNVDLLVVYRELCQKMGDN 743
                                       589*******************************985 PP

  == domain 12  score: 5.4 bits;  conditional E-value: 0.036
                            TPR_19  12 alleqalqedpknaearllLAeallalgqldeAe 45 
                                       a  +++++ d  + e r  LA+al++ g+ deA 
  gi|474934716|ref|YP_007688298.1| 748 AVCRNIIKLDQYDKESRKILADALYKVGRGDEAS 781
                                       6667788888889999999**************7 PP

  == domain 13  score: 12.8 bits;  conditional E-value: 0.00018
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddar 60 
                                       ll+ gd   A ++  +a++ dp+n +  l  A ++  +g++  A a L++++  +p +a 
  gi|474934716|ref|YP_007688298.1| 819 LLEVGDVVGAGRMADKAMESDPDNVDYILFRASVYRRTGDIRVADAFLSQYLTRNPSSAP 878
                                       68889**************************************************99765 PP

  == domain 14  score: 0.3 bits;  conditional E-value: 1.4
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAe 45 
                                       g y +A++ ++ a   +   +++   L +++ ++   d+A 
  gi|474934716|ref|YP_007688298.1| 891 GEYKAAADSYSDA-LRNGARPDVYVKLGNVQEKMDARDAAV 930
                                       8899999999998.667889999999999999988888875 PP

  == domain 15  score: 27.3 bits;  conditional E-value: 5e-09
                            TPR_19   7 yaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasLlAkl 68 
                                        ++A++ +++a + dp++++a  +LA +++++ ++d A + + + +++++  a+  + lA++
  gi|474934716|ref|YP_007688298.1| 926 RDAAVNSYSNAVKIDPHDSDASRALALLQIKTHDYDGALRSIRTSLASEQT-AEGYAILAQI 986
                                       5899***********************************************.99999**997 PP

  == domain 16  score: -1.1 bits;  conditional E-value: 3.7
                            TPR_19   38 lgqldeAealLdal 51  
                                        ++++deA+ lL+ +
  gi|474934716|ref|YP_007688298.1| 1146 AKDVDEAKVLLAYI 1159
                                        57899999999876 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       3.4   2.5e+03       8      40 ..     122     154 ..     118     155 .. 0.87
   2 ?    1.1   0.0       1.2   9.3e+02       8      35 ..     229     256 ..     222     264 .. 0.79
   3 !    9.8   0.0     0.002       1.5       8      42 ..     263     297 ..     257     299 .. 0.88
   4 ?    1.3   0.0       1.1   8.2e+02       7      28 ..     296     317 ..     292     324 .. 0.87
   5 ?    6.4   0.0     0.026        19       9      42 ..     332     365 ..     323     367 .. 0.85
   6 ?    7.1   0.1     0.015        11      11      36 ..     368     393 ..     364     398 .. 0.83
   7 !   11.3   0.0   0.00068      0.51       1      42 [.     392     433 ..     392     435 .. 0.91
   8 !   16.8   0.0   1.2e-05     0.009       3      43 ..     428     468 ..     426     469 .. 0.89
   9 ?    0.7   0.0       1.7   1.3e+03       6      26 ..     495     515 ..     491     515 .. 0.88
  10 !    9.4   0.6    0.0027         2       2      39 ..     525     562 ..     524     568 .. 0.90
  11 ?    7.5   0.1     0.011       8.5      10      39 ..     567     596 ..     564     599 .. 0.87
  12 ?   -1.3   0.0       7.4   5.6e+03      19      38 ..     610     629 ..     604     635 .. 0.76
  13 ?    5.1   0.0     0.065        49       5      38 ..     630     663 ..     627     672 .. 0.85
  14 !   16.9   0.7   1.1e-05    0.0078       5      40 ..     697     732 ..     693     738 .. 0.87
  15 ?    0.1   0.0       2.7     2e+03       4      32 ..     764     791 ..     761     800 .. 0.78
  16 ?    1.6   0.0      0.92   6.9e+02       5      39 ..     813     847 ..     809     850 .. 0.85
  17 !    8.5   0.0    0.0053       3.9       5      44 .]     847     886 ..     843     886 .. 0.92
  18 ?    4.1   0.1      0.14   1.1e+02       6      35 ..     882     910 ..     879     917 .. 0.77
  19 !    8.4   0.0    0.0057       4.3       1      42 [.     910     951 ..     910     953 .. 0.91
  20 ?    1.8   0.3      0.78   5.8e+02       5      43 ..     948     985 ..     945     986 .. 0.79
  21 ?   -0.8   0.1       5.1   3.8e+03      12      38 ..     971     997 ..     963    1001 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 3.4
                            TPR_14   8 aeallalGdpdeAiallrralalaPddaeawll 40 
                                       ae+l a + ++eA++ l   l+ +P +  a+ +
  gi|474934716|ref|YP_007688298.1| 122 AEVLVADQHTQEAAKSLMGSLRSDPLNVKAYEF 154
                                       8999*************9999999999888865 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 1.2
                            TPR_14   8 aeallalGdpdeAiallrralalaPdda 35 
                                       a+  +  Gd+  A +++++a +  Pdd 
  gi|474934716|ref|YP_007688298.1| 229 ARMARDEGDWVNAQRMYEKASKSMPDDI 256
                                       66677889************88778875 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.002
                            TPR_14   8 aeallalGdpdeAiallrralalaPddaeawllla 42 
                                       ++ +l+ Gd ++A+a +r a a++P+++ + + l 
  gi|474934716|ref|YP_007688298.1| 263 GDSYLNGGDAETALARFRSAEAHDPANPIVVRGLI 297
                                       56799**********************98877765 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 1.1
                            TPR_14   7 laeallalGdpdeAiallrral 28 
                                       l + ++ lG+  eA+++l++ l
  gi|474934716|ref|YP_007688298.1| 296 LIRGYMSLGKNSEALEILNEFL 317
                                       7899**************9876 PP

  == domain 5  score: 6.4 bits;  conditional E-value: 0.026
                            TPR_14   9 eallalGdpdeAiallrralalaPddaeawllla 42 
                                       + +l+ G  +eA +++ ++l ++P+da+a + + 
  gi|474934716|ref|YP_007688298.1| 332 REMLRMGYSAEASEVASAILNTYPGDATACIVMS 365
                                       446899***********************99886 PP

  == domain 6  score: 7.1 bits;  conditional E-value: 0.015
                            TPR_14  11 llalGdpdeAiallrralalaPddae 36 
                                       + a G+++eA+a++++a++ + +d+e
  gi|474934716|ref|YP_007688298.1| 368 MVAEGNLREAEAYAKAAVSNNRKDPE 393
                                       6789***************8888776 PP

  == domain 7  score: 11.3 bits;  conditional E-value: 0.00068
                            TPR_14   1 peallalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       pe l+++ +++l l+ + +A+++++ra++++ ++ +a++ l+
  gi|474934716|ref|YP_007688298.1| 392 PESLAQMSRVYLVLRHTSKAVRYAKRAVSADAKSVTALTTLM 433
                                       678999****************************99997765 PP

  == domain 8  score: 16.8 bits;  conditional E-value: 1.2e-05
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                       al  l e+++++G+ d A++ +r++l+ +P ++ea   l +
  gi|474934716|ref|YP_007688298.1| 428 ALTTLMEVYREAGENDMAMETCRKILEIDPHNDEAANVLSK 468
                                       566799**************************999877766 PP

  == domain 9  score: 0.7 bits;  conditional E-value: 1.7
                            TPR_14   6 alaeallalGdpdeAiallrr 26 
                                       +l + l a ++++eA++l+r+
  gi|474934716|ref|YP_007688298.1| 495 RLISTLIAERKYAEAEKLCRD 515
                                       6889999***********996 PP

  == domain 10  score: 9.4 bits;  conditional E-value: 0.0027
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawl 39 
                                       +++++++ a++alG++ +A a +  a al P+ ae+w 
  gi|474934716|ref|YP_007688298.1| 525 AVRRLRGNAEYALGEFLKASASFASAAALEPECAEIWH 562
                                       567899******************************95 PP

  == domain 11  score: 7.5 bits;  conditional E-value: 0.011
                            TPR_14  10 allalGdpdeAiallrralalaPddaeawl 39 
                                       a +a Gd+d A+a++++a+ l+ +++ +w+
  gi|474934716|ref|YP_007688298.1| 567 ADEAFGDLDSAEAAYNQAVLLDMKNPHYWI 596
                                       56889**************99999998886 PP

  == domain 12  score: -1.3 bits;  conditional E-value: 7.4
                            TPR_14  19 eAiallrralalaPddaeaw 38 
                                       +A++ ++ra++l+ ++  a+
  gi|474934716|ref|YP_007688298.1| 610 AAVDSFNRAIELDQSSTYAL 629
                                       799********987766655 PP

  == domain 13  score: 5.1 bits;  conditional E-value: 0.065
                            TPR_14   5 lalaeallalGdpdeAiallrralalaPddaeaw 38 
                                        + a+++++ G++ +Ai+  + a a++P++ +++
  gi|474934716|ref|YP_007688298.1| 630 VKKASIMAEYGRFSDAINFMDLAEATDPKNNDIQ 663
                                       5678999*********************986655 PP

  == domain 14  score: 16.9 bits;  conditional E-value: 1.1e-05
                            TPR_14   5 lalaeallalGdpdeAiallrralalaPddaeawll 40 
                                       ++la+a   l+d+++A++ll++ala++Pd+ +++  
  gi|474934716|ref|YP_007688298.1| 697 ACLARADIGLDDTAAARKLLDKALADDPDNVDLLVV 732
                                       799***************************877654 PP

  == domain 15  score: 0.1 bits;  conditional E-value: 2.7
                            TPR_14   4 llalaeallalGdpdeAiallrralalaP 32 
                                       ++ la+al+  G+ deA  l+  + ++ P
  gi|474934716|ref|YP_007688298.1| 764 RKILADALYKVGRGDEASMLYSSL-DRTP 791
                                       6779*************9999887.4444 PP

  == domain 16  score: 1.6 bits;  conditional E-value: 0.92
                            TPR_14   5 lalaeallalGdpdeAiallrralalaPddaeawl 39 
                                        ++a+ ll+ Gd  +A +++++a + +Pd+ ++ l
  gi|474934716|ref|YP_007688298.1| 813 FQIAKSLLEVGDVVGAGRMADKAMESDPDNVDYIL 847
                                       688999***********************987655 PP

  == domain 17  score: 8.5 bits;  conditional E-value: 0.0053
                            TPR_14   5 lalaeallalGdpdeAiallrralalaPddaeawlllaql 44 
                                       l +a+++++ Gd + A a l ++l ++P++a ++ ++++l
  gi|474934716|ref|YP_007688298.1| 847 LFRASVYRRTGDIRVADAFLSQYLTRNPSSAPILEAMGDL 886
                                       5689*****************************9999875 PP

  == domain 18  score: 4.1 bits;  conditional E-value: 0.14
                            TPR_14   6 alaeallalGdpdeAiallrralalaPdda 35 
                                       a++++ ++ G++++A++ + +al+ +   +
  gi|474934716|ref|YP_007688298.1| 882 AMGDLKAEVGEYKAAADSYSDALRNGAR-P 910
                                       678888999**************95433.3 PP

  == domain 19  score: 8.4 bits;  conditional E-value: 0.0057
                            TPR_14   1 peallalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       p+++ +l+ + +  +  d+A++ +  a++ +P d +a ++la
  gi|474934716|ref|YP_007688298.1| 910 PDVYVKLGNVQEKMDARDAAVNSYSNAVKIDPHDSDASRALA 951
                                       56788999**************************99999998 PP

  == domain 20  score: 1.8 bits;  conditional E-value: 0.78
                            TPR_14   5 lalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                       +ala +     d+d+A++  r  la   + ae +  laq
  gi|474934716|ref|YP_007688298.1| 948 RALALLQIKTHDYDGALRSIRTSLA-SEQTAEGYAILAQ 985
                                       6888889999***********9998.6666666666666 PP

  == domain 21  score: -0.8 bits;  conditional E-value: 5.1
                            TPR_14  12 lalGdpdeAiallrralalaPddaeaw 38 
                                       la+++++e  a+l ++++l  d + ++
  gi|474934716|ref|YP_007688298.1| 971 LASEQTAEGYAILAQICQLRKDREGVR 997
                                       678999999999999999999887766 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1         3   2.2e+03       7      25 ..      88     106 ..      83     106 .. 0.86
   2 ?    3.3   0.0      0.14   1.1e+02       8      34 .]     229     255 ..     223     255 .. 0.88
   3 ?    4.9   0.0     0.047        35       3      34 .]     258     289 ..     256     289 .. 0.92
   4 ?   -0.2   0.0       1.9   1.4e+03      11      27 ..     300     316 ..     298     319 .. 0.85
   5 ?    4.4   0.0     0.066        50       3      33 ..     360     390 ..     358     391 .. 0.81
   6 ?    4.9   0.0     0.046        35       2      30 ..     393     421 ..     392     424 .. 0.89
   7 !    7.6   0.0     0.006       4.5      10      34 .]     435     459 ..     434     459 .. 0.95
   8 ?   -1.0   0.1       3.5   2.6e+03      12      24 ..     501     513 ..     499     515 .. 0.76
   9 !    9.9   0.5    0.0011      0.85       5      33 ..     528     556 ..     524     557 .. 0.91
  10 !   12.6   0.2   0.00016      0.12       1      34 []     558     591 ..     558     591 .. 0.94
  11 !   11.1   0.0   0.00048      0.36       3      32 ..     594     623 ..     592     625 .. 0.92
  12 ?    2.5   0.0      0.26   1.9e+02       3      34 .]     628     659 ..     626     659 .. 0.88
  13 ?   -1.0   0.0       3.6   2.7e+03       9      33 ..     668     692 ..     668     693 .. 0.90
  14 !    9.8   0.0    0.0012       0.9       6      34 .]     698     726 ..     694     726 .. 0.94
  15 ?   -1.7   0.0       5.7   4.3e+03       7      20 ..     767     780 ..     765     781 .. 0.89
  16 ?    0.6   0.0         1   7.8e+02       5      34 .]     813     842 ..     809     842 .. 0.92
  17 ?    0.3   0.0       1.4     1e+03       7      33 ..     849     875 ..     844     876 .. 0.89
  18 ?    2.9   0.1       0.2   1.5e+02       3      29 ..     879     905 ..     877     906 .. 0.87
  19 !   10.5   0.0   0.00074      0.56       2      34 .]     911     943 ..     910     943 .. 0.94
  20 ?    4.0   0.0      0.09        68       5      29 ..     948     972 ..     944     976 .. 0.87
  21 ?   -2.3   0.1       9.4     7e+03       1      24 [.     977    1000 ..     977    1001 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 3
                             TPR_2   7 lGlayyklgdyeeAleafe 25 
                                        + +++++g  +eA+ ++e
  gi|474934716|ref|YP_007688298.1|  88 AASCLARKGIVNEARTYLE 106
                                       578999*********9986 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.14
                             TPR_2   8 GlayyklgdyeeAleafekAleldPnn 34 
                                       ++ ++  gd+  A + +ekA +  P++
  gi|474934716|ref|YP_007688298.1| 229 ARMARDEGDWVNAQRMYEKASKSMPDD 255
                                       5677889*************9999986 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.047
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                       +l++ G++y++ gd e Al+ f+ A ++dP n
  gi|474934716|ref|YP_007688298.1| 258 VLCETGDSYLNGGDAETALARFRSAEAHDPAN 289
                                       67889************************976 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 1.9
                             TPR_2  11 yyklgdyeeAleafekA 27 
                                       y+ lg+  eAle +++ 
  gi|474934716|ref|YP_007688298.1| 300 YMSLGKNSEALEILNEF 316
                                       999********988875 PP

  == domain 5  score: 4.4 bits;  conditional E-value: 0.066
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                       a+  + ++  + g++ eA+++ ++A++ + +
  gi|474934716|ref|YP_007688298.1| 360 ACIVMSKSMVAEGNLREAEAYAKAAVSNNRK 390
                                       566667778899*************988765 PP

  == domain 6  score: 4.9 bits;  conditional E-value: 0.046
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAlel 30 
                                       e l ++ ++y+ l +  +A+++ ++A++ 
  gi|474934716|ref|YP_007688298.1| 393 ESLAQMSRVYLVLRHTSKAVRYAKRAVSA 421
                                       6788999*******************976 PP

  == domain 7  score: 7.6 bits;  conditional E-value: 0.006
                             TPR_2  10 ayyklgdyeeAleafekAleldPnn 34 
                                       +y+++g+ + A e ++k le+dP+n
  gi|474934716|ref|YP_007688298.1| 435 VYREAGENDMAMETCRKILEIDPHN 459
                                       799********************97 PP

  == domain 8  score: -1.0 bits;  conditional E-value: 3.5
                             TPR_2  12 yklgdyeeAleaf 24 
                                       ++  +y+eA++++
  gi|474934716|ref|YP_007688298.1| 501 IAERKYAEAEKLC 513
                                       5678999999986 PP

  == domain 9  score: 9.9 bits;  conditional E-value: 0.0011
                             TPR_2   5 ynlGlayyklgdyeeAleafekAleldPn 33 
                                         +G+a y+lg++ +A + f  A +l+P+
  gi|474934716|ref|YP_007688298.1| 528 RLRGNAEYALGEFLKASASFASAAALEPE 556
                                       679*************************7 PP

  == domain 10  score: 12.6 bits;  conditional E-value: 0.00016
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       ae+++  Gla ++ gd++ A++a+++A+ ld +n
  gi|474934716|ref|YP_007688298.1| 558 AEIWHSKGLADEAFGDLDSAEAAYNQAVLLDMKN 591
                                       799**************************99765 PP

  == domain 11  score: 11.1 bits;  conditional E-value: 0.00048
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldP 32 
                                       ++   G++ + +g+   A++ f++A+eld 
  gi|474934716|ref|YP_007688298.1| 594 YWISKGCVQEMKGNKVAAVDSFNRAIELDQ 623
                                       79999***********************95 PP

  == domain 12  score: 2.5 bits;  conditional E-value: 0.26
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                       al   + + ++ g++ +A+++++ A + dP+n
  gi|474934716|ref|YP_007688298.1| 628 ALVKKASIMAEYGRFSDAINFMDLAEATDPKN 659
                                       677788899999*************9999987 PP

  == domain 13  score: -1.0 bits;  conditional E-value: 3.6
                             TPR_2   9 layyklgdyeeAleafekAleldPn 33 
                                       ++y+++ ++ +A+   +k ++ dP+
  gi|474934716|ref|YP_007688298.1| 668 QIYLAATRFTDAAYIGKKLVKKDPD 692
                                       5899999*******99*******98 PP

  == domain 14  score: 9.8 bits;  conditional E-value: 0.0012
                             TPR_2   6 nlGlayyklgdyeeAleafekAleldPnn 34 
                                       +l++a + l+d + A+++++kAl+ dP+n
  gi|474934716|ref|YP_007688298.1| 698 CLARADIGLDDTAAARKLLDKALADDPDN 726
                                       68999999*******************98 PP

  == domain 15  score: -1.7 bits;  conditional E-value: 5.7
                             TPR_2   7 lGlayyklgdyeeA 20 
                                       l++a+yk g+ +eA
  gi|474934716|ref|YP_007688298.1| 767 LADALYKVGRGDEA 780
                                       899******99998 PP

  == domain 16  score: 0.6 bits;  conditional E-value: 1
                             TPR_2   5 ynlGlayyklgdyeeAleafekAleldPnn 34 
                                       +++++++++ gd   A +  +kA e dP+n
  gi|474934716|ref|YP_007688298.1| 813 FQIAKSLLEVGDVVGAGRMADKAMESDPDN 842
                                       7899999*********************98 PP

  == domain 17  score: 0.3 bits;  conditional E-value: 1.4
                             TPR_2   7 lGlayyklgdyeeAleafekAleldPn 33 
                                       ++ +y++ gd   A +++ + l  +P 
  gi|474934716|ref|YP_007688298.1| 849 RASVYRRTGDIRVADAFLSQYLTRNPS 875
                                       8999**********9999999999985 PP

  == domain 18  score: 2.9 bits;  conditional E-value: 0.2
                             TPR_2   3 alynlGlayyklgdyeeAleafekAle 29 
                                       +l ++G++ ++ g+y+ A++ +  Al+
  gi|474934716|ref|YP_007688298.1| 879 ILEAMGDLKAEVGEYKAAADSYSDALR 905
                                       567789999999***********9996 PP

  == domain 19  score: 10.5 bits;  conditional E-value: 0.00074
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       +++  lG++ +k++  + A++ +  A+++dP++
  gi|474934716|ref|YP_007688298.1| 911 DVYVKLGNVQEKMDARDAAVNSYSNAVKIDPHD 943
                                       78999**************************86 PP

  == domain 20  score: 4.0 bits;  conditional E-value: 0.09
                             TPR_2   5 ynlGlayyklgdyeeAleafekAle 29 
                                        +l+l+ +k  dy+ Al+  + +l+
  gi|474934716|ref|YP_007688298.1| 948 RALALLQIKTHDYDGALRSIRTSLA 972
                                       689***************9998886 PP

  == domain 21  score: -2.3 bits;  conditional E-value: 9.4
                             TPR_2    1 aealynlGlayyklgdyeeAleaf 24  
                                        ae++  l++++  ++d e  ++a+
  gi|474934716|ref|YP_007688298.1|  977 AEGYAILAQICQLRKDREGVRDAY 1000
                                        788999******999999888877 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       9.5   7.1e+03      19      30 ..     240     251 ..     229     255 .. 0.80
   2 ?    1.0   0.1       0.9   6.7e+02      11      28 ..     300     317 ..     300     320 .. 0.89
   3 ?    3.4   0.1      0.14   1.1e+02      14      33 ..     371     390 ..     358     391 .. 0.85
   4 ?    3.9   0.0       0.1        75       2      33 ..     393     424 ..     392     425 .. 0.91
   5 !   11.2   0.0   0.00047      0.35      10      34 .]     435     459 ..     433     459 .. 0.93
   6 ?   -0.8   0.1       3.2   2.4e+03       8      34 .]     531     557 ..     529     557 .. 0.86
   7 !   12.7   0.1   0.00015      0.11       1      31 [.     558     588 ..     558     591 .. 0.94
   8 !    8.2   0.0    0.0043       3.2       2      32 ..     593     623 ..     592     625 .. 0.92
   9 ?    0.6   0.0       1.2   8.7e+02       9      33 ..     701     725 ..     699     726 .. 0.79
  10 ?    0.5   0.1       1.2   9.2e+02      10      32 ..     736     758 ..     735     760 .. 0.89
  11 ?    6.4   0.0     0.016        12       5      33 ..     847     875 ..     843     876 .. 0.90
  12 ?    0.9   0.1      0.96   7.2e+02       2      28 ..     878     904 ..     877     905 .. 0.85
  13 !   12.8   0.0   0.00014      0.11       2      33 ..     911     942 ..     910     943 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 9.5
                                       HHHHHHHHHHHH CS
                             TPR_8  19 eAkeyyekalel 30 
                                       +A+  yeka + 
  gi|474934716|ref|YP_007688298.1| 240 NAQRMYEKASKS 251
                                       688899999875 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.9
                                       HHHTT-HHHHHHHHHHHH CS
                             TPR_8  11 ylklgdyeeAkeyyekal 28 
                                       y++lg+  eA e +++ l
  gi|474934716|ref|YP_007688298.1| 300 YMSLGKNSEALEILNEFL 317
                                       99***********99876 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.14
                                       TT-HHHHHHHHHHHHHHHHH CS
                             TPR_8  14 lgdyeeAkeyyekaleldpd 33 
                                        g++ eA++y + a++ +++
  gi|474934716|ref|YP_007688298.1| 371 EGNLREAEAYAKAAVSNNRK 390
                                       79*************99887 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.1
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       e++ +++++yl l    +A+ y ++a+++d +
  gi|474934716|ref|YP_007688298.1| 393 ESLAQMSRVYLVLRHTSKAVRYAKRAVSADAK 424
                                       68899999********************9986 PP

  == domain 5  score: 11.2 bits;  conditional E-value: 0.00047
                                       HHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8  10 iylklgdyeeAkeyyekaleldpdn 34 
                                       +y++ g+ ++A+e+++k le+dp n
  gi|474934716|ref|YP_007688298.1| 435 VYREAGENDMAMETCRKILEIDPHN 459
                                       6999*******************75 PP

  == domain 6  score: -0.8 bits;  conditional E-value: 3.2
                                       HHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   8 gsiylklgdyeeAkeyyekaleldpdn 34 
                                       g++   lg++ +A +++  a  l+p++
  gi|474934716|ref|YP_007688298.1| 531 GNAEYALGEFLKASASFASAAALEPEC 557
                                       7777889***********999999985 PP

  == domain 7  score: 12.7 bits;  conditional E-value: 0.00015
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleld 31 
                                       ae+++ +g++ +  gd+++A+++y++a+ ld
  gi|474934716|ref|YP_007688298.1| 558 AEIWHSKGLADEAFGDLDSAEAAYNQAVLLD 588
                                       799************************9887 PP

  == domain 8  score: 8.2 bits;  conditional E-value: 0.0043
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       +++  +g++ + +g++ +A+ ++++a+eld+
  gi|474934716|ref|YP_007688298.1| 593 HYWISKGCVQEMKGNKVAAVDSFNRAIELDQ 623
                                       589999***********************97 PP

  == domain 9  score: 0.6 bits;  conditional E-value: 1.2
                                       HHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   9 siylklgdyeeAkeyyekaleldpd 33 
                                       ++ + l d  +A + + kal  dpd
  gi|474934716|ref|YP_007688298.1| 701 RADIGLDDTAAARKLLDKALADDPD 725
                                       5557899************976665 PP

  == domain 10  score: 0.5 bits;  conditional E-value: 1.2
                                       HHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8  10 iylklgdyeeAkeyyekaleldp 32 
                                       +++k+gd e+ +++++  ++ld+
  gi|474934716|ref|YP_007688298.1| 736 LCQKMGDNEALIAVCRNIIKLDQ 758
                                       6789****************996 PP

  == domain 11  score: 6.4 bits;  conditional E-value: 0.016
                                       HHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   5 ynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       +  +s+y+ +gd+  A +++ ++l+ +p+
  gi|474934716|ref|YP_007688298.1| 847 LFRASVYRRTGDIRVADAFLSQYLTRNPS 875
                                       5689**********************996 PP

  == domain 12  score: 0.9 bits;  conditional E-value: 0.96
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekal 28 
                                       +++  +g++  + g+y++A  +y  al
  gi|474934716|ref|YP_007688298.1| 878 PILEAMGDLKAEVGEYKAAADSYSDAL 904
                                       567788999999**********99887 PP

  == domain 13  score: 12.8 bits;  conditional E-value: 0.00014
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       ++y++lg++ +k+   ++A+ +y  a+++dp 
  gi|474934716|ref|YP_007688298.1| 911 DVYVKLGNVQEKMDARDAAVNSYSNAVKIDPH 942
                                       69*****************************7 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       3.5   2.6e+03      31      57 ..      79     105 ..      74     108 .. 0.81
   2 ?    2.9   0.0      0.23   1.7e+02       3      40 ..     121     155 ..     119     155 .. 0.91
   3 !   12.4   0.1   0.00026      0.19       4      68 .]     229     290 ..     226     290 .. 0.94
   4 ?   -1.5   0.0       5.6   4.2e+03       5      26 ..     298     319 ..     294     320 .. 0.86
   5 ?    6.4   0.4     0.019        14      10      33 ..     371     394 ..     367     401 .. 0.86
   6 ?    7.2   0.0     0.011       8.3       5      67 ..     400     459 ..     396     460 .. 0.94
   7 !   18.4   3.2   3.5e-06    0.0026       3      61 ..     530     585 ..     528     593 .. 0.93
   8 ?    2.0   0.0      0.44   3.3e+02      14      67 ..     609     659 ..     605     660 .. 0.90
   9 ?    0.7   0.0       1.2   8.9e+02      30      67 ..     656     693 ..     640     694 .. 0.76
  10 ?    6.8   0.6     0.014        11       3      37 ..     699     730 ..     699     733 .. 0.87
  11 ?    0.7   0.0       1.2   8.9e+02      34      53 ..     761     780 ..     750     793 .. 0.81
  12 !    8.6   0.0     0.004         3       3      66 ..     815     875 ..     813     878 .. 0.89
  13 !    9.8   0.1    0.0017       1.3       2      65 ..     882     941 ..     881     944 .. 0.77
  14 !    9.4   0.0    0.0021       1.6      13      58 ..     926     968 ..     914     975 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 3.5
                            TPR_16  31 PdaaeAllllgdaalrqgrlaeAaaly 57 
                                       P++  A+l+ + +++r+g + eA+ ++
  gi|474934716|ref|YP_007688298.1|  79 PQDCKASLAAASCLARKGIVNEARTYL 105
                                       5666799999********999999776 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.23
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllll 40 
                                       +a  +++ ++ ++Aa+ l   l++d   P+++ A+ +l
  gi|474934716|ref|YP_007688298.1| 121 KAEVLVADQHTQEAAKSLMGSLRSD---PLNVKAYEFL 155
                                       688999999****************...******9886 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.00026
                            TPR_16   4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapdap 68 
                                       ar a++ gd+  A++++e a k+    Pd+   l + gd++l  g+ + A+a +r+a +++p +p
  gi|474934716|ref|YP_007688298.1| 229 ARMARDEGDWVNAQRMYEKASKSM---PDDINVLCETGDSYLNGGDAETALARFRSAEAHDPANP 290
                                       6668899*****************...***********************************997 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 5.6
                            TPR_16   5 raalragdyddAaaaleaalkr 26 
                                       r ++ +g+  +A++ l+++l++
  gi|474934716|ref|YP_007688298.1| 298 RGYMSLGKNSEALEILNEFLDS 319
                                       678999**********999987 PP

  == domain 5  score: 6.4 bits;  conditional E-value: 0.019
                            TPR_16  10 agdyddAaaaleaalkrdpssPda 33 
                                        g+ ++A+a+++aa+ +++++P+ 
  gi|474934716|ref|YP_007688298.1| 371 EGNLREAEAYAKAAVSNNRKDPES 394
                                       69********************83 PP

  == domain 6  score: 7.2 bits;  conditional E-value: 0.011
                            TPR_16   5 raalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       r +l +++  +A++++++a+ +d      + Al  l +++ ++g+ + A + +r+ l+ +p +
  gi|474934716|ref|YP_007688298.1| 400 RVYLVLRHTSKAVRYAKRAVSAD---AKSVTALTTLMEVYREAGENDMAMETCRKILEIDPHN 459
                                       789999*****************...********************************99976 PP

  == domain 7  score: 18.4 bits;  conditional E-value: 3.5e-06
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraal 61 
                                       +++a +++g++ +A a +  a ++    P++ae +  +g+a  ++g+l+ A+a+y+ a+
  gi|474934716|ref|YP_007688298.1| 530 RGNAEYALGEFLKASASFASAAALE---PECAEIWHSKGLADEAFGDLDSAEAAYNQAV 585
                                       799**********************...************************9999886 PP

  == domain 8  score: 2.0 bits;  conditional E-value: 0.44
                            TPR_16  14 ddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                        +A+  +++a+++d        Al  ++ + ++ gr+ +A+ + + a + +p++
  gi|474934716|ref|YP_007688298.1| 609 VAAVDSFNRAIELD---QSSTYALVKKASIMAEYGRFSDAINFMDLAEATDPKN 659
                                       58999*********...99**********************9999999998875 PP

  == domain 9  score: 0.7 bits;  conditional E-value: 1.2
                            TPR_16  30 sPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       +P + + +  + +++l++ r+++Aa   +++++ +pda
  gi|474934716|ref|YP_007688298.1| 656 DPKNNDIQKIKMQIYLAATRFTDAAYIGKKLVKKDPDA 693
                                       57788888888888999999999999999998888886 PP

  == domain 10  score: 6.8 bits;  conditional E-value: 0.014
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAl 37 
                                       lara + + d ++A+++l+ al++d   Pd+++ l
  gi|474934716|ref|YP_007688298.1| 699 LARADIGLDDTAAARKLLDKALADD---PDNVDLL 730
                                       57888888999**************...9998865 PP

  == domain 11  score: 0.7 bits;  conditional E-value: 1.2
                            TPR_16  34 aeAllllgdaalrqgrlaeA 53 
                                        e++  l+da+++ gr +eA
  gi|474934716|ref|YP_007688298.1| 761 KESRKILADALYKVGRGDEA 780
                                       56777899999999998888 PP

  == domain 12  score: 8.6 bits;  conditional E-value: 0.004
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                        a+++l+ gd   A ++++ a ++d   Pd+++  l+++ ++ r g+   A a++  +l+  p+
  gi|474934716|ref|YP_007688298.1| 815 IAKSLLEVGDVVGAGRMADKAMESD---PDNVDYILFRASVYRRTGDIRVADAFLSQYLTRNPS 875
                                       6999*********************...*******************99888888888866665 PP

  == domain 13  score: 9.8 bits;  conditional E-value: 0.0017
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                       a++++ ++ g+y +Aa  +  al+++     +++ +  lg++  +    ++A+  y  a++ +p
  gi|474934716|ref|YP_007688298.1| 882 AMGDLKAEVGEYKAAADSYSDALRNG---A-RPDVYVKLGNVQEKMDARDAAVNSYSNAVKIDP 941
                                       5789999*******************...4.899999999998766565555544444455555 PP

  == domain 14  score: 9.4 bits;  conditional E-value: 0.0021
                            TPR_16  13 yddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyr 58 
                                        d+A++ +  a+k d   P + +A+ +l+++  +  ++++A+  +r
  gi|474934716|ref|YP_007688298.1| 926 RDAAVNSYSNAVKID---PHDSDASRALALLQIKTHDYDGALRSIR 968
                                       589************...*********************9986555 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.026        20       5      40 ..     233     268 ..     229     270 .. 0.89
   2 !    9.0   0.0    0.0014       1.1       1      29 [.     263     291 ..     263     296 .. 0.94
   3 ?    0.1   0.0      0.86   6.4e+02       4      15 ..     300     311 ..     299     315 .. 0.87
   4 ?    3.4   0.0      0.08        60       3      30 ..     435     462 ..     434     466 .. 0.94
   5 ?   -1.2   0.1       2.3   1.7e+03      16      31 ..     505     520 ..     504     526 .. 0.82
   6 !   12.8   0.1   9.4e-05      0.07       1      37 [.     531     567 ..     531     568 .. 0.98
   7 !    7.7   0.0    0.0038       2.8       8      42 .]     572     606 ..     570     606 .. 0.87
   8 ?    5.4   0.0      0.02        15      12      31 ..     610     629 ..     604     640 .. 0.83
   9 !    6.3   0.1      0.01       7.4      11      30 ..     710     729 ..     706     731 .. 0.88
  10 ?   -1.2   0.0       2.3   1.7e+03      19      38 ..     834     853 ..     833     857 .. 0.73
  11 !    9.4   0.2    0.0011      0.85       1      41 [.     884     923 ..     884     924 .. 0.92
  12 !   14.3   0.1   3.3e-05     0.025      11      38 ..     927     954 ..     927     957 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.026
                            TPR_11   5 yeqGkyeeAieaYkkAlkldPdnaeayynLGlayyk 40 
                                       ++ G++ +A   Y+kA k  Pd+ +++++ G+ y++
  gi|474934716|ref|YP_007688298.1| 233 RDEGDWVNAQRMYEKASKSMPDDINVLCETGDSYLN 268
                                       678999999999*******************99985 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0014
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnae 29 
                                       Gd y   G+ e A+++++ A + dP n+ 
  gi|474934716|ref|YP_007688298.1| 263 GDSYLNGGDAETALARFRSAEAHDPANPI 291
                                       99*************************96 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.86
                            TPR_11   4 yyeqGkyeeAie 15 
                                       y+++Gk+ eA+e
  gi|474934716|ref|YP_007688298.1| 300 YMSLGKNSEALE 311
                                       89********98 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.08
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaea 30 
                                       +y+e G+++ A+e  +k l++dP n ea
  gi|474934716|ref|YP_007688298.1| 435 VYREAGENDMAMETCRKILEIDPHNDEA 462
                                       79**********************9987 PP

  == domain 5  score: -1.2 bits;  conditional E-value: 2.3
                            TPR_11  16 aYkkAlkldPdnaeay 31 
                                       +Y +A kl+ dn + y
  gi|474934716|ref|YP_007688298.1| 505 KYAEAEKLCRDNDDKY 520
                                       699*********9866 PP

  == domain 6  score: 12.8 bits;  conditional E-value: 9.4e-05
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGla 37 
                                       G+a y++G++ +A +++  A +l P+ ae+++  Gla
  gi|474934716|ref|YP_007688298.1| 531 GNAEYALGEFLKASASFASAAALEPECAEIWHSKGLA 567
                                       9*******************************99987 PP

  == domain 7  score: 7.7 bits;  conditional E-value: 0.0038
                            TPR_11   8 GkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G+++ A +aY++A+ ld +n+  +   G ++ ++G
  gi|474934716|ref|YP_007688298.1| 572 GDLDSAEAAYNQAVLLDMKNPHYWISKGCVQEMKG 606
                                       899******************99888887776665 PP

  == domain 8  score: 5.4 bits;  conditional E-value: 0.02
                            TPR_11  12 eAieaYkkAlkldPdnaeay 31 
                                       +A+ ++++A++ld+++  a+
  gi|474934716|ref|YP_007688298.1| 610 AAVDSFNRAIELDQSSTYAL 629
                                       79***********9987665 PP

  == domain 9  score: 6.3 bits;  conditional E-value: 0.01
                            TPR_11  11 eeAieaYkkAlkldPdnaea 30 
                                        +A + + kAl+ dPdn+++
  gi|474934716|ref|YP_007688298.1| 710 AAARKLLDKALADDPDNVDL 729
                                       579999***********996 PP

  == domain 10  score: -1.2 bits;  conditional E-value: 2.3
                            TPR_11  19 kAlkldPdnaeayynLGlay 38 
                                       kA + dPdn++  + ++ +y
  gi|474934716|ref|YP_007688298.1| 834 KAMESDPDNVDYILFRASVY 853
                                       78999*****9765555555 PP

  == domain 11  score: 9.4 bits;  conditional E-value: 0.0011
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykq 41 
                                       Gd+  e G+y++A  +Y+ Al+ +   +++y +LG+++ k+
  gi|474934716|ref|YP_007688298.1| 884 GDLKAEVGEYKAAADSYSDALR-NGARPDVYVKLGNVQEKM 923
                                       7777888**************9.9999***********997 PP

  == domain 12  score: 14.3 bits;  conditional E-value: 3.3e-05
                            TPR_11  11 eeAieaYkkAlkldPdnaeayynLGlay 38 
                                       ++A+++Y++A+k+dP + +a  +L+l++
  gi|474934716|ref|YP_007688298.1| 927 DAAVNSYSNAVKIDPHDSDASRALALLQ 954
                                       68*******************9999876 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   3.4e-05     0.025      12      79 ..      71     138 ..      61     141 .. 0.93
   2 !    8.6   0.0    0.0028       2.1       4      80 ..     237     314 ..     234     316 .. 0.78
   3 ?    2.5   0.1      0.23   1.7e+02      11      75 ..     346     411 ..     336     414 .. 0.65
   4 !    7.0   0.3    0.0092       6.9       3      62 ..     372     432 ..     370     448 .. 0.86
   5 !    7.7   0.0    0.0055       4.1       5      62 ..     408     466 ..     405     473 .. 0.90
   6 ?    0.1   0.1       1.3   9.5e+02      34      77 ..     501     545 ..     491     550 .. 0.83
   7 ?    1.5   0.1      0.48   3.6e+02       3      81 ..     640     718 ..     638     719 .. 0.76
   8 !   10.1   0.1   0.00099      0.74       8      79 ..     712     784 ..     706     787 .. 0.88
   9 !   10.2   0.0   0.00089      0.66      11      79 ..     831     900 ..     827     903 .. 0.93
  10 ?    5.6   0.1     0.025        19       8      67 ..     929     989 ..     923    1002 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.4e-05
                                       HHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHHH CS
                            ANAPC3  12 aerllaaetespedayllAlclylngqykrAyellrkaklnskslgcrylfAqcllkLkkyeeAiaaL 79 
                                       a+++ ++ +++++++++ A cl + g  ++A ++l+        + + y++A++l++ ++ +eA + L
  gi|474934716|ref|YP_007688298.1|  71 ADLVSKQRPQDCKASLAAASCLARKGIVNEARTYLEGVHGSVDIPTYSYVKAEVLVADQHTQEAAKSL 138
                                       78888999******************************8889999*******************9887 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0028
                                       -HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHH...HHHHHTT-HHHHHH CS
                            ANAPC3   4 nyknAiflaerllaaetespedayllAlclylngqykrAyellrkaklnskslgcrylfA...qcllkLkkyeeAia 77 
                                       ++ nA  ++e++ ++++++ + +   + ++++ g+ ++A+  +r+a  + ++++  ++     + +  L+k  eA+ 
  gi|474934716|ref|YP_007688298.1| 237 DWVNAQRMYEKASKSMPDDINVLCETGDSYLNGGDAETALARFRSA--EAHDPANPIVVRgliRGYMSLGKNSEALE 311
                                       67799999*****9999999999999********************..44444444444334477778888888887 PP

                                       HH- CS
                            ANAPC3  78 aLe 80 
                                       +L 
  gi|474934716|ref|YP_007688298.1| 312 ILN 314
                                       776 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.23
                                       HHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHH CS
                            ANAPC3  11 laerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeA 75 
                                       +a+ +l++ + ++ +    ++++   g+  +A  +++ a   n k+++++  + +++l L +  +A
  gi|474934716|ref|YP_007688298.1| 346 VASAILNTYPGDATACIVMSKSMVAEGNLREAEAYAKAAvSNNRKDPESLAQMSRVYLVLRHTSKA 411
                                       555555555556666666666677777777777777777777777777777777777777666666 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.0092
                                       T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHH CS
                            ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylf 62 
                                       +n+++A+ +a  +++ ++++pe++   + +++ +    +A +++++a   + ks  ++ ++
  gi|474934716|ref|YP_007688298.1| 372 GNLREAEAYAKAAVSNNRKDPESLAQMSRVYLVLRHTSKAVRYAKRAvSADAKSVTALTTL 432
                                       68999*********999******************************88888887776655 PP

  == domain 5  score: 7.7 bits;  conditional E-value: 0.0055
                                       HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHH CS
                            ANAPC3   5 yknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylf 62 
                                       + +A+ +a r+++a+++s  ++  l +++ ++g+ + A+e +rk  ++++++ +++ ++
  gi|474934716|ref|YP_007688298.1| 408 TSKAVRYAKRAVSADAKSVTALTTLMEVYREAGENDMAMETCRKIlEIDPHNDEAANVL 466
                                       678999***************************************99999888877665 PP

  == domain 6  score: 0.1 bits;  conditional E-value: 1.3
                                       HHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHH CS
                            ANAPC3  34 ylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAia 77 
                                           +y +A +l+r++ +++++  ++r l + + ++L+++ +A a
  gi|474934716|ref|YP_007688298.1| 501 IAERKYAEAEKLCRDNdDKYGNVAAVRRLRGNAEYALGEFLKASA 545
                                       567899999999999999999999999999999999998877765 PP

  == domain 7  score: 1.5 bits;  conditional E-value: 0.48
                                       T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                            ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78 
                                       +++ +Ai + +++ a+++++++    + + ++ + +++ A ++ +k+ k+++       ++A++ + L+    A+++
  gi|474934716|ref|YP_007688298.1| 640 GRFSDAINFMDLAEATDPKNNDIQKIKMQIYLAATRFTDAAYIGKKLvKKDPDA-ITVACLARADIGLDDTAAARKL 715
                                       6788999999999988888888888899***************99994444444.4445667777777777777777 PP

                                       H-S CS
                            ANAPC3  79 Lek 81 
                                       L+k
  gi|474934716|ref|YP_007688298.1| 716 LDK 718
                                       765 PP

  == domain 8  score: 10.1 bits;  conditional E-value: 0.00099
                                       HHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH CS
                            ANAPC3   8 AiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaL 79 
                                       A  l++++la ++++ + +  + +   ++g+ +  + ++r+  kl+  ++++r ++A +l+k ++ +eA +++
  gi|474934716|ref|YP_007688298.1| 712 ARKLLDKALADDPDNVDLLVVYRELCQKMGDNEALIAVCRNIiKLDQYDKESRKILADALYKVGRGDEASMLY 784
                                       5668888887777777778889***********************************************8876 PP

  == domain 9  score: 10.2 bits;  conditional E-value: 0.00089
                                       HHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH CS
                            ANAPC3  11 laerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaL 79 
                                       +a++++++++++ + +++ A ++ ++g+   A  +l+++   n++s  ++  ++    + ++y+ A + +
  gi|474934716|ref|YP_007688298.1| 831 MADKAMESDPDNVDYILFRASVYRRTGDIRVADAFLSQYlTRNPSSAPILEAMGDLKAEVGEYKAAADSY 900
                                       7999**999******************************9******999999999999999999998866 PP

  == domain 10  score: 5.6 bits;  conditional E-value: 0.025
                                       HHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHH CS
                            ANAPC3   8 AiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcll 67 
                                       A+  ++ +++ ++++++++ +lAl   ++ +y+ A++ +r++  ++ + +g+++l+  c+l
  gi|474934716|ref|YP_007688298.1| 929 AVNSYSNAVKIDPHDSDASRALALLQIKTHDYDGALRSIRTSlASEQTAEGYAILAQICQL 989
                                       5555667777899*****************************6666666677777766666 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       6.6   4.9e+03      14      27 ..     235     248 ..     231     251 .. 0.75
   2 ?   -0.6   0.0       1.8   1.4e+03      11      22 ..     300     311 ..     300     315 .. 0.89
   3 ?   -0.5   0.2       1.7   1.3e+03      15      33 ..     372     390 ..     370     391 .. 0.85
   4 ?   -2.8   0.0       8.9   6.7e+03      11      29 ..     402     420 ..     401     422 .. 0.79
   5 !   13.5   0.0   6.4e-05     0.048      10      34 .]     435     459 ..     434     459 .. 0.95
   6 ?   -1.8   0.0       4.2   3.2e+03      13      25 ..     502     514 ..     494     514 .. 0.79
   7 ?    5.1   0.1     0.028        21       6      34 .]     529     557 ..     524     557 .. 0.90
   8 ?    6.4   0.1     0.011       8.6       1      31 [.     558     588 ..     558     588 .. 0.85
   9 !   14.0   0.0   4.4e-05     0.033       4      33 ..     595     624 ..     593     625 .. 0.94
  10 ?    2.0   0.2      0.28   2.1e+02      12      29 ..     888     905 ..     879     906 .. 0.84
  11 !   15.3   0.0   1.8e-05     0.013       2      34 .]     911     943 ..     910     943 .. 0.95
  12 ?   -1.3   0.0         3   2.3e+03       7      25 ..     950     968 ..     946     972 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 6.6
                                       TT-HHHHHHHHHHH CS
                             TPR_1  14 lgkydeAleyyekA 27 
                                        g++  A   yekA
  gi|474934716|ref|YP_007688298.1| 235 EGDWVNAQRMYEKA 248
                                       57777788888887 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.8
                                       HHHTT-HHHHHH CS
                             TPR_1  11 yfklgkydeAle 22 
                                       y++lgk  eAle
  gi|474934716|ref|YP_007688298.1| 300 YMSLGKNSEALE 311
                                       99********98 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1.7
                                       T-HHHHHHHHHHHHHHSTT CS
                             TPR_1  15 gkydeAleyyekALelnPn 33 
                                       g++ eA++y + A++ n +
  gi|474934716|ref|YP_007688298.1| 372 GNLREAEAYAKAAVSNNRK 390
                                       999*******999988876 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 8.9
                                       HHHTT-HHHHHHHHHHHHH CS
                             TPR_1  11 yfklgkydeAleyyekALe 29 
                                       y+ l    +A+ y ++A++
  gi|474934716|ref|YP_007688298.1| 402 YLVLRHTSKAVRYAKRAVS 420
                                       666777789******9975 PP

  == domain 5  score: 13.5 bits;  conditional E-value: 6.4e-05
                                       HHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  10 ayfklgkydeAleyyekALelnPnn 34 
                                       +y++ g+ d A e ++k Le++P+n
  gi|474934716|ref|YP_007688298.1| 435 VYREAGENDMAMETCRKILEIDPHN 459
                                       799********************98 PP

  == domain 6  score: -1.8 bits;  conditional E-value: 4.2
                                       HTT-HHHHHHHHH CS
                             TPR_1  13 klgkydeAleyye 25 
                                          ky eA++ ++
  gi|474934716|ref|YP_007688298.1| 502 AERKYAEAEKLCR 514
                                       6689*****9885 PP

  == domain 7  score: 5.1 bits;  conditional E-value: 0.028
                                       HHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   6 nlGnayfklgkydeAleyyekALelnPnn 34 
                                        +Gna + lg++ +A + +  A  l+P++
  gi|474934716|ref|YP_007688298.1| 529 LRGNAEYALGEFLKASASFASAAALEPEC 557
                                       59******************999999975 PP

  == domain 8  score: 6.4 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALeln 31 
                                       a+++  +G+a    g++d A+++y++A+ l+
  gi|474934716|ref|YP_007688298.1| 558 AEIWHSKGLADEAFGDLDSAEAAYNQAVLLD 588
                                       67788888888888*************9886 PP

  == domain 9  score: 14.0 bits;  conditional E-value: 4.4e-05
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   4 lynlGnayfklgkydeAleyyekALelnPn 33 
                                       +  +G +   +g+   A++ +++A+el+ +
  gi|474934716|ref|YP_007688298.1| 595 WISKGCVQEMKGNKVAAVDSFNRAIELDQS 624
                                       8899***********************976 PP

  == domain 10  score: 2.0 bits;  conditional E-value: 0.28
                                       HHTT-HHHHHHHHHHHHH CS
                             TPR_1  12 fklgkydeAleyyekALe 29 
                                        + g+y+ A + y+ AL+
  gi|474934716|ref|YP_007688298.1| 888 AEVGEYKAAADSYSDALR 905
                                       6679**********9995 PP

  == domain 11  score: 15.3 bits;  conditional E-value: 1.8e-05
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       +++  lGn+  k+   d A+  y+ A++++P++
  gi|474934716|ref|YP_007688298.1| 911 DVYVKLGNVQEKMDARDAAVNSYSNAVKIDPHD 943
                                       78999**************************86 PP

  == domain 12  score: -1.3 bits;  conditional E-value: 3
                                       HHHHHHHTT-HHHHHHHHH CS
                             TPR_1   7 lGnayfklgkydeAleyye 25 
                                       l+++  k  +yd Al   +
  gi|474934716|ref|YP_007688298.1| 950 LALLQIKTHDYDGALRSIR 968
                                       789999999*****98765 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.021        15       1      33 [.     244     276 ..     244     277 .. 0.94
   2 ?   -0.7   0.0       3.2   2.4e+03       3      29 ..     382     408 ..     380     413 .. 0.80
   3 ?    1.1   0.0       0.9   6.7e+02       2      32 ..     415     445 ..     414     447 .. 0.91
   4 ?    2.8   0.0      0.24   1.8e+02       2      22 ..     449     469 ..     448     479 .. 0.87
   5 ?    3.2   0.0      0.19   1.4e+02       2      32 ..     581     611 ..     580     613 .. 0.92
   6 ?    5.3   0.0     0.041        31       2      32 ..     615     645 ..     614     647 .. 0.91
   7 ?    3.8   0.0      0.12        88       1      16 [.     715     730 ..     715     744 .. 0.87
   8 ?    4.4   0.0     0.077        57       2      28 ..     832     858 ..     831     862 .. 0.83
   9 ?    1.6   0.0      0.62   4.7e+02       6      32 ..     870     896 ..     866     897 .. 0.90
  10 ?    6.6   0.0     0.015        11       2      33 ..     933     964 ..     932     965 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.021
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       +y+ka +  P++ +++++ +  +l+ Gd +tA+
  gi|474934716|ref|YP_007688298.1| 244 MYEKASKSMPDDINVLCETGDSYLNGGDAETAL 276
                                       699999999**********************97 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 3.2
                            TPR_17   3 lkaleldPnnadaynnLAelllknGdl 29 
                                       + a+ ++ ++++++ ++ +++l +  +
  gi|474934716|ref|YP_007688298.1| 382 KAAVSNNRKDPESLAQMSRVYLVLRHT 408
                                       67899999*********9999976555 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.9
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtA 32 
                                        ++a+  d +++ a++ L e+++++G+ ++A
  gi|474934716|ref|YP_007688298.1| 415 AKRAVSADAKSVTALTTLMEVYREAGENDMA 445
                                       6899999********************9999 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.24
                            TPR_17   2 ylkaleldPnnadaynnLAel 22 
                                       ++k le+dP n +a n L +l
  gi|474934716|ref|YP_007688298.1| 449 CRKILEIDPHNDEAANVLSKL 469
                                       789***********9999877 PP

  == domain 5  score: 3.2 bits;  conditional E-value: 0.19
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtA 32 
                                       y +a+ ld +n+  +  ++ +++++G++  A
  gi|474934716|ref|YP_007688298.1| 581 YNQAVLLDMKNPHYWISKGCVQEMKGNKVAA 611
                                       99************************99887 PP

  == domain 6  score: 5.3 bits;  conditional E-value: 0.041
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtA 32 
                                       + +a+eld ++ +a+  +A ++++ G++ +A
  gi|474934716|ref|YP_007688298.1| 615 FNRAIELDQSSTYALVKKASIMAEYGRFSDA 645
                                       789*******************999998777 PP

  == domain 7  score: 3.8 bits;  conditional E-value: 0.12
                            TPR_17   1 lylkaleldPnnaday 16 
                                       l+ kal+ dP+n+d++
  gi|474934716|ref|YP_007688298.1| 715 LLDKALADDPDNVDLL 730
                                       578**********987 PP

  == domain 8  score: 4.4 bits;  conditional E-value: 0.077
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGd 28 
                                         ka+e dP+n+d    +A ++++ Gd
  gi|474934716|ref|YP_007688298.1| 832 ADKAMESDPDNVDYILFRASVYRRTGD 858
                                       579*********988888888877776 PP

  == domain 9  score: 1.6 bits;  conditional E-value: 0.62
                            TPR_17   6 leldPnnadaynnLAelllknGdlmtA 32 
                                       l ++P++a+ +  ++ l ++ G+++ A
  gi|474934716|ref|YP_007688298.1| 870 LTRNPSSAPILEAMGDLKAEVGEYKAA 896
                                       789****************99999877 PP

  == domain 10  score: 6.6 bits;  conditional E-value: 0.015
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       y +a+++dP ++da   LA l+ k +d++ A+
  gi|474934716|ref|YP_007688298.1| 933 YSNAVKIDPHDSDASRALALLQIKTHDYDGAL 964
                                       7799************************9986 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       3.3   2.5e+03      19      53 ..      72     106 ..      69     107 .. 0.84
   2 ?    6.1   0.0     0.016        12       5      65 ..     232     292 ..     227     298 .. 0.92
   3 ?   -1.4   0.0       3.6   2.7e+03      39      58 ..     300     319 ..     294     336 .. 0.79
   4 ?   -0.2   0.0       1.6   1.2e+03       9      61 ..     406     458 ..     398     469 .. 0.54
   5 !    6.9   0.1    0.0092       6.9      31      61 ..     526     556 ..     522     563 .. 0.91
   6 !   10.3   0.0   0.00082      0.62      10      61 ..     573     624 ..     564     633 .. 0.92
   7 ?    4.8   0.0     0.041        31      20      72 ..     617     669 ..     616     670 .. 0.94
   8 ?    3.3   0.3      0.12        92      36      66 ..     700     730 ..     696     736 .. 0.87
   9 ?    0.6   0.0      0.84   6.3e+02       8      50 ..     740     782 ..     733     801 .. 0.78
  10 !    8.6   0.0    0.0028       2.1       9      66 ..     823     881 ..     805     886 .. 0.83
  11 ?    1.2   0.1      0.55   4.1e+02      36      58 ..     884     906 ..     879     915 .. 0.82
  12 !   10.1   0.1   0.00095      0.71      35      73 .]     916     954 ..     908     954 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 3.3
                             TPR_9  19 erllllaPddpeerrdRGlllaqlGclsaAladLe 53 
                                       +++    P+d+   +  + +la+ G +++A+  Le
  gi|474934716|ref|YP_007688298.1|  72 DLVSKQRPQDCKASLAAASCLARKGIVNEARTYLE 106
                                       55555679999999999*************99997 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.016
                             TPR_9   5 aireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                       a  e dw  a +++e      Pdd+  + + G  +   G+ ++Ala +  + a++p++p +
  gi|474934716|ref|YP_007688298.1| 232 ARDEGDWVNAQRMYEKASKSMPDDINVLCETGDSYLNGGDAETALARFRSAEAHDPANPIV 292
                                       567899**************************************************98865 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 3.6
                             TPR_9  39 laqlGclsaAladLeaylal 58 
                                       ++ lG  s+Al+ L+ +l+ 
  gi|474934716|ref|YP_007688298.1| 300 YMSLGKNSEALEILNEFLDS 319
                                       7899999**********965 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 1.6
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                       ++ ++a +++ r +  + +++  +     ++ + G    A++     l+++p+
  gi|474934716|ref|YP_007688298.1| 406 RHTSKAVRYAKRAVSADAKSVTALTTLMEVYREAGENDMAMETCRKILEIDPH 458
                                       55666666666666555555555555555555555444444444444444444 PP

  == domain 5  score: 6.9 bits;  conditional E-value: 0.0092
                             TPR_9  31 errdRGlllaqlGclsaAladLeaylalapd 61 
                                        rr RG +++ lG + +A a +  ++al+p+
  gi|474934716|ref|YP_007688298.1| 526 VRRLRGNAEYALGEFLKASASFASAAALEPE 556
                                       5899************************996 PP

  == domain 6  score: 10.3 bits;  conditional E-value: 0.00082
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                       d + a a+++  +ll+ + p+ +   G +++  G+  aA++ ++++++l+ +
  gi|474934716|ref|YP_007688298.1| 573 DLDSAEAAYNQAVLLDMKNPHYWISKGCVQEMKGNKVAAVDSFNRAIELDQS 624
                                       7899*******************************************99854 PP

  == domain 7  score: 4.8 bits;  conditional E-value: 0.041
                             TPR_9  20 rllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdaeairaqL 72 
                                       r + l+  + + +   + + a+ G++s A++ ++ + a +p++ d+  i++q+
  gi|474934716|ref|YP_007688298.1| 617 RAIELDQSSTYALVKKASIMAEYGRFSDAINFMDLAEATDPKNNDIQKIKMQI 669
                                       788999999**************************************999986 PP

  == domain 8  score: 3.3 bits;  conditional E-value: 0.12
                             TPR_9  36 GlllaqlGclsaAladLeaylalapdapdae 66 
                                       +++   l++++aA++ L+ +la +pd+ d  
  gi|474934716|ref|YP_007688298.1| 700 ARADIGLDDTAAARKLLDKALADDPDNVDLL 730
                                       5667789*******************98875 PP

  == domain 9  score: 0.6 bits;  conditional E-value: 0.84
                             TPR_9   8 eedweralavverllllaPddpeerrdRGlllaqlGclsaAla 50 
                                         d+e+++av+  ++ l+  d e r   + +l+++G+  +A +
  gi|474934716|ref|YP_007688298.1| 740 MGDNEALIAVCRNIIKLDQYDKESRKILADALYKVGRGDEASM 782
                                       5799*******************99999999999999888754 PP

  == domain 10  score: 8.6 bits;  conditional E-value: 0.0028
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap.dapdae 66 
                                        d   a ++++  +  +Pd ++ ++ R+ ++ + G++++A a L +yl  +p +ap  e
  gi|474934716|ref|YP_007688298.1| 823 GDVVGAGRMADKAMESDPDNVDYILFRASVYRRTGDIRVADAFLSQYLTRNPsSAPILE 881
                                       55556667778888889*******************************99995555555 PP

  == domain 11  score: 1.2 bits;  conditional E-value: 0.55
                             TPR_9  36 GlllaqlGclsaAladLeaylal 58 
                                       G l a++G ++aA++    +l++
  gi|474934716|ref|YP_007688298.1| 884 GDLKAEVGEYKAAADSYSDALRN 906
                                       88999*********999988876 PP

  == domain 12  score: 10.1 bits;  conditional E-value: 0.00095
                             TPR_9  35 RGlllaqlGclsaAladLeaylalapdapdaeairaqLn 73 
                                        G +++++++  aA++    ++ ++p++ da ++ a+L+
  gi|474934716|ref|YP_007688298.1| 916 LGNVQEKMDARDAAVNSYSNAVKIDPHDSDASRALALLQ 954
                                       68899******************************9996 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   9.9e-06    0.0074     142     241 ..     218     317 ..     193     350 .. 0.87
   2 !   10.8   0.9   0.00027       0.2     108     180 ..     390     460 ..     375     466 .. 0.49
   3 ?    1.6   0.0      0.18   1.4e+02     144     180 ..     590     626 ..     574     635 .. 0.84
   4 !    6.5   0.4    0.0057       4.3     193     270 ..     706     783 ..     667     793 .. 0.88
   5 ?    0.4   0.0      0.42   3.1e+02     147     184 ..     844     881 ..     810     883 .. 0.81
   6 !    7.8   0.2    0.0023       1.7     146     198 ..     910     962 ..     895     982 .. 0.82
   7 ?    1.6   0.1      0.18   1.3e+02      13      72 ..     949    1005 ..     942    1011 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 9.9e-06
                            TPR_15 142 aeqsaafllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkara...esdas 215
                                        e+++ + l+ a+++r+eg++ +A r+y++A +  pd+ ++  +    +++ g ++    +l++++ ++    +++ 
  gi|474934716|ref|YP_007688298.1| 218 KEEDPDYILLSARMARDEGDWVNAQRMYEKASKSMPDDINVLCETGDSYLNGGDAE---TALARFRSAEahdPANPI 291
                                       468999**********************************9999999999777554...7******99977778888 PP

                            TPR_15 216 LwgplaaAlllLgrpkkALeylrkqa 241
                                           l  +++ Lg++++ALe l+  +
  gi|474934716|ref|YP_007688298.1| 292 VVRGLIRGYMSLGKNSEALEILNEFL 317
                                       9999****************987755 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00027
                            TPR_15 108 rsprlLssalellerakdydriaellksleeeeaaeqsaafllaraelyrqegqtdaAlrdyreAlalapdss 180
                                       ++p+ L ++  ++  ++  ++ ++  k++   +a ++s + l  + e+yr++g++d A++  r+ l+ +p ++
  gi|474934716|ref|YP_007688298.1| 390 KDPESLAQMSRVYLVLRHTSKAVRYAKRAV--SADAKSVTALTTLMEVYREAGENDMAMETCRKILEIDPHND 460
                                       344444444444444444444444444422..22224555555555555555555555555555555555555 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.18
                            TPR_15 144 qsaafllaraelyrqegqtdaAlrdyreAlalapdss 180
                                       +++ +++  + +++ +g++ aA+  + +A++l+  s+
  gi|474934716|ref|YP_007688298.1| 590 KNPHYWISKGCVQEMKGNKVAAVDSFNRAIELDQSST 626
                                       7899****************************99877 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.0057
                            TPR_15 193 lgrraeLrellkawkaraesdasLwgplaaAlllLgrpkkALeylrkqakenrkdplwllaYADaleqagradeAwr 269
                                       l+ +a +r+ll +  a+   + +L  ++    +++g++++  +  r+  k  + d   +   ADal++ gr deA  
  gi|474934716|ref|YP_007688298.1| 706 LDDTAAARKLLDKALADDPDNVDLLVVYRELCQKMGDNEALIAVCRNIIKLDQYDKESRKILADALYKVGRGDEASM 782
                                       56677799999999999999******************99999*******************************986 PP

                            TPR_15 270 l 270
                                       l
  gi|474934716|ref|YP_007688298.1| 783 L 783
                                       6 PP

  == domain 5  score: 0.4 bits;  conditional E-value: 0.42
                            TPR_15 147 afllaraelyrqegqtdaAlrdyreAlalapdsselra 184
                                        + l ra++yr++g+   A   + + l+++p s+ + +
  gi|474934716|ref|YP_007688298.1| 844 DYILFRASVYRRTGDIRVADAFLSQYLTRNPSSAPILE 881
                                       578899*****************999999999988876 PP

  == domain 6  score: 7.8 bits;  conditional E-value: 0.0023
                            TPR_15 146 aafllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrrae 198
                                       + +++ +++++++ ++ daA++ y +A++ +p +s++  al  l i +  ++ 
  gi|474934716|ref|YP_007688298.1| 910 PDVYVKLGNVQEKMDARDAAVNSYSNAVKIDPHDSDASRALALLQIKTHDYDG 962
                                       5577788999***************************9999888887766664 PP

  == domain 7  score: 1.6 bits;  conditional E-value: 0.18
                            TPR_15   13 klatllykqgdvkkAlevLkeaaqkaapskdteyWrtladLAwalqqedearkAyrqLla 72  
                                        +la l  k+ d+++Al+ + +     a+++ +e + +la+  +  ++ + +r+Ay+  l+
  gi|474934716|ref|YP_007688298.1|  949 ALALLQIKTHDYDGALRSIRT---SLASEQTAEGYAILAQICQLRKDREGVRDAYKGFLR 1005
                                        678899999999999999954...444567778889999999999999999999987766 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       9.7   7.2e+03       8      27 ..      87     106 ..      81     109 .. 0.79
   2 !   10.0   0.0    0.0011      0.83       9      74 ..     228     285 ..     224     288 .. 0.89
   3 ?   -1.5   0.0       4.3   3.2e+03      15      70 ..     302     315 ..     295     330 .. 0.65
   4 ?    4.5   0.1     0.056        42      26      73 ..     340     386 ..     338     390 .. 0.88
   5 ?    2.1   0.7      0.33   2.5e+02      17      73 ..     372     420 ..     369     424 .. 0.69
   6 ?    4.2   0.0     0.073        55       5      51 ..     428     469 ..     425     475 .. 0.85
   7 !   12.8   2.5   0.00015      0.11       6      71 ..     520     584 ..     515     587 .. 0.86
   8 ?    1.4   0.0      0.54     4e+02      52      76 ..     599     623 ..     594     624 .. 0.87
   9 ?    1.3   0.1      0.55   4.1e+02       9      31 ..     699     721 ..     692     736 .. 0.66
  10 ?    0.4   0.0       1.1   8.1e+02       9      26 ..     767     784 ..     761     787 .. 0.76
  11 ?    2.0   0.0      0.35   2.6e+02      47      74 ..     845     872 ..     810     875 .. 0.73
  12 ?    6.7   0.1     0.011       8.5      37      73 ..     869     905 ..     846     907 .. 0.79
  13 ?    3.2   0.1      0.14   1.1e+02       6      73 ..     913     972 ..     909     992 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 9.7
                            TPR_12   8 nlaavlrrlgrydeAlelle 27 
                                         a++l+r g   eA+++le
  gi|474934716|ref|YP_007688298.1|  87 AAASCLARKGIVNEARTYLE 106
                                       46889999999999999987 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0011
                            TPR_12   9 laavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                        a + r  g++  A++++eka   +     pd    +++l+  g+ y+  g+ e Al++++ a a 
  gi|474934716|ref|YP_007688298.1| 228 SARMARDEGDWVNAQRMYEKASKSM-----PDD---INVLCETGDSYLNGGDAETALARFRSAEAH 285
                                       5788999**************7777.....886...99***********************99876 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 4.3
                            TPR_12  15 rlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlellee 70 
                                        lg+  eAle+l                                          +e
  gi|474934716|ref|YP_007688298.1| 302 SLGKNSEALEIL------------------------------------------NE 315
                                       455555555555..........................................44 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.056
                            TPR_12  26 lekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                         +a e+a+++l++ +p+ at+ + ++    a g+++eA+++ + a+ 
  gi|474934716|ref|YP_007688298.1| 340 SAEASEVASAILNT-YPGDATACIVMSKSMVAEGNLREAEAYAKAAVS 386
                                       5689999*999985.9**************************999876 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 0.33
                            TPR_12  17 grydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                       g++ eA+++ ++a+   r+   p      ++l  ++r+y+ l ++ +A+++ ++a+ 
  gi|474934716|ref|YP_007688298.1| 372 GNLREAEAYAKAAVSNNRKD--P------ESLAQMSRVYLVLRHTSKAVRYAKRAVS 420
                                       66666666666665555433..3......4688899999877799999999999976 PP

  == domain 6  score: 4.2 bits;  conditional E-value: 0.073
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnL 51 
                                       al+ l +v+r++g+ d A e ++k lei      p+++++a++l  L
  gi|474934716|ref|YP_007688298.1| 428 ALTTLMEVYREAGENDMAMETCRKILEID-----PHNDEAANVLSKL 469
                                       5666889*********************9.....8888888888766 PP

  == domain 7  score: 12.8 bits;  conditional E-value: 0.00015
                            TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleea 71 
                                       + n+aav r +g+ + Al  + ka + + ++     p+ a++ +  g + +a+g+++ A++++++a
  gi|474934716|ref|YP_007688298.1| 520 YGNVAAVRRLRGNAEYALGEFLKASASFASA-AALEPECAEIWHSKGLADEAFGDLDSAEAAYNQA 584
                                       6688999999999999999999999998555.3667889**************************9 PP

  == domain 8  score: 1.4 bits;  conditional E-value: 0.54
                            TPR_12  52 grlyralgryeeAlelleealaiae 76 
                                       g ++++ g+  +A++ +++a+++++
  gi|474934716|ref|YP_007688298.1| 599 GCVQEMKGNKVAAVDSFNRAIELDQ 623
                                       7788899***************987 PP

  == domain 9  score: 1.3 bits;  conditional E-value: 0.55
                            TPR_12   9 laavlrrlgrydeAlellekale 31 
                                       la +   l + + A++ll+kal+
  gi|474934716|ref|YP_007688298.1| 699 LARADIGLDDTAAARKLLDKALA 721
                                       66666667777777777777776 PP

  == domain 10  score: 0.4 bits;  conditional E-value: 1.1
                            TPR_12   9 laavlrrlgrydeAlell 26 
                                       la++l++ gr deA  l+
  gi|474934716|ref|YP_007688298.1| 767 LADALYKVGRGDEASMLY 784
                                       788888888888887776 PP

  == domain 11  score: 2.0 bits;  conditional E-value: 0.35
                            TPR_12  47 tlrnLgrlyralgryeeAlelleealai 74 
                                       +    + +yr++g+ + A ++l + l +
  gi|474934716|ref|YP_007688298.1| 845 YILFRASVYRRTGDIRVADAFLSQYLTR 872
                                       5566789999999999999999998865 PP

  == domain 12  score: 6.7 bits;  conditional E-value: 0.011
                            TPR_12  37 lGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                       + + +p  a +l ++g+l  + g+y++A + + +al+
  gi|474934716|ref|YP_007688298.1| 869 YLTRNPSSAPILEAMGDLKAEVGEYKAAADSYSDALR 905
                                       33678889999**********************9997 PP

  == domain 13  score: 3.2 bits;  conditional E-value: 0.14
                            TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                       +++l++v  ++   d A   +  a+ i      p h   + + r+L+ l+ ++ +y+ Al+  + +la
  gi|474934716|ref|YP_007688298.1| 913 YVKLGNVQEKMDARDAAVNSYSNAVKID-----P-H--DSDASRALALLQIKTHDYDGALRSIRTSLA 972
                                       6677777777777777777777777776.....5.5..577888999999999999999887777765 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.58   4.3e+02      11      82 ..      89     159 ..      81     182 .. 0.83
   2 ?    3.9   0.3     0.028        21     199     256 ..     399     456 ..     354     460 .. 0.81
   3 ?    4.8   0.0     0.014        11     210     268 ..     542     602 ..     533     610 .. 0.80
   4 !   11.8   0.3   0.00011     0.082     207     280 ..     607     680 ..     592     697 .. 0.80
   5 !    6.2   0.3    0.0053         4     206     260 ..     707     761 ..     695     805 .. 0.86
   6 !   11.8   0.0   0.00011     0.082     196     248 ..     813     865 ..     782     873 .. 0.84
   7 !   11.5   0.0   0.00014       0.1       5     122 ..     844     960 ..     841     968 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.58
                                       HHHHHHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHHHHHT CS
                             NARP1  11 nqiieeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpenskYyeglekak 82 
                                       ++ ++ +g ++eA   Le ++   vD  +++ +kae+l++ ++++eA++ +   l+  p n k ye lek  
  gi|474934716|ref|YP_007688298.1|  89 ASCLARKGIVNEARTYLEGVHG-SVDIPTYSYVKAEVLVADQHTQEAAKSLMGSLRSDPLNVKAYEFLEKLI 159
                                       5667788888899888887765.589999**********************999999999999999998865 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.028
                                       HHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                             NARP1 199 AqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                       +  y  l++++kA++y  +a++ + ++v   +t  ++++ aG+ + A+e+  +  ++D
  gi|474934716|ref|YP_007688298.1| 399 SRVYLVLRHTSKAVRYAKRAVSADAKSVTALTTLMEVYREAGENDMAMETCRKILEID 456
                                       45566788899************************************99987766665 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.014
                                       HHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT-H.H.HHHHHHH CS
                             NARP1 210 kAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaDR.y.iNskcak 268
                                       kA     +a + +p++ e++  K+   +  Gdl+ A ++ ++a  lD +   y i   c++
  gi|474934716|ref|YP_007688298.1| 542 KASASFASAAALEPECAEIWHSKGLADEAFGDLDSAEAAYNQAVLLDMKNPhYwISKGCVQ 602
                                       777778889999***********************************98631314444554 PP

  == domain 4  score: 11.8 bits;  conditional E-value: 0.00011
                                       -SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT-HHHHHHHHHHHHHTT-HHHHH CS
                             NARP1 207 srekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaDRyiNskcakymLradeveeAe 280
                                       ++  A++  ++aie + +++   + Ka i+  +G +++A++ m+ a + D +   i     +  L a +   A+
  gi|474934716|ref|YP_007688298.1| 607 NKVAAVDSFNRAIELDQSSTYALVKKASIMAEYGRFSDAINFMDLAEATDPKNNDIQKIKMQIYLAATRFTDAA 680
                                       4448999*****************************************99987766666666666666666655 PP

  == domain 5  score: 6.2 bits;  conditional E-value: 0.0053
                                       T-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT-H CS
                             NARP1 206 gsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaDR 260
                                        ++  A +++dka++ +p  v+l ++  ++++++Gd ++ ++v  +  klD+ D+
  gi|474934716|ref|YP_007688298.1| 707 DDTAAARKLLDKALADDPDNVDLLVVYRELCQKMGDNEALIAVCRNIIKLDQYDK 761
                                       45668999******************************99999999999999986 PP

  == domain 6  score: 11.8 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHH CS
                             NARP1 196 yflAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaev 248
                                       + +A+   ++g++  A ++ dka+e++p  v++ l +a +++++Gd++ A + 
  gi|474934716|ref|YP_007688298.1| 813 FQIAKSLLEVGDVVGAGRMADKAMESDPDNVDYILFRASVYRRTGDIRVADAF 865
                                       556777778888899999*****************************998765 PP

  == domain 7  score: 11.5 bits;  conditional E-value: 0.00014
                                       HHHHHHHHHHHHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHHHHH CS
                             NARP1   5 ellLyknqiieeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpenskYyegleka 81 
                                       + +L+++++ + +g++  A + L+++ ++      ++e++++l  ++g+++ A+  y++ l rn    + y +l ++
  gi|474934716|ref|YP_007688298.1| 844 DYILFRASVYRRTGDIRVADAFLSQYLTRNPSSAPILEAMGDLKAEVGEYKAAADSYSDAL-RNGARPDVYVKLGNV 919
                                       679********************************************************99.677788888899999 PP

                                       T..SSS-HHHHHHHHHHTTTS-.TT-SHHHHTHHHH--HHHH CS
                             NARP1  82 kklskedeeallalydelaeky.prsdaprRlpLdfleGeeF 122
                                       ++ + + ++a ++ y+++++     sda+r l+L  ++ +++
  gi|474934716|ref|YP_007688298.1| 920 QE-KMDARDAAVNSYSNAVKIDpHDSDASRALALLQIKTHDY 960
                                       98.555678889999988887725699999999987776666 PP

>> ChAPs  ChAPs (Chs5p-Arf1p-binding proteins)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.048        36     196     293 ..     218     315 ..     202     345 .. 0.81
   2 !    6.3   0.2    0.0055       4.1     197     267 ..     389     459 ..     375     473 .. 0.83
   3 !   12.8   0.0     6e-05     0.045     175     262 ..     666     755 ..     649     851 .. 0.83
   4 ?   -0.4   0.0      0.59   4.4e+02     250     292 ..     926     968 ..     914     987 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.048
                                       HTT-GGGHHHHHHHHHHTT-HHHHHHHHHHHH-SSS-HHHHHHHHHHHHHHSS--HHHHHHHHHHHHH-TT-HHHHH CS
                             ChAPs 196 keeepevvillarvllladeEvdavkllneeleeeekdaelLllqaefllskkkeelAlevakravksaPsefktWa 272
                                       kee+p+ + l ar+     + v+a ++ +++ ++ ++d ++L+   +  l+  + e Al+  ++a    P +     
  gi|474934716|ref|YP_007688298.1| 218 KEEDPDYILLSARMARDEGDWVNAQRMYEKASKSMPDDINVLCETGDSYLNGGDAETALARFRSAEAHDPANPIVVR 294
                                       56667777777777777777788888888888888899999999999999999999999999999999999999999 PP

                                       HHHHHHHHTT-HHHHHHHHHT CS
                             ChAPs 273 lLvkvYikledienALltLNs 293
                                        L + Y++l+  ++AL +LN 
  gi|474934716|ref|YP_007688298.1| 295 GLIRGYMSLGKNSEALEILNE 315
                                       999999999999999999995 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0055
                                       TT-GGGHHHHHHHHHHTT-HHHHHHHHHHHH-SSS-HHHHHHHHHHHHHHSS--HHHHHHHHHHHHH-TT- CS
                             ChAPs 197 eeepevvillarvllladeEvdavkllneeleeeekdaelLllqaefllskkkeelAlevakravksaPse 267
                                       +++pe  + ++rv+l+  +  +av+  +++++ + k++  L++  e   +  ++++A+e+ ++  ++ P +
  gi|474934716|ref|YP_007688298.1| 389 RKDPESLAQMSRVYLVLRHTSKAVRYAKRAVSADAKSVTALTTLMEVYREAGENDMAMETCRKILEIDPHN 459
                                       46788888899999999999999999999999999999999999999999999999999988888877766 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 6e-05
                                       HHHHHHHHT-HHHHHHHHHHHHTT-GGGHHH..HHHHHHHTT-HHHHHHHHHHHH-SSS-HHHHHHHHHHHHHHSS- CS
                             ChAPs 175 llklvrltkrydralellekLkeeepevvil..larvllladeEvdavkllneeleeeekdaelLllqaefllskkk 249
                                        +++   ++r++ a+ + +kL +++p+++++  lar  +  d+   a kll ++l++++++++lL++  e +++  +
  gi|474934716|ref|YP_007688298.1| 666 KMQIYLAATRFTDAAYIGKKLVKKDPDAITVacLARADIGLDDTAAARKLLDKALADDPDNVDLLVVYRELCQKMGD 742
                                       466777788999999************9765449**************************************99988 PP

                                       -HHHHHHHHHHHH CS
                             ChAPs 250 eelAlevakravk 262
                                       +e  ++v ++ +k
  gi|474934716|ref|YP_007688298.1| 743 NEALIAVCRNIIK 755
                                       8766666666555 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 0.59
                                       -HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHH CS
                             ChAPs 250 eelAlevakravksaPsefktWalLvkvYikledienALltLN 292
                                        + A++  ++avk+ P ++     L+   ik +d++ AL ++ 
  gi|474934716|ref|YP_007688298.1| 926 RDAAVNSYSNAVKIDPHDSDASRALALLQIKTHDYDGALRSIR 968
                                       378899999*****************************98764 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       3.2   2.4e+03      68     131 ..     255     318 ..     225     324 .. 0.75
   2 ?    1.2   0.1      0.64   4.8e+02      58     114 ..     347     403 ..     340     412 .. 0.78
   3 !    8.6   0.2    0.0033       2.5      57     109 ..     413     466 ..     404     483 .. 0.75
   4 ?    2.7   0.0      0.22   1.6e+02      69     120 ..     626     677 ..     607     682 .. 0.86
   5 ?    6.5   0.0     0.014        10      72     123 ..     696     781 ..     678     790 .. 0.64
   6 !    7.0   0.0    0.0099       7.4      68     120 ..     808     860 ..     785     876 .. 0.85
   7 ?   -2.0   0.0         6   4.5e+03     109     130 ..     909     930 ..     881     973 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 3.2
                                       SHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHHHHHHHHH CS
                   Alkyl_sulf_dimr  68 gaekvlekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesatwRniYls 131
                                       + + ++e   ++l+ gd++ a+     + + dp n    + +++ + +lg+ +e+    n +l 
  gi|474934716|ref|YP_007688298.1| 255 DINVLCETGDSYLNGGDAETALARFRSAEAHDPANPIVVRGLIRGYMSLGKNSEALEILNEFLD 318
                                       4455667777788889999999999988888999988888888888889888888877777765 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.64
                                       HHHHHHHHTTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHH CS
                   Alkyl_sulf_dimr  58 kakrlvelmGgaekvlekakealkegdyrwaaellnhlvfadpenaeakelkadale 114
                                       +++ l+ + G+a + + + k+ ++eg++r a   ++ +v ++ ++ e  +   +++ 
  gi|474934716|ref|YP_007688298.1| 347 ASAILNTYPGDATACIVMSKSMVAEGNLREAEAYAKAAVSNNRKDPESLAQMSRVYL 403
                                       455677889***************************999998887666555555555 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0033
                                       HHHHHHHHHTT.SHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHH CS
                   Alkyl_sulf_dimr  57 ekakrlvelmG.gaekvlekakealkegdyrwaaellnhlvfadpenaeakelk 109
                                       + akr v++   ++ ++ + ++ ++++g+  +a+e + ++++ dp+n+ea +++
  gi|474934716|ref|YP_007688298.1| 413 RYAKRAVSADAkSVTALTTLMEVYREAGENDMAMETCRKILEIDPHNDEAANVL 466
                                       45666666633145566666777779*********************9998874 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.22
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH- CS
                   Alkyl_sulf_dimr  69 aekvlekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqa 120
                                         ++++ka+  ++ g +  a+++++ + + dp+n++ +++k++++ +  +++
  gi|474934716|ref|YP_007688298.1| 626 TYALVKKASIMAEYGRFSDAINFMDLAEATDPKNNDIQKIKMQIYLAATRFT 677
                                       567889999999999999***************************9887765 PP

  == domain 5  score: 6.5 bits;  conditional E-value: 0.014
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-..................................HHHHHHHHHHHH CS
                   Alkyl_sulf_dimr  72 vlekakealkegdyrwaaellnhlvfadpen..................................aeakelkadale 114
                                       v+  a++++  +d  +a +ll+++++ dp+n                                  +e ++++adal 
  gi|474934716|ref|YP_007688298.1| 696 VACLARADIGLDDTAAARKLLDKALADDPDNvdllvvyrelcqkmgdnealiavcrniikldqydKESRKILADALY 772
                                       55555666666666666666666666555555555555555555555555555555555555554999999999999 PP

                                       HHHHH-SSH CS
                   Alkyl_sulf_dimr 115 qlgyqaesa 123
                                       ++g++ e+ 
  gi|474934716|ref|YP_007688298.1| 773 KVGRGDEAS 781
                                       999998865 PP

  == domain 6  score: 7.0 bits;  conditional E-value: 0.0099
                                       SHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH- CS
                   Alkyl_sulf_dimr  68 gaekvlekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqa 120
                                       + + v + ak+ l+ gd+  a  ++++++++dp+n +    +a+++++ g   
  gi|474934716|ref|YP_007688298.1| 808 DPASVFQIAKSLLEVGDVVGAGRMADKAMESDPDNVDYILFRASVYRRTGDIR 860
                                       56889******************************************998765 PP

  == domain 7  score: -2.0 bits;  conditional E-value: 6
                                       HHHHHHHHHHH-SSHHHHHHHH CS
                   Alkyl_sulf_dimr 109 kadaleqlgyqaesatwRniYl 130
                                       + d++ +lg+ +e + +R + +
  gi|474934716|ref|YP_007688298.1| 909 RPDVYVKLGNVQEKMDARDAAV 930
                                       4455555555555555554433 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       7.3   5.5e+03       6      24 ..      88     106 ..      84     109 .. 0.80
   2 ?    2.1   0.0      0.48   3.6e+02       5      29 ..     227     251 ..     223     255 .. 0.76
   3 ?    4.7   0.0     0.074        56       7      25 ..     263     281 ..     261     287 .. 0.89
   4 ?    2.0   0.0      0.54     4e+02      10      28 ..     300     318 ..     296     320 .. 0.87
   5 ?   -1.9   0.0       9.5   7.1e+03      17      32 ..     341     356 ..     334     357 .. 0.71
   6 ?    1.9   0.1      0.58   4.3e+02       2      28 ..     394     420 ..     393     425 .. 0.84
   7 ?    4.2   0.0       0.1        78       6      32 ..     432     458 ..     428     459 .. 0.89
   8 ?    0.3   0.0       1.9   1.4e+03      13      28 ..     591     620 ..     576     622 .. 0.66
   9 ?   -1.8   0.1       8.7   6.5e+03       1      23 [.     627     649 ..     627     654 .. 0.87
  10 ?    4.5   0.1     0.087        65       7      33 .]     700     726 ..     699     726 .. 0.86
  11 ?   -1.8   0.0         9   6.7e+03       6      23 ..     767     784 ..     766     788 .. 0.63
  12 ?    0.2   0.0         2   1.5e+03       4      32 ..     813     841 ..     810     842 .. 0.82
  13 ?    4.0   0.0      0.12        91       7      33 .]     850     876 ..     846     876 .. 0.92
  14 ?    4.7   0.0     0.077        57       1      31 [.     911     941 ..     911     943 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 7.3
                                       HHHHHHHHHHHHHHHHHHH CS
                             TPR_6   6 lalsyrklgdtdkAleale 24 
                                       +a ++ + g   +A+++le
  gi|474934716|ref|YP_007688298.1|  88 AASCLARKGIVNEARTYLE 106
                                       678888888999*****98 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.48
                                       HHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   5 klalsyrklgdtdkAlealerlike 29 
                                       + a+  r  gd+ +A +++e+  k+
  gi|474934716|ref|YP_007688298.1| 227 LSARMARDEGDWVNAQRMYEKASKS 251
                                       5676666667**********98765 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.074
                                       HHHHHHHHHHHHHHHHHHH CS
                             TPR_6   7 alsyrklgdtdkAlealer 25 
                                       + sy+++gd+++Al+ +++
  gi|474934716|ref|YP_007688298.1| 263 GDSYLNGGDAETALARFRS 281
                                       89****99*******9986 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.54
                                       HHHHHHHHHHHHHHHHHHH CS
                             TPR_6  10 yrklgdtdkAlealerlik 28 
                                       y +lg+ ++Ale+l+++++
  gi|474934716|ref|YP_007688298.1| 300 YMSLGKNSEALEILNEFLD 318
                                       5668999**********97 PP

  == domain 5  score: -1.9 bits;  conditional E-value: 9.5
                                       HHHHHHHHHHHHH-TT CS
                             TPR_6  17 dkAlealerlikeYPd 32 
                                       ++A e    +++ YP+
  gi|474934716|ref|YP_007688298.1| 341 AEASEVASAILNTYPG 356
                                       5777888888888885 PP

  == domain 6  score: 1.9 bits;  conditional E-value: 0.58
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerlik 28 
                                       +l ++ + y+ l  t+kA+++ +r ++
  gi|474934716|ref|YP_007688298.1| 394 SLAQMSRVYLVLRHTSKAVRYAKRAVS 420
                                       6778999999988*********99986 PP

  == domain 7  score: 4.2 bits;  conditional E-value: 0.1
                                       HHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   6 lalsyrklgdtdkAlealerlikeYPd 32 
                                       l + yr++g+ d A+e+ +++++  P 
  gi|474934716|ref|YP_007688298.1| 432 LMEVYREAGENDMAMETCRKILEIDPH 458
                                       6789***99*************99885 PP

  == domain 8  score: 0.3 bits;  conditional E-value: 1.9
                                       H..............HHHHHHHHHHHHHHH CS
                             TPR_6  13 l..............gdtdkAlealerlik 28 
                                                      g++ +A++ ++r i+
  gi|474934716|ref|YP_007688298.1| 591 NphywiskgcvqemkGNKVAAVDSFNRAIE 620
                                       25555555555555589999*****99987 PP

  == domain 9  score: -1.8 bits;  conditional E-value: 8.7
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   1 dAlyklalsyrklgdtdkAleal 23 
                                       +Al k a  + + g+ ++A+  +
  gi|474934716|ref|YP_007688298.1| 627 YALVKKASIMAEYGRFSDAINFM 649
                                       7999********77**9999765 PP

  == domain 10  score: 4.5 bits;  conditional E-value: 0.087
                                       HHHHHHHHHHHHHHHHHHHHHHH-TT- CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYPdS 33 
                                       a++ + l+dt++A+++l++ + + Pd+
  gi|474934716|ref|YP_007688298.1| 700 ARADIGLDDTAAARKLLDKALADDPDN 726
                                       66667778****************995 PP

  == domain 11  score: -1.8 bits;  conditional E-value: 9
                                       HHHHHHHHHHHHHHHHHH CS
                             TPR_6   6 lalsyrklgdtdkAleal 23 
                                       la +++k g+ d+A  ++
  gi|474934716|ref|YP_007688298.1| 767 LADALYKVGRGDEASMLY 784
                                       566777744777776666 PP

  == domain 12  score: 0.2 bits;  conditional E-value: 2
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   4 yklalsyrklgdtdkAlealerlikeYPd 32 
                                       +++a+s+++ gd   A ++ ++  ++ Pd
  gi|474934716|ref|YP_007688298.1| 813 FQIAKSLLEVGDVVGAGRMADKAMESDPD 841
                                       89*******55998888888888888887 PP

  == domain 13  score: 4.0 bits;  conditional E-value: 0.12
                                       HHHHHHHHHHHHHHHHHHHHHHH-TT- CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYPdS 33 
                                       a  yr++gd + A + l + +++ P S
  gi|474934716|ref|YP_007688298.1| 850 ASVYRRTGDIRVADAFLSQYLTRNPSS 876
                                       7789**99*****************98 PP

  == domain 14  score: 4.7 bits;  conditional E-value: 0.077
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerlikeYP 31 
                                       d++ kl+  ++k++  d+A+  + + +k  P
  gi|474934716|ref|YP_007688298.1| 911 DVYVKLGNVQEKMDARDAAVNSYSNAVKIDP 941
                                       6899*********88889999**99999887 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00061      0.46      71     121 ..     265     315 ..     234     322 .. 0.87
   2 ?    4.9   1.7     0.045        33       8     118 ..     326     448 ..     317     466 .. 0.64
   3 ?   -0.1   0.4       1.5   1.1e+03      64     122 ..     526     584 ..     522     588 .. 0.86
   4 ?   -0.9   0.0       2.7     2e+03      22      95 ..     567     659 ..     558     679 .. 0.52
   5 !   10.2   0.1     0.001      0.76      64     125 ..     732     790 ..     700     806 .. 0.89
   6 ?    0.9   0.1      0.73   5.5e+02      64     124 ..     879     938 ..     847     954 .. 0.79
   7 ?   -1.5   0.0       4.1   3.1e+03      75     107 ..     923     955 ..     909     968 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00061
                                       HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHH CS
                              BTAD  71 aelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYer 121
                                         l  G+ae ala+ +++ a++P +   +r l+r ++ +G+++eALe  ++
  gi|474934716|ref|YP_007688298.1| 265 SYLNGGDAETALARFRSAEAHDPANPIVVRGLIRGYMSLGKNSEALEILNE 315
                                       5567799***************************************98766 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.045
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHTT--SSTTGGGTT............STTHHHHHHHHHHHHHHHHHHHHHHH CS
                              BTAD   8 alvaagraalaagdpeeaaelleaAlalwrGpaladlea............gewleaererleelrlealealaeae 72 
                                       +++ a+r+ l+ g  +ea e ++a l+ + G+a a +               e   ++++  +++  e l+++ +  
  gi|474934716|ref|YP_007688298.1| 326 DYEYASREMLRMGYSAEASEVASAILNTYPGDATACIVMsksmvaegnlreAEAYAKAAVSNNRKDPESLAQMSRVY 402
                                       55667777778888888888888888888888777766656444333333322222222233333334444444455 PP

                                       HHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHH CS
                              BTAD  73 lrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALev 118
                                       l l + ++a+++++++v+++    ++   lm+ ++  G++  A+e+
  gi|474934716|ref|YP_007688298.1| 403 LVLRHTSKAVRYAKRAVSADAKSVTALTTLMEVYREAGENDMAMET 448
                                       6666777888888888888888888888888888888888888765 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 1.5
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                              BTAD  64 alealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                       + + + +ae +lG+  +a a  ++++a++P   + +    +A  + G+   A ++Y+++
  gi|474934716|ref|YP_007688298.1| 526 VRRLRGNAEYALGEFLKASASFASAAALEPECAEIWHSKGLADEAFGDLDSAEAAYNQA 584
                                       45678889999999999999999999999999999999999999999999999999876 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 2.7
                                       HHHHHHHHHHHHTT--SSTTGGGTT...................STTHHHHHHHHHHHHHHHHHHHHHHHHHTT-HH CS
                              BTAD  22 peeaaelleaAlalwrGpaladlea...................gewleaererleelrlealealaeaelrlGrae 79 
                                        +ea   l+ A a ++  +l d++                          ++ +l+++   al + a   +++Gr +
  gi|474934716|ref|YP_007688298.1| 567 ADEAFGDLDSAEAAYNQAVLLDMKNphywiskgcvqemkgnkvaAVDSFNRAIELDQSSTYALVKKASIMAEYGRFS 643
                                       55566666666666666666666555433333333333222211111122333455555555555566666666666 PP

                                       HHHHHHHHHHHHSTT- CS
                              BTAD  80 ealaelealvaehPlr 95 
                                       +a+  ++ + a +P +
  gi|474934716|ref|YP_007688298.1| 644 DAINFMDLAEATDPKN 659
                                       6666555555555555 PP

  == domain 5  score: 10.2 bits;  conditional E-value: 0.001
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                              BTAD  64 alealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrrl 125
                                       ++++l++   ++G+ e+++a  +++++++ ++ ++++ l  Al+++Gr  eA   Y +l r+
  gi|474934716|ref|YP_007688298.1| 732 VYRELCQ---KMGDNEALIAVCRNIIKLDQYDKESRKILADALYKVGRGDEASMLYSSLDRT 790
                                       5556666...89****************************************9999998776 PP

  == domain 6  score: 0.9 bits;  conditional E-value: 0.73
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              BTAD  64 alealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                       +lea+ ++++++G++++a++ +++++++   r + + +l     +++ + +A + Y ++++
  gi|474934716|ref|YP_007688298.1| 879 ILEAMGDLKAEVGEYKAAADSYSDALRN-GARPDVYVKLGNVQEKMDARDAAVNSYSNAVK 938
                                       5788888899999999998888888765.46667777777777777777777777777655 PP

  == domain 7  score: -1.5 bits;  conditional E-value: 4.1
                                       TT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHH CS
                              BTAD  75 lGraeealaelealvaehPlrErlhrqlmrAla 107
                                       +  +++a+  ++++v+ +P++ ++ r+l +   
  gi|474934716|ref|YP_007688298.1| 923 MDARDAAVNSYSNAVKIDPHDSDASRALALLQI 955
                                       456678899999999999999999998876555 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1       2.8   2.1e+03      23      54 ..      31      63 ..      15      75 .. 0.57
   2 ?   -0.1   0.0       1.6   1.2e+03      16      41 ..      76     101 ..      69     106 .. 0.88
   3 ?    1.5   0.0       0.5   3.7e+02      28      52 ..     121     145 ..     116     148 .. 0.89
   4 ?    5.5   0.0     0.029        22      12      45 ..     246     279 ..     240     288 .. 0.89
   5 ?    1.0   0.0      0.71   5.3e+02      11      54 ..     279     322 ..     276     328 .. 0.80
   6 ?   -1.1   0.0       3.4   2.5e+03      13      54 ..     349     390 ..     340     399 .. 0.77
   7 ?    5.3   0.3     0.033        25      11      85 ..     381     453 ..     370     455 .. 0.88
   8 ?    4.3   0.1     0.069        51       4      57 ..     408     461 ..     405     479 .. 0.85
   9 ?    4.9   0.3     0.044        33      10      77 ..     715     780 ..     707     786 .. 0.77
  10 ?   -2.4   0.0       8.3   6.2e+03      15      40 ..     802     827 ..     789     831 .. 0.76
  11 ?    0.5   0.0       1.1     8e+02      12      52 ..     833     873 ..     827     878 .. 0.83
  12 ?   -1.8   0.0       5.5   4.1e+03      13      49 ..     868     904 ..     863     908 .. 0.76
  13 !   11.1   0.3   0.00053      0.39       4      55 ..     926     977 ..     923     990 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2.8
                            TPR_20 23 darldlAlallaagryeeAl.eqLleilkrdrk 54
                                      ++  +l++ l ++g++  Al ++++ei++++ +
  gi|474934716|ref|YP_007688298.1| 31 ALSAALSKILTSEGEVSSALlARMIEIVSAEEA 63
                                      344456666667777777743667777765543 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.6
                            TPR_20  16 aanpddldarldlAlallaagryeeA 41 
                                       +++p+d +a l+ A  l+ +g + eA
  gi|474934716|ref|YP_007688298.1|  76 KQRPQDCKASLAAASCLARKGIVNEA 101
                                       689***************99999888 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.5
                            TPR_20  28 lAlallaagryeeAleqLleilkrd 52 
                                        A++l+a ++ +eA++ L+  l++d
  gi|474934716|ref|YP_007688298.1| 121 KAEVLVADQHTQEAAKSLMGSLRSD 145
                                       5899***************999987 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.029
                            TPR_20  12 eaalaanpddldarldlAlallaagryeeAleqL 45 
                                       e+a ++ pdd++  ++  + +l +g+ e Al+++
  gi|474934716|ref|YP_007688298.1| 246 EKASKSMPDDINVLCETGDSYLNGGDAETALARF 279
                                       7788899************************986 PP

  == domain 5  score: 1.0 bits;  conditional E-value: 0.71
                            TPR_20  11 leaalaanpddldarldlAlallaagryeeAleqLleilkrdrk 54 
                                       +++a a +p++      l + +++ g++ eAle L e+l ++ +
  gi|474934716|ref|YP_007688298.1| 279 FRSAEAHDPANPIVVRGLIRGYMSLGKNSEALEILNEFLDSEMA 322
                                       5667778888888888888999***************9987765 PP

  == domain 6  score: -1.1 bits;  conditional E-value: 3.4
                            TPR_20  13 aalaanpddldarldlAlallaagryeeAleqLleilkrdrk 54 
                                       a l++ p d  a + +++  +a+g+ +eA +   + ++++rk
  gi|474934716|ref|YP_007688298.1| 349 AILNTYPGDATACIVMSKSMVAEGNLREAEAYAKAAVSNNRK 390
                                       4577899999999999*9999999999997766666666666 PP

  == domain 7  score: 5.3 bits;  conditional E-value: 0.033
                            TPR_20  11 leaalaanpddldarldlAlallaagryeeAleqLleilkrdrkweddaarkqllkifealgsqdplvakyRrkL 85 
                                        +aa+ +n +d +   ++++++l   +  +A+    + +++d k     a ++l+++   +g++d ++++ R+ L
  gi|474934716|ref|YP_007688298.1| 381 AKAAVSNNRKDPESLAQMSRVYLVLRHTSKAVRYAKRAVSADAKS--VTALTTLMEVYREAGENDMAMETCRKIL 453
                                       468889999***********************9999999988877..8899999999999999999999999865 PP

  == domain 8  score: 4.3 bits;  conditional E-value: 0.069
                            TPR_20   4 dapelaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkwed 57 
                                       +++ ++  ++a+ a+ + + a   l +++ +ag+++ A+e   +il+ d + ++
  gi|474934716|ref|YP_007688298.1| 408 TSKAVRYAKRAVSADAKSVTALTTLMEVYREAGENDMAMETCRKILEIDPHNDE 461
                                       5667778889999999999*********************99999999987644 PP

  == domain 9  score: 4.9 bits;  conditional E-value: 0.044
                            TPR_20  10 eleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkweddaarkqllkifealgsqdpl 77 
                                        l++ala++pd++d+ + + ++  + g++e+ ++   +i+k d ++ d++ rk l + +  +g +d++
  gi|474934716|ref|YP_007688298.1| 715 LLDKALADDPDNVDLLVVYRELCQKMGDNEALIAVCRNIIKLD-QY-DKESRKILADALYKVGRGDEA 780
                                       57899**********9999888888888776666666666644.44.688899999999999999976 PP

  == domain 10  score: -2.4 bits;  conditional E-value: 8.3
                            TPR_20  15 laanpddldarldlAlallaagryee 40 
                                        + + dd +  ++ A+ ll+ g++  
  gi|474934716|ref|YP_007688298.1| 802 SEVQHDDPASVFQIAKSLLEVGDVVG 827
                                       45677999999999999999998755 PP

  == domain 11  score: 0.5 bits;  conditional E-value: 1.1
                            TPR_20  12 eaalaanpddldarldlAlallaagryeeAleqLleilkrd 52 
                                       ++a++++pd++d  l  A ++   g+ + A + L + l r+
  gi|474934716|ref|YP_007688298.1| 833 DKAMESDPDNVDYILFRASVYRRTGDIRVADAFLSQYLTRN 873
                                       67899****************99999988877776666665 PP

  == domain 12  score: -1.8 bits;  conditional E-value: 5.5
                            TPR_20  13 aalaanpddldarldlAlallaagryeeAleqLleil 49 
                                       + l+ np+   +  ++ ++ ++ g+y++A++   + l
  gi|474934716|ref|YP_007688298.1| 868 QYLTRNPSSAPILEAMGDLKAEVGEYKAAADSYSDAL 904
                                       6677788888888888899999999999988765555 PP

  == domain 13  score: 11.1 bits;  conditional E-value: 0.00053
                            TPR_20   4 dapelaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkw 55 
                                       +++ + +  +a++ +p d da  +lAl++++  +y+ Al  + + l++++++
  gi|474934716|ref|YP_007688298.1| 926 RDAAVNSYSNAVKIDPHDSDASRALALLQIKTHDYDGALRSIRTSLASEQTA 977
                                       56677888999****************************9988887776665 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       9.6   7.2e+03      10      31 ..     299     320 ..     299     320 .. 0.84
   2 !   10.2   0.0   0.00083      0.62      15      40 ..     440     465 ..     437     477 .. 0.82
   3 ?   -0.4   0.0       1.7   1.3e+03      15      41 ..     640     666 ..     637     679 .. 0.83
   4 ?    0.9   0.0      0.64   4.8e+02      15      34 ..     707     726 ..     699     730 .. 0.80
   5 ?    3.2   0.1      0.12        93       7      45 ..     950     988 ..     949     996 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 9.6
                                       HHHHHT-HHHHHHHHHHHHHHT CS
                        Fis1_TPR_C  10 GhyklgeYseArryvdalLeiE 31 
                                       G++ lg+ seA++ ++ +L  E
  gi|474934716|ref|YP_007688298.1| 299 GYMSLGKNSEALEILNEFLDSE 320
                                       677788999*******999876 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00083
                                       T-HHHHHHHHHHHHHHTTS-HHHHHH CS
                        Fis1_TPR_C  15 geYseArryvdalLeiEPenrQaqsL 40 
                                       ge ++A++ ++ +Lei+P n  a++ 
  gi|474934716|ref|YP_007688298.1| 440 GENDMAMETCRKILEIDPHNDEAANV 465
                                       56689****************99874 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.7
                                       T-HHHHHHHHHHHHHHTTS-HHHHHHH CS
                        Fis1_TPR_C  15 geYseArryvdalLeiEPenrQaqsLk 41 
                                       g++s+A +++d   + +P+n+  q+ k
  gi|474934716|ref|YP_007688298.1| 640 GRFSDAINFMDLAEATDPKNNDIQKIK 666
                                       788999999999999999999988765 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.64
                                       T-HHHHHHHHHHHHHHTTS- CS
                        Fis1_TPR_C  15 geYseArryvdalLeiEPen 34 
                                        +   Ar+++d  L+ +P+n
  gi|474934716|ref|YP_007688298.1| 707 DDTAAARKLLDKALADDPDN 726
                                       55567**************9 PP

  == domain 5  score: 3.2 bits;  conditional E-value: 0.12
                                       HHHHHHHHT-HHHHHHHHHHHHHHTTS-HHHHHHHHHHH CS
                        Fis1_TPR_C   7 lAlGhyklgeYseArryvdalLeiEPenrQaqsLkelie 45 
                                       lAl ++k ++Y+ A+r +++ L+ E   +  + L ++++
  gi|474934716|ref|YP_007688298.1| 950 LALLQIKTHDYDGALRSIRTSLASEQTAEGYAILAQICQ 988
                                       566689****************99976666555555555 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1     0.018        13       6      26 ..     229     249 ..     225     290 .. 0.88
   2 ?   -1.4   0.0       4.4   3.3e+03       9      23 ..     300     314 ..     298     326 .. 0.80
   3 ?    0.4   0.0       1.1   8.6e+02       1      28 [.     394     419 ..     394     426 .. 0.83
   4 ?    3.8   0.0     0.096        71       7      30 ..     434     457 ..     428     463 .. 0.81
   5 ?   -0.3   0.0         2   1.5e+03      12      34 ..     706     726 ..     697     728 .. 0.85
   6 ?    2.0   0.0      0.36   2.7e+02       8      35 ..     736     761 ..     734     762 .. 0.85
   7 ?    0.7   0.0       0.9   6.8e+02       5      33 ..     849     875 ..     846     878 .. 0.83
   8 ?    3.5   0.0      0.12        86       2      28 ..     880     904 ..     879     911 .. 0.84
   9 ?   -0.7   0.0       2.5   1.9e+03       2      32 ..     913     941 ..     912     945 .. 0.79
  10 ?   -0.2   0.1       1.8   1.3e+03       4      30 ..     949     975 ..     948     997 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.018
                             TPR_7   6 arlysrlGdyeeAielyeqsL 26 
                                       ar+ +++Gd+ +A + ye++ 
  gi|474934716|ref|YP_007688298.1| 229 ARMARDEGDWVNAQRMYEKAS 249
                                       88999**************43 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.4
                             TPR_7   9 ysrlGdyeeAielye 23 
                                       y +lG+ +eA+e++ 
  gi|474934716|ref|YP_007688298.1| 300 YMSLGKNSEALEILN 314
                                       899********9875 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 1.1
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLal 28 
                                       +L ++ r+y  l+++++A+++ ++  a+
  gi|474934716|ref|YP_007688298.1| 394 SLAQMSRVYLVLRHTSKAVRYAKR--AV 419
                                       577888899999*********999..65 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.096
                             TPR_7   7 rlysrlGdyeeAielyeqsLaltk 30 
                                       ++y++ G+ + A e +++ L+++ 
  gi|474934716|ref|YP_007688298.1| 434 EVYREAGENDMAMETCRKILEIDP 457
                                       68****************888874 PP

  == domain 5  score: -0.3 bits;  conditional E-value: 2
                             TPR_7  12 lGdyeeAielyeqsLaltkdped 34 
                                       l d++ A +l+ +  al++dp++
  gi|474934716|ref|YP_007688298.1| 706 LDDTAAARKLLDK--ALADDPDN 726
                                       56899999*****..*****987 PP

  == domain 6  score: 2.0 bits;  conditional E-value: 0.36
                             TPR_7   8 lysrlGdyeeAielyeqsLaltkdpeda 35 
                                       l++++Gd e +i +++    +  d++d+
  gi|474934716|ref|YP_007688298.1| 736 LCQKMGDNEALIAVCRN--IIKLDQYDK 761
                                       89*************99..777777776 PP

  == domain 7  score: 0.7 bits;  conditional E-value: 0.9
                             TPR_7   5 LarlysrlGdyeeAielyeqsLaltkdpe 33 
                                        a++y+r Gd + A  ++ q   lt+ p+
  gi|474934716|ref|YP_007688298.1| 849 RASVYRRTGDIRVADAFLSQ--YLTRNPS 875
                                       599*******9999999988..8888776 PP

  == domain 8  score: 3.5 bits;  conditional E-value: 0.12
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLal 28 
                                       L ++++l  ++G+y+ A++ y    al
  gi|474934716|ref|YP_007688298.1| 880 LEAMGDLKAEVGEYKAAADSYSD--AL 904
                                       56899999***********9977..44 PP

  == domain 9  score: -0.7 bits;  conditional E-value: 2.5
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdp 32 
                                       ++ L+++++++  ++ A+  y    a+  dp
  gi|474934716|ref|YP_007688298.1| 913 YVKLGNVQEKMDARDAAVNSYSN--AVKIDP 941
                                       67799*******9****999977..665555 PP

  == domain 10  score: -0.2 bits;  conditional E-value: 1.8
                             TPR_7   4 nLarlysrlGdyeeAielyeqsLaltk 30 
                                       +La l+ +  dy+ A++  + sLa + 
  gi|474934716|ref|YP_007688298.1| 949 ALALLQIKTHDYDGALRSIRTSLASEQ 975
                                       688888889999999999999887664 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       8.4   6.3e+03       5      51 ..     192     236 ..     191     246 .. 0.80
   2 ?   -3.6   0.0       7.5   5.6e+03     210     232 ..     299     321 ..     284     325 .. 0.75
   3 ?    2.2   0.3      0.13        98     213     244 ..     370     401 ..     341     473 .. 0.66
   4 !   13.0   0.2   6.8e-05     0.051     176     264 ..     669     758 ..     622     775 .. 0.89
   5 ?    1.0   0.0       0.3   2.3e+02      80     135 ..     924     977 ..     901     998 .. 0.63

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 8.4
                                       THHHHHHHHTT-HHHHHHHHHS---SHHHHHHHHHHHHHHHHHTT-H CS
                        Coatomer_E   5 LfdvrnefYlGaYqkaineadvaslseeekeerdvylyrsylAlgsa 51 
                                       L+ +  e+Y G +  a   + + s++  ++e+ d +l  + +A ++ 
  gi|474934716|ref|YP_007688298.1| 192 LYRIYHEWYRGTHDGAN--SLLISSEGYKEEDPDYILLSARMARDEG 236
                                       89999999999998874..6777777788888899999999998876 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 7.5
                                       HHHHTT-HHHHHHHHHHHHHH-T CS
                        Coatomer_E 210 vslllgryeeAeslLkeaLdkda 232
                                         + lg+  eA ++L+e Ld++ 
  gi|474934716|ref|YP_007688298.1| 299 GYMSLGKNSEALEILNEFLDSEM 321
                                       56889999999999999999875 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.13
                                       HTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHH CS
                        Coatomer_E 213 llgryeeAeslLkeaLdkdakdeetLiNlvva 244
                                       + g+  eAe   k a   + kd+e L+ +  +
  gi|474934716|ref|YP_007688298.1| 370 AEGNLREAEAYAKAAVSNNRKDPESLAQMSRV 401
                                       34566677777777788888888888876432 PP

  == domain 4  score: 13.0 bits;  conditional E-value: 6.8e-05
                                       HHH-TTHHHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--H CS
                        Coatomer_E 176 lavggekiqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkda 252
                                       +  ++ ++ dA yi + l  k ++  ++    A +++ l++ ++A +lL +aL  d+ + + L+    ++q++g ++
  gi|474934716|ref|YP_007688298.1| 669 IYLAATRFTDAAYIGKKLVKK-DPDAITVACLARADIGLDDTAAARKLLDKALADDPDNVDLLVVYRELCQKMGDNE 744
                                       666788999************.*****************************************99999999999886 PP

                                       H..HHHHHHHHHHH CS
                        Coatomer_E 253 e..vsernlsqlkl 264
                                          ++ rn+ +l +
  gi|474934716|ref|YP_007688298.1| 745 AliAVCRNIIKLDQ 758
                                       52245577776665 PP

  == domain 5  score: 1.0 bits;  conditional E-value: 0.3
                                       TTHHHHHHHHHHHHHS----S-HHHHHHHHHHHHHTT-HHHHHHHHTT--SHHHHH CS
                        Coatomer_E  80 srkeeilaelkeeladseiesnevlrllaaivflkegdfddalkllkksenLeavA 135
                                       +++++++++ ++ +  +  +s+  +  + a++++k  d+d al+ ++ s   e +A
  gi|474934716|ref|YP_007688298.1| 924 DARDAAVNSYSNAVKIDPHDSD--ASRALALLQIKTHDYDGALRSIRTSLASEQTA 977
                                       6667777777766644443344..34445677888888888888776653333333 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.1   0.00076      0.57       6      28 ..     296     318 ..     293     321 .. 0.91
   2 ?    2.5   0.1      0.28   2.1e+02       4      28 ..     430     454 ..     427     456 .. 0.88
   3 ?    2.8   0.0      0.23   1.7e+02       5      25 ..     766     786 ..     764     789 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00076
                               PPR   6 lIsgycknGkleeAlelfkeMke 28 
                                       lI+gy + Gk +eAle+++e ++
  gi|474934716|ref|YP_007688298.1| 296 LIRGYMSLGKNSEALEILNEFLD 318
                                       9******************9765 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.28
                               PPR   4 nslIsgycknGkleeAlelfkeMke 28 
                                       ++l+ +y  +G+ ++A+e  ++++e
  gi|474934716|ref|YP_007688298.1| 430 TTLMEVYREAGENDMAMETCRKILE 454
                                       89***************99888765 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.23
                               PPR   5 slIsgycknGkleeAlelfke 25 
                                       +l +++ k G+ +eA  l+  
  gi|474934716|ref|YP_007688298.1| 766 ILADALYKVGRGDEASMLYSS 786
                                       57799***********99975 PP

>> FAT  FAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1    0.0062       4.6     145     338 ..     424     627 ..     393     632 .. 0.66
   2 ?    4.5   0.0     0.023        17     247     296 ..     912     954 ..     852    1005 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0062
                                       -STTCCCCCCCCHCHHHHCCSTTHHCCCCCHCTT.....TT.TSSCCCHHHHHHHCCHHHHHSSCCHHHHCCTSSCC CS
                               FAT 145 vkaemwlkfanlarksgrlslAekaLkelleedpeewlprappevvyaylKylwssgeqkealqkLreftsellekk 221
                                        ++++ +   ++ r++g+ ++A+++ +++le dp      +++e     +K++ +++ +++  +++  ++s  +e+ 
  gi|474934716|ref|YP_007688298.1| 424 KSVTALTTLMEVYREAGENDMAMETCRKILEIDP------HNDEAANVLSKLEMAQVIKDSDASSILPEVS-GSEDF 493
                                       5677778888899999999999999999999999......2334445567777777776555555545555.33443 PP

                                       CSS-SS---....................HHHHCCCTCCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTC CS
                               FAT 222 eelqsgleaq........keptnleeftkllarcylkkGewqealqkldwseekieeilqsysaateidpswykawh 290
                                        +l s l+a+         + +n  ++  ++a +  ++G    al++       + ++ +s++ a+ + p++++ wh
  gi|474934716|ref|YP_007688298.1| 494 IRLISTLIAErkyaeaekLCRDNDDKYG-NVAAVRRLRGNAEYALGE-------FLKASASFASAAALEPECAEIWH 562
                                       3444444443233322221122222222.224555666777777777.......8899999**************** PP

                                       C..CCHHHHHCCHHHHHHSSSS...................S-TCCHHHHCCT..CCHHHHTTTSSTT CS
                               FAT 291 t..walfnfevvskeeeqkeeee..................pedlqeyvvpavkgflksislssensl 338
                                       +  +a+  f  +   e      +                   ++++   v av+ f ++i l +++++
  gi|474934716|ref|YP_007688298.1| 563 SkgLADEAFGDLDSAEAAY---NqavlldmknphywiskgcVQEMKGNKVAAVDSFNRAIELDQSSTY 627
                                       *444444444444443333...23457888888888888886788889999**********9999765 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.023
                                       CCCTCCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCCCCHHH CS
                               FAT 247 cylkkGewqealqkldwseekieeilqsysaateidpswykawhtwalfn 296
                                       +y k+G  qe++         ++++++sys a++idp+  +a  ++al+ 
  gi|474934716|ref|YP_007688298.1| 912 VYVKLGNVQEKMDA-------RDAAVNSYSNAVKIDPHDSDASRALALLQ 954
                                       67788888888888.......9***************9999999998875 PP

>> HrpB1_HrpK  Bacterial type III secretion protein (HrpB1_HrpK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.26     2e+02       5      74 ..      45     111 ..      41     137 .. 0.78
   2 ?    0.6   0.2      0.56   4.1e+02       7      86 ..     422     502 ..     417     514 .. 0.79
   3 ?    4.7   0.3     0.029        21       6     111 ..     621     726 ..     617     740 .. 0.78
   4 ?    6.6   0.0    0.0079       5.9      51      94 ..     950     992 ..     936    1006 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.26
                        HrpB1_HrpK   5 qcskelvggLievlslalasedtedaellLdalrvLrPevaeldllegvlliergrweeAlrlLreveae 74 
                                       ++s +l++ +ie++s+  a++ ++d+++l+      rP+  ++ l  +  l ++g ++eA+ +L+ v ++
  gi|474934716|ref|YP_007688298.1|  45 EVSSALLARMIEIVSAEEAEGWKDDVADLVSK---QRPQDCKASLAAASCLARKGIVNEARTYLEGVHGS 111
                                       66778888888888888888888888888765...579999999*****9**************999843 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.56
                        HrpB1_HrpK   7 skelvggLievlslalasedtedaellLdalrvLrPevaeldllegvllierg.rweeAlrlLreveaeasgtpyak 82 
                                       + + v++L  ++ +  ++++ + a +  + +  + P++ e++ +   l +++  + ++A  +L ev++++ +  + +
  gi|474934716|ref|YP_007688298.1| 422 DAKSVTALTTLMEVYREAGENDMAMETCRKILEIDPHNDEAANVLSKLEMAQViKDSDASSILPEVSGSEDFIRLIS 498
                                       566777777777777777888888888888888889999988888888887752567999*******9999999999 PP

                        HrpB1_HrpK  83 aLlA 86 
                                        L+A
  gi|474934716|ref|YP_007688298.1| 499 TLIA 502
                                       9988 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.029
                        HrpB1_HrpK   6 cskelvggLievlslalasedtedaellLdalrvLrPevaeldllegvlliergrweeAlrlLreveaeasgtpyak 82 
                                       ++++   +L++ +s  ++ +++ da + +d   +  P++ +++ +  +++++  r+++A+ + +++ ++ + + +++
  gi|474934716|ref|YP_007688298.1| 621 LDQSSTYALVKKASIMAEYGRFSDAINFMDLAEATDPKNNDIQKIKMQIYLAATRFTDAAYIGKKLVKKDPDAITVA 697
                                       56667779999999999*********************************************999998888877776 PP

                        HrpB1_HrpK  83 aLlAlcLaalrD.eeWrayAeevlesdadp 111
                                        L A +   l+D ++ r++ +++l+ d+d+
  gi|474934716|ref|YP_007688298.1| 698 CL-ARADIGLDDtAAARKLLDKALADDPDN 726
                                       55.444444444144566666666655554 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.0079
                        HrpB1_HrpK  51 egvlliergrweeAlrlLreveaeasgtpyakaLlAlcLaalrD 94 
                                        ++l+i+ +++++Alr +r+  a+++  + + a+lA   + ++D
  gi|474934716|ref|YP_007688298.1| 950 LALLQIKTHDYDGALRSIRTSLASEQT-AEGYAILAQICQLRKD 992
                                       589****************99866554.4555666655555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 1.06u 0.33s 00:00:01.39 Elapsed: 00:00:00.59
# Mc/sec: 6154.44
//
Query:       gi|474934717|ref|YP_007688299.1|  [L=235]
Description: Glycerol uptake facilitator and related permeases (Major Intrinsic Protein Family) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.6e-48  163.6  22.9    6.3e-48  163.4  22.9    1.0  1  MIP           Major intrinsic protein
  ------ inclusion threshold ------
        8.8    5.4   7.2         16    4.6   7.2    1.5  1  Bac_export_2  FlhB HrpN YscU SpaS Family


Domain annotation for each model (and alignments):
>> MIP  Major intrinsic protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.4  22.9   7.1e-52   6.3e-48       7     223 ..       4     222 ..       1     226 [. 0.93

  Alignments for each domain:
  == domain 1  score: 163.4 bits;  conditional E-value: 7.1e-52
                                       HHHHHHHHHHHHHHHHHHHHHHHHCCCSSCSSSSTTSSHHHHHHHHHHHHHHHHHHHHHHHCHT-S-SHHHHHHHHH CS
                               MIP   7 flravlAEflatlllvfigvgsalnvkkkvsslaslvsvtleavalafglalavlvylaagiSGaHlNPavTlallv 83 
                                       + r+++AE ++t++lv++g+g+a+ +   v        ++ +a+alafgl+++v   ++++iSGaHlNPav l++++
  gi|474934717|ref|YP_007688299.1|   4 AFRSYFAELIGTMVLVLFGCGAAVFLGGVV-------GGGALAIALAFGLTVVVMSVTVGNISGAHLNPAVSLGMFL 73 
                                       4799*****************999666655.......46899*********************************** PP

                                       TTSSSHHHHHHHHHHHHHHHHHHHHHHHHHCHHH......HHHTTTTSSSSSTTSSHHHHHHHHHHHHHHHHHHHHH CS
                               MIP  84 arkisllrailYivaQllGaivaaallklltkgl......esraglfanslkpglsagqalvvEiiltfvLvlvvfa 154
                                        ++i+l+  ++Y++ Ql+Gai++aall ++ +g+         + ++a+  ++g++++ a+++Ei+lt+++vl+ +a
  gi|474934717|ref|YP_007688299.1|  74 DKRIDLKTFVMYFIFQLVGAIIGAALLAVFAMGAfdcgfgDLGNLAMATNDAEGVGVAYAMIIEIVLTMIFVLIALA 150
                                       *********************************99999986777777888999********************9999 PP

                                       HCSTTSSSSTCHGHHHHHHHHHHHHHHHHHHHHST-SSHHHHHHHHHHHTH......STTTTHHHHHHHHHHHHH CS
                               MIP 155 ltddkrkvslgelaplaigllvaliilvgipltGaamNpArslgpavvlnk......fedhwvylvGPliGailg 223
                                       +t ++   +   +a+l igl +++++lvgipltG+++NpArslg+++++ +       ++++v+l++PliGa+++
  gi|474934717|ref|YP_007688299.1| 151 ATAKNGMDK---FAGLYIGLGLTMVHLVGIPLTGCSVNPARSLGASILHVAegadfvASEFYVFLIAPLIGAAIA 222
                                       998765555...9************************************999***9999**************98 PP

>> Bac_export_2  FlhB HrpN YscU SpaS Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   7.2    0.0018        16      80     189 ..      38     151 ..       1     159 [. 0.58

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0018
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.....XXX....XXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      Bac_export_2  80 llvlllaallanllqvgflfstkalkpklsklnplkgl.....kri....fslrslvellksllkvvlvgavaylvl 147
                                       l      a++  +  + +++s+   ++   +lnp+  l     kri    f +  +++l+ +++ ++l++++a+ ++
  gi|474934717|ref|YP_007688299.1|  38 L------AIALAFGLTVVVMSVTVGNISGAHLNPAVSLgmfldKRIdlktFVMYFIFQLVGAIIGAALLAVFAMGAF 108
                                       2......2222233333333444444444445553333111112222123666667889999999999999999999 PP

                                       XXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      Bac_export_2 148 kseleellala.eldleaalelllslllkllllvllallvial 189
                                       +  +++l +la +++ ++ + ++  ++++++l+++++l+++a+
  gi|474934717|ref|YP_007688299.1| 109 DCGFGDLGNLAmATNDAEGVGVAYAMIIEIVLTMIFVLIALAA 151
                                       989999998873556779999**************99999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       960  (0.0535445); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1607.64
//
Query:       gi|474934718|ref|YP_007688300.1|  [L=338]
Description: protoporphyrin IX magnesium-chelatase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-17   63.5   0.4    1.9e-17   62.9   0.4    1.4  1  AAA_lid_2        AAA lid domain
    1.4e-11   44.5   0.0    1.3e-06   28.5   0.0    2.5  2  AAA_5            AAA domain (dynein-related subfamily)
    1.8e-08   34.0   0.1    9.6e-06   25.1   0.0    2.9  3  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00046   19.9   0.0       0.39   10.4   0.0    2.2  2  Sigma54_activat  Sigma-54 interaction domain
    0.00074   18.7   0.0       0.07   12.2   0.0    2.6  2  MCM              MCM P-loop domain
     0.0035   17.4   0.1     0.0087   16.2   0.1    1.7  1  TIP49_C          TIP49 AAA-lid domain
     0.0055   16.6   0.0       0.24   11.3   0.0    2.4  2  AAA_3            ATPase family associated with various cellul
  ------ inclusion threshold ------
      0.054   13.9   0.2       0.14   12.5   0.2    1.8  1  AAA_16           AAA ATPase domain


Domain annotation for each model (and alignments):
>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.9   0.4   8.5e-21   1.9e-17       2      72 ..     262     332 ..     261     333 .. 0.96

  Alignments for each domain:
  == domain 1  score: 62.9 bits;  conditional E-value: 8.5e-21
                         AAA_lid_2   2 atrahlaielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlrrepeaegetteeivee 72 
                                       +++a+l++ ++++g+R dl+l+raArA+Aaleg d++   D + +a lVLaHR++ +++++ + ++++v+e
  gi|474934718|ref|YP_007688300.1| 262 EMAARLSMHYNMEGHRSDLTLIRAARANAALEGHDHIDVKDMESVASLVLAHRIKGKAFEKVQFDDSEVRE 332
                                       6789999******************************************************9*99999997 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   2.5e-05     0.056       1      26 [.      28      53 ..      28      60 .. 0.86
   2 !   28.5   0.0   5.7e-10   1.3e-06      23     138 .]      88     197 ..      81     197 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.5e-05
                                      EEEEE--SSSSHHHHHHHGGGGBS-- CS
                             AAA_5  1 dvlLvGppGtgKselaerlaaalnre 26
                                      +vl++G++Gt+Ks+ +++++++l ++
  gi|474934718|ref|YP_007688300.1| 28 GVLIKGEKGTAKSTAVRSMSQFLPSR 53
                                      599******************99544 PP

  == domain 2  score: 28.5 bits;  conditional E-value: 5.7e-10
                                       BS--EEEEE--TT--HHHHH--B--.............--------G-SEEEEESGGG--HHHHHHHHHHHHSSEEE CS
                             AAA_5  23 lnreveyvqltrdtteedlkgrreik....ngttslvdsplvraaregeilvlDEveraesevlnsLlslleerrll 95 
                                       ++ ++ +v l+ + te+ + g ++++     g++++++++l   a +g il++DE++ +++++++ L   l+   + 
  gi|474934718|ref|YP_007688300.1|  88 ITVPMKVVELPLNATEDRVSGTLDLEyvlkTGKKKFEPGVLA--AANGNILYVDEINLLDDHIVDLL---LDSAAMG 159
                                       566778888888999******999999999***********8..89***********9999999988...7777777 PP

                                       ..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHTT- CS
                             AAA_5  96 leeggelvkaknddllerfrviatanpldrslnelspalrsRf 138
                                       ++   ++    +  +  rf +++t+np +    +l p+l++Rf
  gi|474934718|ref|YP_007688300.1| 160 VNYVEREGVSFS--HPARFVLVGTMNPEE---GNLRPQLLDRF 197
                                       555444433222..2234*********99...66789999998 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   0.0     0.005        11       2      48 ..       4      52 ..       3      57 .. 0.84
   2 !   25.1   0.0   4.3e-09   9.6e-06      92     159 ..     118     185 ..     112     193 .. 0.93
   3 ?   -1.1   0.0      0.45     1e+03     185     202 ..     189     206 ..     186     210 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.005
                      Mg_chelatase  2 lkdvkGqeeakraleiaaa..GgHnlllvGppGsGKtmlakrlpsllpp 48
                                      ++ v+ qe+ kral + ++      +l+ G  G+ K+   + +++ lp+
  gi|474934718|ref|YP_007688300.1|  4 FTRVVKQEKMKRALLLNVIdpTIGGVLIKGEKGTAKSTAVRSMSQFLPS 52
                                      56799999****99888762235679*********************96 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 4.3e-09
                      Mg_chelatase  92 GggskpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpc 159
                                        g +k +pG ++ a+  +L++DE+  ++ ++++ L +    g   ++r   ++++parf lv +mNp 
  gi|474934718|ref|YP_007688300.1| 118 TGKKKFEPGVLAAANGNILYVDEINLLDDHIVDLLLDSAAMGVNYVEREGVSFSHPARFVLVGTMNPE 185
                                       577899************************************************************95 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.45
                      Mg_chelatase 185 lsgplldRidlqvevkkl 202
                                       l   lldR+ l+vev+  
  gi|474934718|ref|YP_007688300.1| 189 LRPQLLDRFGLSVEVEGE 206
                                       55679*********9765 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0015       3.3      23      45 ..      27      53 ..       7      84 .. 0.67
   2 !   10.4   0.0   0.00018      0.39      79     133 ..     118     174 ..     115     196 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0015
                                      S-EEEECSTTSSHHHHHHHHHH....H CS
                   Sigma54_activat 23 lsvlitGesGtGKellaraihe....a 45
                                        vli+Ge+Gt K++  r++ +    +
  gi|474934718|ref|YP_007688300.1| 27 GGVLIKGEKGTAKSTAVRSMSQflpsR 53
                                      579***************998854440 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00018
                                       TTTSS-BEHHHHHTTTSEEEEETGGGS-HHHHHHHHH..HHHHSEEESBTSSSEEE- CS
                   Sigma54_activat  79 tGAekekkGlfekadgGtlfLDeigelplelQekLlr..vlqegevervGsskeikv 133
                                       tG +k + G + +a+g +l++Dei+ l+ ++   Ll   ++  + ver G s ++++
  gi|474934718|ref|YP_007688300.1| 118 TGKKKFEPGVLAAANGNILYVDEINLLDDHIVDLLLDsaAMGVNYVEREGVSFSHPA 174
                                       77788889*****************99998888887522344455566665555555 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.012        26      60      84 ..      29      53 ..       4      60 .. 0.82
   2 !   12.2   0.0   3.1e-05      0.07     107     179 ..     118     190 ..     109     210 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.012
                                      EEEEESSTSTHHHHHHHHHHHSSSE CS
                               MCM 60 vllvgdpgtaKsqlLkyveklapra 84
                                      vl+ g+ gtaKs+ ++++++++p  
  gi|474934718|ref|YP_007688300.1| 29 VLIKGEKGTAKSTAVRSMSQFLPSR 53
                                      8999**************9999865 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 3.1e-05
                                       SSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--SSSSCC CS
                               MCM 107 tgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAanpkagryd 179
                                       tg+  +e G l  a++ ++++De++  +++  + l++        + + G+  + +ar  ++  +np++g+  
  gi|474934718|ref|YP_007688300.1| 118 TGKKKFEPGVLAAANGNILYVDEINLLDDHIVDLLLDSAAMGVNYVEREGVSFSHPARFVLVGTMNPEEGNLR 190
                                       5667789*****************************99999999999*********************99765 PP

>> TIP49_C  TIP49 AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   3.9e-06    0.0087       1      63 [.     244     309 ..     244     311 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.9e-06
                           TIP49_C   1 IlkiRakeEgvkldeeAldlLakigtetSL...RYaiqLltpasilakkrkkkevevedveeveeL 63 
                                       I+k R    ++ +de+A+++ a+++++  +   R  + L+ +a+  a +++++ ++v+d e+v++L
  gi|474934718|ref|YP_007688300.1| 244 IVKARELIPKIPIDEKAMEMAARLSMHYNMeghRSDLTLIRAARANAALEGHDHIDVKDMESVASL 309
                                       7888999999*********99998887544444******************************998 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.043        95       2      23 ..      29      50 ..      28      55 .. 0.91
   2 !   11.3   0.0   0.00011      0.24      53     115 ..     120     187 ..      99     199 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.043
                             AAA_3  2 vllegvPGlaktllvkalakal 23
                                      vl++g  G+ak ++v+++++ l
  gi|474934718|ref|YP_007688300.1| 29 VLIKGEKGTAKSTAVRSMSQFL 50
                                      89****************9987 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00011
                             AAA_3  53 efefkkGpvfa...nllladeinrappktqsalle..ameerqvtvegethklpepflvlatqnPieq 115
                                       + +f++G + a   n+l +dein    ++   ll+  am  + v  eg +++ p  f+++ t nP e 
  gi|474934718|ref|YP_007688300.1| 120 KKKFEPGVLAAangNILYVDEINLLDDHIVDLLLDsaAMGVNYVEREGVSFSHPARFVLVGTMNPEEG 187
                                       4455566554323389******************8557999************************774 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   6.4e-05      0.14      14      51 ..      16      53 ..       6     161 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.4e-05
                            AAA_16 14 salervrsgrpelvllsGesGvGKsslvrellralekd 51
                                      ++l +v +++ + vl+ Ge+G+ Ks+ vr+  + l  +
  gi|474934718|ref|YP_007688300.1| 16 ALLLNVIDPTIGGVLIKGEKGTAKSTAVRSMSQFLPSR 53
                                      4555788888899****************999766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       708  (0.0394891); expected 358.6 (0.02)
Passed bias filter:                      606  (0.0338); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2064.84
//
Query:       gi|474934719|ref|YP_007688301.1|  [L=659]
Description: Mg-chelatase subunit ChlI [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-16   60.0   1.3    3.5e-16   58.8   0.4    2.1  2  AAA_lid_2        AAA lid domain
    4.4e-13   49.8   0.0    1.2e-12   48.4   0.0    1.8  1  VWA_2            von Willebrand factor type A domain
    2.1e-09   37.9   0.0    8.6e-09   35.9   0.0    2.0  2  VWA              von Willebrand factor type A domain
    3.2e-08   33.2   0.1     0.0064   15.9   0.0    2.5  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00013   21.9   0.0    0.00047   20.2   0.0    2.0  1  AAA_5            AAA domain (dynein-related subfamily)
    0.00038   20.4   0.0    0.00099   19.1   0.0    1.7  1  VWA_3            von Willebrand factor type A domain
     0.0013   18.5   0.0     0.0038   16.9   0.0    1.8  2  Sigma54_activat  Sigma-54 interaction domain
     0.0052   15.9   0.0      0.014   14.5   0.0    1.7  1  MCM              MCM P-loop domain
  ------ inclusion threshold ------
       0.09   12.3   0.0       0.19   11.3   0.0    1.6  1  Sec23_trunk      Sec23/Sec24 trunk domain
       0.11   12.1   0.2       0.28   10.7   0.0    1.7  2  AAA_7            P-loop containing dynein motor region
       0.16   12.4   0.8       0.78   10.1   0.0    2.6  3  AAA_16           AAA ATPase domain


Domain annotation for each model (and alignments):
>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   0.4   2.1e-19   3.5e-16       3      63 ..     238     298 ..     236     309 .. 0.86
   2 ?   -3.9   0.0       7.8   1.3e+04      24      34 ..     479     489 ..     476     500 .. 0.79

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 2.1e-19
                         AAA_lid_2   3 trahlaielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlrrepeaeg 63 
                                        +++++  lgv g R+++ ++++A+AlAal+gr++Vt++Dv  aa l+L HR + ++e+ +
  gi|474934719|ref|YP_007688301.1| 238 NISRICKLLGVKGCRGAISTAHTAKALAALAGRKRVTDDDVANAAVLCLDHRRTVSAEDLK 298
                                       57788999********************************************995554433 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 7.8
                         AAA_lid_2  24 raArAlAaleg 34 
                                       r+A++ Aa+e 
  gi|474934719|ref|YP_007688301.1| 479 RMAKVKAAIES 489
                                       78999999875 PP

>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.4   0.0   7.2e-16   1.2e-12       2     107 .]     465     571 ..     464     571 .. 0.88

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 7.2e-16
                             VWA_2   2 vfvlDtSgSmrngdygptrleaakdaveallksl..pgdrvglvtfsdgp.evlipltkdkakilnalrnleakggg 75 
                                       +f+lDtSgS   +    +r++++k+a+e++l++   ++drvgl+tf++++  ++ ++++  ++++++++++   g g
  gi|474934719|ref|YP_007688301.1| 465 LFLLDTSGSLIIR----NRMAKVKAAIESMLQTHyvKRDRVGLMTFNEEAiDLIMQPSRATEQLEQIIDKIAV-GTG 536
                                       8********9666....48*************66679***********7548999*****************8.6** PP

                             VWA_2  76 tnlaaaLqlarkalkkrr...kgekrvivlitDge 107
                                       t l aaL ++ + +   +     e++ ivl+tDg+
  gi|474934719|ref|YP_007688301.1| 537 TPLSAALMKVYDYMLPYSikhPDERCHIVLLTDGK 571
                                       ************884333455689*********95 PP

>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.6   2.6e+03     119     156 ..     328     369 ..     320     386 .. 0.64
   2 !   35.9   0.0   5.3e-12   8.6e-09       4     122 ..     466     584 ..     464     632 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.6
                                       HTHHHHHHHH.....GCTEEEEEEEESSSHHHHHHHHHSSSSC CS
                               VWA 119 dpkeaaneak.....eqgikvfavGvgnadekelLnkiasepg 156
                                       d k+++ e++     + g++v+ +G g  +++e +++  ++ +
  gi|474934719|ref|YP_007688301.1| 328 DKKPEVIELQpgaegSGGVEVVQIGDGFMNDDE-VKQVITKAA 369
                                       555555555555555668888888887777777.666655555 PP

  == domain 2  score: 35.9 bits;  conditional E-value: 5.3e-12
                                       EEEE-STTS.CHHHHHHHHHHHHHHHHHHTBTTTTEEEEEEEESSS.EEEEEETTSHCHHHHHHHHHHTGSGGGGSS CS
                               VWA   4 fvlDgSgsm.geenfekvkefikklveklevgpegtrvglvqfsse.vktefslndysskeellsalnnlkysgggt 78 
                                       f+lD+Sgs   ++++ kvk +i+++++  +   +++rvgl++f++e +  +++ ++ +  e+l + ++++   g+gt
  gi|474934719|ref|YP_007688301.1| 466 FLLDTSGSLiIRNRMAKVKAAIESMLQTHY--VKRDRVGLMTFNEEaIDLIMQPSRAT--EQLEQIIDKI-AVGTGT 537
                                       9*******87899999**************..8889**********666668888866..9999999996.778888 PP

                                       C-HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CSS.....HTHH CS
                               VWA  79 tntgkalkyaleklfkssagaRenakkviilltdGksndg.....dpke 122
                                         + +al ++++ ++  s +  ++ + +i+lltdGk ++       p e
  gi|474934719|ref|YP_007688301.1| 538 P-LSAALMKVYDYMLPYSIK-HPDERCHIVLLTDGKATKAldfrkTPIE 584
                                       8.9*********88888888.6779************985555554444 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   9.9e-06     0.016       2      47 ..      14      61 ..      13      69 .. 0.88
   2 !   15.9   0.0   3.9e-06    0.0064     103     161 ..     100     158 ..      84     178 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.9e-06
                      Mg_chelatase  2 lkdvkGqeeakraleiaaaG..gHnlllvGppGsGKtmlakrlpsllp 47
                                      ++ + G+  ak+al +aa       ++l G++G+ Kt+la+ ++s+ p
  gi|474934719|ref|YP_007688301.1| 14 FSAIYGNVPAKTALMVAAVSpsIRAVMLKGASGTAKTVLARSIMSIDP 61
                                      57899*************8622579******************99976 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 3.9e-06
                      Mg_chelatase 103 slahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpcpc 161
                                        +a++  L+LD++  f+ + l  L + + dg+v+++r + ++++  +++++a+m  ++ 
  gi|474934719|ref|YP_007688301.1| 100 LRANKNYLYLDDCDLFDPNLLTGLMDDVVDGTVRVERENVSTQYRVSTTVIASMHSSRK 158
                                       579999************************************************98774 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   2.9e-07   0.00047       2     124 ..      39     157 ..      38     167 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.9e-07
                                       EEEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT--HHHHH--B--.............--------G-SEEEEES CS
                             AAA_5   2 vlLvGppGtgKselaerlaaal.nreveyvqltrdtteedlkgrreik....ngttslvdsplvraaregeilvlDE 73 
                                       v+L+G++Gt+K+ la+++ +   ++++     + + t e+l+g+++++     g+ +l d +l ra  ++  l+lD+
  gi|474934719|ref|YP_007688301.1|  39 VMLKGASGTAKTVLARSIMSIDpGKKLIN--VPLNVTDEQLFGSIDLEhavaTGKVELGDCILLRA--NKNYLYLDD 111
                                       89****************99885555555..55567***********9998888889999999976..678999**9 PP

                                       GGG--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS-- CS
                             AAA_5  74 veraesevlnsLlslleerrllleeggelvkaknddllerfrviatanpld 124
                                        +  +++ l  L+    + ++++e  +  ++ +       ++via++++ +
  gi|474934719|ref|YP_007688301.1| 112 CDLFDPNLLTGLMDDVVDGTVRVERENVSTQYRVS-----TTVIASMHSSR 157
                                       99999999888876666666654433333322222.....77777777665 PP

>> VWA_3  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0     6e-07   0.00099       5     113 ..     466     581 ..     463     623 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 6e-07
                             VWA_3   5 ivvDvsssmsaen..klvkdaLsvalrq.Lptndkiavllfgtkprplfpgsravsaaelqealqkikelelslgas 78 
                                       +++D+s s    n  + vk+a+  +l++   ++d++ ++ f  ++  l+ +   +  ++l+++ +ki+       ++
  gi|474934719|ref|YP_007688301.1| 466 FLLDTSGSLIIRNrmAKVKAAIESMLQThYVKRDRVGLMTFNEEAIDLIMQPSRAT-EQLEQIIDKIAV----GTGT 537
                                       899****977666689************999*************999997776666.577777777776....678* PP

                             VWA_3  79 nlegaLkealrqp.....akpgevrsvilltDgssaqge....e 113
                                       +l +aL ++ +       ++p e+ +++lltDg +++      +
  gi|474934719|ref|YP_007688301.1| 538 PLSAALMKVYDYMlpysiKHPDERCHIVLLTDGKATKALdfrkT 581
                                       **********954558889***************7664344443 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.3e-06    0.0038      15     143 ..      29     155 ..      20     164 .. 0.74
   2 ?   -3.4   0.0       4.1   6.7e+03      38      55 ..     392     409 ..     389     420 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.3e-06
                                       HHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BEHHHHH CS
                   Sigma54_activat  15 ikkvaktdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAekekkGlfek 91 
                                       +++v ++   v+++G sGt K++lar+i +  +   k++++v    + e+l+ s     e+   tG  +     + +
  gi|474934719|ref|YP_007688301.1|  29 VAAVSPSIRAVMLKGASGTAKTVLARSIMSIDP--GKKLINVPLNVTDEQLFGS--IDLEHAVATGKVELGDCILLR 101
                                       5566667789******************98887..5566666555555666666..345667778999999999*** PP

                                       TTTSEEEEETGGGS-HHHHHHHHHHHHHSEE..ESBTSSSEEE--EEEEEEESS CS
                   Sigma54_activat  92 adgGtlfLDeigelplelQekLlrvlqegev..ervGsskeikvdvriiaatne 143
                                       a++  l+LD+   ++++l + L+  + +g+v  er   s++ +v++ +ia+ ++
  gi|474934719|ref|YP_007688301.1| 102 ANKNYLYLDDCDLFDPNLLTGLMDDVVDGTVrvERENVSTQYRVSTTVIASMHS 155
                                       ***********9999999999998766665511444445666777777777665 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 4.1
                                       HHHHHHHHSTTTTS-EEE CS
                   Sigma54_activat  38 laraiheaskrkekpfva 55 
                                       +a+ ++++sk +++++v+
  gi|474934719|ref|YP_007688301.1| 392 VAKRMYAESKDRNGKYVR 409
                                       899999999999999886 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   8.5e-06     0.014      59     182 ..      38     164 ..      14     173 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 8.5e-06
                                       EEEEEESSTSTHHHHHHHHHHHSSSEEEEESS.SSSSSHSSSEEEEESS..SSSEEEEETHHHHTTTSEEEEESGGG CS
                               MCM  59 nvllvgdpgtaKsqlLkyveklapravytsgk.gssaagLtaavvrdee..tgefvleaGalvladkGvcciDefdk 132
                                        v+l g +gtaK+ l +++ ++ p    ++     + + L  ++  +++  tg++ l    l+ a+k  +++D+ d 
  gi|474934719|ref|YP_007688301.1|  38 AVMLKGASGTAKTVLARSIMSIDPGKKLINVPlNVTDEQLFGSIDLEHAvaTGKVELGDCILLRANKNYLYLDDCDL 114
                                       48999*********************99998626789999888776665115556666667999************* PP

                                       STCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--SSSSCCTTS CS
                               MCM 133 mkeedrsalhEamEqqtisiaKaGivatLnartsvlaAanpkagrydkkk 182
                                        + +  + l++ + + t+ + +  + ++ +  t+v+a++ ++  ++d++ 
  gi|474934719|ref|YP_007688301.1| 115 FDPNLLTGLMDDVVDGTVRVERENVSTQYRVSTTVIASMHSSRKHFDSHV 164
                                       **********************************************9876 PP

>> Sec23_trunk  Sec23/Sec24 trunk domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00011      0.19       4      51 ..     462     508 ..     459     532 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                                       -EEEEEEE-SHHHHHHTHHHHHHHHHHHHCTTSSTSTT-EEEEEEESS CS
                       Sec23_trunk   4 pvflFviDvsleaikegelkalkeslkqsLdllPeepralvglitfds 51 
                                        +flF++D+s + i  + ++ +k +++++L+     +r +vgl+tf++
  gi|474934719|ref|YP_007688301.1| 462 STFLFLLDTSGSLIIRNRMAKVKAAIESMLQTHY-VKRDRVGLMTFNE 508
                                       68****************************8766.6999*******96 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00017      0.28      27      68 ..      30      71 ..      21      76 .. 0.78
   2 ?   -3.2   0.1       3.1     5e+03     104     117 ..     627     640 ..     623     641 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00017
                             AAA_7 27 elllknkkpvllvGptGtGKtviikdllkkldkekylsltin 68
                                        +  + + v+l G +Gt+Ktv+++++++  + +k++ + +n
  gi|474934719|ref|YP_007688301.1| 30 AAVSPSIRAVMLKGASGTAKTVLARSIMSIDPGKKLINVPLN 71
                                      555566789*****************9988777777766666 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.1
                             AAA_7 104 vFvDDlnmpakeky 117
                                       + +DDl +p+ +++
  gi|474934719|ref|YP_007688301.1| 627 FLLDDLQVPEDNTF 640
                                       568*******9987 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00048      0.78      18      47 ..      30      58 ..      24      87 .. 0.85
   2 ?   -2.1   0.1       2.7   4.4e+03     137     158 ..     105     123 ..      93     131 .. 0.74
   3 ?   -3.0   0.0       4.9     8e+03     135     146 ..     623     634 ..     567     653 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00048
                            AAA_16 18 rvrsgrpelvllsGesGvGKsslvrellra 47
                                      ++ s++ ++v+l G+sG+ K+ l+r+++ +
  gi|474934719|ref|YP_007688301.1| 30 AAVSPSIRAVMLKGASGTAKTVLARSIM-S 58
                                      5666777******************998.3 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.7
                            AAA_16 137 lvlvlDdlqwadeaslqllaaL 158
                                        +l lDd + +d+   +ll  L
  gi|474934719|ref|YP_007688301.1| 105 NYLYLDDCDLFDP---NLLTGL 123
                                       4899*******99...555555 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 4.9
                            AAA_16 135 rplvlvlDdlqw 146
                                       +   ++lDdlq 
  gi|474934719|ref|YP_007688301.1| 623 HAKFFLLDDLQV 634
                                       345788999984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (659 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       896  (0.0499749); expected 358.6 (0.02)
Passed bias filter:                      617  (0.0344135); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.73u 0.31s 00:00:01.04 Elapsed: 00:00:00.49
# Mc/sec: 4046.30
//
Query:       gi|474934720|ref|YP_007688302.1|  [L=298]
Description: putative membrane protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.8e-35  120.8  22.2    6.8e-35  120.8  22.2    2.3  2  DUF368    Domain of unknown function (DUF368)
  ------ inclusion threshold ------
       0.12   12.0   0.3       0.22   11.2   0.3    1.4  1  SAT       Starter unit:ACP transacylase in aflatoxin biosynth
       0.17   11.5   0.0        0.3   10.6   0.0    1.5  1  DUF1972   Domain of unknown function (DUF1972)
       0.26   11.3   3.2        4.7    7.3   1.1    3.6  3  UPF0370   Uncharacterised protein family (UPF0370)
        7.5    6.1  41.6         25    4.4  23.4    4.3  3  TauE      Sulfite exporter TauE/SafE


Domain annotation for each model (and alignments):
>> DUF368  Domain of unknown function (DUF368)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.8  22.2   1.9e-38   6.8e-35       1     230 [.      24     254 ..      24     265 .. 0.86
   2 ?    0.9   0.1     0.078   2.8e+02     214     242 ..     267     295 ..     263     298 .] 0.67

  Alignments for each domain:
  == domain 1  score: 120.8 bits;  conditional E-value: 1.9e-38
                            DUF368   1 mGaAdvvPGvSGGtiAlitGiYeelieslksinlealklllrarlkaalkkinlkfLlalvlGivvsilvlakllsy 77 
                                       +G+A ++PG+SG ++A+++GiYe+l++ l+++              + + k++++f++  ++G +v+ ++ akll+ 
  gi|474934720|ref|YP_007688302.1|  24 IGIAAMLPGISGAVLAVLFGIYERLVRDLAKL--------------HYYIKADFWFIILFLIGGIVGTVISAKLLNE 86 
                                       79*****************************9..............566678999********************** PP

                            DUF368  78 llekypillwslffGlilasvvvlikevkk.....wsvkkiialllglaiallltvle..........pveteeslv 139
                                        +++yp     +f+Gli++ ++ l+k   +      ++++++a+++g++++  + +++           ++ + ++ 
  gi|474934720|ref|YP_007688302.1|  87 AMDRYPAECLMFFVGLIAGQIPALYKLTATsscekPAAHNMLAFIIGIIAMGSMIAVDlleissgdveLLHDSYGYA 163
                                       ***********************999877756654577788888888888777777773444444332222333666 PP

                            DUF368 140 fvflaGaiaicAmilPGiSGSfiLlllGlYelllealkeldvkvllvfllGavvGllsfsrvlsallkkyrsltlav 216
                                       ++f+ G++ +++ ++PGiS S+iL+++Gl+  + +a+ ++dv+++ +++lG++ G l+fs+v++++l++++++++ +
  gi|474934720|ref|YP_007688302.1| 164 VMFVIGVVVAISALVPGISHSTILIVFGLFAAFTAAVGDVDVAFIGCMMLGILAGALLFSKVIHYALDHHHRTMMFL 240
                                       677777776666678************************************************************** PP

                            DUF368 217 liGlmlGslrkvwp 230
                                       ++Gl +Gsl +++ 
  gi|474934720|ref|YP_007688302.1| 241 ILGLTIGSLAALLF 254
                                       *********99876 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.078
                            DUF368 214 lavliGlmlGslrkvwpwketletlkdss 242
                                       la+++ l +G  +++w +k   + +  ++
  gi|474934720|ref|YP_007688302.1| 267 LACICTLAVGLAVSIWSMKMSHKNMVREH 295
                                       67777777777777777777766666555 PP

>> SAT  Starter unit:ACP transacylase in aflatoxin biosynthesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3     6e-05      0.22      87     152 ..     224     286 ..     201     297 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6e-05
                               SAT  87 qfivyleenpeeypspestylvGlCtGllaAaavacskslseLvplaveavrvafrlGlevarvaa 152
                                       ++i+y+ +++++ +      ++Gl +G+laA +  ++++++ L+ +   + ++a+ l++ ++ ++ 
  gi|474934720|ref|YP_007688302.1| 224 KVIHYALDHHHRTM---MFLILGLTIGSLAALLFTSADKVDGLMHILACICTLAVGLAVSIWSMKM 286
                                       44555433333333...5789**************************9999999999998888665 PP

>> DUF1972  Domain of unknown function (DUF1972)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   8.4e-05       0.3      76     124 ..     218     266 ..     192     293 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 8.4e-05
                           DUF1972  76 dilalnyalklikeknikepifyilgntiGafiahfakkihklgGklfv 124
                                         l + + ++++ +++ ++ +f ilg tiG+++a      +k++G +++
  gi|474934720|ref|YP_007688302.1| 218 GALLFSKVIHYALDHHHRTMMFLILGLTIGSLAALLFTSADKVDGLMHI 266
                                       4556778999***********************************9987 PP

>> UPF0370  Uncharacterised protein family (UPF0370)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.56     2e+03      11      30 ..      37      56 ..      36      61 .. 0.87
   2 ?    7.3   1.1    0.0013       4.7       5      23 ..      61      79 ..      57      92 .. 0.75
   3 ?    0.9   0.0      0.13   4.7e+02      12      32 ..      96     116 ..      89     122 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.56
                           UPF0370 11 illllvGillngikeLkrvd 30
                                      +l +l Gi    +++L ++ 
  gi|474934720|ref|YP_007688302.1| 37 VLAVLFGIYERLVRDLAKLH 56
                                      7899****999999999886 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0013
                           UPF0370  5 adYWWvillllvGillngi 23
                                      ad+W++il l+ Gi+  +i
  gi|474934720|ref|YP_007688302.1| 61 ADFWFIILFLIGGIVGTVI 79
                                      6899999888777776665 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.13
                           UPF0370  12 llllvGillngikeLkrvdhk 32 
                                       l+++vG++   i +L ++ ++
  gi|474934720|ref|YP_007688302.1|  96 LMFFVGLIAGQIPALYKLTAT 116
                                       899**********99998765 PP

>> TauE  Sulfite exporter TauE/SafE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   4.1      0.04   1.4e+02     123     153 ..      12      42 ..       4      53 .. 0.72
   2 ?    4.4  23.4    0.0068        25      61     229 ..      61     242 ..      48     242 .. 0.63
   3 ?    2.2  18.3     0.033   1.2e+02       2     111 ..     166     285 ..     165     298 .] 0.57

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.04
                              TauE 123 ptaillvligglvGllsGllGiGgGfllvpl 153
                                       ++++ +++ig+++G+++ l Gi+g +l v +
  gi|474934720|ref|YP_007688302.1|  12 KGLLKMLPIGIIIGIAAMLPGISGAVLAVLF 42 
                                       5666677777778888888888877766655 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0068
                              TauE  61 vdwrlllllllgsliGallGallllllpsellkllfgvlllllallm..llrkkrsrakgrerrptaillvliggl. 134
                                        d+  ++l+l+g+++G+++ a ll+   +++   ++ +++ l+a ++  l++ + ++ + ++++    l+++ig++ 
  gi|474934720|ref|YP_007688302.1|  61 ADFWFIILFLIGGIVGTVISAKLLNEAMDRYPAECLMFFVGLIAGQIpaLYKLT-ATSSCEKPAAHNMLAFIIGIIa 136
                                       566777889999999999999999966666656666666666666665333333.3333334555555577778777 PP

                              TauE 135 vGllsG..llGiGgGfllvpllllllglplkkavatsllli....lvislagalgy..al.....agavdwplllll 198
                                       +G + +  ll i+ G   v ll   +g+ +  ++++ ++++     ++  + ++++  ++      g+vd+ +++ +
  gi|474934720|ref|YP_007688302.1| 137 MGSMIAvdLLEISSGD--VELLHDSYGYAVMFVIGVVVAISalvpGISHSTILIVFglFAaftaaVGDVDVAFIGCM 211
                                       8877663467777776..444544456666665555544441001444444444444311455568999**99999* PP

                              TauE 199 lpgallGallGarlarrlsertlrrlfalll 229
                                       ++g+l+Gall +++ ++  + + r +++l+l
  gi|474934720|ref|YP_007688302.1| 212 MLGILAGALLFSKVIHYALDHHHRTMMFLIL 242
                                       *************999988888888877765 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.033
                              TauE   2 llagllaGfvagllGiGggliavPlLll.ll.....ppav.avatsllavvatsls.galahrrrgnvdwrllllll 70 
                                       +++g+++ + a + Gi  ++i++ + l+ ++     +  v  ++  +l ++a++l  + + h+     + r++++l+
  gi|474934720|ref|YP_007688302.1| 166 FVIGVVVAISALVPGISHSTILIVFGLFaAFtaavgDVDVaFIGCMMLGILAGALLfSKVIHYA-LDHHHRTMMFLI 241
                                       6677777777777787776665554444234456674444366777777777777644444444.345678888888 PP

                              TauE  71 lgsliGallGallllllpse..llkllfgvlllllallm.ll.rk 111
                                       lg  iG+l++ l+ +  ++   l+++l ++  l+++l + ++ +k
  gi|474934720|ref|YP_007688302.1| 242 LGLTIGSLAALLFTS-ADKVdgLMHILACICTLAVGLAVsIWsMK 285
                                       888888888555544.34323555555555555555555333133 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       984  (0.0548832); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.64u 0.35s 00:00:00.99 Elapsed: 00:00:00.51
# Mc/sec: 1774.66
//
Query:       gi|474934721|ref|YP_007688303.1|  [L=167]
Description: hypothetical protein TALC_01155 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.013   15.3   2.2       0.15   11.9   2.2    2.1  1  DUF2157    Predicted membrane protein (DUF2157)
      0.018   15.6   0.3      0.018   15.6   0.3    2.0  2  PAP2_C     PAP2 superfamily C-terminal
       0.13   12.4   0.0       0.23   11.6   0.0    1.4  1  P5-ATPase  P5-type ATPase cation transporter


Domain annotation for each model (and alignments):
>> DUF2157  Predicted membrane protein (DUF2157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   2.2   2.5e-05      0.15       7     106 ..      14     158 ..      13     166 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.5e-05
                           DUF2157   7 glIteeqaqallaryeaeeresarrrsf....leallvlGalllglGlilfvAanW................qglsr 63 
                                       +lI+++ +++ll++  aee e +++r +    ++++l++++ + g+Gl++++  +W                   s+
  gi|474934721|ref|YP_007688303.1|  14 HLISRKLRDDLLQEQPAEETEVRTGRTAeasiYQIFLTVSVAVCGIGLMSLFF-FWipdttgfallvddslhGPGSD 89 
                                       58999*********999998888666667788******************995.55588888888888666555567 PP

                           DUF2157  64 lvkfllllvllllslllg.avlwrdr.........................rvpprlgeallllaalll 106
                                       l++f+ + v l+ +++++ +v +r r                          v p +g +++++a++++
  gi|474934721|ref|YP_007688303.1|  90 LLRFAPVTVSLASAVAGTvIVSGRYRfliipmgltmtvmaffflielrnhySVDPSFGAYAAFAAGIIV 158
                                       888888888887777777344443334444444444444444444444444444444444444444333 PP

>> PAP2_C  PAP2 superfamily C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.2       1.2   7.2e+03      61      64 ..      58      61 ..      43      70 .. 0.52
   2 ?   15.6   0.3     3e-06     0.018      29      66 ..     115     152 ..      96     160 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.2
                            PAP2_C 61 glyi 64
                                      g+ +
  gi|474934721|ref|YP_007688303.1| 58 GIGL 61
                                      3333 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 3e-06
                            PAP2_C  29 lailkvillllallglfliiasrkHYtvDVllglyitt 66 
                                        +++  + l+++++ +f++i  r+HY+vD  +g+y ++
  gi|474934721|ref|YP_007688303.1| 115 RFLIIPMGLTMTVMAFFFLIELRNHYSVDPSFGAYAAF 152
                                       44566778899999***************999999875 PP

>> P5-ATPase  P5-type ATPase cation transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   3.8e-05      0.23      13      42 ..      44      73 ..      40      88 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.8e-05
                         P5-ATPase 13 srwrlalyilgciltlGlllLlfrWlPewr 42
                                      s ++ +l++ + ++ +Gl+ L f W+P   
  gi|474934721|ref|YP_007688303.1| 44 SIYQIFLTVSVAVCGIGLMSLFFFWIPDTT 73
                                      6788899999*****************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       878  (0.0489709); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1321.58
//
Query:       gi|474934722|ref|YP_007688304.1|  [L=566]
Description: Queuine tRNA-ribosyltransferase containing PUA domain [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-49  168.2   0.0    1.6e-49  167.7   0.0    1.3  1  DUF5591        Domain of unknown function (DUF5591)
    1.2e-09   38.0   1.6      3e-09   36.7   1.6    1.7  1  PUA            PUA domain
    1.8e-08   34.3   0.0    6.4e-08   32.6   0.0    1.9  1  TGT_C2         Patch-forming domain C2 of tRNA-guanine transg
  ------ inclusion threshold ------
      0.017   14.3   0.0      0.028   13.6   0.0    1.3  1  TGT            Queuine tRNA-ribosyltransferase
      0.096   12.4   0.0       0.18   11.5   0.0    1.3  1  DUF1647        Protein of unknown function (DUF1647)
       0.11   12.7   0.0       0.57   10.4   0.0    2.2  3  Peptidase_C36  Beet necrotic yellow vein furovirus-type papai
        0.2   11.8   0.1         20    5.4   0.0    2.5  2  TcpQ           Toxin co-regulated pilus biosynthesis protein 


Domain annotation for each model (and alignments):
>> DUF5591  Domain of unknown function (DUF5591)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.7   0.0   6.4e-53   1.6e-49       1     154 []     257     406 ..     257     406 .. 0.96

  Alignments for each domain:
  == domain 1  score: 167.7 bits;  conditional E-value: 6.4e-53
                                       X-HHHHHHHHH---S..SSEEEEEE--SSSSGGGSHHHHHHHHHS---.....SEEEEE-SS-.EEEGGGTT----- CS
                           DUF5591   1 vkrfrervlerYeppeekkvlvLlPcsakkPyseskshrkfaeaikkrka..kvheviltsPlGvvPreleevYPaa 75 
                                       + r+++r+++ Y+pp++kkvl+LlPcsakkPy+ s++hr+fa+ai+++++   vhevi+tsPlG+vPrel+ +YPa+
  gi|474934722|ref|YP_007688304.1| 257 IARYENRMRDLYSPPKHKKVLLLLPCSAKKPYHISRTHRMFASAIHTAQHdtLVHEVIVTSPLGIVPRELDAMYPAN 333
                                       78*********************************************997779************************ PP

                                       -----------HHHHHHHHHHHHHHHHHHT-SEEEE---THHHHHHHHHHTT-SSEEEE--.SS-TTSHHHHHHHHH CS
                           DUF5591  76 qYdiavtgewseeeiefvaellakylektkyekviahleeeyreiveevaeelgleiiytvvedkptskeslknLke 152
                                       +Ydi+vtgew+ ee++ ++++l++ ++k  yekv+ h+ e+  e+v++       +++ t   ++p+s++sl+nL++
  gi|474934722|ref|YP_007688304.1| 334 SYDIPVTGEWKPEEKDRIRRMLKDLVSKGGYEKVVSHMGED-DELVRDLF----PDMVSTF-VGDPVSPASLDNLDK 404
                                       ****************************************9.99999988....7899998.788***********9 PP

                                       HH CS
                           DUF5591 153 aL 154
                                       aL
  gi|474934722|ref|YP_007688304.1| 405 AL 406
                                       97 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   1.6   1.2e-12     3e-09       8      72 ..     506     564 ..     501     566 .] 0.90

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 1.2e-12
                                       HHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEE CS
                               PUA   8 gAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveier 72 
                                        Avk      sL+a Gv +++  ++ gd+ ++v   g+l +vG+a++ + e++++ +g+++++++
  gi|474934722|ref|YP_007688304.1| 506 FAVKG-----SLYAVGVKKADHGIRIGDEAVVVYN-GQLRGVGVAMMCGREMEQARRGVAIRMRH 564
                                       44444.....*******************999999.**************************998 PP

>> TGT_C2  Patch-forming domain C2 of tRNA-guanine transglycosylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.0   2.5e-11   6.4e-08       2      66 ..     425     494 ..     424     496 .. 0.86

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 2.5e-11
                            TGT_C2   2 rlraiadYqFGagagdaLfpedvtitrsatgrirqvlv.........dgerlatlraqdgrltLsleGarrlhe 66 
                                       ++r+ + YqFG +++da+++  ++    + g++++  v         ++++++ + a+ g+++Ls eGa+ l++
  gi|474934722|ref|YP_007688304.1| 425 TVRSALTYQFGPEIADAIMD--ANTV--SMGKYPYWKVfrvdpenpkKKTQICMMSAERGMFSLSPEGAQILVD 494
                                       799****************4..4444..58888876666698887777***********************997 PP

>> TGT  Queuine tRNA-ribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.1e-05     0.028     197     283 ..     104     190 ..      87     212 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.1e-05
                                       SSSSSSHHHHHHHHHHHHGGGS-TTS-EEETTB-SHHHHHHHHHTT--EEEESHHHHHHHTTEEEETTEEEETTSGG CS
                               TGT 197 GlsvgeekeellevveavtellpedkprylmGvgtPedlleavalGvDmfdcvyptrtarngraltsegelnlknak 273
                                       +++v+e+ + +++ v ++++     +  ++ G+  P++ + +  +GvD++d  +++ ++ ng +  +e ++ + + +
  gi|474934722|ref|YP_007688304.1| 104 AFEVKEDFRRMVDQVMKARNAAGFGRLLVMLGIAEPSNAAFLAYMGVDVVDDGFCNVAGMNGILTLPEAKMAIGKDC 180
                                       4889999999999999999999999************************************************9999 PP

                                       GTT--SBSSS CS
                               TGT 274 yaedfsplde 283
                                        +e+ ++l+ 
  gi|474934722|ref|YP_007688304.1| 181 TSENAEELER 190
                                       9999888776 PP

>> DUF1647  Protein of unknown function (DUF1647)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0     7e-05      0.18      23      90 ..     238     307 ..     229     319 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7e-05
                           DUF1647  23 ssiGkkFdCslvetleklklleeeeklvdlselikneedvvFv..satsddhlkeakksiksirkyypkk 90 
                                       s+ G +F+C+ v++l + ++   e+++ dl +  k+++ ++    sa    h+++++++++s  +   ++
  gi|474934722|ref|YP_007688304.1| 238 SVTGVRFSCNTVQALRRPDIARYENRMRDLYSPPKHKKVLLLLpcSAKKPYHISRTHRMFASAIHTAQHD 307
                                       678*****************************99999887764337888889999999999876665554 PP

>> Peptidase_C36  Beet necrotic yellow vein furovirus-type papain-like endopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       3.5     9e+03      50      64 ..     290     304 ..     283     321 .. 0.73
   2 ?   -1.9   0.0       1.5   3.9e+03      12      71 ..     313     369 ..     302     375 .. 0.65
   3 ?   10.4   0.0   0.00022      0.57      23     100 ..     437     522 ..     426     526 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.5
                     Peptidase_C36  50 twqdcrmfadalkvs 64 
                                         +  rmfa a++ +
  gi|474934722|ref|YP_007688304.1| 290 ISRTHRMFASAIHTA 304
                                       455679999988765 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.5
                     Peptidase_C36  12 vaiseclgvtlekldnlmqanavtldkyhawlskkspstwqdcrmfadalkvsmyvkvls 71 
                                       v ++  lg+   +ld +  an+  +     w  ++     +  rm+ d +    y kv+s
  gi|474934722|ref|YP_007688304.1| 313 VIVTSPLGIVPRELDAMYPANSYDIPVTGEWKPEEK---DRIRRMLKDLVSKGGYEKVVS 369
                                       556677888888888888888777666666643332...233466666666666666666 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00022
                     Peptidase_C36  23 ekldnlmqanavtldkyhawlskk....sp.stwqdcrmfadalkvsmy...vkvlsdkpydltyevdgagssvtlh 91 
                                       e  d +m+an+v++ ky  w   +     p    q c m a+    s+     ++l d  y l   vd      +l+
  gi|474934722|ref|YP_007688304.1| 437 EIADAIMDANTVSMGKYPYWKVFRvdpeNPkKKTQICMMSAERGMFSLSpegAQILVDLGYHLVETVDDFAVKGSLY 513
                                       55799***************75431111342357899**9*99888875334789**************99999999 PP

                     Peptidase_C36  92 lvgkesdgh 100
                                        vg +   h
  gi|474934722|ref|YP_007688304.1| 514 AVGVKKADH 522
                                       999776666 PP

>> TcpQ  Toxin co-regulated pilus biosynthesis protein Q
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0    0.0077        20      34      60 ..      99     125 ..      94     130 .. 0.85
   2 ?    3.6   0.0     0.029        74      25      43 ..     415     433 ..     402     454 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0077
                              TcpQ  34 ypieadatfsgdfedavsqvlealaaa 60 
                                       + ++++++++ df++ v+qv++a +aa
  gi|474934722|ref|YP_007688304.1|  99 VVVPNAFEVKEDFRRMVDQVMKARNAA 125
                                       57999*****************95554 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.029
                              TcpQ  25 tvvWeadedypieadatfs 43 
                                       ++ W+ad+d ++++++t++
  gi|474934722|ref|YP_007688304.1| 415 NLSWNADRDATVRSALTYQ 433
                                       467*******999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (566 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 3946.00
//
Query:       gi|474934723|ref|YP_007688305.1|  [L=310]
Description: aspartate carbamoyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.9e-47  159.0   0.0    2.7e-46  157.3   0.0    1.8  2  OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl
      1e-35  123.2   0.0    1.4e-35  122.7   0.0    1.2  1  OTCace    Aspartate/ornithine carbamoyltransferase, Asp/Orn b


Domain annotation for each model (and alignments):
>> OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.3   0.0     3e-50   2.7e-46       1     148 []       6     148 ..       6     148 .. 0.95
   2 ?   -1.1   0.0       0.2   1.8e+03      51      79 ..     167     194 ..     151     210 .. 0.78

  Alignments for each domain:
  == domain 1  score: 157.3 bits;  conditional E-value: 3e-50
                                       S-BSSGGGS-HHHHHHHHHHHHHHHHHHHTTT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTS CS
                          OTCace_N   1 rhllsledlskeeieelldlaaelkekvkkekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaedi 77 
                                       ++l+s++dls+++ie++l l++++    k ek ++ l+gk+l++lF+epStRT++Sfe+Aa+rlG++v+ +se   +
  gi|474934723|ref|YP_007688305.1|   6 KDLVSIRDLSRDDIESILALSKKMVPYAKGEKVKRALDGKILGNLFFEPSTRTKLSFESAAYRLGCDVIDVSE---M 79 
                                       789***********************9999*****************************************94...5 PP

                                       CTTTGGSTTSSCHHHHHHHHHHHTSEEEEEES..SHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHHH CS
                          OTCace_N  78 qlssvskgrkEsleDtarvlsryvdaiviRhp..gaeeleelakyasvpviNagdgdgeHPtQaLaDlltire 148
                                        ++s++kg  E+l+Dt+r++++y+daiv+Rhp  ga  ++  a+ ++ pviNagdg+g+HPtQ+L+Dl+t++e
  gi|474934723|ref|YP_007688305.1|  80 SMTSIAKG--ETLADTIRMVDAYCDAIVLRHPfeGA--ARLAADVSENPVINAGDGAGSHPTQMLLDLFTMEE 148
                                       788899**..**********************8777..77778899*************************97 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.2
                                       HHHHHHHHHHHHHTTSEEEEEESTTTSCT CS
                          OTCace_N  51 tRTrvSfevAakrlGgkvlslseaediql 79 
                                        RT  S   A +  G + + +  ++++q+
  gi|474934723|ref|YP_007688305.1| 167 GRTVHSLAQALTMFGVNLTLVA-PDSLQM 194
                                       6999999999999999988887.767776 PP

>> OTCace  Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.7   0.0   1.5e-39   1.4e-35       1     156 [.     154     303 ..     154     304 .. 0.94

  Alignments for each domain:
  == domain 1  score: 122.7 bits;  conditional E-value: 1.5e-39
                                       CC.EEEEESS.TTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEE CS
                            OTCace   1 kglkiafvGd.kknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvy 76 
                                       +gl++++vGd k++++++sl+++l+++g++++lvaP++l++ +++ +++k+    +g   + t dlee++ ++Dv+y
  gi|474934723|ref|YP_007688305.1| 154 DGLNVTLVGDlKYGRTVHSLAQALTMFGVNLTLVAPDSLQMPEDITARLKE----KGCMRKQTADLEEVIPDTDVLY 226
                                       599***********************************9998787766555....69999999************** PP

                                       E--SSETTCCGGHH...HHHHHHCC.CSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHH CS
                            OTCace  77 tdvwvsmgeekere...erlkklkd.yqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlht 149
                                        ++++     +er+   ++++k+++ y+++++ll+ a++d+i++H+LP  r +E+++eV++ p++ +f+qa N++ +
  gi|474934723|ref|YP_007688305.1| 227 VTRIQ-----RERFpdpSEYQKVAGtYRIDNALLRSARDDMIIMHPLP--RVNEIATEVDSTPHARYFQQAFNGVPV 296
                                       *****.....8888888999999999**********************..*************************** PP

                                       HHHHHHH CS
                            OTCace 150 ikAllvl 156
                                       ++A+l++
  gi|474934723|ref|YP_007688305.1| 297 RMAILCA 303
                                       *****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2021.27
//
Query:       gi|474934724|ref|YP_007688306.1|  [L=158]
Description: aspartate carbamoyltransferase, regulatory subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-29  100.8   2.1    4.7e-29  100.5   2.1    1.1  1  PyrI      Aspartate carbamoyltransferase regulatory chain, al
    4.9e-17   61.6   0.9    8.8e-17   60.8   0.9    1.4  1  PyrI_C    Aspartate carbamoyltransferase regulatory chain, me


Domain annotation for each model (and alignments):
>> PyrI  Aspartate carbamoyltransferase regulatory chain, allosteric domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.5   2.1   5.3e-33   4.7e-29       2      94 .]       9     103 ..       8     103 .. 0.95

  Alignments for each domain:
  == domain 1  score: 100.5 bits;  conditional E-value: 5.3e-33
                                       -----SCEEEEEEEETT-HHHHHHHCT--T...TS-EEEEEEEEETTTE..EEEEEEEET----HHHHHHHCCC-TT CS
                              PyrI   2 kvkkienGiViDHIkagkalkvlklLkldklkseekvaiiknvkskklg..kKdiikiegkelseeeldklaliapn 76 
                                       k+ +i+nG+ViDHIkag+al+vlk+L++++ + +++++i++ v ++k g   Kdi+k+e++el+ + +dk+aliap+
  gi|474934724|ref|YP_007688306.1|   9 KIPPIRNGTVIDHIKAGQALNVLKILGVSEDTIDSTISIAMRVATEKHGmkWKDIVKLEDMELDPDAADKIALIAPD 85 
                                       799***************************************99998764489************************ PP

                                       -EEEEEETTEEEEEE--. CS
                              PyrI  77 atiniIkdgevveKkkve 94 
                                       ati+iI+d+ v+eK +v+
  gi|474934724|ref|YP_007688306.1|  86 ATISIIRDYYVAEKSQVK 103
                                       ***************985 PP

>> PyrI_C  Aspartate carbamoyltransferase regulatory chain, metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.8   0.9   9.8e-21   8.8e-17       2      42 ..     108     149 ..     107     153 .. 0.95

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 9.8e-21
                                       EESSS--S-TTBGGGT.TS-.-EEEEEETTTTEEEETTT--E CS
                            PyrI_C   2 iegvlkCpNpnCItnn.epveskFkvedkekvklkCkYCeke 42 
                                       + g++kC+NpnCItn+ epv+++F+ve++++ +l+C YC+++
  gi|474934724|ref|YP_007688306.1| 108 VVGLVKCSNPNCITNKgEPVSPQFYVESRNPPRLRCMYCDRV 149
                                       89**************99**********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 944.14
//
Query:       gi|474934725|ref|YP_007688307.1|  [L=177]
Description: Dephospho-CoA kinase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-11   43.8   0.0    4.5e-11   43.3   0.0    1.2  1  AAA_17    AAA domain
    1.7e-07   31.9   0.1    4.8e-07   30.4   0.1    1.8  1  AAA_18    AAA domain
  ------ inclusion threshold ------
      0.026   14.7   0.3        0.4   10.8   0.3    2.2  1  AAA_33    AAA domain


Domain annotation for each model (and alignments):
>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3   0.0   7.6e-15   4.5e-11       1     132 [.       7     130 ..       7     134 .. 0.72

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 7.6e-15
                                       EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTS.HSSHHHHCTSHHHHHHHHHHHHHHHHHHHH.HSSEEE CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrggl.akardemrklpleekkelqkeaaekiaeea.kkkgvl 75 
                                       +G+PG+GK + + ++   ++++++ +Gd++re  + + + ++  +  + + +e+k + +++ a++++ +a +++ +l
  gi|474934725|ref|YP_007688307.1|   7 TGMPGAGKEEFL-QVGAGLDIPFFRMGDVVREAYAASDSnDRGMSVGEFAGNERKLHGTDIWAKRVMAKAeGNSLAL 82 
                                       7***********.******************887777651222333334577777778888888887776477889* PP

                                       EEE-SEEEETTEEEESSHHHHHHHH..SEEEE.EE--HHHHHHHHHHHTTST-TS-SH CS
                            AAA_17  76 vdghprikeqagfldglpkevleelkpdaiil.leadpeeilerrlkdrtrgrdddne 132
                                       +dg  +++e a+         +++l  d+i++ ++a+p + +er++  r+r+++ ++e
  gi|474934725|ref|YP_007688307.1|  83 IDGCRSLDEIAE---------FRNLGADIIVVgIHASPSVRFERLKL-RGRDDAPKDE 130
                                       ****99865444.........355666666666*****987777766.4555544555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.1   8.1e-11   4.8e-07       1     125 [.       4     132 ..       4     139 .. 0.74

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 8.1e-11
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.gvnlrdvakenglllevdpe.....aldeskrldedkldklldaleenssal 71 
                                       I++tG+pG+GK ++ +  + +  +  ++ +dv++e +   + ++      ++  ++r   +  d + + +++     
  gi|474934725|ref|YP_007688307.1|   4 IVVTGMPGAGKEEFLQVGAGL-DIpFFRMGDVVREAYAASDSNDRgmsvgEFAGNERKLHGT-DIWAKRVMAK---- 74 
                                       99***********99987655.6799999999999888888888877665444444443333.3333444443.... PP

                            AAA_18  72 eegknl.vidghlaeleseaakdikk....vvLtaspeelleRlekRgyeeakikenee 125
                                       +eg++l +idg+++  e ++++ ++     v ++asp++++eRl+ Rg+ +a + ++ e
  gi|474934725|ref|YP_007688307.1|  75 AEGNSLaLIDGCRSLDEIAEFRNLGAdiivVGIHASPSVRFERLKLRGRDDAPK-DEQE 132
                                       3456666**************99999**9999****************766544.4444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.3   6.8e-05       0.4       1     132 [.       3     132 ..       3     140 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.8e-05
                            AAA_33   1 lvllvGlpGsGKstlaerllkklg.avllssdtlrrrlfgtdqqskt..........dytrvldrlyqilnelarka 66 
                                       l+++ G+pG+GK  +++  +  l+  ++   d++r++++++d ++            +  +    +  i ++++  a
  gi|474934725|ref|YP_007688307.1|   3 LIVVTGMPGAGKEEFLQVGA-GLDiPFFRMGDVVREAYAASDSNDRGmsvgefagneRKLHG---TD-IWAKRV-MA 73 
                                       57777888888887777655.44443333456666666664444222333333221111111...22.222333.24 PP

                            AAA_33  67 lsagrnvildatnlsrrerarflklarrlgvpvrivvvetdeetlkeRlakRaangddrsevpeea 132
                                        ++g+++ l  +++s +e a+f++l       + +v +++++++  eRl+ R ++ d++   +e+ 
  gi|474934725|ref|YP_007688307.1|  74 KAEGNSLALIDGCRSLDEIAEFRNLGA----DIIVVGIHASPSVRFERLKLRGRD-DAP--KDEQE 132
                                       466777777778888888888887765....799******************996.444..44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 1205.64
//
Query:       gi|474934726|ref|YP_007688308.1|  [L=88]
Description: hypothetical protein TALC_01160 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 659.62
//
Query:       gi|474934727|ref|YP_007688309.1|  [L=240]
Description: putative membrane protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-38  131.6  12.9    3.8e-38  131.2  12.9    1.1  1  DUF92     Integral membrane protein DUF92
  ------ inclusion threshold ------
       0.22   11.8   6.5      0.034   14.4   2.5    1.7  2  DUF3522   Protein of unknown function (DUF3522)


Domain annotation for each model (and alignments):
>> DUF92  Integral membrane protein DUF92
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.2  12.9   4.2e-42   3.8e-38       2     202 ..      13     218 ..      12     233 .. 0.88

  Alignments for each domain:
  == domain 1  score: 131.2 bits;  conditional E-value: 4.2e-42
                             DUF92   2 ltlllalralrkksLtpsGalaavlvgvlialaplgllffllllvFfllgslltkvkkkvKa..kleeekegaRdav 76 
                                       ++++l++++++ +++t  +++++++++++i +a +   ++l++++F  ++ + tk++ k+K+  +l+e k+g+R+  
  gi|474934727|ref|YP_007688309.1|  13 IVVALCIFSYKVNLMTAGACVVSFFMATAIGAAAGI-WWTLAFFTFPAIAFASTKIGFKKKSeeGLQEGKRGERSTL 88 
                                       6899*************************9999555.5*****************9999999889************ PP

                             DUF92  77 qVlanslvalllally.......lasdlllvgivasyAavaaDTlaSElGkilskskprlittlkkvppGtnGgVsl 146
                                       ++l+ +++++++al+y       +     +v++v+++A++++DT+aSE+G +  k + ++ittlk+++ G nGg+s 
  gi|474934727|ref|YP_007688309.1|  89 NILGVGTIPTVIALAYfftdgagF---EQTVAFVSALAVSCSDTVASEIG-VRDK-RVYMITTLKPCEVGLNGGISR 160
                                       ****************76554331...3479*******************.6666.9******************** PP

                             DUF92 147 lGllasllGalliallavlllllel...lillltlaGllGsllDSlLGatlqasvvdkr 202
                                       +G+++s++ all +++a+ l+ ++     +l+ ++aG++G+++DSl+Ga+++++++ ++
  gi|474934727|ref|YP_007688309.1| 161 FGMFVSAASALLFSFVAFSLV-MQDldvRFLIPAFAGIMGNIFDSLFGALFENKGRMSK 218
                                       **************8843333.2234669999*********************976654 PP

>> DUF3522  Protein of unknown function (DUF3522)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   2.5   3.8e-06     0.034      65     171 ..       5     106 ..       1     121 [. 0.76
   2 ?   -1.7   0.1      0.34     3e+03     103     103 ..     182     182 ..     159     237 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.8e-06
                           DUF3522  65 sdfilsilavwvtlvyladldeklksllhylglllvailqekdrwsla.ntiip.ilvgllillvswliecvkkrkl 139
                                         fi+ i++v++++++  +++  +  ++ +++++ +ai+++ + w+   ++++p i+++ + + ++     ++++ l
  gi|474934727|ref|YP_007688309.1|   5 AEFIVIIAIVVALCIFSYKVNLMTAGACVVSFFMATAIGAAAGIWWTLaFFTFPaIAFASTKIGFKK----KSEEGL 77 
                                       479999*************************************986550455554444444444443....444444 PP

                           DUF3522 140 ypsllrrrlkrlnlqqllpgllllalAlfllg 171
                                             +r +r  l+ l +g +  ++Al++++
  gi|474934727|ref|YP_007688309.1|  78 QEG---KRGERSTLNILGVGTIPTVIALAYFF 106
                                       444...78888888888888888888887665 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.34
                           DUF3522 103 l 103
                                       +
  gi|474934727|ref|YP_007688309.1| 182 M 182
                                       2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       910  (0.0507558); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.57
# Mc/sec: 1276.87
//
Query:       gi|474934728|ref|YP_007688310.1|  [L=691]
Description: hypothetical protein TALC_01162 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.2e-09   35.4  12.1    4.6e-05   23.5   0.3    3.4  3  Flg_new       Listeria-Bacteroides repeat domain (List_Bact_r
  ------ inclusion threshold ------
      0.065   13.2   0.1       0.17   11.8   0.1    1.7  1  Tcp10_C       T-complex protein 10 C-terminus
        0.1   12.7   0.1         11    6.2   0.0    2.4  2  Nucleoporin2  Nucleoporin autopeptidase
       0.15   11.0   0.0       0.22   10.4   0.0    1.2  1  AMA-1         Apical membrane antigen 1


Domain annotation for each model (and alignments):
>> Flg_new  Listeria-Bacteroides repeat domain (List_Bact_rpt)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   1.8   5.6e-07    0.0025       1      65 []     354     419 ..     354     419 .. 0.78
   2 !   23.5   0.3     1e-08   4.6e-05       1      65 []     432     497 ..     432     497 .. 0.82
   3 ?   -3.4   0.1       2.5   1.1e+04       8      22 ..     625     642 ..     620     652 .. 0.52

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 5.6e-07
                                       EEEEEEETTEE.EEEEEET.TSB----B-.-E.ETTEEEEEEESSTTCCSB--TTT-B--SS-EEEEEE CS
                           Flg_new   1 YtvtFdanGgt.vsqtvty.getitlpan.pt.keGYtFaGWytdsdgttaydfgtkvtptgdvtLyAk 65 
                                       +t++F+anGgt +  +v++ + ++tlpan +t  ++  F+ W+    g+ + + g+ +t+t++v ++A+
  gi|474934728|ref|YP_007688310.1| 354 HTISFNANGGTgTMANVENtTGSYTLPANgFTaPANKAFKCWSV---GGVEKNVGDVITVTQNVEVTAV 419
                                       69*******995334665525689999662563699******98...68888999999999***99995 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 1e-08
                                       EEEEEEETTEEEEE..EEETTSB----B-.-E.ETTEEEEEEESSTTCCSB--TTT-B--SS-EEEEEE CS
                           Flg_new   1 YtvtFdanGgtvsq..tvtygetitlpan.pt.keGYtFaGWytdsdgttaydfgtkvtptgdvtLyAk 65 
                                       +tvtFdanGgt +    ++ + ++tlpan +t  +  tF+ W+    g+++++ g+k++++++vt+ A+
  gi|474934728|ref|YP_007688310.1| 432 FTVTFDANGGTGEMapVADVSGEYTLPANgFTaPAEKTFKCWSV---GDAQFKVGEKINVAANVTVKAV 497
                                       7*********9654215777999****763563699*******9...6799999***********9995 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 2.5
                                       TTEE...EEEEEETTSB- CS
                           Flg_new   8 nGgt...vsqtvtygeti 22 
                                       nG t   ++ t+++g+ +
  gi|474934728|ref|YP_007688310.1| 625 NGDTkekMDATYENGKVV 642
                                       565532234455555544 PP

>> Tcp10_C  T-complex protein 10 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   3.8e-05      0.17      12      63 ..     597     658 ..     588     664 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.8e-05
                                       E-TTS-EEEE......-TTSS-EEEE-TTS-EEEE-....TTS-EEEEETTTTEEEEE-TTS CS
                           Tcp10_C  12 tyanGtvkev......sadgktvtvsffNgDvketl....edgrviYyyaeaqtthttypdg 63 
                                        +anGt+k +      +++gk  +v+f+NgD+ke +    e+g+v+++  + +t+ +  +d 
  gi|474934728|ref|YP_007688310.1| 597 LFANGTAKVTvpftqeVPEGKELVVYFINGDTKEKMdatyENGKVVFTTNHFSTYAIVFEDE 658
                                       699999997622222257999************97644447888888888877777776665 PP

>> Nucleoporin2  Nucleoporin autopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0    0.0024        11      76      96 ..     480     500 ..     466     530 .. 0.81
   2 ?    4.0   0.0     0.011        51     132     148 ..     636     652 ..     612     653 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0024
                                       --TTSTT-S-EEEEESS---B CS
                      Nucleoporin2  76 ppvGegLNkpaeitLenvwpk 96 
                                        +vGe++N++a++t++ vw+ 
  gi|474934728|ref|YP_007688310.1| 480 FKVGEKINVAANVTVKAVWKD 500
                                       589****************86 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.011
                                       TTTTEEEEEES--XXXX CS
                      Nucleoporin2 132 petgtwtfkVeHFsrYg 148
                                        e+g+ +f+ +HFs+Y+
  gi|474934728|ref|YP_007688310.1| 636 YENGKVVFTTNHFSTYA 652
                                       468999**********7 PP

>> AMA-1  Apical membrane antigen 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0     5e-05      0.22     395     458 ..     622     690 ..     600     691 .] 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 5e-05
                                       XEEXXSSXXXEE.EXTTSXEEEXHHHHTTXXX....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             AMA-1 395 fyvCsevekrae.ikennevvlkeekrdeyed....ksnkdvlviiifiilavavvvlavlayllkrkk 458
                                       +++  ++++++    en +vv++ ++ + y+     +s+ + + i + i++a+av+++ vl yl  r+k
  gi|474934728|ref|YP_007688310.1| 622 YFINGDTKEKMDaTYENGKVVFTTNHFSTYAIvfedESDDTLMWIEVGIVAALAVIAISVLLYLQFRRK 690
                                       77777777666514577789998877777653343399999***********************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (691 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.69u 0.27s 00:00:00.96 Elapsed: 00:00:01.02
# Mc/sec: 2041.28
//
Query:       gi|474934729|ref|YP_007688311.1|  [L=155]
Description: hypothetical protein TALC_01163 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-24   86.3  15.1    2.4e-24   86.1  15.1    1.0  1  DUF3021          Protein of unknown function (DUF3021)
  ------ inclusion threshold ------
        1.3    7.6  11.2        1.5    7.4  11.2    1.1  1  EMP70            Endomembrane protein 70
          5    5.3  12.0        5.7    5.1  12.0    1.1  1  DUF2070          Predicted membrane protein (DUF2070)
        6.3    5.5   8.7       0.82    8.4   1.2    2.0  2  DUF2254          Predicted membrane protein (DUF2254)
        6.5    6.4  12.9       0.38   10.4   6.7    1.8  2  DUF21            Cyclin M transmembrane N-terminal domain


Domain annotation for each model (and alignments):
>> DUF3021  Protein of unknown function (DUF3021)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.1  15.1   6.7e-28   2.4e-24       4     130 .]       8     147 ..       4     147 .. 0.94

  Alignments for each domain:
  == domain 1  score: 86.1 bits;  conditional E-value: 6.7e-28
                           DUF3021   4 illgiliGiliglii..slvislfsgettll...........estavlkqvllsaliGvlfalaslifeserlsllk 67 
                                       +l++ liGi++g+i+  +++i ++sget l+            ++a++ q+++s+++G++++ ++++++ser+s+l+
  gi|474934729|ref|YP_007688311.1|   8 VLRAGLIGIVLGMIMcnGITIAFTSGETGLAlvaprleeefgLAAAFILQTIVSGILGFVMFATTAVYYSERFSILS 84 
                                       688999*******997777878888877777********************************************** PP

                           DUF3021  68 qtlihflvvlllvlllalllgWfplsvigilivilifiiiyliiwlifylsekkevkkiNekL 130
                                       +tlih  + ++ + l++++l+W++ +v+g l+++l+ ++iyl+iw+ + ls+k +v++iN+ +
  gi|474934729|ref|YP_007688311.1|  85 ATLIHGSIAMVSMALVSYFLWWTDRTVKGTLLFLLFILMIYLLIWFSITLSFKIRVDQINRAI 147
                                       ********************************97777***********************976 PP

>> EMP70  Endomembrane protein 70
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4  11.2   0.00042       1.5     299     384 ..      50     133 ..       4     146 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00042
                             EMP70 299 ltvalllyvllgliaGYvsarlyktfggekwkkntlltalllpgl.lflvffllnlilwakessgalpfgtlvllll 374
                                       l +a++l ++++ i G+v   + + +   + ++ ++l a+l+ g   ++ + l+  +lw  + + +  +  l+++l+
  gi|474934729|ref|YP_007688311.1|  50 LAAAFILQTIVSGILGFVMFATTAVY---YSERFSILSATLIHGSiAMVSMALVSYFLWWTDRTVKGTLLFLLFILM 123
                                       34445555555555566655555444...678888999988888736777888899******999999999999999 PP

                             EMP70 375 lwflisvPlv 384
                                       +++li + ++
  gi|474934729|ref|YP_007688311.1| 124 IYLLIWFSIT 133
                                       9998876655 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1  12.0    0.0016       5.7      81     176 ..      26     132 ..       6     142 .. 0.62

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0016
                           DUF2070  81 ivviisllaillsall..........qalvllalvls.lalvfalrllvlvavsdesllkavlpaliqpllailllv 146
                                       i ++++   + l+++           +a++l+ +v + l +v++ ++ v+++   + l+  ++  +i  ++++l+++
  gi|474934729|ref|YP_007688311.1|  26 ITIAFTSGETGLALVAprleeefglaAAFILQTIVSGiLGFVMFATTAVYYSERFSILSATLIHGSIAMVSMALVSY 102
                                       44444444444444444444433332333333333335555555555555555555555555777777777777777 PP

                           DUF2070 147 lyfspesfllllllslifalavylfivvvd 176
                                       ++  ++++++  ll l+f+l++yl+i++  
  gi|474934729|ref|YP_007688311.1| 103 FLWWTDRTVKGTLLFLLFILMIYLLIWFSI 132
                                       777888899999999999999999998765 PP

>> DUF2254  Predicted membrane protein (DUF2254)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   1.1     0.026        93      27      64 ..      33      71 ..       6      81 .. 0.63
   2 ?    8.4   1.2   0.00023      0.82     118     161 ..     102     150 ..      79     154 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.026
                           DUF2254 27 ealslsldleel.kegaeaaralLstiagsmltvagfvf 64
                                       + +l+l  ++l +e   aa  +L+ti++++l+++ f+ 
  gi|474934729|ref|YP_007688311.1| 33 GETGLALVAPRLeEEFGLAAAFILQTIVSGILGFVMFAT 71
                                      33344444444422356678899*********9987754 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00023
                           DUF2254 118 e.....vpqlsvlvalllaivsvllLiyFihhlarsiqvsnviarveee 161
                                       +       ++  ++ +ll i+ ++lLi+F   l+  i+v+++ + +ee+
  gi|474934729|ref|YP_007688311.1| 102 YflwwtDRTVKGTLLFLLFILMIYLLIWFSITLSFKIRVDQINRAIEER 150
                                       25554333478888899**************************999976 PP

>> DUF21  Cyclin M transmembrane N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   6.7   0.00011      0.38      53     131 ..      13      95 ..       9     115 .. 0.76
   2 ?   -0.1   4.0      0.19   6.7e+02      53     100 ..      83     130 ..      82     134 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00011
                             DUF21  53 Lstlligntlvn.illsalatalfvellae...galavviatvivtllilvfgEilPkslalkyaekialalapplr 125
                                       L+ +++g+ ++n i ++   + +   l+a+   +++++++a+++ t++  ++g ++  + a+ y+e+++ ++a++++
  gi|474934729|ref|YP_007688311.1|  13 LIGIVLGMIMCNgITIAFTSGETGLALVAPrleEEFGLAAAFILQTIVSGILGFVMFATTAVYYSERFSILSATLIH 89 
                                       55667777777634555566666777777788899******9999*******************************8 PP

                             DUF21 126 vlmvll 131
                                         +  +
  gi|474934729|ref|YP_007688311.1|  90 GSIAMV 95 
                                       544333 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.19
                             DUF21  53 Lstlligntlvnillsalatalfvellaegalavviatvivtllilvf 100
                                       Ls++li  +++++ ++++  +l+    + +++ +++ ++++ +l++ f
  gi|474934729|ref|YP_007688311.1|  83 LSATLIHGSIAMVSMALVSYFLWWTDRTVKGTLLFLLFILMIYLLIWF 130
                                       677777777777777777766644433336778888888888887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1223  (0.0682135); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 953.82
//
Query:       gi|474934730|ref|YP_007688312.1|  [L=144]
Description: Response regulator of the LytR/AlgR family [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-18   66.0   0.3    4.4e-18   65.3   0.3    1.4  2  LytTR     LytTr DNA-binding domain


Domain annotation for each model (and alignments):
>> LytTR  LytTr DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       0.5   8.9e+03      20      34 ..      15      29 ..       5      35 .. 0.64
   2 !   65.3   0.3   2.4e-22   4.4e-18       3      97 ..      50     143 ..      48     144 .] 0.97

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.5
                             LytTR 20 yvtlvteneeylfrg 34
                                      +vt+++ ++++++++
  gi|474934730|ref|YP_007688312.1| 15 RVTVQAPSRSVEVDD 29
                                      566666677776665 PP

  == domain 2  score: 65.3 bits;  conditional E-value: 2.4e-22
                             LytTR   3 iilvplddilyieaeekyvtlvteneeylfrgtLkeleeklppdsffrvhRsylVnlkkikeidrdfngtleltlkn 79 
                                       +++++ ++++ +++++k+v++ t ++++ ++ +L++lee+lp ++f+r++ s +Vn++ki ++d +  gt++++l++
  gi|474934730|ref|YP_007688312.1|  50 VVKIAKKSVIRFYSRDKRVYVDTLEGSFSVKSPLYQLEEELP-NNFVRISNSEIVNIDKILRLDMNLAGTIRIHLEG 125
                                       689999***********************************8.********************************** PP

                             LytTR  80 geklpvSrrylkelkell 97 
                                       + +  vSrryl+++k +l
  gi|474934730|ref|YP_007688312.1| 126 DIESRVSRRYLSKVKGVL 143
                                       **************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 987.68
//
Query:       gi|474934731|ref|YP_007688313.1|  [L=317]
Description: Pyruvate:ferredoxin oxidoreductase-related 2-oxoacid:ferredoxin oxidoreductase, beta subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-24   85.8   0.7    3.4e-24   85.4   0.7    1.1  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.4   0.7   1.9e-28   3.4e-24       2     152 ..      51     217 ..      50     218 .. 0.85

  Alignments for each domain:
  == domain 1  score: 85.4 bits;  conditional E-value: 1.9e-28
                                       SSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHH..........STTSEEEEEEEHHHHHHT.GGGHHH CS
                      TPP_enzyme_C   2 iGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGakla..........kpdrevvaivGDGgflmi.lqelat 67 
                                       +Gc+++ +  +    + +s+  + +++++G+g ++  G++ a          ++d + v ++GDG++++i lq+l+ 
  gi|474934731|ref|YP_007688313.1|  51 TGCFEVSTTIF----PYTSWNVPMIHTAFGNGAAGCAGVETAyrslkrqgkiDKDIKFVNFAGDGATYDIgLQALSG 123
                                       68888855555....344566699*****************555666666555578********************* PP

                                       HHHTT-SEEEEEEE-SBCCCHHHH...HHHHTCCTTTTSBB........BS----HHHHHHHTTSE.EEEESSH.HH CS
                      TPP_enzyme_C  68 avrrnlpitvvvlnNegygmtggq...qepfggkrksgpagk.......dlkpvdfaklaealGak.garvekadve 133
                                       a++r++++++v+lnNe+y++tg q    + +g++++++   +       ++ ++d+ +++ a+ ++ +a+v +++++
  gi|474934731|ref|YP_007688313.1| 124 AMERGHDMLFVCLNNEAYMNTGIQsssATAKGASTTTSW--NgavaygkKEASKDVTAIMVAHNIPyVAQVAPHNWK 198
                                       ************************755555555555544..3559999879999************999******** PP

                                       HHHHHHHHHHCSSSEEEEE CS
                      TPP_enzyme_C 134 eleealkealekkgpalie 152
                                       +l  + ++a+e +gp++i+
  gi|474934731|ref|YP_007688313.1| 199 DLVGKARKAFECGGPSFIN 217
                                       *****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1928.16
//
Query:       gi|474934732|ref|YP_007688314.1|  [L=391]
Description: Pyruvate:ferredoxin oxidoreductase-related 2-oxoacid:ferredoxin oxidoreductase, alpha subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-64  216.3   0.6    6.2e-64  215.9   0.6    1.1  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
      5e-26   91.0   0.0    1.1e-25   89.8   0.0    1.6  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
    4.1e-06   26.7   0.0      1e-05   25.4   0.0    1.6  1  Transketolase_C  Transketolase, C-terminal domain


Domain annotation for each model (and alignments):
>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.9   0.6     1e-67   6.2e-64       4     229 ..      22     243 ..      19     245 .. 0.97

  Alignments for each domain:
  == domain 1  score: 215.9 bits;  conditional E-value: 1e-67
                                       HHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCCHH CS
                             POR_N   4 iaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmienlg 80 
                                       +++++dv+aaYPITP++ i+e +++++a+gev d+e++ +esE++a   +  ++ aGar++TaT++qGl++m e+l 
  gi|474934732|ref|YP_007688314.1|  22 KQINPDVVAAYPITPQTIIVEDFSKYVANGEV-DTEFIDVESEHSALTLCSTSSSAGARTFTATASQGLAYMWEMLP 97 
                                       7899***************************9.8******************************************* PP

                                       HHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHHS---EEEE-SSHHHHHHHHHHHHHHHHH..CTSEEEEEEEH CS
                             POR_N  81 laageelPvvivvvaRalpstglsirtdqsDlmaardtglivlasenvqeafdlalvAfnlAek..vrvPvivlfDg 155
                                       ++a +++Pv+++v++R+++ + ++i +d++D+m ardtg++ +++envqea+d+ +++ ++Ae+  v++P++v +Dg
  gi|474934732|ref|YP_007688314.1|  98 ITAAMRVPVMMAVANRTVSGP-ININNDHGDVMSARDTGWLSIFAENVQEAYDMSIIGPRIAEHheVQLPILVNLDG 173
                                       *********************.******************************************************* PP

                                       HHH.HEEEEEEC-SGG.GS-----SBXXXXXXXXSXXXBXXTXXTSSXXEEESBXBXTTSXBXXXXHHHHHHHH CS
                             POR_N 156 fllshevekvelpdeedelklikekleeyerkeyaldpekpiargtaanpdtglehrekgneaedaaekvveev 229
                                       f+l+h++e+++ +d +    +++++  e ++ ++ ld+++p++ +  + p  ++ h++++  a+++a  v +ev
  gi|474934732|ref|YP_007688314.1| 174 FILTHAIERMTPLDTQ----HVRDFVGEFKPLYPLLDTDHPVTHNLMDGPLFYFPHKYQMVVAMNKALDVAREV 243
                                       *************999....9999999999999********************************999888887 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.8   0.0   1.9e-29   1.1e-25       1     101 [.     266     368 ..     266     369 .. 0.96

  Alignments for each domain:
  == domain 1  score: 89.8 bits;  conditional E-value: 1.9e-29
                                       -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHH CS
                           PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaa 77 
                                       A+++ +++Gs+ gt+k+avd+lR+eg+kvG+  +r++rP P++e++ l k++k+v+v+dr  s+g+ G+++ ev a+
  gi|474934732|ref|YP_007688314.1| 266 ADYIAIVLGSSFGTMKQAVDNLRDEGMKVGVAMPRVYRPWPADEIAALCKGKKAVIVMDRHLSIGAYGPMFPEVCAS 342
                                       9*************************************************************************999 PP

                                       TGGG..TSEEEEEE--GGG----HHH CS
                           PFOR_II  78 lkks..kvkvvnfvaglgGrditved 101
                                       +  +   ++++nf++glgG d +v+d
  gi|474934732|ref|YP_007688314.1| 343 IAVNgkMPEMYNFIYGLGGADTMVSD 368
                                       88777799*************99987 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   1.7e-09     1e-05      11      86 ..     267     342 ..     260     362 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.7e-09
                                       SEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHHHHHHHHHHH CS
                   Transketolase_C  11 dvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGigsevaaalae 86 
                                       d + +  Gs + ++ +A+++L++eg+++ V  +r  +p+  + i+++ k ++ ++v++ +  +g+ g  + +++a 
  gi|474934732|ref|YP_007688314.1| 267 DYIAIVLGSSFGTMKQAVDNLRDEGMKVGVAMPRVYRPWPADEIAALCKGKKAVIVMDRHLSIGAYGPMFPEVCAS 342
                                       55556789********************************************************999888777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2619.57
//
Query:       gi|474934733|ref|YP_007688315.1|  [L=94]
Description: 2-oxoacid:acceptor oxidoreductase, delta subunit, pyruvate/2-ketoisovalerate family [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.6e-12   45.0  15.8    1.1e-11   44.7  15.8    1.1  1  Fer4_21         4Fe-4S dicluster domain
    2.2e-10   39.9  18.4      6e-07   29.0   2.8    2.3  2  Fer4            4Fe-4S binding domain
    1.9e-07   31.5  23.5    0.00024   21.6  13.3    2.1  3  Fer4_7          4Fe-4S dicluster domain
    2.6e-06   27.5  12.7    8.4e-06   25.9  13.2    1.5  2  Fer4_9          4Fe-4S dicluster domain
    3.7e-06   27.8  12.1     0.0003   21.6   3.0    2.2  2  Fer4_16         4Fe-4S double cluster binding domain
    2.4e-05   24.1  17.0    0.00089   19.2   4.1    2.5  2  Fer4_2          4Fe-4S binding domain
    0.00013   22.0  27.0     0.0012   19.0  15.7    1.9  2  Fer4_10         4Fe-4S dicluster domain
    0.00024   21.1  18.4     0.0069   16.4   2.7    2.5  2  Fer4_6          4Fe-4S binding domain
    0.00076   20.0   7.0      0.046   14.3   0.9    2.2  2  Fer4_17         4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.011   16.7   4.9      0.011   16.7   4.9    2.5  2  Fer4_3          4Fe-4S binding domain
      0.032   14.8  15.5       0.16   12.5   5.1    2.2  2  Fer4_13         4Fe-4S single cluster domain of Ferredoxin I
      0.035   14.8  15.2       0.19   12.5   4.3    2.4  2  Fer4_15         4Fe-4S single cluster domain
       0.75   10.3  14.8       0.29   11.6   3.7    2.2  2  Fer4_8          4Fe-4S dicluster domain
        0.8    9.6   6.2        2.6    8.0   0.6    2.2  2  Ribosomal_L40e  Ribosomal L40e family
        1.1   10.1  14.3        0.5   11.3   3.5    2.2  3  Fer4_22         4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7  15.8   8.9e-15   1.1e-11       2      59 .]      36      89 ..      35      89 .. 0.97

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 8.9e-15
                           Fer4_21  2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedciem 59
                                      +id++ Ci+C +C i C+d   ++i +d++  + v + +C GC +Cs+vCP +d+i+m
  gi|474934733|ref|YP_007688315.1| 36 VIDKSICISCLSCWIDCPD---NCIVVDEDGLVDVKTTHCKGCGICSQVCP-KDAITM 89
                                      79****************9...9****************************.7***99 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   7.8   3.7e-06    0.0044       1      23 [.      35      57 ..      35      58 .. 0.95
   2 !   29.0   2.8     5e-10     6e-07       5      24 .]      69      88 ..      65      88 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.7e-06
                                      EEEETTTSSS-THHHHHSTTTEE CS
                              Fer4  1 vvideekCigCGaCvevCPvgAI 23
                                      +vid++ Ci C  C   CP ++I
  gi|474934733|ref|YP_007688315.1| 35 PVIDKSICISCLSCWIDCPDNCI 57
                                      69********************9 PP

  == domain 2  score: 29.0 bits;  conditional E-value: 5e-10
                                      TTTSSS-THHHHHSTTTEEE CS
                              Fer4  5 eekCigCGaCvevCPvgAIt 24
                                      +  C gCG+C +vCP +AIt
  gi|474934733|ref|YP_007688315.1| 69 TTHCKGCGICSQVCPKDAIT 88
                                      678****************7 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   2.7    0.0014       1.6      29      51 ..      33      55 ..      14      56 .. 0.74
   2 !   21.6  13.3     2e-07   0.00024       2      52 .]      42      86 ..      41      86 .. 0.95
   3 !   21.4   2.5   2.4e-07   0.00029       1      21 [.      71      91 ..      71      93 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0014
                            Fer4_7 29 ekveidpekClgCgaCvavCPtg 51
                                      + ++id + C++C +C   CP +
  gi|474934733|ref|YP_007688315.1| 33 QVPVIDKSICISCLSCWIDCPDN 55
                                      566899999***********965 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 2e-07
                            Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      Ci C  C   Cp ++i +de+        v+++ + C gCg C +vCP++a
  gi|474934733|ref|YP_007688315.1| 42 CISCLSCWIDCPDNCIVVDED------GLVDVKTTHCKGCGICSQVCPKDA 86
                                      ******************997......47999****************997 PP

  == domain 3  score: 21.4 bits;  conditional E-value: 2.4e-07
                            Fer4_7  1 rCigCgaCvaaCpvkaielde 21
                                      +C gCg C ++Cp +ai+++e
  gi|474934733|ref|YP_007688315.1| 71 HCKGCGICSQVCPKDAITMKE 91
                                      6*****************987 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   3.8    0.0002      0.24      21      51 .]      21      57 ..      14      57 .. 0.71
   2 !   25.9  13.2     7e-09   8.4e-06       2      51 .]      42      87 ..      41      87 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0002
                            Fer4_9 21 aaerkarlraase......eaCigCgaCveaCpkgai 51
                                      ++e+++  +++s+      + Ci+C +C   Cp ++i
  gi|474934733|ref|YP_007688315.1| 21 NSEKFRTGDWRSQvpvidkSICISCLSCWIDCPDNCI 57
                                      555555555555577777778************9976 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 7e-09
                            Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                      C++C +C   Cp + +v d+ +  +  +      C gCg C ++Cpk+ai
  gi|474934733|ref|YP_007688315.1| 42 CISCLSCWIDCPDNCIVVDEDGLVDVKTT----HCKGCGICSQVCPKDAI 87
                                      ********************999988755....6*************998 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   1.8   0.00034      0.41       2      26 ..      42      66 ..      41      70 .. 0.85
   2 !   21.6   3.0   2.5e-07    0.0003       1      21 [.      71      91 ..      71      94 .] 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00034
                           Fer4_16  2 CgtCgkCaevCPtnaikekkekeie 26
                                      C++C  C   CP n+i  +++  ++
  gi|474934733|ref|YP_007688315.1| 42 CISCLSCWIDCPDNCIVVDEDGLVD 66
                                      ****************999776665 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 2.5e-07
                           Fer4_16  1 rCgtCgkCaevCPtnaikekk 21
                                      +C++Cg C +vCP +ai++k+
  gi|474934733|ref|YP_007688315.1| 71 HCKGCGICSQVCPKDAITMKE 91
                                      7*****************994 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   5.0   0.00039      0.47       2      21 ..      34      53 ..      33      59 .. 0.93
   2 !   19.2   4.1   7.4e-07   0.00089       5      21 ..      67      83 ..      57      84 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00039
                            Fer4_2  2 pvvvdtdrCigCgaCvsa.CP 21
                                      ++v+d  +Ci+C +C +  CP
  gi|474934733|ref|YP_007688315.1| 34 VPVIDKSICISCLSC-WIdCP 53
                                      589************.99998 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 7.4e-07
                            Fer4_2  5 vdtdrCigCgaCvsaCP 21
                                      v t +C gCg+C ++CP
  gi|474934733|ref|YP_007688315.1| 67 VKTTHCKGCGICSQVCP 83
                                      45669***********9 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0  15.7   9.6e-07    0.0012       3      56 .]      36      83 ..      34      83 .. 0.87
   2 !   14.7   3.5   2.1e-05     0.025       6      22 ..      69      85 ..      64      93 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 9.6e-07
                           Fer4_10  3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      vid++ Ci C  C   CP       +    +e++ v++k  +C gcg C ++CP
  gi|474934733|ref|YP_007688315.1| 36 VIDKSICISCLSCWIDCPD------NCIVVDEDGLVDVKTTHCKGCGICSQVCP 83
                                      89*****************......555566666777789*************9 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2.1e-05
                           Fer4_10  6 ddtCirCgkCvkaCPad 22
                                      +  C +Cg C ++CP d
  gi|474934733|ref|YP_007688315.1| 69 TTHCKGCGICSQVCPKD 85
                                      56799999999999984 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   7.6   0.00044      0.52       1      24 []      34      57 ..      34      59 .. 0.93
   2 !   16.4   2.7   5.7e-06    0.0069       9      24 .]      72      87 ..      65      87 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00044
                            Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                      v++id++ Ci+C  C + CP + i
  gi|474934733|ref|YP_007688315.1| 34 VPVIDKSICISCLSCWIDCPDNCI 57
                                      79******************9865 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 5.7e-06
                            Fer4_6  9 CigCgdCvrvCPegai 24
                                      C gCg C  vCP +ai
  gi|474934733|ref|YP_007688315.1| 72 CKGCGICSQVCPKDAI 87
                                      ************9998 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.6    0.0012       1.5      44      59 ..      40      55 ..       9      56 .. 0.84
   2 !   14.3   0.9   3.8e-05     0.046      45      59 ..      71      85 ..      61      91 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0012
                           Fer4_17 44 slCieCgeCerkCPqg 59
                                      s Ci+C  C  +CP +
  gi|474934733|ref|YP_007688315.1| 40 SICISCLSCWIDCPDN 55
                                      67***********976 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 3.8e-05
                           Fer4_17 45 lCieCgeCerkCPqg 59
                                       C +Cg C+++CP++
  gi|474934733|ref|YP_007688315.1| 71 HCKGCGICSQVCPKD 85
                                      566666666666654 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   3.3       6.8   8.1e+03       1       7 [.      42      48 ..      42      59 .. 0.53
   2 ?   16.7   4.9     9e-06     0.011       1      15 []      72      86 ..      72      86 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 6.8
                            Fer4_3  1 CtgCgaC 7 
                                      C+ C  C
  gi|474934733|ref|YP_007688315.1| 42 CISCLSC 48
                                      6666323 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 9e-06
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C gCg C +vCP++A
  gi|474934733|ref|YP_007688315.1| 72 CKGCGICSQVCPKDA 86
                                      9************98 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   5.1   0.00014      0.16       1      28 [.      37      64 ..      37      70 .. 0.83
   2 ?    8.1   3.0    0.0033       3.9       4      18 ..      70      84 ..      65      85 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                           Fer4_13  1 VDrdtCiacgaCvelaPdvFeeddegga 28
                                      +D++ Ci+c +C+  +Pd     de+g 
  gi|474934733|ref|YP_007688315.1| 37 IDKSICISCLSCWIDCPDNCIVVDEDGL 64
                                      899***************8776666665 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0033
                           Fer4_13  4 dtCiacgaCvelaPd 18
                                        C +cg+C +++P+
  gi|474934733|ref|YP_007688315.1| 70 THCKGCGICSQVCPK 84
                                      57************6 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   4.3   0.00016      0.19       2      33 ..      36      68 ..      36      71 .. 0.86
   2 ?    8.7   3.6    0.0024       2.9       4      20 ..      68      84 ..      65      93 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00016
                           Fer4_15  2 vvDrdaCigcglCvaea.pevfeldedglasvl 33
                                      v+D++ Ci+c  C+  + ++ ++ dedgl +v+
  gi|474934733|ref|YP_007688315.1| 36 VIDKSICISCLSCWIDCpDNCIVVDEDGLVDVK 68
                                      69***************5568999****98776 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0024
                           Fer4_15  4 DrdaCigcglCvaeape 20
                                        + C gcg C +++p+
  gi|474934733|ref|YP_007688315.1| 68 KTTHCKGCGICSQVCPK 84
                                      5689***********64 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   3.0      0.03        36       5      63 ..      42      54 ..      38      71 .. 0.65
   2 ?   11.6   3.7   0.00024      0.29      48      64 ..      69      85 ..      58      86 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.03
                            Fer4_8  5 CieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63
                                      Ci C  C                                                 Cp 
  gi|474934733|ref|YP_007688315.1| 42 CISCLSCW----------------------------------------------IDCPD 54
                                      55555555..............................................44443 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00024
                            Fer4_8 48 lwsCttcgaCtevCpvg 64
                                        +C +cg C++vCp++
  gi|474934733|ref|YP_007688315.1| 69 TTHCKGCGICSQVCPKD 85
                                      56899999999999975 PP

>> Ribosomal_L40e  Ribosomal L40e family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.6     0.023        28      14      33 ..      37      56 ..      35      58 .. 0.88
   2 ?    8.0   0.6    0.0022       2.6      28      47 ..      67      84 ..      64      87 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.023
                    Ribosomal_L40e 14 cdKmiCrkCYArlpprAtnC 33
                                      +dK+iC  C ++   +  nC
  gi|474934733|ref|YP_007688315.1| 37 IDKSICISCLSCWIDCPDNC 56
                                      69********9998888888 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0022
                    Ribosomal_L40e 28 prAtnCrkkkCghsnnlrpK 47
                                      +++t+C+   Cg +++++pK
  gi|474934733|ref|YP_007688315.1| 67 VKTTHCK--GCGICSQVCPK 84
                                      5778886..**********9 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   3.2     0.062        74      78      94 ..      38      54 ..       7      57 .. 0.72
   2 ?    4.2   3.0     0.067        80       2      16 ..      42      57 ..      41      65 .. 0.78
   3 ?   11.3   3.5   0.00042       0.5      77      95 ..      67      85 ..      60      86 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.062
                           Fer4_22 78 gesgCvGCgRCieacpv 94
                                      ++s C+ C  C   cp 
  gi|474934733|ref|YP_007688315.1| 38 DKSICISCLSCWIDCPD 54
                                      55556666666555554 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.067
                           Fer4_22  2 ClsCgaCtlvCpt.Cs 16
                                      C+sC +C + Cp  C+
  gi|474934733|ref|YP_007688315.1| 42 CISCLSCWIDCPDnCI 57
                                      ***********95244 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00042
                           Fer4_22 77 fgesgCvGCgRCieacpvk 95
                                      +++++C GCg C+++cp++
  gi|474934733|ref|YP_007688315.1| 67 VKTTHCKGCGICSQVCPKD 85
                                      57889***********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 638.72
//
Query:       gi|474934734|ref|YP_007688316.1|  [L=185]
Description: 2-oxoacid:acceptor oxidoreductase, gamma subunit, pyruvate/2-ketoisovalerate family [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-35  123.1   0.1    1.5e-35  122.9   0.1    1.0  1  POR       Pyruvate ferredoxin/flavodoxin oxidoreductase


Domain annotation for each model (and alignments):
>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.9   0.1   8.4e-40   1.5e-35       1     177 []      11     182 ..      11     182 .. 0.93

  Alignments for each domain:
  == domain 1  score: 122.9 bits;  conditional E-value: 8.4e-40
                                       CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHH..HHGGG CS
                               POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetls..ehldg 75 
                                       GGqGvvta++ila++a ++G+yv+a++e+g+e++G++  +  risd+p + + +v+e+d++++ d++++   ++++g
  gi|474934734|ref|YP_007688316.1|  11 GGQGVVTANEILAESAIYSGKYVKAFPEFGPERMGAPIRAFARISDTPVRVHTQVYEPDIVIVIDPTLIGkvDVAKG 87 
                                       9**********************************************99999999************99779***** PP

                                       EEEEEEEEEECTCGTT-CCHHHCTS-HHHHHHHT-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHT.S-HHHHH CS
                               POR  76 lkpggiiiynseelkpdelkkakeeerelkerlgvrvygvdatkiakeiggneraaNtvmlGalaallg.lpleale 151
                                       lk+gg+i++n e   ++el+ka    +        +  +v+a+kia e  g ++++Nt mlGal+++   ++  ++e
  gi|474934734|ref|YP_007688316.1|  88 LKKGGFILANYEG-TSAELQKAIGTTA--------ECHAVKASKIALEEIG-KPLVNTSMLGALIKIRPiISYSEME 154
                                       ***********77.5555556555543........567*************.*****************9999**** PP

                                       HHHHCCS-CH...HHHHHHHHHHHHHHH CS
                               POR 152 eaikkrfpkkk..eviekNlkafragye 177
                                       ++i ++f +k   ++i kNl a++++y+
  gi|474934734|ref|YP_007688316.1| 155 DHITDKFTGKLsdKLIVKNLTALKRAYD 182
                                       *********99***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1222.83
//
Query:       gi|474934735|ref|YP_007688317.1|  [L=780]
Description: phosphoenolpyruvate synthase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.2e-102  343.6   0.0   1.9e-102  342.9   0.0    1.3  1  PPDK_N           Pyruvate phosphate dikinase, PEP/pyruvate bi
    2.9e-72  243.3   0.0    4.3e-72  242.7   0.0    1.2  1  PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
    5.5e-26   90.1   3.4    1.3e-25   88.9   3.4    1.7  1  PEP-utilizers    PEP-utilising enzyme, mobile domain


Domain annotation for each model (and alignments):
>> PPDK_N  Pyruvate phosphate dikinase, PEP/pyruvate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  342.9   0.0  3.1e-106  1.9e-102       2     321 ..      22     333 ..      21     336 .. 0.98

  Alignments for each domain:
  == domain 1  score: 342.9 bits;  conditional E-value: 3.1e-106
                            PPDK_N   2 elvGGKganLaellneagipvPpgfaitadafrefleengleekideelkeldvddvdelrkaskeirelilsaelP 78 
                                       ++vGGKganL+el +++g pvP+ f+ t+  ++ef+++n+l  ki +e+k +d ++ d+l +as++ir+++ ++++P
  gi|474934735|ref|YP_007688317.1|  22 PIVGGKGANLGEL-TSSGFPVPHAFVLTTVSYDEFVNANKLMPKIMKEIKGIDPNSDDSLVAASEKIRAIFDKSKIP 97 
                                       68***********.77************************************************************* PP

                            PPDK_N  79 eeleeaikeayeelgkkfgdeelpvaVRSSataEDlpkasfaGqqdtyLnvggeeevleaikavfaSlfnerAilYr 155
                                       + l+++i++ y+ l+ + +++ + vaVRSSataEDlp+asfaGqq+tyLnv++  e++e+i  +++Slf++rAi+Yr
  gi|474934735|ref|YP_007688317.1|  98 AALKKDIEDNYKILCGSSKQK-TFVAVRSSATAEDLPDASFAGQQETYLNVASLTELYEKIIMCWSSLFTARAISYR 173
                                       ***************866665.9****************************************************** PP

                            PPDK_N 156 kekgldheevalavvvqkmvnsdlgasGVafsldpetGfkdevlinasyGlGeaVVaGrvtpdefvvekstrkilek 232
                                       +++g++heev+lavvvq+mvns+   sG++f+++p++G +++++++  yGlGea+V+G++tpd+++++k +  i+++
  gi|474934735|ref|YP_007688317.1| 174 EKQGYSHEEVKLAVVVQRMVNSE--FSGIMFTVNPNNG-AKNIIVEGGYGLGEAIVGGEITPDTYTIDKVKMDITDR 247
                                       ***********************..*************.999*********************************** PP

                            PPDK_N 233 kigekeikivydekeegtkevevpeeereklaLsdeeveeLaeiakkiekhygtpmdiEfaideeegklyllQaRpe 309
                                       + ++++ k+ + +k+ g ++v++pe+ +++++++d++v+e+aei++++e hy++pmd+E++i+  eg++yl+QaRp+
  gi|474934735|ref|YP_007688317.1| 248 RFSTQKWKYARGPKG-GLVKVDIPEDLQKAQKIDDAHVREIAEIGRQVEIHYEKPMDMEWCIE--EGNVYLVQARPI 321
                                       *************99.88*********************************************..************ PP

                            PPDK_N 310 trtsekkekkaa 321
                                       t+ ++ ke++++
  gi|474934735|ref|YP_007688317.1| 322 TTLNKIKEANTS 333
                                       ****99998765 PP

>> PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  242.7   0.0   7.1e-76   4.3e-72      11     293 ..     465     763 ..     455     764 .. 0.94

  Alignments for each domain:
  == domain 1  score: 242.7 bits;  conditional E-value: 7.1e-76
                                       CCCHCCCXBCEEEEEESSCHHHHHHHHCTXSSEEEEEHHHHCTTS..CCHHHHHH..........HHHHHHHHHHHT CS
                   PEP-utilizers_C  11 lavtkdgkkikvlaNidtpedaekalengaeGiGLlRtEflfmar..eelpteee..........qaeaykkvleam 75 
                                        a   +++ +kv++N+++p++ae+ ++ + +G+GLlR+Eflf++   e++ +++           +a+   kv++a+
  gi|474934735|ref|YP_007688317.1| 465 FAEQVPITGTKVMVNMSMPNKAEEIAQLPCDGVGLLRSEFLFTNYigEHPCAVIAdgrsqelidkLADGVGKVARAF 541
                                       5666788999**********************************9844566666689*******99*********** PP

                                       TTSEEEEEXXXSSCC..GGSGGC.HHHH.XSXGGGSSXTHHHHCCS..HHHHHHHHHHHHHHCCCC...EEEEEESS CS
                   PEP-utilizers_C  76 ngrpvvvRtlDiggd..kelpel.keepeevNPmlGfRgirlglse..pelfetqlrAllrasaag...kleimlPm 144
                                       ++rpv++Rt D++++  + ++ + ++ep+e NPm+G+Rg+++++se  +e f  +l+A+++++ ++   +++imlP+
  gi|474934735|ref|YP_007688317.1| 542 YPRPVTLRTSDFKTNeyRDMKGGaNYEPNEDNPMIGWRGCSRYVSEnyREAFMCELKAIKKVRDEMgmkNVNIMLPF 618
                                       **************9778899865789***************9998779**************966677******** PP

                                       XXSHHHHHHHHHHHHHHHHHHHHCTCTXXTTXEEEEEEXSHHHHHTHHHHCTTSSEEEEXHHHHHHHHHTXXCCCHC CS
                   PEP-utilizers_C 145 vasveeleeakkiieevkeelekegvkkkkkvkvGiMiEvpsaalladklakevdFfSiGtNDLtQytlavdRdnee 221
                                       v++++e++e  +++e+v       g+k+  ++k+  M Evp  +++a++++k+ d fSiG+NDLtQ+t+++dRd++ 
  gi|474934735|ref|YP_007688317.1| 619 VRTIDEVKEITAMMESV-------GLKRGLDLKLYFMAEVPVNIFMAEEFCKYCDWFSIGSNDLTQLTMGCDRDSDI 688
                                       *****************.......89999************************************************ PP

                                       HHHH..SXTTTCHHCCCHHHHHHHHHHCCXEEEEESCCCC.SCCCHHHHHHCTXSEEEEXGGGHHHHHHHHHCTT CS
                   PEP-utilizers_C 222 vakl..ydplepavlrlikevikaaeekglkvgiCGelag.dpsavellvglGldelSmsaasvpaaraalaqve 293
                                       + k+  +d+ +p v+++ik++ik+a+++g +v+iCG++++ +p   e+lv+ G+d +S++++   ++++ +a++e
  gi|474934735|ref|YP_007688317.1| 689 LGKMgyFDERNPGVKAAIKHLIKVAHKYGNHVSICGQAPSvYPDFCEFLVETGIDCISLNPDTFVKTKKIIASAE 763
                                       **9999**********************************9****************************999875 PP

>> PEP-utilizers  PEP-utilising enzyme, mobile domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.9   3.4   2.2e-29   1.3e-25       2      73 .]     370     441 ..     369     441 .. 0.98

  Alignments for each domain:
  == domain 1  score: 88.9 bits;  conditional E-value: 2.2e-29
                                       --S-EEEEES---HHHHTTS-GEEEEEES--TTHHHHHHHHHHTT--EEE--SSHH.HH--TEEEEEETTTT CS
                     PEP-utilizers   2 leegvILvaeetspsdiagldkaaGivterGGmtSHaAivArelgiPaVvgvgeatielkegdlitvDgstG 73 
                                       +++g++Lv+++t p++++++++  +ivt++GGmt+HaAi++relg P+Vvg+geat+ lk+gd++tvDgstG
  gi|474934735|ref|YP_007688317.1| 370 IKDGDVLVTKMTMPDMVPAMSRSVAIVTDEGGMTCHAAIISRELGTPCVVGTGEATSALKNGDIVTVDGSTG 441
                                       5789****************************************************999999*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (780 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:00.47
# Mc/sec: 4946.42
//
Query:       gi|474934736|ref|YP_007688318.1|  [L=51]
Description: hypothetical protein TALC_01170 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.052   13.7   0.0      0.052   13.7   0.0    1.0  1  DUF4143   Domain of unknown function (DUF4143)


Domain annotation for each model (and alignments):
>> DUF4143  Domain of unknown function (DUF4143)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.9e-06     0.052      53      89 ..       2      38 ..       1      50 [. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.9e-06
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DUF4143 53 allgldkeelledsenkGallEnlVaqeLlkysekeg 89
                                      +++g+++e+ ++d + +G+++E l+ ++Ll y+e+ +
  gi|474934736|ref|YP_007688318.1|  2 TAIGMTPETAMKDLNAFGFMFEALCERDLLVYAEATK 38
                                      5688999************************944433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       153  (0.00853366); expected 358.6 (0.02)
Passed bias filter:                      132  (0.00736237); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 330.04
//
Query:       gi|474934737|ref|YP_007688319.1|  [L=72]
Description: hypothetical protein TALC_01171 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.60
# Mc/sec: 363.59
//
Query:       gi|474934738|ref|YP_007688320.1|  [L=310]
Description: putative transcriptional regulator, contains C-terminal CBS domains [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-24   84.8   4.7    4.9e-14   52.5   0.1    3.1  3  CBS       CBS domain
    6.2e-12   45.6   0.0    1.5e-11   44.4   0.0    1.6  1  ParBc     ParB-like nuclease domain
  ------ inclusion threshold ------
      0.044   13.9   0.2        0.3   11.1   0.2    2.0  1  ParBc_2   Putative ParB-like nuclease


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.5   0.1   8.2e-18   4.9e-14       1      56 [.       5      59 ..       5      60 .. 0.97
   2 !   32.7   0.3   1.3e-11   7.6e-08       5      54 ..      69     118 ..      64     121 .. 0.92
   3 ?   -0.6   0.1      0.32   1.9e+03      28      41 ..     186     199 ..     178     201 .. 0.75

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 8.2e-18
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56
                                      Vgd+m rdv +v+pd+t+ee+ e++++++++++PVV e+g l+G+vt + llr++ 
  gi|474934738|ref|YP_007688320.1|  5 VGDYMVRDVEYVTPDMTIEEVKEKLIDSNFHGYPVV-ENGYLLGYVTAKELLRYMD 59
                                      89**********************99**********.9***************986 PP

  == domain 2  score: 32.7 bits;  conditional E-value: 1.3e-11
                                       SBSSCEEEETTSBHHHHHHH.HHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS   5 mtrdvvtvppdttleealel.mrekgvsrlPVVdedgklvGivtlrDllra 54 
                                       m+r  ++v p++++ +a +  + ++g++ lPVVd+++++vGi++  D++r 
  gi|474934738|ref|YP_007688320.1|  69 MSRGTLCVIPSMSIDDATRVlF-RYGLRNLPVVDDEKRIVGIISNIDIVRS 118
                                       7888899*************77.999**********************985 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.32
                                       HTSSEEEEEETTTB CS
                               CBS  28 kgvsrlPVVdedgk 41 
                                       k++++++VVd+ ++
  gi|474934738|ref|YP_007688320.1| 186 KRHNGYLVVDGHHR 199
                                       5578888**98776 PP

>> ParBc  ParB-like nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   0.0   2.5e-15   1.5e-11       2      75 ..     149     217 ..     148     224 .. 0.94

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 2.5e-15
                             ParBc   2 evplseirpnplqprkdspekieelvasIkkkGllqPiivrktrqgryeiiaGerRlrAakrlglkevpvivle 75 
                                       e+p++++ p+++ ++    +++   + ++k +Gl +P+iv k   + y +++G++R  Aakrlglk++ +ivle
  gi|474934738|ref|YP_007688320.1| 149 EIPIDQMIPTQKEVY---MDELIGRQYELK-RGLNEPLIVIKRH-NGYLVVDGHHRIMAAKRLGLKTFNCIVLE 217
                                       89*************...779*********.************7.***************************98 PP

>> ParBc_2  Putative ParB-like nuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   5.1e-05       0.3       2      81 ..     149     215 ..     148     224 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.1e-05
                                       EEEGGGCB-SBSEE-HHHHHHHHHHHHT------.---TT-BEEEEEE-STT-EEE-S-HHHHHHHHHTT-....-E CS
                           ParBc_2   2 eveiadLrPTQlavGldeveyklgeleelkekkkldkflekklvpvVigpdgelYliDhHHllrallesgvggaekk 78 
                                       e+ i+++ PTQ  v +de+  ++ el++  +              +Vi +++ + ++D+HH + a  + g   ++ +
  gi|474934738|ref|YP_007688320.1| 149 EIPIDQMIPTQKEVYMDELIGRQYELKRGLN-----------EPLIVIKRHNGYLVVDGHHRIMAAKRLGL--KTFN 212
                                       5678889999999999988888777733221...........233677778888899*****999888554..4555 PP

                                       EEE CS
                           ParBc_2  79 vlv 81 
                                       ++v
  gi|474934738|ref|YP_007688320.1| 213 CIV 215
                                       555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2068.90
//
Query:       gi|474934739|ref|YP_007688321.1|  [L=292]
Description: ABC-type Fe3+-siderophore transport system, permease component [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-80  270.6  24.8    1.6e-80  270.5  24.8    1.0  1  FecCD     FecCD transport family


Domain annotation for each model (and alignments):
>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  270.5  24.8   8.7e-85   1.6e-80      34     312 .]       5     285 ..       1     285 [. 0.96

  Alignments for each domain:
  == domain 1  score: 270.5 bits;  conditional E-value: 8.7e-85
                             FecCD  34 eaeivlelrlprvlaallvGaaLavaGallQtvtrNpLadPsilGissgaalgavlallll....lgslslfalpla 106
                                       ++  ++++r pr++ a+++GaaLa+aGa++Q  ++NpLa+P+++Gissga lga+l+++ +     + ++   +++ 
  gi|474934739|ref|YP_007688321.1|   5 DDYYIWDIRTPRAIGAIVTGAALALAGAVMQNDFKNPLAEPYTMGISSGAFLGACLSIISGfsilPFISGPLVTMAN 81 
                                       56789********************************************************7776666777777777 PP

                             FecCD 107 aflgallalllvlllarkrkgasplkliLaGiavsallsaltsllllllneealesilfwllGslsgaswskvllll 183
                                       af+++l+ ++++++++ k k+++p+ +iL+Giav +l+s+++++l++++ +e+l++++ w +Gsl+++sw+ + +++
  gi|474934739|ref|YP_007688321.1|  82 AFVFSLIPTAVIVVIS-KFKKMTPAAMILTGIAVMFLFSSISQVLMVTAPSESLADAYSWRVGSLNRVSWDVLPVMV 157
                                       8888888899999999.************************************************************ PP

                             FecCD 184 vllllllllllllarkldllalgdetAkslGvnvervrllllllvalltavavalvGpigFvGLivPhiarllvgad 260
                                        ++++l + l+++ +kl+++  gd+ A +lG + +r+r+++l++ +++ta++v+++G+igF+GL+ Phiar++vg++
  gi|474934739|ref|YP_007688321.1| 158 SATVVLGVSLYFFVNKLNVMYAGDKSALTLGEDANRIRIATLIILSFMTASVVSFTGTIGFIGLVGPHIARIFVGSN 234
                                       ***************************************************************************** PP

                             FecCD 261 hrkllplsallGallllladllarlllsptelpvgivtaliGapffiylllr 312
                                       +r+ lp+sa +Ga+++llad++a++   ++ lpvg++ a++G+p+fi++l+r
  gi|474934739|ref|YP_007688321.1| 235 NRYFLPASAAFGAAFILLADTVAKVSG-SSGLPVGVISAMVGGPLFIWILIR 285
                                       ************************886.7999*****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       778  (0.0433934); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1798.62
//
Query:       gi|474934740|ref|YP_007688322.1|  [L=363]
Description: ABC-type Fe3+-siderophore transport system, permease component [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-76  255.7  45.7    3.5e-75  252.9  45.6    1.9  2  FecCD     FecCD transport family
  ------ inclusion threshold ------
       0.25   10.8  37.9      0.025   14.1  32.9    1.8  2  ABC-3     ABC 3 transport family
        6.2    6.6   6.0          5    6.9   0.1    3.2  2  DUF4538   Domain of unknown function (DUF4538)


Domain annotation for each model (and alignments):
>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   1.3     0.039   2.3e+02     234     248 ..      28      42 ..      21      48 .. 0.86
   2 !  252.9  45.6   5.9e-79   3.5e-75      24     311 ..      57     353 ..      27     354 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.039
                             FecCD 234 vavalvGpigFvGLi 248
                                       +av++vG+i F GL 
  gi|474934740|ref|YP_007688322.1|  28 LAVCVVGIILFAGLF 42 
                                       7899*********95 PP

  == domain 2  score: 252.9 bits;  conditional E-value: 5.9e-79
                             FecCD  24 eallgka..........dsleaeivlelrlprvlaallvGaaLavaGallQtvtrNpLadPsilGissgaalgavla 90 
                                       e++ ++           + +++  ++++ +p+v+aa+l+Ga+La++G+l+Q+++ NpLadP+  Gissga +gav+a
  gi|474934740|ref|YP_007688322.1|  57 ELIWNHIlgneypprsyEWWADRNLWNTAMPQVVAAILAGASLAICGTLMQAIMANPLADPYSTGISSGACFGAVAA 133
                                       3333333444477766666667789**************************************************** PP

                             FecCD  91 llll...lgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsaltsllllllneealesil 164
                                       ++++   +g +++ +l++ aflga++ ++ +++++ +r +++p++liL G a+s++++al++++++++++++l+s++
  gi|474934740|ref|YP_007688322.1| 134 IIVGisfSGVAGETGLVANAFLGAMVPAITIIIIS-ERIRMTPATLILLGTAISYFFNALITYMMVTTDADTLKSAY 209
                                       *****99999*************************.***************************************** PP

                             FecCD 165 fwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrllllllvalltavavalvGp 241
                                        w +Gsls++ w+++ +++ +++++ ++++l ++k+++++lgd+ A slG++v ++r+l+l l+a++ta++va++G+
  gi|474934740|ref|YP_007688322.1| 210 LWQVGSLSSIGWDSMPVMAGVTIIGSIFVMLATSKMNVMSLGDNSAISLGIDVHKFRVLCLGLMAIMTASIVAFTGI 286
                                       ***************************************************************************** PP

                             FecCD 242 igFvGLivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivtaliGapffiylll 311
                                       igFvGL++Ph++rl++g+d+r + p+s+ lGallll+++++a ll+   ++pvg+v++liGap+f++l++
  gi|474934740|ref|YP_007688322.1| 287 IGFVGLVAPHLVRLVIGSDNRFVTPISMALGALLLLISNYIAYLLA---NIPVGVVMSLIGAPLFFLLIV 353
                                       ********************************************95...7****************9987 PP

>> ABC-3  ABC 3 transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.2      0.27   1.6e+03     174     189 ..      26      41 ..      17      47 .. 0.62
   2 ?   14.1  32.9   4.2e-06     0.025      35     257 ..     119     354 ..      83     355 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.27
                             ABC-3 174 alialavvvalqavGv 189
                                       +l+a++vv ++ ++G+
  gi|474934740|ref|YP_007688322.1|  26 MLLAVCVVGIILFAGL 41 
                                       4555555555544443 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 4.2e-06
                             ABC-3  35 gdalsHaalpGvalayllgvn.........lllgailvgliaavalellkrktklkedtai..givlsvflalglvl 100
                                       + ++s  a  G + a+++g++         l++ a+l +++ a+++ +++++ ++   t+i  g  +s f+   +  
  gi|474934740|ref|YP_007688322.1| 119 STGISSGACFGAVAAIIVGISfsgvagetgLVANAFLGAMVPAITIIIISERIRMTPATLIllGTAISYFFNALITY 195
                                       34455555555555555555577778888899**********************99887643388999999765555 PP

                             ABC-3 101 vslikkskvdldsyL..fGniltisqedliliaiieavvllllllfwkelllitfdeelAkveglsvkllkllllal 175
                                       +  + +++   ++yL   G++ +i  + + ++a ++++  + ++l   ++ ++++  + A + g+ v+ +++l l l
  gi|474934740|ref|YP_007688322.1| 196 MMVTTDADTLKSAYLwqVGSLSSIGWDSMPVMAGVTIIGSIFVMLATSKMNVMSLGDNSAISLGIDVHKFRVLCLGL 272
                                       555554444445566336*********************************************************** PP

                             ABC-3 176 ialavvvalqavGviLvialliiPaatArrltrslesllivAillglvsvvaGlllSyyld.latGavivlvatllf 251
                                       +a+  + ++ + G+i  +  l++P  + + ++++ + +  ++++lg++ +++  ++ y l  ++ G v+ l+ + lf
  gi|474934740|ref|YP_007688322.1| 273 MAIMTASIVAFTGIIGFVG-LVAPHLVRLVIGSDNRFVTPISMALGALLLLISNYIAYLLAnIPVGVVMSLIGAPLF 348
                                       *************998887.689***********************************9877***********9999 PP

                             ABC-3 252 llallv 257
                                       +l +++
  gi|474934740|ref|YP_007688322.1| 349 FLLIVF 354
                                       988776 PP

>> DUF4538  Domain of unknown function (DUF4538)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1   0.00083         5       4      33 ..      23      53 ..      22      57 .. 0.83
   2 ?   -0.7   1.8      0.21   1.2e+03       7      19 ..     280     292 ..     275     294 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00083
                           DUF4538  4 lkyvllvggvvgligla.lYPiiiaPllhpe 33
                                      ++++ll ++vvg+i  a l++i ++P l  +
  gi|474934740|ref|YP_007688322.1| 23 RRIMLLAVCVVGIILFAgLFSIKMYPELSLS 53
                                      6999********9976559******988765 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.21
                           DUF4538   7 vllvggvvgligl 19 
                                       ++++ g++g++gl
  gi|474934740|ref|YP_007688322.1| 280 IVAFTGIIGFVGL 292
                                       5778999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       833  (0.046461); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2303.94
//
Query:       gi|474934741|ref|YP_007688323.1|  [L=451]
Description: hypothetical protein TALC_01175 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    0.00019   21.5  11.7    0.00034   20.7  10.1    2.4  2  Dockerin_1  Dockerin type I domain
  ------ inclusion threshold ------
       0.16   12.4   1.7       0.43   11.1   0.1    2.4  2  EF-hand_7   EF-hand domain pair


Domain annotation for each model (and alignments):
>> Dockerin_1  Dockerin type I domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7  10.1   3.8e-08   0.00034       5      54 ..      43      89 ..      39      93 .. 0.93
   2 ?   -2.3   0.0      0.61   5.4e+03      19      40 ..     419     444 ..     417     445 .. 0.65

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 3.8e-08
                                      TSSSC-SHHHHHHHHHHCTSSEBTTSCCCHGGGSTT-SSCESHHHHHHHH CS
                        Dockerin_1  5 NgDgkVnalDalliinylnqregqssssngkaaDvNgDGrvnalDallvi 54
                                      N+D ++n+ D+++++  +n   g+ ++ +   aDvN DG+vn +D++l+ 
  gi|474934741|ref|YP_007688323.1| 43 NDDHTINSDDMAIVQDIIN---GTRNKDDFPLADVNDDGKVNETDVSLLQ 89
                                      9******************...999999999***************9986 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.61
                                       HHHCT....SSEBTTSCCCHGGGSTT CS
                        Dockerin_1  19 inyln....qregqssssngkaaDvN 40 
                                       + y+n      +gq+ ss   + DvN
  gi|474934741|ref|YP_007688323.1| 419 KDYINtgtmPLKGQTLSSICSYIDVN 444
                                       66666665545567777777888888 PP

>> EF-hand_7  EF-hand domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   4.8e-05      0.43       5      35 ..      66      95 ..      63     121 .. 0.80
   2 ?   -1.1   0.2       0.3   2.7e+03      49      60 ..     360     371 ..     342     373 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.8e-05
                         EF-hand_7  5 keaFkelDtdgdgyldkeellrllrkifqga 35
                                      k+ F + D+++dg+++++++  ll+ +++ +
  gi|474934741|ref|YP_007688323.1| 66 KDDFPLADVNDDGKVNETDVS-LLQDLIDRK 95
                                      67799**************99.***998765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.3
                         EF-hand_7  49 lfkefDtdkdGv 60 
                                       +++ +D+d+dGv
  gi|474934741|ref|YP_007688323.1| 360 IIDTWDHDNDGV 371
                                       677789999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3222.05
//
Query:       gi|474934742|ref|YP_007688324.1|  [L=441]
Description: ABC-type Fe3+-hydroxamate transport system, periplasmic component [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.9e-09   36.1   0.4    9.4e-09   35.2   0.4    1.5  1  Peripla_BP_2  Periplasmic binding protein
     0.0075   16.4   1.0     0.0075   16.4   1.0    2.2  2  Dockerin_1    Dockerin type I domain


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.4     1e-12   9.4e-09       1     231 [.     133     379 ..     133     385 .. 0.72

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 1e-12
                                       EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT.......TS-BSBESSSB-HHHHHHH--SEEEE-GGG... CS
                      Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadklee.....aivevgadgeidvEklaalkPDlvilskgl..g 70 
                                       i++ ++   ++ + lG+td++v+   +  d +   +  +     + ++vg ++e+++E++ + + D +++ +++   
  gi|474934742|ref|YP_007688324.1| 133 IIVNTQRALDLCINLGITDRIVALNDYIFDQAINVDTIKykgfsSYPSVGDRKEPNLETITKTDADTIFAGTTGtyM 209
                                       566677788999999********99999988888765446556677****************************544 PP

                                       ..GGGHHHHHHHS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT.-EEEEEEEETT CS
                      Peripla_BP_2  71 ltdedeellksgiptvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidsekpkpvlvfggad 147
                                        + +++        ++   +++   +++  + +lg  ++  d+a+k+v++ d+  +   +a+++  ++++  + +a 
  gi|474934742|ref|YP_007688324.1| 210 KNISASAATYGEKTVLRLATWER-GEFCSGALTLGFFTDADDNAQKYVKWNDKINEVTSDALAKV-NTKATKMLNAS 284
                                       44444444444455666666664.************************98776666666666666.66677777777 PP

                                       E..EEEE-TTSTTTHHHHTS--EESTTT--........STT-EEE-HHHHHHH--SEEEEEEH.........HHHT- CS
                      Peripla_BP_2 148 eggyvvagsnsyigdlldalgieniaaesk........kseyeeisaEqilasdpdvifvsgr.........aeadn 207
                                       +++++ a s++  ++l+   g+ ni   ++        ++++ +   E+i++++p vi+ s +              
  gi|474934742|ref|YP_007688324.1| 285 SATWFGAQSDGVSTALTA-TGVTNI---GNdiivkttgSGGSVTTYKENIVKANPSVIVLSYTvgynwtqeqM---- 353
                                       777788877777777777.555555...222234555599999999***************999966533222.... PP

                                       S--HHHHT-S..HHHHTSHHHHTT-E CS
                      Peripla_BP_2 208 ktgleflken..pllaelpAvkngrV 231
                                       + +  ++ ++      +++A+ n++V
  gi|474934742|ref|YP_007688324.1| 354 DDKFNGIVTTmkGSIGATTAITNNNV 379
                                       22222232222233555666666666 PP

>> Dockerin_1  Dockerin type I domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   1.0   8.4e-07    0.0075       2      38 ..      74     107 ..      60     110 .. 0.74
   2 ?   -1.7   0.1      0.38   3.4e+03      37      43 ..     405     411 ..     401     415 .. 0.56

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 8.4e-07
                                       TETTSSSC-SHHHHHHHHHHCTSSEBTTSCCCHGGGS CS
                        Dockerin_1   2 gDVNgDgkVnalDalliinylnqregqssssngkaaD 38 
                                       +D N D kV+a Da  +++ +     ++s++ ++aaD
  gi|474934742|ref|YP_007688324.1|  74 ADANHDDKVDAADAEFVKKLID---LKKSNTGKAAAD 107
                                       4777777777777777777777...666666666666 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.38
                                       GSTT-SS CS
                        Dockerin_1  37 aDvNgDG 43 
                                        DvN D 
  gi|474934742|ref|YP_007688324.1| 405 SDVNVDK 411
                                       5555553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       910  (0.0507558); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3069.12
//
Query:       gi|474934743|ref|YP_007688325.1|  [L=372]
Description: ABC-type Fe3+-siderophore transport system, permease component [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-91  306.8  36.2    1.7e-91  306.5  36.2    1.1  1  FecCD     FecCD transport family


Domain annotation for each model (and alignments):
>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  306.5  36.2   9.3e-96   1.7e-91       3     312 .]      52     366 ..      42     366 .. 0.96

  Alignments for each domain:
  == domain 1  score: 306.5 bits;  conditional E-value: 9.3e-96
                             FecCD   3 llllllslllgavkispsevfeallgka.....dsleaeivlelrlprvlaallvGaaLavaGallQtvtrNpLadP 74 
                                       +l+  +s+++g+++i + e + +  ++      d +++++++e+rlpr++a++++G++La++Ga++Q++++NpLadP
  gi|474934743|ref|YP_007688325.1|  52 ILVSGISMTIGEYDIGFFESYVIAWNHLfgdvgDTTKDFVIWEIRLPRIIAGIISGVGLATCGAVMQSTMKNPLADP 128
                                       566778899999999998876666555566669999***************************************** PP

                             FecCD  75 silGissgaalgavlallll.lgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsaltsl 150
                                       ++ Gissga++ga+la++l+ +  ++ +a++l af++al+ ++l++l++ + ++++ +++iL+Giav +l++a+t++
  gi|474934743|ref|YP_007688325.1| 129 YTTGISSGASFGATLAIILGlTIIAGDYAIVLNAFIFALIPMALIMLIS-SIRKTTATMIILCGIAVMYLFNAMTTV 204
                                       ********************98899************************.99************************* PP

                             FecCD 151 lllllneealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrllllll 227
                                       ++l++n+++l++++ w +G+l++ sw+++ +++ ++l+++++l ll++k+++la gde+AkslG+n e++rl++ll+
  gi|474934743|ref|YP_007688325.1| 205 MMLMANPNDLAAVYSWQVGTLGSSSWNTIPIMFTFVLVGFVILELLSSKINVLASGDENAKSLGLNAEQLRLICLLV 281
                                       ***************************************************************************** PP

                             FecCD 228 valltavavalvGpigFvGLivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivtaliGap 304
                                       v+l++a++v+++G+igFvGL+ Ph++r+++g+d+r+l+p+s+ lGa+l++++dl++r++++p+ l+vg+vta+iG+p
  gi|474934743|ref|YP_007688325.1| 282 VSLVAASVVSFTGIIGFVGLVCPHMCRMILGSDNRYLIPASGALGATLMVACDLIGRTIIAPSVLQVGVVTAFIGGP 358
                                       ***************************************************************************** PP

                             FecCD 305 ffiylllr 312
                                       +f++lllr
  gi|474934743|ref|YP_007688325.1| 359 MFLWLLLR 366
                                       ******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1056  (0.058899); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2246.28
//
Query:       gi|474934744|ref|YP_007688326.1|  [L=280]
Description: ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase component [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.2e-30  104.5   0.0    8.4e-30  104.1   0.0    1.2  1  ABC_tran      ABC transporter
    5.2e-09   36.3   0.7    0.00026   20.9   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    5.1e-08   33.0   0.3    2.1e-05   24.4   0.0    2.1  2  AAA_15        AAA ATPase domain
    1.8e-06   28.6   0.0      3e-06   27.9   0.0    1.3  1  AAA_23        AAA domain
      4e-06   26.5   0.0      8e-06   25.5   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
    5.4e-06   26.0   0.6    5.2e-05   22.8   0.6    2.0  1  SMC_N         RecF/RecN/SMC N terminal domain
    0.00011   22.6   0.0    0.00019   21.9   0.0    1.4  1  AAA_16        AAA ATPase domain
    0.00014   22.2   0.6     0.0012   19.1   0.6    2.1  1  AAA_22        AAA domain
    0.00073   18.4   0.0      0.001   17.9   0.0    1.2  1  RNA12         RNA12 protein
     0.0036   16.7   0.3       0.48    9.8   0.0    2.3  2  TniB          Bacterial TniB protein
     0.0048   16.8   0.0     0.0095   15.9   0.0    1.5  1  RsgA_GTPase   RsgA GTPase
     0.0062   16.3   0.3      0.019   14.7   0.0    1.8  2  AAA_24        AAA domain
     0.0068   17.0   0.1      0.015   15.9   0.1    1.8  1  AAA_18        AAA domain
     0.0068   15.5   0.0      0.011   14.8   0.0    1.3  1  T2SSE         Type II/IV secretion system protein
     0.0084   15.7   0.0      0.015   14.9   0.0    1.3  1  AAA_27        AAA domain
  ------ inclusion threshold ------
      0.016   15.3   0.1      0.059   13.5   0.0    1.9  2  MMR_HSR1      50S ribosome-binding GTPase
       0.02   15.3   0.0       0.12   12.8   0.0    2.3  3  RNA_helicase  RNA helicase
       0.02   13.7   0.2        2.3    6.9   0.0    2.1  2  ABC_ATPase    Predicted ATPase of the ABC class
      0.022   14.8   0.0      0.066   13.2   0.0    1.8  1  AAA_5         AAA domain (dynein-related subfamily)
      0.022   15.2   0.3       0.17   12.3   0.3    2.1  1  AAA           ATPase family associated with various cellular 
       0.03   13.5   0.1      0.087   12.0   0.1    1.8  1  NB-ARC        NB-ARC domain
      0.036   13.4   0.0       0.06   12.7   0.0    1.4  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.037   13.7   0.1          1    9.1   0.0    2.4  2  IstB_IS21     IstB-like ATP binding protein
       0.06   13.4   0.0      0.088   12.9   0.0    1.3  1  DUF87         Helicase HerA, central domain
      0.061   12.2   0.0       0.51    9.2   0.0    2.2  3  AAA_10        AAA-like domain
      0.063   13.4   0.1       0.15   12.2   0.1    1.8  1  AAA_33        AAA domain
      0.066   13.1   0.0       0.14   12.0   0.0    1.5  1  NACHT         NACHT domain
      0.082   12.8   0.4       0.24   11.3   0.1    1.8  2  NTPase_1      NTPase
       0.12   11.6   0.0        0.2   10.9   0.0    1.3  1  Zeta_toxin    Zeta toxin
       0.12   12.4   0.0       0.54   10.3   0.0    1.9  2  AAA_14        AAA domain
       0.14   12.3   0.0       0.37   11.0   0.0    1.7  1  AAA_28        AAA domain
        0.2   11.3   0.0       0.34   10.6   0.0    1.6  1  AAA_30        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.1   0.0   1.5e-32   8.4e-30       1     137 []      20     167 ..      20     167 .. 0.93

  Alignments for each domain:
  == domain 1  score: 104.1 bits;  conditional E-value: 1.5e-32
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l++++l++ +  ++ i+G+nG GKStL+k++ +ll+pteG++l+d+k+++e +++ l   +g++p  ++ +  ++v 
  gi|474934744|ref|YP_007688326.1|  20 LRDINLSIDRPGLICIIGPNGVGKSTLVKCINRLLTPTEGNVLIDDKPISEYRTRDLATVVGYVPAFSTDDFAMSVV 96 
                                       6899***************************************************************9999999999 PP

                                       HH...............HHHTC...HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx...............xxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en...............esdee...iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       ++               e   +   ++++l++lg+++l+ ++      +LS Gq q+v+lar l++ p++l+lDEpt
  gi|474934744|ref|YP_007688326.1|  97 DTvmmgrhpyrrmgstrE---DlhiVYEVLKELGITHLAMRNF----DELSAGQHQKVSLARGLAQSPDILILDEPT 166
                                       998999999998865444...1556************999999....*****************************9 PP

                                       T CS
                                       x RF
                          ABC_tran 137 a 137
                                       a
  gi|474934744|ref|YP_007688326.1| 167 A 167
                                       7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   4.6e-07   0.00026       2      23 ..      33      54 ..      32      77 .. 0.77
   2 !   13.9   0.3   6.3e-05     0.035     252     300 ..     151     200 ..     111     202 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 4.6e-07
                            AAA_21  2 nvliGpNgsGKSnLLdaldlla 23
                                       ++iGpNg+GKS+L +++  l 
  gi|474934744|ref|YP_007688326.1| 33 ICIIGPNGVGKSTLVKCINRLL 54
                                      68****************9995 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 6.3e-05
                            AAA_21 252 lralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHSpl 300
                                         +++++++l++DEp ++L+ k + ++ +l+ ++ +++++  ++ +H+  
  gi|474934744|ref|YP_007688326.1| 151 RGLAQSPDILILDEPTANLDIKHQVEVTRLMrDISHEKNITTVMISHDLN 200
                                       4455666************************65555599********975 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   3.7e-08   2.1e-05      14      69 ..      20      72 ..      18      80 .. 0.80
   2 !    6.9   0.1    0.0082       4.6     318     357 ..     151     190 ..     120     201 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 3.7e-08
                            AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleife 69
                                      l+d+ ++++   l ++iG+N++GKS++++ ++ +l+ +    +  + i+++ +++++
  gi|474934744|ref|YP_007688326.1| 20 LRDINLSIDRPgLICIIGPNGVGKSTLVKCINRLLTPT----EGNVLIDDKPISEYR 72
                                      678777777779***********************988....555677776666655 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0082
                            AAA_15 318 dekeeknvilliEEPEahLHpqaqkvlikllkelandnkt 357
                                       ++  ++++il+++EP a+L +++q ++ +l+++++ +++ 
  gi|474934744|ref|YP_007688326.1| 151 RGLAQSPDILILDEPTANLDIKHQVEVTRLMRDISHEKNI 190
                                       5567899****************************99874 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   5.3e-09     3e-06      15      44 ..      23      55 ..      11      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 5.3e-09
                            AAA_23 15 idF...skgltlItGpNGaGKTTildAiklaLy 44
                                      i++    +gl +I+GpNG GK+T++ +i   L+
  gi|474934744|ref|YP_007688326.1| 23 INLsidRPGLICIIGPNGVGKSTLVKCINRLLT 55
                                      56666778********************98887 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   1.4e-08     8e-06      17      50 ..      25      58 ..      19      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.4e-08
                            AAA_29 17 ieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      ++id+ g + ++Gp+G+GKSTl+  i+ lL+p++
  gi|474934744|ref|YP_007688326.1| 25 LSIDRPGLICIIGPNGVGKSTLVKCINRLLTPTE 58
                                      6788889999**********************86 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.6   9.2e-08   5.2e-05      24     204 ..      30     204 ..      18     216 .. 0.71

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 9.2e-08
                                       SSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--..BTTCSSTTEEEEEEEEEETTEESSSSSSCEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk..skekasvkkaeveitfdnedkklkiekeevs 98 
                                       +++ +i+GpNG GKs l+  i  +L          ++ + li     +e +  + a+v  ++      +++++  +s
  gi|474934744|ref|YP_007688326.1|  30 PGLICIIGPNGVGKSTLVKCINRLLT--------PTEGNVLIDDkpISEYRTRDLATVVGYVPA----FSTDDFAMS 94 
                                       67889****************66666........555677777655455566666666665322....233345567 PP

                                       EEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  99 isrrvkrkgeseykingkevtkkevsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDeida 169
                                       +  +v+ + +   ++  ++   + v e+l++ gi+        +LS G+ + v+la  +A    +   + +lDe  a
  gi|474934744|ref|YP_007688326.1|  95 VVDTVMMGRHPYRRMGSTREDLHIVYEVLKELGITHLamrnfdELSAGQHQKVSLARGLA----QSPDILILDEPTA 167
                                       76666666665555555555667778888888887654555559********99998876....3445899****** PP

                                       TS-HHHHHHHHHHHH..HHCTTSEEEEE-SSHHHCCC CS
                                       xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 170 aLDeknvkkvaellk..eksknaQfivislreemlek 204
                                       +LD k+  +v +l++  +++kn   ++is++ ++  k
  gi|474934744|ref|YP_007688326.1| 168 NLDIKHQVEVTRLMRdiSHEKNITTVMISHDLNVSCK 204
                                       **************96667788889999998776543 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   3.3e-07   0.00019      20      61 ..      26      68 ..      17     108 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 3.3e-07
                            AAA_16 20 rsgrpelvllsGesGvGKsslvrellralekdggif.lrgkcd 61
                                      + +rp+l+ ++G+ GvGKs+lv+++ r l+ ++g + +  k  
  gi|474934744|ref|YP_007688326.1| 26 SIDRPGLICIIGPNGVGKSTLVKCINRLLTPTEGNVlIDDKPI 68
                                      66899*********************99988864443555554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.6   2.1e-06    0.0012       4     126 ..      29     193 ..      26     200 .. 0.53

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.1e-06
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee............................erpevvfvtlpssts 52 
                                       + g+++++G+ G+GK+tl++ + + l+     +e                                           
  gi|474934744|ref|YP_007688326.1|  29 RPGLICIIGPNGVGKSTLVKCINRLLTP----TEgnvliddkpiseyrtrdlatvvgyvpafS-------------- 87 
                                       6799******************999953....3345678888888885543333333333330.............. PP

                            AAA_22  53 skdllrellralglelka..........................erlsseell.ealeqalrarav...ielliiDE 99 
                                        +d++  ++  +  +++                           +  + +el   + ++ + ar+    + +li+DE
  gi|474934744|ref|YP_007688326.1|  88 TDDFAMSVVDTVMMGRHPyrrmgstredlhivyevlkelgithlAMRNFDELSaGQHQKVSLARGLaqsPDILILDE 164
                                       44554444444444444444333333333333333322222222244444444444444444444466777777777 PP

                            AAA_22 100 aqh.lr...seealeeLrsllnlsrkgvqli 126
                                           l+   + e+ +  r+++   +k+++ +
  gi|474934744|ref|YP_007688326.1| 165 PTAnLDikhQVEVTRLMRDISH--EKNITTV 193
                                       6555655422333333366655..6666665 PP

>> RNA12  RNA12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.8e-06     0.001      19      92 ..      32     102 ..      22     148 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.8e-06
                             RNA12  19 FivvkGPrGSGkkeLv..ldrvlkdrkkvlvidCdelvkarndaelisaaAsqlGYfPvFswlnsissliDlavqg 92 
                                        i + GP G Gk+ Lv  ++r l+  +  + id + + + r+     + +A+ +GY+P Fs  +   s++D  + g
  gi|474934744|ref|YP_007688326.1|  32 LICIIGPNGVGKSTLVkcINRLLTPTEGNVLIDDKPISEYRT-----RDLATVVGYVPAFSTDDFAMSVVDTVMMG 102
                                       6899***********9778999****************9997.....679***********999888888876665 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0   0.00085      0.48      33     138 ..      28     146 ..       7     153 .. 0.74
   2 !    7.2   0.5    0.0054         3      82     161 ..     114     196 ..     106     210 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00085
                              TniB  33 krmpnlllvGdsnnGKtmivekFarlhppekd....edae.....kv.pvlvvqappkpdekrlyaaiLealga... 96 
                                       +r+  + ++G+  +GK+++v+   rl +p++      d+      ++    vv + p  +++++  ++++++++   
  gi|474934744|ref|YP_007688326.1|  28 DRPGLICIIGPNGVGKSTLVKCINRLLTPTEGnvliDDKPiseyrTRdLATVVGYVPAFSTDDFAMSVVDTVMMgrh 104
                                       5666789**************99999888753233222212333333134567788888999999999999865322 PP

                              TniB  97 plkararvskleqqvlrllrelkvrvLiiDEihnllagsark 138
                                       p++   ++ +  + v+++l+el++  L +  +++l ag+++k
  gi|474934744|ref|YP_007688326.1| 105 PYRRMGSTREDLHIVYEVLKELGITHLAMRNFDELSAGQHQK 146
                                       677777888888899999999999999999999999998876 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0054
                              TniB  82 dekrlyaaiLealgaplkara...rvskleqqvlrllr..elkvrvLiiDEihnllagsarkqreflnalksLgnel 153
                                       ++ ++  ++L++lg  + a +   ++s+ ++q ++l r  + ++ +Li+DE    l    ++q e++ +++ ++ e 
  gi|474934744|ref|YP_007688326.1| 114 EDLHIVYEVLKELGITHLAMRnfdELSAGQHQKVSLARglAQSPDILILDEPTANL--DIKHQVEVTRLMRDISHEK 188
                                       555666677777777655544111444445566666662245789******99888..8999*************** PP

                              TniB 154 kipivlvG 161
                                       +i+ v++ 
  gi|474934744|ref|YP_007688326.1| 189 NITTVMIS 196
                                       ***99875 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.7e-05    0.0095      87     120 ..      17      51 ..       4      71 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.7e-05
                                       HTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase  87 kegleelkellkd.ktsvlvGqSGvGKStLinall 120
                                        + l++++  ++   +++++G+ GvGKStL++ ++
  gi|474934744|ref|YP_007688326.1|  17 AKILRDINLSIDRpGLICIIGPNGVGKSTLVKCIN 51 
                                       55667777777777899*************98775 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   3.3e-05     0.019       5      33 ..      33      59 ..      31     102 .. 0.67
   2 ?   -1.3   0.1       2.7   1.5e+03     108     130 ..     174     197 ..     172     213 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.3e-05
                            AAA_24  5 iliyGpsgiGKTtlakelgpkplfidtek 33
                                      i+i+Gp+g+GK+tl+k +  + l+  te+
  gi|474934744|ref|YP_007688326.1| 33 ICIIGPNGVGKSTLVKCI--NRLLTPTEG 59
                                      89***************9..667777777 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.7
                            AAA_24 108 aeefrrllkklqelrk.nvifiah 130
                                       + e++rl++++++ ++ + ++i+h
  gi|474934744|ref|YP_007688326.1| 174 QVEVTRLMRDISHEKNiTTVMISH 197
                                       5689999****9999999999998 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   2.6e-05     0.015       1      32 [.      33      77 ..      33     168 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.6e-05
                            AAA_18  1 IlltGtpGvGKttlakeLskrl.gf............gvnlrdva 32
                                      I++ G+ GvGK+tl k ++++l                ++ rd+a
  gi|474934744|ref|YP_007688326.1| 33 ICIIGPNGVGKSTLVKCINRLLtPTegnvliddkpisEYRTRDLA 77
                                      9****************9998633364455555555555555555 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0     2e-05     0.011     102     165 ..       3      65 ..       1      82 [. 0.83

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2e-05
                             T2SSE 102 eltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderivtvED 165
                                       +l+++++ +e + k+ki + ++ ++ + gli + G+ g GK+tl+  +   +  ++ + v++ D
  gi|474934744|ref|YP_007688326.1|   3 SLRFENVYFEYNSKAKILRDINLSIDRPGLICIIGPNGVGKSTLVKCINRLLTPTEGN-VLIDD 65 
                                       6788899999999********************************9998888888555.45555 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.7e-05     0.015      18      50 ..      22      54 ..      20      58 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.7e-05
                            AAA_27 18 sldfsaeeadlhliyGpNEAGKstalrAisdll 50
                                       +++s ++++l  i+GpN  GKst+++ i++ll
  gi|474934744|ref|YP_007688326.1| 22 DINLSIDRPGLICIIGPNGVGKSTLVKCINRLL 54
                                      56777889*********************9998 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   0.00011     0.059       2      54 ..      33      99 ..      32     149 .. 0.69
   2 ?   -1.6   0.0       4.9   2.7e+03      28      57 ..     186     218 ..     177     237 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00011
                                      EEEEESTTSSHHHHHHHHHT.....S.TEEESSST...TSSSSEEEEEEE.....ETTEEEEEEECG CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltg.....e.kaivsdkp...gtTrdinegrvk.....lkgkeielvDtp 54
                                      ++i+G   vGKStL++ + +     e ++ + dkp     Trd  +         +++  + +vDt+
  gi|474934744|ref|YP_007688326.1| 33 ICIIGPNGVGKSTLVKCINRlltptEgNVLIDDKPiseYRTRDLATVVGYvpafsTDDFAMSVVDTV 99
                                      89************75554322243247788888766667777765543233443445556677765 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.9
                                       SSTTSSSSEEEEEEE..ETT.EEEEEEECGGCS CS
                          MMR_HSR1  28 dkpgtTrdinegrvk..lkg.keielvDtpGli 57 
                                       +++  T+ ++ + ++   k  +e++++  pG+i
  gi|474934744|ref|YP_007688326.1| 186 HEKNITTVMISHDLNvsCKYaDEVIVMSSPGII 218
                                       444444444444444333333678888888865 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00022      0.12       1      23 [.      33      54 ..      33      95 .. 0.78
   2 ?   -1.9   0.0       7.8   4.4e+03      75      88 ..     182     195 ..     149     219 .. 0.50
   3 ?   -1.5   0.0       5.9   3.3e+03      48      81 ..     236     271 ..     223     275 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00022
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakall 23
                                      i++ Gp+g+GKStl+k  +++ll
  gi|474934744|ref|YP_007688326.1| 33 ICIIGPNGVGKSTLVKC-INRLL 54
                                      799************99.55554 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 7.8
                      RNA_helicase  75 rlvsstpyplnmas 88 
                                       r +s  + ++ +  
  gi|474934744|ref|YP_007688326.1| 182 RDISHEKNITTVMI 195
                                       33333332222222 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 5.9
                      RNA_helicase  48 t.gqevvvidDfgqvkdee.npsdlaelirlvsstp 81 
                                         g +++++dD g+ +    +p  ++e+  l s+ p
  gi|474934744|ref|YP_007688326.1| 236 VyGMNCLIVDDNGRPHVILqEPIPEEEFRALHSTDP 271
                                       337789999998887655444557777777766665 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0     0.004       2.3     244     265 ..      30      51 ..      17      54 .. 0.90
   2 ?    4.6   0.1      0.02        11     378     412 ..     179     213 ..     157     220 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.004
                                       SSEEEEEE-TTSSHHHHHHHHH CS
                        ABC_ATPase 244 kGvtlIvGggfhGKsTLLeAle 265
                                        G++ I+G++  GKsTL++ ++
  gi|474934744|ref|YP_007688326.1|  30 PGLICIIGPNGVGKSTLVKCIN 51 
                                       599****************997 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.02
                                       HCHHHHHHHH--EEEEEESS-GCCTTT-SEEEEEE CS
                        ABC_ATPase 378 drvrelykklgvstilvvggsgdyldvAdtvilme 412
                                        ++r++ ++ +++t++++  ++   + Ad+vi+m 
  gi|474934744|ref|YP_007688326.1| 179 RLMRDISHEKNITTVMISHDLNVSCKYADEVIVMS 213
                                       456788899*************************7 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00012     0.066       2      24 ..      33      56 ..      32      66 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00012
                                      EEEE--SSSSHHHHHHHGGGGB.S CS
                             AAA_5  2 vlLvGppGtgKselaerlaaal.n 24
                                      ++++Gp G+gKs+l++ + ++l  
  gi|474934744|ref|YP_007688326.1| 33 ICIIGPNGVGKSTLVKCINRLLtP 56
                                      69***************9999952 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.3   0.00031      0.17       1      22 [.      33      54 ..      33     200 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00031
                                      EEEESSTTSSHHHHHHHHHHHH CS
                               AAA  1 vllyGppGtGKTllakavakel 22
                                      ++++Gp G+GK++l+k + + l
  gi|474934744|ref|YP_007688326.1| 33 ICIIGPNGVGKSTLVKCINRLL 54
                                      6899************997765 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00016     0.087      17      49 ..      29      59 ..      16     195 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                                      TSCSEEEEEEESTTSSHHHHHHHHCCSHCCCCC CS
                            NB-ARC 17 elqslvvalvGmgGvGKttlakqilnksdeveg 49
                                       ++  ++ + G  GvGK+tl+k i++ +  +eg
  gi|474934744|ref|YP_007688326.1| 29 RPG--LICIIGPNGVGKSTLVKCINRLLTPTEG 59
                                      566..899***************9987666665 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00011      0.06      25      57 ..      33      65 ..      20     105 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                      Mg_chelatase 25 lllvGppGsGKtmlakrlpsllpplseeealev 57
                                      + ++Gp G GK+ l k+++ ll+p + +  ++ 
  gi|474934744|ref|YP_007688326.1| 33 ICIIGPNGVGKSTLVKCINRLLTPTEGNVLIDD 65
                                      5689*******************9987766665 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0    0.0018         1      44      67 ..      27      50 ..       6      62 .. 0.83
   2 ?    2.0   0.1      0.27   1.5e+02      96     151 ..     146     201 ..     113     210 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0018
                         IstB_IS21 44 iekkenivllGpsGvGKshlaial 67
                                      i++   i+++Gp GvGKs l   +
  gi|474934744|ref|YP_007688326.1| 27 IDRPGLICIIGPNGVGKSTLVKCI 50
                                      6677789***********997765 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.27
                         IstB_IS21  96 dgklaralkrllkvdllilDdlg.llpl.dqaeaellfeviekryerrsiiitsnlpf 151
                                       + +lar l+  + +d+lilD+    l++  q e + l++ i++  + ++++i+ +l++
  gi|474934744|ref|YP_007688326.1| 146 KVSLARGLA--QSPDILILDEPTaNLDIkHQVEVTRLMRDISHEKNITTVMISHDLNV 201
                                       334444443..3569*****95413344145566777777777777777788777665 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00016     0.088      26     123 ..      33     151 ..      20     195 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00016
                             DUF87  26 lAilgsTGsGKSntvavLleellekkgatililD.pHGEYgkal.............ekllsekvkvitpspsa... 85 
                                       ++i+g  G+GKS++v+ + + l     +++li D p +EY + +                             a   
  gi|474934744|ref|YP_007688326.1|  33 ICIIGPNGVGKSTLVKCINRLLT-PTEGNVLIDDkPISEYRTRDlatvvgyvpafstD-------------DFAmsv 95 
                                       579999***********977777.5555666655778899999944444444433331.............222333 PP

                             DUF87  86 ................kdkelkinpwsldpeelldllee..ddkpaaavqrsvlee 123
                                                         + l+i +  l+   + +l++   d+ +a + q+  l++
  gi|474934744|ref|YP_007688326.1|  96 vdtvmmgrhpyrrmgsTREDLHIVYEVLKELGITHLAMRnfDELSAGQHQKVSLAR 151
                                       33344444445567666777777777777777777777765555555555555555 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00091      0.51      22      57 ..      31      66 ..       7     101 .. 0.80
   2 ?   -2.2   0.0       2.6   1.5e+03     110     128 ..     178     196 ..     117     213 .. 0.59
   3 ?    0.3   0.0      0.46   2.6e+02     336     361 ..     240     265 ..     220     266 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00091
                            AAA_10 22 sasliiGdlGnGKSvlakllvlyisllggkaliiDp 57
                                          iiG+ G GKS l+k +   ++  +g +li D+
  gi|474934744|ref|YP_007688326.1| 31 GLICIIGPNGVGKSTLVKCINRLLTPTEGNVLIDDK 66
                                      44589****************999999999887553 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.6
                            AAA_10 110 lelllgvkkkesekkaals 128
                                       + l+ +++++++  ++++s
  gi|474934744|ref|YP_007688326.1| 178 TRLMRDISHEKNITTVMIS 196
                                       2223333333333333333 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.46
                            AAA_10 336 qCLmkDllgrvgkikidvlfeellea 361
                                       +CL+ D  gr  +i  ++++ee ++a
  gi|474934744|ref|YP_007688326.1| 240 NCLIVDDNGRPHVILQEPIPEEEFRA 265
                                       7********************98776 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00027      0.15       1      31 [.      32      65 ..      32     200 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00027
                            AAA_33  1 lvllvGlpGsGKstlaerllkklg...avllssd 31
                                      l+ ++G++G+GKstl++ + + l+   + +l  d
  gi|474934744|ref|YP_007688326.1| 32 LICIIGPNGVGKSTLVKCINRLLTpteGNVLIDD 65
                                      6889***********9854333333335555555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00026      0.14       2      23 ..      32      53 ..      31      60 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00026
                                      CEEEEC-TTTCHHHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqklala 23
                                      l+++ G++G+GK+tL++ + ++
  gi|474934744|ref|YP_007688326.1| 32 LICIIGPNGVGKSTLVKCINRL 53
                                      689*************988765 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00043      0.24       2      24 ..      33      55 ..      32      63 .. 0.86
   2 ?   -1.5   0.0       3.6     2e+03      94     103 ..     155     164 ..     135     205 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00043
                                      EEEE--TTSSHHHHHHHHHHHH. CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellk 24
                                      ++i Gp GvGK+Tlvk + +ll 
  gi|474934744|ref|YP_007688326.1| 33 ICIIGPNGVGKSTLVKCINRLLT 55
                                      6799************9999885 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.6
                                       HHH-EEEE-- CS
                          NTPase_1  94 seadviviDE 103
                                       +++d++++DE
  gi|474934744|ref|YP_007688326.1| 155 QSPDILILDE 164
                                       6677777777 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00035       0.2       3      50 ..      18      64 ..      16      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00035
                        Zeta_toxin  3 ellkdkkypsqerPklillgGqpGAGKselaellkdelerqgnvvrld 50
                                      ++l+d++  s +rP li + G  G GKs+l + +++ l+++++ v +d
  gi|474934744|ref|YP_007688326.1| 18 KILRDIN-LSIDRPGLICIIGPNGVGKSTLVKCINRLLTPTEGNVLID 64
                                      5677776.7779***************************888888887 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00096      0.54       4      34 ..      32      61 ..      29      90 .. 0.71
   2 ?   -0.6   0.0       2.2   1.2e+03      32      73 ..     130     165 ..     107     195 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00096
                            AAA_14  4 ilvitGaRrvGKTtllkqlikellvkkesil 34
                                      +++i G+  vGK+tl+k +i++ll++ e  +
  gi|474934744|ref|YP_007688326.1| 32 LICIIGPNGVGKSTLVK-CINRLLTPTEGNV 61
                                      689************85.5556664444444 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.2
                            AAA_14  32 silyinldderdkkladpekllelileklkeekktylflDEi 73 
                                       +    n+d+ +  ++++  +l + + +        +l+lDE 
  gi|474934744|ref|YP_007688326.1| 130 HLAMRNFDELSAGQHQKV-SLARGLAQ-----SPDILILDEP 165
                                       444455555544443332.22222222.....4578888885 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00065      0.37       2      20 ..      33      51 ..      32      92 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00065
                            AAA_28  2 ivitGgestGKTtlleaLa 20
                                      i+i+G+ + GK+tl++ ++
  gi|474934744|ref|YP_007688326.1| 33 ICIIGPNGVGKSTLVKCIN 51
                                      9*************98665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0    0.0006      0.34      20      49 ..      32      61 ..      23     193 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0006
                            AAA_30 20 vavltGpAGtGKttalkalreaweaaggrv 49
                                      + ++ Gp G GK+t++k ++++++  +g+v
  gi|474934744|ref|YP_007688326.1| 32 LICIIGPNGVGKSTLVKCINRLLTPTEGNV 61
                                      67899**************99998886555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        32  (0.00178482); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              32  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 1781.79
//
Query:       gi|474934745|ref|YP_007688327.1|  [L=199]
Description: isochorismatase family protein Amidases nicotinamidase -like protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.8e-20   72.0   0.0    9.2e-20   71.5   0.0    1.2  1  Isochorismatase  Isochorismatase family
  ------ inclusion threshold ------
      0.047   12.0   0.1        1.5    7.0   0.0    2.0  2  DUF2070          Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> Isochorismatase  Isochorismatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.5   0.0     1e-23   9.2e-20       2     152 ..      18     152 ..      17     164 .. 0.94

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 1e-23
                   Isochorismatase   2 alvviDmqndfveegvkeseeisavveninkllkaarkagipviftrdvheleevkgdlderkaaphfkpgttgael 78 
                                       +l+v+D+qn f++e +++++e++a++  ++k +ka+ +++  ++++++  +                 k+g+++ +l
  gi|474934745|ref|YP_007688327.1|  18 CLIVVDLQNCFFDEDRPRTPEDDAAIGVVAKTVKAFNENSRDIFVVKHIGS----------------HKEGPSDDRL 78 
                                       69*************************************************................9********* PP

                   Isochorismatase  79 vpelaplegdvvvdKtrfsafagtdldeiLkelgiktivlaGiatdvCVeatardaldlGyevvvvsDAvaals 152
                                       v+e++ l    +  K +++af +t l +++k++g +  +++G+ t++CV+a+  +al+++  +++++ ++  + 
  gi|474934745|ref|YP_007688327.1|  79 VEEIRDLVPREFTGKFHMGAFQDTCLADLIKSKGYDSAIICGAYTEYCVMASYWSALEHDIAPFLLAGGTVPYR 152
                                       ********999999***********************************************9999887776555 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0   0.00017       1.5     360     395 ..      19      54 ..       1      59 [. 0.77
   2 ?    4.5   0.0   0.00095       8.5     263     294 ..      55      89 ..      46     101 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00017
                           DUF2070 360 vllVDaHNsfseeagevlpgsedaeeliraaekale 395
                                       +++VD +N+f +e+ + +p+++ a   +    ka++
  gi|474934745|ref|YP_007688327.1|  19 LIVVDLQNCFFDEDRPRTPEDDAAIGVVAKTVKAFN 54 
                                       69**************99998888777766666665 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.00095
                           DUF2070 263 el...vlvlHgtatHdfNlvserevekiveavkea 294
                                       e+   ++v + +++H++ ++++r ve+i + v ++
  gi|474934745|ref|YP_007688327.1|  55 ENsrdIFVVKHIGSHKEGPSDDRLVEEIRDLVPRE 89 
                                       334559**********************9998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.36s 00:00:00.94 Elapsed: 00:00:00.56
# Mc/sec: 1066.18
//
Query:       gi|474934746|ref|YP_007688328.1|  [L=369]
Description: hypothetical protein TALC_01181 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.023   14.6   0.4       0.21   11.6   0.1    2.3  2  ADH_zinc_N  Zinc-binding dehydrogenase


Domain annotation for each model (and alignments):
>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0     0.031   5.5e+02      57      81 ..     129     153 ..     110     196 .. 0.83
   2 ?   11.6   0.1   1.2e-05      0.21       3      62 ..     234     301 ..     234     304 .. 0.67

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.031
                                       SSEEEEEESSCSHHHHHHHHHCEEE CS
                        ADH_zinc_N  57 egvdvvfecvGsgatleaalkllkp 81 
                                       +  dvv+ +vGs +t ++ +++l+ 
  gi|474934746|ref|YP_007688328.1| 129 KEKDVVMITVGSASTTSTGINVLNL 153
                                       5669999999999999999998875 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 1.2e-05
                                       HHHHHHHHHHTT-EEEEEESSHHHHHHHHHT.......TESEEEET..TTC.HHHHHHHHHTTTSSEEEE CS
                        ADH_zinc_N   3 GlaavqlAkalGaeviavdsseeklelakkl.......Gadeviny..kea.dlverikeltggegvdvv 62 
                                       G+++  lA a+Ga+v+++d s+e   +a+ l       G d v+ +  + a    +++++   g++v++v
  gi|474934746|ref|YP_007688328.1| 234 GSLGTSLALAAGANVVTIDASKEP-TYAANLtdligtyGTDTVVFAdgSMAsARLSELRDKV-GNDVKIV 301
                                       788999****************94.5555555556666988888884322223444444444.6666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 2133.83
//
Query:       gi|474934747|ref|YP_007688329.1|  [L=333]
Description: ABC-type Fe3+-siderophore transport system, permease component [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.5e-87  293.6  33.1    1.8e-87  293.2  33.1    1.0  1  FecCD       FecCD transport family
    0.00024   20.7  26.2    0.00024   20.7  26.2    2.1  2  ABC-3       ABC 3 transport family


Domain annotation for each model (and alignments):
>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  293.2  33.1   2.1e-91   1.8e-87       3     311 ..      13     324 ..       9     325 .. 0.96

  Alignments for each domain:
  == domain 1  score: 293.2 bits;  conditional E-value: 2.1e-91
                             FecCD   3 llllllslllgav..kispsevfeallgkadsleaeivlelrlprvlaallvGaaLavaGallQtvtrNpLadPsil 77 
                                       +++++l l+  ++  ++s+sevf+al+g+a+ ++++ v e  lprv ++++vGa+La++G+ +Q+v++NpLa+P+il
  gi|474934747|ref|YP_007688329.1|  13 VVCVFLDLSWVSAtkSYSFSEVFDALFGNASWSANKNVREEGLPRVTIGIFVGAGLAISGCAMQAVFKNPLASPYIL 89 
                                       66777777555443499*************9999999**************************************** PP

                             FecCD  78 Gissgaalgavlallll.lgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsaltsllll 153
                                       G+ssga++ga++++l+  ++ + ++++p++af+  + +++lv++++r ++++++++liL+G+avs+llsal+s+l++
  gi|474934747|ref|YP_007688329.1|  90 GLSSGASVGAAVGMLFAiSFIPVAIQVPALAFVTCFGTMMLVYTMSRIGGTIRTETLILSGVAVSSLLSALVSFLTF 166
                                       ***************998899999****************************************************9 PP

                             FecCD 154 llneealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrllllllval 230
                                       +   ++l+ i+fw++G+ls+a+w+++++++++++++ ++l+  a++l++++lgd  A  lGv+v+++rl++l+l+++
  gi|474934747|ref|YP_007688329.1| 167 I-AGDQLSGIVFWTMGDLSHADWEEICFAAPIIVVSSVFLITQAKNLNVMMLGDIHALDLGVDVKKTRLFVLILTTF 242
                                       9.779************************************************************************ PP

                             FecCD 231 ltavavalvGpigFvGLivPhiarllvgadhrkllplsallGallllladllarllls.ptelpvgivtaliGapff 306
                                       ++a+av++vG+igF+GL++Phi+r+l+g+d+r ++pls++ Ga+++l++d+l+++++    +lp+g+ taliGap+f
  gi|474934747|ref|YP_007688329.1| 243 IVAAAVSFVGIIGFIGLVIPHILRMLLGPDNRVIMPLSMVGGACFILICDYLSHIVAPlYGTLPIGVTTALIGAPIF 319
                                       *********************************************************95566*************** PP

                             FecCD 307 iylll 311
                                       iyll+
  gi|474934747|ref|YP_007688329.1| 320 IYLLI 324
                                       ***97 PP

>> ABC-3  ABC 3 transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.2     0.053   4.8e+02     176     192 ..       3      19 ..       1      50 [. 0.53
   2 !   20.7  26.2   2.7e-08   0.00024      39     236 ..      92     299 ..      57     325 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.053
                             ABC-3 176 ialavvvalqavGviLv 192
                                       ial+v va+ +v v L 
  gi|474934747|ref|YP_007688329.1|   3 IALTVLVAVTVVCVFLD 19 
                                       55555555555555443 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 2.7e-08
                             ABC-3  39 sHaalpGvalayllgvn......lllgailvgliaavalellkrk....tklkedtaigivlsvflalglvlvslik 105
                                       s  a  G a+++l++++       + + ++v+ +++++l++ +++     ++++ ++ g+ +s+ l+  + +++ i 
  gi|474934747|ref|YP_007688329.1|  92 SSGASVGAAVGMLFAISfipvaiQVPALAFVTCFGTMMLVYTMSRiggtIRTETLILSGVAVSSLLSALVSFLTFIA 168
                                       5556678888888888866655422334455555666555554441111566666667*********9888999988 PP

                             ABC-3 106 k.skvdldsyLfGniltisqedliliaiieavvllllllfwkelllitfdeelAkveglsvkllkllllalialavv 181
                                       +   +++  + +G++   + e+++  a i +v  + l+ + k+l ++++   +A   g+ vk  +l  l+l+   v+
  gi|474934747|ref|YP_007688329.1| 169 GdQLSGIVFWTMGDLSHADWEEICFAAPIIVVSSVFLITQAKNLNVMMLGDIHALDLGVDVKKTRLFVLILTTFIVA 245
                                       767788899999***************************************************************** PP

                             ABC-3 182 valqavGviLvialliiPaatArrltrslesllivAillglvsvvaGlllSyyld 236
                                       +a+ +vG+i  i l +iP ++ ++l+ + + ++ ++++ g+ ++++  +lS ++ 
  gi|474934747|ref|YP_007688329.1| 246 AAVSFVGIIGFIGL-VIPHILRMLLGPDNRVIMPLSMVGGACFILICDYLSHIVA 299
                                       *********99996.78*******************************9998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       969  (0.0540465); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2006.69
//
Query:       gi|474934748|ref|YP_007688330.1|  [L=263]
Description: ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase component [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.8e-34  117.1   0.0    1.1e-33  116.7   0.0    1.2  1  ABC_tran      ABC transporter
    5.5e-11   42.8   0.7    3.5e-06   27.1   0.0    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    1.2e-05   25.2   0.0      0.085   12.5   0.0    2.1  2  AAA_15        AAA ATPase domain
    0.00011   21.7   0.5     0.0036   16.8   0.5    2.1  1  SMC_N         RecF/RecN/SMC N terminal domain
    0.00011   22.8   0.0    0.00013   22.6   0.0    1.2  1  AAA_23        AAA domain
    0.00016   22.1   0.1     0.0023   18.4   0.1    2.3  1  AAA           ATPase family associated with various cellular 
    0.00032   21.1   0.0    0.00051   20.5   0.0    1.4  1  AAA_16        AAA ATPase domain
    0.00032   21.0   0.2      0.033   14.5   0.0    2.2  2  AAA_22        AAA domain
    0.00054   18.9   0.2        1.2    7.9   0.1    3.0  2  ABC_ATPase    Predicted ATPase of the ABC class
    0.00054   19.9   0.0     0.0018   18.2   0.0    1.8  1  ATPase_2      ATPase domain predominantly from Archaea
     0.0007   19.6   0.0     0.0014   18.6   0.0    1.4  1  Rad17         Rad17 P-loop domain
      0.001   19.1   0.0     0.0038   17.2   0.0    1.9  2  AAA_14        AAA domain
     0.0018   18.5   0.1      0.033   14.5   0.0    2.3  2  AAA_28        AAA domain
     0.0029   18.2   0.1     0.0062   17.1   0.1    1.9  1  AAA_18        AAA domain
      0.003   16.8   0.0     0.0052   16.1   0.0    1.3  1  Zeta_toxin    Zeta toxin
     0.0067   15.6   0.1      0.017   14.3   0.0    1.7  2  NB-ARC        NB-ARC domain
     0.0084   14.9   0.0      0.071   11.9   0.0    2.0  2  Adeno_IVa2    Adenovirus IVa2 protein
     0.0087   16.2   0.0      0.012   15.7   0.0    1.5  1  AAA_33        AAA domain
  ------ inclusion threshold ------
      0.022   14.7   0.0      0.054   13.4   0.0    1.7  1  NACHT         NACHT domain
      0.026   14.3   0.0      0.097   12.4   0.0    1.9  2  AAA_29        P-loop containing region of AAA domain
      0.041   13.3   0.0       0.07   12.5   0.0    1.3  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.057   13.1   0.0      0.064   12.9   0.0    1.4  1  ATP-synt_ab   ATP synthase alpha/beta family, nucleotide-bind
      0.096   12.3   0.0       0.17   11.5   0.0    1.5  1  cobW          CobW/HypB/UreG, nucleotide-binding domain
       0.11   13.0   0.1        1.1    9.6   0.0    2.3  2  AAA_17        AAA domain
       0.11   12.4   0.0       0.73    9.8   0.0    2.1  2  AAA_5         AAA domain (dynein-related subfamily)
       0.12   12.7   0.1       0.82    9.9   0.1    2.1  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
       0.12   12.0   0.0        1.1    8.9   0.0    2.0  2  SRP54         SRP54-type protein, GTPase domain
       0.13   12.1   0.0       0.31   11.0   0.0    1.6  1  MobB          Molybdopterin guanine dinucleotide synthesis pr
       0.15   12.5   0.0       0.26   11.7   0.0    1.5  1  RNA_helicase  RNA helicase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.7   0.0   1.8e-36   1.1e-33       1     136 [.      19     167 ..      19     168 .. 0.96

  Alignments for each domain:
  == domain 1  score: 116.7 bits;  conditional E-value: 1.8e-36
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l+ ++l+++ege+++i+G+nG+GK+tLl+ l ++l+p  G + ldg d+++++++ + k ++v+pq++++    tvr
  gi|474934748|ref|YP_007688330.1|  19 LDGIDLDIREGEVLGILGPNGCGKTTLLRNLNKNLSPYGGCVMLDGSDMEDISKRDVAKTVAVVPQTNEIRFSFTVR 95 
                                       6899************************************************************************* PP

                                       HH.................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx.................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       e                  e+++ ie+a++k g + ++d+++    +++SgG++qr  +ara+++kpk+ll+DEpt
  gi|474934748|ref|YP_007688330.1|  96 EIvsmgrmpfqglmsgesrEDRDIIEEAMRKTGVDRFADRRI----NTMSGGERQRAIIARAIAQKPKILLMDEPT 167
                                       **************9987555555******************....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.2   3.7e-05     0.023       3      17 ..      33      47 ..      31      96 .. 0.88
   2 !   27.1   0.0   5.6e-09   3.5e-06     220     302 ..     123     203 ..      83     204 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.7e-05
                            AAA_21  3 vliGpNgsGKSnLLd 17
                                      ++ GpNg+GK++LL+
  gi|474934748|ref|YP_007688330.1| 33 GILGPNGCGKTTLLR 47
                                      799***********8 PP

  == domain 2  score: 27.1 bits;  conditional E-value: 5.6e-09
                            AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQvilt 295
                                        ++    ++  ++ ++ +S G ++  a+++  +++ +  ++ll DEp ++L+ +++   l l+ +ls+ +g  v+++
  gi|474934748|ref|YP_007688330.1| 123 AMRKTGVDRFADRRINTMSGGERQR-AIIARAIAQKP--KILLMDEPTLHLDVSMQFDALNLVYRLSKeEGLTVVIV 196
                                       66666667777888999********.99998888776..8***********************8888889******* PP

                            AAA_21 296 THSplll 302
                                       +H+ + +
  gi|474934748|ref|YP_007688330.1| 197 SHDLSMV 203
                                       ***8876 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0    0.0003      0.19      19      45 ..      24      51 ..      18     125 .. 0.75
   2 !   12.5   0.0   0.00014     0.085     318     369 .]     152     203 ..      67     203 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0003
                            AAA_15 19 idlsee.ltvliGkNnsGKSsilealdl 45
                                      +d+ e  +  + G+N++GK+++l+ l++
  gi|474934748|ref|YP_007688330.1| 24 LDIREGeVLGILGPNGCGKTTLLRNLNK 51
                                      444444577799***********99954 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00014
                            AAA_15 318 dekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSphii 369
                                       + + +k++ill++EP +hL  ++q    +l ++l++++   v+i +H   ++
  gi|474934748|ref|YP_007688330.1| 152 RAIAQKPKILLMDEPTLHLDVSMQFDALNLVYRLSKEEGLTVVIVSHDLSMV 203
                                       568899********************************99*******87775 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.5   5.8e-06    0.0036      26     211 ..      31     213 ..      19     220 .. 0.60

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.8e-06
                                       EEEEEESTTSSHHHHHHHHHHHCTT..TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  26 ftaivGpNGSGKsnlldAilFvLGer.sakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisr 101
                                       +  i+GpNG+GK+ ll  +   L+       l  ++++d+ ++     + + a v  t  ne + + + +e vs+ r
  gi|474934748|ref|YP_007688330.1|  31 VLGILGPNGCGKTTLLRNLNKNLSPYgGCVMLDGSDMEDISKR---DVAKTVAVVPQT--NEIRFSFTVREIVSMGR 102
                                       56799**************999986523446777777776555...222222333222..22222222222233333 PP

                                       E.....EETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-H CS
                                       x.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 102 r.....vkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDe 173
                                             ++ + + +  i ++ ++k+ v + +++ +i  +++SgGe++ + +a  +A    ++  + l+De   +LD 
  gi|474934748|ref|YP_007688330.1| 103 MpfqglMSGESREDRDIIEEAMRKTGVDR-FADRRI--NTMSGGERQRAIIARAIA----QKPKILLMDEPTLHLDV 172
                                       30000022233344455555555555544.344444..58*****99776665443....4455889********** PP

                                       HHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC-.SCEEEE CS
                                       xxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx.xxxxxx RF
                             SMC_N 174 knvkkvaellkekskn..aQfivislreemleka.dklvgv 211
                                       +      +l+ + sk+    ++++s++  m+++  d+++ +
  gi|474934748|ref|YP_007688330.1| 173 SMQFDALNLVYRLSKEegLTVVIVSHDLSMVARYcDRILMI 213
                                       **999999999888774467777777777776553555444 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   2.1e-07   0.00013       2      82 ..       4      93 ..       3     170 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 2.1e-07
                            AAA_23  2 LkienfrsfrdqeidF........skgltlItGpNGaGKTTildAiklaL..ygetprlsrksgrgfeksdveiesegk 70
                                      L+ +++r + d++i +        +  +  I GpNG+GKTT+l+ +   L  yg    l++++ +++ k+dv+  + + 
  gi|474934748|ref|YP_007688330.1|  4 LSTKGLRYLYDKHIVLdgidldirEGEVLGILGPNGCGKTTLLRNLNKNLspYGGCVMLDGSDMEDISKRDVAK-TVAV 81
                                      67788888888887776666688888899**************9888555447777777777777777777773.3456 PP

                            AAA_23 71 vkayveltfenk 82
                                      v++  e++f+ +
  gi|474934748|ref|YP_007688330.1| 82 VPQTNEIRFSFT 93
                                      666666665554 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   3.7e-06    0.0023       3      66 ..      34     165 ..      32     170 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.7e-06
                                       EESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSS........................................ CS
                               AAA   3 lyGppGtGKTllakavakelg..vefleisgsellsk........................................ 37 
                                       + Gp G+GKT+l + + k+l+    ++ ++gs++ +                                         
  gi|474934748|ref|YP_007688330.1|  34 ILGPNGCGKTTLLRNLNKNLSpyGGCVMLDGSDMEDIskrdvaktvavvpqtneirfsftvreivsmgrmpfqglms 110
                                       57*****************9643447777777777223466666677777777777777777777778888888877 PP

                                       ...........................STTHHHHHHHHHHHHHHHTSTSEEEEEET CS
                               AAA  38 ...........................yvgesekkirelfkeakekakpsilfiDE 66 
                                                                      + ++ r+++++a +++ p+il++DE
  gi|474934748|ref|YP_007688330.1| 111 gesredrdiieeamrktgvdrfadrriNTMSGGERQRAIIARAIAQK-PKILLMDE 165
                                       78888888888888888777777777755566666677776666665.78888887 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   8.3e-07   0.00051      24     142 ..      29     164 ..      19     196 .. 0.61

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 8.3e-07
                            AAA_16  24 pelvllsGesGvGKsslvrellralekdggif.lrgkcdql..esa....ipysalaqalareellrqllde..... 88 
                                       +e++ + G+ G+GK++l+r l + l+  gg + l g   +   +++    ++ ++ ++ + ++  +r++ ++     
  gi|474934748|ref|YP_007688330.1|  29 GEVLGILGPNGCGKTTLLRNLNKNLSPYGGCVmLDGSDMEDisKRDvaktVAVVPQTNEIRFSFTVREIVSMgrmpf 105
                                       477889********************997555466666666543334444222333333333333344444466677 PP

                            AAA_16  89 ..aesaeleawrekleealaavpelagaea........srllellkrllallsrderplvlvlD 142
                                         + s e +++r+ +eea++ ++ ++ a++        +r ++ ++r++      ++p +l++D
  gi|474934748|ref|YP_007688330.1| 106 qgLMSGESREDRDIIEEAMRKTGVDRFADRrintmsggERQRAIIARAI----A-QKPKILLMD 164
                                       7877888889999999998844444444445555333344444444544....3.556666666 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   5.4e-05     0.033       7      29 ..      31      53 ..      26      86 .. 0.87
   2 ?    4.5   0.1     0.062        38      54     128 ..     117     196 ..     106     201 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.4e-05
                            AAA_22  7 ilvvtGesGtGKTtllrrlleql 29
                                      +l + G+ G+GKTtllr+l ++l
  gi|474934748|ref|YP_007688330.1| 31 VLGILGPNGCGKTTLLRNLNKNL 53
                                      56689**************9987 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.062
                            AAA_22  54 kdllrellralglelka....erlsseell.ealeqalrarav...ielliiDEaqh.lr...seealeeLrsllnl 118
                                       +d+ +e  r++g+++ a    +      +     ++a+ ara    +++l+ DE    l+   + +al+ + +l++ 
  gi|474934748|ref|YP_007688330.1| 117 RDIIEEAMRKTGVDRFAdrriN-----TMSgGERQRAIIARAIaqkPKILLMDEPTLhLDvsmQFDALNLVYRLSK- 187
                                       6666667777777666643332.....222222233333333334457******9888988555************. PP

                            AAA_22 119 srkgvqliLv 128
                                        + g+++++v
  gi|474934748|ref|YP_007688330.1| 188 -EEGLTVVIV 196
                                       .999999876 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.0     0.005       3.1     241     266 ..      25      51 ..      19      55 .. 0.90
   2 !    7.9   0.1    0.0019       1.2     377     420 ..     179     222 ..     131     240 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.005
                                       EE-SS.EEEEEE-TTSSHHHHHHHHHH CS
                        ABC_ATPase 241 gipkG.vtlIvGggfhGKsTLLeAlek 266
                                        i++G v  I G++  GK+TLL+ l+k
  gi|474934748|ref|YP_007688330.1|  25 DIREGeVLGILGPNGCGKTTLLRNLNK 51 
                                       589999999**************9986 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0019
                                       HHCHHHHHHHH--EEEEEESS-GCCTTT-SEEEEEETTEEEE-H CS
                        ABC_ATPase 377 vdrvrelykklgvstilvvggsgdyldvAdtvilmeeykpkdvt 420
                                       +++v +l k+ g+++++v+  ++   +  d++++++++k++ + 
  gi|474934748|ref|YP_007688330.1| 179 LNLVYRLSKEEGLTVVIVSHDLSMVARYCDRILMIKDHKVHSIG 222
                                       5688899999*****************************99875 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   2.9e-06    0.0018      21     172 ..      30     205 ..      24     220 .. 0.58

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.9e-06
                          ATPase_2  21 eiyfiYGpegsGKtaLlkeiienledkdkyviy.yialreesiskldefie......eeeekkklekal........ 82 
                                       e++ i Gp g+GKt+Ll+++ +nl+ ++  v+   ++++++s   + ++++      e                   
  gi|474934748|ref|YP_007688330.1|  30 EVLGILGPNGCGKTTLLRNLNKNLSPYGGCVMLdGSDMEDISKRDVAKTVAvvpqtnE----I-----Rfsftvrei 97 
                                       677799*****************98877533321234444444444444445533221....2.....122223455 PP

                          ATPase_2  83 .......................giavpkaeleeilk...eksklvfkaielllekikkkgkkiiiiiDelqklidl 133
                                                               +a++k+ ++++ +   ++    +++ + + ++i +k k  i+++De     d+
  gi|474934748|ref|YP_007688330.1|  98 vsmgrmpfqglmsgesredrdiiEEAMRKTGVDRFADrriNTMSGGERQRAIIARAIAQKPK--ILLMDEPTLHLDV 172
                                       66666666666666666666666666666666666554333333334444445555555544..7777776555544 PP

                          ATPase_2 134 glngaellvkeLlnliesltkekhlcvviclsSeglfie 172
                                        ++       + lnl+ +l+ke+ l+vvi++   +++ +
  gi|474934748|ref|YP_007688330.1| 173 SMQ------FDALNLVYRLSKEEGLTVVIVSHDLSMVAR 205
                                       444......556677777777777777777766666666 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   2.3e-06    0.0014      38      70 ..      22      54 ..      12      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.3e-06
                             Rad17 38 dvLesrkkriLLisGPsGCgkstvvkvLskelg 70
                                        L+ r+ ++L i GP GCgk+t ++ L k+l+
  gi|474934748|ref|YP_007688330.1| 22 IDLDIREGEVLGILGPNGCGKTTLLRNLNKNLS 54
                                      5577777889********************986 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   6.2e-06    0.0038       3      49 ..      30      75 ..      28      91 .. 0.81
   2 ?   -1.2   0.0       3.2     2e+03      55      74 ..     148     167 ..     120     199 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 6.2e-06
                            AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladp 49
                                      ++l i G+  +GKTtll++l k+l  +   ++ ++  d +d +++d 
  gi|474934748|ref|YP_007688330.1| 30 EVLGILGPNGCGKTTLLRNLNKNLS-PYGGCVMLDGSDMEDISKRDV 75
                                      7899****************98887.888888888888888766654 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.2
                            AAA_14  55 lilek.lkeekktylflDEiq 74 
                                       +i ++ + + k ++l++DE  
  gi|474934748|ref|YP_007688330.1| 148 AIIARaIAQ-KPKILLMDEPT 167
                                       333332444.77888888855 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   5.3e-05     0.033       4      22 ..      34      52 ..      32      96 .. 0.79
   2 ?    1.6   0.0      0.46   2.8e+02      32      84 ..     117     169 ..     113     192 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.3e-05
                            AAA_28  4 itGgestGKTtlleaLaar 22
                                      i+G+ ++GKTtll++L+++
  gi|474934748|ref|YP_007688330.1| 34 ILGPNGCGKTTLLRNLNKN 52
                                      89**************987 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.46
                            AAA_28  32 reileeklakgedalpwvedllafaervleeqleeeaaa..aankvlfcDrglld 84 
                                       r+i+ee ++k++ +  + +++++  ++ +  q++  a+a  +++k+l++D  +l 
  gi|474934748|ref|YP_007688330.1| 117 RDIIEEAMRKTGVDRFA-DRRINTMSGGE-RQRAIIARAiaQKPKILLMDEPTLH 169
                                       78999999988887777.46666666633.4444555555699999999987765 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1     1e-05    0.0062       3      29 ..      34      73 ..      32     206 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1e-05
                            AAA_18  3 ltGtpGvGKttlakeLskrl.gf............gvnlr 29
                                      + G+ G+GKttl ++L+k l  +             +  r
  gi|474934748|ref|YP_007688330.1| 34 ILGPNGCGKTTLLRNLNKNLsPYggcvmldgsdmeDISKR 73
                                      89***************99866677777766666433333 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   8.5e-06    0.0052      23      56 ..      36      69 ..      29     106 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.5e-06
                        Zeta_toxin 23 GqpGAGKselaellkdelerqgnvvrldpDdlRe 56
                                      G  G+GK++l++ l+++l ++g++v ld+ d+  
  gi|474934748|ref|YP_007688330.1| 36 GPNGCGKTTLLRNLNKNLSPYGGCVMLDGSDMED 69
                                      778*************************999865 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   2.7e-05     0.017      21      46 ..      30      55 ..      21      99 .. 0.88
   2 ?   -2.1   0.0       2.8   1.7e+03      86     110 ..     140     164 ..     113     205 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.7e-05
                                      EEEEEEESTTSSHHHHHHHHCCSHCC CS
                            NB-ARC 21 lvvalvGmgGvGKttlakqilnksde 46
                                       v+++ G  G+GKttl+++ +++++ 
  gi|474934748|ref|YP_007688330.1| 30 EVLGILGPNGCGKTTLLRNLNKNLSP 55
                                      499****************9998765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.8
                                       S-STTSHHHHHHHHCCCTTEEEEEE CS
                            NB-ARC  86 keeveslkrklvrlLltkrfllvlD 110
                                       ++ +e     + r++ +k  +l++D
  gi|474934748|ref|YP_007688330.1| 140 MSGGERQRAIIARAIAQKPKILLMD 164
                                       4444434455677777887777777 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00011     0.071      88     121 ..      31      61 ..      10      77 .. 0.79
   2 ?    0.7   0.0      0.29   1.8e+02     186     265 ..     147     219 ..     141     226 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                        Adeno_IVa2  88 viGviyGPtGsGksqllrnlissklisPiPetvi 121
                                       v+G i GP G+Gk+ llrnl  +k +sP    v+
  gi|474934748|ref|YP_007688330.1|  31 VLG-ILGPNGCGKTTLLRNL--NKNLSPYGGCVM 61 
                                       666.56*************9..566777766665 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.29
                        Adeno_IVa2 186 knifvkaakrGpvaiildecmeklidkksvsklfhalPsklsakfkkctgfsvlvvlhnlnPrsdiagniadlkiqa 262
                                       ++i ++a ++ p  +++de       + +vs  f al   l  + +k  g +v++v h+l+  +  ++ i  +k + 
  gi|474934748|ref|YP_007688330.1| 147 RAIIARAIAQKPKILLMDEPT----LHLDVSMQFDAL--NLVYRLSKEEGLTVVIVSHDLSMVARYCDRILMIK-DH 216
                                       567777777777777777764....456899999999..5888899999*********9998888877777666.44 PP

                        Adeno_IVa2 263 klh 265
                                       k+h
  gi|474934748|ref|YP_007688330.1| 217 KVH 219
                                       555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0     2e-05     0.012       4      32 ..      34      66 ..      31     199 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2e-05
                            AAA_33  4 lvGlpGsGKstlaerllkklg....avllssdt 32
                                      + G++G+GK+tl+++l k+l     +v l+  +
  gi|474934748|ref|YP_007688330.1| 34 ILGPNGCGKTTLLRNLNKNLSpyggCVMLDGSD 66
                                      57**************99998888877777665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   8.8e-05     0.054       3      22 ..      32      51 ..      30      56 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.8e-05
                                      EEEEC-TTTCHHHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqklal 22
                                      + + G++G+GKTtLl+ l  
  gi|474934748|ref|YP_007688330.1| 32 LGILGPNGCGKTTLLRNLNK 51
                                      5689************9866 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00016     0.097      15      39 ..      22      46 ..      13      56 .. 0.81
   2 ?   -2.2   0.0       5.9   3.6e+03      45      58 ..     227     241 ..     225     242 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00016
                            AAA_29 15 htieidlkgatlltGpsGsGKSTll 39
                                       +++i++ ++  + Gp+G GK+Tll
  gi|474934748|ref|YP_007688330.1| 22 IDLDIREGEVLGILGPNGCGKTTLL 46
                                      567777555888************8 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.9
                            AAA_29  45 lLvpak.kvrfNkaa 58 
                                       +L+p++ +  fN  a
  gi|474934748|ref|YP_007688330.1| 227 VLTPESmREVFNVDA 241
                                       899999899999755 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00011      0.07      27     103 ..      34     110 ..      26     114 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                      Mg_chelatase  27 lvGppGsGKtmlakrlpsllpplseeealevakiasvagkkeeekllkrrpfraphhsaskaalvGggskpkpGeis 103
                                       ++Gp G+GKt l + l++ l+p     +l+ + ++ +++++ ++++   +  ++ + s +   +v  g+ p  G +s
  gi|474934748|ref|YP_007688330.1|  34 ILGPNGCGKTTLLRNLNKNLSPYGGCVMLDGSDMEDISKRDVAKTVAVVPQTNEIRFSFTVREIVSMGRMPFQGLMS 110
                                       78*************************************98888888888888899999999999988888888665 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0    0.0001     0.064      11      46 ..      26      61 ..      17     262 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.0001
                                      EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab 11 ivqGqrtlipgafgvGktvisqslskqsnsddaiiy 46
                                      i +G+ ++i+g +g+Gkt+++++l k+ +    +++
  gi|474934748|ref|YP_007688330.1| 26 IREGEVLGILGPNGCGKTTLLRNLNKNLSPYGGCVM 61
                                      678999******************999644434444 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00027      0.17       2      23 ..      31      52 ..      30      86 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00027
                                      EEEEEESTTCCHHHHHHHHHCT CS
                              cobW  2 vtvltGflGsGKTtLlnhllen 23
                                      v+++ G+ G GKTtLl++l +n
  gi|474934748|ref|YP_007688330.1| 31 VLGILGPNGCGKTTLLRNLNKN 52
                                      67899*************9876 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0    0.0018       1.1       1      24 [.      35      62 ..      35      79 .. 0.81
   2 ?    0.9   0.0      0.92   5.7e+02      46      66 ..     108     128 ..      88     168 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0018
                                      EE-TTSSHHHHHHHHHHHH....TEEEE CS
                            AAA_17  1 lGgPGsGKgtqceklveky....gfthl 24
                                      lG+ G+GK+t++++l +++    g  +l
  gi|474934748|ref|YP_007688330.1| 35 LGPNGCGKTTLLRNLNKNLspygGCVML 62
                                      79*************9988555555555 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.92
                                       HCTSHHHHHHHHHHHHHHHHH CS
                            AAA_17  46 mrklpleekkelqkeaaekia 66 
                                       ++ ++ +e++++ +ea++k  
  gi|474934748|ref|YP_007688330.1| 108 LMSGESREDRDIIEEAMRKTG 128
                                       334555555555555555443 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0    0.0012      0.73       4      23 ..      34      53 ..      32      98 .. 0.83
   2 ?   -0.1   0.0       1.3   8.3e+02      45      73 ..     137     165 ..     121     203 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0012
                                      EE--SSSSHHHHHHHGGGGB CS
                             AAA_5  4 LvGppGtgKselaerlaaal 23
                                      ++Gp G+gK++l + l + l
  gi|474934748|ref|YP_007688330.1| 34 ILGPNGCGKTTLLRNLNKNL 53
                                      68************999877 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.3
                                       B--.........------.--G-SEEEEES CS
                             AAA_5  45 reikngttslvdsplvra.aregeilvlDE 73 
                                       +++ +++ +++  ++ ra a++++il++DE
  gi|474934748|ref|YP_007688330.1| 137 INT-MSGGERQRAIIARAiAQKPKILLMDE 165
                                       232.44444444444444155888988888 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1    0.0013      0.82      17      42 ..     123     149 ..     113     184 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0013
                           SbcCD_C  17 r.dedgkekelsrssgtlSGGekqfla 42 
                                         +++g ++  +r+++t+SGGe+q ++
  gi|474934748|ref|YP_007688330.1| 123 AmRKTGVDRFADRRINTMSGGERQRAI 149
                                       35788888889************8654 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0018       1.1       5      38 ..      33      66 ..      30      75 .. 0.83
   2 ?    0.6   0.0      0.58   3.6e+02      92     148 ..     141     197 ..     104     202 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0018
                                      EEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                             SRP54  5 llvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                       ++G++G GKTt l  L + l+  g  v+l   D
  gi|474934748|ref|YP_007688330.1| 33 GILGPNGCGKTTLLRNLNKNLSPYGGCVMLDGSD 66
                                      589************9999988777777766655 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.58
                                       --SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEE CS
                             SRP54  92 aGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgvilt 148
                                       +G  ++ + + + +++  k++  de  l ld +++ +a++ +++ +++ g+t vi++
  gi|474934748|ref|YP_007688330.1| 141 SGGERQRAIIARAIAQKPKILLMDEPTLHLDVSMQFDALNLVYRLSKEEGLTVVIVS 197
                                       555555555666666667777788888999999999999999999999999999886 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00049      0.31       1      24 [.      31      54 ..      31      62 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00049
                              MobB  1 vlgivgksgsGKTtLleklipelk 24
                                      vlgi g +g+GKTtLl +l + l+
  gi|474934748|ref|YP_007688330.1| 31 VLGILGPNGCGKTTLLRNLNKNLS 54
                                      799**************9988876 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00042      0.26       3      23 ..      34      54 ..      32     100 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00042
                      RNA_helicase  3 lyGpsgeGKStlakeLakall 23
                                      + Gp+g+GK+tl ++L k+l+
  gi|474934748|ref|YP_007688330.1| 34 ILGPNGCGKTTLLRNLNKNLS 54
                                      68*************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 0.68u 0.35s 00:00:01.03 Elapsed: 00:00:00.53
# Mc/sec: 1494.36
//
Query:       gi|474934749|ref|YP_007688331.1|  [L=112]
Description: L-aspartate 1-decarboxylase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-41  141.2   0.0    1.4e-41  141.0   0.0    1.0  1  Asp_decarbox  Aspartate decarboxylase
  ------ inclusion threshold ------
      0.028   14.6   0.0        3.6    7.8   0.1    2.2  2  CDC48_N       Cell division protein 48 (CDC48), N-terminal do


Domain annotation for each model (and alignments):
>> Asp_decarbox  Aspartate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.0   0.0   1.5e-45   1.4e-41       5     114 ..       1     106 [.       1     107 [. 0.98

  Alignments for each domain:
  == domain 1  score: 141.0 bits;  conditional E-value: 1.5e-45
                                       EEEEEEEEEEXXEEETTXXXXEEEEHHHHHHCT--TTBEEEEEETTT--EEEEEEEEESTTTT-EEEEGGGGGG--T CS
                      Asp_decarbox   5 llksKihratvteaelnYeGSitideelleaagileyekvqvvnvnngeRletYvikgergsgviclnGaaarlvqv 81 
                                       +l+sKihratvtea+l+YeGSitid++ll+ ag++ +ekv+vv +++g+R+etY+++gergsg+i lnGaaarl++v
  gi|474934749|ref|YP_007688331.1|   1 MLRSKIHRATVTEARLDYEGSITIDADLLDGAGMWVGEKVTVVVIETGARFETYTLPGERGSGIIALNGAAARLASV 77 
                                       89*************************************************************************** PP

                                       T-EEEEEEEEEEEHHHHHH---EEEEE-TTS-E CS
                      Asp_decarbox  82 gdkviiiayaqleeeeakelkpkvvlvdeknri 114
                                       gdkvii+ y+ +++     +++kv+lvd++nr+
  gi|474934749|ref|YP_007688331.1|  78 GDKVIIMGYELTDD----PIRAKVLLVDQHNRV 106
                                       **********9988....679**********97 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1    0.0004       3.6      45      82 ..       9      44 ..       3      47 .. 0.80
   2 ?    4.6   0.0     0.004        36      53      82 ..      58      85 ..      51      88 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0004
                                      EEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEEEEE CS
                           CDC48_N 45 aivwpaepedegkgiIrmdgvtRknagvsiGdkVtVrk 82
                                      a v +a+ +   +g+I +d+ +   ag+ +G+kVtV  
  gi|474934749|ref|YP_007688331.1|  9 ATVTEARLD-Y-EGSITIDADLLDGAGMWVGEKVTVVV 44
                                      556666555.4.7**********************965 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.004
                                      TSTTTTEEEE-HHHHHHHT--TTEEEEEEE CS
                           CDC48_N 53 edegkgiIrmdgvtRknagvsiGdkVtVrk 82
                                       ++g giI+++g + + a  s+GdkV++  
  gi|474934749|ref|YP_007688331.1| 58 GERGSGIIALNGAAARLA--SVGDKVIIMG 85
                                      457899999999987776..6799999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.51
# Mc/sec: 666.03
//
Query:       gi|474934750|ref|YP_007688332.1|  [L=134]
Description: Ribonuclease HI [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      9e-14   51.4   0.0      1e-13   51.1   0.0    1.0  1  RVT_3     Reverse transcriptase-like
    6.2e-07   29.7   0.0      7e-07   29.5   0.0    1.1  1  RNase_H   RNase H


Domain annotation for each model (and alignments):
>> RVT_3  Reverse transcriptase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.1   0.0   1.2e-17     1e-13       3     113 ..       9     117 ..       7     126 .. 0.94

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 1.2e-17
                             RVT_3   3 dgafkkksgaggagvvirdsnGevllagaeklqgkasveeAElqALlrGLqlalklgirrlvvegDsktvvqllngr 79 
                                       dg  + + g +++++vi  +nG++++  +e   g  ++  AE+++L+  ++++ +lg  + ++  Ds+ v+++++g+
  gi|474934750|ref|YP_007688332.1|   9 DGGSRGNPGPSAFAIVIS-ENGKIIFEHSEF-LGVHTNNYAEYRGLIANIRKCIELGADEAEFIMDSQLVIRQMTGE 83 
                                       888889999999999986.79******9988.77889**************************************** PP

                             RVT_3  80 ekvksselanlldeirkllksfesvsvehipReq 113
                                        +vks ++  l++e+ +l++   +v+++ ++R++
  gi|474934750|ref|YP_007688332.1|  84 YRVKSADMVPLHNEAEELCELIPKVKFTNVRRSE 117
                                       ********************************86 PP

>> RNase_H  RNase H
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0   7.8e-11     7e-07       4      79 ..       4      82 ..       1     118 [. 0.73

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 7.8e-11
                                      EEEEEEEEEECTTTCEEEEEEECTT..EEEEEEEC.CCCHHHHHHHHHHHHHHH.TT.SC.SEEEEEES-HHHHHHHHC CS
                           RNase_H  4 vvvYtDGsclgnpgeggagavlykegarnisaple.eaqtnnraELsAvieaLk.alksd.ekvniytDSkYvvkgitq 79
                                      +  Y+DG ++gnpg++  ++v++++g+  ++++   +  tnn+aE + +i+ ++   + +  + + + DS+ v+  +t 
  gi|474934750|ref|YP_007688332.1|  4 LKCYSDGGSRGNPGPSAFAIVISENGKIIFEHSEFlGVHTNNYAEYRGLIANIRkCIELGaDEAEFIMDSQLVIRQMTG 82
                                      678*****************99877555666555579*****************4434335777899999999986664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 998.81
//
Query:       gi|474934751|ref|YP_007688333.1|  [L=277]
Description: TPR repeat protein, SEL1 subfamily [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      8e-29   99.4  15.4    3.4e-07   30.7   0.3    6.5  6  Sel1      Sel1 repeat
  ------ inclusion threshold ------
      0.037   14.8   0.0        1.8    9.3   0.0    2.3  2  DUF2877   Protein of unknown function (DUF2877)


Domain annotation for each model (and alignments):
>> Sel1  Sel1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0   0.00015       1.4       1      38 []      47      80 ..      47      80 .. 0.87
   2 !   22.8   0.6   1.2e-08   0.00011       2      38 .]      82     116 ..      81     116 .. 0.94
   3 !   30.7   0.3   3.8e-11   3.4e-07       3      38 .]     119     152 ..     118     152 .. 0.94
   4 !   21.5   0.1   3.1e-08   0.00027       3      31 ..     155     181 ..     154     183 .. 0.92
   5 !    8.1   0.3   0.00049       4.4       2      36 ..     187     218 ..     186     220 .. 0.85
   6 !   12.1   0.0   2.8e-05      0.25      15      38 .]     227     251 ..     221     251 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00015
                              Sel1  1 aeAmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38
                                      +++m  LG   ++ nG   p  +++A++++e A ++G+
  gi|474934751|ref|YP_007688333.1| 47 PASMVLLG--VILINGG--PEEKSEAVRLFEEAGKLGN 80
                                      57999999..7779995..7789************997 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 1.2e-08
                              Sel1   2 eAmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                       + + +LG  y+y  Glgv+kD+ k+ e y ++A++G+
  gi|474934751|ref|YP_007688333.1|  82 SGYRNLG--YCYAVGLGVEKDKAKGAEIYALSADMGN 116
                                       6789***..**************************97 PP

  == domain 3  score: 30.7 bits;  conditional E-value: 3.8e-11
                              Sel1   3 AmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                       Am++LG   +y +G gv++D ekA+++y  +Ae+G+
  gi|474934751|ref|YP_007688333.1| 119 AMCNLG--VMYSFGNGVEQDDEKAFQCYLASAEKGY 152
                                       9*****..777***********************96 PP

  == domain 4  score: 21.5 bits;  conditional E-value: 3.1e-08
                              Sel1   3 AmyrLGmfylylnGlgvpkDpekAiewye 31 
                                        m +LG  ++yl G+g+ kD+ +A++w++
  gi|474934751|ref|YP_007688333.1| 155 GMTNLG--EYYLWGRGTLKDVAQAEKWFH 181
                                       599***..888****************96 PP

  == domain 5  score: 8.1 bits;  conditional E-value: 0.00049
                              Sel1   2 eAmyrLGmfylylnGlgvpk.DpekAiewyekAAeq 36 
                                        A yrL+  ++yl+    ++ Dpe +  ++e+A+e+
  gi|474934751|ref|YP_007688333.1| 187 RADYRLA--EIYLDEP--DWkDPEIGNAYLERACEK 218
                                       6789***..8889995..778*************97 PP

  == domain 6  score: 12.1 bits;  conditional E-value: 2.8e-05
                              Sel1  15 nGlgvpk.DpekAiewyekAAeqGd 38 
                                       +G  +++ D+ekAi +y  AA++G+
  gi|474934751|ref|YP_007688333.1| 227 YGETIEAaDREKAISLYNEAASKGN 251
                                       67766666***************97 PP

>> DUF2877  Protein of unknown function (DUF2877)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.017   1.6e+02      42      99 ..      24      84 ..       2      92 .. 0.66
   2 ?    9.3   0.0    0.0002       1.8      47      95 ..     203     251 ..     168     256 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.017
                           DUF2877 42 akakkrttdvS..aalLkaalegefseellallkalsseeeeel.ekalekllaiGhtSGa 99
                                      ++ ++ ++d+S  +++L++  +  +s  ll ++    + ee+++  + +e+  ++G++SG 
  gi|474934751|ref|YP_007688333.1| 24 KAYESGKQDLSeeKEMLRKNSDDPASMVLLGVILINGGPEEKSEaVRLFEEAGKLGNSSGY 84
                                      255556666662246888888888888888877666665555545888999999*****96 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0002
                           DUF2877  47 rttdvSaalLkaalegefseellallkalsseeeeelekalekllaiGh 95 
                                       +  ++ +a+L+ a+e ++s+++++  ++++++++e++ + +++ ++ G+
  gi|474934751|ref|YP_007688333.1| 203 KDPEIGNAYLERACEKKYSRAMVRYGETIEAADREKAISLYNEAASKGN 251
                                       566899***************************9999888888777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.54
# Mc/sec: 1536.16
//
Query:       gi|474934752|ref|YP_007688334.1|  [L=251]
Description: ABC-2 type transporter [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-24   86.1  12.8    2.1e-24   86.1  12.8    1.7  2  ABC2_membrane    ABC-2 type transporter
    1.6e-06   27.4  25.3    1.6e-06   27.4  25.3    1.7  2  ABC2_membrane_3  ABC-2 family transporter protein
     0.0026   17.2   1.2     0.0026   17.2   1.2    2.1  2  YndJ             YndJ-like protein


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.1  12.8   3.6e-28   2.1e-24      16     208 ..      20     218 ..       8     220 .. 0.90
   2 ?   -0.7   0.8      0.13     8e+02     103     124 ..     222     243 ..     217     248 .. 0.61

  Alignments for each domain:
  == domain 1  score: 86.1 bits;  conditional E-value: 3.6e-28
                     ABC2_membrane  16 rdpslgllwrliqplllalvfgtvfgn.lgnsedglnr..............pgllffsvlflafsaltsvapvfer 77 
                                       r+  ++l +++i+pll+++ fg   g+ ++       +              pg++  ++l+ +fs++++  +v  r
  gi|474934752|ref|YP_007688334.1|  20 RNILILLSTSVITPLLYLIAFGWGLGDgIE-------EtidgktftyiaymiPGVVSLTTLTSSFSTVANKLLVQKR 89 
                                       4444455689****************6533.......122333335577788************************* PP

                     ABC2_membrane  78 ergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflv.gldlsrfflflllllltalaasslgllisa 153
                                         +++++++  p+ s  +++++k l+ ++ ++l+a i+l++ yfl+ +l+++  +l++l +ll+++++ +l+++ ++
  gi|474934752|ref|YP_007688334.1|  90 FYESFDELMLCPI-SKTSIIVGKSLLGMIKGMLCAGIMLVLGYFLTdDLEIN--ALLILCMLLSSFTFAFLAVAAGM 163
                                       *************.*******************************9999998..999******************** PP

                     ABC2_membrane 154 lapsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrsn 208
                                       l+p++  ++++ s+++lp+++l+G ++p+d+mp++ ++i  ++Plt a + +r++
  gi|474934752|ref|YP_007688334.1| 164 LMPDLPYMNLFNSFIILPMTFLCGTMFPTDKMPGVAKAIIDYLPLTQASSCIRAS 218
                                       ************************************************9999986 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.13
                     ABC2_membrane 103 velpvsllqalifll.ivyflvg 124
                                       +e+p+  +++l ++l i+y+l g
  gi|474934752|ref|YP_007688334.1| 222 LEFPWVSAAILFVWLlIFYVL-G 243
                                       567776666666666255544.4 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   1.4       0.1   6.1e+02       7     255 ..      29      73 ..      12      86 .. 0.42
   2 !   27.4  25.3   2.8e-10   1.6e-06     194     341 ..      96     241 ..      55     245 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.1
                   ABC2_membrane_3   7 tlllPiilvlllglifsnsveddentpiavvdednsslsqqlvealeaspsvelvyevdseeeakkalkngdidgil 83 
                                       +++ P+++++ +g+ ++ + e                                                        
  gi|474934752|ref|YP_007688334.1|  29 SVITPLLYLIAFGWGLGDGIE-------------------------------------------------------- 49 
                                       222233332222222222222........................................................ PP

                   ABC2_membrane_3  84 vipkgfskdllkgesatvtvlinssnlnsskailnalnsllqqlnasalvlqseatstsaninvestqleeelsnva 160
                                                                                                                    
  gi|474934752|ref|YP_007688334.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                   ABC2_membrane_3 161 sflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilllafglgipfg. 236
                                                                                                                  + 
  gi|474934752|ref|YP_007688334.1|  50 --------------------------------------------------------------------------ETi 52 
                                       ..........................................................................222 PP

                   ABC2_membrane_3 237 ..nlglllllfllfglayial 255
                                           +  + +++++  ++++l
  gi|474934752|ref|YP_007688334.1|  53 dgKTFTYIAYMIPGVVSLTTL 73 
                                       222233334444444444444 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 2.8e-10
                   ABC2_membrane_3 194 lqlvsgvsplqywlskilgdflvyllqlllilllafglgipfg.nlglll.llfllfglayialgyllsslfknset 268
                                        ++++++s+++++++k l  +++++l++ ++l+l +   ++ + ++ +ll l++ll ++++++l+ + + l+ +   
  gi|474934752|ref|YP_007688334.1|  96 ELMLCPISKTSIIVGKSLLGMIKGMLCAGIMLVLGYF--LTDDlEINALLiLCMLLSSFTFAFLAVAAGMLMPDLPY 170
                                       467999****************************998..99998886655599999********************* PP

                   ABC2_membrane_3 269 aqilifivilllsgffgglfpledlpsalkwifsiiPffapglgllrlitgd..plweillsliilalfavvyll 341
                                       ++++ +++il++ +++g +fp++++p+ +k i  ++P+++ +  +   + g   p+++ ++ +++l++f     +
  gi|474934752|ref|YP_007688334.1| 171 MNLFNSFIILPMTFLCGTMFPTDKMPGVAKAIIDYLPLTQASSCIRASALGLefPWVSAAILFVWLLIF----YV 241
                                       *******************************************99888876633555555555555555....44 PP

>> YndJ  YndJ-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.12   7.1e+02       3      47 ..      24      71 ..       6      86 .. 0.55
   2 !   17.2   1.2   4.3e-07    0.0026     159     241 ..     119     200 ..      98     210 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.12
                              YndJ  3 valgalvvvPlgLrlves...ktklerllrvasklwplaaalavvalv 47
                                      ++l+  v+ Pl+  ++         e  +    +++++ ++++vv+l 
  gi|474934752|ref|YP_007688334.1| 24 ILLSTSVITPLLYLIAFGwglGDGIEETIDGKTFTYIAYMIPGVVSLT 71
                                      444444444444444443344333333444444555555555555554 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 4.3e-07
                              YndJ 159 vvvlvgpllvavGitvsdlvelvgvlvltaalwlvallalrtalpavrsrlarlllrvsalvllvtmllallyalge 235
                                        ++ +g++lv +G+++ d +e+ + l+l + l  +++++l+ a++ +   l ++ l  s+++l++t l   ++   +
  gi|474934752|ref|YP_007688334.1| 119 GMLCAGIMLV-LGYFLTDDLEINALLILCMLLSSFTFAFLAVAAGMLMPDLPYMNLFNSFIILPMTFLCGTMFPTDK 194
                                       5567787777.6*********************************************************99999998 PP

                              YndJ 236 ltgvph 241
                                       + gv+ 
  gi|474934752|ref|YP_007688334.1| 195 MPGVAK 200
                                       888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 1639.09
//
Query:       gi|474934753|ref|YP_007688335.1|  [L=298]
Description: ABC-type multidrug transport system, ATPase component [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      8e-29  100.9   0.0    1.1e-28  100.4   0.0    1.2  1  ABC_tran  ABC transporter
    3.3e-12   46.8   0.0    2.4e-07   30.8   0.0    2.2  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    0.00016   21.6   0.0       0.26   10.9   0.0    2.1  2  AAA_15    AAA ATPase domain
     0.0016   18.8   0.1     0.0084   16.5   0.1    2.1  1  AAA       ATPase family associated with various cellular acti
     0.0077   16.8   0.1      0.014   15.9   0.1    1.3  1  AAA_23    AAA domain
  ------ inclusion threshold ------
      0.011   15.2   0.0       0.46    9.9   0.0    2.1  2  SMC_N     RecF/RecN/SMC N terminal domain
      0.047   13.9   0.0       0.52   10.6   0.0    2.3  1  SbcCD_C   Putative exonuclease SbcCD, C subunit
      0.065   13.0   0.0       0.15   11.8   0.0    1.6  1  RHS       RHS protein
      0.081   11.6   0.0        2.1    6.9   0.1    2.0  2  AAA_13    AAA domain
       0.19   11.5   0.2       0.33   10.7   0.2    1.4  1  AAA_29    P-loop containing region of AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.4   0.0   6.3e-32   1.1e-28       2     137 .]      27     170 ..      26     170 .. 0.95

  Alignments for each domain:
  == domain 1  score: 100.4 bits;  conditional E-value: 6.3e-32
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       +++++++  ge+ +++G+nGaGK+t +k+l+ + kpt+G+i + g+  +e +  s+r+ igv++q+  l+ +++vre
  gi|474934753|ref|YP_007688335.1|  27 DDIEVHVGDGEIFGFLGPNGAGKTTTVKVLTTMRKPTAGTISIGGNLASE-NPLSVRSLIGVVQQHIALDMDISVRE 102
                                       7999*************************************998777777.78899********************* PP

                                       H.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       x.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       n               +e+++++ + +gl++  d+++    + LSgG+k++ a+++al+ +pk+l+lDEpta
  gi|474934753|ref|YP_007688335.1| 103 NiisratlhkvpkpLIKERMKDLCDAIGLTDYLDKTA----RDLSGGWKRKTAIVCALMHEPKILFLDEPTA 170
                                       ***9999999999888999************999999....*****************************97 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   1.8e-05     0.032       2     103 ..      39     126 ..      38     138 .. 0.78
   2 !   30.8   0.0   1.4e-10   2.4e-07     233     297 ..     138     199 ..     132     202 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.8e-05
                            AAA_21   2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrl 78 
                                        ++ GpNg+GK++  + l  ++                 + + i+   +l ++++ ++ +++ +++q++  +  + +
  gi|474934753|ref|YP_007688335.1|  39 FGFLGPNGAGKTTTVKVLTTMRKP---------------TAGTISIGGNLASENPLSVRSLIGVVQQHIALDMDISV 100
                                       6789**************998653...............66777777888888888888888888888888888888 PP

                            AAA_21  79 ersqv.eeklssvetllesgllldkr 103
                                        ++++ +++l  v+++l +  ++d  
  gi|474934753|ref|YP_007688335.1| 101 RENIIsRATLHKVPKPLIKERMKDLC 126
                                       88888888888888888877777665 PP

  == domain 2  score: 30.8 bits;  conditional E-value: 1.4e-10
                            AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                       +ar+lS G kr  a++ al   +   ++l++DEp +gL+ +  + l++++++l+++g+ v++tTH
  gi|474934753|ref|YP_007688335.1| 138 TARDLSGGWKRKTAIVCALMHEP---KILFLDEPTAGLDTQSRHMLWDVIRLLNKRGTTVFITTH 199
                                       6899********88888888888...9************************************** PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0007       1.3      14      48 ..      26      61 ..      18     124 .. 0.86
   2 !   10.9   0.0   0.00015      0.26     323     364 ..     159     199 ..     156     200 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0007
                            AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsilealdlFln 48
                                       +d+e+++ +  +  + G+N++GK++ +++l  + +
  gi|474934753|ref|YP_007688335.1| 26 VDDIEVHVGDGeIFGFLGPNGAGKTTTVKVLTTMRK 61
                                      56777777777677899*************987765 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00015
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                       +++il+++EP a L +q   +l++ ++ l + + t v+itTH
  gi|474934753|ref|YP_007688335.1| 159 EPKILFLDEPTAGLDTQSRHMLWDVIRLLNKRG-TTVFITTH 199
                                       578*********************998777777.59****** PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   4.7e-06    0.0084       3     114 ..      41     203 ..      39     215 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.7e-06
                                       EESSTTSSHHHHHHHHHHHHTHEEEEEETTTCS.SS......................................... CS
                               AAA   3 lyGppGtGKTllakavakelgvefleisgsell.sk......................................... 37 
                                       + Gp G GKT+++k + +  + +  +is    l s+                                         
  gi|474934753|ref|YP_007688335.1|  41 FLGPNGAGKTTTVKVLTTMRKPTAGTISIGGNLaSEnplsvrsligvvqqhialdmdisvreniisratlhkvpkpl 117
                                       68****************97755555554444423356666666777777777777777777788888888888899 PP

                                       ................STTHHHHHHHHHHHHHHHTS......TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHH CS
                               AAA  38 ................yvgesekkirelfkeakeka......kpsilfiDEidalaksrsgseseeeervvnqLlte 92 
                                                       y+ ++++++++ +k+  +        +p+ilf+DE  a   ++              L  +
  gi|474934753|ref|YP_007688335.1| 118 ikermkdlcdaigltdYLDKTARDLSGGWKRKTA-IvcalmhEPKILFLDEPTAGLDTQ----------SRHMLWDV 183
                                       99999999999******************98443.258899999*******88887777..........23333444 PP

                                       HHHTTTSSSTEEEEEEESSGGG CS
                               AAA  93 ldgvkkkeskvivigatnrpdk 114
                                       +  ++k+   ++v ++t+++d+
  gi|474934753|ref|YP_007688335.1| 184 IRLLNKR--GTTVFITTHYMDE 203
                                       4444332..3566666666665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   7.6e-06     0.014      12      40 ..      28      57 ..      18      59 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.6e-06
                            AAA_23 12 dqeidF.skgltlItGpNGaGKTTildAik 40
                                      d e++  +  ++ + GpNGaGKTT +  ++
  gi|474934753|ref|YP_007688335.1| 28 DIEVHVgDGEIFGFLGPNGAGKTTTVKVLT 57
                                      44444455579*************887665 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.026        47      29      41 ..      41      53 ..      23      59 .. 0.83
   2 ?    9.9   0.0   0.00026      0.46     136     204 ..     141     206 ..      83     220 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.026
                                      EEESTTSSHHHHH CS
                                      xxxxxxxxxxxxx RF
                             SMC_N 29 ivGpNGSGKsnll 41
                                       +GpNG+GK+  +
  gi|474934753|ref|YP_007688335.1| 41 FLGPNGAGKTTTV 53
                                      57*******9766 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00026
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlek 204
                                        LSgG k  +a+  + A  + +p+   +lDe  a LD + ++ + ++++  +k+ + ++++++  +  e 
  gi|474934753|ref|YP_007688335.1| 141 DLSGGWKRKTAI--VCA-LMHEPKI-LFLDEPTAGLDTQSRHMLWDVIRLLNKRgTTVFITTHYMDEAET 206
                                       688887765543..333.3456665.569********************887776888888886655544 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00029      0.52      62      88 ..     158     184 ..     120     185 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00029
                           SbcCD_C  62 palrlvfLDEAFsklDeesiatllell 88 
                                       + ++++fLDE  ++lD +s++ l +++
  gi|474934753|ref|YP_007688335.1| 158 HEPKILFLDEPTAGLDTQSRHMLWDVI 184
                                       4589****************9998876 PP

>> RHS  RHS protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   8.3e-05      0.15       7      20 ..     220     233 ..     214     236 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.3e-05
                               RHS   7 DhlGtPeeLtDanG 20 
                                       +h+GtP+e++D+ G
  gi|474934753|ref|YP_007688335.1| 220 EHVGTPREMCDSLG 233
                                       7**********977 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1    0.0012       2.1      23      43 ..      43      63 ..      37      92 .. 0.78
   2 ?    2.5   0.0     0.025        45     525     570 ..     158     200 ..     155     211 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0012
                            AAA_13 23 GwNGaGKTtLSrllrslelge 43
                                      G NGaGKTt  ++l  + +  
  gi|474934753|ref|YP_007688335.1| 43 GPNGAGKTTTVKVLTTMRKPT 63
                                      99************9985544 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.025
                            AAA_13 525 gkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHn 570
                                        + ki ++D P   LD++s  +    i+      k    +fi TH 
  gi|474934753|ref|YP_007688335.1| 158 HEPKILFLDEPTAGLDTQSRHMLWDVIRLLN---KRGTTVFITTHY 200
                                       5789**************9999888888775...88899******6 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   0.00019      0.33      12      40 ..      23      54 ..      16      75 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00019
                            AAA_29 12 fdg.htieidlkg..atlltGpsGsGKSTllD 40
                                      f+   +ie+++ +  ++ + Gp+G+GK+T + 
  gi|474934753|ref|YP_007688335.1| 23 FTAvDDIEVHVGDgeIFGFLGPNGAGKTTTVK 54
                                      5665666676665578899**********875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1909.99
//
Query:       gi|474934754|ref|YP_007688336.1|  [L=197]
Description: precorrin-8X methylmutase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-68  228.7   0.2    5.3e-68  228.5   0.2    1.0  1  CbiC      Precorrin-8X methylmutase
  ------ inclusion threshold ------
      0.096   12.5   0.0       0.12   12.1   0.0    1.2  1  PocR      Sensory domain found in PocR


Domain annotation for each model (and alignments):
>> CbiC  Precorrin-8X methylmutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  228.5   0.2   5.9e-72   5.3e-68       7     195 ..       1     193 [.       1     194 [. 0.97

  Alignments for each domain:
  == domain 1  score: 228.5 bits;  conditional E-value: 5.9e-72
                                       HHHHHCHC-TT.S-CHHHHHHHHHHHHHT-CCHHHHEEE-TTHHHHHHHHHHCT-EEEESSHHHHCCS-HHHHHTTC CS
                              CbiC   7 faiideelgeeelseeeeevvrRvihatadfelaellrfspdaveaglealkagapivtDvemvkaGitkkrleklg 83 
                                       +a+i +el+ ++++e e ++v+R+ih++adf++a++l+f  da ++g+e lk+ga+++tD++m+ aGi+k++l+k g
  gi|474934754|ref|YP_007688336.1|   1 MATIVKELNGRTWPEPEFSIVKRCIHTSADFDYADNLVFGLDAANRGVELLKNGADVITDTKMAMAGINKNALAKHG 77 
                                       688999**9999***************************************************************** PP

                                       -EEEECTC-HHHHHHHHHHTS-HHHHHHHHHHHCTTTCEEEESS-HHHHHHHHHHHHHS..HTSEEEE----SCCHH CS
                              CbiC  84 nevlclladpevaelakekgitrsaaamekaaeelegaivviGnAPtALlellelieegkvkpalvigvPvGFvgaa 160
                                        e+ c+++dp+v ++ak++g trs++a+eka ++ +  i+v+GnAPtAL+e+ +l++egk kpa+++gvPvGFv+++
  gi|474934754|ref|YP_007688336.1|  78 GEAFCFVSDPDVVDEAKARGCTRSTVAVEKASKHAKPTIYVCGNAPTALIEIDKLVREGKYKPAMIVGVPVGFVNVV 154
                                       ***************************************************************************** PP

                                       HHHHHHHCSS....S-EEEESSS---HHHHHHHHHHHHH CS
                              CbiC 161 esKealaese....vpyitveGrkGGsavAaaivnaLle 195
                                       esKe+++++     +pyi+++GrkGGs++ a+i+na+l+
  gi|474934754|ref|YP_007688336.1| 155 ESKELIIKTAeefgIPYIVAKGRKGGSNIGATIINAMLY 193
                                       *******8555677***********************97 PP

>> PocR  Sensory domain found in PocR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.4e-05      0.12      18      79 ..      58     120 ..      49     171 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.4e-05
                              PocR  18 atglaivivdtdgepltepsnftdfCklvrstp.....egrkrCrksdarggeeavksgkpyiykCh 79 
                                       +t  ++++  ++ + l+++ + ++fC +v s+p       ++ C++s + + e+a k  kp+iy C 
  gi|474934754|ref|YP_007688336.1|  58 ITDTKMAMAGINKNALAKHGG-EAFC-FV-SDPdvvdeAKARGCTRS-TVAVEKASKHAKPTIYVCG 120
                                       6788888899999******76.9***.55.44456775778889888.55557899999*******4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1417.83
//
Query:       gi|474934755|ref|YP_007688337.1|  [L=250]
Description: precorrin-3 methyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-37  130.2   0.2    1.2e-37  129.9   0.2    1.0  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
  ------ inclusion threshold ------
       0.14   11.9   0.0       0.21   11.3   0.0    1.3  1  RuvB_N        Holliday junction DNA helicase RuvB P-loop doma


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.9   0.2   1.3e-41   1.2e-37       1     212 [.       4     211 ..       4     212 .. 0.88

  Alignments for each domain:
  == domain 1  score: 129.9 bits;  conditional E-value: 1.3e-41
                      TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealr 77 
                                       kl++VG GpG+ e++TvrA++a+k ad+v g++  + +il+++ +e+        + k +   +  +  ++ +e++ 
  gi|474934755|ref|YP_007688337.1|   4 KLTVVGFGPGSYEDMTVRAVEAIKGADIVTGYT-TYIKILKEFFPEK--------EYKATGMMKEVDRCRMAIEDAL 71 
                                       79*******************************.9*****9988773........33333333345567777***** PP

                      TP_methylase  78 agkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl..lpglakeeer 152
                                       +gk+V++++sGD  +yg+++ +++ + + +a+ie+  + Gv+++++ aa lg+pl ++    s++   ++++  +  
  gi|474934755|ref|YP_007688337.1|  72 SGKNVAMVSSGDSGIYGMTGLIYQLADEMGADIEITSVAGVTAASSSAAILGAPLMHDVALISLSdlMTPIE--KIM 146
                                       ****************************9999*************************999999998877767..444 PP

                      TP_methylase 153 eleallangdtlvllkapr.k.....laelaelLkealyddttpvavveragtedervvrgtleel 212
                                       ++ +l+ +gd++++l++p+ k     la++a++L++++ + +tpv +v++ag++d+  + +tl++l
  gi|474934755|ref|YP_007688337.1| 147 KRVELAGEGDFVIALYNPKsKgrteyLAQAADILLKCRSP-DTPVGIVRQAGRKDQGSTITTLGKL 211
                                       556677789**********75899*************666.56********************987 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.3e-05      0.21      37      91 ..      79     134 ..      47     165 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.3e-05
                            RuvB_N  37 llyGpPGl.GkttlakiiakelgvklkitsgPvlekagdlaalltnleekdvlfid 91 
                                       + +G  G+ G t l   +a+e+g++++its   +  a+  aa+l     +dv +i 
  gi|474934755|ref|YP_007688337.1|  79 VSSGDSGIyGMTGLIYQLADEMGADIEITSVAGVTAASSSAAILGAPLMHDVALIS 134
                                       45677775599*********************************998888888774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1929.56
//
Query:       gi|474934756|ref|YP_007688338.1|  [L=251]
Description: precorrin-4 C11-methyltransferase/cobalt-factor II C20-methyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.9e-40  138.1   0.1    4.6e-40  137.8   0.1    1.0  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
  ------ inclusion threshold ------
      0.087   13.2   0.0       0.26   11.6   0.0    1.9  1  Radical_SAM   Radical SAM superfamily


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.8   0.1   5.1e-44   4.6e-40       1     212 [.       1     207 [.       1     208 [. 0.87

  Alignments for each domain:
  == domain 1  score: 137.8 bits;  conditional E-value: 5.1e-44
                      TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleea...yeeiaealae 74 
                                       ++++VG+GpGdpel+T+++ +++ +ad+++ ++s++   +l+            +k++ + + a    +e+ + ++ 
  gi|474934756|ref|YP_007688338.1|   1 MVHFVGAGPGDPELITIKGKKLIDQADIIIFAGSLVNPAVLEG----------RKKDAVVYDSAymnLDEVMDVTIP 67 
                                       689******************************8988888654..........3344445555522277777777** PP

                      TP_methylase  75 alragkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl....lpgla 147
                                       a++agk+Vv++++GDP++yg+ +e + +l a  +gie++v PGvss++a aa+++ + t   ++++v+    + ++ 
  gi|474934756|ref|YP_007688338.1|  68 AAKAGKKVVRVHTGDPSIYGAIREQMVRLDA--EGIEYDVTPGVSSFCASAAAVKKEFTLPSVSQTVIitrmEGRTP 142
                                       **************************99999..***************************************66666 PP

                      TP_methylase 148 keeereleallangdtlvllkaprklaelaelLkea.lyddttpvavveragtedervvrgtleel 212
                                       ++e+++l +l+++  ++ ++ ++  ++el + L+ea + +dt p+avv +a++++++++ gt+e++
  gi|474934756|ref|YP_007688338.1| 143 MPEKEKLIDLAKHHSSMCIFLSVGFMDELTKTLLEAgYEPDT-PMAVVYKASWPEQKIIYGTVETM 207
                                       7788888888888888888877777***********777755.*******************9976 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.9e-05      0.26      25      61 ..      52     144 ..      47     235 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.9e-05
                                       HHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS......................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................................... RF
                       Radical_SAM  25 rgrslsveeileevkelkaekgvkevilgggeplly......................................... 60 
                                       +++++ ++e+++    + a+ g+k+v ++ g+p+ y                                         
  gi|474934756|ref|YP_007688338.1|  52 DSAYMNLDEVMDVTIPA-AKAGKKVVRVHTGDPSIYgaireqmvrldaegieydvtpgvssfcasaaavkkeftlps 127
                                       6789999*******999.8999**************55555555555555555555555555555555555555555 PP

                                       ................T CS
                                       ................x RF
                       Radical_SAM  61 ................p 61 
                                                       p
  gi|474934756|ref|YP_007688338.1| 128 vsqtviitrmegrtpmP 144
                                       55555555555554433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1524.11
//
Query:       gi|474934757|ref|YP_007688339.1|  [L=233]
Description: precorrin-2 C20-methyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-43  149.7   0.1    1.3e-43  149.5   0.1    1.0  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.5   0.1   7.1e-48   1.3e-43       1     204 [.       4     212 ..       4     216 .. 0.95

  Alignments for each domain:
  == domain 1  score: 149.5 bits;  conditional E-value: 7.1e-48
                      TP_methylase   1 klylVGvGpGdpellTvrAlralktadvv......lgddsraleilldllaeel....eleapmgkekepleeayee 67 
                                       kly++GvGpG+p+l+T+rA ++l++++v+      lg+d  alei++++++       el ++m +++e++ +  ++
  gi|474934757|ref|YP_007688339.1|   4 KLYGIGVGPGNPDLMTIRAKELLEDSQVIaypvrkLGEDGTALEIIKKKVDVSGkevvELLFKMDPDDEVRKKCRAK 80 
                                       79***************************666666566656*****99999888*********************** PP

                      TP_methylase  68 iaealaealragkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvllp 144
                                       + e++  +l++gk++++++ GD  vy+t++++ + +r+  +g+e+ev+PG++s++  aa +++pl  g+e+l+vl  
  gi|474934757|ref|YP_007688339.1|  81 ALEKVCSLLDEGKNIAMVTLGDVAVYSTYMYIDRDVRD--RGYETEVVPGIPSFCHGAALARLPLMIGEESLAVL-- 153
                                       **************************************..9**********************************.. PP

                      TP_methylase 145 glakeeereleallangdtlvllkaprklaelaelLkealyddttpvavveragtederv 204
                                       ++ak +++++e++l+  d++v++ka   + e+++ L ++ + ++ +++v++++g++de +
  gi|474934757|ref|YP_007688339.1| 154 SMAKHNRAKVEKALDCIDNVVVMKAFASIGEIVDMLNQR-DIPLSNATVMSNVGMDDEYI 212
                                       77888**********************************.77789************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1532.71
//
Query:       gi|474934758|ref|YP_007688340.1|  [L=289]
Description: ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase component [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.8e-31  107.4   0.0    1.3e-30  106.7   0.0    1.3  1  ABC_tran      ABC transporter
    3.5e-10   39.7   0.1    5.8e-08   32.4   0.1    2.1  1  SMC_N         RecF/RecN/SMC N terminal domain
    3.2e-05   23.6   0.0    7.8e-05   22.3   0.0    1.6  1  AAA_29        P-loop containing region of AAA domain
    3.6e-05   23.7   1.1      0.053   13.3   0.1    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    0.00012   22.5   0.0    0.00015   22.2   0.0    1.4  1  AAA_16        AAA ATPase domain
    0.00015   22.4   0.0    0.00026   21.5   0.0    1.4  1  AAA_23        AAA domain
    0.00073   18.4   0.0     0.0011   17.8   0.0    1.2  1  RNA12         RNA12 protein
    0.00077   19.3   1.5     0.0054   16.5   0.1    2.0  2  AAA_15        AAA ATPase domain
     0.0023   17.8   0.0     0.0041   17.0   0.0    1.5  1  RsgA_GTPase   RsgA GTPase
     0.0052   16.0   0.5      0.045   12.9   0.5    2.2  1  NB-ARC        NB-ARC domain
     0.0064   15.9   0.0      0.011   15.1   0.0    1.4  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
     0.0085   16.5   0.3      0.093   13.2   0.3    2.2  1  AAA           ATPase family associated with various cellular 
  ------ inclusion threshold ------
      0.013   15.2   0.0      0.031   14.0   0.0    1.5  1  AAA_24        AAA domain
      0.016   15.1   0.1       0.28   11.1   0.0    2.2  2  Rad17         Rad17 P-loop domain
      0.021   14.7   0.0      0.042   13.8   0.0    1.5  1  NTPase_1      NTPase
      0.047   13.3   0.0      0.081   12.5   0.0    1.3  1  AAA_27        AAA domain
      0.061   13.4   0.3       0.12   12.4   0.3    1.8  1  MMR_HSR1      50S ribosome-binding GTPase
       0.11   12.4   0.0       0.19   11.6   0.0    1.5  1  ATPase_2      ATPase domain predominantly from Archaea
       0.12   12.7   0.6       0.55   10.5   0.6    2.0  1  AAA_22        AAA domain
       0.13   12.3   0.0        0.6   10.1   0.0    1.9  2  AAA_14        AAA domain
       0.19   11.1   1.5        1.2    8.5   0.5    2.2  2  TniB          Bacterial TniB protein


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.7   0.0   1.5e-33   1.3e-30       1     137 []      18     165 ..      18     165 .. 0.90

  Alignments for each domain:
  == domain 1  score: 106.7 bits;  conditional E-value: 1.5e-33
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l++++l+l+  + v i+G+nG GKStL+ ++ + l+pteG++ +dgkd+ke++++++ k++g++p  ++    ltv 
  gi|474934758|ref|YP_007688340.1|  18 LNDITLNLEGPRFVSILGPNGVGKSTLIHCINKILSPTEGNVFIDGKDVKEITIKEMAKQVGYVPYSANDTFPLTVV 94 
                                       789****************************************************************7666666688 PP

                                       HH...............HHHTC...HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx...............xxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en...............esdee...iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       ++               +   +   +++ l+ lg+++l+ +      ++LS Gq q+v+lar l+++pk+lllDEpt
  gi|474934758|ref|YP_007688340.1|  95 DTvlmgrhphskwksldN---DldiVYDTLKMLGISHLAMRAF----NELSAGQHQKVMLARGLVQEPKILLLDEPT 164
                                       888****99777654433...1556999999999999999999....*****************************9 PP

                                       T CS
                                       x RF
                          ABC_tran 137 a 137
                                       +
  gi|474934758|ref|YP_007688340.1| 165 S 165
                                       6 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.1   6.8e-11   5.8e-08      24     217 ..      28     213 ..      18     215 .. 0.70

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 6.8e-11
                                       SSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTT.TCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersakkl.rseklsdlihkskekasvkkaeveitfdnedkklkiekeevsi 99 
                                       ++f +i+GpNG GKs l+  i  +L+ ++ + +   ++++++  k   + + + ++v      +d   +     +++
  gi|474934758|ref|YP_007688340.1|  28 PRFVSILGPNGVGKSTLIHCINKILSPTEGNVFiDGKDVKEITIK---EMAKQVGYVPYS--ANDTF-P-----LTV 93 
                                       789**********************98877655155666666555...666777888773..34443.3.....333 PP

                                       EEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 100 srrvkrkgeseykingkevtkkevsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDeidaa 170
                                         +v  + + + k +  +     v + l++ gis        +LS G+ + v+la       v+   + llDe  ++
  gi|474934758|ref|YP_007688340.1|  94 VDTVLMGRHPHSKWKSLDNDLDIVYDTLKMLGISHLamrafnELSAGQHQKVMLAR----GLVQEPKILLLDEPTSN 166
                                       3333333333333333333444444555555554433334449*****99887764....456777799******** PP

                                       S-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEEEEETT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 171 LDeknvkkvaellkeksknaQfivislreemlekadklvgvtkveng 217
                                       LD ++   v ++lk+ s + Q+++i +++++   a+    v + ++g
  gi|474934758|ref|YP_007688340.1| 167 LDVRHQLDVTKMLKRLSVEKQILIIMISHDINIAAKYSDEVIMMHQG 213
                                       *************************9999998888888888777776 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   9.1e-08   7.8e-05      17      50 ..      21      56 ..      17      60 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 9.1e-08
                            AAA_29 17 ieidlkg..atlltGpsGsGKSTllDAiqalLvpak 50
                                      i+++l+g  ++ + Gp+G+GKSTl+  i+ +L p++
  gi|474934758|ref|YP_007688340.1| 21 ITLNLEGprFVSILGPNGVGKSTLIHCINKILSPTE 56
                                      566777777899*********************987 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.1   6.2e-05     0.053       3      20 ..      32      49 ..      30      76 .. 0.80
   2 !    9.4   0.1   0.00097      0.83     256     301 ..     153     199 ..     127     201 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.2e-05
                            AAA_21  3 vliGpNgsGKSnLLdald 20
                                       + GpNg+GKS+L+ ++ 
  gi|474934758|ref|YP_007688340.1| 32 SILGPNGVGKSTLIHCIN 49
                                      699***********9984 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00097
                            AAA_21 256 kkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSpll 301
                                       +++++ll+DEp ++L+ + +  + ++lk+ls  + + +i+ +H+  +
  gi|474934758|ref|YP_007688340.1| 153 QEPKILLLDEPTSNLDVRHQLDVTKMLKRLSVeKQILIIMISHDINI 199
                                       4459*************777444444433333445889999998665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   1.8e-07   0.00015      23      63 ..      27      68 ..      18     191 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.8e-07
                            AAA_16 23 rpelvllsGesGvGKsslvrellralekdg.giflrgkcdql 63
                                      +p+ v + G+ GvGKs+l+ ++ + l+ ++  +f+ gk ++ 
  gi|474934758|ref|YP_007688340.1| 27 GPRFVSILGPNGVGKSTLIHCINKILSPTEgNVFIDGKDVKE 68
                                      6899********************999996488899998887 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   3.1e-07   0.00026      12      43 ..      20      52 ..      11      84 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 3.1e-07
                            AAA_23 12 dqeidF.skgltlItGpNGaGKTTildAiklaL 43
                                      d ++++ ++ ++ I GpNG GK+T++ +i  +L
  gi|474934758|ref|YP_007688340.1| 20 DITLNLeGPRFVSILGPNGVGKSTLIHCINKIL 52
                                      567777888999*****************8776 PP

>> RNA12  RNA12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.3e-06    0.0011      18      74 ..      29      82 ..      20      92 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.3e-06
                             RNA12 18 tFivvkGPrGSGkkeLv..ldrvlkdrkkvlvidCdelvkarndaelisaaAsqlGYfP 74
                                       F+ + GP G Gk+ L+  ++++l+  +  ++id +++ +      +i+++A+q+GY+P
  gi|474934758|ref|YP_007688340.1| 29 RFVSILGPNGVGKSTLIhcINKILSPTEGNVFIDGKDVKE-----ITIKEMAKQVGYVP 82
                                      59**************8667999999999********975.....68***********9 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   6.3e-06    0.0054      16      68 ..      20      69 ..      17      79 .. 0.77
   2 ?    1.7   0.2       0.2   1.7e+02     300     361 ..     125     190 ..     105     200 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.3e-06
                            AAA_15 16 dveidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleif 68
                                      d++++l+   +  + G+N++GKS++++ ++++l+ +    +  ++i+ +d+++ 
  gi|474934758|ref|YP_007688340.1| 20 DITLNLEGPrFVSILGPNGVGKSTLIHCINKILSPT----EGNVFIDGKDVKEI 69
                                      566666655789999*******************99....56677777776655 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.2
                            AAA_15 300 Gvqrllllillileaekk......dekeeknvilliEEPEahLHpqaqkvlikllkelandnktQvii 361
                                       G++ l   ++ +l+a +       ++  ++++ill++EP  +L   +q  + k lk+l+ ++  Q++i
  gi|474934758|ref|YP_007688340.1| 125 GISHLAMRAFNELSAGQHqkvmlaRGLVQEPKILLLDEPTSNLDVRHQLDVTKMLKRLSVEK--QILI 190
                                       55555555555555555555666566668899**************************9999..5443 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   4.8e-06    0.0041      89     121 ..      17      50 ..       2      77 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.8e-06
                                       THHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  89 gleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                        l++++ +l++ +++ ++G+ GvGKStLi  ++ 
  gi|474934758|ref|YP_007688340.1|  17 VLNDITLNLEGpRFVSILGPNGVGKSTLIHCINK 50 
                                       67888999999999**************987765 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.5   5.3e-05     0.045      17      49 ..      27      57 ..      18     218 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.3e-05
                                      TSCSEEEEEEESTTSSHHHHHHHHCCSHCCCCC CS
                            NB-ARC 17 elqslvvalvGmgGvGKttlakqilnksdeveg 49
                                      ++   +v++ G  GvGK+tl++ i++ ++ +eg
  gi|474934758|ref|YP_007688340.1| 27 GPR--FVSILGPNGVGKSTLIHCINKILSPTEG 57
                                      455..9****************99998777766 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.3e-05     0.011      24      78 ..      30      83 ..      19     100 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.3e-05
                      Mg_chelatase 24 nlllvGppGsGKtmlakrlpsllpplseeealevakiasvagkkeeekllkrrpf 78
                                       + ++Gp G GK+ l+++++++l+p + +  ++ + ++ ++  ke +k++   p+
  gi|474934758|ref|YP_007688340.1| 30 FVSILGPNGVGKSTLIHCINKILSPTEGNVFIDGKDVKEITI-KEMAKQVGYVPY 83
                                      56789************************9999999999988.444555555555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.3   0.00011     0.093       3      38 ..      33      93 ..      31     202 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
                                      EESSTTSSHHHHHHHHHHHH..........THEEEEEETTTCSSS...............S CS
                               AAA  3 lyGppGtGKTllakavakel..........gvefleisgsellsk...............y 38
                                      + Gp G+GK++l++ + k l          g ++ ei  +e+ ++               +
  gi|474934758|ref|YP_007688340.1| 33 ILGPNGVGKSTLIHCINKILsptegnvfidGKDVKEITIKEMAKQvgyvpysandtfpltV 93
                                      68*****************944333222222345555555555334545544444444550 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.6e-05     0.031       6      74 ..      32      97 ..      28     101 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.6e-05
                            AAA_24  6 liyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdieswedfldevvel.aaeladyktlviDti 74
                                       i Gp+g+GK+tl+  +  + ++  te+ +  +d++++++i +++++ ++v ++ + +++++   v+Dt+
  gi|474934758|ref|YP_007688340.1| 32 SILGPNGVGKSTLIHCI--NKILSPTEGNV-FIDGKDVKEI-TIKEMAKQVGYVpYSANDTFPLTVVDTV 97
                                      699**************..889999*9944.6777777766.9999999999999999999*******97 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00033      0.28      46      72 ..      29      55 ..      16      90 .. 0.79
   2 ?    1.9   0.1      0.21   1.8e+02     106     177 ..     131     199 ..     104     205 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00033
                             Rad17 46 riLLisGPsGCgkstvvkvLskelgik 72
                                      r + i GP G gkst ++ + k+l++ 
  gi|474934758|ref|YP_007688340.1| 29 RFVSILGPNGVGKSTLIHCINKILSPT 55
                                      677899*****************9875 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.21
                             Rad17 106 iesfkeleLkdakylklqklGddlrtdkklilvedlPnkfyrdsdalrevirkylrssealplilviteies 177
                                       + +f+el   + +++k+ +l   l  + k++l+++  ++     +     ++k l +++ + +i++  +i++
  gi|474934758|ref|YP_007688340.1| 131 MRAFNEL--SAGQHQKV-MLARGLVQEPKILLLDEPTSNLDVRHQLDVTKMLKRLSVEKQILIIMISHDINI 199
                                       6778887..34444333.356668888999999997676655543333445666777777677777666665 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.9e-05     0.042       3      46 ..      32      79 ..      30      97 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.9e-05
                                      EEE--TTSSHHHHHHHHHHHH.....GGGEEEEEEEEE-..------E CS
                          NTPase_1  3 fiTGppGvGKtTlvkkvlellkss..gvkvgGfyteevr..eggrrig 46
                                       i Gp GvGK+Tl++ + + l+    +v ++G  ++e++  e  +++g
  gi|474934758|ref|YP_007688340.1| 32 SILGPNGVGKSTLIHCINKILSPTegNVFIDGKDVKEITikEMAKQVG 79
                                      678**************9999754338888998888876445555555 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   9.5e-05     0.081      16      50 ..      20      52 ..      17      56 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.5e-05
                            AAA_27 16 drsldfsaeeadlhliyGpNEAGKstalrAisdll 50
                                      d +l++  e +++  i+GpN  GKst+++ i+++l
  gi|474934758|ref|YP_007688340.1| 20 DITLNL--EGPRFVSILGPNGVGKSTLIHCINKIL 52
                                      445555..599******************999876 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   0.00014      0.12       2      54 ..      31      97 ..      30     214 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                                      EEEEESTTSSHHHHHHHHHT.......STE.EESSSTTSSSSEEEEEEE.....ETT.EEEEEEECG CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltg.......eka.ivsdkpgtTrdinegrvk.....lkg.keielvDtp 54
                                      v i+G   vGKStLi  + +       ++    +d +  T++   ++v       ++  ++++vDt+
  gi|474934758|ref|YP_007688340.1| 31 VSILGPNGVGKSTLIHCINKilsptegNVFiDGKDVKEITIKEMAKQVGyvpysANDtFPLTVVDTV 97
                                      789***********98887622232211111223444444444444433444332223557777776 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00023      0.19      16      62 ..      24      71 ..      18     125 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00023
                          ATPase_2 16 erepneiyfiYGpegsGKtaLlkeiienledkdkyviyyi..alreesi 62
                                      + e  +++ i Gp g+GK++L+   i++ ++  +  ++++  +++e+ i
  gi|474934758|ref|YP_007688340.1| 24 NLEGPRFVSILGPNGVGKSTLIH-CINKILSPTEGNVFIDgkDVKEITI 71
                                      455678899************96.5666666677788875224444444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.6   0.00065      0.55       4      29 ..      27      52 ..      24     199 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00065
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleql 29
                                      + +++ + G+ G+GK+tl+  + + l
  gi|474934758|ref|YP_007688340.1| 27 GPRFVSILGPNGVGKSTLIHCINKIL 52
                                      568999************98877766 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0    0.0007       0.6       4      47 ..      30      72 ..      28      91 .. 0.76
   2 ?   -0.8   0.0       1.7   1.4e+03      57      75 ..     147     165 ..     115     198 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0007
                            AAA_14  4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkla 47
                                       + i G+  vGK+tl++ +i++ l + e  ++i+ +d ++ +++
  gi|474934758|ref|YP_007688340.1| 30 FVSILGPNGVGKSTLIH-CINKILSPTEGNVFIDGKDVKEITIK 72
                                      6889***********85.55566668888888888887765544 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.7
                            AAA_14  57 lek.lkeekktylflDEiqe 75 
                                       l++ l  ++ ++l+lDE   
  gi|474934758|ref|YP_007688340.1| 147 LARgLV-QEPKILLLDEPTS 165
                                       333233.3678888888654 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.23     2e+02      38      53 ..      31      46 ..      19      74 .. 0.86
   2 ?    8.5   0.5    0.0015       1.2     118     162 ..     153     195 ..     121     209 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.23
                              TniB 38 lllvGdsnnGKtmive 53
                                      + ++G+  +GK+++++
  gi|474934758|ref|YP_007688340.1| 31 VSILGPNGVGKSTLIH 46
                                      6799*********997 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0015
                              TniB 118 lkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlvGt 162
                                        ++++L++DE  + l   +r+q  ++ +lk+L+ e +i i+++  
  gi|474934758|ref|YP_007688340.1| 153 QEPKILLLDEPTSNL--DVRHQLDVTKMLKRLSVEKQILIIMISH 195
                                       4789******99999..89*******************9998755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.65u 0.40s 00:00:01.05 Elapsed: 00:00:00.57
# Mc/sec: 1524.51
//
Query:       gi|474934759|ref|YP_007688341.1|  [L=306]
Description: ABC-type multidrug transport system, ATPase component [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.4e-32  110.7   0.0    1.2e-31  110.0   0.0    1.4  1  ABC_tran      ABC transporter
    1.6e-11   44.6   0.0    1.8e-06   28.0   0.0    2.3  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    3.4e-06   27.0   0.0      0.028   14.1   0.0    2.1  2  AAA_15        AAA ATPase domain
     0.0017   17.8   0.0     0.0076   15.7   0.0    1.9  1  SMC_N         RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
       0.01   15.5   0.0      0.017   14.8   0.0    1.5  1  SRP54         SRP54-type protein, GTPase domain
      0.016   15.7   0.3       0.04   14.4   0.2    1.7  1  AAA_23        AAA domain
      0.019   14.8   0.0      0.039   13.9   0.0    1.5  1  RsgA_GTPase   RsgA GTPase
       0.02   14.6   0.1       0.11   12.2   0.1    1.8  2  AAA_30        AAA domain
      0.023   15.2   0.0      0.042   14.4   0.0    1.4  1  AAA_18        AAA domain
      0.027   14.2   0.1      0.053   13.3   0.1    1.4  1  AAA_29        P-loop containing region of AAA domain
      0.042   13.8   0.0      0.064   13.2   0.0    1.2  1  Rad17         Rad17 P-loop domain
      0.077   13.2   0.0       0.13   12.4   0.0    1.4  1  AAA_33        AAA domain
      0.092   13.2   0.2       0.24   11.8   0.2    1.9  1  AAA           ATPase family associated with various cellular 
       0.14   10.8   0.0       0.18   10.4   0.0    1.1  1  AAA_13        AAA domain
       0.15   12.1   0.1       0.24   11.4   0.1    1.4  1  BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette 


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.0   0.0     1e-34   1.2e-31       2     136 ..      23     165 ..      22     166 .. 0.97

  Alignments for each domain:
  == domain 1  score: 110.0 bits;  conditional E-value: 1e-34
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       +n+++++k+ge++a++G+nGaGK+t +++l+ l++ +eG++ +dg dl + + +++++ +gv++q+ +l+++ltv e
  gi|474934759|ref|YP_007688341.1|  23 NNITMTVKKGEMYAFLGPNGAGKTTTVRVLSTLTNFDEGKVIIDGYDLLK-NPKEAKSCMGVIQQHISLDKDLTVWE 98 
                                       89***********************************************9.889999******************** PP

                                       H.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n             e++++i+++ + +gl e  + +v     +LSgG+k+rva+++al+ +pkll+lDEpt
  gi|474934759|ref|YP_007688341.1|  99 NmmahamyqqipkaERKKRIDELSEYIGLGEYYNYKV----DKLSGGWKKRVAIVCALVHRPKLLFLDEPT 165
                                       ***********99999999************999999....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   2.1e-05     0.025       3      45 ..      36      68 ..      34      97 .. 0.74
   2 !   28.0   0.0   1.5e-09   1.8e-06     235     297 ..     136     195 ..     106     199 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.1e-05
                            AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirki 45
                                      ++ GpNg+GK++  + l+ l            ++ g++ i+++
  gi|474934759|ref|YP_007688341.1| 36 AFLGPNGAGKTTTVRVLSTLTN----------FDEGKVIIDGY 68
                                      789**************99854..........44444444443 PP

  == domain 2  score: 28.0 bits;  conditional E-value: 1.5e-09
                            AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                       ++lS G k+  a++ al  ++   +ll++DEp  gL+ ++ r l++ll++l++ g  ++ltTH
  gi|474934759|ref|YP_007688341.1| 136 DKLSGGWKKRVAIVCALVHRP---KLLFLDEPTVGLDIQARRGLWDLLRKLNDDGMTIFLTTH 195
                                       566777777778888888888...9************************************** PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   2.4e-05     0.028      17     128 ..      25     134 ..      17     147 .. 0.65
   2 !   10.4   0.0   0.00031      0.37     324     364 ..     156     195 ..     150     196 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.4e-05
                            AAA_15  17 veidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskdikIdvefaek.....e 87 
                                       +++ +++  +  + G+N++GK++ +++l  + n +    + ++ i+  dl ++ ++++s +  I+ +   +     +
  gi|474934759|ref|YP_007688341.1|  25 ITMTVKKGeMYAFLGPNGAGKTTTVRVLSTLTNFD----EGKVIIDGYDLLKNPKEAKSCMGVIQQHI--SldkdlT 95 
                                       5555555557899***************9999977....66667777777666666666666666666..1112111 PP

                            AAA_15  88 kakeyektlkskekkkadlllkkkesdlkktikdkklklkk 128
                                        ++  +  ++   ++ ++ + kk +++l+++i   +++++k
  gi|474934759|ref|YP_007688341.1|  96 VWE--NMMAHAMYQQIPKAERKKRIDELSEYIGLGEYYNYK 134
                                       111..234444445555556666677777777777777665 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00031
                            AAA_15 324 nvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                       +++l+++EP + L +qa + l++ll++l +d+   +++tTH
  gi|474934759|ref|YP_007688341.1| 156 PKLLFLDEPTVGLDIQARRGLWDLLRKLNDDGM-TIFLTTH 195
                                       789*************************99997.9****** PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   6.4e-06    0.0076      11     203 ..      14     198 ..       6     214 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.4e-06
                                       TTEECEEEEEETTS.....SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEE CS
                                       xxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  11 ksyagktvilpfsk.....sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveit 82 
                                       k y++kt+i +++      ++ a +GpNG+GK+  +  ++ +  +++ k +   +  dl+++  ++a++  + ++ +
  gi|474934759|ref|YP_007688341.1|  14 KRYKNKTAINNITMtvkkgEMYAFLGPNGAGKTTTVRVLSTLTNFDEGKVI-I-DGYDLLKN-PKEAKSCMGVIQQH 87 
                                       666666666555431111157799***********9999666666666443.3.44688888.67777777888888 PP

                                       EEETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  83 fdnedkklkiekeevsisrrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpa 159
                                       ++ +++ ++ e+     + + + k e + +i+    + +e+  l e  + + + LSgG k+ va  ++ A+ +  + 
  gi|474934759|ref|YP_007688341.1|  88 ISLDKDLTVWENMMAHAMYQQIPKAERKKRID----ELSEYIGLGEYYNYKVDKLSGGWKKRVA--IVCALVH--RP 156
                                       87777776677777777777777777677776....478999999***************9665..5655543..44 PP

                                       SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                             SMC_N 160 plyllDeidaaLDeknvkkvaellkekskn.aQfivislreemle 203
                                        l +lDe    LD + ++ + +ll++ +++ + ++ +++    +e
  gi|474934759|ref|YP_007688341.1| 157 KLLFLDEPTVGLDIQARRGLWDLLRKLNDDgMTIFLTTHY---IE 198
                                       47789********************999774555555553...33 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.4e-05     0.017       3      39 ..      34      70 ..      32     120 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.4e-05
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDt 39
                                      +++++G++GaGKTtt+  L+ l + ++ kv++   D 
  gi|474934759|ref|YP_007688341.1| 34 MYAFLGPNGAGKTTTVRVLSTLTNFDEGKVIIDGYDL 70
                                      5789****************99999999999887775 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.2   3.3e-05      0.04      19      39 ..      32      52 ..       7      62 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.3e-05
                            AAA_23 19 kgltlItGpNGaGKTTildAi 39
                                        ++++ GpNGaGKTT ++ +
  gi|474934759|ref|YP_007688341.1| 32 GEMYAFLGPNGAGKTTTVRVL 52
                                      46899***********98766 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.2e-05     0.039      80     122 ..      12      55 ..       4      67 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.2e-05
                                       EE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  80 llvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                       l+ + k+k+++++++  +k+ ++ +++G+ G+GK+t + +l   
  gi|474934759|ref|YP_007688341.1|  12 LVKRYKNKTAINNITMTVKKgEMYAFLGPNGAGKTTTVRVLSTL 55 
                                       56667889999***9999998****************9999765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   9.5e-05      0.11      16      50 ..      30      64 ..      19      67 .. 0.79
   2 ?   -0.3   0.0      0.65   7.7e+02      41     121 ..     100     192 ..      94     194 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.5e-05
                            AAA_30 16 sgdrvavltGpAGtGKttalkalreaweaaggrvi 50
                                      ++  + +  Gp G+GKtt++++l  + + ++g+vi
  gi|474934759|ref|YP_007688341.1| 30 KKGEMYAFLGPNGAGKTTTVRVLSTLTNFDEGKVI 64
                                      344588999**************999887766766 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.65
                            AAA_30  41 aweaaggrviglAptgkaAkvLaeelgi...eastiakllkrlk.....grarlepgtllivDEagmv....dtkql 105
                                       ++++a ++ i  A  +k  ++L+e +g+     + ++kl   +k       a +++ +ll  DE  +     + + l
  gi|474934759|ref|YP_007688341.1| 100 MMAHAMYQQIPKAERKKRIDELSEYIGLgeyYNYKVDKLSGGWKkrvaiVCALVHRPKLLFLDEPTVGldiqARRGL 176
                                       55555666677777777778888877755557777888888888888885456677799999997765433355556 PP

                            AAA_30 106 aallkaaekagakvil 121
                                        +ll++++++g+++ l
  gi|474934759|ref|YP_007688341.1| 177 WDLLRKLNDDGMTIFL 192
                                       6677777777777665 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.5e-05     0.042       4      61 ..      38     105 ..      36     140 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.5e-05
                            AAA_18   4 tGtpGvGKttlakeLskrlgf........gvnlrdvakenglllevdpe..aldeskrldedkldkll 61 
                                        G+ G+GKtt  + Ls +++f        g+ l ++ ke  ++ +v ++   ld+ + + e++++ ++
  gi|474934759|ref|YP_007688341.1|  38 LGPNGAGKTTTVRVLSTLTNFdegkviidGYDLLKNPKEAKSCMGVIQQhiSLDKDLTVWENMMAHAM 105
                                       69***************9999**999999888888888888888888887777777777777766665 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   4.4e-05     0.053      13      39 ..      23      49 ..      16      57 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.4e-05
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTll 39
                                      ++ t++++  +++ + Gp+G+GK+T +
  gi|474934759|ref|YP_007688341.1| 23 NNITMTVKKGEMYAFLGPNGAGKTTTV 49
                                      55678888555**************77 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   5.3e-05     0.064      37     122 ..      24     109 ..      14     123 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.3e-05
                             Rad17  37 advLesrkkriLLisGPsGCgkstvvkvLskelgikl.rewlnpvslkepdnqksdfkgltekesrflsqiesfkel 112
                                         ++  +k ++    GP G gk+t+v+vLs    ++  +  +++  l + + + +   g+++++ ++   + +++++
  gi|474934759|ref|YP_007688341.1|  24 NITMTVKKGEMYAFLGPNGAGKTTTVRVLSTLTNFDEgKVIIDGYDLLKNPKEAKSCMGVIQQHISLDKDLTVWENM 100
                                       555556666788889***************98776541345567666666666666666666666666666666666 PP

                             Rad17 113 eLkdakylkl 122
                                        +  a y+++
  gi|474934759|ref|YP_007688341.1| 101 -MAHAMYQQI 109
                                       .555666555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00011      0.13       4      70 ..      37     113 ..      34     120 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                            AAA_33   4 lvGlpGsGKstlaerllkklg...........avllssdtlrrrlfgtdqqsktdytrvldrlyqilnelarkalsa 69 
                                       + G++G+GK+t ++ l   l+           + ll  +++ + + g  qq+++  ++++ + + + +++ ++  +a
  gi|474934759|ref|YP_007688341.1|  37 FLGPNGAGKTTTVRVLS-TLTnfdegkviidgYDLLKNPKEAKSCMGVIQQHISLDKDLTVWENMMAHAMYQQIPKA 112
                                       88************885.34446677788888999999999999999778888777776666666666666665555 PP

                            AAA_33  70 g 70 
                                       +
  gi|474934759|ref|YP_007688341.1| 113 E 113
                                       4 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2    0.0002      0.24       3      35 ..      37      71 ..      35     164 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0002
                                      EESSTTSSHHHHHHHHHHHHTHE..EEEEETTTCS CS
                               AAA  3 lyGppGtGKTllakavakelgve..fleisgsell 35
                                      + Gp G GKT++++ + + ++++   + i+g +ll
  gi|474934759|ref|YP_007688341.1| 37 FLGPNGAGKTTTVRVLSTLTNFDegKVIIDGYDLL 71
                                      78*************99988754224677777777 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00015      0.18      21      53 ..      37      63 ..      20      97 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00015
                            AAA_13 21 iYGwNGaGKTtLSrllrslelgetepkfangsi 53
                                      + G NGaGKTt  r+l+ l++      f +g++
  gi|474934759|ref|YP_007688341.1| 37 FLGPNGAGKTTTVRVLSTLTN------FDEGKV 63
                                      679***************954......555555 PP

>> BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1    0.0002      0.24       2      10 ..     215     223 ..     214     226 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0002
                      BCA_ABC_TP_C   2 vIAeGtPaE 10 
                                       +IAeGtP+E
  gi|474934759|ref|YP_007688341.1| 215 IIAEGTPDE 223
                                       8*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.62u 0.35s 00:00:00.97 Elapsed: 00:00:00.54
# Mc/sec: 1710.53
//
Query:       gi|474934760|ref|YP_007688342.1|  [L=253]
Description: ABC-2 type transporter [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-22   80.6  15.6      1e-22   80.6  15.6    1.4  2  ABC2_membrane    ABC-2 type transporter
    3.2e-05   23.2  23.9    3.2e-05   23.2  23.9    1.5  1  ABC2_membrane_3  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.6  15.6   1.2e-26     1e-22       6     208 ..      10     218 ..       5     220 .. 0.91
   2 ?   -3.8   1.4      0.77   6.9e+03     111     122 ..     231     242 ..     222     247 .. 0.41

  Alignments for each domain:
  == domain 1  score: 80.6 bits;  conditional E-value: 1.2e-26
                     ABC2_membrane   6 llkreflqrwrdpslgllwrliqplllalvfgtvfgnlg..nsedglnr.......pgllffsvlflafsaltsvap 73 
                                       + + +++ ++++ + +++++l+ p+l++l fg+    +g  + e+ +         pg+++ s l+ ++ ++++ ++
  gi|474934760|ref|YP_007688342.1|  10 VAWADLRFMKHNAMNIVISSLMAPILYLLAFGYGLN-AGdvEIEGHM-VpyldfviPGIIALSSLNGSYGSTATRMN 84 
                                       67889999999************************8.4544444444.145889*********************** PP

                     ABC2_membrane  74 vferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldls..rf.flflllllltalaassl 147
                                       v     +++++++  pl s sa++++k+++ ++++++ ++++++i + l   +++  +f  +f+++l+ +++++s l
  gi|474934760|ref|YP_007688342.1|  85 VQRLYYRSFDEMMMCPL-SNSAIIIGKATLGILRGMFSCMLMFIIGFAL---EPDfmNFtPWFVVTLVTCTFTFSLL 157
                                       *****************.*****************************97...3333356679*************** PP

                     ABC2_membrane 148 gllisalapsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrsn 208
                                       g   + +++s++ +++++slv++p+++l+G f+++ ++p+w q++ y++Plt a + +r++
  gi|474934760|ref|YP_007688342.1| 158 GETCALMVSSHQGMATFGSLVITPMTFLCGTFFNVANLPEWAQAVLYALPLTEASSCFRAA 218
                                       **************************************99**************9999986 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 0.77
                     ABC2_membrane 111 qalifllivyfl 122
                                       ++++ + +++fl
  gi|474934760|ref|YP_007688342.1| 231 LVIVAFGVAFFL 242
                                       222222233333 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2  23.9   3.6e-09   3.2e-05     191     342 ..      92     243 ..      56     246 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 3.6e-09
                   ABC2_membrane_3 191 ikelqlvsgvsplqywlskilgdflvyllqlllilllafglgipfg..nlglll.llfllfglayialgyllsslfk 264
                                           ++++++s+++++++k +   l ++++++l++++ f+  ++ +  n+   + + ++   ++++ lg  +  +++
  gi|474934760|ref|YP_007688342.1|  92 SFDEMMMCPLSNSAIIIGKATLGILRGMFSCMLMFIIGFA--LEPDfmNFTPWFvVTLVTCTFTFSLLGETCALMVS 166
                                       555689*******************************999..66665577655515555558899999********* PP

                   ABC2_membrane_3 265 nsetaqilifivilllsgffgglfpledlpsalkwifsiiPffapglgllrlitgdplweillsliilalfavvyll 341
                                       ++  + ++ ++vi ++ +++g +f + +lp++++ +++ +P++  +  +       + ++il+ l+i  +f+v+++l
  gi|474934760|ref|YP_007688342.1| 167 SHQGMATFGSLVITPMTFLCGTFFNVANLPEWAQAVLYALPLTEASSCFRAATLDIYAFPILQYLVIV-AFGVAFFL 242
                                       **9999********88888888888************************8888766778988887775.66666666 PP

                   ABC2_membrane_3 342 l 342
                                       +
  gi|474934760|ref|YP_007688342.1| 243 I 243
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.55
# Mc/sec: 1378.52
//
Query:       gi|474934761|ref|YP_007688343.1|  [L=281]
Description: Cobalamin biosynthesis protein CobN-related Mg-chelatase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.8e-92  309.2   0.3    6.5e-92  309.0   0.3    1.0  1  CobN-Mg_chel  CobN/Magnesium Chelatase


Domain annotation for each model (and alignments):
>> CobN-Mg_chel  CobN/Magnesium Chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  309.0   0.3   3.6e-96   6.5e-92     833    1088 ..       1     260 [.       1     261 [. 0.98

  Alignments for each domain:
  == domain 1  score: 309.0 bits;  conditional E-value: 3.6e-96
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  833 lvaeldEpeedNfvrkhvleeeaeleeke....eaeeratyRvFgskpGaYgagvqeliessnWedeedLaeaYl 903 
                                        ++a+ldE++++N++++++++++ e  +++    ea+++a+yR+Fg++pG+Yg g+++l++++nW++ +dL ++Y+
  gi|474934761|ref|YP_007688343.1|    1 MIAALDEDDDQNYLAANIRRDTVEAIAQGvpvdEAQREASYRIFGDAPGQYGCGISDLVQTGNWKSVDDLRDTYV 75  
                                        699*******************99999656555888*************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  904 nwssyaYgkgaegeeaeeafearLkrvdvvvqnqdsrehdlldsddyyqflGGltaavrslsgkkpeayfgdssn 978 
                                        ++++y+Ygkg +ge+++e+f++rLk +dv+v+n+++r +d+ld+dd ++ lGG+taav++ +g+kp +++gdss+
  gi|474934761|ref|YP_007688343.1|   76 KHGCYVYGKGLKGEAKPEMFRKRLKIMDVTVKNHNTRAVDMLDMDDDFDCLGGFTAAVTAEKGQKPVSFMGDSSD 150 
                                        *************************************************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  979 penpkvrtlkeeiarelrsrvlNPkWiegmmrhGykGafelaatvdnlfgwdatadvvddwvyeevaetYvlDee 1053
                                        ++n k+rt +ee++  +rs++ NPkW++g+++hG++Ga+el++ +d+++gw+at+d++++w+y+++a+++vlD+e
  gi|474934761|ref|YP_007688343.1|  151 TQNLKLRTTEEECRFIFRSKIDNPKWLNGLKQHGFAGAKELSKLFDYTMGWSATEDIIENWMYDDLANRFVLDKE 225 
                                        *************************************************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel 1054 vrefleekNpwAlreiaerLlEaarrglWeaseet 1088
                                        ++e+++++Np+A+ ++ +rL Ea +rg+W+as+e+
  gi|474934761|ref|YP_007688343.1|  226 TQEWIKDENPYAMMAMLARLQEAVDRGFWDASDEM 260 
                                        ********************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1789.29
//
Query:       gi|474934762|ref|YP_007688344.1|  [L=963]
Description: Cobalamin biosynthesis protein CobN-related Mg-chelatase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   6.2e-249  828.9   0.0   7.5e-249  828.6   0.0    1.0  1  CobN-Mg_chel  CobN/Magnesium Chelatase
  ------ inclusion threshold ------
      0.021   14.0   0.3      0.053   12.7   0.1    1.7  2  PLU-1         PLU-1-like protein
      0.068   12.0   0.1        0.1   11.5   0.1    1.1  1  CALCOCO1      Calcium binding and coiled-coil domain (CALCOCO
       0.14   11.8   0.0       0.25   11.0   0.0    1.3  1  Maelstrom     piRNA pathway germ-plasm component
       0.15   11.8   0.1         24    4.7   0.0    2.8  3  DUF2635       Protein of unknown function (DUF2635)


Domain annotation for each model (and alignments):
>> CobN-Mg_chel  CobN/Magnesium Chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  828.6   0.0  2.1e-252  7.5e-249       7     831 ..     123     963 .]     119     963 .] 0.92

  Alignments for each domain:
  == domain 1  score: 828.6 bits;  conditional E-value: 2.1e-252
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel   7 ggveNlknllryladkllgkkeeeveppvelpeegiyhpdakelfesleeylewykkakkekaptvgilfyrahlla 83 
                                       gg+eN  ++++ l + + +    +v++pv+  ++g+y p   + f    +++e +k+  ++ +p+v i+f ++ ++ 
  gi|474934762|ref|YP_007688344.1| 123 GGDENNFSVVKKLLNMFDN-AGLKVPDPVRPMAQGVYVPGRGA-F----TFEEGLKDVGSTGRPVVLITFVYTFYIR 193
                                       6777877888888887775.556889999999*****988654.2....233344456899**************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx..x....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  84 gntavidaliraleerglnvlpvfvssl..d....seaqealeelftkegeekvdalinttsfalvkgpaeeeeeea 154
                                       +nt+++d+l +a+e++g ++l++f++++  +      +++ +++++ ++g++ vda+int++f+ +  ++ +  e+ 
  gi|474934762|ref|YP_007688344.1| 194 HNTRAMDELYHAVERAGGEPLAIFYKTYadEvvgsIGVSAIVDRYLLRDGKPIVDAVINTIGFSSTLIASPGCGEQV 270
                                       ***************************99625566999*************************87766655555444 PP

                                       xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel 155 eeea.lkelnvPvlqailssqsreeWeessqGlspldlamsvalpEldGriepvvisfkeeeeeetevekyepiper 230
                                       +e++ +++lnvPv+qai +++  ++W+es+ Gl p d+amsv+ pE+dG+i+ v++ ++e  + e++  k +pi+er
  gi|474934762|ref|YP_007688344.1| 271 SEDNfYERLNVPVIQAINLYGPAKAWRESPFGLGPADIAMSVVDPEFDGQIDGVPYCGTE--KMENGDYKQVPIEER 345
                                       444469****************************************************65..4688899******** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel 231 vervadlaarwarLrrkpnaekkvaiilanyppgegrlgnavgLdvpaSlvnlLkalkeeGYdveelpesgdeLiel 307
                                       ++++a++a rw +L + +++ekkvai+++ ypp+++  g + gLd++aS+ ++L+++k++GY ++  pe+g++L+++
  gi|474934762|ref|YP_007688344.1| 346 CSALAEMAVRWGTLTHRKQSEKKVAILIYMYPPRQDLAGGGYGLDTFASVTSMLERMKDAGYALDWVPEDGKDLVNR 422
                                       ****************************************************************877********** PP

                                       xxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel 308 lleggtndpew...eelkvgaaallpaeeYeewfeeLpeelreeveerWgeppgemveeeksgekklvipglqlGnv 381
                                       +leg tnd +w   ++++  a++++++e+Y +wf+e+ e++r++ +e+Wg+ pg    + +  ++k+++pg+  Gnv
  gi|474934762|ref|YP_007688344.1| 423 MLEGITNDDNWrseAQMREAAVDMVTKEQYDAWFDEIAESARKRFVEAWGDTPG----DIHVLDGKILLPGIMNGNV 495
                                       ***********876555669**********************************....5666789************ PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel 382 fvgvQPargyeedpsklyhdpdlpPthqYlAfYlWlreefgadavvHvGkHGtlEwlPGKqvglseecyPdillgdl 458
                                       f+g QP rg  + +++ +hdp ++P+hqYl fY+Wl+ ++gadavvH+G+HGtlEwlPGK++gls+ec Pdi+l +l
  gi|474934762|ref|YP_007688344.1| 496 FIGFQPDRG--KCTTESVHDPWTAPPHQYLGFYRWLKYVWGADAVVHIGTHGTLEWLPGKSAGLSDECDPDIVLSKL 570
                                       *********..446678************************************************************ PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                      CobN-Mg_chel 459 PhlYpYivnnpgEGtqAKRRsyAviidHltPpmtraelygelaeLeelideYeeaesldpe.rlkalreqilelvee 534
                                       P++ pYi++npgEG+q KRR+yAv+  Hl+P+m+r++ y+e++eLe++++++ +a++++++ +l+ + e++++l+++
  gi|474934762|ref|YP_007688344.1| 571 PNINPYIIDNPGEGMQSKRRQYAVTTTHLIPAMARSGGYDEINELESAVQSFLKAKEQKQTdKLPLIMEKVISLCVK 647
                                       ********************************************************997777*************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel 535 lnldkdlgleeakeeeeeefeellekldgyleelkeaqirdglhilGeapegeqlvdlvvailrleneegeslteal 611
                                       ln+ +dl+l+  +++++ee+++ ++kl++y+ e+k+a+i+dglhilG+ pege+++++++ ++r++n++ +sl+ea+
  gi|474934762|ref|YP_007688344.1| 648 LNMMSDLNLS--ADATAEEMDSKIDKLYDYILEVKDALIKDGLHILGQIPEGERMAETLYMLVRYRNGDVPSLREAV 722
                                       *******777..56789999999****************************************************** PP

                                       xxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......... RF
                      CobN-Mg_chel 612 aealgldlde...leeksekelrtagdalealeeeaeelveelleeeaeeeeaeaeeleeeeeeeee.......... 675
                                       a+++gl++++     +  + + + +g++++ +++   el+e++ e +++++ea   +  +  ++ e+          
  gi|474934762|ref|YP_007688344.1| 723 AHTYGLEMEDllkDPSGVQPDGHLNGEMTDIIDAGMYELIEKCQEYDFDASEAIGFAVGRYPNAGEDmkqaiefvcg 799
                                       *********9655334455667889999999**************9999887755555444444444889******* PP

                                       .......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel 676 .......eteeEitallraLdGeyippgpsGdptrgraevLPTGrNfysvDpraiPteaAwevGkklaeellerylq 745
                                              ++ +Ei ++l+aL G+++ppgpsG p rgra++LPTGrNfys+Dp++iP +++we+G k+ae+++ery q
  gi|474934762|ref|YP_007688344.1| 800 flidavrHMGDEIGNVLKALGGGFVPPGPSGCPGRGRAQILPTGRNFYSIDPDSIPWHSSWEIGSKMAEQMVERYIQ 876
                                       ******8777******************************************************************* PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel 746 ehgeyPekvglslwgtetmrteGediAqiLallGvrPvwdaa.grvvdlelipleeLgRPRiDVtvriSGffRDafp 821
                                       ++g  P+++g++lw+t+tm+t+G+d+A iL l+G rPvwd+  grv+d+e+ip+eeLgRPRiDVtvriSG+fRD+fp
  gi|474934762|ref|YP_007688344.1| 877 DNGVCPQTIGIILWATDTMKTGGDDVAYILRLMGLRPVWDGYgGRVKDVEVIPIEELGRPRIDVTVRISGLFRDTFP 953
                                       ***************************************************************************** PP

                                       xxxxxxxxxx RF
                      CobN-Mg_chel 822 nlielldkav 831
                                       nl +l+d+ v
  gi|474934762|ref|YP_007688344.1| 954 NLSNLIDRGV 963
                                       *******976 PP

>> PLU-1  PLU-1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   1.5e-05     0.053     212     276 ..     609     674 ..     595     696 .. 0.91
   2 ?   -3.0   0.0      0.87   3.1e+03      87     103 ..     758     774 ..     755     776 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.5e-05
                             PLU-1 212 leaaekweekakelLeareklsleeLeallneaqeipvslpslaale.eilkkarewqrkveelik 276
                                       +++ +++e+ ++ +L+a+e+ + ++L  +++++ +++v l+ +++l+ ++   a+e+ +k+++l+ 
  gi|474934762|ref|YP_007688344.1| 609 YDEINELESAVQSFLKAKEQKQTDKLPLIMEKVISLCVKLNMMSDLNlSADATAEEMDSKIDKLYD 674
                                       67899*****************************************98777899999999999975 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.87
                             PLU-1  87 lekLleeldslpFdlpe 103
                                       ++ L+e+ + ++Fd++e
  gi|474934762|ref|YP_007688344.1| 758 MYELIEKCQEYDFDASE 774
                                       45555555555555554 PP

>> CALCOCO1  Calcium binding and coiled-coil domain (CALCOCO1) like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   2.8e-05       0.1     365     421 ..     611     668 ..     604     681 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.8e-05
                          CALCOCO1 365 eLqElkaslrvaQkEkEqlqaekqEl.leyirqLEqrlekvadakWseaaltekeeaa 421
                                       e++El ++++ + k kEq+q++k  l +e +  L  +l++++d   s++a++e+ +  
  gi|474934762|ref|YP_007688344.1| 611 EINELESAVQSFLKAKEQKQTDKLPLiMEKVISLCVKLNMMSDLNLSADATAEEMDSK 668
                                       99*********************986599*********************99988765 PP

>> Maelstrom  piRNA pathway germ-plasm component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   7.1e-05      0.25      37     137 ..     581     685 ..     573     696 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.1e-05
                                       --------HHHHHH.HTT----TTS--SB--HHHHHHHHHHHHHHHH-SS..S-EEEEE-GGGHHHHHHHHHHH-.. CS
                         Maelstrom  37 lilgqardaqrhsd.etHqlplppnalgesdlkklveeilsflessseksneksliiltkeeeisvvksclknla.. 110
                                       +  g++++  +++  +tH +p   +  g +++++l + ++sfl+ +++k+ +k+++i+ k  ++ v  ++++ l+  
  gi|474934762|ref|YP_007688344.1| 581 PGEGMQSKRRQYAVtTTHLIPAMARSGGYDEINELESAVQSFLKAKEQKQTDKLPLIMEKVISLCVKLNMMSDLNls 657
                                       4567666666665549******************************9988899999999999999999999999988 PP

                                       .---HHHH-EEEEEHHHHHHHHHHHHHH CS
                         Maelstrom 111 .edvkfeeevsvydiqelfldlkkevld 137
                                        + + +e++ ++ ++ + +l++k ++++
  gi|474934762|ref|YP_007688344.1| 658 aDATAEEMDSKIDKLYDYILEVKDALIK 685
                                       7777777889999999999999888775 PP

>> DUF2635  Protein of unknown function (DUF2635)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1     0.012        44       5      22 ..     142     163 ..     141     166 .. 0.76
   2 ?   -2.7   0.0       1.5   5.2e+03      22      33 ..     267     278 ..     264     278 .. 0.88
   3 ?    4.7   0.0    0.0068        24      20      40 ..     695     715 ..     694     721 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.012
                           DUF2635   5 aGlkVRdPet....gelLpaeG 22 
                                       aGlkV+dP+     g ++p  G
  gi|474934762|ref|YP_007688344.1| 142 AGLKVPDPVRpmaqGVYVPGRG 163
                                       8*******97666666666555 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.5
                           DUF2635  22 GeevprtlyWlR 33 
                                       Ge+v  + ++ R
  gi|474934762|ref|YP_007688344.1| 267 GEQVSEDNFYER 278
                                       9********987 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.0068
                           DUF2635  20 aeGeevprtlyWlRRlkdGDv 40 
                                       +eGe+   tly l R ++GDv
  gi|474934762|ref|YP_007688344.1| 695 PEGERMAETLYMLVRYRNGDV 715
                                       69******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (963 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.80u 0.38s 00:00:01.18 Elapsed: 00:00:00.51
# Mc/sec: 5728.04
//
Query:       gi|474934763|ref|YP_007688345.1|  [L=1251]
Description: Cobalamin biosynthesis protein CobN-related Mg-chelatase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
          0 1169.4   0.0          0 1169.2   0.0    1.0  1  CobN-Mg_chel  CobN/Magnesium Chelatase
     0.0059   16.7   0.6      0.018   15.2   0.6    1.8  1  DUF3479       Domain of unknown function (DUF3479)
  ------ inclusion threshold ------
       0.79   10.6   6.2         33    5.4   0.3    4.1  4  FliT          Flagellar protein FliT


Domain annotation for each model (and alignments):
>> CobN-Mg_chel  CobN/Magnesium Chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1169.2   0.0         0         0       2    1087 ..     119    1229 ..     118    1231 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1169.2 bits;  conditional E-value: 0
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel    2 aYlkeggveNlknllryladkllgkkeeeveppvelpeegiyhpdakelfesleeylewykkakkekaptvgilf 76  
                                        +Y ++ g eN   +++y+a+ l + +++++++pve  ++g+yh  +++ +++ e+yl++     ++++ t+gilf
  gi|474934763|ref|YP_007688345.1|  119 RYSAARGFENEYGMMHYMARLLGK-TQTTPPEPVEQRRDGYYHKGMDRDISR-EDYLKT----LDPSKMTIGILF 187 
                                        79999************9998886.777999************777665544.477766....79********** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....x..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel   77 yrahllagntavidaliraleerglnvlpvfvssl....d..seaqealeelftkegeekvdalinttsfalvkg 145 
                                          + +l +n+a+idal +++e+rg+n lp+f+s++    d  + ++++++++ft++g++ +da+i  tsf+++ +
  gi|474934763|ref|YP_007688345.1|  188 ASSLWLYDNLAAIDALTDEIERRGMNSLPLFYSAVsyktDgeEGTRATIRKYFTDNGKPIPDAVIIHTSFSVMYN 262 
                                        *********************************99987625589999*************************999 PP

                                        xxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  146 paeeeeeeaeeea...lkelnvPvlqailssqsreeWeessqGlspldlamsvalpEldGriepvvisfkeeeee 217 
                                        +++++  e +e++    + lnvP+l++++++++++++e+++ G ++ +++ +va pE+dG i++v+i+ +    +
  gi|474934763|ref|YP_007688345.1|  263 SRQDMGVEIQERDnyyRSLLNVPMLNTLTITGEYSDFENDKVGADKHTVTNNVAFPEIDGDIITVPIAWTP---R 334 
                                        98888776666668977889*************************************************43...5 PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  218 etevekyepipervervadlaarwarLrrkpnaekkvaiilanyppgegrlgnavgLdvpaSlvnlLkalkeeGY 292 
                                        +++++k +pip+r+erv+dla rwa+Lr++pn+ekkvai+l+++ p+ g +gna+gLd+++S++ lL+++ + GY
  gi|474934763|ref|YP_007688345.1|  335 KSGMKKNVPIPDRIERVVDLAYRWAKLRHMPNSEKKVAILLWQSRPNSGVIGNAAGLDSVESIAGLLRRMSASGY 409 
                                        799************************************************************************ PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  293 dveelpesgdeLiellleggtndpew...eelkvgaaallpaeeYeewfeeLpeelreeveerWgeppgemveee 364 
                                         ve+ p+sg +L++++l+g+tnd +    e+++ +aa+l+pa++Y + ++++p+  re  e++Wg+ppg    + 
  gi|474934763|ref|YP_007688345.1|  410 IVENVPDSGRALVDEILDGVTNDLDNmsaEAMRKKAADLVPASDYIKEYSKVPQWDREMTEKDWGDPPG----DI 480 
                                        **999******************99988766677***********************************....55 PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  365 ksgekklvipglqlGnvfvgvQPargyeedpsklyhdpdlpPthqYlAfYlWlreefgadavvHvGkHGtlEwlP 439 
                                          ++++++ipg+  Gnvfvg QP rg  e  ++++hdp l  +hqYl +Y+W+r++f+ad+v+HvG+HGt+EwlP
  gi|474934763|ref|YP_007688345.1|  481 CVDRDRIIIPGIVKGNVFVGYQPLRGRAEKMEQNIHDPVLFAQHQYLEYYRWIRDVFKADMVIHVGTHGTIEWLP 555 
                                        66799*********************999999******************************************* PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  440 GKqvglseecyPdillgdlPhlYpYivnnpgEGtqAKRRsyAviidHltPpmtraelygelaeLeelideYeeae 514 
                                        GK+vg+s++c Pd++lg lP+lY+Yiv++pgEG+q KRR ++v+i+H+ P m+ra+ y+e+a+ e+ i+eY e +
  gi|474934763|ref|YP_007688345.1|  556 GKNVGMSQKCDPDVVLGGLPNLYIYIVDDPGEGIQCKRRIESVLIEHMPPSMARAGQYDEIAQVERPIQEYLEHK 630 
                                        *************************************************************************99 PP

                                        xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  515 sl.dperlkalreqilelveelnldkdlgleeakeeeeeefeellekldgyleelkeaqirdglhilGeapegeq 588 
                                        ++ d++r+  l ++i e ++e+++ +d+gl ++k+  +e fe  + +l++yl+e+k++++r +lh+lG++p++++
  gi|474934763|ref|YP_007688345.1|  631 ATnDSKRRAVLVKNIYEAAKEHKMLNDIGLGDDKDPGPEGFEPHIVELHEYLSEVKDTLVRADLHVLGRVPKEDH 705 
                                        9845559999999****************9999****************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  589 lvdlvvailrleneegesltealaealgldlde...leeksekelrtagdalealeeeaeelveelleeeaeeee 660 
                                          ++v++++rl+n++ +sl++a+a+++g+d+++     + +  + + +++a++++++  +e+++ + + + + ++
  gi|474934763|ref|YP_007688345.1|  706 YDEMVYSLMRLDNGDVKSLRDAFADSMGIDIQKaidDPAGRLPSGELNSSAVDRVDDLLQEFLKYARSVKYDIQS 780 
                                        ********************************9776333344444556666777777767766666666555555 PP

                                        xxxxxxxxxxxxxxx.................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  661 aeaeeleeeeeeeee.................eteeEitallraLdGeyippgpsGdptrgraevLPTGrNfysv 718 
                                          ++ +++  +++++                  +++Ei+++l++++G+y+ pgp+G+ptrg+a++LP GrNfys+
  gi|474934763|ref|YP_007688345.1|  781 CISKLENDLGKASKDlresvsfmcsrvvpgidGMTDEIDNILHGMNGGYVLPGPAGAPTRGNAHILPMGRNFYSL 855 
                                        5555555544444448889999999******97789*************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                      CobN-Mg_chel  719 DpraiPteaAwevGkklaeellerylqehgeyPekvglslwgtetmrteGediAqiLallGvrPvwdaa.grvvd 792 
                                        Dp+++P++a+we+Gkk+a++++e+y++e+ge+P++vg+++w+t+tm+t+G+d+A iL+llGvrPvw+ a g+v +
  gi|474934763|ref|YP_007688345.1|  856 DPDTVPSRASWEIGKKMADQMIEKYVAEKGEFPREVGFIIWATDTMKTGGDDVAYILWLLGVRPVWSMAgGQVIG 930 
                                        *************************************************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xx RF
                      CobN-Mg_chel  793 lelipleeLgRPRiDVtvriSGffRDafpnlielldkavelvaeldEpeedNfvrkhvleeeaeleeke....ea 863 
                                        le++p eeL+RPR+DV v+i+G+fRD+fpnli+l+d+av+lvaeldE++edN ++++ +++  e  +++    ea
  gi|474934763|ref|YP_007688345.1|  931 LEVVPKEELKRPRVDVSVNITGLFRDTFPNLIDLIDDAVKLVAELDESDEDNALAANLRRDIVEGIAEGltpdEA 1005
                                        **************************************************************9999944544477 PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  864 eeratyRvFgskpGaYgagvqeliessnWedeedLaeaYlnwssyaYgkgaegeeaeeafearLkrvdvvvqnqd 938 
                                        ++r ++R+Fg++ G Yg+gv+ +ies++W++ +dLa++Y++w s+ Y+kg++g++ +  f +r+++v v+v+n  
  gi|474934763|ref|YP_007688345.1| 1006 RQRNSVRIFGAPLGGYGTGVNFAIESGAWKTVNDLADVYIDWCSNGYSKGNYGQKMRGEFIRRFSKVGVTVKNMP 1080
                                        7************************************************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  939 srehdlldsddyyqflGGltaavrslsgkkpeayfgdssnpenpkvrtlkeeiarelrsrvlNPkWiegmmrhGy 1013
                                         re+dlld+dd+y++lGG++a vr++  k++ +y+gd s+p+++kvr+ k+e++  +rs+vlNPk+i+g+++hGy
  gi|474934763|ref|YP_007688345.1| 1081 DREIDLLDCDDVYEYLGGMNAFVRAYGRKDAVTYMGDDSDPKKTKVRSTKDELRFAFRSKVLNPKFINGLKEHGY 1155
                                        *************************************************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel 1014 kGafelaatvdnlfgwdatadvvddwvyeevaetYvlDeevrefleekNpwAlreiaerLlEaarrglWeasee 1087
                                        +Ga e+a+  +++++w at+dv +dw+ye++a+++++D++++e++++ Np+A+ +i +rL Ea++rglW+a++e
  gi|474934763|ref|YP_007688345.1| 1156 RGAAEMANLTEYTMAWGATSDVAEDWMYEGLADKFLFDKDTQEWMQDVNPYAMMNILNRLQEAIERGLWNADDE 1229
                                        ************************************************************************98 PP

>> DUF3479  Domain of unknown function (DUF3479)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.6     3e-06     0.018       2     101 ..       5     104 ..       4     105 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3e-06
                           DUF3479   2 vvlvtlesfnasalkraaaelnrelpelelsvfadeelrekpealeelaaavaeAdifiasllfdedq...vealre 75 
                                       +v++  +s  a ++++ a++l++   + ++   +  +++++   ++++ + v++Ad+++   + d +    +e+l++
  gi|474934763|ref|YP_007688345.1|   5 IVIISVQSADAATMAEPAQKLRELGIAPNVLALNSDDIDDDVLVYQDVVRHVRNADFIFIRCMSDTNRfkrFEKLEK 81 
                                       89999****************8766699999*******************************999998333567777 PP

                           DUF3479  76 aleaarekldavlvfeSapelmrltk 101
                                       +le+   +   vl+f  + e+  +t+
  gi|474934763|ref|YP_007688345.1|  82 VLEE---TSAYVLIFSGNAEVTMMTR 104
                                       7777...4569**********99997 PP

>> FliT  Flagellar protein FliT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1     0.016        93       4      31 ..     607     634 ..     606     655 .. 0.81
   2 ?    0.9   0.0      0.14   8.4e+02      32      77 ..     749     794 ..     735     797 .. 0.85
   3 ?    5.4   0.3    0.0056        33      12      49 ..     960     998 ..     956    1009 .. 0.86
   4 ?   -2.5   0.0       1.6   9.4e+03       4      20 ..    1028    1044 ..    1027    1048 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.016
                                       HHHCT-HHHHHHHHHHHHHHHHHHHCS- CS
                              FliT   4 aAragdWdelaaleaerqqlverlreld 31 
                                       +Arag++de+a+ e+  q+++e+ + +d
  gi|474934763|ref|YP_007688345.1| 607 MARAGQYDEIAQVERPIQEYLEHKATND 634
                                       79*****************999877777 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.14
                                       -ST--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHTHH CS
                              FliT  32 aaplspaereekrellrrilandaeirallqprldelqkllgalrr 77 
                                       + +l++++  + ++ll++ l+  + ++  +q   ++l+++lg++++
  gi|474934763|ref|YP_007688345.1| 749 SGELNSSAVDRVDDLLQEFLKYARSVKYDIQSCISKLENDLGKASK 794
                                       5578899999999999999999999999999999999999999987 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.0056
                                       HHHHHHHHHHHHHHHHHCS-.-ST--HHHHHHHHHHHHH CS
                              FliT  12 elaaleaerqqlverlreld.aaplspaereekrellrr 49 
                                       +l++l ++ ++lv++l+e d    l++++r+++ e + +
  gi|474934763|ref|YP_007688345.1| 960 NLIDLIDDAVKLVAELDESDeDNALAANLRRDIVEGIAE 998
                                       799*****************9999999999999998875 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 1.6
                                        HHHCT-HHHHHHHHHHH CS
                              FliT    4 aAragdWdelaaleaer 20  
                                        a+++g W ++++l + +
  gi|474934763|ref|YP_007688345.1| 1028 AIESGAWKTVNDLADVY 1044
                                        7899********99877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.85u 0.31s 00:00:01.15 Elapsed: 00:00:00.48
# Mc/sec: 7770.15
//
Query:       gi|474934764|ref|YP_007688346.1|  [L=75]
Description: hypothetical protein TALC_01199 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0023   16.6   0.6     0.0024   16.5   0.6    1.0  1  MFS_2        MFS/sugar transport protein
     0.0029   17.7   1.8     0.0031   17.6   1.8    1.0  1  DUF3043      Protein of unknown function (DUF3043)
     0.0057   17.0   0.1      0.006   16.9   0.1    1.0  1  DUF1772      Domain of unknown function (DUF1772)
  ------ inclusion threshold ------
      0.016   15.3   2.0      0.016   15.3   2.0    1.0  1  DUF3278      Protein of unknown function (DUF3278)
      0.017   15.3   4.8      0.019   15.2   4.8    1.0  1  CD47         CD47 transmembrane region
      0.028   14.7   0.1      0.033   14.5   0.1    1.1  1  DUF3382      Domain of unknown function (DUF3382)
      0.035   13.2   1.8      0.039   13.0   1.8    1.0  1  ArAE_2_N     Putative ER transporter, 6TM, N-terminal
       0.11   12.7   0.1        0.2   11.9   0.0    1.4  2  UPF0239      Uncharacterised protein family (UPF0239)
       0.13   11.6   4.4       0.14   11.4   4.4    1.1  1  EpsG         EpsG family
       0.27   10.9   1.8       0.37   10.5   1.8    1.3  1  Tetraspanin  Tetraspanin family
       0.52   10.2   5.7       0.22   11.4   0.7    2.2  2  DUF1514      Protein of unknown function (DUF1514)
        3.7    8.5   5.4        2.4    9.1   0.1    2.0  2  EphA2_TM     Ephrin type-A receptor 2 transmembrane domain
        5.2    6.2   4.5        5.6    6.1   4.5    1.0  1  Herpes_LMP1  Herpesvirus latent membrane protein 1 (LMP1)


Domain annotation for each model (and alignments):
>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.6   1.8e-06    0.0024     145     210 ..       7      70 ..       1      73 [. 0.75

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.8e-06
                             MFS_2 145 lggvlaailafllvlilgglkserkgylifaliialLmllgviivvlgtkervem..rkkekteqkek 210
                                       +  vl ai+++++v i +    ++++ +++ ++ ++Lml++++ +vl  ++r ++  +k+ +++++e+
  gi|474934764|ref|YP_007688346.1|   7 IYAVLLAIFIYVVVSIDS----DNTRLMAMYALSTILMLVTIVSAVLLMRNRSNEeiAKRFEEMDREW 70 
                                       334555555555555555....6*****************************9987777777777665 PP

>> DUF3043  Protein of unknown function (DUF3043)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   1.8   2.3e-06    0.0031      82     143 ..       4      69 ..       1      73 [. 0.51

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.3e-06
                           DUF3043  82 flplalvvlvlllv..slvkvpevqavvsl.lllvllllvvidgillgr.kvkkkvrekFpetese 143
                                       fl +  v+l++++     + + +++ ++ + l ++l+l++++ ++ll+r + + +++++F e ++e
  gi|474934764|ref|YP_007688346.1|   4 FLAIYAVLLAIFIYvvVSIDSDNTRLMAMYaLSTILMLVTIVSAVLLMRnRSNEEIAKRFEEMDRE 69 
                                       5555555555522212233334444433332334455666666555554278899*****955554 PP

>> DUF1772  Domain of unknown function (DUF1772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   4.3e-06     0.006      42     103 ..       9      70 ..       1      75 [] 0.60

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.3e-06
                           DUF1772  42 lallsalafaylaaraasrgarllylaaaallllsivpyTllvmvPtNnkLaalk.eedakek 103
                                       ++ll++  +++++ ++ +++  ++y a++ +l+l++++  +l+m+   n+ +a++ ee  +e+
  gi|474934764|ref|YP_007688346.1|   9 AVLLAIFIYVVVSIDSDNTRLMAMY-ALSTILMLVTIVSAVLLMRNRSNEEIAKRfEEMDREW 70 
                                       4444444444444888888888899.6677788889999999999955454444434443333 PP

>> DUF3278  Protein of unknown function (DUF3278)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   2.0   1.1e-05     0.016      36      96 ..       2      62 ..       1      75 [] 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.1e-05
                           DUF3278 36 nafillwlyllilslvalllakktpeselilglvltnlllvvlvsglYiliaskklglatk 96
                                      ++f+ ++ +ll++++ +++   + ++ ++++  ++t+l+lv++vs + ++++ ++ ++a++
  gi|474934764|ref|YP_007688346.1|  2 TVFLAIYAVLLAIFIYVVVSIDSDNTRLMAMYALSTILMLVTIVSAVLLMRNRSNEEIAKR 62
                                      6899999999999999999999999999998888899999999999999999999888865 PP

>> CD47  CD47 transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   4.8   1.4e-05     0.019       3      55 ..       2      53 ..       1      60 [. 0.87

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.4e-05
                              CD47  3 villilaiiLlwgqlgiitlkyksvskklilllvagliitlivvvgaillipg 55
                                       ++l ++ +Ll   ++++ ++++s +++l+ +++ + i+ l+ +v a+ll+ +
  gi|474934764|ref|YP_007688346.1|  2 TVFLAIYAVLLA-IFIYVVVSIDSDNTRLMAMYALSTILMLVTIVSAVLLMRN 53
                                      688999999875.5888889999999***********************9875 PP

>> DUF3382  Domain of unknown function (DUF3382)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   2.4e-05     0.033       8      64 ..       7      61 ..       2      73 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.4e-05
                           DUF3382  8 iaallalvlfvpilGlqleldgtrlvleprwglvaiavavvfvgqLlrplllqalka 64
                                      i a+l+++ +++++ +    d+trl     + +++++v +v ++ L+r+   + +++
  gi|474934764|ref|YP_007688346.1|  7 IYAVLLAIFIYVVVSI--DSDNTRLMAMYALSTILMLVTIVSAVLLMRNRSNEEIAK 61
                                      4566666666666666..**************************9999887766665 PP

>> ArAE_2_N  Putative ER transporter, 6TM, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.8   2.8e-05     0.039     142     189 ..       6      53 ..       2      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.8e-05
                          ArAE_2_N 142 vvyavllcvflffvgrlrakspkfalgaifgiIaadvfltyapmlPlf 189
                                       ++yavll++f+++v ++ + +  +   +  ++I + v++ +a++l  +
  gi|474934764|ref|YP_007688346.1|   6 AIYAVLLAIFIYVVVSIDSDNTRLMAMYALSTILMLVTIVSAVLLMRN 53 
                                       8****************************************9988655 PP

>> UPF0239  Uncharacterised protein family (UPF0239)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       4.6   6.3e+03      39      42 ..      17      20 ..       6      32 .. 0.51
   2 ?   11.9   0.0   0.00014       0.2      29      65 ..      37      73 ..      32      75 .] 0.84

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4.6
                           UPF0239 39 iill 42
                                       +++
  gi|474934764|ref|YP_007688346.1| 17 YVVV 20
                                      2222 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00014
                           UPF0239 29 AifqlvCilAiillpsskseesveeeaesseeksseq 65
                                       i+ lv i  ++ll  ++s+e++ +  e+++++  e+
  gi|474934764|ref|YP_007688346.1| 37 TILMLVTIVSAVLLMRNRSNEEIAKRFEEMDREWEEK 73
                                      6899*****9999********9999999999965554 PP

>> EpsG  EpsG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   4.4    0.0001      0.14      65     104 ..       2      47 ..       1      56 [. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0001
                              EpsG  65 qfflfilalitllllfvfikkyskn......lflslllfllslffl 104
                                       ++fl+i+a++  ++++v++   s+n      + ls++l+l+++  +
  gi|474934764|ref|YP_007688346.1|   2 TVFLAIYAVLLAIFIYVVVSIDSDNtrlmamYALSTILMLVTIVSA 47 
                                       68***********************888877777777776666555 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.8   0.00027      0.37      53     119 ..       4      63 ..       1      75 [] 0.67

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00027
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--HHH........HHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Tetraspanin  53 livvGvllfllgflGcigalkenkcllltfsllllvlfllelaagilgfvfsdkargkvseiinnai 119
                                       ++++ ++l+++ +  ++ +  +n+ l+++++l  ++++++ ++a++l+   s+++       i + +
  gi|474934764|ref|YP_007688346.1|   4 FLAIYAVLLAIFIYVVVSIDSDNTRLMAMYALSTILMLVTIVSAVLLMRNRSNEE-------IAKRF 63 
                                       4455556666666778889999*********998888888888777777777664.......44433 PP

>> DUF1514  Protein of unknown function (DUF1514)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.7   0.00016      0.22       6      26 ..       9      29 ..       1      38 [. 0.84
   2 ?    1.6   0.9      0.18   2.5e+02       4      14 ..      41      51 ..      30      67 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00016
                           DUF1514  6 sivlailLLvllsiisdkake 26
                                      ++ lai++ v++si sd  + 
  gi|474934764|ref|YP_007688346.1|  9 AVLLAIFIYVVVSIDSDNTRL 29
                                      6789*************9885 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.18
                           DUF1514  4 visivlailLL 14
                                       ++iv a+lL+
  gi|474934764|ref|YP_007688346.1| 41 LVTIVSAVLLM 51
                                      34566555554 PP

>> EphA2_TM  Ephrin type-A receptor 2 transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   1.7      0.31   4.3e+02       7      22 ..       6      21 ..       1      33 [. 0.46
   2 ?    9.1   0.1    0.0018       2.4       6      33 ..      34      61 ..      29      75 .] 0.48

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.31
                          EphA2_TM  7 aglvllvilvilvlvl 22
                                      a   +l+++ i v+v 
  gi|474934764|ref|YP_007688346.1|  6 AIYAVLLAIFIYVVVS 21
                                      3333444433333332 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0018
                          EphA2_TM  6 vaglvllvilvilvlvlvrrrsknrkqk 33
                                      ++  +l++++++ +++l+r+rs+++ +k
  gi|474934764|ref|YP_007688346.1| 34 ALSTILMLVTIVSAVLLMRNRSNEEIAK 61
                                      3444444444555555554554444333 PP

>> Herpes_LMP1  Herpesvirus latent membrane protein 1 (LMP1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   4.5     0.004       5.6      27      73 ..       5      52 ..       1      57 [. 0.58

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.004
                                      XXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXX..XXXXXXXXXXXXXX CS
                       Herpes_LMP1 27 lallllllallfwlyivms.dwtggallvlysfa..llliiiiliififr 73
                                      la+  +lla++  +y+v+s d     l+ +y+++  l+l+ i+  ++++r
  gi|474934764|ref|YP_007688346.1|  5 LAIYAVLLAIF--IYVVVSiDSDNTRLMAMYALStiLMLVTIVSAVLLMR 52
                                      56666666654..4555543666677888887761155555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1815  (0.101233); expected 358.6 (0.02)
Passed bias filter:                      923  (0.0514808); expected 358.6 (0.02)
Passed Vit filter:                       138  (0.00769703); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 470.57
//
Query:       gi|474934765|ref|YP_007688347.1|  [L=343]
Description: protoporphyrin IX magnesium-chelatase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-24   85.1   0.2    4.6e-24   84.0   0.2    1.6  1  AAA_lid_2        AAA lid domain
    6.7e-10   38.7   0.0    4.8e-05   22.8   0.0    2.5  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    1.8e-09   37.7   0.2    2.9e-05   24.1   0.0    2.9  3  AAA_5            AAA domain (dynein-related subfamily)
    0.00062   18.9   0.0       0.14   11.2   0.0    3.4  2  MCM              MCM P-loop domain
     0.0092   15.7   0.0       0.59    9.8   0.0    2.2  2  Sigma54_activat  Sigma-54 interaction domain
  ------ inclusion threshold ------
      0.048   14.0   0.2       0.12   12.7   0.2    1.8  1  AAA_16           AAA ATPase domain
      0.074   12.9   0.0        1.1    9.2   0.0    2.3  2  AAA_3            ATPase family associated with various cellul


Domain annotation for each model (and alignments):
>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.0   0.2   1.8e-27   4.6e-24       3      71 ..     269     337 ..     267     339 .. 0.93

  Alignments for each domain:
  == domain 1  score: 84.0 bits;  conditional E-value: 1.8e-27
                         AAA_lid_2   3 trahlaielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlrrepeaegetteeive 71 
                                       ++++ ++ +g++g+Rad++l++aA+A+Aalegr++Vt++D+++ a+lVL+HRl+r+p++e+  ++e++e
  gi|474934765|ref|YP_007688347.1| 269 MIVSVMVHFGIDGHRADITLMKAAKANAALEGRNKVTKDDIRQTAELVLSHRLKRKPFEEKALDREELE 337
                                       5788999****************************************************9977777665 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   1.6e-05     0.042       2      48 ..      10      58 ..       9      64 .. 0.87
   2 !   22.8   0.0   1.9e-08   4.8e-05      92     158 ..     124     190 ..     117     198 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.6e-05
                      Mg_chelatase  2 lkdvkGqeeakraleiaaa..GgHnlllvGppGsGKtmlakrlpsllpp 48
                                      +++v+Gq++ kral + ++  G   +l+ G  G+ K+   + l+ +lp 
  gi|474934765|ref|YP_007688347.1| 10 FTEVVGQDDMKRALLLNIIdpGIGGVLIKGEKGTAKSTTVRSLNWILPY 58
                                      689**********865554339*************************96 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 1.9e-08
                      Mg_chelatase  92 GggskpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNp 158
                                        g +k +pG ++ a+  +L++DE+  ++ + ++ L +    g   ++r   ++++pa+f lv +mNp
  gi|474934765|ref|YP_007688347.1| 124 TGEKKFEPGVLAAANGNILYVDEVNLLDDHLVDLLLDSAAMGINYVEREGVSFSHPAKFVLVGTMNP 190
                                       577899************************************************************9 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00021      0.53       1      23 [.      34      56 ..      34      65 .. 0.85
   2 !   24.1   0.0   1.1e-08   2.9e-05      32     138 .]     103     203 ..      89     203 .. 0.77
   3 ?   -1.6   0.0      0.94   2.4e+03      40      63 ..     208     231 ..     206     238 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00021
                                      EEEEE--SSSSHHHHHHHGGGGB CS
                             AAA_5  1 dvlLvGppGtgKselaerlaaal 23
                                      +vl++G++Gt+Ks+ +++l   l
  gi|474934765|ref|YP_007688347.1| 34 GVLIKGEKGTAKSTTVRSLNWIL 56
                                      599**************997665 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 1.1e-08
                                       --TT--HHHHH--B--.............--------G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE CS
                             AAA_5  32 ltrdtteedlkgrreik....ngttslvdsplvraaregeilvlDEveraesevlnsLlslleerrllleeggelvk 104
                                       l+ + te+ + g ++++     g++++++++l   a +g il++DEv+ ++++ ++ L   l+   + ++   ++  
  gi|474934765|ref|YP_007688347.1| 103 LPLSATEDRVSGTLDLEhvlkTGEKKFEPGVLA--AANGNILYVDEVNLLDDHLVDLL---LDSAAMGINYVEREG- 173
                                       5556788999999999889889*********98..89***********8888888877...777777754443333. PP

                                       ---.......-EEEEEESS--.-TT-TTHHHHTT- CS
                             AAA_5 105 akndd.llerfrviatanpldrslnelspalrsRf 138
                                       ++  +  + +f +++t+np +    +l p+l++Rf
  gi|474934765|ref|YP_007688347.1| 174 VSF-ShPA-KFVLVGTMNPEE---GDLRPQLLDRF 203
                                       322.2123.3*********99...67788999998 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.94
                                       HHH--B--.........------- CS
                             AAA_5  40 dlkgrreikngttslvdsplvraa 63 
                                       d+kg+r++k++ ++ ++ ++++a 
  gi|474934765|ref|YP_007688347.1| 208 DIKGERDVKMRAEVVKKRVAYDAD 231
                                       899999*99999999999988775 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.015        39      25      81 ..      12      56 ..       5      65 .. 0.66
   2 !   11.2   0.0   5.6e-05      0.14     106     178 ..     123     195 ..     112     227 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.015
                                      TSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHHHHS CS
                               MCM 25 siyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyvekla 81
                                      +++g++d+k+a+ll ++ +                vl+ g+ gtaKs+ +++++ ++
  gi|474934765|ref|YP_007688347.1| 12 EVVGQDDMKRALLLNIIDPGI------------GGVLIKGEKGTAKSTTVRSLNWIL 56
                                      677777777777777765433............136777777777777776666555 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 5.6e-05
                                       SSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--SSSSC CS
                               MCM 106 etgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAanpkagry 178
                                       +tge  +e G l  a++ ++++De++  +++  + l++        + + G+  + +a+  ++  +np++g  
  gi|474934765|ref|YP_007688347.1| 123 KTGEKKFEPGVLAAANGNILYVDEVNLLDDHLVDLLLDSAAMGINYVEREGVSFSHPAKFVLVGTMNPEEGDL 195
                                       6788899*****************************999888888999********************99864 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.02        52      25      42 ..      35      52 ..      19      65 .. 0.88
   2 !    9.8   0.0   0.00023      0.59      79     136 ..     124     183 ..     122     200 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.02
                                      EEEECSTTSSHHHHHHHH CS
                   Sigma54_activat 25 vlitGesGtGKellarai 42
                                      vli+Ge+Gt K++  r++
  gi|474934765|ref|YP_007688347.1| 35 VLIKGEKGTAKSTTVRSL 52
                                      9**********9988765 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00023
                                       TTTSS-BEHHHHHTTTSEEEEETGGGS-HHHHHHHHH..HHHHSEEESBTSSSEEE--EE CS
                   Sigma54_activat  79 tGAekekkGlfekadgGtlfLDeigelplelQekLlr..vlqegevervGsskeikvdvr 136
                                       tG +k + G + +a+g +l++De++ l+ +l   Ll   ++  + ver G s ++++++ 
  gi|474934765|ref|YP_007688347.1| 124 TGEKKFEPGVLAAANGNILYVDEVNLLDDHLVDLLLDsaAMGINYVEREGVSFSHPAKFV 183
                                       67788889*****************99999888887521344455666666555555555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   4.9e-05      0.12      16      63 ..      24      69 ..      12     167 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.9e-05
                            AAA_16 16 lervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                      l ++ +++ + vl+ Ge+G+ Ks+ vr+l   l  ++  +++g   ++
  gi|474934765|ref|YP_007688347.1| 24 LLNIIDPGIGGVLIKGEKGTAKSTTVRSLNWILPYRE--AVKGCPFRC 69
                                      34555666689*****************987666553..244444444 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.13   3.3e+02       2      22 ..      35      55 ..      34      61 .. 0.88
   2 ?    9.2   0.0   0.00042       1.1      55     114 ..     128     192 ..     105     205 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.13
                             AAA_3  2 vllegvPGlaktllvkalaka 22
                                      vl++g  G+ak ++v++l  +
  gi|474934765|ref|YP_007688347.1| 35 VLIKGEKGTAKSTTVRSLNWI 55
                                      89**************99765 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00042
                             AAA_3  55 efkkGpvfa...nllladeinrappktqsalle..ameerqvtvegethklpepflvlatqnPie 114
                                       +f++G + a   n+l +de+n    +    ll+  am  + v  eg +++ p +f+++ t nP e
  gi|474934765|ref|YP_007688347.1| 128 KFEPGVLAAangNILYVDEVNLLDDHLVDLLLDsaAMGINYVEREGVSFSHPAKFVLVGTMNPEE 192
                                       45555544322389*****************985579999***********************77 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.65u 0.36s 00:00:01.01 Elapsed: 00:00:00.56
# Mc/sec: 1852.05
//
Query:       gi|474934766|ref|YP_007688348.1|  [L=610]
Description: Mg-chelatase subunit ChlI [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-21   75.2   0.0    1.3e-20   73.0   0.0    2.2  2  AAA_lid_2        AAA lid domain
    4.8e-12   46.5   0.0    1.2e-11   45.2   0.0    1.7  1  VWA_2            von Willebrand factor type A domain
    5.7e-10   39.3   0.0    9.7e-10   38.6   0.0    1.4  1  AAA_5            AAA domain (dynein-related subfamily)
    5.2e-09   35.8   0.1    8.7e-06   25.3   0.0    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    2.9e-08   33.1   0.0    7.7e-08   31.7   0.0    1.6  1  MCM              MCM P-loop domain
    1.1e-07   32.2   0.0    1.9e-07   31.5   0.0    1.3  1  VWA              von Willebrand factor type A domain
    8.4e-05   22.3   0.0    0.00018   21.3   0.0    1.5  1  Sigma54_activat  Sigma-54 interaction domain
  ------ inclusion threshold ------
      0.039   14.1   0.0       0.12   12.5   0.0    1.7  1  Sigma54_activ_2  Sigma-54 interaction domain
      0.066   13.4   0.0       0.16   12.1   0.0    1.7  1  TIP49_C          TIP49 AAA-lid domain


Domain annotation for each model (and alignments):
>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       1.7   3.3e+03      26      36 ..      34      44 ..      29      48 .. 0.64
   2 !   73.0   0.0   6.4e-24   1.3e-20       4      69 ..     212     278 ..     209     288 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.7
                         AAA_lid_2 26 ArAlAalegrd 36
                                      ArA A + gr+
  gi|474934766|ref|YP_007688348.1| 34 ARAAAGVSGRK 44
                                      66666666665 PP

  == domain 2  score: 73.0 bits;  conditional E-value: 6.4e-24
                         AAA_lid_2   4 rahlaielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlr.repeaegetteei 69 
                                       +++l+i++g++g+R+dla++++A+AlAal+grd+V + D++eaa l+L+HR    +p+ e+ +  e 
  gi|474934766|ref|YP_007688348.1| 212 ISELCIKVGADGLRGDLAMINCAKALAALNGRDEVMKKDIEEAAVLCLPHRRNySQPPPEPPEPPEP 278
                                       789*************************************************996676666454444 PP

>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.0     6e-15   1.2e-11       1     106 [.     427     533 ..     427     534 .. 0.92

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 6e-15
                             VWA_2   1 lvfvlDtSgSmrngdygptrleaakdaveallksl..pgdrvglvtfsd.gpevlipltkdkakilnalrnleakgg 74 
                                       l+f++D SgS + +    +r++++k a+ ++l +   ++dr+gl++f+  ++  ++p+tk+ +   + l++l + gg
  gi|474934766|ref|YP_007688348.1| 427 LLFLVDASGSLGVR----RRMATVKGAILSMLRDSyvKRDRIGLMAFRRdSADMILPPTKSVEYSYKQLEELPT-GG 498
                                       68***********9....5**************55569**********96689********************7.7* PP

                             VWA_2  75 gtnlaaaLqlarkalkkrr...kgekrvivlitDg 106
                                       +t l++aL ++ + + +      ge++ i+l+tDg
  gi|474934766|ref|YP_007688348.1| 499 KTPLGEALMKVDEYMTAYArchVGERCFIILVTDG 533
                                       *************9987777899***********9 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   0.0   4.8e-13   9.7e-10       2     138 .]      20     148 ..      19     148 .. 0.83

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 4.8e-13
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.............--------G-SEEEEESG CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik....ngttslvdsplvraaregeilvlDEv 74 
                                       vl+ G  G++K++la+  a + +r+  +v+++ + t e+l+g+++i+    +g+ +++++ l ra   g il++D+v
  gi|474934766|ref|YP_007688348.1|  20 VLIRGGEGSAKTTLARAAAGVSGRK--IVNCPLNVTDEQLFGGMDIErtirEGRPVFEPGLLQRA--DGNILYIDDV 92 
                                       7999***************999987..67888899***********9999999999999999976..8********* PP

                                       GG--HHHH.HHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHTT- CS
                             AAA_5  75 eraesevl.nsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrsRf 138
                                       + +++++l ++L s+l   ++ +e g    k +  d    ++++at+np+d   ++ls+ +++Rf
  gi|474934766|ref|YP_007688348.1|  93 NLMDRAMLaGILDSVLT-GTVTVERGSISAKYPV-D----TTLVATMNPND---SDLSSHVLDRF 148
                                       ****6665156666665.5555555555555554.4....9**********...99999999999 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.1   0.00071       1.4      10      45 ..       3      40 ..       1      73 [. 0.87
   2 !   25.3   0.0   4.4e-09   8.7e-06      96     161 ..      73     138 ..      63     152 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00071
                      Mg_chelatase 10 eakraleiaaaGgH..nlllvGppGsGKtmlakrlpsl 45
                                      +akrale a +  H   +l+ G  Gs Kt la++ +++
  gi|474934766|ref|YP_007688348.1|  3 DAKRALECALSSPHikTVLIRGGEGSAKTTLARAAAGV 40
                                      79**********996679**************998766 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 4.4e-09
                      Mg_chelatase  96 kpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpcpc 161
                                         +pG + +a   +L++D++  ++r +l  + + + +g+vt++r + ++++p +++lva+mNp  +
  gi|474934766|ref|YP_007688348.1|  73 VFEPGLLQRADGNILYIDDVNLMDRAMLAGILDSVLTGTVTVERGSISAKYPVDTTLVATMNPNDS 138
                                       678************************************************************765 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.0   3.9e-11   7.7e-08      60     177 ..      20     139 ..      13     161 .. 0.91

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 3.9e-11
                                       EEEEESSTSTHHHHHHHHHHHSSSEEEEESSSSSSSHS..SSEEEEESSSSSEEEEETHHHHTTTSEEEEESGGGST CS
                               MCM  60 vllvgdpgtaKsqlLkyveklapravytsgkgssaagL..taavvrdeetgefvleaGalvladkGvcciDefdkmk 134
                                       vl+ g  g aK++l ++++ ++ r +  +    + + L     + r  ++g  v+e G l  ad+ +++iD+++ m+
  gi|474934766|ref|YP_007688348.1|  20 VLIRGGEGSAKTTLARAAAGVSGRKIVNCPLNVTDEQLfgGMDIERTIREGRPVFEPGLLQRADGNILYIDDVNLMD 96 
                                       899999********************************65566778888888************************* PP

                                       CHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--SSSS CS
                               MCM 135 eedrsalhEamEqqtisiaKaGivatLnartsvlaAanpkagr 177
                                       ++    +++ +   t+++ +++i a+ +  t+++a +np+ + 
  gi|474934766|ref|YP_007688348.1|  97 RAMLAGILDSVLTGTVTVERGSISAKYPVDTTLVATMNPNDSD 139
                                       ***************************************9764 PP

>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.0   9.8e-11   1.9e-07       2     167 ..     427     596 ..     427     602 .. 0.79

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 9.8e-11
                                       EEEEEE-STTSC.HHHHHHHHHHHHHHHHHHTBTTTTEEEEEEEESSS.EEEEEETTSHCHHHHHHHHHHTGSGGGG CS
                               VWA   2 ivfvlDgSgsmg.eenfekvkefikklveklevgpegtrvglvqfsse.vktefslndysskeellsalnnlkysgg 76 
                                       + f++D+Sgs g ++++ +vk +i +++++ +   +++r+gl+ f  + +  + + ++  s e   ++l++l   +g
  gi|474934766|ref|YP_007688348.1| 427 LLFLVDASGSLGvRRRMATVKGAILSMLRDSY--VKRDRIGLMAFRRDsADMILPPTK--SVEYSYKQLEEL--PTG 497
                                       57*********6266788**************..8889********886888899999..66999******8..666 PP

                                       SSC-HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CSS.........HTHHHHHHHHGCTEEEEEEEE..SSS CS
                               VWA  77 gttntgkalkyaleklfkssagaRenakkviilltdGksndg.........dpkeaaneakeqgikvfavGv..gna 142
                                       g+t +g+al ++ e ++++ a+   + + +iil+tdG+ n           ++++ a+ +k   +k ++v    g  
  gi|474934766|ref|YP_007688348.1| 498 GKTPLGEALMKVDE-YMTAYARCHVGERCFIILVTDGRANVPlqagadaneEVQKMAEDLKIPSVKWIVVDAasGFP 573
                                       6666********88.555555546699************99668999555555555555555556666665577888 PP

                                       HHHHHHHHHSSSSCHHCEEEESSHH CS
                               VWA 143 dekelLnkiasepgeghvftvtdfe 167
                                       + ++  +++a++ g  ++f+++d +
  gi|474934766|ref|YP_007688348.1| 574 HFDN-AERLAEKLG-ARYFKLEDLD 596
                                       8888.888888888.8888888876 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0     9e-08   0.00018      22     144 ..      15     136 ..       1     150 [. 0.77

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 9e-08
                                       S..S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHE...BSSSSSTTTSS-BEHHHHHTT CS
                   Sigma54_activat  22 d..lsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFG...hekGaFtGAekekkGlfekad 93 
                                       +   +vli+G  G+ K++lara    s rk      vnc   p ++ + +LFG   +e+    G    + Gl+++ad
  gi|474934766|ref|YP_007688348.1|  15 PhiKTVLIRGGEGSAKTTLARAAAGVSGRK-----IVNC---PLNVTDEQLFGgmdIERTIREGRPVFEPGLLQRAD 83 
                                       34479*****************99999976.....4687...7788999999944445666677778889******* PP

                                       TSEEEEETGGGS-HHHHHHHHHHHHHSEEE.SBTS.SSEEE--EEEEEEESS- CS
                   Sigma54_activat  94 gGtlfLDeigelplelQekLlrvlqegeve.rvGs.skeikvdvriiaatned 144
                                       g +l++D+++ ++ ++ + +l  + +g+v+   Gs s++ +vd+ ++a+ n +
  gi|474934766|ref|YP_007688348.1|  84 GNILYIDDVNLMDRAMLAGILDSVLTGTVTvERGSiSAKYPVDTTLVATMNPN 136
                                       ********************986666654315566367899**9999998865 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.9e-05      0.12      23      90 ..      19     104 ..       4     112 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.9e-05
                                       -EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH-H....................HHHHHHTTTSEEEEEE-T CS
                   Sigma54_activ_2  23 pvfltGekGsgkelvArlLhknsgpwleifvverlaklp....................ldlleqakggtLylkdia 79 
                                        v++ G++Gs k++ Ar+ +  sg+  +i+++   ++                        ll++a+g +Ly+ d++
  gi|474934766|ref|YP_007688348.1|  19 TVLIRGGEGSAKTTLARAAAGVSGR--KIVNCPLNVTDEqlfggmdiertiregrpvfePGLLQRADGNILYIDDVN 93 
                                       69******************99999..78888666654456788889999999999998899*************** PP

                                       T--HHHHHHHH CS
                   Sigma54_activ_2  80 dlskaeqkeLl 90 
                                        +++a ++++l
  gi|474934766|ref|YP_007688348.1|  94 LMDRAMLAGIL 104
                                       ****9999876 PP

>> TIP49_C  TIP49 AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   8.1e-05      0.16      28      63 ..     222     257 ..     202     259 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.1e-05
                           TIP49_C  28 tSLRYaiqLltpasilakkrkkkevevedveeveeL 63 
                                        +LR  + +++ a+ la +++++ev ++d+ee++ L
  gi|474934766|ref|YP_007688348.1| 222 DGLRGDLAMINCAKALAALNGRDEVMKKDIEEAAVL 257
                                       468888999***********************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (610 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.72u 0.30s 00:00:01.02 Elapsed: 00:00:00.48
# Mc/sec: 3849.48
//
Query:       gi|474934767|ref|YP_007688349.1|  [L=63]
Description: hypothetical protein TALC_01202 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.5e-08   32.6   0.0    8.9e-08   32.3   0.0    1.1  1  DUF4177   Domain of unknown function (DUF4177)


Domain annotation for each model (and alignments):
>> DUF4177  Domain of unknown function (DUF4177)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.0     5e-12   8.9e-08       3      64 ..       5      61 ..       4      62 .. 0.80

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 5e-12
                           DUF4177  3 YkvvevkegglgngkieeeeleeyqeilnelAkeGWrlvsiipvkesrgvgaaesilliFeR 64
                                      Yk+v++  +   +g+++   +ee ++ ln+ +k+GW+lv+++    ++ +++++++ + F++
  gi|474934767|ref|YP_007688349.1|  5 YKTVNFNFDLTESGRLD--DVEEASDKLNDSGKDGWELVNTVV--SRMDPTYVSGFFI-FKK 61
                                      9****777555577777..888888***************773..7888888888865.776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.31s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 418.68
//
Query:       gi|474934768|ref|YP_007688350.1|  [L=2736]
Description: Listeria/Bacterioides repeat protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-37  127.1  59.7    1.6e-10   41.0   1.2   12.4 11  Flg_new   Listeria-Bacteroides repeat domain (List_Bact_rpt)


Domain annotation for each model (and alignments):
>> Flg_new  Listeria-Bacteroides repeat domain (List_Bact_rpt)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   3.3         1   1.8e+04       2      52 ..      15      70 ..      14      83 .. 0.65
   2 ?   -0.9   0.1      0.11   1.9e+03      34      45 ..      85      96 ..      67     117 .. 0.66
   3 !    3.5   0.0    0.0044        80      15      45 ..     692     722 ..     674     738 .. 0.71
   4 ?   -1.0   0.0      0.12   2.1e+03       3      23 ..    1250    1271 ..    1249    1285 .. 0.79
   5 !   25.3   0.8     7e-10   1.3e-05       3      64 ..    1492    1553 ..    1491    1554 .. 0.81
   6 !   41.0   1.2   8.7e-15   1.6e-10       1      65 []    1557    1629 ..    1557    1629 .. 0.85
   7 !   23.8   0.5   2.1e-09   3.8e-05       5      63 ..    1875    1938 ..    1873    1940 .. 0.77
   8 !   11.8   2.6   1.2e-05      0.21      30      64 ..    2170    2202 ..    2111    2203 .. 0.79
   9 !    7.1   1.0   0.00034       6.1       8      62 ..    2306    2353 ..    2304    2358 .. 0.74
  10 !   15.5   0.0     8e-07     0.014       4      64 ..    2384    2442 ..    2384    2443 .. 0.86
  11 !   31.1   0.9   1.1e-11   1.9e-07       1      55 [.    2449    2508 ..    2449    2523 .. 0.80

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 1
                                      EEEEEETTEE...EEEEEETTSB----B--EETTEEEEEEESSTTCC..SB--TTT CS
                           Flg_new  2 tvtFdanGgt...vsqtvtygetitlpanptkeGYtFaGWytdsdgt..taydfgt 52
                                       vt+  n      v+ tv y+  i +  np     tF+G + ds  +  t++++ +
  gi|474934768|ref|YP_007688350.1| 15 EVTYYRNQNAndnVTVTVSYEGIIATEYNPAYWKGTFTGDFSDSGVKlaTNWTPPS 70
                                      68999987552223458889998988889999888999988887654446666554 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.11
                                      EEEEEESSTTCC CS
                           Flg_new 34 tFaGWytdsdgt 45
                                      +FaGW+t  + +
  gi|474934768|ref|YP_007688350.1| 85 VFAGWSTVRTPS 96
                                      7****9955433 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.0044
                                       EEETTSB----B--EETTEEEEEEESSTTCC CS
                           Flg_new  15 tvtygetitlpanptkeGYtFaGWytdsdgt 45 
                                       +v +++ +++    t +G+ F+ W+ +++ +
  gi|474934768|ref|YP_007688350.1| 692 QVVESDYYSKVILATDSGFIFNDWFAKATSD 722
                                       4555666666667899*********998753 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 0.12
                                        EEEEETTEE.EEEEEETTSB-- CS
                           Flg_new    3 vtFdanGgt.vsqtvtygetit 23  
                                        vtFd+  g  v+q++++++ i+
  gi|474934768|ref|YP_007688350.1| 1250 VTFDSASGVmVPQNINSSTCID 1271
                                        9****99995699999987665 PP

  == domain 5  score: 25.3 bits;  conditional E-value: 7e-10
                                        EEEEE..TTEE.EEEEEETTSB----B--EETTEEEEEEESSTTCCSB--TTT-B--SS-EEEEE CS
                           Flg_new    3 vtFda..nGgt.vsqtvtygetitlpanptkeGYtFaGWytdsdgttaydfgtkvtptgdvtLyA 64  
                                        +tF    +Gg+  s  +tyg+ i+  + p  +  +F+GWy+ds++++ y+f+t+ t  + +tLyA
  gi|474934768|ref|YP_007688350.1| 1492 ITFYDryDGGNhFSRDFTYGTVISGGDCP-ATSDNFVGWYQDSSFNNPYNFNTPLT--APITLYA 1553
                                        56655457888568899999888876655.56669******************986..9*****9 PP

  == domain 6  score: 41.0 bits;  conditional E-value: 8.7e-15
                                        EEEEEEETTEEEEEE.EET.TSB----.B--EETTEEEEEEESSTTCCSB--TTT-.....B--SS-EEEEEE CS
                           Flg_new    1 YtvtFdanGgtvsqt.vty.getitlp.anptkeGYtFaGWytdsdgttaydfgtk.....vtptgdvtLyAk 65  
                                        ++vtF++ +gt s   +++ g+t+++p ++pt  GY+F+GWyt  dg+ +++f+++      t++gdv +yA+
  gi|474934768|ref|YP_007688350.1| 1557 FSVTFNNMNGTSSMVyIESeGTTLSTPrPDPTWVGYEFQGWYTTLDGNVKWNFSDDlipgaDTINGDVVIYAH 1629
                                        68*****8888887515444899999999*************************9987777567899999997 PP

  == domain 7  score: 23.8 bits;  conditional E-value: 2.1e-09
                                        EEETTEEE.EE..EEETTSB----B--EETTEEEEEEESSTTCC..SB--TTT-B--SS-EEEE CS
                           Flg_new    5 FdanGgtv.sq..tvtygetitlpanptkeGYtFaGWytdsdgt..taydfgtkvtptgdvtLy 63  
                                        Fd  G  v ++  tv+yg+t+tl+ +p  +GY F+ Wy + +g+  +a+   +  t+tg+  +y
  gi|474934768|ref|YP_007688350.1| 1875 FDEHGARVvETtlTVHYGDTYTLSYAPGDSGYIFNNWYLNGEGSfdDAVGNPAVLTVTGNCAVY 1938
                                        88899775244356**************************998643455555557777777766 PP

  == domain 8  score: 11.8 bits;  conditional E-value: 1.2e-05
                                        ETTEEEEEEESSTTCCSB--TTT-B--SS-EEEEE CS
                           Flg_new   30 keGYtFaGWytdsdgttaydfgtkvtptgdvtLyA 64  
                                         +G+   GW+td d ++ ++   +v+++gd+tLyA
  gi|474934768|ref|YP_007688350.1| 2170 QDGFILMGWFTDVDHNNPVSW--PVSIEGDTTLYA 2202
                                        79****************976..56678******9 PP

  == domain 9  score: 7.1 bits;  conditional E-value: 0.00034
                                        TTEEEEEEEETTSB----B--EETTEEEEEEESSTTCCSB--TTT-B--SS-EEE CS
                           Flg_new    8 nGgtvsqtvtygetitlpanptkeGYtFaGWytdsdgttaydfgtkvtptgdvtL 62  
                                        nG ++s+tv+y+e++tlp   +k+GY  + W  +    +ay+  t ++  ++vtL
  gi|474934768|ref|YP_007688350.1| 2306 NGLSMSKTVEYQESLTLPV-LSKTGYR-QNWTVNG---NAYAQAT-YV-FSSVTL 2353
                                        8999*************97.******9.8898874...4454333.22.244444 PP

  == domain 10  score: 15.5 bits;  conditional E-value: 8e-07
                                        EEEETTEEEEE.EEETTSB----.B--EETTEEEEEEESSTTCCSB--TTT-B--SS-EEEEE CS
                           Flg_new    4 tFdanGgtvsq.tvtygetitlp.anptkeGYtFaGWytdsdgttaydfgtkvtptgdvtLyA 64  
                                        +F +nG +v   +v+y++ i+   ++p+ +GY  +GW  +   + a+d ++  +p++d+ L A
  gi|474934768|ref|YP_007688350.1| 2384 SFPSNGASVVHiSVEYNSVISAYvETPVATGYYVTGWKHA---GVAFDVDS-LMPAEDLELNA 2442
                                        6889**9975549*******99879*************96...89999876.68999999988 PP

  == domain 11  score: 31.1 bits;  conditional E-value: 1.1e-11
                                        EEEEEEETTEEEEE...EEETTSB----B.--EETTEEEEEEESSTTC.CSB--TTT-B- CS
                           Flg_new    1 YtvtFdanGgtvsq...tvtygetitlpa.nptkeGYtFaGWytdsdg.ttaydfgtkvt 55  
                                        Ytv F++nGg+ s     +ty++ ++ p+ ++t +G++F+ W+ ++dg +t++d+g++v 
  gi|474934768|ref|YP_007688350.1| 2449 YTVAFNSNGGSGSMapiVATYDTPFNMPQcSFTYSGHDFVSWNGANDGsGTSFDAGQSVR 2508
                                        *********9954422269*********658*****************66******9952 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (2736 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 1.09u 0.33s 00:00:01.42 Elapsed: 00:00:00.51
# Mc/sec: 16213.53
//
Query:       gi|474934769|ref|YP_007688351.1|  [L=581]
Description: threonyl-tRNA synthetase/Ser-tRNA(Thr) hydrolase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-39  136.2   0.0    2.1e-39  135.4   0.0    1.4  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
    3.9e-23   81.4   2.2    8.6e-23   80.3   2.2    1.6  1  HGTP_anticodon  Anticodon binding domain
    3.6e-14   52.6   0.0    9.1e-14   51.3   0.0    1.7  1  tRNA_SAD        Threonyl and Alanyl tRNA synthetase second ad
  ------ inclusion threshold ------
      0.074   13.1   0.0         17    5.5   0.1    2.8  2  DUF1447         Protein of unknown function (DUF1447)


Domain annotation for each model (and alignments):
>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.4   0.0   4.6e-43   2.1e-39       9     179 .]     269     472 ..     262     472 .. 0.94

  Alignments for each domain:
  == domain 1  score: 135.4 bits;  conditional E-value: 4.6e-43
                                       EEEEE-SSSHHHHHHHHHHHEEEBGG.SSEEEEEEEEEEBTTTS.TBCTTTB-SEEEEEEEEEEESGGGHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b   9 reyiLkPtneetfvelirdevlrskr.LPlklyqiqtkyRdEks.dsrGLlRvreFhqkdgyvfhaeaslddslrdl 83 
                                       +  ++kP+n+++ + ++ +e  rs+r LPl+l +++ ++R+E+s  ++GL+Rvr F+q+d + +++++++ d+++ +
  gi|474934769|ref|YP_007688351.1| 269 QPCCIKPMNCPGSTLVFANE-SRSYRdLPLRLGEFGIVHRHERSgTLHGLFRVRCFTQDDSHLYVTPEQIGDEIKRV 344
                                       5789****************.***777****************99999***************************** PP

                                       HHHHHHHHHHTT.SCEEEEEEGTTSC.................................BTTSEEEEEEEEETTTSE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.................................xxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  84 ikaisriferlglefraiielmsaks.................................adykdkkefeavsesltk 127
                                       +  i+r+++++g++ + ++++++ ++                                 a+y++k +f + +  +++
  gi|474934769|ref|YP_007688351.1| 345 VSIIDRVYKQFGFK-YNVELSTRPEDsmgsdedwenatnglknalesiglpysinegdgAFYGPKIDFHLEDS-IGR 419
                                       ************98.67888866555667788*************************************9999.*** PP

                                       EEEEEEEEEEETHHHHHTTEEEECTTSSEEEEEEEEEE.EE.HHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.xxxxxxxxxxxx RF
                      tRNA-synt_2b 128 gieigtiqklgtrlserlgatvldennreksvimicaa.ig.veRllsaileqn 179
                                       ++++gtiq + +++++r++++++  +++++++imi++  +g veR++++++e++
  gi|474934769|ref|YP_007688351.1| 420 TWQCGTIQLD-FQMPQRFNLEYVGADGEKHHPIMIHRVvFGsVERFMGILIEHY 472
                                       **********.****************************************986 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.3   2.2   1.9e-26   8.6e-23       1      93 [.     484     574 ..     484     575 .. 0.97

  Alignments for each domain:
  == domain 1  score: 80.3 bits;  conditional E-value: 1.9e-26
                                       SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHH.TEEEEEETTT CS
                    HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelek.gtvtvrdrdt 76 
                                       qv v+ ++e   +  +ya k+ e+L aagirve d ++e+ig+kirea+l ++p+++v+Geke+e+ ++v+vr+rd 
  gi|474934769|ref|YP_007688351.1| 484 QVKVLSVSE---KSRDYAAKVTEKLMAAGIRVENDARDEKIGYKIREAQLEKVPYMLVIGEKEAESgDSVAVRNRDR 557
                                       79999****...889************************************************************** PP

                                       CEEEEEETTHHHHHHHH CS
                    HGTP_anticodon  77 reqervsldelveklke 93 
                                       ++   ++ +el+e +++
  gi|474934769|ref|YP_007688351.1| 558 GDLGVMKTSELIETVRK 574
                                       **************997 PP

>> tRNA_SAD  Threonyl and Alanyl tRNA synthetase second additional domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.3   0.0     2e-17   9.1e-14       1      44 []     114     163 ..     114     163 .. 0.98

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 2e-17
                                       EEEEEETT.EEEEESS---SBGGGC-SEEEE.......CCECCCTCEEEEE CS
                          tRNA_SAD   1 vrvvsiGdisvelCgGtHvpnTgeIgafkil.......seesiakglrRIy 44 
                                       ++++++G+ +v+lC G+Hv  T++++afk++       ++++ +k+l+RIy
  gi|474934769|ref|YP_007688351.1| 114 ISFYKQGE-FVDLCAGPHVLYTKQCKAFKLTsvagaywRGDEHNKMLTRIY 163
                                       689****8.*****************************************9 PP

>> DUF1447  Protein of unknown function (DUF1447)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1    0.0039        17      30      54 ..      87     112 ..      66     121 .. 0.77
   2 ?    4.7   0.0     0.007        31      45      67 ..     121     143 ..     117     144 .. 0.95

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0039
                           DUF1447  30 eevrklveen.teyniEfieelsgka 54 
                                       +e+ ++++e+ ++y++E i+ l +++
  gi|474934769|ref|YP_007688351.1|  87 AEAIEYMKERgEDYKVELIQDLPEDS 112
                                       56888888888999999999997654 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.007
                           DUF1447  45 EfieelsgkaLeYEkesedfklt 67 
                                       Ef++   g ++ Y k+ ++fklt
  gi|474934769|ref|YP_007688351.1| 121 EFVDLCAGPHVLYTKQCKAFKLT 143
                                       9********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (581 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.52
# Mc/sec: 3382.02
//
Query:       gi|474934770|ref|YP_007688352.1|  [L=481]
Description: Amino acid transporter [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      9e-55  186.2  31.9    1.1e-54  185.9  31.9    1.0  1  AA_permease_2  Amino acid permease
    8.5e-12   44.4  25.2    1.1e-11   44.0  24.7    1.4  1  AA_permease    Amino acid permease


Domain annotation for each model (and alignments):
>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.9  31.9   1.2e-58   1.1e-54       2     410 ..      18     451 ..      17     469 .. 0.78

  Alignments for each domain:
  == domain 1  score: 185.9 bits;  conditional E-value: 1.2e-58
                     AA_permease_2   2 sllsafalvigsvig.sgifvknlaasggpa.lilwvwiavligslavllvyaEl.ssalprsgGiyvytkaaf... 72 
                                       s+ +  ++++g+++  ++++    ++s++ a  i+++ ++vl g + + ++yaE+ ++ +p   Gi + ++a+f   
  gi|474934770|ref|YP_007688352.1|  18 SWKDGMFVALGVPLLiLPGLYD--VGSMIWAlCIFTWTVGVLQG-FVQNIAYAEMvTT-FPQATGIPGCAQAVFqse 90 
                                       6777777888887443667766..99988774677777777777.8*********666.***************999 PP

                     AA_permease_2  73 .........gkkvaflsawfnwfayvpvlasilsvaasyllnalgpdlqgntw..ltyliaiaililvalinirgik 138
                                                +k+++ +++w++wfa+ pv+++ + ++++y+  +++ dl +     l++ ++ +++++  ++ +rg  
  gi|474934770|ref|YP_007688352.1|  91 navkgqidkSKFIGAFASWCYWFAWTPVVYIFSGLIVEYIGVMFDLDLSDVEHlgLSMAVILIVVAGMYILGSRGLE 167
                                       9999999999**********************************997765332124555555555666778888899 PP

                     AA_permease_2 139 esakiqnilgilkillpliiliilglitvdgggfsslstetdtffpngwpgv.....llgllivlwsfdGfesaanv 210
                                       +++k++ il+++++ +p+i+++   +  ++   f++++++++  +p+ ++++     l+ ++  +ws +++e+aa +
  gi|474934770|ref|YP_007688352.1| 168 GGGKLALILALISL-IPIIVIL---FGDIGDFEFDNITDAWKFPTPGYSDSMsivliLGCFGLGQWSSCAWETAAIY 240
                                       99************.8*65555...22222333333478999999998887555565667888************** PP

                     AA_permease_2 211 seevkk..kdvpkaifigllivlvlyllvniaflgvvpddeianlsnlgsvaalffeavggkvvaiivvilialsll 285
                                         e k   +d+pka+f+++li+l ly+lv+++++g +++ +++  ++ +s+  +  +a+g  ++  i+ ++++++++
  gi|474934770|ref|YP_007688352.1| 241 GPEYKDpgRDTPKALFSCGLICLALYFLVPFLMYGEIGQVGLED-AGYHSLHPIAIAAFG-NIGGKIALVVLIIAMI 315
                                       ***777669*********************************65.444544444444444.6666666678889999 PP

                     AA_permease_2 286 gaintavigssrvlealardgvlPrffakvnkfgspiraiiltaivslillllfllas....saaynfllsvsslgl 358
                                       ++i t ++gssr l++++++g lP++f k n++g p+ a+ ++a ++++l++++ + +    ++++ ++ls+s++g+
  gi|474934770|ref|YP_007688352.1| 316 LIIQTGFLGSSRALYSMSTEGNLPSWFGKLNEHGMPVHAMLFVAGFNSLLMFVLEVLPmlgaDTSVMTVLSASAMGY 392
                                       99*********************************************9887655544444459************** PP

                     AA_permease_2 359 iisyllliigalilrkkrphl..kr......pgkilvaiigalfllfllvalffppkgpa 410
                                        i +++++++ ++ r++++ +  +r      ++   v++i++++ ++llv l + + +++
  gi|474934770|ref|YP_007688352.1| 393 AIANFVALAAFVKSRRDPRFKdlPRpfqapsFYT-YVGMIMCCLQIVLLVCLVYWSYVAS 451
                                       *****************88666677777743333.3777777777777666655444444 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0  24.7   1.2e-15   1.1e-11      73     436 ..     102     450 ..      47     479 .. 0.70

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 1.2e-15
                       AA_permease  73 elGfviGlnylfswitvlaleltaasiliqfwelvtdlpkawvt........gavflvvlliinlvgvkvygeaefi 141
                                         G + ++ y+f w    ++ ++ ++ ++++++ + dl   +v         ++++++ + i+   g+++ g+  +i
  gi|474934770|ref|YP_007688352.1| 102 FIGAFASWCYWFAWT---PVVYIFSGLIVEYIGVMFDLDLSDVEhlglsmavILIVVAGMYILGSRGLEGGGKLALI 175
                                       568888888888774...33333344444444444444422222444455557777777888888889999998888 PP

                       AA_permease 142 lalikiiaiiafiivgiillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielv 218
                                       lali +i ii  + + i + ++        f +++d++     + +pg+  ++++++  ++++f     +    e  
  gi|474934770|ref|YP_007688352.1| 176 LALISLIPIIVILFGDI-GDFE--------FDNITDAWK----FPTPGY--SDSMSIVLILGCFGLGQWSSCAWETA 237
                                       88888888776665553.3333........556677787....778884..455558888888888888888899** PP

                       AA_permease 219 aiiagEvkdPeksiPkailqvviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinav 295
                                       ai + E kdP ++ Pka  +  ++ + +Y l+ +l+   ++      l+d+    s+  i+i   g+++ +  ++++
  gi|474934770|ref|YP_007688352.1| 238 AIYGPEYKDPGRDTPKALFSCGLICLALYFLVPFLMYGEIGQVG---LEDAGYH-SLHPIAIAAFGNIGGKIALVVL 310
                                       *******************9999999999999888776665544...2323333.5666888888888888888888 PP

                       AA_permease 296 iltaalssansslysasRvlyslakdglaPkvlkkvskrgvPlraillsmiisllal....llaslnlaapivfnfl 368
                                       i++ +l +  ++   +sR+lys++ +g +P++++k++ +g P+ a+l+++ +  l++    +l +l ++ ++v+++l
  gi|474934770|ref|YP_007688352.1| 311 IIAMILIIQTGF-LGSSRALYSMSTEGNLPSWFGKLNEHGMPVHAMLFVAGFNSLLMfvleVLPMLGAD-TSVMTVL 385
                                       777777766665.589**********************************9998888888899999999.9****** PP

                       AA_permease 369 laisaliglivwlliilsylrfRkalkyqgrsieelgfkaallplgvilvlaaliiillilalyaylt 436
                                       +a+++ ++++++++ ++ +++ R+  + +    + +++ + +  +  +++  + i +l+ l ++ y++
  gi|474934770|ref|YP_007688352.1| 386 SASAMGYAIANFVALAA-FVKSRRDPRFKDL-PRPFQAPSFY-TYVGMIMCCLQIVLLVCLVYWSYVA 450
                                       *****999999987655.5555555333332.2233333322.2333333333334444455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (481 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       830  (0.0462937); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.71u 0.35s 00:00:01.06 Elapsed: 00:00:00.56
# Mc/sec: 2592.14
//
Query:       gi|474934771|ref|YP_007688353.1|  [L=416]
Description: histidyl-tRNA synthetase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-58  199.0   0.0    1.4e-58  198.7   0.0    1.1  1  tRNA-synt_His    Histidyl-tRNA synthetase
    6.9e-17   61.4   0.0    1.3e-16   60.5   0.0    1.5  1  HGTP_anticodon   Anticodon binding domain
    1.4e-16   60.9   0.0    3.5e-16   59.7   0.0    1.7  1  tRNA-synt_2b     tRNA synthetase class II core domain (G, H, 
    4.8e-05   23.0   0.0    9.4e-05   22.0   0.0    1.4  1  tRNA-synt_2d     tRNA synthetases class II core domain (F)
    6.9e-05   22.1   0.3      0.014   14.5   0.0    2.9  3  tRNA-synt_2      tRNA synthetases class II (D, K and N)
  ------ inclusion threshold ------
      0.028   13.9   0.0      0.046   13.2   0.0    1.3  1  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
       0.37   10.5   1.5        1.3    8.8   1.5    2.0  1  DUF1127          Domain of unknown function (DUF1127)


Domain annotation for each model (and alignments):
>> tRNA-synt_His  Histidyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.7   0.0   5.3e-62   1.4e-58       1     310 []       7     310 ..       7     310 .. 0.95

  Alignments for each domain:
  == domain 1  score: 198.7 bits;  conditional E-value: 5.3e-62
                                       T---EETCHHHHHHHHHHHHHHHHHHTT-EEEE--SEEEHHHHCTTSTCC.HHHS-EEE-TTSSEEEE-SSSHHHHH CS
                     tRNA-synt_His   1 glrdllpeeaekieelrrrlldlfeswGYelVspPllEyldslltgaged.ldqtfklvDqsgrllglRaDiTpqva 76 
                                       g+rd+lp+e ek+++ +++l +++ + G++++ +P++E  + +  ++g + l++++ ++D+ +r ++lR+++T+ v+
  gi|474934771|ref|YP_007688353.1|   7 GTRDFLPDELEKRRSYEATLRSVALRFGFREIETPIFEEAELFILRSGPNvLKELYNFKDKGDRDIALRPEMTAPVV 83 
                                       78***************************************999999777589************************ PP

                                       HHHHHHHH.TSS-EEEEEEEEEEESS-SSTT--CCEEEEEEEEESS-SHHHHHHHHHHHHHHHHHHCTSSSEEEEEE CS
                     tRNA-synt_His  77 Riaahrln.rerplRlcYaGsvlrtrpdglgrsreplQvGaEliGaegleadlEvlslllealeaaagvkelrldlg 152
                                       R+  + ++  ++p ++ Y+G+++r ++ + gr re++Q+GaE+iG++++e d+E + ++  +++ ++g+k+ ++ +g
  gi|474934771|ref|YP_007688353.1|  84 RAFVNGMSnDPKPIKVFYFGQCFRYERPQSGRYREFFQFGAEIIGSATPETDAEAIGMASFMIK-SLGLKNYKVRIG 159
                                       *****8866******************************************************7.************ PP

                                       ETCHHHHHHHHTT--HHHHHHHHHHHHCT-HHHHHHHHHCCTTHHHCCHCC....HCCHCCCHHHHCHCCHCTHHHH CS
                     tRNA-synt_His 153 hvglvralleaaglsesleeallaalarkdlaelkelaaeaglkealrellkal.elygdaevleealealaaapal 228
                                       h+g++r+ ++++g+++++++++l+ l++k+++e + ++++ g++++ +++l  l e+ g+ evl++          +
  gi|474934771|ref|YP_007688353.1| 160 HIGVLRQRIADIGVPKERTAEVLQKLDKKNYEEARPILEDIGVRREDIDALFELtETVGGTEVLDKV--------PI 228
                                       *******************************************************999**9999996........25 PP

                                       HHHHHHHHHHHHHHHHHHHH-TTEEE-TT--TTTTT--SEEEEEEETT-S..S-SEEEEEECTTTGGG.T---EEEE CS
                     tRNA-synt_His 229 qaaldeleelaallealakpevrvtlDlaelrgyeYytGlvFaayaegvg..qaiarGGrYdelgaaf.grarpAtG 302
                                        +a + l+e++++le+++    ++ +Dl+ +rg++YytG+vF+a a+  g  ++i +GG Y  l++ f g++  +tG
  gi|474934771|ref|YP_007688353.1| 229 GEAGEYLREVVSYLERMG--VDDLEIDLGVVRGLDYYTGMVFEAEAPVLGaeKQICGGGSY-TLSELFgGEKVFSTG 302
                                       678899**********98..69**********************998655216********.9*****999****** PP

                                       EEEEHHHH CS
                     tRNA-synt_His 303 fsldleal 310
                                       f++  +++
  gi|474934771|ref|YP_007688353.1| 303 FAIGFDRI 310
                                       **988875 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.5   0.0   5.2e-20   1.3e-16       1      91 [.     327     414 ..     327     416 .] 0.97

  Alignments for each domain:
  == domain 1  score: 60.5 bits;  conditional E-value: 5.2e-20
                                       SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTC CS
                    HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtr 77 
                                       +++vip+++   ++ ++   +a +Lraag+++++d  ++++gk++++a  + ++fav++G+ el+kg+ t+rd++++
  gi|474934771|ref|YP_007688353.1| 327 DAFVIPVSD---DVRKESFAVATQLRAAGVSADIDLMGRKMGKALKYASGIPCRFAVIIGKAELDKGVATLRDMESG 400
                                       589******...89*************************************************************** PP

                                       EEEEEETTHHHHHH CS
                    HGTP_anticodon  78 eqervsldelvekl 91 
                                       +q +v+l++l++++
  gi|474934771|ref|YP_007688353.1| 401 DQKEVALADLPKAI 414
                                       **********9987 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7   0.0   1.4e-19   3.5e-16       1     174 [.      62     313 ..      62     317 .. 0.88

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 1.4e-19
                                       EEEEETTSEEEEE-SSSHHHHHHHHHHHEEEB.GGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b   1 YkledrndreyiLkPtneetfvelirdevlrs.krLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeasl 76 
                                       Y ++d+ dr+ +L+P+ ++++v+++ + + ++ k  P+k+++++ ++R+E++ ++G  R+reF q ++++++++   
  gi|474934771|ref|YP_007688353.1|  62 YNFKDKGDRDIALRPEMTAPVVRAFVNGMSNDpK--PIKVFYFGQCFRYERP-QSG--RYREFFQFGAEIIGSAT-- 131
                                       99**************************889888..****************.***..**************998.. PP

                                       HHHHHHHHHHHHHHHHHTT.SCEEEEEE.GTTSC........................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx........................................... RF
                      tRNA-synt_2b  77 ddslrdlikaisriferlglefraiiel.msaks........................................... 109
                                       ++ +++ i  +s + ++lgl+ ++++    +                                              
  gi|474934771|ref|YP_007688353.1| 132 PETDAEAIGMASFMIKSLGLKNYKVRIGhIGVLRqriadigvpkertaevlqkldkknyeearpiledigvrredid 208
                                       9********************99887544443336677899999999999999999999999999999999999999 PP

                                       ...................................................BTTSEEEEEEEEETTTSEEEEEEEEE CS
                                       ...................................................xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b 110 ...................................................adykdkkefeavsesltkgieigtiq 135
                                                                                          +dy+   +fea  + l+++ +i   +
  gi|474934771|ref|YP_007688353.1| 209 alfeltetvggtevldkvpigeageylrevvsylermgvddleidlgvvrgLDYYTGMVFEAEAPVLGAEKQICGGG 285
                                       99999999999999999999999999999999999999999999999999999999999999999999999886555 PP

                                       EEETHHHHHTTEEEECTTSSEEEEEEEEEEEEHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b 136 klgtrlserlgatvldennreksvimicaaigveRllsa 174
                                            lse +g++          v+ +++aig  R+l+a
  gi|474934771|ref|YP_007688353.1| 286 SY--TLSELFGGEK---------VFSTGFAIGFDRILLA 313
                                       44..7888888765.........6777788888887776 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   3.7e-08   9.4e-05      34     160 ..      34     157 ..      11     160 .. 0.69

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 3.7e-08
                                       TCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-ECESEEE-SSTHHHHHHHH....TTS-SSEEEEE CS
                      tRNA-synt_2d  34 gfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpekaveekllLRthttavqirtl....ekkkppikiis 106
                                       gf+e+e p           L++ ++ p   +++ + +k++    +++  LR  +ta  +r+     ++  +pik++ 
  gi|474934771|ref|YP_007688353.1|  34 GFREIETPIF-----EEAELFILRSGP-NVLKELYNFKDKG---DRDIALRPEMTAPVVRAFvngmSNDPKPIKVFY 101
                                       5554444443.....334455555555.3566667773333...6899*********9999888889999******* PP

                                       EEEEEBSST-SSSB-SEEEEEEEEEEETT-..-HHHHHHHHHHHHHHHCTST.EEEE CS
                      tRNA-synt_2d 107 igrvfRrdavDathlaeFhqveglvvdenv..sladlkgvleellkklfgae.vkvr 160
                                       +g++fR +   + +  eF+q    ++++    + a+ +g+++ ++k+l g +  kvr
  gi|474934771|ref|YP_007688353.1| 102 FGQCFRYERPQSGRYREFFQFGAEIIGSATpeTDAEAIGMASFMIKSL-GLKnYKVR 157
                                       ********************8877777655113344556666666666.66545555 PP

>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.033        85      22      52 ..      16      46 ..       8      62 .. 0.83
   2 !   14.5   0.0   5.5e-06     0.014      93     181 ..      98     198 ..      95     271 .. 0.77
   3 ?    2.1   0.0     0.033        85     285     298 ..     301     314 ..     285     319 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.033
                                      HHHHHHHHHHHHHHHHHTT-EE----SEESS CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 22 lrlrstvtkavrkyleengfieietPiLsks 52
                                      l+ r +  + +r++  + gf eietPi+ ++
  gi|474934771|ref|YP_007688353.1| 16 LEKRRSYEATLRSVALRFGFREIETPIFEEA 46
                                      667777778888888899*********8765 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 5.5e-06
                                       EEEEEEEEE--S--BTTB-S-CEEEEEEEE..ET-SCHH..HHHHHHHHHHHHHHHHHHCSCCCCCHTTTTTS.... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.... RF
                       tRNA-synt_2  93 rvfqiaraFRaEdsrtdrhlaEFtqieaem..sfieeed..imqvleelikslvkevlessakdiefvirrns.... 161
                                       +vf ++++FR E+ ++ r   EF q+ ae+  s + e d   + ++  +iksl  +  +   ++i    +r      
  gi|474934771|ref|YP_007688353.1|  98 KVFYFGQCFRYERPQSGRYR-EFFQFGAEIigSATPETDaeAIGMASFMIKSLGLKNYKVRIGHIGVLRQRIAdigv 173
                                       89*****************9.********977444443335788888888888766656665555555555556677 PP

                                       .....EE-SSS-EEEEHHHHHHHHH CS
                                       .....xxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 162 .....kdlkkpfkrltykeaiekln 181
                                             ++ +++ + +y+ea  +l+
  gi|474934771|ref|YP_007688353.1| 174 pkertAEVLQKLDKKNYEEARPILE 198
                                       7776666666677777777776655 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.033
                                       EEEEEEHHHHHHHH CS
                                       xxxxxxxxxxxxxx RF
                       tRNA-synt_2 285 gGlglGldRlvmll 298
                                        G+++G+dR++  +
  gi|474934771|ref|YP_007688353.1| 301 TGFAIGFDRILLAM 314
                                       7********98765 PP

>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.8e-05     0.046      14     198 ..      15     239 ..       8     248 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.8e-05
                   tRNA_synthFbeta  14 elnkeqklrrklrdllagaGlnEvitysfvsekeldklleddderkavelanPlsedqs..vlRtsLlpglLevlar 88 
                                       el+k++ ++ +lr++   +G+ E+ t  f   +el  l  ++  + + el n  ++     +lR+ +++ ++ +  +
  gi|474934771|ref|YP_007688353.1|  15 ELEKRRSYEATLRSVALRFGFREIETPIFEE-AELFIL--RSGPNVLKELYNFKDKGDRdiALRPEMTAPVVRAFVN 88 
                                       578999999999***********99877755.555566..47888888888887654333389************** PP

                   tRNA_synthFbeta  89 NlargnedvrlFEigkvflkd.seeelpeeerhlaivltgkreeeswsekaravdfydlkgivealleslgiekvef 164
                                        +++  + +++F +g++f+ +  ++ +++e  ++++ + g++          ++  +++ g++  + +slg++++++
  gi|474934771|ref|YP_007688353.1|  89 GMSNDPKPIKVFYFGQCFRYErPQSGRYREFFQFGAEIIGSA---------TPETDAEAIGMASFMIKSLGLKNYKV 156
                                       *********************999999***************.........8899999**************88876 PP

                   tRNA_synthFbeta 165 epaehpalhpgrsAei..................................................kvdgkevGvlG 191
                                       +  +      +r A+i                                                  ++d++++G +G
  gi|474934771|ref|YP_007688353.1| 157 RIGH-IGVLRQRIADIgvpkertaevlqkldkknyeearpiledigvrredidalfeltetvggteVLDKVPIGEAG 232
                                       6544.444445777777777777777999999999999999999999999999999999999999888999999999 PP

                   tRNA_synthFbeta 192 elhpevl 198
                                       e   ev+
  gi|474934771|ref|YP_007688353.1| 233 EYLREVV 239
                                       9888776 PP

>> DUF1127  Domain of unknown function (DUF1127)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.5   0.00049       1.3      26      36 ..     197     207 ..     196     208 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00049
                           DUF1127  26 LaDIGlsRsdi 36 
                                       L DIG++R+di
  gi|474934771|ref|YP_007688353.1| 197 LEDIGVRREDI 207
                                       99********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.53
# Mc/sec: 2378.94
//
Query:       gi|474934772|ref|YP_007688354.1|  [L=402]
Description: glutamyl-tRNA reductase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-34  118.6   0.6    4.5e-34  117.5   0.6    1.6  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    1.5e-32  112.4   0.2    4.5e-32  110.8   0.2    1.8  1  GlutR_N          Glutamyl-tRNAGlu reductase, N-terminal domai
    1.1e-16   61.0   7.8    6.6e-16   58.5   4.4    2.7  2  GlutR_dimer      Glutamyl-tRNAGlu reductase, dimerisation dom
      1e-09   38.9   0.2      3e-09   37.3   0.2    1.9  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    0.00038   20.7   0.1    0.00097   19.3   0.1    1.7  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
     0.0014   18.0   0.1     0.0025   17.2   0.1    1.4  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
  ------ inclusion threshold ------
      0.045   14.2   1.1       0.11   13.0   0.1    2.2  2  NAD_binding_7    Putative NAD(P)-binding
      0.082   13.2   0.2      0.082   13.2   0.2    2.7  3  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
          1    9.8   7.4        3.9    7.9   0.1    2.9  3  Latarcin         Latarcin precursor


Domain annotation for each model (and alignments):
>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.5   0.6   2.2e-37   4.5e-34       1     138 []     152     287 ..     152     287 .. 0.98

  Alignments for each domain:
  == domain 1  score: 117.5 bits;  conditional E-value: 2.2e-37
                                       HHHHHHHS..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-S CS
                      Shikimate_DH   1 elakkkleslkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaead 77 
                                       ela++ ++sl+++ + ++GaG ma  +ak+L+ k+ k v+v NRt+era+ela+elkg+   a+ l+ l ++l+++d
  gi|474934772|ref|YP_007688354.1| 152 ELAENHIGSLENRSIAILGAGDMAGVIAKNLAGKNPKTVIVSNRTFERAQELAKELKGT---AVGLDRLGDILRDSD 225
                                       79******************************************************999...*************** PP

                                       EEEE-SSSSS-SB-HHHHHCCHHH.S...EEEEE--SS-SB-TTGGGSTTCCCEEHHHHHHH CS
                      Shikimate_DH  78 vvisataseepilekeeveealkkrk.kplllvDiavPRdvepevaeledvrlytvDdLkev 138
                                       ++++at++++ +++k++ve a+++r+ +pll++D++vP +v+++v e+e+v+l t++ L ++
  gi|474934772|ref|YP_007688354.1| 226 LILVATSAKHDVIKKADVEYAMQQRDgRPLLIIDVSVPTNVSKDVTEIEGVSLSTMESLDSI 287
                                       ********************************************************999765 PP

>> GlutR_N  Glutamyl-tRNAGlu reductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.8   0.2   2.3e-35   4.5e-32      24     146 .]      16     137 ..       8     137 .. 0.83

  Alignments for each domain:
  == domain 1  score: 110.8 bits;  conditional E-value: 2.3e-35
                           GlutR_N  24 kellkeleekvkeaviLsTCNRtEiylsaeeeeeaseellellaevsleelk....eklyvlegeeavrHlfrVasG 96 
                                       +e++++ +++v+e+v++ TCNR+E y++++++ + ++    +l ++ +++++    +  y+le++++++Hlf+V +G
  gi|474934772|ref|YP_007688354.1|  16 AEAVRA-DKDVREYVLIRTCNRLEAYIATDDNVRVKA----MLDRTVRKNVEfgdrQFWYILEDKACIKHLFTVICG 87 
                                       334444.35788**************87766544444....45444445555556799******************* PP

                           GlutR_N  97 LdSlvlGEdqIlgQvkeayelakeagtlgkvLerlfqkaikvakrvrtet 146
                                       +dSl++GEdqI++Q+ke++e+a+++g ++k L  lf ka+ v+krvrtet
  gi|474934772|ref|YP_007688354.1|  88 IDSLIVGEDQIQHQIKESFEQARKEGHVKKKLYALFCKALVVGKRVRTET 137
                                       *************************************************8 PP

>> GlutR_dimer  Glutamyl-tRNAGlu reductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1     0.076   1.5e+02      34      68 ..      23      59 ..       5      62 .. 0.82
   2 !   58.5   4.4   3.3e-19   6.6e-16       1      97 []     301     396 ..     301     396 .. 0.95

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.076
                                      HHHHHHHHHHHHS-S....--------TTHHHHHHHH CS
                       GlutR_dimer 34 eeireeeleralkkla..ldgedreelekltrslvnk 68
                                      +++re  l r+ ++l+  + ++d+  +++++++ v+k
  gi|474934772|ref|YP_007688354.1| 23 KDVREYVLIRTCNRLEayIATDDNVRVKAMLDRTVRK 59
                                      568999999********877777777********998 PP

  == domain 2  score: 58.5 bits;  conditional E-value: 3.3e-19
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-S..--------TTHHHHHHHHHHHHHHHHH CS
                       GlutR_dimer   1 kAeaiIeeeveefeawlkslevvptIkalrekaeeireeeleralkklaldgedreelekltrslvnkllheptarL 77 
                                       +Ae+iI++e+e++ ++ k+ +++ +I++l   +e++r++e + a+  l  + ed +++++++r+l+nk++ e +++L
  gi|474934772|ref|YP_007688354.1| 301 RAESIIRQEMEDIDREEKQEAADRAIRDLSLMFETVRKREADVAKGML--SSEDSAVIDDMSRALINKIFSEVIKNL 375
                                       59*******************************************999..6999999******************** PP

                                       HSS.-TTTTHHHHHHHHH... CS
                       GlutR_dimer  78 kea.edeeeellealrrlFnl 97 
                                       ++a  +e++ ++ea+++lF+l
  gi|474934772|ref|YP_007688354.1| 376 RKAaLEEDDLTIEAASKLFGL 396
                                       ***766666**********97 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.2   1.5e-12     3e-09       2      73 ..     166     235 ..     165     263 .. 0.76

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 1.5e-12
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECH.HHHHHH-SEEEE-S-HHH CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdn.eeaaeeadvvvlavkped 73 
                                       i+i+GaG+m+  +a++l+ ++  p+ ++v  +r+ e+a+ela+el+ ++ + d   + ++++d +++a   ++
  gi|474934772|ref|YP_007688354.1| 166 IAILGAGDMAGVIAKNLAGKN--PKTVIVS-NRTFERAQELAKELKGTAVGLDRlGDILRDSDLILVATSAKH 235
                                       9****************9998..9999955.***************888877652689999999999986654 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   4.9e-07   0.00097       2      71 ..     166     239 ..     165     272 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4.9e-07
                                       EEEE--SHHHHHHHHHHH.HTT-EEEEE-SSHHHHHHHHHTT...EEE-SSHHHHHHHCSEEEE-SSSHHHHHH CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnll.kagykvavynrtkekveelvaeg...akaaesieelvasldvvitmvkagkavde 71 
                                       i+++G G M   +a+nl+ k+  +v+v nrt e+++el++e    a++++ + +++++ d++++  +a+++v +
  gi|474934772|ref|YP_007688354.1| 166 IAILGAGDMAGVIAKNLAgKNPKTVIVSNRTFERAQELAKELkgtAVGLDRLGDILRDSDLILVATSAKHDVIK 239
                                       99***************8588899***************99566899***************999999888865 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   1.2e-06    0.0025      28     103 ..     155     235 ..     131     246 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.2e-06
                                       CGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-.EEEEESSSHHHHH....CHHHHTCEECSHHHHHHH-SEEEE-S CS
                      2-Hacid_dh_C  28 allgkelsgktvGiiGlGrIGqavakrlkafgm.kviaydrskkkee....eeeelgvelvsleellaesDivslhl 99 
                                       + ++ +l+++ ++i+G+G+++  +ak l++ +   vi+ +r+ ++ +    e + + v l+ l ++l++sD + +++
  gi|474934772|ref|YP_007688354.1| 155 ENHIGSLENRSIAILGAGDMAGVIAKNLAGKNPkTVIVSNRTFERAQelakELKGTAVGLDRLGDILRDSDLILVAT 231
                                       5566789**********************999945666666655554565555566668889999********9998 PP

                                       --ST CS
                      2-Hacid_dh_C 100 pltp 103
                                        +++
  gi|474934772|ref|YP_007688354.1| 232 SAKH 235
                                       8765 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.9   3.7e+03      44      71 ..      57      90 ..      16     111 .. 0.57
   2 ?   13.0   0.1   5.4e-05      0.11       5      72 ..     161     234 ..     158     267 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.9
                     NAD_binding_7 44 leelvklaeeel......ekdlegadlviaatdd 71
                                      + ++v++ ++++      ++ ++  ++vi+ +d 
  gi|474934772|ref|YP_007688354.1| 57 VRKNVEFGDRQFwyiledKACIKHLFTVICGIDS 90
                                      3344444444443333222336666666666654 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 5.4e-05
                     NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvk.laeeel.....ekdlegadlviaatddr 72 
                                       l+++++ + G+G++A   +++l+ ++ k ++v+++++e ++el k l+ + +      + l + dl+++at+ +
  gi|474934772|ref|YP_007688354.1| 161 LENRSIAILGAGDMAGVIAKNLAGKNPKTVIVSNRTFERAQELAKeLKGTAVgldrlGDILRDSDLILVATSAK 234
                                       799********************************988888777743333322232267799999999999754 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.57   1.1e+03       9      51 ..      11      51 ..      10      58 .. 0.85
   2 ?   13.2   0.2   4.1e-05     0.082       1      49 [.     166     212 ..     166     272 .. 0.85
   3 ?   -2.6   0.1       3.2   6.4e+03      32      62 ..     315     321 ..     287     357 .. 0.51

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.57
                                      HHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEE CS
                   Sacchrp_dh_NADP  9 vGqavaellarhfdvdaeitvadrskeklealaakalgvrfea 51
                                      ++ avae + + +dv  +  v  r+ ++lea +a+  +vr++a
  gi|474934772|ref|YP_007688354.1| 11 ISDAVAEAVRADKDV--REYVLIRTCNRLEAYIATDDNVRVKA 51
                                      788999999999999..88888899999999999888888876 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 4.1e-05
                                       EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCE CS
                   Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrf 49 
                                       + i+GaG ++ ++a+ la +++   +++v  r+ e++++la++++g+ +
  gi|474934772|ref|YP_007688354.1| 166 IAILGAGDMAGVIAKNLAGKNPK--TVIVSNRTFERAQELAKELKGTAV 212
                                       789*****************998..9**************998865544 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 3.2
                                       SSHHHHHHHHCHHTTTCEEEEE--TTTHHHH CS
                   Sacchrp_dh_NADP  32 rskeklealaakalgvrfeaialdaenyeav 62 
                                       r++++                        + 
  gi|474934772|ref|YP_007688354.1| 315 REEKQ------------------------EA 321
                                       22222........................22 PP

>> Latarcin  Latarcin precursor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.7   7.5e+03      54      70 ..     104     119 ..      96     126 .. 0.65
   2 ?    4.9   1.1     0.018        36       7      37 ..     311     340 ..     307     353 .. 0.90
   3 ?    7.9   0.1     0.002       3.9      14      57 ..     356     400 ..     345     402 .] 0.79

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.7
                          Latarcin  54 edtEEARgafkklkdkf 70 
                                       e  E AR   +++k+k+
  gi|474934772|ref|YP_007688354.1| 104 ESFEQARK-EGHVKKKL 119
                                       55677777.66666665 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.018
                          Latarcin   7 eeleaeeLdelergainrklmemvnnlRkvq 37 
                                       e+++ ee +e+ ++ai r l  m+  +Rk +
  gi|474934772|ref|YP_007688354.1| 311 EDIDREEKQEAADRAI-RDLSLMFETVRKRE 340
                                       9***************.***********965 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.002
                          Latarcin  14 LdelergainrklmemvnnlRkvqgRLee.mvenlrkvedledtE 57 
                                       +d+ +r+ in+ + e + nlRk +    +  +e+  k+++l+  E
  gi|474934772|ref|YP_007688354.1| 356 IDDMSRALINKIFSEVIKNLRKAALEEDDlTIEAASKLFGLDSKE 400
                                       899*******************98443333478888888876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1137  (0.0634168); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 2545.67
//
Query:       gi|474934773|ref|YP_007688355.1|  [L=333]
Description: porphobilinogen synthase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.8e-138  461.0   0.7   2.1e-138  460.9   0.7    1.0  1  ALAD      Delta-aminolevulinic acid dehydratase


Domain annotation for each model (and alignments):
>> ALAD  Delta-aminolevulinic acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  460.9   0.7  1.1e-142  2.1e-138       2     316 ..       7     330 ..       6     331 .. 0.97

  Alignments for each domain:
  == domain 1  score: 460.9 bits;  conditional E-value: 1.1e-142
                                       --GGGGGSSHHHHHHC-S----GGGEEEEEEEESS-SS-EE-TTSTT-EEEEGGGHHHHHHHHHHTT--EEEEEEE- CS
                              ALAD   2 krlrrlrksealrelvretrlsasdlilplfvkegeeekeeiksmpgvyrlsvdelvkeveelvklgikavllFgvp 78 
                                       +r rrlr+++a+r lvretrl+asdlilplf + + +e +  +smp+v +++++  ++ v++++++g+++vl+Fgvp
  gi|474934773|ref|YP_007688355.1|   7 NRGRRLRQTPAIRGLVRETRLDASDLILPLFFDANISEIKYTDSMPDVPTYPLSGYADIVKDVMDSGVSSVLVFGVP 83 
                                       699************************************************************************** PP

                                       SS-BSS-GGGGSTTSHHHHHHHHHHHH-...TTSEEEEEE-STTTBSS-SSSEEE.SS.EEHHHHHHHHHHHHHHHH CS
                              ALAD  79 eekdeegsealnedglvqrairaikeev...pelvvitDvclceytshGhcgile.ekevdndetlellakvavsqa 151
                                       ++kd egs+a+++dg+vq air +k+++   ++l+vi+D+c+ceyt+hGhcgil+ +++vdnd+t+e++ ++avsqa
  gi|474934773|ref|YP_007688355.1|  84 ARKDGEGSDAYSDDGVVQVAIRGLKAALkdpQDLIVISDLCMCEYTDHGHCGILReDGDVDNDATIEYYGRIAVSQA 160
                                       *************************99866577*********************62556****************** PP

                                       HCT-SEEEE-S--TTHHHHHHHHHHHTT-TT-EEB---EEB--CGGHHHHHHHT--.....-S.S--TTTSB-TT-H CS
                              ALAD 152 eaGadivapSdmmDgrvaaireaLdeagfeevailsYsaKyaSafYgPFrdaaesa.....psfgdrktYqmdpans 223
                                       +aGad++apS+mmDg++ air+ Ld+agf++v+i++YsaKy+SafYgPFrd+a+sa      +++dr tYqmdpan+
  gi|474934773|ref|YP_007688355.1| 161 KAGADMIAPSGMMDGQIDAIRSVLDAAGFQDVPIMAYSAKYQSAFYGPFRDIANSAptcscHAKKDRATYQMDPANR 237
                                       ********************************************************666665578************ PP

                                       HHHHHHHHHHHHTT-SBEEEES-TTGHHHHHHHHTT-SS-EEEEE-HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH CS
                              ALAD 224 realreveldleeGADivmvKPalaylDiirevkeefdlpvaayqvSGEYamikaaaengwldekkvvlEsllsikR 300
                                       realre++ dl+eGADi+mvKPa +ylDi+re++++f +p++ayqvSGEYam kaaa+ngw+de+++++Esll+ikR
  gi|474934773|ref|YP_007688355.1| 238 REALREIAEDLDEGADIIMVKPAGPYLDIVREAADTFPVPICAYQVSGEYAMTKAAAKNGWIDEERIMMESLLGIKR 314
                                       ***************************************************************************** PP

                                       TT-SEEEETTHHHHHH CS
                              ALAD 301 AGadliltYfakevak 316
                                       AGad+i+tY+ak +a+
  gi|474934773|ref|YP_007688355.1| 315 AGADMIITYYAKVAAR 330
                                       ************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2132.26
//
Query:       gi|474934774|ref|YP_007688356.1|  [L=425]
Description: glutamate-1-semialdehyde 2,1-aminomutase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-71  241.4   0.0    1.7e-71  241.1   0.0    1.0  1  Aminotran_3    Aminotransferase class-III
    4.6e-06   26.0   0.0    6.7e-06   25.5   0.0    1.1  1  Aminotran_1_2  Aminotransferase class I and II


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  241.1   0.0   1.9e-75   1.7e-71       9     386 ..      31     400 ..      24     418 .. 0.84

  Alignments for each domain:
  == domain 1  score: 241.1 bits;  conditional E-value: 1.9e-75
                                       SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT- CS
                       Aminotran_3   9 lllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapk 85 
                                        ++v++ ++G+++tdvdg+ y+Dl  ++ ++++Gh+ P+v+kav++q  k s      + +ep l+l ek+++++p 
  gi|474934774|ref|YP_007688356.1|  31 YPVVMDSGQGCIITDVDGNDYIDLCMAYGPLIVGHSCPRVTKAVRDQTRKGSVFG---TPSEPELRLLEKITSVVPS 104
                                       568999*********************************************5554...899***************9 PP

                                       ..SEEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-T CS
                       Aminotran_3  86 gldkvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlky 162
                                         d+  lansG+eA++ A++lar       +t ++ i++++g+fHG  ++ l ++gs  +  ++  p++ +v+    
  gi|474934774|ref|YP_007688356.1| 105 -ADMCRLANSGTEATMHAVRLARG------YTGRNGIVKLNGGFHGAHNTMLVAAGS--GSVSG-TPSSLGVPADDV 171
                                       .9**********************......9****************9999999999..33333.344555555555 PP

                                       TBGGGTB-HHHHHHHHHHHHHHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTTT CS
                       Aminotran_3 163 pdeevlkeneeeeaalleelealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvqtGfG 239
                                         ++ +++n+      +  +e+l   +++++aA+i+Ep+ g+ Gvv++++++l+++r++++khdvlli+DEv tGf 
  gi|474934774|ref|YP_007688356.1| 172 RNTYLVEYND------AGSFESLL-DSNEDIAAIIMEPVMGNVGVVPPKDGYLKEMRKITEKHDVLLIFDEVITGF- 240
                                       5566666666......66789988.7899***********************************************. PP

                                       TTSSSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTS...B--TTTT-HHHHHHHHHHHHHHHH... CS
                       Aminotran_3 240 rTGklfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgs...hgsTfgGnplacavalavleiiee... 310
                                       r G   A   +gv+pDl+t++K ++gG+p+ a+++++++m+++ap +    ++Tf+Gnp+  a+ l++++i++e   
  gi|474934774|ref|YP_007688356.1| 241 RAGPASAQGRYGVTPDLTTMGKIIGGGYPAGAFMGKRKIMEMVAPAGqvyAAGTFAGNPISSAAGLETINIMAEsgr 317
                                       99*******************************************998989***********************555 PP

                                       .TTHHHHHHHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTC............HHHHHHHHHCTEE- CS
                       Aminotran_3 311 .ekllenaqelgaalkegLeelqkkyevikevRgkGlmiaielkeeaevke............keilkkakekGvli 374
                                        + l +++ +l a+++++Le+        + v  +  m+++ ++ + ev++             ++++ +++ Gv+ 
  gi|474934774|ref|YP_007688356.1| 318 yDSLEKRTMDLVARMRDALEDSG----IPGCVQTVASMFSV-FFGPGEVTNgneaqtadraafGRMFNYMLDRGVY- 388
                                       55666666666666666666655....66777777777777.6666665555666677887776678888888888. PP

                                       EEETTTEEEE-- CS
                       Aminotran_3 375 lsaGdnvirllp 386
                                       l+ G+  + ++ 
  gi|474934774|ref|YP_007688356.1| 389 LPPGPLEVEFMS 400
                                       566666666665 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   7.5e-10   6.7e-06     130     360 ..     180     408 ..     172     412 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 7.5e-10
                                       E-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHH.HHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHG CS
                     Aminotran_1_2 130 ldlealeealkeapegnkktkvilvesphNPtGtvatlee.leklldlakkynlllfvDeaYagfvfgsldavatra 205
                                       +d+ ++e +l+++      +  i+ e +  + G+v++++  l+++ ++++k+ +ll++De+  gf  g+ +a+  r 
  gi|474934774|ref|YP_007688356.1| 180 NDAGSFESLLDSNE----DIAAIIMEPVMGNVGVVPPKDGyLKEMRKITEKHDVLLIFDEVITGFRAGPASAQG-RY 251
                                       68999999999943....3589***************99647899999********************777766.99 PP

                                       GSTTSTTEEEEEESSSTT..SSGGG-EEEEEEEHHHHHHHHHHHHHHTS.SHHHHHHHHHHHHHHHHHHH...HHHH CS
                     Aminotran_1_2 206 nveeepnllivgslsKaf..GlaGeRvGyilgnaavvsqlrklsrpfls.ssllqaavaaalsdallkqs...elee 276
                                       +v ++       +++K    G +    G++ g+ ++ + ++ + + +   + ++ ++ +aa   +  ++    + + 
  gi|474934774|ref|YP_007688356.1| 252 GVTPDLT-----TMGKIIggGYPA---GAFMGKRKIMEMVAPAGQVYAAgTFAGNPISSAAGLETINIMAesgRYDS 320
                                       9999855.....*****9666788...*******9999999999988888666666666665565656655778888 PP

                                       HHHHHHHHHHHHHHHHHHSTEE.EECCSCSSEEEEEETHH..........CHHHHHHH.........HHHTCTEEEE CS
                     Aminotran_1_2 277 mrqrlqkrrkelrdeLaelglk.vlasqsgmflltdlsae..........takelskk.........Lleevgvyvt 333
                                         +r  ++  ++rd+L++ g++ +++  + mf++  ++ e          +                +l++ gvy+ 
  gi|474934774|ref|YP_007688356.1| 321 LEKRTMDLVARMRDALEDSGIPgCVQTVASMFSVFFGPGEvtngneaqtaD------RaafgrmfnyMLDR-GVYLP 390
                                       9999999999999999888998355555************99775444321......2566667999****.***99 PP

                                       EGGGGTSTTEEEEECTTS-HHHHHHHH CS
                     Aminotran_1_2 334 pgtsftvpgrlRitvAglteeeleelv 360
                                       p       g l + +  +++++  e++
  gi|474934774|ref|YP_007688356.1| 391 P-------GPLEVEF--MSAATDSEAC 408
                                       9.......4555555..5555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2851.10
//
Query:       gi|474934775|ref|YP_007688357.1|  [L=287]
Description: porphobilinogen deaminase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-64  217.0   0.1    2.5e-64  216.6   0.1    1.2  1  Porphobil_deam   Porphobilinogen deaminase, dipyromethane cof
    6.5e-11   42.5   0.0    1.6e-10   41.2   0.0    1.7  1  Porphobil_deamC  Porphobilinogen deaminase, C-terminal domain
  ------ inclusion threshold ------
      0.023   14.0   0.0      0.044   13.1   0.0    1.4  1  DegV             Uncharacterised protein, DegV family COG1307


Domain annotation for each model (and alignments):
>> Porphobil_deam  Porphobilinogen deaminase, dipyromethane cofactor binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.6   0.1   4.1e-68   2.5e-64       2     203 ..       2     204 ..       1     205 [. 0.94

  Alignments for each domain:
  == domain 1  score: 216.6 bits;  conditional E-value: 4.1e-68
                    Porphobil_deam   2 rigtRkSkLAlaqaelvaeaLke...eeeveivtiktkGDkildkpLakiggkglFtkeleeaLlegeidlaVhSlK 75 
                                        +g+R+S+LA++q+e+++++Lk+   e e+e+  i+++GD +l+++L+++gg+g+F++el++ L +geid+ V SlK
  gi|474934775|ref|YP_007688357.1|   2 IVGSRESQLAMLQTEEFIRRLKKkmpEIECETRGITSSGDIDLKTSLKDMGGTGVFVRELDDLLKKGEIDVTVNSLK 78 
                                       69*******************765555568*********************************************** PP

                    Porphobil_deam  76 DlptelpeglelaavlkredprDvlvvkssleelpegavvgTsSlRRkaqlkklrpdlevkdlRGnvdtRlrkldeg 152
                                       D+p+ ++e+l+++avl+r+ ++D+l     +e+l  ga+vgTsS+RR++ ++++ pd+++kd+RGn++tRl+k++++
  gi|474934775|ref|YP_007688357.1|  79 DIPAFIDEELTIGAVLPRAAVEDALYP-IPWEKLSCGAIVGTSSMRRAMMIRARKPDIRIKDIRGNMNTRLQKVNDE 154
                                       *************************93.379********************************************9* PP

                    Porphobil_deam 153 eydaiiLAaAGLkRlgleerisevlspeellpavgQGalavevrkedeell 203
                                        y+ai++A+A+++R+g + ++   ++++ ++pa+gQGa+ave+rk+d+e+l
  gi|474934775|ref|YP_007688357.1| 155 VYNAIVVAKAAMDRMGEDLNVYP-IDKNIVIPAAGQGAIAVECRKDDKETL 204
                                       ****************4444443.***********************9975 PP

>> Porphobil_deamC  Porphobilinogen deaminase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.0   2.6e-14   1.6e-10       2      69 ..     217     284 ..     216     287 .] 0.82

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 2.6e-14
                                       HHHHHHHHHHHHTT--TTSSEEEEEEEETTE.EEEEEEEE-TTS..S-EEEEEEEE-GGGHHHHHHHH CS
                   Porphobil_deamC   2 levlaERallkeLeGGCsvPiGvyaeveaneelkLkglvlsldglksaveeaeakgeleeaeelGkkl 69 
                                       +ev+ ER +l+++++GCs PiGv aev++++e+k  ++   +d  +   e+  + +++e+a+e+  kl
  gi|474934775|ref|YP_007688357.1| 217 IEVTFERDVLRYMNAGCSSPIGVNAEVTEDDEIKVLAASFVPDVPVRLSETFPVDDAPEKAKEIAAKL 284
                                       589*************************5555************886666666777777777766655 PP

>> DegV  Uncharacterised protein, DegV family COG1307
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   7.4e-06     0.044      96     169 ..     156     232 ..     154     237 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.4e-06
                                       HHHHHHHHHTS....STTCEEEEE-SS-HHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHTEEEEEEES-THHHHH CS
                              DegV  96 fqsaklaaeel....eekkvrvvDsksvsaglgllvleaarlakqGksfeeilkkleeikektklyfvvddLdyLvk 168
                                       ++++++a+ ++    e+ +v+ +D  +v  + g + + a + +k+ k++ eilkk+++ k++++++f  d L+y+  
  gi|474934775|ref|YP_007688357.1| 156 YNAIVVAKAAMdrmgEDLNVYPIDKNIVIPAAG-QGAIAVECRKDDKETLEILKKVDHAKTRIEVTFERDVLRYMNA 231
                                       8888888888888899999*****988854444.3334566789****************************99987 PP

                                       H CS
                              DegV 169 g 169
                                       g
  gi|474934775|ref|YP_007688357.1| 232 G 232
                                       7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2164.56
//
Query:       gi|474934776|ref|YP_007688358.1|  [L=247]
Description: uroporphyrin-III C-methyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-46  158.1   0.0    3.3e-46  157.9   0.0    1.0  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
  ------ inclusion threshold ------
       0.13   12.6   0.0       0.49   10.8   0.0    2.0  1  Radical_SAM   Radical SAM superfamily


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.9   0.0   3.7e-50   3.3e-46       1     212 [.       4     216 ..       4     217 .. 0.88

  Alignments for each domain:
  == domain 1  score: 157.9 bits;  conditional E-value: 3.7e-50
                      TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealr 77 
                                       k+ylVG+GpGd  l T++++++l++advv++d+   +e+l + ++e +el +  ++ ++ +  ++ + ++ l+e+++
  gi|474934776|ref|YP_007688358.1|   4 KVYLVGAGPGDLGLFTIKGMQVLREADVVMYDALANPELL-EECKEGAELIDAGKRAADHH-LRQWQTNDLLVEYAK 78 
                                       79*******************************4455555.55666544444444444444.4455589999***** PP

                      TP_methylase  78 agkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl.....lpglake 149
                                       +gk+Vv+l++GDP+++g+g+e++e+lr+  ag+ev+v+PGvss  +++  +gip+t+++ +++v+     +++   e
  gi|474934776|ref|YP_007688358.1|  79 QGKTVVRLKGGDPFLFGRGAEEAEKLRN--AGVEVHVVPGVSSSISVPELAGIPVTHRDHASMVTfitghEKSDRSE 153
                                       ****************************..***************************************96666778 PP

                      TP_methylase 150 eereleallangdtlvllkaprklaelaelLkea.lyddttpvavveragtedervvrgtleel 212
                                       ++ +++ l++  +tlv+l++++++ ++ + L+e  + +d  p+a++++++t+d++v+++ +++l
  gi|474934776|ref|YP_007688358.1| 154 DRVDWASLVKGHGTLVILMGLENACNISKGLIEGgMSPDF-PAAIISKGSTPDQKVFKTVVSKL 216
                                       999*******************************999966.*****************998877 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   5.5e-05      0.49      39      83 ..      74     114 ..      55     228 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.5e-05
                                       HHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  39 kelkaekgvkevilgggepllypdfvellerlaklavpgiritve 83 
                                        e+ a++g+ +v l gg+p+l  + +e++e+l+     g++++v+
  gi|474934776|ref|YP_007688358.1|  74 VEY-AKQGKTVVRLKGGDPFLFGRGAEEAEKLRNA---GVEVHVV 114
                                       456.6788************************998...5555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1898.42
//
Query:       gi|474934777|ref|YP_007688359.1|  [L=263]
Description: Uroporphyrinogen-III synthase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-33  114.3   0.1    6.7e-33  114.0   0.1    1.1  1  HEM4      Uroporphyrinogen-III synthase HemD


Domain annotation for each model (and alignments):
>> HEM4  Uroporphyrinogen-III synthase HemD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.0   0.1   3.7e-37   6.7e-33       3     231 ..      16     250 ..      14     251 .. 0.94

  Alignments for each domain:
  == domain 1  score: 114.0 bits;  conditional E-value: 3.7e-37
                                       HHHHHHHTTEEEEE---EECCECCHHHHHHHHH.T.....--SEEEE--HHHHHHHHHHHHHTT---HHHHHCSEEE CS
                              HEM4   3 laealearGaeplelPlieiepaedraelraal.ddleagkydwliftSanavealfealkreeedvkalaslkvaa 78 
                                        ++++++rG +p  +P +  ++   r+++ +++ + l +g+  + +f S +ave+++e    +e +++ l+++ va+
  gi|474934777|ref|YP_007688359.1|  16 AEQEIRKRGMQPYGAPSLVSVR--GRDSVFEEIeETLSSGEAYFTVFASITAVECVVEEYG-KEKVLALLSETNVAC 89 
                                       5789***************999..78888888877788999*******************8.9************** PP

                                       SSHHHHHHHHHT.T---SEE-..SSSHHHHGGGS-.---EEEEEE-SS.S--HHHHHHHHHTTEEEEEE-SEEE..E CS
                              HEM4  79 vGpaTaraLeel.glrvdlvpseegtaegLaeelaeslagkrvlllrgeiarddlaegLeergaevdevevYet..v 152
                                        Gp+T +a+++l g   dlvp+  ++++g a e+a ++ +k+vl+lr+ +++  ++  Lee+ga v +  vY     
  gi|474934777|ref|YP_007688359.1|  90 TGPSTEAAMQRLlGRGCDLVPE-VYSGVGIATEIADEVCDKTVLILRSAEGDGGIVTILEEAGAVVLDEAVYAMepA 165
                                       ***********76********9.***************************************************555 PP

                                       E-HHHHHHHHHHHHTT--SEEEESSHHHHHHHHHH-S-HH......HHHCTSEEEEESHHHHHHHHHTT---SEEET CS
                              HEM4 153 paeeepeelkealkagevdavvftSpstvrnllellkdeg......delkevkvaaiGptTaealkklglkvdvvae 223
                                       p +++ + l +al +ge+d+ +ftSp + + lle +++        + l++v  +aiG  T++a++k+gl++ + +e
  gi|474934777|ref|YP_007688359.1| 166 PFSPAHSALLDALGDGEIDVMLFTSPKSFTILLEQAEKWLgagrahSSLESVCKMAIGLPTSKAMEKYGLEPQILPE 242
                                       555699999999999*********************974499999999***************************** PP

                                       S--HHHHH CS
                              HEM4 224 eptaeglv 231
                                       + t  g++
  gi|474934777|ref|YP_007688359.1| 243 KSTFAGML 250
                                       ****9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1845.31
//
Query:       gi|474934778|ref|YP_007688360.1|  [L=370]
Description: small GTP-binding protein domain protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.3e-29   99.7   0.2    1.5e-28   98.9   0.2    1.4  1  MMR_HSR1_Xtn   C-terminal region of MMR_HSR1 domain
      3e-23   82.1   0.1    8.7e-23   80.6   0.0    1.8  2  MMR_HSR1       50S ribosome-binding GTPase
    1.5e-18   66.6   0.0      3e-18   65.6   0.0    1.6  1  TGS            TGS domain
    1.9e-17   63.2   1.2    4.4e-15   55.5   0.0    3.0  3  FeoB_N         Ferrous iron transport protein B
    8.5e-08   32.3   1.6      0.006   16.5   0.1    2.9  3  RsgA_GTPase    RsgA GTPase
    4.4e-06   26.4   1.3       0.03   13.9   0.1    3.5  3  GTP_EFTU       Elongation factor Tu GTP binding domain
    7.1e-06   26.2   1.6      0.054   13.5   0.0    2.7  3  Dynamin_N      Dynamin family
     0.0043   16.7   1.6        1.3    8.6   0.2    2.3  2  cobW           CobW/HypB/UreG, nucleotide-binding domain
  ------ inclusion threshold ------
      0.015   14.3   0.8      0.039   12.9   0.1    1.9  2  MeaB           Methylmalonyl Co-A mutase-associated GTPase Me
      0.023   14.9   0.1       0.35   11.1   0.1    2.6  1  YchF-GTPase_C  Protein of unknown function (DUF933)
      0.024   14.2   0.3        2.5    7.7   0.0    2.6  2  Ras            Ras family
      0.057   13.9   0.0       0.17   12.4   0.0    1.9  1  ABC_tran       ABC transporter
      0.087   13.1   0.0       0.17   12.1   0.0    1.6  1  AAA_28         AAA domain
       0.12   12.8   0.1       0.28   11.6   0.1    1.7  1  AAA_16         AAA ATPase domain
       0.78    9.8   4.9         11    6.1   0.4    2.7  2  FlxA           FlxA-like protein


Domain annotation for each model (and alignments):
>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.9   0.2   1.3e-31   1.5e-28       1     106 []     185     293 ..     185     293 .. 0.92

  Alignments for each domain:
  == domain 1  score: 98.9 bits;  conditional E-value: 1.3e-31
                      MMR_HSR1_Xtn   1 kgGikitstvkltkldeetvkkilkeykihnaevliredvtvDdlidviegnrvYipclyvlNKiDlisleeldela 77 
                                       +gGi+i+ t++ltk++ et +++++ ++  n++v+ired+++++l dv++gnrvYi++++++NK+Dl++  +l++++
  gi|474934778|ref|YP_007688360.1| 185 QGGINIQPTLPLTKITVETAREMISAFGHINCTVVIREDIDTEQLLDVLAGNRVYIKAVMAINKVDLAKPGQLEAVQ 261
                                       69*****************************************************************8877777777 PP

                      MMR_HSR1_Xtn  78 re...pnsvviSaekelnldeLkekiweeLnL 106
                                       ++    +sv +Sa++++n+d+Lk++i++++++
  gi|474934778|ref|YP_007688360.1| 262 EMhkqFKSVGVSAATGYNMDALKQEIYDQIDM 293
                                       65332699********************9986 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.6   0.0   7.3e-26   8.7e-23       2      93 ..      68     160 ..      67     185 .. 0.85
   2 ?   -2.6   0.0       4.8   5.7e+03      64      86 ..     261     283 ..     233     311 .. 0.59

  Alignments for each domain:
  == domain 1  score: 80.6 bits;  conditional E-value: 7.3e-26
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHC.TS CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflalee.ad 77 
                                       va+vG p vGKStL+n+ltg++++v+++++tT+d++ g +++++ +i+++D+pGli++as++kg g+++ a  + +d
  gi|474934778|ref|YP_007688360.1|  68 VALVGFPSVGKSTLLNQLTGAHSEVGAYHFTTLDVVPGVMEYNHAKIQILDMPGLIKDASRGKGRGREVIAAARsSD 144
                                       9****************************************999*******************9999999988857* PP

                                       EEEEEEETTTTCSHHH CS
                          MMR_HSR1  78 lillvvdaseeklkpl 93 
                                       +illvvd+ + +++ l
  gi|474934778|ref|YP_007688360.1| 145 VILLVVDIFQPDMHVL 160
                                       *******983333333 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.8
                                       HHHHHHHHHHHCTSEEEEEEETT CS
                          MMR_HSR1  64 kglgkaflaleeadlillvvdas 86 
                                       +++ k+f+++  + +  + +da 
  gi|474934778|ref|YP_007688360.1| 261 QEMHKQFKSVGVSAATGYNMDAL 283
                                       35566666655555555666644 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.6   0.0   2.5e-21     3e-18       1      59 [.     294     366 ..     294     367 .. 0.98

  Alignments for each domain:
  == domain 1  score: 65.6 bits;  conditional E-value: 2.5e-21
                                       EEEEE.TTSSEEE......EETTB-HHHHHHHHSTTHHHHEEEEEECS.......EEEETTSBB-SSEEEEEE CS
                               TGS   1 irvyt.PdGkvpd......lprgatveDfAykIhrslakkfiyAlVnG.......qrvgldhvLedgdvveIv 59 
                                       ir+y+ P+G++ d      ++rg  v D+A  Ihr++ ++f+yA+V+G       q vg+dhvL+d+dv+ I+
  gi|474934778|ref|YP_007688360.1| 294 IRIYLkPQGQEADmkepliVKRGNNVGDVAELIHRDFRNAFRYAQVWGksakfpgQTVGMDHVLQDEDVLCII 366
                                       89********************************************************************997 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   0.0   3.7e-18   4.4e-15       2      94 ..      67     158 ..      66     172 .. 0.90
   2 ?    2.2   0.1       0.1   1.2e+02      88     136 ..     187     235 ..     168     243 .. 0.81
   3 ?    3.2   0.1     0.049        59     106     156 .]     240     287 ..     236     287 .. 0.82

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 3.7e-18
                                       EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHH.CT CS
                            FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardfll.ee 77 
                                       tvalvG p vGk+tl+n+ltga+++vg +  +t +   g +++++ +++i+D+PG   +++ s+ +   r++++  +
  gi|474934778|ref|YP_007688360.1|  67 TVALVGFPSVGKSTLLNQLTGAHSEVGAYHFTTLDVVPGVMEYNHAKIQILDMPGL--IKDASRGKGRGREVIAaAR 141
                                       79*****************************************************8..78999999999**998456 PP

                                       SSSEEEEEEEGGGHHHH CS
                            FeoB_N  78 epdvvvnvvdatnlern 94 
                                       + dv++ vvd  + + +
  gi|474934778|ref|YP_007688360.1| 142 SSDVILLVVDIFQPDMH 158
                                       789******98766555 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.1
                                       GGGHHHHHHHHHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS CS
                            FeoB_N  88 atnlernLyLtlqllelgvpvvlalnmideaekkgieidlkkLsekLgv 136
                                         n++ +L Lt   +e+  +++ a+  i+     + +id+++L + L  
  gi|474934778|ref|YP_007688360.1| 187 GINIQPTLPLTKITVETAREMISAFGHINCTVVIREDIDTEQLLDVLAG 235
                                       4689999***********************************9888865 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.049
                                       SSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTHHHHHHHH CS
                            FeoB_N 106 vpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkegieellkai 156
                                       ++ v+a+n++d a+  ++e  ++++++++  + v +sa+++ ++++l+++i
  gi|474934778|ref|YP_007688360.1| 240 IKAVMAINKVDLAKPGQLE-AVQEMHKQF--KSVGVSAATGYNMDALKQEI 287
                                       6899*******99887776.577888876..56999999999999999876 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1     5e-06     0.006      54     125 ..      18      90 ..       7     133 .. 0.73
   2 ?    0.0   0.0      0.58   6.9e+02      46      86 ..     189     225 ..     180     238 .. 0.70
   3 !   13.4   0.1   4.6e-05     0.056      45     102 ..     238     292 ..     216     295 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5e-06
                                       E-GGG--HHH..HHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT--- CS
                       RsgA_GTPase  54 nKiDlleeee..eleelkeelealgyevllvsaktkegleelkellkdktsvlvGqSGvGKStLinallpelel 125
                                       +K + ++e +  ++++  ++l+a   + l  s+ ++ +     ++  + t++lvG   vGKStL+n+l++  + 
  gi|474934778|ref|YP_007688360.1|  18 TKKNKATEGHigKIKARIAKLSAEKEKRLEASKASGGTKGFYVKKAGNATVALVGFPSVGKSTLLNQLTGA-HS 90 
                                       55555555554444444444444455555555555555555566667799******************997.34 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.58
                                       T-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTT CS
                       RsgA_GTPase  46 giepvivlnKiDlleeeeeleelkeelealgyevllvsakt 86 
                                       +i+p++ l+Ki + + +e    + +++ +++++v++ +  +
  gi|474934778|ref|YP_007688360.1| 189 NIQPTLPLTKITVETARE----MISAFGHINCTVVIREDID 225
                                       689999999998877777....7777777777777665443 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 4.6e-05
                                       TT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTTSEE CS
                       RsgA_GTPase  45 kgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkellkdkts 102
                                         i+ v+++nK+Dl++  + le+++e  +++  + + vsa t+ ++++lk+++ d++ 
  gi|474934778|ref|YP_007688360.1| 238 VYIKAVMAINKVDLAKPGQ-LEAVQEMHKQF--KSVGVSAATGYNMDALKQEIYDQID 292
                                       46899*************9.88888888777..8889999999********9999876 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.11   1.3e+02       6      29 ..      68      91 ..      65     101 .. 0.78
   2 !    7.6   0.0    0.0021       2.5      63     104 ..     107     153 ..      90     174 .. 0.74
   3 !   13.9   0.1   2.5e-05      0.03     111     154 ..     226     280 ..     206     345 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.11
                                      EEEEESTTSSHHHHHHHHHHHTTS CS
                          GTP_EFTU  6 igiighvDhGKtTLtdrLlyktga 29
                                      ++++g    GK+TL+ +L+ ++++
  gi|474934778|ref|YP_007688360.1| 68 VALVGFPSVGKSTLLNQLTGAHSE 91
                                      566777778*********966555 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0021
                                       EETTCSSEEEEEEEESSSGG.......GHHHHHHHHHT-SEEEEEEETT CS
                          GTP_EFTU  63 leketkkylinliDtPGHvd.......FskevirglrvlDgavlvvdav 104
                                       +  e+++ +i+++D PG ++         +evi+++r  D+ +lvvd+ 
  gi|474934778|ref|YP_007688360.1| 107 M--EYNHAKIQILDMPGLIKdasrgkgRGREVIAAARSSDVILLVVDIF 153
                                       3..4888999999999976522111223479****************75 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 2.5e-05
                                       HHHHHHHHHHTTTE..EEEEEESCGSTHHHHHHHHHHHHHHHHHH.........H CS
                          GTP_EFTU 111 teevlrlalkegvp..iivfiNKmDrlkaelkeiveevkqklsrk.........e 154
                                       te++l ++  ++v    +++iNK+D +k    e v+e++++++++         +
  gi|474934778|ref|YP_007688360.1| 226 TEQLLDVLAGNRVYikAVMAINKVDLAKPGQLEAVQEMHKQFKSVgvsaatgynM 280
                                       77777777666665559*************************6656666666652 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.1       9.4   1.1e+04      65      81 ..       8      24 ..       5      45 .. 0.55
   2 !   13.5   0.0   4.5e-05     0.054       1      22 [.      68      89 ..      68     103 .. 0.86
   3 !   11.2   0.0   0.00024      0.29      99     138 ..     110     152 ..     104     173 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 9.4
                                      CHHHHHHHHHHHHHHHT CS
                         Dynamin_N 65 fsevreeieketekiag 81
                                      + e+++ei + ++++a+
  gi|474934778|ref|YP_007688360.1|  8 IAELEKEIANTKKNKAT 24
                                      44555555554444442 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 4.5e-05
                                      EEEEEBTTTTHHHHHHHHHTS- CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLlged 22
                                      +a+vG  S GKS++ln+L+g++
  gi|474934778|ref|YP_007688360.1| 68 VALVGFPSVGKSTLLNQLTGAH 89
                                      799*****************97 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00024
                                       TS-SEEEEE---B-SSSGTTS...HHHHHHHSTTEEEEEEEET CS
                         Dynamin_N  99 lvkgltlvDlPGldsvnkrdq...elvkeyikkadiilavtsa 138
                                       +  ++ ++D+PGl++ + r +   + v  +++++d+il+v++ 
  gi|474934778|ref|YP_007688360.1| 110 NHAKIQILDMPGLIKDASRGKgrgREVIAAARSSDVILLVVDI 152
                                       56789**********9999999998888899*********986 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.1    0.0032       3.9       3      21 ..      68      86 ..      66      95 .. 0.83
   2 !    8.6   0.2    0.0011       1.3      68     170 ..     163     268 ..     156     274 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0032
                                      EEEEESTTCCHHHHHHHHH CS
                              cobW  3 tvltGflGsGKTtLlnhll 21
                                      + l+Gf+  GK+tLln+l+
  gi|474934778|ref|YP_007688360.1| 68 VALVGFPSVGKSTLLNQLT 86
                                      679**************98 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0011
                                       -HHHHHHHHHHHHTT-SEEEEEECT.TTTHHHH..HTT....SHHHHH.CCCECEEEEEEETTTH.CCHCCHHHHHH CS
                              cobW  68 dllkelealeereerldviliEttG.laePapv..aft....eeelks.dltldavvavvDaknleaeeekieekae 136
                                       +l +++ +l ++  ++++i   ++G + +P+           ++e+ s    ++++v++   + + + e+    +a+
  gi|474934778|ref|YP_007688360.1| 163 ELYNSAIRLNQTAPDVNIITTQQGGiNIQPTLPltK-ItvetAREMISaFGHINCTVVI--REDI-DTEQLLDVLAG 235
                                       555566666777777888888888887888765341.1323433333302333333333..3344.77888889999 PP

                                       HHHHTSSEEEEE-HHHHCHC..HHHHHHHHHHHH CS
                              cobW 137 dqlaaadllvlnKtDlldeeallekleerlrqln 170
                                       + +    ++ +nK+Dl++  +l e+++e+ +q++
  gi|474934778|ref|YP_007688360.1| 236 NRVYIKAVMAINKVDLAKPGQL-EAVQEMHKQFK 268
                                       99999************99965.88888777765 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   3.2e-05     0.039      24      57 ..      61      93 ..      55     106 .. 0.84
   2 ?   -1.3   0.1      0.72   8.6e+02     172     191 ..     244     266 ..     218     309 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.2e-05
                                      GG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT CS
                              MeaB 24 akaGraqvvGltGvPGaGkstlvealglelrrrG 57
                                      +kaG+a+ v l G+P +Gkstl+++l+    + G
  gi|474934778|ref|YP_007688360.1| 61 KKAGNAT-VALVGFPSVGKSTLLNQLTGAHSEVG 93
                                      6899997.6899*************997766665 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.72
                                       EEEE---...HHHHHHHHHHHHH CS
                              MeaB 172 ivvnkaD...kkeaekaarelra 191
                                       +++nk D   + + e ++++ ++
  gi|474934778|ref|YP_007688360.1| 244 MAINKVDlakPGQLEAVQEMHKQ 266
                                       55555553322222222222222 PP

>> YchF-GTPase_C  Protein of unknown function (DUF933)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00029      0.35      17      44 ..     313     340 ..     305     367 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00029
                     YchF-GTPase_C  17 ikkgttapqaAgviHsDfekgFiraevi 44 
                                       +k+g ++ + A  iH Df++ F  a+v 
  gi|474934778|ref|YP_007688360.1| 313 VKRGNNVGDVAELIHRDFRNAFRYAQVW 340
                                       78999999*****************996 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0021       2.5       2      56 ..      68     120 ..      67     212 .. 0.67
   2 ?    4.0   0.1     0.028        33     105     160 ..     240     291 ..     220     293 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0021
                                       EEEEESTTSSHHHHHHHHHHSSCS.SSCTTTSSEEEEEEEEEETTEEEEEEEEEET CS
                               Ras   2 lvlvGdsavGKtslllrfvkdkFk.eeyesTigvdfytkeievdgkevkleiwDTA 56 
                                       + lvG  +vGK++ll++ +  + +   y+ T   d     +e+++  +k++i+D  
  gi|474934778|ref|YP_007688360.1|  68 VALVGFPSVGKSTLLNQLTGAHSEvGAYHFTT-LDVVPGVMEYNH--AKIQILDMP 120
                                       679**************987655413555555.666666665554..444555544 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.028
                                       SEEEEEEETTTGGGG-SS-HHHHHHHHHHHTSEEEEEBTTTTCTHHHHHHHHHHHH CS
                               Ras 105 vpivLvGnKvDleekravsteegeelakelglkfletSAktnenveeafeellrei 160
                                       ++ v+  nKvDl++    + e ++e++k++  k + +SA t +n++ + +e+ ++i
  gi|474934778|ref|YP_007688360.1| 240 IKAVMAINKVDLAK--PGQLEAVQEMHKQF--KSVGVSAATGYNMDALKQEIYDQI 291
                                       67788889999996..55567778888765..56899*******999988888776 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00014      0.17      11      43 ..      65      96 ..      55     141 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                                      TSEEEEEESTTSSHHHHHHHHTTSS--SEEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 11 gekvaivGenGaGKStLlkllagllkpteGeil 43
                                      + +va+vG    GKStLl+ l+g ++ + G  +
  gi|474934778|ref|YP_007688360.1| 65 NATVALVGFPSVGKSTLLNQLTGAHS-EVGAYH 96
                                      5689******************9976.455555 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00014      0.17       2      22 ..      68      89 ..      67     151 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                            AAA_28  2 ivitGgestGKTtlleaLa.ar 22
                                      ++++G +s GK+tll++L+ a+
  gi|474934778|ref|YP_007688360.1| 68 VALVGFPSVGKSTLLNQLTgAH 89
                                      899***************9544 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00023      0.28      25      51 ..      66      92 ..      59     160 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00023
                            AAA_16 25 elvllsGesGvGKsslvrellralekd 51
                                        v l+G + vGKs+l+++l  a ++ 
  gi|474934778|ref|YP_007688360.1| 66 ATVALVGFPSVGKSTLLNQLTGAHSEV 92
                                      5799***************99655554 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.5     0.028        34      48      80 ..      18      50 ..       2      62 .. 0.61
   2 ?    6.1   0.4    0.0092        11      26      66 ..     260     299 ..     256     310 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.028
                              FlxA 48 kkqqqliqaQIqqlqaQIaqlqqqqaekaqekq 80
                                       k+ +  +  I +++a Ia+l +++++  + ++
  gi|474934778|ref|YP_007688360.1| 18 TKKNKATEGHIGKIKARIAKLSAEKEKRLEASK 50
                                      255666677777777777777777766655555 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0092
                              FlxA  26 iknlqkqLkelsesdeltkeekkkqqqliqaQIqqlqaQIa 66 
                                       ++++ kq k+++ s + t  +  + +q+i  QI++++  ++
  gi|474934778|ref|YP_007688360.1| 260 VQEMHKQFKSVGVS-AATGYNMDALKQEIYDQIDMIRIYLK 299
                                       578999*******9.88888788*************86655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 2351.48
//
Query:       gi|474934779|ref|YP_007688361.1|  [L=379]
Description: hypothetical protein TALC_01214 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.5e-12   45.1  35.0    1.8e-07   31.1  10.0    2.3  3  DZR              Double zinc ribbon
    3.6e-10   39.2  26.9    1.6e-05   24.4   5.7    3.3  3  zinc_ribbon_2    zinc-ribbon domain
    2.4e-08   33.1  22.0     0.0012   18.2   2.6    3.4  3  zf-ribbon_3      zinc-ribbon domain
    7.2e-07   29.9  14.3      0.016   15.9   7.2    3.4  3  zinc_ribbon_15   zinc-ribbon family
     0.0012   18.7  22.6       0.38   10.7   1.8    3.6  3  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
     0.0089   15.5   0.5     0.0089   15.5   0.5    4.4  4  TF_Zn_Ribbon     TFIIB zinc-binding
  ------ inclusion threshold ------
      0.013   15.9   2.8      0.013   15.9   2.8    2.0  2  zf-C4H2          Zinc finger-containing protein
      0.028   14.5   3.3      0.028   14.5   3.3    3.7  4  UPF0547          Uncharacterised protein family UPF0547
       0.11   12.1   0.3       0.17   11.4   0.3    1.3  1  DUF334           Domain of unknown function (DUF334)
       0.18   11.8  14.0       0.66   10.0   2.9    2.9  3  zinc-ribbons_6   zinc-ribbons
       0.24   11.1  12.9        2.1    8.0   7.8    2.5  1  TackOD1          Thaumarchaeal output domain 1
       0.26   10.9  13.9        7.3    6.3   0.1    5.0  5  zf_UBZ           Ubiquitin-Binding Zinc Finger
       0.29   11.1  17.8         11    6.1   1.4    3.2  2  HypA             Hydrogenase/urease nickel incorporation, met
        0.3   11.1  16.3       0.23   11.4   2.7    3.9  5  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
       0.38   11.5   9.5        1.1   10.0   0.2    3.2  3  zinc-ribbon_6    zinc-ribbon domain
        0.5   10.7   4.4       0.25   11.7   0.6    2.4  2  zf-Di19          Drought induced 19 protein (Di19), zinc-bind
        2.2    8.5  24.8       0.84    9.8   2.9    4.4  5  Zn-ribbon_8      Zinc ribbon domain
        5.5    7.0  14.3        5.8    7.0   1.3    3.8  4  RNHCP            RNHCP domain
        7.3    7.0   9.5        6.7    7.1   0.6    3.3  3  C1_2             C1 domain
        9.9    6.0  24.6       0.11   12.2   1.8    4.4  4  Rubredoxin_2     Rubredoxin metal binding domain


Domain annotation for each model (and alignments):
>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   7.3   4.1e-09   3.7e-06       1      49 []     275     330 ..     275     330 .. 0.96
   2 !   31.1  10.0     2e-10   1.8e-07       1      48 [.     312     373 ..     312     374 .. 0.97
   3 !   14.2   2.1   3.8e-05     0.034       1      23 [.     356     378 ..     356     379 .] 0.92

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 4.1e-09
                               DZR   1 CpqCgeelppdarfCseCgtklkavaa.......edrCpsCgekvdpearfCpeCG 49 
                                       C  Cg+ + p+   C +Cg+ ++++++       + +C +Cg++v+ +a +Cp+CG
  gi|474934779|ref|YP_007688361.1| 275 CTFCGSIVLPGEVECRKCGAYIDRPESmkkqkhdMFQCTNCGAEVPGNADVCPKCG 330
                                       99*******************998777999999999*******************9 PP

  == domain 2  score: 31.1 bits;  conditional E-value: 2e-10
                               DZR   1 CpqCgeelppdarfCseCgtklkavaa..............edrCpsCgekvdpearfCpeC 48 
                                       C +Cg+e+p +a +C++Cg+k + v++              +  Cp Cg+ v+++a  Cp+C
  gi|474934779|ref|YP_007688361.1| 312 CTNCGAEVPGNADVCPKCGAKFDGVENevqhidgtvdvsdeSVECPFCGAVVPANADHCPKC 373
                                       *********************9988889999******************************* PP

  == domain 3  score: 14.2 bits;  conditional E-value: 3.8e-05
                               DZR   1 CpqCgeelppdarfCseCgtklk 23 
                                       Cp Cg+ +p++a  C++C +kl+
  gi|474934779|ref|YP_007688361.1| 356 CPFCGAVVPANADHCPKCFKKLR 378
                                       99****************99997 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   1.1   2.7e-05     0.025       1      21 [.     274     294 ..     274     296 .. 0.95
   2 !   24.4   5.7   1.8e-08   1.6e-05       2      22 ..     312     332 ..     311     333 .. 0.96
   3 !   11.8   5.1   0.00016      0.15       2      19 ..     356     373 ..     355     373 .. 0.99

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.7e-05
                     zinc_ribbon_2   1 fCpnCGaelqdnakFCpyCGt 21 
                                       +C+ CG  + ++++ C +CG+
  gi|474934779|ref|YP_007688361.1| 274 RCTFCGSIVLPGEVECRKCGA 294
                                       6*******************8 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 1.8e-08
                     zinc_ribbon_2   2 CpnCGaelqdnakFCpyCGtp 22 
                                       C+nCGae++ na  Cp+CG++
  gi|474934779|ref|YP_007688361.1| 312 CTNCGAEVPGNADVCPKCGAK 332
                                       *******************98 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.00016
                     zinc_ribbon_2   2 CpnCGaelqdnakFCpyC 19 
                                       Cp CGa ++ na  Cp+C
  gi|474934779|ref|YP_007688361.1| 356 CPFCGAVVPANADHCPKC 373
                                       ****************** PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   1.2    0.0006      0.53       4      24 ..     274     294 ..     273     296 .. 0.93
   2 !   16.2   3.5   5.5e-06     0.005       2      25 ..     309     332 ..     308     333 .. 0.91
   3 !   18.2   2.6   1.3e-06    0.0012       3      22 ..     354     373 ..     352     377 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0006
                       zf-ribbon_3   4 rCPnCGaplssddnvCpyCGt 24 
                                       rC  CG+++ ++ + C +CG+
  gi|474934779|ref|YP_007688361.1| 274 RCTFCGSIVLPGEVECRKCGA 294
                                       7999***99***********6 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 5.5e-06
                       zf-ribbon_3   2 tvrCPnCGa.plssddnvCpyCGtk 25 
                                       + +C nCGa +    + vCp+CG+k
  gi|474934779|ref|YP_007688361.1| 309 MFQCTNCGAeV-PGNADVCPKCGAK 332
                                       679******77.***********98 PP

  == domain 3  score: 18.2 bits;  conditional E-value: 1.3e-06
                       zf-ribbon_3   3 vrCPnCGaplssddnvCpyC 22 
                                       v+CP CGa++ + + +Cp+C
  gi|474934779|ref|YP_007688361.1| 354 VECPFCGAVVPANADHCPKC 373
                                       79******99********** PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.5     0.021        19      64      86 .]     262     293 ..     235     293 .. 0.77
   2 !   15.9   7.2   1.8e-05     0.016      38      86 .]     287     330 ..     286     330 .. 0.87
   3 !   14.6   0.3   4.5e-05     0.041      64      85 ..     350     373 ..     333     374 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.021
                    zinc_ribbon_15  64 e.........kkeCknCgkeveeefkyCpkCg 86 
                                       e         + +C  Cg+ v +    C kCg
  gi|474934779|ref|YP_007688361.1| 262 EaqgrlypqgYGRCTFCGSIVLPGEVECRKCG 293
                                       122345566799*******************9 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.8e-05
                    zinc_ribbon_15  38 lacskCkslleaskelgkeiekkessekkeCknCgkeveeefkyCpkCg 86 
                                       + c+kC++ +   +       kk+++++ +C nCg+ev  + + CpkCg
  gi|474934779|ref|YP_007688361.1| 287 VECRKCGAYIDRPE-----SMKKQKHDMFQCTNCGAEVPGNADVCPKCG 330
                                       6799**99998887.....4455667799*******************9 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 4.5e-05
                    zinc_ribbon_15  64 e..kkeCknCgkeveeefkyCpkC 85 
                                       +  + eC+ Cg++v ++ ++CpkC
  gi|474934779|ref|YP_007688361.1| 350 SdeSVECPFCGAVVPANADHCPKC 373
                                       144889****************** PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   1.8   0.00043      0.38      12      33 ..     273     294 ..     272     294 .. 0.93
   2 !    7.8   1.6    0.0033       2.9      13      33 ..     311     331 ..     311     334 .. 0.89
   3 !   10.6   4.2   0.00044       0.4      14      32 ..     356     374 ..     355     376 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00043
                           DUF35_N  12 qrCpdCGtvqfPPravCphCgs 33 
                                       +rC+ CG+ + P +  C++Cg+
  gi|474934779|ref|YP_007688361.1| 273 GRCTFCGSIVLPGEVECRKCGA 294
                                       8**********999******95 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0033
                           DUF35_N  13 rCpdCGtvqfPPr.avCphCgs 33 
                                       +C++CG+  +P    vCp+Cg+
  gi|474934779|ref|YP_007688361.1| 311 QCTNCGAE-VPGNaDVCPKCGA 331
                                       7*******.69999******97 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00044
                           DUF35_N  14 CpdCGtvqfPPr.avCphCg 32 
                                       Cp CG+v +P+   +Cp+C+
  gi|474934779|ref|YP_007688361.1| 356 CPFCGAV-VPANaDHCPKCF 374
                                       *******.7**********8 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.5     0.051        46      21      29 ..     274     282 ..     268     284 .. 0.80
   2 ?    1.4   3.5      0.26   2.4e+02       3      27 ..     275     294 ..     273     308 .. 0.69
   3 ?    1.0   2.9      0.35   3.1e+02      19      28 ..     309     318 ..     287     323 .. 0.65
   4 !   15.5   0.5   9.9e-06    0.0089       2      30 ..     325     364 ..     324     369 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.051
                                       EESSSSBEE CS
                      TF_Zn_Ribbon  21 vCtdCGlVl 29 
                                       +Ct+CG+++
  gi|474934779|ref|YP_007688361.1| 274 RCTFCGSIV 282
                                       8*****986 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.26
                                       ETTTTCEECHEETSTTCEEESSSSB CS
                      TF_Zn_Ribbon   3 CPnCgstnlveDpergelvCtdCGl 27 
                                       C  Cgs  +v++   ge+ C +CG+
  gi|474934779|ref|YP_007688361.1| 275 CTFCGS--IVLP---GEVECRKCGA 294
                                       666666..5666...6677777776 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.35
                                       CEEESSSSBE CS
                      TF_Zn_Ribbon  19 elvCtdCGlV 28 
                                        + Ct+CG+ 
  gi|474934779|ref|YP_007688361.1| 309 MFQCTNCGAE 318
                                       5678888865 PP

  == domain 4  score: 15.5 bits;  conditional E-value: 9.9e-06
                                       EETTTTCEEC...........HEETSTTCEEESSSSBEEE CS
                      TF_Zn_Ribbon   2 kCPnCgstnl...........veDpergelvCtdCGlVle 30 
                                       +CP+Cg +++           ++D +   + C++CG+V+ 
  gi|474934779|ref|YP_007688361.1| 325 VCPKCGAKFDgvenevqhidgTVDVSDESVECPFCGAVVP 364
                                       7*******999***************************96 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.9   2.8   1.4e-05     0.013     166     201 ..     297     332 ..     250     334 .. 0.87
   2 ?    0.3   1.4      0.84   7.6e+02     181     203 ..     356     378 ..     354     379 .] 0.88

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.4e-05
                           zf-C4H2 166 tatasfrqqpPPMKsClsChqqIHRNAPiCPlCKaK 201
                                       + ++s+++q   M +C++C +++  NA +CP C aK
  gi|474934779|ref|YP_007688361.1| 297 DRPESMKKQKHDMFQCTNCGAEVPGNADVCPKCGAK 332
                                       5668999**************************998 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.84
                           zf-C4H2 181 ClsChqqIHRNAPiCPlCKaKsR 203
                                       C  C + +  NA  CP C  K R
  gi|474934779|ref|YP_007688361.1| 356 CPFCGAVVPANADHCPKCFKKLR 378
                                       889999999*********88865 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   1.2       4.6   4.2e+03      16      21 ..     274     279 ..     273     279 .. 0.87
   2 ?   -0.5   0.3       1.5   1.4e+03      16      21 ..     288     293 ..     287     295 .. 0.86
   3 ?   14.5   3.3   3.2e-05     0.028       3      21 ..     312     330 ..     311     334 .. 0.89
   4 ?   10.3   7.0   0.00066      0.59       2      20 ..     355     373 ..     355     373 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 4.6
                           UPF0547  16 fCphCG 21 
                                       +C +CG
  gi|474934779|ref|YP_007688361.1| 274 RCTFCG 279
                                       69***9 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.5
                           UPF0547  16 fCphCG 21 
                                       +C+ CG
  gi|474934779|ref|YP_007688361.1| 288 ECRKCG 293
                                       799998 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 3.2e-05
                           UPF0547   3 CPeCeakvPvaaqfCphCG 21 
                                       C  C a+vP +a +Cp CG
  gi|474934779|ref|YP_007688361.1| 312 CTNCGAEVPGNADVCPKCG 330
                                       889**************** PP

  == domain 4  score: 10.3 bits;  conditional E-value: 0.00066
                           UPF0547   2 vCPeCeakvPvaaqfCphC 20 
                                       +CP C a vP++a  Cp C
  gi|474934779|ref|YP_007688361.1| 355 ECPFCGAVVPANADHCPKC 373
                                       5*****************9 PP

>> DUF334  Domain of unknown function (DUF334)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3   0.00019      0.17     181     224 ..     205     249 ..     199     255 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00019
                            DUF334 181 dvlqnaiasklkasegfisvlwy.iayglpyvlaiglfiglyewi 224
                                       d+  na+++    +    ++ wy  aygl y +ai  f+ l  w 
  gi|474934779|ref|YP_007688361.1| 205 DTKSNALCTGAYFTGSESTMAWYgAAYGLAYTMAIFYFLVLATWF 249
                                       66666666554444444578899568****************995 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.3      0.27   2.4e+02      18      39 ..     274     296 ..     258     301 .. 0.67
   2 ?    9.8   4.9   0.00084      0.75       2      39 ..     288     333 ..     287     338 .. 0.76
   3 ?   10.0   2.9   0.00073      0.66       3      39 ..     326     377 ..     324     379 .] 0.84

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.27
                                       E-TTT--.EEEEEEE-SSS-S-- CS
                    zinc-ribbons_6  18 hCeaCqe.dlkkealCpeCeqel 39 
                                       +C  C +  l  e  C +C+  +
  gi|474934779|ref|YP_007688361.1| 274 RCTFCGSiVLPGEVECRKCGAYI 296
                                       67777773445567777777654 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00084
                                       --SSS-S--EE-S.......SEEE-TTT--EEE.EEEE-SSS-S-- CS
                    zinc-ribbons_6   2 kCpeCqqelekrg.......eqyhCeaCqedlk.kealCpeCeqel 39 
                                       +C++C + +++ +       + ++C +C +++  +  +Cp+C+ + 
  gi|474934779|ref|YP_007688361.1| 288 ECRKCGAYIDRPEsmkkqkhDMFQCTNCGAEVPgNADVCPKCGAKF 333
                                       6999998777444467777799********99725569****9986 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00073
                                       -SSS-S--E.E-S.............SEEE-TTT--EEE.EEEE-SSS-S-- CS
                    zinc-ribbons_6   3 CpeCqqele.krg.............eqyhCeaCqedlk.kealCpeCeqel 39 
                                       Cp+C ++ +  ++             e+++C  C + +  +  +Cp+C ++l
  gi|474934779|ref|YP_007688361.1| 326 CPKCGAKFDgVENevqhidgtvdvsdESVECPFCGAVVPaNADHCPKCFKKL 377
                                       ******9995444799********************77515679****9988 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   7.8    0.0023       2.1      74     135 ..     273     335 ..     233     362 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0023
                           TackOD1  74 rlCpsCksghlnvrevCpkC.......kSidieeqelihhftCgnvgpeeeflkegkleCpkCktkLrh 135
                                         C+ C s  l    +C+kC       +S++ +++ ++++ +Cg+  p      +++ +CpkC  k   
  gi|474934779|ref|YP_007688361.1| 273 GRCTFCGSIVLPGEVECRKCgayidrpESMKKQKHDMFQCTNCGAEVP------GNADVCPKCGAKFDG 335
                                       46******************3333333356666666777777776554......567789999765433 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1     0.065        59       3      16 ..     287     300 ..     285     303 .. 0.83
   2 ?    6.3   0.1    0.0081       7.3       1      14 [.     308     321 ..     308     325 .. 0.88
   3 ?    4.9   0.2     0.022        19       4      13 ..     325     334 ..     322     342 .. 0.85
   4 ?    3.2   0.0     0.073        66       2      15 ..     353     366 ..     352     369 .. 0.85
   5 ?   -1.3   0.2       1.9   1.7e+03       5      10 ..     370     375 ..     366     378 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.065
                            zf_UBZ   3 ylCerCgkeipese 16 
                                       + C +Cg++i  +e
  gi|474934779|ref|YP_007688361.1| 287 VECRKCGAYIDRPE 300
                                       57*******98775 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0081
                            zf_UBZ   1 dtylCerCgkeipe 14 
                                       d+++C  Cg+e+p 
  gi|474934779|ref|YP_007688361.1| 308 DMFQCTNCGAEVPG 321
                                       789********995 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.022
                            zf_UBZ   4 lCerCgkeip 13 
                                       +C++Cg+++ 
  gi|474934779|ref|YP_007688361.1| 325 VCPKCGAKFD 334
                                       8*****9985 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.073
                            zf_UBZ   2 tylCerCgkeipes 15 
                                       ++ C+ Cg+ +p +
  gi|474934779|ref|YP_007688361.1| 353 SVECPFCGAVVPAN 366
                                       789********976 PP

  == domain 5  score: -1.3 bits;  conditional E-value: 1.9
                            zf_UBZ   5 CerCgk 10 
                                       C++C k
  gi|474934779|ref|YP_007688361.1| 370 CPKCFK 375
                                       ****66 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   9.1     0.023        21      68      95 ..     307     332 ..     268     345 .. 0.74
   2 ?    6.1   1.4     0.012        11      67      94 ..     350     375 ..     339     378 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.023
                                       --EEEETTTS-EEECHHHHHS-TTTSSS CS
                              HypA  68 pvkvrCreCgkefeleekalrCpkCgsa 95 
                                       +  ++C++Cg+e+  +++   CpkCg++
  gi|474934779|ref|YP_007688361.1| 307 HDMFQCTNCGAEVPGNAD--VCPKCGAK 332
                                       445678888877775544..79999985 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.012
                                       E--EEEETTTS-EEECHHHHHS-TTTSS CS
                              HypA  67 vpvkvrCreCgkefeleekalrCpkCgs 94 
                                        + +v+C  Cg+ +  +++  +CpkC +
  gi|474934779|ref|YP_007688361.1| 350 SDESVECPFCGAVVPANAD--HCPKCFK 375
                                       56789******99998755..8****65 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.6    0.0091       8.1      30      58 ..     274     298 ..     273     299 .. 0.90
   2 ?   11.4   2.7   0.00025      0.23      30      59 ..     288     324 ..     287     325 .. 0.86
   3 ?    4.2   1.6     0.046        41      30      57 ..     311     334 ..     310     340 .. 0.80
   4 ?    4.8   1.9      0.03        27      30      59 ..     325     368 ..     321     370 .. 0.75
   5 ?    4.9   0.6     0.029        26      25      52 ..     350     373 ..     345     378 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0091
                    OrfB_Zn_ribbon  30 tCseCgsknkealsgrtfkCpnCgfeadr 58 
                                       +C  Cgs++ +     +++C++Cg+++dr
  gi|474934779|ref|YP_007688361.1| 274 RCTFCGSIVLP----GEVECRKCGAYIDR 298
                                       58889999988....99**********99 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00025
                    OrfB_Zn_ribbon  30 tCseCgsknke.....alsgrtfkCpnCgfe..adrD 59 
                                       +C +Cg+  ++     +++++ f+C+nCg+e   ++D
  gi|474934779|ref|YP_007688361.1| 288 ECRKCGAYIDRpesmkKQKHDMFQCTNCGAEvpGNAD 324
                                       8******99999*999999**********98455665 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.046
                    OrfB_Zn_ribbon  30 tCseCgsknkealsgrtfkCpnCgfead 57 
                                       +C +Cg+++      +  +Cp+Cg+++d
  gi|474934779|ref|YP_007688361.1| 311 QCTNCGAEVPG----NADVCPKCGAKFD 334
                                       58888887766....6678999998887 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.03
                    OrfB_Zn_ribbon  30 tCseCgsknke............alsgrtfkCpnCgfe..adrD 59 
                                        C++Cg+k +             ++s++ ++Cp Cg++  a++D
  gi|474934779|ref|YP_007688361.1| 325 VCPKCGAKFDGvenevqhidgtvDVSDESVECPFCGAVvpANAD 368
                                       58888888766667778888888888888888888887556666 PP

  == domain 5  score: 4.9 bits;  conditional E-value: 0.029
                    OrfB_Zn_ribbon  25 ayTSktCseCgsknkealsgrtfkCpnC 52 
                                       +  S +C+ Cg+++      +  +Cp+C
  gi|474934779|ref|YP_007688361.1| 350 SDESVECPFCGAVVPA----NADHCPKC 373
                                       5569999999999888....44456666 PP

>> zinc-ribbon_6  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.2     0.051        46       3      25 ..     274     296 ..     272     304 .. 0.90
   2 ?   10.0   0.2    0.0012       1.1       1      25 [.     309     333 ..     309     352 .. 0.86
   3 ?    1.2   0.7      0.67     6e+02       3      25 ..     355     377 ..     353     378 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.051
                     zinc-ribbon_6   3 eCeqCgqllffenssClkCgaal 25 
                                       +C+ Cg+ +   +++C kCga +
  gi|474934779|ref|YP_007688361.1| 274 RCTFCGSIVLPGEVECRKCGAYI 296
                                       69*****************9865 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0012
                     zinc-ribbon_6   1 lfeCeqCgqllffenssClkCgaal 25 
                                       +f+C++Cg ++  +   C kCga+ 
  gi|474934779|ref|YP_007688361.1| 309 MFQCTNCGAEVPGNADVCPKCGAKF 333
                                       69********************985 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.67
                     zinc-ribbon_6   3 eCeqCgqllffenssClkCgaal 25 
                                       eC  Cg  +  +  +C kC ++l
  gi|474934779|ref|YP_007688361.1| 355 ECPFCGAVVPANADHCPKCFKKL 377
                                       799****************8776 PP

>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.6   0.00028      0.25       5      44 ..     326     366 ..     322     369 .. 0.86
   2 ?   -1.1   0.2       2.7   2.4e+03       5      12 ..     370     377 ..     365     379 .] 0.66

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00028
                           zf-Di19   5 CPyCgkelt.vkeLveHvedeHrveskevvCPvCaekvtkd 44 
                                       CP Cg +++ v++ v+H++    v+ ++v CP C + v ++
  gi|474934779|ref|YP_007688361.1| 326 CPKCGAKFDgVENEVQHIDGTVDVSDESVECPFCGAVVPAN 366
                                       ******998345579*******************9988776 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.7
                           zf-Di19   5 CPyCgkel 12 
                                       CP C k+l
  gi|474934779|ref|YP_007688361.1| 370 CPKCFKKL 377
                                       77776654 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1       1.6   1.4e+03       7      13 ..     274     280 ..     274     282 .. 0.81
   2 ?    9.8   2.9   0.00093      0.84       5      36 ..     286     319 ..     286     321 .. 0.85
   3 ?    8.6   2.3    0.0022         2       6      35 ..     310     332 ..     308     336 .. 0.75
   4 ?    9.0   3.1    0.0016       1.5       8      34 ..     326     361 ..     325     366 .. 0.75
   5 ?   -0.1   4.3       1.2   1.1e+03       8      36 ..     356     377 ..     355     379 .] 0.55

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.6
                       Zn-ribbon_8   7 rCeeCgh 13 
                                       rC+ Cg+
  gi|474934779|ref|YP_007688361.1| 274 RCTFCGS 280
                                       7999996 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00093
                       Zn-ribbon_8   5 eYrCeeCghefevlqsis.daplta.CPeCgsev 36 
                                       e +C++Cg   ++  s++ ++ +   C +Cg+ev
  gi|474934779|ref|YP_007688361.1| 286 EVECRKCGAYIDRPESMKkQKHDMFqCTNCGAEV 319
                                       569*********99999976667767*****986 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0022
                       Zn-ribbon_8   6 YrCeeCghefevlqsisdapltaCPeCgse 35 
                                       ++C++Cg e       +     +CP+Cg++
  gi|474934779|ref|YP_007688361.1| 310 FQCTNCGAEVP----GN---ADVCPKCGAK 332
                                       89*****4444....33...456*****85 PP

  == domain 4  score: 9.0 bits;  conditional E-value: 0.0016
                       Zn-ribbon_8   8 CeeCghefe....vlqsis.dap...lta.CPeCgs 34 
                                       C +Cg +f+    ++q i+   +   + + CP Cg+
  gi|474934779|ref|YP_007688361.1| 326 CPKCGAKFDgvenEVQHIDgTVDvsdESVeCPFCGA 361
                                       **********99966666543335566677****98 PP

  == domain 5  score: -0.1 bits;  conditional E-value: 1.2
                       Zn-ribbon_8   8 CeeCghefevlqsisdapltaCPeCgsev 36 
                                       C  Cg    ++++++     +CP+C +++
  gi|474934779|ref|YP_007688361.1| 356 CPFCG----AVVPAN---ADHCPKCFKKL 377
                                       66666....333333...33499996655 PP

>> RNHCP  RNHCP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       2.3   2.1e+03      40      71 ..      95     126 ..      90     143 .. 0.77
   2 ?   -0.1   0.1         1     9e+02       4      18 ..     287     301 ..     284     308 .. 0.64
   3 ?    5.4   1.7     0.019        17       2      29 ..     308     329 ..     307     334 .. 0.82
   4 ?    7.0   1.3    0.0065       5.8       2      30 ..     352     374 ..     351     377 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.3
                             RNHCP  40 gdraseCkglmepiavevkkkkewvivhrCek 71 
                                       +d +++ +g++ +++++++ +++++i+   ++
  gi|474934779|ref|YP_007688361.1|  95 DDTEADAEGSFGAVSISYDGTGGLTITSSWST 126
                                       78899999999999999999999988766555 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1
                             RNHCP   4 ftCeeCgkeveklaa 18 
                                        +C++Cg+ + + ++
  gi|474934779|ref|YP_007688361.1| 287 VECRKCGAYIDRPES 301
                                       578888888775544 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.019
                             RNHCP   2 esftCeeCgkeveklaagsakrnHCpsC 29 
                                       + f+C++Cg+ev     g+   + Cp+C
  gi|474934779|ref|YP_007688361.1| 308 DMFQCTNCGAEVP----GN--ADVCPKC 329
                                       67**********9....33..6779998 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.0065
                             RNHCP   2 esftCeeCgkeveklaagsakrnHCpsCL 30 
                                       es +C  Cg+ v +      + +HCp+C 
  gi|474934779|ref|YP_007688361.1| 352 ESVECPFCGAVVPA------NADHCPKCF 374
                                       7889*****99993......469*****7 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1      0.15   1.3e+02      15      42 ..     269     296 ..     250     299 .. 0.74
   2 ?    7.1   0.6    0.0074       6.7      13      43 ..     304     334 ..     301     336 .. 0.85
   3 ?    1.0   0.4      0.59   5.3e+02      15      38 ..     350     373 ..     346     377 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.15
                              C1_2  15 ssesfnCsaCgrkidgffYsCseCdfsl 42 
                                        ++ ++C  Cg  + + + +C +C   +
  gi|474934779|ref|YP_007688361.1| 269 PQGYGRCTFCGSIVLPGEVECRKCGAYI 296
                                       5667899999999767778998897655 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0074
                              C1_2  13 edssesfnCsaCgrkidgffYsCseCdfslh 43 
                                       ++++++f+C  Cg ++ g+   C++C  +++
  gi|474934779|ref|YP_007688361.1| 304 KQKHDMFQCTNCGAEVPGNADVCPKCGAKFD 334
                                       67899**********9999999*99976665 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.59
                              C1_2  15 ssesfnCsaCgrkidgffYsCseC 38 
                                       s+es +C  Cg  +  +  +C++C
  gi|474934779|ref|YP_007688361.1| 350 SDESVECPFCGAVVPANADHCPKC 373
                                       788999****99976666788888 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.9     0.041        37       7      22 ..     265     280 ..     265     280 .. 0.85
   2 ?    0.9   0.5      0.44   3.9e+02       3       8 ..     289     294 ..     288     295 .. 0.73
   3 ?   12.2   1.8   0.00013      0.11       1      22 [.     310     331 ..     310     331 .. 0.96
   4 ?    2.6   1.5      0.13   1.1e+02       3      20 ..     356     373 ..     355     374 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.041
                      Rubredoxin_2   7 GfesakwfGrCpsCgs 22 
                                       G  +++ +GrC  Cgs
  gi|474934779|ref|YP_007688361.1| 265 GRLYPQGYGRCTFCGS 280
                                       5668999*******97 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.44
                      Rubredoxin_2   3 CsqCGf 8  
                                       C++CG+
  gi|474934779|ref|YP_007688361.1| 289 CRKCGA 294
                                       888885 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 0.00013
                      Rubredoxin_2   1 YvCsqCGfesakwfGrCpsCgs 22 
                                       ++C +CG+e +     Cp Cg+
  gi|474934779|ref|YP_007688361.1| 310 FQCTNCGAEVPGNADVCPKCGA 331
                                       89******************96 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.13
                      Rubredoxin_2   3 CsqCGfesakwfGrCpsC 20 
                                       C  CG++ ++   +Cp C
  gi|474934779|ref|YP_007688361.1| 356 CPFCGAVVPANADHCPKC 373
                                       7779999999999****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1072  (0.0597914); expected 358.6 (0.02)
Passed bias filter:                      689  (0.0384294); expected 358.6 (0.02)
Passed Vit filter:                       139  (0.0077528); expected 17.9 (0.001)
Passed Fwd filter:                        61  (0.00340231); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.71u 0.28s 00:00:00.99 Elapsed: 00:00:00.49
# Mc/sec: 2313.31
//
Query:       gi|474934780|ref|YP_007688362.1|  [L=684]
Description: DNA topoisomerase VI, B subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-59  199.2   0.0    5.6e-59  198.5   0.0    1.3  1  Topo-VIb_trans  Topoisomerase VI B subunit, transducer
    2.1e-09   37.9   0.1    4.6e-09   36.8   0.1    1.5  1  HATPase_c       Histidine kinase-, DNA gyrase B-, and HSP90-l
    1.8e-07   31.0   0.0    3.8e-07   30.0   0.0    1.5  1  HATPase_c_3     Histidine kinase-, DNA gyrase B-, and HSP90-l
    1.7e-05   24.9   0.0    6.5e-05   23.1   0.0    2.0  1  Top6b_C         Type 2 DNA topoisomerase 6 subunit B C-termin
     0.0011   19.5   0.1       0.17   12.5   0.0    3.3  4  PAS_10          PAS domain
  ------ inclusion threshold ------
      0.041   13.6   0.0      0.087   12.5   0.0    1.5  1  MAF_flag10      Protein of unknown function DUF115


Domain annotation for each model (and alignments):
>> Topo-VIb_trans  Topoisomerase VI B subunit, transducer
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.5   0.0   1.9e-62   5.6e-59       1     159 []     325     493 ..     325     493 .. 0.96

  Alignments for each domain:
  == domain 1  score: 198.5 bits;  conditional E-value: 1.9e-62
                    Topo-VIb_trans   1 Pstdclspigeeliekglkkel...kpefvaa.vtrkpkvyeghpfivEvgiayGGelekeekaeilRfaNrvPLly 73 
                                       P+++clspige+li+kgl+++l   kpef+a+ vtr+++v++g+pf+vE+gi+yGG+++ e +++++RfaNrvPLl+
  gi|474934780|ref|YP_007688362.1| 325 PPSECLSPIGETLIKKGLMHILdgeKPEFYATpVTRPAHVVNGNPFTVEAGIVYGGQIPAEGQVTVMRFANRVPLLF 401
                                       99*****************96533389****99******************************************** PP

                    Topo-VIb_trans  74 degadvitkavksinwkrYkleq......pedpvvvlvhvastkvPfksegKeaiadveeiekeiklalqevarkLk 144
                                       + gad+itka+ +i+w+rY+leq      p +p+++lvhvastkvPf+segK+aia+++eie+ei +al+ +ar+Lk
  gi|474934780|ref|YP_007688362.1| 402 QPGADIITKAIGEIDWRRYGLEQrggkgvPFGPAIFLVHVASTKVPFTSEGKDAIAAIPEIEEEIITALKGCARSLK 478
                                       *****************************9*********************************************** PP

                    Topo-VIb_trans 145 kylskkekekeekek 159
                                       ++l+k +k+ +++ek
  gi|474934780|ref|YP_007688362.1| 479 SHLNKMAKKDKTHEK 493
                                       ******999998775 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.1   1.5e-12   4.6e-09      10      94 ..      54     148 ..      46     170 .. 0.71

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 1.5e-12
                                       HHHHHHHHHHHHSTTTEE....EEEEEEEE...TEEEEEEEESSSSSTTHHHTGTCS.TTCH....HCSTCHTSTSS CS
                         HATPase_c  10 isnlvdNavkfatkagei....eveikase...ddlvisveDnGiGipkedlkklfe.kfsq....ddstkrggggt 74 
                                       ++++vdN++++  ++ ei     v+++  +   d++++s+eDnG+Gi    ++++f+  ++     +  ++rg++g 
  gi|474934780|ref|YP_007688362.1|  54 VKEAVDNSLDA-CEEAEIlpdiIVKVE--KtgdDEYKVSIEDNGPGIVHRAMPNVFGrLLYGsrfhAMRQSRGQQGI 127
                                       89********8.445544341155555..33468*******************99996333358887999999**** PP

                                       SHHHHHHHH.HHHHTTTEEEE CS
                         HATPase_c  75 GlGlsivkk.lvelmgGeiwv 94 
                                       G++++++ + +++ +  +i+ 
  gi|474934780|ref|YP_007688362.1| 128 GISATVMYAnISTGHPAHIQS 148
                                       *******99888754444444 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   1.3e-10   3.8e-07       7      99 ..      54     155 ..      49     188 .. 0.73

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 1.3e-10
                       HATPase_c_3   7 laelvdNsldAdaen.....vkievnknrgktgeivieDdGkGmseeelknal.rlatsskeakrkstslGkkGiGl 77 
                                       + e vdNsldA  e      + ++v+k   ++ +++ieD+G G+  + + n++ rl   s+  +  ++s+G+ GiG 
  gi|474934780|ref|YP_007688362.1|  54 VKEAVDNSLDACEEAeilpdIIVKVEKTGDDEYKVSIEDNGPGIVHRAMPNVFgRLLYGSRF-HAMRQSRGQQGIG- 128
                                       789********999999999777777776778*******************77589999999.579**********. PP

                       HATPase_c_3  78 klAsl.....slgkkltvitkkegess 99 
                                        +A++     s g  + + ++ ege +
  gi|474934780|ref|YP_007688362.1| 129 ISATVmyaniSTGHPAHIQSRIEGEDE 155
                                       454440111145556666666665555 PP

>> Top6b_C  Type 2 DNA topoisomerase 6 subunit B C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   2.2e-08   6.5e-05       2     109 ..     514     629 ..     513     634 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 2.2e-08
                                       SS---SHHHHHHHTT-EEEE..EEE--SSS-EEEEEEE---------EEE--EES---.--------.EEE-SSSEE CS
                           Top6b_C   2 reepdidpvvArimgnvlve..reveengdgvevslkvkNfsdkkeefelheilpaei.eeaspeak.vvemdneyd 74 
                                       r++pdi +++ +im+ v  e  r+ e++++ v+ + ++ N++ + ++f +h  lp e   +a  +++   +++++  
  gi|474934780|ref|YP_007688362.1| 514 RPVPDISRTISKIMNVVWFEpeRKREQENNSVRFTYTIFNYTVRPHTFMVHLALPPESvGDAVTKSEfFDSVNKDGK 590
                                       789**************98622666666566888999**************99987652444444441457899999 PP

                                       E-EEE.---TT-EEEE----SS-GGGS--...B------ CS
                           Top6b_C  75 lkWel.svsageskvleYsvdseaeeels...liveGve 109
                                        +W +  +++ +s +l+++++ +  +  +   + + G++
  gi|474934780|ref|YP_007688362.1| 591 AQWIIrDLQPTSSVQLSFELTGDMADTFDmdeVYISGIN 629
                                       999884599999999999998776665554577777776 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   5.6e-05      0.17      13      87 ..      32     103 ..      25     105 .. 0.92
   2 ?   -1.1   0.0      0.96   2.9e+03      11      59 ..     220     272 ..     177     277 .. 0.77
   3 ?    2.3   0.0     0.083   2.5e+02      31      70 ..     504     545 ..     499     571 .. 0.70
   4 ?   -2.2   0.0       2.1   6.3e+03      31      69 ..     564     605 ..     546     615 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.6e-05
                            PAS_10  13 tflDdnlqirrFtpaakklfklipadvGrpladihpkkavknveeviealrtgekdevevvvpkngkwvlvrylp 87 
                                        f+ +n qi+ F  ++k+l+  +++ v ++l+++   ++ + + ++i ++ ++ +de +v ++ ng  +++r +p
  gi|474934780|ref|YP_007688362.1|  32 EFFEKNKQILGFDSRQKSLLMGVKEAVDNSLDAC---EEAEILPDIIVKVEKTGDDEYKVSIEDNGPGIVHRAMP 103
                                       5999******************************...677778889999***********************998 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.96
                            PAS_10  11 eltflDdnlqirrFtpaak....klfklipadvGrpladihpkkavknveevi 59 
                                       +++f D + +i  F +a++    k  +++p   G ++ d+ + +++++++ v 
  gi|474934780|ref|YP_007688362.1| 220 KIVFHDPDGKIWTFERATEtkppKAQEIKPHPAGMEIGDMMTYSSLTQTKTVR 272
                                       67888899999999886532333777777777777777777776666666665 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.083
                            PAS_10  31 lfklipadvGrpladihpk.kavknveevi.ealrtgekdev 70 
                                       l++  ++++Grp+ di+ + +++ nv ++  e+ r++e++ v
  gi|474934780|ref|YP_007688362.1| 504 LANKLAEELGRPVPDISRTiSKIMNVVWFEpERKREQENNSV 545
                                       67778999********88777777777765233444444444 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 2.1
                            PAS_10  31 lfklipadvGrpladih..pk.kavknveeviealrtgekde 69 
                                       ++ l p+ vG+ +++     + ++  +++++i +l+ + +++
  gi|474934780|ref|YP_007688362.1| 564 HLALPPESVGDAVTKSEffDSvNKDGKAQWIIRDLQPTSSVQ 605
                                       567888899998887642222366666777887777766655 PP

>> MAF_flag10  Protein of unknown function DUF115
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.9e-05     0.087      55      90 ..      57      93 ..      54     123 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.9e-05
                        MAF_flag10 55 aadtalkaLlkegIkPDivvslDp.qeasyevfkeae 90
                                      a+d +l a++++ I PDi+v +++ ++ +y+v+ e +
  gi|474934780|ref|YP_007688362.1| 57 AVDNSLDACEEAEILPDIIVKVEKtGDDEYKVSIEDN 93
                                      89*********************97888888776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (684 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.48
# Mc/sec: 4266.54
//
Query:       gi|474934781|ref|YP_007688363.1|  [L=362]
Description: DNA topoisomerase VI, subunit A [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-13   48.2   0.1    1.5e-12   47.3   0.1    1.5  1  TP6A_N    Type IIB DNA topoisomerase
  ------ inclusion threshold ------
      0.012   14.5   0.0      0.018   13.9   0.0    1.2  1  RE_AlwI   AlwI restriction endonuclease
       0.14   12.0   0.0       0.45   10.4   0.0    1.8  2  DUF2399   Protein of unknown function C-terminus (DUF2399)


Domain annotation for each model (and alignments):
>> TP6A_N  Type IIB DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.1   2.5e-16   1.5e-12       3      61 ..      70     132 ..      68     133 .. 0.95

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 2.5e-16
                                       HHHHHHHHHHHHHHHHTT--EEHHHHHHH....GGGS-SSHHHHHHHHHHHHHHHTS-GGGGT CS
                            TP6A_N   3 faqllkvlelihelleegkvvTkRdiYYr....dvelFksQaesdrliddievllgvsReeLn 61 
                                       + ++ ++ ++i+++++ +k++T+R++YY     + ++F+s +es+ l++d+e++ +++Re++ 
  gi|474934781|ref|YP_007688363.1|  70 MLRTAYTTKFINDMIRDNKSSTLREMYYVsegwNNAKFHSEDESNLLVEDLETISSCLREDFK 132
                                       578999***********************999999**************************96 PP

>> RE_AlwI  AlwI restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0     3e-06     0.018     167     237 ..      62     134 ..      41     153 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3e-06
                           RE_AlwI 167 k.skgklvilakekk.eeIekLleeaaiknkddylelmskinkaelplenisnnlleqlnrivsnlskqlnik 237
                                       k  +g+ + l   +  ++I+ ++ + +  + ++++++++ +n+a+   e+ sn l+e+l+ i s l ++++++
  gi|474934781|ref|YP_007688363.1|  62 KtVQGATMMLRTAYTtKFINDMIRDNKSSTLREMYYVSEGWNNAKFHSEDESNLLVEDLETISSCLREDFKLR 134
                                       3456888888888888*******999999***********************************999999875 PP

>> DUF2399  Protein of unknown function C-terminus (DUF2399)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   7.6e-05      0.45      22      83 ..     191     255 ..     159     267 .. 0.79
   2 ?   -2.0   0.0      0.51   3.1e+03     118     145 ..     314     340 ..     290     342 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 7.6e-05
                           DUF2399  22 vyVvENpavlaaaadr..lgakaaplvctsGqpsaaalelldkl.aaagarlrYhGDfDwpGlai 83 
                                       v+  E   + a ++++   +++ a lv +sGqp++a  +ll++l  ++g  + +  D D+   +i
  gi|474934781|ref|YP_007688363.1| 191 VMALETGGMYARLIENgfPEKSGAVLVHLSGQPARAIRRLLKRLnEEQGLPIVVFTDGDPWSFRI 255
                                       66666666666667664334467889******************778999999988888765555 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.51
                           DUF2399 118 rrldaewddelaeamaelgvaiyeEavl 145
                                       r +d  wd+e+  am ++g ++++ +++
  gi|474934781|ref|YP_007688363.1| 314 RFTDEFWDTEIH-AMLDMGKKAEQQSLA 340
                                       344567888875.678888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 2155.55
//
Query:       gi|474934782|ref|YP_007688364.1|  [L=327]
Description: Lactate dehydrogenase-related dehydrogenase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.4e-50  169.5   0.2    1.1e-49  168.2   0.1    1.7  2  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    1.9e-18   66.4   0.0    2.3e-18   66.2   0.0    1.0  1  2-Hacid_dh     D-isomer specific 2-hydroxyacid dehydrogenase,
    0.00037   20.6   0.0    0.00097   19.2   0.0    1.6  2  Shikimate_DH   Shikimate / quinate 5-dehydrogenase
    0.00042   19.7   0.4     0.0072   15.6   0.4    2.2  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
    0.00043   20.5   0.0    0.00091   19.4   0.0    1.6  1  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
     0.0039   16.6   0.4     0.0075   15.6   0.4    1.4  1  ThiF           ThiF family
  ------ inclusion threshold ------
       0.03   14.2   0.0      0.056   13.3   0.0    1.4  1  Rossmann-like  Rossmann-like domain


Domain annotation for each model (and alignments):
>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.61   1.6e+03      87     107 ..      41      62 ..      30      77 .. 0.69
   2 !  168.2   0.1   4.4e-53   1.1e-49       1     178 []     109     295 ..     109     295 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.61
                                       HHHHH-SEEEE.-S--STTTTT CS
                      2-Hacid_dh_C  87 ellaesDivsl.hlpltpetrh 107
                                        l   sD++s+ ++p+tpe  +
  gi|474934782|ref|YP_007688364.1|  41 HLADGSDFISViTTPITPEMMD 62 
                                       5677899998624677777655 PP

  == domain 2  score: 168.2 bits;  conditional E-value: 4.4e-53
                                       HHHHHHHHTTHHHHHHHHHTTCCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHH CS
                      2-Hacid_dh_C   1 lalllallrrlaeadeevregewksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeee 77 
                                       ++++l+++r++  + e++ ++++ + k +l  +l+++ vGiiG+G+IG +v + l++fg+++++ +rs ++e+   e
  gi|474934782|ref|YP_007688364.1| 109 VMMMLMVVRKIVPILERCARNDF-TLKGVLAGKLKNMSVGIIGAGKIGVTVLRDLSGFGCRLYYCNRSMNAEA---E 181
                                       68*********************.888888999***********************************99554...5 PP

                                       HTCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEES-- CS
                      2-Hacid_dh_C  78 lgvelvsleellaesDivslhlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiagaalDvf 154
                                       + +e  s++e+l  +Di+slhl l++et h+i++++++kmk+g++l+NtaRG+lvd+ aL++aL+sg++++aalDv+
  gi|474934782|ref|YP_007688364.1| 182 KYAERLSMDEILGACDIISLHLELNQETFHMIDEKAISKMKRGSVLVNTARGPLVDTGALIKALDSGQLGAAALDVI 258
                                       566899*********************************************************************** PP

                                       SSS.............SSGTCHHHHHSTTEEE-SS-T CS
                      2-Hacid_dh_C 155 eee.............plpedspllelpnviltPHia 178
                                       e e             +  + ++l+  +nv+lt H+a
  gi|474934782|ref|YP_007688364.1| 259 EDEfglyyndctkmeiKNRALNELRGRDNVLLTHHMA 295
                                       *********999885433344899************8 PP

>> 2-Hacid_dh  D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.2   0.0   8.9e-22   2.3e-18      10     128 ..      16     321 ..       3     326 .. 0.91

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 8.9e-22
                                       HHHHHHHHTTEEEEEESCSSHHHCHHHHTTESEEEE-TTS-BSHHHHHHH..TT--EEEESSSSCTTB-HHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh  10 eelellkeegvevevkdellteellekakdadalivrsntkvtaevleal..pkLkviaragvGvDnvDldaakerG 84 
                                       + ++++++ g+e+ ++++ +t +++  a + d++ v ++  +t e+++++   ++k+i+++++G++++Dl++ak+ G
  gi|474934782|ref|YP_007688364.1|  16 YFRKFAEDFGFELGYTEQDPTMDTCHLADGSDFISVITTP-ITPEMMDRFkaGGVKMISTRTIGYNHIDLEYAKKIG 91 
                                       3444555544499999*99******************987.*******9999************************* PP

                                       -EEEE-TTTTHHHHHHHH........................................................... CS
                                       xxxxxxxxxxxxxxxxxx........................................................... RF
                        2-Hacid_dh  85 ilVtnvpgystesvAElt........................................................... 102
                                       ++V+++  y +e vAE+t                                                           
  gi|474934782|ref|YP_007688364.1|  92 MAVSHIT-YDPEGVAEYTvmmmlmvvrkivpilercarndftlkgvlagklknmsvgiigagkigvtvlrdlsgfgc 167
                                       *****98.********************************************************************* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                        2-Hacid_dh 103 ............................................................................. 102
                                                                                                                    
  gi|474934782|ref|YP_007688364.1| 168 rlyycnrsmnaeaekyaerlsmdeilgacdiislhlelnqetfhmidekaiskmkrgsvlvntargplvdtgalika 244
                                       ********************************************999999999999999999999999999999999 PP

                                       ...................................................T-BHHHHHHHHHHHHHHHHHHHTTCC CS
                                       ...................................................xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh 103 ...................................................aaTeeaqeniaeeaaenlvaflkges 128
                                                                                          ++ e+a+++++ +++  ++  ++g++
  gi|474934782|ref|YP_007688364.1| 245 ldsgqlgaaaldviedefglyyndctkmeiknralnelrgrdnvllthhmaFYYENAVRDMVYNCLYGMKMLAEGKD 321
                                       99999999999999999999999999999999999999999999999999999999999999998887777777766 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   3.8e-07   0.00097       8      60 ..     139     191 ..     133     210 .. 0.83
   2 ?   -2.9   0.0       2.6   6.6e+03      31      46 ..     264     279 ..     263     282 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3.8e-07
                                       S..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHH.HHHHHHHHHT.ET CS
                      Shikimate_DH   8 eslkekkvlliGaGemaelvakhLlakgvkkvvvaNRtle.rakelaeelkgee 60 
                                       ++lk+  v +iGaG+++  v++ L+  g++ +   NR+++  a++ ae+l+ +e
  gi|474934782|ref|YP_007688364.1| 139 GKLKNMSVGIIGAGKIGVTVLRDLSGFGCR-LYYCNRSMNaEAEKYAERLSMDE 191
                                       589999************************.9*****98527888898886554 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.6
                                       HHCCT-CEEEEEESSH CS
                      Shikimate_DH  31 LlakgvkkvvvaNRtl 46 
                                       L+ + ++k+ + NR l
  gi|474934782|ref|YP_007688364.1| 264 LYYNDCTKMEIKNRAL 279
                                       6778999999999976 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.4   2.8e-06    0.0072      12     128 ..     130     231 ..     123     250 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.8e-06
                                       GCTSEEETTCEETCB---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHH CS
                       AlaDh_PNT_C  12 ffggkgtlaGgvpgvepakvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeellaea 88 
                                        f+ kg+laG+++   +  v +iG+G  G+  ++  +g+g + + ++ ++++  + e+         ++++ +++e 
  gi|474934782|ref|YP_007688364.1| 130 DFTLKGVLAGKLK---NMSVGIIGAGKIGVTVLRDLSGFGCRLYYCNRSMNA--EAEK---------YAERLSMDEI 192
                                       678899*******...99**********************999998766554..3344.........4555778888 PP

                                       HHH-SEEEE---BTTSS---SC-HHHHHTS-TTEEEEETT CS
                       AlaDh_PNT_C  89 vkeadvvigtvlipGkkaPkLvteemvksMkpgsVivDvA 128
                                       +  +d+ i+  l   +++ ++++e+ +++Mk gsV+v  A
  gi|474934782|ref|YP_007688364.1| 193 LGACDI-ISLHLELNQETFHMIDEKAISKMKRGSVLVNTA 231
                                       999996.6666777889999*****************887 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   3.5e-07   0.00091       2     105 ..     146     246 ..     145     257 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 3.5e-07
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS.HC CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieg.ll 77 
                                       +g+iG G++G    + l   g++++  nr+ ++  e  ae++    s+ e++ ++d++ + ++ ++++ ++i++  +
  gi|474934782|ref|YP_007688364.1| 146 VGIIGAGKIGVTVLRDLSGFGCRLYYCNRSMNAEAEKYAERL----SMDEILGACDIISLHLELNQETFHMIDEkAI 218
                                       8*****************************777776666665....8999***********************99** PP

                                       CC--TT-EEEE-S---HHHHHHHHHHHH CS
                     NAD_binding_2  78 ealkkgdilidgstsspedtrelakelk 105
                                       +++k+g++l++++     dt  l k+l 
  gi|474934782|ref|YP_007688364.1| 219 SKMKRGSVLVNTARGPLVDTGALIKALD 246
                                       **********998777777777766665 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.4   2.9e-06    0.0075      13      43 ..     138     168 ..     126     173 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.9e-06
                                       HHHHHTSEEEEE--SHHHHHHHHHHHHHTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  13 qekLrdskvllvGaGglGsellknLalsGvg 43 
                                       + kL++++v ++GaG +G  +l++L + G++
  gi|474934782|ref|YP_007688364.1| 138 AGKLKNMSVGIIGAGKIGVTVLRDLSGFGCR 168
                                       569**************************97 PP

>> Rossmann-like  Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.2e-05     0.056      10      65 ..     143     198 ..     135     209 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.2e-05
                     Rossmann-like  10 rlsvGiisaGrvGtalgaaleraghvvvgisaisaasreraerrlPdvpvlevedv 65 
                                        +svGii+aG++G+++   l + g  +  ++   +a  e+  +rl   ++l   d+
  gi|474934782|ref|YP_007688364.1| 143 NMSVGIIGAGKIGVTVLRDLSGFGCRLYYCNRSMNAEAEKYAERLSMDEILGACDI 198
                                       689*********************99999999999998888888887777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2044.69
//
Query:       gi|474934783|ref|YP_007688365.1|  [L=516]
Description: lysyl-tRNA synthetase, archaeal and spirochete [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   1.5e-111  372.8   0.0     2e-111  372.4   0.0    1.1  1  tRNA-synt_1f  tRNA synthetases class I (K)


Domain annotation for each model (and alignments):
>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  372.4   0.0  1.1e-115    2e-111       1     359 [.       1     350 [.       1     351 [. 0.97

  Alignments for each domain:
  == domain 1  score: 372.4 bits;  conditional E-value: 1.1e-115
                      tRNA-synt_1f   1 kaWadklaeklieerkkkkaekdevvvesGispSGliHiGnlrevltadlvaralrkrgeevrlilisDdmDglRkv 77 
                                       ++Wad++a+++ e+        ++ ++++Gisp G iH+G+lre +t++ ++ a++ +g++vrli+++D +D+lRk 
  gi|474934783|ref|YP_007688365.1|   1 MHWADVIAKDIAEKA-------EHPLIATGISPTGIIHVGSLREAITGESIRSAVEGLGKDVRLIYLIDSFDPLRKR 70 
                                       69**********444.......468**************************************************** PP

                      tRNA-synt_1f  78 penlpekllekylgkpltsiPdpkgkhesyaehfnaelvesLdelgievefisatelYksglydeaikealenreki 154
                                       +++lp + +e+y+g+p+++iP+p gkh++ya+hf +++++++d+lg+++e+i +++lYk+g +d+ai+   ++r++i
  gi|474934783|ref|YP_007688365.1|  71 YDFLPPE-YENYVGMPISRIPCPCGKHKNYAHHFVQPFLDAVDSLGVHCEIIWTSDLYKEGKFDKAIDLTFKKRQDI 146
                                       *******.********************************************************************* PP

                      tRNA-synt_1f 155 keilekyrgeereetyspylpvcekcgrvdttevvevdaeeeeieYkceecGeeeevdiregngKLqWkvdwamrWa 231
                                        +il+++ g++++ +y py+p+c kcgr  t ++ e+  e  ++eY+c +cG+++++dir+ +gKL+W+ +w+++W 
  gi|474934783|ref|YP_007688365.1| 147 IRILHEVSGKPENPDYAPYNPLCAKCGR-YTKPIFETY-EYPYVEYQC-DCGFRGKADIRTDDGKLTWRCEWPAKWL 220
                                       ****************************.888888887.8********.**************************** PP

                      tRNA-synt_1f 232 algVdfEpaGkDhaaaGgSvdvsskia.eilggeaPekvvYelillkggekmssSkGnvltledwlevaepevlrfl 307
                                       ++g   Ep+GkDhaaaGgS+d++++i+ ei+g eaP++++Ye+++lkg ++m++S+G  +t  d++++ +pevl++l
  gi|474934783|ref|YP_007688365.1| 221 IFGTSAEPFGKDHAAAGGSYDTGKRIVrEIFGAEAPYPIPYEFVQLKGVGQMHKSTGSSVTGLDAIRMTPPEVLNYL 297
                                       ***************************************************************************** PP

                      tRNA-synt_1f 308 ilrrkPkkakkldldleilrlvdeYdklerkyf.aeqeeeeekekrvyelsav 359
                                       +lr +P +a++ d +l++l++ deYd++e+++f  e +e+ee++ r+ye++++
  gi|474934783|ref|YP_007688365.1| 298 FLRVQPSRAIDYDSGLGLLDMSDEYDRMEEAFFsGEFSESEENTVRAYEIAQH 350
                                       *********************************66667888888999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (516 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.49
# Mc/sec: 3149.31
//
Query:       gi|474934784|ref|YP_007688366.1|  [L=383]
Description: cobalt transport protein ATP-binding subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-31  109.5   0.0    2.9e-31  108.8   0.0    1.4  1  ABC_tran     ABC transporter
    2.4e-16   60.4   0.2    1.1e-10   41.8   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    4.9e-05   23.0   0.2     0.0001   22.0   0.2    1.5  1  AAA_29       P-loop containing region of AAA domain
    6.6e-05   22.5   0.2    0.00054   19.5   0.2    2.0  1  SMC_N        RecF/RecN/SMC N terminal domain
    0.00011   22.0   0.1       0.21   11.3   0.1    2.1  2  AAA_15       AAA ATPase domain
     0.0083   16.6   0.0      0.013   16.0   0.0    1.3  1  AAA_23       AAA domain
  ------ inclusion threshold ------
      0.022   15.0   0.0      0.037   14.3   0.0    1.2  1  DHquinase_I  Type I 3-dehydroquinase
       0.14   11.3   0.0       0.18   11.0   0.0    1.2  1  G-alpha      G-protein alpha subunit
       0.14   11.7   0.0       0.32   10.6   0.0    1.7  1  ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-bindi


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.8   0.0   1.4e-34   2.9e-31       1     137 []      23     171 ..      23     171 .. 0.93

  Alignments for each domain:
  == domain 1  score: 108.8 bits;  conditional E-value: 1.4e-34
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG..B-HHHCCHCEEEE-SS..--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx..xxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke..qeleslrkeigvlpqe..pqlfpe 73 
                                       l++v++ + +g k+ai+G nGaGKStL+++l  l+kp+eG++l++g ++++  +++ ++r+++++l+q+  + lf+ 
  gi|474934784|ref|YP_007688366.1|  23 LNDVNMRIGKGVKTAILGANGAGKSTLFSVLNALYKPDEGTVLFNGSPVSYrhKNIIKMRSQVSILFQNpnDMLFRP 99 
                                       799***********************************************9999999************54334443 PP

                                       SBHHHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                         v++              e ++++++al  +g++e+k++++     +LS+Gq++r+ la +l+ +p++l++DEpta
  gi|474934784|ref|YP_007688366.1| 100 N-VEQDvaygpenmklpkdEIERRVDDALFAVGMSEFKKSPI----MKLSYGQRKRITLAGVLAMEPQVLIMDEPTA 171
                                       3.444499*********999999*******************....*****************************97 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.6   2.1e-06    0.0043       2      51 ..      36      76 ..      35     106 .. 0.63
   2 !   41.8   0.0   5.8e-14   1.1e-10     173     301 ..     104     204 ..      72     205 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.1e-06
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldl 51
                                      +++ G+Ng+GKS+L+  l  l           ++++    +++  s+   
  gi|474934784|ref|YP_007688366.1| 36 TAILGANGAGKSTLFSVLNALYK---------PDEGTVLFNGSPVSYRHK 76
                                      89****************99853.........333333444444444444 PP

  == domain 2  score: 41.8 bits;  conditional E-value: 5.8e-14
                            AAA_21 173 adyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllallt 249
                                       +  +g+ + k   ++ +r+++++ + + ++                           ++ p+ +lS G+++ + l+ 
  gi|474934784|ref|YP_007688366.1| 104 DVAYGPENMKLPKDEIERRVDDALFAVGMS-------------------------EFKKSPIMKLSYGQRKRITLAG 155
                                       444444444444555555555555555555.........................456668889************* PP

                            AAA_21 250 allralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpll 301
                                        l+  +    +l+ DEp +gL+P++  +++e+ ++l+r+g+ vi+++H++ l
  gi|474934784|ref|YP_007688366.1| 156 VLAMEP---QVLIMDEPTAGLDPQMAYEVMEIAEQLHRTGVTVIMSSHDTNL 204
                                       ****99...9***************************************876 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.2   5.1e-08    0.0001      16      57 ..      27      69 ..      22      72 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 5.1e-08
                            AAA_29 16 tieidlkg.atlltGpsGsGKSTllDAiqalLvpak.kvrfNka 57
                                       ++i  kg  t + G++G+GKSTl+  ++al  p++ +v fN +
  gi|474934784|ref|YP_007688366.1| 27 NMRIG-KGvKTAILGANGAGKSTLFSVLNALYKPDEgTVLFNGS 69
                                      56666.6779***************9999999999999999976 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.2   2.7e-07   0.00054      27     212 ..      36     215 ..      24     222 .. 0.67

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.7e-07
                                       EEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  27 taivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrv 103
                                       tai+G+NG+GKs l+  +  +   ++ + l   + s + + ++++   ++ +v+i+f+n+++ l   + e  +    
  gi|474934784|ref|YP_007688366.1|  36 TAILGANGAGKSTLFSVLNALYKPDEGTVL--FNGSPVSY-RHKNIIKMRSQVSILFQNPNDMLFRPNVEQDV---- 105
                                       89***********99877433333333333..33344444.478888999***********994444444333.... PP

                                       ETTSEEEEEETTEEE-HHHHHHHHHCTT-STT..........CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 104 krkgeseykingkevtkkevsellesagiske..........lLSgGektLvalaLlfAiqkvkpaplyllDeidaa 170
                                              y  ++ +  k e+++ + +a +              LS G+++ + la ++A++   p+ + ++De  a 
  gi|474934784|ref|YP_007688366.1| 106 ------AYGPENMKLPKDEIERRVDDALFAVGmsefkkspimKLSYGQRKRITLAGVLAME---PQ-VLIMDEPTAG 172
                                       ......3444444444444444444444443334444445558************999975...55.569******* PP

                                       S-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 171 LDeknvkkvaellkekskn.aQfivislreemlekadklvgvt 212
                                       LD +   +v e+ ++ + + + +i+ s++++++      + v+
  gi|474934784|ref|YP_007688366.1| 173 LDPQMAYEVMEIAEQLHRTgVTVIMSSHDTNLTYSWADEIHVM 215
                                       ****999999998876655489999999988766655545554 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.1    0.0001      0.21      16      58 ..      25      64 ..      22     118 .. 0.74
   2 !    8.8   0.0   0.00058       1.2     287     367 ..     124     203 ..     100     205 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0001
                            AAA_15 16 dveidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvi 58
                                      dv + + +   t + G+N++GKS++  +l+ + + +    + ++
  gi|474934784|ref|YP_007688366.1| 25 DVNMRIGKGvKTAILGANGAGKSTLFSVLNALYKPD----EGTV 64
                                      556666666789*****************9999877....3444 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00058
                            AAA_15 287 k.........ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkeland 354
                                                 +  ++p+ k ++G++  + l+  ++ +e          +l+++EP a L pq+ +++++    l ++
  gi|474934784|ref|YP_007688366.1| 124 DdalfavgmsEFKKSPIMKLSYGQRKRITLAGVLA-MEP--------QVLIMDEPTAGLDPQMAYEVMEIAEQLHRT 191
                                       15555666656678888899999999988887554.344........48**************************** PP

                            AAA_15 355 nktQviitTHSph 367
                                       +   vi+++H   
  gi|474934784|ref|YP_007688366.1| 192 GV-TVIMSSHDTN 203
                                       97.9******865 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   6.5e-06     0.013      22      40 ..      36      54 ..      24     126 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6.5e-06
                            AAA_23 22 tlItGpNGaGKTTildAik 40
                                      t+I G NGaGK+T++  + 
  gi|474934784|ref|YP_007688366.1| 36 TAILGANGAGKSTLFSVLN 54
                                      89************98765 PP

>> DHquinase_I  Type I 3-dehydroquinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.9e-05     0.037     104     140 ..     180     216 ..     159     221 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.9e-05
                                       HHHHHHHHHHHTT-EEEEEEEESS----HHHHHHHHH CS
                       DHquinase_I 104 skkrlieekreggtkvIvSyhdfegtpsaeelkalle 140
                                       ++ +++e+ +++g+ vI+S+hd++ t s+ + +++++
  gi|474934784|ref|YP_007688366.1| 180 EVMEIAEQLHRTGVTVIMSSHDTNLTYSWADEIHVMQ 216
                                       567999***********************97666665 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   8.8e-05      0.18      22      69 ..      32      80 ..      18     204 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.8e-05
                                      .EEEEEEEESTTSSHHHHHHHHHHHCS--.....--HHHHHCCHHHHHHHHHH CS
                           G-alpha 22 revkllllGqseSGKsTilkqlkllykkg.....fseeelatwraviqlnivr 69
                                      + vk  +lG+++ GKsT++  l  lyk+      f+ + +    ++ ++ni++
  gi|474934784|ref|YP_007688366.1| 32 KGVKTAILGANGAGKSTLFSVLNALYKPDegtvlFNGSPV----SYRHKNIIK 80
                                      479999********************99866666554422....223344444 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00016      0.32       6      42 ..      25      61 ..      22     275 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00016
                                      HHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSS CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  6 DalfpivqGqrtlipgafgvGktvisqslskqsnsdd 42
                                      D+ + i++G +t+i+ga+g Gk+++ + l    + d+
  gi|474934784|ref|YP_007688366.1| 25 DVNMRIGKGVKTAILGANGAGKSTLFSVLNALYKPDE 61
                                      5667799*****************9977765554454 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2617.38
//
Query:       gi|474934785|ref|YP_007688367.1|  [L=366]
Description: cobalt transport protein ATP-binding subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-33  116.3   0.0    2.2e-33  115.7   0.0    1.3  1  ABC_tran     ABC transporter
    9.9e-16   58.4   0.2    5.3e-10   39.6   0.0    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    1.9e-05   24.2   0.0    6.4e-05   22.5   0.0    1.7  1  SMC_N        RecF/RecN/SMC N terminal domain
    0.00034   20.5   0.0       0.49   10.0   0.0    2.2  2  AAA_15       AAA ATPase domain
     0.0027   17.4   0.0     0.0052   16.5   0.0    1.4  1  AAA_29       P-loop containing region of AAA domain
      0.004   17.7   0.1     0.0064   17.0   0.1    1.3  1  AAA_23       AAA domain
  ------ inclusion threshold ------
      0.033   11.7   0.1      0.046   11.2   0.1    1.1  1  DUF3584      Protein of unknown function (DUF3584)
      0.048   13.9   0.0       0.56   10.5   0.0    2.2  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
      0.049   12.3   0.1        1.2    7.7   0.1    2.0  2  AAA_13       AAA domain
       0.15   12.1   0.0        0.3   11.2   0.0    1.6  1  MMR_HSR1     50S ribosome-binding GTPase
       0.17   11.5   0.0       0.47   10.1   0.0    1.4  1  ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-bindi


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.7   0.0   1.3e-36   2.2e-33       1     137 []      10     158 ..      10     158 .. 0.94

  Alignments for each domain:
  == domain 1  score: 115.7 bits;  conditional E-value: 1.3e-36
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG..B-HHHCCHCEEEE-SS--S-TTSB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke..qeleslrkeigvlpqepqlfpelt 75 
                                       l+  +++++eg+++ai+G nGaGK+tL+ +l+g +kp+eGe+l++g+++++  + l+++r+ ++v+ q+p  +   +
  gi|474934785|ref|YP_007688367.1|  10 LDGFNIEIEEGSRTAILGANGAGKTTLFYTLTGVYKPQEGEVLYRGQPIEYtkEGLTRVRSDVAVVLQNPDEQMFCS 86 
                                       678999*********************************************99999*************77777777 PP

                                       .HHHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       .xxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  76 .vren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                        v+e              e d++iekal+ ++++e + +++    ++LSgGq++r+a+a al+ +p++l++DEpta
  gi|474934785|ref|YP_007688367.1|  87 iVEEDiafgplnlgvdrdEVDARIEKALRDVRMTEYRRRPL----QQLSGGQRKRIAIAGALAVQPEVLIMDEPTA 158
                                       25555***********9999999******************....*****************************97 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2   3.1e-06     0.005       2      22 ..      23      43 ..      22      67 .. 0.86
   2 !   39.6   0.0   3.2e-13   5.3e-10     220     299 ..     113     189 ..      86     192 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.1e-06
                            AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                                      +++ G+Ng+GK++L+++l ++
  gi|474934785|ref|YP_007688367.1| 23 TAILGANGAGKTTLFYTLTGV 43
                                      79****************876 PP

  == domain 2  score: 39.6 bits;  conditional E-value: 3.2e-13
                            AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltT 296
                                        ++ + ++ ++ +p+ +lS G+++ +a++ al+ ++    +l+ DEp +gL+P++  +++el ++ s  g+ v+++T
  gi|474934785|ref|YP_007688367.1| 113 ALRDVRMTEYRRRPLQQLSGGQRKRIAIAGALAVQP---EVLIMDEPTAGLDPQASMEVIELAEKMSLSGVTVLIST 186
                                       7788889999************************99...9***********************99999********* PP

                            AAA_21 297 HSp 299
                                       H+ 
  gi|474934785|ref|YP_007688367.1| 187 HDV 189
                                       *95 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0     4e-08   6.4e-05      25     200 ..      21     190 ..      12     208 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 4e-08
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisr 101
                                       s tai+G+NG+GK+ l+  +  v   ++ +        + i ++ke+    + +v+++++n+d++       +si  
  gi|474934785|ref|YP_007688367.1|  21 SRTAILGANGAGKTTLFYTLTGVYKPQEGEV---LYRGQPIEYTKEGLTRVRSDVAVVLQNPDEQ-----MFCSIVE 89 
                                       569*****************77777666644...45556688889999999*************9.....4567777 PP

                                       EEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 102 rvkrkgeseykingkevtkkevsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLD 172
                                       + +  g  +  +++ ev  + +++ l+++++++       +LSgG+++ +a+a  +A+q   p+ + ++De  a LD
  gi|474934785|ref|YP_007688367.1|  90 EDIAFGPLNLGVDRDEVD-ARIEKALRDVRMTEYrrrplqQLSGGQRKRIAIAGALAVQ---PE-VLIMDEPTAGLD 161
                                       777778888888888775.568888888888776666666*************999986...55.569********* PP

                                       HHHHHHHHHHHHHHCTT.SEEEEE-SSHH CS
                                       xxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                             SMC_N 173 eknvkkvaellkekskn.aQfivislree 200
                                        +   +v el ++ s + + +++ +++ +
  gi|474934785|ref|YP_007688367.1| 162 PQASMEVIELAEKMSLSgVTVLISTHDVD 190
                                       ****9999999887755467777777655 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0013         2      16      43 ..      12      40 ..       8      63 .. 0.87
   2 !   10.0   0.0    0.0003      0.49     324     365 ..     148     188 ..     124     192 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0013
                            AAA_15 16 dveidlsee.ltvliGkNnsGKSsileal 43
                                       + i+++e   t + G+N++GK+++ + l
  gi|474934785|ref|YP_007688367.1| 12 GFNIEIEEGsRTAILGANGAGKTTLFYTL 40
                                      57788888889*************98766 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0003
                            AAA_15 324 nvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                       + +l+++EP a L pqa +++i+l  +++ ++   v+i+TH 
  gi|474934785|ref|YP_007688367.1| 148 PEVLIMDEPTAGLDPQASMEVIELAEKMSLSGV-TVLISTHD 188
                                       5689****************************7.9******6 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   3.2e-06    0.0052      13      44 ..      11      42 ..       8      52 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.2e-06
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqa 44
                                      dg  iei++ + t + G++G+GK+Tl+  ++ 
  gi|474934785|ref|YP_007688367.1| 11 DGFNIEIEEGSRTAILGANGAGKTTLFYTLTG 42
                                      66678898656***************866555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1     4e-06    0.0064      13      39 ..      13      40 ..       8      64 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4e-06
                            AAA_23 13 qeidFsk.gltlItGpNGaGKTTildAi 39
                                      ++i+ +    t+I G NGaGKTT++  +
  gi|474934785|ref|YP_007688367.1| 13 FNIEIEEgSRTAILGANGAGKTTLFYTL 40
                                      56666431459*************9655 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   2.8e-05     0.046       9      35 ..      12      38 ..       8      44 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.8e-05
                           DUF3584  9 GrvaeldldghtnieGtNaaGKTtLlr 35
                                      G+ +e++   +t i G+N+aGKTtL  
  gi|474934785|ref|YP_007688367.1| 12 GFNIEIEEGSRTAILGANGAGKTTLFY 38
                                      6667999999**************975 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00034      0.56      24      89 ..     121     173 ..     102     174 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00034
                           SbcCD_C  24 kelsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                       +  +r  ++lSGG++     +a+a ala +          ++++++DE  ++lD++ + +++el e
  gi|474934785|ref|YP_007688367.1| 121 EYRRRPLQQLSGGQR---KRIAIAGALAVQ----------PEVLIMDEPTAGLDPQASMEVIELAE 173
                                       347889999999999...555666555544..........56799***********9999999976 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1   0.00075       1.2      21      39 ..      25      43 ..      19     136 .. 0.73
   2 ?    2.6   0.0     0.026        42     526     582 ..     147     200 ..     135     238 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00075
                            AAA_13 21 iYGwNGaGKTtLSrllrsl 39
                                      i G+NGaGKTtL   l  +
  gi|474934785|ref|YP_007688367.1| 25 ILGANGAGKTTLFYTLTGV 43
                                      88**********8777766 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.026
                            AAA_13 526 kdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkevkkntk 582
                                       + ++ ++D P   LD ++++ v+ l ++      +   ++i+TH +++   + + + 
  gi|474934785|ref|YP_007688367.1| 147 QPEVLIMDEPTAGLDPQASMEVIELAEKMS---LSGVTVLISTHDVDLAYSWADSVA 200
                                       57899********************99997...677789*******99887777655 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00018       0.3       2      22 ..      23      47 ..      22     124 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00018
                                      EEEEESTTSSHHHHHHHHHT....S CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltg....e 22
                                       ai+G   +GK+tL+ +ltg    +
  gi|474934785|ref|YP_007688367.1| 23 TAILGANGAGKTTLFYTLTGvykpQ 47
                                      69*****************844430 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00029      0.47       4      35 ..       9      41 ..       7      55 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00029
                                      HHHHH.S-EBTT-EEEEEESTTSSHHHHHHHHH CS
                                      xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  4 vlDal.fpivqGqrtlipgafgvGktvisqsls 35
                                      vlD + + i +G rt+i+ga+g Gkt++  +l+
  gi|474934785|ref|YP_007688367.1|  9 VLDGFnIEIEEGSRTAILGANGAGKTTLFYTLT 41
                                      67766356889****************997776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2452.22
//
Query:       gi|474934786|ref|YP_007688368.1|  [L=220]
Description: ABC-type cobalt transport system, permease component CbiQ-related transporter [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.7e-23   81.5   1.0    1.1e-22   80.8   1.0    1.3  1  CbiQ      Cobalt transport protein


Domain annotation for each model (and alignments):
>> CbiQ  Cobalt transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.8   1.0     6e-27   1.1e-22      73     211 ..      25     171 ..       4     175 .. 0.83

  Alignments for each domain:
  == domain 1  score: 80.8 bits;  conditional E-value: 6e-27
                                       E.............EECTTEEE.....E..-TTHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHCCCSS--HHH CS
                              CbiQ  73 f......qlittegefvfaggg..qisi..tseGllrglllalRiltllslllllalTTppeeltsslerlgvPlel 139
                                       +        ++ ++   ++ g+  +++i  t+ + +++ l+++R ++ ++l+l +a +Tp++ l+++l++++ P e+
  gi|474934786|ref|YP_007688368.1|  25 VlgsgmiSIMGDSSDPALWDGKflWFTIhmTDSSFQKAWLIFFRAVAGVTLMLSFASSTPIPHLAHALRSIKCPIEI 101
                                       3456665334444444444444575555116667******************************************* PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS-SS CS
                              CbiQ 140 alillLayRfiflLleevqrikqAqklRlgdsklgirrslrslgkliaalflralkraervalAmeaRGYtg 211
                                        +++ L+yR+ flLle + ++ +A + Rlg+   g +  ++s++ ++   f+ +l+ +e+ + A++ R+Y+g
  gi|474934786|ref|YP_007688368.1| 102 CELIVLIYRYAFLLLERFLVMLDAAQCRLGYN--GTKTAIKSYAGAMTGTFIFSLELGEKSEAALACRNYQG 171
                                       ********************************..*************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1532.60
//
Query:       gi|474934787|ref|YP_007688369.1|  [L=108]
Description: ABC-type cobalt transport system, periplasmic component [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.5e-13   47.9   0.1    1.7e-12   47.1   0.1    1.4  1  CbiN      Cobalt transport protein component CbiN
  ------ inclusion threshold ------
      0.025   14.5   1.3       0.15   11.9   0.2    2.2  2  DUF5325   Family of unknown function (DUF5325)
       0.25   11.4   0.4       0.25   11.4   0.4    1.6  2  UPF0154   Uncharacterised protein family (UPF0154)
        7.7    6.4   7.0          4    7.3   1.0    2.2  2  DUF2374   Protein  of unknown function (Duf2374)


Domain annotation for each model (and alignments):
>> CbiN  Cobalt transport protein component CbiN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.1   3.8e-16   1.7e-12       4      67 .]      13      81 ..       9      81 .. 0.88

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 3.8e-16
                              CbiN  4 llllvvllavvplflvkgaeFgGaDdqaeevIeeiapdyepwfeplwep........psGEiESlLFalQAA 67
                                      +++++++++v+ l+lv + eFgG+Dd++ e   +   +ye w+  +++          +GE+ES+LFa+QAA
  gi|474934787|ref|YP_007688369.1| 13 CFIVIAVMCVATLALV-NGEFGGSDDAGGEEADK--YGYEAWTGDILTIitgdedyeLPGETESMLFAVQAA 81
                                      5677788888888887.788**********9997..69********99888999999**************8 PP

>> DUF5325  Family of unknown function (DUF5325)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1     0.065   2.9e+02       8      19 ..      14      25 ..       5      31 .. 0.58
   2 ?   11.9   0.2   3.4e-05      0.15       8      31 ..      73      96 ..      70     102 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.065
                           DUF5325  8 fllyAilAvasl 19
                                      f+++A++ va l
  gi|474934787|ref|YP_007688369.1| 14 FIVIAVMCVATL 25
                                      444444444443 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 3.4e-05
                           DUF5325  8 fllyAilAvaslmgiGiaigersi 31
                                       +l+A+ A++  + iG +ig++s+
  gi|474934787|ref|YP_007688369.1| 73 SMLFAVQAAIGAIIIGYFIGANSM 96
                                      689******************997 PP

>> UPF0154  Uncharacterised protein family (UPF0154)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       1.8   8.2e+03      10      20 ..      10      20 ..       9      21 .. 0.66
   2 ?   11.4   0.4   5.5e-05      0.25       4      25 ..      80     101 ..      77     103 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.8
                           UPF0154 10 vlGffiarkym 20
                                      +lG fi+  +m
  gi|474934787|ref|YP_007688369.1| 10 YLGCFIVIAVM 20
                                      57777776655 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 5.5e-05
                           UPF0154   4 alivGlvlGffiarkymkkqlk 25 
                                       a i  +++G+fi ++ mkk+++
  gi|474934787|ref|YP_007688369.1|  80 AAIGAIIIGYFIGANSMKKKME 101
                                       678889**************97 PP

>> DUF2374  Protein  of unknown function (Duf2374)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   1.0   0.00089         4      21      38 ..      10      27 ..       8      30 .. 0.87
   2 ?    2.4   0.6     0.032   1.4e+02      15      27 ..      80      92 ..      72      96 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00089
                           DUF2374 21 iLgGFvaVavvaillLsl 38
                                       Lg F+++av++++ L l
  gi|474934787|ref|YP_007688369.1| 10 YLGCFIVIAVMCVATLAL 27
                                      6999*********99976 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.032
                           DUF2374 15 aAmPvIiLgGFva 27
                                      aA+ +Ii+g F++
  gi|474934787|ref|YP_007688369.1| 80 AAIGAIIIGYFIG 92
                                      899******9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 777.89
//
Query:       gi|474934788|ref|YP_007688370.1|  [L=209]
Description: cobalamin biosynthesis protein CbiM [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.7e-39  133.4  17.4    1.1e-38  133.2  17.4    1.0  1  CbiM      Cobalt uptake substrate-specific transmembrane regi
  ------ inclusion threshold ------
       0.13   12.3   0.1       0.19   11.8   0.1    1.3  1  AlphaC_N  Alpha C protein N terminal


Domain annotation for each model (and alignments):
>> CbiM  Cobalt uptake substrate-specific transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.2  17.4   1.2e-42   1.1e-38      20     206 ..       2     192 ..       1     193 [. 0.93

  Alignments for each domain:
  == domain 1  score: 133.2 bits;  conditional E-value: 1.2e-42
                              CbiM  20 lallalalrrlrkeldear..vpllallaafifaaqminipipggtslHllgavlaaiLlGpwaaflavavvlllqa 94 
                                       +++ ++++ +lr+ l+++    + +al +afif+++++++p  +g+s+H++g+++a ++ G  ++++  ++vl++qa
  gi|474934788|ref|YP_007688370.1|   2 IPFFYIGVIKLRQILRDHPdqKMIVALSGAFIFLISSLKLPSVTGSSAHPTGTGIAVVFYGVGVCAVLSTIVLIFQA 78 
                                       678999999999998865556999***************************************************** PP

                              CbiM  95 llfgdGGitaLGaNilnmavigvllaylvyrllsrlasskkrvalaaflaallsvvlaallvalelalsgleas... 168
                                       ll ++GG+t+LGaN+++m++ig++++ +v+++l+r+   +  v+++ ++aa+++ +++++++a++++l   +a+   
  gi|474934788|ref|YP_007688370.1|  79 LLIAHGGFTTLGANCVSMGIIGPFFGLIVWKILRRT---NVGVFVSMACAAAVADLMTYVVTAIQMTLNVVTANnan 152
                                       *******************************88665...689**************************955444788 PP

                              CbiM 169 ..lsltaalaamllvhlpvgilEgviTaaivkalkkvrpe 206
                                          ++  ++ + +++++p++i+Eg++ ++ +++l  +rp+
  gi|474934788|ref|YP_007688370.1| 153 fgEAFIDFMSVYAVTQVPLAIIEGIVLGMFAHYLSTTRPD 192
                                       8888999999999**************************8 PP

>> AlphaC_N  Alpha C protein N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   2.1e-05      0.19       2      62 ..     135     195 ..     134     207 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.1e-05
                          AlphaC_N   2 vvsgsavtlntamtknvqngrayidlydvklgkidplqliklespdlkaiyvirqgskvya 62 
                                       vv+   +tln   + n + g+a+id+  v      pl +i+    ++ a y+ +   +v+ 
  gi|474934788|ref|YP_007688370.1| 135 VVTAIQMTLNVVTANNANFGEAFIDFMSVYAVTQVPLAIIEGIVLGMFAHYLSTTRPDVFE 195
                                       6777789************************9999*****988899999998888777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       953  (0.0531541); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1353.54
//
Query:       gi|474934789|ref|YP_007688371.1|  [L=55]
Description: Preprotein translocase subunit Sec61beta [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      2e-16   59.7   0.5    2.3e-16   59.5   0.5    1.1  1  Sec61_beta  Sec61beta family


Domain annotation for each model (and alignments):
>> Sec61_beta  Sec61beta family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.5   0.5   1.3e-20   2.3e-16       1      40 [.      11      51 ..      11      52 .. 0.96

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 1.3e-20
                                      XXXXXXXXXX.----SS-B-THHHHHHHHHHHHHHHHHTSS CS
                        Sec61_beta  1 SsaGLlryye.edapgikidPkvVlvlsvafiasVilLhil 40
                                      SsaGL+ry++ ed++gik++P +V+++++af +++++L ++
  gi|474934789|ref|YP_007688371.1| 11 SSAGLMRYFDsEDDKGIKLGPRTVIAIAIAFTVLILVLPVF 51
                                      9************************************9775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 400.87
//
Query:       gi|474934790|ref|YP_007688372.1|  [L=441]
Description: Kef-type K+ transport systems, membrane components [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-57  195.6  40.2    1.4e-57  195.3  40.2    1.1  1  Na_H_Exchanger  Sodium/hydrogen exchanger family
  ------ inclusion threshold ------
      0.063   13.7   0.0      0.063   13.7   0.0    4.6  6  DUF3262         Protein of unknown function (DUF3262)
       0.16   12.4   0.1       0.48   10.9   0.1    1.8  1  DUF4094         Domain of unknown function (DUF4094)


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.3  40.2   2.3e-61   1.4e-57       5     379 ..      11     425 ..       6     427 .. 0.88

  Alignments for each domain:
  == domain 1  score: 195.3 bits;  conditional E-value: 2.3e-61
                                       HHHHHHHHH...HHHHTTSXHHHHHHHHHHHHTTTTTS...............................HHHCHCCH CS
                    Na_H_Exchanger   5 illallvgl...larrlklpeivgliiaGlllGpsglg....lieps......................eedlevls 52 
                                       ++l +l+++   +++ +++p ++g+ii+G+l+++++      l                           ++l v +
  gi|474934790|ref|YP_007688372.1|  11 VVLFTLARVgnrVFEHFGVPGLIGEIIVGILIANIVIWdgetL---VellhaavpavganpgdlettefYSVLYVAA 84 
                                       2223333335557***********************9855552...0555777899999999*************** PP

                                       HHHCHHCCHHHHCTCGCCTGCCTHHHHHHHHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHH CS
                    Na_H_Exchanger  53 elglilllFlaGleldlrelrknlksilllallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlai 129
                                       elg+i+llF +Gle++ ++l+ ++ks++l+a+lgv++++vl G+++ +  + + ++++a++++a++ at++++++++
  gi|474934790|ref|YP_007688372.1|  85 ELGVIFLLFSVGLETKVEQLLNVGKSAMLVAVLGVVVPFVL-GFAFIM--FQDGNFHHAMFLAAAMVATSVGITARV 158
                                       *****************************************.**9997..7899*********************** PP

                                       C.CCCTSTCCCCCCHHHHHHHHHHHCCCCCHHHHHHTX..XXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Na_H_Exchanger 130 lkeegrvperlgtlllgesvlnDavavvllavllalak..eeaggetslllllliflvvavgglllglvigwllrli 204
                                        k+++++++r  ++++g++v++D++++++la++ ++a+  ++++  + l+ ++ ++ +v++ +++++++++ +    
  gi|474934790|ref|YP_007688372.1| 159 IKDMHLMEKRESRIIIGAAVIDDVLGMIVLAIVKGVAGsdSGVSISSILIIIVEAIGFVLITIWAAKVLVPKFDDWN 235
                                       *************************************8777777777777888888888888888999998888777 PP

                                       HHHS.........CTHHHHHHHHHHHHHHHHHHHHHTSXXXHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHH CS
                    Na_H_Exchanger 205 trft.........dddrelevllvlllallaallaellgvsgilgaflaGlvlseyefsnklseklesfreglfnpl 272
                                       +r+          + +    ++++l+++l+ a +ae +g+ +i+gaflaG+++++ + ++ l +k+e +   +f+ +
  gi|474934790|ref|YP_007688372.1| 236 ERRKlaymeknkrSPQGYNDLVVALIVCLAFATFAEFIGLAAIIGAFLAGMLFANKAWESGLDKKFETVT-TVFISF 311
                                       77778999988654455567888888899999**********************8888888*********.9***** PP

                                       HHHHHHHHSXHHHHHXXHHHHHHHHHHHHHHHTHHHHHHHHHTTTX..SSXHHHHHHCCCCSS.BHHHHHHHHHHHH CS
                    Na_H_Exchanger 273 fFvlvGlsldlkvlnnhlsvlilvllilvaillgrilavflllrll..glslrealiigfgglqrgavalalaalgp 347
                                       fF+ vG+++d + l   +  + +v++i++a+ ++++++  l ++l    l+ ++  iig+g+++rg+v +++a++g 
  gi|474934790|ref|YP_007688372.1| 312 FFLNVGMQVDASQLSDTTIIIDVVIVIILAV-ISKFVGCGLGAKLGdaSLDKNSVSIIGVGMVPRGEVGIIVASIGL 387
                                       **********999965777777777777777.8***********998778888889999****************** PP

                                       HH......XHHHHTTSSTTTCSTSXHHHHHHHHHHHHH CS
                    Na_H_Exchanger 348 al......gllarelyallivvvlftvlvqGlslkpll 379
                                       +       ++l+ +ly++++++++ t+++++  l+ ++
  gi|474934790|ref|YP_007688372.1| 388 SIvlsdgtQALSGDLYTVIVLMAVATTVIAPPLLTKVF 425
                                       9988899999999***************8888777665 PP

>> DUF3262  Protein of unknown function (DUF3262)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   1.1         3   1.8e+04      65      75 ..       6      16 ..       3      17 .. 0.59
   2 ?   -2.6   0.1       1.2   7.3e+03      23      35 ..      36      48 ..      33      50 .. 0.87
   3 ?    0.9   0.3      0.11   6.3e+02      26      61 ..     111     146 ..     101     155 .. 0.63
   4 ?   13.7   0.0   1.1e-05     0.063      12      52 ..     198     239 ..     196     245 .. 0.86
   5 ?   -1.7   0.5      0.64   3.8e+03      34      34 ..     278     278 ..     255     317 .. 0.55
   6 ?   -1.2   0.2      0.47   2.8e+03      15      36 ..     320     341 ..     310     346 .. 0.62

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 3
                           DUF3262 65 vvlllvlgflf 75
                                      ++++lv++f +
  gi|474934790|ref|YP_007688372.1|  6 IAMMLVVLFTL 16
                                      56666666654 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.2
                           DUF3262 23 liagillvvllLw 35
                                      +i+gil++ +++w
  gi|474934790|ref|YP_007688372.1| 36 IIVGILIANIVIW 48
                                      6999999999999 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.11
                           DUF3262  26 gillvvllLwaaWalvsvYkgWaeekiseadllslv 61 
                                       ++l++vl + + ++l  ++ ++++++  +a +l+++
  gi|474934790|ref|YP_007688372.1| 111 AMLVAVLGVVVPFVLGFAFIMFQDGNFHHAMFLAAA 146
                                       455566666666666666666666666666666555 PP

  == domain 4  score: 13.7 bits;  conditional E-value: 1.1e-05
                           DUF3262  12 asGvspsalkllia.gillvvllLwaaWalvsvYkgWaeeki 52 
                                        sGvs+s++ ++i+ +i +v++++waa +lv  +  W+e++ 
  gi|474934790|ref|YP_007688372.1| 198 DSGVSISSILIIIVeAIGFVLITIWAAKVLVPKFDDWNERRK 239
                                       5999999999988835779999****************9986 PP

  == domain 5  score: -1.7 bits;  conditional E-value: 0.64
                           DUF3262  34 L 34 
                                       +
  gi|474934790|ref|YP_007688372.1| 278 I 278
                                       2 PP

  == domain 6  score: -1.2 bits;  conditional E-value: 0.47
                           DUF3262  15 vspsalklliagillvvllLwa 36 
                                       v++s+l+ + ++i +v+++++a
  gi|474934790|ref|YP_007688372.1| 320 VDASQLSDTTIIIDVVIVIILA 341
                                       5666666665555555555544 PP

>> DUF4094  Domain of unknown function (DUF4094)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   8.1e-05      0.48      10      26 ..     279     295 ..     275     313 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8.1e-05
                           DUF4094  10 vasflagllftnRlwtv 26 
                                       +++flag+lf+n+ w++
  gi|474934790|ref|YP_007688372.1| 279 IGAFLAGMLFANKAWES 295
                                       789************55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       887  (0.0494729); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 2689.79
//
Query:       gi|474934791|ref|YP_007688373.1|  [L=333]
Description: hypothetical protein TALC_01226 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.019   15.0   0.3      0.034   14.2   0.3    1.4  1  DZR            Double zinc ribbon
      0.026   14.2   3.3       0.81    9.5   0.5    2.4  2  zinc_ribbon_2  zinc-ribbon domain
      0.028   14.6   0.1         13    6.0   0.0    2.9  3  MSV199         MSV199 domain
      0.032   14.2   0.2      0.049   13.6   0.2    1.3  1  zf-C2HC5       Putative zinc finger motif, C2HC5-type
      0.051   13.9   0.1       0.15   12.4   0.0    1.9  1  Rpr2           RNAse P Rpr2/Rpp21/SNM1 subunit domain
       0.06   13.6   0.0       0.15   12.3   0.0    1.6  1  ANAPC3         Anaphase-promoting complex, cyclosome, subunit
       0.14   12.1   1.8        5.9    6.9   0.1    2.4  2  Nudix_N_2      Nudix N-terminal
       0.19   11.9   1.1       0.68   10.2   0.1    2.5  2  TPR_2          Tetratricopeptide repeat
       0.38   11.4   3.6       0.16   12.7   0.9    1.8  2  TPR_16         Tetratricopeptide repeat
       0.46   10.4   2.0         32    4.5   0.0    2.8  3  DUF3966        Protein of unknown function (DUF3966)
       0.51    9.8   5.8        8.3    6.0   0.2    2.3  2  zf-ribbon_3    zinc-ribbon domain
        2.6    7.6   5.1        7.8    6.1   5.1    1.9  1  TF_Zn_Ribbon   TFIIB zinc-binding


Domain annotation for each model (and alignments):
>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.3   2.3e-05     0.034      11      38 ..       4      33 ..       1      39 [. 0.73

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.3e-05
                               DZR 11 darfCseCgtklkavaa...edrCpsCgekv 38
                                      +a +C+eCg +++   +   + +C  Cg+++
  gi|474934791|ref|YP_007688373.1|  4 KAVVCPECGGTVQMD-EglkKGFCTYCGKPI 33
                                      567899999998743.358899999999885 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.016        23      13      20 ..       5      12 ..       3      15 .. 0.75
   2 ?    9.5   0.5   0.00054      0.81      15      23 .]      25      33 ..      24      37 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.016
                     zinc_ribbon_2 13 akFCpyCG 20
                                      a+ Cp+CG
  gi|474934791|ref|YP_007688373.1|  5 AVVCPECG 12
                                      66788886 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00054
                     zinc_ribbon_2 15 FCpyCGtpl 23
                                      FC+yCG p+
  gi|474934791|ref|YP_007688373.1| 25 FCTYCGKPI 33
                                      666666653 PP

>> MSV199  MSV199 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.89   1.3e+03      48      82 ..      47      81 ..      26      95 .. 0.79
   2 ?    4.9   0.0      0.02        30       9      55 ..     119     171 ..     114     182 .. 0.77
   3 ?    6.0   0.0    0.0089        13      39      76 ..     245     282 ..     209     307 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.89
                            MSV199 48 kkqkkkfkklLkrnnieykelkykdeeielypslk 82
                                      ++ +k++ +lL   +i +k+ +  d +++  + l 
  gi|474934791|ref|YP_007688373.1| 47 ETRRKDVDNLLTLARIAFKQNNFVDARMKAEEALA 81
                                      67899999999999999999888887777666655 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.02
                            MSV199   9 ennyeldlliswF....wqplvdkkdvlitneiLeflgyeGeykk..qkkkfk 55 
                                       + n  ++++++ F      p+ +++ + i+++ L+ + ye ++ k   k++f+
  gi|474934791|ref|YP_007688373.1| 119 DRNAYFEIMSDGFnrflLSPYANNTLTEIAKKHLKKFDYERKLGKaeSKNAFI 171
                                       5677788999888887889********************87654311455555 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0089
                            MSV199  39 eflgyeGeykkqkkkfkklLkrnnieykelkykdeeie 76 
                                       +  g eG+y     k+ ++++rn ++ ++l++  +ei 
  gi|474934791|ref|YP_007688373.1| 245 SSTGSEGTYGAEMIKLYNMVDRNYVNIRKLSHVRNEIY 282
                                       3334599************************9999874 PP

>> zf-C2HC5  Putative zinc finger motif, C2HC5-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   3.3e-05     0.049      17      47 ..       5      36 ..       1      43 [. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.3e-05
                          zf-C2HC5 17 apnClnCGkiiCakegls.kpCsfCgspllss 47
                                      a  C +CG  +   egl+ + C++Cg+p++++
  gi|474934791|ref|YP_007688373.1|  5 AVVCPECGGTVQMDEGLKkGFCTYCGKPIVND 36
                                      678**************9999*******9986 PP

>> Rpr2  RNAse P Rpr2/Rpp21/SNM1 subunit domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   9.9e-05      0.15      36      73 ..      14      50 ..      10      86 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.9e-05
                                      T---SSTCCCTB-TTT--B--CTTTEEEEEE-SSS-E. CS
                              Rpr2 36 qlrlppsvkrtvCkkCgsvlipgvtcsvrvenkskkkk 73
                                      ++++++ +k+ +C  Cg+ ++   t++v +  ++++ +
  gi|474934791|ref|YP_007688373.1| 14 TVQMDEGLKKGFCTYCGKPIVNDGTARVVLDDSETR-R 50
                                      6899************************99764433.3 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0    0.0001      0.15      18      76 ..      48     107 ..      37     112 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0001
                                       HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHH CS
                            ANAPC3  18 aetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAi 76 
                                       + +++ ++++ lA   ++++++  A   +++a  ++ +   +++++A ++l L   e A 
  gi|474934791|ref|YP_007688373.1|  48 TRRKDVDNLLTLARIAFKQNNFVDARMKAEEAlAIDARCTDAWIIKAFASLYLADKETAF 107
                                       6789999********************************************998777765 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.3     0.029        44       3      11 ..       8      16 ..       7      18 .. 0.80
   2 ?    6.9   0.1    0.0039       5.9       2      22 ..      25      49 ..      24      50 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.029
                                      -TTT--B-E CS
                         Nudix_N_2  3 CsqCGtpve 11
                                      C++CG++v+
  gi|474934791|ref|YP_007688373.1|  8 CPECGGTVQ 16
                                      999998886 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0039
                                      B-TTT--B-E....EE--TT-SS-E CS
                         Nudix_N_2  2 FCsqCGtpve....lripdgDnreR 22
                                      FC+ CG+p+      r+  +D+++R
  gi|474934791|ref|YP_007688373.1| 25 FCTYCGKPIVndgtARVVLDDSETR 49
                                      9*******65466666666776666 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00046      0.68       4      31 ..      56      83 ..      53      86 .. 0.91
   2 ?   -1.5   0.1       2.5   3.8e+03       3      31 ..      89     117 ..      88     119 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00046
                             TPR_2  4 lynlGlayyklgdyeeAleafekAleld 31
                                      l  l+++++k++++ +A+   e+Al++d
  gi|474934791|ref|YP_007688373.1| 56 LLTLARIAFKQNNFVDARMKAEEALAID 83
                                      678**********************998 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.5
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleld 31 
                                       a+   + a ++l d e A +a +   el+
  gi|474934791|ref|YP_007688373.1|  89 AWIIKAFASLYLADKETAFNAADTGFELA 117
                                       78889999999999999988877776665 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.9    0.0001      0.16       1      43 [.      57      96 ..      57     110 .. 0.92
   2 ?   -3.2   0.1       9.2   1.4e+04      49      63 ..     317     331 ..     313     332 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0001
                            TPR_16  1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgda 43
                                      l lar+a++++++ dA+  +e+al+ d    ++ +A+  ++ a
  gi|474934791|ref|YP_007688373.1| 57 LTLARIAFKQNNFVDARMKAEEALAID---ARCTDAWIIKAFA 96
                                      679************************...******9888876 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 9.2
                            TPR_16  49 rlaeAaalyraalra 63 
                                       + ++ +++++++l+a
  gi|474934791|ref|YP_007688373.1| 317 EIDAEIEAVKRELGA 331
                                       667777999998876 PP

>> DUF3966  Protein of unknown function (DUF3966)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.2     0.026        39       7      20 ..     153     166 ..     152     184 .. 0.73
   2 ?   -2.8   0.0       4.2   6.2e+03      14      24 ..     226     236 ..     223     239 .. 0.74
   3 ?    4.5   0.0     0.021        32      17      30 ..     315     328 ..     312     330 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.026
                           DUF3966   7 RKFkQEReLaKSEI 20 
                                       +KF  ER L K E 
  gi|474934791|ref|YP_007688373.1| 153 KKFDYERKLGKAES 166
                                       69*********995 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.2
                           DUF3966  14 eLaKSEITAeL 24 
                                       e    +ITA L
  gi|474934791|ref|YP_007688373.1| 226 EVSPADITARL 236
                                       556678***98 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.021
                           DUF3966  17 KSEITAeLeMLarE 30 
                                       KSEI Ae+e   rE
  gi|474934791|ref|YP_007688373.1| 315 KSEIDAEIEAVKRE 328
                                       9********99998 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.2    0.0056       8.3      17      23 ..       6      12 ..       4      15 .. 0.70
   2 ?    5.9   1.1    0.0059       8.7      18      26 .]      25      33 ..      24      33 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0056
                       zf-ribbon_3 17 nvCpyCG 23
                                      +vCp CG
  gi|474934791|ref|YP_007688373.1|  6 VVCPECG 12
                                      5777777 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0059
                       zf-ribbon_3 18 vCpyCGtkl 26
                                      +C+yCG+++
  gi|474934791|ref|YP_007688373.1| 25 FCTYCGKPI 33
                                      7*****986 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   5.1    0.0052       7.8       2      26 ..       7      30 ..       6      37 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0052
                                      EETTTTCEECHEETSTTCEEESSSS CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCG 26
                                      +CP+Cg+t +  D+     +Ct CG
  gi|474934791|ref|YP_007688373.1|  7 VCPECGGT-VQMDEGLKKGFCTYCG 30
                                      79999998.6789999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       981  (0.0547158); expected 358.6 (0.02)
Passed bias filter:                      775  (0.0432261); expected 358.6 (0.02)
Passed Vit filter:                       113  (0.00630264); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.60u 0.24s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2189.78
//
Query:       gi|474934792|ref|YP_007688374.1|  [L=493]
Description: hypothetical protein TALC_01227 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (493 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 3690.62
//
Query:       gi|474934793|ref|YP_007688375.1|  [L=127]
Description: putative transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain and a metal-binding domain [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-09   36.9   0.8    1.2e-08   35.0   0.5    2.2  2  NikR_C    NikR C terminal nickel binding domain
  ------ inclusion threshold ------
      0.013   15.4   0.0      0.027   14.4   0.0    1.5  1  RHH_1     Ribbon-helix-helix protein, copG family
      0.045   13.9   0.0       0.12   12.5   0.0    1.8  2  K-box     K-box region


Domain annotation for each model (and alignments):
>> NikR_C  NikR C terminal nickel binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.052   3.1e+02      15      33 ..      53      71 ..      47      72 .. 0.78
   2 !   35.0   0.5     2e-12   1.2e-08      10      68 ..      64     118 ..      55     127 .] 0.83

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.052
                                      HHHHHHHHHHHHSSEEEEE CS
                            NikR_C 15 lserltdiqheyhdliiss 33
                                      ++  l++i+h++ d   s+
  gi|474934793|ref|YP_007688375.1| 53 VEGVLITIRHDHADPWMST 71
                                      6667999*****9977665 PP

  == domain 2  score: 35.0 bits;  conditional E-value: 2e-12
                                       TTSTTHHHHHHHHHHHHSSEEEEEEEEEESSSEEEEEEEEEE-HHHHHHHHHHHHTSTT CS
                            NikR_C  10 hhqrelserltdiqheyhdliisslhvhldhdncLevivlkGeaeeikelaeklralkg 68 
                                       h     +  +++iq +y + i+++lh hl++++cLev+++  +a+++++++ ++ ++  
  gi|474934793|ref|YP_007688375.1|  64 H----ADPWMSTIQARYVNAIKTQLHSHLKDKKCLEVMIVSCSADDLRSMMFEIEGTGK 118
                                       4....4556899*************************************9988877655 PP

>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   4.5e-06     0.027       2      34 ..       4      37 ..       3      39 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.5e-06
                                      EEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHH CS
                             RHH_1  2 vsirldeellerLdelarrrg.rSrSelIReAlr 34
                                      +s++l e+ +e Ld++ +  g + rS+++R A+ 
  gi|474934793|ref|YP_007688375.1|  4 ISVSLGEDNIEDLDRIQKLYGlKGRSDAVRTAIN 37
                                      9*******************************96 PP

>> K-box  K-box region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     2e-05      0.12      36      72 ..      37      73 ..      13      95 .. 0.83
   2 ?   -0.9   0.0      0.32   1.9e+03      37      48 ..      98     109 ..      74     116 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2e-05
                             K-box 36 dleslslkeLqqLEqqLekslkkiRsrKeqllleeie 72
                                      +l++ ++++L++LE  +e  l +iR+  ++ ++  i+
  gi|474934793|ref|YP_007688375.1| 37 NLATSEVQDLKELEGSVEGVLITIRHDHADPWMSTIQ 73
                                      577889********************99887777665 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.32
                             K-box  37 leslslkeLqqL 48 
                                       + s+s ++L+++
  gi|474934793|ref|YP_007688375.1|  98 IVSCSADDLRSM 109
                                       456777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.33s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 754.73
//
Query:       gi|474934794|ref|YP_007688376.1|  [L=258]
Description: putative divalent heavy-metal cations transporter [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-27   95.6  19.4    2.3e-16   59.9   8.7    2.1  2  Zip              ZIP Zinc transporter
     0.0057   16.8   0.1     0.0057   16.8   0.1    3.2  3  DUF2178          Predicted membrane protein (DUF2178)
  ------ inclusion threshold ------
       0.11   12.4  12.4        1.3    8.9   2.6    3.3  2  DUF4271          Domain of unknown function (DUF4271)
       0.19   11.3  11.8        7.5    6.1   3.2    2.2  1  TauE             Sulfite exporter TauE/SafE
       0.31   10.5   9.3       0.22   11.0   1.7    2.4  2  DUF1129          Protein of unknown function (DUF1129)
       0.48    9.8   9.7       0.71    9.2   3.7    2.1  2  TssN             Type VI secretion system, TssN
       0.77   10.4   6.9        3.8    8.1   0.3    3.0  2  DUF2818          Protein of unknown function (DUF2818)
        1.5    8.3  22.2        0.2   11.2   4.7    3.1  3  ABC2_membrane_5  ABC-2 family transporter protein
        1.7    8.0   5.3        6.4    6.2   0.9    2.8  3  EBP              Emopamil binding protein


Domain annotation for each model (and alignments):
>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   1.2   3.7e-15   7.3e-12       3     104 ..       6     101 ..       4     111 .. 0.87
   2 !   59.9   8.7   1.2e-19   2.3e-16     181     331 ..     103     244 ..      96     249 .. 0.85

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 3.7e-15
                               Zip   3 lkilaiiaililsllgllgpllvpkiskllsklllslllafavGvllgtaflhLlPealealeesqleeehthplag 79 
                                       + ++ i +++++sl++  +p++++     +++++l+l+ af++G+++g  f+ LlPeale  e+   e     ++ag
  gi|474934794|ref|YP_007688376.1|   6 TLLIYIAVLFAVSLAAARLPYFMN-----SQESRLHLMIAFSAGIMIGVLFVMLLPEALERTEDGGYEY----TWAG 73 
                                       5678899*****************.....77899******************************98655....**** PP

                               Zip  80 llvllGflllllveklltmivek...ks 104
                                        ++l G ++ ll++ l+++++++   ++
  gi|474934794|ref|YP_007688376.1|  74 YMILAGVIVALLFDCLVKHLMPEgdnEE 101
                                       **********************943322 PP

  == domain 2  score: 59.9 bits;  conditional E-value: 1.2e-19
                               Zip 181 slkvraiilllglilHsfidGLAlG..vssssstgislfiAvllHelpeelglgaiLlkaglsrkkavllnllfalt 255
                                        + + ++   lgl +H f+dGL+l+  + ++ + g+ ++iA++lH+++++++l + +  +g ++  a+ + +lf l 
  gi|474934794|ref|YP_007688376.1| 103 DHDITSMSAFLGLAIHCFFDGLSLAaaFVAGEEIGVLVLIALCLHKVVVVFSLSTTMS-MGSKKDEAWKYLVLFCLI 178
                                       5678889999********************************************9985.6888999*********** PP

                               Zip 256 aplGiliGilvrsisessgaeivsgillalsaGtflYvalvellphEllnek.gssslkqsllqllglllGfalmll 331
                                       +pl+++   lv     ++++   +g+ l +s G+f  v+l+++lp E  +e+ g      s   l +l+lG+a++++
  gi|474934794|ref|YP_007688376.1| 179 TPLAAIPSYLV----IDGQDIGFAGLALCFSVGIFAFVTLCDMLP-ESFHENeG------STQRLGLLMLGIAIVIA 244
                                       **********4....566777889999******************.55555513......55555666677777665 PP

>> DUF2178  Predicted membrane protein (DUF2178)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   1.1     0.025        50       2      38 ..       8      50 ..       6      65 .. 0.70
   2 !   16.8   0.1   2.9e-06    0.0057      23      96 ..      70     147 ..      64     156 .. 0.85
   3 ?   -1.2   1.1       1.2   2.3e+03      25      30 ..     235     240 ..     195     256 .. 0.55

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.025
                           DUF2178  2 liivavialvglgiwa......aignvllaviavaaGvllail 38
                                      li +av+++v+l+++       +++++l ++ia+ aG+++ +l
  gi|474934794|ref|YP_007688376.1|  8 LIYIAVLFAVSLAAARlpyfmnSQESRLHLMIAFSAGIMIGVL 50
                                      5677888888888822466678777777777777777776544 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 2.9e-06
                           DUF2178  23 llaviavaaGvllaillkkkve....evveDERlariaekAsrktlqillfliallgvvlivlksdfpeytrvgfll 95 
                                         a+ +++aGv++a+l    v+    e  + ER++ i+  ++ + l i +f  +l+ +  +v+ +++     ++++l
  gi|474934794|ref|YP_007688376.1|  70 TWAGYMILAGVIVALLFDCLVKhlmpEGDNEERDHDITSMSAFLGLAIHCFFDGLSLAAAFVAGEEIGVLVLIALCL 146
                                       567889********99998888777788899*******************************988886667777766 PP

                           DUF2178  96 a 96 
                                        
  gi|474934794|ref|YP_007688376.1| 147 H 147
                                       5 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.2
                           DUF2178  25 aviava 30 
                                       +++ +a
  gi|474934794|ref|YP_007688376.1| 235 LMLGIA 240
                                       222222 PP

>> DUF4271  Domain of unknown function (DUF4271)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   2.6   0.00067       1.3      44     101 ..      29      86 ..      19     176 .. 0.57
   2 ?    8.6   0.2   0.00081       1.6      53     109 ..     197     253 ..     189     256 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00067
                           DUF4271  44 tksesrfqlflllltclllglllylllse.fgslfgsylassllllliiflilllylll 101
                                       +++esr +l++ +   +++g+l++ ll e    +++  ++ ++  ++i++++++++l +
  gi|474934794|ref|YP_007688376.1|  29 NSQESRLHLMIAFSAGIMIGVLFVMLLPEaLERTEDGGYEYTWAGYMILAGVIVALL-F 86 
                                       589*****************6666666660444444433366666666666555443.3 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00081
                           DUF4271  53 flllltclllglllylllsefgslfgsylassllllliiflilllylllKlllykll 109
                                       f  l  c+++g++ +++l ++ +++  +++ s + l++++l++++++ + l+   l+
  gi|474934794|ref|YP_007688376.1| 197 FAGLALCFSVGIFAFVTLCDMLPESFHENEGSTQRLGLLMLGIAIVIAVALISHELM 253
                                       678999**************9999988888777777777777777777776666665 PP

>> TauE  Sulfite exporter TauE/SafE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   3.2    0.0037       7.5      42     138 ..     149     248 ..     139     256 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0037
                              TauE  42 lavvatslsgalahrrrgnvdwrlllllllgsliGallGallllllpsel....lkllfgvlllllallmllrkkrs 114
                                       + vv+ sls +++   ++   w+ l+l++l + ++a+   l+    +  +    l + +g++  ++   ml +++ +
  gi|474934794|ref|YP_007688376.1| 149 V-VVVFSLSTTMSMGSKKDEAWKYLVLFCLITPLAAIPSYLVIDGQDIGFaglaLCFSVGIFAFVTLCDMLPESF-H 223
                                       3.4445555566666655566***999999999999998888886664442222566666666666666665555.6 PP

                              TauE 115 rakgrerrptaillvliggl.vGll 138
                                       +++g+++r +++ l+++ ++ v+l+
  gi|474934794|ref|YP_007688376.1| 224 ENEGSTQRLGLLMLGIAIVIaVALI 248
                                       6666777777777777766666665 PP

>> DUF1129  Protein of unknown function (DUF1129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.7   0.00011      0.22      82     171 ..       1      95 [.       1     122 [. 0.78
   2 ?    3.9   1.3     0.016        33      83     166 ..     166     248 ..     110     255 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
                           DUF1129  82 lDnsLlllalfallfgila......lfskkkqtasiGlitlllvalvgGlamvlvy.rlltrekkkkkrpplwkrll 151
                                       +D+ L+ll+ +a+lf++        +f +++++    l+  ++ +++ G+++v++  + l+r  +    + +w   +
  gi|474934794|ref|YP_007688376.1|   1 MDEFLTLLIYIAVLFAVSLaaarlpYFMNSQESR-LHLMIAFSAGIMIGVLFVMLLpEALER-TEDGGYEYTWAGYM 75 
                                       6888999999999999865222222577655554.59999************9876255665.88888888999999 PP

                           DUF1129 152 illlllvvwlvlftlvallp 171
                                       il++++v++l+ +++  l+p
  gi|474934794|ref|YP_007688376.1|  76 ILAGVIVALLFDCLVKHLMP 95 
                                       99999999998777777766 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.016
                           DUF1129  83 DnsLlllalfallfgilalfskkkqtas.iGlitlllvalvgGlamvlvyrlltrekkkkkrpplwkrllilllllv 158
                                       D+++ +l+lf+l++ + a+ s      + iG+  l+l+  vg +a+v++ ++l   ++ ++ ++  +rl +l+l ++
  gi|474934794|ref|YP_007688376.1| 166 DEAWKYLVLFCLITPLAAIPSYLVIDGQdIGFAGLALCFSVGIFAFVTLCDMLP--ESFHENEGSTQRLGLLMLGIA 240
                                       667777777777666555444433333347888877766666667777777775..477777888888888777777 PP

                           DUF1129 159 vwlvlftl 166
                                       + +++ ++
  gi|474934794|ref|YP_007688376.1| 241 IVIAVALI 248
                                       77776655 PP

>> TssN  Type VI secretion system, TssN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.3     0.013        26      38     141 ..      13      86 ..       2     102 .. 0.41
   2 ?    9.2   3.7   0.00036      0.71       4     110 ..     138     247 ..     136     254 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.013
                              TssN  38 LlaglvlalpgllgflknefvpygyillqilylllGilhlylllkkffkelkekkilfeilltlivillglvlfvlv 114
                                       +l+++ la   l  f++ +     ++++  + +++G+l+++ll + +                              
  gi|474934794|ref|YP_007688376.1|  13 VLFAVSLAAARLPYFMNSQESRLHLMIAFSAGIMIGVLFVMLLPEAL------------------------------ 59 
                                       22333333333333444444444444444444444444444222222.............................. PP

                              TssN 115 fnllselqygv.waatsllvfiipllfl 141
                                        +++++  y++ wa   +l+ +i+ l++
  gi|474934794|ref|YP_007688376.1|  60 -ERTEDGGYEYtWAGYMILAGVIVALLF 86 
                                       .233333343334444444433333322 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00036
                              TssN   4 ylllpllavilllilsliakknkll.kkkkliiyiLlaglvlalpgllgflknefvpygyillqilylllGilhlyl 79 
                                       +l+l++l++  +++++++++++ +  kk ++  y++l+ l+  l ++ ++l  +   +g+  l +++  +Gi+  ++
  gi|474934794|ref|YP_007688376.1| 138 VLVLIALCLHKVVVVFSLSTTMSMGsKKDEAWKYLVLFCLITPLAAIPSYLVIDGQDIGFAGLALCFS-VGIFAFVT 213
                                       566677776666666666665555405557999*****************************999875.69999998 PP

                              TssN  80 llkkffkelkekk...ilfeilltlivillglvl 110
                                       l + + + ++e++       +l++ i+i+++++l
  gi|474934794|ref|YP_007688376.1| 214 LCDMLPESFHENEgstQRLGLLMLGIAIVIAVAL 247
                                       ****999999999432233344444444444444 PP

>> DUF2818  Protein of unknown function (DUF2818)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   1.6     0.046        92       3      74 ..      12      77 ..      10      94 .. 0.55
   2 ?    8.1   0.3    0.0019       3.8      37      87 ..     138     188 ..     124     190 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.046
                           DUF2818  3 wlllllalvaANLPflse....rlflviplkkaeKslalrllEllvlylvvgllalllEaragnvaaqgWeFYavt 74
                                      ++l++++l aA LP++++    rl l+i++           + +++  l v+ll  +lE++    ++  W  Y + 
  gi|474934794|ref|YP_007688376.1| 12 AVLFAVSLAAARLPYFMNsqesRLHLMIAF----------SAGIMIGVLFVMLLPEALERTEDGGYEYTWAGYMIL 77
                                      678889999999999865111133333332..........222233333344555666655555566666666655 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0019
                           DUF2818  37 lrllEllvlylvvgllalllEaragnvaaqgWeFYavtlslflvfafpgfv 87 
                                       + +l  l+l+ vv++++l    ++g+ +++ W++ +  + +    a+p+++
  gi|474934794|ref|YP_007688376.1| 138 VLVLIALCLHKVVVVFSLSTTMSMGSKKDEAWKYLVLFCLITPLAAIPSYL 188
                                       555667889999*********************766555555566788875 PP

>> ABC2_membrane_5  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   4.7     0.068   1.4e+02      83     132 ..       4      53 ..       2      56 .. 0.78
   2 ?   11.2   4.7    0.0001       0.2      91     195 ..      77     184 ..      68     190 .. 0.70
   3 ?    2.8   3.1     0.037        73     128     197 ..     177     249 ..     172     253 .. 0.59

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.068
                   ABC2_membrane_5  83 Ylfvlililiailitlllliiavlikgnvtisevllsiliglvialifla 132
                                       +l++li+i++ + ++l+++ + ++++++     +++++ +g++i+++f+ 
  gi|474934794|ref|YP_007688376.1|   4 FLTLLIYIAVLFAVSLAAARLPYFMNSQESRLHLMIAFSAGIMIGVLFVM 53 
                                       67889999999999999999988999887767777888888888877754 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0001
                   ABC2_membrane_5  91 liailitlll.liiavlikgn.....vtisevllsiliglvialiflaivlPlyfkfgvekgrivliiiifgiifll 161
                                       l+++++ ll+ +++++l+  +      + + + +s+++gl+i ++f  ++l   f  g+e g +vli++++  ++++
  gi|474934794|ref|YP_007688376.1|  77 LAGVIVALLFdCLVKHLMP-EgdneeRDHDITSMSAFLGLAIHCFFDGLSLAAAFVAGEEIGVLVLIALCLHKVVVV 152
                                       3333333344234444433.235666555678999*****************************9999999998999 PP

                   ABC2_membrane_5 162 vaifslsklelslidlsnyilliillviilllii 195
                                       ++++ +++   +  +  +y++l++l+  +    i
  gi|474934794|ref|YP_007688376.1| 153 FSLSTTMSMGSKKDEAWKYLVLFCLITPL--AAI 184
                                       98888888877777777777666666544..333 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.037
                   ABC2_membrane_5 128 liflaivlPlyfkfgvekgrivliiiifgiif.llvaifsl..sklelslidlsnyilliillviillliivS 197
                                       li     +P y+    + + ++ ++++f + +  +v ++ +  ++++ +  +++ + ll++ ++i++++ ++S
  gi|474934794|ref|YP_007688376.1| 177 LITPLAAIPSYLVIDGQDIGFAGLALCFSVGIfAFVTLCDMlpESFHENEGSTQRLGLLMLGIAIVIAVALIS 249
                                       5556667777777777777776666665432213333444345677666677777766666666666666665 PP

>> EBP  Emopamil binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.9    0.0032       6.4      79     155 ..       2      76 ..       1      84 [. 0.79
   2 ?    3.5   0.0     0.022        44       6      55 ..      80     131 ..      75     141 .. 0.69
   3 ?   -1.0   0.1      0.53   1.1e+03     149     156 ..     168     175 ..     134     194 .. 0.48

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0032
                               EBP  79 dltvvslelltvllagplallvvyaiakekplrhllqivlataelyGg.vlyfatewlegslnldtseplylwvYlv 154
                                       d ++  l  + vl+a  la   +  ++++++ r  l+i+ + + ++G+ ++  ++e le   + ++    y w+ ++
  gi|474934794|ref|YP_007688376.1|   2 DEFLTLLIYIAVLFAVSLAAARLPYFMNSQESRLHLMIAFSAGIMIGVlFVMLLPEALE---RTEDGGYEYTWAGYM 75 
                                       67778888899999999999999999998999999************934566899998...455556667777666 PP

                               EBP 155 f 155
                                       +
  gi|474934794|ref|YP_007688376.1|  76 I 76 
                                       5 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.022
                               EBP   6 lavllaalllskrllpk.sklkkdrllfiWfafda.liHlilEGsflynsff 55 
                                       ++v+l+  +l k+l+p+  + ++d  ++   af +  iH++++G  l  +f 
  gi|474934794|ref|YP_007688376.1|  80 VIVALLFDCLVKHLMPEgDNEERDHDITSMSAFLGlAIHCFFDGLSLAAAFV 131
                                       5566666677788888866665555555556666648*******99987665 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.53
                               EBP 149 lwvYlvff 156
                                        w Ylv+f
  gi|474934794|ref|YP_007688376.1| 168 AWKYLVLF 175
                                       23333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       977  (0.0544927); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 1676.09
//
Query:       gi|474934795|ref|YP_007688377.1|  [L=443]
Description: hydrogenobyrinic acid a,c-diamide synthase (glutamine-hydrolysing)/cobyrinate a,c-diamide synthase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.2e-27   96.8   0.0    2.1e-27   96.0   0.0    1.4  1  GATase_3   CobB/CobQ-like glutamine amidotransferase domain
    9.3e-15   55.0   0.1    1.8e-08   34.4   0.0    2.4  2  AAA_26     AAA domain
    7.6e-11   42.2   0.0    1.5e-10   41.2   0.0    1.5  1  CbiA       CobQ/CobB/MinD/ParA nucleotide binding domain
     0.0025   17.8   1.7       0.33   10.8   0.0    2.9  3  NTPase_1   NTPase
  ------ inclusion threshold ------
      0.055   13.4   0.0       0.14   12.1   0.0    1.7  1  MobB       Molybdopterin guanine dinucleotide synthesis prote
       0.11   11.9   0.2        8.9    5.7   0.0    2.2  2  Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/


Domain annotation for each model (and alignments):
>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.0   0.0   6.9e-31   2.1e-27       1     174 [.     240     415 ..     240     421 .. 0.88

  Alignments for each domain:
  == domain 1  score: 96.0 bits;  conditional E-value: 6.9e-31
                          GATase_3   1 kiavirlpaisnyt..dldpLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeag 75 
                                       ki++++++ + + +  ++ +Le+ +++ vrf+p++d+++++ +  +il Gg+++++  al+ ++++ +++k+++ ag
  gi|474934795|ref|YP_007688377.1| 240 KIGLAYDDTFCFTYedNIALLEECGAEIVRFSPMHDRKIPDGVCGIILSGGYPELHGEALSSNKSMLQDLKSKVDAG 316
                                       6999******99888************************************************************** PP

                          GATase_3  76 gpvlgiCGGlqmLGeeiedpegvegeageveglglLdietefekekltgqvegevel......aaegeevkGyEiHs 146
                                       +p+l++CGG+++L e++ed++g+      +++ g+++ e++ +  klt    g+v l      +  g+  kG+E+H+
  gi|474934795|ref|YP_007688377.1| 317 MPCLAECGGFMYLHERMEDADGK-----VWPMAGVIQGEVRNTG-KLT--RFGYVALtsgsrdSILGSGAKGHEFHY 385
                                       ***********************.....****************.***..8888777888776555699******** PP

                          GATase_3 147 Grtilkekakpllkvkvggnng..ekdGav 174
                                         +++  +  +++k + ++ +   ekdG+ 
  gi|474934795|ref|YP_007688377.1| 386 WDSSNPGESWTAVKSSGKTYTCghEKDGLA 415
                                       977766655555544333333356888876 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   5.6e-07    0.0017       4      36 ..       1      33 [.       1      54 [. 0.96
   2 !   34.4   0.0   6.1e-12   1.8e-08      88     195 ..      65     178 ..      40     181 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 5.6e-07
                            AAA_26  4 fvtgtdtgvGKTvvslgLvralkrkgvkvgyfK 36
                                      ++t+   g+GKT+v+ g+++al ++g+kv+ fK
  gi|474934795|ref|YP_007688377.1|  1 MITAPASGSGKTLVTCGILQALVNRGMKVSSFK 33
                                      89***************************9998 PP

  == domain 2  score: 34.4 bits;  conditional E-value: 6.1e-12
                            AAA_26  88 lekivkelekdadivvVEGagglgvpitee...llnadiaknlgapvilVargglgtinqllltiealrq.knvrvl 160
                                       l+ i+k+ ++ +di v+E++ g  ++  ++    + +++ ++l apvil+++++  +i  + +ti+ +++ +++r++
  gi|474934795|ref|YP_007688377.1|  65 LKYIFKRSAEPSDISVIEAVMGFYDGMRSGdtrGSSYEVSEKLEAPVILLVNTRGTSISCV-ATIKGFKEfRKNRIA 140
                                       444558899999********99999988872234689***************998888765.566666654999*** PP

                            AAA_26 161 GvilNkvrnp....envetlekksgipvlGvvPylpdle 195
                                       GvilN++ +p    +    +e  +g++v+G vP  +dl 
  gi|474934795|ref|YP_007688377.1| 141 GVILNNM-SPgvyaDVSPIIEREIGLKVIGYVPKMKDLV 178
                                       ******5.6657755666677789***********9985 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.0     5e-14   1.5e-10       2     119 ..       1     178 [.       1     187 [. 0.83

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 5e-14
                                       EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................ RF
                              CbiA   2 aiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep........................ 54 
                                       +i++  +G+GKT +++++++al +rg +V  ++++p+    + ++  ++  +                         
  gi|474934795|ref|YP_007688377.1|   1 MITAPASGSGKTLVTCGILQALVNRGMKVSSFKCGPDYIDPM-FHARVIGTRSrnldtffcddgtlkyifkrsaeps 76 
                                       69999********************************65555.333333333367888******************* PP

                                       ..............................................CCHCCCHHHHHHCHCHHHH....EEEEEEEE CS
                                       ..............................................xxxxxxxxxxxxxxxxxxx..xxxxxxxxxx RF
                              CbiA  55 ..............................................dlkrllellealgkkkall..lkiagvvlnr 83 
                                                                                     ++        +++ +++ +   +iagv+ln 
  gi|474934795|ref|YP_007688377.1|  77 disvieavmgfydgmrsgdtrgssyevsekleapvillvntrgtsiSCVA------TIK-GFKEFrkNRIAGVILNN 146
                                       ***************************************86653332222......333.33333456********* PP

                                       ESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  84 vdgeneetllkealeelkqrygvpvlgviprdeava 119
                                         +   ++  +  +e+++   g++v+g +p+ ++++
  gi|474934795|ref|YP_007688377.1| 147 MSPG-VYADVSPIIEREI---GLKVIGYVPKMKDLV 178
                                       *999.57889******99...**********99984 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9   0.1    0.0073        22       4      35 ..       2      34 ..       1      36 [. 0.87
   2 ?   -1.3   0.1      0.62   1.8e+03      94     124 ..     182     212 ..     171     217 .. 0.82
   3 !   10.8   0.0   0.00011      0.33      25      61 ..     338     374 ..     328     384 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0073
                                      EE--.TTSSHHHHHHHHHHHH...GGGEEEEEE CS
                          NTPase_1  4 iTGp.pGvGKtTlvkkvlellkssgvkvgGfyt 35
                                      iT+p +G+GKt +   +l++l ++g+kv+ f +
  gi|474934795|ref|YP_007688377.1|  2 ITAPaSGSGKTLVTCGILQALVNRGMKVSSFKC 34
                                      566526**********************99877 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.62
                                       HHH-EEEE---STTGGG-HHHHHHHHHHHTT CS
                          NTPase_1  94 seadviviDEiGkmElkskkfkeaveevLks 124
                                       ++ ++++ DE+ ++  + ++++e +ee+L+ 
  gi|474934795|ref|YP_007688377.1| 182 RHLGLVLPDEVSQLKENLNTLAERLEETLDI 212
                                       55678888*****************999984 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00011
                                       ..GGGEEEEEEEEE-------EEEEEET.T--EEEEE CS
                          NTPase_1  25 ssgvkvgGfyteevreggrrigFkivdlasgeegiLa 61 
                                        + ++++G++  evr++g+ + F +v+l+sg+++ + 
  gi|474934795|ref|YP_007688377.1| 338 GKVWPMAGVIQGEVRNTGKLTRFGYVALTSGSRDSIL 374
                                       5567899************************998765 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   4.5e-05      0.14       7      34 ..       6      33 ..       1      42 [. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.5e-05
                              MobB  7 ksgsGKTtLleklipelkarglrvgtiK 34
                                       sgsGKT     ++++l +rg++v+  K
  gi|474934795|ref|YP_007688377.1|  6 ASGSGKTLVTCGILQALVNRGMKVSSFK 33
                                      69***********************998 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0    0.0095        29      10      39 ..       8      37 ..       5      50 .. 0.91
   2 ?    5.7   0.0     0.003       8.9     163     215 ..     126     178 ..     114     212 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0095
                         Fer4_NifH 10 GiGksttsqnlsaalaemgkkvlivGCDPk 39
                                      G+Gk+  ++ +++al+++g kv    C P 
  gi|474934795|ref|YP_007688377.1|  8 GSGKTLVTCGILQALVNRGMKVSSFKCGPD 37
                                      99*********************9999985 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.003
                         Fer4_NifH 163 kgiekyaksggvrlgGliinsrkvddereliekfaeelgtkvlevvPrdeivr 215
                                       ++i+ +++  + r++G+i n+ +     ++   + +e+g+kv+  vP+ +++ 
  gi|474934795|ref|YP_007688377.1| 126 ATIKGFKEFRKNRIAGVILNNMSPGVYADVSPIIEREIGLKVIGYVPKMKDLV 178
                                       567778888889********999888999999999************987664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2882.13
//
Query:       gi|474934796|ref|YP_007688378.1|  [L=667]
Description: precorrin-6x reductase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-66  223.8   0.0    3.5e-66  223.1   0.0    1.3  1  CbiJ             Precorrin-6x reductase CbiJ/CobK
    6.3e-16   59.0   0.0    6.1e-15   55.7   0.0    2.6  2  TP_methylase     Tetrapyrrole (Corrin/Porphyrin) Methylases
    0.00025   20.9   0.0      0.012   15.4   0.0    2.2  2  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    0.00062   19.6   0.3     0.0016   18.2   0.0    1.7  2  Met_10           Met-10+ like-protein
    0.00064   19.6   0.0     0.0012   18.6   0.0    1.5  1  Methyltransf_31  Methyltransferase domain
    0.00094   18.8   0.0     0.0021   17.6   0.0    1.5  1  DOT1             Histone methylation protein DOT1
     0.0024   17.4   0.1     0.0072   15.9   0.0    1.7  2  MTS              Methyltransferase small domain
     0.0025   18.1   0.0      0.011   16.0   0.0    2.1  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.003   18.2   0.1      0.013   16.2   0.0    2.2  2  Methyltransf_25  Methyltransferase domain
     0.0065   16.1   0.0      0.014   15.0   0.0    1.5  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
      0.008   15.7   0.1      0.022   14.2   0.0    1.7  2  Methyltransf_4   Putative methyltransferase
     0.0093   15.1   0.1      0.015   14.4   0.1    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
     0.0096   15.5   0.1         12    5.4   0.0    3.2  3  LDcluster4       SLOG cluster4 family
  ------ inclusion threshold ------
      0.016   14.6   0.0      0.031   13.6   0.0    1.5  1  GidB             rRNA small subunit methyltransferase G
      0.019   14.6   0.0      0.037   13.7   0.0    1.5  1  Cons_hypoth95    Conserved hypothetical protein 95
       0.11   12.2   0.0       0.19   11.4   0.0    1.3  1  GCD14            tRNA methyltransferase complex GCD14 subunit


Domain annotation for each model (and alignments):
>> CbiJ  Precorrin-6x reductase CbiJ/CobK
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  223.1   0.0   3.1e-69   3.5e-66       2     235 ..       4     245 ..       3     246 .. 0.97

  Alignments for each domain:
  == domain 1  score: 223.1 bits;  conditional E-value: 3.1e-69
                                       EEEE-SSHHHHHHHHHHHHTT--EEEEE---SSS----S...S-EEES--SHHHHHHHHHHHT--EEEE-S-TT-HH CS
                              CbiJ   2 ililgGTsearelaeaLaeagievvvsvateygaellpe.kklevrvgrlgeeglaellreekidlvvDATHPfAae 77 
                                       +l+++GT+e+ ++ + L++ag++v+++vat+yg+  +p+ +++ev  ++l+ e++++l+re    +vvDATHP+A+ 
  gi|474934796|ref|YP_007688378.1|   4 VLVFAGTTEGGAISAYLDRAGVKVHACVATDYGTTSVPKgRNIEVSAHPLDPEEMRDLMREY--PVVVDATHPYATS 78 
                                       9**********************************************************997..79*********** PP

                                       HHHHHHHHHHHHT-EEEEE-------...EEEEESSHHHHH.........EEEESTSTTGGGGSTT....SEEEEEE CS
                              CbiJ  78 isanaaeackelgipylrleRpswea...kiievdsleeaaella.....vllttGskelaafaealkk.erllaRv 145
                                       i+ +++eac+++g +y+r++Rps      +i+ev+s++ea+e+l+     +l+ttGsk+l++++++ +  +r++aRv
  gi|474934796|ref|YP_007688378.1|  79 ITGHIREACHDTGAEYIRIQRPSIPIsgdDIREVKSIDEAVEFLKwtdgnILVTTGSKDLEKYTAIPNYkSRVFARV 155
                                       ***********************998*************************************77655569****** PP

                                       SS--SS.--SSS....SEEEEE--SS--HHHHHHHHHHTT--EEEEES--SS.TTTHHHHHHHHTT-EEEEE----- CS
                              CbiJ 146 lptpeslekalplglkakeiiamrGpfskelerallreykidvlVtKeSGgaGgteeKleaArelgipvivikRpev 222
                                       l  p + +++ +lg++ k+++am+Gpf +el+  +l ++k+++lVtK+ Gg Gg++eK+  Ar+++++++++ Rp +
  gi|474934796|ref|YP_007688378.1| 156 LSLPGVAQRCSELGFEGKNLFAMQGPFCEELDYGMLLQTKAKYLVTKDTGGPGGFAEKVCSARKAKATIVLVGRPPE 232
                                       ***************************************************************************66 PP

                                       EEE-SHHHHHHHH CS
                              CbiJ 223 eevsdveellewl 235
                                       +e+++++e+ e+l
  gi|474934796|ref|YP_007688378.1| 233 KEGMTYDEATEYL 245
                                       77*******9987 PP

>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       6.2   6.9e+03     159     188 ..     219     251 ..     207     261 .. 0.59
   2 !   55.7   0.0   5.4e-18   6.1e-15       2     212 ..     270     455 ..     267     456 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 6.2
                      TP_methylase 159 angdtlvllkapr.k....laelaelLkealyddt 188
                                       +++ t+vl+ +p  k    ++e+ e L+++   d+
  gi|474934796|ref|YP_007688378.1| 219 KAKATIVLVGRPPeKegmtYDEATEYLAKK--LDL 251
                                       445677777665533555566666666655..444 PP

  == domain 2  score: 55.7 bits;  conditional E-value: 5.4e-18
                      TP_methylase   2 lylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealra 78 
                                       l++ GvGpG    lT +A +a+++ad+v+g++ r lei +++              k++l e +      +     +
  gi|474934796|ref|YP_007688378.1| 270 LIGTGVGPG--TGLTEAASAAVREADLVVGAE-RMLEIPEAI-------------GKQQLKEYMPSRIFDYLNMHPE 330
                                       455555555..5********************.877777543.............3445544433333333333334 PP

                      TP_methylase  79 gkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvllpglakeeerele 155
                                        +++++l sGD  +y++++ ++  +    +++++    G+ss+q ++ar+gip+++ + v+++  +g     +  + 
  gi|474934796|ref|YP_007688378.1| 331 FRNIAVLLSGDVGFYSAARSILGTVDP--KEFDTFAYCGISSVQYLCARAGIPWQDVRLVSAHG-KG-----ANIVG 399
                                       477*******************99999..89************************999999999.54.....44555 PP

                      TP_methylase 156 allangdtlvllkaprklaelaelLkea.lyddttpvavveragtedervvrgtleel 212
                                       ++   +   +ll + + ++e+++ L e+ + +    v+v++++g+++e  v gt +e+
  gi|474934796|ref|YP_007688378.1| 400 EVRRSPACFFLLNGKEGVKEMCAGLCEYgFSN--VSVIVGSDLGYPEENFVFGTPQEV 455
                                       55556778888877779***********6666..89*************998887665 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.064        72      80     113 ..     275     307 ..     266     331 .. 0.78
   2 !   15.4   0.0   1.1e-05     0.012      56     131 ..     493     567 ..     481     608 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.064
                                       ES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHH CS
                              PCMT  80 vGsGsGyltavlarlvgekgrvvsierikelvee 113
                                       vG G+G   a  +  v+e  +vv+ er+ e+ e+
  gi|474934796|ref|YP_007688378.1| 275 VGPGTGLTEAA-SAAVREADLVVGAERMLEIPEA 307
                                       78899987775.566888888*******999764 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.1e-05
                                       E--HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES CS
                              PCMT  56 iSaphmvalalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvg 131
                                       + +  + al +  l+l++ + v +vG+G+G  +  +ar+   +g+v +ie+  e ++  + n kk ++ nv+v+ g
  gi|474934796|ref|YP_007688378.1| 493 MTKSEVRALSVAKLKLSEDSVVYDVGAGTGSCSIEMARV-AVEGTVYAIEKETEAADLIETNKKKFATPNVQVIRG 567
                                       5566778999999*****************999999986.56788***********99999999999999999876 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.5e-06    0.0016      97     145 ..     506     555 ..     495     566 .. 0.89
   2 ?   -2.9   0.0       4.2   4.7e+03      25      43 ..     594     613 ..     590     625 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.5e-06
                                       T.--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHH CS
                            Met_10  97 l.veegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkenik 145
                                       l  +e+ vV dv AG G  +i +a+ + + +v+ai+++ e+  +++ n k
  gi|474934796|ref|YP_007688378.1| 506 LkLSEDSVVYDVGAGTGSCSIEMARVAVEGTVYAIEKETEAADLIETNKK 555
                                       4478899*************************************999855 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.2
                                       HHHHHHHHS.S-SCEEEE-S CS
                            Met_10  25 igevildkt.kvktvlrkvs 43 
                                       i+ ++l+k+ +v+ v++ v+
  gi|474934796|ref|YP_007688378.1| 594 IVMAVLEKNpNVRLVVNSVT 613
                                       56666777777777777654 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.1e-06    0.0012       3      61 ..     510     567 ..     508     579 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.1e-06
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqg 61 
                                       ++ +v+D+G+GtG  ++e+a ++  +++v+ i+ + ea  l ++n +k    nv++ +g
  gi|474934796|ref|YP_007688378.1| 510 EDSVVYDVGAGTGSCSIEMA-RVAVEGTVYAIEKETEAADLIETNKKKFATPNVQVIRG 567
                                       6789****************.99999******************988877779988765 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.9e-06    0.0021      35      90 ..     503     558 ..     494     562 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.9e-06
                                       HHHTT--TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE--HHHHHHHHHHHHHHH CS
                              DOT1  35 ldkvnlkkedvFvDLGSGvGnvvlqaalevgcklsvGvEimdnaselaekqkeelk 90 
                                       + k++l++++v +D G G G + + +a  +   + + +E+ ++a++l e++k+ + 
  gi|474934796|ref|YP_007688378.1| 503 VAKLKLSEDSVVYDVGAGTGSCSIEMARVAVEGTVYAIEKETEAADLIETNKKKFA 558
                                       6799************************999999*****************99885 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       2.9   3.2e+03      17      40 ..     239     262 ..     236     332 .. 0.74
   2 !   15.9   0.0   6.5e-06    0.0072      26      81 ..     505     560 ..     499     574 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.9
                                       -HHHHHHHHHCHCCTCSEEEEET- CS
                               MTS  17 DkGsklLletlpkelsgkvlDlGc 40 
                                       D +++ L+++l+     ++ D+G+
  gi|474934796|ref|YP_007688378.1| 239 DEATEYLAKKLDLLDVADASDFGA 262
                                       788888888888876667777776 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 6.5e-06
                                       HCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC CS
                               MTS  26 tlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle 81 
                                       +l+ +++  v D+G+G+G  ++++a+   e +v +++++++A ++ ++n ++ +  
  gi|474934796|ref|YP_007688378.1| 505 KLKLSEDSVVYDVGAGTGSCSIEMARVAVEGTVYAIEKETEAADLIETNKKKFATP 560
                                       55555677899**********************************99998876554 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0     1e-05     0.011      44      99 ..      43      97 ..       9     122 .. 0.79
   2 ?   -2.5   0.0       5.2   5.9e+03       7      41 ..     589     621 ..     582     641 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1e-05
                                      HTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SSGG...GHHHHHHHHHHHT-EEEES CS
                   Sacchrp_dh_NADP 44 algvrfeaialdaenyeavLaallkegdlvvnlsppi...ssldvlkaCietgvhyvdt 99
                                       ++++++a+ ld+e+ ++    l++e+ +vv+++ p+    +  + +aC++tg+ y+ +
  gi|474934796|ref|YP_007688378.1| 43 GRNIEVSAHPLDPEEMRD----LMREYPVVVDATHPYatsITGHIREACHDTGAEYIRI 97
                                      378888888888888888....9**************987788*************974 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.2
                                       SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHH CS
                   Sacchrp_dh_NADP   7 GsvGqavaellarhfdvdaeitvadrskekleala 41 
                                       G+  + v+ +l+++ +v  +++v + ++e   +++
  gi|474934796|ref|YP_007688378.1| 589 GNLDEIVMAVLEKNPNV--RLVVNSVTLETISEVL 621
                                       55555677777777777..7777777777665554 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       7.6   8.5e+03       5      25 ..     274     296 ..     273     315 .. 0.58
   2 !   16.2   0.0   1.1e-05     0.013       1      55 [.     514     569 ..     514     601 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 7.6
                                       T-TTSHHHHHHHCTS..TSSEEE CS
                   Methyltransf_25   5 GcGtGrltlalakrl..gkakvt 25 
                                       G G+G+ + ++a +   ++  v+
  gi|474934796|ref|YP_007688378.1| 274 GVGPGTGLTEAASAAvrEADLVV 296
                                       56666666665555422233333 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.1e-05
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHH.TTTTEEEEESBC CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraee.eglnvefvqgda 55 
                                       v d+G+GtG  ++++a+   +++v++++   e+ + ++++ ++ + +nv++++g a
  gi|474934796|ref|YP_007688378.1| 514 VYDVGAGTGSCSIEMARVAVEGTVYAIEKETEAADLIETNKKKfATPNVQVIRGLA 569
                                       78**************99758**********9999999888776677999998766 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.3e-05     0.014       3      65 ..     505     566 ..     503     572 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.3e-05
                                       HH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEE CS
                   Methyltr_RsmB-F   3 lLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivle 65 
                                        L++ e+  + D+ a+ G+    +a + + +gtv+A+++++e ++ +++n k++   n++v++
  gi|474934796|ref|YP_007688378.1| 505 KLKLSEDSVVYDVGAGTGSCSIEMARV-AVEGTVYAIEKETEAADLIETNKKKFATPNVQVIR 566
                                       68999**********************.99**************************9999987 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0     2e-05     0.022       3      65 ..     512     574 ..     510     583 .. 0.90
   2 ?   -2.0   0.0       1.8   2.1e+03       3      60 ..     579     639 ..     577     647 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2e-05
                                       EEEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCHHH CS
                    Methyltransf_4   3 pvvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkvll 65 
                                       +vv ++G G G+  +++A    + ++ +iE++++  + +  + ++    N++++rg a   l 
  gi|474934796|ref|YP_007688378.1| 512 SVVYDVGAGTGSCSIEMARVAVEGTVYAIEKETEAADLIETNKKKFATPNVQVIRGLAPSALA 574
                                       6899*******************************99999999999********998877775 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.8
                                       EEEEEET-TTSH...HHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-C CS
                    Methyltransf_4   3 pvvleiGcGkGe...flvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgda 60 
                                       p+++ iG  +G+   +++a  +knP++ ++   +  + + +vl+  ++  ++ l++++ + 
  gi|474934796|ref|YP_007688378.1| 579 PTHVFIGGSSGNldeIVMAVLEKNPNVRLVVNSVTLETISEVLRLPDKCAVEQLEVVCLNV 639
                                       5666677666642125777778999999998899999999999999999999999988885 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   1.3e-05     0.015      23      81 ..     503     565 ..     494     567 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.3e-05
                                       HHHH-GGTTSEEEEES-TTTCCHHHHHCC-..SEEEEE-S-H...HHHHHHHCHTTTCCCEEEE CS
                            RrnaAD  23 ldklnleekltvleigpGkGilTeeLakra..kqvvvlElde...rLakllqkklskdeklkvv 81 
                                       + kl+l+e+  v+++g+G+G  + e+a  a    v ++E+ +   +L++  +kk+   ++++v+
  gi|474934796|ref|YP_007688378.1| 503 VAKLKLSEDSVVYDVGAGTGSCSIEMARVAveGTVYAIEKETeaaDLIETNKKKFA-TPNVQVI 565
                                       78999************************99889999**99722246666666666.9999998 PP

>> LDcluster4  SLOG cluster4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.28   3.2e+02      38      66 ..     204     233 ..     188     271 .. 0.67
   2 ?    5.4   0.0     0.011        12      31      99 ..     265     342 ..     241     355 .. 0.77
   3 ?    5.3   0.0     0.012        13     101     127 ..     582     608 ..     567     632 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.28
                        LDcluster4  38 tGgrtGvmeaaskGakeagGlt.vGilpas 66 
                                       tGg +G+ e ++ + k ++ ++ vG  p++
  gi|474934796|ref|YP_007688378.1| 204 TGGPGGFAEKVCSARKAKATIVlVGRPPEK 233
                                       799999999999998877766536666653 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.011
                        LDcluster4  31 kegavll...tGgrtGvmeaaskGakeagGltvGilpassekehsnk.....yvdiiiyT..GlglagRnlilvlss 97 
                                       ++++ l+    G  tG+ eaas +++ea+ l+vG  +  +  e+  k     y+   i+   ++  + Rn+ + ls 
  gi|474934796|ref|YP_007688378.1| 265 RRKMSLIgtgVGPGTGLTEAASAAVREAD-LVVGAERMLEIPEAIGKqqlkeYMPSRIFDylNMHPEFRNIAVLLSG 340
                                       55555553113445899999999999987.9***987777666665566666887777665589999********99 PP

                        LDcluster4  98 dv 99 
                                       dv
  gi|474934796|ref|YP_007688378.1| 341 DV 342
                                       97 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.012
                        LDcluster4 101 iaiggrsGTlsEialaleegkpvivlk 127
                                       ++igg+sG l Ei++a+ e++p + l 
  gi|474934796|ref|YP_007688378.1| 582 VFIGGSSGNLDEIVMAVLEKNPNVRLV 608
                                       89***************9999977765 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.8e-05     0.031      42     107 ..     504     569 ..     496     645 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.8e-05
                                       GGCS-CCC-.EEEETSTTTTTHHHHHHH-TTSEEEEEES-HHHHHHHHHHHHHCT-SSEEEEES-C CS
                              GidB  42 lellkekrdkviDvGsGaGlPGipLaiarpelkltLleslekkiaFLeevkeelklenveiveara 107
                                       ++l  ++++ v DvG+G G  +i +a +  e  ++ +e++   +  +e  k++++  nv++++  a
  gi|474934796|ref|YP_007688378.1| 504 AKLKLSEDSVVYDVGAGTGSCSIEMARVAVEGTVYAIEKETEAADLIETNKKKFATPNVQVIRGLA 569
                                       44433444349***************************************************9755 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.3e-05     0.037      41     107 ..     510     576 ..     475     584 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.3e-05
                                       CC-EEEETT-TTSHHHHHHHHTT-S..EEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS CS
                     Cons_hypoth95  41 egarvLDlfaGsGalglEAlSRgak..kavlvekdkeavkilkenleelkleeetaelkedaleallkl 107
                                       e++ v D+ aG+G+ ++E   R a    ++++ek+ ea+ ++++n +++ + + +++++  a +al +l
  gi|474934796|ref|YP_007688378.1| 510 EDSVVYDVGAGTGSCSIEM-ARVAVegTVYAIEKETEAADLIETNKKKFATPN-VQVIRGLAPSALASL 576
                                       556788************6.56664125789*******************997.888887776666665 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00017      0.19      31      79 ..     501     548 ..     496     566 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00017
                             GCD14  31 liimkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqrae 79 
                                       l + kL+l + svv + G+G+gs s  +ar va  G ++++e   + a+
  gi|474934796|ref|YP_007688378.1| 501 LSVAKLKLSEDSVVYDVGAGTGSCSIEMAR-VAVEGTVYAIEKETEAAD 548
                                       56789************************9.8999*****997665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (667 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.68u 0.31s 00:00:00.99 Elapsed: 00:00:00.47
# Mc/sec: 4302.57
//
Query:       gi|474934797|ref|YP_007688379.1|  [L=348]
Description: Cobalamin biosynthesis protein CbiG [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-33  114.8   0.1    2.7e-33  113.8   0.1    1.5  1  CbiG_N    Cobalamin synthesis G N-terminal
    1.6e-33  115.7   0.3    3.1e-33  114.8   0.1    1.6  2  CbiG_C    Cobalamin synthesis G C-terminus
    1.8e-05   24.8   0.0    4.3e-05   23.5   0.0    1.7  1  CbiG_mid  Cobalamin biosynthesis central region
  ------ inclusion threshold ------
       0.18   12.6   0.0        8.3    7.3   0.0    2.3  2  DUF3744   ATP-binding cassette cobalt transporter


Domain annotation for each model (and alignments):
>> CbiG_N  Cobalamin synthesis G N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.8   0.1   5.9e-37   2.7e-33       2      82 .]      51     131 ..      50     131 .. 0.99

  Alignments for each domain:
  == domain 1  score: 113.8 bits;  conditional E-value: 5.9e-37
                                       .HHHHCCC-SEEEEES-HHHHHHHHHHH---TTT--EEEEE-TT--EEEEEE-TT.TTHHHHHHHHHHHTT-EE-XX CS
                            CbiG_N   2 llrelfkeydalvfilaaGivvRliapllkdKktDpaVvvvdeagrfvisllsGhlggAnelAeeiaallgaepviT 78 
                                       ++r++f+e+da+vf++++Gi+vR iap++k+K+ Dpa+v +de grf+i+llsGh+ggAnel+ +ia  +ga+pv+T
  gi|474934797|ref|YP_007688379.1|  51 WTRKAFEECDAIVFVGSVGIAVREIAPFIKSKDVDPAIVDLDELGRFCIPLLSGHIGGANELSLRIAGSVGATPVVT 127
                                       899************************************************************************** PP

                                       XXX. CS
                            CbiG_N  79 tatd 82 
                                       tatd
  gi|474934797|ref|YP_007688379.1| 128 TATD 131
                                       ***8 PP

>> CbiG_C  Cobalamin synthesis G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.6   1.2e+04      76      91 ..      31      46 ..      12      48 .. 0.64
   2 !  114.8   0.1     7e-37   3.1e-33       2     116 .]     216     333 ..     215     333 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.6
                                      T-CHHHCCCSSS-HHH CS
                            CbiG_C 76 psefvkkevGvpsVaE 91
                                        +++  ++G++ V+E
  gi|474934797|ref|YP_007688379.1| 31 FAKTTMDTLGIEKVSE 46
                                      4456667777777777 PP

  == domain 2  score: 114.8 bits;  conditional E-value: 7e-37
                                       EEEEEE-SS--HHHHHHHHHHHHHHCT--GGGEEEEEESSCCSHHHHHHHHHHHCTSTEEEE-HHHHHCHH..CSCT CS
                            CbiG_C   2 vvGiGcrrgtsaeeieeaieealeeaglseeavaalatidlKadepgllelaeklglplktfsaeeLaave..vpnp 76 
                                       v+GiGc++gt++e+iee +  al+eag+++++++a a+id+K+de+gll +a++++lp++++++eeL+av+  + ++
  gi|474934797|ref|YP_007688379.1| 216 VLGIGCKKGTPREAIEERVGLALKEAGITIKSIRACASIDIKSDEEGLLSFAAEHRLPITFYTSEELNAVPgeF-SK 291
                                       89********************************************************************8857.** PP

                                       -CHHHCCCSSS-HHHHHHHHHC...EECSCEEEETTEEEEEE CS
                            CbiG_C  77 sefvkkevGvpsVaEaaAllaa..arllvpKqakggvTvAia 116
                                       s+fv++ + v+ V+E++A+ a+  +rl+++K a +gvT+Aia
  gi|474934797|ref|YP_007688379.1| 292 SDFVRSVTSVDCVCERSAVKASrdGRLVLRKFAGEGVTAAIA 333
                                       ********************98556****************8 PP

>> CbiG_mid  Cobalamin biosynthesis central region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   9.6e-09   4.3e-05       2      48 ..     137     183 ..     136     207 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 9.6e-09
                          CbiG_mid   2 alDilgrpfGwriegegaltevsaalvngepvavlqdvrlegterle 48 
                                       ++D +++  G++i++ +  ++vsa++++g pv+++ d++ +g+  +e
  gi|474934797|ref|YP_007688379.1| 137 SIDAFAVTHGLSIDRLKPAKDVSARILEGSPVGLISDFPIKGEVPKE 183
                                       89*************************************99998776 PP

>> DUF3744  ATP-binding cassette cobalt transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.042   1.9e+02      32      56 ..      34      58 ..      29      64 .. 0.89
   2 ?    7.3   0.0    0.0019       8.3      17      59 ..     237     276 ..     236     283 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.042
                           DUF3744 32 snleklalsqdkeklkewfekqkap 56
                                      + +++l +++++e +++w +k +++
  gi|474934797|ref|YP_007688379.1| 34 TTMDTLGIEKVSESMRSWTRKAFEE 58
                                      57899****************9987 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0019
                           DUF3744  17 aLKkagidltslnqlsnleklalsqdkeklkewfekqkapkke 59 
                                       aLK+agi+++s+   ++   +++++d+e l+++ ++++ p + 
  gi|474934797|ref|YP_007688379.1| 237 ALKEAGITIKSIRACAS---IDIKSDEEGLLSFAAEHRLPITF 276
                                       9*******999877766...56888999999999888877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       248  (0.0138323); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2439.52
//
Query:       gi|474934798|ref|YP_007688380.1|  [L=383]
Description: cobalamin biosynthesis protein CbiD [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-92  310.0   0.3    1.5e-92  309.4   0.3    1.2  1  CbiD      CbiD


Domain annotation for each model (and alignments):
>> CbiD  CbiD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  309.4   0.3   8.6e-97   1.5e-92       1     252 []      18     277 ..      18     277 .. 0.98

  Alignments for each domain:
  == domain 1  score: 309.4 bits;  conditional E-value: 8.6e-97
                              CbiD   1 lrsGyTtGscAaAAakaAllallkgekleeveielpkgekleipiekvalleee..aavikdaGddpDvTngaeiva 75 
                                       lr+GyTtGscAaAA+kaA+++l++g+++e+v+i +p+g+ l+i++e+++++e    +av+kd+Gdd D Tnga i++
  gi|474934798|ref|YP_007688380.1|  18 LRRGYTTGSCAAAASKAAAEMLISGKRVETVDILTPRGIPLHISVEDIEMSEGAvsCAVRKDGGDDADDTNGALIYS 94 
                                       69************************************************77769********************** PP

                              CbiD  76 eve....eeieiegGeGvGrvtkpgLevevgeaAInpvprkmieenveevleea..kegvevtisvpeGeelAkkTl 146
                                       +v+    e i+i+gG+GvGrvt++gL++++g+aAIn+vpr+mi+e +++v+++   +  ++v isv++Ge++Ak+T+
  gi|474934798|ref|YP_007688380.1|  95 RVSrsaeEGIHIDGGKGVGRVTRKGLDQPPGNAAINHVPRSMITECITDVCDAFrtTPAFDVVISVKDGETIAKRTF 171
                                       *******88******************************************98888889****************** PP

                              CbiD 147 NprlGivgGiSiLGTtGivepmSeeallesireelkvaaaeglkelvlvtGnkgeklakkklglpeealvkvsnfvg 223
                                       NprlGi+gGiSi+GT+GivepmSe all si++e++v +a g+k l+ v+Gn+g++++k+   l+ ++ v++snf+g
  gi|474934798|ref|YP_007688380.1| 172 NPRLGIEGGISIIGTSGIVEPMSETALLGSIKAEMSVFMAPGRKFLLTVPGNYGKDFVKDFPALEGQQPVECSNFIG 248
                                       ************************************************************88*************** PP

                              CbiD 224 ealeeaaekgvkkvllvghiGKlvKlagG 252
                                       + l++a+e+g++ vllvg +GKlvK+agG
  gi|474934798|ref|YP_007688380.1| 249 DFLDMAVEMGAEGVLLVGNLGKLVKIAGG 277
                                       ***************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2613.90
//
Query:       gi|474934799|ref|YP_007688381.1|  [L=256]
Description: hypothetical protein TALC_01234 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.2e-37  125.6   0.0    5.7e-19   68.4   0.0    2.0  2  CbiX            CbiX
    6.1e-08   32.3   0.0       0.01   15.2   0.0    2.3  2  CbiK            Cobalt chelatase (CbiK)
    3.2e-06   26.4   0.0    0.00028   20.1   0.0    2.5  2  Ferrochelatase  Ferrochelatase


Domain annotation for each model (and alignments):
>> CbiX  CbiX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   0.0   9.8e-19   5.9e-15       2     106 ..      10     119 ..       9     120 .. 0.94
   2 !   68.4   0.0   9.5e-23   5.7e-19       1     106 [.     138     248 ..     138     249 .. 0.95

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 9.8e-19
                                       STSSCCHHHHHHHHHHHHHHHCCSCCCEECESCCCECCSCCSSHHHHC-SBSEEEEEEESSSSSHHHHTHHHHHCT- CS
                              CbiX   2 GSrdpesneeveklaeelrekgpfkpvelgfleleepsleealrelaeqgvkrivvvPlflfaGvhvkeDIpeelee 78 
                                       GS++p++++++ + +e+l++ ++ ++v ++   +++p + ++++++a+ gv+r +v+P+f+++G  +k+ Ip+e+++
  gi|474934799|ref|YP_007688381.1|  10 GSSLPYAEAALKAQCERLQNLRS-EKVYYASHRANKPLIADTVKQIAADGVDRLLVIPFFIADGEITKDYIPREMGL 85 
                                       9*******************999.****************************************************7 PP

                                       -SSSS-......TTEEEEE---CCCSCCHHHHHH CS
                              CbiX  79 aeeahp......kdveieytepLGthplvaevlk 106
                                                   k++ei+ ++++Gt+p +a+v++
  gi|474934799|ref|YP_007688381.1|  86 KSYGDRclevdgKKIEIIWGSAIGTDPGIADVII 119
                                       666666777888*******************996 PP

  == domain 2  score: 68.4 bits;  conditional E-value: 9.5e-23
                                       -STSSCCHHHHHHHHHHHHHHHCCSCCCEECESCCCECCSCCSSHHHHC-SBSEEEEEEESSSSSHHHHTHHHHHCT CS
                              CbiX   1 HGSrdpesneeveklaeelrekgpfkpvelgfleleepsleealrelaeqgvkrivvvPlflfaGvhvkeDIpeele 77 
                                       HGSr++e  e+ve++ae +r  g  + v+++++e++ p++e+++ e+++ + + i++vP+f++ G h k  Ipe l+
  gi|474934799|ref|YP_007688381.1| 138 HGSRNKELPEAVEAAAESVRLAGY-RNVRVAYNEFNGPYIEDVFPEMVALNEDAIIIVPMFIACGLHLKVEIPEKLG 213
                                       *******************99666.**************************************************** PP

                                       --SSSS-......TTEEEEE---CCCSCCHHHHHH CS
                              CbiX  78 eaeeahp......kdveieytepLGthplvaevlk 106
                                         +++ +      k++e++yt+++G+++ vaevl+
  gi|474934799|ref|YP_007688381.1| 214 IPDNRGGivkhngKSIEVRYTPAVGEDEYVAEVLA 248
                                       88888888899999******************996 PP

>> CbiK  Cobalt chelatase (CbiK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.7e-06      0.01     167     259 ..      28     124 ..       2     126 .. 0.76
   2 !   15.2   0.0   1.7e-06      0.01     141     259 ..     130     253 ..     125     256 .] 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.7e-06
                                       HHCT-S.EEEEETT.SSS-HHHHHHHHHHHT--EEEEEE-SSS--HHHHCCCCSSST.TSHH.HHHHHTT--EEE.- CS
                              CbiK 167 kekdfkqvvvgtve.gyPeveevieelkkkgikevkliPlmlvAGdHaknDmasdee.dswk.ealeaaGikvei.i 239
                                       ++ + ++v+ +     +P + + ++++  +g+ +  +iP+++  G+  k  +  +   +s+    le +G k+ei +
  gi|474934799|ref|YP_007688381.1|  28 QNLRSEKVYYASHRaNKPLIADTVKQIAADGVDRLLVIPFFIADGEITKDYIPREMGlKSYGdRCLEVDGKKIEIiW 104
                                       45444555555444157****************************988777766543368862569*******9846 PP

                                       ---GGGSHHHHHHHHHHHHH CS
                              CbiK 240 lkgLGeieeirsifikhike 259
                                        +++G ++ i+++ ik+ik+
  gi|474934799|ref|YP_007688381.1| 105 GSAIGTDPGIADVIIKRIKD 124
                                       79****************98 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.7e-06
                                       TEEEEEEE---SCH.HHHHHHHHHHHHHHCT-S.EEEEETT.SSS-HHHHHHHHHHHT--EEEEEE-SSS--HHHHC CS
                              CbiK 141 dealvfvgHGtehe.snavyaeldkvlkekdfkqvvvgtve.gyPeveevieelkkkgikevkliPlmlvAGdHakn 215
                                       d  ++ +gHG++ +   ++ +   + ++  ++++v v+  e   P +e+v  e+   +  ++ ++P+++  G H k 
  gi|474934799|ref|YP_007688381.1| 130 DTPVLIIGHGSRNKeLPEAVEAAAESVRLAGYRNVRVAYNEfNGPYIEDVFPEMVALNEDAIIIVPMFIACGLHLKV 206
                                       6778999***976515677777888889999********99456********************************* PP

                                       CCCSSS..TTSHHHHHHHTT--EEE.----GGGSHHHHHHHHHHHHH CS
                              CbiK 216 Dmasde..edswkealeaaGikvei.ilkgLGeieeirsifikhike 259
                                       ++ +     d+   +++++G  +e+ +  ++Ge+e ++++ +k+  +
  gi|474934799|ref|YP_007688381.1| 207 EIPEKLgiPDNRGGIVKHNGKSIEVrYTPAVGEDEYVAEVLAKRAAK 253
                                       **87642258889999****99999556799*999999999888665 PP

>> Ferrochelatase  Ferrochelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   4.7e-08   0.00028      72     130 ..      21      75 ..       7      86 .. 0.76
   2 !    3.0   0.0    0.0071        43      91     123 ..     164     197 ..     135     199 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.7e-08
                                       HHHHHHHHHHHHHH---EEEEEEESSSSSBHHHHHHHHHCTT-SEEEEEES-SS--TTT CS
                    Ferrochelatase  72 rkqaealekelaergidvkvylamrywePsiedaleelkadgvervvvlplyPqysast 130
                                       ++q+e l++       +   y   r  +P+i+d++++++adgv+r++v+p +  ++  t
  gi|474934799|ref|YP_007688381.1|  21 KAQCERLQNLR----SEKVYYASHRANKPLIADTVKQIAADGVDRLLVIPFFIADGEIT 75 
                                       33444444333....45567777899************************988777766 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.0071
                                       EEEE.ESSSSSBHHHHHHHHHCTT-SEEEEEES- CS
                    Ferrochelatase  91 vyla.mrywePsiedaleelkadgvervvvlply 123
                                       v +a +++  P+ied+  e+ a + + ++++p++
  gi|474934799|ref|YP_007688381.1| 164 VRVAyNEFNGPYIEDVFPEMVALNEDAIIIVPMF 197
                                       4444144566999999999999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.34s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 1521.80
//
Query:       gi|474934800|ref|YP_007688382.1|  [L=259]
Description: NAD+ synthetase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-79  267.0   0.1    1.3e-79  266.7   0.1    1.0  1  NAD_synthase   NAD synthase
      5e-05   22.3   0.2    0.00022   20.1   0.2    2.0  2  tRNA_Me_trans  tRNA methyl transferase
    0.00054   19.5   0.0      0.016   14.7   0.0    2.3  2  QueC           Queuosine biosynthesis protein QueC
  ------ inclusion threshold ------
       0.03   13.9   0.2      0.075   12.6   0.0    1.7  2  ThiI           Thiamine biosynthesis protein (ThiI)
      0.055   13.2   0.0       0.11   12.2   0.0    1.6  2  ATP_bind_3     PP-loop family


Domain annotation for each model (and alignments):
>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  266.7   0.1   3.7e-83   1.3e-79       4     239 ..      16     252 ..      14     255 .. 0.97

  Alignments for each domain:
  == domain 1  score: 266.7 bits;  conditional E-value: 3.7e-83
                                       HHHHHHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE-- CS
                      NAD_synthase   4 elvdflkeyvkkagakgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktid 80 
                                       +l+df++  v+kagakg+v+G+SGGvDS++va+l+ +alg envl + +P+ v+s ed+ +++++++  gi+++t++
  gi|474934800|ref|YP_007688382.1|  16 KLTDFIRTTVQKAGAKGAVVGISGGVDSAVVAKLCADALGGENVLCVFMPTAVTSAEDYIQTKKMCQTWGINYNTVS 92 
                                       789************************************************************************** PP

                                       -HHHHHHHHH.HHHHHH-HHHHHHHHHHHHHHHHHHHHHHHTEEEB---BHHHHTTT-S-TTTTT--SBETTTTS-H CS
                      NAD_synthase  81 ikpivrafeq.elkeakedlakgNlkaRiRmailyaianklnllvlgTgnksElvvGyfTkyGDgaadlapiaellK 156
                                       i+p+v af+   l+ ++  l kgN+ aR Rm++ly+ a+k+n+lv+gT n+sEl++Gy+Tk+GDga d+ p+++++K
  gi|474934800|ref|YP_007688382.1|  93 IQPAVDAFSGmLLTGKEAPLEKGNIMARCRMIVLYDKAKKENYLVVGTTNRSELLMGYMTKFGDGAEDVMPMHGIYK 169
                                       **********544555579********************************************************** PP

                                       HHHHHHHHHTT--HHHHCS--B--SSTT-BHHHHHSS-HHHHHHHHTHSSSS...HHHHHTTT--HHHHHHHHHHHH CS
                      NAD_synthase 157 tevkeLakelnvPervlkkpPsAdLkpgqtDeeeLgikYdelDeiLklvekkkspeeiikekelpaevvekieklvk 233
                                       t+v eLak ++vP+++++k P+A+L++gqtDeee+gi+Y+ lD  L+l+e +  +e ++k++++++e++ +i + v 
  gi|474934800|ref|YP_007688382.1| 170 TQVWELAKIIGVPQEIIDKVPTAGLWEGQTDEEEMGITYHDLDIALSLMEGGADDEAMAKSANISKEKAAEIRRQVA 246
                                       ***************************************************************************** PP

                                       HTGGGG CS
                      NAD_synthase 234 ksehKr 239
                                         +hK 
  gi|474934800|ref|YP_007688382.1| 247 CMKHKS 252
                                       *99996 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.2   6.3e-08   0.00022       4      70 ..      34      93 ..      31      99 .. 0.81
   2 ?   -1.2   0.0      0.18   6.6e+02     165     185 ..     161     181 ..     158     188 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 6.3e-08
                     tRNA_Me_trans  4 vvalSgGVDSsvaaallkeq..gyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdf 70
                                      vv++SgGVDS+v+a l +++  g +v  vf+ +  +         + ed+ + ++++++ gi++++v++
  gi|474934800|ref|YP_007688382.1| 34 VVGISGGVDSAVVAKLCADAlgGENVLCVFMPTAVT---------SAEDYIQTKKMCQTWGINYNTVSI 93
                                      89***************99754799*****986544.........567788888888888888888776 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.18
                     tRNA_Me_trans 165 lfPlgeltKeevrkiAkeagl 185
                                       ++P++ + K++v ++Ak +g+
  gi|474934800|ref|YP_007688382.1| 161 VMPMHGIYKTQVWELAKIIGV 181
                                       78**************98776 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   4.4e-06     0.016       2      82 ..      33     115 ..      32     131 .. 0.83
   2 ?    2.3   0.0     0.028     1e+02     155     178 ..     161     184 ..     148     188 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.4e-06
                                       EEEE--SSHHHHHHHHHHHHH..-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-G.GGGGGSCGGG--- CS
                              QueC   2 avvllSGGlDSttvlalakke..gkevealtfdYgqrhkkeleaakkiakelgveehkildld.llkelggsaLtde 75 
                                       avv +SGG+DS++v+ l  ++  g++v ++ +      +++    kk++++ g+ + ++++++  + +++g  Lt +
  gi|474934800|ref|YP_007688382.1|  33 AVVGISGGVDSAVVAKLCADAlgGENVLCVFMPTAVTSAEDYIQTKKMCQTWGI-NYNTVSIQpAVDAFSGMLLTGK 108
                                       89************988776522588999999999999999999**********.7777776537899999999999 PP

                                       ------- CS
                              QueC  76 eievpke 82 
                                       e+ ++k 
  gi|474934800|ref|YP_007688382.1| 109 EAPLEKG 115
                                       9888874 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.028
                                       E-TTTT--HHHHHHHHHHTTHHHH CS
                              QueC 155 eaPlidlsKaeivklgkelgvple 178
                                       ++P+  + K+++++l+k +gvp e
  gi|474934800|ref|YP_007688382.1| 161 VMPMHGIYKTQVWELAKIIGVPQE 184
                                       589*****************9876 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.1e-05     0.075       6      78 ..      33     106 ..      29     141 .. 0.64
   2 ?   -2.2   0.0      0.72   2.6e+03     143     161 ..     163     181 ..     161     187 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.1e-05
                              ThiI   6 vlaLlSgGiDSpVaaylllkR..Gcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlke 78 
                                       +++ +SgG+DS V a l      G +v +v++  + +ts+e   + +k+ + +  +  +++++  v  f  +l  
  gi|474934800|ref|YP_007688382.1|  33 AVVGISGGVDSAVVAKLCADAlgGENVLCVFMP-TAVTSAEDYIQTKKMCQTWGINYNTVSIQPAVDAFSGMLLT 106
                                       45569********99998763326777777775.67777777777777777776444448877777666666554 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.72
                              ThiI 143 PLigldKeeiiklAkeigt 161
                                       P+ g+ K ++ +lAk ig 
  gi|474934800|ref|YP_007688382.1| 163 PMHGIYKTQVWELAKIIGV 181
                                       889999*********9985 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   3.2e-05      0.11       3      68 ..      34      95 ..      32     144 .. 0.74
   2 ?   -3.6   0.0       2.2   7.8e+03       8      33 ..     220     246 ..     217     252 .. 0.49

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.2e-05
                                      EEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H CS
                        ATP_bind_3  3 lvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvdv 68
                                      +v++SgG+DS +  +l a+     g ++ +  v   +  +s+e+    k++c++++i++ + +++ 
  gi|474934800|ref|YP_007688382.1| 34 VVGISGGVDSAVVAKLCADALG--GENVLC--VFMPTAVTSAEDYIQTKKMCQTWGINYNTVSIQP 95
                                      89************99999854..333333..3334555677777788999999999999888875 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.2
                                       SCHHHHHHHHHHHHHCTTTTT.EEEEE CS
                        ATP_bind_3   8 gGlDSmaLllllaklkkklgi.klvai 33 
                                       gG+D  a+ + ++ +k+k +  +  ++
  gi|474934800|ref|YP_007688382.1| 220 GGADDEAMAKSANISKEKAAEiRRQVA 246
                                       566665555555554444332244444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1659.32
//
Query:       gi|474934801|ref|YP_007688383.1|  [L=189]
Description: putative amidohydrolase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-24   85.3   0.0    4.7e-24   85.1   0.0    1.0  1  CN_hydrolase     Carbon-nitrogen hydrolase
  ------ inclusion threshold ------
       0.19   10.3   0.0       0.21   10.1   0.0    1.1  1  Nucleopor_Nup85  Nup85 Nucleoporin


Domain annotation for each model (and alignments):
>> CN_hydrolase  Carbon-nitrogen hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.1   0.0   5.2e-28   4.7e-24      15     214 ..       8     185 ..       4     189 .] 0.88

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 5.2e-28
                                       HHHHHHHHHHHHHHHHTTESEEEEETTTTTBSSSHHHHHHHHBHSSSHHHHHHHHHHHHHTEEEEEEEEEEECCTTE CS
                      CN_hydrolase  15 eanlqklleliaeAarkgadLivlPElfitgykeeahfleaAeaglgetlallaalarkngiavvigliereltngk 91 
                                       e nl++++ +i +   + adL v+PElf+  y +   f + ++    +  ++l+ l+ + ++av+ig + ++ +ng+
  gi|474934801|ref|YP_007688383.1|   8 EDNLKRAEGAILQ---NEADLYVFPELFLSSY-DTTTFNPEDT---PTAEKRLRLLCGERDCAVAIGAPVQW-YNGV 76 
                                       5566666666666...9***************.5555554444...245589********************.**** PP

                                       EEEEEEEEEEETTSEEEEEEE-SS--EECTTSCECCGHHTSCS-SSS-EEEETTEEEEEEEGGGGGSHHHHHHHHHT CS
                      CN_hydrolase  92 lqayntavlldldgklvgkyrKlhLfpgeprpptaverelfepgdgipvfdtpvgkiGaaiCyeigfpellralalk 168
                                            + +++ ++ ++  +y+K+ L      + + ++++ fepg++ ++++ ++ kiG++iCy+ +fpel r++a++
  gi|474934801|ref|YP_007688383.1|  77 T---DSLLFITPTETF--RYDKIYLA-----NFGIYNESAFEPGKSPAIVEWKGMKIGLEICYDVTFPELHRFYATH 143
                                       9...9*****999997..******96.....7999**********999999************************** PP

                                       T-SEEEE.BH.GCCCTCHHHHHHHHHHHHHHHHHHTSEEEEEEBEEE CS
                      CN_hydrolase 169 gaeilvn.lserapvpksmgppqwellgraralengcfviaanqvgg 214
                                       + +i++            +++++++++  +r++en ++++++n++g 
  gi|474934801|ref|YP_007688383.1| 144 DCDIVIVsA-----ASAEPSKKVLMNILPTRSVENTVYTVYVNSIGK 185
                                       *******51.....45799*************************997 PP

>> Nucleopor_Nup85  Nup85 Nucleoporin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   2.3e-05      0.21     235     287 ..      37      92 ..      30     129 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 2.3e-05
                                       S---S-HHHHHHHHHHHHHHHT-HH..HHHHT-SSHHHHHHHHHHHT---T.HH.H CS
                   Nucleopor_Nup85 235 seqkisgelrdnledllkilsGnes..kileysetWyellvglllYyiPtl.kkle 287
                                       ++++ ++e  +  e+ l++l+G+++    + +  +Wy  ++  ll++ Pt    ++
  gi|474934801|ref|YP_007688383.1|  37 DTTTFNPEDTPTAEKRLRLLCGERDcaVAIGAPVQWYNGVTDSLLFITPTEtFRYD 92 
                                       456678999999*************766677779***************9754445 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1416.58
//
Query:       gi|474934802|ref|YP_007688384.1|  [L=38]
Description: hypothetical protein TALC_01237 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.30s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 255.87
//
Query:       gi|474934803|ref|YP_007688385.1|  [L=56]
Description: hypothetical protein TALC_01239 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0001   22.3   3.6    0.00013   21.9   3.6    1.3  1  DZR             Double zinc ribbon
    0.00035   20.2   6.5     0.0005   19.7   6.5    1.3  1  zinc_ribbon_2   zinc-ribbon domain
    0.00059   19.2   4.0     0.0008   18.7   4.0    1.2  1  zf-ribbon_3     zinc-ribbon domain
  ------ inclusion threshold ------
      0.018   14.9   6.1       0.63   10.0   1.4    2.3  2  Nudix_N_2       Nudix N-terminal
       0.17   11.8   5.1       0.28   11.1   0.2    2.1  2  Prok-RING_1     Prokaryotic RING finger family 1
       0.61   10.1   6.2        4.6    7.2   2.1    2.1  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain


Domain annotation for each model (and alignments):
>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   3.6   4.4e-08   0.00013       1      23 [.      32      54 ..      24      56 .] 0.95

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 4.4e-08
                               DZR  1 CpqCgeelppdarfCseCgtklk 23
                                      C +Cg++++ +++fCs Cg++l+
  gi|474934803|ref|YP_007688385.1| 32 CTECGAANRRGSKFCSCCGSRLR 54
                                      99******************997 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   6.5   1.7e-07    0.0005       1      23 []      31      53 ..      31      53 .. 0.95

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.7e-07
                     zinc_ribbon_2  1 fCpnCGaelqdnakFCpyCGtpl 23
                                      +C++CGa +  ++kFC+ CG+ l
  gi|474934803|ref|YP_007688385.1| 31 YCTECGAANRRGSKFCSCCGSRL 53
                                      8*******************875 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   4.0   2.7e-07    0.0008       2      26 .]      29      53 ..      28      53 .. 0.96

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.7e-07
                       zf-ribbon_3  2 tvrCPnCGa.plssddnvCpyCGtkl 26
                                      tv+C +CGa + + + ++C  CG++l
  gi|474934803|ref|YP_007688385.1| 29 TVYCTECGAaN-RRGSKFCSCCGSRL 53
                                      79*********.***********987 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.2    0.0013       3.9       2       9 ..      31      38 ..      30      42 .. 0.83
   2 ?   10.0   1.4   0.00021      0.63       1      11 [.      44      54 ..      44      56 .] 0.90

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0013
                                      B-TTT--B CS
                         Nudix_N_2  2 FCsqCGtp 9 
                                      +C++CG++
  gi|474934803|ref|YP_007688385.1| 31 YCTECGAA 38
                                      9*****87 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00021
                                      -B-TTT--B-E CS
                         Nudix_N_2  1 kFCsqCGtpve 11
                                      kFCs CG++++
  gi|474934803|ref|YP_007688385.1| 44 KFCSCCGSRLR 54
                                      9*******986 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   9.5e-05      0.28      17      30 ..      26      39 ..      21      42 .. 0.84
   2 ?    3.4   0.7     0.024        73       5      16 ..      44      55 ..      40      56 .] 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.5e-05
                       Prok-RING_1 17 edDiVvCpeCgtpy 30
                                      + D V C+eCg+  
  gi|474934803|ref|YP_007688385.1| 26 QADTVYCTECGAAN 39
                                      579********976 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.024
                       Prok-RING_1  5 kkCpvCgkelke 16
                                      k C++Cg +l++
  gi|474934803|ref|YP_007688385.1| 44 KFCSCCGSRLRN 55
                                      56*****99986 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.2    0.0043        13      44      57 ..      27      40 ..      16      42 .. 0.74
   2 ?    7.2   2.1    0.0015       4.6      27      39 ..      42      54 ..      38      56 .] 0.84

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0043
                    OrfB_Zn_ribbon 44 grtfkCpnCgfead 57
                                       +t++C++Cg+   
  gi|474934803|ref|YP_007688385.1| 27 ADTVYCTECGAANR 40
                                      57888888887654 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0015
                    OrfB_Zn_ribbon 27 TSktCseCgsknk 39
                                       Sk Cs+Cgs+++
  gi|474934803|ref|YP_007688385.1| 42 GSKFCSCCGSRLR 54
                                      59********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 377.18
//
Query:       gi|474934804|ref|YP_007688386.1|  [L=759]
Description: Excinuclease ATPase subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-26   92.5   0.0    5.4e-15   56.1   0.0    3.6  3  ABC_tran         ABC transporter
    8.8e-11   41.6   0.8     0.0012   18.3   0.0    4.1  4  SMC_N            RecF/RecN/SMC N terminal domain
      2e-08   34.8   0.0     0.0034   17.8   0.0    2.7  2  AAA_16           AAA ATPase domain
    1.7e-07   30.9   0.4     0.0033   17.1   0.0    2.5  2  AAA_29           P-loop containing region of AAA domain
      2e-06   27.5   0.0       0.08   12.5   0.0    2.6  2  AAA_25           AAA domain
      2e-05   24.5   9.2      0.081   12.7   0.0    4.1  4  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    8.6e-05   22.8   0.6       0.98    9.8   0.1    3.4  3  DnaJ_CXXCXGXG    DnaJ central domain
      9e-05   22.8   0.0    0.00038   20.8   0.0    2.0  1  UvrA_DNA-bind    UvrA DNA-binding domain
     0.0001   22.3   0.1       0.13   12.1   0.0    2.4  2  RsgA_GTPase      RsgA GTPase
    0.00011   22.4   0.0       0.34   11.1   0.0    2.9  2  AAA_33           AAA domain
    0.00014   21.6   0.0      0.012   15.3   0.1    2.5  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    0.00027   20.6   0.1       0.06   12.9   0.0    2.4  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
    0.00039   20.4   0.0       0.54   10.2   0.1    2.4  2  NACHT            NACHT domain
    0.00067   19.9   0.0       0.63   10.3   0.0    3.1  3  AAA_22           AAA domain
    0.00069   19.0   0.1        1.1    8.5   0.0    2.5  2  ATPase           KaiC
    0.00077   20.0   0.0        4.5    7.8   0.0    3.4  3  AAA_18           AAA domain
     0.0011   18.9   5.1          3    7.9   0.7    3.4  3  Anti-TRAP        Tryptophan RNA-binding attenuator protein in
     0.0015   17.8   0.1       0.52    9.5   0.0    2.8  3  NB-ARC           NB-ARC domain
     0.0024   17.2   0.0       0.79    8.9   0.0    2.3  2  DUF2075          Uncharacterized conserved protein (DUF2075)
     0.0032   17.2   0.2        1.7    8.3   0.0    3.7  4  AAA_15           AAA ATPase domain
     0.0036   17.3   0.0        3.8    7.5   0.0    2.5  2  AAA_14           AAA domain
     0.0097   15.2   0.0       0.48    9.7   0.0    2.4  2  Zeta_toxin       Zeta toxin
  ------ inclusion threshold ------
      0.014   15.3   0.3        1.6    8.6   0.0    2.5  2  APS_kinase       Adenylylsulphate kinase
      0.021   14.6   0.3          6    6.5   0.0    2.6  2  AAA_24           AAA domain
      0.022   14.2   0.1        1.2    8.5   0.0    2.3  2  RecA             recA bacterial DNA recombination protein
      0.027   14.2   0.6          1    9.1   0.1    2.8  3  AAA_30           AAA domain
      0.036   14.3   0.2         29    5.0   0.0    3.2  2  SbcCD_C          Putative exonuclease SbcCD, C subunit
      0.096   12.2   0.0         15    5.0   0.0    2.6  2  AAA_7            P-loop containing dynein motor region
      0.099   12.5   0.0       0.33   10.8   0.0    1.8  2  CPT              Chloramphenicol phosphotransferase-like prot
       0.13   12.8   0.7        4.2    7.8   0.1    2.4  2  AAA_23           AAA domain
       0.17   11.0   0.1        1.5    7.9   0.0    2.1  2  DAP3             Mitochondrial ribosomal death-associated pro
       0.17   10.6   0.0        5.4    5.6   0.0    2.1  2  RNA12            RNA12 protein
       0.24   11.5   0.5         14    5.8   0.0    2.9  2  MMR_HSR1         50S ribosome-binding GTPase
       0.34   10.7   0.9        2.4    7.9   0.1    2.6  3  ATP_bind_1       Conserved hypothetical ATP binding protein


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   5.6e-06     0.003       1      28 [.      16      43 ..      16      54 .. 0.91
   2 !   14.1   0.0   9.7e-05     0.051      79     137 .]     304     371 ..     240     371 .. 0.80
   3 !   56.1   0.0     1e-17   5.4e-15       1     137 []     472     676 ..     472     676 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 5.6e-06
                                      EEEEEEEEETTSEEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  1 lknvslklkegekvaivGenGaGKStLl 28
                                      lk +++++ +g++v++ G +G+GKS+L+
  gi|474934804|ref|YP_007688386.1| 16 LKGIDVDIPKGKIVVLAGVSGSGKSSLA 43
                                      7899**********************95 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 9.7e-05
                                       H.......HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSS..EEEEESTTT CS
                                       x.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxx RF
                          ABC_tran  79 n.......esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpk..llllDEpta 137
                                       +       +  ++i++ l+++ +++l    +++++ sLSgG+ qr++++r l +  +   +++DEpta
  gi|474934804|ref|YP_007688386.1| 304 RiddplgkAIARQISDSLAHMVDVGLGYLSLSRRTDSLSGGEVQRLKMVRHLGSSLSdiTYIFDEPTA 371
                                       14445665677899999********99999*9999***************9976533226899***96 PP

  == domain 3  score: 56.1 bits;  conditional E-value: 1e-17
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       lk+vs+++ +g ++a++G  G+GKStL+  +    +p  + i +d+k++ +++++      gv+    +lf e ++ 
  gi|474934804|ref|YP_007688386.1| 472 LKDVSVTIPKGILTAVTGVAGSGKSTLICQVFASRHP--EAIVIDQKPIGSTSRSTPATYTGVFDRIRKLFAEANNV 546
                                       79**************************999999888..67889*******99999999999999999999999633 PP

                                       HH......................................................................HHHTC CS
                                       xx......................................................................xxxxx RF
                          ABC_tran  78 en......................................................................esdee 84 
                                                                                                                +d++
  gi|474934804|ref|YP_007688386.1| 547 GLewfsfnskggcpickgkgeivpdvafadpvailcegcqgkryndlalsyrykgktieevnnltieqamefFEDRQ 623
                                       3379************************************************9999999988888888777777777 PP

                                       HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  85 iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       i   l+ l ++++   ++++++s+LSgG+ qr++la  l +k  +++lDEpt+
  gi|474934804|ref|YP_007688386.1| 624 IRSRLQCLMDVGMGYMTLGQQTSTLSGGENQRLKLASELHRKGAIYVLDEPTS 676
                                       88888888888899999**********************************96 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1      0.14        76      25      40 ..      27      42 ..       7      48 .. 0.80
   2 !    9.9   0.0   0.00086      0.45     136     211 ..     340     414 ..      98     420 .. 0.78
   3 ?    6.0   0.1     0.013       6.9       9      41 ..     468     499 ..     463     506 .. 0.70
   4 !   18.3   0.0   2.3e-06    0.0012     125     211 ..     617     719 ..     587     725 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.14
                                      SEEEEEESTTSSHHHH CS
                                      xxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnl 40
                                      ++ ++ G  GSGKs+l
  gi|474934804|ref|YP_007688386.1| 27 KIVVLAGVSGSGKSSL 42
                                      478999********98 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00086
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlekadklvgv 211
                                       +LSgGe     l ++  + +      y++De  a L  +  +++ +l+   +++   ++v+ +++ m++ ad+++ +
  gi|474934804|ref|YP_007688386.1| 340 SLSGGEV--QRLKMVRHLGSSLSDITYIFDEPTAGLHPEDASRIGKLMMDLRDKhNTVLVVEHNRLMINLADHVIEI 414
                                       7888874..44555555566667778********************98866554399***************99987 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.013
                                       SETTEECEEEEEETTSSEEEEEESTTSSHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N   9 nFksyagktvilpfsksftaivGpNGSGKsnll 41 
                                       n  ++++ +v++p    +ta++G  GSGKs l+
  gi|474934804|ref|YP_007688386.1| 468 NLHNLKDVSVTIPKG-ILTAVTGVAGSGKSTLI 499
                                       556665444444433.489***********987 PP

  == domain 4  score: 18.3 bits;  conditional E-value: 2.3e-06
                                       HHHHCTT-STT...................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHH CS
                                       xxxxxxxxxxx...................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 125 ellesagiske...................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvael 182
                                       e++e+ +i +                    +LSgGe +     L +A +  ++ ++y+lDe  + L +k v ++ +l
  gi|474934804|ref|YP_007688386.1| 617 EFFEDRQIRSRlqclmdvgmgymtlgqqtsTLSGGENQ----RLKLASELHRKGAIYVLDEPTSGLHAKDVGNLLSL 689
                                       4555555555566666666666666666669*****97....677899999************************** PP

                                       HHHHCTT.SEEEEE-SSHHHCCC-SCEEEE CS
                                       xxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 183 lkekskn.aQfivislreemlekadklvgv 211
                                       l++       +i++ +r em+++ad ++ +
  gi|474934804|ref|YP_007688386.1| 690 LRRMVAAdNTVIIVEHRLEMVSQADWIIDM 719
                                       **76544399**************988765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   9.7e-05     0.051      22      51 ..      24      54 ..      13     101 .. 0.78
   2 !   17.8   0.0   6.4e-06    0.0034      26      89 ..     484     543 ..     467     572 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.7e-05
                            AAA_16 22 grpelvllsGesGvGKsslv.rellralekd 51
                                      + + +v+l G sG+GKssl+ ++++++  ++
  gi|474934804|ref|YP_007688386.1| 24 PKGKIVVLAGVSGSGKSSLAfDTVAKESHRQ 54
                                      45689***************99998887777 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 6.4e-06
                            AAA_16  26 lvllsGesGvGKsslvrellralekdggiflrgkcdql.esaipysalaqalareellrqlldea 89 
                                       l+ ++G +G+GKs+l+ +++ +   + +i++ +k   + ++++p ++++ ++   + +r+l +ea
  gi|474934804|ref|YP_007688386.1| 484 LTAVTGVAGSGKSTLICQVFASRHPE-AIVIDQKPIGStSRSTP-ATYTGVF---DRIRKLFAEA 543
                                       678*************9999666655.9*******999433344.3344444...4466666664 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.1    0.0004      0.21      17      38 ..      21      42 ..      13      49 .. 0.79
   2 !   17.1   0.0   6.3e-06    0.0033       7      39 ..     467     499 ..     463     504 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0004
                            AAA_29 17 ieidlkg.atlltGpsGsGKSTl 38
                                      ++i  kg +++l+G sGsGKS+l
  gi|474934804|ref|YP_007688386.1| 21 VDIP-KGkIVVLAGVSGSGKSSL 42
                                      5665.56699***********98 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 6.3e-06
                            AAA_29   7 vNWgtfdghtieidlkg.atlltGpsGsGKSTll 39 
                                       +N + +++ +++i  kg  t +tG  GsGKSTl+
  gi|474934804|ref|YP_007688386.1| 467 ANLHNLKDVSVTIP-KGiLTAVTGVAGSGKSTLI 499
                                       57777888888886.888***************8 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   0.00015      0.08      30      58 ..      23      51 ..      10      66 .. 0.86
   2 !   12.0   0.0   0.00022      0.11      29      55 ..     478     504 ..     456     507 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00015
                            AAA_25 30 lpagelallaGapgtGKttlaldlalava 58
                                      +p+g++++laG +g+GK+ la d +++ +
  gi|474934804|ref|YP_007688386.1| 23 IPKGKIVVLAGVSGSGKSSLAFDTVAKES 51
                                      8*********************9988765 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00022
                            AAA_25  29 llpagelallaGapgtGKttlaldlal 55 
                                        +p+g l++++G  g+GK+tl +++ +
  gi|474934804|ref|YP_007688386.1| 478 TIPKGILTAVTGVAGSGKSTLICQVFA 504
                                       58*********************9876 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.7       0.5   2.6e+02       1      15 [.      28      42 ..      28      43 .. 0.92
   2 !   12.7   0.0   0.00015     0.081     244     295 ..     348     398 ..     335     406 .. 0.75
   3 ?    1.2   0.8      0.49   2.6e+02       1      16 [.     484     499 ..     484     499 .. 0.92
   4 !   11.4   0.0   0.00039       0.2     246     285 ..     657     693 ..     646     705 .. 0.67

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.5
                            AAA_21  1 lnvliGpNgsGKSnL 15
                                      + vl G  gsGKS+L
  gi|474934804|ref|YP_007688386.1| 28 IVVLAGVSGSGKSSL 42
                                      679**********98 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00015
                            AAA_21 244 llalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQvilt 295
                                        l+++  l + l+   ++++DEp +gLHP+  +r+ +l+ +l+++   v+++
  gi|474934804|ref|YP_007688386.1| 348 RLKMVRHLGSSLSD-ITYIFDEPTAGLHPEDASRIGKLMMDLRDKHNTVLVV 398
                                       44666666666766.899*******************997777766677665 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.49
                            AAA_21   1 lnvliGpNgsGKSnLL 16 
                                       l++++G  gsGKS+L+
  gi|474934804|ref|YP_007688386.1| 484 LTAVTGVAGSGKSTLI 499
                                       6999**********97 PP

  == domain 4  score: 11.4 bits;  conditional E-value: 0.00039
                            AAA_21 246 alltallralkkgsllliDEpEngLHPkllrrllellkel 285
                                       +l++ l+r   kg+++++DEp +gLH k +  ll ll++ 
  gi|474934804|ref|YP_007688386.1| 657 KLASELHR---KGAIYVLDEPTSGLHAKDVGNLLSLLRRM 693
                                       66666665...55*************97666666666443 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0      0.11        58      16      25 ..     136     145 ..     127     161 .. 0.70
   2 ?    4.8   0.0     0.071        37      16      24 ..     264     272 ..     251     289 .. 0.69
   3 !    9.8   0.1    0.0018      0.98      16      50 ..     558     588 ..     543     592 .. 0.60

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.11
                     DnaJ_CXXCXGXG  16 tCktCkGsGv 25 
                                        C++C+G G+
  gi|474934804|ref|YP_007688386.1| 136 MCPDCHGIGK 145
                                       4666666663 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.071
                     DnaJ_CXXCXGXG  16 tCktCkGsG 24 
                                        C+tC+G+G
  gi|474934804|ref|YP_007688386.1| 264 PCDTCGGTG 272
                                       366666666 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.0018
                     DnaJ_CXXCXGXG  16 tCktCkGsGvvreeqktlgpfvqqsqstCpeCeGt 50 
                                        C+ CkG+G+++        f   +   C+ C+G+
  gi|474934804|ref|YP_007688386.1| 558 GCPICKGKGEIVPDVA----FADPVAILCEGCQGK 588
                                       4777777774433331....333445567777776 PP

>> UvrA_DNA-bind  UvrA DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   7.1e-07   0.00038       1     100 [.     150     244 ..     150     257 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 7.1e-07
                                       -S----.-----------GGG..TT-HHHHHHHHHHHTTTS------------S-THHHHH----............ CS
                     UvrA_DNA-bind   1 DpdlvvpdpslslaegAiapwsskkssyyrqlleavaehygidldtpfkeLpeeqkdilLyGsgeekikveyksggr 77 
                                       D d+++ d ++s++e Ai+  + +++s++  l+         d  +++++++e + + l yG +++ +k+ y s+++
  gi|474934804|ref|YP_007688386.1| 150 DIDKML-DLDKSINENAIRFTQFSTGSWQGWLYYHCP---VLDPAKKLRDYSETEWKNLVYGPDTT-VKMMYISNNT 221
                                       788888.99********************99986543...47999*******************85.5666666666 PP

                                       .......---HHHHHHHHHH--- CS
                     UvrA_DNA-bind  78 krsyektfeGvipnlerryrete 100
                                           ++ +eG++p  +r y + +
  gi|474934804|ref|YP_007688386.1| 222 GLGQYTDYEGIVPRFNRLYLSRD 244
                                       6666678**********998765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   0.00025      0.13      88     116 ..      14      43 ..       4      58 .. 0.75
   2 !    7.5   0.0    0.0068       3.6      83     120 ..     465     503 ..     438     523 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00025
                                       TTHHHHHHHCTT.SEEEEECSTTSSHHHHH CS
                       RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLi 116
                                       ++l+ +   + + k++vl+G SG GKS+L 
  gi|474934804|ref|YP_007688386.1|  14 NNLKGIDVDIPKgKIVVLAGVSGSGKSSLA 43 
                                       5666666666555***************96 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0068
                                       -TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase  83 saktkegleelkellkd.ktsvlvGqSGvGKStLinall 120
                                       ++ + ++l++++  + +  ++++ G  G GKStLi ++ 
  gi|474934804|ref|YP_007688386.1| 465 KNANLHNLKDVSVTIPKgILTAVTGVAGSGKSTLICQVF 503
                                       5555667777777776657899************98765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0051       2.7       1      22 [.      28      49 ..      28      92 .. 0.76
   2 !   11.1   0.0   0.00065      0.34       3      31 ..     486     516 ..     484     704 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0051
                            AAA_33  1 lvllvGlpGsGKstlaerllkk 22
                                      +v+l G++GsGKs la   ++k
  gi|474934804|ref|YP_007688386.1| 28 IVVLAGVSGSGKSSLAFDTVAK 49
                                      5899**********99665444 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00065
                            AAA_33   3 llvGlpGsGKstlaerllkklg..avllssd 31 
                                        + G++GsGKstl+ ++ + ++  a+++++ 
  gi|474934804|ref|YP_007688386.1| 486 AVTGVAGSGKSTLICQVFASRHpeAIVIDQK 516
                                       678*************976666588888875 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.094        49       2      18 ..      30      46 ..      29      89 .. 0.79
   2 !   15.3   0.1   2.4e-05     0.012       2      22 ..     486     506 ..     485     533 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.094
                   Viral_helicase1  2 vvhGvpGcGKStlirkl 18
                                      v +Gv G+GKS+l  + 
  gi|474934804|ref|YP_007688386.1| 30 VLAGVSGSGKSSLAFDT 46
                                      789********986554 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2.4e-05
                   Viral_helicase1   2 vvhGvpGcGKStlirkllrts 22 
                                        v Gv+G+GKStli +++ ++
  gi|474934804|ref|YP_007688386.1| 486 AVTGVAGSGKSTLICQVFASR 506
                                       699***********9999883 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.027        14       2      29 ..      28      55 ..      27      57 .. 0.87
   2 !   12.9   0.0   0.00011      0.06       3      28 ..     485     510 ..     483     522 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.027
                                      EEEEEESTTCCHHHHHHHHHCT--SS-E CS
                              cobW  2 vtvltGflGsGKTtLlnhllenraglkl 29
                                      ++vl+G  GsGK++L   ++++++++++
  gi|474934804|ref|YP_007688386.1| 28 IVVLAGVSGSGKSSLAFDTVAKESHRQW 55
                                      689************9999988888776 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00011
                                       EEEEESTTCCHHHHHHHHHCT--SS- CS
                              cobW   3 tvltGflGsGKTtLlnhllenraglk 28 
                                       t +tG  GsGK+tL++++ + r+ + 
  gi|474934804|ref|YP_007688386.1| 485 TAVTGVAGSGKSTLICQVFASRHPEA 510
                                       789***************98877655 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0059       3.1       2      43 ..      28      66 ..      27      98 .. 0.73
   2 !   10.2   0.1     0.001      0.54       3      20 ..     485     502 ..     484     507 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0059
                                      CEEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETT CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalawaegklpqgafklvFflslr 43
                                      +v+l G +GsGK+ L+   + +  +++    + +++++l+ r
  gi|474934804|ref|YP_007688386.1| 28 IVVLAGVSGSGKSSLAFDTVAKESHRQ---WQLSYPLYLRNR 66
                                      699************965554444333...334666666655 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.001
                                       EEEEC-TTTCHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqkl 20 
                                        +++G aGsGK+tL++++
  gi|474934804|ref|YP_007688386.1| 485 TAVTGVAGSGKSTLICQV 502
                                       5799***********997 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0      0.03        16       5      22 ..      26      43 ..      23      85 .. 0.83
   2 !   10.3   0.0    0.0012      0.63       8      42 ..     485     510 ..     481     545 .. 0.76
   3 ?   -2.4   0.0       9.8   5.2e+03      83     123 ..     659     699 ..     649     703 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.03
                            AAA_22  5 agilvvtGesGtGKTtll 22
                                       +i+v+ G sG+GK+ l+
  gi|474934804|ref|YP_007688386.1| 26 GKIVVLAGVSGSGKSSLA 43
                                      6799***********987 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0012
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpev 42 
                                       ++vtG +G+GK+tl+ +++ + +          e 
  gi|474934804|ref|YP_007688386.1| 485 TAVTGVAGSGKSTLICQVFASRHP---------EA 510
                                       78************9988888743.........33 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 9.8
                            AAA_22  83 eqalraravielliiDEaqh.lrs....eealeeLrsllnlsrkgv 123
                                       +  l+++++  + ++DE    l +     ++l+ Lr+++    +++
  gi|474934804|ref|YP_007688386.1| 659 ASELHRKGA--IYVLDEPTSgL-HakdvGNLLSLLRRMVA--ADNT 699
                                       455666666..88999988888.43356777777777766..5555 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0035       1.8      16      36 ..      23      43 ..      16      53 .. 0.89
   2 !    8.5   0.0    0.0021       1.1      16      40 ..     479     504 ..     470     510 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0035
                            ATPase 16 ipegrvvlitGepGtGKtifa 36
                                      ip+g++v ++G++G+GK+ +a
  gi|474934804|ref|YP_007688386.1| 23 IPKGKIVVLAGVSGSGKSSLA 43
                                      8*****************887 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0021
                            ATPase  16 ipegrvvlitGepGtGKtif.alqFl 40 
                                       ip+g  + +tG++G+GK+++ ++ F+
  gi|474934804|ref|YP_007688386.1| 479 IPKGILTAVTGVAGSGKSTLiCQVFA 504
                                       89999************765156565 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0      0.01       5.5       1      16 [.      29      44 ..      29      90 .. 0.87
   2 !    7.8   0.0    0.0085       4.5       3      15 ..     487     499 ..     486     548 .. 0.83
   3 ?   -0.8   0.0       3.9     2e+03      58      99 ..     684     732 ..     657     743 .. 0.51

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.01
                            AAA_18  1 IlltGtpGvGKttlak 16
                                      ++l+G++G+GK++la 
  gi|474934804|ref|YP_007688386.1| 29 VVLAGVSGSGKSSLAF 44
                                      78***********996 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0085
                            AAA_18   3 ltGtpGvGKttla 15 
                                       +tG++G+GK+tl 
  gi|474934804|ref|YP_007688386.1| 487 VTGVAGSGKSTLI 499
                                       9**********85 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 3.9
                            AAA_18  58 dklldaleenssaleegknlvidghlaeleseaakdikk..........vvL 99 
                                        +ll++l++  +  +++ + +i  h+ e++s a+++i +          +  
  gi|474934804|ref|YP_007688386.1| 684 GNLLSLLRRMVA--ADNTV-IIVEHRLEMVSQADWIIDMgpeggnlggrILF 732
                                       444444444433..23344.55555555555554444333555555555555 PP

>> Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.023        12      33      52 ..     137     156 ..     124     161 .. 0.88
   2 ?    5.1   0.1     0.041        22       9      25 ..     261     277 ..     255     283 .. 0.78
   3 !    7.9   0.7    0.0058         3      13      40 ..     559     589 ..     556     595 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.023
                                       -TTTTTSSEEE-HHHHHHHH CS
                         Anti-TRAP  33 CPkCsGkglipTaqGqkLld 52 
                                       CP+C G g  +T +  k+ld
  gi|474934804|ref|YP_007688386.1| 137 CPDCHGIGKRLTVDIDKMLD 156
                                       ************99999988 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.041
                                       CEEE-TTTTTTSEETTE CS
                         Anti-TRAP   9 LEtkCdaCngsGkiepe 25 
                                       +E +Cd+C g+G  + +
  gi|474934804|ref|YP_007688386.1| 261 IEGPCDTCGGTGLNPKA 277
                                       68999999999977655 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0058
                                       -TTTTTTSEETTE..........E-TTTTTSS CS
                         Anti-TRAP  13 CdaCngsGkiepe....eprasleCPkCsGkg 40 
                                       C+ C+g G+i p+    +p  ++ C  C+Gk 
  gi|474934804|ref|YP_007688386.1| 559 CPICKGKGEIVPDvafaDPV-AILCEGCQGKR 589
                                       9*********9998885555.56699999986 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.029        15      21      43 ..      27      49 ..      17      63 .. 0.79
   2 !    9.5   0.0   0.00098      0.52      21      43 ..     483     505 ..     474     510 .. 0.87
   3 ?   -1.3   0.0       1.9     1e+03     151     196 ..     602     651 ..     589     665 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.029
                                      EEEEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC 21 lvvalvGmgGvGKttlakqilnk 43
                                       +v l G  G+GK+ la + + k
  gi|474934804|ref|YP_007688386.1| 27 KIVVLAGVSGSGKSSLAFDTVAK 49
                                      6999************9876666 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00098
                                       EEEEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC  21 lvvalvGmgGvGKttlakqilnk 43 
                                       ++ a+ G +G+GK+tl+ q++ +
  gi|474934804|ref|YP_007688386.1| 483 ILTAVTGVAGSGKSTLICQVFAS 505
                                       56789***************976 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.9
                                       EEEEEESS--HHHHHHHHHHCCTS-GGCHH......CHHHHHHHHHHCTT CS
                            NB-ARC 151 sekievelLekdeawellenkvfekkleekes....leevakeivekckG 196
                                       ++  ev+ L++++a e++e   ++ +l+   +       +++++++ ++G
  gi|474934804|ref|YP_007688386.1| 602 KTIEEVNNLTIEQAMEFFEDRQIRSRLQCLMDvgmgYMTLGQQTSTLSGG 651
                                       66778999**********99998888773333454555555555555555 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.012       6.1       2      27 ..      27      52 ..      26      91 .. 0.82
   2 !    8.9   0.0    0.0015      0.79       5      25 ..     486     506 ..     483     529 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.012
                           DUF2075  2 avvlVtGvaGtGKtvvllnllaeled 27
                                      ++v+  Gv+G+GK+ +++  +a+ ++
  gi|474934804|ref|YP_007688386.1| 27 KIVVLAGVSGSGKSSLAFDTVAKESH 52
                                      68999*************99998733 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0015
                           DUF2075   5 lVtGvaGtGKtvvllnllael 25 
                                        VtGvaG+GK+ +  +++a  
  gi|474934804|ref|YP_007688386.1| 486 AVTGVAGSGKSTLICQVFASR 506
                                       69***************9876 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.2       1.6   8.6e+02      14      39 ..      19      42 ..      14      45 .. 0.72
   2 !    8.3   0.0    0.0032       1.7     324     368 ..     361     404 ..     347     405 .. 0.86
   3 ?    1.4   0.0       0.4   2.1e+02      10      40 ..     468     499 ..     463     510 .. 0.88
   4 ?    1.8   0.0       0.3   1.6e+02     318     362 ..     660     703 ..     633     710 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.6
                            AAA_15 14 lkdveidlseeltvliGkNnsGKSsi 39
                                      ++ v+i+  + + vl G  +sGKSs+
  gi|474934804|ref|YP_007688386.1| 19 ID-VDIPKGK-IVVLAGVSGSGKSSL 42
                                      33.4444444.99************8 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0032
                            AAA_15 324 nvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSphi 368
                                        ++++++EP a LHp+  + + kl+ +l ++++  v++  H+  +
  gi|474934804|ref|YP_007688386.1| 361 DITYIFDEPTAGLHPEDASRIGKLMMDLRDKHN-TVLVVEHNRLM 404
                                       6789***************************99.67777677666 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.4
                            AAA_15  10 NFRslkdveidlsee.ltvliGkNnsGKSsil 40 
                                       N   lkdv++ + +  lt + G  +sGKS+++
  gi|474934804|ref|YP_007688386.1| 468 NLHNLKDVSVTIPKGiLTAVTGVAGSGKSTLI 499
                                       6667899999998889**************86 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.3
                            AAA_15 318 dekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviit 362
                                       +e + k +i++++EP   LH +    l  ll++++  ++  vii 
  gi|474934804|ref|YP_007688386.1| 660 SELHRKGAIYVLDEPTSGLHAKDVGNLLSLLRRMVAADN-TVIIV 703
                                       55567899**************99999999999999988.45554 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0    0.0095         5       2      27 ..      26      51 ..      25      85 .. 0.84
   2 !    7.5   0.0    0.0073       3.8       5      27 ..     485     507 ..     481     542 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0095
                            AAA_14  2 rkilvitGaRrvGKTtllkqlikell 27
                                      +ki+v+ G+  +GK+ l+++ + ++ 
  gi|474934804|ref|YP_007688386.1| 26 GKIVVLAGVSGSGKSSLAFDTVAKES 51
                                      69*****************9988776 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0073
                            AAA_14   5 lvitGaRrvGKTtllkqlikell 27 
                                        ++tG+  +GK+tl+ q++ ++ 
  gi|474934804|ref|YP_007688386.1| 485 TAVTGVAGSGKSTLICQVFASRH 507
                                       689***************98877 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0    0.0009      0.48      16      62 ..      26      71 ..      15      82 .. 0.76
   2 ?    2.8   0.0      0.12        63      18      50 ..     484     514 ..     469     518 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0009
                        Zeta_toxin 16 PklillgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPeye 62
                                       k+++l+G +G+GKs+la ++ ++  ++++    +p  lR++ P+ye
  gi|474934804|ref|YP_007688386.1| 26 GKIVVLAGVSGSGKSSLAFDTVAKE-SHRQWQLSYPLYLRNRMPRYE 71
                                      589**************97776663.355555555666666666665 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.12
                        Zeta_toxin  18 lillgGqpGAGKselaellkdelerqgnvvrld 50 
                                       l  + G  G+GKs+l+  + ++   + +++++d
  gi|474934804|ref|YP_007688386.1| 484 LTAVTGVAGSGKSTLICQVFASR--HPEAIVID 514
                                       5568899********98877774..66666666 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0031       1.6       1      22 [.      25      46 ..      25      61 .. 0.80
   2 ?    4.2   0.1     0.067        35       3      22 ..     483     502 ..     481     513 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0031
                                      S-EEEEEESSTTSSHHHHHHHH CS
                        APS_kinase  1 rgvvvwltGlsgsGKstianal 22
                                      +g +v l+G+sgsGKs++a+  
  gi|474934804|ref|YP_007688386.1| 25 KGKIVVLAGVSGSGKSSLAFDT 46
                                      57899*************9854 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.067
                                       EEEEEESSTTSSHHHHHHHH CS
                        APS_kinase   3 vvvwltGlsgsGKstianal 22 
                                       +   +tG++gsGKst+ +++
  gi|474934804|ref|YP_007688386.1| 483 ILTAVTGVAGSGKSTLICQV 502
                                       55678**********98876 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.024        12       2      20 ..      26      44 ..      25      52 .. 0.85
   2 ?    6.5   0.0     0.011         6       5      30 ..     485     514 ..     481     546 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.024
                            AAA_24  2 klkiliyGpsgiGKTtlak 20
                                      ++ +++ G sg+GK++la 
  gi|474934804|ref|YP_007688386.1| 26 GKIVVLAGVSGSGKSSLAF 44
                                      56799***********997 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.011
                            AAA_24   5 iliyGpsgiGKTtlakel....gpkplfid 30 
                                        +++G +g+GK+tl+ +      p++++id
  gi|474934804|ref|YP_007688386.1| 485 TAVTGVAGSGKSTLICQVfasrHPEAIVID 514
                                       5799***********999999999999997 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0023       1.2      49      78 ..      22      51 ..      11      59 .. 0.87
   2 ?    3.1   0.0       0.1        53      50      76 ..     479     505 ..     470     514 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0023
                                      SEETTSEEEEEESTTSSHHHHHHHHHHHHH CS
                              RecA 49 GlpkGriieiyGpessGkttlalhaiaeaq 78
                                       +pkG+i+ + G+  sGk++la++++a+  
  gi|474934804|ref|YP_007688386.1| 22 DIPKGKIVVLAGVSGSGKSSLAFDTVAKES 51
                                      48************************9865 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.1
                                       EETTSEEEEEESTTSSHHHHHHHHHHH CS
                              RecA  50 lpkGriieiyGpessGkttlalhaiae 76 
                                       +pkG ++ + G+  sGk+tl  ++ a+
  gi|474934804|ref|YP_007688386.1| 479 IPKGILTAVTGVAGSGKSTLICQVFAS 505
                                       8*******************9999886 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.33   1.7e+02      19      34 ..      27      42 ..      23      56 .. 0.83
   2 ?    9.1   0.1    0.0019         1      19      38 ..     483     502 ..     475     512 .. 0.83
   3 ?   -1.5   0.0       3.2   1.7e+03      89     121 ..     665     702 ..     634     751 .. 0.63

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.33
                            AAA_30 19 rvavltGpAGtGKtta 34
                                      +++vl G+ G+GK+ +
  gi|474934804|ref|YP_007688386.1| 27 KIVVLAGVSGSGKSSL 42
                                      589**********986 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0019
                            AAA_30  19 rvavltGpAGtGKttalkal 38 
                                        ++++tG+AG+GK+t++ ++
  gi|474934804|ref|YP_007688386.1| 483 ILTAVTGVAGSGKSTLICQV 502
                                       5789***********98665 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 3.2
                            AAA_30  89 g.tllivDE.agmv...dtkqlaallkaaekagakvil 121
                                       +  +++ DE ++ +   d  +l +ll+++ +a+ +vi+
  gi|474934804|ref|YP_007688386.1| 665 KgAIYVLDEpTSGLhakDVGNLLSLLRRMVAADNTVII 702
                                       33666666632333223333333444444444444444 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.055        29      26      44 ..     334     352 ..     324     373 .. 0.84
   2 ?    4.9   0.1      0.06        32      26      41 ..     641     656 ..     619     692 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.055
                           SbcCD_C  26 lsrssgtlSGGekqflayl 44 
                                       lsr++ +lSGGe q l ++
  gi|474934804|ref|YP_007688386.1| 334 LSRRTDSLSGGEVQRLKMV 352
                                       799**********998766 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.06
                           SbcCD_C  26 lsrssgtlSGGekqfl 41 
                                       l ++++tlSGGe+q l
  gi|474934804|ref|YP_007688386.1| 641 LGQQTSTLSGGENQRL 656
                                       6688999999999865 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.029        15      31      63 ..      24      56 ..      19      60 .. 0.81
   2 ?    4.1   0.0     0.056        29      33      62 ..     482     511 ..     467     530 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.029
                             AAA_7 31 knkkpvllvGptGtGKtviikdllkkldkekyl 63
                                       ++k v+l G +G+GK++++ d++ k ++++++
  gi|474934804|ref|YP_007688386.1| 24 PKGKIVVLAGVSGSGKSSLAFDTVAKESHRQWQ 56
                                      578899*************99977766666665 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.056
                             AAA_7  33 kkpvllvGptGtGKtviikdllkkldkeky 62 
                                       +  + ++G +G+GK+++i +++ + ++e +
  gi|474934804|ref|YP_007688386.1| 482 GILTAVTGVAGSGKSTLICQVFASRHPEAI 511
                                       5556789***********997666665655 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00063      0.33       1      19 [.      26      44 ..      26      90 .. 0.79
   2 ?   -1.9   0.0         5   2.6e+03       7      92 ..     488     503 ..     459     511 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00063
                                      --EEEEEE-TTSSHHHHHH CS
                               CPT  1 ariilLnGgsssGKsslar 19
                                      ++i++L G+s sGKssla 
  gi|474934804|ref|YP_007688386.1| 26 GKIVVLAGVSGSGKSSLAF 44
                                      79**************984 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5
                                       EE-TTSSHHHHHHHHHHHSSS-EEEEEHHHHHHHS-GGGGTSTTSEEEETTSEEE-HHHHHHHHHHHHHHHHHHHTT CS
                               CPT   7 nGgsssGKsslaralqevldepwlhlgvDafvealppkrqdeadglefeteleeigpeldlllaalyeavaamaraG 83 
                                        G++ sGKs+                                                                   
  gi|474934804|ref|YP_007688386.1| 488 TGVAGSGKST------------------------------------------------------------------- 497
                                       3555555555................................................................... PP

                                       -EEEEEE-- CS
                               CPT  84 nnvivDdvi 92 
                                          ++ +v+
  gi|474934804|ref|YP_007688386.1| 498 ---LICQVF 503
                                       ...444444 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1       0.3   1.6e+02      18      35 ..      25      42 ..      14      43 .. 0.79
   2 ?    7.8   0.1    0.0079       4.2      10      37 ..     472     500 ..     463     503 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.3
                            AAA_23 18 skgltlItGpNGaGKTTi 35
                                      + +++++ G  G+GK+++
  gi|474934804|ref|YP_007688386.1| 25 KGKIVVLAGVSGSGKSSL 42
                                      56899***********98 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0079
                            AAA_23  10 frdqeidF.skgltlItGpNGaGKTTild 37 
                                       ++d+++   +  lt++tG  G+GK+T+++
  gi|474934804|ref|YP_007688386.1| 472 LKDVSVTIpKGILTAVTGVAGSGKSTLIC 500
                                       4666666634459**************96 PP

>> DAP3  Mitochondrial ribosomal death-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.53   2.8e+02      25      39 ..      28      42 ..      15      55 .. 0.81
   2 ?    7.9   0.0    0.0028       1.5      28      46 ..     487     505 ..     480     514 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.53
                                      EEEEE-SSSSSTTTT CS
                              DAP3 25 rlvltGekgsGKSvl 39
                                       +vl G  gsGKS l
  gi|474934804|ref|YP_007688386.1| 28 IVVLAGVSGSGKSSL 42
                                      579**********76 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0028
                                       EE-SSSSSTTTTHHHHHHH CS
                              DAP3  28 ltGekgsGKSvlLlqalay 46 
                                       +tG  gsGKS+l++q+ a 
  gi|474934804|ref|YP_007688386.1| 487 VTGVAGSGKSTLICQVFAS 505
                                       89*************9886 PP

>> RNA12  RNA12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.093        49      20      44 ..      29      53 ..      24      59 .. 0.86
   2 ?    5.6   0.0      0.01       5.4      21      58 ..     486     524 ..     478     533 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.093
                             RNA12 20 ivvkGPrGSGkkeLvldrvlkdrkk 44
                                      +v+ G  GSGk++L +d v k++++
  gi|474934804|ref|YP_007688386.1| 29 VVLAGVSGSGKSSLAFDTVAKESHR 53
                                      8999*************99988765 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.01
                             RNA12  21 vvkGPrGSGkkeLvldrvlkdrkkvlvidCdelvk.arn 58 
                                        v+G  GSGk+ L+ +   +++ +++vid + + + +r+
  gi|474934804|ref|YP_007688386.1| 486 AVTGVAGSGKSTLICQVFASRHPEAIVIDQKPIGStSRS 524
                                       699***********6666666677*****9999874555 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1      0.28   1.5e+02       2      16 ..      29      43 ..      28      53 .. 0.88
   2 ?    5.8   0.0     0.027        14       3      29 ..     486     515 ..     484     538 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.28
                                      EEEEESTTSSHHHHH CS
                          MMR_HSR1  2 vaivGrpNvGKStLi 16
                                      v+++G + +GKS+L 
  gi|474934804|ref|YP_007688386.1| 29 VVLAGVSGSGKSSLA 43
                                      799**********95 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.027
                                       EEEESTTSSHHHHHHHHHTS...TEEESSS CS
                          MMR_HSR1   3 aivGrpNvGKStLinaltge...kaivsdk 29 
                                       a+ G   +GKStLi + + +   +aiv d+
  gi|474934804|ref|YP_007688386.1| 486 AVTGVAGSGKSTLICQVFASrhpEAIVIDQ 515
                                       78999*********9998865555666433 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       2.3   1.2e+03       2      13 ..      32      43 ..      31      54 .. 0.84
   2 ?    7.9   0.1    0.0045       2.4       1      17 [.     487     503 ..     487     512 .. 0.82
   3 ?   -1.1   0.0       2.6   1.4e+03     118     170 ..     658     711 ..     607     720 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.3
                        ATP_bind_1  2 vGpaGsGKttfv 13
                                      +G+ GsGK+++ 
  gi|474934804|ref|YP_007688386.1| 32 AGVSGSGKSSLA 43
                                      799******985 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0045
                        ATP_bind_1   1 vvGpaGsGKttfvgals 17 
                                       v+G+aGsGK+t++ ++ 
  gi|474934804|ref|YP_007688386.1| 487 VTGVAGSGKSTLICQVF 503
                                       89*********987664 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 2.6
                        ATP_bind_1 118 Les.efalvvvyLvDsqrltdptkfisgllsalsamlrlelPhvvvlnkfDllk 170
                                       L+s  ++ +++y++D +++   +k + +lls l+ m+ ++ + ++v  ++++++
  gi|474934804|ref|YP_007688386.1| 658 LASeLHRKGAIYVLDEPTSGLHAKDVGNLLSLLRRMVAADNTVIIVEHRLEMVS 711
                                       555456788899999999888888899999999999998888888877777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (759 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                        36  (0.00200792); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              34  [number of targets reported over threshold]
# CPU time: 0.80u 0.33s 00:00:01.13 Elapsed: 00:00:00.52
# Mc/sec: 4412.43
//
Query:       gi|474934805|ref|YP_007688387.1|  [L=282]
Description: isochorismatase family protein Amidases nicotinamidase -like protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-27   96.1   0.1    3.7e-27   95.6   0.1    1.2  1  Isochorismatase  Isochorismatase family
  ------ inclusion threshold ------
      0.052   13.9   0.1       0.82   10.0   0.1    2.6  2  AlbA_2           Putative DNA-binding domain


Domain annotation for each model (and alignments):
>> Isochorismatase  Isochorismatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.6   0.1   4.1e-31   3.7e-27       2     155 ..      12     153 ..      11     169 .. 0.93

  Alignments for each domain:
  == domain 1  score: 95.6 bits;  conditional E-value: 4.1e-31
                   Isochorismatase   2 alvviDmqndfveegvkeseeisavveninkllkaarkagipviftrdvheleevkgdlderkaaphfkpgttgael 78 
                                        lvviD q++f+++  + se+++++v +in+l   +r+ag pv++++++                 +  +gt g e 
  gi|474934805|ref|YP_007688387.1|  12 GLVVIDAQRKFCNDRPDWSEKVDELVFRINRLMFMFRQAGRPVVVVQYEGV------------THCRPYEGTDGDEY 76 
                                       59***********************************************99............3444457******* PP

                   Isochorismatase  79 vpelaplegdvvvdKtrfsafagtdldeiLkelgiktivlaGiatdvCVeatardaldlGyevvvvsDAvaalspel 155
                                       +  la+ +gd+vv+K+++++f++tdl+++L++lg + i+l+G   ++CV++t   ald++  ++ + DA+ +   e 
  gi|474934805|ref|YP_007688387.1|  77 FRGLAVEPGDIVVTKHTMNSFKETDLEDVLRKLGYDMILLCGTVSQYCVMSTYFGALDREIIPYFAHDATISTADEI 153
                                       *********************************************************************98877654 PP

>> AlbA_2  Putative DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.11     1e+03      79     113 ..      44      78 ..      12      80 .. 0.82
   2 ?   10.0   0.1   9.1e-05      0.82      22      40 ..     198     216 ..     187     280 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.11
                            AlbA_2  79 iervelkgkkvlvvkvekskkkplyeneegvvyiR 113
                                       ++ ++  g+ v+vv+ e  +++  ye  +g+ y+R
  gi|474934805|ref|YP_007688387.1|  44 MFMFRQAGRPVVVVQYEGVTHCRPYEGTDGDEYFR 78 
                                       555677888999***99999999999999999998 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 9.1e-05
                            AlbA_2  22 iakticAfaNsegGtlliG 40 
                                       ++ t++A+aN egG+ ++G
  gi|474934805|ref|YP_007688387.1| 198 LICTVAALANGEGGHFMLG 216
                                       899*************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1816.45
//
Query:       gi|474934806|ref|YP_007688388.1|  [L=114]
Description: hypothetical protein TALC_01242 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       242  (0.0134977); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 785.36
//
Query:       gi|474934807|ref|YP_007688389.1|  [L=234]
Description: TPR repeat protein, SEL1 subfamily [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-31  107.1  26.7    1.8e-09   37.9   0.4    5.7  6  Sel1      Sel1 repeat
  ------ inclusion threshold ------
      0.012   16.3   6.0       0.13   12.9   1.2    3.4  3  TPR_16    Tetratricopeptide repeat
      0.046   14.1   0.2         27    5.4   0.0    3.8  4  TPR_17    Tetratricopeptide repeat
       0.14   12.8   5.5         23    5.9   0.1    4.2  4  TPR_6     Tetratricopeptide repeat
        1.5    8.8  17.8        8.2    6.4   0.3    5.1  5  TPR_1     Tetratricopeptide repeat
        6.1    7.2  21.9        6.8    7.1   2.1    5.7  6  TPR_2     Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> Sel1  Sel1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       4.2   1.3e+04      31      38 .]      31      38 ..      31      38 .. 0.82
   2 !   37.9   0.4   6.2e-13   1.8e-09       1      38 []      39      74 ..      39      74 .. 0.96
   3 !   21.4   0.4   9.8e-08   0.00029       2      38 .]      76     110 ..      75     110 .. 0.87
   4 !   19.1   0.2   5.2e-07    0.0015       3      34 ..     113     142 ..     112     145 .. 0.87
   5 !   19.6   0.8   3.5e-07     0.001       7      38 .]     153     182 ..     148     182 .. 0.95
   6 !   26.6   0.1   2.3e-09   6.7e-06       1      37 [.     183     217 ..     183     217 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.2
                              Sel1 31 ekAAeqGd 38
                                      ++AAe G+
  gi|474934807|ref|YP_007688389.1| 31 KQAAEEGS 38
                                      58***996 PP

  == domain 2  score: 37.9 bits;  conditional E-value: 6.2e-13
                              Sel1  1 aeAmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38
                                      aeA++r+G +   + G+ vpk++e A++w++kAA+qG+
  gi|474934807|ref|YP_007688389.1| 39 AEAQFRMGGYS--YWGQIVPKNEEDALKWFRKAADQGH 74
                                      79******777..************************9 PP

  == domain 3  score: 21.4 bits;  conditional E-value: 9.8e-08
                              Sel1   2 eAmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                       +Am  +G +y   + +gv   p++A++w  kAA++G+
  gi|474934807|ref|YP_007688389.1|  76 AAMTEVGRMY--AYSDGVAHSPDLAFKWTYKAAQAGS 110
                                       69*****666..666669****************996 PP

  == domain 4  score: 19.1 bits;  conditional E-value: 5.2e-07
                              Sel1   3 AmyrLGmfylylnGlgvpkDpekAiewyekAA 34 
                                       A+y+LG++y  + G gv +D  +A + y+ A 
  gi|474934807|ref|YP_007688389.1| 113 AYYNLGTLY--EQGIGVSRDLPSAAQMYKVAG 142
                                       9*****888..**********99999998665 PP

  == domain 5  score: 19.6 bits;  conditional E-value: 3.5e-07
                              Sel1   7 LGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                       L+  +ly++G+gvpkD++ A  +  kAA++G+
  gi|474934807|ref|YP_007688389.1| 153 LA--QLYHAGKGVPKDRKAAAGYCIKAADMGN 182
                                       78..999************************7 PP

  == domain 6  score: 26.6 bits;  conditional E-value: 2.3e-09
                              Sel1   1 aeAmyrLGmfylylnGlgvpkDpekAiewyekAAeqG 37 
                                       a A+ + +  ++y++G+gv+kD + A+ +++kA ++G
  gi|474934807|ref|YP_007688389.1| 183 AQACIDTA--MCYYDGDGVEKDDKIALSYFQKALDLG 217
                                       5799999*..666********************9998 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.2   4.4e-05      0.13       1      63 [.      11      72 ..      11      77 .. 0.88
   2 ?    3.7   0.1     0.033        99      31      57 ..     108     138 ..      98     144 .. 0.73
   3 ?   -1.1   0.0         1   3.1e+03      16      28 ..     206     218 ..     205     224 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.4e-05
                            TPR_16  1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrq...grlaeAaalyraalra 63
                                      l+++ +a+++++y++A  a ++a + +   ++ a+++++ g +++ q   ++ ++A+ ++r+a+++
  gi|474934807|ref|YP_007688389.1| 11 LKEGIEAFENKKYAEAYSAIKQAAEEG---SAEAQFRMG-GYSYWGQivpKNEEDALKWFRKAADQ 72
                                      67899**********************...888888888.88888999988888888999998865 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.033
                            TPR_16  31 PdaaeAllllgdaalrq....grlaeAaaly 57 
                                           +A+++lg ++ +      +l+ Aa+ y
  gi|474934807|ref|YP_007688389.1| 108 AGSMQAYYNLGTLYEQGigvsRDLPSAAQMY 138
                                       45889*******9999888877777777665 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1
                            TPR_16  16 Aaaaleaalkrdp 28 
                                       A+ +++ al++++
  gi|474934807|ref|YP_007688389.1| 206 ALSYFQKALDLGR 218
                                       7778888888874 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.1   3.3e+03      19      29 ..      23      33 ..      19      41 .. 0.76
   2 ?    5.4   0.0     0.009        27      14      24 ..     112     122 ..     108     136 .. 0.88
   3 ?    3.6   0.0     0.035     1e+02      13      24 ..     147     158 ..     140     187 .. 0.80
   4 ?   -1.5   0.0       1.4   4.3e+03       7      20 ..     200     213 ..     198     215 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.1
                            TPR_17 19 LAelllknGdl 29
                                      +Ae+++ +++ 
  gi|474934807|ref|YP_007688389.1| 23 YAEAYSAIKQA 33
                                      78888877775 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.009
                            TPR_17  14 daynnLAelll 24 
                                        ay+nL++l++
  gi|474934807|ref|YP_007688389.1| 112 QAYYNLGTLYE 122
                                       59*******97 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.035
                            TPR_17  13 adaynnLAelll 24 
                                       +d y+ LA+l++
  gi|474934807|ref|YP_007688389.1| 147 SDGYHCLAQLYH 158
                                       789********7 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 1.4
                            TPR_17   7 eldPnnadaynnLA 20 
                                       e+d + a +y+++A
  gi|474934807|ref|YP_007688389.1| 200 EKDDKIALSYFQKA 213
                                       66777788999887 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       1.6   4.8e+03      14      26 ..      21      33 ..      11      36 .. 0.62
   2 ?    1.4   0.0      0.21   6.4e+02       1      21 [.      40      64 ..      40      72 .. 0.77
   3 ?    5.9   0.1    0.0076        23       1      23 [.     112     138 ..     112     142 .. 0.75
   4 ?    5.0   0.0     0.015        45       7      28 ..     190     215 ..     188     216 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.6
                                      HHHHHHHHHHHHH CS
                             TPR_6 14 gdtdkAlealerl 26
                                      +++++A  a ++ 
  gi|474934807|ref|YP_007688389.1| 21 KKYAEAYSAIKQA 33
                                      3677776665554 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.21
                                      HHHHHHH.HHHHHH...HHHHHHHH CS
                             TPR_6  1 dAlykla.lsyrkl...gdtdkAle 21
                                      +A+++++ +sy  +   ++ ++Al+
  gi|474934807|ref|YP_007688389.1| 40 EAQFRMGgYSYWGQivpKNEEDALK 64
                                      7999999999998778888888876 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.0076
                                       HHHHHHHHHHHHH....HHHHHHHHHH CS
                             TPR_6   1 dAlyklalsyrkl....gdtdkAleal 23 
                                       +A+y+l+ +y+++     d   A +++
  gi|474934807|ref|YP_007688389.1| 112 QAYYNLGTLYEQGigvsRDLPSAAQMY 138
                                       69*********9766665665666655 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.015
                                       HHHHHHH....HHHHHHHHHHHHHHH CS
                             TPR_6   7 alsyrkl....gdtdkAlealerlik 28 
                                       a++y+ +    +d   Al ++++ ++
  gi|474934807|ref|YP_007688389.1| 190 AMCYYDGdgveKDDKIALSYFQKALD 215
                                       99***99899989999999***9876 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   2.0     0.025        73       8      28 ..      14      34 ..       7      36 .. 0.84
   2 ?    2.0   0.1     0.067     2e+02      18      27 ..      60      69 ..      57      71 .. 0.86
   3 ?    6.4   0.3    0.0028       8.2       2      13 ..     112     123 ..     112     123 .. 0.88
   4 ?   -2.5   0.1       1.9   5.6e+03       2      12 ..     148     158 ..     147     159 .. 0.81
   5 ?    5.3   0.0    0.0063        19      20      30 ..     206     216 ..     201     219 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.025
                                      HHHHHHTT-HHHHHHHHHHHH CS
                             TPR_1  8 GnayfklgkydeAleyyekAL 28
                                      G   f+++ky eA  + ++A 
  gi|474934807|ref|YP_007688389.1| 14 GIEAFENKKYAEAYSAIKQAA 34
                                      88899*********9999996 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.067
                                      HHHHHHHHHH CS
                             TPR_1 18 deAleyyekA 27
                                      ++Al+ ++kA
  gi|474934807|ref|YP_007688389.1| 60 EDALKWFRKA 69
                                      89*******9 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0028
                                       HHHHHHHHHHHH CS
                             TPR_1   2 kalynlGnayfk 13 
                                       +a+ynlG +y +
  gi|474934807|ref|YP_007688389.1| 112 QAYYNLGTLYEQ 123
                                       59********75 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHH CS
                             TPR_1   2 kalynlGnayf 12 
                                       + +  l+++y+
  gi|474934807|ref|YP_007688389.1| 148 DGYHCLAQLYH 158
                                       67889999997 PP

  == domain 5  score: 5.3 bits;  conditional E-value: 0.0063
                                       HHHHHHHHHHH CS
                             TPR_1  20 AleyyekALel 30 
                                       Al y++kAL l
  gi|474934807|ref|YP_007688389.1| 206 ALSYFQKALDL 216
                                       99*******97 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   2.1    0.0023       6.8       2      29 ..       8      35 ..       7      37 .. 0.89
   2 ?    4.2   0.2     0.019        57      16      28 ..      58      70 ..      57      72 .. 0.85
   3 ?    2.3   0.2     0.079   2.4e+02       3      13 ..     113     123 ..     111     124 .. 0.86
   4 ?   -1.2   0.1         1     3e+03       2      12 ..     148     158 ..     147     160 .. 0.83
   5 ?   -2.4   0.0       2.4   7.3e+03       1      12 [.     183     194 ..     183     195 .. 0.78
   6 ?    5.0   0.0      0.01        30      19      30 ..     205     216 ..     200     219 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0023
                             TPR_2  2 ealynlGlayyklgdyeeAleafekAle 29
                                      e +   G  ++++++y+eA  a ++A e
  gi|474934807|ref|YP_007688389.1|  8 EKHLKEGIEAFENKKYAEAYSAIKQAAE 35
                                      667889999****************987 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.019
                             TPR_2 16 dyeeAleafekAl 28
                                      + e+Al++f+kA 
  gi|474934807|ref|YP_007688389.1| 58 NEEDALKWFRKAA 70
                                      6699*******96 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.079
                             TPR_2   3 alynlGlayyk 13 
                                       a+ynlG +y++
  gi|474934807|ref|YP_007688389.1| 113 AYYNLGTLYEQ 123
                                       89****99975 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 1
                             TPR_2   2 ealynlGlayy 12 
                                       +++++l+++y 
  gi|474934807|ref|YP_007688389.1| 148 DGYHCLAQLYH 158
                                       57999***996 PP

  == domain 5  score: -2.4 bits;  conditional E-value: 2.4
                             TPR_2   1 aealynlGlayy 12 
                                       a+a+   +++yy
  gi|474934807|ref|YP_007688389.1| 183 AQACIDTAMCYY 194
                                       567888899998 PP

  == domain 6  score: 5.0 bits;  conditional E-value: 0.01
                             TPR_2  19 eAleafekAlel 30 
                                        Al +f+kAl l
  gi|474934807|ref|YP_007688389.1| 205 IALSYFQKALDL 216
                                       59********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1513.33
//
Query:       gi|474934808|ref|YP_007688390.1|  [L=233]
Description: TPR repeat protein, SEL1 subfamily [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-42  142.3  18.4    2.6e-10   40.6   0.3    6.1  6  Sel1      Sel1 repeat
    7.8e-05   23.2  13.0       0.69   10.6   0.2    4.1  5  TPR_16    Tetratricopeptide repeat
  ------ inclusion threshold ------
       0.19   12.5  11.8        3.1    8.6   0.2    4.8  6  TPR_6     Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> Sel1  Sel1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.1    0.0027        16      14      38 .]      11      37 ..       4      37 .. 0.77
   2 !   40.6   0.3   4.4e-14   2.6e-10       1      38 []      38      73 ..      38      73 .. 0.95
   3 !   26.9   0.1   8.9e-10   5.3e-06       2      37 ..      75     108 ..      74     109 .. 0.91
   4 !   29.7   0.0   1.2e-10   7.2e-07       2      34 ..     111     141 ..     110     144 .. 0.93
   5 !   21.6   0.0   4.2e-08   0.00025       1      38 []     146     181 ..     146     181 .. 0.94
   6 !   26.6   0.6   1.1e-09   6.7e-06       1      34 [.     182     213 ..     182     216 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0027
                              Sel1 14 lnGlgvpk..DpekAiewyekAAeqGd 38
                                      ++Gl   +  D   A+ ++ +AA+ Gd
  gi|474934808|ref|YP_007688390.1| 11 EAGLEAFRqnDLTNAFALLLQAAKEGD 37
                                      56664444568999**********997 PP

  == domain 2  score: 40.6 bits;  conditional E-value: 4.4e-14
                              Sel1  1 aeAmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38
                                      aeA+yr G  ++y+ G+ v kD+++A++w++k+A+q++
  gi|474934808|ref|YP_007688390.1| 38 AEAQYRIG--EFYYWGRVVGKDEKEAFKWFRKSAKQDH 73
                                      79******..666***********************98 PP

  == domain 3  score: 26.9 bits;  conditional E-value: 8.9e-10
                              Sel1   2 eAmyrLGmfylylnGlgvpkDpekAiewyekAAeqG 37 
                                        Am+ +G  ++y  G+ + + p+kA+ew++kAA +G
  gi|474934808|ref|YP_007688390.1|  75 GAMNEVG--LMYASGTQTQRSPDKALEWMKKAALKG 108
                                       59*****..777*********************988 PP

  == domain 4  score: 29.7 bits;  conditional E-value: 1.2e-10
                              Sel1   2 eAmyrLGmfylylnGlgvpkDpekAiewyekAA 34 
                                        A y+LG+fy  + G g p D+++A+++ye+A 
  gi|474934808|ref|YP_007688390.1| 111 QAVYNLGTFY--ERGIGCPVDYKRAVKLYEMAS 141
                                       689*******..********************7 PP

  == domain 5  score: 21.6 bits;  conditional E-value: 4.2e-08
                              Sel1   1 aeAmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                       ++A y L+   l+++G+g ++D+ +A e+ +kAA++G+
  gi|474934808|ref|YP_007688390.1| 146 PSADYSLA--RLLHDGTGCKQDIPRAAELCKKAADKGH 181
                                       578899**..777************************9 PP

  == domain 6  score: 26.6 bits;  conditional E-value: 1.1e-09
                              Sel1   1 aeAmyrLGmfylylnGlgvpkDpekAiewyekAA 34 
                                       a Amy+ G  +ly+nG+g +kD  +A+ +++kA 
  gi|474934808|ref|YP_007688390.1| 182 AQAMYDTG--LLYYNGDGFEKDDGEALIYFQKAR 213
                                       68******..777*******************95 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   4.9   0.00013      0.77       3      62 ..      12      70 ..      10      76 .. 0.85
   2 !    6.6   0.0    0.0021        12      18      66 ..      60     111 ..      59     113 .. 0.88
   3 ?    2.7   0.0     0.034   2.1e+02      13      59 ..      94     139 ..      89     146 .. 0.73
   4 !    5.5   0.1    0.0046        28      12      62 ..     129     178 ..     128     180 .. 0.89
   5 !   10.6   0.2   0.00011      0.69      12      60 ..     165     212 ..     163     221 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00013
                            TPR_16  3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaal.rq...grlaeAaalyraalr 62
                                      ++++a+r++d + A a+l +a k +     +aeA++  g+ ++  +   ++ +eA  ++r+ ++
  gi|474934808|ref|YP_007688390.1| 12 AGLEAFRQNDLTNAFALLLQAAKEG-----DAEAQYRIGEFYYwGRvvgKDEKEAFKWFRKSAK 70
                                      7999*********************.....************9655786666666699998775 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0021
                            TPR_16  18 aaleaalkrdpssPdaaeAllllgdaalrq....grlaeAaalyraal.raapd 66 
                                       +a+++++k+++   d+a A+++ g++++         ++A+++ ++a+ +  p+
  gi|474934808|ref|YP_007688390.1|  60 EAFKWFRKSAK--QDHAGAMNEVGLMYASGtqtqRSPDKALEWMKKAAlKGFPQ 111
                                       68999999998..88*************99899999999999999998777776 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.034
                            TPR_16  13 yddAaaal.eaalkrdpssPdaaeAllllgdaalrq....grlaeAaalyra 59 
                                       +d+A++   +aalk +   P+   A ++lg  + r      ++++A+ ly+ 
  gi|474934808|ref|YP_007688390.1|  94 PDKALEWMkKAALKGF---PQ---AVYNLGTFYERGigcpVDYKRAVKLYEM 139
                                       5555555556777777...76...9999998888888888888888888776 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.0046
                            TPR_16  12 dyddAaaaleaalkrdpssPdaaeAllllgdaalrq....grlaeAaalyraalr 62 
                                       dy +A++++e a   +      + A + l++++       ++ ++Aa+l+++a++
  gi|474934808|ref|YP_007688390.1| 129 DYKRAVKLYEMASQVG-----LPSADYSLARLLHDGtgckQDIPRAAELCKKAAD 178
                                       6888888898888888.....999**********999**************9986 PP

  == domain 5  score: 10.6 bits;  conditional E-value: 0.00011
                            TPR_16  12 dyddAaaaleaalkrdpssPdaaeAllllgdaalrq....grlaeAaalyraa 60 
                                       d ++Aa++ + a +++     +a+A++  g++++      ++  eA+ ++++a
  gi|474934808|ref|YP_007688390.1| 165 DIPRAAELCKKAADKG-----HAQAMYDTGLLYYNGdgfeKDDGEALIYFQKA 212
                                       778999999*******.....*************9999999999999999987 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.2      0.62   3.7e+03      11      25 ..      17      31 ..       4      35 .. 0.61
   2 ?    4.5   0.0     0.011        66       1      16 [.      39      58 ..      39      77 .. 0.79
   3 ?   -3.3   0.0         3   1.8e+04       7      18 ..      81      92 ..      80      93 .. 0.72
   4 ?    4.5   0.0     0.011        64       1      25 [.     111     139 ..     111     142 .. 0.87
   5 ?   -2.3   0.0       1.6   9.4e+03       7      25 ..     153     175 ..     148     179 .. 0.52
   6 ?    8.6   0.2   0.00052       3.1       1      26 [.     183     212 ..     183     215 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.62
                                      HHHHHHHHHHHHHHH CS
                             TPR_6 11 rklgdtdkAlealer 25
                                      ++++d ++A ++l +
  gi|474934808|ref|YP_007688390.1| 17 FRQNDLTNAFALLLQ 31
                                      344677777776654 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.011
                                      HHHHHHHHHHHHH....HHH CS
                             TPR_6  1 dAlyklalsyrkl....gdt 16
                                      +A+y++++ y+ +    +d 
  gi|474934808|ref|YP_007688390.1| 39 EAQYRIGEFYYWGrvvgKDE 58
                                      79********9875664344 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 3
                                      HHHHHHHHHHHH CS
                             TPR_6  7 alsyrklgdtdk 18
                                      +l y ++++t++
  gi|474934808|ref|YP_007688390.1| 81 GLMYASGTQTQR 92
                                      666777889876 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHHHH...H.HHHHHHHHHHH CS
                             TPR_6   1 dAlyklalsyrkl...g.dtdkAlealer 25 
                                       +A y+l+  y+++     d+ +A++++e 
  gi|474934808|ref|YP_007688390.1| 111 QAVYNLGTFYERGigcPvDYKRAVKLYEM 139
                                       6889****9*99889977999*****996 PP

  == domain 5  score: -2.3 bits;  conditional E-value: 1.6
                                       HHHHHHH....HHHHHHHHHHHH CS
                             TPR_6   7 alsyrkl....gdtdkAlealer 25 
                                       a+++  +    +d  +A e+ ++
  gi|474934808|ref|YP_007688390.1| 153 ARLLHDGtgckQDIPRAAELCKK 175
                                       54444433444466667666555 PP

  == domain 6  score: 8.6 bits;  conditional E-value: 0.00052
                                       HHHHHHHHHHHHH....HHHHHHHHHHHHH CS
                             TPR_6   1 dAlyklalsyrkl....gdtdkAlealerl 26 
                                       +A+y  +l+y+++    +d  +Al ++++ 
  gi|474934808|ref|YP_007688390.1| 183 QAMYDTGLLYYNGdgfeKDDGEALIYFQKA 212
                                       69**********9888777779**9*9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.31s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1584.31
//
Query:       gi|474934809|ref|YP_007688391.1|  [L=274]
Description: TPR repeat protein, SEL1 subfamily [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.8e-40  134.6  14.2    3.2e-08   34.0   0.2    6.3  6  Sel1      Sel1 repeat


Domain annotation for each model (and alignments):
>> Sel1  Sel1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0   0.00025       4.6      19      38 .]      60      79 ..      46      79 .. 0.90
   2 !   25.7   0.0   7.5e-10   1.3e-05       3      38 .]      82     115 ..      80     115 .. 0.94
   3 !   20.4   0.0   3.5e-08   0.00062       2      35 ..     117     148 ..     116     151 .. 0.87
   4 !   31.9   0.0   8.3e-12   1.5e-07       2      37 ..     153     186 ..     152     187 .. 0.93
   5 !   19.9   0.8   4.7e-08   0.00084       2      38 .]     189     223 ..     188     223 .. 0.93
   6 !   34.0   0.2   1.8e-12   3.2e-08       1      37 [.     224     258 ..     224     259 .. 0.94

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00025
                              Sel1 19 vpkDpekAiewyekAAeqGd 38
                                      +++ p+++++++e+AA+ G+
  gi|474934809|ref|YP_007688391.1| 60 IERSPIEGYRFMEMAADSGY 79
                                      7899*************996 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 7.5e-10
                              Sel1   3 AmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                       A+y +G f+   +G g  + pekA  w+++AAeqG+
  gi|474934809|ref|YP_007688391.1|  82 AQYCMGIFC--STGFGCNASPEKAKDWFQMAAEQGH 115
                                       9999**777..************************9 PP

  == domain 3  score: 20.4 bits;  conditional E-value: 3.5e-08
                              Sel1   2 eAmyrLGmfylylnGlgvpkDpekAiewyekAAe 35 
                                        +++ LG   +y +G+g +kD ++A+ew  kAA 
  gi|474934809|ref|YP_007688391.1| 117 QSQNELG--VIYREGKGCKKDDDLAFEWIWKAAI 148
                                       589****..777****************988885 PP

  == domain 4  score: 31.9 bits;  conditional E-value: 8.3e-12
                              Sel1   2 eAmyrLGmfylylnGlgvpkDpekAiewyekAAeqG 37 
                                        A+y+L+   +y++G g+      A++wy +AA+qG
  gi|474934809|ref|YP_007688391.1| 153 NAQYNLA--VMYETGEGTSVSMGDAFKWYSQAASQG 186
                                       6******..777***********************9 PP

  == domain 5  score: 19.9 bits;  conditional E-value: 4.7e-08
                              Sel1   2 eAmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                       eA+y LG   ly+ G+g+  +  kA  wy  AA+ G+
  gi|474934809|ref|YP_007688391.1| 189 EAQYCLG--ALYHLGKGTAENHTKAAFWYGEAARSGH 223
                                       8******..666****99*****************98 PP

  == domain 6  score: 34.0 bits;  conditional E-value: 1.8e-12
                              Sel1   1 aeAmyrLGmfylylnGlgvpkDpekAiewyekAAeqG 37 
                                       ++A y+LG  ++y++G+g+p+D+ekA  ++e AA++G
  gi|474934809|ref|YP_007688391.1| 224 PDAEYNLG--LMYMEGDGIPADYEKASALFESAASKG 258
                                       68******..777**********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1852.08
//
Query:       gi|474934810|ref|YP_007688392.1|  [L=197]
Description: Sel1 repeat protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.7e-46  153.3   7.7    9.4e-12   45.2   0.6    5.1  5  Sel1      Sel1 repeat
    6.7e-05   23.4   5.6      0.069   13.8   0.1    3.4  3  TPR_16    Tetratricopeptide repeat
    0.00018   21.7   0.1       0.29   11.4   0.0    3.3  4  Flu_M1_C  Influenza Matrix protein (M1) C-terminal domain
     0.0027   17.2   0.3        0.2   11.1   0.0    3.0  3  SPO22     Meiosis protein SPO22/ZIP4 like
     0.0086   16.6   3.3        2.5    8.7   0.1    4.1  4  TPR_19    Tetratricopeptide repeat
  ------ inclusion threshold ------
       0.01   15.5   9.0        5.2    6.8   0.1    5.9  5  TPR_11    TPR repeat
      0.053   13.7  12.3         41    4.6   0.1    6.6  8  TPR_2     Tetratricopeptide repeat
      0.089   13.5   4.7         12    6.7   0.0    4.0  4  TPR_6     Tetratricopeptide repeat
      0.092   13.1   1.7          8    6.9   0.0    2.7  3  TPR_20    Tetratricopeptide repeat
       0.21   11.5   0.0         23    4.9   0.0    3.0  3  NIL       NIL domain
       0.28   11.4   1.5          2    8.7   0.1    2.7  4  ANAPC3    Anaphase-promoting complex, cyclosome, subunit 3
        1.7    9.1  10.7         18    5.8   0.1    5.4  7  TPR_8     Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> Sel1  Sel1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.071   1.1e+02      23      38 .]      22      37 ..      13      37 .. 0.85
   2 !   38.6   0.1   7.7e-13   1.1e-09       1      37 [.      38      72 ..      38      73 .. 0.96
   3 !   29.2   0.0     7e-10     1e-06       1      36 [.      74     107 ..      74     109 .. 0.94
   4 !   37.4   0.0   1.8e-12   2.7e-09       1      38 []     110     145 ..     110     145 .. 0.91
   5 !   45.2   0.6   6.3e-15   9.4e-12       2      38 .]     147     181 ..     146     181 .. 0.95

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.071
                              Sel1 23 pekAiewyekAAeqGd 38
                                      +++A+ ++++AA++++
  gi|474934810|ref|YP_007688392.1| 22 YDQAVMFLKMAAQRNN 37
                                      789*********9875 PP

  == domain 2  score: 38.6 bits;  conditional E-value: 7.7e-13
                              Sel1  1 aeAmyrLGmfylylnGlgvpkDpekAiewyekAAeqG 37
                                      ++A+y LG  ++y  G+gvp   e+A++w++kAAe+G
  gi|474934810|ref|YP_007688392.1| 38 PSAQYVLG--QMYASGKGVPESMEEAVKWFRKAAENG 72
                                      69******..888**********************99 PP

  == domain 3  score: 29.2 bits;  conditional E-value: 7e-10
                              Sel1   1 aeAmyrLGmfylylnGlgvpkDpekAiewyekAAeq 36 
                                       ++A ++LG   +y+nG gv++D++ A+e+++ AAe 
  gi|474934810|ref|YP_007688392.1|  74 PYANADLG--VCYFNGMGVDADVNTALEYFRTAAES 107
                                       68999***..999*********************96 PP

  == domain 4  score: 37.4 bits;  conditional E-value: 1.8e-12
                              Sel1   1 aeAmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                       +eA+  LG   +y +G+gv+kD+++A++w++kAAe+G+
  gi|474934810|ref|YP_007688392.1| 110 PEAQLCLG--NMYITGDGVKKDQIEAVKWFRKAAERGN 145
                                       688888**..556***********************97 PP

  == domain 5  score: 45.2 bits;  conditional E-value: 6.3e-15
                              Sel1   2 eAmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                       +A++++G   +y+nG+gv+kD ++A++wy++AAeqGd
  gi|474934810|ref|YP_007688392.1| 147 DAQFNMG--AAYENGDGVDKDLNEALRWYRLAAEQGD 181
                                       7******..777************************7 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   4.6e-05     0.069       2      65 ..      11      73 ..      10      76 .. 0.85
   2 ?    4.4   0.1      0.04        60      14      61 ..      95     141 ..      91     144 .. 0.76
   3 !    6.7   1.7    0.0077        12      16      66 ..     133     182 ..     131     184 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.6e-05
                            TPR_16  2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrq....grlaeAaalyraalraap 65
                                      + a+ ++++  yd+A+  l+ a  r+     ++ A++ lg++++        ++eA+ ++r+a+++++
  gi|474934810|ref|YP_007688392.1| 11 DNALRLIENESYDQAVMFLKMAAQRN-----NPSAQYVLGQMYASGkgvpESMEEAVKWFRKAAENGM 73
                                      67888999999999996666666777.....888**********999****************99986 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.04
                            TPR_16  14 ddAaaaleaalkrdpssPdaaeAllllgdaalrq....grlaeAaalyraal 61 
                                         A++++++a +++      +eA+l lg+++       ++  eA+ ++r+a+
  gi|474934810|ref|YP_007688392.1|  95 NTALEYFRTAAESN-----VPEAQLCLGNMYITGdgvkKDQIEAVKWFRKAA 141
                                       5699**********.....999999999988766666666666666666665 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0077
                            TPR_16  16 AaaaleaalkrdpssPdaaeAllllgdaalrq....grlaeAaalyraalraapd 66 
                                       A++ ++ a +r+     +++A+++ g a+       ++l eA+ +yr a++++  
  gi|474934810|ref|YP_007688392.1| 133 AVKWFRKAAERG-----NVDAQFNMGAAYENGdgvdKDLNEALRWYRLAAEQGDA 182
                                       555577777777.....*************999****************987655 PP

>> Flu_M1_C  Influenza Matrix protein (M1) C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.26   3.9e+02      40      85 ..      23      67 ..      16      75 .. 0.78
   2 ?   -0.8   0.0       1.2   1.8e+03      61      81 ..      79      99 ..      46     110 .. 0.68
   3 ?    5.3   0.0     0.016        23      57      85 ..     111     139 ..      78     143 .. 0.73
   4 !   11.4   0.0   0.00019      0.29      53      84 ..     143     174 ..     138     187 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.26
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Flu_M1_C 40 ekaeevqklaeelrqnvqvlrslGasqksseGlkkdllevlkayqk 85
                                      ++a    k+a + r+n  +   lG    s++G+ + + e +k ++k
  gi|474934810|ref|YP_007688392.1| 23 DQAVMFLKMAAQ-RNNPSAQYVLGQMYASGKGVPESMEEAVKWFRK 67
                                      566666677766.6778889999999999***99999999887665 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.2
                                      XXXXXXXXXXXXXXXXXXXXX CS
                          Flu_M1_C 61 slGasqksseGlkkdllevlk 81
                                       lG    ++ G+  d+   l+
  gi|474934810|ref|YP_007688392.1| 79 DLGVCYFNGMGVDADVNTALE 99
                                      566677777888888776666 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.016
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Flu_M1_C  57 qvlrslGasqksseGlkkdllevlkayqk 85 
                                       ++   lG    +++G+kkd +e +k ++k
  gi|474934810|ref|YP_007688392.1| 111 EAQLCLGNMYITGDGVKKDQIEAVKWFRK 139
                                       456679999999***********997766 PP

  == domain 4  score: 11.4 bits;  conditional E-value: 0.00019
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Flu_M1_C  53 rqnvqvlrslGasqksseGlkkdllevlkayq 84 
                                       r nv++   +Ga  ++++G+ kdl e l+ y+
  gi|474934810|ref|YP_007688392.1| 143 RGNVDAQFNMGAAYENGDGVDKDLNEALRWYR 174
                                       678999999*******************9875 PP

>> SPO22  Meiosis protein SPO22/ZIP4 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00013       0.2       5      64 ..      19      70 ..      12      76 .. 0.87
   2 ?    0.8   0.0      0.19   2.8e+02      39      66 ..     119     144 ..      92     158 .. 0.71
   3 ?    1.8   0.0     0.095   1.4e+02     261     275 ..     163     177 ..     148     178 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00013
                             SPO22  5 egdldlAehmlskakceenllrldpeeaeeLarllyniGksllskkkyeeavkWLqrald 64
                                      ++ +d A+++l+ a      ++ + ++a+++  ++y  Gk +   ++ eeavkW+++a +
  gi|474934810|ref|YP_007688392.1| 19 NESYDQAVMFLKMA------AQRNNPSAQYVLGQMYASGKGVP--ESMEEAVKWFRKAAE 70
                                      56778888888774......4667999****************..99**********976 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.19
                             SPO22  39 lyniGksllskkkyeeavkWLqraldil 66 
                                       +y  G  +   k+  eavkW+++a + +
  gi|474934810|ref|YP_007688392.1| 119 MYITGDGVK--KDQIEAVKWFRKAAERG 144
                                       444444444..66667779999987755 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.095
                             SPO22 261 aknydeAaewyelsl 275
                                        k+ +eA++wy+l+ 
  gi|474934810|ref|YP_007688392.1| 163 DKDLNEALRWYRLAA 177
                                       6999********995 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.1    0.0017       2.5       1      35 [.      16      48 ..      16      59 .. 0.86
   2 ?    4.6   0.0     0.031        46       8      36 ..      59      85 ..      55      87 .. 0.88
   3 ?   -0.1   0.0      0.94   1.4e+03       6      35 ..      93     120 ..      88     123 .. 0.73
   4 ?   -0.0   0.2      0.88   1.3e+03      10      35 ..     133     156 ..     129     189 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0017
                            TPR_19  1 llaegdyaeAlalleqalqedpknaearllLAeal 35
                                      l++++ y++A+ +l+ a q   +n+ a++ L + +
  gi|474934810|ref|YP_007688392.1| 16 LIENESYDQAVMFLKMAAQR--NNPSAQYVLGQMY 48
                                      7899************9666..8999999998877 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.031
                            TPR_19  8 aeAlalleqalqedpknaearllLAeall 36
                                      +eA++ +++a  +++++++a ++L  +++
  gi|474934810|ref|YP_007688392.1| 59 EEAVKWFRKA--AENGMPYANADLGVCYF 85
                                      7999999997..7889************8 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.94
                            TPR_19   6 dyaeAlalleqalqedpknaearllLAeal 35 
                                       d   Al++++ a  ++ + +ea+l L + +
  gi|474934810|ref|YP_007688392.1|  93 DVNTALEYFRTA--AESNVPEAQLCLGNMY 120
                                       667899999997..5666777777666666 PP

  == domain 4  score: -0.0 bits;  conditional E-value: 0.88
                            TPR_19  10 AlalleqalqedpknaearllLAeal 35 
                                       A++ +++a  ++ +n +a+ ++  a+
  gi|474934810|ref|YP_007688392.1| 133 AVKWFRKA--AERGNVDAQFNMGAAY 156
                                       55555554..3445555555554444 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1     0.028        41      25      39 ..      35      49 ..      13      50 .. 0.86
   2 ?    2.3   0.0     0.091   1.4e+02      11      21 ..      59      69 ..      56      70 .. 0.87
   3 ?    0.3   0.0      0.37   5.6e+02      26      38 ..     108     120 ..      95     122 .. 0.85
   4 ?    6.8   0.1    0.0035       5.2      26      39 ..     144     157 ..     128     159 .. 0.76
   5 ?    1.4   0.1      0.17   2.6e+02       9      20 ..     165     176 ..     164     179 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.028
                            TPR_11 25 PdnaeayynLGlayy 39
                                       +n++a y LG+ y+
  gi|474934810|ref|YP_007688392.1| 35 RNNPSAQYVLGQMYA 49
                                      69*********9885 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.091
                            TPR_11 11 eeAieaYkkAl 21
                                      eeA+++++kA 
  gi|474934810|ref|YP_007688392.1| 59 EEAVKWFRKAA 69
                                      9********96 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.37
                            TPR_11  26 dnaeayynLGlay 38 
                                       + +ea ++LG+ y
  gi|474934810|ref|YP_007688392.1| 108 NVPEAQLCLGNMY 120
                                       55999999*9977 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.0035
                            TPR_11  26 dnaeayynLGlayy 39 
                                        n++a +n+G+ay 
  gi|474934810|ref|YP_007688392.1| 144 GNVDAQFNMGAAYE 157
                                       599**********7 PP

  == domain 5  score: 1.4 bits;  conditional E-value: 0.17
                            TPR_11   9 kyeeAieaYkkA 20 
                                       +++eA+ +Y+ A
  gi|474934810|ref|YP_007688392.1| 165 DLNEALRWYRLA 176
                                       699******966 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       4.6   6.8e+03       3      12 ..      40      49 ..      38      50 .. 0.79
   2 ?    4.6   0.1     0.027        41      18      29 ..      59      70 ..      58      71 .. 0.91
   3 ?   -0.8   0.0       1.5   2.3e+03       2      13 ..      75      86 ..      74      86 .. 0.81
   4 ?    2.0   0.0      0.19   2.8e+02      19      29 ..      96     106 ..      93     108 .. 0.81
   5 ?   -2.0   0.0       3.7   5.5e+03       1      11 [.     110     120 ..     110     121 .. 0.80
   6 ?    3.8   0.2      0.05        74      18      29 ..     131     142 ..     127     143 .. 0.83
   7 ?    0.4   0.0      0.62   9.3e+02       2      13 ..     147     158 ..     146     160 .. 0.84
   8 ?    3.7   0.1     0.054        81      15      29 ..     164     178 ..     162     180 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4.6
                             TPR_2  3 alynlGlayy 12
                                      a y lG+ y+
  gi|474934810|ref|YP_007688392.1| 40 AQYVLGQMYA 49
                                      7899999986 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.027
                             TPR_2 18 eeAleafekAle 29
                                      eeA+++f+kA e
  gi|474934810|ref|YP_007688392.1| 59 EEAVKWFRKAAE 70
                                      8*********86 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.5
                             TPR_2  2 ealynlGlayyk 13
                                      +a+  lG +y++
  gi|474934810|ref|YP_007688392.1| 75 YANADLGVCYFN 86
                                      67889*****85 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.19
                             TPR_2  19 eAleafekAle 29 
                                        Ale+f+ A e
  gi|474934810|ref|YP_007688392.1|  96 TALEYFRTAAE 106
                                       59******987 PP

  == domain 5  score: -2.0 bits;  conditional E-value: 3.7
                             TPR_2   1 aealynlGlay 11 
                                       +ea  +lG+ y
  gi|474934810|ref|YP_007688392.1| 110 PEAQLCLGNMY 120
                                       57889999998 PP

  == domain 6  score: 3.8 bits;  conditional E-value: 0.05
                             TPR_2  18 eeAleafekAle 29 
                                        eA+++f+kA e
  gi|474934810|ref|YP_007688392.1| 131 IEAVKWFRKAAE 142
                                       69********87 PP

  == domain 7  score: 0.4 bits;  conditional E-value: 0.62
                             TPR_2   2 ealynlGlayyk 13 
                                       +a +n+G ay++
  gi|474934810|ref|YP_007688392.1| 147 DAQFNMGAAYEN 158
                                       6899*****975 PP

  == domain 8  score: 3.7 bits;  conditional E-value: 0.054
                             TPR_2  15 gdyeeAleafekAle 29 
                                       +d++eAl++++ A e
  gi|474934810|ref|YP_007688392.1| 164 KDLNEALRWYRLAAE 178
                                       6899******99976 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       2.1   3.1e+03      16      29 ..      22      35 ..      13      38 .. 0.76
   2 ?   -1.0   0.0       2.5   3.7e+03       2      14 ..      40      52 ..      39      70 .. 0.72
   3 ?    6.7   0.0    0.0083        12       6      27 ..      80     105 ..      75     108 .. 0.78
   4 ?    5.6   0.3     0.019        29       1      20 [.     147     170 ..     147     193 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 2.1
                                      HHHHHHHHHHHHHH CS
                             TPR_6 16 tdkAlealerlike 29
                                      +d+A+  l+   ++
  gi|474934810|ref|YP_007688392.1| 22 YDQAVMFLKMAAQR 35
                                      78999888877665 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.5
                                      HHHHHHHHHHHHH CS
                             TPR_6  2 Alyklalsyrklg 14
                                      A+y l++ y +++
  gi|474934810|ref|YP_007688392.1| 40 AQYVLGQMYASGK 52
                                      7888999998864 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0083
                                       HHHHHHH.HH.HHH..HHHHHHHHHH CS
                             TPR_6   6 lalsyrk.lg.dtd..kAlealerli 27 
                                       l+ +y++ +g d+d  +Ale+++   
  gi|474934810|ref|YP_007688392.1|  80 LGVCYFNgMGvDADvnTALEYFRTAA 105
                                       89*****775555555******9876 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.019
                                       HHHHHHHHHHHHH....HHHHHHH CS
                             TPR_6   1 dAlyklalsyrkl....gdtdkAl 20 
                                       dA+++++ +y+++    +d  +Al
  gi|474934810|ref|YP_007688392.1| 147 DAQFNMGAAYENGdgvdKDLNEAL 170
                                       89*********9866665555665 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       1.3     2e+03      23      45 ..       7      29 ..       2      36 .. 0.69
   2 ?    6.9   0.0    0.0054         8      14      53 ..      30      69 ..      18      78 .. 0.90
   3 ?    4.3   0.7     0.033        50      16      62 ..     140     186 ..     127     196 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.3
                            TPR_20 23 darldlAlallaagryeeAleqL 45
                                      d +ld Al l++++ y++A+  L
  gi|474934810|ref|YP_007688392.1|  7 DPELDNALRLIENESYDQAVMFL 29
                                      45678888888888888887655 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0054
                            TPR_20 14 alaanpddldarldlAlallaagryeeAleqLleilkrdr 53
                                      ++aa+ ++  a++ l + +++++ + e++e+ ++++++  
  gi|474934810|ref|YP_007688392.1| 30 KMAAQRNNPSAQYVLGQMYASGKGVPESMEEAVKWFRKAA 69
                                      689999***************************9999765 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.033
                            TPR_20  16 aanpddldarldlAlallaagryeeAleqLleilkrdrkweddaark 62 
                                       aa+  ++da++++  a+  +  +++ l++ l++ +   +  d +ark
  gi|474934810|ref|YP_007688392.1| 140 AAERGNVDAQFNMGAAYENGDGVDKDLNEALRWYRLAAEQGDASARK 186
                                       67889***************************999999999999998 PP

>> NIL  NIL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.015        23      42      67 ..      43      68 ..      40      71 .. 0.91
   2 ?   -1.0   0.0         1   1.6e+03      54      66 ..      91     103 ..      83     106 .. 0.83
   3 ?    2.3   0.0       0.1   1.5e+02      43      66 ..     116     139 ..     114     147 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.015
                                      EEEEEEEEEES-HHHHHHHHHHHHHT CS
                               NIL 42 pfGqlvielsgsqesiaaalqylrkr 67
                                      ++Gq+  + +g +es ++a++++rk 
  gi|474934810|ref|YP_007688392.1| 43 VLGQMYASGKGVPESMEEAVKWFRKA 68
                                      68**********************96 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1
                                       HHHHHHHHHHHHH CS
                               NIL  54 qesiaaalqylrk 66 
                                       ++++++al+y+r 
  gi|474934810|ref|YP_007688392.1|  91 DADVNTALEYFRT 103
                                       578999****996 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.1
                                       EEEEEEEEES.-HHHHHHHHHHHHH CS
                               NIL  43 fGqlvielsg.sqesiaaalqylrk 66 
                                       +G++ i+  g ++++i+a++ ++rk
  gi|474934810|ref|YP_007688392.1| 116 LGNMYITGDGvKKDQIEAVK-WFRK 139
                                       699*******7777777665.5554 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1    0.0014         2       2      49 ..      19      68 ..      10      76 .. 0.72
   2 ?    2.2   0.0      0.14   2.2e+02       6      49 ..      59     104 ..      56     121 .. 0.69
   3 ?   -3.0   0.0       5.8   8.7e+03      41      50 ..     132     141 ..     128     156 .. 0.63
   4 ?   -3.0   0.0       6.1   9.1e+03      38      49 ..     165     176 ..     163     188 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0014
                                      TT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-....HHHHHHHHHCT CS
                            ANAPC3  2 qnnyknAiflaerllaaetespedayllAlclylngq....ykrAyellrka 49
                                      ++ y+ A++++  +   ++++p++ y l++ + + +      ++A +++rka
  gi|474934810|ref|YP_007688392.1| 19 NESYDQAVMFLKMAA--QRNNPSAQYVLGQMYASGKGvpesMEEAVKWFRKA 68
                                      667777777765555..99999999999998877664555577777777777 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHH.HHH--HHHHHHHHHHHHH....TT-HHHHHHHHHCT CS
                            ANAPC3   6 knAiflaerllaaetespedayllAlclyl....ngqykrAyellrka 49 
                                       ++A+ ++ ++   e+ +p++   l+ c+++    + + ++A+e++r+a
  gi|474934810|ref|YP_007688392.1|  59 EEAVKWFRKAA--ENGMPYANADLGVCYFNgmgvDADVNTALEYFRTA 104
                                       67777887777..88888888888888887444456677777777777 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 5.8
                                       HHHHHHHCTS CS
                            ANAPC3  41 rAyellrkak 50 
                                       +A +++rka 
  gi|474934810|ref|YP_007688392.1| 132 EAVKWFRKAA 141
                                       5666777662 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 6.1
                                       -HHHHHHHHHCT CS
                            ANAPC3  38 qykrAyellrka 49 
                                       + ++A++++r a
  gi|474934810|ref|YP_007688392.1| 165 DLNEALRWYRLA 176
                                       555666665544 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       2.2   3.3e+03      13      25 ..      18      30 ..      16      36 .. 0.75
   2 ?   -1.6   0.0       3.1   4.6e+03       3      12 ..      40      49 ..      38      53 .. 0.78
   3 ?    5.8   0.1     0.012        18      17      29 ..      58      70 ..      56      71 .. 0.88
   4 ?    0.2   0.0      0.79   1.2e+03      18      29 ..      95     106 ..      92     108 .. 0.79
   5 ?    4.2   0.1      0.04        59      15      29 ..     128     142 ..     127     143 .. 0.86
   6 ?   -2.1   0.0       4.3   6.5e+03       2      13 ..     147     158 ..     146     158 .. 0.78
   7 ?   -0.2   0.0       1.1   1.6e+03      15      27 ..     164     176 ..     163     178 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.2
                                      HTT-HHHHHHHHH CS
                             TPR_8 13 klgdyeeAkeyye 25
                                      + + y++A+ +++
  gi|474934810|ref|YP_007688392.1| 18 ENESYDQAVMFLK 30
                                      5678999988876 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.1
                                      HHHHHHHHHH CS
                             TPR_8  3 ayynlgsiyl 12
                                      a y lg+ y 
  gi|474934810|ref|YP_007688392.1| 40 AQYVLGQMYA 49
                                      7899999995 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.012
                                      HHHHHHHHHHHHH CS
                             TPR_8 17 yeeAkeyyekale 29
                                      +eeA+++++ka e
  gi|474934810|ref|YP_007688392.1| 58 MEEAVKWFRKAAE 70
                                      89********976 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 0.79
                                       HHHHHHHHHHHH CS
                             TPR_8  18 eeAkeyyekale 29 
                                       + A ey++ a e
  gi|474934810|ref|YP_007688392.1|  95 NTALEYFRTAAE 106
                                       6799****9987 PP

  == domain 5  score: 4.2 bits;  conditional E-value: 0.04
                                       T-HHHHHHHHHHHHH CS
                             TPR_8  15 gdyeeAkeyyekale 29 
                                       +d  eA+++++ka e
  gi|474934810|ref|YP_007688392.1| 128 KDQIEAVKWFRKAAE 142
                                       7888*********76 PP

  == domain 6  score: -2.1 bits;  conditional E-value: 4.3
                                       CHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylk 13 
                                       +a +n+g +y++
  gi|474934810|ref|YP_007688392.1| 147 DAQFNMGAAYEN 158
                                       678999999975 PP

  == domain 7  score: -0.2 bits;  conditional E-value: 1.1
                                       T-HHHHHHHHHHH CS
                             TPR_8  15 gdyeeAkeyyeka 27 
                                       +d++eA  +y+ a
  gi|474934810|ref|YP_007688392.1| 164 KDLNEALRWYRLA 176
                                       6888888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1401.17
//
Query:       gi|474934811|ref|YP_007688393.1|  [L=214]
Description: putative HD superfamily hydrolase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-09   36.6   0.6    1.3e-08   35.1   0.1    2.0  2  HD        HD domain
  ------ inclusion threshold ------
      0.022   14.3   0.0        0.1   12.1   0.0    2.1  2  DUF761    Cotton fibre expressed protein


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.1   1.5e-12   1.3e-08       4     121 ..      28     125 ..      26     126 .. 0.82
   2 ?   -3.2   0.0         1   9.2e+03      81      89 ..     188     196 ..     162     204 .. 0.57

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 1.5e-12
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHH..H CS
                                HD   4 HsleVaklarrlaedlgeeedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgld..l 78 
                                       Hs++V ++a  +++ +  e+dr l+ +aaLlHD+   + g              ++  v++  lr+++ + ++   +
  gi|474934811|ref|YP_007688393.1|  28 HSVRVRNIAMSICDTEP-EADRTLVAVAALLHDVDDRKLGG--------D---WKNLPVAEGFLRDNGVSGDEIlqV 92 
                                       ****************9.*****************999775........1...236778888888888888554776 PP

                                       HHHHHHHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHHHHHHH CS
                                HD  79 edvaklirehheswegkkrprglaerqlslearivklaDrlaa 121
                                       +++++ i+ + +++e           + sle riv++aDrl+a
  gi|474934811|ref|YP_007688393.1|  93 KEIIAKISFKGKDSE----------VPDSLEGRIVQDADRLDA 125
                                       666666666666666..........69**************98 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1
                                       HHHHHHTTC CS
                                HD  81 vaklirehh 89 
                                         +l+++ h
  gi|474934811|ref|YP_007688393.1| 188 GRRLAEHRH 196
                                       333333333 PP

>> DUF761  Cotton fibre expressed protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.1e-05       0.1       4      17 ..       5      18 ..       2      19 .. 0.87
   2 ?   -1.2   0.0      0.17   1.5e+03      12      19 ..     169     176 ..     167     180 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.1e-05
                            DUF761  4 vDakAEeFIakFre 17
                                      + +kAE+FI+ F+e
  gi|474934811|ref|YP_007688393.1|  5 ISEKAERFIRGFYE 18
                                      668**********8 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.17
                            DUF761  12 IakFreql 19 
                                       I  F+e+l
  gi|474934811|ref|YP_007688393.1| 169 ITHFHEKL 176
                                       44566666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       244  (0.0136092); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1339.52
//
Query:       gi|474934812|ref|YP_007688394.1|  [L=206]
Description: siroheme synthase, N-terminal domain protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.1e-15   55.1   0.0    1.5e-14   54.3   0.0    1.4  1  NAD_binding_7   Putative NAD(P)-binding
  ------ inclusion threshold ------
      0.052   12.8   0.0       0.12   11.5   0.0    1.6  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
       0.16   11.9   0.1       0.29   11.0   0.1    1.5  2  DUF386          YhcH/YjgK/YiaL
       0.17   11.6   0.0        0.3   10.8   0.0    1.4  1  CysG_dimeriser  Sirohaem synthase dimerisation region


Domain annotation for each model (and alignments):
>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3   0.0   3.3e-18   1.5e-14       6      93 ..       5      96 ..       3     105 .. 0.82

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 3.3e-18
                     NAD_binding_7  6 kgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvk......laeeelekdlegadlviaatddrelneri 78
                                      k++k++v+GgG+vA+rk+r+++ +  ++tv+a ++ + +e+ ++      + +++l + l+ga+++iaatd ++ln++i
  gi|474934812|ref|YP_007688394.1|  5 KDRKIVVFGGGNVALRKCRQFAGF--DITVIADRTVPGIEDACDrvviehFDSSDLGRYLDGAFIAIAATDSQSLNAEI 81
                                      799******************877..********8666664444322222345666666******************** PP

                     NAD_binding_7 79 aeaakarrilvnvad 93
                                      a++  ++++l n a 
  gi|474934812|ref|YP_007688394.1| 82 AKTSLSAGVLTNSAH 96
                                      ************985 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.8e-05      0.12     141     182 ..       5      54 ..       1      68 [. 0.75
   2 ?   -1.8   0.0      0.33   1.5e+03      20      54 ..     108     141 ..     105     183 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.8e-05
                                       -TSEEEEES-SHHHHHHHHHHHHHT-EEE.......EEESSSSSS.TTS- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxx.xxxx RF
                       Pyr_redox_2 141 lpkrivvvGgGyiGvElAaalaklgkevt.......lveardrll.rald 182
                                       ++++ivv GgG++++  + ++a +   v        + +a+dr++ + +d
  gi|474934812|ref|YP_007688394.1|   5 KDRKIVVFGGGNVALRKCRQFAGFDITVIadrtvpgIEDACDRVViEHFD 54 
                                       4589*****************99966555555566677777777766665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.33
                                       HHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  20 aqagakvtlvelegtclnggcllskallgvaedae 54 
                                       ++ g+ v++  +eg ++ + ++++k + ++ +++ 
  gi|474934812|ref|YP_007688394.1| 108 RKRGYTVAVS-SEGSVPAFPPIVAKDIDAFLGEEY 141
                                       5567888888.888888888888888877665543 PP

>> DUF386  YhcH/YjgK/YiaL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0         2   8.8e+03      13      32 ..      58      77 ..      43      84 .. 0.59
   2 ?   11.0   0.1   6.4e-05      0.29      39      71 ..     173     205 ..     140     206 .] 0.89

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2
                                      --HHHHHHHHHHHTS-GCC- CS
                            DUF386 13 lkpklkkaleylketdlenl 32
                                      l++ l+ a+ ++++td ++l
  gi|474934812|ref|YP_007688394.1| 58 LGRYLDGAFIAIAATDSQSL 77
                                      33445555555555555555 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 6.4e-05
                                       -.SSS-EEEEE--B-B-GGGS-EEE-SSEEEEE CS
                            DUF386  39 idgdklfvnvqeyetkpaeeakfEsHrkyiDiq 71 
                                       +d+++++ n+++ +t+ ae+a f + +ky Di+
  gi|474934812|ref|YP_007688394.1| 173 LDNEDIWHNLKDGDTEGAEKAAFAIREKYSDIH 205
                                       5999****************************9 PP

>> CysG_dimeriser  Sirohaem synthase dimerisation region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   6.8e-05       0.3       2      53 ..     141     193 ..     140     196 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.8e-05
                                       HHHHHHHHHHHHHHHHHH-SSHHHHHHHHHHHT.-HHHHHHHHTT-HHHHHHH CS
                    CysG_dimeriser   2 lGrLAelagrlRdrVkarlpdvaaRRrFWerff.dgpvaelvlaGdeeeAeal 53 
                                       +  + +l+ ++R+ +k+ +++ + R +   +++ ++++ + ++ Gd+e Ae++
  gi|474934812|ref|YP_007688394.1| 141 YDLMLDLLIKIRQDIKSVISTQPMRAKCLAEILdNEDIWHNLKDGDTEGAEKA 193
                                       667899999******************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1388.96
//
Query:       gi|474934813|ref|YP_007688395.1|  [L=447]
Description: cobyrinic acid a,c-diamide synthase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-31  109.4   0.0    2.7e-31  108.7   0.0    1.3  1  GATase_3  CobB/CobQ-like glutamine amidotransferase domain
    4.1e-18   65.7   0.0    7.6e-18   64.8   0.0    1.4  1  CbiA      CobQ/CobB/MinD/ParA nucleotide binding domain
    3.3e-17   63.0   0.2    1.7e-10   41.1   0.0    2.2  2  AAA_26    AAA domain
  ------ inclusion threshold ------
      0.021   14.2   0.4        3.8    6.9   0.1    2.7  3  PALP      Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.7   0.0   6.1e-35   2.7e-31       3     194 ..     245     431 ..     243     433 .. 0.89

  Alignments for each domain:
  == domain 1  score: 108.7 bits;  conditional E-value: 6.1e-35
                          GATase_3   3 avirlpaisnyt..dldpLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggp 77 
                                       av++++a s+y+  +++ Lea +     f p  +e++++ ad+ +l+Gg++++ + +++ +s++ e +k+++ +g p
  gi|474934813|ref|YP_007688395.1| 245 AVPMDDAYSFYYreNIECLEASGIRVKTFRPADGEDIPN-ADMAYLGGGYPELYAREISSNSNFLEGVKNMSDEGCP 320
                                       8999*******************999999999*****76.************************************* PP

                          GATase_3  78 vlgiCGGlqmLGeeiedpegvegeageveglglLdietefekekltgqvegevel....aaegeevkGyEiHsGrti 150
                                       vlg+CGGl+ L+ +++ ++       +  + g++d++  +  ++      ++ ++       + evkG+E H++++ 
  gi|474934813|ref|YP_007688395.1| 321 VLGECGGLMTLCGSMKLKDS------KFRMAGVFDARADMVGKRHGPTYMIT-RAtasnPLFEGEVKGHEYHYSEVC 390
                                       **************998775......6***************6654333333.44355544559************* PP

                          GATase_3 151 lkekakpllkvkvggnng.ekdGavkksedgnvlGtYlHglfdnr 194
                                        +e+ +  ++v++g+++  ++dG+  +    n++GtY+H +++++
  gi|474934813|ref|YP_007688395.1| 391 PAEGSTFGFEVSRGEGICgGRDGLTVR----NTVGTYMHQHCLSN 431
                                       *999999999988777778******99....**********9876 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.8   0.0   1.7e-21   7.6e-18       2     117 ..       5     182 ..       4     188 .. 0.91

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 1.7e-21
                                       EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH...HTTEB-HHHH..................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxx..................... RF
                              CbiA   2 aiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai...leglendiep..................... 54 
                                       +ia+t +GvGKT++a++L+  l++ +++V++++++p+    ++   +                              
  gi|474934813|ref|YP_007688395.1|   5 VIAGTGSGVGKTSIATGLMSVLSK-RYKVQPFKVGPDFIDPMYhsaA--------Sgrhgrnldsfmmddatirnlv 72 
                                       89**********************.************7777764431........02222356788899999999** PP

                                       ..............................................CCHCCCHHHHHHCHCHHHH.....EEEEEEE CS
                                       ..............................................xxxxxxxxxxxxxxxxxxx...xxxxxxxxx RF
                              CbiA  55 ..............................................dlkrllellealgkkkall...lkiagvvln 82 
                                                                                     ++ +l ++++a++++++ +   ++iagv++n
  gi|474934813|ref|YP_007688395.1|  73 gyasrgadlciiegvrglyegfqgdgdigstahiaktlglpvilvvNAGSLNRSAAAIVNGFRSFdpdVNIAGVIFN 149
                                       ***************************************************************************** PP

                                       EESS...-TTCHHHHHHHHHHCTS-EEEEEE--CC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  83 rvdgeneetllkealeelkqrygvpvlgviprdea 117
                                        + g++++ +l    e++++  g++vlg+ip+d +
  gi|474934813|ref|YP_007688395.1| 150 NISGKQHSDKLDVVAETYCK--GLRVLGKIPKDRK 182
                                       *******************9..*********9976 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.5   1.5e-07   0.00067       2      36 ..       3      36 ..       2      38 .. 0.87
   2 !   41.1   0.0   3.7e-14   1.7e-10      85     192 ..      65     181 ..      41     184 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.5e-07
                            AAA_26  2 tifvtgtdtgvGKTvvslgLvralkrkgvkvgyfK 36
                                      +++++gt+ gvGKT++++gL++ l +k +kv+ fK
  gi|474934813|ref|YP_007688395.1|  3 GFVIAGTGSGVGKTSIATGLMSVL-SKRYKVQPFK 36
                                      689******************999.7778877665 PP

  == domain 2  score: 41.1 bits;  conditional E-value: 3.7e-14
                            AAA_26  85 didlekivkelekdadivvVEGagglgvpitee...llnadiaknlgapvilVarggl..gtinqllltiealrqkn 156
                                       d ++ ++v   +  ad+ ++EG+ gl ++   +    ++a iak+lg+pvilV+++g+  ++ ++++    ++   +
  gi|474934813|ref|YP_007688395.1|  65 DATIRNLVGYASRGADLCIIEGVRGLYEGFQGDgdiGSTAHIAKTLGLPVILVVNAGSlnRSAAAIVNGFRSFD-PD 140
                                       445556666677889************9965544456899***************9763234444444444444.58 PP

                            AAA_26 157 vrvlGvilNkvrnp...envetlekk..sgipvlGvvPylp 192
                                       v+++Gvi+N++  +   ++++ + ++  +g++vlG +P ++
  gi|474934813|ref|YP_007688395.1| 141 VNIAGVIFNNISGKqhsDKLDVVAETycKGLRVLGKIPKDR 181
                                       **********988855545555555434689*******986 PP

>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1   0.00084       3.8     161     208 ..       5      55 ..       2      80 .. 0.88
   2 ?    2.9   0.1     0.014        61      69      93 ..     102     126 ..      65     132 .. 0.84
   3 ?    4.3   0.1    0.0049        22      71     190 ..     104     146 ..      91     195 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00084
                                       EEEE-SSSHHHHHHHHHHHH...HSTT-EEEEEEECTTCGGTTCCS..S.S CS
                              PALP 161 vvvpvGgGgliaGiaaglke...rrpdvrvigvepegsdalarslragrrv 208
                                       v++++G+G   + ia+gl++   +r +v+ + v p+  d++++s++ gr+ 
  gi|474934813|ref|YP_007688395.1|   5 VIAGTGSGVGKTSIATGLMSvlsKRYKVQPFKVGPDFIDPMYHSAASGRHG 55 
                                       89999***************8877888******************888774 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.014
                                       HHHHHHHHHT-EEEEEEETTS-HHH CS
                              PALP  69 alAaaaallGlkvtivvpadaspek 93 
                                       ++A++a+ lGl+v++vv a++ +  
  gi|474934813|ref|YP_007688395.1| 102 STAHIAKTLGLPVILVVNAGSLNRS 126
                                       79***************99987655 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.0049
                                       HHHHHHHT-EEEEEEETTS-HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHH CS
                              PALP  71 AaaaallGlkvtivvpadaspekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtig 147
                                       A++a+ lGl+v                                                                  
  gi|474934813|ref|YP_007688395.1| 104 AHIAKTLGLPV------------------------------------------------------------------ 114
                                       34444444444.................................................................. PP

                                       HHHHHHTTTTEEEEEEE-SSS.HHHHHHHHHHHHHSTT-EEEEE CS
                              PALP 148 lEileqlggkpdavvvpvGgG.gliaGiaaglkerrpdvrvigv 190
                                                    +vv +G+    +a+i+ g+++ +pdv++ gv
  gi|474934813|ref|YP_007688395.1| 115 ------------ILVVNAGSLnRSAAAIVNGFRSFDPDVNIAGV 146
                                       ............45555555534566666666666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 3312.26
//
Query:       gi|474934814|ref|YP_007688396.1|  [L=363]
Description: putative methanogenesis marker 13 metalloprotein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-25   89.4   0.6      3e-25   88.8   0.5    1.4  1  Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase


Domain annotation for each model (and alignments):
>> Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.8   0.5   1.6e-29     3e-25       6     151 ..      14     155 ..      10     216 .. 0.86

  Alignments for each domain:
  == domain 1  score: 88.8 bits;  conditional E-value: 1.6e-29
                                       HH.HHHTTBTTEEEEEES-HHHHHCCCCHHHCHHSS-HS-EEEE--HHHHSSSSHHHHHHHHHHHHHHC-TSEEEEE CS
                    Oxidored_nitro   6 Aa.lvllgikdalplvhGpqGCatyaralltrhfrepiplastdltekdavfGgeekLkeaikeivkrykpkaIgVi 81 
                                       Aa + l  ++  +++ hGp GC+++a++ l    ++ i +++++++ekd++fGg + L++++ e+ ++++pk+++V+
  gi|474934814|ref|YP_007688396.1|  14 AAlYTLRDMDVQVIVEHGPSGCSFMASRPLE---NDGIRVVTSAMKEKDLIFGGIDPLVRTLNEVKREFNPKVVAVV 87 
                                       4437788888889999*********999885...55669************************************** PP

                                       E-HHHHHTTTTHHHHHHHHHHHHTSSEEEEEE--TTSSSHHHHHHHHHHHHHHHCTT-TT---SSEEEEE CS
                    Oxidored_nitro  82 ttClteliGdDieavareaeeelgeipvipvstpgfggsqseGydaalealvrklvgkkgekeprkvnil 151
                                        tC++ +iGdDi+a +r+++   ++ +v++v++ g++g  +eG   al a +++ v  ++e+  r+ ++l
  gi|474934814|ref|YP_007688396.1|  88 GTCASTIIGDDIGAAVRRVDMG-PDCKVFHVDCHGCIGANTEGAIRALVAGAKAGVI-PQEECDRQTALL 155
                                       *******************864.567*******************999998887766.444444555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 2129.78
//
Query:       gi|474934815|ref|YP_007688397.1|  [L=405]
Description: UDP-N-acetylmuramoylalanine-D-glutamate ligase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      4e-07   30.2   0.0      6e-07   29.6   0.0    1.2  1  Mur_ligase_M  Mur ligase middle domain


Domain annotation for each model (and alignments):
>> Mur_ligase_M  Mur ligase middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   3.4e-11     6e-07       1      70 [.     103     185 ..     103     196 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 3.4e-11
                                       EESSS-HHHHHHHHHHHHHCTEEEEETTC..............SS-THHHHHHHHHHHHHTT-SEEEEE--HCHHHC CS
                      Mur_ligase_M   1 vTGtnGKTTtteliaailekagkvigtvg..............ttnneiglpktlaemekkeaeyavlEvsshglge 63 
                                       +TG +GKT+t +++a+il++agk +++                t  ++i  p+tl+++ ++e+e++v+Evs  g g 
  gi|474934815|ref|YP_007688397.1| 103 ITGVKGKTSTCYVLAHILDAAGKRTFLHTsrgmgpyakgqhviTDFQSI-APSTLLNLPRTEYEVLVCEVSLGGSGR 178
                                       8********************66666555566*********96555555.68888899999***********98888 PP

                                       TTTCCHC CS
                      Mur_ligase_M  64 krlegll 70 
                                       + ++g++
  gi|474934815|ref|YP_007688397.1| 179 ADIAGIT 185
                                       8777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2423.47
//
Query:       gi|474934816|ref|YP_007688398.1|  [L=260]
Description: hypothetical protein TALC_01253 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-27   95.8   0.0    1.4e-13   51.1   0.0    2.1  2  CbiX            CbiX
    2.3e-09   36.8   0.0    8.5e-09   34.9   0.0    1.7  1  Ferrochelatase  Ferrochelatase
    2.3e-05   23.9   0.0     0.0044   16.4   0.0    2.2  2  CbiK            Cobalt chelatase (CbiK)


Domain annotation for each model (and alignments):
>> CbiX  CbiX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   0.0   7.3e-15   4.4e-11       2     106 ..      11     120 ..      10     121 .. 0.94
   2 !   51.1   0.0   2.4e-17   1.4e-13       1     104 [.     139     249 ..     139     252 .. 0.85

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 7.3e-15
                                       STSSCCHHHHHHHHHHHHHHHCCSCCCEECESCCCECCSCCSSHHHHC-SBSEEEEEEESSSSSHHHHTHHHHHCT- CS
                              CbiX   2 GSrdpesneeveklaeelrekgpfkpvelgfleleepsleealrelaeqgvkrivvvPlflfaGvhvkeDIpeelee 78 
                                       G+r  +  + +e  a++lr++g+ k + +++  ++ep++++a++++a+ g+++++++P+ +++G ++ e Ipe l+ 
  gi|474934816|ref|YP_007688398.1|  11 GTRTGNLTDILESQAARLRARGR-KNIYVSYFRISEPTIPDAIAKMAADGIDDVLAIPYYIAEGRMTLELIPEKLGI 86 
                                       67777777778999*********.***************************************************** PP

                                       -SSSS-......TTEEEEE---CCCSCCHHHHHH CS
                              CbiX  79 aeeahp......kdveieytepLGthplvaevlk 106
                                        ++ h+      ++v++++++++G    ++++l 
  gi|474934816|ref|YP_007688398.1|  87 GHTSHGvadiggRKVKVTVAPAFGRTRMLTNILT 120
                                       **************************99999986 PP

  == domain 2  score: 51.1 bits;  conditional E-value: 2.4e-17
                                       -STSS.CCHHHHHHHHHHHHHHHCCSCCCEECESCCCECCSCCSSHHHHC-SBSEEEEEEESSSSSHHHHTHHHHHC CS
                              CbiX   1 HGSrd.pesneeveklaeelrekgpfkpvelgfleleepsleealrelaeqgvkrivvvPlflfaGvhvkeDIpeel 76 
                                       HGSrd ++sn+e+ +l ++     ++++v +gf+e++ p++ +al++l +++ ++++v Plf+++Gvh  e I e l
  gi|474934816|ref|YP_007688398.1| 139 HGSRDmHDSNREIVELNARRLGDMGYRHVAYGFNEFCGPEISDALASL-AKETDEVIVTPLFIANGVHLGEEIAEKL 214
                                       9****99*******998777777777*********************9.779***********************99 PP

                                       T--SSSS-.......TTEEEEE---CCCSCCHHHH CS
                              CbiX  77 eeaeeahp.......kdveieytepLGthplvaev 104
                                       +  +  ++       k + + y  p+ ++ ++ e 
  gi|474934816|ref|YP_007688398.1| 215 GISNYSKGgkvdiggKMICVKYMAPVEDDVRLLES 249
                                       97776666667777777777777777777777665 PP

>> Ferrochelatase  Ferrochelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.0   1.4e-12   8.5e-09      67     277 ..      17     210 ..      12     224 .. 0.81

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 1.4e-12
                                       HHHHHHHHHHHHHHHHHHH---EEEEEEESSSSSBHHHHHHHHHCTT-SEEEEEES-SS--TTTHHHHHHHHHHHHH CS
                    Ferrochelatase  67 lneitrkqaealekelaergidvkvylamrywePsiedaleelkadgvervvvlplyPqysasttgssleeleralk 143
                                       l +i ++qa+ l+++ +++   +     +r +eP i da+++++adg+++v+++p y  ++++t + + e+l    +
  gi|474934816|ref|YP_007688398.1|  17 LTDILESQAARLRARGRKN---I-YVSYFRISEPTIPDAIAKMAADGIDDVLAIPYYIAEGRMTLELIPEKLGIGHT 89 
                                       5677888888888888764...3.33348*****************************************9976664 PP

                                       H......TT-SSEEEEE---TT-HHHHHHHHHHHHHHHTTS-HC.C-EEEEEEE--BHHHHT.TT-SHHHHHHHHHH CS
                    Ferrochelatase 144 k......kreapevrvirqfydhpgyiealaesikealeelpeekkakllfsaHglPeravkkkgdpYqqqveetar 214
                                       +      + ++++v+v + f +   + ++l+++i +a  +    + + +l+  Hg    ++  ++       +e ++
  gi|474934816|ref|YP_007688398.1|  90 ShgvadiGGRKVKVTVAPAFGRTRMLTNILTDRIAQAGGSK---D-TGILVIGHGSRDMHD--SN-------REIVE 153
                                       44567798999*************************98865...5.9********866664..33.......78888 PP

                                       HHHHHTTT-S-EEEEEE---SSS-BSSSBHHHHHHHHCCC.-S-EEEE-TT-SS--HHHHIII CS
                    Ferrochelatase 215 lvaealglkeevelayqSrvGpeeWlePdtddtleelaekgvkaivvvpigFvsDhlEtleel 277
                                       l a++lg     ++a     G +e  +P+++d+l++la++  ++++v p+ F++  +   ee+
  gi|474934816|ref|YP_007688398.1| 154 LNARRLGDMGYRHVA----YGFNEFCGPEISDALASLAKET-DEVIVTPL-FIANGVHLGEEI 210
                                       888888755522344....488999999*********9986.78777775.777766666666 PP

>> CbiK  Cobalt chelatase (CbiK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   0.0    0.0017        10     145     210 ..       6      73 ..       2      80 .. 0.77
   2 !   16.4   0.0   7.3e-07    0.0044     127     219 ..     115     212 ..     106     221 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0017
                                       EEEE---SCH.HHHHHHHHHHHHHHCT-S.EEEEETT.SSS-HHHHHHHHHHHT--EEEEEE-SSS-- CS
                              CbiK 145 vfvgHGtehe.snavyaeldkvlkekdfkqvvvgtve.gyPeveevieelkkkgikevkliPlmlvAG 210
                                       + vg Gt+    +++ +     l++++ k+++v+    + P++ + i+++  +gi +v  iP+ +  G
  gi|474934816|ref|YP_007688398.1|   6 LIVGYGTRTGnLTDILESQAARLRARGRKNIYVSYFRiSEPTIPDAIAKMAADGIDDVLAIPYYIAEG 73 
                                       5566666654034445555566888889999999886589**********************988776 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 7.3e-07
                                       HHHHHHTTS----..TTEEEEEEE---..SCHHHHHHHHHHH.HHHHCT-S.EEEEETT.SSS-HHHHHHHHHHHT- CS
                              CbiK 127 vvealkdeierar..kdealvfvgHGt..ehesnavyaeldk.vlkekdfkqvvvgtve.gyPeveevieelkkkgi 197
                                       + ++l+d+i +a   kd  ++ +gHG+  +h sn    el+   l + ++++v  g  e   Pe+++ +++l k ++
  gi|474934816|ref|YP_007688398.1| 115 LTNILTDRIAQAGgsKDTGILVIGHGSrdMHDSNREIVELNArRLGDMGYRHVAYGFNEfCGPEISDALASLAK-ET 190
                                       6788999999987779999999****844699999999998626999*********999567**********86.68 PP

                                       -EEEEEE-SSS--HHHHCCCCS CS
                              CbiK 198 kevkliPlmlvAGdHaknDmas 219
                                        ev + Pl++  G H  +++a+
  gi|474934816|ref|YP_007688398.1| 191 DEVIVTPLFIANGVHLGEEIAE 212
                                       9**************9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1755.86
//
Query:       gi|474934817|ref|YP_007688399.1|  [L=268]
Description: Mo-nitrogenase iron protein subunit NifH [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.6e-91  304.7   0.2    6.9e-91  304.4   0.2    1.0  1  Fer4_NifH     4Fe-4S iron sulfur cluster binding proteins, Ni
    5.3e-12   45.9   0.0    7.7e-12   45.4   0.0    1.2  1  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain
    4.2e-10   39.8   0.0    7.6e-10   39.0   0.0    1.4  2  AAA_31        AAA domain
    4.3e-08   32.9   0.1    7.3e-05   22.3   0.1    2.2  2  ParA          NUBPL iron-transfer P-loop NTPase
    1.4e-06   27.8   0.2    2.4e-06   27.0   0.2    1.4  1  ArsA_ATPase   Anion-transporting ATPase
    0.00058   19.2   0.0      0.001   18.4   0.0    1.3  1  MipZ          ATPase MipZ
     0.0038   16.2   0.0     0.0052   15.8   0.0    1.2  1  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
     0.0048   16.7   0.0     0.0065   16.2   0.0    1.2  1  AAA_24        AAA domain
  ------ inclusion threshold ------
      0.014   15.8   0.0      0.028   14.8   0.0    1.5  2  AAA_16        AAA ATPase domain
      0.028   14.3   0.1      0.087   12.7   0.1    1.8  1  NTPase_1      NTPase
       0.08   12.6   0.2       0.15   11.7   0.2    1.4  1  SRP54         SRP54-type protein, GTPase domain
        0.1   12.7   0.1       0.16   12.1   0.1    1.2  1  DUF87         Helicase HerA, central domain
       0.14   11.3   0.0       0.24   10.5   0.0    1.3  1  DUF815        Protein of unknown function (DUF815)
       0.15   12.4   0.0       0.39   11.1   0.0    1.7  2  RNA_helicase  RNA helicase
       0.16   11.1   0.1       0.29   10.3   0.1    1.3  1  NB-ARC        NB-ARC domain


Domain annotation for each model (and alignments):
>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  304.4   0.2   5.8e-94   6.9e-91       1     246 [.       2     246 ..       2     252 .. 0.97

  Alignments for each domain:
  == domain 1  score: 304.4 bits;  conditional E-value: 5.8e-94
                         Fer4_NifH   1 rkiaiyGkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllggkaqetvldtlrekgavedvkvedvvkkG 77 
                                       r+iaiyGkGGiGkstts+n++ alae+g kvl++GCDPkaDst+ll g+  ++ vl++lre++   d+ +ed+v +G
  gi|474934817|ref|YP_007688399.1|   2 RRIAIYGKGGIGKSTTSANVTDALAEKGLKVLQIGCDPKADSTKLLAGANRKDPVLQVLREND---DISLEDIVAEG 75 
                                       68**********************************************************998...7********** PP

                         Fer4_NifH  78 yggvkcvesGGPepGvGCaGrgvitaielleelgayd..dlDfvlyDvLGDvvCGGfalPiredkaqevyivtsgel 152
                                       ++g  cve GGP pG+GCaGrg+i a+e le+l+a +    D+++yDvLGDvvCGGfa+Pir+++a +v++vtsge+
  gi|474934817|ref|YP_007688399.1|  76 SHGSLCVECGGPRPGMGCAGRGIIAAFEELERLDAIEvyRPDVIVYDVLGDVVCGGFAMPIRNGYARDVFVVTSGEM 152
                                       ***********************************996459************************************ PP

                         Fer4_NifH 153 malyaanniakgiekyaksggvrlgGliinsrkvddereliekfaeelgtkvlevvPrdeivrkaelrkktvieyap 229
                                       m+lyaa nia++++ ++  g  r+gGli nsr+v+ e+el+++ a+e+gt+v+  +Pr+ +v+k e+   tv++ ap
  gi|474934817|ref|YP_007688399.1| 153 MSLYAASNIAEAVNGFRADGYARFGGLIQNSRNVEGEDELVDRAAAEIGTEVVYRIPRSPEVQKCEALGTTVVSGAP 229
                                       ***************************************************************************** PP

                         Fer4_NifH 230 eseqakeyrelarkile 246
                                       +seqa+eyr+la+ +++
  gi|474934817|ref|YP_007688399.1| 230 DSEQADEYRHLAQLLYN 246
                                       ************97765 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.0   6.4e-15   7.7e-12       4     125 ..       6     221 ..       4     224 .. 0.87

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 6.4e-15
                                       EESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH.......................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................... RF
                              CbiA   4 astkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep.......................... 54 
                                       + +kGG GK+t++an   ala++gl+Vl + +Dp a +++ l    n+++p                          
  gi|474934817|ref|YP_007688399.1|   6 IYGKGGIGKSTTSANVTDALAEKGLKVLQIGCDPKADSTK-LLAGANRKDPvlqvlrenddisledivaegshgslc 81 
                                       679*************************************.666666666679999********************* PP

                                       ........................................................................CCHCC CS
                                       ........................................................................xxxxx RF
                              CbiA  55 ........................................................................dlkrl 59 
                                                                                                               +l   
  gi|474934817|ref|YP_007688399.1|  82 vecggprpgmgcagrgiiaafeelerldaievyrpdvivydvlgdvvcggfampirngyardvfvvtsgemmSLYAA 158
                                       ******************************************************************88887766666 PP

                                       CHHHHHHCHCHHHH....EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHT CS
                                       xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  60 lellealgkkkall..lkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeaparg 125
                                       ++++ea+ +  a     ++ g++ n  + e e++l   a +e+    g +v+  ipr+ +v +++a g
  gi|474934817|ref|YP_007688399.1| 159 SNIAEAVNGFRA-DgyARFGGLIQNSRNVEGEDELVDRAAAEI----GTEVVYRIPRSPEVQKCEALG 221
                                       666666664433.358999999999988887666666666665....**************9988766 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.0   6.4e-13   7.6e-10       4      73 ..       4      72 ..       1      81 [. 0.77
   2 ?   -3.8   0.0       8.6     1e+04     143     166 ..     144     167 ..     141     171 .. 0.72

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 6.4e-13
                            AAA_31  4 IaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekneiektlyevl..ieeknikeai 73
                                      Iai+  KGG+GK+Tts n+  ala++g kvL + +Dp a +t  l     +++  +++vl  ++++++++++
  gi|474934817|ref|YP_007688399.1|  4 IAIY-GKGGIGKSTTSANVTDALAEKGLKVLQIGCDPKADSTKLLA--GANRKDPVLQVLreNDDISLEDIV 72
                                      6665.5************************************9664..445556677776333555555555 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 8.6
                            AAA_31 143 viipvqaeayaleGleqllktiee 166
                                       v +++  e ++l+ ++++ + ++ 
  gi|474934817|ref|YP_007688399.1| 144 VFVVTSGEMMSLYAASNIAEAVNG 167
                                       667777788888888888888775 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.1   6.1e-08   7.3e-05      10      56 ..       7      53 ..       2      67 .. 0.81
   2 !    8.6   0.0   0.00096       1.1     194     243 ..     193     242 ..     180     245 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 6.1e-08
                              ParA 10 SgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveee 56
                                       gKGG+GKSt+++n++ aLa+kglkv  +  D    s   l g++++
  gi|474934817|ref|YP_007688399.1|  7 YGKGGIGKSTTSANVTDALAEKGLKVLQIGCDPKADSTKLLAGANRK 53
                                      59***********************9877777766666666666665 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00096
                              ParA 194 geklaeelgvpllgeipldpeireasdegkplvlkepeseaakaleeiae 243
                                       ++++a+e+g++++ +ip +pe++++   g+++v  +p+se+a++++++a+
  gi|474934817|ref|YP_007688399.1| 193 VDRAAAEIGTEVVYRIPRSPEVQKCEALGTTVVSGAPDSEQADEYRHLAQ 242
                                       6788999***************************************9987 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.2     2e-09   2.4e-06       1      39 [.       1      39 [.       1      53 [. 0.93

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 2e-09
                                      -EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-ST CS
                       ArsA_ATPase  1 lkvilvgGKGGVGKttvsaatavklsekgkkvllistDP 39
                                      ++ i + GKGG+GK+t sa +   l+ekg kvl i  DP
  gi|474934817|ref|YP_007688399.1|  1 MRRIAIYGKGGIGKSTTSANVTDALAEKGLKVLQIGCDP 39
                                      6889999******************************** PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   8.4e-07     0.001       9      44 ..       9      44 ..       4      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 8.4e-07
                                      STTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HH CS
                              MipZ  9 kGGsGksttavhvavaLlkkGarvaaidldlrqrtl 44
                                      kGG Gkstt+  v  aL++kG++v  i  d +  + 
  gi|474934817|ref|YP_007688399.1|  9 KGGIGKSTTSANVTDALAEKGLKVLQIGCDPKADST 44
                                      9**************************999876665 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   4.4e-06    0.0052      31      71 ..       3      43 ..       1      82 [. 0.89

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.4e-06
                                      EEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE------ CS
                              MeaB 31 vvGltGvPGaGkstlvealglelrrrGkrvavlavDPsspf 71
                                      ++ + G  G Gkst+  +++  l+++G +v  +  DP +  
  gi|474934817|ref|YP_007688399.1|  3 RIAIYGKGGIGKSTTSANVTDALAEKGLKVLQIGCDPKADS 43
                                      89999********************************8765 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   5.4e-06    0.0065       4      39 ..       3      34 ..       1      70 [. 0.77

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.4e-06
                            AAA_24  4 kiliyGpsgiGKTtlakelgpkplfidtekGlksld 39
                                      +i+iyG+ giGK+t+ ++   ++l    ekGlk l+
  gi|474934817|ref|YP_007688399.1|  3 RIAIYGKGGIGKSTTSANV-TDAL---AEKGLKVLQ 34
                                      89***************99.5554...244444444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   2.4e-05     0.028      27      69 ..       4      46 ..       2     109 .. 0.77
   2 ?   -2.9   0.0       6.5   7.7e+03      62      62 ..     231     231 ..     185     252 .. 0.53

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.4e-05
                            AAA_16 27 vllsGesGvGKsslvrellralekdggiflrgkcdqlesaipy 69
                                      + ++G  G+GKs+    + +al ++g  +l+  cd    ++ +
  gi|474934817|ref|YP_007688399.1|  4 IAIYGKGGIGKSTTSANVTDALAEKGLKVLQIGCDPKADSTKL 46
                                      679********************************99555444 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.5
                            AAA_16  62 q 62 
                                       +
  gi|474934817|ref|YP_007688399.1| 231 S 231
                                       1 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   7.3e-05     0.087       1      30 [.       3      32 ..       3      40 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.3e-05
                                      EEEEE--TTSSHHHHHHHHHHHH...GGGE CS
                          NTPase_1  1 kvfiTGppGvGKtTlvkkvlellkssgvkv 30
                                      +++i G+ G+GK+T   +v+++l+++g+kv
  gi|474934817|ref|YP_007688399.1|  3 RIAIYGKGGIGKSTTSANVTDALAEKGLKV 32
                                      58899***********************98 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   0.00013      0.15       4      38 ..       4      38 ..       1      45 [. 0.93

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                                      EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                             SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                      i++ G  G+GK tt a + + l ++g kvl + +D
  gi|474934817|ref|YP_007688399.1|  4 IAIYGKGGIGKSTTSANVTDALAEKGLKVLQIGCD 38
                                      7899**************************99999 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00013      0.16      24      56 ..       2      33 ..       1      38 [. 0.92

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                             DUF87 24 rHlAilgsTGsGKSntvavLleellekkgatil 56
                                      r++Ai g+ G GKS+t a   + l+ +kg+++l
  gi|474934817|ref|YP_007688399.1|  2 RRIAIYGKGGIGKSTTSANVTDALA-EKGLKVL 33
                                      899***************9999999.9998887 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0    0.0002      0.24      57      94 ..       5      42 ..       2      74 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0002
                            DUF815 57 LLwGarGtGKSslvkallneyaeegLrlievekedlke 94
                                       ++G+ G GKS++   ++ ++ae+gL+++++  +  ++
  gi|474934817|ref|YP_007688399.1|  5 AIYGKGGIGKSTTSANVTDALAEKGLKVLQIGCDPKAD 42
                                      689***************************97665544 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00032      0.39       1      26 [.       4      29 ..       4      63 .. 0.83
   2 ?   -2.7   0.0       6.6   7.9e+03      32      49 ..     222     239 ..     207     245 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00032
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkkl 26
                                      i +yG+ g+GKSt++ ++++al++k 
  gi|474934817|ref|YP_007688399.1|  4 IAIYGKGGIGKSTTSANVTDALAEKG 29
                                      679**************999999765 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6.6
                      RNA_helicase  32 dsvysrnpeddfwdgYtg 49 
                                        +v+s++p+++  d Y++
  gi|474934817|ref|YP_007688399.1| 222 TTVVSGAPDSEQADEYRH 239
                                       567778899999999885 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00024      0.29      23      44 ..       4      25 ..       2      31 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00024
                                      EEEEESTTSSHHHHHHHHCCSH CS
                            NB-ARC 23 valvGmgGvGKttlakqilnks 44
                                      +a++G+gG+GK+t ++++   +
  gi|474934817|ref|YP_007688399.1|  4 IAIYGKGGIGKSTTSANVTDAL 25
                                      79************99998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 1632.80
//
Query:       gi|474934818|ref|YP_007688400.1|  [L=168]
Description: hypothetical protein TALC_01255 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0009   19.3   0.0     0.0014   18.7   0.0    1.3  1  PA-IL           PA-IL-like protein
     0.0065   16.2   2.7      0.011   15.5   2.7    1.3  1  zinc_ribbon_2   zinc-ribbon domain
  ------ inclusion threshold ------
      0.011   14.7  10.2      0.013   14.5  10.2    1.0  1  MFS_1           Major Facilitator Superfamily
      0.042   13.9   0.4      0.075   13.1   0.4    1.4  1  DZR             Double zinc ribbon
       0.15   12.8   2.1       0.29   11.9   2.1    1.5  1  zinc_ribbon_15  zinc-ribbon family
        3.3    8.1  12.0        0.5   10.7   3.7    2.5  2  DUF3040         Protein of unknown function (DUF3040)


Domain annotation for each model (and alignments):
>> PA-IL  PA-IL-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   4.6e-07    0.0014      60     101 ..      38      79 ..      25      89 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 4.6e-07
                                       TTCTCEEEEETTCEEEETTCEEEEEE-STTSBEEEEEEE--- CS
                             PA-IL  60 asiaalvakiankktiivntvlfktvapnnvdGelillyndv 101
                                        s++al a +a ++++ +n  lf +va + v G l l++ d 
  gi|474934818|ref|YP_007688400.1|  38 ESVSALTAEVARSNYLFTNFLLFAWVAASMVYGTLALIFPDT 79 
                                       5899***********************************996 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   2.7   3.6e-06     0.011       2      22 ..       2      22 ..       1      23 [. 0.96

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.6e-06
                     zinc_ribbon_2  2 CpnCGaelqdnakFCpyCGtp 22
                                      C +CGa+++ +  FC  CG++
  gi|474934818|ref|YP_007688400.1|  2 CRECGAPIDGEYGFCVFCGAE 22
                                      *******************97 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5  10.2   4.2e-06     0.013     201     313 ..      45     154 ..      14     160 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.2e-06
                             MFS_1 201 kallkdpvlw..illialllfffgfsglltllplylqevlgls.glllaglllallalvgailallagrlsdrlgrr 274
                                        ++ ++++l+  +ll+a++ +++++ +l   +p  + ev +++ +   a+ +++++ +++ i+all+g   +r +++
  gi|474934818|ref|YP_007688400.1|  45 AEVARSNYLFtnFLLFAWVAASMVYGTLALIFPDTMIEVGKMAyS-PAALRVMGVSLIGSGIFALLSGVCCTRRSNW 120
                                       345555555456699999999999999888888877888777742.3344446666666666699999999887777 PP

                             MFS_1 275 rrlllallllllaalglallavtssavllllvlvliGfg 313
                                       ++ +  + +++++ + +++l+ ++  +l+l     +Gf 
  gi|474934818|ref|YP_007688400.1| 121 KQAVYLCMAAAALPFVILILGDSTGLLLAL-----VGFV 154
                                       777777777777777777777773433333.....3332 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.4   2.5e-05     0.075       1      20 [.       2      21 ..       1      33 [. 0.69

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.5e-05
                               DZR  1 CpqCgeelppdarfCseCgt 20
                                      C +Cg++++ +  fC  Cg+
  gi|474934818|ref|YP_007688400.1|  2 CRECGAPIDGEYGFCVFCGA 21
                                      66666666666666666666 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   2.1   9.7e-05      0.29      68      86 .]       2      20 ..       1      20 [. 0.97

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.7e-05
                    zinc_ribbon_15 68 CknCgkeveeefkyCpkCg 86
                                      C++Cg+ ++ e+ +C +Cg
  gi|474934818|ref|YP_007688400.1|  2 CRECGAPIDGEYGFCVFCG 20
                                      ******************9 PP

>> DUF3040  Protein of unknown function (DUF3040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   2.1      0.12   3.7e+02      45      77 ..      67     100 ..      35     113 .. 0.68
   2 ?   10.7   3.7   0.00017       0.5      37      79 ..     116     157 ..     107     160 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.12
                           DUF3040  45 avlavllfvaGllllvlG.vaaaavvlgvvGfvv 77 
                                       +v ++l+++++ +++ +G +a +  +l v+G+ +
  gi|474934818|ref|YP_007688400.1|  67 MVYGTLALIFPDTMIEVGkMAYSPAALRVMGVSL 100
                                       4555666666666666666666664444444433 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00017
                           DUF3040  37 rrrslrrlavlavllfvaGllllvlGvaaaavvlgvvGfvvml 79 
                                       rr++ +++++l+++++++++++l+lG ++   +l++vGfvv+l
  gi|474934818|ref|YP_007688400.1| 116 RRSNWKQAVYLCMAAAALPFVILILGDSTGL-LLALVGFVVAL 157
                                       444456666677777777********77775.9*******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       939  (0.0523733); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1052.00
//
Query:       gi|474934819|ref|YP_007688401.1|  [L=140]
Description: Universal stress protein UspA-related nucleotide-binding protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-31  109.2   0.2    2.6e-31  109.0   0.2    1.0  1  Usp              Universal stress protein family
  ------ inclusion threshold ------
      0.066   13.9   0.0      0.091   13.5   0.0    1.3  1  DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomer


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.0   0.2   2.9e-35   2.6e-31       1     141 []       1     139 [.       1     139 [. 0.97

  Alignments for each domain:
  == domain 1  score: 109.0 bits;  conditional E-value: 2.9e-35
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaea 77 
                                       m+k I+V +Dgse+ k A++++le ak +ga++++l v d  ++g+v+++    ee e++ ++ae ++    ++ ++
  gi|474934819|ref|YP_007688401.1|   1 MFKEIMVTTDGSESNKVAVDQGLEIAKGSGARVTALCVFDIGSYGHVAQGYGFGEEREYMIKAAEDALRYVVTRGKE 77 
                                       99**************************************************************9999999****** PP

                                       TTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  78 ggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                        gv+v+ ++  g+pae+i+e+ +  + dl+V+G+ gr+g +r+llGSv+e+v+r a+cpVlv+r
  gi|474934819|ref|YP_007688401.1|  78 VGVEVVPKIITGHPAEAIVEESK--NFDLVVCGTIGRTGMQRVLLGSVAEKVVRLAHCPVLVCR 139
                                       ******************98765..59***********************************97 PP

>> DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     1e-05     0.091      69     126 ..      80     137 ..      44     139 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1e-05
                                       TTSSSEEEESHHHHHHHHCHTT-SEEEE--SSGGGHHHHHHHHHTTSEEEE--SHHHH CS
                   DXP_reductoisom  69 kelktevlvGeealkelaeeeeadvvvaaivGaaGLkptlaaikagkriaLANKEsLV 126
                                        e+ +++++G+ a + + e+++ d+vv + +G +G++  l    a+k + LA    LV
  gi|474934819|ref|YP_007688401.1|  80 VEVVPKIITGHPAEAIVEESKNFDLVVCGTIGRTGMQRVLLGSVAEKVVRLAHCPVLV 137
                                       4567899*****999999*******************************999776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 904.05
//
Query:       gi|474934820|ref|YP_007688402.1|  [L=165]
Description: ACT-domain-containing protein, predicted allosteric regulator of homoserine dehydrogenase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.019   14.9   0.1       0.63    9.9   0.0    2.2  2  DUF2726   Protein of unknown function (DUF2726)


Domain annotation for each model (and alignments):
>> DUF2726  Protein of unknown function (DUF2726)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.006   1.1e+02      87     117 ..      95     125 ..      90     134 .. 0.81
   2 ?    9.9   0.0   3.5e-05      0.63      85     107 ..     140     162 ..     130     163 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.006
                           DUF2726  87 arkrDalkraalaaAgipllrvkakksytve 117
                                       a+  D+l++aa +a+gi  ++v+ ++s++ +
  gi|474934820|ref|YP_007688402.1|  95 AAYMDELIDAAGKAVGIEDVEVSYSASDKSS 125
                                       66789*****************887776655 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 3.5e-05
                           DUF2726  85 gkarkrDalkraalaaAgipllr 107
                                       ++ ++ D +++ a+++Ag++l+r
  gi|474934820|ref|YP_007688402.1| 140 EDIEALDSFFEDACKKAGLTLIR 162
                                       566889***************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1180.83
//
Query:       gi|474934821|ref|YP_007688403.1|  [L=339]
Description: homoserine dehydrogenase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.8e-56  189.7   0.0      6e-56  189.1   0.0    1.3  1  Homoserine_dh  Homoserine dehydrogenase
    2.3e-09   37.9   0.0    5.4e-09   36.7   0.0    1.7  1  NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
     0.0049   16.6   0.1      0.042   13.6   0.1    2.3  2  ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydro


Domain annotation for each model (and alignments):
>> Homoserine_dh  Homoserine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.1   0.0     1e-59     6e-56       1     173 []     154     326 ..     154     326 .. 0.98

  Alignments for each domain:
  == domain 1  score: 189.1 bits;  conditional E-value: 1e-59
                                       --HHHHHHTCTTSEEEEEEEE--HHHHHHHHHHHCHTT-HHHHHHHHHHTTSS-SSTHHHHTTHHHHHHHHHHHHHH CS
                     Homoserine_dh   1 PiiktlkeilsgdritrieGilngtlnyiltemeeegasfsevlkeaqelGyaeaDptdDveGlDaarKlailarla 77 
                                       Pii+  +e l g+++++i+Gi+ngt+nyil++m++ g+ f+ +lkeaq++Gyae+Dpt+DveG+Daa+K++ila+ +
  gi|474934821|ref|YP_007688403.1| 154 PIINLCHENLMGEKVRSIRGIFNGTCNYILSKMDK-GQPFEPALKEAQQRGYAETDPTNDVEGFDAAAKVTILANSV 229
                                       9*********************************7.888************************************** PP

                                       CTTT--GGGSEE--STTS-HHHHHHHHCTTEEEEEEEEE..CEEEEEEEEEETTSGGGHSSST-EEEEEEESSSEEE CS
                     Homoserine_dh  78 fgleveledvevegiskltaedikeakeegkvlklvasa..vearVkpelvpkshplasvkgsenavlvetdrlgel 152
                                       f+ +v+++dv+++gis++t+e ++ a+++++v++l++++  ++++V+p+lvpk +pla + g+ n+ ++++d +g++
  gi|474934821|ref|YP_007688403.1| 230 FHRNVTIRDVKITGISSITPEAVALAASRNMVIRLIGEVsdTKLEVSPRLVPKGSPLA-IGGTLNVAVIDADLAGPI 305
                                       **************************************8777****************.****************** PP

                                       EEEES-SSHHHHHHHHHHHHH CS
                     Homoserine_dh 153 viqGpgaGaepTAsavlsDll 173
                                       +i G+gaG+ +TAsa+lsDll
  gi|474934821|ref|YP_007688403.1| 306 TINGRGAGRIETASAILSDLL 326
                                       *******************96 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.0   9.1e-13   5.4e-09       1     117 []       7     146 ..       7     146 .. 0.82

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 9.1e-13
                                       --SHHHHHHHHHHHH---S........SEEEEEEEEESSEEE-TT............HHHHHT--CB---HHHHHHH CS
                     NAD_binding_3   1 GlGaiGsavleqlkrqqse........ielelvavadrdsllskd............rkallasealtldlddliah 57 
                                       G+G++G+++++ l++ ++            ++vav+d+++ ++++            +++ +   ++++d  ++++ 
  gi|474934821|ref|YP_007688403.1|   7 GYGTVGKGFADVLAKRRDLlasrygeeNLPRVVAVMDSRTVARNPdgidlkalearkAEKGTVGDETYSDSIAVMDS 83 
                                       99***************999***99986679********4444446****999997755555566666677777887 PP

                                       HS-EEEEE-S--HHHH.....TTHHHHHHTTEEEE-S--CGGG-HHHHHHHTSSSTTS--.EE-G CS
                     NAD_binding_3  58 ldpdvvVEcasseava.....elvlkaLkagkdvvtankgaladealyeeLreaaeangakiyve 117
                                       +  d++VE+ + +        + +  aL++gkdv+t+nkg la    ++eL+++a++n++k+++e
  gi|474934821|ref|YP_007688403.1|  84 VSYDLLVEVSPTNIRDggvglKNIRHALERGKDVITVNKGPLA--LCFRELIDLAQKNECKLRFE 146
                                       89*******88777652222235689*****************..9***************9987 PP

>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.1     7e-06     0.042      56      93 ..      36      73 ..       1      93 [. 0.73
   2 ?    0.1   0.0     0.093   5.6e+02      41      78 ..     100     137 ..      98     153 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7e-06
                                      -EEEEEEESSEEEEETTEE-HHHHHHHHHCSSSSTTHS CS
                     ELFV_dehydrog 56 akvvavsDssGviydpeGldieellelkeerksvkeyk 93
                                       +vvav+Ds+ v  +p+G+d+++l + k+e+++v + +
  gi|474934821|ref|YP_007688403.1| 36 PRVVAVMDSRTVARNPDGIDLKALEARKAEKGTVGDET 73
                                      379****************************9975544 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.093
                                       SHHHHHHHHHHHHCT-EEEEEEESSEEEEETTEE-HHH CS
                     ELFV_dehydrog  41 GnvgsyaallltelgakvvavsDssGviydpeGldiee 78 
                                       G vg   ++++ e+g+ v++v  +  +++  e +d+++
  gi|474934821|ref|YP_007688403.1| 100 GGVGLKNIRHALERGKDVITVNKGPLALCFRELIDLAQ 137
                                       889999**************998877777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 2261.57
//
Query:       gi|474934822|ref|YP_007688404.1|  [L=92]
Description: ACT domain-containing protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.8e-11   43.2   0.0    3.1e-11   43.1   0.0    1.1  1  ACT_6        ACT domain
    1.1e-06   28.3   0.2    2.1e-06   27.4   0.1    1.5  2  ACT          ACT domain
    0.00019   21.9   0.5    0.00034   21.2   0.5    1.4  1  ACT_4        ACT domain
     0.0041   16.9   0.2     0.0061   16.3   0.2    1.3  1  ACT_7        ACT domain
  ------ inclusion threshold ------
      0.019   14.7   0.2       0.02   14.6   0.2    1.0  1  Endotoxin_N  delta endotoxin, N-terminal domain
      0.054   13.3   0.1      0.054   13.3   0.1    1.1  1  TrpP         Tryptophan transporter TrpP
       0.14   12.1   0.0       0.14   12.1   0.0    1.0  1  SLATT_1      SMODS and SLOG-associating 2TM effector domain 1


Domain annotation for each model (and alignments):
>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   0.0   1.2e-14   3.1e-11       4      75 ..       7      80 ..       4      81 .. 0.96

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 1.2e-14
                             ACT_6  4 litvtGpdrpGltasLtsvlaefgvnilDieqavihgrlsLgllvsgp..edalarlekaLlflakelgltvef 75
                                      +it++G+d++G++a+++   ae+++nilD+ + ++ +    ++ v+++  ++ + +l k+L+++ak+ g t++ 
  gi|474934822|ref|YP_007688404.1|  7 IITLVGADHAGIIAAVCTYFAENDINILDLSMTTVQEFINMMMIVDLSkyKKSFPELSKDLDEVAKKVGCTIHA 80
                                      8***********************************************9999*****************99975 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.1   8.2e-10   2.1e-06       2      53 ..       7      54 ..       6      75 .. 0.82
   2 ?   -1.5   0.0      0.89   2.3e+03      40      55 ..      70      85 ..      61      89 .. 0.63

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 8.2e-10
                                      EEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHH CS
                               ACT  2 vlrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdee 53
                                      ++ +  +D+ G++a+v++ +a+++iNi  ++ +++ +    +++++ +vd +
  gi|474934822|ref|YP_007688404.1|  7 IITLVGADHAGIIAAVCTYFAENDINILDLSMTTVQE----FINMMMIVDLS 54
                                      5666778****************************76....77776666655 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.89
                                      ECEEEEEEEEEEHHHH CS
                               ACT 40 vagivfvvivvdeedl 55
                                      va+ v ++i++ +ed+
  gi|474934822|ref|YP_007688404.1| 70 VAKKVGCTIHAQHEDI 85
                                      4555666666666665 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.5   1.3e-07   0.00034       9      57 ..       8      54 ..       3      58 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.3e-07
                             ACT_4  9 leveaedrkglLaditqviseekanivsvnaktrkkdglaeikitveVk 57
                                      +++++ d  g++a +++ ++e+++ni +++++t +  ++ ++ + v ++
  gi|474934822|ref|YP_007688404.1|  8 ITLVGADHAGIIAAVCTYFAENDINILDLSMTTVQ--EFINMMMIVDLS 54
                                      8899*****************************65..699999888765 PP

>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.2   2.4e-06    0.0061      10      43 ..       9      38 ..       4      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.4e-06
                                      EE-S-.---SS--HHHHHHHHHHTTT---EEEE- CS
                             ACT_7 10 svvgsglpfdvtGivaklaspLaeagIsifqiSt 43
                                      ++vg+    d+ Gi+a++++  ae++I+i+ +S+
  gi|474934822|ref|YP_007688404.1|  9 TLVGA----DHAGIIAAVCTYFAENDINILDLSM 38
                                      55666....99**********************5 PP

>> Endotoxin_N  delta endotoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.2   7.7e-06      0.02       5      79 ..       4      74 ..       1      91 [. 0.85

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 7.7e-06
                       Endotoxin_N  5 alslipevGgvlsfivdliftylieedksiaelvnsyrkeiqdlidnsltqyddnklkallkglslslkdfrkev 79
                                        ++i+ vG   ++i+ ++ ty+ e+d  i +l     + +q+ i+  +   d +k k ++  ls+ l++ +k+v
  gi|474934822|ref|YP_007688404.1|  4 NRTIITLVGADHAGIIAAVCTYFAENDINILDLSM---TTVQEFINMMM-IVDLSKYKKSFPELSKDLDEVAKKV 74
                                      5799*********************9988887555...999**998655.6789999999999999999988876 PP

>> TrpP  Tryptophan transporter TrpP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   2.1e-05     0.054      45      94 ..       3      51 ..       1      80 [. 0.78

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.1e-05
                              TrpP 45 nddvkivlvsGvvaGilaalttkfpgGqlpniidkivtallvflllalfk 94
                                      n++  i+lv    aGi+aa+ t f    + ni+d  +t++  f+ ++++ 
  gi|474934822|ref|YP_007688404.1|  3 NNRTIITLVGADHAGIIAAVCTYFAENDI-NILDLSMTTVQEFINMMMIV 51
                                      5666778888889***********99998.9*******998888776654 PP

>> SLATT_1  SMODS and SLOG-associating 2TM effector domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   5.6e-05      0.14      25      96 ..       4      75 ..       1      90 [. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.6e-05
                           SLATT_1 25 krwrlllillellalllaalrafgelsvdlvgvlaavaaallaWlelkqyeelaaaYslaaeeLeiiraale 96
                                      +r+ ++l+ +  +++++a+   f e +++++++  + +  ++  + + ++++ ++++    ++L+++ +++ 
  gi|474934822|ref|YP_007688404.1|  4 NRTIITLVGADHAGIIAAVCTYFAENDINILDLSMTTVQEFINMMMIVDLSKYKKSFPELSKDLDEVAKKVG 75
                                      566678899999*******************************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       871  (0.0485805); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 633.14
//
Query:       gi|474934823|ref|YP_007688405.1|  [L=454]
Description: hypothetical protein TALC_01260 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   3.3e-175  582.9  13.6   3.9e-175  582.6  13.6    1.0  1  DUF711    Uncharacterised ACR (DUF711)
  ------ inclusion threshold ------
      0.027   14.7   0.4          9    6.5   0.0    3.2  2  EF1_GNE   EF-1 guanine nucleotide exchange domain


Domain annotation for each model (and alignments):
>> DUF711  Uncharacterised ACR (DUF711)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  582.6  13.6  4.4e-179  3.9e-175       1     404 [.      13     417 ..      13     419 .. 0.99

  Alignments for each domain:
  == domain 1  score: 582.6 bits;  conditional E-value: 4.4e-179
                            DUF711   1 mieeekldiRtvTlgislldcasedleklaekiyekiikkaaklvktveeieeeyGievvtkRisvtpisellaeas 77 
                                       m+++e+ld+Rt+T+gislldc++ dl+ l+++iy ki+++a++lv++++ei  e G++v++kRisvtpi+ ++ +++
  gi|474934823|ref|YP_007688405.1|  13 MVSSENLDVRTITMGISLLDCITPDLDVLCDNIYAKITESAKNLVSVGDEIALEIGVPVINKRISVTPIA-IVGASA 88 
                                       999*******************************************************************.888877 PP

                            DUF711  78 aeea...velaktldelakevgvdfiggfsalvekgltkgdkeliesipealaetervcssvnvastkaginmdavr 151
                                       ++++   ve+a++l+++ ++vgv+figgfsalv+kg+t++d+ +i+sipeala+te++cssv +astk+gi+mdav+
  gi|474934823|ref|YP_007688405.1|  89 CRKTedfVEIAEALEKASQKVGVNFIGGFSALVQKGMTDSDRLMIDSIPEALAKTEHLCSSVSLASTKTGIDMDAVK 165
                                       777779*********************************************************************** PP

                            DUF711 152 aaaevikeiaeltkdkdglgnaklvvfanvpednPFfpgAfhgvgeaeavinvGvsgpgvvkkaleeakkeasleel 228
                                        ++e + e+a+ltkd+d++g+aklvvf+n  +dnPF++gAfhgv+eae vinvGvsgpgvv++a++++ +++s+e+l
  gi|474934823|ref|YP_007688405.1| 166 LMGEKVVETAQLTKDRDSIGCAKLVVFCNPTDDNPFMAGAFHGVTEAERVINVGVSGPGVVRTAISKV-RGESFETL 241
                                       ********************************************************************.6699**** PP

                            DUF711 229 aeaikktafkitrlgelvarevakrlgvefggiDlSlaPtpavgdSvaeileelglesfGapGtlaalalltdavkk 305
                                       +e+ikktafk+tr+g+lva+e+++rl+v+fg++DlSlaPtpavgdS+a+i++e+g+e +GapGt+aala+l+d+vkk
  gi|474934823|ref|YP_007688405.1| 242 CETIKKTAFKVTRVGQLVAKEASARLNVPFGIVDLSLAPTPAVGDSIADIIKEMGMEYCGAPGTTAALAILNDQVKK 318
                                       ***************************************************************************** PP

                            DUF711 306 GGvmasskvgGlsGlflpvsEDaglaeaaeegaltiekLlamsaVCsvGLDmvpipgdtsaetiaaliaDeaalavr 382
                                       GG+mass+vgGlsG+f+pv+ED+ +ae+a+ ga+++ekL+am++VCsvGLDm++ipgdt+a+ti+++iaDe+a++++
  gi|474934823|ref|YP_007688405.1| 319 GGIMASSYVGGLSGAFIPVTEDSSMAESAKIGAISLEKLEAMTCVCSVGLDMIAIPGDTPATTISGIIADEMAIGMV 395
                                       ***************************************************************************** PP

                            DUF711 383 lnKtlavRliPvpgkkaGdkve 404
                                       ++Kt+avRliPv+gkkaGd+++
  gi|474934823|ref|YP_007688405.1| 396 NQKTTAVRLIPVIGKKAGDSIS 417
                                       *******************986 PP

>> EF1_GNE  EF-1 guanine nucleotide exchange domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.2    0.0034        31      22      79 ..       4      57 ..       1     157 [. 0.86
   2 ?    6.5   0.0     0.001         9       3      50 ..     230     278 ..     228     322 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0034
                                      HHH..HS-TSEE--.--EEE-SSS-EEEEEEEEESSS-GGGGHHHHHHTTS-S......S CS
                           EF1_GNE 22 vks.ikleglvwgeasklepiafGlkkLqiscvieddkvstdeleekieeiege.ledlV 79
                                      +++ i+ +++v  e+ ++  i  G+  L   c+++d  v  d++  ki+    e  ++lV
  gi|474934823|ref|YP_007688405.1|  4 INEvIETNQMVSSENLDVRTITMGISLL--DCITPDLDVLCDNIYAKIT----EsAKNLV 57
                                      5666888888888899999999999998..59************99999....3244444 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.001
                                       EEEEEESSS---HHHHHHHHHH.HS-T.SEE--.--EEE-SSS-EEEEE CS
                           EF1_GNE   3 vlevkPeddetdleelekkvksikleg.lvwgeasklepiafGlkkLqi 50 
                                       + +v  e+ et  e ++k   +++  g lv +eas +  ++fG+  L +
  gi|474934823|ref|YP_007688405.1| 230 ISKVRGESFETLCETIKKTAFKVTRVGqLVAKEASARLNVPFGIVDLSL 278
                                       5678888899999999999999888888****************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 2665.06
//
Query:       gi|474934824|ref|YP_007688406.1|  [L=191]
Description: hypothetical protein TALC_01261 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0033   17.3   0.5     0.0033   17.3   0.5    3.9  5  Syndecan  Syndecan domain
  ------ inclusion threshold ------
      0.023   14.4   2.9      0.048   13.4   2.9    1.4  1  HlyIII    Haemolysin-III related
      0.025   14.1   1.6      0.044   13.3   0.6    1.9  1  Smim3     Small integral membrane protein 3
       0.21   11.7   0.0       0.24   11.6   0.0    1.2  1  DUF2236   Uncharacterized protein conserved in bacteria (DUF2
       0.53   10.7  13.4       0.22   11.9   1.9    2.4  2  DUF4199   Protein of unknown function (DUF4199)
       0.85    9.5   8.1       0.37   10.7   4.7    2.0  2  DUF1275   Protein of unknown function (DUF1275)
        6.5    6.4  18.7       0.63    9.7   1.7    3.0  2  Wzy_C     O-Antigen ligase


Domain annotation for each model (and alignments):
>> Syndecan  Syndecan domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.5   1.3e-06    0.0033      12      42 ..       9      41 ..       3      46 .. 0.70
   2 ?   -0.2   1.1      0.36   9.3e+02      15      32 ..      45      62 ..      43      65 .. 0.79
   3 ?   -4.0   0.3       5.8   1.5e+04      20      27 ..      94     101 ..      92     105 .. 0.59
   4 ?    3.0   0.1     0.038        98       6      22 ..     123     139 ..     120     143 .. 0.81
   5 ?   -1.6   0.0         1   2.6e+03      39      55 ..     169     186 ..     158     191 .] 0.70

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.3e-06
                          Syndecan 12 viggvv.vgllfaillvlf.lvYRmrKKDEGSY 42
                                      +i g + ++l++a  lv+f +vY  rK DEG Y
  gi|474934824|ref|YP_007688406.1|  9 IINGNLsAILMLAAGLVAFlIVYEYRKDDEGGY 41
                                      5666551445556666655279*********99 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.36
                          Syndecan 15 gvvvgllfaillvlflvY 32
                                      +v++g+++ i+l+ f v 
  gi|474934824|ref|YP_007688406.1| 45 SVLIGFILGICLMFFGVT 62
                                      578899999999998775 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 5.8
                          Syndecan  20 llfaillv 27 
                                       ll+ail +
  gi|474934824|ref|YP_007688406.1|  94 LLLAILAM 101
                                       66666644 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.038
                          Syndecan   6 pevlaaviggvvvgllf 22 
                                       p ++  v++g+vv ++f
  gi|474934824|ref|YP_007688406.1| 123 PRIILSVVVGAVVYMVF 139
                                       67888999999999887 PP

  == domain 5  score: -1.6 bits;  conditional E-value: 1
                          Syndecan  39 EGSYaLdepkk.snaaYk 55 
                                       EGS  L +     n++Y 
  gi|474934824|ref|YP_007688406.1| 169 EGSLLLADAPSlINYYYD 186
                                       788877777665666664 PP

>> HlyIII  Haemolysin-III related
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   2.9   1.9e-05     0.048      82     222 ..      15     166 ..      14     168 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.9e-05
                            HlyIII  82 sgIslliagsylplilyalakapkagllylslilalgvlgiisklvplfsr..................pearplra 140
                                       s+I +l ag +  li+y + k    g  y  ++l+  +lgi + ++ + +r                    +rplr 
  gi|474934824|ref|YP_007688406.1|  15 SAILMLAAGLVAFLIVYEYRK-DDEGGYYKLSVLIGFILGICLMFFGV-TRyegwssfdaalivlsgfvLFIRPLRD 89 
                                       689999999999999999977.6677778888888889**99999888.44588***********9986666***** PP

                            HlyIII 141 vlfillgllgvipllhlllvltqlgeaaelalvllvlggvlylvGavfYalrvPErlkpgkfdivghsHqiFHvfvv 217
                                       v f+ll  l++++++ ++++l++l+   e+ +      +++++vGav+Y+++    +  +  + vg+  + + ++++
  gi|474934824|ref|YP_007688406.1|  90 VPFALL--LAILAMAWMYVFLGGLSGDLEILSEGYPRIILSVVVGAVVYMVF---NFLEKLTQLVGKILNCWPILLI 161
                                       ***999..8888888889999999955588888888889999**********...999999**************** PP

                            HlyIII 218 lgalf 222
                                       lg+++
  gi|474934824|ref|YP_007688406.1| 162 LGSVC 166
                                       99988 PP

>> Smim3  Small integral membrane protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.6   1.7e-05     0.044      16      48 ..     151     183 ..     143     186 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.7e-05
                             Smim3  16 hiLDiWvivLiiLativimtsLlLCPataviiY 48 
                                        iL+ W i+Li+ +  +i  sLlL  a + i Y
  gi|474934824|ref|YP_007688406.1| 151 KILNCWPILLILGSVCIIEGSLLLADAPSLINY 183
                                       79********999999999********999987 PP

>> DUF2236  Uncharacterized protein conserved in bacteria (DUF2236)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   9.5e-05      0.24      97     157 ..      19      74 ..       7     143 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.5e-05
                           DUF2236  97 vhatfsasflraygrtvgpltaeeeeayyhewrrvgrllGvpdrllpa.traafdayldemv 157
                                       ++a+   +fl +y++     + ++e  yy +++++g+ lG+   + ++ tr++ ++ +d+ +
  gi|474934824|ref|YP_007688406.1|  19 MLAAGLVAFLIVYEY-----RKDDEGGYYKLSVLIGFILGI-CLMFFGvTRYEGWSSFDAAL 74 
                                       456666666667775.....59*******************.8888777*********9874 PP

>> DUF4199  Protein of unknown function (DUF4199)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.9   8.5e-05      0.22      36      80 ..      14      60 ..       2      84 .. 0.69
   2 ?    4.2   4.0      0.02        51       2      51 ..      92     138 ..      91     173 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.5e-05
                           DUF4199 36 lallllllvpflvylalkkyrkknlgG..fisfgqafgfgflislva 80
                                      l+ +l+l+  ++++l + +yrk ++gG  ++s   +f++g+ +++++
  gi|474934824|ref|YP_007688406.1| 14 LSAILMLAAGLVAFLIVYEYRKDDEGGyyKLSVLIGFILGICLMFFG 60
                                      44344444456678888888888887744556666666666666665 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.02
                           DUF4199   2 fGlilglvwilifllilyllglh...qilstgpllglla..llllllvpflvyla 51 
                                       f+l+l+++ ++++++  +l gl+   +i      l+  +  ++l+++v ++vy+ 
  gi|474934824|ref|YP_007688406.1|  92 FALLLAILAMAWMYV--FLGGLSgdlEI------LSEGYprIILSVVVGAVVYMV 138
                                       7999**********8..55555320333......333335455555543333322 PP

>> DUF1275  Protein of unknown function (DUF1275)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   4.7   0.00014      0.37      32     113 ..      25     104 ..      12     119 .. 0.70
   2 ?   -1.3   0.1      0.68   1.7e+03     158     168 ..     125     135 ..     117     163 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00014
                           DUF1275  32 tvllglalaegnakaalaalvsllaFvlGaalagllarrggrrrrlvllleallllaaallvpagsvsp.....lal 103
                                       + +l++   +++ +   ++l  l+ F+lG+ l+ +      +r+  +  + a+l+++ ++++      p     +al
  gi|474934824|ref|YP_007688406.1|  25 VAFLIVYEYRKDDEGGYYKLSVLIGFILGICLMFFGV----TRYEGWSSFDAALIVLSGFVLFIR---PlrdvpFAL 94 
                                       44555554444445555678889*******9998875....99*************999997644...234655555 PP

                           DUF1275 104 allafamGlq 113
                                       +l  +am+  
  gi|474934824|ref|YP_007688406.1|  95 LLAILAMAWM 104
                                       5555555544 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.68
                           DUF1275 158 iilafllGavv 168
                                       iil+ ++Gavv
  gi|474934824|ref|YP_007688406.1| 125 IILSVVVGAVV 135
                                       45555555554 PP

>> Wzy_C  O-Antigen ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.7   0.00024      0.63      17      70 ..      15      71 ..       9      78 .. 0.58
   2 ?   -2.4  16.7       1.2   3.1e+03       1      59 [.      48     142 ..      48     191 .] 0.58

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00024
                             Wzy_C 17 sgiigllvalivlliifykrri..pfllllg.ilvgvilliilfvls.tnletlknit 70
                                      s+i+ l +a +v+++i+y+ r      ++++ +l+g il+i l++++ t++e++ +  
  gi|474934824|ref|YP_007688406.1| 15 SAILML-AAGLVAFLIVYEYRKddEGGYYKLsVLIGFILGICLMFFGvTRYEGWSSFD 71
                                      455555.555555555555555585555555566666666666654316788887655 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.2
                             Wzy_C   1 ialllsllalflstsRs.giigl..lvalivlliifykrri...................pfllllgilvgvillii 55 
                                       i+++l+++++f+  +R  g+ ++  +++++ ++++f+++++                   +                
  gi|474934824|ref|YP_007688406.1|  48 IGFILGICLMFFGVTRYeGWSSFdaALIVLSGFVLFIRPLRdvpfalllailamawmyvfL---------------- 108
                                       6899999999999999989999977777777899999999966333333333333333330................ PP

                             Wzy_C  56 lfv................................l 59 
                                                                          l
  gi|474934824|ref|YP_007688406.1| 109 --GglsgdleilsegypriilsvvvgavvymvfnfL 142
                                       ..1444444444444444444444444444433332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       937  (0.0522617); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 1164.07
//
Query:       gi|474934825|ref|YP_007688407.1|  [L=619]
Description: Molecular chaperone, HSP90 family [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     4e-103  346.1   2.3   3.2e-101  339.8   2.3    2.0  1  HSP90        Hsp90 protein
    1.1e-11   44.8   0.6      2e-11   43.8   0.6    1.5  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
    2.9e-11   43.9   0.1    6.1e-11   42.8   0.1    1.6  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
  ------ inclusion threshold ------
      0.054   13.6   0.2        3.1    7.9   0.0    3.1  3  DcrB         DcrB


Domain annotation for each model (and alignments):
>> HSP90  Hsp90 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  339.8   2.3  7.2e-105  3.2e-101       1     485 [.     168     619 .]     168     619 .] 0.88

  Alignments for each domain:
  == domain 1  score: 339.8 bits;  conditional E-value: 7.2e-105
                                       GGGSHHHHHHHHHHCCTTSSS-EEEEEEEEXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXEEE CS
                             HSP90   1 eyleekklkelvkkySeFinfpiyllkekeeekeveeeeeeeeeeeeeeeeeakveeeeeeeeekkktkkvketvke 77 
                                       e+le+++l+el++kyS++i +pi++         v+e + +e+ e     +++k          ++k + v+++   
  gi|474934825|ref|YP_007688407.1| 168 EFLETERLRELIEKYSDYIRWPIHME--------VDESDWQETGE-----KDDKG---------EPKRELVSKK--V 220
                                       89*********************993........32222222111.....11122.........2333334433..2 PP

                                       EEEESXXSXGGGSXGGGSXHHHHHHHHHHTTTTTSXXSEEEEEEEXSSSXEEEEEEEXSSXXTTTTTTTTTSXXTTE CS
                             HSP90  78 wellNkqkpiWlrkpkevteeeYkeFYkslskdsedplavkhfsaegevefkaiLfvPkrapsdlfekykkkkknni 154
                                        + +N+  piW ++++e  +++  eFYk   +d+edp++v+  saeg v++ka+Lf+P +ap+d++++   + +  +
  gi|474934825|ref|YP_007688407.1| 221 DKVINSMVPIWRKSKEEAPDDKCIEFYKDKFRDWEDPVSVVRVSAEGAVSYKALLFIPAKAPYDFYTR---DFRPGL 294
                                       346****************************************************************6...56899* PP

                                       EEEETTEEEESXXTTSSXGGGTTXEEEEEESSSXSSSTHHHHHTCHHHHHHHHHHHHHHHHHHHTS.XHHH..HHTH CS
                             HSP90 155 kLYvrrVfitdefedllPkyLsFvkGvvdsddLPLNvsREtlqqnkilkvikkklvrKvlemlkkl.aeekeeykkf 230
                                       +LY   V+i+d++edllP  ++Fv+Gvvds d+ LN+sRE+lq+++ l+ +   l ++v + l++l ++e e+y++f
  gi|474934825|ref|YP_007688407.1| 295 QLYANGVLIMDRCEDLLPYCFRFVRGVVDSPDFSLNISREVLQHDRQLQSVGSYLTKQVKKELQRLmSDEPEKYATF 371
                                       *******************************************************999999988872556688**** PP

                                       HHHHHHHHHHHHHHXGGG.HHHHHTTXEEEETTEEEEEEEHHHHHHHSXTTXXEEEEEEXSSHHHHHTSGGGHHHHH CS
                             HSP90 231 ykefsknlklGiiedsan.rkklakLlrfksskseeeltsLedYvermkekqksiYyiageskeevekspflerlkk 306
                                       +++f++++k+G+++      + l ++l+f+s+k e++ +sL+ Y + m e+qk+iYy+++e+ +++++ p  e++ +
  gi|474934825|ref|YP_007688407.1| 372 WQSFGRQIKYGCVDGYGRdADLLKDILMFRSAK-EDKDISLDGYAKAMPEGQKKIYYVTAENAAHAKELPQAEQVID 447
                                       **************98861556778*****998.6779*************************************** PP

                                       TTXXEEEEXSTTHHHHHHTXSEETTEEEEETTBSTXXXXXXHHHHHHHHHHHHHHHHHHHHHHHTTTTTESEEEEXS CS
                             HSP90 307 kgyevlylvdpiDeyvvqqlkeyegkklvnvakegleleeeeeekkkkeelkkkfeeltkllkevlkdkvekvkvse 383
                                       kgy+vl ++d+iD +v + l++++gk++ nv+ e+l l e+eeekk+ e+++++++el++++ke+l+d+v +vk+s+
  gi|474934825|ref|YP_007688407.1| 448 KGYDVLVFTDEIDSFVANVLRDFDGKEFCNVTTEDLGL-ESEEEKKEAEKKDEEYKELLDFCKETLGDEVANVKISH 523
                                       **************************************.678899999999************************** PP

                                       SXSSXSEEEEBXTTSXXHHHHHHHHHHHHHHHSSTSSSSSXEEEEEXTTSHHHHHHHHHHHHTTTXHHHHHHHHHHH CS
                             HSP90 384 rlvdsPcvlvtseygwsanmerimkaqalrdkskssymsskktleinprhpiikeLkkkveedkedeeakdlaelly 460
                                       +l++ +++l +++  ++ + e+  +            +++ ++le+n + ++  +L+  +++d   e ak++++++y
  gi|474934825|ref|YP_007688407.1| 524 KLKSHAVLL-STQGNITFETEKYFREMPGMA---GDGVKAARVLELNTESQVFASLQAAFKDD--RERAKKIVKVMY 594
                                       **9876555.577789999999998776543...33455679*******************99..579********* PP

                                       HHHHHHTTXXXSXHHHHHHHHHHHH CS
                             HSP90 461 etallesGfsledpasfakrierll 485
                                        +a+l +G  +++p ++++ + ++l
  gi|474934825|ref|YP_007688407.1| 595 GQACLMAGQPVANPVEYSDLVLSML 619
                                       ******************9998876 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.6   4.6e-15     2e-11       4     108 ..      10     136 ..       6     162 .. 0.82

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 4.6e-15
                       HATPase_c_3   4 ekAlaelvdNsldAdaen..................vkievnknrgktgeivieDdGkGmseeelknalr.latssk 61 
                                       e+ l e++ N+ dA  +                   ++++++++     ++++ D+G Gm+ ee+++ l  +a+s +
  gi|474934825|ref|YP_007688407.1|  10 EIFLREIISNASDAIDKLnykaledsslgigrddfrIDVKIDRDA---RTVTVSDNGIGMNAEEMEKNLGyIAHSGT 83 
                                       67789********966656999************99888888865...79*****************8854888877 PP

                       HATPase_c_3  62 eakr.......kstslGkkGiGlklAslslgkkltvitkkegesstltldvdki 108
                                        + +       +s+ +G++G+G + +++++++k++v++k+ g+ ++++++ + +
  gi|474934825|ref|YP_007688407.1|  84 LEYKeslgenaDSEAIGQFGVG-FYSAFMVADKVDVVSKAFGSDTANKWSSSGS 136
                                       755434555556778*******.************************9997655 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.8   0.1   1.4e-14   6.1e-11       2     111 ..       9     160 ..       8     161 .. 0.65

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 1.4e-14
                                       HHHHHHHHHHHHHHHHHHH......HSTTT.........EEEEEEEEEETEEEEEEEESSSSSTTHHHT.......G CS
                         HATPase_c   2 dekrLrqiisnlvdNavkf......atkag.........eieveikaseddlvisveDnGiGipkedlk.......k 56 
                                       +e++Lr+iisn++d+ +k           +         +i+v+i+   d  +++v+DnGiG++ e+++       +
  gi|474934825|ref|YP_007688407.1|   9 KEIFLREIISNASDAIDKLnykaleD---SslgigrddfRIDVKID--RDARTVTVSDNGIGMNAEEMEknlgyiaH 80 
                                       799***************97754440...23444444445566666..679******************99999998 PP

                                       TCS.TTCH.....HCSTCHTSTSSSH..HHHHH...............HHHHHHTTTEEEE.............EEE CS
                         HATPase_c  57 lfe.kfsq.....ddstkrggggtGl..Glsiv...............kklvelmgGeiwv.............ese 97 
                                       +++  + +     +ds+++g++g+G+   ++++               +                          ++
  gi|474934825|ref|YP_007688407.1|  81 SGTlEYKEslgenADSEAIGQFGVGFysAFMVAdkvdvvskafgsdtaN-----------KwsssgsdgysiseCEK 146
                                       8888888899977777777777777663444445433333333332222...........13344444444443444 PP

                                       TTTEEEEEEEEESS CS
                         HATPase_c  98 pgrGttftftlple 111
                                       +  Gt+++++++++
  gi|474934825|ref|YP_007688407.1| 147 ESPGTDIVMHIKED 160
                                       44599998888875 PP

>> DcrB  DcrB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.34   1.5e+03      24      49 ..     148     173 ..     142     185 .. 0.83
   2 ?    7.9   0.0    0.0007       3.1      26      62 ..     326     362 ..     320     381 .. 0.85
   3 ?    1.3   0.0     0.075   3.3e+02       6      38 ..     439     473 ..     438     532 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.34
                                       TT-EEEEEEEE---TTS-HHHHHHHH CS
                              DcrB  24 atgaslvIsRdeleegetleeylerq 49 
                                       + g+ +v+ ++e+++ge+  e+le +
  gi|474934825|ref|YP_007688407.1| 148 SPGTDIVMHIKEDADGEEYSEFLETE 173
                                       34999*****************9865 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0007
                                       -EEEEEEEE---TTS-HHHHHHHHHHHHHHHSTT-EE CS
                              DcrB  26 gaslvIsRdeleegetleeylerqlkqlrkrlkgfql 62 
                                       ++sl+IsR+ l+ + +l+++   + kq++k+l+++  
  gi|474934825|ref|YP_007688407.1| 326 DFSLNISREVLQHDRQLQSVGSYLTKQVKKELQRLMS 362
                                       79******************99999999999998765 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.075
                                       EE..TTSEE--BEEEEE--BTT-EEEEEEEE---T CS
                              DcrB   6 LP..agwqDrSvnvlvfpdeatgaslvIsRdelee 38 
                                       LP  ++++D+   vlvf+de   + +++ Rd + +
  gi|474934825|ref|YP_007688407.1| 439 LPqaEQVIDKGYDVLVFTDEIDSFVANVLRDFDGK 473
                                       6666789999999*****98779999999997654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (619 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       898  (0.0500865); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.71u 0.33s 00:00:01.04 Elapsed: 00:00:00.51
# Mc/sec: 3657.14
//
Query:       gi|474934826|ref|YP_007688408.1|  [L=185]
Description: hypothetical protein TALC_01263 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-11   42.8   8.5    5.8e-05   22.5   0.4    3.3  3  TF_Zn_Ribbon    TFIIB zinc-binding
    7.2e-05   22.8  14.3     0.0067   16.5   0.4    4.0  3  Zn-ribbon_8     Zinc ribbon domain
    0.00015   21.6   2.7      0.087   12.7   0.0    2.6  3  MCM_OB          MCM OB domain
    0.00026   21.0  15.8     0.0079   16.2  10.6    2.9  3  DZR             Double zinc ribbon
    0.00036   20.5  10.7        0.1   12.6   0.9    3.3  3  HypA            Hydrogenase/urease nickel incorporation, meta
     0.0038   16.9   9.8      0.019   14.7   9.9    1.8  1  TackOD1         Thaumarchaeal output domain 1
     0.0042   17.7   8.6       0.45   11.2   0.7    2.8  3  FYDLN_acid      Protein of unknown function (FYDLN_acid)
  ------ inclusion threshold ------
      0.011   15.4   0.8      0.011   15.4   0.8    4.5  4  zinc_ribbon_2   zinc-ribbon domain
      0.031   14.4  14.6        0.2   11.9   0.4    3.1  3  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
      0.048   13.6  13.2       0.43   10.5   0.9    2.9  3  C1_1            Phorbol esters/diacylglycerol binding domain 
      0.048   13.6   1.9      0.048   13.6   1.9    3.4  4  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
      0.063   13.0  23.2        0.7    9.6   3.5    4.9  4  zf-RRN7         Zinc-finger of RNA-polymerase I-specific TFII
      0.065   12.9  19.6       0.23   11.2   3.7    3.8  3  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
       0.15   12.1  15.5          1    9.4   0.8    4.4  3  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
       0.17   11.6   0.2       0.17   11.6   0.2    3.5  3  A2L_zn_ribbon   A2L zinc ribbon domain
       0.29   11.8  18.5          9    7.1   0.1    5.2  5  zf-ISL3         zinc-finger of transposase IS204/IS1001/IS109
       0.42   10.7  10.9         13    6.0   1.9    4.2  4  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
       0.68   10.0   8.9      0.073   13.2   4.0    1.9  2  Mut7-C          Mut7-C RNAse domain
        1.1    9.3  28.2        6.2    6.9   3.8    4.0  4  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
        1.5    9.0   6.3       0.33   11.1   1.6    2.2  3  DUF2318         Predicted membrane protein (DUF2318)
        1.7    8.6   7.5        1.4    8.8   0.1    2.8  2  NinF            NinF protein
        2.2    8.6  10.4        7.9    6.7   0.2    3.0  3  DUF2072         Zn-ribbon containing protein
        2.3    8.5  13.2        9.7    6.5   0.1    4.5  4  zf-RING_7       C4-type zinc ribbon domain
        2.6    8.4   0.0        2.6    8.4   0.0    4.3  4  zinc_ribbon_9   zinc-ribbon
        2.8    7.5  25.2        4.4    6.8   0.5    5.1  4  zf-ribbon_3     zinc-ribbon domain
        5.2    6.8  15.8        7.5    6.2   0.1    4.9  5  zf_UBZ          Ubiquitin-Binding Zinc Finger
          6    6.9  10.5        7.3    6.6   0.1    2.9  3  DUF1451         Zinc-ribbon containing domain
          6    7.1   8.8         49    4.2   8.9    2.4  1  FYVE_2          FYVE-type zinc finger
        7.9    6.5  21.3        9.6    6.2   0.7    5.1  5  zinc_ribbon_4   zinc-ribbon domain


Domain annotation for each model (and alignments):
>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.9   1.6e-05    0.0097       2      28 ..      16      41 ..      15      42 .. 0.90
   2 !   22.5   0.4   9.4e-08   5.8e-05       2      27 ..      51      74 ..      50      76 .. 0.94
   3 !    8.2   0.0    0.0028       1.7       2      18 ..      87     103 ..      86     104 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.6e-05
                                      EETTTTCEECHEE.TSTTCEEESSSSBE CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveD.pergelvCtdCGlV 28
                                      +CP C+s  ++++ ++  ++vC++CG  
  gi|474934826|ref|YP_007688408.1| 16 RCPRCNS--ILWNcTDLKTHVCKRCGHK 41
                                      7*****9..9***9999999******86 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 9.4e-08
                                      EETTTTCEECHEETSTTCEEESSSSB CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGl 27
                                      +CPnC s+  ++D++  +++C++CG 
  gi|474934826|ref|YP_007688408.1| 51 RCPNCRSK--LWDADVETFICGSCGH 74
                                      7******9..9**************6 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0028
                                       EETTTTCEECHEETSTT CS
                      TF_Zn_Ribbon   2 kCPnCgstnlveDperg 18 
                                       +CP Cgs n  +Dp++g
  gi|474934826|ref|YP_007688408.1|  87 TCPACGSGNWFVDPKSG 103
                                       7******9988888877 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.2     0.097        60      27      34 ..      14      22 ..       2      24 .. 0.76
   2 !    8.8   2.2    0.0027       1.7       7      35 ..      34      58 ..      29      60 .. 0.72
   3 !   16.5   0.4   1.1e-05    0.0067       6      34 ..      67      93 ..      66      96 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.097
                       Zn-ribbon_8 27 ta.CPeCgs 34
                                      +  CP+C+s
  gi|474934826|ref|YP_007688408.1| 14 PRrCPRCNS 22
                                      445****87 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0027
                       Zn-ribbon_8  7 rCeeCghefevlqsisdapltaCPeCgse 35
                                       C++Cgh+   +    d+ +  CP+C s+
  gi|474934826|ref|YP_007688408.1| 34 VCKRCGHKWLGRT---DD-PLRCPNCRSK 58
                                      5*****7766333...43.355****986 PP

  == domain 3  score: 16.5 bits;  conditional E-value: 1.1e-05
                       Zn-ribbon_8  6 YrCeeCghefevlqsisdapltaCPeCgs 34
                                      + C +Cgh+     ++ ++++ +CP+Cgs
  gi|474934826|ref|YP_007688408.1| 67 FICGSCGHKAL--YRVGRSAPATCPACGS 93
                                      78*****6655..4455556677*****9 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.2       2.2   1.4e+03      49      61 ..      12      22 ..       2      33 .. 0.72
   2 !    7.0   2.0    0.0082       5.1      33      62 ..      31      58 ..      19      66 .. 0.78
   3 !   12.7   0.0   0.00014     0.087      33     104 ..      65     137 ..      60     146 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2.2
                                      ---SB-..TTT-H CS
                            MCM_OB 49 eePrkCeekeCes 61
                                      + Pr+C  ++C+s
  gi|474934826|ref|YP_007688408.1| 12 TVPRRC--PRCNS 22
                                      459999..88884 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0082
                                      EEEEETTT-.-EEES----SB-..TTT-HH CS
                            MCM_OB 33 avfeckkcgktveveleePrkCeekeCesk 62
                                       ++ ck+cg++   ++ +P +C  ++C+sk
  gi|474934826|ref|YP_007688408.1| 31 KTHVCKRCGHKWLGRTDDPLRC--PNCRSK 58
                                      5799*****966669999****..99*953 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 0.00014
                                       EEEEETTT-.-EEES---..-SB-..TTT-HHH-EEE-GGGSEEEEEEEEEEE------..-------EEEEEEEG CS
                            MCM_OB  33 avfeckkcgktvevelee..PrkCeekeCeskdpfkletekskfvdfqklklQEspeev..paGelPrsleviled 104
                                        +f c +cg++  +++ +  P +C  ++C+ ++++ +++++ +   + + ++ E+ e++    G +P  +++++++
  gi|474934826|ref|YP_007688408.1|  65 ETFICGSCGHKALYRVGRsaPATC--PACG-SGNWFVDPKSGQDAVTDSTRVAEQVERAfrAGGGIPAMVSILVSE 137
                                       6899*****96665544455****..99**.799999999666655566666666666654788899999888765 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   4.5     0.013       8.2      27      49 .]      11      39 ..       1      39 [. 0.66
   2 !   16.2  10.6   1.3e-05    0.0079       1      49 []      17      73 ..      17      73 .. 0.82
   3 !   12.7   6.5   0.00015     0.095       1      36 [.      52      93 ..      52      96 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.013
                               DZR 27 a..edrCpsCgek....vdpearfCpeCG 49
                                      +  ++rCp+C++     +d+++ +C+ CG
  gi|474934826|ref|YP_007688408.1| 11 NtvPRRCPRCNSIlwncTDLKTHVCKRCG 39
                                      35579999999873323478888899998 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.3e-05
                               DZR  1 CpqCgee....lppdarfCseCgtk.lkavaaedrCpsCgek...vdpearfCpeCG 49
                                      Cp+C++     ++ + ++C++Cg+k l ++ ++ rCp+C +k   +d e+ +C++CG
  gi|474934826|ref|YP_007688408.1| 17 CPRCNSIlwncTDLKTHVCKRCGHKwLGRTDDPLRCPNCRSKlwdADVETFICGSCG 73
                                      9***9998887899999********6666666*********97434555566****9 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 0.00015
                               DZR  1 CpqCgee...lppdarfCseCgtk.lkavaa..edrCpsCge 36
                                      Cp+C+++    + +   C+ Cg+k l +v +  + +Cp+Cg+
  gi|474934826|ref|YP_007688408.1| 52 CPNCRSKlwdADVETFICGSCGHKaLYRVGRsaPATCPACGS 93
                                      *******666666777*******9755444477*******97 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.2     0.076        47      76      95 ..       2      23 ..       1      32 [. 0.74
   2 !   12.6   0.9   0.00017       0.1      72      95 ..      34      58 ..      28      66 .. 0.82
   3 !   10.0   0.2    0.0011      0.65      70      97 ..      66      96 ..      60     113 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.076
                                      TS-EEECHHH..HHS-TTTSSS CS
                              HypA 76 Cgkefeleek..alrCpkCgsa 95
                                      Cg+ ++++ +    rCp+C+s 
  gi|474934826|ref|YP_007688408.1|  2 CGYGWKKRGNtvPRRCPRCNSI 23
                                      899998766434559****986 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00017
                                      EETTTS-EEECHHH.HHS-TTTSSS CS
                              HypA 72 rCreCgkefeleek.alrCpkCgsa 95
                                       C++Cg+++  +++  lrCp+C s+
  gi|474934826|ref|YP_007688408.1| 34 VCKRCGHKWLGRTDdPLRCPNCRSK 58
                                      7********96665589*****996 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.0011
                                      EEEETTTS-EEECHH.H..HHS-TTTSSS-E CS
                              HypA 70 kvrCreCgkefelee.k..alrCpkCgsadv 97
                                      ++ C +Cg++   +  +   ++Cp+Cgs + 
  gi|474934826|ref|YP_007688408.1| 66 TFICGSCGHKALYRVgRsaPATCPACGSGNW 96
                                      578*****99886554335569*****9763 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   9.9   3.1e-05     0.019      88     169 ..      15      92 ..       9      95 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.1e-05
                           TackOD1  88 evCpkCkSidieeqelihhftCgnvgpeeeflkegkleCpkCktkLrhiGvDYdrplevykCnsCkslfsep...ev 161
                                         Cp C+Si  +++ l  h+ C + g +   ++++ l Cp+C++kL      +d   e+++C sC++ + +    ++
  gi|474934826|ref|YP_007688408.1|  15 RRCPRCNSILWNCTDLKTHV-CKRCGHKWLGRTDDPLRCPNCRSKL------WDADVETFICGSCGHKALYRvgrSA 84 
                                       56888888877777665553.6666667777888888888888888......5555678888888886655411145 PP

                           TackOD1 162 karClsCe 169
                                        a+C  C+
  gi|474934826|ref|YP_007688408.1|  85 PATCPACG 92 
                                       56666665 PP

>> FYDLN_acid  Protein of unknown function (FYDLN_acid)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       5.6   3.4e+03      26      34 ..      14      22 ..      11      26 .. 0.69
   2 !   11.2   0.7   0.00073      0.45      10      36 ..      33      59 ..      30      67 .. 0.86
   3 !   11.0   0.2   0.00083      0.51      11      35 ..      68      94 ..      66     123 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 5.6
                        FYDLN_acid 26 Pivcpkcge 34
                                      P  cp c++
  gi|474934826|ref|YP_007688408.1| 14 PRRCPRCNS 22
                                      667777765 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00073
                        FYDLN_acid 10 riCpscgakFYDLnkdPivcpkcgeef 36
                                      ++C+ cg+k+   + dP  cp+c ++ 
  gi|474934826|ref|YP_007688408.1| 33 HVCKRCGHKWLGRTDDPLRCPNCRSKL 59
                                      79********99999********9765 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00083
                        FYDLN_acid 11 iCpscgak.FYDLnk.dPivcpkcgee 35
                                      iC scg+k  Y  ++  P++cp+cg+ 
  gi|474934826|ref|YP_007688408.1| 68 ICGSCGHKaLYRVGRsAPATCPACGSG 94
                                      799**98868*****89*******984 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.2      0.26   1.6e+02       1       6 [.      16      21 ..      16      24 .. 0.76
   2 ?    3.5   1.1       0.1        64       2       8 ..      35      41 ..      33      41 .. 0.76
   3 ?   15.4   0.8   1.8e-05     0.011       1      22 [.      51      75 ..      51      76 .. 0.94
   4 ?    4.5   0.7      0.05        31      16      21 ..      88      93 ..      86      95 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.26
                     zinc_ribbon_2  1 fCpnCG 6 
                                      +Cp+C 
  gi|474934826|ref|YP_007688408.1| 16 RCPRCN 21
                                      599996 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.1
                     zinc_ribbon_2  2 CpnCGae 8 
                                      C++CG++
  gi|474934826|ref|YP_007688408.1| 35 CKRCGHK 41
                                      8888876 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 1.8e-05
                     zinc_ribbon_2  1 fCpnCGael.q.dnakF.CpyCGtp 22
                                      +CpnC  +l + d ++F C  CG++
  gi|474934826|ref|YP_007688408.1| 51 RCPNCRSKLwDaDVETFiCGSCGHK 75
                                      6*********9899999******97 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.05
                     zinc_ribbon_2 16 CpyCGt 21
                                      Cp CG+
  gi|474934826|ref|YP_007688408.1| 88 CPACGS 93
                                      888886 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   2.8    0.0014      0.86       9      37 ..      15      46 ..       8      48 .. 0.83
   2 ?   11.9   0.4   0.00032       0.2       9      38 ..      50      81 ..      49      87 .. 0.82
   3 ?   -0.1   0.2       1.8   1.1e+03      26      31 ..      88      93 ..      83      96 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0014
                      NOB1_Zn_bind  9 lrChaCfkvt...kdmtkkFCpkCGnktLkrv 37
                                       rC  C ++    +d + + C++CG+k L r+
  gi|474934826|ref|YP_007688408.1| 15 RRCPRCNSILwncTDLKTHVCKRCGHKWLGRT 46
                                      589999997655599************99986 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00032
                      NOB1_Zn_bind  9 lrChaCfkvt..kdmtkkFCpkCGnktLkrva 38
                                      lrC  C +     d +   C +CG+k L rv 
  gi|474934826|ref|YP_007688408.1| 50 LRCPNCRSKLwdADVETFICGSCGHKALYRVG 81
                                      79****9977445678888***********96 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 1.8
                      NOB1_Zn_bind 26 CpkCGn 31
                                      Cp CG+
  gi|474934826|ref|YP_007688408.1| 88 CPACGS 93
                                      9***97 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   3.8    0.0062       3.8       3      35 ..       6      39 ..       5      39 .. 0.93
   2 ?   10.5   0.9    0.0007      0.43       1      35 [.      40      73 ..      40      76 .. 0.93
   3 ?    0.1   0.0       1.3   7.9e+02      10      20 ..      84      94 ..      78     103 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0062
                                      EEEE--SS--B-TTT-SB--S.SSS-EEEETTT- CS
                              C1_1  3 wvhrnfkqptfCkhCgeflwg.kekqglkCswCk 35
                                      w++r    p +C  C+++lw    +    C+ C+
  gi|474934826|ref|YP_007688408.1|  6 WKKRGNTVPRRCPRCNSILWNcTDLKTHVCKRCG 39
                                      99998899************************95 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0007
                                      --EEEE--SS--B-TTT-SB--SSSS-EEEETTT- CS
                              C1_1  1 HhwvhrnfkqptfCkhCgeflwgkekqglkCswCk 35
                                      H+w  r+ ++p +C  C++ lw      + C  C+
  gi|474934826|ref|YP_007688408.1| 40 HKWLGRT-DDPLRCPNCRSKLWDADVETFICGSCG 73
                                      99****9.***************99999*9*9997 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.3
                                      S--B-TTT-SB CS
                              C1_1 10 qptfCkhCgef 20
                                       p++C  Cg+ 
  gi|474934826|ref|YP_007688408.1| 84 APATCPACGSG 94
                                      68999999975 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   4.4     0.008         5      30      56 ..      16      42 ..      11      46 .. 0.93
   2 ?   13.6   1.9   7.8e-05     0.048      31      61 ..      35      65 ..      34      68 .. 0.93
   3 ?   11.0   1.4    0.0005      0.31      30      56 ..      51      76 ..      50      79 .. 0.93
   4 ?    1.1   0.3       0.6   3.7e+02      30      36 ..      87      93 ..      84      96 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.008
                    OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfea 56
                                      +C++C s++ +  + +t++C++Cg+++
  gi|474934826|ref|YP_007688408.1| 16 RCPRCNSILWNCTDLKTHVCKRCGHKW 42
                                      7**********9999*********986 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 7.8e-05
                    OrfB_Zn_ribbon 31 CseCgsknkealsgrtfkCpnCgfe.adrDvn 61
                                      C +Cg+k    ++++ ++CpnC  + +d+Dv 
  gi|474934826|ref|YP_007688408.1| 35 CKRCGHKWLG-RTDDPLRCPNCRSKlWDADVE 65
                                      *******999.9******************95 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.0005
                    OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfea 56
                                      +C++C sk+ +  + +tf C +Cg++a
  gi|474934826|ref|YP_007688408.1| 51 RCPNCRSKLWD-ADVETFICGSCGHKA 76
                                      6**********.9***********985 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.6
                    OrfB_Zn_ribbon 30 tCseCgs 36
                                      tC+ Cgs
  gi|474934826|ref|YP_007688408.1| 87 TCPACGS 93
                                      7999997 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.3       0.3   1.8e+02       6      15 ..      16      25 ..      15      26 .. 0.84
   2 ?    7.1   0.6    0.0068       4.2      22      31 ..      33      42 ..      32      43 .. 0.85
   3 ?    9.6   3.5    0.0011       0.7       5      30 ..      50      75 ..      47      77 .. 0.88
   4 ?    5.2   0.6     0.027        17       7      16 ..      88      97 ..      87      99 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.3
                           zf-RRN7  6 pCgvCgcrsf 15
                                      +C+ C++ ++
  gi|474934826|ref|YP_007688408.1| 16 RCPRCNSILW 25
                                      7999999887 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0068
                           zf-RRN7 22 yyCrrChtqe 31
                                       +C+rC++++
  gi|474934826|ref|YP_007688408.1| 33 HVCKRCGHKW 42
                                      69*****986 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0011
                           zf-RRN7  5 ppCgvCgcrsftl.ddGfyyCrrChtq 30
                                       +C+ C++++++   + +++C +C+++
  gi|474934826|ref|YP_007688408.1| 50 LRCPNCRSKLWDAdVE-TFICGSCGHK 75
                                      69***********777.9999999997 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.027
                           zf-RRN7  7 CgvCgcrsft 16
                                      C++Cg+ +++
  gi|474934826|ref|YP_007688408.1| 88 CPACGSGNWF 97
                                      ******9996 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.4         3   1.8e+03      19      23 ..      16      20 ..      11      22 .. 0.79
   2 ?   11.2   3.7   0.00037      0.23       2      24 ..      34      56 ..      33      59 .. 0.91
   3 ?   10.4   2.0   0.00065       0.4       2      25 ..      68      93 ..      67      94 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 3
                                      --SSS CS
                    DNA_RNApol_7kD 19 RCkeC 23
                                      RC  C
  gi|474934826|ref|YP_007688408.1| 16 RCPRC 20
                                      88888 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00037
                                      B-SSS--B----SSS----SSS- CS
                    DNA_RNApol_7kD  2 iCgeCgaevslkkgdpiRCkeCG 24
                                       C +Cg++   +  dp+RC +C 
  gi|474934826|ref|YP_007688408.1| 34 VCKRCGHKWLGRTDDPLRCPNCR 56
                                      599*******************5 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00065
                                      B-SSS--B--..--SSS----SSS-- CS
                    DNA_RNApol_7kD  2 iCgeCgaevs..lkkgdpiRCkeCGh 25
                                      iCg Cg++    + +++p  C  CG+
  gi|474934826|ref|YP_007688408.1| 68 ICGSCGHKALyrVGRSAPATCPACGS 93
                                      9*****9975459999********96 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   4.2     0.096        59       4      29 ..      16      42 ..      12      43 .. 0.79
   2 ?    9.4   0.8    0.0016         1       4      27 ..      51      74 ..      49      75 .. 0.91
   3 ?    2.9   0.1      0.18   1.1e+02       5      10 ..      88      93 ..      83     101 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.096
                    PhnA_Zn_Ribbon  4 kCplCaSeytY.edgallvCpeCahEw 29
                                       Cp C+S+     d    vC  C+h w
  gi|474934826|ref|YP_007688408.1| 16 RCPRCNSILWNcTDLKTHVCKRCGHKW 42
                                      69***9985435888888999999988 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0016
                    PhnA_Zn_Ribbon  4 kCplCaSeytYedgallvCpeCah 27
                                       Cp+C S    +d + ++C  C+h
  gi|474934826|ref|YP_007688408.1| 51 RCPNCRSKLWDADVETFICGSCGH 74
                                      5*****98777***********99 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.18
                    PhnA_Zn_Ribbon  5 CplCaS 10
                                      Cp C+S
  gi|474934826|ref|YP_007688408.1| 88 CPACGS 93
                                      888887 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.5   9.2e+02      24      30 ..      17      23 ..      15      24 .. 0.85
   2 ?   11.6   0.2   0.00028      0.17       4      27 ..      33      55 ..      30      57 .. 0.92
   3 ?   -1.8   3.6       4.5   2.8e+03       6      15 ..      69      78 ..      67      94 .. 0.56

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.5
                     A2L_zn_ribbon 24 CieCgas 30
                                      C+ C+++
  gi|474934826|ref|YP_007688408.1| 17 CPRCNSI 23
                                      999*986 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00028
                     A2L_zn_ribbon  4 kvCsvCggngilnseqgylvCieC 27
                                       vC+ Cg+  +  ++++ l C++C
  gi|474934826|ref|YP_007688408.1| 33 HVCKRCGHKWLG-RTDDPLRCPNC 55
                                      59**********.*********** PP

  == domain 3  score: -1.8 bits;  conditional E-value: 4.5
                     A2L_zn_ribbon  6 CsvCggngil 15
                                      C  Cg+  ++
  gi|474934826|ref|YP_007688408.1| 69 CGSCGHKALY 78
                                      7777776555 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   1.7      0.22   1.4e+02       2      10 ..      14      22 ..      13      27 .. 0.89
   2 ?    2.5   0.3      0.37   2.3e+02       2      11 ..      32      41 ..      31      47 .. 0.85
   3 ?    6.3   0.1     0.025        16       2      11 ..      49      58 ..      48      63 .. 0.85
   4 ?    2.1   0.1       0.5   3.1e+02       4      17 ..      68      81 ..      65      83 .. 0.80
   5 ?    7.1   0.1     0.015         9       1      10 [.      84      93 ..      84     108 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.22
                           zf-ISL3  2 phrCPnCgs 10
                                      p+rCP+C+s
  gi|474934826|ref|YP_007688408.1| 14 PRRCPRCNS 22
                                      78*****86 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.37
                           zf-ISL3  2 phrCPnCgsk 11
                                      +h+C +Cg k
  gi|474934826|ref|YP_007688408.1| 32 THVCKRCGHK 41
                                      699*****86 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.025
                           zf-ISL3  2 phrCPnCgsk 11
                                      p rCPnC+sk
  gi|474934826|ref|YP_007688408.1| 49 PLRCPNCRSK 58
                                      679****997 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.5
                           zf-ISL3  4 rCPnCgsktvvkhg 17
                                       C  Cg k +++ g
  gi|474934826|ref|YP_007688408.1| 68 ICGSCGHKALYRVG 81
                                      7*******998765 PP

  == domain 5  score: 7.1 bits;  conditional E-value: 0.015
                           zf-ISL3  1 aphrCPnCgs 10
                                      ap +CP Cgs
  gi|474934826|ref|YP_007688408.1| 84 APATCPACGS 93
                                      589******8 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0      0.11        68       1       7 [.      16      22 ..      16      25 .. 0.85
   2 ?    4.2   0.0      0.07        43       1       9 [.      51      59 ..      51      63 .. 0.87
   3 ?   -1.2   0.1       3.6   2.2e+03       4       9 ..      71      76 ..      68      79 .. 0.67
   4 ?    6.0   1.9      0.02        13       1       7 [.      87      93 ..      87      94 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.11
                    DNA_ligase_ZBD  1 hCPvCGs 7 
                                      +CP C+s
  gi|474934826|ref|YP_007688408.1| 16 RCPRCNS 22
                                      5****99 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.07
                    DNA_ligase_ZBD  1 hCPvCGsav 9 
                                      +CP C s++
  gi|474934826|ref|YP_007688408.1| 51 RCPNCRSKL 59
                                      5****9987 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 3.6
                    DNA_ligase_ZBD  4 vCGsav 9 
                                      +CG+++
  gi|474934826|ref|YP_007688408.1| 71 SCGHKA 76
                                      688765 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.02
                    DNA_ligase_ZBD  1 hCPvCGs 7 
                                      +CP+CGs
  gi|474934826|ref|YP_007688408.1| 87 TCPACGS 93
                                      7*****9 PP

>> Mut7-C  Mut7-C RNAse domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   4.0   0.00012     0.073      83     135 ..       7      61 ..       3      68 .. 0.85
   2 ?   -2.3   0.1         7   4.3e+03     124     134 ..      86      96 ..      74     103 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00012
                            Mut7-C  83 klslkpelsrCvaCngeleeve..keevkervpekvyeeadeftrCekCrkvfWk 135
                                       k + + + +rC +Cn+ l + +  k++v +r  +k   + d+  rC++Cr   W 
  gi|474934826|ref|YP_007688408.1|   7 KKRGNTVPRRCPRCNSILWNCTdlKTHVCKRCGHKWLGRTDDPLRCPNCRSKLWD 61 
                                       56678889********9988763478899*********************99997 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 7
                            Mut7-C 124 trCekCrkvfW 134
                                       ++C++C+   W
  gi|474934826|ref|YP_007688408.1|  86 ATCPACGSGNW 96 
                                       57888886555 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   9.5     0.019        12      14      45 ..       5      40 ..       1      41 [. 0.79
   2 ?    6.9   3.8      0.01       6.2      19      45 ..      50      74 ..      42      75 .. 0.76
   3 ?    4.3   4.0     0.066        41      18      43 ..      66      91 ..      58      92 .. 0.76
   4 ?    4.7   0.9     0.048        30      19      26 ..      86      93 ..      81      98 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.019
                     Zn_Tnp_IS1595 14 rWpng.....fvCPhCgsrkayriktrglfqCkeCrk 45
                                       W+ +     ++CP+C  + ++  ++ + + Ck+C++
  gi|474934826|ref|YP_007688408.1|  5 GWKKRgntvpRRCPRCN-SILWNCTDLKTHVCKRCGH 40
                                      588778888788****9.56777777778******98 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.01
                     Zn_Tnp_IS1595 19 fvCPhCgsrkayriktrglfqCkeCrk 45
                                       +CP+C  +k++     + f C +C++
  gi|474934826|ref|YP_007688408.1| 50 LRCPNCR-SKLWDADV-ETFICGSCGH 74
                                      68*****.66777664.88******98 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.066
                     Zn_Tnp_IS1595 18 gfvCPhCgsrkayriktrglfqCkeC 43
                                      +f+C  Cg++ +yr+ +     C +C
  gi|474934826|ref|YP_007688408.1| 66 TFICGSCGHKALYRVGRSAPATCPAC 91
                                      48999999999999988766677776 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.048
                     Zn_Tnp_IS1595 19 fvCPhCgs 26
                                       +CP+Cgs
  gi|474934826|ref|YP_007688408.1| 86 ATCPACGS 93
                                      68*****7 PP

>> DUF2318  Predicted membrane protein (DUF2318)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.4      0.11        66      35      61 ..      15      42 ..       5      46 .. 0.78
   2 ?   11.1   1.6   0.00054      0.33      35      77 ..      33      76 ..      26      87 .. 0.88
   3 ?   -1.4   0.0       4.2   2.6e+03      34      45 ..      85      96 ..      78     131 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.11
                           DUF2318 35 daCevCekkgYv.qegeelvCknCgvrf 61
                                        C  C++  +   + ++ vCk+Cg ++
  gi|474934826|ref|YP_007688408.1| 15 RRCPRCNSILWNcTDLKTHVCKRCGHKW 42
                                      5688888888885666888******998 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00054
                           DUF2318 35 daCevCekkgYvqegeelvCknCgvrfaldsige.kkGGCnpip 77
                                       +C+ C++k    +++ l C nC +++  +++++ + G+C   +
  gi|474934826|ref|YP_007688408.1| 33 HVCKRCGHKWLGRTDDPLRCPNCRSKLWDADVETfICGSCGHKA 76
                                      68**************************9999997889997655 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 4.2
                           DUF2318 34 ldaCevCekkgY 45
                                        +C  C++  +
  gi|474934826|ref|YP_007688408.1| 85 PATCPACGSGNW 96
                                      557777744433 PP

>> NinF  NinF protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   1.0      0.14        88      29      40 ..      29      40 ..      13      49 .. 0.75
   2 ?    8.8   0.1    0.0023       1.4      19      44 ..      50      78 ..      45      86 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.14
                              NinF 29 vdevhvCeeCva 40
                                       + +hvC  C  
  gi|474934826|ref|YP_007688408.1| 29 DLKTHVCKRCGH 40
                                      5789******65 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0023
                              NinF 19 L.CanCskkL..evdevhvCeeCvaeliy 44
                                      L C nC  kL     e+ +C  C  +++y
  gi|474934826|ref|YP_007688408.1| 50 LrCPNCRSKLwdADVETFICGSCGHKALY 78
                                      66****99994334699*******99996 PP

>> DUF2072  Zn-ribbon containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   3.0      0.15        92       1      28 [.      14      41 ..      14      44 .. 0.90
   2 ?    3.5   0.6      0.13        78       1      30 [.      49      77 ..      49      87 .. 0.82
   3 ?    6.7   0.2     0.013       7.9       4      55 ..      69     118 ..      68     173 .. 0.62

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.15
                           DUF2072  1 PHkCtkCekvfedgskeilkGCpsCGgk 28
                                      P +C +C++++ + ++   + C  CG k
  gi|474934826|ref|YP_007688408.1| 14 PRRCPRCNSILWNCTDLKTHVCKRCGHK 41
                                      899**********99977889*****87 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.13
                           DUF2072  1 PHkCtkCekvfedgskeilkGCpsCGgkkF 30
                                      P +C +C + + d++ e    C sCG k  
  gi|474934826|ref|YP_007688408.1| 49 PLRCPNCRSKLWDADVET-FICGSCGHKAL 77
                                      779*********999864.56*****9865 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.013
                           DUF2072   4 CtkCek..vfedgskeilkGCpsCGgkkFlyvkeeekkedvseekeelvaeaee 55 
                                       C +C++  +++ g++     Cp+CG   + +v +++ ++ v+++++  vae+ e
  gi|474934826|ref|YP_007688408.1|  69 CGSCGHkaLYRVGRS-APATCPACGSGNW-FVDPKSGQDAVTDSTR--VAEQVE 118
                                       566654213555555.6678*****9886.7888876665555444..333333 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.5      0.03        18      25      33 .]      16      24 ..       8      24 .. 0.80
   2 ?    6.5   0.1     0.016       9.7      19      29 ..      45      55 ..      42      57 .. 0.81
   3 ?   -2.0   0.4       6.8   4.2e+03       2       6 ..      69      73 ..      65      75 .. 0.72
   4 ?    2.9   0.1      0.21   1.3e+02      24      30 ..      86      92 ..      76      93 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.03
                                      E-TTT--EE CS
                         zf-RING_7 25 tCpeCGRIL 33
                                      +Cp C+ IL
  gi|474934826|ref|YP_007688408.1| 16 RCPRCNSIL 24
                                      9*******8 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.016
                                      CSTB-EE-TTT CS
                         zf-RING_7 19 agdevvtCpeC 29
                                      ++d+  +Cp+C
  gi|474934826|ref|YP_007688408.1| 45 RTDDPLRCPNC 55
                                      567889***** PP

  == domain 3  score: -2.0 bits;  conditional E-value: 6.8
                                      ETTT- CS
                         zf-RING_7  2 CgGCh 6 
                                      Cg C+
  gi|474934826|ref|YP_007688408.1| 69 CGSCG 73
                                      67775 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.21
                                      EE-TTT- CS
                         zf-RING_7 24 vtCpeCG 30
                                      +tCp CG
  gi|474934826|ref|YP_007688408.1| 86 ATCPACG 92
                                      89****9 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.6      0.22   1.3e+02      24      29 ..      17      22 ..       7      24 .. 0.82
   2 ?    3.0   3.6       0.2   1.2e+02      16      29 ..      45      57 ..      33      59 .. 0.59
   3 ?   -1.2   0.1       4.1   2.5e+03      22      28 ..      66      73 ..      60      75 .. 0.65
   4 ?    8.4   0.0    0.0042       2.6      21      30 ..      84      94 ..      76      99 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.22
                     zinc_ribbon_9 24 CPhCgg 29
                                      CP+C++
  gi|474934826|ref|YP_007688408.1| 17 CPRCNS 22
                                      ****97 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.2
                     zinc_ribbon_9 16 pdedsdvlCPhCgg 29
                                      +++d+   CP+C++
  gi|474934826|ref|YP_007688408.1| 45 RTDDPL-RCPNCRS 57
                                      334444.5****97 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 4.1
                     zinc_ribbon_9 22 v.lCPhCg 28
                                      + +C +Cg
  gi|474934826|ref|YP_007688408.1| 66 TfICGSCG 73
                                      35799998 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.0042
                     zinc_ribbon_9 21 dv.lCPhCggg 30
                                      ++ +CP Cg+g
  gi|474934826|ref|YP_007688408.1| 84 APaTCPACGSG 94
                                      3337*****97 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.2     0.012       7.3       3      11 ..      15      23 ..      15      24 .. 0.82
   2 ?    2.5   0.2      0.17   1.1e+02      18      25 ..      34      41 ..      32      43 .. 0.83
   3 ?    0.2   8.2      0.87   5.4e+02       4      25 ..      51      75 ..      50      76 .. 0.76
   4 ?    6.8   0.5    0.0071       4.4       4      10 ..      87      93 ..      86      97 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.012
                       zf-ribbon_3  3 vrCPnCGap 11
                                      +rCP+C+++
  gi|474934826|ref|YP_007688408.1| 15 RRCPRCNSI 23
                                      59****995 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.17
                       zf-ribbon_3 18 vCpyCGtk 25
                                      vC+ CG+k
  gi|474934826|ref|YP_007688408.1| 34 VCKRCGHK 41
                                      69999986 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.87
                       zf-ribbon_3  4 rCPnCGa.plssddn..vCpyCGtk 25
                                      rCPnC + + ++d+   +C +CG+k
  gi|474934826|ref|YP_007688408.1| 51 RCPNCRSkLWDADVEtfICGSCGHK 75
                                      8999999776666664479999986 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.0071
                       zf-ribbon_3  4 rCPnCGa 10
                                      +CP+CG+
  gi|474934826|ref|YP_007688408.1| 87 TCPACGS 93
                                      6888887 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.087        54       5      10 ..      17      22 ..      15      25 .. 0.84
   2 ?    6.2   0.1     0.012       7.5       2      11 ..      32      41 ..      31      43 .. 0.86
   3 ?    2.2   0.1      0.22   1.4e+02       4      17 ..      51      64 ..      48      66 .. 0.81
   4 ?    2.7   0.2      0.16        98       1      11 [.      65      75 ..      65      77 .. 0.88
   5 ?    0.5   0.2      0.78   4.8e+02       4      10 ..      87      93 ..      86      94 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.087
                            zf_UBZ  5 CerCgk 10
                                      C+rC++
  gi|474934826|ref|YP_007688408.1| 17 CPRCNS 22
                                      ****97 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.012
                            zf_UBZ  2 tylCerCgke 11
                                      t++C+rCg++
  gi|474934826|ref|YP_007688408.1| 32 THVCKRCGHK 41
                                      89******85 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.22
                            zf_UBZ  4 lCerCgkeipesel 17
                                       C+ C +++ ++++
  gi|474934826|ref|YP_007688408.1| 51 RCPNCRSKLWDADV 64
                                      6*****99988776 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.16
                            zf_UBZ  1 dtylCerCgke 11
                                      +t++C  Cg++
  gi|474934826|ref|YP_007688408.1| 65 ETFICGSCGHK 75
                                      69*******85 PP

  == domain 5  score: 0.5 bits;  conditional E-value: 0.78
                            zf_UBZ  4 lCerCgk 10
                                      +C+ Cg+
  gi|474934826|ref|YP_007688408.1| 87 TCPACGS 93
                                      7****95 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.2       8.3   5.2e+03     133     140 ..      15      22 ..       2      24 .. 0.74
   2 ?    5.8   1.6     0.021        13     114     141 ..      32      58 ..      26      61 .. 0.76
   3 ?    6.6   0.1     0.012       7.3     114     140 ..      66      93 ..      62      97 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 8.3
                           DUF1451 133 ppCpkCga 140
                                        +Cp+C++
  gi|474934826|ref|YP_007688408.1|  15 RRCPRCNS 22 
                                       57999975 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.021
                           DUF1451 114 tlvCekCgkelalkkteeippCpkCgat 141
                                       t vC++Cg++    +t+   +Cp+C+++
  gi|474934826|ref|YP_007688408.1|  32 THVCKRCGHKWL-GRTDDPLRCPNCRSK 58 
                                       679******985.55555568****986 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.012
                           DUF1451 114 tlvCekCgkelalkkteeip.pCpkCga 140
                                       t++C +Cg++  ++  +  p +Cp+Cg+
  gi|474934826|ref|YP_007688408.1|  66 TFICGSCGHKALYRVGRSAPaTCPACGS 93 
                                       789*******988877666537****97 PP

>> FYVE_2  FYVE-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   8.9      0.08        49      73     102 ..      26      57 ..      15      99 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.08
                            FYVE_2  73 qCldCklnvCkkCsve..nkkekvwlCkiCse 102
                                       +C+d k++vCk+C+++  ++++    C +C+ 
  gi|474934826|ref|YP_007688408.1|  26 NCTDLKTHVCKRCGHKwlGRTDDPLRCPNCRS 57 
                                       7**************99967777777777765 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.3     0.089        55       4       9 ..      16      21 ..       8      23 .. 0.74
   2 ?    6.2   0.7     0.016       9.6      28      35 ..      35      42 ..      34      43 .. 0.95
   3 ?    5.0   0.2     0.039        24      27      32 ..      51      56 ..      49      59 .. 0.56
   4 ?    0.7   0.2       0.8     5e+02      28      34 ..      69      75 ..      65      75 .. 0.84
   5 ?    2.9   0.2      0.17     1e+02       4       9 ..      87      92 ..      82      94 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.089
                     zinc_ribbon_4  4 tCpsCk 9 
                                      +Cp+C+
  gi|474934826|ref|YP_007688408.1| 16 RCPRCN 21
                                      566666 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.016
                     zinc_ribbon_4 28 CskCghvF 35
                                      C++Cgh++
  gi|474934826|ref|YP_007688408.1| 35 CKRCGHKW 42
                                      *******9 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.039
                     zinc_ribbon_4 27 rCskCg 32
                                      rC++C+
  gi|474934826|ref|YP_007688408.1| 51 RCPNCR 56
                                      555554 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.8
                     zinc_ribbon_4 28 CskCghv 34
                                      C  Cgh+
  gi|474934826|ref|YP_007688408.1| 69 CGSCGHK 75
                                      9999995 PP

  == domain 5  score: 2.9 bits;  conditional E-value: 0.17
                     zinc_ribbon_4  4 tCpsCk 9 
                                      tCp+C+
  gi|474934826|ref|YP_007688408.1| 87 TCPACG 92
                                      566665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); expected 17.9 (0.001)
Passed Fwd filter:                        64  (0.00356964); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 0.68u 0.33s 00:00:01.01 Elapsed: 00:00:00.56
# Mc/sec: 998.36
//
Query:       gi|474934827|ref|YP_007688409.1|  [L=201]
Description: Acetyltransferase (isoleucine patch superfamily) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-13   50.4   4.9    5.5e-12   45.2   2.3    2.3  2  Hexapep_2  Hexapeptide repeat of succinyl-transferase
    4.7e-13   48.3   7.2    2.8e-11   42.7   2.9    2.6  2  Hexapep    Bacterial transferase hexapeptide (six repeats)


Domain annotation for each model (and alignments):
>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   0.0    0.0013        12       2      16 ..     111     125 ..     110     129 .. 0.88
   2 !   45.2   2.3   6.2e-16   5.5e-12       1      34 []     146     181 ..     146     181 .. 0.97

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0013
                                       EEE-TT-EE-TT-EE CS
                         Hexapep_2   2 viIGdnCliGanagi 16 
                                       ++IG+ +++G+++ i
  gi|474934827|ref|YP_007688409.1| 111 IRIGAHTMVGPDCHI 125
                                       79**********965 PP

  == domain 2  score: 45.2 bits;  conditional E-value: 6.2e-16
                                       .EEE-TT-EE-TT-EE..SEEE-TT-EE-TT-EE-S CS
                         Hexapep_2   1 pviIGdnCliGanagi..GvslGdncvvgaGvvita 34 
                                       pv+IG ++ +Gan ++  Gv++Gd+cvvgaG v+t+
  gi|474934827|ref|YP_007688409.1| 146 PVRIGRDVWLGANVTVlpGVTIGDGCVVGAGAVVTK 181
                                       8**************99******************7 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.1   0.00042       3.8       3      17 ..     112     126 ..     110     130 .. 0.73
   2 !   42.7   2.9   3.1e-15   2.8e-11       2      36 .]     147     181 ..     146     181 .. 0.96

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00042
                                       EEETTEEE-TTEEEE CS
                           Hexapep   3 vIGsnvlIgpfavig 17 
                                       +IG ++++gp ++i 
  gi|474934827|ref|YP_007688409.1| 112 RIGAHTMVGPDCHIV 126
                                       688888888888886 PP

  == domain 2  score: 42.7 bits;  conditional E-value: 3.1e-15
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                                       ++IG +v++g++++++++V+IGd++++gag+v+++
  gi|474934827|ref|YP_007688409.1| 147 VRIGRDVWLGANVTVLPGVTIGDGCVVGAGAVVTK 181
                                       78*******************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1358.54
//
Query:       gi|474934828|ref|YP_007688410.1|  [L=472]
Description: amidophosphoribosyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-19   70.7   0.0    2.5e-19   69.8   0.0    1.4  1  GATase_6      Glutamine amidotransferase domain
    1.1e-17   64.0   0.0    2.1e-17   63.2   0.0    1.5  1  GATase_7      Glutamine amidotransferase domain
    1.4e-07   30.8   0.0      2e-07   30.2   0.0    1.2  1  GATase_4      Glutamine amidotransferases class-II
    1.3e-06   28.0   0.1    3.6e-06   26.6   0.1    1.7  1  Pribosyltran  Phosphoribosyl transferase domain
  ------ inclusion threshold ------
      0.062   12.0   1.4        1.2    7.8   0.2    2.6  3  GATase_2      Glutamine amidotransferases class-II


Domain annotation for each model (and alignments):
>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.8   0.0   6.9e-23   2.5e-19      10     134 .]      70     202 ..      49     202 .. 0.86

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 6.9e-23
                          GATase_6  10 vedevalaHvRlaivglaeeegaqPf..psedgrlllvhNGeiynykelreelpalkglafrsrsDtevllall... 81 
                                       ++ +v+++HvR a++g ++ + aqP+   + +g+++++hNG+  +y+++++++ + +g  f ++sDte+++++l   
  gi|474934828|ref|YP_007688410.1|  70 YG-NVGIGHVRYATTGGKNVKNAQPItvATGSGQIAVAHNGDLTTYEKVKNKYLE-AGEVFLTDSDTELIIKILsky 144
                                       33.49*************88888***66666778********************9.****************88766 PP

                          GATase_6  82 eelG.......eevlerlrGmfafaiwdkrentlilardrlgvkplyyavdesglafase 134
                                        + G        +++ +++G++a a++   +++++ +rd +g++pl+++   +g ++ase
  gi|474934828|ref|YP_007688410.1| 145 LKSGsdpilamRQTMGEIDGAYALALM--INGRMFGIRDPHGIRPLVIGKLSDGYMIASE 202
                                       333477777788888899998888765..6999**************************8 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.2   0.0   5.9e-21   2.1e-17       9     122 ..      87     207 ..      77     208 .. 0.93

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 5.9e-21
                          GATase_7   9 seagaQPmvs.sedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea.........ewgeealerln 75 
                                         ++aQP++  + +g++++++nG ++ y+++++++ ++g  f t+sDte+++++l++           +++++ +++
  gi|474934828|ref|YP_007688410.1|  87 NVKNAQPITVaTGSGQIAVAHNGDLTTYEKVKNKYLEAGEVFLTDSDTELIIKILSKylksgsdpiLAMRQTMGEID 163
                                       56889***998899******************************************9********999********* PP

                          GATase_7  76 GmfAfaiwdeeekrlllaRDrlGikPLyygedkgdallfaSelkall 122
                                       G +A+a++ + +  ++ +RD+ Gi+PL +g+ + d++++aSe  a+ 
  gi|474934828|ref|YP_007688410.1| 164 GAYALALMINGR--MFGIRDPHGIRPLVIGKLS-DGYMIASESCAID 207
                                       ********9988..******************7.7********9986 PP

>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   5.5e-11     2e-07      33     139 ..      35     143 ..       8     172 .. 0.73

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 5.5e-11
                          GATase_4  33 adGwGiafyegkaarvfkdpepsaesplaelvreypiksknvvaHiRkatqGevklenthpFvRelwgrewifAHnG 109
                                       +d  Gi+ ++g  ++++kd    +++     +   ++  ++ + H+R at+G  + +n++p +   +  ++  AHnG
  gi|474934828|ref|YP_007688410.1|  35 QDTAGISVFDGMEIHTVKDAGLVQTALPKDRI--AQLYGNVGIGHVRYATTGGKNVKNAQPITVATGSGQIAVAHNG 109
                                       46679999999999999987666655444433..34888999*********************************** PP

                          GATase_4 110 dlkeykpklegrfePvGs...T..DsElafCelle 139
                                       dl+ y++   +++   G+   T  D+El++ +l +
  gi|474934828|ref|YP_007688410.1| 110 DLTTYEKVK-NKYLEAGEvflTdsDTELIIKILSK 143
                                       **9988776.3444444322250055555544433 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.1   9.9e-10   3.6e-06      29     120 ..     281     379 ..     260     381 .. 0.66

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 9.9e-10
                                       GGEEEEEEETTTHHHHHHHHHHS.......TT-EE..-EEEEEE-TTT--EE........EE----TTSEEEEE-SE CS
                      Pribosyltran  29 kpdvvvgiargGvpfakiladeL.......evpla..yvrkvkyrpdgseeaargssdesrlledpagkkVliVDDi 96 
                                         d+v++i+  G  +a   +++           +   + +++   pd++e    +s++ +   + + gk+++iVDD 
  gi|474934828|ref|YP_007688410.1| 281 DVDLVMPIPDSGRAHAIGFSNASgipyeegF--MKnrFAERTFILPDQKERELAVSTKMNPIKSTVNGKRIIIVDDS 355
                                       5666666666666666666666633333210..11223333334455555555555555578999************ PP

                                       ESSSHHHHHHHHHHHCC-BSEEEE CS
                      Pribosyltran  97 ldtGgTllaalelLkekgpeevri 120
                                       +  G+Tl+  +  L+++g++ev++
  gi|474934828|ref|YP_007688410.1| 356 IVRGTTLKQLIGMLRKAGATEVHV 379
                                       *********************985 PP

>> GATase_2  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.2   0.00034       1.2      12      80 ..      14      81 ..       8     105 .. 0.81
   2 ?    1.6   0.0     0.025        91     204     243 ..      72     119 ..      64     151 .. 0.68
   3 ?    1.7   0.1     0.023        83     328     394 ..     162     225 ..     155     231 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00034
                                      --BSHHHHHHHHHHHHGGGGS-B-TTSSSBSEEEEEEE--HHHHHHHHHHTT-----GGG-EEEEEEE- CS
                          GATase_2 12 kkshkivekalealenleHRGavgadektGDGaGillqiPdeflrkeakekgielpeageyavgmlflp 80
                                      +++h+iv    +al  l+HRG  +a  +  DG  i + +   ++++++ +  i     g++++g++   
  gi|474934828|ref|YP_007688410.1| 14 NADHNIVAALQKALMILQHRGQDTAGISVFDGMEIHTVKDAGLVQTALPKDRIAQL-YGNVGIGHVRYA 81
                                      578********************************999999999999888777664.488888877554 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.025
                                       SEEEEEE---SSSS--GGGSSS-SS........EEEEE--TTHHHHHH CS
                          GATase_2 204 alalvHsRfstntfPsWelaqPlRl........laHnGEintlrGnkn 243
                                       ++ + H R++t    + + aqP+ +        +aHnG++ t +  kn
  gi|474934828|ref|YP_007688410.1|  72 NVGIGHVRYATTGGKNVKNAQPITVatgsgqiaVAHNGDLTTYEKVKN 119
                                       677889999999999999999997633333333678888777765544 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.023
                                       --SS.EEEEEE-SSEEEEEE-TT--S--EEEEETT--EEEESSTTSS---GGGEEEEEE--TT-EEEE CS
                          GATase_2 328 WDGP.alivftdGkvvgavLDRnGLRPaRylvtkddlvvlasEvGvldleeeevvekgrlqPGrmllv 394
                                        DG  al  + +G++ g   D  G+RP  +   +d++++ asE+  +d    e+v+   + PG+++ v
  gi|474934828|ref|YP_007688410.1| 162 IDGAyALALMINGRMFGIR-DPHGIRPLVIGKLSDGYMI-ASESCAIDALGGELVR--DVAPGEIIEV 225
                                       5776245567899999965.********99999999975.8999999888777775..4788888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 2949.05
//
Query:       gi|474934829|ref|YP_007688411.1|  [L=56]
Description: LSU ribosomal protein L37E [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-21   76.0  10.2    2.1e-21   75.8  10.2    1.0  1  Ribosomal_L37e  Ribosomal protein L37e
  ------ inclusion threshold ------
      0.017   15.2   0.4      0.019   15.0   0.4    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta


Domain annotation for each model (and alignments):
>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.8  10.2   2.3e-25   2.1e-21       2      51 ..       3      53 ..       2      55 .. 0.97

  Alignments for each domain:
  == domain 1  score: 75.8 bits;  conditional E-value: 2.3e-25
                    Ribosomal_L37e  2 kGtssfGkrqkkktHilCrrCgkrsyhvqkktCascGy.psaklrkynWsa 51
                                       Gt+++G+++k+ktHi CrrCgkrsy+++k +CascGy ++a++r y+W++
  gi|474934829|ref|YP_007688411.1|  3 AGTAAQGRHNKHKTHIPCRRCGKRSYNIRKGYCASCGYgKTARIRGYEWAK 53
                                      6************************************************86 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.4   2.1e-06     0.019      65     104 ..      12      50 ..       3      52 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.1e-06
                                       EEE--EEEETTTS-EEECHHHHHS-TTTSSS-EEEEESSS CS
                              HypA  65 eevpvkvrCreCgkefeleekalrCpkCgsadveivsGee 104
                                       ++ + ++ Cr+Cgk+    +k   C +Cg  ++  ++G e
  gi|474934829|ref|YP_007688411.1|  12 NKHKTHIPCRRCGKRSYNIRK-GYCASCGYGKTARIRGYE 50 
                                       56788999*****99885544.46*****99998888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.28s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 415.28
//
Query:       gi|474934830|ref|YP_007688412.1|  [L=372]
Description: putative Fe-S-cluster oxidoreductase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.3e-06   28.2  11.5    4.3e-06   27.3  11.5    1.4  1  CxxCxxCC     Putative zinc- or iron-chelating domain
  ------ inclusion threshold ------
       0.15   12.6   0.3         13    6.3   0.0    2.2  2  KinB_sensor  Sensor domain of alginate biosynthesis sensor pr


Domain annotation for each model (and alignments):
>> CxxCxxCC  Putative zinc- or iron-chelating domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3  11.5   4.8e-10   4.3e-06       1      73 [.      17      98 ..      17     110 .. 0.66

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 4.8e-10
                          CxxCxxCC  1 eCke.CgaCCkelkvklteedlerlkaae..vaeeeeeskkiak.....adgrCvfldeetklCkiYeeRpkicrlfpa 71
                                      eC + Cg+CC   ++++ +e++  +k+ +   +e+++  ++++        g Cvfl+e  ++Ck+Y +R   cr fp 
  gi|474934830|ref|YP_007688412.1| 17 ECIDgCGMCCL-CQPEILPEERPFFKKNHpdCIEKSRGPEHYTAiklknDRGSCVFLNEC-RRCKVYDHRTAYCRQFPY 93
                                      68888******.555555555555544331123333334444435666599********9.5****************9 PP

                          CxxCxxCC 72 s...e 73
                                      +   +
  gi|474934830|ref|YP_007688412.1| 94 HiyvS 98
                                      75543 PP

>> KinB_sensor  Sensor domain of alginate biosynthesis sensor protein KinB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0014        13      55      89 ..     127     161 ..     120     178 .. 0.80
   2 ?    4.6   0.1    0.0049        44      59      96 ..     193     228 ..     163     238 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0014
                                       HHH--SHHHHHHHHHHHHHHHHH..HHHHHHHHHS CS
                       KinB_sensor  55 laskvdeaerqaleqiasayrqflqalespatsrr 89 
                                       l +++d+  r+al q+++ y qf+  +++++  ++
  gi|474934830|ref|YP_007688412.1| 127 LVANADARIREALPQARDIYSQFYSFAREAGVMAD 161
                                       567789999*****************999776554 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0049
                                       -SHHHHHHHHHHHHHHHHH..HHHHHHHHHS-SSSSHH CS
                       KinB_sensor  59 vdeaerqaleqiasayrqflqalespatsrrelldndd 96 
                                        + +  ++l+q++++y+++++a++++a   ++l  +d+
  gi|474934830|ref|YP_007688412.1| 193 PQMTIADGLKQTKVDYKELEDAARETA--LESLSSEDP 228
                                       56667789***************9954..445555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2623.50
//
Query:       gi|474934831|ref|YP_007688413.1|  [L=423]
Description: dihydroorotase, multifunctional complex type [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-21   77.4   0.2      6e-21   75.1   0.2    1.9  1  Amidohydro_1  Amidohydrolase family
      3e-10   40.2   0.7    9.9e-06   25.3   0.0    2.8  2  Amidohydro_3  Amidohydrolase family


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.1   0.2   6.7e-25     6e-21       1     322 [.      52     385 ..      52     406 .. 0.71

  Alignments for each domain:
  == domain 1  score: 75.1 bits;  conditional E-value: 6.7e-25
                                       EEEE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTH..HHHHHHHHHHTSSS CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattst..giealleaaeelpl 75 
                                       +vlPG+ D HvHl+             +p++t +e + +g++ al +G+t v+dm++t ++   i+ l++   +  +
  gi|474934831|ref|YP_007688413.1|  52 TVLPGFMDPHVHLR-------------DPGMTQKEDFVTGTTSALYGGVTCVLDMPNTKPPvtDIPTLMDKKAA--V 113
                                       69***********9.............******************************98867655555553333..4 PP

                                       EEEEEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHHHHHHHTTEEEEEE CS
                      Amidohydro_1  76 glrilggkvsldrgsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealkeakkrdlpvaiHa 152
                                       + r+++ ++ ++  +++ + +     ++ +         ++++ + +      + d+e++ +++e ++ ++ +++Ha
  gi|474934831|ref|YP_007688413.1| 114 KGRAFVDYGLFAALTPSAPVDMLAPHVPAF---------KLFM-GSTTGNILLNDDAEIAPLMEEIARTGKVLSVHA 180
                                       677777777777688787777777776776.........2333.2222233456788******************** PP

                                       TSSCHHHHHHHHHHTTTEEEETTTTSTCC.HHTTTHCCEEEHCTCEEE.HH......HHHHHHHHHHHHCEE..... CS
                      Amidohydro_1 153 letkgevedaeaafgetiehgthlevaes.lglldeiklilahgvhlt.pt......eaellkerlkeagva..... 216
                                        +++ +v  +++    ++ ++ + e   s +  l +++ + + ++h t ++      e          +g +     
  gi|474934831|ref|YP_007688413.1| 181 EDDSLIVHGVQENCCQDHLRNRPAEAEYSaIRRLSKYRGTKVNICHTTnAEqvgmarE----------VGFTtevtm 247
                                       8888888888888887777766666633356667777888888888885332222220..........333344456 PP

                                       .HHHHHHHH................SEHHHHHHHHHHHHTSCEEEEEECT.....TSSCCGGHHHHHHHHHHHHHHC CS
                      Amidohydro_1 217 .hcpfsnsi................lrsgrealrkaldeGvkvglgtDga.....asgnslnlleelrlalklqrgl 271
                                        h+ f+ ++                +r+g+    +  ++G + ++gtD+a      +   ++   +++ +++++++ 
  gi|474934831|ref|YP_007688413.1| 248 hHLLFNAERntsafyktnppvrdenSRKGL---FESFRKGDITMFGTDHAphtydEKSQEFDAAPGGIPGVETTMPM 321
                                       644444444455555555554411155554...566777889********999995556677778899999999999 PP

                                       CTT.TTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECC....CT..........C CS
                      Amidohydro_1 272 lye.deegglslkealrmaTingAkalglddkvGsievGkdADlvvvdl....di..........l 322
                                        +e + +g ++   a+rm   ++A+++++   +G+i++G dAD++++d      i           
  gi|474934831|ref|YP_007688413.1| 322 VMEmVRAGTITMDLAVRMGAEKPAEVFSV--GKGRIAPGCDADFAIFDFrrvtEIdqkklhskagW 385
                                       999988999********************..8***************9986652244455555553 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.1   9.4e-06     0.084       8      25 ..      51      68 ..      45      83 .. 0.78
   2 !   25.3   0.0   1.1e-09   9.9e-06     401     471 ..     325     405 ..     151     406 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.4e-06
                      Amidohydro_3  8 rlvlPGFvDsHtHlaggg 25
                                      ++vlPGF D+H Hl   g
  gi|474934831|ref|YP_007688413.1| 51 MTVLPGFMDPHVHLRDPG 68
                                      69***********65555 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 1.1e-09
                      Amidohydro_3 401 vlrpdeelsleealalyTrgpAkalgledrkGtLevGadADlvvld.adpldvdppelaear............vrl 464
                                        +r+   +++  a+++  ++pA++++  +  G++++G+dAD++++d +   ++d+++l+++             +  
  gi|474934831|ref|YP_007688413.1| 325 MVRA-GTITMDLAVRMGAEKPAEVFSVGK--GRIAPGCDADFAIFDfRRVTEIDQKKLHSKAgwsvyhgmkaifPDT 398
                                       4443.37888889***************9..***************999999*******999888888888888888 PP

                      Amidohydro_3 465 tvvdGrv 471
                                       ++++G+v
  gi|474934831|ref|YP_007688413.1| 399 VIIRGQV 405
                                       8888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 2617.19
//
Query:       gi|474934832|ref|YP_007688414.1|  [L=197]
Description: conserved hypothetical protein TIGR00296 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-41  141.4   0.0    2.4e-41  141.1   0.0    1.0  1  AMMECR1   AMMECR1


Domain annotation for each model (and alignments):
>> AMMECR1  AMMECR1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.1   0.0   1.3e-45   2.4e-41       4     166 .]      14     184 ..      11     184 .. 0.87

  Alignments for each domain:
  == domain 1  score: 141.1 bits;  conditional E-value: 1.3e-45
                                       HHHHH.HHHTTSS-S-HH---HHHHSEEEEEEEEE.EE..CCECCCECEEEEEEHHHHHHHHHHHHHHT-TTS---- CS
                           AMMECR1   4 areai.eealkeekkleeeakeelkekaglFVtlk.ekkgeLRGCiGtleperpLaeevaenAlaaAfeDpRFspvt 78 
                                       area  +e  +++ +l ++   e++ ++g+FVt++   +++LR CiG+ ep +pL+e+v+  A   A++DpRF+++t
  gi|474934832|ref|YP_007688414.1|  14 AREAAyAESENSGYVLPKDLGGEFSVNSGAFVTVSeFPSRRLRACIGYPEPIMPLGESVMMSA-RGAVHDPRFPKLT 89 
                                       55555333333333344677779999*********86778*****************999888.689********** PP

                                       HHHHTTEEEEEEEE---EE-...-....GGG--TTT-EEEEEETTEEEEE-THHHHHTT--HHHHHHHHHHHHTS-T CS
                           AMMECR1  79 aeElpeleveVsvLtepepi...v....ledlevgkhGliiekgsrsatlLPqvaveqgwdkeeflasllrKaglrp 148
                                       +eE + +++eV+vLt+pep+   +    ++++ +g++Gli+e+g ++a++LPqv+veqgw +ee++++l+ Kag+rp
  gi|474934832|ref|YP_007688414.1|  90 REEAEACTFEVTVLTKPEPLeytDvpdlMSRIVIGRDGLIVEYGPYRALFLPQVPVEQGWGVEEYISELCYKAGMRP 166
                                       ********************66515666888********************************************** PP

                                       TCCCSTTSEEEEE-EEEE CS
                           AMMECR1 149 dewkdseikltryevekf 166
                                       d+w++++++++++++e+f
  gi|474934832|ref|YP_007688414.1| 167 DAWRNNRLTFETFRGEIF 184
                                       *************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       189  (0.0105416); expected 358.6 (0.02)
Passed bias filter:                      186  (0.0103743); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1271.31
//
Query:       gi|474934833|ref|YP_007688415.1|  [L=237]
Description: hypothetical protein TALC_01271 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.25   12.0  13.0       0.21   12.2   3.6    2.7  3  DUF883       Bacterial protein of unknown function (DUF883)
       0.33   11.6   5.9       0.51   10.9   5.9    1.4  1  Hemerythrin  Hemerythrin HHE cation binding domain


Domain annotation for each model (and alignments):
>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   2.5   2.4e-05      0.21      11      51 ..      43      83 ..       9      87 .. 0.77
   2 ?   12.2   3.6   2.4e-05      0.21      11      58 ..      43      90 ..      37     105 .. 0.80
   3 ?    3.1   3.4     0.017   1.5e+02      33      61 ..      98     126 ..      91     140 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.4e-05
                            DUF883 11 ladleellkeaadeageeaeelRerleerlerarerlrdae 51
                                       +++ee +++ ad+a  +++  R+r++++++++r++lrd +
  gi|474934833|ref|YP_007688415.1| 43 AEKMEEAVRDGADRAYGDYRYGRDRAMDAFDETRDTLRDFA 83
                                      56777888888888888888888888888888888887766 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 2.4e-05
                            DUF883 11 ladleellkeaadeageeaeelRerleerlerarerlrdaeeavaera 58
                                       +++ee +++ ad+a  +++  R+r++++++++r++lrd ++   +  
  gi|474934833|ref|YP_007688415.1| 43 AEKMEEAVRDGADRAYGDYRYGRDRAMDAFDETRDTLRDFADVESDYF 90
                                      6899***********************************998754444 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.017
                            DUF883  33 Rerleerlerarerlrdaeeavaerakea 61 
                                       Rer++ ++e+ ++ +r+ +e+ ++r +e 
  gi|474934833|ref|YP_007688415.1|  98 RERARRYAEAEKAYARRRYEESRDRFRED 126
                                       45555555555555555555555554443 PP

>> Hemerythrin  Hemerythrin HHE cation binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   5.9   5.7e-05      0.51      14     117 ..      40     146 ..      20     154 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.7e-05
                                       HHHHHHHHHHHHH.HHHHCCC....HCCHHHHHHHHHHHHHHHHHHHHHHCHHHHH.CCC.HHHHHHHHHHHHHHHH CS
                       Hemerythrin  14 rallerlralada.aaevhga....lrklaelldelvdeleaHhaaEEellfPlledrpggravldvlereHdeire 85 
                                       r+ +e +++++++ a+++ g+    ++++ +++de +d l++    E ++++ +++  ++ +   +  e+e + +r+
  gi|474934833|ref|YP_007688415.1|  40 RERAEKMEEAVRDgADRAYGDyrygRDRAMDAFDETRDTLRDFADVESDYFYRMMR--EERERARRYAEAEKAYARR 114
                                       6666777666666466666669999*******************************..6666667777888888888 PP

                                       HHHHHH.HHCHTCGGSTCHHHHHHHHHHHHHHH CS
                       Hemerythrin  86 lleelr.ellkgleepsaaafaelleeladllr 117
                                       + ee r ++ +++   +++ f++++e+++ +++
  gi|474934833|ref|YP_007688415.1| 115 RYEESRdRFREDFG-RAKGRFEDEFEGFFGWIA 146
                                       88888866666666.888888889999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       955  (0.0532657); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 1574.53
//
Query:       gi|474934834|ref|YP_007688416.1|  [L=394]
Description: arsenite-activated ATPase (arsA) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-86  290.5   1.0    1.6e-86  290.3   1.0    1.0  1  ArsA_ATPase  Anion-transporting ATPase
    1.4e-14   53.4   0.0    2.6e-14   52.5   0.0    1.5  1  ArsA_HSP20   HSP20-like domain found in ArsA
    8.3e-10   38.9   0.1    2.4e-09   37.4   0.0    1.8  2  AAA_31       AAA domain
    3.6e-08   33.5   0.0    2.2e-07   31.0   0.0    2.1  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    5.6e-08   32.5   0.6    2.2e-07   30.6   0.2    2.0  2  ParA         NUBPL iron-transfer P-loop NTPase
  ------ inclusion threshold ------
      0.035   13.7   2.3        2.1    7.9   0.3    2.9  3  SRP54        SRP54-type protein, GTPase domain
      0.056   12.9   0.0       0.14   11.6   0.0    1.7  1  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
       0.23   10.9   0.3       0.49    9.8   0.3    1.5  1  CBP_BcsQ     Cellulose biosynthesis protein BcsQ


Domain annotation for each model (and alignments):
>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  290.3   1.0   7.2e-90   1.6e-86       1     303 [.       1     301 [.       1     303 [. 0.98

  Alignments for each domain:
  == domain 1  score: 290.3 bits;  conditional E-value: 7.2e-90
                                       -EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS--BSS-EEETSSEEEEE--HHHHHHHHH CS
                       ArsA_ATPase   1 lkvilvgGKGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdqklgkeptkvkeNLsavEidpeveleeak 77 
                                       +++i+  GKGGVGKt+vs+ata++l++ g++++l+s+D Ahs+ D++d klg ept v  NL + E+d+  e++ ++
  gi|474934834|ref|YP_007688416.1|   1 MRLIIYNGKGGVGKTSVSTATALRLAKLGHRTILMSVDTAHSIGDALDMKLGPEPTNVAPNLDVLELDIVHEMKTKW 77 
                                       799************************************************************************** PP

                                       CCHHGGGSCCHHHHHHHHHHHHHHTSSTTHHHHHHHHHHHHHHHCSSSSEEEEESBSCCHTCGGGGHHHHHHHHHHH CS
                       ArsA_ATPase  78 qevqkeeeallgleeledvlaeelaslPGideilsfeellkyvkeeeydvvvlDtaPTGhtlrllslpevlekllek 154
                                       ++ ++++ a++ +++ e++ a+ela++PG++ + ++ ++l + +e +ydvv++DtaPTG+tlrl+s+p+v +++++k
  gi|474934834|ref|YP_007688416.1|  78 SAIKDYISAFMLSQGIEGISADELAIFPGMEMVSALLYVLTFEREGKYDVVIIDTAPTGETLRLMSFPDVSNWYIDK 154
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHCCCSHCHHHHHH..HHHHHHHHHHHHHHHHHHHHTSTTTEEEEEEEESSHHHHHHHHHHHHH CS
                       ArsA_ATPase 155 lvklkeklsplakqlvkllglggvsie..ealeeleetkeeikkveeiltdpertsfrlVvipEklslkEteRaike 229
                                       ++++  kl+ +a+ +v+  +++++ ++  +++++++  k+++k+v+ il+d + t++rlV++pE+++++Et+R+ ++
  gi|474934834|ref|YP_007688416.1| 155 MFSIVSKLMGVARFTVG--HIVDFPLPskKVMNQIKVLKDQMKDVKRILEDSKNTTVRLVLNPERMAINETRRSYAY 229
                                       **************988..57777777779*********************************************** PP

                                       HHHTT-EEEEEEEEEE-TTCSSSTSHHHHHHHHHHHHHHHHHHHHTTTSEEEEEE--SS-S-SHHHHHHHHHHH CS
                       ArsA_ATPase 230 LkkygikvdavivNkllpeeeqenCeflearkkiqkkylkeieelfedlevvklplleeEvvGlekleklsell 303
                                       +++y+ +v+ +++Nk++p++ +    f++++ k q++ ++ei++ f++l+++++ ++++E++G+ekle l++++
  gi|474934834|ref|YP_007688416.1| 230 MSLYNKNVECLVINKVIPDDADG--AFIKEKLKEQREHMEEIHSSFDPLKIMTAYMMKTEMRGTEKLEALADMI 301
                                       ********************996..9*********************************************987 PP

>> ArsA_HSP20  HSP20-like domain found in ArsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.5   0.0   1.2e-17   2.6e-14       1      63 []     324     387 ..     324     387 .. 0.97

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 1.2e-17
                        ArsA_HSP20   1 ddeyvlkldLPfvdkeeidlsrs.gdeLtIkignfrRqitLPsvlarkevtsAkfedgvLeIrF 63 
                                       d+ ++l++++Pfvd +e++l++  ++++++++g+++R+++LP++l++ e  +A+f d++L I+F
  gi|474934834|ref|YP_007688416.1| 324 DGTVELRIKMPFVDSDEVELFKGnENTIILHVGSQKRTVSLPMTLSDSELLGAEFGDECLIIKF 387
                                       68899****************9879*************************************99 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.0   1.1e-12   2.4e-09       6     131 ..       5     138 ..       1     151 [. 0.70
   2 ?   -2.4   0.1       1.7   3.8e+03      83      89 ..     245     251 ..     187     288 .. 0.53

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 1.1e-12
                            AAA_31   6 ianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekne......iektlyevl.ieeknikeaiik 75 
                                       i+n KGGvGKT  s++ a  laklg++++l+ +D+  +   +l+++          + +++e+  ++e+++k  +ik
  gi|474934834|ref|YP_007688416.1|   5 IYNGKGGVGKTSVSTATALRLAKLGHRTILMSVDTAHSIGDALDMKLGPeptnvaPNLDVLELDiVHEMKTKWSAIK 81 
                                       89**********************************99999877765442333331223333322466666666664 PP

                            AAA_31  76 tkvenldlipssid.Laeaeielvelekkeeil.kellekvkdeYDyiiiDcpPsLgl 131
                                       + ++   ++   i+ +++ e  ++  ++  ++l   l  + + +YD++iiD+ P+ ++
  gi|474934834|ref|YP_007688416.1|  82 DYIS-AFMLSQGIEgISADELAIFPGMEMVSALlYVLTFEREGKYDVVIIDTAPTGET 138
                                       4433.455666666255556666666666555515555688999**********8665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.7
                            AAA_31  83 lipssid 89 
                                       +ip + d
  gi|474934834|ref|YP_007688416.1| 245 VIPDDAD 251
                                       3333222 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   9.8e-11   2.2e-07       1     117 [.       3     251 ..       3     264 .. 0.83

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 9.8e-11
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep....................... 54 
                                       ++i ++kGGvGKT+++++ a  la+ g+r++l  +D+  +    l+ + + + +                       
  gi|474934834|ref|YP_007688416.1|   3 LIIYNGKGGVGKTSVSTATALRLAKLGHRTILMSVDTAHSIGDALDMKLGPEPTnvapnldvleldivhemktkwsa 79 
                                       5899********************************995554443333333333688999999999*********** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|474934834|ref|YP_007688416.1|  80 ikdyisafmlsqgiegisadelaifpgmemvsallyvltferegkydvviidtaptgetlrlmsfpdvsnwyidkmf 156
                                       ***************************************************************************** PP

                                       ....................................CCHCCCHHHHHHCHCHHHH...EEEEEEEEESS...-TTCH CS
                                       ....................................xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ....................................dlkrllellealgkkkall.lkiagvvlnrvdgeneetllk 94 
                                                                            +k ++++le+ ++++  l l++ ++ +n  + +      +
  gi|474934834|ref|YP_007688416.1| 157 sivsklmgvarftvghivdfplpskkvmnqikvlkdQMKDVKRILEDSKNTTVRLvLNPERMAINETRRS------Y 227
                                       **********************999999999999998888888998888886666888888888887666......3 PP

                                       HHHHHHHHHCTS-EEE.EEE--CC CS
                                       xxxxxxxxxxxxxxxx.xxxxxxx RF
                              CbiA  95 ealeelkqrygvpvlg.viprdea 117
                                         +  +++  +  v++ vip d +
  gi|474934834|ref|YP_007688416.1| 228 AYMSLYNKNVECLVINkVIPDDAD 251
                                       333333332233333356666665 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.2   9.9e-11   2.2e-07       6     122 ..       3     135 ..       1     170 [. 0.84
   2 ?   -0.6   0.0      0.33   7.4e+02     136     173 ..     206     243 ..     196     271 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 9.9e-11
                              ParA   6 iavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgvee................ekpeqsekkli 66 
                                       +++  gKGGVGK++v++  Al Lak g+++ l+ +D   +si + l+++                 + +++ ++k+ 
  gi|474934834|ref|YP_007688416.1|   3 LIIYNGKGGVGKTSVSTATALRLAKLGHRTILMSVDT-AHSIGDALDMKLgpeptnvapnldvlelDIVHEMKTKWS 78 
                                       67899*******************************5.689999999887777888888887776544455576788 PP

                              ParA  67 Pvea.kgikvmSigfllesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPG 122
                                        ++   +  ++S g+   s de  ++ G  + +a+  +l+  + g+ D++iiD+ P 
  gi|474934834|ref|YP_007688416.1|  79 AIKDyISAFMLSQGIEGISADELAIFPGMEMVSALLYVLTFEREGKYDVVIIDTAPT 135
                                       7777455667788887778999999999999999999999999999*******9984 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.33
                              ParA 136 lagaviVttpqevaladvkkaiemfkkvkvkvlGvveN 173
                                        + + +V  p+++a+++++++ + ++  + +v  +v N
  gi|474934834|ref|YP_007688416.1| 206 NTTVRLVLNPERMAINETRRSYAYMSLYNKNVECLVIN 243
                                       55666788999999999999999999998888888877 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.3   0.00093       2.1       4      39 ..       4      39 ..       1      44 [. 0.91
   2 ?    4.1   0.0     0.014        31      77      92 ..     118     133 ..     100     139 .. 0.83
   3 ?   -1.4   0.1      0.65   1.5e+03     101     122 ..     190     214 ..     184     261 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00093
                                      EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                             SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllvaaDt 39
                                      i+  G  G+GKT+  +  a +l k g++++l+++Dt
  gi|474934834|ref|YP_007688416.1|  4 IIYNGKGGVGKTSVSTATALRLAKLGHRTILMSVDT 39
                                      6677999****************************9 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.014
                                       HHHHHTTSSEEEEEE- CS
                             SRP54  77 ekakeekidvvlvDTa 92 
                                         ++e k+dvv++DTa
  gi|474934834|ref|YP_007688416.1| 118 TFEREGKYDVVIIDTA 133
                                       5567789********9 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.65
                                       HHHHHHHHHHHH...SSSEEEEEEE CS
                             SRP54 101 lmeelkkikkvv...kpdevllvld 122
                                       l +++k++k+++   k++ v lvl+
  gi|474934834|ref|YP_007688416.1| 190 LKDQMKDVKRILedsKNTTVRLVLN 214
                                       5667777777775556777777775 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   6.3e-05      0.14       4      38 ..       4      39 ..       1      57 [. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.3e-05
                         Fer4_NifH  4 aiy.GkGGiGksttsqnlsaalaemgkkvlivGCDP 38
                                       iy GkGG+Gk+  s+ ++  la+ g++ +++  D 
  gi|474934834|ref|YP_007688416.1|  4 IIYnGKGGVGKTSVSTATALRLAKLGHRTILMSVDT 39
                                      4555************************99998886 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.3   0.00022      0.49       1      37 [.       1      36 [.       1      52 [. 0.83

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00022
                          CBP_BcsQ  1 mkvlalqGvRGGvGttsllaaLawalhelgesvlviD 37
                                      m+++  +G +GGvG+ts+++a a  l +lg++ +++ 
  gi|474934834|ref|YP_007688416.1|  1 MRLIIYNG-KGGVGKTSVSTATALRLAKLGHRTILMS 36
                                      66666666.8**********************99864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       835  (0.0465726); expected 358.6 (0.02)
Passed bias filter:                      650  (0.0362541); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 2615.07
//
Query:       gi|474934835|ref|YP_007688417.1|  [L=238]
Description: Ribosomal protein S3AE [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.6e-58  196.1   6.6    5.3e-58  195.9   6.6    1.0  1  Ribosomal_S3Ae  Ribosomal S3Ae family
  ------ inclusion threshold ------
      0.016   14.9   0.4       0.23   11.2   0.1    2.1  2  BppU_N          BppU N-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_S3Ae  Ribosomal S3Ae family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.9   6.6   5.9e-62   5.3e-58       3     201 ..      11     198 ..       9     199 .. 0.98

  Alignments for each domain:
  == domain 1  score: 195.9 bits;  conditional E-value: 5.9e-62
                                       ----S-TCCSEEEEEEEB-TTSSSSEEEEEEEE--BSSSESHHSHTT-EEEEESHHHHTCSHTSSSEEEEEEEEEEE CS
                    Ribosomal_S3Ae   3 kkkvvDkfkkKeWydvkaPslfgkreiGktlvnrtqgtkiaseklkgrvvevslaDLtndekeqafrklklkieevq 79 
                                       +kk +Dk+k+KeWy+++aP++f+++ iG+t++        ++e l+gr  ev+++DLt+d+ ++ ++kl++ki+  +
  gi|474934835|ref|YP_007688417.1|  11 AKKSKDKWKAKEWYNIHAPRMFNETVIGETPA-------ADPEILIGRQAEVTVQDLTGDF-SKMHIKLQFKITGAD 79 
                                       799*****************************.......**********************.667************ PP

                                       SSEEEEEEEEEEE-HHHHHHH--SSB-EEEEEEEEEESSSEEEEEEEEEEE-STTB---HHHHHHHHHHHHHHHHHH CS
                    Ribosomal_S3Ae  80 gknaltnFkgmeltrDklrslvrkwsslIeaivdvktkDgyllrvfvvafTkkrnsYakssqkkaIrkkmveiltee 156
                                       g++a+t+F g+ lt+D++r+l+r+++++ + +vdv tkD y+lr++++ + ++r   +++sq+  +r++++ +lt+ 
  gi|474934835|ref|YP_007688417.1|  80 GHEAKTEFIGHTLTSDYVRRLTRRKKTKTDHVVDVVTKDKYVLRIKTMSIADRR---IQASQEDGMRAQIKIFLTQY 153
                                       ******************************************************...******************** PP

                                       HHHS-HHHHHHHHTTTHHHHHHHHHHTTTS-EEEEEEEEEEEEE- CS
                    Ribosomal_S3Ae 157 aseldlkelvkklipeslgkeiekeakkIyplrnveirKvkvlkk 201
                                        +e++l +++k++i+ +l+ke  k+++ I+p+++veirK++vl+k
  gi|474934835|ref|YP_007688417.1| 154 GKENNLADIIKAVISGDLAKETAKACHIIVPIKRVEIRKTEVLRK 198
                                       ***************55*************************986 PP

>> BppU_N  BppU N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.02   1.8e+02      42      65 ..      56      83 ..      46      91 .. 0.74
   2 ?   11.2   0.1   2.5e-05      0.23      13      58 ..     126     172 ..     103     184 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.02
                            BppU_N 42 spldLtg....ltarlefkkekaedgsg 65
                                      +  dLtg    ++++l+fk + a+++  
  gi|474934835|ref|YP_007688417.1| 56 TVQDLTGdfskMHIKLQFKITGADGHEA 83
                                      5678888887799999999986665553 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 2.5e-05
                            BppU_N  13 nnkvisqgiqfrsgDtgtaklnikltkngspldLtg.ltarlefkke 58 
                                       + ++ +  iq++++D   a+++i lt+ g++ +L++ ++a++ + ++
  gi|474934835|ref|YP_007688417.1| 126 TMSIADRRIQASQEDGMRAQIKIFLTQYGKENNLADiIKAVISGDLA 172
                                       33458999**************************9999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1649.29
//
Query:       gi|474934836|ref|YP_007688418.1|  [L=39]
Description: hypothetical protein TALC_01275 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 269.39
//
Query:       gi|474934837|ref|YP_007688419.1|  [L=285]
Description: CoB--CoM heterodisulfide reductase subunit B [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.1e-34  117.1   4.6    1.8e-16   60.1   0.2    3.1  4  CCG           Cysteine-rich domain
  ------ inclusion threshold ------
      0.024   14.5   0.1        6.6    6.5   0.0    2.2  2  Asp_Glu_race  Asp/Glu/Hydantoin racemase
       0.14   12.1   0.0       0.41   10.5   0.0    1.7  1  DUF2024       Domain of unknown function (DUF2024)


Domain annotation for each model (and alignments):
>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.2   0.1   2.4e-19   1.4e-15       1      84 [.       7      89 ..       7      90 .. 0.93
   2 ?   -2.6   0.0       1.1   6.8e+03      14      30 ..      99     115 ..      94     123 .. 0.77
   3 ?   -0.4   0.0      0.23   1.4e+03      65      78 ..     132     145 ..     114     146 .. 0.88
   4 !   60.1   0.2     3e-20   1.8e-16       2      85 .]     153     244 ..     152     244 .. 0.95

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 2.4e-19
                               CCG  1 vayfdgChllraaypevrkalkkllealgveleelekesCCGagggrsgkeelae.alakrnvetaeetgadaivtacp 78
                                      +a+f gC ++  +yp  +k+++ + e+lgvele+l ++sCC+a+g+ + + ++++ a a+rn+  ae+ +  +ivt+c+
  gi|474934837|ref|YP_007688419.1|  7 YAFFLGC-IAPLRYPGIEKSTRVVCEKLGVELEDLTDASCCPAPGVIRAFSRTTWlAAAARNLVLAEQ-KGLPIVTICN 83
                                      79*****.*******************************************96664999999999999.6899****** PP

                               CCG 79 gCllql 84
                                      gC+++l
  gi|474934837|ref|YP_007688419.1| 84 GCYGSL 89
                                      **9886 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.1
                               CCG  14 ypevrkalkkllealgv 30 
                                       + e+r ++ ++l+a+gv
  gi|474934837|ref|YP_007688419.1|  99 NAELRANVNEILKAAGV 115
                                       66778888888888876 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.23
                               CCG  65 aeetgadaivtacp 78 
                                       ++e+g+++i++ac+
  gi|474934837|ref|YP_007688419.1| 132 FREVGVEKIAAACS 145
                                       78999999*99998 PP

  == domain 4  score: 60.1 bits;  conditional E-value: 3e-20
                               CCG   2 ayfdgChllraa......ypevrkalkkllealgveleel.ekesCCGagggrsgkee.laealakrnvetaeetga 70 
                                       a f+gCh+l++         ev+++l  l+ea+g++ ++  +k  CCG+ggg +     +a++++k n+e+++  ga
  gi|474934837|ref|YP_007688419.1| 153 ATFYGCHFLKPTdikgidDAEVPHILDDLVEATGCTSMPRkQKMLCCGSGGGLKAAFGdVAKEFTKTNLENMQASGA 229
                                       78*******9999**********************999988*********998888777****************** PP

                               CCG  71 daivtacpgCllqlk 85 
                                       ++iv  cp+C+lq++
  gi|474934837|ref|YP_007688419.1| 230 QFIVDVCPFCHLQFD 244
                                       *************96 PP

>> Asp_Glu_race  Asp/Glu/Hydantoin racemase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0    0.0018        11     121     192 ..      79     145 ..      76     151 .. 0.80
   2 ?    6.5   0.0    0.0011       6.6      54      98 ..     212     259 ..     181     274 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0018
                                       HHHHCTHHHHHHHHHGT.EEE....T-CCCHHCCHC.HHHHTT-TTSHHHHHHHHHHHHHHTTT-SEEEE-ST CS
                      Asp_Glu_race 121 gtlksglyqkeleanqgievvvpseelqssvnqaiy.eelkaGevteearrailkllerlaergadaviLGCT 192
                                        t+ +g+y + +ea++++     ++el+ +vn++ + + +++ + t+e +++ + l++   e g++++  +C 
  gi|474934837|ref|YP_007688419.1|  79 VTICNGCYGSLFEAAHEL---NHNAELRANVNEILKaAGVVEYKGTTEVFHFAEVLFR---EVGVEKIAAACS 145
                                       68999*********9888...88999999**988886555555555666677777777...999999999997 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0011
                                       THH.HHHHHHHHHHCTTESEEEE--CHHHHHHHHHHHH..-SSEEEEC CS
                      Asp_Glu_race  54 pvl.klleaakkLekagadaiviaCnTahavadelqkk..ikiPvlgi 98 
                                       +++ +++ ++++++++ga++iv  C   h  +d  +k    +iPvl++
  gi|474934837|ref|YP_007688419.1| 212 VAKeFTKTNLENMQASGAQFIVDVCPFCHLQFDTSEKDlgFNIPVLHL 259
                                       55669***************************9999553378999996 PP

>> DUF2024  Domain of unknown function (DUF2024)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   6.9e-05      0.41      32      64 ..     213     245 ..     207     253 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 6.9e-05
                                       HHHHHHHHHHHHT---S---TTTEEEEEEEE-- CS
                           DUF2024  32 aleyakeyLkskgeeeakvtskeCkfCHseeae 64 
                                       a e++k  L+++  ++a+   + C fCH +  +
  gi|474934837|ref|YP_007688419.1| 213 AKEFTKTNLENMQASGAQFIVDVCPFCHLQFDT 245
                                       7899************************99655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2015.50
//
Query:       gi|474934838|ref|YP_007688420.1|  [L=166]
Description: CoB--CoM heterodisulfide reductase, subunit C [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.9e-10   38.7   8.0    1.6e-09   38.1   8.0    1.3  1  Fer4_8    4Fe-4S dicluster domain
      2e-09   37.5   7.7    3.5e-09   36.7   7.7    1.4  1  Fer4_9    4Fe-4S dicluster domain
    5.5e-09   36.0   6.3    9.2e-09   35.3   6.3    1.3  1  Fer4_10   4Fe-4S dicluster domain
    5.7e-09   36.4   8.4    8.9e-09   35.8   8.4    1.3  1  Fer4_17   4Fe-4S dicluster domain
    6.2e-07   29.9   7.6    1.1e-06   29.1   7.6    1.4  1  Fer4_7    4Fe-4S dicluster domain
    0.00042   20.6  11.3     0.0015   18.9   2.8    2.2  2  Fer4_4    4Fe-4S binding domain
     0.0011   18.9  11.2      0.029   14.4   2.2    2.4  2  Fer4_2    4Fe-4S binding domain
      0.004   16.9  13.4       0.13   12.1   2.4    2.4  2  Fer4      4Fe-4S binding domain
  ------ inclusion threshold ------
      0.023   14.8   6.9      0.069   13.3   6.9    1.7  1  Fer4_21   4Fe-4S dicluster domain
      0.074   14.0  12.8       0.72   10.8  12.8    2.2  2  Fer4_16   4Fe-4S double cluster binding domain
       0.08   13.1   6.3       0.35   11.1   0.4    2.2  2  Fer4_18   4Fe-4S dicluster domain
       0.23   12.5  17.9       0.79   10.8   4.3    2.3  2  Fer4_3    4Fe-4S binding domain
       0.74   10.0  13.0       0.21   11.7   1.7    2.3  2  Fer4_6    4Fe-4S binding domain
        2.2    9.1   8.2       0.69   10.7   0.7    2.7  2  Fer4_15   4Fe-4S single cluster domain
        6.5    7.7  12.4        9.8    7.1   1.1    2.3  2  Fer4_22   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   8.0   1.3e-12   1.6e-09       2      64 ..      21      81 ..      20      82 .. 0.81

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 1.3e-12
                            Fer4_8  2 lekCieCgaCqsaCpvlrrtk.khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                      ++ C +Cg C++ Cp+ rrt  + ++  r  + + ++e     + e lw C+tc  C+e+Cp  
  gi|474934838|ref|YP_007688420.1| 21 VSLCFQCGTCTAGCPSGRRTSyRVRKLVRMAQLDMKEEIL---NSEELWMCSTCYTCVERCPRR 81
                                      567*****************97777777777666333333...3789***************86 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   7.7   2.9e-12   3.5e-09       2      49 ..      24      81 ..      22      82 .. 0.96

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 2.9e-12
                            Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraase..........eaCigCgaCveaCpkg 49
                                      C +Cg+C++ Cp+g  +  ++++ +r+ + ++          + C +C +Cve+Cp+ 
  gi|474934838|ref|YP_007688420.1| 24 CFQCGTCTAGCPSGRRTSYRVRKLVRMAQLDMkeeilnseelWMCSTCYTCVERCPRR 81
                                      **************************99988899**********************96 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   6.3   7.7e-12   9.2e-09       5      56 .]      20      79 ..      18      79 .. 0.92

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 7.7e-12
                           Fer4_10  5 dddtCirCgkCvkaCPadl.......tsvgakgeaseeeavrk.kvekCtgcgaCveaCP 56
                                      d + C +Cg+C++ CP+         + v+  + +++ee  +   ++ C +c  Cve CP
  gi|474934838|ref|YP_007688420.1| 20 DVSLCFQCGTCTAGCPSGRrtsyrvrKLVRMAQLDMKEEILNSeELWMCSTCYTCVERCP 79
                                      6789*************98*******999999999999998888***************9 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   8.4   7.5e-12   8.9e-09       2      60 ..      24      82 ..      23      83 .. 0.96

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 7.5e-12
                           Fer4_17  2 CiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqgl 60
                                      C qCg C++ Cps+++++ + +kl+r a+l ++ee+ ++e+   C++C  C+++CP  +
  gi|474934838|ref|YP_007688420.1| 24 CFQCGTCTAGCPSGRRTSYRVRKLVRMAQLDMKEEILNSEELWMCSTCYTCVERCPRRV 82
                                      ************************************999*****************876 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   7.6   9.3e-10   1.1e-06       2      50 ..      24      80 ..      23      82 .. 0.70

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 9.3e-10
                            Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgtekv........eidpekClgCgaCvavCPt 50
                                      C +Cg C+a Cp++ ++   + +  +++++          + ++C++C+ Cv++CP 
  gi|474934838|ref|YP_007688420.1| 24 CFQCGTCTAGCPSGRRTSYRVRKLVRMAQLdmkeeilnSEELWMCSTCYTCVERCPR 80
                                      ************99999876655555544422222233334568************7 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   2.8   1.2e-06    0.0015       4      17 .]      24      37 ..      21      42 .. 0.92
   2 ?    6.5   1.4     0.012        14       4      16 ..      68      80 ..      62      88 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.2e-06
                            Fer4_4  4 CigCgsCvaaCPqg 17
                                      C++Cg C+a CP+g
  gi|474934838|ref|YP_007688420.1| 24 CFQCGTCTAGCPSG 37
                                      ************75 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.012
                            Fer4_4  4 CigCgsCvaaCPq 16
                                      C  C  Cv  CP 
  gi|474934838|ref|YP_007688420.1| 68 CSTCYTCVERCPR 80
                                      99*********95 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   2.2   2.5e-05     0.029       5      21 ..      19      35 ..      16      36 .. 0.87
   2 !    9.3   1.8    0.0011       1.3       9      21 ..      67      79 ..      60      80 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.5e-05
                            Fer4_2  5 vdtdrCigCgaCvsaCP 21
                                      +d   C +Cg+C+  CP
  gi|474934838|ref|YP_007688420.1| 19 ADVSLCFQCGTCTAGCP 35
                                      57889*******888** PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0011
                            Fer4_2  9 rCigCgaCvsaCP 21
                                      +C  C +Cv  CP
  gi|474934838|ref|YP_007688420.1| 67 MCSTCYTCVERCP 79
                                      8***********9 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   2.4   0.00011      0.13       4      21 ..      20      37 ..      19      37 .. 0.91
   2 !   10.1   3.4   0.00049      0.58       8      20 ..      68      80 ..      67      83 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                                      ETTTSSS-THHHHHSTTT CS
                              Fer4  4 deekCigCGaCvevCPvg 21
                                      d ++C  CG+C   CP g
  gi|474934838|ref|YP_007688420.1| 20 DVSLCFQCGTCTAGCPSG 37
                                      6799************76 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00049
                                      SSS-THHHHHSTT CS
                              Fer4  8 CigCGaCvevCPv 20
                                      C  C +Cve CP 
  gi|474934838|ref|YP_007688420.1| 68 CSTCYTCVERCPR 80
                                      999*********7 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   6.9   5.7e-05     0.069       6      52 ..      22      79 ..      19      85 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.7e-05
                           Fer4_21  6 dkCigCgkCliaCedtshqai.........eidaktvlkvved..eCvGCnlCssvCP 52
                                      + C +Cg C+  C+ +  +           ++d k+ +   e+   C  C  C++ CP
  gi|474934838|ref|YP_007688420.1| 22 SLCFQCGTCTAGCPSGRRTSYrvrklvrmaQLDMKEEILNSEElwMCSTCYTCVERCP 79
                                      68***********987666554445554443444444333444457************ PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8  12.8    0.0006      0.72       2      65 ..      24      79 ..      23      81 .. 0.77
   2 ?    8.0   3.4    0.0047       5.6       2      16 ..      68      82 ..      67     120 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0006
                           Fer4_16  2 CgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCP 65
                                      C +Cg C+  CP++  ++    ++++   ++     + d++e++ + ++ + +  C +C++ CP
  gi|474934838|ref|YP_007688420.1| 24 CFQCGTCTAGCPSGRRTSY---RVRKLVRMA-----QLDMKEEILNSEELWMCSTCYTCVERCP 79
                                      9************988877...344333433.....3567777777777888***********9 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0047
                           Fer4_16  2 CgtCgkCaevCPtna 16
                                      C tC  C+e CP ++
  gi|474934838|ref|YP_007688420.1| 68 CSTCYTCVERCPRRV 82
                                      9***********876 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.9      0.02        23      56      74 ..      19      37 ..       4      46 .. 0.80
   2 ?   11.1   0.4   0.00029      0.35      45      78 ..      52      85 ..      37      94 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.02
                           Fer4_18 56 kgagdcidcescvkvcPtg 74
                                      ++++ c +c++c + cP g
  gi|474934838|ref|YP_007688420.1| 19 ADVSLCFQCGTCTAGCPSG 37
                                      56677************86 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00029
                           Fer4_18 45 kalkekeerkekgagdcidcescvkvcPtgidir 78
                                      +  +++e  ++++   c +c +cv+ cP  + i 
  gi|474934838|ref|YP_007688420.1| 52 QLDMKEEILNSEELWMCSTCYTCVERCPRRVPIV 85
                                      4445556667778889************998775 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   5.7    0.0078       9.3       1      14 [.      24      37 ..      24      37 .. 0.95
   2 ?   10.8   4.3   0.00066      0.79       1      13 [.      68      80 ..      67      82 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0078
                            Fer4_3  1 CtgCgaCvevCPvg 14
                                      C +Cg+C   CP+g
  gi|474934838|ref|YP_007688420.1| 24 CFQCGTCTAGCPSG 37
                                      99**********97 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00066
                            Fer4_3  1 CtgCgaCvevCPv 13
                                      C  C++Cve CP 
  gi|474934838|ref|YP_007688420.1| 68 CSTCYTCVERCPR 80
                                      899*********7 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.7   0.00018      0.21       5      22 ..      20      37 ..      19      38 .. 0.89
   2 ?    3.3   3.9     0.081        97       9      20 ..      68      79 ..      67      87 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00018
                            Fer4_6  5 dpdkCigCgdCvrvCPeg 22
                                      d ++C +Cg C++ CP g
  gi|474934838|ref|YP_007688420.1| 20 DVSLCFQCGTCTAGCPSG 37
                                      778999**********86 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.081
                            Fer4_6  9 CigCgdCvrvCP 20
                                      C  C+ Cv  CP
  gi|474934838|ref|YP_007688420.1| 68 CSTCYTCVERCP 79
                                      889********9 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   1.5      0.33     4e+02       4      20 ..      20      36 ..      19      65 .. 0.80
   2 ?   10.7   0.7   0.00058      0.69       7      55 ..      67     130 ..      63     151 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.33
                           Fer4_15  4 DrdaCigcglCvaeape 20
                                      D ++C  cg C a +p 
  gi|474934838|ref|YP_007688420.1| 20 DVSLCFQCGTCTAGCPS 36
                                      6689*******999985 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00058
                           Fer4_15   7 aCigcglCvaeapevfeldedglasvl..........lddgeiaeg.............evpddeeeaaqeA 55 
                                        C  c  Cv+++p+++ + +  +a ++          +       +             +vp ++e +a +A
  gi|474934838|ref|YP_007688420.1|  67 MCSTCYTCVERCPRRVPIVDIVIA-LRnmavadghikA-------AhkktasnlyttghTVPINDEVKALRA 130
                                       6***********999998877666.3334433333331.......234444445555566666666666665 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   4.6      0.03        36       2      14 ..      24      36 ..      23      46 .. 0.88
   2 ?    7.1   1.1    0.0082       9.8      64      95 ..      50      81 ..      36      82 .. 0.63

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.03
                           Fer4_22  2 ClsCgaCtlvCpt 14
                                      C++Cg+Ct+ Cp+
  gi|474934838|ref|YP_007688420.1| 24 CFQCGTCTAGCPS 36
                                      9**********97 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0082
                           Fer4_22 64 qrllhklsefkekfgesgCvGCgRCieacpvk 95
                                         l+  +e+ ++ +  +C  C  C+e+cp +
  gi|474934838|ref|YP_007688420.1| 50 MAQLDMKEEILNSEELWMCSTCYTCVERCPRR 81
                                      33333334555556889************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       833  (0.046461); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1070.35
//
Query:       gi|474934839|ref|YP_007688421.1|  [L=240]
Description: Transcriptional regulator [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-08   32.6   0.0    9.5e-08   31.9   0.0    1.4  1  HTH_1     Bacterial regulatory helix-turn-helix protein, lysR
  ------ inclusion threshold ------
       0.16   12.3   0.0       0.43   10.9   0.0    1.7  1  NUMOD1    NUMOD1 domain


Domain annotation for each model (and alignments):
>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   1.1e-11   9.5e-08      14      60 .]       2      48 ..       1      48 [. 0.97

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 1.1e-11
                                      SSHHHHHHHHTS-HHHHHHHHHHHHHHHTS-SEEESSSEEEE-HHHH CS
                             HTH_1 14 gsftrAAeeLglsqpavsrqikrLEeelgvpLfeRtgrglrLTeaGe 60
                                      gs+++AA+ +g+s p v r i++ E++ g+   + t  g+ LT+aG+
  gi|474934839|ref|YP_007688421.1|  2 GSMSAAAKSMGISVPVVHRYIANIEAAAGEAVTHSTPSGTFLTPAGK 48
                                      9********************************************95 PP

>> NUMOD1  NUMOD1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   4.8e-05      0.43      18      37 .]       3      22 ..       3      22 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.8e-05
                            NUMOD1 18 SireAakyLgishntInkyl 37
                                      S+++Aak++gis + + +y+
  gi|474934839|ref|YP_007688421.1|  3 SMSAAAKSMGISVPVVHRYI 22
                                      89*************99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1480.27
//
Query:       gi|474934840|ref|YP_007688422.1|  [L=167]
Description: hydrogenase maturation protease [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-09   37.8   0.2    2.4e-09   37.1   0.2    1.4  2  HycI      Hydrogenase maturation protease


Domain annotation for each model (and alignments):
>> HycI  Hydrogenase maturation protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.18   3.3e+03      95     119 ..       9      33 ..       5      43 .. 0.68
   2 !   37.1   0.2   1.3e-13   2.4e-09      25     128 ..      46     151 ..      24     153 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.18
                                       EEEEEE--S-BST.CCS--HHHHCC CS
                              HycI  95 villgvqpesledvgielseevkka 119
                                       vi+lg +  + + vg+ +se ++++
  gi|474934840|ref|YP_007688422.1|   9 VIGLGSPVMTDDSVGLRVSEDIERM 33 
                                       5555555555555888888888876 PP

  == domain 2  score: 37.1 bits;  conditional E-value: 1.3e-13
                                       -SGGGHHHHCC-SEEEEEEE--S.SS-TT-EEEEECCHHHHHHTTC.CGCCCHCHHHHHHHHHHC..CS--SEEEEE CS
                              HycI  25 qglelvgtleeadkliivDavdf.glepGevkiikddevpkklkakkmsaHqlplaevlklleek..geipkevill 98 
                                       +glel+++++ +++++ivDa++  + +pG++ i+++ +    + ++ m aH++++a ++   +++  + +p +v ++
  gi|474934840|ref|YP_007688422.1|  46 GGLELLPLMKGYSYVVIVDAIQTfQYDPGTILIFDVADFES-TVNNGMPAHDINVATAIGIGRQMdpDSMPLQVRFV 121
                                       7999*****************988****************7.55555*********99965544411479******* PP

                                       EE--S-BST.CCS--HHHHCCHHHHHHHCC CS
                              HycI  99 gvqpesledvgielseevkkavekavelil 128
                                       +++ +++++++ el++ v+ +   +v+++l
  gi|474934840|ref|YP_007688422.1| 122 AMEIKDMQTMSEELTPIVASKESSMVDAAL 151
                                       *******************99999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1100.22
//
Query:       gi|474934841|ref|YP_007688423.1|  [L=423]
Description: putative Zn-dependent peptidase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.4e-33  114.5   0.0    2.7e-30  105.8   0.0    2.7  3  Peptidase_M16_C  Peptidase M16 inactive domain
    4.4e-29  101.4   0.0    8.6e-29  100.4   0.0    1.4  1  Peptidase_M16    Insulinase (Peptidase family M16)


Domain annotation for each model (and alignments):
>> Peptidase_M16_C  Peptidase M16 inactive domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.29   2.6e+03      63     101 ..      11      49 ..       5      71 .. 0.75
   2 !  105.8   0.0     3e-34   2.7e-30       2     183 .]     169     342 ..     168     342 .. 0.94
   3 !    5.7   0.0    0.0015        13       1      30 [.     382     411 ..     382     416 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.29
                                       GSSEEEEEEEESSSSSEEEEEEEEEECTCTHTTHHHHHH CS
                   Peptidase_M16_C  63 tlkkppvvlkkldeeqahlslafegpskendeddlalav 101
                                       t ++ pvv ++ +  +a + +a ++ s++ ++ ++ l+ 
  gi|474934841|ref|YP_007688423.1|  11 TGSGIPVVTENVPGANAAFLVAVRTGSRDEHDGIFGLSH 49 
                                       556778888888889999999999999977777766653 PP

  == domain 2  score: 105.8 bits;  conditional E-value: 3e-34
                                       H-HHHHHHHHHHHSSGGGEEEEEEESS-HHHHHHHHHHHHTTSTHHSHCSGSCTSSSSSGGGSSEEEEEEEESSSSS CS
                   Peptidase_M16_C   2 ltredlkefykkfYrpenmvlaivGdvdheelvkliekyfgdlkaskappakptgepltpatlkkppvvlkkldeeq 78 
                                       lt+edl+++y++ Y   n+ +++ G +d +e+v+++e+ f+++ as  + ++ ++ p++        +++ +  ++ 
  gi|474934841|ref|YP_007688423.1| 169 LTYEDLRKYYEERYGLPNIAVFATGSFDKKEVVDWAENSFSGMSASVVNRREAPKMPVS-------KFRITDNGVDH 238
                                       89*******************************************97665666666666.......7788888889* PP

                                       EEEEEEEEEECTCTHTTHHHHHHHHHHHHSSTTSHHHHHHHTTTTSESEEEEEEEEESSCEEEEEEEEEECTTHHHH CS
                   Peptidase_M16_C  79 ahlslafegpskendeddlalavlntlLgggmesrLytnlrekeglaysvsafndsyrdsglfgisatadpenveev 155
                                       a + l+f++p   +  +  +++vl+ ++g+g +sr ++++rek  l+y ++    +y+d g+ +  + + ++n+++ 
  gi|474934841|ref|YP_007688423.1| 239 ANIGLGFPTPKV-DGHQRTVNQVLSAVIGSGSSSRMFQEVREKNALVYAIYNQTGNYSDAGYVSTFLNCVDKNILKS 314
                                       ************.**************************************************************** PP

                                       HHHHHHHHHHHHHHTS-HHHHHHHHHHH CS
                   Peptidase_M16_C 156 vevilkelrklkkeglteeeleraknql 183
                                       ++ ++++ r++k+eglte el+r kn l
  gi|474934841|ref|YP_007688423.1| 315 LDECFRVYREFKREGLTEGELDRTKNIL 342
                                       *************************976 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.0015
                                       CH-HHHHHHHHHHHSSGGGEEEEEEESS-H CS
                   Peptidase_M16_C   1 sltredlkefykkfYrpenmvlaivGdvdh 30 
                                       s+t e++ +  +++  pe++ l i G+v+ 
  gi|474934841|ref|YP_007688423.1| 382 SVTEEEVMAAAERYLVPERLNLTILGKVPK 411
                                       57999**********************986 PP

>> Peptidase_M16  Insulinase (Peptidase family M16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.4   0.0   9.6e-33   8.6e-29       2     142 ..      17     156 ..      16     161 .. 0.96

  Alignments for each domain:
  == domain 1  score: 100.4 bits;  conditional E-value: 9.6e-33
                                       EEEEE-TSSSEEEEEEEES-SGGGSCTTTTTHHHHHHHHTTSBBSSSCHHHHHHHHHHTTCEEEEEEESSEEEEEEE CS
                     Peptidase_M16   2 valesdppaktsavglvvdaGSryepkdlnGlAHllehmafkgTkkypsnklaeeleklGgslnAttsrentvYyve 78 
                                       v++e+  p   +a+ + v +GSr+e + + Gl+Hlleh +f  Tk+ +s ++ +++e  Gg lnA+t +e t+Yy  
  gi|474934841|ref|YP_007688423.1|  17 VVTENV-PGANAAFLVAVRTGSRDEHDGIFGLSHLLEHTVFRETKNMTSFEMSKVMEGAGGMLNAFTAKEMTAYYGI 92 
                                       566777.88999***************************************************************** PP

                                       EEGGGHHHHHHHHHHHHHSBTTSHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHTTTSGGG CS
                     Peptidase_M16  79 vlskdlekaldvladvfkaplleesevererkvvekeveavdaepekvveenlhaaayrekalg 142
                                       +l++   +a+d+ ad++++pl++e+++e+e+++v++e+++v++epe  +++  +++ +  ++lg
  gi|474934841|ref|YP_007688423.1|  93 TLAETGRTAMDLVADIVANPLINEKDTEMEKDIVLQELSMVKSEPETYIHDLFEQNLWDGDPLG 156
                                       ***************************************************9999999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2607.84
//
Query:       gi|474934842|ref|YP_007688424.1|  [L=265]
Description: Archaeal enzymes of ATP-grasp superfamily [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.5e-38  131.4   0.0    5.2e-38  131.2   0.0    1.0  1  PAC2            PAC2 family
  ------ inclusion threshold ------
      0.025   14.8   0.0      0.057   13.7   0.0    1.6  1  Transgly_assoc  Transglycosylase associated protein


Domain annotation for each model (and alignments):
>> PAC2  PAC2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.2   0.0   5.8e-42   5.2e-38       1     212 [.      19     252 ..      19     253 .. 0.95

  Alignments for each domain:
  == domain 1  score: 131.2 bits;  conditional E-value: 5.8e-42
                                       EEEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETTEEE-SEEEEEE.TTT........... CS
                              PAC2   1 LilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveegrelepprlyak.dsg........... 65 
                                       +i+Gfp +G+Vg+++++++++ l+++  g i s++ lp     p++lv++g++l+++r+ya   ++           
  gi|474934842|ref|YP_007688424.1|  19 AIIGFPTVGLVGSIVASFIARDLKLDITGGITSRD-LP-----PYTLVQSGQPLPQIRIYAGsLPKakrkkktevse 89 
                                       69*********************************.9*.....****************99984445899******* PP

                                       ................SEEEEEEE...E-HSCHHHHHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEE CS
                              PAC2  66 ...............srdllvlqg...repilqyeefakalldwaeelgvkevvvLggldageradvphtrpekvtg 124
                                                       rd++++++   + p+ +y+ ++k++ + ++++g +++++L+g++ + + d       +++g
  gi|474934842|ref|YP_007688424.1|  90 qpaadevpakkprakTRDVIIVTSevaPKPEDTYD-LSKCVYETVRAMGATTIICLEGVPRMGQDD-------RIMG 158
                                       ***********************************.************************887643.......89** PP

                                       EESSHHHHHHHHCT.....-CEEEEHHHHHHHHHHHHTT-EEEEEEEEEECCC--HHHHHHHHHHHHHHH.T---HC CS
                              PAC2 125 aatdeelleelees.....eyggivgitglLlsaakergipavgllaevphylpdPkaaaalleflskll.glevdt 195
                                       +at++e +  lee       +g++ gitg++l+++ +  +++ ++l++++++lpdP++aa+++  l++++ +l+vdt
  gi|474934842|ref|YP_007688424.1| 159 VATTREGAIFLEEIgltvmGEGIVRGITGVILMLGMKDRVDVKAILCPANPQLPDPRSAARIIGPLQAIMpRLSVDT 235
                                       ********99964456788999************************************************99***** PP

                                       HHHHHHHHHHHHHHHHH CS
                              PAC2 196 edLeedaeeleeqleel 212
                                       ++L ++aee++++++ +
  gi|474934842|ref|YP_007688424.1| 236 DPLFKEAEEIDNRIQAQ 252
                                       *************9986 PP

>> Transgly_assoc  Transglycosylase associated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   6.4e-06     0.057       3      30 ..      26      48 ..      25      53 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.4e-06
                    Transgly_assoc  3 lGivGAfvGgfllgllgigvgggelasl 30
                                      +G+vG++v+ f+++ l +     ++ + 
  gi|474934842|ref|YP_007688424.1| 26 VGLVGSIVASFIARDLKL-----DITGG 48
                                      7***************99.....33333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2021.93
//
Query:       gi|474934843|ref|YP_007688425.1|  [L=159]
Description: hypothetical protein TALC_01282 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-35  122.4   0.0    1.6e-35  122.3   0.0    1.0  1  PvlArgDC  Pyruvoyl-dependent arginine decarboxylase (PvlArgDC


Domain annotation for each model (and alignments):
>> PvlArgDC  Pyruvoyl-dependent arginine decarboxylase (PvlArgDC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.3   0.0   9.1e-40   1.6e-35       1     161 [.       5     154 ..       5     155 .. 0.96

  Alignments for each domain:
  == domain 1  score: 122.3 bits;  conditional E-value: 9.1e-40
                          PvlArgDC   1 vPkkvfltkGvgesk.eelasFdlALldAgIenfNLvkvSSilPpeaeivsveeglkelppGsivevvmarassnep 76 
                                       vP+++f+t+++++s+ ++l++FdlALl+Ag +++NLv+vSS++P +a+  +ve++  +lp+G ++++v+++++++  
  gi|474934843|ref|YP_007688425.1|   5 VPSAYFVTSAAATSPvSDLNAFDLALLKAGLSEQNLVAVSSVIPDGAR--EVEQF--DLPMGMVTFCVLSQMRGR-G 76 
                                       79*************89*******************************..9****..****************96.5 PP

                          PvlArgDC  77 grliaaavgvaipkdekkgGyiaEysgfgeseeeaeeeaeelaaemlattrglleekiietkeievaaveakvekyg 153
                                       g++++a+++++++kd   gGy+aE + +g s++  ++e  ++++em +  rg+    ++ + e+++++ +  +++yg
  gi|474934843|ref|YP_007688425.1|  77 GDIVSAGIAYTRRKD-GYGGYVAEGHLHG-SADCLRDELGRKMNEMSRI-RGV----EFGEIEYRIEELKIPEDEYG 146
                                       559********9999.99*********99.******************6.**9....8888999999********** PP

                          PvlArgDC 154 tvlaaavf 161
                                       ++l+a+vf
  gi|474934843|ref|YP_007688425.1| 147 CALSALVF 154
                                       *******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1156.02
//
Query:       gi|474934844|ref|YP_007688426.1|  [L=144]
Description: hypothetical protein TALC_01283 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.061   13.4   3.0       0.21   11.6   2.8    1.9  2  Zn_Tnp_IS91  Transposase zinc-binding domain
       0.12   12.3   0.0       0.23   11.5   0.0    1.4  1  PUA          PUA domain
       0.36   11.0   4.6          2    8.6   4.6    2.1  1  UPF0547      Uncharacterised protein family UPF0547


Domain annotation for each model (and alignments):
>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   2.8   3.5e-05      0.21      37      69 ..       4      36 ..       2      48 .. 0.90
   2 ?    1.0   0.1     0.076   4.5e+02      19      36 ..      34      51 ..      32      57 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.5e-05
                       Zn_Tnp_IS91 37 faryeCeeCghekivyfsCksrhCpsCqkkate 69
                                      fa++ C++C+  +iv  s k   C  C++k+  
  gi|474934844|ref|YP_007688426.1|  4 FAVVTCPGCKRMRIVDLSAKTSECAFCGTKSVV 36
                                      67899***********************99865 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.076
                       Zn_Tnp_IS91 19 sqrkavekilrCrtaalG 36
                                      s+ k+++ + rCrt++  
  gi|474934844|ref|YP_007688426.1| 34 SVVKELQPVCRCRTQETA 51
                                      6788999999***98865 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.8e-05      0.23      18      43 ..      95     120 ..      83     135 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.8e-05
                                       EEEGGGEEEEETT--TTSEEEEEETT CS
                               PUA  18 sLlapGvvevegdfeegdvVaivded 43 
                                        ++ +G++++ g+f e+dvV++  + 
  gi|474934844|ref|YP_007688426.1|  95 EVMSKGLTRIYGEFTEDDVVRLDPKH 120
                                       79******************987665 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   4.6   0.00033         2       2      22 ..       8      32 ..       8      33 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00033
                           UPF0547  2 vCPeCea....kvPvaaqfCphCGy 22
                                      +CP+C +     +++ + +C++CG+
  gi|474934844|ref|YP_007688426.1|  8 TCPGCKRmrivDLSAKTSECAFCGT 32
                                      7****97443346777779*****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 886.02
//
Query:       gi|474934845|ref|YP_007688427.1|  [L=230]
Description: hypothetical protein TALC_01284 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
        2.8    8.5  22.1         43    4.6   2.0    3.2  2  SNARE_assoc  SNARE associated Golgi protein
        4.2    7.3  11.5        1.3    8.9   5.8    2.3  2  DUF2678      Protein of unknown function (DUF2678)
        6.9    6.6  13.8       0.21   11.5   1.6    3.0  3  DUF3487      Protein of unknown function (DUF3487)


Domain annotation for each model (and alignments):
>> SNARE_assoc  SNARE associated Golgi protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4  16.0     0.036   2.2e+02       2      90 ..      28     145 ..      28     176 .. 0.71
   2 ?    4.6   2.0    0.0073        43      18      44 ..     176     210 ..     160     230 .] 0.66

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.036
                       SNARE_assoc   2 PsevllvaaGvlfglllgtlvtslgallGaslayllgrylgr...........................kalrrkll 51 
                                       Ps ++l+a G+++g+++ ++++++  ++ a+++y ++++l+                             + +  ++
  gi|474934845|ref|YP_007688427.1|  28 PSFFMLFAIGLVAGTVMFLVYSYVMNSIVAVIMYSVIQVLLIvvcmnlkryrgksdsifyglgfglgagGSTGTGFI 104
                                       8899**********************************999777755555555555555444444444433333333 PP

                       SNARE_assoc  52 sekrvka..lerlverygflallllrllpivPrdlvnyvaG 90 
                                       ++ +v    l  +v+  g+++l+++ l+ i+ +++v++++G
  gi|474934845|ref|YP_007688427.1| 105 YYIAVSSdqLGGSVDAAGWVFLVVVALSMIFQYSAVGVTVG 145
                                       44333334455555778888888888888888888887776 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0073
                       SNARE_assoc  18 l.....gtlvtslgallGaslayllgrylgr...k 44 
                                       +     +++++++ga l+ s+ yl  +y  +    
  gi|474934845|ref|YP_007688427.1| 176 MnsdsgAIMYLMAGAALAISVFYLWFAYTKEiakL 210
                                       13333589****************99998765550 PP

>> DUF2678  Protein of unknown function (DUF2678)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   5.8   0.00023       1.3      40     111 ..       5      75 ..       1      80 [. 0.74
   2 ?    1.6   0.3     0.043   2.6e+02      81     105 ..     152     176 ..     120     199 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00023
                           DUF2678  40 llvlvtvvssfvfpslpp...kplniffavcillisssvivlifwyrqgdlepkfrnliyyilasivllclcanl 111
                                       ll++  ++  + +p ++         f+ + i l++++v+ l++ y        +  +i y+++ ++l+++c nl
  gi|474934845|ref|YP_007688427.1|   5 LLLMYLLLRKYTYPAVENpyfSDPSFFMLFAIGLVAGTVMFLVYSYVMNS----IVAVIMYSVIQVLLIVVCMNL 75 
                                       556666666677776543111233467778999*************8765....5789****************9 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.043
                           DUF2678  81 wyrqgdlepkfrnliyyilasivll 105
                                       +  q  ++  + nl+y+++++i+l+
  gi|474934845|ref|YP_007688427.1| 152 YPMQFAMQAMIYNLVYWVVFTIMLM 176
                                       4556667777889999999988876 PP

>> DUF3487  Protein of unknown function (DUF3487)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.6   3.5e-05      0.21      23      69 ..      28      74 ..      24      88 .. 0.82
   2 ?    1.0   0.7     0.063   3.8e+02      48      87 ..     122     160 ..      98     172 .. 0.70
   3 ?    1.0   0.7     0.062   3.7e+02      25      61 ..     174     210 ..     161     226 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.5e-05
                           DUF3487 23 dEllvlaglglvvglvlglllallvgslaliptialllvllvvlvgg 69
                                      + +++l+ +glv+g v+ l+   +++s++ ++   ++ vll+v+++ 
  gi|474934845|ref|YP_007688427.1| 28 PSFFMLFAIGLVAGTVMFLVYSYVMNSIVAVIMYSVIQVLLIVVCMN 74
                                      66899999*************99999999999999999988887764 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.063
                           DUF3487  48 gslaliptialllvllvvlvggkllarlKRgkPdtylyrr 87 
                                       g +++++ +al +++   +vg ++ + + R  P ++  + 
  gi|474934845|ref|YP_007688427.1| 122 G-WVFLVVVALSMIFQYSAVGVTVGEGIARHYPMQFAMQA 160
                                       3.67777777777777777777776677777776666655 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.062
                           DUF3487  25 llvlaglglvvglvlglllallvgslaliptialllv 61 
                                       +l+   +g++++l++g  la+ v +l +  t  ++ +
  gi|474934845|ref|YP_007688427.1| 174 MLMNSDSGAIMYLMAGAALAISVFYLWFAYTKEIAKL 210
                                       4455566777777777777766666666655555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1281  (0.0714485); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 1396.92
//
Query:       gi|474934846|ref|YP_007688428.1|  [L=67]
Description: hypothetical protein TALC_01285 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.7e-08   31.9   0.3      8e-08   31.6   0.3    1.0  1  FecCD     FecCD transport family


Domain annotation for each model (and alignments):
>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.3   4.5e-12     8e-08     124     177 ..      11      64 ..       7      66 .. 0.94

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 4.5e-12
                             FecCD 124 krkgasplkliLaGiavsallsaltsllllllneealesilfwllGslsgasws 177
                                       k ++asp+++i++Gi + ++++altsl+++ +  ++++++ +wl+G+++ ++w+
  gi|474934846|ref|YP_007688428.1|  11 KITNASPITIIMTGIGIMYVFNALTSLVKIKMGGTSTARLENWLMGDVQLVTWD 64 
                                       66899***********************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 459.53
//
Query:       gi|474934847|ref|YP_007688429.1|  [L=685]
Description: 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase-related enzyme [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.5e-38  131.4   0.0    5.1e-38  130.8   0.0    1.2  1  PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
    0.00017   22.1  12.2    0.00017   22.1  12.2    3.4  3  Fer4_7       4Fe-4S dicluster domain
    0.00079   19.5  12.6    0.00079   19.5  12.6    3.8  4  Fer4_10      4Fe-4S dicluster domain
     0.0019   18.2   2.1     0.0019   18.2   2.1    4.0  4  Fer4_6       4Fe-4S binding domain
     0.0023   17.7  25.6     0.0028   17.4   2.3    4.3  4  Fer4         4Fe-4S binding domain
     0.0035   17.4   9.2     0.0035   17.4   9.2    3.4  4  Fer4_21      4Fe-4S dicluster domain
     0.0038   17.4   0.1     0.0038   17.4   0.1    4.8  5  Fer4_9       4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.41   10.1   0.0       0.41   10.1   0.0    2.8  5  QueC         Queuosine biosynthesis protein QueC


Domain annotation for each model (and alignments):
>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.8   0.0   2.3e-41   5.1e-38       3     173 ..     251     422 ..     249     423 .. 0.97

  Alignments for each domain:
  == domain 1  score: 130.8 bits;  conditional E-value: 2.3e-41
                                       EEE--SSCTCHHHHHHHHHHCTTHEEEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-THHH CS
                       PAPS_reduct   3 vvsvsgGkdslVllhLalkafkpvpvvfvdtghefpetiefvdeleeryglrlkvyepeeevaekinaekhgsslye 79 
                                        vs+sgGkdsl+   +a++a ++++++f dtg efpet+++v+e++e+ +l+l+ +e   ++++++ +++ + ++++
  gi|474934847|ref|YP_007688429.1| 251 TVSFSGGKDSLAAYGIASRAVDNIELLFTDTGLEFPETLAYVEEFAEKNKLKLHRAEAGSGFRDNVDTFGPPAKDFR 327
                                       79*************************************************************************** PP

                                       CHHHHHHTHHHHHHHHHCT..TECEEE----CCCTTTTTTSSSEEECTTT-SCEEE-CCCT--HHHHHHHHHHCT-- CS
                       PAPS_reduct  80 eaaeriaKveplkkaLekl..dedalltGaRrdesksraklpiveidedfekslrvfPllnWteedvwqyilrenip 154
                                       + +++++K+ p++  + +   + +++  G R  es+sra +++v ++   +++ +++P+ +W   ++w yi++++++
  gi|474934847|ref|YP_007688429.1| 328 W-CCKVCKLGPITDLIARDfpKGTITCEGNRSLESFSRADTQLVTRNPFVPNQTNLNPVRDWCAAEIWGYIWMRGLD 403
                                       *.************8877667889***************************************************** PP

                                       B-CCCCTT-SS--BCTTB- CS
                       PAPS_reduct 155 ynpLydqgfrsiGcvpctg 173
                                       ynpLy++ f++iGc+ c +
  gi|474934847|ref|YP_007688429.1| 404 YNPLYERDFERIGCYLCAS 422
                                       ***************9976 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -5.8   5.3         8   1.8e+04      37      45 ..      21      29 ..       9      42 .. 0.69
   2 ?   -4.3   4.4         8   1.8e+04      37      44 ..     416     423 ..     329     426 .. 0.75
   3 !   22.1  12.2   7.7e-08   0.00017       2      49 ..     588     627 ..     587     629 .. 0.93

  Alignments for each domain:
  == domain 1  score: -5.8 bits;  conditional E-value: 8
                            Fer4_7 37 kClgCgaCv 45
                                      +C  C+ C 
  gi|474934847|ref|YP_007688429.1| 21 ECRWCDTCG 29
                                      566666663 PP

  == domain 2  score: -4.3 bits;  conditional E-value: 8
                            Fer4_7  37 kClgCgaC 44 
                                        C+ C +C
  gi|474934847|ref|YP_007688429.1| 416 GCYLCASC 423
                                       46666666 PP

  == domain 3  score: 22.1 bits;  conditional E-value: 7.7e-08
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCP 49 
                                       C++Cg C+++C  kai ++          +++dp kC++Cg+C++ C 
  gi|474934847|ref|YP_007688429.1| 588 CTECGICAKTCARKAIHIKGG--------MRVDPGKCTSCGRCERSCM 627
                                       ******************664........9*****************7 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -5.1   6.1         8   1.8e+04      35      49 ..      15      29 ..       5      41 .. 0.60
   2 ?   -1.0   0.4       0.9     2e+03       9      16 ..     417     424 ..     410     426 .. 0.60
   3 !   19.5  12.6   3.5e-07   0.00079       2      55 ..     581     626 ..     580     627 .. 0.93
   4 ?   -3.0   0.1       3.7   8.3e+03      18      31 ..     646     654 ..     644     666 .. 0.55

  Alignments for each domain:
  == domain 1  score: -5.1 bits;  conditional E-value: 8
                           Fer4_10 35 eeavrkkvekCtgcg 49
                                      ++  ++ +  C++cg
  gi|474934847|ref|YP_007688429.1| 15 IANGKEECRWCDTCG 29
                                      444555666677765 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.9
                           Fer4_10   9 CirCgkCv 16 
                                       C  C+ C 
  gi|474934847|ref|YP_007688429.1| 417 CYLCASCL 424
                                       55555554 PP

  == domain 3  score: 19.5 bits;  conditional E-value: 3.5e-07
                           Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                       + i ++ C++Cg C k C        a++++ +++  r++++kCt cg C ++C
  gi|474934847|ref|YP_007688429.1| 581 ALIRAELCTECGICAKTC--------ARKAIHIKGGMRVDPGKCTSCGRCERSC 626
                                       5688999***********........59************************** PP

  == domain 4  score: -3.0 bits;  conditional E-value: 3.7
                           Fer4_10  18 aCPadltsvgakge 31 
                                       +CP+     + k++
  gi|474934847|ref|YP_007688429.1| 646 SCPV-----RRKDK 654
                                       7999.....33333 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.5       2.7   6.1e+03       7      14 ..      35      42 ..      35      42 .. 0.77
   2 ?   -2.2   1.8       2.4   5.5e+03      10      16 ..     415     421 ..     415     423 .. 0.84
   3 !   12.6   2.0   4.9e-05      0.11       4      24 .]     583     603 ..     580     603 .. 0.85
   4 !   18.2   2.1   8.4e-07    0.0019       3      19 ..     610     626 ..     609     631 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.7
                            Fer4_6  7 dkCigCgd 14
                                      ++C  Cg+
  gi|474934847|ref|YP_007688429.1| 35 ERCARCGK 42
                                      58999986 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.4
                            Fer4_6  10 igCgdCv 16 
                                       igC+ C+
  gi|474934847|ref|YP_007688429.1| 415 IGCYLCA 421
                                       79***97 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 4.9e-05
                            Fer4_6   4 idpdkCigCgdCvrvCPegai 24 
                                       i +++C+ Cg C++ C  +ai
  gi|474934847|ref|YP_007688429.1| 583 IRAELCTECGICAKTCARKAI 603
                                       7789************87776 PP

  == domain 4  score: 18.2 bits;  conditional E-value: 8.4e-07
                            Fer4_6   3 eidpdkCigCgdCvrvC 19 
                                       ++dp kC++Cg+C+r C
  gi|474934847|ref|YP_007688429.1| 610 RVDPGKCTSCGRCERSC 626
                                       79*************** PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.7       1.3   2.9e+03       6      12 ..      35      41 ..      35      42 .. 0.85
   2 ?    0.6   0.5      0.26   5.8e+02       9      15 ..     415     421 ..     415     422 .. 0.89
   3 !   14.2   2.1   1.2e-05     0.028       3      18 ..     583     598 ..     581     604 .. 0.85
   4 !   17.4   2.3   1.2e-06    0.0028       2      18 ..     610     626 ..     609     626 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.3
                                      TTSSS-T CS
                              Fer4  6 ekCigCG 12
                                      e+C +CG
  gi|474934847|ref|YP_007688429.1| 35 ERCARCG 41
                                      79999*9 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.26
                                       SS-THHH CS
                              Fer4   9 igCGaCv 15 
                                       igC +C+
  gi|474934847|ref|YP_007688429.1| 415 IGCYLCA 421
                                       8*****8 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 1.2e-05
                                       EETTTSSS-THHHHHS CS
                              Fer4   3 ideekCigCGaCvevC 18 
                                       i  e+C+ CG+C++ C
  gi|474934847|ref|YP_007688429.1| 583 IRAELCTECGICAKTC 598
                                       6789************ PP

  == domain 4  score: 17.4 bits;  conditional E-value: 1.2e-06
                                       EEETTTSSS-THHHHHS CS
                              Fer4   2 videekCigCGaCvevC 18 
                                        +d+ kC+ CG+C+  C
  gi|474934847|ref|YP_007688429.1| 610 RVDPGKCTSCGRCERSC 626
                                       69*************99 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.3      0.71   1.6e+03      37      47 ..      18      28 ..       6      31 .. 0.76
   2 ?   -4.1   0.7         8   1.8e+04      47      51 ..     329     333 ..     328     342 .. 0.52
   3 ?   -0.5   0.2      0.62   1.4e+03      42      49 ..     415     422 ..     405     425 .. 0.78
   4 !   17.4   9.2   1.6e-06    0.0035       1      53 [.     581     628 ..     581     633 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.71
                           Fer4_21 37 vedeCvGCnlC 47
                                       ++eC  C+ C
  gi|474934847|ref|YP_007688429.1| 18 GKEECRWCDTC 28
                                      47899999999 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 8
                           Fer4_21  47 CssvC 51 
                                       C +vC
  gi|474934847|ref|YP_007688429.1| 329 CCKVC 333
                                       44555 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.62
                           Fer4_21  42 vGCnlCss 49 
                                       +GC lC+s
  gi|474934847|ref|YP_007688429.1| 415 IGCYLCAS 422
                                       68888875 PP

  == domain 4  score: 17.4 bits;  conditional E-value: 1.6e-06
                           Fer4_21   1 AridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPv 53 
                                       A i  + C +Cg C+++C     +ai+i++   ++v   +C+ C  C   C v
  gi|474934847|ref|YP_007688429.1| 581 ALIRAELCTECGICAKTCA---RKAIHIKG--GMRVDPGKCTSCGRCERSCMV 628
                                       78999*************9...69**9965..56799**************87 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   5.6       5.2   1.2e+04      34      42 ..      20      28 ..       3      43 .. 0.51
   2 ?   -3.4   0.3       5.2   1.2e+04      42      47 ..     329     334 ..     322     340 .. 0.69
   3 ?    1.5   0.1      0.15   3.4e+02      34      43 ..     415     424 ..     379     426 .. 0.69
   4 !   17.4   0.1   1.7e-06    0.0038      33      51 .]     574     603 ..     502     603 .. 0.82
   5 !   12.0   1.6     8e-05      0.18       1      14 [.     615     633 ..     613     658 .. 0.70

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 5.2
                            Fer4_9 34 eaCigCgaC 42
                                      e+C  C +C
  gi|474934847|ref|YP_007688429.1| 20 EECRWCDTC 28
                                      234334443 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 5.2
                            Fer4_9  42 CveaCp 47 
                                       C ++C+
  gi|474934847|ref|YP_007688429.1| 329 CCKVCK 334
                                       444443 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.15
                            Fer4_9  34 eaCigCgaCv 43 
                                         C+ C +C+
  gi|474934847|ref|YP_007688429.1| 415 IGCYLCASCL 424
                                       5688888887 PP

  == domain 4  score: 17.4 bits;  conditional E-value: 1.7e-06
                            Fer4_9  33 e...........eaCigCgaCveaCpkgai 51 
                                       +           e C++Cg C++ C ++ai
  gi|474934847|ref|YP_007688429.1| 574 MfersvkaliraELCTECGICAKTCARKAI 603
                                       03334445666689*************987 PP

  == domain 5  score: 12.0 bits;  conditional E-value: 8e-05
                            Fer4_9   1 kCtgCgaCveaC.....pa 14 
                                       kCt+Cg+C+++C       
  gi|474934847|ref|YP_007688429.1| 615 KCTSCGRCERSCmvihyYD 633
                                       79**********4444433 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.5   1.6       5.6   1.3e+04     191     199 ..      20      28 ..      16      30 .. 0.77
   2 ?   10.1   0.0   0.00018      0.41       4      54 ..     252     302 ..     249     308 .. 0.90
   3 ?   -1.4   0.1       0.6   1.3e+03     184     200 ..     408     424 ..     384     428 .. 0.86
   4 ?   -4.7   0.8       6.2   1.4e+04     190     200 ..     585     595 ..     567     601 .. 0.72
   5 ?   -6.3   3.2         8   1.8e+04     191     199 ..     617     626 ..     612     628 .. 0.55

  Alignments for each domain:
  == domain 1  score: -4.5 bits;  conditional E-value: 5.6
                                       TTTSSSHHH CS
                              QueC 191 kaCgeCdaC 199
                                       ++C+ Cd+C
  gi|474934847|ref|YP_007688429.1|  20 EECRWCDTC 28 
                                       579999999 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00018
                                       EE--SSHHHHHHHHHHHHH-SEEEEEEEESS-TTSHHHHHHHHHHHHT--. CS
                              QueC   4 vllSGGlDSttvlalakkegkevealtfdYgqrhkkeleaakkiakelgve 54 
                                       v +SGG DS ++  +a+++++++e+l  d g    ++l +++++a++ +++
  gi|474934847|ref|YP_007688429.1| 252 VSFSGGKDSLAAYGIASRAVDNIELLFTDTGLEFPETLAYVEEFAEKNKLK 302
                                       779*****************************9999999999999998884 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.6
                                       TTS.-BTTTTSSSHHHH CS
                              QueC 184 YegeeegkaCgeCdaCa 200
                                       Ye + e+ +C  C +C 
  gi|474934847|ref|YP_007688429.1| 408 YERDFERIGCYLCASCL 424
                                       88888899********7 PP

  == domain 4  score: -4.7 bits;  conditional E-value: 6.2
                                       TTTTSSSHHHH CS
                              QueC 190 gkaCgeCdaCa 200
                                       ++ C eC  Ca
  gi|474934847|ref|YP_007688429.1| 585 AELCTECGICA 595
                                       45677777775 PP

  == domain 5  score: -6.3 bits;  conditional E-value: 8
                                       TTTSSSH.HH CS
                              QueC 191 kaCgeCd.aC 199
                                       ++Cg+C+ +C
  gi|474934847|ref|YP_007688429.1| 617 TSCGRCErSC 626
                                       4566664345 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (685 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 4459.80
//
Query:       gi|474934848|ref|YP_007688430.1|  [L=220]
Description: Zn-dependent protease [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.7e-07   29.3  15.2    6.8e-05   22.3   1.9    3.2  2  Peptidase_M50  Peptidase family M50


Domain annotation for each model (and alignments):
>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   5.9   5.7e-05         1       4     106 ..      64     147 ..      60     151 .. 0.68
   2 !   22.3   1.9   3.8e-09   6.8e-05     190     220 ..     160     190 ..     151     198 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 5.7e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50   4 lllgilvvvHElGHflvAklcgvkve..efsigfGpkllsfkkgeteYaiallpLGGyVkmageepeeelseeeaka 78 
                                       ++ +++ v HE+GH ++A+++g+  e   +  g+              ++al+   G+V +    p +  ++     
  gi|474934848|ref|YP_007688430.1|  64 VITILSFVGHEMGHKFTAQRFGMWSEyrMYPAGL--------------FFALIM--GFVGFLFAAPGAVMIRS---- 120
                                       333344555*************966410333333..............456666..77777777777775555.... PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50  79 flkkspwqrllivlAGplanfilailvf 106
                                        +  +  +  +i +AGp++n++l+ + +
  gi|474934848|ref|YP_007688430.1| 121 -NYITERENGIISIAGPMVNMVLSAVGI 147
                                       .557777899999999999999988765 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 3.8e-09
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 190 sflqllalisvnLgilNLlPipvLDGghllf 220
                                        +++l+++++ +L+++N++Pi+++DG ++++
  gi|474934848|ref|YP_007688430.1| 160 VVFYLMMMLNGSLALFNMIPIMPFDGAKIIK 190
                                       5799************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1293.55
//
Query:       gi|474934849|ref|YP_007688431.1|  [L=479]
Description: FAD/FMN-containing dehydrogenase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.8e-53  179.3   0.0    1.3e-52  178.9   0.0    1.2  1  FAD-oxidase_C  FAD linked oxidases, C-terminal domain
    2.4e-45  153.7   0.9    1.1e-44  151.6   0.2    2.3  3  FAD_binding_4  FAD binding domain
  ------ inclusion threshold ------
      0.039   13.4   0.0        1.8    8.0   0.0    2.2  2  AP_endonuc_2   Xylose isomerase-like TIM barrel
       0.07   13.8   0.0       0.31   11.7   0.0    2.1  2  NAD_binding_3  Homoserine dehydrogenase, NAD binding domain


Domain annotation for each model (and alignments):
>> FAD-oxidase_C  FAD linked oxidases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.9   0.0   2.9e-56   1.3e-52       1     249 [.     216     459 ..     216     460 .. 0.98

  Alignments for each domain:
  == domain 1  score: 178.9 bits;  conditional E-value: 2.9e-56
                                       --SEEEEEEEEESSHHHHHHHHHHHHHHT---SEEEEE-HHHHHHHHHTS-SSTTS-TTT-EEEEEEEEE-HHHHHH CS
                     FAD-oxidase_C   1 lpearavalvafpsfeaavkavreiaqagiipaalelmdkkaldlveatkgakkglpdeeealllvefegddeeeae 77 
                                       +p++ a+ l++f+++ +a k++++i+++ +ipa++el+d++++ +v++++g    + +++++l++ve++g   e ++
  gi|474934849|ref|YP_007688431.1| 216 KPKKSASCLISFDDVVDAGKCISAIIAKPLIPASCELLDSTSITAVNKVLGN---PLPNANSLIIVEVDGETDEIIQ 289
                                       689999**********************************************...9999****************** PP

                                       HHHHHHHHHTTT-EEEEE..........ETGGGGGGGGHHHHHHHHHCTTEEEEEEEEEEEHHHHHHHHHHHHHHHH CS
                     FAD-oxidase_C  78 eelealveaileatgaadvlvaqdeaeaealwkaRkaalpylrdallkagvavlseDtsvPvsrladlvrdikalld 154
                                       ++l+  ve+ +++  a++v+ + d++e++++ +aRk++l  l+ ++ +++ + l  D+ vP+s+++++vr+++a+++
  gi|474934849|ref|YP_007688431.1| 290 RDLK-IVEEVAHEQNAKTVTPSFDKDEIQRWTNARKSVLSSLSALKPGYSCVSLADDMGVPISKVSEAVRRFQAAAE 365
                                       ****.************************************************************************ PP

                                       HHHEEEEEEEEEETTEEEEEEEEEEE..--TT--THHHHHHHHHHHHTT-----------------------THHHH CS
                     FAD-oxidase_C 155 kyglevvlfgHagdgnlhlyilfdladeaeeeraeklvdevvdlavelgGsisgEHGvGldkkaylerekgeeglal 231
                                       + +++v+++gHa dgnlh  + +d+ de++++ra k + e++d+ ++lgG+++gEHGvGl k++  ++e+   +l++
  gi|474934849|ref|YP_007688431.1| 366 RNDVTVAVYGHASDGNLHSKMVIDVTDEDMWKRAIKTASEIFDASIDLGGTVTGEHGVGLSKAKDFQKERAT-ELET 441
                                       ******************************************************************999955.9*** PP

                                       HHHHHHHH-TT--BSTT- CS
                     FAD-oxidase_C 232 mrriKaalDPkgiLNPgk 249
                                       + +iK+a DPk+iLNPgk
  gi|474934849|ref|YP_007688431.1| 442 ILEIKKAMDPKNILNPGK 459
                                       *****************9 PP

>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.6   0.2   2.4e-48   1.1e-44       1     139 []      41     180 ..      41     180 .. 0.99
   2 ?   -3.2   0.0       1.4   6.3e+03      53      89 ..     292     328 ..     288     336 .. 0.75
   3 ?   -0.4   0.0       0.2     9e+02      11      37 ..     355     381 ..     351     432 .. 0.75

  Alignments for each domain:
  == domain 1  score: 151.6 bits;  conditional E-value: 2.4e-48
                                       EEEEEEESSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTC.SCCEEEEEETTS--EEEEETTTTEEEEETTSBHHH CS
                     FAD_binding_4   1 paavvrpeseeevaaalrlaneaglpvlvrGgGssllgqav.atggvvldlsrlnrileideeegtatveaGvtlgd 76 
                                       p++vv+p+s+e+v++++++a ++g+pv++rG+G++l+g+av  +gg+ + l+++nri+e++ ++ ++ veaGv++++
  gi|474934849|ref|YP_007688431.1|  41 PDIVVQPTSTEQVSEIMKIAYKHGIPVVPRGAGTGLCGAAVpIEGGICIALQKMNRIIEVSVADLWVDVEAGVVYNN 117
                                       899*************************************999********************************** PP

                                       HHHHHHHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETTSEEEEEE CS
                     FAD_binding_4  77 lvealaakglllglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvladGevvrls 139
                                       l+ +la++g+++++ pgs + + +GG++atna+G+++ kyG++rd+vlg+++v a+G +vr++
  gi|474934849|ref|YP_007688431.1| 118 LNDELAKYGFFFPPSPGSAEACQIGGMVATNASGMRAVKYGATRDFVLGMTFVKANGDIVRCG 180
                                       *************************************************************96 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.4
                                       S--EEEEETTTTEEEEETTSBHHHHHHHHHHHTTECS CS
                     FAD_binding_4  53 lnrileideeegtatveaGvtlgdlvealaakglllg 89 
                                       l+ ++e+  e++  tv +    ++++++++a++ +l 
  gi|474934849|ref|YP_007688431.1| 292 LKIVEEVAHEQNAKTVTPSFDKDEIQRWTNARKSVLS 328
                                       6677888888888888888888999999988877765 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.2
                                       HHHHHHHHHHHHCTSCEEEESSSTTEE CS
                     FAD_binding_4  11 eevaaalrlaneaglpvlvrGgGssll 37 
                                       e v++  ++a++++++v v+G  s+ +
  gi|474934849|ref|YP_007688431.1| 355 EAVRRFQAAAERNDVTVAVYGHASDGN 381
                                       567777788888899999998877655 PP

>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.011        48      60     119 ..      38     100 ..       4     125 .. 0.76
   2 ?    8.0   0.0    0.0004       1.8       8      89 ..     336     416 ..     331     454 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.011
                                       HTTCS...HHHHHHHHHHHHHHHHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHH CS
                      AP_endonuc_2  60 erear...reesvdalkraielaaaLGapllvlhpGtagagpkgseeeawerlaeslnelady 119
                                       +r+++   +  s +++ + +++a++ G+p++  ++Gt   g+  ++e  +  + +++n+++++
  gi|474934849|ref|YP_007688431.1|  38 HRNPDivvQPTSTEQVSEIMKIAYKHGIPVVPRGAGTGLCGAAVPIEGGICIALQKMNRIIEV 100
                                       55666666667899999*************999999877777777777777777777777765 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0004
                                       T-SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHC.HTTCSHHHHHHHHHHHHHHHHHH. CS
                      AP_endonuc_2   8 GfdgvElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypded.erearreesvdalkraielaaaL. 82 
                                       G+ +v l+ + +vp+s    e++r++++a++++++++a+    ++ +         ++     d +krai++a+++ 
  gi|474934849|ref|YP_007688431.1| 336 GYSCVSLADDMGVPISKV-SEAVRRFQAAAERNDVTVAVYGHASDGNLHSKMvIDVTD----EDMWKRAIKTASEIf 407
                                       99*************975.9****************8776655555553332433333....567777777777654 PP

                                       ..TBSEEEE CS
                      AP_endonuc_2  83 ..Gapllvl 89 
                                          ++l  +
  gi|474934849|ref|YP_007688431.1| 408 daSIDLGGT 416
                                       443444444 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   6.9e-05      0.31      50      87 ..      31      68 ..      13      74 .. 0.86
   2 ?   -2.5   0.0       1.7   7.7e+03      95      95 ..     284     284 ..     252     311 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.9e-05
                                      -HHHHHHHHS-EEEEE-S--HHHHTTHHHHHHTTEEEE CS
                     NAD_binding_3 50 dlddliahldpdvvVEcasseavaelvlkaLkagkdvv 87
                                       +d+ i h +pd+vV  +s e+v e++  a k+g+ vv
  gi|474934849|ref|YP_007688431.1| 31 GFDASIYHRNPDIVVQPTSTEQVSEIMKIAYKHGIPVV 68
                                      5667777778***************************9 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.7
                                       G CS
                     NAD_binding_3  95 a 95 
                                       +
  gi|474934849|ref|YP_007688431.1| 284 T 284
                                       2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3352.17
//
Query:       gi|474934850|ref|YP_007688432.1|  [L=207]
Description: Adenylate kinase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.1e-51  171.9   0.0    1.1e-50  171.7   0.0    1.0  1  ADK             Adenylate kinase
      1e-22   81.0   0.0    1.6e-22   80.4   0.0    1.3  1  AAA_17          AAA domain
    4.4e-17   61.8   4.3    6.7e-17   61.2   4.3    1.3  1  ADK_lid         Adenylate kinase, active site lid
    5.7e-07   30.1   0.0    9.1e-07   29.5   0.0    1.3  1  AAA_18          AAA domain
    1.7e-06   28.2   0.0    3.5e-06   27.2   0.0    1.5  1  AAA_33          AAA domain
     0.0013   18.3   0.8     0.0022   17.5   0.8    1.4  1  TF_Zn_Ribbon    TFIIB zinc-binding
     0.0098   15.6   0.0      0.045   13.5   0.0    1.9  2  Cytidylate_kin  Cytidylate kinase
  ------ inclusion threshold ------
      0.018   15.1   1.9       0.48   10.5   0.2    2.4  2  zf-ACC          Acetyl-coA carboxylase zinc finger domain
      0.043   13.8   0.1      0.069   13.2   0.1    1.3  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.049   13.4   0.9        1.2    9.0   0.1    2.3  2  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
      0.059   13.3   2.7       0.17   11.8   2.7    1.8  1  zinc_ribbon_4   zinc-ribbon domain
      0.096   12.5   0.6        0.2   11.4   0.6    1.5  1  zinc_ribbon_5   zinc-ribbon domain
       0.12   11.7   0.0       0.15   11.3   0.0    1.3  1  Zeta_toxin      Zeta toxin
       0.14   12.4   0.0        8.7    6.6   0.0    2.3  2  Hydin_ADK       Hydin Adenylate kinase-like domain
       0.16   12.0   2.0       0.36   10.9   2.0    1.5  1  DZR             Double zinc ribbon
       0.16   11.7   1.5        1.5    8.6   0.2    2.2  2  zf-RRN7         Zinc-finger of RNA-polymerase I-specific TFII
       0.19   11.1   0.0       0.32   10.4   0.0    1.3  1  DUF1116         Protein of unknown function (DUF1116)
        0.2   11.6   1.0       0.38   10.7   1.0    1.4  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.24   11.7   0.9       0.84   10.0   0.0    2.0  2  GFA             Glutathione-dependent formaldehyde-activating
       0.27   11.2   2.6        3.6    7.6   0.1    2.3  2  Prok-RING_1     Prokaryotic RING finger family 1


Domain annotation for each model (and alignments):
>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.7   0.0   1.2e-53   1.1e-50       1     150 [.       4     184 ..       4     185 .. 0.99

  Alignments for each domain:
  == domain 1  score: 171.7 bits;  conditional E-value: 1.2e-53
                                       EEESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHCT-HHHHHHHHHHHTTSS--HHHHHHHHHHHHHCHGTTTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK   1 llGaPgaGKGtqaeklvkkyglahlstGdllRaevksgtelGkeakevmdkgelvpdevvvklvkeelekedkkkgf 77 
                                       llG+PgaGKGtq ek+ +++g+++lstGd+lR++v++gt+lGk ak++md+g+lvp++v+++l+ke++++  k  g 
  gi|474934850|ref|YP_007688432.1|   4 LLGPPGAGKGTQGEKMETELGYVRLSTGDMLREAVRNGTDLGKLAKKYMDAGDLVPNDVIINLMKEKIQSLGKVPGI 80 
                                       79*************************************************************************** PP

                                       EEESB-SSHHHHHHHHHHHHHHTSEESEEEEEE--HHHHHHHHHT................................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................ RF
                               ADK  78 llDGfPRtveqaealeelleeekvkldlvleldvpeevlveRltg................................ 122
                                       ++DGfPRtveqaeal++     + ++dl l++dv+++vl++Rlt+                                
  gi|474934850|ref|YP_007688432.1|  81 IFDGFPRTVEQAEALDK-----ELNIDLALNFDVEDQVLIDRLTQrrscpdcnavyhlsnnppkkegvcdkcgaqly 152
                                       *****************.....889**************************************************** PP

                                       ....GSHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                                       ....xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK 123 ....DneetvkkRletykkqtkplidyykkkg 150
                                           D+e tvk+Rl+ty+++t pli yy+k g
  gi|474934850|ref|YP_007688432.1| 153 qrddDKEATVKNRLSTYREKTFPLIAYYEKAG 184
                                       *****************************986 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.4   0.0   1.8e-25   1.6e-22       1     124 [.       5     123 ..       5     129 .. 0.92

  Alignments for each domain:
  == domain 1  score: 80.4 bits;  conditional E-value: 1.8e-25
                                       EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTT.TS.HSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEE CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrg.gl.akardemrklpleekkelqkeaaekiaeeakkkgvl 75 
                                       lG+PG+GKgtq ek+  ++g+  ls+Gd+lre +++g  l + a+++m+ ++l++++ +  +++eki+   k  g++
  gi|474934850|ref|YP_007688432.1|   5 LGPPGAGKGTQGEKMETELGYVRLSTGDMLREAVRNGtDLgKLAKKYMDAGDLVPNDVIINLMKEKIQSLGKVPGII 81 
                                       7******************************99988844658899************************9999**** PP

                                       EEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHTT CS
                            AAA_17  76 vdghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkdrt 124
                                       +dg+pr+ eqa++ld       +el++d+ + ++++++++++r+ ++r+
  gi|474934850|ref|YP_007688432.1|  82 FDGFPRTVEQAEALD-------KELNIDLALNFDVEDQVLIDRLTQRRS 123
                                       *******99999766.......589*******************99864 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.2   4.3   7.5e-20   6.7e-17       1      36 []     121     156 ..     121     156 .. 0.98

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 7.5e-20
                                       EEE-TTT--EEETTTB--SSTTB-TTT--.-B--GG CS
                           ADK_lid   1 RrvCpkCGrsYhvvfnpPkveglCDkCGepLvqRsD 36 
                                       Rr Cp+C+++Yh+  npPk+eg+CDkCG +L+qR+D
  gi|474934850|ref|YP_007688432.1| 121 RRSCPDCNAVYHLSNNPPKKEGVCDKCGAQLYQRDD 156
                                       9***********889********************9 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0     1e-09   9.1e-07       1     116 [.       2     124 ..       2     132 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 1e-09
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpealdeskrldedkldklldaleenssale 72 
                                       I+l G+pG+GK t ++  + +lg+     g+ lr+ ++++  l    ++  d  + +  d+   ++++++e +++l+
  gi|474934850|ref|YP_007688432.1|   2 IVLLGPPGAGKGTQGEKMETELGYvrlstGDMLREAVRNGTDLGKLAKKYMDAGDLVPNDV---IINLMKEKIQSLG 75 
                                       89******************99999999999999999997777777777777777777788...6777777766799 PP

                            AAA_18  73 egknlvidghlaeleseaakdikk.....vvLtaspeelleRlekRgye 116
                                       +   +++dg++   e+++a d+          ++++++l++Rl +R+  
  gi|474934850|ref|YP_007688432.1|  76 KVPGIIFDGFPRTVEQAEALDKELnidlaLNFDVEDQVLIDRLTQRRSC 124
                                       9*******************9999*999999999************865 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0   3.9e-09   3.5e-06       1     119 [.       1     122 [.       1     129 [. 0.75

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 3.9e-09
                            AAA_33   1 lvllvGlpGsGKstlaerllkklgavllssdtlrr.rlfg..tdqqsktdytrvldrlyq..ilnelarkalsagrn 72 
                                       +++l G+pG+GK t  e++  +lg+v+ls+ +++r ++++  +  +  ++y ++ d + +  i+n + +k +s g+ 
  gi|474934850|ref|YP_007688432.1|   1 MIVLLGPPGAGKGTQGEKMETELGYVRLSTGDMLReAVRNgtDLGKLAKKYMDAGDLVPNdvIINLMKEKIQSLGKV 77 
                                       6899*************************988777477777644555567888777755555555555666666643 PP

                            AAA_33  73 ..vildatnlsrrerarflklarrlgvpvrivvvetdeetlkeRlakRa 119
                                         +i+d   ++ ++ ++++k ++     ++++ +++ +++l +Rl +R 
  gi|474934850|ref|YP_007688432.1|  78 pgIIFDGFPRTVEQAEALDKELN----IDLALNFDVEDQVLIDRLTQRR 122
                                       34788876666777778887776....6699999999999999999996 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.8   2.4e-06    0.0022       2      32 ..     123     154 ..     122     161 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.4e-06
                                       EETTTTCEE.CHEETSTTCEEESSSSBEEEEC CS
                      TF_Zn_Ribbon   2 kCPnCgstn.lveDpergelvCtdCGlVledn 32 
                                        CP+C+  + l ++p   e vC +CG+ l  +
  gi|474934850|ref|YP_007688432.1| 123 SCPDCNAVYhLSNNPPKKEGVCDKCGAQLYQR 154
                                       5******999****************987655 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0     5e-05     0.045       2      35 ..       3      36 ..       2      49 .. 0.92
   2 ?   -0.5   0.0      0.96   8.6e+02      99     119 ..      64      84 ..      52      92 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5e-05
                                      EEE-STTSSHHHHHHHHHHHHT-EEEEHHHHHHH CS
                    Cytidylate_kin  2 aiDGPagsGKssvaralaeklglkyldtgalYRa 35
                                       + GP g+GK++ + ++ ++lg+  l+tg + R 
  gi|474934850|ref|YP_007688432.1|  3 VLLGPPGAGKGTQGEKMETELGYVRLSTGDMLRE 36
                                      566****************************996 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.96
                                       HHHHHHHHHTT-BSSBEEEEE CS
                    Cytidylate_kin  99 RailvkklrelvkkarvvveG 119
                                        + +++k+++l k  +++++G
  gi|474934850|ref|YP_007688432.1|  64 INLMKEKIQSLGKVPGIIFDG 84 
                                       578999*************99 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.084        75       3      10 ..     123     130 ..     122     132 .. 0.85
   2 ?   10.5   0.2   0.00054      0.48       4      15 ..     144     155 ..     144     159 .. 0.95

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.084
                            zf-ACC   3 KCpsCgem 10 
                                        Cp C+++
  gi|474934850|ref|YP_007688432.1| 123 SCPDCNAV 130
                                       6****986 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00054
                            zf-ACC   4 CpsCgemlykke 15 
                                       C++Cg++ly+++
  gi|474934850|ref|YP_007688432.1| 144 CDKCGAQLYQRD 155
                                       *********997 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   7.7e-05     0.069      62     108 ..     113     163 ..      84     165 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.7e-05
                                       EEEEEE--EEEETTTS-EEECHH...H.HHS-TTTSSS-EEEEESSSEEEE CS
                              HypA  62 LeieevpvkvrCreCgkefelee...k.alrCpkCgsadveivsGeellvk 108
                                       + i++   +  C +C++ ++l++   k +  C kCg++  +  + +e +vk
  gi|474934850|ref|YP_007688432.1| 113 VLIDRLTQRRSCPDCNAVYHLSNnppKkEGVCDKCGAQLYQRDDDKEATVK 163
                                       44788888999*********77745435669******99999999998887 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1      0.12   1.1e+02       2       9 ..     122     129 ..     121     135 .. 0.80
   2 ?    9.0   0.1    0.0013       1.2       2      15 ..     142     155 ..     141     159 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.12
                                       EE-SSS-- CS
                    zf-C4_Topoisom   2 ekCPkCgg 9  
                                       + CP C++
  gi|474934850|ref|YP_007688432.1| 122 RSCPDCNA 129
                                       67999986 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0013
                                       EE-SSS--EEEEEE CS
                    zf-C4_Topoisom   2 ekCPkCggdLvlkr 15 
                                       + C+kCg++L ++ 
  gi|474934850|ref|YP_007688432.1| 142 GVCDKCGAQLYQRD 155
                                       67********9995 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   2.7   0.00019      0.17       4      33 ..     123     149 ..     121     151 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00019
                     zinc_ribbon_4   4 tCpsCkakyeiddeklpakgvkvrCskCgh 33 
                                       +Cp C+a+y ++++  +++gv   C kCg+
  gi|474934850|ref|YP_007688432.1| 123 SCPDCNAVYHLSNNPPKKEGV---CDKCGA 149
                                       7************95445544...888875 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.6   0.00022       0.2       4      29 ..     123     148 ..     121     150 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00022
                     zinc_ribbon_5   4 rCpdCdtkFklvdsklKksgkkVrCa 29 
                                       +CpdC+  + l +   Kk g+  +C+
  gi|474934850|ref|YP_007688432.1| 123 SCPDCNAVYHLSNNPPKKEGVCDKCG 148
                                       8*******************977776 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00017      0.15      18      76 ..       1      58 [.       1     110 [. 0.75

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                        Zeta_toxin 18 lillgGqpGAGKselaellkdelerqgnvvrld.pDdlRelhPeyeeilk..adpkkaselt 76
                                      +i+l G pGAGK++  e++++el    ++vrl+ +D lRe  ++  ++ k  ++ ++a +l+
  gi|474934850|ref|YP_007688432.1|  1 MIVLLGPPGAGKGTQGEKMETEL----GYVRLStGDMLREAVRNGTDLGKlaKKYMDAGDLV 58
                                      58899*****************9....89*99735888998888776655334555555555 PP

>> Hydin_ADK  Hydin Adenylate kinase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.076        68       2      42 ..       2      42 ..       1      52 [. 0.90
   2 ?    6.6   0.0    0.0097       8.7     170     197 ..      57      84 ..      51      85 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.076
                         Hydin_ADK  2 iivhGaPlsGKtatavtLakkYeaAlltiDsvvleAisdgn 42
                                      i++ G+P +GK +   ++  + +   l+  +++ eA+ +g+
  gi|474934850|ref|YP_007688432.1|  2 IVLLGPPGAGKGTQGEKMETELGYVRLSTGDMLREAVRNGT 42
                                      8899********************************99986 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0097
                         Hydin_ADK 170 vLPedllveIlsERlqlndCyrGvvfDg 197
                                       + P+d++++++ E++q      G++fDg
  gi|474934850|ref|YP_007688432.1|  57 LVPNDVIINLMKEKIQSLGKVPGIIFDG 84 
                                       57*************************9 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   2.0    0.0004      0.36      15      38 ..     124     151 ..     116     158 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0004
                               DZR  15 CseCgtk..lkavaa....edrCpsCgekv 38 
                                       C++C++   l++  +    e +C++Cg+++
  gi|474934850|ref|YP_007688432.1| 124 CPDCNAVyhLSN--NppkkEGVCDKCGAQL 151
                                       555555533221..1223455566665553 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.19   1.7e+02       6      13 ..     123     130 ..     119     134 .. 0.82
   2 ?    8.6   0.2    0.0017       1.5       3      18 ..     140     156 ..     139     157 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.19
                           zf-RRN7   6 pCgvCgcr 13 
                                        C+ C+++
  gi|474934850|ref|YP_007688432.1| 123 SCPDCNAV 130
                                       5*****94 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0017
                           zf-RRN7   3 kgppCgvCgcrsftl.d 18 
                                       k+ +C+ Cg+ +++  d
  gi|474934850|ref|YP_007688432.1| 140 KEGVCDKCGAQLYQRdD 156
                                       5789*********9944 PP

>> DUF1116  Protein of unknown function (DUF1116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00036      0.32      52      97 ..      13      56 ..       9      61 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00036
                                      T--SHHHHHHHHHHHHTHHHHHHHHHH-TT-EEHHHHHHHHTTTT- CS
                           DUF1116 52 GayseevlerLrwmrdvlapvlkealekeggidlkaliaqalqmGD 97
                                      G ++e+  ++L ++r + +++l+ea++  +g dl +l+++ +++GD
  gi|474934850|ref|YP_007688432.1| 13 GTQGEKMETELGYVRLSTGDMLREAVR--NGTDLGKLAKKYMDAGD 56
                                      788899999******************..6***************9 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.0   0.00043      0.38      30      59 ..     123     155 ..     114     157 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00043
                    OrfB_Zn_ribbon  30 tCseCgsknke..alsgrtfkCpnCgfe.adrD 59 
                                       +C+ C ++     ++ +++ +C++Cg++ ++rD
  gi|474934850|ref|YP_007688432.1| 123 SCPDCNAVYHLsnNPPKKEGVCDKCGAQlYQRD 155
                                       799999887777799*************99998 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.79   7.1e+02      48      59 ..     120     131 ..     111     141 .. 0.75
   2 ?   10.0   0.0   0.00094      0.84      43      69 ..     135     161 ..     128     174 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.79
                               GFA  48 trsfCpeCgspl 59 
                                       +r+ Cp+C +  
  gi|474934850|ref|YP_007688432.1| 120 QRRSCPDCNAVY 131
                                       6799****8754 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00094
                               GFA  43 sgnkvtrsfCpeCgsplyseesaapev 69 
                                       ++ ++++ +C++Cg++ly + + ++ +
  gi|474934850|ref|YP_007688432.1| 135 NNPPKKEGVCDKCGAQLYQRDDDKEAT 161
                                       55667779**********755554444 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1    0.0041       3.6      23      32 ..     124     133 ..     122     136 .. 0.91
   2 ?    3.4   0.3     0.083        75       6      18 ..     143     155 ..     138     157 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0041
                       Prok-RING_1  23 CpeCgtpyHr 32 
                                       Cp+C ++yH 
  gi|474934850|ref|YP_007688432.1| 124 CPDCNAVYHL 133
                                       *********6 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.083
                       Prok-RING_1   6 kCpvCgkelkeed 18 
                                        C  Cg +l + d
  gi|474934850|ref|YP_007688432.1| 143 VCDKCGAQLYQRD 155
                                       4666666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       778  (0.0433934); expected 358.6 (0.02)
Passed bias filter:                      669  (0.0373138); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1392.09
//
Query:       gi|474934851|ref|YP_007688433.1|  [L=123]
Description: crcB protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.7e-22   77.3   7.9      1e-21   77.0   7.9    1.0  1  CRCB      CrcB-like protein, Camphor Resistance (CrcB)


Domain annotation for each model (and alignments):
>> CRCB  CrcB-like protein, Camphor Resistance (CrcB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.0   7.9   5.7e-26     1e-21       2      94 ..      11     116 ..      10     117 .. 0.92

  Alignments for each domain:
  == domain 1  score: 77.0 bits;  conditional E-value: 5.7e-26
                                       HHHHHHHHHHHHHHHH.HHHHBE...BHHHHHHHHHHHHHHHHHHH...........HHTTTHHHHHS-SHHHHHHH CS
                              CRCB   2 lvalggalGallRyllssllnkr...plgtlavNvlGsfllgllla...........llttGflGglTTfStfvlel 64 
                                       +v++ggalGa+lR+++ +++  +   p++t+avN++Gsfll+ll+            ll tG++G++TT+Stf++++
  gi|474934851|ref|YP_007688433.1|  11 IVGAGGALGAVLRFGMGQAID-SdqfPWATFAVNIIGSFLLALLMFswtdisdgyrlLLFTGLFGAFTTMSTFTVDT 86 
                                       799*************66555.55**9****************9998899999988889****************** PP

                                       HHHHHHT-HHHHHHHHHHHHHHHHHHHHHH CS
                              CRCB  65 vslleegellaallyvllsvvlgllavvlg 94 
                                       v+l+ +g + +al++++l+ v++ll +++g
  gi|474934851|ref|YP_007688433.1|  87 VELFVDGYVGKALMNFVLNPVVCLLGAFAG 116
                                       ************************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 706.20
//
Query:       gi|474934852|ref|YP_007688434.1|  [L=194]
Description: hypothetical protein TALC_01292 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-13   49.6   0.0    5.6e-13   48.5   0.0    1.6  1  TrkA_C          TrkA-C domain
    9.8e-08   32.4   2.1    1.7e-07   31.6   2.1    1.3  1  PhoU            PhoU domain
  ------ inclusion threshold ------
      0.026   13.1   0.2      0.031   12.9   0.2    1.1  1  Zw10            Centromere/kinetochore Zw10
       0.12   12.7   0.3       0.29   11.5   0.3    1.6  2  Mobilization_B  Mobilization protein B


Domain annotation for each model (and alignments):
>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   0.0   1.2e-16   5.6e-13       5      68 ..     119     184 ..     115     186 .. 0.94

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 1.2e-16
                                       EEE--GGGTTSBHHHHTHHHH.S-EEEEEE-T.-EEES--TT-B--TT-EEEEEEEHHHHHHHHHH CS
                            TrkA_C   5 tvpagsplvGktlkelnlrar.gvlvvairRg.geliipsgdtvLeeGDvllvvgspsdlaelrel 68 
                                       +++++s l+Gkt + + l ++ g +v+airR+ + ++ p+++t +e+GD+l+  g+ +++a +++l
  gi|474934852|ref|YP_007688434.1| 119 KIAEDSVLAGKTFGSVSLSTNsGMFVIAIRRDqDYIFGPGPNTSIEAGDILIARGPEDAVAYFKDL 184
                                       799*****************************999999999********************99986 PP

>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   2.1   3.7e-11   1.7e-07       1      83 [.       9      95 ..       9      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 3.7e-11
                                      HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SH.....HHHHHHHHHHHHHH CS
                              PhoU  1 lrrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplae.....dlrellsllriard 74
                                      + ++++++  m+d+a+++l  ++te+a+evi +  ++ +l ++i++s +  ++k+ p++        r l ++l+ia  
  gi|474934852|ref|YP_007688434.1|  9 ILELKDTTDMMVDLAYSSLLYNNTEIAEEVITLSTSMSDLADRIQDS-IADVGKSAPEEIaraivTTRLLDGILDIAEA 86
                                      57899******************************************.7788887777664456555555569999999 PP

                                      HHHHHHHHH CS
                              PhoU 75 lERigDhav 83
                                       E i+D +v
  gi|474934852|ref|YP_007688434.1| 87 AESIADVVV 95
                                      999999776 PP

>> Zw10  Centromere/kinetochore Zw10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   6.9e-06     0.031      16     107 ..       2      90 ..       1      97 [. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.9e-06
                              Zw10  16 isklekkveeikeevskmivkkYseflelsssaeellerveslskeidalkkkveneieqdlkaaveelaelkqqlk 92 
                                       +++le+ + e+k     m++  Ys +l +++   e+ e+v  ls  +++l  +++++i    k+a+ee+a      +
  gi|474934852|ref|YP_007688434.1|   2 MTRLEEMILELKDTTDMMVDLAYSSLLYNNT---EIAEEVITLSTSMSDLADRIQDSIADVGKSAPEEIARAIVTTR 75 
                                       57999999999999999*******9987664...6788888999**************************9999999 PP

                              Zw10  93 ekevvlellealkki 107
                                         + +l++ ea + i
  gi|474934852|ref|YP_007688434.1|  76 LLDGILDIAEAAESI 90 
                                       999999998876665 PP

>> Mobilization_B  Mobilization protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.3   6.5e-05      0.29      14      52 ..      32      70 ..      26      96 .. 0.83
   2 ?   -1.2   0.0      0.52   2.3e+03       8      33 ..      75     101 ..      68     121 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.5e-05
                    Mobilization_B 14 nelaeeieplaqsmatladearqviaevqqaseeqaaew 52
                                       e+aee+  l+ sm+ lad  ++ ia+v +++ e+ a  
  gi|474934852|ref|YP_007688434.1| 32 TEIAEEVITLSTSMSDLADRIQDSIADVGKSAPEEIARA 70
                                      599*************************88776665544 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.52
                    Mobilization_B   8 kksrginelaeeieplaqsma.tlade 33 
                                       +   gi ++ae  e +a+ +   lad 
  gi|474934852|ref|YP_007688434.1|  75 RLLDGILDIAEAAESIADVVVrGLADH 101
                                       555677888888888877643156665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1188.69
//
Query:       gi|474934853|ref|YP_007688435.1|  [L=239]
Description: hypothetical protein TALC_01293 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-13   49.3   0.0    7.3e-13   48.2   0.0    1.7  1  TrkA_C    TrkA-C domain
    5.6e-08   33.1   4.3    1.2e-07   32.1   4.3    1.6  1  PhoU      PhoU domain
  ------ inclusion threshold ------
      0.091   12.1   0.8       0.14   11.5   0.8    1.3  1  CorA      CorA-like Mg2+ transporter protein


Domain annotation for each model (and alignments):
>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.2   0.0   1.2e-16   7.3e-13       2      68 ..     127     195 ..     126     197 .. 0.93

  Alignments for each domain:
  == domain 1  score: 48.2 bits;  conditional E-value: 1.2e-16
                                       EEEEEE--GGGTTSBHHHHTHHHH.S-EEEEE.E-T-EEES--TT-B--TT-EEEEEEEHHHHHHHHHH CS
                            TrkA_C   2 vevtvpagsplvGktlkelnlrar.gvlvvai.rRggeliipsgdtvLeeGDvllvvgspsdlaelrel 68 
                                       ++++v+++s +vG t+  l+++a  g+ v+ai  R+g+ + p++++++++GD ++v g++++ + l+e+
  gi|474934853|ref|YP_007688435.1| 127 RMMRVRPESDMVGNTIEKLGIEAQtGCKVIAIkNRHGWTYDPDDNMKIRSGDDIIVRGTDEGADLLQEY 195
                                       6789****************************64669**************************999886 PP

>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   4.3     2e-11   1.2e-07       2      87 ..      22     103 ..      21     105 .. 0.90

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 2e-11
                                       HHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHH CS
                              PhoU   2 rrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERi 78 
                                        +m++++e ++d+a+ +l  +   +a++v+e+++e+d+l ++++ ++l a  +r+    d +++ +ll++a+    i
  gi|474934853|ref|YP_007688435.1|  22 TEMKDTSEVIVDLAYACLMYNSQSMAEKVRELEKEMDDLKFAVRYKVLLATRTRD----DAKQMAGLLEVASAADKI 94 
                                       59****************99999********************999887776555....5677899*********** PP

                                       HHHHHHHHH CS
                              PhoU  79 gDhavniae 87 
                                       +D a ++++
  gi|474934853|ref|YP_007688435.1|  95 SDAASDMVD 103
                                       ****99976 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.8   2.3e-05      0.14      95     195 ..      21     127 ..       8     145 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.3e-05
                              CorA  95 ikrlkdeggkpkspgellyrlldeivdrlfellekleeeldeledel........edstkkeilrelaqlrrrlvkl 163
                                       + ++k   +  +   +l y++l  + ++++e +++le+e+d+l   +        +++ +++++  l+++   + k+
  gi|474934853|ref|YP_007688435.1|  21 MTEMK---DTSEVIVDLAYACLMYNSQSMAEKVRELEKEMDDLKFAVrykvllatRTRDDAKQMAGLLEVASAADKI 94 
                                       44444...5566677999**********************************9999999999999999999999999 PP

                              CorA 164 rralapnrevlkrlla..kaddkllddedkeylr 195
                                        +a++++ ++l r+    + + +++ +e+ e +r
  gi|474934853|ref|YP_007688435.1|  95 SDAASDMVDLL-RFPVekRPFISKILQEADEKIR 127
                                       99999999999.8776444555555555544455 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1008  (0.0562218); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1453.79
//
Query:       gi|474934854|ref|YP_007688436.1|  [L=418]
Description: putative divalent cation transporter [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-29  102.5  24.0    7.1e-17   62.0   8.6    3.7  4  MgtE           Divalent cation transporter
  ------ inclusion threshold ------
       0.15   12.4   0.1       0.51   10.6   0.1    1.9  1  Viral_Beta_CD  Viral Beta C/D like family
       0.28   12.0   0.2       0.28   12.0   0.2    3.7  3  HKR_ArcB_TM    Histidine kinase receptor ArcB trans-membrane 


Domain annotation for each model (and alignments):
>> MgtE  Divalent cation transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.4      0.26   1.6e+03      42      78 ..      21      58 ..       6      61 .. 0.48
   2 !   54.3   7.4   2.7e-18   1.6e-14       5     123 ..      61     187 ..      59     188 .. 0.90
   3 ?   -0.7   2.4      0.29   1.7e+03      71      85 ..     209     223 ..     184     279 .. 0.57
   4 !   62.0   8.6   1.2e-20   7.1e-17       1     123 [.     280     411 ..     280     412 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.26
                                      HHHHHHHHHHHHHHHHHHHHT-..CTSHHHHHHHHHHH CS
                              MgtE 42 vvlllgvilgllifllalllgw.slllalvvglalvlv 78
                                      ++++ +vi g++ ++  ll+ + + +l+l++g++++++
  gi|474934854|ref|YP_007688436.1| 21 MGITALVIAGTADLFAGLLMDQmEEYLTLIIGMMVLIY 58
                                      23333333333333333334435555555666665554 PP

  == domain 2  score: 54.3 bits;  conditional E-value: 2.7e-18
                                       HHHHHHHHHHHHHHHHHHHHTTSS-GG..HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-......CTSHHHHHHH CS
                              MgtE   5 lglgGnlgaqlasristalhlgelekk..lkkvllkelrvvlllgvilgllifllalllgw.....slllalvvgla 74 
                                       +g++Gn+   + sri ta+++g++e +     vl+ +l  +l l +i++++ ++ ++ +++     ++ ++ ++ ++
  gi|474934854|ref|YP_007688436.1|  61 IGMRGNIFGAMGSRIGTAMNIGTFEMSfrRGTVLRANLESALALTLIMSIATGIATWGVAKlffggDAEIWDFIYIS 137
                                       79********************9977765799999************99999999775444555669999999**** PP

                                       HHHHHHHHHHH...HHHHHHHHHHTTS-GGGSHHHHHHHHHHHHHHHHHH CS
                              MgtE  75 lvlvllaaall.ilgvllplllwklglDPdnaaiPlltalgDllgtlllv 123
                                        +  ++a +++ ++ +l++++ +k+++D dn+++Pl++a+gD++++ + +
  gi|474934854|ref|YP_007688436.1| 138 TFGGVTAGLIVmMFNILIAYVGNKRNWDVDNITAPLIAAIGDIVTMPMVF 187
                                       *********************************************98876 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.29
                                       HHHHHHHHHHHHHHH CS
                              MgtE  71 vglalvlvllaaall 85 
                                       +++ ++++ la + +
  gi|474934854|ref|YP_007688436.1| 209 LSVVFIIATLALTAY 223
                                       222222222222221 PP

  == domain 4  score: 62.0 bits;  conditional E-value: 1.2e-20
                                       HHHHHHHHHHHHHHHHHHHHHHHHTTSS-GG..HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-.......CTSHH CS
                              MgtE   1 iPvilglgGnlgaqlasristalhlgelekk..lkkvllkelrvvlllgvilgllifllalllgw......slllal 69 
                                       +P+ l+ g +l  +l+sr+s+++h+g+le++    k  + +++++++++++ +l+i+++ +          sl +a 
  gi|474934854|ref|YP_007688436.1| 280 MPAYLNQGNALSGMLTSRLSSMIHMGTLEERmlPGKGAIDNFLLMFFCAAVTFLYIGIISFAACVltggsgSLSIAE 356
                                       78889999999*****************9996448888888888888888866666666553222445677778888 PP

                                       HHHHHHHHHHHHHHHH...HHHHHHHHHHTTS-GGGSHHHHHHHHHHHHHHHHHH CS
                              MgtE  70 vvglalvlvllaaall.ilgvllplllwklglDPdnaaiPlltalgDllgtlllv 123
                                       ++++ +v+ ++a+++l il +++++++ ++glDPd ++iP+ ++++Dl+g l+lv
  gi|474934854|ref|YP_007688436.1| 357 CLAIIMVAGMIATLILnILSYYVAIAADRFGLDPDDHCIPITSSVMDLFGALVLV 411
                                       8***************************************************997 PP

>> Viral_Beta_CD  Viral Beta C/D like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   8.6e-05      0.51      36      76 ..     188     228 ..     173     236 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 8.6e-05
                     Viral_Beta_CD  36 vektaaasvladnlddqyvlllaflfviaalllcvylksik 76 
                                       v   ++  +  + + d+ vl+l+++f+ia+l l  y+ + k
  gi|474934854|ref|YP_007688436.1| 188 VATWSFIRMDGQSFGDDLVLILSVVFIIATLALTAYIAMRK 228
                                       555678899999************************97655 PP

>> HKR_ArcB_TM  Histidine kinase receptor ArcB trans-membrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   4.7e-05      0.28      13      66 ..     105     158 ..      96     163 .. 0.79
   2 ?   -0.9   0.3      0.49   2.9e+03      17      32 ..     210     225 ..     205     236 .. 0.44
   3 ?   -2.7   2.6       1.8   1.1e+04       9      28 ..     352     371 ..     321     382 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.7e-05
                       HKR_ArcB_TM  13 lvlllivlalliqillslllsgeveiedllrsilfgllsaPwvlYFlsvlveqL 66 
                                        +++ i++ +++  + +l++ g+ ei d++   +fg ++a +++  +++l+  +
  gi|474934854|ref|YP_007688436.1| 105 TLIMSIATGIATWGVAKLFFGGDAEIWDFIYISTFGGVTAGLIVMMFNILIAYV 158
                                       33444455566667889*********************************9866 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.49
                       HKR_ArcB_TM  17 livlalliqillslll 32 
                                        +v+ +++ +l+ ++ 
  gi|474934854|ref|YP_007688436.1| 210 SVVFIIATLALTAYIA 225
                                       2333333333333333 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 1.8
                       HKR_ArcB_TM   9 fSlllvlllivlalliqill 28 
                                       +S+   l++i++a +i +l+
  gi|474934854|ref|YP_007688436.1| 352 LSIAECLAIIMVAGMIATLI 371
                                       34444444444444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1079  (0.0601818); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 3116.70
//
Query:       gi|474934855|ref|YP_007688437.1|  [L=391]
Description: ATP-utilizing enzymes of ATP-grasp superfamily (probably carboligases) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-72  243.1   0.0      2e-72  242.7   0.0    1.1  1  DUF1297   Domain of unknown function (DUF1297)
    1.4e-43  147.7   0.0    2.6e-43  146.9   0.0    1.4  1  DUF1246   Protein of unknown function (DUF1246)


Domain annotation for each model (and alignments):
>> DUF1297  Domain of unknown function (DUF1297)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  242.7   0.0   2.2e-76     2e-72       2     188 .]     198     391 .]     197     391 .] 0.98

  Alignments for each domain:
  == domain 1  score: 242.7 bits;  conditional E-value: 2.2e-76
                                       HHHHHHHHHCTTSSSHHHHCCEEEEE---SEEEEEEEEEETTT...TEEEEEEEEEEEEEECCCHCCS-HHHHHCCT CS
                           DUF1297   2 feekleellekglieeedlkkasieeyvvGanfnlnyfysplk...eevellgidrRyesnldglvrlpakeqlele 75 
                                       + ek++el+++g+++e+  ++a++e+y++G  fnl++fy pl+   e+vel+gid+R+es+ldg+ rlp k+q+ele
  gi|474934855|ref|YP_007688437.1| 198 YVEKSQELIKQGVLDEDFEQHARMEQYIIGPVFNLDFFYDPLEekgEKVELVGIDWRFESSLDGYARLPGKQQVELE 274
                                       889****************************************99999****************************9 PP

                                       -...---EEEEEEEEEEE-GGGHHHHHHHHHHHHHHHHHHSTT---EEEEEEEEE-TTS-EEEEEEESSB-GGGGGG CS
                           DUF1297  76 v...epeyvvvGnipvvlREsllekvfelgekfveaakklvppGiiGpFcLqsvvtkdlelvvfdvsaRivggtnvy 149
                                            pey+v+G+++++lREsll+++f ++ek+v+a+++l++pGiiGpFcLq++v+kdl+++++dv++Ri+ggtnv+
  gi|474934855|ref|YP_007688437.1| 275 NdgiIPEYTVCGHNSATLRESLLDNAFAMAEKYVKATQDLYKPGIIGPFCLQTCVDKDLHFYIYDVAPRIGGGTNVH 351
                                       87779************************************************************************ PP

                                       TT.--CCHHHTTSS---HHHHHHHHHHHHHHCT-GGGCEE CS
                           DUF1297 150 me.gspyskllfgeplsmGrrialEikeaiekdrleeivt 188
                                       m+ g+py ++l+++++s+Grr++  +++ ie++rleei+t
  gi|474934855|ref|YP_007688437.1| 352 MSvGHPYGNTLWRTNMSTGRRLSKMVRDGIEQERLEEIIT 391
                                       ***************************************8 PP

>> DUF1246  Protein of unknown function (DUF1246)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.9   0.0   2.9e-47   2.6e-43       1     121 [.      27     163 ..      27     164 .. 0.99

  Alignments for each domain:
  == domain 1  score: 146.9 bits;  conditional E-value: 2.9e-47
                                       EEEESSTTHHHHHHHHHHTT--EEEEC-CCCHHHHHTT.............TT-SEEEE.S.S..TTSS--HHHHHH CS
                           DUF1246   1 iatlaSHsalqilkgAkkegfrtlavcekgreklYekf.............kvidevivldkfkdilkeevqeklre 64 
                                       i++laSHs+l++++gA +egf+tlavc+kgre++++++             +v+d++++ldkf++il+ ++qe l++
  gi|474934855|ref|YP_007688437.1|  27 IGVLASHSSLDTCDGAISEGFKTLAVCQKGRERTFNNYfrcqrdaagnvirGVVDDTMILDKFNEILQPQNQEFLMK 103
                                       89************************************************99************************* PP

                                       TTCEE--BTTHHHHC-HHHHH.C-SS-EES-TTHHHHHCSHHHHHHH..HHHTT-BB--B CS
                           DUF1246  65 enailvPhgsfveYvgiekie.elkvpifGnrkllrwEerrekkrky..LekAgiriPkk 121
                                       +n+++vP++sf++Y++i+++e ++kvp++G+r+llr+Eer   +++y  LekA++++Pkk
  gi|474934855|ref|YP_007688437.1| 104 TNTLWVPNRSFTSYCSIDQVEnDFKVPMVGSRNLLRSEERGGPQDYYwlLEKANLPFPKK 163
                                       **********************************************99**********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 2224.10
//
Query:       gi|474934856|ref|YP_007688438.1|  [L=233]
Description: hypothetical protein TALC_01296 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0043   17.1   0.2     0.0043   17.1   0.2    1.8  2  DUF2561          Protein of unknown function (DUF2561)
     0.0043   16.9   0.4      0.018   14.9   0.1    1.9  2  SpoIIIAH         SpoIIIAH-like protein
     0.0061   16.5   0.1      0.014   15.4   0.1    1.5  1  DUF3290          Protein of unknown function (DUF3290)
     0.0086   17.0   0.1      0.017   16.0   0.1    1.5  1  DUF756           Domain of unknown function (DUF756)
  ------ inclusion threshold ------
      0.013   15.6   0.0      0.023   14.8   0.0    1.4  1  Peptidase_S49_N  Peptidase family S49 N-terminal
      0.034   14.4   0.6      0.061   13.6   0.6    1.5  1  CBM_4_9          Carbohydrate binding domain
      0.042   13.2   0.0      0.068   12.5   0.0    1.3  1  DUF929           Domain of unknown function (DUF929)
      0.045   13.5   2.2       0.95    9.3   0.0    2.3  2  Form-deh_trans   Formate dehydrogenase N, transmembrane
      0.045   14.7   0.0       0.11   13.5   0.0    1.6  1  DUF4834          Domain of unknown function (DUF4834)
      0.053   12.4   0.1      0.099   11.6   0.0    1.4  2  MFS_1            Major Facilitator Superfamily
      0.074   13.0   3.0       0.18   11.7   1.3    2.3  2  TMEM154          TMEM154 protein family
      0.081   13.9   3.7       0.23   12.4   0.1    2.8  2  Pilin_N          Archaeal Type IV pilin, N-terminal
       0.23   11.8   0.1       0.23   11.8   0.1    1.5  1  BatA             Aerotolerance regulator N-terminal
       0.43   11.7   5.1        1.7    9.8   4.6    2.2  2  PPC              Bacterial pre-peptidase C-terminal domain
       0.51   10.7   5.1        7.1    7.1   0.5    2.7  3  Lipoprotein_17   Lipoprotein associated domain
       0.86    9.4   4.5       0.54   10.1   3.2    1.4  1  RIFIN            Rifin
        1.1    9.5   4.0       0.27   11.5   0.5    1.7  1  Pox_EPC_I2-L1    Poxvirus entry protein complex L1 and I2
        3.5    7.5   6.6        2.1    8.3   2.3    2.4  2  PKD              PKD domain


Domain annotation for each model (and alignments):
>> DUF2561  Protein of unknown function (DUF2561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.3       1.1   1.1e+03      32      50 ..       9      27 ..       4      37 .. 0.77
   2 !   17.1   0.2   4.3e-06    0.0043      60     144 ..     131     218 ..     123     222 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.1
                           DUF2561 32 wLvllGvsvaatvaLvdLg 50
                                       L+++ v+v+a va+ d g
  gi|474934856|ref|YP_007688438.1|  9 LLAFMFVAVSAFVAVSDDG 27
                                      5778888889999888865 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 4.3e-06
                           DUF2561  60 shttwvLyavivvsalvivgavPlLLrarrvaeae..Paarargaperaaaapargadapaeraeaeea.saekaea 133
                                         ++ + y+ i+v a+++v a+ l Lr r  ++     ++ ++ ++++ ++ap + a++++++ + e+a + e +e 
  gi|474934856|ref|YP_007688438.1| 131 VWSGSLPYIAIIVIAIIVVIAIFLYLRNRPKTKPSitFTELEAQKKAEKGEAPSKPAQQSTDKKRYEAApKDEDSEP 207
                                       44555779********************9887766432333344445556677788888888877777745555666 PP

                           DUF2561 134 lreaaewssaa 144
                                       ++e +++ +++
  gi|474934856|ref|YP_007688438.1| 208 VQEGQAPAAKK 218
                                       66666666555 PP

>> SpoIIIAH  SpoIIIAH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.75   7.5e+02       6      30 ..       7      30 ..       6     101 .. 0.69
   2 !   14.9   0.1   1.8e-05     0.018       4      83 ..     141     217 ..     138     229 .. 0.47

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.75
                                      XXXXX.XXXXXXXXXXXXXXX..XXX CS
                          SpoIIIAH  6 itaLa.lmiavagYlnftedsgkkaa 30
                                      i++La + +av++++ +++d  +  a
  gi|474934856|ref|YP_007688438.1|  7 IALLAfMFVAVSAFVAVSDDGSD--A 30
                                      66777344778889888887633..2 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.8e-05
                                       XXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          SpoIIIAH   4 iiitaLalmiavagYlnftedsgkkaaetaeteqeesekaeigddkekdessaasaeaesssetesesseksdiass 80 
                                       ii++a++++ia+  Yl       k++++ + te e+++kae g++ +k ++++++++  + + ++++s+  ++ ++ 
  gi|474934856|ref|YP_007688438.1| 141 IIVIAIIVVIAIFLYLRNRP---KTKPSITFTELEAQKKAEKGEAPSKPAQQSTDKKRYEAAPKDEDSEPVQEGQAP 214
                                       44444445555555554444...477778888888888888888333333333333333333333333333333333 PP

                                       XXX CS
                          SpoIIIAH  81 ded 83 
                                        ++
  gi|474934856|ref|YP_007688438.1| 215 AAK 217
                                       222 PP

>> DUF3290  Protein of unknown function (DUF3290)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   1.4e-05     0.014      14      45 ..     132     163 ..     124     164 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.4e-05
                           DUF3290  14 lndllryililvlllllivvlilylrnrldtk 45 
                                       ++  l yi i+v++++++++++lylrnr +tk
  gi|474934856|ref|YP_007688438.1| 132 WSGSLPYIAIIVIAIIVVIAIFLYLRNRPKTK 163
                                       5567889*********************9998 PP

>> DUF756  Domain of unknown function (DUF756)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   1.7e-05     0.017      12      67 ..      51     111 ..      28     114 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.7e-05
                            DUF756  12 gnlrltlrNtgkaaarftVydnaka....pwtytveagdqledhwklassg.gwYdltVtg 67 
                                       g+++l+     ++ +rftV+++++a      t tv+ gd  + ++k + ++ g Y ++Vt 
  gi|474934856|ref|YP_007688438.1|  51 GSIKLKVIVPTTQDVRFTVTSKDGAvsyyDGTQTVASGDPQTVKLKFSIDDtGTYTVKVTM 111
                                       7788888888999*********999**999********888877777777779******96 PP

>> Peptidase_S49_N  Peptidase family S49 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   2.3e-05     0.023      13      85 ..     139     210 ..     135     230 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.3e-05
                   Peptidase_S49_N  13 lvtlvvailvvvvlivalaakkkkekgelevtkLneeykelkeeleealldeeelkaaekkekkeekeekkae 85 
                                       ++++v+ai+vv+++++ l+++ k +k ++++t+L+ + k  k e  ++  ++++ k++  +  k+e +e  +e
  gi|474934856|ref|YP_007688438.1| 139 IAIIVIAIIVVIAIFLYLRNRPK-TKPSITFTELEAQKKAEKGEAPSKPAQQSTDKKRYEAAPKDEDSEPVQE 210
                                       56788999999888887777776.7899********9999998887777766666655555555544444444 PP

>> CBM_4_9  Carbohydrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.6   6.1e-05     0.061      67     130 ..      53     111 ..      21     120 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.1e-05
                                       EEEEEEESSTSEEEEEEEEEESSTTSCTCEEEEEEEEEESTSEEEEEEEEE-SSCSCCEEEEEE CS
                           CBM_4_9  67 vsfwvkassgksrtikvkigdtdadganydevadekvelkgewktlegtFtipkstdenvelyv 130
                                       ++++v   +   ++++++++ +d+   +y+  +  +++ +g+ +t++ +F+i+++ + +v+++ 
  gi|474934856|ref|YP_007688438.1|  53 IKLKVIVPTT--QDVRFTVTSKDGA-VSYYDGT--QTVASGDPQTVKLKFSIDDTGTYTVKVTM 111
                                       5555555555..**********992.5555555..9*****************77766666655 PP

>> DUF929  Domain of unknown function (DUF929)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.8e-05     0.068       3      38 ..     138     179 ..     136     208 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.8e-05
                            DUF929   3 liviaiivliivvivvvslsai......vsnalvelskqvya 38 
                                       +i+i++i++i+v++++++l+        ++    e++k++++
  gi|474934856|ref|YP_007688438.1| 138 YIAIIVIAIIVVIAIFLYLRNRpktkpsITFTELEAQKKAEK 179
                                       799*****************9966666633333333333333 PP

>> Form-deh_trans  Formate dehydrogenase N, transmembrane
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   1.3      0.11     1e+02      13      28 ..       5      20 ..       4      21 .. 0.91
   2 ?    9.3   0.0   0.00095      0.95       6      38 ..     130     162 ..     127     165 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.11
                                      HHHHHHHHHHHHHHHH CS
                    Form-deh_trans 13 Kplgalgmaatalagf 28
                                      K +++l+++++a+ +f
  gi|474934856|ref|YP_007688438.1|  5 KSIALLAFMFVAVSAF 20
                                      789**********998 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00095
                                       HHHHTTHHHHHHHHHHHHHHHHHHHHHHH--B- CS
                    Form-deh_trans   6 elWKGvlKplgalgmaatalagffHYitvGPne 38 
                                       ++W G l +++++++a+ ++ ++f Y++  P++
  gi|474934856|ref|YP_007688438.1| 130 SVWSGSLPYIAIIVIAIIVVIAIFLYLRNRPKT 162
                                       579************************999986 PP

>> DUF4834  Domain of unknown function (DUF4834)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   0.00011      0.11       9      79 ..     139     213 ..     134     227 .. 0.42

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00011
                           DUF4834   9 ifiiailviglsilsvilrtv.....fglgsrkkss........ksaqkqfgnstnsnqqksqsrsetkeegeiiee 72 
                                       i ii+i++i+++ ++  lr+                        k+a+k+ +   +  qq++++++++ + +++ +e
  gi|474934856|ref|YP_007688438.1| 139 IAIIVIAIIVVIAIFLYLRNRpktkpS--------ItfteleaqKKAEKG-EAPSKPAQQSTDKKRYEAAPKDEDSE 206
                                       555666666666666666666333330........245444431222222.22222223333334444444444444 PP

                           DUF4834  73 ersekea 79 
                                         +e +a
  gi|474934856|ref|YP_007688438.1| 207 PVQEGQA 213
                                       4444333 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       2.5   2.5e+03     155     158 ..      13      16 ..       5      32 .. 0.46
   2 ?   11.6   0.0   9.9e-05     0.099     148     189 ..     132     179 ..     126     221 .. 0.65

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.5
                             MFS_1 155 yila 158
                                       +++a
  gi|474934856|ref|YP_007688438.1|  13 MFVA 16 
                                       1111 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 9.9e-05
                             MFS_1 148 lgWravfyilaivsllafvlfllllpeepperkrkspkeee.......k 189
                                       ++ +++++++ ++++++ v++++l+++++p+ k++ + +e+       k
  gi|474934856|ref|YP_007688438.1| 132 WSGSLPYIAIIVIAIIV-VIAIFLYLRNRPKTKPSITFTELeaqkkaeK 179
                                       44445566666666665.4456777677776666666666546555331 PP

>> TMEM154  TMEM154 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.2   1.2e+03      97     112 ..      98     113 ..      88     122 .. 0.83
   2 ?   11.7   1.3   0.00018      0.18      64      93 ..     136     165 ..     131     179 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.2
                           TMEM154  97 esdeldsenvkvpifE 112
                                       + d+ +  +vkv ++E
  gi|474934856|ref|YP_007688438.1|  98 SIDDTGTYTVKVTMYE 113
                                       67899999*******9 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00018
                           TMEM154  64 iPlvllillllvviiliqkkkrkrsKddek 93 
                                       +P +++i++ ++v+i i  + r+r K +++
  gi|474934856|ref|YP_007688438.1| 136 LPYIAIIVIAIIVVIAIFLYLRNRPKTKPS 165
                                       699***********************9965 PP

>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   1.1      0.75   7.4e+02      38      76 ..      90     127 ..       7     131 .. 0.73
   2 ?   12.4   0.1   0.00023      0.23      13      50 ..     139     175 ..     134     191 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.75
                           Pilin_N  38 pq.asievkidssastgknavsle.hkgGdsidtkdlkivl 76 
                                       pq ++++++id++++++   v+++ ++gG  i+ + + + +
  gi|474934856|ref|YP_007688438.1|  90 PQtVKLKFSIDDTGTYT---VKVTmYEGGAEIQSDIVDVKV 127
                                       33355656666666553...555424677777776666555 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00023
                           Pilin_N  13 vaitvIlaAviaafvlglasneekapqasievkidssa 50 
                                       +ai+vI++ v+ a+ l l + ++++p++++ +++++++
  gi|474934856|ref|YP_007688438.1| 139 IAIIVIAIIVVIAIFLYLRNRPKTKPSITF-TELEAQK 175
                                       6788888888888888889***********.4433333 PP

>> BatA  Aerotolerance regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00023      0.23      10      46 ..     140     179 ..     135     191 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00023
                              BatA  10 Llallllplpiillyllkrrpqev...vfsslrlleevek 46 
                                        +  ++++++i++ ++l+ rp+++   +f  l+  +++ek
  gi|474934856|ref|YP_007688438.1| 140 AIIVIAIIVVIAIFLYLRNRPKTKpsiTFTELEAQKKAEK 179
                                       4455555665888888888888876666666666666555 PP

>> PPC  Bacterial pre-peptidase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   4.6    0.0017       1.7       3      69 ..      41     110 ..      39     110 .. 0.76
   2 ?   -1.6   0.0       6.3   6.3e+03      51      61 ..     163     173 ..     150     175 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0017
                                       EEEEEEE-TT-EEEEEE..S-TT..SEEEEE-TT..-SS-EE-ST...T-TTS-TTS-EE-SSSEEEEEEE. CS
                               PPC   3 Dvysfevpagdsltidi..dggtidldLylldsngtsvaaydans...apsgsdeyieftapqaGtYyvaVs 69 
                                       Dvy+f+  +++s+++ +   +++ d+  ++   + + v+ yd+++   + ++    ++f+  ++GtY v+V+
  gi|474934856|ref|YP_007688438.1|  41 DVYKFTEDSTGSIKLKVivPTTQ-DVRFTVTSKD-GAVSYYDGTQtvaSGDPQTVKLKFSIDDTGTYTVKVT 110
                                       9***********99885226666.7778888888.88888888887533333445566999********995 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 6.3
                                       -TTS-EE-SSS CS
                               PPC  51 deyieftapqa 61 
                                       +++i+ft ++a
  gi|474934856|ref|YP_007688438.1| 163 KPSITFTELEA 173
                                       59999999887 PP

>> Lipoprotein_17  Lipoprotein associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.3     0.028        28      53      77 ..      46      69 ..      25      84 .. 0.71
   2 ?    7.1   0.5    0.0071       7.1      46      70 ..      94     115 ..      68     129 .. 0.73
   3 ?   -1.8   0.0       4.1   4.1e+03      72      80 ..     160     169 ..     147     196 .. 0.62

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.028
                                      HHHHHTEEEEEEEE.TTT--EEEEEE CS
                    Lipoprotein_17 53 anDeeGtLkvkvtl.sknnksetkti 77
                                        D++G++k+kv + + ++  + +t+
  gi|474934856|ref|YP_007688438.1| 46 TEDSTGSIKLKVIVpTTQD--VRFTV 69
                                      67**********9964433..44444 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0071
                                       EEEEE-THHHHHTEEEEEEEETTT- CS
                    Lipoprotein_17  46 sikivssanDeeGtLkvkvtlsknn 70 
                                       ++k+   + D++Gt +vkvt++ ++
  gi|474934856|ref|YP_007688438.1|  94 KLKF---SIDDTGTYTVKVTMYEGG 115
                                       3333...459**********98887 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 4.1
                                       EEEE.EEEEE CS
                    Lipoprotein_17  72 setk.titit 80 
                                       ++tk +it+t
  gi|474934856|ref|YP_007688438.1| 160 PKTKpSITFT 169
                                       4444333333 PP

>> RIFIN  Rifin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   3.2   0.00054      0.54     270     308 ..     124     163 ..      42     172 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00054
                             RIFIN 270 eattaslqtaiiasivaivvIvLimvI.IYLiLRYrRKkK 308
                                       + +++s+  +     +ai+vI +i+vI I+L LR r K K
  gi|474934856|ref|YP_007688438.1| 124 DVKVSSSVWSGSLPYIAIIVIAIIVVIaIFLYLRNRPKTK 163
                                       44444444455556799999988887779*******9988 PP

>> Pox_EPC_I2-L1  Poxvirus entry protein complex L1 and I2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.5   0.00027      0.27      43      70 ..     129     157 ..     119     158 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00027
                     Pox_EPC_I2-L1  43 sgtklwlt.lliiliavlilvlllflylK 70 
                                       s+ +  +   ++i+++++i+v+ +flyl+
  gi|474934856|ref|YP_007688438.1| 129 SSVWSGSLpYIAIIVIAIIVVIAIFLYLR 157
                                       333333445899***************96 PP

>> PKD  PKD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.69   6.9e+02      15      34 ..      19      40 ..      16      56 .. 0.73
   2 ?    8.3   2.3    0.0021       2.1       8      61 ..      59     110 ..      55     112 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.69
                                      EEEEES.-SS-SEEE..EE--S CS
                               PKD 15 aftaavpdganvtys..Wdfgd 34
                                      af a+++dg++++    + f+d
  gi|474934856|ref|YP_007688438.1| 19 AFVAVSDDGSDAAVGngFAFED 40
                                      7999999999999876677777 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0021
                                       -BSSEEEEEEEES.-SS-SEEEEE--SS--EEEEETTEEEEEE-S..SEEEEEEEE CS
                               PKD   8 lvpgatvaftaavpdganvtysWdfgdgsvvqvlseptvthtYls..pGeYeVtvt 61 
                                       +++++ v+ft ++ dga   y    g   +v+++  +tv+++++   +G+Y+V+vt
  gi|474934856|ref|YP_007688438.1|  59 VPTTQDVRFTVTSKDGAVSYYD---GT-QTVASGDPQTVKLKFSIddTGTYTVKVT 110
                                       7899999999999888776663...44.779999999******9777*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1534  (0.0855597); expected 358.6 (0.02)
Passed bias filter:                      941  (0.0524848); expected 358.6 (0.02)
Passed Vit filter:                       133  (0.00741815); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 1461.29
//
Query:       gi|474934857|ref|YP_007688439.1|  [L=91]
Description: hypothetical protein TALC_01297 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00027   20.5   0.5    0.00031   20.4   0.5    1.0  1  Saf_2TM          SAVED-fused 2TM effector domain
     0.0023   17.7   0.0     0.0028   17.4   0.0    1.1  1  Yip1             Yip1 domain
     0.0063   16.8   0.2     0.0074   16.6   0.2    1.1  1  DUF1772          Domain of unknown function (DUF1772)
  ------ inclusion threshold ------
      0.012   15.3   0.0      0.013   15.2   0.0    1.0  1  Cation_efflux    Cation efflux family
      0.015   15.3   0.3      0.017   15.1   0.3    1.0  1  Abhydrolase_9_N  Alpha/beta-hydrolase family N-terminus
      0.022   15.0   0.4      0.026   14.7   0.4    1.1  1  CD47             CD47 transmembrane region
      0.045   13.6   1.4      0.053   13.4   1.4    1.0  1  Imp-YgjV         Bacterial inner membrane protein
       0.05   13.8   0.4       0.23   11.7   0.0    1.9  2  DUF2985          Protein of unknown function (DUF2985)
       0.27   11.3   3.0       0.88    9.7   0.6    2.1  2  DUF2973          Protein of unknown function (DUF2973)
       0.29   10.9   1.2       0.35   10.7   0.6    1.4  1  ATP-synt_S1      Vacuolar ATP synthase subunit S1 (ATP6S1)
       0.33   10.8   3.0        1.4    8.8   0.5    2.1  2  LapA_dom         Lipopolysaccharide assembly protein A domain


Domain annotation for each model (and alignments):
>> Saf_2TM  SAVED-fused 2TM effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.5   1.9e-07   0.00031      21     101 ..       9      86 ..       5      88 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.9e-07
                           Saf_2TM  21 aelllftigvalllailgtdwalkialklaggslevsfssseipeivlaiilvigvllivvGavllilryvneakrq 97 
                                       ++l ++++  al+++++g   al+   +++ +++   f++ +  e++ +++ ++ v++++v a +li r+ n akrq
  gi|474934857|ref|YP_007688439.1|   9 FKLQFLETMSALIISAFGLVAALAWNETIK-TAVAKVFDEDG--ELLGLFVYALLVTILAVAATMLITRATNKAKRQ 82 
                                       5566788888999999***99999988887.889999**999..89******************************9 PP

                           Saf_2TM  98 skkk 101
                                        k+k
  gi|474934857|ref|YP_007688439.1|  83 LKAK 86 
                                       9876 PP

>> Yip1  Yip1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.7e-06    0.0028      59     124 ..      13      75 ..       2      79 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.7e-06
                              Yip1  59 lssllgaiiggylglllgllllalllhliakllggkgsfkqtlsvvgyallPlilgaliailllll 124
                                       ++  ++a+i++++gl+++l+    + + +ak+++ +g    +l + +yall++il++ +++l+  +
  gi|474934857|ref|YP_007688439.1|  13 FLETMSALIISAFGLVAALAWNETIKTAVAKVFDEDGE---LLGLFVYALLVTILAVAATMLITRA 75 
                                       5555566666666544444444445555**********...******************9998765 PP

>> DUF1772  Domain of unknown function (DUF1772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.2   4.6e-06    0.0074      41      96 ..      16      87 ..       6      91 .] 0.66

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.6e-06
                           DUF1772 41 plallsalafa.yla.............araasrgarllylaaaallllsivpyTllvmvPtN...nkLaalk 96
                                      ++++l+++af+ ++a             + + + +  +l+ + a+l+++  v  T+l+ + tN   ++L+a+k
  gi|474934857|ref|YP_007688439.1| 16 TMSALIISAFGlVAAlawnetiktavakVFDEDGELLGLF-VYALLVTILAVAATMLITRATNkakRQLKAKK 87
                                      4444444444422335589999999998666677777777.669999999*************4322233332 PP

>> Cation_efflux  Cation efflux family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   8.2e-06     0.013      56     131 ..       4      83 ..       1      89 [. 0.78

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8.2e-06
                     Cation_efflux  56 derfpfGygrlevlgalvsgllllglav...fllleaiqkli.kegereihaglalvvalvslvvnlalllilrrag 128
                                       de+ pf ++ le++ al+ +++ l++a+     + +a+ k++ + ge +    +al+v++++++ ++++ +++ +a 
  gi|474934857|ref|YP_007688439.1|   4 DEEKPFKLQFLETMSALIISAFGLVAALawnETIKTAVAKVFdEDGELLGLFVYALLVTILAVAATMLITRATNKAK 80 
                                       78889999*************99999987778888999999954455556677777777777777777777777776 PP

                     Cation_efflux 129 rkl 131
                                       r+l
  gi|474934857|ref|YP_007688439.1|  81 RQL 83 
                                       655 PP

>> Abhydrolase_9_N  Alpha/beta-hydrolase family N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.3     1e-05     0.017      56     122 ..      19      85 ..       6      89 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1e-05
                   Abhydrolase_9_N  56 lavvalvvllvalvlaarwQrelralmgaeplgaaeyllvllvallvfalllllgrllralvrllar 122
                                       ++++++ +l++al++  + ++ ++++++ ++     ++ +llv++l +a+ +l+ r++ ++ r l++
  gi|474934857|ref|YP_007688439.1|  19 ALIISAFGLVAALAWNETIKTAVAKVFDEDGELLGLFVYALLVTILAVAATMLITRATNKAKRQLKA 85 
                                       5667778899999999999999999999999999999999999999999999999999999888874 PP

>> CD47  CD47 transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.4   1.6e-05     0.026       1      59 [.      20      79 ..      20      83 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.6e-05
                              CD47  1 livillilaiiLlwgqlgiitlkyks.vskklilllvagliitlivvvgaillipgeysv 59
                                      li++   l+  L w + + +++   + ++ +l  l+v +l++t+++v + +l+  +    
  gi|474934857|ref|YP_007688439.1| 20 LIISAFGLVAALAWNETIKTAVAKVFdEDGELLGLFVYALLVTILAVAATMLITRATNKA 79
                                      68889999999***9987766654444999****************99999987666554 PP

>> Imp-YgjV  Bacterial inner membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.4   3.2e-05     0.053      43     107 ..      13      77 ..       9      85 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.2e-05
                          Imp-YgjV  43 lLgaytaalsnllsavRtllslktrkkkvmllfilltlvlglltwqglisllpiaasllatialf 107
                                       +L+ ++a +++++ +v +l+   t k  v+ +f   + +lgl+ +  l+ +l++aa++l t a  
  gi|474934857|ref|YP_007688439.1|  13 FLETMSALIISAFGLVAALAWNETIKTAVAKVFDEDGELLGLFVYALLVTILAVAATMLITRATN 77 
                                       7999*********************************************************9875 PP

>> DUF2985  Protein of unknown function (DUF2985)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.44   7.2e+02       9      28 ..      13      32 ..       9      46 .. 0.64
   2 ?   11.7   0.0   0.00014      0.23      11      43 ..      54      87 ..      50      91 .] 0.84

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.44
                           DUF2985  9 flvtiYglnvvawgamlfLl 28
                                      fl t+ +l++ a+g++  L 
  gi|474934857|ref|YP_007688439.1| 13 FLETMSALIISAFGLVAALA 32
                                      55566666777777666655 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00014
                           DUF2985 11 vtiYglnvvawgamlfLlLlgaapamnin.sark 43
                                      +++Y+l+v++  ++  +l+++a+++++ + +a+k
  gi|474934857|ref|YP_007688439.1| 54 LFVYALLVTILAVAATMLITRATNKAKRQlKAKK 87
                                      689**********************885545444 PP

>> DUF2973  Protein of unknown function (DUF2973)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.12   1.9e+02       5      31 ..      20      46 ..      17      53 .. 0.79
   2 ?    9.7   0.6   0.00054      0.88       4      34 ..      55      85 ..      51      91 .] 0.80

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.12
                           DUF2973  5 lYilaftvlaflAvanLirslitlsad 31
                                      l i af ++a lA +  i+  ++  +d
  gi|474934857|ref|YP_007688439.1| 20 LIISAFGLVAALAWNETIKTAVAKVFD 46
                                      6688999*****999999887776665 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00054
                           DUF2973  4 llYilaftvlaflAvanLirslitlsadsqr 34
                                      ++Y+l +t+la+ A + + r    ++++ ++
  gi|474934857|ref|YP_007688439.1| 55 FVYALLVTILAVAATMLITRATNKAKRQLKA 85
                                      69************99999988877777666 PP

>> ATP-synt_S1  Vacuolar ATP synthase subunit S1 (ATP6S1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.6   0.00021      0.35     105     132 ..      51      78 ..      44      89 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00021
                       ATP-synt_S1 105 wmgLvvslillliltyglhmimdlktmd 132
                                       + gL+v ++l++il+++ +m+++  t+ 
  gi|474934857|ref|YP_007688439.1|  51 LLGLFVYALLVTILAVAATMLITRATNK 78 
                                       68*******************9877765 PP

>> LapA_dom  Lipopolysaccharide assembly protein A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1     0.078   1.3e+02      20      35 ..      18      33 ..      15      40 .. 0.88
   2 ?    8.8   0.5   0.00086       1.4      27      61 ..      55      88 ..      50      91 .] 0.45

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.078
                          LapA_dom 20 sllllvafgiGallgw 35
                                      s l++ afg+ a l+w
  gi|474934857|ref|YP_007688439.1| 18 SALIISAFGLVAALAW 33
                                      6789999999999999 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00086
                          LapA_dom 27 fgiGallgwllslwsylrlrrelrrlkkkikklek 61
                                      f+  +l+++l+ + + +   r+ +++k+++k+ +k
  gi|474934857|ref|YP_007688439.1| 55 FVYALLVTILAVA-ATMLITRATNKAKRQLKAKKK 88
                                      3333344444444.444455555555555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1235  (0.0688828); expected 358.6 (0.02)
Passed bias filter:                      610  (0.0340231); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 594.49
//
Query:       gi|474934858|ref|YP_007688440.1|  [L=167]
Description: Sortase-related acyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-08   34.6   0.0    2.1e-08   34.4   0.0    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    5.4e-07   29.4   0.0    6.6e-07   29.1   0.0    1.2  1  DUF1999          Protein of unknown function (DUF1999)
    2.7e-05   24.5   0.0    3.8e-05   24.0   0.0    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.031   14.2   0.0      0.044   13.7   0.0    1.3  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
      0.042   13.8   0.0      0.061   13.3   0.0    1.4  1  FR47             FR47-like protein
       0.06   14.0   0.1        0.1   13.2   0.1    1.4  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
       0.08   12.9   0.6       0.12   12.3   0.6    1.2  1  Sds3             Sds3-like


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.0   8.4e-12   2.1e-08      10     117 .]      37     148 ..      16     148 .. 0.81

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 8.4e-12
                                       HHTHHHHHHHHHHH....HHHHHHSTTCEEEEEEETTEEEEEEEEEEEET..TSTTEEEEEEEEESGGGTTSSHHHH CS
                    Acetyltransf_1  10 esffppnedaseee....feesfsleaegllvaeedgeliGfisllkipd..ekggvayieslaVspeyrgkGlGsa 80 
                                       e+f  +++d   +     f+++  l+ +  +vaeedge+ Gfi + +  +     + ++ie + V+p  r++ +G +
  gi|474934858|ref|YP_007688440.1|  37 EDFSQEWKDNLGASspnhFRPY--LDSGLSFVAEEDGEIYGFIFAQMLHHvaDCSNLVWIENMGVDPIVRRNEIGYR 111
                                       4444555555555555456666..44458888***********888888888899********************** PP

                                       HHHHHHHHHHHTTESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  81 LlealeerareegikkivlaveedndaairlYeklGF 117
                                       Ll++ ++  +  g++     + + n ++i l++k GF
  gi|474934858|ref|YP_007688440.1| 112 LLRETLRAGKAAGAEVAHSMIGQGNAPSIMLHKKIGF 148
                                       *******99999997765557888********88**9 PP

>> DUF1999  Protein of unknown function (DUF1999)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   2.6e-10   6.6e-07       1      77 [.       3      84 ..       3     144 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 2.6e-10
                           DUF1999  1 meyRtleeaDfaalqaldlavlree.....dpafdalpereregrlrtslaaLkfyeRsehsfvaeeegelrGlvlaqs 74
                                      me+R ++ +D +++++l+l+ +re      +++++ +++  ++    +s+   + y  s+ sfvaee+ge+ G+++aq 
  gi|474934858|ref|YP_007688440.1|  3 MEFRPMKLKDLKRVRELELSCIREYfaetiENKWEDFSQEWKDNLGASSPNHFRPYLDSGLSFVAEEDGEIYGFIFAQM 81
                                      89*****************99886421112556666777777777889999***************************9 PP

                           DUF1999 75 vWq 77
                                      +  
  gi|474934858|ref|YP_007688440.1| 82 LHH 84
                                      865 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   1.5e-08   3.8e-05       5      74 ..      64     148 ..      60     149 .. 0.69

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.5e-08
                                       EEEEEETTEEEEEEEEEEES........TCTEEEEE-GGGTTSSHHHHHHHH.....TTSEEEEE.EEEE...THHH CS
                    Acetyltransf_7   5 vfVaeddgkivGfialslld........aeitrlaVdpeyrgkGiGraLlea.....aekgiile.qlel...naek 64 
                                        fVae+dg+i Gfi ++ l          +i+++ Vdp  r++ iG +Ll+      ++ g + + ++     na +
  gi|474934858|ref|YP_007688440.1|  64 SFVAEEDGEIYGFIFAQMLHhvadcsnlVWIENMGVDPIVRRNEIGYRLLREtlragKAAGAE-VaHSMIgqgNA-P 138
                                       69************9999999999988888888*****************9644433113321.11112222121.4 PP

                                       HHHHHHHTTE CS
                    Acetyltransf_7  65 aikfYeklGF 74 
                                       +i + +k GF
  gi|474934858|ref|YP_007688440.1| 139 SIMLHKKIGF 148
                                       4556666666 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.7e-05     0.044      32     108 ..      63     150 ..      32     156 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.7e-05
                   Acetyltransf_10  32 lllvaeeggkivGvi......elrdgs.......hisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnas 94 
                                       l +vaee+g+i G+i                    i+ + Vdp  r++ ig +Ll + +++ + +g ++ +  + + 
  gi|474934858|ref|YP_007688440.1|  63 LSFVAEEDGEIYGFIfaqmlhH----VadcsnlvWIENMGVDPIVRRNEIGYRLLRETLRAGKAAGAEVaHSMIGQG 135
                                       569************7654433....144557999999*********************999888888887777777 PP

                   Acetyltransf_10  95 p.yavpfYeklGFka 108
                                       +   + + +k+GF +
  gi|474934858|ref|YP_007688440.1| 136 NaPSIMLHKKIGFFM 150
                                       768888888888865 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.4e-05     0.061      25      81 ..      95     152 ..      75     157 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.4e-05
                                       EEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-E.EEEEETT-HHHHHHHHHHT-EEEE CS
                              FR47  25 galqvlpehrrrGlgsrlvkalakeiaergktv.llvvvasNtpsirlyeklGfekie 81 
                                         + v+p +rr   g rl ++  ++  ++g +v   +++++N psi l +k+Gf  ++
  gi|474934858|ref|YP_007688440.1|  95 ENMGVDPIVRRNEIGYRLLRETLRAGKAAGAEVaHSMIGQGNAPSIMLHKKIGFFMDR 152
                                       56778999999999999999988888887766515789****************7764 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   4.1e-05       0.1       1     137 [.       2     148 ..       2     149 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.1e-05
                    Acetyltransf_3   1 RLlLrplteeDlealfelrsdpevmrylpepltleeaeewlera............waeeseeegygwaivlkdtgv 65 
                                       R+ +rp++ +Dl+++ e ++   +++y+ e  t e+ +e +++             ++ ++ ++g+ ++  ++d+++
  gi|474934858|ref|YP_007688440.1|   2 RMEFRPMKLKDLKRVRE-LELSCIREYFAE--TIENKWEDFSQEwkdnlgasspnhFR-PYLDSGLSFVA-EEDGEI 73 
                                       8899**********977.343456666433..33333333332212223555565444.35567777888.444436 PP

                    Acetyltransf_3  66 iGsvglrdleeedee...aelg.ymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGf 137
                                        G++  + l++  +    + ++ + ++p ++++ ++   +r  l++  +  g+e   + i + N  Si +++k+Gf
  gi|474934858|ref|YP_007688440.1|  74 YGFIFAQMLHHVADCsnlVWIEnMGVDPIVRRNEIGYRLLRETLRAG-KAAGAEVAHSMIGQGNAPSIMLHKKIGF 148
                                       99997777776655555544441445666899999999999999999.788899999*****************99 PP

>> Sds3  Sds3-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.6   4.9e-05      0.12      51      91 ..       4      44 ..       2      46 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.9e-05
                              Sds3 51 eerDaeLkrlrlreeyqlkriekefkadiekakqeheklvk 91
                                      e+r  +Lk l++ +e +l++i++ f ++ie  ++++ ++ k
  gi|474934858|ref|YP_007688440.1|  4 EFRPMKLKDLKRVRELELSCIREYFAETIENKWEDFSQEWK 44
                                      788899******************************98766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1094.04
//
Query:       gi|474934859|ref|YP_007688441.1|  [L=589]
Description: arginyl-tRNA synthetase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.2e-37  127.6   0.3    9.2e-37  126.8   0.3    1.4  1  tRNA-synt_1d     tRNA synthetases class I (R)
    5.4e-25   87.9   0.1    1.1e-24   86.9   0.1    1.5  1  DALR_1           DALR anticodon binding domain
    4.3e-09   36.8   0.1    1.4e-08   35.2   0.1    1.9  1  Arg_tRNA_synt_N  Arginyl tRNA synthetase N terminal domain
    5.6e-05   22.2   0.0       0.15   10.9   0.0    2.3  2  tRNA-synt_1f     tRNA synthetases class I (K)
    0.00068   19.1   0.1     0.0013   18.2   0.1    1.4  1  tRNA-synt_1e     tRNA synthetases class I (C) catalytic domai
     0.0029   16.4   0.0       0.05   12.4   0.0    2.4  2  tRNA-synt_1g     tRNA synthetases class I (M)
  ------ inclusion threshold ------
      0.024   12.9   0.1      0.056   11.7   0.1    1.5  1  tRNA-synt_1      tRNA synthetases class I (I, L, M and V)


Domain annotation for each model (and alignments):
>> tRNA-synt_1d  tRNA synthetases class I (R)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.8   0.3   3.6e-40   9.2e-37      11     349 .]     106     462 ..      96     462 .. 0.84

  Alignments for each domain:
  == domain 1  score: 126.8 bits;  conditional E-value: 3.6e-40
                                       TT.---SST-EEEEE----BTTS--BHHHHHHHHHHHHHHHHHHHCT-EEEEEE--B-SSTCHHHHHHHHHHHTTTT CS
                      tRNA-synt_1d  11 klqkksrekkkvvvdfssPniakemhvGhLrstiiGdavsrlleflGydvirlnhvGDWGtqfGlLiaylekkqdek 87 
                                        ++k ++   +v v+++s n   ++hvG  r  iiGd+++r l + G+dv+   +v D G+q   L+ ++ + ++e+
  gi|474934859|ref|YP_007688441.1| 106 DFGKSAPTGIRVNVEHTSTNPTGPVHVGRARNPIIGDTLARCLRMRGHDVTTEYYVNDVGKQVVTLAWGVANVTEEE 182
                                       5566677777899**************************************************99998888888777 PP

                                       TTS-----S.............CCCHHHHHHHHCCCSHC.............CCHHHHHHHHHHHCT-HHHHHHHHH CS
                      tRNA-synt_1d  88 llqeqelqd.............Leafykeakkdydeeei.............faerarnyvvkLqsgdedirklwkl 138
                                       +   qe+++             L   y+ a k+     i             ++++  +++ ++++gd ++     +
  gi|474934859|ref|YP_007688441.1| 183 VE--QEIAEtntaderdkvdhrLVYNYRVATKK-----IhgnaekgipanpeLEGQIADMMRRFENGDREVIDYVGK 252
                                       44..44433000001111111233334444444.....144444799***99******************9999999 PP

                                       HHHHHHHHHHHHHHHCT---EC.--CC..CCCCCHHHHHHHHHCTT-E.EECTTCEEEEECCC...TSSCCEECC-T CS
                      tRNA-synt_1d 139 lvditrtelqklydrldvtlie.rGes..lykeslneivkelkkkglv.kesdGalvvfldef...gkrlgvvvqks 208
                                       +   +    +++ ++++v+l +   es  +     ++iv +l +  ++ + +dGa  v+l++f   gk+   +  + 
  gi|474934859|ref|YP_007688441.1| 253 VARTMLGGINETLAAMNVALDKyTWESaiIAGGAAKDIVSKLDASKYAgQSEDGAHFVDLKDFgihGKNTKFTYTRA 329
                                       999999999***********888789987788999********9998847789**********999999999***** PP

                                       TS-B-HHHHHHHHHHHHHHTT--SEEEEEEECCCHHHHHHHHHHHHCTTSSTTTSEEEEEEE--EE-TTSSBSBCSS CS
                      tRNA-synt_1d 209 DGgylytttDiaaakerkeelkadkvlyvidsrqslhlqqiflilkkigyvpeskdlehanfGmvlgkdkkkfktrk 285
                                       DG++lytt+D+a   ++    + d+++ v+ + q+l  qq+ ++l  +g +    +l++a   +     + +++trk
  gi|474934859|ref|YP_007688441.1| 330 DGTTLYTTRDLAYHEDKF--SRSDRIIDVLGEDQKLGSQQLCAALEIMGEQKRPEPLFYAFVSLP----EGRMSTRK 400
                                       ***********9877655..579**************************8777888887765555....668***** PP

                                       STC-BHHHHHHHHHHHHHHHHCCCCCCTS-CCCCHCHHHHHHHHHHHHCCCCTS-TTS-EE--H CS
                      tRNA-synt_1d 286 GetvkLadlLdealeralqlikeknkdkvlqadelekvaeavgvgaikyaDlsknrindyifdw 349
                                       G +v L+dl+dea +ra + ik + +d  l+ +++  +a a+gvga++y+ ++    ++++f+w
  gi|474934859|ref|YP_007688441.1| 401 GVVVYLDDLIDEATDRAYEEIKKRRND--LSEEKMRTIARAIGVGAVRYNIVKVGADKQFVFKW 462
                                       **********************99999..999******************99999999999998 PP

>> DALR_1  DALR anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.9   0.1   4.2e-28   1.1e-24       1     119 []     476     589 .]     476     589 .] 0.94

  Alignments for each domain:
  == domain 1  score: 86.9 bits;  conditional E-value: 4.2e-28
                                       HHHHHHHHHHHHHHTTCTTCCCCHCCHCCS-SHHHHHHHHHHHTHHHHHHHHHHHT-THHHHHHHHHHHHHHHHHHH CS
                            DALR_1   1 vqyahaRiksilrkaeeegekleeealalleeeeekeLlkalaqfpevleeaaeelephklaeylyeLaatfhkfYn 77 
                                       +qy haR++sil ka++ +   +++ ++l ++e e +L+k la+++ +l+++ e+ +++ +  y +e+aa+f++fY 
  gi|474934859|ref|YP_007688441.1| 476 LQYVHARACSILAKAGDFQ--RDTDGSKL-TDEFEVKLAKVLAKYEGILKQIDETKKVNLMPAYGHEVAAAFNQFYV 549
                                       6************999655..55666666.99********************************************* PP

                                       HCTSTTSCTHHH.HHHHHHHHHHHHHHHHHHHHTT----S-- CS
                            DALR_1  78 kervlkeeeeelaaaRLaLvkavrqvLangLdlLGieapekm 119
                                       +++vl++ ++  ++aRL Lv++++ vLa+ Ld+LG+eape+m
  gi|474934859|ref|YP_007688441.1| 550 NVNVLNSGDA--KNARLTLVECTKFVLASVLDCLGMEAPEEM 589
                                       *****99998..48***************************9 PP

>> Arg_tRNA_synt_N  Arginyl tRNA synthetase N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.1   5.5e-12   1.4e-08       4      84 ..      12      86 ..       9      87 .. 0.86

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 5.5e-12
                                      HHHHHHHHHHHHSS-HHHHGGG-E-.SSGGG-SEEEEGGGG--TT-..-HHHHHHHHHHT---TTT.EEEEEEETT.EE CS
                   Arg_tRNA_synt_N  4 keaiaealkkaagadleeeeiviekpknpkfGDyatnvamqlakklkknPreiAeeiaekleksei.iekvevagpGFi 81
                                      ++a+ +al+++ g   ++  ++i k   p+ +D+a++ +++++k+lk++P +iAeeia++++ + + i+ +++   G++
  gi|474934859|ref|YP_007688441.1| 12 EDAVVKALADM-G---APAGLKIVK-EIPDNADLAIP-CFTFSKALKNAPVKIAEEIASRIQVPCGlIAGLTALN-GYL 83
                                      67888999999.3...344456665.89*********.8*************************999****9977.9** PP

                                      EEE CS
                   Arg_tRNA_synt_N 82 Nff 84
                                      Nf+
  gi|474934859|ref|YP_007688441.1| 84 NFT 86
                                      **7 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0     6e-05      0.15      29      71 ..     122     164 ..     108     187 .. 0.90
   2 !    8.9   0.0   0.00025      0.63     249     297 ..     364     411 ..     353     423 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6e-05
                      tRNA-synt_1f  29 sGispSGliHiGnlrevltadlvaralrkrgeevrlilisDdm 71 
                                       + + p G++H+G++r+ + +d +ar lr rg++v + ++++d+
  gi|474934859|ref|YP_007688441.1| 122 TSTNPTGPVHVGRARNPIIGDTLARCLRMRGHDVTTEYYVNDV 164
                                       66789****************************9988887776 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00025
                      tRNA-synt_1f 249 gSvdvsskiaeilggeaPekvvYelillkggekmssSkGnvltledwle 297
                                       gS ++ +++  + + ++Pe++ Y++++l +g  ms  kG+v+ l+d+++
  gi|474934859|ref|YP_007688441.1| 364 GSQQLCAALEIMGEQKRPEPLFYAFVSLPEG-RMSTRKGVVVYLDDLID 411
                                       55555555443445678************99.9***********99886 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   4.9e-07    0.0013      23     139 ..     130     318 ..     120     347 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4.9e-07
                                       -BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-............................ CS
                      tRNA-synt_1e  23 shlGhaRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeks............................ 71 
                                       +h+G+aR+ ++ D l+r+l+++g+dv+    v D+  ++++ a    +                             
  gi|474934859|ref|YP_007688441.1| 130 VHVGRARNPIIGDTLARCLRMRGHDVTTEYYVNDVGKQVVTLAWGVANVteeeveqeiaetntaderdkvdhrlvyn 206
                                       7***************************************9998766665677888888888888888888888888 PP

                                       ...........................................HHHHHHHHHHHHHHHHHHTT----SB--BGGGGH CS
                      tRNA-synt_1e  72 ...........................................vkelaekfieefkkdleaLnvlkptleprvsekv 105
                                                                                  v ++a ++    ++ l+a+nv   +++   s  +
  gi|474934859|ref|YP_007688441.1| 207 yrvatkkihgnaekgipanpelegqiadmmrrfengdrevidyVGKVARTMLGGINETLAAMNVALDKYTWE-SAII 282
                                       888888888888888888888888888888888888888888888888888888888888888877554433.3333 PP

                                       H..HHHHHHHHHHHTTSEEE-TTS-EEE-GGG-TTT CS
                      tRNA-synt_1e 106 d..eiielvekliekgyaYavsdgdvyfdvskkeeY 139
                                       +  +  ++v kl +  ya +++dg    d +++  +
  gi|474934859|ref|YP_007688441.1| 283 AggAAKDIVSKLDASKYAGQSEDGAHFVDLKDFGIH 318
                                       312677888888888888888887777766655555 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   1.9e-05      0.05      11      43 ..     127     159 ..     120     231 .. 0.79
   2 ?    1.1   0.0     0.051   1.3e+02     319     345 ..     387     413 ..     334     419 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.9e-05
                                       SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEE CS
                      tRNA-synt_1g  11 ngklHlGhllevisaDifaRykrlrgeevlfvc 43 
                                       +g++H+G +++ i++D +aR  r+rg++v+   
  gi|474934859|ref|YP_007688441.1| 127 TGPVHVGRARNPIIGDTLARCLRMRGHDVTTEY 159
                                       699*************************97544 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.051
                                       --EEE--------------HHHHHHHH CS
                      tRNA-synt_1g 319 eyltvegkKlSkSrgvvvkakealerl 345
                                        ++ + ++++S+ +gvvv+ ++++++ 
  gi|474934859|ref|YP_007688441.1| 387 AFVSLPEGRMSTRKGVVVYLDDLIDEA 413
                                       5899999**************999874 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   2.2e-05     0.056      33      66 ..     125     158 ..     119     219 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.2e-05
                       tRNA-synt_1  33 yvtGslHiGhalaktlkdivirykrmkGkevlyv 66 
                                       + tG +H+G a + ++ d++ r  rm+G++v+  
  gi|474934859|ref|YP_007688441.1| 125 NPTGPVHVGRARNPIIGDTLARCLRMRGHDVTTE 158
                                       679**************************98754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (589 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.69u 0.27s 00:00:00.96 Elapsed: 00:00:00.48
# Mc/sec: 3700.39
//
Query:       gi|474934860|ref|YP_007688442.1|  [L=411]
Description: peptide chain release factor subunit 1 (aeRF-1) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-38  131.1   0.0    5.3e-38  130.3   0.0    1.3  1  eRF1_2          eRF1 domain 2
    8.3e-27   93.9   0.0    2.7e-26   92.3   0.0    1.9  2  eRF1_3          eRF1 domain 3
      2e-10   41.1   0.0    3.6e-10   40.2   0.0    1.4  1  acVLRF1         Actinobacteria/chloroflexi VLRF1 release fact
    6.4e-09   35.9   0.0    9.7e-09   35.3   0.0    1.3  1  eRF1_1          eRF1 domain 1
      6e-08   33.0   0.0    1.2e-07   32.0   0.0    1.6  1  baeRF_family10  Bacterial archaeo-eukaryotic release factor f
  ------ inclusion threshold ------
      0.026   15.3   0.7      0.058   14.1   0.7    1.5  1  ATPase-cat_bd   Putative metal-binding domain of cation trans
      0.044   13.9   3.9       0.17   12.1   3.9    2.0  1  Zn-ribbon_8     Zinc ribbon domain


Domain annotation for each model (and alignments):
>> eRF1_2  eRF1 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.3   0.0   2.1e-41   5.3e-38       2     131 ..     143     272 ..     142     274 .. 0.96

  Alignments for each domain:
  == domain 1  score: 130.3 bits;  conditional E-value: 2.1e-41
                                       EEEEEEETTEEEEEEEESSCEEEEEEEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTTES CS
                            eRF1_2   2 vglivldegeAtigllkgsrtevlkkievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaankafllvdkdklk 78 
                                       +gliv+d++eAtig+l g++++vlk+ ++ vP Kh++Ggqs+ rfeRl+e +++ef+kkva+  ++ fl   + +l+
  gi|474934860|ref|YP_007688442.1| 143 YGLIVIDRKEATIGMLAGTTIKVLKHYDSLVPSKHHQGGQSSVRFERLIEIAAHEFFKKVADGCTTCFL-DSILDLE 218
                                       89*******************************************************************.489**** PP

                                       EEEEEESSTHHHHHHHHHHHHHHHHTCCEE.EEE-S-TSCHHHHHHHHCCHHHH CS
                            eRF1_2  79 giilagpgfvkeefldkdlldaelkkkvik.lvdvsyggesglnevlekaaevl 131
                                       gi+++gpg +k+ f+++d+l++el kkv+k  +d++y++esgl+e++++ + ++
  gi|474934860|ref|YP_007688442.1| 219 GILVGGPGMTKDFFINNDYLHHELLKKVVKpFFDTGYTDESGLKELVDAGQGAI 272
                                       ****************************9999***************9877665 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.7   4.4e+03      49      75 ..      48      76 ..      15     106 .. 0.61
   2 !   92.3   0.0     1e-29   2.7e-26       1     113 []     277     410 ..     277     410 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.7
                                      TSSSH.HHHHS-HHH-HHHHHH.HHHHHH CS
                            eRF1_3 49 rsrdt.lkekvketgeelelve.lieelv 75
                                      + rd+  + +  ++ ++++ v+ +i++++
  gi|474934860|ref|YP_007688442.1| 48 YLRDEqGQASNIKSKTTMKNVTsAIDSIM 76
                                      33333222222222222333333333333 PP

  == domain 2  score: 92.3 bits;  conditional E-value: 1e-29
                                       HHHHHHHHHHHHHHHHC.TCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSHHHHHS.................- CS
                            eRF1_3   1 liqekklleefleelak.dtgkavYGveevlkalemgAvetLLvseelersrdtlkekv.................k 59 
                                       + qek++++++++e++k d+g+ +YG++ v++++ mgAv+t L+s  l+++r + +++                  +
  gi|474934860|ref|YP_007688442.1| 277 ITQEKEMVQRLFREIRKsDGGLSAYGEDMVRRCADMGAVDTFLISSMLRKYRCQCQCNNghsfavtvddpendvvcP 353
                                       579**************9*********************************988555558****************9 PP

                                       HHH-HHHHHH...HHHHHHHHHHHTT-EEEEE-TTSHHHHHHHHHTTTEEEEESS-- CS
                            eRF1_3  60 etgeelelve...lieelvenveesgakveiisseseeGeqlvkafgGiaaiLRykv 113
                                       e++++++++e   l++++ e+ e+++ ++++is +seeGe+l++afgGiaa+LRy++
  gi|474934860|ref|YP_007688442.1| 354 ECNAKAKVLEskdLVDDFFEMSETYNSNMQLISGDSEEGEMLLRAFGGIAALLRYRI 410
                                       ***999999999*******************************************96 PP

>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.0   1.4e-13   3.6e-10       4     123 ..     145     267 ..     141     272 .. 0.87

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 1.4e-13
                           acVLRF1   4 gvllvrrggfavgvveggelvaskvgtrdvqgrtaaGGwSqqRfaRrrenqadalleavaeaaarllaeesae...v 77 
                                       +++++r+ + ++g++ g+++   k+  + v +++ +GG+S  Rf+R +e  a + +++va+   + + +   +   +
  gi|474934860|ref|YP_007688442.1| 145 LIVIDRKEA-TIGMLAGTTIKVLKHYDSLVPSKHHQGGQSSVRFERLIEIAAHEFFKKVADGCTTCFLDSILDlegI 220
                                       345555555.*********************************************************9888888989 PP

                           acVLRF1  78 vlgGdrslvaevledar.laplatlareelldvpdprravLedavrr 123
                                       ++gG+  + + + ++    ++l + ++++++d++  +++ L++ v+ 
  gi|474934860|ref|YP_007688442.1| 221 LVGGPGMTKDFFINNDYlHHELLKKVVKPFFDTGYTDESGLKELVDA 267
                                       99999999999988855255688888889999999999999998876 PP

>> eRF1_1  eRF1 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.0   3.8e-12   9.7e-09       6     126 ..      20     134 ..      15     137 .. 0.91

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 3.8e-12
                                       E..CTBTTSCCEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH.......--CEEEEEEEEEEEEEEECTT... CS
                            eRF1_1   6 r..dlekdgsgsvtLipeddedlwhlynliapgdsvrastvrkvqresstgsreservklkLtikvekvdfdkd... 77 
                                       +   ++++g+++++++++  + +++++ ++++++++++++++k +          ++v++++ + + +++   +   
  gi|474934860|ref|YP_007688442.1|  20 ElrGFRGRGTELISVYVPYGKLISDVMAYLRDEQGQASNIKSKTTM---------KNVTSAIDSIMARLKTFDKipe 87 
                                       555899*************************************977.........9*************87777788 PP

                                       SSEEEEEEEEEEGGGG--TTSEEEEEE-TTSEEEEEECE.ESHHHHHHHH CS
                            eRF1_1  78 agvlrisGkvieenehvklgafhtldlelkrpftiikee.wdsfalerLk 126
                                       +gv+ ++G+v    +   +++++ +++++++p+t + ++ +  f +++L+
  gi|474934860|ref|YP_007688442.1|  88 NGVVIFCGEVPRAGD---QTKMVQYTIQPPEPITAFLYRcDAAFFTDPLD 134
                                       ***************...89*****************9989999999987 PP

>> baeRF_family10  Bacterial archaeo-eukaryotic release factor family 10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.0   4.9e-11   1.2e-07       4     119 ..     131     249 ..     129     267 .. 0.85

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 4.9e-11
                    baeRF_family10   4 apLlealdeyerygvvlvdreraRlfevylgeleeveevegevpgrtktggwksqdrfqrreeeqaerhlkevAell 80 
                                        pL   l + + yg++++dr++a +   ++  ++  ++  + vp ++++gg+ s  rf+r  e  a++++k+vA+  
  gi|474934860|ref|YP_007688442.1| 131 DPLDVMLVDKRFYGLIVIDRKEATIGMLAGTTIKVLKHYDSLVPSKHHQGGQ-SSVRFERLIEIAAHEFFKKVADGC 206
                                       577778889999****************************************.************************ PP

                    baeRF_family10  81 aklleerg..verlvlgGdeeetaal..ldrlpkalrarvvgt 119
                                       +  + ++   +e +++gG+   ++ +   d l+ +l ++vv +
  gi|474934860|ref|YP_007688442.1| 207 TTCFLDSIldLEGILVGGPGMTKDFFinNDYLHHELLKKVVKP 249
                                       **99999767999999999665555523455777777777666 PP

>> ATPase-cat_bd  Putative metal-binding domain of cation transport ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.7   2.2e-05     0.058       3      53 ..     327     378 ..     326     395 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.2e-05
                     ATPase-cat_bd   3 yHCglpveesaklkaeiegeerefCCkGCqavaqliveagl.esyYklrtek 53 
                                       y C+ ++++++++ +++++ e+++ C+ C+a a+++ +++l ++++++ ++ 
  gi|474934860|ref|YP_007688442.1| 327 YRCQCQCNNGHSFAVTVDDPENDVVCPECNAKAKVLESKDLvDDFFEMSETY 378
                                       56*************************************9835677655543 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   3.9   6.5e-05      0.17       6      36 ..     327     359 ..     326     361 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.5e-05
                       Zn-ribbon_8   6 YrCee.Cghefevlqsisdaplta.CPeCgsev 36 
                                       YrC+  C++ +   ++++d+++ + CPeC++++
  gi|474934860|ref|YP_007688442.1| 327 YRCQCqCNNGHSFAVTVDDPENDVvCPECNAKA 359
                                       8877667777777777889998888****9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       836  (0.0466284); expected 358.6 (0.02)
Passed bias filter:                      671  (0.0374254); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2701.60
//
Query:       gi|474934861|ref|YP_007688443.1|  [L=229]
Description: putative uridylate kinase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    9.5e-25   87.6   5.1    6.4e-24   84.9   5.1    1.9  1  AA_kinase  Amino acid kinase family


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.9   5.1   3.6e-28   6.4e-24       2     241 .]       5     205 ..       4     205 .. 0.92

  Alignments for each domain:
  == domain 1  score: 84.9 bits;  conditional E-value: 3.6e-28
                                       EEEEEE-TTCCC.CTCC.HHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC....E..HHHHHH CS
                         AA_kinase   2 rvVvKlGGsslt.dkee.aslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaaglrstleeagev 76 
                                       +vV+ +GGs+l  d+++  ++ +lae + ++ e++ +++vV+Ggg++++ +++  +gl  +e ++            
  gi|474934861|ref|YP_007688443.1|   5 KVVISIGGSILIpDNDDaVFIGKLAEMLLRA-EKKVDIAVVVGGGKIARYYSNTGRGLGGNEDQL------------ 68 
                                       79*******666477778*************.**********************99999999985............ PP

                                       HHHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTT CS
                         AA_kinase  77 atrdalaslgerlvaallaaglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfigldeeg 153
                                          d l++ ++rl+aalla +l +v+    +l++++                      ++ g ++v++g    +e+g
  gi|474934861|ref|YP_007688443.1|  69 ---DTLGIGATRLNAALLALALGDVSSMKIPLTVRDSAS------------------KFAPGRIVVMGG----TEPG 120
                                       ...*******************99998888888765444..................568899******....6799 PP

                                       EEEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH.CSSS.TTTHHHHCHHHHHHH CS
                         AA_kinase 154 elgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaee.saselatgGmkvkhpaalaa 229
                                       +    ++D +aa+lA+++gA +++++t+Vd Vy++dp+k+pda+++++++++++++ +    + g   v++p  +++
  gi|474934861|ref|YP_007688443.1| 121 H----TTDAVAAMLAKEIGAARVVNATSVDAVYSDDPRKNPDAVKYDRLTIEQLDAlVYHDHGAGKSSVFDPLGVQI 193
                                       8....9***************************************************99999*************** PP

                                       HHCTT-EEEEEE CS
                         AA_kinase 230 arrggipvvItn 241
                                       a++++i+++ +n
  gi|474934861|ref|YP_007688443.1| 194 AKENKIDIMMVN 205
                                       ******998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1609.69
//
Query:       gi|474934862|ref|YP_007688444.1|  [L=281]
Description: archaeal conserved hypothetical protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      8e-65  218.2   0.0    9.9e-65  217.9   0.0    1.1  1  tRNA_deacylase  D-aminoacyl-tRNA deacylase


Domain annotation for each model (and alignments):
>> tRNA_deacylase  D-aminoacyl-tRNA deacylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  217.9   0.0   5.5e-69   9.9e-65       3     204 ..      68     268 ..      66     269 .. 0.95

  Alignments for each domain:
  == domain 1  score: 217.9 bits;  conditional E-value: 5.5e-69
                                       ---SEEEEEEEEE-TT---EEEEE--B-SS--TTSS-TT-B--B-HHHHHHHHHHHHGGGGGSTT-EEEE--S-SS- CS
                    tRNA_deacylase   3 edvdliiflSrHssesgkplLTvHvtGnlgeaelGGkpeelapaaPrllkallralkkiaekleefevtlEatHHGP 79 
                                        ++d++if S H+s+sg p+LTvH++Gn++ ++lGG+++ela+++P++++ +lr +k+ + +l+ef++++EatHHGP
  gi|474934862|ref|YP_007688444.1|  68 FTPDVVIFPSEHASTSGMPALTVHPMGNFNGNDLGGNERELAIPCPAMMTDCLRMIKERC-TLPEFNICFEATHHGP 143
                                       579*********************************************************.**************** PP

                                       ----S-EEEEEEEESHHHHT-HHHHHHHHHHHHHHHH------EEEEEE-S-TT-HHHHHHHHHBSEEEEEEE-GGG CS
                    tRNA_deacylase  80 telkvPslFvEiGSteeeWkdedaaeavaeavlelleseeekekvlvgiGGgHYaprftklvletevavGhilskya 156
                                       + +++Ps+F+EiGS+e++W ++daae++a+++ ++ e++  + +++vg+GGgHYaprft+l+l+ +v+++h+l++y+
  gi|474934862|ref|YP_007688444.1| 144 F-VDTPSFFIEIGSDENYWPRKDAAELLASVIRDVPETN--DYPAVVGFGGGHYAPRFTELALSYKVNFAHMLPNYQ 217
                                       *.*********************************7777..9**********************************9 PP

                                       GGG--HH....HHHHHHHHH.T-SEEEE-TTT--HHHHHHHHHHHHHHT-EE CS
                    tRNA_deacylase 157 leelkee....vikqaleksegadvalidkkslkseqkeaieelleelgiev 204
                                           ++e    +ik a+++s g+++ +i++ks+k+ + ++++el e+ g e+
  gi|474934862|ref|YP_007688444.1| 218 WMGHDDEdiarMIKLAIDRS-GTKLSFIHRKSMKGMEAQKLRELGESVGAEW 268
                                       99999996666777777777.***************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       224  (0.0124937); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2014.31
//
Query:       gi|474934863|ref|YP_007688445.1|  [L=361]
Description: hypothetical protein TALC_01303 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0043   17.2   0.4      0.028   14.6   0.1    2.4  2  DUF3175   Protein of unknown function (DUF3175)
     0.0073   16.8   0.1        3.3    8.3   0.0    2.8  2  TPR_19    Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.013   16.0   0.0       0.35   11.5   0.0    2.3  2  UAE_UbL   Ubiquitin/SUMO-activating enzyme ubiquitin-like dom
      0.023   14.8   0.0        1.5    9.2   0.0    2.8  2  TPR_2     Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> DUF3175  Protein of unknown function (DUF3175)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.45     2e+03      41      80 ..     206     247 ..     194     251 .. 0.69
   2 !   14.6   0.1   6.3e-06     0.028      23      66 ..     312     355 ..     302     358 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.45
                           DUF3175  41 rRkaepfrsamsmLtfyinRagknLske..rrkiLekakdeL 80 
                                        R +e+ + a  ++ f + R    L +   r + Le a ++L
  gi|474934863|ref|YP_007688445.1| 206 GRTTEAKHYASTLMEFDVGRGTTLLARAelRESHLESATKNL 247
                                       566666667777888999998888865422677888888776 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 6.3e-06
                           DUF3175  23 ddpkkiakslkrsaekskrRkaepfrsamsmLtfyinRagknLs 66 
                                       ddp++i   +  s  +s+ R+     sams+   y   +gknL 
  gi|474934863|ref|YP_007688445.1| 312 DDPTAIMYIMDASKASSEYRRKMMISSAMSLCELYGQTTGKNLI 355
                                       89****************************************96 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   0.0    0.0048        22      32      57 ..     199     224 ..     186     233 .. 0.80
   2 !    8.3   0.0   0.00074       3.3      28      55 ..     260     287 ..     234     302 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0048
                            TPR_19  32 AeallalgqldeAealLdalpeedpd 57 
                                       Ae+ +++g+++eA+   ++l+e d  
  gi|474934863|ref|YP_007688445.1| 199 AELAIETGRTTEAKHYASTLMEFDVG 224
                                       9*************988888887655 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00074
                            TPR_19  28 rllLAeallalgqldeAealLdalpeed 55 
                                       ++  Ae ++a g+l++A + Lda+ +  
  gi|474934863|ref|YP_007688445.1| 260 LITCAESMFAHGNLEKASEYLDAARDRL 287
                                       4568999****************98865 PP

>> UAE_UbL  Ubiquitin/SUMO-activating enzyme ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   7.8e-05      0.35      33      70 ..      17      54 ..      12      58 .. 0.84
   2 ?    1.8   0.0     0.083   3.7e+02      44      75 ..     206     237 ..     191     241 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.8e-05
                           UAE_UbL 33 ggatilYlsseedeeeddnldkkLaelgikngsiLtvd 70
                                      + +++ Y  ++ + +e++nl+k L++ gi ++siL++d
  gi|474934863|ref|YP_007688445.1| 17 HSKRLAYSLTSMGRQEASNLKKQLESDGIDHDSILNID 54
                                      667777844567788999*****************997 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.083
                           UAE_UbL  44 edeeeddnldkkLaelgikngsiLtvdDfsqe 75 
                                       +  +e++ +  +L e+++  g++L + ++  e
  gi|474934863|ref|YP_007688445.1| 206 GRTTEAKHYASTLMEFDVGRGTTLLARAELRE 237
                                       5668899999**************99888766 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.047   2.1e+02       4      26 ..     195     217 ..     193     222 .. 0.83
   2 ?    9.2   0.0   0.00032       1.5       2      27 ..     258     283 ..     257     286 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.047
                             TPR_2   4 lynlGlayyklgdyeeAleafek 26 
                                       l  +++++++ g+  eA+++   
  gi|474934863|ref|YP_007688445.1| 195 LSLQAELAIETGRTTEAKHYAST 217
                                       6788999***********99766 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00032
                             TPR_2   2 ealynlGlayyklgdyeeAleafekA 27 
                                       ++l   +++ ++ g++e+A e++++A
  gi|474934863|ref|YP_007688445.1| 258 DYLITCAESMFAHGNLEKASEYLDAA 283
                                       6788999****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2671.26
//
Query:       gi|474934864|ref|YP_007688446.1|  [L=509]
Description: phenylalanyl-tRNA synthetase, alpha subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.2e-86  287.8   0.0    8.2e-86  287.5   0.0    1.1  1  tRNA-synt_2d     tRNA synthetases class II core domain (F)
    2.3e-07   30.5   0.0    2.7e-05   23.7   0.0    2.2  2  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
    2.7e-05   23.4   0.0     0.0014   17.8   0.0    2.4  2  tRNA-synt_2      tRNA synthetases class II (D, K and N)
     0.0029   17.6   0.0     0.0082   16.1   0.0    1.7  2  tRNA-synt_2b     tRNA synthetase class II core domain (G, H, 


Domain annotation for each model (and alignments):
>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  287.5   0.0   1.8e-89   8.2e-86       2     244 ..     236     505 ..     235     506 .. 0.98

  Alignments for each domain:
  == domain 1  score: 287.5 bits;  conditional E-value: 1.8e-89
                                       .-TSSCTSCTSHSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-.. CS
                      tRNA-synt_2d   2 idvtlpgkrieagklhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpeka.. 76 
                                       +d t +++ ++a+k++plt++ ++i+++f+e+gf+e+++++v+  f+n d+L++pqdhpaRdmqdtF+l++p+++  
  gi|474934864|ref|YP_007688446.1| 236 YDYTTFAPAVYAAKKNPLTRLGNDIRRMFIEMGFTEMTSEYVQPAFWNMDCLFIPQDHPARDMQDTFFLDNPKRIdl 312
                                       8999999**************************************************************999999** PP

                                       ...............................ECESEEE-SSTHHHHHHHH.TTS-SSEEEEEEEEEEBSST-SSSB- CS
                      tRNA-synt_2d  77 ...............................veekllLRthttavqirtl.ekkkppikiisigrvfRrdavDathl 121
                                                                      ++++ lLRth t+ ++r+l +++++p+k +si r+fR++++Dathl
  gi|474934864|ref|YP_007688446.1| 313 kdcalvqkvkeiqlnggdtgstgwggewsveKASQALLRTHSTCSSVRYLaAHPDAPQKAFSISRIFRKESIDATHL 389
                                       ******************************9899****************88889********************** PP

                                       SEEEEEEEEEEETT--HHHHHHHHHHHHHHHCTSTEEEEEEECEETTEEEEEEEEEEECCSSSSEEEEEEEEEE-HH CS
                      tRNA-synt_2d 122 aeFhqveglvvdenvsladlkgvleellkklfgaevkvrfrpsyfpftePsaevdvylvekkkkwlEllgaGmvrpe 198
                                       +eF q+eg+++den +l+ l+++++e+++++ g++ k+ +rpsyfp+tePs+e++v++   ++kwlEl+gaG++rpe
  gi|474934864|ref|YP_007688446.1| 390 PEFSQIEGIIIDENANLDMLIAIIREFYSRM-GFD-KIHVRPSYFPYTEPSLEFEVFF---NGKWLELGGAGIFRPE 461
                                       *******************************.***.**********************...9*************** PP

                                       HHHHTT-.TTSEEEEEEEEHHHHHHHHHT-SSGHHHHTT.HHHHGG CS
                      tRNA-synt_2d 199 vleavgideevsgfafGlGveRlamlkygieDiRelvendlrflrq 244
                                       vl+++g+  +++++a+G+G+eRlamlk +i+DiR+l+  d++flr+
  gi|474934864|ref|YP_007688446.1| 462 VLAPFGV--KYPVLAWGFGFERLAMLKWNIKDIRDLYIADIDFLRK 505
                                       *******..**********************************986 PP

>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.5   0.0    0.0047        21      12      39 ..     247     274 ..     239     312 .. 0.82
   2 !   23.7   0.0     6e-09   2.7e-05      85     209 ..     358     474 ..     345     478 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0047
                   tRNA_synthFbeta  12 egelnkeqklrrklrdllagaGlnEvit 39 
                                       ++++n+  +l + +r++ +++G++E+ +
  gi|474934864|ref|YP_007688446.1| 247 AAKKNPLTRLGNDIRRMFIEMGFTEMTS 274
                                       44589********************864 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 6e-09
                   tRNA_synthFbeta  85 vlarNlargnedvrlFEigkvflkd.seeelpeeerhlaivltgkreeeswsekaravdfydlkgivealleslgie 160
                                        +++  a+     ++F i+++f+k+  + +   e +++ +++  ++           ++   l +i++++ +++g++
  gi|474934864|ref|YP_007688446.1| 358 SVRYLAAHPDAPQKAFSISRIFRKEsIDATHLPEFSQIEGIIIDEN-----------ANLDMLIAIIREFYSRMGFD 423
                                       56666777788899***********867788999************...........9******************* PP

                   tRNA_synthFbeta 161 kvefepaehpalhpgrsAeikvdgk..evGvlGelhpevleafdlkqrvyv 209
                                       k++++p+  p+ +p    e+ ++gk  e+G +G + pevl+ f++k++v +
  gi|474934864|ref|YP_007688446.1| 424 KIHVRPSYFPYTEPSLEFEVFFNGKwlELGGAGIFRPEVLAPFGVKYPVLA 474
                                       *************************9*********************9976 PP

>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0     3e-07    0.0014      91     119 ..     369     396 ..     354     427 .. 0.80
   2 ?    2.8   0.0     0.011        51     287     307 ..     475     495 ..     468     497 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3e-07
                                       HSEEEEEEEEE--S--BTTB-S-CEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  91 idrvfqiaraFRaEdsrtdrhlaEFtqie 119
                                        ++ f+i+r FR+E++++++ + EF qie
  gi|474934864|ref|YP_007688446.1| 369 PQKAFSISRIFRKESIDATHLP-EFSQIE 396
                                       5799******************.****98 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.011
                                       EEEEHHHHHHHHCT-SSGGGC CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 287 lglGldRlvmlllgsesIrdv 307
                                       +g+G++Rl ml  + ++Ird+
  gi|474934864|ref|YP_007688446.1| 475 WGFGFERLAMLKWNIKDIRDL 495
                                       79*****************97 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.97   4.4e+03     105     155 ..      50      98 ..      36     109 .. 0.76
   2 !   16.1   0.0   1.8e-06    0.0082      35     134 ..     368     455 ..     350     470 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.97
                                       GTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b 105 msaksadykdkkefeavsesltkgieigtiqklgtrlserlgatvldennr 155
                                       m+  sa+  ++k + a+ e+++k+  ++ +++  ++l+er  ++++d ++ 
  gi|474934864|ref|YP_007688446.1|  50 MG--SASWLQSKGLAAIREESRKFYALSDVEESRKGLPERKALKAIDAAGG 98 
                                       44..45667788888999999999999999999899999888888777665 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.8e-06
                                       SSEEEEEEEEEEBTTTS.TBCTTTB-SEEEEEEEEEEESGGGHHHHHHHHHHHHHHHHHHTT.SCEEEEEEGTTSCB CS
                                       xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  35 LPlklyqiqtkyRdEks.dsrGLlRvreFhqkdgyvfhaeaslddslrdlikaisriferlglefraiielmsaksa 110
                                        P+k + i++++R+E   +++    + eF q +g ++  +a     l  li  i ++++r+g+ + +++ +     +
  gi|474934864|ref|YP_007688446.1| 368 APQKAFSISRIFRKESIdATH----LPEFSQIEGIIIDENA----NLDMLIAIIREFYSRMGFDKIHVRPSYF---P 433
                                       59*************983444....56**********9988....566789999**********999999966...4 PP

                                       TTSEEEEEEEEETTTSEEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b 111 dykdkkefeavsesltkgieigti 134
                                         ++++efe+ ++  +k +e+g +
  gi|474934864|ref|YP_007688446.1| 434 YTEPSLEFEVFFN--GKWLELGGA 455
                                       589*********9..888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (509 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 3507.38
//
Query:       gi|474934865|ref|YP_007688447.1|  [L=373]
Description: tryptophanyl-tRNA synthetase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      4e-25   88.7   0.0    1.7e-24   86.6   0.0    1.9  1  tRNA-synt_1b  tRNA synthetases class I (W and Y)
  ------ inclusion threshold ------
       0.13   12.6   0.3        0.3   11.4   0.3    1.6  1  Kelch_3       Galactose oxidase, central domain
        0.2   12.4   0.1       0.44   11.3   0.1    1.5  1  DUF4666       Domain of unknown function (DUF4666)


Domain annotation for each model (and alignments):
>> tRNA-synt_1b  tRNA synthetases class I (W and Y)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.6   0.0   2.9e-28   1.7e-24       4     292 ..      70     349 ..      67     350 .. 0.87

  Alignments for each domain:
  == domain 1  score: 86.6 bits;  conditional E-value: 2.9e-28
                                       S--EEEEEEETSSS-BGGGHHHHHHHHHHHHTTSEEEEEEEHHHHHTTTTT..-SSHHHHHHHHHHHHHHHHHHHHH CS
                      tRNA-synt_1b   4 rplrvysGidPTgklHlGylvplkklvelqkaghevffliaDlhAiigdps..kaeerklrkreevlenaikaqlak 78 
                                       +++ +y+G  P+g+ HlG+++p     ++q+     +f +  l  +++d +   +++  + +r+  +ena    +a 
  gi|474934865|ref|YP_007688447.1|  70 NRFYIYTGRGPSGNTHLGHMMPWIFNKWIQD-----VFRVPMLFQMTDDEKflFKDLTLHDTRNMAYENA-LDFIAL 140
                                       67899*****************999999993.....3444445566666665444556677777777777.88**** PP

                                       TCHTTTEEEEETHHHHTTH.HHHHHHHHHHTTCBHHHHHHHHHCCHHCSSSC--BHHHHHHHHHHHHHHHHTCHS.. CS
                      tRNA-synt_1b  79 gldpekaevvlqsewlehl.elaellrdlgklgslnrmlqfksvkkrleegegislgeftYplLqaaDilllkad.. 152
                                       g+dp+ ++++l ++ +e+l  la  +++ +++ + + +  f       e+    ++g + +  + +a  +l      
  gi|474934865|ref|YP_007688447.1| 141 GFDPDTTKIILDTKNIETLyPLALEVAKKVTFSTAKAVFGFTG-----ES----NIGRIFFTTMESAPAFLPTIIeg 208
                                       *****************99888999999999999999999999.....44....68889999999999887665567 PP

                                       .....EEEEEGGGHHHHHHHHHHHHHHHHHSTTSS-EEEEET-BBSTTSSSBTTCETTCGC-BTTCCHHHHHHHHHH CS
                      tRNA-synt_1b 153 .....lvpgGsDQkqnielgrdlarrfnkkevfkkpegltvplltgldGekKmSKSagnsaIfLddekesvkkkiqk 224
                                            + p G DQ+ +++++rd+a+ +++     kp+ ++ ++ +gl+G+ KmS+S++ ++I+ +d +++vkkk+++
  gi|474934865|ref|YP_007688447.1| 209 kptkvMIPCGIDQDPHFRVTRDVAPGMGYP----KPSLIYCKMCPGLSGGDKMSSSDEMATIYTTDTPKQVKKKVGR 281
                                       78899**********************997....******************************************* PP

                                       CHCSTTC..SHHHHHHHHHTHHHCHHHHHHHHCCSEEESSHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH CS
                      tRNA-synt_1b 225 avtdsde..evekllklktelsnelierleavsgkkpkreaeellaeevtklvhggdlkkalaealnell 292
                                       a+t      e ++ + +++e++  ++++  ++ ++++  +++e++ +++++++ +g++k al++++n +l
  gi|474934865|ref|YP_007688447.1| 282 AFTGGCVsiEEQREKGGNPEVCA-VYKYNYYLFEHDD-AKLQEMADKCRRGEILCGECKVALTQKINVFL 349
                                       *****99899999**********.8887777777776.89**************************9988 PP

>> Kelch_3  Galactose oxidase, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3     5e-05       0.3       1      19 [.      69      87 ..      69      89 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5e-05
                           Kelch_3  1 gdrlyifGGlgddgqdrln 19
                                      g+r+yi++G+g++g+++l+
  gi|474934865|ref|YP_007688447.1| 69 GNRFYIYTGRGPSGNTHLG 87
                                      89**************987 PP

>> DUF4666  Domain of unknown function (DUF4666)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   7.3e-05      0.44      73     107 ..     221     256 ..     212     260 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.3e-05
                           DUF4666  73 aqrvfr.tkrvsPavdPpsPrvsacilCsifgkkgk 107
                                       ++ +fr t++v+P +  p P +  c +C  +++ +k
  gi|474934865|ref|YP_007688447.1| 221 QDPHFRvTRDVAPGMGYPKPSLIYCKMCPGLSGGDK 256
                                       5669999*********************88876554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 2207.12
//
Query:       gi|474934866|ref|YP_007688448.1|  [L=144]
Description: hypothetical protein TALC_01306 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 949.03
//
Query:       gi|474934867|ref|YP_007688449.1|  [L=370]
Description: hypothetical protein TALC_01307 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1208  (0.0673769); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.70u 0.30s 00:00:01.00 Elapsed: 00:00:00.52
# Mc/sec: 2156.29
//
Query:       gi|474934868|ref|YP_007688450.1|  [L=114]
Description: hypothetical protein TALC_01308 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 744.70
//
Query:       gi|474934869|ref|YP_007688451.1|  [L=503]
Description: putative rRNA pseudouridine synthase, putative/cytidylate kinase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-25   89.4   0.1    5.9e-22   78.6   0.1    3.3  1  TruB_N           TruB family pseudouridylate synthase (N term
    1.6e-21   76.2   0.2    4.7e-21   74.7   0.2    1.9  1  TruB_C_2         tRNA pseudouridylate synthase B C-terminal d
    9.8e-20   71.4   0.2    5.3e-18   65.8   0.2    2.3  1  Cytidylate_kin2  Cytidylate kinase-like family
    2.8e-18   65.6   0.3    5.8e-18   64.6   0.3    1.6  1  PUA              PUA domain
    6.8e-16   59.0   0.0    1.4e-15   58.0   0.0    1.5  1  AAA_18           AAA domain
    4.5e-14   53.0   0.5    1.5e-13   51.4   0.1    2.1  1  AAA_17           AAA domain
    1.8e-12   47.1   0.0    4.6e-12   45.8   0.0    1.7  1  DKCLD            DKCLD (NUC011) domain
      1e-11   45.0   3.5    5.6e-05   23.0   0.0    3.2  3  Cytidylate_kin   Cytidylate kinase
    2.3e-05   24.5   0.7    0.00056   20.0   0.7    2.5  1  ADK              Adenylate kinase
    4.4e-05   23.7   0.3     0.0015   18.7   0.3    2.5  1  AAA_33           AAA domain
    4.8e-05   23.5   2.1     0.0014   18.8   2.1    2.3  1  SKI              Shikimate kinase
    0.00018   21.2   0.5      0.022   14.5   0.1    2.3  2  Thymidylate_kin  Thymidylate kinase
    0.00022   21.5   0.1    0.00041   20.6   0.1    1.6  1  AAA_28           AAA domain
     0.0003   21.0   0.0      0.002   18.4   0.0    2.2  2  UPF0113          UPF0113 PUA domain
    0.00036   20.4   1.3       0.24   11.3   0.0    2.3  2  dNK              Deoxynucleoside kinase
     0.0024   17.8   0.1     0.0062   16.5   0.1    1.7  1  NTPase_1         NTPase
     0.0057   17.1   0.1      0.014   15.8   0.1    1.7  1  AAA              ATPase family associated with various cellul
  ------ inclusion threshold ------
      0.011   16.1   0.4      0.092   13.0   0.1    2.6  4  AAA_22           AAA domain
      0.013   15.9   0.0      0.026   14.9   0.0    1.5  1  AAA_16           AAA ATPase domain
      0.018   14.8   0.5       0.03   14.1   0.1    1.6  1  ATP_bind_1       Conserved hypothetical ATP binding protein
      0.034   14.1   0.0      0.077   12.9   0.0    1.5  1  Rad17            Rad17 P-loop domain
      0.092   12.5   0.4        1.2    8.8   0.1    2.2  2  PRK              Phosphoribulokinase / Uridine kinase family
      0.095   12.4   0.1       0.52   10.0   0.0    2.1  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
       0.11   12.9   0.0       0.22   12.0   0.0    1.5  1  RNA_helicase     RNA helicase
       0.11   12.1   0.1       0.19   11.3   0.1    1.4  1  SRP54            SRP54-type protein, GTPase domain
       0.12   12.0   0.4        2.3    7.9   0.2    2.5  2  AAA_30           AAA domain


Domain annotation for each model (and alignments):
>> TruB_N  TruB family pseudouridylate synthase (N terminal domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.6   0.1   8.6e-25   5.9e-22       2     149 .]     227     339 ..     226     339 .. 0.94

  Alignments for each domain:
  == domain 1  score: 78.6 bits;  conditional E-value: 8.6e-25
                                       HHTT-S-EEESS---TT-EEEEEEEEGGGGGGHHHCTTS-EEEEEEEEETEEETTSBTTS-EEE-.--TT--HHHHH CS
                            TruB_N   2 rllkakkvGhtGtLDplatGvLvvavgeaTklleylleadKeYeatirlgaetdteDaegeileeekveklteekle 78 
                                        +++++ vGh+GtLDp ++GvL++++g+a +l++++l++dKeY++ +rl+a+ +                  e++++
  gi|474934869|ref|YP_007688451.1| 227 SAIHMDSVGHGGTLDPYVSGVLPICTGKAVRLTDIVLSSDKEYICLMRLHADRS------------------EKQIR 285
                                       5678899******************************************98654..................45699 PP

                                       HHHHHC-EEE---------------------------------EEEEEEEEEEEEEEEEEEEEEESTTTTH CS
                            TruB_N  79 evlkkftGeieqvppmySAvkvnGkrlyelaregeeverkkrkvtiyelelleveepevelevecskGtYi 149
                                       e+++kf G+i+q pp+ SAvk                 r+ r  +++ele+le++ ++v ++++c +GtY+
  gi|474934869|ref|YP_007688451.1| 286 EAMSKFVGRIYQLPPVRSAVK-----------------RQLRIRRVRELEVLEINGRDVLFRISCDAGTYV 339
                                       9********************.................999*****************************8 PP

>> TruB_C_2  tRNA pseudouridylate synthase B C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.7   0.2   6.8e-24   4.7e-21       1      63 [.     340     405 ..     340     406 .. 0.94

  Alignments for each domain:
  == domain 1  score: 74.7 bits;  conditional E-value: 6.8e-24
                                       HHHHHHHHHHTTS-EEEEEEEEEEETTEGG-..B-HHHHHHHHHHHHT..--H.HHHHEEEGGGGG CS
                          TruB_C_2   1 RtLcdDiGeaLgcgAhveeLRRtrvgpfdeedmvtledLedavllyke..dee.LdrlllPlesal 63 
                                       RtLc DiGe+L cgA ++eLRR r+g ++e+ +vtl+dL+da+ ++++  +++ L+ +++P+e ++
  gi|474934869|ref|YP_007688451.1| 340 RTLCIDIGEMLLCGASMTELRRSRSGRLKEDSAVTLQDLTDAYVFWQQegHGDwLRGMIRPMEMLV 405
                                       9**********************************************955555**********998 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.8   0.2   7.7e-21   5.3e-18       2     178 ..       3     158 ..       2     159 .. 0.84

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 7.7e-21
                   Cytidylate_kin2   2 ITIsreyGsgGetigeaLAekLglpfydr.eiieevakelglseeeveevdersrlssflskllaarvagdtldekl 77 
                                       ITIs+  Gsg++t++ +L+++Lgl+ +   ++++ +a e+g++  e+ e+ e+ +                    ++
  gi|474934869|ref|YP_007688451.1|   3 ITISGPPGSGKTTVCGKLSQELGLKAVVFgQVFRDLAAEKGMTLGELGELAEKDP--------------------SI 59 
                                       9***********************998877*****************88888333....................45 PP

                   Cytidylate_kin2  78 ddelfeaqervirelaaeesvVivGRgadliLkdrp.nvlrvfltapledrvkrvaereglseeearekiketDkrr 153
                                       d+    +++r+++++ +  ++++  R ++++L+++   +lr++l+a+ e+r+ r+  reg + e+a  +  e+ + +
  gi|474934869|ref|YP_007688451.1|  60 DEG---IDARIVETARQTPDIILESRLSAYMLTRNNiPALRIYLDASPEVRMSRIGGREGKDLEKAVAETIERQESE 133
                                       555...455566666677799999********995557*********************998555555555555666 PP

                   Cytidylate_kin2 154 akyykkytgqdwgdaenYdlvlnts 178
                                       ak+y ky++ d++d + Yd+v+nt+
  gi|474934869|ref|YP_007688451.1| 134 AKRYMKYYNIDIKDLSVYDMVINTD 158
                                       788888999**************97 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.6   0.3   8.5e-21   5.8e-18       1      74 []     409     482 ..     409     482 .. 0.98

  Alignments for each domain:
  == domain 1  score: 64.6 bits;  conditional E-value: 8.5e-21
                                       CEEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEEEE CS
                               PUA   1 grvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveiervl 74 
                                       + ++v++ Av+a+++ga+L ++Gv   + +++++  Va+++  gelv++G +++sse l++++ g++v++ rvl
  gi|474934869|ref|YP_007688451.1| 409 PWIIVKATAVDAVCHGADLSVKGVHMLDPEIRKNALVALMTARGELVGLGQMQMSSEKLMSAEQGVAVKVTRVL 482
                                       579********************************************************************997 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.0   0.0   2.1e-18   1.4e-15       1     122 [.       3     128 ..       3     138 .. 0.87

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 2.1e-18
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpealdeskrldedkldklldaleenssale 72 
                                       I ++G+pG+GKtt++  Ls++lg+     g++ rd+a+e+g+ l++  e  ++   +de+ +++++++ ++ ++   
  gi|474934869|ref|YP_007688451.1|   3 ITISGPPGSGKTTVCGKLSQELGLkavvfGQVFRDLAAEKGMTLGELGELAEKDPSIDEGIDARIVETARQTPD--- 76 
                                       89*******************999*************************9999999***************985... PP

                            AAA_18  73 egknlvidghlaeleseaakdikk.vvLtaspeelleRlekRgyeeakik.....e 122
                                           ++++++l+ +  +++ +    ++L+aspe+++ R+  R+ ++ +++     e
  gi|474934869|ref|YP_007688451.1|  77 ----IILESRLSAYMLTRNNIPALrIYLDASPEVRMSRIGGREGKDLEKAvaetiE 128
                                       ....9***99988776655544445*****************98877766665554 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.4   0.1   2.1e-16   1.5e-13       2     135 ..       7     127 ..       6     128 .. 0.80

  Alignments for each domain:
  == domain 1  score: 51.4 bits;  conditional E-value: 2.1e-16
                                       E-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHH.HSSEEEEE CS
                            AAA_17   2 GgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrklpleekkelqkeaaekiaeea.kkkgvlvd 77 
                                       G+PGsGK+t+c kl +++g++ + +G+++r+ a+++g+  + +e+ +l  e++  +++ + ++i e+a ++ +++++
  gi|474934869|ref|YP_007688451.1|   7 GPPGSGKTTVCGKLSQELGLKAVVFGQVFRDLAAEKGM--TLGELGELA-EKDPSIDEGIDARIVETArQTPDIILE 80 
                                       9************************************8..777787776.445567888888888887345678887 PP

                                       E-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHTTST-TS-SHHHH CS
                            AAA_17  78 ghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkdrtrgrdddneesi 135
                                          +      +   l+    +++ p + i+l+a+pe+ ++r   +++++ +   +e+i
  gi|474934869|ref|YP_007688451.1|  81 SRLSA-----Y--MLT---RNNI-PALRIYLDASPEVRMSRIGGREGKDLEKAVAETI 127
                                       77653.....1..122...2455.89****************9999988888888777 PP

>> DKCLD  DKCLD (NUC011) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.0   6.7e-15   4.6e-12      11      56 ..     175     220 ..     169     222 .. 0.95

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 6.7e-15
                                       XX-EEESS-----TTSS--GGG--HHHHHHTEEEEEEE-SSS-HHH CS
                             DKCLD  11 ydkllvrtehytplpaGssPlkRpieeyikyGvinLDKPsnPsSHE 56 
                                       ++++lv+  +  p ++G  P  R+i e+++ Gvi LDKPs+P+SH+
  gi|474934869|ref|YP_007688451.1| 175 IRSMLVKDPKAIPDRWGKRPSDRSIGELLQAGVIALDKPSGPTSHQ 220
                                       689******************************************7 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   8.1e-08   5.6e-05       1      37 [.       3      39 ..       3      45 .. 0.96
   2 !   18.5   0.3   1.9e-06    0.0013     131     209 ..      95     173 ..      52     175 .. 0.70
   3 ?    2.8   0.1      0.12        84      76     130 ..     280     335 ..     256     339 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 8.1e-08
                                      EEEE-STTSSHHHHHHHHHHHHT-EEEEHHHHHHHHH CS
                    Cytidylate_kin  1 iaiDGPagsGKssvaralaeklglkyldtgalYRala 37
                                      i+i GP gsGK +v+ +l+++lglk +  g+++R la
  gi|474934869|ref|YP_007688451.1|  3 ITISGPPGSGKTTVCGKLSQELGLKAVVFGQVFRDLA 39
                                      89********************************987 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 1.9e-06
                                       SEEEEEE--HHHHHHHHHHHHHHTT----HHHHHHHHHHHHHHHHCTSSS-S--.....-TT-EEEETTTS-HHHHH CS
                    Cytidylate_kin 131 elKifldAsveeRakRRlkqlkakgtsvsleellaeikeRDklDkerevgpLkl.....aedaliidtskltieevv 202
                                        l+i+ldAs+e+R +R       +g  ++le+ +ae +eR +   +r ++  ++     +   ++i+t++lt eev+
  gi|474934869|ref|YP_007688451.1|  95 ALRIYLDASPEVRMSRIGGR---EG--KDLEKAVAETIERQESEAKRYMKYYNIdikdlSVYDMVINTDNLTPEEVL 166
                                       589**********9986554...22..46888899999999999999776655411111444589************ PP

                                       HHHHHHH CS
                    Cytidylate_kin 203 ekileli 209
                                       +kil+++
  gi|474934869|ref|YP_007688451.1| 167 QKILDAV 173
                                       ***9987 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.12
                                       -TTGGGSHHHHHHHHHHTTSHHHHHHHHHH..HHTT-BSSBEEEEESSIIIIISTT- CS
                    Cytidylate_kin  76 veeelrsdevekavSavaaipavRailvkk..lrelvkkarvvveGRDigtvvfpda 130
                                        e+++r ++++k+v  + + p vR++++++  +r++ + + + ++GRD+  ++  da
  gi|474934869|ref|YP_007688451.1| 280 SEKQIR-EAMSKFVGRIYQLPPVRSAVKRQlrIRRVRELEVLEINGRDVLFRISCDA 335
                                       444555.67899999999********9886115667777778899***977776665 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.7   8.1e-07   0.00056       1      45 [.       5      49 ..       5     146 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 8.1e-07
                                      EEESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHC.T-HHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                               ADK  1 llGaPgaGKGtqaeklvkkyglahlstGdllRaevks.gtelGkea 45
                                      + G+Pg+GK t++ kl +++gl+ +  G+++R+  ++ g  lG+ +
  gi|474934869|ref|YP_007688451.1|  5 ISGPPGSGKTTVCGKLSQELGLKAVVFGQVFRDLAAEkGMTLGE-L 49
                                      57******************************977550444553.3 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.3   2.2e-06    0.0015       4     139 ..       5     133 ..       3     137 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.2e-06
                            AAA_33   4 lvGlpGsGKstlaerllkklgavllssdtlrrrlfgtdqqsktdytrvldr...lyqilnelarkalsagrnvilda 77 
                                       + G+pGsGK+t+  +l ++lg   +   +++r l++++  ++ ++ +++++   + + + +++ +++++  ++il +
  gi|474934869|ref|YP_007688451.1|   5 ISGPPGSGKTTVCGKLSQELGLKAVVFGQVFRDLAAEKGMTLGELGELAEKdpsIDEGIDARIVETARQTPDIILES 81 
                                       57*******************66666666788888877777766555444344599999999999999999999864 PP

                            AAA_33  78 tnlsrrerarflklarrlgvpvrivvvetdeetlkeRlakRaangddrsevpeealdrqkar 139
                                               +    ++ r + p + +++++++e+  +R+  R+ +     ++  e+++rq + 
  gi|474934869|ref|YP_007688451.1|  82 --------RLSAYMLTRNNIPALRIYLDASPEVRMSRIGGREGKD--LEKAVAETIERQESE 133
                                       ........2233445568999999999999999999999999974..346888888888765 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   2.1     2e-06    0.0014       1     157 [.       9     173 ..       9     174 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2e-06
                                       TTSSHHHHHHHHHHHHTSEEEEHHHHH...HHHHTS-HHHH..HHHHHHHHHHHHHHHHHHHHCCCSSEEEEE-TT. CS
                               SKI   1 mGaGKstvGkllAkklglefiDlDeli...ekrtgksiaei..feeegeegFrelEsevlkelleeeglViatGGG. 71 
                                       +G+GK+tv  +l+++lgl+ +   +++     + g++  e+  ++e++ + +   ++++++   ++ ++++    + 
  gi|474934869|ref|YP_007688451.1|   9 PGSGKTTVCGKLSQELGLKAVVFGQVFrdlAAEKGMTLGELgeLAEKDPSIDEGIDARIVETARQTPDIILESRLSa 85 
                                       69*****************9999998844355667999988334466667788888888888888878888764441 PP

                                       GGGSHHHHHHHHHHSEEEEEE--HHHHHHHHHHTTSSGGGCSCHHHHHHHHHHHHHHHHHCCS.......SCEEEEC CS
                               SKI  72 avlseenrellkekgiviyLdvsleellerlkadkeRPllqekskeeelleelaereplyeea.......advvvde 141
                                        +l+++n  +l+     iyLd+s+e+ ++r+  ++ + l ++  ++ e++e++a+r   y ++        d+v+++
  gi|474934869|ref|YP_007688451.1|  86 YMLTRNNIPALR-----IYLDASPEVRMSRIGGREGKDLEKAVAETIERQESEAKRYMKYYNIdikdlsvYDMVINT 157
                                       445556666777.....***************999987777777777777888888888888766666667899999 PP

                                       TSSHHHHHHHHHHHHH CS
                               SKI 142 seeskeevaeeileal 157
                                       ++ ++eev ++il+a+
  gi|474934869|ref|YP_007688451.1| 158 DNLTPEEVLQKILDAV 173
                                       99999*******9976 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.027        19       2      20 ..       6      24 ..       5      32 .. 0.84
   2 !   14.5   0.1   3.2e-05     0.022     117     166 ..      93     145 ..      71     169 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.027
                                      EESTTSSHHHHHHHHHHHH CS
                   Thymidylate_kin  2 EGlDGaGKttqaellkerl 20
                                       G  G+GKtt++ +l + l
  gi|474934869|ref|YP_007688451.1|  6 SGPPGSGKTTVCGKLSQEL 24
                                      5888**********99876 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 3.2e-05
                                       E-SEEEEEESSHHHHHTSCCTTSS..TTTSHHHHHHHHHHHHHHHHHHHH.TT CS
                   Thymidylate_kin 117 kPdltflldvdpevalkRlakrde..ldeeeeeqldflrkvrerylelak.ed 166
                                        P l ++ld +pev++ R++ r+   l+++++e ++ +++  +ry++ ++ + 
  gi|474934869|ref|YP_007688451.1|  93 IPALRIYLDASPEVRMSRIGGREGkdLEKAVAETIERQESEAKRYMKYYNiDI 145
                                       599******************99967678888999999999999988886443 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.1   5.9e-07   0.00041       1      44 [.       2      48 ..       2     162 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 5.9e-07
                            AAA_28  1 kivitGgestGKTtlleaLaar...gypvvpEaareileeklakged 44
                                      +i i+G++++GKTt++ +L+++   + +v+  ++r++  ek+ + ++
  gi|474934869|ref|YP_007688451.1|  2 RITISGPPGSGKTTVCGKLSQElglKAVVFGQVFRDLAAEKGMTLGE 48
                                      799*****************9884444566*******9999866664 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       2.2   1.5e+03      60      75 ..     325     340 ..     318     341 .. 0.79
   2 !   18.4   0.0   2.9e-06     0.002       2      60 ..     411     472 ..     410     490 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2.2
                           UPF0113  60 gkivvknlaDiGeYlR 75 
                                       ++++++  +D G+Y+R
  gi|474934869|ref|YP_007688451.1| 325 RDVLFRISCDAGTYVR 340
                                       566777789******9 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 2.9e-06
                           UPF0113   2 vvvkekaeklFLYGrdvlkesilkitesvkenqvvvVlnengeplGiGkirkdt...kaspg 60 
                                       ++vk  a   +  G d+  ++++ +++++++n  v+++  +ge++G+G ++ ++    + ++
  gi|474934869|ref|YP_007688451.1| 411 IIVKATAVDAVCHGADLSVKGVHMLDPEIRKNALVALMTARGELVGLGQMQMSSeklMSAEQ 472
                                       789999999999**************************************998885413333 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00034      0.24       1      26 [.       3      28 ..       3      39 .. 0.91
   2 !    7.9   0.2    0.0036       2.5     113     186 ..      83     154 ..      68     175 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00034
                                      EEEEESTTSSHHHHHHHHHCCSTCEE CS
                               dNK  1 ivveGnIgaGKstlvklLskklgvkv 26
                                      i+++G+ g+GK+t+   Ls++lg k+
  gi|474934869|ref|YP_007688451.1|  3 ITISGPPGSGKTTVCGKLSQELGLKA 28
                                      89********************9765 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0036
                                       HHHHHHHCCH.-SEEEEEE--HHHHHHHHHHCTTCCCTTS-HHHHHHHHHHHHHHHTSGGCS-EEEEETSS.-TT CS
                               dNK 113 ldnlleelak.pdlliYLkasletclerikkRgreeekkieldYlekLhekyeewlkklnevpvlvidveeldlv 186
                                       l++++ + ++ p l iYL+as+e+ + ri  R+ ++    e++  e+++++ +e+ + +++  + + d + +d+v
  gi|474934869|ref|YP_007688451.1|  83 LSAYMLTRNNiPALRIYLDASPEVRMSRIGGREGKD---LEKAVAETIERQESEAKRYMKYYNIDIKDLSVYDMV 154
                                       555553333348999**************9887665...444444444444444444444444444444433333 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   8.9e-06    0.0062       1      24 [.       2      25 ..       2      45 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 8.9e-06
                                      EEEEE--TTSSHHHHHHHHHHHH. CS
                          NTPase_1  1 kvfiTGppGvGKtTlvkkvlellk 24
                                      ++ i+GppG+GKtT++ k++++l 
  gi|474934869|ref|YP_007688451.1|  2 RITISGPPGSGKTTVCGKLSQELG 25
                                      589******************994 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1     2e-05     0.014       3      27 ..       5      29 ..       3      59 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2e-05
                                      EESSTTSSHHHHHHHHHHHHTHEEE CS
                               AAA  3 lyGppGtGKTllakavakelgvefl 27
                                      ++GppG GKT+++  + +elg + +
  gi|474934869|ref|YP_007688451.1|  5 ISGPPGSGKTTVCGKLSQELGLKAV 29
                                      79*****************986643 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   0.00013     0.092       8      29 ..       3      24 ..       2      46 .. 0.90
   2 ?   -2.2   0.0       6.5   4.5e+03      38      64 ..     146     173 ..     117     186 .. 0.55
   3 ?   -1.4   0.0       3.8   2.6e+03      39      65 ..     266     293 ..     188     322 .. 0.59
   4 ?   -2.0   0.0       5.7   3.9e+03      38      65 ..     323     351 ..     301     377 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00013
                            AAA_22  8 lvvtGesGtGKTtllrrlleql 29
                                      +++ G++G+GKTt++ +l ++l
  gi|474934869|ref|YP_007688451.1|  3 ITISGPPGSGKTTVCGKLSQEL 24
                                      6899***********9998887 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.5
                            AAA_22  38 erpevvfvtlpsst.sskdllrellral 64 
                                       ++ +v+ + ++ ++ +++++l+++l a+
  gi|474934869|ref|YP_007688451.1| 146 KDLSVYDMVINTDNlTPEEVLQKILDAV 173
                                       4444443333444444555555555444 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 3.8
                            AAA_22  39 rpevv.fvtlpsstsskdllrellralg 65 
                                       ++e++ ++ l ++ s k++++++ +++g
  gi|474934869|ref|YP_007688451.1| 266 DKEYIcLMRLHADRSEKQIREAMSKFVG 293
                                       3333444555555555555555555555 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 5.7
                            AAA_22  38 erpevv.fvtlpsstsskdllrellralg 65 
                                       ++++v+ ++ + ++t  ++l+ ++ + l 
  gi|474934869|ref|YP_007688451.1| 323 NGRDVLfRISCDAGTYVRTLCIDIGEMLL 351
                                       45566668999999999999999887765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   3.8e-05     0.026      28      63 ..       4      38 ..       2     132 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.8e-05
                            AAA_16 28 llsGesGvGKsslvrellralekdggiflrgkcdql 63
                                       +sG++G+GK+++  +l ++l  + ++++ + +++l
  gi|474934869|ref|YP_007688451.1|  4 TISGPPGSGKTTVCGKLSQELGLK-AVVFGQVFRDL 38
                                      69*****************99999.77766666666 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   4.3e-05      0.03       1      23 [.       5      27 ..       5      42 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.3e-05
                        ATP_bind_1  1 vvGpaGsGKttfvgalseilelr 23
                                      + Gp+GsGKtt +g+ls+ l l+
  gi|474934869|ref|YP_007688451.1|  5 ISGPPGSGKTTVCGKLSQELGLK 27
                                      67***************977655 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00011     0.077      49      73 ..       4      28 ..       2      44 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                             Rad17 49 LisGPsGCgkstvvkvLskelgikl 73
                                       isGP+G gk+tv   Ls+elg k 
  gi|474934869|ref|YP_007688451.1|  4 TISGPPGSGKTTVCGKLSQELGLKA 28
                                      59*******************9875 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1    0.0017       1.2       2      29 ..       3      30 ..       2      47 .. 0.85
   2 ?    1.4   0.0      0.33   2.3e+02     127     177 ..      91     138 ..      61     150 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0017
                               PRK  2 IgvagsSGaGkttvarklekifgrekvk 29
                                      I ++g+ G+Gkttv  kl + +g ++v 
  gi|474934869|ref|YP_007688451.1|  3 ITISGPPGSGKTTVCGKLSQELGLKAVV 30
                                      89*******************9955554 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.33
                               PRK 127 aelldlkiyvdisidlelarklqRDiaeRGrsle.avldsilrrkpdyvnyi 177
                                        +   l+iy+d+s +++++r         G++le av ++i+r+  + ++y+
  gi|474934869|ref|YP_007688451.1|  91 NNIPALRIYLDASPEVRMSRIG----GREGKDLEkAVAETIERQESEAKRYM 138
                                       5677899********9877544....44577776457777777777777665 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00076      0.52      36      60 ..       3      27 ..       2      40 .. 0.89
   2 ?   -1.4   0.0       2.4   1.7e+03     102     139 ..     318     355 ..     309     363 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00076
                            RuvB_N 36 vllyGpPGlGkttlakiiakelgvk 60
                                      + ++GpPG Gktt++  +++elg k
  gi|474934869|ref|YP_007688451.1|  3 ITISGPPGSGKTTVCGKLSQELGLK 27
                                      5689*****************9976 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.4
                            RuvB_N 102 evlysamedfrldivigkGpsarsikldlpkftlvgat 139
                                       evl     d+ + i  + G+  r++ +d+ ++ l ga+
  gi|474934869|ref|YP_007688451.1| 318 EVLEINGRDVLFRISCDAGTYVRTLCIDIGEMLLCGAS 355
                                       666677778889999999***********999999996 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00031      0.22       1      23 [.       3      25 ..       3      42 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00031
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakall 23
                                      i ++Gp+g GK+t++ +L+++l 
  gi|474934869|ref|YP_007688451.1|  3 ITISGPPGSGKTTVCGKLSQELG 25
                                      6799**************99986 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00027      0.19       4      26 ..       3      25 ..       1      54 [. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00027
                                      EEEEESTTSSHHHHHHHHHHHHH CS
                             SRP54  4 illvGlqGaGKTttlaKLaallk 26
                                      i + G+ G+GKTt ++KL++ l 
  gi|474934869|ref|YP_007688451.1|  3 ITISGPPGSGKTTVCGKLSQELG 25
                                      66889*************98664 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.2    0.0033       2.3      22      39 ..       4      21 ..       2      25 .. 0.85
   2 ?    0.8   0.0       0.5   3.5e+02     128     153 ..      26      51 ..      25      59 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0033
                            AAA_30 22 vltGpAGtGKttalkalr 39
                                      ++ Gp+G+GKtt+ ++l 
  gi|474934869|ref|YP_007688451.1|  4 TISGPPGSGKTTVCGKLS 21
                                      589**********98875 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.5
                            AAA_30 128 lasVeaGgvlrdlveaagigtaeLte 153
                                       l++V  G+v+rdl++++g++  eL e
  gi|474934869|ref|YP_007688451.1|  26 LKAVVFGQVFRDLAAEKGMTLGELGE 51 
                                       789999*******9888888777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (503 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); expected 358.6 (0.02)
Passed bias filter:                      666  (0.0371465); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.73u 0.32s 00:00:01.05 Elapsed: 00:00:00.49
# Mc/sec: 3107.69
//
Query:       gi|474934870|ref|YP_007688452.1|  [L=232]
Description: putative membrane protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      6e-27   94.4   9.3      6e-27   94.4   9.3    2.1  2  EMC3_TMCO1       Integral membrane protein EMC3/TMCO1-like
  ------ inclusion threshold ------
      0.017   15.1   0.7      0.017   15.1   0.7    1.7  2  EOS1             N-glycosylation protein
      0.024   13.9   3.3      0.034   13.4   3.3    1.2  1  Choline_transpo  Plasma-membrane choline transporter
       0.34   11.3  14.0        4.1    7.8  11.6    3.0  2  DUF4199          Protein of unknown function (DUF4199)
       0.48   10.9   3.1       0.26   11.8   0.7    1.8  2  Vps39_2          Vacuolar sorting protein 39 domain 2
       0.64    9.6  16.6        1.6    8.3   3.9    2.6  3  DUF2208          Predicted membrane protein (DUF2208)
        1.3   10.0   6.3          1   10.3   0.5    2.6  2  DUF4834          Domain of unknown function (DUF4834)


Domain annotation for each model (and alignments):
>> EMC3_TMCO1  Integral membrane protein EMC3/TMCO1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   6.0     0.014        36      84     115 ..       6      37 ..       3      52 .. 0.83
   2 !   94.4   9.3   2.3e-30     6e-27      15     167 ..      56     208 ..      43     210 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.014
                        EMC3_TMCO1  84 qsemmmdqmkpmivtmipqiliffwlnsffsg 115
                                       q++ m+ + k++++ m++ +li++++++f ++
  gi|474934870|ref|YP_007688452.1|   6 QQQAMQPMPKGTMIAMLFVLLIMMVVMQFREQ 37 
                                       788999*********************99774 PP

  == domain 2  score: 94.4 bits;  conditional E-value: 2.3e-30
                        EMC3_TMCO1  15 Pivivillvgiltgllsellqkllidkkkmekeqkrekelqkrarelqkngdklklkklekrqeelmedqsemmmdq 91 
                                       P+ +++++ g++   ls++++++l+d  km ++q +++++q+++r+++ +++  k kkl+++q+ ++++++em+ +q
  gi|474934870|ref|YP_007688452.1|  56 PV-LTLVIGGLIMITLSTVIRSFLTDAIKMARTQHIQRQFQEEMRKARTENNLYKMKKLQEQQMVMTQASMEMSAQQ 131
                                       44.889999******************************************************************** PP

                        EMC3_TMCO1  92 mkpmivtmipqiliffwlnsffsgfvv......aklpfpltgrfksllqrglesldvrfvssiswYflcsfglsqii 162
                                       mk+m +tm+++i+i++w+++f++ +        a+l++ l +        +l ++++ ++s+i++Y+l+s+ + q+ 
  gi|474934870|ref|YP_007688452.1| 132 MKSMPITMVVIIPIYAWVWYFINSIHNgdlgdpANLVIDLPWGT-----ANLYNNVWFMPSWIIIYTLISLPIGQLE 203
                                       ***********************777644344445555544444.....55579*********************** PP

                        EMC3_TMCO1 163 rklLg 167
                                       +kl++
  gi|474934870|ref|YP_007688452.1| 204 NKLMQ 208
                                       **987 PP

>> EOS1  N-glycosylation protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.7   6.6e-06     0.017      54     161 ..      43     145 ..      18     156 .. 0.59
   2 ?   -2.0   0.5       1.1   2.9e+03      26      36 ..     185     195 ..     178     199 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.6e-06
                              EOS1  54 llllsvlsadkeqplaaWivistt.ltlseivqswvtSnladaeldsrevksrssaaerleskasslrqgksrhkrs 129
                                        ++ +v+++  + p+ + ++ + +  tls ++ s++t  +++a++++ + +  + +  + +++++ ++ +k +++++
  gi|474934870|ref|YP_007688452.1|  43 DVVFHVIDFGGDNPVLTLVIGGLImITLSTVIRSFLTDAIKMARTQHIQRQF-QEEMRKARTENNLYKMKKLQEQQM 118
                                       5677888888889999988888652699************998766322222.111222222222333332222222 PP

                              EOS1 130 vskseakkkrertsskrtldleeivvravvPv 161
                                       v     ++++    s ++++   i++  ++P+
  gi|474934870|ref|YP_007688452.1| 119 V-----MTQASMEMSAQQMKSMPITMVVIIPI 145
                                       2.....23333334444555555555555665 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.1
                              EOS1  26 lvrWlvyYsil 36 
                                       +  W++ Y+++
  gi|474934870|ref|YP_007688452.1| 185 MPSWIIIYTLI 195
                                       45566666554 PP

>> Choline_transpo  Plasma-membrane choline transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   3.3   1.3e-05     0.034       2     118 ..      19     156 ..      18     158 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.3e-05
                   Choline_transpo   2 illivavllllllivlrkrirlaiallkvaskaiksnpslllvplltllllllvsafwivvavalylassgestdkv 78 
                                       i++++ +l++++++ +r++i  a  ++ +++++ ++np l ++++  l++++l +++ ++++ a+ +a ++ +   +
  gi|474934870|ref|YP_007688452.1|  19 IAMLFVLLIMMVVMQFREQIGKALDVVFHVIDFGGDNPVL-TLVIGGLIMITLSTVIRSFLTDAIKMARTQHI---Q 91 
                                       67788999999999************************55.45566666666666666666655633333333...1 PP

                   Choline_transpo  79 ............................nsgsesglaavefessskvkalllyllfgllWtleflral 118
                                                                       ++ +  ++ + ++++ + +++ + ++ W++ f++ +
  gi|474934870|ref|YP_007688452.1|  92 rqfqeemrkartennlykmkklqeqqmvM---TQASMEMSAQQMKSMPITMVVIIPIYAWVWYFINSI 156
                                       346889999*************9996642...2333334566789999*****************986 PP

>> DUF4199  Protein of unknown function (DUF4199)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8  11.6    0.0016       4.1      46     160 ..      25     156 ..       4     159 .. 0.51
   2 ?    1.7   0.0      0.12     3e+02     147     164 ..     184     201 ..     173     205 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0016
                           DUF4199  46 flvylalkkyrkknlgGfisfgqafgfg....flislvagllsavfqyiyfnfidpd............fienyiae 106
                                       +l+ + ++++r+++ +      + + fg    +l+ +++gl+++ +  ++ +f+               f e++ ++
  gi|474934870|ref|YP_007688452.1|  25 LLIMMVVMQFREQIGKALDVVFHVIDFGgdnpVLTLVIGGLIMITLSTVIRSFLTDAikmartqhiqrqFQEEMRKA 101
                                       34555555666666222222334444444444667777777777777777777744445544443333366666554 PP

                           DUF4199 107 ilekleeakeesaeeenaemseeeikealesls..piivalqsflgnliiGlilsl 160
                                         e+   +++  + e+++ m+++ +++ +++++  pi ++++  ++  ++++i s+
  gi|474934870|ref|YP_007688452.1| 102 RTENNLYKMKKLQ-EQQMVMTQASMEMSAQQMKsmPITMVVIIPIYAWVWYFINSI 156
                                       4444332222222.233334444443333344456667777777777777777665 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.12
                           DUF4199 147 sflgnliiGlilsliiAl 164
                                       ++ + +ii++++sl+i+ 
  gi|474934870|ref|YP_007688452.1| 184 FMPSWIIIYTLISLPIGQ 201
                                       577889999999999986 PP

>> Vps39_2  Vacuolar sorting protein 39 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       2.2   5.5e+03      11      37 ..       4      30 ..       2      40 .. 0.72
   2 ?   11.8   0.7    0.0001      0.26      28      80 ..      73     125 ..      57     147 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.2
                           Vps39_2 11 ldplevLdllPdelplkdlesflekal 37
                                      l+  ++++ +P+ + ++ l+ +l  ++
  gi|474934870|ref|YP_007688452.1|  4 LQQQQAMQPMPKGTMIAMLFVLLIMMV 30
                                      566788888999888888877776554 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.0001
                           Vps39_2  28 dlesflekalrnslekkreeqvvkklrkaeklsveeellklrskkvvvteekv 80 
                                        ++sfl  a++ + +++ ++q ++++rka++++   ++ kl+++++v+t+ ++
  gi|474934870|ref|YP_007688452.1|  73 VIRSFLTDAIKMARTQHIQRQFQEEMRKARTENNLYKMKKLQEQQMVMTQASM 125
                                       48999999**9999999999*********999999999999999999999876 PP

>> DUF2208  Predicted membrane protein (DUF2208)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   3.9   0.00064       1.6      74     148 ..       1      79 [.       1      95 [. 0.82
   2 ?    6.0   6.9    0.0031       7.9      40     109 ..      84     155 ..      57     163 .. 0.63
   3 ?   -2.4   0.0       1.1   2.9e+03      97     119 ..     185     207 ..     174     220 .. 0.51

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00064
                           DUF2208  74 ekDeelqkelkeqlkasmitllllliviilffllyryiiplassllgev....leeklarflaflalFealflismf 146
                                       + D + q+ ++ + k +mi +l++l+++++++ +++ i+++++ ++  +     + +l   +  l++    ++i +f
  gi|474934870|ref|YP_007688452.1|   1 MRDLQQQQAMQPMPKGTMIAMLFVLLIMMVVMQFREQIGKALDVVFHVIdfggDNPVLTLVIGGLIMITLSTVIRSF 77 
                                       6799999*********************************9999998778886677777778888888888888888 PP

                           DUF2208 147 lr 148
                                       l+
  gi|474934870|ref|YP_007688452.1|  78 LT 79 
                                       76 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0031
                           DUF2208  40 svltsrsllrerkkleevesgktLfeEknalkliekDeelqkelkeqlkasmitlll..lliviilffllyr 109
                                       ++ t+   ++ + ++++    + L++ k+ ++ ++  ++ + e+++q ++sm  +++  ++i+ ++++++++
  gi|474934870|ref|YP_007688452.1|  84 MARTQHIQRQFQEEMRKARTENNLYKMKKLQEQQMVMTQASMEMSAQQMKSMPITMVviIPIYAWVWYFINS 155
                                       333333233444555555556679999999999999999999998766655544444246777777777665 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.1
                           DUF2208  97 lliviilffllyryiiplassll 119
                                       ++ +ii+++l+   i++l ++l+
  gi|474934870|ref|YP_007688452.1| 185 MPSWIIIYTLISLPIGQLENKLM 207
                                       44444444444444444444444 PP

>> DUF4834  Domain of unknown function (DUF4834)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.8      0.19   4.8e+02       3      19 ..      18      34 ..      16      54 .. 0.70
   2 ?   10.3   0.5    0.0004         1      13      69 ..      61     118 ..      56     136 .. 0.64

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.19
                           DUF4834  3 fLlfilifiiailvigl 19
                                      +++++++++i+++v+ +
  gi|474934870|ref|YP_007688452.1| 18 MIAMLFVLLIMMVVMQF 34
                                      56677777777777655 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0004
                           DUF4834  13 ailviglsilsvilrtvfglgsrkkssksaqkqfgnstnsnqqksq.......srsetkeegei 69 
                                       +i  + ++ ls+++r+++    ++  +++ q+qf+++  + +++++       +      e+++
  gi|474934870|ref|YP_007688452.1|  61 VIGGLIMITLSTVIRSFLTDAIKMARTQHIQRQFQEEMRKARTENNlykmkklQ------EQQM 118
                                       2223344567889999999999999999********999999888854332220......2222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2302  (0.128395); expected 358.6 (0.02)
Passed bias filter:                      744  (0.041497); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 1528.90
//
Query:       gi|474934871|ref|YP_007688453.1|  [L=512]
Description: protein translocase subunit secY/sec61 alpha [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.3e-71  238.9  15.8    1.1e-70  238.4  15.8    1.2  1  SecY             SecY translocase
    1.7e-12   46.9   2.1    6.2e-12   45.1   0.5    2.7  2  Plug_translocon  Plug domain of Sec61p
  ------ inclusion threshold ------
      0.052   13.9   0.2      0.052   13.9   0.2    3.2  4  Phage_holin_5_2  Phage holin family Hol44, in holin superfami
       0.19   10.6   3.9        3.5    6.5   0.0    2.6  2  MMPL             MMPL family
        0.7   10.3   0.0        0.7   10.3   0.0    3.7  4  Phage_holin_5_1  Bacteriophage A118-like holin, Hol118


Domain annotation for each model (and alignments):
>> SecY  SecY translocase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  238.4  15.8     3e-74   1.1e-70       1     306 []      78     490 ..      78     490 .. 0.82

  Alignments for each domain:
  == domain 1  score: 238.4 bits;  conditional E-value: 3e-74
                                       BTTSSTCHHHHHHHHHHHHH.HHHSSSSSSTS.-S.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC......... CS
                              SecY   1 sifaLGImPyitasIilqLl.tvvipkleelk.ke.geegrkkinqitryltvvlalvqalgialslg......... 65 
                                       +i++LGI+P++tasIi+qL+ ++     ++++ +  ++++++ ++++ ++l++v+++++a+  ++++          
  gi|474934871|ref|YP_007688453.1|  78 TILQLGIGPIVTASIIMQLFvGA-----KIIRlDLtNRKDKACYQSVLKLLVIVMIFIEAVPQVFGYLvpsdqftdt 149
                                       89******************999.....5555444599***********************9887655899****** PP

                                       ....HH.HHHHHHHHHHHHHHHHHHHHHHHHSSTTHHHHHHHHHHHHHHC.CHSS.................-HHHH CS
                              SecY  66 ....lalllivlqltagtvllmwLgEqitekGiGnGisllifagivarlp.kals.................gliel 120
                                           +a lli+lql++g++l+++++E+i+++GiG+Gisl+i+ag+++ ++ +al+                 g   +
  gi|474934871|ref|YP_007688453.1| 150 fggvGAKLLIILQLFIGSYLVFLFDEVISKWGIGSGISLFIAAGVAQAVFtGALNwyavdnsaayslsnppaG---T 223
                                       ****889*******************************************66666666666655555555551...0 PP

                                       .............SS.............THHHHHHHHHHHHHHHHHCHHHHBEEEECBBBSTT....S.S-EEEEET CS
                              SecY 121 .............ale...........gilallllllvtllvillvvyveeaerripvqyakrgrkggqssylPlkl 173
                                                    + e           g  + l++l+ t++++l+vvy+e++++++p+++ +    +g+++++P+kl
  gi|474934871|ref|YP_007688453.1| 224 ipkaiyvlmntnsS-EmasggyemillGQPNPLIALIGTVVIFLVVVYLESSRIELPLSHGNA---RGARGRYPIKL 296
                                       44445555544440.044555554445445899***************************955...49********* PP

                                       TCCCSCHHHHHHHHHH..............................................HHHCCCCS....... CS
                              SecY 174 nyagviPiIfasslla..............................................lpstiaqfl...... 198
                                       +ya++iP+I+ s+lla                                              +p+ ++ +l      
  gi|474934871|ref|YP_007688453.1| 297 MYASNIPVILMSALLAnismvclllysndflsgipliggneyigyyasgsttasdgiawflsTPQGLTDWLlpilnp 373
                                       ****************8888888888888888888888888888888887777777766655577777777555555 PP

                                       TCCCS........THHHHHHHHHHHHHH....HHHHHHTCT.THHHHHHHCCHHTBSSSCTTT.TCHHHHHHHHHHH CS
                              SecY 199 lalls........psvlyvvlyvlliif....Fayfyteit.fnpkevaenlkksggfipgir.pgketakyLekvl 261
                                       +   s        +++++v++y++++++    Fa+f++e+t + +++va+n+ +sg++ipg+r + + ++++L++++
  gi|474934871|ref|YP_007688453.1| 374 V---SygnghgvlENLCHVAIYMTVMVIgsilFAKFWVETTnLGSESVAKNILRSGMQIPGFRrDPRVLKRVLDRYI 447
                                       1...0444545554455666666666655666*******************************999*********** PP

                                       HHHHHHHHHHHHHHHHHHHHHTTS.TT.TTHHHHHHHHHHHHHHH CS
                              SecY 262 sritliGalflaliavlpdllgasligafggtslLivVgvaletv 306
                                       ++it++++++++l+a+++d++g+  +g+ +gt+lL++Vg++++++
  gi|474934871|ref|YP_007688453.1| 448 PTITVLSGALIGLLAACADMIGT--TGNATGTGLLLTVGIIIRFY 490
                                       ***********************..8899************9875 PP

>> Plug_translocon  Plug domain of Sec61p
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   0.5   1.7e-15   6.2e-12       1      35 []      43      77 ..      43      77 .. 0.98
   2 ?   -0.2   0.0      0.26   9.3e+02       5      13 ..     326     334 ..     326     356 .. 0.83

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 1.7e-15
                                      HHHHHHCCSB-TT--SSS-TCCHTTTCCCCTSSTT CS
                   Plug_translocon  1 llYlvlsqiPLyGissssssDpfywlRaifAsnrG 35
                                      +lY+v+s+++++G+++++s D+f+++R+i+A+++G
  gi|474934871|ref|YP_007688453.1| 43 ILYFVMSNVYIWGLDQTDSLDIFAQYRTIMAGASG 77
                                      89******************************998 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.26
                                       HHCCSB-TT CS
                   Plug_translocon   5 vlsqiPLyG 13 
                                       +ls iPL G
  gi|474934871|ref|YP_007688453.1| 326 FLSGIPLIG 334
                                       789999998 PP

>> Phage_holin_5_2  Phage holin family Hol44, in holin superfamily V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.2         5   1.8e+04      54      63 ..     257     266 ..     247     272 .. 0.49
   2 ?   -1.8   0.1       1.2   4.2e+03      23      48 ..     302     330 ..     297     351 .. 0.54
   3 ?   -3.3   0.1       3.4   1.2e+04      26      39 ..     395     408 ..     389     422 .. 0.57
   4 ?   13.9   0.2   1.4e-05     0.052      16      61 ..     440     487 ..     437     495 .. 0.76

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 5
                   Phage_holin_5_2  54 aiiqGilsgg 63 
                                       a+i  +++ +
  gi|474934871|ref|YP_007688453.1| 257 ALIGTVVIFL 266
                                       2233333333 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.2
                   Phage_holin_5_2  23 IPlilgiiGiilgvvivfta.....dfqaed 48 
                                       IP+il+  +++l+ + ++       df    
  gi|474934871|ref|YP_007688453.1| 302 IPVILM--SALLANISMVCLllysnDFLSGI 330
                                       677664..55555555544223334444444 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 3.4
                   Phage_holin_5_2  26 ilgiiGiilgvviv 39 
                                       +++i +i+++  +v
  gi|474934871|ref|YP_007688453.1| 395 VMVIGSILFAKFWV 408
                                       33444455554444 PP

  == domain 4  score: 13.9 bits;  conditional E-value: 1.4e-05
                   Phage_holin_5_2  16 ekvkdkyIPlilgiiGiilgvvivft.a...dfqaedilifgaiiqGils 61 
                                       ++v d+yIP+i ++ G+++g+++  + +   + +a  + +   +++Gi++
  gi|474934871|ref|YP_007688453.1| 440 KRVLDRYIPTITVLSGALIGLLAACAdMigtTGNATGTGL--LLTVGIII 487
                                       56789***************88888855644444444444..89999986 PP

>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0   0.00098       3.5     239     275 ..     293     329 ..     282     335 .. 0.82
   2 ?    2.1   3.0     0.021        77     257     291 ..     452     486 ..     448     493 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.00098
                              MMPL 239 aviravastgkvvtaaGltvaiamlgLvvarlpvlaq 275
                                        +  ++as  +v+++++l   i+m++L++ +  +l++
  gi|474934871|ref|YP_007688453.1| 293 PIKLMYASNIPVILMSALLANISMVCLLLYSNDFLSG 329
                                       57889**********************9988777665 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.021
                              MMPL 257 tvaiamlgLvvarlpvlaqvGvaialGvlvdvliv 291
                                       ++ +a++gL++a   +++++G a ++G+l++v i+
  gi|474934871|ref|YP_007688453.1| 452 VLSGALIGLLAACADMIGTTGNATGTGLLLTVGII 486
                                       56789*************************98666 PP

>> Phage_holin_5_1  Bacteriophage A118-like holin, Hol118
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1      0.55     2e+03      35      77 ..      37      80 ..      32      83 .. 0.75
   2 ?   -1.8   2.2       1.2   4.3e+03       7      50 ..     123     172 ..     115     214 .. 0.46
   3 ?   -1.0   0.0      0.65   2.3e+03       8      24 ..     390     406 ..     384     423 .. 0.72
   4 ?   10.3   0.0    0.0002       0.7      31      69 ..     442     480 ..     428     496 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.55
                   Phage_holin_5_1 35 wlptvsilvgailgalatsldgsgslatmi.wagalagaggtgl 77
                                      w+  v il   +       ld + sl  +  +   +aga gt l
  gi|474934871|ref|YP_007688453.1| 37 WVAVVLILYFVMSNVYIWGLDQTDSLDIFAqYRTIMAGASGTIL 80
                                      77778888777777788889999998876426778899999865 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.2
                   Phage_holin_5_1   7 llvymtflvvvtpvfvqai...kktel...vpskwlptvsilvgailgal 50 
                                       l++ m f+  v  vf   +   + t+    v +k l  + +++g+ l  l
  gi|474934871|ref|YP_007688453.1| 123 LVIVMIFIEAVPQVFGYLVpsdQFTDTfggVGAKLLIILQLFIGSYLVFL 172
                                       34444455444444432220001111111144555555555555555444 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.65
                   Phage_holin_5_1   8 lvymtflvvvtpvfvqa 24 
                                        +ymt++v+ + +f + 
  gi|474934871|ref|YP_007688453.1| 390 AIYMTVMVIGSILFAKF 406
                                       68999998887777664 PP

  == domain 4  score: 10.3 bits;  conditional E-value: 0.0002
                   Phage_holin_5_1  31 vpskwlptvsilvgailgalatsldgsgslatmiwagal 69 
                                       v  +++pt+++l ga++g la+  d  g+      +g l
  gi|474934871|ref|YP_007688453.1| 442 VLDRYIPTITVLSGALIGLLAACADMIGTTGNATGTGLL 480
                                       56789*****************99988877666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (512 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.26s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 3429.13
//
Query:       gi|474934872|ref|YP_007688454.1|  [L=140]
Description: Ribosomal protein L15 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-16   60.3   2.4    4.2e-16   59.8   2.4    1.2  1  Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27
  ------ inclusion threshold ------
       0.13   13.3   5.4       0.19   12.8   5.4    1.3  1  DUF5320         Family of unknown function (DUF5320)


Domain annotation for each model (and alignments):
>> Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.8   2.4   4.7e-20   4.2e-16       2     126 ..      17     138 ..      16     140 .] 0.82

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 4.7e-20
                                       GGGTSST..TTTTTTTT-S--......S--..........---.GGG..---EEEEHHHHHHTTTTGTTS.--...- CS
                    Ribosomal_L27A   2 GktgGrG..hkGqkkrsgvkkkpgfeGGqmplyrr.lpkrGfk.nskfkkeykvvnlkdLdelideerle.la...d 70 
                                       Gk++GrG  + G + +sg  k  ++  G  +  r    +rGfk  +   k ++++n+ +L++ +d+ + +  a   +
  gi|474934872|ref|YP_007688454.1|  17 GKKSGRGagMIGGRGQSGLCKTGKI--GMLKYDRDhWGRRGFKrPQSMVKANTTINVAELKKSMDRFVTSgFAtqdG 91 
                                       7788776446777777775555556..6565555415679***8444578889*************99987779888 PP

                                       ---EEEGGGTTTTSSS....SE.EEE--S---.--EEEESEE-HHHHHHHHHTT-EE CS
                    Ribosomal_L27A  71 eaeeidleelaeaglikkkdgv.KvlgkgeltkklkvkaskfSkkAkekIeaaGGkv 126
                                       ++ +++l+e           g+ K+lg+g++  +++v++ ++S+kAkekIeaaGG++
  gi|474934872|ref|YP_007688454.1|  92 DKFTVNLTEA----------GIdKLLGSGNIDIAVDVTVAEVSAKAKEKIEAAGGSI 138
                                       99********..........***********************************97 PP

>> DUF5320  Family of unknown function (DUF5320)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   5.4   2.1e-05      0.19      10      59 ..      14      65 ..       7      88 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.1e-05
                           DUF5320 10 mGlGpmtGrglGyCagadapgyansagfGr..grg.grglgrgfgrrrragga 59
                                       G+G ++Grg+G+ +g  ++g  +   +G+        + +rgf r + +  a
  gi|474934872|ref|YP_007688454.1| 14 HGRGKKSGRGAGMIGGRGQSGLCKTGKIGMlkY-DrDHWGRRGFKRPQSMVKA 65
                                      69********************99988888642.2366667777764444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 951.80
//
Query:       gi|474934873|ref|YP_007688455.1|  [L=157]
Description: LSU ribosomal protein L30P [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-12   46.5   0.0    4.3e-12   45.7   0.0    1.4  1  Ribosomal_L30  Ribosomal protein L30p/L7e


Domain annotation for each model (and alignments):
>> Ribosomal_L30  Ribosomal protein L30p/L7e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   0.0   2.4e-16   4.3e-12       2      51 .]       7      56 ..       6      56 .. 0.96

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 2.4e-16
                                      EEEE-S-STTS-HHHHHHHHHTT-SSTTEEEE--SSHHHHHHHHHCCCGE CS
                     Ribosomal_L30  2 fVtrirsiigvppkvrktLqlLgLrkingtvvklntpsirGmLkkVkhlV 51
                                       V+r+r ++gv  +++ t++l gL++ n+ vv++ + s+rGmL+k k++V
  gi|474934873|ref|YP_007688455.1|  7 IVIRVRATVGVRGDIQETMKLVGLNRPNHAVVLPESDSYRGMLQKMKDYV 56
                                      69**************************99999999*************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1041.46
//
Query:       gi|474934874|ref|YP_007688456.1|  [L=213]
Description: SSU ribosomal protein S5P [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-22   79.3   0.5    2.9e-22   78.4   0.5    1.5  1  Ribosomal_S5    Ribosomal protein S5, N-terminal domain
      4e-20   71.0   0.1    6.4e-20   70.4   0.1    1.3  1  Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain
  ------ inclusion threshold ------
       0.19   12.0   0.0       0.43   10.8   0.0    1.5  2  RyR             RyR domain


Domain annotation for each model (and alignments):
>> Ribosomal_S5  Ribosomal protein S5, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.4   0.5   4.9e-26   2.9e-22       1      64 [.      33      96 ..      33      97 .. 0.98

  Alignments for each domain:
  == domain 1  score: 78.4 bits;  conditional E-value: 4.9e-26
                                      XEEEEEEEEEEEEEETTEEEEEEEEEEEEEETTTEEEEEEEEESSHHHHHHHHHHHHHHTEEE- CS
                      Ribosomal_S5  1 lkekvlkikrvqkvtkgGrrtsfsalvvvGdgnGlvGlGvgkakevatAirkAiekAkknlvpv 64
                                      l+++v+++++vq++t++Grr +f+++++vG+g+G +G+G +k+kev  +i+kAi++Ak+n++++
  gi|474934874|ref|YP_007688456.1| 33 LQDEVIDLNMVQRMTDSGRRVRFAVTCIVGNGDGFIGVGRAKGKEVGPSIKKAIDNAKLNIIEI 96
                                      799***********************************************************98 PP

>> Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.4   0.1   1.1e-23   6.4e-20       2      70 ..     119     188 ..     118     190 .. 0.96

  Alignments for each domain:
  == domain 1  score: 70.4 bits;  conditional E-value: 1.1e-23
                                       EEETTEEEEEEE--TT--EES-HHHHHHHHHHT--SEE---BS.-SSHHHHHHHHHHHHHHTTTT-.-GG CS
                    Ribosomal_S5_C   2 gkfgavkvllkpaprGtGiiaggavravlelaGikDvlakslg.srnpinvvkAtfeALkklrspeevaa 70 
                                       g++g+v+v+l+paprG G+ +g++++++l laG++D +  + g +++++n   Atf+AL+++++++ +++
  gi|474934874|ref|YP_007688456.1| 119 GRCGSVTVYLRPAPRGIGLAVGDVAKSLLTLAGVHDAWGFATGnTKTKVNYCMATFDALRQTSKMRVTPE 188
                                       99*************************************************************9987765 PP

>> RyR  RyR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.3   7.6e+03      12      27 ..       2      17 ..       1      18 [. 0.81
   2 ?   10.8   0.0   7.2e-05      0.43      40      81 ..     155     195 ..     149     198 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.3
                                      ---HHHHTTHHHHHHH CS
                               RyR 12 tLpeeleklveklAen 27
                                      +L+ e++++ e lA +
  gi|474934874|ref|YP_007688456.1|  2 VLNGEVTTMSEALATK 17
                                      6888999999999975 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 7.2e-05
                                       T-EE-SS-BTTTTEETT-S-GGGS-HHHHHHHHHHHHHHHHH CS
                               RyR  40 gwsygeerdekkkthplLvpydaLsekekekdrekaqetlkt 81 
                                        w + ++ ++k+k+++++  +daL +++k +++ + +e lk+
  gi|474934874|ref|YP_007688456.1| 155 AWGFATG-NTKTKVNYCMATFDALRQTSKMRVTPEQTERLKI 195
                                       5666666.8899********************9999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       265  (0.0147805); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1385.62
//
Query:       gi|474934875|ref|YP_007688457.1|  [L=166]
Description: LSU ribosomal protein L18P [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-25   89.4   3.0    2.7e-19   69.7   1.6    2.2  2  Ribosomal_L5e    Ribosomal large subunit proteins 60S L5, and
    7.3e-09   36.0   0.2    9.3e-09   35.7   0.2    1.2  1  Ribosomal_L18p   Ribosomal L18 of archaea, bacteria, mitoch. 
  ------ inclusion threshold ------
      0.021   14.9   0.0      0.032   14.3   0.0    1.3  1  Acetyltransf_14  YopJ Serine/Threonine acetyltransferase


Domain annotation for each model (and alignments):
>> Ribosomal_L5e  Ribosomal large subunit proteins 60S L5, and 50S L18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.7   1.6   4.6e-23   2.7e-19       2      96 ..       6      93 ..       5      99 .. 0.93
   2 !   19.4   0.0   1.4e-07   0.00084     130     162 ..     100     132 ..      92     133 .. 0.90

  Alignments for each domain:
  == domain 1  score: 69.7 bits;  conditional E-value: 4.6e-23
                     Ribosomal_L5e  2 rfqvkfrrrregktdYyarkrliiqdknkyntpkyRlvVrvtnkdiicqiayakiegdkvlaaayskelpkygvkvglt 80
                                      r++v frrrre++tdYyar++l++        +  R vVr +nk+i++q++   +egdk++a+a++k+l k+g +++  
  gi|474934875|ref|YP_007688457.1|  6 RYKVAFRRRRECRTDYYARRKLLAS-------HETRAVVRRSNKNITVQFVDFAMEGDKIIASADTKQLAKMGWEHSCS 77
                                      9*********************975.......5569******************************************* PP

                     Ribosomal_L5e 81 nyaaaYatglllarrl 96
                                         aaY++g+  + r+
  gi|474934875|ref|YP_007688457.1| 78 TLPAAYLVGYAAGLRA 93
                                      *********9877665 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 1.4e-07
                     Ribosomal_L5e 130 kaiLdvGLartttgakvfgalkgavdgglsiph 162
                                        a+Ld G++   +g  +f++ kg++d+gl+ip 
  gi|474934875|ref|YP_007688457.1| 100 YAVLDLGMQNPQHGGVLFAVAKGMIDAGLEIPC 132
                                       689****************************96 PP

>> Ribosomal_L18p  Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.2   1.6e-12   9.3e-09       5     116 .]      10     130 ..       6     130 .. 0.80

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 1.6e-12
                                       HHHCHHHHH....HTTT--TTSSS-EEEEEE-SS-EEEEEE-TT..T--EEEEECS-SCCCT..S-SSSCHHHHHHH CS
                    Ribosomal_L18p   5 earkrRhkR....irkklsgtaerprlvvfrsnrhiyaQviddv..kgktlasastlekelk..lkstknkeaakkv 73 
                                       + r+rR+ R    +r+kl       r vv rsn++i +Q +d +   +k++asa+t + +     +s ++  aa  v
  gi|474934875|ref|YP_007688457.1|  10 AFRRRRECRtdyyARRKLLASH-ETRAVVRRSNKNITVQFVDFAmeGDKIIASADTKQLAKMgwEHSCSTLPAAYLV 85 
                                       5577777774433688888655.6899***************8622569999999987655556788889999**** PP

                                       HHHHHHHHCHHCHTC-EE--TTS..SS-CHHHHHHHHHHCTSSB- CS
                    Ribosomal_L18p  74 geliAerakekgiekvvfDrggy..kYhGrvaalAdaaReaGlkf 116
                                       g +   rak+++ie +v D g +  +  G++ a+A+++ +aGl++
  gi|474934875|ref|YP_007688457.1|  86 GYAAGLRAKKAEIEYAVLDLGMQnpQHGGVLFAVAKGMIDAGLEI 130
                                       *******************9865326778889**********985 PP

>> Acetyltransf_14  YopJ Serine/Threonine acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   5.4e-06     0.032      70     157 ..      31     120 ..      10     126 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.4e-06
                   Acetyltransf_14  70 rsrravVnlgssgiHhvaldvrvkpdgktsiivlepA.......pvkslgaallaaeytklleaalkkkgpdaklav 139
                                       ++ ravV++++++i +  +d+ ++ d+      + +A         +  + ++l a y    +a l+ k  +++ av
  gi|474934875|ref|YP_007688457.1|  31 HETRAVVRRSNKNITVQFVDFAMEGDKI-----IASAdtkqlakMGWEHSCSTLPAAYLVGYAAGLRAKKAEIEYAV 102
                                       3446999999999999999999994442.....23333345555557888889999999999*************** PP

                   Acetyltransf_14 140 veldiQkSssdCaiFsLs 157
                                       ++l++Q  ++++++F+++
  gi|474934875|ref|YP_007688457.1| 103 LDLGMQNPQHGGVLFAVA 120
                                       ***************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1071.04
//
Query:       gi|474934876|ref|YP_007688458.1|  [L=153]
Description: LSU ribosomal protein L19E [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-56  190.4   4.1    1.7e-56  190.3   4.1    1.0  1  Ribosomal_L19e  Ribosomal protein L19e
  ------ inclusion threshold ------
      0.049   13.3   2.0      0.062   13.0   2.0    1.2  1  Ribosomal_L4    Ribosomal protein L4/L1 family
       0.16   11.5   0.0       0.18   11.4   0.0    1.1  1  Lant_dehydr_C   Lantibiotic biosynthesis dehydratase C-term


Domain annotation for each model (and alignments):
>> Ribosomal_L19e  Ribosomal protein L19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.3   4.1   2.9e-60   1.7e-56       1     141 [.       3     143 ..       3     146 .. 0.98

  Alignments for each domain:
  == domain 1  score: 190.3 bits;  conditional E-value: 2.9e-60
                                       -THHHHHHHHHHTTS-GGGEEE-GGGHHHHHH--SHHHHHHHHHTTSEEE-------THHHHHHHHHHHTT-S-SGG CS
                    Ribosomal_L19e   1 dlklqkrlaasvlkvGknrvwldpeeleeiaeAitredirklikdglIikkpkkgnsrararerkekkrkgrrrgsG 77 
                                       dl++qkrlaa++lk+G+nrvw+dpe++ee++++itr d+r+ i++glI++kpk+g+sr+r+r+ +++k++g+r+g+G
  gi|474934876|ref|YP_007688458.1|   3 DLRNQKRLAADILKCGENRVWIDPEHIEEVQDCITRGDVRTAIDSGLIKAKPKNGTSRGRIRHAAKQKASGKRKGPG 79 
                                       5899************************************************************************* PP

                                       G--S-HHHHS-HHHHHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHTT--SSHHHHHHHHT CS
                    Ribosomal_L19e  78 krkGtkeaRlpekelWikriRalRrlLkelrekkkidkktYrelYrkakGgefknkavLkeyie 141
                                       +rkGt++aR+pek++Wi riR +R++Lk+lr+++ki+ + Yr +YrkakGg++ ++++Lk+++ 
  gi|474934876|ref|YP_007688458.1|  80 SRKGTANARVPEKRQWIARIRPIRDELKQLRADGKITPSIYRLYYRKAKGGSYTSRRNLKQHMI 143
                                       *************************************************************996 PP

>> Ribosomal_L4  Ribosomal protein L4/L1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   2.0     1e-05     0.062      35      67 ..      65      97 ..      50     127 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1e-05
                                      ---TTTSS---S-SS-SSSSSS---S-TTSTTS CS
                      Ribosomal_L4 35 tkarsevsgsgrklwkQKGtGrARvgsirspia 67
                                      + a+++ sg+++ +++ KGt++ARv++ r  ia
  gi|474934876|ref|YP_007688458.1| 65 HAAKQKASGKRKGPGSRKGTANARVPEKRQWIA 97
                                      5588999********************994443 PP

>> Lant_dehydr_C  Lantibiotic biosynthesis dehydratase C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.9e-05      0.18     242     278 ..      80     119 ..      37     142 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.9e-05
                                       ..........HHHHHHHHHHHHHHHHHHHHHHTTS-----TTTTTH CS
                     Lant_dehydr_C 242 p.........pflaewaerlrelrrrlealeasgeltldsldaagl 278
                                       +         p  ++w++r r++r+ l++l a+g++t       ++
  gi|474934876|ref|YP_007688458.1|  80 SrkgtanarvPEKRQWIARIRPIRDELKQLRADGKITP------SI 119
                                       1222444566999**********************998......44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 887.69
//
Query:       gi|474934877|ref|YP_007688459.1|  [L=224]
Description: Ribosomal protein L32E [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-38  130.5   0.0    5.6e-38  129.7   0.0    1.4  1  Ribosomal_L32e  Ribosomal protein L32
    7.8e-05   23.2   0.6     0.0015   19.1   0.2    3.0  3  HHH_5           Helix-hairpin-helix domain
  ------ inclusion threshold ------
      0.096   12.8   0.0       0.24   11.5   0.0    1.6  1  Trans_reg_C     Transcriptional regulatory protein, C termina
       0.12   12.3   0.1        1.1    9.2   0.1    2.5  2  HHH             Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> Ribosomal_L32e  Ribosomal protein L32
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.7   0.0   1.2e-41   5.6e-38       2     108 .]     113     217 ..     112     217 .. 0.99

  Alignments for each domain:
  == domain 1  score: 129.7 bits;  conditional E-value: 1.2e-41
                                       -----TTTTT-TTS-SS------TT-TTTTT-TTS-----GGG---TTTTT--TTS-EEEEESSGGGGTT--TTTE. CS
                    Ribosomal_L32e   2 kkFirhqsdryvklkeswrkprGidnrvrrrfkgqilmpkiGYgspkktrgllpsGfkkvlVhnvkeLevllmenks 78 
                                       + F+r+++ ry  l+++wr+p+Gi++++rr fk +++m++iGY+ p + r+l+psGf++vlV+nv+ Le+++++++ 
  gi|474934877|ref|YP_007688459.1| 113 PAFKRQEWYRYSMLGDKWRRPKGIHSKMRRGFKRRPPMVEIGYRGPVAARNLHPSGFEEVLVYNVDGLENIDPKTQ- 188
                                       78**************************************************************************. PP

                                       .EEEE-TTS-HHHHHHHHHHHHHTT-EBSS CS
                    Ribosomal_L32e  79 yaaeiahsVsskkrkeiverAaelgikVtN 108
                                        aa+i+ +V+ kkr++i++rA+elgi+V+N
  gi|474934877|ref|YP_007688459.1| 189 -AARIGGTVGVKKRIMIEDRAKELGIRVLN 217
                                       .****************************9 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.35   1.6e+03      33      46 ..       2      15 ..       1      20 [. 0.79
   2 !   19.1   0.2   3.3e-07    0.0015      20      54 ..      21      62 ..      16      64 .. 0.79
   3 ?   -0.6   0.0      0.46   2.1e+03      11      26 ..     157     172 ..     157     200 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.35
                                      -HHHHHTSTTS-HH CS
                             HHH_5 33 dveeLakipGiGkk 46
                                      +v+e+ ++pG+  +
  gi|474934877|ref|YP_007688459.1|  2 TVKEFKDLPGFKDE 15
                                      6899******9665 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 3.3e-07
                                      TT.T--SHHHHHHS......-HHHHHTSTTS-HHHHHHHHHH CS
                             HHH_5 20 sa.Giesvedlaaa......dveeLakipGiGkktAeriile 54
                                      +  Gi+sve+l +a      +++ + ++ G+G+kt ++++++
  gi|474934877|ref|YP_007688459.1| 21 ESiGITSVEQLRDAvnddekAKDIIKTLSGVGPKTIDKWKEA 62
                                      5559*******9997653323344888************986 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.46
                                       -HHHHHHHHTTT--SH CS
                             HHH_5  11 GpktAlallsaGiesv 26 
                                       Gp+ A++l+  G+e v
  gi|474934877|ref|YP_007688459.1| 157 GPVAARNLHPSGFEEV 172
                                       7888888888877743 PP

>> Trans_reg_C  Transcriptional regulatory protein, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   5.3e-05      0.24      49      74 ..      27      52 ..      22      53 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.3e-05
                                      HHHHHHHHHHTTTTSSSSEEEETTTE CS
                       Trans_reg_C 49 hisrLRkkLeddekkprlIetvrgvG 74
                                       + +LR+ ++ddek+++ I+t+ gvG
  gi|474934877|ref|YP_007688459.1| 27 SVEQLRDAVNDDEKAKDIIKTLSGVG 52
                                      5899********************99 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.34   1.5e+03       9      18 ..       2      11 ..       2      11 .. 0.93
   2 ?    9.2   0.1   0.00025       1.1      13      25 ..      45      57 ..      39      58 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.34
                                      SHHHHHTSTT CS
                               HHH  9 sreeLlalPG 18
                                      +++e ++lPG
  gi|474934877|ref|YP_007688459.1|  2 TVKEFKDLPG 11
                                      799******9 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00025
                                      HHTSTT-SHHHHH CS
                               HHH 13 LlalPGVGpktAe 25
                                      +++l+GVGpkt +
  gi|474934877|ref|YP_007688459.1| 45 IKTLSGVGPKTID 57
                                      677********65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1546.01
//
Query:       gi|474934878|ref|YP_007688460.1|  [L=185]
Description: LSU ribosomal protein L6P [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-25   88.9   3.1    7.7e-21   74.6   0.2    2.3  2  Ribosomal_L6  Ribosomal protein L6
  ------ inclusion threshold ------
      0.056   13.9   0.1       0.51   10.8   0.0    2.0  2  HtaA          Htaa
       0.18   11.8   0.0       0.35   10.9   0.0    1.4  1  TubC_N        TubC N-terminal docking domain


Domain annotation for each model (and alignments):
>> Ribosomal_L6  Ribosomal protein L6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.6   0.2   1.3e-24   7.7e-21       1      76 []      13      85 ..      13      85 .. 0.95
   2 !   15.0   0.3   4.8e-06     0.029       1      63 [.      97     160 ..      97     173 .. 0.85

  Alignments for each domain:
  == domain 1  score: 74.6 bits;  conditional E-value: 1.3e-24
                                      CSTTEEEEEETTTEEEEEESSEEEEEE-CTT.SEEEEEECSTEEEEEECSESCHHHHHHHHHHHHHHHHHHHHHHTC CS
                      Ribosomal_L6  1 iPvgvrvsikggqlvlvlGpkgeltreipeg.vtvevkvegnkvtvivvsgidkekvAligtvrslinnmikGVteg 76
                                      iP+gv+vs++g ++++v+Gpkgel+r++++  v+++  v ++kv v +     k k+ ++gt+r++++nm +GVteg
  gi|474934878|ref|YP_007688460.1| 13 IPDGVTVSLDG-NVLKVKGPKGELSRTFSHPrVNIA--VADGKVSVSCEYPRIKDKA-MVGTFRAHVRNMFHGVTEG 85
                                      8*********8.******************955555..88*****************.*****************98 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 4.8e-06
                                       CSTTEEEEEET..TTEEEEEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHH....HHHHHHH CS
                      Ribosomal_L6   1 iPvgvrvsikg..gqlvlvlGpkgeltreipegvtvevkvegnkvtvivvsgidkekv....Aligtvr 63 
                                       +P++v v+ k+  +++++  G + ++ + i  + +v+++     +++++v+gi++e+v    A+ ++++
  gi|474934878|ref|YP_007688460.1|  97 FPMKVAVNDKEkrVEVNNYMGGRAPRYAVIVGDSKVKIS-----GQDVTVTGISIEDVgqtaANMEKCT 160
                                       68888888888889*************************.....9999**********88887777766 PP

>> HtaA  Htaa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   8.5e-05      0.51      55      95 ..      17      58 ..       8      78 .. 0.83
   2 ?    1.1   0.0     0.084     5e+02      67     102 ..      85     131 ..      69     163 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 8.5e-05
                              HtaA 55 geirfkGs.vhftghngaLdltlsnpkievsgetgtLladvs 95
                                      ++++++G+ ++++g +g L  t+s+p+++++ + g++++  +
  gi|474934878|ref|YP_007688460.1| 17 VTVSLDGNvLKVKGPKGELSRTFSHPRVNIAVADGKVSVSCE 58
                                      7899****889*******************999998888766 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.084
                              HtaA  67 ghngaLdltlsnpkievsgetgtLladvsskdkeg............g 102
                                       g++++L++ +s++ ++v+ + ++  ++v++ ++ g            +
  gi|474934878|ref|YP_007688460.1|  85 GYTYTLKIVFSHFPMKVAVNDKEKRVEVNN-YMGGrapryavivgdsK 131
                                       557777777777666555555555555543.22222222223333322 PP

>> TubC_N  TubC N-terminal docking domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   5.8e-05      0.35      12      33 ..      16      37 ..      13      40 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.8e-05
                            TubC_N 12 gIkLwleggrLrfrApkgaltp 33
                                      g++++l+g+ L+++ pkg l++
  gi|474934878|ref|YP_007688460.1| 16 GVTVSLDGNVLKVKGPKGELSR 37
                                      9*****************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1255.11
//
Query:       gi|474934879|ref|YP_007688461.1|  [L=129]
Description: SSU ribosomal protein S8P [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.9e-25   86.9   0.0    1.2e-24   86.7   0.0    1.1  1  Ribosomal_S8  Ribosomal protein S8
  ------ inclusion threshold ------
      0.044   14.2   0.1       0.08   13.3   0.1    1.4  1  Retro_M       Retroviral M domain


Domain annotation for each model (and alignments):
>> Ribosomal_S8  Ribosomal protein S8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.7   0.0   1.3e-28   1.2e-24       1     127 []       4     129 .]       4     129 .] 0.90

  Alignments for each domain:
  == domain 1  score: 86.7 bits;  conditional E-value: 1.3e-28
                                       -HHHHHHHHHHHHHHTT-SEEEE.E--HHHHHHHHHHHHCTSEEEEEEE.CCCCCCEEEEE-BSSS-SBSSSEEEE- CS
                      Ribosomal_S8   1 DpiadmltrirNaekakkeevev.pasklkeeilkvLkeeGyikdfeve.eekkkkikielkynkkkksvikklkrv 75 
                                       D+++d+++ i+Na+  +k e+e+ p+skl+ ++lkvL+++Gyi++fe++ + k  k++++lk   ++++vik    v
  gi|474934879|ref|YP_007688461.1|   4 DTLNDAMCVIKNASLSGKAECEIaPSSKLIGHVLKVLQDNGYISQFEYVdDGKAGKFRVQLKGAINDCGVIKPRYSV 80 
                                       89**********************************************9777788888888888888*****87777 PP

                                       SBTTC--EE-CCC---CGGGTSEEEEEETTEEEEHHHHHHCT--EEEEEEEE CS
                      Ribosomal_S8  76 skpgrrvYakvkelpkvlnglGiaivsTskGvmtdkeArkkkvGGevlayvw 127
                                       +    + Y  ++ lp   + +G++i +T+ Gv+++ +A++ ++GG++layv+
  gi|474934879|ref|YP_007688461.1|  81 KAVDIEKYE-ARYLP--AQDFGVLIFTTTDGVVSQFKAKELGIGGKLLAYVY 129
                                       777777554.34555..578*******************************9 PP

>> Retro_M  Retroviral M domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   8.9e-06      0.08       2      38 ..      11      46 ..      10      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.9e-06
                           Retro_M  2 avikvissacktycgkispskkeigamlsllqkegll 38
                                      +vik  s + k+ c  i+ps k ig +l +lq +g +
  gi|474934879|ref|YP_007688461.1| 11 CVIKNASLSGKAEC-EIAPSSKLIGHVLKVLQDNGYI 46
                                      58999999999999.6*****************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 798.76
//
Query:       gi|474934880|ref|YP_007688462.1|  [L=48]
Description: SSU ribosomal protein S14P [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.7e-13   48.0   4.7    8.5e-13   47.9   4.7    1.1  1  Ribosomal_S14  Ribosomal protein S14p/S29e


Domain annotation for each model (and alignments):
>> Ribosomal_S14  Ribosomal protein S14p/S29e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   4.7   4.7e-17   8.5e-13      18      54 .]      13      48 .]       2      48 .] 0.94

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 4.7e-17
                                      -SSS--SSSEE-GGG-..EHHHHHHHTTT...TT-EE-- CS
                     Ribosomal_S14 18 CrvtGrprGvirkfgL..sRicfRelAlkgelpGvkKaS 54
                                      C  +Gr+rG+irk+g+  +R+cfR++A +    G+kK+S
  gi|474934880|ref|YP_007688462.1| 13 CDRCGRRRGIIRKYGMhlCRQCFRDMAPE---LGFKKYS 48
                                      *****************************...******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.47
# Mc/sec: 308.09
//
Query:       gi|474934881|ref|YP_007688463.1|  [L=174]
Description: LSU ribosomal protein L5P [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-24   85.0   0.0    5.1e-24   84.3   0.0    1.4  1  Ribosomal_L5_C  ribosomal L5P family C-terminus
    1.1e-16   60.9   0.7    1.9e-16   60.1   0.7    1.4  1  Ribosomal_L5    Ribosomal protein L5


Domain annotation for each model (and alignments):
>> Ribosomal_L5_C  ribosomal L5P family C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.3   0.0   5.7e-28   5.1e-24       1      94 []      63     163 ..      63     163 .. 0.89

  Alignments for each domain:
  == domain 1  score: 84.3 bits;  conditional E-value: 5.7e-28
                    Ribosomal_L5_C   1 piGvkvtLrgekmyefldkllevvlprlrdFkGiskssfdgrGnvsfGikeqiifpeieydkdkgifGmditivtta 77 
                                       p+G+kvtLrge +++fl+++l + ++r+       ++sfd++Gn+sfGi+++++f +++yd+++gifGmd+++v+++
  gi|474934881|ref|YP_007688463.1|  63 PLGCKVTLRGEIAEDFLKRALIIRENRVY------SYSFDKEGNMSFGISDYTDFDGMKYDPEIGIFGMDVNVVVRR 133
                                       78***************************......99**************************************** PP

                    Ribosomal_L5_C  78 k....tde..........earallkelgipf 94 
                                       +    +++          e+r +l++++i+f
  gi|474934881|ref|YP_007688463.1| 134 TggtrVERralqarripkEHR-VLRDEAIEF 163
                                       *97553336777777776666.888777776 PP

>> Ribosomal_L5  Ribosomal protein L5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   0.7   2.1e-20   1.9e-16       1      57 []       6      59 ..       6      59 .. 0.96

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 2.1e-20
                                      SCTTS-EEEEEEEEEE-SSSSSCHHHHHCCHHHHCCCHSS--EECC--TTCTTTCSC CS
                      Ribosomal_L5  1 NvMqvPrleKivinmgvGeagedkkllekaakeLaeItGQkPvvtkakksianFkiR 57
                                      N+ +  r+eK+++n+gvGeage+   l ka+k+L+ +tGQkPv+t +k   ++ +iR
  gi|474934881|ref|YP_007688463.1|  6 NPLRALRIEKVTVNIGVGEAGEK---LVKAMKVLEMVTGQKPVQTISKTVNRDLGIR 59
                                      8999*******************...**********************998888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 1261.52
//
Query:       gi|474934882|ref|YP_007688464.1|  [L=234]
Description: Ribosomal protein S4E [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.7e-19   67.8   0.0    1.1e-18   66.9   0.0    1.5  1  Ribosomal_S4e  Ribosomal family S4e
    4.4e-09   36.3   1.6    4.4e-09   36.3   1.6    1.9  2  RS4NT          RS4NT (NUC023) domain
    8.4e-08   31.8   0.0    1.9e-07   30.7   0.0    1.6  1  S4             S4 domain
  ------ inclusion threshold ------
      0.026   14.2   0.2       0.15   11.7   0.1    2.4  2  40S_S4_C       40S ribosomal protein S4 C-terminus
      0.033   14.0   0.3       0.31   10.9   0.0    2.3  2  S4_2           S4 domain
      0.081   12.9   0.3       0.26   11.3   0.3    2.0  1  KOW            KOW motif


Domain annotation for each model (and alignments):
>> Ribosomal_S4e  Ribosomal family S4e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.9   0.0   3.8e-22   1.1e-18       2      75 .]      92     164 ..      91     164 .. 0.98

  Alignments for each domain:
  == domain 1  score: 66.9 bits;  conditional E-value: 3.8e-22
                                       TEEEEEEE-TTSSEEEEEE-TTCCCEEEEEECEEEEECCCEEEEEETTS-EEEESSTT-STTEEEEEETTTTEE CS
                     Ribosomal_S4e   2 genyrllydtkgrfalhkItseeakyKLcKikkkttvkkgipqlvthdGrtirypdpdikvnDtvkidleenkI 75 
                                       ++n+r+++ +kg+++l++I + ++k+ + ++++kt+v++g++ql+++ Gr+i+ +++   v+D+vk++l++n+I
  gi|474934882|ref|YP_007688464.1|  92 EKNFRVVLTPKGKITLVEIPEANSKWIMARVEGKTIVSGGKTQLNLSGGRNILSEEK-LAVGDSVKLQLDNNEI 164
                                       79******************************************************9.**************98 PP

>> RS4NT  RS4NT (NUC023) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   1.6   1.5e-12   4.4e-09       4      35 ..       2      33 ..       1      35 [. 0.95
   2 ?   -3.0   0.0       2.8   8.4e+03      14      24 ..     115     125 ..     113     125 .. 0.77

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 1.5e-12
                                      ---EETTTS-TTS---SSSSSEE----SSSS- CS
                             RS4NT  4 kkHLKrlaAPkhWpldkkegvfavkPspGPHk 35
                                      + H+Kr+a Pk+Wp++kk +v+a+k ++G+H+
  gi|474934882|ref|YP_007688464.1|  2 SDHIKRIAMPKTWPIPKKAHVYATKQRAGAHS 33
                                      68*****************************8 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.8
                                       TTS---SSSSS CS
                             RS4NT  14 khWpldkkegv 24 
                                       + W +++ eg+
  gi|474934882|ref|YP_007688464.1| 115 SKWIMARVEGK 125
                                       68999998875 PP

>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0   6.2e-11   1.9e-07      10      48 .]      48      86 ..      42      86 .. 0.95

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 6.2e-11
                                      TTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTCEE CS
                                S4 10 lglassrreArqlIehGrVlVNGkvvkdpsyrVkpgDvi 48
                                      l+ + + reA+++I  +   VNGk vkd++++V+ +Dv+
  gi|474934882|ref|YP_007688464.1| 48 LKVCDTAREAKKIIANRDLFVNGKAVKDAKTPVGIMDVV 86
                                      789**********************************98 PP

>> 40S_S4_C  40S ribosomal protein S4 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.5   4.5e+03      24      29 ..      85      90 ..      84      92 .. 0.84
   2 ?   11.7   0.1     5e-05      0.15      11      30 ..     214     232 ..     210     233 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.5
                                      SS---S CS
                          40S_S4_C 24 wvsLPk 29
                                      +vsLPk
  gi|474934882|ref|YP_007688464.1| 85 VVSLPK 90
                                      69***9 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 5e-05
                                       GGGEEE--STTS-SS---SS CS
                          40S_S4_C  11 lsNvFvIGkgnkpwvsLPkg 30 
                                        +NvFvIG g++ +  LP+g
  gi|474934882|ref|YP_007688464.1| 214 KENVFVIGTGSSEI-VLPEG 232
                                       58******988765.57765 PP

>> S4_2  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0    0.0001      0.31      13      56 ..      47      87 ..      41      98 .. 0.70
   2 ?    0.6   0.0      0.16   4.9e+02      47      58 ..     147     158 ..     122     165 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0001
                              S4_2 13 lLKlaglvesGgeaKafiaegeVkvNGevetrRgkKlraGdvVe 56
                                      +LK   ++++  eaK +ia+ + +vNG+  +  +  +   dvV+
  gi|474934882|ref|YP_007688464.1| 47 MLK---VCDTAREAKKIIANRDLFVNGKAVKDAKTPVGIMDVVS 87
                                      555...5566679**************98765555555555555 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.16
                              S4_2  47 kKlraGdvVeid 58 
                                        Kl  Gd V+++
  gi|474934882|ref|YP_007688464.1| 147 EKLAVGDSVKLQ 158
                                       699999999984 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3   8.7e-05      0.26       1      16 [.     172     187 ..     172     206 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.7e-05
                                       TTSEEEESSSTTTTCE CS
                               KOW   1 pGdhVkVvsGphkGkt 16 
                                       +G +V V+sG h Gk+
  gi|474934882|ref|YP_007688464.1| 172 KGAYVLVISGSHSGKV 187
                                       79************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1773.90
//
Query:       gi|474934883|ref|YP_007688465.1|  [L=123]
Description: ribosomal protein L24p/L26e, archaeal/eukaryotic [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-29  101.6   0.2      3e-29  101.3   0.2    1.1  1  Ribosomal_L26  Ribosomal proteins L26 eukaryotic, L24P archae
  ------ inclusion threshold ------
      0.083   12.7   0.0      0.091   12.6   0.0    1.1  1  NYAP_C         Neuronal tyrosine-phosphorylated phosphoinosit


Domain annotation for each model (and alignments):
>> Ribosomal_L26  Ribosomal proteins L26 eukaryotic, L24P archaeal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.3   0.2   3.3e-33     3e-29       1      82 []       3     119 ..       3     119 .. 0.99

  Alignments for each domain:
  == domain 1  score: 101.3 bits;  conditional E-value: 3.3e-33
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................. RF
                     Ribosomal_L26   1 sssrrkqrKahfnapshirrklmsapLskeLrekygvrslpir.................................. 43 
                                       ss+ r qrKa++nap+h++rk++sa+LskeL ekyg+r+ ++                                   
  gi|474934883|ref|YP_007688465.1|   3 SSKARVQRKAQYNAPAHTKRKMLSAHLSKELAEKYGRRTARVCvgdtvavvrgeekvkgveakvievftktgrvsid 79 
                                       89*************************************************************************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                     Ribosomal_L26  44 gvtrekangttvpvgihpSkvvItklkl.DkdrkkiLerk 82 
                                       gvt ++a+gt v ++ih+S++vItkl+l D  r ++L++k
  gi|474934883|ref|YP_007688465.1|  80 GVTINQADGTAVARPIHASNLVITKLNLdDPLRAEALNNK 119
                                       ****************************999*****9987 PP

>> NYAP_C  Neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adapter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0     1e-05     0.091      53     138 ..      14      99 ..       4     117 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1e-05
                            NYAP_C  53 fgsgwalqRKlsssrksketeekssedearawngsteallrldkeergagasgiPvkasgaeghsvdgspgfra.ls 128
                                       +++    +RK+ s++ ske +ek  +  ar+  g t a+ r +++ +g  a+ i v ++     s+dg +  +a  +
  gi|474934883|ref|YP_007688465.1|  14 YNAPAHTKRKMLSAHLSKELAEKYGRRTARVCVGDTVAVVRGEEKVKGVEAKVIEVFTKTGRV-SIDGVTINQAdGT 89 
                                       55666779****************9999*******************9888888876655443.5566554443134 PP

                            NYAP_C 129 Rvglplpcqt 138
                                        v++p+ +  
  gi|474934883|ref|YP_007688465.1|  90 AVARPIHASN 99 
                                       4556655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 812.27
//
Query:       gi|474934884|ref|YP_007688466.1|  [L=132]
Description: LSU ribosomal protein L14P [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.8e-38  129.3   0.5    9.4e-38  129.0   0.5    1.0  1  Ribosomal_L14  Ribosomal protein L14p/L23e


Domain annotation for each model (and alignments):
>> Ribosomal_L14  Ribosomal protein L14p/L23e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.0   0.5   5.2e-42   9.4e-38       4     122 .]      14     132 .]      12     132 .] 0.95

  Alignments for each domain:
  == domain 1  score: 129.0 bits;  conditional E-value: 5.2e-42
                                       SS-EEE--SSSSBSEEEEEEETT-.....---EE-SSSEEEEEESSS-T...TTSSCEEEEEEEE-SS-EE-TTS-E CS
                     Ribosomal_L14   4 lktrlkvaDNsgakevecikvlggk....krkaasvGdiivvsvkkakpkgkvkkgdvvkavvvrtkkevrrkdGsv 76 
                                        +t+l+v+DN+gak +++i+v  ++    + ++a vGd+i++svkk++p    +++++v avvvr+k+++rr+dG++
  gi|474934884|ref|YP_007688466.1|  14 EQTQLNVIDNTGAKIIQIITVPSYHgvtrRLPQAGVGDMIIASVKKGTP---AMRRQIVFAVVVRQKRPYRRPDGTM 87 
                                       69*******************9887666455******************...99*********************** PP

                                       EEESS-EEEEB-TTS-BSS-.B-SBEEHHHHHH.-HHHHHTBSBE. CS
                     Ribosomal_L14  77 irfddnaaVllnkkgeplGtrifgpvarelrekkflkivslApevl 122
                                       ++f+dnaaVl++++ge +Gt i+gpvare++++ +++i+++A++++
  gi|474934884|ref|YP_007688466.1|  88 VSFEDNAAVLVTDTGETKGTDIKGPVAREAADR-WPRIAATASTIV 132
                                       ********************************9.********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 754.36
//
Query:       gi|474934885|ref|YP_007688467.1|  [L=112]
Description: SSU ribosomal protein S17P [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-24   86.2   0.9    1.5e-24   85.9   0.9    1.1  1  Ribosomal_S17    Ribosomal protein S17
     0.0029   18.0   0.3     0.0065   16.8   0.0    1.7  2  Ribosomal_S17_N  Ribosomal_S17 N-terminal


Domain annotation for each model (and alignments):
>> Ribosomal_S17  Ribosomal protein S17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.9   0.9   1.7e-28   1.5e-24       1      68 []      39     107 ..      39     107 .. 0.98

  Alignments for each domain:
  == domain 1  score: 85.9 bits;  conditional E-value: 1.7e-28
                                       EEEEE--STTEEEEEEEEEEEETTTTEEEEEEEEEEEE-TTTS.--TT-EEEEEEECECSSSEEEEEEE CS
                     Ribosomal_S17   1 GvVvsdkmdkTvvVrverlvkhpkykkyvkrrkkylahdenns.vkvGDiVrieecrPlSktkrfvvve 68 
                                       GvV s kmdkTv+V++++++  +ky++y+kr+ +y ah  ++  +kvGD V+i+ecrP+Skt++fv ve
  gi|474934885|ref|YP_007688467.1|  39 GVVDSIKMDKTVIVKRDYFKFEQKYERYEKRSVRYAAHAAPCLgLKVGDSVKIMECRPISKTVSFVAVE 107
                                       899999***********************************************************9875 PP

>> Ribosomal_S17_N  Ribosomal_S17 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   7.3e-07    0.0065      45      69 .]      13      37 ..       4      37 .. 0.86
   2 ?   -2.3   0.1      0.65   5.8e+03      30      30 ..      64      64 ..      48      77 .. 0.50

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.3e-07
                                      GGGS-----TTSSSSSS----S-EE CS
                   Ribosomal_S17_N 45 eAiegtYiDkKCPFtGnvsirGriL 69
                                      +A eg+  D  CPF G+ s+rG+++
  gi|474934885|ref|YP_007688467.1| 13 AAPEGECTDPNCPFHGTLSVRGQVI 37
                                      4779999***************985 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.65
                                      - CS
                   Ribosomal_S17_N 30 k 30
                                      +
  gi|474934885|ref|YP_007688467.1| 64 E 64
                                      1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 665.31
//
Query:       gi|474934886|ref|YP_007688468.1|  [L=84]
Description: RNase P/RNase MRP subunit p29 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-18   64.9   0.1    5.4e-18   64.7   0.1    1.1  1  UPF0086   Domain of unknown function UPF0086


Domain annotation for each model (and alignments):
>> UPF0086  Domain of unknown function UPF0086
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.7   0.1     3e-22   5.4e-18       3      84 .]       6      82 ..       4      82 .. 0.93

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 3e-22
                                      HCCSXXSS-EEEEEECSSTTTTTEEEEEEEEETTEEEEEECTTEEEEEESTTCEEEEEE.TTEEEEEECCCCSSXHHHH CS
                           UPF0086  3 LlkadlhGaeveVvrsknpslvgikGiVvkEtkntlkivtkksrvktvpKegsvFefevkdvlevevdGsqlryrpadR 81
                                      +++ +++G++v V+++      gi+G+Vv+Etknt+ i++     ++vpK+g  F+f++ ++ +++++Gs++++rp+dR
  gi|474934886|ref|YP_007688468.1|  6 MMRTEFIGLDVVVLSAP---FSGISGVVVDETKNTFTIES-AGTERMVPKSGNEFRFTY-RNEQIDIEGSKILHRPEDR 79
                                      789**********9875...67*****************9.7899**************.6999*************** PP

                                      HCH CS
                           UPF0086 82 aer 84
                                      +++
  gi|474934886|ref|YP_007688468.1| 80 IKK 82
                                      997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 527.36
//
Query:       gi|474934887|ref|YP_007688469.1|  [L=99]
Description: translation initiation factor 1 (eIF-1/SUI1) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-22   79.2   0.5    2.8e-22   79.0   0.5    1.1  1  SUI1          Translation initiation factor SUI1
    1.9e-05   24.8   0.1    2.5e-05   24.5   0.1    1.2  1  Img2          Mitochondrial large subunit ribosomal protein (
     0.0015   18.3   0.7      0.002   17.9   0.7    1.2  1  DTW           DTW domain
     0.0057   16.9   0.4      0.009   16.3   0.2    1.5  1  PG_binding_4  Putative peptidoglycan binding domain
  ------ inclusion threshold ------
      0.072   13.3   0.0      0.086   13.0   0.0    1.1  1  ExbD          Biopolymer transport protein ExbD/TolR


Domain annotation for each model (and alignments):
>> SUI1  Translation initiation factor SUI1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.0   0.5   7.9e-26   2.8e-22       2      76 ..      24      94 ..      23      95 .. 0.96

  Alignments for each domain:
  == domain 1  score: 79.0 bits;  conditional E-value: 7.9e-26
                              SUI1  2 kpkihirleqrggrKkvTtvsgleafgidlkklakelkkkfacsgsvvkdggeeiqvQGdqrkkvaelLtekygv 76
                                      ++ ++i++++r+ +K+vT++ g++ ++id+ +lak+lk+k+a++g+v kdg   i++QGd++kkv  +L e+ g+
  gi|474934887|ref|YP_007688469.1| 24 QQSVRISVDTRRYGKTVTVIDGIDGNDIDIADLAKKLKSKCAAGGTV-KDG--RIELQGDHKKKVDAALKEM-GF 94
                                      899*******************************************8.999..9*****************9.87 PP

>> Img2  Mitochondrial large subunit ribosomal protein (Img2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.1   6.8e-09   2.5e-05      19      80 .]      33      94 ..      21      94 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 6.8e-09
                              Img2 19 vkrggtkkltvirkieG...DiaalredLrkaleelvkvnevtgkieikGdrveevkkfLeskgF 80
                                      ++r   k++tvi  i+G   Dia+l+++L++ ++  +  + + g+ie++Gd++++v + L++ gF
  gi|474934887|ref|YP_007688469.1| 33 TRR-YGKTVTVIDGIDGndiDIADLAKKLKSKCA--AGGTVKDGRIELQGDHKKKVDAALKEMGF 94
                                      444.45789********77778899999999999..5677789*********************9 PP

>> DTW  DTW domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.7   5.6e-07     0.002       2      29 ..       3      29 ..       2      38 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 5.6e-07
                               DTW  2 elCerCllpaevclcsslppleklpikv 29
                                      e+C++C lp+e+c+c++l + e++ +++
  gi|474934887|ref|YP_007688469.1|  3 EICPKCGLPMELCMCEELAR-EQQSVRI 29
                                      68*****************9.6665766 PP

>> PG_binding_4  Putative peptidoglycan binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.2   2.5e-06     0.009      78     109 ..      36      67 ..      18      72 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.5e-06
                      PG_binding_4  78 kggsvkvspekyGwkidkdkllkdliealkkg 109
                                        g++v+v+++++G+ id+++l+k+l+++ ++g
  gi|474934887|ref|YP_007688469.1|  36 YGKTVTVIDGIDGNDIDIADLAKKLKSKCAAG 67 
                                       699**********************9998777 PP

>> ExbD  Biopolymer transport protein ExbD/TolR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.4e-05     0.086      50     107 ..      21      87 ..      11      93 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.4e-05
                              ExbD  50 veekelirisisad..gsiy.....ldkkavsveelaqklkerkakppdk..ltvaikadkdvsygk 107
                                       + e++++ris++++  g+       +d++++++++la+klk + a   +     + +++d + ++++
  gi|474934887|ref|YP_007688469.1|  21 AREQQSVRISVDTRryGKTVtvidgIDGNDIDIADLAKKLKSKCAAGGTVkdGRIELQGDHKKKVDA 87 
                                       6799********884433224555699999*************999887777789999988776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       820  (0.045736); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 614.78
//
Query:       gi|474934888|ref|YP_007688470.1|  [L=69]
Description: LSU ribosomal protein L29P [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-16   60.5   0.1    1.4e-16   60.2   0.1    1.1  1  Ribosomal_L29  Ribosomal L29 protein


Domain annotation for each model (and alignments):
>> Ribosomal_L29  Ribosomal L29 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.2   0.1   7.9e-21   1.4e-16       2      56 ..      10      65 ..       9      65 .. 0.98

  Alignments for each domain:
  == domain 1  score: 60.2 bits;  conditional E-value: 7.9e-21
                                      HHHHS-HHHHHHHHHHHHHHHHHHHHHHHHT.SSS-CHHHHHHHHHHHHHHHHHHH CS
                     Ribosomal_L29  2 elrelsdeeLkeklkelkkeLfnLrfqkatg.qlenpsrirkvRkdIARikTvlre 56
                                      ++r++s ee +eklkel++eL+  r   a+g +++ p+ ir +R +IARi+Tv++e
  gi|474934888|ref|YP_007688470.1| 10 DIRNMSAEERNEKLKELRNELMHERGVSAMGgAPSSPGIIRSIRLSIARILTVQKE 65
                                      9******************************9*********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 475.83
//
Query:       gi|474934889|ref|YP_007688471.1|  [L=227]
Description: SSU ribosomal protein S3P [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.4e-24   84.8   1.0    8.2e-24   83.9   0.5    1.7  2  Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
    7.1e-14   51.4   0.0    1.4e-13   50.5   0.0    1.5  1  KH_2            KH domain
     0.0077   16.1   0.1      0.017   15.0   0.1    1.5  1  KH_4            KH domain
  ------ inclusion threshold ------
      0.036   13.9   0.2       0.24   11.3   0.1    2.2  2  KH_1            KH domain
        0.3   11.4   1.1         20    5.6   0.1    2.9  3  DUF190          Uncharacterized ACR, COG1993


Domain annotation for each model (and alignments):
>> Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.7   6.2e+03      17      33 ..      20      36 ..      10      37 .. 0.70
   2 !   83.9   0.5   2.3e-27   8.2e-24       2      83 .]     100     182 ..      99     182 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.7
                                      HHHHHHHHCC-SEEEEE CS
                    Ribosomal_S3_C 17 kairramkagakGikiq 33
                                      + ++++ +ag  G ++q
  gi|474934889|ref|YP_007688471.1| 20 YLMKEVSRAGFGGLEVQ 36
                                      46788888999998886 PP

  == domain 2  score: 83.9 bits;  conditional E-value: 2.3e-27
                                       HHHHHTT--HHHHHHHHHHHHHHCC-SEEEEEEEC-SS.TTT--EEEEEEC----..TCHHHH-EEEEEEEEETTEE CS
                    Ribosomal_S3_C   2 aeqlekrvsfRramkkairramkagakGikiqvsGrLggaeiarsekykeGrvpl..htlradidyavaeaktkyGi 76 
                                       a +le++++fRra + ++rr+m+aga+G+ i+v+G+L+ +++ r+ek+keG+++   ++  + +d+++a ak+k+G+
  gi|474934889|ref|YP_007688471.1| 100 AFSLERGWHFRRAGHATLRRVMEAGARGCYIVVAGKLS-GQRHRTEKFKEGSIKYcgEPKIQFVDEGYAVAKLKMGV 175
                                       779***********************************.9************************************* PP

                                       EEEEEEE CS
                    Ribosomal_S3_C  77 iGvkVwI 83 
                                       iGv+V+I
  gi|474934889|ref|YP_007688471.1| 176 IGVTVRI 182
                                       *****98 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5   0.0   3.8e-17   1.4e-13       2      71 ..      17      85 ..      16      92 .. 0.93

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 3.8e-17
                                      HHHHHHHHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEEEEE CS
                              KH_2  2 ipeslaveikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkkVklniv 71
                                      ++e+l +e++ ag +++e++rt+ ++++++ +++pg+vIG++G++ik+++ +++k+++ +e+ +++++ v
  gi|474934889|ref|YP_007688471.1| 17 LKEYLMKEVSRAGFGGLEVQRTPMGTRVILSTERPGLVIGHKGQTIKNLTYAIEKNFG-FENPQIEVQEV 85
                                      5799*****************************************************8.*****997644 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   4.8e-06     0.017      32      56 ..      43      67 ..      32      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.8e-06
                              KH_4 32 elnvegedlGrvIGkrGrtldAlqy 56
                                      ++ +++e  G+vIG +G+t++ l y
  gi|474934889|ref|YP_007688471.1| 43 RVILSTERPGLVIGHKGQTIKNLTY 67
                                      688999**************98766 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   6.6e-05      0.24       3      25 ..      43      65 ..      41      67 .. 0.84
   2 ?   -0.4   0.0      0.29     1e+03      20      36 ..     115     133 ..     112     152 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.6e-05
                                      EEEEGGGHHHHHHTGGGHHHHHH CS
                              KH_1  3 rilvPsslvgriIGkgGsnIkeI 25
                                      r+++ ++  g++IG +G++Ik++
  gi|474934889|ref|YP_007688471.1| 43 RVILSTERPGLVIGHKGQTIKNL 65
                                      6677777789***********98 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.29
                                       HHHHHHHHH.H.T-EEEEE CS
                              KH_1  20 snIkeIree.t.gakIkvp 36 
                                       +++++ +e    g++I+v 
  gi|474934889|ref|YP_007688471.1| 115 ATLRRVMEAgArGCYIVVA 133
                                       6888888844558888876 PP

>> DUF190  Uncharacterized ACR, COG1993
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.063   2.2e+02      13      43 ..      12      42 ..       7      49 .. 0.87
   2 ?    0.7   0.0      0.19   6.8e+02      13      51 ..     107     145 ..     101     171 .. 0.70
   3 ?    5.6   0.1    0.0056        20      51      79 ..     179     207 ..     164     216 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.063
                                      ETTEEHHHHHHHHHHHTT-S--EEEE-S--- CS
                            DUF190 13 legkplyeaivelareeglagatvlrGieGf 43
                                      +++  l e++++++ ++g+ g  v r  +G 
  gi|474934889|ref|YP_007688471.1| 12 VRRVLLKEYLMKEVSRAGFGGLEVQRTPMGT 42
                                      55778999******************99996 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.19
                                       ETTEEHHHHHHHHHHHTT-S--EEEE-S----------- CS
                            DUF190  13 legkplyeaivelareeglagatvlrGieGfgassriht 51 
                                       ++ + + +a +++++e+g++g+ ++ +    g+++r+++
  gi|474934889|ref|YP_007688471.1| 107 WHFRRAGHATLRRVMEAGARGCYIVVAGKLSGQRHRTEK 145
                                       677778889999999999999987765555555555544 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.0056
                                       -----------EEEEEEEE-HHHHHHHHH CS
                            DUF190  51 takllelsedlPvvieivdteekieaflp 79 
                                       t ++++ +++lP  i ivd+++++e++ +
  gi|474934889|ref|YP_007688471.1| 179 TVRIMQSDSKLPADINIVDKTTAAERLPD 207
                                       679999***************99998755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1518.25
//
Query:       gi|474934890|ref|YP_007688472.1|  [L=151]
Description: ribosomal protein L22(archaeal)/L17(eukaryotic/archaeal) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-24   86.5   0.1    1.5e-24   86.2   0.1    1.1  1  Ribosomal_L22  Ribosomal protein L22p/L17e


Domain annotation for each model (and alignments):
>> Ribosomal_L22  Ribosomal protein L22p/L17e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.2   0.1   8.1e-29   1.5e-24       3     102 ..      21     147 ..      19     148 .. 0.96

  Alignments for each domain:
  == domain 1  score: 86.2 bits;  conditional E-value: 8.1e-29
                                       EEEESS-HHHHHHHHHHHTTSBHHHHHHHHHT..-SST.........................THHHHHHHHHHHHH CS
                     Ribosomal_L22   3 gsnlrvsfkklrevarlIrgmkveeAlkyLkf..skkk.........................aakfvlklLknaea 52 
                                       +++ ++s+k +reva+++rgm+v++A + L++  +k++                         ++k vl +L++a +
  gi|474934890|ref|YP_007688472.1|  21 SKEQPISPKLAREVACMVRGMTVSDARTALEEviDKERpvrmnrynkrvahkpgvgpgkypvkVSKAVLACLESAAS 97 
                                       67899***************************955555*************************************** PP

                                       HHH..HT-GGGEEEEEEEEEEEEEEEEEEEESTTEEEEEEEEEEEEEEEE CS
                     Ribosomal_L22  53 naelkgldvdslvIeeiqvnkgpklkrrtyrArGrinpirkspchievvl 102
                                       na++kgld  s+ I++i v +g+ + + ++rA+Gr++ +++ +++ie+v+
  gi|474934890|ref|YP_007688472.1|  98 NADYKGLDSASMKITTISVARGRVIPGHRPRAQGRATEWNQDTVNIEIVI 147
                                       ************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1045.56
//
Query:       gi|474934891|ref|YP_007688473.1|  [L=155]
Description: SSU ribosomal protein S19P [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-22   78.8   0.3    5.7e-22   77.4   0.0    1.7  2  Ribosomal_S19  Ribosomal protein S19


Domain annotation for each model (and alignments):
>> Ribosomal_S19  Ribosomal protein S19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.2      0.12   2.1e+03      22      38 ..       8      24 ..       2      32 .. 0.67
   2 !   77.4   0.0   3.2e-26   5.7e-22       5      81 .]      64     138 ..      60     138 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.12
                                      TS-----EEES-TT-B- CS
                     Ribosomal_S19 22 aekkkevikthsRdstI 38
                                       ++k  v  t  R+s I
  gi|474934891|ref|YP_007688473.1|  8 GSHKAAVRATRKRNSQI 24
                                      44566777777777776 PP

  == domain 2  score: 77.4 bits;  conditional E-value: 3.2e-26
                                       SS.TTCCCHHHHHHHHHHTS-----EEES-TT-B--GGGTT-EEEEE-SSSEEEEE--CCCTTSBCGGGT-SS---- CS
                     Ribosomal_S19   5 kg.pfvqesllkkvrkakaekkkevikthsRdstIlPemvgltvgVynGktfvpveikeemvGhkLgEFspTrkpvk 80 
                                       +g +++q+ +++k+ +    +++ +i+th Rd  IlP++vg +v+VynGk+f+++ i +em+G+ LgEF+p rk  +
  gi|474934891|ref|YP_007688473.1|  64 RGlNYEQQLVFDKLTAE---EAEGTIRTHRRDLPILPSFVGKRVAVYNGKEFIEFSIVPEMIGCMLGEFVPNRKNPQ 137
                                       56566666666666555...47889*************************************************988 PP

                                       S CS
                     Ribosomal_S19  81 h 81 
                                       h
  gi|474934891|ref|YP_007688473.1| 138 H 138
                                       7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1003.74
//
Query:       gi|474934892|ref|YP_007688474.1|  [L=208]
Description: LSU ribosomal protein L2P [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.3e-38  129.8   4.6      1e-37  129.2   4.6    1.3  1  Ribosomal_L2_C   Ribosomal Proteins L2, C-terminal domain
    2.2e-05   24.3   0.0    4.8e-05   23.2   0.0    1.6  1  Ribosomal_L2     Ribosomal Proteins L2, RNA binding domain
  ------ inclusion threshold ------
       0.17   12.0   2.0       0.38   10.9   2.0    1.6  1  Chlorovi_GP_rpt  Chlorovirus glycoprotein repeat


Domain annotation for each model (and alignments):
>> Ribosomal_L2_C  Ribosomal Proteins L2, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.2   4.6   1.7e-41     1e-37       2     113 ..      61     181 ..      60     195 .. 0.88

  Alignments for each domain:
  == domain 1  score: 129.2 bits;  conditional E-value: 1.7e-41
                                       SSS-EBSSSS-TTB-BBSE-SSTTS--SSS-SSSB-EEBB-B.SSEEEEEETTS-EEEEETTSBEBES-BS-TTCTT CS
                    Ribosomal_L2_C   2 vGnvlplknipeGtivhnielkpgkggklarsaGtyaqvvakegkkvtvklpSgevrkvssecrAtiGvvsngehke 78 
                                       +Gn+l l+nipeGt+vhn+e +pg+ggk++++aGt+a vv++  k v++ +pSg  ++++ +crA++Gvv++g++ +
  gi|474934892|ref|YP_007688474.1|  61 PGNILALSNIPEGTLVHNVEGQPGDGGKFVKTAGTSALVVSRG-KVVILSMPSGVLKEFNPNCRAVVGVVAGGGRVD 136
                                       8****************************************75.********************************* PP

                                       ----STTHHHHT.....TBS----SSSS-TTTSSS--SS.....S CS
                    Ribosomal_L2_C  79 kklgkAgrkrwl.....grrpkvrGvamnpvdHphGGGe.....G 113
                                       k+l kAg++         +  ++ Gvamn+vdHphGGG+     G
  gi|474934892|ref|YP_007688474.1| 137 KPLAKAGKNVLTmrsrsVTTRHTSGVAMNAVDHPHGGGShphvgG 181
                                       *******99988655544445899**************9766642 PP

>> Ribosomal_L2  Ribosomal Proteins L2, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   8.1e-09   4.8e-05      33      76 ..      11      53 ..       1      54 [. 0.89

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 8.1e-09
                                      --EEEEEEE--TT-SS-EEEEEETTTEEEEEE--SS--SS-EE- CS
                      Ribosomal_L2 33 vkgkVveieyDpgRsApiAlvkyedgekryiiapeglkvGdtvv 76
                                       +g+++++++ pgR++p+A + +   +k+y +a+eg  vG+tv+
  gi|474934892|ref|YP_007688474.1| 11 AQGTIKDLIQAPGRTSPLAVIDFDG-KKTYQLAVEGTAVGQTVE 53
                                      67999******************76.****************98 PP

>> Chlorovi_GP_rpt  Chlorovirus glycoprotein repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   2.0   6.3e-05      0.38      20      34 .]      50      64 ..      45      64 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6.3e-05
                   Chlorovi_GP_rpt 20 qniDIiGNVvatgNV 34
                                      q++ I GNVv++gN+
  gi|474934892|ref|YP_007688474.1| 50 QTVEIGGNVVSPGNI 64
                                      8999**********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1463.36
//
Query:       gi|474934893|ref|YP_007688475.1|  [L=93]
Description: Ribosomal protein L23 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-15   56.3   0.4    2.4e-14   53.4   0.4    1.9  1  Ribosomal_L23  Ribosomal protein L23


Domain annotation for each model (and alignments):
>> Ribosomal_L23  Ribosomal protein L23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   0.4   1.3e-18   2.4e-14       1      58 [.       5      71 ..       5      85 .. 0.87

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 1.3e-18
                                      SSEEEE--SHHHHHHH........TT.E.EEEEE-SS-THHHHHHHHHHHHT--EEEEEEEEE--EB CS
                     Ribosomal_L23  1 dvilkPvitEkstkla........ek.nkyvFeVakdanKleikkaveklFgVkVekVntlnvkgkk 58
                                      d+++kP++tEks +l+        ++ nk+ F V++da K +ik a+e+ F+VkV kV t ++k  k
  gi|474934893|ref|YP_007688475.1|  5 DILIKPYVTEKSLNLMngtpvqnyKDgNKIEFLVHRDADKQDIKTAFEERFEVKVVKVWTRIQKDGK 71
                                      79***********9999999988744589*******************************9988644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 708.64
//
Query:       gi|474934894|ref|YP_007688476.1|  [L=258]
Description: 50S ribosomal protein L4P [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.1e-40  137.5   0.3    4.8e-40  137.3   0.3    1.0  1  Ribosomal_L4  Ribosomal protein L4/L1 family
  ------ inclusion threshold ------
      0.047   13.7   0.3       0.88    9.7   0.2    2.4  2  CMD           Carboxymuconolactone decarboxylase family


Domain annotation for each model (and alignments):
>> Ribosomal_L4  Ribosomal protein L4/L1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.3   0.3   5.3e-44   4.8e-40       1     191 [.      17     255 ..      17     256 .. 0.88

  Alignments for each domain:
  == domain 1  score: 137.3 bits;  conditional E-value: 5.3e-44
                                       EEE-HHHHSS---HHHHHHHHHHHHHSS-EE-----.-TTTSS---S-SS-SSSSSS---S-TT.......STTSTT CS
                      Ribosomal_L4   1 veLspkvFaapirrdlihravvaylanrrqgtastk.arsevsgsgrklwkQKGtGrARvgsir.......spiarg 69 
                                       +e+ p+ F++ +r+dli++av+a +an+rq+++ +k +++++s s   ++k  G+G ARv +++       sp   +
  gi|474934894|ref|YP_007688476.1|  17 IEV-PAAFETAYRPDLIKKAVLAANANKRQPYGPNKmSGMRHSVS--TWGK--GRGVARVQRLHdgrratqSPNNIS 88 
                                       678.99**************************************6..7777..************************ PP

                                       ---SS---S.EEHHHHHHHHHHHHHHHHHHHHHHHTT-EEEES.---..-S...........S--HHHHHHHHHHTT CS
                      Ribosomal_L4  70 GgvahgpkperdystklnkKvrrlAlrsaLsakakqglllvvd.nle.ple...........esktkelvellkklg 133
                                       G++ah+pk+e+ +++k+nkK+ rlA  saL+ +a ++ ++ ++ +++ ++             + + e++el++ +g
  gi|474934894|ref|YP_007688476.1|  89 GRRAHPPKVEKIWEQKVNKKEARLARLSALACTACADCVKQRGhKFDdKVTfpvvvddalndVKTAAEVKELFDIIG 165
                                       *******************************************9554344455778888776666777777888777 PP

                                       -..........................TTSSEEEEESSSSC..HHHHHHTT-TTEEEEESTT--CHHHHHSSE.... CS
                      Ribosomal_L4 134 l..........................ksksvLivvsekde..nlvlaarnlpgvevieveslnvydllkadk.... 178
                                       +                          ++ svLiv+s+kd+   +++ a+nlpgv+v e+  ln   l+++ +    
  gi|474934894|ref|YP_007688476.1| 166 IgydverakdgtkiragrgtmrnrkyrTPVSVLIVISDKDRnaAVFKGANNLPGVQVEEISTLNTSLLAPGGDagrl 242
                                       788888887777777788888777777777*******765522689******************************* PP

                                       EEEEHHHHHHHHH CS
                      Ribosomal_L4 179 vvitksaveklee 191
                                       +v+tksa+ek+ e
  gi|474934894|ref|YP_007688476.1| 243 TVYTKSAIEKIGE 255
                                       **********987 PP

>> CMD  Carboxymuconolactone decarboxylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.2   9.8e-05      0.88      15      44 ..     100     130 ..      98     133 .. 0.88
   2 ?    1.2   0.0     0.043   3.9e+02      47      77 ..     144     174 ..     137     179 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 9.8e-05
                                       CCGSSTS-HHHHHHHHHHHHHHTT-HHHH..H CS
                               CMD  15 lareggLdpkereLialavsaangceyCv..d 44 
                                       ++ e ++++ke  L+ l ++a + c++Cv  +
  gi|474934894|ref|YP_007688476.1| 100 IW-EQKVNKKEARLARLSALACTACADCVkqR 130
                                       68.899**********************9655 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.043
                                       HHHHHHTT--HHHHHHHHHHHHHHHSHHHHH CS
                               CMD  47 traAleaGvteeeiaevlaqaaayagwpaar 77 
                                       + +Al++ +t+ e++e++++  +  ++++a+
  gi|474934894|ref|YP_007688476.1| 144 VDDALNDVKTAAEVKELFDIIGIGYDVERAK 174
                                       56899999*********99987766666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1887.01
//
Query:       gi|474934895|ref|YP_007688477.1|  [L=283]
Description: archaeal ribosomal protein L3 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.1e-73  246.9   3.7    1.2e-71  241.6   3.7    2.0  1  Ribosomal_L3  Ribosomal protein L3


Domain annotation for each model (and alignments):
>> Ribosomal_L3  Ribosomal protein L3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  241.6   3.7   6.9e-76   1.2e-71      53     369 .]       1     282 [.       1     282 [. 0.93

  Alignments for each domain:
  == domain 1  score: 241.6 bits;  conditional E-value: 6.9e-76
                                       EEEEEEECHHTTSCCCCCEEEEEEEEEEC--EEEEEEEEEEEETTEEEEEEEEESSS.SHHHHCCCSTSTTTSSSSS CS
                      Ribosomal_L3  53 mthiVrevdkpgskldkkevveavtvvetppmvivgvvgyvetprGlrslktvwaehlseevkrrlyknwykskkka 129
                                       mth   +++++ s + ++e+  +vtv+e ppm+i++v+ y++t +Gl++  +vwa ++   ++rr+  n        
  gi|474934895|ref|YP_007688477.1|   1 MTHAFVVDKRAKSTTSGMEIQTPVTVIEVPPMKIAAVRFYENTILGLKTAGEVWAADVDPLLNRRV--NVP------ 69 
                                       8999999**********************************************************9..322...... PP

                                       SHCCCCHCSSCCCCCCHHH.HHHHHHHSCSCEEEEEEEECCCSS-SCCSSHHEEEEECHCSCHHHHHHHHHHCCTCE CS
                      Ribosomal_L3 130 ftkyskkyeskdvkkliea.dleeikkeasvvrviahtvirktkslaqKkahllEiqvngGtiaekldfarealekt 205
                                                 k+++    + d   i++    vrv+a+t+ + +k++ +K ++l+E++++gG i++++++a+  l k 
  gi|474934895|ref|YP_007688477.1|  70 ----------KKGEPDFSRfDNMDIED----VRVLAYTQPKMLKGVPKKVPDLMELRIGGGAISDRVEYAKGILGKE 132
                                       ..........23333444445666777....9********************************************* PP

                                       EECCCCS-TTSEEEEEEEE---EEE-HHHHCT----STTTSSSSSS-S-SS-SSSSS--TTS--SEEESCCEEEEEE CS
                      Ribosomal_L3 206 vavaavFrqgeliDvigvtkGkGfeGvvkRWgvkklprkthrglRkvaaigawdparVsstvaraGqkGyhhRteln 282
                                       v++++  ++g liDvi++t GkGf+Gv+kRWgvk l  k  + +R +a++g+  p+ V+stv+ aGq+Gyh+Rteln
  gi|474934895|ref|YP_007688477.1| 133 VTINDFTAEGTLIDVIAITTGKGFQGVTKRWGVKLLSHKNSKHRRGIANLGPKRPGYVRSTVPAAGQMGYHQRTELN 209
                                       ***************************************************************************** PP

                                       EEEEEEETTTSSTTTSSTTT.SS..SS.TTTCTTCB..TSCEEEEES--SSSTTEEEEEEE-SS.GGGSCCCSS-EE CS
                      Ribosomal_L3 283 kkiyrigkgedaknastefdltekeitPmGGfvhyGevkndfilvkGsvpGpkkrlvklrksll.tqtsrkaeeevs 358
                                       kk+++ig+              ++e++P+GGf +yGev++ ++lv+GsvpGp krl+++r++ + +++ ++   e+ 
  gi|474934895|ref|YP_007688477.1| 210 KKVMKIGT-------------DGQEVNPKGGFLNYGEVQGTYVLVHGSVPGPTKRLIRFRDATRiPAKADQSAAEI- 272
                                       ********.............5789************************************986266678888888. PP

                                       EEEE-TTCTSS CS
                      Ribosomal_L3 359 lkfidtaskfg 369
                                         f++t+s++g
  gi|474934895|ref|YP_007688477.1| 273 -TFVSTQSQQG 282
                                       .9******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1819.26
//
Query:       gi|474934896|ref|YP_007688478.1|  [L=38]
Description: hypothetical protein TALC_01336 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       178  (0.00992805); expected 358.6 (0.02)
Passed bias filter:                      115  (0.00641419); expected 358.6 (0.02)
Passed Vit filter:                         3  (0.000167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.48
# Mc/sec: 240.09
//
Query:       gi|474934897|ref|YP_007688479.1|  [L=112]
Description: archaeal conserved hypothetical protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.4e-27   94.2   1.4    8.5e-27   94.0   1.4    1.0  1  DUF5611   Domain of unknown function (DUF5611)


Domain annotation for each model (and alignments):
>> DUF5611  Domain of unknown function (DUF5611)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.0   1.4   4.7e-31   8.5e-27       1     103 []       4     105 ..       4     105 .. 0.95

  Alignments for each domain:
  == domain 1  score: 94.0 bits;  conditional E-value: 4.7e-31
                                       -EEE---SSS--SH..HHHHHHHHHHT.-EEEEETTEEEEE-TTBS-EEEEE..-SS-EEEEE--.B...-TTS-HH CS
                           DUF5611   1 mreYkiKrGfkkeee.erlkelleeyfggeveeegdllvvsfgaikklevkisskkkklvvdteerdaeeeddeaal 76 
                                       m++++iK+G++k++e + lk++++ +f g+++ egd++v+sfg+++++e+k   +k  l v++++ da+e +de++l
  gi|474934897|ref|YP_007688479.1|   4 MTDFDIKKGCYKNIEgDGLKNIMQAVF-GNATVEGDMVVSSFGVMARIEAKPV-SKTVLDVKVTNVDAKEFKDEDVL 78 
                                       99*************************.8***********************5.677888888888*********** PP

                                       HHHHHHHHHHHHHH---GGGHHHHH-- CS
                           DUF5611  77 dtvkkfndFLeeaTGydaKeRkkkakk 103
                                       ++++k+n+FLe+aTG+daK+R+k+a++
  gi|474934897|ref|YP_007688479.1|  79 NSKRKLNEFLEKATGFDAKARMKRAQQ 105
                                       ************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 717.07
//
Query:       gi|474934898|ref|YP_007688480.1|  [L=332]
Description: conserved hypothetical protein TIGR01210 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.047   14.1   0.0      0.082   13.3   0.0    1.3  1  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.5e-06     0.082       8     154 ..      44     186 ..      33     195 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.5e-06
                                       SS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTC.CCTEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                       Radical_SAM   8 nlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlakla.vpgiritv 82 
                                       n++C+ C  ++  + +g+ +     +i + + ++    g + + i ++g  ++  ++ + +++++  + +   ri v
  gi|474934898|ref|YP_007688480.1|  44 NGGCTMCGYRTA-SLNGVTEADLNAQIDQALSKYN---GeKFVKIYTSGSFFDENEIPVSVRERVFDEyKGCSRILV 116
                                       778999999985.8888888888888888888884...447778888999999999*******99998888888999 PP

                                       EECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  83 etngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglpG 154
                                       e+ +  ++++ +  l +    +v+lgle+ ++e vl+ +  +g t  + ++a e++++ag+ + ++ ++ +p 
  gi|474934898|ref|YP_007688480.1| 117 ESRPEFINRDLVSSLPK--SLTVALGLESSNEE-VLRTCIhKGFTAAQSKAAGETIKDAGLMVRTYLLLKPPF 186
                                       99999998999999999..47************.888887799999**************9877777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 2015.66
//
Query:       gi|474934899|ref|YP_007688481.1|  [L=455]
Description: NAD(P)H-nitrite reductase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-54  185.6   2.0    1.7e-54  185.1   2.0    1.2  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
      4e-24   85.0   4.0    2.5e-20   72.8   0.4    3.4  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
      6e-12   45.8  11.3    0.00077   19.1   0.6    4.8  5  DAO             FAD dependent oxidoreductase
    7.4e-12   45.5   0.4    3.7e-11   43.3   0.0    2.3  2  Pyr_redox_dim   Pyridine nucleotide-disulphide oxidoreductase
    2.6e-11   42.9   4.1      0.063   12.0   0.1    4.5  5  HI0933_like     HI0933-like protein
      3e-10   39.8   3.1    6.1e-08   32.3   1.2    3.3  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    1.3e-07   31.7   0.9     0.0071   16.5   0.0    3.0  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    6.6e-06   25.5   6.3      0.018   14.2   0.2    2.8  3  FAD_binding_2   FAD binding domain
    1.1e-05   24.9   3.8      0.053   12.8   0.4    2.6  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
    1.8e-05   25.1   0.6     0.0056   17.1   0.2    2.5  2  NAD_binding_7   Putative NAD(P)-binding
    0.00029   20.2   0.7       0.11   11.7   0.0    2.5  2  Thi4            Thi4 family
    0.00051   19.4   4.8     0.0028   17.0   0.2    2.2  2  FAD_binding_3   FAD binding domain
    0.00066   18.9   0.2     0.0091   15.2   0.0    2.3  3  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
    0.00078   18.6   3.5       0.76    8.8   0.4    3.1  3  Lycopene_cycl   Lycopene cyclase protein
    0.00085   19.6   0.9     0.0053   17.0   0.2    2.3  2  TrkA_N          TrkA-N domain
     0.0012   18.8   0.4     0.0021   18.1   0.4    1.3  1  Sigma70_r1_1    Sigma-70 factor, region 1.1
     0.0019   17.4   5.9        1.3    8.0   0.1    4.1  4  GIDA            Glucose inhibited division protein A
     0.0058   16.0   0.3        4.3    6.5   0.0    3.0  3  Amino_oxidase   Flavin containing amine oxidoreductase
     0.0059   16.6   2.9        3.6    7.6   0.0    4.0  4  NAD_binding_9   FAD-NAD(P)-binding
  ------ inclusion threshold ------
      0.012   15.5   0.2        4.7    7.1   0.0    2.9  2  SIS             SIS domain
      0.018   15.0   1.2      0.045   13.6   0.1    2.0  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      0.019   14.4   0.3       0.16   11.3   0.1    2.2  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
      0.021   14.5   0.2      0.021   14.5   0.2    2.1  2  ApbA            Ketopantoate reductase PanE/ApbA
      0.024   14.2   0.4      0.089   12.4   0.2    2.0  2  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
      0.026   14.1   0.1          1    8.9   0.0    2.7  2  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
      0.032   13.1   6.1         11    4.7   0.0    3.8  4  Trp_halogenase  Tryptophan halogenase
      0.049   13.8   0.0       0.17   12.0   0.0    2.0  2  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
      0.063   12.6   0.4       0.49    9.7   0.1    2.3  2  ThiF            ThiF family
      0.089   12.7   0.1       0.22   11.4   0.1    1.7  1  LpxI_N          LpxI N-terminal domain
      0.091   12.7   0.0       0.67    9.9   0.0    2.1  2  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
        2.1    7.0   3.2        2.3    6.9   0.0    2.3  2  MCRA            MCRA family
        2.3    7.5   9.4         17    4.6   1.4    3.5  4  FAD_oxidored    FAD dependent oxidoreductase


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.1   2.0     3e-57   1.7e-54       2     279 ..       4     295 ..       3     313 .. 0.87

  Alignments for each domain:
  == domain 1  score: 185.1 bits;  conditional E-value: 3e-57
                                       SEEEE--SHHHHHHHHHHHH..HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH........HHHHCHHHHCC CS
                                       xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq..agakvtlvelegtclnggcllskallgvaedaeias........evvkklnqgie 68 
                                       ++vviG+G+AGl+aa  +++    a++t++ ++  + +  c++ +++lg ++  e +         +     + +i+
  gi|474934899|ref|YP_007688481.1|   4 KIVVIGSGAAGLSAASSARAvdPDAEITVYTQDVDVAYSPCMI-PWVLGGKSTWENMImhtpewyaK-----ERNIR 74 
                                       89******************877*******9999999998888.55555555555555589766542.....45788 PP

                                       CCHCCTCEEEEESC.EEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T.S CS
                                       xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                       Pyr_redox_2  69 lllgeevvkidpgk.kkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp.k 143
                                        ++g++v +  +++ k+ + +k+++ ++e++ ydkl+lAtG++ ++++i+Gv+  +++ vrt++  +++++ l + k
  gi|474934899|ref|YP_007688481.1|  75 IVTGTTVEAAAYDRaKDGTMTKTVTVNGETVPYDKLILATGGKVFIPPIEGVNLPGVFTVRTVEGGRKMQEYLAKsK 151
                                       88887766666666568888889999**************************999999************999999* PP

                                       EEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSS.TTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 144 rivvvGgGyiGvElAaalaklgkevtlveardrll.raldkelsaaleealekeGvevklgtsvkeidgngeklevv 219
                                       r+v+ G+G+iG+ElA +l+++gk+vt++e +d++  r  dk++++ ++++le++Gve++l++ v++++g+++ +e v
  gi|474934899|ref|YP_007688481.1| 152 RVVIAGAGVIGLELALHLKEAGKDVTIIEMMDQVIpRIADKDMADPIQKYLEDKGVEIVLKAPVQAVNGKDR-VESV 227
                                       ********************************************************************9997.99** PP

                                       ETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBE....S.STTEEE-GGGC....T CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....x.xxxxxxxxxxx....x RF
                       Pyr_redox_2 220 ledgeeidadlvvvavGvrpstelleeklglelderggivvdeflrt....n.vpgiyaiGDva....g 279
                                        + g+e+++d+v++a+Gvr++ +l+ + ++l + + g++ v ++l+       vp+++++GDv      
  gi|474934899|ref|YP_007688481.1| 228 SSLGKEYPCDMVIFATGVRANVDLA-KMMNLDIGQLGALCVAPTLQAyqrgRlVPDVFVCGDVMqcqsA 295
                                       *************************.*****************9975566656**********954440 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0     0.011       6.4       1      21 [.       4      24 ..       4      36 .. 0.83
   2 ?    4.2   0.0      0.11        64      49      69 ..      67      87 ..      57     103 .. 0.77
   3 !   72.8   0.4   4.4e-23   2.5e-20       1      76 [.     152     227 ..     152     229 .. 0.97

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.011
                                      EEEEECSSHHHHHHHHHHHHT CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalael 21
                                      k+vv+G+G  gl +A+ +++ 
  gi|474934899|ref|YP_007688481.1|  4 KIVVIGSGAAGLSAASSARAV 24
                                      79*************998875 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.11
                                      HHHHTTEEEECSEEEEEEEEE CS
                         Pyr_redox 49 klekngievllntkveeiegs 69
                                      + ++++i+++++t+ve+   +
  gi|474934899|ref|YP_007688481.1| 67 YAKERNIRIVTGTTVEAAAYD 87
                                      67899***********98743 PP

  == domain 3  score: 72.8 bits;  conditional E-value: 4.4e-23
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS.TTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEE CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkll.rllDeeaskilqeklekngievllntkveeiegsedgvesv 76 
                                       +vv+ G+G+iglElA  l+e gk+Vt++e++d++  r  D+++++ +q++le++g+e++l++ v++++g+++ vesv
  gi|474934899|ref|YP_007688481.1| 152 RVVIAGAGVIGLELALHLKEAGKDVTIIEMMDQVIpRIADKDMADPIQKYLEDKGVEIVLKAPVQAVNGKDR-VESV 227
                                       79*******************************************************************999.8888 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.2    0.0012      0.67       1      29 [.       4      36 ..       4      42 .. 0.78
   2 !    7.8   0.1     0.004       2.2     156     203 ..      68     117 ..      65     136 .. 0.71
   3 !   19.1   0.6   1.4e-06   0.00077       1      29 [.     152     182 ..     152     186 .. 0.92
   4 !   13.2   0.0   8.7e-05     0.049     152     210 ..     198     255 ..     188     276 .. 0.74
   5 ?   -1.1   0.0         2   1.1e+03     294     345 ..     278     331 ..     269     336 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0012
                                      EEEEECTSHHHHHHHHHHHHT..T...EEEEESS CS
                               DAO  1 dvviiGGGiiGlstAyeLarr..g...Vtllekg 29
                                      ++v+iG+G +Gls+A  + r+  +   +t++ ++
  gi|474934899|ref|YP_007688481.1|  4 KIVVIGSGAAGLSAASSA-RAvdPdaeITVYTQD 36
                                      59*************999.444336888888776 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.004
                                       HHHTT-EEEESECEEEE...EEEETCEEEEE..EECTEEEEEEEEEEE--GGG CS
                               DAO 156 aealGveilegtevtgl...eeedgkvwgve..rttpgendaadavVnaaGaw 203
                                       a+++ ++i++gt+v++    +++dg        +t +ge++ +d++++a+G  
  gi|474934899|ref|YP_007688481.1|  68 AKERNIRIVTGTTVEAAaydRAKDGT---MTktVTVNGETVPYDKLILATGGK 117
                                       78999***********8332223333...32323444888788********76 PP

  == domain 3  score: 19.1 bits;  conditional E-value: 1.4e-06
                                       EEEEECTSHHHHHHHHHHHHTT..EEEEESS CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllekg 29 
                                       +vvi G+G+iGl  A++L ++g  Vt++e+ 
  gi|474934899|ref|YP_007688481.1| 152 RVVIAGAGVIGLELALHLKEAGkdVTIIEMM 182
                                       59****************99999******85 PP

  == domain 4  score: 13.2 bits;  conditional E-value: 8.7e-05
                                       HHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHH.HH.HTT CS
                               DAO 152 laraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsd.ll.gll 210
                                       +++ +e++Gvei+++++v++++ + ++v  v   ++ g +  +d v+ a+G+ ++  l +++
  gi|474934899|ref|YP_007688481.1| 198 IQKYLEDKGVEIVLKAPVQAVNGK-DRVESV---SSlGKEYPCDMVIFATGVRANvDLaKMM 255
                                       678899**************9332.345555...55587766799********998554555 PP

  == domain 5  score: -1.1 bits;  conditional E-value: 2
                                       HHSGGG...CGEEEEEEEEEEETTSSEEEEEEETEEEEEEEEECTTTHHHHHHHH CS
                               DAO 294 klfPql...gdvlrkwaGlrplpdglpligetpgvkglylatGhsghGltlapat 345
                                       +l+P++   gdv ++++ ++p p     +g +   +g +  +++ g Gl+++p++
  gi|474934899|ref|YP_007688481.1| 278 RLVPDVfvcGDVMQCQSAVYPGPTM-SQLGSSAVREGKVAGANAAGAGLSFGPVA 331
                                       5678844679999999999994444.44444334558899999999999999986 PP

>> Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       6.7   3.7e+03      20      77 ..     168     225 ..     152     230 .. 0.72
   2 !   43.3   0.0   6.6e-14   3.7e-11       5      95 ..     337     427 ..     334     441 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 6.7
                                       HHHHHHSGEEEEEEEEECGHHHCHTTHTEEEEEEEEETTTTBEEEEEEECTTHHHHHH CS
                     Pyr_redox_dim  20 eAkaagieikvgkfpfkangralayaetkgfvKlvadaktgkvlGahivGpgageliq 77 
                                        +k+ag +++++++  + + r   +++++ ++K + d+  + vl a + + + +++++
  gi|474934899|ref|YP_007688481.1| 168 HLKEAGKDVTIIEMMDQVIPRIADKDMADPIQKYLEDKGVEIVLKAPVQAVNGKDRVE 225
                                       5778888888888887777777777778888888888888877777777766666665 PP

  == domain 2  score: 43.3 bits;  conditional E-value: 6.6e-14
                                       EESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTH.TEEEEEEEEETTTTBEEEEEEEC.TTHHHHHHHH CS
                     Pyr_redox_dim   5 vftdpevasvGlteeeAkaagieikvgkfpfkangralayae.tkgfvKlvadaktgkvlGahivG.pgageliqel 79 
                                       v  d ++a +G++ + A   g   k ++++ + ++ra++y++ ++ +vK++adakt++++Ga+i+G ++ + +i+ l
  gi|474934899|ref|YP_007688481.1| 337 VIGDIQIAGTGMSTALASWYG--EKLISAKATGSTRARYYPDgKELTVKVMADAKTHRLVGAQIIGgEDITGRIDWL 411
                                       567899*********999999..899***************************************9899999***** PP

                                       HHHHHTTSBHHHHHTS CS
                     Pyr_redox_dim  80 avaikagltvedladt 95 
                                       ++ai  g+t+e++a  
  gi|474934899|ref|YP_007688481.1| 412 NQAIVDGITAEEFAVR 427
                                       ***********98754 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.1   0.00011     0.063       2      26 ..       4      30 ..       3      39 .. 0.76
   2 !    9.8   0.0   0.00052      0.29     119     165 ..      68     117 ..      58     122 .. 0.77
   3 !   10.8   0.6   0.00025      0.14       2      36 ..     152     186 ..     151     191 .. 0.91
   4 !    7.7   0.0    0.0022       1.2     111     164 ..     194     245 ..     187     251 .. 0.83
   5 ?   -2.4   0.0       2.7   1.5e+03     373     387 ..     278     292 ..     276     295 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                                      SEEEE--SHHHHHHHHHH..HHTT--E CS
                       HI0933_like  2 dviviGgGaAGlmaAisa..akrgkrV 26
                                      +++viG GaAGl aA sa   + ++++
  gi|474934899|ref|YP_007688481.1|  4 KIVVIGSGAAGLSAASSAraVDPDAEI 30
                                      79*************999333444454 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00052
                                       HHHHT-EEE-S--EEEE..ECETTE.EEEEE..TTEEEEESEEEE----S CS
                       HI0933_like 119 lkeagvklrletevksv..ekeedgkfrvkt.kseeeleadklvlAtGGl 165
                                       +ke+++++ + t+v+++  ++ +dg+++ ++  ++e++  dkl+lAtGG+
  gi|474934899|ref|YP_007688481.1|  68 AKERNIRIVTGTTVEAAayDRAKDGTMTKTVtVNGETVPYDKLILATGGK 117
                                       6899999999999999844334455444444349***************8 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00025
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36 
                                       +v++ G+G  Gl  A++++++gk+V+++e ++++ 
  gi|474934899|ref|YP_007688481.1| 152 RVVIAGAGVIGLELALHLKEAGKDVTIIEMMDQVI 186
                                       79****************************99875 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0022
                                       HHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE---- CS
                       HI0933_like 111 ivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGG 164
                                       + d ++k l+++gv++ l+  v++v+  +d++ +v+   ++e+ +d +++AtG 
  gi|474934899|ref|YP_007688481.1| 194 MADPIQKYLEDKGVEIVLKAPVQAVNG-KDRVESVSS-LGKEYPCDMVIFATGV 245
                                       556678889****************55.555577777.89************96 PP

  == domain 5  score: -2.4 bits;  conditional E-value: 2.7
                                       TTSTTEEE-GGGBSE CS
                       HI0933_like 373 kkvpgLffaGEvlDv 387
                                       + vp++f++G v+  
  gi|474934899|ref|YP_007688481.1| 278 RLVPDVFVCGDVMQC 292
                                       579*********976 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.016       8.9       1      19 [.       6      24 ..       6      36 .. 0.89
   2 !   32.3   1.2   1.1e-10   6.1e-08      90     305 .]      67     287 ..      53     287 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.016
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkka 19
                                      ++iG G+aGl+aa  ++ +
  gi|474934899|ref|YP_007688481.1|  6 VVIGSGAAGLSAASSARAV 24
                                      79***********999876 PP

  == domain 2  score: 32.3 bits;  conditional E-value: 1.1e-10
                       Pyr_redox_3  90 vaksfelpiklfeeVesvkk..edeg...fevetsketyeAkkviiAtGe.fdkPnk..lnipGeeklvkhyskvke 158
                                       +ak+ +++i + ++Ve+ +   +++g    +v+ + et+  +k+i+AtG    +P     n pG    v      ++
  gi|474934899|ref|YP_007688481.1|  67 YAKERNIRIVTGTTVEAAAYdrAKDGtmtKTVTVNGETVPYDKLILATGGkVFIPPIegVNLPGVFT-VRTVEGGRK 142
                                       6888999999999998876532333323478999999***********9523344440134445543.222222234 PP

                       Pyr_redox_3 159 fhky..agqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfna 233
                                       +++y  + ++vv+ G++  + + Al+l ++g++Vt++   +++  + +        d+ + ++++++ + ++++ +a
  gi|474934899|ref|YP_007688481.1| 143 MQEYlaKSKRVVIAGAGVIGLELALHLKEAGKDVTIIEMMDQVIPRIA------DKDMADPIQKYLEDKGVEIVLKA 213
                                       44442258899999***********************99987666543......4456677777777767******* PP

                       Pyr_redox_3 234 evkeikekeeeykvktedgkkvevkddvvlatGykpdlsflkkslfeldedg....rpvlteeteetnvpglflaG 305
                                        v++++ k++ ++  ++ gk+    d v++atG + ++++ k + +++ + g     p+l+  +    vp++f++G
  gi|474934899|ref|YP_007688481.1| 214 PVQAVNGKDR-VESVSSLGKEYPC-DMVIFATGVRANVDLAKMMNLDIGQLGalcvAPTLQAYQRGRLVPDVFVCG 287
                                       ******9866.6666777899886.889************998888877766444457788888888888888887 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.1    0.0002      0.11       1      25 [.       7      33 ..       7      39 .. 0.85
   2 !   16.5   0.0   1.3e-05    0.0071       1      51 [.     155     209 ..     155     220 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0002
                                      EE--SHHHHHHHHHHHCC..TEEEEEE CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLaka..gfdvlll 25
                                      ++G+G++Gl+aA+ ++    +++++++
  gi|474934899|ref|YP_007688481.1|  7 VIGSGAAGLSAASSARAVdpDAEITVY 33
                                      8***********999984358888887 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.3e-05
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECE....TTCEECTS--- CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyev....pgvrvdygahi 51 
                                       I GaG+ Gl +A +L++ag+dv+++e+ d++  r+a++++    +++  d g+ i
  gi|474934899|ref|YP_007688481.1| 155 IAGAGVIGLELALHLKEAGKDVTIIEMMDQVIPRIADKDMadpiQKYLEDKGVEI 209
                                       67*************************9998777777777443333666666665 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.2   3.1e-05     0.018       2      19 ..       5      22 ..       4      38 .. 0.86
   2 !   13.6   0.6   4.6e-05     0.026       2      32 ..     153     183 ..     152     186 .. 0.93
   3 ?   -3.0   0.0       5.2   2.9e+03     371     404 ..     260     291 ..     252     300 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.1e-05
                                      EEEE--SHHHHHHHHHHH CS
                     FAD_binding_2  2 viViGsGlAGLaAAleaa 19
                                      ++ViGsG+AGL+AA +a+
  gi|474934899|ref|YP_007688481.1|  5 IVVIGSGAAGLSAASSAR 22
                                      79************9886 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 4.6e-05
                                       EEEE--SHHHHHHHHHHHHTTT-EEEEESSS CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeq 32 
                                       v++ G+G+ GL  Al ++eaG++v+++e ++
  gi|474934899|ref|YP_007688481.1| 153 VVIAGAGVIGLELALHLKEAGKDVTIIEMMD 183
                                       9**************************9776 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 5.2
                                       EES-EEEBETTSBESTTEEESSBTEEE-STCEES CS
                     FAD_binding_2 371 ytmgGvetdengrvldadgqpipGLYAaGevaag 404
                                       +++g + + +++++  + g+ +p+ + +G v+  
  gi|474934899|ref|YP_007688481.1| 260 GQLGALCVAPTLQA-YQRGRLVPDVFVCGDVM-Q 291
                                       55555666677888.899999*********99.3 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.4   9.4e-05     0.053      29      56 ..       3      32 ..       1      42 [. 0.76
   2 !   12.4   0.2   0.00012     0.069      28      67 ..     150     189 ..     136     218 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.4e-05
                                      -EEEEESTSHHHHHHHHHHHHTT..-EEEE CS
                       AlaDh_PNT_C 29 akvlviGgGvaGlqAiatakglg..akVtv 56
                                       k++viG G aGl+A++ a++++  a++tv
  gi|474934899|ref|YP_007688481.1|  3 TKIVVIGSGAAGLSAASSARAVDpdAEITV 32
                                      79****************998852244444 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00012
                                       --EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHH CS
                       AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakglgakVtvlDvrparleql 67 
                                         +v++ G+Gv Gl+ +   k+ g +Vt++++  +++ ++
  gi|474934899|ref|YP_007688481.1| 150 SKRVVIAGAGVIGLELALHLKEAGKDVTIIEMMDQVIPRI 189
                                       558***************************9988877655 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.035        20       9      43 ..       4      40 ..       2     108 .. 0.68
   2 !   17.1   0.2   9.9e-06    0.0056       6      40 ..     149     183 ..     147     253 .. 0.61

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.035
                     NAD_binding_7  9 kvlvvGgGevAarkvrklleag..akvtvvapevkee 43
                                      k++v+G G  +++ +++  + +  a++tv++++v  +
  gi|474934899|ref|YP_007688481.1|  4 KIVVIGSGAAGLSAASSARAVDpdAEITVYTQDVDVA 40
                                      799*********999887665444*****99997333 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 9.9e-06
                     NAD_binding_7   6 kgkkvlvvGgGevAarkvrklleagakvtvvapev 40 
                                       k k+v+++G+G ++++ + +l eag++vt++    
  gi|474934899|ref|YP_007688481.1| 149 KSKRVVIAGAGVIGLELALHLKEAGKDVTIIEMMD 183
                                       679***************************86652 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0    0.0002      0.11      18      53 ..       3      39 ..       1      99 [. 0.74
   2 !    6.4   0.1     0.008       4.5      18      49 ..     151     181 ..     136     185 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0002
                                      EEEEEE--SHHHHHHHHHHHHC.TTS-EEEEESSSS- CS
                              Thi4 18 sDvvivGaGssGLtaayylakk.pdlkvailersvsp 53
                                      + +v++G+G++GL+aa       pd ++++  + v +
  gi|474934899|ref|YP_007688481.1|  3 TKIVVIGSGAAGLSAASSARAVdPDAEITVYTQDVDV 39
                                      679************9876544599999998877643 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.008
                                       EEEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                              Thi4  18 sDvvivGaGssGLtaayylakkpdlkvailer 49 
                                         vvi GaG  GL  a  l ++ +  v+i+e 
  gi|474934899|ref|YP_007688481.1| 151 KRVVIAGAGVIGLELALHLKEA-GKDVTIIEM 181
                                       469****************999.888999885 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   1.0     0.049        27       2      18 ..       3      19 ..       2      21 .. 0.91
   2 !   17.0   0.2     5e-06    0.0028       3      35 ..     152     184 ..     150     191 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.049
                                      EEEEEE--SHHHHHHHH CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlal 18
                                      t+++++G+G aGl++a+
  gi|474934899|ref|YP_007688481.1|  3 TKIVVIGSGAAGLSAAS 19
                                      7899***********95 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 5e-06
                                       EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                     FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrst 35 
                                        V+I GaG  Gl lal L+eaG +v+++e +++
  gi|474934899|ref|YP_007688481.1| 152 RVVIAGAGVIGLELALHLKEAGKDVTIIEMMDQ 184
                                       59***************************8876 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.31   1.7e+02     192     223 ..       3      34 ..       1      41 [. 0.76
   2 !   15.2   0.0   1.6e-05    0.0091     104     221 ..      66     180 ..      64     219 .. 0.74
   3 ?   -3.6   0.0       8.3   4.7e+03     330     340 ..     235     245 ..     228     246 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.31
                       K_oxygenase 192 kriaVvGsGqSaaeifedllrrqkkvelklvt 223
                                        +i+V+GsG  +   +  + +  +++e++++t
  gi|474934899|ref|YP_007688481.1|   3 TKIVVIGSGAAGLSAASSARAVDPDAEITVYT 34 
                                       68999999988887777777777777777766 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.6e-05
                       K_oxygenase 104 Wvasqleeqvrfgeeveevepdeeeee.elltveskdaegeeeelearnlvlgvGtepkiPevleklegkervvHss 179
                                       W a++ + ++  g++ve+  +d++++     tv++     + e++   +l+l++G++  iP++   ++  + v+   
  gi|474934899|ref|YP_007688481.1|  66 WYAKERNIRIVTGTTVEAAAYDRAKDGtMTKTVTV-----NGETVPYDKLILATGGKVFIPPIEG-VN-LPGVFTVR 135
                                       66666666677789999999999987745556665.....56789999*************9754.44.25555555 PP

                       K_oxygenase 180 eylerkee...llakkriaVvGsGqSaaeifedllrrqkkvelkl 221
                                       ++   ++    l+++kr+++ G+G  + e++ +l +  k+v++  
  gi|474934899|ref|YP_007688481.1| 136 TVEGGRKMqeyLAKSKRVVIAGAGVIGLELALHLKEAGKDVTIIE 180
                                       44433222235999********************99988765543 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 8.3
                       K_oxygenase 330 evdavvlATGY 340
                                        +d+v++ATG 
  gi|474934899|ref|YP_007688481.1| 235 PCDMVIFATGV 245
                                       589*******6 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0034       1.9       2      29 ..       5      32 ..       4      98 .. 0.77
   2 !    8.8   0.4    0.0014      0.76       2      36 ..     153     185 ..     152     189 .. 0.90
   3 ?    1.7   0.0      0.19   1.1e+02      83     143 ..     188     247 ..     187     260 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0034
                     Lycopene_cycl  2 vvviGaGpAglslAarlteakpglkvvl 29
                                      +vviG+G+Agls A    +  p+ ++++
  gi|474934899|ref|YP_007688481.1|  5 IVVIGSGAAGLSAASSARAVDPDAEITV 32
                                      89**********9987755555555544 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0014
                     Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlieaspsl 36 
                                       vv+ GaG  gl lA +l  +++g  v++ie  +++
  gi|474934899|ref|YP_007688481.1| 153 VVIAGAGVIGLELALHL--KEAGKDVTIIEMMDQV 185
                                       89***************..9999999999987766 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.19
                     Lycopene_cycl  83 rvsskrlkeellerlvengvk.lleakvesveeeeageslvvleggrkirarlvvdarglas 143
                                       r+  k+++  +++ l ++gv+  l+a v++v+ ++   +  v + g++ ++ +v+ a+g+ +
  gi|474934899|ref|YP_007688481.1| 188 RIADKDMADPIQKYLEDKGVEiVLKAPVQAVNGKDR--VESVSSLGKEYPCDMVIFATGVRA 247
                                       5777889999999999888852689*******9999..7778899**************544 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       1.4   7.9e+02       1      95 [.       5      33 ..       3      42 .. 0.53
   2 !   17.0   0.2   9.5e-06    0.0053       1      41 [.     153     193 ..     153     211 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.4
                                      EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHHHH CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeanila 79
                                      i++iG G  G s                                                                  a
  gi|474934899|ref|YP_007688481.1|  5 IVVIGSGAAGLS------------------------------------------------------------------A 17
                                      455555555555..................................................................5 PP

                                      HHHHHHHTSSSEEEEE CS
                            TrkA_N 80 vllakelnpkkkiiar 95
                                      + +a+   p+++i + 
  gi|474934899|ref|YP_007688481.1| 18 ASSARAVDPDAEITVY 33
                                      5555555555444444 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 9.5e-06
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTT CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeg 41 
                                       ++i+G+G +G +la  L+e+gkdv++i+  ++++ +++++ 
  gi|474934899|ref|YP_007688481.1| 153 VVIAGAGVIGLELALHLKEAGKDVTIIEMMDQVIPRIADKD 193
                                       79*****************7779*********999999886 PP

>> Sigma70_r1_1  Sigma-70 factor, region 1.1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.4   3.7e-06    0.0021      14      58 ..     169     214 ..     164     230 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.7e-06
                                       HHHHSC.EEHHHHHHHGCCSS--HHHHHHHHHHHHCCT-EEE-SS- CS
                      Sigma70_r1_1  14 gKkkGy.LtyeEindaLpddeldseqiediiemLedmgIdvveeae 58 
                                        K++G  +t  E++d   + + d++  + i+++Led g+++v +a+
  gi|474934899|ref|YP_007688481.1| 169 LKEAGKdVTIIEMMDQVIPRIADKDMADPIQKYLEDKGVEIVLKAP 214
                                       6999999**********99***********************9999 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.1    0.0023       1.3       1      20 [.       4      23 ..       4      45 .. 0.73
   2 ?    1.9   0.0      0.17        93     108     150 ..      70     116 ..      62     132 .. 0.80
   3 ?    5.5   0.5     0.013       7.6       2      31 ..     153     181 ..     152     193 .. 0.86
   4 ?    1.5   0.0      0.23   1.3e+02     100     170 ..     197     264 ..     187     279 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0023
                                      CEEEE-SSHHHHHHHHHHHH CS
                              GIDA  1 dviViGgGhAGceAAlaaar 20
                                      +++ViG G AG+ AA  a  
  gi|474934899|ref|YP_007688481.1|  4 KIVVIGSGAAGLSAASSARA 23
                                      69*************87754 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.17
                                       STTEEEEES-EEEEEECT....TEEEEEEETTS-EEEECEEEE--TT CS
                              GIDA 108 epnleiieeeveelivee....kkvkgvvtedgetikakavviatGt 150
                                       e n+ i++++  e    +    ++++  vt +get+  ++ ++atG 
  gi|474934899|ref|YP_007688481.1|  70 ERNIRIVTGTTVEAAAYDrakdGTMTKTVTVNGETVPYDKLILATGG 116
                                       567777777666665544566688899999****************6 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.013
                                       EEEE-SSHHHHHHHHHHHHTT--EEEEES- CS
                              GIDA   2 viViGgGhAGceAAlaaarlGakvlLithk 31 
                                       v++ G+G  G+e Al+++++G +v++i + 
  gi|474934899|ref|YP_007688481.1| 153 VVIAGAGVIGLELALHLKEAGKDVTII-EM 181
                                       8999*********************99.33 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.23
                                       HHHHHHHTSTTEEEE.ES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT-BT-EEEETTEEEESSCTTC CS
                              GIDA 100 evteklenepnleii.eeeveeliveekkvkgvvtedgetikakavviatGtflkgkihigekelsaGrlge 170
                                        ++++le+ + +ei+ ++ v+ +   +++v+ v  + g+++ ++ v+ atG   +     ++ +l+ G+lg 
  gi|474934899|ref|YP_007688481.1| 197 PIQKYLED-KGVEIVlKAPVQAV-NGKDRVESV-SSLGKEYPCDMVIFATGV-RANVDLAKMMNLDIGQLGA 264
                                       56777777.66665514445555.435666665.678999***********8.4444455555555555555 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.44   2.5e+02     223     264 ..      73     118 ..      61     123 .. 0.75
   2 !    6.5   0.0    0.0077       4.3       3      26 ..     162     185 ..     162     189 .. 0.92
   3 ?    5.2   0.0     0.019        11     217     263 ..     199     246 ..     182     251 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.44
                                       EEEETSEEEEEEEE....ETTCEEEEETTSTEEEESEEEE-S-HHH CS
                     Amino_oxidase 223 ldirlntrVkeikr....egdgvtvtledgevveaDaVvvTvplgv 264
                                        +i ++t V   ++    +g   ++ +++ge+v++D+ ++++   v
  gi|474934899|ref|YP_007688481.1|  73 IRIVTGTTVEAAAYdrakDGTMTKTVTVNGETVPYDKLILATGGKV 118
                                       5666677777777755445555888899*************97665 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0077
                                       HHHHHHHHHHTTEEEEEEESSSSS CS
                     Amino_oxidase   3 GLaaArqLlsaGfdVtvlEardrv 26 
                                       GL  A +L++aG dVt++E  d+v
  gi|474934899|ref|YP_007688481.1| 162 GLELALHLKEAGKDVTIIEMMDQV 185
                                       8889***************98875 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.019
                                       HH..TTTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S-HH CS
                     Amino_oxidase 217 ae..elrgldirlntrVkeikregdgvtvtledgevveaDaVvvTvplg 263
                                       ++  e +g++i l ++V  ++  +d v    + g+++++D V+ ++ ++
  gi|474934899|ref|YP_007688481.1| 199 QKylEDKGVEIVLKAPVQAVNG-KDRVESVSSLGKEYPCDMVIFATGVR 246
                                       2255589**************5.8889998999***********99875 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.57   3.2e+02       1      17 [.       6      22 ..       6      40 .. 0.74
   2 !    7.6   0.0    0.0065       3.6     118     155 ..      79     116 ..      62     117 .. 0.70
   3 ?    2.2   0.2      0.28   1.6e+02       1      32 [.     154     183 ..     154     194 .. 0.78
   4 ?    2.7   0.0       0.2   1.1e+02     116     154 ..     206     244 ..     191     246 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.57
                     NAD_binding_9  1 aivGaGprGlavlerLl 17
                                      +++G G++Gl+++    
  gi|474934899|ref|YP_007688481.1|  6 VVIGSGAAGLSAASSAR 22
                                      69*********997654 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0065
                     NAD_binding_9 118 evhraevvdleeradgqavlladgaslaadaVvLAlGh 155
                                       + ++a + d +++++  + ++ +g+++ +d+++LA+G 
  gi|474934899|ref|YP_007688481.1|  79 TTVEAAAYDRAKDGTMTKTVTVNGETVPYDKLILATGG 116
                                       334444455555555568999***************95 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.28
                     NAD_binding_9   1 aivGaGprGlavlerLlarakkkspleitlfd 32 
                                       +i GaG+ Gl ++ +L +    k+ + i ++d
  gi|474934899|ref|YP_007688481.1| 154 VIAGAGVIGLELALHLKEAG--KDVTIIEMMD 183
                                       699*************8885..5555555555 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.2
                     NAD_binding_9 116 tvevhraevvdleeradgqavlladgaslaadaVvLAlG 154
                                        ve++ +  v+  + +d+++ + + g+++ +d V+ A+G
  gi|474934899|ref|YP_007688481.1| 206 GVEIVLKAPVQAVNGKDRVESVSSLGKEYPCDMVIFATG 244
                                       56665555555566778888999***************9 PP

>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.026        15       6      41 ..       3      41 ..       1      45 [. 0.84
   2 ?    7.1   0.0    0.0084       4.7       2      42 ..     147     184 ..     146     198 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.026
                                      SEEEEEESHHHHHHHHHHHHHH...HHHHTSEEEEEEHH CS
                               SIS  6 kriyvlGaGtsyaiakelalkl...eeiggivvevedas 41
                                       +i+v+G+G+ + +a+ +a+++   +ei++++++v+ a+
  gi|474934899|ref|YP_007688481.1|  3 TKIVVIGSGAAGLSAASSARAVdpdAEITVYTQDVDVAY 41
                                      68*****************99977778888888877665 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0084
                                       HCTSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHH CS
                               SIS   2 LakakriyvlGaGtsyaiakelalkleeiggivvevedase 42 
                                       Lak+kr+++ GaG    i++elal+l+e g+ v  +e  ++
  gi|474934899|ref|YP_007688481.1| 147 LAKSKRVVIAGAGV---IGLELALHLKEAGKDVTIIEMMDQ 184
                                       89**********96...9**********9987777665555 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1       1.7   9.7e+02       1      18 [.       4      21 ..       4      40 .. 0.70
   2 ?   13.6   0.1     8e-05     0.045       2      82 ..     153     239 ..     152     244 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.7
                                      EEEEE--SCCHHHHHHHH CS
                           3HCDH_N  1 kvaviGaGtmGagiaavf 18
                                      k+ viG+G  G + a+ +
  gi|474934899|ref|YP_007688481.1|  4 KIVVIGSGAAGLSAASSA 21
                                      689*******99988765 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 8e-05
                                       EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHH.HHHHHHHHHHCCTTTTSS-.....HHHHCCCHHCEEEES- CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealek.alekieksleklvekgklk.....eeeveaalarisfttd 72 
                                       v + GaG++G ++a  + +ag +V+++++ ++ + + a + +++ ++k  e++ ++       ++ +  +r++  ++
  gi|474934899|ref|YP_007688481.1| 153 VVIAGAGVIGLELALHLKEAGKDVTIIEMMDQVIPRiADKDMADPIQKYLEDKGVEivlkaPVQAVNGKDRVESVSS 229
                                       8899*************************877776514455666677766666666444222233333445555555 PP

                                       HHHHHC-SEE CS
                           3HCDH_N  73 leeavdadlv 82 
                                       l +   +d+v
  gi|474934899|ref|YP_007688481.1| 230 LGKEYPCDMV 239
                                       5555555555 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.68   3.8e+02      38      60 ..       4      26 ..       2      40 .. 0.77
   2 ?   11.3   0.1   0.00029      0.16      28      72 ..     142     186 ..     133     216 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.68
                                      EEEEES-SHHHHHHHHHHHHTT- CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgm 60
                                      ++ +iG G+ G ++a  ++a++ 
  gi|474934899|ref|YP_007688481.1|  4 KIVVIGSGAAGLSAASSARAVDP 26
                                      789*************9999864 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00029
                                       CGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHH CS
                      2-Hacid_dh_C  28 allgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkke 72 
                                       +++ +  + k+v i G+G IG ++a  lk+ g +v++++   +  
  gi|474934899|ref|YP_007688481.1| 142 KMQEYLAKSKRVVIAGAGVIGLELALHLKEAGKDVTIIEMMDQVI 186
                                       566667789*************************99998876654 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   1.2       5.2   2.9e+03       1      12 [.       5      16 ..       5      21 .. 0.84
   2 ?   14.5   0.2   3.7e-05     0.021       1      28 [.     153     180 ..     153     243 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5.2
                                      EEEES-SHHHHH CS
                              ApbA  1 iailGaGaiGsl 12
                                      i+++G+Ga G  
  gi|474934899|ref|YP_007688481.1|  5 IVVIGSGAAGLS 16
                                      89******9975 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 3.7e-05
                                       EEEES-SHHHHHHHHHHHHHTHCEEEE- CS
                              ApbA   1 iailGaGaiGsllaakLakagadvtlil 28 
                                       ++i+GaG iG  la +L++ag dvt+i 
  gi|474934899|ref|YP_007688481.1| 153 VVIAGAGVIGLELALHLKEAGKDVTIIE 180
                                       68***********************985 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       2.2   1.2e+03       2      17 ..       4      19 ..       3      38 .. 0.84
   2 ?   12.4   0.2   0.00016     0.089       2      43 ..     152     193 ..     151     232 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.2
                                      EEEEE--STTHHHHHH CS
                    UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaa 17
                                      ki+viG+G  Gl  a 
  gi|474934899|ref|YP_007688481.1|  4 KIVVIGSGAAGLSAAS 19
                                      89******99998765 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00016
                                       EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS CS
                    UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighevigvDideekvdklnsgk 43 
                                       ++++ G+G +Gl  a+ l e+g++v+++ + ++ +  +  ++
  gi|474934899|ref|YP_007688481.1| 152 RVVIAGAGVIGLELALHLKEAGKDVTIIEMMDQVIPRIADKD 193
                                       899**************************9999998887665 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0       0.2   1.1e+02       5      35 ..       3      33 ..       1      44 [. 0.77
   2 ?    8.9   0.0    0.0018         1       3      38 ..     149     184 ..     147     216 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.2
                                      S-EEEES-SHHHHHHHHHHHHTT--EEEEE- CS
                              IlvN  5 kkiaviGyGsqGhaqalnlrdsgldvvvglr 35
                                       ki+viG G+ G + a   r    d  ++++
  gi|474934899|ref|YP_007688481.1|  3 TKIVVIGSGAAGLSAASSARAVDPDAEITVY 33
                                      58***********999998876666555555 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0018
                                       HTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT- CS
                              IlvN   3 kgkkiaviGyGsqGhaqalnlrdsgldvvvglregs 38 
                                       k+k++++ G G  G   al l+++g dv++    ++
  gi|474934899|ref|YP_007688481.1| 149 KSKRVVIAGAGVIGLELALHLKEAGKDVTIIEMMDQ 184
                                       79**************************99766555 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.026        15       1      30 [.       4      32 ..       4      37 .. 0.76
   2 ?    0.1   0.0      0.49   2.7e+02     163     210 ..      67     117 ..      65     120 .. 0.82
   3 ?    3.7   0.6     0.041        23       1      34 [.     152     182 ..     152     191 .. 0.79
   4 ?    4.7   0.0      0.02        11     156     212 ..     194     248 ..     188     257 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.026
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEE CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtl 30
                                      kiv++G G aG  aA+   +a++ ++e+t+
  gi|474934899|ref|YP_007688481.1|  4 KIVVIGSGAAGLSAASSA-RAVDPDAEITV 32
                                      79*********8888765.55546688876 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.49
                                       HHHHCT-EEEE--EEEEEE.-T..TS-EEEEEETTS-EEE-SEEEE-SGGG CS
                    Trp_halogenase 163 vaearGvtrvegkvvevql.de..dgrveslrledgreveadlfiDcsGfr 210
                                       +a++r++++v g+ ve+   d   dg  ++  + +g++v +d  i ++G +
  gi|474934899|ref|YP_007688481.1|  67 YAKERNIRIVTGTTVEAAAyDRakDGTMTKTVTVNGETVPYDKLILATGGK 117
                                       799*******999877654122469*****9999********999999975 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.041
                                       EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-S CS
                    Trp_halogenase   1 kivivGGGtaGwlaAaalakalkgklevtlvese 34 
                                       ++vi+G+G  G   A +l++a+    +vt++e  
  gi|474934899|ref|YP_007688481.1| 152 RVVIAGAGVIGLELALHLKEAG---KDVTIIEMM 182
                                       69********************...457777753 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.02
                                       HHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGGG-I CS
                    Trp_halogenase 156 yakfLrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsGfrgl 212
                                       +a+ ++++ e++Gv++v    v++ ++ ++rves+    g+e+  d++i ++G r+ 
  gi|474934899|ref|YP_007688481.1| 194 MADPIQKYLEDKGVEIVLKAPVQA-VNGKDRVESVSS-LGKEYPCDMVIFATGVRAN 248
                                       567788999*******99988665.456899***998.899************9975 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       7.8   4.4e+03       1      30 [.       4      35 ..       4      40 .. 0.77
   2 ?   12.0   0.0   0.00031      0.17       4      42 ..     155     193 ..     152     242 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 7.8
                                      EEEEE--SHHHHHHHHHH..HHTT-EEEEE-S CS
                     NAD_binding_2  1 kigfiGlGvMGsnmalnl..lkagykvavynr 30
                                      ki +iG G  G + a+    ++ + +++vy  
  gi|474934899|ref|YP_007688481.1|  4 KIVVIGSGAAGLSAASSAraVDPDAEITVYTQ 35
                                      57899999999999987644788888888875 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00031
                                       EE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT CS
                     NAD_binding_2   4 fiGlGvMGsnmalnllkagykvavynrtkekveelvaeg 42 
                                       + G Gv+G ++al+l++ag +v++++   + + +++++ 
  gi|474934899|ref|YP_007688481.1| 155 IAGAGVIGLELALHLKEAGKDVTIIEMMDQVIPRIADKD 193
                                       67************************9999998888876 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.76   4.3e+02      21      92 ..       5      32 ..       2      45 .. 0.57
   2 ?    9.7   0.1   0.00087      0.49      11      42 ..     142     174 ..     132     185 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.76
                                      EEEE--SHHHHHHHHHHHHHTTTEEEEEESSB--GGGGGTBTTS-GGGTTSBHHHHHHHHHHHT-TTSEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF 21 vllvGaGglGsellknLalsGvgkltlvDnDkielsNlnRqflfreediGkpKaevaaealqeinpdvevea 92
                                      ++++G G+ G  +                                            a +++++ pd+e++ 
  gi|474934899|ref|YP_007688481.1|  5 IVVIGSGAAGLSA--------------------------------------------ASSARAVDPDAEITV 32
                                      5555555555544............................................444444445555554 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00087
                                       HHHHHHHT.SEEEEE--SHHHHHHHHHHHHHTT CS
                                       xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  11 dgqekLrd.skvllvGaGglGsellknLalsGv 42 
                                       + qe L++ ++v++ GaG +G el+  L  +G 
  gi|474934899|ref|YP_007688481.1| 142 KMQEYLAKsKRVVIAGAGVIGLELALHLKEAGK 174
                                       67777877689***************9998883 PP

>> LpxI_N  LpxI N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00039      0.22       4      41 ..     154     191 ..     151     211 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00039
                            LpxI_N   4 liAGsGrlPllvaeaakaagrevvvvalegeadeelek 41 
                                       +iAG+G + l++a ++k+ag++v ++ + +++ +++++
  gi|474934899|ref|YP_007688481.1| 154 VIAGAGVIGLELALHLKEAGKDVTIIEMMDQVIPRIAD 191
                                       8***************************9998888776 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       1.2   6.8e+02       1      17 [.       4      20 ..       4      40 .. 0.77
   2 ?    9.9   0.0    0.0012      0.67       2      43 ..     153     194 ..     152     227 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.2
                                      -EEEE--SHHHHHHHHH CS
                    NAD_Gly3P_dh_N  1 kiavlGaGswGtalAkv 17
                                      ki v+G+G+ G + A +
  gi|474934899|ref|YP_007688481.1|  4 KIVVIGSGAAGLSAASS 20
                                      799******99988765 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0012
                                       EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHSS CS
                    NAD_Gly3P_dh_N   2 iavlGaGswGtalAkvlaenghevrlwvreeelieeineehe 43 
                                       + + GaG  G  lA +l+e+g++v+++ + +++i +i ++  
  gi|474934899|ref|YP_007688481.1| 153 VVIAGAGVIGLELALHLKEAGKDVTIIEMMDQVIPRIADKDM 194
                                       7899***************************99999987764 PP

>> MCRA  MCRA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   1.1       1.1     6e+02       3      17 ..       4      18 ..       2      22 .. 0.88
   2 ?    6.9   0.0     0.004       2.3     208     236 ..     194     222 ..     190     234 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.1
                                      EEEEE--SHHHHHHH CS
                              MCRA  3 kaylvGsGiasLaaA 17
                                      k+ ++GsG a+L+aA
  gi|474934899|ref|YP_007688481.1|  4 KIVVIGSGAAGLSAA 18
                                      6779**********9 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.004
                                       CCHHHHHHHHHTT-EEE-SEEEEEEEEEE CS
                              MCRA 208 lilPlvkyLkeqgVdfqfntkVtdiefee 236
                                       +  P++kyL+++gV++ +++ V+ ++ ++
  gi|474934899|ref|YP_007688481.1| 194 MADPIQKYLEDKGVEIVLKAPVQAVNGKD 222
                                       789*******************9998773 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   1.4      0.03        17       2      19 ..       5      22 ..       4      26 .. 0.92
   2 ?   -1.8   0.0       2.6   1.5e+03      90     125 ..      53     100 ..      50     111 .. 0.67
   3 ?    1.7   0.3      0.23   1.3e+02       2      30 ..     153     181 ..     152     185 .. 0.94
   4 ?    4.0   0.0     0.045        25      93     144 ..     198     244 ..     187     254 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.03
                      FAD_oxidored  2 vvVvGGgpaGvaAAiaAa 19
                                      +vV+G+g+aG+ AA +A 
  gi|474934899|ref|YP_007688481.1|  5 IVVIGSGAAGLSAASSAR 22
                                      8*************9995 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.6
                      FAD_oxidored  90 kavleeml........aeagvtvllntrlveveke...gkr.iesvtv 125
                                       k+++e+m+        +e +++++++t+++++  +   +++  + vtv
  gi|474934899|ref|YP_007688481.1|  53 KSTWENMImhtpewyaKERNIRIVTGTTVEAAAYDrakDGTmTKTVTV 100
                                       566677777777777899999999999998877752222222444544 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.23
                      FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLvee 30 
                                       vv+ G+g+ G+  A+  ++aG+ v ++e 
  gi|474934899|ref|YP_007688481.1| 153 VVIAGAGVIGLELALHLKEAGKDVTIIEM 181
                                       9**************************95 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.045
                      FAD_oxidored  93 leemlaeagvtvllntrlvevekegkriesvtveskegrktirAkvfiDATg 144
                                       +++ l+++gv+++l++ +++v+ ++ r+esv       +k++ ++++i ATg
  gi|474934899|ref|YP_007688481.1| 198 IQKYLEDKGVEIVLKAPVQAVNGKD-RVESVSSL----GKEYPCDMVIFATG 244
                                       688999*****************98.*****998....78888888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        32  (0.00178482); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              32  [number of targets reported over threshold]
# CPU time: 0.71u 0.32s 00:00:01.03 Elapsed: 00:00:00.49
# Mc/sec: 2765.28
//
Query:       gi|474934900|ref|YP_007688482.1|  [L=257]
Description: hypothetical protein TALC_01340 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-41  140.1   0.0    7.6e-41  139.2   0.0    1.4  1  TPD       Protein of unknown function TPD sequence-motif
    0.00068   18.9   0.4     0.0011   18.2   0.0    1.5  2  RmuC      RmuC family
  ------ inclusion threshold ------
      0.044   13.7   0.0       0.11   12.4   0.0    1.6  1  DUF4224   Domain of unknown function (DUF4224)


Domain annotation for each model (and alignments):
>> TPD  Protein of unknown function TPD sequence-motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.2   0.0   1.3e-44   7.6e-41       3     134 ..     110     244 ..     108     245 .. 0.93

  Alignments for each domain:
  == domain 1  score: 139.2 bits;  conditional E-value: 1.3e-44
                               TPD   3 krlakevkeaieedsvyspladairssvGeeyEellekllkekgiafkteedlrekgl...dktPDvkLevpvaveg 76 
                                       ++ a+e++ea+e+d vysp+ad++++++G+++E ll+++l+++gi+++te+d re++    +ktPD++L+vp+ ++g
  gi|474934900|ref|YP_007688482.1| 110 EEAAEELREASEKDLVYSPAADEKSKERGKWGEGLLWEWLDAQGIEYQTEADEREMDSsqgTKTPDCLLKVPMDYKG 186
                                       67789**********************************************999776511167************** PP

                               TPD  77 kvvnWiesKalfgdeeehkkylkkQlssYvnrfGpGlviYwfGyvdelesekgvlikd 134
                                       +++ WiesKa+fgd  e k +  +Ql+ Y++ fGpG+v+Yw+G+vd le++ +v+++d
  gi|474934900|ref|YP_007688482.1| 187 HKIFWIESKASFGDAAELKYNSLHQLIPYTEIFGPGVVVYWTGHVDGLECPPNVFLED 244
                                       ***************************************************9988876 PP

>> RmuC  RmuC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1      0.58   3.4e+03      27      36 ..      43      52 ..      29      64 .. 0.43
   2 !   18.2   0.0   1.8e-07    0.0011      62     125 ..     133     199 ..     110     207 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.58
                              RmuC 27 eeaeeleslk 36
                                      +++++++++k
  gi|474934900|ref|YP_007688482.1| 43 TVKKRFHQVK 52
                                      1122222221 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 1.8e-07
                              RmuC  62 nsktrGnwGEvqLerilessgleegeeyetqvslkdeegelrpDvvvklpgg....kklviDsKvple 125
                                       +sk rG+wGE  L + l++ g e + e ++ +   +++g+  pD+++k+p +    k   i sK+++ 
  gi|474934900|ref|YP_007688482.1| 133 KSKERGKWGEGLLWEWLDAQGIEYQTEADEREM-DSSQGTKTPDCLLKVPMDykghKIFWIESKASFG 199
                                       789******************988866554444.4445767*********999998999999999975 PP

>> DUF4224  Domain of unknown function (DUF4224)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.8e-05      0.11      21      36 ..     147     162 ..     142     163 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.8e-05
                           DUF4224  21 kwLranGipfvvradG 36 
                                       +wL+a+Gi+++++ad 
  gi|474934900|ref|YP_007688482.1| 147 EWLDAQGIEYQTEADE 162
                                       8************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1797.44
//
Query:       gi|474934901|ref|YP_007688483.1|  [L=301]
Description: conserved hypothetical protein TIGR00294 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-71  240.0   0.1    3.7e-71  239.7   0.1    1.0  1  GCHY-1    Type I GTP cyclohydrolase folE2
  ------ inclusion threshold ------
      0.043   14.1   0.1         16    5.9   0.0    2.6  2  ACDC      AP2-coincident C-terminal


Domain annotation for each model (and alignments):
>> GCHY-1  Type I GTP cyclohydrolase folE2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  239.7   0.1   4.1e-75   3.7e-71       3     259 .]       6     281 ..       5     281 .. 0.90

  Alignments for each domain:
  == domain 1  score: 239.7 bits;  conditional E-value: 4.1e-75
                                       XXXXXXXXX----SEEEEEEEEEEEEE--TT...TS-EEEEEEEEEEEES-SS--GGGGGHHHHHHH.HS-SSEEG. CS
                            GCHY-1   3 DvqsekderkipldrVGvkgvklpvkvkdke...kkaqtlvaevdlfvdLpaekkGihmSRlvevle.eaeeelee. 74 
                                       Dvq  k +  ++l++VGv+gv++pv +++++   + +  +++e+++fvdLpa ++G h+SR+vevl+  a+e++++ 
  gi|474934901|ref|YP_007688483.1|   6 DVQYGKGSSGFKLTKVGVSGVRKPVLIARPGinnSASSVVNCEIEIFVDLPAAQRGSHLSRNVEVLRaVADESVKKp 82 
                                       9***************************9763224558999**************************6667888878 PP

                                       ....GGHHH....HHHHHHHHTT.-SEEEEEEEEEEEEEEE-TTT--EEEEEEEEEEEEEE..TTEEEEEEEEEEEE CS
                            GCHY-1  75 ....kslee....ileellekleyaeraevelkfeyfiekkapvsgkeglesyevtleaelerkeevkltvgvevpv 143
                                           +   +    ++++ll k+eyae+a+v++ +eyf  +k+p sg+e+lesy++++ a+++r  ++++t+gve+ +
  gi|474934901|ref|YP_007688483.1|  83 ypglE---NlavdMVKQLLVKHEYAENAYVSICAEYFRANKTP-SGRETLESYSLIAGAHATRGGDIRKTIGVEAIG 155
                                       85553...44447*****************************9.777**************99558*********** PP

                                       EEE-HHHHHHS...........SS---EEEEEEEEEEEE......--HHHHHHHHHHHSSEE--S---HHHHHHHHH CS
                            GCHY-1 144 ttlCPCskeisrell.......eagaHnQRsvvtvkvelaeeekeveiedlielvessassevyellKReDEkavte 213
                                       +t+CPC++e+++e+l       ++++HnQR+v+++ +++ +++ +ve++dli+l+e+s+ss++yellKReDE  v+ 
  gi|474934901|ref|YP_007688483.1| 156 MTACPCAQETVSEMLrvekpgfPMMSHNQRNVCSIILTM-DDDVNVEADDLIDLAEKSVSSPTYELLKREDEGSVVI 231
                                       ***********9998***********************5.68999******************************** PP

                                       HHHTS---HHHHHHHHHHHHHS-TTEEEE.........EEEEEEE-TTTSSEEEE CS
                            GCHY-1 214 kayenpkFvEDvvRevaaaleeeerveef.........sveveneESiHnHnavA 259
                                       +a++n++FvEDvvR+  + +     v+++          v + +eESiH+Hna+A
  gi|474934901|ref|YP_007688483.1| 232 NAHTNTRFVEDVVRNGLTLV-----VHNYeslpddvevCVISDSEESIHKHNAYA 281
                                       ***************88888.....33333346667779999************9 PP

>> ACDC  AP2-coincident C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0    0.0018        16      61      88 ..     107     134 ..      46     135 .. 0.87
   2 ?    5.5   0.0    0.0024        22      16      60 ..     241     291 ..     237     294 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0018
                              ACDC  61 pylklFstcilknklPSqlsleeqllll 88 
                                        y+++++++ ++nk+PS  ++ e ++l+
  gi|474934901|ref|YP_007688483.1| 107 AYVSICAEYFRANKTPSGRETLESYSLI 134
                                       7****************99988888887 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0024
                              ACDC  16 eDLlnnclpqlasslanktss......kelkrvieahikyvenakslkelq 60 
                                       eD+ +n l  + +++++ + +      ++ +++i++h  y+e+++s+ el+
  gi|474934901|ref|YP_007688483.1| 241 EDVVRNGLTLVVHNYESLPDDvevcviSDSEESIHKHNAYAERTASMGELR 291
                                       78899999999999999988899999999******************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1933.72
//
Query:       gi|474934902|ref|YP_007688484.1|  [L=214]
Description: ribonuclease H, mammalian HI/archaeal HII subfamily [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.9e-44  151.3   0.0    3.5e-44  151.0   0.0    1.1  1  RNase_HII  Ribonuclease HII


Domain annotation for each model (and alignments):
>> RNase_HII  Ribonuclease HII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.0   0.0   1.9e-48   3.5e-44       1     197 [.       4     198 ..       4     199 .. 0.90

  Alignments for each domain:
  == domain 1  score: 151.0 bits;  conditional E-value: 1.9e-48
                                       EEEEEE-TT-SBS-EEEEEEEECGHHHHHHHCTTGTTGTTS-HHHHHHHHHHHH...SEEEEEEE-HHHHH.HHTTT CS
                         RNase_HII   1 iGiDEaGrGpvlGplvvaavavekereeelkklgvkDSKkLskqkreeLaklik...kkiekrklvaeeikyasene 74 
                                       +G+DEaGrGp++Gplvv av  e++    l+++gvkDSK+Ls+ +re ++++i    ++ e   ++aee++ ++++e
  gi|474934902|ref|YP_007688484.1|   4 CGVDEAGRGPMMGPLVVGAVWTEDDSV--LRNIGVKDSKQLSPAQREIMFSEISdtaAHWEVVIVSAEELD-RRMAE 77 
                                       7****************9999988877..*************************77777777888888888.88*** PP

                                       S-HHHHHHHHHHHHHHHHHHTCEECCECCCE--SSHHHHHHHHHHHHC.CEEEEETTGGGT-HHHHHHHHHHHHHHH CS
                         RNase_HII  75 inlneikaaltlaviklleklgvkvdeilvdgvttpeslkkkleqiik.ikvtvekkadekyllvaaASiiAkverd 150
                                        nlne++  +++++i +   + v++d    +     +++   + + ++ ++v +e+kad++++ v+aASi+Akv+rd
  gi|474934902|ref|YP_007688484.1|  78 KNLNEVEMGMFAEAIMKHPSDIVYIDCPETN----TQRFGAIMSNLTGgRRVDAENKADALFPTVSAASIMAKVTRD 150
                                       ************9999877766665555554....5566666777788999************************** PP

                                       HHHHHHHHHCSH.--TTSSTTSHHHHHHHHHHHHH..S--TTB-TTSHH CS
                         RNase_HII 151 eelellkrkpgtldkgsGyasdektrallkkgats..klpdivrlsfkt 197
                                         +e ++r+ g  d+gsGy+sd+ t+a+++k++++   +p ++r+s+k 
  gi|474934902|ref|YP_007688484.1| 151 RLIEDIAREFG-CDIGSGYPSDPVTKAFVEKWIKDngSPPPHTRRSWKP 198
                                       *********96.***********************9999********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1271.29
//
Query:       gi|474934903|ref|YP_007688485.1|  [L=110]
Description: SCP-2 sterol transfer family [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.9e-11   42.5   0.1    8.4e-11   42.3   0.1    1.1  1  SCP2          SCP-2 sterol transfer family
    4.1e-05   23.8   0.0    4.6e-05   23.7   0.0    1.2  1  Alkyl_sulf_C  Alkyl sulfatase C-terminal


Domain annotation for each model (and alignments):
>> SCP2  SCP-2 sterol transfer family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.1   9.4e-15   8.4e-11       3      99 ..      13     109 ..      11     110 .] 0.80

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 9.4e-15
                                       HHHHHHHHH.HHHHHHCCH-EEEEEEECTC.TEEEEEETTSTEEE.SSCTTBS-SEEEEEEHHHHHHHHCTSS-HHH CS
                              SCP2   3 qllerlkdp.ekkealkklagvlrfdltdlkgsltldlkegqldv.aakdegkadvtlslsledllelaegklnpqk 77 
                                       ++ +r++++ + ++++++l  ++ +dl ++  ++ + l +  ++    ++   adv+l+ ++e+l +l++g ++p++
  gi|474934903|ref|YP_007688485.1|  13 KANQRMSEDeKVRKEVENLVKTFNIDLGEE--KYSFKLENAVISDfRCEMLPAADVVLTSTPETLTKLIDGDMRPMR 87 
                                       677788555499******************..566666653333332222258************************ PP

                                       HHHTTSSEEEC-HHHHHHHHHH CS
                              SCP2  78 afmqgkLkieGDielaqkleal 99 
                                       a++++k+ki+G i+ ++ l++ 
  gi|474934903|ref|YP_007688485.1|  88 AYVTKKIKIQGKINDLMVLKKF 109
                                       ***********99999988876 PP

>> Alkyl_sulf_C  Alkyl sulfatase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   5.2e-09   4.6e-05      38     111 ..      35     107 ..       3     110 .] 0.85

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 5.2e-09
                                       EEETTT.TEEEEEEEETTEEEE.ECT---TTSSEEEEE-HHHHHHHHTTSS-HHHHHHTTTEEEEE-TCHHHHHH CS
                      Alkyl_sulf_C  38 lvvtDv.dekyllrlsngvLthtrkaaqaddadltvtltreqLvalllgkatlgkevaagklkieGdaealakll 111
                                       +++ D  +eky  +l+n+v+    + +  + ad+ +t t e+L++l+ g++ +  +  ++k+ki+G+   l  l 
  gi|474934903|ref|YP_007688485.1|  35 FNI-DLgEEKYSFKLENAVISD-FRCEMLPAADVVLTSTPETLTKLIDGDMRPMRAYVTKKIKIQGKINDLMVLK 107
                                       333.55468*************.6656669************************************999887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       904  (0.0504211); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 687.19
//
Query:       gi|474934904|ref|YP_007688486.1|  [L=181]
Description: Tetratricopeptide repeat protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.5e-08   32.6   1.2       0.11   13.3   0.0    4.4  5  TPR_14    Tetratricopeptide repeat
    2.6e-07   30.6   0.4     0.0056   17.0   0.0    3.1  3  TPR_17    Tetratricopeptide repeat
      4e-07   29.6  14.8    0.00097   19.1   0.5    6.1  6  TPR_2     Tetratricopeptide repeat
    6.2e-07   29.1  14.6    0.00063   19.8   1.0    5.3  5  TPR_8     Tetratricopeptide repeat
    9.9e-07   29.3   2.7       0.13   12.9   0.6    3.9  4  TPR_16    Tetratricopeptide repeat
    1.3e-05   25.6   3.4      0.064   13.8   0.0    3.9  4  TPR_19    Tetratricopeptide repeat
    0.00029   20.4  12.1      0.031   14.0   2.9    4.3  5  TPR_11    TPR repeat
    0.00062   19.5  19.5     0.0031   17.2   0.2    6.1  7  TPR_1     Tetratricopeptide repeat
    0.00066   19.0   0.2    0.00089   18.6   0.2    1.2  1  FAT       FAT domain
     0.0027   17.9   6.1      0.021   15.1   1.2    3.8  4  TPR_12    Tetratricopeptide repeat
     0.0062   16.7   0.4       0.21   11.8   0.2    2.6  2  ANAPC3    Anaphase-promoting complex, cyclosome, subunit 3
     0.0093   16.5   5.2       0.22   12.2   0.1    4.1  3  TPR_6     Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.015   15.4   2.6      0.022   14.9   2.6    1.3  1  TPR_18    Tetratricopeptide repeat
      0.022   14.9   0.3        1.2    9.3   0.0    2.7  3  TPR_9     Tetratricopeptide repeat
      0.049   13.7   2.9        4.8    7.4   0.0    4.3  5  TPR_7     Tetratricopeptide repeat
       0.74    9.3   4.6       0.23   10.9   1.6    1.7  2  14-3-3    14-3-3 protein


Domain annotation for each model (and alignments):
>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0    0.0001      0.11      12      43 ..      27      58 ..      14      59 .. 0.84
   2 ?    2.2   0.0      0.37   4.1e+02      18      39 ..      74      95 ..      72      98 .. 0.86
   3 !   10.8   0.0   0.00066      0.74       1      33 [.      91     123 ..      91     131 .. 0.88
   4 ?    3.0   0.0      0.21   2.4e+02      20      43 ..     133     159 ..     129     161 .. 0.86
   5 ?    1.2   0.0      0.81     9e+02       8      29 ..     142     163 ..     139     180 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.0001
                            TPR_14 12 lalGdpdeAiallrralalaPddaeawlllaq 43
                                      +  Gd+++A  ++++  + +Pddae w+  a+
  gi|474934904|ref|YP_007688486.1| 27 MDMGDFKGAFSAFKKFTEEYPDDAEGWYSRAE 58
                                      678************************97776 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.37
                            TPR_14 18 deAiallrralalaPddaeawl 39
                                      de +a++ +a++l+ +++e++ 
  gi|474934904|ref|YP_007688486.1| 74 DEIEAAYTKAIELDDSHPEYYQ 95
                                      7899**********99999876 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00066
                            TPR_14   1 peallalaeallalGdpdeAiallrralalaPd 33 
                                       pe ++ ++ ++   G+++eA++++++a a + +
  gi|474934904|ref|YP_007688486.1|  91 PEYYQSYGLFCISIGKYEEAEKAYNEAAAIDES 123
                                       577889999******************998765 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.21
                            TPR_14  20 AiallrralalaP...ddaeawlllaq 43 
                                       Ai++++ +la++    dd+ a+  +a+
  gi|474934904|ref|YP_007688486.1| 133 AIEYYNNVLAQYGeilDDPKARVKYAK 159
                                       899*******99767799999998885 PP

  == domain 5  score: 1.2 bits;  conditional E-value: 0.81
                            TPR_14   8 aeallalGdpdeAiallrrala 29 
                                       a++ + l+dp++ ++++++al+
  gi|474934904|ref|YP_007688486.1| 142 AQYGEILDDPKARVKYAKKALD 163
                                       5555556666666666666654 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   0.00058      0.65       2      22 ..      39      59 ..      38      64 .. 0.94
   2 !   17.0   0.0     5e-06    0.0056       1      34 []      79     112 ..      79     112 .. 0.96
   3 ?   -2.5   0.0         8     9e+03      15      24 ..     140     149 ..     139     162 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00058
                            TPR_17  2 ylkaleldPnnadaynnLAel 22
                                      ++k+ e +P++a+ ++ +Ae+
  gi|474934904|ref|YP_007688486.1| 39 FKKFTEEYPDDAEGWYSRAEC 59
                                      89*****************86 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 5e-06
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                       +y+ka+eld ++++ y+ ++ +  ++G++++A++
  gi|474934904|ref|YP_007688486.1|  79 AYTKAIELDDSHPEYYQSYGLFCISIGKYEEAEK 112
                                       59******************************86 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 8
                            TPR_17  15 aynnLAelll 24 
                                       ++ +++e+l 
  gi|474934904|ref|YP_007688486.1| 140 VLAQYGEILD 149
                                       5566666664 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.1    0.0045       5.1      12      34 .]      27      49 ..      16      49 .. 0.87
   2 ?   -1.7   0.1       3.8   4.3e+03       1      10 [.      50      59 ..      50      59 .. 0.79
   3 ?    3.5   0.0     0.083        93      22      33 ..      78      89 ..      77      90 .. 0.84
   4 !   19.1   0.5   8.7e-07   0.00097       1      32 [.      91     122 ..      91     123 .. 0.91
   5 ?    1.3   0.0      0.43   4.9e+02      20      31 ..     133     144 ..     130     146 .. 0.85
   6 ?    3.3   0.1     0.096   1.1e+02      18      29 ..     159     170 ..     155     175 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0045
                             TPR_2 12 yklgdyeeAleafekAleldPnn 34
                                      + +gd++ A  af+k  e +P++
  gi|474934904|ref|YP_007688486.1| 27 MDMGDFKGAFSAFKKFTEEYPDD 49
                                      789******************96 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.8
                             TPR_2  1 aealynlGla 10
                                      ae++y ++++
  gi|474934904|ref|YP_007688486.1| 50 AEGWYSRAEC 59
                                      7899999875 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.083
                             TPR_2 22 eafekAleldPn 33
                                      +a+ kA+eld  
  gi|474934904|ref|YP_007688486.1| 78 AAYTKAIELDDS 89
                                      69*******975 PP

  == domain 4  score: 19.1 bits;  conditional E-value: 8.7e-07
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldP 32 
                                       +e++   Gl ++  g+yeeA++a+++A ++d+
  gi|474934904|ref|YP_007688486.1|  91 PEYYQSYGLFCISIGKYEEAEKAYNEAAAIDE 122
                                       5889999999******************9986 PP

  == domain 5  score: 1.3 bits;  conditional E-value: 0.43
                             TPR_2  20 AleafekAleld 31 
                                       A+e+++ +l+ +
  gi|474934904|ref|YP_007688486.1| 133 AIEYYNNVLAQY 144
                                       9*****999865 PP

  == domain 6  score: 3.3 bits;  conditional E-value: 0.096
                             TPR_2  18 eeAleafekAle 29 
                                       ++Al+++ kAl 
  gi|474934904|ref|YP_007688486.1| 159 KKALDYMLKALD 170
                                       79********97 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       4.1   4.6e+03      14      22 ..      17      25 ..      16      25 .. 0.82
   2 ?    6.2   0.1     0.013        14      12      34 .]      27      49 ..      19      49 .. 0.89
   3 ?    4.8   0.1     0.036        40      19      33 ..      75      89 ..      72      90 .. 0.81
   4 !   19.8   1.0   5.6e-07   0.00063       2      32 ..      92     122 ..      91     124 .. 0.93
   5 ?    4.7   0.4     0.037        42       6      29 ..     140     163 ..     134     171 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 4.1
                                      TT-HHHHHH CS
                             TPR_8 14 lgdyeeAke 22
                                      +++y++A++
  gi|474934904|ref|YP_007688486.1| 17 QKKYDAAMK 25
                                      6899*9986 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.013
                                      HHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8 12 lklgdyeeAkeyyekaleldpdn 34
                                      +++gd++ A ++++k +e  pd+
  gi|474934904|ref|YP_007688486.1| 27 MDMGDFKGAFSAFKKFTEEYPDD 49
                                      79*************99988875 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.036
                                      HHHHHHHHHHHHHHH CS
                             TPR_8 19 eAkeyyekaleldpd 33
                                      e +++y ka+eld +
  gi|474934904|ref|YP_007688486.1| 75 EIEAAYTKAIELDDS 89
                                      55799*******975 PP

  == domain 4  score: 19.8 bits;  conditional E-value: 5.6e-07
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       e+y+  g+ +++ g+yeeA+++y++a  +d+
  gi|474934904|ref|YP_007688486.1|  92 EYYQSYGLFCISIGKYEEAEKAYNEAAAIDE 122
                                       799***********************99997 PP

  == domain 5  score: 4.7 bits;  conditional E-value: 0.037
                                       HHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_8   6 nlgsiylklgdyeeAkeyyekale 29 
                                        l++  + l d ++ ++y +kal+
  gi|474934904|ref|YP_007688486.1| 140 VLAQYGEILDDPKARVKYAKKALD 163
                                       566777888899999999999986 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   0.00016      0.18       1      43 [.      20      59 ..      20      61 .. 0.94
   2 !   12.9   0.6   0.00012      0.13      17      64 ..      77     121 ..      77     126 .. 0.84
   3 ?    0.2   0.0       1.1   1.2e+03      16      40 ..     133     157 ..     133     162 .. 0.81
   4 ?   -2.2   0.0       6.3     7e+03      51      66 ..     159     174 ..     151     176 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00016
                            TPR_16  1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgda 43
                                      +++a+  ++ gd+  A  a++ +++ +   Pd+ae ++ ++++
  gi|474934904|ref|YP_007688486.1| 20 YDAAMKKMDMGDFKGAFSAFKKFTEEY---PDDAEGWYSRAEC 59
                                      67888899*******************...***********99 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00012
                            TPR_16  17 aaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraa 64 
                                       +aa++ a+++d     ++e +  +g+ +   g ++eA+ +y++a++ +
  gi|474934904|ref|YP_007688486.1|  77 EAAYTKAIELD---DSHPEYYQSYGLFCISIGKYEEAEKAYNEAAAID 121
                                       589999*****...6677799999**************8888877554 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1.1
                            TPR_16  16 AaaaleaalkrdpssPdaaeAllll 40 
                                       A+++++ +l+++++  d++ A+  +
  gi|474934904|ref|YP_007688486.1| 133 AIEYYNNVLAQYGEILDDPKARVKY 157
                                       8899999999998877787777665 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 6.3
                            TPR_16  51 aeAaalyraalraapd 66 
                                       ++A+++ ++al+ + d
  gi|474934904|ref|YP_007688486.1| 159 KKALDYMLKALDMGED 174
                                       4566777777776655 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       2.1   2.3e+03       3      12 ..      16      25 ..      15      28 .. 0.76
   2 !   13.8   0.0   5.7e-05     0.064       2      34 ..      27      59 ..      26      59 .. 0.96
   3 !    8.5   0.2    0.0025       2.8       9      55 ..      75     121 ..      72     130 .. 0.87
   4 ?    1.2   0.2      0.48   5.4e+02      10      33 ..     133     159 ..     132     181 .] 0.73

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 2.1
                            TPR_19  3 aegdyaeAla 12
                                      a+++y++A++
  gi|474934904|ref|YP_007688486.1| 16 AQKKYDAAMK 25
                                      7889999987 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 5.7e-05
                            TPR_19  2 laegdyaeAlalleqalqedpknaearllLAea 34
                                      +++gd+  A +++++  +e+p++ae ++  Ae+
  gi|474934904|ref|YP_007688486.1| 27 MDMGDFKGAFSAFKKFTEEYPDDAEGWYSRAEC 59
                                      79*************99***********99998 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0025
                            TPR_19   9 eAlalleqalqedpknaearllLAeallalgqldeAealLdalpeed 55 
                                       e  a++++a++ d  ++e    +   +++ g ++eAe++ +++ + d
  gi|474934904|ref|YP_007688486.1|  75 EIEAAYTKAIELDDSHPEYYQSYGLFCISIGKYEEAEKAYNEAAAID 121
                                       677899999999999999999999**************999887655 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.48
                            TPR_19  10 Alalleqalqedpk...naearllLAe 33 
                                       A++++ ++l+++ +   ++ ar  +A+
  gi|474934904|ref|YP_007688486.1| 133 AIEYYNNVLAQYGEildDPKARVKYAK 159
                                       677777777777776666666666664 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.1   1.3e+03       6      15 ..      16      25 ..      15      26 .. 0.81
   2 ?    2.2   0.0      0.13   1.4e+02       7      35 ..      29      57 ..      25      58 .. 0.74
   3 !    7.5   0.2    0.0029       3.2      15      32 ..      78      95 ..      78     100 .. 0.86
   4 !   14.0   2.9   2.8e-05     0.031       5      27 ..     102     124 ..      98     140 .. 0.82
   5 ?   -2.0   0.0       2.6   2.9e+03      13      22 ..     133     142 ..     131     143 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.1
                            TPR_11  6 eqGkyeeAie 15
                                      +q ky++A++
  gi|474934904|ref|YP_007688486.1| 16 AQKKYDAAMK 25
                                      6889999986 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.13
                            TPR_11  7 qGkyeeAieaYkkAlkldPdnaeayynLG 35
                                       G++++A  a+kk  +  Pd+ae +y ++
  gi|474934904|ref|YP_007688486.1| 29 MGDFKGAFSAFKKFTEEYPDDAEGWYSRA 57
                                      6667777777777667779*******986 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0029
                            TPR_11 15 eaYkkAlkldPdnaeayy 32
                                      +aY kA++ld + +e y 
  gi|474934904|ref|YP_007688486.1| 78 AAYTKAIELDDSHPEYYQ 95
                                      58*************995 PP

  == domain 4  score: 14.0 bits;  conditional E-value: 2.8e-05
                            TPR_11   5 yeqGkyeeAieaYkkAlkldPdn 27 
                                        + GkyeeA +aY++A ++d++ 
  gi|474934904|ref|YP_007688486.1| 102 ISIGKYEEAEKAYNEAAAIDESM 124
                                       577*****************874 PP

  == domain 5  score: -2.0 bits;  conditional E-value: 2.6
                            TPR_11  13 AieaYkkAlk 22 
                                       Aie Y++ l+
  gi|474934904|ref|YP_007688486.1| 133 AIEYYNNVLA 142
                                       8999998875 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.5       0.6   6.7e+02      13      22 ..      16      25 ..      15      25 .. 0.85
   2 ?    1.1   0.0      0.37   4.1e+02      12      26 ..      27      41 ..      26      49 .. 0.81
   3 ?   -0.6   0.0       1.2   1.4e+03       1      10 [.      50      59 ..      50      59 .. 0.86
   4 ?    5.8   0.0     0.012        13      22      33 ..      78      89 ..      77      90 .. 0.84
   5 !   17.2   0.2   2.8e-06    0.0031      11      33 ..     101     123 ..      98     124 .. 0.86
   6 ?    3.9   0.1     0.048        54      20      29 ..     133     142 ..     131     145 .. 0.85
   7 ?   -1.8   0.1       2.9   3.2e+03      19      28 ..     160     169 ..     156     171 .. 0.63

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.6
                                      HTT-HHHHHH CS
                             TPR_1 13 klgkydeAle 22
                                       ++kyd A +
  gi|474934904|ref|YP_007688486.1| 16 AQKKYDAAMK 25
                                      69*****975 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.37
                                      HHTT-HHHHHHHHHH CS
                             TPR_1 12 fklgkydeAleyyek 26
                                      + +g+++ A  +++k
  gi|474934904|ref|YP_007688486.1| 27 MDMGDFKGAFSAFKK 41
                                      579******999998 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.2
                                      HHHHHHHHHH CS
                             TPR_1  1 akalynlGna 10
                                      a+ +y ++ +
  gi|474934904|ref|YP_007688486.1| 50 AEGWYSRAEC 59
                                      789***9987 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.012
                                      HHHHHHHHHSTT CS
                             TPR_1 22 eyyekALelnPn 33
                                      ++y kA+el+ +
  gi|474934904|ref|YP_007688486.1| 78 AAYTKAIELDDS 89
                                      79*******965 PP

  == domain 5  score: 17.2 bits;  conditional E-value: 2.8e-06
                                       HHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1  11 yfklgkydeAleyyekALelnPn 33 
                                       + + gky+eA+++y++A  ++++
  gi|474934904|ref|YP_007688486.1| 101 CISIGKYEEAEKAYNEAAAIDES 123
                                       6678**************99975 PP

  == domain 6  score: 3.9 bits;  conditional E-value: 0.048
                                       HHHHHHHHHH CS
                             TPR_1  20 AleyyekALe 29 
                                       A+eyy+ +L 
  gi|474934904|ref|YP_007688486.1| 133 AIEYYNNVLA 142
                                       9*****9996 PP

  == domain 7  score: -1.8 bits;  conditional E-value: 2.9
                                       HHHHHHHHHH CS
                             TPR_1  19 eAleyyekAL 28 
                                       +Al+y  kAL
  gi|474934904|ref|YP_007688486.1| 160 KALDYMLKAL 169
                                       6666655665 PP

>> FAT  FAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.2   7.9e-07   0.00089     266     339 ..      71     178 ..      15     180 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 7.9e-07
                                       ..-SSCCHHHHCCHHCTCCCHSTTCCCCHHHHHCCHHHHHHSSSS................................ CS
                               FAT 266 ekieeilqsysaateidpswykawhtwalfnfevvskeeeqkeeee............................... 311
                                        k +ei+++y++a e+d+s  + + + +lf+  + + ee +k  +e                               
  gi|474934904|ref|YP_007688486.1|  71 VKEDEIEAAYTKAIELDDSHPEYYQSYGLFCISIGKYEEAEKAYNEaaaidesmapslysefaieyynnvlaqygei 147
                                       34567777777777777777777777777777777766666555556667777777777777777777777777777 PP

                                       ...S-TCCHHHHCCT..CCHHHHTTTSSTTT CS
                               FAT 312 ...pedlqeyvvpavkgflksislssenslq 339
                                          p+   +y+ +a++ +lk++  ++ ++++
  gi|474934904|ref|YP_007688486.1| 148 lddPKARVKYAKKALDYMLKALDMGEDEARN 178
                                       776888889***************9999886 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0         4   4.5e+03      15      27 ..      28      40 ..      16      42 .. 0.61
   2 !   15.1   1.2   1.9e-05     0.021      21      76 ..      75     122 ..      72     123 .. 0.77
   3 ?    1.3   0.0      0.37   4.1e+02      22      37 ..     133     148 ..     131     155 .. 0.79
   4 ?    0.5   0.0       0.7   7.8e+02      63      74 ..     160     171 ..     154     174 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 4
                            TPR_12 15 rlgrydeAlelle 27
                                       +g++  A++ ++
  gi|474934904|ref|YP_007688486.1| 28 DMGDFKGAFSAFK 40
                                      4566666655554 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.9e-05
                            TPR_12  21 eAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       e ++ + ka+e+      + hp+   +++ +g  +   g+yeeA+++++ea ai+e
  gi|474934904|ref|YP_007688486.1|  75 EIEAAYTKAIELD-----DSHPE---YYQSYGLFCISIGKYEEAEKAYNEAAAIDE 122
                                       5555566665555.....55555...79999999999***************9988 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.37
                            TPR_12  22 Alellekaleiarrll 37 
                                       A+e+++ +l+++ ++l
  gi|474934904|ref|YP_007688486.1| 133 AIEYYNNVLAQYGEIL 148
                                       9999999999997774 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.7
                            TPR_12  63 eAlelleealai 74 
                                       +Al++  +al++
  gi|474934904|ref|YP_007688486.1| 160 KALDYMLKALDM 171
                                       566666666665 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.21   2.4e+02      36      65 ..      29      59 ..      26      62 .. 0.90
   2 !   11.8   0.2   0.00019      0.21      42      81 ..      79     116 ..      71     117 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.21
                                      TT-HHHHHHHHHCT.SHHHC-HHHHHHHHHH CS
                            ANAPC3 36 ngqykrAyellrka.klnskslgcrylfAqc 65
                                      +g++k A+  ++k+ ++++ + + +y  A+c
  gi|474934904|ref|YP_007688486.1| 29 MGDFKGAFSAFKKFtEEYPDDAEGWYSRAEC 59
                                      79************99999999999988888 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00019
                                       HHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  42 AyellrkaklnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       Ay+ +   +l+++++++   ++  ++ ++kyeeA++a+ +
  gi|474934904|ref|YP_007688486.1|  79 AYTKAI--ELDDSHPEYYQSYGLFCISIGKYEEAEKAYNE 116
                                       444444..55999**********************99876 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.1    0.0002      0.22      13      32 ..      29      48 ..      15      49 .. 0.86
   2 ?    1.7   0.1      0.44   4.9e+02      13      26 ..     104     117 ..      92     120 .. 0.76
   3 ?    2.2   0.1      0.31   3.5e+02      19      30 ..     133     144 ..     133     146 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0002
                                      HHHHHHHHHHHHHHHHH-TT CS
                             TPR_6 13 lgdtdkAlealerlikeYPd 32
                                      +gd   A  a++++ +eYPd
  gi|474934904|ref|YP_007688486.1| 29 MGDFKGAFSAFKKFTEEYPD 48
                                      59*****************9 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.44
                                       HHHHHHHHHHHHHH CS
                             TPR_6  13 lgdtdkAlealerl 26 
                                        g++++A +a+++ 
  gi|474934904|ref|YP_007688486.1| 104 IGKYEEAEKAYNEA 117
                                       389*******9875 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.31
                                       HHHHHHHHHHH- CS
                             TPR_6  19 AlealerlikeY 30 
                                       A+e++++++ +Y
  gi|474934904|ref|YP_007688486.1| 133 AIEYYNNVLAQY 144
                                       99********99 PP

>> TPR_18  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   2.6     2e-05     0.022       8     133 ..      14     145 ..       8     161 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2e-05
                            TPR_18   8 vpeaelyqeaqkaldegnyltaieqLealdtryP...fGaYaeqa....qLDLiYakykskdyelavasidrfirln 77 
                                        + ++ y +a k++d g++++a    +++   yP    G Y+       +  +  a+ k+++ e+a +++      +
  gi|474934904|ref|YP_007688486.1|  14 PAAQKKYDAAMKKMDMGDFKGAFSAFKKFTEEYPddaEGWYSRAEcgnyASGMFGARVKEDEIEAAYTKAIELDDSH 90 
                                       456789****************************5555889875411114567789999999999999998888888 PP

                            TPR_18  78 PahpkiDyvlYlrglanmaldksslqslvsldrsdrdteaakaafrdfkrLlsryP 133
                                       P+  +  y l+  ++ + +  +++ ++ +++d+s   + + + a + ++++l +y 
  gi|474934904|ref|YP_007688486.1|  91 PEYYQ-SYGLFCISIGKYEEAEKAYNEAAAIDESMAPSLYSEFAIEYYNNVLAQYG 145
                                       88776.6999***********************99999999999999999999986 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0011       1.2      32      63 ..      19      50 ..      13      52 .. 0.89
   2 ?    2.4   0.0      0.15   1.7e+02      20      60 ..      82     122 ..      73     129 .. 0.84
   3 ?   -1.7   0.0       2.9   3.2e+03      47      60 ..     157     170 ..     154     180 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0011
                             TPR_9 32 rrdRGlllaqlGclsaAladLeaylalapdap 63
                                       +d ++  + +G++++A  ++  + +  pd++
  gi|474934904|ref|YP_007688486.1| 19 KYDAAMKKMDMGDFKGAFSAFKKFTEEYPDDA 50
                                      6789999999*******************996 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.15
                             TPR_9  20 rllllaPddpeerrdRGlllaqlGclsaAladLeaylalap 60 
                                         + l+  +pe +   Gl     G +++A ++ + ++a+++
  gi|474934904|ref|YP_007688486.1|  82 KAIELDDSHPEYYQSYGLFCISIGKYEEAEKAYNEAAAIDE 122
                                       567889999999999**************999999988776 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.9
                             TPR_9  47 aAladLeaylalap 60 
                                        A ++L+++l   +
  gi|474934904|ref|YP_007688486.1| 157 YAKKALDYMLKALD 170
                                       57778888874433 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       6.1   6.9e+03      11      22 ..      28      39 ..      27      41 .. 0.72
   2 ?    0.8   0.1      0.55   6.2e+02      19      35 ..      77      91 ..      74      92 .. 0.72
   3 ?    7.4   0.0    0.0043       4.8       9      31 ..     101     123 ..      98     126 .. 0.84
   4 ?    0.5   0.0      0.71   7.9e+02      16      27 ..     131     142 ..     129     151 .. 0.78
   5 ?    0.2   0.1      0.87   9.7e+02      16      31 ..     159     174 ..     154     177 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 6.1
                             TPR_7 11 rlGdyeeAiely 22
                                      ++Gd++ A + +
  gi|474934904|ref|YP_007688486.1| 28 DMGDFKGAFSAF 39
                                      689*99886555 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.55
                             TPR_7 19 ielyeqsLaltkdpeda 35
                                      +  y++  a++ d++++
  gi|474934904|ref|YP_007688486.1| 77 EAAYTK--AIELDDSHP 91
                                      667999..888888776 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0043
                             TPR_7   9 ysrlGdyeeAielyeqsLaltkd 31 
                                       + + G+yeeA++ y ++ a++++
  gi|474934904|ref|YP_007688486.1| 101 CISIGKYEEAEKAYNEAAAIDES 123
                                       7789***********98888876 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.71
                             TPR_7  16 eeAielyeqsLa 27 
                                       e Aie+y  +La
  gi|474934904|ref|YP_007688486.1| 131 EFAIEYYNNVLA 142
                                       679****88554 PP

  == domain 5  score: 0.2 bits;  conditional E-value: 0.87
                             TPR_7  16 eeAielyeqsLaltkd 31 
                                       ++A+++  ++L + +d
  gi|474934904|ref|YP_007688486.1| 159 KKALDYMLKALDMGED 174
                                       6999999996655444 PP

>> 14-3-3  14-3-3 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       4.7   5.3e+03     138     149 ..      76      87 ..      72      93 .. 0.69
   2 ?   10.9   1.6   0.00021      0.23     136     202 ..     108     175 ..     105     179 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4.7
                                       HHHHHHHHHHHH CS
                            14-3-3 138 akeaYeeAleia 149
                                        ++aY +A+e+ 
  gi|474934904|ref|YP_007688486.1|  76 IEAAYTKAIELD 87 
                                       567888887765 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00021
                                       HHHHHHHHHHHHHHHTTTGC.C-HHHHHHHHHHHHHHHCTT--HHHHHHHHHHHHHCCHCCCCCS.TT CS
                            14-3-3 136 ekakeaYeeAleiakkelqp.thpirLglaLNySVflyeilnspekAcelakkafdeaiaeldelsee 202
                                       e+a++aY+eA  i ++  ++ ++   ++ + N+   + eil++p+  ++ akka+d  +++ld  ++e
  gi|474934904|ref|YP_007688486.1| 108 EEAEKAYNEAAAIDESMAPSlYSEFAIEYYNNVLAQYGEILDDPKARVKYAKKALDYMLKALDMGEDE 175
                                       789**********9554444677788888888888899************************977665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1195.58
//
Query:       gi|474934905|ref|YP_007688487.1|  [L=114]
Description: hypothetical protein TALC_01346 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-17   64.1  13.7    1.4e-17   63.9  13.7    1.0  1  DUF3795   Protein of unknown function (DUF3795)


Domain annotation for each model (and alignments):
>> DUF3795  Protein of unknown function (DUF3795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.9  13.7   7.7e-22   1.4e-17       2      83 ..       5      94 ..       4      96 .. 0.94

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 7.7e-22
                           DUF3795  2 iapCGldCeeCeayeakekeekkkkkk.....eafeelllaleeikCeGCreeekkalaee..CkirkCakekglefCa 73
                                      +a+CGldC++C+a  a+ +++++++ k     +  +++++++++++C+GCr +++k++++e  C+ir+Ca+ kg+ +Ca
  gi|474934905|ref|YP_007688487.1|  5 VAYCGLDCSKCKARIATVNDDDEMRSKiaeewSRLNNVEITPDMVNCDGCRMNGRKTVYCEslCPIRQCAMAKGYATCA 83
                                      79****************999999999999998899999*****************999999***************** PP

                           DUF3795 74 eCeef.pCekl 83
                                      eC+e+ +Cek+
  gi|474934905|ref|YP_007688487.1| 84 ECSEMaDCEKV 94
                                      *****99*997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       762  (0.042501); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 841.88
//
Query:       gi|474934906|ref|YP_007688488.1|  [L=185]
Description: putative metal-binding protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-32  110.8   1.6    6.6e-32  110.5   1.6    1.0  1  DUF2284   Predicted metal-binding protein (DUF2284)


Domain annotation for each model (and alignments):
>> DUF2284  Predicted metal-binding protein (DUF2284)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.5   1.6   3.7e-36   6.6e-32      11     164 .]      33     179 ..      25     179 .. 0.96

  Alignments for each domain:
  == domain 1  score: 110.5 bits;  conditional E-value: 3.7e-36
                           DUF2284  11 eervrlkCek.gCknYgknlsCPPavptveefrkilkeYkkallvqtkaeledeeddkeemkevkeelekillelek 86 
                                       +e  r+ Ce+  C+ Yg ++ CPP ++t+ e+   lk+++ka++v +k ++++++ +   + +++ ++++ + ++++
  gi|474934906|ref|YP_007688488.1|  33 AEYCRKLCEQnACHCYGVTWGCPPGAGTLGECLSALKKFSKAVIVYCKFKVDHKDRV--MIDRLSSDTQTYIRKFNN 107
                                       567899************************************************999..999*************** PP

                           DUF2284  87 eafeagypkalalsagsCtlCetCayeegepCrhpekarpsmealGidvfktaekaglelevgkeeketvslvglvL 163
                                        + ++gy k+lal+ g C+ C++C y+e  +C +p+++ ps++a+Gi +++ +e++gl++++ +   ++v+l+g+vL
  gi|474934906|ref|YP_007688488.1| 108 GLRSEGY-KTLALADGGCNNCDHCRYPE--ACDNPDQRVPSISAYGIIMMQYLEDNGLDFKFED---GYVTLYGIVL 178
                                       ******9.********************..5*********************************...9********9 PP

                           DUF2284 164 l 164
                                       +
  gi|474934906|ref|YP_007688488.1| 179 Y 179
                                       6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1279.05
//
Query:       gi|474934907|ref|YP_007688489.1|  [L=90]
Description: glutamyl-tRNA(Gln) and/or aspartyl-tRNA(Asn) amidotransferase, C subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-09   38.5   0.3    1.3e-09   38.2   0.3    1.1  1  Glu-tRNAGln  Glu-tRNAGln amidotransferase C subunit


Domain annotation for each model (and alignments):
>> Glu-tRNAGln  Glu-tRNAGln amidotransferase C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.3   7.4e-14   1.3e-09       1      57 [.      17      81 ..      17      85 .. 0.78

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 7.4e-14
                                      --HHHHHHHHHHHHHHHHHHTTCGCS-...-TT----S....-EB-S--.....HHHHHTT-SSEET CS
                       Glu-tRNAGln  1 lseeEleklakelnsildyveqLqevd...ttgveplthp..vlReDev.....reelLknApeted 57
                                      ls+eElek+ ++l++ildy++ L+e       gv+p   +  vlR+D++     ++elLk  +   +
  gi|474934907|ref|YP_007688489.1| 17 LSDEELEKYSSDLQDILDYFKVLDEAPghdGVGVNPVD-IsdVLRDDVPdqeidSAELLKDMKTY-E 81
                                      79************************965334778843.379*****866678777788887544.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 676.52
//
Query:       gi|474934908|ref|YP_007688490.1|  [L=442]
Description: Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit-related amidase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   4.2e-100  335.8   0.0   5.1e-100  335.5   0.0    1.0  1  Amidase   Amidase


Domain annotation for each model (and alignments):
>> Amidase  Amidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  335.5   0.0  2.9e-104  5.1e-100      53     451 .]      36     423 ..      34     423 .. 0.97

  Alignments for each domain:
  == domain 1  score: 335.5 bits;  conditional E-value: 2.9e-104
                                       EEEETTB--TTSB--TTSGGGTT-B-SS--HHHHHHHHTT-EEEEEE--SGGG-SSSSTT-TT---BBTTCTCCB-- CS
                           Amidase  53 isvKDnidvkgvpttaGskalenypaekDatvverLkkaGavilgkTnmdefamgsstensvfgptrNPwdksrtpG 129
                                       +s KDn++  +++t+aGs++le+y++ +Dat +++++kaG +++gkTnmdef++g+ + ns fg  rNP+d++r++G
  gi|474934908|ref|YP_007688490.1|  36 FSAKDNLTSVDFETCAGSRILEGYRPVFDATPIAKMRKAGGMLVGKTNMDEFGFGTFSANSGFGVPRNPFDTNRSCG 112
                                       578************************************************************************** PP

                                       SSSHHHHHHHHTTSSSCEEEEESSSTTHHHHHHCTSEEEE--TTSC--TTB--SSTTT-EEEEEESSHHHHHHHHHH CS
                           Amidase 130 GSSGGsAAavAaglvplaiGtDtGGSiRiPAsfcglvGlKPtygrvSragvvalessldvvGplarsvedlalllrv 206
                                       GSSGGsA a A     +++G  tGGS+ +PAsfcg++G+ PtygrvSr+g++++ +sld vG l+ + + l  +l v
  gi|474934908|ref|YP_007688490.1| 113 GSSGGSACAAAVLDDHVSLGVSTGGSVCCPASFCGTYGIVPTYGRVSRYGLIDYGNSLDKVGLLSVDPKKLSEYLPV 189
                                       ***************************************************************************** PP

                                       HBS--TT-TTS----HHHHHHHHCTT---TT-EEEEEGGGCSS---CCHHHHHHHHHHHHHCTT-EEEEEE-CCGGG CS
                           Amidase 207 ilgedpkdstssvipeesedlaeelkkslkglriGvvkedgvasldpevqravekalkaLeeaGhevvevelpslee 283
                                       i+g+d+kd+ts + p       e +  + k + ++v+ke   + + ++v  a+++ l++L+ +G+ v+ v++p+l +
  gi|474934908|ref|YP_007688490.1| 190 ISGKDEKDPTSCCQP-------ELQIRHAKMKSVAVPKEAV-DGIAKDVLGAFNDGLETLKGMGIDVEYVDMPELRY 258
                                       ***********9944.......45555666678*******9.8********************************** PP

                                       HHHHHHHHHHHHHHHHTTT-SSSSS..---SS-SCCCCCCCHHHHCCS-HHHHHHHHHHHHHCSCCCCCCCHHHHHH CS
                           Amidase 284 alslyylilvaeassnlarylgvry..erlsetkvlsellpksraellgeevkrrielgnyalsaeasskyylkaqk 358
                                       a+++yy ++++eas+nlary g+ry  +  + t  ++ ++++ r + +gee krri lg+y+  ++ ++ yy ka +
  gi|474934908|ref|YP_007688490.1| 259 AMPAYYVLATSEASTNLARYVGMRYghQDGDYTLGFDAYFTSFRNKYFGEEAKRRILLGTYTRMEGFRDRYYAKALQ 335
                                       **************************988999999****************************************** PP

                                       HHHHHHHHHHHHCCCBSEEEEESSSSS--BCCCCCHHHCSHHHHHGCCTTT...HHHHHTT--EEEEECCCCT.TEC CS
                           Amidase 359 vrrllrrefakafeelDvllsPtaptpaprlgekdktidsytvlynlldftavvvpvnlaglpalsvpagksedglP 435
                                       vr  ++++++++fe+ D++l+Pt+p   pr ++ +k   ++ ++y+ + +t   vp nlag+p l+ p+g+++dg+P
  gi|474934908|ref|YP_007688490.1| 336 VRMGVIDAYKAIFERHDAVLTPTMPFVSPRFDDISKM--TPVESYKADFLT---VPPNLAGTPHLNCPCGYNADGMP 407
                                       **********************************996..5*******9999...*********************** PP

                                       EEEEEEESTT-HHHHH CS
                           Amidase 436 vGvqvigkafqeetlL 451
                                       vG+q+++++++e +lL
  gi|474934908|ref|YP_007688490.1| 408 VGMQFVTDHWNEDMLL 423
                                       **************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2918.19
//
Query:       gi|474934909|ref|YP_007688491.1|  [L=450]
Description: glutamyl-tRNA(Gln) and/or aspartyl-tRNA(Asn) amidotransferase, B subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.1e-82  277.5   0.0    1.5e-82  277.0   0.0    1.1  1  GatB_N     GatB/GatE catalytic domain
    1.7e-09   37.7   0.2    7.5e-09   35.6   0.2    2.0  1  GatB_Yqey  GatB domain


Domain annotation for each model (and alignments):
>> GatB_N  GatB/GatE catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  277.0   0.0   1.7e-86   1.5e-82       1     268 [.       1     271 [.       1     275 [. 0.94

  Alignments for each domain:
  == domain 1  score: 277.0 bits;  conditional E-value: 1.7e-86
                                       EEEEEEEEEEB--SB-SSSSSBSSSSCESTTSS--TTTTTSTT..--EEHHHHHHHHHHHHHTTEEE-SEE-EEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N   1 lviGlEiHaqlktksKlFssasteeegeepnsevsevdlalPGtlPvlnkeavelaikaalalnceiaeeskfdRKn 77 
                                       ++iGlEiH+ql t+sK+F+s++t+ +  +pn++v++v+l++PG+ Pvln++++ + i++a++l+c++++++ f RK+
  gi|474934909|ref|YP_007688491.1|   1 MKIGLEIHVQLPTRSKMFCSCPTT-DAPAPNTHVCPVCLGMPGSRPVLNRQVLVYGIMLAKMLGCTVTDTTWFSRKT 76 
                                       58********************65.7778************************************************ PP

                                       -TCTTCTTSEEEEESSS.SEEEEEEEE......TEEEEEEEEEEEE---EEEEEETTEEEEETTSTT-EEEEEEE-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N  78 yfypdlpkgyQitqkeeplakeGslel......ekkvrierihlEeDaaksvheekeeslvdlnRaGvpLiEivtep 148
                                       yfypd++k  Qitq+++p+ ++G+  l      +k +ri+rihlEeD +k+ ++++ + lvd+nR+G+pL Eivtep
  gi|474934909|ref|YP_007688491.1|  77 YFYPDMSKSVQITQYDHPVGERGMYYLntkdgqTKPIRITRIHLEEDPGKTKRTSDMHALVDYNRSGIPLAEIVTEP 153
                                       ***********************76666699988899*****************999******************** PP

                                       TB-SHHHHHHHHHHHHHHHHHHTSB--SGGGTTEEEEEEEEECTSETTSSS.--EEEEEE-SHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N 149 dlrspeearavveklrellralgvsdgnmeeGslRcDvNvSvreeekgeeegtrvEiKnlnslksiekaieyeierq 225
                                       dl sp+eara++++l + +r++     +  e s+RcD+N+Sv +        +r+EiKn+  lk++e a++ye+ rq
  gi|474934909|ref|YP_007688491.1| 154 DLASPAEARAFLTQLVQDIRHTIDLPEGG-ERSIRCDCNISVGK--------ERCEIKNVTGLKNVEVALNYEMVRQ 221
                                       **************988888775555555.47***********3........6************************ PP

                                       HHHH.......-EEEEEETTTTEEEEECC----...-EEE-TTS--EE-- CS
                                       xxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N 226 iell.......qeTrkfdedkgetvslRskeeaedYryfpepdlppleis 268
                                       i++l       + T++fde++g t+  R+ke ++dY y+ epdl  ++i 
  gi|474934909|ref|YP_007688491.1| 222 IKVLkaggkieRATMNFDESRGVTYGARKKEFEADYGYIDEPDLGIFHIA 271
                                       *******************************999**********999886 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.2   8.4e-13   7.5e-09       2     139 ..     314     437 ..     313     448 .. 0.71

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 8.4e-13
                                       HHHHHHHHSS.HHHHHHHHHTCHHHHHHHHTXXTTCSSTTHHHHHHHHHHHHTTSSGHHHHHHHHHHHHHHTXXHHH CS
                         GatB_Yqey   2 ffeevvkegadaklaanwllnellgelnkegleieelkltpeqlaellkliaegkIskkiakevleelleegkspee 78 
                                       ffe+v+++   +  a++w+++ + ++ +k     ee   + e++  +++ + +g+I+++     ++ l+++   +e+
  gi|474934909|ref|YP_007688491.1| 314 FFETVIEKF-GKDNAVKWVAGPVTANWKKF----EERDGNVEDILPIIEDFVSGRITDTECTLKIKSLMTGIDAAEA 385
                                       677777666.56666677766666655554....3333456667777777777777777777777777765555555 PP

                                       HHHHCTXXXXXXSSXHHHHHHHHHHTXHHHHHHHTTXXTTSTHHHHHHHHHTTSSXSXHHH CS
                         GatB_Yqey  79 iieekgLkqisdeeeleklveeviaenpkavedyksgkekalkflvGqvMkktkGkadpkl 139
                                       + + +          l k++ + +++npk v+dy +g+eka +  +G vMk t G+   + 
  gi|474934909|ref|YP_007688491.1| 386 AASSE---------GLDKMISDFLDKNPKIVDDYGKGNEKAANSVIGYVMKSTGGQYSSAD 437
                                       54444.........5679999**********************************987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2802.58
//
Query:       gi|474934910|ref|YP_007688492.1|  [L=606]
Description: aspartyl-tRNA synthetase, bacterial type [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-94  315.6   0.0    3.6e-94  315.4   0.0    1.1  1  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    2.4e-18   66.2   0.0    4.7e-18   65.2   0.0    1.5  1  GAD              GAD domain
    1.9e-12   47.0   0.0    3.6e-12   46.1   0.0    1.5  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
     0.0063   16.5   0.0      0.016   15.2   0.0    1.8  1  tRNA-synt_2b     tRNA synthetase class II core domain (G, H, 
  ------ inclusion threshold ------
      0.051   13.0   0.0       0.18   11.3   0.0    1.8  2  tRNA-synt_2d     tRNA synthetases class II core domain (F)


Domain annotation for each model (and alignments):
>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  315.4   0.0     1e-97   3.6e-94       1     313 [.     130     561 ..     130     562 .. 0.98

  Alignments for each domain:
  == domain 1  score: 315.4 bits;  conditional E-value: 1e-97
                                       .CCHHHHTHHHHCCSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE-E-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2   1 seelrlknryldlrtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeffaLtq 77 
                                       +e++r+k+ryldlr+ ++ +++++rs+++++ r yle++gf+eietP+L +s t+egar++ ++sr+++++f+aL+q
  gi|474934910|ref|YP_007688492.1| 130 DEDTRMKYRYLDLRRTDMIRTMEFRSRLVHLARVYLESQGFLEIETPVLGRS-TPEGARDYIIPSRVHPGTFYALPQ 205
                                       689*************************************************.************************ PP

                                       -SHHHHHHHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCCCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  78 spqlylellivagidrvfqiaraFRaEdsrtdrhlaEFtqieaemsfieeedimqvleelikslvkevlessakdie 154
                                       spq+++++l+v+g+dr++q+ar+FR+Edsr+dr++ EFtq+++emsf + +di +++e+++++++k +  ++     
  gi|474934910|ref|YP_007688492.1| 206 SPQQFKQMLMVGGMDRYYQVARCFRDEDSRKDRQP-EFTQLDIEMSFCDSKDIQDLIEGMVSYMWKGL-YGT----- 275
                                       ***********************************.********************************.556..... PP

                                       HTTTTTSEE-SSS-EEEEHHHHHHHHHTS-SS--HHHHHHHHH.................................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................. RF
                       tRNA-synt_2 155 fvirrnskdlkkpfkrltykeaieklneigkdldkaderalvk.................................. 197
                                               +lk+pf+++ y++a+e+      ++dk+d+r+ ++                                  
  gi|474934910|ref|YP_007688492.1| 276 --------ELKTPFPHIGYRDAMER-----FGSDKPDMRYGLEftkltdvvrdvpykifqsimseggivagmcikke 339
                                       ........8****************.....9********************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                       tRNA-synt_2 198 ............................................................................. 197
                                                                                                                    
  gi|474934910|ref|YP_007688492.1| 340 mgevgrnevdryiqyakkcglggltwmrcengvltsnitkyftpeilenikttlgaeegdlcfliagpwkstyeggg 416
                                       ***************************************************************************** PP

                                       ..............HS--SEEEEEEEB............GGGSTTCBBBSTTS..TTBBSEEEEEETTEEEEEEEEB CS
                                       ..............xxxxxxxxxxxxx............xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 198 ..............keknepvfvtdfP............aelkpFyarkeedd..kkltesyDllingvElvgGslR 246
                                                      +++ ++++ + P            a ++pF  +  + d  ++  + +Dl +ng El++Gs R
  gi|474934910|ref|YP_007688492.1| 417 flrrkiaedlgmvpDNEFMFFWMDQNPmfeidpvsgkrdAFHHPFVLPTGDLDdpDCGGACFDLCLNGNELGSGSER 493
                                       *************99999999999999*******************9987766669999****************** PP

                                       --SHHHHHHHHHHCCHH.SSSGGGGHHHHHHHHCT--SEEEEEEEHHHHHHHHCT-SSGGGCSSS-XX CS
                                       xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 247 iedpeeleeklkskgld.eeaeekfswylealeyGapphgGlglGldRlvmlllgsesIrdviaFPkl 313
                                       i+d e + e++++ gl+ e+ +++f+ ++eal+yGapphgG+++G+dRl+++ll+++ Ir+viaFPk+
  gi|474934910|ref|YP_007688492.1| 494 IHDAETQIEVFHRLGLSdETIQARFDYFVEALSYGAPPHGGIAIGIDRLCAILLNKDTIREVIAFPKN 561
                                       *****************9999*********************************************98 PP

>> GAD  GAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.2   0.0   1.3e-21   4.7e-18       1      91 [.     321     411 ..     321     413 .. 0.97

  Alignments for each domain:
  == domain 1  score: 65.2 bits;  conditional E-value: 1.3e-21
                                       HHHHHHSTEEEEEEEETTG-TTTSHHHHHHHHHHHHHTTHSHCEEEEESSGGEETTTCCCS-HHHHHHHHHHCT--T CS
                               GAD   1 fsealksggsvkalrvpggaaklsrkeideleefakelgakglawikvegegltgpiakflteeevkklleavgaee 77 
                                       f++ +++gg+v+++++++ + +  r e+d + + ak+ g  gl+w++ e++ lt++i k++t e +++++ ++gaee
  gi|474934910|ref|YP_007688492.1| 321 FQSIMSEGGIVAGMCIKKEMGEVGRNEVDRYIQYAKKCGLGGLTWMRCENGVLTSNITKYFTPEILENIKTTLGAEE 397
                                       7888999********************************************************************** PP

                                       TEEEEEEEEEHHHH CS
                               GAD  78 gDillfvAdkkktv 91 
                                       gD+++++A+++k++
  gi|474934910|ref|YP_007688492.1| 398 GDLCFLIAGPWKST 411
                                       **********9976 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   0.0     1e-15   3.6e-12       1      76 []      19     110 ..      19     110 .. 0.94

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 1e-15
                                       EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET.........HHHHHHHTTS-TTSEEEEEEEEEEC....... CS
                   tRNA_anti-codon   1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfr.........eeatklaenlkeGdvvrvtGrvkrr....... 61 
                                       V+++G+v+    r++g+v fidl D+ g+ qvv+++         ++  k+++++ ++++v + G+v++r       
  gi|474934910|ref|YP_007688492.1|  19 VCLEGWVRFS--RDHGGVRFIDLADRYGITQVVFDPedlpsnanrDAIAKTMDTFSRESCVLINGKVRARvegtave 93 
                                       789*******..**********************************************************8877777 PP

                                       ..TTSSEEEEEEEEEEE CS
                   tRNA_anti-codon  62 ..pggelelkveeiell 76 
                                         p+ge+e+ ++  ell
  gi|474934910|ref|YP_007688492.1|  94 snPTGEIEVLITHAELL 110
                                       77777******999876 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   4.4e-06     0.016      38      88 ..     221     269 ..     220     550 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.4e-06
                                       EEEEEEEEEBTTTSTBCTTTB-SEEEEEEEE.EEESGGGHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  38 klyqiqtkyRdEksdsrGLlRvreFhqkdgy.vfhaeaslddslrdlikais 88 
                                       ++yq+ +++RdE s  +   R+ eF+q d + +f+  ++++d ++ ++  + 
  gi|474934910|ref|YP_007688492.1| 221 RYYQVARCFRDEDS-RKD--RQPEFTQLDIEmSFCDSKDIQDLIEGMVSYMW 269
                                       79***********9.889..*********86368889999999998876553 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0     5e-05      0.18      88     159 ..     206     279 ..     204     284 .. 0.78
   2 ?   -2.1   0.0      0.59   2.1e+03     216     235 ..     537     556 ..     530     558 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5e-05
                                       HHHHHHHHTTS-SSEEEEEEEEEEBSST-SSSB-SEEEE..EEEEEEETT--HHHHHHHHHHHHHHHCTSTEEE CS
                      tRNA-synt_2d  88 tavqirtlekkkppikiisigrvfRrdavDathlaeFhq..veglvvdenvsladlkgvleellkklfgaevkv 159
                                       ++ q++++       ++  + r+fR ++  + +++eF+q  +e+ ++d++   + + g+++ + k l+g+e+k+
  gi|474934910|ref|YP_007688492.1| 206 SPQQFKQMLMVGGMDRYYQVARCFRDEDSRKDRQPEFTQldIEMSFCDSKDIQDLIEGMVSYMWKGLYGTELKT 279
                                       6778888888888889999********************33456677765444445688899999999998775 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.59
                                       EEHHHHHHHHHT-SSGHHHH CS
                      tRNA-synt_2d 216 lGveRlamlkygieDiRelv 235
                                       +G++Rl  + ++ + iRe++
  gi|474934910|ref|YP_007688492.1| 537 IGIDRLCAILLNKDTIREVI 556
                                       89***************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (606 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.68u 0.25s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 3806.67
//
Query:       gi|474934911|ref|YP_007688493.1|  [L=159]
Description: Transcriptional regulator [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.4e-17   60.9   0.4    1.8e-16   59.9   0.4    1.5  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    7.1e-10   38.6   0.0    1.6e-09   37.4   0.0    1.6  2  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    1.8e-08   33.8   0.0    2.8e-08   33.2   0.0    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
    3.3e-05   23.7   0.0    0.00012   21.9   0.0    1.9  2  HTH_11          HTH domain
    0.00019   21.2   0.0    0.00041   20.1   0.0    1.5  1  HTH_30          PucR C-terminal helix-turn-helix domain
     0.0002   20.9   0.0    0.00048   19.7   0.0    1.7  1  HTH_50          Helix-turn-helix domain
    0.00027   20.9   1.3    0.00051   20.1   1.3    1.4  1  NapD            NapD protein
    0.00039   20.3   0.0     0.0011   18.9   0.0    1.7  2  MarR            MarR family
     0.0022   17.9   0.0     0.0037   17.2   0.0    1.3  1  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.003   17.6   0.0      0.005   16.9   0.0    1.3  1  HTH_20          Helix-turn-helix domain
     0.0039   16.9   0.0     0.0065   16.2   0.0    1.3  1  HTH_23          Homeodomain-like domain
     0.0053   16.7   0.0       0.33   11.0   0.0    2.3  2  HTH_29          Winged helix-turn helix
     0.0072   16.1   0.0      0.018   14.8   0.0    1.7  1  HTH_8           Bacterial regulatory protein, Fis family
     0.0075   16.2   0.1      0.018   15.0   0.0    1.6  1  HTH_36          Helix-turn-helix domain
     0.0076   16.0   0.0      0.014   15.2   0.0    1.4  1  HTH_38          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.011   15.1   0.0      0.018   14.4   0.0    1.3  1  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
      0.012   15.5   0.0       0.02   14.8   0.0    1.3  1  HTH_5           Bacterial regulatory protein, arsR family
      0.017   14.9   0.0      0.028   14.2   0.0    1.3  1  LexA_DNA_bind   LexA DNA binding domain
       0.03   14.3   0.0       0.16   11.9   0.0    2.0  2  HTH_1           Bacterial regulatory helix-turn-helix protein
      0.031   14.4   0.0      0.049   13.8   0.0    1.3  1  HTH_28          Helix-turn-helix domain
      0.038   13.9   0.0      0.075   12.9   0.0    1.5  1  MarR_2          MarR family
      0.045   13.9   0.0        5.8    7.2   0.0    2.2  2  HTH_34          Winged helix DNA-binding domain
      0.057   13.6   0.1       0.22   11.8   0.0    1.9  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.097   12.5   0.0       0.24   11.2   0.0    1.6  1  HTH_10          HTH DNA binding domain
       0.11   12.3   0.0       0.27   11.1   0.0    1.7  1  TFIIE_alpha     TFIIE alpha subunit
       0.14   11.8   0.0        1.1    9.0   0.0    2.1  2  DUF3755         Protein of unknown function (DUF3755)
       0.17   11.7   0.0       0.28   11.0   0.0    1.4  1  HxlR            HxlR-like helix-turn-helix


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.9   0.4   2.7e-19   1.8e-16      10      74 ..      77     140 ..      72     141 .. 0.94

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 2.7e-19
                                       TTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                    AsnC_trans_reg  10 peqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74 
                                       ++++e++e++++++peVv +y vtG++d ++ v++   +++++++++ ++sl+gv +t+ts+vl+
  gi|474934911|ref|YP_007688493.1|  77 SDNIEKVEKEIRDIPEVVAVYDVTGEADAIVVVTCLGRDEFSAVVKR-INSLEGVNKTNTSVVLN 140
                                       3569****************************************999.***************97 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.0   2.4e-12   1.6e-09       2      42 .]       8      48 ..       7      48 .. 0.98
   2 ?   -2.2   0.0       5.6   3.7e+03      32      42 .]     118     128 ..     118     128 .. 0.85

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 2.4e-12
                     HTH_AsnC-type  2 DeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                      D++Dr+I+e L   +  sy++LA+++G+ ++t ++Rv++Le
  gi|474934911|ref|YP_007688493.1|  8 DQLDRRIIEMLCTSSQGSYRQLAKQLGVHPTTLIQRVKALE 48
                                      9***************************************8 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.6
                     HTH_AsnC-type  32 stvlrRvrrLe 42 
                                       s+v +R++ Le
  gi|474934911|ref|YP_007688493.1| 118 SAVVKRINSLE 128
                                       68999**9997 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.0   4.3e-11   2.8e-08       2      47 ..       8      53 ..       7      54 .. 0.98

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 4.3e-11
                            HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      d++dr+I+e L   +  s+r+LA++lg+ p+t+ +r+k Le++G+I
  gi|474934911|ref|YP_007688493.1|  8 DQLDRRIIEMLCTSSQGSYRQLAKQLGVHPTTLIQRVKALEDKGVI 53
                                      899******************************************9 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   1.8e-07   0.00012       3      44 ..      12      52 ..      11      67 .. 0.84
   2 ?   -1.0   0.0       2.7   1.8e+03      31      41 ..     119     129 ..     118     143 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.8e-07
                            HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                      + i+e+L  + ++ s  +LA++L+v  +t  +++kaLe++gv
  gi|474934911|ref|YP_007688493.1| 12 RRIIEML-CTSSQGSYRQLAKQLGVHPTTLIQRVKALEDKGV 52
                                      5799999.555668***************************3 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.7
                            HTH_11  31 tvrrdIkaLee 41 
                                       +v+++I +Le 
  gi|474934911|ref|YP_007688493.1| 119 AVVKRINSLEG 129
                                       89999999985 PP

>> HTH_30  PucR C-terminal helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   6.1e-07   0.00041      11      37 ..      22      48 ..      14      50 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 6.1e-07
                                      TTT-HHHHHHHHTS-HHHHHHHHHHHH CS
                            HTH_30 11 nggnisatAkaLhvHrnTlryRLrrie 37
                                      ++g++++ Ak+L+vH+ Tl +R++ +e
  gi|474934911|ref|YP_007688493.1| 22 SQGSYRQLAKQLGVHPTTLIQRVKALE 48
                                      689********************9887 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   7.2e-07   0.00048       4      45 ..       4      45 ..       1      47 [. 0.84

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 7.2e-07
                            HTH_50  4 LkeyveefErelikkay.ekYpStRklAkrLGvShtaianklr 45
                                      Lke  ++ +r +i+ +  ++ +S R lAk+LGv  t+ +++++
  gi|474934911|ref|YP_007688493.1|  4 LKEF-DQLDRRIIEMLCtSSQGSYRQLAKQLGVHPTTLIQRVK 45
                                      5553.78899999998625789*******************98 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   1.3   7.6e-07   0.00051       7      68 ..      72     134 ..      71     138 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 7.6e-07
                              NapD   7 vVqarperlaavkaalaalpg.vEvhasdeegklVvviEaesedeladtieaiealpgVlsas 68 
                                       +Vq+  +++++v ++++++p+ v v+ +++e   +vv+    +de  + +++i++l+gV  ++
  gi|474934911|ref|YP_007688493.1|  72 LVQVFSDNIEKVEKEIRDIPEvVAVYDVTGEADAIVVVTCLGRDEFSAVVKRINSLEGVNKTN 134
                                       79*****************9835899*********************************8875 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.6e-06    0.0011      21      51 ..      27      57 ..      12      61 .. 0.84
   2 ?   -2.1   0.0       5.6   3.7e+03      22      37 ..     123     138 ..     108     140 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.6e-06
                                      HHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR 21 seLakklgvskstvtrvldrLekkGlieRsk 51
                                       +Lak+lgv+++t+   +++Le+kG i+ ++
  gi|474934911|ref|YP_007688493.1| 27 RQLAKQLGVHPTTLIQRVKALEDKGVINGYR 57
                                      59***********************998665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.6
                                       HHHHHHTS-HHHHHHH CS
                              MarR  22 eLakklgvskstvtrv 37 
                                        + +  gv+k++++ v
  gi|474934911|ref|YP_007688493.1| 123 RINSLEGVNKTNTSVV 138
                                       4455556666666655 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   5.5e-06    0.0037      23      54 ..      25      57 ..      11      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.5e-06
                                      HHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ET CS
                         HTH_Crp_2 23 tqeelAsmlGltretvsrilseLkreglis.rg 54
                                      + ++lA  lG+++ t+ +  ++L+++g+i   +
  gi|474934911|ref|YP_007688493.1| 25 SYRQLAKQLGVHPTTLIQRVKALEDKGVINgYR 57
                                      679**************************9433 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   7.5e-06     0.005      13      58 ..      12      57 ..       8      59 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 7.5e-06
                                      HHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20 13 rrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                      rri  +L++    +  +la++l+++++tl +++++Le+ g + + r
  gi|474934911|ref|YP_007688493.1| 12 RRIIEMLCTSSQGSYRQLAKQLGVHPTTLIQRVKALEDKGVINGYR 57
                                      89**************************************998765 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   9.8e-06    0.0065       9      46 ..      13      52 ..      12      55 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 9.8e-06
                            HTH_23  9 rillllae..GlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                      ri+ +l      s+r+ A++Lgv++ T+ + +k+ + +G+
  gi|474934911|ref|YP_007688493.1| 13 RIIEMLCTssQGSYRQLAKQLGVHPTTLIQRVKALEDKGV 52
                                      688888866778*****************99999866884 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0    0.0005      0.33      10      40 ..      23      51 ..      15      59 .. 0.79
   2 ?    3.5   0.0      0.11        73      16      38 ..     104     126 ..     100     134 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0005
                            HTH_29 10 eGvstvsqiAkllglsrrtvyrwlkrfeegG 40
                                      +G  + +q+Ak+lg++++t    +k+ e +G
  gi|474934911|ref|YP_007688493.1| 23 QG--SYRQLAKQLGVHPTTLIQRVKALEDKG 51
                                      33..59*************998888888888 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.11
                            HTH_29  16 sqiAkllglsrrtvyrwlkrfee 38 
                                         i+ +++l r+ +  ++kr + 
  gi|474934911|ref|YP_007688493.1| 104 DAIVVVTCLGRDEFSAVVKRINS 126
                                       57999***************996 PP

>> HTH_8  Bacterial regulatory protein, Fis family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   2.7e-05     0.018       4      41 ..       9      46 ..       7      47 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.7e-05
                                      HHHHHHHHHHHHHTTT-HHHHHHHHTS-HHHHHHHHHH CS
                             HTH_8  4 evEkelIeaALertgGnkskAArlLGisRrtLyrKLkk 41
                                      ++++++Ie    +++G   + A+ LG++++tL  + k+
  gi|474934911|ref|YP_007688493.1|  9 QLDRRIIEMLCTSSQGSYRQLAKQLGVHPTTLIQRVKA 46
                                      678888888889999999***************99886 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.7e-05     0.018      27      55 .]      25      53 ..      10      53 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.7e-05
                            HTH_36 27 sqetlakrlglsknTvsraikeLeqlGyi 55
                                      s++ lak+lg++  T +  +k Le++G i
  gi|474934911|ref|YP_007688493.1| 25 SYRQLAKQLGVHPTTLIQRVKALEDKGVI 53
                                      89************************976 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0     2e-05     0.014       9      36 ..      11      39 ..       6      44 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2e-05
                            HTH_38  9 eReeIerll.aeGlslreIArrLgrspsT 36
                                      +R+ Ie l  +   s+r+ A++Lg++p+T
  gi|474934911|ref|YP_007688493.1| 11 DRRIIEMLCtSSQGSYRQLAKQLGVHPTT 39
                                      89999999646779**************9 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.7e-05     0.018      20      50 ..      15      46 ..      10      47 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.7e-05
                      HTH_Tnp_ISL3 20 ilellles.rsvkavArqlgvSwtTVwrildr 50
                                      i +l+++s  s ++ A+qlgv++tT++ ++++
  gi|474934911|ref|YP_007688493.1| 15 IEMLCTSSqGSYRQLAKQLGVHPTTLIQRVKA 46
                                      66899999******************998875 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0     3e-05      0.02       5      46 ..      12      54 ..       8      54 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3e-05
                                      HHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  5 lkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      ++I+ +L+  ++ +  +la++lg+ + t+ +  k+L++ G+++
  gi|474934911|ref|YP_007688493.1| 12 RRIIEMLCTsSQGSYRQLAKQLGVHPTTLIQRVKALEDKGVIN 54
                                      68*******66699**************************996 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   4.2e-05     0.028      27      57 ..      25      54 ..      14      59 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.2e-05
                                      -HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE CS
                     LexA_DNA_bind 27 sireiaralglkSpsaveehLkaLerKGyie 57
                                      s r++a++lg++ p +  ++ kaLe KG+i+
  gi|474934911|ref|YP_007688493.1| 25 SYRQLAKQLGVH-PTTLIQRVKALEDKGVIN 54
                                      88**********.99999***********97 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00024      0.16      12      39 ..      22      49 ..      16      50 .. 0.90
   2 ?   -0.8   0.0       2.4   1.6e+03      28      38 ..     118     128 ..     117     130 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00024
                                      HHSSHHHHHHHHTS-HHHHHHHHHHHHH CS
                             HTH_1 12 eegsftrAAeeLglsqpavsrqikrLEe 39
                                       +gs ++ A++Lg+ + ++ +++k+LE+
  gi|474934911|ref|YP_007688493.1| 22 SQGSYRQLAKQLGVHPTTLIQRVKALED 49
                                      68999999*******************7 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.4
                                       HHHHHHHHHHH CS
                             HTH_1  28 pavsrqikrLE 38 
                                       +av ++i++LE
  gi|474934911|ref|YP_007688493.1| 118 SAVVKRINSLE 128
                                       79999****99 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   7.3e-05     0.049      10      40 ..      21      51 ..      12      59 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.3e-05
                            HTH_28 10 aaGhsvreaArelgisrrtvyrWikryeegG 40
                                       +++s+r++A++lg++++t+ + +k++e  G
  gi|474934911|ref|YP_007688493.1| 21 SSQGSYRQLAKQLGVHPTTLIQRVKALEDKG 51
                                      4789****************88888888777 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00011     0.075      23      51 ..      25      53 ..       7      61 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                                      EHHHHHHHHTSSHHHHHHHHHHHHHTTSE CS
                            MarR_2 23 tvgelarrlglsksavsrilkrLvaaGLv 51
                                      + ++la+ lg+ + ++ +++k L+++G +
  gi|474934911|ref|YP_007688493.1| 25 SYRQLAKQLGVHPTTLIQRVKALEDKGVI 53
                                      5689***********************98 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0087       5.8       5      45 ..      14      54 ..      12      62 .. 0.92
   2 ?    4.5   0.0      0.06        40      58      78 ..     106     126 ..      97     127 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0087
                            HTH_34  5 vlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYie 45
                                      ++ +L + ++ ++++l ++l++    L   +k+Le++g i+
  gi|474934911|ref|YP_007688493.1| 14 IIEMLCTSSQGSYRQLAKQLGVHPTTLIQRVKALEDKGVIN 54
                                      78899999*****************************9886 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.06
                            HTH_34  58 llriTpeGreafkkyvkaLks 78 
                                       ++ +T  Gr++f+++vk ++s
  gi|474934911|ref|YP_007688493.1| 106 IVVVTCLGRDEFSAVVKRINS 126
                                       6789************99876 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00033      0.22      26      51 ..      27      52 ..      19      58 .. 0.90
   2 ?   -2.1   0.0         7   4.6e+03      23      38 ..     130     145 ..     122     146 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00033
                                      HHHHHHHTS-HHHHHHHHHHHHHTTS CS
                    Fe_dep_repress 26 kdlaerLnvspssVsemlkkLekdGy 51
                                       +la+ L+v+p +  + +k Le++G 
  gi|474934911|ref|YP_007688493.1| 27 RQLAKQLGVHPTTLIQRVKALEDKGV 52
                                      69*********************995 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 7
                                       B-HHHHHHHHTS-HHH CS
                    Fe_dep_repress  23 vktkdlaerLnvspss 38 
                                       v +++ + +Ln+ +ss
  gi|474934911|ref|YP_007688493.1| 130 VNKTNTSVVLNIVKSS 145
                                       6677778899998887 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00036      0.24      26      50 ..      26      50 ..      22      52 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00036
                            HTH_10 26 lkeLAkelGIskstlsehLrkaesk 50
                                       ++LAk+lG+ ++tl +++++ e k
  gi|474934911|ref|YP_007688493.1| 26 YRQLAKQLGVHPTTLIQRVKALEDK 50
                                      689***************9988876 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00041      0.27      16      97 ..      12      88 ..       4      93 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00041
                                      HHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEECCCHCCCHHHHHHHHHH CS
                       TFIIE_alpha 16 vlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrinyeklvdvvkrkleevvk 94
                                        ++++L + ++ +  +lak+l++ ++ l + + +L ++++++  r++ +   +       +y  lv+v ++ +e+v k
  gi|474934911|ref|YP_007688493.1| 12 RRIIEMLCTSSQGSYRQLAKQLGVHPTTLIQRVKALEDKGVINGYRAKVDYVAM-----GYDYTGLVQVFSDNIEKVEK 85
                                      57999*************************************977766443322.....22345566666666666666 PP

                                      HHH CS
                       TFIIE_alpha 95 kLe 97
                                      +++
  gi|474934911|ref|YP_007688493.1| 86 EIR 88
                                      665 PP

>> DUF3755  Protein of unknown function (DUF3755)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0    0.0017       1.1      15      31 ..      77      93 ..      75      95 .. 0.91
   2 ?   -0.0   0.0       1.1     7e+02      15      33 ..     114     132 ..     113     133 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0017
                           DUF3755 15 RdNImaIlndMsdmpGi 31
                                       dNI +++++++d p++
  gi|474934911|ref|YP_007688493.1| 77 SDNIEKVEKEIRDIPEV 93
                                      69*************97 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.1
                           DUF3755  15 RdNImaIlndMsdmpGiMs 33 
                                       Rd   a+ ++++ + G+++
  gi|474934911|ref|YP_007688493.1| 114 RDEFSAVVKRINSLEGVNK 132
                                       66678999********986 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00043      0.28      18      66 ..      23      70 ..      11      90 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00043
                                      -EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE- CS
                              HxlR 18 kkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYslt 66
                                      +  + +l+++l ++   +L+qr ++Le +g+i+    +   + + Y  t
  gi|474934911|ref|YP_007688493.1| 23 QGSYRQLAKQL-GVHPTTLIQRVKALEDKGVINGYRAKVDYVAMGYDYT 70
                                      44577999999.89999***************98877777777777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       850  (0.0474092); expected 358.6 (0.02)
Passed bias filter:                      702  (0.0391544); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.46u 0.32s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1010.54
//
Query:       gi|474934912|ref|YP_007688494.1|  [L=393]
Description: Alanyl-tRNA synthetase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-16   61.4   1.3    2.5e-16   60.3   1.3    1.6  1  DHHA1         DHHA1 domain
    8.5e-10   37.8   0.0    1.3e-09   37.1   0.0    1.2  1  tRNA-synt_2c  tRNA synthetases class II (A)
    5.2e-06   26.5   2.1    4.2e-05   23.5   0.1    2.5  2  tRNA_SAD      Threonyl and Alanyl tRNA synthetase second addi
  ------ inclusion threshold ------
      0.014   15.6   0.0      0.046   13.9   0.0    1.8  2  MatP_C        MatP C-terminal ribbon-helix-helix domain


Domain annotation for each model (and alignments):
>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   1.3   5.6e-20   2.5e-16       3     138 .]     249     388 ..     247     388 .. 0.82

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 5.6e-20
                                       HHCHHHHHHHHHHHCHHHHHHHHHHHHHHHTCEEEC........TCEEEEEECHCCHHHHHHHHHHHHHHTHGBTTC CS
                             DHHA1   3 slneerkelekeleelkealaklkaeellekaeevk........gvkvlvaevgeewdagalgiaadklksklkkpv 71 
                                       + n + +++ k ++++k+ la ++++   +  + ++        g++v+++ + +++d+++l  aa++++s  k + 
  gi|474934912|ref|YP_007688494.1| 249 EANSKPQDIVKTVANMKKDLAVAAEARKASAKQAIRnlrprdvnGTPVYASMF-ADADRKTLSDAAEEFRS--KGAA 322
                                       56667777777777777777777666655555555577788899*********.*****************..6688 PP

                                       EEEEEEEECTEEEEEEEESSHSS-HHHHHHHHHHHTTCCEEEE.TCEEEEEEEHCHHHHHHHHHHHHH CS
                             DHHA1  72 ivfvakeegdkvkvsarskkdgvdagelakeaaaklgggGGGH.dlAaGagipaekleealealeeai 138
                                       +vfv++ e    +++a  ++ +vd ++++ e+ +++gg+GGG+ ++A+G+  ++ k++e+ +al +a+
  gi|474934912|ref|YP_007688494.1| 323 VVFVSVGES-VSALIASGTS-KVDCRKILPEVLSAFGGRGGGKpENAQGGIPDKAKAQELFDALVAAV 388
                                       888888776.6666666666.*****************************************998875 PP

>> tRNA-synt_2c  tRNA synthetases class II (A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.0     3e-13   1.3e-09     473     552 .]      13      87 ..       6      87 .. 0.93

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 3e-13
                                       SEEEEEEEEEETTEEEESEEXXXXSSSSCSXXXEEEEESSEEEEESEEEEET.TEEEEEXSS.XSXXXTTSEEEEEE CS
                      tRNA-synt_2c 473 kefveeveegeevgvvLdrTpfYaesGGqigDeGliekegaefrvkdvqkak.gvvlhkgkleegklkvgdkvkaev 548
                                       +ef++ + +++ + +++d T+fY+ +GGq  D+G+i++    frv+dv+  + g ++h++  +  +l+vg +v++++
  gi|474934912|ref|YP_007688494.1|  13 SEFEAGIVSINGDEIIMDCTCFYPGGGGQVCDTGTING----FRVTDVHYNDsGEIVHVVPGH--DLSVGLRVWCSL 83 
                                       78999999****************************85....99*****9999******9995..9*********** PP

                                       XHHH CS
                      tRNA-synt_2c 549 deer 552
                                       d++r
  gi|474934912|ref|YP_007688494.1|  84 DWDR 87 
                                       *986 PP

>> tRNA_SAD  Threonyl and Alanyl tRNA synthetase second additional domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.4      0.06   2.7e+02      12      32 ..      35      61 ..      18      65 .. 0.66
   2 !   23.5   0.1   9.5e-09   4.2e-05       1      26 [.     182     207 ..     182     220 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.06
                                      EEESS---SBGGGC-SEEEE......C CS
                          tRNA_SAD 12 elCgGtHvpnTgeIgafkil......s 32
                                       + gG  v  Tg I+ f+++      s
  gi|474934912|ref|YP_007688494.1| 35 YPGGGGQVCDTGTINGFRVTdvhyndS 61
                                      6779999**********9995555444 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 9.5e-09
                                       EEEEEETT.EEEEESS---SBGGGC- CS
                          tRNA_SAD   1 vrvvsiGdisvelCgGtHvpnTgeIg 26 
                                       ++vvsiGdi++ +C G Hv  Tge++
  gi|474934912|ref|YP_007688494.1| 182 ITVVSIGDIDYSACSGVHVMETGELE 207
                                       69**********************84 PP

>> MatP_C  MatP C-terminal ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0     1e-05     0.046      18      56 ..     229     268 ..     224     270 .. 0.88
   2 ?   -2.6   0.0       1.5   6.6e+03      21      32 ..     302     313 ..     299     316 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1e-05
                            MatP_C  18 sklsqrrgsTLSetivqLieeaerk.ekyeeqvsslkedL 56 
                                        + +++  + L +   q+i+ea++k + + ++v+++k+dL
  gi|474934912|ref|YP_007688494.1| 229 GRAAREAAMQLANICLQVIDEANSKpQDIVKTVANMKKDL 268
                                       56799999**************99945699*********9 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.5
                            MatP_C  21 sqrrgsTLSeti 32 
                                       +     TLS++ 
  gi|474934912|ref|YP_007688494.1| 302 ADADRKTLSDAA 313
                                       566678999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      587  (0.0327403); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2640.52
//
Query:       gi|474934913|ref|YP_007688495.1|  [L=125]
Description: alpha-NAC-related protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-13   50.6   1.0    2.2e-13   49.9   1.0    1.3  1  NAC              NAC domain
     0.0021   17.9   0.0     0.0041   16.9   0.0    1.5  1  UBA_4            UBA-like domain
  ------ inclusion threshold ------
      0.052   13.5   0.3      0.072   13.0   0.3    1.1  1  Glyco_hydro_3_C  Glycosyl hydrolase family 3 C-terminal domai
       0.23   11.6   1.6        1.2    9.3   0.1    2.3  2  DUF1296          Protein of unknown function (DUF1296)


Domain annotation for each model (and alignments):
>> NAC  NAC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9   1.0     5e-17   2.2e-13       1      55 [.      10      67 ..      10      68 .. 0.96

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 5e-17
                               NAC  1 ekKlrkalkklgl..keipgieeVtirksdgkvlvfdnPkVq..kspgsntyvvfGeae 55
                                      +++++ka++ +g+   +++g+++V+i+ +d k +v++n++V+  +++g+++y v+G + 
  gi|474934913|ref|YP_007688495.1| 10 PRQMQKAMRSMGItqSTVAGVQQVIIKCND-KDIVITNASVTciEMKGQKSYEVSGVVT 67
                                      79****************************.*************************876 PP

>> UBA_4  UBA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   9.2e-07    0.0041       1      27 [.      87     113 ..      87     121 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 9.2e-07
                             UBA_4   1 deliaqFqaiTGadeekArqlLeannW 27 
                                       de i+  ++ TG+d+ekA++ Le +++
  gi|474934913|ref|YP_007688495.1|  87 DEDIELVMSQTGCDREKAVKALEECDG 113
                                       6888889999***************98 PP

>> Glyco_hydro_3_C  Glycosyl hydrolase family 3 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3   1.6e-05     0.072     103     152 ..      28      79 ..      14      81 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.6e-05
                                       HHHHHHH.HTT.SSEEEEEEESSGG--TTTGTTTEEEEEE-S--GCCHHHHH CS
                                       xxxxxxx.xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Glyco_hydro_3_C 103 elikava.aan.knvvvvlqsggpvavepwkeenvkAilaawlpGqegGtai 152
                                       + +++v  + n k +v+   s + ++++  k+ +v++++  + pG +gG+a+
  gi|474934913|ref|YP_007688495.1|  28 AGVQQVIiKCNdKDIVITNASVTCIEMKGQKSYEVSGVVTEMTPGAAGGEAV 79 
                                       5556665333336799999999*****99999******************97 PP

>> DUF1296  Protein of unknown function (DUF1296)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.2     0.091   4.1e+02       6      25 ..      24      43 ..      22      47 .. 0.85
   2 ?    9.3   0.1   0.00026       1.2      16      44 ..      97     124 ..      84     125 .] 0.86

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.091
                           DUF1296  6 rkviqsikEivgkhsdeeIy 25
                                      + ++  ++ +  k++d++I 
  gi|474934913|ref|YP_007688495.1| 24 QSTVAGVQQVIIKCNDKDIV 43
                                      5689999999999*****96 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00026
                           DUF1296  16 vgkhsdeeIyamLkecnmDpneavqkLLs 44 
                                       +g + +e+  ++L+ec+  p ea+ k +s
  gi|474934913|ref|YP_007688495.1|  97 TG-CDREKAVKALEECDGQPAEAIIKIMS 124
                                       44.999999***************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       799  (0.0445647); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 847.96
//
Query:       gi|474934914|ref|YP_007688496.1|  [L=79]
Description: hydrogenase assembly chaperone HypC/HupF [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.1e-27   93.8   1.4    6.2e-27   93.5   1.4    1.1  1  HupF_HypC  HupF/HypC family
  ------ inclusion threshold ------
        0.1   12.3   0.0       0.11   12.3   0.0    1.1  1  DUF5105    Domain of unknown function (DUF5105)
       0.11   13.3   0.0       0.14   13.1   0.0    1.1  1  DUF5611    Domain of unknown function (DUF5611)
       0.33   10.4   2.0        1.4    8.4   0.2    2.2  2  ProQ_C     ProQ C-terminal domain


Domain annotation for each model (and alignments):
>> HupF_HypC  HupF/HypC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.5   1.4   1.4e-30   6.2e-27       1      65 []       1      64 [.       1      64 [. 0.98

  Alignments for each domain:
  == domain 1  score: 93.5 bits;  conditional E-value: 1.4e-30
                                      CCEEEEEEEEEEETTEEEEECTTEEEEEEGTTCTTB-TT-EEEEETTEEEEEE-HHHHHHHHHHH CS
                         HupF_HypC  1 MCLaiPgkvveiedelAlvdvgGvrrevslalveevkvGdyVLvhvGfAiekideeeaeetlell 65
                                      MCLa+P+k+v+i+++ A+vd+gG+ + +++++v+ vkvGd+V+vh+GfAie++deeea+et++l+
  gi|474934914|ref|YP_007688496.1|  1 MCLAVPAKIVAIDGDEAQVDFGGTMKPANISMVD-VKVGDWVVVHAGFAIEVMDEEEAAETIKLW 64
                                      *********************************6.***************************987 PP

>> DUF5105  Domain of unknown function (DUF5105)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.4e-05      0.11      87     125 ..       5      45 ..       3      76 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.4e-05
                                       EEEEEEEEETTEEEEEE..EEE-EE-TTHHHHHHHHHHHHH CS
                           DUF5105  87 vetkvvsisgdkAeVev..tvkpidlselkdkleeekeeyl 125
                                       v +k+v+i+gd+A+V +  t+kp ++s +  k+ +     +
  gi|474934914|ref|YP_007688496.1|   5 VPAKIVAIDGDEAQVDFggTMKPANISMVDVKVGDWVVVHA 45 
                                       679*************9779******999999877665555 PP

>> DUF5611  Domain of unknown function (DUF5611)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     3e-05      0.14      44      87 ..      30      69 ..       7      71 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3e-05
                                      BS-EEEEE..-SS-EEEEE--.B...-TTS-HHHHHHHHHHHHH CS
                           DUF5611 44 ikklevkisskkkklvvdteerdaeeeddeaaldtvkkfndFLe 87
                                      i+ ++vk+   ++ +vv+      e +d+e+a++t+k +ndF++
  gi|474934914|ref|YP_007688496.1| 30 ISMVDVKV---GDWVVVHAGF-AIEVMDEEEAAETIKLWNDFID 69
                                      33444444...6777777777.6788****************97 PP

>> ProQ_C  ProQ C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.2   0.00032       1.4      19      35 ..       4      20 ..       3      26 .. 0.91
   2 ?    1.6   0.1      0.04   1.8e+02       4      16 ..      34      46 ..      31      49 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00032
                                      ---EEEEEE-SSSEEEE CS
                            ProQ_C 19 pmpAtileiaKddVrVq 35
                                      ++pA i+ i+ d+++V 
  gi|474934914|ref|YP_007688496.1|  4 AVPAKIVAIDGDEAQVD 20
                                      69**************6 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.04
                                      SS-TT--B---SS CS
                            ProQ_C  4 eLkvGqqVkVklG 16
                                      ++kvG+ V V +G
  gi|474934914|ref|YP_007688496.1| 34 DVKVGDWVVVHAG 46
                                      5677777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 517.21
//
Query:       gi|474934915|ref|YP_007688497.1|  [L=362]
Description: Na+/proline symporter [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.4e-66  225.0  22.7    1.7e-66  224.8  22.7    1.1  1  SSF        Sodium:solute symporter family


Domain annotation for each model (and alignments):
>> SSF  Sodium:solute symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  224.8  22.7   9.4e-71   1.7e-66       1     326 [.      33     358 ..      33     362 .] 0.93

  Alignments for each domain:
  == domain 1  score: 224.8 bits;  conditional E-value: 9.4e-71
                               SSF   1 yflagrsltgfvlglslaasnisaasfvGlaGavaasGlavvllelgalllvlllllllaerlr.....nagalTlp 72 
                                       y+l+gr+l ++v +ls+ as++s+++++Gl+G++++ G++ +++ +g+ ++ ++++ll+a+rlr      +  lTl 
  gi|474934915|ref|YP_007688497.1|  33 YILGGRKLNPYVAALSAQASDMSGWLLLGLPGSIYLFGIGQAWIGIGLAIGSYFAWLLIAKRLRnytkkAKDSLTLS 109
                                       9***************************************************************888777789**** PP

                               SSF  73 dylskRfkgkr.ilvylsalslllvitlklsvdlvggaklielalGlnyetavlllaaltalYtviGGllAvvytdt 148
                                       +++s+Rf++++  l+ +sa++++++++ ++++++v+++ ++ + + l+y   +l+++++++ Ytv+GG+ A+ +td+
  gi|474934915|ref|YP_007688497.1| 110 QFFSNRFRDQKnYLKTMSAIAIIVFFIPYVASGFVSAGNILMSFVDLDYVPCMLIGVVVIIAYTVLGGFKAICWTDV 186
                                       ********99989**************************************************************** PP

                               SSF 149 iqavlmlvgalilliivllevGgleslveklkeaapkv.vdllt.pdslkllrdpltalslwlglvlGvaglphilv 223
                                       +qa+lm+v+ +i+++ ++ e+Gg ++++  +   a ++  d+++ +d+      +l+++s  l+++lG++g+ph++v
  gi|474934915|ref|YP_007688497.1| 187 LQAMLMIVAIIIVPLAAIGELGGWDEVMAVADRPAFSGfFDFFKnADGS--TIAALSIISS-LAWGLGYFGMPHVVV 260
                                       ****************************999988887789998855553..4455666665.8************** PP

                               SSF 224 RflaakdakailkgvlkltivlilvligmisiilfaiklagavpkavgtevgvsniaypeLvvkllpnllaGlllav 300
                                       R +a +d k++  +++ +t+++i+ l+ +i ++l ++++         t+   ++ +++ +v  ++ ++++G+l ++
  gi|474934915|ref|YP_007688497.1| 261 RYMALEDPKEAKVARRVGTGWIIVALAFAILVGLVGQAYHPG---F--TTKSDAQTIFIVMVGGIFAPIIMGVLYSA 332
                                       ************************************998544...3..4556678899******************* PP

                               SSF 301 mlAaimstltslllsassaftkDlYk 326
                                        +Aa+mst +s+ll+as+a+t+Dl +
  gi|474934915|ref|YP_007688497.1| 333 LMAAVMSTSDSQLLVASAAVTNDLMS 358
                                       ***********************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       975  (0.0543812); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 2413.94
//
Query:       gi|474934916|ref|YP_007688498.1|  [L=135]
Description: Na+/proline symporter [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-15   55.9   5.1    3.2e-15   55.9   5.1    1.3  2  SSF              Sodium:solute symporter family
  ------ inclusion threshold ------
       0.53   10.4   0.2       0.53   10.4   0.2    2.3  2  Bacteriocin_IIc  Bacteriocin class II with double-glycine lea
        2.3    8.4  16.5         13    6.0  16.5    1.9  1  DUF5518          Family of unknown function (DUF5518)


Domain annotation for each model (and alignments):
>> SSF  Sodium:solute symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.9   5.1   5.4e-19   3.2e-15     340     406 .]       1      66 [.       1      66 [. 0.97
   2 ?   -3.4   0.1      0.53   3.2e+03     289     297 ..      96     104 ..      76     113 .. 0.51

  Alignments for each domain:
  == domain 1  score: 55.9 bits;  conditional E-value: 5.4e-19
                               SSF 340 vgvsriivlvvislaillavqeeqkgvlklvelafaglasavlavillalfwkrvneqGAlagliiG 406
                                       ++++r +v++++ +a ++a+++e++ +++lv++a+ag+++a+++v+ll+l+w r n  GAlag+i+G
  gi|474934916|ref|YP_007688498.1|   1 MWMARAVVVIIAIVAAAIALDPESS-IMDLVSFAWAGFGAAFGPVVLLSLYWRRSNGWGALAGMITG 66 
                                       6899999****************99.***************************************99 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.53
                               SSF 289 lpnllaGll 297
                                       +p +l++l+
  gi|474934916|ref|YP_007688498.1|  96 VPGFLFALI 104
                                       333333332 PP

>> Bacteriocin_IIc  Bacteriocin class II with double-glycine leader peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   1.8       0.2   1.2e+03      45      57 ..      32      44 ..       7      47 .. 0.77
   2 ?   10.4   0.2   8.8e-05      0.53      29      50 ..      56      77 ..      53      81 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.2
                   Bacteriocin_IIc 45 ilgaavGavvGav 57
                                       ++a++Ga++G v
  gi|474934916|ref|YP_007688498.1| 32 FAWAGFGAAFGPV 44
                                      4677777777755 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 8.8e-05
                   Bacteriocin_IIc 29 vggalaGaatGaatlgilgaav 50
                                      ++galaG++tG++t +i+ +  
  gi|474934916|ref|YP_007688498.1| 56 GWGALAGMITGFITVIIWNTFL 77
                                      79***********999987755 PP

>> DUF5518  Family of unknown function (DUF5518)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0  16.5    0.0022        13       5     102 ..       6     109 ..       2     114 .. 0.53

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0022
                           DUF5518   5 liGavvaivlslllglllpsvgsllgllvgGlvaGy........laggdskdgavaGalaGligaipv.lvlllvll 72 
                                        +  ++aiv  +++     s+++l+++ ++G+ a++          +++ + ga+aG+++G+i++i+  + l++  +
  gi|474934916|ref|YP_007688498.1|   6 AVVVIIAIVAAAIALDPESSIMDLVSFAWAGFGAAFgpvvllslYWRRSNGWGALAGMITGFITVIIWnTFLSADSV 82 
                                       44455555555555557788888888888888887544432221233444566666666666666666555555555 PP

                           DUF5518  73 lglvaaigglagfvallvalllvvllllvv 102
                                       +gl a  +gl  +v +++++l++   +++v
  gi|474934916|ref|YP_007688498.1|  83 FGLCAYDTGLYELVPGFLFALIA---IIAV 109
                                       44555545544444444444444...3332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 818.94
//
Query:       gi|474934917|ref|YP_007688499.1|  [L=259]
Description: putative archaeal kinase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.4e-39  136.2   0.1    1.6e-39  136.0   0.1    1.0  1  AA_kinase  Amino acid kinase family


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.0   0.1   8.7e-44   1.6e-39       3     241 .]       2     233 ..       1     233 [. 0.94

  Alignments for each domain:
  == domain 1  score: 136.0 bits;  conditional E-value: 8.7e-44
                                       EEEEE-TTCCCCTCC......HHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC....E..HHH CS
                         AA_kinase   3 vVvKlGGssltdkee......aslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaaglrstleea 73 
                                       + +KlGGs++t k +      + + rla++ia+    g+++++VhG+gsf++  +++ + l++g+++     ++++ 
  gi|474934917|ref|YP_007688499.1|   2 ILIKLGGSVITGKADyrtfnrETVARLADEIARS---GKDVIIVHGAGSFGHIVAKE-NRLQEGFKD-----KSQIP 69 
                                       89*********77777*99999999999999999...********************.********9.....57777 PP

                                       HHHHHHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEE CS
                         AA_kinase  74 gevatrdalaslgerlvaallaaglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfigld 150
                                       + + t+     l + +v++lla+ +pav++++ ++ + ++g+       +   ++e +++l++ g+ pv+ g+++ d
  gi|474934917|ref|YP_007688499.1|  70 AAARTMCDTRELSSMVVEELLAHNIPAVSVPPGSCFVMDNGK-------LIIDNEEPLRRLVDLGIMPVMFGDVVTD 139
                                       788888999999999*********************998888.......999************************* PP

                                       TTTEEEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH....CSSS.TTTHHHHCH CS
                         AA_kinase 151 eegelgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaee....saselatgGmkvkh 223
                                       +  ++g++s+D++  +l+ +++++++i+++d+dG+yd++pk + +ar+l +++  +++e    s+  ++tgG++ k+
  gi|474934917|ref|YP_007688499.1| 140 RSTGFGILSGDQCMEALCRMFDPEEVIFVSDIDGLYDRNPKTDRHARMLGTVTRAKLDEleteSNVADVTGGIRGKM 216
                                       ****************************************************99999999999999*********** PP

                                       HHHHHHHHCTT-EEEEEE CS
                         AA_kinase 224 paalaaarrggipvvItn 241
                                        a+l++      ++v++n
  gi|474934917|ref|YP_007688499.1| 217 IAMLKMTTAD-RRCVLVN 233
                                       *****99887.7777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1722.16
//
Query:       gi|474934918|ref|YP_007688500.1|  [L=357]
Description: isopentenyl-diphosphate delta-isomerase, type 2 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      9e-22   77.6   1.4    3.9e-14   52.4   2.1    2.4  2  FMN_dh    FMN-dependent dehydrogenase
     0.0016   17.9   0.4     0.0016   17.9   0.4    1.6  2  NMO       Nitronate monooxygenase
     0.0086   15.1   2.3        2.6    7.0   0.2    2.8  3  IMPDH     IMP dehydrogenase / GMP reductase domain
  ------ inclusion threshold ------
      0.068   13.6   0.0       0.21   12.0   0.0    1.8  1  GP67      Gene product 67


Domain annotation for each model (and alignments):
>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   1.7e-08   7.5e-05      29      95 ..      28      96 ..       6     105 .. 0.85
   2 !   52.4   2.1   8.7e-18   3.9e-14     214     344 ..     185     338 ..     158     342 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.7e-08
                                      GGGGEEE---SSS..S-SS-B--EEETTEEESSSEEE--BSTGGGTSTTHHHHHHHHHHHHTS-EEEET CS
                            FMN_dh 29 aferirlrprvlr..dvskvdlsttllGqklslPvliaPvglaklahpdgelalaraaakagipfvlst 95
                                       ++++rl++++l   d+ ++dl+ ++lG+kl++P+++ ++      +++ + ++a a+a++gi +++++
  gi|474934918|ref|YP_007688500.1| 28 YWDDVRLVHNALPeiDMDEIDLTADVLGKKLDFPLIVTAITGGFSGARKINANIASACADLGIGMGVGS 96
                                      699*********82245788********************88888888999**************9876 PP

  == domain 2  score: 52.4 bits;  conditional E-value: 8.7e-18
                                       HHSSEEEEEEE...-SHHHHHHHHHTTESEEEE--GGG....................TSSTT---HHHCHHHHHHH CS
                            FMN_dh 214 qtklplvvKGv...ltaedakraveaGvdgivvSNHGG....................RqldgapatidvLpeivea 267
                                       ++k p++vK+    ++a +a+r+  +Gv +i v+  GG                                       
  gi|474934918|ref|YP_007688500.1| 185 AVKYPIIVKETgagIDAFTAERLRGIGVRAIDVAGMGGtsfsavemyraqladdelhtE------------------ 243
                                       4689*****99888889999******************555555555444444333320.................. PP

                                       H.....................SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            FMN_dh 268 v...................ggrievlvDgGirrGsDvlkAlalGAdavllGRpflyglaagGeeGvervleilrae 325
                                       +                     +++++++gG   G++ + A+a+GA a + +R++l   a++ +e v++ l ++r+e
  gi|474934918|ref|YP_007688500.1| 244 LgttffdwgiptpvslreakCAKLPLIASGGLLDGTHLASAIAMGAVAGGCARAILRD-AMESAEAVKKKLMLFREE 319
                                       13333333333333333322459********************************888.89**************** PP

                                       HHHHHHHHT-SBHHHHHCG CS
                            FMN_dh 326 lertmallGvksvaeldrs 344
                                       l+++m l+G++++++l+++
  gi|474934918|ref|YP_007688500.1| 320 LRAAMMLTGCTDIKQLSNA 338
                                       ****************875 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1      0.87   3.9e+03     194     213 ..      60      82 ..      43      93 .. 0.63
   2 !   17.9   0.4   3.7e-07    0.0016     191     242 ..     264     315 ..     256     335 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.87
                               NMO 194 iPviA...aGGiidrrgvaaaLa 213
                                        P+i    +GG+  +r ++a +a
  gi|474934918|ref|YP_007688500.1|  60 FPLIVtaiTGGFSGARKINANIA 82 
                                       45443112577777777777654 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 3.7e-07
                               NMO 191 avdiPviAaGGiidrrgvaaaLalGAsgvqigtrfLltkesdakdahkkkll 242
                                         ++P+iA GG+ d+  +a a+a+GA +   + + L      a+++ kk +l
  gi|474934918|ref|YP_007688500.1| 264 CAKLPLIASGGLLDGTHLASAIAMGAVAGGCARAILRDAMESAEAVKKKLML 315
                                       4569***********************9999988887666666666665554 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.35   1.6e+03     146     178 ..      64      96 ..      29      97 .. 0.58
   2 !    7.0   0.2   0.00058       2.6     202     231 ..     261     290 ..     256     297 .. 0.89
   3 !    6.9   0.0   0.00062       2.8     295     333 ..     305     342 ..     299     354 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.35
                                       SEEEEEEE-SHHHHHHHHHTT-SEEEE-SS-ST CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 146 veviaGnvataegakaLieagadavkvGiGpGs 178
                                       v+ i+G    a  ++a i+     + +G+G Gs
  gi|474934918|ref|YP_007688500.1|  64 VTAITGGFSGARKINANIASACADLGIGMGVGS 96 
                                       444555555555555444444444566666665 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00058
                                       HHCTCT-EEEEES---SHHHHHHHHHTT-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 202 aakkagvpviaDGGikysgdivkAlaaGad 231
                                        ak a+ p+ia GG+    +++ A+a+Ga 
  gi|474934918|ref|YP_007688500.1| 261 EAKCAKLPLIASGGLLDGTHLASAIAMGAV 290
                                       5677899*********************95 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.00062
                                       --B-HHHHHHHHHHHHHHHHHHHT-SSHHHHHHH-EEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 295 ykgsvkevveqlvgglrsgmgylGaktieelkekakfvr 333
                                        +  vk+ +  + ++lr++m  +G+++i++l  +a++v 
  gi|474934918|ref|YP_007688500.1| 305 SAEAVKKKLMLFREELRAAMMLTGCTDIKQLS-NARYVV 342
                                       56678899999999*****************6.566655 PP

>> GP67  Gene product 67
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.6e-05      0.21      16      53 ..     134     171 ..     120     180 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.6e-05
                              GP67  16 arklfaeamaartidlikeekiaiarnfliegeepede 53 
                                       ++ +f++ m  ++ dli  + +a+  nfl e  +pe +
  gi|474934918|ref|YP_007688500.1| 134 SKDIFSDDMVGQAKDLIDADYVAVHLNFLQEVVQPEGD 171
                                       5789******************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 1986.78
//
Query:       gi|474934919|ref|YP_007688501.1|  [L=327]
Description: Geranylgeranyl pyrophosphate synthase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.2e-64  215.8   0.4    6.5e-64  215.5   0.4    1.1  1  polyprenyl_synt  Polyprenyl synthetase
  ------ inclusion threshold ------
       0.14   12.5   0.4        0.5   10.7   0.1    2.1  2  TFIIE_beta       TFIIE beta subunit core domain


Domain annotation for each model (and alignments):
>> polyprenyl_synt  Polyprenyl synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.5   0.4   7.2e-68   6.5e-64       4     255 ..      31     278 ..      28     279 .. 0.92

  Alignments for each domain:
  == domain 1  score: 215.5 bits;  conditional E-value: 7.2e-68
                                       HHHHHHHHHHSSS--HHHHHHHHHHHHHSCGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEETTEE-HHHCTCH CS
                   polyprenyl_synt   4 leealeylveagGKrlRpllvllaaealkeeeeelekaavlawivellhaasLvhDDimDdsetRRGqpcahrlvGn 80 
                                       +e++ +y   agGKr+Rp++vl+a+ a++ ++   +ka  la+++e +h+++L+hDD+mD +e+RRG +++h  +++
  gi|474934919|ref|YP_007688501.1|  31 IEASRQYPY-AGGKRMRPAIVLAACGAVGGDK---KKAMPLAVAIEYIHNFTLIHDDLMDGDEMRRGMKTIHVGYDE 103
                                       445555666.*******************445...89**************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHH..STT.HHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC.SHHHHHHHHHHHTHHH CS
                   polyprenyl_synt  81 klAindgdfllarafellaklf..eks.lellelfsevllqtveGqlldleeekdddlskfsleeyleivkyKTayl 154
                                       ++Ai++gd+l+a+af+++a+l    +   e+l+ +++++ ++++Gq +d+ +e  + ++   +++y e +  KT++l
  gi|474934919|ref|YP_007688501.1| 104 PTAILAGDALFAKAFQIIAELDipAEAmREVLRFVTKAVWDLARGQEMDILNE-GKLID---EAHYTETIFLKTSVL 176
                                       *********************99844459*********************888.35555...9************** PP

                                       CHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHSS-TSHHHHTT---HHHHHHHH.CT-HH CS
                   polyprenyl_synt 155 falpvalaallagasdeelealkdiglelGlaFQiqDDylDlfgdpevlgKpagtDiqegkctlpilkale.laspe 230
                                       fa+++a +al++ga++++++a+++++l +Gl FQ+ DDyl + gd++++gK +g+D+++gkctl++ ++le l++++
  gi|474934919|ref|YP_007688501.1| 177 FAAAAAGGALCGGADKKVVDAINRYALDMGLGFQMFDDYLGIAGDTSKTGKSVGNDLRKGKCTLMVTYTLEhLKDEK 253
                                       **************99*******************************************************445555 PP

                                       HHHHHHHHTTSSHHHHHHHHHHHHH CS
                   polyprenyl_synt 231 qrkvlkeilgkkaekeedvkealel 255
                                       + +++k+ilg+ +++e++v+e +e+
  gi|474934919|ref|YP_007688501.1| 254 KLAKFKSILGNMKATEAEVREGMEI 278
                                       6689******99999*999987776 PP

>> TFIIE_beta  TFIIE beta subunit core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.99   8.9e+03      10      17 ..       5      12 ..       2      19 .. 0.67
   2 ?   10.7   0.1   5.6e-05       0.5       5      56 ..     242     290 ..     239     297 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.99
                        TFIIE_beta 10 eylKkkdg 17
                                      +ylKk+++
  gi|474934919|ref|YP_007688501.1|  5 DYLKKTSA 12
                                      89999654 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 5.6e-05
                        TFIIE_beta   5 LakiveylKkkdgplsleeIlsylslqldlsdknwllleaLknnpkieyDpk 56 
                                       +++  e+lK  ++  +++ Il +++  ++   + ++ +e+++++  iey++k
  gi|474934919|ref|YP_007688501.1| 242 VTYTLEHLKDEKKLAKFKSILGNMKA-TE--AEVREGMEIMREIGAIEYNKK 290
                                       7899*********************5.44..667999************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2009.93
//
Query:       gi|474934920|ref|YP_007688502.1|  [L=206]
Description: RecA/RadA recombinase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-23   83.9   0.5    1.3e-23   83.6   0.5    1.1  1  Rad51            Rad51
    1.6e-12   47.3   3.5      7e-11   41.9   3.5    2.0  1  ATPase           KaiC
    3.3e-10   39.9   0.0    4.5e-10   39.4   0.0    1.2  1  AAA_25           AAA domain
    5.6e-10   39.2   0.2    6.6e-10   38.9   0.2    1.1  1  Zot              Zonular occludens toxin (Zot)
    7.2e-08   32.1   0.5    0.00075   18.9   0.1    2.3  3  DnaB_C           DnaB-like helicase C terminal domain
    1.5e-07   31.2   0.1    1.7e-07   31.0   0.1    1.3  1  RecA             recA bacterial DNA recombination protein
    3.1e-07   30.3   0.0      4e-07   30.0   0.0    1.2  1  AAA_24           AAA domain
    1.2e-05   25.1   0.7    5.6e-05   23.0   0.1    2.0  2  IstB_IS21        IstB-like ATP binding protein
    0.00022   21.6   0.0    0.00029   21.3   0.0    1.2  1  AAA_16           AAA ATPase domain
    0.00026   21.4   0.0     0.0004   20.8   0.0    1.3  1  AAA              ATPase family associated with various cellul
     0.0015   18.7   0.0     0.0031   17.7   0.0    1.5  1  Isochorismatase  Isochorismatase family
     0.0017   18.6   0.1     0.0029   17.9   0.1    1.4  1  AAA_22           AAA domain
     0.0019   18.2   0.0     0.0026   17.7   0.0    1.4  1  ATPase_2         ATPase domain predominantly from Archaea
     0.0031   16.5   0.0     0.0089   15.0   0.0    1.7  2  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
     0.0045   17.1   0.0     0.0065   16.5   0.0    1.5  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
     0.0075   15.8   0.2      0.014   14.9   0.2    1.4  1  PhoH             PhoH-like protein
  ------ inclusion threshold ------
      0.011   15.0   0.0      0.017   14.3   0.0    1.2  1  PIF1             PIF1-like helicase
      0.025   14.4   0.0      0.065   13.0   0.0    1.7  2  CLP1_P           mRNA cleavage and polyadenylation factor CLP
       0.03   14.0   0.2       0.11   12.2   0.1    2.0  2  SRP54            SRP54-type protein, GTPase domain
       0.04   13.8   0.1      0.087   12.6   0.0    1.5  2  Bac_DnaA         Bacterial dnaA  protein
      0.046   14.1   0.1       0.13   12.7   0.0    1.8  2  RNA_helicase     RNA helicase
       0.05   13.5   0.1      0.064   13.2   0.1    1.3  1  AAA_31           AAA domain
      0.078   13.0   0.0       0.12   12.4   0.0    1.3  1  Hpr_kinase_N     HPr Serine kinase N terminus
       0.11   12.7   1.9        3.9    7.7   1.9    2.1  1  CobA_CobO_BtuR   ATP:corrinoid adenosyltransferase BtuR/CobO/
       0.13   12.5   0.0       0.25   11.6   0.0    1.5  1  PucR             Purine catabolism regulatory protein-like fa
       0.13   12.7   0.0        0.2   12.2   0.0    1.5  1  ABC_tran         ABC transporter
       0.15   11.7   0.0       0.23   11.1   0.0    1.3  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b


Domain annotation for each model (and alignments):
>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.6   0.5     2e-26   1.3e-23      29     254 ..       1     205 [.       1     206 [] 0.86

  Alignments for each domain:
  == domain 1  score: 83.6 bits;  conditional E-value: 2e-26
                                       HHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS---GGGGHHHHHHTT--HHHHGGG CS
                             Rad51  29 lLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegtfrperlveiaerykldkeevlen 105
                                       +LgGGietg++t  +Ge ++Gkt +c +++  +          +k++y+dteg +  +r+ +i      ++++++++
  gi|474934920|ref|YP_007688502.1|   1 MLGGGIETGAVTLFYGEAGCGKTNICLQMAANA------CRRGKKVAYVDTEG-LSYDRVHQIF-----KDDALMKE 65 
                                       69************************9887654......45679********7.8999**9994.....46788999 PP

                                       EEEEE--STTHHHHHHHHTHHHHHHS-EEEEEEETTTGGGCH-------THHHHHHHHHHHHHHHHHHHHH--EEEE CS
                             Rad51 106 vayaRaytiehqeellqqaaallaedkfallivDsvtalyRtdfsgrgelakRqqklgkllrtLrkladefevavvi 182
                                         +  +++ ++q++ ++q++   ++  ++l++vDs+t  yR ++ + +    R+  + +  ++L ++a e+e+ vvi
  gi|474934920|ref|YP_007688502.1|  66 LLVFSVHSFQEQSDRVEQISRIAKNGIIGLIVVDSMTMFYRLNYDDMD---MRN-DFIRQTEQLLHVAREYEIPVVI 138
                                       9999****************************************8766...565.45566788999*********** PP

                                       EEE-------.------------HHHHHHHH-SE..EEEEEE-STTEEEEEEES-SSS-S.-EEEEEEETTEEE- CS
                             Rad51 183 tnqvvaqvdgqaalfsadpkkPigGlvlahastt..RlalrkgkgeeRivkvvdsPnlpe.leavfaigeeGied 254
                                       t qv  ++++ +  f        gG+ + h+++t  R+ lr      R + +++  +lpe + a f i+e+G+ d
  gi|474934920|ref|YP_007688502.1| 139 TSQVYTNINTGSIEF-------LGGHAMHHNAKTiiRFDLRG-AAGVRTAVIIKHRSLPEgRTALFRITEDGVRD 205
                                       ********9966666.......68******998733566665.4557999999999***9346789*******98 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   3.5   1.1e-13     7e-11      12     224 ..       2     203 ..       1     204 [. 0.79

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 1.1e-13
                            ATPase  12 lkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepa.edlrenakslGwdlekleeegklaiid 87 
                                       l gGi  g+v+l +Ge+G+GKt ++lq + + +++ g+++ +v +e  +   +++ +k      ++l +e +++ ++
  gi|474934920|ref|YP_007688502.1|   2 LGGGIETGAVTLFYGEAGCGKTNICLQMAANACRR-GKKVAYVDTEGLSyDRVHQIFKD-----DALMKELLVFSVH 72 
                                       579********************************.*******9998772334443332.....6788884555555 PP

                            ATPase  88 asesaeesaeekdkedleelieelaeaikeikakrvviDsitgl.ayeekeavaReil....rqlvrvlkklgvTai 159
                                        +++++        +     +e++ ++ k+  +  +v+Ds t +   + +++ +R+ +     ql++v +++++  +
  gi|474934920|ref|YP_007688502.1|  73 SFQEQS--------DR----VEQISRIAKNGIIGLIVVDSMTMFyRLNYDDMDMRNDFirqtEQLLHVAREYEIPVV 137
                                       555543........34....456777888888899*********7777788889986622225788888******** PP

                            ATPase 160 lvsekss.....seeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteegi 224
                                       ++s++ +     s e  gg++  +  ++ +i+ d  +     vRt  i+k R+ +   ++  f Ite+g+
  gi|474934920|ref|YP_007688502.1| 138 ITSQVYTnintgSIEFLGGHAMHH-NAKTIIRFD--LRGAAGVRTAVIIKHRSLPEG-RTALFRITEDGV 203
                                       ****99999887667778888888.999999999..5566789**********9965.567899999998 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.0   6.7e-13   4.5e-10      28     188 ..       4     141 ..       1     144 [. 0.82

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 6.7e-13
                            AAA_25  28 gllpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgealrddarl 103
                                       g +  g+++l++G  g+GKt ++l++a+  + +Gk           kV yv++E+       R+++++++ ++ ++l
  gi|474934920|ref|YP_007688502.1|   4 GGIETGAVTLFYGEAGCGKTNICLQMAANACrRGK-----------KVAYVDTEGLS---YDRVHQIFKDDALMKEL 66 
                                       56789**************************6666...........9*********9...99******998889999 PP

                            AAA_25 104 lvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralgg...densnsdvgalvealeriar 177
                                       lv +++++      +++         v+++ + ++    ++l+v+D+++ +++    d +  +d  +  e+l ++ar
  gi|474934920|ref|YP_007688502.1|  67 LVFSVHSF------QEQ------SDRVEQISRIAKN-GIIGLIVVDSMTMFYRLnydDMDMRNDFIRQTEQLLHVAR 130
                                       99987665......322......2447888888888.67**************966555556666677778888899 PP

                            AAA_25 178 rtgaavllvhH 188
                                       ++ + v+++ +
  gi|474934920|ref|YP_007688502.1| 131 EYEIPVVITSQ 141
                                       99999998876 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.2     1e-12   6.6e-10       1     150 [.      10     167 ..      10     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 1e-12
                               Zot   1 aislvtGapGsgKtsgavkkdllpalkegRkiit.nidGlrlerieqvlgekvstarliridnpegaetlkefakwa 76 
                                       a+ l++G+ G gKt   +++ + +a + g+k++  + +Gl  +r++q+++++   ++l+  + + ++e+++++++  
  gi|474934920|ref|YP_007688502.1|  10 AVTLFYGEAGCGKTNICLQM-AANACRRGKKVAYvDTEGLSYDRVHQIFKDDALMKELLVFSVHSFQEQSDRVEQIS 85 
                                       6899****************.77777777766544*****************9988999999999*********999 PP

                               Zot  77 tidkg...allviDEcqeifpvrakegrkd.....pevinaftehRhlgwDivlltqdiskihk.evralaekavkl 144
                                       +i+k+   +l+v+D    ++  +     ++      + ++ +  +R +   +v++ q  ++i+   +  l ++a ++
  gi|474934920|ref|YP_007688502.1|  86 RIAKNgiiGLIVVDSMTMFYRLNYDD-MDMrndfiRQTEQLLHVAREYEIPVVITSQVYTNINTgSIEFLGGHAMHH 161
                                       99966233689**********99995.55567787777889999******************973566777777888 PP

                               Zot 145 krkaai 150
                                       + k+ i
  gi|474934920|ref|YP_007688502.1| 162 NAKTII 167
                                       877644 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00019      0.13      14      58 ..       4      47 ..       1      65 [. 0.83
   2 !   18.9   0.1   1.1e-06   0.00075     118     181 ..      81     145 ..      48     150 .. 0.76
   3 ?   -3.9   0.0        10   6.6e+03     226     242 ..     177     193 ..     165     196 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00019
                                      TSBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSS CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C 14 sGlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslem 58
                                      +G++ g +++  + +++Gkt ++l++a+na+  + ++va++  e 
  gi|474934920|ref|YP_007688502.1|  4 GGIETGAVTLFYGEAGCGKTNICLQMAANACR-RGKKVAYVDTEG 47
                                      68999999999******************997.566899988875 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 1.1e-06
                                       HHHHHHHHHHTTEEEEEEEEGGGTBTSCS.SSCCCHHHHHHHHHHHHHHHHCTSXEEEEEEXSGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C 118 rskarrlkkekglgliviDyLqlmegsee.kenreqevseisrsLkalakelnvpvialsqLsra 181
                                        +++ r++k++ +gliv+D + +    +  + + +++  + + +L ++a+e ++pv++ sq+  +
  gi|474934920|ref|YP_007688502.1|  81 VEQISRIAKNGIIGLIVVDSMTMFYRLNYdDMDMRNDFIRQTEQLLHVAREYEIPVVITSQVYTN 145
                                       456778889999***********99664433355566667799******************8655 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 10
                                       EEEEEEEEETTSXXEEE CS
                                       xxxxxxxxxxxxxxxxx RF
                            DnaB_C 226 kaeiiiaKhRnGptgtv 242
                                       + + +i KhR+ p g+ 
  gi|474934920|ref|YP_007688502.1| 177 VRTAVIIKHRSLPEGRT 193
                                       55778899998777665 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.1   2.6e-10   1.7e-07      46     145 ..       3     106 ..       1     178 [. 0.80

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 2.6e-10
                                       SSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS-.---HHHH.HHTT--GGG-EE.E--SSHHHH CS
                              RecA  46 GiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafidaeh.aldpkya.kklGvdidellv.sqpdtGeqa 119
                                       G GG+  G ++  yG    Gkt ++l++ a+a ++g+ +a++d+e  + d ++   k    ++ellv s     eq+
  gi|474934920|ref|YP_007688502.1|   3 G-GGIETGAVTLFYGEAGCGKTNICLQMAANACRRGKKVAYVDTEGlSYDRVHQiFKDDALMKELLVfSVHSFQEQS 78 
                                       4.9*****************************************963556544312333335566552666667775 PP

                                       ..HHHHHHHHTTT--SEEEEE-TTT--- CS
                              RecA 120 ..leiadalvrsgaidlivvdsvaalvp 145
                                         +e +  + + g i livvds++ +  
  gi|474934920|ref|YP_007688502.1|  79 drVEQISRIAKNGIIGLIVVDSMTMFYR 106
                                       3367788899************987655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0     6e-10     4e-07       3      89 ..      10     116 ..       8     128 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 6e-10
                            AAA_24   3 lkiliyGpsgiGKTtlakel.......gpkplfidtek.Glksldadkfpdie...............swedfldev 56 
                                       +  l yG++g GKT +++++       g+k++++dte+ +++++  +                     s+++  d v
  gi|474934920|ref|YP_007688502.1|  10 AVTLFYGEAGCGKTNICLQMaanacrrGKKVAYVDTEGlSYDRVHQI-----FkddalmkellvfsvhSFQEQSDRV 81 
                                       66789*********************************555555544.....4444458999999888888888888 PP

                            AAA_24  57 vel..aaeladyktlviDtideleelclaevirqn 89 
                                       +++   a++  +  +v+D+ + +++l  ++++ +n
  gi|474934920|ref|YP_007688502.1|  82 EQIsrIAKNGIIGLIVVDSMTMFYRLNYDDMDMRN 116
                                       888887777779*************9988887665 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.1   8.4e-08   5.6e-05      45      87 ..       7      49 ..       5      71 .. 0.83
   2 ?    0.3   0.1      0.77   5.1e+02      88     149 ..      82     142 ..      65     146 .. 0.56

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 8.4e-08
                         IstB_IS21 45 ekkenivllGpsGvGKshlaialgveavraglsvlfvrvedLv 87
                                      e+ +  ++ G +G GK+ +   ++ +a+r+g++v +v +e L 
  gi|474934920|ref|YP_007688502.1|  7 ETGAVTLFYGEAGCGKTNICLQMAANACRRGKKVAYVDTEGLS 49
                                      566777899****************************999885 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.77
                         IstB_IS21  88 eelkrarrdgklara.lkrllkvdllilDdlgllpldqaeaellfeviekryerrsiiitsnl 149
                                       e+++r  ++g +  + +++++++  l  Dd+ + +    ++e+l++v ++ ye  +++its++
  gi|474934920|ref|YP_007688502.1|  82 EQISRIAKNGIIGLIvVDSMTMFYRLNYDDMDMRNDFIRQTEQLLHV-AREYE-IPVVITSQV 142
                                       44444444444443213444444555556666665555666777775.45565.577788875 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   4.4e-07   0.00029      25     138 ..      10     137 ..       3     140 .. 0.63

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 4.4e-07
                            AAA_16  25 elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde..aesaeleawre 99 
                                        ++l++Ge+G+GK+ +  + +  ++++g  +++ +    +++++y+ + q+++ + l+++ll    ++ +e+++  e
  gi|474934920|ref|YP_007688502.1|  10 AVTLFYGEAGCGKTNICLQMAANACRRGKKVAYVD----TEGLSYDRVHQIFKDDALMKELLVFsvHSFQEQSDRVE 82 
                                       5789*************99999***9953343333....55569999*****8877777665333334434444444 PP

                            AAA_16 100 kleeala................avpelagaeasrllellkrllallsrderplv 138
                                       ++ + ++                  + ++ + ++++ ++  +ll  +++ e p+v
  gi|474934920|ref|YP_007688502.1|  83 QISRIAKngiiglivvdsmtmfyRLNYDDMDMRNDFIRQTEQLLHVAREYEIPVV 137
                                       4444333666666666666666655555555556666666666655555555555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   6.1e-07    0.0004       2      97 ..      13     133 ..      12     150 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 6.1e-07
                                       EEESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCSSS...................STTHHHHHHHHHHHHHH CS
                               AAA   2 llyGppGtGKTllakavakel.....gvefleisgsellsk...................yvgesekkirelfkeak 54 
                                       l+yG  G+GKT ++ ++a ++     +v ++ ++g +                        ++e++++++++ + ak
  gi|474934920|ref|YP_007688502.1|  13 LFYGEAGCGKTNICLQMAANAcrrgkKVAYVDTEGLSYDRVhqifkddalmkellvfsvhSFQEQSDRVEQISRIAK 89 
                                       8*******************867655455555555555533667777777778888888889999999999999998 PP

                                       HTSTSEEEEEETGGGHHHHH..TTCCCHHHHHHHHHHHHHHHHTT CS
                               AAA  55 ekakpsilfiDEidalaksr..sgseseeeervvnqLlteldgvk 97 
                                       +      +++D +  + + +  + + +++  r  +qLl++  +++
  gi|474934920|ref|YP_007688502.1|  90 NGI-IGLIVVDSMTMFYRLNydDMDMRNDFIRQTEQLLHVAREYE 133
                                       886.79999999988887775544455555666666666665555 PP

>> Isochorismatase  Isochorismatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   4.7e-06    0.0031       3      59 ..      95     152 ..      94     178 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.7e-06
                   Isochorismatase   3 lvviDmqndfveegvkeseeisavveninkllkaarkagipviftrdvhe.leevkgd 59 
                                       l+v+D    f+   ++++   +++++++++ll+ ar+ +ipv++t +v+  +++ + +
  gi|474934920|ref|YP_007688502.1|  95 LIVVDSMTMFYRLNYDDMDMRNDFIRQTEQLLHVAREYEIPVVITSQVYTnINTGSIE 152
                                       899****999988889999999***********************9999864444444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   4.3e-06    0.0029       4     104 ..       8     105 ..       6     141 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 4.3e-06
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst..sskdllrellralglelka...erlss 75 
                                       t  +++ +Ge+G+GKT  + +++ +++++      +++v++v+  +++     +++++ +   +        + +s 
  gi|474934920|ref|YP_007688502.1|   8 TGAVTLFYGEAGCGKTNICLQMAANACRR------GKKVAYVDTEGLSydRVHQIFKDDALMKE----LlvfSVHSF 74 
                                       5678999*******************987......99999**9999995544444444333333....133435555 PP

                            AAA_22  76 eellealeqalrarav..ielliiDEaqhlr 104
                                       +e  +++eq +r ++   i+l+++D +  + 
  gi|474934920|ref|YP_007688502.1|  75 QEQSDRVEQISRIAKNgiIGLIVVDSMTMFY 105
                                       5555666666665555666999999887654 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   3.9e-06    0.0026      19      57 ..       8      46 ..       5     140 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.9e-06
                          ATPase_2 19 pneiyfiYGpegsGKtaLlkeiienledkdkyviyyial 57
                                      +  + + YG  g+GKt +  +++ n    +k+v y++  
  gi|474934920|ref|YP_007688502.1|  8 TGAVTLFYGEAGCGKTNICLQMAANACRRGKKVAYVDTE 46
                                      6778999*******************999*****99753 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.3e-05    0.0089      18      61 ..      12      55 ..       6      66 .. 0.87
   2 ?   -1.9   0.0       1.7   1.2e+03     258     285 ..     119     146 ..     115     148 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.3e-05
                     TrwB_AAD_bind 18 ilivGttGsGKtqalekllrairargdraivlDltGafvsrfyd 61
                                      +l+ G +G GKt+   ++ +++ +rg+++  +D++G  ++r ++
  gi|474934920|ref|YP_007688502.1| 12 TLFYGEAGCGKTNICLQMAANACRRGKKVAYVDTEGLSYDRVHQ 55
                                      7899********************************99998776 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.7
                     TrwB_AAD_bind 258 leelksllaegRkfGgavvlglqsiaql 285
                                       +++ ++ll  +R++ + vv++ q +  +
  gi|474934920|ref|YP_007688502.1| 119 IRQTEQLLHVAREYEIPVVITSQVYTNI 146
                                       5677899999999999999999988765 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   9.8e-06    0.0065       6      35 ..      16      45 ..      11     152 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 9.8e-06
                                      SSTTSSHHHHHHHHHHHHHHTT--EEEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  6 tkGGvGKTtlaanLaralarrglrVllvDa 35
                                      +  G GKT +++ +a+   rrg++V+ vD+
  gi|474934920|ref|YP_007688502.1| 16 GEAGCGKTNICLQMAANACRRGKKVAYVDT 45
                                      6779*************************6 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.2   2.1e-05     0.014      18      48 ..       8      38 ..       4      43 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.1e-05
                                      H-SEEEEE--TTSSTTHHHHHHHHHHHHTTS CS
                              PhoH 18 kndivfaiGpaGtGKtylavalavealkkkk 48
                                      +  ++   G+aG+GKt + +++a++a++++k
  gi|474934920|ref|YP_007688502.1|  8 TGAVTLFYGEAGCGKTNICLQMAANACRRGK 38
                                      5578999*******************99854 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.5e-05     0.017      21     133 ..       8     123 ..       5     132 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.5e-05
                                       CTS-EEEEESTTSSCHHHHHHHHHHCHCTCCCEEEEESSHHHHHCC.TSEECHHHHT-TTSSS-HHHHHHHTSCCCH CS
                              PIF1  21 kgklfFvtGsgGtgKtflwkallkklrsegkivlavAssGvAalllegGrtahsrfkiplekdeestckikrgskla 97 
                                        g +  ++G +G gKt +  ++ +    +gk+v+ v   G+    +++     +++k  l  + +   + +++s++ 
  gi|474934920|ref|YP_007688502.1|   8 TGAVTLFYGEAGCGKTNICLQMAANACRRGKKVAYVDTEGLSYDRVHQIFKDDALMKELLVFSVH---SFQEQSDRV 81 
                                       6778889***************9999999************998884444444444433333333...444455554 PP

                                       HHHHC......-SEEEEECGGGSBHHHHHHHHHHHHHHCT-. CS
                              PIF1  98 ellkk......tsliiwDEapmverecfealdrtlrdilkek 133
                                       e++++      + li++D + m  r  ++ +d     i++++
  gi|474934920|ref|YP_007688502.1|  82 EQISRiakngiIGLIVVDSMTMFYRLNYDDMDMRNDFIRQTE 123
                                       444431112224689*****************8776666654 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   9.8e-05     0.065       1      30 [.      16      45 ..      16      47 .. 0.95
   2 ?   -2.2   0.0       4.4   2.9e+03      40     111 ..      90     101 ..      66     126 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.8e-05
                            CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDl 30
                                      G+  +GK+ ++  ++ +a+r+g+k++yvD+
  gi|474934920|ref|YP_007688502.1| 16 GEAGCGKTNICLQMAANACRRGKKVAYVDT 45
                                      78899************************7 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.4
                            CLP1_P  40 PgtislalverpidveegfsldaplvyffGdtspsdnpslylalvkelareveekleenkkakasgliIntp 111
                                       +g+i+l                                                            ++++++
  gi|474934920|ref|YP_007688502.1|  90 NGIIGL------------------------------------------------------------IVVDSM 101
                                       233333............................................................333333 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00016      0.11       3      35 ..      11      43 ..       9     101 .. 0.86
   2 ?   -1.1   0.0       1.9   1.2e+03      45      61 ..     122     138 ..     114     168 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEE CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllv 35
                                      v+l+ G  G GKT  + ++aa   ++gkkv+ v
  gi|474934920|ref|YP_007688502.1| 11 VTLFYGEAGCGKTNICLQMAANACRRGKKVAYV 43
                                      889**************************9876 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHTTEEEEE CS
                             SRP54  45 veQLktlaeklgvpvik 61 
                                       +eQL ++a+++++pv+ 
  gi|474934920|ref|YP_007688502.1| 122 TEQLLHVAREYEIPVVI 138
                                       47777777777777664 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00013     0.087      38      87 ..      13      60 ..       9      70 .. 0.79
   2 ?   -2.8   0.0       6.8   4.5e+03     163     201 ..     107     145 ..     100     148 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
                                      EEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT- CS
                          Bac_DnaA 38 fiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkk 87
                                      ++yge G Gkt +      ++ +  + ++v Y+ +e    + v+ + +++
  gi|474934920|ref|YP_007688502.1| 13 LFYGEAGCGKTNICLQ--MAANACRRGKKVAYVDTEGLSYDRVHQIFKDD 60
                                      79*********98544..4444556899********99999988876554 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6.8
                                       -----HHHHHHHHHHHHHHTT----TTHHHHHHHH--S- CS
                          Bac_DnaA 163 ieppdletrlailkkkieaeklevpeevlefiaervtdn 201
                                       ++  d+++r + +++  +  ++    e+   i+++v +n
  gi|474934920|ref|YP_007688502.1| 107 LNYDDMDMRNDFIRQTEQLLHVAREYEIPVVITSQVYTN 145
                                       566677777777777777666666666666666666555 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0    0.0002      0.13       2      26 ..      13      37 ..      12      59 .. 0.85
   2 ?   -1.9   0.0       6.4   4.2e+03      67      96 ..     109     138 ..      97     145 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0002
                      RNA_helicase  2 wlyGpsgeGKStlakeLakallkkl 26
                                      ++yG++g+GK++++ ++a++ +++ 
  gi|474934920|ref|YP_007688502.1| 13 LFYGEAGCGKTNICLQMAANACRRG 37
                                      69**************999988554 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 6.4
                      RNA_helicase  67 psdlaelirlvsstpyplnmasleekgtlf 96 
                                       ++d+ + +  +  t+  l++a+  e  +++
  gi|474934920|ref|YP_007688502.1| 109 YDDMDMRNDFIRQTEQLLHVAREYEIPVVI 138
                                       334444444444444444444444444444 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   9.7e-05     0.064      12      40 ..      19      47 ..      10     140 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.7e-05
                            AAA_31 12 GvGKTTtsvnlaaalaklgkkvLlvDlDp 40
                                      G GKT  ++++aa   ++gkkv  vD   
  gi|474934920|ref|YP_007688502.1| 19 GCGKTNICLQMAANACRRGKKVAYVDTEG 47
                                      99************************875 PP

>> Hpr_kinase_N  HPr Serine kinase N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00018      0.12      66     125 .]      77     154 ..      71     154 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00018
                                       HHHH..HHHHHHTT--S-EEEETTT-..................--HHHHHHHHHH---EEEESS-HHHHHTTHHHH CS
                      Hpr_kinase_N  66 eeerkerleklfskkipciiltrgle..................ppeellelaeeygvpllrtklstsefiaeliry 124
                                       +++r e+++++ + +i  +i+ ++++                   +e+ll +a+ey++p++ t++  +++ +  i++
  gi|474934920|ref|YP_007688502.1|  77 QSDRVEQISRIAKNGIIGLIVVDSMTmfyrlnyddmdmrndfirQTEQLLHVAREYEIPVVITSQVYTNINTGSIEF 153
                                       568999999999999999999999999999999999999999999*******************9999998877776 PP

                                       H CS
                      Hpr_kinase_N 125 L 125
                                       L
  gi|474934920|ref|YP_007688502.1| 154 L 154
                                       6 PP

>> CobA_CobO_BtuR  ATP:corrinoid adenosyltransferase BtuR/CobO/CobP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   1.9    0.0058       3.9       2     127 ..       8     123 ..       7     131 .. 0.54

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0058
                    CobA_CobO_BtuR   2 kglihvytGd.GKGKttAAlGlalRalgaglkvlvvqFlKgekesgEl.aalkkleielerlgkegfvkmeeeekee 76 
                                       +g + +++G+ G GKt   l +a  a+ +g+kv++v     +  ++ + +++k  +  +++l    f         +
  gi|474934920|ref|YP_007688502.1|   8 TGAVTLFYGEaGCGKTNICLQMAANACRRGKKVAYVDTEGLS--YDRVhQIFKD-DALMKELL--VFS---V----H 72 
                                       688889999658999999999999999999999887532221..2211011111.11111111..122...1....1 PP

                    CobA_CobO_BtuR  77 daaaakealekakealaseeydlvvlDEinyalklglldeeevlellkkkp 127
                                         ++ ++ +e++ + ++++ + l+v+D +++ ++l++ d++   +++++ +
  gi|474934920|ref|YP_007688502.1|  73 SFQEQSDRVEQISRIAKNGIIGLIVVDSMTMFYRLNYDDMDMRNDFIRQTE 123
                                       222333334444444444556666666666666666666666666666655 PP

>> PucR  Purine catabolism regulatory protein-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00038      0.25      42     101 ..      64     140 ..      47     148 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00038
                              PucR  42 geLllttglalkddpealaelvrelaeagvaaLviklg.......r...........eipeelieaadelglPliel 100
                                       +eLl+ +  +++ ++++  e + ++a+ g+ +L++          +           +  e+l+++a+e+++P++  
  gi|474934920|ref|YP_007688502.1|  64 KELLVFSVHSFQ-EQSDRVEQISRIAKNGIIGLIVVDSmtmfyrlNyddmdmrndfiRQTEQLLHVAREYEIPVVIT 139
                                       699999999**8.8899999***************9976777644144443334444446*************9976 PP

                              PucR 101 p 101
                                       +
  gi|474934920|ref|YP_007688502.1| 140 S 140
                                       5 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0    0.0003       0.2       7      79 ..       5      71 ..       2     145 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0003
                                      EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  7 klkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren 79
                                       ++ g ++ + Ge G+GK+ ++  +a +      ++ +       +++  +  ++  +++++ l +el v + 
  gi|474934920|ref|YP_007688502.1|  5 GIETGAVTLFYGEAGCGKTNICLQMAANACRRGKKVAYV------DTEGLSYDRVHQIFKDDALMKELLVFSV 71
                                      5889*****************999988876655555333......2233334444444444444444444444 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00035      0.23      13      87 ..       8      81 ..       5      92 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00035
                                      TT-EEEEEESTTSSHHHHHHHHHHHSSTSS.EEEEEEESEEHHHHHHHHHHCHHSSGGGGEEEEEEETTS-HHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab 13 qGqrtlipgafgvGktvisqslskqsnsdd.aiiyvgiGergnevaevleefpegtimkrtvlvantsnepvaare 87
                                       G  tl  g++g+Gkt i+ +++ ++  +   + y  +   g +  +v + f+++ +mk+  ++  +s +    r+
  gi|474934920|ref|YP_007688502.1|  8 TGAVTLFYGEAGCGKTNICLQMAANACRRGkKVAY--VDTEGLSYDRVHQIFKDDALMKELLVFSVHSFQEQSDRV 81
                                      68889999***********6666665555324444..567788888888888888888888888777766666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       800  (0.0446204); expected 358.6 (0.02)
Passed bias filter:                      669  (0.0373138); expected 358.6 (0.02)
Passed Vit filter:                       117  (0.00652574); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 1464.88
//
Query:       gi|474934921|ref|YP_007688503.1|  [L=211]
Description: Mn2+-dependent serine/threonine protein kinase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-09   38.6   1.0    0.00014   21.9   0.1    2.1  2  APH             Phosphotransferase enzyme family
    9.7e-09   35.1   0.0    1.3e-08   34.7   0.0    1.2  1  RIO1            RIO1 family
    9.9e-09   34.8   0.0    1.5e-08   34.3   0.0    1.2  1  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
    2.1e-07   30.6   0.0    2.2e-07   30.5   0.0    1.2  1  Pkinase         Protein kinase domain
    9.5e-05   21.8   0.0    0.00011   21.6   0.0    1.1  1  Pkinase_Tyr     Protein tyrosine kinase
      0.002   17.8   0.0     0.0028   17.3   0.0    1.3  1  Choline_kinase  Choline/ethanolamine kinase
  ------ inclusion threshold ------
        0.2   10.9   0.1        1.9    7.7   0.1    2.0  2  EcKinase        Ecdysteroid kinase


Domain annotation for each model (and alignments):
>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.1   5.4e-08   0.00014      33     108 ..      49     121 ..       9     124 .. 0.74
   2 !   16.4   0.0   2.6e-06    0.0067     168     194 ..     123     147 ..     120     192 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 5.4e-08
                                       -HHHHHHHHHHHHHHHHTT-B--B-CTTBS-EEETTEEEEEEE----EE-SSHHHHHHHHHHHHHHHHHHCCHHCH CS
                               APH  33 aaeeirrevallrlLakagvpvPevlagdtddeeigllfalieyvpgrsllrklsaaqlpellealgeflaalhqv 108
                                         ++ir+e+++ r  + ag+++P+++  dt ++ i   ++ i +v ++ +l+ +++++++++++++g  la lh++
  gi|474934921|ref|YP_007688503.1|  49 RSRRIRAEARIIRDARLAGLRTPVIYSVDTVEGSIV--MEDIRGVTAKRFLD-ENPSEAERVCRQIGHNLALLHNA 121
                                       56789999999999999999*******655555555..77777777777777.9********************98 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 2.6e-06
                                       EE-SS-SGGGEEEC..TTEEEEE---T CS
                               APH 168 llHgDlhpgNllvdpddgrvtGviDfe 194
                                       l HgDl + N++v  +dgr+ ++iDf 
  gi|474934921|ref|YP_007688503.1| 123 LSHGDLTTSNIIVM-EDGRL-CFIDFS 147
                                       78************.99**9.*****4 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.0   4.9e-12   1.3e-08      56     150 ..      54     147 ..      37     176 .. 0.86

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 4.9e-12
                                       HHHHHHHHHHHHTT--S--EEEE..ETTEEEEE--EETTEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHHTSTEEES CS
                              RIO1  56 ekEfrnLkrleeagvpvPkpiel..krhvlvmefigedgvaapklkdveeeeeaeelyeevleemrklykeaglvHa 130
                                       + E r+++ ++ ag++ P  + +   +  +vme i   gv a++  d +  +eae++ +++ ++++ l+++a+l H+
  gi|474934921|ref|YP_007688503.1|  54 RAEARIIRDARLAGLRTPVIYSVdtVEGSIVMEDIR--GVTAKRFLDEN-PSEAERVCRQIGHNLA-LLHNANLSHG 126
                                       67899999999999999976655116899*******..******99999.89*********99866.556******* PP

                                       S-STTSEEEETT.EEEE--GT CS
                              RIO1 131 DLSeyNvlvded.kvviIDvs 150
                                       DL   N++v ed ++ +ID+s
  gi|474934921|ref|YP_007688503.1| 127 DLTTSNIIVMEDgRLCFIDFS 147
                                       **********999******98 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.0   5.8e-12   1.5e-08      53     195 ..      48     174 ..      38     187 .. 0.82

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 5.8e-12
                               Kdo  53 lgrtravrEfrllkrLeeagvavpkpvaagavkvgleyrAlllterlegaqdLedllakwaelaeelkrallkavgr 129
                                       +   r+++E r+++  + ag+++p  v + +  v++     +++e++ g+   + +l +    + +  ++  +++g 
  gi|474934921|ref|YP_007688503.1|  48 IRSRRIRAEARIIRDARLAGLRTP--VIYSVDTVEG----SIVMEDIRGVTA-KRFLDE----NPSEAERVCRQIGH 113
                                       55678999999**99999999986..6666666665....69*******986.555655....6888999******* PP

                               Kdo 130 liaklhragvnHadlyaknillqqeeeeeaeiwliDldkarlrlradrwrekdLarLkrsflkiel 195
                                         a lh+a++ H+dl   ni + +++    ++++iD+  ++  + ++ +   d++ L+r f + + 
  gi|474934921|ref|YP_007688503.1| 114 NLALLHNANLSHGDLTTSNIIVMEDG----RLCFIDFSMGNSLV-ETEDMGVDIRLLERAFSSAHP 174
                                       **************************....********999888.899999999999999884433 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   8.8e-11   2.2e-07      44     153 ..      52     157 ..      13     189 .. 0.84

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 8.8e-11
                                       HHHHHHHHHHHHSCTTB--EEEEEEESSEEEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE CS
                           Pkinase  44 kvlrEikilkklkhpnivrlyevfeekdelylvleyveggeladllerkgslseeeakkiakqilegleylHskgii 120
                                       ++++E +i++  +   + + + +  ++ e  +v+e ++g + +++l +    +++ea+++++qi + l+ lH++++ 
  gi|474934921|ref|YP_007688503.1|  52 RIRAEARIIRDARLAGLRTPVIYSVDTVEGSIVMEDIRGVTAKRFLDE----NPSEAERVCRQIGHNLALLHNANLS 124
                                       566666666666655555555555566677789999998888888875....7889********************* PP

                                       -SS-SGGGEEEETTTEEEE-SGTTSEESSSSCS CS
                           Pkinase 121 HrDlKpeNiLidekgelKitDFGlakelesssk 153
                                       H Dl ++Ni++ e+g l  +DF + + l ++++
  gi|474934921|ref|YP_007688503.1| 125 HGDLTTSNIIVMEDGRLCFIDFSMGNSLVETED 157
                                       **********************99998887765 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   4.2e-08   0.00011      51     157 ..      56     156 ..       8     164 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 4.2e-08
                                       HHHHHHTS-BTTB--EEEEEESSSSEEEEEE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEES CS
                       Pkinase_Tyr  51 eakimkklkhpnivkllgvctkeepllivteyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHr 127
                                       ea+i+++ +   +   +   +++ +  iv+e ++g + + fL ++       ++  +++ q+ + ++ L++ +l H 
  gi|474934921|ref|YP_007688503.1|  56 EARIIRDARLAGLRTPVIYSVDTVEGSIVMEDIRGVTAKRFLDEN------PSEAERVCRQIGHNLALLHNANLSHG 126
                                       555555555555444444444555667888888888888888888......6667789******************* PP

                                       T-SGGGEEEEETTEEEE-STTTHEETTTSS CS
                       Pkinase_Tyr 128 dlaarNvLlsenkvvkisDfGLardiekdd 157
                                       dl++ N+++ e+      Df + +++ +++
  gi|474934921|ref|YP_007688503.1| 127 DLTTSNIIVMEDGRLCFIDFSMGNSLVETE 156
                                       *********************998886555 PP

>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.1e-06    0.0028     144     171 ..     120     146 ..      86     171 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.1e-06
                                       -EEEE-S--SGGGEEE.-CTTEEEE--G CS
                    Choline_kinase 144 pvvfcHnDlqegNillnkeekklvlIDF 171
                                       + +++H Dl  +Ni++  e+++l++IDF
  gi|474934921|ref|YP_007688503.1| 120 NANLSHGDLTTSNIIV-MEDGRLCFIDF 146
                                       37899***********.9********** PP

>> EcKinase  Ecdysteroid kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.066   1.7e+02      67     122 ..      59     109 ..      42     122 .. 0.67
   2 ?    7.7   0.1   0.00073       1.9     216     248 ..     122     149 ..     117     190 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.066
                          EcKinase  67 llreagdefklapkcykaeeeeeeevlvleDLkekgyknadRlkgldlehlklvlk 122
                                       ++r+a      +p +y +++ e+   +v+eD++      a+R    +  ++++v +
  gi|474934921|ref|YP_007688503.1|  59 IIRDARLAGLRTPVIYSVDTVEG--SIVMEDIRGVT---AKRFLDENPSEAERVCR 109
                                       55566556666899999998888..9*****98743...44444444444444444 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00073
                          EcKinase 216 vlnHGDlwvnNimfkydeegepedvilvDFQls 248
                                        l HGDl ++Ni++  d      +++++DF + 
  gi|474934921|ref|YP_007688503.1| 122 NLSHGDLTTSNIIVMEDG-----RLCFIDFSMG 149
                                       599***********8775.....4999*99764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1508.00
//
Query:       gi|474934922|ref|YP_007688504.1|  [L=185]
Description: dITPase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.3e-45  154.8   0.0    2.6e-45  154.6   0.0    1.0  1  Ham1p_like  Ham1 family


Domain annotation for each model (and alignments):
>> Ham1p_like  Ham1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.6   0.0   1.5e-49   2.6e-45       1     186 [.       3     177 ..       3     178 .. 0.84

  Alignments for each domain:
  == domain 1  score: 154.6 bits;  conditional E-value: 1.5e-49
                                       EEEC-S-HHHHHHHHHHTTTECCCE.EECCCCEE----BS.SSHHHHHHHHHHHHHHHTS-.EEEEEEEEEEGGGTT CS
                        Ham1p_like   1 ivfaTgNkgKlrevkeilaeellevkslkelelpeveEtq.gtfeenalkKaraaaeaglp.vladDsgLevdaLng 75 
                                       ++++T+N+gK+re +  +++ ++e++++    + e++E+q + +ee++ k ++++  +gl  +++dDsgL+v+aL+g
  gi|474934922|ref|YP_007688504.1|   3 LNVVTHNPGKVREYQLAFDGFGVEMVHV----NREYDEVQtAYLEEVVDKGMKQLHGEGLRdFMIDDSGLFVEALGG 75 
                                       679***********99998888888877....56788***5555556666666666455556*************** PP

                                       TBGGGTTTTTHTTCHHHHHHHHHHHHCTHTTS--EEEEEEEEEEEETTTTEEEEEEEEEEEEE-SS.--SSSSTTGG CS
                        Ham1p_like  76 lPGvysarfagegaedeenlaklleeleeeeedrsArfvcvlaladpeeeeellfeGeveGeiveeprgeggfGyDp 152
                                       +PGvysa+ ++     + ++a +l+ +e++e dr+A f+c++++  + +e+ ++++G++ G i+ e+rgeggfGyDp
  gi|474934922|ref|YP_007688504.1|  76 FPGVYSAYGQK-----TIGNAGILKLMEGVE-DRRAVFKCCIGCWVG-DER-IVVTGKCPGYILFEERGEGGFGYDP 144
                                       *******8743.....456777777776544.8*********99775.555.9************************ PP

                                       GEEETT-SSBTTTS.CHHHHHHSHHHHHHHHHHH CS
                        Ham1p_like 153 iFvpeegektfaelskeeknaiShRgkAleklle 186
                                       iF p +ge++fae++++ekn iShRg A + l++
  gi|474934922|ref|YP_007688504.1| 145 IFTP-DGEHSFAEIPTDEKNVISHRGLATKMLID 177
                                       ****.7689********************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1302.15
//
Query:       gi|474934923|ref|YP_007688505.1|  [L=203]
Description: hypothetical protein TALC_01366 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00039   20.4   1.7    0.00083   19.3   1.7    1.7  1  VIT1         VIT family
  ------ inclusion threshold ------
       0.41   10.3   3.7          8    6.2   0.7    2.4  2  Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase cha


Domain annotation for each model (and alignments):
>> VIT1  VIT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   1.7   9.3e-08   0.00083      90     194 ..      76     182 ..       2     202 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 9.3e-08
                              VIT1  90 learglseelaqevaaellk.npdallelmlreelg..psaseelasplkaAlssalsfliGgliPllpylfvesvg 163
                                       +++  +se +a+  ++ + +  +d++ +l+l+ + +  p a  ++ + + +A+  ++  ++ ++ P l +lf+++++
  gi|474934923|ref|YP_007688505.1|  76 YRDEVVSELDATI-VDLMDDrTKDEIIDLVLQGKINhkPLA-GRYRQYFVNAMGAFAVTFTTAIPPALCVLFISDQT 150
                                       4444444444422.332222255556666666554422333.445567889************************** PP

                              VIT1 164 lalvvsiavtllalllfGavkalltgssk.lv 194
                                       +a++++   +++ ++++G+  a +  ++  +v
  gi|474934923|ref|YP_007688505.1| 151 DAFFWASFTSSVLMFFIGYYFAPFKALWAkAV 182
                                       *******************9887775444333 PP

>> Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1    0.0019        17       3      49 ..      10      56 ..       7     147 .. 0.80
   2 ?    6.2   0.7   0.00089         8       4      44 ..     159     199 ..     156     201 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0019
                                      HHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHHHHHHHC. CS
                       Oxidored_q2  3 llliallfliGlygvllrrnllkvliglelisnavnlllvlagvfte 49
                                      +l+++++  +G++    rr l+  +++++++  a+ ++ +  +  t 
  gi|474934923|ref|YP_007688505.1| 10 ALTLVTAAQLGIVHYDERRTLIIAILAMDFVWGAIDMFAFFRSDVTA 56
                                      444555555555555559*****************999988777764 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.00089
                                       HHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHHHH CS
                       Oxidored_q2   4 lliallfliGlygvllrrnllkvliglelisnavnlllvla 44 
                                       + ++l+f+iG y   ++    k + gl l+++a+ l++++a
  gi|474934923|ref|YP_007688505.1| 159 TSSVLMFFIGYYFAPFKALWAKAVWGLTLVGTALSLTFFAA 199
                                       5689*********************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       777  (0.0433376); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1474.36
//
Query:       gi|474934924|ref|YP_007688506.1|  [L=123]
Description: MarR family [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-05   24.7   0.2      5e-05   23.7   0.0    1.6  2  HTH_27        Winged helix DNA-binding domain
     0.0012   18.9   0.0     0.0028   17.7   0.0    1.6  1  HTH_20        Helix-turn-helix domain
     0.0017   18.3   0.0     0.0034   17.3   0.0    1.6  1  HTH_Crp_2     Crp-like helix-turn-helix domain
     0.0017   18.3   0.2     0.0071   16.2   0.0    1.9  2  MarR          MarR family
     0.0033   17.3   0.1     0.0067   16.3   0.0    1.5  2  MarR_2        MarR family
  ------ inclusion threshold ------
      0.013   15.1   0.1      0.082   12.5   0.0    1.9  2  SMC_ScpB      Segregation and condensation complex subunit Sc
      0.031   13.8   0.1      0.097   12.2   0.0    1.8  2  HTH_24        Winged helix-turn-helix DNA-binding
      0.066   13.3   0.0      0.083   13.0   0.0    1.1  1  Replic_Relax  Replication-relaxation
       0.11   12.4   0.2       0.39   10.6   0.0    1.9  2  HTH_5         Bacterial regulatory protein, arsR family


Domain annotation for each model (and alignments):
>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   2.5e-08     5e-05      16      68 .]       2      53 ..       1      53 [. 0.92
   2 ?   -2.5   0.0       3.9   7.7e+03      18      28 ..      97     107 ..      91     109 .. 0.54

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.5e-08
                            HTH_27 16 rrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      r++ ++++lc  l v+++++s ++ ++ e+G +++ ++  ++r+  ++lT+kG
  gi|474934924|ref|YP_007688506.1|  2 RAPLTEKQLCHLLGVDKANTSRAVMAMLEAGIIKKGRK-VSGRSYEFELTEKG 53
                                      788999***************************55555.8************9 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.9
                            HTH_27  18 rkkladlcgrl 28 
                                         ++a+++  l
  gi|474934924|ref|YP_007688506.1|  97 DLEIAEIIAQL 107
                                       44555555544 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.4e-06    0.0028      22      56 ..       2      36 ..       1      39 [. 0.93

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.4e-06
                                      CTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20 22 aegltaselaerldlskntlsyHLrvLeeagLvev 56
                                      +++lt ++l+++l+++k++ s+ + ++ eag+++ 
  gi|474934924|ref|YP_007688506.1|  2 RAPLTEKQLCHLLGVDKANTSRAVMAMLEAGIIKK 36
                                      689*****************************985 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.7e-06    0.0034      20      56 ..       3      39 ..       1      46 [. 0.90

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.7e-06
                                      EEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEE CS
                         HTH_Crp_2 20 lpltqeelAsmlGltretvsrilseLkreglisrgrr 56
                                       plt ++l ++lG+    +sr+  ++ ++g+i++gr+
  gi|474934924|ref|YP_007688506.1|  3 APLTEKQLCHLLGVDKANTSRAVMAMLEAGIIKKGRK 39
                                      59*******************************8753 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   3.6e-06    0.0071      17      52 ..       4      39 ..       2      43 .. 0.91
   2 ?   -0.7   0.0      0.71   1.4e+03      11      28 ..      91     108 ..      90     111 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.6e-06
                                      TEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
                              MarR 17 plsvseLakklgvskstvtrvldrLekkGlieRsks 52
                                      pl+ ++L   lgv+k++++r++ ++ ++G i++ ++
  gi|474934924|ref|YP_007688506.1|  4 PLTEKQLCHLLGVDKANTSRAVMAMLEAGIIKKGRK 39
                                      78999**************************98765 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.71
                                       HHHHSTTEEHHHHHHHHT CS
                              MarR  11 ilyeqgplsvseLakklg 28 
                                       ++++q++l ++e+  +l+
  gi|474934924|ref|YP_007688506.1|  91 CIASQEDLEIAEIIAQLK 108
                                       889999999999977776 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   3.4e-06    0.0067      19      53 ..       4      36 ..       1      44 [. 0.87
   2 ?   -2.8   0.0       3.1   6.1e+03      21      32 ..      97     108 ..      86     109 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.4e-06
                                      TSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2 19 grdltvgelarrlglsksavsrilkrLvaaGLver 53
                                      +  lt ++l+  lg++k+++sr++  + +aG + +
  gi|474934924|ref|YP_007688506.1|  4 P--LTEKQLCHLLGVDKANTSRAVMAMLEAGIIKK 36
                                      4..88899************************976 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.1
                                       EEEHHHHHHHHT CS
                            MarR_2  21 dltvgelarrlg 32 
                                       dl ++e+ + l+
  gi|474934924|ref|YP_007688506.1|  97 DLEIAEIIAQLK 108
                                       466777777776 PP

>> SMC_ScpB  Segregation and condensation complex subunit ScpB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.1e-05     0.082      95     144 ..       2      52 ..       1      60 [. 0.85
   2 ?    0.7   0.0      0.18   3.6e+02      25      65 ..      75     115 ..      62     121 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.1e-05
                          SMC_ScpB  95 kqpvtraeieeiRGvn...sdsvvrtLlerglieekgrkeepgrpilYgtTek 144
                                       + p+t +++ ++ Gv+   ++++v  +le g+i++ +  +++gr++ +++Tek
  gi|474934924|ref|YP_007688506.1|   2 RAPLTEKQLCHLLGVDkanTSRAVMAMLEAGIIKKGR--KVSGRSYEFELTEK 52 
                                       67999999999999875447899**********9988..679*********98 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.18
                          SMC_ScpB  25 lskeeveealeeLkeeyeeedrglelvevaggyrlvtkpel 65 
                                       +  ee+ + l  +++ + ++++ le+ e+  + +lv+  ++
  gi|474934924|ref|YP_007688506.1|  75 IPDEEMLAFLSVMEKICIASQEDLEIAEIIAQLKLVVGRKV 115
                                       55677777777777777777777777777666666665555 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.9e-05     0.097      18      48 .]       5      35 ..       3      35 .. 0.94
   2 ?   -2.4   0.0       1.8   3.6e+03      18      27 ..      98     107 ..      91     112 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.9e-05
                            HTH_24 18 isqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      ++ ++L+  lg+ +++++r +  + e+G+Ik
  gi|474934924|ref|YP_007688506.1|  5 LTEKQLCHLLGVDKANTSRAVMAMLEAGIIK 35
                                      6789**************************8 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.8
                            HTH_24  18 isqreLAerl 27 
                                       + ++e+  +l
  gi|474934924|ref|YP_007688506.1|  98 LEIAEIIAQL 107
                                       4455555555 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.1e-05     0.083       9      68 ..       4      56 ..       2      74 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.1e-05
                      Replic_Relax  9 vlTtrqiarllfashratarrrLarLrelgllsrlrkrvggarggsepyvYaLtpkGarl 68
                                      +lT++q+ +ll  ++ +t r ++a L e g++++ rk     +   ++y + Lt+kG+++
  gi|474934924|ref|YP_007688506.1|  4 PLTEKQLCHLLGVDKANTSRAVMAML-EAGIIKKGRKV---SG---RSYEFELTEKGHEI 56
                                      69***************777788887.999****7777...33...3799*******986 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0    0.0002      0.39      14      47 .]       3      36 ..       1      36 [. 0.92
   2 ?   -1.0   0.1      0.84   1.7e+03      14      27 ..      96     109 ..      90     112 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0002
                                      SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5 14 gelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                       +l+  +l+  lg+ ++++S+   ++ eaG+++k
  gi|474934924|ref|YP_007688506.1|  3 APLTEKQLCHLLGVDKANTSRAVMAMLEAGIIKK 36
                                      688999*************************986 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.84
                                       SSEEHHHHHHHHTS CS
                             HTH_5  14 gelcvcelaeelgl 27 
                                       + l + e+ ++l+l
  gi|474934924|ref|YP_007688506.1|  96 EDLEIAEIIAQLKL 109
                                       55888899999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.50
# Mc/sec: 740.97
//
Query:       gi|474934925|ref|YP_007688507.1|  [L=66]
Description: hypothetical protein TALC_01368 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 449.21
//
Query:       gi|474934926|ref|YP_007688508.1|  [L=281]
Description: hypothetical protein TALC_01369 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-08   34.9   0.0      2e-08   34.2   0.0    1.3  1  bPH_5     Bacterial PH domain
  ------ inclusion threshold ------
       0.02   14.8   3.4      0.085   12.7   3.4    2.1  1  DUF4027   Protein of unknown function (DUF4027)


Domain annotation for each model (and alignments):
>> bPH_5  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0   2.2e-12     2e-08       3      84 ..     180     262 ..     178     279 .. 0.90

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 2.2e-12
                             bPH_5   3 yildeeglvIrwifgkeeIplseIeavrvsegvikgvrlfgtskpgyalGrfkikdigkarmyatr.lkrvlllktk 78 
                                       ++  e+++ I+ ++  e++ +s+I+++r + ++  g r++g+++ + ++G+f+  d+g++++ a +  +  ++++t 
  gi|474934926|ref|YP_007688508.1| 180 VTAGEDSVAIKAPMVSETVRYSDITEIRMDADFHHGTRISGYGGSSIHSGTFRNSDLGTYTLAAYSsCDACIVIHTS 256
                                       56678999********************************************************998999******9 PP

                             bPH_5  79 dkiygi 84 
                                        + +++
  gi|474934926|ref|YP_007688508.1| 257 GGYIAF 262
                                       877665 PP

>> DUF4027  Protein of unknown function (DUF4027)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   3.4   9.5e-06     0.085      13      28 ..      81      96 ..      79     102 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.5e-06
                           DUF4027 13 VsLICLGGFvaSVlLA 28
                                      Vs ICLGG  +SVlL 
  gi|474934926|ref|YP_007688508.1| 81 VSRICLGGILSSVLLC 96
                                      899***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       737  (0.0411066); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1676.61
//
Query:       gi|474934927|ref|YP_007688509.1|  [L=745]
Description: Lhr-like helicase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.6e-24   84.6   0.0    4.8e-23   81.8   0.0    2.1  2  DEAD        DEAD/DEAH box helicase
    1.6e-15   57.4   0.0    9.5e-15   54.9   0.0    2.2  2  Helicase_C  Helicase conserved C-terminal domain
    0.00084   19.4   0.0     0.0014   18.6   0.0    1.3  1  ResIII      Type III restriction enzyme, res subunit


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.8   0.0   8.1e-27   4.8e-23       3     170 ..      28     196 ..      26     201 .. 0.91
   2 ?    0.1   0.0     0.097   5.8e+02      44      73 ..     272     301 ..     247     347 .. 0.69

  Alignments for each domain:
  == domain 1  score: 81.8 bits;  conditional E-value: 8.1e-27
                                       HHHHHHHHHH.TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEE CS
                                       xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   3 iQaeaiplil.gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrv 78 
                                       iQ +a ++i  ++++vl+ a T+sGKT+a+++p+l  ++e +      a+++ P+++L+++++++l+++++++d+ v
  gi|474934927|ref|YP_007688509.1|  28 IQMAAADAIFnSEENVLLTASTASGKTEAAFFPILTLLSE-NPPASVGAIYIGPLKALINDQFERLNQLCQEADIPV 103
                                       89999999996678*********************99987.8899999***************************** PP

                                       EEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHH..HCTSSH..CTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  79 lliiggvaardqlskldngvdivvgtpgrlddll..stgkln..lsqvrflVlDEadrlldqgfsdfinrilnqlpq 151
                                         + g+v+++++ + +++   i+  tp+ l  +l  + g +   + ++rf+V+DE++ l   +++ +   i+++l++
  gi|474934927|ref|YP_007688509.1| 104 WHWHGDVNQSHKEKFIRHPSGILQITPESLEGMLlhKHGDIVrlFGDLRFIVIDEVHSLIRGDRGGQTLCIIERLSR 180
                                       ****************777*************886766776678*******************************87 PP

                                       HCTTSTTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxxxxxxx RF
                              DEAD 152 itcdgklqrqvivlSATlp 170
                                            +   + i lSAT+ 
  gi|474934927|ref|YP_007688509.1| 181 LAGCNP---RRIGLSATIG 196
                                       766555...59******86 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.097
                                       TSTS-EEEEEESSHHHHHHHHHHHHHHTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  44 gktgpkalivePtreLaeqtlnnlkkfkky 73 
                                       ++ g+k+li + +re +e ++++l+ +++ 
  gi|474934927|ref|YP_007688509.1| 272 HTLGKKCLIFSNSREECEAVCSTLRHYCED 301
                                       566789999999999999999999988874 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.38   2.3e+03      32      60 ..      92     120 ..      82     125 .. 0.77
   2 !   54.9   0.0   1.6e-18   9.5e-15      13     111 .]     272     377 ..     265     377 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.38
                                       HHHHHHHTTSTEEEESTTSTHHHHHHHHH CS
                        Helicase_C  32 vklllekkgikvavlhgelpqnereeile 60 
                                       ++ l+++ +i v   hg+ +q+++e+ ++
  gi|474934927|ref|YP_007688509.1|  92 LNQLCQEADIPVWHWHGDVNQSHKEKFIR 120
                                       35566666899************999886 PP

  == domain 2  score: 54.9 bits;  conditional E-value: 1.6e-18
                                       TTTTSEEEEEESSHHHHHH....HHHHHHHT..TSTEEEESTTSTHHHHHHHHHHHHTTSSS.EEEESGGGTSSSTS CS
                        Helicase_C  13 eeeggkilifvntidrlek....vklllekk..gikvavlhgelpqnereeileqfnkgesd.vLiatdvaerGidi 82 
                                       +  g+k+lif+n+++++e     ++  +e k    ++ ++hg+++   re + ++++++e++  + +t  +e Gid+
  gi|474934927|ref|YP_007688509.1| 272 HTLGKKCLIFSNSREECEAvcstLRHYCEDKgePDRFMIHHGNISPALRETAEKAMKDEERNlSICTTATLELGIDV 348
                                       55699************9885553333555556699**********************9***89999999******* PP

                                       TTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                        Helicase_C  83 pkvnlVinfdlprnvtsyiqriGRtgRag 111
                                        +++  +++d+p++v+ + qr+GRtgR g
  gi|474934927|ref|YP_007688509.1| 349 GRLERAFQIDAPWTVSAFLQRMGRTGRRG 377
                                       ***************************75 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   2.4e-07    0.0014       5     169 ..      26     195 ..      18     197 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.4e-07
                                       -HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.......-EEEEESSHHHHHHHHHHGGGGTG CS
                            ResIII   5 reyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkee..kflflvprkslleqtleefkkfls 79 
                                       r  Q+ a +++      + ++++l+ + T +GKT  a+  i  ll++++     ++ + p k+l++   e+++++ +
  gi|474934927|ref|YP_007688509.1|  26 RGIQMAAADAIF-----NSEENVLLTASTASGKTEAAFFPILTLLSENPPAsvGAIYIGPLKALINDQFERLNQLCQ 97 
                                       444555555554.....8999****************888877777666556899*********************9 PP

                                       G........GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T...T CS
                            ResIII  80 eayke....igkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk...s 149
                                       ea+      +g + ++ k+k+    ++ + il +t +sl   +  ++  +   l +   +i+iDE+H l + +   +
  gi|474934927|ref|YP_007688509.1|  98 EADIPvwhwHGDVNQSHKEKF---IRHPSGILQITPESLEGML-LHKHGDIVRLFGDLRFIVIDEVHSLIRGDrggQ 170
                                       996545554333333333333...5677888889999999988.445555555666666***********9855432 PP

                                       THHHHHT---.....SEEEEEESS- CS
                            ResIII 150 wreilekfke.....avllglTATp 169
                                          i+e +++       ++gl+AT+
  gi|474934927|ref|YP_007688509.1| 171 TLCIIERLSRlagcnPRRIGLSATI 195
                                       222466665566666999*****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (745 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 4903.22
//
Query:       gi|474934928|ref|YP_007688510.1|  [L=434]
Description: hypothetical protein TALC_01371 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   1.3e-170  567.8   0.0   1.4e-170  567.6   0.0    1.0  1  DUF2791     P-loop Domain of unknown function (DUF2791)
      1e-05   26.0   0.0    3.5e-05   24.3   0.0    1.9  2  AAA_16      AAA ATPase domain
     0.0052   17.0   0.3        2.5    8.4   0.2    3.4  3  Phage_DsbA  Transcriptional regulator DsbA
     0.0081   15.4   0.0      0.015   14.6   0.0    1.4  1  Zeta_toxin  Zeta toxin
  ------ inclusion threshold ------
      0.031   14.5   0.0        7.5    6.8   0.0    2.5  2  AAA_22      AAA domain
       0.04   13.6   0.0      0.066   12.9   0.0    1.3  1  AAA_30      AAA domain
      0.045   13.7   0.0        2.6    7.9   0.0    2.2  2  ATPase_2    ATPase domain predominantly from Archaea


Domain annotation for each model (and alignments):
>> DUF2791  P-loop Domain of unknown function (DUF2791)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  567.6   0.0  5.6e-174  1.4e-170       1     412 [.       3     412 ..       3     414 .. 0.99

  Alignments for each domain:
  == domain 1  score: 567.6 bits;  conditional E-value: 5.6e-174
                           DUF2791   1 iskrereaiinsLraGvVPriGleliaVGrereiealledlervaeggaafrfirGeYGsGKtFllqllreralerg 77 
                                       i+kr ++++insL++GvVPriGl++i+VGr++e++all+d+e +a+gga+frfi G+YGsGK+Fllq++r+++++r+
  gi|474934928|ref|YP_007688510.1|   3 IPKRVASTVINSLKGGVVPRIGLPYITVGRRTEVDALLNDVEIIADGGATFRFIEGRYGSGKSFLLQAVRNYVMDRN 79 
                                       899************************************************************************** PP

                           DUF2791  78 fvvaeadlsperrLhgtkgqlealYrelvenlstktkpeggALrsildrwiseveeevaaegkeeddealeaavekk 154
                                       fvv++ dlsper+Lhg+kgq++a+Yrel++n+st+tkpeggAL+ ildrwise+++++ ++ + +d++++ +avek+
  gi|474934928|ref|YP_007688510.1|  80 FVVIDGDLSPERKLHGNKGQGLATYRELIRNMSTRTKPEGGALTLILDRWISEAQSQTSQTVS-PDSPDFPKAVEKR 155
                                       *********************************************************998886.************* PP

                           DUF2791 155 ieerlaelselvegfdfakvlrayyrakeegdeelksaalrWLrGeyktktearkelgvkgiidddnaydylkllaa 231
                                       i e + +++e+v+gfdfa++l  yyra +egd+  k++++rW+rGey+ ktea+++lgv+  i+dd++y+y+kl+a 
  gi|474934928|ref|YP_007688510.1| 156 IGEIVLSMNEMVHGFDFARLLILYYRAFAEGDDMAKAKVVRWFRGEYQNKTEAKNDLGVNIVITDDDWYEYVKLFAF 232
                                       ***************************************************************************** PP

                           DUF2791 232 fvrkaGykGLlvvlDElvnlyklsnsdaReknyekllqilndvlqgkaeglgllltGTpeflederrGvysyeaLrs 308
                                       f+++aGy+G+++++DElvn+yk++n+ +Re+nyek+l+++ndvlqgka++lg++++GTpe++e+++rGvysyeaLrs
  gi|474934928|ref|YP_007688510.1| 233 FLKQAGYAGMMMLVDELVNIYKIPNRISRENNYEKILTMYNDVLQGKARYLGIIMCGTPECIENTQRGVYSYEALRS 309
                                       ***************************************************************************** PP

                           DUF2791 309 RlaedrfakeaglkdlrapvirLkplteeellvlleklrdiyaegyeeevlvsdeelkafleevtgrlgakvgvtpR 385
                                       Rl+++rfa+e g kd+ apvi+L+plt+ee++vl+ekl+di+a  +++e ++++ +l +f++ +++r+ga++++tpR
  gi|474934928|ref|YP_007688510.1| 310 RLSDGRFASE-GRKDMLAPVIKLDPLTYEEMTVLVEKLSDIHAILFDYERRLTEGDLVTFIKIEYSRVGADSHITPR 385
                                       *********6.9***************************************************************** PP

                           DUF2791 386 evirdfvdvLdileqnpdldpeellke 412
                                       e+irdf+++Ldil+q+pd+d+++ll++
  gi|474934928|ref|YP_007688510.1| 386 EIIRDFIELLDILYQHPDTDVAQLLNS 412
                                       ***********************9976 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   1.4e-08   3.5e-05       3      63 ..      30      90 ..      29     165 .. 0.81
   2 ?   -2.0   0.0       1.6     4e+03       5      26 ..     261     282 ..     259     287 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.4e-08
                            AAA_16  3 vGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                      vGR+ e+++Ll+ +e +++g+    ++ G  G+GKs l++++++++ +++++++ g+    
  gi|474934928|ref|YP_007688510.1| 30 VGRRTEVDALLNDVEIIADGGATFRFIEGRYGSGKSFLLQAVRNYVMDRNFVVIDGDLSPE 90
                                      8*******************************************99999999999887665 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.6
                            AAA_16   5 ReeeleqLlsalervrsgrpel 26 
                                       Re+  e++l+++++v +g  ++
  gi|474934928|ref|YP_007688510.1| 261 RENNYEKILTMYNDVLQGKARY 282
                                       99*************9998755 PP

>> Phage_DsbA  Transcriptional regulator DsbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.063   1.6e+02      13      28 ..     103     118 ..      99     125 .. 0.89
   2 ?    1.3   0.0      0.15   3.9e+02      31      47 ..     167     183 ..     162     199 .. 0.77
   3 !    8.4   0.2   0.00097       2.5      38      66 ..     248     276 ..     242     277 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.063
                        Phage_DsbA  13 sereLikDiaiRakee 28 
                                       ++reLi+++  R k e
  gi|474934928|ref|YP_007688510.1| 103 TYRELIRNMSTRTKPE 118
                                       79************88 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.15
                        Phage_DsbA  31 vdgkdFnkllklYhkdn 47 
                                       v+g dF +ll lY++  
  gi|474934928|ref|YP_007688510.1| 167 VHGFDFARLLILYYRAF 183
                                       7899*********9865 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.00097
                        Phage_DsbA  38 kllklYhkdnRdveeaktekvveLYeklF 66 
                                        l+++Y   nR   e ++ek+  +Y+ + 
  gi|474934928|ref|YP_007688510.1| 248 ELVNIYKIPNRISRENNYEKILTMYNDVL 276
                                       699**********************9885 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   5.9e-06     0.015      20      53 ..      55      87 ..      38     122 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.9e-06
                        Zeta_toxin 20 llgGqpGAGKselaellkdelerqgnvvrldpDd 53
                                      ++ G  G+GKs l++++++++ +++n+v++d+D 
  gi|474934928|ref|YP_007688510.1| 55 FIEGRYGSGKSFLLQAVRNYV-MDRNFVVIDGDL 87
                                      778999**************9.7*********96 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0029       7.5       4      27 ..      50      73 ..      47     118 .. 0.89
   2 ?    5.2   0.0    0.0095        24      83     133 ..     234     293 ..     167     296 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0029
                            AAA_22  4 tagilvvtGesGtGKTtllrrlle 27
                                      +a++ ++ G  G+GK++ll+ +++
  gi|474934928|ref|YP_007688510.1| 50 GATFRFIEGRYGSGKSFLLQAVRN 73
                                      67788899************9987 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0095
                            AAA_22  83 eqalraravielliiDEaqhlr......s.eealeeLrsllnl....srkgvqliLvGtpel 133
                                        +++  +++  ++++DE  ++       s e+++e++ +++n+    +   + +i++Gtpe+
  gi|474934928|ref|YP_007688510.1| 234 LKQAGYAGM--MMLVDELVNIYkipnriSrENNYEKILTMYNDvlqgKARYLGIIMCGTPEC 293
                                       445555555..7899999998777765527****************99999*********85 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.6e-05     0.066      12      49 ..      45      82 ..      41     127 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.6e-05
                            AAA_30 12 alltsgdrvavltGpAGtGKttalkalreaweaaggrv 49
                                       ++ +g+ + +++G+ G+GK+++l+a+r+ + ++++ v
  gi|474934928|ref|YP_007688510.1| 45 IIADGGATFRFIEGRYGSGKSFLLQAVRNYVMDRNFVV 82
                                      567788999*******************9988777555 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0     0.001       2.6      11      49 ..      43      80 ..      30      87 .. 0.75
   2 ?    3.6   0.0     0.021        53      57     154 ..     172     278 ..     153     311 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.001
                          ATPase_2 11 leeilerepneiyfiYGpegsGKtaLlkeiienledkdk 49
                                      + ei+  + +++ fi G+ gsGK+ Ll+ + +   d ++
  gi|474934928|ref|YP_007688510.1| 43 V-EIIADGGATFRFIEGRYGSGKSFLLQAVRNYVMDRNF 80
                                      3.466677899***************9988776666655 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.021
                          ATPase_2  57 lreesiskldefie..eeeekkklekal..........giavpkaeleeilk....eksklvfkaielllekikkkg 117
                                       + +  i +++ f e  +  ++      +          +    k+e+++ l      +  + +++++l+   +k+ g
  gi|474934928|ref|YP_007688510.1| 172 FARLLILYYRAFAEgdDMAKA------KvvrwfrgeyqN----KTEAKNDLGvnivITDDDWYEYVKLFAFFLKQAG 238
                                       455555556666332211111......112333433321....222222222223367889999************* PP

                          ATPase_2 118 kk.iiiiiDelqklidl..glngaellvkeLlnliesltk 154
                                          + +++Del ++ ++   + +++++ k L  + + l  
  gi|474934928|ref|YP_007688510.1| 239 YAgMMMLVDELVNIYKIpnRISRENNYEKILTMYNDVLQG 278
                                       999**********996622333666676666666655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 3012.98
//
Query:       gi|474934929|ref|YP_007688511.1|  [L=603]
Description: hypothetical protein TALC_01372 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-21   77.4   0.2    2.2e-21   76.7   0.2    1.3  1  TerB_C    TerB-C domain
    2.5e-21   76.3   0.0    3.6e-21   75.8   0.0    1.2  1  TerB_N    TerB N-terminal domain
  ------ inclusion threshold ------
      0.055   13.3   0.0       0.37   10.6   0.0    2.4  2  rve_3     Integrase core domain


Domain annotation for each model (and alignments):
>> TerB_C  TerB-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.7   0.2   3.7e-25   2.2e-21       4     151 .]     473     598 ..     470     598 .. 0.89

  Alignments for each domain:
  == domain 1  score: 76.7 bits;  conditional E-value: 3.7e-25
                            TerB_C   4 eeqeekaeaakkkislDlsrlaairketaavselLaeifeeeereeeeepakpevteepeaeeaetaladkvaeseg 80 
                                       e+ eek+ ++ +k+++D+srl  ir++++ ++e+++   + eer      a+++v+ee+ +e ++++         +
  gi|474934929|ref|YP_007688511.1| 473 EWFEEKRIRSIPKVEVDTSRLVDIRRDAETTMEKIM---TSEER------AQEPVPEEELREVPADT---------P 531
                                       6789999999**************************...88884......55555555555555553.........9 PP

                            TerB_C  81 LdeaeaalLraLlareswpreeveslarekglmpdvliesINekafdefddtvie.dddppeinedyleelk 151
                                       L+++e+++ r+Ll++     ++ ++++++k +m++v+++sIN k+fdef+d v+  + + pei  dy+eelk
  gi|474934929|ref|YP_007688511.1| 532 LTPDEYEFVRRLLYG-----GAWDEVLKSKRMMLSVVVDSINGKLFDEFGDSVLTeESGRPEIVGDYVEELK 598
                                       ***************.....*******************************99998**************97 PP

>> TerB_N  TerB N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.8   0.0   6.1e-25   3.6e-21       9     202 ..     155     363 ..     149     370 .. 0.79

  Alignments for each domain:
  == domain 1  score: 75.8 bits;  conditional E-value: 6.1e-25
                            TerB_N   9 agleipgglvyvge.kseagyr..ereeafidpalsvas.edgsdkevpfmsywpsYsslspaqrrtYLdWlaqgRk 81 
                                       +++ +p+++  ++    +++y+  ++  +f++ a  +++ ed+   e+ f +   +Y+ +  aq r+Y++W++++Rk
  gi|474934929|ref|YP_007688511.1| 155 EPEDVPERIREMRNlFTRDDYHmlSEPVIFYRMARFMEDyEDDCPFEGSFSQPFQTYRMMGNAQIRGYFTWRTGVRK 231
                                       6778899999999975566666789999************************************************* PP

                            TerB_N  82 g..pdtslsYvflYfygLerrvgvdnpqegyeklielpeiyeeld....rllkeygddysfreyatelldlarlles 152
                                       g  ++t  sY++ Y+++L++ +g+++p+eg  +l+ + ++y+++d     +  ++++d     y+ e  d+ r  + 
  gi|474934929|ref|YP_007688511.1| 232 GvlEETYPSYAYTYVCELINGIGWKDPEEGFGMLKGFLDDYAKIDvalfPYDYIWLSDF-AACYNIESPDINRTGSE 307
                                       *****************************************666622226777888888.44555555555555444 PP

                            TerB_N 153 ddaylllpdpeeksakelplslrvalgqyaad........qeplpaelalawalldpe 202
                                       +  yl l d ++  +++l  sl   +++y+++         e+ ++++++a++ +d  
  gi|474934929|ref|YP_007688511.1| 308 EA-YLCLSDLKNCPPEKL-MSLAPLISSYRIEsmkvnalyPEDTQEVFVRALRNADAA 363
                                       44.777766666666666.777777777777766666777666666666666666665 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   6.3e-05      0.37      12      48 ..     456     492 ..     447     496 .. 0.88
   2 ?   -1.8   0.0      0.48   2.8e+03      18      33 ..     563     578 ..     556     584 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 6.3e-05
                             rve_3  12 kPqqNglvEsfngtlrdellneelfrslaeareklea 48 
                                       kP +N  vE f +t  de+  e+  rs+++++  + +
  gi|474934929|ref|YP_007688511.1| 456 KPRENDAVEDFVRTAADEWFEEKRIRSIPKVEVDTSR 492
                                       9***************************999877665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.48
                             rve_3  18 lvEsfngtlrdellne 33 
                                        v s+ng+l de+ ++
  gi|474934929|ref|YP_007688511.1| 563 VVDSINGKLFDEFGDS 578
                                       689******9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (603 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 3888.83
//
Query:       gi|474934930|ref|YP_007688512.1|  [L=130]
Description: hypothetical protein TALC_01373 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1488  (0.082994); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 869.43
//
Query:       gi|474934931|ref|YP_007688513.1|  [L=602]
Description: heavy metal-(Cd/Co/Hg/Pb/Zn)-translocating P-type ATPase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-47  161.8   2.0    1.2e-47  161.8   2.0    2.4  2  E1-E2_ATPase  E1-E2 ATPase
    1.1e-42  146.7   0.1      2e-42  145.9   0.1    1.4  1  Hydrolase     haloacid dehalogenase-like hydrolase
     0.0042   16.9   0.5      0.041   13.6   0.4    2.1  2  Hydrolase_3   haloacid dehalogenase-like hydrolase
     0.0071   16.8   0.0      0.019   15.3   0.0    1.7  1  HAD           haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.8   2.0   2.7e-51   1.2e-47       2     180 ..     107     277 ..     106     278 .. 0.98
   2 ?   -1.4   2.0      0.33   1.5e+03     113     157 ..     545     590 ..     540     600 .. 0.76

  Alignments for each domain:
  == domain 1  score: 161.8 bits;  conditional E-value: 2.7e-51
                                       SS--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE CS
                      E1-E2_ATPase   2 llpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvs 78 
                                       + p++a+virdg+e+e++a+ + +G  + + ag+++p+Dg +v+g ++vd+s+LTGEs+pv+k +gd+vfsGtv+  
  gi|474934931|ref|YP_007688513.1| 107 MVPTRARVIRDGEETEVEAESVSVGEKLRVIAGESIPLDGFVVSGRTSVDQSSLTGESMPVDKAEGDEVFSGTVNQM 183
                                       7899************************************************************************* PP

                                       -EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHH CS
                      E1-E2_ATPase  79 geakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralall 155
                                       g+++++Vt+t++++ ++k++++ve+a +++t++++ +d+ + +lv++v+ i+l+++l++        + + ral+++
  gi|474934931|ref|YP_007688513.1| 184 GTFEMEVTKTASESSFQKLVAMVESADADRTRIVRTADRWATYLVALVFGITLVTYLAF--------RDVERALTVM 252
                                       **********************************************************9........9999****** PP

                                       HHHS-TTHHHHHHHHHHHHHHHHHH CS
                      E1-E2_ATPase 156 vaaiPcaLplavplalalgarrlak 180
                                       ++++Pca++la+p+a+++++++la+
  gi|474934931|ref|YP_007688513.1| 253 IVFCPCAFILATPTAVVAAIGNLAH 277
                                       ***********************97 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.33
                                       HHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHH.HHHHHHH CS
                      E1-E2_ATPase 113 kkldklgkvlvpvvlliallvflialllgkslaeallr.alallva 157
                                       ++++k+ + +v+++++ +++v+l+ + + +++  a+++ + +++v+
  gi|474934931|ref|YP_007688513.1| 545 RMMSKIRNNIVFAMCWNFMAVALAVFGIVGPVLGAIVHnVGSVAVV 590
                                       6889999999999999999999999999999998888834344443 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.9   0.1   4.4e-46     2e-42       3     210 .]     296     507 ..     294     507 .. 0.92

  Alignments for each domain:
  == domain 1  score: 145.9 bits;  conditional E-value: 4.4e-46
                                       EEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHH......HHCHHHHHHHHHHHHH.....HHHHHHHHHETTTE. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxx. RF
                         Hydrolase   3 tvvfDkdGTLttgepsvedvivsaalalaaaletg......sehpigkalvaaakar.....sgaltgfatfigrg. 67 
                                        vvfDk+GTLt+g+p ve+v+    ++++++l ++      sehp+gka++   +a+     s+++       g g 
  gi|474934931|ref|YP_007688513.1| 296 RVVFDKTGTLTEGRPKVERVVSAGGMEEGEILSLAasaeslSEHPLGKAIASSSDAEkpddfSISV-------GGGv 365
                                       69**********************99999999999999999*********9999999666664444.......3333 PP

                                       .......HHHHTHHHHHHHH..HCHHHHHHHHHHHHHHCHHHHHH..TTHHHHHHHHHHTHHBHTTHHHHHHHHHHT CS
                                       .......xxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  68 .......ayaigkpewltal..dippdlgaaigsaqsqgrtvall..qaralavftiadplkvkpeaaeavasLkaa 133
                                              ++++g+ +++++    +p+ lg+a ++a + g + +++  ++ra +v+ ++dp  ++++ aeav +++a 
  gi|474934931|ref|YP_007688513.1| 366 sasvsgrKVLVGSSRFMEESgiAVPDALGEAASEATGGGSICVFVsvDGRAEGVIVLSDP--IRQDSAEAVSEIRAE 440
                                       3334445**************************************9**************..*************** PP

                                       TEEEEEEESSEHHHHHHHHHHTTGGGESEEEEHHCES.STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 134 gievvlltgdnpetaeraanqlGddyfdaviasdiet.vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaA 209
                                       g e vlltgd+++ta ++a ++G           i++  a+  pe+k   ir +q ++++v+mVGDg+nDa+ l+aA
  gi|474934931|ref|YP_007688513.1| 441 GAECVLLTGDSENTASHIAGEAG-----------ISEfRAECRPEDKMSRIRDMQSEGHRVCMVGDGINDAPSLKAA 506
                                       ***********************...........8888*************************************** PP

                                       T CS
                                       x RF
                         Hydrolase 210 g 210
                                       +
  gi|474934931|ref|YP_007688513.1| 507 D 507
                                       8 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.08   3.6e+02      16      55 ..     426     465 ..     423     471 .. 0.88
   2 !   13.6   0.4   9.2e-06     0.041     202     242 ..     486     527 ..     479     532 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.08
                                       --HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCC CS
                       Hydrolase_3  16 isektkeaikklkekgikvviATGRslravlpvleelgld 55 
                                       i + ++ea+ +++++g + v+ TG s  ++++++ e g++
  gi|474934931|ref|YP_007688513.1| 426 IRQDSAEAVSEIRAEGAECVLLTGDSENTASHIAGEAGIS 465
                                       678899*********************9999999988876 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 9.2e-06
                                       -GGGEEEEESSGGGHHHHHHSSEEEEET.TS-HHHHHHSSEE CS
                       Hydrolase_3 202 sleeviafGDgeNDieMLeaaglgvAmg.naseevkkaAdyv 242
                                       +  +v  +GDg ND + L+aa++g+Amg  ++  +  aAd+v
  gi|474934931|ref|YP_007688513.1| 486 EGHRVCMVGDGINDAPSLKAADVGIAMGgTGTGIALDAADMV 527
                                       6678999********************736777777777776 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   4.3e-06     0.019      89     188 .]     432     504 ..     415     504 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.3e-06
                               HAD  89 galellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgegkvaalrewlaae 165
                                       +a+  ++   a+G ++v+++g  +  +  ++ e g    +++       + +e       +r e+k +++r+ ++ e
  gi|474934931|ref|YP_007688513.1| 432 EAVSEIR---AEGAECVLLTGDSENTASHIAGEAG----ISE-------FRAE-------CRPEDKMSRIRD-MQSE 486
                                       5666666...*************************....***.......9999.......999999999999.4444 PP

                               HAD 166 gegidleevvayGDspsDlpllr 188
                                       g     ++v+ +GD+++D p l+
  gi|474934931|ref|YP_007688513.1| 487 G-----HRVCMVGDGINDAPSLK 504
                                       4.....45999*******99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (602 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.46
# Mc/sec: 3944.96
//
Query:       gi|474934932|ref|YP_007688514.1|  [L=221]
Description: hypothetical protein TALC_01375 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-18   64.3   2.8    2.5e-17   62.5   0.0    2.4  2  DUF4357   Domain of unknown function (DUF4357)


Domain annotation for each model (and alignments):
>> DUF4357  Domain of unknown function (DUF4357)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   1.1     0.027   4.8e+02      40      49 ..       5      14 ..       3      17 .. 0.83
   2 !   62.5   0.0   1.4e-21   2.5e-17       1      53 [.     166     214 ..     166     215 .. 0.97

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.027
                           DUF4357 40 aNGwteWkde 49
                                      +NG +eW+d 
  gi|474934932|ref|YP_007688514.1|  5 NNGDKEWQDW 14
                                      6******985 PP

  == domain 2  score: 62.5 bits;  conditional E-value: 1.4e-21
                           DUF4357   1 RekliedgvlvkeggllvfteDyeFsSPSaAAsvvlGrsaNGwteWkdedGkt 53 
                                       Rekli+dgv+v++    +f  Dy+FsS SaAAsv++G+s+NG+++W ++d+++
  gi|474934932|ref|YP_007688514.1| 166 REKLINDGVIVND----IFVTDYLFSSYSAAASVICGNSTNGRQAWVNDDHQS 214
                                       9**********88....*********************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1477.52
//
Query:       gi|474934933|ref|YP_007688515.1|  [L=40]
Description: hypothetical protein TALC_01376 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       168  (0.00937029); expected 358.6 (0.02)
Passed bias filter:                      133  (0.00741815); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 302.66
//
Query:       gi|474934934|ref|YP_007688516.1|  [L=815]
Description: Superfamily I DNA and RNA helicase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-36  126.9  10.0      1e-19   71.2   0.4    2.6  3  UvrD-helicase    UvrD/REP helicase N-terminal domain
    1.3e-28  100.2   0.0    2.2e-27   96.2   0.0    2.3  1  AAA_19           AAA domain
    3.1e-18   66.3   0.1    2.8e-16   59.8   0.0    2.6  3  UvrD_C           UvrD-like helicase C-terminal domain
    2.4e-13   49.6   4.5    4.5e-13   48.7   4.5    1.5  1  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
    8.4e-11   41.5   0.3    2.3e-09   36.9   0.3    2.6  1  UvrD_C_2         UvrD-like helicase C-terminal domain
      2e-08   34.3   0.0    3.8e-08   33.4   0.0    1.4  1  AAA_11           AAA domain
    5.5e-08   32.7   0.1    0.00014   21.6   0.1    2.3  2  AAA_30           AAA domain
    7.9e-06   25.8   0.1       0.41   10.4   0.0    3.6  4  Viral_helicase1  Viral (Superfamily 1) RNA helicase
     0.0024   17.9   1.4          1    9.4   0.1    3.2  3  AAA_14           AAA domain
     0.0052   16.1   1.2     0.0089   15.3   0.0    1.9  2  DUF2075          Uncharacterized conserved protein (DUF2075)
  ------ inclusion threshold ------
      0.016   15.5   0.8          5    7.4   0.0    3.1  4  AAA_22           AAA domain
      0.023   14.7   0.1      0.055   13.5   0.1    1.6  1  ResIII           Type III restriction enzyme, res subunit
      0.043   13.4   0.0        1.2    8.7   0.0    2.4  2  AAA_12           AAA domain
      0.057   13.1   0.0       0.11   12.2   0.0    1.4  1  DUF4122          Domain of unknown function (DUF4122)


Domain annotation for each model (and alignments):
>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       6.3   8.1e+03     186     221 ..      38      78 ..      31      81 .. 0.62
   2 !   60.0   2.0   2.2e-19   2.8e-16       3     101 ..     113     192 ..     111     201 .. 0.85
   3 !   71.2   0.4   8.2e-23     1e-19     209     312 ..     454     552 ..     401     554 .. 0.93

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 6.3
                                       HHHHHHTTCCTTHHCHSS.....TSCSHHHHHHHHHHHHHH CS
                     UvrD-helicase 186 vskakekqlspkelkkaf.....ekasdlqkkiaeflkeyq 221
                                        +  k+   s+k++ k +       ++++++ i+eflk+y+
  gi|474934934|ref|YP_007688516.1|  38 KNSTKQTVESAKKRSKGIffrlgLVNKPFKSSIIEFLKRYE 78 
                                       44444444444444444366666678888899999999886 PP

  == domain 2  score: 60.0 bits;  conditional E-value: 2.2e-19
                                       HHHHHHHHS-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHHHHHCCHHCTT- CS
                     UvrD-helicase   3 peqreaiaslggpilveAsAGsGKTfvlaerilrlikeeeiepdrilvvTFTnkAaeElkeRieealkkaeqessdd 79 
                                       ++q   ia   ++ lv+A+AG+GKT++++ ++ +l+ +e+ +p++il++ FTn++ +ElkeRi + + k+       
  gi|474934934|ref|YP_007688516.1| 113 RQQLTSIAMDVNTRLVIAGAGTGKTTTIIGLVKELLMTEKAQPEEILLLSFTNASVNELKERILKETSKR------- 182
                                       6788889998999***************************************************988775....... PP

                                       HHHHHHHHHCTTSEEEEHHHHH CS
                     UvrD-helicase  80 erlrlalqnlseanisTlHsfc 101
                                                   ++  T+H ++
  gi|474934934|ref|YP_007688516.1| 183 ------------IDTTTFHRLG 192
                                       ............4444444444 PP

  == domain 3  score: 71.2 bits;  conditional E-value: 8.2e-23
                                       HHHHHHHHHHHHHHHHHHHTCEEHHHHHHHHHHHHHHCHHHHHHHHHHSSEEEESSGGG-BHHHHHHHHHHHTTTTT CS
                     UvrD-helicase 209 lqkkiaeflkeyqeqkkeenalDfsdllhallelleeneelaealrerykeiliDEyQDTnkiQyrilkllasghee 285
                                       l+k ++ +++eyq+q+ +++ +Df+d+l+ + e  +e       +   y+++ +DEyQD +++ +++lk + +++++
  gi|474934934|ref|YP_007688516.1| 454 LEKVLRPIYEEYQDQLAINDEIDFEDMLNMASECVKE------GYIHPYRYVIVDEYQDISRSRFNLLKEMRTSKDY 524
                                       6788899************************998876......7999*************************99999 PP

                                       .EEEEE-GGG--GGGGTB-THHHHHHHH CS
                     UvrD-helicase 286 .lfmvGDpkQsIYgFRgAdielflkkkk 312
                                        lf+vGD+ QsIY+F g+d++ +l +++
  gi|474934934|ref|YP_007688516.1| 525 rLFCVGDDWQSIYRFNGSDVSYILDFED 552
                                       9***********************9875 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.2   0.0   1.7e-30   2.2e-27       7     146 .]     120     540 ..     114     540 .. 0.96

  Alignments for each domain:
  == domain 1  score: 96.2 bits;  conditional E-value: 1.7e-30
                            AAA_19   7 alkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae.....atTiHrlal. 77 
                                       a+  ++ lv+aG+GtGKT+++ + v++l+ +++ +peeill++ft+ +++el+er+ +         +tT+Hrl+l 
  gi|474934934|ref|YP_007688516.1| 120 AMDVNTRLVIAGAGTGKTTTIIGLVKELLMTEKAQPEEILLLSFTNASVNELKERILKE--TskridTTTFHRLGLk 194
                                       56677889***********************************************9433..255899********9* PP

                            AAA_19  78 ............................................................................. 77 
                                                                                                                    
  gi|474934934|ref|YP_007688516.1| 195 iiastrgktpnvshtdlnqfvtdelqrrvsdpqfladfnsyiafdynsqtdefafatnedyvryvkenplitlngek 271
                                       ***************************************************************************** PP

                            AAA_19  78 ............................................................................. 77 
                                                                                                                    
  gi|474934934|ref|YP_007688516.1| 272 vksfgeadianflaingvpytyedaypvdtsdakhghyhpdfhingtniyieyfgtdrygnvaqfmldanpnaaedy 348
                                       ***************************************************************************** PP

                            AAA_19  78 ............................................................................. 77 
                                                                                                                    
  gi|474934934|ref|YP_007688516.1| 349 rqsmewkrtihrinntelvelfaynrsegtlledlknhltrlgvemspaspsdlfdrmfnsgrlkfsmiassmttai 425
                                       ***************************************************************************** PP

                            AAA_19  78 .................................................ldfddlltealelleeaeeekklqeee. 104
                                                                                        +df+d l++a e ++    e  + + + 
  gi|474934934|ref|YP_007688516.1| 426 llikgygkpwnevyptskdrrvkqslirlekvlrpiyeeyqdqlaindeIDFEDMLNMASECVK----EGYI-HPYr 497
                                       *******************************************999988888888877777755....5677.5666 PP

                            AAA_19 105 llivDEfqdvdelqyrLlkallgek.kklllvGDpdQliyvfr 146
                                       ++ivDE+qd++   ++Llk++ ++k  +l+ vGD+ Q+iy f+
  gi|474934934|ref|YP_007688516.1| 498 YVIVDEYQDISRSRFNLLKEMRTSKdYRLFCVGDDWQSIYRFN 540
                                       **********************999788************995 PP

>> UvrD_C  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.1       5.2   6.7e+03     132     150 ..     172     190 ..     140     195 .. 0.55
   2 ?    3.5   0.0     0.029        37       4      89 ..     563     643 ..     560     645 .. 0.77
   3 !   59.8   0.0   2.2e-19   2.8e-16     286     347 ..     669     742 ..     656     744 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 5.2
                                       xxxxxxxxxxxxxxxxxxx RF
                            UvrD_C 132 lkrilkrlvlgigkatver 150
                                        +rilk+  ++i+++t+ r
  gi|474934934|ref|YP_007688516.1| 172 KERILKETSKRIDTTTFHR 190
                                       2345555555555555544 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.029
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C   4 ekNyRStksLlkaankflenilnrralekek...ktvekge...kivvleaeteeeEaekiaatikalleknekled 74 
                                       e+ yR + +Ll+ +++f+ ++  +     +k       k +   +i+ l+a+te + ++ +a+++ +++     +e+
  gi|474934934|ref|YP_007688516.1| 563 ETTYRFSGELLQKSSEFIMRNPRQ----FKKdlvG---KADvdcRIIRLSAKTEADAYQRVAEELAQIP----GNET 628
                                       666999999999999999666555....3332432...3333369********************9999....8888 PP

                                       xxxxxxxxxxxxxxx RF
                            UvrD_C  75 iavLvRsnkdadkis 89 
                                       i  L R  +d++k++
  gi|474934934|ref|YP_007688516.1| 629 ILFLGRYRHDIVKLE 643
                                       888889899888886 PP

  == domain 3  score: 59.8 bits;  conditional E-value: 2.2e-19
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C 286 kipiiTiHqAKGlEFdvVflagleegt..fPsyrskk..........ekrleEEkRlfYVaiTRAkkrLfisys 347
                                       k + +TiH +KGl    Vf+++ + g   fP+ r +            ++l+EE+RlfYVa+TRAkkr+++ + 
  gi|474934934|ref|YP_007688516.1| 669 KMTFMTIHGSKGLQASRVFILNNKTGSygFPNVRDEPpiiplllnsqDNQLDEERRLFYVAMTRAKKRVYLVAV 742
                                       5678******************999874479888777999999999999*********************9775 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   4.5   3.5e-16   4.5e-13       3      36 ..     768     803 ..     766     806 .. 0.93

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 3.5e-16
                                       E-SSS--EEEEEE-SSSEEEEESST.T..----EEB CS
                    zf-C4_Topoisom   3 kCPkCggdLvlkrgkkGkFvGCsnYPe..Ckftkkl 36 
                                       +CP Cggd+vl++gk+G F+GCsn+P+  Ck+t+k 
  gi|474934934|ref|YP_007688516.1| 768 TCPMCGGDMVLRKGKYGLFYGCSNFPKtgCKYTVKY 803
                                       8*************************999****986 PP

>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.3   1.8e-12   2.3e-09       3      52 .]     671     740 ..     669     740 .. 0.94

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 1.8e-12
                          UvrD_C_2   3 yaltihkaQGsefpaVivfdpdlaaarmgel....................rrrlLYtavTRAreklilv 52 
                                       +++tih ++G+++  V++ +  + ++  +++                     rrl+Y+a+TRA+++++lv
  gi|474934934|ref|YP_007688516.1| 671 TFMTIHGSKGLQASRVFILNNKTGSYGFPNVrdeppiiplllnsqdnqldeERRLFYVAMTRAKKRVYLV 740
                                       679***************999988888777799***********************************98 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.0     3e-11   3.8e-08       2     119 ..     111     221 ..     110     273 .. 0.74

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 3e-11
                            AAA_11   2 lndsqreaiksalseseitliqGPPGtgKTktivellsqllsrrkseeeksakpriLvCapSNaAvDellerllrgl 78 
                                       l+++q+++i+  ++++   +i G  GtgKT+ti++l+++l       +ek+++++iL+ + +Na+v+el er+l+  
  gi|474934934|ref|YP_007688516.1| 111 LDRQQLTSIAMDVNTRL--VIAGA-GTGKTTTIIGLVKEL-----LMTEKAQPEEILLLSFTNASVNELKERILK-- 177
                                       67778888888787774..67777.***************.....45789*************************.. PP

                            AAA_11  79 ldsegekykpkivRvgnee....eriseavksvsleekvekrlek 119
                                        +++++  +  + R+g +     +  +++v+   l++ v ++l+ 
  gi|474934934|ref|YP_007688516.1| 178 -ETSKRIDTTTFHRLGLKIiastRGKTPNVSHTDLNQFVTDELQR 221
                                       .55555556666666655554443335555555555555555544 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.1   1.1e-07   0.00014      13      76 ..     119     191 ..     111     220 .. 0.72
   2 !    8.6   0.0    0.0011       1.4      84     127 ..     491     534 ..     443     536 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.1e-07
                            AAA_30  13 lltsgdrvavltGpAGtGKttalkal.reaweaag...grviglAptgkaAkvLae......elgieastiakl 76 
                                       ++++ + + ++ ++AGtGKtt++ +l +e++ +++   +++++l+ t++  ++L+e      +  i++ t ++l
  gi|474934934|ref|YP_007688516.1| 119 IAMDVN-TRLVIAGAGTGKTTTIIGLvKELLMTEKaqpEEILLLSFTNASVNELKErilketSKRIDTTTFHRL 191
                                       555554.78999********9887775787776655679****************8333322333677777776 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0011
                            AAA_30  84 arlepgtllivDEagmvdtkqlaallkaaekagakvilvGDerQ 127
                                         ++p + +ivDE   ++ + ++ l +  ++++ ++ +vGD+ Q
  gi|474934934|ref|YP_007688516.1| 491 GYIHPYRYVIVDEYQDISRSRFNLLKEMRTSKDYRLFCVGDDWQ 534
                                       46788899**********999987777777789*********99 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.014        18       4      32 ..     129     158 ..     127     194 .. 0.51
   2 !    6.0   0.0     0.007         9      62     140 ..     495     578 ..     455     621 .. 0.78
   3 ?   -3.3   0.0       4.9   6.3e+03     182     202 ..     670     689 ..     664     694 .. 0.81
   4 !   10.4   0.0   0.00032      0.41     203     233 ..     711     740 ..     705     741 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.014
                   Viral_helicase1   4 hGvpGcGKStlirkllrts.liltvnrpta 32 
                                        + +G GK+t i  l+++  +  ++ ++ +
  gi|474934934|ref|YP_007688516.1| 129 IAGAGTGKTTTIIGLVKELlMTEKAQPEEI 158
                                       4669************99432222222222 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.007
                   Viral_helicase1  62 kgkililDEylllhaGyilllaalskak..lvilfGDplQipfhsrnasfllahlpssl...shrvgrrttyllpsd 133
                                        ++++i+DEy+   +  ++ll  + ++k   ++++GD  Q+ +  + +++++   +  +   s+  +  tty++   
  gi|474934934|ref|YP_007688516.1| 495 PYRYVIVDEYQDISRSRFNLLKEMRTSKdyRLFCVGDDWQSIYRFNGSDVSYILDFEDYwgpSEICKIETTYRFSGE 571
                                       3899***********99999877666653379999******999888887777777777788888888888887765 PP

                   Viral_helicase1 134 vaeilsa 140
                                         ++ s+
  gi|474934934|ref|YP_007688516.1| 572 LLQKSSE 578
                                       5555555 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 4.9
                   Viral_helicase1 182 vrevttvhevqGltfdkVtlv 202
                                        + ++t h+  Gl++++V ++
  gi|474934934|ref|YP_007688516.1| 670 MT-FMTIHGSKGLQASRVFIL 689
                                       55.89************9987 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 0.00032
                   Viral_helicase1 203 llketdlelisesrenllvAlTRhrkslvil 233
                                       ll++ d++l +e r  ++vA+TR++k+++++
  gi|474934934|ref|YP_007688516.1| 711 LLNSQDNQLDEE-RRLFYVAMTRAKKRVYLV 740
                                       566777786665.*************99875 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       2.1   2.7e+03      64      78 ..       3      17 ..       1      51 [. 0.78
   2 !    9.4   0.1    0.0008         1       7      55 ..     129     178 ..     124     197 .. 0.79
   3 ?    5.6   0.2     0.012        16      46      99 ..     474     530 ..     447     536 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.1
                            AAA_14 64 kktylflDEiqevpe 78
                                      +k  +++DE+ ++ e
  gi|474934934|ref|YP_007688516.1|  3 EKDRILFDEVNRSLE 17
                                      56779*****98744 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0008
                            AAA_14   7 itGaRrvGKTtllkqlikell....vkkesilyinldderdkkladpekllel 55 
                                       i Ga  +GKTt +  l+kell    +++e+il +++ + +  +l++   +l++
  gi|474934934|ref|YP_007688516.1| 129 IAGA-GTGKTTTIIGLVKELLmtekAQPEEILLLSFTNASVNELKER--ILKE 178
                                       5555.68*******************************998776643..4443 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.012
                            AAA_14  46 ladpekllelileklke...ekktylflDEiqevpewekalkslvdegknldvivtG 99 
                                       + d+e++l++  e +ke   +  +y++ DE q +++ +  l + ++++k++++++ G
  gi|474934934|ref|YP_007688516.1| 474 EIDFEDMLNMASECVKEgyiHPYRYVIVDEYQDISRSRFNLLKEMRTSKDYRLFCVG 530
                                       2245556666666544456656889********988665555555555588888877 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0     7e-06    0.0089       9     102 ..     131     224 ..     125     257 .. 0.83
   2 ?   -2.5   0.3       1.8   2.3e+03     346     362 ..     726     742 ..     723     743 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 7e-06
                           DUF2075   9 vaGtGKtvvllnllael..eddeeertavylsvNhplvlvlrealakkeekkkkkeafeklssfinnlsefkkaeek 83 
                                       +aGtGKt   + l+ el  +++++ ++  +ls  ++ v+ l+e++ k+++k+  +++f++l   i + +  + ++ +
  gi|474934934|ref|YP_007688516.1| 131 GAGTGKTTTIIGLVKELlmTEKAQPEEILLLSFTNASVNELKERILKETSKRIDTTTFHRLGLKIIAST--RGKTPN 205
                                       69***************755555556666778899************99999********998887777..788888 PP

                           DUF2075  84 keepkedvvivDEAhrllt 102
                                        ++ +++  + DE +r  +
  gi|474934934|ref|YP_007688516.1| 206 VSHTDLNQFVTDELQRRVS 224
                                       9999999999999999776 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.8
                           DUF2075 346 yrVLLtRGrkGlyiyae 362
                                       ++V +tR+ k +y++a+
  gi|474934934|ref|YP_007688516.1| 726 FYVAMTRAKKRVYLVAV 742
                                       6899**********986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0039         5       9      70 ..     127     185 ..     125     246 .. 0.54
   2 ?   -3.4   0.0       8.6   1.1e+04      71      89 ..     372     390 ..     346     409 .. 0.44
   3 ?    5.0   0.0     0.021        28      75     129 ..     477     530 ..     447     534 .. 0.65
   4 ?   -3.4   0.0       8.3   1.1e+04      38      67 ..     733     760 ..     712     766 .. 0.60

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0039
                            AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka 70 
                                       +v++ +GtGKTt++  l+++l   +ka+ e+  ++++t +s     +l +++l+++  + ++
  gi|474934934|ref|YP_007688516.1| 127 LVIAGAGTGKTTTIIGLVKELLMTEKAQPEEILLLSFTNAS---VNELKERILKETSKRIDT 185
                                       578889********999999976666655444444333333...445555555555544444 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 8.6
                            AAA_22  71 erlsseellealeqalrar 89 
                                       ++ s+  lle l ++l + 
  gi|474934934|ref|YP_007688516.1| 372 YNRSEGTLLEDLKNHLTRL 390
                                       2222222333333333222 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.021
                            AAA_22  75 seellealeqalrarav..ielliiDEaqhlrseealeeLrsllnlsrkgvqliLvG 129
                                        e++l++  + +++ +    + +i+DE q + s   ++ L+++    +k+ +l+ vG
  gi|474934934|ref|YP_007688516.1| 477 FEDMLNMASECVKEGYIhpYRYVIVDEYQDI-SRSRFNLLKEMRT--SKDYRLFCVG 530
                                       3444444444444444477789*********.9999999988887..7777766666 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 8.3
                            AAA_22  38 erpevvfvtlpsstsskdllrellralgle 67 
                                       ++++v++v +++++  + +++e+++  g +
  gi|474934934|ref|YP_007688516.1| 733 AKKRVYLVAVNNKE--SRFYKEIASSSGGQ 760
                                       45555555555555..78888888877765 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   4.3e-05     0.055      28      94 ..     127     202 ..     100     246 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.3e-05
                                       EEEESTTSTHHHHHHHHHHHH-S.......-EEEEESSHHHHHHHHHHGGGGTGG...........GEEEESSS-B CS
                            ResIII  28 likmaTGtGKTlvaaklierllkkgkee..kflflvprkslleqtleefkkflseayke.......igkkvsgdkk 94 
                                       l+ +  GtGKT +++ l+++ll  +k +  ++l+l  +++ ++ ++e++ k +s+  +         + + s ++k
  gi|474934934|ref|YP_007688516.1| 127 LVIAGAGTGKTTTIIGLVKELLMTEKAQpeEILLLSFTNASVNELKERILKETSKRIDTttfhrlgLKIIASTRGK 202
                                       455567**************99877766779****99986666666666555555433322235543333333333 PP

>> AAA_12  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.096   1.2e+02      93     138 ..     138     182 ..     133     202 .. 0.83
   2 ?    8.7   0.0   0.00096       1.2     143     196 ..     670     741 ..     559     744 .. 0.65

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.096
                            AAA_12  93 elvvklvekllkkgseeerkkigvitpYraqvellkkklkekeeek 138
                                       ++++ lv++ll + +++  ++i  +++ +a v+ lk+++ ++ +++
  gi|474934934|ref|YP_007688516.1| 138 TTIIGLVKELLMTEKAQ-PEEILLLSFTNASVNELKERILKETSKR 182
                                       67889999999999999.8******************998665554 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00096
                            AAA_12 143 ievntvdgfQGrekdviilslVRsn..................ekkeigflkderrlNValTRAkskliivG 196
                                       ++  t+ g  G + + +++   ++                   ++++  + +++r + Va+TRAk+++++v 
  gi|474934934|ref|YP_007688516.1| 670 MTFMTIHGSKGLQASRVFILNNKTGsygfpnvrdeppiiplllNSQDNQLDEERRLFYVAMTRAKKRVYLVA 741
                                       6666666666666666666666663222222222233333333222333445555568*********99986 PP

>> DUF4122  Domain of unknown function (DUF4122)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   8.6e-05      0.11     141     192 ..     332     384 ..     322     391 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.6e-05
                           DUF4122 141 nlgdvllkln.eadedeekslraaltlhsiretdlfevfssqvenkevieell 192
                                       n+++++l+ n +a ed  +s+   +t+h i +t+l+e+f  +  +  ++e+l 
  gi|474934934|ref|YP_007688516.1| 332 NVAQFMLDANpNAAEDYRQSMEWKRTIHRINNTELVELFAYNRSEGTLLEDLK 384
                                       78888887764788**************************9999999998885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (815 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       781  (0.0435607); expected 358.6 (0.02)
Passed bias filter:                      669  (0.0373138); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.85u 0.33s 00:00:01.18 Elapsed: 00:00:00.55
# Mc/sec: 4487.98
//
Query:       gi|474934935|ref|YP_007688517.1|  [L=63]
Description: DNA-directed RNA polymerase, subunit N [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.1e-29  100.6   0.6    4.6e-29  100.5   0.6    1.0  1  RNA_pol_N       RNA polymerases N / 8 kDa subunit
  ------ inclusion threshold ------
      0.061   13.6   0.3      0.092   13.0   0.3    1.3  1  Chordopox_RPO7  Chordopoxvirus DNA-directed RNA polymerase 7 


Domain annotation for each model (and alignments):
>> RNA_pol_N  RNA polymerases N / 8 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.5   0.6   5.1e-33   4.6e-29       1      58 [.       1      58 [.       1      59 [. 0.98

  Alignments for each domain:
  == domain 1  score: 100.5 bits;  conditional E-value: 5.1e-33
                                      ----SS-TTT--B-STHHHHHHHHHHTT--HHHHHHHHT--SHHHHHHHHTB--THHH CS
                         RNA_pol_N  1 MiiPVrCFtCGkvigekweeylellekgeepkdaLdaLglkryCCrrmllthvdliek 58
                                      MiiPVrCFtCGkv+g+ + ey ++++ g +pk++Ld++g++ryCCrrm+++h dli +
  gi|474934935|ref|YP_007688517.1|  1 MIIPVRCFTCGKVVGSAYSEYINRVKMGDDPKKVLDDMGFERYCCRRMIVSHADLIGE 58
                                      9******************************************************976 PP

>> Chordopox_RPO7  Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3     1e-05     0.092       1      41 [.       1      46 [.       1      54 [. 0.72

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1e-05
                    Chordopox_RPO7  1 mvfplvCstCGrDlseeryrLlvkkkkL....kdvlat..vkrkCCr 41
                                      m+ p+ C tCG+ +  + y   +++ k+    k+vl+   ++r CCr
  gi|474934935|ref|YP_007688517.1|  1 MIIPVRCFTCGKVVGSA-YSEYINRVKMgddpKKVLDDmgFERYCCR 46
                                      8999********88776.5555555444333489**8633699***9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 426.46
//
Query:       gi|474934936|ref|YP_007688518.1|  [L=132]
Description: SSU ribosomal protein S9P [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-33  115.3   0.5    2.6e-33  115.1   0.5    1.0  1  Ribosomal_S9  Ribosomal protein S9/S16


Domain annotation for each model (and alignments):
>> Ribosomal_S9  Ribosomal protein S9/S16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.1   0.5   1.5e-37   2.6e-33       1     121 []       8     132 .]       8     132 .] 0.92

  Alignments for each domain:
  == domain 1  score: 115.1 bits;  conditional E-value: 1.5e-37
                                       EECTTEEEEEEEEESSSEEEETTEECCHHSTTSCHHHHHCHHHHHTTTSS.SEEEEEEEESS-HHHHHHHHHHHHHH CS
                      Ribosomal_S9   1 GrrKesvArvwikegkgkilvngksleeYfkeeaarekvleplkltgllg.kfdvfvkvkgGGlsgqaeAirlgiar 76 
                                       G+rK+++Ar+ +keg+gk++vn+++++  f+ e ar k++epl+l+ ++  k+d+ v+v+gGG++gqa+A+r++iar
  gi|474934936|ref|YP_007688518.1|   8 GKRKTAIARAVVKEGTGKVTVNKTPIDI-FTPELARLKIKEPLELVPEKAaKVDISVTVSGGGVMGQAAAVRTAIAR 83 
                                       8***************************.6559************9887736************************* PP

                                       HHHHHHHHH..HHHHC..TCCCTS-B--------TTSSCTTB----S-- CS
                      Ribosomal_S9  77 aLvalekee..kkeLk..kaglltrDpRvvErkKtgkkkARkkyqwskR 121
                                       +Lv++++++  +  +k  +++l+ +D R++ +kK+  ++AR+k q+s+R
  gi|474934936|ref|YP_007688518.1|  84 GLVEFYNDKdlEAMFKayDRTLMINDDRRKLPKKPLGPGARAKKQKSYR 132
                                       *****99433355555889****************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 869.08
//
Query:       gi|474934937|ref|YP_007688519.1|  [L=141]
Description: ribosomal protein L13, archaeal/eukaryotic [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.4e-10   39.4   0.0    1.2e-08   35.3   0.0    2.1  1  Ribosomal_L13  Ribosomal protein L13


Domain annotation for each model (and alignments):
>> Ribosomal_L13  Ribosomal protein L13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.0   6.5e-13   1.2e-08      33     117 ..      21     105 ..       2     113 .. 0.82

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 6.5e-13
                                       TTS--S-EEEEEEGGCBB-SSTHHTT-EEEEE-SSTTSEEEEEHHHHHCCSHHHHHHHHHHCCS-S.SHHHHHHGCT CS
                     Ribosomal_L13  33 phvdcGdyvvvinaekvaltgkkleqkvyyrhtgypgglkevtakellekkpeeilekaVkgmLpk.nklgrrrlkr 108
                                       + +  G+ vvv+naek+ +tg+++e  + ++h+   g++ +++   +  ++ + +++++V+gm+p+ ++ gr+ ++ 
  gi|474934937|ref|YP_007688519.1|  21 NMIMSGEEVVVLNAEKIIVTGERAEVLKDFKHKVDLGEVTKRKG-PFYPRRADLLFKRCVRGMIPRyTTTGREAYRA 96 
                                       445689********************999999999999988765.5778889*************9567899999** PP

                                       EEEESSSTT CS
                     Ribosomal_L13 109 Lkvyageeh 117
                                       L+v+ g   
  gi|474934937|ref|YP_007688519.1|  97 LHVFVGVPK 105
                                       ****99654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 879.68
//
Query:       gi|474934938|ref|YP_007688520.1|  [L=122]
Description: LSU ribosomal protein L18AE [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.9e-09   36.9   2.5    6.2e-09   36.6   2.5    1.3  1  Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27
    9.5e-09   34.9   0.1    9.6e-09   34.9   0.1    1.1  1  Ribosomal_L18   Ribosomal protein 60S L18 and 50S L18e
  ------ inclusion threshold ------
      0.015   15.3   0.0        0.6   10.2   0.0    2.6  2  Dimerisation    Dimerisation domain
       0.15   12.2   0.0       0.27   11.4   0.0    1.4  1  Fer4_19         Divergent 4Fe-4S mono-cluster


Domain annotation for each model (and alignments):
>> Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   2.5   1.4e-12   6.2e-09      88     127 ..      56     103 ..       3     104 .. 0.77

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 1.4e-12
                                       .........SE..EEE--S---.--EEEESEE-HHHHHHHHHTT-EEE CS
                    Ribosomal_L27A  88 k......kdgv..KvlgkgeltkklkvkaskfSkkAkekIeaaGGkve 127
                                       k      +  v  Kvl+ geltkk++v a +fS+kAke+I aaGGk++
  gi|474934938|ref|YP_007688520.1|  56 KyakdgeTIAVpgKVLAAGELTKKVNVAAYSFSAKAKEAIVAAGGKAM 103
                                       2333455333345********************************986 PP

>> Ribosomal_L18  Ribosomal protein 60S L18 and 50S L18e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.1   2.1e-12   9.6e-09      46     137 ..      35     120 ..       2     122 .] 0.83

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 2.1e-12
                     Ribosomal_L18  46 vlkrLfmsrinrpplslsrlvkkvkkkeeekkiavvvgtvtdDvrllevPklsvaALrftetararilkaGGeiltl 122
                                       +  rL +  + r+   ls++ k+ k    +++++ v g+v+    l++  k++vaA  f+++a++ i++aGG+ +tl
  gi|474934938|ref|YP_007688520.1|  35 IALRLESPIRVRAEANLSKIEKYAK----DGETIAVPGKVLAAGELTK--KVNVAAYSFSAKAKEAIVAAGGKAMTL 105
                                       5667777778888899999988887....5689999******999986..9************************** PP

                     Ribosomal_L18 123 DqLalraPtGkntvL 137
                                        +L  + P G+++ +
  gi|474934938|ref|YP_007688520.1| 106 RELMDECPSGSKVRI 120
                                       **********98765 PP

>> Dimerisation  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.042   1.9e+02      13      33 ..      62      81 ..      61      91 .. 0.85
   2 ?   10.2   0.0   0.00013       0.6      13      33 ..      93     113 ..      92     119 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.042
                      Dimerisation 13 diiakaggkplspsEiaskLp 33
                                      ++ia  g k l++ E+ +k++
  gi|474934938|ref|YP_007688520.1| 62 ETIAVPG-KVLAAGELTKKVN 81
                                      7888887.*********9987 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00013
                      Dimerisation  13 diiakaggkplspsEiaskLp 33 
                                       ++i++aggk++++ E++   p
  gi|474934938|ref|YP_007688520.1|  93 EAIVAAGGKAMTLRELMDECP 113
                                       79**************97766 PP

>> Fer4_19  Divergent 4Fe-4S mono-cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0     6e-05      0.27      29      57 ..      87     115 ..      80     118 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6e-05
                           Fer4_19  29 FdpkrkpwikpdeasteeiievverCPSG 57 
                                       F  k+k  i   ++++ +++e  ++CPSG
  gi|474934938|ref|YP_007688520.1|  87 FSAKAKEAIVAAGGKAMTLRELMDECPSG 115
                                       78888999999999*************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 895.94
//
Query:       gi|474934939|ref|YP_007688521.1|  [L=377]
Description: Endonuclease IV [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.2e-09   35.6   0.0    1.7e-08   34.1   0.0    1.7  1  AP_endonuc_2  Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0   9.7e-13   1.7e-08      33     182 ..     108     266 ..      95     278 .. 0.85

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 9.7e-13
                                       HHHHHHHTTSEEEEEEECCCHSTCTHC.HTTCS...HHHHHHHHHHHHHHHHHHTBSEEEEEBCCGBCTTTSGHHHH CS
                      AP_endonuc_2  33 lrkaldelglriaslslftrfgypded.erear...reesvdalkraielaaaLGapllvlhpGtagagpkgseeea 105
                                       l + ++++++ ++ +++++ +   d     ++r     +  + +++a  + +aLG++++v+++G  ++ +++s+ee+
  gi|474934939|ref|YP_007688521.1| 108 LGNVARRHDVSLSIHTPYYMDLTADITdMDDPRaglTMQYYESVRQAGFILNALGGDIVVTNIG--PYSDDRSREET 182
                                       556677777777777777766665554433333556667789999999****************..9********** PP

                                       HHHHHHHHHHHHHHHHHHT..SEEEEE--TTTTSSSTCHHHHHHHHHHTTTTEEEEEEHHHHHHH.......TTTHH CS
                      AP_endonuc_2 106 werlaeslneladyaekeg..vklalEtlagsgvelgdeelarlldavdspnvgvclDtgHllia.......eedvd 173
                                        + ++++l  l +  ++     +l++E +  ++v+   +++++l+d+++   +  +++++H++ +        +d++
  gi|474934939|ref|YP_007688521.1| 183 DDIVRNNLGMLTEWWQDMKftPRLGIEVTGHQDVFGSLDQVLDLCDEIPG--LTPVMNFAHYQSRtkgslltATDFA 257
                                       **************996554499***********9999***********8..************************* PP

                                       HHHHHHHGG CS
                      AP_endonuc_2 174 dalraladr 182
                                       d+l++l+++
  gi|474934939|ref|YP_007688521.1| 258 DILQKLEPY 266
                                       *****9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2413.52
//
Query:       gi|474934940|ref|YP_007688522.1|  [L=177]
Description: putative sugar phosphate isomerase involved in capsule formation [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-17   63.1   0.1    2.8e-17   62.8   0.1    1.1  1  SIS       SIS domain
    8.8e-07   29.0   3.9      0.011   15.8   0.2    2.4  3  SIS_2     SIS domain
  ------ inclusion threshold ------
      0.068   12.8   0.0       0.15   11.7   0.0    1.5  1  DUF2529   Domain of unknown function (DUF2529)
       0.16   12.1   0.0       0.22   11.6   0.0    1.3  1  DUF1398   Protein of unknown function (DUF1398)


Domain annotation for each model (and alignments):
>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.8   0.1   6.3e-21   2.8e-17       2     110 ..      30     132 ..      29     149 .. 0.94

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 6.3e-21
                                       HCTSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHH CS
                               SIS   2 LakakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelake 78 
                                       + +a+ri+++G G+s+ +a+ +a  l ++g +v++v d ++      + i +ddl+il+s +g+t ++v++a+ a+ 
  gi|474934940|ref|YP_007688522.1|  30 IVSAERIFIFGVGRSGLVAQTFAIRLVQMGLRVYFVGDMTT------PIIGKDDLLILVSNTGNTMSVVKTAQIAQG 100
                                       6789*************************************......9***************************** PP

                                       TTSEEEEEESSTTSHHHHHSSEEEEEEEECHC CS
                               SIS  79 rgakiiaITdskgsplareadlalyinaepet 110
                                        g + i+IT + +s+la+ +d+++ i a++ +
  gi|474934940|ref|YP_007688522.1| 101 IGTRRISITANGKSSLAKTSDEVIVISASNPE 132
                                       **********************9999887655 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   5.7e-06     0.026      22      59 ..      20      57 ..       4      67 .. 0.85
   2 !   15.8   0.2   2.4e-06     0.011     102     137 ..      74     109 ..      68     110 .. 0.92
   3 ?   -3.6   0.1       2.3     1e+04     101     113 ..     117     129 ..     114     130 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.7e-06
                                      HHHHHHHHHHHHTT--EEEEESGGGHHHHHHTSSSTT- CS
                             SIS_2 22 ekaaeliadslenggkvlvfGsGhSaalaeelaaragg 59
                                      e+  + + +s+ + +++++fG G S + a+ +a r++ 
  gi|474934940|ref|YP_007688522.1| 20 EECGRSLIESIVSAERIFIFGVGRSGLVAQTFAIRLVQ 57
                                      566788999*************************9985 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 2.4e-06
                                       -TT-EEEEE-SS--SHHHHHHHHHHHHHT-EEEEEE CS
                             SIS_2 102 kpgDvLlviSnsGnnavvveaaeaakergmkviAlt 137
                                        + D+L+ +Sn Gn  +vv+ a+ a+ +g + i +t
  gi|474934940|ref|YP_007688522.1|  74 GKDDLLILVSNTGNTMSVVKTAQIAQGIGTRRISIT 109
                                       689***************************999998 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 2.3
                                       --TT-EEEEE-SS CS
                             SIS_2 101 lkpgDvLlviSns 113
                                       +k++D  +viS+s
  gi|474934940|ref|YP_007688522.1| 117 AKTSDEVIVISAS 129
                                       5778888999986 PP

>> DUF2529  Domain of unknown function (DUF2529)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.4e-05      0.15      25     133 ..      20     129 ..      10     135 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.4e-05
                                       HHHHHHHHHHHHTT--EEEEE-GGGGGGH..HHHHCSTT--TTEEE--TT-.---TT-EEEEEES-S--HHHHHHHH CS
                           DUF2529  25 edaarlLaqavigdgkvyikgfgeleave..aealegkeklpsvkkleeek.eltetDrvllfsresndkealklak 98 
                                       e+ +r L+ ++++  +++i g+g    v+   ++   +  l      + +   + + D  +l+s+  n+ +++k a+
  gi|474934940|ref|YP_007688522.1|  20 EECGRSLIESIVSAERIFIFGVGRSGLVAqtFAIRLVQMGLRVYFVGDMTTpIIGKDDLLILVSNTGNTMSVVKTAQ 96 
                                       7889***************9998655544104444444455544444444446667777777788888889999999 PP

                                       HHHHHT--EEEEESS---T..TGGGSSS-EE---- CS
                           DUF2529  99 kleekgievvavsskvkeedalteladvfidlklk 133
                                        ++  g+  + ++++ k++  l++++d  i ++ +
  gi|474934940|ref|YP_007688522.1|  97 IAQGIGTRRISITANGKSS--LAKTSDEVIVISAS 129
                                       8888888888888888877..56666666666555 PP

>> DUF1398  Protein of unknown function (DUF1398)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   4.8e-05      0.22       9      66 ..      44      99 ..      38     129 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.8e-05
                                      HH---HHHHHHHHHH-SSEEEEETTTSEEEEE-SSS-EEEEE-STT-----S---HHH CS
                           DUF1398  9 sdadfpafiqelkrlgvskYeyfvadgnvkyvgendevvevkakrellkvaekknael 66
                                      s+   ++f+  l ++g++ Y  fv d ++ ++g++d  + v+++++ ++v ++++ ++
  gi|474934940|ref|YP_007688522.1| 44 SGLVAQTFAIRLVQMGLRVY--FVGDMTTPIIGKDDLLILVSNTGNTMSVVKTAQIAQ 99
                                      55666788888888888865..****************************99988665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1249.63
//
Query:       gi|474934941|ref|YP_007688523.1|  [L=136]
Description: hypothetical protein TALC_01385 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       186  (0.0103743); expected 358.6 (0.02)
Passed bias filter:                      174  (0.00970495); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1081.04
//
Query:       gi|474934942|ref|YP_007688524.1|  [L=185]
Description: Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 2 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-10   39.7   0.0    4.4e-10   39.3   0.0    1.1  1  ThiF      ThiF family
     0.0013   17.7   0.0     0.0019   17.2   0.0    1.2  1  DUF4910   Domain of unknown function (DUF4910)


Domain annotation for each model (and alignments):
>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.0   4.9e-14   4.4e-10     109     242 ..      45     166 ..      24     173 .. 0.82

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 4.9e-14
                                       T-SEEEEESSSHHHHHHHHHHHHHHT-EEEEEEEETTEEEEEEEEECCS-ECTSS-TGGS.EECCCCEEHHHHHHCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF 109 svDlVvdalDniearrlvnracvkkgiplieagtlgfegqvvviipgktgcyeCldpsstedptekkvplctsiagn 185
                                       ++Dl++ +l     r++vn+++ +++ipli++++ g  g++++++  + +c+eC        +++++ +    +a+ 
  gi|474934942|ref|YP_007688524.1|  45 NYDLIICCLGDAGKRLYVNSRAKEYRIPLIDGTVDGGRGRIQTVL-PEGPCLECGLD-----RSRRTSSKA--AAS- 112
                                       68******************************************9.59*******63.....333333333..111. PP

                                       E-B-HHHHHHHHHHHHHHHHHHHTTBCGGGCCEEEECCTTTTEEEEECCEEEEEEC- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF 186 ipaiatttavvaglaalellkllsgkeklenslltqvdllesrfenvelerakkskc 242
                                        p  + ++a  a ++  e+lk+l g+ +++ +   ++d +e + + +++ +++  kc
  gi|474934942|ref|YP_007688524.1| 113 EP-DSGAVAETARIIREEALKILAGEADRCLKGIIYYDSEEGTSSVLPMGKDP--KC 166
                                       13.4456788899999*******999888888888999999988888886666..55 PP

>> DUF4910  Domain of unknown function (DUF4910)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.1e-07    0.0019     114     160 ..      24      70 ..      23      79 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.1e-07
                                       E-TTHHHHHHHHH-GGGGGGEEEEEE--S--SSS-EEEE--TTSSSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DUF4910 114 vPetiGsitylsrneeklkkikaGlvltcvGdegalsykksrrgdae 160
                                       +P+t G +t l ++ +++++ +  l++ c+Gd+g+  y +sr ++  
  gi|474934942|ref|YP_007688524.1|  24 IPGTDGRVTVLRKEPNAMDSWNYDLIICCLGDAGKRLYVNSRAKEYR 70 
                                       7*****************************************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1512.97
//
Query:       gi|474934943|ref|YP_007688525.1|  [L=65]
Description: Uncharacterized protein containing a Zn-ribbon (DUF2116) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-10   40.9   0.3    1.8e-10   40.6   0.3    1.1  1  DUF2116   Uncharacterized protein containing a Zn-ribbon (DUF
  ------ inclusion threshold ------
      0.013   15.2   0.9      0.015   15.0   0.9    1.1  1  DUF2616   Protein of unknown function (DUF2616)


Domain annotation for each model (and alignments):
>> DUF2116  Uncharacterized protein containing a Zn-ribbon (DUF2116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.3     2e-14   1.8e-10       2      55 ..       7      59 ..       6      64 .. 0.77

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 2e-14
                           DUF2116  2 pHkHCivCGkaIpldesfCsekCqeeyekkrkkvarsqqilfgililllavvlv 55
                                       H HC  CG+a+p ++  C e+C  + ++k kk  r++  l+++++++ av ++
  gi|474934943|ref|YP_007688525.1|  7 DHDHCRYCGAAVPFEQAYCCEDCYWRDQEKMKK-DRQREALLAAIAVIGAVAIL 59
                                      6**********************9998888888.55566666666665555554 PP

>> DUF2616  Protein of unknown function (DUF2616)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.9   1.7e-06     0.015      51      85 ..       7      39 ..       2      52 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.7e-06
                           DUF2616 51 aedkCefClevveeedklfCkkClfPllcsesvde 85
                                       +d+C++C ++v  e++++C+ C++     e++++
  gi|474934943|ref|YP_007688525.1|  7 DHDHCRYCGAAVPFEQAYCCEDCYWRDQ--EKMKK 39
                                      4689*******************99663..33333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1080  (0.0602376); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 464.08
//
Query:       gi|474934944|ref|YP_007688526.1|  [L=339]
Description: hypothetical protein TALC_01388 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.051   13.6   0.0      0.095   12.8   0.0    1.4  1  Coiled-coil_56  Coiled-coil domain-containing protein 56
      0.087   12.2   0.2        0.2   11.1   0.2    1.6  1  Chalcone        Chalcone-flavanone isomerase


Domain annotation for each model (and alignments):
>> Coiled-coil_56  Coiled-coil domain-containing protein 56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.1e-05     0.095      62      85 ..      11      34 ..       3      48 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.1e-05
                    Coiled-coil_56 62 lvlgiygytfysvkqekfldelee 85
                                      +vl+i gy+fy++++e + d++ e
  gi|474934944|ref|YP_007688526.1| 11 VVLAIVGYSFYTIAKESLPDNFSE 34
                                      79******************9954 PP

>> Chalcone  Chalcone-flavanone isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   2.2e-05       0.2      91     158 ..     189     258 ..     179     295 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.2e-05
                                       -EEHHHHHHHHTTTHHHHHHHT...T---HHHHHHHHHHHHHHTT-EE-TT-EEEEEE-TTSEEE.EEEESS CS
                          Chalcone  91 pLtGaeysekvaencvailksv...giytdaeakaiekflevfkdetfpPGssilfavspkgsLt.vsfskd 158
                                       +++G + s  v+e ++a + s+   g+  da ++ ie++ +++    + PG  i+f++s +gs +  s s +
  gi|474934944|ref|YP_007688526.1| 189 NVSGVNVSAPVVEGTKASMTSTitdGMIKDAVNDLIEEYDDIIG--GYTPGDEIVFKTSNSGSEAqFSVSYE 258
                                       5789999************9864446777888888888888886..589*********99987431333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2446.36
//
Query:       gi|474934945|ref|YP_007688527.1|  [L=216]
Description: hypothetical protein TALC_01389 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.9    8.2   7.3        6.1    5.5   7.3    1.9  1  DUF2207   Predicted membrane protein (DUF2207)
        3.6    8.1   8.9       0.74   10.3   0.2    2.5  2  HRG       Haem-transporter, endosomal/lysosomal, haem-respons


Domain annotation for each model (and alignments):
>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   7.3   0.00068       6.1     341     409 ..       8     113 ..       2     201 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.00068
                           DUF2207 341 kyakkskkkakkfkkalkkwksavkkkergyfdkkgkkklkklsalglgliilglilillallllvll......... 408
                                       k a+   +k k+ kk l+++ ++ +k++++y+++k++  + ++  ++  +++++++l+++a    + +         
  gi|474934945|ref|YP_007688527.1|   8 KAAR---EKEKERKKGLDSFDRGKEKEYKKYLNSKSRFVKGIVYSVIEYILVIVFVLAIVAY---TQGddmshfqdd 78 
                                       3333...3888999999999999999999999999655554444444444444444443332...222678****** PP

                           DUF2207 409 ..................................l 409
                                                                          
  gi|474934945|ref|YP_007688527.1|  79 viemlkpgnfiftalvsflpiiilgnistyfgigT 113
                                       *****998764444444444444444444433330 PP

>> HRG  Haem-transporter, endosomal/lysosomal, haem-responsive gene
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.2   8.3e-05      0.74       8      48 ..      45      97 ..      39     100 .. 0.63
   2 ?    0.1   4.1      0.12   1.1e+03       5      27 ..     117     139 ..     116     178 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 8.3e-05
                               HRG  8 gifgsilglsaflvylvlaivnkq............gvsl.ptSfylsavWsll 48
                                      gi+ s++  +  +v+  + + + q            ++ l p +f+++a+ s+l
  gi|474934945|ref|YP_007688527.1| 45 GIVYSVIEYILVIVFVLAIVAYTQgddmshfqddviEM-LkPGNFIFTALVSFL 97
                                      56666666555555555444444448666555544433.55***********98 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.12
                               HRG   5 iaygifgsilglsaflvylvlai 27 
                                       +a+gi+  ++ ++++ v l++a+
  gi|474934945|ref|YP_007688527.1| 117 MAIGIIRCLILVVWIYVVLIAAG 139
                                       78899999999999999999864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1074  (0.059903); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 1448.15
//
Query:       gi|474934946|ref|YP_007688528.1|  [L=264]
Description: dihydropteroate synthase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-71  241.0   0.0    1.6e-71  240.9   0.0    1.0  1  Pterin_bind  Pterin binding enzyme
  ------ inclusion threshold ------
      0.047   13.7   0.0      0.077   13.0   0.0    1.3  1  CAT_RBD      CAT RNA binding domain


Domain annotation for each model (and alignments):
>> Pterin_bind  Pterin binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  240.9   0.0   1.8e-75   1.6e-71       1     244 []      18     255 ..      18     255 .. 0.96

  Alignments for each domain:
  == domain 1  score: 240.9 bits;  conditional E-value: 1.8e-75
                                       EEEEETTTTTCHCCHHCTHHHHHHHHHHHHHHTT-SEEEEESS-TSTT--CCHHHHHHHHHHHHHHHHHHHCTSEEE CS
                       Pterin_bind   1 mgilNvtpdsfsdggkfedldkalaqarkmveeGAdilDiggestrPgaervdeeeelervvpvlealrdeadvpis 77 
                                       mgilNvtpdsfsdggk  ++++ala+a +++e+GAdi+DiggestrPga++v+ eeel+r++pvl++l   +dvp+s
  gi|474934946|ref|YP_007688528.1|  18 MGILNVTPDSFSDGGKWDSPKTALAHALDLIEQGADIIDIGGESTRPGATPVSREEELSRLLPVLKELIPSIDVPVS 94 
                                       9*********************************************************************99***** PP

                                       EE-S-HHHHHHHHHTTSEEEEETTTTSSSTTHHHHHHHHT-EEEEESECSSTTTHCCCCCCCSSHHHHHHHHHHHHH CS
                       Pterin_bind  78 iDttkaevaeaAlkagadivNdvsgeerdpkmlelvaeagaavvvmhmrgtpktmqeeegqyedvveeveaflearv 154
                                       +Dt+ka+vaea+++ ga+i+Ndvsg+  dp+m+ ++a+ g+++v+m + g+p t+++++    d v   +  l   +
  gi|474934946|ref|YP_007688528.1|  95 VDTMKADVAEACVALGASIINDVSGLG-DPDMAMTAADCGVPLVLMSSYGDPSTFRTQT-IPGDGVLYAREKLAGLT 169
                                       **************************9.*******************************.77777777788888899 PP

                                       HHHHHTT--GGGEEEETTTTSSTTHHHHHHHHHTHHHHHHTTSSEBEEEGTTGHHHHHHHCTTCHGHHHHHHHHHHH CS
                       Pterin_bind 155 eaaeeaGvaperillDpgigfgkteehnlellrrldelrealevpvllGvSrksflgrllelgkaeeRdagtaafla 231
                                       e+a eaGv++e i+lDpgigfg ++ +  e+l++ +++ +  ++pvl+G Srk+fl    +    ++ da+ta ++ 
  gi|474934946|ref|YP_007688528.1| 170 EKALEAGVREEMIILDPGIGFGTSPGQATEMLAHSSDF-SLGRYPVLIGPSRKRFLSHAFP---GKDPDAATAEACE 242
                                       99999*********************************.9999**************9763...469********** PP

                                       HHHHTT-SEEEES CS
                       Pterin_bind 232 laaaaGadivrVh 244
                                       +aa  Gadi+rVh
  gi|474934946|ref|YP_007688528.1| 243 IAASSGADILRVH 255
                                       ************9 PP

>> CAT_RBD  CAT RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   8.6e-06     0.077      19      40 ..     178     199 ..     172     209 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.6e-06
                                       CSEEEEE-TTTTTT--TTSEEE CS
                           CAT_RBD  19 gkEvilmGkGIGFgkkkgdeid 40 
                                        +E+i++  GIGFg  +g+  +
  gi|474934946|ref|YP_007688528.1| 178 REEMIILDPGIGFGTSPGQATE 199
                                       69****************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1879.89
//
Query:       gi|474934947|ref|YP_007688529.1|  [L=354]
Description: Fe-S oxidoreductase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-27   95.0   1.9    2.1e-14   53.5   0.1    2.8  2  CCG       Cysteine-rich domain
    2.3e-08   34.4   4.9    2.3e-08   34.4   4.9    2.3  2  Fer4_8    4Fe-4S dicluster domain
    4.3e-08   33.6   4.5    4.3e-08   33.6   4.5    3.2  4  Fer4_17   4Fe-4S dicluster domain
      3e-07   30.4   5.7      3e-07   30.4   5.7    2.6  3  Fer4_10   4Fe-4S dicluster domain
    1.4e-06   28.8   6.2    1.4e-06   28.8   6.2    2.7  3  Fer4_7    4Fe-4S dicluster domain
     0.0013   18.8  13.4      0.034   14.3   0.2    3.8  4  Fer4_9    4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.027   14.3   2.4      0.027   14.3   2.4    3.1  2  Fer4      4Fe-4S binding domain
      0.048   14.2   1.0      0.048   14.2   1.0    4.3  4  Fer4_4    4Fe-4S binding domain
       0.35   11.0  12.4       0.28   11.4   0.8    3.3  3  Fer4_21   4Fe-4S dicluster domain
        2.4    9.2  15.2        4.8    8.2  12.3    2.9  4  Fer4_16   4Fe-4S double cluster binding domain
          5    7.4  16.8        4.5    7.5   1.3    3.6  4  Fer4_18   4Fe-4S dicluster domain
        7.9    6.7  17.9      0.095   12.8   1.6    3.6  3  Fer4_6    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   0.2   4.3e-16   6.5e-13       1      85 []     129     212 ..     129     212 .. 0.94
   2 !   53.5   0.1   1.4e-17   2.1e-14       1      85 []     247     333 ..     247     333 .. 0.96

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 4.3e-16
                               CCG   1 vayfdgChllraaypevrkalkkllealgveleelekesCCGagggrsgkee.laealakrnvetaeetgadaivta 76 
                                       vayf gC  + +++ ++ ka   +l +lgv+  +l +e CCG+   r g  +    +l++rnv+++ ++g++ +v  
  gi|474934947|ref|YP_007688529.1| 129 VAYFAGC-TATYRATKTAKASMSILDKLGVDWTTL-DEVCCGSVMQRVGWPQeDVTKLMQRNVDAITSLGVKTLVLS 203
                                       89*****.9**************************.*******9888877665999********************* PP

                               CCG  77 cpgCllqlk 85 
                                       c+gC+ ++k
  gi|474934947|ref|YP_007688529.1| 204 CAGCYRMFK 212
                                       *****9985 PP

  == domain 2  score: 53.5 bits;  conditional E-value: 1.4e-17
                               CCG   1 vayfdgChllraa..ypevrkalkkllealgveleel.ekesCCGagggrsgkee.laealakrnvetaeetgadai 73 
                                       v+y+d+Chl+r+   y+++r ++++ + +++ e++++ + + CCG ggg++   + +a ++a+ ++++a    ad+i
  gi|474934947|ref|YP_007688529.1| 247 VTYHDPCHLGRHCgvYDAPRDVIRQFPDVDFKEMQFNrDLSHCCGGGGGVRAAFPeEAADIANTRLDEASF--ADMI 321
                                       89*********************************************999998877999***********9..8*** PP

                               CCG  74 vtacpgCllqlk 85 
                                       +t+cp+C ++lk
  gi|474934947|ref|YP_007688529.1| 322 ITTCPFCVTNLK 333
                                       *******99885 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   4.9   1.5e-11   2.3e-08       2      65 .]       5      73 ..       4      73 .. 0.80
   2 ?   -2.2   0.1       3.9   5.8e+03      45      54 ..     198     207 ..     166     209 .. 0.58

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 1.5e-11
                            Fer4_8  2 lekCieCgaCqsaCpvlrrtkkhlldargeaae.........dvqeeqvlee....eealwsCttcgaCtevCpvgi 65
                                      l +C+ Cg+C+s Cp++++ + +   +rg+            +              +++++Cttc  C+++C  ++
  gi|474934947|ref|YP_007688529.1|  5 LTSCTMCGFCKSVCPSFKSINWDTDLSRGRIVLtyglavgqiE--------PdesvVKSMYTCTTCADCVRRCTSKV 73
                                      578*****************98888888887776776655442........03334588**************9875 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.9
                            Fer4_8  45 eealwsCttc 54 
                                       ++ + sC +c
  gi|474934947|ref|YP_007688529.1| 198 KTLVLSCAGC 207
                                       6666677777 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   4.5   2.9e-11   4.3e-08       2      60 ..       8      73 ..       7      74 .. 0.75
   2 ?   -3.1   0.0       8.4   1.2e+04      11      25 ..      99     116 ..      94     137 .. 0.56
   3 ?   -2.1   0.0       3.8   5.7e+03      44      49 ..     202     207 ..     169     210 .. 0.66
   4 ?    0.1   0.0      0.82   1.2e+03      20      48 ..     263     291 ..     250     294 .. 0.75

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 2.9e-11
                           Fer4_17  2 CiqCgyClpeCpsyeaydnepkkllraakl......glleeaeke.ekaslCieCgeCerkCPqgl 60
                                      C+ Cg+C  +Cps++ ++++ +  + ++ l      g++e  e   + + +C++C  C+r+C +++
  gi|474934947|ref|YP_007688529.1|  8 CTMCGFCKSVCPSFKSINWDTDLSRGRIVLtyglavGQIEPDESVvKSMYTCTTCADCVRRCTSKV 73
                                      ****************9997664444443333333377777655469***************9876 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 8.4
                           Fer4_17  11 eCpsyeaydn...epkkl 25 
                                       +C    +y n   e+k++
  gi|474934947|ref|YP_007688529.1|  99 MCENIVNYHNpfaEKKSV 116
                                       566555555433223333 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 3.8
                           Fer4_17  44 slCieC 49 
                                        +C++C
  gi|474934947|ref|YP_007688529.1| 202 LSCAGC 207
                                       555555 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.82
                           Fer4_17  20 nepkkllraaklglleeaekeekaslCie 48 
                                       + p+ ++r++   +++e++ ++  s C++
  gi|474934947|ref|YP_007688529.1| 263 DAPRDVIRQFPDVDFKEMQFNRDLSHCCG 291
                                       35888999999989999999999999986 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   5.7     2e-10     3e-07       7      55 ..       6      69 ..       1      70 [. 0.94
   2 ?   -2.8   0.1       4.8   7.2e+03      44      48 ..     203     207 ..     195     209 .. 0.60
   3 ?   -1.3   0.0       1.6   2.4e+03      17      28 ..     323     331 ..     312     345 .. 0.64

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 2e-10
                           Fer4_10  7 dtCirCgkCvkaCPadl...............tsvgakgeaseeeavrkkvekCtgcgaCveaC 55
                                       +C+ Cg C+++CP+                 t   a g+++++e v k ++ Ct+c  Cv+ C
  gi|474934947|ref|YP_007688529.1|  6 TSCTMCGFCKSVCPSFKsinwdtdlsrgrivlTYGLAVGQIEPDESVVKSMYTCTTCADCVRRC 69
                                      68*************66***************9999**************************** PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.8
                           Fer4_10  44 kCtgc 48 
                                       +C gc
  gi|474934947|ref|YP_007688529.1| 203 SCAGC 207
                                       44444 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.6
                           Fer4_10  17 kaCPadltsvga 28 
                                       + CP+   +v +
  gi|474934947|ref|YP_007688529.1| 323 TTCPF---CVTN 331
                                       45777...3433 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   6.2   9.4e-10   1.4e-06       1      51 [.       7      72 ..       7      73 .. 0.73
   2 ?   -2.4   0.0       5.1   7.6e+03      37      42 ..     203     208 ..     171     212 .. 0.76
   3 ?   -2.3   0.0       4.8   7.1e+03       4       9 ..     324     329 ..     301     331 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 9.4e-10
                            Fer4_7  1 rCigCgaCvaaCp.vkaieldeeenek..............gtekveidpekClgCgaCvavCPtg 51
                                      +C+ Cg+C ++Cp  k i++d + +                + e+v+ ++ +C++C  Cv++C ++
  gi|474934947|ref|YP_007688529.1|  7 SCTMCGFCKSVCPsFKSINWDTDLSRGrivltyglavgqiePDESVVKSMYTCTTCADCVRRCTSK 72
                                      5************999****9753332233444333322224478899999************986 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.1
                            Fer4_7  37 kClgCg 42 
                                       +C gC+
  gi|474934947|ref|YP_007688529.1| 203 SCAGCY 208
                                       466665 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 4.8
                            Fer4_7   4 gCgaCv 9  
                                        C +Cv
  gi|474934947|ref|YP_007688529.1| 324 TCPFCV 329
                                       355555 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   1.7   0.00035      0.52      34      48 ..       6      20 ..       1      24 [. 0.81
   2 !   14.3   0.2   2.3e-05     0.034      34      49 ..      57      72 ..      25      75 .. 0.79
   3 ?   -1.2   0.2       1.6   2.3e+03      33      39 ..     191     207 ..     164     209 .. 0.51
   4 ?   -1.2   0.0       1.6   2.4e+03      11      21 ..     324     334 ..     306     342 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00035
                            Fer4_9 34 eaCigCgaCveaCpk 48
                                      ++C++Cg C  +Cp+
  gi|474934947|ref|YP_007688529.1|  6 TSCTMCGFCKSVCPS 20
                                      579999999999996 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 2.3e-05
                            Fer4_9 34 eaCigCgaCveaCpkg 49
                                        C++C +Cv +C ++
  gi|474934947|ref|YP_007688529.1| 57 YTCTTCADCVRRCTSK 72
                                      47***********876 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.6
                            Fer4_9  33 e..........eaCigC 39 
                                       +           +C gC
  gi|474934947|ref|YP_007688529.1| 191 AitslgvktlvLSCAGC 207
                                       04444555445456666 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 1.6
                            Fer4_9  11 aCpagvvveda 21 
                                        Cp++v++ +a
  gi|474934947|ref|YP_007688529.1| 324 TCPFCVTNLKA 334
                                       57777776665 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   2.4   1.8e-05     0.027       7      19 ..       7      19 ..       5      20 .. 0.92
   2 ?    2.4   2.1      0.11   1.6e+02       6      18 ..      57      69 ..      52      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.8e-05
                                      TSSS-THHHHHST CS
                              Fer4  7 kCigCGaCvevCP 19
                                       C+ CG C +vCP
  gi|474934947|ref|YP_007688529.1|  7 SCTMCGFCKSVCP 19
                                      6************ PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.11
                                      TTSSS-THHHHHS CS
                              Fer4  6 ekCigCGaCvevC 18
                                        C+ C  Cv  C
  gi|474934947|ref|YP_007688529.1| 57 YTCTTCADCVRRC 69
                                      57*********99 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   1.0   3.2e-05     0.048       3      15 ..       7      19 ..       5      30 .. 0.91
   2 ?    1.4   4.3       0.4     6e+02       3      15 ..      58      70 ..      56      72 .. 0.84
   3 ?   -1.4   0.2       3.1   4.6e+03       4       7 ..     204     207 ..     202     209 .. 0.62
   4 ?   -0.6   0.2       1.7   2.6e+03       6      11 ..     324     329 ..     323     330 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.2e-05
                            Fer4_4  3 rCigCgsCvaaCP 15
                                      +C+ Cg C ++CP
  gi|474934947|ref|YP_007688529.1|  7 SCTMCGFCKSVCP 19
                                      7************ PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.4
                            Fer4_4  3 rCigCgsCvaaCP 15
                                      +C+ C  Cv+ C 
  gi|474934947|ref|YP_007688529.1| 58 TCTTCADCVRRCT 70
                                      7********9885 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 3.1
                            Fer4_4   4 CigC 7  
                                       C gC
  gi|474934947|ref|YP_007688529.1| 204 CAGC 207
                                       7777 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 1.7
                            Fer4_4   6 gCgsCv 11 
                                        C+ Cv
  gi|474934947|ref|YP_007688529.1| 324 TCPFCV 329
                                       699998 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.8   0.00018      0.28      40      57 ..       7      24 ..       2      26 .. 0.83
   2 ?    5.2   2.0     0.016        23       7      19 ..      58      70 ..      42      91 .. 0.65
   3 ?   -2.6   0.1       4.2   6.2e+03      40      44 ..     203     207 ..     190     210 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00018
                           Fer4_21 40 eCvGCnlCssvCPvedci 57
                                      +C+ C  C svCP  + i
  gi|474934947|ref|YP_007688529.1|  7 SCTMCGFCKSVCPSFKSI 24
                                      7************76655 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.016
                           Fer4_21  7 kCigCgkCliaCe 19
                                      +C  C  C+  C 
  gi|474934947|ref|YP_007688529.1| 58 TCTTCADCVRRCT 70
                                      4555555555555 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 4.2
                           Fer4_21  40 eCvGC 44 
                                       +C GC
  gi|474934947|ref|YP_007688529.1| 203 SCAGC 207
                                       46666 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   3.0    0.0039       5.8      53      65 ..       7      19 ..       2      21 .. 0.66
   2 ?    8.2  12.3    0.0032       4.8       2      65 ..       8      70 ..       7      72 .. 0.84
   3 ?    2.7   5.2      0.17   2.5e+02       1      16 [.      58      73 ..      58     107 .. 0.83
   4 ?   -2.3   0.0       6.1   9.1e+03      42      60 ..     313     328 ..     297     330 .. 0.54

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0039
                           Fer4_16 53 aitgCdiCqdvCP 65
                                       +t C+ C+ vCP
  gi|474934947|ref|YP_007688529.1|  7 SCTMCGFCKSVCP 19
                                      5666666666666 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0032
                           Fer4_16  2 CgtCgkCaevCPt.naikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCP 65
                                      C+ Cg C +vCP+ + i+ +  + +   + + +      ++++de   k+ + +t C+ C++ C 
  gi|474934947|ref|YP_007688529.1|  8 CTMCGFCKSVCPSfKSINWD--TDLSRGRIVLTYGLAVGQIEPDESVVKSMYTCTTCADCVRRCT 70
                                      ************97889988..677777766665667788999999999999************6 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.17
                           Fer4_16  1 rCgtCgkCaevCPtna 16
                                      +C+tC  C+  C +++
  gi|474934947|ref|YP_007688529.1| 58 TCTTCADCVRRCTSKV 73
                                      5999999999998765 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 6.1
                           Fer4_16  42 aedeekckkqeaitgCdiC 60 
                                        e +++++    it C  C
  gi|474934947|ref|YP_007688529.1| 313 DEASFADM---IITTCPFC 328
                                       34444444...44666666 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   1.3     0.003       4.5      55      74 ..       2      21 ..       1      31 [. 0.84
   2 ?    6.6   3.7    0.0057       8.5      49      80 ..      47      78 ..      23     108 .. 0.82
   3 ?   -0.1   0.0      0.69     1e+03      94     107 ..     166     179 ..     125     184 .. 0.82
   4 ?   -2.2   0.0       3.1   4.6e+03      61      70 ..     322     331 ..     296     344 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.003
                           Fer4_18 55 ekgagdcidcescvkvcPtg 74
                                      +++ + c+ c++c +vcP  
  gi|474934947|ref|YP_007688529.1|  2 QQALTSCTMCGFCKSVCPSF 21
                                      567789************75 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0057
                           Fer4_18 49 ekeerkekgagdcidcescvkvcPtgidirkG 80
                                      e +e   k++  c++c  cv+ c  ++ i + 
  gi|474934947|ref|YP_007688529.1| 47 EPDESVVKSMYTCTTCADCVRRCTSKVKIVDI 78
                                      566777888999***********999988765 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.69
                           Fer4_18  94 acdkvmeklgkpkg 107
                                        c +vm+++g+p+ 
  gi|474934947|ref|YP_007688529.1| 166 CCGSVMQRVGWPQE 179
                                       59999999999975 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 3.1
                           Fer4_18  61 cidcescvkv 70 
                                        ++c +cv+ 
  gi|474934947|ref|YP_007688529.1| 322 ITTCPFCVTN 331
                                       3467777765 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.6   6.3e-05     0.095       8      20 ..       7      19 ..       6      24 .. 0.90
   2 ?    2.4   2.9      0.12   1.8e+02       9      19 ..      59      69 ..      53      73 .. 0.86
   3 ?   -1.2   0.4       1.7   2.6e+03       8      14 ..     203     209 ..     203     209 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.3e-05
                            Fer4_6  8 kCigCgdCvrvCP 20
                                      +C+ Cg C +vCP
  gi|474934947|ref|YP_007688529.1|  7 SCTMCGFCKSVCP 19
                                      7************ PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.12
                            Fer4_6  9 CigCgdCvrvC 19
                                      C+ C dCvr C
  gi|474934947|ref|YP_007688529.1| 59 CTTCADCVRRC 69
                                      99999999876 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.7
                            Fer4_6   8 kCigCgd 14 
                                       +C gC++
  gi|474934947|ref|YP_007688529.1| 203 SCAGCYR 209
                                       5999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2298.12
//
Query:       gi|474934948|ref|YP_007688530.1|  [L=415]
Description: hypothetical protein TALC_01392 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-55  187.6   0.0    2.5e-55  186.8   0.0    1.4  1  Lar_N     Lactate racemase N-terminal domain
     0.0003   21.1   0.0    0.00057   20.2   0.0    1.5  1  DUF362    Domain of unknown function (DUF362)
  ------ inclusion threshold ------
       0.14   12.7   0.0        0.3   11.6   0.0    1.6  1  DUF4179   Domain of unknown function (DUF4179)


Domain annotation for each model (and alignments):
>> Lar_N  Lactate racemase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.8   0.0   4.1e-59   2.5e-55       1     200 [.       7     201 ..       7     205 .. 0.92

  Alignments for each domain:
  == domain 1  score: 186.8 bits;  conditional E-value: 4.1e-59
                             Lar_N   1 ygkk.kleleipeenllgvlepkevkeekdeeeaieeaLenpigsekleelvkekekvvivvsDiTRptpskiilpl 76 
                                       ygk+  +++eip+enl+g++ p  v    +  e i+++L+npig ++lee++  ++++v++v+D TRptp++++l +
  gi|474934948|ref|YP_007688530.1|   7 YGKDgVQKVEIPDENLIGTYYPADVV-CGNADEVINKSLDNPIGYASLEEFLDGGKDIVFIVNDGTRPTPTAQVLDA 82 
                                       66664789***************965.6778889******************************************* PP

                             Lar_N  77 lleelkeagvkdeditilvAtGlHrkqteeelkkilGeevvkri..kvvnhdaedksslvklGttskGtpveinklv 151
                                       +  +++      +  + l+AtG+Hr+ teee+++i+G ++ + +  +++ hda ++s++v+lGt+++Gtp+e+nk++
  gi|474934948|ref|YP_007688530.1|  83 IAGRMDL-----RSARYLIATGTHRAPTEEEYNNIFGRHLES-LrdRIIVHDA-KNSECVNLGTSKNGTPMEVNKIA 152
                                       ****998.....67799********************99854.447******9.8999******************* PP

                             Lar_N 152 aeadlviltGfiepHyfaGfsGGrKsilpGvasretimanHkavlaepr 200
                                       ++ad+++++ ++epHyfaG++GGrKs+lpGvas++ti++nHk+++  ++
  gi|474934948|ref|YP_007688530.1| 153 VDADRLVIITSVEPHYFAGWTGGRKSFLPGVASFRTIETNHKMAVGMEA 201
                                       *******************************************885555 PP

>> DUF362  Domain of unknown function (DUF362)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   9.5e-08   0.00057      71     169 ..     125     236 ..      67     278 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 9.5e-08
                                       xxxxxxxxxxxxxxxxx.xxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx. RF
                            DUF362  71 diadglegedevvvpvk.gkhlkke..lkiakavleaDviInlpklKgHalagvtgalKn.lfGcisgsgkaeiHs. 142
                                       ++ d    +++++v++   k+      +++ k +++aD ++ ++ +  H  ag tg+ K  l G++s ++    H+ 
  gi|474934948|ref|YP_007688530.1| 125 IVHD---AKNSECVNLGtSKN---GtpMEVNKIAVDADRLVIITSVEPHYFAGWTGGRKSfLPGVASFRTIETNHKm 195
                                       3333...23344444422222...13499****9**************************999**888876666666 PP

                                       .........xxxxxxxxxxxxxxxxxxx.xx...x.xxxxx RF
                            DUF362 143 .........krdsekfaekiadlakalk.pd...l.nvvdg 169
                                                k d + ++e ++d+++++k ++   + +v+d 
  gi|474934948|ref|YP_007688530.1| 196 avgmeaqalKLDGNPVHEDMMDALEIVKgKKifsIqVVMDR 236
                                       777788875224678***********854664444555554 PP

>> DUF4179  Domain of unknown function (DUF4179)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0     5e-05       0.3      50      88 ..     125     165 ..      90     166 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5e-05
                                       -..HHHHSEEEEEEEEETTEEEEEEEEEE-SSEEEEEEEEE CS
                           DUF4179  50 g..eqeyvkpvnksaednGitvtvnevvaDgnklivsysvk 88 
                                            + ++ vn   ++nG  ++vn++++D  +l++++sv+
  gi|474934948|ref|YP_007688530.1| 125 IvhDAKNSECVNLGTSKNGTPMEVNKIAVDADRLVIITSVE 165
                                       344455556699999************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2530.83
//
Query:       gi|474934949|ref|YP_007688531.1|  [L=316]
Description: thiamine-monophosphate kinase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-20   72.5   3.2    6.7e-20   71.6   2.1    2.0  2  AIRS      AIR synthase related protein, N-terminal domain
    7.5e-12   45.6   0.0    1.2e-11   44.9   0.0    1.3  1  AIRS_C    AIR synthase related protein, C-terminal domain


Domain annotation for each model (and alignments):
>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.6   2.1   7.5e-24   6.7e-20       1      93 [.      33     140 ..      33     141 .. 0.91
   2 ?   -1.2   0.0      0.38   3.4e+03      33      66 ..     213     249 ..     187     262 .. 0.54

  Alignments for each domain:
  == domain 1  score: 71.6 bits;  conditional E-value: 7.5e-24
                                       SSSEE.......EEEEEEEE.EECCTCCCC........HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HHH CS
                              AIRS   1 dDaav.......vvttdshnrpvlvepvhf........iGakavavnlsDlaamGArPlalllslalp......wle 56 
                                       dDaav       vv+td     v+ +++h+        +G++a+avn sDla+mGArP+++l +++ p      +l 
  gi|474934949|ref|YP_007688531.1|  33 DDAAVvkcpgdlVVSTD-----VVSAERHMpsgmtyeqFGWTAAAVNFSDLASMGARPVGFLAAISAPgdmeeaDLY 104
                                       89**5555555599999.....88888888888889999************************************** PP

                                       HHHHHHHHHHHHTT-EEEEEEEEEESSEEEEEEEEEE CS
                              AIRS  57 evvrglaeaaeelgvplvgGdtsfsneptisvtavGl 93 
                                       ++v+g+ +++e++g++++gGdt+ +  ++++ tavG 
  gi|474934949|ref|YP_007688531.1| 105 DIVSGIDQCCEHVGTDVIGGDTKPGA-LSVAGTAVGS 140
                                       ************************97.9*******97 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.38
                                       HHHHHTTTEEEEEEEEEEEEC...HHHHHHHHHHHHH CS
                              AIRS  33 lsDlaamGArPlalllslalp...wleevvrglaeaa 66 
                                       lsD +a  Ar ++    + ++   ++  v + +++ +
  gi|474934949|ref|YP_007688531.1| 213 LSDGLANAARTICRQSHVGMEiewEFLPVGENVEDIC 249
                                       4444455555555444444445553333333333333 PP

>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.9   0.0   1.4e-15   1.2e-11       1     149 [.     153     298 ..     153     303 .. 0.80

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 1.4e-15
                                       STTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHH CS
                            AIRS_C   1 kpGdvliltgslGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgala 77 
                                       +pGd++ +tg+lGl +ag+++++ ++ee++ +     +  +     +i+   ++a + g v+++ D+++ GL++a+ 
  gi|474934949|ref|YP_007688531.1| 153 RPGDLVAVTGTLGLAAAGYYSIEAGIEEADDE-----RFALNVPLPHIDDGIRMAKS-GIVTSCMDLSD-GLANAAR 222
                                       79************************999966.....33333333678888888887.***********.8****** PP

                                       HHHHTTTEEEEEECGTHHHHHHHH.........HHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEE CS
                            AIRS_C  78 emapasgvgaeidldkvpifdele.........splemllsensGrllvavppeeadavlaileeeglpeaavIGev 145
                                        ++++s vg+ei+++ +p+ +++e          +  +l+      l++++++++     ++l + gl  +++IG v
  gi|474934949|ref|YP_007688531.1| 223 TICRQSHVGMEIEWEFLPVGENVEdicrqagkdVKDAVLRWGGDYELMFTFRKDKV----QKLYDSGL-VFSIIGIV 294
                                       ***************88888877666666677766777777888888888888888....66666777.58888887 PP

                                       EESS CS
                            AIRS_C 146 take 149
                                        ++ 
  gi|474934949|ref|YP_007688531.1| 295 NNDS 298
                                       7765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1958.65
//
Query:       gi|474934950|ref|YP_007688532.1|  [L=337]
Description: Pyruvate-formate lyase-activating enzyme [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.1e-19   69.0   0.2    1.8e-18   67.5   0.3    1.7  2  Radical_SAM   Radical SAM superfamily
  ------ inclusion threshold ------
      0.018   15.2   2.7       0.13   12.4   0.1    2.9  3  Fer4_14       4Fe-4S single cluster domain
      0.018   15.3   1.2       0.03   14.6   0.0    2.0  3  Fer4_12       4Fe-4S single cluster domain
       0.02   14.9   0.1       0.02   14.9   0.1    2.9  4  DZR           Double zinc ribbon
      0.036   14.2   0.8       0.12   12.6   0.1    2.2  2  NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
       0.15   11.5   4.2       0.34   10.4   0.1    3.3  3  zf-ribbon_3   zinc-ribbon domain
       0.35   11.0   0.0       0.35   11.0   0.0    3.6  4  Zn-ribbon_8   Zinc ribbon domain
       0.49   10.6   6.7       0.14   12.3   1.2    2.7  3  Tat           Transactivating regulatory protein (Tat)


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.5   0.3     8e-22   1.8e-18       6     167 .]      86     236 ..      82     236 .. 0.93
   2 ?   -3.0   0.0       3.7   8.4e+03     112     143 ..     254     284 ..     247     291 .. 0.61

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 8e-22
                                       EESS--TTTSCCTT...HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEE CS
                                       xxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   6 gCnlrCsfCarpet...vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgir 79 
                                       gCnlrC +C+++         +r  ++s+e+i+++ ++ k     + + ++  ep+ ++++++++ ++     p++ 
  gi|474934950|ref|YP_007688532.1|  86 GCNLRCQYCQNYPIsmdAFGKKRTTYKSPEDIVALCRQQK----FGRIAFTYNEPSIWYEYIMDVMEED----PDLD 154
                                       9****************9999******************9....9************998877776665....58** PP

                                       EEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  80 itvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGen 156
                                       ++++tng+   ee l+ l +     ++++++a+++  + kl+  g+ +e v++++e+ +++ ++    +++++pG+n
  gi|474934950|ref|YP_007688532.1| 155 LVLVTNGMIE-EEPLRDLCKVT-GAMNIDVKAFNESFYSKLC--GGKLEYVKKTCEIVHASKVH-LELTYLVIPGYN 226
                                       *********9.*********77.*************555555..59****************99.************ PP

                                       HHHHHHHHHHH CS
                                       xxxxxxxxxxx RF
                       Radical_SAM 157 deeleellell 167
                                       d+e +++le++
  gi|474934950|ref|YP_007688532.1| 227 DDE-DDILEFV 236
                                       ***.*999986 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.7
                                       SSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 112 addekvlklmnrghtfeevlealeklreagik 143
                                       ++++ +  ++ ++   e +l++ e++ ++g++
  gi|474934950|ref|YP_007688532.1| 254 FHPD-YNMMTVPMTPAETLLRCKEIAEDNGLN 284
                                       5666.666665556666666666666666655 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.3       1.6   3.6e+03       8      19 ..      25      43 ..      21      59 .. 0.75
   2 ?   12.4   0.1   5.8e-05      0.13       7      94 ..      86     166 ..      81     184 .. 0.79
   3 ?    1.6   0.0      0.13   2.8e+02      64      86 ..     229     252 ..     198     265 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.6
                           Fer4_14  8 CnlsCk.......gCdnke 19
                                      C+++C+        C  ++
  gi|474934950|ref|YP_007688532.1| 25 CPHHCRikkdgfgLCNSRK 43
                                      99***97777776676555 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 5.8e-05
                           Fer4_14   7 gCnlsCkgCdnketwkselgkp.qteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekk 82 
                                       gCnl C+ C n    ++  gk+  t++  e+i++   ++++    + +t  eP ++      ++ +  + ee p+++
  gi|474934950|ref|YP_007688532.1|  86 GCNLRCQYCQNYPISMDAFGKKrTTYKSPEDIVALCRQQKF--GRIAFTYNEPSIW------YEYIMDVMEEDPDLD 154
                                       8*********9887777665541566777888888899999..4479998888866......999************ PP

                           Fer4_14  83 iwletngtleie 94 
                                         l tng++e e
  gi|474934950|ref|YP_007688532.1| 155 LVLVTNGMIEEE 166
                                       *******99955 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.13
                           Fer4_14  64 kkellklvkrlkeey.pekkiwle 86 
                                       ++++l++vk+++++  p+++++++
  gi|474934950|ref|YP_007688532.1| 229 EDDILEFVKWVRDSLsPDVPVHFN 252
                                       67899********99899999986 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.5   0.4         8   1.8e+04      15      20 ..      25      30 ..      23      31 .. 0.88
   2 ?   14.6   0.0   1.3e-05      0.03      13      68 ..      85     141 ..      76     188 .. 0.78
   3 ?   -3.3   0.0       4.4   9.8e+03      70      84 ..     230     244 ..     226     254 .. 0.73

  Alignments for each domain:
  == domain 1  score: -4.5 bits;  conditional E-value: 8
                           Fer4_12 15 CnlsCk 20
                                      C+++C+
  gi|474934950|ref|YP_007688532.1| 25 CPHHCR 30
                                      *****7 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1.3e-05
                           Fer4_12  13 sgCnlsCkgCfnketwsfksgkef.tkelleeiiedlkkesiegltllGGEPllpen 68 
                                        gCnl+C++C n  +     gk+  t +  e i++ + +++   + ++  EP+ +++
  gi|474934950|ref|YP_007688532.1|  85 IGCNLRCQYCQNYPISMDAFGKKRtTYKSPEDIVALCRQQKFGRIAFTYNEPSIWYE 141
                                       59**********9887666555551699999******99999999999999999543 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 4.4
                           Fer4_12  70 eallelvkevkeekp 84 
                                       +++le+vk+v+   +
  gi|474934950|ref|YP_007688532.1| 230 DDILEFVKWVRDSLS 244
                                       578999999998776 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   3.7       2.5   5.5e+03      29      36 ..      89      96 ..      18     107 .. 0.71
   2 ?   -0.0   0.4      0.42   9.3e+02      15      21 ..      91      97 ..      85     122 .. 0.72
   3 ?   -3.1   0.0       3.7   8.3e+03      18      23 ..     194     199 ..     187     206 .. 0.55
   4 ?   14.9   0.1   9.1e-06      0.02      10      38 ..     296     333 ..     289     336 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.5
                               DZR 29 drCpsCge 36
                                       rC  C+ 
  gi|474934950|ref|YP_007688532.1| 89 LRCQYCQN 96
                                      45666654 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.42
                               DZR 15 CseCgtk 21
                                      C++C++ 
  gi|474934950|ref|YP_007688532.1| 91 CQYCQNY 97
                                      5555444 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 3.7
                               DZR  18 Cgtklk 23 
                                       Cg kl+
  gi|474934950|ref|YP_007688532.1| 194 CGGKLE 199
                                       555553 PP

  == domain 4  score: 14.9 bits;  conditional E-value: 9.1e-06
                               DZR  10 pdarfCseCgtklkavaa.........edrCpsCgekv 38 
                                       + + +C+eCg+++ + +           drC  C++k+
  gi|474934950|ref|YP_007688532.1| 296 ATDTYCPECGASVIKRTGysvsilgldGDRCAFCKHKL 333
                                       4567*********977779***************9985 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       1.3     3e+03       9      16 ..      89      96 ..      88     137 .. 0.64
   2 ?   12.6   0.1   5.2e-05      0.12      19      42 ..     294     317 ..     270     332 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.3
                      NOB1_Zn_bind  9 lrChaCfk 16
                                      lrC+ C +
  gi|474934950|ref|YP_007688532.1| 89 LRCQYCQN 96
                                      56777765 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 5.2e-05
                      NOB1_Zn_bind  19 kdmtkkFCpkCGnktLkrvavsvd 42 
                                        d t  +Cp+CG + +kr+ +sv+
  gi|474934950|ref|YP_007688532.1| 294 DDATDTYCPECGASVIKRTGYSVS 317
                                       578999*************99986 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.74   1.7e+03       5      10 ..      91      96 ..      89     103 .. 0.60
   2 ?   10.4   0.1   0.00015      0.34       3      13 ..     299     310 ..     298     312 .. 0.83
   3 ?    0.3   0.1      0.23   5.2e+02      19      26 .]     326     333 ..     324     333 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.74
                       zf-ribbon_3  5 CPnCGa 10
                                      C +C +
  gi|474934950|ref|YP_007688532.1| 91 CQYCQN 96
                                      555544 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00015
                       zf-ribbon_3   3 vrCPnCGa.pls 13 
                                       ++CP+CGa +++
  gi|474934950|ref|YP_007688532.1| 299 TYCPECGAsVIK 310
                                       59******8876 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.23
                       zf-ribbon_3  19 CpyCGtkl 26 
                                       C+ C +kl
  gi|474934950|ref|YP_007688532.1| 326 CAFCKHKL 333
                                       88888776 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.7         2   4.6e+03       7      12 ..      90      95 ..      69      97 .. 0.62
   2 ?   -1.9   0.0       1.7   3.9e+03      22      34 ..     163     177 ..     159     180 .. 0.77
   3 ?   11.0   0.0   0.00016      0.35      22      38 ..     294     310 ..     288     312 .. 0.75
   4 ?   -0.6   0.2      0.66   1.5e+03       7      16 ..     325     334 ..     325     337 .] 0.80

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2
                       Zn-ribbon_8  7 rCeeCg 12
                                      rC+ C+
  gi|474934950|ref|YP_007688532.1| 90 RCQYCQ 95
                                      577776 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.7
                       Zn-ribbon_8  22 s.daplta.CPeCgs 34 
                                         ++pl + C+  g+
  gi|474934950|ref|YP_007688532.1| 163 IeEEPLRDlCKVTGA 177
                                       448999999*99887 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00016
                       Zn-ribbon_8  22 sdapltaCPeCgsevrr 38 
                                       +da +t CPeCg+ v +
  gi|474934950|ref|YP_007688532.1| 294 DDATDTYCPECGASVIK 310
                                       4677788*****96644 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 0.66
                       Zn-ribbon_8   7 rCeeCghefe 16 
                                       rC  C+h+ +
  gi|474934950|ref|YP_007688532.1| 325 RCAFCKHKLN 334
                                       8****99876 PP

>> Tat  Transactivating regulatory protein (Tat)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.2   6.4e-05      0.14      11      51 ..       7      45 ..       3      53 .. 0.84
   2 ?   -0.7   0.1      0.71   1.6e+03      29      37 ..      87      95 ..      63     111 .. 0.81
   3 ?   -2.1   0.0       2.1   4.6e+03      21      30 ..     296     305 ..     287     309 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.4e-05
                                      GS-B-S-SS---S--SCCHHTSSHHHHHHCTT---S-XXXX CS
                               Tat 11 khpgsqpktactncyckkcsfhcqvcfikkalGisyerkkr 51
                                      +hp    ++  t+c c  c  hc++   k ++G+   rk+ 
  gi|474934950|ref|YP_007688532.1|  7 NHPAKYWHSEGTDCVCDLCPHHCRI--KKDGFGLCNSRKNV 45
                                      68888999999************97..68899999999975 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.71
                                      HHTSSHHHH CS
                               Tat 29 csfhcqvcf 37
                                      c + cq c 
  gi|474934950|ref|YP_007688532.1| 87 CNLRCQYCQ 95
                                      888888884 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 2.1
                                       --S--SCCHH CS
                               Tat  21 ctncyckkcs 30 
                                        t+ yc  c 
  gi|474934950|ref|YP_007688532.1| 296 ATDTYCPECG 305
                                       6889999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       763  (0.0425568); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 1898.91
//
Query:       gi|474934951|ref|YP_007688533.1|  [L=280]
Description: hypothetical protein TALC_01395 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0033   17.8  14.5     0.0044   17.4   9.2    3.1  3  Peptidase_A24    Type IV leader peptidase family
     0.0058   17.1   0.0      0.013   16.0   0.0    1.5  1  Arc_PepC_II      Archaeal Peptidase A24 C-terminus Type II
  ------ inclusion threshold ------
       0.75   10.0   9.4       0.38   10.9   4.1    3.2  3  Phage_holin_3_3  LydA holin phage, holin superfamily III


Domain annotation for each model (and alignments):
>> Peptidase_A24  Type IV leader peptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   9.2   7.3e-07    0.0044       2      99 ..      14     169 ..      13     186 .. 0.69
   2 ?   -0.8   0.4      0.33     2e+03      46      74 ..     171     199 ..     157     199 .. 0.54
   3 ?   -0.7   0.1      0.32   1.9e+03      47      62 ..     257     272 ..     248     276 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 7.3e-07
                     Peptidase_A24   2 vlltillvlsviDldtrtlpdeltlpllllgvlfa...................qllllglpnlaqavlgalvgalv 59 
                                       v++++++++++ D+++r++ d+ + +++ + +l+                     ll++ ++               
  gi|474934951|ref|YP_007688533.1|  14 VVAAFMFAAALEDIRKREVRDCWWGAIAACHFLYLvqmyfedrvcweipvsgaaALLSFAAA--------------- 75 
                                       7899**********************999999999755555555555555554423233333............... PP

                     Peptidase_A24  60 llli.............................................slvdeq.amGgGDvklaavlgaflgwer 90 
                                                                                         +++++   Gg+D+k +++l+++++++ 
  gi|474934951|ref|YP_007688533.1|  76 ---AwaegrtaltlaagviascltvillgnadravlnsllipvfvsvycAMYRLGvLRGGADCKCLMALSVAFPVYP 149
                                       ...2444444455555555555777888899999888888888887777777888677****************776 PP

                     Peptidase_A24  91 l...............llavlvai 99 
                                                       +    +a+
  gi|474934951|ref|YP_007688533.1| 150 EvgrfpilgtdgtlsvV----FAF 169
                                       55666777777754332....333 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.33
                     Peptidase_A24  46 laqavlgalvgalvlllislvdeqamGgG 74 
                                       +   ++ga+++ ++ ++ +lv+++++G G
  gi|474934951|ref|YP_007688533.1| 171 ISVLFVGAVATTAFHVANVLVRNRGLGRG 199
                                       33334444444444444456667777765 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.32
                     Peptidase_A24  47 aqavlgalvgalvlll 62 
                                       +  +++al++a+v+++
  gi|474934951|ref|YP_007688533.1| 257 MMPFIAALAAAFVFVI 272
                                       4456666666666665 PP

>> Arc_PepC_II  Archaeal Peptidase A24 C-terminus Type II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.1e-06     0.013       8      90 ..     201     275 ..     198     276 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.1e-06
                       Arc_PepC_II   8 igyrvkvkellkkflflleefeekdgkikrkfisvekeldeelrkelkkykkkglieetvWvtygvPflipitaGfi 84 
                                       +gy + ++  +++f+ +le++ +  g+++r  +  ++e   +++++l++ ++ +       vt+ +Pf+  + a f+
  gi|474934951|ref|YP_007688533.1| 201 SGYVMPIDRAERSFVWPLEDVVD--GETRRVPVP-DDETVPDIYRRLRESERTE-----ALVTPMMPFIAALAAAFV 269
                                       79******************988..444553333.3355566666666666655.....89**************** PP

                       Arc_PepC_II  85 ialvlG 90 
                                       + + +G
  gi|474934951|ref|YP_007688533.1| 270 FVITVG 275
                                       *99988 PP

>> Phage_holin_3_3  LydA holin phage, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   4.1   6.3e-05      0.38      30      66 ..      56      92 ..      12      96 .. 0.88
   2 ?   -3.2   0.0       1.6   9.4e+03      28      43 ..     108     123 ..     102     125 .. 0.66
   3 ?   -0.5   0.2      0.22   1.3e+03      39      54 ..     174     189 ..     161     215 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6.3e-05
                   Phage_holin_3_3 30 ellleivvSgfvGllvfllceelglsqlltlaiagls 66
                                      ++ +ei+vSg ++ll f+++++++    ltla+  ++
  gi|474934951|ref|YP_007688533.1| 56 RVCWEIPVSGAAALLSFAAAAWAEGRTALTLAAGVIA 92
                                      589***************************9998776 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.6
                   Phage_holin_3_3  28 ikellleivvSgfvGl 43 
                                       +++ll+ ++vS+ +++
  gi|474934951|ref|YP_007688533.1| 108 LNSLLIPVFVSVYCAM 123
                                       5567777777776665 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.22
                   Phage_holin_3_3  39 gfvGllvfllceelgl 54 
                                       +fvG ++  + + +++
  gi|474934951|ref|YP_007688533.1| 174 LFVGAVATTAFHVANV 189
                                       3444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1865.29
//
Query:       gi|474934952|ref|YP_007688534.1|  [L=538]
Description: Small-conductance mechanosensitive channel [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-38  132.7   8.8    2.4e-38  131.7   8.8    1.5  1  MS_channel       Mechanosensitive ion channel
  ------ inclusion threshold ------
       0.54   10.2  13.1        0.1   12.6   3.5    2.7  3  Colicin_V        Colicin V production protein


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.7   8.8   2.7e-42   2.4e-38       5     206 .]     308     510 ..     304     510 .. 0.92

  Alignments for each domain:
  == domain 1  score: 131.7 bits;  conditional E-value: 2.7e-42
                                       HHHHHHHHHHHHHHTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESS..SEEEEEEEE CS
                        MS_channel   5 kiliivvgilivlsllgvnvsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveig..dieGtVedi 79 
                                        i+i +v++++++sllg+n++a+++++G+++l+++++++d+++++++G+ +l+++pfk GDl+++g  + +++V+ +
  gi|474934952|ref|YP_007688534.1| 308 EIIIAIVATMLIMSLLGFNLTAIITSAGLVSLGISMGAQDVLKQFFSGLEILATRPFKKGDLITVGtdTTIYRVRRV 384
                                       6899**************************************************************999******** PP

                                       -SSEEEEEETTSEEE.EEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-T... CS
                        MS_channel  80 glrttkirtfdgriv.tiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlk... 152
                                       +   t ++++d++ v ++Pns ++t++i+N +re+  +++ +++ v+y+sd   ++ v+  +++a++e+ +v++   
  gi|474934952|ref|YP_007688534.1| 385 NVMNTFLENWDNTDVsIMPNSLITTNKIQNITRETLVTKVYITVDVAYGSD---VNLVRTLMQQAANENHHVINdgs 458
                                       ************976266*********************************...66666666666666666666444 PP

                                       TS-EEEEEEEE-SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHHHHHHT--- CS
                        MS_channel 153 dkellvvldefgdsslnfevrvfvktvvpeeylsvqseinlrikkileeegiei 206
                                          +  +l++fg s+ln++  ++v +  ++ ++++  +i+++i++++ +++++i
  gi|474934952|ref|YP_007688534.1| 459 VTRPYTRLEAFGESNLNVKMGFYVDN--FSSKWAISGQIRQSIIEKFAANNVSI 510
                                       88999*********************..***********************986 PP

>> Colicin_V  Colicin V production protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1      0.95   8.5e+03     109     122 ..      13      25 ..       9      35 .. 0.55
   2 ?    4.0   0.4    0.0052        46      38      86 ..     153     205 ..     142     242 .. 0.79
   3 ?   12.6   3.5   1.1e-05       0.1      21      91 ..     249     336 ..     249     345 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.95
                         Colicin_V 109 llvvllllllalvp 122
                                       l +vl+ll+la+vp
  gi|474934952|ref|YP_007688534.1|  13 L-AVLALLMLAAVP 25 
                                       3.334444555555 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.0052
                         Colicin_V  38 asllypslaellae....lilspalaaiiaflllfllvllivsllgallsklv 86 
                                       +s  y+++  ++ +      +s ++ a+++f+ l+l++++++ +   ++s++v
  gi|474934952|ref|YP_007688534.1| 153 TSEKYNKFLGWFPNeldgALGSVWFTAAVSFVGLLLIGYAAMFIAVPVCSRIV 205
                                       5555667777777778886688899999***9999999999988877777766 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 1.1e-05
                         Colicin_V  21 fvrevlsllgwvvafvvasllypslaellae.................lilspalaaiiaflllfllvllivsllga 80 
                                       ++ ++++l+ +vv++vv+++ly+ + + +                    +  p + +i  ++++ ++++li+sllg 
  gi|474934952|ref|YP_007688534.1| 249 LINRLFYLAYIVVGVVVGWQLYKLIIDTVVRrlvvradeydidrktdfESFRPLFLYIGEIIIAIVATMLIMSLLGF 325
                                       57899*****************************************97434788888888899************** PP

                         Colicin_V  81 llsklvsktgl 91 
                                        l+ +++  gl
  gi|474934952|ref|YP_007688534.1| 326 NLTAIITSAGL 336
                                       ****9998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (538 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1109  (0.0618551); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 3344.13
//
Query:       gi|474934953|ref|YP_007688535.1|  [L=140]
Description: Transcriptional regulator [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.4e-16   58.2   0.7    5.7e-15   54.6   0.1    2.4  2  HTH_24          Winged helix-turn-helix DNA-binding
    5.4e-15   54.9   0.0    1.5e-14   53.5   0.0    1.7  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    4.7e-12   45.7   0.5    7.8e-12   45.0   0.5    1.4  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    2.2e-06   27.2   0.0    2.2e-06   27.2   0.0    2.5  3  Sigma70_r4_2    Sigma-70, region 4
    1.4e-05   24.5   0.0    3.4e-05   23.3   0.0    1.7  1  Sigma70_r4      Sigma-70, region 4
    2.9e-05   23.9   0.2    9.2e-05   22.3   0.0    2.0  1  HTH_11          HTH domain
    4.1e-05   23.5   0.0    9.7e-05   22.3   0.0    1.8  1  HTH_Mga         M protein trans-acting positive regulator (MG
    0.00033   20.4   0.0    0.00098   18.8   0.0    1.8  1  HTH_DeoR        DeoR-like helix-turn-helix domain
      0.001   19.2   0.1     0.0029   17.8   0.0    1.7  2  PaaX            PaaX-like protein
     0.0017   18.1   0.0     0.0034   17.1   0.0    1.5  1  HTH_23          Homeodomain-like domain
     0.0017   18.4   0.0     0.0034   17.5   0.0    1.5  1  HTH_28          Helix-turn-helix domain
     0.0043   16.9   0.4       0.02   14.8   0.0    2.2  2  MarR            MarR family
     0.0046   17.0   0.0      0.028   14.5   0.0    2.2  3  HTH_20          Helix-turn-helix domain
     0.0066   16.3   0.0      0.014   15.3   0.0    1.6  1  MarR_2          MarR family
     0.0073   16.2   0.1      0.018   15.0   0.0    1.8  2  GYD             GYD domain
  ------ inclusion threshold ------
      0.013   15.5   1.5      0.025   14.6   1.1    1.7  1  NapD            NapD protein
      0.015   15.2   0.1      0.026   14.5   0.1    1.4  1  DUF2621         Protein of unknown function (DUF2621)
      0.017   15.3   0.0      0.046   13.9   0.0    1.8  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.018   14.8   0.0      0.044   13.6   0.0    1.7  1  HTH_IclR        IclR helix-turn-helix domain
      0.019   14.5   1.9      0.033   13.7   0.0    2.4  2  GerE            Bacterial regulatory proteins, luxR family
       0.02   14.9   0.0       0.03   14.3   0.0    1.4  1  HTH_29          Winged helix-turn helix
       0.02   14.6   0.0      0.043   13.6   0.0    1.6  1  HTH_39          Helix-turn-helix domain
      0.022   14.9   0.0      0.033   14.3   0.0    1.4  1  MIase           Muconolactone delta-isomerase
      0.026   14.4   0.0      0.097   12.6   0.0    2.0  1  HTH_5           Bacterial regulatory protein, arsR family
      0.032   14.8   2.2        1.8    9.2   0.1    2.3  2  ACT_4           ACT domain
      0.037   14.0   0.0       0.12   12.4   0.0    1.9  1  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.039   13.9   0.3      0.054   13.4   0.2    1.5  2  PAX             'Paired box' domain
      0.055   13.9   1.0       0.37   11.3   1.0    2.1  1  HTH_40          Helix-turn-helix domain
      0.062   13.7   0.1       0.26   11.7   0.0    2.0  2  Rrf2            Transcriptional regulator
      0.065   14.2   0.2      0.096   13.7   0.2    1.4  1  LAGLIDADG_1     LAGLIDADG endonuclease
      0.069   13.5   0.0       0.28   11.6   0.0    1.9  2  FaeA            FaeA-like protein
      0.074   12.5   0.0       0.16   11.4   0.0    1.5  1  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
        0.1   12.2   0.5        1.1    8.9   0.0    2.6  3  HrcA_DNA-bdg    Winged helix-turn-helix transcription repress
       0.22   11.8   1.7         14    6.0   0.0    2.9  3  DUF4777         Domain of unknown function (DUF4777)


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6   0.1   1.1e-17   5.7e-15       2      48 .]       3      49 ..       2      49 .. 0.97
   2 ?    1.6   0.1      0.39   2.1e+02       5      27 ..      96     118 ..      96     122 .. 0.89

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 1.1e-17
                            HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      d +d++ILe+++k++r+++ e+Ae+lg+S +tv+ r+ +++e+G+I+
  gi|474934953|ref|YP_007688535.1|  3 DNLDKRILEIMKKDSRCPYVEIAEKLGVSEGTVRSRVHKMTEDGIIR 49
                                      899*******************************************7 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.39
                            HTH_24   5 drkILelLqknprisqreLAerl 27 
                                       d +I+ ++  ++  s +eL e++
  gi|474934953|ref|YP_007688535.1|  96 DQDIIAIVDVESPQSLNELIEKV 118
                                       67899999999999*****9998 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   0.0   2.8e-17   1.5e-14       1      41 [.       2      42 ..       2      43 .. 0.98

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 2.8e-17
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrL 41
                                      +D +D++ILe++ +d+R +y e+Ae++G+Se tv+ Rv+++
  gi|474934953|ref|YP_007688535.1|  2 IDNLDKRILEIMKKDSRCPYVEIAEKLGVSEGTVRSRVHKM 42
                                      69**************************************9 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.5   1.5e-14   7.8e-12       1      75 []      66     135 ..      64     135 .. 0.92

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 1.5e-14
                                       EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEEE CS
                    AsnC_trans_reg   1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivlet 75 
                                       +++ ++  +   +e++++ la+++ V+e+  +tGd d++++v v++ ++l++++++ +++ ++v++t t ++l++
  gi|474934953|ref|YP_007688535.1|  66 IMIDVN-TD---TEDIAKDLAKYEGVTEVLEITGDQDIIAIVDVESPQSLNELIEK-VRKYKNVKSTMTRLILKE 135
                                       456666.55...9****************************************999.***************985 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0   4.2e-09   2.2e-06      26      49 ..      18      41 ..      12      42 .. 0.89
   2 ?   -1.6   0.0       4.3   2.2e+03      31      40 ..      76      89 ..      72      90 .. 0.55
   3 ?   -2.3   0.1       7.1   3.8e+03      40      49 ..     121     130 ..     119     131 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 4.2e-09
                                      ---HHHHHHHHT--HHHHHHHHHH CS
                      Sigma70_r4_2 26 glsykEIAellgisegtVksrlsR 49
                                       ++y EIAe+lg+segtV+sr+++
  gi|474934953|ref|YP_007688535.1| 18 RCPYVEIAEKLGVSEGTVRSRVHK 41
                                      589*******************97 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.3
                                      HHHHHH....T--H CS
                      Sigma70_r4_2 31 EIAell....gise 40
                                      +IA+ l    g++e
  gi|474934953|ref|YP_007688535.1| 76 DIAKDLakyeGVTE 89
                                      66665533337765 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 7.1
                                       HHHHHHHHHH CS
                      Sigma70_r4_2  40 egtVksrlsR 49 
                                        ++Vks + R
  gi|474934953|ref|YP_007688535.1| 121 YKNVKSTMTR 130
                                       5799999987 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   6.4e-08   3.4e-05      22      43 ..      20      41 ..       5      44 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 6.4e-08
                                      -HHHHHHHHTS-HHHHHHHHHH CS
                        Sigma70_r4 22 TleEIgerlgiSrerVrqiekr 43
                                      ++ EI+e+lg+S+++Vr++ ++
  gi|474934953|ref|YP_007688535.1| 20 PYVEIAEKLGVSEGTVRSRVHK 41
                                      689****************997 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   1.8e-07   9.2e-05       4      44 ..       8      51 ..       6      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.8e-07
                            HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg....v 44
                                       ile+  ++++  +  e+Ae+L+vS+ tvr ++ +++e g    +
  gi|474934953|ref|YP_007688535.1|  8 RILEIM-KKDSRCPYVEIAEKLGVSEGTVRSRVHKMTEDGiirgF 51
                                      577777.888889999***********************955555 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   1.8e-07   9.7e-05       7      46 ..       6      44 ..       2      59 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.8e-07
                           HTH_Mga  7 klkLlelLteneksltldelakeLglseltlqsdiseLne 46
                                      + ++le+  + +++ +++e+a++Lg se t++s++++++e
  gi|474934953|ref|YP_007688535.1|  6 DKRILEIMKK-DSRCPYVEIAEKLGVSEGTVRSRVHKMTE 44
                                      6789999999.**************************985 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.9e-06   0.00098       3      44 ..       7      48 ..       6      51 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.9e-06
                          HTH_DeoR  3 eqilellkqqgklsveelvellgvSeaTiRRDLneLeeqgll 44
                                      + ile  k++  +   e++e lgvSe T+R    +++e+g++
  gi|474934953|ref|YP_007688535.1|  7 KRILEIMKKDSRCPYVEIAEKLGVSEGTVRSRVHKMTEDGII 48
                                      679***************************999999999996 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   5.6e-06    0.0029      27      55 ..      22      50 ..      20      60 .. 0.91
   2 ?   -2.2   0.0       9.6   5.1e+03      23      35 ..      60      72 ..      51      76 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5.6e-06
                              PaaX 27 irllaelGiseslvRaalsRlakaGwlvr 55
                                      +++ ++lG+se++vR+ ++ ++++G +++
  gi|474934953|ref|YP_007688535.1| 22 VEIAEKLGVSEGTVRSRVHKMTEDGIIRG 50
                                      7999*********************9975 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 9.6
                              PaaX 23 lgsLirllaelGi 35
                                      ++ L++++ ++  
  gi|474934953|ref|YP_007688535.1| 60 VKALVEIMIDVNT 72
                                      7889999877765 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   6.5e-06    0.0034      20      46 ..      21      47 ..      14      49 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.5e-06
                            HTH_23 20 vreIAreLgvsrrTvyrwlkryreeGl 46
                                      + eIA++Lgvs+ Tv+  +++  e+G+
  gi|474934953|ref|YP_007688535.1| 21 YVEIAEKLGVSEGTVRSRVHKMTEDGI 47
                                      789*************66665567876 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   6.5e-06    0.0034      13      41 ..      18      47 ..       8      54 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6.5e-06
                            HTH_28 13 h.svreaArelgisrrtvyrWikryeegGi 41
                                      + ++ e+A++lg+s+ tv++ +++  e Gi
  gi|474934953|ref|YP_007688535.1| 18 RcPYVEIAEKLGVSEGTVRSRVHKMTEDGI 47
                                      56899*****************99888775 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   3.7e-05      0.02       8      48 ..       9      49 ..       6      60 .. 0.87
   2 ?   -0.4   0.1       2.2   1.2e+03      31      38 ..     125     132 ..      98     134 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.7e-05
                                      HHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR  8 iLrilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                      iL+i +    +   e+a+klgvs +tv   ++++ ++G i+
  gi|474934953|ref|YP_007688535.1|  9 ILEIMKKDSRCPYVEIAEKLGVSEGTVRSRVHKMTEDGIIR 49
                                      66666667778888*************************97 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2.2
                                       HHHHHHHH CS
                              MarR  31 kstvtrvl 38 
                                       kst+tr++
  gi|474934953|ref|YP_007688535.1| 125 KSTMTRLI 132
                                       67888776 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   5.2e-05     0.028      14      56 ..       8      50 ..       2      54 .. 0.85
   2 ?   -1.7   0.0       5.9   3.1e+03      38      50 ..      53      65 ..      50      72 .. 0.83
   3 ?   -1.4   0.0       4.7   2.5e+03      15      34 ..      99     118 ..      97     130 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.2e-05
                                      HHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20 14 rilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                      ril   + +      e+ae l++s  t++ +++++ e g++++
  gi|474934953|ref|YP_007688535.1|  8 RILEIMKKDSRCPYVEIAEKLGVSEGTVRSRVHKMTEDGIIRG 50
                                      566666666667778*************************985 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 5.9
                                      HHHHHHHHHHHHH CS
                            HTH_20 38 kntlsyHLrvLee 50
                                       +t s+++++L+e
  gi|474934953|ref|YP_007688535.1| 53 IKTSSKNVKALVE 65
                                      5688999999987 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 4.7
                                       HHHHHSTCTTB-HHHHHHHH CS
                            HTH_20  15 ilraLaraegltaselaerl 34 
                                       i +    + +++++el e +
  gi|474934953|ref|YP_007688535.1|  99 IIAIVDVESPQSLNELIEKV 118
                                       55666677888888887765 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   2.6e-05     0.014      23      52 ..      20      49 ..       7      63 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.6e-05
                                      EHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2 23 tvgelarrlglsksavsrilkrLvaaGLve 52
                                         e+a++lg+s ++v  ++ ++ + G ++
  gi|474934953|ref|YP_007688535.1| 20 PYVEIAEKLGVSEGTVRSRVHKMTEDGIIR 49
                                      5569***********************996 PP

>> GYD  GYD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       5.6     3e+03      70      82 ..      31      43 ..      24      49 .. 0.78
   2 !   15.0   0.0   3.4e-05     0.018      23      88 ..      75     138 ..      52     140 .] 0.82

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 5.6
                               GYD 70 asGtvrtetlraf 82
                                      + Gtvr+++++++
  gi|474934953|ref|YP_007688535.1| 31 SEGTVRSRVHKMT 43
                                      6789998887765 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 3.4e-05
                               GYD  23 eeakealveslGgkleslyatlGeyDvvvivEapDdetaaalslalaasGtvrtetlrafteeefd 88 
                                       e++++ l ++ +g + ++  ++G++D+++iv+++  ++   l  +++++ +v+++++r++ +e f 
  gi|474934953|ref|YP_007688535.1|  75 EDIAKDL-AKYEG-VTEVLEITGDQDIIAIVDVESPQSLNELIEKVRKYKNVKSTMTRLILKEHFG 138
                                       5555555.44443.45677789*************************************9888775 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   1.1   4.7e-05     0.025      14      67 ..      73     127 ..      57     129 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.7e-05
                              NapD  14 rlaavkaalaalpgv.EvhasdeegklVvviEaesedeladtieaiealpgVlsa 67 
                                       ++++++++la+ +gv Ev   ++++ ++ +++ es ++l + ie++++ ++V s+
  gi|474934953|ref|YP_007688535.1|  73 DTEDIAKDLAKYEGVtEVLEITGDQDIIAIVDVESPQSLNELIEKVRKYKNVKST 127
                                       6899*********97699999999****************************886 PP

>> DUF2621  Protein of unknown function (DUF2621)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1     5e-05     0.026      84     134 ..      24      76 ..       4      81 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5e-05
                           DUF2621  84 iagkig..elaleekakeitedliikGyilatpkrdhkflkkklkekeidlep 134
                                       ia k+g  e ++ ++++++ted ii+G+ + t  ++ k l++ + + + d+e+
  gi|474934953|ref|YP_007688535.1|  24 IAEKLGvsEGTVRSRVHKMTEDGIIRGFTIKTSSKNVKALVEIMIDVNTDTED 76 
                                       66665422778999****************************99999999875 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   8.8e-05     0.046      26      51 ..      22      47 ..       7      49 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.8e-05
                                      HHHHHHHTS-HHHHHHHHHHHHHTTS CS
                    Fe_dep_repress 26 kdlaerLnvspssVsemlkkLekdGy 51
                                       ++ae L+vs  +V   + k+ +dG 
  gi|474934953|ref|YP_007688535.1| 22 VEIAEKLGVSEGTVRSRVHKMTEDGI 47
                                      58**********************95 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   8.4e-05     0.044       8      49 ..       9      49 ..       8      50 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.4e-05
                                      HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR  8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      iL++  +  +     e+A+++g++  tv+  ++ ++e G+++
  gi|474934953|ref|YP_007688535.1|  9 ILEIMKKDSR-CPYVEIAEKLGVSEGTVRSRVHKMTEDGIIR 49
                                      6666666666.5889**********************99986 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   6.3e-05     0.033      22      41 ..      23      42 ..      20      44 .. 0.88
   2 ?   -2.4   0.2       6.9   3.7e+03      30      42 ..     120     132 ..     119     134 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.3e-05
                                      HHHHHHTS-HHHHHHHHHHH CS
                              GerE 22 eIAeelniSekTVkvhksni 41
                                      eIAe+l++Se TV++ +  +
  gi|474934953|ref|YP_007688535.1| 23 EIAEKLGVSEGTVRSRVHKM 42
                                      8*************988766 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6.9
                                       -HHHHHHHHHHHH CS
                              GerE  30 SekTVkvhksnim 42 
                                       ++k+Vk+ ++++ 
  gi|474934953|ref|YP_007688535.1| 120 KYKNVKSTMTRLI 132
                                       5788888888775 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   5.7e-05      0.03      15      43 ..      21      49 ..       8      64 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.7e-05
                            HTH_29 15 vsqiAkllglsrrtvyrwlkrfeegGlaa 43
                                        +iA+ lg+s+ tv+  ++ + e+G+  
  gi|474934953|ref|YP_007688535.1| 21 YVEIAEKLGVSEGTVRSRVHKMTEDGIIR 49
                                      679***********************755 PP

>> HTH_39  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   8.2e-05     0.043       3      49 ..       6      58 ..       4      62 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.2e-05
                            HTH_39  3 carilaaLrqhgsittleamrelditr..laaRIkeLre....kGyeIkterv 49
                                      ++ril++++++++   +e  ++l++ +   ++R++ + e    +G+ Ikt  +
  gi|474934953|ref|YP_007688535.1|  6 DKRILEIMKKDSRCPYVEIAEKLGVSEgtVRSRVHKMTEdgiiRGFTIKTSSK 58
                                      79*************************999********933334577777765 PP

>> MIase  Muconolactone delta-isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   6.3e-05     0.033      23      82 ..      70     129 ..      51     136 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.3e-05
                             MIase  23 lkarekaraqelqrqGklvrlwrvvgeyanisifdvedndeLhelLssLPlfpymtievt 82 
                                       ++++ ++ a++l++   + ++  + g    i+i+dve++++L+el++++  ++ ++ + t
  gi|474934953|ref|YP_007688535.1|  70 VNTDTEDIAKDLAKYEGVTEVLEITGDQDIIAIVDVESPQSLNELIEKVRKYKNVKSTMT 129
                                       56667777888888777889999***********************99877777776666 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00018     0.097       6      45 ..       8      48 ..       7      49 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00018
                                      HHHHHHTTSSEEHH.HHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  6 kILklLaegelcvc.elaeelglsqstvShHLkkLreaGLV 45
                                      +IL ++ + ++c   e+ae+lg+s++tv+    k+ e G++
  gi|474934953|ref|YP_007688535.1|  8 RILEIMKKDSRCPYvEIAEKLGVSEGTVRSRVHKMTEDGII 48
                                      799999998877755*************9877777777776 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.3     0.059        31      32      78 ..      46      90 ..      39      91 .. 0.85
   2 ?    9.2   0.1    0.0034       1.8      52      77 ..     101     126 ..      93     127 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.059
                             ACT_4 32 anivsvnaktrkkdglaeikitveVkdvehLsrviakLraipgVisV 78
                                      + i+  ++kt   ++ ++  +++ +    + +++ + L + +gV++V
  gi|474934953|ref|YP_007688535.1| 46 GIIRGFTIKTS--SKNVKALVEIMIDVNTDTEDIAKDLAKYEGVTEV 90
                                      56888889995..5679999999999999999************998 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0034
                             ACT_4  52 itveVkdvehLsrviakLraipgVis 77 
                                         v V++ + L+++i+k+r+ ++V+s
  gi|474934953|ref|YP_007688535.1| 101 AIVDVESPQSLNELIEKVRKYKNVKS 126
                                       6699********************86 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00022      0.12      26      65 ..      23      63 ..       7      66 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00022
                                      HHHHHTTSSHHHHHHHHHHHHHTTSEE.ET.EEEEES-HHHH CS
                         HTH_Crp_2 26 elAsmlGltretvsrilseLkreglis.rg.rririldleaL 65
                                      e+A+ lG++  tv    +++ ++g+i+    +    ++++aL
  gi|474934953|ref|YP_007688535.1| 23 EIAEKLGVSEGTVRSRVHKMTEDGIIRgFTiK-TSSKNVKAL 63
                                      9*************************953323.455555555 PP

>> PAX  'Paired box' domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2    0.0001     0.054      20      76 ..       3      61 ..       1     116 [. 0.85
   2 ?   -1.5   0.0       4.1   2.2e+03      78      93 ..     112     127 ..      71     136 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.0001
                               PAX 20 dsirqkivelahsgvrp..cvisrqlrvshgcvskilgryqetgsirpgviggskpkva 76
                                      d++ ++i+e+ ++  r   ++i+ +l vs+g v   + +  e g ir  +i  s  +v 
  gi|474934953|ref|YP_007688535.1|  3 DNLDKRILEIMKKDSRCpyVEIAEKLGVSEGTVRSRVHKMTEDGIIRGFTIKTSSKNVK 61
                                      5678999**9999888423689**************************99998877664 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.1
                               PAX  78 pevvkkieeykrenps 93 
                                        e+++k+ +yk+   +
  gi|474934953|ref|YP_007688535.1| 112 NELIEKVRKYKNVKST 127
                                       3555666666665555 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.0    0.0007      0.37      17      67 ..      23      73 ..      17     140 .] 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0007
                            HTH_40 17 eIAkerglkesTIegHLaelieegeeidlerl...vseeeekeIeeaiekvgse 67
                                      eIA++ g++e+T+ + + ++ e+g    ++ +   +s++  k++ e++ +v+++
  gi|474934953|ref|YP_007688535.1| 23 EIAEKLGVSEGTVRSRVHKMTEDGI---IRGFtikTSSKNVKALVEIMIDVNTD 73
                                      9**********************84...33331112566666666666666544 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0    0.0005      0.26      21      56 ..      14      49 ..       8      52 .. 0.86
   2 ?   -1.6   0.0       6.6   3.5e+03       7      35 ..      60      85 ..      55      92 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0005
                                      STCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 21 eeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                      ++++ +   eiae+ ++s+  ++  ++k+++ g+++
  gi|474934953|ref|YP_007688535.1| 14 KKDSRCPYVEIAEKLGVSEGTVRSRVHKMTEDGIIR 49
                                      445559999*************************97 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 6.6
                                      HHHHHHHHHHHHHSSTCC-B-HHHHHHHH CS
                              Rrf2  7 teyalhallyLakeeeeepvsseeiaerq 35
                                      ++  + ++++  +  e+    ++++a+  
  gi|474934953|ref|YP_007688535.1| 60 VKALVEIMIDVNTDTEDI---AKDLAKYE 85
                                      555566666666666554...55555555 PP

>> LAGLIDADG_1  LAGLIDADG endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   0.00018     0.096      13      87 ..      53     123 ..      31     132 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00018
                                       EEEEETTTTTTSEEEEEEEEEEEEGGGHHHHHHHHHHHTECEEEEETTTEEEEEEE-S.HHHHHHTHHHHHHHST- CS
                       LAGLIDADG_1  13 itvtkskskktslkvqlefqielkkkdesllekikeylglgsikkrkkdkyvsyiisn.sskslkilipyfdkypl 87 
                                       i++++++     +k  +e+ i+++++ e++ + +++y g++ +   + d++++ i+   s +sl+ li+   ky+ 
  gi|474934953|ref|YP_007688535.1|  53 IKTSSKN-----VKALVEIMIDVNTDTEDIAKDLAKYEGVTEVLEITGDQDIIAIVDVeSPQSLNELIEKVRKYKN 123
                                       3333333.....4566788888889**************999988888888888887778**************74 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00053      0.28       4      46 ..       8      49 ..       5      57 .. 0.88
   2 ?   -1.1   0.0       4.9   2.6e+03      14      25 ..      70      81 ..      61      85 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00053
                                      HHHHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEE CS
                              FaeA  4 eIleylnsikapckTreiAdalglsaYQaRyYLeqLekegkik 46
                                       Ile +++  + c   eiA+ lg+s   +R+   ++   g i+
  gi|474934953|ref|YP_007688535.1|  8 RILEIMKK-DSRCPYVEIAEKLGVSEGTVRSRVHKMTEDGIIR 49
                                      68888888.899999****************999999999886 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 4.9
                                      ----HHHHHHHH CS
                              FaeA 14 apckTreiAdal 25
                                          T +iA+ l
  gi|474934953|ref|YP_007688535.1| 70 VNTDTEDIAKDL 81
                                      556799999876 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00031      0.16      29      49 ..      20      40 ..      12      41 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00031
                      HTH_Tnp_ISL3 29 svkavArqlgvSwtTVwrild 49
                                      +  ++A+ lgvS+ TV+ +++
  gi|474934953|ref|YP_007688535.1| 20 PYVEIAEKLGVSEGTVRSRVH 40
                                      6679*************9986 PP

>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0021       1.1      27      51 ..      22      46 ..       5      52 .. 0.78
   2 ?    0.1   0.0       1.2   6.5e+02      25      39 ..      73      87 ..      54      91 .. 0.72
   3 ?   -1.2   0.0       3.2   1.7e+03      10      28 ..     111     128 ..     107     138 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0021
                      HrcA_DNA-bdg 27 eeiAevlkrneGtvRNqlqsLkalg 51
                                       eiAe+l+  eGtvR  ++ +   g
  gi|474934953|ref|YP_007688535.1| 22 VEIAEKLGVSEGTVRSRVHKMTEDG 46
                                      69*************9988776555 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.2
                      HrcA_DNA-bdg 25 KgeeiAevlkrneGt 39
                                       +e+iA+ l + eG 
  gi|474934953|ref|YP_007688535.1| 73 DTEDIAKDLAKYEGV 87
                                      478999999998885 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 3.2
                      HrcA_DNA-bdg  10 lqaLielyrkkkravKgee 28 
                                       l++Lie  rk  + vK++ 
  gi|474934953|ref|YP_007688535.1| 111 LNELIEKVRK-YKNVKSTM 128
                                       5677776655.45677765 PP

>> DUF4777  Domain of unknown function (DUF4777)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.027        14      28      59 ..      23      54 ..      21      58 .. 0.91
   2 ?   -1.7   0.0         7   3.7e+03       4      18 ..      58      72 ..      55      90 .. 0.71
   3 ?    4.1   0.0       0.1        55      12      39 ..     101     128 ..      94     136 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.027
                           DUF4777 28 rvaerydlseeelkkvVkntLeaAvrhGFlkk 59
                                       +ae++++se  ++  V ++ e++ + GF  k
  gi|474934953|ref|YP_007688535.1| 23 EIAEKLGVSEGTVRSRVHKMTEDGIIRGFTIK 54
                                      589**************************766 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 7
                           DUF4777  4 qngalvlealkvlnr 18
                                      +n++ ++e + ++n+
  gi|474934953|ref|YP_007688535.1| 58 KNVKALVEIMIDVNT 72
                                      567777777777664 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.1
                           DUF4777  12 alkvlnrPaTldEivervaerydlseee 39 
                                       a+ ++  P +l E++e+v++  ++++ +
  gi|474934953|ref|YP_007688535.1| 101 AIVDVESPQSLNELIEKVRKYKNVKSTM 128
                                       5667899************999888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1077  (0.0600703); expected 358.6 (0.02)
Passed bias filter:                      644  (0.0359195); expected 358.6 (0.02)
Passed Vit filter:                       122  (0.00680462); expected 17.9 (0.001)
Passed Fwd filter:                        34  (0.00189637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              34  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 834.96
//
Query:       gi|474934954|ref|YP_007688536.1|  [L=295]
Description: dihydrodipicolinate synthase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-88  295.7   0.0    2.5e-88  295.6   0.0    1.0  1  DHDPS     Dihydrodipicolinate synthetase family
  ------ inclusion threshold ------
      0.044   13.2   0.0        5.6    6.4   0.0    2.1  2  TMEM215   TMEM215 family
       0.19   12.0   0.2        1.1    9.5   0.0    2.3  3  CCG       Cysteine-rich domain


Domain annotation for each model (and alignments):
>> DHDPS  Dihydrodipicolinate synthetase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  295.6   0.0   4.2e-92   2.5e-88       2     287 ..       8     291 ..       7     293 .. 0.98

  Alignments for each domain:
  == domain 1  score: 295.6 bits;  conditional E-value: 4.2e-92
                                       -SEEEEE----B-TTSSB-HHHHHHHHHHHHHCT-SEEEESSCCCTGGGS-HHHHHHHHHHHHHHHTTSSEEEEE-- CS
                             DHDPS   2 fsgiitalvtpfdedgkldkealrklieflinkgvdglvvaGttGEsatlsteekeqlveiaveaakgripviagvG 78 
                                       f+g  talvtp+++dg +d+ealr+l++f+ ++gvd l+ +G+tGE+atl  e++ +++ i+ + ak r +v+ag+G
  gi|474934954|ref|YP_007688536.1|   8 FRGTGTALVTPMKKDGSIDEEALRRLVDFQEENGVDMLLPCGSTGEAATLAREDHLKVISIVIDQAK-RAKVVAGAG 83 
                                       78999************************************************************98.89******* PP

                                       -SSHHHHHHHHHCCCCCT-SEEEEE---SS---HHHHHHHHHHHHHCHSS-EEEEE-HHHHSHHHHHHHHHHHHTST CS
                             DHDPS  79 snstseaiklakkaeeaGadgvlavtPYYnkpsqeglyqhfkaiieatdlpvilYnvpsrtgadlspetvkrLaele 155
                                       sn t+eai+l+++a ++Gad++l++ PYY+kp+qeg+ qh++ai+ea + p+i+Ynvp+rtg++++ +t+ r+ae++
  gi|474934954|ref|YP_007688536.1|  84 SNCTREAIDLTRNACDMGADAILSISPYYVKPTQEGIFQHYRAIAEASSKPIIVYNVPGRTGSNITAQTMLRMAEVD 160
                                       ***************************************************************************** PP

                                       TEEEEEE-SS-CTHHHHHHCCCSTTSEEEES-GGGHHHHHHTT-SEEEESCHHCHHHHHHHHHHHHHTT-HHHHHHH CS
                             DHDPS 156 nivgvKeavgdleevikikkevgkdlviysGddelllsalslGadGvisvtsniagermrqlikalkeGdlaeaael 232
                                       ni+gvKea+g +e+v++i +   kd+v++sG d+++ +++  GadGv sv+sn  ++ + ++++ +k+G+ + a+ l
  gi|474934954|ref|YP_007688536.1| 161 NILGVKEASGIMEQVQEILAGRPKDFVVLSGNDDMTFDMMCCGADGVFSVASNPLPKMVSDMVNHMKKGERDPARDL 237
                                       ***************************************************************************** PP

                                       HHHHHHHHHHCCCCSCCHHHHHHHHCTTSSSBB.--TTS--S-HHHHHHHHHHHH CS
                             DHDPS 233 nekllplikilfaepnvilvktalellGlvveatlrkPltpleeeekeeleallk 287
                                       n+kl+p+++ lf+e+n+i+vk++++ lG      lr Pltpl+   + +l  +l 
  gi|474934954|ref|YP_007688536.1| 238 NQKLMPIFQSLFVESNPIPVKYVMAKLGYGEDV-LRLPLTPLSAAGRAKLDPVLA 291
                                       ******************************999.***********9999987765 PP

>> TMEM215  TMEM215 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0   0.00093       5.6     100     175 ..      23      99 ..      13     126 .. 0.82
   2 ?    4.9   0.0    0.0026        16     160     210 ..     152     202 ..     136     209 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.00093
                           TMEM215 100 Gssde..lakkaekkekrkgevsvsssitvgeakslikkvdqdevlryldacypsnvlsgvgdvstysvldkkcsar 174
                                       Gs de  l ++  + ++++g +    + ++gea +l ++ + + ++  +d++   +v++g+g++ t  ++d ++ a 
  gi|474934954|ref|YP_007688536.1|  23 GSIDEeaL-RRLVDFQEENGVDMLLPCGSTGEAATLAREDHLKVISIVIDQAKRAKVVAGAGSNCTREAIDLTRNAC 98 
                                       66665223.33344444589999999999******************************************998876 PP

                           TMEM215 175 d 175
                                       d
  gi|474934954|ref|YP_007688536.1|  99 D 99 
                                       6 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0026
                           TMEM215 160 dvstysvldkkcsardrsayseaedkvll.vPrdsiivysykdnspydrycc 210
                                       ++  ++ +d+   +++ s ++e+ +++l   P+d  +v+s +d+  +d  cc
  gi|474934954|ref|YP_007688536.1| 152 TMLRMAEVDNILGVKEASGIMEQVQEILAgRPKD-FVVLSGNDDMTFDMMCC 202
                                       5566777888888899998888888887725666.678899999******** PP

>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.59   3.5e+03      41      80 ..      48      86 ..      25      89 .. 0.54
   2 ?   -2.8   0.0       1.2   7.4e+03      63      77 ..      95     109 ..      90     110 .. 0.80
   3 ?    9.5   0.0   0.00018       1.1      37      69 ..     198     230 ..     191     235 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.59
                               CCG 41 CGagggrsgkee.laealakrnvetaeetgadaivtacpgC 80
                                      CG+ g  +   +  ++++    +++a++  a++++ a ++C
  gi|474934954|ref|YP_007688536.1| 48 CGSTGEAATLAReDHLKVISIVIDQAKR--AKVVAGAGSNC 86
                                      4444433333222555555555666666..56666666666 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.2
                               CCG  63 etaeetgadaivtac 77 
                                       ++a ++gadai++++
  gi|474934954|ref|YP_007688536.1|  95 RNACDMGADAILSIS 109
                                       678899999999876 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00018
                               CCG  37 kesCCGagggrsgkeelaealakrnvetaeetg 69 
                                       + +CCGa g++s+  +   +++  +v+++++ +
  gi|474934954|ref|YP_007688536.1| 198 DMMCCGADGVFSVASNPLPKMVSDMVNHMKKGE 230
                                       579**********99988888888888888755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1782.72
//
Query:       gi|474934955|ref|YP_007688537.1|  [L=453]
Description: aspartate kinase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.8e-49  168.5   0.0    3.3e-49  167.7   0.0    1.4  1  AA_kinase  Amino acid kinase family
    0.00053   19.7   0.2      0.045   13.5   0.1    3.3  3  ACT        ACT domain


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.7   0.0   3.6e-53   3.3e-49       1     241 []       1     280 [.       1     280 [. 0.84

  Alignments for each domain:
  == domain 1  score: 167.7 bits;  conditional E-value: 3.6e-53
                                       TEEEEEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC.............. CS
                         AA_kinase   1 krvVvKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaa............g 65 
                                       +++V+K+GG+s++++e+  ++r+a+++     +g k vvV++ +++t++l+ l+ +++ ++++             +
  gi|474934955|ref|YP_007688537.1|   1 MLTVMKFGGTSVGSPEA--IERVANIVTGT--EGQKAVVVSAMSGITNFLVGLCEDVPGKRNEVlktfeqkhldvaH 73 
                                       689**************..*********99..88898888888**********555555555523333322555552 PP

                                       ..E..HHHHHHHHH.....................................HHHHHHHHHHHHHHHHTTHGEEEE-G CS
                         AA_kinase  66 lrstleeagevatr.....................................dalaslgerlvaallaaglpavglsa 105
                                                                                          d ++s ger ++ ll + l+++g  +
  gi|474934955|ref|YP_007688537.1|  74 -------------AlfddrqfaefmkefaprleafrnllndekamsdpyyrDNVTSQGERFSSLLLCHKLRSMGFES 137
                                       .............33333444444455777788888888888888888888****************9997777777 PP

                                       GGTCEECCCE..........HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTTE...EEEE-HHHHHHHHHHHC CS
                         AA_kinase 106 aaldateagr........degsdgnvesvdaeaieelleagvvpvltgfigldeege...lgrgssDtiaallAeal 171
                                        al++++ g          e    + e+ +  +++ ++e++ +pv+tgf+g+  +g    +grg+sD++aa +A+al
  gi|474934955|ref|YP_007688537.1| 138 VALTSEDCGTravgkplnGEADLTETERGMGVQVMPYVERNCIPVITGFYGCMADGRpltFGRGGSDYAAAVVANAL 214
                                       77777777777776677666666666677799********************************************* PP

                                       TSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHHCSSS.TTTHHHHCHHHHHHHHHCTT-EEEEEE CS
                         AA_kinase 172 gAdkliiltdVdGVydadpkkvpdarllpeisvdeaeesaselatgGmkvkhpaalaaarrggipvvItn 241
                                       +Ad+l+i+tdVdG ++adp++vp a++++e+++ ea e    la++G+kv+hp++++++r++ ip+ ++n
  gi|474934955|ref|YP_007688537.1| 215 NADMLEIWTDVDGFMSADPRVVPAAVKIDEMTYAEASE----LAYFGAKVLHPRTIEPVRKKHIPLKVKN 280
                                       **************************************....************************9987 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0     0.055   4.9e+02       6      31 ..      49      74 ..      44      75 .. 0.87
   2 ?    0.7   0.0     0.051   4.5e+02      42      66 ..     348     372 ..     328     373 .. 0.80
   3 !   13.5   0.1     5e-06     0.045      12      47 ..     400     432 ..     399     440 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.055
                                      EEESSTTHHHHHHHHHHHTTSEEEEE CS
                               ACT  6 gvpDrPGlLarvfgaladrgiNidsi 31
                                      +++D+PG  ++v+ ++ + ++ ++++
  gi|474934955|ref|YP_007688537.1| 49 LCEDVPGKRNEVLKTFEQKHLDVAHA 74
                                      69999999999999999999999987 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.051
                                       EEEEEEEEEEHHHHHHHHHHHHTTC CS
                               ACT  42 givfvvivvdeedleevlealkkle 66 
                                       +++++ +++  +d++++l++l++l 
  gi|474934955|ref|YP_007688537.1| 348 SLSTLAVLIHNNDVKATLKKLNELD 372
                                       57788889999999******99985 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 5e-06
                                       THHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEE CS
                               ACT  12 GlLarvfgaladrgiNidsieqrssedkvagivfvv 47 
                                       G+ +++f+a+ ++  N+++i+ +sse    ++ fvv
  gi|474934955|ref|YP_007688537.1| 400 GVSGDIFSAVKEAKANVVMISEGSSEV---SLNFVV 432
                                       8899*********************98...444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.68u 0.35s 00:00:01.03 Elapsed: 00:00:00.56
# Mc/sec: 2425.40
//
Query:       gi|474934956|ref|YP_007688538.1|  [L=419]
Description: diaminopimelate decarboxylase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-54  184.2   0.1    3.4e-54  183.8   0.1    1.1  1  Orn_Arg_deC_N    Pyridoxal-dependent decarboxylase, pyridoxal
    4.4e-25   87.8   0.0    1.5e-24   86.1   0.0    2.2  1  Orn_DAP_Arg_deC  Pyridoxal-dependent decarboxylase, C-termina
      2e-05   24.4   0.0    3.1e-05   23.7   0.0    1.3  1  Ala_racemase_N   Alanine racemase, N-terminal domain
  ------ inclusion threshold ------
       0.13   11.4   0.1       0.19   10.9   0.1    1.2  1  Peptidase_M19    Membrane dipeptidase (Peptidase family M19)


Domain annotation for each model (and alignments):
>> Orn_Arg_deC_N  Pyridoxal-dependent decarboxylase, pyridoxal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.8   0.1   7.5e-58   3.4e-54       2     246 ..      35     278 ..      34     279 .. 0.95

  Alignments for each domain:
  == domain 1  score: 183.8 bits;  conditional E-value: 7.5e-58
                                       HHHHHHHHHHHHHCT...CCEEEEEGGG---HHHHHHHHHTTEEEEESSHHHHHHHHHCTTTGGGEEEEESS--HHH CS
                     Orn_Arg_deC_N   2 asierklkrwkkalp...rikvfYavKansdlavlellaelGlgldcaSkaElelvlaagvsperiifanpckqree 75 
                                       a+i++++++  +a+    + +++Ya Kan++lavl++l+++G+g+d++S +E+++ l+ag+sp++i++++ + + ee
  gi|474934956|ref|YP_007688538.1|  35 ARIRENYHALYDAFSrymPTEIHYACKANTNLAVLSILRQEGAGIDAVSIGEVMTCLKAGFSPSKIMYTGVNVSDEE 111
                                       5788888888888887778999******************************************************* PP

                                       HHHHHHCTHTEEEESSHHHHHHHHHHHCCEEEEEEEE-SCCSSSSTCCCSSSTTSSSSEEHCHHHHHHHHHHHHTTE CS
                     Orn_Arg_deC_N  76 lryalekgvkvvtvdnveeleklaklapeakvllRiktdvsaatcelistggessKFGaaleeavealleaakeenl 152
                                       l++++e+gv+ +++d+v+e+e+la++  + +v+ Ri++++ +++ e + tg++  KFG+  e+ ve++l+a+  ++l
  gi|474934956|ref|YP_007688538.1| 112 LKAVVESGVM-INLDSVSEMERLARIKTGIPVSFRITPGIGSGHGEKVITGNKGAKFGIPKEKVVETYLRAID-LGL 186
                                       *********9.**************************************************999999999885.799 PP

                                       EEEEEE---BSSC-SCHHHHHHHHHHHHHHHHHH.HHT---SEEE--S-BS-HCSTTSSSSTHHHHHHHHHHHHHHH CS
                     Orn_Arg_deC_N 153 qlvGvsfHvGSgvsdleafvkavekalklfdela.elGvklkiLdvGGGfgveyeeeeeplkleeiaekirealeea 228
                                         +G++ H+GSg + +e+f + +  +++l+++++   G++l+++d+GGG gv y+ +e++++++e+a+++ +  ++ 
  gi|474934956|ref|YP_007688538.1| 187 RPIGIHAHIGSGGQTVEPFIDEAMVLAELINQIEeACGIHLEFVDIGGGIGVPYKPNEDEMDVQEMASEVTDVFQQE 263
                                       999*******************************999*******************************999999887 PP

                                       HHTSSS-EEEE--SHHHH CS
                     Orn_Arg_deC_N 229 fpgdkevtiiaEpGRalv 246
                                              +ii+EpGR++v
  gi|474934956|ref|YP_007688538.1| 264 TD---VDRIILEPGRYIV 278
                                       64...457********98 PP

>> Orn_DAP_Arg_deC  Pyridoxal-dependent decarboxylase, C-terminal sheet domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.1   0.0   3.3e-28   1.5e-24       5      98 .]     231     369 ..      16     369 .. 0.71

  Alignments for each domain:
  == domain 1  score: 86.1 bits;  conditional E-value: 3.3e-28
                                       E................................................GGEEEEEEEEEEEEETCEEEEEES--TT CS
                                       x................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Orn_DAP_Arg_deC   5 d................................................eagvLvtrViavkesekkkfvivdaGmn 33 
                                       d                                                +a+vL+t+ ++vk+  +kk++ vdaG+n
  gi|474934956|ref|YP_007688538.1| 231 DigggigvpykpnedemdvqemasevtdvfqqetdvdriilepgryivcDAVVLLTKCVDVKDAITKKYIGVDAGFN 307
                                       05555555555555555555555555555556666666666666666669************99999********** PP

                                       TS-HHHHCTT-S-E.ESBTT-SCEEC.EEEEEEEE-SSSSTT-EEEEEEEEEE--TT-EEEESS-S CS
                                       xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Orn_DAP_Arg_deC  34 dllrpalygsfhei.pvkeeeaekeeeeeeevdvvGptCesgDvlakdrelpelevGdllafedaG 98 
                                       +l+rpa+y+sfh i + ++      ++++ ++d++Gp+Ce+gD+l++dr +pe+e+Gd++++ +aG
  gi|474934956|ref|YP_007688538.1| 308 TLIRPAMYDSFHYIqNGSR----FGKAATGRYDIAGPICETGDYLGHDRVMPETEEGDIIVVYNAG 369
                                       **************55542....33445678*********************************98 PP

>> Ala_racemase_N  Alanine racemase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   6.8e-09   3.1e-05       1     186 [.      32     226 ..      32     244 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 6.8e-09
                                       EEHHHHHHHHHHHHHHSCT..TSEEEEE-HHHHHTTHHHHHHHHHHHTTESEEEESSHHHHHHHHHTTS.CSEEEEE CS
                    Ala_racemase_N   1 idldalrhNlrrlralagp..gaklmavvKanayghgavevaralaeggadgfgvatleEalelreagi.tapilvl 74 
                                       +d +++r+N+ +l +++++  ++++    Ka   ++ ++ ++r ++     g+   ++ E  ++ +ag+   +i++ 
  gi|474934956|ref|YP_007688538.1|  32 VDEARIRENYHALYDAFSRymPTEIHYACKA-NTNLAVLSILR-QEG---AGIDAVSIGEVMTCLKAGFsPSKIMYT 103
                                       6999*************445999********.45555656666.333...45557789999999999998999*999 PP

                                       SC.STGGGHHHHHHTTEEEEESSHHHHHHHHHHHHHTTS-EEEEEEBESSSS..........SSSBSCHHHHHHHHH CS
                    Ala_racemase_N  75 eg.fspeelaalaeydltvtvdsleqlealaaaareagkplrvhlkidtgmg..........RlGftpeeleellea 140
                                       +  +s eel+a++e ++ + +ds  ++e+la+++      +r+   i +g g          + G++ e++ e + +
  gi|474934956|ref|YP_007688538.1| 104 GVnVSDEELKAVVESGVMINLDSVSEMERLARIKTGIPVSFRITPGIGSGHGekvitgnkgaKFGIPKEKVVETYLR 180
                                       9999*****************************98755555555555555558888888899******999999999 PP

                                       HHHTTTEEEEEEE-S-SSTTSTSHHHHHHHHHHHHHHHHHHHTT.GG CS
                    Ala_racemase_N 141 laalpglrleglmtHfasadepdeeteaqlarfeealeelekag.lr 186
                                       + +l glr++g+  H +s  +  e++  +  +++e+++++e+a  ++
  gi|474934956|ref|YP_007688538.1| 181 AIDL-GLRPIGIHAHIGSGGQTVEPFIDEAMVLAELINQIEEACgIH 226
                                       9888.6*********99987644555556666777777776555455 PP

>> Peptidase_M19  Membrane dipeptidase (Peptidase family M19)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   4.2e-05      0.19     211     271 ..     103     200 ..      96     270 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.2e-05
                                       -TTSB-HHHHHHHHHTT-EEEE-SSHHHCTTT....................................S--BHHHHH CS
                     Peptidase_M19 211 hpRNltDeqlkaiaesgGvvgvtfvpaflkek....................................aeatledvv 251
                                          N++De+lka++esg ++ +  v+++ + +                                    +e  +e+++
  gi|474934956|ref|YP_007688538.1| 103 TGVNVSDEELKAVVESGVMINLDSVSEMERLAriktgipvsfritpgigsghgekvitgnkgakfgipKEKVVETYL 179
                                       566********************99999333367999******************************999999**** PP

                                       HHHHHHHHHT-G.GGEEE--- CS
                     Peptidase_M19 252 dhidyivelaGi.dhVGlGsD 271
                                       ++id  ++ +Gi +h+G G+ 
  gi|474934956|ref|YP_007688538.1| 180 RAIDLGLRPIGIhAHIGSGGQ 200
                                       ****99999996368987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.51
# Mc/sec: 2449.53
//
Query:       gi|474934957|ref|YP_007688539.1|  [L=281]
Description: diaminopimelate epimerase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.5e-52  175.1   0.0    5.5e-30  104.0   0.0    2.0  2  DAP_epimerase  Diaminopimelate epimerase
    0.00047   19.3   0.0     0.0027   16.8   0.0    1.8  2  Pro_racemase   Proline racemase


Domain annotation for each model (and alignments):
>> DAP_epimerase  Diaminopimelate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.0   0.0   6.2e-34   5.5e-30       1     118 [.       3     126 ..       3     128 .. 0.96
   2 !   69.3   0.0   3.6e-23   3.2e-19       2     120 ..     157     271 ..     156     272 .. 0.93

  Alignments for each domain:
  == domain 1  score: 104.0 bits;  conditional E-value: 6.2e-34
                                       EEEECSSEEEEEEECCTTCSSHHHHHHHHHHHTTTTSTT-SEEEEEE.EEETTEEEEEEEETTTEEESTTHCCHHHH CS
                     DAP_epimerase   1 fakshGnpndvvvvddveaelvleaelvaalcdreagpgadgvlfvk.psgeediklryfnrdgseaemCGnGvrvf 76 
                                       f+k+hG +nd++v+d +   ++  ++  +++cdr++g+gadgvl +   ++ +di++r+ n+d+seaemCGnG+r++
  gi|474934957|ref|YP_007688539.1|   3 FWKYHGIGNDFIVLDCISDPVPVDPAWCEQVCDRHFGIGADGVLYILpGEKGTDITMRIINADSSEAEMCGNGIRCV 79 
                                       89*********************************************777899************************ PP

                                       HHHHHCTTS-S-SEEEEEETTEEEEEEEECTTSS.....EEEEEE-- CS
                     DAP_epimerase  77 aaylreggletkkevtvetlgGeleievkddgek.....vkvdmGka 118
                                       a+ +++ gl++ +e+t+ t  G l+++v++d e      v+ dmG +
  gi|474934957|ref|YP_007688539.1|  80 AKHAADTGLVSGDEFTIMTGRGVLKAKVRKDPEDdyvsfVQIDMGAP 126
                                       ******************************99889999999999987 PP

  == domain 2  score: 69.3 bits;  conditional E-value: 3.6e-23
                                       EEECSSEEEEEEECCTTCSSHHHHHHHHHHHTTTTSTT-SEEEEEEEEETTEEEEEEEETTTEEESTTHCC.HHHHH CS
                     DAP_epimerase   2 akshGnpndvvvvddveaelvleaelvaalcdreagpgadgvlfvkpsgeediklryfnrdgseaemCGnG.vrvfa 77 
                                       a+s+Gnp+++ +  d+  e+v +  l+++l++++++p +++v+f   +++ +i++ +++r++  + +CG+G ++  +
  gi|474934957|ref|YP_007688539.1| 157 AVSMGNPHFITF-SDISDEDVRR--LGPQLEKHPFFPRKTNVEFAR-VKDGKIEITVYERGAAWTLACGTGaCATTV 229
                                       799*****8777.5666689999..*********************.699*************************** PP

                                       HHHHCTTS-S-SEEEEEETTEEEEEEEECTTSSEEEEEE--EE CS
                     DAP_epimerase  78 aylreggletkkevtvetlgGeleievkddgekvkvdmGkasl 120
                                       a++ ++ +  ++++ v+++gG l+i+  ++ +  + + G+a+l
  gi|474934957|ref|YP_007688539.1| 230 AAALNKLVPFDEPIDVRLPGGWLKITADSKLR-YVLMEGPAEL 271
                                       *************************9999887.7999999987 PP

>> Pro_racemase  Proline racemase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0     3e-07    0.0027      62     151 ..      50     138 ..      42     141 .. 0.79
   2 ?   -0.1   0.0     0.041   3.7e+02      82     124 ..     219     258 ..     206     264 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3e-07
                                       -SSTTSSEEEEEEESSS.B-SSTHHHHHHHHHHHHHTTSS-SEEEECEEEEEETTEEEEEEEECTST..SEEEEEEE CS
                      Pro_racemase  62 pkepdadlgvifletsg.ylpmcGsntigvvtvlletGlvevqepetklsletpaGlvevtaecrdg..kvervsle 135
                                       p e+ +d+ + +++++     mcG++  +v++ +++tGlv+  e +    + t  G+++++++++ +   v+ v+++
  gi|474934957|ref|YP_007688539.1|  50 PGEKGTDITMRIINADSsEAEMCGNGIRCVAKHAADTGLVSGDEFT----IMTGRGVLKAKVRKDPEddYVSFVQID 122
                                       556667777777776541568*******************998777....999***999998876443399999999 PP

                                       -S-BEEEEEEEEEEET CS
                      Pro_racemase 136 nvpsfvyaldvevevp 151
                                       + +  ++ ++v v+ +
  gi|474934957|ref|YP_007688539.1| 123 MGAPILDGRQVPVDFD 138
                                       9888888888888866 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.041
                                       STHHHHHHHHHHHHHTTSS-SEEEECEEEEEETTEEEEEEEEC CS
                      Pro_racemase  82 mcGsntigvvtvlletGlvevqepetklsletpaGlvevtaec 124
                                        cG ++ +++ +++ + lv+  ep     +  p+G +++ta+ 
  gi|474934957|ref|YP_007688539.1| 219 ACGTGACATTVAAALNKLVPFDEPI---DVRLPGGWLKITADS 258
                                       6999998888888888999999998...677799999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1748.82
//
Query:       gi|474934958|ref|YP_007688540.1|  [L=387]
Description: Aspartate/tyrosine/aromatic aminotransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-53  180.8   0.0      5e-53  180.6   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    0.00028   19.9   0.0       0.25   10.2   0.0    2.2  2  Alliinase_C      Allinase
  ------ inclusion threshold ------
      0.018   14.8   0.0      0.031   14.1   0.0    1.4  1  PAZ              PAZ domain
      0.083   11.4   0.0       0.12   10.9   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
      0.096   12.2   0.1       0.15   11.6   0.1    1.2  1  DUF4918          Domain of unknown function (DUF4918)


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.6   0.0   1.4e-56     5e-53       2     362 ..      35     381 ..      34     382 .. 0.94

  Alignments for each domain:
  == domain 1  score: 180.6 bits;  conditional E-value: 1.4e-56
                                       EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHH CS
                     Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGag 78 
                                       d+i++g+++++       + e+++a+k+ a++ +++ +y+ ++g ++l++a+a+++++++++kl+++++++v+ G++
  gi|474934958|ref|YP_007688540.1|  35 DMIDFGIGDPDLP----CPGEIVRAMKK-AADVNENQKYSSSQGEKDLRQAIAEYYRKKYNVKLNPDTEICVTIGSK 106
                                       79********999....***********.************************************************ PP

                                       HHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSE.EEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEE CS
                     Aminotran_1_2  79 aliealifllklnpgdeilvpdptyasyknilrlsgge.vvryplyseedfhldlealeealkeapegnkktkvilv 154
                                       ++i  +++++ +n g++i++p+p y+ y+ ++ +   + + +++l++e+++ ld+++  +            +++++
  gi|474934958|ref|YP_007688540.1| 107 EGIFNIAQAF-VNDGEKIIAPSPGYPVYSGAAPIFNNAvCEKVALRKEKNWLLDVKDCPT----------DARLMYL 172
                                       **********.9****************999877554448899999************99..........4569*** PP

                                       ESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EE CS
                     Aminotran_1_2 155 esphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvG 231
                                       + p+NPtG+ ++ + ++ +++ ak+++ +  +D aY ++ f+     ++ + ++++ +++   s+sK f ++G+R+G
  gi|474934958|ref|YP_007688540.1| 173 CYPNNPTGATCDVDYIKNVYKWAKRNKTIMAFDNAYNELTFDGY---RAPSALQAGKDCIEFCSFSKTFDMTGFRIG 246
                                       *****************************************954...34889999999******************* PP

                                       EEEEEHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHSTEEEECCS CS
                     Aminotran_1_2 232 yilgnaavvsqlrklsrpfls..ssllqaavaaalsdallkqs...eleemrqrlqkrrkelrdeLaelglkvlasq 303
                                       +++gn++++  l+k + ++ s  +   q+a+   l+  ++        + +++++ +rrk l+++L++lg ++ +++
  gi|474934958|ref|YP_007688540.1| 247 WAAGNEELIAGLTKCKGQIDSgaPIFIQKAAKFGLEMYNDDGTlpaAAQRNVDEFGERRKMLVEGLRDLGYECDMPK 323
                                       ***********************99999999888877776666777******************************* PP

                                       CSSEEEEEETHHCHHHHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHH CS
                     Aminotran_1_2 304 sgmflltdlsaetakelskkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelvea 362
                                       ++++++ d+ +    e+ ++++ + gv+vtpg  f+    g +R+ v + +++ + e++++
  gi|474934958|ref|YP_007688540.1| 324 GTFYVWFDCGKD-SGEFTQEMIRK-GVIVTPGDGFGEagAGYIRMAV-TRSKDRIAEALRR 381
                                       **********99.9**********.************9999999999.9999999999876 PP

>> Alliinase_C  Allinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0     7e-05      0.25      96     211 ..     120     253 ..     101     260 .. 0.71
   2 !    7.5   0.0   0.00045       1.6     304     359 ..     327     382 ..     319     385 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 7e-05
                                       SEEEEE-SS--THHHHHTTTT-BTTEEEEE..ESTT-....--S..S-EEEEEESS-TTT----.....----...- CS
                       Alliinase_C  96 pvkvvaavPyysvykeqtslldsklykweG..daaayv...kkknpeefielvtsPnnPdgllr.....eavv...k 159
                                         k++a  P y+vy   + +++++  +     + +++    k+  ++  +     PnnP g+       ++v    k
  gi|474934958|ref|YP_007688540.1| 120 GEKIIAPSPGYPVYSGAAPIFNNAVCEKVAlrKEKNWLldvKDCPTDARLMYLCYPNNPTGATCdvdyiKNVYkwaK 196
                                       57899**************999988765431245566555456666777888999****997531111144446667 PP

                                       TT-EEEEEE-TT-STTT....S---S-B--SEEEE.EHHHHHS-GGG-EEEEEES-H CS
                       Alliinase_C 160 gseakviyDlayYWPhy....tpitskadedimLf.tlskltGhaGsrlGWalvkdk 211
                                       ++++++ +D ay    +    +p   +a +d + f ++sk+   +G r+GWa   ++
  gi|474934958|ref|YP_007688540.1| 197 RNKTIMAFDNAYNELTFdgyrAPSALQAGKDCIEFcSFSKTFDMTGFRIGWAAGNEE 253
                                       77888889999976555222356666777886655389*************976555 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00045
                                       EEEEEESSSS..-HHHHHHTTTEEEEEGGGGTS-TTEEEEESSS-HHHHHHHHHHH CS
                       Alliinase_C 304 yaWlkcekeededcaevlrekkiltrsGevfeaesryvrlsllkrdddfdvllerl 359
                                       y W+ c k++ e  +e++r++ i+t +    ea++ y+r+++ +++d     l+r+
  gi|474934958|ref|YP_007688540.1| 327 YVWFDCGKDSGEFTQEMIRKGVIVTPGDGFGEAGAGYIRMAVTRSKDRIAEALRRM 382
                                       99*******999999999999999887777789*************9998888876 PP

>> PAZ  PAZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   8.6e-06     0.031      48      93 ..      62     105 ..      56     155 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.6e-06
                                       EESS--TTSEECCTTCT..CECCHHHHCCT---ST-TT--EEEEEE CS
                               PAZ  48 ittdlapsstFpdkdkeneitfaeYfkkkYnieikdqdqplldvdk 93 
                                       + ++++ ss+   kd   ++ +aeY++kkYn++++     ++  ++
  gi|474934958|ref|YP_007688540.1|  62 VNENQKYSSSQGEKD--LRQAIAEYYRKKYNVKLNPDTEICVTIGS 105
                                       444444444444443..4589*************655777777776 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   3.4e-05      0.12      80     176 ..     109     208 ..      92     224 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.4e-05
                                       HHHHHHTTS-TTEEEEEEST...SSHHHHHHHHHTHHH.TTCEEEEESTTSHHHHHHHCCTTEEEEEEESS-TTTT- CS
                   Cys_Met_Meta_PP  80 iaaailallkaGdeivvsdd...lYggtqrllkkvlkk.lgievkfvdtsdleelekaikentklvylEtptnpllk 152
                                       i+++ +a+++ G++i++ +    +Y+g+  ++++ + + + ++ +     d     k +    +l+yl  p np+  
  gi|474934958|ref|YP_007688540.1| 109 IFNIAQAFVNDGEKIIAPSPgypVYSGAAPIFNNAVCEkVALRKEKNWLLD----VKDCPTDARLMYLCYPNNPTGA 181
                                       66788999999*****98753337888888877655430333332222222....3345557899999999999988 PP

                                       ---...HHHHHHHHHHTT-EEEEEGTT CS
                   Cys_Met_Meta_PP 153 vvD...iekiaklakkagvlvvvDntf 176
                                       ++D   i+++ k ak +++++  Dn++
  gi|474934958|ref|YP_007688540.1| 182 TCDvdyIKNVYKWAKRNKTIMAFDNAY 208
                                       888333567788889999*******87 PP

>> DUF4918  Domain of unknown function (DUF4918)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   4.2e-05      0.15     122     179 ..      47     106 ..      45     121 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.2e-05
                                       SS-SEEEEE-TTS-EEE--T.TSSHHHHHHHHHHHHHHHHHHH..TTTEEECEEEEE-TTH CS
                           DUF4918 122 vfPlglvkkaskgneknyny.Yddkklekalkpfiieslkeql..elgldtsvcfvlGkgk 179
                                       ++P  +v+ ++k+ ++n n  Y + + ek l+++i e  +++   +l+ dt++c+ +G+ k
  gi|474934958|ref|YP_007688540.1|  47 PCPGEIVRAMKKAADVNENQkYSSSQGEKDLRQAIAEYYRKKYnvKLNPDTEICVTIGS-K 106
                                       68999************99659*****************99873366777888888887.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 2663.71
//
Query:       gi|474934959|ref|YP_007688541.1|  [L=311]
Description: hypothetical protein TALC_01403 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1955.41
//
Query:       gi|474934960|ref|YP_007688542.1|  [L=72]
Description: hypothetical protein TALC_01404 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       217  (0.0121033); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 461.12
//
Query:       gi|474934961|ref|YP_007688543.1|  [L=412]
Description: 3-phosphoglycerate kinase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.9e-107  359.5   0.0   2.2e-107  359.3   0.0    1.0  1  PGK       Phosphoglycerate kinase


Domain annotation for each model (and alignments):
>> PGK  Phosphoglycerate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  359.3   0.0  1.2e-111  2.2e-107       3     375 ..       9     390 ..       7     393 .. 0.92

  Alignments for each domain:
  == domain 1  score: 359.3 bits;  conditional E-value: 1.2e-111
                                       GS--TT-EEEEEE-----EECT.TEES--HHHHHHHHHHHHHHHTT-EEEEEE--S--TTS-GGG-SHHHHHHHHHH CS
                               PGK   3 dldlkgkrvlvRvDfNvplkke.gkitddtriraalpTikyllekgakvvllsHlgrpkgekeklslkpvaerLsel 78 
                                       dl+ kg+rvl+RvD+N+p++k+  ki +d rira +pTi++l+ k+ak+v+l+H++r kg+ + ++l+++a+ Ls+ 
  gi|474934961|ref|YP_007688543.1|   9 DLNYKGRRVLLRVDINCPMDKKtLKIINDVRIRAVVPTIRELMGKEAKLVILAHQSR-KGKWDFTDLSQHAALLSRN 84 
                                       899****************99889*********************************.599**************** PP

                                       HTT-EEEESSTTSHHHHHHHHT-TTT-EEEES-GGGSTTTTTT-H.......HHHHHHHHT-SEEEE--GGGTTS-- CS
                               PGK  79 lgkeVkfvedvvgeeveeaiaelkegevllLeNvrfykeEeknde.......elakklasladvyVnDAFgtahrah 148
                                       l+ +Vk+v+dv+g+e+++ai+elk+gevllL Nvr  + E+++++       e++++la l+d+yV DAFg+ahr++
  gi|474934961|ref|YP_007688543.1|  85 LNAPVKYVDDVIGDEAKKAIQELKDGEVLLLGNVRAIDSESESKPmeehakgEIVSNLAPLFDFYVCDAFGAAHRSQ 161
                                       *************************************9997765566666667************************ PP

                                       TTTTHHHHCSEEEE-HHHHHHHHHHHHHHHS--SSEEEEEEES-HHHCHHHHHHHTTT-..SEEEEETCHHHHHHHH CS
                               PGK 149 aStvgiakvlsaaaGllmekElealskvlenperplvailGGakvsdkikvienLlekv..dkliigGgmantFlka 223
                                       aS+vg++ vl++aaG+lm+kE+ al++++++p+rp v+ilGGak +d   +i+++l +   d++ii G+  n+Fl+a
  gi|474934961|ref|YP_007688543.1| 162 ASLVGFEAVLPSAAGRLMSKEIYALRTIFNEPRRPSVFILGGAKFDDVPYMIDRVLGNGtaDQVIIVGLAGNAFLAA 238
                                       **********99********************************************98777**************** PP

                                       TT-B-TTSS-.......-GGGHHHHHHHHHHHHHHT-EEE--SEEEEESSSSTTS.EEEECCG--TT-EEEEE-HHH CS
                               PGK 224 qgleigkslv.......eedklelakellekakkkgvkillpvDvvvakeeaekeakvveveaipedemalDigpkt 293
                                       +g +ig+           e++   a+e++ek++   +ki+lpvDv+v+  +   e+  v++ ++ +   a+Dig+k+
  gi|474934961|ref|YP_007688543.1| 239 RGRDIGEASRaplkedlTEENFRNAQEIMEKYS---EKIILPVDVAVEGPN--GERVSVNIGDMAKAGAAIDIGNKS 310
                                       ******666633322223357999*******98...79**********732..324566899999999********* PP

                                       HHHHHHHHCC-SEEEEES-SS-TTSGCCCHHHHHHHHHHHHHCHTSEEEEESHHHHHHHHHTT-GGGSSEEESSSHH CS
                               PGK 294 ielfaeaikeaktvvwnGpmGvfeiekfakGTkaiakalaeatkgalsivGGgdsaaaveklgladkvshvStGGgA 370
                                       ie+f ++i+ ++t ++ Gp+G+fe + f+ GT+++++a+ e++   l++ GGg++ aa+ek++lad++s++StGGgA
  gi|474934961|ref|YP_007688543.1| 311 IERFVKVIRGSRTSFMSGPAGMFEKPGFDVGTRSLMEAMVESKG--LTVLGGGHTSAAAEKFDLADSMSYLSTGGGA 385
                                       *****************************************855..******************************* PP

                                       HHHHH CS
                               PGK 371 sLelL 375
                                       + ++L
  gi|474934961|ref|YP_007688543.1| 386 LETFL 390
                                       87766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 3254.04
//
Query:       gi|474934962|ref|YP_007688544.1|  [L=337]
Description: glyceraldehyde-3-phosphate dehydrogenase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.1e-26   90.9   0.1    9.2e-26   90.3   0.1    1.3  1  Gp_dh_C         Glyceraldehyde 3-phosphate dehydrogenase, C-t
    4.7e-09   36.4   0.2    1.2e-08   35.1   0.0    1.8  2  DapB_N          Dihydrodipicolinate reductase, N-terminus
    2.2e-06   27.9   0.6    1.8e-05   25.0   0.0    2.6  3  Gp_dh_N         Glyceraldehyde 3-phosphate dehydrogenase, NAD
     0.0001   21.7   0.1     0.0018   17.6   0.1    2.4  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
     0.0015   19.2   0.0      0.011   16.3   0.0    2.2  2  NAD_binding_3   Homoserine dehydrogenase, NAD binding domain
     0.0046   17.8   0.0      0.009   16.8   0.0    1.5  1  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
  ------ inclusion threshold ------
      0.014   15.8   0.0      0.031   14.7   0.0    1.5  1  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai
       0.12   12.3   0.1       0.32   11.0   0.1    1.8  1  RHH_1           Ribbon-helix-helix protein, copG family
       0.12   12.6   0.1       0.41   10.9   0.1    2.0  1  TrkA_N          TrkA-N domain


Domain annotation for each model (and alignments):
>> Gp_dh_C  Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.3   0.1   4.6e-29   9.2e-26       1     158 []     146     299 ..     146     299 .. 0.96

  Alignments for each domain:
  == domain 1  score: 90.3 bits;  conditional E-value: 4.6e-29
                                       HHHHHHHHHHHHEEEEEEEEEEEECTTTSBSSSS--.SSTTTTSBTT.CSSEEEE-THHHHHHHHSGGGTTTEEEEE CS
                           Gp_dh_C   1 LaplakvlndkfgikkglmttvhaytndQkllDgpskkdlrraraaa.eniiptstgaakavglVlpelkgkldglA 76 
                                       L +++  l+++f+ik++++t+v++++++          d ++++++a e  +  +t+++ +v++V+p    +++++A
  gi|474934962|ref|YP_007688544.1| 146 LLRTLAPLDKEFKIKNAYVTIVRRAADP---------GDSKNGPINAlEPSVSLPTHHGVDVKSVMPW--LDITTMA 211
                                       678999**********************.........89********9999****************6..689**** PP

                                       EEESSSSEEEEEEEEEESSTS-HHHHHHHHHHHHH....TTTTTTEEEEHSHHHGGGGTTGCS..SEEEEGGGCEEE CS
                           Gp_dh_C  77 vrVPtpnvsvvdlvvelekevtveevnaalkeaae....galkgilsyteeelvssDlvgdph..ssifdaketivv 147
                                       ++VPt+ +++  +vv++++e + eev ++++   +    ++ +gi s+++ ++ +++l +++   ++i+ +k + +v
  gi|474934962|ref|YP_007688544.1| 212 IKVPTTLMHIQTVVVKFDREISTEEVLRVFEGCHRvrlvSSKDGIKSTAQIMELARELGRSRSdmYEIVIWKDGVKV 288
                                       *********************************9999*99*******************999989************ PP

                                       TTTEEEEEEEE CS
                           Gp_dh_C 148 eenlvkvvawy 158
                                        ++ +++++++
  gi|474934962|ref|YP_007688544.1| 289 VGDTLYYYQAV 299
                                       **999999986 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.0     6e-12   1.2e-08       1      96 [.       4     108 ..       4     129 .. 0.82
   2 ?   -2.1   0.0         2     4e+03      68     101 ..     222     256 ..     195     273 .. 0.64

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 6e-12
                                       EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTC..STTTTTBHH........HHSSSS--S-BEBSSHHHHHHH CS
                            DapB_N   1 ikvavvGasGrmGkevvkaveeaedlelvaavdrke..selegkdag........ellglgklgvavtddleevlek 67 
                                       ikv+++G+ G++Gk+v+ av+ ++d+e+ ++ ++++  ++  + +ag        ++  ++k g++v  +++++l k
  gi|474934962|ref|YP_007688544.1|   4 IKVGINGY-GTIGKRVATAVSLQDDMEVIGVTKTRPtyEAKTAAEAGypiyvpaeSIPAFEKAGLKVAGTVDDLLGK 79 
                                       79******.*************************9944444455555*******7777778**************** PP

                                       -SEEEE-S-HHHHHHHHHHHHHTT-EEEE CS
                            DapB_N  68 advliDFTtpeavlenlklalekgvklVi 96 
                                       ad+++D T  +   e+ + + ++g+k+++
  gi|474934962|ref|YP_007688544.1|  80 ADIIVDCTPGDIGPEYKAKYEKAGIKAIF 108
                                       ********544444444444444777765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2
                                       -SEEEE-S-HHHHHHHHHHHHHT.T-EEEE--SS- CS
                            DapB_N  68 advliDFTtpeavlenlklalek.gvklViGTTGl 101
                                       + v++ F +  ++ e+l++     +v+lV    G+
  gi|474934962|ref|YP_007688544.1| 222 QTVVVKFDREISTEEVLRVFEGChRVRLVSSKDGI 256
                                       56777777777777777665544466666655555 PP

>> Gp_dh_N  Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   9.2e-09   1.8e-05       1      33 [.       4      36 ..       4      49 .. 0.85
   2 ?   -2.3   0.0       2.8   5.6e+03      88      96 ..      80      88 ..      78      89 .. 0.86
   3 ?   -0.8   0.0      0.96   1.9e+03      38      77 ..     214     254 ..     195     260 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 9.2e-09
                                      CEEEEESTSHHHHHHHHHHHHHTTCEEEEEE-T CS
                           Gp_dh_N  1 vkvainGfGRIGrlvlralleekelevvaindl 33
                                      +kv+inG+G IG+ v+ a+  ++++ev+ + ++
  gi|474934962|ref|YP_007688544.1|  4 IKVGINGYGTIGKRVATAVSLQDDMEVIGVTKT 36
                                      69****************************984 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.8
                                      SSEEEE-SS CS
                           Gp_dh_N 88 vdlVvestG 96
                                      +d++v++t 
  gi|474934962|ref|YP_007688544.1| 80 ADIIVDCTP 88
                                      79*****95 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.96
                                       HHHHHHHEETTTEC-SS-EEEETTEEEETT.EEEEEE--SS CS
                           Gp_dh_N  38 tlayllkyDsvhgrfkgeveaeeealvvng.kkikvlaekd 77 
                                         + l++  +v  +f++e+++ee   v +g ++++++++kd
  gi|474934962|ref|YP_007688544.1| 214 VPTTLMHIQTVVVKFDREISTEEVLRVFEGcHRVRLVSSKD 254
                                       45567788888899999999877666666656777777665 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   9.3e-07    0.0018      37      73 ..       4      41 ..       1      94 [. 0.83

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 9.3e-07
                                      SEEEEES-SHHHHHHHHHHH.HTT-EEEEESSSHHHHH CS
                      2-Hacid_dh_C 37 ktvGiiGlGrIGqavakrlk.afgmkviaydrskkkee 73
                                       +vGi G+G IG++va  ++ + +m+vi++ +++ + e
  gi|474934962|ref|YP_007688544.1|  4 IKVGINGYGTIGKRVATAVSlQDDMEVIGVTKTRPTYE 41
                                      58******************999*******99988555 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   5.6e-06     0.011       1      83 [.      10     103 ..      10     108 .. 0.84
   2 ?   -0.1   0.0      0.73   1.5e+03      75      94 ..     294     313 ..     290     332 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.6e-06
                                       --SHHHHHHHHHHHH---SSEEEEEEEEESS.EEE-TT...............HHHHHT--CB---HHHHHHHHS-E CS
                     NAD_binding_3   1 GlGaiGsavleqlkrqqseielelvavadrd.sllskd...............rkallasealtldlddliahldpd 61 
                                       G+G+iG++v+ ++  q +   +e+ +v++ + + ++k                ++ + a  ++   +ddl+   ++d
  gi|474934962|ref|YP_007688544.1|  10 GYGTIGKRVATAVSLQDD---MEVIGVTKTRpTYEAKTaaeagypiyvpaesiPAFEKAGLKVAGTVDDLLG--KAD 81 
                                       99************9995...8*********6666665999*******999998888899999999999999..*** PP

                                       EEEE-S--HHHHTTHHHHHHTT CS
                     NAD_binding_3  62 vvVEcasseavaelvlkaLkag 83 
                                       ++V+c++ +   e+ +k  kag
  gi|474934962|ref|YP_007688544.1|  82 IIVDCTPGDIGPEYKAKYEKAG 103
                                       ******8776666666655555 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.73
                                       THHHHHHTTEEEE-S--CGG CS
                     NAD_binding_3  75 lvlkaLkagkdvvtankgal 94 
                                       ++++a+ +  dvv  n++ +
  gi|474934962|ref|YP_007688544.1| 294 YYYQAVHQESDVVPENVDCI 313
                                       6999*********9999866 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   4.5e-06     0.009       1      90 [.       4     108 ..       4     110 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.5e-06
                                       EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESS.................HHHHHTC CS
                      GFO_IDH_MocA   1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysd.................leellad 60 
                                       ++v+i G+G ig++ + ++  + ++ ev+++ ++++    + a++ g + y                   +++ll  
  gi|474934962|ref|YP_007688544.1|   4 IKVGINGYGTIGKRVATAVSLQ-DDMEVIGVTKTRPTYEAKTAAEAGYPIYVPaesipafekaglkvagtVDDLLG- 78 
                                       68**************666666.*******************9999999665556788888899999998999999. PP

                                       TTESEEEE-S-GGGHHHHHHHHHHTT-.EEE CS
                      GFO_IDH_MocA  61 peidavivatpngtheelakaaleagk.hvl 90 
                                        ++d+++ +tp + + e+  +  +ag+ +++
  gi|474934962|ref|YP_007688544.1|  79 -KADIIVDCTPGDIGPEYKAKYEKAGIkAIF 108
                                       .99*********9999999999999986666 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.5e-05     0.031       1      94 [.       5     107 ..       5     109 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.5e-05
                                       EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTT.TTTSBHHHHSG.........GGTTTECEBEEEGGGGGCTT- CS
                    Semialdhyde_dh   1 kvaivGatGyvGqellrlLeehpevelvvllsssr.saGkklaeavk.........aleegkdlkvedvdeeelkev 67 
                                       kv+i G  G +G+++++ ++ + ++e++ ++ ++   + k+ aea              e++ lkv  + ++ l ++
  gi|474934962|ref|YP_007688544.1|   5 KVGING-YGTIGKRVATAVSLQDDMEVIGVTKTRPtYEAKTAAEAGYpiyvpaesiPAFEKAGLKVAGTVDDLLGKA 80 
                                       577778.8999999999999999999999999998744444444433599999975445566677777888899*** PP

                                       SEEEE-SCHHHHHHHHHHHHHTTSEEE CS
                    Semialdhyde_dh  68 divflalpagvskelapklaeagvkvi 94 
                                       di++ ++p+++  e+ +k+ +ag+k i
  gi|474934962|ref|YP_007688544.1|  81 DIIVDCTPGDIGPEYKAKYEKAGIKAI 107
                                       ***********************9876 PP

>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00016      0.32      12      28 ..     260     276 ..     257     281 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00016
                                       HHHHHHHHHHTSSHHHH CS
                             RHH_1  12 erLdelarrrgrSrSel 28 
                                       +++ elar++grSrS++
  gi|474934962|ref|YP_007688544.1| 260 AQIMELARELGRSRSDM 276
                                       7888***********97 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1    0.0002      0.41       3      46 ..       8      54 ..       6      84 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0002
                                      EES-SHHHHHHHHHHHH.TTEEEEEEESSHHH..HHHHHHTTSEEEE CS
                            TrkA_N  3 iiGlGrvGrslaeeLse.ggkdvvvidkdeer..veelreeglevvv 46
                                      i G+G++G+++a  +s  + ++v+++ k + +  +++++e g++++v
  gi|474934962|ref|YP_007688544.1|  8 INGYGTIGKRVATAVSLqDDMEVIGVTKTRPTyeAKTAAEAGYPIYV 54
                                      77*************9966678******9966447777888887654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2279.29
//
Query:       gi|474934963|ref|YP_007688545.1|  [L=554]
Description: acetolactate synthase, large subunit, biosynthetic type [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-59  200.8   0.0    5.7e-58  195.3   0.0    2.5  2  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
    2.1e-51  173.7   0.0    6.3e-51  172.2   0.0    1.9  2  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    3.9e-38  130.3   0.0    1.2e-37  128.7   0.0    1.8  2  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
     0.0043   16.8   0.0     0.0093   15.7   0.0    1.5  1  CO_dh         CO dehydrogenase beta subunit/acetyl-CoA syntha
  ------ inclusion threshold ------
      0.062   12.1   0.1       0.11   11.2   0.1    1.3  1  XFP_N         XFP N-terminal domain
      0.087   12.5   0.8        1.8    8.2   0.1    2.6  3  DAGK_cat      Diacylglycerol kinase catalytic domain


Domain annotation for each model (and alignments):
>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.3   0.0   1.9e-61   5.7e-58       1     170 [.       1     168 [.       1     170 [. 0.98
   2 ?    2.9   0.0     0.024        72     111     144 ..     484     517 ..     414     521 .. 0.73

  Alignments for each domain:
  == domain 1  score: 195.3 bits;  conditional E-value: 1.9e-61
                                       EEHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHH CS
                      TPP_enzyme_N   1 mtvaealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGat 77 
                                       m++++al+++L++  v++vfg+pG  i p++d++ ++ g+r+vl+rhEq+aa++Adgyara+g+pgv+l+tsgpG+t
  gi|474934963|ref|YP_007688545.1|   1 MKGSKALLKMLEDRHVDTVFGYPGAVIIPIYDSFIDS-GVRHVLVRHEQCAAHMADGYARASGRPGVCLATSGPGTT 76 
                                       799**********************************.7************************************** PP

                                       HCHHHHHHHHHHT--EEEEEEE--CCCHHS..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--E CS
                      TPP_enzyme_N  78 naltalaeAkvdriPllvlsgdrptslrgqgvlqqeldqlalfrpvtkyaervtspeelpealrrAirtalsgrpgP 154
                                       n++t++a+A+ d++Pl++l+g+++ts  g +++q e+d  +l+ pvtk+++rv +pe+lp+a+++A+++++ grpgP
  gi|474934963|ref|YP_007688545.1|  77 NLVTGIATAYADSVPLIALTGQVGTSFLGAEAFQ-EVDSYSLMMPVTKHNFRVLDPERLPHAIDEAWKICQIGRPGP 152
                                       **********************************.****************************************** PP

                                       EEEEEEHHHCC-EEEH CS
                      TPP_enzyme_N 155 vylelpkdvlleevde 170
                                       v+++ p d l++++++
  gi|474934963|ref|YP_007688545.1| 153 VHIDMPTDQLSADIPD 168
                                       ********99998876 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.024
                                       C--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHH CS
                      TPP_enzyme_N 111 qqeldqlalfrpvtkyaervtspeelpealrrAi 144
                                        +  d +++++++  +  rv++p+e++eal+r i
  gi|474934963|ref|YP_007688545.1| 484 RPDPDFVKVAESFGAWGIRVEKPSEIREALERGI 517
                                       34558889999*******************9976 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.7     5e+03      48      69 ..     199     219 ..     173     231 .. 0.52
   2 !  172.2   0.0   2.1e-54   6.3e-51       1     153 []     379     527 ..     379     527 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.7
                                       EEEEEEEHHHHHHTGGGHHHHH CS
                      TPP_enzyme_C  48 evvaivGDGgflmilqelatav 69 
                                       + v +vG G+ +    e++  +
  gi|474934963|ref|YP_007688545.1| 199 RPVMLVGGGA-MGASKEVVRLA 219
                                       3333444333.33334444444 PP

  == domain 2  score: 172.2 bits;  conditional E-value: 2.1e-54
                                       ESSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEE CS
                      TPP_enzyme_C   1 diGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnlpitv 77 
                                       d+G++++wa ++l+vk pr+++tsg +gtmG+glp A+Gak+a+pd++vv ivGDGg++m +qelat+v +++p+t+
  gi|474934963|ref|YP_007688545.1| 379 DVGQNQMWAMHCLDVKYPRQFITSGSFGTMGFGLPSAMGAKMARPDAKVVTIVGDGGLQMVIQELATSVAEDIPVTI 455
                                       89*************************************************************************** PP

                                       EEEE-SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                      TPP_enzyme_C  78 vvlnNegygmtggqqepfggkrksgpagkdlkpvdfaklaealGakgarvekadveeleealkealekkgpaliev 153
                                       v+lnN+++gm++++q+ f ++r+sg++    +++df+k+ae++Ga g+rvek+  +e++eal++ +++++++li++
  gi|474934963|ref|YP_007688545.1| 456 VLLNNGWLGMVRQWQKLFWDRRFSGTD--LRPDPDFVKVAESFGAWGIRVEKP--SEIREALERGINSDRTCLIDI 527
                                       *************************99..6999*****************999..*******************97 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.7   0.0     4e-41   1.2e-37       1     125 [.     187     308 ..     187     322 .. 0.92
   2 ?   -3.2   0.0       2.2   6.6e+03      13      41 ..     426     452 ..     422     462 .. 0.69

  Alignments for each domain:
  == domain 1  score: 128.7 bits;  conditional E-value: 4e-41
                                       HHHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEEESGGGSCHHHHHHHHH CS
                      TPP_enzyme_M   1 iekaaellkaakrpvilvGggvarsgaseelrelaeklgiPvvttlmgkgvipedhplylgmlglhgskaanealee 77 
                                       +e+aa ++++a+rpv+lvGgg+   gas+e+++lae +++Pv+ttlm  gvip++hpl++g lg+hg+  a +a+++
  gi|474934963|ref|YP_007688545.1| 187 VEEAARMIREAQRPVMLVGGGAM--GASKEVVRLAEYTNMPVITTLMSLGVIPSTHPLCMGPLGMHGKLGALDAFQQ 261
                                       689********************..**************************************************** PP

                                       -SEEEEES-SSSTCCCTTTTTTTTTT-EEEEEESSCCCCTTCC--SEE CS
                      TPP_enzyme_M  78 aDlvlalGarfddirttgsepefapeakiihididpaeigknyqvdla 125
                                       aDl+la+G++f+d rt+++++  ap+ k+i+idid++++gk+ + ++ 
  gi|474934963|ref|YP_007688545.1| 262 ADLILAVGTKFSD-RTYNPHTMPAPDCKVIQIDIDATQFGKSQRCSIN 308
                                       *************.9987666555555**************9876655 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.2
                                       SEEEEE-CHHCHTTGHHHHHHHHHHHT-E CS
                      TPP_enzyme_M  13 rpvilvGggvarsgaseelrelaeklgiP 41 
                                       ++v +vG g  +   +e ++++ae +  P
  gi|474934963|ref|YP_007688545.1| 426 KVVTIVGDGGLQMVIQELATSVAEDI--P 452
                                       66778888888777777777777743..4 PP

>> CO_dh  CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   3.1e-06    0.0093      23      70 ..     185     230 ..     170     243 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.1e-06
                                       --SHHHHHHHHHSSSEEEEE-S--.-HH.HHHHHHHHHTSSSEEEEET CS
                             CO_dh  23 ealkvvakmikkakrPllivGpqvlkaeneeakekkilekklkvvata 70 
                                       + ++++a+mi+ a+rP+++vG+ +  a    + ++  +  +++v+ t 
  gi|474934963|ref|YP_007688545.1| 185 SGVEEAARMIREAQRPVMLVGGGAMGAS--KEVVRLAEYTNMPVITTL 230
                                       55689*****************998887..566778888899988886 PP

>> XFP_N  XFP N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   3.8e-05      0.11     140     169 ..     406     435 ..     399     447 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.8e-05
                             XFP_N 140 GelGyalshayGavldnPdlivacvvGdGe 169
                                       G +G+ l  a+Ga + +Pd  v+++vGdG 
  gi|474934963|ref|YP_007688545.1| 406 GTMGFGLPSAMGAKMARPDAKVVTIVGDGG 435
                                       889*************************95 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0         2     6e+03      57      76 ..      65      84 ..      40      94 .. 0.59
   2 ?    1.8   0.0     0.056   1.7e+02      27      89 ..     173     237 ..     168     238 .. 0.67
   3 ?    8.2   0.1   0.00059       1.8      56      88 ..     424     456 ..     359     458 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2
                                      SEEEEEESHHHHHHHHHHHC CS
                          DAGK_cat 57 dlivvaGGDGtvsevlngll 76
                                       + ++ +G Gt + v +   
  gi|474934963|ref|YP_007688545.1| 65 GVCLATSGPGTTNLVTGIAT 84
                                      56678888899887766554 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.056
                                       HHCTCEEEEEE--STTHHHHHHHHHHHCC-SEEEEEESH.HHHHHHHHHHCT....HHCTTSEEEEEE CS
                          DAGK_cat  27 eeagvelelieteepgdakelakeakeegvdlivvaGGD.Gtvsevlnglle....elatkpplgiiP 89 
                                       ++ gv++ l ++++ ++a ++++ea++    + +v GG  G  +ev+            t + lg+iP
  gi|474934963|ref|YP_007688545.1| 173 KDYGVKIPLEDVSGVEEAARMIREAQR---PVMLVGGGAmGASKEVVRLAEYtnmpVITTLMSLGVIP 237
                                       567888889999999999999999999...56666666447777777654444444444446666666 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.00059
                                       -SEEEEEESHHHHHHHHHHHCTHHCTTSEEEEE CS
                          DAGK_cat  56 vdlivvaGGDGtvsevlnglleelatkpplgii 88 
                                          +v + GDG ++ v++ l+   a+++p++i+
  gi|474934963|ref|YP_007688545.1| 424 DAKVVTIVGDGGLQMVIQELATSVAEDIPVTIV 456
                                       46799999**************99******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (554 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 3495.91
//
Query:       gi|474934964|ref|YP_007688546.1|  [L=345]
Description: hypothetical protein TALC_01408 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00029   21.5   0.0       0.49   11.1   0.0    2.4  2  Methyltransf_25  Methyltransferase domain
  ------ inclusion threshold ------
      0.046   13.4   0.0       0.69    9.6   0.0    2.1  2  UPF0020          Putative RNA methylase family UPF0020
      0.063   13.9   0.0        4.8    7.9   0.0    2.4  2  Methyltransf_11  Methyltransferase domain
       0.16   11.7   0.0       0.31   10.7   0.0    1.5  1  N6_N4_Mtase      DNA methylase


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0011       4.8       2      32 ..      25      53 ..      24      89 .. 0.81
   2 !   11.1   0.0   0.00011      0.49      23      85 ..     150     212 ..     139     220 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0011
                                      EEET-TTSHHHHHHHCTSTSSEEEEEESSHH CS
                   Methyltransf_25  2 LdlGcGtGrltlalakrlgkakvtgvDisee 32
                                      Ld  cG+G ++ a+a r+   +vtg++ ++ 
  gi|474934964|ref|YP_007688546.1| 25 LDPFCGSGSVSYACAMRG--WNVTGLESNPF 53
                                      7889*************5..******98874 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00011
                                       EEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSS.STTTEEEEEEESTGGGSSHHHHHHH CS
                   Methyltransf_25  23 kvtgvDiseemleaareraeeegl.nvefvqgdaedlpf.edgsfDlvvssgalhhlsdedleka 85 
                                       + +g Di ++ +e++re ++ +    ++++ +d +d+p+   +++Dl+vss   ++ +++d +++
  gi|474934964|ref|YP_007688546.1| 150 DRVGADIFSASVETVREPVSVNPKaTAQIHLCDSRDMPYtLRRKYDLIVSSLP-EISPNPD-AEL 212
                                       5689**************97654369999*********73677*******743.4444455.334 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00015      0.69      33      54 ..      25      46 ..      14      87 .. 0.79
   2 ?    1.5   0.0     0.044     2e+02      61     130 ..     132     202 ..     120     202 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00015
                                      EETT-TTSHHHHHHHHHHTT-- CS
                           UPF0020 33 lDPmCGsGtilIEaallgania 54
                                      lDP+CGsG++    a+ g n+ 
  gi|474934964|ref|YP_007688546.1| 25 LDPFCGSGSVSYACAMRGWNVT 46
                                      8********9877777766665 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.044
                                       --SSHHHHHHHHHHHH--.EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--.STTS---EEEE--- CS
                           UPF0020  61 fvlelkaeaeeearaelk.lygsDldrrvvqgareNaekagvgdliefsqadaakLr.lkegevdvivtnpP 130
                                        +++ ++ ++++ ++     +g+D+ ++ v++ re   + + + + ++   d ++++   + ++d+iv+ +P
  gi|474934964|ref|YP_007688546.1| 132 AFCHCLEGIRASDEDGFDdRVGADIFSASVETVREPV-SVNPKATAQIHLCDSRDMPyTLRRKYDLIVSSLP 202
                                       5555566666666655555789999999999888764.5778888888889999999867779*****9988 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0011       4.8       1      35 [.      25      58 ..      25      81 .. 0.82
   2 ?    3.5   0.0     0.026   1.2e+02      21      68 ..     151     200 ..     138     202 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0011
                                      EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHH CS
                   Methyltransf_11  1 LdvGcGtGrlaealakrgarvvgvDlskemlklak 35
                                      Ld  cG+G+++ a+a rg +v+g++ s+ +l++a 
  gi|474934964|ref|YP_007688546.1| 25 LDPFCGSGSVSYACAMRGWNVTGLE-SNPFLRWAA 58
                                      5677*********************.777777774 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.026
                                       EEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-T.T-EEEEEEE CS
                   Methyltransf_11  21 vvgvDlskemlklakekaseegl.kvefvvadaeklpfed.nsfDlvvss 68 
                                        vg D+  + +++++e +s ++  + +++ +d +++p+    ++Dl+vss
  gi|474934964|ref|YP_007688546.1| 151 RVGADIFSASVETVREPVSVNPKaTAQIHLCDSRDMPYTLrRKYDLIVSS 200
                                       5899**********99999999898999********98764699999987 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   6.9e-05      0.31     195     223 ..      24      52 ..       8      60 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 6.9e-05
                                       EEETT-TTTHHHHHHHHTT-EEEEEESSH CS
                       N6_N4_Mtase 195 vlDpFaGSGtTavaakelgrkfiGieiee 223
                                        lDpF+GSG+   a++  g +  G e ++
  gi|474934964|ref|YP_007688546.1|  24 ALDPFCGSGSVSYACAMRGWNVTGLESNP 52 
                                       59****************99999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       258  (0.0143901); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2266.69
//
Query:       gi|474934965|ref|YP_007688547.1|  [L=554]
Description: acetolactate synthase, large subunit, biosynthetic type [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-58  196.8   0.0    1.6e-57  193.9   0.0    2.2  2  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
    6.7e-48  162.3   0.0    4.1e-47  159.8   0.0    2.2  2  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    8.9e-42  142.1   0.1    5.2e-41  139.6   0.1    2.2  2  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain


Domain annotation for each model (and alignments):
>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.9   0.0   2.6e-61   1.6e-57       1     170 [.       1     168 [.       1     170 [. 0.99
   2 ?    0.1   0.0     0.092   5.5e+02      70     101 ..     430     461 ..     414     520 .. 0.62

  Alignments for each domain:
  == domain 1  score: 193.9 bits;  conditional E-value: 2.6e-61
                                       EEHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHH CS
                      TPP_enzyme_N   1 mtvaealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGat 77 
                                       m++++al+++L++ gve++fg+pG+++ p++d+++e+ +ir++l+rhEq+a++aAdg+aratg+ gv+l tsgpGat
  gi|474934965|ref|YP_007688547.1|   1 MKGSRALLKMLEDKGVETMFGYPGGSVIPIYDEIKES-SIRHILVRHEQCAGHAADGFARATGQTGVCLSTSGPGAT 76 
                                       799**********************************.6************************************** PP

                                       HCHHHHHHHHHHT--EEEEEEE--CCCHHS..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--E CS
                      TPP_enzyme_N  78 naltalaeAkvdriPllvlsgdrptslrgqgvlqqeldqlalfrpvtkyaervtspeelpealrrAirtalsgrpgP 154
                                       n++t++a+A+ d++P+l+l+g+++t++ g +++q e+d+ +l+ ++tk+++rvt+ ++lp+a+ +A+++a +grpgP
  gi|474934965|ref|YP_007688547.1|  77 NMVTGIATAYADSVPMLALTGQVGTTMLGSDAFQ-EVDAYSLMMSITKHNFRVTDIKRLPHAISEAWEIARTGRPGP 152
                                       **********************************.****************************************** PP

                                       EEEEEEHHHCC-EEEH CS
                      TPP_enzyme_N 155 vylelpkdvlleevde 170
                                       v+++lp d +++++de
  gi|474934965|ref|YP_007688547.1| 153 VHIDLPVDQVNADIDE 168
                                       **********999987 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.092
                                       E-CHHHHHHCHHHHHHHHHHT--EEEEEEE-- CS
                      TPP_enzyme_N  70 vtsgpGatnaltalaeAkvdriPllvlsgdrp 101
                                            G+  ++  la+   +++P++v+  +++
  gi|474934965|ref|YP_007688547.1| 430 IVGDGGLQMVIQELATSVAEKLPVVVVLLNNG 461
                                       44444788888899999999999999876654 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.16   9.6e+02     107     151 ..     108     155 ..      75     157 .. 0.67
   2 !  159.8   0.0   6.9e-51   4.1e-47       1     153 []     379     527 ..     379     527 .. 0.98

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.16
                                       BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHH.....CSSSEEEE CS
                      TPP_enzyme_C 107 dlkpvdfaklaealGakgarvekadveeleealkeal.....ekkgpali 151
                                        +++vd   l+ ++  + +rv++   + l  a+ ea       + gp+ i
  gi|474934965|ref|YP_007688547.1| 108 AFQEVDAYSLMMSITKHNFRVTDI--KRLPHAISEAWeiartGRPGPVHI 155
                                       367777777777775556675555..999999988865565555555555 PP

  == domain 2  score: 159.8 bits;  conditional E-value: 6.9e-51
                                       ESSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEE CS
                      TPP_enzyme_C   1 diGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnlpitv 77 
                                       d+G++++wa ++l++krpr++l+sg +gtmG+glpaAiGak+ +pd +v aivGDGg++m +qelat+v ++lp++v
  gi|474934965|ref|YP_007688547.1| 379 DVGQNQMWAMHFLDIKRPRQLLSSGSFGTMGFGLPAAIGAKAGRPDCKVAAIVGDGGLQMVIQELATSVAEKLPVVV 455
                                       89*************************************************************************** PP

                                       EEEE-SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                      TPP_enzyme_C  78 vvlnNegygmtggqqepfggkrksgpagkdlkpvdfaklaealGakgarvekadveeleealkealekkgpaliev 153
                                       v+lnN+++gm++++q+ f ++r+s+++   l+++df ++a+a+ a+g++v++a   ++++alkea++ ++++++++
  gi|474934965|ref|YP_007688547.1| 456 VLLNNGWLGMVKQWQKLFWDQRYSETE--LLDDPDFGMIAKAYHARGITVDRA--GDVHDALKEAFDCGETCIVDI 527
                                       ************************988..69999*******************..***********9999999986 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.6   0.1   8.6e-45   5.2e-41       3     136 ..     189     321 ..     187     322 .. 0.95
   2 ?   -0.9   0.0      0.21   1.3e+03      14      45 ..     427     458 ..     424     474 .. 0.79

  Alignments for each domain:
  == domain 1  score: 139.6 bits;  conditional E-value: 8.6e-45
                                       HHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEEESGGGSCHHHHHHHHH-S CS
                      TPP_enzyme_M   3 kaaellkaakrpvilvGggvarsgaseelrelaeklgiPvvttlmgkgvipedhplylgmlglhgskaanealeeaD 79 
                                       +a++l+++a++pvi++Gggv++++aseel++lae lg+Pvvt lmg g+ip+ hpl++g lg+hg   a ea+ +aD
  gi|474934965|ref|YP_007688547.1| 189 DAVALIRSAQKPVIFAGGGVISANASEELVRLAEMLGAPVVTPLMGIGSIPSAHPLCMGALGMHGRMCAMEAFSHAD 265
                                       699************************************************************************** PP

                                       EEEEES-SSSTCCCTTTTTTTTTT-.EEEEEESSCCCCTTCC--SEEEECTHHHHHHH CS
                      TPP_enzyme_M  80 lvlalGarfddirttgsepefapea.kiihididpaeigknyqvdlaivgdvketlea 136
                                       l++a+G++f+d rt++++ + + e+ ++++idid++++gk+ +  + i +d+k +l+a
  gi|474934965|ref|YP_007688547.1| 266 LIIAVGTKFSD-RTYSPH-TKPGETcRVVQIDIDATQLGKSGRDGVNIKADAKRALRA 321
                                       ***********.887644.5577778****************988***********98 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.21
                                       EEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEE CS
                      TPP_enzyme_M  14 pvilvGggvarsgaseelrelaeklgiPvvtt 45 
                                       ++ +vG g  +   +e ++++aekl + vv  
  gi|474934965|ref|YP_007688547.1| 427 VAAIVGDGGLQMVIQELATSVAEKLPVVVVLL 458
                                       66789999999999999999999998888755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (554 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 3536.79
//
Query:       gi|474934966|ref|YP_007688548.1|  [L=354]
Description: hypothetical protein TALC_01410 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00035   19.4   0.0     0.0024   16.7   0.0    1.9  1  Prismane  Prismane/CO dehydrogenase family


Domain annotation for each model (and alignments):
>> Prismane  Prismane/CO dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.3e-07    0.0024     202     334 ..     181     300 ..     121     308 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.3e-07
                                       -.SSSEEEEEESS-HHHHHHHHHHHCTTCCCCCCCGCCCCCCHHHHHHHHHCCEEEEECSSGGGHHHHHCCHECEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane 202 ldkdkvnIlvsGHdladleelleqtegkglnvythgemLpghcctalklkyrhlvgnvGnawqqekaeftgavdaiv 278
                                        +k++++++v+G dl dleell+q++  g+       m p+++ + +  + ++l+g v       +     ++ +++
  gi|474934966|ref|YP_007688548.1| 181 PKKEMPCLVVTGLDLPDLEELLKQASAAGIGICLSDGMAPAMAIPFFL-NHPNLAGYV-------ELDGGPLPAPVL 249
                                       35788******************************99********999.666666655.......67778899**** PP

                                       ESSSS--TTHHHHHHCHCCEEEEECTTB-TTSEEE--CTTCHHHHHHHHHHHHCCH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Prismane 279 vdtnCivpplasvaekyktrlittsevakpgakhieeeekadkdaseiiekAiela 334
                                       +    ++ p as     k+ ++tt++v +pg+ hi    +  k +++++ekA e+ 
  gi|474934966|ref|YP_007688548.1| 250 FVSDSVLRPEAS----DKDMIFTTGPVQFPGCVHIG-GCQRPKIFTPALEKAAECG 300
                                       *********555....69*****************8.56667***********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       243  (0.0135535); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 2356.33
//
Query:       gi|474934967|ref|YP_007688549.1|  [L=333]
Description: ketol-acid reductoisomerase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-70  235.6   0.4    2.7e-70  235.2   0.4    1.2  1  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
      4e-47  160.1   0.0    5.8e-47  159.6   0.0    1.2  1  IlvC            Acetohydroxy acid isomeroreductase, catalytic
    6.5e-08   33.1   0.0    1.5e-07   31.9   0.0    1.7  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
    7.8e-06   25.4   0.0    1.5e-05   24.4   0.0    1.4  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    0.00073   19.6   1.2     0.0011   19.1   0.2    1.7  2  AdoHcyase_NAD   S-adenosyl-L-homocysteine hydrolase, NAD bind
     0.0013   18.9   0.0     0.0036   17.5   0.0    1.7  2  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
     0.0082   16.1   0.1       0.96    9.4   0.1    2.6  2  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
  ------ inclusion threshold ------
      0.013   15.2   0.1      0.037   13.7   0.0    1.8  2  ApbA            Ketopantoate reductase PanE/ApbA
       0.17   10.9   0.0       0.28   10.1   0.0    1.3  1  PDH             Prephenate dehydrogenase


Domain annotation for each model (and alignments):
>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.2   0.4   1.4e-73   2.7e-70       1     165 []      15     180 ..      15     180 .. 0.99

  Alignments for each domain:
  == domain 1  score: 235.2 bits;  conditional E-value: 1.4e-73
                                       HHHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHT.T-EEEEHHHHHHT-SEEEE-S-HHHHHHH CS
                              IlvN   1 llkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkee.gfevltvaeavkkadvvmiliPDelqkev 76 
                                       +lkgkkiav+GyG+qG+aqal lrdsgldv+vg+r++++s++kAke+ g+ev+++++avkk dvvmil+PDe+q e+
  gi|474934967|ref|YP_007688549.1|  15 VLKGKKIAVLGYGAQGRAQALCLRDSGLDVIVGVRKDGESWNKAKEDgGMEVTDMTDAVKKGDVVMILLPDEIQPEI 91 
                                       59******************************************998469*************************** PP

                                       HHHHTGGG--TT-EEEESSSHHHHTTSS---TTSEEEEEEESS-SHHHHHHHHTT----EEEEEEE-SSS-HHHHHH CS
                              IlvN  77 yeeeiepnlkegkalafahGfnihfglikppkdvdvvlvAPkgpGhlvreeyeegkGvpaliaveqdasgkakelal 153
                                       y++ +++nlk+g+al fahGf i ++li+ppkdvdv+++APk+pG++ r+++ eg+Gvpaliav+qda+g+ak++al
  gi|474934967|ref|YP_007688549.1|  92 YDKYVKDNLKSGAALDFAHGFAITYKLIVPPKDVDVIMMAPKSPGDAERQQFLEGFGVPALIAVHQDATGNAKKIAL 168
                                       ***************************************************************************** PP

                                       HHHHHTTHHHH- CS
                              IlvN 154 ayakgiGatraG 165
                                       a+akg+Ga raG
  gi|474934967|ref|YP_007688549.1| 169 ALAKGLGALRAG 180
                                       ***********9 PP

>> IlvC  Acetohydroxy acid isomeroreductase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.6   0.0   2.9e-50   5.8e-47       1     143 [.     187     330 ..     187     331 .. 0.97

  Alignments for each domain:
  == domain 1  score: 159.6 bits;  conditional E-value: 2.9e-50
                                       HHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHTT--HHHHHHHHTHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHH CS
                              IlvC   1 FkeEtetDlfgEqavLcGgvselveagFetlveaGyspelAyfeclhelklivdliyegGiakmresiSdtaeygdl 77 
                                       F  Et++DlfgEq + cGg+s+l+e gF+tlv++G++p +Ayfec+he+kli+dl+ +gG+ +m++ +S+ta+yg+l
  gi|474934967|ref|YP_007688549.1| 187 FDLETKSDLFGEQSIECGGLSKLIEEGFQTLVDQGFPPIVAYFECCHECKLIIDLVVSGGMPYMWRVCSNTAKYGGL 263
                                       778************************************************************************** PP

                                       HHHHHHS-HHHHHHHHHHHHHHHTTHHHHHHHHHHHT.TSHHHHHHHHHHHTSHHHHHHHHHHHCHT CS
                              IlvC  78 tagprviteevkeemkeileeiqsGefakevieenka.grpelkklrkeeaeheiekvgkklralmp 143
                                       t+++ +i++++ e mk++++ i+sGef ke+ +e+++ + ++l++l+++e++  +e++gk++ral++
  gi|474934967|ref|YP_007688549.1| 264 TRRDLIINDQSVEGMKKVYQMIDSGEFKKEWRAEYEQnHLQKLHALMDAEDKMLLETTGKEVRALFQ 330
                                       **********************************8776899**********************9975 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   7.5e-11   1.5e-07       1      87 [.      20     101 ..      20     111 .. 0.90

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 7.5e-11
                                       EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHH CS
                     F420_oxidored   1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveev 77 
                                       ki+++G+G +g+a a+ l  +g    +++v+ +++ e+ ++++e+ g +vt     +a+++ dvv + ++ e  +e+
  gi|474934967|ref|YP_007688549.1|  20 KIAVLGYGAQGRAQALCLRDSG---LDVIVGVRKDGESWNKAKEDGGMEVTD--MTDAVKKGDVVMILLPDEIQPEI 91 
                                       7*********************...********************9988888..99**************9999999 PP

                                       HHHCGHHHHT CS
                     F420_oxidored  78 lselakdalk 87 
                                        ++  kd+lk
  gi|474934967|ref|YP_007688549.1|  92 YDKYVKDNLK 101
                                       8888666665 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   7.5e-09   1.5e-05      28     101 ..      10      85 ..       2     106 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 7.5e-09
                                       CGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH..CHHHHTCEECSHHHHHHH-SEEEE-S-- CS
                      2-Hacid_dh_C  28 allgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkee..eeeelgvelvsleellaesDivslhlpl 101
                                       + +   l+gk+++++G+G+ G+a a +l+  g++vi+  r+  ++   ++e+ g+e++++ +++++ D+v++ lp 
  gi|474934967|ref|YP_007688549.1|  10 DATFDVLKGKKIAVLGYGAQGRAQALCLRDSGLDVIVGVRKDGESWnkAKEDGGMEVTDMTDAVKKGDVVMILLPD 85 
                                       5556679****************************99888866444645566677******************994 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.2   5.4e-07    0.0011      17      83 ..      12      80 ..       7      87 .. 0.85
   2 ?   -2.6   0.0       2.5     5e+03      91     130 ..     269     308 ..     264     326 .. 0.57

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 5.4e-07
                                      H-S--TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE.-S-HHHHHHHHCT.T-EE--HHHCTTT-SEEE CS
                     AdoHcyase_NAD 17 tdvllaGkvavvaGyGdvGkGcaaslkglGarvivt.evdPicalqaame.Gfevvtleevvkkadivv 83
                                      t  +l Gk++ v GyG  G+  a +l+  G  viv    d  +  +a  + G+ev+ + ++vkk+d+v+
  gi|474934967|ref|YP_007688549.1| 12 TFDVLKGKKIAVLGYGAQGRAQALCLRDSGLDVIVGvRKDGESWNKAKEDgGMEVTDMTDAVKKGDVVM 80
                                      4456899***************************9724567677777776469*************986 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.5
                                       SB-HHHHCCS-TTEEEEE-SSTTTTBTHHHHHTTT-EEEE CS
                     AdoHcyase_NAD  91 iitlehlkkmkddaivcniGhfdseidvaaleanalkkee 130
                                       ii+ + ++ mk+   + + G f++e   +  +++ +k + 
  gi|474934967|ref|YP_007688549.1| 269 IINDQSVEGMKKVYQMIDSGEFKKEWRAEYEQNHLQKLHA 308
                                       5556667777777777777777777655554444444444 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.8e-06    0.0036       1      84 [.      20     104 ..      20     107 .. 0.86
   2 ?   -3.0   0.0       3.6   7.2e+03      37      65 ..     216     244 ..     211     247 .. 0.58

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.8e-06
                                       EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSH.HHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS. CS
                     NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtk.ekveelvaegakaaesieelvasldvvitmvkagkavdevieg. 75 
                                       ki+++G G  G+  al l ++g +v+v  r+  e+ +++ ++g   ++++ ++v++ dvv+++++++ +  e++++ 
  gi|474934967|ref|YP_007688549.1|  20 KIAVLGYGAQGRAQALCLRDSGLDVIVGVRKDgESWNKAKEDGGMEVTDMTDAVKKGDVVMILLPDEIQ-PEIYDKy 95 
                                       79***********************99887753888999999999********************9655.4555555 PP

                                       HCCC--TT- CS
                     NAD_binding_2  76 llealkkgd 84 
                                       ++++lk+g+
  gi|474934967|ref|YP_007688549.1|  96 VKDNLKSGA 104
                                       778887776 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.6
                                       HHHHTTEEE-SSHHHHHHHCSEEEE-SSS CS
                     NAD_binding_2  37 elvaegakaaesieelvasldvvitmvka 65 
                                       +lv++g+ ++    e++++++++i +v +
  gi|474934967|ref|YP_007688549.1| 216 TLVDQGFPPIVAYFECCHECKLIIDLVVS 244
                                       55666666666666666666666655543 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.1   0.00048      0.96       1      80 [.      20      86 ..      20     120 .. 0.64
   2 ?   -2.8   0.0       2.7   5.4e+03      55     103 ..     151     171 ..     139     180 .. 0.53

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00048
                                      -EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHSSBTTTBTT----TTEEEES-HHHHHTT--EEEE---H CS
                    NAD_Gly3P_dh_N  1 kiavlGaGswGtalAkvlaenghevrlwvreeelieeineehenvkyLpgiklpenlvattdlaealkgadiivlvvPs 79
                                      kiavlG G+ G a A  l + g +v + vr++   e+ n+++e+               +td+++a+k+ d++++ +P 
  gi|474934967|ref|YP_007688549.1| 20 KIAVLGYGAQGRAQALCLRDSGLDVIVGVRKDG--ESWNKAKEDGG-----------MEVTDMTDAVKKGDVVMILLPD 85
                                      799999999999999999999988887776652..33333333332...........2345555555555555555555 PP

                                      H CS
                    NAD_Gly3P_dh_N 80 q 80
                                      +
  gi|474934967|ref|YP_007688549.1| 86 E 86
                                      5 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.7
                                       TTEEEES-HHHHHTT--EEEE---HHHHHHHHHHHCCC--TT-EEEE-- CS
                    NAD_Gly3P_dh_N  55 enlvattdlaealkgadiivlvvPsqalrevlkklkgllkkkailvsli 103
                                       + + + +d +                             ++k+i++ l+
  gi|474934967|ref|YP_007688549.1| 151 ALIAVHQDATG----------------------------NAKKIALALA 171
                                       44444444433............................3444444555 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.9e-05     0.037       1      38 [.      21      57 ..      21      80 .. 0.87
   2 ?   -1.9   0.0       1.2   2.4e+03      67     112 ..     123     167 ..     101     179 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.9e-05
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCHHHHHHHH CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsrrlealkk 38
                                      ia+lG Ga+G+  a +L   g dv++ +r++  e+++k
  gi|474934967|ref|YP_007688549.1| 21 IAVLGYGAQGRAQALCLRDSGLDVIVGVRKD-GESWNK 57
                                      89***************99*********999.555555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.2
                                       S-ESEEEE-SSGGGHHHHHHHHGGGECTCEEEEEESSSSCHHHHHT CS
                              ApbA  67 epidlvivtvKayqteealeeikplldpntvvlllqNGlgheeelr 112
                                       +++d+++ + K+  ++e  + ++ +  p + + + q   g++++++
  gi|474934967|ref|YP_007688549.1| 123 KDVDVIMMAPKSPGDAERQQFLEGFGVP-ALIAVHQDATGNAKKIA 167
                                       5688999999988888854445444444.47777777777777766 PP

>> PDH  Prephenate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00014      0.28       2      65 ..      34      95 ..      33     107 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00014
                                      HHHHHHTT--SEEEEE-SSHHHHHHH.HHTTSSSEEES-GGGGCCGSEEEE-S-GGGHHHHHHHH CS
                               PDH  2 aralrrkgfkvtvigydideekaeaa.lelglvdeatddieavkeadivvlavPvevilevlkel 65
                                      a+ lr +g +v+v g+ +d e+ ++a ++ g   e+td  +avk++d+v++  P e   e+  + 
  gi|474934967|ref|YP_007688549.1| 34 ALCLRDSGLDVIV-GVRKDGESWNKAkEDGG--MEVTDMTDAVKKGDVVMILLPDEIQPEIYDKY 95
                                      78899***77765.66666666666604444..45555568***********9988776666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       731  (0.0407719); expected 358.6 (0.02)
Passed bias filter:                      619  (0.0345251); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2079.94
//
Query:       gi|474934968|ref|YP_007688550.1|  [L=129]
Description: hypothetical protein TALC_01412 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-20   73.5   0.0    1.4e-20   73.3   0.0    1.0  1  Cyclophil_like   Cyclophilin-like
      3e-06   27.2   0.0    5.7e-06   26.3   0.0    1.5  1  Cyclophil_like2  Cyclophilin-like family


Domain annotation for each model (and alignments):
>> Cyclophil_like  Cyclophilin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.3   0.0   1.6e-24   1.4e-20       4     116 ..       6     121 ..       3     124 .. 0.91

  Alignments for each domain:
  == domain 1  score: 73.3 bits;  conditional E-value: 1.6e-24
                                       EEEETTEEEEEEEETT.HHHHHHHHC-SEEEEEEECTTEEEEE-S-----SSSEESSB-TTEEEEECCCTEEEEESS CS
                    Cyclophil_like   4 kidiesseveveLddt.etaraikealPiesrvntWgeEiYfstpvklekeenakevveagdiaywppGkalclffG 79 
                                       ki+  ++e  +eLd++ ++a+a++ +lP+++++n+ g  iYf++p++ + e++ ++v e+gdi +wp  +al++ fG
  gi|474934968|ref|YP_007688550.1|   6 KIRTRNGEYDAELDEStDMANAVWLSLPFRADINMLGSSIYFEMPIDPKIEDEKTNVFEVGDICWWPGVNALVILFG 82 
                                       67888999*******999*********************************************************** PP

                                       --TT-..TTSB--SSSEEEEEEEEC-GGGGGG--TTEEE CS
                    Cyclophil_like  80 ktPis..ddeirpaspvnviGrivedlellkkvkdgekv 116
                                       + P+s  d+++        iGri++d +++    d +++
  gi|474934968|ref|YP_007688550.1|  83 PMPLSgeDGKPVTSHKMIRIGRIIGDCSSMEDAGDRQRI 121
                                       *****544556666788999********99998888777 PP

>> Cyclophil_like2  Cyclophilin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   6.4e-10   5.7e-06       3      95 ..       9     107 ..       7     124 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 6.4e-10
                   Cyclophil_like2   3 iggqtftatL.ednaaaralleklPltltmedyngnEkiaylpeklptddapegssikaGdlayyapwgnlvlfy.. 76 
                                         + +++a+L e ++ a+a +  lP+  +++ ++    ++++p   +++d+ +++  ++Gd++ +++ + lv+++  
  gi|474934968|ref|YP_007688550.1|   9 TRNGEYDAELdESTDMANAVWLSLPFRADINMLG-SSIYFEMPIDPKIEDE-KTNVFEVGDICWWPGVNALVILFgp 83 
                                       5678999***445689**************9999.89***********999.99********************933 PP

                   Cyclophil_like2  77 .....kdfeesysygltrlGriee 95 
                                            +d +  +s +++r+Gri +
  gi|474934968|ref|YP_007688550.1|  84 mplsgEDGKPVTSHKMIRIGRIIG 107
                                       333333555666889999999833 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 838.81
//
Query:       gi|474934969|ref|YP_007688551.1|  [L=362]
Description: Xaa-Pro aminopeptidase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-63  214.4   0.0      2e-63  213.9   0.0    1.3  1  Peptidase_M24  Metallopeptidase family M24
  ------ inclusion threshold ------
        0.1   12.7   0.0       0.19   11.8   0.0    1.4  1  HTH_20         Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.9   0.0   2.3e-67     2e-63       1     209 []     143     346 ..     143     346 .. 0.97

  Alignments for each domain:
  == domain 1  score: 213.9 bits;  conditional E-value: 2.3e-67
                                       HHHHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBCSSSB--TTEEE CS
                     Peptidase_M24   1 elirkaariasaaleavleaikpgvterelaaeieattlkrhgarglafppivasgenaavlhytpndrvlkegdlv 77 
                                       e+irka+ i+s++  ++ + + +gv+e e+aa +e  ++++ g++glaf++i+a+g+n++++hy+p d +lk+gd  
  gi|474934969|ref|YP_007688551.1| 143 EAIRKACSITSEVACEIPDYLSEGVSETEVAARME-IRMQELGGKGLAFDTIAAFGPNSSMPHYSPADYRLKKGDAA 218
                                       579********************************.669************************************** PP

                                       EEEEEEEETTEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSSCSE CS
                     Peptidase_M24  78 lidagaeydgyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffphglG 154
                                       l+d+g+++ gy+sD trTv++Gk+ +e +++ye+v++aq+a+i++ ++G+++++ d aar+v+   +++  f h+ G
  gi|474934969|ref|YP_007688551.1| 219 LFDFGCKWGGYCSDLTRTVFFGKPPEELERAYEVVRQAQQAGIDEYRAGAKAKDADLAARKVIDGSEFKGKFIHSFG 295
                                       ************************99**************************************889*9999***** PP

                                       EEESSSSSEEEEE.ESSSTTCSSB--TTBEEEEEEEEEEETTTEEEEEBEEEEEES CS
                     Peptidase_M24 155 HgvGlevhdegps.vsresndgrkleeGmvftiEpgiyfapgeggvriedtvlvte 209
                                       Hg+G++vh+  p+ vs  +++ ++l++G++++ Epgiy +pg+gg+riedtvl+te
  gi|474934969|ref|YP_007688551.1| 296 HGIGMDVHQ--PIhVS--PKSAQVLKAGNIVSAEPGIY-IPGVGGIRIEDTVLITE 346
                                       ********5..65488..789*****************.9***************7 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.2e-05      0.19       7      41 ..     151     183 ..     142     184 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.2e-05
                                       HS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHH CS
                            HTH_20   7 LahPvRrrilraLaraegltaselaerldlskntl 41 
                                       ++++v ++i ++L   eg++ +e+a+r+++++++l
  gi|474934969|ref|YP_007688551.1| 151 ITSEVACEIPDYL--SEGVSETEVAARMEIRMQEL 183
                                       678999*******..******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 2067.99
//
Query:       gi|474934970|ref|YP_007688552.1|  [L=219]
Description: hypothetical protein TALC_01414 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-30  107.1   0.6    1.9e-30  106.9   0.6    1.0  1  SIMPL     Protein of unknown function (DUF541)


Domain annotation for each model (and alignments):
>> SIMPL  Protein of unknown function (DUF541)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.9   0.6     1e-34   1.9e-30       1     200 []       5     215 ..       5     215 .. 0.89

  Alignments for each domain:
  == domain 1  score: 106.9 bits;  conditional E-value: 1e-34
                             SIMPL   1 ItVtGsaevevapDqatltlsvesegkdaaeakaevaekmnavlealkklgikekdiqtsslslkpeysy....... 70 
                                       I++tG+a v++++++ +++ ++e  +++ ++a ++++++++++ +++ klgi++++i+ts+ls+k +y++       
  gi|474934970|ref|YP_007688552.1|   5 IRITGNAVVNAPANTTVVRAEIEGLEETFEDAVESLTKATRHIKDSISKLGIQRDSIKTSQLSIKAHYRKvkkgvde 81 
                                       899***************************************************9********************99 PP

                             SIMPL  71 ...engknkitgyeasqsltvkfr.dldklgevldaavka.anein.gvsfslsdedelrdeareeAvkdArakAea 141
                                            +  k++gy +sq+++++f  d++kl ++++++ +  a  +  + sf  +d++ +++ea+ +A+++A++ Aea
  gi|474934970|ref|YP_007688552.1|  82 dkkPIYVDKFDGYAFSQNISFRFPnDNEKLTAAVKRIYDVrAS-VKvYFSFVNDDPERMYREALVRATEKAKTEAEA 157
                                       888888889999***********85555699999999885444.333455555577999****************** PP

                             SIMPL 142 lAkalgvklgkvvsisesgsnpyappapamaaaaaaaasaatpfepgeievtasVtvvf 200
                                       +++a+g+klg++v++  ++  +++ +++++++a++     ++++ p++ + + s+t ++
  gi|474934970|ref|YP_007688552.1| 158 IVSAAGSKLGRLVDVKKGSDYYDGDYCRKSYSAPM-VMGKPLDIDPEDDSASQSITLTW 215
                                       ****************9888888888888888877.77778888899999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       858  (0.0478554); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1349.86
//
Query:       gi|474934971|ref|YP_007688553.1|  [L=268]
Description: putative dinucleotide-utilizing enzyme [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.6e-33  113.0   0.5    1.2e-32  112.2   0.5    1.4  1  DUF108           Domain of unknown function DUF108
    4.8e-16   59.5   0.7    8.1e-16   58.7   0.7    1.4  1  NAD_binding_3    Homoserine dehydrogenase, NAD binding domain
    3.1e-05   24.1   1.0    5.4e-05   23.3   1.0    1.4  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
    3.9e-05   24.1   0.5      8e-05   23.1   0.5    1.6  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
    8.3e-05   22.7   1.0    0.00018   21.6   0.6    1.9  2  Ldh_1_N          lactate/malate dehydrogenase, NAD binding do
    0.00017   21.8   0.6    0.00037   20.8   0.6    1.6  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    0.00034   20.9   0.7    0.00087   19.5   0.7    1.9  1  TrkA_N           TrkA-N domain
     0.0009   18.0   0.6     0.0013   17.5   0.6    1.1  1  DUF2827          Protein of unknown function (DUF2827)
     0.0022   18.8   0.2     0.0054   17.6   0.2    1.6  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
     0.0052   15.8   1.1     0.0073   15.3   1.1    1.2  1  OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin famil
     0.0083   16.7   0.9      0.018   15.6   0.9    1.5  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
      0.045   13.0   1.7      0.066   12.4   1.7    1.3  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
      0.056   12.8   0.1      0.082   12.3   0.1    1.3  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
      0.067   13.4   0.4      0.096   12.9   0.4    1.3  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
      0.084   12.7   2.2       0.16   11.8   2.2    1.5  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
       0.12   12.7   0.7        1.4    9.3   0.4    2.4  2  Gp_dh_N          Glyceraldehyde 3-phosphate dehydrogenase, NA


Domain annotation for each model (and alignments):
>> DUF108  Domain of unknown function DUF108
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.2   0.5     1e-35   1.2e-32       1      88 [.     166     253 ..     166     254 .. 0.98

  Alignments for each domain:
  == domain 1  score: 112.2 bits;  conditional E-value: 1e-35
                                       .SS-EEEEEEEHHHHHHHSTTS-CHHHHHHHHHH.CCGEEEEEEEETT-SSEEEEEEEEETTEEEEEEEEE-EETTE CS
                            DUF108   1 lteptvlFeGsareaikkfPknvNvaaalaLaalgfdrvkvelvadpnldkniheieveGsfgefslevenkpspen 77 
                                       +tept++++G+area+k+fPknvNvaa+++L ++gfd+++v++v dp++++n he++ +G+fg++  ++ n p+p+n
  gi|474934971|ref|YP_007688553.1| 166 ITEPTTVYSGPAREAVKLFPKNVNVAATVSLSGIGFDKTQVTIVLDPAATSNSHELRYSGNFGHAVSHTYNLPEPDN 242
                                       689************************************************************************** PP

                                       EEEEHHHHHHH CS
                            DUF108  78 Pktsalaalsv 88 
                                       Pktsala+ls+
  gi|474934971|ref|YP_007688553.1| 243 PKTSALAVLSA 253
                                       *********97 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.7   0.7   7.2e-19   8.1e-16       1     117 []       7     118 ..       7     118 .. 0.90

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 7.2e-19
                                       --SHHHHHHHHHHHH---SSEEEEEEEEESSEEE-TTHHHHHT--CB---HHHHHHHHS-EEEEE-S--HHHHTTHH CS
                     NAD_binding_3   1 GlGaiGsavleqlkrqqseielelvavadrdsllskdrkallasealtldlddliahldpdvvVEcasseavaelvl 77 
                                       G+G iGs+++++ +++ +    ++++v  r+ +++++ +a l+++ ++++++d +     d+v+E+as++ ++e+v+
  gi|474934971|ref|YP_007688553.1|   7 GCGSIGSRLAAAADQMDEVK--RIYLVDIRK-EVADKVAAGLNKAIVVDSVEDELY--HTDLVIEAASQATAKEVVP 78 
                                       9**********999998753..344443344.779999**************9777..9****************** PP

                                       HHHHTTEEEE-S--CGGG-HHHHHHHTSSSTTS--.EE-G CS
                     NAD_binding_3  78 kaLkagkdvvtankgaladealyeeLreaaeangakiyve 117
                                       k++++g+d++++++g ++d++ +e+ +e+a++++ak++++
  gi|474934971|ref|YP_007688553.1|  79 KVVSRGVDMMVMSVGSFVDDDFREMVFEKAKEHEAKVFFP 118
                                       *************************************997 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   1.0   4.8e-08   5.4e-05       1     100 [.       1      93 [.       1     118 [. 0.85

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 4.8e-08
                                       EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH-SEEEE-S-H CS
                            DapB_N   1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavtddleevlekadvliDFTtp 77 
                                       +++++vG+ G +G++++ a+++ ++++    vd ++      ++ + +  g ++  v d++e+ l ++d +i+  + 
  gi|474934971|ref|YP_007688553.1|   1 MRITIVGC-GSIGSRLAAAADQMDEVKRIYLVDIRK------EVADKVAAGLNKAIVVDSVEDELYHTDLVIEAASQ 70 
                                       89******.*************************98......4444455556778899******************* PP

                                       HHHHHHHHHHHHTT-EEEE--SS CS
                            DapB_N  78 eavlenlklalekgvklViGTTG 100
                                       + ++e++  ++++gv++ + + G
  gi|474934971|ref|YP_007688553.1|  71 ATAKEVVPKVVSRGVDMMVMSVG 93 
                                       ***************99875555 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.5   7.2e-08     8e-05       1      94 [.       2      88 ..       2     115 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 7.2e-08
                                      EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SCHHHH CS
                    Semialdhyde_dh  1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeelkevdivflalpagvs 79
                                      ++ ivG  G +G++l+   ++  ev+ ++l+  +++   k+a+  +      +  v d  e+el + d+v+ a+++ ++
  gi|474934971|ref|YP_007688553.1|  2 RITIVG-CGSIGSRLAAAADQMDEVKRIYLVDIRKEVADKVAAGLN------KAIVVDSVEDELYHTDLVIEAASQATA 73
                                      688***.9************************99977777766644......4555555889999************** PP

                                      HHHHHHHHHTTSEEE CS
                    Semialdhyde_dh 80 kelapklaeagvkvi 94
                                      ke++pk++++gv + 
  gi|474934971|ref|YP_007688553.1| 74 KEVVPKVVSRGVDMM 88
                                      ***********9543 PP

>> Ldh_1_N  lactate/malate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.6   1.6e-07   0.00018       1      61 [.       1      60 [.       1      94 [. 0.90
   2 ?   -3.4   0.0       8.5   9.6e+03      90     101 ..     183     194 ..     175     220 .. 0.63

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.6e-07
                                      EEEEEETTTSHHHHHHHHHHHHTTSSSEEEEE-SSHHHHHHHHHHHHHCHCCSTS-EEEEE CS
                           Ldh_1_N  1 vkvavvGaaGgiGqslalllankkladelaLlDiakekleGvaldlshistflsvkvkvse 61
                                      +++++vG  G iG+ la +  + + ++++ L+Di+ke+++ va+ l+ + +  sv+ + ++
  gi|474934971|ref|YP_007688553.1|  1 MRITIVGC-GSIGSRLAAAADQMDEVKRIYLVDIRKEVADKVAAGLNKAIVVDSVEDELYH 60
                                      69******.**************99999*******************99999888877666 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 8.5
                                       HHHHHHHHHHHH CS
                           Ldh_1_N  90 LlkvNakIvkei 101
                                       L+ +N+++ +++
  gi|474934971|ref|YP_007688553.1| 183 LFPKNVNVAATV 194
                                       556666555443 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.6   3.3e-07   0.00037       1     101 [.       3      92 ..       3     117 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.3e-07
                                       EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-S CS
                   Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnls 77 
                                       + i+G+Gs+G+ +a    + ++v+ +i ++d  ke ++++aa +      ++a+ ++ +e+     l ++dlv+ ++
  gi|474934971|ref|YP_007688553.1|   3 ITIVGCGSIGSRLAAAADQMDEVK-RIYLVDIRKEVADKVAAGL------NKAIVVDSVED----ELYHTDLVIEAA 68 
                                       679********************6.***************9643......45566666666....456679999999 PP

                                       SGGGHHHHHHHHHHHT-EEEESS- CS
                   Sacchrp_dh_NADP  78 ppissldvlkaCietgvhyvdtsi 101
                                        +  + +v+   +++gv+++  s+
  gi|474934971|ref|YP_007688553.1|  69 SQATAKEVVPKVVSRGVDMMVMSV 92 
                                       999999999999999999887666 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.7   7.7e-07   0.00087       1      54 [.       3      58 ..       3     113 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 7.7e-07
                                      EEEES-SHHHHHHHHHHHH.TT.EEEEEEESSHHHHHHHHHTTSEEEES-TTSHHH CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLse.gg.kdvvvidkdeerveelreeglevvvgdatdeev 54
                                      i i+G+G +G++la    + ++ k+++++d ++e+++++++   +++v d  ++e+
  gi|474934971|ref|YP_007688553.1|  3 ITIVGCGSIGSRLAAAADQmDEvKRIYLVDIRKEVADKVAAGLNKAIVVDSVEDEL 58
                                      67*****************777988**************98888899999887765 PP

>> DUF2827  Protein of unknown function (DUF2827)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.6   1.1e-06    0.0013      27     122 ..      16     111 ..      13     118 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.1e-06
                           DUF2827  27 aelLkqsplveevvlvnggdakklpealelelld.vplvsleeakkelDvlIelgaql.daewlrevrarGakivsy 101
                                       a +  q++ v++++lv+   +k++++++ + l + + + s+e+   ++D++Ie + q   +e + +v +rG+ ++++
  gi|474934971|ref|YP_007688553.1|  16 AAAADQMDEVKRIYLVDI--RKEVADKVAAGLNKaIVVDSVEDELYHTDLVIEAASQAtAKEVVPKVVSRGVDMMVM 90 
                                       56667999*********4..44444555444444044667889999*******998861568899************ PP

                           DUF2827 102 rvgndyvedveailfekpsgk 122
                                        vg+    d  +++fek++++
  gi|474934971|ref|YP_007688553.1|  91 SVGSFVDDDFREMVFEKAKEH 111
                                       *****************9865 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.2   4.8e-06    0.0054       1      89 [.       1      87 [.       1      90 [. 0.82

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.8e-06
                                      EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHE.EESSHHHHHTCTTESEEEE-S-GGGHHHH CS
                      GFO_IDH_MocA  1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgve.aysdleelladpeidavivatpngtheel 78
                                      +r+ i+G+G igs+ +++  +  ++ + + l+d+++e a++va+ ++ + +++++e+ l   + d+vi a    t +e+
  gi|474934971|ref|YP_007688553.1|  1 MRITIVGCGSIGSRLAAAADQM-DEVKRIYLVDIRKEVADKVAAGLNKAiVVDSVEDELY--HTDLVIEAASQATAKEV 76
                                      6899***********9555555.9999999************888887778888998888..66888888888888888 PP

                                      HHHHHHTT-EE CS
                      GFO_IDH_MocA 79 akaaleagkhv 89
                                      + +++ +g++ 
  gi|474934971|ref|YP_007688553.1| 77 VPKVVSRGVDM 87
                                      88888888765 PP

>> OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   1.1   6.5e-06    0.0073     132     239 ..       3     107 ..       1     114 [. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.5e-06
                                       EEEE--SHHHHHHHHHHCCCS--SEEEEE-SSHHHHHHHHHHCCS.CTT-EEECSCHHHHTTSSEEEE--.--SS-S CS
                   OCD_Mu_crystall 132 laiiGaGvqaetqlealkavldikevriydrdeeaaekfaenlqefefevsackseeeavegadivvtvT.aakapi 207
                                       ++i+G+G      + a  ++ ++k++ + d+++e a+k+a  l++      +++s+e++    d v+ +   a+a  
  gi|474934971|ref|YP_007688553.1|   3 ITIVGCGSIGSRLAAAADQMDEVKRIYLVDIRKEVADKVAAGLNK----AIVVDSVEDELYHTDLVIEAAsQATAKE 75 
                                       79*******9999999999999**********************7....55789**********9996551556688 PP

                                       B-GGGS-TT-EEEE-S--STT--SB-HHHHHC CS
                   OCD_Mu_crystall 208 lkaewvkpGahinavgadapgkteLdddilkr 239
                                       ++ + v+ G+ ++ +  + + + +  + +  +
  gi|474934971|ref|YP_007688553.1|  76 VVPKVVSRGVDMMVMSVGSFVDDDFREMVFEK 107
                                       99999999999999888877776666666555 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.9   1.6e-05     0.018       1      81 [.       2      80 ..       2      93 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.6e-05
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHH CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevls 79
                                      +i i+G+G++g+ la  + + + + + i+++ +  +e a++ a+ l+  +   + e+ + ++d v+ a   + ++ev+ 
  gi|474934971|ref|YP_007688553.1|  2 RITIVGCGSIGSRLAAAADQMD-EVKRIYLV-DIRKEVADKVAAGLNKAIVVDSVEDELYHTDLVIEAASQATAKEVVP 78
                                      699*************877777.99****88.999999*********999999**************999999999998 PP

                                      HC CS
                     F420_oxidored 80 el 81
                                      ++
  gi|474934971|ref|YP_007688553.1| 79 KV 80
                                      77 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.7   5.9e-05     0.066     144     245 ..       2     102 ..       1     115 [. 0.70

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.9e-05
                                       EEEEES-SHHHHHHHHHHHHH..T-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCE..EEEEEETTEEE CS
                                       xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxx RF
                       Pyr_redox_2 144 rivvvGgGyiGvElAaalakl..gkevtlveardrllraldkelsaaleealekeGvevklgts..vkeidgngekl 216
                                       ri++vG G iG+ lAaa+ ++   k+++lv+ r+++     ++++a l++a+  + ve  l ++  v e+ ++ +  
  gi|474934971|ref|YP_007688553.1|   2 RITIVGCGSIGSRLAAAADQMdeVKRIYLVDIRKEVA----DKVAAGLNKAIVVDSVEDELYHTdlVIEAASQATAK 74 
                                       799**************98885233699999999999....667777777777777764443330033444444333 PP

                                       EEEETTSCEEEESEEEE-S-EEES-HHCS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 217 evvledgeeidadlvvvavGvrpstelle 245
                                       evv +  ++  +d++v++vG   +++++e
  gi|474934971|ref|YP_007688553.1|  75 EVVPKVVSR-GVDMMVMSVGSFVDDDFRE 102
                                       466666665.9999999999988888764 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   7.3e-05     0.082      38      94 ..       2      63 ..       1      75 [. 0.67

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.3e-05
                                      EEEEES-SHHHHHHHHHHHHTT-..EEEEESSSHHHHH...CHHHHTCEECSHHHHHHH-SE CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgm..kviaydrskkkee...eeeelgvelvsleellaesDi 94
                                      ++ i+G+G+IG+++a  + +++   +++ +d +k+  +   +  ++ + ++s+e+ l ++D 
  gi|474934971|ref|YP_007688553.1|  2 RITIVGCGSIGSRLAAAADQMDEvkRIYLVDIRKEVADkvaAGLNKAIVVDSVEDELYHTDL 63
                                      689****************9996656777777766555322111222234455555555555 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.4   8.5e-05     0.096       2      97 ..       3     100 ..       2     132 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.5e-05
                                       EEEE--SHHHHHHHHHH..HHTT-EEEEE-SSHHHHHHHHHTT..EEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHH CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnl..lkagykvavynrtkekveelvaeg..akaaesieelvasldvvitmvkagkavdevie 74 
                                       i ++G G +Gs +a     +++  ++++++ +ke +++++a    a +++s+e+ + + d+vi   ++ +  +ev+ 
  gi|474934971|ref|YP_007688553.1|   3 ITIVGCGSIGSRLAAAAdqMDEVKRIYLVDIRKEVADKVAAGLnkAIVVDSVEDELYHTDLVIEAASQ-ATAKEVVP 78 
                                       899***********99965788899*********99999987456999*****999999999876544.56677777 PP

                                       SHCCC--TT-EEEE-S---HHHH CS
                     NAD_binding_2  75 gllealkkgdilidgstsspedt 97 
                                       +++++   + +++ +++   +d 
  gi|474934971|ref|YP_007688553.1|  79 KVVSRG-VDMMVMSVGSFVDDDF 100
                                       765543.3444444444444444 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   2.2   0.00015      0.16       2      81 ..       3      87 ..       2     113 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                                      EEEE--SCCHHHHHHHHHHT..T-EEEEE-S-HHHHHHHHHHHHH.HHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasa..gleVvlvdiseealekalekiek.sleklvekgklkeeeveaalarisfttdleeav 77
                                      ++++G+G +G+ +aa++ +     ++ lvdi++e ++k+++ ++k  +   ve++ ++++ v +a+++ ++++ + ++v
  gi|474934971|ref|YP_007688553.1|  3 ITIVGCGSIGSRLAAAADQMdeVKRIYLVDIRKEVADKVAAGLNKaIVVDSVEDELYHTDLVIEAASQATAKEVVPKVV 81
                                      89************999776425689***************99995566777777777777777777777666666665 PP

                                      ..C-SE CS
                           3HCDH_N 78 ..dadl 81
                                        ++d+
  gi|474934971|ref|YP_007688553.1| 82 srGVDM 87
                                      555555 PP

>> Gp_dh_N  Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.4    0.0012       1.4       1      52 [.       1      58 [.       1      98 [. 0.61
   2 ?    1.1   0.0      0.43   4.9e+02      65      95 ..     183     213 ..     131     219 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0012
                                      CEEEEESTSHHHHHHHHHHH...HHTTCEEEEEE-.TS-..HHHHHHHHHEETTTEC- CS
                           Gp_dh_N  1 vkvainGfGRIGrlvlrall...eekelevvaind.ltd..letlayllkyDsvhgrf 52
                                      +++ i G G IG  ++ a+    e k++ +v i++ ++d  ++ l + +  Dsv  ++
  gi|474934971|ref|YP_007688553.1|  1 MRITIVGCGSIGSRLAAAADqmdEVKRIYLVDIRKeVADkvAAGLNKAIVVDSVEDEL 58
                                      79**********9999888845455567777777754431133344555555554443 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.43
                                       ETTEEEEEE--SSGGGS-CHHHTSSEEEE-S CS
                           Gp_dh_N  65 vngkkikvlaekdpeelpwkelgvdlVvest 95 
                                       +  k+++v a+ + + + +++++v +V++  
  gi|474934971|ref|YP_007688553.1| 183 LFPKNVNVAATVSLSGIGFDKTQVTIVLDPA 213
                                       455789999999999999********99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       697  (0.0388756); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 1737.52
//
Query:       gi|474934972|ref|YP_007688554.1|  [L=135]
Description: hypothetical protein TALC_01416 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-35  122.3   0.0    1.8e-35  122.2   0.0    1.0  1  Archease  Archease protein family (MTH1598/TM1083)
  ------ inclusion threshold ------
      0.097   12.9   0.0       0.17   12.1   0.0    1.4  1  DUF779    Protein of unknown function (DUF779)


Domain annotation for each model (and alignments):
>> Archease  Archease protein family (MTH1598/TM1083)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.2   0.0     2e-39   1.8e-35       1     138 []       4     135 .]       4     135 .] 0.97

  Alignments for each domain:
  == domain 1  score: 122.2 bits;  conditional E-value: 2e-39
                                       EEE---SSEEEEEEE-SSSHHHHHHHHHHHHHHHS--TT---S-EEEEEEEESSSHHHHHHHHHHHHHHHHHT--S- CS
                          Archease   1 yeyldhtADviieawGksleeafesaalalfeymtdlskvepkeekeieveaedledlLfdfLdellylfdteyfvf 77 
                                       ye+l+htAD+ i+++G++lee++ ++a ++f+ ++dls+v+p e++++eve+ed ed L++fL+ell+  + e++++
  gi|474934972|ref|YP_007688554.1|   4 YEVLEHTADLLIRGKGSTLEECYGNLAYGMFDQTVDLSSVRPLERRHVEVEGEDAEDALYSFLSELLFIENYEDLIL 80 
                                       9**************************************************************************** PP

                                       ---EEEE.E-SSSEEEEEEEE----.-TT--------B--S---EEEEETTEEEEEEEEE- CS
                          Archease  78 kevkvdeeeeeeeleleaeargekfdkekhevqtevKAvTyhelrieeeddgweayvvvDi 138
                                       +++    +++ ++ ++ + + ge++d+++ +++ e+KAvT+h++ i+      +++v++D+
  gi|474934972|ref|YP_007688554.1|  81 CQF----SVSIDGNRIVCDCAGERLDRSRMHIRGEIKAVTFHMMDINAAV--PQVTVLFDV 135
                                       ***....5677899********************************9876..889999998 PP

>> DUF779  Protein of unknown function (DUF779)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.9e-05      0.17       7      64 ..      73     130 ..      66     135 .] 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.9e-05
                            DUF779   7 akhgplmfhqsggccdgssPmcypageflvgdadvllgeiegvpfyiskeqfeywkht 64 
                                       +++ +l+++q     dg   +c  age l +++ ++ gei++v+f++++ ++++ + t
  gi|474934972|ref|YP_007688554.1|  73 ENYEDLILCQFSVSIDGNRIVCDCAGERLDRSRMHIRGEIKAVTFHMMDINAAVPQVT 130
                                       7899*******************************************98877766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 926.43
//
Query:       gi|474934973|ref|YP_007688555.1|  [L=345]
Description: Uroporphyrinogen-III decarboxylase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-50  171.6   0.0    2.8e-50  171.4   0.0    1.0  1  URO-D         Uroporphyrinogen decarboxylase (URO-D)
     0.0093   15.3   0.0      0.015   14.7   0.0    1.2  1  APO_RNA-bind  APO RNA-binding


Domain annotation for each model (and alignments):
>> URO-D  Uroporphyrinogen decarboxylase (URO-D)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.4   0.0   3.2e-54   2.8e-50       1     345 [.       2     342 ..       2     343 .. 0.95

  Alignments for each domain:
  == domain 1  score: 171.4 bits;  conditional E-value: 3.2e-54
                                       ----HHHHHHTT---SS--B--TT-SSTTSHHHHHHHTSSSHHHHHH-HHHHHHHHHHHHHHH--S-EE-S--TTGG CS
                             URO-D   1 tknerllralrgekvdrvPvwlmRqaGrylpeyraeragvsflelcknpelaaevtlqpvrrfglDaailfsdilve 77 
                                       t++er l+++ ge +dr Pv+       +       ++g++++e+  n +l   +     +  g D+++ ++    +
  gi|474934973|ref|YP_007688555.1|   2 TSRERGLAVFHGEIPDRAPVCD------FGNAAMLGYTGHTMKECRGNTALTDSIMKEWAKATGADIFFGPMETKGI 72 
                                       6899*****************9......7888888999*********************************999777 PP

                                       GGGG.T-EEEEETTTEEEEE--S-.....GGGS----GGG.....G..HHHHHHHHHHHHH.--SS-EEEEEE-HHH CS
                             URO-D  78 aeal.GlevefeegegPvvekpvr.taedveklevpddvee....grlpyvleaikllkkelggevpligfvgaPft 148
                                       +  l  l+++++++++ ++++  + ++edve  + +d+++     +  +yvl+  k  +++l+ +v   + + + +t
  gi|474934973|ref|YP_007688555.1|  73 FMDLpDLQIKLPDDDQGSLQNTYFsSPEDVESKPLYDPFNPeespNFRKYVLDVFKSERAALP-DVMTPAWCEGVLT 148
                                       7666478******999999999999******988888886566766789*************6.9************ PP

                                       HHHHHHCTT-SS-HHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHH.HTT-SEEEEEE..TTGGGS-HHHHHHHTHH CS
                             URO-D 149 lasylveGgskgfekllkllykdpeevhklldkltdvvieylkaqi.eagAdaiqifD..swagllspedfeefvlp 222
                                       +   l      g++ l+ +l+++p+e++k++++ +d++ + ++aq+ e  Ad +++ D  s+a++++  +f+ef l 
  gi|474934973|ref|YP_007688555.1| 149 TSGFLR-----GIDTLILMLLTEPDEAKKVIRRGADFSRDIVSAQLeEVDADYVVYTDpvSSADMIDDVMFREFNLD 220
                                       ******.....***********************************8899*************************** PP

                                       HHHHHHHHHHH.H--S-EEEEESSHH.HHHHHHTTS--SEEE--TTS-HHHHHHSS....EEE--B-G.GGGG.S-H CS
                             URO-D 223 ylkrivdevkaegpkvpvilfikgagaeiledlaelgadvlsldwtvdlkeaarevgdkvalqGnldPialLl.gsp 298
                                        l r +++ k ++ +v  +l+i+g+++++l+d+a++ga+v+sld++v+lk a++++g k a++GnldP++l+l gs 
  gi|474934973|ref|YP_007688555.1| 221 LLHRNITHWKNKY-GVGTMLHICGDTTPMLKDFAKTGAEVMSLDHKVNLKTAKADFGGKLAVMGNLDPVSLILnGSA 296
                                       ***********98.6**********************************99999***************9999**** PP

                                       HHHHHHHHHHHT.T---SSSEEB-BSS---TTS-HHHHHHHHHHHHT CS
                             URO-D 299 eeiekevkeilekgaggkkgyilnlGhgippetppenvkalveavke 345
                                       +++ ++++++ e +ag+ +gyi+  G+  p  tp++n++a+ve+ k+
  gi|474934973|ref|YP_007688555.1| 297 ADVAAAAEKCFE-DAGKDGGYIFGAGCAEPKATPIANIQAMVEVSKK 342
                                       ************.5999**************************9887 PP

>> APO_RNA-bind  APO RNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.7e-06     0.015      97     139 ..      22      64 ..      14      78 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.7e-06
                      APO_RNA-bind  97 ckecsevhvgkvGheikdckGpssskrkglheWvkgsiedvlv 139
                                       c   +   +g +Gh++k+c+G+++ + + + eW+k++  d++ 
  gi|474934973|ref|YP_007688555.1|  22 CDFGNAAMLGYTGHTMKECRGNTALTDSIMKEWAKATGADIFF 64 
                                       777888899***************************9999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 2491.06
//
Query:       gi|474934974|ref|YP_007688556.1|  [L=272]
Description: Folate-dependent phosphoribosylglycinamide formyltransferase PurN [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-10   41.4   0.0    2.2e-10   40.6   0.0    1.3  1  Formyl_trans_N  Formyl transferase
    0.00085   19.2   0.9     0.0053   16.6   0.1    2.3  2  DUF1086         Domain of Unknown Function (DUF1086)


Domain annotation for each model (and alignments):
>> Formyl_trans_N  Formyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.0   2.4e-14   2.2e-10      10     157 ..      15     183 ..      12     205 .. 0.82

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 2.4e-14
                                       SSHHHHHHHHHHHHTTSECEEEEEEESCTTEHCHH.HHHHCCHCCCECHHCC......................SCC CS
                    Formyl_trans_N  10 tgsnlqalldalkkgsleadvvlvvsnkdkaagle.kaeaasiptkvfeekk......................lep 63 
                                       + + l+a++d+ +kg+l+ ++ +v++n d+ +  + ++e+ +  + ++++++                      +  
  gi|474934974|ref|YP_007688556.1|  15 SRNLLKAVMDEKEKGNLDIEIPFVFCNWDNTEVPNsRKEQRQMFFDMVARYGipletasfkkfmpelrekdkeaWG- 90 
                                       55678999*********************99987615555555555566666999999999999999877643222. PP

                                       CCCCCHHHHHHHHCTT-SEEEEES--S---HHHHHSSTTSEEEEESSSTTTTBS..S-HHHHHHHTTSSEEEEEEEE CS
                    Formyl_trans_N  64 rsqfeeelaeelkelkadlivlagymkllpkelvqavrlkilniHpSLLPrfkG..aaaiqraleaGdketGvtihf 138
                                        +++ + l e+ ++++++l +lagym+ + +e  + +    ln+Hp+L+   kG   ++i + + + ++e+Gv+ h 
  gi|474934974|ref|YP_007688556.1|  91 -NAYGKVLREKTQKYRPELGILAGYMLWMDDETCEVYDM--LNLHPALPWGPKGtwQEVIWQLISENAEEQGVMMHI 164
                                       .45777889999************************998..********8888866799999*************** PP

                                       --SSSSTS-EEEEEEEE-- CS
                    Formyl_trans_N 139 vdeelDtGailaqkkveii 157
                                        + e D G+ l     +i 
  gi|474934974|ref|YP_007688556.1| 165 CTKEHDRGDALTYCGFPIR 183
                                       *********9987666665 PP

>> DUF1086  Domain of Unknown Function (DUF1086)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   5.9e-07    0.0053      12      76 ..      26      93 ..      17     101 .. 0.82
   2 ?   -0.1   0.0     0.084   7.5e+02      55      75 ..     188     208 ..     175     226 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.9e-07
                           DUF1086 12 karsdkdeplPllegegkslevLGFnerqRkaflnalmRyGv..gdfdskelvrelkqktedei.kaY 76
                                      k++ + d ++P++  +  + ev    ++qR++f  ++ RyG+  +  + k+++ el++k ++   +aY
  gi|474934974|ref|YP_007688556.1| 26 KEKGNLDIEIPFVFCNWDNTEVPNSRKEQRQMFFDMVARYGIplETASFKKFMPELREKDKEAWgNAY 93
                                      455566677888888888899999999***************999999**********9887653455 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.084
                           DUF1086  55 dfdskelvrelkqktedeika 75 
                                       d  ++ + ++lk+kt d+ik+
  gi|474934974|ref|YP_007688556.1| 188 DALWERMNEKLKTKTLDQIKE 208
                                       444778889999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1789.31
//
Query:       gi|474934975|ref|YP_007688557.1|  [L=379]
Description: archaeal conserved hypothetical protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.027   14.3   0.0    1.7  1  NIF       NLI interacting factor-like phosphatase


Domain annotation for each model (and alignments):
>> NIF  NLI interacting factor-like phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.5e-06     0.027      36     101 ..     102     167 ..      81     201 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.5e-06
                               NIF  36 RpgldefLkelsklyevvifTasseeyaeavidildpekkllshr.lyrescvkkkgeyvKdLsllg 101
                                        pg+++ +++l  l+ ++i T  +++ a++++d+ld + +l ++  l  +++   ++++ +dL+++ 
  gi|474934975|ref|YP_007688557.1| 102 NPGAEDCIRYLKALMPMYIDTVMYQHAADDICDKLDLNDCLAGASsLDLDHS-EMTKKEARDLRKMA 167
                                       49*************************************9877767777887.34778899999864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 2155.07
//
Query:       gi|474934976|ref|YP_007688558.1|  [L=649]
Description: Amino acid transporter [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.6e-44  150.9  39.3    4.6e-44  150.9  39.3    2.2  2  AA_permease_2  Amino acid permease
    2.4e-17   62.7  37.7    2.4e-17   62.7  37.7    1.7  2  AA_permease    Amino acid permease


Domain annotation for each model (and alignments):
>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.9  39.3   5.1e-48   4.6e-44       2     403 ..      21     450 ..      20     473 .. 0.80
   2 ?   -8.1  13.5         2   1.8e+04      82     182 ..     510     605 ..     453     639 .. 0.57

  Alignments for each domain:
  == domain 1  score: 150.9 bits;  conditional E-value: 5.1e-48
                     AA_permease_2   2 sllsafalvigsvig.sgifvknlaasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaaf..... 72 
                                       ++ + +++++g++i  ++++   +++ + +++i+ ++++vl g + + + + E+++  +   Gi +  ++++     
  gi|474934976|ref|YP_007688558.1|  21 DWKQGLIIAMGIPILiVPSLCDLSVTLWSMSIII-WVLSVLSG-FLLNIPLGEMCA-TFGVAGIGGSIQYVYkdder 94 
                                       5666666666666553444444377777776665.66778888.5799999***66.59999999999999888888 PP

                     AA_permease_2  73 ........gkkvaflsawfnwfayvpvlasilsvaasyllnalgp..dlqgntwltyliaiaililvalinirgike 139
                                               g+ +++l aw+++  +vpv+++ +++ + y+   +    d++++t +++++++ai+ ++++   +g  +
  gi|474934976|ref|YP_007688558.1|  95 yagkkinrGRMIGSLGAWAYFATWVPVIPIFTIMTGVYINDYFELgiDGFNSTLFYLVLGAAIYGFIIVSGRKGLEG 171
                                       8888888899999**************************88764345999*************************** PP

                     AA_permease_2 140 sakiqnilgilkillpliiliilglitvdgggfssl...stetdt.........ffpngwpg.v.llgllivlwsfd 202
                                       +akiq il+ ++i +p++++ +++li +d++ +        +++t         ++ ng+++ + l+ +++++ws +
  gi|474934976|ref|YP_007688558.1| 172 GAKIQLILAAITI-VPILVICVVPLINGDFSLSAITdelIPKHHTfgdgavseaWVWNGNSLlMiLGCFTVAQWSAV 247
                                       *************.7***************87765577744444444454444433344443433666888****** PP

                     AA_permease_2 203 Gfesaanvseevkk..kdvpkaifigllivlvlyllvniaflgvvpddeianlsnlgsvaalffeavggkvvaiivv 277
                                       G+esaa +  e k+  +dvpka++ ++l++l++y+++++ ++g++++d+i + +    ++ +  e  +g+++ +++v
  gi|474934976|ref|YP_007688558.1| 248 GWESAATYGAEYKEpnRDVPKALIACGLLCLFMYFVIAFCMYGALGIDGIYEAGA-A-TLIPISESDFGDIGGAVAV 322
                                       ***********66444**********************************76444.3.34455555566******** PP

                     AA_permease_2 278 ilialsllgaintavigssrvlealardgvlPrffakvnkfgspiraiiltaivslillllfllassaaynfllsvs 354
                                       +l++ +++ +i ta+++++r+++ +a+dg +P +f+ +n++g pi+a+++ a + ++++l+ ++      + +l+vs
  gi|474934976|ref|YP_007688558.1| 323 FLLIAGMVMIIQTAFLATARTIQVMAKDGNFPFVFSLTNEYGVPIYAMFFEAFIGFVVILAGIT-----ASQILAVS 394
                                       *******************************************************665543333.....489***** PP

                     AA_permease_2 355 slgliisyllliigalilrkkrphl..kr.....pgkilvaiigalfllfllvalf 403
                                       +lg+ i  ++++++ ++ r +++ +  +r     +++ + a ++a+f +f+++ + 
  gi|474934976|ref|YP_007688558.1| 395 ALGFAIALGMCMLAFIKSRHDPRFKdiERiyrapKWALPGAYFMAIFEFFFMIPGL 450
                                       *********************98777666544554445666666666666665444 PP

  == domain 2  score: -8.1 bits;  conditional E-value: 2
                     AA_permease_2  82 wfnwfayvpvlasilsvaasyl......lnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilki 152
                                        f+ ++ +++l+s l++ ++ +      +  l+ d+  +  ++y+ +++ li+va++ + g + ++++ + ++++++
  gi|474934976|ref|YP_007688558.1| 510 VFAIVGSILMLTSCLAAWVNGYelfngmAV-LNADWA-DGLFQYIPVVFSLIGVAIMVCEGLNFLKRAESSVALCVV 584
                                       333333333332222222222211111022.344663.37899999999999999999****999999999999999 PP

                     AA_permease_2 153 llpliiliilglitvdgggfsslstetdtf 182
                                        l+l i+ ++       ++f      +d f
  gi|474934976|ref|YP_007688558.1| 585 CLVLSIVGLALG-----TYFC----TWDIF 605
                                       755555444333.....3333....23323 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.7  37.7   2.7e-21   2.4e-17      32     473 ..      52     487 ..      32     493 .. 0.77
   2 ?   -3.6   1.4      0.34     3e+03     405     414 ..     578     587 ..     510     634 .. 0.63

  Alignments for each domain:
  == domain 1  score: 62.7 bits;  conditional E-value: 2.7e-21
                       AA_permease  32 llayllagvviflvmlslgeiatngp..ksggfytyasrflgpelGfviGln..........ylfswitvlalelta 96 
                                       +++++l+++  fl  + lge+   +    +gg  +y+ +  ++ +G  i+            y+ +w+ v+++ ++ 
  gi|474934976|ref|YP_007688558.1|  52 IIIWVLSVLSGFLLNIPLGEMCATFGvaGIGGSIQYVYKDDERYAGKKINRGrmigslgawaYFATWVPVIPIFTIM 128
                                       78999999999999999999976666587788888887665555555555554455556666******999876555 PP

                       AA_permease  97 a.siliqfwel.vtdlpkawvt....gavflvvlliinlvgvkvygeaefilalikiiaiiafiivg.....iilla 162
                                         +++  + el ++  +++  +    ga +++++++    g+++ +++++ila i i+ i+   +v      ++l+a
  gi|474934976|ref|YP_007688558.1| 129 TgVYINDYFELgIDGFNSTL-FylvlGAAIYGFIIVSGRKGLEGGAKIQLILAAITIVPILVICVVPlingdFSLSA 204
                                       40455567877555555433.25899***************************999999887777766554544444 PP

                       AA_permease 163 ggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPeksiPkailqv 239
                                         +       +++  +g++ ++++ +g       +++ ++++f ++  ++ G e+ a+ ++E k+P +++Pka +  
  gi|474934976|ref|YP_007688558.1| 205 ITDELIP--KHHTFGDGAVSEAWVWNG------NSLLMILGCFTVAQWSAVGWESAATYGAEYKEPNRDVPKALIAC 273
                                       4433333..456666667678888888......569***************************************** PP

                       AA_permease 240 viritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssansslysasRvly 316
                                        ++ +++Y  +++++   ++ +   + ++ a +  ++ i  +  g ++ a+ + ++i + ++ +  ++l ++ R+++
  gi|474934976|ref|YP_007688558.1| 274 GLLCLFMYFVIAFCMYGALGIDG--IYEAGAAT--LIPISESDFGDIGGAVAVFLLIAGMVMIIQTAFL-ATARTIQ 345
                                       ********999999988887654..77766644..8888999999999888888777777766666666.567**** PP

                       AA_permease 317 slakdglaPkvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwlliilsylrfRka 393
                                        +akdg +P+v++  + +gvP+ a+++ ++i+++++l+   +++       +la+sal + i +++++l++++ R  
  gi|474934976|ref|YP_007688558.1| 346 VMAKDGNFPFVFSLTNEYGVPIYAMFFEAFIGFVVILAGITASQ-------ILAVSALGFAIALGMCMLAFIKSRHD 415
                                       ************************************99998888.......9********************99998 PP

                       AA_permease 394 lkyqgrsieelgfkaallplgvilvlaaliiillilalyayltvkkgpkdwgaasfaaaylivllfliilvgvklhv 470
                                        + + +   e  ++a+   l   + +a++ ++++i +l +y+      ++++ ++ +  +   ++++ +++ ++++ 
  gi|474934976|ref|YP_007688558.1| 416 PRFKDI---ERIYRAPKWALPGAYFMAIFEFFFMIPGLLYYVY-----STMSIGYCVVGIAATMMYVPCWIFIQWWN 484
                                       776666...3355555555555566666666666666666666.....55666776666666666666666666666 PP

                       AA_permease 471 knk 473
                                        + 
  gi|474934976|ref|YP_007688558.1| 485 TQA 487
                                       555 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 0.34
                       AA_permease 405 gfkaallplg 414
                                       ++ ++++ l 
  gi|474934976|ref|YP_007688558.1| 578 SVALCVVCLV 587
                                       3333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (649 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1022  (0.0570026); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.78u 0.33s 00:00:01.11 Elapsed: 00:00:00.51
# Mc/sec: 3825.22
//
Query:       gi|474934977|ref|YP_007688559.1|  [L=456]
Description: glutamate dehydrogenase (NADP) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-90  302.9   3.7    2.4e-90  302.5   3.7    1.1  1  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd
    2.3e-52  176.3   0.0    4.2e-52  175.4   0.0    1.5  1  ELFV_dehydrog_N  Glu/Leu/Phe/Val dehydrogenase, dimerisation 


Domain annotation for each model (and alignments):
>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  302.5   3.7   2.7e-94   2.4e-90       1     243 []     203     453 ..     203     453 .. 0.98

  Alignments for each domain:
  == domain 1  score: 302.5 bits;  conditional E-value: 2.7e-94
                                       T--TTTTTHHHHHHHHHHHHHHHHTTTS-STTEEEEEE--SHHHHHHHHHHHHCT-EEEEEEESSEEEEETTEE-HH CS
                     ELFV_dehydrog   1 GGsldrpeaTglGvvyyveemlkklkldslegkrvaisGsGnvgsyaallltelgakvvavsDssGviydpeGldie 77 
                                       GGsl+r+eaTg+G++y v++mlk+ ++ s++gk v isGsGnv+ ya +++t+lgakvv++sDs+G+iydpeG++++
  gi|474934977|ref|YP_007688559.1| 203 GGSLARTEATGYGLCYLVDAMLKD-NGMSFDGKIVDISGSGNVAIYATEKATQLGAKVVTLSDSNGYIYDPEGIELD 278
                                       9***********************.7788************************************************ PP

                                       HHHHHHHCSSS.STTHSHH.STSTSEEESHHSHHHHSS-SEEEE-SSTTSB-HHHHTHTHHTT-SEEE-SSSS-B-H CS
                     ELFV_dehydrog  78 ellelkeerks.vkeykks.sekkaeyieneeellelkvdilvPcAtqneideenakalikngvklvvEgANlpttq 152
                                        ++++ke +++ +key  + ++k++ey+e++++++++k+di++PcAtqneide++ak+l+kng+ +v+EgAN+p+t+
  gi|474934977|ref|YP_007688559.1| 279 LVKQIKEVERGrIKEYLGRtKHKGVEYHEGSTNVWNVKCDIALPCATQNEIDEASAKTLVKNGCVCVAEGANMPSTP 355
                                       *******99999****9987667899*************************************************** PP

                                       HHHHHHHHTT-EEE-HHHHTTHHHHHHHHHHHHHHCT----HHHHHHHHHHHHHHHHHHHHHHHHHCT-T....... CS
                     ELFV_dehydrog 153 eAkeileeagvlvvpdkaaNaGGVtvSslEmlqnlarlswteeevdeklkkimkeifkavveeaeeykqe....... 222
                                       eA+++++++g+l++p+kaaNaGGV++S+lEm+qn++rlsw+ eevd+klk im++i+++++++a++y+ +       
  gi|474934977|ref|YP_007688559.1| 356 EAIKVYQDNGLLFAPGKAANAGGVATSALEMSQNSERLSWSFEEVDAKLKGIMENIYHNIAAAARKYNLKtkggkdn 432
                                       ********************************************************************9999***** PP

                                       HHHHHHHHHHHHHHHHHHHCT CS
                     ELFV_dehydrog 223 lvkganiagfekvaeamkaqG 243
                                       lv+ganiagfekva+am  qG
  gi|474934977|ref|YP_007688559.1| 433 LVAGANIAGFEKVADAMIWQG 453
                                       *****************9887 PP

>> ELFV_dehydrog_N  Glu/Leu/Phe/Val dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.4   0.0   4.7e-56   4.2e-52       1     130 []      58     186 ..      58     186 .. 0.99

  Alignments for each domain:
  == domain 1  score: 175.4 bits;  conditional E-value: 4.7e-56
                                       -SEEEEEEEEEE-TTSBEEEEEEEEEEEE-TTSSEEEEEEEETT--HHHHHHHHHHHHHHHHHTTSS-EEEEEEEES CS
                   ELFV_dehydrog_N   1 pervlqvtvpvkrdnGelevikgyraqhssalgPakGGiRfhpsvnldevkaLaalmtyKnalvdlpfGGakggvki 77 
                                       per++ ++v++ +d+G+++v++gyr+q++sa+gP+kGG+R+hpsvnl+ +k+L++++++Kn+l++lp+GG+kgg+++
  gi|474934977|ref|YP_007688559.1|  58 PERTIMFRVTWVDDSGKVQVNRGYRVQYNSAIGPYKGGLRLHPSVNLSILKFLGFEQIFKNSLTGLPIGGGKGGSDF 134
                                       89*************************************************************************** PP

                                       -GGGS-HHHHHHHHHHHHHHHG.GG-BTTTEEEEBBTTB-HHHHHHHHHHHHH CS
                   ELFV_dehydrog_N  78 dpkklseeeleritrrfvrelakkfiGpgiDvpApDvgtgaremawladeykk 130
                                       dpk++s++e++r++++f++el  k+iGp++DvpA D+gtg re+++++++yk+
  gi|474934977|ref|YP_007688559.1| 135 DPKGKSDAEVMRFCQSFMTELV-KHIGPDTDVPAGDIGTGGREIGYMFGQYKR 186
                                       **********************.****************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 3041.90
//
Query:       gi|474934978|ref|YP_007688560.1|  [L=108]
Description: translation initiation factor 1A (aeIF-1A) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.4e-17   60.7   0.1    1.2e-16   60.2   0.1    1.2  1  eIF-1a    Translation initiation factor 1A / IF-1


Domain annotation for each model (and alignments):
>> eIF-1a  Translation initiation factor 1A / IF-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.2   0.1   6.7e-21   1.2e-16       1      64 []      24      86 ..      24      86 .. 0.96

  Alignments for each domain:
  == domain 1  score: 60.2 bits;  conditional E-value: 6.7e-21
                                      EEEEEEEEEEETTTEEEEEE.SSSSBEEEEE-HHHHCT----TT-EEEEEE-TT-TTEEEEES- CS
                            eIF-1a  1 gevigkViealgnnlfrVelpdngkevlaeipgkfRnkiwikrGdyVlVelspydltkGrIvyr 64
                                      ge+ g+  ++lg ++++V ++ +g+ ++++ipgk+++++wi++Gd  +V++++++++k+++ +r
  gi|474934978|ref|YP_007688560.1| 24 GEMFGIADQLLGASKIKVMCE-DGQSRVGRIPGKIKKRMWIREGDLLIVSVWDFEPSKCDVRFR 86
                                      6899****************7.6*************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       234  (0.0130515); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 752.42
//
Query:       gi|474934979|ref|YP_007688561.1|  [L=279]
Description: Serine/threonine protein kinase involved in cell cycle control [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-59  200.2   0.0    2.9e-59  199.8   0.0    1.1  1  RIO1            RIO1 family
    2.1e-10   40.9   0.1    4.2e-06   26.9   0.1    2.8  2  APH             Phosphotransferase enzyme family
    3.8e-05   23.2   0.0     0.0035   16.7   0.0    2.1  2  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
  ------ inclusion threshold ------
       0.05   12.4   0.1      0.072   11.8   0.1    1.2  1  Pkinase_fungal  Fungal protein kinase
      0.077   12.4   0.0       0.18   11.2   0.0    1.7  1  APH_6_hur       Aminoglycoside/hydroxyurea antibiotic resista
        9.7    5.4   7.7         16    4.7   7.7    1.4  1  NOA36           NOA36 protein


Domain annotation for each model (and alignments):
>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.8   0.0   9.8e-63   2.9e-59       1     185 [.      67     248 ..      67     251 .. 0.97

  Alignments for each domain:
  == domain 1  score: 199.8 bits;  conditional E-value: 9.8e-63
                                       EEEEEEETTTEEEEEEEE-S---SS-HHHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEE CS
                              RIO1   1 nVyhavsedgkevaiKiyktstteFkkrkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpie 77 
                                       nV++a++edg+ va+Kiy+tst++Fk++ kyv+g++rfk +  + n+ k + +w  kEfrnL r +eag+pvP+pi+
  gi|474934979|ref|YP_007688561.1|  67 NVFYATDEDGDPVALKIYRTSTSTFKRVAKYVEGDPRFKGT--TGNRWKFIYAWCSKEFRNLDRYYEAGLPVPEPIA 141
                                       7*************************************966..99******************************** PP

                                       EETTEEEEE--EETTEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETTEEEE--GTTEEE CS
                              RIO1  78 lkrhvlvmefigedgvaapklkdveeeeeaeelyeevleemrklykeaglvHaDLSeyNvlvdedkvviIDvsQave 154
                                         +++l+me+ig+++ aap+lkd+e  ++ +++y+ev++ ++   +ea+lvH+DLSeyN+l++++++++IDv+Qa++
  gi|474934979|ref|YP_007688561.1| 142 NYENCLLMEYIGDENRAAPQLKDAE-MDDPTDVYDEVISFIIDGWQEAHLVHGDLSEYNILMTDEGPIVIDVGQAMT 217
                                       *************************.668999********************************************* PP

                                       TTSTTHHHHHHHHHHHHHHHHHTTC-----H CS
                              RIO1 155 ldhpnalefLerDveniikfFrrkgvekvde 185
                                        d  na+e+LerD++ni++fF+++g++++d 
  gi|474934979|ref|YP_007688561.1| 218 SDWYNAQELLERDIRNINRFFKNRGADIIDP 248
                                       *************************998775 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   1.9e-05     0.057       5      87 ..      60     166 ..      58     183 .. 0.71
   2 !   26.9   0.1   1.4e-09   4.2e-06     131     201 ..     157     220 ..     152     222 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.9e-05
                                       E--.SSCEEEEEEETT-.-EEEEEE-TT.S-HHHHHHHHH.........................HHHHHHHTT-B- CS
                               APH   5 lsggasnrtylvttpag.ryvlrrnppa.raaeeirreva.........................llrlLakagvpv 54 
                                       +s g +  +++ t+++g +++l++++++  +  +++++v+                          l+   +ag+pv
  gi|474934979|ref|YP_007688561.1|  60 ISTGKEGNVFYATDEDGdPVALKIYRTStSTFKRVAKYVEgdprfkgttgnrwkfiyawcskefrNLDRYYEAGLPV 136
                                       566777777777777744888888777766666666666677777777777777777777776668888899***** PP

                                       -B-CTTBS-EEETTEEEEEEE----EE-SS....HHH CS
                               APH  55 Pevlagdtddeeigllfalieyvpgrsllr....kls 87 
                                       Pe++a       ++   +l+ey++ + ++        
  gi|474934979|ref|YP_007688561.1| 137 PEPIA-------NYENCLLMEYIGDENRAApqlkDAE 166
                                       *****.......6667789999999999985554334 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 1.4e-09
                                       CHHHCCCGCCTCCHHHHHHHHHHHHHHHH--SSS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-EEEEC CS
                               APH 131 satarllaselldlleeleeqvlaalaallpgelptvllHgDlhpgNllvdpddgrvtGviDfedaglgpp 201
                                       +a+++l+++e +d   ++ ++v+  + + ++   ++ l+HgDl+  N+l++ d+g++  viD + a++++ 
  gi|474934979|ref|YP_007688561.1| 157 RAAPQLKDAEMDD-PTDVYDEVISFIIDGWQ---EAHLVHGDLSEYNILMT-DEGPI--VIDVGQAMTSDW 220
                                       4555666677777.44555559999999999...8****************.99***..*********985 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.2e-06    0.0035      51      83 ..     112     144 ..     107     154 .. 0.86
   2 !    4.4   0.0     0.007        21     131     191 ..     182     239 ..     163     253 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.2e-06
                               Kdo  51 fklgrtravrEfrllkrLeeagvavpkpvaaga 83 
                                       +k+ ++   +Efr+l+r++eag++vp+p+a ++
  gi|474934979|ref|YP_007688561.1| 112 WKFIYAWCSKEFRNLDRYYEAGLPVPEPIANYE 144
                                       6666777889*******************9876 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.007
                               Kdo 131 iaklhragvnHadlyaknillqqeeeeeaeiwliDldkarlrlr..adrwrekdLarLkrsfl 191
                                       i    +a++ H+dl   nil+  e+      ++iD  +a +     a+   e+d+++++r f+
  gi|474934979|ref|YP_007688561.1| 182 IDGWQEAHLVHGDLSEYNILMTDEG-----PIVIDVGQAMTSDWynAQELLERDIRNINRFFK 239
                                       55667899*************9998.....788888777665433355555666666666555 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   2.4e-05     0.072     325     363 ..     187     219 ..     175     234 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.4e-05
                    Pkinase_fungal 325 kagiLHrDiSenNilitdskkegerkglLiDLDlakels 363
                                       +a ++H D Se+Nil+t      ++  ++iD+  a++ +
  gi|474934979|ref|YP_007688561.1| 187 EAHLVHGDLSEYNILMT------DEGPIVIDVGQAMTSD 219
                                       7889*************......6778888888888766 PP

>> APH_6_hur  Aminoglycoside/hydroxyurea antibiotic resistance kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   5.9e-05      0.18     143     200 ..     172     228 ..     135     256 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.9e-05
                         APH_6_hur 143 veaaaiaaeLleepselrpLHgdlhhenvLagerrgWlaidPkglvGergfdlanllr 200
                                       +    +   ++++ +e  + Hgdl   n+L ++ +g ++id  + +    +++ +ll+
  gi|474934979|ref|YP_007688561.1| 172 DVYDEVISFIIDGWQEAHLVHGDLSEYNILMTD-EGPIVIDVGQAMTSDWYNAQELLE 228
                                       44445666788999******************9.9999**987777777777777665 PP

>> NOA36  NOA36 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   7.7    0.0054        16     272     291 ..     258     277 ..     214     279 .] 0.50

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0054
                             NOA36 272 egdedddddddeedddeeed 291
                                       + dedd+d+++++++d+eed
  gi|474934979|ref|YP_007688561.1| 258 SPDEDDEDEEEDDEEDYEED 277
                                       12222222222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 1645.22
//
Query:       gi|474934980|ref|YP_007688562.1|  [L=182]
Description: universal archaeal KH domain protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-09   37.2   0.9    2.9e-05   23.8   0.1    2.4  2  KH_1      KH domain
     0.0012   18.9   0.0     0.0032   17.5   0.0    1.7  2  KH_8      Krr1 KH1 domain
     0.0016   18.2   1.4       0.12   12.2   0.1    2.4  2  KH_2      KH domain
  ------ inclusion threshold ------
      0.012   15.4   1.0       0.32   10.9   0.1    2.6  2  KH_4      KH domain


Domain annotation for each model (and alignments):
>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.1   6.6e-09   2.9e-05       3      45 ..       3      46 ..       1      50 [. 0.82
   2 !   12.0   0.1   3.2e-05      0.14       9      55 ..     103     141 ..      96     155 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 6.6e-09
                                      EEEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT....T. CS
                              KH_1  3 rilvPsslvgriIGkgGsnIkeIreetgakIkvpksedeg.sde 45
                                      +i +P + vg+++Gk G++ k ++e+tg + ++ k+ +   +de
  gi|474934980|ref|YP_007688562.1|  3 SIRIPEDRVGALVGKEGASKKMLEERTGIRLDITKDGEVTyDDE 46
                                      689*****************************985333324555 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 3.2e-05
                                       GHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEESHH CS
                              KH_1   9 slvgriIGkgGsnIkeIreetgakIkvpksedegsderevtisGspe 55 
                                       +  gr+IGk G++ k I++   +++ v  +       ++v ++G+  
  gi|474934980|ref|YP_007688562.1| 103 RARGRLIGKDGKTRKIIEDLADVYMSVY-G-------NTVSLIGNSI 141
                                       568**************99769988875.3.......4677777544 PP

>> KH_8  Krr1 KH1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   7.2e-07    0.0032      19      81 .]      18      80 ..       3      80 .. 0.77
   2 ?   -2.2   0.0         1   4.5e+03      62      76 ..     133     147 ..     124     150 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 7.2e-07
                              KH_8 19 eekikkllee.kklklevdlkerslkvsTtekTrDPyiilkardlikLisrgvpleeakkvleD 81
                                      e + kk+lee   ++l++  k++ ++    ++  DP   lk  d+ik ++rg + ++a k+l+D
  gi|474934980|ref|YP_007688562.1| 18 EGASKKMLEErTGIRLDI-TKDGEVTYDDEREGVDPLNALKLMDVIKAVARGFNPDKAAKILDD 80
                                      555566664413455555.36788888999999*****************************99 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1
                              KH_8  62 likLisrgvpleeak 76 
                                        ++Li+ +++l  ak
  gi|474934980|ref|YP_007688562.1| 133 TVSLIGNSISLPVAK 147
                                       689999999998876 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.1   2.6e-05      0.12      33      66 ..       8      41 ..       3      50 .. 0.87
   2 !    4.7   0.1    0.0058        26      36      58 ..     105     127 ..      99     138 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.6e-05
                                      ESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCE CS
                              KH_2 33 esqpgivIGkgGsnikkigkelrkdieklegkkV 66
                                      e + g ++Gk+G+  k++++  + ++++ ++++V
  gi|474934980|ref|YP_007688562.1|  8 EDRVGALVGKEGASKKMLEERTGIRLDITKDGEV 41
                                      7799*****************9999988888877 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0058
                                       HHHHHTGGGHHHHHHHHHHHHHH CS
                              KH_2  36 pgivIGkgGsnikkigkelrkdi 58 
                                        g++IGk G++ k i+  +   +
  gi|474934980|ref|YP_007688562.1| 105 RGRLIGKDGKTRKIIEDLADVYM 127
                                       599********999998887666 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.027   1.2e+02      33      48 ..       4      19 ..       3      25 .. 0.88
   2 ?   10.9   0.1   7.2e-05      0.32      40      70 ..     105     135 ..      76     137 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.027
                              KH_4 33 lnvegedlGrvIGkrG 48
                                      +++ ++ +G ++Gk+G
  gi|474934980|ref|YP_007688562.1|  4 IRIPEDRVGALVGKEG 19
                                      6788999********9 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 7.2e-05
                              KH_4  40 lGrvIGkrGrtldAlqylvsaaankegkrvr 70 
                                        Gr+IGk+G+t + +  l+ ++++ +g+ v+
  gi|474934980|ref|YP_007688562.1| 105 RGRLIGKDGKTRKIIEDLADVYMSVYGNTVS 135
                                       6**********99998888888887777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 1215.25
//
Query:       gi|474934981|ref|YP_007688563.1|  [L=412]
Description: conserved hypothetical protein TIGR01213 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00011   22.3   0.8    0.00027   21.1   0.8    1.6  1  THUMP          THUMP domain
  ------ inclusion threshold ------
        5.7    7.4  12.7       0.15   12.4   4.1    2.6  2  DnaJ_CXXCXGXG  DnaJ central domain


Domain annotation for each model (and alignments):
>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.8     3e-08   0.00027      56     138 ..      59     159 ..      50     165 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3e-08
                                       E..EEEEESSHHHHHHHHHHHHHHHHHHCT-EEEEEEEESSSTS................SSHHHHHHHHHHHHHHC CS
                             THUMP  56 v..cevceadledileaakeivkkkfeeeketFaVrvkrrgkhf................eftsreinrevGkaive 114
                                       +  c +ce+ ++ + ++a ++ +k  e e+  F V+++    ++                e  + e+nre+Gka   
  gi|474934981|ref|YP_007688563.1|  59 EeiCPICENVFDMVPRFADAVAEKVNEVESHNFLVGCRIDAAQAknekelvekyglwetfEPLKTELNREIGKACIH 135
                                       4457789999999999999999999999999*******99888899999**************************** PP

                                       CTT-EE-SSS-SEEEEEEEETTEE CS
                             THUMP 115 ktglkVdlenPdivvrveiikdka 138
                                        ++  V++++P++v +++ +  ++
  gi|474934981|ref|YP_007688563.1| 136 DINRPVEFKEPELVAIIDTRFAEV 159
                                       **************9998776665 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   1.5       0.3   2.7e+03      17      24 ..      21      28 ..      11      68 .. 0.49
   2 ?   12.4   4.1   1.7e-05      0.15       1      52 [.     186     232 ..     186     244 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.3
                     DnaJ_CXXCXGXG 17 CktCkGsG 24
                                      C++C G+ 
  gi|474934981|ref|YP_007688563.1| 21 CDHCLGRM 28
                                      44444443 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 1.7e-05
                     DnaJ_CXXCXGXG   1 CkkCkGsgakkgkkktCktCkGsGvvreeqk.t.lgp.fvqqsqstCpeCeGtGk 52 
                                       Ck C+G+g        C +C+G G++ ++++ + +g   ++ +  + ++ +G G+
  gi|474934981|ref|YP_007688563.1| 186 CKICHGKG--------CARCHGMGKMYMQSVqEiIGDiAMEMTGGDANAFHGMGR 232
                                       99******........********7544433245777444444558888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 2448.97
//
Query:       gi|474934982|ref|YP_007688564.1|  [L=97]
Description: LSU ribosomal protein L21E [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-34  118.0   2.2    1.6e-34  117.8   2.2    1.0  1  Ribosomal_L21e   Ribosomal protein L21e
  ------ inclusion threshold ------
       0.15   11.9   0.3       0.36   10.7   0.3    1.6  1  HlyD             HlyD membrane-fusion protein of T1SS
       0.17   12.4   0.3       0.74   10.3   0.3    1.8  1  Phage_sheath_1N  Phage tail sheath protein beta-sandwich doma


Domain annotation for each model (and alignments):
>> Ribosomal_L21e  Ribosomal protein L21e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.8   2.2   2.7e-38   1.6e-34       1      97 [.       1      93 [.       1      96 [. 0.98

  Alignments for each domain:
  == domain 1  score: 117.8 bits;  conditional E-value: 2.7e-38
                                      X--S-STTTT-TTTTS--GGG-SS--SHHHH----TT-EEEE---TT--SS---GGGTT-EEEE..EEEETTEEEEEEE CS
                    Ribosomal_L21e  1 mknskglrrgtrklfskkfrkkgvpplstylreykkGdkVdikidpsvqkgmphkryhGktgrvynvtkravgvivnkk 79
                                      m++s+g+r +tr+l++kk+r +g++p+++ +++++ G+kV+i+idps++kgmph r+hG tg+v  v++r+ ++ v++k
  gi|474934982|ref|YP_007688564.1|  1 MQRSRGFRTKTRQLLQKKPRARGLSPITKGFQTFETGQKVNIVIDPSIHKGMPHSRFHGLTGVV--VGQRGTAYEVSVK 77
                                      89**************************************************************..************* PP

                                      ETTE..EEEEEE-GGGEE CS
                    Ribosomal_L21e 80 vggkileKriivriehlk 97
                                      vg+k  +K ++ r+ehl 
  gi|474934982|ref|YP_007688564.1| 78 VGDK--TKMVVSRPEHLV 93
                                      ****..**********96 PP

>> HlyD  HlyD membrane-fusion protein of T1SS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3   6.1e-05      0.36      21      66 ..      36      82 ..      31      90 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 6.1e-05
                                      CEEEEEEEGC.....GEEECTTTSEEEEEEECTSBEEEEEEEEEEEETTEE CS
                                      xxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              HlyD 21 vgqpvevrfd.....AfpqtktgkftgvVvgispdrvpvrvvvekaqgpyy 66
                                      +gq+v+++ d     + p++++++ tgvVvg+ ++      +v +++g+++
  gi|474934982|ref|YP_007688564.1| 36 TGQKVNIVIDpsihkGMPHSRFHGLTGVVVGQRGT----AYEVSVKVGDKT 82
                                      566666665544444789*****************....444444444444 PP

>> Phage_sheath_1N  Phage tail sheath protein beta-sandwich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.3   0.00012      0.74      22      54 ..      32      82 ..       9      95 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00012
                                      SSSGGGGGEEEEEEEHSS..................STTSEEEEEEETTEE CS
                   Phage_sheath_1N 22 ypgerGnritvevtsgad..................dsnqfdvivregdri 54
                                      +++e+G+++++ +++++                     ++++v+v++gd++
  gi|474934982|ref|YP_007688564.1| 32 QTFETGQKVNIVIDPSIHkgmphsrfhgltgvvvgqRGTAYEVSVKVGDKT 82
                                      556666666666666666666666666666666666566666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 663.70
//
Query:       gi|474934983|ref|YP_007688565.1|  [L=92]
Description: archaeal conserved hypothetical protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.023   15.0   0.2      0.026   14.9   0.2    1.1  1  RNA_pol_Rpb4  RNA polymerase Rpb4
      0.081   12.7   0.2      0.084   12.7   0.2    1.1  1  Phage_Nu1     Phage DNA packaging protein Nu1


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb4  RNA polymerase Rpb4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.2   2.9e-06     0.026      56     122 ..      17      91 ..       5      92 .] 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.9e-06
                                       HHTTSSHHH.......HHHHHHHHTTST.STHHHHHHHHHCSTSSHHHHHHHSTTGTTTSTSHHHHHHHHHHHHH CS
                      RNA_pol_Rpb4  56 fsrlkneek.......fnelvellksfe.LtkaEklqlvnlkPesavelktlieeleerfedeqleeiLdelkev 122
                                       +++l ++ek       ++elv +l++ +  +   ++++ +++P+   e+++ + + +  ++ + +++ Ld+++++
  gi|474934983|ref|YP_007688565.1|  17 KNALSQAEKyalpadkAKELVAQLSELDfVESDVAVKIADILPKFPSEVRAAFYKKRITLDADMIQKVLDIVNQY 91 
                                       5556666666777777************66777788************************************998 PP

>> Phage_Nu1  Phage DNA packaging protein Nu1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   9.3e-06     0.084      90     151 ..      19      81 ..       3      91 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.3e-06
                         Phage_Nu1  90 ikaqadaqelknaeakkevvelelvtkvlarvaaeiaailstiPlllqrr.ykelenrhvdvl 151
                                         +qa++  l   +ak+ v++l  +++v + va  ia il + P  ++   yk+      d++
  gi|474934983|ref|YP_007688565.1|  19 ALSQAEKYALPADKAKELVAQLSELDFVESDVAVKIADILPKFPSEVRAAfYKKRITLDADMI 81 
                                       45688888899999999***************************8885541444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.32s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 608.10
//
Query:       gi|474934984|ref|YP_007688566.1|  [L=189]
Description: putative RNA-binding protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-54  182.8   0.4    6.6e-54  182.6   0.4    1.0  1  DUF655    Protein of unknown function (DUF655)
    2.1e-06   27.9   0.0    2.9e-06   27.4   0.0    1.4  1  HHH_6     Helix-hairpin-helix motif
     0.0043   17.3   0.0     0.0084   16.4   0.0    1.4  1  HHH_3     Helix-hairpin-helix motif
     0.0053   17.3   0.9        0.2   12.3   0.1    2.1  3  HHH_5     Helix-hairpin-helix domain
  ------ inclusion threshold ------
       0.04   13.6   0.0       0.06   13.0   0.0    1.2  1  YecM      YecM protein


Domain annotation for each model (and alignments):
>> DUF655  Protein of unknown function (DUF655)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.6   0.4   1.8e-57   6.6e-54       1     180 [.       1     180 [.       1     181 [. 0.97

  Alignments for each domain:
  == domain 1  score: 182.6 bits;  conditional E-value: 1.8e-57
                                       X--EEEEEEEETT--TT--S-GGG---EEEEEETTT--EEEEEE-TT----TT-EEE-SSS..--SSEEEEEEE--G CS
                            DUF655   1 leeeaivLDylpeGypddkhrehrdkpvvqalgereltLlelvplkevdilkldevaigkg..ksdkivkikreisy 75 
                                       +ee+a+vLDylp+G p +k    + +p+v+alge+e++L+elv +++v i+ +d+v+igk+  k+d i+++kr+++ 
  gi|474934984|ref|YP_007688566.1|   1 MEEYAYVLDYLPNGIPGGKY--DKAEPLVYALGESEFKLFELVAKPNVSINFEDRVYIGKDsaKRDVIDHVKRRVNS 75 
                                       79***************996..799*********************************997336899********** PP

                                       GGS-HHHHHHHHHHHHHHHHTTHHHHHHHH-----B-SSSBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHHHST CS
                            DUF655  76 edLtdvaraeLpdvvekivkekEdrfveffneaepitiRlHaLelLpgvgkklarkileeRerrrFesFedvkkrvk 152
                                       +d++++a++eL+++v+ iv+++  +f+ ffn+a pit++ HaLe Lpg+gkk + +il+eR++ +F+ Fed++ rv 
  gi|474934984|ref|YP_007688566.1|  76 DDISSTAHNELEYAVKMIVENDVPKFIAFFNNAGPITLKKHALEELPGLGKKSMLAILDERKKGNFKDFEDLAARVP 152
                                       ***************************************************************************** PP

                                       T---HHHHHHHHHHHHHH-TTSS--SS- CS
                            DUF655 153 glkdpaeilverileEiedktekYylFv 180
                                       ++k+p+++++ ri+ Eied+++k y+F+
  gi|474934984|ref|YP_007688566.1| 153 SVKQPEKLIIARIVLEIEDPNRKRYIFA 180
                                       ***************************8 PP

>> HHH_6  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0     8e-10   2.9e-06      28      78 ..     117     164 ..      72     177 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 8e-10
                             HHH_6  28 GLaaikglgeaaaerivaeRekegpfksledlarrvdslnkrqleaLakaG 78 
                                       +L+++ glg++ + +i++eR+ +g+fk++edla rv   +++q e+L+ a 
  gi|474934984|ref|YP_007688566.1| 117 ALEELPGLGKKSMLAILDERK-KGNFKDFEDLAARVP--SVKQPEKLIIAR 164
                                       789999**************9.8**************..899999998775 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   2.3e-06    0.0084      13      47 ..     115     148 ..     112     156 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.3e-06
                             HHH_3  13 aeeLqklpGlgpklAknIvayReknGpfksreeLl 47 
                                       +  L+ lpGlg+k   +I++ R k+G+fk++e+L 
  gi|474934984|ref|YP_007688566.1| 115 KHALEELPGLGKKSMLAILDER-KKGNFKDFEDLA 148
                                       6789******************.999********7 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       2.6   9.2e+03      43      50 ..      56      63 ..      54      63 .. 0.88
   2 !   10.5   0.1    0.0002      0.73      34      57 .]     115     138 ..      90     138 .. 0.83
   3 !   12.3   0.1   5.6e-05       0.2       4      32 ..     118     150 ..     115     171 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.6
                                      S-HHHHHH CS
                             HHH_5 43 iGkktAer 50
                                      iGk+ A+r
  gi|474934984|ref|YP_007688566.1| 56 IGKDSAKR 63
                                      99**9998 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0002
                                       HHHHHTSTTS-HHHHHHHHHHHHH CS
                             HHH_5  34 veeLakipGiGkktAeriilelkd 57 
                                       +++L ++pG+Gkk    i++e k+
  gi|474934984|ref|YP_007688566.1| 115 KHALEELPGLGKKSMLAILDERKK 138
                                       567999999999999999998875 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 5.6e-05
                                       HHTSTT--HHHHHHHHTT...T.--SHHHHHHS CS
                             HHH_5   4 LlsvsGiGpktAlallsa...G.iesvedlaaa 32 
                                       L +++G+G+k  la+l+    G ++ +edlaa 
  gi|474934984|ref|YP_007688566.1| 118 LEELPGLGKKSMLAILDErkkGnFKDFEDLAAR 150
                                       778899999999999988777778888888876 PP

>> YecM  YecM protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.7e-05      0.06      31      96 ..      65     127 ..      49     131 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.7e-05
                                       EEEEEEEE-S-HHHHHHHHHHHTTTEEEEEEEEETTEEEEEEEEEEEEEETTEEEEEEEEE---SS CS
                              YecM  31 eiDHialRvneeetaeawkeallqegellseneiNGRpIllfkLeqplqveeqkidvvELPypkek 96 
                                        iDH+  Rvn+ +  ++++++l    +++ en +  + I  f+ + p+++++++++  ELP  ++k
  gi|474934984|ref|YP_007688566.1|  65 VIDHVKRRVNSDDISSTAHNELEYAVKMIVENDVP-KFIAFFNNAGPITLKKHALE--ELPGLGKK 127
                                       69*******************************96.89999999999999999876..77766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.36s 00:00:00.95 Elapsed: 00:00:00.56
# Mc/sec: 1012.74
//
Query:       gi|474934985|ref|YP_007688567.1|  [L=263]
Description: dimethyladenosine transferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-53  181.2   0.0    2.4e-53  180.9   0.0    1.0  1  RrnaAD           Ribosomal RNA adenine dimethylase
    7.6e-05   23.3   0.0    0.00081   20.0   0.0    2.1  2  Methyltransf_25  Methyltransferase domain
  ------ inclusion threshold ------
      0.012   15.3   0.0       0.03   14.1   0.0    1.7  2  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.023   15.3   0.0      0.055   14.1   0.0    1.6  2  Methyltransf_11  Methyltransferase domain
       0.17   11.1   0.0       0.25   10.6   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
        0.2   11.3   0.0       0.31   10.6   0.0    1.2  1  NodS             Nodulation protein S (NodS)


Domain annotation for each model (and alignments):
>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.9   0.0   7.9e-57   2.4e-53       5     230 ..      18     228 ..      16     257 .. 0.92

  Alignments for each domain:
  == domain 1  score: 180.9 bits;  conditional E-value: 7.9e-57
                                       XXGCG--EE--HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTTTCCCEEEE CS
                            RrnaAD   5 rksygqnflknkkvineIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkklskdeklkvv 81 
                                       rks gqnfl++  ++++ ++ +++++ + vle+gpG GilT++L++++++++ +E+d++La   +   +++ +l+++
  gi|474934985|ref|YP_007688567.1|  18 RKSRGQNFLTDGRIADRHVQYADIQPGDRVLEVGPGLGILTKRLVEISDSLTCIEIDTALADYIEG--ELGDRLTLI 92 
                                       7899**************************************************************..899****** PP

                                       -S-CCGHHHHHHHCTTTCCCCEEEEEEE--TTTHHHHHHHHHHGGGGCEEEEEEEEEHHHHHHHH--TTSTT-SHHH CS
                            RrnaAD  82 hqDflkfetpeevtekdsihqeflvvanlPyeistqlvkqlleesrfglvkmllwlqkefarrllarpgskkrsrls 158
                                         D+ k e+p +           ++v+nlPy +st+++++ll+  r+ ++k+++++qkef  r++a+ gs ++srl+
  gi|474934985|ref|YP_007688567.1|  93 RGDATKVEFPPFD----------RFVSNLPYSVSTPIIFKLLD--RP-FKKAVVMVQKEFGDRMVADVGSPDYSRLT 156
                                       ***********77..........8******************8..55.69*************************** PP

                                       HHHHHHEEEEEEEEC-GGCECS--SSSEEEEEEEE-SS-S--S-HHHHHHHHHHHHCTTTSBCCCHCCCTST CS
                            RrnaAD 159 vlreaftdvklvakveksifsPppkvdsalvelerkdedlpqkdlkkyesvvrkllnrkrktlstslksllp 230
                                       v++ + ++ +++++v++s f+P+p+vds lv +++++ ++p+kd k +  +v+ ++  +rk++ tslk    
  gi|474934985|ref|YP_007688567.1| 157 VNLFYRAECQILENVPRSRFKPEPRVDSCLVSITPRPAPFPVKDEKTFFDIVKVCFDHRRKKIGTSLKAAHL 228
                                       ******************************************************************996544 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   2.7e-07   0.00081       1      74 [.      47     111 ..      47     128 .. 0.87
   2 ?    0.8   0.0      0.27   8.2e+02      24      64 ..     202     241 ..     194     248 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.7e-07
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgal 74 
                                       vL++G G G lt++l +     ++t+++i+ ++ ++++ ++   g ++++++gda++++f+   fD  vs+  l
  gi|474934985|ref|YP_007688567.1|  47 VLEVGPGLGILTKRLVEIS--DSLTCIEIDTALADYIEGEL---GDRLTLIRGDATKVEFPP--FDRFVSN--L 111
                                       9***************984..********************...569*************97..**99995..3 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.27
                                       EEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTT CS
                   Methyltransf_25  24 vtgvDiseemleaareraeeeglnvefvqgdaedlpfedgs 64 
                                        t +Di + + ++ r+++   +l++  ++ +ae +p++d++
  gi|474934985|ref|YP_007688567.1| 202 KTFFDIVKVCFDHRRKKIGT-SLKAAHLVDSAEGIPYADDR 241
                                       57899999999999999954.47999999999999998876 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0     1e-05      0.03      64      94 ..      34      64 ..      21     105 .. 0.85
   2 ?   -2.5   0.0       1.2   3.6e+03      23      36 ..     166     179 ..     163     185 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1e-05
                                      HHHHHTT--TT-EEEEES-TTSHHHHHHHHH CS
                              PCMT 64 lalellelkkgarvLevGsGsGyltavlarl 94
                                      + +++ ++++g+rvLevG G G+lt  l ++
  gi|474934985|ref|YP_007688567.1| 34 RHVQYADIQPGDRVLEVGPGLGILTKRLVEI 64
                                      568999******************9877665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.2
                                       HHHHHS-GGGGSSC CS
                              PCMT  23 ealeevdReefvpe 36 
                                       ++le+v+R++f pe
  gi|474934985|ref|YP_007688567.1| 166 QILENVPRSRFKPE 179
                                       6899*******998 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.9e-05     0.055       1      68 [.      48     110 ..      48     117 .. 0.92
   2 ?   -3.1   0.0       4.3   1.3e+04      46      60 ..     226     240 ..     203     245 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.9e-05
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEE CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvss 68 
                                       L+vG G G+l++ l +   +++++++++++ ++ + +  ++   ++++++da+k+ f+   fD  vs+
  gi|474934985|ref|YP_007688567.1|  48 LEVGPGLGILTKRLVEISDSLTCIEIDTALADYIEGELGDR---LTLIRGDATKVEFPP--FDRFVSN 110
                                       89*************999****************9999988...799**********98..8877765 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4.3
                                       EETTEECCCTSS-TT CS
                   Methyltransf_11  46 efvvadaeklpfedn 60 
                                         +v +ae +p++d+
  gi|474934985|ref|YP_007688567.1| 226 AHLVDSAEGIPYADD 240
                                       336666777777775 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   8.2e-05      0.25      52      82 ..      33      63 ..      28      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 8.2e-05
                                      HHHHTTTT--TT-EEEEES-TTSHHHHHHHH CS
                              CMAS 52 dlileklelkpGmtlLdiGcGWGslvrrave 82
                                      d+ ++ ++++pG+++L++G G G l++r ve
  gi|474934985|ref|YP_007688567.1| 33 DRHVQYADIQPGDRVLEVGPGLGILTKRLVE 63
                                      56678899*****************999887 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00011      0.31      46      74 ..      46      74 ..      34      82 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00011
                              NodS 46 dalevGcaaGalterlapyckrltvvdvv 74
                                       +levG   G lt+rl  ++++lt +++ 
  gi|474934985|ref|YP_007688567.1| 46 RVLEVGPGLGILTKRLVEISDSLTCIEID 74
                                      58************************984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1651.26
//
Query:       gi|474934986|ref|YP_007688568.1|  [L=380]
Description: GTP-binding conserved hypothetical protein TIGR00650 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.9e-30  104.7   0.0    6.2e-30  104.0   0.0    1.3  1  MMR_HSR1_C     GTPase of unknown function C-terminal
    2.6e-13   49.8   0.1    1.1e-12   47.8   0.0    2.0  2  TGS            TGS domain
    3.1e-08   33.7   0.0      1e-07   32.0   0.0    1.9  2  MMR_HSR1       50S ribosome-binding GTPase
      5e-05   23.4   0.0     0.0097   16.1   0.0    2.4  2  YchF-GTPase_C  Protein of unknown function (DUF933)
  ------ inclusion threshold ------
      0.014   15.0   0.4        1.2    8.6   0.1    2.9  3  FeoB_N         Ferrous iron transport protein B
      0.033   14.2   0.0      0.072   13.1   0.0    1.5  1  MMR_HSR1_Xtn   C-terminal region of MMR_HSR1 domain
       0.21   11.1   0.1       0.85    9.1   0.0    1.8  2  GTP_EFTU       Elongation factor Tu GTP binding domain


Domain annotation for each model (and alignments):
>> MMR_HSR1_C  GTPase of unknown function C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.0   0.0   2.4e-33   6.2e-30       1     112 []     207     311 ..     207     311 .. 0.97

  Alignments for each domain:
  == domain 1  score: 104.0 bits;  conditional E-value: 2.4e-33
                        MMR_HSR1_C   1 alNKaDlpaadenieklkekypkdkkvvpvsAaaElaLrkaakqglikYepgdedfeikedklkeldekqkkaLeki 77 
                                       a+NKaD+ +++en+++l +  +   ++vp+ A++ElaL+ka+k+gl++Y+pg+ +f+i++ +  +l+++q+ka++++
  gi|474934986|ref|YP_007688568.1| 207 AMNKADI-TPQENLDRLSDLGE---EAVPTMAETELALKKAEKAGLVEYIPGSPEFRIRDPS--KLNDAQMKAMQYM 277
                                       89*****.************88...69********************************995..5************ PP

                        MMR_HSR1_C  78 rdlvlkrygsTGVqealnaavfelldlivVYPVed 112
                                        d  +++yg+TG+q++l+ av+++ld+i+V+PVed
  gi|474934986|ref|YP_007688568.1| 278 AD-NMRKYGGTGIQKCLEDAVYKTLDYIPVFPVED 311
                                       **.88****************************97 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       0.9   2.3e+03      28      42 ..     135     152 ..     132     172 .. 0.78
   2 !   47.8   0.0   4.4e-16   1.1e-12       6      59 ..     324     377 ..     319     378 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.9
                                       TTHHHHEEEEEECS...E CS
                               TGS  28 rslakkfiyAlVnG...q 42 
                                        +l+k ++ A+ nG   +
  gi|474934986|ref|YP_007688568.1| 135 DGLGKIARQARMNGskpE 152
                                       578999999999997663 PP

  == domain 2  score: 47.8 bits;  conditional E-value: 4.4e-16
                                       TTSSEEE...EETTB-HHHHHHHHSTTHHHHEEEEEECS..EEEETTSBB-SSEEEEEE CS
                               TGS   6 PdGkvpd...lprgatveDfAykIhrslakkfiyAlVnG..qrvgldhvLedgdvveIv 59 
                                       P     d   +prg+t++D+Ay+Ih++l++kfi A      + vg d+vLe gd+++Iv
  gi|474934986|ref|YP_007688568.1| 324 P-----DchlVPRGSTAKDLAYRIHTDLGDKFIRAVNCRthRTVGADYVLEPGDIIRIV 377
                                       3.....34449************************9999999****************9 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.0     4e-11     1e-07      21      87 ..       7     106 ..       1     143 [. 0.73
   2 ?   -2.0   0.0       1.5   3.7e+03     101     114 .]     197     210 ..     179     210 .. 0.72

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 4e-11
                                       TSTEEESSSTTSSSSEEEEEEEETTEE.........................EEEEECGGCSSHHHHHHHHHHHHHH CS
                          MMR_HSR1  21 gekaivsdkpgtTrdinegrvklkgke.........................ielvDtpGliegaseekglgkafla 72 
                                        + ++++++p+tT+++n+g   ++  +                         + l+D++Gl+ +a ++kglg++fl+
  gi|474934986|ref|YP_007688568.1|   7 MAPVEIANYPFTTIEPNKGVGYVRY-PcpckelgvtcnphnslcvdgtrmvpVDLLDVAGLVPDAWQGKGLGNKFLD 82 
                                       456899*************766442.23444555555566666666666666********9999999*********9 PP

                                       HHC.TSEEEEEEETT........T CS
                          MMR_HSR1  73 lee.adlillvvdas........e 87 
                                         + ad+++ vvdas         
  gi|474934986|ref|YP_007688568.1|  83 DLRqADALVNVVDASgstniegvP 106
                                       77769********98655554440 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.5
                                       HHHTTSEEEEEEES CS
                          MMR_HSR1 101 leeakkplilvlnk 114
                                       +++  kp+i+++nk
  gi|474934986|ref|YP_007688568.1| 197 IRKLSKPMIIAMNK 210
                                       2346799***9998 PP

>> YchF-GTPase_C  Protein of unknown function (DUF933)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   3.8e-06    0.0097      17      43 ..     329     355 ..     325     360 .. 0.89
   2 !    5.3   0.0     0.009        23      64      84 .]     359     379 ..     354     379 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.8e-06
                     YchF-GTPase_C  17 ikkgttapqaAgviHsDfekgFiraev 43 
                                       + +g+ta++ A  iH+D+  +Fira  
  gi|474934986|ref|YP_007688568.1| 329 VPRGSTAKDLAYRIHTDLGDKFIRAVN 355
                                       689*********************965 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.009
                     YchF-GTPase_C  64 lrlegkdyvvqdgDiilfkfN 84 
                                        r+ g dyv++ gDii + +N
  gi|474934986|ref|YP_007688568.1| 359 HRTVGADYVLEPGDIIRIVAN 379
                                       5889************98665 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.039        99      17      41 ..       2      26 ..       1      31 [. 0.85
   2 ?   -0.2   0.0      0.25   6.3e+02      77      89 ..      85      97 ..      59     102 .. 0.87
   3 ?    8.6   0.1   0.00049       1.2      95     144 ..     191     235 ..     187     246 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.039
                                      HHHHHTTSEEEEESTTSSSEEEEEE CS
                            FeoB_N 17 fnaltgakqkvgNwpGvtvekkegk 41
                                      f a t a  +++N+p +t+e ++g 
  gi|474934986|ref|YP_007688568.1|  2 FGAATMAPVEIANYPFTTIEPNKGV 26
                                      778889999***********88875 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.25
                                      TSSSEEEEEEEGG CS
                            FeoB_N 77 eepdvvvnvvdat 89
                                      +++d++vnvvda+
  gi|474934986|ref|YP_007688568.1| 85 RQADALVNVVDAS 97
                                      5789*******96 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.00049
                                       HHHHHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTT CS
                            FeoB_N  95 LyLtlqllelgvpvvlalnmideaekkgieidlkkLsekLgvpvvktsak 144
                                       L L++++  l++p+++a+n+ d   ++++    ++Ls  Lg + v+t+a+
  gi|474934986|ref|YP_007688568.1| 191 LALMTEIRKLSKPMIIAMNKADITPQENL----DRLS-DLGEEAVPTMAE 235
                                       889*******************9887754....3443.355555555555 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.8e-05     0.072      53      95 ..     199     242 ..     168     247 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.8e-05
                      MMR_HSR1_Xtn  53 rvYipclyvlNKiDlisleeldelare.pnsvviSaekelnlde 95 
                                       +  +p+++++NK+D   +e+ld+l+   +++v++ ae+el l++
  gi|474934986|ref|YP_007688568.1| 199 KLSKPMIIAMNKADITPQENLDRLSDLgEEAVPTMAETELALKK 242
                                       35589*********************65899**99999998865 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.38   9.9e+02      91     105 ..      84      98 ..      78     105 .. 0.75
   2 ?    9.1   0.0   0.00033      0.85     116     174 ..     195     255 ..     191     305 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.38
                                       HHT-SEEEEEEETTT CS
                          GTP_EFTU  91 lrvlDgavlvvdave 105
                                       lr++D  v vvda+ 
  gi|474934986|ref|YP_007688568.1|  84 LRQADALVNVVDASG 98 
                                       678888888888863 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00033
                                       HHHHHTTTEEEEEEESCGST....HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEB CS
                          GTP_EFTU 116 rlalkegvpiivfiNKmDrl....kaelkeiveevkqklsrkeeklekygekgekevpvvfgS 174
                                         ++k+  p+i+++NK+D +     ++l+ + ee+  ++ ++e +l+k++  g   v+ ++gS
  gi|474934986|ref|YP_007688568.1| 195 TEIRKLSKPMIIAMNKADITpqenLDRLSDLGEEAVPTMAETELALKKAEKAG--LVEYIPGS 255
                                       56789999***********9955555555555666655544444444443333..56666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2402.43
//
Query:       gi|474934987|ref|YP_007688569.1|  [L=825]
Description: DNA polymerase elongation subunit (family B) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      7e-60  203.0   0.0    1.4e-59  202.0   0.0    1.5  1  DNA_pol_B       DNA polymerase family B
    1.2e-19   70.6   0.3    5.4e-18   65.2   0.3    2.5  1  DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain


Domain annotation for each model (and alignments):
>> DNA_pol_B  DNA polymerase family B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.0   0.0   1.6e-63   1.4e-59       2     413 ..     368     732 ..     367     769 .. 0.89

  Alignments for each domain:
  == domain 1  score: 202.0 bits;  conditional E-value: 1.6e-63
                                       -HHHHHHS-HHHHHHHHHHHHHHHTTBE-B-----.--SS.-S----BE----EEESS-EEEEEETTHHHHHHHHTT CS
                         DNA_pol_B   2 plsrvledgqqirveslLlrlakeegfilpdrtekkgkeeegYqGatVlePkkglydkpvlvlDFaSLYPsiiqahN 78 
                                       pl+ vl  g ++   slL+r+a++ g+ +p ++  ++ ++++ +G+ V   k gly+  v+vlDF+S+YPs+i+a+N
  gi|474934987|ref|YP_007688569.1| 368 PLEDVLVSGTSTLADSLLIRAADRSGVGVP-MNGRRSARDDQIEGGYVHVMKPGLYH-WVCVLDFKSMYPSLIIANN 442
                                       67789999**********************.99999999989**************7.79***************** PP

                                       -STTTCE-HCCHCCT--BTT...TEEE-TCC-EEE-TTS---HHHHHHHHHHHHHHHHHHHHHCS--HHHHHHHHHH CS
                         DNA_pol_B  79 lcyttlvaseeeakeleaedeyleveveprlvefvkksvregllpklLkdllakRkaikkelkeekdefekalldkq 155
                                       +c+ttl+ + e               v+p++ +++++++++gllp +L dl+a+R  ikk++k+++d+ e+a +d  
  gi|474934987|ref|YP_007688569.1| 443 VCFTTLCDDGEI--------------VSPSGARYASPERKKGLLPAILMDLMAQRDDIKKKMKAARDAREHAYYDGL 505
                                       *******99877..............457788999****************************************** PP

                                       HHHHHHHHHHHHHHHTSTTSTT--HHHHHHHHHHHHHHHHHHHHHHHHT...SSGGGT-SS.....T-EEEEEBSSE CS
                         DNA_pol_B 156 QlalKvtaNsvYGftGvansrlpclalAasvTtiGRemLektkelvekkaellskllalpeeaeeeklkviYGDTDS 232
                                       Q+a+Kv++N++YG+   +  r+  +++ as+T+  R +++ + + ++++                 ++ viYGDTDS
  gi|474934987|ref|YP_007688569.1| 506 QAAVKVVMNTFYGVFASSFYRFTDKSIGASITAFARFTIKGIINQLNDD-----------------GYPVIYGDTDS 565
                                       ***************************************9999999977.................9********** PP

                                       EEEE-S-SSHHHHHHHHHHHHHHHHT.TSTTT--EEEEEEEEEEEEEE.TTEEEEEEEEESSTTSEEEEESSGGGST CS
                         DNA_pol_B 233 vfielkvkdveellkigkelaeevseklfkkplklefekvykkllLis.KKkYaglkvektskanklliKGvdlvRr 308
                                       vf+     d+e ++++gke a++ s+        lefek +++l  +  KK+Y+g +v  ++k++kll++G ++ R 
  gi|474934987|ref|YP_007688569.1| 566 VFVLSPYHDIEGAARFGKEQAARFSQ--GAR--VLEFEKLLEPLFSHGvKKRYVGKIVW-PEKQDKLLVRGYEIRRS 637
                                       **************************..444..69*********98855******9999.99999************ PP

                                       TS-HHHHHHHHHHHHHHSSS....S-HHHHHHHHHHHHHHHHHHHHTT-S-GGGG-EEEEESS.CCCS.SGCCSHHH CS
                         DNA_pol_B 309 dncklvkevikkvlelllkdeteersleeglealksilkdvleeleenkvplekfvlskelskepeny.ksknlphl 384
                                       d+ +l++++ +++ e++l++     + e +l+ +++++    ++ +++kv+  ++v+s++ +   ++y +  +++++
  gi|474934987|ref|YP_007688569.1| 638 DSFDLQSRMLTELFEKILEE-----DNEGALALVRNTV----RDTMNGKVEPGDLVISRTCKG-LDAYeNPDRMANV 704
                                       *******************9.....99999**9*9999....9999**************998.999967789**** PP

                                       HHHHHHHHHCSS---TTCEEEEEEBETSS CS
                         DNA_pol_B 385 evakrlkkrneeapevgdrisYvivekkk 413
                                       + ak+l +  + +  +g ++s+++++++ 
  gi|474934987|ref|YP_007688569.1| 705 QCAKKLIRM-GYNFIPGMKVSWIVTNASA 732
                                       *****9987.5566677888888887765 PP

>> DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.2   0.3     6e-22   5.4e-18       2     337 .]      30     306 ..      29     306 .. 0.73

  Alignments for each domain:
  == domain 1  score: 65.2 bits;  conditional E-value: 6e-22
                                       ECTTSEEEEEEEE---EEEEEESSCGGHHHHHHHHHHHCCTTCCCEEEEEEEECCCCEECCTSSCCHHCEEEEEESS CS
                    DNA_pol_B_exo1   2 teegksvcvnvfgfkpyfYceapdgkeleevkeelkelyeelskkvtkivkvelvlkkslygyekkpvpylkvsvsn 78 
                                       t+e +s+ + vfgf++yfY+  p    +++v+e l++ +e +   +t  +      + +l++ + + ++ lkv++++
  gi|474934987|ref|YP_007688569.1|  30 TRERQSITIAVFGFRNYFYIVDP----TQSVEEDLSKDKEVY---GT--E------HVRLFYKGGE-HDTLKVTLQH 90 
                                       78999**************9999....224444444433333...33..2......2234444333.45******** PP

                                       TCHHHHHHHHHHHCCCCCCCCSSS--HHHHHHHHCTS-TTCEEEEETEEEEGCC--C-.SEEEEEETTTSCEETTTC CS
                    DNA_pol_B_exo1  79 pnelkkirkelspleeivdvyeydvdylerflidnkivgfgwysvkkylvraegkisncdveidcdvddliakpkes 155
                                       p  l  +rk+++     +++  +d++y  r+++d +   +++++v  +     + + ++ + +  +  ++i  p++ 
  gi|474934987|ref|YP_007688569.1|  91 PWVLAGFRKRFMTR---FKILAGDISYNDRYIYDTDM--GSCIRVTGD-E--VDLGYSTAITVRLERFENIE-PFD- 157
                                       ***********766...******************97..456888822.2..22222333333333333333.334. PP

                                       CS-EEEEEEEEEETEETTSEETTTT..--EEEEEEEECCTC.SS.SEEEEEEECCCTSS----EE--SSTCSTTEEE CS
                    DNA_pol_B_exo1 156 epplrvlsFDIeckskkgkfpdaensedpiiqIscvldglgekepearklftlrecaseeeedfeltpkpeypgvkv 232
                                        p lr  sFDIe           +++++ i  I++ +++ g        +ft  e                      
  gi|474934987|ref|YP_007688569.1| 158 -PGLRYFSFDIEN----------SIEDQHIYCICTRVEEDG--------VFTTPEPL-------------------- 195
                                       .***********9..........344588**********99........66655555.................... PP

                                       EEESSHHHHHHHHHHHHHHH--SEEEESSTTTTHHHHHHHHHHHCCTCCHCG.SCCS.....CTCEECCCCESEE.. CS
                    DNA_pol_B_exo1 233 lefdsEkelLqaflefikqydPdvitgYNidnFDlpYilnRakelykvklsklgrln.....kggrskvseigfs.. 302
                                         + +Ek+++ +f ++i+++dPdvitgYNidn+D++ i++Ra++l   +  + gr       ++g+ +      +  
  gi|474934987|ref|YP_007688569.1| 196 --YGDEKDIILGFSDLIQKIDPDVITGYNIDNYDIRKIKERADALRLKNAMRWGRDIrtrddDFGKGDS-----Nys 265
                                       ..89****************************************9986655555542221442222222.....123 PP

                                       ......EEEECEEEETTSEEEEHHHHHHHHSSSSG-SHHHH CS
                    DNA_pol_B_exo1 303 ......kqarekvkisgrihlDlyrvvkrklklpsYkLnav 337
                                               +++  +++gr+++D    +kr+l+ +  +Lnav
  gi|474934987|ref|YP_007688569.1| 266 kageprLFNERFWRVKGRLIVDAWWAAKRELRPKQETLNAV 306
                                       4456675566678999*****************99999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (825 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:00.48
# Mc/sec: 5183.69
//
Query:       gi|474934988|ref|YP_007688570.1|  [L=470]
Description: Glutamate synthase domain 2 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-97  327.2   1.1    1.7e-97  326.9   1.1    1.0  1  Glu_synthase  Conserved region in glutamate synthase
    3.5e-11   42.7   1.1    1.6e-07   30.7   0.2    3.0  3  FMN_dh        FMN-dependent dehydrogenase
    8.4e-11   41.7   4.6    7.9e-10   38.6   4.6    2.4  1  Rubredoxin    Rubredoxin
      3e-06   26.5   0.2    6.7e-06   25.3   0.2    1.5  1  IMPDH         IMP dehydrogenase / GMP reductase domain
  ------ inclusion threshold ------
      0.011   15.9   0.7      0.027   14.6   0.7    1.7  1  Zn-ribbon_8   Zinc ribbon domain
      0.014   14.8   0.3      0.029   13.8   0.3    1.4  1  NMO           Nitronate monooxygenase
      0.029   13.8   0.0      0.046   13.2   0.0    1.3  1  His_biosynth  Histidine biosynthesis protein
       0.05   13.7   0.3       0.11   12.6   0.3    1.6  1  PHD_4         PHD-finger
       0.11   12.2   1.9         15    5.4   0.0    3.5  4  SpoVS         Stage V sporulation protein S (SpoVS)
       0.15   12.1   0.4       0.45   10.5   0.1    2.0  3  HypA          Hydrogenase/urease nickel incorporation, metall
       0.17   12.0   1.2       0.51   10.4   1.2    1.8  1  zf-NF-X1      NF-X1 type zinc finger
        3.6    7.2   6.2         24    4.6   1.4    3.0  2  TF_Zn_Ribbon  TFIIB zinc-binding


Domain annotation for each model (and alignments):
>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  326.9   1.1  1.1e-100   1.7e-97      55     366 ..     135     442 ..     106     444 .. 0.95

  Alignments for each domain:
  == domain 1  score: 326.9 bits;  conditional E-value: 1.1e-100
                                       GGGS--HHHHHTTEE---B-TTTS-HHHHHHHHHHHHHHT-B-EETTS---GGGGS-----SEEEE-TT-TT--HHH CS
                      Glu_synthase  55 leevepalkikkriltsamSyGalseeahealakamnrlgtksntGEGGedeerlktakdvaikQvasgrFGvteey 131
                                        ++ +++l +++++ +s+mS+Gals +a+ alak+++ +gt++ +GEGG    +++  + + i  + + ++ v++e 
  gi|474934988|ref|YP_007688570.1| 135 GKKAKKPLVLENPVFISHMSFGALSGNAKVALAKGAEAAGTAMCSGEGGALYDEMSASSRY-IFEYVPNKYSVNDET 210
                                       356677799****************************************************.*************** PP

                                       HHH-SEEEEE---TTSTTS--EE-GGG--HHHHHHHTS-TT--EE--SS-TT-SSHHHHHHHHHHHHHH-TTSEEEE CS
                      Glu_synthase 132 LnnakaleikiaQGakpgeGgqlpgeKvseeiakiRkikpgvdliSPaphhdiysiedlaqliedLkevnkeakvsv 208
                                        + ++a+eiki+QG+kpg+Gg+lp+ Kv++ ia++R+ + g+d++SP+++ +i+s+edl++++  L++ +  ++++v
  gi|474934988|ref|YP_007688570.1| 211 FEGCSAVEIKIGQGTKPGMGGHLPALKVTKAIAAMRGKSMGKDILSPSHFPEISSPEDLKDMVDMLRKRSGGKPIGV 287
                                       ***************************************************************************** PP

                                       EEE-STTHHHHHHHHHHTT-SEEEEE-TT---SSEEHHHHHHB---HHHHHHHHHHHHHHTT-GGG-EEEEESS--S CS
                      Glu_synthase 209 KlvaeagvetiaagvakanadiilidGleGGTGAspkssikhaGlPlelalaevdqtlkeeglrdrvsliadGglkt 285
                                       K++a++ +e+++  ++k+++d+i+idG  G TG sp  + + + +P++ ala++ + ++e+g+ ++  l ++Ggl+t
  gi|474934988|ref|YP_007688570.1| 288 KIAAGHIEEDLEF-ISKSGCDFITIDGRGGATGSSPMFLKDASSVPTVYALARARKYMNEHGMDQE--LVITGGLRT 361
                                       ***********99.************************************************9997..5679***** PP

                                       HHHHHHHHHHT-SEEE-SHHHHHHTT--S---GGGT--TTSSS---HHHH..TT----HHHHHHHHHHHHHHHHHHH CS
                      Glu_synthase 286 gadvvkalalGAdavgigtaalialgCimarvChtntCpvGvatqdpeLrkrlkveekaervvnyikalaeevrell 362
                                       ++d vkala+GAdav i++aa+ialgC++ rvCht++Cp+G+atqd +L+krl+ve+ a+rv+ny+ a+aee+r ++
  gi|474934988|ref|YP_007688570.1| 362 SRDFVKALAMGADAVAIASAAVIALGCQRYRVCHTGNCPMGIATQDRDLEKRLDVEKGAKRVANYLNAVAEELRVFC 438
                                       **************************************************************************999 PP

                                       HHHT CS
                      Glu_synthase 363 aalg 366
                                          g
  gi|474934988|ref|YP_007688570.1| 439 RVSG 442
                                       8776 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0     0.002         3      58      96 ..     145     182 ..     129     221 .. 0.78
   2 !   30.7   0.2   1.1e-10   1.6e-07     226     309 ..     294     388 ..     236     395 .. 0.82
   3 ?    2.5   0.0      0.04        59     310     343 ..     418     451 ..     416     456 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.002
                                       SSSEEE--BSTGGGTSTTHHHHHHHHHHHHTS-EEEETT CS
                            FMN_dh  58 slPvliaPvglaklahpdgelalaraaakagipfvlstv 96 
                                       + Pv+i+ +++  l   ++++ala++a++ag+ ++ ++ 
  gi|474934988|ref|YP_007688570.1| 145 ENPVFISHMSFGALSG-NAKVALAKGAEAAGTAMCSGEG 182
                                       579********99987.99***************98766 PP

  == domain 2  score: 30.7 bits;  conditional E-value: 1.1e-10
                                       SHHHHHHHHHTTESEEEE--GGG........TSSTT---HHHCHHHHHHHH.....SS-EEEESS--SHHHHHHHHH CS
                            FMN_dh 226 taedakraveaGvdgivvSNHGG........RqldgapatidvLpeiveavgg...rievlvDgGirrGsDvlkAla 291
                                        +ed + + + G+d i +   GG         +  ++++t+ +L + ++++++   + e+++ gG r+  D +kAla
  gi|474934988|ref|YP_007688570.1| 294 IEEDLEFISKSGCDFITIDGRGGatgsspmfLKDASSVPTVYALARARKYMNEhgmDQELVITGGLRTSRDFVKALA 370
                                       468888888899999999999998888887744456788999*****99999767789******************* PP

                                       TT-SEEEESHHHHHHHHH CS
                            FMN_dh 292 lGAdavllGRpflyglaa 309
                                       +GAdav+++ +++ +l +
  gi|474934988|ref|YP_007688570.1| 371 MGADAVAIASAAVIALGC 388
                                       ************999986 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.04
                                       HHHHHHHHHHHHHHHHHHHHHHHHT-SBHHHHHC CS
                            FMN_dh 310 gGeeGvervleilraelertmallGvksvaeldr 343
                                       +G+++v+++l+ + +el+   ++ G  s++el+ 
  gi|474934988|ref|YP_007688570.1| 418 KGAKRVANYLNAVAEELRVFCRVSGHDSIDELGL 451
                                       699****************************975 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   4.6   5.3e-13   7.9e-10       1      47 []       3      41 ..       3      41 .. 0.93

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 5.3e-13
                                      EEEETTT-BEEETTTBBGGGTB-TT--GGGS-TT-BBTTTB-BGGGE CS
                        Rubredoxin  1 kyeCkvCgyvYdpakGdpdegiapgTkFedlPddWvCPdCgvekeqF 47
                                      ky+C vCg +Yd+++         g kF+dlPddW+CP Cg+ k++F
  gi|474934988|ref|YP_007688570.1|  3 KYRCGVCGEIYDEER--------EGVKFADLPDDWRCPLCGAAKSEF 41
                                      7***********985........4779******************99 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.2   4.5e-09   6.7e-06     134     237 ..     271     380 ..     264     385 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 4.5e-09
                                       HHHHHHHHHTT...T.SEEEEEEE-SHHHHHHHHHTT-SEEEE-SS-STTBHHHHH..CSB---HHHHHHHHHHHHC CS
                                       xxxxxxxxxxx...x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxx RF
                             IMPDH 134 eavkeikkkve...e.veviaGnvataegakaLieagadavkvGiGpGsiCttrvv..agvGvpqltAvaevaeaak 204
                                       ++v+ ++k+       v++ aG +  +e  + + + g d++ +    G+     +    +  vp + A+a++ ++++
  gi|474934988|ref|YP_007688570.1| 271 DMVDMLRKRSGgkpIgVKIAAGHI--EEDLEFISKSGCDFITIDGRGGATGSSPMFlkDASSVPTVYALARARKYMN 345
                                       555555555532222477788887..577888999999999995444444444433126889**************9 PP

                                       TCT..-EEEEES---SHHHHHHHHHTT-SEEEESC CS
                                       xxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 205 kag..vpviaDGGikysgdivkAlaaGadavmlGs 237
                                       ++g   +++  GG+++s+d vkAla+Gadav + s
  gi|474934988|ref|YP_007688570.1| 346 EHGmdQELVITGGLRTSRDFVKALAMGADAVAIAS 380
                                       99744689999********************8865 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.7   1.8e-05     0.027       6      35 ..       4      38 ..       3      40 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.8e-05
                       Zn-ribbon_8  6 YrCeeCghefe...vlqsisdaplta.CPeCgs.e 35
                                      YrC  Cg+ ++   + ++++d p+   CP Cg+ +
  gi|474934988|ref|YP_007688570.1|  4 YRCGVCGEIYDeerEGVKFADLPDDWrCPLCGAaK 38
                                      ***********9876677779999999*****955 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.3   1.9e-05     0.029     150     229 ..     299     386 ..     270     395 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.9e-05
                               NMO 150 rkvearGaDalivqGpeaGGhqG.....tpevgd...kglfaLvpqvldavd.....iPviAaGGiidrrgvaaaLa 213
                                         + ++G D + ++G   GG +G         +d   + ++  ++++++ ++       ++ +GG+ + r+   aLa
  gi|474934988|ref|YP_007688570.1| 299 EFISKSGCDFITIDGR--GGATGsspmfL---KDassVPTVYALARARKYMNehgmdQELVITGGLRTSRDFVKALA 370
                                       4566677777777774..66666443221...221223444444444444446676667889*************** PP

                               NMO 214 lGAsgvqigtrfLltk 229
                                       +GA +v+i+++ +++ 
  gi|474934988|ref|YP_007688570.1| 371 MGADAVAIASAAVIAL 386
                                       **********988775 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.1e-05     0.046      74     109 ..     351     386 ..     339     435 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.1e-05
                                       SEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-T CS
                      His_biosynth  74 ipvqvGGGIrsledveelleagadkviigtaavknp 109
                                        ++ + GG r+  d+ ++l +gad v i++aav   
  gi|474934988|ref|YP_007688570.1| 351 QELVITGGLRTSRDFVKALAMGADAVAIASAAVIAL 386
                                       568899999999999999999999999999998665 PP

>> PHD_4  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.3   7.6e-05      0.11      33      67 ..       6      34 ..       2      35 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.6e-05
                             PHD_4 33 CsvCyeivHpeClkekegegvvnedlpnsWeCpkC 67
                                      C vC ei        +e egv   dlp +W+Cp C
  gi|474934988|ref|YP_007688570.1|  6 CGVCGEIY------DEEREGVKFADLPDDWRCPLC 34
                                      66666654......237899**************9 PP

>> SpoVS  Stage V sporulation protein S (SpoVS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       5.5   8.2e+03      57      69 ..      65      77 ..      63      93 .. 0.73
   2 ?   -1.6   0.0       1.5   2.3e+03      41      68 ..     238     263 ..     234     270 .. 0.72
   3 ?    5.4   0.0    0.0099        15      41      58 ..     333     350 ..     328     356 .. 0.87
   4 ?    3.1   1.1     0.053        79      19      46 ..     356     384 ..     352     391 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 5.5
                                      EEEEEEEEEEEEE CS
                             SpoVS 57 idlvvvPaFveve 69
                                       d+   P Fv+ +
  gi|474934988|ref|YP_007688570.1| 65 DDISYDPRFVKTD 77
                                      5888899998764 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.5
                                       HHHHHHHHHHHHGGGTEEEEEEEEEEEE CS
                             SpoVS  41 avkAiaiargflapegidlvvvPaFvev 68 
                                         kAia  rg  +  g+d+    +F e+
  gi|474934988|ref|YP_007688570.1| 238 VTKAIAAMRG--KSMGKDILSPSHFPEI 263
                                       5688888888..5667777777777666 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.0099
                                       HHHHHHHHHHHHGGGTEE CS
                             SpoVS  41 avkAiaiargflapegid 58 
                                       +v A+a ar++++++g+d
  gi|474934988|ref|YP_007688570.1| 333 TVYALARARKYMNEHGMD 350
                                       799*************99 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.053
                                       HHHHHHTS.EEEEEE-SHHHHHHHHHHHH CS
                             SpoVS  19 agvlrekg.kvevqaiGagAvnqavkAia 46 
                                        g lr++   v+  a Ga+Av  a  A++
  gi|474934988|ref|YP_007688570.1| 356 TGGLRTSRdFVKALAMGADAVAIASAAVI 384
                                       55666666478999**********99997 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1    0.0003      0.45      69      99 ..       2      41 ..       1      50 [. 0.79
   2 ?   -4.0   0.0        10   1.5e+04      21      35 ..     209     223 ..     195     225 .. 0.61
   3 ?   -3.1   0.0       5.1   7.6e+03      62      79 ..     427     444 ..     412     457 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0003
                                      -EEEETTTS-EEECHHH..HH.......S-TTTSSS-EEE CS
                              HypA 69 vkvrCreCgkefeleek..al.......rCpkCgsadvei 99
                                      +k+rC +Cg+ +++e++  ++       rCp Cg+a+ e+
  gi|474934988|ref|YP_007688570.1|  2 AKYRCGVCGEIYDEEREgvKFadlpddwRCPLCGAAKSEF 41
                                      5789******999876433337889999*******98776 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 10
                                       TT..EEEEEEEEEET CS
                              HypA  21 aaarkvtkvkvevGe 35 
                                       ++++  ++v++++G+
  gi|474934988|ref|YP_007688570.1| 209 ETFEGCSAVEIKIGQ 223
                                       445556667777765 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 5.1
                                       EEEEEE--EEEETTTS-E CS
                              HypA  62 LeieevpvkvrCreCgke 79 
                                       L+   ++++v Cr+ g++
  gi|474934988|ref|YP_007688570.1| 427 LNAVAEELRVFCRVSGHD 444
                                       666777888899888765 PP

>> zf-NF-X1  NF-X1 type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.2   0.00034      0.51       8      16 ..     392     400 ..     388     401 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00034
                          zf-NF-X1   8 klCHeGpCp 16 
                                       ++CH+G+Cp
  gi|474934988|ref|YP_007688570.1| 392 RVCHTGNCP 400
                                       79******9 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.2     0.032        48      20      32 ..       4      16 ..       2      18 .. 0.82
   2 ?    4.6   1.4     0.016        24      21      42 ..      30      57 ..      28      58 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.032
                                      EEESSSSBEEEEC CS
                      TF_Zn_Ribbon 20 lvCtdCGlVledn 32
                                      ++C+ CG++ +++
  gi|474934988|ref|YP_007688570.1|  4 YRCGVCGEIYDEE 16
                                      89*****987775 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.016
                                      EESSSS......BEEEECCCCCCCHHHH CS
                      TF_Zn_Ribbon 21 vCtdCG......lVlednsidegpewre 42
                                      +C+ CG      +++e+++i++++e+ +
  gi|474934988|ref|YP_007688570.1| 30 RCPLCGaaksefSMIEEDDIVPKKEEPA 57
                                      58888844444469**********9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (470 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 3256.33
//
Query:       gi|474934989|ref|YP_007688571.1|  [L=487]
Description: anthranilate synthase, component I [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.7e-94  314.3   0.0    1.3e-93  313.3   0.0    1.4  2  Chorismate_bind  chorismate binding enzyme
    3.3e-31  108.4   0.0    2.2e-30  105.7   0.0    2.1  2  Anth_synt_I_N    Anthranilate synthase component I, N termina


Domain annotation for each model (and alignments):
>> Chorismate_bind  chorismate binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.46   4.1e+03      39      78 ..      33      77 ..      23      99 .. 0.68
   2 !  313.3   0.0   1.4e-97   1.3e-93       1     258 []     217     471 ..     217     471 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.46
                                      -HHHHHHHHHCTBSSSEEEEE.....EETTEEEEEEESSEEEEEE CS
                   Chorismate_bind 39 dplalyralrarnpapysfll.....eledsellgaSPElllkve 78
                                      +p++++ral++  ++++++       + +++++lg  P   +++ 
  gi|474934989|ref|YP_007688571.1| 33 TPVEVMRALMNVDEHCFMLESadsskKWGRYSFLGYAPKAEITCL 77
                                      578899999998888888777443333333777888777666555 PP

  == domain 2  score: 313.3 bits;  conditional E-value: 1.4e-97
                                       .HCHHHHHHHHHHHHHHTTS-SEEEEEEEEEECESS-B-HHHHHHHHHCTBSSSEEEEEEETTEEEEEEESSEEEEE CS
                   Chorismate_bind   1 sredYaeavekvkeeiragdlykvvlsrrlkaeleaavdplalyralrarnpapysflleledsellgaSPElllkv 77 
                                       sre+Y+++vek+k++i +gd+++vvls+rl+a +e   + +++yr lr+ np+py+f+++  d+e+ gaSPE+l+k+
  gi|474934989|ref|YP_007688571.1| 217 SREEYCSMVEKAKKHITEGDIFQVVLSNRLEAGFE--GSLFNTYRVLRTLNPSPYMFYFSGTDMEVAGASPETLVKL 291
                                       689******************************55..667************************************* PP

                                       ETTSEEEEECEEEEEEHSSSHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCBSCCEEEEECCEEEEEETTEEE CS
                   Chorismate_bind  78 eggrrietepiaGTrargktpeedealeeelledeKeraEhlmivdlirndLgkvakpgsvkvpelfkverysevlh 154
                                       e+g  ++t p+aGTr+rgkt+eed ale+elledeKe+aEh m+vdl rnd+gkv+++gsv+v+++ ++erys+v+h
  gi|474934989|ref|YP_007688571.1| 292 EDG-VLHTFPLAGTRPRGKTDEEDLALEKELLEDEKELAEHNMLVDLGRNDIGKVSEFGSVEVEKYHTIERYSHVMH 367
                                       *66.************************************************************************* PP

                                       EEEEEEEEESTT--HHHHHHHCSS-CCCSEESHHHHHHHHHHHSSS--TTTTSEEEEEETTS-EEEEEE-SEEEEET CS
                   Chorismate_bind 155 lvstiegelkedvslldllkalfPtgavtGaPkkrameiidelEearRgvYaGavgyldadgeaelavvIRtavvkd 231
                                       + st++g+l+ d+++ld+++a++P+g+++GaPk ra++ii++lE  +Rg+Y+G +gy+d++g+++l+++IR a  k+
  gi|474934989|ref|YP_007688571.1| 368 IGSTVRGTLRRDKDALDAVSAILPAGTLSGAPKIRACQIINDLEDNKRGIYGGGIGYIDFSGNLDLCIAIRIAYKKN 444
                                       ***************************************************************************** PP

                                       TEEEEEEEEEEETT--HHHHHHHHHHH CS
                   Chorismate_bind 232 kelrlgaGaGIvadSdpeaEyeEtlaK 258
                                       +++ +++GaGIvadS p++E++E l+K
  gi|474934989|ref|YP_007688571.1| 445 GKVFIRSGAGIVADSVPDKEFDESLNK 471
                                       ************************998 PP

>> Anth_synt_I_N  Anthranilate synthase component I, N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.7   0.0   2.5e-34   2.2e-30       3     141 ..      32     167 ..      30     168 .. 0.92
   2 ?    0.1   0.0     0.096   8.6e+02      78      98 ..     405     425 ..     347     428 .. 0.78

  Alignments for each domain:
  == domain 1  score: 105.7 bits;  conditional E-value: 2.5e-34
                     Anth_synt_I_N   3 ltplsvylklaeee.hkflLeSaeneggegrySfigldpflelkskngevevegpegeeleeeepldalrellerfr 78 
                                        tp++v+++l   + h+f+LeSa++++++grySf+g++p++e+++ ng++ ++g   +e+++ +p   +r++l+++r
  gi|474934989|ref|YP_007688571.1|  32 RTPVEVMRALMNVDeHCFMLESADSSKKWGRYSFLGYAPKAEITCLNGSIVING---REHRTDDPAVDIRKILAEHR 105
                                       69********99889***************************************...67777777777********* PP

                     Anth_synt_I_N  79 saedseptelpfvgGlvGylgYDlvreie.klpksakddlnlpdarlilydtlivfDhkerrly 141
                                       s +   ++ +pf+gGlvGy++YD+ ++ e kl   akd+  + d++l+l+d+l+vfD+  +++ 
  gi|474934989|ref|YP_007688571.1| 106 SPK--VEGFPPFTGGLVGYFSYDYLKYAEpKLRLDAKDTEGFKDVDLMLFDKLVVFDNFAQKML 167
                                       664..48999**********************988888888******************99976 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.096
                     Anth_synt_I_N  78 rsaedseptelpfvgGlvGyl 98 
                                       ++++d e+++  ++gG +Gy+
  gi|474934989|ref|YP_007688571.1| 405 QIINDLEDNKRGIYGGGIGYI 425
                                       44444446666799******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (487 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.53
# Mc/sec: 2777.55
//
Query:       gi|474934990|ref|YP_007688572.1|  [L=196]
Description: anthranilate synthase, component II [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.8e-49  166.2   0.0    7.6e-49  166.1   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
    3.8e-10   39.9   0.0    6.7e-10   39.1   0.0    1.4  1  Peptidase_C26  Peptidase C26
  ------ inclusion threshold ------
      0.057   13.2   0.0       0.16   11.7   0.0    1.7  2  NETI           NETI protein


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.1   0.0   1.3e-52   7.6e-49       2     188 ..       4     186 ..       3     188 .. 0.95

  Alignments for each domain:
  == domain 1  score: 166.1 bits;  conditional E-value: 1.3e-52
                                       EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.TTTHHHHHHHHCTSTS-EEEE CS
                            GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.vegkieaikearenkiPiLGI 77 
                                       ++Dnyds+++nl + + +l  ++ vv++d+   + + + ++p++i++s+Gpg p+ ++ ++++i+ a    iPiLG+
  gi|474934990|ref|YP_007688572.1|   4 IVDNYDSFSYNLYQMVGSLYPDIRVVRNDTVTPQDI-MDMEPEAIIISPGPGRPEdAGICVDLIRAAGP-TIPILGV 78 
                                       89***************************9555554.589*************************9999.******* PP

                                       THHHHHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEE CS
                            GATase  78 CLGmQllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeel 154
                                       CLG+Q++++++g+k+  +k   +hg+++ ++  +  l++gl+++  ++++H+++++  ++ p++le + +++++ e+
  gi|474934990|ref|YP_007688572.1|  79 CLGHQAICLAYGGKITYAK-HLMHGKQSVVTLAKDPLFEGLPDREPVARYHSLAADG-DSIPQCLETISATDEG-EI 152
                                       *******************.9***********999*********************9.99*******9999777.9* PP

                                       EEEEEETTTEEEESSBTTSTTSTTHHHHHHHHHH CS
                            GATase 155 meiiekknpfvgvQFHPEststpegpellfnfli 188
                                       m+++++++p++g+QFHPEs++tp g+++l+nfl 
  gi|474934990|ref|YP_007688572.1| 153 MAVRHREYPIYGLQFHPESVMTPCGKTILRNFLK 186
                                       *******************************975 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.0   1.1e-13   6.7e-10     101     216 .]      68     170 ..      59     170 .. 0.84

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 1.1e-13
                     Peptidase_C26 101 alergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllaellgseeievnslHhqa 177
                                       a    +Pilg+C+G+q +  a+GG++  + +         +h    ++  v++ k+ l++ l    +  v+ +H+ a
  gi|474934990|ref|YP_007688572.1|  68 AAGPTIPILGVCLGHQAICLAYGGKITYAKH--------LMH---GKQSVVTLAKDPLFEGLPD--REPVARYHSLA 131
                                       456789******************9876544........333...344569999******9999..7789******* PP

                     Peptidase_C26 178 ike..laeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                        +   + + l+ ++ ++ g i a++++e  ++++g+Q+HPE
  gi|474934990|ref|YP_007688572.1| 132 ADGdsIPQCLETISATDEGEIMAVRHRE--YPIYGLQFHPE 170
                                       9865599999999999999999999998..78********9 PP

>> NETI  NETI protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       0.9   5.4e+03      40      55 ..     102     117 ..      98     118 .. 0.79
   2 ?   11.7   0.0   2.6e-05      0.16       6      51 ..     133     180 ..     131     183 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.9
                              NETI  40 gkkeiepvrqkIvFeg 55 
                                       gk++++++ ++  Feg
  gi|474934990|ref|YP_007688572.1| 102 GKQSVVTLAKDPLFEG 117
                                       6788888888888988 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 2.6e-05
                              NETI   6 eneTIedcLeRmkk..eG.YmPvrRiEkPvFkevkkngkkeiepvrqkI 51 
                                       ++++I +cLe + +  eG  m+vr +E P++   +   +  ++p+++ I
  gi|474934990|ref|YP_007688572.1| 133 DGDSIPQCLETISAtdEGeIMAVRHREYPIYGL-QFHPESVMTPCGKTI 180
                                       6789*******9753378689***********9.578888999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1401.34
//
Query:       gi|474934991|ref|YP_007688573.1|  [L=338]
Description: anthranilate phosphoribosyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.9e-94  314.4   0.0    2.7e-93  312.2   0.0    1.8  2  Glycos_transf_3  Glycosyl transferase family, a/b domain
    2.1e-19   69.1   2.9    4.4e-19   68.1   2.9    1.6  1  Glycos_trans_3N  Glycosyl transferase family, helical bundle 


Domain annotation for each model (and alignments):
>> Glycos_transf_3  Glycosyl transferase family, a/b domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1     0.069   6.2e+02     194     231 ..      32      69 ..      15      73 .. 0.66
   2 !  312.2   0.0     3e-97   2.7e-93       3     252 ..      76     325 ..      74     326 .. 0.99

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.069
                                       SSHHHHHHHHTTHHTSCHHHHHHHHHHHHHHHHHHHTT CS
                   Glycos_transf_3 194 gepkenaeilkavlegkksaakrdlvllnagaalvlag 231
                                        +p++na++l a+ ++++ a++ + ++  a+a+   a 
  gi|474934991|ref|YP_007688573.1|  32 TSPTQNAAFLAALTTKNTRAETEEEIAGCAAAMAAHAS 69 
                                       36788888888776666666556666666665555444 PP

  == domain 2  score: 312.2 bits;  conditional E-value: 3e-97
                                       TBEEEEESS-SSSTHHHHHHHHHHHHHHTT-BEEEEE-STCTTCS-HHHHHCTST--ST--HHHHHHHHHHHSEEEE CS
                   Glycos_transf_3   3 dlvDivgTGGdgantfNiStaaaivvAaaGvkvakhgnrsvssksGsaDvLealgvnleltpeeveklleevgvgfl 79 
                                       +++DivgTGGd +ntfNiSt++++v+Aa G+kvakhgnr++ss+sG+aD Lealgvnl++ pe++++ll++ g++f+
  gi|474934991|ref|YP_007688573.1|  76 KVLDIVGTGGDCSNTFNISTTSSFVIAASGTKVAKHGNRAASSSSGAADCLEALGVNLQQPPEKAASLLDDPGICFM 152
                                       789************************************************************************** PP

                                       EHHSSSSHHHHHHHHHHHHTT.-SSHHHCHHHHHT..SEEEEHHHHHHHHTCHSEEEEEEEESTTSSCCS.TSHHHH CS
                   Glycos_transf_3  80 fapeyhkamkhvapvrrelgirTvfnlLGPLinparvkkqllgvyskelaeklaevlkelgveralvvhg.dGldev 155
                                       fa+ yh++mk+vap+r+elg+rTvfn+LGPL+npar+ +q+lgvy+ +l+e+la+vl+ lgve+++vv g d +de+
  gi|474934991|ref|YP_007688573.1| 153 FAQIYHSSMKYVAPIRKELGFRTVFNILGPLTNPARPAYQVLGVYDRNLVEPLAHVLSSLGVEKGMVVYGeDRMDEL 229
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHTTEEEEEEEEEGSSTSSSEEESHHHHSSHHHHHHHHTTHHTSCHHHHHHHHHHHHHHHHHHHTTS CS
                   Glycos_transf_3 156 sllakttvaelkdgeiteytlepedfglkraelealeggepkenaeilkavlegkksaakrdlvllnagaalvlagk 232
                                       +  + t v + ++++ ++yt++pe++gl r+  ++l gg++ ena i  ++l+gk +   +d+vl+n +a l+++gk
  gi|474934991|ref|YP_007688573.1| 230 TCSSPTFVCDFENDDFRTYTVTPEELGLYRCLKSDLVGGDAAENASITLGILSGKGGPR-YDTVLVNSAAGLYVSGK 305
                                       *********************************************************96.***************** PP

                                       SSSHHHHHHHHHHHHHTSHH CS
                   Glycos_transf_3 233 adslkegvakaeevidsGkA 252
                                       a++lk+g++ a ++i +G A
  gi|474934991|ref|YP_007688573.1| 306 ASDLKDGIELADKLIGDGRA 325
                                       ******************99 PP

>> Glycos_trans_3N  Glycosyl transferase family, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.1   2.9   4.9e-23   4.4e-19       1      63 []       3      68 ..       3      68 .. 0.98

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 4.9e-23
                                      HHHHHHHHTT.---HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH-...--HHHHHHHHHHHHHHS CS
                   Glycos_trans_3N  1 kdiikklrdgeeLtaeeirfaihgilkgevtdaqiaAfLmAlrlkG...etaeEiaalaeAmresg 63
                                      k++i+kl+++++Lt++e++ ++++i++g  ++ q aAfL+Al +k    et+eEia++a Am +++
  gi|474934991|ref|YP_007688573.1|  3 KEAIIKLVNKQDLTYDEAYSVMSEIMDGATSPTQNAAFLAALTTKNtraETEEEIAGCAAAMAAHA 68
                                      589************************************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2238.29
//
Query:       gi|474934992|ref|YP_007688574.1|  [L=263]
Description: Indole-3-glycerol phosphate synthase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-81  273.5   0.1    1.5e-81  273.3   0.1    1.0  1  IGPS          Indole-3-glycerol phosphate synthase
    0.00015   21.0   0.1     0.0006   19.1   0.1    1.8  2  NanE          Putative N-acetylmannosamine-6-phosphate epimer
     0.0074   15.8   0.1      0.038   13.4   0.0    1.9  2  His_biosynth  Histidine biosynthesis protein
  ------ inclusion threshold ------
      0.016   15.0   0.6      0.028   14.2   0.1    1.6  2  QRPTase_C     Quinolinate phosphoribosyl transferase, C-termi


Domain annotation for each model (and alignments):
>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  273.3   0.1   3.4e-85   1.5e-81       4     254 .]       9     259 ..       6     259 .. 0.92

  Alignments for each domain:
  == domain 1  score: 273.3 bits;  conditional E-value: 3.4e-85
                                       CHHHHHHHHHHHHCCS-GGCCCCG....-SS-SS-HHHHCHCHTTS-EEEEEE-SEETTTEESBSS--HHHHHHHHT CS
                              IGPS   4 ivaekkeevaeakkrqsladleaav..klakpkrsfaeaLresekklaliaEvKkaSPskgliredfdpaeiAkkye 78 
                                       ++++ k++v++ +k +s  ++ + +  ++ +    f +aL++  + +++i EvK+aSPskg+i+edf + +iA++ye
  gi|474934992|ref|YP_007688574.1|   9 LADTAKIRVQNSRKLVSPMEMSHLAtrMECDTGFPFEKALAR--DGMQFICEVKRASPSKGVIAEDFPYLDIAREYE 83 
                                       566677778777777665555555522355555667788887..********************************* PP

                                       TT.-SEEEEE--CCCC---CCHHHHHHHH-SS-EEEES---SHHHHHHHHHCT-SEEEEECCCS-HHHHHHHHHHHC CS
                              IGPS  79 eagAsaiSVLteekyFqGsledLrevrqavslpvlrKdFiideyqieearalgadaiLLivkvledeeleelaeaak 155
                                       +agA+aiSVLte++ F G+  +L+e+++ vs+p lrKdFi+dey+i+ea++lga a+LLi ++l+++ l+++ + a+
  gi|474934992|ref|YP_007688574.1|  84 AAGAAAISVLTEPSRFLGEGRFLKEISADVSVPCLRKDFIVDEYMIYEAKTLGASAVLLICAILNKDDLARFINIAH 160
                                       ***************************************************************************** PP

                                       CTT-EEEEEESSHHHHHHHHHTT-SEEEEESEETTTTEE-CHHHHHHCHCC-TTSEEEEESSS-SHHHHHHHCCTT- CS
                              IGPS 156 slglevLvEvhdeeeleralklgakiiGvNnRnLktlevdlntteeLaklvpkdvllvaeSGiktredveklkeegv 232
                                       +lg+ +L Ev +++e+  a+++ga++iGvNnR+L++++v+l+t+  L+ lvpk++l vaeSGi++redve+l+++gv
  gi|474934992|ref|YP_007688574.1| 161 RLGMSALCEVRTASEIRMAVEAGARVIGVNNRDLTDFSVNLETSIILRRLVPKHILFVAESGISSREDVEALEKAGV 237
                                       ***************************************************************************** PP

                                       SEEEESHHHHC-TTHHHHHHHH CS
                              IGPS 233 nafLvGeslmrqedvekairel 254
                                       +a+L+Ge+lmr++d++++++el
  gi|474934992|ref|YP_007688574.1| 238 DAVLIGETLMRSDDKKAKLAEL 259
                                       ****************999886 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.24   1.1e+03     132     158 ..      40      66 ..      31      73 .. 0.81
   2 !   19.1   0.1   1.3e-07    0.0006      80     180 ..     151     250 ..     132     258 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.24
                                       --HHHHHHHHHTT--EEEES---SHHH CS
                              NanE 132 pDfalvkalseaglkviaeGrintPek 158
                                         f + kal  +g++ i e +  +P k
  gi|474934992|ref|YP_007688574.1|  40 TGFPFEKALARDGMQFICEVKRASPSK 66 
                                       4577789999999******99999987 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 1.3e-07
                                       -HHHHHHHHHHH--EEEEE-SSHHHHHHHHHTT-SEEE-TTTTSSTTS-.SS--HHHHHHHHHTT--EEEES---SH CS
                              NanE  80 tieelikkikekyqllmaDistleeglvakklGvdivGttlsGytkeeekaepDfalvkalseaglkviaeGrintP 156
                                       +++++i+  ++ ++ +++++ t  e  +a ++G+ ++G      t+ + + e  + +++ l+ + +  +ae  i + 
  gi|474934992|ref|YP_007688574.1| 151 DLARFINIAHRLGMSALCEVRTASEIRMAVEAGARVIGVNNRDLTDFSVNLETSI-ILRRLVPKHILFVAESGISSR 226
                                       5678899999999*********************************999988765.7899***************** PP

                                       HHHHHHHTT--SEEEE-HHHH-HH CS
                              NanE 157 ekakkaieiGvdavvvGsaitrle 180
                                       e  +   + Gvdav +G  + r +
  gi|474934992|ref|YP_007688574.1| 227 EDVEALEKAGVDAVLIGETLMRSD 250
                                       ********************9976 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.48   2.1e+03      32      48 ..      76      92 ..      65      94 .. 0.73
   2 !   13.4   0.0   8.6e-06     0.038     192     224 ..     215     247 ..     197     252 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.48
                                      HHHHHHHHHHT-SEEEE CS
                      His_biosynth 32 velakryeeegadelhv 48
                                      +++a++ye++ga  + v
  gi|474934992|ref|YP_007688574.1| 76 LDIAREYEAAGAAAISV 92
                                      56788888888877766 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 8.6e-06
                                       SEEEEESS--SHHHHHHHHHTTCSEEEESHHHH CS
                      His_biosynth 192 ipviasGGvgsledlkelksegvdavivgsaly 224
                                       i ++a  G++s ed+++l+++gvdav++g+ l 
  gi|474934992|ref|YP_007688574.1| 215 ILFVAESGISSREDVEALEKAGVDAVLIGETLM 247
                                       556677788888888888888888888887765 PP

>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.91   4.1e+03       5      25 ..       2      23 ..       1      27 [. 0.78
   2 ?   14.2   0.1   6.2e-06     0.028      84     157 ..     167     245 ..     151     251 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.91
                                      HHHHHHHHHCT.SSEEEE-S-- CS
                         QRPTase_C  5 tarmveaaksa.kvrildTRkt 25
                                      t+++ +a++++ k+r+ + Rk 
  gi|474934992|ref|YP_007688574.1|  2 TSNILKALADTaKIRVQNSRKL 23
                                      7778888888779999999985 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 6.2e-06
                                       EEEESSHHHHHHHHHHT-SEEEEES--HHHHHHHHHHH...HHHSTT..SEEEEESS--TTTHHHHHCTT-SEEEEC CS
                         QRPTase_C  84 evevesleeleevleaeadiimLDnfsveelkkaveel...keknkr..vlievSGgvtlenveeyaksgvdvisvg 155
                                         ev++  e++ ++ea+a +i + n + +++   +e+    ++  ++  + +  SG  + e+ve++ k gvd++ +g
  gi|474934992|ref|YP_007688574.1| 167 LCEVRTASEIRMAVEAGARVIGVNNRDLTDFSVNLETSiilRRLVPKhiLFVAESGISSREDVEALEKAGVDAVLIG 243
                                       5799**********************9999988877432225555555455556888899*************9998 PP

                                       HH CS
                         QRPTase_C 156 al 157
                                         
  gi|474934992|ref|YP_007688574.1| 244 ET 245
                                       65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 2064.55
//
Query:       gi|474934993|ref|YP_007688575.1|  [L=199]
Description: Phosphoribosylanthranilate isomerase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-46  159.0   0.0    1.3e-46  158.8   0.0    1.0  1  PRAI      N-(5'phosphoribosyl)anthranilate (PRA) isomerase


Domain annotation for each model (and alignments):
>> PRAI  N-(5'phosphoribosyl)anthranilate (PRA) isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.8   0.0   7.4e-51   1.3e-46       1     193 [.       4     188 ..       4     189 .. 0.91

  Alignments for each domain:
  == domain 1  score: 158.8 bits;  conditional E-value: 7.4e-51
                                       TCE----SHHHHHHHHHHTSSEEEEE--TTBTTB--HHHHHHHCCCS--E..EEEEESSS-HHHHHHHHHHCTECEE CS
                              PRAI   1 akicgltrasdvkaavkagadelglifaesskrevseeqaqellekvpak..lVGVfvNqpieevlriaqelgldvv 75 
                                       +kicgl+r +d+      gad+ g++f + s+r vs+  a+ ++ +  ++   VGVfv++++  +++ia++  + +v
  gi|474934993|ref|YP_007688575.1|   4 VKICGLRRREDAEYCNRYGADYAGFVFWKGSRRFVSPAAAKDVSDNLLPRivPVGVFVDEDVRVISSIADSGTIRMV 80 
                                       69*******************************************999886789*********************** PP

                                       EE-CGG.-HHHHHHHHHHS..-TTSEEEEEEE-SSS--S-SSTT-SEEEEESSS-SSSXXXXGGGGTTSXX.TTEEE CS
                              PRAI  76 QLHGdedeqeyeellktel..pvikalkvaesvdevkearradhvdllllDsgaGGtGelldwsliskllkslkviL 150
                                       QLHGde +qey++ll++++  p+i+a+++         ++r  h+d  ++D gaG  G+++dws+++++    +++L
  gi|474934993|ref|YP_007688575.1|  81 QLHGDE-DQEYIDLLRENVniPIIRAYRPG--------CSRRFHADYSMFDGGAG-DGKTFDWSSLKDVH--GPFFL 145
                                       ******.*********76511344444433........345555599*****988.**************..6**** PP

                                       ESSXXTTTHHHHHT.TXXSEEEEXGGGEEETEEXHHHHHHHHH CS
                              PRAI 151 AGGLtpeNvaeaiklegvlgvDvssGVEtnGvkDlekirkfvq 193
                                       AGGL++eNv +ai++ ++++vDvs GVEt+G kD ekir f++
  gi|474934993|ref|YP_007688575.1| 146 AGGLSAENVPDAIRTLRPFAVDVSTGVETDGYKDPEKIRLFIE 188
                                       *****************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1515.75
//
Query:       gi|474934994|ref|YP_007688576.1|  [L=396]
Description: tryptophan synthase, beta subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-43  149.5   1.2    1.6e-43  149.2   1.2    1.1  1  PALP      Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.2   1.2   9.1e-48   1.6e-43       3     294 .]      51     377 ..      49     377 .. 0.83

  Alignments for each domain:
  == domain 1  score: 149.2 bits;  conditional E-value: 9.1e-48
                                       GCSSS--EEEECCTCCCCCCE.EEEEEGGGSTTSBTTHHHHH.HHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHH CS
                              PALP   3 lgigpTPlvrlprlskelgvp.lflKlEslnptgSfKdRgae.yllarlkegtgaktvveassGNhgralAaaaall 77 
                                       ++ +p++l  ++++++elg++ ++lK+E+ln+tg++K++ +   +l++ k g +++ ++e+++G+hg+a+A aaall
  gi|474934994|ref|YP_007688576.1|  51 YANRPSRLYFAKKMTEELGGAkIYLKREDLNHTGAHKINNVLgQALLAKKMG-KTRLIAETGAGQHGVATATAAALL 126
                                       678999***********************************96666666777.************************ PP

                                       T-EEEEEEETTS-...HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHH......STTCEE--TTT.....SHHHH CS
                              PALP  78 Glkvtivvpadas...pekvallrllGaevvevggdydeavaaaaelaae......gegaylvsqfd.....nptvi 140
                                       G+++ +++   +    + +v ++rllGae++ v++++ + ++a+ +  +e      +   +++  +       pt++
  gi|474934994|ref|YP_007688576.1| 127 GMECLVYMGVEDMerqKLNVYRMRLLGAEIRGVPTGTGTLKDAVSQCMREwtsrisD--THYCLGSVmgphpFPTIV 201
                                       *******9988884555999*************877777777766666664444542..322222224464446688 PP

                                       HH.HHTHHHHHHHHTT....TTEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEEC....TTCGGTTCCS..S.S CS
                              PALP 141 eg.ygtiglEileqlg....gkpdavvvpvGgGgliaGiaaglkerrpdvrvigvepe....gsdalarslragrrv 208
                                          ++ ig Ei eq+     + pd ++++vGgG+++ G+   + + + +v+++g+e++      +  a+++ +g++ 
  gi|474934994|ref|YP_007688576.1| 202 RDfQSVIGKEIREQIMekegRLPDMLIACVGGGSNAIGTFYDFIK-DEEVELVGAEAAgkgvDTPLTAATMNTGSVG 277
                                       878********955555555************************7.6679*******98844344444444444444 PP

                                       S..B................SSS.CCSTCSCGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHH CS
                              PALP 209 tvpvs...............dtiadglavgspselafelldrlvdeivtvsdeealeamrllarregivvepssaaa 270
                                         + +                +i  gl+ +  ++++  l+d    ++v+++deea++a + + r egi++   s +a
  gi|474934994|ref|YP_007688576.1| 278 IFHGMksyfcqdkygqiapvYSISAGLDYPGIGPEHAHLADIGRAKYVAITDEEAVQAFEYVSRCEGIIPAIESSHA 354
                                       444448888888888888879******************************************************** PP

                                       HHHHHHHHHHCCTTCEEEEEEE-B CS
                              PALP 271 laalklreagelkegdrvvviltg 294
                                       la + ++ a  ++++  +vv ++g
  gi|474934994|ref|YP_007688576.1| 355 LAYA-MKVAPTMGKDRIIVVTVSG 377
                                       ****.**********999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 2344.75
//
Query:       gi|474934995|ref|YP_007688577.1|  [L=258]
Description: tryptophan synthase, alpha chain [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-87  292.1   0.1    2.9e-87  291.8   0.1    1.0  1  Trp_syntA     Tryptophan synthase alpha chain
     0.0014   18.1   0.2      0.059   12.8   0.1    2.4  3  PcrB          PcrB family
     0.0091   15.5   0.1      0.031   13.7   0.1    1.8  3  His_biosynth  Histidine biosynthesis protein
  ------ inclusion threshold ------
      0.092   12.2   0.2       0.26   10.7   0.1    1.7  2  BtpA          BtpA family


Domain annotation for each model (and alignments):
>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  291.8   0.1   6.5e-91   2.9e-87       9     242 ..      11     242 ..       5     256 .. 0.95

  Alignments for each domain:
  == domain 1  score: 291.8 bits;  conditional E-value: 6.5e-91
                                       B-EEEEEEETTSS-HHHHHHHHHHHHHCT-SSEEEE---S--TTS-HHHHHHHHCCCCTT--HHHHHHHHHHHHHHC CS
                         Trp_syntA   9 raafvpyvtagdpdleqsleilkalekagadviElGlpfsdPladGPvIqaanlraLakgvtlekvlelveevrkke 85 
                                        +af+++vt gdpdle++  +++a++++gad+iElG+pfsdP a+GPvI  a++raL+ gvt+++++ + +e+r k+
  gi|474934995|ref|YP_007688577.1|  11 GKAFIAFVTCGDPDLETTGRVVRAMAENGADLIELGIPFSDPTAEGPVIMDADKRALDGGVTTDDIFAFTKEIR-KT 86 
                                       68************************************************************************.** PP

                                       SSS-EEEEE-CHHHCCC-HHHHCHHHHHCTEEEEEETTSBCCCHHHHHHHHHHTT-EEEEEE-TTS-HHHHHHHHHH CS
                         Trp_syntA  86 vevPivlltylnlvlsygeerflaelkeagvdglivpDlPleeaeelveaakkkglelvflvapttsderlkevveq 162
                                       v+vP+v +ty+n+v++yg e+f+ ++ +agv g+i+pD+P ee++e+ ++++++gl+l+++vap ts++r+++++++
  gi|474934995|ref|YP_007688577.1|  87 VTVPMVYMTYANVVFHYGAEEFCSRASDAGVSGIILPDVPFEEKAEFESVCDRYGLDLISMVAP-TSEDRISKIASE 162
                                       ****************************************************************.9999******** PP

                                       --S-EEEESTTC-SSTTSSB-TTHHHHHHHHHHCTSS-EEEESSS-SHHHHHHHHTT-SEEEE-HHHHHHHHCTTTS CS
                         Trp_syntA 163 aegfvYvvsraGvTgaenavaaevdelverlkkltavPvavGFGistkeqvkqvakvadGvivGSalvkkieeeaee 239
                                       a+gfvY+vs+ GvTg+++++++++  +ve +++ t+ P avGFGis++eq +++a+v+dG+ivGSa+v++++++ ++
  gi|474934995|ref|YP_007688577.1| 163 AKGFVYIVSSLGVTGTRSSITTDIGPMVELIRRSTEIPCAVGFGISNPEQCQRMASVSDGAIVGSAIVRIVAQHGKD 239
                                       ************************************************************************88776 PP

                                       HHH CS
                         Trp_syntA 240 keq 242
                                       ++ 
  gi|474934995|ref|YP_007688577.1| 240 SAG 242
                                       654 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.018        81       8      37 ..      17      46 ..      11      54 .. 0.90
   2 ?   -2.7   0.0      0.74   3.3e+03     139     161 ..      74      96 ..      68     106 .. 0.53
   3 !   12.8   0.1   1.3e-05     0.059     162     211 ..     180     229 ..     155     237 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.018
                                      EEEEE-TTSS-CHHHHHHHHCTT-SEEEEE CS
                              PcrB  8 hltklDPeeenpdEiveiviesgtDavmig 37
                                      ++t  DP+ e++  +v++++e+g+D + +g
  gi|474934995|ref|YP_007688577.1| 17 FVTCGDPDLETTGRVVRAMAENGADLIELG 46
                                      68888********************88665 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.74
                                       HHHHHHHHHHHHHTT-SEEEEE- CS
                              PcrB 139 ediaayallaakllglrliYlEa 161
                                       +di a+     k + ++++Y+ +
  gi|474934995|ref|YP_007688577.1|  74 DDIFAFTKEIRKTVTVPMVYMTY 96 
                                       34444444444444445555444 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 1.3e-05
                                       TTSSS-HHHHHHHHHHHSSSEEEEESS--SHHHHHHHHCCSSEEEE-CHH CS
                              PcrB 162 sGaledveevialkkklekarlivGGGirsaEkAkevveaADvivvGnvv 211
                                       s ++ d+  +++l ++ +++   vG Gi ++E+ ++++   D  +vG ++
  gi|474934995|ref|YP_007688577.1| 180 SSITTDIGPMVELIRRSTEIPCAVGFGISNPEQCQRMASVSDGAIVGSAI 229
                                       556677888999***********************************987 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       1.3   5.7e+03     181     194 ..      78      91 ..      58      94 .. 0.67
   2 ?   -2.9   0.0      0.85   3.8e+03     150     169 ..     106     125 ..     101     142 .. 0.67
   3 !   13.7   0.1   6.9e-06     0.031      63     107 ..     188     231 ..     168     236 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHSSEE CS
                      His_biosynth 181 eltkelaeavkipv 194
                                        +tke++++v++p+
  gi|474934995|ref|YP_007688577.1|  78 AFTKEIRKTVTVPM 91 
                                       45677777777766 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.85
                                       HHHHHHHHHTT-SEEEEEET CS
                      His_biosynth 150 velakkleelgageilltdi 169
                                       +e+ ++++++g++ i+l d+
  gi|474934995|ref|YP_007688577.1| 106 EEFCSRASDAGVSGIILPDV 125
                                       56666666667777766655 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 6.9e-06
                                       HHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH CS
                      His_biosynth  63 dlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavk 107
                                        +ve i+++++ip+ vG GI++ e+ +++ +   d  i+g+a v+
  gi|474934995|ref|YP_007688577.1| 188 PMVELIRRSTEIPCAVGFGISNPEQCQRMASV-SDGAIVGSAIVR 231
                                       789999**********************9998.899999999875 PP

>> BtpA  BtpA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.34   1.5e+03      36      63 ..     110     134 ..      94     138 .. 0.74
   2 ?   10.7   0.1   5.8e-05      0.26     175     232 ..     172     231 ..     147     248 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.34
                              BtpA  36 kaleegGvDavilenygdaPflkevdpe 63 
                                       +   ++Gv ++il    d Pf  +++ e
  gi|474934995|ref|YP_007688577.1| 110 SRASDAGVSGIILP---DVPFEEKAEFE 134
                                       56689999999985...77888877655 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 5.8e-05
                              BtpA 175 avilsGkatGgevdlee.lklaketvkvkvlvgsGvse.enlekllsiadGvivgtsikk 232
                                       ++ ++G ++  ++d+   ++l+++  +++  vg G+s+ e  +++ s++dG ivg+ i +
  gi|474934995|ref|YP_007688577.1| 172 SLGVTGTRSSITTDIGPmVELIRRSTEIPCAVGFGISNpEQCQRMASVSDGAIVGSAIVR 231
                                       566889999999999752678888999********975388999************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1574.96
//
Query:       gi|474934996|ref|YP_007688578.1|  [L=208]
Description: LSU ribosomal protein L15E [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-73  247.1  10.6    1.2e-73  246.9  10.6    1.0  1  Ribosomal_L15e  Ribosomal L15
  ------ inclusion threshold ------
        8.2    6.7   9.2         34    4.7   4.7    2.4  2  Mitoc_mL59      Mitochondrial ribosomal protein mL59


Domain annotation for each model (and alignments):
>> Ribosomal_L15e  Ribosomal L15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  246.9  10.6   1.3e-77   1.2e-73       1     190 [.      16     202 ..      16     203 .. 0.98

  Alignments for each domain:
  == domain 1  score: 246.9 bits;  conditional E-value: 1.3e-77
                                       -SHHHHHHHTTSTTSHHHHHHHHHHHHHHTTS-SEEEESS-SSHHHHHHHT--SSTTEEEEEEEEE-SS---..--- CS
                    Ribosomal_L15e   1 gaykylrelwkkkqsdvlrellrerlweyrqepavvrverptrldrArrLGYkakqGivvvrvrvrrGgrkkkvskg 77 
                                       ++y+y++e+w + +++++++l  er +++r+e+++ r+e+ptrldrAr++GYkakqG+v+vr++vrrGg +k  +k+
  gi|474934996|ref|YP_007688578.1|  16 SMYRYIAEAWADADNTYVKALNYERRIQWRKEENFLRIEKPTRLDRARAVGYKAKQGYVLVRAKVRRGGLRK--RKI 90 
                                       79**********************************************************************..*** PP

                                       SS---GGGG-SSS---SS-HHHHHHHHHHHHSTTSEEEEEEEEEEESSEEEEEEEEE-TTSHHHHT-TTTGGGGSGG CS
                    Ribosomal_L15e  78 ktgrkpkrqgvnklkpakslqaiaeervgrklpnlrvLnSYwvgeDgtykyyEvilvDpshkairndkkinwickkv 154
                                       ++gr++kr+  +++   kslq+iaeer++++++nl+vLnSYwvg Dg++ +yEvilvDp++++i +dkki wi++++
  gi|474934996|ref|YP_007688578.1|  91 NAGRRAKRKVEQQQIVGKSLQRIAEERAQKRYQNLEVLNSYWVGADGQHEWYEVILVDPACPVIMHDKKIGWIANNK 167
                                       ***************************************************************************** PP

                                       GTTGGGGT-SHHHHHHTT-S-SS.TT-TTTSS-TGG CS
                    Ribosomal_L15e 155 hkhRelrGltsagkksRGlrkkglkgaekirgsrra 190
                                       hk+R++rGlt+ag+k+RGl +kg +g ek+r+s  a
  gi|474934996|ref|YP_007688578.1| 168 HKNRVYRGLTAAGNKGRGLLNKG-HGGEKVRPSAAA 202
                                       ***********************.777888999877 PP

>> Mitoc_mL59  Mitochondrial ribosomal protein mL59
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   4.7    0.0038        34      78     118 ..      87     126 ..       3     131 .. 0.84
   2 ?    4.3   0.1    0.0053        48      75     109 ..     166     200 ..     163     206 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0038
                        Mitoc_mL59  78 eraverglrvkgtagkkkmfkGhkwERtkeerlekrrkale 118
                                       +r++++g r+k++  ++++  G+  +R +eer++kr ++le
  gi|474934996|ref|YP_007688578.1|  87 KRKINAGRRAKRK-VEQQQIVGKSLQRIAEERAQKRYQNLE 126
                                       3455666666666.7788888****************9998 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0053
                        Mitoc_mL59  75 fkeeraverglrvkgtagkkkmfkGhkwERtkeer 109
                                        k++++v rgl++ g++g++   kGh  E+ +++ 
  gi|474934996|ref|YP_007688578.1| 166 NKHKNRVYRGLTAAGNKGRGLLNKGHGGEKVRPSA 200
                                       678899999********************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       858  (0.0478554); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1237.21
//
Query:       gi|474934997|ref|YP_007688579.1|  [L=246]
Description: hypothetical protein TALC_01442 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-41  141.3   0.0    4.3e-41  141.1   0.0    1.0  1  DUF169    Uncharacterised ArCR, COG2043


Domain annotation for each model (and alignments):
>> DUF169  Uncharacterised ArCR, COG2043
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.1   0.0   2.4e-45   4.3e-41       2     204 ..       4     225 ..       3     227 .. 0.91

  Alignments for each domain:
  == domain 1  score: 141.1 bits;  conditional E-value: 2.4e-45
                            DUF169   2 LaealrlktePVavkfsdekpe.lpekke.kieekkrlCqmvalara..kgktvvftaetlgCpgGaaalGf..... 69 
                                       L+++l+lk ePVa++ +d+ pe      + +     ++C+   l +a  kg+ ++++ e++gC+g  ++lGf     
  gi|474934997|ref|YP_007688579.1|   4 LKDLLQLKCEPVAIYRADSIPEdA--HVGgE-----HCCIPPLLLMAakKGRRAATDMEHIGCHGSVSGLGFgkinl 73 
                                       899******************933..33313.....7888777666677**************************** PP

                            DUF169  70 ..............kelpeklksgegylkspeaakkfveslprleagevkyvvvapLekaefe...Pdvvvffanpe 129
                                                     ++++++  +g++ +++pe+a +++++++ +e+g+  ++v++pL++a++    ++vvvf+a+p 
  gi|474934997|ref|YP_007688579.1|  74 qkmswsystvpkevMDSHPRQGDGKHEFCCPEVALAHFSRTKEYEEGG--AIVFEPLDRAKERgadIEVVVFLADPV 148
                                       *****9988887654556666777*****************9887766..************9************** PP

                            DUF169 130 qlmrLvqlalydrgggrlnvsfpgngaaCadivaypykegepn.....iglgdpgarkfaklkddelafgiPyelle 201
                                       ++++L+ la ++r +g ++v++   g aC++i ++p +ege++     +g++d+ ar+f  + +de++f++Py+l++
  gi|474934997|ref|YP_007688579.1| 149 RISALSILAGFERMDGSDPVKIVH-GLACQQIYVMPKAEGEKEnpcaiLGFTDLYARRF--IGRDEFSFSVPYRLYK 222
                                       ***********************9.**********************************..**************** PP

                            DUF169 202 emv 204
                                       +m+
  gi|474934997|ref|YP_007688579.1| 223 QME 225
                                       *97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1498.96
//
Query:       gi|474934998|ref|YP_007688580.1|  [L=285]
Description: Thiamine biosynthesis ATP pyrophosphatase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-24   84.7   0.1      9e-24   84.2   0.1    1.2  1  THUMP     THUMP domain
  ------ inclusion threshold ------
      0.023   14.3   0.0        1.6    8.3   0.0    2.3  2  ThiI      Thiamine biosynthesis protein (ThiI)
       0.18   12.0   0.1       0.35   11.1   0.1    1.5  1  Mtf2_C    Polycomb-like MTF2 factor 2


Domain annotation for each model (and alignments):
>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.2   0.1   1.5e-27     9e-24       6     141 ..      33     161 ..      28     163 .. 0.93

  Alignments for each domain:
  == domain 1  score: 84.2 bits;  conditional E-value: 1.5e-27
                                       HHHHTT.H-SEEEEETTEEEEECTEEEEEETHHHHHHHHHTSTTECEEEEEEEEEESSHHHHHHHHHHHHHHHHHHC CS
                             THUMP   6 llkegkvnverveagkgrivvelkgekpeedeellkealekargiqrvipvcevceadledileaakeivkkkfeee 82 
                                       +l   +v+++++++ + r+++  +      d  ++ + + k++g+ +++++ e+ce +++di +++ e+ k ++ ++
  gi|474934998|ref|YP_007688580.1|  33 MLAADGVEALVERG-DSRFFIQAS------DLDAAVRSCRKVFGVASISIA-ETCEPNIDDICASVAEYSKSRMVKG 101
                                       56667778776666.689999999......99*******************.************************9 PP

                                       T-EEEEEEEESSSTSSSHHHHHHHHHHHHHHCCTT...-EE-SSS-SEEEEEEEETTEEEEE CS
                             THUMP  83 ketFaVrvkrrgkhfeftsreinrevGkaivektg...lkVdlenPdivvrveiikdkayis 141
                                       k +FaV+++r g++ +fts+e+++  G+ai+++     +kVdl+nPd+++ +e++ ++ayi+
  gi|474934998|ref|YP_007688580.1| 102 K-SFAVKARRAGNQ-KFTSMEVAKLAGDAIWNANLdkdPKVDLTNPDVRFYIEVRPRRAYIF 161
                                       8.************.*****************999*************************97 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0   0.00027       1.6      18      31 ..     190     203 ..     174     209 .. 0.71
   2 ?    3.6   0.0    0.0073        44     116     157 ..     231     273 ..     225     281 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00027
                              ThiI  18 VaaylllkRGcrvv 31 
                                        +a++++kRGc+v 
  gi|474934998|ref|YP_007688580.1| 190 LSAWMMMKRGCKVY 203
                                       689*********96 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.0073
                              ThiI 116 esLgqVaSqtleNlrvisavv.nllilrPLigldKeeiiklAk 157
                                       ++Lg V   t++ +   + +  +l+++ P ig+   e+  +  
  gi|474934998|ref|YP_007688580.1| 231 KNLGYVKGWTIDDILGFDPAEyDLPVFMPTIGMTDGEVESMLA 273
                                       589999999**99999887766***********9988877655 PP

>> Mtf2_C  Polycomb-like MTF2 factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   5.8e-05      0.35       2      33 ..      83     112 ..      82     115 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.8e-05
                            Mtf2_C   2 ledLkssvnkYFGaanRiasGEkfavlAkRvt 33 
                                       ++d+ +sv++Y     R+  G +fav+A+R +
  gi|474934998|ref|YP_007688580.1|  83 IDDICASVAEY--SKSRMVKGKSFAVKARRAG 112
                                       57888899999..789**************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 1620.45
//
Query:       gi|474934999|ref|YP_007688581.1|  [L=273]
Description: putative permease [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-43  149.1  33.7    1.9e-43  148.8  33.7    1.0  1  TauE          Sulfite exporter TauE/SafE
  ------ inclusion threshold ------
       0.15   11.9   0.2       0.15   11.9   0.2    3.2  3  Trp_oprn_chp  Tryptophan-associated transmembrane protein (Tr
       0.42   10.4   4.4       0.75    9.6   0.6    2.6  2  DDDD          Putative mitochondrial precursor protein
        4.9    7.1  22.8       0.12   12.2   2.3    3.4  3  DUF3487       Protein of unknown function (DUF3487)


Domain annotation for each model (and alignments):
>> TauE  Sulfite exporter TauE/SafE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.8  33.7   4.2e-47   1.9e-43       2     235 ..      10     264 ..       9     265 .. 0.91

  Alignments for each domain:
  == domain 1  score: 148.8 bits;  conditional E-value: 4.2e-47
                              TauE   2 llagllaGfvagllGiGggliavPlLll.l.lppavavatsllavvatslsgalahrrrgnvdwrlllllllgsliG 76 
                                       l++++ aG++++l+G+Ggg+i++P+L++ + l++ +ava+sl+ +vats+++a+ +  rg  ++rl+++l + + +G
  gi|474934999|ref|YP_007688581.1|  10 LVIAVGAGIIGALFGLGGGIIFIPVLTIlFdLSATEAVAASLVGIVATSTGSAYHYVNRGLSNIRLGMMLEITTSVG 86 
                                       678999**********************66879999************************9**************** PP

                              TauE  77 allGallllllpsellkllfgvlllllallmllrkkr...................srak..grerrptaillvlig 132
                                       a++Ga ++ +l + +l+++f++++l++++ m++++++                      +   r + ++  + +++ 
  gi|474934999|ref|YP_007688581.1|  87 AIIGAAVAVYLENWILLAIFACVMLYSGFKMAVSPEKtvssgpsgesemsfsyedaV--EgeVRYTVQNTGGGMAVS 161
                                       *******************************99887788999998888888766542..153444455555555555 PP

                              TauE 133 glvGllsGllGiGgGfllvpllllllglplkkavatslllilvislagalgyalagavdwpllllllpgallGallG 209
                                        ++G++s+++G+GgG++ vp++ + +++p+k a ats+ +i +++++ga++y++ g v +++++++++ga +Ga++G
  gi|474934999|ref|YP_007688581.1| 162 TIAGMVSSMTGVGGGSIKVPIMNIYMHVPIKAASATSSYMIGITAFSGAVIYFIEGVVLLDVAAAVAVGAYIGAMIG 238
                                       66*************************************************************************** PP

                              TauE 210 arlarrlsertlrrlfallllvlgvk 235
                                       +r+a+r+s++ ++r++ ++ +++++ 
  gi|474934999|ref|YP_007688581.1| 239 SRIATRVSTASIKRCMPAVYFCIAAI 264
                                       ****************9999999875 PP

>> Trp_oprn_chp  Tryptophan-associated transmembrane protein (Trp_oprn_chp)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   4.1    0.0035        16      59     134 ..       8      95 ..       4      97 .. 0.64
   2 ?   11.9   0.2   3.3e-05      0.15      52     134 ..      88     173 ..      77     176 .. 0.84
   3 ?    0.7   2.2     0.087   3.9e+02      82      98 ..     213     229 ..     188     273 .] 0.45

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0035
                      Trp_oprn_chp  59 vlavrglgrrvvgvllalagagaavaalslltdpadaaraaaaaatgvasaaaave..lta...........wpvla 122
                                       +l+v  +g  ++g+l  l g ++ +++l++l d +++++ aa+ ++ va+++ ++   + +             + +
  gi|474934999|ref|YP_007688581.1|   8 ALLVIAVGAGIIGALFGLGGGIIFIPVLTILFDLSATEAVAASLVGIVATSTGSAYhyV-NrglsnirlgmmLEITT 83 
                                       5667778889***********************88888888744444443333333351.14555588855544444 PP

                      Trp_oprn_chp 123 laggvllllagv 134
                                        +g+++ ++ +v
  gi|474934999|ref|YP_007688581.1|  84 SVGAIIGAAVAV 95 
                                       444444444444 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 3.3e-05
                      Trp_oprn_chp  52 llAaavAvlavrglgrrvvgvllalagagaavaalslltdpadaaraaaaaatgvasaaaavelta...wpvlalag 125
                                       ++ aavAv++ + +++ +++ +++ +g+ +av++ + ++++++ + + + + +++ +++ ++++ +   +++++ ++
  gi|474934999|ref|YP_007688581.1|  88 IIGAAVAVYLENWILLAIFACVMLYSGFKMAVSPEKTVSSGPSGESEMSFSYEDAVEGEVRYTVQNtggGMAVSTIA 164
                                       56799999999999****************************99999996667777777777743345699999999 PP

                      Trp_oprn_chp 126 gvllllagv 134
                                       g++  ++gv
  gi|474934999|ref|YP_007688581.1| 165 GMVSSMTGV 173
                                       999888887 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.087
                      Trp_oprn_chp  82 avaalslltdpadaara 98 
                                        +    +l+d a+a++ 
  gi|474934999|ref|YP_007688581.1| 213 YFIEGVVLLDVAAAVAV 229
                                       33222222222222222 PP

>> DDDD  Putative mitochondrial precursor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1     0.078   3.5e+02      46      63 ..      82      99 ..      69     106 .. 0.78
   2 ?    9.6   0.6   0.00017      0.75      36      59 ..     220     243 ..     195     250 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.078
                              DDDD 46 gllvGtliSknvAnlLee 63
                                         vG+ i   vA +Le+
  gi|474934999|ref|YP_007688581.1| 82 TTSVGAIIGAAVAVYLEN 99
                                      456899999999999986 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00017
                              DDDD  36 LlrvilvVipgllvGtliSknvAn 59 
                                       Ll v ++V +g ++G++i  ++A 
  gi|474934999|ref|YP_007688581.1| 220 LLDVAAAVAVGAYIGAMIGSRIAT 243
                                       99*****************99996 PP

>> DUF3487  Protein of unknown function (DUF3487)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   3.8      0.46   2.1e+03      30      67 ..      18      56 ..       5      63 .. 0.62
   2 ?   12.2   2.3   2.7e-05      0.12      16      62 ..      66     112 ..      61     120 .. 0.88
   3 ?    7.3   1.7   0.00094       4.2      26      84 ..     203     259 ..     193     271 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.46
                           DUF3487 30 glglvvglvlglllallvgsla.liptialllvllvvlv 67
                                       +g+++gl  g+++++++  l  l  t a+++ l++++ 
  gi|474934999|ref|YP_007688581.1| 18 IIGALFGLGGGIIFIPVLTILFdLSATEAVAASLVGIVA 56
                                      578888888899888877633213444445555555555 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 2.7e-05
                           DUF3487  16 VfrGltadEllvlaglglvvglvlglllallvgslaliptialllvl 62 
                                       V rGl+   l++++ + + vg+++g  +a+ +++++l+  +a +++ 
  gi|474934999|ref|YP_007688581.1|  66 VNRGLSNIRLGMMLEITTSVGAIIGAAVAVYLENWILLAIFACVMLY 112
                                       88**********************************99888877765 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.00094
                           DUF3487  26 lvlaglglvvglvlglllallvgslaliptialllvllvvlvggkllarlKRgkPdtyl 84 
                                       +++a +g+v++++ g++l+ ++   a+ +++ + +++ + + +    a++KR  P  y+
  gi|474934999|ref|YP_007688581.1| 203 GITAFSGAVIYFIEGVVLLDVAA--AVAVGAYIGAMIGSRIATRVSTASIKRCMPAVYF 259
                                       678999***********977777..5555555555566666677778999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       787  (0.0438954); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1717.85
//
Query:       gi|474935000|ref|YP_007688582.1|  [L=90]
Description: hypothetical protein TALC_01445 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0016   18.5   5.5     0.0016   18.5   5.5    2.1  2  DUF1634          Protein of unknown function (DUF1634)
  ------ inclusion threshold ------
      0.075   13.3   0.4      0.075   13.3   0.4    2.2  2  YiaAB            yiaA/B two helix domain
       0.51   10.3   9.1        1.1    9.2   0.6    2.7  3  SecE             SecE/Sec61-gamma subunits of protein translo
        1.4    9.1   0.1        1.4    9.1   0.1    2.6  3  Herpes_UL49_5    Herpesvirus UL49.5 envelope/tegument protein
        1.6    8.8  13.5       0.38   10.8   7.9    2.0  2  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
        2.1    8.0   8.5        2.8    7.6   8.5    1.2  1  PRA1             PRA1 family protein
        5.2    6.7   9.3          6    6.5   9.3    1.2  1  Tetraspanin      Tetraspanin family
        8.9    6.6  11.0        2.6    8.3   4.0    2.0  2  DUF3784          Domain of unknown function (DUF3784)


Domain annotation for each model (and alignments):
>> DUF1634  Protein of unknown function (DUF1634)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   1.4      0.07   1.6e+02       4      22 ..      11      29 ..       8      36 .. 0.77
   2 !   18.5   5.5     7e-07    0.0016      54      98 ..      37      80 ..      32      85 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.07
                           DUF1634  4 lLriGvllsaavvllGlil 22
                                      +L + +l+ +a++++Gl+l
  gi|474935000|ref|YP_007688582.1| 11 VLHYMTLVGIAILVIGLLL 29
                                      7788888888888888876 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 7e-07
                           DUF1634 54 aiiqlGllvLiatPvlrVvlsliaFlkekdilyviitliVLliLl 98
                                       i+++G l+L++tP++ V++s    ++ ++  +   t++VL++++
  gi|474935000|ref|YP_007688582.1| 37 RILLVGALILVFTPMAGVIVSTACLARLRNAYWL-KTAVVLILVI 80
                                      6899******************999999997555.5555554433 PP

>> YiaAB  yiaA/B two helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.4   3.3e-05     0.075       7      42 ..      14      49 ..      10      63 .. 0.87
   2 ?    0.5   0.8      0.33   7.5e+02       4      17 ..      73      86 ..      69      89 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.3e-05
                             YiaAB  7 lsfllalvlllvGlwyl.pldlseKgfyamgllfllf 42
                                      ++ l++++ l++Gl  l p d s ++ ++ +l+++ +
  gi|474935000|ref|YP_007688582.1| 14 YMTLVGIAILVIGLL-LhPCDISDRILLVGALILVFT 49
                                      5789***********.66********99988887655 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.33
                             YiaAB  4 qswlsfllalvlll 17
                                      +++l +++a++l+l
  gi|474935000|ref|YP_007688582.1| 73 AVVLILVIAVGLVL 86
                                      56677788887776 PP

>> SecE  SecE/Sec61-gamma subunits of protein translocation complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0031       6.9      25      46 ..       7      28 ..       2      34 .. 0.58
   2 ?   -1.9   0.6       1.5   3.3e+03      31      31 ..      47      47 ..      38      60 .. 0.52
   3 ?    9.2   0.6    0.0005       1.1      20      41 ..      66      87 ..      65      90 .] 0.85

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0031
                                      HHHHHHHHHHHHHHHHHHHHHH CS
                              SecE 25 ttvvVlvfvvimglflflvDlv 46
                                      +t++Vl  ++++g+ + ++ l+
  gi|474935000|ref|YP_007688582.1|  7 STAAVLHYMTLVGIAILVIGLL 28
                                      5555555555555555555444 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.5
                                      H CS
                              SecE 31 v 31
                                      v
  gi|474935000|ref|YP_007688582.1| 47 V 47
                                      2 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0005
                                      CHHHHHHHHHHHHHHHHHHHHH CS
                              SecE 20 kEllkttvvVlvfvvimglflf 41
                                      + ++  t+vVl+ v+ +gl+l 
  gi|474935000|ref|YP_007688582.1| 66 NAYWLKTAVVLILVIAVGLVLT 87
                                      567888*************986 PP

>> Herpes_UL49_5  Herpesvirus UL49.5 envelope/tegument protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1   0.00062       1.4      59      85 ..       6      32 ..       4      35 .. 0.87
   2 ?    0.2   1.0      0.35   7.8e+02      62      81 ..      43      62 ..      40      76 .. 0.78
   3 ?   -0.1   0.2      0.46     1e+03      11      23 ..      70      82 ..      63      88 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00062
                     Herpes_UL49_5 59 ssaasvlFYisLlavlvallavaynac 85
                                       s+a+vl Y++L+++ + ++ ++ + c
  gi|474935000|ref|YP_007688582.1|  6 RSTAAVLHYMTLVGIAILVIGLLLHPC 32
                                      589************999998888777 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.35
                     Herpes_UL49_5 62 asvlFYisLlavlvallava 81
                                      a +l +  +++v+v+ +++a
  gi|474935000|ref|YP_007688582.1| 43 ALILVFTPMAGVIVSTACLA 62
                                      77888899999999888766 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.46
                     Herpes_UL49_5 11 lllavvvllllal 23
                                      l++avv++l++a+
  gi|474935000|ref|YP_007688582.1| 70 LKTAVVLILVIAV 82
                                      5667777777765 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.2      0.13   2.9e+02      70      82 ..      16      28 ..       5      32 .. 0.51
   2 ?   10.8   7.9   0.00017      0.38      37      84 ..      39      87 ..      34      90 .] 0.74

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.13
                   Phage_holin_3_6 70 livaavllvlagv 82
                                      ++v+++ lv++++
  gi|474935000|ref|YP_007688582.1| 16 TLVGIAILVIGLL 28
                                      2344444444444 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00017
                   Phage_holin_3_6 37 agllgaagvlallalllllvalalala.alwlaalivaavllvlagvla 84
                                      +++ ++ +v++ +a ++++ a+++ l  a+wl + +v ++++++++vl 
  gi|474935000|ref|YP_007688582.1| 39 LLVGALILVFTPMAGVIVSTACLARLRnAYWLKTAVVLILVIAVGLVLT 87
                                      44455666666667777777777888877********999999998886 PP

>> PRA1  PRA1 family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   8.5    0.0012       2.8      41     107 ..      13      88 ..       8      90 .] 0.64

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0012
                              PRA1  41 NYlivv.llvlllslltnplslivllllvlawlflyflr......seplvlfgrel..sdrvvlivllvvsvlllf 107
                                       +Y+ +v +++l++ ll++p ++   +llv a+++++         ++ l ++ +    ++ vvli++++v ++l +
  gi|474935000|ref|YP_007688582.1|  13 HYMTLVgIAILVIGLLLHPCDISDRILLVGALILVFTPMagvivsTACLARLRNAYwlKTAVVLILVIAVGLVLTY 88 
                                       57666648999999**********9999999999999441333323333333333322333555555555555554 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   9.3    0.0027         6      12     101 ..      15      87 ..       4      90 .] 0.78

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0027
                                       XXXXXXXXXXXXXXXXXXXX.....................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Tetraspanin  12 fwligivllavGvwlrlkhaeaalacllsesaedpailaillivvGvllfllgflGcigalkenkcllltfsllllv 88 
                                       + l+gi++l++G+ l                 ++++i   +l+v   +l+++ ++G+i +      l   + l   v
  gi|474935000|ref|YP_007688582.1|  15 MTLVGIAILVIGLLL-----------------HPCDISDRILLVGALILVFTPMAGVIVSTACLARLRNAYWLKTAV 74 
                                       679999999999777.................4455554445555558888889******************99999 PP

                                       XXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxx RF
                       Tetraspanin  89 lfllelaagilgf 101
                                       +++l +a+g+++ 
  gi|474935000|ref|YP_007688582.1|  75 VLILVIAVGLVLT 87 
                                       9999999998543 PP

>> DUF3784  Domain of unknown function (DUF3784)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   4.0    0.0012       2.6      47      89 ..      12      57 ..       2      62 .. 0.78
   2 ?    4.0   3.4     0.026        58      50      88 ..      48      86 ..      46      90 .] 0.68

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0012
                           DUF3784 47 givllligilflllgll...saiesealliialiviiiiviylivy 89
                                        +++l+gi++l++gll     i +  ll++ali+++  + ++iv 
  gi|474935000|ref|YP_007688582.1| 12 LHYMTLVGIAILVIGLLlhpCDISDRILLVGALILVFTPMAGVIVS 57
                                      5689999999999999999767777777777888888888888876 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.026
                           DUF3784 50 llligilflllgllsaiesealliialiviiiiviyliv 88
                                      ++ ++ +++ +++l+ + ++++l  a+++i++i+++l++
  gi|474935000|ref|YP_007688582.1| 48 FTPMAGVIVSTACLARLRNAYWLKTAVVLILVIAVGLVL 86
                                      566777888888887777777777777766666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       992  (0.0553294); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 735.68
//
Query:       gi|474935001|ref|YP_007688583.1|  [L=451]
Description: Recombination protein MgsA [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-63  212.5   0.3    6.1e-63  211.7   0.0    1.5  1  MgsA_C           MgsA AAA+ ATPase C terminal
      1e-25   89.9   0.1    2.3e-25   88.7   0.1    1.6  1  AAA_assoc_2      AAA C-terminal domain
    2.2e-16   60.0   0.0      7e-16   58.4   0.0    1.9  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    3.3e-15   56.7   0.0    7.8e-15   55.5   0.0    1.7  1  AAA              ATPase family associated with various cellul
    7.7e-06   26.4   0.0      0.042   14.2   0.0    2.7  2  AAA_16           AAA ATPase domain
    1.7e-05   24.6   0.0     0.0031   17.2   0.0    2.4  2  Sigma54_activat  Sigma-54 interaction domain
    2.1e-05   24.5   0.1    0.00052   20.0   0.1    2.6  1  AAA_5            AAA domain (dynein-related subfamily)
     0.0001   21.8   0.1       0.14   11.5   0.0    2.2  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00029   21.0   0.0     0.0005   20.2   0.0    1.4  1  AAA_2            AAA domain (Cdc48 subfamily)
    0.00045   20.5   0.2       0.24   11.7   0.0    2.5  2  AAA_22           AAA domain
     0.0007   20.2   0.2        3.1    8.9   0.0    3.7  3  TPR_14           Tetratricopeptide repeat
    0.00097   19.2   0.0     0.0065   16.5   0.0    2.1  2  AAA_14           AAA domain
     0.0024   17.7   0.0       0.51   10.1   0.0    2.3  2  DNA_pol3_delta2  DNA polymerase III, delta subunit
     0.0029   16.9   0.0     0.0067   15.7   0.0    1.6  1  TIP49            TIP49 P-loop domain
     0.0033   17.3   0.0      0.013   15.4   0.0    2.0  1  AAA_3            ATPase family associated with various cellul
     0.0046   16.7   0.0     0.0078   16.0   0.0    1.3  1  IstB_IS21        IstB-like ATP binding protein
     0.0074   16.3   0.1        1.8    8.5   0.0    2.2  2  ResIII           Type III restriction enzyme, res subunit
     0.0097   15.6   0.1       0.11   12.2   0.1    2.5  1  AAA_30           AAA domain
  ------ inclusion threshold ------
      0.015   15.9   0.0      0.033   14.7   0.0    1.7  1  AAA_18           AAA domain
      0.016   14.4   0.0      0.051   12.7   0.0    1.7  2  NB-ARC           NB-ARC domain
      0.022   14.9   0.0      0.048   13.8   0.0    1.5  1  Sigma54_activ_2  Sigma-54 interaction domain
      0.048   13.3   0.1        1.3    8.6   0.1    2.4  2  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
       0.06   13.5   0.0       0.12   12.5   0.0    1.6  1  AAA_33           AAA domain
      0.079   12.5   0.0       0.19   11.3   0.0    1.5  1  AAA_7            P-loop containing dynein motor region
      0.079   12.9   0.0       0.26   11.2   0.0    1.8  2  RsgA_GTPase      RsgA GTPase
      0.088   12.7   0.0        6.1    6.7   0.0    2.6  2  ATPase_2         ATPase domain predominantly from Archaea
      0.096   12.9   1.2         13    6.0   0.3    2.5  2  TAF              TATA box binding protein associated factor (
       0.12   12.8   0.0       0.25   11.8   0.0    1.6  1  RNA_helicase     RNA helicase
       0.15   11.5   0.1        3.9    6.8   0.0    2.7  3  TniB             Bacterial TniB protein
       0.15   11.7   0.0       0.57    9.9   0.0    1.9  2  AAA_24           AAA domain
       0.17   12.2   0.1         14    6.0   0.1    2.5  2  AAA_19           AAA domain
       0.18   12.3   0.0       0.67   10.5   0.0    1.9  2  ABC_tran         ABC transporter


Domain annotation for each model (and alignments):
>> MgsA_C  MgsA AAA+ ATPase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.7   0.0   1.1e-65   6.1e-63       1     166 [.     273     438 ..     273     439 .. 0.99

  Alignments for each domain:
  == domain 1  score: 211.7 bits;  conditional E-value: 1.1e-65
                                       TT-HHHHHHHHHHHHHTT--HHHHHHHHHHHHHHTTGGGSTTHHHHHHHHHHHHHHH-TTTTHHHHHHHHHHHHCS- CS
                            MgsA_C   1 GSdpdAAlyylarmleaGedprfiaRRlviiAseDiGlAdpqalqlavaaaeaveriGlpEariaLaqavvylalap 77 
                                       +SdpdAA+y+larml++Gedp fiaRRl+ +A +D+GlAdp+a ++av++++a++ +G+pE+r+aLa++vvyl+lap
  gi|474935001|ref|YP_007688583.1| 273 NSDPDAAIYWLARMLAGGEDPLFIARRLIEFAGDDVGLADPNAHVMAVTCFDACRDLGMPECRYALAETVVYLSLAP 349
                                       59*************************************************************************** PP

                                       ---GG.GHHHHHHHHH---------GGGST...........T-T---GGG--SS------S-CCG--..-------- CS
                            MgsA_C  78 KSnaaykAikkaledvkekkslevPlhLrnaptklakklgygkgYkyphdypegvvkqqylpdelkkkkfYepterg 154
                                       +Sn++  Ai++a++d+++  +++vPl +rna+tkl+++lgygkgY+y+  ++e+++k+q+lpd+lk++++Yep +rg
  gi|474935001|ref|YP_007688583.1| 350 RSNSIAVAISQAMDDAEKMLAEPVPLRIRNASTKLMEDLGYGKGYEYAEGTDEKIAKMQCLPDSLKDRRYYEPGDRG 426
                                       ***************************************************************************** PP

                                       HHHHHHH-XXX. CS
                            MgsA_C 155 lekkikerlekl 166
                                       +e  +++r++++
  gi|474935001|ref|YP_007688583.1| 427 NEVYYRKRIDAI 438
                                       ******999876 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.7   0.1   4.1e-28   2.3e-25       4      81 .]     195     272 ..     193     272 .. 0.98

  Alignments for each domain:
  == domain 1  score: 88.7 bits;  conditional E-value: 4.1e-28
                                       .XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXHHHHHHHHHHHH CS
                       AAA_assoc_2   4 klkleddalealaeladGDaRkaLnlLElaaeaaeakegkieitledleealqrkalryDkagdehYdliSAlhKSi 80 
                                       ++ ++d++l ++a +a+GDaR+a+n+LE+a++ + ++eg+++i ++++ e++ rk+l+yDk+g++hYdliSAlhKS+
  gi|474935001|ref|YP_007688583.1| 195 NIVVSDEVLGLIAGYANGDARTAMNVLEAAVSVTPEAEGQVRIGKHTVVEVTARKSLLYDKDGEMHYDLISALHKSM 271
                                       6899************************************************************************* PP

                                       H CS
                       AAA_assoc_2  81 R 81 
                                       R
  gi|474935001|ref|YP_007688583.1| 272 R 272
                                       9 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.4   0.0   1.3e-18     7e-16       1     116 [.      27     145 ..      27     162 .. 0.80
   2 ?   -2.7   0.0       7.9   4.4e+03     127     145 ..     234     252 ..     223     254 .. 0.80

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 1.3e-18
                            RuvB_N   1 lrPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvklkitsgPv..lekagdl 75 
                                       +rP+ l+e++gqek+    +++ +  +  ++ +  +++ GpPG+Gkttla iia+  ++++ + s+ +  +++ +d+
  gi|474935001|ref|YP_007688583.1|  27 MRPRCLDEFVGQEKLVGPGRVLRNMIE--QDRVTSMIFWGPPGVGKTTLAGIIANSTDAEFVQYSAVTggIKEVKDI 101
                                       7***************99888766544..5667789**********************9998777643338888887 PP

                            RuvB_N  76 aa...lltnleekdvlfideihrlsraveevlysamedfrldiv 116
                                       ++   +  +  ++ vlf+deihr+++a ++ + + +e  ++ ++
  gi|474935001|ref|YP_007688583.1| 102 MTaaeMRRRHGKRTVLFVDEIHRFNKAQQDAFLPFVEKGSITLI 145
                                       54111445566889****************99999998888764 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7.9
                            RuvB_N 127 kldlpkftlvgattragll 145
                                       ++++ k t+v  t+r++ll
  gi|474935001|ref|YP_007688583.1| 234 QVRIGKHTVVEVTARKSLL 252
                                       5678888999999998877 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   0.0   1.4e-17   7.8e-15       1     127 [.      60     167 ..      60     172 .. 0.87

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 1.4e-17
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS...TSEEEEEETGGGHHHHH CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakeka...kpsilfiDEidalaksr 74 
                                       ++++GppG+GKT+la  +a+++++ef++ s+ +          k++++++++a+  +   k ++lf+DEi++++k++
  gi|474935001|ref|YP_007688583.1|  60 MIFWGPPGVGKTTLAGIIANSTDAEFVQYSAVTGG-------IKEVKDIMTAAEMRRrhgKRTVLFVDEIHRFNKAQ 129
                                       79***************************998877.......67777777777555566567*************** PP

                                       TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS..GGGSTHHHHSTTSSEE CS
                               AAA  75 sgseseeeervvnqLlteldgvkkkeskvivigatnr..pdkldpallrgRfdrk 127
                                                  ++++l+++++ +      ++igat++    ++++all +R+ + 
  gi|474935001|ref|YP_007688583.1| 130 -----------QDAFLPFVEKGSI-----TLIGATTEnpSFEVNSALL-SRCRVF 167
                                       ...........********98866.....89****9988889999999.9*9876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   7.4e-05     0.042      18      48 ..      51      81 ..      34      95 .. 0.75
   2 !    9.5   0.0    0.0022       1.2     120     156 ..      99     135 ..      80     145 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.4e-05
                            AAA_16 18 rvrsgrpelvllsGesGvGKsslvrellral 48
                                      ++ ++r  ++++ G++GvGK++l+  ++++ 
  gi|474935001|ref|YP_007688583.1| 51 MIEQDRVTSMIFWGPPGVGKTTLAGIIANST 81
                                      455677799**************98887654 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0022
                            AAA_16 120 lellkrllallsrderplvlvlDdlqwadeaslql.la 156
                                        + ++++ ++ ++++  +vl++D+++++  a++++ l+
  gi|474935001|ref|YP_007688583.1|  99 KDIMTAAEMRRRHGK-RTVLFVDEIHRFNKAQQDAfLP 135
                                       566677777788855.5****************99554 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.028        16      18      49 ..      51      84 ..      38     107 .. 0.76
   2 !   17.2   0.0   5.5e-06    0.0031      93     132 ..     113     152 ..      90     181 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.028
                                      HCTSS..S-EEEECSTTSSHHHHHHHHHHHSTTT CS
                   Sigma54_activat 18 vaktd..lsvlitGesGtGKellaraiheaskrk 49
                                      ++++d  +s++  G  G+GK++la  i ++++ +
  gi|474935001|ref|YP_007688583.1| 51 MIEQDrvTSMIFWGPPGVGKTTLAGIIANSTDAE 84
                                      4444444667789************998876654 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 5.5e-06
                                       TTSEEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSEEE CS
                   Sigma54_activat  93 dgGtlfLDeigelplelQekLlrvlqegevervGsskeik 132
                                       +  +lf+Dei++++ + Q  +l ++++g+++ +G+++e +
  gi|474935001|ref|YP_007688583.1| 113 KRTVLFVDEIHRFNKAQQDAFLPFVEKGSITLIGATTENP 152
                                       5679******************************987654 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   9.3e-07   0.00052       2     100 ..      60     148 ..      59     171 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 9.3e-07
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG-- CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEverae 78 
                                       ++  GppG+gK++la  +a  + +e++        +++ ++g+++  + +  ++  ++ r   +  +l++DE++r +
  gi|474935001|ref|YP_007688583.1|  60 MIFWGPPGVGKTTLAGIIANSTDAEFV--------QYSAVTGGIK--EVKDIMTAAEMRRRHGKRTVLFVDEIHRFN 126
                                       6889*****************987754........4555777777..566666667788888899************ PP

                                       HHHHHHHHHHHHSSEEE..-SS CS
                             AAA_5  79 sevlnsLlslleerrllleegg 100
                                       ++ ++++l+  e+  + l   +
  gi|474935001|ref|YP_007688583.1| 127 KAQQDAFLPFVEKGSITLIGAT 148
                                       ********99999888766554 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00026      0.14      24      78 ..      59     107 ..      56     114 .. 0.72
   2 !    8.2   0.0    0.0026       1.4     106     143 ..     113     150 ..     110     165 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00026
                      Mg_chelatase  24 nlllvGppGsGKtmlakrlpsllpplseeealevakiasvagkkeeekllkrrpf 78 
                                       ++++ GppG GKt la    +++++ +++e ++ ++++     ke +++++++++
  gi|474935001|ref|YP_007688583.1|  59 SMIFWGPPGVGKTTLA----GIIANSTDAEFVQYSAVTGG--IKEVKDIMTAAEM 107
                                       689**********987....78888888888888887743..3345555555555 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0026
                      Mg_chelatase 106 hnGvLfLDElpefkrkvlevLRePledgevtisrakak 143
                                       ++ vLf+DE+  f++   +++   +e+g++t+  a+++
  gi|474935001|ref|YP_007688583.1| 113 KRTVLFVDEIHRFNKAQQDAFLPFVEKGSITLIGATTE 150
                                       578***************************98766543 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   8.9e-07    0.0005       2     109 ..      56     143 ..      55     159 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 8.9e-07
                                       ----EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTSEEEEETGG CS
                             AAA_2   2 piisilllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegGivllDEid 78 
                                       ++ s+++ gp gvGkt la  +a+  ++    +++   a +        + v+  + a+++  ++ ++ ++++DEi 
  gi|474935001|ref|YP_007688583.1|  56 RVTSMIFWGPPGVGKTTLAGIIANSTDA----EFVQYSAVTGGI-----KEVKDIMTAAEMRRRHGKRTVLFVDEIH 123
                                       57899*********************96....999999988888.....89************************** PP

                                       G-------------HHHHHHHHHHHH--EE- CS
                             AAA_2  79 KihpkessgadvSregVqrdLLqileggtlt 109
                                       +  +             q+++L+ +e+g +t
  gi|474935001|ref|YP_007688583.1| 124 RFNK-----------AQQDAFLPFVEKGSIT 143
                                       **99...........7789999999999987 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00042      0.24       6      30 ..      58      82 ..      53     104 .. 0.79
   2 ?    6.4   0.0     0.018        10      86     108 ..     109     130 ..      92     150 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00042
                            AAA_22  6 gilvvtGesGtGKTtllrrlleqld 30
                                      ++++ +G++G+GKTtl+  ++++ d
  gi|474935001|ref|YP_007688583.1| 58 TSMIFWGPPGVGKTTLAGIIANSTD 82
                                      578999**********988888773 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.018
                            AAA_22  86 lrarav.ielliiDEaqhlrseea 108
                                        r+    + +l +DE+++++++++
  gi|474935001|ref|YP_007688583.1| 109 RRH--GkRTVLFVDEIHRFNKAQQ 130
                                       222..2469**********63333 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       4.2   2.4e+03      18      30 ..     175     187 ..     159     195 .. 0.79
   2 !    8.9   0.0    0.0055       3.1      12      35 ..     209     232 ..     203     239 .. 0.85
   3 ?    6.2   0.1     0.041        23       3      41 ..     259     300 ..     258     303 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 4.2
                            TPR_14  18 deAiallrralal 30 
                                       ++ ++llrra+++
  gi|474935001|ref|YP_007688583.1| 175 EDIVKLLRRAVED 187
                                       46899*****984 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0055
                            TPR_14  12 lalGdpdeAiallrralalaPdda 35 
                                       +a+Gd ++A+++l++a++  P+ +
  gi|474935001|ref|YP_007688583.1| 209 YANGDARTAMNVLEAAVSVTPEAE 232
                                       689****************99854 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.041
                            TPR_14   3 allalaeal...lalGdpdeAiallrralalaPddaeawlll 41 
                                       ++++l +al   +++ dpd+Ai  l r+la + d++ + ++l
  gi|474935001|ref|YP_007688583.1| 259 MHYDLISALhksMRNSDPDAAIYWLARMLAGGEDPLFIARRL 300
                                       6788888886667999**************777766666666 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.2e-05    0.0065       7     109 ..      62     156 ..      58     177 .. 0.65
   2 ?   -0.3   0.0       1.8     1e+03       9      50 ..     233     275 ..     232     296 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.2e-05
                            AAA_14   7 itGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelilek.lkeekktylflDEiqevpewek. 81 
                                         G+  vGKTtl+  ++++      +++ ++  +   k+ +d    +++   +  ++ k+t+lf DEi++ +++++ 
  gi|474935001|ref|YP_007688583.1|  62 FWGPPGVGKTTLAGIIANSTD---AEFVQYSAVTGGIKEVKDI---MTAAEMRrRHG-KRTVLFVDEIHRFNKAQQd 131
                                       569999******877765555...7888888888777777766...33333321345.89***********988641 PP

                            AAA_14  82 alkslvdegknldvivtGSnskllskei 109
                                       a   +v++g    + + G    + s e+
  gi|474935001|ref|YP_007688583.1| 132 AFLPFVEKG---SITLIGATTENPSFEV 156
                                       455555544...5555555555555555 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.8
                            AAA_14   9 GaRrvGKTtllkqlikell.vkkesilyinldderdkkladpe 50 
                                       G  r+GK t+++  ++++l  +k+  + ++l +   k++++++
  gi|474935001|ref|YP_007688583.1| 233 GQVRIGKHTVVEVTARKSLlYDKDGEMHYDLISALHKSMRNSD 275
                                       66699*******9999999877777777777777666666544 PP

>> DNA_pol3_delta2  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.027        15       7      42 ..      46      80 ..      42      87 .. 0.88
   2 !   10.1   0.0   0.00091      0.51      85     160 ..      95     170 ..      80     173 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.027
                   DNA_pol3_delta2  7 kilskalksgrlahayLfeGdegigkkelalnlaka 42
                                      ++l+++++++r++ +++f G+ g+gk +la  +a++
  gi|474935001|ref|YP_007688583.1| 46 RVLRNMIEQDRVT-SMIFWGPPGVGKTTLAGIIANS 80
                                      67999******97.689*************998875 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00091
                   DNA_pol3_delta2  85 ldqirelieelsrkpreskkkiiiiedaekmtksAaNalLktlEEPsenaifiLitsdtn.klLktirSRcqelkfs 160
                                       + ++++++  ++ + r +k+ ++ ++++ + +k+ + a+L ++E  s   i   +t++++ ++   + SRc ++ ++
  gi|474935001|ref|YP_007688583.1|  95 IKEVKDIMTAAEMRRRHGKRTVLFVDEIHRFNKAQQDAFLPFVEKGSITLI-GATTENPSfEVNSALLSRCRVFVLE 170
                                       7899****************************************9844333.3344444325689999999988776 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.2e-05    0.0067      24      85 ..      33      90 ..      18     116 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.2e-05
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 24 eglvGqkkareaagvivelikekklaGravLlaGpsgtGktalaiaiskelgedvpfvalsg 85
                                      + +vGq+k      v+ ++i++++++  ++++ Gp+g Gkt la  i+++      fv+ s+
  gi|474935001|ref|YP_007688583.1| 33 DEFVGQEKLVGPGRVLRNMIEQDRVT--SMIFWGPPGVGKTTLAGIIANSTD--AEFVQYSA 90
                                      579*********************99..999*************99998765..44444433 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   2.3e-05     0.013       4      99 ..      62     150 ..      59     158 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.3e-05
                             AAA_3   4 legvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeeke..kefefkkGpvfanllladeinrappkt 78 
                                       + g PG++kt+l+  +a++ d+ef  +q+ +  + + i     +++     e++ ++G     +l++dei r +   
  gi|474935001|ref|YP_007688583.1|  62 FWGPPGVGKTTLAGIIANSTDAEF--VQYSA--VTGGIK---EVKDIMtaAEMRRRHGK--RTVLFVDEIHRFNKAQ 129
                                       5688*****************999..67754..233333...33322212556666665..789************* PP

                             AAA_3  79 qsalleameerqvtvegethk 99 
                                       q a+l  +e   +t+ g+t++
  gi|474935001|ref|YP_007688583.1| 130 QDAFLPFVEKGSITLIGATTE 150
                                       **************9999876 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.4e-05    0.0078      47     130 ..      57     133 ..      30     150 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.4e-05
                         IstB_IS21  47 kenivllGpsGvGKshlaialgveavraglsvlfvrvedLveelkrarrdgklaralkrllkvdllilDdlgllpld 123
                                         ++++ Gp+GvGK+ la  ++ +     +   fv+ +++   +k  ++   +a++ +r  k ++l +D++   +  
  gi|474935001|ref|YP_007688583.1|  57 VTSMIFWGPPGVGKTTLAGIIANS-----TDAEFVQYSAVTGGIKEVKDIMTAAEMRRRHGKRTVLFVDEIHRFNKA 128
                                       56799*************876654.....556677777777888888888889999999999********8655444 PP

                         IstB_IS21 124 qaeaell 130
                                       q+    +
  gi|474935001|ref|YP_007688583.1| 129 QQ--DAF 133
                                       44..444 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.026        15      17      45 ..      50      78 ..      38      86 .. 0.77
   2 !    8.5   0.0    0.0032       1.8     122     147 ..     103     128 ..      80     151 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.026
                                      ......TTSEEEEEESTTSTHHHHHHHHH CS
                            ResIII 17 eklkskrdkrglikmaTGtGKTlvaakli 45
                                      + ++++r + ++++ + G+GKT +a  ++
  gi|474935001|ref|YP_007688583.1| 50 NMIEQDRVTSMIFWGPPGVGKTTLAGIIA 78
                                      444546777999**********9886555 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0032
                                       .....HHHTTT-SEEEEETGGGTTS. CS
                            ResIII 122 eeeseellrdrfdviiiDEaHrlgak 147
                                       + ++ + ++++  v+++DE Hr++++
  gi|474935001|ref|YP_007688583.1| 103 TAAEMRRRHGKRTVLFVDEIHRFNKA 128
                                       5566777888999**********994 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.1    0.0002      0.11      21     124 ..      60     147 ..      45     164 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0002
                            AAA_30  21 avltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlkgrarlepgtllivDEa 97 
                                       ++  Gp+G GKtt+ + +++  +a+   v   A tg   k+++     + +t a++ +r+++      +t+l vDE+
  gi|474935001|ref|YP_007688583.1|  60 MIFWGPPGVGKTTLAGIIANSTDAEF--VQYSAVTGGI-KEVK-----DIMTAAEMRRRHGK------RTVLFVDEI 122
                                       5678**********999999999875..7788888776.3344.....35677777766665......599999999 PP

                            AAA_30  98 gmvdtkqlaallkaaekagakvilvGD 124
                                          + +q +a+l  +ek   ++ l+G 
  gi|474935001|ref|YP_007688583.1| 123 HRFNKAQQDAFLPFVEK--GSITLIGA 147
                                       99999999999999988..66666665 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   5.9e-05     0.033       4      59 ..      63     132 ..      61     203 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.9e-05
                            AAA_18   4 tGtpGvGKttlakeLskrlgf...........gvnlrdvakenglllevdpe...aldeskrldedkldk 59 
                                        G+pGvGKttla  +++++               +++d+ +  +++    +     +de +r+++ ++d+
  gi|474935001|ref|YP_007688583.1|  63 WGPPGVGKTTLAGIIANSTDAefvqysavtggIKEVKDIMTAAEMRRRHGKRtvlFVDEIHRFNKAQQDA 132
                                       6**************9987333466666666544555555555555555555656566666666666555 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   9.2e-05     0.051       7      45 ..      46      82 ..      44      93 .. 0.79
   2 ?   -1.8   0.0       2.6   1.4e+03     102     172 ..     112     185 ..      87     191 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.2e-05
                                      HHHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCSHC CS
                            NB-ARC  7 kviekLlekdelqslvvalvGmgGvGKttlakqilnksd 45
                                      +v  ++ e+d +    + + G +GvGKttla  i n+ d
  gi|474935001|ref|YP_007688583.1| 46 RVLRNMIEQDRVT--SMIFWGPPGVGKTTLAGIIANSTD 82
                                      5667777777777..8999************99999855 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.6
                                       CTTEEEEEEEE-SHHHH.....HHHHCHTTSEEEE..EESB..CCCCCCS-S-EEEEEESS--HHHHHHHHHHCC CS
                            NB-ARC 102 tkrfllvlDDVweeedwdkigvvlparenrlrvll..TTRd..eevanavsatsekievelLekdeawellenkv 172
                                       +kr++l  D +   ++  +  + lp  e+++  l+  TT +   ev +a   ++ ++ +e L k++  +ll   v
  gi|474935001|ref|YP_007688583.1| 112 GKRTVLFVDEIHRFNKA-QQDAFLPFVEKGSITLIgaTTENpsFEVNSALLSRCRVFVLEGLGKEDIVKLLRRAV 185
                                       46888888888776663.334444544444444433366541146777777778888888888888888887665 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   8.5e-05     0.048      26     110 ..      62     151 ..      50     165 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.5e-05
                                       EEEETT--HHHHHHCC--TT.S-EE--SSTTHHHH-HHHHHHHT.......TTSEEEEEE-TT--HHHHHHHHHHHH CS
                   Sigma54_activ_2  26 ltGekGsgkelvArlLhkns.gpwleifvverlaklpldlleqa.......kggtLylkdiadlskaeqkeLlella 94 
                                         G++G gk++ A++++++  ++ ++   v  ++k+ +d++  a       k  +L++ +i+ ++ka+q   l  ++
  gi|474935001|ref|YP_007688583.1|  62 FWGPPGVGKTTLAGIIANSTdAEFVQYSAVTGGIKEVKDIMTAAemrrrhgKRTVLFVDEIHRFNKAQQDAFLPFVE 138
                                       579*************9875156678888888889999999998788888899****************98877776 PP

                                       HHTTTT-EEEEEEEE- CS
                   Sigma54_activ_2  95 kaeksslrlVstsskd 110
                                       k+   s+ l+ ++ ++
  gi|474935001|ref|YP_007688583.1| 139 KG---SITLIGATTEN 151
                                       66...77777776665 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1    0.0023       1.3      17      76 ..      60     119 ..      46     122 .. 0.83
   2 ?    7.3   0.0    0.0057       3.2      94     122 ..     102     130 ..      95     139 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0023
                                       EEEEESTTSSHHHHHHHHHHHSSTSSEEEEEEESEEHHHHHHHHHHCHHSS.GGGGEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                       ATP-synt_ab  17 tlipgafgvGktvisqslskqsnsddaiiyvgiGergnevaevleefpegt.imkrtvlva 76 
                                       ++  g  gvGkt+++  +++ ++++  + y ++    +ev+++++  + ++   krtvl++
  gi|474935001|ref|YP_007688583.1|  60 MIFWGPPGVGKTTLAGIIANSTDAE-FVQYSAVTGGIKEVKDIMTAAEMRRrHGKRTVLFV 119
                                       5567999**************8766.99999**9999*****9998888555889999987 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0057
                                       HHHHHHHHHTTSEEEEEEETHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  94 itlAEyfrdqgknvlliadslsrwaeAlr 122
                                       +t+AE+ r +gk+ +l++d++ r+ +A++
  gi|474935001|ref|YP_007688583.1| 102 MTAAEMRRRHGKRTVLFVDEIHRFNKAQQ 130
                                       799***********************987 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00022      0.12       3      32 ..      61      90 ..      60     139 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00022
                            AAA_33  3 llvGlpGsGKstlaerllkklgavllssdt 32
                                      ++ G+pG+GK+tla  +++ ++a+++   +
  gi|474935001|ref|YP_007688583.1| 61 IFWGPPGVGKTTLAGIIANSTDAEFVQYSA 90
                                      899***********9998888888876555 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00033      0.19      34     111 ..      58     124 ..      44     135 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00033
                             AAA_7  34 kpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiiesklekrrkgvygPpggkklvvFvDDln 110
                                        ++++ Gp G+GKt+++  + ++ d       +++ sa t   +  + i+   e rr+       gk+ v+FvD+++
  gi|474935001|ref|YP_007688583.1|  58 TSMIFWGPPGVGKTTLAGIIANSTD-----AEFVQYSAVTGGIKEVKDIMTAAEMRRR------HGKRTVLFVDEIH 123
                                       46899***********999999999.....6778888888876666666666666663......7999999999987 PP

                             AAA_7 111 m 111
                                        
  gi|474935001|ref|YP_007688583.1| 124 R 124
                                       5 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00046      0.26     100     131 ..      58      89 ..      44     107 .. 0.80
   2 ?   -1.9   0.0         5   2.8e+03     119     143 ..     221     244 ..     146     254 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00046
                                       SEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                       RsgA_GTPase 100 ktsvlvGqSGvGKStLinallpelelktgevs 131
                                         +++ G+ GvGK+tL   ++++++++  + s
  gi|474935001|ref|YP_007688583.1|  58 TSMIFWGPPGVGKTTLAGIIANSTDAEFVQYS 89 
                                       46799*************99999888766665 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5
                                       HCTT-----S--------------S CS
                       RsgA_GTPase 119 llpelelktgevseklgrGkhTTta 143
                                       l       t e   + + GkhT  +
  gi|474935001|ref|YP_007688583.1| 221 LEAA-VSVTPEAEGQVRIGKHTVVE 244
                                       3333.44455666666777777655 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0     0.011       6.1      11      44 ..      48      81 ..      46      97 .. 0.77
   2 ?    3.3   0.0      0.12        67     111     141 ..     106     134 ..      83     215 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.011
                          ATPase_2 11 leeilerepneiyfiYGpegsGKtaLlkeiienl 44
                                      l++++e+++ + +  +Gp g+GKt+L   i++  
  gi|474935001|ref|YP_007688583.1| 48 LRNMIEQDRVTSMIFWGPPGVGKTTLAGIIANST 81
                                      6678888888888899*********987665544 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.12
                          ATPase_2 111 ekikkkgkkiiiiiDelqklidlglngaell 141
                                       e  ++ gk+ ++++De+ +    + +++++l
  gi|474935001|ref|YP_007688583.1| 106 EMRRRHGKRTVLFVDEIHRFN--KAQQDAFL 134
                                       444677888999999998888..54433333 PP

>> TAF  TATA box binding protein associated factor (TAF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.3     0.023        13      37      62 ..      98     123 ..      95     125 .. 0.89
   2 ?    5.0   0.0     0.049        27      17      40 ..     357     380 ..     352     386 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.023
                                       HHHHHHHHHHHHHHTT-SSB-HHHHH CS
                               TAF  37 lkeivqeaakfmrhskRqkLtvaDvd 62 
                                       +k i+  a    rh+kR++L v+ + 
  gi|474935001|ref|YP_007688583.1|  98 VKDIMTAAEMRRRHGKRTVLFVDEIH 123
                                       79999999999*********999885 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.049
                                       T---B-HHHHHHHHHHHHHHHHHH CS
                               TAF  17 GitnLsdeaaalLaedveyrlkei 40 
                                        i++  d+a ++Lae v  r++++
  gi|474935001|ref|YP_007688583.1| 357 AISQAMDDAEKMLAEPVPLRIRNA 380
                                       588899***************975 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00044      0.25       2      26 ..      61      85 ..      60     140 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00044
                      RNA_helicase  2 wlyGpsgeGKStlakeLakallkkl 26
                                      +++Gp+g+GK+tla  +a++   ++
  gi|474935001|ref|YP_007688583.1| 61 IFWGPPGVGKTTLAGIIANSTDAEF 85
                                      799************9998877666 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0     0.007       3.9      27      52 ..      49      74 ..      45      92 .. 0.85
   2 ?    1.2   0.0      0.38   2.1e+02     119     140 ..     113     131 ..      94     139 .. 0.73
   3 ?   -3.3   0.0       9.1   5.1e+03     120     146 ..     194     221 ..     193     223 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.007
                              TniB 27 leypkrkrmpnlllvGdsnnGKtmiv 52
                                       ++ +++r+ +++++G++ +GKt+++
  gi|474935001|ref|YP_007688583.1| 49 RNMIEQDRVTSMIFWGPPGVGKTTLA 74
                                      5678899****************987 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.38
                              TniB 119 kvrvLiiDEihnllagsarkqr 140
                                       k  vL +DEih++ ++   +q 
  gi|474935001|ref|YP_007688583.1| 113 KRTVLFVDEIHRFNKA---QQD 131
                                       55799******98754...444 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 9.1
                              TniB 120 vrvLiiDEihnllagsar.kqreflnal 146
                                       + +++ DE+  l+ag a+ + r+++n+l
  gi|474935001|ref|YP_007688583.1| 194 MNIVVSDEVLGLIAGYANgDARTAMNVL 221
                                       5688999999999998873556777776 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0     0.001      0.57       4      20 ..      59      75 ..      57     130 .. 0.83
   2 ?   -2.1   0.0       4.7   2.6e+03      75     107 ..     363     397 ..     318     403 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.001
                            AAA_24  4 kiliyGpsgiGKTtlak 20
                                      +++ +Gp+g+GKTtla 
  gi|474935001|ref|YP_007688583.1| 59 SMIFWGPPGVGKTTLAG 75
                                      5788**********996 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.7
                            AAA_24  75 deleelclaevirqnekaesk..edkgdgkGygel 107
                                       d++e++  + v  + ++a++k  ed g+gkGy ++
  gi|474935001|ref|YP_007688583.1| 363 DDAEKMLAEPVPLRIRNASTKlmEDLGYGKGYEYA 397
                                       55555555555434444455566899999998765 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1     0.024        14      11      35 ..      58      81 ..      49      93 .. 0.71
   2 ?    3.3   0.0      0.17        94      93     136 ..     104     146 ..      87     154 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.024
                            AAA_19 11 kvllvtaGpGtGKTrvlkhivallv 35
                                      + ++  ++pG GKT++  +i+a   
  gi|474935001|ref|YP_007688583.1| 58 TSMIFWGPPGVGKTTL-AGIIANST 81
                                      567889*******975.55555544 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.17
                            AAA_19  93 eaeeekklqeeellivDEfqdvd.elqyrLlkallgekkklllvG 136
                                        ae ++   ++++l+vDE+   +  +q ++l  +  ++  ++l+G
  gi|474935001|ref|YP_007688583.1| 104 AAEMRRRHGKRTVLFVDEIHRFNkAQQDAFLPFVE-KGS-ITLIG 146
                                       3333444446779**********666666666555.555.88888 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0    0.0012      0.67      14      37 ..      60      83 ..      52     157 .. 0.77
   2 ?   -1.3   0.0         5   2.8e+03      75      80 ..     241     258 ..     170     302 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0012
                                      EEEEESTTSSHHHHHHHHTTSS-- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 14 vaivGenGaGKStLlkllagllkp 37
                                      + + G+ G GK+tL+ ++a+ ++ 
  gi|474935001|ref|YP_007688583.1| 60 MIFWGPPGVGKTTLAGIIANSTDA 83
                                      5678***************99887 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 5
                                       BHHHH............H CS
                                       xxxxx............x RF
                          ABC_tran  75 tvren............e 80 
                                       tv e             e
  gi|474935001|ref|YP_007688583.1| 241 TVVEVtarksllydkdgE 258
                                       222223333344333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        32  (0.00178482); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              32  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.45
# Mc/sec: 2985.39
//
Query:       gi|474935002|ref|YP_007688584.1|  [L=74]
Description: hypothetical protein TALC_01448 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.1   12.2   0.0        0.1   12.2   0.0    1.1  1  Relaxase  Relaxase/Mobilisation nuclease domain
       0.12   12.2   0.1        8.6    6.3   0.0    2.1  2  PASTA     PASTA domain


Domain annotation for each model (and alignments):
>> Relaxase  Relaxase/Mobilisation nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.1e-05       0.1     182     209 ..      39      67 ..       8      74 .] 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.1e-05
                          Relaxase 182 e..nasdfedlkealkekglelrrktgkkl 209
                                           + ++ed+  alk++gl++  ++g+++
  gi|474935002|ref|YP_007688584.1|  39 NrlDVISWEDFEAALKKRGLQIY-ASGSWM 67 
                                       344599****************8.777776 PP

>> PASTA  PASTA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0   0.00096       8.6      10      37 ..       7      37 ..       3      45 .. 0.71
   2 ?    4.8   0.0    0.0029        26      10      25 ..      45      60 ..      42      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.00096
                                      BHHHHHHHHHHTT--CCCEEE...ECTCCGT CS
                             PASTA 10 svdeAkatLkalGlkiktvee...tsddvpe 37
                                      s+d Ak ++k+ Glk + v+    ++ ++++
  gi|474935002|ref|YP_007688584.1|  7 SIDKAKIIAKNTGLKPGRVKGtegVQFTKGT 37
                                      89************55555543336666665 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0029
                                      BHHHHHHHHHHTT--C CS
                             PASTA 10 svdeAkatLkalGlki 25
                                      s+++ +a+Lk+ Gl+i
  gi|474935002|ref|YP_007688584.1| 45 SWEDFEAALKKRGLQI 60
                                      89************65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 542.92
//
Query:       gi|474935003|ref|YP_007688585.1|  [L=445]
Description: Phosphomannomutase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.5e-10   40.1   0.0      1e-07   32.5   0.0    2.4  2  PGM_PMM_II  Phosphoglucomutase/phosphomannomutase, alpha/beta
    1.4e-07   31.3   0.0    2.7e-07   30.4   0.0    1.5  1  PGM_PMM_I   Phosphoglucomutase/phosphomannomutase, alpha/beta


Domain annotation for each model (and alignments):
>> PGM_PMM_II  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.0   1.1e-11     1e-07      13     103 .]     151     238 ..     143     238 .. 0.91
   2 !    5.1   0.0    0.0039        35      70      91 ..     298     319 ..     285     321 .. 0.88

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 1.1e-11
                                       HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TTSS----TT-TTTTHHHHGGGGG-SEEEEE CS
                        PGM_PMM_II  13 seaikksglkvvidplhGaggeilkellkelgvdvvelnaepdpdfptkapnpeekealkllielvkkegadlglaf 89 
                                       ++ i+ +g+ +++d++ G+++ +++++l+e+g+d+ ++n++  ++ p ++p  ++  +l  l+  v+++  ++g+a 
  gi|474935003|ref|YP_007688585.1| 151 NSGIQADGF-IILDCGCGSTSLVAPRALSEAGADISSMNSHIGKKAP-RNPGINK-TDLLPLGGFVNESVGSIGIAY 224
                                       456788888.9*********************************999.7898888.9999999************** PP

                                       -TTS-BEEEEETTE CS
                        PGM_PMM_II  90 DgDaDRlgvvderG 103
                                        gD+ Rl+v+de+G
  gi|474935003|ref|YP_007688585.1| 225 NGDGTRLAVMDESG 238
                                       ***********998 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0039
                                       TTTTHHHHGGGGG-SEEEEE-T CS
                        PGM_PMM_II  70 alkllielvkkegadlglafDg 91 
                                       ++ ++i+++k+++ad+g+ +Dg
  gi|474935003|ref|YP_007688585.1| 298 DINSVIKAIKDNDADIGALTDG 319
                                       78899****************8 PP

>> PGM_PMM_I  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   3.1e-11   2.7e-07      17     124 ..      16     115 ..       5     122 .. 0.81

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 3.1e-11
                                       TBSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB-HHHHHHHHHHCCECE CS
                         PGM_PMM_I  17 eltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillgllptPavsfairklkada 93 
                                        +tpe ++++g  +++++++      v+v+ Dt  ss+ + +a+ agl a+G++vi++g+ p Pa+ fa  +     
  gi|474935003|ref|YP_007688585.1|  16 RMTPEDALEVGIRLGSVFSS------VAVSCDTDSSSPVILSAFTAGLNAAGADVIDIGVSPAPAACFAYAH--SVE 84 
                                       39999999999999999997......*******************************************999..333 PP

                                       EEEE--TTS-TTCCCEEEEETTTCE--CHHH CS
                         PGM_PMM_I  94 gimitaSHnppeyngiKvylsnGgpispeve 124
                                        i   +S n ++   i +  ++G ++++e+ 
  gi|474935003|ref|YP_007688585.1|  85 VIANIGSPNGYTLPSITLRHPDGSQFEEEEV 115
                                       3444466666666667777777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2816.45
//
Query:       gi|474935004|ref|YP_007688586.1|  [L=132]
Description: hypothetical protein TALC_01450 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0032   17.2   0.5      0.004   16.9   0.5    1.3  1  Prok-JAB  Prokaryotic homologs of the JAB domain


Domain annotation for each model (and alignments):
>> Prok-JAB  Prokaryotic homologs of the JAB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.5   2.2e-07     0.004      55     116 ..      52     109 ..      10     111 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.2e-07
                          Prok-JAB  55 slarlkfearerglevvgiwHSHpggsarPSetDrrdaaalarvkalliivgdkaeelrawr 116
                                       s + ++ +++  + +  g +HSHpg sa+ Se D+  +  ++  ++++i ++  ++++++w 
  gi|474935004|ref|YP_007688586.1|  52 SHSFINDWMDPIDYHRAGSAHSHPGYSAEASEDDLTVFGMMG--GIHFITCQ--PYDRKSWV 109
                                       34444448888899999*****************99998775..56666665..47777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 851.22
//
Query:       gi|474935005|ref|YP_007688587.1|  [L=533]
Description: putative sugar kinase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.7e-52  176.3   0.8    3.5e-51  174.1   0.7    1.8  2  NAD_kinase  ATP-NAD kinase
    1.8e-27   96.5   0.0    2.6e-27   96.0   0.0    1.2  1  Inositol_P  Inositol monophosphatase family
  ------ inclusion threshold ------
       0.14   11.8   0.2       0.29   10.8   0.2    1.5  1  DAGK_cat    Diacylglycerol kinase catalytic domain


Domain annotation for each model (and alignments):
>> NAD_kinase  ATP-NAD kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0     0.071   4.2e+02       3      35 ..     269     300 ..     267     311 .. 0.78
   2 !  174.1   0.7   5.9e-55   3.5e-51      72     291 ..     310     516 ..     304     517 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.071
                                       EEEESSCGGTCSHHHHHHHHHHHCT.-..EEEEE CS
                        NAD_kinase   3 givvnpikkeaieraeevarwLlda.lsrvlevt 35 
                                       g+v+np+ + +++++++va+ L +  l  v+  t
  gi|474935005|ref|YP_007688587.1| 269 GLVANPNVPDLENYVRRVADALGQEtL--VCDAT 300
                                       89*******************999833..55444 PP

  == domain 2  score: 174.1 bits;  conditional E-value: 5.9e-55
                                       -TTTTTSSSEEEEEE-HHHHHHHHHHHHHCT-EEEEEESSS--SS-SEEGGGHHHHHHHHHHT-SEEEEEEEEEEEE CS
                        NAD_kinase  72 eafadagvdliivvGGDGTaldvarllqkaeiPvlgvnaGvkgfltefepeaaaellekllegeirvekrevldavi 148
                                        ++ d++vd++i++GGDGT+l++a  +++   P++g+naG +gfl+e++p+ + e +++l  g++++++r++ld ++
  gi|474935005|ref|YP_007688587.1| 310 TDVRDMDVDVVITIGGDGTILRAAMGTRA---PIMGINAGGVGFLAEITPDRIEEGIARLRSGDFTISERFKLDSFL 383
                                       567899******************99995...******************************************999 PP

                                       EETTE......EEEEEEESSEEEEEESSSSS-EEEEEEETTEEEEEEEESEEEEE-TGGGGTHHHHTT--EE-TT-- CS
                        NAD_kinase 149 mrskgeediadiviensvlnevviirgpgstlielelyvdtelleadqldglivstPtGstayslsaGgplisPgvl 225
                                       + +k          e++ +ne v+++ + +++ ++++yvd++l++++++dg+i+stPtGst y++s G p+++Pgv+
  gi|474935005|ref|YP_007688587.1| 384 NGKKM---------EPT-INEAVVHTDSVAKIRQFKVYVDGKLATEVRADGIIISTPTGSTSYAMSLGAPMVDPGVD 450
                                       99999.........465.9********************************************************** PP

                                       -EEEEEESESSS----EEE-TT-EEEEEE-SS--EEEEETTTEEEEE-TT-EEEEEEESSEEEEEE CS
                        NAD_kinase 226 ailivpicPhslssrpiVvssssklrirvasrseallaldGseelelspgdevrvtasdkkfklir 291
                                       a+livp+ + + +srp Vv+s  k++++  +++ +ll+ldG+ e  ++ g  + +++s++ ++++ 
  gi|474935005|ref|YP_007688587.1| 451 ALLIVPMAAYKFASRPFVVPSGVKVTVECVRDKGCLLVLDGQAEHPIEGGSKLDFVRSSERVRFVS 516
                                       **************************9999*******************************99985 PP

>> Inositol_P  Inositol monophosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.0   0.0   4.4e-31   2.6e-27      11     254 ..      10     246 ..       1     263 [. 0.79

  Alignments for each domain:
  == domain 1  score: 96.0 bits;  conditional E-value: 4.4e-31
                                       HHHHHHHHHHHHHTTTSEEEESTTTCCHHHHHHHHHHHHHHHHHHHHHHHHSTTSEEEHHCHHHHCCCT.SSSSSEE CS
                        Inositol_P  11 elaakagevlreefsenelvieekskegeedlvtaadeaveelilealaekfpshkilgeetlakgekseltedglt 87 
                                       ++++++g + + e++   ++ie +    +  + +++d+++e ++l+ + +++    +l+ee +        + d  t
  gi|474935005|ref|YP_007688587.1|  10 AVVKAVGLIPTLEER--GKDIEMGA---DGTPTSEIDKVAENTVLDFIVRNRVPLNVLSEEIGFVDY----GYD-ET 76 
                                       445555544444443..33333333...446899*************98888888999999888888....788.8* PP

                                       EEEEEEETHHHHHHT-SG-EEEEEEEE..TTEEEEEEEEETTTTEEECEETTTEEEETCEEEEECTTSEGGGTEEEE CS
                        Inositol_P  88 wivDPiDGTknFvrgipqvaVsigllv..egkpvlGviaqPllgqlysaakgkGaflngeklplsrappiseallvt 162
                                        ++DPiDGT+n + g p ++Vs+++     + ++ + + + ++g++++a kg+Gaf +g+++++++ +    ++l+ 
  gi|474935005|ref|YP_007688587.1|  77 LVLDPIDGTSNAIAGVPLFTVSLAVGNkdLDGIHTAYLRNIATGESMWAEKGRGAFKDGRRISVRSPD---FKHLFV 150
                                       *************************995557899*************************988888888...455555 PP

                                       EESSSSSSHHHHCHHHHHHHCCCCCHEEEBESSHHHHHHHHHHTSTSEEEEEC......EBHHHHHHHHHHHHHTTE CS
                        Inositol_P 163 lfavssrkdtseasllekvesavsaegvrsvgssalklaavaeGkadaylefg.....rekkWDhAAGeaileeaGG 234
                                        + + +  d++       + + v+    rs+g + l++a+vaeG++day+  +      + + D+AA  +il+eaGG
  gi|474935005|ref|YP_007688587.1| 151 MIYMGNGADPKS----FELAKNVKSS--RSYGCASLEMALVAEGQCDAYYMNSerynrGIRIVDIAASYLILREAGG 221
                                       566666666666....2333444555..7999*****************9998899999****************** PP

                                       EEEESSSC....SSSTTSS.EEEEE CS
                        Inositol_P 235 vvtdakge....grlllar.giiaa 254
                                        v d++g+    +++l ar + +a+
  gi|474935005|ref|YP_007688587.1| 222 HVYDLSGKafnmPFDLSARsNFVAC 246
                                       ********99998888554255555 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   4.8e-05      0.29      48      72 ..     312     333 ..     269     346 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4.8e-05
                                       HHHHHHCC-SEEEEEESHHHHHHHH CS
                          DAGK_cat  48 akeakeegvdlivvaGGDGtvsevl 72 
                                       +++    +vd+++ +GGDGt+  ++
  gi|474935005|ref|YP_007688587.1| 312 VRD---MDVDVVITIGGDGTILRAA 333
                                       333...3579**********96655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (533 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 3288.87
//
Query:       gi|474935006|ref|YP_007688588.1|  [L=219]
Description: rRNA 2'-O-methyltransferase fibrillarin [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.4e-79  263.8   0.0      1e-78  263.6   0.0    1.0  1  Fibrillarin      Fibrillarin
  ------ inclusion threshold ------
      0.011   16.4   0.0      0.023   15.4   0.0    1.6  1  Methyltransf_25  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  263.6   0.0   1.1e-82     1e-78      18     223 ..      15     217 ..       9     219 .] 0.97

  Alignments for each domain:
  == domain 1  score: 263.6 bits;  conditional E-value: 1.1e-82
                                       SEEEEEE-SSTT--SSSSEEEEETTEEEEEE-TTTSHHHHHHHTT-S--S--TTSEEEEESTTTSHHHHHHHHHHTT CS
                       Fibrillarin  18 darlatknlvpgekvYgEklikveeeEyRvWnpfrsKlaaailkglkelpikkgskvLYlGaasGttvsHvsDivge 94 
                                         r+ t + +pg++vYgE+l++++++EyR+Wnp+rsKlaa i +g +++pi + s+vLYlGa+sGtt+sHvsD+v  
  gi|474935006|ref|YP_007688588.1|  15 MRRIYTLSSAPGTRVYGERLVTSKGKEYREWNPMRSKLAAYIANGGRSVPITRKSNVLYLGASSGTTPSHVSDMVS- 90 
                                       45799**********************************************************************9. PP

                                       TSEEEEEESSHHHHHHHHHHHTTSTTEEEEES-TTSGGGGTTTS--EEEEEEESSSTTHHHHHHHHHHHHEEEEEEE CS
                       Fibrillarin  95 egvvyavefsprvlrelievakkRknivPileDArkPekYralvekvDvifaDvaqpdqarilaknaklflkeggyl 171
                                       eg+vy+vef+pr++rel+  a  R+n++Pil+DA+kP++Y+ +ve vDv+++Dvaq +qa+ila+n+++f  +  y 
  gi|474935006|ref|YP_007688588.1|  91 EGKVYCVEFAPRMFRELVGNAGPRPNMMPILADATKPSEYQFMVEDVDVVYQDVAQKNQADILADNMDMFGAR--YG 165
                                       **********************************************************************876..56 PP

                                       EEEEEHHHHHSSSSHHHHHHHHHHHHHHTTEEEEEEEE-TTTSTTEEEEEEE CS
                       Fibrillarin 172 lisikarsidvtkepeevfkeeveklkeeglkvleqvklepyekdhalvvgk 223
                                       ++++kars dv++ep+ +fk+ +++lke+g+++l++ +lep+e  h+++v++
  gi|474935006|ref|YP_007688588.1| 166 MVAVKARSEDVAEEPKVIFKRSESRLKERGFRILDSRSLEPFEDSHVMIVVE 217
                                       89***********************************************975 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0   2.6e-06     0.023       1      70 [.      71     142 ..      71     158 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.6e-06
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCG...BSSSTTTEEEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaed...lpfedgsfDlvvs 70 
                                       vL lG+ +G++  ++++ ++++kv++v+++++m ++   +a   ++n+  + +da++   ++f  + +D+v+ 
  gi|474935006|ref|YP_007688588.1|  71 VLYLGASSGTTPSHVSDMVSEGKVYCVEFAPRMFRELVGNAG-PRPNMMPILADATKpseYQFMVEDVDVVYQ 142
                                       899***************989******************995.446999999999663336788889999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1491.33
//
Query:       gi|474935007|ref|YP_007688589.1|  [L=118]
Description: ADP-ribose pyrophosphatase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-12   46.3   0.3      5e-12   46.0   0.3    1.2  1  NUDIX     NUDIX domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.0   0.3   2.8e-16     5e-12       6      66 ..       8      65 ..       4     116 .. 0.67

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 2.8e-16
                                      EEEEEEETTSEEEEEEESSSSTTTEESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEE CS
                             NUDIX  6 vgvvllnekgevLlvrrskkpfpgWelPgGkvepgEtpeeAArREleEEtGleaellellg 66
                                      v  v ++++ ++L+v     + +gWe+PgG+v++gE+ e+AA RE+ EE G++ e +e+ +
  gi|474935007|ref|YP_007688589.1|  8 VYTVAFQGE-RFLMVYNE--KRKGWEMPGGHVREGESREDAAKREFLEESGYDIEIVEIRD 65
                                      555555555.48888744..8899***************************9888886654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 793.36
//
Query:       gi|474935008|ref|YP_007688590.1|  [L=134]
Description: SSU ribosomal protein S15P [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-14   53.0   0.1      4e-14   52.6   0.1    1.2  1  Ribosomal_S15    Ribosomal protein S15
      3e-12   46.4   0.0      5e-12   45.7   0.0    1.4  1  Ribosomal_S13_N  Ribosomal S13/S15 N-terminal domain
  ------ inclusion threshold ------
      0.028   14.3   0.2      0.048   13.5   0.2    1.4  1  GatB_Yqey        GatB domain


Domain annotation for each model (and alignments):
>> Ribosomal_S15  Ribosomal protein S15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   0.1   6.8e-18     4e-14      14      80 ..      63     131 ..      52     132 .. 0.90

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 6.8e-18
                                       -TSSHHHHHHHHHHHHHHHHHHHHCTTT-HHHHHHHHHHHHHHHHHHHHHHHH-H..HHHHHHHHHCTS CS
                     Ribosomal_S15  14 DtGspevqiallterInnltehlkenkkDkhsrrgLlklvskRrkllkYLkrkdv..erYkklieklgl 80 
                                         G++++++  l+ r+ nl+ h+k n+kD+++ rgL ++++k+r+l +Y+kr+ v  +++k+ +++++l
  gi|474935008|ref|YP_007688590.1|  63 LKGNLPEDLQQLMVRAINLNVHVKANPKDVANIRGLALIEAKIRRLERYYKRNGVlpATWKYSLANAEL 131
                                       3579***********************************************************999876 PP

>> Ribosomal_S13_N  Ribosomal S13/S15 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   0.0   8.3e-16     5e-12      20      60 .]       3      43 ..       1      43 [. 0.94

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 8.3e-16
                                      SS--TTS---HHHHHHHHHHHHHTT--HHHHHHHHHHCCT- CS
                   Ribosomal_S13_N 20 reapsWlklskeeveelivklakkGltpSqIGviLRDqyGv 60
                                       e+p W+ l+++e+e+++ ++ak+G+++++IG+iLRDq +v
  gi|474935008|ref|YP_007688590.1|  3 SENPDWVPLTATEIEDKVAEFAKDGISSAMIGMILRDQWAV 43
                                      579***********************************876 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   8.1e-06     0.048      38     105 ..       9      82 ..       3      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.1e-06
                                       SSTTHHHHHHHHHHHHTTSSGHHHHHHHHHHHH.......HHTXXHHHHHHHCTXXXXXXSSXHHHHHHHHHHTX CS
                         GatB_Yqey  38 lkltpeqlaellkliaegkIskkiakevleell.......eegkspeeiieekgLkqisdeeeleklveeviaen 105
                                       ++lt+ ++++ ++ +a++ Is+ ++ ++l+  +       ++gk++ ei++ekgLk    +e l++l+  +i+ n
  gi|474935008|ref|YP_007688590.1|   9 VPLTATEIEDKVAEFAKDGISSAMIGMILRDQWavpnvklATGKTVTEILKEKGLKGNL-PEDLQQLMVRAINLN 82 
                                       5799999**********************9999899988788*************9876.588888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 798.51
//
Query:       gi|474935009|ref|YP_007688591.1|  [L=451]
Description: Single-stranded DNA-specific exonuclease [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-11   43.8   0.9    4.3e-11   43.4   0.1    1.7  2  DHHA1     DHHA1 domain
    1.5e-06   28.3   0.3    3.8e-06   27.1   0.3    1.6  1  DHH       DHH family
  ------ inclusion threshold ------
      0.042   14.1   0.0       0.11   12.7   0.0    1.7  1  DUF1884   Domain of unknown function (DUF1884)


Domain annotation for each model (and alignments):
>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1         2   1.2e+04     118     135 ..     212     229 ..     211     231 .. 0.82
   2 !   43.4   0.1   7.2e-15   4.3e-11      32     138 .]     336     442 ..     309     442 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2
                                       EEEEEEHCHHHHHHHHHH CS
                             DHHA1 118 aGagipaekleealeale 135
                                       aG + +a+ + ++l++++
  gi|474935009|ref|YP_007688591.1| 212 AGITGDADAVTAFLKEAR 229
                                       788889999999999987 PP

  == domain 2  score: 43.4 bits;  conditional E-value: 7.2e-15
                                       HTCEEECTCEEEEEECHCCHHHHHHHHHHHHHHTHGBT.TCEEEEEEEECTEEEEEEEESSH....SS-HHHHHHHH CS
                             DHHA1  32 ekaeevkgvkvlvaevgeewdagalgiaadklksklkk.pvivfvakeegdkvkvsarskkd....gvdagelakea 103
                                        k+ + ++ + + + +  +    + g + + + +  ++ p+i +  +ee+  +++s r +      gvd+++++k+ 
  gi|474935009|ref|YP_007688591.1| 336 GKLHQMENIQWFDSSS-SGFTGMICGVIMSFIGD--PDkPTIGINCSEED--ANISSRGTFPlldkGVDLADAMKRG 407
                                       4444443444444444.66666666777777777..77777777777774..89999999779999*********** PP

                                       HHHTTCCEEEETCEEEEEEEHCHHHHHHHHHHHHH CS
                             DHHA1 104 aaklgggGGGHdlAaGagipaekleealealeeai 138
                                       +a +gg GGGH+ AaG++i+  k +e+l+ +++++
  gi|474935009|ref|YP_007688591.1| 408 CASVGGEGGGHRIAAGGSIKSAKRDEFLANVDKIV 442
                                       ******************************99875 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.3   6.4e-10   3.8e-06       4      82 ..      27     141 ..      26     159 .. 0.62

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 6.4e-10
                                       EE-ECSSSHHHHHH.HHHHHH.............................CECS--TCGGCGCCHHCCCSEEEEEEE CS
                                       xxxxxxxxxxxxxx.xxxxxx.............................xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH   4 ivghknpDtDsigS.aialan.............................llvDhneksqavegeakeeaedviiiD 50 
                                       i  + ++D+D++++ ai+ ++                              +v + +   + ++++++ + dvi++D
  gi|474935009|ref|YP_007688591.1|  27 IHVYSHYDADGLTAaAIVCKAlmragkefqvttfhtltdpqmqiieenrdACVLMTDLGASYIDRLEKLGGDVIVLD 103
                                       55599*********66666666666666666666666666666555555524445555555555577********** PP

                                       -S---SS---SS--EEEE-SS........S-HHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxx RF
                               DHH  51 HHrlgeefetlapilflnepv........gstaeivaell 82 
                                       HH lg   ++ +++++ n+++        g++a++++ ++
  gi|474935009|ref|YP_007688591.1| 104 HHTLGV--TNTEKVIYANPHLygidgmtsGCGATMAFLFA 141
                                       ****95..44445555555432222222288888888765 PP

>> DUF1884  Domain of unknown function (DUF1884)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.9e-05      0.11      53      82 ..      82     111 ..      51     118 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.9e-05
                                       -EETTEEEEE-GGGTTEEEEE-TTTTTTST CS
                           DUF1884  53 telsnlkveileeLGgDavvvDskvLGqik 82 
                                       t+l    + +le LGgD +v+D ++LG  +
  gi|474935009|ref|YP_007688591.1|  82 TDLGASYIDRLEKLGGDVIVLDHHTLGVTN 111
                                       566666799******************865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 3002.23
//
Query:       gi|474935010|ref|YP_007688592.1|  [L=327]
Description: O-sialoglycoprotein endopeptidase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-85  286.4   0.0    3.3e-85  286.1   0.0    1.0  1  Peptidase_M22   Glycoprotease family
  ------ inclusion threshold ------
      0.061   12.8   0.1       0.62    9.5   0.1    2.0  2  BcrAD_BadFG     BadF/BadG/BcrA/BcrD ATPase family
       0.08   12.6   0.0          4    7.0   0.0    2.2  2  Carbam_trans_N  Carbamoyltransferase N-terminus
      0.082   12.7   0.2       0.19   11.5   0.2    1.5  1  DUF348          G5-linked-Ubiquitin-like domain


Domain annotation for each model (and alignments):
>> Peptidase_M22  Glycoprotease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  286.1   0.0   7.3e-89   3.3e-85       2     271 .]      24     293 ..      22     293 .. 0.96

  Alignments for each domain:
  == domain 1  score: 286.1 bits;  conditional E-value: 7.3e-89
                                       CEXEEEEEEEEE....SSSSHHHHHHHHHHHHHHHHHHHHHHHTSTGGGEEEEEEEEESS-HHHHHHHHHHHHHHHH CS
                     Peptidase_M22   2 vlanvvasqkelhakyGGvvPelasraHserllplieealaeaglsledldaIavtkgPGlftgLrvGvsfAkglal 78 
                                       vlanv+  ++   +++GG +P++a+ +H+e +   i++a ++ag+sl+d+d + ++ gPGl+++Lrv+ ++A+ la+
  gi|474935010|ref|YP_007688592.1|  24 VLANVIDMYR---PPQGGLHPREAANHHAEVVAGDIQKAVEQAGISLKDVDLVSFSMGPGLGPCLRVAGTAARSLAF 97 
                                       6777777776...889************************************************************* PP

                                       HCT--EEEEEHHHHHHHCCHCTSECSSCEEEEESSSTEEEEEECTTEEEEEEEESSSEHHHHHHHHHHHHT..SSCC CS
                     Peptidase_M22  79 alnkPlvgVnhleahalaarleekeefPvvllvsGghtqvylvkegryeilgetlddaagealdkvarllglpypgg 155
                                       +l++P+vgVnh++ h++ ++ +++ ++P +l+ sGg+tqv++++++ry+i+get d  +g+++dk++r lgl++ +g
  gi|474935010|ref|YP_007688592.1|  98 TLGVPIVGVNHCISHIEIGNATTGCHDPCLLYASGGNTQVIAYSDRRYRIFGETQDVGVGNMFDKLGRDLGLGFYAG 174
                                       *******************9887669*****************99******************************** PP

                                       HHHHHHHCTC.S.......EETTEEE.CHHHHHHHHHHST.T.HHHHHHHHHHHHHHHHHHHHHHHHHHCTBSEEEE CS
                     Peptidase_M22 156 pkieklakeg.kkiefprplkgldfsfsGlktavlkelek.e.vedlaasfqeavvdhlvekteralklpkakelvi 229
                                       pkie+la++g k +++p+ +kg+d+sfsG+ ta++   +k e  ed+++s+qe+++++l+e+tera+++ +++e+++
  gi|474935010|ref|YP_007688592.1| 175 PKIEELARSGdKLLDLPYSVKGMDISFSGILTAAVAYRQKgErLEDICYSVQETAFSMLTEVTERAMAHVGKDEVLL 251
                                       **********666*************************88757********************************** PP

                                       ESGGGGXHHHHHCHCCHHHHTTSEEEXXXHHHHSSXCHHHHH CS
                     Peptidase_M22 230 lGGvaankrLrealeeeaeelglkliiPplkyctdnaamiaw 271
                                       +GGva+n+rLr ++ e+a+e+g+k+++P++++c+dn+amiaw
  gi|474935010|ref|YP_007688592.1| 252 GGGVAQNNRLRDMVGEMAKERGAKMFVPEKQFCRDNGAMIAW 293
                                       *****************************************9 PP

>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0     0.051   2.3e+02      38      65 ..      46      73 ..       7     112 .. 0.82
   2 ?    9.5   0.1   0.00014      0.62     185     246 ..     212     275 ..     202     292 .. 0.63

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.051
                                      ........HHHHHHHHHHT--GGGECEE CS
                       BcrAD_BadFG 38 eaaekvleealtealerageeeadieet 65
                                      +  ++v+ + +++a+e+ag + +d++ +
  gi|474935010|ref|YP_007688592.1| 46 NHHAEVVAGDIQKAVEQAGISLKDVDLV 73
                                      4567788999999999999999998865 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00014
                                       HHTT--HHHHHHHHHHHHHHHHHHHHHTT..---SS.EEEESGGGG-HHHHHHH.....HHHH- CS
                       BcrAD_BadFG 185 lsggekaedIlaglhraialrvialisrs..ggvtdevtltGGvakneaavkelrklvkenyge 246
                                       +++ge  edI   + +   + + ++ +r      +dev+l GGva+n+ +  ++ ++ ke+  +
  gi|474935010|ref|YP_007688592.1| 212 RQKGERLEDICYSVQETAFSMLTEVTERAmaHVGKDEVLLGGGVAQNNRLRDMVGEMAKERGAK 275
                                       6677777777555544444444444444311233478**********66655555555555554 PP

>> Carbam_trans_N  Carbamoyltransferase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.011        47      37      68 ..      46      76 ..       3      81 .. 0.68
   2 ?    7.0   0.0    0.0009         4     257     306 ..     207     259 ..     176     271 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.011
                    Carbam_trans_N 37 krdqklpklkaidyaleeagvelsdiDqivfd 68
                                      ++ +++    +i+ a+e+ag++l+d+D + f 
  gi|474935010|ref|YP_007688592.1| 46 NHHAEVVA-GDIQKAVEQAGISLKDVDLVSFS 76
                                      34444444.589***************98775 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0009
                    Carbam_trans_N 257 rlkearekde...dlaAsiqvflErlvvevlnivyeklkirnLclaGGvalNi 306
                                          ++r+k+e   d+  s+q+    ++ ev++ ++++++     l GGva N 
  gi|474935010|ref|YP_007688592.1| 207 AAVAYRQKGErleDICYSVQETAFSMLTEVTERAMAHVGKDEVLLGGGVAQNN 259
                                       4455666655555*************************************995 PP

>> DUF348  G5-linked-Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   4.3e-05      0.19      16      37 ..      53      74 ..      49      76 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.3e-05
                                      -SSHHHHHHHTT----TT-EEE CS
                            DUF348 16 adTVgdlLeeagitlgeqDkVs 37
                                      a++ + + e+agi+l+++D Vs
  gi|474935010|ref|YP_007688592.1| 53 AGDIQKAVEQAGISLKDVDLVS 74
                                      889999**************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1962.34
//
Query:       gi|474935011|ref|YP_007688593.1|  [L=297]
Description: Permeases of the drug/metabolite transporter (DMT) superfamily [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-28   98.8  31.8    3.7e-17   62.8  10.7    2.0  2  EamA             EamA-like transporter family
    0.00033   20.1  12.3       0.12   11.7   2.3    2.2  2  TPT              Triose-phosphate Transporter family
     0.0052   16.2   3.5     0.0052   16.2   3.5    2.4  3  Sugar_transport  Sugar transport protein
     0.0098   15.8   0.5     0.0098   15.8   0.5    3.4  3  DUF981           Protein of unknown function (DUF981)


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3  13.1   1.8e-14     8e-11       7     136 ..      10     137 ..       8     138 .. 0.93
   2 !   62.8  10.7   8.2e-21   3.7e-17       2     136 ..     148     282 ..     147     283 .. 0.93

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 1.8e-14
                              EamA   7 allaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegkl.aklslkdwllllllgllgtvlafllf 82 
                                       +++a+++ ++++++ +   ++ +++ ++f+r+l+a+++ +++al+k +   a++ ++d+l  +l g+  +++    +
  gi|474935011|ref|YP_007688593.1|  10 IICASVMVSFSAIFYRL--SDAPSMVMVFYRMLFASAIIVPVALWKCRGEfASMERRDVLVSILSGI-VFAVHLATY 83 
                                       89999999999999976..7**************************99999*******999988886.45555689* PP

                              EamA  83 fyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                       f +l ++s +   ++t +++ f++++ ++++ge+++ + +  ++l + G+++i 
  gi|474935011|ref|YP_007688593.1|  84 FESLDRVSIASCLVLTDTAVFFVALIMIVFFGESVSRRGWGIMALTFGGCVIIA 137
                                       ***************************************************985 PP

  == domain 2  score: 62.8 bits;  conditional E-value: 8.2e-21
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvla 78 
                                       +g+ lal ++l++a+y+++ +++  ++s+l++t++ +  a++  l++ +  +        +++l+ l l++++t+++
  gi|474935011|ref|YP_007688593.1| 148 IGDGLALFSSLLFAVYAIIGRRVRGRMSTLAYTAILYSSAALTSLVMVASGDAGELDCGTENLLYALGLAVFCTIFG 224
                                       67889*******************************99888877776666666666999****************** PP

                              EamA  79 fllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                       + +++++l++ +as++++ t+lePvf  +l+ +++ge ++ + ++g +++l+Gv++ +
  gi|474935011|ref|YP_007688593.1| 225 HTVYNWGLRYEKASFVAITTLLEPVFGSVLGLAVFGEIPGALVIAGSAVVLIGVYMFS 282
                                       *******************************************************976 PP

>> TPT  Triose-phosphate Transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   5.6     3e-05      0.13      29     190 ..      28     194 ..      10     200 .. 0.71
   2 !   11.7   2.3   2.7e-05      0.12      65     136 ..     210     282 ..     180     285 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3e-05
                               TPT  29 pyPltvsav.q..llvgsvlilvlwalglkkrpkisse.flkailplalvktlghvlavv.slskvaVSfthtvKas 100
                                         P++v ++ +  +++ +++ ++lw+ + +  + ++ + +l++il  ++v +++h+++ + sl +v++    ++  +
  gi|474935011|ref|YP_007688593.1|  28 DAPSMVMVFyRmlFASAIIVPVALWKCRGE-FASMERRdVLVSIL-SGIV-FAVHLATYFeSLDRVSIASCLVLTDT 101
                                       566666554221133444444455555443.45565552444444.4444.56677776659*************** PP

                               TPT 101 ePiFtvilsrlllgeklsllvylsLlpivgGvalasvtElsFn..ligfisAlisnltfslrnifsKkllkklkd.l 174
                                       + +F +++ ++++ge++s   +  +    gG+++ ++ ++s +  +ig   Al+s l f++  i+ +++   +    
  gi|474935011|ref|YP_007688593.1| 102 AVFFVALIMIVFFGESVSRRGWGIMALTFGGCVIIAIDDMSGDsgIIGDGLALFSSLLFAVYAIIGRRVRGRMSTlA 178
                                       ****************************************98744677788*************9999866632223 PP

                               TPT 175 dalnlfaiitilslll 190
                                        +  l++  ++ sl++
  gi|474935011|ref|YP_007688593.1| 179 YTAILYSSAALTSLVM 194
                                       3333455555555554 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 2.7e-05
                               TPT  65 lkailplal.vktlghvlavvslskvaVSfthtvKasePiFtvilsrlllgeklsllvylsLlpivgGvalas 136
                                       l + l la+ + ++gh + +  l     Sf  +   +eP+F  +l   ++ge +  lv+    +++ Gv + s
  gi|474935011|ref|YP_007688593.1| 210 LLYALGLAVfCTIFGHTVYNWGLRYEKASFVAITTLLEPVFGSVLGLAVFGEIPGALVIAGSAVVLIGVYMFS 282
                                       44455555438899*******************************************************9977 PP

>> Sugar_transport  Sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   3.5   1.2e-06    0.0052     177     271 ..      39     136 ..       5     141 .. 0.71
   2 ?   -1.5   0.2      0.29   1.3e+03     148     194 ..     178     226 ..     159     258 .. 0.65
   3 ?    0.6   0.2     0.064   2.9e+02      87     135 ..     242     286 ..     232     292 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.2e-06
                   Sugar_transport 177 ilpqaiGmvivalilalakkkalvekvslkniisGllwaignlflllsaqkvGvatafslsqlsvvistlggillLk 253
                                       +l+ +  +v val     +   + ++ +l  i+sG+++a+   +++ s  +v +a   +l+ ++v +  l  i++++
  gi|474935011|ref|YP_007688593.1|  39 MLFASAIIVPVALWKCRGEFASMERRDVLVSILSGIVFAVHLATYFESLDRVSIASCLVLTDTAVFFVALIMIVFFG 115
                                       444444444455444444444777888999*********************************************** PP

                   Sugar_transport 254 ekktkkel...vlviiGivli 271
                                       e  +++ +    l++ G v+i
  gi|474935011|ref|YP_007688593.1| 116 ESVSRRGWgimALTFGGCVII 136
                                       **9999761113344455554 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.29
                   Sugar_transport 148 gllllllstigyviyvvla..qlvkvdgleailpqaiGmvivalilala 194
                                       +++++l+s+  ++  v++a  ++ ++d  +  l  a+G+ +   i++++
  gi|474935011|ref|YP_007688593.1| 178 AYTAILYSSAALTSLVMVAsgDAGELDCGTENLLYALGLAVFCTIFGHT 226
                                       5556666666665555544113456776666677777777766666554 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.064
                   Sugar_transport  87 istglqLvgasLigvlvlgeWstsiqvilGllaliliviGivltslkek 135
                                       i+t l  v +s++g  v+ge +++   ++   a  +++iG+++ s +++
  gi|474935011|ref|YP_007688593.1| 242 ITTLLEPVFGSVLGLAVFGEIPGAL--VIAGSA--VVLIGVYMFSCESR 286
                                       6777777889999999999987754..444445..45679999887765 PP

>> DUF981  Protein of unknown function (DUF981)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.5   2.2e-06    0.0098     111     175 ..      14      78 ..       8      85 .. 0.93
   2 ?   -4.1   7.2       2.8   1.3e+04     103     144 ..     152     194 ..      83     226 .. 0.68
   3 ?   -2.4   2.8      0.86   3.9e+03     105     120 ..     214     229 ..     174     282 .. 0.50

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.2e-06
                            DUF981 111 livygvailklgLtaePlaalllyilvGLagllsplvllkldksrsvllvlaavlliiagllall 175
                                        +++ ++ + ++L+ +P+++++ y ++  +++++p++l+k + + +++ +  +++ i++g+++++
  gi|474935011|ref|YP_007688593.1|  14 SVMVSFSAIFYRLSDAPSMVMVFYRMLFASAIIVPVALWKCRGEFASMERRDVLVSILSGIVFAV 78 
                                       56788999**********************************9999****************997 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 2.8
                            DUF981 103 lalflGlilivygvailklgLtaeP.laalllyilvGLaglls 144
                                       lalf +l+  vy++ + + +   +  +++++ly  ++L++l++
  gi|474935011|ref|YP_007688593.1| 152 LALFSSLLFAVYAIIGRRVRGRMSTlAYTAILYSSAALTSLVM 194
                                       4555555666665555443322222134555666666666655 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.86
                            DUF981 105 lflGlilivygvailk 120
                                       l l ++  + g  +++
  gi|474935011|ref|YP_007688593.1| 214 LGLAVFCTIFGHTVYN 229
                                       2333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 1800.43
//
Query:       gi|474935012|ref|YP_007688594.1|  [L=187]
Description: pyridoxal phosphate synthase yaaE subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-54  184.3   0.0    2.2e-54  184.2   0.0    1.0  1  SNO            SNO glutamine amidotransferase family
    3.1e-08   33.5   0.0    4.7e-08   32.9   0.0    1.4  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    0.00033   20.4   0.0    0.00035   20.3   0.0    1.2  1  Peptidase_S51  Peptidase family S51
     0.0023   17.7   0.0     0.0033   17.2   0.0    1.2  1  GATase         Glutamine amidotransferase class-I


Domain annotation for each model (and alignments):
>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.2   0.0   4.9e-58   2.2e-54       1     186 [.       4     184 ..       4     186 .. 0.97

  Alignments for each domain:
  == domain 1  score: 184.2 bits;  conditional E-value: 4.9e-58
                                       EESSSSSHHHHHHHHHHTTSEEEEE-SGGGGC.C-SEEEE-SS-HHHHHHHHHHTT-HHHHHHHHHTT.--EEEETH CS
                               SNO   1 vlalqGaveehveaikkclaenktvkrkedla.evdaliiPGGestamskliertglyedllefvknsekvvlGtCa 76 
                                       vlalqGa+ eh++ +++ + e   +++ke+l+  +daliiPGGest m+kl+   g++e l+  v  + + v+GtCa
  gi|474935012|ref|YP_007688594.1|   4 VLALQGAFAEHERCLERLGFEYAEIRKKEHLDvPLDALIIPGGESTVMGKLLADLGMLERLRGTVLSG-LSVFGTCA 79 
                                       8******************************8459******************************999.9******* PP

                                       HHHHHCCEETTBSS-SS--CCEEEETTTT-SCCGEEEEEEEETTTCSEEEEEESS--EEEEE-.TTTCEEEEECTTE CS
                               SNO  77 GlillskelenelvktlellkvkvkrnafGrqvdsfekeldfknliekftavfiraPvieeilddeavkvlyeldge 153
                                       Gli+ls e+e+ +   l+ ++v+  rna+Grq  sf    dfk+l+ k++  firaP +e ++    v+vl e dg+
  gi|474935012|ref|YP_007688594.1|  80 GLIILSSEVEGGKAS-LGTMDVRTVRNAYGRQLGSFSTVSDFKGLG-KIPMRFIRAPFVESVG--SDVEVLAEVDGR 152
                                       ***********9988.******************************.****************..6799******** PP

                                       EEEEEETTEEEESS-GGGSTTHCHHHHHHHHHH CS
                               SNO 154 ivvakqkkilatsfhPelaeddirvhdyfveev 186
                                       iv+++q++ lat+fhPel++d   vh +f+e+v
  gi|474935012|ref|YP_007688594.1| 153 IVAVRQNRQLATAFHPELTDD-LSVHRFFLEDV 184
                                       *******************98.********987 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0   1.1e-11   4.7e-08      30     118 ..      28     105 ..      11     127 .. 0.81

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 1.1e-11
                          GATase_3  30 vplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGeeiedpegvegeageve 106
                                       ++ k+e l+  +d++i+pGg++t+  + l++  g+ e ++  + +g  v+g C+Gl++L++e+e  +          
  gi|474935012|ref|YP_007688594.1|  28 IR-KKEHLDVPLDALIIPGGESTVMGKLLADL-GMLERLRGTVLSGLSVFGTCAGLIILSSEVEGGK---------A 93 
                                       34.567777559************99888888.*****************************99744.........4 PP

                          GATase_3 107 glglLdietefe 118
                                        lg +d++t+ +
  gi|474935012|ref|YP_007688594.1|  94 SLGTMDVRTVRN 105
                                       477777777655 PP

>> Peptidase_S51  Peptidase family S51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   7.8e-08   0.00035      82     137 ..      37      92 ..       7     160 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 7.8e-08
                                       HSSEEEE--S-HHHHHHHHHHTTHHHHHHHHHHTT-EEEEETHHHHTTSSB-GGGT CS
                     Peptidase_S51  82 eadviyvgGGntfrLlkllketgldkllreavqqglvyiGvSAGaivagesietts 137
                                         d++++ GG+   + kll++ g+ + lr  v +gl ++G+ AG i+ ++++e  +
  gi|474935012|ref|YP_007688594.1|  37 PLDALIIPGGESTVMGKLLADLGMLERLRGTVLSGLSVFGTCAGLIILSSEVEGGK 92 
                                       3489*********************************************9988655 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   7.3e-07    0.0033      39     176 ..      34     173 ..      10     184 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 7.3e-07
                                       THHSTSEEEEEEESSCTT.....TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTT..........EEEEEECEEE CS
                            GATase  39 llknpdgilvsgGpgspg.....vegkieaikearenkiPiLGICLGmQllaiefgr..........kvvkekekeh 100
                                       l    d+++++gG  ++        g++e ++    +++ ++G C G+ +l  e+ +           +v++    +
  gi|474935012|ref|YP_007688594.1|  34 LDVPLDALIIPGGESTVMgkllaDLGMLERLRGTVLSGLSVFGTCAGLIILSSEVEGgkaslgtmdvRTVRNAYGRQ 110
                                       356789*******999998966555666666666669******************9988888877665555554556 PP

                                       EEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEETTTEEEESSBTTSTTS CS
                            GATase 101 hggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelmeiiekknpfvgvQFHPEstst 176
                                       +g  + + d     ++gl  ++  r+     v+    + +++ev+a+  d+ ++++++++++   ++ FHPE t  
  gi|474935012|ref|YP_007688594.1| 111 LGSFSTVSD-----FKGL-GKIPMRFIRAPFVES---VGSDVEVLAEV-DG-RIVAVRQNRQ--LATAFHPELTDD 173
                                       666666666.....9999.788999999999998...9999***8888.65.8*****9998..99******9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1233.88
//
Query:       gi|474935013|ref|YP_007688595.1|  [L=291]
Description: pyridoxal phosphate synthase yaaD subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   4.1e-108  359.9   3.3   5.3e-108  359.5   3.3    1.1  1  SOR_SNZ    SOR/SNZ family
    7.7e-08   31.9   3.5    2.8e-05   23.5   0.2    2.2  2  ThiG       Thiazole biosynthesis protein ThiG
    0.00015   21.2   3.7     0.0035   16.8   0.1    2.3  2  NMO        Nitronate monooxygenase
    0.00023   20.4   0.9       0.17   11.0   0.0    2.6  3  Dus        Dihydrouridine synthase (Dus)
     0.0016   17.6   0.1        1.1    8.4   0.0    3.2  3  IGPS       Indole-3-glycerol phosphate synthase
  ------ inclusion threshold ------
      0.032   13.4   3.1       0.65    9.2   0.1    3.0  3  NanE       Putative N-acetylmannosamine-6-phosphate epimerase
      0.043   13.9   0.0       0.11   12.5   0.0    1.7  1  TetR_C_27  Tetracyclin repressor-like, C-terminal domain
      0.065   13.6   0.0        1.2    9.5   0.0    2.5  2  DUF1871    Domain of unknown function (DUF1871)


Domain annotation for each model (and alignments):
>> SOR_SNZ  SOR/SNZ family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  359.5   3.3  2.3e-111  5.3e-108       3     207 .]       7     211 ..       5     211 .. 0.99

  Alignments for each domain:
  == domain 1  score: 359.5 bits;  conditional E-value: 2.3e-111
                                       HHHHHHHHTTTSSEEEEESSHHHHHHHHHHT-SEEEE-SS-HHHHHHH-S------HHHHHHHHHH-SS-EEEEEET CS
                           SOR_SNZ   3 kvkaglaemlkgGvimdvvnaeqakiaeeaGavavmalervpadirkeggvarmsdpklikeikeavsipvmakvri 79 
                                       +++++la+mlkgGvimdv+++eqak+ae+aGa avmaler+padir++ggv+rmsdpk+ik i+eavsipvmakvri
  gi|474935013|ref|YP_007688595.1|   7 ELNKELAQMLKGGVIMDVTTPEQAKVAEKAGAAAVMALERIPADIRAAGGVSRMSDPKMIKGIQEAVSIPVMAKVRI 83 
                                       6889************************************************************************* PP

                                       T-HHHHHHHHHTT-SEEEEETTS--S-SS----GGG-SS-EEEEESSHHHHHHHHHHT-SEEEEES-TTS--THHHH CS
                           SOR_SNZ  80 GhfveaqilealgvdyiDesevltpadeeahidkkkfkvpfvcGarnlgealrriaeGaamirtkGeagtGdvveav 156
                                       Ghfveaqileal++dyiDesevltpad+ +hidk++f+vpfvcGarnlgealrri+eGa+mirtkGe+gtGd+v+av
  gi|474935013|ref|YP_007688595.1|  84 GHFVEAQILEALEIDYIDESEVLTPADDVYHIDKTQFRVPFVCGARNLGEALRRISEGASMIRTKGEPGTGDIVQAV 160
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHTTS-HHHHHHHHHHHHGGGHHHHHHHHHTTS-S---T. CS
                           SOR_SNZ 157 rhvrkikeeirklkslseeelvalakelkaplelvkevaelgrlpvvnfaa 207
                                        h+r++++ ir++++ +++el+++ak+l++p++lv+ v+e+grlpvvnfaa
  gi|474935013|ref|YP_007688595.1| 161 SHMRAMNSAIRDIQNRRTDELFETAKQLQVPMDLVRYVHENGRLPVVNFAA 211
                                       *************************************************98 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.3   0.00028      0.62     134     191 ..      27      90 ..       1     117 [. 0.69
   2 !   23.5   0.2   1.3e-08   2.8e-05     166     225 ..     194     255 ..     184     264 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00028
                                       HHHHHHHHHTT-SEBEEB...SSSTTS----...S-HHHHHHHHHH-SS-BEEES---SHHHHH CS
                              ThiG 134 lvlarrleevGcaavmPl...aapiGsglGl...lnkealkiiieeakvPvivDAGigspsdaa 191
                                       +  a+  e++G+aavm l    a i ++ G+   ++++++k i e +++Pv+    ig+  +a 
  gi|474935013|ref|YP_007688595.1|  27 PEQAKVAEKAGAAAVMALeriPADIRAAGGVsrmSDPKMIKGIQEAVSIPVMAKVRIGHFVEAQ 90 
                                       335677788999999987333588988888622156899*************999999765553 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 1.3e-08
                                       HHHHHHHH-SS-BEEES..---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHHH CS
                              ThiG 166 alkiiieeakvPvivDA..GigspsdaaqamelGadavllntavaeakdpvamArafklave 225
                                        ++ + e+ ++Pv+  A  G+ +p daa  m lGa++v++ + +  + +p + A+a+ +av+
  gi|474935013|ref|YP_007688595.1| 194 LVRYVHENGRLPVVNFAagGVATPADAALMMYLGAEGVFVGSGIFASGNPEKRAAAIVQAVT 255
                                       56778888899*99654459***************************************996 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.1   0.9    0.0055        12     139     198 ..      20      79 ..       7      92 .. 0.74
   2 !   16.8   0.1   1.6e-06    0.0035     182     228 ..     192     240 ..     177     282 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0055
                               NMO 139 liptissvkearkvearGaDalivqG......peaGGhqGtpevgdkglfaLvpqvldavdiPviA 198
                                       +i+ +++ ++a+++e++Ga a+ +         +aGG          +  ++++ +++av+iPv+A
  gi|474935013|ref|YP_007688595.1|  20 VIMDVTTPEQAKVAEKAGAAAVMALEripadiRAAGGVSR------MSDPKMIKGIQEAVSIPVMA 79 
                                       5677888999999999998877764411111134454444......456789*************9 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 1.6e-06
                               NMO 182 faLvpqvldavdiPvi..AaGGiidrrgvaaaLalGAsgvqigtrfLlt 228
                                       + Lv  v +   +Pv+  AaGG+ +  + a ++ lGA+gv +g+   + 
  gi|474935013|ref|YP_007688595.1| 192 MDLVRYVHENGRLPVVnfAAGGVATPADAALMMYLGAEGVFVGSGIFAS 240
                                       455666666666***877*************************986654 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.71   1.6e+03     192     212 ..      24      43 ..      22      63 .. 0.70
   2 !    7.3   0.1   0.00097       2.2     112     133 ..      64      85 ..      58      97 .. 0.86
   3 !   11.0   0.0   7.5e-05      0.17     169     238 ..     189     262 ..     162     286 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.71
                                       --SHHHHHHHHHHH--SEEEE CS
                               Dus 192 IkdaedaqaileetGadgvmi 212
                                       ++++e+a+   e+ Ga +vm+
  gi|474935013|ref|YP_007688595.1|  24 VTTPEQAKV-AEKAGAAAVMA 43 
                                       555555543.34446666664 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00097
                                       HHHHHHHCCSSS-EEEEEESES CS
                               Dus 112 qivkavvkaveiPvtvkirigi 133
                                       +++k +++av+iPv +k+rig 
  gi|474935013|ref|YP_007688595.1|  64 KMIKGIQEAVSIPVMAKVRIGH 85 
                                       68999***************96 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 7.5e-05
                                       G--CHHHHHHHHH-SS-E..EEESS--SHHHHHHHHHHH--SEEEESCH..HCCSTTHHHH.HHHHHHSC----- CS
                               Dus 169 tadweaIkevkqavsipv..iaNGdIkdaedaqaileetGadgvmigrg..algnPwlfae.stavktgeaepap 238
                                       ++  + +++v ++ ++pv  +a G++ ++ da  ++   Ga+gv +g g  a gnP   a+   ++ t++++p+ 
  gi|474935013|ref|YP_007688595.1| 189 QVPMDLVRYVHENGRLPVvnFAAGGVATPADAALMMYL-GAEGVFVGSGifASGNPEKRAAaIVQAVTNYNDPEK 262
                                       5556779999999886662279*********9877755.********9966789998887666666666766665 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.4   0.1    0.0078        17      61      88 ..      17      44 ..      13      98 .. 0.80
   2 !    8.4   0.0   0.00049       1.1     191     250 ..     187     246 ..     173     250 .. 0.79
   3 ?    0.5   0.0      0.12   2.7e+02     163     192 ..     255     285 ..     247     289 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0078
                                      TEESBSS--HHHHHHHHTTT.-SEEEEE CS
                              IGPS 61 kgliredfdpaeiAkkyeeagAsaiSVL 88
                                      kg + +d+  +e+Ak+ e+agA+a+  L
  gi|474935013|ref|YP_007688595.1| 17 KGGVIMDVTTPEQAKVAEKAGAAAVMAL 44
                                      788999****************998655 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00049
                                       TTEE-CHHHHHHCHCC-TTSEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC-TTHHHH CS
                              IGPS 191 tlevdlntteeLaklvpkdvllvaeSGiktredveklkeegvnafLvGeslmrqedveka 250
                                       +l+v ++ ++ + +  +  v+  a  G++t++d+  +   g++++ vG+ + ++ + ek 
  gi|474935013|ref|YP_007688595.1| 187 QLQVPMDLVRYVHENGRLPVVNFAAGGVATPADAALMMYLGAEGVFVGSGIFASGNPEKR 246
                                       4555555555555555556778899*************************9999887776 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.12
                                       EEESSHHHHHHHH.HTT-SEEEEESEETTTT CS
                              IGPS 163 vEvhdeeeleral.klgakiiGvNnRnLktl 192
                                       +  +d e l+    +lg  ++G+N+ ++kt+
  gi|474935013|ref|YP_007688595.1| 255 TNYNDPEKLAELSyDLGRAMVGINSEEIKTI 285
                                       5667777777665599********9999886 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1     0.023        51     153     171 ..      24      42 ..       5      49 .. 0.76
   2 ?   -0.6   0.1      0.28   6.2e+02      20      39 ..      62      81 ..      48     119 .. 0.74
   3 ?    9.2   0.1   0.00029      0.65     135     176 ..     193     237 ..     182     256 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.023
                                       --SHHHHHHHHTT--SEEE CS
                              NanE 153 intPekakkaieiGvdavv 171
                                       + tPe+ak a + G++av+
  gi|474935013|ref|YP_007688595.1|  24 VTTPEQAKVAEKAGAAAVM 42 
                                       5689999999999988875 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.28
                                      SHHHHHHHHTT--S-EEEE- CS
                              NanE 20 gvedikaikavvdlPiiGiv 39
                                        + ik i+++v++P++  v
  gi|474935013|ref|YP_007688595.1| 62 DPKMIKGIQEAVSIPVMAKV 81
                                      44567778888888877655 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00029
                                       HHHHHHHHTT--...EEEES---SHHHHHHHHTT--SEEEE-HHH CS
                              NanE 135 alvkalseaglk...viaeGrintPekakkaieiGvdavvvGsai 176
                                       +lv+ + e+g       a G + tP+ a+ ++ +G++ v vGs i
  gi|474935013|ref|YP_007688595.1| 193 DLVRYVHENGRLpvvNFAAGGVATPADAALMMYLGAEGVFVGSGI 237
                                       5666666655322224689************************88 PP

>> TetR_C_27  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     5e-05      0.11      61      94 ..     234     267 ..     228     275 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5e-05
                                       HCT-STT--HHHHHHHHHHHSGGGTSHHHHHHHG CS
                         TetR_C_27  61 aaGeFkaadpeaaaravfdatarfhhPalaaews 94 
                                        +G F++ +pe+ a a+++a++++ +P  +ae s
  gi|474935013|ref|YP_007688595.1| 234 GSGIFASGNPEKRAAAIVQAVTNYNDPEKLAELS 267
                                       689************************9999876 PP

>> DUF1871  Domain of unknown function (DUF1871)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.25   5.7e+02      23      45 ..     153     175 ..     148     195 .. 0.83
   2 ?    9.5   0.0   0.00054       1.2      20      41 ..     244     265 ..     238     268 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.25
                                       HHHHHHHHTT-S-HHHHHHHHHH CS
                           DUF1871  23 aadvvqavyelddpkklakkiqe 45 
                                       + d+vqav+++   ++  ++iq+
  gi|474935013|ref|YP_007688595.1| 153 TGDIVQAVSHMRAMNSAIRDIQN 175
                                       679******99998888888885 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00054
                                       HHHHHHHHHHHTT-S-HHHHHH CS
                           DUF1871  20 etEaadvvqavyelddpkklak 41 
                                       e  aa +vqav + +dp+kla+
  gi|474935013|ref|YP_007688595.1| 244 EKRAAAIVQAVTNYNDPEKLAE 265
                                       56799***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 1910.84
//
Query:       gi|474935014|ref|YP_007688596.1|  [L=148]
Description: transcriptional regulator, BadM/Rrf2 family [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-23   83.3   0.0    1.6e-23   82.8   0.0    1.2  1  Rrf2          Transcriptional regulator
  ------ inclusion threshold ------
       0.02   14.4   0.1      0.041   13.4   0.0    1.6  2  HTH_24        Winged helix-turn-helix DNA-binding
      0.058   13.0   0.0       0.09   12.3   0.0    1.3  1  HTH_47        winged helix-turn-helix
      0.074   12.7   0.1       0.14   11.8   0.1    1.5  1  HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor
       0.14   12.3   1.6       0.61   10.2   0.0    2.2  2  FeoC          FeoC like transcriptional regulator


Domain annotation for each model (and alignments):
>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.8   0.0   4.5e-27   1.6e-23       3      82 ..       5      84 ..       4      85 .. 0.98

  Alignments for each domain:
  == domain 1  score: 82.8 bits;  conditional E-value: 4.5e-27
                                      --HHHHHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEEESSHCCCSBHHHHHH CS
                              Rrf2  3 lsskteyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGkgGGyrLakppeeItlldvvr 81
                                      +s+k++ya+++l++La+++ ++ v ++e+aerqnis +y+e i+  L k+glv    GkgGGy+L  ppe+I++++v+r
  gi|474935014|ref|YP_007688596.1|  5 ISTKGRYAIRILIDLAEHSADGRVPLKEMAERQNISLKYMETIMPLLVKEGLVSGSHGKGGGYKLVVPPEDIKIGKVLR 83
                                      79****************************************************************************9 PP

                                      H CS
                              Rrf2 82 a 82
                                      a
  gi|474935014|ref|YP_007688596.1| 84 A 84
                                      8 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.1e-05     0.041       8      47 ..      15      57 ..      10      58 .. 0.85
   2 ?   -3.4   0.0       2.1   7.6e+03      37      44 ..     116     123 ..     113     123 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.1e-05
                            HTH_24  8 ILelLqk...nprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      IL  L +   ++r + +e Aer ++S+    + +  L++eGl+
  gi|474935014|ref|YP_007688596.1| 15 ILIDLAEhsaDGRVPLKEMAERQNISLKYMETIMPLLVKEGLV 57
                                      5555555566*******************************98 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.1
                            HTH_24  37 rlkrLeee 44 
                                       +l+rL+++
  gi|474935014|ref|YP_007688596.1| 116 HLDRLISD 123
                                       89999875 PP

>> HTH_47  winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.5e-05      0.09      43      77 ..      24      58 ..       5      59 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.5e-05
                                      -EEEEEHHHHHHHHT--HHHHHHHHHHHHHTT-EE CS
                            HTH_47 43 aDGkrsLldiAeriglpfdrvaaiaraLaeaglla 77
                                      aDG+  L ++Aer +++ + ++ i+  L ++gl++
  gi|474935014|ref|YP_007688596.1| 24 ADGRVPLKEMAERQNISLKYMETIMPLLVKEGLVS 58
                                      8*******************************986 PP

>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1     4e-05      0.14      10      64 ..      13      68 ..       5      76 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4e-05
                      HrcA_DNA-bdg 10 lqaLielyrkk.kravKgeeiAevlkrneGtvRNqlqsLkalgLvegvpGPkGGYk 64
                                      ++ Li+l +++ +  v  +e+Ae  +    ++  ++  L   gLv+g  G  GGYk
  gi|474935014|ref|YP_007688596.1| 13 IRILIDLAEHSaDGRVPLKEMAERQNISLKYMETIMPLLVKEGLVSGSHGKGGGYK 68
                                      678999999987889****************************************8 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00017      0.61       1      45 [.      15      58 ..      15      65 .. 0.90
   2 ?    0.8   0.5      0.15   5.4e+02      40      63 ..      77     105 ..      76     110 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00017
                              FeoC  1 iLtelkeyleergrvslkeLsrhfkaspealeamLeqwvrkGrve 45
                                      iL +l e   + grv lke++ + ++s + +e ++ ++v+ G v 
  gi|474935014|ref|YP_007688596.1| 15 ILIDLAEH-SADGRVPLKEMAERQNISLKYMETIMPLLVKEGLVS 58
                                      57778888.889*****************************9986 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.15
                              FeoC  40 rkGrvekvaataccsgsCkk.....Cggk 63 
                                       + G+v + ++++ ++ sC +     C+ +
  gi|474935014|ref|YP_007688596.1|  77 KIGKVLRATEGTIAAVSCLNggemgCERA 105
                                       56999999999999999977666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 972.22
//
Query:       gi|474935015|ref|YP_007688597.1|  [L=308]
Description: cysteine synthase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      9e-72  242.0   0.4      1e-71  241.8   0.4    1.0  1  PALP      Pyridoxal-phosphate dependent enzyme
     0.0037   17.1   0.1     0.0068   16.3   0.1    1.4  1  DFP       DNA / pantothenate metabolism flavoprotein


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  241.8   0.4   1.1e-75     1e-71       3     293 ..       8     294 ..       6     295 .. 0.94

  Alignments for each domain:
  == domain 1  score: 241.8 bits;  conditional E-value: 1.1e-75
                                       GCSSS--EEEECCTCCCCCCE..EEEEEGGGSTTSBTTHHHHHHHHHHHHTT...TTTSEEEEEBSSHHHHHHHHHH CS
                              PALP   3 lgigpTPlvrlprlskelgvp..lflKlEslnptgSfKdRgaeyllarlkeg...tgaktvveassGNhgralAaaa 74 
                                         ig+TPlv+l +++kelg +  +f K E++np gS+KdR a  ++ +l+++   ++ ++++e +sGN+g+alA +a
  gi|474935015|ref|YP_007688597.1|   8 ETIGGTPLVELTNIEKELGLKakIFGKVEFFNPAGSVKDRIAKAMIDDLEKQgkiNKDTVLIEPTSGNTGIALASIA 84 
                                       679*********************************************66666************************ PP

                                       HHHT-EEEEEEETTS-HHHHHHHHHTT-EEEEECCH..HHHHHHHHHHHHHHSTTCEE--TTTSHHHHHH.HHTHHH CS
                              PALP  75 allGlkvtivvpadaspekvallrllGaevvevggd..ydeavaaaaelaaegegaylvsqfdnptvieg.ygtigl 148
                                        + G+k  iv+p+++s e+++l++++Gae+++++g    + ava+a+el +e+++ ++  qf np++ e  y+t+g+
  gi|474935015|ref|YP_007688597.1|  85 TARGYKIKIVMPETMSIERRKLIKAYGAELILTEGAkgMKGAVAKAEELSKEIPNSVIPGQFVNPANPEIhYNTTGP 161
                                       *********************************55444*************************************** PP

                                       HHHHHTTTTEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCS.C CS
                              PALP 149 EileqlggkpdavvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvsdtiadglavg.s 224
                                       Ei+++l+gk+d +v++vG+Gg+++G++++lke++pdv+v++vep+gs+ l ++           +++ ++g+++g  
  gi|474935015|ref|YP_007688597.1| 162 EIYKDLDGKVDILVAGVGTGGTLSGVGKYLKEKKPDVKVVAVEPKGSPLLSEGK---------AGPHKIQGIGAGfI 229
                                       ******************************************************.........5599********** PP

                                       GTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH.HHHHHHCCTTCEEEEEEE- CS
                              PALP 225 pselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaal.klreagelkegdrvvvilt 293
                                       p +l+ +++dr +     v de+a++  rl  ++eg +v+ s++aal a+ +l+++ + +++ ++v+il 
  gi|474935015|ref|YP_007688597.1| 230 PDTLDTKIYDRVIA----VADEDAFANGRLIGKKEGFLVGISAGAALTAAlELAKDPANAGK-NIVAILA 294
                                       *********87777....***********************999999999677777777777.9**9986 PP

>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   7.6e-07    0.0068      25      79 ..      70     130 ..      61     138 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7.6e-07
                                       E----HHHHHHHHHHHHTT-EEEEEE-S-.SS--.....-TT-EEEE--SHHHHHHHHHHH CS
                               DFP  25 NrSSGkmGyalAeaaaarGaeVtlvsgpv.slet.....pegvevvkvesaeemleaveea 79 
                                        + SG +G+alA+ a arG ++++v  ++ s+e        g+e++  e a+ m+ av +a
  gi|474935015|ref|YP_007688597.1|  70 EPTSGNTGIALASIATARGYKIKIVMPETmSIERrklikAYGAELILTEGAKGMKGAVAKA 130
                                       568**********************999647775344424478899999999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1955.19
//
Query:       gi|474935016|ref|YP_007688598.1|  [L=430]
Description: O-acetylhomoserine sulfhydrolase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     2e-136  454.5   0.0   2.3e-136  454.3   0.0    1.0  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    7.6e-12   45.2   0.0    1.2e-11   44.6   0.0    1.3  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    2.4e-09   36.6   0.3    4.6e-09   35.7   0.3    1.4  1  Aminotran_5      Aminotransferase class-V
      8e-09   35.1   0.0    1.2e-08   34.5   0.0    1.3  1  Aminotran_1_2    Aminotransferase class I and II
    0.00028   19.8   0.0    0.00042   19.3   0.0    1.2  1  GDC-P            Glycine cleavage system P-protein
    0.00069   19.0   0.0     0.0017   17.7   0.0    1.6  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.025   13.3   0.0      0.034   12.8   0.0    1.2  1  SepSecS          O-phosphoseryl-tRNA(Sec) selenium transferas
      0.037   13.0   0.8       0.22   10.5   0.8    1.9  1  SelA             L-seryl-tRNA selenium transferase


Domain annotation for each model (and alignments):
>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  454.3   0.0    1e-139  2.3e-136       1     381 [.       9     425 ..       9     426 .. 0.98

  Alignments for each domain:
  == domain 1  score: 454.3 bits;  conditional E-value: 1e-139
                                       HHHHHHTTTTCHT.TTTBSS--B---SBBBESSHHHH...CTTCSSS-SBTTT--HHHHHHHHHHHHHHT-SEEEEE CS
                   Cys_Met_Meta_PP   1 eTllvhagqekde.qtgavavpiyltstykfkdvdea...fageekgyeYsRsgnptrsvleeriaaLeggeaalav 73 
                                       eTl+vhagqe+ + +t+a+avpiy t++y+fkd+++a   fa  e g++Y+R++npt+sv+eer+ aLegg aala+
  gi|474935016|ref|YP_007688598.1|   9 ETLQVHAGQESPDpTTDARAVPIYMTTSYVFKDSAQAagrFALAEPGNIYTRLMNPTSSVFEERMVALEGGIAALAT 85 
                                       69******998666********************999999************************************* PP

                                       SSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHHHHHHCCTTEEEEEEESS-TTT CS
                   Cys_Met_Meta_PP  74 ssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdtsdleelekaikentklvylEtptnpl 150
                                       +sG aAi+ a+++++ aGd+iv+s+++Yggt++l++++l++ gie++fvd+sd++++ekai+entkl+y+E ++np 
  gi|474935016|ref|YP_007688598.1|  86 ASGAAAITYAVQNIALAGDHIVSSSNVYGGTFNLFENTLREQGIETTFVDPSDPKNFEKAIRENTKLLYTEVLGNPN 162
                                       ***************************************************************************** PP

                                       T----HHHHHHHHHHTT-EEEEEGTTTHTTTS-GGGGT-SEEEEETTTTTTCSSS--EEEEEESSCHHHHHHHHHHH CS
                   Cys_Met_Meta_PP 151 lkvvDiekiaklakkagvlvvvDntfaspllqrplklgaDivvhSaTKylgGhsdvvaGvivvkgkeelkkelkflq 227
                                        +v+Di +i+k+a+k+g++++vD tf+ p ++rp+++gaDivvhSaTK++gGh+ +++G+i+++g+++++++ kf +
  gi|474935016|ref|YP_007688598.1| 163 SDVADIDEISKIAHKHGIPLIVDSTFTPPSVFRPIEHGADIVVHSATKFIGGHGVAMGGIIIDSGNFDWAQNDKFPT 239
                                       ***********************************************************************999877 PP

                                       ...............................HHHT-B--HHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHTSTTE CS
                   Cys_Met_Meta_PP 228 ...............................nalGavlspfdawlllrGlkTLslRlerhqenAlkvAefLekhpkv 273
                                                                      ++ Ga++spf+++lll Gl+TLslR +rh enAlkv  +L++hp+v
  gi|474935016|ref|YP_007688598.1| 240 lskpnpsyhgvvfteavgkaafvvkirttlmRDQGAAISPFNSFLLLLGLETLSLRTDRHIENALKVVDYLKNHPQV 316
                                       99*************************************************************************** PP

                                       EEEE-TTSTTSTTHHHHHHHSSSG-S.EEEEEESSHHHHHHHHHHC-SSSEECSS-SSSS-EEEETTTTTTTTSCHH CS
                   Cys_Met_Meta_PP 274 ekvyYpglpshpqhelakkqlkgagg.vlsFelkseeekakkfvdnlklfslaeslGgveslielpasmthasipke 349
                                       ekv++p+l++  +  +  +++ +++g +++Fe+k+++ekakkf ++lklfsl++++ +v+sl+++pas+th +++++
  gi|474935016|ref|YP_007688598.1| 317 EKVNHPSLETGAKKAVYDRFFPKGAGsIFTFEIKGGAEKAKKFTESLKLFSLLANVADVKSLVIHPASTTHSQLEED 393
                                       *******************98655555************************************************** PP

                                       HHHHTTS-TTEEEEE--SS-HHHHHHHHHHHH CS
                   Cys_Met_Meta_PP 350 ereaagvtddliRlsvGiEdvdDliaDlkqal 381
                                       +  a+g++++ +Rls+G E++dD+iaDl+q++
  gi|474935016|ref|YP_007688598.1| 394 ALLASGIKPNTVRLSIGTENIDDIIADLEQGF 425
                                       ******************************98 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   0.0   5.3e-15   1.2e-11      17     145 ..      56     186 ..      40     201 .. 0.85

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 5.3e-15
                                       S-SSS..SHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHH....HHHHHTT-EE CS
                   DegT_DnrJ_EryC1  17 gwlts..gpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvata....navlelgakp 87 
                                       + +t+  +p+ + FE+++ a  g   a+a++sG aA+  a +++ +  gd ++  s+ + +t     n+ +e g ++
  gi|474935016|ref|YP_007688598.1|  56 NIYTRlmNPTSSVFEERMVALEGGIAALATASGAAAITYAVQNIALA-GDHIVSSSNVYGGTFnlfeNTLREQGIET 131
                                       455556699***********************************999.*********9999972222578999**** PP

                                       EEE-B-TTTSSB-GGGCGGG--TTEEEEEEB-GGGB....---HHHHHHHHHHCT-EEEEE- CS
                   DegT_DnrJ_EryC1  88 vfvDvdpdtynidpaaieaaitertkaIlpVhlyGq....vadmdalkaiaakhglkvieDa 145
                                        fvD        dp++ e+ai e+tk     +++G+    vad+d++ +ia+khg+++i D+
  gi|474935016|ref|YP_007688598.1| 132 TFVDPS------DPKNFEKAIRENTKLL-YTEVLGNpnsdVADIDEISKIAHKHGIPLIVDS 186
                                       *****9......*************965.4555554111178******************98 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.3     2e-12   4.6e-09      67     209 ..      85     218 ..      73     224 .. 0.90

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 2e-12
                                       ESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEE CS
                       Aminotran_5  67 tsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklv 143
                                       t +++ ai+ +++++     +gd+iv +++ + ++++  ++  +++g++ +++        d++++ek+++e+tkl+
  gi|474935016|ref|YP_007688598.1|  85 TASGAAAITYAVQNI---ALAGDHIVSSSNVYGGTFNLFENTLREQGIETTFVDP-----SDPKNFEKAIRENTKLL 153
                                       455566777777777...89******************************99998.....899************** PP

                                       EEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTTTTSSTT-E CS
                       Aminotran_5 144 aithvsnvtGtiqpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghKllgPtGiG 209
                                       +     n    + +++ei k+a+k+g+ ++vD++ + ++      + g+D+++ s+ K++g  G+ 
  gi|474935016|ref|YP_007688598.1| 154 YTEVLGNPNSDVADIDEISKIAHKHGIPLIVDSTFTPPSVFR-PIEHGADIVVHSATKFIGGHGVA 218
                                       ********************************9988777655.5578****************995 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.0   5.5e-12   1.2e-08      44     253 ..      65     245 ..      30     277 .. 0.75

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 5.5e-12
                                       THHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-TH....HHHHHHHTTSE CS
                     Aminotran_1_2  44 dglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyas....yknilrlsgge 116
                                       + +  +ee++  + g          aa+ + sGa a+  a+  ++   +gd i++++ +y+     ++n lr  g+e
  gi|474935016|ref|YP_007688598.1|  65 T-SSVFEERMVALEG--------GIAALATASGAAAITYAVQNIAL--AGDHIVSSSNVYGGtfnlFENTLREQGIE 130
                                       4.6667777777777........7789999****999999999996..9*****99987765333388888999999 PP

                                       EEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTC CS
                     Aminotran_1_2 117 vvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagf 193
                                          +          d +++e+a++e       tk++++e   NP  +va+ +e+ k+   a+k+++ l+vD ++   
  gi|474935016|ref|YP_007688598.1| 131 TTFVD-------PSDPKNFEKAIRE------NTKLLYTEVLGNPNSDVADIDEISKI---AHKHGIPLIVDSTFTPP 191
                                       99999.......88***********......99************************...***********987533 PP

                                       BSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTS...S CS
                     Aminotran_1_2 194 vfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsrpfls...s 253
                                                 ++   e+ ++++v s  K  G  G  +G i++++   +++++ + p ls   +
  gi|474935016|ref|YP_007688598.1| 192 S---------VFRPIEHGADIVVHSATKFIGGHGVAMGGIIIDSGNFDWAQNDKFPTLSkpnP 245
                                       2.........34444444559999999999999998898888887777777766666666444 PP

>> GDC-P  Glycine cleavage system P-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.9e-07   0.00042     136     260 ..      84     211 ..      76     223 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.9e-07
                                       HHHH.HHHHHHHHHH-SSS--EEEEETTS-HHHHHHHHHHHGGGT-EEEEE-GGG--S-........S-EEEEEEEE CS
                             GDC-P 136 gtAa.aEAvllaaraskkkakkvvvdkkvhpqtlevlktrakglgieivevdlteekvtd.....kekevagvlvqy 206
                                       +tA+ a A++ a+++     +++v +++v+  t +  +   +++gie+  vd ++ k  +     ++k + + ++  
  gi|474935016|ref|YP_007688598.1|  84 ATASgAAAITYAVQNIALAGDHIVSSSNVYGGTFNLFENTLREQGIETTFVDPSDPKNFEkaireNTKLLYTEVL-- 158
                                       456514566777788888899***************************999988777666343222222333333.. PP

                                       S-TTSB----HHHHHHHHHTT-EEEEEE-TTGGGTB--HHHHT-SEEEEE-TTT CS
                             GDC-P 207 pnteGriedlkelvekakkkkslvvvaadllaLtllkpPgelgaDivvGsaqrf 260
                                        n +  + d++e+++ a+k+ + ++v +     ++++ P e gaDivv sa +f
  gi|474935016|ref|YP_007688598.1| 159 GNPNSDVADIDEISKIAHKHGIPLIVDSTFTPPSVFR-PIEHGADIVVHSATKF 211
                                       345567**********************999999987.789**********998 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   7.5e-07    0.0017      31     208 ..      63     223 ..      61     316 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 7.5e-07
                                       -HHHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHC...C--EEEEE-EB CS
                   Beta_elim_lyase  31 dktvnrLedavaelfgkeaalfvpqGtaAnsillkillqrgeevivtepahihfdetgaiael...agvklrdlknk 104
                                       ++t  ++e+++ +l g  aal +++G aA   +++ ++  g+ ++ +  ++++  +    +     +g+  +++  +
  gi|474935016|ref|YP_007688598.1|  63 NPTSSVFEERMVALEGGIAALATASGAAAITYAVQNIALAGDHIVSS--SNVYGGTFNLFENTlreQGI-ETTFVDP 136
                                       57778888999999999999999999999999998888777777655..45554444333322221333.3344444 PP

                                       TTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS- CS
                   Beta_elim_lyase 105 eaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgei 181
                                       +    d++++e+ai+e      ++kl++++v  n        ++ ++e+++ia+k+gipl++D++       +    
  gi|474935016|ref|YP_007688598.1| 137 S----DPKNFEKAIRE------NTKLLYTEVLGNP----NSDVADIDEISKIAHKHGIPLIVDSTF------TPPSV 193
                                       4....79999999999......799***9998874....6789********************972......33333 PP

                                       CHHHHTTSSEEEEESSS...TT--SS-EEE CS
                   Beta_elim_lyase 182 vkemfsyvDsvtmslkK...dllanvGgvl 208
                                        + +  ++D+v+ s++K   + ++ +Gg++
  gi|474935016|ref|YP_007688598.1| 194 FRPIEHGADIVVHSATKfigGHGVAMGGII 223
                                       555556666666666665544456666666 PP

>> SepSecS  O-phosphoseryl-tRNA(Sec) selenium transferase, SepSecS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.5e-05     0.034     138     196 ..     133     190 ..     100     272 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.5e-05
                                       EEHHHHHHHHHHCCTCCCEEEEEECSSTTTTB----HHHHHHHHHCCT--EEEEGCCCC CS
                           SepSecS 138 itdvedveeiiekkreevilavlstlsffaprspDdvkeiakiCaeydvPhlvNgAYai 196
                                        +d++d ++ ++ +re+ +  + + + +++     d++ei+ki +++++P++v + ++ 
  gi|474935016|ref|YP_007688598.1| 133 FVDPSDPKNFEKAIREN-TKLLYTEVLGNPNSDVADIDEISKIAHKHGIPLIVDSTFTP 190
                                       45666666666776666.666777777777666556*****************998865 PP

>> SelA  L-seryl-tRNA selenium transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.8   9.9e-05      0.22      52     224 ..      69     224 ..      63     234 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 9.9e-05
                                       HHHHHHHHHT-SEEEEES-HHHHHHHHHHHHHBTSEEEEETTSGTEETTTEEHHH.HHHHHTBEEEEESBSSB--HH CS
                              SelA  52 veellkeltgaedalvvnnnaaavllvLntlaagkeviisrGeLveiGGsfriPd.vmkkaGvkLvevGttnkthlk 127
                                        ee +  l g  +al     aaa+  +++ +a   + i+s  ++   GG+f + +  +++ G++ + v  +     k
  gi|474935016|ref|YP_007688598.1|  69 FEERMVALEGGIAALATASGAAAITYAVQNIALAGDHIVSSSNV--YGGTFNLFEnTLREQGIETTFVDPS---DPK 140
                                       5777888999999999999*********************9997..6****98642889999988877665...579 PP

                                       HHHHT--TTEEEEEEE---SEEEEES-B---HHHHHHHHHHHT--EEEEEES-B-S-GGGGT-----BHHHHHHTT- CS
                              SelA 128 DyekainentalllkvhtsnyrieGftkevelaeLvelgkekglpvleDlGsGllvdlseyglskePtvqealaeGv 204
                                       ++ekai ent ll      n +     +  +++e+ ++++++g+p++ D               + P v   +++G+
  gi|474935016|ref|YP_007688598.1| 141 NFEKAIRENTKLLYTEVLGNPN----SDVADIDEISKIAHKHGIPLIVDST------------FTPPSVFRPIEHGA 201
                                       9***********9875555533....44568999***********999842............35699999999999 PP

                                       SEEEEETTSTT-SS...S-EEEE CS
                              SelA 205 dlvsfsGDkllGgp...qaGiiv 224
                                       d+v  s  k++Gg      Gii+
  gi|474935016|ref|YP_007688598.1| 202 DIVVHSATKFIGGHgvaMGGIII 224
                                       99999999999985111345665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 2573.64
//
Query:       gi|474935017|ref|YP_007688599.1|  [L=379]
Description: cysteine desulfurase NifS [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-83  280.0   0.0    3.2e-83  279.7   0.0    1.0  1  Aminotran_5      Aminotransferase class-V
    5.1e-07   29.3   0.1    6.5e-07   28.9   0.1    1.2  1  Beta_elim_lyase  Beta-eliminating lyase
    2.6e-05   23.7   0.5    4.1e-05   23.1   0.5    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
     0.0039   15.8   0.0     0.0053   15.3   0.0    1.1  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  279.7   0.0   7.1e-87   3.2e-83      13     370 ..       3     352 ..       1     353 [. 0.97

  Alignments for each domain:
  == domain 1  score: 279.7 bits;  conditional E-value: 7.1e-87
                                       HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC.-TTT CS
                       Aminotran_5  13 qeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlvalslars.lkpg 88 
                                       +e+l+a+  +++  +an+ +s+h l+ +  +av+ear ++a+++na++  ei+ftsG+te+ n +++s a+   ++g
  gi|474935017|ref|YP_007688599.1|   3 KEALEAMLPFFSIEYANP-SSIHFLSRDPRDAVKEARVRIAKVLNADD-TEIYFTSGGTESDNWALISGAEMsKNKG 77 
                                       689***************.****************************7.************999999988888**** PP

                                       SEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHH CS
                       Aminotran_5  89 deivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGtiqpveeigkla 165
                                       ++i+v+++ehha l +   la ++g++++++ +d++g +d+d l+k ++++t l++++ ++n++Gt+qp++eigk+a
  gi|474935017|ref|YP_007688599.1|  78 KHIIVSAIEHHAILETVDYLA-KHGYEITKVGVDADGVIDMDGLKKSIRPDTVLISVMTANNEIGTVQPIAEIGKIA 153
                                       **************9999999.78***************************************************** PP

                                       HHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTTTTSSTT-EEEEEEHHHHHTS..SS.STTSEEEEETTEEEEH CS
                       Aminotran_5 166 kkkgalvlvDaaqavghipidvkklgvDflafsghKllgPtGiGvlyvrkellekleplllggemveevsleettfa 242
                                       ++kg+l+++Da+qa+ghip+dvk++++D+l++sghK+ gP+G+G+lyvrk    +l+p++ gge       +e +  
  gi|474935017|ref|YP_007688599.1| 154 REKGILFHTDAVQAFGHIPLDVKAMNIDMLSASGHKFGGPKGVGFLYVRK--GIRLPPFMHGGE-------QENG-- 219
                                       **************************************************..999*********.......8888.. PP

                                       CTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCT.STTEEEES.-B-CTCBSEEEEEETT CS
                       Aminotran_5 243 eapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlks.lpgvrlygpdkaerrasivsfnfkg 318
                                             +aGT+nv+gi+g+g a+e+  + +le+  ++  e+++++ er+++ +p  +l+g ++++r ++ v+f fk 
  gi|474935017|ref|YP_007688599.1| 220 -----RRAGTTNVPGIVGMGVAAEIS-ARDLEKNSARLIEMRDHAIERISKeIPYSKLNG-HRTQRLPGNVNFGFKF 289
                                       .....89*****************98.99********************8769999**99.799************* PP

                                       CSHHHHHHHHHHTTEEEEEE-TTT....HHHHHHTT.S.......-EEEEE--TTS-HHHHHH CS
                       Aminotran_5 319 vhaedvatlLdeegIavrsGhhca....qplmkrlale.......gtvRaSlyiynteeevdr 370
                                       ++ e v + L  +g+++++G++ca     p++++la+        g+vR+Sl  +nt ee+d+
  gi|474935017|ref|YP_007688599.1| 290 IEGESVLMSLGMKGVCISTGSACAsgslDPSHVLLAIGlphgdahGSVRISLSENNTMEEIDY 352
                                       ************************9999999999999999*********************95 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.1   1.5e-10   6.5e-07      40     199 ..      40     190 ..      28     278 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 1.5e-10
                                       HHHHHTT-S..EEEEES-HHHHHHHHH....HHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTTTBE- CS
                   Beta_elim_lyase  40 avaelfgke..aalfvpqGtaAnsill....killqrgeevivtepahihfdetgaiaelagvklrdlknkeaGkmd 110
                                       ++a+++ ++   + f+  Gt +++ +l    ++  ++g+ +iv+   h    et  + +  g + +++  +++G +d
  gi|474935017|ref|YP_007688599.1|  40 RIAKVLNADdtEIYFTSGGTESDNWALisgaEMSKNKGKHIIVSAIEHHAILETVDYLAKHGYEITKVGVDADGVID 116
                                       5556665553234477789999999998875444478899999999888888888888889999************* PP

                                       HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHT CS
                   Beta_elim_lyase 111 lekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgeivkemfs 187
                                       ++ l++ i++      ++ lis+ ++nn     + +++ ++e+ +ia+++gi +h D+     a  ++  +vk m  
  gi|474935017|ref|YP_007688599.1| 117 MDGLKKSIRP------DTVLISVMTANNE----IGTVQPIAEIGKIAREKGILFHTDAV---QAFGHIPLDVKAM-- 178
                                       **********......488*******995....445666788999************84...4444555555554.. PP

                                       TSSEEEEESSST CS
                   Beta_elim_lyase 188 yvDsvtmslkKd 199
                                        +D++++s+ K 
  gi|474935017|ref|YP_007688599.1| 179 NIDMLSASGHKF 190
                                       477777777775 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.5   9.1e-09   4.1e-05      47     150 ..      58     169 ..      48     181 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 9.1e-09
                                       HHHHHHHHHHH...TTTTTT-EEEEESSS-TH...HHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTE...EE CS
                   DegT_DnrJ_EryC1  47 GtaAlhlaLra...lgvgpgdeVIvpsltFva...tanavlelgakpvfvDvdpdtynidpaaieaaitert...ka 114
                                       Gt++   aL     ++ ++g+ +Iv ++   a   t+   ++ g++   v vd ++  id + +++ i + t   + 
  gi|474935017|ref|YP_007688599.1|  58 GTESDNWALISgaeMSKNKGKHIIVSAIEHHAileTVDYLAKHGYEITKVGVD-ADGVIDMDGLKKSIRPDTvliSV 133
                                       5666666665544566679********99999333455556779*********.8899**************77444 PP

                                       EEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT CS
                   DegT_DnrJ_EryC1 115 IlpVhlyGqvadmdalkaiaakhglkvieDaAhAlG 150
                                        ++ +  G v  ++++ +ia+++g+ +  Da +A+G
  gi|474935017|ref|YP_007688599.1| 134 MTANNEIGTVQPIAEIGKIAREKGILFHTDAVQAFG 169
                                       4555679****************************9 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.2e-06    0.0053      88     198 ..      74     189 ..      24     195 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.2e-06
                                       S-TTEEEEEESTSSHHHHHHHHHTHHH.TTCEEEEEST...TSHHHHHHHCCTTEEEEEEESS-TTTT----HHHHH CS
                   Cys_Met_Meta_PP  88 lkaGdeivvsddlYggtqrllkkvlkk.lgievkfvdt...sdleelekaikentklvylEtptnpllkvvDiekia 160
                                        ++G++i+vs   +    + +++++k+  +i+   vd     d++ l+k i++ t l+ + t  n    v  i++i 
  gi|474935017|ref|YP_007688599.1|  74 KNKGKHIIVSAIEHHAILETVDYLAKHgYEITKVGVDAdgvIDMDGLKKSIRPDTVLISVMTANNEIGTVQPIAEIG 150
                                       345999999877777766666666555444444455542226899******************************** PP

                                       HHHHHTT-EEEEEGTTTHTTTS-GG.GGT-SEEEEETTT CS
                   Cys_Met_Meta_PP 161 klakkagvlvvvDntfaspllqrpl.klgaDivvhSaTK 198
                                       k+a+++g+l   D++ a + +   + ++++D+   S+ K
  gi|474935017|ref|YP_007688599.1| 151 KIAREKGILFHTDAVQAFGHIPLDVkAMNIDMLSASGHK 189
                                       **********99998777644222213456666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 2311.99
//
Query:       gi|474935018|ref|YP_007688600.1|  [L=142]
Description: FeS cluster assembly scaffold protein NifU, Clostridium type [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.4e-49  166.8   0.2    2.7e-49  166.6   0.2    1.0  1  NifU_N      NifU-like N terminal domain
  ------ inclusion threshold ------
      0.022   14.3   0.0      0.035   13.6   0.0    1.3  1  Proteasome  Proteasome subunit


Domain annotation for each model (and alignments):
>> NifU_N  NifU-like N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.6   0.2     3e-53   2.7e-49       2     126 ..       6     126 ..       5     129 .. 0.98

  Alignments for each domain:
  == domain 1  score: 166.6 bits;  conditional E-value: 3e-53
                                       SCHHHHHHHHSSSSBSS-TTSSS--EEEEEEETTTTEEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHHHHHT CS
                            NifU_N   2 ysdkvldhyknPrnvGvleeedakvgvgevgapacGDavrLqikvdeetdriedakFktfGCgsaiAssslltelvk 78 
                                       ysdkv+dh++nPrnvG +e+++   gvg+vg+  cGD +r+ + +de+ ++i d kFktfGCg+aiAsss++te+vk
  gi|474935018|ref|YP_007688600.1|   6 YSDKVVDHFTNPRNVGEIENAS---GVGTVGNAKCGDIMRIFLDIDEN-GIIRDCKFKTFGCGAAIASSSMATEMVK 78 
                                       9********************9...8*********************6.**************************** PP

                                       TSBHHHHCCCCHHHHHHHHTCSCSSSCHCSCHHHHHHHHHHHHHHHHC CS
                            NifU_N  79 gktleealkitnkeiaeelgglpkeklhcsvlaedalkaavkkYkakk 126
                                       gk+++eal+itnk ++e+lgglp++k+hcs lae+a++aa+ +Y +k+
  gi|474935018|ref|YP_007688600.1|  79 GKSIHEALEITNKAVMEALGGLPQVKIHCSLLAEEAIHAALWDYAQKN 126
                                       *********************************************998 PP

>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0     4e-06     0.035     124     175 ..      47      97 ..      41     103 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4e-06
                                       EETTSEEEEESSEEEESTTHHHHHHHHHHHHSTTBSHHHHHHHHHHHHHHHH CS
                        Proteasome 124 idpsGsyieekdavaiGsgseaaktalekeykedltleeavelavkalkeal 175
                                       id +G + ++k + + G+g+  a + +  e+ +  +  ea+e+  ka+ eal
  gi|474935018|ref|YP_007688600.1|  47 IDENGIIRDCK-FKTFGCGAAIASSSMATEMVKGKSIHEALEITNKAVMEAL 97 
                                       8999******8.************************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1007.35
//
Query:       gi|474935019|ref|YP_007688601.1|  [L=309]
Description: Arsenite efflux pump ACR3-related permease [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.2e-20   71.5   7.7    7.2e-20   71.5   7.7    1.8  2  SBF       Sodium Bile acid symporter family


Domain annotation for each model (and alignments):
>> SBF  Sodium Bile acid symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.5   7.7     4e-24   7.2e-20       2     189 ..      27     206 ..      26     212 .. 0.91
   2 ?   -1.1   1.3     0.072   1.3e+03      59      98 ..     244     283 ..     195     305 .. 0.56

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 4e-24
                               SBF   2 ilLilmmfpmglkveveklkellkrpkalllglvlqwvikPllmfilakillrdlklepelavGlilvglapggams 78 
                                       ++L++m+f++ l v++ ++++ + ++   + ++++++v  P+l+++l     ++++ +  +++Gli++ + p++   
  gi|474935019|ref|YP_007688601.1|  27 PFLVIMLFSVFLAVDFGDMRRSFDNRSFFASAVIINFVWTPVLAYVLGL---AFFDGSLDMRIGLIMLLVTPCTDWY 100
                                       579**********************************************...569999******************* PP

                               SBF  79 nvwtylakGdlelsvvlvalstllailltPlllyllaksleqttlkvpieeivksvlivviiPliaGillryillkh 155
                                       +v+t +akG++++s +l  ++ +l+ill+P++++++a++        ++ ++++  + +v+iP++a ++l+  + + 
  gi|474935019|ref|YP_007688601.1| 101 LVFTSVAKGNVPMSSSLLPINLILQILLLPVYIKVFAGED----SSFDMLGMFLD-MWIVLIPFAAAFILKAASGRN 172
                                       ***************************************9....99999999999.78899*********9999887 PP

                               SBF 156 kGrewfeskllpavspisligllltivvifalkg 189
                                            +   l      i l++l + i+v+fa + 
  gi|474935019|ref|YP_007688601.1| 173 NSARSVVDGLNSRSDGIQLAFLCMAIAVMFAAES 206
                                       7777777777777777888888888888888765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.072
                               SBF  59 epelavGlilvglapggamsnvwtylakGdlelsvvlval 98 
                                       +    + li + la+ + ++++++ +a +d++l + + ++
  gi|474935019|ref|YP_007688601.1| 244 PYADGTSLIFTTLARNSPLALAIAVMAFPDRPLIMLVLVI 283
                                       4444555666666666666666666666666655444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2299.62
//
Query:       gi|474935020|ref|YP_007688602.1|  [L=374]
Description: glutamate 5-kinase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.8e-39  134.7   3.2    5.6e-39  134.2   3.2    1.3  1  AA_kinase  Amino acid kinase family
    4.8e-16   58.5   2.6    1.9e-15   56.6   0.6    2.6  2  PUA        PUA domain


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.2   3.2   6.2e-43   5.6e-39       2     240 ..      13     242 ..      12     243 .. 0.88

  Alignments for each domain:
  == domain 1  score: 134.2 bits;  conditional E-value: 6.2e-43
                                       EEEEEE-TTCCC.CTCC...HHHHHHHHHHHHHHHHTTEEEEEE--.HHHHHHHHHHTCCCCCHHHC....E..HHH CS
                         AA_kinase   2 rvVvKlGGsslt.dkee...aslrrlaeqiaalkesgnklvvVhGg.gsftdgllalksglssgelaaglrstleea 73 
                                       rvV K+G ss+  d++    + ++++a+q+a+lk++g+++ +V++g  +++ + l+++ + ++ ++           
  gi|474935020|ref|YP_007688602.1|  13 RVVFKIGTSSIIkDGNVvseELMDSVARQVAELKKRGKEVLIVSSGaIGIGLRVLDARPKPNEVPI----------- 78 
                                       89*******66648888**************************99933666666666444444444........... PP

                                       HHHHHHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEE CS
                         AA_kinase  74 gevatrdalaslgerlvaallaaglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfigld 150
                                            ++a+a++g+ ++++ ++  ++++g+++a+++++ ++    s+++   +  +++ +ll+ g vp++++++++ 
  gi|474935020|ref|YP_007688602.1|  79 -----KQAAAAVGQGVLMQKWNDSFQKYGITVAQILISLDDY---SNRDTVLNLNNTMTTLLKYGAVPIFNENDAIA 147
                                       .....4*********************************999...999999999*********************** PP

                                       TTTE.EEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH.....CSSS.TTTHHHH CS
                         AA_kinase 151 eege.lgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaee.....saselatgGmkv 221
                                       +++    +g++Dt++a +A   +Ad l+il+dV G+yd++p ++ da+l+p ++  e  +        +++tgGmk+
  gi|474935020|ref|YP_007688602.1| 148 TKEIgPMFGDNDTLSAVIASRADADLLVILSDVAGLYDKNPQVHGDAKLIPVVTDIESVQavaggAGTKMGTGGMKT 224
                                       **99988**********************************************6666666699************** PP

                                       CHHHHHHHHHCTT-EEEEE CS
                         AA_kinase 222 khpaalaaarrggipvvIt 240
                                       k++aa ++++ +g+ +vI+
  gi|474935020|ref|YP_007688602.1| 225 KLKAA-KICQDAGCLMVIA 242
                                       99776.5555555888886 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1     0.074   6.6e+02      32      56 ..      47      69 ..      34      70 .. 0.84
   2 !   56.6   0.6   2.1e-19   1.9e-15       1      74 []     283     355 ..     283     355 .. 0.98

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.074
                                      -TTSEEEEEETTSCEEEEEEESS-H CS
                               PUA 32 eegdvVaivdedgelvavGlanyss 56
                                      ++g +V iv+    ++++Gl  +++
  gi|474935020|ref|YP_007688602.1| 47 KRGKEVLIVSS--GAIGIGLRVLDA 69
                                      78999***999..899999988775 PP

  == domain 2  score: 56.6 bits;  conditional E-value: 2.1e-19
                                       CEEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEEEE CS
                               PUA   1 grvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveiervl 74 
                                       g++v+d+gA ka+l+ +sLl+ Gv  + g fe+g  V+iv e g ++a+G+  y se++ ++kg +s+e ++vl
  gi|474935020|ref|YP_007688602.1| 283 GKIVIDAGAGKAILEHRSLLPVGVKCASGPFEAGKPVDIVCE-GVVIARGIPDYGSEDINSVKGMRSDEAKKVL 355
                                       79****************************************.**************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 2100.26
//
Query:       gi|474935021|ref|YP_007688603.1|  [L=434]
Description: glutamate-5-semialdehyde dehydrogenase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.5e-19   67.2   1.3    7.1e-14   51.2   0.1    2.1  2  Aldedh    Aldehyde dehydrogenase family
  ------ inclusion threshold ------
      0.029   14.4   0.4        3.9    7.4   0.0    2.3  2  IMS       impB/mucB/samB family


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   0.1     8e-18   7.1e-14      34     298 ..       7     281 ..       2     290 .. 0.82
   2 !   14.9   0.1   7.7e-07    0.0069     374     430 ..     314     370 ..     314     382 .. 0.92

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 8e-18
                                       HHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH....---HHHHHHHHHHHHHHHHHHHHHHHH CS
                            Aldedh  34 avaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaeletlet....Gkplaearaeveeaidvlryyaelaek 106
                                        ++aAk a  ++a+l+ e + + L+ +a+++ +r++e+ ++ + ++    Gk  ae+ + ++     ++ +++ +++
  gi|474935021|ref|YP_007688603.1|   7 EIKAAKTAALKMAALTTEVKDRALQLMAEAVDSRRKEILDANAEDVreaeGKIPAEMLKRLKVNDAKVDEMIASLND 83 
                                       5899***********************************99998762223555555444333333333333333333 PP

                                       HSEEE......EEEC.....TTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEEEEE-TTSHHHHHHH CS
                            Aldedh 107 legev......lpss.....egklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvvlKPaeetplsalll 172
                                       ++++       +  +     +g + + +r P+G +g++  ++    ++ + +  +l  GN+v +K  +e+  s  +l
  gi|474935021|ref|YP_007688603.1|  84 VKKQKdpvgetM--RsmlldDGLTLYQVRCPIGLIGIV--FEARPDVIPQIMSLCLKSGNAVCFKGGSEAKRSNRAL 156
                                       333332323221..1344559999999999******98..88888888888999*********************** PP

                                       HHHHHHT....TS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSEEEEEE---EEEEE- CS
                            Aldedh 173 aelfeea....glPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlkrvtlElGGknplivl 245
                                       + +++ea    g+P++ + ++  s +e++e l  ++ +d++   Gs    r i ++      +v+    G  ++ v 
  gi|474935021|ref|YP_007688603.1| 157 FDILREAagraGVPEDGFVLL-ESREEISEILKLDEYIDLMIPRGSYGFVRYIKENTR---IPVLGHAAGVCHVYVD 229
                                       ******88999*******666.5599*****************************988...9*************** PP

                                       TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--B CS
                            Aldedh 246 edaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkv 298
                                       ++aDl+ka + +  + + +   vC aa++llv+e+i+  f+ ++++ +++  v
  gi|474935021|ref|YP_007688603.1| 230 SEADLNKAFNVAYDSKVQYP-AVCNAAEKLLVNEKIASFFLPRMADLYAEAGV 281
                                       **************999886.8**********************998877655 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 7.7e-07
                                       EEEEEEESSHHHHHHHHHSSSEESEEEEE-SBHHHHHHHHHHS-SSEEEESSSST-- CS
                            Aldedh 374 VlsvikfkdeeeaieiaNdteyGLaagvftkdleraervaerleaGnvyiNdsttga 430
                                       ++++  +++ eeai+i+N +    + +++t++ ++  +++++++   + +N st++a
  gi|474935021|ref|YP_007688603.1| 314 IIAIRMVRSAEEAIDIMNTCGSHHTEAIITENRATFDKFVKNVDSADIVMNASTRFA 370
                                       57788899*******************************************997765 PP

>> IMS  impB/mucB/samB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0   0.00044       3.9      64     132 ..      43     109 ..       6     169 .. 0.78
   2 ?    5.1   0.1    0.0024        21      79     146 ..     326     391 ..     296     392 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00044
                                       EEEEEE-HHHHHHHHHHH.HHHHHH-S..EEEEETTEEEEE-HHHHHHHH-SHHHHHHHHHHHHHHHH-- CS
                               IMS  64 ivvkvdlekyrraskkil.eilkrfispkvekasiDEayldltgleelaesegaalakelrkaikeelgl 132
                                        ++ ++ e++r+a  ki  e+lkr  +  v  a++DE+ + l++++++++  g+ + ++l ++  +  ++
  gi|474935021|ref|YP_007688603.1|  43 EILDANAEDVREAEGKIPaEMLKRL-K--VNDAKVDEMIASLNDVKKQKDPVGETMRSMLLDDGLTLYQV 109
                                       566999999***9999961566666.5..***************99998877666666655555555555 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0024
                                       HHHHHHHHH-S..EEEEETTEEEEE-HHHHHHHH-SHHHHHHHHHHHHHH..HH---EEEEEESSHHHHH CS
                               IMS  79 kileilkrfispkvekasiDEayldltgleelaesegaalakelrkaike..elgltvsiGiasnkllAK 146
                                       +i +i+++ +s ++ +a i E  + + +++++ +s  a+++ + + + ++  +lg+ + +Gi++nk+ A+
  gi|474935021|ref|YP_007688603.1| 326 AI-DIMNTCGS-HHTEAIITENRATFDKFVKNVDS--ADIVMNASTRFADgfRLGMGAEVGISTNKVHAR 391
                                       33.66666644.66777788888888888888887..799999999999844568999********9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 2680.24
//
Query:       gi|474935022|ref|YP_007688604.1|  [L=396]
Description: putative ATPase (AAA+ superfamily) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-35  122.4   0.0    1.9e-35  121.7   0.0    1.3  1  AAA_14        AAA domain
    3.3e-05   23.9   0.0    6.1e-05   23.0   0.0    1.5  1  ATPase_2      ATPase domain predominantly from Archaea
    0.00088   19.4   0.0     0.0015   18.7   0.0    1.3  1  DUF4143       Domain of unknown function (DUF4143)
     0.0024   18.3   0.0     0.0057   17.1   0.0    1.8  1  AAA_16        AAA ATPase domain
  ------ inclusion threshold ------
      0.064   12.2   0.0       0.12   11.3   0.0    1.3  1  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
      0.082   12.8   0.0       0.16   11.9   0.0    1.4  1  NACHT         NACHT domain
      0.085   13.3   0.0       0.23   11.9   0.0    1.7  1  RNA_helicase  RNA helicase
       0.11   12.8   0.0       0.58   10.4   0.0    2.0  1  AAA_22        AAA domain
       0.19   10.9   0.1        2.2    7.4   0.1    2.1  1  NB-ARC        NB-ARC domain


Domain annotation for each model (and alignments):
>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.7   0.0   9.6e-39   1.9e-35       4     131 .]      24     152 ..      21     152 .. 0.94

  Alignments for each domain:
  == domain 1  score: 121.7 bits;  conditional E-value: 9.6e-39
                            AAA_14   4 ilvitGaRrvGKTtllkqlikell...vkkesilyinldderdkkladpekllelileklkeekktylflDEiqevp 77 
                                       ++vitG+Rr+GK+tl++q++++l    +++++i+ +n+++ + ++ + pe+l + i+e+  +++  y++lDEiqev+
  gi|474935022|ref|YP_007688604.1|  24 VKVITGMRRCGKSTLMEQFADDLRsegTDDSHIFHVNFETFEGRDVSSPEELRSRIRELP-GDGIVYILLDEIQEVD 99 
                                       79******************9999***********************9*99999999974.4599************ PP

                            AAA_14  78 ewekalkslvdegknldvivtGSnskllskeiatslagrvaeielyplsfaEfl 131
                                       +we+++  l   gkn+dv++tGSns +ls ++at+l+gr+ ei++ plsfaE+l
  gi|474935022|ref|YP_007688604.1| 100 GWETIVAALET-GKNYDVYITGSNSNMLSTDLATHLSGRYIEIRMLPLSFAEYL 152
                                       ****9998877.55**************************************97 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   3.1e-08   6.1e-05      19      68 ..      21      72 ..       7     125 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 3.1e-08
                          ATPase_2 19 pneiyfiYGpegsGKtaLlkeiienledkdk..yviyyialreesiskldef 68
                                      +  + +i+G +++GK++L+ +++  l++ +    +i+  ++++ +   +++ 
  gi|474935022|ref|YP_007688604.1| 21 TGVVKVITGMRRCGKSTLMEQFADDLRSEGTddSHIFHVNFETFEGRDVSSP 72
                                      67899*******************9965544349999999998877777766 PP

>> DUF4143  Domain of unknown function (DUF4143)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   7.6e-07    0.0015       7     107 ..     223     329 ..     197     342 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 7.6e-07
                                       xxxxxxxxxxxx...................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DUF4143   7 lagvrdpeelrk...................glverlppwsespnskkrlrkspKlyfvDtGLlvallgldkeelle 64 
                                       +++v++++++ k                    l++ ++++      kk l ++ K+y  D G+   +l+ + +++++
  gi|474935022|ref|YP_007688604.1| 223 IGNVTNIANIAKgtglnpgtvdryiggmeaaLLFYHAEKY--DIVGKKLLSTNGKYYASDLGMRLMALKGSGTDDMS 297
                                       4555555555558888888888899999888888888888..8889999999***********99999888888666 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DUF4143  65 dsenkGallEnlVaqeLlkysekegaklyyyrdkngaEvDfvi 107
                                       ++      lEn+V+ eL++ +++  +++  yrd   +E+Df  
  gi|474935022|ref|YP_007688604.1| 298 RP------LENAVYLELMR-RGY-TVRVGSYRD---KEIDFTA 329
                                       55......***********.444.578999998...69*9966 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.9e-06    0.0057      25      99 ..      23     103 ..       5     215 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.9e-06
                            AAA_16  25 elvllsGesGvGKsslvrellralekd........ggif..lrgkcdqlesaipy.salaqalareellrqlldeae 90 
                                        + +++G++ +GKs+l++++++ l+ +        ++ f  ++g+ +++    ++ s + ++   ++++  llde  
  gi|474935022|ref|YP_007688604.1|  23 VVKVITGMRRCGKSTLMEQFADDLRSEgtddshifHVNFetFEGRDVSS--PEELrSRIRELP-GDGIVYILLDE-- 94 
                                       55689*****************999998876533322222122222222..222212233333.55555555555.. PP

                            AAA_16  91 saeleawre 99 
                                        +e++ w +
  gi|474935022|ref|YP_007688604.1|  95 IQEVDGWET 103
                                       334555555 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   6.1e-05      0.12      18      58 ..      10      51 ..       3      56 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.1e-05
                                      HHHHHGGG-S-SEEEE.EEE-TTSSHHHHHHHHHHHHHCTT- CS
                              MeaB 18 llerllakaGraqvvG.ltGvPGaGkstlvealglelrrrGk 58
                                       le+l  + G + vv  +tG+   Gkstl+e+++  lr++G+
  gi|474935022|ref|YP_007688604.1| 10 YLEQLHGSKGATGVVKvITGMRRCGKSTLMEQFADDLRSEGT 51
                                      578888889999888637********************9996 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   7.8e-05      0.16       4      51 ..      26      70 ..      24      90 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.8e-05
                                      EEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-.. CS
                             NACHT  4 ilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgna 51
                                      +++G   +GK+tL++++a++++++  +    +++F++++ +++ +  +
  gi|474935022|ref|YP_007688604.1| 26 VITGMRRCGKSTLMEQFADDLRSEGTDD---SHIFHVNFETFEGRDVS 70
                                      57777789****************9877...78999999999877654 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00011      0.23       2      26 ..      26      50 ..      25      63 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                      RNA_helicase  2 wlyGpsgeGKStlakeLakallkkl 26
                                      +++G +++GKStl++++a++l ++ 
  gi|474935022|ref|YP_007688604.1| 26 VITGMRRCGKSTLMEQFADDLRSEG 50
                                      5899****************99665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00029      0.58       9      61 ..      26      80 ..      21     142 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00029
                            AAA_22  9 vvtGesGtGKTtllrrlleqldeeakaee..erpevvfvtlpsstsskdllrell 61
                                      v+tG   +GK+tl++++++ l  e   +    ++ + +++    +s+++l++++ 
  gi|474935022|ref|YP_007688604.1| 26 VITGMRRCGKSTLMEQFADDLRSEGTDDShiFHVNFETFEGRDVSSPEELRSRIR 80
                                      79*****************995433222233222222444444446666666665 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1    0.0011       2.2      18      54 ..      20      55 ..       8     131 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0011
                                      SCSEEEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEE CS
                            NB-ARC 18 lqslvvalvGmgGvGKttlakqilnksdevegrFdsv 54
                                         +v  + Gm  +GK+tl++q   +    eg+ ds+
  gi|474935022|ref|YP_007688604.1| 20 ATGVVKVITGMRRCGKSTLMEQFADD-LRSEGTDDSH 55
                                      444666799***********999888.4445555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 2417.27
//
Query:       gi|474935023|ref|YP_007688605.1|  [L=206]
Description: Methylase involved in ubiquinone/menaquinone biosynthesis [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-14   53.7   0.0    2.7e-14   53.3   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    9.2e-14   51.9   0.0    1.5e-13   51.2   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    4.6e-13   49.7   0.0    8.8e-13   48.8   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
      2e-08   34.2   0.0    2.8e-08   33.7   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    3.7e-06   27.6   0.0    5.7e-06   27.0   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    8.2e-05   22.0   0.0    0.00094   18.6   0.0    2.0  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
     0.0016   18.0   0.0      0.035   13.7   0.0    2.0  2  MTS              Methyltransferase small domain
     0.0054   16.2   0.0      0.031   13.7   0.0    2.0  2  Methyltransf_4   Putative methyltransferase


Domain annotation for each model (and alignments):
>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.3   0.0   1.2e-17   2.7e-14      16     161 ..      36     187 ..      19     191 .. 0.81

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 1.2e-17
                   Methyltransf_23  16 llpklraggrvLdiGcGtGillevlrengf..svtgvDlspeaveiae.......kakkaqkdqfdeqeaaepqgkf 83 
                                       + p   +++  LdiGcG G +l+  + ++    ++g+D+s   v+          +a   + + +  +++++p+g f
  gi|474935023|ref|YP_007688605.1|  36 FIPDSIRPKHSLDIGCGGGLVLRMTAFEWPkcLCEGIDISQTSVDFTLrsnsyfvSAGRIRAQVASVEDIPFPDGEF 112
                                       45557789999********9999775554324788****976555433889999855555555555579******** PP

                   Methyltransf_23  84 dlIvlrevlehvpdppellrqiatllkpgGylllseplaslkedrllldwlylvpagrhisffsarslkelleeaGl 160
                                       dlI++ e+    pd++++l+++a+ l+ gGy+ + +     ++ r  ++++ l ++  h+++   ++lk l+e+aGl
  gi|474935023|ref|YP_007688605.1| 113 DLITAVETYFFWPDLEKNLAHAASKLNAGGYMAVVTEQ--YPNGRNDEEIGRLCEE-YHMKLVPNDELKSLMEKAGL 186
                                       *******************************9999973..4688899999777777.8******************9 PP

                   Methyltransf_23 161 e 161
                                       +
  gi|474935023|ref|YP_007688605.1| 187 K 187
                                       7 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   0.0   6.5e-17   1.5e-13       1      95 [.      47     145 ..      47     146 .. 0.87

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 6.5e-17
                                       EEET-TTSHHHHHHH.HTT..SEEEEEES-HHHHHHH.HHHCCHHT-....EEEETTEECCCTSS-TT-EEEEEEES CS
                   Methyltransf_11   1 LdvGcGtGrlaeala.krg..arvvgvDlskemlkla.kekaseegl....kvefvvadaeklpfednsfDlvvsse 69 
                                       Ld+GcG+G++++  a +    + + g+D+s++ ++   ++++    +    +++ +va++e++pf+d+ fDl+++ e
  gi|474935023|ref|YP_007688605.1|  47 LDIGCGGGLVLRMTAfE-WpkCLCEGIDISQTSVDFTlRSNSY---FvsagRIRAQVASVEDIPFPDGEFDLITAVE 119
                                       8**************54.34899***********777222222...2345899************************ PP

                                       -CCC-CCHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  70 vlhhvedpekalkeiaRvLkpgGllv 95 
                                       + ++++d+ek l+ +a  L  gG+++
  gi|474935023|ref|YP_007688605.1| 120 TYFFWPDLEKNLAHAASKLNAGGYMA 145
                                       ************************87 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.0   3.9e-16   8.8e-13       2      97 .]      47     142 ..      47     142 .. 0.89

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 3.9e-16
                                       EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHH..TTT.TEEEEESBCCGBSSSTTTEEEEEEESTGG CS
                   Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraee..egl.nvefvqgdaedlpfedgsfDlvvssgalh 75 
                                       Ld+GcG G ++++ a +++k+   g+Dis++ ++ + + ++   + + +++ +++++ed+pf+dg+fDl++++ +  
  gi|474935023|ref|YP_007688605.1|  47 LDIGCGGGLVLRMTAFEWPKCLCEGIDISQTSVDFTLRSNSYfvS-AgRIRAQVASVEDIPFPDGEFDLITAVET-Y 121
                                       8**************99999***************9988866543.26************************866.3 PP

                                       GSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  76 hlsdedlekalkeiarvLkpgG 97 
                                       +++ +dlek l+++a+ L+ gG
  gi|474935023|ref|YP_007688605.1| 122 FFW-PDLEKNLAHAASKLNAGG 142
                                       344.79**********999998 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.0   1.3e-11   2.8e-08       6     130 ..      45     170 ..      42     196 .. 0.77

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 1.3e-11
                   Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld..nveFeqgdieeleklledekfDlils 80 
                                       + lD+GCG G  +   a    pk+   GiDis++++ +     +  +++  +++ +++++e+++  + d  fDli++
  gi|474935023|ref|YP_007688605.1|  45 HSLDIGCGGGLVLRMTA-FEWPKCLCEGIDISQTSVDFTLRSNS-YFVSagRIRAQVASVEDIP--FPDGEFDLITA 117
                                       569*****987777777.6689999*************988433.333357*************..*********** PP

                   Methyltransf_31  81 nevlnaladpdkileeiervlkpggilliedpr....llaelpakveeeskay..e 130
                                        e+    +d++k l  + + l+ gg++++ + +        +++++ + +++y  +
  gi|474935023|ref|YP_007688605.1| 118 VETYFFWPDLEKNLAHAASKLNAGGYMAVVTEQypngR---NDEEIGRLCEEYhmK 170
                                       ****************************9888843331...225555555544332 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   2.5e-09   5.7e-06       1      98 [.      47     143 ..      47     144 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 2.5e-09
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.ssfDlvvasnvl 76 
                                       L+iGcG G +lr+ + + p +   g+Dis+ +++ + +  +     ++ +++ ++ +++d + + + fDl++a ++ 
  gi|474935023|ref|YP_007688605.1|  47 LDIGCGGGLVLRMTAFEWPKCLCEGIDISQTSVDFTLRSNSYF--VSAGRIRAQVASVEDIPFPdGEFDLITAVETY 121
                                       8****************9999999*********3333333322..234455555555444433367*********** PP

                   Methyltransf_12  77 hhlkdirevldnirklLkpgGr 98 
                                         ++d+++ l+++++ L+ gG+
  gi|474935023|ref|YP_007688605.1| 122 FFWPDLEKNLAHAASKLNAGGY 143
                                       ********************97 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   4.2e-07   0.00094      46     152 ..      41     147 ..      21     174 .. 0.86
   2 ?    1.8   0.0     0.058   1.3e+02     201     215 ..     174     188 ..     156     195 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 4.2e-07
                                       --TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE--TTT-TTS-T-EEEEE CS
                   Ubie_methyltran  46 krgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.nieflqanaeeLpfeddsfDvvt 121
                                        r+++ lD+ +G g l ++++     k   +++Di+++ ++ + +         +i+  +a+ e++pf d+ fD++t
  gi|474935023|ref|YP_007688605.1|  41 IRPKHSLDIGCGGG-LVLRMTAFEWPKCLCEGIDISQTSVDFTLRSNSYFVSAgRIRAQVASVEDIPFPDGEFDLIT 116
                                       578899*****966.889*****9**************9998765544433336*********************** PP

                                       EES-GGG-S-HHHHHHHHHHHEEEEEEEEEE CS
                   Ubie_methyltran 122 vsfGlrnvtDklkaLkeayrvlkpGGrlvvl 152
                                               +D +k L +a   l +GG + v+
  gi|474935023|ref|YP_007688605.1| 117 AVETYFFWPDLEKNLAHAASKLNAGGYMAVV 147
                                       *999999*******************99887 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.058
                                       HHHHHHHHHHTTEEE CS
                   Ubie_methyltran 201 qetlkeliedaGfks 215
                                       +++lk+l+e+aG+k+
  gi|474935023|ref|YP_007688605.1| 174 NDELKSLMEKAGLKT 188
                                       589*********985 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   1.5e-05     0.035      32      73 ..      43      84 ..      32     118 .. 0.77
   2 ?    2.3   0.0     0.047   1.1e+02     122     141 ..     131     150 ..     123     167 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.5e-05
                                      CSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHH CS
                               MTS 32 sgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesake 73
                                       ++ lD+GcG G++  + a e+p+   + +d++  +++++ +
  gi|474935023|ref|YP_007688605.1| 43 PKHSLDIGCGGGLVLRMTAFEWPKCLCEGIDISQTSVDFTLR 84
                                      4568********************************998644 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.047
                                       HHHHHHHEEEEEEEEEEEET CS
                               MTS 122 iaeAkeaLkegGeLliVanr 141
                                       +a+A++ L+ gG + +V+++
  gi|474935023|ref|YP_007688605.1| 131 LAHAASKLNAGGYMAVVTEQ 150
                                       789**************876 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   1.4e-05     0.031       5      40 ..      46      81 ..      42      87 .. 0.90
   2 ?   -0.2   0.0      0.27   6.1e+02     100     119 ..     131     150 ..     128     192 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.4e-05
                                      EEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHH CS
                    Methyltransf_4  5 vleiGcGkGeflvalAkknPdknflGiEirvkvvak 40
                                       l+iGcG G +l   A + P++++ Gi+i++++v+ 
  gi|474935023|ref|YP_007688605.1| 46 SLDIGCGGGLVLRMTAFEWPKCLCEGIDISQTSVDF 81
                                      58******************************9985 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.27
                                       HHHHHHHEEEEEEEEEEESH CS
                    Methyltransf_4 100 lkelarvLkkgGvlelaTDv 119
                                       l+++a++L+ gG++ ++T  
  gi|474935023|ref|YP_007688605.1| 131 LAHAASKLNAGGYMAVVTEQ 150
                                       67889999999999999874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1483.60
//
Query:       gi|474935024|ref|YP_007688606.1|  [L=185]
Description: hypothetical protein TALC_01472 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.016   14.8   0.8      0.021   14.5   0.8    1.3  1  Wzy_C     O-Antigen ligase
      0.067   13.3   0.1       0.11   12.5   0.1    1.3  1  bPH_5     Bacterial PH domain
      0.074   12.5   0.2       0.18   11.3   0.1    1.6  1  SoxE      Sulfocyanin (SoxE) domain
       0.92   10.0   3.3        1.7    9.1   3.3    1.4  1  DUF983    Protein of unknown function (DUF983)


Domain annotation for each model (and alignments):
>> Wzy_C  O-Antigen ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.8   4.6e-06     0.021      19      80 ..       8      79 ..       4     145 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.6e-06
                             Wzy_C 19 iigllvalivlliifykrri...pfllllgilvgvilliilfvlstnletlknitkafgkldkk.......k 80
                                      iig++ ++ ++ +i++ ++    + l+  ++lvg ++l++lf+l +n + ++ni++    +dk        k
  gi|474935024|ref|YP_007688606.1|  8 IIGFVYLFAAVSVIVISNFTsgfLPLWTQIALVGSAVLLMLFALYRNKKVVANIEFSTLENDKFrhtvvteK 79
                                      566655555555555555555558888999************************988777776666666651 PP

>> bPH_5  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   2.6e-05      0.11       5      65 ..      84     144 ..      81     165 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.6e-05
                             bPH_5   5 ldeeglvIrwifgkeeIplseIeavrvsegvikgvrlfgtskpgyalGrfkikdigkarmy 65 
                                       ld  +l+I+  +   +I l +I ++ + ++ + g r fg+s  + a+G++   + g++ + 
  gi|474935024|ref|YP_007688606.1|  84 LDSLSLHITASMMDLRIALADIMEIGKITSIKVGKRRFGVSNGKQASGVWHNSEWGDYGLA 144
                                       6777899*******************************************99998887655 PP

>> SoxE  Sulfocyanin (SoxE) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1     4e-05      0.18      96     124 ..     119     147 ..     100     159 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4e-05
                              SoxE  96 avsGissGqsasGlledlsaGtywlacgi 124
                                       +  G+s G++asG++++   G+y la  +
  gi|474935024|ref|YP_007688606.1| 119 RRFGVSNGKQASGVWHNSEWGDYGLAIDV 147
                                       3469*******************998765 PP

>> DUF983  Protein of unknown function (DUF983)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   3.3   0.00038       1.7      32      77 ..      10      56 ..       5      60 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00038
                            DUF983 32 ilivghlvvplallvevayep.plwvhlliwlpltlllsllllrplK 77
                                       ++ ++ +v ++++ +++    plw++++++   +ll+ ++l+r  K
  gi|474935024|ref|YP_007688606.1| 10 GFVYLFAAVSVIVISNFTSGFlPLWTQIALVGSAVLLMLFALYRNKK 56
                                      3445555566667777777767*********************9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       845  (0.0471303); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 1213.12
//
Query:       gi|474935025|ref|YP_007688607.1|  [L=390]
Description: Arabinose efflux permease [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-42  144.3  40.7    4.3e-42  144.3  40.7    1.8  2  MFS_1     Major Facilitator Superfamily
    1.2e-13   50.8   5.0    1.2e-13   50.8   5.0    3.2  3  Sugar_tr  Sugar (and other) transporter
    4.6e-07   28.8  28.5    2.4e-06   26.4   4.6    3.0  3  MFS_2     MFS/sugar transport protein


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.3  40.7   7.2e-46   4.3e-42       7     353 .]      12     346 ..       6     346 .. 0.90
   2 !    4.8   6.6    0.0019        11     100     169 ..     309     375 ..     308     385 .. 0.70

  Alignments for each domain:
  == domain 1  score: 144.3 bits;  conditional E-value: 7.2e-46
                             MFS_1   7 lsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfas 83 
                                       +  ++ +++++ +p  +a dl  +p++++++l +++l +av++l++G+++dr+Gr+ +l+ +l+ +++++++++f+ 
  gi|474935025|ref|YP_007688607.1|  12 FGPISTDMFLSDIP-NMAVDLDTDPATMNMVLYGFMLSMAVSILLFGPFTDRYGRKHLLIGCLAEYVAASMIAAFVD 87 
                                       55677889999999.9*****************************************************8888899* PP

                             MFS_1  84 slwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaiv 160
                                       ++++l+v+rvlqG+gag++++++ ali d f++  r++++ ++s+   +G++ +p++g++++s + Wr +f++ ++v
  gi|474935025|ref|YP_007688607.1|  88 NIYILVVFRVLQGIGAGGVITISTALIKDCFTGLTRAKVLNVISLIGVVGPLAAPIVGAYIISIWDWRMTFIAPGVV 164
                                       ***************************************************************************** PP

                             MFS_1 161 sllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlw.illialllfffgfsglltllplylqe 236
                                       ++l+++     ++ +++ +   ++ +       ap++ a + +l +p++  +ll++ +++++++ +l++ + +y   
  gi|474935025|ref|YP_007688607.1| 165 AALCLI---PAFMLSETLKDEHRDYKG-----IAPMFHAMEGILVSPPFGsFLLMVTIFNMMFMGYLSVSSYIY-EG 232
                                       ****88...555555555555555444.....6688888999999999976678888888888888999999*9.** PP

                             MFS_1 237 vlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfg 313
                                        +g s     +l+la++ l+g  ++++++r s+ lg rr++ +++++++++a+++++++   ++v+ll  ++ + ++
  gi|474935025|ref|YP_007688607.1| 233 MFGVS-STNYTLFLAAALLFGSLMMPFFARGSRSLGYRRMIPVFFSVMFAGAFSMFMVGDGGKYVFLLT-FLPCMCA 307
                                       *****.688888899999999999*************************************77777775.4445557 PP

                             MFS_1 314 lgfvfpsllalasdlappeeagtasglfntagslggalgp 353
                                        + ++p  +++++ ++ +  +g++s+l+n+++ l g++g+
  gi|474935025|ref|YP_007688607.1| 308 CAAIRPYGMTVLMASH-EGDNGMVSSLINFIFFLTGCIGM 346
                                       7778***********9.5******************9996 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0019
                             MFS_1 100 galfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivslla.fv.lfl 169
                                       +a+ p g++++ +   + + g++ +l++  f l   +g++++ +      W+   y l +++l+a ++ l++
  gi|474935025|ref|YP_007688607.1| 309 AAIRPYGMTVLMASHEG-DNGMVSSLINFIFFLTGCIGMVVSTMSF----WPNYVYGLSAIGLIAcAIfLAM 375
                                       56667777777777777.9999999999999999999999999888....5555555555555551443333 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   5.0     2e-17   1.2e-13      48     194 ..      38     178 ..      20     187 .. 0.94
   2 ?   -2.4   8.3      0.26   1.6e+03      28      98 ..     215     291 ..     204     301 .. 0.63
   3 ?   -1.7   5.4      0.16   9.8e+02     317     371 ..     294     348 ..     291     356 .. 0.62

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 2e-17
                                       HHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHH CS
                          Sugar_tr  48 sglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvP 124
                                       + +++  f++  +++ l++g+++dr+GRk  l+ + + +v+++++ a+ +   ++++l+v Rvl Gig+G++ ++++
  gi|474935025|ref|YP_007688607.1|  38 MNMVLYGFMLSMAVSILLFGPFTDRYGRKHLLIGCLAEYVAASMIAAFVD---NIYILVVFRVLQGIGAGGVITIST 111
                                       5666777899999*************************************...************************ PP

                                       HHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS--- CS
                          Sugar_tr 125 myisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllflPES 194
                                        +i+   +   R ++  +  l  ++G l a i+g+ +  + +   wr+++    v a l li  ++l E+
  gi|474935025|ref|YP_007688607.1| 112 ALIKDCFTGLTRAKVLNVISLIGVVGPLAAPIVGAYIISIWD---WRMTFIAPGVVAALCLIPAFMLSET 178
                                       **************************************9999...************9999999999987 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.26
                                       HHHTSTT--SHHHHHH..........HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TT CS
                          Sugar_tr  28 faknfglsksksskee.......ssvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaak 97 
                                       f ++f  + s+ss+         s+ ++ ++++++l+G+++  +fa   +  +G++  + ++  ++++ga+ +++  
  gi|474935025|ref|YP_007688607.1| 215 FNMMFMGYLSVSSYIYegmfgvsSTNYTLFLAAALLFGSLMMPFFAR-GSRSLGYRRMIPVFFSVMFAGAFSMFMVG 290
                                       33333344444433334444443444456777777778877777776.78999999999999999999999888766 PP

                                       T CS
                          Sugar_tr  98 g 98 
                                       +
  gi|474935025|ref|YP_007688607.1| 291 D 291
                                       4 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.16
                                       HHHHHHHHHHHHHHHHHHH....HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHH CS
                          Sugar_tr 317 RtllllGaagmaicfvilg..ivalllvakskaasivaivfialfialfalgwgpvp 371
                                       ++++ll ++ ++++++ +   +++ l+ + +    ++++  ++ fi++ + ++g v+
  gi|474935025|ref|YP_007688607.1| 294 KYVFLLTFLPCMCACAAIRpyGMTVLMASHE--GDNGMVSSLINFIFFLTGCIGMVV 348
                                       7889999999999999888864444444443..455555555555555555555544 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   4.6   3.9e-10   2.4e-06     257     343 ..      34     118 ..      26     122 .. 0.93
   2 !   16.0  15.9   5.6e-07    0.0033     171     324 ..     154     307 ..     122     327 .. 0.71
   3 ?   -3.7   5.0      0.54   3.2e+03     300     339 ..     340     379 ..     320     384 .. 0.53

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 3.9e-10
                             MFS_2 257 ngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlllqpsnlllflvllviagfgvgvaal 333
                                       + + ++++l+ +++s++++i+l+ p++ r+g+k++ + +++ +++ ++++ ++   n+++++v+ v+ g+g+g+  +
  gi|474935025|ref|YP_007688607.1|  34 DPATMNMVLYGFMLSMAVSILLFGPFTDRYGRKHLLIGCLAEYVAASMIAAFV--DNIYILVVFRVLQGIGAGGVIT 108
                                       677899999999***************************************99..9********************* PP

                             MFS_2 334 lpwsmladvv 343
                                       + ++++ d++
  gi|474935025|ref|YP_007688607.1| 109 ISTALIKDCF 118
                                       ********96 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 5.6e-07
                             MFS_2 171 ylifaliialLmllgviivvlgtkervemrkkekteqkeklslleqlkevfrnraflillllfllaalalgvlngll 247
                                       ++++ +   ++++l+ i +++         k+e    k+  +++ +++ ++ +++f  +ll++ ++ ++++ + + +
  gi|474935025|ref|YP_007688607.1| 154 WRMTFIAPGVVAALCLIPAFMLSETL----KDEHRDYKGIAPMFHAMEGILVSPPFGSFLLMVTIFNMMFMGYLSVS 226
                                       33444444444444444443333322....233447899999*********************************** PP

                             MFS_2 248 lYyltyvlg.ngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlll...qpsnlllflvl 320
                                        Y ++ + g + +++++fl+++ + + l++p++++  + lg ++++ +++++++++ + ++++   +++  ll+++ 
  gi|474935025|ref|YP_007688607.1| 227 SYIYEGMFGvSSTNYTLFLAAALLFGSLMMPFFARGSRSLGYRRMIPVFFSVMFAGAFSMFMVgdgGKYVFLLTFLP 303
                                       ***************************************************************74433333333333 PP

                             MFS_2 321 lvia 324
                                       +++a
  gi|474935025|ref|YP_007688607.1| 304 CMCA 307
                                       3222 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 0.54
                             MFS_2 300 ivllvlvlllqpsnlllflvllviagfgvgvaallpwsml 339
                                       + + +++++ + s +  ++  l ++g+++++++l++w+++
  gi|474935025|ref|YP_007688607.1| 340 LTGCIGMVVSTMSFWPNYVYGLSAIGLIACAIFLAMWAIM 379
                                       2222222222333444444455566666666666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       801  (0.0446762); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 2796.06
//
Query:       gi|474935026|ref|YP_007688608.1|  [L=161]
Description: hypothetical protein TALC_01474 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.016   15.6   0.1        0.3   11.5   0.0    2.3  2  V-SNARE   Vesicle transport v-SNARE protein N-terminus
        0.1   13.4   3.1       0.17   12.7   3.1    1.4  1  Stm1_N    Stm1


Domain annotation for each model (and alignments):
>> V-SNARE  Vesicle transport v-SNARE protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.3e-05       0.3      10      44 ..      61      97 ..      53     104 .. 0.81
   2 ?    1.7   0.1     0.037   3.4e+02      21      38 ..     134     151 ..     114     156 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.3e-05
                           V-SNARE 10 sklarls.slag.eerkaalreiekkldeaeelldqM 44
                                      +++ar+  +++g  +r+a++re+++++++++++++q 
  gi|474935026|ref|YP_007688608.1| 61 NAIARVEtTEEGtPDRRAMIRELDQAFNNMKTCVEQC 97
                                      67777773444666*********************95 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.037
                           V-SNARE  21 eerkaalreiekkldeae 38 
                                       + r+ a+ e++++ld ++
  gi|474935026|ref|YP_007688608.1| 134 SVRNVAIEEADRALDALD 151
                                       378888888888888664 PP

>> Stm1_N  Stm1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   3.1   1.9e-05      0.17      24      60 ..       4      40 ..       1      45 [. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.9e-05
                            Stm1_N 24 apppkevdkkstrsaKrptkpepPsqavrearnegar 60
                                      + p+k++++k+t+s+K p+ +++P q ++ a++ +++
  gi|474935026|ref|YP_007688608.1|  4 KTPAKKAEQKKTASKKEPSIKLTPEQEAVLAQKPESG 40
                                      67999*********************99998666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       913  (0.0509231); expected 358.6 (0.02)
Passed bias filter:                      610  (0.0340231); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 946.46
//
Query:       gi|474935027|ref|YP_007688609.1|  [L=222]
Description: hypothetical protein TALC_01475 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       203  (0.0113224); expected 358.6 (0.02)
Passed bias filter:                      188  (0.0104858); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 1284.21
//
Query:       gi|474935028|ref|YP_007688610.1|  [L=300]
Description: Membrane protein TerC, possibly involved in tellurium resistance [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-52  178.2   6.7    1.2e-52  178.2   6.7    2.1  3  TerC         Integral membrane protein TerC family
  ------ inclusion threshold ------
       0.84    9.3   7.5        4.2    7.1   0.2    3.6  3  DUF3961      Domain of unknown function (DUF3961)
        7.9    6.3  19.5        3.6    7.4   1.8    3.0  3  DUF2157      Predicted membrane protein (DUF2157)


Domain annotation for each model (and alignments):
>> TerC  Integral membrane protein TerC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.4       0.3   1.8e+03     132     143 ..      24      35 ..      12      44 .. 0.49
   2 !  178.2   6.7     2e-56   1.2e-52       3     180 ..      53     253 ..      51     254 .. 0.95
   3 ?   -3.0   0.7       0.8   4.8e+03     119     127 ..     265     273 ..     258     285 .. 0.42

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.3
                              TerC 132 fivitavilsil 143
                                       +i+++av+++  
  gi|474935028|ref|YP_007688610.1|  24 VIIYVAVAMAFG 35 
                                       233333333332 PP

  == domain 2  score: 178.2 bits;  conditional E-value: 2e-56
                              TerC   3 lvlleivLsiDNlvviallvkk..lpeeqqkkalllGilgAlvlRillillavallelfdlilligglfLlytavke 77 
                                        +++e ++s+DNl+v++++++   +pee+q+++l++GilgA+ +R+++i++++ ll+ fd++++++g++L+yta+++
  gi|474935028|ref|YP_007688610.1|  53 SYVIEFAMSVDNLFVFIIIFAAflIPEEHQHRVLFYGILGAICFRAAFIFVGAELLDTFDWMMYVFGVILIYTAWHT 129
                                       589************************************************************************** PP

                              TerC  78 llekr....lenklvkeekkkkkktkst.................llavviqielaDlvfslDSvlaavaitsdlfi 133
                                         +k     +e++l  + ++k k+t++t                 +++ ++ iel+D++f++DS++aa++it+d+fi
  gi|474935028|ref|YP_007688610.1| 130 ACSKGgekpPEETLPYKLSRKIKSTDDTrggrffvkengrrlattMFLCLVVIELSDVMFAFDSIPAALSITTDMFI 206
                                       **988998755778888888888888889999********************************************* PP

                              TerC 134 vitavilsilvlrflakllakllerfptlkylalalllligvklvle 180
                                       v+t++il++l+lr++++++++++ ++ +lky++ ++l++ig+k++++
  gi|474935028|ref|YP_007688610.1| 207 VFTSNILAVLGLRSMYFVVSHAIGSLVYLKYGLGVILAFIGIKMLIS 253
                                       ********************************************985 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 0.8
                              TerC 119 DSvlaavai 127
                                         +la++a+
  gi|474935028|ref|YP_007688610.1| 265 VFILAVLAL 273
                                       222222222 PP

>> DUF3961  Domain of unknown function (DUF3961)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.012        69      12      23 ..      81      92 ..      72     103 .. 0.83
   2 ?    7.1   0.2    0.0007       4.2      26      38 ..     198     212 ..     195     213 .. 0.74
   3 ?    0.7   0.8     0.071   4.2e+02      26      35 ..     258     267 ..     256     270 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.012
                           DUF3961 12 KeDrvWFYGFYG 23
                                       + rv FYG  G
  gi|474935028|ref|YP_007688610.1| 81 HQHRVLFYGILG 92
                                      6899*****988 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0007
                           DUF3961  26 vSiV..LFmVFvSNi 38 
                                       +Si   +F+VF+SNi
  gi|474935028|ref|YP_007688610.1| 198 LSITtdMFIVFTSNI 212
                                       5554338*******9 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.071
                           DUF3961  26 vSiVLFmVFv 35 
                                       +S+VL +VF+
  gi|474935028|ref|YP_007688610.1| 258 ISVVLSLVFI 267
                                       9********7 PP

>> DUF2157  Predicted membrane protein (DUF2157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.36   2.2e+03     101     112 ..      28      39 ..      12      61 .. 0.60
   2 ?    7.4   1.8    0.0006       3.6      35      81 ..      85     131 ..      72     235 .. 0.74
   3 ?    6.4   7.0    0.0012       7.3      39      81 ..     237     278 ..     218     292 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.36
                           DUF2157 101 laalllgaaial 112
                                       +a+ +  + ++l
  gi|474935028|ref|YP_007688610.1|  28 VAVAMAFGVLIL 39 
                                       222222222222 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0006
                           DUF2157  35 leallvlGalllglGlilfvAanWqglsrlvkfllllvllllslllg 81 
                                       + +  +lGa+++ ++ i++ A + +++  ++ +  ++++  + + + 
  gi|474935028|ref|YP_007688610.1|  85 VLFYGILGAICFRAAFIFVGAELLDTFDWMMYVFGVILIYTAWHTAC 131
                                       3444579****************999998777766666666655544 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0012
                           DUF2157  39 lvlGalllglGlilfvAanWqglsrlvkfllllvllllslllg 81 
                                       ++lG++l  +G+ +++ +nW+++s ++ ++ +l++l+l+++l 
  gi|474935028|ref|YP_007688610.1| 237 YGLGVILAFIGIKMLI-SNWAEISVVLSLVFILAVLALTVVLS 278
                                       789***********99.6******9999999999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1044  (0.0582297); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 1883.80
//
Query:       gi|474935029|ref|YP_007688611.1|  [L=161]
Description: Family of unknown function (DUF1790) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.8e-08   32.8   0.0    7.2e-08   32.5   0.0    1.1  1  YbjN             Putative bacterial sensory transduction regu
  ------ inclusion threshold ------
       0.17   12.0   0.0        0.4   10.7   0.0    1.6  1  Molybdopterin_N  Molybdopterin oxidoreductase N-terminal doma


Domain annotation for each model (and alignments):
>> YbjN  Putative bacterial sensory transduction regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.0     8e-12   7.2e-08       5     107 ..      22     128 ..      19     146 .. 0.82

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 8e-12
                                       HHHHHHHH--S-EEEEETTEE.EEEEEETTEEEEEEE--SSTT-EE..EEEEEEES--TTHHHHHHHHHHHTTTTTT CS
                              YbjN   5 leevLeeagleyertedddgaivvvgtwggyrftiallgeseelll..vlafvarvpeedreallellnrwNrellf 79 
                                       + ++L++ g+++ +++ +   ++ +++++++++ +a++ ++e   l      +++ p++  +++l  ln +N +l f
  gi|474935029|ref|YP_007688611.1|  22 VTKALTSKGIKFNESDAEKNTVYTTFEGDDFPVKLAITVDDELPVLcfNSLLDFQAPPNSYKEILDGLNLINSNLHF 98 
                                       7899*******999999999999*********9999999998877733556666666******************** PP

                                       T-EEE.EETTEEEEEEEEE-..TT--HHHH CS
                              YbjN  80 gkayl.dedgdvlvehdldl.dagltpeql 107
                                       g++ l  e+g v++++++++ +  ++++ +
  gi|474935029|ref|YP_007688611.1|  99 GAFILdPENGRVVFRYHFLFaEYVPSKDMI 128
                                       *****88888888****9994444444444 PP

>> Molybdopterin_N  Molybdopterin oxidoreductase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   4.5e-05       0.4       4      18 ..      97     111 ..      96     112 .. 0.97

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 4.5e-05
                   Molybdopterin_N   4 HWGafraevkdGkiv 18 
                                       H+Gaf  ++++G++v
  gi|474935029|ref|YP_007688611.1|  97 HFGAFILDPENGRVV 111
                                       *************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1025.89
//
Query:       gi|474935030|ref|YP_007688612.1|  [L=379]
Description: chaperone protein DnaJ [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-34  117.8   0.0    5.2e-34  117.5   0.0    1.1  1  DnaJ_C           DnaJ C terminal domain
    1.9e-27   95.2   2.1    2.8e-27   94.6   2.1    1.3  1  DnaJ             DnaJ domain
    3.6e-13   49.6  16.4      6e-13   49.0  16.4    1.4  1  DnaJ_CXXCXGXG    DnaJ central domain
    0.00013   21.8  14.7      0.012   15.5   4.5    2.5  2  Anti-TRAP        Tryptophan RNA-binding attenuator protein in
    0.00091   19.2   3.7      0.064   13.3   0.1    2.3  2  HypA             Hydrogenase/urease nickel incorporation, met
  ------ inclusion threshold ------
      0.015   15.6  13.1        1.9    8.9   0.2    3.8  4  Lar_restr_allev  Restriction alleviation protein Lar
       0.23   10.8  11.9       0.27   10.6   3.2    3.3  3  zf-TFIIB         Transcription factor zinc-finger
       0.35    9.6   8.3        0.9    8.2   1.3    2.1  2  NRDD             Anaerobic ribonucleoside-triphosphate reduct
       0.44   10.5   5.7        1.5    8.8   0.3    2.2  2  zf-C3HC4_3       Zinc finger, C3HC4 type (RING finger)
        1.1    9.3  10.2        5.9    7.0  10.2    2.0  1  DZR              Double zinc ribbon
        4.6    7.3   8.4         24    5.0   0.3    3.3  3  Ogr_Delta        Ogr/Delta-like zinc finger
        5.1    6.7   5.5        7.6    6.2   0.6    2.2  2  TackOD1          Thaumarchaeal output domain 1
        8.7    6.3  12.3         24    4.9   0.1    4.1  4  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)


Domain annotation for each model (and alignments):
>> DnaJ_C  DnaJ C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.5   0.0   3.8e-37   5.2e-34       2     148 .]     129     346 ..     128     346 .. 0.95

  Alignments for each domain:
  == domain 1  score: 117.5 bits;  conditional E-value: 3.8e-37
                                       EEEEEE-HHHHHH-.EEE.EEEE...................................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx................................................... RF
                            DnaJ_C   2 eveleisleelykGktkkikikrnvi................................................... 27 
                                       +++ ei+l +++kGk+++i++ +  i                                                   
  gi|474935030|ref|YP_007688612.1| 129 RYDTEIDLLDVLKGKDTEINVPHSAIcsdchgtggkdgktnvcptcggrgqvqsvrrtpfgnavsispcpkcggtgk 205
                                       7999******************9999*************************************************** PP

                                       ..................TEEEEEE-TT--TT-EEEETT-SS..SS..S---EEEEEEE---SS-EEETTEEEEEEE CS
                                       ..............xxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaJ_C  28 ..............kkekktlevkipaGikdgqkirlegeGd..eeggepGDlivtikvkphpvFkrkgndlyveve 88 
                                                     ++++++++v+ipaGi+dg+++r++g Gd   +gg pGDl+v+++v+++  F+r+g dl+  +e
  gi|474935030|ref|YP_007688612.1| 206 tfdtpcpkcrgrgrVNKTTKVSVHIPAGIEDGMRLRVPGAGDagTNGGAPGDLFVVVHVRENGSFERDGTDLWAVAE 282
                                       *************7666669**********************87677**************************9999 PP

                                       EEHHHHHHTEEEEEE-S.S-EEEEEE...--TT-EEEETT-S-EET...TEE--EEEEEEEE-- CS
                                       xxxxxxxxxxxxxxxxx.xxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaJ_C  89 islaeallGgklevptl.dgkvklki...tqpgevlrikgkGmpklkkpgkrGdlyvevkvefP 148
                                        ++   +lGg++ev+ + ++++++++   tq g v+r++g+G+p++++p+ rG+lyv+v +++P
  gi|474935030|ref|YP_007688612.1| 283 TTYPRLVLGGTVEVKNVeGKTIEINVpagTQVGGVIRVPGQGLPSVNRPSDRGNLYVRVAIKVP 346
                                       ***************99555677888************************************99 PP

>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.6   2.1     2e-30   2.8e-27       1      63 []       8      71 ..       8      71 .. 0.95

  Alignments for each domain:
  == domain 1  score: 94.6 bits;  conditional E-value: 2e-30
                                      HHHHHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHH.HHHHHHHHHHHHHHHHTSHHHHHHHH CS
                              DnaJ  1 dyYeiLgvskdasedeIkkaYrklalkyHPDknpkdp.eaeekFkeineAyevLsdpekRkqYD 63
                                      dyYe+Lgvsk as+deIkkaYr++a+kyHPD +++ +  ae kFkei+eAyevLsdp+kR++YD
  gi|474935030|ref|YP_007688612.1|  8 DYYEVLGVSKGASADEIKKAYRQMAKKYHPDVSTEPKdVAEAKFKEISEAYEVLSDPDKRSRYD 71
                                      8******************************88555568999*********************9 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0  16.4   4.4e-16     6e-13       1      67 []     155     218 ..     155     218 .. 0.90

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 4.4e-16
                     DnaJ_CXXCXGXG   1 CkkCkGsgakkgkkktCktCkGsGvvreeqkt.lgpfvqqsqstCpeCeGtGkvikekdkCkkCkGkg 67 
                                       C++C+G+g k+gk++ C+tC+G+G+v++ ++t +g+ v  s s+Cp+C+GtGk++  +++C+kC+G+g
  gi|474935030|ref|YP_007688612.1| 155 CSDCHGTGGKDGKTNVCPTCGGRGQVQSVRRTpFGNAV--SISPCPKCGGTGKTF--DTPCPKCRGRG 218
                                       ************************98888877798866..568************..778******86 PP

>> Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   2.5   0.00018      0.25      12      42 ..     154     180 ..     147     184 .. 0.89
   2 !   15.5   4.5   8.8e-06     0.012      12      42 ..     196     220 ..     194     227 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00018
                                       E-TTTTTTSEETTE......E-TTTTTSSEE CS
                         Anti-TRAP  12 kCdaCngsGkiepeeprasleCPkCsGkgli 42 
                                        C  C+g+G  +++    +  CP C+G+g +
  gi|474935030|ref|YP_007688612.1| 154 ICSDCHGTGGKDGK----TNVCPTCGGRGQV 180
                                       5*********9999....678******9965 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 8.8e-06
                                       E-TTTTTTSEETTE......E-TTTTTSSEE CS
                         Anti-TRAP  12 kCdaCngsGkiepeeprasleCPkCsGkgli 42 
                                       +C++C g+Gk   +      +CPkC G+g +
  gi|474935030|ref|YP_007688612.1| 196 PCPKCGGTGKTFDT------PCPKCRGRGRV 220
                                       8*************......*******9965 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.1   4.6e-05     0.064      66      96 ..     148     178 ..     134     187 .. 0.81
   2 !    6.5   0.6    0.0059       8.2      73      96 ..     197     218 ..     190     230 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.6e-05
                                       EE--EEEETTTS-EEECHHHHHS-TTTSSS- CS
                              HypA  66 evpvkvrCreCgkefeleekalrCpkCgsad 96 
                                       +vp ++ C++C+ ++ ++ k+  Cp+Cg+++
  gi|474935030|ref|YP_007688612.1| 148 NVPHSAICSDCHGTGGKDGKTNVCPTCGGRG 178
                                       58999*******99998877678*****973 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0059
                                       ETTTS-EEECHHHHHS-TTTSSS- CS
                              HypA  73 CreCgkefeleekalrCpkCgsad 96 
                                       C +Cg ++++   ++ CpkC +++
  gi|474935030|ref|YP_007688612.1| 197 CPKCGGTGKTF--DTPCPKCRGRG 218
                                       *****999966..458****9864 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       5.4   7.4e+03      28      36 ..     152     160 ..     137     165 .. 0.74
   2 ?    6.5   0.1    0.0077        11       5      20 ..     170     185 ..     166     191 .. 0.80
   3 ?    7.0   1.3    0.0056       7.7       3      15 ..     194     206 ..     192     209 .. 0.82
   4 ?    8.9   0.2    0.0014       1.9       5      23 ..     210     228 ..     206     234 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 5.4
                   Lar_restr_allev  28 cvyCadCga 36 
                                         +C dC  
  gi|474935030|ref|YP_007688612.1| 152 SAICSDCHG 160
                                       568999975 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0077
                   Lar_restr_allev   5 pCPfCggravlersqr 20 
                                        CP Cggr+ ++   r
  gi|474935030|ref|YP_007688612.1| 170 VCPTCGGRGQVQSVRR 185
                                       6*******99887665 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0056
                   Lar_restr_allev   3 LkpCPfCggravl 15 
                                       + pCP Cgg ++ 
  gi|474935030|ref|YP_007688612.1| 194 ISPCPKCGGTGKT 206
                                       57*******9875 PP

  == domain 4  score: 8.9 bits;  conditional E-value: 0.0014
                   Lar_restr_allev   5 pCPfCggravlersqrvva 23 
                                       pCP C gr+ + ++++v+ 
  gi|474935030|ref|YP_007688612.1| 210 PCPKCRGRGRVNKTTKVSV 228
                                       9***********9999876 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.28   3.9e+02      21      27 ..     154     160 ..     146     161 .. 0.88
   2 ?   10.6   3.2    0.0002      0.27       2      27 ..     171     202 ..     170     203 .. 0.80
   3 ?    3.6   0.2     0.029        40      22      27 ..     211     216 ..     210     229 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.28
                          zf-TFIIB  21 yCpqCrG 27 
                                        C +C+G
  gi|474935030|ref|YP_007688612.1| 154 ICSDCHG 160
                                       6*****9 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0002
                          zf-TFIIB   2 CPkCqdele..eser....ggveidyCpqCrG 27 
                                       CP+C+   +   ++r    + v i  Cp+C+G
  gi|474935030|ref|YP_007688612.1| 171 CPTCGGRGQvqSVRRtpfgNAVSISPCPKCGG 202
                                       ****87544336666999777*********** PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.029
                          zf-TFIIB  22 CpqCrG 27 
                                       Cp+CrG
  gi|474935030|ref|YP_007688612.1| 211 CPKCRG 216
                                       666666 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   1.3   0.00065       0.9     505     537 ..     150     186 ..     145     187 .. 0.75
   2 ?    5.4   0.8    0.0048       6.6     506     533 ..     193     222 ..     188     227 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00065
                                       --EEEETT.--....EESSSB-TTT--BE.EEEEEES CS
                              NRDD 505 pkidvCnecgy....kgeiekCpkCgseeevevirRi 537
                                       p++ +C +c+     +g ++ Cp+Cg + +v+ +rR+
  gi|474935030|ref|YP_007688612.1| 150 PHSAICSDCHGtggkDGKTNVCPTCGGRGQVQSVRRT 186
                                       34679**99884444555599*****9999**99996 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0048
                                       -EEEETT.--EESS..SB-TTT--BE.EEE CS
                              NRDD 506 kidvCnecgykgei..ekCpkCgseeevev 533
                                        i+ C++cg +g +  + CpkC  + +v+ 
  gi|474935030|ref|YP_007688612.1| 193 SISPCPKCGGTGKTfdTPCPKCRGRGRVNK 222
                                       6889******99888888****96655555 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.3    0.0011       1.5      22      44 ..     151     175 ..     147     182 .. 0.91
   2 ?    3.9   0.9     0.036        50      26      45 ..     197     216 ..     193     219 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0011
                                       EEEE-HHHHHHHHH..TT-B-TTT- CS
                        zf-C3HC4_3  22 HlvlCeeCaekllk..rkkkCpiCr 44 
                                       H ++C++C  +  k  +++ Cp C 
  gi|474935030|ref|YP_007688612.1| 151 HSAICSDCHGTGGKdgKTNVCPTCG 175
                                       999*********999*********6 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.036
                                       -HHHHHHHHHTT-B-TTT-- CS
                        zf-C3HC4_3  26 CeeCaekllkrkkkCpiCrr 45 
                                       C +C  + +  ++ Cp Cr 
  gi|474935030|ref|YP_007688612.1| 197 CPKCGGTGKTFDTPCPKCRG 216
                                       999999998899******95 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0  10.2    0.0043       5.9       1      48 [.     155     214 ..     145     216 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0043
                               DZR   1 CpqCgee..lppdarfCseCgtk..lkavaa..........edrCpsCgekvdpearfCpeC 48 
                                       C+ C+     + + ++C++Cg +  +++                Cp+Cg   +  ++ Cp+C
  gi|474935030|ref|YP_007688612.1| 155 CSDCHGTggKDGKTNVCPTCGGRgqVQS--VrrtpfgnavsISPCPKCGGTGKTFDTPCPKC 214
                                       8888888555556679*****9944443..255999****999******************9 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.3      0.04        55       2      17 ..     171     186 ..     170     187 .. 0.88
   2 ?    2.2   0.2      0.13   1.8e+02       2       9 ..     197     204 ..     196     209 .. 0.77
   3 ?    5.0   0.3     0.017        24       2      18 ..     211     227 ..     210     230 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.04
                         Ogr_Delta   2 CPhCgapaaartsrnl 17 
                                       CP Cg +  + ++r++
  gi|474935030|ref|YP_007688612.1| 171 CPTCGGRGQVQSVRRT 186
                                       *******999998875 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.13
                         Ogr_Delta   2 CPhCgapa 9  
                                       CP+Cg   
  gi|474935030|ref|YP_007688612.1| 197 CPKCGGTG 204
                                       *****765 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.017
                         Ogr_Delta   2 CPhCgapaaartsrnls 18 
                                       CP+C+ + ++ +++  s
  gi|474935030|ref|YP_007688612.1| 211 CPKCRGRGRVNKTTKVS 227
                                       **********9999877 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.4     0.055        76     147     171 ..     153     177 ..     142     192 .. 0.55
   2 ?    6.2   0.6    0.0055       7.6      73      95 ..     194     216 ..     189     229 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.055
                           TackOD1 147 ykCnsCkslfsepevkarClsCeke 171
                                        +C +C+ +  +     +C  C+ +
  gi|474935030|ref|YP_007688612.1| 153 AICSDCHGTGGKDGKTNVCPTCGGR 177
                                       3444444444444444444444443 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0055
                           TackOD1  73 irlCpsCksghlnvrevCpkCkS 95 
                                       i  Cp+C +   ++   CpkC+ 
  gi|474935030|ref|YP_007688612.1| 194 ISPCPKCGGTGKTFDTPCPKCRG 216
                                       677******************85 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0      0.04        56      21      34 ..     148     161 ..     143     163 .. 0.84
   2 ?    4.9   0.1     0.017        24      25      35 ..     168     178 ..     167     180 .. 0.79
   3 ?    2.3   0.3      0.11   1.6e+02      28      34 ..     197     203 ..     195     208 .. 0.80
   4 ?    0.6   0.5       0.4   5.5e+02      28      34 ..     211     217 ..     209     220 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.04
                           DUF35_N  21 qfPPravCphCgsd 34 
                                        +P  a+C+ C+++
  gi|474935030|ref|YP_007688612.1| 148 NVPHSAICSDCHGT 161
                                       57999******986 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.017
                           DUF35_N  25 ravCphCgsdd 35 
                                       ++vCp Cg++ 
  gi|474935030|ref|YP_007688612.1| 168 TNVCPTCGGRG 178
                                       579****9875 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.11
                           DUF35_N  28 CphCgsd 34 
                                       Cp+Cg++
  gi|474935030|ref|YP_007688612.1| 197 CPKCGGT 203
                                       9999886 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.4
                           DUF35_N  28 CphCgsd 34 
                                       Cp+C+++
  gi|474935030|ref|YP_007688612.1| 211 CPKCRGR 217
                                       9999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       745  (0.0415528); expected 358.6 (0.02)
Passed bias filter:                      622  (0.0346924); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        33  (0.00184059); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 2308.39
//
Query:       gi|474935031|ref|YP_007688613.1|  [L=628]
Description: chaperone protein DnaK [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     6e-225  748.0  15.0   5.1e-204  678.9  11.0    2.1  2  HSP70     Hsp70 protein
    4.8e-21   74.9   5.3    3.2e-20   72.2   5.3    2.2  1  MreB_Mbl  MreB/Mbl protein
     0.0035   16.6   0.9      0.072   12.3   0.5    2.4  2  StbA      StbA protein
  ------ inclusion threshold ------
       0.14   12.3   1.4       0.42   10.7   1.4    1.9  1  SGS       SGS domain
       0.51   10.8   2.9        1.2    9.6   2.9    1.6  1  HMG_box   HMG (high mobility group) box
       0.59   10.6   7.8        9.8    6.7   0.1    3.6  3  FtsA      Cell division protein FtsA
       0.68    8.8   5.8        1.3    7.9   5.8    1.4  1  DUF2362   Uncharacterized conserved protein (DUF2362)


Domain annotation for each model (and alignments):
>> HSP70  Hsp70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.0   0.1   1.2e-23     3e-20       1      72 [.       4      80 ..       4      85 .. 0.91
   2 !  678.9  11.0    2e-207  5.1e-204     100     599 .]      82     580 ..      79     580 .. 0.99

  Alignments for each domain:
  == domain 1  score: 72.0 bits;  conditional E-value: 1.2e-23
                                      EEEEEEXSSEEEEEEEETTEEEEEXXTTSX....SSEESEEEEXTT.SEEETHHHHHCTTTTGGGEEEXGGGTTTXB CS
                             HSP70  1 viGiDLGttnsvvavmeggkievianeegn....rttPsvvaFtkk.erlvGeaAkrqavtnpkntvfsvKrliGrk 72
                                      +iGiDLGt ns+ avmegg+++vi  +eg+    ++ Ps+vaFtk+ + lvGe+A+rqavtnp+ t+ +vKr +G +
  gi|474935031|ref|YP_007688613.1|  4 IIGIDLGTSNSAAAVMEGGRPTVIPSAEGTsvggKSFPSYVAFTKDgQLLVGEPARRQAVTNPEGTIKNVKRKMGSN 80
                                      69***********************998753333789*********9999*************************84 PP

  == domain 2  score: 678.9 bits;  conditional E-value: 2e-207
                                       EEEETTEEEEHHHHHHHHHHHHHHHHHHHHTSBEEEEEEEEXTTXXHHHHHHHHHHHHHTTXEEEEEEEHHHHHHHH CS
                             HSP70 100 eveaagekftpeqisamvLkklketaeaylgkkvtdavitvPaYfndaqRqatkdAgkiAGLnvlRivNepTAaala 176
                                       +v+a g+++tp+qisa +L+k+k++aea++g+++++avitvPaYfnd+qRqatkdAgkiAGL+v+Ri+NepTAaala
  gi|474935031|ref|YP_007688613.1|  82 KVSALGKEYTPQQISAYILMKIKKDAEAFVGEPIDKAVITVPAYFNDNQRQATKDAGKIAGLDVVRIINEPTAAALA 158
                                       68899************************************************************************ PP

                                       HHTCCSSSCEEEEEEEEXSSXEEEEEEEEETTEEEEEEEEEETTXSHHHHHHHHHHHHHHHHHHHHSXXGGGSHHHH CS
                             HSP70 177 YGldkkdkernvlvyDlGggtfdvSilelekGvfevkaTagDthlGGedfDealvehlveefkkkegidlskdkkal 253
                                       YGldk+  ++++lv+DlGggt dv i+++++Gvf+v++T+gDt+lGG d+Dea++++++++f++++gidl kd  a 
  gi|474935031|ref|YP_007688613.1| 159 YGLDKSGVSQKILVFDLGGGTLDVTIMDFDDGVFQVLSTSGDTQLGGSDMDEAITDFVIKQFQNETGIDLGKDAAAR 235
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHTTTSSCSEEEEEEEEEETTT.EEEEEEEEHHHHHHHHHHHHHHTHHHHHHHHHHCTEEGGGCSE CS
                             HSP70 254 qrlkeaaekaKkeLSsskqteinleietvdedg.kdlseklsRakfeelvedllertlepvekalkdaklkkeeide 329
                                        r++ea+ekaK+eLS+++qteinl+++t+d++g k+l ++l+Rak+eelv+ ++er+  p+e+al+dakl+++ id+
  gi|474935031|ref|YP_007688613.1| 236 VRVREACEKAKIELSTTMQTEINLPFITADASGpKHLVQTLTRAKLEELVTSIVERCRGPIEQALSDAKLTTSGIDK 312
                                       ***************************************************************************** PP

                                       EEEESGGGGSHHHHHHHHHHTTCHHBSSSHTTTHHHHHHHHHHHHHCTCGCSHCCEEEEBESS-EEEEETTTEEEEE CS
                             HSP70 330 vvlvGGstRiPkvqelvkelfgkepsktvnpDeavaiGAAvqagvlsgeeevkdllllDvtpLslgietlggvmtkl 406
                                       v++vGG tR+P +q+ v++++g + +++v+p e+v  GAA+q++vlsg  +vkd+lllDvtpL+lgietlggv+t l
  gi|474935031|ref|YP_007688613.1| 313 VIMVGGPTRMPIIQNFVESIVGPKIQHGVDPMECVCSGAAIQGAVLSG--DVKDVLLLDVTPLTLGIETLGGVATPL 387
                                       ************************************************..*************************** PP

                                       ESTTCBSSEEEEEEEEESSTTSSSEEEEEEESSSSBGGGSEEEEEEEEECESSCSTTCSEEEEEEEEETTSCEEEEE CS
                             HSP70 407 iernttiptkksqvfstaadnqtaveievlqgerelvkdnkllgsfeldgippaprGvpqieVtfdidanGiltvsa 483
                                       iernttiptkksq+fstaadnq++vei+v+qger++++dn++lg+f ldgippaprG+pqieVtfdidanGi++v+a
  gi|474935031|ref|YP_007688613.1| 388 IERNTTIPTKKSQIFSTAADNQPSVEINVVQGERKMAADNTSLGRFVLDGIPPAPRGMPQIEVTFDIDANGIINVTA 464
                                       ***************************************************************************** PP

                                       EETTTCCEEEEEEECCSSSBHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGSTHHHHHHH CS
                             HSP70 484 kdketgkeeeitieaseglseeeiekmvkdaeesaeedkkkkeaieakneaeelvyslekkleeeaekvseaekekv 560
                                       kdk+tgke++iti++s++ls+e+i+  +kdae++a++dkkk+e i+a+n+ae+l ys++k+++e ++kv+++e+++v
  gi|474935031|ref|YP_007688613.1| 465 KDKGTGKEQKITIASSNKLSKEDIDAAIKDAEKFADADKKKEELINARNSAETLGYSAKKAMDELGDKVTQEERASV 541
                                       ***************************************************************************** PP

                                       HHHHHHHHCHTTSSCHHHHHHHHHHHHHHHHHHHHHHHH CS
                             HSP70 561 esaieeLkeeleeeekeeieakteelkkvvekiaeklye 599
                                       e+ai++L++++++e+ eei++kte+l+k++e+i +k+ye
  gi|474935031|ref|YP_007688613.1| 542 EAAINDLNAAAKGEDLEEIKKKTEALSKAMEPISKKIYE 580
                                       ***********************************9985 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.2   5.3   1.2e-23   3.2e-20       4     317 ..       5     353 ..       2     359 .. 0.71

  Alignments for each domain:
  == domain 1  score: 72.2 bits;  conditional E-value: 1.2e-23
                                       EEEEE-SSEEEEEETTTEEEEEEES-EEEETT...........T--EEEESHHHH.TTTTS-GTTEEEE-.SE.ETT CS
                          MreB_Mbl   4 lgiDLGtantlvyvkgkgivlnepsvvAikkk...........tkkvlavGeeAk.kmlgktpgnikavr.Pl.kdG 66 
                                       +giDLGt n  + v + g     ps    +             +   l vGe A+ + +   +g+ik v+  + ++ 
  gi|474935031|ref|YP_007688613.1|   5 IGIDLGTSNSAAAVMEGGRPTVIPSAEGTSVGgksfpsyvaftKDGQLLVGEPARrQAVTNPEGTIKNVKrKMgSNE 81 
                                       78888888876655544433333332222222112223333323334557777752445555667766541342122 PP

                                       EESSH..HHH.HHHHHHHHHHHHT.SS-S...S--EEEEEE-SS--HHHHHHHHHHHHHTT-SEEEEEEHHHHHHHH CS
                          MreB_Mbl  67 viadl..eva.eellkyfikkvkk.kksl...skprvvicvPsgiteverrAvkeaakkaGarevllieeplaAAiG 136
                                        ++ l  e++ +++  y++ k+kk ++++   + ++ vi+vP   ++ +r+A k+a k aG + v +i+ep aAA+ 
  gi|474935031|ref|YP_007688613.1|  82 KVSALgkEYTpQQISAYILMKIKKdAEAFvgePIDKAVITVPAYFNDNQRQATKDAGKIAGLDVVRIINEPTAAALA 158
                                       2332222344144455677777774333333356799**************************************** PP

                                       TT--TTSSS.-EEEEEE-SS-EEEEEEETTEEE.....EEEEES-SHHHHHHHHHHHHHHHHS....EE--HHHHHH CS
                          MreB_Mbl 137 aglpveeps.gnmvvdiGggttevavislggiv.....tsksvrvaGdeldeaiikyirkkyn....lliGertaek 203
                                        gl+ +  s   +v d+Gggt +v+++ + + v     ts   +++G ++deai++++ k+++    + +G+  a +
  gi|474935031|ref|YP_007688613.1| 159 YGLDKSGVSqKILVFDLGGGTLDVTIMDFDDGVfqvlsTSGDTQLGGSDMDEAITDFVIKQFQnetgIDLGKDAAAR 235
                                       ****88765056789*************9875522222456689**************9999733335677777777 PP

                                       HHHHH-BSS--HHHH...EEEEEEEETTTTCEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHTS..-HHHHHHHHHH CS
                          MreB_Mbl 204 ikieigsavkeeeee...kmeikGrdlvtglpkevevsseevrealkepvsaiveavkevLekt..ppeLaadivdr 275
                                       ++++ ++ + + e +   ++ei+   ++       ++ ++  r  l+e v++ive  +  +e++   + L++  +d+
  gi|474935031|ref|YP_007688613.1| 236 VRVREACEKAKIELSttmQTEINLPFITADASGPKHLVQTLTRAKLEELVTSIVERCRGPIEQAlsDAKLTTSGIDK 312
                                       777665555444433446788888888888888899999999999***********999999962256799999999 PP

                                       -EEEESGGGGSBTHHHHHHHHHSS-EEE-SSTTTHHHHHHHH CS
                          MreB_Mbl 276 givltGGgallkgldkllseetglpvkvaedpltcvakGtgk 317
                                        i++ GG + +  +++++++ +g +++ + dp++cv++G+++
  gi|474935031|ref|YP_007688613.1| 313 VIMV-GGPTRMPIIQNFVESIVGPKIQHGVDPMECVCSGAAI 353
                                       8776.**********************************975 PP

>> StbA  StbA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.5   2.8e-05     0.072     162     209 ..     167     216 ..     130     227 .. 0.75
   2 ?    2.0   0.0      0.04     1e+02     228     283 ..     266     321 ..     232     336 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.8e-05
                              StbA 162 leslLiiDlGGttLDvakvr..gklegiskvkgdskiGvslitdavkeal 209
                                        ++ L+ DlGG tLDv+ +     + ++  + gd ++G s + +a+++ +
  gi|474935031|ref|YP_007688613.1| 167 SQKILVFDLGGGTLDVTIMDfdDGVFQVLSTSGDTQLGGSDMDEAITDFV 216
                                       5689***********98764225577788899**********99998865 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.04
                              StbA 228 rkdeeyLkrrindedkresvlevinekvkkLkerviravsefsgythvmvvGGGae 283
                                           ++L ++++ ++  e v++++++    +++ + +a  + sg+ +v++vGG + 
  gi|474935031|ref|YP_007688613.1| 266 ASGPKHLVQTLTRAKLEELVTSIVERCRGPIEQALSDAKLTTSGIDKVIMVGGPTR 321
                                       455677888888888888899999999999********99*************875 PP

>> SGS  SGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.4   0.00017      0.42      14      59 ..     558     606 ..     525     620 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00017
                               SGS  14 ekeekkeeegeaalnklFkklYadadedtrram...mKSyveSnGtvLs 59 
                                       e+ +kk+e  ++a++ + kk+Y+++++++++a     K y e  G   s
  gi|474935031|ref|YP_007688613.1| 558 EEIKKKTEALSKAMEPISKKIYENSTPEQQQAYqeaAKQYSEQAGAQQS 606
                                       3334444678999*****************9963335889988887766 PP

>> HMG_box  HMG (high mobility group) box
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   2.9   0.00047       1.2      28      69 .]     557     598 ..     542     598 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00047
                                       HHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           HMG_box  28 naeiskklgekWkalseeeKkkYeekaekekaryekekpeyk 69 
                                         ei+kk ++  ka+++  Kk Ye+   ++++ y+++ ++y+
  gi|474935031|ref|YP_007688613.1| 557 LEEIKKKTEALSKAMEPISKKIYENSTPEQQQAYQEAAKQYS 598
                                       579************************************995 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1    0.0056        14       1      22 [.       5      26 ..       5     118 .. 0.84
   2 ?    6.7   0.1    0.0038       9.8       2      85 ..     172     332 ..     171     356 .. 0.60
   3 ?   -0.1   0.9       0.5   1.3e+03      37      71 ..     488     550 ..     457     604 .. 0.51

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0056
                                      EEEEE-SSSEEEEEEETTEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxx RF
                              FtsA  1 alvDiGagktdvavaedgalvh 22
                                      +++D+G++ + +av+e+g+++ 
  gi|474935031|ref|YP_007688613.1|  5 IGIDLGTSNSAAAVMEGGRPTV 26
                                      58***************97665 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0038
                                       EEEE-SSSEEEEEEETTEEEEEEEES-......-HHHHHHH..........HHHHHT--HHHHHHHHHHH--S--.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxx.. RF
                              FtsA   2 lvDiGagktdvavaedgalvhlrvigv......ggngitkd..........iakalrtaveeAerikikyGsala.. 60 
                                       + D+G+g+ dv++++ +  v ++v+ +      gg+ +++            ++++    ++A r+ ++ ++  a  
  gi|474935031|ref|YP_007688613.1| 172 VFDLGGGTLDVTIMDFDDGV-FQVLSTsgdtqlGGSDMDEAitdfvikqfqNETGIDLGKDAAARVRVREACEKAki 247
                                       569************96533.55555555567799999998777777777755555556666666665555555444 PP

                                       .........EEEEEHHHHH.......................................................... CS
                                       .........xxxxxxxxxx.......................................................... RF
                              FtsA  61 .........ekeigrkels.......................................................... 70 
                                                         +                                                          
  gi|474935031|ref|YP_007688613.1| 248 elsttmqteI--------Nlpfitadasgpkhlvqtltrakleelvtsivercrgpieqalsdaklttsgidkvimv 316
                                       4433331330........24444455555555555554444446655666666666666666666666666666666 PP

                                       .GGGGSTTHHHHHHHH CS
                                       .xxxxxxxxxxxxxxx RF
                              FtsA  71 .ggsalpnleelaera 85 
                                        g + +p +++++e++
  gi|474935031|ref|YP_007688613.1| 317 gGPTRMPIIQNFVESI 332
                                       6666666666666655 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.5
                                       HHHHHT--HHHHHHHHHHH--S--...........................EEEEEHHHHH................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx...........................xxxxxxxxxx................ RF
                              FtsA  37 iakalrtaveeAerikikyGsala...........................ekeigrkels................ 70 
                                       i      a+++Ae+ +     a +                           +        +                
  gi|474935031|ref|YP_007688613.1| 488 IDA----AIKDAEKFA----DADKkkeelinarnsaetlgysakkamdelgD--------Kvtqeerasveaaindl 548
                                       444....444444444....11111111222222333333333233323320........02233333333333344 PP

                                       .G CS
                                       .x RF
                              FtsA  71 .g 71 
                                         
  gi|474935031|ref|YP_007688613.1| 549 nA 550
                                       41 PP

>> DUF2362  Uncharacterized conserved protein (DUF2362)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   5.8    0.0005       1.3      81     210 ..     471     605 ..     448     625 .. 0.49

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0005
                           DUF2362  81 deeifaqvyhklvhspaletllqlehtyaka...vedlveernk..eleklee............kqteemekaiqe 140
                                       +e++++ +  ++ +++ +++ ++  +++a+a    e+l+++rn+  +l    +            +++ ++e+ai++
  gi|474935031|ref|YP_007688613.1| 471 KEQKITIASSNKLSKEDIDAAIKDAEKFADAdkkKEELINARNSaeTLGYSAKkamdelgdkvtqEERASVEAAIND 547
                                       55555555555555555555554444443321113344444443112223333111111111111555555555555 PP

                           DUF2362 141 ldksltdedvnelaakhfeeqqllkkklnseleelketQkkeYrewvmklveelksptnsslsseikaqs 210
                                       l+  +  ed  e+++k  + +++++   ++ +e+ + +Q++ Y+e+ ++  e+               q+
  gi|474935031|ref|YP_007688613.1| 548 LNAAAKGEDLEEIKKKTEALSKAMEPISKKIYENSTPEQQQAYQEAAKQYSEQAGA------------QQ 605
                                       55555555555555555555555555555556666666666666666666666552............11 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (628 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1699  (0.0947627); expected 358.6 (0.02)
Passed bias filter:                      688  (0.0383736); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.83u 0.32s 00:00:01.14 Elapsed: 00:00:00.51
# Mc/sec: 3724.63
//
Query:       gi|474935032|ref|YP_007688614.1|  [L=191]
Description: Molecular chaperone GrpE (heat shock protein) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-41  140.3   3.8    5.6e-41  140.0   3.8    1.1  1  GrpE             GrpE
  ------ inclusion threshold ------
      0.074   13.3   1.0       0.17   12.2   1.0    1.6  1  KxDL             Uncharacterized conserved protein
       0.11   13.1   0.4        1.8    9.2   0.4    2.3  2  YabA             Initiation control protein YabA
       0.24   11.2   4.9       0.34   10.7   4.9    1.2  1  Erythro_esteras  Erythromycin esterase
       0.51   10.4   3.0       0.76    9.9   1.4    2.0  2  DUF357           Protein of unknown function (DUF357)
        1.3    8.5   6.6        2.8    7.4   6.5    1.5  2  Vps5             Vps5 C terminal like
        2.9    8.0  10.7        1.5    9.0   8.5    1.7  2  ATP-synt_B       ATP synthase B/B' CF(0)


Domain annotation for each model (and alignments):
>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.0   3.8   2.2e-44   5.6e-41       5     166 .]      16     171 ..       7     171 .. 0.95

  Alignments for each domain:
  == domain 1  score: 140.0 bits;  conditional E-value: 2.2e-44
                                       ..CTTTHHHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                              GrpE   5 eeeeeeedeeeeleeeleelekevkelkekllrllaefenlrkrtekekeeakkfaiekfakdLLpvlDnleralks 81 
                                       +   +++ ++ee e++l++++++++e+ +   r +a+fen+r+rteke ++ +k+a  +++++LL+++D+l ral+s
  gi|474935032|ref|YP_007688614.1|  16 KAADKAKSQIEETEAKLAAAQAKADEYLDMARRVQADFENFRRRTEKENADFRKYATVDLVRQLLNTVDDLGRALES 92 
                                       566788999*******************************************************************5 PP

                                       ..HHH-HHHHHHHHHHHHHHHHHHHHHTT-EE---TTSB--TTTEEEEEEECSSC...TBEEEEEE--EEETTEEEE CS
                              GrpE  82 akeneeekslleGvemtlkqllkiLekhgvekiepkgepFDpnlheavstveddekeegtvvevvqkGYklkdrvlR 158
                                          +++ ++l  Gv+ ++++l kiLe +g+ ++++    FDpn+hea+ +ve +e  ++ + +v+qkGY++++rv+R
  gi|474935032|ref|YP_007688614.1|  93 ---AKDDDPLSAGVRAVRDNLVKILEAEGLREVPT-DGRFDPNMHEALTVVEGPE--DDMIAQVYQKGYMMHERVIR 163
                                       ...7899999***********************99.678****************..******************** PP

                                       -EEEEEEE CS
                              GrpE 159 pAmVkVsk 166
                                        A+V+V k
  gi|474935032|ref|YP_007688614.1| 164 YAKVIVTK 171
                                       ******86 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.0   6.6e-05      0.17      34      78 ..      23      67 ..      18      72 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.6e-05
                              KxDL 34 elnalsqerlaklrarfkqgtkllkevkkdLesifkkirslkakl 78
                                       ++++++++la ++a+  ++  ++++v++d e+ ++++++ +a +
  gi|474935032|ref|YP_007688614.1| 23 SQIEETEAKLAAAQAKADEYLDMARRVQADFENFRRRTEKENADF 67
                                      57899********************************99866665 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.4   0.00072       1.8      12      58 ..      20      66 ..      11     115 .. 0.83
   2 ?    2.5   0.0     0.091   2.3e+02      44      81 ..     115     155 ..      69     167 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00072
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXX CS
                              YabA 12 eleeqleelleeleelkeelaelleenaeLeleneklrerleeeekk 58
                                      + ++q+ee+ ++l++ +++  e l+  ++++++ e++r+r e+e+++
  gi|474935032|ref|YP_007688614.1| 20 KAKSQIEETEAKLAAAQAKADEYLDMARRVQADFENFRRRTEKENAD 66
                                      6689************************************9544433 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.091
                                       HHHHHHHHH...XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              YabA  44 eneklrerl...eeeekkekekkkelsegkenLarlYeeGF 81 
                                       e e lre     + + + +++ +   +   + +a++Y++G+
  gi|474935032|ref|YP_007688614.1| 115 EAEGLREVPtdgRFDPNMHEALTVVEGPEDDMIAQVYQKGY 155
                                       33333333354433334444445555667788899999998 PP

>> Erythro_esteras  Erythromycin esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   4.9   0.00013      0.34      91     190 ..      12     109 ..       8     124 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00013
                                       HCHCCCCHHHHHHHCCHGGC.S......TSSCCCCCHHHHHHHHHHHHCCHGGG.....GGTSHHHHHHHHHHHHHH CS
                   Erythro_esteras  91 kvdpelagaareryaclapl.adpraarsaeaaelrscedevvallkellakreeyaaedgeaeeffsaeqnarlvk 166
                                       k dp++a++a+++++++++  a    a++a+a+e+  ++++v+a  + +++++e+  a+ ++  +++ ++q  ++v 
  gi|474935032|ref|YP_007688614.1|  12 KADPKAADKAKSQIEETEAKlA----AAQAKADEYLDMARRVQADFENFRRRTEKENADFRKYATVDLVRQLLNTVD 84 
                                       669**********999977753....6788999****************9999855553336778888888888888 PP

                                       HHHHHC...CSSSSSCHHHHHHHHH CS
                   Erythro_esteras 167 naeryyra.gdeeswnlrllalRDr 190
                                       ++ r  ++ +d++  ++   a+RD 
  gi|474935032|ref|YP_007688614.1|  85 DLGRALESaKDDDPLSAGVRAVRDN 109
                                       8888887664444444444555554 PP

>> DUF357  Protein of unknown function (DUF357)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.4    0.0003      0.76       7      53 ..      19      65 ..      15      68 .. 0.83
   2 ?   -1.5   0.0         1   2.7e+03       4      33 ..     130     157 ..     127     175 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0003
                                      HHHHHHHH.....TS---HHHHHHHHHHHHHHHHHHHHHHTT-HHHH CS
                            DUF357  7 eealekvkiapdeesplgeaaeevlemaesYleDakyflekgdlvnA 53
                                      ++a ++++  + +    +++a+e+l+ma++  +D + f+++ + +nA
  gi|474935032|ref|YP_007688614.1| 19 DKAKSQIEETEAKLAAAQAKADEYLDMARRVQADFENFRRRTEKENA 65
                                      455556665557788888999***********************998 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1
                                       HHHHHHHHHHH.....TS---HHHHHHHHH CS
                            DUF357   4 rlleealekvkiapdeesplgeaaeevlem 33 
                                       +++ eal  v+   +e+  + +++++ + m
  gi|474935032|ref|YP_007688614.1| 130 PNMHEALTVVE--GPEDDMIAQVYQKGYMM 157
                                       57778888888..34444444444443333 PP

>> Vps5  Vps5 C terminal like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   6.5    0.0011       2.8     153     205 ..       6      61 ..       2      81 .. 0.74
   2 ?   -2.2   0.0      0.93   2.4e+03     107     124 ..      77      94 ..      69      95 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0011
                              Vps5 153 Klekaaksqqdklqqlkkeveelerkvqeae...keFeeisetikkElerFeterv 205
                                       K e ++k +++ ++++k+++ee+e+k++ a+   +e+ +++++++ ++e+F +   
  gi|474935032|ref|YP_007688614.1|   6 KEESKTKADPKAADKAKSQIEETEAKLAAAQakaDEYLDMARRVQADFENFRRRTE 61 
                                       5556667778899999**********9887733357999***********976443 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.93
                              Vps5 107 ltLgetideylrligsvk 124
                                        +L +t+d+  r+++s k
  gi|474935032|ref|YP_007688614.1|  77 RQLLNTVDDLGRALESAK 94 
                                       578889999999999988 PP

>> ATP-synt_B  ATP synthase B/B' CF(0)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   8.5   0.00057       1.5      44     107 ..      16      78 ..       7      95 .. 0.82
   2 ?   -2.7   0.0       2.3   5.9e+03      69     101 ..     145     177 ..     140     178 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00057
                        ATP-synt_B  44 errkeaaallaeaeqqlkeAraeAaeiiknAkkeaeklkeeieaeaeaeaerlkesAaaeIeqe 107
                                       +++++a+ +++e e++l+ A+a+A+e+ + A++  +   e+ + ++e+e +  ++ A  ++ ++
  gi|474935032|ref|YP_007688614.1|  16 KAADKAKSQIEETEAKLAAAQAKADEYLDMARR-VQADFENFRRRTEKENADFRKYATVDLVRQ 78 
                                       567889999*********************986.556678889999999888888888888776 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.3
                        ATP-synt_B  69 eiiknAkkeaeklkeeieaeaeaeaerlkesAa 101
                                       ++i++++++++   e  +  a+  +++ ke A+
  gi|474935032|ref|YP_007688614.1| 145 DMIAQVYQKGYMMHERVIRYAKVIVTKKKEPAE 177
                                       567777777777777777777777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1596  (0.0890178); expected 358.6 (0.02)
Passed bias filter:                      762  (0.042501); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.67u 0.35s 00:00:01.02 Elapsed: 00:00:00.56
# Mc/sec: 1018.41
//
Query:       gi|474935033|ref|YP_007688615.1|  [L=539]
Description: thermosome subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   2.7e-174  580.4  19.1     3e-174  580.3  19.1    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family
  ------ inclusion threshold ------
      0.081   13.1   0.2        1.7    8.9   0.0    2.5  2  AAA_lid_1   AAA+ lid domain


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  580.3  19.1  3.4e-178    3e-174       1     489 [.      34     524 ..      34     526 .. 0.98

  Alignments for each domain:
  == domain 1  score: 580.3 bits;  conditional E-value: 3.4e-178
                                       HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHH CS
                        Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleea 77 
                                       +ad+v+++lGP+GmdKmlv++ g+vv+TnDG+tilke++++hPaak+lve+a++qd+evGDGTtt vi+ageLl+++
  gi|474935033|ref|YP_007688615.1|  34 IADAVRSSLGPRGMDKMLVDSLGDVVITNDGVTILKEMDVQHPAAKMLVEVAKTQDQEVGDGTTTSVIIAGELLKKS 110
                                       79*************************************************************************** PP

                                       HHHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHH.HCH CS
                        Cpn60_TCP1  78 ekliaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAv.kli 153
                                        +li+++vhpt i+ gy++a +ka e+Lk++a+++s   +d++ L+++a+ts+ sk++++++e+++++vvdAv +++
  gi|474935033|ref|YP_007688615.1| 111 LDLIDSNVHPTIITAGYRMANDKAQEILKAVAKKVSP--DDDKLLMQIAETSMISKQVNSQKEFFARMVVDAVrTIL 185
                                       *******************************888875..5999******************************7777 PP

                                       CCCS...EECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSC CS
                        Cpn60_TCP1 154 eene...keldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsda 227
                                       e+ +   ++ dl++i++vk+ g ++e+selv+Glv+dk+++sp+mp+ +++ak++l+d  +e +k+e++++++++d+
  gi|474935033|ref|YP_007688615.1| 186 EKGKdgkYTADLKNIQTVKKAGAKMEESELVKGLVIDKEPVSPTMPHIVKKAKIALIDGAFEVKKPEVDAKIQITDP 262
                                       66669*9********************************************************************** PP

                                       CHHHHHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGG CS
                        Cpn60_TCP1 228 eeleklekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledl 304
                                       e l+k+ ++ee++l++l+ +++k+g+nvv+cqkgiddla+hf+ak+gi a rrvkk+d+erlak t+a++v+++ ++
  gi|474935033|ref|YP_007688615.1| 263 EMLQKFIDEEENILRDLVMAVKKAGANVVFCQKGIDDLAQHFFAKEGIYACRRVKKSDIERLAKSTNASIVTKITEI 339
                                       ***************************************************************************** PP

                                       GCGC-EEEEEEEECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHH CS
                        Cpn60_TCP1 305 tpeelGtakkveeekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatel 381
                                       t+++lGta++ve +++g+e++t+i+++k++k+++il+rg t++v de+er++ dA +vv+  ied+ +v GGG+t +
  gi|474935033|ref|YP_007688615.1| 340 TKDDLGTADTVELRHVGDEDMTFITGCKDPKTVSILVRGGTNHVTDEVERSLVDAWSVVRVSIEDGMIVTGGGSTAM 416
                                       ***************************************************************************** PP

                                       HHHHHHHCCCCTSXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCT CS
                        Cpn60_TCP1 382 elakklkeyaksvsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiidlveag 458
                                       e+a  +++ya sv g+eq+aiea+a+A+e+ip tLaeNaGldpi+++ ++r++h++g+k++g++  +g+++d+++ +
  gi|474935033|ref|YP_007688615.1| 417 EIAMGVRDYAASVGGREQIAIEAYASAMEIIPTTLAENAGLDPINMVIEMRKQHKAGKKHAGLNPFTGKVEDMMKLN 493
                                       ***************************************************************************** PP

                                       XEEEHHHHHHHHHHHHHHHHHHHCEEEEEXX CS
                        Cpn60_TCP1 459 vvDplkvkrqalksAteaastiLrideiika 489
                                       v++p+++ +qal+sAt+aa +iLrid++i  
  gi|474935033|ref|YP_007688615.1| 494 VIEPVRIGQQALNSATDAAVMILRIDDVIAS 524
                                       *****************************86 PP

>> AAA_lid_1  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00019       1.7      43      85 ..     103     145 ..      95     159 .. 0.88
   2 ?    1.3   0.1     0.043   3.9e+02      51      88 ..     297     334 ..     265     346 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00019
                         AAA_lid_1  43 saevlkapldlirlylheservygdkmveekdlellekvtlev 85 
                                       + e+lk +ldli   +h +    g +m ++k +e l+ v  +v
  gi|474935033|ref|YP_007688615.1| 103 AGELLKKSLDLIDSNVHPTIITAGYRMANDKAQEILKAVAKKV 145
                                       569*******************************999876554 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.043
                         AAA_lid_1  51 ldlirlylheservygdkmveekdlellekvtlevakk 88 
                                       +d +  ++   e +y  + v++ d+e l k t +++  
  gi|474935033|ref|YP_007688615.1| 297 IDDLAQHFFAKEGIYACRRVKKSDIERLAKSTNASIVT 334
                                       444444556678999999********999988766543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (539 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       933  (0.0520386); expected 358.6 (0.02)
Passed bias filter:                      587  (0.0327403); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.52
# Mc/sec: 3094.22
//
Query:       gi|474935034|ref|YP_007688616.1|  [L=726]
Description: L-glutamine synthetase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.8e-73  244.1   0.0      8e-73  243.4   0.0    1.4  1  GSIII_N         Glutamine synthetase type III N terminal
    1.8e-34  118.1   0.0    3.7e-34  117.1   0.0    1.5  1  Gln-synt_C-ter  Glutamine synthetase C-terminal domain
    1.3e-21   77.0   0.1    4.5e-21   75.2   0.0    1.8  2  Gln-synt_C      Glutamine synthetase, catalytic domain


Domain annotation for each model (and alignments):
>> GSIII_N  Glutamine synthetase type III N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  243.4   0.0   1.3e-76     8e-73       2     160 .]      28     186 ..      27     186 .. 0.99

  Alignments for each domain:
  == domain 1  score: 243.4 bits;  conditional E-value: 1.3e-76
                           GSIII_N   2 selfgskvfnekvmkkrlpkevykklkkaieegekldeevadvvakamkeWalekgathytHwFqPltgltaekhds 78 
                                       s+++g++vfn+++m+++l++++ + + ++ie+g+ ld++va++va++m++Wa++ gathytHwFqPltg taekhds
  gi|474935034|ref|YP_007688616.1|  28 SDYYGCNVFNRRAMRQYLSEDTRRIIYETIERGAVLDKNVAEHVAAGMRRWAMDMGATHYTHWFQPLTGGTAEKHDS 104
                                       689************************************************************************** PP

                           GSIII_N  79 flelekdgkvieefsgkelikgEpDaSSfpsGglratfeArgytawdptspafikektlciPtvfvsytGealDkkt 155
                                       f +++++g+ +e+fsgk l ++E+DaSSfpsGglr+tfeArgytawdp+spafi+ ++lciPtvfvsytGealD+k+
  gi|474935034|ref|YP_007688616.1| 105 FADPRTHGESLEKFSGKLLSQQESDASSFPSGGLRNTFEARGYTAWDPSSPAFIMGDVLCIPTVFVSYTGEALDYKA 181
                                       ***************************************************************************** PP

                           GSIII_N 156 pllrs 160
                                       pl++s
  gi|474935034|ref|YP_007688616.1| 182 PLMKS 186
                                       ***98 PP

>> Gln-synt_C-ter  Glutamine synthetase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.1   0.0   6.2e-38   3.7e-34       6     118 .]     520     632 ..     515     632 .. 0.97

  Alignments for each domain:
  == domain 1  score: 117.1 bits;  conditional E-value: 6.2e-38
                    Gln-synt_C-ter   6 ikktikehkriiFnGdgYseeWeeeaekRgLknlkttvealkalleeknielfeklgvlseeElesryeillekYvk 82 
                                        ++t++++++i+F+G+gYseeW++ea +RgL + ++ + + ++l++ k++++f+++gv++++Elesr+ei++e Y+k
  gi|474935034|ref|YP_007688616.1| 520 TRETFRACRDICFDGNGYSEEWKAEALRRGLDCETSPPLVYDNLTSAKTVKVFNDTGVMNKVELESRKEIFWEMYCK 596
                                       6899************************************************************************* PP

                    Gln-synt_C-ter  83 kieiEaktllelvkkeilPavlkyqkelaeevkkvk 118
                                       k+ iEa++l +l++++++P +++yq+ l+e+v+++k
  gi|474935034|ref|YP_007688616.1| 597 KVDIEARVLSDLTTNHVIPVAVRYQNILLENVRDLK 632
                                       *******************************99876 PP

>> Gln-synt_C  Glutamine synthetase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.2   0.0   7.6e-25   4.5e-21      20     189 ..     208     379 ..     190     409 .. 0.81
   2 ?   -1.5   0.0      0.17     1e+03     236     249 ..     466     479 ..     456     485 .. 0.89

  Alignments for each domain:
  == domain 1  score: 75.2 bits;  conditional E-value: 7.6e-25
                                       CEEEEEEEEEEEEESEECCCESSEEEEEEE.T.....B...B.TSS-TTBHCCCCCTCCHHHHHHHHHHHTT--EEC CS
                        Gln-synt_C  20 ltvvvgpElEFflfdkeedkeasksllevdse.....ekgrpaekggyfsvapvdeaedlrreivealealgievea 91 
                                       ++ ++g E E+fl+dk+ +++  + +l+ + +     + + ++ + +yf   p  ++ ++++++   + +lgi++++
  gi|474935034|ref|YP_007688616.1| 208 IHSYLGWEQEYFLVDKDLYEQRPDLVLTDR-TlighdSAKSQQLEDHYFAAIPS-RVLEFMKDLEFECYKLGIPIKT 282
                                       5889*************9987333333333.24677555666677777777776.8999****************** PP

                                       CEEECCCTEEEEEE--EECHHHHHHHHHHHHHHHHHHHHTT-EEE-SSSSSTTS---BEEEEEEEEECTTEESSB-T CS
                        Gln-synt_C  92 shhEvatgQvEinlkfadalkaaDnvvtfKrvvkevArkhgltatFmpKplegdnGsgmHvhlSlwdkdgknlfade 168
                                        h+Eva+ Q+E+   ++ a  a D+ +++  ++k++ +khg ++ F+ Kp++g nGsg H++ Sl +++g +l++  
  gi|474935034|ref|YP_007688616.1| 283 RHNEVAPNQFEVAPVYEVANLANDHNLMLMSLMKNISEKHGFEVLFHEKPFAGVNGSGKHCNWSLGTESGIALMSPG 359
                                       ******************************************************************88888777655 PP

                                       TSGGGB-HHHHHHHHHHHHHH CS
                        Gln-synt_C 169 ddeyalselarhfigGllkha 189
                                       + + +    ++ f++  lk +
  gi|474935034|ref|YP_007688616.1| 360 K-TDEENLRFLCFMANTLKAV 379
                                       5.3344445555666555555 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.17
                                       CSTEEEECEBTTS- CS
                        Gln-synt_C 236 akrvElRlpdasaN 249
                                       ++r+E+R++++saN
  gi|474935034|ref|YP_007688616.1| 466 GNRFEFRAVGSSAN 479
                                       68***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (726 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.69u 0.31s 00:00:01.00 Elapsed: 00:00:00.49
# Mc/sec: 4418.70
//
Query:       gi|474935035|ref|YP_007688617.1|  [L=271]
Description: hypothetical protein TALC_01483 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1799.97
//
Query:       gi|474935036|ref|YP_007688618.1|  [L=516]
Description: hypothetical protein TALC_01484 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0024   17.2   1.4        1.7    8.1   0.2    2.6  2  zf-ribbon_3    zinc-ribbon domain
  ------ inclusion threshold ------
       0.01   15.9   0.7      0.027   14.5   0.7    1.7  1  DZR            Double zinc ribbon
      0.013   15.2   1.8      0.082   12.6   1.8    2.3  1  zinc_ribbon_2  zinc-ribbon domain
      0.026   14.6   0.7      0.063   13.4   0.7    1.6  1  Zn-ribbon_8    Zinc ribbon domain
       0.16   11.5   0.4         17    5.1   0.1    2.4  2  TF_Zn_Ribbon   TFIIB zinc-binding
       0.18   11.9   0.2       0.41   10.7   0.2    1.5  1  HypA           Hydrogenase/urease nickel incorporation, metal
        0.2   11.6   1.3       0.41   10.6   1.3    1.5  1  Prok-RING_1    Prokaryotic RING finger family 1


Domain annotation for each model (and alignments):
>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.1   0.00098       2.5       4      17 ..      12      25 ..       9      26 .. 0.73
   2 !    8.1   0.2   0.00067       1.7       3      11 ..      32      41 ..      30      47 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00098
                       zf-ribbon_3  4 rCPnCGaplssddn 17
                                      rC +CGapl +dd+
  gi|474935036|ref|YP_007688618.1| 12 RCKYCGAPLPADDV 25
                                      78888887777775 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00067
                       zf-ribbon_3  3 vrCPnCGa.p 11
                                      ++CP+CG+ +
  gi|474935036|ref|YP_007688618.1| 32 ITCPSCGTtQ 41
                                      7888888765 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.7   1.1e-05     0.027      15      39 ..      13      42 ..       7      47 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.1e-05
                               DZR 15 CseCgtklkavaa......edrCpsCgekvd 39
                                      C++Cg++l+a  +       ++CpsCg+  +
  gi|474935036|ref|YP_007688618.1| 13 CKYCGAPLPAD-DvksdapYITCPSCGTTQQ 42
                                      *******9743.26999999******99754 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.8   3.2e-05     0.082       1      21 [.      12      39 ..      12      41 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.2e-05
                     zinc_ribbon_2  1 fCpnCGaelq.dnakF......CpyCGt 21
                                      +C+ CGa+l+ d++k       Cp CGt
  gi|474935036|ref|YP_007688618.1| 12 RCKYCGAPLPaDDVKSdapyitCPSCGT 39
                                      6********9577777***********8 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.7   2.5e-05     0.063       5      37 ..      10      42 ..      10      44 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.5e-05
                       Zn-ribbon_8  5 eYrCeeCghefevlqsisdapltaCPeCgsevr 37
                                      e rC+ Cg    +    sdap ++CP+Cg + +
  gi|474935036|ref|YP_007688618.1| 10 ELRCKYCGAPLPADDVKSDAPYITCPSCGTTQQ 42
                                      679*****9999777556**********98655 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.015        37      19      33 ..      10      24 ..       4      29 .. 0.76
   2 ?    5.1   0.1    0.0065        17       2      14 ..      33      45 ..      31      49 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.015
                                      CEEESSSSBEEEECC CS
                      TF_Zn_Ribbon 19 elvCtdCGlVledns 33
                                      el+C+ CG+ l  ++
  gi|474935036|ref|YP_007688618.1| 10 ELRCKYCGAPLPADD 24
                                      899999998666665 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0065
                                      EETTTTCEECHEE CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveD 14
                                      +CP Cg+t++  D
  gi|474935036|ref|YP_007688618.1| 33 TCPSCGTTQQKID 45
                                      7999999877666 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   0.00016      0.41      69     100 ..       9      45 ..       6      53 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00016
                                       -EEEETTTS-EEECHH.HHH.....S-TTTSSS-EEEE CS
                              HypA  69 vkvrCreCgkefelee.kal.....rCpkCgsadveiv 100
                                       v++rC+ Cg+    ++ k       +Cp+Cg+++ +i 
  gi|474935036|ref|YP_007688618.1|   9 VELRCKYCGAPLPADDvK-SdapyiTCPSCGTTQQKID 45 
                                       689******999977642.123556*******998875 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.3   0.00016      0.41       4      30 ..      10      41 ..       7      45 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00016
                       Prok-RING_1  4 gkkCpvCgkelkee...dDi..VvCpeCgtpy 30
                                      + +C+ Cg +l  +   +D+  ++Cp Cgt +
  gi|474935036|ref|YP_007688618.1| 10 ELRCKYCGAPLPADdvkSDApyITCPSCGTTQ 41
                                      678*******9888555454559*******87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (516 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 3235.53
//
Query:       gi|474935037|ref|YP_007688619.1|  [L=127]
Description: hypothetical protein TALC_01485 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0042   17.0   8.5     0.0073   16.2   8.5    1.4  1  DUF4271   Domain of unknown function (DUF4271)
      0.007   16.6   0.5      0.007   16.6   0.5    2.0  2  DUF2754   Protein of unknown function (DUF2754)
  ------ inclusion threshold ------
      0.038   13.6   8.7      0.049   13.2   8.7    1.1  1  PRA1      PRA1 family protein
       0.21   10.2   5.6       0.69    8.5   1.2    2.1  2  Tweety    Tweety
       0.28   11.4   9.6      0.063   13.5   5.3    1.9  2  DUF1516   Protein of unknown function (DUF1516)
       0.49   10.5  18.5       0.42   10.7   4.5    2.4  2  DUF2892   Protein of unknown function (DUF2892)
        0.9    9.4  10.2       0.44   10.4   4.2    2.5  2  DUF2427   Domain of unknown function (DUF2427)
        3.2    6.6  25.6       0.35    9.7   5.3    1.9  2  MFS_1     Major Facilitator Superfamily
        3.3    8.1  12.7       0.71   10.2   4.2    2.2  2  DUF4133   Domain of unknown function (DUF4133)
        6.3    6.4   9.6        9.3    5.9   9.6    1.4  1  DUF2101   Predicted membrane protein (DUF2101)
        8.3    6.8  15.5         16    5.9  15.5    1.4  1  DUF4395   Domain of unknown function (DUF4395)


Domain annotation for each model (and alignments):
>> DUF4271  Domain of unknown function (DUF4271)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   8.5   4.5e-06    0.0073      54     178 ..      14     125 ..       3     127 .] 0.83

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.5e-06
                           DUF4271  54 lllltclllglllylllsefgslfgsylassllllliiflilllylllKlllykllgwlFfdkkkirqwifsylsyl 130
                                       l++++c+l+gl+l ll                l+ l  ++++l+++    +++  +g++F++k       ++++ ++
  gi|474935037|ref|YP_007688619.1|  14 LVIVFCVLIGLALALLAWG----------AAGLSALAAVGVFLIIFG---GAVVAVGSTFSSKPDKFGPSEQMYRVS 77 
                                       8899999999999999888..........677777777777777766...566689********************* PP

                           DUF4271 131 sllglllfplvlllvyfplssqillililiillliklllllyksirif 178
                                       + l++ll+ +v+++++ + s ++ + +++i + +i l++ l+ s +i 
  gi|474935037|ref|YP_007688619.1|  78 VGLVILLIGVVMVMTLADVSWYVYVAILIIGIAVIGLATGLINSRNIT 125
                                       ********************9999988888777776666677777765 PP

>> DUF2754  Protein of unknown function (DUF2754)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   2.3       3.1     5e+03      28      42 ..      26      40 ..       9      56 .. 0.56
   2 !   16.6   0.5   4.3e-06     0.007      12      63 ..      72     123 ..      62     127 .] 0.86

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.1
                           DUF2754 28 vGllGfeakGwqtya 42
                                      + ll + a G  + a
  gi|474935037|ref|YP_007688619.1| 26 LALLAWGAAGLSALA 40
                                      345555555555443 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 4.3e-06
                           DUF2754  12 hyyavalGlifilnGvvGllGfeakGwqtyavGlvtwvisfwiaGliirrrp 63 
                                         y v++Gl+++l Gvv ++ +    w  y   l+  +  + +a  +i  r+
  gi|474935037|ref|YP_007688619.1|  72 QMYRVSVGLVILLIGVVMVMTLADVSWYVYVAILIIGIAVIGLATGLINSRN 123
                                       5799***************************999999999888866666654 PP

>> PRA1  PRA1 family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   8.7     3e-05     0.049      44     127 ..      14     113 ..       6     126 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3e-05
                              PRA1  44 ivvllvlllslltnplslivllllvlawlflyf.lrseplvlfgrelsdr..............vvlivllvvsvll 105
                                       +v+++++l+ l +  l+  ++ l +la++ +++ ++   +v +g ++s++              v l++ll+ +v++
  gi|474935037|ref|YP_007688619.1|  14 LVIVFCVLIGLALALLAWGAAGLSALAAVGVFLiIFGGAVVAVGSTFSSKpdkfgpseqmyrvsVGLVILLIGVVMV 90 
                                       567788888888888888888888888888888677999999999997777999****9999887777777777778 PP

                              PRA1 106 lfltg.avlvllwalliglllvl 127
                                       + l++ +++v++  l+ig++++ 
  gi|474935037|ref|YP_007688619.1|  91 MTLADvSWYVYVAILIIGIAVIG 113
                                       88888566666667777887775 PP

>> Tweety  Tweety
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   1.2   0.00043      0.69     208     243 ..       8      44 ..       5      46 .. 0.82
   2 ?    4.0   0.2    0.0097        16       6     215 ..      65     101 ..      60     119 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00043
                            Tweety 208 arkskcllivvsvlgllal.vlsWaslglelasavga 243
                                       a + + l+iv++vl  lal +l+W+++gl + +avg+
  gi|474935037|ref|YP_007688619.1|   8 AYRTRQLVIVFCVLIGLALaLLAWGAAGLSALAAVGV 44 
                                       5678999999998766665378************996 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.0097
                            Tweety   6 stfrpedeeyqqsllllasvaaallalsLlflllYlltlCCdrrkeeeeskkdsccvtwsvviatlvccaaigvGfY 82 
                                       ++f p+++ y  s+ l+  + +++++++L  ++ Y+                                         
  gi|474935037|ref|YP_007688619.1|  65 DKFGPSEQMYRVSVGLVILLIGVVMVMTLADVSWYV----------------------------------------- 100
                                       566666666666666666666666666665555554......................................... PP

                            Tweety  83 GNsetndGvlqltyslrkanhtlagikklvseteesleekleeeLtkleeifakrtdlletlrlvqeqveevvqqls 159
                                                                                                                    
  gi|474935037|ref|YP_007688619.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                            Tweety 160 elpflkkkdvsltelaeqvelvelyRWlaylllllldlviClvlllglarkskcll 215
                                                                                               
  gi|474935037|ref|YP_007688619.1| 101 -------------------------------------------------------Y 101
                                       .......................................................3 PP

>> DUF1516  Protein of unknown function (DUF1516)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       1.2     2e+03      93     102 ..      14      23 ..       4      32 .. 0.53
   2 ?   13.5   5.3   3.9e-05     0.063      15      77 ..      54     115 ..      38     124 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.2
                           DUF1516  93 llilfivvlv 102
                                       l+i+f v++ 
  gi|474935037|ref|YP_007688619.1|  14 LVIVFCVLIG 23 
                                       3333333332 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 3.9e-05
                           DUF1516  15 fivalllyskgkskaakilhmilRlfy.llilvtglvllirtfknspllyilKvllgllvIglm 77 
                                       + v+ +++sk  +k +  +  + R+   l+il+ g+v++++ ++ s+++y+   ++g++vIgl 
  gi|474935037|ref|YP_007688619.1|  54 VAVGSTFSSK-PDK-FGPSEQMYRVSVgLVILLIGVVMVMTLADVSWYVYVAILIIGIAVIGLA 115
                                       3444444444.444.555555566654399999****************************986 PP

>> DUF2892  Protein of unknown function (DUF2892)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   6.1      0.01        17      14      48 ..      22      58 ..       3      60 .. 0.72
   2 ?   10.7   4.5   0.00026      0.42       6      49 ..      68     119 ..      67     121 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.01
                           DUF2892 14 ivvGlvllllallglsggw..gwllglvGavllltgl 48
                                      i ++l+ll+++++gls+ +  g++l+++G++ ++ g 
  gi|474935037|ref|YP_007688619.1| 22 IGLALALLAWGAAGLSALAavGVFLIIFGGAVVAVGS 58
                                      4456667777777776655887777777777776665 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00026
                           DUF2892   6 gtldRilrivvGlvllllallglsggw........gwllglvGavllltglt 49 
                                       g+ +   r+ vGlv+ll++++ +++ +        ++l + ++++ l+tgl+
  gi|474935037|ref|YP_007688619.1|  68 GPSEQMYRVSVGLVILLIGVVMVMTLAdvswyvyvAILIIGIAVIGLATGLI 119
                                       5668999****************98889988888877777788888888876 PP

>> DUF2427  Domain of unknown function (DUF2427)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   1.9      0.18     3e+02      86     101 ..      14      29 ..       4      88 .. 0.56
   2 ?   10.4   4.2   0.00027      0.44      30      67 ..      82     119 ..      73     126 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.18
                           DUF2427  86 willillavqvvlavl 101
                                        ++++ +++ ++la+l
  gi|474935037|ref|YP_007688619.1|  14 LVIVFCVLIGLALALL 29 
                                       4444444444444433 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00027
                           DUF2427  30 vvvyPvalvLslaksrwylpvqivnlvlavlglllghi 67 
                                       +++  v +v+ la+ +wy+ v i+ + +av+gl+ g+i
  gi|474935037|ref|YP_007688619.1|  82 ILLIGVVMVMTLADVSWYVYVAILIIGIAVIGLATGLI 119
                                       44556789**************************9987 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6  12.6     0.033        53      60     109 ..      10      60 ..       6      63 .. 0.67
   2 ?    9.7   5.3   0.00021      0.35     269     322 ..      65     120 ..      60     122 .. 0.61

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.033
                             MFS_1  60 Grrr.vlllglllfalglllllfa.sslwlllvlrvlqGlgagalfpagaal 109
                                         r  v+++++l+ ++  +ll+++ ++l +l+++ v+  +++ga++++g ++
  gi|474935037|ref|YP_007688619.1|  10 RTRQlVIVFCVLIGLAL-ALLAWGaAGLSALAAVGVFLIIFGGAVVAVGSTF 60 
                                       55664555555555555.5555544888899999999999999999988776 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00021
                             MFS_1 269 drlgrrrrlllallllllaalglallavt.ssavllllvlvliGf.glgfvfpsll 322
                                       d++g+  +++   ++l+++++g++++ +  + ++ +++++++iG+   g+++++++
  gi|474935037|ref|YP_007688619.1|  65 DKFGPSEQMYRVSVGLVILLIGVVMVMTLaDVSWYVYVAILIIGIaVIGLATGLIN 120
                                       67777555555555555555555544444144555555888899988888888776 PP

>> DUF4133  Domain of unknown function (DUF4133)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   1.3     0.073   1.2e+02      28      59 ..      23      54 ..       9      68 .. 0.47
   2 ?   10.2   4.2   0.00044      0.71      18      57 ..      72     112 ..      69     123 .. 0.65

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.073
                           DUF4133 28 allllvvilyiiGvsqliclalivvagsllvv 59
                                      +l l+++    +G+s l ++++ ++ +  +vv
  gi|474935037|ref|YP_007688619.1| 23 GLALALLAWGAAGLSALAAVGVFLIIFGGAVV 54
                                      33333333333444444444443333333332 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00044
                           DUF4133  18 ylfilagglvallllv.vilyiiGvsqliclalivvagsll 57 
                                        ++ +++glv+ll+ v +++ ++ vs ++ +a+++++++++
  gi|474935037|ref|YP_007688619.1|  72 QMYRVSVGLVILLIGVvMVMTLADVSWYVYVAILIIGIAVI 112
                                       578899********883556666666666665555554444 PP

>> DUF2101  Predicted membrane protein (DUF2101)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   9.6    0.0057       9.3      91     132 ..      73     114 ..       5     119 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0057
                           DUF2101  91 ylavsviailaylgyvllrklslelyyylvyllvivivvlvf 132
                                        + vsv  ++  +g v++++l+ +  y +v +l+i i+v+ +
  gi|474935037|ref|YP_007688619.1|  73 MYRVSVGLVILLIGVVMVMTLADVSWYVYVAILIIGIAVIGL 114
                                       3557777777789**************************976 PP

>> DUF4395  Domain of unknown function (DUF4395)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9  15.5    0.0096        16       5     109 ..       8     110 ..       5     118 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0096
                           DUF4395   5 avRfnaalvvvllvlalltg.apwllallavvfalralagprlsplgllarrlvaprlgpkpeledaapkrFAqliG 80 
                                       a R++++++v+ +++ l+++  +w +a l +  a+++++     ++g  + ++ +  ++ kp    +  + +   +G
  gi|474935037|ref|YP_007688619.1|   8 AYRTRQLVIVFCVLIGLALAlLAWGAAGLSALAAVGVFLI----IFGGAVVAVGS-TFSSKPDKFGPSEQMYRVSVG 79 
                                       7899999999999999999977888888888888888865....45555555555.5667899999999999***** PP

                           DUF4395  81 lvfllvalvlfllgapv..lglvltalllva 109
                                       lv+ll+++v+ ++ a v  + +v+++++ +a
  gi|474935037|ref|YP_007688619.1|  80 LVILLIGVVMVMTLADVswYVYVAILIIGIA 110
                                       **99888877776666621444444444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1345  (0.0750181); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        34  (0.00189637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.48
# Mc/sec: 798.68
//
Query:       gi|474935038|ref|YP_007688620.1|  [L=180]
Description: hypothetical protein TALC_01486 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.028   14.5   0.1       0.08   13.0   0.0    1.7  2  Ribosomal_S16  Ribosomal protein S16
      0.032   14.0   0.7       0.04   13.7   0.7    1.1  1  DUF445         Protein of unknown function (DUF445)
      0.042   13.9   1.1      0.057   13.5   1.0    1.4  1  ADIP           Afadin- and alpha -actinin-Binding
      0.094   13.2   0.9       0.14   12.6   0.9    1.3  1  YicC_N         YicC-like family, N-terminal region
       0.23   11.5   1.5       0.37   10.8   0.2    1.9  2  Noelin-1       Neurogenesis glycoprotein
       0.33   11.1   1.9       0.63   10.2   1.5    1.6  2  MutS_III       MutS domain III
        1.3    9.5   6.4       0.76   10.2   0.3    2.8  2  LPP            Lipoprotein leucine-zipper


Domain annotation for each model (and alignments):
>> Ribosomal_S16  Ribosomal protein S16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.1e-05      0.08      16      51 ..      10      45 ..       8      65 .. 0.88
   2 ?   -1.6   0.0       1.1   2.9e+03      23      36 ..      79      93 ..      66     126 .. 0.47

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.1e-05
                                      ETTSSTTSSESEEEEEEETTTTSSTS.SEEE-HHHH CS
                     Ribosomal_S16 16 dsrkprdgrpiEklGtYdPlakkkekkevelneeri 51
                                      +s+ +r+   iE++G Y P+ +  ++k+++ +e+r+
  gi|474935038|ref|YP_007688620.1| 10 ESSMARNRSLIERIGLYIPFYRGYKQKNLRRDEDRA 45
                                      57889**************87777777899999997 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.1
                                      SSESEEEEEEET.TT CS
                     Ribosomal_S16 23 grpiEklGtYdP.la 36
                                      +r++ k+  Y   ++
  gi|474935038|ref|YP_007688620.1| 79 ERILSKVDRYYSdVK 93
                                      555555555544222 PP

>> DUF445  Protein of unknown function (DUF445)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.7   1.6e-05      0.04     202     327 ..      34     167 ..      10     175 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.6e-05
                            DUF445 202 pdhllreeedkkvreliadllndpelaakveklkkkklsdlevqeyeealwealkdlllkdlneee..sllrerisk 276
                                       +++ lr++ed+++r+lia++l+  +++  +++  ++++ dl+  +  e++ +++ +  ++  +  +  s ++ +++ 
  gi|474935038|ref|YP_007688620.1|  34 KQKNLRRDEDRAIRNLIAQVLD--RAKVDLKNAERATVGDLQAMRDNERILSKVDRYYSDVKKAVNgySGFHDSVKI 108
                                       5789******************..678889999*********99999998777777665554444455444444444 PP

                            DUF445 277 lleklge......klaed.pklrekln.....kflenaaakvlekyrldiskiveetvnafda 327
                                       l+++l +      kl++d ++l+++ +           a + + +  + +++i+ + ++++ +
  gi|474935038|ref|YP_007688620.1| 109 LETELDAliewdaKLIDDvERLKSQTEqmsadA----DAGDSIATDMKIVERIIDDLIDNYRQ 167
                                       444444411111166666555555555433331....23333333344555666665555554 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.0   2.2e-05     0.057      30     131 ..      39     140 ..      15     167 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.2e-05
                              ADIP  30 veeniaaiinviysLlqardrdleqreslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklkt 106
                                       + ++++ai n+i ++l + + dl+  e  +    +   ++er  sk++r    +++  +  +  +   + le++l +
  gi|474935038|ref|YP_007688620.1|  39 RRDEDRAIRNLIAQVLDRAKVDLKNAERATVGDLQAMRDNERILSKVDRYYSDVKKAVNGYSGFHDSVKILETELDA 115
                                       57899************************************************************************ PP

                              ADIP 107 leqklknekeelqrlknalqqiktq 131
                                       l++   ++ ++++rlk++ +q+++ 
  gi|474935038|ref|YP_007688620.1| 116 LIEWDAKLIDDVERLKSQTEQMSAD 140
                                       *******************999875 PP

>> YicC_N  YicC-like family, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.9   5.3e-05      0.14      44     115 ..      43     131 ..      34     172 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.3e-05
                            YicC_N  44 eeeirelikerlsRGkvevsvsleseeeeekalkvneellkaylealkelaeel.g.a...eel.....slaellrl 110
                                       + +ir+li++ l R kv++    +++  + +a++ ne++l+++ +  +++++++ g +   +++     +l+ l+++
  gi|474935038|ref|YP_007688620.1|  43 DRAIRNLIAQVLDRAKVDLKNAERATVGDLQAMRDNERILSKVDRYYSDVKKAVnGySgfhDSVkiletELDALIEW 119
                                       679****************9877776689999999**9988777777777777733423332223455578888888 PP

                            YicC_N 111 pgvl.......e 115
                                       +  l       +
  gi|474935038|ref|YP_007688620.1| 120 DAKLiddverlK 131
                                       755543332221 PP

>> Noelin-1  Neurogenesis glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   0.00014      0.37      37      88 ..      42      94 ..      34     101 .. 0.84
   2 ?   -0.9   0.1      0.65   1.7e+03      50      50 ..     146     146 ..     110     177 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00014
                          Noelin-1 37 rsrqlrqllekvqnlsq.sievldlRtsrdlqyvrktetllktlesklkvvee 88
                                        r +r+l ++v + ++  ++  ++ t  dlq +r+ e +l++++  +++v++
  gi|474935038|ref|YP_007688620.1| 42 EDRAIRNLIAQVLDRAKvDLKNAERATVGDLQAMRDNERILSKVDRYYSDVKK 94
                                      46899*******98776368999999******************998887765 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.65
                          Noelin-1  50 n 50 
                                        
  gi|474935038|ref|YP_007688620.1| 146 S 146
                                       2 PP

>> MutS_III  MutS domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.39     1e+03     152     174 ..      38      61 ..       6      68 .. 0.63
   2 ?   10.2   1.5   0.00025      0.63      68     171 ..      66     169 ..      45     179 .. 0.48

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.39
                                       HHHHHHHHHHHHHHHH.HHTHHHH CS
                                       xxxxxxxxxxxxxxxx.xxxxxxx RF
                          MutS_III 152 iealeqelfqelleev.eealerl 174
                                       +++ e++++++l+++v ++a  +l
  gi|474935038|ref|YP_007688620.1|  38 LRRDEDRAIRNLIAQVlDRAKVDL 61 
                                       666777778888888733344444 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00025
                                       HHHHHHHTT---HHHHHHHHHTT---HHHHHH.......HHHHHHHHHTTTTT---SSTHHHHHHHHHHHHHHHB-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          MutS_III  68 eelrellrrlpDleRllsrislgkakardlka.......llealkaleelvallekeklaeseeeslaelleeaide 137
                                        +   +l+ ++D eR+ls++    ++++   +       +++++k le   ++l +++++  ++    e+l++   e
  gi|474935038|ref|YP_007688620.1|  66 RATVGDLQAMRDNERILSKVDRYYSDVK---KavngysgFHDSVKILETELDALIEWDAKLIDD-V--ERLKS-QTE 135
                                       33335688899********988555544...311223344444444444444444443322211.1..33332.333 PP

                                       S--SSGGGS--B-THHHHHHHHHHHHHHHHHHTH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          MutS_III 138 eplalekegedlraiealeqelfqelleeveeal 171
                                       + +a  ++g  +++  ++ ++++++l+++ +++ 
  gi|474935038|ref|YP_007688620.1| 136 QMSADADAGDSIATDMKIVERIIDDLIDNYRQRE 169
                                       3333333333333344444555555555554443 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   1.2      0.21   5.3e+02      36      47 ..      73      84 ..      34      90 .. 0.77
   2 ?   10.2   0.3    0.0003      0.76       4      25 ..     122     143 ..     121     155 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.21
                               LPP 36 EAaRANqRlDNi 47
                                       A+R N+R+   
  gi|474935038|ref|YP_007688620.1| 73 QAMRDNERILSK 84
                                      599999999555 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0003
                               LPP   4 eLssqVsqLkskvdqlssdvns 25 
                                       +L ++V++Lks+ +q+s+d+++
  gi|474935038|ref|YP_007688620.1| 122 KLIDDVERLKSQTEQMSADADA 143
                                       5778999999999999999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       938  (0.0523175); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 1015.21
//
Query:       gi|474935039|ref|YP_007688621.1|  [L=369]
Description: hypothetical protein TALC_01487 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-26   93.4   0.2    2.2e-26   92.9   0.2    1.1  1  Band_7_1        SPFH domain-Band 7 family
    4.4e-08   33.3   0.1      8e-08   32.5   0.1    1.4  1  Band_7          SPFH domain / Band 7 family
    2.1e-06   27.7  10.6     0.0035   17.3   1.0    2.2  2  DZR             Double zinc ribbon
    0.00025   20.3  18.8      0.056   12.9   4.6    3.7  3  zf-ribbon_3     zinc-ribbon domain
    0.00067   20.4   3.1      0.018   15.8   0.6    2.4  2  zinc_ribbon_15  zinc-ribbon family
     0.0013   18.4  17.1        1.6    8.6   0.3    4.3  4  zinc_ribbon_2   zinc-ribbon domain
  ------ inclusion threshold ------
      0.014   15.7   2.9        4.4    7.7   0.0    3.4  3  zinc_ribbon_9   zinc-ribbon
       0.24   11.6   4.1        9.3    6.5   0.2    3.3  3  zf-RING_7       C4-type zinc ribbon domain
       0.43   10.7  12.8        3.5    7.8   0.2    3.8  3  zf-CHCC         Zinc-finger domain
       0.57    9.9  12.8       0.36   10.5   0.2    4.0  4  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
       0.66   10.7   9.5       0.15   12.8   2.4    2.6  2  FYDLN_acid      Protein of unknown function (FYDLN_acid)
       0.97    9.5   8.5         19    5.3   4.8    2.7  2  zinc-ribbons_6  zinc-ribbons
          2    8.8  11.5         19    5.6   0.1    3.4  3  zf-Di19         Drought induced 19 protein (Di19), zinc-bindi
        2.1    8.0   3.9        9.1    6.0   0.9    2.6  2  zf_C2H2_13      Zinc finger domain


Domain annotation for each model (and alignments):
>> Band_7_1  SPFH domain-Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.9   0.2   1.7e-29   2.2e-26       8     203 ..      25     218 ..      21     225 .. 0.91

  Alignments for each domain:
  == domain 1  score: 92.9 bits;  conditional E-value: 1.7e-29
                          Band_7_1   8 dneiknGakLivregqeavfvneGqiaDvfapGtytLttenlPvlstLkgwkyGfe.sPfkaevYfvntrqftdlkw 83 
                                       d e+++ ++++v e   a+f+++Gq+    +pG++++t+ n+P l++L ++  G++  Pfk  + +++ + f + kw
  gi|474935039|ref|YP_007688621.1|  25 DTELRTLSQVVVPEHAVALFIRDGQLQGTLEPGRHMITSANIPWLTKLYNLALGYRdNPFKVWIVYISLKMF-NGKW 100
                                       67888999**********************************************9638**********9988.67** PP

                          Band_7_1  84 GtknpvilrDpefglvrvrafGtyslrvvdpakllreivGtdgefdteeiseqlkslivtrlsdvlaeskipvldla 160
                                       G ++ +    +   ++ + a+G + +r++d a++ ++++G  ++++t ++++ ++s i++++++ ++++    +dl 
  gi|474935039|ref|YP_007688621.1| 101 GIRGMIRAAKDYEVPITLMANGDFQFRISDVAVFYTQVLGGMKNYSTGNVNDFMRSFIAEQITQQMNNQY--YMDLM 175
                                       ***999876555569**************************************************99875..68*** PP

                          Band_7_1 161 akseelaeklkealkeelaeyGlelekleienislpeevekal 203
                                        + e+ + + k  +++ +++ G+el +l+i + s  +e + ++
  gi|474935039|ref|YP_007688621.1| 176 QNLEKSSTTTKILIDPYFQQRGIELLSLKIVQASTTKEEQDKI 218
                                       ******************************9999877655544 PP

>> Band_7  SPFH domain / Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.1   6.3e-11     8e-08       2     151 ..      35     212 ..      34     230 .. 0.86

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 6.3e-11
                            Band_7   2 iieegevgvvvrfGklsrvlepGlhfi....lPfgrsvtvvsvrvqtldvsv..................sltvptk 56 
                                       +++e  v++ +r G+l+++lepG h i    +P+++++++  +  +   ++v                  ++ +   
  gi|474935039|ref|YP_007688621.1|  35 VVPEHAVALFIRDGQLQGTLEPGRHMItsanIPWLTKLYNLALGYRDNPFKVwivyislkmfngkwgirgMIRAAKD 111
                                       7999*******************666412225699999999999888888889999999999999999865555444 PP

                            Band_7  57 Dglpvti..dvtviyrvpddapklvaav.....eresanldnlirrvlesalrevisemtleellsnreelaeelkn 126
                                         +p+t+  ++ +++r+ +d+++++++v     +++ +n+++++r+ + +++ ++ ++    +l +n e+     k 
  gi|474935039|ref|YP_007688621.1| 112 YEVPITLmaNGDFQFRI-SDVAVFYTQVlggmkNYSTGNVNDFMRSFIAEQITQQMNNQYYMDLMQNLEKSSTTTKI 187
                                       4577776669999****.*********************************************************** PP

                            Band_7 127 elneqlrkyGvevldvritdidppp 151
                                        + + +++ G+e+l+++i + +  +
  gi|474935039|ref|YP_007688621.1| 188 LIDPYFQQRGIELLSLKIVQASTTK 212
                                       *****************65544444 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   1.2     1e-05     0.013      25      49 .]     282     306 ..     270     306 .. 0.81
   2 !   17.3   1.0   2.8e-06    0.0035      12      38 ..     341     368 ..     334     369 .] 0.84

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1e-05
                               DZR  25 vaaedrCpsCgekvdpearfCpeCG 49 
                                       +a++ +Cp Cg  ++   +fC++CG
  gi|474935039|ref|YP_007688621.1| 282 QAQQVMCPYCGGLNPYPYNFCGKCG 306
                                       334899******************9 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 2.8e-06
                               DZR  12 arfCseCgtklkavaa.edrCpsCgekv 38 
                                        + C++Cg++l+  ++ +++Cp C e++
  gi|474935039|ref|YP_007688621.1| 341 FKICPYCGQDLSGLKKtPKFCPYCAEEL 368
                                       6899999999998877899999999875 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.3   6.8e-05     0.087       9      24 ..     279     293 ..     279     295 .. 0.85
   2 ?    3.4   1.3     0.042        54      17      25 ..     300     308 ..     299     310 .. 0.82
   3 !   12.9   4.6   4.3e-05     0.056       2      22 ..     341     364 ..     340     368 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.8e-05
                       zf-ribbon_3   9 GaplssddnvCpyCGt 24 
                                       G++ ++++++CpyCG+
  gi|474935039|ref|YP_007688621.1| 279 GQQ-QAQQVMCPYCGG 293
                                       566.899********7 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.042
                       zf-ribbon_3  17 nvCpyCGtk 25 
                                       n+C +CG++
  gi|474935039|ref|YP_007688621.1| 300 NFCGKCGKP 308
                                       789999975 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 4.3e-05
                       zf-ribbon_3   2 tvrCPnCGa.p..lssddnvCpyC 22 
                                        + CP+CG+ +  l++  ++CpyC
  gi|474935039|ref|YP_007688621.1| 341 FKICPYCGQdLsgLKKTPKFCPYC 364
                                       578*******99************ PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   1.3   0.00077      0.99      58      86 .]     277     306 ..     263     306 .. 0.74
   2 !   15.8   0.6   1.4e-05     0.018      36      85 ..     298     364 ..     297     365 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00077
                    zinc_ribbon_15  58 ekk.essekkeCknCgkeveeefkyCpkCg 86 
                                       +++ +++++  C+ Cg      +++C kCg
  gi|474935039|ref|YP_007688621.1| 277 QQGqQQAQQVMCPYCGGLNPYPYNFCGKCG 306
                                       33303445899******************9 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.4e-05
                    zinc_ribbon_15  36 pylacskCkslleaskelgkeiekkesse..............kkeCknCgkev...eeefkyCpkC 85 
                                       py  c kC++  ++++++ ++ + + ++                k+C+ Cg+ +   ++  k+Cp+C
  gi|474935039|ref|YP_007688621.1| 298 PYNFCGKCGKPSPMQQQQMQQQQPAPQAApaaapaggaaaggsFKICPYCGQDLsglKKTPKFCPYC 364
                                       6788*******99999666666655555599********************98622257799***** PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.018        23      16      20 ..     288     292 ..     280     294 .. 0.84
   2 !    6.0   2.0     0.008        10      14      22 ..     300     308 ..     298     309 .. 0.85
   3 !    8.0   0.2    0.0019       2.4      14      23 .]     342     351 ..     340     351 .. 0.80
   4 !    8.6   0.3    0.0012       1.6      14      23 .]     359     368 ..     354     368 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.018
                     zinc_ribbon_2  16 CpyCG 20 
                                       CpyCG
  gi|474935039|ref|YP_007688621.1| 288 CPYCG 292
                                       99999 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.008
                     zinc_ribbon_2  14 kFCpyCGtp 22 
                                       +FC +CG p
  gi|474935039|ref|YP_007688621.1| 300 NFCGKCGKP 308
                                       799999986 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0019
                     zinc_ribbon_2  14 kFCpyCGtpl 23 
                                       k CpyCG  l
  gi|474935039|ref|YP_007688621.1| 342 KICPYCGQDL 351
                                       66*****865 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.0012
                     zinc_ribbon_2  14 kFCpyCGtpl 23 
                                       kFCpyC ++l
  gi|474935039|ref|YP_007688621.1| 359 KFCPYCAEEL 368
                                       8*****8876 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0034       4.4      17      29 ..     281     293 ..     274     294 .. 0.76
   2 ?    4.5   0.1     0.033        43      22      29 ..     342     349 ..     330     351 .. 0.80
   3 ?    2.0   0.1      0.21   2.6e+02      22      28 ..     359     365 ..     352     367 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0034
                     zinc_ribbon_9  17 dedsdvlCPhCgg 29 
                                        + ++v+CP+Cgg
  gi|474935039|ref|YP_007688621.1| 281 QQAQQVMCPYCGG 293
                                       455668*****98 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.033
                     zinc_ribbon_9  22 vlCPhCgg 29 
                                       ++CP+Cg+
  gi|474935039|ref|YP_007688621.1| 342 KICPYCGQ 349
                                       57****97 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.21
                     zinc_ribbon_9  22 vlCPhCg 28 
                                       ++CP+C 
  gi|474935039|ref|YP_007688621.1| 359 KFCPYCA 365
                                       47****6 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.2    0.0073       9.3      19      30 ..     278     292 ..     262     292 .. 0.68
   2 ?    2.9   0.1     0.099   1.3e+02      24      30 ..     342     348 ..     335     348 .. 0.75
   3 ?    1.7   0.0      0.23     3e+02      18      29 ..     355     364 ..     349     365 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0073
                                       CS...TB-EE-TTT- CS
                         zf-RING_7  19 ag...devvtCpeCG 30 
                                       +g    + v Cp+CG
  gi|474935039|ref|YP_007688621.1| 278 QGqqqAQQVMCPYCG 292
                                       44333447******9 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.099
                                       EE-TTT- CS
                         zf-RING_7  24 vtCpeCG 30 
                                         Cp+CG
  gi|474935039|ref|YP_007688621.1| 342 KICPYCG 348
                                       57****9 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.23
                                       CCSTB-EE-TTT CS
                         zf-RING_7  18 ragdevvtCpeC 29 
                                       +++    +Cp+C
  gi|474935039|ref|YP_007688621.1| 355 KKT--PKFCPYC 364
                                       555..559**** PP

>> zf-CHCC  Zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.2    0.0027       3.5      25      34 ..     283     292 ..     279     294 .. 0.86
   2 ?    5.0   1.1      0.02        25      28      35 ..     342     349 ..     338     351 .. 0.82
   3 ?    4.3   0.6     0.034        43      24      33 ..     355     364 ..     350     367 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0027
                                       TSEEEETTTT CS
                           zf-CHCC  25 kgpvdCgYCg 34 
                                        ++v C+YCg
  gi|474935039|ref|YP_007688621.1| 283 AQQVMCPYCG 292
                                       6899*****9 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.02
                                       EEETTTTE CS
                           zf-CHCC  28 vdCgYCgl 35 
                                         C+YCg+
  gi|474935039|ref|YP_007688621.1| 342 KICPYCGQ 349
                                       67*****7 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.034
                                       TTSEEEETTT CS
                           zf-CHCC  24 kkgpvdCgYC 33 
                                       kk+p  C+YC
  gi|474935039|ref|YP_007688621.1| 355 KKTPKFCPYC 364
                                       789999**** PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.7      0.79     1e+03       6      11 ..     288     293 ..     287     293 .. 0.87
   2 ?   10.5   0.2   0.00028      0.36       4      17 ..     300     313 ..     299     319 .. 0.77
   3 ?    2.2   0.2      0.11   1.4e+02       4      11 ..     342     349 ..     336     351 .. 0.77
   4 ?    3.3   0.0     0.052        67       4      12 ..     359     367 ..     356     369 .] 0.81

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.79
                     zf-NADH-PPase   6 CgrCGa 11 
                                       C+ CG+
  gi|474935039|ref|YP_007688621.1| 288 CPYCGG 293
                                       999996 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00028
                     zf-NADH-PPase   4 rFCgrCGaptepae 17 
                                        FCg+CG p  +++
  gi|474935039|ref|YP_007688621.1| 300 NFCGKCGKPSPMQQ 313
                                       6******9976555 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.11
                     zf-NADH-PPase   4 rFCgrCGa 11 
                                       + C+ CG+
  gi|474935039|ref|YP_007688621.1| 342 KICPYCGQ 349
                                       56888886 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.052
                     zf-NADH-PPase   4 rFCgrCGap 12 
                                       +FC+ C+ +
  gi|474935039|ref|YP_007688621.1| 359 KFCPYCAEE 367
                                       6*****975 PP

>> FYDLN_acid  Protein of unknown function (FYDLN_acid)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.7      0.36   4.7e+02      28      51 ..     287     312 ..     282     338 .. 0.43
   2 ?   12.8   2.4   0.00012      0.15       7      36 ..     339     368 ..     335     369 .] 0.90

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.36
                        FYDLN_acid  28 vcpkcgeefepeev..lksraaaaea 51 
                                       +cp+cg   +  +    k  ++++ +
  gi|474935039|ref|YP_007688621.1| 287 MCPYCGGLNPYPYNfcGKCGKPSPMQ 312
                                       66666654443333222222222111 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00012
                        FYDLN_acid   7 GtKriCpscgakFYDLnkdPivcpkcgeef 36 
                                       G  +iCp cg+    L+k+P  cp+c ee 
  gi|474935039|ref|YP_007688621.1| 339 GSFKICPYCGQDLSGLKKTPKFCPYCAEEL 368
                                       66689*********************9986 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   1.2     0.029        38       9      38 ..     278     308 ..     270     316 .. 0.79
   2 ?    5.3   4.8     0.015        19      18      39 ..     343     368 ..     300     369 .] 0.55

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.029
                                       --EE-SSEEE-TTT--.EEEEEEE-SSS-S- CS
                    zinc-ribbons_6   9 elekrgeqyhCeaCqe.dlkkealCpeCeqe 38 
                                       + +++ +q+ C  C   +    ++C +C+++
  gi|474935039|ref|YP_007688621.1| 278 QGQQQAQQVMCPYCGGlNPYPYNFCGKCGKP 308
                                       4556779999999998677788999999986 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.015
                                       E-TTT--EE....EEEEE-SSS-S-- CS
                    zinc-ribbons_6  18 hCeaCqedl....kkealCpeCeqel 39 
                                        C  C +dl    k  ++Cp C +el
  gi|474935039|ref|YP_007688621.1| 343 ICPYCGQDLsglkKTPKFCPYCAEEL 368
                                       45555553311112334555555554 PP

>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   1.0     0.028        36       2       9 ..     285     292 ..     278     307 .. 0.77
   2 ?    5.6   0.1     0.015        19       5      12 ..     344     351 ..     340     355 .. 0.83
   3 ?    4.1   0.8     0.044        56       4      12 ..     360     368 ..     357     369 .] 0.82

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.028
                           zf-Di19   2 sftCPyCg 9  
                                       ++ CPyCg
  gi|474935039|ref|YP_007688621.1| 285 QVMCPYCG 292
                                       56677776 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.015
                           zf-Di19   5 CPyCgkel 12 
                                       CPyCg++l
  gi|474935039|ref|YP_007688621.1| 344 CPYCGQDL 351
                                       *****987 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.044
                           zf-Di19   4 tCPyCgkel 12 
                                        CPyC +el
  gi|474935039|ref|YP_007688621.1| 360 FCPYCAEEL 368
                                       5****9876 PP

>> zf_C2H2_13  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.9    0.0071       9.1      17      26 ..     299     308 ..     294     312 .. 0.86
   2 ?    1.8   0.1      0.15   1.9e+02      17      27 ..     341     351 ..     336     353 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0071
                        zf_C2H2_13  17 YRvCnkCGkP 26 
                                       Y  C kCGkP
  gi|474935039|ref|YP_007688621.1| 299 YNFCGKCGKP 308
                                       889******9 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.15
                        zf_C2H2_13  17 YRvCnkCGkPi 27 
                                       + +C  CG+ +
  gi|474935039|ref|YP_007688621.1| 341 FKICPYCGQDL 351
                                       99******865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1079  (0.0601818); expected 358.6 (0.02)
Passed bias filter:                      644  (0.0359195); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); expected 17.9 (0.001)
Passed Fwd filter:                        31  (0.00172904); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.70u 0.35s 00:00:01.04 Elapsed: 00:00:00.54
# Mc/sec: 2039.28
//
Query:       gi|474935040|ref|YP_007688622.1|  [L=225]
Description: hypothetical protein TALC_01488 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.016   14.9   0.0      0.018   14.7   0.0    1.1  1  Esterase  Putative esterase


Domain annotation for each model (and alignments):
>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0     1e-06     0.018      65     186 ..      58     173 ..      13     179 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1e-06
                                       SS-TTTTTSBTTSBB.TTEEETTCCCCCCHCHHHHTHHHHHHHHHCSEECCCEEEEEETHHHHHHHHHHHCSTTTCC CS
                          Esterase  65 rggessfysdwdlgarfyenategpgaeayetfltqeLlplldanfrtapdgravaGqSmGGlgALilalkhpdrFg 141
                                       + + +   s w+ + +    ++ g+ga++  + ++ ++ p  ++++   ++  ++ G S++Gl++L++++ + + F 
  gi|474935040|ref|YP_007688622.1|  58 DWDSR--LSPWNAP-QPRGTVPFGDGAPETLKMIERTVIPAAKERMGLGDTPVVIGGYSLSGLFSLWAGTMS-GTFD 130
                                       44444..6777777.445667889999999*************************************99765.6788 PP

                                       EEEEES--S-CCHCHHHC.....TTCCHHHCC-CCCCHCHHCHTTSEEEE CS
                          Esterase 142 svssfSpivnpsnamWgq.....eekeawqendpvllakelsaslkalri 186
                                        +   S      ++ W +     ++k+aw ++  +l+     +++++ +i
  gi|474935040|ref|YP_007688622.1| 131 ICVGCS------PSTWFKgwtdhAKKSAWIARAVYLSLGD-TEHQTRNSI 173
                                       888888......5577666666777777877766666644.555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1503.71
//
Query:       gi|474935041|ref|YP_007688623.1|  [L=275]
Description: Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.7e-55  187.8   0.0    3.2e-55  187.6   0.0    1.0  1  Inositol_P  Inositol monophosphatase family


Domain annotation for each model (and alignments):
>> Inositol_P  Inositol monophosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.6   0.0   1.8e-59   3.2e-55       7     269 ..      16     266 ..       7     269 .. 0.87

  Alignments for each domain:
  == domain 1  score: 187.6 bits;  conditional E-value: 1.8e-59
                                       HHHHHHHHHHHHHHHHHTTTSEEEESTTTCCHHHHHHHHHHHHHHHHHHHHHHHHSTTSEEEHHCHHHHCCCT.SSS CS
                        Inositol_P   7 kaavelaakagevlreefsenelvieekskegeedlvtaadeaveelilealaekfpshkilgeetlakgekselte 83 
                                       +  ++la +ag+++ +  +   +++e k  +++e+ vt +d ++e +++e+l   +p++ +lgee+    e    +e
  gi|474935041|ref|YP_007688623.1|  16 SEVISLAEQAGNMMLDDSG---ITVENK--ATKENYVTSMDVKIEGFLREKLTSLIPGSFFLGEEGDPVSE----GE 83 
                                       4445566666666666655...444444..589******************************99888888....77 PP

                                       SSEEEEEEEEETHHHHHHT-SG-EEEEEEEETTEEEEEEEEETTTTEEECEETTTEEEETCEEEEECTTSEGGGTEE CS
                        Inositol_P  84 dgltwivDPiDGTknFvrgipqvaVsigllvegkpvlGviaqPllgqlysaakgkGaflngeklplsrappiseall 160
                                       ++++wivDPiDGT+nF+rgi++  Vsigl++ g+ vlGv+ +P+lg++ysa+kg+Gaflnge++++s+++  +e++ 
  gi|474935041|ref|YP_007688623.1|  84 KEYMWIVDPIDGTANFARGIRMSVVSIGLAHFGELVLGVVRHPHLGETYSAVKGNGAFLNGEPIHVSDRT--KEHCM 158
                                       77*******************************************************************9..***** PP

                                       EEEESSSSSSHHHHCHH.HHHHHCCCCCHEEEBESSHHHHHHHHHHTSTSEEEEEC.EBHHHHHHHHHHHHHTTEEE CS
                        Inositol_P 161 vtlfavssrkdtseasl.lekvesavsaegvrsvgssalklaavaeGkadaylefgrekkWDhAAGeaileeaGGvv 236
                                       v+l ++  +k+   + +  ++ +  v+   +r++g +a++l++va G+ d+  e++ + +WD A++++il+eaGGv+
  gi|474935041|ref|YP_007688623.1| 159 VSLAWSTYNKKLAPMCFeVSQRLYGVCED-LRRIGTAAYELCQVAKGSEDMLFEIR-LAPWDYAGAAVILREAGGVI 233
                                       *********99999433255666666666.**************************.******************** PP

                                       EESSSCSSSTTSSEEEEESCHHHHHHHHHHHCC CS
                        Inositol_P 237 tdakgegrlllargiiaanqkelaellaaavee 269
                                         ++g+  l  + ++ aan+  ++e l + v++
  gi|474935041|ref|YP_007688623.1| 234 SSVDGDVSLTHSCTVMAANTAGNHEFLSSVVKD 266
                                       ******777788999999999999988777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1789.73
//
Query:       gi|474935042|ref|YP_007688624.1|  [L=181]
Description: adenine phosphoribosyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.2e-15   55.3   0.2    6.7e-15   55.0   0.2    1.1  1  Pribosyltran  Phosphoribosyl transferase domain
    2.6e-06   27.0   0.0    4.1e-06   26.4   0.0    1.3  1  UPRTase       Uracil phosphoribosyltransferase
     0.0019   17.7   0.0     0.0027   17.3   0.0    1.2  1  PRTase_2      Phosphoribosyl transferase


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   0.2   1.1e-18   6.7e-15      15     124 ..      44     155 ..      31     174 .. 0.82

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 1.1e-18
                                       EEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE.............EE----T CS
                      Pribosyltran  15 varlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes.....rlledpa 86 
                                       v+ la+++        d+v+g + +G++f+  +a  ++  ++  rk+ + p  + + +  ++  s     ++ +++ 
  gi|474935042|ref|YP_007688624.1|  44 VDGLAEKLKGV---DFDLVIGTEARGFVFGAPVAYIMNKGFVLARKKGKLPRETVSETYDLEYGSatlemHKDSIKP 117
                                       55555555444...899*****************************99999999999866654449*********** PP

                                       TSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEE CS
                      Pribosyltran  87 gkkVliVDDildtGgTllaalelLkekgpeevriavlv 124
                                       g+kV+iVDD+++tGgT +a+++l+++ g ++ +i+ ++
  gi|474935042|ref|YP_007688624.1| 118 GQKVVIVDDLIATGGTTKAVINLIEKLGGKVEKIVFVM 155
                                       *****************************965555555 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   6.9e-10   4.1e-06     120     161 ..     117     158 ..      87     172 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 6.9e-10
                           UPRTase 120 aertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvla 161
                                         ++v+++D +iaTGg+  a+i+l+ + g ++ekI+++  la
  gi|474935042|ref|YP_007688624.1| 117 PGQKVVIVDDLIATGGTTKAVINLIEKLGGKVEKIVFVMELA 158
                                       4566*********************************98776 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   4.5e-07    0.0027     113     156 ..     110     154 ..     101     175 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.5e-07
                          PRTase_2 113 edeellaaakelvLvDDEistGktalnliralqeklpr.kryvvv 156
                                        +++ ++  +++v+vDD i+tG t+ ++i+ +++   + +++v+v
  gi|474935042|ref|YP_007688624.1| 110 MHKDSIKPGQKVVIVDDLIATGGTTKAVINLIEKLGGKvEKIVFV 154
                                       5677888899***************99999999886666555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1152.42
//
Query:       gi|474935043|ref|YP_007688625.1|  [L=343]
Description: hydrogenase expression/formation protein HypE [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-26   92.3   0.4      5e-26   91.7   0.1    1.4  2  AIRS_C    AIR synthase related protein, C-terminal domain
    1.3e-15   57.9   1.9    2.6e-15   56.9   1.9    1.5  1  AIRS      AIR synthase related protein, N-terminal domain


Domain annotation for each model (and alignments):
>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.1   9.6e+03       7      32 ..      77     100 ..      75     112 .. 0.59
   2 !   91.7   0.1   5.6e-30     5e-26       1     150 [.     171     317 ..     171     322 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.1
                                       EEEETSSCTCCHHHHHHHCHHHCTSH CS
                            AIRS_C   7 iltgslGlggagtslkrkileeegld 32 
                                       ++ +++Gl ++++++  ++l+++++d
  gi|474935043|ref|YP_007688625.1|  77 MGAKPIGLASSVILE--EGLDSDTVD 100
                                       666777777777443..455555555 PP

  == domain 2  score: 91.7 bits;  conditional E-value: 5.6e-30
                                       STTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHH CS
                            AIRS_C   1 kpGdvliltgslGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgala 77 
                                       +pGdv+i+ g  G +g+++++ r++  +e+       ++dv+ ++++i+  ++       + a++D T+GGL+++l+
  gi|474935043|ref|YP_007688625.1| 171 RPGDVIIVSGYVGDHGVSLLSFREGYGFESDV-----KSDVQPLNKMIERGLRVGG----IVAMKDPTRGGLANTLN 238
                                       79**********************99999965.....9**********99987777....8**************** PP

                                       HHHHTTTEEEEEECGTHHHHHHHH.....HHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTC.CCEEEEEEEEES CS
                            AIRS_C  78 emapasgvgaeidldkvpifdele.....splemllsensGrllvavppeeadavlaileeegl.peaavIGevtak 148
                                       e+a++s++++ i+++++p++d +      +++e+l + n+G+ +++v+pe a++vl+++++  + ++aa+IG++ ++
  gi|474935043|ref|YP_007688625.1| 239 EWADKSKCQLDINEADIPLRDGVVsacelLGIEPLNIGNEGKCVISVVPEMAEEVLKAIRATPEgKDAAIIGRASEG 315
                                       ***************88888877777778**********************************9999*******999 PP

                                       SS CS
                            AIRS_C 149 ee 150
                                       ++
  gi|474935043|ref|YP_007688625.1| 316 PS 317
                                       85 PP

>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.9   1.9   2.9e-19   2.6e-15       1      92 [.      35     141 ..      35     143 .. 0.91

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 2.9e-19
                                       SSSE....EEEEEEEEE.EECCTCCCC....HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HHHHHHHHHH CS
                              AIRS   1 dDaa....vvvttdshnrpvlvepvhf....iGakavavnlsDlaamGArPlalllslalp......wleevvrgla 63 
                                       dD a    vv+t+d       v+p  f    iG++av ++++D+ +mGA+P++l  s++l+      ++++v+++++
  gi|474935043|ref|YP_007688625.1|  35 DDSAvvddVVFTID----GHTVQPLFFpggdIGRIAVSGTINDISVMGAKPIGLASSVILEegldsdTVDKVMASMG 107
                                       78885555599***....7778888888899********************************************** PP

                                       HHHHHTT-EEEEEEEEEESS.....EEEEEEEEE CS
                              AIRS  64 eaaeelgvplvgGdtsfsne.....ptisvtavG 92 
                                       + a  +gvp+v+Gdt+++ +     ++i+++a+G
  gi|474935043|ref|YP_007688625.1| 108 KTAGDAGVPIVTGDTKVMGAgeidkMVITTSAIG 141
                                       ****************996668999999999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 2143.33
//
Query:       gi|474935044|ref|YP_007688626.1|  [L=396]
Description: hypothetical protein TALC_01493 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-93  314.1   0.0    1.4e-93  313.9   0.0    1.0  1  DUF1015    Protein of unknown function (DUF1015)
  ------ inclusion threshold ------
      0.035   14.8   0.0       0.11   13.2   0.0    1.8  2  GRDP-like  Glycine-rich domain-containing protein-like


Domain annotation for each model (and alignments):
>> DUF1015  Protein of unknown function (DUF1015)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  313.9   0.0   1.6e-97   1.4e-93       2     393 ..       5     393 ..       4     394 .. 0.90

  Alignments for each domain:
  == domain 1  score: 313.9 bits;  conditional E-value: 1.6e-97
                           DUF1015   2 kPfrglrypkekv..laevasppYDviseeearelakknpysflrlilpeadledeedeedryekaaetleewleeg 76 
                                       +Pf g+r +  +   +a+ +sppYDvis+ee ++l +++p+++++l+l      d +   +ry+  ++ l++++++g
  gi|474935044|ref|YP_007688626.1|   5 LPFAGFRPDLGAGeaIADRVSPPYDVISDEELAKL-QSKPNNVTNLTLKP----DAD---KRYKGSRKLLDKMVDDG 73 
                                       79*****66555589******************99.699*********53....222...3**************** PP

                           DUF1015  77 vlvqdekpalyvyeqtfed.g.grvrrGlvaavsledyeegvIlpHEkTlaekeedRlkllratkanlepifllyrd 151
                                        l ++++p++y+y+q+f+  g +++rrGlv+ +++edy++g+I pHE+T+++ ++dRl+llr ++++le if+++++
  gi|474935044|ref|YP_007688626.1|  74 FL-KQDSPSFYIYDQKFTSdGkEYKRRGLVGILRCEDYDQGHIIPHEETFSKVKADRLNLLRDMETHLESIFGIFPG 149
                                       **.6678**********99956******************************************************* PP

                           DUF1015 152 pe.eieelieelkkkeeeplydfttdedgvrhrlwaitdpeaiekiaealadkklyIADGHHRyatalavreerkae 227
                                        + e+++l+++++    + ly+   d+dgv+hr  +i d++++++i+e+l+d++++IADGHHRy+tal++++e    
  gi|474935044|ref|YP_007688626.1| 150 LGdELNRLVDNTC----RLLYRH-VDKDGVEHRYSRILDSDVCAQISEKLKDQNMLIADGHHRYETALNYAKE---- 217
                                       *999******994....479999.899********************************************33.... PP

                           DUF1015 228 eeaatgeepanyflavlvnledpgLkilpihRvvkdlnglseeelleklaeafev............ap..fglylk 290
                                       ++   g+e+ +++l+++v+++dpgL+i p+hR+v   +++ e + ++kl++++ +             +  +g+++k
  gi|474935044|ref|YP_007688626.1| 218 NA---GDEKKQFVLCTMVAADDPGLVIWPTHRLVDA-EDIGETSAIKKLEKNVAMkevsgeemeaqlPQhmLGMMFK 290
                                       32...68999************************76.5788999*******99777778877776651156*****9 PP

                           DUF1015 291 dgkwyklltlkdka...vrsLdvsvlqelllepilgiedprkderidyvhgleeavekvdsgeagvafllnptsvee 364
                                       +g+ + +  l++ +   + sLd++ +q+ +l+ + + ++   ++++++  +l  +++ + +++++va++lnp s ++
  gi|474935044|ref|YP_007688626.1| 291 SGRCFLVDPLEK-DgniMMSLDTYFAQQKILNGVYKADE--GKSKVSFDAELPSVKKVMGEKKHDVAIVLNPPSLKT 364
                                       998877777666.3457***************9999765..69****************99999************* PP

                           DUF1015 365 lfavadagevmPrKSTyfePKlrsGlvle 393
                                       + +++d+g++mP+K+Tyf PK+ sG v++
  gi|474935044|ref|YP_007688626.1| 365 IWDLSDQGKRMPKKTTYFFPKIWSGWVFY 393
                                       **************************997 PP

>> GRDP-like  Glycine-rich domain-containing protein-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       0.7   6.3e+03      94     113 ..      53      72 ..      38      86 .. 0.71
   2 ?   13.2   0.0   1.2e-05      0.11      76     135 ..     184     248 ..     175     251 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.7
                         GRDP-like  94 keAvqRYkrfLyLlkkneee 113
                                        +A +RYk+   Ll k  ++
  gi|474935044|ref|YP_007688626.1|  53 PDADKRYKGSRKLLDKMVDD 72 
                                       56889999877777776655 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.2e-05
                         GRDP-like  76 skfvykvssphiseevflkeAvqRYkrfLyLlkkneeegskrflvPty....DidL.iWhtHqlh 135
                                       s++++++s+   ++++ + +  +RY+  L   k+n+ +  k+f+  t+    D  L iW tH+l 
  gi|474935044|ref|YP_007688626.1| 184 SDVCAQISEKLKDQNMLIADGHHRYETALNYAKENAGDEKKQFVLCTMvaadDPGLvIWPTHRLV 248
                                       56899999999999999**************************999888998765538****996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2628.46
//
Query:       gi|474935045|ref|YP_007688627.1|  [L=649]
Description: putative RNA-binding protein, eukaryotic snRNP -like protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-66  225.6   0.2    1.3e-66  225.3   0.2    1.1  1  FbpA           Fibronectin-binding protein A N-terminus (FbpA
      8e-22   78.0   0.0    2.8e-21   76.2   0.0    1.9  2  NFACT-R_1      NFACT protein RNA binding domain
      0.003   17.5   4.7      0.003   17.5   4.7    2.1  2  Bap31_Bap29_C  Bap31/Bap29 cytoplasmic coiled-coil domain
  ------ inclusion threshold ------
      0.026   14.5   0.3      0.062   13.3   0.3    1.6  1  MCC-bdg_PDZ    PDZ domain of MCC-2 bdg protein for Usher synd
      0.053   13.9   1.7       0.56   10.6   0.0    2.6  3  Ribosomal_S13  Ribosomal protein S13/S18
       0.07   12.4   4.3       0.13   11.5   1.6    2.1  2  DUF3450        Protein of unknown function (DUF3450)
       0.66   10.0   2.4        2.7    8.0   0.5    2.6  3  DUF1664        Protein of unknown function (DUF1664)
        0.8   10.2   5.6       0.24   11.9   1.8    2.1  2  DUF16          Protein of unknown function DUF16
       0.85    9.6  10.0        0.8    9.7   0.8    2.3  2  YscO-like      YscO-like protein
       0.88    9.6   5.3        3.8    7.5   0.9    2.3  2  Laminin_II     Laminin Domain II
       0.89    9.9   5.3       0.99    9.8   2.8    2.4  3  Csm1_N         Csm1 N-terminal domain
        2.6    8.4   6.5       0.35   11.2   1.8    1.9  2  DUF641         Plant protein of unknown function (DUF641)
        3.2    7.9   9.7       0.95    9.7   4.1    2.1  2  ATG16          Autophagy protein 16 (ATG16)


Domain annotation for each model (and alignments):
>> FbpA  Fibronectin-binding protein A N-terminus (FbpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.3   0.2   9.5e-70   1.3e-66       2     421 ..       7     428 ..       6     437 .. 0.92

  Alignments for each domain:
  == domain 1  score: 225.3 bits;  conditional E-value: 9.5e-70
                                       HHHHHHHHHHHHHHHTTXEEEEEEEEETTEEEEEEE.ETTEEEEEEEEXXTTTXEEEEXXXXXXXXSSXXHHHHHHH CS
                              FbpA   2 glvlaavvaELqkellggridkiyqpekdelvltlr.anrgrhkLllsahpsyarihltekpkenpkeppnFcmlLR 77 
                                       ++++ +vv+E+   l++++ dkiyq ++ ++ +++  +n+g+ +L        + + l+    e p++p++F+ ++R
  gi|474935045|ref|YP_007688627.1|   7 SFDVSSVVREMAI-LEDAHMDKIYQWGEGNVLFRINtKNDGKADLFFKD---KKWLFLSPDRPETPETPTSFATFMR 79 
                                       789**********.**********************77888878***99...888889888999************* PP

                                       HHHTTXEEEEEEEXTTSSEEEEEEEEEXTTSXEEEEEEEEEXXGGGXEEEEEETTTEEEEESSXBXXXSSXSXXBST CS
                              FbpA  78 kyLkgarivsieqlgfdRivelsiekrdElgdeeeytLivEimgrhSNiiLvdeenkIidaikhvspkqsrvReilp 154
                                       kyL +ari + +q+gfdRiv l++ k+     ++ y++i+E++g  +N++Lv +++kI+ ++ + +++   +R   p
  gi|474935045|ref|YP_007688627.1|  80 KYLTNARIGKASQIGFDRIVTLEVFKA-----DADYQIIFEMFGG-GNVLLV-QDGKIVNCLTQRTFR---DRATRP 146
                                       ***************************.....9************.******.588************...9***** PP

                                       TXBXXXSXXXSXBXTTSXXH.HHHHHHHHHS.XXXHHHHHHHBTTXXHHHHHHHHTTXSSSH............... CS
                              FbpA 155 gekYelPpsqdklnPleaeeleefkellskkekdlvkaLvkafqGlspllaeelleragldketsakelseedlerl 231
                                       ge Y++P +  + nPl a+e eef++ ++++e+d v++L++   +l++++aee+++r g+dk+ +a+e  + +++++
  gi|474935045|ref|YP_007688627.1| 147 GEDYVMPKE--RFNPLAATE-EEFSDEFRTSEGDTVRTLATVT-NLGGQYAEEVCARSGVDKTLPAAEQGDGEIKSM 219
                                       *********..*****9999.99****99999*********96.********************************* PP

                                       HHHHHHHHTXXX....XXEE.....XSSSEESSXXTTXX.SSXXXXSXHHHHHHHHTTTXXX--SHHHHHHHHHHHH CS
                              FbpA 232 yealqelleeleeekfepqlvlkeekpeefsvvplkslselekesfdslsealdeyYakkaerdrveqkrsdlekrv 308
                                       yeal+ ++e+++ e+ +p+++  + k e++++v+ k  +++ek+++ds+s+a+ ++ a+ a +++ve++  ++ek +
  gi|474935045|ref|YP_007688627.1| 220 YEALHAIVEDIK-EHPQPTVFRYDGKIEDIAPVDMKVHDGCEKQPYDSISKAIGAFIAEAAMQQKVERTDPEIEK-L 294
                                       ***********9.79*******************88889*********************************987.7 PP

                                       HHHHHHHHHHHHHHHHHHHCCGGH.....HHHHCCHH-----------------------.--.............. CS
                              FbpA 309 eneleklekklkklekelekaeka.....enyrligelltaylyaikkgmsevelenyydege.............. 366
                                       ++++ek++++ +++  ++e+ +++      +y+++ ell ++ ++  k+ s+ +l    + g               
  gi|474935045|ref|YP_007688627.1| 295 KRRIEKQQETVDEYTVNAERLKTQadslyTEYKKVSELLAVLGEQS-KKLSWEKLT---E-GAlkipyvayidpskn 366
                                       8999**********99999999988999***********9998777.455555555...2.3344677888999999 PP

                                       .......---------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              FbpA 367 .......evtIpLdprkspsenAqkyfkkykKlkraveaveeqieetkeeleylesveaale 421
                                               ++I+Ld +k++  nA   + k k   ++++++ +++   +eel + e+  + ++
  gi|474935045|ref|YP_007688627.1| 367 tvavrigLLEIELDYTKNIDANASDIYAKGKEQSEKAANAMKALNDSREELGKKEKGFEKVK 428
                                       999999888******************************************99887666665 PP

>> NFACT-R_1  NFACT protein RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       7.5     1e+04       8      31 ..     305     328 ..     299     340 .. 0.66
   2 !   76.2   0.0     2e-24   2.8e-21       2     109 .]     446     554 ..     445     554 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 7.5
                         NFACT-R_1   8 sdgylvimGkDkqeneelikkyle 31 
                                        d+y+v + + k++ + l+ +y +
  gi|474935045|ref|YP_007688627.1| 305 VDEYTVNAERLKTQADSLYTEYKK 328
                                       455666666667777777766655 PP

  == domain 2  score: 76.2 bits;  conditional E-value: 2e-24
                         NFACT-R_1   2 vfwFkssdgylvimGkDkqeneelikkyleesdvwfhvdkessahvylrlsegeleeipeelleeaaqlakanSia. 77 
                                       + wF++s+g l ++G+D ++n+ ++kk+++e+d++ h+d++++++v+l+  eg   + +++  +ea+ +a a+S+a 
  gi|474935045|ref|YP_007688627.1| 446 FKWFITSEGRLALAGRDTHSNDSVVKKHMKEKDIYAHADIHGAPSVVLK--EGL--SATPDEFREACWFALAQSKAw 518
                                       78***********************************************..777..8999***************** PP

                         NFACT-R_1  78 gnklssvdvvyvpasnlsktap....ldtGsvgfkg 109
                                        +  ++  +++ +++++skt++    +++G+++++g
  gi|474935045|ref|YP_007688627.1| 519 TAGSPEGGAFWAYPDQVSKTPNagefVPRGAFIIRG 554
                                       **********************99999999999986 PP

>> Bap31_Bap29_C  Bap31/Bap29 cytoplasmic coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   4.7   2.2e-06     0.003       2      47 ..     290     341 ..     289     343 .. 0.90
   2 ?   -2.5   1.4       3.8   5.2e+03      21      43 ..     397     421 ..     397     428 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.2e-06
                     Bap31_Bap29_C   2 eiekLkkeLkkkk.......kDlealKkQaeglakEYDrLadehskldesedK 47 
                                       eiekLk  ++k++        ++e lK Qa++l  EY ++++  + l+e+ +K
  gi|474935045|ref|YP_007688627.1| 290 EIEKLKRRIEKQQetvdeytVNAERLKTQADSLYTEYKKVSELLAVLGEQ-SK 341
                                       9***********9*****************************99999333.33 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.8
                     Bap31_Bap29_C  21 KkQaeglakEYDrLadehskl..de 43 
                                       K+Q+e  a +   L+d +++l  +e
  gi|474935045|ref|YP_007688627.1| 397 KEQSEKAANAMKALNDSREELgkKE 421
                                       7888888888888889888884333 PP

>> MCC-bdg_PDZ  PDZ domain of MCC-2 bdg protein for Usher syndrome
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   4.5e-05     0.062       1      36 [.     293     328 ..     293     334 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.5e-05
                       MCC-bdg_PDZ   1 rLksrIeeLkaqnelLsltleerkqqseeLsldlgk 36 
                                       +Lk+rIe+ + + +  ++++e+ k+q+++L+   +k
  gi|474935045|ref|YP_007688627.1| 293 KLKRRIEKQQETVDEYTVNAERLKTQADSLYTEYKK 328
                                       7******************************99888 PP

>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0    0.0004      0.56      15      62 ..     180     227 ..     174     256 .. 0.86
   2 ?    1.5   0.2      0.26   3.6e+02      44      74 ..     284     314 ..     267     333 .. 0.69
   3 ?   -3.2   0.0       7.5     1e+04       4      36 ..     376     408 ..     374     434 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0004
                     Ribosomal_S13  15 ialtaikGiGrrkakiilkkadvdedkrigelteeeiekieeivenka 62 
                                        +l++++ +G ++a++++++ +vd++  + e  + ei+ + e ++  +
  gi|474935045|ref|YP_007688627.1| 180 RTLATVTNLGGQYAEEVCARSGVDKTLPAAEQGDGEIKSMYEALHAIV 227
                                       67999999******************************9998887744 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.26
                     Ribosomal_S13  44 gelteeeiekieeivenkaqykipnwi.nrqk 74 
                                        e t+ eiek++ ++e++ q+ +++++ n  +
  gi|474935045|ref|YP_007688627.1| 284 VERTDPEIEKLKRRIEKQ-QETVDEYTvNAER 314
                                       4668999*********95.5555555536543 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 7.5
                     Ribosomal_S13   4 gtdidgkkkveialtaikGiGrrkakiilkkad 36 
                                       ++++d +k++      i+  G++++++ +++++
  gi|474935045|ref|YP_007688627.1| 376 EIELDYTKNIDANASDIYAKGKEQSEKAANAMK 408
                                       567777777777777777777777766555444 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.6   9.6e-05      0.13      29      86 ..     274     331 ..     255     344 .. 0.84
   2 ?    1.0   0.0      0.16   2.2e+02     152     177 ..     374     399 ..     368     429 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.6e-05
                           DUF3450  29 vaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiaslee 86 
                                         a+a++q+k+++ d e ++l++++++ +e +++ +v  e+l+ + +s+ +e +++ e
  gi|474935045|ref|YP_007688627.1| 274 FIAEAAMQQKVERTDPEIEKLKRRIEKQQETVDEYTVNAERLKTQADSLYTEYKKVSE 331
                                       5578999**************************************9999999887765 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.16
                           DUF3450 152 ayqiEaeYgrtievyqgeleldGeev 177
                                       +++iE +Y ++i++   ++   G+e 
  gi|474935045|ref|YP_007688627.1| 374 LLEIELDYTKNIDANASDIYAKGKEQ 399
                                       67899999999999999988888775 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.8   2.4e+03      82     105 ..     209     232 ..     184     249 .. 0.55
   2 ?    8.0   0.5     0.002       2.7      56     116 ..     279     339 ..     261     346 .. 0.66
   3 ?   -0.2   0.0       0.7   9.6e+02      58     116 ..     362     420 ..     357     427 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.8
                           DUF1664  82 skeikeevtevredlseigedves 105
                                       +++ + e++++ e l++i ed+++
  gi|474935045|ref|YP_007688627.1| 209 AEQGDGEIKSMYEALHAIVEDIKE 232
                                       334444455555555555555443 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.002
                           DUF1664  56 slaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesk 116
                                       ++++  ++   +i+++ +++++q+e+  e + + ++++ + +++ ++ ++v+e+   l+++
  gi|474935045|ref|YP_007688627.1| 279 AMQQKVERTDPEIEKLKRRIEKQQETVDEYTVNAERLKTQADSLYTEYKKVSELLAVLGEQ 339
                                       3333344555678888888888888888888888888888888888888888877777665 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.7
                           DUF1664  58 aatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesk 116
                                          k+  + ri  ++ +ld +k+i ++ ++  ++ +e+ ++  + ++++++  e+l++k
  gi|474935045|ref|YP_007688627.1| 362 DPSKNTVAVRIGLLEIELDYTKNIDANASDIYAKGKEQSEKAANAMKALNDSREELGKK 420
                                       56788888999999999999999999999888889999999999999888888888776 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.8   0.00017      0.24      39      88 ..     280     336 ..     274     346 .. 0.65
   2 ?   -3.1   0.1       8.3   1.1e+04      76      86 ..     401     411 ..     380     429 .. 0.41

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00017
                                       HHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH..............HHHHH CS
                             DUF16  39 ieakvdklgeqinkleqkvekqgekikelkveqkaqgeeln.......kvdetleli 88 
                                       +++kv+  + +i+kl+  +ekq+e ++e +v+ +  + + +       kv e l ++
  gi|474935045|ref|YP_007688627.1| 280 MQQKVERTDPEIEKLKRRIEKQQETVDEYTVNAERLKTQADslyteykKVSELLAVL 336
                                       567777777888888888888888888888777777776664333333444444444 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 8.3
                                       H.......HHH CS
                             DUF16  76 eelnkvdetle 86 
                                       e+  +  ++l+
  gi|474935045|ref|YP_007688627.1| 401 EKAANAMKALN 411
                                       21111112222 PP

>> YscO-like  YscO-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   2.8     0.036        49      20      64 ..     276     320 ..     272     342 .. 0.73
   2 ?    9.7   0.8   0.00058       0.8      77     125 ..     380     428 ..     372     435 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.036
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         YscO-like  20 AEkvvkdkkkaLekEkeklrkleeerdkvkkhkkaKvaqlreeld 64 
                                       AE ++++k++  + E ekl++++e++++++ ++    + l+ + d
  gi|474935045|ref|YP_007688627.1| 276 AEAAMQQKVERTDPEIEKLKRRIEKQQETVDEYTVNAERLKTQAD 320
                                       677777777777777777777777777777777766666666544 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00058
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         YscO-like  77 ryikvvkeelkqeekkvekQkekVkvAerkvEqareelakkrkevekle 125
                                        y k ++ + +    k ++Q ek   A + +   reel kk+k  ek++
  gi|474935045|ref|YP_007688627.1| 380 DYTKNIDANASDIYAKGKEQSEKAANAMKALNDSREELGKKEKGFEKVK 428
                                       688999999999999999*************************999987 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.9    0.0028       3.8      14      78 ..     279     343 ..     271     354 .. 0.69
   2 ?    3.6   0.2     0.045        61      12      62 ..     367     418 ..     362     429 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0028
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHH CS
                        Laminin_II  14 evleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkel 78 
                                       + +++++  + ++e++k  +++ +++v+e + +++ ++++ ++  ++ kk+ +l+ +L ++ k+l
  gi|474935045|ref|YP_007688627.1| 279 AMQQKVERTDPEIEKLKRRIEKQQETVDEYTVNAERLKTQADSLYTEYKKVSELLAVLGEQSKKL 343
                                       45666666667777777777777777777777777777777777777777777777777776665 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.045
                                       XXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II  12 akevleqlaplsqn.lentkeklseinrsveetnekvkdankairdArrsvk 62 
                                       +++v   l +++ + ++n+ +++s i ++ +e  ek+ +a+ka++d r++  
  gi|474935045|ref|YP_007688627.1| 367 TVAVRIGLLEIELDyTKNIDANASDIYAKGKEQSEKAANAMKALNDSREELG 418
                                       66677777777765368999*************************9998765 PP

>> Csm1_N  Csm1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       5.6   7.7e+03      37      59 ..     210     232 ..     208     235 .. 0.82
   2 ?    9.8   2.8   0.00072      0.99      32      61 ..     280     309 ..     269     321 .. 0.86
   3 ?    0.2   0.5      0.69   9.5e+02      34      62 ..     303     331 ..     300     346 .. 0.65

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 5.6
                            Csm1_N  37 etkdqeiesLkeqlaeleekvke 59 
                                       e+ d ei+s+ e l+++ e++ke
  gi|474935045|ref|YP_007688627.1| 210 EQGDGEIKSMYEALHAIVEDIKE 232
                                       66788999999999999998887 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00072
                            Csm1_N  32 LsqkletkdqeiesLkeqlaeleekvkele 61 
                                       ++qk+e  d eie+Lk+++++ +e v+e  
  gi|474935045|ref|YP_007688627.1| 280 MQQKVERTDPEIEKLKRRIEKQQETVDEYT 309
                                       689*********************999865 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.69
                            Csm1_N  34 qkletkdqeiesLkeqlaeleekvkelee 62 
                                       ++++ ++   e+Lk q ++l ++ k+  e
  gi|474935045|ref|YP_007688627.1| 303 ETVDEYTVNAERLKTQADSLYTEYKKVSE 331
                                       55666666777777777777666666554 PP

>> DUF641  Plant protein of unknown function (DUF641)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.8   0.00025      0.35      65     125 ..     283     343 ..     267     346 .. 0.85
   2 ?   -2.9   0.2       5.7   7.8e+03      76     109 ..     392     425 ..     380     438 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00025
                            DUF641  65 kkkaseaeeseleaeiqeqrsllktyeitvkkleaelkakdseieeLkekLeeaeksnkkl 125
                                       k +++++e ++l+++i++q++ ++ y + +++l+++ ++  +e +++ e L+ + +++kkl
  gi|474935045|ref|YP_007688627.1| 283 KVERTDPEIEKLKRRIEKQQETVDEYTVNAERLKTQADSLYTEYKKVSELLAVLGEQSKKL 343
                                       333335999******************************9999999999999888888877 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.7
                            DUF641  76 leaeiqeqrsllktyeitvkkleaelkakdseie 109
                                       + a+ +eq ++ +   +++++ ++el +k++  e
  gi|474935045|ref|YP_007688627.1| 392 IYAKGKEQSEKAANAMKALNDSREELGKKEKGFE 425
                                       4444444444444444444444455544444444 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   4.1   0.00069      0.95      98     154 ..     278     334 ..     275     346 .. 0.89
   2 ?    1.1   0.3      0.28   3.9e+02     127     157 ..     398     428 ..     371     434 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00069
                             ATG16  98 gelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvq 154
                                       + ++q++ ++  e++kl++++++++e+++e + + ++l+t+ +++  e +   +l+ 
  gi|474935045|ref|YP_007688627.1| 278 AAMQQKVERTDPEIEKLKRRIEKQQETVDEYTVNAERLKTQADSLYTEYKKVSELLA 334
                                       679***************************************999999988887776 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.28
                             ATG16 127 eleaeraaletklkdreeelrekeklvqdlq 157
                                       e +++ a+  ++l+d +eel  kek  ++++
  gi|474935045|ref|YP_007688627.1| 398 EQSEKAANAMKALNDSREELGKKEKGFEKVK 428
                                       4455666677778888888888888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (649 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1300  (0.0725082); expected 358.6 (0.02)
Passed bias filter:                      841  (0.0469072); expected 358.6 (0.02)
Passed Vit filter:                       137  (0.00764125); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.80u 0.33s 00:00:01.13 Elapsed: 00:00:00.49
# Mc/sec: 3973.26
//
Query:       gi|474935046|ref|YP_007688628.1|  [L=63]
Description: SSU ribosomal protein S17E [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-13   51.2   0.0    1.1e-13   51.1   0.0    1.0  1  Ribosomal_S17e  Ribosomal S17
  ------ inclusion threshold ------
      0.094   12.4   0.0        0.1   12.3   0.0    1.1  1  DUF5507         Family of unknown function (DUF5507)


Domain annotation for each model (and alignments):
>> Ribosomal_S17e  Ribosomal S17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.1   0.0   1.3e-17   1.1e-13       1      59 [.       1      59 [.       1      63 [] 0.96

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 1.3e-17
                                      XX----HHHHHHHHHHHHS-TTT--S-HHHHHHHHHHHS----SHHHHHHHHHHHHHHH CS
                    Ribosomal_S17e  1 mgrvrtktvKkaarviiekyyskltndFhtnkkvceevaiipskklrnkiaGyvthlmk 59
                                      mgr+r   +K+++ ++++ky + +++dF++nk+++   + ++   +rnkiaGy+t+++ 
  gi|474935046|ref|YP_007688628.1|  1 MGRIRPTYIKRVSIELVNKYPQAFNRDFNNNKEMVAALTDVAYVPMRNKIAGYITRYLS 59
                                      9******************************************************9986 PP

>> DUF5507  Family of unknown function (DUF5507)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.1e-05       0.1      80     108 ..       9      37 ..       3      51 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.1e-05
                           DUF5507  80 lkrikyevgennlkvfnvhfnnnhelvss 108
                                       +kr+  e+ ++  + fn  fnnn+e+v++
  gi|474935046|ref|YP_007688628.1|   9 IKRVSIELVNKYPQAFNRDFNNNKEMVAA 37 
                                       79************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 415.64
//
Query:       gi|474935047|ref|YP_007688629.1|  [L=223]
Description: thymidylate synthase (FAD) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-73  245.2   0.1    4.6e-73  245.0   0.1    1.0  1  Thy1      Thymidylate synthase complementing protein


Domain annotation for each model (and alignments):
>> Thy1  Thymidylate synthase complementing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  245.0   0.1   2.6e-77   4.6e-73       1     187 [.       4     191 ..       4     192 .. 0.95

  Alignments for each domain:
  == domain 1  score: 245.0 bits;  conditional E-value: 2.6e-77
                                       EEEEEE.CHHHHHHHHHHHHHTTCSSHHHH..SGCCHHHHHHHHHHTTGGGGGGG-EEEEEEEEEEHHHHHHHTT-T CS
                              Thy1   1 kLldyt.dpeklvaaaarvcygsseeaeele.eeekkeklikkllkhghgsplehasftfeiegvSravlrqlvrHR 75 
                                       +Ll+yt d+++++aaaar cy+ +++a+el    ++ e+++ ++++ gh+s++eha+ftf +egvSr++++qlvrHR
  gi|474935047|ref|YP_007688629.1|   4 TLLAYTqDADRICAAAARSCYS-DKGASELRdTVKNPEEFLSHVVSMGHHSVIEHANFTFSVEGVSRSLTHQLVRHR 79 
                                       69*******************5.5566666642355669************************************** PP

                                       TSEEEE--TTTSGCCC.TCBS--GGGCC.HHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHGGGSBTTBEEEEEEEEE CS
                              Thy1  76 iasfsqqSqRYvessk.eafvippeieqkeeleelyeeamekaleaykelleagvarEdaryvLPlatktklvvtmN 151
                                       iasfsqqSqRYv+ ++ + fv+p+++++++e+e+ly ++m+++++ay +l ++g++ EdaryvLP++++t++++tmN
  gi|474935047|ref|YP_007688629.1|  80 IASFSQQSQRYVSLKDpT-FVVPETVKGNPEAEKLYLDTMDAIWKAYGKLEDMGIPAEDARYVLPNGCTTNITITMN 155
                                       ****************88.*******9999*********************************************** PP

                                       HHHHHHHHHHHSSTTS-HHHHHHHHHHHHHHHHHSH CS
                              Thy1 152 lrsLlhflelracsrAqwEirelaeemleelkkvaP 187
                                       +r+L hf++lr+c+rAqwEire+a++mle+++kv P
  gi|474935047|ref|YP_007688629.1| 156 ARELWHFFNLRCCNRAQWEIREMAKQMLELVQKVSP 191
                                       **********************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1333.04
//
Query:       gi|474935048|ref|YP_007688630.1|  [L=251]
Description: pheromone shutdown -like protein (traB) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-14   55.0   0.0    4.6e-14   52.9   0.0    1.8  1  TraB            TraB family
      0.001   19.2   0.4     0.0089   16.2   0.3    2.4  2  HGTP_anticodon  Anticodon binding domain
  ------ inclusion threshold ------
      0.029   14.5   0.2      0.054   13.7   0.2    1.3  1  DIRP            DIRP
      0.093   13.2   0.0       0.17   12.3   0.0    1.4  1  ACP_PD          Acyl carrier protein phosphodiesterase
          1    9.3   6.8       0.12   12.3   2.3    1.9  2  Cofac_haem_bdg  Haem-binding uptake, Tiki superfamily, ChaN


Domain annotation for each model (and alignments):
>> TraB  TraB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.0   1.3e-17   4.6e-14      14     246 ..       4     213 ..       2     225 .. 0.72

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 1.3e-17
                              TraB  14 LfGTiHvskksvyplspeveealeksdtvvvEldlsdd.....tdeatqkelaklkllpdgktlsdllse.....el 80 
                                       ++GT Hv k +   ++  v+     +d+v+vEld  ++     + ea +k+l + ++ +d +t + ++ +       
  gi|474935048|ref|YP_007688630.1|   4 IIGTGHVFKIGDS-VAFIVKHL--WPDAVCVELDDLRYhaligDREAVKKDLEARGIESD-GTPKGHMKNappvyRK 76 
                                       6788888874444.44444443..69****************999999999999999994.3333333320111134 PP

                              TraB  81 yarlqkalakrglplaaldkmkPwllalllslaelakkkagldpel..vDrylaktakragkpvgglEtveeqlsll 155
                                        ar+q+++++ + +       +P  +a +l++     k+++ +     +D++ ++ + +++ ++g +E++++ +s +
  gi|474935048|ref|YP_007688630.1|  77 NARYQERMSR-EHGS------QP--GADMLAAVTA-GKALDAH--IfcIDKDAQQVMAKMWNEMGTMERLRYRFSQI 141
                                       5566666666.5555......99..7777777775.3555553..236***********************888888 PP

                              TraB 156 ss.lpdeeqlealeetldeleeakdlleelveaykegdlealeleaeaeeefpelkevlldeRnrrwaekieallke 231
                                       s+ +  + ++ + +++       kd+ +  ve              ++++++p+l +vl+deRn+++a ki++ +++
  gi|474935048|ref|YP_007688630.1| 142 SDkIGGKRKVGKTQKDY---S--KDE-AAYVE--------------DFRRKYPTLVRVLIDERNEYMAAKIREVMET 198
                                       42255555444444333...3..332.45666..............8999*************************99 PP

                              TraB 232 pgsvfvaVGagHlaG 246
                                         +v v+VG gH+ G
  gi|474935048|ref|YP_007688630.1| 199 HSNVIVVVGDGHVDG 213
                                       9***********976 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0       0.2     7e+02      54      77 ..      37      60 ..      31      77 .. 0.66
   2 !   16.2   0.3   2.5e-06    0.0089      19      71 ..     167     217 ..     113     244 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.2
                                      SEEEEE-HHHHHHTEEEEEETTTC CS
                    HGTP_anticodon 54 pfavvvGekelekgtvtvrdrdtr 77
                                      ++   +G++e+ k+ ++ r  +++
  gi|474935048|ref|YP_007688630.1| 37 RYHALIGDREAVKKDLEARGIESD 60
                                      566677777777777777666555 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 2.5e-06
                                       HHHHHHHHTTT......SEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEE CS
                    HGTP_anticodon  19 kklaeeLraag......irvelddsnesigkkireadllgipfavvvGekelekgtvtv 71 
                                       ++               +rv +d++ne +  kire  +   +++vvvG+  + +g +++
  gi|474935048|ref|YP_007688630.1| 167 EDF-------RrkyptlVRVLIDERNEYMAAKIREVMETHSNVIVVVGDGHV-DGLLKL 217
                                       333.......13334449*******************************999.555544 PP

>> DIRP  DIRP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   1.5e-05     0.054       5     103 ..     106     204 ..     104     206 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.5e-05
                              DIRP   5 iDkplfeekndfeelLkesfpklktrrltraewrkirrllgkpRrfS...eaFleeEreeLeqkRekiRelqqrkve 78 
                                       +D ++f  ++d +++++++  ++ t +  r  +++i +++g  R++    + + ++E   +e+ R+k  +l +  ++
  gi|474935048|ref|YP_007688630.1| 106 LDAHIFCIDKDAQQVMAKMWNEMGTMERLRYRFSQISDKIGGKRKVGktqKDYSKDEAAYVEDFRRKYPTLVRVLID 182
                                       899**************************************999876222579999999999999998888777444 PP

                              DIRP  79 dleqllkdlpkeiplpLevgtkVta 103
                                       +    ++ ++++i + +e+  +V++
  gi|474935048|ref|YP_007688630.1| 183 E---RNEYMAAKIREVMETHSNVIV 204
                                       3...345577777777777777765 PP

>> ACP_PD  Acyl carrier protein phosphodiesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.8e-05      0.17      27     104 ..     105     177 ..      96     178 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.8e-05
                            ACP_PD  27 qlekneealPerlqrllprmieedwLesYaelegieralqrmarrlkrasklaeaieeleenyaeleadFleffpel 103
                                       +l+++   + +++q+++++m+     +++ ++e ++  +++++ ++  + k+ ++ ++  +++a++ +dF++ +p l
  gi|474935048|ref|YP_007688630.1| 105 ALDAHIFCIDKDAQQVMAKMW-----NEMGTMERLRYRFSQISDKIGGKRKVGKTQKDYSKDEAAYVEDFRRKYPTL 176
                                       566666677788999999999.....789**********************************************99 PP

                            ACP_PD 104 l 104
                                       +
  gi|474935048|ref|YP_007688630.1| 177 V 177
                                       6 PP

>> Cofac_haem_bdg  Haem-binding uptake, Tiki superfamily, ChaN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       1.8   6.5e+03     196     204 ..       2      10 ..       1      14 [. 0.79
   2 ?   12.3   2.3   3.4e-05      0.12     157     205 ..     117     212 ..      31     215 .. 0.63

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.8
                                       EEEEEHHHH CS
                    Cofac_haem_bdg 196 vviaGsgHv 204
                                       + i+G+gHv
  gi|474935048|ref|YP_007688630.1|   2 LTIIGTGHV 10 
                                       789*****9 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 3.4e-05
                                       -.................................................TTTHHHHHHHHHHHH.HHHHHHHHHHH CS
                    Cofac_haem_bdg 157 g.................................................eakeealerfveaQv.lwDetMAesia 183
                                       +                                                 e   ++++++v++ +  ++e MA +i+
  gi|474935048|ref|YP_007688630.1| 117 AqqvmakmwnemgtmerlryrfsqisdkiggkrkvgktqkdyskdeaayvEDFRRKYPTLVRVLIdERNEYMAAKIR 193
                                       03333333333333355566666666666666666666666665555544444444444444433236788*****9 PP

                                       H-SS.E.....EEEEEEHHHH- CS
                    Cofac_haem_bdg 184 aalkarnpgklvvviaGsgHve 205
                                       ++++    ++ v+v++G gHv+
  gi|474935048|ref|YP_007688630.1| 194 EVMET---HSNVIVVVGDGHVD 212
                                       88883...789*********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       768  (0.0428356); expected 358.6 (0.02)
Passed bias filter:                      612  (0.0341346); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:00.54
# Mc/sec: 1392.52
//
Query:       gi|474935049|ref|YP_007688631.1|  [L=80]
Description: hypothetical protein TALC_01500 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 461.13
//
Query:       gi|474935050|ref|YP_007688632.1|  [L=221]
Description: Haloacid Dehalogenase superfamily, subfamily IB, phosphoserine phosphatase-like protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.5e-16   60.6   0.0    3.8e-16   60.1   0.0    1.3  1  HAD          haloacid dehalogenase-like hydrolase
    9.8e-11   42.3   0.0    1.5e-06   28.7   0.0    2.1  2  Hydrolase    haloacid dehalogenase-like hydrolase
    6.2e-10   39.2   0.0      3e-07   30.4   0.0    3.0  3  Hydrolase_3  haloacid dehalogenase-like hydrolase
    1.5e-05   25.2   0.0      0.005   16.9   0.0    2.9  3  HAD_2        Haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   0.0   8.4e-20   3.8e-16       1     188 []       8     179 ..       8     179 .. 0.81

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 8.4e-20
                               HAD   1 alfDfDgTLldgdslelllrfllrrgaprlwralreklllalfrellrldraglaelleallagls.eelaaelerf 76 
                                       + fD+DgTL+   s + +++  l++++++ ++a +++    +       d++++++   al+ g + +  + +l + 
  gi|474935050|ref|YP_007688632.1|   8 VCFDMDGTLTKMRSSWKWIHDCLGVDSEPNYQAFLRQ---EI-------DEDEFMRRDIALWTGKRpGFSEGDLIHC 74 
                                       68**********9999888889999887664444444...33.......4456666778888888878889999999 PP

                               HAD  77 vaevirpklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevdd..rltgelglegkpvrg 151
                                       ++++    l+  g+ e +a  ++ G ++v++Sgg++  ++ l++e+g+d+++a ++ ++    l g     +k+v  
  gi|474935050|ref|YP_007688632.1|  75 FQDMP---LI-DGIQETVASLQECGMKCVIISGGIDLAAKMLMNEFGFDDCVADHVVTNPdgTLAGY---GEKIVDL 144
                                       95444...34.59999999999********************************9888755433333...3344444 PP

                               HAD 152 egkvaalrewlaaegegidleevvayGDspsDlpllr 188
                                       ++k  ++ e  +++ +g ++ ++v +G+s +D+p++r
  gi|474935050|ref|YP_007688632.1| 145 ADKGVWVTE--YQKRYGTTPGRTVSIGNSFTDIPMFR 179
                                       7888*****..************************97 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.1   4.4e-05       0.2       1      18 [.       5      22 ..       5      44 .. 0.86
   2 !   28.7   0.0   3.3e-10   1.5e-06     118     210 .]      79     182 ..      35     182 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.4e-05
                                      SSEEEEESBTTTBCHHHH CS
                                      xxxxxxxxxxxxxxxxxx RF
                         Hydrolase  1 iktvvfDkdGTLttgeps 18
                                      +++v+fD+dGTLt+ ++s
  gi|474935050|ref|YP_007688632.1|  5 YDLVCFDMDGTLTKMRSS 22
                                      589**********87765 PP

  == domain 2  score: 28.7 bits;  conditional E-value: 3.3e-10
                                       HBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT.GGGE.SEEEEHHCES.....STTTSHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxxxxx.....xxxxxxxxxxxxxxxxx RF
                         Hydrolase 118 kvkpeaaeavasLkaagievvlltgdnpetaeraanqlG.ddyf.daviasdiet.....vakpspegkvaaireLq 187
                                       ++ +++ e+vasL++ g + v+++g+    a+ ++n++G dd++ d+v++  + t      + ++  +k   + e+q
  gi|474935050|ref|YP_007688632.1|  79 PLIDGIQETVASLQECGMKCVIISGGIDLAAKMLMNEFGfDDCVaDHVVTNPDGTlagygEKIVDLADKGVWVTEYQ 155
                                       5899************************************9999899999999996665555558899999999998 PP

                                       ....STGGGEEEEESSHHHHHHHHHTT CS
                                       ....xxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 188 ....gkpeevamVGDgvnDaaalaaAg 210
                                             p +++ +G +++D++++++ g
  gi|474935050|ref|YP_007688632.1| 156 krygTTPGRTVSIGNSFTDIPMFRRSG 182
                                       777566****************99865 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.7   0.0    0.0096        43       1      11 [.       8      18 ..       8      27 .. 0.83
   2 ?    1.7   0.0      0.04   1.8e+02      19      57 ..      83     121 ..      75     144 .. 0.80
   3 !   30.4   0.0   6.8e-11     3e-07     186     248 ..     145     207 ..     132     214 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.0096
                                      EEEEIIIIIS- CS
                       Hydrolase_3  1 ialDlDGTLln 11
                                      +++D+DGTL +
  gi|474935050|ref|YP_007688632.1|  8 VCFDMDGTLTK 18
                                      689******76 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.04
                                       HHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSE CS
                       Hydrolase_3  19 ktkeaikklkekgikvviATGRslravlpvleelgldlp 57 
                                        ++e+++ l+e g+k vi +G    a++ +++e+g+d  
  gi|474935050|ref|YP_007688632.1|  83 GIQETVASLQECGMKCVIISGGIDLAAKMLMNEFGFDDC 121
                                       57899999*************999999999999998833 PP

  == domain 3  score: 30.4 bits;  conditional E-value: 6.8e-11
                                       -SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GGG CS
                       Hydrolase_3 186 vsKgtalkklakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnne 248
                                       ++Kg  +++++k+++ ++ +++++G++  Di+M+ ++g+++A +  +e    aA+ v+ks n 
  gi|474935050|ref|YP_007688632.1| 145 ADKGVWVTEYQKRYGTTPGRTVSIGNSFTDIPMFRRSGRSIAFNPMDEYTSGAATDVVKSDNI 207
                                       69********************************************************99986 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.011        51       2      13 ..       9      20 ..       8      54 .. 0.86
   2 !   16.9   0.0   1.1e-06     0.005      78     126 ..      78     126 ..      66     134 .. 0.87
   3 ?    0.8   0.0       0.1   4.6e+02     143     172 ..     153     182 ..     147     187 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.011
                             HAD_2  2 iFDlDgTlldte 13
                                       FD+DgTl   +
  gi|474935050|ref|YP_007688632.1|  9 CFDMDGTLTKMR 20
                                      6*******8765 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 1.1e-06
                             HAD_2  78 vkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdviv 126
                                       + ++dg++e++ +L+e g+k+ i++ + + a+++ ++++g+++     v
  gi|474935050|ref|YP_007688632.1|  78 MPLIDGIQETVASLQECGMKCVIISGGIDLAAKMLMNEFGFDDCVADHV 126
                                       6789*************************************98764433 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.1
                             HAD_2 143 kaleklklkkeeviyvGDsptDieaakkag 172
                                       +  +++++++ +++ +G s+tDi   ++ g
  gi|474935050|ref|YP_007688632.1| 153 EYQKRYGTTPGRTVSIGNSFTDIPMFRRSG 182
                                       556889999**************8887777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1341.46
//
Query:       gi|474935051|ref|YP_007688633.1|  [L=223]
Description: putative archaeal Zn-finger protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0032   17.6   0.1       0.65   10.2   0.0    2.7  2  Zn-ribbon_8     Zinc ribbon domain
     0.0052   16.7   1.0      0.014   15.3   1.0    1.8  1  Zn_ribbon_SprT  SprT-like zinc ribbon domain
     0.0095   16.3   0.3        1.2    9.7   0.0    2.4  2  zf-H2C2_2       Zinc-finger double domain
     0.0099   15.6   0.0       0.02   14.7   0.0    1.4  1  zf-C2H2_11      zinc-finger C2H2-type
  ------ inclusion threshold ------
        0.1   12.4   3.0        0.4   10.5   3.0    2.1  1  zinc_ribbon_5   zinc-ribbon domain
       0.17   11.7   4.0        5.8    6.9   0.3    2.6  2  TFIIS_C         Transcription factor S-II (TFIIS)
       0.35   10.4   5.8        2.4    7.7   5.8    2.4  1  TF_Zn_Ribbon    TFIIB zinc-binding
       0.67   10.9   2.8        3.9    8.6   0.2    2.5  2  zf-C2H2_4       C2H2-type zinc finger
        1.2    9.7   6.3        1.3    9.7   0.8    2.4  2  zf-C2H2         Zinc finger, C2H2 type
        2.4    8.3   5.6       0.41   10.7   0.5    2.1  2  zf-C2H2_6       C2H2-type zinc finger


Domain annotation for each model (and alignments):
>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1     0.022        39       6      16 ..      11      21 ..       8      28 .. 0.71
   2 !   10.2   0.0   0.00036      0.65       6      16 ..      38      48 ..      37      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.022
                       Zn-ribbon_8  6 YrCeeCghefe 16
                                      Y+C +C  + e
  gi|474935051|ref|YP_007688633.1| 11 YECPDCRDTTE 21
                                      77777776665 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00036
                       Zn-ribbon_8  6 YrCeeCghefe 16
                                      +rC+eCg++f+
  gi|474935051|ref|YP_007688633.1| 38 FRCTECGRVFT 48
                                      9*********8 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   1.0   7.8e-06     0.014       2      36 ..       8      49 ..       7      51 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 7.8e-06
                    Zn_ribbon_SprT  2 kyvYrCtgCgreythhlsi.rrhn......YrCrrCkgtLrg 36
                                      + vY C++C+++ +h   + r  n       rC  C+ +++g
  gi|474935051|ref|YP_007688633.1|  8 TIVYECPDCRDTTEHKILKaRLGNsnvtgtFRCTECGRVFTG 49
                                      569************98888****************988876 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0   0.00068       1.2      12      26 .]       7      22 ..       1      22 [. 0.80
   2 ?    4.6   0.1     0.028        49      15      25 ..      38      48 ..      31      48 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00068
                         zf-H2C2_2 12 ekp.yeCplCdkaFkt 26
                                      +++ yeCp C++++ +
  gi|474935051|ref|YP_007688633.1|  7 DTIvYECPDCRDTTEH 22
                                      5666********9865 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.028
                         zf-H2C2_2 15 yeCplCdkaFk 25
                                      + C +C+ +F+
  gi|474935051|ref|YP_007688633.1| 38 FRCTECGRVFT 48
                                      89******996 PP

>> zf-C2H2_11  zinc-finger C2H2-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.1e-05      0.02       3      20 ..      36      53 ..      35      56 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.1e-05
                        zf-C2H2_11  3 stcqCleCGlcftSqlsL 20
                                       t++C+eCG+ ft  + L
  gi|474935051|ref|YP_007688633.1| 36 GTFRCTECGRVFTGTIRL 53
                                      69***********87765 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   3.0   0.00023       0.4       4      36 ..      12      48 ..       9      49 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00023
                     zinc_ribbon_5  4 rCpdCd..tkFklvdsklKksg..kkVrCakCaevFd 36
                                       CpdC+  t  k+   +l +s   +  rC  C+ vF+
  gi|474935051|ref|YP_007688633.1| 12 ECPDCRdtTEHKILKARLGNSNvtGTFRCTECGRVFT 48
                                      7****8667899999999887622579*********8 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.3    0.0032       5.8      21      35 ..       2      17 ..       1      20 [. 0.84
   2 ?    5.6   0.3    0.0079        14      28      39 .]      37      48 ..      32      48 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0032
                           TFIIS_C 21 aDE.pmtvfykCtkCg 35
                                      aDE p t+ y+C +C 
  gi|474935051|ref|YP_007688633.1|  2 ADElPDTIVYECPDCR 17
                                      677699*********7 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0079
                           TFIIS_C 28 fykCtkCghrWr 39
                                       ++Ct+Cg  ++
  gi|474935051|ref|YP_007688633.1| 37 TFRCTECGRVFT 48
                                      699*****9885 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   5.8    0.0013       2.4       1      28 [.      11      46 ..      11      48 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0013
                                      EEETTTTCEE.C......HEE.TSTTCEEESSSSBE CS
                      TF_Zn_Ribbon  1 ykCPnCgstn.l......veD.pergelvCtdCGlV 28
                                      y CP+C  t+        + + + +g+++Ct+CG V
  gi|474935051|ref|YP_007688633.1| 11 YECPDCRDTTeHkilkarLGNsNVTGTFRCTECGRV 46
                                      5688888765347787776665779*********98 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.2      0.25   4.4e+02       1       7 [.      11      17 ..      11      23 .. 0.83
   2 ?    8.6   0.2    0.0022       3.9       1      11 [.      38      48 ..      38      53 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.25
                         zf-C2H2_4  1 fkCpiCg 7 
                                      ++Cp C+
  gi|474935051|ref|YP_007688633.1| 11 YECPDCR 17
                                      89****5 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0022
                         zf-C2H2_4  1 fkCpiCgksFs 11
                                      f+C+ Cg++F+
  gi|474935051|ref|YP_007688633.1| 38 FRCTECGRVFT 48
                                      89********6 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.5      0.13   2.4e+02       1       6 [.      11      16 ..      11      23 .. 0.89
   2 ?    9.7   0.8    0.0007       1.3       1      11 [.      38      48 ..      38      50 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.13
                                      EEETTT CS
                           zf-C2H2  1 ykCpdC 6 
                                      y+CpdC
  gi|474935051|ref|YP_007688633.1| 11 YECPDC 16
                                      99**** PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0007
                                      EEETTTTEEES CS
                           zf-C2H2  1 ykCpdCgksFk 11
                                      ++C++Cg++F+
  gi|474935051|ref|YP_007688633.1| 38 FRCTECGRVFT 48
                                      89********7 PP

>> zf-C2H2_6  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.5      0.94   1.7e+03       1       7 [.      10      16 ..      10      17 .. 0.88
   2 ?   10.7   0.5   0.00023      0.41       2      11 ..      38      47 ..      37      48 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.94
                         zf-C2H2_6  1 vheCsvC 7 
                                      v+eC+ C
  gi|474935051|ref|YP_007688633.1| 10 VYECPDC 16
                                      7***988 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00023
                         zf-C2H2_6  2 heCsvCsksF 11
                                      ++C++C+++F
  gi|474935051|ref|YP_007688633.1| 38 FRCTECGRVF 47
                                      9********* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1404.49
//
Query:       gi|474935052|ref|YP_007688634.1|  [L=195]
Description: Zn-dependent hydrolase, including glyoxylase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-21   76.2   0.3    5.9e-19   68.9   0.3    2.1  1  Lactamase_B    Metallo-beta-lactamase superfamily
    3.4e-05   23.4   0.1    8.2e-05   22.2   0.1    1.8  1  Lactamase_B_2  Beta-lactamase superfamily domain
    4.4e-05   23.4   0.0    8.1e-05   22.6   0.0    1.4  1  Lactamase_B_3  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.018   14.5   0.0      0.027   13.9   0.0    1.2  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.9   0.3   1.3e-22   5.9e-19       2     197 .]      23     186 ..      22     186 .. 0.86

  Alignments for each domain:
  == domain 1  score: 68.9 bits;  conditional E-value: 1.3e-22
                                       CCCSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHT.SGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEH CS
                       Lactamase_B   2 gpdpvnsyliegdggviLiDtGtsteaaraalelaalg.lkpkdvdavilTHlHlDHiGglgglveatdvpvgavae 77 
                                       g+++++s+li+ +g++i++Dt +++ ++ ++ +l+++g + p+d+d+v+lTH H+DHiG++g +++a  +    ++ 
  gi|474935052|ref|YP_007688634.1|  23 GETFSTSTLIRCPGHNIVVDTSGESMKPGIKIALKQIGkVFPEDIDTVVLTHVHPDHIGNNGMFPKAKVII---HSG 96 
                                       67899***************************999997479***********************9876544...333 PP

                                       HHHCCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSS CS
                       Lactamase_B  78 eapalfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDalla 154
                                       e+ ++                         +++e+++++ + ++ l++t+g+  g++++ ve ++++++++GDa+++
  gi|474935052|ref|YP_007688634.1|  97 EELEGA------------------------EVIEVDEVEIAKGVKLVHTPGHSAGSMSVFVEGEDRRYAIAGDAIPT 149
                                       333333........................4566888**************************************** PP

                                       HHCCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                       Lactamase_B 155 getgridltlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                        +++  +      ++r  +d +++l+s+ ++    a+v+vpgH
  gi|474935052|ref|YP_007688634.1| 150 KDNLVKGI-----PPRLNVDEKQALESMNRI-SKWADVIVPGH 186
                                       ********.....777777777777777755.77899999998 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.1   1.8e-08   8.2e-05       1      48 [.      37      83 ..      37     157 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.8e-08
                                      SEEEES--TTHHHH.HTCGGS--SSS--..SEEEEE-SS--HHHHGGGG CS
                     Lactamase_B_2  1 rriLiDagpdlrqq.alralqPvelrdelppidaVllthaHyDHlagll 48
                                      ++i++D++ + +++  + al++   +  +++id V+lth H DH+ +  
  gi|474935052|ref|YP_007688634.1| 37 HNIVVDTSGESMKPgIKIALKQIG-KVFPEDIDTVVLTHVHPDHIGN-N 83
                                      89******9988888666663333.333569**************44.3 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   1.8e-08   8.1e-05       8      99 ..      28     132 ..      26     143 .. 0.69

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.8e-08
                     Lactamase_B_3   8 nsflletagarilvDPfkanlgyeppa...........eeaDlvlisqaledHahletlkqlaenvkvlee.ges.. 70 
                                       +s l++ +g +i+vD   ++++ ++ +           e++D v++++ ++dH   + + +   ++kv+ + ge+  
  gi|474935052|ref|YP_007688634.1|  28 TSTLIRCPGHNIVVDTSGESMKPGI-KialkqigkvfpEDIDTVVLTHVHPDHIGNNGMFP---KAKVIIHsGEEle 100
                                       7999***********8743222222.134566888999*******************9999...6666655244455 PP

                     Lactamase_B_3  71 ....levggleir.avatshdavggsergenngf 99 
                                           +ev+++ei  +v+  h  ++g+  g  ++f
  gi|474935052|ref|YP_007688634.1| 101 gaevIEVDEVEIAkGVKLVH--TPGHSAGSMSVF 132
                                       55557788887751445555..455555555555 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   5.9e-06     0.027       4      52 ..      34      83 ..      31      96 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.9e-06
                     Lactamase_B_6  4 ldnvkiLlDvGwdeskvslesalkelekvip.tvdliLLshatlehlGay 52
                                        + +i +D + ++ k  ++ alk++ kv p ++d ++L+h  ++h+G  
  gi|474935052|ref|YP_007688634.1| 34 CPGHNIVVDTSGESMKPGIKIALKQIGKVFPeDIDTVVLTHVHPDHIGNN 83
                                      556789*********999**********98648***************65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1233.31
//
Query:       gi|474935053|ref|YP_007688635.1|  [L=188]
Description: HemK-related putative methylase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.6e-19   67.9   0.0    5.1e-18   65.2   0.0    1.9  1  MTS              Methyltransferase small domain
    5.7e-11   43.0   0.0    1.1e-10   42.1   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    7.1e-11   42.0   0.1    1.1e-10   41.4   0.1    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    2.4e-10   40.4   0.0    2.9e-10   40.1   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    4.5e-08   33.1   0.0      2e-07   31.0   0.0    1.8  2  Methyltransf_23  Methyltransferase domain
    8.8e-08   32.7   0.0    1.6e-07   31.9   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    3.5e-07   29.8   0.0      5e-07   29.3   0.0    1.2  1  TehB             Tellurite resistance protein TehB
    1.9e-06   28.6   0.2    4.1e-06   27.5   0.0    1.6  1  Methyltransf_12  Methyltransferase domain
    5.1e-05   23.1   0.1    7.2e-05   22.6   0.1    1.2  1  Methyltransf_16  Lysine methyltransferase
    9.9e-05   21.8   0.0    0.00013   21.4   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
    0.00014   21.7   0.0    0.00021   21.1   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0015   18.2   0.0     0.0018   17.9   0.0    1.1  1  NodS             Nodulation protein S (NodS)
     0.0033   17.2   0.1     0.0046   16.7   0.1    1.1  1  Met_10           Met-10+ like-protein
     0.0046   16.9   0.0     0.0063   16.4   0.0    1.2  1  Methyltransf_18  Methyltransferase domain
     0.0063   16.1   0.1     0.0076   15.8   0.1    1.1  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
  ------ inclusion threshold ------
      0.017   14.3   0.0       0.02   14.0   0.0    1.1  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
       0.02   14.6   0.1        0.1   12.2   0.2    2.0  2  UPF0020          Putative RNA methylase family UPF0020
      0.031   14.0   0.0      0.049   13.3   0.0    1.2  1  GCD14            tRNA methyltransferase complex GCD14 subunit
      0.043   13.4   0.0       0.06   13.0   0.0    1.2  1  Cons_hypoth95    Conserved hypothetical protein 95
       0.15   12.1   0.0       0.29   11.1   0.0    1.5  2  rRNA_methylase   Putative rRNA methylase
       0.22   10.4   0.0       0.29   10.1   0.0    1.1  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase


Domain annotation for each model (and alignments):
>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.2   0.0     6e-21   5.1e-18      20     153 ..      22     163 ..       6     175 .. 0.79

  Alignments for each domain:
  == domain 1  score: 65.2 bits;  conditional E-value: 6e-21
                                       HHHHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS CS
                               MTS  20 sklLletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveek 96 
                                       s +++e+l+ ++  +vl +GcG Gv+++++a +  e  vt+ dv+ +A+e+a++n+ean++++++v +dv++ ++ +
  gi|474935053|ref|YP_007688635.1|  22 SVMFIEALEIRRGMRVLEIGCGSGVVSIHCALNGAE--VTCGDVNPKAVELANRNAEANGVRINAVGTDVYSGID-G 95 
                                       678999****9999*****************97666..9************************************.* PP

                                       -EEEEEE---S............TTTCHCHHHHHHHHHHHHHHHEEEEEEEEEEEETTSCHHHHHHHHH CS
                               MTS  97 kfdlivsNPPf............hagkatelavaeeliaeAkeaLkegGeLliVanrklgyeslleelf 153
                                       kfdli+ N P+             +g +       +l++ A+e+L +gG+  +V+++ ++ ++ lee++
  gi|474935053|ref|YP_007688635.1|  96 KFDLILFNLPYlpvdeegelakaWSGGEDGMGPLPRLLEGAPEHLLPGGRVAVVVSSLMDRKR-LEEVI 163
                                       ********8873222111111111223333445679*****************9988776544.45555 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.0   1.2e-13   1.1e-10       1      80 [.      37     110 ..      37     120 .. 0.86

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 1.2e-13
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGS CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhl 77 
                                       vL++GcG+G +++++a ++  a+vt+ D++++++e a+++ae++g++++ v  d+ +    dg+fDl++ +  l +l
  gi|474935053|ref|YP_007688635.1|  37 VLEIGCGSGVVSIHCALNG--AEVTCGDVNPKAVELANRNAEANGVRINAVGTDVYSG--IDGKFDLILFN--LPYL 107
                                       9***************884..********************************99664..589*****995..5666 PP

                                       SHH CS
                   Methyltransf_25  78 sde 80 
                                       + +
  gi|474935053|ref|YP_007688635.1| 108 PVD 110
                                       544 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.1   1.3e-13   1.1e-10     152     233 ..      26     103 ..      19     108 .. 0.79

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 1.3e-13
                              PrmA 152 lealeklvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellk..eek 226
                                       +eale  +++g +vl +G+GSG+ +i  a+ ga +v+  D+++ Av+ a++Nae N+v+ +  v    ++ +  ++k
  gi|474935053|ref|YP_007688635.1|  26 IEALE--IRRGMRVLEIGCGSGVVSIHCALNGA-EVTCGDVNPKAVELANRNAEANGVRINA-V--GTDVYSgiDGK 96 
                                       44444..78999**************9987776.57777*******************9987.3..33333333499 PP

                              PrmA 227 advivaN 233
                                       +d+i+ N
  gi|474935053|ref|YP_007688635.1|  97 FDLILFN 103
                                       9999988 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.0   3.4e-13   2.9e-10       2     113 ..      32     152 ..      31     180 .. 0.86

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 3.4e-13
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDl 77 
                                       ++g+rvl++GCG+G  ++  a     +aev+  D +++a+elA+ na+ +g+ +++    d+ + ++      kfDl
  gi|474935053|ref|YP_007688635.1|  32 RRGMRVLEIGCGSGVVSIHCA---LNGAEVTCGDVNPKAVELANRNAEANGV-RINAVGTDVYSgID-----GKFDL 99 
                                       689******************...3479************************.5**********999.....99*** PP

                   Methyltransf_31  78 ilsnevl.................naladpdkileeiervlkpggilliedpr 113
                                       il n +                  + +  ++  le++++ l pgg++++   +
  gi|474935053|ref|YP_007688635.1| 100 ILFNLPYlpvdeegelakawsggeDGMGPLPRLLEGAPEHLLPGGRVAVVVSS 152
                                       ****5545555555556778999999999999999999999999999987666 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   2.3e-10     2e-07      20      88 ..      31     102 ..      15     106 .. 0.74
   2 ?   -0.4   0.0         1   8.8e+02      98     127 ..     129     156 ..     124     180 .. 0.77

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 2.3e-10
                   Methyltransf_23  20 lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfdeqeaaepqg...kfdlIvl 88 
                                        r+g+rvL+iGcG+G ++ +++ ng++vt  D +p+ave+a     a+ +  ++   ++ +g   kfdlI  
  gi|474935053|ref|YP_007688635.1|  31 IRRGMRVLEIGCGSGVVSIHCALNGAEVTCGDVNPKAVELANRNAEANGVRINAVGTDVYSGidgKFDLILF 102
                                       6999************************************96444333333333333443335558888865 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1
                   Methyltransf_23  98 ppellrqiatllkpgGylllseplaslked 127
                                       +p+ll  + ++l pgG++ + ++  sl  +
  gi|474935053|ref|YP_007688635.1| 129 LPRLLEGAPEHLLPGGRVAVVVS--SLMDR 156
                                       6888999999999**99988887..33344 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   1.8e-10   1.6e-07       1      68 [.      38     103 ..      38     119 .. 0.91

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 1.8e-10
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEE CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvss 68 
                                       L++GcG+G ++ ++a +ga+v++ D+++++++la+++a+ +g++++ v  d+ +    d++fDl++ +
  gi|474935053|ref|YP_007688635.1|  38 LEIGCGSGVVSIHCALNGAEVTCGDVNPKAVELANRNAEANGVRINAVGTDVYS--GIDGKFDLILFN 103
                                       89****************************************987777777776..7899****9876 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   5.9e-10     5e-07      22     101 ..      25     102 ..      14     113 .. 0.90

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 5.9e-10
                                       HHHHCCCS-S-EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG----S-EEE CS
                              TehB  22 vveavkivkpgkvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydineaklderydf 98 
                                        +ea +i +  +vl++gcg+g  s++ +l+g +vt+ d n ++++  ++ +e + ++ i++   d+ +  +d ++d+
  gi|474935053|ref|YP_007688635.1|  25 FIEALEIRRGMRVLEIGCGSGVVSIHCALNGAEVTCGDVNPKAVELANRNAEANGVR-INAVGTDVYS-GIDGKFDL 99 
                                       47999*********************************************9999998.9999999875.69999999 PP

                                       EEE CS
                              TehB  99 ils 101
                                       il 
  gi|474935053|ref|YP_007688635.1| 100 ILF 102
                                       986 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   4.8e-09   4.1e-06       1      72 [.      38     102 ..      38     106 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 4.8e-09
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvva 72 
                                       LeiGcG+G ++ +++ +  ++e+t+ D++p+a+   +++ a+ ++ + n v  ++ + +d     +fDl++ 
  gi|474935053|ref|YP_007688635.1|  38 LEIGCGSGVVSIHCALN--GAEVTCGDVNPKAV-ELANRNAEANGVRINAVGTDVYSGIDG----KFDLILF 102
                                       8****************..**************.888888999999999999999998876....9***985 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.1   8.4e-08   7.2e-05      45      94 ..      32      80 ..      13      93 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 8.4e-08
                   Methyltransf_16 45 lsklsvlELGsGtGlvGlavaellpeakviltDlee.llellkknielnkn 94
                                      +++++vlE+G G+G+v +  a+   +a+v+  D++  ++el ++n e+n+ 
  gi|474935053|ref|YP_007688635.1| 32 RRGMRVLEIGCGSGVVSIHCALN--GAEVTCGDVNPkAVELANRNAEANGV 80
                                      57899****************99..********98669**********873 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.5e-07   0.00013      53     131 ..      24     100 ..      19     102 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.5e-07
                                       HHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-----S CS
                              CMAS  53 lileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedldekvd 129
                                       + +e le++ Gm++L+iGcG G + ++ + + +++v    +  +  +la+++ ++ +  r + v    y  +d+k+d
  gi|474935053|ref|YP_007688635.1|  24 MFIEALEIRRGMRVLEIGCGSGVVSIHCALN-GAEVTCGDVNPKAVELANRNAEANG-VRINAVGTDVYSGIDGKFD 98 
                                       56799************************99.****999999999999999888888.6788899999999999999 PP

                                       EE CS
                              CMAS 130 rv 131
                                        +
  gi|474935053|ref|YP_007688635.1|  99 LI 100
                                       76 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   2.5e-07   0.00021      64      89 ..      24      49 ..       6      99 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.5e-07
                                      HHHHHTT--TT-EEEEES-TTSHHHH CS
                              PCMT 64 lalellelkkgarvLevGsGsGylta 89
                                      +++e le+++g+rvLe+G+GsG  + 
  gi|474935053|ref|YP_007688635.1| 24 MFIEALEIRRGMRVLEIGCGSGVVSI 49
                                      789*******************8654 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   2.2e-06    0.0018      39     112 ..      29     102 ..      12     118 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.2e-06
                              NodS  39 laqgsiadalevGcaaGalterlapyckrltvvdvveeaiararervk.esshiswivsdvqqfstdekfdlivv 112
                                       l+ ++   +le+Gc +G ++ + a     +t  dv ++a++ a++  + +   i+ + +dv     d kfdli+ 
  gi|474935053|ref|YP_007688635.1|  29 LEIRRGMRVLEIGCGSGVVSIHCALNGAEVTCGDVNPKAVELANRNAEaNGVRINAVGTDVYS-GIDGKFDLILF 102
                                       555666789********************************9977665156789999999975.68999999975 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   5.4e-06    0.0046      98     177 ..      31     105 ..      22     111 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.4e-06
                                       --TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---TT-EEEEEE CS
                            Met_10  98 veegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevireqladrvvm 174
                                       ++ g +V+++  G G  +i +a   ++ +v   d+nP++v++ ++n + N v   ++++ +D+   i + ++d ++ 
  gi|474935053|ref|YP_007688635.1|  31 IRRGMRVLEIGCGSGVVSIHCAL--NGAEVTCGDVNPKAVELANRNAEANGVR--INAVGTDVYSGI-DGKFDLILF 102
                                       567889999*************9..9999*********************995..777888887776.777777777 PP

                                       --T CS
                            Met_10 175 nlp 177
                                       nlp
  gi|474935053|ref|YP_007688635.1| 103 NLP 105
                                       776 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   7.4e-06    0.0063      12      78 ..      31      93 ..      26     102 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.4e-06
                   Methyltransf_18 12 vekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGlekl 78
                                      +++g rv+ iG+  g+++i+ + +g   +v+  D+n++++e a++n+e +g+  +i+++ +d  + +
  gi|474935053|ref|YP_007688635.1| 31 IRRGMRVLEIGCGSGVVSIHCALNGA--EVTCGDVNPKAVELANRNAEANGV--RINAVGTDVYSGI 93
                                      678999****************9996..59*******************999..5666666655555 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   8.9e-06    0.0076       4      58 ..      37      89 ..      34     125 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8.9e-06
                   Methyltransf_15  4 ilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdv 58
                                      +l + +G+G  +i+ al++ +v + ++n++ +++a++Nae+ gv  +i  v  dv
  gi|474935053|ref|YP_007688635.1| 37 VLEIGCGSGVVSIHCALNGAEVTCGDVNPKAVELANRNAEANGV--RINAVGTDV 89
                                      79999************************************987..566666665 PP

>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.4e-05      0.02      47     100 ..      31      81 ..       7     100 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.4e-05
                                       H-S-EEEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHHHTT-- CS
                               TRM  47 lgekikvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNvklneve 100
                                       + + ++vl+   +sG+ +i  al      ev   D+++kAvel ++N++ n v 
  gi|474935053|ref|YP_007688635.1|  31 IRRGMRVLEIGCGSGVVSIHCALN---GAEVTCGDVNPKAVELANRNAEANGVR 81 
                                       44568999999***********98...778999**************9999987 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   0.00012       0.1      49     131 ..      54     106 ..      25     117 .. 0.70
   2 ?   -2.8   0.0       4.9   4.2e+03     153     182 ..     137     169 ..     130     177 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                                       HHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EE CS
                           UPF0020  49 lganiapgllrefvlelkaeaeeearaelklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvi 125
                                        ga                          ++ + D ++++v+ a++Nae+ gv   i+++  d+ +    +g++d+i
  gi|474935053|ref|YP_007688635.1|  54 NGA--------------------------EVTCGDVNPKAVELANRNAEANGVR--INAVGTDVYSGI--DGKFDLI 100
                                       444..........................4568888888888888888877764..555665665333..4678888 PP

                                       EE---- CS
                           UPF0020 126 vtnpPY 131
                                       + n+PY
  gi|474935053|ref|YP_007688635.1| 101 LFNLPY 106
                                       888888 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.9
                                       HHH-TT..-EEEEEES...SHHHHHCC---ESE CS
                           UPF0020 153 krvlrgggrlvlltse...nkalekaleeralr 182
                                        ++l  ggr ++++s+   +k le++++ r  r
  gi|474935053|ref|YP_007688635.1| 137 PEHLLPGGRVAVVVSSlmdRKRLEEVIGGRPCR 169
                                       556666677766665411155666666666555 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   5.7e-05     0.049      28      56 ..      21      49 ..      15      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.7e-05
                             GCD14 28 DisliimkLelkpGsvvvesGtGsgslsh 56
                                      D  + i  Le++ G +v+e G Gsg +s 
  gi|474935053|ref|YP_007688635.1| 21 DSVMFIEALEIRRGMRVLEIGCGSGVVSI 49
                                      6778899******************9995 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     7e-05      0.06      41     123 ..      33     106 ..      22     117 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7e-05
                                       CC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEE CS
                     Cons_hypoth95  41 egarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdiv 117
                                       +g rvL++ +GsG++++ ++  g +++++ + +++av++ ++n e+ +++  ++++  d ++ ++ +      fd++
  gi|474935053|ref|YP_007688635.1|  33 RGMRVLEIGCGSGVVSIHCALNG-AEVTCGDVNPKAVELANRNAEANGVR--INAVGTDVYSGIDGK------FDLI 100
                                       5789*****************99.579******************99965..566666666655444......7888 PP

                                       EE--SS CS
                     Cons_hypoth95 118 flDPPy 123
                                        ++ Py
  gi|474935053|ref|YP_007688635.1| 101 LFNLPY 106
                                       777777 PP

>> rRNA_methylase  Putative rRNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00034      0.29       2      59 ..      59     111 ..      58     121 .. 0.83
   2 ?   -3.2   0.0         9   7.6e+03      74      90 ..     134     150 ..     131     151 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00034
                                       EEEES-HHHHHHHHHHHHHTT-GGSEEEEES-GGGGGGT--S-EEEEEEEESB-CTS- CS
                    rRNA_methylase   2 yafDiQeeAleatkerleeekleervelildsHekleeyvkekvkavifNLGYLPggd 59 
                                       ++ D+  +A+e ++++ e+++++     i++  +++ + +++k+++++fNL YLP  +
  gi|474935053|ref|YP_007688635.1|  59 TCGDVNPKAVELANRNAEANGVR-----INAVGTDVYSGIDGKFDLILFNLPYLPVDE 111
                                       56688888888888888888886.....7777888999999**************765 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 9
                                       HHHHHHEEEEEEEEEEE CS
                    rRNA_methylase  74 ekalelLkkgGlitivv 90 
                                       e a e L +gG++++vv
  gi|474935053|ref|YP_007688635.1| 134 EGAPEHLLPGGRVAVVV 150
                                       66778899999999986 PP

>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00034      0.29     202     248 ..      33      80 ..      21      86 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00034
                   tRNA_U5-meth_tr 202 kg.dllelycGnGnfslalarnfekvlateiakssveaaqyniaanki 248
                                       +g  +le+ cG G  s+  a n   v   ++   +ve a  n +an +
  gi|474935053|ref|YP_007688635.1|  33 RGmRVLEIGCGSGVVSIHCALNGAEVTCGDVNPKAVELANRNAEANGV 80 
                                       44378*****************************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.40u 0.18s 00:00:00.58 Elapsed: 00:00:00.36
# Mc/sec: 1576.37
//
Query:       gi|474935054|ref|YP_007688636.1|  [L=218]
Description: haloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-38  132.1   0.0    2.8e-38  131.8   0.0    1.1  1  HAD_2           Haloacid dehalogenase-like hydrolase
    4.2e-20   73.0   0.1    2.7e-17   63.8   0.1    2.1  1  Hydrolase       haloacid dehalogenase-like hydrolase
    3.1e-08   34.2   0.0    4.1e-08   33.9   0.0    1.2  1  HAD             haloacid dehalogenase-like hydrolase
    5.5e-06   26.2   0.0    4.6e-05   23.2   0.0    2.0  1  NIF             NLI interacting factor-like phosphatase
    7.8e-06   25.9   0.0    1.4e-05   25.0   0.0    1.5  1  Hydrolase_like  HAD-hyrolase-like
    0.00015   21.8   0.0      0.005   16.9   0.0    3.1  1  Hydrolase_6     Haloacid dehalogenase-like hydrolase
     0.0012   18.7   0.1       0.82    9.4   0.0    2.1  2  Hydrolase_3     haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.8   0.0   1.1e-41   2.8e-38       1     178 []       4     184 ..       4     184 .. 0.94

  Alignments for each domain:
  == domain 1  score: 131.8 bits;  conditional E-value: 1.1e-41
                             HAD_2   1 iiFDlDgTlldteeliiqafnelleeyglselseeelrkliglslrellrklgeseeeee....kieellrkyneek 73 
                                       +iFD+DgTl+dte++ i ++ e+ +++g+  ++++++ ++  l++r + +++ e+   +      + e +r ++++ 
  gi|474935054|ref|YP_007688636.1|   4 VIFDMDGTLIDTEKFNIMFWCEAGKKFGF-GITPDDVIHIRSLDSRLVAKYFRERFGDSFdfetVRGERRRLMRAHV 79 
                                       7****************************.89999**********99998888877766666766677777788888 PP

                             HAD_2  74 kkkevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekaleklkl 150
                                       + + ++p +g++e+L++Lk  g kl+++T +++e +++ leq+g++++Fd +++++ ve+ KP+p+v++ a++ l++
  gi|474935054|ref|YP_007688636.1|  80 EANGIEPKPGIREVLDYLKGTGAKLAVATASTQEHADDYLEQIGVKDMFDMVISTHSVENGKPAPDVYLYACRCLGF 156
                                       889************************************************************************** PP

                             HAD_2 151 kkeeviyvGDsptDieaakkagikviav 178
                                       ++++++ v+D p++ie+a +ag++v+ v
  gi|474935054|ref|YP_007688636.1| 157 DPKDCVAVEDAPFGIESAYRAGCHVVTV 184
                                       ************************9976 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.8   0.1     1e-20   2.7e-17       1     210 []       1     178 [.       1     178 [. 0.76

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 1e-20
                                       SSEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrgayaigkpewl 77 
                                       +k+v+fD+dGTL+++e+    ++++a                gk++         ++  ++ +  r  +a+      
  gi|474935054|ref|YP_007688636.1|   1 MKAVIFDMDGTLIDTEKFNIMFWCEA----------------GKKFGFGITPD--DVIHIRSLDSR-LVAKY----- 53 
                                       79**************8888899999................33332222222..22222221111.22222..... PP

                                       HHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  78 taldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanq 154
                                           + + +g+  + +  +g+   l   ra+ +    +   +kp+++e++ +Lk  g +++++t + +e+a+  ++q
  gi|474935054|ref|YP_007688636.1|  54 ----FRERFGDSFDFETVRGERRRLM--RAHVEANGIE---PKPGIREVLDYLKGTGAKLAVATASTQEHADDYLEQ 121
                                       ....2333455555566666666666..5555555554...6*********************************** PP

                                       TT.GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 155 lG.ddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                       +G +d fd vi++  ++ +kp p+ +++a+r L+ +p+++++V+D + +++ + +Ag
  gi|474935054|ref|YP_007688636.1| 122 IGvKDMFDMVISTHSVENGKPAPDVYLYACRCLGFDPKDCVAVEDAPFGIESAYRAG 178
                                       **********************************************99999887776 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0   1.6e-11   4.1e-08       1     134 [.       4     139 ..       4     177 .. 0.73

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 1.6e-11
                               HAD   1 alfDfDgTLldgdsle.lllrfllrrgaprlwralreklllalfrellrldraglaelleallagls.eelaaeler 75 
                                       ++fD+DgTL+d++ +  +++   +++++         +++  +   ++ ++r+ ++ + e++  +++ e +  e +r
  gi|474935054|ref|YP_007688636.1|   4 VIFDMDGTLIDTEKFNiMFWCEAGKKFGFGI------TPDDVI-HIRSLDSRLVAKYFRERFGDSFDfETVRGERRR 73 
                                       79**********6666677775776655442......222222.445555566777788888888888888888888 PP

                               HAD  76 fv.....aevirpklldpgalellaahraaGdrvvvvSgglrplvepllaelg....adevlat.elev 134
                                       ++     a  i+pk   pg++e+l+  +  G +++v +++ ++ +   l++ g    +d v++t ++e 
  gi|474935054|ref|YP_007688636.1|  74 LMrahveANGIEPK---PGIREVLDYLKGTGAKLAVATASTQEHADDYLEQIGvkdmFDMVISThSVEN 139
                                       88544444455555...8***********************************99999999*9933333 PP

>> NIF  NLI interacting factor-like phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   1.8e-08   4.6e-05       2     149 ..       3     205 ..       2     213 .. 0.72

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.8e-08
                               NIF   2 tLVLDLDetLvhskleksk...........................................klkvegekvevsvlk 35 
                                        +++D+D+tL+ ++    +                                           +  +e+ + e + l+
  gi|474935054|ref|YP_007688636.1|   3 AVIFDMDGTLIDTEK-F-NimfwceagkkfgfgitpddvihirsldsrlvakyfrerfgdsfD--FETVRGERRRLM 75 
                                       688999999997772.2.122445555567777777777777777777766666666666441..222223333333 PP

                               NIF  36 R...........pgldefLkelskl.yevvifTasseeyaeavidildpekkllshrlyrescvkkkg.....eyvK 95 
                                       R           pg +e L++l    +++ + Tas++e a++ ++++  +   ++ +++ +s+   +g      y+ 
  gi|474935054|ref|YP_007688636.1|  76 RahveangiepkPGIREVLDYLKGTgAKLAVATASTQEHADDYLEQIGVKDM-FDMVISTHSVE--NGkpapdVYLY 149
                                       344444455555*********98777*********************99875.99999999994..44235667888 PP

                               NIF  96 dLsllgrdlsrvvivDdspdsfelqpengipiksf..fsdkkDneLlkllpllkel 149
                                         + lg d ++ v v+d p  +e+  + g+++ +   +s++++++L  l  + ++l
  gi|474935054|ref|YP_007688636.1| 150 ACRCLGFDPKDCVAVEDAPFGIESAYRAGCHVVTVpdVSEPDEKQLDMLECVAETL 205
                                       888899******************99999999998656688888888776666655 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   5.6e-09   1.4e-05       3      49 ..     140     185 ..     138     206 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 5.6e-09
                                       STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEES CS
                    Hydrolase_like   3 gKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVl 49 
                                       gKP+p +y +a + lg dp++++++ D     i++A +aG++ v V 
  gi|474935054|ref|YP_007688636.1| 140 GKPAPDVYLYACRCLGFDPKDCVAVEDA-PFGIESAYRAGCHVVTVP 185
                                       9***************************.9*************9985 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0     2e-06     0.005       1      55 [.       4     123 ..       4     148 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2e-06
                                       EEEESTTTSE................................................................... CS
                       Hydrolase_6   1 flfDidGvLw................................................................... 10 
                                       ++fD+dG+L+                                                                   
  gi|474935054|ref|YP_007688636.1|   4 VIFDMDGTLIdtekfnimfwceagkkfgfgitpddvihirsldsrlvakyfrerfgdsfdfetvrgerrrlmrahve 80 
                                       689***********************************************************************999 PP

                                       .ETTEE-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHHHHTT CS
                       Hydrolase_6  11 .rgdkaipgaaealnalraagkpvvllTNnsskseeeyakkleklg 55 
                                        +g ++ pg  e+l++l+ +g ++++ T +++++ ++y++++   g
  gi|474935054|ref|YP_007688636.1|  81 aNGIEPKPGIREVLDYLKGTGAKLAVATASTQEHADDYLEQI---G 123
                                       99***************************9999999998775...3 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.2    0.0015       3.7       1      14 [.       4      17 ..       4      21 .. 0.87
   2 !    9.4   0.0   0.00032      0.82      18      60 ..      88     133 ..      81     146 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0015
                                      EEEEIIIIIS-TTS CS
                       Hydrolase_3  1 ialDlDGTLlnsdk 14
                                      +++D+DGTL++ +k
  gi|474935054|ref|YP_007688636.1|  4 VIFDMDGTLIDTEK 17
                                      69********9876 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00032
                                       HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCC...SEEEE CS
                       Hydrolase_3  18 ektkeaikklkekgikvviATGRslravlpvleelgld...lpvia 60 
                                       + ++e++ +lk  g k+++AT+   + + ++le++g++    +vi+
  gi|474935054|ref|YP_007688636.1|  88 PGIREVLDYLKGTGAKLAVATASTQEHADDYLEQIGVKdmfDMVIS 133
                                       67899*******************************9977666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1316.99
//
Query:       gi|474935055|ref|YP_007688637.1|  [L=624]
Description: glutamyl-tRNA(Gln) amidotransferase, subunit E [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.2e-61  208.5   0.0    1.6e-61  208.1   0.0    1.2  1  GatB_N     GatB/GatE catalytic domain
    2.4e-15   56.7   0.1    3.9e-15   56.0   0.1    1.3  1  GatB_Yqey  GatB domain
    1.8e-08   34.5   0.0    5.6e-08   32.9   0.0    1.9  1  GAD        GAD domain
     0.0018   18.3   0.6     0.0066   16.5   0.3    2.0  2  YqeY       Yqey-like protein


Domain annotation for each model (and alignments):
>> GatB_N  GatB/GatE catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.1   0.0   3.6e-65   1.6e-61       2     271 ..      10     440 ..       9     442 .. 0.96

  Alignments for each domain:
  == domain 1  score: 208.1 bits;  conditional E-value: 3.6e-65
                                       EEEEEEEEEB--SB-SSSSSBSS..SSCE.........S.TTSS--TTTTTS......................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxx..xxxx.........x.xxxxxxxxxxxx......................... RF
                            GatB_N   2 viGlEiHaqlktksKlFssaste..eege.........e.pnsevsevdlal......................... 41 
                                       ++G+EiH+ql+tk KlF+++ +   e  e         + ++se++evd a+                         
  gi|474935055|ref|YP_007688637.1|  10 MCGIEIHQQLDTK-KLFCNCDSClsE--EgsgaiyrrlRpTTSEMGEVDRAAlaqfnrgygyqyqscpgttclveld 83 
                                       79*********96.******965432..234778888854899********9************************9 PP

                                       ..TT..--.EEHHHHHHHHHHHHHTTEEE-SEE-EEEEE-TCTTCTTSEEEEESSS.SEEEEEEEE.TEEEEEEEEE CS
                                       ..xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                            GatB_N  42 ..PGtlPv.lnkeavelaikaalalnceiaeeskfdRKnyfypdlpkgyQitqkeeplakeGslel.ekkvrierih 114
                                         P   P+ +n++ +e+++ ++  +++++ +e++f+RK+++++++++g+Q+t+    +a +G++e+  +k++i +++
  gi|474935055|ref|YP_007688637.1|  84 eeP---PHeVNADSMETTLIFSELVHASVIDEVQFMRKIVVDGSNTSGFQRTS---LVAVDGYVEAiGRKIGILSVC 154
                                       998...999********************************************...677******87899******* PP

                                       EEE---EEEEEETTEEEEETTSTT-EEEEEEE-STB-SHHHHHHHHHHHHHHHHHHTSB--SGGGTTEEEEEEEEEC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N 115 lEeDaaksvheekeeslvdlnRaGvpLiEivtepdlrspeearavveklrellralgvsdgnmeeGslRcDvNvSvr 191
                                       lEeDa++++ ++++ ++ + +R+G+pLiE++t+pd+r+p+e+++v+ ++++llra++ +++++  G++R D+N+S+ 
  gi|474935055|ref|YP_007688637.1| 155 LEEDACRKIDTTDTDVVWRTDRLGIPLIEVATAPDMRTPQEVMEVALRIGTLLRATKRVKRGI--GTIREDLNISIP 229
                                       **********9999*************************************************..************ PP

                                       TSETTSSS.--EEEEEE-SHHHHHHHHHHHHHHHHHHH....................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................................... RF
                            GatB_N 192 eeekgeeegtrvEiKnlnslksiekaieyeierqiell....................................... 229
                                       e       g+r+EiK++++l+++ + +++e++rq  l+                                       
  gi|474935055|ref|YP_007688637.1| 230 E-------GARIEIKGVQELRMLPDFVTNEVKRQKMLVrvkkilaergtkavpvdlvdvtdifktceskiivsalkd 299
                                       4.......59******************************************************************* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                            GatB_N 230 ............................................................................. 229
                                                                                                                    
  gi|474935055|ref|YP_007688637.1| 300 kgrvlacrlpgfagvmngdnktlrlgsemaqyartvgvkgifhsdelpnygieqeyvdrlrealgmtgefdafvica 376
                                       ***************************************************************************** PP

                                       .........................-EEEEEETTTTEEEEECC----...-EEE-TTS--EE--HHH CS
                                       .........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N 230 .........................qeTrkfdedkgetvslRskeeaedYryfpepdlppleiseel 271
                                                                +eTr   +d g+t++ R+ + a   r++pe+d+pp  i+++ 
  gi|474935055|ref|YP_007688637.1| 377 akekkakdaltlavnranaalegvpEETRDPLPD-GTTKYSRPLPGA--ARMYPETDVPPTPITRQR 440
                                       **********************************.**********77..5************99876 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.0   0.1   8.7e-19   3.9e-15       2     148 .]     481     619 ..     480     619 .. 0.92

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 8.7e-19
                                       HHHHHHHHSS.HHHHHHHHHTCHHHHHHHHTXXTTCSSTTHHHHHHHHHHHHTTSSGHHHHHHHHHHHHHHTXXHHH CS
                         GatB_Yqey   2 ffeevvkegadaklaanwllnellgelnkegleieelkltpeqlaellkliaegkIskkiakevleelleegkspee 78 
                                       +f ++++e    + +a+ +++++ +el++eg++ ++  lt +++  +++ ++e++ +k+++  +l+e++ +g ++++
  gi|474935055|ref|YP_007688637.1| 481 VFCKIADEF-GMAAVAATTFQNTFSELEHEGINTDA--LTYDDMYNVFAGLKENRFAKEAIPALLKEIA-SGTDMDA 553
                                       566777776.567788889999999***********..9*****************************9.8****** PP

                                       HHHHCTXXXXXXSSXHHHHHHHHHHTXHHHHHHHTTXXTTSTHHHHHHHHHTTSSXSXHHHHHHHHHHHS CS
                         GatB_Yqey  79 iieekgLkqisdeeeleklveeviaenpkavedyksgkekalkflvGqvMkktkGkadpklvnellkekL 148
                                       +i + gL+++   +e e++++++++e     e ++s+ + a++ l+G vM +++Gk+d+k+++++l +++
  gi|474935055|ref|YP_007688637.1| 554 AIMKLGLTAVD-AGEAEAIIAKIVRER---EEFVRSKGMAAIGPLMGPVMGALRGKIDGKQASDILTKEI 619
                                       *********95.6**************...677789999***************************9986 PP

>> GAD  GAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0   1.3e-11   5.6e-08       3      95 .]     295     386 ..     293     386 .. 0.92

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 1.3e-11
                                       HHHHSTEEEEEEEETTG-TTTSHHHHHHHHHHHHHTTHSHCEEEEESSGGEETTTCCC.S-HHHHHHHHHHCT--TT CS
                               GAD   3 ealksggsvkalrvpggaaklsrkeideleefakelgakglawikvegegltgpiakf.lteeevkklleavgaeeg 78 
                                       +alk++g+v a r+pg +a+  + + + l +++ e++ ++++  +v+g +++++++ + + +e v +l+ea+g+  +
  gi|474935055|ref|YP_007688637.1| 295 SALKDKGRVLACRLPG-FAGVMNGDNKTL-RLGSEMAQYARTV-GVKGIFHSDELPNYgIEQEYVDRLREALGMTGE 368
                                       799*************.688877776555.799*******998.*******************************99 PP

                                       .EEEEEEEEEHHHHHHHH CS
                               GAD  79 .DillfvAdkkktvnkal 95 
                                        D++++ A k+k++++al
  gi|474935055|ref|YP_007688637.1| 369 fDAFVICAAKEKKAKDAL 386
                                       9**************997 PP

>> YqeY  Yqey-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.66   2.9e+03      78     111 ..     240     273 ..     236     316 .. 0.80
   2 !   16.5   0.3   1.5e-06    0.0066      96     141 ..     568     617 ..     552     619 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.66
                                       HHHHHHGGGS-----HHHHHHHHHHHHHHTT--B CS
                              YqeY  78 aEievleeYlPeqlseeeiealvkeaiaevgaes 111
                                       +E+++l +++ ++++++++   vk+++ae g + 
  gi|474935055|ref|YP_007688637.1| 240 QELRMLPDFVTNEVKRQKMLVRVKKILAERGTKA 273
                                       6888888888888888888888888888887764 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.5e-06
                                       HHHHHHHHHHH....TT--BGGGHHHHHHHHHHHHTTTS-HHHHHHHHHH CS
                              YqeY  96 iealvkeaiae....vgaesmkdmGkvmkalkpkvkGkaDgkkvsalvke 141
                                        ea++++++ e    v  ++m+++G +m+ ++  ++Gk+Dgk++s ++ +
  gi|474935055|ref|YP_007688637.1| 568 AEAIIAKIVREreefVRSKGMAAIGPLMGPVMGALRGKIDGKQASDILTK 617
                                       5555555555511116788**************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (624 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.49
# Mc/sec: 3857.38
//
Query:       gi|474935056|ref|YP_007688638.1|  [L=118]
Description: L-asparaginase/archaeal Glu-tRNAGln amidotransferase subunit D [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-26   91.6   0.3      4e-26   91.5   0.3    1.0  1  Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
    0.00086   17.8   0.4     0.0011   17.4   0.4    1.1  1  Gly_reductase   Glycine/sarcosine/betaine reductase component


Domain annotation for each model (and alignments):
>> Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.5   0.3   4.5e-30     4e-26      11     112 ..       1     101 [.       1     103 [. 0.93

  Alignments for each domain:
  == domain 1  score: 91.5 bits;  conditional E-value: 4.5e-30
                                       --HHHHHHHHHTT--EEEEEEBTTTB--HHHHHHHHHHHTTT-EEEEEESSSBS-----H.....HHHHHTEEE-TT CS
                    Asparaginase_C  11 mdtkvlkallkkgakGvvlegtGvGnlpsallealkeakargivvvatsqcpsgsvsnseyeagkelerlgvisadd 87 
                                       md+++++ ++  + kGvv+ g G G++++++++++kea+++givvv+t+qc++g+++ ++y++g+++ ++g++   d
  gi|474935056|ref|YP_007688638.1|   1 MDPSLFRDVV-MKSKGVVISGSGLGHVNENMVPLIKEATDAGIVVVITTQCINGRTNLNVYNTGRDMLNAGAVPVLD 76 
                                       7999999998.699*************************************************************** PP

                                       --HHHHHHHHHHHCTT---HHHHHH CS
                    Asparaginase_C  88 mtpeaarikLmlllgkgldpaevrk 112
                                       m pe+a++kLm++l++ +  ++  +
  gi|474935056|ref|YP_007688638.1|  77 MLPETAYAKLMWVLANVKGREAAVE 101
                                       ***************9886665544 PP

>> Gly_reductase  Glycine/sarcosine/betaine reductase component B subunits
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.4   1.2e-07    0.0011     301     347 ..      10      56 ..       7      66 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.2e-07
                     Gly_reductase 301 lLgadgvivseeGyGnpdtdlimnikklekaGiktvlitdelaGrdg 347
                                       +++ +gv++s  G G+ + +++  ik++++aGi +v+ t+ ++Gr +
  gi|474935056|ref|YP_007688638.1|  10 VMKSKGVVISGSGLGHVNENMVPLIKEATDAGIVVVITTQCINGRTN 56 
                                       57889***************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 731.89
//
Query:       gi|474935057|ref|YP_007688639.1|  [L=302]
Description: L-asparaginase/archaeal Glu-tRNAGln amidotransferase subunit D [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.6e-63  212.2   0.2    5.9e-63  211.9   0.2    1.1  1  Asparaginase  Asparaginase, N-terminal
    2.6e-17   61.9   0.0    4.7e-17   61.0   0.0    1.4  1  GatD_N        GatD N-terminal domain


Domain annotation for each model (and alignments):
>> Asparaginase  Asparaginase, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.9   0.2   6.6e-67   5.9e-63       2     186 ..      92     284 ..      91     288 .. 0.96

  Alignments for each domain:
  == domain 1  score: 211.9 bits;  conditional E-value: 6.6e-67
                                       EEEEEEESGGGEEECTTS--CCEES-HHHHHCCTTTCCCCSEEEEEEEEEE-GGG--HHHHHHHHHHHHHHCCT.-S CS
                      Asparaginase   2 vlvlatGGTiasekdesggalapalsaeellealpelekiaeleseqlanidSsnmtpadwlklaeaieealee.yd 77 
                                       +++++tGGTias++d+++ga++pals +++++a+pe+ +ia+l++++l++i S+nmt  +w+klaeai+e+l++ +d
  gi|474935057|ref|YP_007688639.1|  92 IVLIGTGGTIASYVDYRTGAVHPALSTADMINAVPEIMDIANLQAKVLFSIFSENMTVPHWQKLAEAIAEELNNgAD 168
                                       89**********************************************************************666** PP

                                       EEEEE--STTHHHHHHHHHHHEES.SSEEEEE--SS-TTSTT-SHHHHHHHHHHHHHCGGTTSECEEEETTE..... CS
                      Asparaginase  78 gfVvlhGTDTlaytAsaLslmlknldkpvvltGsqrplselrsDgpeNlldAllvaasseriagvlvvfngk..... 149
                                       g++v hGTDT+ ytA+a+s+ml +++kpvv++G+qr++++++sD+ +Nl++A+++  +  + agv+v+++++     
  gi|474935057|ref|YP_007688639.1| 169 GVIVPHGTDTMGYTAAAVSFMLGDVSKPVVFVGAQRSSDRPSSDASSNLMAAARFIVNG-NRAGVFVCMHDTpgdds 244
                                       **********************************************************9.9**************** PP

                                       ..EEETTTEEE-BSSSSS-EEETTT--SEEE.ETTEEEES CS
                      Asparaginase 150 ..llranrvtKvhtssldaFespnlgplaev.egskvkvn 186
                                         +++++rv+K+h+s++daF+s+n++p+a + +++k+++n
  gi|474935057|ref|YP_007688639.1| 245 faIHAGTRVRKMHSSRRDAFQSINVPPVAHLdRDGKITFN 284
                                       *****************************99556666665 PP

>> GatD_N  GatD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.0   0.0   5.3e-21   4.7e-17       2      54 ..      17      69 ..      16      69 .. 0.94

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 5.3e-21
                                      -TT-EEEEE-SS-EEEEEE----TTS-SSEEEEEETTS-EEEEE-TT-.---E CS
                            GatD_N  2 evGDlikvekkgreyeGilmPrselsdddiivlKLdnGYNiGikieeiekiel 54
                                      ++G ++ ve+ g++y+G+lmP++e+s +di++lK+++GYN+Gi++++ +++++
  gi|474935057|ref|YP_007688639.1| 17 DEGCMLTVESSGKSYRGVLMPHHEFSGEDILILKMKSGYNVGIRMDKDSSVKV 69
                                      6788999****************************************999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1845.94
//
Query:       gi|474935058|ref|YP_007688640.1|  [L=209]
Description: hydrogenase accessory protein HypB [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-21   76.6   0.6    2.1e-21   76.3   0.6    1.1  1  cobW           CobW/HypB/UreG, nucleotide-binding domain
      2e-12   46.7   1.0    1.6e-05   24.0   0.1    2.1  2  MeaB           Methylmalonyl Co-A mutase-associated GTPase Me
    0.00013   21.6   0.4    0.00013   21.6   0.4    1.8  2  SRP54          SRP54-type protein, GTPase domain
    0.00051   20.0   0.3     0.0012   18.7   0.3    1.7  1  MobB           Molybdopterin guanine dinucleotide synthesis p
     0.0015   18.6   0.0     0.0019   18.2   0.0    1.3  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
     0.0025   17.7   0.1     0.0041   17.0   0.1    1.3  1  APS_kinase     Adenylylsulphate kinase
     0.0065   16.4   0.9      0.016   15.1   0.8    1.7  1  AAA_31         AAA domain
  ------ inclusion threshold ------
      0.036   14.6   0.2      0.095   13.2   0.2    1.8  1  AAA_18         AAA domain
      0.045   13.5   0.0      0.085   12.6   0.0    1.4  1  AAA_29         P-loop containing region of AAA domain
      0.079   13.0   0.0       0.15   12.1   0.0    1.5  1  TsaE           Threonylcarbamoyl adenosine biosynthesis prote
       0.09   11.9   0.0       0.13   11.4   0.0    1.3  1  LpxK           Tetraacyldisaccharide-1-P 4'-kinase
       0.09   11.7   0.3       0.13   11.2   0.3    1.1  1  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
       0.11   12.3   0.2       0.21   11.3   0.2    1.5  1  ATP_bind_1     Conserved hypothetical ATP binding protein
       0.11   12.3   0.1       0.25   11.2   0.0    1.5  2  TK             Thymidine kinase
       0.12   12.2   0.1       0.89    9.4   0.0    2.0  2  RsgA_GTPase    RsgA GTPase
       0.16   11.7   0.1       0.39   10.5   0.1    1.6  2  CLP1_P         mRNA cleavage and polyadenylation factor CLP1 


Domain annotation for each model (and alignments):
>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.3   0.6   1.8e-24   2.1e-21       5     160 ..      30     173 ..      26     189 .. 0.90

  Alignments for each domain:
  == domain 1  score: 76.3 bits;  conditional E-value: 1.8e-24
                                       EEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCCHCCCT.EEEETTTTECCHCTT-HHHHHHHHHHH CS
                              cobW   5 ltGflGsGKTtLlnhll..enraglklavivNefgevsiDaellretgveivelenGciCctlredllkelealeer 79 
                                       + G++GsGKTtL+ +l     ++g+k+ vi +++   + D ++ ++ g  +++ ++G+ C+  + d++++ +++   
  gi|474935058|ref|YP_007688640.1|  30 FMGSIGSGKTTLIIELGkrLVAQGKKVCVIAGDVT-GDDDFKRFKAGGLDAINCNTGKECHLEARDIQRVTRDVDLS 105
                                       679*************9776789************.99999*********************999999999998877 PP

                                       HTT-SEEEEEECT.TTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHHCH CS
                              cobW  80 eerldviliEttG.laePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDllde 155
                                       +  +d+++iE++G l++Pa           +l  d+ vav++     +e+++  +k +  ++ +d+ +lnK+D +d+
  gi|474935058|ref|YP_007688640.1| 106 R--YDIVFIENVGnLVCPADF---------NLGTDFRVAVIST----TEGDDMVRKHHAIFQHSDMAILNKIDIADA 167
                                       7..9*****************.........9************....9***************************99 PP

                                       C...HH CS
                              cobW 156 e.alle 160
                                       +  + +
  gi|474935058|ref|YP_007688640.1| 168 VgVDPQ 173
                                       855544 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.1   8.3e-08   9.3e-05      29      67 ..      25      63 ..      14      68 .. 0.88
   2 !   24.0   0.1   1.4e-08   1.6e-05     115     222 ..     100     204 ..      84     207 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 8.3e-08
                                      SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE-- CS
                              MeaB 29 aqvvGltGvPGaGkstlvealglelrrrGkrvavlavDP 67
                                       + v + G+ G+Gk tl+ +lg +l+++Gk+v v+a D 
  gi|474935058|ref|YP_007688640.1| 25 VKTVDFMGSIGSGKTTLIIELGKRLVAQGKKVCVIAGDV 63
                                      5678999*****************************885 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 1.4e-08
                                       HHHHHTT-SEEEEEEESSTTHHHHHHTT-SEEEEEEESSTTTTTTT--CCCHHH-SEEEEE---HHHHHHHHHHHHH CS
                              MeaB 115 llleaaGfDvvlietvGvGqsevdvaevvdtfvvlllpeaGDelqgikkGileiaDiivvnkaDkkeaekaarelra 191
                                       + ++   +D+v ie vG      d    +d  v+++ +  GD++    + i+  +D+ ++nk D ++a  +  +   
  gi|474935058|ref|YP_007688640.1| 100 RDVDLSRYDIVFIENVGNLVCPADFNLGTDFRVAVISTTEGDDMVRKHHAIFQHSDMAILNKIDIADAVGVDPQ--I 174
                                       5567778*********************************************************9999877654..4 PP

                                       HHHHCSTTBTTB--EEEEEBCCCTBSHHHHH CS
                              MeaB 192 aleleeekekeWrpkvlktsavegeGidelv 222
                                       +l+  ++ + e   ++++t+a++g+G+de++
  gi|474935058|ref|YP_007688640.1| 175 ILDDYKKLTGEL-KPMITTAAKKGDGVDEVL 204
                                       555444445555.5678999********986 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.4   1.2e-07   0.00013       6      40 ..      30      64 ..      25     120 .. 0.75
   2 ?   -1.9   0.1       1.9   2.1e+03     119     152 ..     133     164 ..     125     171 .. 0.64

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.2e-07
                                      EEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTS CS
                             SRP54  6 lvGlqGaGKTttlaKLaallkkegkkvllvaaDtf 40
                                      ++G  G+GKTt +  L ++l ++gkkv+++a D+ 
  gi|474935058|ref|YP_007688640.1| 30 FMGSIGSGKTTLIIELGKRLVAQGKKVCVIAGDVT 64
                                      89*******************************86 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.9
                                       EEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTS CS
                             SRP54 119 lvldattgqeavkqakaFkeavgitgviltklDg 152
                                        v+++t g ++v++ +a  ++   + +il k+D 
  gi|474935058|ref|YP_007688640.1| 133 AVISTTEGDDMVRKHHAIFQHS--DMAILNKIDI 164
                                       5677777777777666666655..5567777775 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.3   1.1e-06    0.0012       2      63 ..      28      82 ..      27     116 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.1e-06
                              MobB  2 lgivgksgsGKTtLleklipelkarglrvgtiKhahhgfdvdkpgkDsyrhrkAGAkevlva 63
                                      + ++g  gsGKTtL+ +l + l a+g +v++i         d +g D ++  kAG    +  
  gi|474935058|ref|YP_007688640.1| 28 VDFMGSIGSGKTTLIIELGKRLVAQGKKVCVIA-------GDVTGDDDFKRFKAGGLDAINC 82
                                      678999*************************95.......4667777777777776554443 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.7e-06    0.0019       9      44 ..      35      70 ..      32     195 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.7e-06
                                      TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  9 GvGKTtlaanLaralarrglrVllvDaDpqannlai 44
                                      G+GKTtl + L++ l  +g++V ++  D+ +  ++ 
  gi|474935058|ref|YP_007688640.1| 35 GSGKTTLIIELGKRLVAQGKKVCVIAGDVTGDDDFK 70
                                      9************************99999888775 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   3.6e-06    0.0041       4      40 ..      27      63 ..      24      70 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.6e-06
                                      EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHH CS
                        APS_kinase  4 vvwltGlsgsGKstianalekkLvekgisvylLdGdn 40
                                      +v + G  gsGK+t+  +l k+Lv++g++v ++ Gd+
  gi|474935058|ref|YP_007688640.1| 27 TVDFMGSIGSGKTTLIIELGKRLVAQGKKVCVIAGDV 63
                                      67799******************************96 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.8   1.4e-05     0.016      12      41 ..      35      64 ..      28     128 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.4e-05
                            AAA_31 12 GvGKTTtsvnlaaalaklgkkvLlvDlDpQ 41
                                      G GKTT  ++l++ l  +gkkv ++  D  
  gi|474935058|ref|YP_007688640.1| 35 GSGKTTLIIELGKRLVAQGKKVCVIAGDVT 64
                                      99***********************98865 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   8.5e-05     0.095       4      47 ..      31      72 ..      29     182 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.5e-05
                            AAA_18  4 tGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpeald 47
                                      +G +G+GKttl  eL krl  + + ++v+   g ++++d+++  
  gi|474935058|ref|YP_007688640.1| 31 MGSIGSGKTTLIIELGKRL--VAQGKKVCVIAGDVTGDDDFKRF 72
                                      6899**************9..77777777666666666666333 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   7.6e-05     0.085      14      39 ..      15      42 ..       6      52 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.6e-05
                            AAA_29 14 ghtieidlkg..atlltGpsGsGKSTll 39
                                      ++ ++++++g  ++ ++G +GsGK+Tl+
  gi|474935058|ref|YP_007688640.1| 15 ENYHMFKTNGvkTVDFMGSIGSGKTTLI 42
                                      5556677777766779***********8 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00013      0.15      18      45 ..      20      51 ..       2      58 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                                      H....TEEEEEEESTTSSHHHHHHHHHHHTT- CS
                              TsaE 18 l....gdvilLeGdLGaGKTtlvrglakalgv 45
                                      +     +++ + G +G+GKTtl+ +l k l  
  gi|474935058|ref|YP_007688640.1| 20 FktngVKTVDFMGSIGSGKTTLIIELGKRLVA 51
                                      23333456999************999998855 PP

>> LpxK  Tetraacyldisaccharide-1-P 4'-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00011      0.13      47      72 ..      35      60 ..      27      98 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                                      -HSHHHHHHHHHHHTTTS..-EEEEE CS
                              LpxK 47 GtGKTPlvialvkllqarglkvgvlS 72
                                      G+GKT l+i l k+l+a+g kv v++
  gi|474935058|ref|YP_007688640.1| 35 GSGKTTLIIELGKRLVAQGKKVCVIA 60
                                      99*********************995 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3   0.00011      0.13      18      54 ..      28      66 ..      15      80 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                     TrwB_AAD_bind 18 ilivGttGsGKtqalekllrairargdraivl..DltGa 54
                                      + ++G++GsGKt+ + +l + + a+g+++ v+  D tG+
  gi|474935058|ref|YP_007688640.1| 28 VDFMGSIGSGKTTLIIELGKRLVAQGKKVCVIagDVTGD 66
                                      5679**********************9987754577775 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00019      0.21       2      30 ..      31      59 ..      30      66 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00019
                        ATP_bind_1  2 vGpaGsGKttfvgalseilelrgrsvavv 30
                                      +G  GsGKtt++ +l + l ++g++v v+
  gi|474935058|ref|YP_007688640.1| 31 MGSIGSGKTTLIIELGKRLVAQGKKVCVI 59
                                      89*********************999987 PP

>> TK  Thymidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00022      0.25       7      85 ..      31     114 ..      27     119 .. 0.73
   2 ?   -2.4   0.0       3.3   3.7e+03      55      84 ..     142     171 ..     128     186 .. 0.48

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00022
                                TK   7 lgpmfaGKsteLlrrvkryqlaekkvvvik..aakdn...Rysegkvvthdgisleakksktssleeikeeleeedv 78 
                                       +g++ +GK+t +++  kr+  + kkv vi    + d+   R+++g + + + ++ +  + ++  ++++++ ++ + +
  gi|474935058|ref|YP_007688640.1|  31 MGSIGSGKTTLIIELGKRLVAQGKKVCVIAgdVTGDDdfkRFKAGGLDAINCNTGKECHLEARDIQRVTRDVDLSRY 107
                                       68999********************9999622455652225555554444444444447788888888888898999 PP

                                TK  79 dvvlvDE 85 
                                       d+v++  
  gi|474935058|ref|YP_007688640.1| 108 DIVFIEN 114
                                       9999875 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.3
                                TK  55 sleakksktssleeikeeleeedvdvvlvD 84 
                                        +  k++++ + +++    + +  d+v+vD
  gi|474935058|ref|YP_007688640.1| 142 DMVRKHHAIFQHSDMAILNKIDIADAVGVD 171
                                       333333333333333333333333444444 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00079      0.89      99     125 ..      24      51 ..       2      62 .. 0.76
   2 ?    0.4   0.0      0.48   5.4e+02      51      93 ..     157     203 ..     145     207 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00079
                                       T.SEEEEECSTTSSHHHHHHHHCTT--- CS
                       RsgA_GTPase  99 d.ktsvlvGqSGvGKStLinallpelel 125
                                       + kt+ ++G+ G GK+tLi +l  +l +
  gi|474935058|ref|YP_007688640.1|  24 GvKTVDFMGSIGSGKTTLIIELGKRLVA 51 
                                       348999*************998776655 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.48
                                       EEEE-GGG--HHH.HHHHHHHHHHHTT...SEEEE--TTTHTTHHHH CS
                       RsgA_GTPase  51 ivlnKiDlleeee.eleelkeelealg...yevllvsaktkegleel 93 
                                        +lnKiD+++    + + + +++++l     +++++ ak+++g++e+
  gi|474935058|ref|YP_007688640.1| 157 AILNKIDIADAVGvDPQIILDDYKKLTgelKPMITTAAKKGDGVDEV 203
                                       57999999998876455556666665422134555666666776665 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00034      0.39       1      32 [.      32      63 ..      32      69 .. 0.91
   2 ?   -2.6   0.0       3.7   4.2e+03     124     148 ..     163     188 ..     154     195 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00034
                            CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDv 32
                                      G+  sGK+Tl+  L  +++ +g+k++++  Dv
  gi|474935058|ref|YP_007688640.1| 32 GSIGSGKTTLIIELGKRLVAQGKKVCVIAGDV 63
                                      6778***********************99997 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.7
                            CLP1_P 124 eliealepdvvvvldq.eellnelkr 148
                                       ++++a+ +d  ++ld+ ++l  elk 
  gi|474935058|ref|YP_007688640.1| 163 DIADAVGVDPQIILDDyKKLTGELKP 188
                                       46888888888888888888877775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      616  (0.0343577); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1292.06
//
Query:       gi|474935059|ref|YP_007688641.1|  [L=441]
Description: phosphoribosylamine--glycine ligase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.4e-60  203.2   0.2    4.6e-60  202.7   0.2    1.2  1  GARS_A       Phosphoribosylglycinamide synthetase, ATP-grasp 
    1.8e-21   76.7   0.2    5.4e-21   75.2   0.1    1.8  2  GARS_N       Phosphoribosylglycinamide synthetase, N domain
    7.8e-13   48.5   0.3    4.1e-12   46.2   0.1    2.4  3  GARS_C       Phosphoribosylglycinamide synthetase, C domain
    5.8e-05   23.2   0.0    0.00019   21.5   0.0    1.9  1  ATP-grasp_3  ATP-grasp domain
  ------ inclusion threshold ------
      0.013   15.0   0.0      0.084   12.4   0.0    2.0  2  CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP bindin
      0.016   15.3   0.0       0.05   13.7   0.0    1.9  2  DpaA_N       Dipicolinate synthase subunit A N-terminal domai
      0.017   14.7   0.1      0.045   13.4   0.0    1.7  2  ATP-grasp_4  ATP-grasp domain


Domain annotation for each model (and alignments):
>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.7   0.2   1.8e-63   4.6e-60       1     194 []     102     299 ..     102     299 .. 0.96

  Alignments for each domain:
  == domain 1  score: 202.7 bits;  conditional E-value: 1.8e-63
                                       HBHHHHHHHHHHTT--B-.-EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEE....SSHHHHHHHHHHHCT CS
                            GARS_A   1 asKsfakdllkkagipta.eyeaftdpeeakeyieeatakalVvKadglaagKgviva....kseeealkavkeile 72 
                                       ++Ksf+++l++k++i++   +++f+d+++a +y++++  ++  vK++gl++gKgv+v     k+ ++++++++ei++
  gi|474935059|ref|YP_007688641.1| 102 TNKSFMRELVQKYEIEGNlGFRSFDDAASAIDYVKTVPYEV-AVKPVGLTGGKGVKVQgdqlKDLQDTIDYINEIFD 177
                                       68***************989*********************.9**************988889999**********8 PP

                                       S-TTCCCCSSEEEEE---SEEEEEEEEECTTEEEE---BEEEEEEECCCEEEEECECEEEE....S-TTS-HHHHHH CS
                            GARS_A  73 kkkfGeagekvviEelleGeEvsllalvdgktvkplplaqdhkrvlegDkgpnTGGmGays....papvvteellek 145
                                        +  G  g kv+iEe+ eGeE++ ++++dg++v+p+pl+qdhkr++egD+gpnTGGmG+ys     +p++ ee+ +k
  gi|474935059|ref|YP_007688641.1| 178 GN-VG--GGKVIIEEKAEGEEFTQMVFTDGSDVIPMPLVQDHKRAYEGDTGPNTGGMGSYSdsnhLLPFIGEEDRQK 251
                                       55.55..59****************************************************988889********** PP

                                       HHHHTHHHHHHHHHCTT---EEEEEEEEEEETTEEEEEEEESS--TTCH CS
                            GARS_A 146 ikeeileptveglkkegipfkGvLyaglmlvedgpkvlefnvRfgDpet 194
                                       + + i++ ++++lkkeg+p++G +y+++ml+++gpk++e+n+RfgDpe+
  gi|474935059|ref|YP_007688641.1| 252 AID-IVKAIIDALKKEGCPYRGTMYGQFMLTKNGPKIIEINARFGDPEA 299
                                       **9.*******************************************97 PP

>> GARS_N  Phosphoribosylglycinamide synthetase, N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.2   0.1   2.1e-24   5.4e-21       1      90 []       1     101 [.       1     101 [. 0.92
   2 ?   -2.9   0.0       4.8   1.2e+04      63      79 ..     255     270 ..     236     273 .. 0.72

  Alignments for each domain:
  == domain 1  score: 75.2 bits;  conditional E-value: 2.1e-24
                                       EEEEEEESSHHHHHHHHHHTTSTTESEEEEEE..--CGG............TTHHHHHHHHHHCTESEEEE-SHHHH CS
                            GARS_N   1 mkvLvvGsGGRehalawklaqspkvekvyvap..gNagt............edlealvefakeekidlvvvGpeapL 63 
                                       mkvL +G+G+Reha +++la+     ++y+++   N+g+            +d++++ +fa ++ i++++vGpeapL
  gi|474935059|ref|YP_007688641.1|   1 MKVLTIGGGAREHAAVEALARAG--AEIYAVMknVNPGIekratktlisseNDIDKICDFAINNFIEYAFVGPEAPL 75 
                                       9*******************985..57888884567888******9999999999********************** PP

                                       HTTHHHHHHHHHT-EEES--CCCCHHH CS
                            GARS_N  64 vaGvadaleeekgikvfGpskeaAqlE 90 
                                         G++dal++  gik+ +p+k+aA++E
  gi|474935059|ref|YP_007688641.1|  76 SVGIVDALQDL-GIKCASPTKAAARIE 101
                                       ********666.**************9 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.8
                                       HHTTHHHHHHHHHT-EE CS
                            GARS_N  63 LvaGvadaleeekgikv 79 
                                       +v+ + dal++e g++ 
  gi|474935059|ref|YP_007688641.1| 255 IVKAIIDALKKE-GCPY 270
                                       577888888666.7665 PP

>> GARS_C  Phosphoribosylglycinamide synthetase, C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.1       6.3   1.6e+04      50      66 ..      17      33 ..      13      36 .. 0.74
   2 ?   -2.1   0.0       1.9   4.9e+03      50      74 ..     247     271 ..     234     272 .. 0.84
   3 !   46.2   0.1   1.6e-15   4.1e-12       1      79 [.     334     424 ..     334     425 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 6.3
                                      SSHHHHHHHHHHHHTTC CS
                            GARS_C 50 etleeArakayeavkki 66
                                      e l+ A a++y+ +k++
  gi|474935059|ref|YP_007688641.1| 17 EALARAGAEIYAVMKNV 33
                                      55778888888888776 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.9
                                       SSHHHHHHHHHHHHTTCB-TTEE-- CS
                            GARS_C  50 etleeArakayeavkkikfeglfyR 74 
                                       e+ ++A++ + + ++++k eg+ yR
  gi|474935059|ref|YP_007688641.1| 247 EDRQKAIDIVKAIIDALKKEGCPYR 271
                                       5678888888889999999999998 PP

  == domain 3  score: 46.2 bits;  conditional E-value: 1.6e-15
                                       EEEEEEEETTTTSS--ST-EEBS.......TTEEEEESSEE.....EEE-SSEEEEEEEEESSHHHHHHHHHHHHTT CS
                            GARS_C   1 avgvvlaskGYPgsyekgkeitg.......egvkvfhagtk.....lvtsGGRvlavvavgetleeArakayeavkk 65 
                                       +v+ +++++GY  ++e g++i+        eg  v+  +       +vt  +R ++vv++g++++eA+a++++++++
  gi|474935059|ref|YP_007688641.1| 334 TVCKYIVPRGYGVKPEPGHTISFdmeaierEGSIVYFGSIDkngdkFVTGTSRSVGVVGIGDSISEAEANCESGLSH 410
                                       69*******************66999999855545555544677779****************************** PP

                                       CB-TTEE--STTTH CS
                            GARS_C  66 ikfeglfyRkDIGa 79 
                                       ik++ + +R+DIG+
  gi|474935059|ref|YP_007688641.1| 411 IKCDAMEVRHDIGT 424
                                       *************7 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   7.2e-08   0.00019      28     159 ..     136     295 ..     126     297 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 7.2e-08
                                       S--SSSEEEEESS-------B--SS-.-TTE...................EEEE---SEEEEEEEEE.SSSEEEEEE CS
                       ATP-grasp_3  28 eeeekklvvKprdGaggesvrvveek.eeaeaaieeve............lvqefieGkplSvsllsdgekvlvlav 91 
                                       + +++++ vKp+   gg++v v  ++ ++++ +i++++            ++ e  eG++++  +  dg++v ++ +
  gi|474935059|ref|YP_007688641.1| 136 KTVPYEVAVKPVGLTGGKGVKVQGDQlKDLQDTIDYINeifdgnvgggkvIIEEKAEGEEFTQMVFTDGSDVIPMPL 212
                                       56689999***********98875552667788999999*********************************99988 PP

                                       EEEEEET..............TEEEEEEES----H.HHHHHHHHHHHHTTST....T--EEEEEEEEESS.SEEEEE CS
                       ATP-grasp_3  92 nrqliekaeke..........fvyaGnvtpietel.keevvelaeevvekle....glaGyvGvDlvlkdeepyviE 153
                                        + +    e +          ++ +  + p+  e+ +++++++++ ++ +l+    + +G +   ++l++++p +iE
  gi|474935059|ref|YP_007688641.1| 213 VQDHKRAYEGDtgpntggmgsYSDSNHLLPFIGEEdRQKAIDIVKAIIDALKkegcPYRGTMYGQFMLTKNGPKIIE 289
                                       77776554433788877775444455667777666699*************99866678888889************ PP

                                       EESS-- CS
                       ATP-grasp_3 154 vNPRlt 159
                                       +N+R+ 
  gi|474935059|ref|YP_007688641.1| 290 INARFG 295
                                       ****95 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.3e-05     0.084       5      85 ..     107     187 ..     103     206 .. 0.76
   2 ?   -0.1   0.0      0.21   5.3e+02     153     180 ..     269     294 ..     243     301 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.3e-05
                                       HHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSH.HHHHHHHHHHHHHHHHHHST CS
                       CPSase_L_D2   5 akealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarne.eelaelvkkalaeakaafgn 80 
                                       ++e+++k +++   ++    +++  a++ +k++ y v +k+    GGkG +v  ++ ++l++++    +      g 
  gi|474935059|ref|YP_007688641.1| 107 MRELVQKYEIEGNLGFRS-FDDAASAIDYVKTVPYEVAVKPVGLTGGKGVKVQGDQlKDLQDTIDYINEIFDGNVGG 182
                                       567777777777777777.89999***************************97654256666665555555555555 PP

                                       S-EEE CS
                       CPSase_L_D2  81 kqvlv 85 
                                        +v +
  gi|474935059|ref|YP_007688641.1| 183 GKVII 187
                                       55555 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.21
                                       T-EEEEEEEEEEETTTTEEEEEEEESS- CS
                       CPSase_L_D2 153 gvvgagtveflldpkskeyyviEvNtRl 180
                                        ++g    +f+l +  +   +iE+N+R 
  gi|474935059|ref|YP_007688641.1| 269 PYRGTMYGQFMLTK--NGPKIIEINARF 294
                                       45566666888885..67789*****96 PP

>> DpaA_N  Dipicolinate synthase subunit A N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0     2e-05      0.05       2      34 ..       3      41 ..       2      59 .. 0.70
   2 ?   -4.0   0.0       5.9   1.5e+04      56      66 ..     207     217 ..     202     220 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2e-05
                                      EEEESB-HHHHHHHHHHHHTT-EEEEE......S-TSSS CS
                            DpaA_N  2 iaviGGDaRqlylarkLaekgakvsly......glelee 34
                                      ++ iGG aR+ + ++ La+ ga+++++      g+e+  
  gi|474935059|ref|YP_007688641.1|  3 VLTIGGGAREHAAVEALARAGAEIYAVmknvnpGIEKRA 41
                                      789**********************99443333333333 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 5.9
                                       E--TT-BETTT CS
                            DpaA_N  56 ilPvpgtkdgg 66 
                                       + P+p+++d++
  gi|474935059|ref|YP_007688641.1| 207 VIPMPLVQDHK 217
                                       67999999976 PP

>> ATP-grasp_4  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.7e-05     0.045       2      80 ..     139     208 ..     138     225 .. 0.71
   2 ?   -2.9   0.0       1.8   4.6e+03     135     154 ..     278     295 ..     244     297 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.7e-05
                       ATP-grasp_4   2 slPvviKPsvgffSlGVyki.nneeewkaavaaieeeleqakeeykeevveeesflvEeyieGeEfavdayfdeeGe 77 
                                       ++ v +KP+  ++  GV +  ++ ++++++++ i+       e ++   v ++++++Ee  eGeEf   ++   +G 
  gi|474935059|ref|YP_007688641.1| 139 PYEVAVKPVGLTGGKGVKVQgDQLKDLQDTIDYIN-------EIFD-GNVGGGKVIIEEKAEGEEFTQMVFT--DGS 205
                                       57788999999999999764134456666555555.......4455.5688***************976665..677 PP

                       ATP-grasp_4  78 pvi 80 
                                        vi
  gi|474935059|ref|YP_007688641.1| 206 DVI 208
                                       776 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.8
                       ATP-grasp_4 135 lrvsedgkiipiEvnplrfa 154
                                       + ++++g+ i iE+n+ rf+
  gi|474935059|ref|YP_007688641.1| 278 FMLTKNGPKI-IEINA-RFG 295
                                       4555666444.68887.666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2721.04
//
Query:       gi|474935060|ref|YP_007688642.1|  [L=262]
Description: Pseudouridylate synthase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.2e-25   87.6   0.0    2.3e-19   69.8   0.0    2.2  2  PseudoU_synth_1  tRNA pseudouridine synthase
  ------ inclusion threshold ------
       0.11   12.6   0.1       0.18   11.9   0.1    1.5  1  DUF3641          Protein of unknown function (DUF3641)


Domain annotation for each model (and alignments):
>> PseudoU_synth_1  tRNA pseudouridine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.7e-06     0.015       4      68 ..       9      72 ..       7     106 .. 0.66
   2 !   69.8   0.0   2.6e-23   2.3e-19       1     108 []     130     229 ..     130     229 .. 0.96

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.7e-06
                   PseudoU_synth_1  4 elvGthdfgsfckqkqekkntvrtileaaieevsgeekellvvtvkgsgFldhqVRamvgvl.fav 68
                                      +++G  ++gs  + ++ + +tv++ +  +i  v+    +  ++++k+s+++d++V a+++v+ f+ 
  gi|474935060|ref|YP_007688642.1|  9 AYLGDGFSGSQIQPRARNLRTVQSEILEKILLVDHV--PCDDIEIKFSSRTDAGVSALGNVVcFHT 72
                                      588888888554444555566666666666644444..677********************94443 PP

  == domain 2  score: 69.8 bits;  conditional E-value: 2.6e-23
                   PseudoU_synth_1   1 AakelvGthdfgsfckqkqekkntvrtileaaieevsgeekellvvtvkgsgFldhqVRamvgvlfavgqgklsped 77 
                                       Aak ++G+hdf+ f ++++ +k+tv  i  ++++    +e++ll+v+++++ F+++++R++++++++vg+g  + ed
  gi|474935060|ref|YP_007688642.1| 130 AAKLFEGHHDFKRF-AKNETGKTTVMCIDTVDVR----HEGNLLTVDFCANYFMWNMIRRIMAAVIQVGKGMTDCED 201
                                       89************.6777779************....99************************************* PP

                   PseudoU_synth_1  78 vkellnakkrkkiavetapavglvlfhvrYd 108
                                       vk+ l+ ++     +  a+++gl+l +v Y+
  gi|474935060|ref|YP_007688642.1| 202 VKRKLAGEDG---TFGLAKPTGLTLLDVTYP 229
                                       *********6...57***************8 PP

>> DUF3641  Protein of unknown function (DUF3641)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1     2e-05      0.18      45      89 ..     131     175 ..     109     213 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2e-05
                           DUF3641  45 kgkleeYlellkeafneetveklmCrsllsvdwdGklydCdfnqm 89 
                                        + +e   ++ + a ne+  +++mC +++ v ++G+l   df   
  gi|474935060|ref|YP_007688642.1| 131 AKLFEGHHDFKRFAKNETGKTTVMCIDTVDVRHEGNLLTVDFCAN 175
                                       5555556666666677888899*******************9654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1677.16
//
Query:       gi|474935061|ref|YP_007688643.1|  [L=194]
Description: putative RNA-binding protein of the translin family [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.013   15.5   0.0      0.051   13.6   0.0    1.7  2  Translin  Translin family


Domain annotation for each model (and alignments):
>> Translin  Translin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.17   3.1e+03     195     205 .]      87      97 ..      82      97 .. 0.91
   2 ?   13.6   0.0   2.8e-06     0.051     118     187 ..     106     173 ..      92     179 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.17
                                       HHHHHHHHHHT CS
                          Translin 195 EdvvYdlsvRg 205
                                       E+v+Yd+++Rg
  gi|474935061|ref|YP_007688643.1|  87 ETVIYDYALRG 97 
                                       99*******98 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 2.8e-06
                                       S---HHHHHHHHHHHHHHHHHHHHHHHCTT--S.HHHHHHHHHHHHHHHHHTS----HH...HHHHHTTH CS
                          Translin 118 fhltpedYllGlfdLtgELmRfainsvalgdkeekplqilkflrelragfellnlkndsakdlrkKldvl 187
                                       +++tp  +  Gl+d +gEL R   +++  g  e ++    + +++l +++  ++++ d+   lr+K+d  
  gi|474935061|ref|YP_007688643.1| 106 LEITPGSWAEGLADSIGELRRDMLTALMDGRLE-DAVALFQTMEQLSDALMTFDVR-DGIAPLRRKQDIA 173
                                       6788889999********************977.9********************9.66689***99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1271.89
//
Query:       gi|474935062|ref|YP_007688644.1|  [L=274]
Description: hypothetical protein TALC_01513 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.7e-05   24.4  10.1    0.00041   20.6   0.6    3.1  2  CARDB        CARDB
    5.9e-05   23.1   4.8      0.011   15.8   0.8    2.2  2  Wzt_C        Wzt C-terminal domain
     0.0005   20.6   0.3      0.011   16.4   0.1    2.6  3  YtkA         YtkA-like
  ------ inclusion threshold ------
      0.062   13.2   0.0       0.14   12.0   0.0    1.6  1  DUF2610      Domain of unknown function (DUF2610)
      0.067   13.6   0.3       0.45   11.0   0.1    2.2  2  MG2          MG2 domain
      0.074   13.1   0.0       0.21   11.7   0.0    1.8  1  SecG         Preprotein translocase SecG subunit
        0.1   12.7   0.3         13    5.9   0.0    2.3  2  DUF2057      Uncharacterized protein conserved in bacteria (D
       0.18   10.7   0.0       0.26   10.1   0.0    1.3  1  MFS_1        Major Facilitator Superfamily
       0.18   12.1  15.6       0.25   11.7   6.4    2.7  3  Invasin_D3   Invasin, domain 3
        1.2    9.6   4.7         21    5.6   0.2    3.2  4  Copper-bind  Copper binding proteins, plastocyanin/azurin fam
        2.4    8.2   9.9       0.97    9.5   0.4    3.0  2  Big_1        Bacterial Ig-like domain (group 1)


Domain annotation for each model (and alignments):
>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   3.3    0.0076        12      59     100 ..      95     136 ..      21     138 .. 0.82
   2 !   20.6   0.6   2.5e-07   0.00041      19      83 ..     147     212 ..     139     222 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0076
                                       CTEEEEEEEEEE-S-S-CEEEEEEEESTT-SS--SSCCCSEE CS
                             CARDB  59 agesttvsftwtteategevtltvvvDpdnevaEsnEtNNel 100
                                       +g++ ++s+t+  + ++g++tl++++ ++++ ++++E NN+ 
  gi|474935062|ref|YP_007688644.1|  95 SGGKGSISLTVNSQSKAGNYTLEFKTTETGTYSDGTEINNVE 136
                                       45666666676677789***********************85 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 2.5e-07
                                       SEEEEEEEEEE-SSS-EEEEEEEEEETTEEE.EEEEESEE-CTEEEEEEEEEE-S-S-CEEEEEEE CS
                             CARDB  19 eentitvtvkNqGtaasgatkvalyldgelv.gtvtvpsLaagesttvsftwtteategevtltvv 83 
                                       e +t+tvt++N+ + +  +  v +y+dg++  g+ +   ++ag++++v+f +t e+++g++t+ v 
  gi|474935062|ref|YP_007688644.1| 147 EPVTLTVTLENTSNVNIADLGVYFYIDGNKIdGSLKTVDIEAGKTSEVTFDYTGELKSGKHTFYVE 212
                                       6789***************************97788889********************9997665 PP

>> Wzt_C  Wzt C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.8   6.7e-06     0.011      19     111 ..      31     124 ..      16     139 .. 0.75
   2 !    9.2   0.2   0.00074       1.2      32     113 ..     147     219 ..     132     241 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.7e-06
                             Wzt_C  19 d...aegeetst.fesgeevtlrikvkahedvedpvfg..faikdrngqevfgtntelekksfeleel.kagervev 88 
                                       +   ++++ ts+ + +ge++++ i +   ++v+++++   +a+ d +g  v+g+ t+       +++l   g+++ +
  gi|474935062|ref|YP_007688644.1|  31 TftiDDEQVTSYrIGTGESFKVSIGFYEYATVNSLTVSyeVALLDDDGDKVTGATTRE------NGTLtMSGGKGSI 101
                                       3333666677777*************889999866665116778**********9943......3444489999999 PP

                             Wzt_C  89 efefklpLapGeYlltvaledrd 111
                                       +++++ + ++G+Y+l +  ++++
  gi|474935062|ref|YP_007688644.1| 102 SLTVNSQSKAGNYTLEFKTTETG 124
                                       999977889*****998876655 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00074
                             Wzt_C  32 eevtlrikvkahedvedpvfgfaikdrngqevfgtntelekksfeleelkagervevefefklpLapGeYlltvale 108
                                       e+vtl ++++  + v+  ++g+ ++  +g+ + g+         ++ +++ag++ ev+f+ +  L+ G+ ++ v   
  gi|474935062|ref|YP_007688644.1| 147 EPVTLTVTLENTSNVNIADLGVYFY-IDGNKIDGS--------LKTVDIEAGKTSEVTFDYTGELKSGKHTFYVESS 214
                                       6777777776666666666666666.667777442........347889************779******9999876 PP

                             Wzt_C 109 drdge 113
                                       +++++
  gi|474935062|ref|YP_007688644.1| 215 SANSN 219
                                       65554 PP

>> YtkA  YtkA-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   6.6e-06     0.011      20      81 ..      63     126 ..      47     127 .. 0.78
   2 ?   -1.5   0.0       2.5   4.1e+03      27      46 ..     152     172 ..     138     193 .. 0.53
   3 ?    1.0   0.0      0.41   6.7e+02       4      36 ..     189     221 ..     186     224 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.6e-06
                              YtkA  20 gentivvt...vtqggkpVedadvkvefwmpameGmeemttkvelke.sedGvYeaevnfsmeGtW 81 
                                       ++ t++++    +++g++V++a+ + +++ + m+G++  +  +++   s+ G Y +e + ++ Gt+
  gi|474935062|ref|YP_007688644.1|  63 NSLTVSYEvalLDDDGDKVTGATTRENGTLT-MSGGK-GSISLTVNSqSKAGNYTLEFKTTETGTY 126
                                       4445544223599*********977777766.77787.68999998899****************9 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.5
                              YtkA  27 tvt.qggkpVedadvkvefwm 46 
                                       tvt ++ + V+ ad  v f+ 
  gi|474935062|ref|YP_007688644.1| 152 TVTlENTSNVNIADLGVYFYI 172
                                       333344555555554333333 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.41
                              YtkA   4 sddlevelvspeepkagentivvtvtqggkpVe 36 
                                        ++ ev++  + e+k g++t+ v+ +  ++ V+
  gi|474935062|ref|YP_007688644.1| 189 GKTSEVTFDYTGELKSGKHTFYVESSSANSNVS 221
                                       567799999999*********998777776665 PP

>> DUF2610  Domain of unknown function (DUF2610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   8.9e-05      0.14      41      75 ..     136     170 ..     117     176 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.9e-05
                           DUF2610  41 eRggqvpeevveslskLfklakennvsfeeLivya 75 
                                       eR g++p ++ve ++  ++l +  nv++++L vy+
  gi|474935062|ref|YP_007688644.1| 136 ERVGKLPVKIVEPVTLTVTLENTSNVNIADLGVYF 170
                                       89********************************8 PP

>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00027      0.45      35      87 ..      68     125 ..      42     134 .. 0.70
   2 ?    0.0   0.0      0.74   1.2e+03      53      88 ..     184     219 ..     143     223 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00027
                                       EEEEEEE-TTSSEEEEEEE....EE-CTTE.EEEEEE--TT--SEEEEEEEEECSTTT CS
                               MG2  35 plkltirdpdgkevkelpl....atdetgg.aesefalpeaaklGeysvelsadsaee 87 
                                       ++++ + d+dg +v   +     + + +gg  + ++++++++k G+y++e+++ ++++
  gi|474935062|ref|YP_007688644.1|  68 SYEVALLDDDGDKVTGATTrengTLTMSGGkGSISLTVNSQSKAGNYTLEFKTTETGT 125
                                       5677778888877776666444433333445899*****************5544443 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.74
                                       EEE-CTTEEEEEEE--TT--SEEEEEEEEECSTTT- CS
                               MG2  53 latdetggaesefalpeaaklGeysvelsadsaees 88 
                                       ++ ++  + e++f+   + k G+ + +++ +sa+++
  gi|474935062|ref|YP_007688644.1| 184 VDIEAGKTSEVTFDYTGELKSGKHTFYVESSSANSN 219
                                       344555568888888999999999988866655554 PP

>> SecG  Preprotein translocase SecG subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00013      0.21      24      66 ..     220     258 ..     212     260 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                                       CSCCHHTT...SS-SS--SSCCCHHCCHHHHHHHHHHHHHHHH CS
                              SecG  24 gaglsgafgggasdslfgsrgaekfLtkiTvilavlFfvlslv 66 
                                        +gl+ a    + ++++  +g  + L+ i+ il v+F++l++ 
  gi|474935062|ref|YP_007688644.1| 220 VSGLGEAC---S-STFYYDQGDYDYLNYIMGILLVVFIILCIW 258
                                       34555333...2.3466999*********************95 PP

>> DUF2057  Uncharacterized protein conserved in bacteria (DUF2057)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.016        27       2      49 ..      65     112 ..      64     122 .. 0.89
   2 ?    5.9   0.0    0.0082        13       9      60 ..     168     213 ..     160     225 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.016
                           DUF2057   2 LkvpdniellavdgqkvksslfkgaksltLtpGkhqivvrykdlfkdd 49 
                                       L+v+ ++ ll  dg kv++  ++++ +lt+  Gk  i +++++  k +
  gi|474935062|ref|YP_007688644.1|  65 LTVSYEVALLDDDGDKVTGATTRENGTLTMSGGKGSISLTVNSQSKAG 112
                                       899999999999***************************999877555 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0082
                           DUF2057   9 ellavdgqkvksslfkga.ksltLtpGkh.qivvrykdlfkddsdsdsqdlvkS 60 
                                        ++++dg k+      g+ k+++++ Gk  ++++ y+  +k+++    + +v+S
  gi|474935062|ref|YP_007688644.1| 168 VYFYIDGNKID-----GSlKTVDIEAGKTsEVTFDYTGELKSGKH---TFYVES 213
                                       6889*******.....4449****9887538*********55443...346666 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00016      0.26     141     183 ..     228     270 ..     214     274 .] 0.70

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00016
                             MFS_1 141 gglla.sslgWravfyilaivsllafvlfllllpeepperkrks 183
                                       ++ ++ +++ + ++ yi++i+++++++l +++++ +p+++  k+
  gi|474935062|ref|YP_007688644.1| 228 SSTFYyDQGDYDYLNYIMGILLVVFIILCIWVFR-KPVKNYGKP 270
                                       4444449999***************996555555.555444443 PP

>> Invasin_D3  Invasin, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       2.4   3.9e+03      21      35 ..      27      41 ..      14      68 .. 0.63
   2 ?   11.7   6.4   0.00015      0.25      24      85 ..      69     137 ..      59     148 .. 0.65
   3 ?    6.0   0.9    0.0088        14      22      62 ..     149     191 ..     146     221 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.4
                        Invasin_D3 21 tstltvtlkDangnp 35
                                       s  t+t+ D++   
  gi|474935062|ref|YP_007688644.1| 27 VSHTTFTIDDEQVTS 41
                                      444566666665544 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00015
                        Invasin_D3  24 ltvtlkDangnpvsgltvtfstt.....sagtls.avt.dngdGtytatLtattagtatitptvnGvai 85 
                                        +v l D++g+ v+g+t   + t      +g++s +v  ++++G yt +++ t++gt++   ++n+v+ 
  gi|474935062|ref|YP_007688644.1|  69 YEVALLDDDGDKVTGATTRENGTltmsgGKGSISlTVNsQSKAGNYTLEFKTTETGTYSDGTEINNVER 137
                                       578999******999885544444442333343333333566688888888888888887777777554 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0088
                        Invasin_D3  22 stltvtlkDangnpvsgltvtfstt...sagtlsavtdngdGty 62 
                                        tltvtl+++++  ++ l v f  +    +g+l++v d ++G  
  gi|474935062|ref|YP_007688644.1| 149 VTLTVTLENTSNVNIADLGVYFYIDgnkIDGSLKTV-DIEAGKT 191
                                       69********************98854444577777.5555543 PP

>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0         2   3.3e+03      59      74 ..      36      54 ..      15      67 .. 0.65
   2 ?   -1.0   0.1       1.5   2.4e+03      60      80 ..      90     114 ..      46     125 .. 0.57
   3 ?    5.6   0.4     0.013        22      33      82 ..     155     209 ..     104     212 .. 0.80
   4 ?    5.6   0.2     0.013        21      46      82 ..     202     240 ..     199     242 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2
                                      C...EEEEBSTTEEEEEEE CS
                       Copper-bind 59 d...etkliggGekdsvtf 74
                                      d     + ig+Ge+++v +
  gi|474935062|ref|YP_007688644.1| 36 DeqvTSYRIGTGESFKVSI 54
                                      2334456688888888765 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.5
                                       EEEEBSTTE.EEEEEEE...SSEEE CS
                       Copper-bind  60 etkliggGe.kdsvtfd...eagtY 80 
                                        t+ ++gG+ + s+t++   +ag+Y
  gi|474935062|ref|YP_007688644.1|  90 GTLTMSGGKgSISLTVNsqsKAGNY 114
                                       2333333321344444454333435 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.013
                                       SSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEE.....SSEEEEE CS
                       Copper-bind  33 avmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfd.....eagtYkf 82 
                                            Nv ++  gv   +d +k++ + +t  i +G++++vtfd     ++g+ +f
  gi|474935062|ref|YP_007688644.1| 155 LENTSNVNIADLGVYFYIDGNKIDGSLKTVDIEAGKTSEVTFDytgelKSGKHTF 209
                                       4456688888888999999999999999999************555544444555 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.013
                                       STTTGGGTTSCTTC.EEEEBSTTEEEEEEEE.SSEEEEE CS
                       Copper-bind  46 vpagvdkdkvkaed.etkliggGekdsvtfd.eagtYkf 82 
                                       +++g  +++v+ +  + ++ g Ge+ s tf  ++g+Y++
  gi|474935062|ref|YP_007688644.1| 202 LKSGKHTFYVESSSaNSNVSGLGEACSSTFYyDQGDYDY 240
                                       677888888888776788*************88888*99 PP

>> Big_1  Bacterial Ig-like domain (group 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   3.4      0.18   2.9e+02      11      60 ..      71     126 ..      63     127 .. 0.64
   2 ?    9.5   0.4   0.00059      0.97       5      42 ..     147     185 ..     146     219 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.18
                             Big_1  11 atvkDangnpvagatV....tfsvsg..galsassgtTdanGkatvtltstkagtv 60 
                                       + + D +g  v gat     t+++sg  g++s +     + G++t +++ t+ gt+
  gi|474935062|ref|YP_007688644.1|  71 VALLDDDGDKVTGATTrengTLTMSGgkGSISLTVNSQSKAGNYTLEFKTTETGTY 126
                                       55566666666665432222788888545555555555667999999999999998 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00059
                             Big_1   5 dtntltatvkDangnpvagatVtfsvsggals.assgtT 42 
                                       + +tlt+t+ + ++  +a+  V f ++g+++  + +++ 
  gi|474935062|ref|YP_007688644.1| 147 EPVTLTVTLENTSNVNIADLGVYFYIDGNKIDgSLKTVD 185
                                       689*************************99875555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       818  (0.0456244); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 1680.13
//
Query:       gi|474935063|ref|YP_007688645.1|  [L=1865]
Description: putative membrane protein, required for N-linked glycosylation [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1865 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       999  (0.0557198); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 1.01u 0.31s 00:00:01.32 Elapsed: 00:00:00.52
# Mc/sec: 10725.36
//
Query:       gi|474935064|ref|YP_007688646.1|  [L=216]
Description: orotidine-5'-phosphate decarboxylase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      7e-41  140.3   0.2    8.4e-41  140.0   0.2    1.1  1  OMPdecase       Orotidine 5'-phosphate decarboxylase / HUMPS 
  ------ inclusion threshold ------
      0.012   15.6   1.7      0.017   15.1   0.0    2.0  2  DUF1471         Protein of unknown function (DUF1471)
       0.03   13.6   0.4       0.03   13.6   0.4    1.6  2  ThiG            Thiazole biosynthesis protein ThiG
      0.044   13.2   0.0       0.06   12.7   0.0    1.2  1  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
        0.1   12.9   0.0       0.24   11.7   0.0    1.7  1  SepF            Cell division protein SepF


Domain annotation for each model (and alignments):
>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.0   0.2   2.3e-44   8.4e-41       1     224 [.       5     207 ..       5     208 .. 0.91

  Alignments for each domain:
  == domain 1  score: 140.0 bits;  conditional E-value: 2.3e-44
                                       SEEEEEE-SSSHHHHHHHHHHHGGGSSEEEEEHHHHHHHTHH.HHTHHHHHHHHHTSEEEEEEEE-S-HHHHHHHHH CS
                         OMPdecase   1 snLclalDvatarelleladkvgpsivvlKthydlvegwgfegtgaklaalarkhgflifeDrKfaDIGntvekqat 77 
                                       s+L+lalD ++++++l++ad v   ++ +K++++lv + g      +++ ++ k+   +++D+K+aDI+ntv ++++
  gi|474935064|ref|YP_007688646.1|   5 SRLILALDETDREKALRIADSVSGTVDAIKINWPLVLSAG-----PEMITELSKRS-DVICDFKVADIPNTVHLIVE 75 
                                       68**************************************.....**********6.*******************9 PP

                                       STCHHHHTTESEEEEEGTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHHHSHHHHHHHHHHHHHHHTTESE CS
                         OMPdecase  78 agsarikewadivtvhavaGkasvkalaeaaekwgnrgllilaqmsskgnlmlqekgytqacveaarehkaedfvmG 154
                                            i+ +a +v++ha+ G++s+++++++a++ g + ++++++ms++g++++         +e+++    e++v G
  gi|474935064|ref|YP_007688646.1|  76 ---NSIDRGASAVICHAFTGSDSMREAVQVANAKG-ASIYAVTEMSHPGGQEFTA-----PNAERLAHVGVECGVKG 143
                                       ...78*****************************8.9*************88888.....999999999999***** PP

                                       EECCCHTHHHHHHTTCSCEEEHHHTT.EEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHHHHHH CS
                         OMPdecase 155 fvaqetlnateedaddfihltpgigl.eqggdgkgqqyntpekligiagadiiivGRgIlkagdpveeaer 224
                                       f+a +t++      + +  +++ ig  e  + g g q   +  +i+ agad++ivGR+I+ka+dp++ a +
  gi|474935064|ref|YP_007688646.1| 144 FIAPATRP------ERIAAIRQIIGDrEILSPGVGAQGGSASSAIR-AGADYVIVGRAIYKAEDPAAVADE 207
                                       ******99......45566666666555666666677776777777.89******************9986 PP

>> DUF1471  Protein of unknown function (DUF1471)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   4.8e-06     0.017      17      52 ..      93     126 ..      88     127 .. 0.82
   2 ?   -1.7   0.3      0.81   2.9e+03      27      35 ..     181     189 ..     178     199 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.8e-06
                                       HHHHHHHHHHHHHCT-SEEEECCECC..CTTEEEEE CS
                           DUF1471  17 sdledalskkAdekGAkyYrItsarennggnlhatA 52 
                                       sd  ++  + A++kGA+ Y +t+++   +g ++ tA
  gi|474935064|ref|YP_007688646.1|  93 SDSMREAVQVANAKGASIYAVTEMSH--PGGQEFTA 126
                                       5677888999**************99..66666555 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.81
                                       HHHCT-SEE CS
                           DUF1471  27 AdekGAkyY 35 
                                       A ++GA+y 
  gi|474935064|ref|YP_007688646.1| 181 AIRAGADYV 189
                                       888999984 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1      0.88   3.2e+03      70      83 ..      91     104 ..      73     114 .. 0.65
   2 ?   13.6   0.4   8.5e-06      0.03     179     223 ..     166     211 ..     128     214 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.88
                                       TT-SSHHHHHHHHH CS
                              ThiG  70 aGaktaeeAvriar 83 
                                       +G+ + +eAv++a+
  gi|474935064|ref|YP_007688646.1|  91 TGSDSMREAVQVAN 104
                                       35555555555553 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 8.5e-06
                                       EEES---SH.HHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHH CS
                              ThiG 179 ivDAGigsp.sdaaqamelGadavllntavaeakdpvamArafkla 223
                                       i+  G+g     a  a+  Gad v++  a+ +a+dp+a+A  +++ 
  gi|474935064|ref|YP_007688646.1| 166 ILSPGVGAQgGSASSAIRAGADYVIVGRAIYKAEDPAAVADEIAAE 211
                                       677788865157889*************************987765 PP

>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.7e-05      0.06      43     198 .]      42     196 ..      30     196 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.7e-05
                                       -B-HHHHHHHGGGE-S-EEEEE..ESSSHHHCHHHHHHCT-SEEEEE-S.T-TTHHHHHHHHHHTTSEEEEEE-TT- CS
                    Ribul_P_3_epim  43 tigplvvealrkltelpldvHL..mveevdrivpefaeagasiisvHaE.alehlkrtiqeikeaGakaglvlnpat 116
                                       + gp+++ +l k +++  d+ +  + + v  iv++ ++ gas +  Ha   ++ +++ +q   ++Ga    v + + 
  gi|474935064|ref|YP_007688646.1|  42 SAGPEMITELSKRSDVICDFKVadIPNTVHLIVENSIDRGASAVICHAFtGSDSMREAVQVANAKGASIYAVTEMSH 118
                                       5677778888887777777665223456788999999*****99999985789999999999999*99998888888 PP

                                       -GGGGTTTCCC-SEEEEESS-TT-SS----CCHHHHHHHHHHHHHHHT.---EEEEESS--TTTCHHHHHHT--EEE CS
                    Ribul_P_3_epim 117 plealeyllekldlvllmsvePgfgGQkFipevlekikkvrklideke.ldlkievDGGvkldnieqiaeagadvlV 192
                                       p    e ++++ + +    ve g  G     +  e+i ++r++i ++e l+  + + GG    +++ +++agad ++
  gi|474935064|ref|YP_007688646.1| 119 PGG-QEFTAPNAERLAHVGVECGVKGFIAPATRPERIAAIRQIIGDREiLSPGVGAQGG----SASSAIRAGADYVI 190
                                       854.588889999999999******9766677789*********987767888888888....5667778******* PP

                                       ESHHHH CS
                    Ribul_P_3_epim 193 agsavf 198
                                       +g+a++
  gi|474935064|ref|YP_007688646.1| 191 VGRAIY 196
                                       ****98 PP

>> SepF  Cell division protein SepF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   6.6e-05      0.24      25      52 ..       7      34 ..       1      40 [. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.6e-05
                                      EEEE-CCCTCHHHHHHHHHHHHHHHHCT CS
                              SepF 25 Vilnledldkeeakrivdflsgvvyald 52
                                      +il l+++d+e+a ri d +sg+v a++
  gi|474935064|ref|YP_007688646.1|  7 LILALDETDREKALRIADSVSGTVDAIK 34
                                      7999*********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1386.55
//
Query:       gi|474935065|ref|YP_007688647.1|  [L=353]
Description: Radical SAM domain protein, pyruvate formate-lyase activating enzyme -like protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-07   31.9   0.1    5.2e-07   30.2   0.0    1.8  2  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
      0.016   15.5   0.0      0.028   14.7   0.0    1.3  1  Fer4_12      4Fe-4S single cluster domain
      0.018   15.2   0.0      0.031   14.4   0.0    1.4  1  Fer4_14      4Fe-4S single cluster domain
        0.1   12.3   0.1       0.49   10.1   0.0    2.0  2  MukB_hinge   MukB hinge domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   1.2e-10   5.2e-07       3     105 ..      33     135 ..      31     141 .. 0.95
   2 ?   -1.6   0.0      0.67     3e+03      13      42 ..     243     270 ..     242     309 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 1.2e-10
                                       EESEESS--TTTSCCTT.....HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC CS
                                       xxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpet.....vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla 74 
                                       vt  C+ +C +C+++       v     gr+ s  eilee ++++    +++  ++gg+p+   d +  +  l k a
  gi|474935065|ref|YP_007688647.1|  33 VTGRCRAGCFYCPVSAEkkgkdVVYANEGRVDSDGEILEECRAMA----AEGAGITGGDPSETLDRTLHYISLLKDA 105
                                       7889***********99***************************9....9*************************** PP

                                       .CCTEEEEEEECSSCHGHHHHHHHHHTT-SEE CS
                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  75 .vpgiritvetngtlpdeeklerllelgvdrv 105
                                         +++++++ t+ + +  e +++l  +g+d +
  gi|474935065|ref|YP_007688647.1| 106 fGKDFHLHMYTSVISL--ENAKKLEAAGLDEI 135
                                       ***************6..9*******999876 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.67
                                       TTSCCTTHHHHHHHHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  13 fCarpetvrregrgrslsveeileevkelk 42 
                                       fC+ +++  +++  r++ +++ ++ ++e+ 
  gi|474935065|ref|YP_007688647.1| 243 FCSSTFK--DGVQLRNRLKRRAENTAREYD 270
                                       8999985..888889998888888888885 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   6.4e-06     0.028       8     100 ..      30     125 ..      23     135 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.4e-06
                           Fer4_12   8 lslfvsgCnlsCkgC...fnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpena.eallelvkevk 80 
                                       ++l +++C+  C +C     k+ +++ + +e   +   ei+e++     eg  ++GG+P++   +    ++l+k   
  gi|474935065|ref|YP_007688647.1|  30 VLLVTGRCRAGCFYCpvsAEKKGKDVVYANEGRVDSDGEILEECRAMAAEGAGITGGDPSETLDRtLHYISLLKDAF 106
                                       344467799999999322344444555777777888999*********************97665245678888887 PP

                           Fer4_12  81 eekpekdiwlytgytleels 100
                                        + +   ++ +++ +le+ +
  gi|474935065|ref|YP_007688647.1| 107 GKDF-HLHMYTSVISLENAK 125
                                       7777.466666666666654 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0     7e-06     0.031       4      90 ..      33     119 ..      30     134 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7e-06
                           Fer4_14   4 rlsgCnlsCkgCdnketwkselgkpqteelle...qilkdlkkseikiqglvltGGePLhyenkkellklvkrlkee 77 
                                        +++C+  C  C  ++++k +   + +e  ++   +il   + + ++++g  +tGG+P   e  +  l+ ++ lk+ 
  gi|474935065|ref|YP_007688647.1|  33 VTGRCRAGCFYCPVSAEKKGKDVVYANEGRVDsdgEIL--EECRAMAAEGAGITGGDPS--ETLDRTLHYISLLKDA 105
                                       489*********95555555444444444444000555..55566677999*******9..77999999******99 PP

                           Fer4_14  78 y.pekkiwletngt 90 
                                       + ++++ +++t+  
  gi|474935065|ref|YP_007688647.1| 106 FgKDFHLHMYTSVI 119
                                       97889999999864 PP

>> MukB_hinge  MukB hinge domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.31   1.4e+03      34      60 ..     102     129 ..      97     136 .. 0.81
   2 ?   10.1   0.0   0.00011      0.49      68     111 ..     281     325 ..     275     332 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.31
                        MukB_hinge  34 laerlggvLLseiydd.isledapyfea 60 
                                       l++++g  +  ++y   isle+a+++ea
  gi|474935065|ref|YP_007688647.1| 102 LKDAFGKDFHLHMYTSvISLENAKKLEA 129
                                       7788888888888876379******998 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00011
                        MukB_hinge  68 Aivv.kDleavkeklegledcpddlyliegdpdafdesvfeaeel 111
                                        iv  +Dle+++++++++ ++pd+l +i++d + ++ ++  +ee+
  gi|474935065|ref|YP_007688647.1| 281 GIVYaDDLEKAASYMREQYEVPDELMFIDRDRNRMEIAAWILEEI 325
                                       555426899***********************9888777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 2100.80
//
Query:       gi|474935066|ref|YP_007688648.1|  [L=142]
Description: NusA family KH domain protein, archaeal [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-13   49.4   3.4    2.5e-07   30.4   0.1    2.1  2  KH_2      KH domain
    2.1e-10   40.5   1.9      2e-09   37.4   0.3    2.3  2  KH_5      NusA-like KH domain
    1.5e-05   24.7   0.7       0.15   11.9   0.0    2.3  2  KH_1      KH domain
    0.00014   21.6   0.3    0.00045   20.0   0.1    1.9  2  KH_4      KH domain
  ------ inclusion threshold ------
      0.067   13.1   0.1       0.14   12.1   0.1    1.5  1  DUF1979   Domain of unknown function (DUF1979)


Domain annotation for each model (and alignments):
>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.1   6.8e-11   2.5e-07      15      74 ..      24      87 ..      12      91 .. 0.81
   2 !   21.1   0.4   5.6e-08    0.0002      10      53 ..      84     129 ..      75     137 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 6.8e-11
                                      EEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTC....EEEEEEEET CS
                              KH_2 15 vskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkk....VklnivkVk 74
                                      ++ v+  +t++++++v+ ++q  i++Gk+G  +kk++   +k+i+++e+++      ln++++ 
  gi|474935066|ref|YP_007688648.1| 24 TNAVDCMDTEEKLVFVVEKGQGNIAVGKNGDHMKKLKDLTGKNIQVVEYSDdpkqFVLNVFHIY 87
                                      5566777899**************************************9987777555666555 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 5.6e-08
                                       TECETEEEEEEEC.CS.CEEEEEEEESCHHHHHTGGGHHHHHHHHH CS
                              KH_2  10 ikkagvskveIer.ta.nrviiviresqpgivIGkgGsnikkigke 53 
                                       +   +  +v+Ie+      +++++  +++g++IGk+G+n++  +  
  gi|474935066|ref|YP_007688648.1|  84 FHIYEPTNVVIEQrGDiTHATVTVNPEKKGRAIGKNGKNLRIARDI 129
                                       556667778888853348899*******************988765 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.3   5.5e-13     2e-09       2      68 ..      33      93 ..      32      94 .. 0.86
   2 ?    2.6   0.1     0.041   1.5e+02       7      31 ..     105     124 ..      98     137 .. 0.79

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 5.5e-13
                              KH_5  2 GertkvaVkshnpnvdpvGaivgkkGsrikavsseLkgekidvvewseDlaefianalsPaevlsVk 68
                                      +e+ +++V++++        +vgk+G+ +k++++ L g++i+vve+s+D+++f+ n+++ +e ++V 
  gi|474935066|ref|YP_007688648.1| 33 EEKLVFVVEKGQ-----GNIAVGKNGDHMKKLKD-LTGKNIQVVEYSDDPKQFVLNVFHIYEPTNVV 93
                                      577888999998.....3346**********987.55*********************999988885 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.041
                              KH_5   7 vaVkshnpnvdpvGaivgkkGsrik 31 
                                       v V  ++      G ++gk+G++ +
  gi|474935066|ref|YP_007688648.1| 105 VTVNPEK-----KGRAIGKNGKNLR 124
                                       5555555.....89*******9875 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   4.1e-05      0.15      15      42 ..      49      77 ..      37     100 .. 0.81
   2 !   11.3   0.1   6.6e-05      0.24       3      23 ..     104     124 ..     102     129 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.1e-05
                                      HTGGGHHHHHHHHHHT-EEEEES.STT.. CS
                              KH_1 15 IGkgGsnIkeIreetgakIkvpk.sedeg 42
                                      +Gk+G + k++++ tg +I+v++ s+d++
  gi|474935066|ref|YP_007688648.1| 49 VGKNGDHMKKLKDLTGKNIQVVEySDDPK 77
                                      6*********************8777764 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 6.6e-05
                                       EEEEGGGHHHHHHTGGGHHHH CS
                              KH_1   3 rilvPsslvgriIGkgGsnIk 23 
                                       +++v+ ++ gr IGk+G+n++
  gi|474935066|ref|YP_007688648.1| 104 TVTVNPEKKGRAIGKNGKNLR 124
                                       78999**************98 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.39   1.4e+03      20      49 ..      27      54 ..      15      65 .. 0.54
   2 !   20.0   0.1   1.3e-07   0.00045       7      57 ..      79     129 ..      74     141 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.39
                              KH_4 20 vteeeeeeeveielnvegedlGrvIGkrGr 49
                                      v+++++e  +++   ve+ +  + +Gk+G 
  gi|474935066|ref|YP_007688648.1| 27 VDCMDTE--EKLVFVVEKGQGNIAVGKNGD 54
                                      5555333..333333333333334555554 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 1.3e-07
                              KH_4   7 ilkalvddpeevevteeeeeeeveielnvegedlGrvIGkrGrtldAlqyl 57 
                                       ++ ++++  e  +v +e+  + +  +++v++e++Gr IGk+G++l+  + +
  gi|474935066|ref|YP_007688648.1|  79 FVLNVFHIYEPTNVVIEQRGDITHATVTVNPEKKGRAIGKNGKNLRIARDI 129
                                       555666666777788887789999********************9855555 PP

>> DUF1979  Domain of unknown function (DUF1979)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   3.8e-05      0.14       3      27 ..      34      58 ..      32      68 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.8e-05
                           DUF1979  3 sklifdivyGeGnvrfGqdGvDLse 27
                                      +kl+f +  G Gn+ +G++G  +  
  gi|474935066|ref|YP_007688648.1| 34 EKLVFVVEKGQGNIAVGKNGDHMKK 58
                                      69******************76655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 866.49
//
Query:       gi|474935067|ref|YP_007688649.1|  [L=94]
Description: Ribosomal protein L30E [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.9e-13   47.8   0.5    2.4e-12   46.4   0.5    1.6  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil
  ------ inclusion threshold ------
      0.071   13.6   0.1       0.13   12.8   0.1    1.4  1  eRF1_3          eRF1 domain 3


Domain annotation for each model (and alignments):
>> Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.5   2.7e-16   2.4e-12       4      94 ..       8      92 ..       6      93 .. 0.93

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 2.7e-16
                                      HHHHHHHHHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHHHTTEEEEEESCHHHHHHHTTSSSECSE CS
                    Ribosomal_L7Ae  4 eevlkkakkagklvlGlkevtkalergeaklvilAedvepeekkkllealckekevpyvkvkskkeLGelvgkkrpvsa 82
                                       ++lk+a  +gk+  G+ ++ ka++ g+a+++i++e+++ +          k+ +v+++++++  eLG+l+g +  v+a
  gi|474935067|ref|YP_007688649.1|  8 GKALKAAISTGKVEFGTVQTEKAVKAGKAQMIIVSENCPSAFLAN-----NKDVKVHVFSGNN-MELGALCGVPYSVAA 80
                                      5899***********************************988777.....6799999999999.**********99*** PP

                                      EEEEESTTTHHH CS
                    Ribosomal_L7Ae 83 laikdegdskdl 94
                                      la++d+g s++l
  gi|474935067|ref|YP_007688649.1| 81 LAVIDKGTSNIL 92
                                      *********997 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   1.4e-05      0.13      18      50 ..      16      48 ..       1      70 [. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.4e-05
                                      TCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTS CS
                            eRF1_3 18 dtgkavYGveevlkalemgAvetLLvseelers 50
                                       tgk+ +G  +++ka++ g  + ++vse+  + 
  gi|474935067|ref|YP_007688649.1| 16 STGKVEFGTVQTEKAVKAGKAQMIIVSENCPSA 48
                                      478*************************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 652.68
//
Query:       gi|474935068|ref|YP_007688650.1|  [L=494]
Description: DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.3e-47  160.0   0.3    1.2e-46  159.3   0.3    1.5  1  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
    0.00015   21.8   0.3    0.00061   19.8   0.1    2.2  2  HHH_2           Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.3   0.3   1.4e-50   1.2e-46      66     265 ..     128     436 ..      13     438 .. 0.88

  Alignments for each domain:
  == domain 1  score: 159.3 bits;  conditional E-value: 1.4e-50
                                       S...........................B--TT-BHHHHHHHHHHHHHHCCCSSTTSSTCSSTSSSSSSHHHHHHHH CS
                                       x...........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5  66 g...........................lvepGeavGiiaaQSiGePgTQltlnTFHfaGvasknvtlGvprlkeil 115
                                       +                            +   e+ G++aa SiGePgTQ++l+TFHfaG    +vt+G+prl ei+
  gi|474935068|ref|YP_007688650.1| 128 VaekvgididdetverlvtragemydshKMAQNESAGVMAAHSIGEPGTQMNLRTFHFAGDTFLSVTQGLPRLIEIV 204
                                       144444444555555555555555555678889******************************************** PP

                                       TT-SS-SS-EEEEEB-SSSSSCHHHCHHHHHHHSE.......................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................................... RF
                    RNA_pol_Rpb1_5 116 nvskniksksltvllvdeeakelekakkvkkaiek.......................................... 150
                                       ++ ++ +++s+t+ l+  ++++++ a +++++i+                                           
  gi|474935068|ref|YP_007688650.1| 205 DARREPSTPSMTIPLMGLAKTDKNIASHIASNIQIttlsdvadlttditnmrimvkpspkildekglniddivdrln 281
                                       *******************9999999888888877899*************************************** PP

                                       ..........................................CBTTEEEEEEEEEEEEEEETEEEEEEECS--HHHH CS
                                       ..........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5 151 ..........................................gikkikrilvkeaekgkeeekelvletegvnlsev 185
                                                                                 gi +ikr+lvke+ +++ + k +++ teg nl e+
  gi|474935068|ref|YP_007688650.1| 282 kvkavrgmvtktddyniviasdepsfskmqamydairntklkGIDGIKRALVKEDVDKTGQ-KYYTILTEGSNLGEI 357
                                       *****************************************************99988888.89************* PP

                                       TTSTTTBETTTEEESSHHHHHHHHCHHHHHHHHHHHHHHHHHHTTS---HHHHHHHHHHHTTTSS---SSTTCHCCS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5 186 lkveevvdageilsndiaeileilgieaarkallkeiqevykvqgvsvndrHlelivdqmtkkgeivavnrsGinka 262
                                       lkv+e v+a ++++n+i e++ +lgieaar+ ++ e ++++k+ g++v+ rH++l++d+mt  g++ a++r+G+  +
  gi|474935068|ref|YP_007688650.1| 358 LKVPE-VEAPKVMTNSILEVADVLGIEAARNSIVYEATSTLKNAGLDVDIRHIMLVADLMTNDGTVRAIGRHGVSGK 433
                                       *****.********************************************************************988 PP

                                       SSH CS
                                       xxx RF
                    RNA_pol_Rpb1_5 263 els 265
                                       ++s
  gi|474935068|ref|YP_007688650.1| 434 KSS 436
                                       876 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1   6.8e-08   0.00061      11      55 ..      17      59 ..       9      66 .. 0.88
   2 ?   -3.3   0.0       1.1     1e+04      29      45 ..     451     467 ..     446     469 .. 0.60

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 6.8e-08
                             HHH_2 11 VGektAklLakrFksldaLkkasleeLlevddiGeeiAqsivefF 55
                                      +  +tA lL++++ sl a k+a +eeL+e+  +Gee+Aq++ + +
  gi|474935068|ref|YP_007688650.1| 17 INDETASLLVSKYSSLGAVKDAGAEELAEL--VGEEMAQEVMSKL 59
                                      5578************************98..9********8765 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.1
                             HHH_2  29 LkkasleeLlevddiGe 45 
                                       L +a + e+ +++++ e
  gi|474935068|ref|YP_007688650.1| 451 LHAAMVGEIDHLEGVTE 467
                                       45556666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (494 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       768  (0.0428356); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.28s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 3092.02
//
Query:       gi|474935069|ref|YP_007688651.1|  [L=951]
Description: DNA-directed RNA polymerase, subunit A' [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.5e-96  321.9   0.0    5.8e-96  321.5   0.0    1.1  1  RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
    5.8e-63  212.0   0.1    1.2e-62  211.0   0.1    1.5  1  RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
    9.6e-34  116.6   0.0    1.8e-33  115.7   0.0    1.5  1  RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
    1.3e-27   96.9   0.1    2.2e-27   96.2   0.1    1.3  1  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
    3.1e-27   94.6   0.0    6.9e-27   93.5   0.0    1.6  1  RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
  ------ inclusion threshold ------
       0.16   11.8   0.8       0.44   10.4   0.1    2.1  2  Rad50_zn_hook   Rad50 zinc hook motif


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  321.5   0.0     2e-99   5.8e-96       2     312 .]       6     328 ..       5     328 .. 0.92

  Alignments for each domain:
  == domain 1  score: 321.5 bits;  conditional E-value: 2e-99
                                       E---EEEEEE--HHHHHHH-SBB--STTSTCSTSSSSBBSSSSSSSSS-SSSSSTSTTTSSTTTT-----EEEEEEC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1   2 kkikeiqfgiaspeeirkwSvvevtkaetieekslkPeegGllDerlgtidkdleCetCgkkkkeCeghfGhieLak 78 
                                       k+i +i+f+ +speeirk+++v++ +a+t++++   P e+Gl+D ++g+i+  l+C+tCg k  eC+ghfG+i+La+
  gi|474935069|ref|YP_007688651.1|   6 KRIGSIKFSCLSPEEIRKMAAVKIITADTYDDEG-HPIEQGLMDMHMGVIEPGLRCKTCGCKVDECPGHFGYIDLAE 81 
                                       899****************************995.****************************************** PP

                                       EEE-HHHHHHHHHHCTTCETT..TTEBSS-TTSH....HHHHHHCSSSCC.......CCHHHHHHHHCCS-BE-SSS CS
                                       xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1  79 Pvfhigffklilkilecvcke..cskllldeekkkllsklkkrekleelk.......krlkaieelckkinlcekCg 146
                                       Pv h+gf+k i+ +le +c++  c++l+l+ee+  + + +k+++ + e+          +k+i++  ++ + c  Cg
  gi|474935069|ref|YP_007688651.1|  82 PVTHVGFVKDIKMLLEATCRNpkCGRLMLTEEQ--IGKMQKRMDSILEFGgdtidqkVYSKEIAKEASNNTSCPICG 156
                                       *******************95559*****9983..355555555555555666665588999*************** PP

                                       SB-EEEEEETTEEEEEESSSST......SCEEEE-HHHHHHHHHCSTHHHHHHTTSBTTTB-GGGCCECCEEE--GG CS
                                       xxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1 147 avqpkleeegeklkaalkkske......eekeklsaekvkkllkriededvevlgfkssgsrPewliltvlPVpPpe 217
                                       a q k++ ++ +   ++++s+        ++++l++++++  l+ i+d+d++vlg++++ +rPew+ilt l VpP++
  gi|474935069|ref|YP_007688651.1| 157 ADQMKIKLDKPTRFREVEPSHGkddnspARSHDLTPKEIRARLELIPDDDLRVLGIDPATCRPEWMILTALAVPPVT 233
                                       *99999766666666666655555667677899******************************************** PP

                                       GS-BEESSSSSEEBECCCCHHHHHHHHHHHHHHHHHSSSSSTCHHHHHHHHHHHHHHCC-TTSSSSSEEBSTTSSS- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1 218 iRPsvqldggrrsedDlteklrdiikrNnrLkkaeeegapeliieeekelLQehvatlfdneisglkpatqkskrpl 294
                                       +RPs++ld+g rsedDlt+kl+d++++N+rL++++++gap+liie+ +elLQ+h++t+fdn+ sg++pa+++s+r+l
  gi|474935069|ref|YP_007688651.1| 234 VRPSITLDSGDRSEDDLTHKLVDVLRINQRLRENRDAGAPQLIIEDLRELLQYHITTYFDNQTSGTPPARHRSGRSL 310
                                       ***************************************************************************** PP

                                       -THHHHHTSSSSCCCCCT CS
                                       xxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1 295 kslsqrLkGKeGrfRgnL 312
                                       k+l qrLkGKeGrfR nL
  gi|474935069|ref|YP_007688651.1| 311 KTLAQRLKGKEGRFRSNL 328
                                       *****************9 PP

>> RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.0   0.1   3.9e-66   1.2e-62       1     166 []     330     503 ..     330     503 .. 0.94

  Alignments for each domain:
  == domain 1  score: 211.0 bits;  conditional E-value: 3.9e-66
                                       SEEESSEEEEEEEEESSS-TTEEEEEHHHHTTSEEEEE-STTTHHHHHHHHHHTTTSSS.......SEEEEESTTSS CS
                    RNA_pol_Rpb1_2   1 GkrvdysaRsvispdpnlkldevgvPisvakkltvpeivtelnikklrklvengpevyP.......gasyvkredgs 70 
                                       Gkrv++saR+vispdpnl+++evgvP+  a+ l+vp  v+e ni+k+r++v++gp+ +        g +yv+r+dg+
  gi|474935069|ref|YP_007688651.1| 330 GKRVNFSARTVISPDPNLSINEVGVPVIAARELSVPMHVNERNIEKMREYVKRGPSPADdengyvfGVNYVIRNDGR 406
                                       9*****************************************************97432222222399********* PP

                                       EEETTTT-S.CHHCCTTTTSEEEEE--TTSEEEEE-SSTTSGGGEEEEEEEEESSSSEEEEGGGHCCCT--SSS-EE CS
                    RNA_pol_Rpb1_2  71 ekklkakkr.klakelekgdiverhvkdgdvvllNRqPsLhklsimahrvkvlekktlrlnlsvttayNaDFDGDem 146
                                       + +++ +++ ++a+ l++ ++v r+++dgd+vl+NRqPsLh++simahrv+v++++t+r+nl+v+++yNaDFDGDem
  gi|474935069|ref|YP_007688651.1| 407 KIRVTPDNAeTVAEGLSIDYVVWRQLIDGDIVLFNRQPSLHRMSIMAHRVRVMKGRTFRFNLCVCAPYNADFDGDEM 483
                                       *****999978****************************************************************** PP

                                       EEE--SSHHHHHHHHHCSBT CS
                    RNA_pol_Rpb1_2 147 nlhlpqseearaEaeelllv 166
                                       nlh+ qseearaEa+ +++v
  gi|474935069|ref|YP_007688651.1| 484 NLHVLQSEEARAEARIIMQV 503
                                       ***************99975 PP

>> RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.7   0.0     6e-37   1.8e-33       1     156 [.     506     668 ..     506     669 .. 0.89

  Alignments for each domain:
  == domain 1  score: 115.7 bits;  conditional E-value: 6e-37
                                       CSEETTTTEESSS--THHHHHHHHHSSTTEEEEHHHHHHHHHHSSSCCSSSSSS.SSSBESS..SEBEEHHHHHHCC CS
                    RNA_pol_Rpb1_3   1 nilspqsgkPvigivQDsllGvyllTkedvfidreeaqqllykgvgsdsktvtl.rpailkp..kelwtgkqtfsri 74 
                                       nilsp+ g P+ig ++D+++G+y lT+ +  + + e +++l+k      +++++ +pa      ++ wtg+q+fs++
  gi|474935069|ref|YP_007688651.1| 506 NILSPRYGGPIIGGIHDHISGSYFLTHGNPHFGKWETMNILMKL-----PEIEPpEPAGTDEngEPYWTGRQLFSLV 577
                                       9****************************999999999999999.....34444044444433445*********** PP

                                       CHCCCCEEEE.SSSS.........STSEEECSSEEEES--SHHHHSSSSTTSHHHHHHHHCHHHHHHHHHHHHHHHH CS
                    RNA_pol_Rpb1_3  75 lpneinyerk.neek.........dgkvlikngelikGvidkkvvgkksqgslihvlakeygiketvrfldslqrlg 141
                                       lp+++n++ k ++ k         dg v+i+ng+l++G+id++++g +s+g++++ +a++yg++++++fl+ ++rl+
  gi|474935069|ref|YP_007688651.1| 578 LPDNFNIKFKsSITKsldkddpdfDGLVIIRNGQLLEGTIDESAIG-NSKGKILEKIARDYGSDRAAKFLNEVTRLA 653
                                       *********96333367789999***********************.9***************************** PP

                                       HHHHHHHCEB-TGGG CS
                    RNA_pol_Rpb1_3 142 fkyllqsgftigigD 156
                                        + ++++gf++gi+D
  gi|474935069|ref|YP_007688651.1| 654 LGTIMNHGFSTGISD 668
                                       *************99 PP

>> RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.2   0.1   7.3e-31   2.2e-27       1      66 [.     807     872 ..     807     915 .. 0.89

  Alignments for each domain:
  == domain 1  score: 96.2 bits;  conditional E-value: 7.3e-31
                                       B--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTEEEETTSEEEETTS-EEESSGGGTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5   1 GLkvkefffhtmggReGLiDtAvkTaesGYlqRrlvkaledvvvkyddtvrnsggeivqflygedg 66 
                                       GL+++efffh+mggReGL+DtAv+T++sGY+qRrl+ aled+  + d+t+rn+ g ivqf+ygedg
  gi|474935069|ref|YP_007688651.1| 807 GLTPTEFFFHAMGGREGLVDTAVRTSRSGYMQRRLISALEDLKLTSDGTIRNTVGAIVQFKYGEDG 872
                                       9****************************************************************8 PP

>> RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.5   0.0   2.3e-30   6.9e-27       2     107 ..     695     799 ..     694     800 .. 0.95

  Alignments for each domain:
  == domain 1  score: 93.5 bits;  conditional E-value: 2.3e-30
                                       HHHCTHTCCHHHTTHCHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTTSHHHHHHHCTSSS-HHHHHHHHTB-EEEEB CS
                    RNA_pol_Rpb1_4   2 eeaerygkledlpgksleelfeakinkilnkardkagkiaskslaasNsiliMvksGaKGsiinisqiagclGqqnv 78 
                                       e++ + + le   g + e ++e++i+k+l +ar +ag+ia ++l  sN+ +iM+k+Ga+Gs++n+sq+agc+Gqq+v
  gi|474935069|ref|YP_007688651.1| 695 ESFHD-QTLEASQGGTAETTLENQIMKVLGDARTTAGNIAGSKLGMSNPAVIMAKTGARGSMTNLSQMAGCVGQQTV 770
                                       56666.8899999********************************88****************************** PP

                                       TTBSS--SSTSCSSTTSSSSESSTTTSSE CS
                    RNA_pol_Rpb1_4  79 egkripkgfsgrtlphfkkidespesrGF 107
                                       +g+ri++g+ +rtlphf + d ++ ++GF
  gi|474935069|ref|YP_007688651.1| 771 RGERISRGYWQRTLPHFPREDLGAYAKGF 799
                                       ****************************9 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.9   5.6e+03      12      33 ..      92     113 ..      88     125 .. 0.64
   2 ?   10.4   0.1   0.00015      0.44       7      27 ..     137     157 ..     135     158 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.9
                                       HHHHTT-SEE-TTT--EE-HHH CS
                     Rad50_zn_hook  12 ieelkeakgcCPlCgReldeeh 33 
                                       i++l ea+ + P CgR + +e+
  gi|474935069|ref|YP_007688651.1|  92 IKMLLEATCRNPKCGRLMLTEE 113
                                       6666666644488999776665 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00015
                                       HHHHHHHHHTT-SEE-TTT-- CS
                     Rad50_zn_hook   7 elnkkieelkeakgcCPlCgR 27 
                                        + k i + ++++ +CP Cg 
  gi|474935069|ref|YP_007688651.1| 137 VYSKEIAKEASNNTSCPICGA 157
                                       6999999***9********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (951 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.82u 0.36s 00:00:01.18 Elapsed: 00:00:00.54
# Mc/sec: 5256.44
//
Query:       gi|474935070|ref|YP_007688652.1|  [L=1207]
Description: DNA-directed RNA polymerase, subunit B' [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     1e-123  413.3   0.1   1.5e-123  412.8   0.1    1.2  1  RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
    3.2e-31  108.4   0.0    4.9e-30  104.6   0.0    2.7  2  RNA_pol_Rpb2_1  RNA polymerase beta subunit
    3.3e-27   94.7   0.1    9.2e-27   93.3   0.1    1.9  1  RNA_pol_Rpb2_7  RNA polymerase Rpb2, domain 7
    3.9e-26   91.9   0.5    6.9e-26   91.1   0.5    1.4  1  RNA_pol_Rpb2_2  RNA polymerase Rpb2, domain 2
    1.4e-25   89.2   0.1      3e-25   88.2   0.1    1.6  1  RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3
    1.2e-19   70.3   0.5    3.5e-19   68.8   0.5    1.9  1  RNA_pol_Rpb2_4  RNA polymerase Rpb2, domain 4
    6.3e-15   55.5   0.2    1.5e-14   54.3   0.2    1.7  1  RNA_pol_Rpb2_5  RNA polymerase Rpb2, domain 5
     0.0036   17.2   6.3     0.0076   16.2   0.4    2.6  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
  ------ inclusion threshold ------
        1.4    9.0   4.1        4.8    7.3   0.4    2.6  2  Elf1            Transcription elongation factor Elf1 like
        1.8    8.7   5.6        4.3    7.5   0.3    2.5  2  TerY_C          TerY-C metal binding domain
          2    8.5   4.3         74    3.4   0.6    3.4  3  Ogr_Delta       Ogr/Delta-like zinc finger
        3.4    7.7   4.4        5.2    7.1   0.0    3.0  3  zf_CopZ         Zinc binding domain


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  412.8   0.1  9.9e-127  1.5e-123       2     390 .]     738    1109 ..     737    1109 .. 0.96

  Alignments for each domain:
  == domain 1  score: 412.8 bits;  conditional E-value: 9.9e-127
                                        HHT-SS-TTB-HHHHHHHHHHGGGB-S---TTTTT---SSEEEESS----SSB-S.TTTTTS........GGGS- CS
                    RNA_pol_Rpb2_6    2 aklapvvehvqspriiiqaamekqalgiyslnkfkrsnqktyllcinqkPlvktgdkveagqvldgpatekgela 76  
                                        a ++p++eh+++pr+++ a m+kqalgi+++n+  r +++ ++++++q P+v+t+ ++++++        ++  +
  gi|474935070|ref|YP_007688652.1|  738 AGIVPYPEHNSAPRVTMGAGMAKQALGIAAANYRIRPDTRGHVMHYPQVPMVQTQ-TMDYIG--------YKYRP 803 
                                        7889***************************************************.******........***** PP

                                        SEEEEEBBBS--TTTTTTT-EEEBCHHHHTTTT-EEEEEE..EEE--SSSS---.-S--..-.....-SS-GGGS CS
                    RNA_pol_Rpb2_6   77 lGqnavVAvmsyeGYniEDaiilnerlvdrdvftsihikeyeveardtklgeeeitrdipnv.....seealkkL 146 
                                        +Gqn+++Avmsy+GYniEDai++n+++vdr++ +++++++y+ e r++++g+e+ ++ ++++      +ea++ L
  gi|474935070|ref|YP_007688652.1|  804 AGQNFCIAVMSYHGYNIEDAIVMNKSSVDRGLGRTTFLRSYRAEERRYPGGQEDRFEIPSEEivgirADEAYAAL 878 
                                        ****************************************************99999888889***99******* PP

                                        -TTSB--SS-EEETT-EEE---..B-----...-----------..-B---EE--TT-EEEEEEEEE.......E CS
                    RNA_pol_Rpb2_6  147 dedGivrvgaevkegdilvgkvtkgeteltpeekllraifgekarevkdtslrvksgeegvVdkvkvfsrekgde 221 
                                        ++dGi+++++ vk  d+l+gk+  ++ ++  e+   + +++ek    ++ts++v++ge+g+Vd+v+v       +
  gi|474935070|ref|YP_007688652.1|  879 EDDGIISPETFVKGSDVLIGKT--SPPRFI-EDPAGELMTNEK---RRETSVTVRPGEQGYVDSVIV-------T 940 
                                        *********************8..666665.333333333333...589******************.......8 PP

                                        E-TT--EEEEEEEEEEE---TT-BEEETTS---BBEEEB-TTTSEEETTS---SEEE-GGGCHHH-BTTHHHHHH CS
                    RNA_pol_Rpb2_6  222 lkagvnklvkvyvaqkRklqvGDKfasrhGqKGvvslilpqeDmPfledGivvDivlNPlgvPSRmtigqllEtl 296 
                                        +++++++lv+v+v+++R +++GDKf+sr GqKGvv+++++q DmPf++dG+++Div+NP+g+PSRmtig++lE++
  gi|474935070|ref|YP_007688652.1|  941 ESDNGSRLVRVKVRDERIPELGDKFCSRFGQKGVVGRLVDQCDMPFTADGVTPDIVVNPHGIPSRMTIGHVLEMI 1015
                                        999************************************************************************ PP

                                        HHHCCCSSSS--B--TT-...-HHHHHHHHHTTS-TT-EE-EEETTTS-B-SS-EEB-EEEEEEBS--CCCS--- CS
                    RNA_pol_Rpb2_6  297 lgkaaalegkkvdatvFdgakeeeikelLeeagleasGkevlydGrtGekleaeifvGviYylkLkhlvedKiha 371 
                                        +gk++++e + +d+t+F+g++e+ i++ L ++g++++Gke++y+GrtG++++++++ Gvi+y kL+h+v+ K+h+
  gi|474935070|ref|YP_007688652.1| 1016 AGKVGSMEARTIDGTAFSGESEDSIRDGLVRNGFARTGKEIMYNGRTGHMVQTDVYTGVIFYEKLHHMVSGKLHV 1090
                                        *************************************************************************** PP

                                        -SS--B-TTT--B-SCGGG CS
                    RNA_pol_Rpb2_6  372 RstGpyslltqQPlgGkaq 390 
                                        Rs+Gp++ lt+QP++G+++
  gi|474935070|ref|YP_007688652.1| 1091 RSRGPVQILTRQPTEGRSR 1109
                                        *****************86 PP

>> RNA_pol_Rpb2_1  RNA polymerase beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.6   0.0   3.3e-33   4.9e-30       2     194 ..      16     440 ..      15     449 .. 0.87
   2 ?   -1.1   0.0      0.73   1.1e+03      94     115 ..    1142    1163 ..    1129    1179 .. 0.75

  Alignments for each domain:
  == domain 1  score: 104.6 bits;  conditional E-value: 3.3e-33
                                       TTHHHHHHHHHH.............................HHTHHHHHCTTSSECCHCSSSHCSSSCEEEEEEEEE CS
                                       xxxxxxxxxxxx.............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb2_1   2 LvsqqldSFnkf.............................veqdlekiikeeaaieseeeiqssgeelelkfvsir 49 
                                       +v+ ++ SF++f                             ++ d e+  + e +i++  + ++ g+    +   ir
  gi|474935070|ref|YP_007688652.1|  16 IVNHHIASFDDFlctkdnpnsrmqkivddirvptddaargiIRLDTERTGGREIEIRIGRRRREDGTVDPQDKPTIR 92 
                                       577788888888888888888888877777777555555555555555555555555555554444445556678** PP

                                       EESCSSECTTSCEEES.HHHHHHCTSBXEEEEEEEEEEEECCCCTCCEEEEEEEEEEEEEXBTTSTTSSST...... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...... RF
                    RNA_pol_Rpb2_1  50 lgkPvvdesdasereiyPkearlrnltYsaplyvklklvvyekdnkeeikeeevyiGelPlMlrskacvls...... 120
                                       +++P   e+++  ++i P+earlrnl Y +p++v+ + ++ + ++ e ++   v +Ge+P+M++sk c+l+      
  gi|474935070|ref|YP_007688652.1|  93 IDHPQLIEANGYAHDIHPMEARLRNLNYMSPVSVHFEVTI-DGEEMELENGGWVRVGEMPMMIKSKGCNLYrgnlee 168
                                       **************************************99.677888888999***************996322222 PP

                                       ....TS.H....HHHHHTTS.TTS..SSEEETTCEEEEXEEEE.................................. CS
                                       ....xxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................. RF
                    RNA_pol_Rpb2_1 121 ....ease....eelvelkEcpldqGGyFiinGtekvivaqek.................................. 155
                                           ++++    eelv+ kE+p ++GGyFii Gte+v++ +e+                                  
  gi|474935070|ref|YP_007688652.1| 169 qlerKLNDeeyaEELVKQKEDPREPGGYFIIGGTERVLITLEDlapnrvmceyderygtavetakvfsqregyralt 245
                                       22111111222268*************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                    RNA_pol_Rpb2_1 156 ............................................................................. 155
                                                                                                                    
  gi|474935070|ref|YP_007688652.1| 246 qvekkkdgilmvsvpvvtseiplialmkalgmesdseiydtivskeyesdmanivyaniedsmdpkkyapnafhtte 322
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                    RNA_pol_Rpb2_1 156 ............................................................................. 155
                                                                                                                    
  gi|474935070|ref|YP_007688652.1| 323 daiaylernfaagqakeyrtkkvesildrsllphlgdtkedrkkkaiylgriaksvlemsigkrkaddkdhysnkrl 399
                                       ***************************************************************************** PP

                                       .XHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSS.SSSHHH CS
                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                    RNA_pol_Rpb2_1 156 .laGeLlaslfrvllkklerdvkerlqkslekld.dlmlql 194
                                        l G+L+++lfr+ +  l +d+k +l++++++++ +++ + 
  gi|474935070|ref|YP_007688652.1| 400 kLSGDLMEDLFRNSFSALMKDLKYQLERNMGRKRnEINIAS 440
                                       ******************************99883355555 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.73
                                        TCCEEEEEEEEEEEEEXBTTST CS
                                        xxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb2_1   94 nkeeikeeevyiGelPlMlrsk 115 
                                         +++    + ++G++ +M+r+ 
  gi|474935070|ref|YP_007688652.1| 1142 GTQQYVCGNPKCGHIAIMTRNG 1163
                                        55556666779*********94 PP

>> RNA_pol_Rpb2_7  RNA polymerase Rpb2, domain 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.3   0.1   6.2e-30   9.2e-27       1      86 [.    1111    1203 ..    1111    1204 .. 0.94

  Alignments for each domain:
  == domain 1  score: 93.3 bits;  conditional E-value: 6.2e-30
                                        BBEEEEHHHHHHHHHHTBHHHHHHHHTTTTTEEEEEEESS..SSSCCCEE.....EBTTTTCSSSEEEEEEEHHH CS
                    RNA_pol_Rpb2_7    1 GGlrfGEMErdaliayGaaalLkerltikSDavevdvcgr..ckllaaan.....eCkivkseekiekveipeaf 68  
                                        GGlrfGEMErd+li++G a+++k+rl+++SD ++ +vcg+  c+++a+++     +C+++ ++++i+ v++++af
  gi|474935070|ref|YP_007688652.1| 1111 GGLRFGEMERDCLIGHGVAMVIKDRLLDESDGTQQYVCGNpkCGHIAIMTrngqlYCPVCGNNSSIHLVQTSYAF 1185
                                        9*************************************9633778888779************************ PP

                                        HHHHHHHHHTTBEEEEES CS
                    RNA_pol_Rpb2_7   69 klLlqeLqslgialklll 86  
                                        klL++eL slg+a++l+l
  gi|474935070|ref|YP_007688652.1| 1186 KLLMDELLSLGVAMRLQL 1203
                                        **************9875 PP

>> RNA_pol_Rpb2_2  RNA polymerase Rpb2, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.1   0.5   4.6e-29   6.9e-26       2     190 .]     214     400 ..     213     400 .. 0.88

  Alignments for each domain:
  == domain 1  score: 91.1 bits;  conditional E-value: 4.6e-29
                                       TSCEEEEE-SSSSSE..SSSCCEECCCEEEEECCCCSTSCEEEEECTTSSSEEEHHHHHHHTT--STTHHHHHHTS. CS
                    RNA_pol_Rpb2_2   2 sngiyvekekdknki..satvtsslisqrgsvlklekdgktliwtriskkrkipivivlkAlglvsdreIlericy. 75 
                                        n++++e +++       a+v s ++ +r+++ +++k++++l+++ + ++++ip++ ++kAlg+ sd eI++ i+  
  gi|474935070|ref|YP_007688652.1| 214 PNRVMCEYDERYGTAveTAKVFSQREGYRALTQVEKKKDGILMVSVPVVTSEIPLIALMKALGMESDSEIYDTIVSk 290
                                       58888888888777777789999999*************************************************66 PP

                                       .......SSTTHHHHHHHHHHHHHHCTSSSCHHHHHHHHHCSSTTSSSCCCCCHHHHHHHCHHHHHHHTTTTSSTTT CS
                    RNA_pol_Rpb2_2  76 .......dsedsqlleelleeleekeeiqtqeealdyigkvvalrrgeearlqsareilqkrydlgeigreklnkhl 145
                                              +  + ++++ + +++   +   t+e+a+ y+ + +a+++ +e r ++ + il         +r  l+ hl
  gi|474935070|ref|YP_007688652.1| 291 eyesdmaNIVYANIEDSMDPKKYAPNAFHTTEDAIAYLERNFAAGQAKEYRTKKVESIL---------DRSLLP-HL 357
                                       77888844445555556666666667789*****************************9.........799999.** PP

                                       TTSSSTCHH..HHHHHHHHHHHHHHHHTTSSSS--TTSGGGEEEE CS
                    RNA_pol_Rpb2_2 146 glseslenkrlkaqdilymidrLlslklgrrevDDiDhlgnkRvr 190
                                       g  ++  +  +ka +++ +++ +l+++ g+r+ DD+Dh+ nkR++
  gi|474935070|ref|YP_007688652.1| 358 GDTKEDRK--KKAIYLGRIAKSVLEMSIGKRKADDKDHYSNKRLK 400
                                       *9999444..6********************************96 PP

>> RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.2   0.1     2e-28     3e-25       1      67 [.     469     532 ..     469     533 .. 0.96

  Alignments for each domain:
  == domain 1  score: 88.2 bits;  conditional E-value: 2e-28
                    RNA_pol_Rpb2_3   1 qvldrlnplselshlrrvsslrgglskerkttevRdlhpshwGriCpveTPEGencGlvksLallar 67 
                                       q+ldr++ +s++shlrr++s    l++++ ++e+Rdlhp++wGr+Cp+eTPEG+ncGlvk+ al + 
  gi|474935070|ref|YP_007688652.1| 469 QLLDRTSNMSTVSHLRRITSS---LTRSQPHFEARDLHPTQWGRLCPSETPEGQNCGLVKNAALIID 532
                                       89*****************88...*************************************999876 PP

>> RNA_pol_Rpb2_4  RNA polymerase Rpb2, domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.8   0.5   2.4e-22   3.5e-19       1      61 [.     561     621 ..     561     622 .. 0.98

  Alignments for each domain:
  == domain 1  score: 68.8 bits;  conditional E-value: 2.4e-22
                                       EECTT-BEEE-S-HCCHHHHHHHHCCTTSS-TT-EEEE-TTT--EEEE-SSEEB-EEEEE- CS
                    RNA_pol_Rpb2_4   1 VfvNGrllGvtrdpkklvetlRelRRkgkiseevsivlnekqkevkiatDgGRvcRPliiV 61 
                                       VfvNG+l+G+++d kkl+e+++e RR g+i+++v+i ++e+  e+ i++D GR++RPl+i 
  gi|474935070|ref|YP_007688652.1| 561 VFVNGDLVGTCSDSKKLIEDVKEHRRYGNINNNVNIRYDEEMGEIIINCDDGRLRRPLLIL 621
                                       9**********************************************************97 PP

>> RNA_pol_Rpb2_5  RNA polymerase Rpb2, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3   0.2     1e-17   1.5e-14       1      58 []     643     730 ..     643     730 .. 0.96

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 1e-17
                                       HHHHHHTTSEEEEEHHHHTT--EESSTTTCSST.-SSTTTSS-..............................-TTS CS
                    RNA_pol_Rpb2_5   1 wddLlregvvEylDaeEEetamIamtpedleks.reekealee..............................kens 46 
                                       wd+L++ gv+E++DaeEEe+a++ +tp++++k+ +++++al+e                               ens
  gi|474935070|ref|YP_007688652.1| 643 WDNLFHYGVMEWVDAEEEEDALVLVTPYETPKRcPCCGHALSEtdvdwmnpgkkgdcelscrwcgdkftvpskLENS 719
                                       ***********************************************************************966666 PP

                                       SSST-SEEES-G CS
                    RNA_pol_Rpb2_5  47 kshtyTHcEIhP 58 
                                       k+  yTH+E++P
  gi|474935070|ref|YP_007688652.1| 720 KV-PYTHLEVDP 730
                                       66.********9 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.4   5.1e-06    0.0076      12      50 ..     657     700 ..     651     710 .. 0.75
   2 ?    2.9   1.0     0.072   1.1e+02      32      54 ..    1151    1172 ..    1148    1175 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.1e-06
                    OrfB_Zn_ribbon  12 akeyGikveevnpayTSktCseCgsknke.....alsgrtfkCp 50 
                                       a+e+   +++v p+ T k+C++Cg+ ++e      + g++  C+
  gi|474935070|ref|YP_007688652.1| 657 AEEEEDALVLVTPYETPKRCPCCGHALSEtdvdwMNPGKKGDCE 700
                                       677777899*******************9777774444444443 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.072
                    OrfB_Zn_ribbon   32 seCgsknkealsgrtfkCpnCgf 54  
                                        ++Cg++      + +++Cp Cg 
  gi|474935070|ref|YP_007688652.1| 1151 PKCGHIAIM-TRNGQLYCPVCGN 1172
                                        79****999.899999*****97 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.4    0.0032       4.8      23      58 ..     675     713 ..     665     726 .. 0.73
   2 ?    1.9   0.3      0.16   2.4e+02      43      57 ..    1162    1176 ..    1146    1184 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0032
                              Elf1  23 dCpfCnheks.vevkldk..kekiaevsCkvCgesfetk 58 
                                       +Cp C+h  s  +v+  +  k++  e+sC+ Cg +f++ 
  gi|474935070|ref|YP_007688652.1| 675 RCPCCGHALSeTDVDWMNpgKKGDCELSCRWCGDKFTVP 713
                                       7*****98554445544411666889********99976 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.16
                              Elf1   43 iaevsCkvCgesfet 57  
                                        ++++ C vCg + ++
  gi|474935070|ref|YP_007688652.1| 1162 NGQLYCPVCGNNSSI 1176
                                        667777777766554 PP

>> TerY_C  TerY-C metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.8     0.076   1.1e+02      72     113 ..     671     711 ..     648     721 .. 0.64
   2 ?    7.5   0.3    0.0029       4.3      90     115 ..    1152    1177 ..    1142    1187 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.076
                            TerY_C  72 eGapgCPhCgnalafavCeCgkllCidgeeeatCpwCgkevk 113
                                       e    CP+Cg al+ +  +  +    +g+ e  C wCg + +
  gi|474935070|ref|YP_007688652.1| 671 ETPKRCPCCGHALSETDVDWMNP-GKKGDCELSCRWCGDKFT 711
                                       55568*****8766544443332.235677788888888766 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0029
                            TerY_C   90 eCgkllCidgeeeatCpwCgkevkfg 115 
                                        +Cg++  ++ +++  Cp Cg++ +++
  gi|474935070|ref|YP_007688652.1| 1152 KCGHIAIMTRNGQLYCPVCGNNSSIH 1177
                                        79999999999999999999988766 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.6      0.05        74       1       9 [.     675     683 ..     675     691 .. 0.87
   2 ?    2.7   0.0     0.083   1.2e+02      26      36 ..    1146    1156 ..    1134    1161 .. 0.85
   3 ?    1.1   0.1      0.26   3.9e+02       2      11 ..    1167    1176 ..    1166    1181 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.05
                         Ogr_Delta   1 rCPhCgapa 9  
                                       rCP+Cg++ 
  gi|474935070|ref|YP_007688652.1| 675 RCPCCGHAL 683
                                       7*****985 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.083
                         Ogr_Delta   26 yqCsnfeCgat 36  
                                        y+C n+ Cg+ 
  gi|474935070|ref|YP_007688652.1| 1146 YVCGNPKCGHI 1156
                                        99*******95 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.26
                         Ogr_Delta    2 CPhCgapaaa 11  
                                        CP Cg+++ +
  gi|474935070|ref|YP_007688652.1| 1167 CPVCGNNSSI 1176
                                        *****99876 PP

>> zf_CopZ  Zinc binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   2.0       8.2   1.2e+04       2       9 ..     674     681 ..     673     684 .. 0.85
   2 ?    7.1   0.0    0.0035       5.2      19      44 ..    1128    1153 ..    1126    1155 .. 0.82
   3 ?    0.5   0.0      0.39   5.9e+02       4      11 ..    1167    1174 ..    1164    1192 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 8.2
                                       -B-TTT-- CS
                           zf_CopZ   2 kkCPvCgk 9  
                                       k+CP Cg+
  gi|474935070|ref|YP_007688652.1| 674 KRCPCCGH 681
                                       68****98 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0035
                                        HHHHB-GGGGGG--S-EE.E---TT- CS
                           zf_CopZ   19 vkhllkpellekvkeedYylCknedC 44  
                                        v  ++k+ ll++ ++++ y+C n++C
  gi|474935070|ref|YP_007688652.1| 1128 VAMVIKDRLLDESDGTQQYVCGNPKC 1153
                                        667899******6666666******* PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.39
                                        -TTT--B- CS
                           zf_CopZ    4 CPvCgkkG 11  
                                        CPvCg+++
  gi|474935070|ref|YP_007688652.1| 1167 CPVCGNNS 1174
                                        *****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.89u 0.33s 00:00:01.22 Elapsed: 00:00:00.56
# Mc/sec: 6545.55
//
Query:       gi|474935071|ref|YP_007688653.1|  [L=89]
Description: DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-28   97.3   0.1      4e-28   97.1   0.1    1.0  1  RNA_pol_Rpb5_C  RNA polymerase Rpb5, C-terminal domain
  ------ inclusion threshold ------
      0.076   12.5   0.1      0.091   12.2   0.1    1.1  1  ATP-grasp_5     ATP-grasp domain


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb5_C  RNA polymerase Rpb5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.1   0.1   4.5e-32     4e-28       1      73 []       8      86 ..       8      86 .. 0.94

  Alignments for each domain:
  == domain 1  score: 97.1 bits;  conditional E-value: 4.5e-32
                                      ..-TSSSS--EEEEE-HHHHHHHHHHTT--TTCSS-EETTSHHHHCC......T--TTSEEEEEEEETTTEEEEEEEEE CS
                    RNA_pol_Rpb5_C  1 vnitkHelvPkhevlseeekkellkklkikeeqLPkisksDpvaryl......glkkGdvvkItrksetageavtYRlV 73
                                      +ni++H+lvP+h++lseee++e+l++l+i++eqLPki+++D+++  l       +++G+v+k++rks+tage+++YRlV
  gi|474935071|ref|YP_007688653.1|  8 FNILEHDLVPEHHLLSEEETQEVLSRLGISREQLPKIKTTDAAIMILskirkePITEGSVIKVIRKSDTAGEFEAYRLV 86
                                      7*******************************************6666666669************************9 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1     1e-05     0.091       7      64 ..      19      76 ..      15      79 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1e-05
                       ATP-grasp_5  7 rtlLteaeakelleaygipvvetrlassaeeaveaaeeigypvvlKivspdilhKtdv 64
                                       +lL+e+e++e+l+ +gi+  +   ++++++a+ + ++i         + ++++K+d 
  gi|474935071|ref|YP_007688653.1| 19 HHLLSEEETQEVLSRLGISREQLPKIKTTDAAIMILSKIRKEPITEGSVIKVIRKSDT 76
                                      689***********************************98777667777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 587.79
//
Query:       gi|474935072|ref|YP_007688654.1|  [L=728]
Description: ATPases of the AAA+ class [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-87  290.2   0.0    1.5e-43  148.4   0.0    2.4  2  AAA              ATPase family associated with various cellul
    1.6e-33  114.2   1.7    8.8e-17   60.6   0.2    2.6  2  AAA_lid_3        AAA+ lid domain
    2.2e-14   54.2   0.0    0.00017   22.0   0.0    4.4  4  AAA_16           AAA ATPase domain
    3.4e-12   46.4   0.0    5.3e-05   23.0   0.0    2.9  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    1.9e-10   40.8   0.0    1.4e-09   38.0   0.0    2.3  2  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    3.3e-10   40.1   0.0     0.0025   17.8   0.0    3.8  2  AAA_5            AAA domain (dynein-related subfamily)
      1e-09   38.8   0.0    0.00092   19.4   0.0    3.7  3  AAA_2            AAA domain (Cdc48 subfamily)
    1.9e-09   37.9   0.2      0.009   16.3   0.0    4.0  2  AAA_22           AAA domain
    1.3e-08   34.5   0.1     0.0026   17.0   0.0    2.5  2  TIP49            TIP49 P-loop domain
    1.9e-08   34.9   0.0      0.003   18.1   0.0    2.7  2  AAA_18           AAA domain
    1.9e-08   34.6   0.0     0.0037   17.4   0.0    2.5  2  AAA_33           AAA domain
    5.6e-08   32.7   0.0      0.015   15.1   0.0    2.5  2  IstB_IS21        IstB-like ATP binding protein
    6.4e-08   32.5   0.0    0.00057   19.7   0.0    2.5  2  AAA_24           AAA domain
    3.6e-07   30.6   0.0     0.0074   16.6   0.0    2.4  2  AAA_28           AAA domain
      4e-07   29.6   0.2      0.014   14.8   0.0    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    1.1e-06   28.2   0.4      0.019   14.3   0.0    3.0  3  ATPase           KaiC
    1.2e-06   27.8   0.2      0.018   14.1   0.0    2.2  2  Parvo_NS1        Parvovirus non-structural protein NS1
    1.9e-06   27.5   0.0      0.019   14.5   0.0    2.4  2  AAA_7            P-loop containing dynein motor region
    2.2e-06   28.0   0.0       0.11   12.9   0.0    2.6  2  RNA_helicase     RNA helicase
    3.7e-06   27.0   0.0      0.039   14.0   0.0    2.3  2  AAA_14           AAA domain
    3.7e-06   26.8   0.2       0.12   12.4   0.0    2.6  2  Vps4_C           Vps4 C terminal oligomerisation domain
    7.8e-06   25.7   0.0       0.24   11.1   0.0    3.0  2  Sigma54_activat  Sigma-54 interaction domain
    9.9e-06   25.7   0.0      0.075   13.1   0.0    2.5  2  Sigma54_activ_2  Sigma-54 interaction domain
    1.5e-05   24.7   0.1       0.59    9.7   0.0    4.4  4  AAA_25           AAA domain
    2.2e-05   24.5   0.0       0.14   12.2   0.0    2.8  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      3e-05   23.7   0.1    6.1e-05   22.7   0.1    1.5  1  CDC48_2          Cell division protein 48 (CDC48), domain 2
    4.2e-05   23.4   0.2       0.14   11.9   0.0    2.9  3  AAA_30           AAA domain
    8.5e-05   22.4   0.0       0.67    9.8   0.0    3.2  3  AAA_3            ATPase family associated with various cellul
     0.0001   22.8   0.4        1.5    9.3   0.1    3.3  3  AAA_17           AAA domain
    0.00012   21.9   0.1        2.2    8.0   0.0    4.1  4  DEAD             DEAD/DEAH box helicase
    0.00014   22.1   0.0      0.048   13.8   0.0    2.3  2  Cytidylate_kin2  Cytidylate kinase-like family
    0.00021   20.6   0.1       0.65    9.2   0.0    2.5  2  DUF2075          Uncharacterized conserved protein (DUF2075)
    0.00025   21.6   0.1       0.23   11.9   0.0    2.6  2  ABC_tran         ABC transporter
    0.00035   20.6   0.0       0.17   11.8   0.0    2.9  3  Rad17            Rad17 P-loop domain
    0.00035   20.1   0.2       0.81    9.1   0.0    2.5  2  PhoH             PhoH-like protein
    0.00062   19.7   0.0        6.2    6.7   0.0    3.6  3  NACHT            NACHT domain
    0.00092   19.1   0.0       0.93    9.2   0.0    2.3  2  AAA_11           AAA domain
     0.0011   19.3   0.3        2.1    8.7   0.0    2.4  2  AAA_19           AAA domain
     0.0043   16.5   0.0        2.3    7.6   0.0    2.4  2  IPT              Isopentenyl transferase
     0.0058   15.8   0.0        2.4    7.3   0.0    2.2  2  NB-ARC           NB-ARC domain
  ------ inclusion threshold ------
      0.014   14.7   0.1        5.8    6.1   0.0    2.3  2  Zeta_toxin       Zeta toxin
      0.014   14.6   0.0        1.6    7.8   0.0    2.5  3  DUF815           Protein of unknown function (DUF815)
      0.024   14.8   0.0        1.9    8.6   0.0    2.3  2  SKI              Shikimate kinase
      0.025   14.5   0.0        9.2    6.1   0.0    3.0  3  ATPase_2         ATPase domain predominantly from Archaea
      0.026   14.3   0.0        2.5    7.8   0.0    2.4  2  Cytidylate_kin   Cytidylate kinase
      0.039   13.4   0.0         10    5.5   0.0    2.6  2  TniB             Bacterial TniB protein
      0.042   13.6   0.0         11    5.8   0.0    2.5  2  AAA_29           P-loop containing region of AAA domain
      0.079   12.0   0.0        1.1    8.3   0.0    2.2  2  MCM              MCM P-loop domain
       0.15   12.6   0.4        8.6    6.8   0.1    2.4  2  AAA_23           AAA domain
       0.19   11.6   0.0         15    5.5   0.0    2.6  2  NTPase_1         NTPase
       0.25   11.3   0.0         25    4.8   0.0    2.5  2  ResIII           Type III restriction enzyme, res subunit


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.4   0.0   4.3e-46   1.5e-43       1     131 [.     220     349 ..     220     350 .. 0.97
   2 !  139.6   0.0   2.2e-43   7.7e-41       1     131 [.     495     624 ..     495     625 .. 0.97

  Alignments for each domain:
  == domain 1  score: 148.4 bits;  conditional E-value: 4.3e-46
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgs 77 
                                       vllyGppGtGKTl+a+a+a+e+g++f+++ g+el+ kyvg se++irelf++a  +  psi+f+DEid++a++r+g+
  gi|474935072|ref|YP_007688654.1| 220 VLLYGPPGTGKTLIAEAIANESGASFYSVRGPELVGKYVGWSENNIRELFDRAAGNT-PSIIFFDEIDSIASQRDGR 295
                                       79**************************************************98886.******************* PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       +++  +++++q+lt +dg+ +k++ vivigatnrp +ldpa++r gRfdr+iei+
  gi|474935072|ref|YP_007688654.1| 296 SDDAYRNMLSQILTCMDGLGSKDG-VIVIGATNRPGDLDPAIRRpGRFDREIEIG 349
                                       *********************866.***************************986 PP

  == domain 2  score: 139.6 bits;  conditional E-value: 2.2e-43
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgs 77 
                                       vllyGppGtGKTl+aka+a+e g +f+ ++g+el+  + g++e+ ir++f++ak++a psi+f+DEid++a+ r  +
  gi|474935072|ref|YP_007688654.1| 495 VLLYGPPGTGKTLIAKALANENGYNFIPVNGPELMGRFHGDTEEGIRKVFDRAKSMA-PSIIFFDEIDSVAPMRGAD 570
                                       79******************************************************9.****************888 PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                         ++ +++v+qLlt ldgv++ + +v+v++atnrpd++dpa+lr gR+dr i i+
  gi|474935072|ref|YP_007688654.1| 571 GGRSYDSMVAQLLTCLDGVSELK-DVLVLAATNRPDMIDPAVLRpGRIDRMILIG 624
                                       99999****************75.5*************************99876 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.1   9.6e-17   3.4e-14       1      36 [.     374     409 ..     374     436 .. 0.74
   2 !   60.6   0.2   2.5e-19   8.8e-17       1      44 [.     646     689 ..     646     690 .. 0.98

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 9.6e-17
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgik 36 
                                       dvdl++LA++T+G++GAD+ al reAa+ Al+r+i 
  gi|474935072|ref|YP_007688654.1| 374 DVDLDRLAKMTQGFVGADITALAREAAMQALSRTIG 409
                                       9********************************643 PP

  == domain 2  score: 60.6 bits;  conditional E-value: 2.5e-19
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitmedfe 44 
                                       +vdl+++A +T+Gy+GADlaa+creA+l A  rg +++++edfe
  gi|474935072|ref|YP_007688654.1| 646 SVDLAQIAGMTDGYVGADLAAVCREAGLSAFHRGSDAVGQEDFE 689
                                       69*****************************************9 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0     5e-06    0.0018      24      51 ..     217     244 ..     207     262 .. 0.82
   2 ?    4.5   0.0      0.11        40     123     163 ..     265     312 ..     251     323 .. 0.81
   3 !   22.0   0.0   4.9e-07   0.00017      14      47 ..     482     515 ..     480     528 .. 0.87
   4 ?    3.0   0.0      0.35   1.2e+02     121     169 ..     538     597 ..     524     598 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 5e-06
                            AAA_16  24 pelvllsGesGvGKsslvrellralekd 51 
                                       p+ vll+G++G+GK+ ++++++++  ++
  gi|474935072|ref|YP_007688654.1| 217 PRGVLLYGPPGTGKTLIAEAIANESGAS 244
                                       599******************9876665 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.11
                            AAA_16 123 lkrllallsrderplvlvlDdlq........wadeaslqllaaLlrlle 163
                                       +++l+++++    p ++++D+++        + d+a +++l+++l+ ++
  gi|474935072|ref|YP_007688654.1| 265 IRELFDRAAG-NTPSIIFFDEIDsiasqrdgRSDDAYRNMLSQILTCMD 312
                                       6778888887.889*********99999999999999999998887654 PP

  == domain 3  score: 22.0 bits;  conditional E-value: 4.9e-07
                            AAA_16  14 salervrsgrpelvllsGesGvGKsslvrellra 47 
                                       +a+er+  ++++ vll+G++G+GK+ ++++l+++
  gi|474935072|ref|YP_007688654.1| 482 EAFERLGISQGRGVLLYGPPGTGKTLIAKALANE 515
                                       68999999*********************99975 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.35
                            AAA_16 121 ellkrllallsrderplvlvlDdlq............wadeaslqllaaLlrlleskpllv 169
                                       e +++ ++++++   p ++++D+++              d++ +qll +L   +e k +lv
  gi|474935072|ref|YP_007688654.1| 538 EGIRKVFDRAKS-MAPSIIFFDEIDsvapmrgadggrSYDSMVAQLLTCLDGVSELKDVLV 597
                                       567788889998.677*********999999999999999999999999988888777766 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   1.5e-07   5.3e-05      36      70 ..     220     254 ..     215     342 .. 0.77
   2 !   20.1   0.0   1.2e-06   0.00041      36      70 ..     495     529 ..     486     567 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.5e-07
                            RuvB_N  36 vllyGpPGlGkttlakiiakelgvklkitsgPvle 70 
                                       vllyGpPG Gkt +a+ ia+e g+++ +  gP l 
  gi|474935072|ref|YP_007688654.1| 220 VLLYGPPGTGKTLIAEAIANESGASFYSVRGPELV 254
                                       9*******************************874 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 1.2e-06
                            RuvB_N  36 vllyGpPGlGkttlakiiakelgvklkitsgPvle 70 
                                       vllyGpPG Gkt +ak +a+e g ++    gP l 
  gi|474935072|ref|YP_007688654.1| 495 VLLYGPPGTGKTLIAKALANENGYNFIPVNGPELM 529
                                       9**************************99999874 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.0     4e-12   1.4e-09       2      83 ..       8      89 ..       7      90 .. 0.87
   2 ?   -0.9   0.0       5.4   1.9e+03      20      39 ..     480     499 ..     480     525 .. 0.74

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 4e-12
                                      EEEECCS.S-CSSTTEEEE-HHHHHHHTS.-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEE CS
                           CDC48_N  2 LrVaeap.qedvgrgivridpedmeelgl.epgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkV 78
                                      LrV   +  +d g g+v id   +++lgl e+g +v+i+g+r++ a++  ++ +  + g++ +dg+tR+ ag+s++++V
  gi|474935072|ref|YP_007688654.1|  8 LRVISPKrTSDIGFGKVWIDAGSFRSLGLpESGSFVTITGRRTATAFAEISDSS--QSGTVIIDGPTRTSAGASVNERV 84
                                      56666666899*****************9779**********666666666655..58********************* PP

                                      EEEEE CS
                           CDC48_N 79 tVrka 83
                                       V++a
  gi|474935072|ref|YP_007688654.1| 85 AVSPA 89
                                      **996 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 5.4
                                       -HHHHHHHTS-TTSEEEEEC CS
                           CDC48_N  20 dpedmeelglepgdvveieg 39 
                                       ++e++e+lg+++g  v + g
  gi|474935072|ref|YP_007688654.1| 480 NREAFERLGISQGRGVLLYG 499
                                       6899*********9998866 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0     1e-05    0.0036       1      76 [.     219     287 ..     219     338 .. 0.76
   2 !   17.8   0.0     7e-06    0.0025       1      75 [.     494     561 ..     494     566 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1e-05
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--...........--------G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik..ngttslvdsplvraaregeilvlDEve 75 
                                       +vlL GppGtgK+ +ae +a   ++++  v +++      l+g++     n  ++l d     a+++++i+++DE++
  gi|474935072|ref|YP_007688654.1| 219 GVLLYGPPGTGKTLIAEAIANESGASFYSVRGPE------LVGKYVGWseNNIRELFDR---AAGNTPSIIFFDEID 286
                                       59******************99888888777765......5555552111112222221...233466666666666 PP

                                       G CS
                             AAA_5  76 r 76 
                                        
  gi|474935072|ref|YP_007688654.1| 287 S 287
                                       5 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 7e-06
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------.G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar.egeilvlDEve 75 
                                       +vlL GppGtgK+ +a+ la   + ++  v++++      l gr +  ++t++   +++ ra    ++i+++DE++
  gi|474935072|ref|YP_007688654.1| 494 GVLLYGPPGTGKTLIAKALANENGYNFIPVNGPE------LMGRFH--GDTEEGIRKVFDRAKSmAPSIIFFDEID 561
                                       59******************99999999998886......666666..4555555555554444667777777776 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   0.00015     0.051       7      97 ..     221     305 ..     216     315 .. 0.56
   2 ?   -1.2   0.0       5.5   1.9e+03       5      59 ..     358     410 ..     356     415 .. 0.83
   3 !   19.4   0.0   2.6e-06   0.00092       6     105 ..     495     588 ..     493     594 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00015
                                       EEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG-- CS
                             AAA_2   7 lllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKih 81 
                                       ll gp g+Gkt++a+a+a+   +    ++  +   el      + +  ++   ++   +a+ +   i+++DEid i+
  gi|474935072|ref|YP_007688654.1| 221 LLYGPPGTGKTLIAEAIANESGA----SFYSVRGPELVG----KYVGWSENNIRELFDRAAGNTpsIIFFDEIDSIA 289
                                       66777777777777777777764....666666666665....22222222222222223222257*********** PP

                                       -----------HHHHH CS
                             AAA_2  82 pkessgadvSregVqr 97 
                                       +++  ++d    + + 
  gi|474935072|ref|YP_007688654.1| 290 SQRDGRSDDAYRNMLS 305
                                       *633333333333333 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 5.5
                                       -EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHH CS
                             AAA_2   5 silllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrliga 59 
                                       +il + ++g G++++ +   + l  k ++ ++ ad ++l+  e++ + +sr ig+
  gi|474935072|ref|YP_007688654.1| 358 EILAIRTSGRGMPMADDVDLDRLA-KMTQGFVGADITALAR-EAAMQALSRTIGS 410
                                       578888999999998888887777.7899999999999999.9999999998886 PP

  == domain 3  score: 19.4 bits;  conditional E-value: 2.6e-06
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       +ll gp g+Gkt++akala+        ++i ++  el+     +   + ++g ++   +a+     i+++DEid +
  gi|474935072|ref|YP_007688654.1| 495 VLLYGPPGTGKTLIAKALANENGY----NFIPVNGPELMG----RFHGDTEEGIRKVFDRAKSMApsIIFFDEIDSV 563
                                       5789****************9997....************....99999999999999999999899********** PP

                                       ------------HHHHHHHHHHHH- CS
                             AAA_2  81 hpkessgadvSregVqrdLLqileg 105
                                       +p + +    S +  +  LL  l+g
  gi|474935072|ref|YP_007688654.1| 564 APMRGADGGRSYDSMVAQLLTCLDG 588
                                       **87777788888999999988887 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1     6e-05     0.021       8      65 ..     220     277 ..     216     323 .. 0.64
   2 !   16.3   0.0   2.6e-05     0.009       7      46 ..     494     524 ..     488     602 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee....erpevv.fvtlpsstsskdllrellralg 65 
                                       ++++G++GtGKT+ ++ ++++  +          ++pe+v ++   s+++ ++l+ + + ++ 
  gi|474935072|ref|YP_007688654.1| 220 VLLYGPPGTGKTLIAEAIANESGA-----SfysvRGPELVgKYVGWSENNIRELFDRAAGNTP 277
                                       589*****************9732.....1234567777776666666677777666665555 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 2.6e-05
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvt 46 
                                        ++++G++GtGKT+ ++ l++++         +  ++ v+
  gi|474935072|ref|YP_007688654.1| 494 GVLLYGPPGTGKTLIAKALANEN---------GYNFIPVN 524
                                       5789*****************98.........55555555 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   4.2e-05     0.015      51      89 ..     218     254 ..     214     274 .. 0.81
   2 !   17.0   0.0   7.3e-06    0.0026      49      89 ..     491     529 ..     486     547 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.2e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevy 89 
                                       r+vLl Gp+gtGkt +a ai++e g    f ++ g e+ 
  gi|474935072|ref|YP_007688654.1| 218 RGVLLYGPPGTGKTLIAEAIANESG--ASFYSVRGPELV 254
                                       89********************988..557777777665 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 7.3e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  49 aGravLlaGpsgtGktalaiaiskelgedvpfvalsgsevy 89 
                                        Gr+vLl Gp+gtGkt +a a+++e g    f+ ++g e+ 
  gi|474935072|ref|YP_007688654.1| 491 QGRGVLLYGPPGTGKTLIAKALANENG--YNFIPVNGPELM 529
                                       59**********************987..778888888875 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   0.00016     0.058       1      25 [.     220     262 ..     220     338 .. 0.66
   2 !   18.1   0.0   8.5e-06     0.003       1      29 [.     495     521 ..     495     558 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00016
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf..................g 25 
                                       +ll G+pG+GKt +a++++++ g                    
  gi|474935072|ref|YP_007688654.1| 220 VLLYGPPGTGKTLIAEAIANESGAsfysvrgpelvgkyvgwsE 262
                                       799***************9886333566666555555555552 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 8.5e-06
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlr 29 
                                       +ll G+pG+GKt +ak+L++++  g+n +
  gi|474935072|ref|YP_007688654.1| 495 VLLYGPPGTGKTLIAKALANEN--GYNFI 521
                                       799*****************99..44443 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   8.5e-05      0.03       2      45 ..     220     265 ..     220     328 .. 0.79
   2 !   17.4   0.0     1e-05    0.0037       2      43 ..     495     538 ..     495     557 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 8.5e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqsk 45 
                                       vll G+pG+GK+  ae ++++ g  ++ ++ ++l  +++g  ++++
  gi|474935072|ref|YP_007688654.1| 220 VLLYGPPGTGKTLIAEAIANESGasFYSVRGPELVGKYVGWSENNI 265
                                       7899*******************88888999998888887433333 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 1e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqq 43 
                                       vll G+pG+GK+  a+ l++++g  ++ ++ ++l+ r  g+ ++
  gi|474935072|ref|YP_007688654.1| 495 VLLYGPPGTGKTLIAKALANENGynFIPVNGPELMGRFHGDTEE 538
                                       7899*******************777779999999888885555 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   4.2e-05     0.015      48      74 ..     218     244 ..     204     256 .. 0.82
   2 !   14.9   0.0   4.6e-05     0.016      45      70 ..     490     515 ..     482     560 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.2e-05
                         IstB_IS21  48 enivllGpsGvGKshlaialgveavra 74 
                                        +++l Gp+G+GK+ +a a++ e  ++
  gi|474935072|ref|YP_007688654.1| 218 RGVLLYGPPGTGKTLIAEAIANESGAS 244
                                       6799****************9986555 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 4.6e-05
                         IstB_IS21  45 ekkenivllGpsGvGKshlaialgve 70 
                                       ++  +++l Gp+G+GK+ +a al+ e
  gi|474935072|ref|YP_007688654.1| 490 SQGRGVLLYGPPGTGKTLIAKALANE 515
                                       667889*****************976 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0    0.0012      0.41       5      22 ..     220     237 ..     217     303 .. 0.83
   2 !   19.7   0.0   1.6e-06   0.00057       5      70 ..     495     579 ..     491     596 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0012
                            AAA_24   5 iliyGpsgiGKTtlakel 22 
                                       +l+yGp+g+GKT +a  +
  gi|474935072|ref|YP_007688654.1| 220 VLLYGPPGTGKTLIAEAI 237
                                       79**********999876 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 1.6e-06
                            AAA_24   5 iliyGpsgiGKTtlakel....gpkplfi...........dtekGlksldadkfpdieswedfldevvel.....aa 61 
                                       +l+yGp+g+GKT +ak l    g++++ +           dte+G  +  +d+ +++   + f de++++     a+
  gi|474935072|ref|YP_007688654.1| 495 VLLYGPPGTGKTLIAKALanenGYNFIPVngpelmgrfhgDTEEGI-RKVFDRAKSMAPSIIFFDEIDSVapmrgAD 570
                                       89*****************9777777777*****************.888888899999999999999998888877 PP

                            AAA_24  62 eladyktlv 70 
                                         + y++ v
  gi|474935072|ref|YP_007688654.1| 571 GGRSYDSMV 579
                                       777777766 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00073      0.26       2      33 ..     220     256 ..     219     273 .. 0.78
   2 !   16.6   0.0   2.1e-05    0.0074       2      34 ..     495     528 ..     494     551 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00073
                            AAA_28   2 ivitGgestGKTtlleaLaar....gypvv.pEaare 33 
                                       + + G+++tGKT ++ea+a++     y+v  pE + +
  gi|474935072|ref|YP_007688654.1| 220 VLLYGPPGTGKTLIAEAIANEsgasFYSVRgPELVGK 256
                                       6799***************776444455556666555 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 2.1e-05
                            AAA_28   2 ivitGgestGKTtlleaLaar.gypvvpEaarei 34 
                                       + + G+++tGKT +++aLa++ gy+ +p  + e+
  gi|474935072|ref|YP_007688654.1| 495 VLLYGPPGTGKTLIAKALANEnGYNFIPVNGPEL 528
                                       6799***************766999886555444 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00022     0.076      25      43 ..     220     238 ..     215     240 .. 0.91
   2 !   14.8   0.0   3.9e-05     0.014      22      43 ..     492     513 ..     478     515 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00022
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll+GppG+GKt++a++++
  gi|474935072|ref|YP_007688654.1| 220 VLLYGPPGTGKTLIAEAIA 238
                                       89*************9875 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 3.9e-05
                      Mg_chelatase  22 gHnlllvGppGsGKtmlakrlp 43 
                                       g  +ll+GppG+GKt++ak+l+
  gi|474935072|ref|YP_007688654.1| 492 GRGVLLYGPPGTGKTLIAKALA 513
                                       5679***************986 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00091      0.32      15      38 ..     213     236 ..     205     245 .. 0.83
   2 ?   -1.3   0.0       3.3   1.2e+03     125     155 ..     285     315 ..     283     323 .. 0.89
   3 !   14.3   0.0   5.5e-05     0.019      14      38 ..     487     511 ..     471     521 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00091
                            ATPase  15 GipegrvvlitGepGtGKtifalq 38 
                                       Gi   r vl++G pGtGKt++a+ 
  gi|474935072|ref|YP_007688654.1| 213 GITPPRGVLLYGPPGTGKTLIAEA 236
                                       8888899**************985 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.3
                            ATPase 125 iDsitglayeekeavaReilrqlvrvlkklg 155
                                       iDsi++     +++  R+ l q+++ + +lg
  gi|474935072|ref|YP_007688654.1| 285 IDSIASQRDGRSDDAYRNMLSQILTCMDGLG 315
                                       99**99988889999*********9998876 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 5.5e-05
                            ATPase  14 gGipegrvvlitGepGtGKtifalq 38 
                                        Gi +gr vl++G pGtGKt++a+ 
  gi|474935072|ref|YP_007688654.1| 487 LGISQGRGVLLYGPPGTGKTLIAKA 511
                                       49*******************9975 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   5.1e-05     0.018     117     137 ..     220     240 ..     214     244 .. 0.89
   2 !   11.5   0.0   0.00034      0.12     117     136 ..     495     514 ..     490     517 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.1e-05
                         Parvo_NS1 117 vwfyGpantGktnlaeaIaka 137
                                       v++yGp+ tGkt +aeaIa+ 
  gi|474935072|ref|YP_007688654.1| 220 VLLYGPPGTGKTLIAEAIANE 240
                                       89*****************86 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00034
                         Parvo_NS1 117 vwfyGpantGktnlaeaIak 136
                                       v++yGp+ tGkt +a+a+a+
  gi|474935072|ref|YP_007688654.1| 495 VLLYGPPGTGKTLIAKALAN 514
                                       89****************97 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0    0.0011      0.38      34      57 ..     218     241 ..     208     249 .. 0.82
   2 !   14.5   0.0   5.5e-05     0.019      28      56 ..     487     515 ..     481     524 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0011
                             AAA_7  34 kpvllvGptGtGKtviikdllkkl 57 
                                       + vll+Gp GtGKt+i++ + ++ 
  gi|474935072|ref|YP_007688654.1| 218 RGVLLYGPPGTGKTLIAEAIANES 241
                                       679*************99987765 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 5.5e-05
                             AAA_7  28 lllknkkpvllvGptGtGKtviikdllkk 56 
                                       l +++++ vll+Gp GtGKt+i+k l ++
  gi|474935072|ref|YP_007688654.1| 487 LGISQGRGVLLYGPPGTGKTLIAKALANE 515
                                       558899*****************998776 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   0.00031      0.11       1      27 [.     220     252 ..     220     308 .. 0.70
   2 !   12.4   0.0   0.00044      0.15       1      21 [.     495     515 ..     495     527 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00031
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl......k 27 
                                       ++lyGp+g+GK+++a+ +a++   ++      +
  gi|474935072|ref|YP_007688654.1| 220 VLLYGPPGTGKTLIAEAIANESGASFysvrgpE 252
                                       689**************9988776655554433 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00044
                      RNA_helicase   1 iwlyGpsgeGKStlakeLaka 21 
                                       ++lyGp+g+GK+++ak La++
  gi|474935072|ref|YP_007688654.1| 495 VLLYGPPGTGKTLIAKALANE 515
                                       689**************9986 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0    0.0012      0.43       5      77 ..     220     289 ..     217     326 .. 0.74
   2 !   14.0   0.0   0.00011     0.039       4      77 ..     494     564 ..     491     597 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0012
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderd..kkladpekllelileklkeekktylflDEiqevp 77 
                                       +++ G+  +GKT +++ +++e+        ++++  +++  k    +e++++++++++ ++  +++f+DEi  + 
  gi|474935072|ref|YP_007688654.1| 220 VLLYGPPGTGKTLIAEAIANESG-----ASFYSVRGPELvgKYVGWSENNIRELFDRAAGNTPSIIFFDEIDSIA 289
                                       7899************9998888.....445555555552244445555566666665556999*******9874 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 0.00011
                            AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevp 77 
                                        +++ G+  +GKT ++k l++e+     +++ +n  +   + + d+e+ ++ +++++k+   +++f+DEi  v 
  gi|474935072|ref|YP_007688654.1| 494 GVLLYGPPGTGKTLIAKALANENG---YNFIPVNGPELMGRFHGDTEEGIRKVFDRAKSMAPSIIFFDEIDSVA 564
                                       57899***************9999...6666666665555444455545555555544457899******9884 PP

>> Vps4_C  Vps4 C terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00061      0.22      17      44 ..     417     444 ..     414     446 .. 0.85
   2 !   12.4   0.0   0.00034      0.12      31      55 ..     685     709 ..     681     711 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00061
                            Vps4_C  17 mdipsdkllePpvtlkDflkalkkarpt 44 
                                       + +p   l    vt++Df+ al++++p+
  gi|474935072|ref|YP_007688654.1| 417 QSVPDAVLSDIRVTMDDFVTALASVKPS 444
                                       567766677779***************8 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00034
                            Vps4_C  31 lkDflkalkkarptVskeDLekhee 55 
                                        +Df++al+k+rp+V ++  e +e+
  gi|474935072|ref|YP_007688654.1| 685 QEDFESALEKVRPSVDQKTAEAYEK 709
                                       68***************98888876 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00069      0.24      24      47 ..     219     242 ..     213     249 .. 0.87
   2 !   11.0   0.0   0.00072      0.25      23      57 ..     493     524 ..     479     566 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00069
                                       -EEEECSTTSSHHHHHHHHHHHST CS
                   Sigma54_activat  24 svlitGesGtGKellaraiheask 47 
                                        vl+ G  GtGK+l+a+ai ++s 
  gi|474935072|ref|YP_007688654.1| 219 GVLLYGPPGTGKTLIAEAIANESG 242
                                       69*****************98775 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00072
                                       S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEE CS
                   Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkekpfvavn 57 
                                         vl+ G  GtGK+l+a+a+ +++     +f+ vn
  gi|474935072|ref|YP_007688654.1| 493 RGVLLYGPPGTGKTLIAKALANEN---GYNFIPVN 524
                                       579***************997654...34555555 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0    0.0021      0.75      24      80 ..     220     287 ..     215     293 .. 0.62
   2 !   13.1   0.0   0.00021     0.075      24      57 ..     495     528 ..     488     567 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0021
                                       EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH-H........HHHHHHT...TTSEEEEEE-TT CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpwleifvverlaklp........ldlleqa...kggtLylkdiad 80 
                                       v+l G++G+gk+l+A++++++sg     ++  +l+            +l+++a   ++ ++++ +i++
  gi|474935072|ref|YP_007688654.1| 220 VLLYGPPGTGKTLIAEAIANESGASFYSVRGPELVGKYvgwsenniRELFDRAagnTPSIIFFDEIDS 287
                                       9*******************998754443333333211222223335555555444555566666665 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00021
                                       EEEEEETT--HHHHHHCC--TTS-EE--SSTTHH CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpwleifvverl 57 
                                       v+l G++G+gk+l+A++L++++g +  +++  +l
  gi|474935072|ref|YP_007688654.1| 495 VLLYGPPGTGKTLIAKALANENGYNFIPVNGPEL 528
                                       9********************9988777665444 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       1.7     6e+02     135     168 ..      55      89 ..      28      97 .. 0.75
   2 !    7.2   0.0    0.0096       3.4      36      50 ..     220     234 ..     213     240 .. 0.87
   3 !    9.7   0.0    0.0017      0.59      32      54 ..     491     513 ..     467     515 .. 0.88
   4 ?    0.5   0.0       1.1   3.7e+02     126     185 ..     536     599 ..     521     601 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.7
                            AAA_25 135 aaieevegvrlvviDplsralgg.densnsdvgal 168
                                       a+i +  + + v+iD  +r+ +g + n+  +v+++
  gi|474935072|ref|YP_007688654.1|  55 AEISDSSQSGTVIIDGPTRTSAGaSVNERVAVSPA 89 
                                       33444455789********9999899888777665 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0096
                            AAA_25  36 allaGapgtGKttla 50 
                                       +ll+G+pgtGKt +a
  gi|474935072|ref|YP_007688654.1| 220 VLLYGPPGTGKTLIA 234
                                       69**********998 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0017
                            AAA_25  32 agelallaGapgtGKttlaldla 54 
                                        g  +ll+G+pgtGKt +a  la
  gi|474935072|ref|YP_007688654.1| 491 QGRGVLLYGPPGTGKTLIAKALA 513
                                       566789***********998776 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 1.1
                            AAA_25 126 ltadvdaleaaieevegvrlvviDplsralgg...densnsd..vgalvealeriarrtgaavll 185
                                       +++ ++++ +++++++ +  + +D ++++ +    d  ++ d  v++l+++l+ +++ +++ vl+
  gi|474935072|ref|YP_007688654.1| 536 TEEGIRKVFDRAKSMA-PSIIFFDEIDSVAPMrgaDGGRSYDsmVAQLLTCLDGVSELKDVLVLA 599
                                       4667778888888865.888887777765544434665555543599999999999988888875 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0036       1.3      21      51 ..     219     251 ..     188     261 .. 0.83
   2 !   12.2   0.0   0.00039      0.14      13      51 ..     486     526 ..     472     534 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0036
                                       EEEEEESTTSSHHHHHHHHHHHTT--..----T CS
                              TsaE  21 vilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                        +lL+G+ G+GKT ++ ++a++ g +  +v+ P
  gi|474935072|ref|YP_007688654.1| 219 GVLLYGPPGTGKTLIAEAIANESGASfySVRGP 251
                                       399******************999887777776 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00039
                                       HHHHCHTEEEEEEESTTSSHHHHHHHHHHHTT--..----T CS
                              TsaE  13 klakalgdvilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                       +l+ + g+ +lL+G+ G+GKT ++++la++ g++  +v+ P
  gi|474935072|ref|YP_007688654.1| 486 RLGISQGRGVLLYGPPGTGKTLIAKALANENGYNfiPVNGP 526
                                       333333567********************999987777766 PP

>> CDC48_2  Cell division protein 48 (CDC48), domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.1   1.7e-07   6.1e-05       5      58 ..     111     167 ..     108     173 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.7e-07
                                       CCCHHHHCCCTTEEE-TTEEEEECC...TCCCEEEEEEEECCCCSCEEECTSCCEEE CS
                           CDC48_2   5 demaylkrqFlgrpvtkGdlvvfef...kgqeiklvVvstePkgpvgitetTeielg 58 
                                        ++  +++++ gr +++G+++ +++   +g+ +++++  t+  gp ++t +T  +++
  gi|474935072|ref|YP_007688654.1| 111 SFVRSFRSNIAGRGFSPGQQFIVPNislMGTDLTFRIERTDIDGPFVVTGNTDLKFS 167
                                       566689***************88774447***********************87765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0063       2.2      21      41 ..     220     240 ..     214     251 .. 0.79
   2 !   11.9   0.0    0.0004      0.14       7      39 ..     481     513 ..     476     521 .. 0.89
   3 ?   -1.7   0.0       5.6     2e+03     124     182 ..     648     708 ..     646     718 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0063
                            AAA_30  21 avltGpAGtGKttalkalrea 41 
                                       ++l Gp+GtGKt + +a+++ 
  gi|474935072|ref|YP_007688654.1| 220 VLLYGPPGTGKTLIAEAIANE 240
                                       6789**********9999875 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.0004
                            AAA_30   7 aaavealltsgdrvavltGpAGtGKttalkalr 39 
                                       ++a+e+l  s+ r ++l Gp+GtGKt + kal+
  gi|474935072|ref|YP_007688654.1| 481 REAFERLGISQGRGVLLYGPPGTGKTLIAKALA 513
                                       68899999999999**************99986 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 5.6
                            AAA_30 124 DerQlasVeaGgvlrdlveaagigtaeLtevvRqke.seeraaalalregdae...ealeala 182
                                       D +Q a  + G v +dl  aa  + a L+  +R ++   +++   al++ +++   +  ea++
  gi|474935072|ref|YP_007688654.1| 648 DLAQIAGMTDGYVGADL--AAVCREAGLSAFHRGSDaVGQEDFESALEKVRPSvdqKTAEAYE 708
                                       56788888889999999..67889999999999976555666555555555553334444444 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0049       1.7       2      30 ..     220     248 ..     219     287 .. 0.90
   2 ?   -0.7   0.0       3.5   1.2e+03       8      42 ..     393     428 ..     389     434 .. 0.82
   3 !    9.8   0.0    0.0019      0.67       2      30 ..     495     523 ..     494     622 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0049
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                       vll g PG++ktl+++a+a+  +++f  +
  gi|474935072|ref|YP_007688654.1| 220 VLLYGPPGTGKTLIAEAIANESGASFYSV 248
                                       7999****************999998766 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 3.5
                             AAA_3   8 PGlaktllvkalakaldl.efkriqftpdllPsdil 42 
                                         la+  +++al+++++  +++ +q  pd + sdi 
  gi|474935072|ref|YP_007688654.1| 393 TALAREAAMQALSRTIGSgSVDLVQSVPDAVLSDIR 428
                                       56888899999999998637899*******999985 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.0019
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                       vll g PG++ktl++kala+  + +f  +
  gi|474935072|ref|YP_007688654.1| 495 VLLYGPPGTGKTLIAKALANENGYNFIPV 523
                                       7999***************9988888655 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0       1.9   6.6e+02      59      83 ..      51      75 ..      44      87 .. 0.80
   2 !    9.3   0.1    0.0041       1.5       1      25 [.     223     247 ..     223     257 .. 0.93
   3 !    8.6   0.0     0.007       2.5       1      24 [.     498     521 ..     498     531 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1.9
                                      HHHHHHHHHHHHSSEEEEEE-SEEE CS
                            AAA_17 59 keaaekiaeeakkkgvlvdghprik 83
                                      ++a ++i + +++++v++dg  r+ 
  gi|474935072|ref|YP_007688654.1| 51 ATAFAEISDSSQSGTVIIDGPTRTS 75
                                      56778999999*********88764 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0041
                                       EE-TTSSHHHHHHHHHHHHTEEEEE CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthls 25 
                                       +G+PG GK+ ++e ++ + g +++s
  gi|474935072|ref|YP_007688654.1| 223 YGPPGTGKTLIAEAIANESGASFYS 247
                                       7*****************9999987 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.007
                                       EE-TTSSHHHHHHHHHHHHTEEEE CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthl 24 
                                       +G+PG GK+ +++ l+ + g+ ++
  gi|474935072|ref|YP_007688654.1| 498 YGPPGTGKTLIAKALANENGYNFI 521
                                       7***************99888765 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0       0.7   2.5e+02      15      33 ..     218     236 ..     210     244 .. 0.83
   2 !    8.0   0.0    0.0063       2.2     123     169 ..     278     327 ..     264     333 .. 0.75
   3 ?    4.6   0.0     0.072        25      11      33 ..     489     511 ..     480     526 .. 0.84
   4 ?    1.9   0.0      0.47   1.7e+02     123     170 ..     553     603 ..     535     608 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.7
                                       CEEEEEESTTSSHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxx RF
                              DEAD  15 gdvlvaaeTGsGKTlafli 33 
                                       + vl+ ++ G+GKTl++  
  gi|474935072|ref|YP_007688654.1| 218 RGVLLYGPPGTGKTLIAEA 236
                                       5699999********9865 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0063
                                       EEEEEETHHHHHHT...TTHHHHHHHHHHSHHHCTTST.TTSE.EEEEESSB CS
                                       xxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxxx RF
                              DEAD 123 rflVlDEadrlldq...gfsdfinrilnqlpqitcdgk.lqrq.vivlSATl 169
                                       +++ +DE+d + +q      d ++++l+q+   tc     ++  viv+ AT 
  gi|474935072|ref|YP_007688654.1| 278 SIIFFDEIDSIASQrdgRSDDAYRNMLSQI--LTCMDGlGSKDgVIVIGATN 327
                                       56779*********9944455678899**9..455444344446**999995 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.072
                                       HHTTCEEEEEESTTSSHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  11 ilgggdvlvaaeTGsGKTlafli 33 
                                       i +g+ vl+ ++ G+GKTl++  
  gi|474935072|ref|YP_007688654.1| 489 ISQGRGVLLYGPPGTGKTLIAKA 511
                                       45899**************9755 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.47
                                       EEEEEETHHHHHHT...TTHHHHHHHHHHSHHHCTTST..TTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxx RF
                              DEAD 123 rflVlDEadrlldq...gfsdfinrilnqlpqitcdgk..lqrqvivlSATlp 170
                                       +++ +DE+d +  +   + ++ ++++++ql   tc     + + v+vl AT  
  gi|474935072|ref|YP_007688654.1| 553 SIIFFDEIDSVAPMrgaDGGRSYDSMVAQL--LTCLDGvsELKDVLVLAATNR 603
                                       67789*****999987788999********..455444323345******965 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   0.00014     0.048       8     101 ..     226     323 ..     222     326 .. 0.81
   2 ?    5.8   0.0     0.037        13       8      49 ..     501     542 ..     497     582 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00014
                   Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydreiieevakelglseeev.eevdersrlssflskllaarvagdtldeklddelfe 83 
                                        G+g++ i+ea+A++ g  fy+ + +e v k  g se+ + e +d ++  +  +  +   +  + + d  +dd++++
  gi|474935072|ref|YP_007688654.1| 226 PGTGKTLIAEAIANESGASFYSVRGPELVGKYVGWSENNIrELFDRAAGNTPSIIFFDEIDSIASQRDGRSDDAYRN 302
                                       59**************************************888888666556666666666666677********** PP

                   Cytidylate_kin2  84 aqervirel...aaeesvViv 101
                                       + +++++ +   +++++v+++
  gi|474935072|ref|YP_007688654.1| 303 MLSQILTCMdglGSKDGVIVI 323
                                       ***999977332355455555 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.037
                   Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydreiieevakelglseeevee 49 
                                        G+g++ i++aLA++ g++f+  + +e + +  g +ee +++
  gi|474935072|ref|YP_007688654.1| 501 PGTGKTLIAKALANENGYNFIPVNGPELMGRFHGDTEEGIRK 542
                                       59******************9887777776666666666644 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0028      0.97       4      25 ..     220     241 ..     217     254 .. 0.86
   2 !    9.2   0.0    0.0019      0.65       4      25 ..     495     516 ..     493     548 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0028
                           DUF2075   4 vlVtGvaGtGKtvvllnllael 25 
                                       vl  G +GtGKt+++ ++++e 
  gi|474935072|ref|YP_007688654.1| 220 VLLYGPPGTGKTLIAEAIANES 241
                                       6789************999986 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0019
                           DUF2075   4 vlVtGvaGtGKtvvllnllael 25 
                                       vl  G +GtGKt+++ +l++e 
  gi|474935072|ref|YP_007688654.1| 495 VLLYGPPGTGKTLIAKALANEN 516
                                       5778*************99986 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0     0.025       8.8      12      35 ..     218     241 ..     211     284 .. 0.89
   2 !   11.9   0.0   0.00067      0.23       6      34 ..     487     515 ..     486     557 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.025
                                       SEEEEEESTTSSHHHHHHHHTTSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  12 ekvaivGenGaGKStLlkllagll 35 
                                       + v + G+ G+GK+ +++++a+++
  gi|474935072|ref|YP_007688654.1| 218 RGVLLYGPPGTGKTLIAEAIANES 241
                                       56889***************9875 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00067
                                       EEEETTSEEEEEESTTSSHHHHHHHHTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   6 lklkegekvaivGenGaGKStLlkllagl 34 
                                       l +++g+ v + G+ G+GK+ ++k+la++
  gi|474935072|ref|YP_007688654.1| 487 LGISQGRGVLLYGPPGTGKTLIAKALANE 515
                                       6799**********************986 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.085        30      48      80 ..     220     252 ..     212     292 .. 0.73
   2 ?    0.4   0.0       1.5   5.2e+02     126     167 ..     269     318 ..     258     331 .. 0.67
   3 !   11.8   0.0   0.00048      0.17      48     112 ..     495     560 ..     484     568 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.085
                             Rad17  48 LLisGPsGCgkstvvkvLskelgiklrewlnpv 80 
                                       +L+ GP+G gk+ + + ++ e g ++     p 
  gi|474935072|ref|YP_007688654.1| 220 VLLYGPPGTGKTLIAEAIANESGASFYSVRGPE 252
                                       6899****************9999887666655 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.5
                             Rad17 126 Gddlrtdk.klilvedlP...nkfyrds.dalrevirkylrsseal...p 167
                                        d + ++  ++i+ +++    ++  + s da+r+++ + l+  + l    
  gi|474935072|ref|YP_007688654.1| 269 FDRAAGNTpSIIFFDEIDsiaSQRDGRSdDAYRNMLSQILTCMDGLgskD 318
                                       455555433899999988555565555559*********99887775443 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.00048
                             Rad17  48 LLisGPsGCgkstvvkvLskelgiklrewlnpvslkepdn.qksdfkgltekesrflsqiesfkel 112
                                       +L+ GP+G gk+ + k L+ e g++++    p ++   +   ++ ++ +++  +++ + i  f e+
  gi|474935072|ref|YP_007688654.1| 495 VLLYGPPGTGKTLIAKALANENGYNFIPVNGPELMGRFHGdTEEGIRKVFDRAKSMAPSIIFFDEI 560
                                       6899*********************99877776643332225555666666666666666666665 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0044       1.5      22      40 ..     220     238 ..     215     245 .. 0.88
   2 !    9.1   0.0    0.0023      0.81      22      40 ..     495     513 ..     481     518 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0044
                                       EEEE--TTSSTTHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavala 40 
                                       v   Gp GtGKt++a a+a
  gi|474935072|ref|YP_007688654.1| 220 VLLYGPPGTGKTLIAEAIA 238
                                       5678***********9988 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0023
                                       EEEE--TTSSTTHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavala 40 
                                       v   Gp GtGKt++a ala
  gi|474935072|ref|YP_007688654.1| 495 VLLYGPPGTGKTLIAKALA 513
                                       7789***********9998 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0     0.018       6.2       3      23 ..     220     240 ..     218     245 .. 0.88
   2 ?    1.7   0.0      0.61   2.2e+02     111     155 ..     425     469 ..     412     475 .. 0.83
   3 ?    6.5   0.0      0.02         7       3      22 ..     495     514 ..     493     517 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.018
                                       EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                       v+l G++G GKT  ++ +a +
  gi|474935072|ref|YP_007688654.1| 220 VLLYGPPGTGKTLIAEAIANE 240
                                       899*************99975 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.61
                                       HHHCTTTTT--EEEEEEECCCHHHHCTTSSCE..EEEE--TCCHH CS
                             NACHT 111 elirkkllpeasllltvrpralrdleeqleeaivlevegfsesrr 155
                                       + ir ++   ++ l++v+p++ r++  ++ e  ++ ++g++  rr
  gi|474935072|ref|YP_007688654.1| 425 SDIRVTMDDFVTALASVKPSGMREISGGIPEVSWADIGGMESVRR 469
                                       5577888889999******************99999999987665 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.02
                                       EEEEC-TTTCHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklal 22 
                                       v+l G++G GKT  ++ la 
  gi|474935072|ref|YP_007688654.1| 495 VLLYGPPGTGKTLIAKALAN 514
                                       899************99986 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0097       3.4      20      37 ..     220     237 ..     212     272 .. 0.84
   2 !    9.2   0.0    0.0026      0.93      14      37 ..     489     512 ..     477     543 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0097
                            AAA_11  20 tliqGPPGtgKTktivel 37 
                                       +l+ GPPGtgKT    ++
  gi|474935072|ref|YP_007688654.1| 220 VLLYGPPGTGKTLIAEAI 237
                                       6899********655444 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0026
                            AAA_11  14 lseseitliqGPPGtgKTktivel 37 
                                       +s+   +l+ GPPGtgKT    +l
  gi|474935072|ref|YP_007688654.1| 489 ISQGRGVLLYGPPGTGKTLIAKAL 512
                                       55555689**********765555 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.1    0.0083       2.9      12      31 ..     219     238 ..     214     245 .. 0.82
   2 !    8.7   0.0    0.0059       2.1       9      29 ..     491     511 ..     480     517 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0083
                            AAA_19  12 vllvtaGpGtGKTrvlkhiv 31 
                                        +l+ ++pGtGKT + ++i 
  gi|474935072|ref|YP_007688654.1| 219 GVLLYGPPGTGKTLIAEAIA 238
                                       5899*********9987775 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0059
                            AAA_19   9 kekvllvtaGpGtGKTrvlkh 29 
                                       + + +l+ ++pGtGKT + k+
  gi|474935072|ref|YP_007688654.1| 491 QGRGVLLYGPPGTGKTLIAKA 511
                                       667899**********98776 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.016       5.6       5      28 ..     221     244 ..     218     248 .. 0.91
   2 !    7.6   0.0    0.0064       2.3       5      30 ..     496     521 ..     493     524 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.016
                               IPT   5 lifGatttGKtaeaiklaketgap 28 
                                       l++G+ +tGKt  a ++a+e ga+
  gi|474935072|ref|YP_007688654.1| 221 LLYGPPGTGKTLIAEAIANESGAS 244
                                       89*******************997 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0064
                               IPT   5 lifGatttGKtaeaiklaketgapvi 30 
                                       l++G+ +tGKt  a +la+e+g+  i
  gi|474935072|ref|YP_007688654.1| 496 LLYGPPGTGKTLIAKALANENGYNFI 521
                                       89********************9876 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0069       2.4      23      44 ..     220     241 ..     216     247 .. 0.90
   2 ?    6.1   0.0     0.015       5.3      19      43 ..     494     515 ..     480     519 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0069
                                       EEEEESTTSSHHHHHHHHCCSH CS
                            NB-ARC  23 valvGmgGvGKttlakqilnks 44 
                                       v l+G +G GKt +a+ i n+s
  gi|474935072|ref|YP_007688654.1| 220 VLLYGPPGTGKTLIAEAIANES 241
                                       679***************9984 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.015
                                       CSEEEEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC  19 qslvvalvGmgGvGKttlakqilnk 43 
                                       +   v l+G +G GKt +ak   n+
  gi|474935072|ref|YP_007688654.1| 494 G---VLLYGPPGTGKTLIAKALANE 515
                                       4...889************988776 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.017         6      16      40 ..     217     241 ..     214     249 .. 0.87
   2 ?    6.1   0.0     0.016       5.8      19      51 ..     495     525 ..     490     550 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.017
                        Zeta_toxin  16 PklillgGqpGAGKselaellkdel 40 
                                       P  +ll G pG GK+ +ae++++e 
  gi|474935072|ref|YP_007688654.1| 217 PRGVLLYGPPGTGKTLIAEAIANES 241
                                       67799****************9997 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.016
                        Zeta_toxin  19 illgGqpGAGKselaellkdelerqgnvvrldp 51 
                                       +ll G pG GK+ +a++l++e   + n++ +++
  gi|474935072|ref|YP_007688654.1| 495 VLLYGPPGTGKTLIAKALANEN--GYNFIPVNG 525
                                       7899****************97..888888775 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.08        28      54      77 ..     218     241 ..     205     253 .. 0.87
   2 ?    7.8   0.0    0.0046       1.6      51      77 ..     490     516 ..     448     562 .. 0.79
   3 ?   -2.5   0.0       6.4   2.2e+03     122     155 ..     576     607 ..     569     611 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.08
                            DUF815  54 nnvLLwGarGtGKSslvkallney 77 
                                       + vLL+G  GtGK  +  a+ ne 
  gi|474935072|ref|YP_007688654.1| 218 RGVLLYGPPGTGKTLIAEAIANES 241
                                       679**********99999998875 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0046
                            DUF815  51 lpannvLLwGarGtGKSslvkallney 77 
                                        + + vLL+G  GtGK  + kal ne 
  gi|474935072|ref|YP_007688654.1| 490 SQGRGVLLYGPPGTGKTLIAKALANEN 516
                                       45678******************9875 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 6.4
                            DUF815 122 eeeyksLksvLeGsleakpenvliyaTsNrRhLl 155
                                       ++   +L ++L+G  e   ++vl+ a +Nr +++
  gi|474935072|ref|YP_007688654.1| 576 DSMVAQLLTCLDGVSE--LKDVLVLAATNRPDMI 607
                                       5666778889999654..5689999999998887 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.17        60       1      21 [.     226     246 ..     226     249 .. 0.92
   2 ?    8.6   0.0    0.0054       1.9       1      21 [.     501     521 ..     501     531 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.17
                                       TTSSHHHHHHHHHHHHTSEEE CS
                               SKI   1 mGaGKstvGkllAkklglefi 21 
                                       +G+GK+ +++++A++ g +f+
  gi|474935072|ref|YP_007688654.1| 226 PGTGKTLIAEAIANESGASFY 246
                                       69**************99996 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0054
                                       TTSSHHHHHHHHHHHHTSEEE CS
                               SKI   1 mGaGKstvGkllAkklglefi 21 
                                       +G+GK+ ++k+lA++ g++fi
  gi|474935072|ref|YP_007688654.1| 501 PGTGKTLIAKALANENGYNFI 521
                                       69******************8 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.026       9.2      23      49 ..     220     245 ..     210     298 .. 0.83
   2 ?    4.2   0.0     0.097        34      23      43 ..     495     515 ..     487     523 .. 0.84
   3 ?   -1.2   0.0       4.4   1.5e+03     112     152 ..     542     589 ..     527     608 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.026
                          ATPase_2  23 yfiYGpegsGKtaLlkeiienledkdk 49 
                                       +++YGp g GKt  + e+i n +  ++
  gi|474935072|ref|YP_007688654.1| 220 VLLYGPPGTGKTL-IAEAIANESGASF 245
                                       789********95.5555555544444 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.097
                          ATPase_2  23 yfiYGpegsGKtaLlkeiien 43 
                                       +++YGp g GKt + k ++++
  gi|474935072|ref|YP_007688654.1| 495 VLLYGPPGTGKTLIAKALANE 515
                                       689*********988888776 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 4.4
                          ATPase_2 112 kikkkgkk...iiiiiDelqklidl.gln...gaellvkeLlnliesl 152
                                       k+ +++k     ii++De+  +  + g +   +  ++v++Ll++++  
  gi|474935072|ref|YP_007688654.1| 542 KVFDRAKSmapSIIFFDEIDSVAPMrGADggrSYDSMVAQLLTCLDGV 589
                                       444444444446899999998886534443334445577777777663 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0      0.11        37       4      27 ..     223     246 ..     220     249 .. 0.88
   2 ?    7.8   0.0    0.0072       2.5       4      27 ..     498     521 ..     495     524 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.11
                                       E-STTSSHHHHHHHHHHHHT-EEE CS
                    Cytidylate_kin   4 DGPagsGKssvaralaeklglkyl 27 
                                        GP g+GK  +a a+a++ g+++ 
  gi|474935072|ref|YP_007688654.1| 223 YGPPGTGKTLIAEAIANESGASFY 246
                                       6****************9998875 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0072
                                       E-STTSSHHHHHHHHHHHHT-EEE CS
                    Cytidylate_kin   4 DGPagsGKssvaralaeklglkyl 27 
                                        GP g+GK  +a+ala++ g++++
  gi|474935072|ref|YP_007688654.1| 498 YGPPGTGKTLIAKALANENGYNFI 521
                                       6*******************9987 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.029        10      35      58 ..     217     240 ..     206     249 .. 0.82
   2 ?    4.9   0.0     0.043        15      36      58 ..     493     515 ..     481     522 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.029
                              TniB  35 mpnlllvGdsnnGKtmivekFarl 58 
                                       ++ +ll+G++ +GKt i+e  a++
  gi|474935072|ref|YP_007688654.1| 217 PRGVLLYGPPGTGKTLIAEAIANE 240
                                       6789*************9987765 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.043
                              TniB  36 pnlllvGdsnnGKtmivekFarl 58 
                                       + +ll+G++ +GKt i++  a++
  gi|474935072|ref|YP_007688654.1| 493 RGVLLYGPPGTGKTLIAKALANE 515
                                       689*************9987765 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.032        11      21      42 ..     217     237 ..     204     239 .. 0.80
   2 ?    5.0   0.0     0.058        20      20      38 ..     490     508 ..     480     514 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.032
                            AAA_29  21 lkgatlltGpsGsGKSTllDAi 42 
                                       ++g +ll Gp G+GK+ +  Ai
  gi|474935072|ref|YP_007688654.1| 217 PRG-VLLYGPPGTGKTLIAEAI 237
                                       467.9**********9887777 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.058
                            AAA_29  20 dlkg.atlltGpsGsGKSTl 38 
                                       + +g  +ll Gp G+GK+ +
  gi|474935072|ref|YP_007688654.1| 490 S-QGrGVLLYGPPGTGKTLI 508
                                       4.33469**********866 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.57     2e+02      60      86 ..     220     246 ..     216     258 .. 0.81
   2 ?    8.3   0.0    0.0032       1.1      24      78 ..     459     513 ..     445     524 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.57
                                       EEEEESSTSTHHHHHHHHHHHSSSEEE CS
                               MCM  60 vllvgdpgtaKsqlLkyveklapravy 86 
                                       vll g pgt+K+ + +++++ +  + y
  gi|474935072|ref|YP_007688654.1| 220 VLLYGPPGTGKTLIAEAIANESGASFY 246
                                       89**********999999876665555 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0032
                                       TTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHH CS
                               MCM  24 psiyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyve 78 
                                         i g+e+v++ i+  l+ g+++++ ++  +     vll g pgt+K+ + k+++
  gi|474935072|ref|YP_007688654.1| 459 ADIGGMESVRREIMEDLLPGSNREAFERLGISQGRGVLLYGPPGTGKTLIAKALA 513
                                       5799*********************9*9999999**************9988776 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1     0.024       8.6      23      39 ..     221     237 ..     209     240 .. 0.90
   2 ?    3.3   0.0      0.28        99      23      39 ..     496     512 ..     484     513 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.024
                            AAA_23  23 lItGpNGaGKTTildAi 39 
                                       l++Gp G+GKT i +Ai
  gi|474935072|ref|YP_007688654.1| 221 LLYGPPGTGKTLIAEAI 237
                                       99**************9 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.28
                            AAA_23  23 lItGpNGaGKTTildAi 39 
                                       l++Gp G+GKT i  A+
  gi|474935072|ref|YP_007688654.1| 496 LLYGPPGTGKTLIAKAL 512
                                       89***********9998 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.042        15       2      32 ..     220     250 ..     219     285 .. 0.91
   2 ?    3.4   0.0      0.18        63       2      22 ..     495     515 ..     494     527 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.042
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                       v++ GppG+GKt + + ++++   s ++v+G
  gi|474935072|ref|YP_007688654.1| 220 VLLYGPPGTGKTLIAEAIANESGASFYSVRG 250
                                       6788*************99988777777776 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.18
                                       EEEE--TTSSHHHHHHHHHHH CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlel 22 
                                       v++ GppG+GKt + k ++++
  gi|474935072|ref|YP_007688654.1| 495 VLLYGPPGTGKTLIAKALANE 515
                                       6788*******9887776665 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0      0.17        59      26      46 ..     219     239 ..     199     248 .. 0.83
   2 ?    4.8   0.0     0.071        25      22      45 ..     490     513 ..     464     520 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.17
                                       EEEEEESTTSTHHHHHHHHHH CS
                            ResIII  26 rglikmaTGtGKTlvaaklie 46 
                                        +l+  + GtGKTl+a +++ 
  gi|474935072|ref|YP_007688654.1| 219 GVLLYGPPGTGKTLIAEAIAN 239
                                       56788899*******977765 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.071
                                       .TTSEEEEEESTTSTHHHHHHHHH CS
                            ResIII  22 krdkrglikmaTGtGKTlvaakli 45 
                                        + + +l+  + GtGKTl+a +l+
  gi|474935072|ref|YP_007688654.1| 490 SQGRGVLLYGPPGTGKTLIAKALA 513
                                       6677888999*********97765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (728 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        51  (0.00284455); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              51  [number of targets reported over threshold]
# CPU time: 0.67u 0.27s 00:00:00.94 Elapsed: 00:00:00.43
# Mc/sec: 5058.10
//
Query:       gi|474935073|ref|YP_007688655.1|  [L=510]
Description: histone acetyltransferase, ELP3 family [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.6e-27   93.2   0.0    1.5e-26   92.2   0.0    1.6  1  Radical_SAM_C    Radical_SAM C-terminal domain
    2.5e-22   80.0   0.1    6.2e-22   78.7   0.1    1.6  1  Radical_SAM      Radical SAM superfamily
    3.7e-10   40.0   0.2    7.7e-10   39.0   0.2    1.5  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    1.9e-08   34.3   0.1    8.7e-08   32.2   0.1    2.0  2  Acetyltransf_10  Acetyltransferase (GNAT) domain
     0.0015   19.0   0.2     0.0029   18.0   0.2    1.5  1  Acetyltransf_7   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Radical_SAM_C  Radical_SAM C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.2   0.0   4.3e-30   1.5e-26       1      80 [.     290     369 ..     290     371 .. 0.98

  Alignments for each domain:
  == domain 1  score: 92.2 bits;  conditional E-value: 4.3e-30
                     Radical_SAM_C   1 pdgvKlypllvikgTeLaelyksgeykplsleeyvdlvadilellppdirvhRltgdipkelliagpwhknlrelie 77 
                                       pd++K+yp+lv+ gT L+e++++gey+pl+++ +v+lv ++++++p+ +r++R+++dip ++++ag  ++nlr+l++
  gi|474935073|ref|YP_007688655.1| 290 PDMLKFYPTLVVAGTHLYEMWENGEYEPLDTDTAVELVSKMKAYVPEYVRIQRIQRDIPVPEISAGILKSNLRQLVQ 366
                                       8**************************************************************************** PP

                     Radical_SAM_C  78 krl 80 
                                       +++
  gi|474935073|ref|YP_007688655.1| 367 NNM 369
                                       998 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.7   0.1   1.7e-25   6.2e-22       3     158 ..      81     273 ..      79     278 .. 0.88

  Alignments for each domain:
  == domain 1  score: 78.7 bits;  conditional E-value: 1.7e-25
                                       EESEESS--TTTSCCTT.................HHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGST CS
                                       xxxxxxxxxxxxxxxxx.................xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpet.................vrregrgrslsveeileevkelkaekg.vkevilgggepllyp 61 
                                       ++++ +++C +C+ + +                   ++ ++++    +i+++ +++ ++   ++ +i+gg   + +p
  gi|474935073|ref|YP_007688655.1|  81 PYPCPHGKCAYCPGGVSnvspqsytgkepaarraAMNRFDPYDQVAARIAQLEEIG-HDVSkIDLIIMGGTFTSRNP 156
                                       66777788**********************99966666666666666666666666.55554999999999999999 PP

                                       THHHHHHHHHHTC.................CCTEEEEEEECSSCHG....HHHHHHHHHTT-SEEEEEEBSSSHHHH CS
                                       xxxxxxxxxxxxx.................xxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  62 dfvellerlakla.................vpgiritvetngtlpd....eeklerllelgvdrvslgleaaddekv 117
                                        ++e+  +++  a                   + r+   t +t+pd    ee+++r+ +lg +rv+lg++++dde v
  gi|474935073|ref|YP_007688655.1| 157 QYQEWFVKRCFDAmngvvkpdmasaqeynsRCEHRCIGLTVETRPDyfmkEEQIRRMMDLGATRVELGVQILDDE-V 232
                                       9999999999999*****************9999999999999999999**************************.9 PP

                                       HHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 118 lklmnrghtfeevlealeklreagikrvvdrivglpGende 158
                                       lk + rgh++eev +a+ ++r +g+k+++++++glpG + +
  gi|474935073|ref|YP_007688655.1| 233 LKGVSRGHSVEEVRKATSACRGLGLKVCYHIMPGLPGSSPD 273
                                       99999********************************8865 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.2   2.2e-13   7.7e-10      31     117 .]     409     499 ..     382     499 .. 0.85

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 2.2e-13
                                       TTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEE..........SGGGTTSSHHHHHHHHHHHHHHHTTESEE CS
                    Acetyltransf_1  31 eaegllvaeedgeliGfisllkipdekggvayieslaV..........speyrgkGlGsaLlealeerareegikki 97 
                                         e+++++e+++ l+G+++l+ ++    +va i++l V          +++++++G G++Ll ++e++ar+eg +ki
  gi|474935073|ref|YP_007688655.1| 409 GKERFIAYEYEDSLVGYVRLRTDDS---DVAKIRELKVfgnetavgkaAESWQHRGFGKKLLAHAEDIARSEGKTKI 482
                                       34466669*****************...99999999999999999*******************************9 PP

                                       EEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  98 vlaveedndaairlYeklGF 117
                                        +    + ++ +++Y  +G+
  gi|474935073|ref|YP_007688655.1| 483 TV---TSGVGVREYYASVGY 499
                                       77...689999****77997 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       3.4   1.2e+04      14      29 ..     202     217 ..     194     221 .. 0.74
   2 !   32.2   0.1   2.4e-11   8.7e-08      28     108 ..     408     501 ..     391     508 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 3.4
                   Acetyltransf_10  14 kefispealrerieeg 29 
                                       + f+++e++r++++ g
  gi|474935073|ref|YP_007688655.1| 202 DYFMKEEQIRRMMDLG 217
                                       5588899999999655 PP

  == domain 2  score: 32.2 bits;  conditional E-value: 2.4e-11
                   Acetyltransf_10  28 egealllvaeeggkivGvielrdgs....hisll.......fV...dpeyrgqGigkaLleaveeeaekdgiklelt 90 
                                        g+  ++++e ++++vG+++lr+++    +i  l       +V   +++++++G gk+Ll ++e+ a+ +g   ++t
  gi|474935073|ref|YP_007688655.1| 408 GGKERFIAYEYEDSLVGYVRLRTDDsdvaKIRELkvfgnetAVgkaAESWQHRGFGKKLLAHAEDIARSEGKT-KIT 483
                                       577889999************55555999554443334455553335689*****************777655.*** PP

                   Acetyltransf_10  91 vnaspyavpfYeklGFka 108
                                       v +    +++Y ++G++ 
  gi|474935073|ref|YP_007688655.1| 484 VTSGVGVREYYASVGYRL 501
                                       ****************85 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.2   8.1e-07    0.0029       3      75 ..     411     500 ..     409     501 .. 0.63

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 8.1e-07
                                       EEEEEEEETTEEEEEEEEEEES......TCTEE.......EEE-G...GGTTSSHHHHHHHHTT.....SEEEEEEE CS
                    Acetyltransf_7   3 gevfVaeddgkivGfialslld......aeitr.......laVdp...eyrgkGiGraLleaae.....kgiileql 58 
                                       ++++ +e ++  vG+++l  +d          +        aV +   +++ +G G++Ll++ae     +g + +  
  gi|474935073|ref|YP_007688655.1| 411 ERFIAYEYEDSLVGYVRLRTDDsdvakiR---ElkvfgneTAVGKaaeSWQHRGFGKKLLAHAEdiarsEGKT-K-I 482
                                       6677788889999***9999999985541...33322334455544449***********9833344555522.1.1 PP

                                       EETHH..HHHHHHHHTTEE CS
                    Acetyltransf_7  59 elnae..kaikfYeklGFe 75 
                                       +++ +    +++Y++ G++
  gi|474935073|ref|YP_007688655.1| 483 TVT-SgvGVREYYASVGYR 500
                                       221.1224466******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (510 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 3192.73
//
Query:       gi|474935074|ref|YP_007688656.1|  [L=143]
Description: hypothetical protein TALC_01526 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-07   31.2   0.0    3.7e-07   30.1   0.0    1.5  1  HTH_20          Helix-turn-helix domain
    9.8e-06   25.4   0.0    2.1e-05   24.4   0.0    1.6  1  HTH_11          HTH domain
    8.1e-05   22.4   0.0    0.00014   21.7   0.0    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
     0.0003   20.5   0.0    0.00062   19.5   0.0    1.4  1  HTH_IclR        IclR helix-turn-helix domain
    0.00091   19.2   0.0     0.0015   18.4   0.0    1.3  1  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0024   17.7   0.0     0.0057   16.5   0.0    1.6  2  MarR_2          MarR family
     0.0061   16.7   0.0      0.012   15.8   0.0    1.7  1  HTH_17          Helix-turn-helix domain
     0.0098   15.4   0.0      0.017   14.6   0.0    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.017   15.2   0.0      0.073   13.2   0.0    2.0  2  HTH_22          HTH domain
      0.017   15.3   0.2      0.085   13.1   0.0    1.9  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.026   14.4   0.0      0.045   13.6   0.0    1.4  1  TrmB            Sugar-specific transcriptional regulator TrmB
      0.039   14.3   0.0      0.073   13.4   0.0    1.4  1  Rrf2            Transcriptional regulator
      0.065   13.1   0.0       0.13   12.1   0.0    1.4  1  HTH_23          Homeodomain-like domain
      0.066   12.9   0.0       0.12   12.1   0.0    1.5  1  HrcA_DNA-bdg    Winged helix-turn-helix transcription repress
      0.091   12.8   0.0       0.14   12.2   0.0    1.2  1  Replic_Relax    Replication-relaxation
      0.096   13.3   0.0        0.3   11.7   0.0    1.8  2  Mga             Mga helix-turn-helix domain
        0.1   12.4   0.0       0.22   11.3   0.0    1.5  1  HTH_DeoR        DeoR-like helix-turn-helix domain
       0.13   12.2   0.0       0.23   11.4   0.0    1.3  1  MarR            MarR family


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   3.7e-10   3.7e-07      24      56 ..      55      87 ..      42      91 .. 0.91

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 3.7e-10
                                      TB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20 24 gltaselaerldlskntlsyHLrvLeeagLvev 56
                                        ta+ela++ld++k t+++H+++L + +L+e+
  gi|474935074|ref|YP_007688656.1| 55 VWTAEELAALLDTTKPTVYRHINKLKSMDLLES 87
                                      579****************************96 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   2.1e-08   2.1e-05       7      49 ..      46      95 ..      42     101 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 2.1e-08
                            HTH_11  7 elLleargp.isgeeLAeeLnvSrrtvrrdIkaLeelg......vpIese 49
                                       +++++ ++ +++eeLA  L+ ++ tv+r+I +L+++        ++e+ 
  gi|474935074|ref|YP_007688656.1| 46 DFFMKNPSKvWTAEELAALLDTTKPTVYRHINKLKSMDllesmdTEVEGQ 95
                                      5789999999************************9885555555555555 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   1.4e-07   0.00014      17      47 .]      57      87 ..      49      87 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.4e-07
                                      EHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5 17 cvcelaeelglsqstvShHLkkLreaGLVek 47
                                      ++ ela+ l+ +++tv +H +kL+ ++L+e+
  gi|474935074|ref|YP_007688656.1| 57 TAEELAALLDTTKPTVYRHINKLKSMDLLES 87
                                      5679************************985 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   6.2e-07   0.00062       9      49 ..      45      86 ..      44      88 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 6.2e-07
                                      HCT-CTTBSS-.BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR  9 Ldalaeapqel.tlselArrtglpkStvhRlLqtLvelGyve 49
                                      +d++ + p  + t  elA+ ++ +k+tv+R+++ L  + ++e
  gi|474935074|ref|YP_007688656.1| 45 MDFFMKNPSKVwTAEELAALLDTTKPTVYRHINKLKSMDLLE 86
                                      6788888888669**********************9999987 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.5e-06    0.0015      23      52 ..      57      86 ..      53      99 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.5e-06
                                      HHHHHHHHTTSSHHHHHHHHHHHHHTTSEE CS
                         HTH_Crp_2 23 tqeelAsmlGltretvsrilseLkreglis 52
                                      t eelA++l +t  tv r +++Lk   l++
  gi|474935074|ref|YP_007688656.1| 57 TAEELAALLDTTKPTVYRHINKLKSMDLLE 86
                                      779***********************9998 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   5.8e-06    0.0057      22      52 ..      55      86 ..      38      95 .. 0.86
   2 ?   -2.5   0.0         5     5e+03      21      38 ..     101     118 ..      93     119 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.8e-06
                                      E.EHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2 22 l.tvgelarrlglsksavsrilkrLvaaGLve 52
                                      + t+ ela+ l+ +k++v r++++L +  L+e
  gi|474935074|ref|YP_007688656.1| 55 VwTAEELAALLDTTKPTVYRHINKLKSMDLLE 86
                                      449************************99997 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5
                                       EEEHHHHHHHHTSSHHHH CS
                            MarR_2  21 dltvgelarrlglsksav 38 
                                       +++ g++++++  + s+v
  gi|474935074|ref|YP_007688656.1| 101 RIRYGDIVKAWSFTESNV 118
                                       467789999998888877 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.2e-05     0.012       3      24 ..      57      78 ..      55     109 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.2e-05
                            HTH_17  3 tveEaAelLgvsrstvyrlirr 24
                                      t eE+A+lL+  + tvyr i++
  gi|474935074|ref|YP_007688656.1| 57 TAEELAALLDTTKPTVYRHINK 78
                                      99****************9964 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.7e-05     0.017      21      47 ..      59      85 ..      57      86 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.7e-05
                            HTH_24 21 reLAerlglSpstvnrrlkrLeeeGlI 47
                                       eLA  l+ +++tv r++++L+++ l+
  gi|474935074|ref|YP_007688656.1| 59 EELAALLDTTKPTVYRHINKLKSMDLL 85
                                      69********************99886 PP

>> HTH_22  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       2.9   2.8e+03      35      46 ..      30      41 ..      28      41 .. 0.85
   2 ?   13.2   0.0   7.3e-05     0.073      44      63 .]      58      77 ..      57      77 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.9
                            HTH_22 35 kGiFllkgavek 46
                                      +G++ +++++++
  gi|474935074|ref|YP_007688656.1| 30 AGALSVRDSIPY 41
                                      7999****9985 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 7.3e-05
                            HTH_22 44 vekvAekLgiSraTvYryLr 63
                                      +e++A+ L+ +++TvYr+++
  gi|474935074|ref|YP_007688656.1| 58 AEELAALLDTTKPTVYRHIN 77
                                      6889**************96 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   8.6e-05     0.085      21      53 ..      54      86 ..      49      90 .. 0.90
   2 ?   -0.2   0.0       1.2   1.2e+03       6      20 ..     122     137 ..     120     143 .] 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.6e-05
                                      SSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                    Fe_dep_repress 21 kvvktkdlaerLnvspssVsemlkkLekdGyve 53
                                      kv +  +la  L+  +++V   ++kL+++ ++e
  gi|474935074|ref|YP_007688656.1| 54 KVWTAEELAALLDTTKPTVYRHINKLKSMDLLE 86
                                      6778899**********************9987 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHH.HH CS
                    Fe_dep_repress   6 tEdYLetIYtlse.ek 20 
                                       +E+Y +t+ + +e  k
  gi|474935074|ref|YP_007688656.1| 122 MENYKKTVIRFQElLK 137
                                       8999999999998544 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   4.5e-05     0.045      23      54 ..      56      87 ..      52     102 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.5e-05
                                      CHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
                              TrmB 23 atadeiaeelgvprskvYevLrsLedkGlVer 54
                                       ta+e+a  l+  +++vY+ +++L++++l e 
  gi|474935074|ref|YP_007688656.1| 56 WTAEELAALLDTTKPTVYRHINKLKSMDLLES 87
                                      59*************************99875 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   7.4e-05     0.073      14      58 ..      44      88 ..      33      95 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.4e-05
                                      HHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              Rrf2 14 llyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksv 58
                                       ++  +++ ++  ++ee+a+  ++ ++ + + ++kL+  +l++s 
  gi|474935074|ref|YP_007688656.1| 44 FMDFFMKNPSKVWTAEELAALLDTTKPTVYRHINKLKSMDLLESM 88
                                      5555566666779*****************************995 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00013      0.13      17      40 ..      55      78 ..      48      86 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                            HTH_23 17 GlsvreIAreLgvsrrTvyrwlkr 40
                                       ++ +e A++L+ ++ Tvyr +++
  gi|474935074|ref|YP_007688656.1| 55 VWTAEELAALLDTTKPTVYRHINK 78
                                      69******************8887 PP

>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00012      0.12      17      56 ..      48      88 ..      35      95 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00012
                      HrcA_DNA-bdg 17 yrkk.kravKgeeiAevlkrneGtvRNqlqsLkalgLvegv 56
                                      + k+ ++   +ee+A++l+  + tv   ++ Lk+++L+e++
  gi|474935074|ref|YP_007688656.1| 48 FMKNpSKVWTAEELAALLDTTKPTVYRHINKLKSMDLLESM 88
                                      555534555689**************************996 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00014      0.14       8      52 ..      54      97 ..      52     105 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                      Replic_Relax  8 rvlTtrqiarllfashratarrrLarLrelgllsrlrkrvggarg 52
                                      +v T++ +a+ll  ++ + ++r +++L++ +ll++++ +v+g+ +
  gi|474935074|ref|YP_007688656.1| 54 KVWTAEELAALLDTTKPT-VYRHINKLKSMDLLESMDTEVEGQVR 97
                                      68899******9999999.****************9999988776 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00031       0.3      12      65 ..      34      92 ..      28     110 .. 0.81
   2 ?   -0.8   0.0       2.5   2.5e+03      44      68 ..     115     139 ..     102     142 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00031
                                      HHHHSHHHHHHHHHH...HHSEEEHHHHHHHCT--HHHHHHHHHHHHH..HCHCCT-EE CS
                               Mga 12 llkeslkyqllkflf...eeeevsieelaqelyiSestlkrkikelnk..lLkefdlel 65
                                      ++++s+ y+l   +f    +++ + eela+ l   + t++r+i++l+   lL+++d e+
  gi|474935074|ref|YP_007688656.1| 34 SVRDSIPYRLFMDFFmknPSKVWTAEELAALLDTTKPTVYRHINKLKSmdLLESMDTEV 92
                                      68999***9998888776678899**********************9632577776666 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.5
                                       HHHHHHHHHHHHHHCHCCT-EEETT CS
                               Mga  44 estlkrkikelnklLkefdleltkk 68 
                                       es+++  +++ +k    f+  l+k+
  gi|474935074|ref|YP_007688656.1| 115 ESNVNLAMENYKKTVIRFQELLKKQ 139
                                       6777777788888888888777544 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00022      0.22      16      44 ..      57      85 ..      51      87 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00022
                          HTH_DeoR 16 sveelvellgvSeaTiRRDLneLeeqgll 44
                                      + eel++ll++++ T+ R +n+L+  +ll
  gi|474935074|ref|YP_007688656.1| 57 TAEELAALLDTTKPTVYRHINKLKSMDLL 85
                                      569********************987775 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00023      0.23      19      50 ..      57      88 ..      53      91 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00023
                                      EHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR 19 svseLakklgvskstvtrvldrLekkGlieRs 50
                                      +  eLa  l ++k+tv r + +L   +l+e++
  gi|474935074|ref|YP_007688656.1| 57 TAEELAALLDTTKPTVYRHINKLKSMDLLESM 88
                                      5679********************99999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1036.68
//
Query:       gi|474935075|ref|YP_007688657.1|  [L=171]
Description: putative transcriptional regulator with an HTH domain [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.9e-06   26.8   0.0      8e-06   25.8   0.0    1.5  1  HTH_3       Helix-turn-helix
     0.0023   18.3   0.1      0.006   17.0   0.1    1.7  1  HTH_26      Cro/C1-type HTH DNA-binding domain
  ------ inclusion threshold ------
      0.036   14.4   0.0      0.076   13.4   0.0    1.6  2  HTH_31      Helix-turn-helix domain
      0.038   14.3   0.0      0.083   13.2   0.0    1.6  1  HHH_6       Helix-hairpin-helix motif
      0.065   13.1   0.0       0.14   12.0   0.0    1.5  1  Phage_AlpA  Prophage CP4-57 regulatory protein (AlpA)
       0.08   13.5   0.1       0.12   12.9   0.1    1.5  1  Mga         Mga helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   2.7e-09     8e-06       6      50 ..      26      71 ..      21      75 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 2.7e-09
                                      H.HTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTS CS
                             HTH_3  6 k.qlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgv 50
                                      + +l +s+ e+ +++G+s+st ++i   +r+P+l+t+  + ka ++
  gi|474935075|ref|YP_007688657.1| 26 DdELHMSLNEFCQVSGISQSTMYKILEERREPNLRTIRQIIKAINI 71
                                      55899**************************************994 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1     2e-06     0.006      10      51 ..      30      70 ..      24      71 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2e-06
                            HTH_26 10 gitkseLargtgisaatlsrlvkgkpervsldtLdkiCdaLg 51
                                      +++ +e+++ +gis++t+++++ ++ + ++l t+  i +a +
  gi|474935075|ref|YP_007688657.1| 30 HMSLNEFCQVSGISQSTMYKILEER-REPNLRTIRQIIKAIN 70
                                      699*********************9.89*****999988876 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.6e-05     0.076      15      54 ..      31      69 ..      10      78 .. 0.88
   2 ?   -2.6   0.0       2.5   7.6e+03      52      53 ..     117     118 ..      97     130 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.6e-05
                            HTH_31 15 LsqeevAerlgvsestlsrlEqGrrgrpspavlealaral 54
                                      +s+ e  + +g+s+st+ ++   rr +p +++++++  a 
  gi|474935075|ref|YP_007688657.1| 31 MSLNEFCQVSGISQSTMYKILEERR-EPNLRTIRQIIKAI 69
                                      799999*******************.8*******998876 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.5
                            HTH_31  52 ra 53 
                                       +a
  gi|474935075|ref|YP_007688657.1| 117 DA 118
                                       33 PP

>> HHH_6  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.8e-05     0.083      31      82 ..      38      88 ..      26      96 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.8e-05
                             HHH_6 31 aikglgeaaaerivaeRekegpfksledlarrvdslnkrqleaLakaGalds 82
                                      ++ g++++++ +i++eR+ e + ++++++++ ++ ++ r+ e+ +++ a  s
  gi|474935075|ref|YP_007688657.1| 38 QVSGISQSTMYKILEERR-EPNLRTIRQIIKAINIISSRDTEKFVAVIASTS 88
                                      89***************9.9**************999999999988766555 PP

>> Phage_AlpA  Prophage CP4-57 regulatory protein (AlpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.5e-05      0.14       5      28 ..      32      55 ..      30      62 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.5e-05
                        Phage_AlpA  5 rlreVeqktglsrstiYrlikdge 28
                                      +l+e +q  g+s+st Y+++++++
  gi|474935075|ref|YP_007688657.1| 32 SLNEFCQVSGISQSTMYKILEERR 55
                                      68999**************99875 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   4.1e-05      0.12      28      53 ..      28      53 ..       1      71 [. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.1e-05
                                      HSEEEHHHHHHHCT--HHHHHHHHHH CS
                               Mga 28 eeevsieelaqelyiSestlkrkike 53
                                      e ++s+ e++q   iS+st++++++e
  gi|474935075|ref|YP_007688657.1| 28 ELHMSLNEFCQVSGISQSTMYKILEE 53
                                      55899******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 998.36
//
Query:       gi|474935076|ref|YP_007688658.1|  [L=297]
Description: Thioredoxin reductase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.1e-33  114.3   3.9    8.3e-33  113.9   3.9    1.2  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    7.8e-15   54.9   0.9    1.9e-10   40.5   0.0    2.6  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
      5e-11   42.3   0.7     0.0031   16.6   0.2    3.2  3  GIDA            Glucose inhibited division protein A
    7.9e-09   35.7   1.0     0.0035   17.4   0.0    3.2  3  NAD_binding_9   FAD-NAD(P)-binding
    1.2e-06   27.5   5.2     0.0088   14.8   1.1    3.2  3  HI0933_like     HI0933-like protein
    1.4e-05   24.4   0.9        0.1   11.6   0.1    3.1  3  Lycopene_cycl   Lycopene cyclase protein
    7.9e-05   21.9   2.7      0.026   13.6   0.6    3.0  3  FAD_binding_2   FAD binding domain
    0.00014   21.5   4.9       0.03   13.9   0.2    2.8  2  DAO             FAD dependent oxidoreductase
     0.0048   16.1   0.4       0.11   11.7   0.1    2.2  2  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
     0.0083   15.5   3.4     0.0089   15.4   1.9    1.7  2  FAD_oxidored    FAD dependent oxidoreductase
  ------ inclusion threshold ------
      0.028   13.7   0.5      0.081   12.2   0.0    2.0  3  Amino_oxidase   Flavin containing amine oxidoreductase
      0.032   14.8   0.9         11    6.6   0.0    3.1  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
      0.058   12.2   3.9       0.22   10.4   0.1    2.5  3  Trp_halogenase  Tryptophan halogenase


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.9   3.9     6e-36   8.3e-33       2     294 .]       4     281 ..       3     281 .. 0.83

  Alignments for each domain:
  == domain 1  score: 113.9 bits;  conditional E-value: 6e-36
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH.....HHHHCHHHHCCCCHCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias.....evvkklnqgielllge 73 
                                       dv+viG GpAG++aa+++a++++ v+ +++ +   + g+ + + +  ++ +  i +     e++++l+  +++l   
  gi|474935076|ref|YP_007688658.1|   4 DVAVIGLGPAGIQAAIHAARKKVSVVSIGKIDSSSTYGIKVENYFGLSQTASGIDLlssglEQIRSLG--VRVLEM- 77 
                                       8****************************656566666666665555554444444568887766665..665555. PP

                                       TCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TT.BEECCSECHHHHHHCCSS-TSEEEEES CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  74 evvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaen.vgklvrtldsaealklkllpkrivvvG 149
                                       +v++  ++   +++++   +++e+i +++++lAtG s  +l++pG++e  +g++v++++ ++   +k +   ++vvG
  gi|474935076|ref|YP_007688658.1|  78 NVLSAARNGNGFTITA---ESGETISAKSVILATGISRVKLNVPGEKEFaNGRGVSYCAVCDCNFYKGKT--VAVVG 149
                                       7899988888999965...5588***********************7752578899******99999998..***** PP

                                       -SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 150 gGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgngeklevvledgeei 226
                                       +   + + A  ++k++++v+ + a+++      ++l   +e      G e + ++sv ei+g ++  +v l+dg+ei
  gi|474935076|ref|YP_007688658.1| 150 SESEAAVSAELMTKYASKVYWISANPKAD----PSLVSKAES----AGAESV-RASVAEIRGADRVSSVLLSDGREI 217
                                       ************************99984....444444444....455555.899********9555********* PP

                                       EESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTECCSS--HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 227 dadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDvaggkggpelaqaAvqqG 294
                                       ++d v++  G r s +l+  +l +  + ++ i+vd++++t+vpg++a+GD++   g+p ++ +Av +G
  gi|474935076|ref|YP_007688658.1| 218 QVDGVFIELGGRSSADLA-MDLEVYPEVDDTIKVDRSCATQVPGVFACGDIT---GRPWQIAKAVGEG 281
                                       *****************8.5555555779***********************...9999999999987 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.3   6.6e-05     0.091       2      25 ..       7      29 ..       6      47 .. 0.84
   2 !   40.5   0.0   1.3e-13   1.9e-10     101     305 .]      76     265 ..      66     265 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.6e-05
                       Pyr_redox_3  2 IiGaGPaGlaaaielkkagledyl 25
                                      +iG GPaG++aai++ +++++ ++
  gi|474935076|ref|YP_007688658.1|  7 VIGLGPAGIQAAIHAARKKVS-VV 29
                                      8****************9994.43 PP

  == domain 2  score: 40.5 bits;  conditional E-value: 1.3e-13
                       Pyr_redox_3 101 feeVesvkkedegfevetske.tyeAkkviiAtGefdkPnklnipGeek....lvkhyskvkefhkyagqkvvViGg 172
                                       + +V s +++++gf+++++++ t++Ak+vi+AtG      kln+pGe++      + y  v +++ y+g+ v+V+G 
  gi|474935076|ref|YP_007688658.1|  76 EMNVLSAARNGNGFTITAESGeTISAKSVILATGI--SRVKLNVPGEKEfangRGVSYCAVCDCNFYKGKTVAVVGS 150
                                       56799999**********9976*************..77889*****975444467999999*************97 PP

                       Pyr_redox_3 173 knSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeeykvkt 249
                                       +  a+  A  + ++ ++V ++  +      ++dps        ++ e++ +e       +a+v ei+  ++   v  
  gi|474935076|ref|YP_007688658.1| 151 ESEAAVSAELMTKYASKVYWISANP-----KADPSL------VSKAESAGAE-----SVRASVAEIRGADRVSSVLL 211
                                       65555555556677899*9999987.....345553......3333333222.....3567899*******9***** PP

                       Pyr_redox_3 250 edgkkvevkddvvlatGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                       +dg++++v d v++ +G ++++++  +  +  + d +++++   + t+vpg+f +G
  gi|474935076|ref|YP_007688658.1| 212 SDGREIQV-DGVFIELGGRSSADLAMDLEVYPEVDDTIKVD-RSCATQVPGVFACG 265
                                       *****999.5556669*******999766666566666665.6789*******998 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.2   2.3e-06    0.0031       1      28 [.       4      31 ..       4      55 .. 0.88
   2 !   10.8   0.0   0.00013      0.18     111     168 ..      70     128 ..      58     137 .. 0.71
   3 !   11.7   0.0   7.3e-05       0.1     352     389 ..     256     293 ..     242     296 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.3e-06
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEE CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi 28
                                      dv ViG G AG+ AA++aar+ ++v+ i
  gi|474935076|ref|YP_007688658.1|  4 DVAVIGLGPAGIQAAIHAARKKVSVVSI 31
                                      79*********************99865 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00013
                                       EEEEES-EEEEEECT.TEEEEEEETTS-EEEECEEEE--TT-BT-EEEETTEEEESSCT CS
                              GIDA 111 leiieeeveelivee.kkvkgvvtedgetikakavviatGtflkgkihigekelsaGrl 168
                                       l ++  e++ l+    ++   ++ e+geti+ak+v++atG       + geke+++Gr 
  gi|474935076|ref|YP_007688658.1|  70 LGVRVLEMNVLSAARnGNGFTITAESGETISAKSVILATGISRVKLNVPGEKEFANGRG 128
                                       55555555555432225666799*****************9555556679999999994 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 7.3e-05
                                       BSSSBTEEE-CGGGTB.-SHHHHHHHHHHHHHHHHHHHC CS
                              GIDA 352 tkkvkgLflAGqinGt.eGYeEaaaqGllAGinaarkak 389
                                       t +v+g+f++G+i+G  +    a++ G +AG+ aa +++
  gi|474935076|ref|YP_007688658.1| 256 T-QVPGVFACGDITGRpWQIAKAVGEGAVAGLSAADYVR 293
                                       4.59************444556778*********99876 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.1    0.0018       2.4       1      36 [.       6      39 ..       6      45 .. 0.83
   2 !   17.4   0.0   2.5e-06    0.0035     114     154 ..      69     109 ..      58     111 .. 0.88
   3 !    7.5   0.0    0.0026       3.6     115     154 ..     188     227 ..     179     229 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0018
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsep 36
                                      a++G Gp+G+ ++ + ++++   s ++i  +d s++
  gi|474935076|ref|YP_007688658.1|  6 AVIGLGPAGIQAAIHAARKK--VSVVSIGKIDSSST 39
                                      89***************996..88888887777554 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 2.5e-06
                     NAD_binding_9 114 gvtvevhraevvdleeradgqavlladgaslaadaVvLAlG 154
                                       ++ v+v++ +v++ +++++g++++ ++g+++ a++V+LA+G
  gi|474935076|ref|YP_007688658.1|  69 SLGVRVLEMNVLSAARNGNGFTITAESGETISAKSVILATG 109
                                       467999**********************************9 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0026
                     NAD_binding_9 115 vtvevhraevvdleeradgqavlladgaslaadaVvLAlG 154
                                          e +ra+v +++ +++   vll+dg+++++d V++ lG
  gi|474935076|ref|YP_007688658.1| 188 AGAESVRASVAEIRGADRVSSVLLSDGREIQVDGVFIELG 227
                                       4678899*******999999***************99777 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   1.1   6.4e-06    0.0088       2      31 ..       4      33 ..       3      46 .. 0.83
   2 !   10.9   0.0   9.6e-05      0.13     110     163 ..      58     109 ..      47     113 .. 0.82
   3 ?    1.7   0.0     0.058        80     127     172 ..     192     236 ..     179     259 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.4e-06
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-S CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllek 31
                                      dv+viG G+AG+ aAi+aa+++ +V+ + k
  gi|474935076|ref|YP_007688658.1|  4 DVAVIGLGPAGIQAAIHAARKKVSVVSIGK 33
                                      89****************999999986544 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 9.6e-05
                                       HHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE--- CS
                       HI0933_like 110 divdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtG 163
                                       d+++  l+++++ gv++ le++v s++++ +g f+++++s+e+++a++++lAtG
  gi|474935076|ref|YP_007688658.1|  58 DLLSSGLEQIRSLGVRV-LEMNVLSAARNGNG-FTITAESGETISAKSVILATG 109
                                       45566678899999998.57788888888888.********************9 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.058
                                       E-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS-GGGT- CS
                       HI0933_like 127 rletevksvekeedgkfrvktkseeeleadklvlAtGGlSiPklGs 172
                                        ++ +v+++ + +d++ +v +++++e++ d + + +GG S + l  
  gi|474935076|ref|YP_007688658.1| 192 SVRASVAEI-RGADRVSSVLLSDGREIQVDGVFIELGGRSSADLAM 236
                                       467788999.5567778888889*****************988755 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.1   7.6e-05       0.1       1      31 [.       4      32 ..       4      49 .. 0.87
   2 !    5.1   0.0    0.0073        10      99     145 ..      69     114 ..      52     131 .. 0.80
   3 !    5.0   0.0    0.0075        10      97     144 ..     185     230 ..     161     242 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.6e-05
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlie 31
                                      Dv+viG GpAg++ A +   a+++++vv+i 
  gi|474935076|ref|YP_007688658.1|  4 DVAVIGLGPAGIQAAIHA--ARKKVSVVSIG 32
                                      9*****************..89999998884 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0073
                     Lycopene_cycl  99 engvklleakvesveeeeageslvvleggrkirarlvvdarglaslk 145
                                       + gv+ le  v s++ + +   +++ e g++i a+ v+ a+g+ + k
  gi|474935076|ref|YP_007688658.1|  69 SLGVRVLEMNVLSAARNGN-GFTITAESGETISAKSVILATGISRVK 114
                                       5678888888888888887.7899******************65544 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.0075
                     Lycopene_cycl  97 lvengvklleakvesveeeeageslvvleggrkirarlvvdarglasl 144
                                         ++g++ ++a v++++ ++   s+v l++gr+i+   v+   g +++
  gi|474935076|ref|YP_007688658.1| 185 AESAGAESVRASVAEIRGADR-VSSVLLSDGREIQVDGVFIELG-GRS 230
                                       55789999*********9999.99***********999988777.554 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.6   1.9e-05     0.026       1      31 [.       4      34 ..       4      40 .. 0.85
   2 ?   -1.0   0.0      0.51   7.1e+02     186     200 ..      95     109 ..      58     128 .. 0.74
   3 !    6.4   0.0    0.0028       3.9     378     403 ..     244     269 ..     243     280 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.9e-05
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESS CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavveke 31
                                      Dv ViG G AG  AA+ aa++  +v+ + k 
  gi|474935076|ref|YP_007688658.1|  4 DVAVIGLGPAGIQAAIHAARKKVSVVSIGKI 34
                                      9***************999999888876665 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.51
                                       CEEEEEESEEEE--- CS
                     FAD_binding_2 186 revrirakavvlatg 200
                                       + ++i ak v+latg
  gi|474935076|ref|YP_007688658.1|  95 SGETISAKSVILATG 109
                                       334689999999998 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0028
                                       BETTSBESTTEEESSBTEEE-STCEE CS
                     FAD_binding_2 378 tdengrvldadgqpipGLYAaGevaa 403
                                       +d++ +v+++  +++pG +A+G  ++
  gi|474935076|ref|YP_007688658.1| 244 VDDTIKVDRSCATQVPGVFACGDITG 269
                                       8999999999999*********9884 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.7   0.00069      0.95       1      27 [.       4      30 ..       4      41 .. 0.82
   2 !   13.9   0.2   2.2e-05      0.03     153     203 ..      64     111 ..      48     280 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00069
                                      EEEEECTSHHHHHHHHHHHHTTEEEEE CS
                               DAO  1 dvviiGGGiiGlstAyeLarrgVtlle 27
                                      dv++iG G +G+ +A ++ar++V ++ 
  gi|474935076|ref|YP_007688658.1|  4 DVAVIGLGPAGIQAAIHAARKKVSVVS 30
                                      8*****************998876665 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 2.2e-05
                                       HHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGG CS
                               DAO 153 araaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGaw 203
                                       ++++++lGv++le  +v +   ++g + ++  t++ ge+ +a+ v++a+G+ 
  gi|474935076|ref|YP_007688658.1|  64 LEQIRSLGVRVLEM-NVLSAA-RNGNGFTI--TAEsGETISAKSVILATGIS 111
                                       67899********8.999984.56788999..666698855588******76 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.049        68       4      25 ..       4      25 ..       2      40 .. 0.81
   2 !   11.7   0.1   7.7e-05      0.11     111     236 ..      66     185 ..      60     222 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.049
                       K_oxygenase  4 DligiGiGpsnLsLailleevk 25
                                      D++ iG+Gp+ +  ai+++ +k
  gi|474935076|ref|YP_007688658.1|  4 DVAVIGLGPAGIQAAIHAARKK 25
                                      999*********9999998877 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 7.7e-05
                       K_oxygenase 111 eqvrfgeeveevepdeeeee.elltveskdaegeeeelearnlvlgvG...tepkiPevleklegkervvHsseyle 183
                                       +  + g +v e+++ +++++ + +t++     ++ e+++a++++l++G    + ++P   e  +    v   +    
  gi|474935076|ref|YP_007688658.1|  66 QIRSLGVRVLEMNVLSAARNgNGFTITA----ESGETISAKSVILATGisrVKLNVPGEKEFAN-GRGVSYCAVCDC 137
                                       5556667777777766655558899997....56789***********4333446888777555.355655555555 PP

                       K_oxygenase 184 rkeellakkriaVvGsGqSaaeifedllrrqkkvelklvtrsealeplddspf 236
                                       +     ++k++aVvGs  S a +  +l+++++ +++ +++ +++  p+  s+ 
  gi|474935076|ref|YP_007688658.1| 138 NF---YKGKTVAVVGS-ESEAAVSAELMTKYA-SKVYWISANPKADPSLVSKA 185
                                       55...899*******9.78888999*999987.89******999999877765 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   1.9   6.5e-06    0.0089       1      26 [.       4      29 ..       4      34 .. 0.93
   2 ?   -1.8   0.0       1.1   1.5e+03     103     144 ..      73     109 ..      64     113 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.5e-06
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvl 26
                                      Dv V+G gpaG+ AAi Aar+  +v+
  gi|474935076|ref|YP_007688658.1|  4 DVAVIGLGPAGIQAAIHAARKKVSVV 29
                                      9*******************998887 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.1
                      FAD_oxidored 103 tvllntrlvevekegkriesvtveskegrktirAkvfiDATg 144
                                       +vl + +l++++  g   ++ t+ + e ++ti+Ak +i ATg
  gi|474935076|ref|YP_007688658.1|  73 RVLEMNVLSAARN-G---NGFTI-TAESGETISAKSVILATG 109
                                       5555555554443.2...45555.344599999999999998 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   5.9e-05     0.081     207     269 ..      55     115 ..      33     183 .. 0.81
   2 ?   -2.7   0.0         2   2.7e+03     227     256 ..     193     222 ..     185     223 .. 0.84
   3 ?   -1.4   0.0       0.8   1.1e+03     411     448 ..     251     289 ..     239     292 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.9e-05
                                       THTHHHHHHHHH.TTTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S-HHHHHSSE CS
                     Amino_oxidase 207 gGlsqlpealae.elrgldirlntrVkeikregdgvtvtledgevveaDaVvvTvplgvlkail 269
                                        G++ l   l++ +++g+++ l+  V + +r+g+g t+t e+ge+++a++V++++ ++ +k  l
  gi|474935076|ref|YP_007688658.1|  55 SGIDLLSSGLEQiRSLGVRV-LEMNVLSAARNGNGFTITAESGETISAKSVILATGISRVK--L 115
                                       57888888888855555555.45577777889**************************999..3 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2
                                       TSEEEEEEEEETTCEEEEETTSTEEEESEE CS
                     Amino_oxidase 227 lntrVkeikregdgvtvtledgevveaDaV 256
                                       +++ V ei+  +   +v l+dg+++++D V
  gi|474935076|ref|YP_007688658.1| 193 VRASVAEIRGADRVSSVLLSDGREIQVDGV 222
                                       567888999888889999999999999966 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.8
                                       HHHHCHHCSTTEEE.SGGGCTTTTTS..HHHHHHHHHHHH CS
                     Amino_oxidase 411 dplakpegdprlffAGehtsreypgt..vegAilSGlraA 448
                                       d+++++ ++p++f +G+ t r +  +  v     +Gl+aA
  gi|474935076|ref|YP_007688658.1| 251 DRSCAT-QVPGVFACGDITGRPWQIAkaVGEGAVAGLSAA 289
                                       455566.999999999999876643222333333455555 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2     0.026        36       2      30 ..       5      31 ..       4      63 .. 0.71
   2 ?   -2.1   0.0       4.2   5.8e+03      48      67 ..      65      84 ..      57      95 .. 0.73
   3 ?    6.6   0.0    0.0083        11       2      37 ..     145     180 ..     144     215 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.026
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEES CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvver 30
                                      v+v+G G  g+ +A  +a+  kkV+vv  
  gi|474935076|ref|YP_007688658.1|  5 VAVIGLGPAGIQAAIHAAR--KKVSVVSI 31
                                      89**********9987766..55666654 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.2
                                      HHHHHTTEEEECSEEEEEEE CS
                         Pyr_redox 48 eklekngievllntkveeie 67
                                      e+++ +g++vl  +++ + +
  gi|474935076|ref|YP_007688658.1| 65 EQIRSLGVRVLEMNVLSAAR 84
                                      67888999998777766665 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0083
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTT CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrl 37 
                                       v+vvG+   +   A+ ++++++kV+ + +++k  + 
  gi|474935076|ref|YP_007688658.1| 145 VAVVGSESEAAVSAELMTKYASKVYWISANPKADPS 180
                                       89*************************999886644 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.3     0.036        49       1      36 [.       4      39 ..       4      46 .. 0.80
   2 ?   -2.0   0.0      0.85   1.2e+03     168     211 ..      71     112 ..      65     117 .. 0.82
   3 ?   10.4   0.1   0.00016      0.22     159     241 ..     180     260 ..     144     280 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.036
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlveseei 36
                                      ++ ++G G+aG  aA++ a+     +++  ++s+ +
  gi|474935076|ref|YP_007688658.1|  4 DVAVIGLGPAGIQAAIHAARKKVSVVSIGKIDSSST 39
                                      589**************9999855588887777665 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.85
                                       T-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGGG- CS
                    Trp_halogenase 168 GvtrvegkvvevqldedgrveslrledgreveadlfiDcsGfrg 211
                                       Gv+++e +v ++  + +g+   ++ e+g++++a  +i ++G  +
  gi|474935076|ref|YP_007688658.1|  71 GVRVLEMNVLSAARNGNGF--TITAESGETISAKSVILATGISR 112
                                       8999999998888888887..688899*****999999999865 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00016
                                       HHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-S.EEEE-SGGG-IIIIIIT---EEE-TTT----EE CS
                    Trp_halogenase 159 fLrrvaearGvtrvegkvvevqldedgrveslrledgrevead.lfiDcsGfrgllieqaLktgfedwsdvLltdrA 234
                                        L   ae++G ++v++ v  ++++  +rv+s+ l+dgre+++d  fi   G  +  ++  L+  + ++ d++ +dr+
  gi|474935076|ref|YP_007688658.1| 180 SLVSKAESAGAESVRASV--AEIRGADRVSSVLLSDGREIQVDgVFIELGGRSSADLAMDLE-VYPEVDDTIKVDRS 253
                                       57788999*********9..678899****************9889***9999998888765.68899999999999 PP

                                       EEEEEE- CS
                    Trp_halogenase 235 lavqves 241
                                        a+qv+ 
  gi|474935076|ref|YP_007688658.1| 254 CATQVPG 260
                                       9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 1822.04
//
Query:       gi|474935077|ref|YP_007688659.1|  [L=106]
Description: thioredoxin [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-28   97.7   0.0    3.5e-28   97.6   0.0    1.0  1  Thioredoxin    Thioredoxin
    5.6e-08   33.2   0.1    1.5e-06   28.6   0.1    2.0  1  Thioredoxin_2  Thioredoxin-like domain
    2.8e-06   27.6   0.0      0.017   15.4   0.0    2.2  2  Thioredoxin_8  Thioredoxin-like
    2.3e-05   23.9   0.0    2.7e-05   23.7   0.0    1.2  1  OST3_OST6      OST3 / OST6 family, transporter family
    2.7e-05   24.0   0.0    3.3e-05   23.7   0.0    1.2  1  Thioredoxin_9  Thioredoxin
    0.00022   21.0   0.2    0.00034   20.3   0.2    1.4  1  Redoxin        Redoxin
    0.00096   19.1   0.0      0.004   17.1   0.0    1.7  2  AhpC-TSA       AhpC/TSA family
     0.0072   16.0   0.1      0.019   14.6   0.0    1.6  2  Thioredoxin_5  Thioredoxin
  ------ inclusion threshold ------
      0.015   15.2   0.0      0.024   14.6   0.0    1.3  1  HyaE           Hydrogenase-1 expression protein HyaE
      0.021   15.0   0.0      0.027   14.6   0.0    1.2  1  Thioredoxin_7  Thioredoxin-like
      0.032   14.3   0.0      0.042   13.9   0.0    1.3  1  Thioredoxin_3  Thioredoxin domain
       0.15   11.9   0.0       0.37   10.7   0.0    1.6  1  Thioredoxin_6  Thioredoxin-like domain


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.6   0.0   2.3e-31   3.5e-28       2     102 ..       3     102 ..       2     103 .. 0.97

  Alignments for each domain:
  == domain 1  score: 97.6 bits;  conditional E-value: 2.3e-31
                                       EEESSHHHHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEE CS
                       Thioredoxin   2 vlvltkenFeeevakekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlkl 78 
                                       v +l++++F++ v++ +k  +v+++ApwCg+C+++ Pe++k+ae+l++kv + k+++d+n+d+a+++++++iPtl++
  gi|474935077|ref|YP_007688659.1|   3 VTELNSATFKDFVKN-NKVAMVDCWAPWCGPCRRMGPEVDKVAEALAGKVAVGKLNTDDNQDVAAEFGINAIPTLLI 78 
                                       678999*********.************************************************************* PP

                                       EETTEEEEEEESS-HHHHHHHHHH CS
                       Thioredoxin  79 fkngkevkkyegarekeklaaflk 102
                                       fk+g +++ ++g r++++++++l+
  gi|474935077|ref|YP_007688659.1|  79 FKDGVQQDPLVGLRPADDVISYLE 102
                                       *******************99987 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.1   9.8e-10   1.5e-06       3     108 ..      16     100 ..      15     101 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 9.8e-10
                     Thioredoxin_2   3 gngkpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvr 79 
                                       +n+k  +v+ ++p+C+ C+++  e++++ +         l   + ++av    +++          n+++a ++g++
  gi|474935077|ref|YP_007688659.1|  16 KNNKVAMVDCWAPWCGPCRRMGPEVDKVAEA--------L---AGKVAVGKLNTDD----------NQDVAAEFGIN 71 
                                       799*************************222........3...3334444444444..........569******** PP

                     Thioredoxin_2  80 gtPt.ivfldgkeivarlpGyvpaeeleal 108
                                       + Pt ++f dg   ++ l+G+ pa++   +
  gi|474935077|ref|YP_007688659.1|  72 AIPTlLIFKDGV-QQDPLVGLRPADDVISY 100
                                       ****778*****.99999***999987665 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.1e-05     0.017       1      31 [.      18      48 ..      17      55 .. 0.89
   2 !   10.2   0.0   0.00048      0.72      67      90 ..      57      80 ..      53      84 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.1e-05
                                      .SEEEEEE--SSSHHHHHHHHHHHHHHHHHH CS
                     Thioredoxin_8  1 gkvvlLyfgaswcppckaftpklkelyeklk 31
                                      +kv ++ ++a wc pc+++ p+++++ e l 
  gi|474935077|ref|YP_007688659.1| 18 NKVAMVDCWAPWCGPCRRMGPEVDKVAEALA 48
                                      6999*******************99988875 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00048
                                      -TT-HHHHTT-S--TT-SEEEEE- CS
                     Thioredoxin_8 67 ddkkrnklkkkynvkaiPtlvvld 90
                                      + ++++ ++ +++++aiPtl++ +
  gi|474935077|ref|YP_007688659.1| 57 NTDDNQDVAAEFGINAIPTLLIFK 80
                                      677899**************9975 PP

>> OST3_OST6  OST3 / OST6 family, transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   1.8e-08   2.7e-05      46     105 ..      30      82 ..       2      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.8e-08
                         OST3_OST6  46 CelCrefepefelvakswrkdekskskklfFakvdfdegkdvFqklglnsaPhlllfppk 105
                                       C +Cr + pe+++va++   +       +  +k++ d+++dv +++g+n +P ll+f+  
  gi|474935077|ref|YP_007688659.1|  30 CGPCRRMGPEVDKVAEALAGK-------VAVGKLNTDDNQDVAAEFGINAIPTLLIFKDG 82 
                                       9***************99888.......99***************************974 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   2.2e-08   3.3e-05      50     110 ..      27      85 ..       5      96 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.2e-08
                                       -TT-HHHHHHHHHHHHHHH.H-TTEEEEEE-HHHHHHHTTTTTT-SS--SSEEEEE-TT--E CS
                     Thioredoxin_9  50 edwCgDaavnvPvlakiae.lnpnievkillrdenlelmdqyltngaraiPtliildeegee 110
                                       ++wCg ++++ P ++k+ae l+ ++ v  l  d+n+++  ++   g +aiPtl+i+++++++
  gi|474935077|ref|YP_007688659.1|  27 APWCGPCRRMGPEVDKVAEaLAGKVAVGKLNTDDNQDVAAEF---GINAIPTLLIFKDGVQQ 85 
                                       79****************7367899****************9...88*********999765 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.2   2.3e-07   0.00034      16      76 ..       4      64 ..       1      85 [. 0.77

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.3e-07
                                      TCEEEEEHHH..HTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHHH CS
                           Redoxin 16 tdgnsvslse..fkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndafv 76
                                      t+ ns + ++   ++k+++v  ++  +c++C++  p+++k+ae   ++ v v  +++d+++ v
  gi|474935077|ref|YP_007688659.1|  4 TELNSATFKDfvKNNKVAMVDCWAP-WCGPCRRMGPEVDKVAEA-LAGKVAVGKLNTDDNQDV 64
                                      567788888873456669999****.***************888.777788888999888764 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.6e-06     0.004      16      72 ..       7      63 ..       2      68 .. 0.81
   2 ?    1.7   0.0      0.15   2.2e+02      88     115 ..      58      79 ..      52      83 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.6e-06
                                      EEEECHHH..TTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHH CS
                          AhpC-TSA 16 etvslsdy..kgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspes 72
                                      ++ +++d+  ++k++++ +++  wc +C++  p+  k++e+++  +v v  +++d+ ++
  gi|474935077|ref|YP_007688659.1|  7 NSATFKDFvkNNKVAMVDCWAP-WCGPCRRMGPEVDKVAEALA-GKVAVGKLNTDDNQD 63
                                      567889998555**********.****************9998.557777777777665 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.15
                                       E-TTSHHHHHTT-EETTTTECSCEEEEE CS
                          AhpC-TSA  88 sDeegkvakaygvlkeekglalratfvi 115
                                        D +++va ++g+       a+++  ++
  gi|474935077|ref|YP_007688659.1|  58 TDDNQDVAAEFGIN------AIPTLLIF 79 
                                       699**********9......77777665 PP

>> Thioredoxin_5  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.14   2.1e+02       6      29 ..      28      51 ..      25      58 .. 0.84
   2 !   14.6   0.0   1.3e-05     0.019     126     168 ..      39      83 ..      33      92 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.14
                     Thioredoxin_5  6 PlcseCweiEpelkklkveygeki 29
                                      P+c  C ++ pe+ k+ +    k+
  gi|474935077|ref|YP_007688659.1| 28 PWCGPCRRMGPEVDKVAEALAGKV 51
                                      9*************9988766555 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1.3e-05
                     Thioredoxin_5 126 DveefkeDlesklakkafqcD..lklakemgvtevPtlvffnene 168
                                       +v++  e l  k+a+ ++++D  + +a+e+g++ +Ptl +f + +
  gi|474935077|ref|YP_007688659.1|  39 EVDKVAEALAGKVAVGKLNTDdnQDVAAEFGINAIPTLLIFKDGV 83 
                                       6777778888899999999887789****************8554 PP

>> HyaE  Hydrogenase-1 expression protein HyaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.6e-05     0.024      51     104 ..      38      93 ..      33      97 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.6e-05
                                       HHHHCT-TTS-EEEEEE..THHHHHHHHHCCT-TSSSEEEEEETTEEEEEEESSST CS
                              HyaE  51 pEllkaFpnalraavva..dreqeealaerfgvlktPsllflrdgeylgvlakird 104
                                       pE+ k+ ++++  ++v+  ++++++ +a +fg+   P+ll+++dg     l ++r+
  gi|474935077|ref|YP_007688659.1|  38 PEVDKVAEALAGKVAVGklNTDDNQDVAAEFGINAIPTLLIFKDGVQQDPLVGLRP 93 
                                       77777777888888888667889999******************988777777765 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.8e-05     0.027      15      81 ..      16      79 ..       3      81 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.8e-05
                                      HHT--EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-GGG.-TT---SSEEEEE CS
                     Thioredoxin_7 15 ergkpvlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterdanileldeqgvPvvafl 81
                                      +++k  +v+  a wc++C+++  ++ +    ++ala+k+++ +++ + +++   e+  + +P+++++
  gi|474935077|ref|YP_007688659.1| 16 KNNKVAMVDCWAPWCGPCRRMGPEVDKV---AEALAGKVAVGKLNTDDNQDVAAEFGINAIPTLLIF 79
                                      678889*****************99765...56699********99888775535444779999998 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.8e-05     0.042       8      55 ..      28      78 ..      10      85 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.8e-05
                                      SSSTTCHHHHHHHHHHCHCCTCECEEECC..TTHHHH.HHCT-SSSSEEEC CS
                     Thioredoxin_3  8 pgCakCpklekavkeaaaekgikaevekv..tdfeei.ekygVmsvPalvi 55
                                      p C  C+++   v ++a+ +  k+ v k    d++++ +++g+ ++P+l+i
  gi|474935077|ref|YP_007688659.1| 28 PWCGPCRRMGPEVDKVAEALAGKVAVGKLntDDNQDVaAEFGINAIPTLLI 78
                                      6799****************8888777665589***************976 PP

>> Thioredoxin_6  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00025      0.37     116     159 ..      39      80 ..       2      89 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00025
                                       HHHHHHHHTTTT-EEEEEETTGGHHHHHHTT--GGG-SEEEEEE CS
                     Thioredoxin_6 116 aiekvakefkdkinfaladaksfkrpleylglsssdlPvivivd 159
                                       ++ kva+++ +k+ +  +++++++++  ++g++  ++P++ i++
  gi|474935077|ref|YP_007688659.1|  39 EVDKVAEALAGKVAVGKLNTDDNQDVAAEFGIN--AIPTLLIFK 80 
                                       7899****************************9..999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 656.67
//
Query:       gi|474935078|ref|YP_007688660.1|  [L=177]
Description: putative domain HDIG [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-13   50.2   0.9    4.1e-13   49.6   0.9    1.3  1  HD        HD domain
    3.2e-06   26.8   0.1     0.0034   16.9   0.1    2.4  3  HDOD      HDOD domain
  ------ inclusion threshold ------
       0.11   12.4   1.6          2    8.4   0.0    3.1  3  DUF1409   Protein of unknown function (DUF1409)


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.9   6.9e-17   4.1e-13       4     119 ..      14     116 ..      11     119 .. 0.90

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 6.9e-17
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                                HD   4 HsleVaklarrlaedlgeeedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgldled 80 
                                       H+  V  +a+++a+ +  e+d +++ ++aLlHDiG  + ++             +H+ +ga+il+++++++      
  gi|474935078|ref|YP_007688660.1|  14 HCATVRAVAEEIAKAIP-EADMDIVIAGALLHDIGRSRLHS------------IEHAYIGAQILEQEGLPQ-----C 72 
                                       99999************.********************775............57****************.....8 PP

                                       HHHHHHTTCCHHHHHHHH.H....HHHCCTSCHHHHHHHHHHHH CS
                                HD  81 vaklirehheswegkkrp.r....glaerqlslearivklaDrl 119
                                       +++++r+h++    ++   +      ++ + ++e++iv+ aD+l
  gi|474935078|ref|YP_007688660.1|  73 LVDIVRKHTGAGLDQEDVeEmglpPGDYIPRTIEEKIVAHADNL 116
                                       9***********9665556156779*****************98 PP

>> HDOD  HDOD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   5.7e-07    0.0034      94     133 ..      10      49 ..       5      54 .. 0.88
   2 !    8.5   0.0   0.00022       1.3     163     194 ..      50      81 ..      48      83 .. 0.91
   3 ?   -2.9   0.0      0.67     4e+03      89     112 ..     131     154 ..     113     158 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5.7e-07
                                       HHHHHHHHHHHHHHHHHHHTT-S-HHHHHHHHHTTTHHHH CS
                              HDOD  94 klwehslavAlvarelaeelgledpeeaflaGLLhdiGkl 133
                                       +++ h+ +v +va+e+a+++   d++ +  ++LLhdiG+ 
  gi|474935078|ref|YP_007688660.1|  10 RVVVHCATVRAVAEEIAKAIPEADMDIVIAGALLHDIGRS 49 
                                       66779999999***************************86 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00022
                                       HHHSS-HHHHHHHHHHHTT--HHHHHHHHHTT CS
                              HDOD 163 ellgtdhaevGaallekWnlPeelveaiayhh 194
                                       +l  ++ha +Ga++le+  lP+ lv++++ h 
  gi|474935078|ref|YP_007688660.1|  50 RLHSIEHAYIGAQILEQEGLPQCLVDIVRKHT 81 
                                       567899***********************996 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 0.67
                                       SS-HHHHHHHHHHHHHHHHHHHHH CS
                              HDOD  89 gadlkklwehslavAlvarelaee 112
                                       +++ k+ ++ +++vA + +el + 
  gi|474935078|ref|YP_007688660.1| 131 KLESKGAVRGAQRVADLHKELSQL 154
                                       556666666677777777776665 PP

>> DUF1409  Protein of unknown function (DUF1409)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0   0.00033         2      10      36 ..      12      38 ..      10      46 .. 0.87
   2 ?    1.9   0.1     0.035   2.1e+02      10      25 ..      43      56 ..      40      79 .. 0.81
   3 ?   -1.5   0.0       0.4   2.4e+03      19      27 ..     121     129 ..     114     131 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00033
                           DUF1409 10 vndvGsIRsRveeiqdqlpddladvla 36
                                      v+ +  +R+  eei + +p+  +d++ 
  gi|474935078|ref|YP_007688660.1| 12 VVHCATVRAVAEEIAKAIPEADMDIVI 38
                                      889999***************999875 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.035
                           DUF1409 10 vndvGsIRsRveeiqd 25
                                        d G  RsR++ i +
  gi|474935078|ref|YP_007688660.1| 43 LHDIG--RSRLHSIEH 56
                                      55565..999999976 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.4
                           DUF1409  19 Rveeiqdql 27 
                                       Rv e+q+ +
  gi|474935078|ref|YP_007688660.1| 121 RVVEVQHSI 129
                                       999999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1018.05
//
Query:       gi|474935079|ref|YP_007688661.1|  [L=167]
Description: archaeal conserved hypothetical protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-41  141.4   0.0    1.4e-41  141.1   0.0    1.1  1  Trm56     tRNA ribose 2'-O-methyltransferase, aTrm56


Domain annotation for each model (and alignments):
>> Trm56  tRNA ribose 2'-O-methyltransferase, aTrm56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.1   0.0     8e-46   1.4e-41       1     119 []      49     162 ..      49     162 .. 0.97

  Alignments for each domain:
  == domain 1  score: 141.1 bits;  conditional E-value: 8e-46
                                       H-S--EEE.E--HHHHHHC-S...SEEEEE-TTSEEHHHHHHHHHC-SE.EEEEE------TCHHHHSSEEEESSSS CS
                             Trm56   1 wGgefkvevakslkklikefkkeggivvhltmyGenieevieeikkkekdllvvvGaekvprevyeladynvsvgnq 77 
                                       +Gg++++e+ +++++  k f+   g+vvhltmyG++++e++ +i k  +d++v+vGaekvp evy+ ad+n+svgnq
  gi|474935079|ref|YP_007688661.1|  49 FGGDYSIETGVKWQRATKGFQ---GKVVHLTMYGQRMDEALPKIPKD-EDIMVIVGAEKVPPEVYQRADFNISVGNQ 121
                                       8********************...********************886.56*************************** PP

                                       ---HHHHHHHHHHHHC.--TTT---TT-SSEEE--SSS-EEE CS
                             Trm56  78 PhsevaalaifldrllegkelekefedaklkviPsergkkvv 119
                                       Phse+aalaifl +++ g++l++e  +++++viP+ergk+vv
  gi|474935079|ref|YP_007688661.1| 122 PHSEIAALAIFLYNYTGGEHLYEER-GGEMTVIPNERGKTVV 162
                                       **********************996.5************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.35s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 963.55
//
Query:       gi|474935080|ref|YP_007688662.1|  [L=166]
Description: archaeal conserved hypothetical protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-53  179.0   0.1    5.4e-53  178.8   0.1    1.0  1  ArsR      ArsR transcriptional regulator


Domain annotation for each model (and alignments):
>> ArsR  ArsR transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.8   0.1     3e-57   5.4e-53       1     158 [.       7     163 ..       7     164 .. 0.99

  Alignments for each domain:
  == domain 1  score: 178.8 bits;  conditional E-value: 3e-57
                              ArsR   1 indpveLvpllqvfdsetkkkvyeelskeWlteeeleeklgeeveealklLkkikliEsqWrmpepgekpekeYhts 77 
                                       in+p+eLvp+l+++d++ k++v++e++ eW+t++e+e+k+g e++ea  +++k+kl+E++W +++ g+ pek+Yht+
  gi|474935080|ref|YP_007688662.1|   7 INEPSELVPMLRAVDTPIKREVLKEVTLEWKTADEIEKKFGPEGREATIFFEKMKLVETRWLSTN-GQYPEKSYHTY 82 
                                       8****************************************************************.*********** PP

                              ArsR  78 YskvqanfqcsledlsdiievafmsdeeleelvekiekeveegntsisdlsrklglsplfiralakrsekldvkGqr 154
                                       Y+++++n q+++ ++sd++++a+m+++e+ e+++ki +++ ++ ++ +d++++lgls++++++l++rs k+d++G++
  gi|474935080|ref|YP_007688662.1|  83 YTSFSINAQWPVYEISDVLAAAMMPEDEYAEVENKILEQIGSTGKFSGDVAEALGLSSTMLKSLVRRSVKMDYRGHK 159
                                       ***************************************************************************** PP

                              ArsR 155 lelv 158
                                       +e +
  gi|474935080|ref|YP_007688662.1| 160 IEPI 163
                                       *975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1044.68
//
Query:       gi|474935081|ref|YP_007688663.1|  [L=57]
Description: hypothetical protein TALC_01533 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 416.87
//
Query:       gi|474935082|ref|YP_007688664.1|  [L=102]
Description: archaeal conserved hypothetical protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00069   19.1   0.7     0.0022   17.5   0.1    2.0  2  HTH_24    Winged helix-turn-helix DNA-binding
     0.0016   18.3   0.0     0.0022   17.8   0.0    1.2  1  TrmB      Sugar-specific transcriptional regulator TrmB
      0.003   17.4   0.1     0.0045   16.8   0.1    1.3  1  RuvB_C    RuvB C-terminal winged helix domain
     0.0037   17.2   0.4     0.0086   16.0   0.2    2.0  1  HTH_12    Ribonuclease R winged-helix domain
     0.0038   17.5   0.1      0.006   16.9   0.1    1.3  1  Rrf2      Transcriptional regulator
  ------ inclusion threshold ------
      0.015   15.1   0.0        1.4    8.8   0.0    2.3  2  MerR      MerR family regulatory protein
      0.016   15.2   0.3      0.036   14.1   0.0    1.7  2  HTH_20    Helix-turn-helix domain
      0.024   14.4   0.7      0.042   13.7   0.2    1.7  2  HTH_IclR  IclR helix-turn-helix domain
      0.025   14.3   0.1      0.043   13.6   0.1    1.4  1  HTH_DeoR  DeoR-like helix-turn-helix domain
      0.032   14.1   0.8      0.086   12.7   0.2    2.1  3  HTH_5     Bacterial regulatory protein, arsR family
      0.032   14.1   0.2          4    7.3   0.0    2.2  2  HxlR      HxlR-like helix-turn-helix
      0.049   13.3   0.4       0.13   12.0   0.1    1.9  3  GntR      Bacterial regulatory proteins, gntR family
       0.05   13.5   0.0      0.077   12.9   0.0    1.4  1  MarR_2    MarR family
      0.066   13.5   0.0      0.078   13.3   0.0    1.2  1  DUF2513   Hypothetical protein (DUF2513)
      0.081   13.6   0.0      0.097   13.3   0.0    1.2  1  RPA_C     Replication protein A C terminal


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   1.9e-06    0.0022       5      47 ..      19      61 ..      17      62 .. 0.94
   2 ?   -0.4   0.0      0.72   8.6e+02      21      31 ..      79      89 ..      78      92 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.9e-06
                            HTH_24  5 drkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      ++  L+++++n    +  L+e +g+++  v++ l+ Le++GlI
  gi|474935082|ref|YP_007688664.1| 19 HLMMLKAIKANQPVGIIRLSELTGIPQHKVRYSLRLLERDGLI 61
                                      567899************************************9 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.72
                            HTH_24 21 reLAerlglSp 31
                                      reLAe l+  +
  gi|474935082|ref|YP_007688664.1| 79 RELAESLDKAI 89
                                      89***998665 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.8e-06    0.0022       1      58 [.      10      67 ..      10      75 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.8e-06
                                      HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                      L++l L e    + +a+ +++p  +  ++e +g+p+ kv  +Lr Le+ Gl++  +  
  gi|474935082|ref|YP_007688664.1| 10 LKELELIERHLMMLKAIKANQPVGIIRLSELTGIPQHKVRYSLRLLERDGLIMATQDG 67
                                      566777777777888888899999999**************************99865 PP

>> RuvB_C  RuvB C-terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   3.7e-06    0.0045       6      65 ..      17      72 ..      12      77 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.7e-06
                                      HHHHHHHHHHHHT.TT--B-HHHHHHHTT--HHHHHHTTHHHHHHTTSEEEETTEEEE-H CS
                            RuvB_C  6 eldikyLkllkekfkggpvglktlaailgeeketiedviEPyLlkeglIertsrGRilTk 65
                                      e +  +Lk++k    ++pvg+  l++++g++++++      +L + glI+ t+ G ++T+
  gi|474935082|ref|YP_007688664.1| 17 ERHLMMLKAIK---ANQPVGIIRLSELTGIPQHKVRYSL-RLLERDGLIMATQDGAKITD 72
                                      56778899998...79*******************9655.899999************98 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.2   7.2e-06    0.0086      32      61 ..      45      73 ..      20      84 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 7.2e-06
                            HTH_12 32 eravRyrLrkleergltrrvgyagreltEk 61
                                      +  vRy Lr le++gl+      g+++t++
  gi|474935082|ref|YP_007688664.1| 45 QHKVRYSLRLLERDGLIMATQD-GAKITDR 73
                                      5679************986655.5999987 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1     5e-06     0.006      12      58 ..      18      64 ..       9      69 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5e-06
                                      HHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              Rrf2 12 hallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksv 58
                                      + l++L++ + ++pv +  ++e ++i+++ ++  l+ L++ gl+ ++
  gi|474935082|ref|YP_007688664.1| 18 RHLMMLKAIKANQPVGIIRLSELTGIPQHKVRYSLRLLERDGLIMAT 64
                                      67999*999999*******************************9754 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0011       1.4       5      18 ..      37      50 ..      34      50 .. 0.92
   2 ?    4.1   0.0     0.034        41      16      25 ..      52      61 ..      51      69 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0011
                                      HHHHHTTTHHHHHH CS
                              MerR  5 vAeltGvsprtLRy 18
                                      ++eltG++ +++Ry
  gi|474935082|ref|YP_007688664.1| 37 LSELTGIPQHKVRY 50
                                      89***********9 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.034
                                      HHHHHHTTSS CS
                              MerR 16 LRyYEreGLi 25
                                      LR +Er GLi
  gi|474935082|ref|YP_007688664.1| 52 LRLLERDGLI 61
                                      8********* PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0     3e-05     0.036      18      55 ..      25      62 ..      16      67 .. 0.78
   2 ?   -3.1   0.0       7.4   8.9e+03      29      35 ..      80      86 ..      77      93 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3e-05
                                      HHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20 18 aLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                      a++ ++++    l e+ ++++  ++y Lr Le+ gL+ 
  gi|474935082|ref|YP_007688664.1| 25 AIKANQPVGIIRLSELTGIPQHKVRYSLRLLERDGLIM 62
                                      44666666666788999*******************96 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 7.4
                                      HHHHHHT CS
                            HTH_20 29 elaerld 35
                                      elae ld
  gi|474935082|ref|YP_007688664.1| 80 ELAESLD 86
                                      5566554 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   3.5e-05     0.042       2      48 ..      16      61 ..      15      65 .. 0.91
   2 ?   -2.6   0.0         4   4.8e+03      24      30 ..      81      87 ..      79      92 .. 0.50

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.5e-05
                                      HHHHHHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_IclR  2 ldRalaiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyv 48
                                      ++R l+ L+a+ + ++ +++  l++ tg+p  +v+  L+ L++ G++
  gi|474935082|ref|YP_007688664.1| 16 IERHLMMLKAIKANQP-VGIIRLSELTGIPQHKVRYSLRLLERDGLI 61
                                      6899999999987766.8*************************9986 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4
                                      HHHHHTS CS
                          HTH_IclR 24 lArrtgl 30
                                      lA+ ++ 
  gi|474935082|ref|YP_007688664.1| 81 LAESLDK 87
                                      5555443 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   3.6e-05     0.043       1      55 [.      18      72 ..      18      74 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.6e-05
                          HTH_DeoR  1 RieqilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltRthGGavsis 55
                                      R+  +l+ +k  + + + +l+el g+ +  +R  L+ Le +gl+  t  Ga++ +
  gi|474935082|ref|YP_007688664.1| 18 RHLMMLKAIKANQPVGIIRLSELTGIPQHKVRYSLRLLERDGLIMATQDGAKITD 72
                                      8889*******************************************99999876 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       2.2   2.7e+03      32      40 ..      16      24 ..      12      27 .. 0.80
   2 ?   12.7   0.2   7.2e-05     0.086      21      45 ..      37      61 ..      17      62 .. 0.90
   3 ?   -2.5   0.0         4   4.8e+03      19      27 ..      79      87 ..      78      90 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.2
                                      HHHHHHHHH CS
                             HTH_5 32 vShHLkkLr 40
                                      + +HL +L+
  gi|474935082|ref|YP_007688664.1| 16 IERHLMMLK 24
                                      568998886 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 7.2e-05
                                      HHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5 21 laeelglsqstvShHLkkLreaGLV 45
                                      l+e +g++q +v++ L+ L+  GL+
  gi|474935082|ref|YP_007688664.1| 37 LSELTGIPQHKVRYSLRLLERDGLI 61
                                      89**********************8 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 4
                                      HHHHHHHTS CS
                             HTH_5 19 celaeelgl 27
                                       elae l++
  gi|474935082|ref|YP_007688664.1| 79 RELAESLDK 87
                                      589998886 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1     0.017        21      32      45 ..       2      15 ..       1      35 [. 0.80
   2 ?    7.3   0.0    0.0034         4      28      77 ..      40      86 ..      32      99 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.017
                                      -HHHHHHHHHHHHH CS
                              HxlR 32 sqkmLaqrLreLeq 45
                                      s kmL+ +L+eLe 
  gi|474935082|ref|YP_007688664.1|  2 SGKMLSGTLKELEL 15
                                      78**********83 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0034
                                      STTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHHH CS
                              HxlR 28 lpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvlq 77
                                      l +i+q+    +Lr Le+dgli +    + + k+  +  ++ r+l++ l+
  gi|474935082|ref|YP_007688664.1| 40 LTGIPQHKVRYSLRLLERDGLIMA---TQDGAKITDRYGDFTRELAESLD 86
                                      5689999999***********965...56666777777777777666665 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       1.1   1.3e+03      14      34 ..       6      24 ..       4      30 .. 0.67
   2 ?   12.0   0.1   0.00011      0.13      18      58 ..      26      65 ..      13      69 .. 0.81
   3 ?   -3.1   0.0       5.4   6.4e+03      28      34 ..      79      85 ..      78      90 .. 0.62

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.1
                                      HTTSS-TTSB---HHHHHHHH CS
                              GntR 14 lsgelrpGdkLPsereLaaef 34
                                      lsg+l+  + +  er+L++  
  gi|474935082|ref|YP_007688664.1|  6 LSGTLKELELI--ERHLMMLK 24
                                      56777777777..88887655 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00011
                                      S-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                              GntR 18 lrpGdkLPsereLaaefgVsrttvReALrrLeaeglverrq 58
                                      ++++++      L++  g+  + vR +Lr Le++gl+++ q
  gi|474935082|ref|YP_007688664.1| 26 IKANQPV-GIIRLSELTGIPQHKVRYSLRLLERDGLIMATQ 65
                                      5666666.6667999999999****************9877 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 5.4
                                      HHHHHHH CS
                              GntR 28 reLaaef 34
                                      reLa+ +
  gi|474935082|ref|YP_007688664.1| 79 RELAESL 85
                                      5666654 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.4e-05     0.077       7      54 ..      19      64 ..      13      84 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.4e-05
                                      HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      +++ L a+ ++ +  + +  l + +g++++ v + l+ L++ GL+  +
  gi|474935082|ref|YP_007688664.1| 19 HLMMLKAIKANQP--VGIIRLSELTGIPQHKVRYSLRLLERDGLIMAT 64
                                      5678888999998..89999************************9544 PP

>> DUF2513  Hypothetical protein (DUF2513)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   6.6e-05     0.078       5      64 ..      14      70 ..       9      87 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.6e-05
                           DUF2513  5 dlvRdiLltleeletkeeslddeeeklsaidgyskeeiiyhlkllaeagLieaekkkaks 64
                                      +l+ + L+ l++++++++       +ls+++g ++ ++ y l+ll+ +gLi a+++ ak 
  gi|474935082|ref|YP_007688664.1| 14 ELIERHLMMLKAIKANQPVGII---RLSELTGIPQHKVRYSLRLLERDGLIMATQDGAKI 70
                                      4444445555555555554433...455************************99987665 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   8.1e-05     0.097      58     102 ..      23      66 ..       2      68 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.1e-05
                                       HHH.SXSTTTEEHHHHHHHSTSXHHHHHHHHHHHHHTTSEEESSS CS
                             RPA_C  58 ikqspeseeGvhvdeiaqklrlsvndvkqavdeLsneGiiYsTiD 102
                                       +k  ++ ++ v +  +++ ++++  +v+  ++ L+ +G+i +T+D
  gi|474935082|ref|YP_007688664.1|  23 LKA-IKANQPVGIIRLSELTGIPQHKVRYSLRLLERDGLIMATQD 66 
                                       333.5558888899999999************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 648.71
//
Query:       gi|474935083|ref|YP_007688665.1|  [L=395]
Description: Fe-S oxidoreductase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.1e-34  116.7   9.1    9.1e-22   77.1   0.1    2.7  2  CCG        Cysteine-rich domain
    1.2e-08   35.4   4.9    1.2e-08   35.4   4.9    3.2  4  Fer4_17    4Fe-4S dicluster domain
    6.6e-08   32.9   4.2    6.6e-08   32.9   4.2    2.5  2  Fer4_8     4Fe-4S dicluster domain
    1.1e-06   29.2   8.4    1.1e-06   29.2   8.4    2.9  3  Fer4_7     4Fe-4S dicluster domain
    0.00015   21.8   9.5      0.034   14.2   0.1    3.7  4  Fer4_10    4Fe-4S dicluster domain
    0.00019   21.5  10.4    0.00019   21.5  10.4    3.6  4  Fer4_9     4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.015   15.3   2.6      0.015   15.3   2.6    3.6  4  Fer4_2     4Fe-4S binding domain
      0.018   15.1   3.5      0.018   15.1   3.5    3.2  3  Fer4_6     4Fe-4S binding domain
      0.031   14.8   3.7      0.031   14.8   3.7    3.8  4  Fer4_4     4Fe-4S binding domain
      0.077   13.1  14.1       0.64   10.2   1.0    3.7  4  Fer4_21    4Fe-4S dicluster domain
       0.15   12.1   0.4       0.73    9.9   0.1    2.1  2  DUF2841    Protein of unknown function (DUF2841)
       0.18   11.8   0.4       0.31   11.0   0.4    1.3  1  ApoB100_C  Apolipoprotein B100 C terminal
       0.95    9.7   6.2         15    5.9   0.6    3.1  3  Fer4_18    4Fe-4S dicluster domain
       0.97    9.4  24.1       0.14   12.1   6.7    3.1  3  Fer4       4Fe-4S binding domain
        4.5    8.2  17.4        0.2   12.5   0.7    3.8  3  Fer4_22    4Fe-4S dicluster domain
        5.2    8.1  16.3        1.2   10.2  11.3    2.6  1  Fer4_16    4Fe-4S double cluster binding domain


Domain annotation for each model (and alignments):
>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.3   5.4e-15     6e-12       1      84 [.     146     229 ..     146     230 .. 0.97
   2 !   77.1   0.1   8.2e-25   9.1e-22       1      84 [.     270     357 ..     270     358 .. 0.96

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 5.4e-15
                               CCG   1 vayfdgChllraaypevrkalkkllealgveleel.ekesCCGagggrsgkeelaealakrnvetaeetgadaivta 76 
                                       v +f gC  + ++++  ++   ++l++ gv + +l ++e+CC ++  r+g e ++++ a++ ve a+ +ga+ +v +
  gi|474935083|ref|YP_007688665.1| 146 VIFFAGC-TGSYRQQGIPQTGVRILNRGGVRMNILgSDEWCCTSPLLRTGDESQTLECAEHIVEKADGMGAKDMVMT 221
                                       679****.********************************************************************* PP

                               CCG  77 cpgCllql 84 
                                       c+gC+ ++
  gi|474935083|ref|YP_007688665.1| 222 CSGCYKTI 229
                                       ****9876 PP

  == domain 2  score: 77.1 bits;  conditional E-value: 8.2e-25
                               CCG   1 vayfdgChllraa..ypevrkalkkllealgveleel.ekesCCGagggrsgkee.laealakrnvetaeetgadai 73 
                                       v+y+d+Chl+r++  y+++r++++k+ + +++e++++ ++++CCGaggg++++ +  a ++a  ++++ae tga+++
  gi|474935083|ref|YP_007688665.1| 270 VTYHDPCHLGRHMgvYDAPRNVMAKIKGLELIEMPRNrANSMCCGAGGGYKSQFNnFAVRIASDRIREAEATGAEIL 346
                                       89************************************************999886888****************** PP

                               CCG  74 vtacpgCllql 84 
                                       vt cp+C ++l
  gi|474935083|ref|YP_007688665.1| 347 VTSCPFCVTNL 357
                                       *******9887 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   4.9   1.1e-11   1.2e-08       1      60 [.      10      85 ..      10      86 .. 0.80
   2 ?   -0.5   0.9       1.7   1.9e+03      32      49 ..     208     225 ..     185     227 .. 0.61
   3 ?   -1.3   0.0         3   3.3e+03      20      49 ..     286     315 ..     274     317 .. 0.62
   4 ?   -2.0   0.0         5   5.6e+03      11      22 ..     349     360 ..     347     376 .. 0.68

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 1.1e-11
                           Fer4_17  1 rCiqCgyClpeCpsyeaydnepkkllraakl..............glleeaeke.........ekaslCieCgeCerkC 56
                                      +C qCgyC++ C  ++++++e ++++ ++++              g       +         +++ +C++Cg Ce++C
  gi|474935083|ref|YP_007688665.1| 10 ACVQCGYCIAGCQAHRQTPWESDTPRGKIYYinqinaatpldkplG-------RvatlnpyfvDAMYKCTGCGTCEAVC 81
                                      5**********************99999998876666655554333.......03344456878*************** PP

                           Fer4_17 57 Pqgl 60
                                       +++
  gi|474935083|ref|YP_007688665.1| 82 HAKI 85
                                      8765 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.7
                           Fer4_17  32 glleeaekeekaslCieC 49 
                                       ++ +++ +++++ +C++C
  gi|474935083|ref|YP_007688665.1| 208 EKADGMGAKDMVMTCSGC 225
                                       455666666889999999 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 3
                           Fer4_17  20 nepkkllraaklglleeaekeekaslCieC 49 
                                       + p+++++++k  +l e+ ++++ s C++ 
  gi|474935083|ref|YP_007688665.1| 286 DAPRNVMAKIKGLELIEMPRNRANSMCCGA 315
                                       357788888877555566677888888765 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 5
                           Fer4_17  11 eCpsyeaydnep 22 
                                       +Cp++  + ++ 
  gi|474935083|ref|YP_007688665.1| 349 SCPFCVTNLSQG 360
                                       588887766654 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   4.2   5.9e-11   6.6e-08       2      65 .]       8      85 ..       7      85 .. 0.77
   2 ?   -0.4   0.5       1.4   1.6e+03      36      55 ..     207     226 ..     175     227 .. 0.66

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 5.9e-11
                            Fer4_8  2 lekCieCgaCqsaCpvlrrtkkhlldargeaae.......dvqeeqvlee...............eealwsCttcgaCt 58
                                      l +C++Cg+C + C + r+t  ++ ++rg+                                    +a+++Ct+cg C+
  gi|474935083|ref|YP_007688665.1|  8 LAACVQCGYCIAGCQAHRQTPWESDTPRGKIYYinqinaaT--------PldkplgrvatlnpyfVDAMYKCTGCGTCE 78
                                      579***********999999877788888866544333330........24556667777888889************* PP

                            Fer4_8 59 evCpvgi 65
                                       vC  +i
  gi|474935083|ref|YP_007688665.1| 79 AVCHAKI 85
                                      ***9987 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.4
                            Fer4_8  36 vqeeqvleeeealwsCttcg 55 
                                       v++ ++  +++++ +C++c 
  gi|474935083|ref|YP_007688665.1| 207 VEKADGMGAKDMVMTCSGCY 226
                                       33333333488999999995 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   8.4   9.5e-10   1.1e-06       1      50 [.      10      83 ..      10      85 .. 0.74
   2 ?   -0.5   0.3       1.7   1.9e+03      35      43 ..     219     227 ..     186     231 .. 0.70
   3 ?   -2.6   0.1       7.6   8.5e+03       4      10 ..     349     355 ..     346     360 .. 0.74

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 9.5e-10
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekv........................eidpekClgCgaCvavCPt 50
                                      +C++Cg+C a C ++  + +e++ ++g+ ++                        +  + kC+gCg C+avC +
  gi|474935083|ref|YP_007688665.1| 10 ACVQCGYCIAGCQAHRQTPWESDTPRGKIYYinqinaatpldkplgrvatlnpyfVDAMYKCTGCGTCEAVCHA 83
                                      5*******************99999965333444455555555566666666652444789***********76 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.7
                            Fer4_7  35 pekClgCga 43 
                                        ++C+gC++
  gi|474935083|ref|YP_007688665.1| 219 VMTCSGCYK 227
                                       467888875 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 7.6
                            Fer4_7   4 gCgaCva 10 
                                        C +Cv 
  gi|474935083|ref|YP_007688665.1| 349 SCPFCVT 355
                                       5777765 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.3   0.00029      0.33       7      22 ..       9      22 ..       4      51 .. 0.64
   2 !   14.2   0.1   3.1e-05     0.034      42      55 ..      68      81 ..      61     114 .. 0.80
   3 ?   -1.4   0.3       2.4   2.7e+03      42      49 ..     219     226 ..     201     230 .. 0.65
   4 ?   -0.5   0.0       1.2   1.4e+03      17      23 ..     348     354 ..     336     373 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00029
                           Fer4_10  7 dtCirCgkCvkaCPad 22
                                        C++Cg C + C  +
  gi|474935083|ref|YP_007688665.1|  9 AACVQCGYCIAGC--Q 22
                                      5688888888888..3 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 3.1e-05
                           Fer4_10 42 vekCtgcgaCveaC 55
                                      ++kCtgcg C ++C
  gi|474935083|ref|YP_007688665.1| 68 MYKCTGCGTCEAVC 81
                                      55666666666666 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2.4
                           Fer4_10  42 vekCtgcg 49 
                                       v  C gc 
  gi|474935083|ref|YP_007688665.1| 219 VMTCSGCY 226
                                       55555554 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 1.2
                           Fer4_10  17 kaCPadl 23 
                                       ++CP+++
  gi|474935083|ref|YP_007688665.1| 348 TSCPFCV 354
                                       5666654 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5  10.4   1.7e-07   0.00019       1      49 [.      10      84 ..      10      86 .. 0.74
   2 !   12.5   3.9   0.00012      0.13       1      16 [.      70      85 ..      70      93 .. 0.82
   3 ?   -1.0   0.3       1.8   2.1e+03      13      40 ..     203     226 ..     198     228 .. 0.54
   4 ?   -0.3   0.0       1.1   1.2e+03      10      24 ..     348     362 ..     331     369 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.7e-07
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaa.erkarlraase.........................eaCigCgaCveaCpkg 49
                                      +C++Cg+C++ C+a+  ++ ++ +   ++   ++                          +C+gCg+C+++C  +
  gi|474935083|ref|YP_007688665.1| 10 ACVQCGYCIAGCQAHRQTPWESdTPRGKIYYINQinaatpldkplgrvatlnpyfvdamYKCTGCGTCEAVCHAK 84
                                      6***********77665432220222222222335668999999999************99***********876 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00012
                            Fer4_9  1 kCtgCgaCveaCpagv 16
                                      kCtgCg+C+++C a++
  gi|474935083|ref|YP_007688665.1| 70 KCTGCGTCEAVCHAKI 85
                                      6999999999998876 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.8
                            Fer4_9  13 pagvvvedaaerkarlraaseeaCigCg 40 
                                         ++v++ ++ +   + +     C gC 
  gi|474935083|ref|YP_007688665.1| 203 AEHIVEKADGMGAKDMVM----TCSGCY 226
                                       555555555555555544....366664 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 1.1
                            Fer4_9  10 eaCpagvvvedaaer 24 
                                       ++Cp++v++ +++++
  gi|474935083|ref|YP_007688665.1| 348 TSCPFCVTNLSQGAK 362
                                       578888888777665 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.4   0.00066      0.74       6      20 ..       5      21 ..       1      23 [. 0.75
   2 ?   15.3   2.6   1.4e-05     0.015       3      21 ..      63      82 ..      61      83 .. 0.77
   3 ?   -1.3   0.2       2.7   3.1e+03       9      14 ..     221     226 ..     219     227 .. 0.80
   4 ?   -2.2   0.5       5.3   5.9e+03      12      17 ..     349     354 ..     347     356 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00066
                            Fer4_2  6 dtd..rCigCgaCvsaC 20
                                      ++   +C++Cg C+  C
  gi|474935083|ref|YP_007688665.1|  5 EESlaACVQCGYCIAGC 21
                                      555559*******9989 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.4e-05
                            Fer4_2  3 vvvd.tdrCigCgaCvsaCP 21
                                      ++vd   +C+gCg+C  +C 
  gi|474935083|ref|YP_007688665.1| 63 YFVDaMYKCTGCGTCEAVCH 82
                                      55663459***********6 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 2.7
                            Fer4_2   9 rCigCg 14 
                                       +C gC 
  gi|474935083|ref|YP_007688665.1| 221 TCSGCY 226
                                       699995 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 5.3
                            Fer4_2  12 gCgaCv 17 
                                       +C  Cv
  gi|474935083|ref|YP_007688665.1| 349 SCPFCV 354
                                       455555 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   3.2    0.0048       5.3       8      19 ..      10      21 ..       8      24 .. 0.91
   2 ?   15.1   3.5   1.6e-05     0.018       8      22 ..      70      84 ..      68      86 .. 0.90
   3 ?   -1.9   0.4       3.9   4.4e+03       9      14 ..     222     227 ..     221     227 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0048
                            Fer4_6  8 kCigCgdCvrvC 19
                                      +C++Cg C++ C
  gi|474935083|ref|YP_007688665.1| 10 ACVQCGYCIAGC 21
                                      7********999 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.6e-05
                            Fer4_6  8 kCigCgdCvrvCPeg 22
                                      kC+gCg C++vC ++
  gi|474935083|ref|YP_007688665.1| 70 KCTGCGTCEAVCHAK 84
                                      8***********875 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 3.9
                            Fer4_6   9 CigCgd 14 
                                       C gC++
  gi|474935083|ref|YP_007688665.1| 222 CSGCYK 227
                                       999985 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   3.2    0.0036         4       3      14 ..      10      21 ..       8      26 .. 0.91
   2 ?   14.8   3.7   2.8e-05     0.031       3      15 ..      70      82 ..      68      84 .. 0.89
   3 ?   -1.7   0.2       5.1   5.7e+03       3       8 ..     221     226 ..     220     227 .. 0.75
   4 ?   -0.6   0.3       2.3   2.6e+03       6      11 ..     349     354 ..     347     355 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0036
                            Fer4_4  3 rCigCgsCvaaC 14
                                       C++Cg C+a C
  gi|474935083|ref|YP_007688665.1| 10 ACVQCGYCIAGC 21
                                      6*********** PP

  == domain 2  score: 14.8 bits;  conditional E-value: 2.8e-05
                            Fer4_4  3 rCigCgsCvaaCP 15
                                      +C+gCg C+a+C 
  gi|474935083|ref|YP_007688665.1| 70 KCTGCGTCEAVCH 82
                                      8***********7 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 5.1
                            Fer4_4   3 rCigCg 8  
                                       +C gC 
  gi|474935083|ref|YP_007688665.1| 221 TCSGCY 226
                                       599995 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 2.3
                            Fer4_4   6 gCgsCv 11 
                                        C+ Cv
  gi|474935083|ref|YP_007688665.1| 349 SCPFCV 354
                                       588887 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.8   0.00097       1.1       6      20 ..       9      23 ..       4      35 .. 0.86
   2 ?   10.2   1.0   0.00057      0.64      40      51 ..      70      81 ..      58      87 .. 0.82
   3 ?   -1.2   0.1         2   2.2e+03       9      15 ..     220     226 ..     201     236 .. 0.65
   4 ?   -0.3   0.0       1.1   1.2e+03      36      57 ..     335     354 ..     325     356 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00097
                           Fer4_21  6 dkCigCgkCliaCed 20
                                      + C++Cg C+  C+ 
  gi|474935083|ref|YP_007688665.1|  9 AACVQCGYCIAGCQA 23
                                      57***********94 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00057
                           Fer4_21 40 eCvGCnlCssvC 51
                                      +C+GC  C +vC
  gi|474935083|ref|YP_007688665.1| 70 KCTGCGTCEAVC 81
                                      899999999999 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 2
                           Fer4_21   9 igCgkCl 15 
                                       + C  C+
  gi|474935083|ref|YP_007688665.1| 220 MTCSGCY 226
                                       3344444 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 1.1
                           Fer4_21  36 vvedeCvGCnlCssvCPvedci 57 
                                       ++e e +G ++ ++ CP   c+
  gi|474935083|ref|YP_007688665.1| 335 IREAEATGAEILVTSCPF--CV 354
                                       567788899999999996..65 PP

>> DUF2841  Protein of unknown function (DUF2841)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00065      0.73      41      67 ..     119     146 ..     115     150 .. 0.86
   2 ?   -0.9   0.0       1.4   1.6e+03      56      70 ..     266     280 ..     227     287 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00065
                           DUF2841  41 vkypYnggektkPeWWPkev.rhkePdh 67 
                                       v+ pY g+ +++ +WWP+ev r+  Pd 
  gi|474935083|ref|YP_007688665.1| 119 VRNPYGGNPAARGDWWPAEVpRYDTPDV 146
                                       689****************955778886 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.4
                           DUF2841  56 WPkevrhkePdhlkk 70 
                                        P++v++++P hl +
  gi|474935083|ref|YP_007688665.1| 266 FPHKVTYHDPCHLGR 280
                                       588999999999876 PP

>> ApoB100_C  Apolipoprotein B100 C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.4   0.00027      0.31       2      25 ..     236     259 ..     235     260 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00027
                         ApoB100_C   2 fkakLqefsdqlsdyyEkliaesk 25 
                                       f ak q    ++s+y Ekli+e k
  gi|474935083|ref|YP_007688665.1| 236 FYAKVQQNVYHFSQYAEKLINEKK 259
                                       67899****************976 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.6     0.013        15      57      74 ..       7      24 ..       4      31 .. 0.76
   2 ?    5.2   0.2     0.021        23      57      76 ..      67      86 ..      51      90 .. 0.85
   3 ?   -2.2   0.0       4.1   4.6e+03      59      75 ..     338     354 ..     320     367 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.013
                           Fer4_18 57 gagdcidcescvkvcPtg 74
                                      + + c++c++c++ c  +
  gi|474935083|ref|YP_007688665.1|  7 SLAACVQCGYCIAGCQAH 24
                                      567788888888888665 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.021
                           Fer4_18 57 gagdcidcescvkvcPtgid 76
                                      ++ +c+ c++c +vc  +i 
  gi|474935083|ref|YP_007688665.1| 67 AMYKCTGCGTCEAVCHAKIH 86
                                      5668***********99886 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 4.1
                           Fer4_18  59 gdcidcescvkvcPtgi 75 
                                       ++ +  e  v+ cP  +
  gi|474935083|ref|YP_007688665.1| 338 AEATGAEILVTSCPFCV 354
                                       44444455555555433 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   3.2    0.0028       3.1       7      18 ..      10      21 ..       6      24 .. 0.88
   2 ?   12.1   6.7   0.00012      0.14       7      18 ..      70      81 ..      68      81 .. 0.95
   3 ?   -2.6   0.4       5.1   5.8e+03       8      12 ..     222     226 ..     220     227 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0028
                                      TSSS-THHHHHS CS
                              Fer4  7 kCigCGaCvevC 18
                                       C+ CG+C+  C
  gi|474935083|ref|YP_007688665.1| 10 ACVQCGYCIAGC 21
                                      6********988 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00012
                                      TSSS-THHHHHS CS
                              Fer4  7 kCigCGaCvevC 18
                                      kC+gCG+C+ vC
  gi|474935083|ref|YP_007688665.1| 70 KCTGCGTCEAVC 81
                                      9*********** PP

  == domain 3  score: -2.6 bits;  conditional E-value: 5.1
                                       SSS-T CS
                              Fer4   8 CigCG 12 
                                       C gC 
  gi|474935083|ref|YP_007688665.1| 222 CSGCY 226
                                       99995 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   2.1     0.061        68      80      94 ..       9      23 ..       4      25 .. 0.81
   2 ?   12.5   0.7   0.00018       0.2      79      96 .]      68      85 ..      54      85 .. 0.85
   3 ?    0.1   0.1       1.3   1.5e+03      63      88 ..     203     228 ..     192     236 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.061
                           Fer4_22 80 sgCvGCgRCieacpv 94
                                       +Cv Cg Ci+ c++
  gi|474935083|ref|YP_007688665.1|  9 AACVQCGYCIAGCQA 23
                                      679999999999976 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00018
                           Fer4_22 79 esgCvGCgRCieacpvki 96
                                      +++C+GCg C+++c++ki
  gi|474935083|ref|YP_007688665.1| 68 MYKCTGCGTCEAVCHAKI 85
                                      679***********9987 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.3
                           Fer4_22  63 rqrllhklsefkekfgesgCvGCgRC 88 
                                        +++++k   + +k   ++C GC + 
  gi|474935083|ref|YP_007688665.1| 203 AEHIVEKADGMGAKDMVMTCSGCYKT 228
                                       56677777778888888899999765 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2  11.3     0.001       1.2       2      65 ..      11      82 ..      10      84 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.001
                           Fer4_16  2 CgtCgkCaevCPtnaikekkekeieare.cisy..........ntaekkdlaedeekckkqeaitgCdiCqdvCP 65
                                      C++Cg C+  C ++  +     e ++++ +i y           ++  + ++ +    +  +++tgC++C++vC 
  gi|474935083|ref|YP_007688665.1| 11 CVQCGYCIAGCQAHRQTPW---ESDTPRgKIYYinqinaatplDKPLGRVATLNPYFVDAMYKCTGCGTCEAVCH 82
                                      ***********88776655...33333313333655555555433333334444333445699***********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.50
# Mc/sec: 2390.30
//
Query:       gi|474935084|ref|YP_007688666.1|  [L=915]
Description: Lhr-like helicase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-32  112.8   0.0    2.9e-32  111.8   0.0    1.5  1  DEAD           DEAD/DEAH box helicase
    2.5e-22   79.6   0.0      5e-22   78.6   0.0    1.5  1  DEAD_assoc     DEAD/H associated
    9.5e-21   74.2   0.0    9.3e-19   67.8   0.0    2.6  2  Helicase_C     Helicase conserved C-terminal domain
      5e-09   36.4   0.0      1e-08   35.3   0.0    1.5  1  ResIII         Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
      0.011   16.1   0.0      0.026   14.9   0.0    1.6  1  AAA_19         AAA domain
      0.039   14.8   0.0      0.089   13.7   0.0    1.5  1  Metallophos_C  Iron/zinc purple acid phosphatase-like protein
       0.15   12.0   3.0       0.37   10.8   3.0    1.7  1  Nudix_N_2      Nudix N-terminal


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.8   0.0   1.1e-35   2.9e-32       1     170 [.      23     190 ..      23     196 .. 0.88

  Alignments for each domain:
  == domain 1  score: 111.8 bits;  conditional E-value: 1.1e-35
                                       -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlr 77 
                                       td Q+ aip i +g++vlv a+TG GKT+ +++pv++ +++ ++++g ++++v+P+r+L +++l++++ ++ +++++
  gi|474935084|ref|YP_007688666.1|  23 TDPQRDAIPRIQKGHNVLVVAPTGIGKTESAMLPVFDDLAQLEDRKGIRCIYVTPLRALNRDMLRRMEDLGAELKVS 99 
                                       788************************************999******************************86655 PP

                                       EEEEETTSSHHHHHHHHHTT.CSEEEEEHHHHHHHHHCTSSH..CTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHH CS
                                       xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  78 vlliiggvaardqlskldng.vdivvgtpgrlddllstgkln..lsqvrflVlDEadrlldqgfsdfinrilnqlpq 151
                                       v  + +g++ ++++++++++ ++i+++tp+ ++ ++  ++l+  l++v+++V+DE+++l  ++++ ++   l++l q
  gi|474935084|ref|YP_007688666.1| 100 VG-VRHGDTPQSERNRMSRSpPQILITTPETMQIMFIGKNLRegLKNVKYVVIDEIHELAGNERGAQLAVALERLVQ 175
                                       54.556788888889986557*************9944444455*******************************65 PP

                                       HCTTSTTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxxxxxxx RF
                              DEAD 152 itcdgklqrqvivlSATlp 170
                                          +     q i lSAT+ 
  gi|474935084|ref|YP_007688666.1| 176 LAGE----YQRIGLSATVG 190
                                       5443....55*******85 PP

>> DEAD_assoc  DEAD/H associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.6   0.0     2e-25     5e-22       1     181 [.     588     752 ..     588     758 .. 0.91

  Alignments for each domain:
  == domain 1  score: 78.6 bits;  conditional E-value: 2e-25
                        DEAD_assoc   1 lPtdrtllvErfrdelgdwrlvvhspfGrrvnealalllaarlsrrfgidvqvaanDdgivlll..pleerlpllld 75 
                                       +Ptd+ + +E+ ++       +++ +fG+rvn++l+ +l+a l++r g +++v+ + ++i+l+l  + ++   + + 
  gi|474935084|ref|YP_007688666.1| 588 VPTDNIVTIETGDR-----VAIINCCFGSRVNDTLSKILSALLTARVGESLGVTTDAYRIILQLprNIDR---KVIY 656
                                       68888888887644.....68*****************************************88432222...4567 PP

                        DEAD_assoc  76 ellellspdeleedleaalnaselfkrrFrevAaralllprrypgkrkplwqqrlraaqLldvareypdfpllleav 152
                                       +++ +++p ++e++ +  + +s ++k+rF +vA+++++++++ +          ++  +L+d+ +   d+p ++ av
  gi|474935084|ref|YP_007688666.1| 657 DTFMSIRPGTVEAISRLTVLNSTHLKWRFMNVAKKFGIIEKGADR-------RYINYGRLFDIHK---DTPAYNDAV 723
                                       899***************************************999.......89*********99...********* PP

                        DEAD_assoc 153 revledqlDlerlaellrriaageirvve 181
                                       ++vl ++lD+e+++ +lr i++g+i vv 
  gi|474935084|ref|YP_007688666.1| 724 NKVLWEDLDIENTELALRLIHDGKISVVM 752
                                       **************************997 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.034        87      28      62 ..      85     119 ..      57     162 .. 0.73
   2 !   67.8   0.0   3.6e-22   9.3e-19      16     108 ..     257     351 ..     245     355 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.034
                                       HHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHH CS
                        Helicase_C  28 rlekvklllekkgikvavlhgelpqnereeileqf 62 
                                       +l +++ l  + +++v v hg++pq+er+++ ++ 
  gi|474935084|ref|YP_007688666.1|  85 MLRRMEDLGAELKVSVGVRHGDTPQSERNRMSRSP 119
                                       333344444444899*************9887766 PP

  == domain 2  score: 67.8 bits;  conditional E-value: 3.6e-22
                                       TSEEEEEESSHHHHHH..HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEE CS
                        Helicase_C  16 ggkilifvntidrlek..vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVin 90 
                                          +l fvnt++++e    ++    +++ + v+hg+l++++r e+ ++f+ ++ + Li+t+ +e Gidi +++lVi+
  gi|474935084|ref|YP_007688666.1| 257 VTSTLFFVNTRETAEWlaSRYHMWDEDYPIGVHHGSLSKENRMETEDEFKTQKLKGLICTSSLELGIDIGSADLVIQ 333
                                       5689********996555455555669************************************************** PP

                                       SSSSSSHHHHHHHHTTSS CS
                        Helicase_C  91 fdlprnvtsyiqriGRtg 108
                                       ++ pr+v+++ qr+GR+g
  gi|474935084|ref|YP_007688666.1| 334 YNSPRQVARMTQRAGRAG 351
                                       *****************8 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.0   4.1e-12     1e-08       5     169 ..      23     189 ..      18     191 .. 0.84

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 4.1e-12
                                       -HHHHHHHHHHT......TTSEEEEEESTTSTHHHHH.HHHHHHH-S.......-EEEEESSHHHHHHHHHHGGGGT CS
                            ResIII   5 reyQeeaienlleklkskrdkrglikmaTGtGKTlva.aklierllkkgkee..kflflvprkslleqtleefkkfl 78 
                                        + Q +ai ++      ++ +++l++++TG GKT  a + + + l++ ++++  +++ + p ++l   +l++++++ 
  gi|474935084|ref|YP_007688666.1|  23 TDPQRDAIPRI------QKGHNVLVVAPTGIGKTESAmLPVFDDLAQLEDRKgiRCIYVTPLRALNRDMLRRMEDLG 93 
                                       55666666666......467899***********99878999999999888899**********************9 PP

                                       GG....GEEEESSS-B--.........-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T..... CS
                            ResIII  79 seaykeigkkvsgdkkka..kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk..... 148
                                        e +    ++ +gd+ ++  ++ +++  +il+tt ++++        ++ + + ++ ++++iDE H l++++     
  gi|474935084|ref|YP_007688666.1|  94 AELKV-SVGVRHGDTPQSerNRMSRSPPQILITTPETMQIMF---IGKNLREGLKNVKYVVIDEIHELAGNErgaql 166
                                       98754.6666666666666667788999**************...7899999999999************8566667 PP

                                       ..TTHHHHHT---SEEEEEESS- CS
                            ResIII 149 ..swreilekfkeavllglTATp 169
                                         + +++++   e+ ++gl+AT 
  gi|474935084|ref|YP_007688666.1| 167 avALERLVQLAGEYQRIGLSATV 189
                                       7788888899999*********6 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0     1e-05     0.026       1     115 [.      26     158 ..      26     177 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1e-05
                            AAA_19   1 qreave.alkekvllvtaGpGtGKTrvlk.hivallvelggvkpeeillvaftgrAakelrerlaalgae....... 68 
                                       qr+a+    k +++lv+a+ G GKT+  +  +   l +l+++k  +++ v++ +   + +  r++ lgae       
  gi|474935084|ref|YP_007688666.1|  26 QRDAIPrIQKGHNVLVVAPTGIGKTESAMlPVFDDLAQLEDRKGIRCIYVTPLRALNRDMLRRMEDLGAElkvsvgv 102
                                       7889965888999************9755167799999999999*********999999*****9999995555444 PP

                            AAA_19  69 ..atTiHrlal................ldfddlltealelleeaeeekklqeeellivDEfqdvd 115
                                                                  l +++ +t++  ++  ++ ++ l++ +++++DE+ ++ 
  gi|474935084|ref|YP_007688666.1| 103 rhG-------DtpqsernrmsrsppqiL-ITTPETMQIMFIG-KNLREGLKNVKYVVIDEIHELA 158
                                       441.......044555555566666643.3333445566666.4677888777799999998875 PP

>> Metallophos_C  Iron/zinc purple acid phosphatase-like protein C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.5e-05     0.089      36      55 ..     669     688 ..     655     695 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.5e-05
                     Metallophos_C  36 GygrltvhNathLlwefvrs 55 
                                        ++rltv+N+thL+w f + 
  gi|474935084|ref|YP_007688666.1| 669 AISRLTVLNSTHLKWRFMNV 688
                                       579**************876 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   3.0   0.00014      0.37       3      31 ..     796     822 ..     796     823 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00014
                                       -TTT--B-EEE--TT-SS-EEEETTTTEE CS
                         Nudix_N_2   3 CsqCGtpvelripdgDnreRlvCpaCgti 31 
                                       C +C ++ +lr+  gD   Rl+Cp+C+ +
  gi|474935084|ref|YP_007688666.1| 796 CLNCKNQRRLRV--GDAPKRLRCPSCDGV 822
                                       888988866666..************866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (915 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.71u 0.31s 00:00:01.02 Elapsed: 00:00:00.47
# Mc/sec: 5837.16
//
Query:       gi|474935085|ref|YP_007688667.1|  [L=222]
Description: 23S rRNA Um-2552 2'-O-methyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.9e-59  199.1   0.0    6.8e-59  198.9   0.0    1.0  1  FtsJ             FtsJ-like methyltransferase
    2.4e-05   24.2   0.3     0.0069   16.2   0.4    2.6  2  Methyltransf_31  Methyltransferase domain
  ------ inclusion threshold ------
      0.011   15.5   0.0       0.15   11.8   0.0    2.0  2  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.034   13.3   0.1      0.069   12.3   0.1    1.7  1  Fibrillarin      Fibrillarin
      0.055   14.2   0.8        1.5    9.6   0.4    2.8  2  Methyltransf_25  Methyltransferase domain
      0.078   12.1   0.0       0.11   11.6   0.0    1.1  1  NSP16            Coronavirus NSP16
       0.18   11.1   0.6        4.1    6.7   0.0    2.2  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family


Domain annotation for each model (and alignments):
>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.9   0.0   2.7e-62   6.8e-59       1     177 []      18     193 ..      18     193 .. 0.99

  Alignments for each domain:
  == domain 1  score: 198.9 bits;  conditional E-value: 2.7e-62
                                       CCCCHHHHHHHHHHHHT-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSSHHHTTEEEECS-CCCSSHHH CS
                              FtsJ   1 yrsRsayKLleidekfklfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpmaplpgvttiqgditdpetie 77 
                                       yrsR+++KLl++dekf++f++g+ vvDlga+PGgwsqv+   +g+kgkv++vDl+ ++pl+gv++i gditd +t+ 
  gi|474935085|ref|YP_007688667.1|  18 YRSRASFKLLQLDEKFHIFEEGDSVVDLGACPGGWSQVAYDIVGEKGKVIGVDLRYIHPLEGVQFIIGDITDDNTMI 94 
                                       9**************************************************************************** PP

                                       HHCHCHHHSSEEEEEE--S-SS-CHHHHHHHHHCCCCHHHHCCHCCCCECCCEEEECCCHCCCHHHHHHHHHCCEEE CS
                              FtsJ  78 kikealserkvdlvvsDgapdvsgvhdldeylqsqLllaalelalkllkpggtfvlkifrgeeteallkqlkkfFek 154
                                       ++++++ + kvd+v+sD+ap++ g+ ++d++++++L++ a+ ++ ++lk+gg + +k+f g+ +++l+++lkk F++
  gi|474935085|ref|YP_007688667.1|  95 RLLDMV-GGKVDVVLSDMAPNIAGHYSTDHARSIELCMYAVDVCDRILKKGGKMAMKVFMGDLFQDLERELKKRFDS 170
                                       ***976.56******************************************************************** PP

                                       EEEEE-SS--CCG-EEEEEEEEC CS
                              FtsJ 155 vsvvkPkssrsesseeflvcrgf 177
                                       v v+ Pk+sr++sse+++vcrgf
  gi|474935085|ref|YP_007688667.1| 171 VIVTSPKASRPTSSEVYVVCRGF 193
                                       *********************98 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.4   2.7e-06    0.0069       3     111 ..      38     151 ..      36     170 .. 0.78
   2 ?    2.1   0.0     0.057   1.5e+02      43      83 ..     136     176 ..     132     198 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.7e-06
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.lekl.led...ek 74 
                                       +g +v+DlG+  G  + ++++ +g+k++v+G+D               + l+ v+F +gdi++   +  l d    k
  gi|474935085|ref|YP_007688667.1|  38 EGDSVVDLGACPGGWSQVAYDIVGEKGKVIGVDLR-----------YIHPLEGVQFIIGDITDdNTMIrLLDmvgGK 103
                                       6789*****************************74...........3478999999999999977766666699999 PP

                   Methyltransf_31  75 fDlilsnevl....naladpdkile.......eiervlkpggillied 111
                                       +D++ls+ +     ++ +d +  +e          r lk+gg +++  
  gi|474935085|ref|YP_007688667.1| 104 VDVVLSDMAPniagHYSTDHARSIElcmyavdVCDRILKKGGKMAMKV 151
                                       999999977777786666666666666666767778888888888765 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.057
                   Methyltransf_31  43 lArenaqklgldnveFeqgdiee.leklledekfDlilsnev 83 
                                       ++  +++k g   +++  gd ++ le  l+ ++fD ++  ++
  gi|474935085|ref|YP_007688667.1| 136 VCDRILKKGGKMAMKVFMGDLFQdLERELK-KRFDSVIVTSP 176
                                       555666666666788889999998997666.89*99987665 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.9e-05      0.15      71     105 ..      36      70 ..       4      77 .. 0.84
   2 ?    1.5   0.0     0.084   2.1e+02     163     194 ..     141     173 ..     136     180 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.9e-05
                                       --TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEE CS
                              PCMT  71 lkkgarvLevGsGsGyltavlarlvgekgrvvsie 105
                                       +++g++v+++G+  G  + v + +vgekg+v++++
  gi|474935085|ref|YP_007688667.1|  36 FEEGDSVVDLGACPGGWSQVAYDIVGEKGKVIGVD 70 
                                       6899*****************************98 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.084
                                       EEEEEEEEEEESB.SSSEEEEEEEEETTTEEEE CS
                              PCMT 163 LkeGGrlvvPvge.eeeQvlklvdkkadgkvvi 194
                                       Lk+GG++ + v   +  Q+l++  kk  ++v++
  gi|474935085|ref|YP_007688667.1| 141 LKKGGKMAMKVFMgDLFQDLERELKKRFDSVIV 173
                                       99********9998999**99877766566655 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   2.7e-05     0.069      51     149 ..      18     112 ..       4     151 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.7e-05
                                       TTSHHHHHHHTT-S--S-.-TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHTTSTTEEEEES CS
                       Fibrillarin  51 frsKlaaailkglkelpi.kkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvlrelievakkRknivPile 126
                                       +rs+ +  +l+  ++++i ++g++v+ lGa  G       Divge+g+v +v+     ++ l  v      i  i +
  gi|474935085|ref|YP_007688667.1|  18 YRSRASFKLLQLDEKFHIfEEGDSVVDLGACPGGWSQVAYDIVGEKGKVIGVDLR--YIHPLEGV---QFIIGDITD 89 
                                       5666666666655666653899***********8766667************973..33333333...223444555 PP

                                       -TTSGGGGTTTS--EEEEEEESS CS
                       Fibrillarin 127 DArkPekYralvekvDvifaDva 149
                                       D ++ +   ++  kvDv+ +D+a
  gi|474935085|ref|YP_007688667.1|  90 DNTMIRLLDMVGGKVDVVLSDMA 112
                                       55555555555567777777776 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.4   0.00059       1.5       1      30 [.      42      72 ..      42     145 .. 0.80
   2 ?    1.7   0.0      0.17   4.3e+02      15      70 ..     123     173 ..     116     187 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00059
                                      EEEET-TTSHHHHHHHCTST.SSEEEEEESS CS
                   Methyltransf_25  1 vLdlGcGtGrltlalakrlg.kakvtgvDis 30
                                      v+dlG+ +G +++ + + +g k+kv+gvD+ 
  gi|474935085|ref|YP_007688667.1| 42 VVDLGACPGGWSQVAYDIVGeKGKVIGVDLR 72
                                      89***************99779*******85 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.17
                                       HHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBC.CGBS.SSTTTEEEEEE CS
                   Methyltransf_25  15 lakrlgkakvtgvDiseemleaareraeeeglnvefvqgda.edlp.fedgsfDlvvs 70 
                                        a+ + +  +++vD+ ++ l++  + a      +++  gd+ +dl+ + +++fD v++
  gi|474935085|ref|YP_007688667.1| 123 HARSI-ELCMYAVDVCDRILKKGGKMA------MKVFMGDLfQDLErELKKRFDSVIV 173
                                       55554.456667777777777666665......7777777767787335568888876 PP

>> NSP16  Coronavirus NSP16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   4.2e-05      0.11     121     214 ..     102     197 ..      86     204 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.2e-05
                                       S-EEEEEE----TTS-SS-S------THHHHHHHHHHHHEEEEEEEEEEE-SSS--HHHH.HHHTTEEEEEEEEEGG CS
                             NSP16 121 dkfdllisdlydkrtkeidkenvskdgfftylsgfikeklalGGsiaikitefswnkely.elvqkfafwtvfctsv 196
                                        k d+++sd+  +   + +++     ++ +y  ++    l  GG +a+k+      ++l  el +   f +v +ts 
  gi|474935085|ref|YP_007688667.1| 102 GKVDVVLSDMAPNIAGHYSTDHARSIELCMYAVDVCDRILKKGGKMAMKVFMGDLFQDLErELKK--RFDSVIVTSP 176
                                       689********9999999999999999********999************999999999614544..4667888888 PP

                                       GTT...SS-EEEEEEEE-SS. CS
                             NSP16 197 nas...sseafliGinylgka 214
                                        as   sse +++   +lg+ 
  gi|474935085|ref|YP_007688667.1| 177 KASrptSSEVYVVCRGFLGAH 197
                                       7765559**********9984 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0016       4.1      44      80 ..      35      71 ..      16      74 .. 0.90
   2 ?    2.6   0.2     0.027        70      43      93 ..      88     149 ..      80     173 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0016
                                      -S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES CS
                   Ubie_methyltran 44 avkrgakvlDvagGtgDlafklsdsvgekgkvvvlDi 80
                                         +g +v+D+ +  g ++    d vgekgkv+++D+
  gi|474935085|ref|YP_007688667.1| 35 IFEEGDSVVDLGACPGGWSQVAYDIVGEKGKVIGVDL 71
                                      567899******************************8 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.027
                                       --S--TTEEEEES-TT-HHHH.HHHHHHHHHH..........EEEEEES-HHHHHHHHHHHH CS
                   Ubie_methyltran  43 vavkrgakvlDvagGtgDlaf.klsdsvgekg..........kvvvlDinenmLkvgekklk 93 
                                       + + +  ++lD+ gG  D+ + +++ ++  ++           +  +D+ + +Lk g k ++
  gi|474935085|ref|YP_007688667.1|  88 TDDNTMIRLLDMVGGKVDVVLsDMAPNIAGHYstdharsielCMYAVDVCDRILKKGGKMAM 149
                                       55555667888888888876423444444444566677776667777777777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1372.62
//
Query:       gi|474935086|ref|YP_007688668.1|  [L=338]
Description: phosphoribosylaminoimidazole synthetase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-21   76.9   0.1    2.6e-21   76.4   0.1    1.2  1  AIRS_C    AIR synthase related protein, C-terminal domain
    9.9e-12   45.4   0.6    2.1e-11   44.3   0.6    1.5  1  AIRS      AIR synthase related protein, N-terminal domain


Domain annotation for each model (and alignments):
>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.4   0.1   2.9e-25   2.6e-21       2     152 ..     170     327 ..     169     329 .. 0.91

  Alignments for each domain:
  == domain 1  score: 76.4 bits;  conditional E-value: 2.9e-25
                                       TTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTT......TSEHHHHHHHHHHHHHHHHHHHH.HTTECEEEE--TTH CS
                            AIRS_C   2 pGdvliltgslGlggagtslkrkileeegldds......avqlgdvlleptliyvkralaal.kglvkaahDvTgGG 71 
                                        Gd+++ ++s+Gl+++g+ l+rk++e++  +         + +g +ll+pt iyvk+ l    k++v+++ D+TgGG
  gi|474935086|ref|YP_007688668.1| 170 KGDLIVSLKSSGLHSNGLTLARKVVEANNIKMTdsvsglTKSIGKELLTPTEIYVKQVLGITgKHEVHGLVDITGGG 246
                                       7***************************9887799***7777*********************************99 PP

                                       HHHHHHHHHHTTTEEEEEECG..THHHHHHHH.....HHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEE CS
                            AIRS_C  72 Llgalaemapasgvgaeidld..kvpifdele.....splemllsensGrllvavppeeadavlaileeeglpeaav 141
                                       L  ++ +m +++ ++ +id +    pif+ l+     ++ e++ + n+G ++ +++pe +  + +i++e    +a+v
  gi|474935086|ref|YP_007688668.1| 247 L-RNILRM-RKG-LKYTIDDPvkPQPIFQVLQelgqiEDKEIYQTLNMGMGFTIIAPETE--AEDIARENP--NAQV 316
                                       7.678899.554.9999999999888888888888*************************..888888875..7*** PP

                                       EEEEEESSSEE CS
                            AIRS_C 142 IGevtakeels 152
                                       +G+v+++++++
  gi|474935086|ref|YP_007688668.1| 317 VGRVEEGNGVY 327
                                       ******99765 PP

>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.6   2.3e-15   2.1e-11       5      94 .]      55     157 ..      44     157 .. 0.93

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 2.3e-15
                                       EEEEEEEEE.EECCTCCCC....HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.....HHHHHHHHHHHHHHHTT-E CS
                              AIRS   5 vvvttdshnrpvlvepvhf....iGakavavnlsDlaamGArPlalllslalp.....wleevvrglaeaaeelgvp 72 
                                       v+++td++++++l+++  +    iG  ++a+n++D ++++A+P+ +++++a+        ++v  gl+++ae  +++
  gi|474935086|ref|YP_007688668.1|  55 VTLATDGVGTKILIAEELGiwdtIGIDCIAMNVNDTICVNATPISFVDYIAIDkpdgeVTKQVGIGLNRGAELSDME 131
                                       5789999****999887778999***********************************99***************** PP

                                       EEEEEEEEESS....EEEEEEEEEEE CS
                              AIRS  73 lvgGdtsfsne....ptisvtavGlv 94 
                                       +vgG++++ +e    + +s t++G+v
  gi|474935086|ref|YP_007688668.1| 132 IVGGEIAVLPEivngLDLSGTCMGVV 157
                                       *******99999999*********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2581.13
//
Query:       gi|474935087|ref|YP_007688669.1|  [L=186]
Description: archaeal conserved hypothetical protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-69  232.2   0.0    4.1e-69  232.1   0.0    1.0  1  DUF531           Protein of unknown function (DUF531)
  ------ inclusion threshold ------
       0.14   12.0   0.0        0.2   11.5   0.0    1.2  1  Methyltrn_RNA_4  SAM-dependent RNA methyltransferase


Domain annotation for each model (and alignments):
>> DUF531  Protein of unknown function (DUF531)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  232.1   0.0   4.5e-73   4.1e-69       1     169 [.      11     182 ..      11     183 .. 0.98

  Alignments for each domain:
  == domain 1  score: 232.1 bits;  conditional E-value: 4.5e-73
                            DUF531   1 mltlglvntYDkkklheaHkRaiARaapicyafdfnLalldFplk...keekelvdvvaekttiGesGkylkelaek 74 
                                       ++t+g++n+YD+++++e H+RaiARa++i++af++nLal++Fpl    k++ke++d++a +t+iG++G+++ +lae 
  gi|474935087|ref|YP_007688669.1|  11 RMTVGIYNAYDPNTFREPHRRAIARAGDIAMAFNMNLALFGFPLPedkKTPKEVADYIAGTTSIGNHGDNFVQLAEL 87 
                                       69******************************************9777899************************** PP

                            DUF531  75 nrllvldlpkkgfpaqfGevvattskpdekkaitpeevaeeilrkksvllliGlGrkGlPkellklakyhlditekg 151
                                       +r++++++p kgfp+q+G+v++tt+kp+ kk++t++++a+++ +++svlll+G+G++G+P+++   ++y++++t+ +
  gi|474935087|ref|YP_007688669.1|  88 GRFQTFPYPVKGFPPQLGKVILTTCKPEAKKQLTTAQLADMVDQGQSVLLLFGIGPHGIPDKVRPFSDYDFEVTGGN 164
                                       ***************************************************************************** PP

                            DUF531 152 vslEtctAigaiaaviat 169
                                       +slEtctA+ga+++++++
  gi|474935087|ref|YP_007688669.1| 165 YSLETCTALGAVCGALDC 182
                                       *************99876 PP

>> Methyltrn_RNA_4  SAM-dependent RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.2e-05       0.2     104     153 ..     106     156 ..      97     176 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.2e-05
                                       EEEE--SS.--SS-B-HHHHHHHHHH--S-EEEEE--T.T---HHHHTT-SE CS
                   Methyltrn_RNA_4 104 lvvatsAr.kkentvsyeelrelleeeekpvlllfGtg.wGlaeevlekady 153
                                       +v+ t+ + + ++++++++l +++ ++ ++vlllfG g +G+ ++v   +dy
  gi|474935087|ref|YP_007688669.1| 106 KVILTTCKpEAKKQLTTAQLADMV-DQGQSVLLLFGIGpHGIPDKVRPFSDY 156
                                       466666663677889999999999.999********9978999988666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1400.27
//
Query:       gi|474935088|ref|YP_007688670.1|  [L=51]
Description: hypothetical protein TALC_01542 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       172  (0.0095934); expected 358.6 (0.02)
Passed bias filter:                      171  (0.00953762); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.48
# Mc/sec: 320.96
//
Query:       gi|474935089|ref|YP_007688671.1|  [L=820]
Description: DNA gyrase subunit A [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     2e-153  511.3   0.0   2.5e-153  511.0   0.0    1.1  1  DNA_topoisoIV  DNA gyrase/topoisomerase IV, subunit A
    7.6e-69  227.0  13.7    6.8e-16   57.5   0.3    6.4  6  DNA_gyraseA_C  DNA gyrase C-terminal domain, beta-propeller
  ------ inclusion threshold ------
      0.068   13.6   2.1       0.18   12.2   2.1    1.6  1  Nnf1           Nnf1
       0.14   12.8   0.3       0.64   10.7   0.2    2.2  2  RTP            Replication terminator protein


Domain annotation for each model (and alignments):
>> DNA_topoisoIV  DNA gyrase/topoisomerase IV, subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  511.0   0.0  5.6e-157  2.5e-153       1     425 [.      35     474 ..      35     475 .. 0.98

  Alignments for each domain:
  == domain 1  score: 511.0 bits;  conditional E-value: 5.6e-157
                     DNA_topoisoIV   1 RaiPsvrDGlKPvqRriLyamfkl.lnldkkekKvaqlvGevlgkYhPHGdaslydaivrlaqdfvgniplldpqGn 76 
                                       Ra+P+vrDGlKPv+R+iLyam++l l+ ++++kK+a +vGevlgkYhPHGd++ y a+vrl+qdf++++pl+d+qGn
  gi|474935089|ref|YP_007688671.1|  35 RALPDVRDGLKPVHRKILYAMHELgLSYNRPHKKSATVVGEVLGKYHPHGDSAAYGAMVRLGQDFAMRYPLIDGQGN 111
                                       9**************************************************************************** PP

                     DNA_topoisoIV  77 fGsildgdkdAaaRYietrLskiarellkeidketvdyqenyDgsekEPevlppiiPnlLvnGaeGIavGmatkipp 153
                                       fGs+ dgd++Aa+RY+e+rLsk+a++ll ++dk tvd+ +n+Dgs kEP +lp+++PnlLvnG++GIavGmatk+pp
  gi|474935089|ref|YP_007688671.1| 112 FGSV-DGDPPAAMRYTEARLSKMASDLLLDLDKGTVDFIDNFDGSLKEPSILPSKFPNLLVNGSDGIAVGMATKMPP 187
                                       ****.************************************************************************ PP

                     DNA_topoisoIV 154 hnlkeiidaliallkgeea...ellelvlgPdfptgggiigkeeikeayetgrGkikvrakveie.....ektivit 222
                                       hnl+e++da+i+ +++++a    l+++v+gPdfptgg+i g ++i +ay+tgrG+ikvrak+++e     +++i++ 
  gi|474935089|ref|YP_007688671.1| 188 HNLREVCDAIIYTIDTPDAdvpALMQFVKGPDFPTGGIINGIAGIIDAYTTGRGRIKVRAKTHFEeirggKTAIIVD 264
                                       *****************999999****************************************99***9559***** PP

                     DNA_topoisoIV 223 ElPigvntskliekieelvkkkkik.isdirdesdr.gvrivielkrgaseekvleklykktkLessisvnnlvlfd 297
                                       E+P++vn+++l+++i++lvk+k i  i+d+rdesdr g+r+viel+++a +e+vl++l++kt++e ++ + nl+l++
  gi|474935089|ref|YP_007688671.1| 265 EIPYQVNKAELVKSIADLVKNKAIVgITDLRDESDRkGMRVVIELHKDAIDEVVLQNLFSKTQMEITYGIINLALVN 341
                                       **********************9999*******9999**************************************** PP

                     DNA_topoisoIV 298 kkpkylslkeilkeflevrlevyerrkeyllekleerleilegllkalnkidevievirkskkekkakkeLiee..l 372
                                       +kp++l+lke++ +++++r++v++rr++++l+++ +r++ilegl+ aln++de i++ir+sk+ ++a++ L++   +
  gi|474935089|ref|YP_007688671.1| 342 NKPTTLGLKELIMQYIAHRRTVVTRRTQFELDECAKRFHILEGLMAALNMLDETIKLIRASKDGAEANAGLQNLlhI 418
                                       *************************************************************************9889 PP

                     DNA_topoisoIV 373 seeqaeyllemrlrrLtkeeveklekeieelekeikelekllak...lkklikeel 425
                                       ++ qa+++l+mrl++Lt +e +++++e+e+l++++++l+++lak   + ++ik+el
  gi|474935089|ref|YP_007688671.1| 419 DQIQAQAILDMRLQKLTGLELDSVREEYEQLKARMEDLRDILAKparVDAIIKDEL 474
                                       9*******************************************997777777776 PP

>> DNA_gyraseA_C  DNA gyrase C-terminal domain, beta-propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   0.0   3.3e-13   1.5e-09       3      48 .]     508     553 ..     506     553 .. 0.95
   2 !   32.8   0.0     8e-12   3.6e-08       1      47 [.     556     606 ..     556     607 .. 0.96
   3 !   29.9   0.0   6.3e-11   2.8e-07       3      44 ..     615     654 ..     612     658 .. 0.94
   4 !   41.6   0.2   1.3e-14     6e-11       1      48 []     661     708 ..     661     708 .. 0.97
   5 !   32.1   0.8   1.3e-11   5.8e-08       1      45 [.     711     756 ..     711     759 .. 0.90
   6 !   57.5   0.3   1.5e-19   6.8e-16       1      47 [.     762     808 ..     762     808 .. 0.98

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 3.3e-13
                                       EEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEEEES CS
                     DNA_gyraseA_C   3 llliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvlvvs 48 
                                       + +i++  yvkr+pl ++++q+Rg++G +g ++kegd + s++v+s
  gi|474935089|ref|YP_007688671.1| 508 VYTISEDNYVKRLPLRTYKQQNRGGTGMTGLQTKEGDTVRSMFVAS 553
                                       779****************************************975 PP

  == domain 2  score: 32.8 bits;  conditional E-value: 8e-12
                                       SEEEEEETTSEEEEEEGGGS-BT-TTSCTEEGS....ETTTTSSEEEEEEE CS
                     DNA_gyraseA_C   1 dellliTsnGyvkrfplselpeqgRgakGvkgi....klkegdklvsvlvv 47 
                                       d+l+++T+ G++++++ + +pe +R akG++++    +l eg+ +++v+++
  gi|474935089|ref|YP_007688671.1| 556 DYLMFVTNTGRILWLKGYNIPEGSRQAKGKPVVnllpDLQEGEIVTNVIPT 606
                                       8********************************999999999999999986 PP

  == domain 3  score: 29.9 bits;  conditional E-value: 6.3e-11
                                       EEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEE CS
                     DNA_gyraseA_C   3 llliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsv 44 
                                       l++ T+nG +k++ ls + + +   kG+k+i+l+++d+lv v
  gi|474935089|ref|YP_007688671.1| 615 LVFCTRNGLIKKTQLSAYGNVR--NKGIKAIRLDDDDELVEV 654
                                       799*******************..78*************977 PP

  == domain 4  score: 41.6 bits;  conditional E-value: 1.3e-14
                                       SEEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEEEES CS
                     DNA_gyraseA_C   1 dellliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvlvvs 48 
                                       de++l++  G+++rfp+ e++++gR ++Gv+g++   +++++s+ vv+
  gi|474935089|ref|YP_007688671.1| 661 DEIVLASTDGQAIRFPEFEVSATGRDTRGVRGMTVGRKESVISMTVVK 708
                                       89*********************************999******9995 PP

  == domain 5  score: 32.1 bits;  conditional E-value: 1.3e-11
                                       SEEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTT.SSEEEEE CS
                     DNA_gyraseA_C   1 dellliTsnGyvkrfplselpeqgRgakGvkgiklkeg.dklvsvl 45 
                                       d+ll++T+nG++k   +s+++ ++Rg+kGv+ ik +++ + + sv 
  gi|474935089|ref|YP_007688671.1| 711 DMLLTVTENGFGKISIVSDYRLTHRGGKGVITIKCTKRnGGVMSVR 756
                                       89*******************************9888878887776 PP

  == domain 6  score: 57.5 bits;  conditional E-value: 1.5e-19
                                       SEEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEEEE CS
                     DNA_gyraseA_C   1 dellliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvlvv 47 
                                       del+ i+s G+v+r+++s+++++gR+a Gvk+++lk+g+ +vsv +v
  gi|474935089|ref|YP_007688671.1| 762 DELMAISSSGKVIRMRVSDIRQTGRNAAGVKIMDLKDGETIVSVNPV 808
                                       89******************************************987 PP

>> Nnf1  Nnf1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   2.1   3.9e-05      0.18      31     103 ..     385     458 ..     380     463 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.9e-05
                                       HHHHHHHHHHHHHHHHCCHH-T...........TTSSTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              Nnf1  31 vvekLneLDdlieeAkerreegeeeasrpe.vpphtLpPeeliaahlapakkeeqeeLearlqeleaenaelae 103
                                       + + Ln LD+ i+  +  ++ +e++a+ ++  ++++ +++ +++ +l ++   e+++ ++++++l+a  ++l +
  gi|474935089|ref|YP_007688671.1| 385 LMAALNMLDETIKLIRASKDGAEANAGLQNlLHIDQIQAQAILDMRLQKLTGLELDSVREEYEQLKARMEDLRD 458
                                       6789*****88888887777777777666689***********************************9999976 PP

>> RTP  Replication terminator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.2   5.3e+03      40      55 ..      43      58 ..      40      75 .. 0.85
   2 ?   10.7   0.2   0.00014      0.64      38     113 ..     265     341 ..     262     343 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.2
                                      T----HHHHHHHHHHH CS
                               RTP 40 gykPnhseiyralhel 55
                                      g kP h +i+ a+hel
  gi|474935089|ref|YP_007688671.1| 43 GLKPVHRKILYAMHEL 58
                                      67999*********98 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00014
                                       TTT----HHHHHHHHHHHHHTTSEEEEEEEBTSSSSSEE.EEEEESS..HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               RTP  38 elgykPnhseiyralhelvedgilkrrkelkekaklqev.viYsltdeGkekaklykkqvkidldrckkllekalkd 113
                                       e+ y+ n++e+ +++ +lv++  +  +  l+++++++ + v+ +l+++  +++ l     k++++ + ++++ al +
  gi|474935089|ref|YP_007688671.1| 265 EIPYQVNKAELVKSIADLVKNKAIVGITDLRDESDRKGMrVVIELHKDAIDEVVLQNLFSKTQMEITYGIINLALVN 341
                                       5789***************************99999876467799999***********************998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (820 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.76u 0.30s 00:00:01.06 Elapsed: 00:00:00.50
# Mc/sec: 4977.88
//
Query:       gi|474935090|ref|YP_007688672.1|  [L=440]
Description: hydroxymethylpyrimidine synthase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   1.7e-187  623.4   0.7   1.9e-187  623.2   0.7    1.0  1  ThiC_Rad_SAM  Radical SAM ThiC family


Domain annotation for each model (and alignments):
>> ThiC_Rad_SAM  Radical SAM ThiC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  623.2   0.7    1e-191  1.9e-187       1     417 [.       3     419 ..       3     420 .. 0.99

  Alignments for each domain:
  == domain 1  score: 623.2 bits;  conditional E-value: 1e-191
                      ThiC_Rad_SAM   1 tqleaarkgiiteemeevaekenvepefvreevaeGrivipanknhkekpvaiGkglrtkvnaniGtsadasdieeE 77 
                                       t +e+ar+g+ +e+++++ae+env++ f+ +++a+Griv+p+n  h+  p+aiG+gl++k+naniGts+d+ d+e+E
  gi|474935090|ref|YP_007688672.1|   3 TIMEQARRGESDERIRKIAERENVTERFILDGIASGRIVMPCNPVHDPIPAAIGEGLSVKINANIGTSRDMPDLEAE 79 
                                       789************************************************************************** PP

                      ThiC_Rad_SAM  78 veKlkvalkagadtvmdLstggdideirekileespvpvgtvpiYqalee..kekkveelteeellevieeqaedGv 152
                                       ++K++va+k+gad+vmdLstggdi++ir+++l+++pv++g+vpiY++  +  ++++v+e+te+++++ ie++a+dG+
  gi|474935090|ref|YP_007688672.1|  80 IRKMDVAVKYGADAVMDLSTGGDIEAIRKTLLARCPVMMGSVPIYEVGLTaaRRNAVVEMTEDDIFSGIEQHAKDGM 156
                                       **********************************************9877678999********************* PP

                      ThiC_Rad_SAM 153 dfltiHagvtlellellkkekRltgivSrgGsllaawmlanekenplyeefdelleilkeydvtlSlgdglRpGsia 229
                                       df+t+H+g+t+e+++ +kk++R++++vSrgGs+l+aw+l+ne+enplye+fd+lle++++y+ tlSlgdg+RpG+i+
  gi|474935090|ref|YP_007688672.1| 157 DFMTVHCGITRETVRWIKKSGRIMDVVSRGGSFLTAWILHNERENPLYENFDYLLELARKYEFTLSLGDGFRPGAIN 233
                                       ***************************************************************************** PP

                      ThiC_Rad_SAM 230 DatdeaqlaelivlgelvkrareagvqvmveGPGHvpldeieanvklqkklckeaPfyvlGplvtDiapgYDhitsa 306
                                       Da+d+aq++el++lg+lvkr+r+agvq+mveGPGH+++d+i+an+k++k+lc++aPfy+lGplvtDiapgYDhit+a
  gi|474935090|ref|YP_007688672.1| 234 DASDQAQISELMTLGHLVKRSRDAGVQAMVEGPGHMQMDQIAANMKMEKTLCQGAPFYTLGPLVTDIAPGYDHITAA 310
                                       ***************************************************************************** PP

                      ThiC_Rad_SAM 307 iGaalaaaaGadllCyvtpaEHlglPdeedvkeGviaakiaahaadlakglkkarerdkalskaRkeldwekqfela 383
                                       iG+a+aaa+Gad+lC+vtpaEHl+lPdeedvkeGvia+kiaahaadl++g+   +e+d+++++aRk ldwe++++++
  gi|474935090|ref|YP_007688672.1| 311 IGGAIAAANGADFLCFVTPAEHLSLPDEEDVKEGVIASKIAAHAADLTRGIG--KEKDDRMARARKVLDWEAMYDVC 385
                                       **************************************************65..589******************** PP

                      ThiC_Rad_SAM 384 ldpekareireeklpeeeeaCsmCgekCavkive 417
                                       ldpeka+++r++  +ee++ CsmCg+ Cavkiv+
  gi|474935090|ref|YP_007688672.1| 386 LDPEKAKRYRARGCTEEKDGCSMCGDVCAVKIVN 419
                                       *******************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 2758.03
//
Query:       gi|474935091|ref|YP_007688673.1|  [L=272]
Description: Endonuclease IV [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-22   79.2   0.1    3.6e-22   78.8   0.1    1.1  1  AP_endonuc_2  Xylose isomerase-like TIM barrel
    0.00031   20.1   0.0    0.00049   19.4   0.0    1.3  1  UvdE          UV-endonuclease UvdE


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.8   0.1     4e-26   3.6e-22       2     205 ..      22     225 ..      21     229 .. 0.89

  Alignments for each domain:
  == domain 1  score: 78.8 bits;  conditional E-value: 4e-26
                                       HHHHHCT-SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCS.HHHHHHHHHHHHH CS
                      AP_endonuc_2   2 aaaaeaGfdgvElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypdederear.reesvdalkraie 77 
                                       +  +e+G d+ E+ +  +  +s   +e+++++ k +++l++r++++ ++  + +++    +++  ++svd + +++ 
  gi|474935091|ref|YP_007688673.1|  22 KYTRELGLDALEVEFVRGARIS---EERAKAVGKVAKDLDIRLSCHAPYFISFNSE----SPEtIDKSVDWVVETAV 91 
                                       6789*****************9...59***************88888876655532....34467999********* PP

                                       HHHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHT...SEEEEE--TTTTSSSTCHHHHHHHHHH CS
                      AP_endonuc_2  78 laaaLGapllvlhpGtagagpkgseeeawerlaeslneladyaekeg...vklalEtlagsgvelgdeelarlldav 151
                                       +a+ LGa l+v+h+      +++++e+a e+++++l++  d +++ g   v l++Et+ ++g++   +e+a+++d v
  gi|474935091|ref|YP_007688673.1|  92 AAHNLGAYLIVIHAA----AYGKHPETATENVIKGLRRSKDRLDDLGikdVILGVETMGKQGQFGTLKEIAQVMDSV 164
                                       *************55....9999999999*************9999988899***********9999********** PP

                                       TTTTEEEEEEHHHHHHH.......TTTHHHHHHHHHGG...EEEEEE.EESSTTTTSSTTEEST CS
                      AP_endonuc_2 152 dspnvgvclDtgHllia.......eedvddalraladr...ikhvHikDakgdlgagrdrhvpi 205
                                       d   v+ +lD++H +++       e d++++l ++ +    ++h+Hi+ +k  + +g+  h+p+
  gi|474935091|ref|YP_007688673.1| 165 DG--VRPVLDVAHVHARgigclktEQDMRALLSEFFPFageTAHFHISCIKY-GQKGEISHLPL 225
                                       *8..********************99999999999999999******87777.66666666666 PP

>> UvdE  UV-endonuclease UvdE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   5.4e-08   0.00049      86     126 ..      44      84 ..      33     131 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 5.4e-08
                              UvdE  86 aeeleevGelakelglRltfHPeqftllnSdrkevtesair 126
                                       +e+ ++vG++ak+l++Rl+ H   f+ +nS+ +e  ++++ 
  gi|474935091|ref|YP_007688673.1|  44 EERAKAVGKVAKDLDIRLSCHAPYFISFNSESPETIDKSVD 84 
                                       566789*****************************999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1697.16
//
Query:       gi|474935092|ref|YP_007688674.1|  [L=163]
Description: 8-oxoguanine DNA glycosylase, N-terminal domain protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      5e-16   58.9   0.0    2.4e-14   53.4   0.0    2.1  1  OGG_N     8-oxoguanine DNA glycosylase, N-terminal domain
     0.0073   16.8   0.0      0.011   16.2   0.0    1.3  1  HhH-GPD   HhH-GPD superfamily base excision DNA repair protei


Domain annotation for each model (and alignments):
>> OGG_N  8-oxoguanine DNA glycosylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   0.0   2.7e-18   2.4e-14       8     121 .]       2      99 ..       1      99 [. 0.93

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 2.7e-18
                                       S--HHHHHCSSS-SSEEE-TTS-EEEEETTEEEEEEEETTEEEEET--.............HHHHHHTHHHHTTTTS CS
                             OGG_N   8 eldlkktLkcGQsFrWkktekteyvgvlgdrvveLkqeeddllyrtlesesstkasseeakeeeteeilrdYfnLdv 84 
                                       e++l+ tL cGQ+ rW+k e+ ++ gv+g+ vv+L q++d                    +   + + +++Yf+ + 
  gi|474935092|ref|YP_007688674.1|   2 EVSLDPTLGCGQAHRWRKMEDGSWQGVIGNDVVTLFQTDDGFDC----------------EGAADISAVKEYFREKD 62 
                                       689*********************************88776544................455699*********** PP

                                       -HHHHHHHHTT.SHHHHHHHCCTTT-------HHHHH CS
                             OGG_N  85 dleelykewskkdplfkksadkftGiRllrqdpwEcL 121
                                       dl+ ++ e s++dp++++  +k  G+R+l+q  wEcL
  gi|474935092|ref|YP_007688674.1|  63 DLKAIIGEISEADPEVASLSSKCPGLRILKQPEWECL 99 
                                       ************************************9 PP

>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.2e-06     0.011       4      36 ..     103     143 ..     100     162 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.2e-06
                                       HHHTTS-HHHHHHHHHHHHHHHS........HCSHHHHHHS CS
                                       xxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxx RF
                           HhH-GPD   4 ilsqqtsderanriierlferfg........fptpedlada 36 
                                       +l  +++++r+++++e++++ fg        fptp++++d 
  gi|474935092|ref|YP_007688674.1| 103 VLATNVNVKRIAKMVESVCDHFGtdlgerraFPTPKQILDG 143
                                       7889**********************************984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1053.79
//
Query:       gi|474935093|ref|YP_007688675.1|  [L=88]
Description: hypothetical protein TALC_01549 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00014   21.5   0.0    0.00021   21.0   0.0    1.3  1  HHH       Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.057   13.5   0.0      0.089   12.9   0.0    1.3  1  HHH_2     Helix-hairpin-helix motif
      0.092   13.4   0.0       0.13   12.9   0.0    1.2  1  HHH_5     Helix-hairpin-helix domain
       0.16   12.2   0.0       0.28   11.5   0.0    1.4  1  Cdd1      Pathogenicity locus


Domain annotation for each model (and alignments):
>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   4.7e-08   0.00021      10      30 .]      10      30 ..       5      30 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 4.7e-08
                                      HHHHHTSTT-SHHHHHHHHHH CS
                               HHH 10 reeLlalPGVGpktAeaIlsy 30
                                      ++eL+ + GVGpk+A++++ +
  gi|474935093|ref|YP_007688675.1| 10 VKELQGINGVGPKVADCVALF 30
                                      79***************9865 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     2e-05     0.089      34      53 ..      10      29 ..       4      31 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2e-05
                             HHH_2 34 leeLlevddiGeeiAqsive 53
                                      ++eL+ ++++G+++A+ +  
  gi|474935093|ref|YP_007688675.1| 10 VKELQGINGVGPKVADCVAL 29
                                      78**************9975 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.8e-05      0.13       2      15 ..      11      24 ..      10      39 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.8e-05
                                      HHHHTSTT--HHHH CS
                             HHH_5  2 eeLlsvsGiGpktA 15
                                      +eL++++G+Gpk+A
  gi|474935093|ref|YP_007688675.1| 11 KELQGINGVGPKVA 24
                                      799*********98 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   6.2e-05      0.28       5      32 ..      10      37 ..       6      48 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.2e-05
                              Cdd1  5 lkelqdiPniGkalaedlvelGirsvee 32
                                      +kelq i ++G+++a+ +   G+ ++e 
  gi|474935093|ref|YP_007688675.1| 10 VKELQGINGVGPKVADCVALFGYGHLEA 37
                                      79*********************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.34s 00:00:00.82 Elapsed: 00:00:00.52
# Mc/sec: 513.79
//
Query:       gi|474935094|ref|YP_007688676.1|  [L=130]
Description: putative transcriptional regulator [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.088   13.1   0.0       0.14   12.4   0.0    1.3  1  KORA          TrfB plasmid transcriptional repressor
       0.11   12.2   0.0       0.26   11.0   0.0    1.7  1  Sigma70_r4_2  Sigma-70, region 4
       0.15   12.7   0.0       0.21   12.2   0.0    1.2  1  HNF-1_N       Hepatocyte nuclear factor 1 (HNF-1), N terminus
       0.15   12.1   0.0        0.3   11.2   0.0    1.5  1  HTH_3         Helix-turn-helix


Domain annotation for each model (and alignments):
>> KORA  TrfB plasmid transcriptional repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.2e-05      0.14      19      54 ..      16      52 ..       9      61 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.2e-05
                              KORA 19 qtveiargvL.Vegkkqadvatelgltkqavsqavkr 54
                                      + +eia+++  V + kqadv +  g+t  a+sq  ++
  gi|474935094|ref|YP_007688676.1| 16 IRREIAKELVdVHHMKQADVGRIFGVTDAAISQYLNK 52
                                      568999876559*********************8765 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   5.9e-05      0.26      20      48 ..      23      51 ..      12      54 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.9e-05
                                      HHHHTS---HHHHHHHHT--HHHHHHHHH CS
                      Sigma70_r4_2 20 llryleglsykEIAellgisegtVksrls 48
                                      +l ++++++++++ +++g++++++ ++l 
  gi|474935094|ref|YP_007688676.1| 23 ELVDVHHMKQADVGRIFGVTDAAISQYLN 51
                                      6899********************99986 PP

>> HNF-1_N  Hepatocyte nuclear factor 1 (HNF-1), N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.6e-05      0.21     145     176 ..      20      52 ..      14      63 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.6e-05
                           HNF-1_N 145 i.kaflqqhrIsQrevvdvTGlsQShlSqwLlk 176
                                       i k+ +  h++ Q+ v+ + G+    +Sq+L+k
  gi|474935094|ref|YP_007688676.1|  20 IaKELVDVHHMKQADVGRIFGVTDAAISQYLNK 52 
                                       43778899************************6 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   6.8e-05       0.3       9      34 ..      29      54 ..      20      55 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.8e-05
                                      THHHHHHHHHHTSSHHHHHHHHTTSS CS
                             HTH_3  9 glsqeeLAeklGvsrstisriEnGer 34
                                       + q+++ +  Gv+ ++is++ n +r
  gi|474935094|ref|YP_007688676.1| 29 HMKQADVGRIFGVTDAAISQYLNKKR 54
                                      699********************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 848.53
//
Query:       gi|474935095|ref|YP_007688677.1|  [L=1787]
Description: Lhr-like helicase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-54  183.5   0.0    8.6e-54  182.2   0.0    1.7  1  DEAD_assoc       DEAD/H associated
    4.8e-27   94.8   0.1    7.9e-26   90.9   0.0    2.4  2  DEAD             DEAD/DEAH box helicase
    1.3e-21   77.5   4.8    2.5e-06   27.3   1.3    4.3  3  HTH_42           Winged helix DNA-binding domain
    2.8e-17   63.1   0.0    2.1e-15   57.0   0.0    2.8  2  Helicase_C       Helicase conserved C-terminal domain
    2.5e-08   34.1   0.0      6e-08   32.9   0.0    1.6  1  ResIII           Type III restriction enzyme, res subunit
      0.008   15.3   0.1      0.021   13.9   0.1    1.6  1  T2SSE            Type II/IV secretion system protein
  ------ inclusion threshold ------
      0.014   15.8   1.6        3.5    8.0   0.0    3.3  3  Penicillinase_R  Penicillinase repressor
       0.02   15.7   0.8         15    6.4   0.0    3.1  3  Histone_HNS      H-NS histone family
      0.053   13.6   0.0       0.12   12.4   0.0    1.5  1  DUF3793          Protein of unknown function (DUF3793)
      0.077   13.7   0.0       0.52   11.0   0.0    2.4  2  RPA_C            Replication protein A C terminal
        0.1   12.3   0.3        1.6    8.4   0.0    2.9  3  Ribosom_S30AE_C  Sigma 54 modulation/S30EA ribosomal protein 
       0.13   12.3   0.1       0.96    9.5   0.0    2.6  2  HTH_Crp_2        Crp-like helix-turn-helix domain
       0.16   12.3   0.0       0.45   10.8   0.0    1.8  1  AAA_19           AAA domain
       0.17   12.4   1.2         16    6.0   0.0    4.4  4  HTH_27           Winged helix DNA-binding domain


Domain annotation for each model (and alignments):
>> DEAD_assoc  DEAD/H associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.2   0.0   6.7e-57   8.6e-54       1     191 []     635     822 ..     635     822 .. 0.98

  Alignments for each domain:
  == domain 1  score: 182.2 bits;  conditional E-value: 6.7e-57
                        DEAD_assoc   1 lPtdrtllvErfrdelgdwrlvvhspfGrrvnealalllaarlsrrfgidvqvaanDdgivlllpleerlpllldel 77 
                                       +P++r+l vE++ d  g++rl++h pfGrrvn+al++++a+r+++ +g +++v+++Dd +++  +++++++  +d++
  gi|474935095|ref|YP_007688677.1| 635 VPDARRLAVEEYIDPSGNQRLIFHFPFGRRVNDALSRAYAYRITALTGANASVTITDDNFMI--GTTHKID--IDQV 707
                                       8*************************************************************..8888976..899* PP

                        DEAD_assoc  78 lellspdeleedleaalnaselfkrrFrevAaralllprrypgkrkplwqqrlraaqLldvareypdfpllleavre 154
                                         +l+p++l+++l++a+++se+fk rFr+ Aar+++++r+y g+  ++++q++r+  Lld++r++++ p+++e++re
  gi|474935095|ref|YP_007688677.1| 708 PGMLNPRDLDSVLRKAVKDSEIFKLRFRHTAARSFMILRNYMGRSISVNRQQVRSTYLLDMLRDMENEPVIEETYRE 784
                                       ***************************************************************************** PP

                        DEAD_assoc 155 vledqlDlerlaellrriaageirvveve.tprpSpfA 191
                                       +led++D+ +++ +l+ i++g++ v++++ + +pSpfA
  gi|474935095|ref|YP_007688677.1| 785 ILEDDMDIRNAKYVLELIENGKMGVRTIHfSGTPSPFA 822
                                       *****************************999*****9 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.9   0.0   6.2e-29   7.9e-26       1     170 [.      33     217 ..      33     223 .. 0.83
   2 ?    1.0   0.0      0.24   3.1e+02      43     104 ..     279     341 ..     265     349 .. 0.78

  Alignments for each domain:
  == domain 1  score: 90.9 bits;  conditional E-value: 6.2e-29
                                       -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHS....TTSTS-EEEEEESSHHHHHHHHHHHHHHTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyet....kgktgpkalivePtreLaeqtlnnlkkfkky 73 
                                       t+ Q+ aip i + ++vl++ +TGsGKTl ++  +l+++++       +++  +++++P+++La+++ +nl+  +++
  gi|474935095|ref|YP_007688677.1|  33 TEPQSMAIPVIHQRKNVLISSPTGSGKTLTAFTSILNQLIKYstdgVLEEKIYCIYISPLKALANDVNRNLTVPLEQ 109
                                       5679***********************************998888879999********************777775 PP

                                       ST............SEEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSH..CTTEEEEEEETHHHHHHT CS
                                       xx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxx RF
                              DEAD  74 id............lrvlliiggvaardqlskldngvdivvgtpgrlddllstgkln..lsqvrflVlDEadrlldq 136
                                       ++            +rv +  g++++++ ++ +++ ++i+++tp+ ++ +l + k++  ++++++++lDE++ + d+
  gi|474935095|ref|YP_007688677.1| 110 MKelaaregmhvpeIRVAVRSGDTPQSERQKMVRHPPHILITTPESMALILASPKFRenMKSIEWVILDEIHDICDS 186
                                       555556778888778887666655555555555555*************9955554444****************** PP

                                       TTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 137 gfsdfinrilnqlpqitcdgklqrqvivlSATlp 170
                                       +++ f++  ++ l++  ++   + + i lSAT+ 
  gi|474935095|ref|YP_007688677.1| 187 KRGAFLSLTMEMLRDYVAH---DFTRIGLSATMA 217
                                       *************755544...4569******97 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.24
                                       TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEE.EEETTSSHHHHHHHHHTT.CSEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx.xxxxxxx RF
                              DEAD  43 kgktgpkalivePtreLaeqtlnnlkkfkkyidlrvl.liiggvaardqlskldng.vdivvgt 104
                                         +++  +l+ + tr+ ae ++ +lk+++ + +++v+ + +g +++ d  ++l++g +++vv+ 
  gi|474935095|ref|YP_007688677.1| 279 LVDEHDTTLVFTNTRSGAEAVVYKLKERGLE-NIEVHhSSLGRETRLDVEERLKKGeIKCVVSS 341
                                       45666789********************997.3456557899999999999**88889999875 PP

>> HTH_42  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.7e-07   0.00022     158     230 ..    1020    1091 ..     979    1102 .. 0.73
   2 !   27.3   1.3     2e-09   2.5e-06     100     249 ..    1205    1343 ..    1134    1360 .. 0.68
   3 !   25.9   0.0   5.1e-09   6.5e-06     120     252 ..    1548    1701 ..    1533    1708 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.7e-07
                            HTH_42  158 lPravrseaealreLvrrylrayGpatvadlaawsgltkarlraalaelvaegelve..vrvergrerlfdlped 230 
                                        +P++ + +a a++e++ r+l  yGp t+++ a+ + ++ +++r  l+ +va ge+++  + v +g++  ++l  d
  gi|474935095|ref|YP_007688677.1| 1020 DPPKGD-RATAIDEVLARHLGGYGPTTAQEAAFALSIPDEEVRSSLDSMVAGGEVARgqFVVADGEQ--YMLTSD 1091
                                        333322.9**********************************************9751144445544..444443 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 2e-09
                            HTH_42  100 pltarelgealarrgwwgwkkpgkaskralellrlegelvvarrergfe...kvydlaervlPravrseaealre 171 
                                         +t re+ ++  ++        ++++k a++ l +++++++a  er  +             Pr+   + +  +e
  gi|474935095|ref|YP_007688677.1| 1205 GITMREIVAETHKE--------KEQVKEAVMRLDRSMKVMRAFGEREDWgteN---IYVPFVPRQL--DSDPTDE 1266
                                        44555554443333........4578888888888888888887777774443...4444444444..89999** PP

                            HTH_42  172 LvrrylrayGpatvadlaawsgltkarlraalaelvaegelvevrvergrerlfdlpedl..aelpgadtpv.rl 243 
                                        +v +++rayGp  v+ +++++ ++ +r+++a+++     ++      +++ +++ + ++     +++a++   r+
  gi|474935095|ref|YP_007688677.1| 1267 VVAQAIRAYGPIPVMAMRFLVSVPEERIAQAAQRCG---AVQILVGPGQM-PMWIMQDEVgdLNSAEAPEEKtRI 1337
                                        ********************************8774...33444444444.5999998776644444444434** PP

                            HTH_42  244 LppfDn 249 
                                        L+pfD+
  gi|474935095|ref|YP_007688677.1| 1338 LSPFDP 1343
                                        *****9 PP

  == domain 3  score: 25.9 bits;  conditional E-value: 5.1e-09
                            HTH_42  120 kpgkaskralellrlegelvvarrergfekvydlaerv......lPravrs...................eaeal 169 
                                        kp++a + +  ++  ++++   + +   +++yd++++                                 ++eal
  gi|474935095|ref|YP_007688677.1| 1548 KPSEAEREIEKIVKERMPVSKKEIQFRSKHTYDTTADAisslmkR-----AvicqdednyykwvpdngmtRDEAL 1617
                                        455555555556666666666665544447777777773333330.....13333344555555555555***** PP

                            HTH_42  170 reLvrrylrayGpatvadlaawsgltkarlraalaelvaegelve.vrvergre.rlfdlpedlaelpgadtpvr 242 
                                        re+++ ++r +G+ ++  +  ++g + a++r++l +l++eg lv  + +e g +  ++++++d +++ ++ t   
  gi|474935095|ref|YP_007688677.1| 1618 REVAKLHFRDMGLFSAENMSSFLGARMAETRRVLSDLEEEGFLVKgFFIE-GDStLYWMMKDDVDKRVRQFTGLF 1691
                                        ****************************************9998636666.66668999999889999999999* PP

                            HTH_42  243 lLppfDnlll 252 
                                        lL+  Dnl l
  gi|474935095|ref|YP_007688677.1| 1692 LLNTQDNLSL 1701
                                        ***9999865 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.12   1.6e+02      39      62 ..     117     145 ..      86     156 .. 0.76
   2 !   57.0   0.0   1.7e-18   2.1e-15      10     108 ..     276     376 ..     269     378 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.12
                                       T.....TSTEEEESTTSTHHHHHHHHHHH CS
                        Helicase_C  39 k.....gikvavlhgelpqnereeileqf 62 
                                       +     +i+vav  g++pq+er+++++  
  gi|474935095|ref|YP_007688677.1| 117 EgmhvpEIRVAVRSGDTPQSERQKMVRHP 145
                                       3455668*****************98865 PP

  == domain 2  score: 57.0 bits;  conditional E-value: 1.7e-18
                                       H.HHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTT CS
                        Helicase_C  10 l.kleeeggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipk 84 
                                       l +l  e++++l+f+nt++ +e  v  l+e+   ++ v+h++l  + r+++ e+ +kge++++++++ +e Gidi +
  gi|474935095|ref|YP_007688677.1| 276 LkELVDEHDTTLVFTNTRSGAEAvVYKLKERGLENIEVHHSSLGRETRLDVEERLKKGEIKCVVSSTSLELGIDIGS 352
                                       4345589999*********8887555566666789999*************************************** PP

                                       ESEEEESSSSSSHHHHHHHHTTSS CS
                        Helicase_C  85 vnlVinfdlprnvtsyiqriGRtg 108
                                       v+lV +++ p++v++  qriGR g
  gi|474935095|ref|YP_007688677.1| 353 VDLVCQIGSPKSVAKGLQRIGRSG 376
                                       **********************87 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0   4.7e-11     6e-08      21     169 ..      34     216 ..      10     218 .. 0.75

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 4.7e-11
                                       ...........TTSEEEEEESTTSTHHHHHHHHHHHH-S............-EEEEESSHHHHHHHHHHGGGGTGG. CS
                            ResIII  21 s.........krdkrglikmaTGtGKTlvaaklierllkkgkee.......kflflvprkslleqtleefkkflsea 81 
                                       +         +++k++li  +TG+GKTl+a+  i + l k++ +        ++ + p k+l +   ++++  l++ 
  gi|474935095|ref|YP_007688677.1|  34 EpqsmaipviHQRKNVLISSPTGSGKTLTAFTSILNQLIKYSTDgvleekiYCIYISPLKALANDVNRNLTVPLEQM 110
                                       1444555555899*****************76666666666766799999989999***********9997666665 PP

                                       ..............GEEEESSS-B--.........-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTT CS
                            ResIII  82 yke...........igkkvsgdkkka..kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlg 145
                                       ++               + sgd+ ++  ++  ++  +il+tt +s+  ++    + + +   ++++ +i DE H + 
  gi|474935095|ref|YP_007688677.1| 111 KELaaregmhvpeiRVAVRSGDTPQSerQKMVRHPPHILITTPESMALIL---ASPKFRENMKSIEWVILDEIHDIC 184
                                       443555566655543333555555555566678999**************...5555555566666*********** PP

                                       S.T.......TTHHHHHT---.SEEEEEESS- CS
                            ResIII 146 akk.......swreilekfke.avllglTATp 169
                                       ++k       +++ + +++ + ++++gl+AT+
  gi|474935095|ref|YP_007688677.1| 185 DSKrgaflslTMEMLRDYVAHdFTRIGLSATM 216
                                       *867777777888899998555*********7 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.1   1.6e-05     0.021     126     153 ..      43      71 ..      27      82 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.6e-05
                             T2SSE 126 vrerglilvsGgTgsGKttll.yallkei 153
                                       +++r+++l+s +TgsGKt ++  ++l+++
  gi|474935095|ref|YP_007688677.1|  43 IHQRKNVLISSPTGSGKTLTAfTSILNQL 71 
                                       6789**************99834455554 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.023        29       7      68 ..    1194    1257 ..    1190    1275 .. 0.82
   2 ?   -1.7   0.2       2.8   3.6e+03      28      73 ..    1477    1517 ..    1461    1522 .. 0.68
   3 ?    8.0   0.0    0.0028       3.5       2      64 ..    1550    1607 ..    1549    1638 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.023
                                        HHHHHHHHHS-.EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEE.TTEEEEE----X CS
                   Penicillinase_R    7 evmeilwekge.atvkevveeleeekelaysTVktllrrLvkKgllsreke.grafiYsplvse 68  
                                         +m++++++++ +t++e+v+e ++eke  ++ V+ l r +    ++ ++++ g + iY p v +
  gi|474935095|ref|YP_007688677.1| 1194 LIMDLIRNSDSgITMREIVAETHKEKEQVKEAVMRLDRSMKVMRAFGEREDwGTENIYVPFVPR 1257
                                        69*******999*************999999999988888666666555555888888887776 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.8
                                        -GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE----XXXXXX CS
                   Penicillinase_R   28 eeekelaysTVktllrrLvkKgllsrekegrafiYsplvseeeava 73  
                                        e++  + y+TV+ l   L ++g+l++++e    + sp++ ++++ +
  gi|474935095|ref|YP_007688677.1| 1477 EKT--TRYATVREL---LAQRGYLRSDQEMVCRVMSPTTVKKQLEK 1517
                                        333..455555544...56899999999888888888877777665 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0028
                                        --S-SHHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE- CS
                   Penicillinase_R    2 gelEaevmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsrekegrafiYsp 64  
                                        +e+E+e+ +i+ e+ +++ ke++ + +++    y T++  ++ L+k+ ++ ++ e + + + p
  gi|474935095|ref|YP_007688677.1| 1550 SEAEREIEKIVKERMPVSKKEIQFRSKHT----YDTTADAISSLMKRAVI-CQDEDNYYKWVP 1607
                                        89********************9998888....55555555555544443.334455555555 PP

>> Histone_HNS  H-NS histone family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.012        15      22      73 ..     104     174 ..      92     175 .. 0.82
   2 ?   -2.6   0.0       8.3   1.1e+04      36      56 ..    1205    1225 ..    1202    1245 .. 0.59
   3 ?    6.2   0.1     0.014        18      16      69 ..    1473    1552 ..    1461    1555 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.012
                                       XXXXXXXXXXXXXXX----SSS-----EEEEE.........................---TTT-SSS.-EEE CS
                       Histone_HNS  22 kealaeirelaaeyGltleelaaeakkakkkkakakk....................vpaKYrdpetegetW 73 
                                       +  l++++elaa++G+ + e+  +++++   +++++k                    + +K+r+  + +  W
  gi|474935095|ref|YP_007688677.1| 104 TVPLEQMKELAAREGMHVPEIRVAVRSGDTPQSERQKmvrhpphilittpesmalilASPKFRENMK-SIEW 174
                                       55689****************9999999999988888899999999999999999888889888765.6555 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 8.3
                                        X----SSS-----EEEEE... CS
                       Histone_HNS   36 Gltleelaaeakkakkkkaka 56  
                                        G+t+ e+ ae+ k+k++ ++a
  gi|474935095|ref|YP_007688677.1| 1205 GITMREIVAETHKEKEQVKEA 1225
                                        677777766666555555443 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.014
                                        XXXXXXXXXXXXXXXXXXXXX----SSS--..---EEEEE.............................---TTT CS
                       Histone_HNS   16 leaeerkealaeirelaaeyGltleelaae..akkakkkkakakk........................vpaKYr 64  
                                        +++ e++   a++rel+a+ G+  ++ +    + + +  k++ +k                        ++aKYr
  gi|474935095|ref|YP_007688677.1| 1473 KQRLEKTTRYATVRELLAQRGYLRSDQEMVcrVMSPTTVKKQLEKgnvlkgnllpeyvgyttmsnmsifRAAKYR 1547
                                        567789999************75555433333444444444444477788899999******************* PP

                                        -SSS. CS
                       Histone_HNS   65 dpete 69  
                                        +p+++
  gi|474935095|ref|YP_007688677.1| 1548 KPSEA 1552
                                        **975 PP

>> DUF3793  Protein of unknown function (DUF3793)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   9.4e-05      0.12      43      81 ..    1461    1499 ..    1428    1518 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.4e-05
                           DUF3793   43 ekekkalilvyreekLeeylsdeevrefLkklgY...esesl 81  
                                         ++++al +v+r+++Le++ + ++vre+L++ gY   +    
  gi|474935095|ref|YP_007688677.1| 1461 MTRDEALSMVFRKQRLEKTTRYATVRELLAQRGYlrsD---Q 1499
                                        4678999***************************6432...2 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0         4   5.1e+03      70      89 ..     110     129 ..     107     130 .. 0.76
   2 ?   11.0   0.0   0.00041      0.52      45      91 ..    1186    1229 ..    1170    1232 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 4
                                       HHHHHHHSTSXHHHHHHHHH CS
                             RPA_C  70 vdeiaqklrlsvndvkqavd 89 
                                       ++e+a++ ++ v +++ av+
  gi|474935095|ref|YP_007688677.1| 110 MKELAAREGMHVPEIRVAVR 129
                                       67888888888888888876 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00041
                                        .XSXHHHHHHHHHHHH.SXSTTTEEHHHHHHHSTSXHHHHHHHHHHH CS
                             RPA_C   45 kgltalaqqvlnlikqspeseeGvhvdeiaqklrlsvndvkqavdeL 91  
                                        ++ ++ ++ +++li++   s+ G+ ++ei ++++ ++++vk+av  L
  gi|474935095|ref|YP_007688677.1| 1186 DTTQPGDELIMDLIRN---SDSGITMREIVAETHKEKEQVKEAVMRL 1229
                                        556777899******9...************************9887 PP

>> Ribosom_S30AE_C  Sigma 54 modulation/S30EA ribosomal protein C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0013       1.6      31      52 ..     283     305 ..     276     308 .. 0.83
   2 ?   -0.5   0.0       0.8     1e+03      17      36 ..    1220    1239 ..    1209    1251 .. 0.72
   3 ?   -2.7   0.0       3.8   4.9e+03      12      23 ..    1456    1467 ..    1454    1469 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0013
                                       -S.EEEEEETTTTEEEEEEEETT CS
                   Ribosom_S30AE_C  31 hd.FfvFrnaetgevnVvYrrkd 52 
                                       hd  +vF+n  +g+  VvY+ k+
  gi|474935095|ref|YP_007688677.1| 283 HDtTLVFTNTRSGAEAVVYKLKE 305
                                       44489***************997 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.8
                                        B-HHHHHHHHHHHT-SEEEE CS
                   Ribosom_S30AE_C   17 msveeAilqmellghdFfvF 36  
                                         +v+eA+++++ + +   +F
  gi|474935095|ref|YP_007688677.1| 1220 EQVKEAVMRLDRSMKVMRAF 1239
                                        5799******9876666555 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 3.8
                                        S--S-B-HHHHH CS
                   Ribosom_S30AE_C   12 felkpmsveeAi 23  
                                        f  k+m+ +eA+
  gi|474935095|ref|YP_007688677.1| 1456 FVSKTMTRDEAL 1467
                                        6679*******8 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       5.4   6.9e+03      41      58 ..     768     786 ..     759     791 .. 0.74
   2 ?    9.5   0.0   0.00075      0.96      22      53 ..    1631    1662 ..    1617    1667 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 5.4
                                       HHHHHHHTTSEE.ETEEEE CS
                         HTH_Crp_2  41 ilseLkreglis.rgrrir 58 
                                       +l+++++e +i+ + r+i 
  gi|474935095|ref|YP_007688677.1| 768 MLRDMENEPVIEeTYREIL 786
                                       79999**999994433254 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00075
                                        HHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEE CS
                         HTH_Crp_2   22 ltqeelAsmlGltretvsrilseLkreglisr 53  
                                        ++ e ++s+lG++   + r+ls+L++eg + +
  gi|474935095|ref|YP_007688677.1| 1631 FSAENMSSFLGARMAETRRVLSDLEEEGFLVK 1662
                                        57899***********************8875 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00035      0.45       2     115 ..      37     184 ..      36     201 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00035
                            AAA_19   2 reave.alkekvllvtaGpGtGKTrv.lkhivallvelggvkp....eeillvaftgrAakelrerlaalgaeatTi 72 
                                         a+   +++k++l+  + G+GKT +  + i++ l++  +  +      ++ +++ +  a+ ++ +l   +++ + +
  gi|474935095|ref|YP_007688677.1|  37 SMAIPvIHQRKNVLISSPTGSGKTLTaFTSILNQLIKYSTDGVleekIYCIYISPLKALANDVNRNL---TVPLEQM 110
                                       567766899**************97624556677766655443442255666788888889999888...7777777 PP

                            AAA_19  73 Hrlal.................................ldfddlltealelleeaeeekklqeeellivDEfqdvd 115
                                        +la                                  l ++++   ++ +l + + ++++++ e++i DE+ d+ 
  gi|474935095|ref|YP_007688677.1| 111 KELAAregmhvpeirvavrsgdtpqserqkmvrhpphiLITTPES--MALILASPKFRENMKSIEWVILDEIHDIC 184
                                       777667777888888888888888888888888777753333333..33344566777888777899999999986 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.013        16      16      58 ..     970    1013 ..     959    1018 .. 0.87
   2 ?   -1.1   0.0       2.1   2.7e+03      22      47 ..    1418    1444 ..    1410    1445 .. 0.89
   3 ?   -0.0   0.1         1   1.3e+03      17      50 ..    1462    1497 ..    1456    1504 .. 0.80
   4 ?   -0.8   0.0       1.8   2.3e+03      15      48 ..    1562    1595 ..    1556    1601 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.013
                            HTH_27   16 rrrkkl.adlcgrlnvedshisyslkkLtekGLvertgdeadrr 58  
                                          +++l +d++ +++++   +  s++kL+ + L++rtg  ++ r
  gi|474935095|ref|YP_007688677.1|  970 ITENTLlSDVHSKVDMTEDIVFRSVRKLESMYLITRTGITENNR 1013
                                        5678888***************************9998776665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.1
                            HTH_27   22 adlcgrlnvedshis.yslkkLtekGL 47  
                                         ++++ ln+++++   +++  L  +G+
  gi|474935095|ref|YP_007688677.1| 1418 VRIREILNTDAASLNpEMVGSLKSAGY 1444
                                        57999******************9998 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 1
                            HTH_27   17 rrkkl.adlcgrlnvedshisyslkkLtek.GLver 50  
                                         r+++ +++ ++  +e+++    +++L ++ G++ +
  gi|474935095|ref|YP_007688677.1| 1462 TRDEAlSMVFRKQRLEKTTRYATVRELLAQrGYLRS 1497
                                        4555559999999**************9999**933 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 1.8
                            HTH_27   15 rrrrkkladlcgrlnvedshisyslkkLtekGLv 48  
                                        +r +++++++ +r ++++ +++ +++ L ++ ++
  gi|474935095|ref|YP_007688677.1| 1562 ERMPVSKKEIQFRSKHTYDTTADAISSLMKRAVI 1595
                                        6778999******************999887555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1787 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 1.04u 0.31s 00:00:01.35 Elapsed: 00:00:00.48
# Mc/sec: 11115.48
//
Query:       gi|474935096|ref|YP_007688678.1|  [L=424]
Description: hypothetical protein TALC_01552 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-08   33.8   8.3    0.00093   19.4   0.5    3.6  3  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
  ------ inclusion threshold ------
        5.4    6.9   5.2       0.35   10.7   0.2    1.6  2  LapA_dom         Lipopolysaccharide assembly protein A domain


Domain annotation for each model (and alignments):
>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9   0.1    0.0036        32      14      60 ..      55     102 ..      48     121 .. 0.83
   2 !   12.4   0.3   1.6e-05      0.14       5      61 ..     160     218 ..     158     238 .. 0.83
   3 !   19.4   0.5     1e-07   0.00093      11      64 ..     298     350 ..     287     367 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0036
                   CarboxypepD_reg  14 iagatVtvtnadtgtvastttdadGafrlrglpp..gtysvtvsapGya 60 
                                       i+ at+t+t+++++  +st t+++  ++++g++   ++  v++s pGy 
  gi|474935096|ref|YP_007688678.1|  55 ITSATITITDSADNIAKSTFTAPN-IYTVKGIKDisDDLIVEISCPGYT 102
                                       789******************998.778888777777777777777775 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 1.6e-05
                   CarboxypepD_reg   5 rVtda.sgapiagatVtvtnadtgtvastttdadGafrlrglpp.gtysvtvsapGyat 61 
                                       +V d+ +g p++  tV+   ++ + + s  tda+G  ++    + g++++tv  +Gy  
  gi|474935096|ref|YP_007688678.1| 160 YVMDSeTGLPVPSGTVVSIEDSHKNTLSSSTDAKGFVSVGIGSQkGSFTMTVDLNGYTA 218
                                       6999879****88888777677788999**********9744447************86 PP

  == domain 3  score: 19.4 bits;  conditional E-value: 1e-07
                   CarboxypepD_reg  11 gapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatr 64 
                                        ++i  a+Vtv na tg++ +  t+++G   ++ lp g+y  ++   G++ + +
  gi|474935096|ref|YP_007688678.1| 298 TTGIVDANVTVINAITGVEVTENTNSNGIVVFS-LPSGKYYFVIDVGGFEHYDS 350
                                       3689****************************7.**********9999987654 PP

>> LapA_dom  Lipopolysaccharide assembly protein A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.8   1.1         2   1.8e+04      22      29 ..      13      20 ..       9      24 .. 0.46
   2 ?   10.7   0.2     4e-05      0.35      27      50 ..     393     420 ..     391     422 .. 0.77

  Alignments for each domain:
  == domain 1  score: -4.8 bits;  conditional E-value: 2
                          LapA_dom 22 lllvafgi 29
                                      +l+v++++
  gi|474935096|ref|YP_007688678.1| 13 VLAVVIAA 20
                                      34444444 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 4e-05
                          LapA_dom  27 fgiGallgwllslwsyl....rlrrelr 50 
                                       ++iG+++g++l+l+sy+    r r+el+
  gi|474935096|ref|YP_007688678.1| 393 MLIGVVIGLILALLSYMlytrRFRSELS 420
                                       8999999999999999966666777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1037  (0.0578393); expected 358.6 (0.02)
Passed bias filter:                      672  (0.0374812); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.46
# Mc/sec: 2756.86
//
Query:       gi|474935097|ref|YP_007688679.1|  [L=214]
Description: hydro-lyase, Fe-S type, tartrate/fumarate subfamily, beta region [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      4e-43  147.1   0.0    4.9e-43  146.9   0.0    1.0  1  Fumerase_C  Fumarase C-terminus


Domain annotation for each model (and alignments):
>> Fumerase_C  Fumarase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.9   0.0   2.7e-47   4.9e-43      32     205 ..      28     204 ..      24     205 .. 0.94

  Alignments for each domain:
  == domain 1  score: 146.9 bits;  conditional E-value: 2.7e-47
                        Fumerase_C  32 LnqketeeelskykvgtrlllsGkllvaRDaaHkrlkerlekgeelpeyvklkdrviYyaGPv...ktpedeavgsa 105
                                       L+++ tee+++++k g+++ l+G ++++RD +H r    l++g+++p  ++  + v+Y++GP+   ++++++   +a
  gi|474935097|ref|YP_007688679.1|  28 LTAPLTEEDVRSLKLGEVIALTGPIVTGRDDVHIRALRYLDEGKDVPGCLR--NAVLYHCGPImkkNPNGSWSPVAA 102
                                       456789*****************************************6666..**********8755566778889* PP

                        Fumerase_C 106 GPTTatRmdkyvekllkktgllimlaKgnrskkvleaikkhggvYLgaiGGaAilakkaikkvevvefeelGm.EAi 181
                                       GPTT+ Rm++   ++++++g++++++Kg++ +++ +a+k+ g+vYL a GG A+ +++ +  ++ v++e+lGm EA+
  gi|474935097|ref|YP_007688679.1| 103 GPTTSARMNDLEPRFIREFGIRAIIGKGGMNRATADAMKEVGCVYLAATGGVAVSYAEGLGLCSGVDWEDLGMaEAL 179
                                       ***************************************************************************** PP

                        Fumerase_C 182 yeievedf.pafvvvddkGndlfke 205
                                       ++++ + + p +v++d++Gn+l+++
  gi|474935097|ref|YP_007688679.1| 180 WHFDASRMgPFVVAIDAEGNSLYDQ 204
                                       ********667789*********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       241  (0.0134419); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1644.04
//
Query:       gi|474935098|ref|YP_007688680.1|  [L=290]
Description: hydro-lyase, Fe-S type, tartrate/fumarate subfamily, alpha region [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-87  293.5   0.0    1.7e-87  293.3   0.0    1.0  1  Fumerase  Fumarate hydratase (Fumerase)


Domain annotation for each model (and alignments):
>> Fumerase  Fumarate hydratase (Fumerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  293.3   0.0   9.4e-92   1.7e-87       2     269 ..      11     275 ..      10     276 .. 0.97

  Alignments for each domain:
  == domain 1  score: 293.3 bits;  conditional E-value: 9.4e-92
                          Fumerase   2 eaveealkeastelpedvlealkkalekEesenakevleqlleNaeiAaeeklplCqDTGiavvfvkigeevevetg 78 
                                       + +e++l+ a++++ped+  al++a++ E++++a ++l+++leN++ A++ ++p+CqDTGi++++v+   +     +
  gi|474935098|ref|YP_007688680.1|  11 KVAENLLRLANFKIPEDIGWALESAAAWESNPTAASQLAAILENVRKAEHLSRPMCQDTGIPIFWVRGRFD-----S 82 
                                       567899***********************************************************986554.....4 PP

                          Fumerase  79 dleeaineGvreaykegplRksvvadplerkntgd....nlPavihielvpgdeleitvlakGgGsenksklkmlnp 151
                                       ++ + i+++v++ +++ p+R+++v d ++r+n+g+    ++P  ih+  +++d  eitvl+kG+Gsen++klkmlnp
  gi|474935098|ref|YP_007688680.1|  83 SIAKDIAKAVENCTRSIPMRPNTV-DVITRVNNGNnlgkGMP-EIHFIPTDDDFTEITVLLKGAGSENMTKLKMLNP 157
                                       68888*******************.99********9998999.999999999************************* PP

                          Fumerase 152 sdglegvkkfvletvkeagtnaCpPlvlgvgiGgtseeaallakkallrelgeenpdeelaeleeellekinklgiG 228
                                       sdg eg++kf++++v eag+++CpP+++gvgiGgts+ ++ +ak+all++l+ e+pd+e++++ee+l+ +in+ g+G
  gi|474935098|ref|YP_007688680.1| 158 SDGEEGIRKFIIDSVLEAGGRPCPPGIVGVGIGGTSDDCVAMAKRALLEPLDYEDPDPEIRKMEEDLFVEINQSGLG 234
                                       ***************************************************************************** PP

                          Fumerase 229 pqGlGGkttvldvkierlprhiAslpvavnvsCsadRrakv 269
                                       p+GlGG+ttvl+vki ++ +h+Aslpv+vn+ C+a+Rra++
  gi|474935098|ref|YP_007688680.1| 235 PMGLGGNTTVLGVKIRKADCHTASLPVCVNIGCWATRRASA 275
                                       **************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1782.79
//
Query:       gi|474935099|ref|YP_007688681.1|  [L=345]
Description: NMD protein affecting ribosome stability and mRNA decay [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.8e-45  153.7   1.3    7.3e-45  153.3   1.3    1.1  1  NMD3           NMD3 family
  ------ inclusion threshold ------
       0.36   10.6   2.3        2.3    8.1   0.1    2.8  3  zinc_ribbon_2  zinc-ribbon domain


Domain annotation for each model (and alignments):
>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.3   1.3   8.1e-49   7.3e-45       1     243 []       5     236 ..       5     236 .. 0.87

  Alignments for each domain:
  == domain 1  score: 153.3 bits;  conditional E-value: 8.1e-49
                              NMD3   1 CcrCGkeieelinglCedCllkevditegiekievevCkeCgrylpkgkWvkaeleseellaeclkklvekgLkvse 77 
                                       C++CGkei+++++g+C dC+l++ ++++ +++++ ++C  Cg+++++g+W++   +  + +++ +++    +L++ +
  gi|474935099|ref|YP_007688681.1|   5 CVECGKEIDRTVHGMCMDCFLRDRELVSLPDHVDQNQCTMCGQFHRHGEWLSM--SLDKAVSIAARE----ALSCIK 75 
                                       **************************************************554..444444444444....455444 PP

                              NMD3  78 eveevkvelvdaefiwtephskrikvkvtvqgevrgenetilqqevevevkvkrqqCprCsriaggyyeaivQvRqk 154
                                       e + +     d + + +  ++++++v+++++ +++g    + + + ++ v+vk+++C  Csr++g+yyeai+Q+R+ 
  gi|474935099|ref|YP_007688681.1|  76 EGRVT-----DIRAVIDPLDEYNYQVTLNCTVDIDG---YEAEGTASTIVRVKNTVCRICSRRTGNYYEAILQLRTA 144
                                       44444.....44444555557788888888888866...44579********************************* PP

                              NMD3 155 .relteeehkrtfelleqli...lkhdahafiskikevkeGlDfyfgsksaArklveflksevggkvkeseklvsed 227
                                        + +  e ++++   +e+l+   +  da+afi+k++ v+ G+D+y++    +r  v+ l +++ +++ es+klv++ 
  gi|474935099|ref|YP_007688681.1| 145 eKAMPPELQDEALARVERLVddaAATDANAFITKMEMVPGGVDVYLSLIALGRACVKDLGETYCAETDESSKLVGQT 221
                                       999999**************999888**************************************************9 PP

                              NMD3 228 kksgkevyrltysvrl 243
                                       ++ g ++yr++y+vrl
  gi|474935099|ref|YP_007688681.1| 222 RD-GLDMYRVSYLVRL 236
                                       98.***********97 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1   0.00025       2.3       1      10 [.       4      13 ..       4      17 .. 0.89
   2 ?    1.2   0.1     0.036   3.2e+02      13      20 ..      39      46 ..      38      47 .. 0.72
   3 ?   -3.8   0.0       1.4   1.3e+04      12      16 ..     204     208 ..     202     209 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00025
                     zinc_ribbon_2  1 fCpnCGaelq 10
                                      fC +CG+e++
  gi|474935099|ref|YP_007688681.1|  4 FCVECGKEID 13
                                      8*******97 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.036
                     zinc_ribbon_2 13 akFCpyCG 20
                                      ++ C+ CG
  gi|474935099|ref|YP_007688681.1| 39 QNQCTMCG 46
                                      56788888 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 1.4
                     zinc_ribbon_2  12 nakFC 16 
                                       ++++C
  gi|474935099|ref|YP_007688681.1| 204 GETYC 208
                                       67888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2417.00
//
Query:       gi|474935100|ref|YP_007688682.1|  [L=100]
Description: hypothetical protein TALC_01556 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.1e-29  100.1   0.1      7e-29   99.9   0.1    1.0  1  DUF424    Protein of unknown function (DUF424)


Domain annotation for each model (and alignments):
>> DUF424  Protein of unknown function (DUF424)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.9   0.1   3.9e-33     7e-29       2      92 .]      11     100 .]      10     100 .] 0.97

  Alignments for each domain:
  == domain 1  score: 99.9 bits;  conditional E-value: 3.9e-33
                                       EETTE.EEEEEEEGGGTT-EEEETTEEEE--HHHH--EEE-HHHHHHHHHHHEEEEEESHHHHHHHHHTTSS-GGG- CS
                            DUF424   2 rtddllklvavcdkellgktfkegelllnvsegfyggelaseeeaikeLekatiaNivgeeavvlavkaGlvdpdsV 78 
                                       +++++ +l a+cd+e+lg+tf++g+++++v+e+fygg l +e ++ + + ++ti+Nivg++av+la+++G++dp++V
  gi|474935100|ref|YP_007688682.1|  11 KHPKE-TLFAICDSEILGETFRDGDIRITVEESFYGGDLIEEVDLRSVIGSFTIINIVGNRAVDLAIEEGIIDPECV 86 
                                       66778.99********************************************************************* PP

                                       EEETTEEEEEEEE- CS
                            DUF424  79 lvidgvphaqigkl 92 
                                       +vi+gv+haq ++l
  gi|474935100|ref|YP_007688682.1|  87 IVIGGVKHAQAVTL 100
                                       **********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 675.08
//
Query:       gi|474935101|ref|YP_007688683.1|  [L=714]
Description: putative ATPase involved in replication control, Cdc46/Mcm family [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-93  311.2   0.1    5.7e-93  310.1   0.0    1.6  2  MCM              MCM P-loop domain
      4e-27   94.6   0.0    6.9e-27   93.8   0.0    1.3  1  MCM_OB           MCM OB domain
    5.5e-25   87.6   0.7    1.1e-24   86.6   0.7    1.6  1  MCM_lid          MCM AAA-lid domain
    1.6e-09   37.4   0.1    8.7e-07   28.5   0.0    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    1.9e-06   27.9   0.0    4.2e-06   26.8   0.0    1.6  1  AAA_5            AAA domain (dynein-related subfamily)
    7.7e-05   22.6   0.0    0.00031   20.6   0.0    2.1  1  AAA_3            ATPase family associated with various cellul
    0.00066   19.4   0.1      0.023   14.4   0.0    2.8  2  Sigma54_activat  Sigma-54 interaction domain
     0.0012   19.4   0.1      0.005   17.4   0.0    2.0  2  MCM_N            MCM N-terminal domain
  ------ inclusion threshold ------
      0.028   14.8   0.0      0.088   13.2   0.0    1.8  1  AAA_16           AAA ATPase domain


Domain annotation for each model (and alignments):
>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  310.1   0.0   2.9e-96   5.7e-93       2     224 .]     285     508 ..     284     508 .. 0.97
   2 ?   -3.1   0.0       1.7   3.4e+03      85     103 ..     572     590 ..     567     597 .. 0.83

  Alignments for each domain:
  == domain 1  score: 310.1 bits;  conditional E-value: 2.9e-96
                                       HHHHHHHHTSSTHHHHHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHH CS
                               MCM   2 veeikelakekdiieklvksiapsiyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyve 78 
                                       +++ike++k++ ++e++v+siap+i+g+++vk+ai+lqlfgg++k ++d++++rgd+++ll+gdpg+aKsq+L++++
  gi|474935101|ref|YP_007688683.1| 285 ENAIKEMSKDPLLFEHIVASIAPTIHGMTEVKEAIALQLFGGCHKFNDDGSETRGDMHILLIGDPGVAKSQILRFMS 361
                                       689************************************************************************** PP

                                       HHSSSEEEEESSSSSSSHSSSEEEEESSSSS.EEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEES CS
                               MCM  79 klapravytsgkgssaagLtaavvrdeetge.fvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaK 154
                                       +lapr++++sgk++s+agLtaa v+d++ g  + leaGalvladkG++ciDe+dkm+ edrs+lhEamE+q is+aK
  gi|474935101|ref|YP_007688683.1| 362 TLAPRGIFASGKSASSAGLTAAAVKDDTDGGrWNLEAGALVLADKGLACIDELDKMTAEDRSSLHEAMESQRISVAK 438
                                       ********************998888776655********************************************* PP

                                       SSCEEEEE--EEEEEEE--SSSSCCTTS-HHHHSSSSHHHHHHSSEEEEE-SSTTHHHHHHHHHHHHHHH CS
                               MCM 155 aGivatLnartsvlaAanpkagrydkkksvaeninlsaalLsrFDlifvllDkvdeekDeelaehivslh 224
                                       aGi+atL+ r+s+laAanpk+gr+d++++++ +i+l++al+srFDlifvl Dk+d++kD++la++i+ +h
  gi|474935101|ref|YP_007688683.1| 439 AGITATLQCRCSLLAAANPKFGRFDTDQKIVGQIDLPPALMSRFDLIFVLTDKPDKKKDADLARFILGVH 508
                                       ******************************************************************9876 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.7
                                       EEEESSSSSSSHSSSEEEE CS
                               MCM  85 vytsgkgssaagLtaavvr 103
                                       +yt++++ss+ g t+ ++ 
  gi|474935101|ref|YP_007688683.1| 572 TYTQIRASSEDGVTVPITA 590
                                       79***********987765 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.8   0.0   3.5e-30   6.9e-27       2     124 ..     117     247 ..     116     249 .. 0.90

  Alignments for each domain:
  == domain 1  score: 93.8 bits;  conditional E-value: 3.5e-30
                                       XGG--GGGTTSEEEEEEEEEEE---EEEEEEEEEEETTT-.-EEE.....S----SB-....TTT-HHH.-EEE-GG CS
                            MCM_OB   2 lRdlrsehigklvkveGivtrasevkpklkkavfeckkcgktvev.....eleePrkCe..ekeCeskd.pfklete 70 
                                       +R+lr++h+gklv+++G+v +a+  kp+l+ a f+c++cg+ v        l+eP +C+  + +C+++  +f l+ +
  gi|474935101|ref|YP_007688683.1| 117 VRNLRAKHLGKLVSITGLVRKATIPKPQLTYARFTCSRCGADVWEpqdgmYLREPLMCPnpNGNCNKTAnRFILDEK 193
                                       7***************************************85542456556777****9666689954459999999 PP

                                       GSEEEEEEEEEEE-------------EEEEEEEGGGTT---TT-EEEEEEEEEE CS
                            MCM_OB  71 kskfvdfqklklQEspeevpaGelPrslevileddlvdkvkPGdrvevtGiyra 124
                                       +s+++d+q +++QEspe +  G+ P+ + ++ledd+   +++G+r+ v Gi+r+
  gi|474935101|ref|YP_007688683.1| 194 SSRYTDTQIVEIQESPEGLRGGQQPERKVCFLEDDIAGLISAGNRIVVNGILRS 247
                                       ***************************************************997 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.6   0.7   5.8e-28   1.1e-24       1      85 [.     544     626 ..     544     628 .. 0.95

  Alignments for each domain:
  == domain 1  score: 86.6 bits;  conditional E-value: 5.8e-28
                                       HHHHHHHHHHHHTT--BETCHHHHHHHHHHHHHHHHHTSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHHH CS
                           MCM_lid   1 ellrkYiayarekikPklseeakeklseaYvelRkeeedskrksipitvRqLesliRLseAlAklrlsevvteedve 77 
                                       ++lrkY+aya++++ P + +++ + ++++Y ++R ++e  +  ++pit+RqLe+ +RL+eA+Ak+rls+v++eed +
  gi|474935101|ref|YP_007688683.1| 544 DILRKYVAYAKKNVVPFMPDTVVKDITDTYTQIRASSE--DGVTVPITARQLEAFVRLAEASAKMRLSQVIEEEDSS 618
                                       58*********************************986..3689********************************* PP

                                       HHHHHHHH CS
                           MCM_lid  78 eairllke 85 
                                       +airl+k 
  gi|474935101|ref|YP_007688683.1| 619 RAIRLVKY 626
                                       *****985 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0    0.0031       6.1      21      48 ..     339     366 ..     336     377 .. 0.90
   2 !   28.5   0.0   4.3e-10   8.7e-07      92     159 ..     391     458 ..     381     472 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0031
                      Mg_chelatase  21 GgHnlllvGppGsGKtmlakrlpsllpp 48 
                                       G  ++ll+G pG  K+ + + +++l p+
  gi|474935101|ref|YP_007688683.1| 339 GDMHILLIGDPGVAKSQILRFMSTLAPR 366
                                       8889***************999999885 PP

  == domain 2  score: 28.5 bits;  conditional E-value: 4.3e-10
                      Mg_chelatase  92 GggskpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpc 159
                                       Gg  + + G++ la +G+  +DEl +++++   +L e +e++++++++a  +++  +r+ l+aa+Np 
  gi|474935101|ref|YP_007688683.1| 391 GGRWNLEAGALVLADKGLACIDELDKMTAEDRSSLHEAMESQRISVAKAGITATLQCRCSLLAAANPK 458
                                       777799************************************************************94 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   2.1e-09   4.2e-06       1     124 [.     342     459 ..     342     482 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 2.1e-09
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEE...EE--TT--HHHHH--B--.........--------G-SEEEEESG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnrevey...vqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEv 74 
                                       ++lL+G+pG++Ks++ + ++ +  r ++     + ++++t++ +k  ++  +g+  l+ ++lv     + ++++DE+
  gi|474935101|ref|YP_007688683.1| 342 HILLIGDPGVAKSQILRFMSTLAPRGIFAsgkSASSAGLTAAAVKDDTD--GGRWNLEAGALV--LADKGLACIDEL 414
                                       79*********************888887332588899***********..8***********..88899******* PP

                                       GG--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS-- CS
                             AAA_5  75 eraesevlnsLlslleerrllleeggelvkaknddllerfrviatanpld 124
                                       +++  e  +sL+  +e +r+++++ g     +        +++a+anp  
  gi|474935101|ref|YP_007688683.1| 415 DKMTAEDRSSLHEAMESQRISVAKAGITATLQCR-----CSLLAAANPKF 459
                                       *********************9988877766553.....78888888765 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.5e-07   0.00031       1     113 [.     342     458 ..     342     484 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.5e-07
                             AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeeke.kefefkkGpvf.an..llladeinr 73 
                                       h+ll g PG+ak ++ + +++     +           + ++ + v ++++  ++++++G+++ a+  l   de+++
  gi|474935101|ref|YP_007688683.1| 342 HILLIGDPGVAKSQILRFMSTLAPRGIF--ASGKSASSAGLTAAAVKDDTDgGRWNLEAGALVlADkgLACIDELDK 416
                                       99************99999876544332..223344567788888887766689******965254336777***** PP

                             AAA_3  74 appktqsalleameerqvtve..gethklpepflvlatqnPi 113
                                        ++  +s+l eame ++++v+  g t +l+    +la+ nP 
  gi|474935101|ref|YP_007688683.1| 417 MTAEDRSSLHEAMESQRISVAkaGITATLQCRCSLLAAANPK 458
                                       ****************999862256899************94 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   1.2e-05     0.023      22     144 ..     340     458 ..     330     469 .. 0.75
   2 ?    0.5   0.0      0.22   4.4e+02     113     156 ..     504     548 ..     497     558 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.2e-05
                                       SS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BEHHHHHTTTSEEE CS
                   Sigma54_activat  22 dlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAekekkGlfekadgGtlf 98 
                                       d+++l+ G+ G+ K+ + r + +  +r  + + a   +a ++ l ++ +      +  G  + ++G++  ad+G   
  gi|474935101|ref|YP_007688683.1| 340 DMHILLIGDPGVAKSQILRFMSTLAPR--G-IFASGKSASSAGLTAAAVKD---DTDGGRWNLEAGALVLADKGLAC 410
                                       577777777777777777777666663..3.33444455566666665433...33336667788************ PP

                                       EETGGGS-HHHHHHHHHHHHHSEE..ESBTSSSEEE--EEEEEEESS- CS
                   Sigma54_activat  99 LDeigelplelQekLlrvlqegev..ervGsskeikvdvriiaatned 144
                                       +De+ ++++e  + L ++++++++   + G +++ ++ + ++aa+n +
  gi|474935101|ref|YP_007688683.1| 411 IDELDKMTAEDRSSLHEAMESQRIsvAKAGITATLQCRCSLLAAANPK 458
                                       *******************9997522799***************9876 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.22
                                       HHHHHHHSEEESBTSSSE.EE--EEEEEEESS-HHHHHHTTSS-H CS
                   Sigma54_activat 113 LlrvlqegevervGsske.ikvdvriiaatnedleeaveegkfre 156
                                       +l v q+ge++ vG+++e + vd+  +  ++++ +   e++ +r+
  gi|474935101|ref|YP_007688683.1| 504 ILGVHQRGEIRAVGEEAEiQGVDMEAVKDATQHYKPYYERDILRK 548
                                       688899********9977256999999888888887777777776 PP

>> MCM_N  MCM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   2.5e-06     0.005      16      75 ..      30      91 ..      13     113 .. 0.89
   2 ?   -2.8   0.0       4.9   9.7e+03      73      86 ..     531     544 ..     527     583 .. 0.54

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.5e-06
                             MCM_N 16 ededgekkYrdqlqemaer..ekttLevdlddLaafdeeLaeailenpkeylplleealkev 75
                                      ++ed+++ Y   + e+a++  + ++++v +dd+ a++ ++a+ +le+p +++ l  +++ke 
  gi|474935101|ref|YP_007688683.1| 30 TTEDSSRNYTLLISELADNypDVKSVTVYYDDIDAYSVDFAMCVLEEPDRCIRLGIDVIKES 91
                                      478889***********9988899****************************9999888875 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.9
                             MCM_N  73 kevvkklepsykdd 86 
                                       k+  + ++p y++d
  gi|474935101|ref|YP_007688683.1| 531 KDATQHYKPYYERD 544
                                       44444444433332 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.4e-05     0.088      24     123 ..     339     429 ..     330     441 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.4e-05
                            AAA_16  24 p.elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysa.laqalareellrqlldeaesaeleawr 98 
                                       +   +ll+G++Gv Ks ++r     l  + gif++gk  ++      +   a a + ++     + ea    +   +
  gi|474935101|ref|YP_007688683.1| 339 GdMHILLIGDPGVAKSQILRFMS-TLAPR-GIFASGKSASS------AGlTAAAVKDDTDGGRWNLEAG---ALVLA 404
                                       34789**************8777.67777.9******9999......4422333322222333333322...22222 PP

                            AAA_16  99 ekleealaavpelagaeasrllell 123
                                       +k ++ + + ++++++++s+l+e++
  gi|474935101|ref|YP_007688683.1| 405 DKGLACIDELDKMTAEDRSSLHEAM 429
                                       2233333344466666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (714 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.70u 0.29s 00:00:00.99 Elapsed: 00:00:00.48
# Mc/sec: 4507.27
//
Query:       gi|474935102|ref|YP_007688684.1|  [L=75]
Description: hypothetical protein TALC_01558 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.54
# Mc/sec: 421.01
//
Query:       gi|474935103|ref|YP_007688685.1|  [L=170]
Description: hypothetical protein TALC_01559 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.3e-42  142.3   0.0    7.7e-42  142.0   0.0    1.1  1  Ribo_biogen_C  Ribosome biogenesis protein, C-terminal
    1.1e-11   44.4   1.0    1.7e-11   43.7   1.0    1.3  1  RLI            Possible Fer4-like domain in RNase L inhibitor


Domain annotation for each model (and alignments):
>> Ribo_biogen_C  Ribosome biogenesis protein, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.0   0.0   8.6e-46   7.7e-42       1     127 []      41     164 ..      41     164 .. 0.97

  Alignments for each domain:
  == domain 1  score: 142.0 bits;  conditional E-value: 8.6e-46
                                       EEE-TT-SSB--GGGHHHHHHT-EEEE---TTT--GGGTTT-E....EB--S-B--STTTTT-BS---HHHHHHHHH CS
                     Ribo_biogen_C   1 ivlspkakkvlspaDreiveksgiavvdcsWarleevkfkklkakeerlLPyLvAaNpvnYgkplkLscvEAlaaal 77 
                                       ivls +++k+lspaD++  + +g++v+d +W+++++ +  ++++ + r+LPyLvAaNpvn+gkp++L+++EA+ aal
  gi|474935103|ref|YP_007688685.1|  41 IVLSTEGEKTLSPADAKK-AGRGLVVLDLTWTNIDRLP--HVRGGYARKLPYLVAANPVNFGKPWNLNSAEAVLAAL 114
                                       8**************776.788****************..66679******************************** PP

                                       HHTT-HHHHHHHHTSSTTHHHHHHHCHHHHHHH.TT--HHHHHHHHHHHH CS
                     Ribo_biogen_C  78 yilglkeeaeellskfkwgeeFlelnkelleeYakckdseevvevqkeyl 127
                                       +i+g++e+ae ++ +f+w+ +F+++n+ lle+Y+k++dse+++++q+ey+
  gi|474935103|ref|YP_007688685.1| 115 VIMGYDEQAELFMPRFNWAPTFMKMNEALLEQYRKARDSEDIERIQNEYI 164
                                       ************************************************96 PP

>> RLI  Possible Fer4-like domain in RNase L inhibitor, RLI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   1.0   1.9e-15   1.7e-11       2      33 ..       3      34 ..       2      37 .. 0.89

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 1.9e-15
                                      -EEEES---------TTHHHHHTTSEEEESS- CS
                               RLI  2 rlAivdadqCdPKKCtgkkcarfcpvrlvrtg 33
                                      ++ +vd dqCdPKKCt+k++++f++ r+v ++
  gi|474935103|ref|YP_007688685.1|  3 PVLVVDLDQCDPKKCTAKRMEKFGLCREVPLN 34
                                      689************************97654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1109.30
//
Query:       gi|474935104|ref|YP_007688686.1|  [L=162]
Description: hypothetical protein TALC_01560 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0048   17.2   0.0     0.0083   16.4   0.0    1.4  1  DUF1108   Protein of unknown function (DUF1108)


Domain annotation for each model (and alignments):
>> DUF1108  Protein of unknown function (DUF1108)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   4.6e-07    0.0083      45      83 ..     122     160 ..     116     161 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.6e-07
                           DUF1108  45 sinvideselyialdilrdviyewieentderdklinlv 83 
                                        ++ +d +el   l ++ d + +w++en d+ +kl  lv
  gi|474935104|ref|YP_007688686.1| 122 EFDCTDDAELAQCLLAMADRVRKWVQENMDDPEKLKALV 160
                                       6899*******************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 1023.11
//
Query:       gi|474935105|ref|YP_007688687.1|  [L=146]
Description: Oligosaccharide biosynthesis protein Alg14 like protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-13   48.9   0.0    6.7e-11   42.4   0.0    2.0  2  Alg14     Oligosaccharide biosynthesis protein Alg14 like


Domain annotation for each model (and alignments):
>> Alg14  Oligosaccharide biosynthesis protein Alg14 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9   0.0    0.0013        23       7      34 ..       8      36 ..       3      47 .. 0.75
   2 !   42.4   0.0   3.7e-15   6.7e-11      73     171 ..      52     141 ..      46     146 .] 0.84

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0013
                             Alg14  7 S.GGHTaEmlrllkklekeknikrtyvvs 34
                                      S GGH +Eml + ++  k ++  +ty   
  gi|474935105|ref|YP_007688687.1|  8 SwGGHLQEMLDIKDAWGKYDYEFITYRSI 36
                                      44*********999987777777777654 PP

  == domain 2  score: 42.4 bits;  conditional E-value: 3.7e-15
                             Alg14  73 lssifttllsllsaillvlrekrlpdvilvNGPgtcvpvvlaalllkllallkrskivyvEslarvktlSLsGklll 149
                                        +s+ ++l+sl++a+++v+  +  pd+++  G g     +++  l++ll++     +vy+Es a vk++  +++l+ 
  gi|474935105|ref|YP_007688687.1|  52 WKSVPKFLWSLAKAAVHVTFDR--PDILISTGMGYVD--IFLFPLCRLLGVY----TVYIESGANVKSITGTANLVR 120
                                       67999*************9999..******9988633..3445567777775....9******************** PP

                             Alg14 150 plaDrfvVqwpeLekkykkaey 171
                                        +aDrf+V+w+eL++ +  aey
  gi|474935105|ref|YP_007688687.1| 121 IFADRFIVKWEELAEDIC-AEY 141
                                       **************9854.344 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 980.20
//
Query:       gi|474935106|ref|YP_007688688.1|  [L=180]
Description: hypothetical protein TALC_01562 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-08   33.8   0.0    3.8e-08   33.5   0.0    1.1  1  Glyco_tran_28_C  Glycosyltransferase family 28 C-terminal dom


Domain annotation for each model (and alignments):
>> Glyco_tran_28_C  Glycosyltransferase family 28 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.0   2.1e-12   3.8e-08      47     143 ..      37     134 ..      19     155 .. 0.64

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 2.1e-12
                                       STT.-TTTTCEEEEEESS..SSHHHHHHHH-EEEECS-CHHHHHHHHTT--EEEE--TT....S-HHH.....HHHH CS
                   Glyco_tran_28_C  47 kik.veeltlkvevfefi..dkmaeaikaadLvIsRAGagtiaEllalgkplIlvplpeaaenhqdnN.....akel 115
                                       +i+ v+++    e+f+f   ++++++  +adL+++++G g+i++ l+ + p++lvp      n  +       a+++
  gi|474935106|ref|YP_007688688.1|  37 NIDyVSDY---AETFAFLpdEEIQKVFDRADLIVCHSGIGSILNGLNRNIPMVLVPRNVVDPNVTTDDqqaivARKV 110
                                       34434444...566667511579*********************************977655555555000005555 PP

                                       HHHHHHHSSEEEE-STTCHHHHHHHHCC CS
                   Glyco_tran_28_C 116 ekagaalvleqkeltpekLeeallelaa 143
                                       e+ g a v e+  l    L ++++e ++
  gi|474935106|ref|YP_007688688.1| 111 ESLGRAVVCEDLSL----LPQKVEEARN 134
                                       55555555555555....5555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1266.81
//
Query:       gi|474935107|ref|YP_007688689.1|  [L=492]
Description: Membrane protein involved in the export of O-antigen and teichoic acid [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.9e-08   31.8  27.2    8.9e-08   31.8  27.2    2.7  3  Polysacc_synt  Polysaccharide biosynthesis protein


Domain annotation for each model (and alignments):
>> Polysacc_synt  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8  27.2     5e-12   8.9e-08      13     269 ..       1     268 [.       1     273 [. 0.83
   2 !    1.7  10.4    0.0079   1.4e+02      74     182 ..     287     400 ..     273     413 .. 0.74
   3 ?   -0.9  11.8     0.048   8.7e+02      77     188 ..     321     436 ..     318     486 .. 0.79

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 5e-12
                     Polysacc_synt  13 litkllafvtlvylarilgpegfGlvalalaivtllviltdlGlnaalvreiakyrekkelvslillnvllvllvlv 89 
                                       ++++l++ + ++y+  +lg + +G+  la++++ + +i++d+ l+ a +r+   + ++ e+ ++ ++  +++++ l+
  gi|474935107|ref|YP_007688689.1|   1 MVVALIGVLLVPYYLDTLGLAAYGIIPLATTMTAYVMIISDS-LGSACSRYATLAIDRGEDANKAISTGFFGIVKLS 76 
                                       57899******************************9999995.9999999999998887777777777777777666 PP

                     Polysacc_synt  90 llfllllliaa..........flglpelavlylilalmllllvgvasfrrglfqglermkyaavsqvveqlsrvilv 156
                                       l+ l ++l              ++ +e+    l+++++ l +v+v+s     f++ +    + + ++v+ ++ v+ +
  gi|474935107|ref|YP_007688689.1|  77 LILLPFMLAISflapyvfsmpENMWTEVQEMFLLIMVSSL-IVTVSSALMCVFNAYNTLYELYIARIVYTVVQVAII 152
                                       6666666655566667555676666666666666666666.9***************************99988666 PP

                     Polysacc_synt 157 liavflfld.ivaavlgavlaalvggivslavlrkkf...rprfvilslklvrellsfsapltisslaillytyids 229
                                       +++++   + +v ++++++l+++v +++ +a+ +++    r r +  +++l++++ + + ++++  +++ ly + + 
  gi|474935107|ref|YP_007688689.1| 153 VVMFTVYEPsLVDIGIAYLLSSVVLLVMTYALAKHRHsemRIRLSDYDKALFKKMGTLGEWTVFIKIGNMLYIQASL 229
                                       6666655557***************99999999988864335555555***************************** PP

                     Polysacc_synt 230 illglllgaeavGiYnaayqllvaisgllapivtaalfPv 269
                                       ++   + g++a G++  + +l ++i     + +t ++ P+
  gi|474935107|ref|YP_007688689.1| 230 VIVNIYVGSNAGGEFAIISSLISMIHTACYSVTT-SIAPY 268
                                       *************************987777666.88887 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.0079
                     Polysacc_synt  74 vslillnvllvllvlvllfllllliaa.....flglpelavlylilalmllllvgvasfrrglfqglermkyaavsq 145
                                       ++l ++++l+++ v+++ +++   + a       +l el+++ li  ++++  v  a +++ +++ +   ky++   
  gi|474935107|ref|YP_007688689.1| 287 ITLKFISLLFAMPVAFVMIFAPEIMTAwvggtYDYLGELVFIALICDVAFCASVVLAEVPTVYLKVKSQVKYTLFFG 363
                                       4555666666666666655555544447777544577999999999999999999999*****************99 PP

                     Polysacc_synt 146 vveqlsrvilvliavflfldivaavlgavlaalvggi 182
                                       +++ ++ v+  l+  ++++ ++++ ++ +la++++ +
  gi|474935107|ref|YP_007688689.1| 364 IANIVAGVAVALFTDYGVKGVTTVWMISTLAYVIACV 400
                                       9999999955555555555577777777777777654 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.048
                     Polysacc_synt  77 illnvllvllvlvllfllllliaaflglpelavlylilalmllllvgvasfrrglfqglermkyaavsqvveqlsrv 153
                                       +l +++++ l++ + f ++ ++a++     ++   + ++l++ ++++va + + lf++      ++v+++++   ++
  gi|474935107|ref|YP_007688689.1| 321 YLGELVFIALICDVAFCASVVLAEVPTVYLKVKSQVKYTLFFGIANIVAGVAVALFTDYGVKGVTTVWMISTLAYVI 397
                                       67788899999999999999998877777777777778888889999999999999999999999999999999999 PP

                     Polysacc_synt 154 ilvliavflfld....ivaavlgavlaalvggivslavl 188
                                       + vl++ +  +     ++  ++   +a+ + +iv++ v+
  gi|474935107|ref|YP_007688689.1| 398 ACVLFCERVTGVrpltYLKRIGFGYVAMAACLIVLYFVS 436
                                       999999888887777766666666666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (492 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1174  (0.0654805); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.70u 0.29s 00:00:00.99 Elapsed: 00:00:00.46
# Mc/sec: 3195.68
//
Query:       gi|474935108|ref|YP_007688690.1|  [L=271]
Description: LPS biosynthesis protein [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-31  110.3   0.5      3e-31  109.3   0.5    1.4  1  LicD      LicD family


Domain annotation for each model (and alignments):
>> LicD  LicD family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.3   0.5   1.7e-35     3e-31       4     227 .]      23     230 ..      21     230 .. 0.85

  Alignments for each domain:
  == domain 1  score: 109.3 bits;  conditional E-value: 1.7e-35
                              LicD   4 ngleywLsgGTllGavRhggfIPWDDDiDlqmprkdyerLaevfnqlilk.kedlreaekdknylenfaklldknts 79 
                                        g  y + +GT+lGa Rh gfIPWDDD+D+    +d++ + +++ + +++ k++l+e+ + + + ++f+k+  +n++
  gi|474935108|ref|YP_007688690.1|  23 GGVFYTMYSGTALGAARHHGFIPWDDDMDIVVKAEDLDAFKDALAKYLPEgKYYLQEPLSID-WANSFYKIKLNNST 98 
                                       567799************************************666648888****9976655.5667********** PP

                              LicD  80 iterkngngkndsglyiDIfpldyvpkskllikkkkekeklkkklalkkslskkdkkelkkkillkkksfklkklnk 156
                                         er++  +++++gl+iD+fp  ++p+ k      + k  +     +   l++++  + +   ++ k+ +   ++  
  gi|474935108|ref|YP_007688690.1|  99 GVERSHLHTRMHQGLFIDVFPAREYPNGKF-----RRKMYE-----F--LLFCQKGVRVLSFRNYGKPRRDIIQKPI 163
                                       **************************9874.....211211.....1..2578888888888888888888888888 PP

                              LicD 157 kkklkkleklekkkeydlkkseyiavlksgklrnkeilpleelsplkkvkFegvevpipnnydkyLtelYg 227
                                       +  ++ l +++      +k++ y+ v   g+     il ++++++  +  Feg++++ +++yd++Lt++Yg
  gi|474935108|ref|YP_007688690.1| 164 TAVHRLLLRMMAG--LCEKDCRYYRVDYVGE--PYPILDKKIFEDALDWDFEGHQFKLIRDYDYVLTQMYG 230
                                       8888888888888..7777888888777666..588**********************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1716.70
//
Query:       gi|474935109|ref|YP_007688691.1|  [L=430]
Description: 3-hexulose-6-phosphate synthase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-39  135.3   2.6    1.8e-39  135.3   2.6    2.2  2  RraA-like       Aldolase/RraA
    3.9e-23   82.2   5.5    7.9e-23   81.2   5.5    1.5  1  OMPdecase       Orotidine 5'-phosphate decarboxylase / HUMPS 
    4.6e-07   29.5   3.0      6e-06   25.9   0.9    2.5  2  His_biosynth    Histidine biosynthesis protein
     0.0017   17.9   2.6      0.059   12.8   0.2    2.7  3  PEP_mutase      Phosphoenolpyruvate phosphomutase
     0.0022   17.6   1.6      0.048   13.2   0.2    2.3  2  HMGL-like       HMGL-like
     0.0049   16.2   1.9     0.0066   15.8   0.6    1.9  2  TMP-TENI        Thiamine monophosphate synthase
  ------ inclusion threshold ------
      0.072   12.2   3.0      0.086   12.0   0.1    2.5  3  DUF561          Protein of unknown function (DUF561)
      0.076   12.4   1.8       0.22   10.9   1.8    1.8  1  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
       0.14   11.5   9.1        0.3   10.4   3.0    2.6  2  ThiG            Thiazole biosynthesis protein ThiG


Domain annotation for each model (and alignments):
>> RraA-like  Aldolase/RraA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.55   1.1e+03      98     134 ..     126     172 ..     120     192 .. 0.56
   2 !  135.3   2.6   8.9e-43   1.8e-39       2     150 .]     238     384 ..     237     384 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.55
                                       HTTSSSEEEEEEE..........-SSB-B-S.STS........EESS-EEE.TTEE CS
                         RraA-like  98 lreldfpvfargv..........tprkkpkkkgkg........evnvpvei.ggvt 134
                                       +++l++++ ++++           p                  ev++pv++ gg+t
  gi|474935109|ref|YP_007688691.1| 126 VAKLGVGIICLHMgidtqmrgeeAP---------VdvlrkvvaEVDIPVAVaGGIT 172
                                       5666666666666444322222333.........1333344449999999944444 PP

  == domain 2  score: 135.3 bits;  conditional E-value: 8.9e-43
                                       HHHHHHCEE-SSBSTB.TT..EES..EEEEEEEEEESS.BGHHHHHHHTS--TTEEEEEESTT.SSSSSECE-HHHH CS
                         RraA-like   2 advsDalkklggrsggirp.lers..fvGpavTvkvveadnslvkealeeagpgdvlVvdgggdeslraallGglla 75 
                                       +++sDa++k g+  g ++p l+++  ++G+a+Tv++ ++d+++  ea+++a+pgdv+Vvd gg     a++ G+l +
  gi|474935109|ref|YP_007688691.1| 238 CNISDAYHKKGVVFG-LHPyLKHGakLIGRALTVQTCNGDWAKPVEAIDRAKPGDVIVVDVGG--APVAVW-GELAS 310
                                       9*******7777777.999788845799***********************************..448999.***** PP

                                       HHHHHTTBSEEEEEEEES-HHHHTTSSSEEEEEEE-SSB-B-S.STSEESS-EEETTEEE-TTSEEEEETTEEEE CS
                         RraA-like  76 taakangvaGvvvdGavRDvaelreldfpvfargvtprkkpkkkgkgevnvpveiggvtvkpgdlivaDedGvvv 150
                                       ++a++ gv+G+v+dGavRD++++ +ldfpvfar ++p + + k g g +++++++gg++v++gd+iv+De+G++v
  gi|474935109|ref|YP_007688691.1| 311 NSAMNMGVRGIVIDGAVRDIDDIIDLDFPVFARSAVPCAGEAK-GWGGIGIEITVGGQRVRTGDWIVGDESGLMV 384
                                       **************************************97777.****************************976 PP

>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.2   5.5     4e-26   7.9e-23       2     224 ..       4     205 ..       3     206 .. 0.91

  Alignments for each domain:
  == domain 1  score: 81.2 bits;  conditional E-value: 4e-26
                                       EEEEEE-SSSHHHHHHHHHHHGG.GSSEEEEEHHHHHHHTHH.HHTHHHHHHHHHT..SEEEEEEEE-S-HHHHHHH CS
                         OMPdecase   2 nLclalDvatarelleladkvgp.sivvlKthydlvegwgfegtgaklaalarkhg..flifeDrKfaDIGntvekq 75 
                                        L++alD+++ ++ + +ad++ +  +++++++++l++++g     a++++ ++k++  ++i++D K++D G+ + ++
  gi|474935109|ref|YP_007688691.1|   4 VLQVALDMMQLKRSIGIADEAVAgGADWVEVGTPLIKSEG-----AEAVRTMKKRFpgHKIIADTKTMDTGAFEVEI 75 
                                       59*******************999****************.....**********888******************* PP

                                       HHSTCHHHHTTESEEEEEGTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHH..H..SHHHHHHHHHHHHHH CS
                         OMPdecase  76 atagsarikewadivtvhavaGkasvkalaeaaekwgnrgllilaqmsskgnlmlqe..k..gytqacveaarehka 148
                                       +      +k++adivtv ++a+++++++++e  +k+g    +++++++ +++ ++    +  g+   c++   + + 
  gi|474935109|ref|YP_007688691.1|  76 M------AKAGADIVTVLGLAEDSTISEAVESGRKYG--AEVMVDMINVPDKVKRSIevAklGVGIICLHMGIDTQM 144
                                       *......69***************************9..9************8888754247777777777777773 PP

                                       HTTESEEECCCHTHHHHHHTTCSCEEEHHHTTEEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHHHHHH CS
                         OMPdecase 149 edfvmGfvaqetlnateedaddfihltpgigleqggdgkgqqyntpekligiagadiiivGRgIlkagdpveeaer 224
                                       +        +e+ +      d + +++  +++   ++++g+  +t+ + ++ aga  iivG gI+k +d +++ae 
  gi|474935109|ref|YP_007688691.1| 145 R--------GEEAP-----VDVLRKVVAEVDI-PVAVAGGITADTVGEYVK-AGAYDIIVGGGITKTDDIKAAAEN 205
                                       3........55544.....589*********9.****************99.89********************97 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.029        58      87     136 ..      20      73 ..      16     113 .. 0.73
   2 !   25.9   0.9     3e-09     6e-06      51     144 ..     140     226 ..     120     246 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.029
                                       HHHHHHHCT-SEEEESHHHHH-..THHHHHHHHHHCGGGEEEEEEEEE.C.EEE CS
                      His_biosynth  87 dveelleagadkviigtaavkn..pelikelaekfgsqkivvaiDarr.g.ykv 136
                                        ++e++  gad v +gt  +k+   e ++ + ++f++ ki++   + + g ++v
  gi|474935109|ref|YP_007688691.1|  20 IADEAVAGGADWVEVGTPLIKSegAEAVRTMKKRFPGHKIIADTKTMDtGaFEV 73 
                                       56788899**********998844688**********99998766555434333 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 3e-09
                                       HHHHCTTHHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEE CS
                      His_biosynth  51 ldaakegreanldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpelikelaekfgsqkivva 127
                                       +d  ++g+ea  d++++++ ev+ipv v GGI   ++v e+++aga  +i+g    k  + ik +ae++ +    + 
  gi|474935109|ref|YP_007688691.1| 140 IDTQMRGEEAPVDVLRKVVAEVDIPVAVAGGITA-DTVGEYVKAGAYDIIVGGGITK-TDDIKAAAENIKKAMKGLE 214
                                       78899***************************76.55***************87655.5568999998888776777 PP

                                       EEEEECEEEEETTTTEE CS
                      His_biosynth 128 iDarrgykvaikgwree 144
                                       iD     kv+ k+ +e+
  gi|474935109|ref|YP_007688691.1| 215 ID-----KVVAKKYTED 226
                                       77.....5666666666 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.2     3e-05     0.059     165     220 ..      76     137 ..      59     147 .. 0.78
   2 ?    4.2   0.2     0.013        25     185     225 ..     155     195 ..     139     213 .. 0.57
   3 ?    3.7   0.1     0.018        36     164     192 ..     178     207 ..     174     239 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3e-05
                        PEP_mutase 165 YaeAGAdgvfvpglqkdaeiaelvaavd...vplnvvp.l.kgt.lsvaelaelGvarislg 220
                                        a+AGAd v+v gl +d++i e v+  +   + ++v + + +++     e+a+lGv++i l+
  gi|474935109|ref|YP_007688691.1|  76 MAKAGADIVTVLGLAEDSTISEAVESGRkygAEVMVDMiNvPDKvKRSIEVAKLGVGIICLH 137
                                       689*******************9998844764444444334444256679*******99876 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.013
                        PEP_mutase 185 aelvaavdvplnvvplkgtlsvaelaelGvarislgnhllr 225
                                       +++va+vd+p+ v  + ++ +v e  ++G+  i++g  + +
  gi|474935109|ref|YP_007688691.1| 155 RKVVAEVDIPVAVAGGITADTVGEYVKAGAYDIIVGGGITK 195
                                       56666666666666644446666666666666666655433 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.018
                        PEP_mutase 164 aYaeAGAdgvfvpgl.qkdaeiaelvaavd 192
                                        Y++AGA  ++v g+ +k+++i++ +++++
  gi|474935109|ref|YP_007688691.1| 178 EYVKAGAYDIIVGGGiTKTDDIKAAAENIK 207
                                       59*****99888877477788**9999995 PP

>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.2   2.4e-05     0.048      14     125 ..       6     116 ..       5     137 .. 0.85
   2 ?    3.3   0.1     0.026        52      40      89 ..     161     210 ..     146     233 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.4e-05
                                       HTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHHHHHHH....TT- CS
                         HMGL-like  14 qalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkarilalvrarekdikaavealkgaga 90 
                                       q + + +++++ + ia++ ++ g d +Evg p    +  e+vr+ +k  +  +i+a  +   +  +  ve + +aga
  gi|474935109|ref|YP_007688691.1|   6 QVALDMMQLKRSIGIADEAVAGGADWVEVGTPLIKSEGAEAVRTMKKRFPGHKIIADTKTM-DTGAFEVEIMAKAGA 81 
                                       66778899****************************************9999977665544.444455777899*** PP

                                       SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHH CS
                         HMGL-like  91 krvhvfiatselhlkaklkkdreevakkaeeavka 125
                                       ++v v   + +  ++  ++  r++ a+ ++++++ 
  gi|474935109|ref|YP_007688691.1|  82 DIVTVLGLAEDSTISEAVESGRKYGAEVMVDMINV 116
                                       *******9999999999999999999999999875 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.026
                                       E--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHHHHHHH....TT CS
                         HMGL-like  40 iEvgfpaaseddfevvraiakavkkarilalvrarekdikaavealkgag 89 
                                       + + +++a+    + v + +ka+    i++  + + +dikaa+e +k+a 
  gi|474935109|ref|YP_007688691.1| 161 VDIPVAVAGGITADTVGEYVKAGAYDIIVGGGITKTDDIKAAAENIKKAM 210
                                       44455566666667777777777666699999999*********999985 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.3   2.6e+03      87      87 ..      48      48 ..      18     103 .. 0.55
   2 !   15.8   0.6   3.3e-06    0.0066     135     177 ..     147     189 ..     124     193 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.3
                          TMP-TENI 87 a 87
                                      +
  gi|474935109|ref|YP_007688691.1| 48 R 48
                                      3 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 3.3e-06
                          TMP-TENI 135 eplgleglkelaealeiPvvaiGGitlenvaevleagadgvav 177
                                       e + ++ l+++++++ iPv + GGit+++v e ++aga  + v
  gi|474935109|ref|YP_007688691.1| 147 EEAPVDVLRKVVAEVDIPVAVAGGITADTVGEYVKAGAYDIIV 189
                                       6677899*******************************88877 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       0.6   1.2e+03      76      88 ..      23      35 ..      18      38 .. 0.90
   2 ?   12.0   0.1   4.3e-05     0.086     180     235 ..     156     211 ..     134     219 .. 0.88
   3 ?   -1.9   0.0      0.73   1.5e+03     199     226 ..     309     336 ..     306     338 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.6
                            DUF561 76 eavkaGadlveiG 88
                                      eav+ Gad ve+G
  gi|474935109|ref|YP_007688691.1| 23 EAVAGGADWVEVG 35
                                      799*********9 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 4.3e-05
                            DUF561 180 eiskkvslPvicasGlsdvtvplalslgasGiGigsavsklndeeemvallseikk 235
                                       +++ +v++Pv  a G++  tv   +++ga  i +g  ++k +d+++  + +++  k
  gi|474935109|ref|YP_007688691.1| 156 KVVAEVDIPVAVAGGITADTVGEYVKAGAYDIIVGGGITKTDDIKAAAENIKKAMK 211
                                       68999**************************************9999988887665 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.73
                            DUF561 199 tvplalslgasGiGigsavsklndeeem 226
                                       +++ a+++g  Gi i  av+ ++d++++
  gi|474935109|ref|YP_007688691.1| 309 ASNSAMNMGVRGIVIDGAVRDIDDIIDL 336
                                       5677999**************9999875 PP

>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.8   0.00011      0.22     153     196 ..     151     192 ..      70     194 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHHHT---EEEEESS--TTTCHHHHHHT--EEEESHH CS
                    Ribul_P_3_epim 153 ikkvrklidekeldlkievDGGvkldnieqiaeagadvlVagsa 196
                                       +  +rk+++e  +d+ + v GG+++d++ + ++aga  +++g +
  gi|474935109|ref|YP_007688691.1| 151 VDVLRKVVAE--VDIPVAVAGGITADTVGEYVKAGAYDIIVGGG 192
                                       5567888887..99**********************87777755 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   3.0   0.00015       0.3     165     225 ..     152     211 ..      89     227 .. 0.80
   2 ?    4.0   0.2     0.013        26     191     215 ..     311     335 ..     290     349 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00015
                                       HHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHHH CS
                              ThiG 165 ealkiiieeakvPvivDAGigspsdaaqamelGadavllntavaeakdpvamArafklave 225
                                        +l+ +++e+++Pv v  Gi ++  + + ++ Ga  +++   +++++d+ a A+ +k+a++
  gi|474935109|ref|YP_007688691.1| 152 DVLRKVVAEVDIPVAVAGGI-TADTVGEYVKAGAYDIIVGGGITKTDDIKAAAENIKKAMK 211
                                       468999**********9998.688999*******************************987 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.013
                                       HHHHHTT-SEEEESHHHHTSSSHHH CS
                              ThiG 191 aqamelGadavllntavaeakdpva 215
                                         am++G+ +++++ av   +d++ 
  gi|474935109|ref|YP_007688691.1| 311 NSAMNMGVRGIVIDGAVRDIDDIID 335
                                       579***************9999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 3092.14
//
Query:       gi|474935110|ref|YP_007688692.1|  [L=309]
Description: Zn-dependent protease with chaperone function [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-38  131.1   0.0    5.8e-38  130.6   0.0    1.2  1  Peptidase_M48    Peptidase family M48
    7.6e-06   25.3   0.0    1.6e-05   24.3   0.0    1.5  1  Peptidase_M56    BlaR1 peptidase M56
  ------ inclusion threshold ------
       0.21   11.5   5.1       0.33   10.9   0.9    2.3  2  Claudin_3        Tight junction protein, Claudin-like
        2.8    8.1   7.4        1.1    9.4   3.7    2.1  2  DUF4229          Protein of unknown function (DUF4229)


Domain annotation for each model (and alignments):
>> Peptidase_M48  Peptidase family M48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.6   0.0   1.3e-41   5.8e-38       3     195 ..      62     281 ..      60     282 .. 0.88

  Alignments for each domain:
  == domain 1  score: 130.6 bits;  conditional E-value: 1.3e-41
                                       -SSHHHHHHHHHHHHTT-..-EEEEEEE-GGGT-EEEEESSS-E.EEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48   3 reaelkevveelakeaglpkpltkvyvvnspkrNAFalgggknk.rivltdgLlkqllseeelaaVlGHElGHikhr 78 
                                       +e++l  +ve+lak+aglp p+ +v+++ +p  NAFa+g++ ++  +v t+g+l +ll+++el++V++HEl+H+ +r
  gi|474935110|ref|YP_007688692.1|  62 EEPRLYGIVEKLAKQAGLPMPEVGVTEISMP--NAFATGRNPSNaAVVATRGIL-NLLDDDELEGVIAHELSHVRNR 135
                                       6889999***********7777777777777..********9999*********.********************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHTT-SHHHHHTT--S---HHHHHHHHHHTT...........HHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxx RF
                     Peptidase_M48  79 hsvvslivsllasillllglallisraeedaagafldalavliglliillfl...........alSRkrEyqADeag 144
                                       + +v+ + s la+il + +++ +++ a  +a+++  ++ a  i++++il  l           a+SR+rE+ ADe g
  gi|474935110|ref|YP_007688692.1| 136 DILVMSVASCLATILTYAAFI-VFRGAIFNAISGRNSKDALPILAIGILCYLlvpiaaicmqlAVSRNREFLADETG 211
                                       **************9999997.5555566666666677777777778877778889999****************** PP

                                       HHTTT.HHHHHHHHHHHHHHTT-..-S---HHHH.................HHS-SS--HHHHHHHHHH- CS
                                       xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxx.................xxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48 145 vellkrakdlvraliklakdler..qdvsaslrs.................ellstHPplleRiqalkel 195
                                       ++++ ++ +l+ al+kl ++++   +++++s r+                  l+stHP+++eRi++l++l
  gi|474935110|ref|YP_007688692.1| 212 ARICGKPLALAGALYKLENGCQDprNPYDDSRRAnmwianpisggrksfckRLFSTHPDTQERIRRLEKL 281
                                       *********************864477777777799*******************************986 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   3.5e-09   1.6e-05     116     227 ..      34     152 ..      18     161 .. 0.67

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 3.5e-09
                     Peptidase_M56 116 lllyliaallvlkkr.fvrklgklraeelkeaLkeakeemqlkrniki....rlsssidsPavlgllkp....rIvl 183
                                        ++ +  +++  k++ +  ++ +l   e++ +L  + e+ +  ++  +    +   +i+ P  ++  ++     +v 
  gi|474935110|ref|YP_007688692.1|  34 AVILSFVSYFTSKSSaLRANKVHLVTREEEPRLYGIVEKLA--KQAGLpmpeVGVTEISMPNAFATGRNpsnaAVVA 108
                                       23344455555555534444444445556666666666655..3333300113456799999998877534447999 PP

                     Peptidase_M56 184 PadflkklsdeeleyillHElaHlkrkDllvnllvavlqclfwf 227
                                          +l+ l+d+ele +++HEl+H++++D+lv  ++  l  +  +
  gi|474935110|ref|YP_007688692.1| 109 TRGILNLLDDDELEGVIAHELSHVRNRDILVMSVASCLATILTY 152
                                       999****************************9999888887665 PP

>> Claudin_3  Tight junction protein, Claudin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.2      0.03   1.3e+02       9      25 ..      28      44 ..       2      70 .. 0.71
   2 ?   10.9   0.9   7.4e-05      0.33      85     147 ..     128     195 ..     123     206 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.03
                         Claudin_3  9 gvlvvisfilnivglft 25
                                       ++ +i++il++v+ ft
  gi|474935110|ref|YP_007688692.1| 28 ALMACIAVILSFVSYFT 44
                                      33344444555554444 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 7.4e-05
                         Claudin_3  85 gysksvrklffliallslliviltviaviliavnvskfndsfndss....lqLGYsawlsv.isails 147
                                       + s+   + + +++++s l++ilt +a+i+++  + ++ ++ n ++    l +G   +l v i+ai++
  gi|474935110|ref|YP_007688692.1| 128 ELSHVRNRDILVMSVASCLATILTYAAFIVFRGAIFNAISGRNSKDalpiLAIGILCYLLVpIAAICM 195
                                       555555566789*******************9999888877777667888888888887663444444 PP

>> DUF4229  Protein of unknown function (DUF4229)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   3.7   0.00025       1.1      10      44 ..       1      40 [.       1      56 [. 0.78
   2 ?   -1.1   0.1      0.47   2.1e+03      33      58 ..     138     163 ..     126     172 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00025
                           DUF4229 10 Lfvvltavillvarliglp.....vpllvaallAlvvalp 44
                                      +fvv+t+++ +++++igl      ++l ++a +A++++++
  gi|474935110|ref|YP_007688692.1|  1 MFVVMTLILSGIGYVIGLVfgyglLGLALMACIAVILSFV 40
                                      69****************9996666666666666666653 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.47
                           DUF4229  33 vaallAlvvalplSmvllkklRdrat 58 
                                       +++ +A  +a +l + ++   R ++ 
  gi|474935110|ref|YP_007688692.1| 138 LVMSVASCLATILTYAAFIVFRGAIF 163
                                       55666666777777777666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       885  (0.0493614); expected 358.6 (0.02)
Passed bias filter:                      635  (0.0354175); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 2088.96
//
Query:       gi|474935111|ref|YP_007688693.1|  [L=256]
Description: Metal-dependent hydrolases of the beta-lactamase superfamily II [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.8e-05   23.8   0.0    5.2e-05   23.3   0.0    1.2  1  Lactamase_B  Metallo-beta-lactamase superfamily


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   2.9e-09   5.2e-05       6      98 ..      24     119 ..      21     171 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 2.9e-09
                                       SEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCC CS
                       Lactamase_B   6 vnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapal 82 
                                       ++s++ie dg+  ++ tG+ t++ +    + a ++  +d+d+v+++H++ D  G++g + + +  p++++a  ++++
  gi|474935111|ref|YP_007688693.1|  24 GSSFIIEADGERTMFGTGLRTRYLQTN--MSAMDVSADDLDRVVISHMDKDEWGAVGAVLKDRTKPIAVYAPSDAWG 98 
                                       689**********************96..8*********************************************** PP

                                       HCHHHHHHHHHCCHH.....T CS
                       Lactamase_B  83 fmeeaddaasrkgll.....l 98 
                                       ++   ++   +++ +     +
  gi|474935111|ref|YP_007688693.1|  99 EKKSFGCTGIYFPEEykdrgI 119
                                       999999998888654443330 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1683.50
//
Query:       gi|474935112|ref|YP_007688694.1|  [L=277]
Description: putative metal-dependent hydrolase (urease superfamily) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      9e-21   74.4   0.0      1e-20   74.2   0.0    1.0  1  TatD_DNase  TatD related DNase
  ------ inclusion threshold ------
      0.011   15.2   0.0      0.018   14.5   0.0    1.3  1  PTE         Phosphotriesterase family


Domain annotation for each model (and alignments):
>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.2   0.0   1.2e-24     1e-20       2     255 .]       8     276 ..       7     276 .. 0.83

  Alignments for each domain:
  == domain 1  score: 74.2 bits;  conditional E-value: 1.2e-24
                                       EEEE-TTSCCCTTTHHHHHHHHHHTTEEEEEEE-SSG...............GGHHHHHHHHTT..TTTEEEEE--- CS
                        TatD_DNase   2 DaHcHldskefeedreeileraeeagvaavvvvgtss...............kdskavlelakk.ypnkvyavlGiH 62 
                                       D H H+  +       e+l+++e++g++ +  v++                 k + ++ +l+++  + +v +++G +
  gi|474935112|ref|YP_007688694.1|   8 DDHFHMSPRG---RNVEALKEFEAEGGTGITLVTLPYpevrirsgadfaesyKITYDLAQLSREqTSVEVNVAVGPY 81 
                                       9999999944...57777899999999988877776677888888888877445558999999888899******** PP

                                       G...GGGGC.........C.CCHHHHHHHH.HHCCCTSEEEEEEEEEET-CCCCCGHHHHHHHHHHHHHHHHHTTEE CS
                        TatD_DNase  63 P...nevde.........asedlleelkel.anvkhskvvaiGeiGLDyysreestkeaqeevFeeqlrlAkelklp 126
                                       P       +         a+  +++ ++++ + +++ k+vaiGe+G++++   ++ ++a ++v+ + ++lAke + p
  gi|474935112|ref|YP_007688694.1|  82 PillV---SlaeefgleeAEAMMIRGMDDAaKAIQEGKAVAIGEVGRPHFECPDDIWDASNRVLLHGMQLAKENDVP 155
                                       *5553...44457887755666779*****9999***************9999999********************* PP

                                       EEEEEES-HHHHHHHHHHCGGCCS...EEEETT--S-HHHHHHHHHTTEEEEE-GGGGTTTTHHHHHHHHHS-GGGE CS
                        TatD_DNase 127 lviHlrkaeedlleilkeaaeaka...kvvlHsfsgsaeeakkflklgyyislsglltfknakelrelvkavpldrl 200
                                       ++iH+++a+++ l++ + aa a++    v+ Hs   s   +++    g++ s+++      +k+ ++ + a   dr+
  gi|474935112|ref|YP_007688694.1| 156 VIIHCENADDTDLSLSRLAARAGLdpsLVIKHS---SLPLVTEEETHGVMPSIPA------SKKYIKEALAKGTDRF 223
                                       *******99988888888777777886888888...66666666667*******9......4455555556689*** PP

                                       EE---TTSSEECCCTT.SE--GGGHHHHHHHHHHHHTS-HHHHHHHHHHHHHHHHH CS
                        TatD_DNase 201 LiETDaPyltpkpyrg.krnepanvayvveklaelkaltleelaeitaeNakrlfk 255
                                       ++ETD  y+++ p ++       +v++ v+ + +    ++e + +i+++   r+++
  gi|474935112|ref|YP_007688694.1| 224 MLETD--YIDD-PAKPtSIMACTTVPNKVKWMLASGTCSEESIMRICSDLPNRYYH 276
                                       *****..9999.888879999999**********999*******999999988886 PP

>> PTE  Phosphotriesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0     2e-06     0.018      75     189 ..      68     186 ..      56     197 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2e-06
                                       CCHSSEEEEEECB--CCG--TCCCCS-CHCHHHHHHHHHHT-STT.TS--EEEEEEEE.....-CTBS-HHHHHHHH CS
                               PTE  75 eetgvnivaatGfYvdatvpeaararsveeltdvlvdeiehGidg.teikaGiikeig.....tsgkltpseekvle 145
                                       e+t v++ +a G Y    v+  a+  + ee   ++++ + + +    e ka  i+e+g     +  ++ ++ ++vl 
  gi|474935112|ref|YP_007688694.1|  68 EQTSVEVNVAVGPYPILLVSL-AEEFGLEEAEAMMIRGMDDAAKAiQEGKAVAIGEVGrphfeCPDDIWDASNRVLL 143
                                       689999999999999988875.45668888888999888887765246788899999844433457899******** PP

                                       HHHHHHHHH---EEEEEGCCTTCHHHHHHHHHHTT--GGGEEET CS
                               PTE 146 avaqahkqtGaPisihtsaslragleqlrilqeeGvDlsrvvvg 189
                                          q  k    P++ih + +  + l   r+ + +G D s v + 
  gi|474935112|ref|YP_007688694.1| 144 HGMQLAKENDVPVIIHCENADDTDLSLSRLAARAGLDPSLV-IK 186
                                       *999999******************************9865.44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 2048.92
//
Query:       gi|474935113|ref|YP_007688695.1|  [L=422]
Description: putative DNA primase, eukaryotic-type, small subunit [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-24   86.8   0.0    3.1e-24   86.0   0.0    1.5  1  DNA_primase_S  DNA primase small subunit
  ------ inclusion threshold ------
       0.12   12.7   0.0       0.96    9.9   0.0    2.4  2  EnY2           Transcription factor e(y)2


Domain annotation for each model (and alignments):
>> DNA_primase_S  DNA primase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.0   0.0   3.5e-28   3.1e-24       1     176 [.     109     347 ..     109     348 .. 0.82

  Alignments for each domain:
  == domain 1  score: 86.0 bits;  conditional E-value: 3.5e-28
                                       EEEEEETTT-.TT--HHHHHHHHHHHHHHHHHHHH-----GG..GEEEEE--SEEEEEEE--TTEEES-HHHHHHHH CS
                     DNA_primase_S   1 FDiDmddyddcseatvcekcwkfvsvavkvldellredfgfk..dilwvfsgrrGfHcwvsdkdarpltdeeraaiv 75 
                                       FD+D+d++++ +e+t+ e+ +++ ++ +++ d +l  d+gf   ++++ fsg+rG+H++++ +d+ +l+  er+++v
  gi|474935113|ref|YP_007688695.1| 109 FDLDADHLQGADEMTYSEMMVQIRREMIALCDDYLFSDLGFSedQVHICFSGGRGYHAHIRSNDIYTLGANERRELV 185
                                       9****************************************999********************************* PP

                                       HH........................................................................... CS
                     DNA_primase_S  76 nylnly.........................................rplhpflsrs.mlkivkpvveeiileeqdp 110
                                       +y+++                                          +       +  m++ +k++v++ i ee   
  gi|474935113|ref|YP_007688695.1| 186 DYISCTgldlerifpvhqnamgavsygngtsvakinkyrllpapdegG------WKHkMREALKDIVKD-IREE--- 252
                                       *****99**999999999998888887777777666555443222221......223344444444433.3444... PP

                                       .HCHHHHCT--------................................................------------ CS
                     DNA_primase_S 111 feikkllrllpdkslre..kkkw............................eakedivlvllyprldeqvtkgikhl 157
                                        e+k++ +l+p  ++++   +k+                                ++v  +l  + d++vt +ik+l
  gi|474935113|ref|YP_007688695.1| 253 -EPKRIKKLYPSVKSQNssLEKMgthlrkcgdimfergtmvdlepweqeilMKCLNDVAPRLSSEVDKPVTPDIKRL 328
                                       .677777777766666666445577777777777888888888888*999977888999****************** PP

                                       -----....---------. CS
                     DNA_primase_S 158 lkapfcihgktgnvcvpld 176
                                       +++p+++hgktg +++p++
  gi|474935113|ref|YP_007688695.1| 329 IRLPGSLHGKTGLRVTPIT 347
                                       *****************97 PP

>> EnY2  Transcription factor e(y)2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.29   2.6e+03      48      70 ..     119     141 ..      98     145 .. 0.76
   2 ?    9.9   0.0   0.00011      0.96      26      63 ..     230     267 ..     222     271 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.29
                                       TSS.CHHHHHHHHHHHHHHHS-H CS
                              EnY2  48 eeevsveelveeitpkaralVPd 70 
                                        +e++++e++ +i+ ++ al+ d
  gi|474935113|ref|YP_007688695.1| 119 ADEMTYSEMMVQIRREMIALCDD 141
                                       35589999999999999888765 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00011
                                       HHTTHHHHHHHHHHHHHHH..HTSS.CHHHHHHHHHHH CS
                              EnY2  26 eesGWrdevkelckeiirekgleeevsveelveeitpk 63 
                                       +e GW+ +++e+ k+i+++ ++ee+  +++l+  ++ +
  gi|474935113|ref|YP_007688695.1| 230 DEGGWKHKMREALKDIVKDIREEEPKRIKKLYPSVKSQ 267
                                       588***************97778888899999888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      601  (0.0335211); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 2757.96
//
Query:       gi|474935114|ref|YP_007688696.1|  [L=74]
Description: Ribosomal protein L20A (L18A) [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-06   27.4   0.0    3.5e-06   27.1   0.0    1.2  1  Ribosomal_L18A  Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
  ------ inclusion threshold ------
      0.026   14.6   0.0      0.075   13.1   0.0    1.8  1  LAGLIDADG_WhiA  WhiA LAGLIDADG-like domain


Domain annotation for each model (and alignments):
>> Ribosomal_L18A  Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   3.9e-10   3.5e-06      67     121 .]       2      56 ..       1      56 [. 0.89

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 3.9e-10
                                       ............TEEEEEEEEEEESSHHHHHHHHHHHHHHHS---GGGEEEEEEE CS
                    Ribosomal_L18A  67 knygiwlrydsrsgthnfykeyrdlteegaveqvYselgsrhrakrssIqIekve 121
                                       k + +   +   ++ ++f  e+ +  e+++ e++ s++gsrh++kr +I+I+k+e
  gi|474935114|ref|YP_007688696.1|   2 KAFLVTGSFADPRKEQPFSIEMAADDEASVKEKALSTIGSRHKMKRWQIKIDKIE 56 
                                       55666666777788999***********************************996 PP

>> LAGLIDADG_WhiA  WhiA LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   8.4e-06     0.075       8      36 ..       3      33 ..       2      58 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.4e-06
                    LAGLIDADG_WhiA  8 aflasGsindpekk..yhLEivspdeelaeq 36
                                      afl +Gs++dp+k+  + +E++++de  +++
  gi|474935114|ref|YP_007688696.1|  3 AFLVTGSFADPRKEqpFSIEMAADDEASVKE 33
                                      8**********55549******999987764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 501.09
//
Query:       gi|474935115|ref|YP_007688697.1|  [L=144]
Description: prefoldin, archaeal alpha subunit/eukaryotic subunit 5 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.2e-19   68.3   3.5    6.8e-19   67.9   3.5    1.2  1  Prefoldin        Prefoldin subunit
  ------ inclusion threshold ------
      0.013   15.8   4.3       0.02   15.1   4.3    1.3  1  CENP-Q           CENP-Q, a CENPA-CAD centromere complex subun
       0.03   15.1   2.1        4.4    8.1   0.1    2.1  2  Occludin_ELL     Occludin homology domain
      0.036   13.8   2.1       0.41   10.3   0.1    2.0  2  BAR_3            BAR domain of APPL family
       0.05   13.7   1.5       0.75    9.9   0.4    2.2  2  RasGAP_C         RasGAP C-terminus
      0.067   13.5   2.2        5.4    7.3   0.3    2.2  2  DUF948           Bacterial protein of unknown function (DUF94
       0.08   12.6   0.1       0.12   12.0   0.1    1.3  1  ABC_membrane     ABC transporter transmembrane region
      0.082   12.5   5.0       0.15   11.6   0.3    2.0  2  AAA_27           AAA domain
      0.082   12.9   4.9        1.1    9.3   0.9    2.8  2  DUF2388          Protein of unknown function (DUF2388)
      0.098   13.1   7.1       0.29   11.6   1.5    2.4  2  KELK             KELK-motif containing domain of MRCK Ser/Thr
       0.12   12.6  15.5       0.35   11.1   3.9    2.1  2  FliJ             Flagellar FliJ protein
       0.13   11.8   7.6        0.4   10.3   0.7    2.1  2  Snf7             Snf7
       0.17   12.3   2.7        2.5    8.5   0.1    3.2  3  HHH_8            Helix-hairpin-helix domain
       0.17   12.4   4.0        3.3    8.3   0.5    2.2  2  Syntaxin-6_N     Syntaxin 6, N-terminal
       0.18   10.7   9.7          1    8.1   1.9    2.0  2  Spc7             Spc7 kinetochore protein
       0.18   12.1  11.6       0.57   10.5   4.1    2.3  2  Phasin_2         Phasin protein
        0.2   12.0   4.4        1.2    9.5   0.1    2.4  2  BLOC1_2          Biogenesis of lysosome-related organelles co
        0.2   11.9   9.1        1.9    8.8   0.4    2.5  2  WXG100           Proteins of 100 residues with WXG
       0.22   10.8   7.1       0.32   10.3   7.1    1.2  1  DUF4407          Domain of unknown function (DUF4407)
       0.24   10.9   1.6        5.9    6.5   0.0    2.9  2  KNOX2            KNOX2 domain
       0.25   11.6   2.2       0.32   11.3   0.2    1.9  2  Retrotrans_gag   Retrotransposon gag protein
       0.55   10.4   3.5        2.1    8.5   0.7    2.0  2  Fib_alpha        Fibrinogen alpha/beta chain family
       0.56    9.7   5.3        2.9    7.4   0.4    2.0  2  DUF1974          Domain of unknown function (DUF1974)
        0.9    9.6  11.1        2.8    8.0  11.1    1.6  1  Mod_r            Modifier of rudimentary (Mod(r)) protein
        1.1    9.5   6.7        3.3    8.0   0.9    2.1  2  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
        1.4    9.0   4.8        4.9    7.3   0.5    2.2  2  COG2             COG (conserved oligomeric Golgi) complex com
        1.6    8.9   8.3        4.3    7.5   0.6    2.2  2  PEP-utilisers_N  PEP-utilising enzyme, N-terminal
        1.7    9.2  12.7         23    5.5  12.7    2.0  1  APG6_N           Apg6 coiled-coil region
        1.8    6.0  10.8       0.42    8.1   2.5    2.0  2  DUF3584          Protein of unknown function (DUF3584)
        3.5    7.8  11.7        4.5    7.5   1.6    2.3  2  HR1              Hr1 repeat


Domain annotation for each model (and alignments):
>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.9   3.5   1.1e-21   6.8e-19       1     119 [.      19     136 ..      19     137 .. 0.96

  Alignments for each domain:
  == domain 1  score: 67.9 bits;  conditional E-value: 1.1e-21
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT.-TT-EEEEEEETTEEEEEE--STTEEEEEEETTEEEEEEHHH CS
                         Prefoldin   1 lkeeleslqaelaqlkeaieelektletlktlkkedegkevlvplgaglyvkaevkdtdkvlvdlGagyyvekslee 77 
                                       ++++le+l ++++ l+++ +e  ++  +l+ lk+++eg e++vp+ga+ y+ ++v+  ++++v +G g++veksl++
  gi|474935115|ref|YP_007688697.1|  19 YNKQLETLSRQVKLLQATRDEAARAFRALSALKDAKEGDEIMVPVGASTYITVKVTG-KNAVVGVGNGVAVEKSLDD 94 
                                       789****************************************************55.56789************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  78 Aiellkkkleelekqlekleeeleklkdqittleanlaqlyq 119
                                       A ++ + + +e++++l +   + ++ ++  ++l ++++q y 
  gi|474935115|ref|YP_007688697.1|  95 AQAYMQSQGDEITSALNEAVSAMQEVQSYTQELADAIQQEYR 136
                                       ***************************************996 PP

>> CENP-Q  CENP-Q, a CENPA-CAD centromere complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   4.3   3.3e-05      0.02      53     162 ..       7     133 ..       2     137 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.3e-05
                            CENP-Q  53 aeiekeeralerdyeaLreLeknakaearerke..klkkehvllqesdseelslleassdevlgea........... 116
                                       +e++++ ral +  ++L++L +++k ++++r+e  ++ +++  l+ +++++++ + +  +    ++           
  gi|474935115|ref|YP_007688697.1|   7 EELRQAARALDSYNKQLETLSRQVKLLQATRDEaaRAFRALSALKDAKEGDEIMVPVGASTYITVKvtgknavvgvg 83 
                                       89****************************999666666777777665555555554444444444999******** PP

                            CENP-Q 117 ....sgtvfsdlepeldeellpllqqLgshLesmrgnlaqlegllpaler 162
                                            +++  d +  ++++  ++  +L++ +  m++  + +++l +a+++
  gi|474935115|ref|YP_007688697.1|  84 ngvaVEKSLDDAQAYMQSQGDEITSALNEAVSAMQEVQSYTQELADAIQQ 133
                                       99996666666667788888889999999999999999999999999987 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1    0.0074       4.4      23      74 ..       8      58 ..       5      72 .. 0.85
   2 ?    6.8   0.4     0.018        11      39      71 ..     108     140 ..      90     143 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0074
                      Occludin_ELL 23 eYkelhaeleevskkfseLerelkelkegskeykkieeeilqeykklkkdpe 74
                                      e ++  + l++++k+++ L+r++k l+ +++e +++ +  l+ +k+ k+  e
  gi|474935115|ref|YP_007688697.1|  8 ELRQAARALDSYNKQLETLSRQVKLLQATRDEAARAFRA-LSALKDAKEGDE 58
                                      5677788999****************9999999999999.888888887655 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.018
                      Occludin_ELL  39 seLerelkelkegskeykkieeeilqeykklkk 71 
                                       s L++ +++++e ++ ++++++ i+qey++ + 
  gi|474935115|ref|YP_007688697.1| 108 SALNEAVSAMQEVQSYTQELADAIQQEYRQRQA 140
                                       45677777777777888999999999**99865 PP

>> BAR_3  BAR domain of APPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.2     0.091        55      16      56 ..       8      48 ..       4      60 .. 0.70
   2 ?   10.3   0.1   0.00069      0.41      57     102 ..      90     136 ..      83     140 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.091
                             BAR_3 16 sleevEaeleelekklkkllKlckrlieagkaysaaqkqfa 56
                                      +l++  + l+  +k+l+ l +++k l ++  +  +a+++++
  gi|474935115|ref|YP_007688697.1|  8 ELRQAARALDSYNKQLETLSRQVKLLQATRDEAARAFRALS 48
                                      56666677777777777777777777777777777776664 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00069
                             BAR_3  57 qsLrelkkes.kgdeetdesLkkfsellqelenehtilldqaqrsik 102
                                       +sL + + +  ++ +e++++L++  +++qe+ ++ ++l+d +q+  +
  gi|474935115|ref|YP_007688697.1|  90 KSLDDAQAYMqSQGDEITSALNEAVSAMQEVQSYTQELADAIQQEYR 136
                                       67777776665555678899*********************999875 PP

>> RasGAP_C  RasGAP C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.22   1.3e+02      70      88 ..      13      31 ..       3      72 .. 0.63
   2 ?    9.9   0.4    0.0013      0.75      58     104 ..      88     138 ..      86     143 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.22
                          RasGAP_C 70 esqlesYkayienvleqlk 88
                                         l+sY++ +e+   q+k
  gi|474935115|ref|YP_007688697.1| 13 ARALDSYNKQLETLSRQVK 31
                                      4456666666666655553 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0013
                          RasGAP_C  58 tlktLseknnylesqlesYkayienvleqlkkkk.gk...lpfskqyfkkr 104
                                       + k+L++ ++y++sq ++  + ++++++ +++ + ++       +q +++r
  gi|474935115|ref|YP_007688697.1|  88 VEKSLDDAQAYMQSQGDEITSALNEAVSAMQEVQsYTqelADAIQQEYRQR 138
                                       6799**************************988622245533344444444 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1     0.025        15      22      45 ..      10      33 ..       5      55 .. 0.59
   2 ?    7.3   0.3    0.0091       5.4      23      65 ..      87     129 ..      69     137 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.025
                            DUF948 22 lklkktldeaaatieelekqvdpi 45
                                      +++++ ld+ ++++e+l +qv+ +
  gi|474935115|ref|YP_007688697.1| 10 RQAARALDSYNKQLETLSRQVKLL 33
                                      444555555555555555555433 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0091
                            DUF948  23 klkktldeaaatieelekqvdpilkevedllakvnelledvne 65 
                                        ++k ld a+a +++ ++++++ l+e+  ++++v+  ++++ +
  gi|474935115|ref|YP_007688697.1|  87 AVEKSLDDAQAYMQSQGDEITSALNEAVSAMQEVQSYTQELAD 129
                                       5677888888888888888888888888888888776666554 PP

>> ABC_membrane  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1    0.0002      0.12     160     199 ..      87     126 ..      78     138 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHTTTH CS
                      ABC_membrane 160 viakilkklkkkeqkavakassvaeEslsgirtVkafgre 199
                                        + k l +++  +q++ ++++s ++E++s+++ V++++ e
  gi|474935115|ref|YP_007688697.1|  87 AVEKSLDDAQAYMQSQGDEITSALNEAVSAMQEVQSYTQE 126
                                       56678888999999***********************988 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.7      0.11        64     148     194 ..       9      54 ..       5      60 .. 0.81
   2 ?   11.6   0.3   0.00025      0.15     133     179 ..      95     141 ..      88     144 .] 0.86

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.11
                            AAA_27 148 LfeasaGlaslrevleaLeaeadelfkprkskkrainealeeleeak 194
                                       L +a+ +l s ++ le+L+++ + l ++r ++  ++ +al++l++ak
  gi|474935115|ref|YP_007688697.1|   9 LRQAARALDSYNKQLETLSRQVKLLQATRDEAA-RAFRALSALKDAK 54 
                                       668999999999999999999999999998888.6666777777765 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00025
                            AAA_27 133 GGealleaegelgqlLfeasaGlaslrevleaLeaeadelfkprksk 179
                                           + ++ +e++++L ea ++++++++  ++L +  ++ +++r+++
  gi|474935115|ref|YP_007688697.1|  95 AQAYMQSQGDEITSALNEAVSAMQEVQSYTQELADAIQQEYRQRQAN 141
                                       55567778899*******************************99876 PP

>> DUF2388  Protein of unknown function (DUF2388)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.048        29      10      29 ..      22      41 ..      13      46 .. 0.85
   2 ?    9.3   0.9    0.0019       1.1      21      68 ..      88     131 ..      66     133 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.048
                           DUF2388 10 sltssskddklvlaArdDAa 29
                                      +l++ s+  kl++a rd+Aa
  gi|474935115|ref|YP_007688697.1| 22 QLETLSRQVKLLQATRDEAA 41
                                      66778899***********9 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0019
                           DUF2388  21 vlaArdDAasFVASdGairGarLEaaLqelRsenpelqasDleLAeaI 68 
                                       v +  dDA ++  S+G+    ++ +aL+e  s++ e+q+  +eLA aI
  gi|474935115|ref|YP_007688697.1|  88 VEKSLDDAQAYMQSQGD----EITSALNEAVSAMQEVQSYTQELADAI 131
                                       667789********997....566667777777788888899999998 PP

>> KELK  KELK-motif containing domain of MRCK Ser/Thr protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.4     0.078        46       1      19 [.      22      40 ..       2      56 .. 0.57
   2 ?   11.6   1.5   0.00048      0.29      19      67 ..      88     136 ..      86     141 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.078
                              KELK  1 klkeLekqlrllkqEkeel 19
                                      +l +L +q++ll+  ++e+
  gi|474935115|ref|YP_007688697.1| 22 QLETLSRQVKLLQATRDEA 40
                                      2334444444444444444 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00048
                              KELK  19 lqkelaeaqErlksqkkeLkdaisqrklamqefsevneklselrsqkqk 67 
                                       ++k l +aq  ++sq+ e+  a++    amqe +  ++ l++  +q  +
  gi|474935115|ref|YP_007688697.1|  88 VEKSLDDAQAYMQSQGDEITSALNEAVSAMQEVQSYTQELADAIQQEYR 136
                                       689999********************************99998887654 PP

>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   3.9   0.00058      0.35      64     118 ..       5      59 ..       1      61 [. 0.94
   2 ?    7.3   3.8    0.0086       5.1      19      66 ..      90     136 ..      86     142 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00058
                              FliJ  64 qkqelaqaekqvekareewqearqerkklekLkerekkeeqkeenrrEqkqlDEl 118
                                         +el qa ++++ + +++    +++k l+  ++++++++++  + ++ k+ DE+
  gi|474935115|ref|YP_007688697.1|   5 NDEELRQAARALDSYNKQLETLSRQVKLLQATRDEAARAFRALSALKDAKEGDEI 59 
                                       56899*************************************************8 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0086
                              FliJ  19 ekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkq 66 
                                       + l+  + y+q+   ++ ++  + ++++++ +q++ + l +ai+q  +
  gi|474935115|ref|YP_007688697.1|  90 KSLDDAQAYMQSQGDEITSAL-NEAVSAMQEVQSYTQELADAIQQEYR 136
                                       455555555555555555555.6678999999*******999999655 PP

>> Snf7  Snf7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.7   0.00067       0.4       4      52 ..       7      55 ..       5      63 .. 0.90
   2 ?    5.3   1.2     0.022        13     107     155 ..      89     137 ..      85     143 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00067
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTT-HHHHHHHHHHHHH CS
                              Snf7  4 rsLrkaerkldkkqeslekkikkleaelkklakkgnkdralllLKqkkr 52
                                       +Lr+a r ld++ ++le+   ++++  +   +  +  ral +LK+ k+
  gi|474935115|ref|YP_007688697.1|  7 EELRQAARALDSYNKQLETLSRQVKLLQATRDEAARAFRALSALKDAKE 55
                                      79*********************999888888999999******99875 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.022
                                       HHHHHHHHHHHH.HHTCHHHHHHHHHTT-GGTTHHHHHHHHHHHHHHHHH CS
                              Snf7 107 dklmdeiedqme.kaeeisEalsrslddadeedEeeleaeLdaLeqelgd 155
                                       +k +d+ +  m+ + +ei  al++++    +e    +++  da++qe+ +
  gi|474935115|ref|YP_007688697.1|  89 EKSLDDAQAYMQsQGDEITSALNEAVSA-MQEVQSYTQELADAIQQEYRQ 137
                                       5556666665541557888888888854.444445566666777777655 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1    0.0041       2.5      29      49 ..      10      30 ..       9      36 .. 0.84
   2 ?    0.9   0.1         1   6.1e+02       3      22 ..      39      58 ..      37      61 .. 0.71
   3 ?    0.8   0.0       1.1   6.3e+02      40      61 ..     104     129 ..      94     137 .. 0.50

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0041
                                      HHHHCCCCC-SS-HHHH.TTHC CS
                             HHH_8 29 rrAaraiealpeeitsl.eeel 49
                                      r Aara++++ +++++l ++ +
  gi|474935115|ref|YP_007688697.1| 10 RQAARALDSYNKQLETLsRQ-V 30
                                      89**************9877.3 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1
                                      HHHHHHHHHHHHHHHCT--C CS
                             HHH_8  3 eiadaLeeladllelkgedp 22
                                      e a+a++ l  l + k++d+
  gi|474935115|ref|YP_007688697.1| 39 EAARAFRALSALKDAKEGDE 58
                                      67778888887777777665 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 1.1
                                       S-HHHH.TT...HCTTSTT--HHHHH CS
                             HHH_8  40 eeitsl.ee...eltklpgiGkkiaa 61 
                                       +eits+  e   ++++++   + +a+
  gi|474935115|ref|YP_007688697.1| 104 DEITSAlNEavsAMQEVQSYTQELAD 129
                                       55555543322223333333344444 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.2     0.043        26      44      71 ..      10      37 ..       3      53 .. 0.73
   2 ?    8.3   0.5    0.0056       3.3      10      51 ..      88     132 ..      86     139 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.043
                      Syntaxin-6_N 44 teLrkalrsiewdledLeetvriveknp 71
                                      ++  +al+s +++le L + v+ +++ +
  gi|474935115|ref|YP_007688697.1| 10 RQAARALDSYNKQLETLSRQVKLLQATR 37
                                      4445678888899999999998887754 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0056
                      Syntaxin-6_N  10 Vqkslnkaeslyrrw.erlledtss..stseeldetrteLrkalr 51 
                                       V+ksl+ a++ +++   ++ +  ++  s  +e+++ ++eL  a++
  gi|474935115|ref|YP_007688697.1|  88 VEKSLDDAQAYMQSQgDEITSALNEavSAMQEVQSYTQELADAIQ 132
                                       999999999999999756666666657689999999999999987 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   1.9    0.0017         1     197     243 ..       5      51 ..       1      58 [. 0.56
   2 ?    7.4   1.1     0.003       1.8     142     188 ..      90     136 ..      86     143 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0017
                              Spc7 197 dkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqk 243
                                       + eeL+++ ++l++ ++++e ++++++ lq+ ++e + ++ +l++ k
  gi|474935115|ref|YP_007688697.1|   5 NDEELRQAARALDSYNKQLETLSRQVKLLQATRDEAARAFRALSALK 51 
                                       45566666666666666666666666666666666655555555444 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.003
                              Spc7 142 egleenlegleedkelLekqeeeldellpeleeekaeleeeleklqe 188
                                       ++l++  + ++++ +++++  +e+ ++++e++++ +el + ++++ +
  gi|474935115|ref|YP_007688697.1|  90 KSLDDAQAYMQSQGDEITSALNEAVSAMQEVQSYTQELADAIQQEYR 136
                                       56667777777777777777777777777777777777766666544 PP

>> Phasin_2  Phasin protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.8      0.02        12      26      58 ..      24      55 ..       1      60 [. 0.75
   2 ?   10.5   4.1   0.00095      0.57      19      71 ..      89     140 ..      86     143 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.02
                          Phasin_2 26 eklaelqleaarasleeslaaakallsakdpqe 58
                                      e+l ++q+++++a+ +e++ a++al++ kd++e
  gi|474935115|ref|YP_007688697.1| 24 ETL-SRQVKLLQATRDEAARAFRALSALKDAKE 55
                                      444.46889999999999999999999999877 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00095
                          Phasin_2  19 slalegaeklaelqleaarasleeslaaakallsakdpqell.elqselaqpal 71 
                                       +++l+ a+++++ q + + ++l+e+++a++++ s    qel+ ++q+e+ q+++
  gi|474935115|ref|YP_007688697.1|  89 EKSLDDAQAYMQSQGDEITSALNEAVSAMQEVQSYT--QELAdAIQQEYRQRQA 140
                                       567788888888888888888888888888777776..8888788888888776 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1     0.002       1.2      75      93 ..       7      25 ..       2      28 .. 0.90
   2 ?    3.2   0.6      0.19   1.1e+02      41      68 ..     105     128 ..      88     137 .. 0.49

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.002
                           BLOC1_2 75 teLeeavseLDeyskeLEa 93
                                      +eL +a+ +LD+y k+LE 
  gi|474935115|ref|YP_007688697.1|  7 EELRQAARALDSYNKQLET 25
                                      689**************95 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.19
                           BLOC1_2  41 dvaaslekkleklnekyeelqpylqqid 68 
                                       ++++ l++ +++++    e+q+y q++ 
  gi|474935115|ref|YP_007688697.1| 105 EITSALNEAVSAMQ----EVQSYTQELA 128
                                       33333333333333....3333333332 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.4    0.0031       1.9       4      31 ..       4      31 ..       1      46 [. 0.86
   2 ?    6.5   3.0     0.017        10      45      82 ..      95     132 ..      90     139 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0031
                                      SHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  4 vdpeelrqaaarfqkqaeeledelqrlk 31
                                       + eelrqaa+++++ +++le++ +++k
  gi|474935115|ref|YP_007688697.1|  4 LNDEELRQAARALDSYNKQLETLSRQVK 31
                                      6789****************99999887 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.017
                                       HCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  45 aadafqaefeewkqaaqklvdaLeeisealkqaanafe 82 
                                       a+   q++ +e++ a+++ v a++e+++ +++ a+a +
  gi|474935115|ref|YP_007688697.1|  95 AQAYMQSQGDEITSALNEAVSAMQEVQSYTQELADAIQ 132
                                       33334444457777777777777777777777777665 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   7.1   0.00054      0.32     113     238 ..       9     139 ..       2     143 .. 0.44

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00054
                           DUF4407 113 aeeqqeeakelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk..............gtgt 175
                                        ++++++ ++        ++++l++l +q++ lqa+ d+a ++++al a  ++  +g+                tg 
  gi|474935115|ref|YP_007688697.1|   9 LRQAARALDS--------YNKQLETLSRQVKLLQATRDEAARAFRALSALKDA-KEGDEimvpvgastyitvkVTGK 76 
                                       2222222333........55555555555555555555555555554443332.23333455555547777775555 PP

                           DUF4407 176 tgvaGkgpaakekkaqldaaqaelaelkakld.atarlaalraelaeleaerakeraasqaaaa 238
                                       ++v G g      ++ ld+aqa +++  ++++ a  +  ++ +e ++ ++e+a+++++  ++++
  gi|474935115|ref|YP_007688697.1|  77 NAVVGVGNGVAV-EKSLDDAQAYMQSQGDEITsALNEAVSAMQEVQSYTQELADAIQQEYRQRQ 139
                                       666555544333.333444444444433333354444444445555555555555554444333 PP

>> KNOX2  KNOX2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.3      0.16        98      31      47 ..      10      26 ..       3      50 .. 0.74
   2 ?    6.5   0.0    0.0099       5.9      24      45 ..     104     125 ..      97     131 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.16
                             KNOX2 31 eEAteFlreieqqLqsL 47
                                      + A+ +l +  +qL++L
  gi|474935115|ref|YP_007688697.1| 10 RQAARALDSYNKQLETL 26
                                      56777777777777766 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0099
                             KNOX2  24 eeLtrpveEAteFlreieqqLq 45 
                                       +e t  ++EA+++++e+++  q
  gi|474935115|ref|YP_007688697.1| 104 DEITSALNEAVSAMQEVQSYTQ 125
                                       689999**********998655 PP

>> Retrotrans_gag  Retrotransposon gag protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00053      0.32      55      91 ..       8      45 ..       4      52 .. 0.79
   2 ?   -0.2   0.2         2   1.2e+03      61      70 ..     118     127 ..      90     141 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00053
                    Retrotrans_gag 55 slrQgtesvreYvtrfktladqlde.vlteeakiekfl 91
                                      +lrQ  + ++ Y ++++tl +q++  + t +++ ++f+
  gi|474935115|ref|YP_007688697.1|  8 ELRQAARALDSYNKQLETLSRQVKLlQATRDEAARAFR 45
                                      79**********************99555555555543 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2
                    Retrotrans_gag  61 esvreYvtrf 70 
                                       + v+ Y++++
  gi|474935115|ref|YP_007688697.1| 118 QEVQSYTQEL 127
                                       2233333332 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1       0.2   1.2e+02      32      62 ..      18      48 ..       5      59 .. 0.68
   2 ?    8.5   0.7    0.0035       2.1      22      75 ..      88     141 ..      84     144 .] 0.73

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.2
                                      CCCHHHCCCCCCCCCCCCHHHHHHHHHHHHH CS
                         Fib_alpha 32 dvkkdlekleneleeisnstkeaeelvkeik 62
                                      +++k+le+l ++++ ++ +  ea +  ++++
  gi|474935115|ref|YP_007688697.1| 18 SYNKQLETLSRQVKLLQATRDEAARAFRALS 48
                                      4567777777777777777777766666655 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0035
                                       HHHCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  22 lqdlllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn 75 
                                       +++ l++ +  ++ + +++++ l+e+ +  +e++++++e+ d ++++ ++ + n
  gi|474935115|ref|YP_007688697.1|  88 VEKSLDDAQAYMQSQGDEITSALNEAVSAMQEVQSYTQELADAIQQEYRQRQAN 141
                                       566777777777778888888888888888888888888888877777776654 PP

>> DUF1974  Domain of unknown function (DUF1974)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.7     0.027        16     178     228 ..       5      55 ..       2      79 .. 0.90
   2 ?    7.4   0.4    0.0048       2.9     201     242 ..      95     136 ..      82     143 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.027
                           DUF1974 178 sDklkhevaelllepseardrLtagvylpedeedplgrlekafkavlaaep 228
                                       +D+  ++ a++l + +++ + L ++v l +  +d+ +r  +a++a+ +a++
  gi|474935115|ref|YP_007688697.1|   5 NDEELRQAARALDSYNKQLETLSRQVKLLQATRDEAARAFRALSALKDAKE 55 
                                       68888999******************************9999999998876 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0048
                           DUF1974 201 agvylpedeedplgrlekafkavlaaeplekklkkaikkgkl 242
                                       a+ y++++ ++ + +l++a +a++++++  + l +ai+++  
  gi|474935115|ref|YP_007688697.1|  95 AQAYMQSQGDEITSALNEAVSAMQEVQSYTQELADAIQQEYR 136
                                       378999999999************************998744 PP

>> Mod_r  Modifier of rudimentary (Mod(r)) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0  11.1    0.0047       2.8       3      91 ..       4     135 ..       3     141 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0047
                             Mod_r   3 lSkeeLqelledeeklealvktl.pevkqlkeekeellaenesla................................ 46 
                                       l  eeL++     + +++ ++tl  +vk l++ ++e+  + ++l                                 
  gi|474935115|ref|YP_007688697.1|   4 LNDEELRQAARALDSYNKQLETLsRQVKLLQATRDEAARAFRALSalkdakegdeimvpvgastyitvkvtgknavv 80 
                                       667899999999999999999998889999999999999999999******************************** PP

                             Mod_r  47 ........eknlsl.epeleelrselqekleelkelekefeekeqeldell.qkf 91 
                                               ek l++ +  ++ + +e++++l+e+ ++++e++ ++qel +++ q++
  gi|474935115|ref|YP_007688697.1|  81 gvgngvavEKSLDDaQAYMQSQGDEITSALNEAVSAMQEVQSYTQELADAIqQEY 135
                                       ********999999899******************************88773555 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.9    0.0056       3.3      35      82 ..       6      53 ..       2      61 .. 0.86
   2 ?    4.7   0.6     0.056        34      43      90 ..      90     134 ..      85     141 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0056
                                      HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHH CS
                      Seryl_tRNA_N 35 dekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkee 82
                                      de+ r++  +l++ +++  +ls++++ + +  ++a++     ++lk+ 
  gi|474935115|ref|YP_007688697.1|  6 DEELRQAARALDSYNKQLETLSRQVKLLQATRDEAARAFRALSALKDA 53
                                      89999*********************9999998888888888888875 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.056
                                       HHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  43 veleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleael 90 
                                       + l+++qa   + + eI +a +   +a + ++ev++  +el+++ +++
  gi|474935115|ref|YP_007688697.1|  90 KSLDDAQAYMQSQGDEITSALN---EAVSAMQEVQSYTQELADAIQQE 134
                                       5556666666666666666664...45666777777777776665544 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.3     0.092        55      76     116 ..       7      47 ..       2      61 .. 0.62
   2 ?    7.3   0.5    0.0082       4.9      67     108 ..      99     140 ..      84     143 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.092
                              COG2  76 splaaarkkvesvreklsereeeveskleeakeleekrell 116
                                        +l +a + ++s +++l+  +++v+   + + e++++ + l
  gi|474935115|ref|YP_007688697.1|   7 EELRQAARALDSYNKQLETLSRQVKLLQATRDEAARAFRAL 47 
                                       45666666667777777777777665555555555544444 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0082
                              COG2  67 lqeeleevesplaaarkkvesvreklsereeeveskleeake 108
                                       +q++ +e++s l++a++ +++v++  +e   +++++ +++++
  gi|474935115|ref|YP_007688697.1|  99 MQSQGDEITSALNEAVSAMQEVQSYTQELADAIQQEYRQRQA 140
                                       778888888888888888888888888888888888888765 PP

>> PEP-utilisers_N  PEP-utilising enzyme, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   1.8     0.035        21      30      66 ..       6      47 ..       2      59 .. 0.75
   2 ?    7.5   0.6    0.0072       4.3       2      54 ..      75     131 ..      74     141 .. 0.55

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.035
                                      HHHHHHHHHHHHHHHHHHHHHHHHH.....T-HHHHHHHHHH CS
                   PEP-utilisers_N 30 eaelerleeAlekvreelealaeka.....lgeeeaaifeah 66
                                      ++el++  +Al+   ++le+l++++       +e+a  f+a 
  gi|474935115|ref|YP_007688697.1|  6 DEELRQAARALDSYNKQLETLSRQVkllqaTRDEAARAFRAL 47
                                      6899999*************9988888653333345566654 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0072
                                       -EEEE-SEEEEEEE.....---.-----G.GGHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   PEP-utilisers_N   2 GiaaspGiaiGkav.....eveveeeeveaedveaelerleeAlekvreelealaeka 54 
                                       G+ a+ G++ G av     + ++   + + +++ + l+   +A+++v++  ++la+ +
  gi|474935115|ref|YP_007688697.1|  75 GKNAVVGVGNGVAVeksldD-AQAYMQSQGDEITSALNEAVSAMQEVQSYTQELADAI 131
                                       78888888888888655431.2223333344455555555555555555556555444 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5  12.7     0.039        23      11      90 ..       2     137 ..       1     142 [. 0.78

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.039
                            APG6_N  11 leeldkqleqaekerdaYeeflkklkkekkeeek........................................... 44 
                                       le  d++l+qa +  d+Y++ l++l ++ k  ++                                           
  gi|474935115|ref|YP_007688697.1|   2 LELNDEELRQAARALDSYNKQLETLSRQVKLLQAtrdeaarafralsalkdakegdeimvpvgastyitvkvtgkna 78 
                                       77789999*****************9997766558999999999999999999999999999999999999999999 PP

                            APG6_N  45 .............qdeeleeleeeleklekeeeelleeLkelekereeleaelaaleee 90 
                                                     d+  +  + + +++ ++ +e+++ ++e+++  +el++++++  ++
  gi|474935115|ref|YP_007688697.1|  79 vvgvgngvaveksLDDAQAYMQSQGDEITSALNEAVSAMQEVQSYTQELADAIQQEYRQ 137
                                       99999999966665555555666666677777777777777777777777777666555 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   2.5   0.00071      0.42     471     516 ..       3      48 ..       1      60 [. 0.87
   2 ?    3.1   1.3     0.022        13     608     648 ..      92     132 ..      83     143 .. 0.38

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00071
                           DUF3584 471 eeadealekaqeelekaeaevealqaeeeqlrkkrdeadealqkae 516
                                       e +de+l++a ++l + +++ e l ++ + l++ rdea +a++  +
  gi|474935115|ref|YP_007688697.1|   3 ELNDEELRQAARALDSYNKQLETLSRQVKLLQATRDEAARAFRALS 48 
                                       789************************************9997654 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.022
                           DUF3584 608 lqaleealqsaeakqkqaeeelkqlnaeleeakravaeaat 648
                                       l+ ++  +qs+ +++++a +e++++ +e++   +++a+a++
  gi|474935115|ref|YP_007688697.1|  92 LDDAQAYMQSQGDEITSALNEAVSAMQEVQSYTQELADAIQ 132
                                       33333333333333333333333333333333333333322 PP

>> HR1  Hr1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   2.9     0.029        17      34      65 ..       6      37 ..       1      41 [. 0.69
   2 ?    7.5   1.6    0.0075       4.5      36      67 ..     109     141 ..      88     142 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.029
                               HR1 34 kkvrqeaeselsesnskielLreqLeelqasv 65
                                       + +++a+  l++ n+ +e L +q + lqa +
  gi|474935115|ref|YP_007688697.1|  6 DEELRQAARALDSYNKQLETLSRQVKLLQATR 37
                                      44567777778888888888888877777755 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0075
                               HR1  36 vrqeaeselsesnskielLreqL.eelqasvqn 67 
                                       +++ea s ++e +s  ++L +++ +e+++++ n
  gi|474935115|ref|YP_007688697.1| 109 ALNEAVSAMQEVQSYTQELADAIqQEYRQRQAN 141
                                       899********************9999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1924  (0.107312); expected 358.6 (0.02)
Passed bias filter:                      859  (0.0479112); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                        31  (0.00172904); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 880.69
//
Query:       gi|474935116|ref|YP_007688698.1|  [L=374]
Description: signal recognition particle-docking protein FtsY [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.7e-75  251.0   3.2    8.9e-75  250.6   3.2    1.2  1  SRP54            SRP54-type protein, GTPase domain
    3.7e-12   46.3   1.3    1.2e-10   41.5   0.4    2.8  2  SRP54_N          SRP54-type protein, helical bundle domain
    5.3e-08   32.8   1.5    8.7e-08   32.1   1.5    1.2  1  AAA_30           AAA domain
    5.9e-06   26.7   1.4    6.5e-05   23.4   0.2    2.2  2  AAA_17           AAA domain
    8.6e-05   21.9   0.0    0.00013   21.3   0.0    1.3  1  Zeta_toxin       Zeta toxin
    0.00044   19.3   0.7     0.0015   17.5   0.5    2.0  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
     0.0006   19.4   5.0     0.0016   18.1   5.0    1.6  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
    0.00091   19.5   0.1     0.0025   18.1   0.0    1.8  1  AAA_22           AAA domain
    0.00093   19.1   0.0     0.0022   17.9   0.0    1.6  1  APS_kinase       Adenylylsulphate kinase
     0.0012   18.3   0.4     0.0058   16.1   0.2    2.0  2  KdpD             Osmosensitive K+ channel His kinase sensor d
     0.0016   18.4   2.2       0.23   11.4   2.2    2.4  1  NTPase_1         NTPase
     0.0019   17.5   0.1     0.0028   17.0   0.1    1.2  1  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.002   17.4   0.1     0.0028   16.9   0.1    1.2  1  PIF1             PIF1-like helicase
     0.0025   17.5   0.1      0.006   16.3   0.1    1.6  1  Thymidylate_kin  Thymidylate kinase
      0.006   16.8   0.0      0.012   15.8   0.0    1.5  1  AAA_33           AAA domain
     0.0074   16.7   0.0      0.018   15.4   0.0    1.7  1  AAA_16           AAA ATPase domain
      0.009   16.4   0.6      0.024   15.0   0.6    1.8  1  AAA              ATPase family associated with various cellul
     0.0093   16.0   1.1      0.028   14.5   1.1    1.9  1  MMR_HSR1         50S ribosome-binding GTPase
  ------ inclusion threshold ------
      0.013   15.5   0.7      0.036   14.1   0.7    1.8  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
      0.018   15.6   0.2      0.082   13.4   0.1    2.0  2  ABC_tran         ABC transporter
      0.037   13.7   0.0       0.06   13.1   0.0    1.3  1  AAA_24           AAA domain
      0.043   13.8   0.3       0.26   11.3   0.3    2.1  1  ResIII           Type III restriction enzyme, res subunit
      0.048   12.8   0.0       0.39    9.8   0.0    2.1  2  NB-ARC           NB-ARC domain
      0.058   12.9   0.0       0.12   11.9   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
      0.062   13.2   1.3       0.25   11.2   1.3    2.1  1  MobB             Molybdopterin guanine dinucleotide synthesis
      0.065   12.4   1.5       0.13   11.4   0.5    1.9  2  ArsA_ATPase      Anion-transporting ATPase
      0.068   13.1   0.4        4.7    7.1   0.0    2.8  3  RsgA_GTPase      RsgA GTPase
      0.076   12.8   0.2         10    5.8   0.0    2.2  2  CLP1_P           mRNA cleavage and polyadenylation factor CLP
      0.082   12.9   0.0       0.19   11.8   0.0    1.6  1  AAA_14           AAA domain
      0.086   12.6   0.0       0.13   12.0   0.0    1.4  1  DUF2855          Protein of unknown function (DUF2855)
       0.11   12.2   0.1       0.22   11.2   0.1    1.5  1  DUF4073          Domain of unknown function (DUF4073)
       0.13   12.6   0.9       0.27   11.6   0.9    1.5  1  AAA_19           AAA domain


Domain annotation for each model (and alignments):
>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  250.6   3.2   1.6e-77   8.9e-75       1     195 [.     178     372 ..     178     373 .. 0.99

  Alignments for each domain:
  == domain 1  score: 250.6 bits;  conditional E-value: 1.6e-77
                                       SEEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHH CS
                             SRP54   1 pnvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeave 77 
                                       p vi++vG++G+GKTt++aK+ ++lk++gk+v+l+a+DtfRa+A+eQL ++ eklg++++k++++adpa+va++ave
  gi|474935116|ref|YP_007688698.1| 178 PAVIMFVGINGTGKTTAIAKIGNRLKNQGKSVVLAACDTFRAGAIEQLTIHSEKLGIKIVKSQQDADPASVAYDAVE 254
                                       579************************************************************************** PP

                                       HHHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSS CS
                             SRP54  78 kakeekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgda 154
                                       +a+++  dvvl+DTaGr+q++++l++e+kki kv+kpd +++v d+++g++a++qak F++a+gi+++iltk+D+da
  gi|474935116|ref|YP_007688698.1| 255 HARSKMRDVVLIDTAGRMQTNNNLIAEMKKITKVCKPDLKIFVGDSLAGNDAIEQAKVFDDAIGIDAIILTKIDTDA 331
                                       ***************************************************************************** PP

                                       STTHHHHHHHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHH CS
                             SRP54 155 kgGaalsiaaelklPikfigvGekiedleefdperlvsrll 195
                                       kgGaalsia+ +++Pi+f+  G+++ed+e+fd++++++rl+
  gi|474935116|ref|YP_007688698.1| 332 KGGAALSIAKTIGKPIAFVCDGQEYEDIEKFDADWMLNRLF 372
                                       ***************************************97 PP

>> SRP54_N  SRP54-type protein, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.28   1.6e+02       1      22 [.       5      23 ..       5      31 .. 0.83
   2 !   41.5   0.4   2.1e-13   1.2e-10      15      71 ..      94     149 ..      85     156 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.28
                                      HHHHHHHHHHHHCCSSCGHHHH CS
                           SRP54_N  1 Lgkklnsalkklsgkskideed 22
                                      L++kl++++kk   ++k+de  
  gi|474935116|ref|YP_007688698.1|  5 LKSKLKGIFKK---GEKLDEGS 23
                                      689*******9...99***976 PP

  == domain 2  score: 41.5 bits;  conditional E-value: 2.1e-13
                                       SSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTSS-HHHHHHHHH CS
                           SRP54_N  15 kskideedleealkeleeaLleaDVgvkvvkklienvkkkavgekklkpkqqvkkiv 71 
                                       ++ki+++ l+++l+ele +Lle+DV+++vv+++i  v+++  g kk ++  ++++iv
  gi|474935116|ref|YP_007688698.1|  94 SKKIKDDPLDDILDELEVTLLESDVAYDVVQEIILGVRNNLSG-KKYSREYSLEQIV 149
                                       579************************************8888.8877777776666 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   1.5   1.6e-10   8.7e-08      19     154 ..     179     327 ..     172     340 .. 0.74

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 1.6e-10
                            AAA_30  19 rvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastia.kllkrlk............g 82 
                                        v + +G  GtGKtta++++ + ++++g++v+++A     A +++ +l i+++ +  k++k+++            +
  gi|474935116|ref|YP_007688698.1| 179 AVIMFVGINGTGKTTAIAKIGNRLKNQGKSVVLAACDTFRAGAIE-QLTIHSEKLGiKIVKSQQdadpasvaydavE 254
                                       578899*******************************99999999.4455554443133333335556667778886 PP

                            AAA_30  83 rarlepgtllivDEagmvdtk.....qlaallkaaekagakvilvGDe.rQlasVeaGgvlrdlveaagigtaeLte 153
                                       +ar + ++++++D ag + t+     ++++++k ++  +   i+vGD  +  +++e+ +v++d +   gi+++ Lt+
  gi|474935116|ref|YP_007688698.1| 255 HARSKMRDVVLIDTAGRMQTNnnliaEMKKITKVCKP-DL-KIFVGDSlAGNDAIEQAKVFDDAI---GIDAIILTK 326
                                       6888899*********996541111145555555555.44.4799**856799********9996...577777766 PP

                            AAA_30 154 v 154
                                       +
  gi|474935116|ref|YP_007688698.1| 327 I 327
                                       5 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.41   2.3e+02      54      99 ..      67     112 ..      44     144 .. 0.63
   2 !   23.4   0.2   1.2e-07   6.5e-05       1     108 [.     184     297 ..     184     302 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.41
                                       HHHHHHHHHHHHHHHHHSSEEEEEE-SEEEETTEEEESSHHHHHHH CS
                            AAA_17  54 kkelqkeaaekiaeeakkkgvlvdghprikeqagfldglpkevlee 99 
                                       kke ++ a+++   e++++++l +g+ + k +++ ld++ +e + +
  gi|474935116|ref|YP_007688698.1|  67 KKERMAAAKARHSGEKRSSDMLSEGFLSKKIKDDPLDDILDELEVT 112
                                       222233344444444578899******9888888777776655433 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 1.2e-07
                                       EE-TTSSHHHHHHHHHHHH....TEEEEEHHHHHHHHHHTT.TSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHH..H CS
                            AAA_17   1 lGgPGsGKgtqceklveky....gfthlsaGdllreeakrg.glakardemrklpleekkelqkeaaekiaeea..k 70 
                                       +G+ G GK+t+++k+  ++    +  +l a d +r+ a ++    +++  ++ ++ +++ +    a +++++++   
  gi|474935116|ref|YP_007688698.1| 184 VGINGTGKTTAIAKIGNRLknqgKSVVLAACDTFRAGAIEQlTIHSEKLGIKIVKSQQDADPASVAYDAVEHARskM 260
                                       79*************888876668999********998777345555556667788888888888888887776335 PP

                                       SSEEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEE CS
                            AAA_17  71 kkgvlvdghprikeqagfldglpkevleelkpdaiill 108
                                       ++ vl+d+  r+++++ ++++++k + +  kpd+ i++
  gi|474935116|ref|YP_007688698.1| 261 RDVVLIDTAGRMQTNNNLIAEMKK-ITKVCKPDLKIFV 297
                                       5679***************99996.7788899988776 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   2.4e-07   0.00013      11      56 ..     173     219 ..     164     285 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.4e-07
                        Zeta_toxin  11 psqerPklillgGqpGAGKselaellkdelerqgnvvrldp.DdlRe 56 
                                        +q+rP++i+ +G  G GK+++++++ ++l++qg+ v+l + D++R+
  gi|474935116|ref|YP_007688698.1| 173 EEQSRPAVIMFVGINGTGKTTAIAKIGNRLKNQGKSVVLAAcDTFRA 219
                                       5789***************************7777777764488886 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.5   2.7e-06    0.0015      24      76 ..     173     222 ..     167     306 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.7e-06
                                       GG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE----------- CS
                              MeaB  24 akaGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavDPsspftGGsi 76 
                                       ++  r  v+ + G+ G+Gk t++ ++g +l+++Gk v + a D   +f  G+i
  gi|474935116|ref|YP_007688698.1| 173 EEQSRPAVIMFVGINGTGKTTAIAKIGNRLKNQGKSVVLAACD---TFRAGAI 222
                                       5667889999***************************999988...4555555 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   5.0   2.8e-06    0.0016       2     153 ..     180     330 ..     179     345 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.8e-06
                                       EEEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS.-SSCHCCCCCCHCC..CT.EEEETTTTECCHCTT-HHHHH CS
                              cobW   2 vtvltGflGsGKTtLlnhll..enraglklavivNe.fgevsiDaellret..gveivelenGciCctlredllkel 73 
                                       v++++G  G+GKTt + ++    +++g+++ +   + f   +i++  ++++  g +iv+ ++   + +++ d+++++
  gi|474935116|ref|YP_007688698.1| 180 VIMFVGINGTGKTTAIAKIGnrLKNQGKSVVLAACDtFRAGAIEQLTIHSEklGIKIVKSQQDADPASVAYDAVEHA 256
                                       78899**************9764555555555555514556788888877745666888777777777776666655 PP

                                       HHHHHHHTT-SEEEEEECT.TTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE- CS
                              cobW  74 ealeereerldviliEttG.laePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnK 149
                                       ++     +  dv+li t G + + + ++ + +++++ ++ d +++v D+ +  ++  ++++ ++d +   d ++l+K
  gi|474935116|ref|YP_007688698.1| 257 RS-----KMRDVVLIDTAGrMQTNNNLIAEMKKITKVCKPDLKIFVGDSLAG-NDAIEQAKVFDDAI-GIDAIILTK 326
                                       43.....34589*******65555666888*******************554.55555555666655.56******* PP

                                       HHHH CS
                              cobW 150 tDll 153
                                       +D+ 
  gi|474935116|ref|YP_007688698.1| 327 IDTD 330
                                       **85 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   4.5e-06    0.0025       5     117 ..     178     287 ..     173     300 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 4.5e-06
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst....sskdllrellralglelkaerlssee 77 
                                         +++ +G  GtGKTt ++++ ++l+++      +++vv+  +        ++ ++     ++lg +  +  ++  +
  gi|474935116|ref|YP_007688698.1| 178 PAVIMFVGINGTGKTTAIAKIGNRLKNQ------GKSVVLAACDTFRagaiEQLTI---HSEKLGIKIVK-SQQDAD 244
                                       568999*******************887......9999966666666534444444...23333333333.344444 PP

                            AAA_22  78 llealeqalrarav..ielliiDEaqhlr.seealeeLrslln 117
                                         +  ++a+++++   + +++iD a ++  +++++ e +++ +
  gi|474935116|ref|YP_007688698.1| 245 PASVAYDAVEHARSkmRDVVLIDTAGRMQtNNNLIAEMKKITK 287
                                       444444444444444458*****99999544777777776665 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0     4e-06    0.0022       1      54 [.     177     230 ..     177     239 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 4e-06
                                       S-EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT--SSHH CS
                        APS_kinase   1 rgvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLgfsee 54 
                                       r++v+++ G+ g+GK+t   ++ ++L+++g+sv+l   d+ R g  ++L+ ++e
  gi|474935116|ref|YP_007688698.1| 177 RPAVIMFVGINGTGKTTAIAKIGNRLKNQGKSVVLAACDTFRAGAIEQLTIHSE 230
                                       589*****************************************9999998766 PP

>> KdpD  Osmosensitive K+ channel His kinase sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.77   4.3e+02      51      86 ..     144     181 ..     120     186 .. 0.71
   2 !   16.1   0.2     1e-05    0.0058       8      95 ..     183     273 ..     178     290 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.77
                              KdpD  51 llegleviprkeveykgkeleeldldailar..kpevv 86 
                                        le++  +  +e  ++  +++e+d da l++  +p+v+
  gi|474935116|ref|YP_007688698.1| 144 SLEQIVEFAVREAVSDVLQVNEFDFDAWLEEqsRPAVI 181
                                       45555556667777788899999999999851156665 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1e-05
                              KdpD   8 flGaapGvGktyamLeeaqelkeegvdvviglvethgrketeallegleviprkeveykg.keleeldldai...la 80 
                                       f+G ++G Gkt a+ + +++lk++g+ vv+++ +t +   +e+l+ + e +  k v++++ +    + +da+    +
  gi|474935116|ref|YP_007688698.1| 183 FVG-INGTGKTTAIAKIGNRLKNQGKSVVLAACDTFRAGAIEQLTIHSEKLGIKIVKSQQdADPASVAYDAVehaRS 258
                                       444.68*************************************9988887776666654413344555555510045 PP

                              KdpD  81 rkpevvlvDelahtn 95 
                                       +  +vvl+D  +  +
  gi|474935116|ref|YP_007688698.1| 259 KMRDVVLIDTAGRMQ 273
                                       667899999877654 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   2.2   0.00041      0.23       3      41 ..     182     220 ..     180     311 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00041
                                       EEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE--- CS
                          NTPase_1   3 fiTGppGvGKtTlvkkvlellkssgvkvgGfyteevreg 41 
                                       +  G  G+GKtT + k+ + lk++g +v    +   r g
  gi|474935116|ref|YP_007688698.1| 182 MFVGINGTGKTTAIAKIGNRLKNQGKSVVLAACDTFRAG 220
                                       556889*******************99987777776655 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1     5e-06    0.0028       3     106 ..     180     278 ..     178     300 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5e-06
                           DUF2075   3 vvlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakkeekkkkkeafeklssfinnlsefkk 79 
                                       v++  G  GtGKt    ++ ++l   +++ ++v+l     +++   e+l+ ++  +k + ++ k+++   ++s  ++
  gi|474935116|ref|YP_007688698.1| 180 VIMFVGINGTGKTTAIAKIGNRL---KNQGKSVVLAACDTFRAGAIEQLTIHS--EKLGIKIVKSQQDADPASVAYD 251
                                       6667799****************...677777777788888888777777666..5555555555555555554466 PP

                           DUF2075  80 aeekkeepkedvvivDEAhrlltksdq 106
                                       a e++++++ dvv++D A r+ t+++ 
  gi|474935116|ref|YP_007688698.1| 252 AVEHARSKMRDVVLIDTAGRMQTNNNL 278
                                       99********************94443 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1     5e-06    0.0028      19     115 ..     175     273 ..     168     301 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5e-06
                                       .HCTS-EEEEESTTSSCHHHHHHHHHHCHCTCCCEEEEESSHHHHHCC.TSEECHH.HHT-TTSSS-HHHH..HHHT CS
                              PIF1  19 nekgklfFvtGsgGtgKtflwkallkklrsegkivlavAssGvAalllegGrtahs.rfkiplekdeestc..kikr 92 
                                       ++++ ++ + G  GtgKt    ++ + l+++gk v+  A     a  + +  t+hs + +i + k++++    +++ 
  gi|474935116|ref|YP_007688698.1| 175 QSRPAVIMFVGINGTGKTTAIAKIGNRLKNQGKSVVLAACDTFRAGAI-EQLTIHSeKLGIKIVKSQQDADpaSVAY 250
                                       57789999****************************************.5577777356777766555443337777 PP

                                       SCCCHHHHHC-SEEEEECGGGSB CS
                              PIF1  93 gsklaellkktsliiwDEapmve 115
                                       +  +  + k  +++++D a  ++
  gi|474935116|ref|YP_007688698.1| 251 DAVEHARSKMRDVVLIDTAGRMQ 273
                                       77777777788888888876554 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   1.1e-05     0.006       3      29 ..     185     211 ..     183     217 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.1e-05
                                       ESTTSSHHHHHHHHHHHHHHTTE.EEE CS
                   Thymidylate_kin   3 GlDGaGKttqaellkerlkeegikvvl 29 
                                       G++G+GKtt ++++ +rlk++g++vvl
  gi|474935116|ref|YP_007688698.1| 185 GINGTGKTTAIAKIGNRLKNQGKSVVL 211
                                       9*********************99776 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   2.1e-05     0.012       1      37 [.     180     222 ..     180     290 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.1e-05
                            AAA_33   1 lvllvGlpGsGKstlaerl...lkklg..avllssdtlrr.rl 37 
                                       ++++vG +G+GK+t + ++   lk++g  +vl + dt+r  ++
  gi|474935116|ref|YP_007688698.1| 180 VIMFVGINGTGKTTAIAKIgnrLKNQGksVVLAACDTFRAgAI 222
                                       89***************99444544448555556677665333 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   3.2e-05     0.018      21      76 ..     175     222 ..     168     306 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.2e-05
                            AAA_16  21 sgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqal 76 
                                       ++rp +++++G  G+GK++ + ++ ++l+ +g  ++ + cd ++++        a+
  gi|474935116|ref|YP_007688698.1| 175 QSRPAVIMFVGINGTGKTTAIAKIGNRLKNQGKSVVLAACDTFRAG--------AI 222
                                       5788999************************999999999999222........22 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.6   4.3e-05     0.024       1      74 [.     181     276 ..     181     300 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.3e-05
                                       EEEESSTTSSHHHHHHHHHHHHT...HEEEEEETTTCSSS................STTHHHHHHHHHHHHHHHTS. CS
                               AAA   1 vllyGppGtGKTllakavakelg...vefleisgsellsk................yvgesekkirelfkeakeka. 57 
                                       ++++G  GtGKT+++  + + l+    +++   + +++                  + +++ ++ + +  +a e+a 
  gi|474935116|ref|YP_007688698.1| 181 IMFVGINGTGKTTAIAKIGNRLKnqgKSVVLAACDTFRAGaieqltihseklgikiVKSQQDADPASVAYDAVEHAr 257
                                       589******************96333333333333333224555444444444443222333333333333333334 PP

                                       .TS.EEEEEETGGGHHHHH CS
                               AAA  58 .kp.silfiDEidalaksr 74 
                                        k   +++iD + ++ +++
  gi|474935116|ref|YP_007688698.1| 258 sKMrDVVLIDTAGRMQTNN 276
                                       4333777777777664444 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   1.1   5.1e-05     0.028       2      87 ..     181     304 ..     180     327 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.1e-05
                                       EEEEESTTSSHHHHHHHHHT..............STEEESSSTTSSSSEEEEEEEETTEE................. CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltg..............ekaivsdkpgtTrdinegrvklkgke................. 47 
                                       +++vG   +GK+t i ++ +              ++ +++++ + T++ ++  +k+ +++                 
  gi|474935116|ref|YP_007688698.1| 181 IMFVGINGTGKTTAIAKIGNrlknqgksvvlaacDTFRAGAIEQLTIHSEKLGIKIVKSQqdadpasvaydavehar 257
                                       799************99987666777777776444778888888888887777773332235666777777777777 PP

                                       .....EEEEECGGCSSHHHHHHHHHHHHHHHHC.T..SEEEEEEETT..T CS
                          MMR_HSR1  48 .....ielvDtpGliegaseekglgkaflalee.a..dlillvvdas..e 87 
                                            ++l+Dt+G ++   ++++l  +++++ + +  dl ++v d+   +
  gi|474935116|ref|YP_007688698.1| 258 skmrdVVLIDTAGRMQ---TNNNLIAEMKKITKvCkpDLKIFVGDSLagN 304
                                       77777********554...4555555555544432339999999943432 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.7   6.4e-05     0.036       9      38 ..     188     217 ..     181     348 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.4e-05
                                       TSSHHHHHHHHHHHHHHTT--EEEEEEEES CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpq 38 
                                       G+GKTt  a+++  l+++g+ V+l  +D+ 
  gi|474935116|ref|YP_007688698.1| 188 GTGKTTAIAKIGNRLKNQGKSVVLAACDTF 217
                                       9**************************986 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       2.4   1.4e+03      66      94 ..      51     111 ..       6     136 .. 0.45
   2 ?   13.4   0.1   0.00015     0.082      13      71 ..     180     244 ..     174     295 .. 0.64

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 2.4
                                       SS.--S-TTSBHHHH...............................HHHTCHHHHHHHSTT CS
                                       xx.xxxxxxxxxxxx...............................xxxxxxxxxxxxxxx RF
                          ABC_tran  66 qe.pqlfpeltvren...............................esdeeiekalsklgl 94 
                                       +e p  +p+ + ++                                 +d+ ++++l++l+ 
  gi|474935116|ref|YP_007688698.1|  51 EEsPAEQPREEPKKLskkermaaakarhsgekrssdmlsegflskkIKDDPLDDILDELEV 111
                                       3322222222222222222222222233333334444444444443334445555555555 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00015
                                       EEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG........B-HHHCCHCEEEE-SS--S- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  13 kvaivGenGaGKStLlkllagllkpteGeilldgkdlke........qeleslrkeigvlpqepqlf 71 
                                       ++ +vG nG+GK+t ++ + + lk++  ++ l   d+ +        +  e+l  +i   +q+   +
  gi|474935116|ref|YP_007688698.1| 180 VIMFVGINGTGKTTAIAKIGNRLKNQGKSVVLAACDTFRagaieqltIHSEKLGIKIVKSQQD--AD 244
                                       7899******************99988888555444333344443333334444444444444..33 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00011      0.06       3      77 ..     179     272 ..     177     291 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                            AAA_24   3 lkiliyGpsgiGKTtlakel.......gpkplfidtek.Glksldadkfpdie.swedfldevvel..........a 60 
                                       + i+ +G +g+GKTt ++++       g+++++  ++   + +++   + + + +++ ++++ +++           
  gi|474935116|ref|YP_007688698.1| 179 AVIMFVGINGTGKTTAIAKIgnrlknqGKSVVLAACDTfRAGAIEQLTIHSEKlGIKIVKSQQDADpasvaydaveH 255
                                       78999***************999999777777766666445556666655444766666666666688888888887 PP

                            AAA_24  61 aeladyktlviDtidel 77 
                                       a  +  +++ iDt++ +
  gi|474935116|ref|YP_007688698.1| 256 ARSKMRDVVLIDTAGRM 272
                                       77788899999999877 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3   0.00047      0.26      22      70 ..     176     221 ..     138     298 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00047
                                       .TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHH CS
                            ResIII  22 krdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqt 70 
                                        r   ++++   GtGKT  +ak+  rl+++gk    ++l+   +    +
  gi|474935116|ref|YP_007688698.1| 176 SRPAVIMFVGINGTGKTTAIAKIGNRLKNQGK---SVVLAACDTFRAGA 221
                                       46667889999*****************9865...56666555555555 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.56   3.1e+02     151     172 ..     106     127 ..      94     152 .. 0.72
   2 ?    9.8   0.0    0.0007      0.39      11      45 ..     171     203 ..     167     217 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.56
                                       EEEEEESS--HHHHHHHHHHCC CS
                            NB-ARC 151 sekievelLekdeawellenkv 172
                                        + +ev+lLe d a+++++++ 
  gi|474935116|ref|YP_007688698.1| 106 LDELEVTLLESDVAYDVVQEII 127
                                       567899**********999874 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0007
                                       HHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCSHC CS
                            NB-ARC  11 kLlekdelqslvvalvGmgGvGKttlakqilnksd 45 
                                       +L e+  +   v+ +vG  G GKtt +++i n ++
  gi|474935116|ref|YP_007688698.1| 171 WLEEQSRPA--VIMFVGINGTGKTTAIAKIGNRLK 203
                                       677666677..999***************998755 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00021      0.12      36      62 ..     181     207 ..     166     229 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00021
                             AAA_7  36 vllvGptGtGKtviikdllkkldkeky 62 
                                       +++vG  GtGKt+ i ++ ++l+++  
  gi|474935116|ref|YP_007688698.1| 181 IMFVGINGTGKTTAIAKIGNRLKNQGK 207
                                       89****************999995544 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.3   0.00044      0.25       1      30 [.     180     209 ..     180     285 .. 0.96

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00044
                              MobB   1 vlgivgksgsGKTtLleklipelkarglrv 30 
                                       v+ +vg +g+GKTt + k+ + lk++g +v
  gi|474935116|ref|YP_007688698.1| 180 VIMFVGINGTGKTTAIAKIGNRLKNQGKSV 209
                                       689***********************9887 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.5   0.00023      0.13       3      38 ..     180     215 ..     178     221 .. 0.94
   2 ?   -1.0   0.0       1.4     8e+02     117     134 ..     253     270 ..     217     306 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00023
                                       EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                       ArsA_ATPase   3 vilvgGKGGVGKttvsaatavklsekgkkvllistD 38 
                                       vi++ G  G GKtt+ a ++ +l ++gk+v+l + D
  gi|474935116|ref|YP_007688698.1| 180 VIMFVGINGTGKTTAIAKIGNRLKNQGKSVVLAACD 215
                                       79*****************************98877 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.4
                                       HHHHHCSSSSEEEEESBS CS
                       ArsA_ATPase 117 lkyvkeeeydvvvlDtaP 134
                                       +++ +++  dvv++Dta 
  gi|474935116|ref|YP_007688698.1| 253 VEHARSKMRDVVLIDTAG 270
                                       456677778999999883 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0    0.0083       4.7      93     126 ..     172     205 ..     144     214 .. 0.81
   2 ?    2.9   0.1      0.16        89      80     111 ..     272     303 ..     207     311 .. 0.58
   3 ?   -1.4   0.0       3.4   1.9e+03      50      82 ..     321     350 ..     306     366 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0083
                                       HHHHCTTSEEEEECSTTSSHHHHHHHHCTT---- CS
                       RsgA_GTPase  93 lkellkdktsvlvGqSGvGKStLinallpelelk 126
                                       l+e+ +  ++++vG  G GK+t i ++ ++l+ +
  gi|474935116|ref|YP_007688698.1| 172 LEEQSRPAVIMFVGINGTGKTTAIAKIGNRLKNQ 205
                                       677777899***************9998876655 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.16
                                       EE--TTTHTTHHHHHHHCTTSEEEEECSTTSS CS
                       RsgA_GTPase  80 llvsaktkegleelkellkdktsvlvGqSGvG 111
                                       + ++++  ++++++++++k ++ ++vG S +G
  gi|474935116|ref|YP_007688698.1| 272 MQTNNNLIAEMKKITKVCKPDLKIFVGDSLAG 303
                                       33444455789999999999999999999777 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 3.4
                                       EEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE- CS
                       RsgA_GTPase  50 vivlnKiDlleeeeeleelkeelealgyevllv 82 
                                        i+l+KiD   +     +  +  +++g ++ +v
  gi|474935116|ref|YP_007688698.1| 321 AIILTKIDTDAKGG---AALSIAKTIGKPIAFV 350
                                       58899999988777...6666666777666554 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.019        10       3      31 ..     187     215 ..     185     220 .. 0.90
   2 ?    4.8   0.0     0.038        21      95     148 ..     253     308 ..     243     323 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.019
                            CLP1_P   3 kdsGKSTlarlLlNyalrkgrkpvyvDlD 31 
                                       + +GK+T ++ + N++ ++g+++v+  +D
  gi|474935116|ref|YP_007688698.1| 187 NGTGKTTAIAKIGNRLKNQGKSVVLAACD 215
                                       689********************998888 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.038
                            CLP1_P  95 leenkkakasgliIntpGwvkglg..aellleliealepdvvvvldqeellnelkr 148
                                       +e  ++  +++++I+t G ++  +  +  +++++++ +pd+ ++++++   n+  +
  gi|474935116|ref|YP_007688698.1| 253 VEHARSKMRDVVLIDTAGRMQTNNnlIAEMKKITKVCKPDLKIFVGDSLAGNDAIE 308
                                       34445557889********9876523466788************998766666555 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00033      0.19       4     103 ..     180     303 ..     177     318 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00033
                            AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderd....................kkladpekllelilekl 60 
                                       +++ +G+  +GKTt + ++ ++l  + +s++  ++d+ r                     ++ adp+++     e++
  gi|474935116|ref|YP_007688698.1| 180 VIMFVGINGTGKTTAIAKIGNRLKNQGKSVVLAACDTFRAgaieqltihseklgikivksQQDADPASVAYDAVEHA 256
                                       67889**************9888899999*******99986655555555554444432222223323333333332 PP

                            AAA_14  61 keekktylflDEiqevpewekalkslvd....egknldvivtGSnsk 103
                                       +++ + ++++D + ++++  + + ++ +     +++l+++v  S+++
  gi|474935116|ref|YP_007688698.1| 257 RSKMRDVVLIDTAGRMQTNNNLIAEMKKitkvCKPDLKIFVGDSLAG 303
                                       22567778888776665555555444443223225667777666665 PP

>> DUF2855  Protein of unknown function (DUF2855)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00023      0.13     197     235 ..     246     288 ..     173     315 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00023
                           DUF2855 197 kvvsYddlesleaa.kkvvivDfagrdelleklhealkd...k 235
                                         v+Yd++e++++  + vv++D agr +++++l +++k+    
  gi|474935116|ref|YP_007688698.1| 246 ASVAYDAVEHARSKmRDVVLIDTAGRMQTNNNLIAEMKKitkV 288
                                       5789****988766599******************99985432 PP

>> DUF4073  Domain of unknown function (DUF4073)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1    0.0004      0.22      33     107 ..     182     254 ..     178     265 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0004
                           DUF4073  33 msagpdggekvapdgyafkqglrlkvygndvvvtaydykrdkvikkllirdskieq.lapdvtaddeknvlvnate 107
                                       m  g +g  k++      k g rlk  g+ vv+ a d  r   i +l+i+  k+   +    +  d   v  +a e
  gi|474935116|ref|YP_007688698.1| 182 MFVGINGTGKTTA---IAKIGNRLKNQGKSVVLAACDTFRAGAIEQLTIHSEKLGIkIVKSQQDADPASVAYDAVE 254
                                       5667777777764...4689*******************************9986403333333345555555555 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.9   0.00048      0.27       9      62 ..     177     229 ..     170     301 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00048
                            AAA_19   9 kekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrA..akelrerl 62 
                                       +  v++ ++  GtGKT+ + +i + l+++g+     +l+++ t rA   ++l+   
  gi|474935116|ref|YP_007688698.1| 177 RPAVIMFVGINGTGKTTAIAKIGNRLKNQGKS---VVLAACDTFRAgaIEQLTIHS 229
                                       55677888999***************999943...455665566651034444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       881  (0.0491383); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); expected 17.9 (0.001)
Passed Fwd filter:                        32  (0.00178482); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              32  [number of targets reported over threshold]
# CPU time: 0.69u 0.34s 00:00:01.03 Elapsed: 00:00:00.48
# Mc/sec: 2323.12
//
Query:       gi|474935117|ref|YP_007688699.1|  [L=408]
Description: acetylornithine deacetylase or succinyl-diaminopimelate desuccinylase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-28   98.9   0.0      4e-28   98.6   0.0    1.1  1  Peptidase_M20  Peptidase family M20/M25/M40
    1.1e-12   47.8   0.0    7.8e-12   45.1   0.0    2.1  2  M20_dimer      Peptidase dimerisation domain
    0.00012   21.8   0.0    0.00021   21.0   0.0    1.5  2  Peptidase_M28  Peptidase family M28


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.6   0.0   6.6e-32     4e-28       3     205 ..      89     400 ..      87     402 .. 0.87

  Alignments for each domain:
  == domain 1  score: 98.6 bits;  conditional E-value: 6.6e-32
                                       EEES-BSSTTCGGGSSS.TTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SS.EEEEEEESTTSSTT.T CS
                                       xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx.x RF
                     Peptidase_M20   3 gsHlDvVpeeetdgwtt.pfslteedGklyGrGaddmkggvlaalealralkdegikpkg.tivllfqpdEEggr.g 76 
                                        +H+D+Vp+++  +w+t pf++  +dGk+yGrG+ d+  +vl+ + a r +++    ++g +i ++ ++dEE ++  
  gi|474935117|ref|YP_007688699.1|  89 IAHIDTVPAGNLADWETdPFKGIYRDGKVYGRGTEDNGQSVLSSMFASRFFEKGT--LEGmSIGVAWVADEEMAShY 163
                                       69******999999*********************************97766654..5777***********8777* PP

                                       HHHHHHH.HHHTTTCESEEEEEEEESSSBTCHSTETEEEE..................................... CS
                                       xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................................... RF
                     Peptidase_M20  77 Gakalle.gleerekvdavfelhieepgileagklaigvv..................................... 115
                                       G  +l++ g+   + +d +f  ++ + g ++ gk  i v                                      
  gi|474935117|ref|YP_007688699.1| 164 GVCHLIDnGY---FSPDDIF--LVPDWGSPD-GK-YIEVNeksliwlqfdivgksvhastpdiginafrlgaaiidd 233
                                       *******543...4666666..355566666.44.4555577889999999999*********************** PP

                                       ...........................................................................EE CS
                                       ...........................................................................xx RF
                     Peptidase_M20 116 ...........................................................................kv 117
                                                                                                                  k+
  gi|474935117|ref|YP_007688699.1| 234 vivalnerfpmenpmflpakssfeptkadstvlnvntipgswsfcmdcrilpdykvedvlktaqdiasryeatgaKI 310
                                       *************************************************************************9878 PP

                                       EEEEE.EEESHEEEC.CHHHHHHHHHHHHHHHTSCEEEEEES.SSBHTHHHH..TTTEEEEE.EESSGGCTTSTTTE CS
                                       xxxxx.xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx..xxxxxxxx.xxxxxxxxxxxxxx RF
                     Peptidase_M20 118 evell.eggapvtln.dsplvkalaeaaeelfgekvelivsg.pggtdarff..agiptvmi.fgpgsglaHspnEy 188
                                       +v++l +++   +++ dsp++kal++++ee++g+++e +  g  g+t a+ff  +g  ++++  g  +g+ H+pnEy
  gi|474935117|ref|YP_007688699.1| 311 TVKELqRHESGGKSStDSPVFKALSDSVEEVLGHRPEAT--GvGGATCANFFrlKGYDAYVWeTG--GGTLHGPNEY 383
                                       88877766666666689**************9*555555..5559*******7666666655444..49******** PP

                                       EEHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 189 vdledlekgikvlarll 205
                                       v ++++ + +kv+a l 
  gi|474935117|ref|YP_007688699.1| 384 VPVQNIINDAKVFATLF 400
                                       *************9886 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   0.0   1.3e-15   7.8e-12       3     103 ..     197     302 ..     195     308 .. 0.93
   2 ?    0.9   0.0     0.072   4.3e+02       6      33 ..     305     333 ..     301     341 .. 0.85

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 1.3e-15
                                       B-EEEEEEEEEE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC.........TCCTCCCCCEECCE-C.CCCEESS CS
                         M20_dimer   3 hkGlaggkitvkgkagHsgapgagaNAieklarllaeledeegdia....eerslprttlnvtgiegGs.aknvipd 74 
                                       +k l++    + gk++H++ p+ g+NA+++ a ++++     ++      + + ++++++++t  ++   + n+ip+
  gi|474935117|ref|YP_007688699.1| 197 EKSLIWLQFDIVGKSVHASTPDIGINAFRLGAAIIDDVIVALNERFpmenPMFLPAKSSFEPTKADSTVlNVNTIPG 273
                                       7999*******************************99988877766888999***************99******** PP

                                       EEEEEEEEEHHHHHHHHHHHHHHHHHHTS CS
                         M20_dimer  75 eaeakidiRllpgedpeevleeieeilek 103
                                       + ++ +d+R+lp  ++e+vl++ ++i+++
  gi|474935117|ref|YP_007688699.1| 274 SWSFCMDCRILPDYKVEDVLKTAQDIASR 302
                                       ************************99986 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.072
                                       EEEEEEEEE-B-EEGG.-TTTTB-HHHHH CS
                         M20_dimer   6 laggkitvkgkagHsg.apgagaNAiekl 33 
                                       + g+kitvk  + H +  +   ++++ k+
  gi|474935117|ref|YP_007688699.1| 305 ATGAKITVKELQRHESgGKSSTDSPVFKA 333
                                       5799************9999999987654 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   3.6e-08   0.00021       1      82 [.      73     169 ..      73     272 .. 0.84
   2 ?   -3.4   0.0       1.1   6.4e+03     114     154 ..     294     332 ..     285     334 .. 0.63

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3.6e-08
                                       EEEEEESTTCESEEEEEEEE--B-TTT...............TCC.T---TTTTHHHHHHHHHHHHHCHHGGCCS.S CS
                     Peptidase_M28   1 NviatlegkatdevlllgAHyDsvgvg...............rgp.ifvGAdDnAsgvaalLelarvlaasgsrp.k 60 
                                       N++a+ +gk  + ++ + AH+D+v+ g               +g+    G  Dn+ +v + +  +r++++ g ++  
  gi|474935117|ref|YP_007688699.1|  73 NILAKKNGKR-SGTVWIIAHIDTVPAGnladwetdpfkgiyrDGKvYGRGTEDNGQSVLSSMFASRFFEK-G-TLeG 146
                                       8999999999.99********************9999999886666678********************8.5.4459 PP

                                       EEEEEEEESSCSG.SSHHHHHHH CS
                     Peptidase_M28  61 rgvrflffdaEEa.gllGSkafa 82 
                                       +++ ++++  EE  + +G  +++
  gi|474935117|ref|YP_007688699.1| 147 MSIGVAWVADEEMaSHYGVCHLI 169
                                       ************76777777776 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.1
                                       HHCHHHHHHHHHHHHHTT-TTSCCEEEEESSTT-STTHHHH CS
                     Peptidase_M28 114 kssselekelkalakpvgraaaedpfdersgrgrsDhspfl 154
                                       k+++++   ++a+ ++++++  e +  e++g++ +D  +f+
  gi|474935117|ref|YP_007688699.1| 294 KTAQDIASRYEATGAKITVK--ELQRHESGGKSSTDSPVFK 332
                                       45556666666666666554..3666666788888877775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2546.18
//
Query:       gi|474935118|ref|YP_007688700.1|  [L=393]
Description: acetyl-CoA acetyltransferase [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.5e-93  311.1   1.2    7.4e-93  310.6   1.2    1.2  1  Thiolase_N     Thiolase, N-terminal domain
    5.5e-42  142.3   0.4    1.8e-41  140.6   0.2    2.0  2  Thiolase_C     Thiolase, C-terminal domain
    0.00048   19.8   2.0    0.00092   18.9   0.8    2.1  3  ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
  ------ inclusion threshold ------
      0.032   14.1   0.3        0.2   11.5   0.4    2.1  2  ACP_syn_III    3-Oxoacyl-[acyl-carrier-protein (ACP)] synthas
       0.17   11.0   0.0       0.27   10.3   0.0    1.2  1  BBP2           Putative beta-barrel porin-2, OmpL-like. bbp2


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  310.6   1.2   2.1e-96   7.4e-93       2     259 ..       5     262 ..       4     263 .. 0.99

  Alignments for each domain:
  == domain 1  score: 310.6 bits;  conditional E-value: 2.1e-96
                                       EEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSEE CS
                        Thiolase_N   2 vivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqagegqniarqaalkagipeevpa 78 
                                       vivsa rt+igk+g sl+ +++++L+a  +k+++++a++++ +++e i+G vlqag gqn+arqaa+ ag+p e+ +
  gi|474935118|ref|YP_007688700.1|   5 VIVSACRTAIGKYGKSLSGIKSTDLGALCVKEAVKRANLEATDIEECIMGSVLQAGLGQNPARQAAIGAGLPVEIGS 81 
                                       9**************************************************************************** PP

                                       EEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGSSSSEEEEEHHHHHHTEETTTTSEH CS
                        Thiolase_N  79 vtvnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvrsglklgdekakdllipdgladafneehm 155
                                        tvn vc+Sglka +laa++i+age++++ +gG+Esmsnap+ ++  +r+g++++d++++d++++dgl+d+fn++hm
  gi|474935118|ref|YP_007688700.1|  82 FTVNAVCGSGLKAAMLAADAIKAGEYQCLAVGGMESMSNAPYIMN-GARWGYRMNDQTVVDCMVHDGLWDIFNNQHM 157
                                       ********************************************9.99***************************** PP

                                       HHHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSE.EEE-S-TTS-TT--HHHHHTS-B CS
                        Thiolase_N 156 GltaenlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgk.ktvdkdeairsevtaekLaklkp 231
                                       G t+e +a++++++Re+ d+  v+sh kaa+aqk+gkF++eivPv++++kk     +dkde+ir+++++e+L klkp
  gi|474935118|ref|YP_007688700.1| 158 GFTGEIVAERFNVTREDADQLSVESHLKAAKAQKDGKFDKEIVPVMLHDKKLGdYAFDKDEGIRADSSMESLGKLKP 234
                                       *************************************************996659********************** PP

                                       SSSTTSS-BTTSB--BEEEEEEEEEEEH CS
                        Thiolase_N 232 aFkkeGtvtAgnasqisDGaaavllmse 259
                                       +Fkk+G vtAgn+sq+sDGa+ ++++s+
  gi|474935118|ref|YP_007688700.1| 235 VFKKDGIVTAGNSSQLSDGASSMIVCSR 262
                                       **************************97 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.79   2.8e+03      26      43 ..      32      49 ..      20      53 .. 0.75
   2 !  140.6   0.2     5e-45   1.8e-41       1     122 [.     270     391 ..     270     392 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.79
                                      HHHHHHHHHHT--GGGES CS
                        Thiolase_C 26 yaikkvlkkagltvedid 43
                                        +k+++k+a l+  di+
  gi|474935118|ref|YP_007688700.1| 32 LCVKEAVKRANLEATDIE 49
                                      456778888888888875 PP

  == domain 2  score: 140.6 bits;  conditional E-value: 5e-45
                                       ---SEEEEEEEEEE--GGGGGGHHHHHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--GGGBSTT--HHH CS
                        Thiolase_C   1 lkplakirsyaevgvdpeilglgPayaikkvlkkagltvedidlfEinEAFaaqaLavakaldldlekvNvnGGaia 77 
                                       lkp+a i++y e gv pe +  +P++a+++v+kkag+t++didlfE nEAFa+   av k+l++  e +NvnGGa+a
  gi|474935118|ref|YP_007688700.1| 270 LKPMASIVAYGERGVLPERIMEAPIPASEHVMKKAGMTIDDIDLFEHNEAFASASCAVKKTLNVPDEIFNVNGGAVA 346
                                       589************************************************************************** PP

                                       H-B-TTTHHHHHHHHHHHHHHHCTTSEEEEEEEETTTEEEEEEEE CS
                        Thiolase_C  78 lGHPlGasGaRivvtllselkkeggklgvaalCigggqgvalvie 122
                                       lGHP+G+sG+R+++tll++l+ +++ +g+a+lC ggg++v+++++
  gi|474935118|ref|YP_007688700.1| 347 LGHPIGCSGSRVMTTLLYALQDRQKDVGLATLCLGGGNAVTMIVK 391
                                       *******************************************98 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.85     3e+03      93     125 ..      31      63 ..      26      75 .. 0.73
   2 !   18.9   0.8   2.6e-07   0.00092     168     218 ..      81     131 ..      71     143 .. 0.88
   3 ?   -2.2   0.0       0.7   2.5e+03      19      74 ..     145     199 ..     135     206 .. 0.65

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.85
                                       HHHHHHHHHHHTS-HHTCTTGGEEEEEEESSTH CS
                     ketoacyl-synt  93 leaawealedagltpeeldgsrvgvfiGvgagd 125
                                         +++ea+++a+l+++++++  +g ++ +g g+
  gi|474935118|ref|YP_007688700.1|  31 ALCVKEAVKRANLEATDIEECIMGSVLQAGLGQ 63 
                                       568899999999999998876677666665554 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 2.6e-07
                                       EEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHHHHHTT CS
                     ketoacyl-synt 168 svtvdtACsSslvavhaavqslrsgeadvalaGGvellltpeavagfsaag 218
                                       s+tv + C S+l+a  +a +++++ge ++  +GG+e + ++  ++  +++g
  gi|474935118|ref|YP_007688700.1|  81 SFTVNAVCGSGLKAAMLAADAIKAGEYQCLAVGGMESMSNAPYIMNGARWG 131
                                       79**********************************999887776666665 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.7
                                       HHHHHHHHHTT---EE.ES-TTSSCGTTSBTSSTTEEE-BSS.EEE..STTEGGTTS CS
                     ketoacyl-synt  19 veefwelLlegrdais.elpadrwdadklydpparaagkiktklggfldvddfdpef 74 
                                       ++ +w+   +++ +++ e+ a+r+++++  +++  ++ + k+  +   ++ +fd+e+
  gi|474935118|ref|YP_007688700.1| 145 HDGLWDIFNNQHMGFTgEIVAERFNVTREDADQLSVESHLKA--AKAQKDGKFDKEI 199
                                       567788888888888777777888888886444444444444..3343477777765 PP

>> ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.4   5.6e-05       0.2       1      39 [.      82     120 ..      82     128 .. 0.92
   2 ?   -1.2   0.0      0.52   1.8e+03      52      64 ..     250     262 ..     244     272 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.6e-05
                                       EEEE-GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEGGG CS
                       ACP_syn_III   1 fDlnaaCsgfvyalsvAdaliesgaakrvLvigaetlsk 39 
                                       f +na+C + + a  +A+++i++g++++  v g e +s+
  gi|474935118|ref|YP_007688700.1|  82 FTVNAVCGSGLKAAMLAADAIKAGEYQCLAVGGMESMSN 120
                                       669*************************99999999986 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.52
                                       B-EEEEEEEEEEE CS
                       ACP_syn_III  52 fGDGAgAvvleas 64 
                                       ++DGA  +++   
  gi|474935118|ref|YP_007688700.1| 250 LSDGASSMIVCSR 262
                                       78****9999655 PP

>> BBP2  Putative beta-barrel porin-2, OmpL-like. bbp2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   7.6e-05      0.27     132     175 ..     118     159 ..     117     198 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 7.6e-05
                              BBP2 132 fnngPfihtGvranytitdklslslgvlng.wdaieddsngtpal 175
                                       ++n+P+i +G+r  y ++d+  +  +v +g wd +    n+  ++
  gi|474935118|ref|YP_007688700.1| 118 MSNAPYIMNGARWGYRMNDQTVVDCMVHDGlWDIFN---NQHMGF 159
                                       799***************************998844...443444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2567.81
//
Query:       gi|474935119|ref|YP_007688701.1|  [L=436]
Description: putative DNA-binding protein containing a Zn-ribbon domain [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.7e-30  103.2   0.0    1.4e-29  102.5   0.0    1.3  1  DUF1743          Domain of unknown function (DUF1743)
     0.0002   21.3   0.0    0.00036   20.5   0.0    1.4  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
  ------ inclusion threshold ------
      0.014   15.4   1.0      0.027   14.4   1.0    1.4  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.019   13.5   0.1      0.028   12.9   0.1    1.1  1  DUF4503          Domain of unknown function (DUF4503)
      0.052   13.4   0.5        0.1   12.5   0.5    1.4  1  C1_1             Phorbol esters/diacylglycerol binding domain
      0.081   12.6   5.8       0.21   11.3   5.8    1.7  1  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
       0.54   10.8   6.1        1.4    9.5   6.1    1.6  1  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
       0.86    9.2   3.4         12    5.6   0.0    2.6  3  zf_UBZ           Ubiquitin-Binding Zinc Finger
        1.8    8.3   7.4        3.9    7.2   7.4    1.6  1  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain


Domain annotation for each model (and alignments):
>> DUF1743  Domain of unknown function (DUF1743)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.5   0.0   6.8e-33   1.4e-29       1     116 []     149     260 ..     149     260 .. 0.97

  Alignments for each domain:
  == domain 1  score: 102.5 bits;  conditional E-value: 6.8e-33
                                       TTHHHHHHHHHH-..-TTS-EEEEEEEE-GGGTT.---EEHHHHHHHHHHHTTCECTSEBTTTTCECCS-STTSSEE CS
                           DUF1743   1 grgiiGAtaalganialedstyEllaYreperwg.erevdeesvieadektypetfdnvDlshklvvlvPhtpdpvl 76 
                                       grgiiG+++ l++++   d t+Ell+Yr +erwg ere+d++++ +a+++ + + f++++ + ++v++vP tp+pv+
  gi|474935119|ref|YP_007688701.1| 149 GRGIIGCVCGLAWEPG--DRTFELLVYRPQERWGtEREFDPSTIERAEHE-IGSSFNSWEDRSRKVAMVPGTPCPVM 222
                                       89***********887..69************************999998.79************************ PP

                                       EEEEES-HHHHHHHHHCSEE..S-EECEEEEEESTTS-TT CS
                           DUF1743  77 fGirgedpeallkaakeilskeeeseemavfrtnqgtdah 116
                                       +G+rg+ p++l+  +  i++  e+ ++++vf+tnqgtd+h
  gi|474935119|ref|YP_007688701.1| 223 YGFRGDVPNDLILGHGIIKT--EPQDRWVVFETNQGTDDH 260
                                       ********************..*****************9 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   1.8e-07   0.00036       2      70 ..     277     343 ..     276     351 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.8e-07
                                       EEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET..HHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEE CS
                   tRNA_anti-codon   2 tvaGrvtsisdrsggkvifidlrDgtgriqvvlfr..eeatklaenlkeGdvvrvtGrvkrrpggelelkv 70 
                                        v+G v s++ r  g++ f+ l  + g+++  +     e++  ++ l +Gdv+++ G++++ p+    l++
  gi|474935119|ref|YP_007688701.1| 277 IVRGTVESVE-RIRGGHTFVRLSTEFGSLTGAAYEpsREFRHALDWLARGDVIEILGELRENPRS---LNI 343
                                       599******8.************************9999999999999*************9866...444 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   1.0   1.3e-05     0.027      30      57 ..     362     389 ..     347     391 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.3e-05
                    OrfB_Zn_ribbon  30 tCseCgsknkealsgrtfkCpnCgfead 57 
                                        C++Cg++++ a +g+ ++C++Cg++ d
  gi|474935119|ref|YP_007688701.1| 362 ICARCGRTMSSAGKGQGYRCRRCGTRSD 389
                                       7***********************9866 PP

>> DUF4503  Domain of unknown function (DUF4503)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   1.4e-05     0.028     269     319 ..     349     397 ..     337     409 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.4e-05
                           DUF4503 269 vvgvdestafsWPvCdrCgsekleqspedrgafsCgsCssvvtsPvlrmqL 319
                                       +   de +  s P+C rCg      s+ + + ++C++C +  ++P++r+++
  gi|474935119|ref|YP_007688701.1| 349 ISLADEYSKVSNPICARCGRT--MSSAGKGQGYRCRRCGTRSDEPIMRKNV 397
                                       445699999*********965..56799999****************9876 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.5   5.2e-05       0.1      13      36 ..     362     386 ..     357     390 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.2e-05
                                       B-TTT-SB--S.SSS-EEEETTT-- CS
                              C1_1  13 fCkhCgeflwg.kekqglkCswCkl 36 
                                        C+ Cg  ++  +  qg++C+ C+ 
  gi|474935119|ref|YP_007688701.1| 362 ICARCGRTMSSaGKGQGYRCRRCGT 386
                                       5********999***********86 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   5.8    0.0001      0.21       2      27 ..     362     388 ..     362     388 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0001
                                       B-SSS--B--.--SSS----SSS---- CS
                    DNA_RNApol_7kD   2 iCgeCgaevs.lkkgdpiRCkeCGhRi 27 
                                       iC++Cg  +s   kg   RC+ CG R+
  gi|474935119|ref|YP_007688701.1| 362 ICARCGRTMSsAGKGQGYRCRRCGTRS 388
                                       8********999************995 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   6.1   0.00072       1.4       7      32 ..     362     387 ..     362     396 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00072
                   Zn_ribbon_recom   7 rCgeCGspmtrrkrkgkrhyYrCsty 32 
                                       +C++CG++m+  +++ ++++ rC+t+
  gi|474935119|ref|YP_007688701.1| 362 ICARCGRTMSSAGKGQGYRCRRCGTR 387
                                       6***********99999999999986 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       2.3   4.5e+03      14      21 ..     188     196 ..     187     196 .. 0.75
   2 ?    5.6   0.0    0.0059        12       4      15 ..     362     373 ..     359     376 .. 0.86
   3 ?    4.0   0.1     0.019        39       2      14 ..     378     390 ..     377     394 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.3
                            zf_UBZ  14 es.elqEHe 21 
                                       ++ e++EHe
  gi|474935119|ref|YP_007688701.1| 188 STiERAEHE 196
                                       55599***7 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0059
                            zf_UBZ   4 lCerCgkeipes 15 
                                       +C+rCg++++++
  gi|474935119|ref|YP_007688701.1| 362 ICARCGRTMSSA 373
                                       6*******9975 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.019
                            zf_UBZ   2 tylCerCgkeipe 14 
                                        y C rCg++  e
  gi|474935119|ref|YP_007688701.1| 378 GYRCRRCGTRSDE 390
                                       699*****98766 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   7.4     0.002       3.9       3      30 ..     360     387 ..     359     388 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.002
                     zf-NADH-PPase   3 hrFCgrCGaptepaeggwarvCpaCgle 30 
                                       ++ C+rCG  +  a  g + +C  Cg++
  gi|474935119|ref|YP_007688701.1| 360 NPICARCGRTMSSAGKGQGYRCRRCGTR 387
                                       678***********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3094.04
//
Query:       gi|474935120|ref|YP_007688702.1|  [L=95]
Description: hypothetical protein TALC_01576 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.13   12.4   0.1       0.23   11.6   0.1    1.3  1  BCMA-Tall_bind  BCMA, TALL-1 binding


Domain annotation for each model (and alignments):
>> BCMA-Tall_bind  BCMA, TALL-1 binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   1.3e-05      0.23      19      32 ..      60      74 ..      59      76 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.3e-05
                    BCMA-Tall_bind 19 LRC.sntPPltCqrY 32
                                      +RC s+tPP  C  Y
  gi|474935120|ref|YP_007688702.1| 60 IRCfSKTPPDGCGMY 74
                                      7***********988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 630.25
//
Query:       gi|474935121|ref|YP_007688703.1|  [L=30]
Description: hypothetical protein TALC_01577 [Thermoplasmatales archaeon BRNA1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (30 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       761  (0.0424452); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 209.70
//
[ok]
